diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 75b79443c396085d703b9afb970ea06fdaf7478c..b91e58a83f43476d985fc513a98a77c943ce8789 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -17,6 +17,7 @@ src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
+src/SPIN/* @julient31
src/USER-CGDNA/* @ohenrich
src/USER-CGSDK/* @akohlmey
src/USER-COLVARS/* @giacomofiorin
@@ -44,6 +45,7 @@ src/USER-MISC/*_grem.* @dstelter92
# tools
tools/msi2lmp/* @akohlmey
+tools/emacs/* @HaoZeke
# cmake
cmake/* @junghans @rbberger
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 60a0f5d48fb7ea425858504105e1cce5f9c3e244..f4d3cac5d2d1e67d71c48508c7349adddbd4638b 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -9,6 +9,7 @@ set(SOVERSION 0)
get_filename_component(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src ABSOLUTE)
get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib ABSOLUTE)
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
+get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
# To avoid conflicts with the conventional Makefile build system, we build everything here
@@ -137,8 +138,11 @@ set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIG
add_definitions(-D${LAMMPS_SIZE_LIMIT})
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${LAMMPS_SIZE_LIMIT}")
-set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
-add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
+# posix_memalign is not available on Windows
+if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+ set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
+ add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
+endif()
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
if(LAMMPS_EXCEPTIONS)
@@ -153,14 +157,15 @@ if(ENABLE_TESTING)
enable_testing()
endif(ENABLE_TESTING)
-set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
- KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SPIN SNAP
+set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
+ KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
+set(OTHER_PACKAGES CORESHELL QEQ)
foreach(PKG ${DEFAULT_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
@@ -174,13 +179,12 @@ macro(pkg_depends PKG1 PKG2)
endif()
endmacro()
+# "hard" dependencies between packages resulting
+# in an error instead of skipping over files
pkg_depends(MPIIO MPI)
-pkg_depends(QEQ MANYBODY)
pkg_depends(USER-ATC MANYBODY)
pkg_depends(USER-LB MPI)
-pkg_depends(USER-MISC MANYBODY)
pkg_depends(USER-PHONON KSPACE)
-pkg_depends(CORESHELL KSPACE)
######################################################
# packages with special compiler needs or external libs
@@ -466,6 +470,11 @@ if(PKG_COMPRESS)
list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
endif()
+# the windows version of LAMMPS requires a couple extra libraries
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+ list(APPEND LAMMPS_LINK_LIBS -lwsock32 -lpsapi)
+endif()
+
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
@@ -574,6 +583,41 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
+if(PKG_CORESHELL)
+ set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL)
+ set(CORESHELL_SOURCES)
+ set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}")
+
+ # detects styles which have a CORESHELL version
+ RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES)
+
+ get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES)
+
+ list(APPEND LIB_SOURCES ${CORESHELL_SOURCES})
+ include_directories(${CORESHELL_SOURCES_DIR})
+endif()
+
+# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
+if(PKG_QEQ)
+ set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
+ file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
+ file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
+
+ if(NOT PKG_MANYBODY)
+ list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
+ list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
+ endif()
+ set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
+
+ foreach(MY_HEADER ${QEQ_HEADERS})
+ AddStyleHeader(${MY_HEADER} FIX)
+ endforeach()
+
+ get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
+ list(APPEND LIB_SOURCES ${QEQ_SOURCES})
+ include_directories(${QEQ_SOURCES_DIR})
+endif()
+
if(PKG_USER-OMP)
set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
@@ -585,8 +629,31 @@ if(PKG_USER-OMP)
# detects styles which have USER-OMP version
RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
+
get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
+ # manually add package dependent source files from USER-OMP that do not provide styles
+
+ if(PKG_ASPHERE)
+ list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
+ endif()
+
+ if(PKG_RIGID)
+ list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
+ endif()
+
+ if(PKG_USER-REAXC)
+ list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
+ endif()
+
list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
include_directories(${USER-OMP_SOURCES_DIR})
endif()
@@ -900,6 +967,80 @@ if(BUILD_EXE)
endif()
endif()
+###############################################################################
+# Build documentation
+###############################################################################
+option(BUILD_DOC "Build LAMMPS documentation" OFF)
+if(BUILD_DOC)
+ include(ProcessorCount)
+ ProcessorCount(NPROCS)
+ find_package(PythonInterp 3 REQUIRED)
+
+ set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
+
+ file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/*.txt)
+ file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
+ list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
+
+ add_custom_command(
+ OUTPUT docenv
+ COMMAND ${VIRTUALENV} docenv
+ )
+
+ set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
+
+ add_custom_command(
+ OUTPUT requirements.txt
+ DEPENDS docenv
+ COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
+ COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade
+ COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+ )
+
+ set(RST_FILES "")
+ set(RST_DIR ${CMAKE_BINARY_DIR}/rst)
+ file(MAKE_DIRECTORY ${RST_DIR})
+ foreach(TXT_FILE ${DOC_SOURCES})
+ get_filename_component(FILENAME ${TXT_FILE} NAME_WE)
+ set(RST_FILE ${RST_DIR}/${FILENAME}.rst)
+ list(APPEND RST_FILES ${RST_FILE})
+ add_custom_command(
+ OUTPUT ${RST_FILE}
+ DEPENDS requirements.txt docenv ${TXT_FILE}
+ COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}
+ )
+ endforeach()
+
+ add_custom_command(
+ OUTPUT html
+ DEPENDS ${RST_FILES}
+ COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}
+ COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html
+ )
+
+ add_custom_target(
+ doc ALL
+ DEPENDS html
+ SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
+ )
+
+ install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
+endif()
+
+###############################################################################
+# Install potential files in data directory
+###############################################################################
+set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
+install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials DESTINATION ${CMAKE_INSTALL_DATADIR}/lammps/potentials)
+
+configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
+configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
+install(
+ FILES ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh
+ ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh
+ DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d
+)
+
###############################################################################
# Testing
#
diff --git a/cmake/README.md b/cmake/README.md
index bafd440a64b1a30e376d704d788ddacf446aeaaa..b6644ffda959c45faec16e89e0a6a3275725c796 100644
--- a/cmake/README.md
+++ b/cmake/README.md
@@ -275,6 +275,16 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
</dl>
</td>
</tr>
+<tr>
+ <td><code>BUILD_DOC</code></td>
+ <td>control whether to build LAMMPS documentation</td>
+ <td>
+ <dl>
+ <dt><code>off</code> (default)</dt>
+ <dt><code>on</code></dt>
+ </dl>
+ </td>
+</tr>
<tr>
<td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
<td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
diff --git a/cmake/etc/profile.d/lammps.csh.in b/cmake/etc/profile.d/lammps.csh.in
new file mode 100644
index 0000000000000000000000000000000000000000..def49bf75c0112503f7286dbb68843a258e993f3
--- /dev/null
+++ b/cmake/etc/profile.d/lammps.csh.in
@@ -0,0 +1,2 @@
+# set environment for LAMMPS executables to find potential files
+if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@
diff --git a/cmake/etc/profile.d/lammps.sh.in b/cmake/etc/profile.d/lammps.sh.in
new file mode 100644
index 0000000000000000000000000000000000000000..acd75fa0cff7bae7013d8c32d8453e2083dc217d
--- /dev/null
+++ b/cmake/etc/profile.d/lammps.sh.in
@@ -0,0 +1,2 @@
+# set environment for LAMMPS executables to find potential files
+export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
diff --git a/doc/Makefile b/doc/Makefile
index c4bc80e7bd5de665a857a5488842cd8be63e51cf..81f362349950be2123d2da4bd14255e7f9f27739 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -157,7 +157,7 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
@(\
mkdir -p $(RSTDIR) ; \
. $(VENV)/bin/activate ;\
- txt2rst $< > $@ ;\
+ txt2rst -v $< > $@ ;\
deactivate ;\
)
diff --git a/doc/src/Commands.txt b/doc/src/Commands.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30e3343bd21c1203b8182f5f42dbab92a15c723b
--- /dev/null
+++ b/doc/src/Commands.txt
@@ -0,0 +1,51 @@
+"Previous Section"_Run.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Packages.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html#comm)
+
+:line
+
+Commands :h2
+
+These pages describe how a LAMMPS input script is formatted and the
+commands in it are used to define a LAMMPS simulation.
+
+<!-- RST
+
+.. toctree::
+
+ Commands_input
+ Commands_parse
+ Commands_structure
+ Commands_category
+
+.. toctree::
+
+ Commands_all
+ Commands_fix
+ Commands_compute
+ Commands_pair
+ Commands_bond
+ Commands_kspace
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"LAMMPS input scripts"_Commands_input.html
+"Parsing rules for input scripts"_Commands_parse.html
+"Input script structure"_Commands_structure.html
+"Commands by category"_Commands_category.html :all(b)
+
+"All commands"_Commands_all.html
+"Fix commands"_Commands_fix.html
+"Compute commands"_Commands_compute.html
+"Pair commands"_Commands_pair.html
+"Bond, angle, dihedral, improper commands"_Commands_bond.html
+"KSpace solvers"_Commands_kspace.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13db1272b928e558ceda0853df22162945e6c6e5
--- /dev/null
+++ b/doc/src/Commands_all.txt
@@ -0,0 +1,128 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+All commands :h3
+
+An alphabetic list of all LAMMPS commmands.
+
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"clear"_clear.html,
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"create_box"_create_box.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"dielectric"_dielectric.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"dihedral_style"_dihedral_style.html,
+"dimension"_dimension.html,
+"displace_atoms"_displace_atoms.html,
+"dump"_dump.html,
+"dump image"_dump_image.html,
+"dump_modify"_dump_modify.html,
+"dump movie"_dump_image.html,
+"dump netcdf"_dump_netcdf.html,
+"dump netcdf/mpiio"_dump_netcdf.html,
+"dump vtk"_dump_vtk.html,
+"echo"_echo.html,
+"fix"_fix.html,
+"fix_modify"_fix_modify.html,
+"group"_group.html,
+"group2ndx"_group2ndx.html,
+"if"_if.html,
+"info"_info.html,
+"improper_coeff"_improper_coeff.html,
+"improper_style"_improper_style.html,
+"include"_include.html,
+"jump"_jump.html,
+"kspace_modify"_kspace_modify.html,
+"kspace_style"_kspace_style.html,
+"label"_label.html,
+"lattice"_lattice.html,
+"log"_log.html,
+"mass"_mass.html,
+"minimize"_minimize.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"molecule"_molecule.html,
+"ndx2group"_group2ndx.html,
+"neb"_neb.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"newton"_newton.html,
+"next"_next.html,
+"package"_package.html,
+"pair_coeff"_pair_coeff.html,
+"pair_modify"_pair_modify.html,
+"pair_style"_pair_style.html,
+"pair_write"_pair_write.html,
+"partition"_partition.html,
+"prd"_prd.html,
+"print"_print.html,
+"processors"_processors.html,
+"python"_python.html,
+"quit"_quit.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"region"_region.html,
+"replicate"_replicate.html,
+"rerun"_rerun.html,
+"reset_ids"_reset_ids.html,
+"reset_timestep"_reset_timestep.html,
+"restart"_restart.html,
+"run"_run.html,
+"run_style"_run_style.html,
+"set"_set.html,
+"shell"_shell.html,
+"special_bonds"_special_bonds.html,
+"suffix"_suffix.html,
+"tad"_tad.html,
+"temper"_temper.html,
+"temper/grem"_temper_grem.html,
+"temper/npt"_temper_npt.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html,
+"uncompute"_uncompute.html,
+"undump"_undump.html,
+"unfix"_unfix.html,
+"units"_units.html,
+"variable"_variable.html,
+"velocity"_velocity.html,
+"write_coeff"_write_coeff.html,
+"write_data"_write_data.html,
+"write_dump"_write_dump.html,
+"write_restart"_write_restart.html :tb(c=6,ea=c)
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
new file mode 100644
index 0000000000000000000000000000000000000000..314260cb14bc582a5791912ac055ec50260878f1
--- /dev/null
+++ b/doc/src/Commands_bond.txt
@@ -0,0 +1,124 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Bond, angle, dihedral, and improper commands :h3
+
+:line
+
+Bond_style potentials :h3,link(bond)
+
+All LAMMPS "bond_style"_bond_style.html commands. Some styles have
+accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_bond_none.html,
+"zero"_bond_zero.html,
+"hybrid"_bond_hybrid.html :tb(c=3,ea=c)
+
+"class2 (ko)"_bond_class2.html,
+"fene (iko)"_bond_fene.html,
+"fene/expand (o)"_bond_fene_expand.html,
+"gromos (o)"_bond_gromos.html,
+"harmonic (ko)"_bond_harmonic.html,
+"harmonic/shift (o)"_bond_harmonic_shift.html,
+"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
+"morse (o)"_bond_morse.html,
+"nonlinear (o)"_bond_nonlinear.html,
+"oxdna/fene"_bond_oxdna.html,
+"oxdna2/fene"_bond_oxdna.html,
+"quartic (o)"_bond_quartic.html,
+"table (o)"_bond_table.html :tb(c=4,ea=c)
+
+:line
+
+Angle_style potentials :h3,link(angle)
+
+All LAMMPS "angle_style"_angle_style.html commands. Some styles have
+accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_angle_none.html,
+"zero"_angle_zero.html,
+"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
+
+"charmm (ko)"_angle_charmm.html,
+"class2 (ko)"_angle_class2.html,
+"cosine (o)"_angle_cosine.html,
+"cosine/delta (o)"_angle_cosine_delta.html,
+"cosine/periodic (o)"_angle_cosine_periodic.html,
+"cosine/shift (o)"_angle_cosine_shift.html,
+"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
+"cosine/squared (o)"_angle_cosine_squared.html,
+"dipole (o)"_angle_dipole.html,
+"fourier (o)"_angle_fourier.html,
+"fourier/simple (o)"_angle_fourier_simple.html,
+"harmonic (iko)"_angle_harmonic.html,
+"quartic (o)"_angle_quartic.html,
+"sdk"_angle_sdk.html,
+"table (o)"_angle_table.html :tb(c=4,ea=c)
+
+:line
+
+Dihedral_style potentials :h3,link(dihedral)
+
+All LAMMPS "dihedral_style"_dihedral_style.html commands. Some styles
+have accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_dihedral_none.html,
+"zero"_dihedral_zero.html,
+"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c)
+
+"charmm (iko)"_dihedral_charmm.html,
+"charmmfsw"_dihedral_charmm.html,
+"class2 (ko)"_dihedral_class2.html,
+"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
+"fourier (io)"_dihedral_fourier.html,
+"harmonic (io)"_dihedral_harmonic.html,
+"helix (o)"_dihedral_helix.html,
+"multi/harmonic (o)"_dihedral_multi_harmonic.html,
+"nharmonic (o)"_dihedral_nharmonic.html,
+"opls (iko)"_dihedral_opls.htm;,
+"quadratic (o)"_dihedral_quadratic.html,
+"spherical (o)"_dihedral_spherical.html,
+"table (o)"_dihedral_table.html,
+"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
+
+:line
+
+Improper_style potentials :h3,link(improper)
+
+All LAMMPS "improper_style"_improper_style.html commands. Some styles
+have accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_improper_none.html,
+"zero"_improper_zero.html,
+"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
+
+"class2 (ko)"_improper_class2.html,
+"cossq (o)"_improper_cossq.html,
+"cvff (io)"_improper_cvff.html,
+"distance"_improper_distance.html,
+"fourier (o)"_improper_fourier.html,
+"harmonic (iko)"_improper_harmonic.html,
+"ring (o)"_improper_ring.html,
+"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_category.txt b/doc/src/Commands_category.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d047c67272ef0e8bedb1d2d9e52260ee4be0b2e
--- /dev/null
+++ b/doc/src/Commands_category.txt
@@ -0,0 +1,141 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Commands by category :h3
+
+This page lists most of the LAMMPS commands, grouped by category. The
+"Commands all"_Commands_all.html doc page lists all commands
+alphabetically. It also includes long lists of style options for
+entries that appear in the following categories as a single command
+(fix, compute, pair, etc).
+
+Initialization:
+
+"newton"_newton.html,
+"package"_package.html,
+"processors"_processors.html,
+"suffix"_suffix.html,
+"units"_units.html :ul
+
+Setup simulation box:
+
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"create_box"_create_box.html,
+"dimension"_dimension.html,
+"lattice"_lattice.html,
+"region"_region.html :ul
+
+Setup atoms:
+
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"displace_atoms"_displace_atoms.html,
+"group"_group.html,
+"mass"_mass.html,
+"molecule"_molecule.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"replicate"_replicate.html,
+"set"_set.html,
+"velocity"_velocity.html :ul
+
+Force fields:
+
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
+"dielectric"_dielectric.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"dihedral_style"_dihedral_style.html,
+"improper_coeff"_improper_coeff.html,
+"improper_style"_improper_style.html,
+"kspace_modify"_kspace_modify.html,
+"kspace_style"_kspace_style.html,
+"pair_coeff"_pair_coeff.html,
+"pair_modify"_pair_modify.html,
+"pair_style"_pair_style.html,
+"pair_write"_pair_write.html,
+"special_bonds"_special_bonds.html :ul
+
+Settings:
+
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"info"_info.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"partition"_partition.html,
+"reset_timestep"_reset_timestep.html,
+"run_style"_run_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html :ul
+
+Operations within timestepping (fixes) and diagnostics (computes):
+
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"fix"_fix.html,
+"fix_modify"_fix_modify.html,
+"uncompute"_uncompute.html,
+"unfix"_unfix.html :ul
+
+Output:
+
+"dump image"_dump_image.html,
+"dump movie"_dump_image.html,
+"dump"_dump.html,
+"dump_modify"_dump_modify.html,
+"restart"_restart.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"undump"_undump.html,
+"write_coeff"_write_coeff.html,
+"write_data"_write_data.html,
+"write_dump"_write_dump.html,
+"write_restart"_write_restart.html :ul
+
+Actions:
+
+"minimize"_minimize.html,
+"neb"_neb.html,
+"prd"_prd.html,
+"rerun"_rerun.html,
+"run"_run.html,
+"tad"_tad.html,
+"temper"_temper.html :ul
+
+Input script control:
+
+"clear"_clear.html,
+"echo"_echo.html,
+"if"_if.html,
+"include"_include.html,
+"jump"_jump.html,
+"label"_label.html,
+"log"_log.html,
+"next"_next.html,
+"print"_print.html,
+"python"_python.html,
+"quit"_quit.html,
+"shell"_shell.html,
+"variable"_variable.html :ul
+
diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt
new file mode 100644
index 0000000000000000000000000000000000000000..028e274c9be4a80555dfcab5a417d738b763bfda
--- /dev/null
+++ b/doc/src/Commands_compute.txt
@@ -0,0 +1,153 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Compute commands :h3
+
+An alphabetic list of all LAMMPS "compute"_compute.html commands.
+Some styles have accelerated versions. This is indicated by
+additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+
+"ackland/atom"_compute_ackland_atom.html,
+"aggregate/atom"_compute_cluster_atom.html,
+"angle"_compute_angle.html,
+"angle/local"_compute_angle_local.html,
+"angmom/chunk"_compute_angmom_chunk.html,
+"basal/atom"_compute_basal_atom.html,
+"body/local"_compute_body_local.html,
+"bond"_compute_bond.html,
+"bond/local"_compute_bond_local.html,
+"centro/atom"_compute_centro_atom.html,
+"chunk/atom"_compute_chunk_atom.html,
+"cluster/atom"_compute_cluster_atom.html,
+"cna/atom"_compute_cna_atom.html,
+"cnp/atom"_compute_cnp_atom.html,
+"com"_compute_com.html,
+"com/chunk"_compute_com_chunk.html,
+"contact/atom"_compute_contact_atom.html,
+"coord/atom"_compute_coord_atom.html,
+"damage/atom"_compute_damage_atom.html,
+"dihedral"_compute_dihedral.html,
+"dihedral/local"_compute_dihedral_local.html,
+"dilatation/atom"_compute_dilatation_atom.html,
+"dipole/chunk"_compute_dipole_chunk.html,
+"displace/atom"_compute_displace_atom.html,
+"dpd"_compute_dpd.html,
+"dpd/atom"_compute_dpd_atom.html,
+"edpd/temp/atom"_compute_edpd_temp_atom.html,
+"entropy/atom"_compute_entropy_atom.html,
+"erotate/asphere"_compute_erotate_asphere.html,
+"erotate/rigid"_compute_erotate_rigid.html,
+"erotate/sphere"_compute_erotate_sphere.html,
+"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
+"event/displace"_compute_event_displace.html,
+"fep"_compute_fep.html,
+"force/tally"_compute_tally.html,
+"fragment/atom"_compute_cluster_atom.html,
+"global/atom"_compute_global_atom.html,
+"group/group"_compute_group_group.html,
+"gyration"_compute_gyration.html,
+"gyration/chunk"_compute_gyration_chunk.html,
+"heat/flux"_compute_heat_flux.html,
+"heat/flux/tally"_compute_tally.html,
+"hexorder/atom"_compute_hexorder_atom.html,
+"improper"_compute_improper.html,
+"improper/local"_compute_improper_local.html,
+"inertia/chunk"_compute_inertia_chunk.html,
+"ke"_compute_ke.html,
+"ke/atom"_compute_ke_atom.html,
+"ke/atom/eff"_compute_ke_atom_eff.html,
+"ke/eff"_compute_ke_eff.html,
+"ke/rigid"_compute_ke_rigid.html,
+"meso/e/atom"_compute_meso_e_atom.html,
+"meso/rho/atom"_compute_meso_rho_atom.html,
+"meso/t/atom"_compute_meso_t_atom.html,
+"msd"_compute_msd.html,
+"msd/chunk"_compute_msd_chunk.html,
+"msd/nongauss"_compute_msd_nongauss.html,
+"omega/chunk"_compute_omega_chunk.html,
+"orientorder/atom"_compute_orientorder_atom.html,
+"pair"_compute_pair.html,
+"pair/local"_compute_pair_local.html,
+"pe"_compute_pe.html,
+"pe/atom"_compute_pe_atom.html,
+"pe/mol/tally"_compute_tally.html,
+"pe/tally"_compute_tally.html,
+"plasticity/atom"_compute_plasticity_atom.html,
+"pressure"_compute_pressure.html,
+"pressure/uef"_compute_pressure_uef.html,
+"property/atom"_compute_property_atom.html,
+"property/chunk"_compute_property_chunk.html,
+"property/local"_compute_property_local.html,
+"rdf"_compute_rdf.html,
+"reduce"_compute_reduce.html,
+"reduce/region"_compute_reduce.html,
+"rigid/local"_compute_rigid_local.html,
+"saed"_compute_saed.html,
+"slice"_compute_slice.html,
+"smd/contact/radius"_compute_smd_contact_radius.html,
+"smd/damage"_compute_smd_damage.html,
+"smd/hourglass/error"_compute_smd_hourglass_error.html,
+"smd/internal/energy"_compute_smd_internal_energy.html,
+"smd/plastic/strain"_compute_smd_plastic_strain.html,
+"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
+"smd/rho"_compute_smd_rho.html,
+"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
+"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
+"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
+"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
+"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
+"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
+"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
+"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
+"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
+"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
+"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
+"smd/vol"_compute_smd_vol.html,
+"sna/atom"_compute_sna_atom.html,
+"snad/atom"_compute_sna_atom.html,
+"snav/atom"_compute_sna_atom.html,
+"spin"_compute_spin.html,
+"stress/atom"_compute_stress_atom.html,
+"stress/tally"_compute_tally.html,
+"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
+"temp (k)"_compute_temp.html,
+"temp/asphere"_compute_temp_asphere.html,
+"temp/body"_compute_temp_body.html,
+"temp/chunk"_compute_temp_chunk.html,
+"temp/com"_compute_temp_com.html,
+"temp/deform"_compute_temp_deform.html,
+"temp/deform/eff"_compute_temp_deform_eff.html,
+"temp/drude"_compute_temp_drude.html,
+"temp/eff"_compute_temp_eff.html,
+"temp/partial"_compute_temp_partial.html,
+"temp/profile"_compute_temp_profile.html,
+"temp/ramp"_compute_temp_ramp.html,
+"temp/region"_compute_temp_region.html,
+"temp/region/eff"_compute_temp_region_eff.html,
+"temp/rotate"_compute_temp_rotate.html,
+"temp/sphere"_compute_temp_sphere.html,
+"temp/uef"_compute_temp_uef.html,
+"ti"_compute_ti.html,
+"torque/chunk"_compute_torque_chunk.html,
+"vacf"_compute_vacf.html,
+"vcm/chunk"_compute_vcm_chunk.html,
+"voronoi/atom"_compute_voronoi_atom.html,
+"xrd"_compute_xrd.html :tb(c=6,ea=c)
diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e002c117701110fc6dd33e83865386f52d2bae3e
--- /dev/null
+++ b/doc/src/Commands_fix.txt
@@ -0,0 +1,229 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Fix commands :h3
+
+An alphabetic list of all LAMMPS "fix"_fix.html commands. Some styles
+have accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"adapt"_fix_adapt.html,
+"adapt/fep"_fix_adapt_fep.html,
+"addforce"_fix_addforce.html,
+"addtorque"_fix_addtorque.html,
+"append/atoms"_fix_append_atoms.html,
+"atc"_fix_atc.html,
+"atom/swap"_fix_atom_swap.html,
+"ave/atom"_fix_ave_atom.html,
+"ave/chunk"_fix_ave_chunk.html,
+"ave/correlate"_fix_ave_correlate.html,
+"ave/correlate/long"_fix_ave_correlate_long.html,
+"ave/histo"_fix_ave_histo.html,
+"ave/histo/weight"_fix_ave_histo.html,
+"ave/time"_fix_ave_time.html,
+"aveforce"_fix_aveforce.html,
+"balance"_fix_balance.html,
+"bond/break"_fix_bond_break.html,
+"bond/create"_fix_bond_create.html,
+"bond/react"_fix_bond_react.html,
+"bond/swap"_fix_bond_swap.html,
+"box/relax"_fix_box_relax.html,
+"cmap"_fix_cmap.html,
+"colvars"_fix_colvars.html,
+"controller"_fix_controller.html,
+"deform (k)"_fix_deform.html,
+"deposit"_fix_deposit.html,
+"dpd/energy (k)"_fix_dpd_energy.html,
+"drag"_fix_drag.html,
+"drude"_fix_drude.html,
+"drude/transform/direct"_fix_drude_transform.html,
+"drude/transform/reverse"_fix_drude_transform.html,
+"dt/reset"_fix_dt_reset.html,
+"edpd/source"_fix_dpd_source.html,
+"efield"_fix_efield.html,
+"ehex"_fix_ehex.html,
+"enforce2d (k)"_fix_enforce2d.html,
+"eos/cv"_fix_eos_cv.html,
+"eos/table"_fix_eos_table.html,
+"eos/table/rx (k)"_fix_eos_table_rx.html,
+"evaporate"_fix_evaporate.html,
+"external"_fix_external.html,
+"filter/corotate"_fix_filter_corotate.html,
+"flow/gauss"_fix_flow_gauss.html,
+"freeze"_fix_freeze.html,
+"gcmc"_fix_gcmc.html,
+"gld"_fix_gld.html,
+"gle"_fix_gle.html,
+"gravity (o)"_fix_gravity.html,
+"grem"_fix_grem.html,
+"halt"_fix_halt.html,
+"heat"_fix_heat.html,
+"imd"_fix_imd.html,
+"indent"_fix_indent.html,
+"ipi"_fix_ipi.html,
+"langevin (k)"_fix_langevin.html,
+"langevin/drude"_fix_langevin_drude.html,
+"langevin/eff"_fix_langevin_eff.html,
+"langevin/spin"_fix_langevin_spin.html,
+"latte"_fix_latte.html,
+"lb/fluid"_fix_lb_fluid.html,
+"lb/momentum"_fix_lb_momentum.html,
+"lb/pc"_fix_lb_pc.html,
+"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
+"lb/viscous"_fix_lb_viscous.html,
+"lineforce"_fix_lineforce.html,
+"manifoldforce"_fix_manifoldforce.html,
+"meso"_fix_meso.html,
+"meso/stationary"_fix_meso_stationary.html,
+"momentum (k)"_fix_momentum.html,
+"move"_fix_move.html,
+"mscg"_fix_mscg.html,
+"msst"_fix_msst.html,
+"mvv/dpd"_fix_mvv_dpd.html,
+"mvv/edpd"_fix_mvv_dpd.html,
+"mvv/tdpd"_fix_mvv_dpd.html,
+"neb"_fix_neb.html,
+"nph (ko)"_fix_nh.html,
+"nph/asphere (o)"_fix_nph_asphere.html,
+"nph/body"_fix_nph_body.html,
+"nph/eff"_fix_nh_eff.html,
+"nph/sphere (o)"_fix_nph_sphere.html,
+"nphug (o)"_fix_nphug.html,
+"npt (kio)"_fix_nh.html,
+"npt/asphere (o)"_fix_npt_asphere.html,
+"npt/body"_fix_npt_body.html,
+"npt/eff"_fix_nh_eff.html,
+"npt/sphere (o)"_fix_npt_sphere.html,
+"npt/uef"_fix_nh_uef.html,
+"nve (kio)"_fix_nve.html,
+"nve/asphere (i)"_fix_nve_asphere.html,
+"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
+"nve/body"_fix_nve_body.html,
+"nve/dot"_fix_nve_dot.html,
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
+"nve/eff"_fix_nve_eff.html,
+"nve/limit"_fix_nve_limit.html,
+"nve/line"_fix_nve_line.html,
+"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
+"nve/noforce"_fix_nve_noforce.html,
+"nve/sphere (o)"_fix_nve_sphere.html,
+"nve/spin"_fix_nve_spin.html,
+"nve/tri"_fix_nve_tri.html,
+"nvk"_fix_nvk.html,
+"nvt (iko)"_fix_nh.html,
+"nvt/asphere (o)"_fix_nvt_asphere.html,
+"nvt/body"_fix_nvt_body.html,
+"nvt/eff"_fix_nh_eff.html,
+"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
+"nvt/sllod (io)"_fix_nvt_sllod.html,
+"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
+"nvt/sphere (o)"_fix_nvt_sphere.html,
+"nvt/uef"_fix_nh_uef.html,
+"oneway"_fix_oneway.html,
+"orient/bcc"_fix_orient.html,
+"orient/fcc"_fix_orient.html,
+"phonon"_fix_phonon.html,
+"pimd"_fix_pimd.html,
+"planeforce"_fix_planeforce.html,
+"poems"_fix_poems.html,
+"pour"_fix_pour.html,
+"precession/spin"_fix_precession_spin.html,
+"press/berendsen"_fix_press_berendsen.html,
+"print"_fix_print.html,
+"property/atom (k)"_fix_property_atom.html,
+"python/invoke"_fix_python_invoke.html,
+"python/move"_fix_python_move.html,
+"qbmsst"_fix_qbmsst.html,
+"qeq/comb (o)"_fix_qeq_comb.html,
+"qeq/dynamic"_fix_qeq.html,
+"qeq/fire"_fix_qeq.html,
+"qeq/point"_fix_qeq.html,
+"qeq/reax (ko)"_fix_qeq_reax.html,
+"qeq/shielded"_fix_qeq.html,
+"qeq/slater"_fix_qeq.html,
+"qmmm"_fix_qmmm.html,
+"qtb"_fix_qtb.html,
+"rattle"_fix_shake.html,
+"reax/bonds"_fix_reax_bonds.html,
+"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/species (k)"_fix_reaxc_species.html,
+"recenter"_fix_recenter.html,
+"restrain"_fix_restrain.html,
+"rhok"_fix_rhok.html,
+"rigid (o)"_fix_rigid.html,
+"rigid/nph (o)"_fix_rigid.html,
+"rigid/npt (o)"_fix_rigid.html,
+"rigid/nve (o)"_fix_rigid.html,
+"rigid/nvt (o)"_fix_rigid.html,
+"rigid/small (o)"_fix_rigid.html,
+"rigid/small/nph"_fix_rigid.html,
+"rigid/small/npt"_fix_rigid.html,
+"rigid/small/nve"_fix_rigid.html,
+"rigid/small/nvt"_fix_rigid.html,
+"rx (k)"_fix_rx.html,
+"saed/vtk"_fix_saed_vtk.html,
+"setforce (k)"_fix_setforce.html,
+"shake"_fix_shake.html,
+"shardlow (k)"_fix_shardlow.html,
+"smd"_fix_smd.html,
+"smd/adjust/dt"_fix_smd_adjust_dt.html,
+"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
+"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
+"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
+"smd/setvel"_fix_smd_setvel.html,
+"smd/wall/surface"_fix_smd_wall_surface.html,
+"spring"_fix_spring.html,
+"spring/chunk"_fix_spring_chunk.html,
+"spring/rg"_fix_spring_rg.html,
+"spring/self"_fix_spring_self.html,
+"srd"_fix_srd.html,
+"store/force"_fix_store_force.html,
+"store/state"_fix_store_state.html,
+"tdpd/source"_fix_dpd_source.html,
+"temp/berendsen"_fix_temp_berendsen.html,
+"temp/csld"_fix_temp_csvr.html,
+"temp/csvr"_fix_temp_csvr.html,
+"temp/rescale"_fix_temp_rescale.html,
+"temp/rescale/eff"_fix_temp_rescale_eff.html,
+"tfmc"_fix_tfmc.html,
+"thermal/conductivity"_fix_thermal_conductivity.html,
+"ti/spring"_fix_ti_spring.html,
+"tmd"_fix_tmd.html,
+"ttm"_fix_ttm.html,
+"ttm/mod"_fix_ttm.html,
+"tune/kspace"_fix_tune_kspace.html,
+"vector"_fix_vector.html,
+"viscosity"_fix_viscosity.html,
+"viscous"_fix_viscous.html,
+"wall/body/polygon"_fix_wall_body_polygon.html,
+"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
+"wall/colloid"_fix_wall.html,
+"wall/ees"_fix_wall_ees.html,
+"wall/gran"_fix_wall_gran.html,
+"wall/gran/region"_fix_wall_gran_region.html,
+"wall/harmonic"_fix_wall.html,
+"wall/lj1043"_fix_wall.html,
+"wall/lj126"_fix_wall.html,
+"wall/lj93 (k)"_fix_wall.html,
+"wall/piston"_fix_wall_piston.html,
+"wall/reflect (k)"_fix_wall_reflect.html,
+"wall/region"_fix_wall_region.html,
+"wall/region/ees"_fix_wall_ees.html,
+"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
diff --git a/doc/src/Commands_input.txt b/doc/src/Commands_input.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b3dda741b42dd03bcca359e654ef0ab1ae6a043
--- /dev/null
+++ b/doc/src/Commands_input.txt
@@ -0,0 +1,60 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+LAMMPS input scripts :h3
+
+LAMMPS executes by reading commands from a input script (text file),
+one line at a time. When the input script ends, LAMMPS exits. Each
+command causes LAMMPS to take some action. It may set an internal
+variable, read in a file, or run a simulation. Most commands have
+default settings, which means you only need to use the command if you
+wish to change the default.
+
+In many cases, the ordering of commands in an input script is not
+important. However the following rules apply:
+
+(1) LAMMPS does not read your entire input script and then perform a
+simulation with all the settings. Rather, the input script is read
+one line at a time and each command takes effect when it is read.
+Thus this sequence of commands:
+
+timestep 0.5
+run 100
+run 100 :pre
+
+does something different than this sequence:
+
+run 100
+timestep 0.5
+run 100 :pre
+
+In the first case, the specified timestep (0.5 fs) is used for two
+simulations of 100 timesteps each. In the 2nd case, the default
+timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
+timestep is used for the 2nd one.
+
+(2) Some commands are only valid when they follow other commands. For
+example you cannot set the temperature of a group of atoms until atoms
+have been defined and a group command is used to define which atoms
+belong to the group.
+
+(3) Sometimes command B will use values that can be set by command A.
+This means command A must precede command B in the input script if it
+is to have the desired effect. For example, the
+"read_data"_read_data.html command initializes the system by setting
+up the simulation box and assigning atoms to processors. If default
+values are not desired, the "processors"_processors.html and
+"boundary"_boundary.html commands need to be used before read_data to
+tell LAMMPS how to map processors to the simulation box.
+
+Many input script errors are detected by LAMMPS and an ERROR or
+WARNING message is printed. The "Errors"_Errors.html doc page gives
+more information on what errors mean. The documentation for each
+command lists restrictions on how the command can be used.
+
diff --git a/doc/src/Commands_kspace.txt b/doc/src/Commands_kspace.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1263445050bda692218aa311831d3565d22155c
--- /dev/null
+++ b/doc/src/Commands_kspace.txt
@@ -0,0 +1,36 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+KSpace solvers :h3
+
+All LAMMPS "kspace_style"_kspace_style.html solvers. Some styles have
+accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"ewald (o)"_kspace_style.html,
+"ewald/disp"_kspace_style.html,
+"msm (o)"_kspace_style.html,
+"msm/cg (o)"_kspace_style.html,
+"pppm (gok)"_kspace_style.html,
+"pppm/cg (o)"_kspace_style.html,
+"pppm/disp (i)"_kspace_style.html,
+"pppm/disp/tip4p"_kspace_style.html,
+"pppm/stagger"_kspace_style.html,
+"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eaf272061347931f1fda5dedf9776170ca8eb41a
--- /dev/null
+++ b/doc/src/Commands_pair.txt
@@ -0,0 +1,231 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Pair_style potentials :h3
+
+All LAMMPS "pair_style"_pair_style.html commands. Some styles have
+accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_pair_none.html,
+"zero"_pair_zero.html,
+"hybrid"_pair_hybrid.html,
+"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
+
+"adp (o)"_pair_adp.html,
+"agni (o)"_pair_agni.html,
+"airebo (oi)"_pair_airebo.html,
+"airebo/morse (oi)"_pair_airebo.html,
+"awpmd/cut"_pair_awpmd.html,
+"beck (go)"_pair_beck.html,
+"body/nparticle"_pair_body_nparticle.html,
+"body/rounded/polygon"_pair_body_rounded_polygon.html,
+"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html,
+"bop"_pair_bop.html,
+"born (go)"_pair_born.html,
+"born/coul/dsf"_pair_born.html,
+"born/coul/dsf/cs"_pair_born.html,
+"born/coul/long (go)"_pair_born.html,
+"born/coul/long/cs"_pair_born.html,
+"born/coul/msm (o)"_pair_born.html,
+"born/coul/wolf (go)"_pair_born.html,
+"born/coul/wolf/cs"_pair_born.html,
+"brownian (o)"_pair_brownian.html,
+"brownian/poly (o)"_pair_brownian.html,
+"buck (giko)"_pair_buck.html,
+"buck/coul/cut (giko)"_pair_buck.html,
+"buck/coul/long (giko)"_pair_buck.html,
+"buck/coul/long/cs"_pair_buck.html,
+"buck/coul/msm (o)"_pair_buck.html,
+"buck/long/coul/long (o)"_pair_buck_long.html,
+"buck/mdf"_pair_mdf.html,
+"colloid (go)"_pair_colloid.html,
+"comb (o)"_pair_comb.html,
+"comb3"_pair_comb.html,
+"coul/cut (gko)"_pair_coul.html,
+"coul/cut/soft (o)"_pair_lj_soft.html,
+"coul/debye (gko)"_pair_coul.html,
+"coul/diel (o)"_pair_coul_diel.html,
+"coul/dsf (gko)"_pair_coul.html,
+"coul/long (gko)"_pair_coul.html,
+"coul/long/cs"_pair_coul.html,
+"coul/long/soft (o)"_pair_lj_soft.html,
+"coul/msm"_pair_coul.html,
+"coul/shield"_pair_coul_shield.html,
+"coul/streitz"_pair_coul.html,
+"coul/wolf (ko)"_pair_coul.html,
+"coul/wolf/cs"_pair_coul.html,
+"dpd (gio)"_pair_dpd.html,
+"dpd/fdt"_pair_dpd_fdt.html,
+"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
+"dpd/tstat (go)"_pair_dpd.html,
+"dsmc"_pair_dsmc.html,
+"eam (gikot)"_pair_eam.html,
+"eam/alloy (gikot)"_pair_eam.html,
+"eam/cd (o)"_pair_eam.html,
+"eam/fs (gikot)"_pair_eam.html,
+"edip (o)"_pair_edip.html,
+"edip/multi"_pair_edip.html,
+"edpd"_pair_meso.html,
+"eff/cut"_pair_eff.html,
+"eim (o)"_pair_eim.html,
+"exp6/rx (k)"_pair_exp6_rx.html,
+"extep"_pair_extep.html,
+"gauss (go)"_pair_gauss.html,
+"gauss/cut"_pair_gauss.html,
+"gayberne (gio)"_pair_gayberne.html,
+"gran/hertz/history (o)"_pair_gran.html,
+"gran/hooke (o)"_pair_gran.html,
+"gran/hooke/history (o)"_pair_gran.html,
+"gw"_pair_gw.html,
+"gw/zbl"_pair_gw.html,
+"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
+"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
+"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
+"kim"_pair_kim.html,
+"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
+"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
+"lcbop"_pair_lcbop.html,
+"lennard/mdf"_pair_mdf.html,
+"line/lj"_pair_line_lj.html,
+"list"_pair_list.html,
+"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
+"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
+"lj/charmm/coul/long (giko)"_pair_charmm.html,
+"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
+"lj/charmm/coul/msm"_pair_charmm.html,
+"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
+"lj/charmmfsw/coul/long"_pair_charmm.html,
+"lj/class2 (gko)"_pair_class2.html,
+"lj/class2/coul/cut (ko)"_pair_class2.html,
+"lj/class2/coul/long (gko)"_pair_class2.html,
+"lj/cubic (go)"_pair_lj_cubic.html,
+"lj/cut (gikot)"_pair_lj.html,
+"lj/cut/coul/cut (gko)"_pair_lj.html,
+"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/debye (gko)"_pair_lj.html,
+"lj/cut/coul/dsf (gko)"_pair_lj.html,
+"lj/cut/coul/long (gikot)"_pair_lj.html,
+"lj/cut/coul/long/cs"_pair_lj.html,
+"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/msm (go)"_pair_lj.html,
+"lj/cut/coul/wolf (o)"_pair_lj.html,
+"lj/cut/dipole/cut (go)"_pair_dipole.html,
+"lj/cut/dipole/long"_pair_dipole.html,
+"lj/cut/dipole/sf (go)"_pair_dipole.html,
+"lj/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/thole/long (o)"_pair_thole.html,
+"lj/cut/tip4p/cut (o)"_pair_lj.html,
+"lj/cut/tip4p/long (ot)"_pair_lj.html,
+"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
+"lj/expand (gko)"_pair_lj_expand.html,
+"lj/gromacs (gko)"_pair_gromacs.html,
+"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
+"lj/long/coul/long (io)"_pair_lj_long.html,
+"lj/long/dipole/long"_pair_dipole.html,
+"lj/long/tip4p/long"_pair_lj_long.html,
+"lj/mdf"_pair_mdf.html,
+"lj/sdk (gko)"_pair_sdk.html,
+"lj/sdk/coul/long (go)"_pair_sdk.html,
+"lj/sdk/coul/msm (o)"_pair_sdk.html,
+"lj/smooth (o)"_pair_lj_smooth.html,
+"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
+"lj96/cut (go)"_pair_lj96.html,
+"lubricate (o)"_pair_lubricate.html,
+"lubricate/poly (o)"_pair_lubricate.html,
+"lubricateU"_pair_lubricateU.html,
+"lubricateU/poly"_pair_lubricateU.html,
+"mdpd"_pair_meso.html,
+"mdpd/rhosum"_pair_meso.html,
+"meam"_pair_meam.html,
+"meam/c"_pair_meam.html,
+"meam/spline (o)"_pair_meam_spline.html,
+"meam/sw/spline"_pair_meam_sw_spline.html,
+"mgpt"_pair_mgpt.html,
+"mie/cut (o)"_pair_mie.html,
+"momb"_pair_momb.html,
+"morse (gkot)"_pair_morse.html,
+"morse/smooth/linear"_pair_morse.html,
+"morse/soft"_pair_morse.html,
+"multi/lucy"_pair_multi_lucy.html,
+"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
+"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
+"nm/cut (o)"_pair_nm.html,
+"nm/cut/coul/cut (o)"_pair_nm.html,
+"nm/cut/coul/long (o)"_pair_nm.html,
+"oxdna/coaxstk"_pair_oxdna.html,
+"oxdna/excv"_pair_oxdna.html,
+"oxdna/hbond"_pair_oxdna.html,
+"oxdna/stk"_pair_oxdna.html,
+"oxdna/xstk"_pair_oxdna.html,
+"oxdna2/coaxstk"_pair_oxdna2.html,
+"oxdna2/dh"_pair_oxdna2.html,
+"oxdna2/excv"_pair_oxdna2.html,
+"oxdna2/stk"_pair_oxdna2.html,
+"peri/eps"_pair_peri.html,
+"peri/lps (o)"_pair_peri.html,
+"peri/pmb (o)"_pair_peri.html,
+"peri/ves"_pair_peri.html,
+"polymorphic"_pair_polymorphic.html,
+"python"_pair_python.html,
+"quip"_pair_quip.html,
+"reax"_pair_reax.html,
+"reax/c (ko)"_pair_reaxc.html,
+"rebo (oi)"_pair_airebo.html,
+"resquared (go)"_pair_resquared.html,
+"smd/hertz"_pair_smd_hertz.html,
+"smd/tlsph"_pair_smd_tlsph.html,
+"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
+"smd/ulsph"_pair_smd_ulsph.html,
+"smtbq"_pair_smtbq.html,
+"snap (k)"_pair_snap.html,
+"snap (k)"_pair_snap.html,
+"soft (go)"_pair_soft.html,
+"sph/heatconduction"_pair_sph_heatconduction.html,
+"sph/idealgas"_pair_sph_idealgas.html,
+"sph/lj"_pair_sph_lj.html,
+"sph/rhosum"_pair_sph_rhosum.html,
+"sph/taitwater"_pair_sph_taitwater.html,
+"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
+"spin/dmi"_pair_spin_dmi.html,
+"spin/exchange"_pair_spin_exchange.html,
+"spin/magelec"_pair_spin_magelec.html,
+"spin/neel"_pair_spin_neel.html,
+"srp"_pair_srp.html,
+"sw (giko)"_pair_sw.html,
+"table (gko)"_pair_table.html,
+"table/rx (k)"_pair_table_rx.html,
+"tdpd"_pair_meso.html,
+"tersoff (giko)"_pair_tersoff.html,
+"tersoff/mod (gko)"_pair_tersoff_mod.html,
+"tersoff/mod/c (o)"_pair_tersoff_mod.html,
+"tersoff/table (o)"_pair_tersoff.html,
+"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
+"thole"_pair_thole.html,
+"tip4p/cut (o)"_pair_coul.html,
+"tip4p/long (o)"_pair_coul.html,
+"tip4p/long/soft (o)"_pair_lj_soft.html,
+"tri/lj"_pair_tri_lj.html,
+"ufm (got)"_pair_ufm.html,
+"vashishta (ko)"_pair_vashishta.html,
+"vashishta/table (o)"_pair_vashishta.html,
+"yukawa (gok)"_pair_yukawa.html,
+"yukawa/colloid (go)"_pair_yukawa_colloid.html,
+"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbe2261986bb8f8f96089dac3dff3a03dc39dd42
--- /dev/null
+++ b/doc/src/Commands_parse.txt
@@ -0,0 +1,136 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Parsing rules for input scripts :h3
+
+Each non-blank line in the input script is treated as a command.
+LAMMPS commands are case sensitive. Command names are lower-case, as
+are specified command arguments. Upper case letters may be used in
+file names or user-chosen ID strings.
+
+Here are 6 rulse for how each line in the input script is parsed by
+LAMMPS:
+
+(1) If the last printable character on the line is a "&" character,
+the command is assumed to continue on the next line. The next line is
+concatenated to the previous line by removing the "&" character and
+line break. This allows long commands to be continued across two or
+more lines. See the discussion of triple quotes in (6) for how to
+continue a command across multiple line without using "&" characters.
+
+(2) All characters from the first "#" character onward are treated as
+comment and discarded. See an exception in (6). Note that a
+comment after a trailing "&" character will prevent the command from
+continuing on the next line. Also note that for multi-line commands a
+single leading "#" will comment out the entire command.
+
+(3) The line is searched repeatedly for $ characters, which indicate
+variables that are replaced with a text string. See an exception in
+(6).
+
+If the $ is followed by curly brackets, then the variable name is the
+text inside the curly brackets. If no curly brackets follow the $,
+then the variable name is the single character immediately following
+the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and
+"x".
+
+How the variable is converted to a text string depends on what style
+of variable it is; see the "variable"_variable.html doc page for details.
+It can be a variable that stores multiple text strings, and return one
+of them. The returned text string can be multiple "words" (space
+separated) which will then be interpreted as multiple arguments in the
+input command. The variable can also store a numeric formula which
+will be evaluated and its numeric result returned as a string.
+
+As a special case, if the $ is followed by parenthesis, then the text
+inside the parenthesis is treated as an "immediate" variable and
+evaluated as an "equal-style variable"_variable.html. This is a way
+to use numeric formulas in an input script without having to assign
+them to variable names. For example, these 3 input script lines:
+
+variable X equal (xlo+xhi)/2+sqrt(v_area)
+region 1 block $X 2 INF INF EDGE EDGE
+variable X delete :pre
+
+can be replaced by
+
+region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
+
+so that you do not have to define (or discard) a temporary variable X.
+
+Additionally, the "immediate" variable expression may be followed by a
+colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
+The format string must be appropriate for a double-precision
+floating-point value. The format string is used to output the result
+of the variable expression evaluation. If a format string is not
+specified a high-precision "%.20g" is used as the default.
+
+This can be useful for formatting print output to a desired precion:
+
+print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
+
+Note that neither the curly-bracket or immediate form of variables can
+contain nested $ characters for other variables to substitute for.
+Thus you cannot do this:
+
+variable a equal 2
+variable b2 equal 4
+print "B2 = $\{b$a\}" :pre
+
+Nor can you specify this $($x-1.0) for an immediate variable, but
+you could use $(v_x-1.0), since the latter is valid syntax for an
+"equal-style variable"_variable.html.
+
+See the "variable"_variable.html command for more details of how
+strings are assigned to variables and evaluated, and how they can be
+used in input script commands.
+
+(4) The line is broken into "words" separated by whitespace (tabs,
+spaces). Note that words can thus contain letters, digits,
+underscores, or punctuation characters.
+
+(5) The first word is the command name. All successive words in the
+line are arguments.
+
+(6) If you want text with spaces to be treated as a single argument,
+it can be enclosed in either single or double or triple quotes. A
+long single argument enclosed in single or double quotes can span
+multiple lines if the "&" character is used, as described above. When
+the lines are concatenated together (and the "&" characters and line
+breaks removed), the text will become a single line. If you want
+multiple lines of an argument to retain their line breaks, the text
+can be enclosed in triple quotes, in which case "&" characters are not
+needed. For example:
+
+print "Volume = $v"
+print 'Volume = $v'
+if "$\{steps\} > 1000" then quit
+variable a string "red green blue &
+ purple orange cyan"
+print """
+System volume = $v
+System temperature = $t
+""" :pre
+
+In each case, the single, double, or triple quotes are removed when
+the single argument they enclose is stored internally.
+
+See the "dump modify format"_dump_modify.html, "print"_print.html,
+"if"_if.html, and "python"_python.html commands for examples.
+
+A "#" or "$" character that is between quotes will not be treated as a
+comment indicator in (2) or substituted for as a variable in (3).
+
+NOTE: If the argument is itself a command that requires a quoted
+argument (e.g. using a "print"_print.html command as part of an
+"if"_if.html or "run every"_run.html command), then single, double, or
+triple quotes can be nested in the usual manner. See the doc pages
+for those commands for examples. Only one of level of nesting is
+allowed, but that should be sufficient for most use cases.
+
diff --git a/doc/src/Commands_structure.txt b/doc/src/Commands_structure.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5d2c7b07b1f8b4afdb2d255f4953cfbba0e330b
--- /dev/null
+++ b/doc/src/Commands_structure.txt
@@ -0,0 +1,95 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Input script structure :h3
+
+This page describes the structure of a typical LAMMPS input script.
+The examples directory in the LAMMPS distribution contains many sample
+input scripts; it is discussed on the "Examples"_Examples.html doc
+page.
+
+A LAMMPS input script typically has 4 parts:
+
+Initialization
+Atom definition
+Settings
+Run a simulation :ol
+
+The last 2 parts can be repeated as many times as desired. I.e. run a
+simulation, change some settings, run some more, etc. Each of the 4
+parts is now described in more detail. Remember that almost all
+commands need only be used if a non-default value is desired.
+
+(1) Initialization
+
+Set parameters that need to be defined before atoms are created or
+read-in from a file.
+
+The relevant commands are "units"_units.html,
+"dimension"_dimension.html, "newton"_newton.html,
+"processors"_processors.html, "boundary"_boundary.html,
+"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
+
+If force-field parameters appear in the files that will be read, these
+commands tell LAMMPS what kinds of force fields are being used:
+"pair_style"_pair_style.html, "bond_style"_bond_style.html,
+"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
+"improper_style"_improper_style.html.
+
+(2) Atom definition
+
+There are 3 ways to define atoms in LAMMPS. Read them in from a data
+or restart file via the "read_data"_read_data.html or
+"read_restart"_read_restart.html commands. These files can contain
+molecular topology information. Or create atoms on a lattice (with no
+molecular topology), using these commands: "lattice"_lattice.html,
+"region"_region.html, "create_box"_create_box.html,
+"create_atoms"_create_atoms.html. The entire set of atoms can be
+duplicated to make a larger simulation using the
+"replicate"_replicate.html command.
+
+(3) Settings
+
+Once atoms and molecular topology are defined, a variety of settings
+can be specified: force field coefficients, simulation parameters,
+output options, etc.
+
+Force field coefficients are set by these commands (they can also be
+set in the read-in files): "pair_coeff"_pair_coeff.html,
+"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"improper_coeff"_improper_coeff.html,
+"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
+"special_bonds"_special_bonds.html.
+
+Various simulation parameters are set by these commands:
+"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
+"group"_group.html, "timestep"_timestep.html,
+"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
+"min_style"_min_style.html, "min_modify"_min_modify.html.
+
+Fixes impose a variety of boundary conditions, time integration, and
+diagnostic options. The "fix"_fix.html command comes in many flavors.
+
+Various computations can be specified for execution during a
+simulation using the "compute"_compute.html,
+"compute_modify"_compute_modify.html, and "variable"_variable.html
+commands.
+
+Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
+and "restart"_restart.html commands.
+
+(4) Run a simulation
+
+A molecular dynamics simulation is run using the "run"_run.html
+command. Energy minimization (molecular statics) is performed using
+the "minimize"_minimize.html command. A parallel tempering
+(replica-exchange) simulation can be run using the
+"temper"_temper.html command.
+
diff --git a/doc/src/Eqs/pair_spin_dmi_forces.jpg b/doc/src/Eqs/pair_spin_dmi_forces.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..fba6a91cbf6fdb6ee6736073a114d08c907d6d3c
Binary files /dev/null and b/doc/src/Eqs/pair_spin_dmi_forces.jpg differ
diff --git a/doc/src/Eqs/pair_spin_dmi_forces.tex b/doc/src/Eqs/pair_spin_dmi_forces.tex
new file mode 100644
index 0000000000000000000000000000000000000000..1c0c246db4c70852212f86c9a7ab7e6b518c323c
--- /dev/null
+++ b/doc/src/Eqs/pair_spin_dmi_forces.tex
@@ -0,0 +1,14 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+ \begin{equation}
+ \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right)
+ ~~{\rm and}~~
+ \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right)
+ , \nonumber
+ \end{equation}
+\end{varwidth}
+\end{document}
diff --git a/doc/src/Eqs/pair_spin_dmi_interaction.jpg b/doc/src/Eqs/pair_spin_dmi_interaction.jpg
index 1d15b2199add75eefecb424f75ea2dbd363a1afe..3eb24c67e3b26f97c362fd05982ead5fb0f5c150 100644
Binary files a/doc/src/Eqs/pair_spin_dmi_interaction.jpg and b/doc/src/Eqs/pair_spin_dmi_interaction.jpg differ
diff --git a/doc/src/Eqs/pair_spin_dmi_interaction.tex b/doc/src/Eqs/pair_spin_dmi_interaction.tex
index 5a5a776f030088efe17fcbe5e131e4686e8de2a3..79f63a333a6c823258f5d9012fa40561e00fb9cb 100644
--- a/doc/src/Eqs/pair_spin_dmi_interaction.tex
+++ b/doc/src/Eqs/pair_spin_dmi_interaction.tex
@@ -5,7 +5,7 @@
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
- \bm{H}_{dm} = -\sum_{{ i,j}=1,i\neq j}^{N}
+ \bm{H}_{dm} = \sum_{{ i,j}=1,i\neq j}^{N}
\left( \vec{e}_{ij} \times \vec{D} \right)
\cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right),
\nonumber
diff --git a/doc/src/Eqs/pair_spin_exchange_forces.jpg b/doc/src/Eqs/pair_spin_exchange_forces.jpg
index 2b0469bf4db84885fd8b81679cdd9571ba9e3574..b312a9ccdaaf44b7647f2c444c7d79a740cea88c 100644
Binary files a/doc/src/Eqs/pair_spin_exchange_forces.jpg and b/doc/src/Eqs/pair_spin_exchange_forces.jpg differ
diff --git a/doc/src/Eqs/pair_spin_exchange_forces.tex b/doc/src/Eqs/pair_spin_exchange_forces.tex
index 088696d5efbc8f44b7b9c5f87ca8984984927f2f..ac5ef682f3ca9d9532ff6d258cb1012529058636 100644
--- a/doc/src/Eqs/pair_spin_exchange_forces.tex
+++ b/doc/src/Eqs/pair_spin_exchange_forces.tex
@@ -5,10 +5,12 @@
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
- \vec{F}^{i} = \sum_{j}^{Neighbor} \frac{\partial {J} \left(r_{ij} \right)}{
- \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{r}_{ij}
- ~~{\rm and}~~ \vec{\omega}^{i} = \frac{1}{\hbar} \sum_{j}^{Neighbor} {J}
- \left(r_{ij} \right)\,\vec{s}_{j} \nonumber
+ \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J}
+ \left(r_{ij} \right)\,\vec{s}_{j}
+ ~~{\rm and}~~
+ \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
+ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
+ \nonumber
\end{equation}
\end{varwidth}
\end{document}
diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.jpg b/doc/src/Eqs/pair_spin_exchange_interaction.jpg
index d51524d27ca413ec4ded189107c2219b061f7d7e..c70d8a6554003e37472d648c1944a13ee9d3f859 100644
Binary files a/doc/src/Eqs/pair_spin_exchange_interaction.jpg and b/doc/src/Eqs/pair_spin_exchange_interaction.jpg differ
diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.tex b/doc/src/Eqs/pair_spin_exchange_interaction.tex
index 6e598f75ac04b4318c8d5679c032a75c5e82aeec..f20b3e5740ce2db9cb86a70910ca2b80f263fe4f 100644
--- a/doc/src/Eqs/pair_spin_exchange_interaction.tex
+++ b/doc/src/Eqs/pair_spin_exchange_interaction.tex
@@ -5,7 +5,7 @@
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
- \bm{H}_{exchange} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
+ \bm{H}_{ex} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
\end{equation}
\end{varwidth}
\end{document}
diff --git a/doc/src/Errors.txt b/doc/src/Errors.txt
index 7bc520c19dbacc86aaa7a1bd4083f884bde53752..1b6206c780e7a8e02ea5303ad09889dd070e44a0 100644
--- a/doc/src/Errors.txt
+++ b/doc/src/Errors.txt
@@ -1,10 +1,10 @@
"Previous Section"_Python.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_history.html :c
+Section"_Manual.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Errors_bugs.txt b/doc/src/Errors_bugs.txt
index c0a94c7a44b124bc6d987b40d9f0b25ca9b520b5..4a8e62e77546206de35b1132a3484d731db61af3 100644
--- a/doc/src/Errors_bugs.txt
+++ b/doc/src/Errors_bugs.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Errors_common.txt b/doc/src/Errors_common.txt
index 86a25f7e7d4b262fc4e730b42a5584ce76133d12..43d1a85a7bd0ff2772c5dfeb690073d93d50bb10 100644
--- a/doc/src/Errors_common.txt
+++ b/doc/src/Errors_common.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt
index 1563e029014e2d118fa3c9ae139b656597ced62d..03fc25b5618c3b6803c719cdbb5473edad5cbf6a 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -21,9 +21,9 @@ means that line #78 in the file src/velocity.cpp generated the error.
Looking in the source code may help you figure out what went wrong.
Note that error messages from "user-contributed
-packages"_Section_package.html#table_user are not listed here. If
-such an error occurs and is not self-explanatory, you'll need to look
-in the source code or contact the author of the package.
+packages"_Packages_user.html are not listed here. If such an error
+occurs and is not self-explanatory, you'll need to look in the source
+code or contact the author of the package.
Doc page with "WARNING messages"_Errors_warnings.html
diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt
index 0324f563b6870e8636f15d5cc9a9486b8b7ad334..dd3402ba8641c487f1a6a4210fa27f1b6ae062ff 100644
--- a/doc/src/Errors_warnings.txt
+++ b/doc/src/Errors_warnings.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -21,9 +21,9 @@ means that line #187 in the file src/domain.cpp generated the error.
Looking in the source code may help you figure out what went wrong.
Note that warning messages from "user-contributed
-packages"_Section_start.html#table_user are not listed here. If such
-a warning occurs and is not self-explanatory, you'll need to look in
-the source code or contact the author of the package.
+packages"_Packages_user.html are not listed here. If such a warning
+occurs and is not self-explanatory, you'll need to look in the source
+code or contact the author of the package.
Doc page with "ERROR messages"_Errors_messages.html
diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt
index 08afca8b202df67f941182e7e00320118ecb48e2..5bd8da2409185873b745cc87b1ae95b5a0b6ac1b 100644
--- a/doc/src/Examples.txt
+++ b/doc/src/Examples.txt
@@ -1,10 +1,10 @@
-"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_perf.html :c
+"Previous Section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Tools.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -143,5 +143,5 @@ The USER directory has a large number of sub-directories which
correspond by name to a USER package. They contain scripts that
illustrate how to use the command(s) provided in that package. Many
of the sub-directories have their own README files which give further
-instructions. See the "Section 4"_Section_packages.html doc
+instructions. See the "Packages_details"_Packages_details.html doc
page for more info on specific USER packages.
diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9a60d1ef4b8e8365683794e5bfc96d5fc325b32
--- /dev/null
+++ b/doc/src/Howto.txt
@@ -0,0 +1,128 @@
+"Previous Section"_Performance.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Examples.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html#comm)
+
+:line
+
+How to discussions :h2
+
+These doc pages describe how to perform various tasks with LAMMPS,
+both for users and developers. The
+"glossary"_http://lammps.sandia.gov website page also lists MD
+terminology with links to corresponding LAMMPS manual pages.
+
+The example input scripts included in the examples dir of the LAMMPS
+distribution and highlighted on the "Examples"_Examples.html doc page
+also show how to setup and run various kinds of simulations.
+
+<!-- RST
+
+.. toctree::
+
+ Howto_github
+ Howto_pylammps
+ Howto_bash
+
+.. toctree::
+
+ Howto_restart
+ Howto_viz
+ Howto_multiple
+ Howto_replica
+ Howto_library
+ Howto_couple
+
+.. toctree::
+
+ Howto_output
+ Howto_chunk
+
+.. toctree::
+
+ Howto_2d
+ Howto_triclinic
+ Howto_walls
+ Howto_nemd
+ Howto_granular
+ Howto_spherical
+ Howto_dispersion
+
+.. toctree::
+
+ Howto_temperature
+ Howto_thermostat
+ Howto_barostat
+ Howto_elastic
+ Howto_kappa
+ Howto_viscosity
+ Howto_diffusion
+
+.. toctree::
+
+ Howto_bioFF
+ Howto_tip3p
+ Howto_tip4p
+ Howto_spc
+
+.. toctree::
+
+ Howto_body
+ Howto_polarizable
+ Howto_coreshell
+ Howto_drude
+ Howto_drude2
+ Howto_manifold
+ Howto_spins
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Using GitHub with LAMMPS"_Howto_github.html
+"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
+"Using LAMMPS with bash on Windows"_Howto_bash.html
+
+"Restart a simulation"_Howto_restart.html
+"Visualize LAMMPS snapshots"_Howto_viz.html
+"Run multiple simulations from one input script"_Howto_multiple.html
+"Multi-replica simulations"_Howto_replica.html
+"Library interface to LAMMPS"_Howto_library.html
+"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
+
+"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
+"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
+
+"2d simulations"_Howto_2d.html
+"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
+"Walls"_Howto_walls.html
+"NEMD simulations"_Howto_nemd.html
+"Granular models"_Howto_granular.html
+"Finite-size spherical and aspherical particles"_Howto_spherical.html
+"Long-range dispersion settings"_Howto_dispersion.html :all(b)
+
+"Calculate temperature"_Howto_temperature.html
+"Thermostats"_Howto_thermostat.html
+"Barostats"_Howto_barostat.html
+"Calculate elastic constants"_Howto_elastic.html
+"Calculate thermal conductivity"_Howto_kappa.html
+"Calculate viscosity"_Howto_viscosity.html
+"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
+
+"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
+"TIP3P water model"_Howto_tip3p.html
+"TIP4P water model"_Howto_tip4p.html
+"SPC water model"_Howto_spc.html :all(b)
+
+"Body style particles"_Howto_body.html
+"Polarizable models"_Howto_polarizable.html
+"Adiabatic core/shell model"_Howto_coreshell.html
+"Drude induced dipoles"_Howto_drude.html
+"Drude induced dipoles (extended)"_Howto_drude2.html :all(b)
+"Manifolds (surfaces)"_Howto_manifold.html
+"Magnetic spins"_Howto_spins.html
+
+<!-- END_HTML_ONLY -->
diff --git a/doc/src/Howto_2d.txt b/doc/src/Howto_2d.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1758c05d5ff9fc771e239ba6007f98d3abbbf63
--- /dev/null
+++ b/doc/src/Howto_2d.txt
@@ -0,0 +1,48 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+2d simulations :h3
+
+Use the "dimension"_dimension.html command to specify a 2d simulation.
+
+Make the simulation box periodic in z via the "boundary"_boundary.html
+command. This is the default.
+
+If using the "create box"_create_box.html command to define a
+simulation box, set the z dimensions narrow, but finite, so that the
+create_atoms command will tile the 3d simulation box with a single z
+plane of atoms - e.g.
+
+"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre
+
+If using the "read data"_read_data.html command to read in a file of
+atom coordinates, set the "zlo zhi" values to be finite but narrow,
+similar to the create_box command settings just described. For each
+atom in the file, assign a z coordinate so it falls inside the
+z-boundaries of the box - e.g. 0.0.
+
+Use the "fix enforce2d"_fix_enforce2d.html command as the last
+defined fix to insure that the z-components of velocities and forces
+are zeroed out every timestep. The reason to make it the last fix is
+so that any forces induced by other fixes will be zeroed out.
+
+Many of the example input scripts included in the LAMMPS distribution
+are for 2d models.
+
+NOTE: Some models in LAMMPS treat particles as finite-size spheres, as
+opposed to point particles. See the "atom_style
+sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html
+commands for details. By default, for 2d simulations, such particles
+will still be modeled as 3d spheres, not 2d discs (circles), meaning
+their moment of inertia will be that of a sphere. If you wish to
+model them as 2d discs, see the "set density/disc"_set.html command
+and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html,
+"fix nvt/sphere"_fix_nvt_sphere.html, "fix
+nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html
+commands.
diff --git a/doc/src/Howto_barostat.txt b/doc/src/Howto_barostat.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c3db891524379f49fe38134186764e07eeff959
--- /dev/null
+++ b/doc/src/Howto_barostat.txt
@@ -0,0 +1,75 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Barostats :h3
+
+Barostatting means controlling the pressure in an MD simulation.
+"Thermostatting"_Howto_thermostat.html means controlling the
+temperature of the particles. Since the pressure includes a kinetic
+component due to particle velocities, both these operations require
+calculation of the temperature. Typically a target temperature (T)
+and/or pressure (P) is specified by the user, and the thermostat or
+barostat attempts to equilibrate the system to the requested T and/or
+P.
+
+Barostatting in LAMMPS is performed by "fixes"_fix.html. Two
+barosttating methods are currently available: Nose-Hoover (npt and
+nph) and Berendsen:
+
+"fix npt"_fix_nh.html
+"fix npt/sphere"_fix_npt_sphere.html
+"fix npt/asphere"_fix_npt_asphere.html
+"fix nph"_fix_nh.html
+"fix press/berendsen"_fix_press_berendsen.html :ul
+
+The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat
+and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;
+it does no thermostatting. Both "fix nph"_fix_nh.html and "fix
+press/berendsen"_fix_press_berendsen.html can be used in conjunction
+with any of the thermostatting fixes.
+
+As with the "thermostats"_Howto_thermostat.html, "fix npt"_fix_nh.html
+and "fix nph"_fix_nh.html only use translational motion of the
+particles in computing T and P and performing thermo/barostatting.
+"Fix npt/sphere"_fix_npt_sphere.html and "fix
+npt/asphere"_fix_npt_asphere.html thermo/barostat using not only
+translation velocities but also rotational velocities for spherical
+and aspherical particles.
+
+All of the barostatting fixes use the "compute
+pressure"_compute_pressure.html compute to calculate a current
+pressure. By default, this compute is created with a simple "compute
+temp"_compute_temp.html (see the last argument of the "compute
+pressure"_compute_pressure.html command), which is used to calculated
+the kinetic component of the pressure. The barostatting fixes can
+also use temperature computes that remove bias for the purpose of
+computing the kinetic component which contributes to the current
+pressure. See the doc pages for the individual fixes and for the
+"fix_modify"_fix_modify.html command for instructions on how to assign
+a temperature or pressure compute to a barostatting fix.
+
+NOTE: As with the thermostats, the Nose/Hoover methods ("fix
+npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration.
+"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should
+be used with one of the constant NVE fixes or with one of the NVT
+fixes.
+
+Thermodynamic output, which can be setup via the
+"thermo_style"_thermo_style.html command, often includes pressure
+values. As explained on the doc page for the
+"thermo_style"_thermo_style.html command, the default pressure is
+setup by the thermo command itself. It is NOT the presure associated
+with any barostatting fix you have defined or with any compute you
+have defined that calculates a presure. The doc pages for the
+barostatting fixes explain the ID of the pressure compute they create.
+Thus if you want to view these pressurse, you need to specify them
+explicitly via the "thermo_style custom"_thermo_style.html command.
+Or you can use the "thermo_modify"_thermo_modify.html command to
+re-define what pressure compute is used for default thermodynamic
+output.
diff --git a/doc/src/tutorial_bash_on_windows.txt b/doc/src/Howto_bash.txt
old mode 100644
new mode 100755
similarity index 99%
rename from doc/src/tutorial_bash_on_windows.txt
rename to doc/src/Howto_bash.txt
index 66712bdffafc8173bef83e5883bae8d3e0843ec0..f1438418e78b2bf97118992dea972e73513e0e29
--- a/doc/src/tutorial_bash_on_windows.txt
+++ b/doc/src/Howto_bash.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -10,6 +10,7 @@ Using LAMMPS with Bash on Windows :h3
[written by Richard Berger]
:line
+
Starting with Windows 10 you can install Linux tools directly in Windows. This
allows you to compile LAMMPS following the same procedure as on a real Ubuntu
Linux installation. Software can be easily installed using the package manager
diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afb8a84f2e32ac4397054054c4032ab339629290
--- /dev/null
+++ b/doc/src/Howto_bioFF.txt
@@ -0,0 +1,101 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+CHARMM, AMBER, and DREIDING force fields :h3
+
+A force field has 2 parts: the formulas that define it and the
+coefficients used for a particular system. Here we only discuss
+formulas implemented in LAMMPS that correspond to formulas commonly
+used in the CHARMM, AMBER, and DREIDING force fields. Setting
+coefficients is done in the input data file via the
+"read_data"_read_data.html command or in the input script with
+commands like "pair_coeff"_pair_coeff.html or
+"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for
+additional tools that can use CHARMM or AMBER to assign force field
+coefficients and convert their output into LAMMPS input.
+
+See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
+field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force
+field.
+
+:link(charmm,http://www.scripps.edu/brooks)
+:link(amber,http://amber.scripps.edu)
+
+These style choices compute force field formulas that are consistent
+with common options in CHARMM or AMBER. See each command's
+documentation for the formula it computes.
+
+"bond_style"_bond_harmonic.html harmonic
+"angle_style"_angle_charmm.html charmm
+"dihedral_style"_dihedral_charmm.html charmmfsh
+"dihedral_style"_dihedral_charmm.html charmm
+"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh
+"pair_style"_pair_charmm.html lj/charmmfsw/coul/long
+"pair_style"_pair_charmm.html lj/charmm/coul/charmm
+"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
+"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
+
+"special_bonds"_special_bonds.html charmm
+"special_bonds"_special_bonds.html amber :ul
+
+NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
+released in March 2017. We recommend they be used instead of the
+older {charmm} styles. See discussion of the differences on the "pair
+charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
+doc pages.
+
+DREIDING is a generic force field developed by the "Goddard
+group"_http://www.wag.caltech.edu at Caltech and is useful for
+predicting structures and dynamics of organic, biological and
+main-group inorganic molecules. The philosophy in DREIDING is to use
+general force constants and geometry parameters based on simple
+hybridization considerations, rather than individual force constants
+and geometric parameters that depend on the particular combinations of
+atoms involved in the bond, angle, or torsion terms. DREIDING has an
+"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
+interactions involving a hydrogen atom on very electronegative atoms
+(N, O, F).
+
+See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
+
+These style choices compute force field formulas that are consistent
+with the DREIDING force field. See each command's
+documentation for the formula it computes.
+
+"bond_style"_bond_harmonic.html harmonic
+"bond_style"_bond_morse.html morse :ul
+
+"angle_style"_angle_harmonic.html harmonic
+"angle_style"_angle_cosine.html cosine
+"angle_style"_angle_cosine_periodic.html cosine/periodic :ul
+
+"dihedral_style"_dihedral_charmm.html charmm
+"improper_style"_improper_umbrella.html umbrella :ul
+
+"pair_style"_pair_buck.html buck
+"pair_style"_pair_buck.html buck/coul/cut
+"pair_style"_pair_buck.html buck/coul/long
+"pair_style"_pair_lj.html lj/cut
+"pair_style"_pair_lj.html lj/cut/coul/cut
+"pair_style"_pair_lj.html lj/cut/coul/long :ul
+
+"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj
+"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul
+
+"special_bonds"_special_bonds.html dreiding :ul
+
+:line
+
+:link(howto-MacKerell)
+[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+
+:link(howto-Mayo)
+[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).
diff --git a/doc/src/body.txt b/doc/src/Howto_body.txt
similarity index 96%
rename from doc/src/body.txt
rename to doc/src/Howto_body.txt
index 4a39ac25d8c2719f3c7a24ba8559439c4003c808..3535349b461589aa6ddafdf4e9a3d684a546c2e1 100644
--- a/doc/src/body.txt
+++ b/doc/src/Howto_body.txt
@@ -1,24 +1,24 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-Body particles :h2
+Body particles :h3
[Overview:]
-This doc page is not about a LAMMPS input script command, but about
-body particles, which are generalized finite-size particles.
+In LAMMPS, body particles are generalized finite-size particles.
Individual body particles can represent complex entities, such as
surface meshes of discrete points, collections of sub-particles,
deformable objects, etc. Note that other kinds of finite-size
spherical and aspherical particles are also supported by LAMMPS, such
as spheres, ellipsoids, line segments, and triangles, but they are
-simpler entities that body particles. See "Section
-6.14"_Section_howto.html#howto_14 for a general overview of all
+simpler entities that body particles. See the "Howto
+spherical"_Howto_spherical.html doc page for a general overview of all
these particle types.
Body particles are used via the "atom_style body"_atom_style.html
@@ -151,8 +151,8 @@ center-of-mass position of the particle is specified by the x,y,z
values in the {Atoms} section of the data file, as is the total mass
of the body particle.
-The "pair_style body"_pair_body.html command can be used with this
-body style to compute body/body and body/non-body interactions.
+The "pair_style body/nparticle"_pair_body_nparticle.html command can be used
+with this body style to compute body/body and body/non-body interactions.
For output purposes via the "compute
body/local"_compute_body_local.html and "dump local"_dump.html
diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e52acf4b8693569bac54304bb5f2c0ffd56d0fb
--- /dev/null
+++ b/doc/src/Howto_chunk.txt
@@ -0,0 +1,166 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Use chunks to calculate system properties :h3
+
+In LAMMS, "chunks" are collections of atoms, as defined by the
+"compute chunk/atom"_compute_chunk_atom.html command, which assigns
+each atom to a chunk ID (or to no chunk at all). The number of chunks
+and the assignment of chunk IDs to atoms can be static or change over
+time. Examples of "chunks" are molecules or spatial bins or atoms
+with similar values (e.g. coordination number or potential energy).
+
+The per-atom chunk IDs can be used as input to two other kinds of
+commands, to calculate various properties of a system:
+
+"fix ave/chunk"_fix_ave_chunk.html
+any of the "compute */chunk"_compute.html commands :ul
+
+Here, each of the 3 kinds of chunk-related commands is briefly
+overviewed. Then some examples are given of how to compute different
+properties with chunk commands.
+
+Compute chunk/atom command: :h4
+
+This compute can assign atoms to chunks of various styles. Only atoms
+in the specified group and optional specified region are assigned to a
+chunk. Here are some possible chunk definitions:
+
+atoms in same molecule | chunk ID = molecule ID |
+atoms of same atom type | chunk ID = atom type |
+all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom |
+atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command |
+atoms in same spatial bin | chunk ID = bin ID |
+atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies |
+atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html |
+atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2)
+
+Note that chunk IDs are integer values, so for atom properties or
+computes that produce a floating point value, they will be truncated
+to an integer. You could also use the compute in a variable that
+scales the floating point value to spread it across multiple integers.
+
+Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
+pencils, 3d bins = boxes, spherical bins, cylindrical bins.
+
+This compute also calculates the number of chunks {Nchunk}, which is
+used by other commands to tally per-chunk data. {Nchunk} can be a
+static value or change over time (e.g. the number of clusters). The
+chunk ID for an individual atom can also be static (e.g. a molecule
+ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
+
+Note that this compute allows the per-atom output of other
+"computes"_compute.html, "fixes"_fix.html, and
+"variables"_variable.html to be used to define chunk IDs for each
+atom. This means you can write your own compute or fix to output a
+per-atom quantity to use as chunk ID. See the "Modify"_Modify.html
+doc pages for info on how to do this. You can also define a "per-atom
+variable"_variable.html in the input script that uses a formula to
+generate a chunk ID for each atom.
+
+Fix ave/chunk command: :h4
+
+This fix takes the ID of a "compute
+chunk/atom"_compute_chunk_atom.html command as input. For each chunk,
+it then sums one or more specified per-atom values over the atoms in
+each chunk. The per-atom values can be any atom property, such as
+velocity, force, charge, potential energy, kinetic energy, stress,
+etc. Additional keywords are defined for per-chunk properties like
+density and temperature. More generally any per-atom value generated
+by other "computes"_compute.html, "fixes"_fix.html, and "per-atom
+variables"_variable.html, can be summed over atoms in each chunk.
+
+Similar to other averaging fixes, this fix allows the summed per-chunk
+values to be time-averaged in various ways, and output to a file. The
+fix produces a global array as output with one row of values per
+chunk.
+
+Compute */chunk commands: :h4
+
+Currently the following computes operate on chunks of atoms to produce
+per-chunk values.
+
+"compute com/chunk"_compute_com_chunk.html
+"compute gyration/chunk"_compute_gyration_chunk.html
+"compute inertia/chunk"_compute_inertia_chunk.html
+"compute msd/chunk"_compute_msd_chunk.html
+"compute property/chunk"_compute_property_chunk.html
+"compute temp/chunk"_compute_temp_chunk.html
+"compute torque/chunk"_compute_vcm_chunk.html
+"compute vcm/chunk"_compute_vcm_chunk.html :ul
+
+They each take the ID of a "compute
+chunk/atom"_compute_chunk_atom.html command as input. As their names
+indicate, they calculate the center-of-mass, radius of gyration,
+moments of inertia, mean-squared displacement, temperature, torque,
+and velocity of center-of-mass for each chunk of atoms. The "compute
+property/chunk"_compute_property_chunk.html command can tally the
+count of atoms in each chunk and extract other per-chunk properties.
+
+The reason these various calculations are not part of the "fix
+ave/chunk command"_fix_ave_chunk.html, is that each requires a more
+complicated operation than simply summing and averaging over per-atom
+values in each chunk. For example, many of them require calculation
+of a center of mass, which requires summing mass*position over the
+atoms and then dividing by summed mass.
+
+All of these computes produce a global vector or global array as
+output, wih one or more values per chunk. They can be used
+in various ways:
+
+As input to the "fix ave/time"_fix_ave_time.html command, which can
+write the values to a file and optionally time average them. :ulb,l
+
+As input to the "fix ave/histo"_fix_ave_histo.html command to
+histogram values across chunks. E.g. a histogram of cluster sizes or
+molecule diffusion rates. :l
+
+As input to special functions of "equal-style
+variables"_variable.html, like sum() and max(). E.g. to find the
+largest cluster or fastest diffusing molecule. :l
+:ule
+
+Example calculations with chunks :h4
+
+Here are examples using chunk commands to calculate various
+properties:
+
+(1) Average velocity in each of 1000 2d spatial bins:
+
+compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
+fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre
+
+(2) Temperature in each spatial bin, after subtracting a flow
+velocity:
+
+compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
+compute vbias all temp/profile 1 0 0 y 10
+fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre
+
+(3) Center of mass of each molecule:
+
+compute cc1 all chunk/atom molecule
+compute myChunk all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre
+
+(4) Total force on each molecule and ave/max across all molecules:
+
+compute cc1 all chunk/atom molecule
+fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
+variable xave equal ave(f_1\[2\])
+variable xmax equal max(f_1\[2\])
+thermo 1000
+thermo_style custom step temp v_xave v_xmax :pre
+
+(5) Histogram of cluster sizes:
+
+compute cluster all cluster/atom 1.0
+compute cc1 all chunk/atom c_cluster compress yes
+compute size all property/chunk cc1 count
+fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
diff --git a/doc/src/Howto_coreshell.txt b/doc/src/Howto_coreshell.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f1cd64384e696dbf00eccf023a3a10be8f40cc9
--- /dev/null
+++ b/doc/src/Howto_coreshell.txt
@@ -0,0 +1,253 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Adiabatic core/shell model :h3
+
+The adiabatic core-shell model by "Mitchell and
+Fincham"_#MitchellFincham is a simple method for adding polarizability
+to a system. In order to mimic the electron shell of an ion, a
+satellite particle is attached to it. This way the ions are split into
+a core and a shell where the latter is meant to react to the
+electrostatic environment inducing polarizability. See the "Howto
+polarizable"_Howto_polarizable.html doc page for a discussion of all
+the polarizable models available in LAMMPS.
+
+Technically, shells are attached to the cores by a spring force f =
+k*r where k is a parametrized spring constant and r is the distance
+between the core and the shell. The charges of the core and the shell
+add up to the ion charge, thus q(ion) = q(core) + q(shell). This
+setup introduces the ion polarizability (alpha) given by
+alpha = q(shell)^2 / k. In a
+similar fashion the mass of the ion is distributed on the core and the
+shell with the core having the larger mass.
+
+To run this model in LAMMPS, "atom_style"_atom_style.html {full} can
+be used since atom charge and bonds are needed. Each kind of
+core/shell pair requires two atom types and a bond type. The core and
+shell of a core/shell pair should be bonded to each other with a
+harmonic bond that provides the spring force. For example, a data file
+for NaCl, as found in examples/coreshell, has this format:
+
+432 atoms # core and shell atoms
+216 bonds # number of core/shell springs :pre
+
+4 atom types # 2 cores and 2 shells for Na and Cl
+2 bond types :pre
+
+0.0 24.09597 xlo xhi
+0.0 24.09597 ylo yhi
+0.0 24.09597 zlo zhi :pre
+
+Masses # core/shell mass ratio = 0.1 :pre
+
+1 20.690784 # Na core
+2 31.90500 # Cl core
+3 2.298976 # Na shell
+4 3.54500 # Cl shell :pre
+
+Atoms :pre
+
+1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
+2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
+3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
+4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
+(...) :pre
+
+Bonds # Bond topology for spring forces :pre
+
+1 2 1 2 # spring for core/shell pair 1
+2 2 3 4 # spring for core/shell pair 2
+(...) :pre
+
+Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
+defined between the shells. Coulombic interactions are defined
+between all cores and shells. If desired, additional bonds can be
+specified between cores.
+
+The "special_bonds"_special_bonds.html command should be used to
+turn-off the Coulombic interaction within core/shell pairs, since that
+interaction is set by the bond spring. This is done using the
+"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0,
+which is the default value. It needs to be considered whether one has
+to adjust the "special_bonds"_special_bonds.html weighting according
+to the molecular topology since the interactions of the shells are
+bypassed over an extra bond.
+
+Note that this core/shell implementation does not require all ions to
+be polarized. One can mix core/shell pairs and ions without a
+satellite particle if desired.
+
+Since the core/shell model permits distances of r = 0.0 between the
+core and shell, a pair style with a "cs" suffix needs to be used to
+implement a valid long-range Coulombic correction. Several such pair
+styles are provided in the CORESHELL package. See "this doc
+page"_pair_cs.html for details. All of the core/shell enabled pair
+styles require the use of a long-range Coulombic solver, as specified
+by the "kspace_style"_kspace_style.html command. Either the PPPM or
+Ewald solvers can be used.
+
+For the NaCL example problem, these pair style and bond style settings
+are used:
+
+pair_style born/coul/long/cs 20.0 20.0
+pair_coeff * * 0.0 1.000 0.00 0.00 0.00
+pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
+pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
+pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre
+
+bond_style harmonic
+bond_coeff 1 63.014 0.0
+bond_coeff 2 25.724 0.0 :pre
+
+When running dynamics with the adiabatic core/shell model, the
+following issues should be considered. The relative motion of
+the core and shell particles corresponds to the polarization,
+hereby an instantaneous relaxation of the shells is approximated
+and a fast core/shell spring frequency ensures a nearly constant
+internal kinetic energy during the simulation.
+Thermostats can alter this polarization behaviour, by scaling the
+internal kinetic energy, meaning the shell will not react freely to
+its electrostatic environment.
+Therefore it is typically desirable to decouple the relative motion of
+the core/shell pair, which is an imaginary degree of freedom, from the
+real physical system. To do that, the "compute
+temp/cs"_compute_temp_cs.html command can be used, in conjunction with
+any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
+langevin"_fix_langevin. This compute uses the center-of-mass velocity
+of the core/shell pairs to calculate a temperature, and insures that
+velocity is what is rescaled for thermostatting purposes. This
+compute also works for a system with both core/shell pairs and
+non-polarized ions (ions without an attached satellite particle). The
+"compute temp/cs"_compute_temp_cs.html command requires input of two
+groups, one for the core atoms, another for the shell atoms.
+Non-polarized ions which might also be included in the treated system
+should not be included into either of these groups, they are taken
+into account by the {group-ID} (2nd argument) of the compute. The
+groups can be defined using the "group {type}"_group.html command.
+Note that to perform thermostatting using this definition of
+temperature, the "fix modify temp"_fix_modify.html command should be
+used to assign the compute to the thermostat fix. Likewise the
+"thermo_modify temp"_thermo_modify.html command can be used to make
+this temperature be output for the overall system.
+
+For the NaCl example, this can be done as follows:
+
+group cores type 1 2
+group shells type 3 4
+compute CSequ all temp/cs cores shells
+fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
+fix thermostatequ all nve # integrator as needed for the berendsen thermostat
+fix_modify thermoberendsen temp CSequ
+thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
+
+The pressure for the core/shell system is computed via the regular
+LAMMPS convention by "treating the cores and shells as individual
+particles"_#MitchellFincham2. For the thermo output of the pressure
+as well as for the application of a barostat, it is necessary to
+use an additional "pressure"_compute_pressure compute based on the
+default "temperature"_compute_temp and specifying it as a second
+argument in "fix modify"_fix_modify.html and
+"thermo_modify"_thermo_modify.html resulting in:
+
+(...)
+compute CSequ all temp/cs cores shells
+compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles
+thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure
+fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
+fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre
+
+If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
+relative motion of the core and the shell should in theory be
+stable. However numerical fluctuation can introduce a small
+momentum to the system, which is noticable over long trajectories.
+Therefore it is recommendable to use the "fix
+momentum"_fix_momentum.html command in combination with "compute
+temp/cs"_compute_temp_cs.html when equilibrating the system to
+prevent any drift.
+
+When initializing the velocities of a system with core/shell pairs, it
+is also desirable to not introduce energy into the relative motion of
+the core/shell particles, but only assign a center-of-mass velocity to
+the pairs. This can be done by using the {bias} keyword of the
+"velocity create"_velocity.html command and assigning the "compute
+temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
+"velocity"_velocity.html command, e.g.
+
+velocity all create 1427 134 bias yes temp CSequ
+velocity all scale 1427 temp CSequ :pre
+
+To maintain the correct polarizability of the core/shell pairs, the
+kinetic energy of the internal motion shall remain nearly constant.
+Therefore the choice of spring force and mass ratio need to ensure
+much faster relative motion of the 2 atoms within the core/shell pair
+than their center-of-mass velocity. This allows the shells to
+effectively react instantaneously to the electrostatic environment and
+limits energy transfer to or from the core/shell oscillators.
+This fast movement also dictates the timestep that can be used.
+
+The primary literature of the adiabatic core/shell model suggests that
+the fast relative motion of the core/shell pairs only allows negligible
+energy transfer to the environment.
+The mentioned energy transfer will typically lead to a small drift
+in total energy over time. This internal energy can be monitored
+using the "compute chunk/atom"_compute_chunk_atom.html and "compute
+temp/chunk"_compute_temp_chunk.html commands. The internal kinetic
+energies of each core/shell pair can then be summed using the sum()
+special function of the "variable"_variable.html command. Or they can
+be time/averaged and output using the "fix ave/time"_fix_ave_time.html
+command. To use these commands, each core/shell pair must be defined
+as a "chunk". If each core/shell pair is defined as its own molecule,
+the molecule ID can be used to define the chunks. If cores are bonded
+to each other to form larger molecules, the chunks can be identified
+by the "fix property/atom"_fix_property_atom.html via assigning a
+core/shell ID to each atom using a special field in the data file read
+by the "read_data"_read_data.html command. This field can then be
+accessed by the "compute property/atom"_compute_property_atom.html
+command, to use as input to the "compute
+chunk/atom"_compute_chunk_atom.html command to define the core/shell
+pairs as chunks.
+
+For example if core/shell pairs are the only molecules:
+
+read_data NaCl_CS_x0.1_prop.data
+compute prop all property/atom molecule
+compute cs_chunk all chunk/atom c_prop
+compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
+fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
+
+For example if core/shell pairs and other molecules are present:
+
+fix csinfo all property/atom i_CSID # property/atom command
+read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
+compute prop all property/atom i_CSID
+(...) :pre
+
+The additional section in the date file would be formatted like this:
+
+CS-Info # header of additional section :pre
+
+1 1 # column 1 = atom ID, column 2 = core/shell ID
+2 1
+3 2
+4 2
+5 3
+6 3
+7 4
+8 4
+(...) :pre
+
+:line
+
+:link(MitchellFincham)
+[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter,
+5, 1031-1038 (1993).
+
+:link(MitchellFincham2)
+[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
+6, 393-404 (1994).
diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38595a9d1641ddb869cf5606ce003c2189690813
--- /dev/null
+++ b/doc/src/Howto_couple.txt
@@ -0,0 +1,105 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Coupling LAMMPS to other codes :h3
+
+LAMMPS is designed to allow it to be coupled to other codes. For
+example, a quantum mechanics code might compute forces on a subset of
+atoms and pass those forces to LAMMPS. Or a continuum finite element
+(FE) simulation might use atom positions as boundary conditions on FE
+nodal points, compute a FE solution, and return interpolated forces on
+MD atoms.
+
+LAMMPS can be coupled to other codes in at least 3 ways. Each has
+advantages and disadvantages, which you'll have to think about in the
+context of your application.
+
+(1) Define a new "fix"_fix.html command that calls the other code. In
+this scenario, LAMMPS is the driver code. During its timestepping,
+the fix is invoked, and can make library calls to the other code,
+which has been linked to LAMMPS as a library. This is the way the
+"POEMS"_poems package that performs constrained rigid-body motion on
+groups of atoms is hooked to LAMMPS. See the "fix
+poems"_fix_poems.html command for more details. See the
+"Modify"_Modify.html doc pages for info on how to add a new fix to
+LAMMPS.
+
+:link(poems,http://www.rpi.edu/~anderk5/lab)
+
+(2) Define a new LAMMPS command that calls the other code. This is
+conceptually similar to method (1), but in this case LAMMPS and the
+other code are on a more equal footing. Note that now the other code
+is not called during the timestepping of a LAMMPS run, but between
+runs. The LAMMPS input script can be used to alternate LAMMPS runs
+with calls to the other code, invoked via the new command. The
+"run"_run.html command facilitates this with its {every} option, which
+makes it easy to run a few steps, invoke the command, run a few steps,
+invoke the command, etc.
+
+In this scenario, the other code can be called as a library, as in
+(1), or it could be a stand-alone code, invoked by a system() call
+made by the command (assuming your parallel machine allows one or more
+processors to start up another program). In the latter case the
+stand-alone code could communicate with LAMMPS thru files that the
+command writes and reads.
+
+See the "Modify command"_Modify_command.html doc page for info on how
+to add a new command to LAMMPS.
+
+(3) Use LAMMPS as a library called by another code. In this case the
+other code is the driver and calls LAMMPS as needed. Or a wrapper
+code could link and call both LAMMPS and another code as libraries.
+Again, the "run"_run.html command has options that allow it to be
+invoked with minimal overhead (no setup or clean-up) if you wish to do
+multiple short runs, driven by another program.
+
+Examples of driver codes that call LAMMPS as a library are included in
+the examples/COUPLE directory of the LAMMPS distribution; see
+examples/COUPLE/README for more details:
+
+simple: simple driver programs in C++ and C which invoke LAMMPS as a
+library :ulb,l
+
+lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical
+MD with quantum forces calculated by a density functional code :l
+
+lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple
+a kinetic Monte Carlo model for grain growth using MD to calculate
+strain induced across grain boundaries :l
+:ule
+
+:link(quest,http://dft.sandia.gov/Quest)
+:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
+
+"This section"_Section_start.html#start_5 of the documentation
+describes how to build LAMMPS as a library. Once this is done, you
+can interface with LAMMPS either via C++, C, Fortran, or Python (or
+any other language that supports a vanilla C-like interface). For
+example, from C++ you could create one (or more) "instances" of
+LAMMPS, pass it an input script to process, or execute individual
+commands, all by invoking the correct class methods in LAMMPS. From C
+or Fortran you can make function calls to do the same things. See the
+"Python"_Python.html doc pages for a description of the Python wrapper
+provided with LAMMPS that operates through the LAMMPS library
+interface.
+
+The files src/library.cpp and library.h contain the C-style interface
+to LAMMPS. See the "Howto library"_Howto_library.html doc page for a
+description of the interface and how to extend it for your needs.
+
+Note that the lammps_open() function that creates an instance of
+LAMMPS takes an MPI communicator as an argument. This means that
+instance of LAMMPS will run on the set of processors in the
+communicator. Thus the calling code can run LAMMPS on all or a subset
+of processors. For example, a wrapper script might decide to
+alternate between LAMMPS and another code, allowing them both to run
+on all the processors. Or it might allocate half the processors to
+LAMMPS and half to the other code and run both codes simultaneously
+before syncing them up periodically. Or it might instantiate multiple
+instances of LAMMPS to perform different calculations.
diff --git a/doc/src/Howto_diffusion.txt b/doc/src/Howto_diffusion.txt
new file mode 100644
index 0000000000000000000000000000000000000000..401c1e359c05ee83ef37ecbae44073cdd4ecfacf
--- /dev/null
+++ b/doc/src/Howto_diffusion.txt
@@ -0,0 +1,31 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Calculate a diffusion coefficient :h3
+
+The diffusion coefficient D of a material can be measured in at least
+2 ways using various options in LAMMPS. See the examples/DIFFUSE
+directory for scripts that implement the 2 methods discussed here for
+a simple Lennard-Jones fluid model.
+
+The first method is to measure the mean-squared displacement (MSD) of
+the system, via the "compute msd"_compute_msd.html command. The slope
+of the MSD versus time is proportional to the diffusion coefficient.
+The instantaneous MSD values can be accumulated in a vector via the
+"fix vector"_fix_vector.html command, and a line fit to the vector to
+compute its slope via the "variable slope"_variable.html function, and
+thus extract D.
+
+The second method is to measure the velocity auto-correlation function
+(VACF) of the system, via the "compute vacf"_compute_vacf.html
+command. The time-integral of the VACF is proportional to the
+diffusion coefficient. The instantaneous VACF values can be
+accumulated in a vector via the "fix vector"_fix_vector.html command,
+and time integrated via the "variable trap"_variable.html function,
+and thus extract D.
diff --git a/doc/src/Howto_dispersion.txt b/doc/src/Howto_dispersion.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ea286258e11a38aa07e6e93df4c3e22cb0aca0a
--- /dev/null
+++ b/doc/src/Howto_dispersion.txt
@@ -0,0 +1,108 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Long-raage dispersion settings :h3
+
+The PPPM method computes interactions by splitting the pair potential
+into two parts, one of which is computed in a normal pairwise fashion,
+the so-called real-space part, and one of which is computed using the
+Fourier transform, the so called reciprocal-space or kspace part. For
+both parts, the potential is not computed exactly but is approximated.
+Thus, there is an error in both parts of the computation, the
+real-space and the kspace error. The just mentioned facts are true
+both for the PPPM for Coulomb as well as dispersion interactions. The
+deciding difference - and also the reason why the parameters for
+pppm/disp have to be selected with more care - is the impact of the
+errors on the results: The kspace error of the PPPM for Coulomb and
+dispersion interaction and the real-space error of the PPPM for
+Coulomb interaction have the character of noise. In contrast, the
+real-space error of the PPPM for dispersion has a clear physical
+interpretation: the underprediction of cohesion. As a consequence, the
+real-space error has a much stronger effect than the kspace error on
+simulation results for pppm/disp. Parameters must thus be chosen in a
+way that this error is much smaller than the kspace error.
+
+When using pppm/disp and not making any specifications on the PPPM
+parameters via the kspace modify command, parameters will be tuned
+such that the real-space error and the kspace error are equal. This
+will result in simulations that are either inaccurate or slow, both of
+which is not desirable. For selecting parameters for the pppm/disp
+that provide fast and accurate simulations, there are two approaches,
+which both have their up- and downsides.
+
+The first approach is to set desired real-space an kspace accuracies
+via the {kspace_modify force/disp/real} and {kspace_modify
+force/disp/kspace} commands. Note that the accuracies have to be
+specified in force units and are thus dependent on the chosen unit
+settings. For real units, 0.0001 and 0.002 seem to provide reasonable
+accurate and efficient computations for the real-space and kspace
+accuracies. 0.002 and 0.05 work well for most systems using lj
+units. PPPM parameters will be generated based on the desired
+accuracies. The upside of this approach is that it usually provides a
+good set of parameters and will work for both the {kspace_modify diff
+ad} and {kspace_modify diff ik} options. The downside of the method
+is that setting the PPPM parameters will take some time during the
+initialization of the simulation.
+
+The second approach is to set the parameters for the pppm/disp
+explicitly using the {kspace_modify mesh/disp}, {kspace_modify
+order/disp}, and {kspace_modify gewald/disp} commands. This approach
+requires a more experienced user who understands well the impact of
+the choice of parameters on the simulation accuracy and
+performance. This approach provides a fast initialization of the
+simulation. However, it is sensitive to errors: A combination of
+parameters that will perform well for one system might result in
+far-from-optimal conditions for other simulations. For example,
+parameters that provide accurate and fast computations for
+all-atomistic force fields can provide insufficient accuracy or
+united-atomistic force fields (which is related to that the latter
+typically have larger dispersion coefficients).
+
+To avoid inaccurate or inefficient simulations, the pppm/disp stops
+simulations with an error message if no action is taken to control the
+PPPM parameters. If the automatic parameter generation is desired and
+real-space and kspace accuracies are desired to be equal, this error
+message can be suppressed using the {kspace_modify disp/auto yes}
+command.
+
+A reasonable approach that combines the upsides of both methods is to
+make the first run using the {kspace_modify force/disp/real} and
+{kspace_modify force/disp/kspace} commands, write down the PPPM
+parameters from the outut, and specify these parameters using the
+second approach in subsequent runs (which have the same composition,
+force field, and approximately the same volume).
+
+Concerning the performance of the pppm/disp there are two more things
+to consider. The first is that when using the pppm/disp, the cutoff
+parameter does no longer affect the accuracy of the simulation
+(subject to that gewald/disp is adjusted when changing the cutoff).
+The performance can thus be increased by examining different values
+for the cutoff parameter. A lower bound for the cutoff is only set by
+the truncation error of the repulsive term of pair potentials.
+
+The second is that the mixing rule of the pair style has an impact on
+the computation time when using the pppm/disp. Fastest computations
+are achieved when using the geometric mixing rule. Using the
+arithmetic mixing rule substantially increases the computational cost.
+The computational overhead can be reduced using the {kspace_modify
+mix/disp geom} and {kspace_modify splittol} commands. The first
+command simply enforces geometric mixing of the dispersion
+coefficients in kspace computations. This introduces some error in
+the computations but will also significantly speed-up the
+simulations. The second keyword sets the accuracy with which the
+dispersion coefficients are approximated using a matrix factorization
+approach. This may result in better accuracy then using the first
+command, but will usually also not provide an equally good increase of
+efficiency.
+
+Finally, pppm/disp can also be used when no mixing rules apply.
+This can be achieved using the {kspace_modify mix/disp none} command.
+Note that the code does not check automatically whether any mixing
+rule is fulfilled. If mixing rules do not apply, the user will have
+to specify this command explicitly.
diff --git a/doc/src/Howto_drude.txt b/doc/src/Howto_drude.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebdf5f865824a365220f1a58214fd06f111dcae2
--- /dev/null
+++ b/doc/src/Howto_drude.txt
@@ -0,0 +1,77 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Drude induced dipoles :h3
+
+The thermalized Drude model represents induced dipoles by a pair of
+charges (the core atom and the Drude particle) connected by a harmonic
+spring. See the "Howto polarizable"_Howto_polarizable.html doc page
+for a discussion of all the polarizable models available in LAMMPS.
+
+The Drude model has a number of features aimed at its use in
+molecular systems ("Lamoureux and Roux"_#howto-Lamoureux):
+
+Thermostating of the additional degrees of freedom associated with the
+induced dipoles at very low temperature, in terms of the reduced
+coordinates of the Drude particles with respect to their cores. This
+makes the trajectory close to that of relaxed induced dipoles. :ulb,l
+
+Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
+pair represents a single (polarizable) atom, so the special screening
+factors in a covalent structure should be the same for the core and
+the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
+special neighbor relations from their respective cores. :l
+
+Stabilization of the interactions between induced dipoles. Drude
+dipoles on covalently bonded atoms interact too strongly due to the
+short distances, so an atom may capture the Drude particle of a
+neighbor, or the induced dipoles within the same molecule may align
+too much. To avoid this, damping at short range can be done by Thole
+functions (for which there are physical grounds). This Thole damping
+is applied to the point charges composing the induced dipole (the
+charge of the Drude particle and the opposite charge on the core, not
+to the total charge of the core atom). :l,ule
+
+A detailed tutorial covering the usage of Drude induced dipoles in
+LAMMPS is on the "Howto drude2e"_Howto_drude2.html doc page.
+
+As with the core-shell model, the cores and Drude particles should
+appear in the data file as standard atoms. The same holds for the
+springs between them, which are described by standard harmonic bonds.
+The nature of the atoms (core, Drude particle or non-polarizable) is
+specified via the "fix drude"_fix_drude.html command. The special
+list of neighbors is automatically refactored to account for the
+equivalence of core and Drude particles as regards special 1-2 to 1-4
+screening. It may be necessary to use the {extra/special/per/atom}
+keyword of the "read_data"_read_data.html command. If using "fix
+shake"_fix_shake.html, make sure no Drude particle is in this fix
+group.
+
+There are two ways to thermostat the Drude particles at a low
+temperature: use either "fix langevin/drude"_fix_langevin_drude.html
+for a Langevin thermostat, or "fix
+drude/transform/*"_fix_drude_transform.html for a Nose-Hoover
+thermostat. The former requires use of the command "comm_modify vel
+yes"_comm_modify.html. The latter requires two separate integration
+fixes like {nvt} or {npt}. The correct temperatures of the reduced
+degrees of freedom can be calculated using the "compute
+temp/drude"_compute_temp_drude.html. This requires also to use the
+command {comm_modify vel yes}.
+
+Short-range damping of the induced dipole interactions can be achieved
+using Thole functions through the "pair style
+thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
+with a Coulomb pair style. It may be useful to use {coul/long/cs} or
+similar from the CORESHELL package if the core and Drude particle come
+too close, which can cause numerical issues.
+
+:line
+
+:link(howto-Lamoureux)
+[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
diff --git a/doc/src/tutorial_drude.txt b/doc/src/Howto_drude2.txt
similarity index 99%
rename from doc/src/tutorial_drude.txt
rename to doc/src/Howto_drude2.txt
index f6e7eed40bd84cde46e30213c0a14c22244eae86..a342d4a87d1deec93cbb9820a39099aaf5fb75a6 100644
--- a/doc/src/tutorial_drude.txt
+++ b/doc/src/Howto_drude2.txt
@@ -9,7 +9,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Howto_elastic.txt b/doc/src/Howto_elastic.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68b30970ca33a84308b32bb1516081f49470367e
--- /dev/null
+++ b/doc/src/Howto_elastic.txt
@@ -0,0 +1,47 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Calculate elastic constants :h3
+
+Elastic constants characterize the stiffness of a material. The formal
+definition is provided by the linear relation that holds between the
+stress and strain tensors in the limit of infinitesimal deformation.
+In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where
+the repeated indices imply summation. s_ij are the elements of the
+symmetric stress tensor. e_kl are the elements of the symmetric strain
+tensor. C_ijkl are the elements of the fourth rank tensor of elastic
+constants. In three dimensions, this tensor has 3^4=81 elements. Using
+Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
+is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
+derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
+most 7*6/2 = 21 distinct elements.
+
+At zero temperature, it is easy to estimate these derivatives by
+deforming the simulation box in one of the six directions using the
+"change_box"_change_box.html command and measuring the change in the
+stress tensor. A general-purpose script that does this is given in the
+examples/elastic directory described on the "Examples"_Examples.html
+doc page.
+
+Calculating elastic constants at finite temperature is more
+challenging, because it is necessary to run a simulation that perfoms
+time averages of differential properties. One way to do this is to
+measure the change in average stress tensor in an NVT simulations when
+the cell volume undergoes a finite deformation. In order to balance
+the systematic and statistical errors in this method, the magnitude of
+the deformation must be chosen judiciously, and care must be taken to
+fully equilibrate the deformed cell before sampling the stress
+tensor. Another approach is to sample the triclinic cell fluctuations
+that occur in an NPT simulation. This method can also be slow to
+converge and requires careful post-processing "(Shinoda)"_#Shinoda1
+
+:line
+
+:link(Shinoda1)
+[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
diff --git a/doc/src/tutorial_github.txt b/doc/src/Howto_github.txt
similarity index 98%
rename from doc/src/tutorial_github.txt
rename to doc/src/Howto_github.txt
index fc261bdb958e18bdb19511f4a0ec8ecad8ad8c3e..720b3317f012eb3eaf3f32f65fc1542185359721 100644
--- a/doc/src/tutorial_github.txt
+++ b/doc/src/Howto_github.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -25,8 +25,8 @@ or improvements to LAMMPS, as it significantly reduces the amount of
work required by the LAMMPS developers. Consequently, creating a pull
request will increase your chances to have your contribution included
and will reduce the time until the integration is complete. For more
-information on the requirements to have your code included in LAMMPS,
-see the "Modify contribute"_Modify_contribute.html doc page.
+information on the requirements to have your code included into LAMMPS
+please see the "Modify contribute"_Modify_contribute.html doc page.
:line
@@ -124,7 +124,7 @@ unrelated feature, you should switch branches!
After everything is done, add the files to the branch and commit them:
- $ git add doc/src/tutorial_github.txt
+ $ git add doc/src/Howto_github.txt
$ git add doc/src/JPG/tutorial*.png :pre
IMPORTANT NOTE: Do not use {git commit -a} (or {git add -A}). The -a
@@ -318,7 +318,7 @@ Because the changes are OK with us, we are going to merge by clicking on
Now, since in the meantime our local text for the tutorial also changed,
we need to pull Axel's change back into our branch, and merge them:
- $ git add tutorial_github.txt
+ $ git add Howto_github.txt
$ git add JPG/tutorial_reverse_pull_request*.png
$ git commit -m "Updated text and images on reverse pull requests"
$ git pull :pre
@@ -331,7 +331,7 @@ With Axel's changes merged in and some final text updates, our feature
branch is now perfect as far as we are concerned, so we are going to
commit and push again:
- $ git add tutorial_github.txt
+ $ git add Howto_github.txt
$ git add JPG/tutorial_reverse_pull_request6.png
$ git commit -m "Merged Axel's suggestions and updated text"
$ git push git@github.com:Pakketeretet2/lammps :pre
diff --git a/doc/src/Howto_granular.txt b/doc/src/Howto_granular.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8027369501eb0730dd4008b56503d95642ee9380
--- /dev/null
+++ b/doc/src/Howto_granular.txt
@@ -0,0 +1,57 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Granular models :h3
+
+Granular system are composed of spherical particles with a diameter,
+as opposed to point particles. This means they have an angular
+velocity and torque can be imparted to them to cause them to rotate.
+
+To run a simulation of a granular model, you will want to use
+the following commands:
+
+"atom_style sphere"_atom_style.html
+"fix nve/sphere"_fix_nve_sphere.html
+"fix gravity"_fix_gravity.html :ul
+
+This compute
+
+"compute erotate/sphere"_compute_erotate_sphere.html :ul
+
+calculates rotational kinetic energy which can be "output with
+thermodynamic info"_Howto_output.html.
+
+Use one of these 3 pair potentials, which compute forces and torques
+between interacting pairs of particles:
+
+"pair_style"_pair_style.html gran/history
+"pair_style"_pair_style.html gran/no_history
+"pair_style"_pair_style.html gran/hertzian :ul
+
+These commands implement fix options specific to granular systems:
+
+"fix freeze"_fix_freeze.html
+"fix pour"_fix_pour.html
+"fix viscous"_fix_viscous.html
+"fix wall/gran"_fix_wall_gran.html :ul
+
+The fix style {freeze} zeroes both the force and torque of frozen
+atoms, and should be used for granular system instead of the fix style
+{setforce}.
+
+For computational efficiency, you can eliminate needless pairwise
+computations between frozen atoms by using this command:
+
+"neigh_modify"_neigh_modify.html exclude :ul
+
+NOTE: By default, for 2d systems, granular particles are still modeled
+as 3d spheres, not 2d discs (circles), meaning their moment of inertia
+will be the same as in 3d. If you wish to model granular particles in
+2d as 2d discs, see the note on this topic on the "Howto 2d"_Howto_2d
+doc page, where 2d simulations are discussed.
diff --git a/doc/src/Howto_kappa.txt b/doc/src/Howto_kappa.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2a57ef49b82461b89a72cda29c9785297a877f0
--- /dev/null
+++ b/doc/src/Howto_kappa.txt
@@ -0,0 +1,90 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Calculate thermal conductivity :h3
+
+The thermal conductivity kappa of a material can be measured in at
+least 4 ways using various options in LAMMPS. See the examples/KAPPA
+directory for scripts that implement the 4 methods discussed here for
+a simple Lennard-Jones fluid model. Also, see the "Howto
+viscosity"_Howto_viscosity.html doc page for an analogous discussion
+for viscosity.
+
+The thermal conductivity tensor kappa is a measure of the propensity
+of a material to transmit heat energy in a diffusive manner as given
+by Fourier's law
+
+J = -kappa grad(T)
+
+where J is the heat flux in units of energy per area per time and
+grad(T) is the spatial gradient of temperature. The thermal
+conductivity thus has units of energy per distance per time per degree
+K and is often approximated as an isotropic quantity, i.e. as a
+scalar.
+
+The first method is to setup two thermostatted regions at opposite
+ends of a simulation box, or one in the middle and one at the end of a
+periodic box. By holding the two regions at different temperatures
+with a "thermostatting fix"_Howto_thermostat.html, the energy added to
+the hot region should equal the energy subtracted from the cold region
+and be proportional to the heat flux moving between the regions. See
+the papers by "Ikeshoji and Hafskjold"_#howto-Ikeshoji and
+"Wirnsberger et al"_#howto-Wirnsberger for details of this idea. Note
+that thermostatting fixes such as "fix nvt"_fix_nh.html, "fix
+langevin"_fix_langevin.html, and "fix
+temp/rescale"_fix_temp_rescale.html store the cumulative energy they
+add/subtract.
+
+Alternatively, as a second method, the "fix heat"_fix_heat.html or
+"fix ehex"_fix_ehex.html commands can be used in place of thermostats
+on each of two regions to add/subtract specified amounts of energy to
+both regions. In both cases, the resulting temperatures of the two
+regions can be monitored with the "compute temp/region" command and
+the temperature profile of the intermediate region can be monitored
+with the "fix ave/chunk"_fix_ave_chunk.html and "compute
+ke/atom"_compute_ke_atom.html commands.
+
+The third method is to perform a reverse non-equilibrium MD simulation
+using the "fix thermal/conductivity"_fix_thermal_conductivity.html
+command which implements the rNEMD algorithm of Muller-Plathe.
+Kinetic energy is swapped between atoms in two different layers of the
+simulation box. This induces a temperature gradient between the two
+layers which can be monitored with the "fix
+ave/chunk"_fix_ave_chunk.html and "compute
+ke/atom"_compute_ke_atom.html commands. The fix tallies the
+cumulative energy transfer that it performs. See the "fix
+thermal/conductivity"_fix_thermal_conductivity.html command for
+details.
+
+The fourth method is based on the Green-Kubo (GK) formula which
+relates the ensemble average of the auto-correlation of the heat flux
+to kappa. The heat flux can be calculated from the fluctuations of
+per-atom potential and kinetic energies and per-atom stress tensor in
+a steady-state equilibrated simulation. This is in contrast to the
+two preceding non-equilibrium methods, where energy flows continuously
+between hot and cold regions of the simulation box.
+
+The "compute heat/flux"_compute_heat_flux.html command can calculate
+the needed heat flux and describes how to implement the Green_Kubo
+formalism using additional LAMMPS commands, such as the "fix
+ave/correlate"_fix_ave_correlate.html command to calculate the needed
+auto-correlation. See the doc page for the "compute
+heat/flux"_compute_heat_flux.html command for an example input script
+that calculates the thermal conductivity of solid Ar via the GK
+formalism.
+
+:line
+
+:link(howto-Ikeshoji)
+[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
+(1994).
+
+:link(howto-Wirnsberger)
+[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
+(2015).
diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d4852fbf247adee92be56045d7b98af7e5a3542
--- /dev/null
+++ b/doc/src/Howto_library.txt
@@ -0,0 +1,208 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Library interface to LAMMPS :h3
+
+As described in "Section 2.5"_Section_start.html#start_5, LAMMPS can
+be built as a library, so that it can be called by another code, used
+in a "coupled manner"_Howto_couple.html with other codes, or driven
+through a "Python interface"_Python.html.
+
+All of these methodologies use a C-style interface to LAMMPS that is
+provided in the files src/library.cpp and src/library.h. The
+functions therein have a C-style argument list, but contain C++ code
+you could write yourself in a C++ application that was invoking LAMMPS
+directly. The C++ code in the functions illustrates how to invoke
+internal LAMMPS operations. Note that LAMMPS classes are defined
+within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
+application.
+
+The examples/COUPLE and python/examples directories have example C++
+and C and Python codes which show how a driver code can link to LAMMPS
+as a library, run LAMMPS on a subset of processors, grab data from
+LAMMPS, change it, and put it back into LAMMPS.
+
+The file src/library.cpp contains the following functions for creating
+and destroying an instance of LAMMPS and sending it commands to
+execute. See the documentation in the src/library.cpp file for
+details.
+
+NOTE: You can write code for additional functions as needed to define
+how your code talks to LAMMPS and add them to src/library.cpp and
+src/library.h, as well as to the "Python interface"_Python.html. The
+added functions can access or change any internal LAMMPS data you
+wish.
+
+void lammps_open(int, char **, MPI_Comm, void **)
+void lammps_open_no_mpi(int, char **, void **)
+void lammps_close(void *)
+int lammps_version(void *)
+void lammps_file(void *, char *)
+char *lammps_command(void *, char *)
+void lammps_commands_list(void *, int, char **)
+void lammps_commands_string(void *, char *)
+void lammps_free(void *) :pre
+
+The lammps_open() function is used to initialize LAMMPS, passing in a
+list of strings as if they were "command-line
+arguments"_Section_start.html#start_6 when LAMMPS is run in
+stand-alone mode from the command line, and a MPI communicator for
+LAMMPS to run under. It returns a ptr to the LAMMPS object that is
+created, and which is used in subsequent library calls. The
+lammps_open() function can be called multiple times, to create
+multiple instances of LAMMPS.
+
+LAMMPS will run on the set of processors in the communicator. This
+means the calling code can run LAMMPS on all or a subset of
+processors. For example, a wrapper script might decide to alternate
+between LAMMPS and another code, allowing them both to run on all the
+processors. Or it might allocate half the processors to LAMMPS and
+half to the other code and run both codes simultaneously before
+syncing them up periodically. Or it might instantiate multiple
+instances of LAMMPS to perform different calculations.
+
+The lammps_open_no_mpi() function is similar except that no MPI
+communicator is passed from the caller. Instead, MPI_COMM_WORLD is
+used to instantiate LAMMPS, and MPI is initialized if necessary.
+
+The lammps_close() function is used to shut down an instance of LAMMPS
+and free all its memory.
+
+The lammps_version() function can be used to determined the specific
+version of the underlying LAMMPS code. This is particularly useful
+when loading LAMMPS as a shared library via dlopen(). The code using
+the library interface can than use this information to adapt to
+changes to the LAMMPS command syntax between versions. The returned
+LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
+20150902) that grows with every new LAMMPS version.
+
+The lammps_file(), lammps_command(), lammps_commands_list(), and
+lammps_commands_string() functions are used to pass one or more
+commands to LAMMPS to execute, the same as if they were coming from an
+input script.
+
+Via these functions, the calling code can read or generate a series of
+LAMMPS commands one or multiple at a time and pass it thru the library
+interface to setup a problem and then run it in stages. The caller
+can interleave the command function calls with operations it performs,
+calls to extract information from or set information within LAMMPS, or
+calls to another code's library.
+
+The lammps_file() function passes the filename of an input script.
+The lammps_command() function passes a single command as a string.
+The lammps_commands_list() function passes multiple commands in a
+char** list. In both lammps_command() and lammps_commands_list(),
+individual commands may or may not have a trailing newline. The
+lammps_commands_string() function passes multiple commands
+concatenated into one long string, separated by newline characters.
+In both lammps_commands_list() and lammps_commands_string(), a single
+command can be spread across multiple lines, if the last printable
+character of all but the last line is "&", the same as if the lines
+appeared in an input script.
+
+The lammps_free() function is a clean-up function to free memory that
+the library allocated previously via other function calls. See
+comments in src/library.cpp file for which other functions need this
+clean-up.
+
+The file src/library.cpp also contains these functions for extracting
+information from LAMMPS and setting value within LAMMPS. Again, see
+the documentation in the src/library.cpp file for details, including
+which quantities can be queried by name:
+
+int lammps_extract_setting(void *, char *)
+void *lammps_extract_global(void *, char *)
+void lammps_extract_box(void *, double *, double *,
+ double *, double *, double *, int *, int *)
+void *lammps_extract_atom(void *, char *)
+void *lammps_extract_compute(void *, char *, int, int)
+void *lammps_extract_fix(void *, char *, int, int, int, int)
+void *lammps_extract_variable(void *, char *, char *) :pre
+
+The extract_setting() function returns info on the size
+of data types (e.g. 32-bit or 64-bit atom IDs) used
+by the LAMMPS executable (a compile-time choice).
+
+The other extract functions return a pointer to various global or
+per-atom quantities stored in LAMMPS or to values calculated by a
+compute, fix, or variable. The pointer returned by the
+extract_global() function can be used as a permanent reference to a
+value which may change. For the extract_atom() method, see the
+extract() method in the src/atom.cpp file for a list of valid per-atom
+properties. New names could easily be added if the property you want
+is not listed. For the other extract functions, the underlying
+storage may be reallocated as LAMMPS runs, so you need to re-call the
+function to assure a current pointer or returned value(s).
+
+double lammps_get_thermo(void *, char *)
+int lammps_get_natoms(void *) :pre
+
+int lammps_set_variable(void *, char *, char *)
+void lammps_reset_box(void *, double *, double *, double, double, double) :pre
+
+The lammps_get_thermo() function returns the current value of a thermo
+keyword as a double precision value.
+
+The lammps_get_natoms() function returns the total number of atoms in
+the system and can be used by the caller to allocate memory for the
+lammps_gather_atoms() and lammps_scatter_atoms() functions.
+
+The lammps_set_variable() function can set an existing string-style
+variable to a new string value, so that subsequent LAMMPS commands can
+access the variable.
+
+The lammps_reset_box() function resets the size and shape of the
+simulation box, e.g. as part of restoring a previously extracted and
+saved state of a simulation.
+
+void lammps_gather_atoms(void *, char *, int, int, void *)
+void lammps_gather_atoms_concat(void *, char *, int, int, void *)
+void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *)
+void lammps_scatter_atoms(void *, char *, int, int, void *)
+void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre
+
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
+ imageint *, int) :pre
+
+The gather functions collect peratom info of the requested type (atom
+coords, atom types, forces, etc) from all processors, and returns the
+same vector of values to each callling processor. The scatter
+functions do the inverse. They distribute a vector of peratom values,
+passed by all calling processors, to invididual atoms, which may be
+owned by different processos.
+
+The lammps_gather_atoms() function does this for all N atoms in the
+system, ordered by atom ID, from 1 to N. The
+lammps_gather_atoms_concat() function does it for all N atoms, but
+simply concatenates the subset of atoms owned by each processor. The
+resulting vector is not ordered by atom ID. Atom IDs can be requetsed
+by the same function if the caller needs to know the ordering. The
+lammps_gather_subset() function allows the caller to request values
+for only a subset of atoms (identified by ID).
+For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
+If the count is specified as 1, they are returned
+in a packed format with all three image flags stored in a single integer.
+If the count is specified as 3, the values are unpacked into xyz flags
+by the library before returning them.
+
+The lammps_scatter_atoms() function takes a list of values for all N
+atoms in the system, ordered by atom ID, from 1 to N, and assigns
+those values to each atom in the system. The
+lammps_scatter_atoms_subset() function takes a subset of IDs as an
+argument and only scatters those values to the owning atoms.
+
+The lammps_create_atoms() function takes a list of N atoms as input
+with atom types and coords (required), an optionally atom IDs and
+velocities and image flags. It uses the coords of each atom to assign
+it as a new atom to the processor that owns it. This function is
+useful to add atoms to a simulation or (in tandem with
+lammps_reset_box()) to restore a previously extracted and saved state
+of a simulation. Additional properties for the new atoms can then be
+assigned via the lammps_scatter_atoms() or lammps_extract_atom()
+functions.
diff --git a/doc/src/manifolds.txt b/doc/src/Howto_manifold.txt
similarity index 97%
rename from doc/src/manifolds.txt
rename to doc/src/Howto_manifold.txt
index 1013d8fab68f91cb2d5113b0cde132d7fc1f4385..09a936f7d3adec5cec22b820be9e9c54a2e4dfd0 100644
--- a/doc/src/manifolds.txt
+++ b/doc/src/Howto_manifold.txt
@@ -2,11 +2,11 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-Manifolds (surfaces) :h2
+Manifolds (surfaces) :h3
[Overview:]
diff --git a/doc/src/Howto_multiple.txt b/doc/src/Howto_multiple.txt
new file mode 100644
index 0000000000000000000000000000000000000000..edcb8196cf015543db85b6ab83411d4d13373758
--- /dev/null
+++ b/doc/src/Howto_multiple.txt
@@ -0,0 +1,95 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Run multiple simulations from one input script :h3
+
+This can be done in several ways. See the documentation for
+individual commands for more details on how these examples work.
+
+If "multiple simulations" means continue a previous simulation for
+more timesteps, then you simply use the "run"_run.html command
+multiple times. For example, this script
+
+units lj
+atom_style atomic
+read_data data.lj
+run 10000
+run 10000
+run 10000
+run 10000
+run 10000 :pre
+
+would run 5 successive simulations of the same system for a total of
+50,000 timesteps.
+
+If you wish to run totally different simulations, one after the other,
+the "clear"_clear.html command can be used in between them to
+re-initialize LAMMPS. For example, this script
+
+units lj
+atom_style atomic
+read_data data.lj
+run 10000
+clear
+units lj
+atom_style atomic
+read_data data.lj.new
+run 10000 :pre
+
+would run 2 independent simulations, one after the other.
+
+For large numbers of independent simulations, you can use
+"variables"_variable.html and the "next"_next.html and
+"jump"_jump.html commands to loop over the same input script
+multiple times with different settings. For example, this
+script, named in.polymer
+
+variable d index run1 run2 run3 run4 run5 run6 run7 run8
+shell cd $d
+read_data data.polymer
+run 10000
+shell cd ..
+clear
+next d
+jump in.polymer :pre
+
+would run 8 simulations in different directories, using a data.polymer
+file in each directory. The same concept could be used to run the
+same system at 8 different temperatures, using a temperature variable
+and storing the output in different log and dump files, for example
+
+variable a loop 8
+variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
+log log.$a
+read data.polymer
+velocity all create $t 352839
+fix 1 all nvt $t $t 100.0
+dump 1 all atom 1000 dump.$a
+run 100000
+clear
+next t
+next a
+jump in.polymer :pre
+
+All of the above examples work whether you are running on 1 or
+multiple processors, but assumed you are running LAMMPS on a single
+partition of processors. LAMMPS can be run on multiple partitions via
+the "-partition" command-line switch as described in "this
+section"_Section_start.html#start_6 of the manual.
+
+In the last 2 examples, if LAMMPS were run on 3 partitions, the same
+scripts could be used if the "index" and "loop" variables were
+replaced with {universe}-style variables, as described in the
+"variable"_variable.html command. Also, the "next t" and "next a"
+commands would need to be replaced with a single "next a t" command.
+With these modifications, the 8 simulations of each script would run
+on the 3 partitions one after the other until all were finished.
+Initially, 3 simulations would be started simultaneously, one on each
+partition. When one finished, that partition would then start
+the 4th simulation, and so forth, until all 8 were completed.
diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f787801c36745d934abbfb1c26462734014d1c0c
--- /dev/null
+++ b/doc/src/Howto_nemd.txt
@@ -0,0 +1,48 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+NEMD simulations :h3
+
+Non-equilibrium molecular dynamics or NEMD simulations are typically
+used to measure a fluid's rheological properties such as viscosity.
+In LAMMPS, such simulations can be performed by first setting up a
+non-orthogonal simulation box (see the preceding Howto section).
+
+A shear strain can be applied to the simulation box at a desired
+strain rate by using the "fix deform"_fix_deform.html command. The
+"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
+the sheared fluid and integrate the SLLOD equations of motion for the
+system. Fix nvt/sllod uses "compute
+temp/deform"_compute_temp_deform.html to compute a thermal temperature
+by subtracting out the streaming velocity of the shearing atoms. The
+velocity profile or other properties of the fluid can be monitored via
+the "fix ave/chunk"_fix_ave_chunk.html command.
+
+As discussed in the previous section on non-orthogonal simulation
+boxes, the amount of tilt or skew that can be applied is limited by
+LAMMPS for computational efficiency to be 1/2 of the parallel box
+length. However, "fix deform"_fix_deform.html can continuously strain
+a box by an arbitrary amount. As discussed in the "fix
+deform"_fix_deform.html command, when the tilt value reaches a limit,
+the box is flipped to the opposite limit which is an equivalent tiling
+of periodic space. The strain rate can then continue to change as
+before. In a long NEMD simulation these box re-shaping events may
+occur many times.
+
+In a NEMD simulation, the "remap" option of "fix
+deform"_fix_deform.html should be set to "remap v", since that is what
+"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity
+profile consistent with the applied shear strain rate.
+
+An alternative method for calculating viscosities is provided via the
+"fix viscosity"_fix_viscosity.html command.
+
+NEMD simulations can also be used to measure transport properties of a fluid
+through a pore or channel. Simulations of steady-state flow can be performed
+using the "fix flow/gauss"_fix_flow_gauss.html command.
diff --git a/doc/src/Howto_output.txt b/doc/src/Howto_output.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a204a3cc96c3a0f2cebdc97fbc4ac7d2b78e8420
--- /dev/null
+++ b/doc/src/Howto_output.txt
@@ -0,0 +1,307 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Output from LAMMPS (thermo, dumps, computes, fixes, variables) :h3
+
+There are four basic kinds of LAMMPS output:
+
+"Thermodynamic output"_thermo_style.html, which is a list
+of quantities printed every few timesteps to the screen and logfile. :ulb,l
+
+"Dump files"_dump.html, which contain snapshots of atoms and various
+per-atom values and are written at a specified frequency. :l
+
+Certain fixes can output user-specified quantities to files: "fix
+ave/time"_fix_ave_time.html for time averaging, "fix
+ave/chunk"_fix_ave_chunk.html for spatial or other averaging, and "fix
+print"_fix_print.html for single-line output of
+"variables"_variable.html. Fix print can also output to the
+screen. :l
+
+"Restart files"_restart.html. :l
+:ule
+
+A simulation prints one set of thermodynamic output and (optionally)
+restart files. It can generate any number of dump files and fix
+output files, depending on what "dump"_dump.html and "fix"_fix.html
+commands you specify.
+
+As discussed below, LAMMPS gives you a variety of ways to determine
+what quantities are computed and printed when the thermodynamics,
+dump, or fix commands listed above perform output. Throughout this
+discussion, note that users can also "add their own computes and fixes
+to LAMMPS"_Modify.html which can then generate values that can then be
+output with these commands.
+
+The following sub-sections discuss different LAMMPS command related
+to output and the kind of data they operate on and produce:
+
+"Global/per-atom/local data"_#global
+"Scalar/vector/array data"_#scalar
+"Thermodynamic output"_#thermo
+"Dump file output"_#dump
+"Fixes that write output files"_#fixoutput
+"Computes that process output quantities"_#computeoutput
+"Fixes that process output quantities"_#fixprocoutput
+"Computes that generate values to output"_#compute
+"Fixes that generate values to output"_#fix
+"Variables that generate values to output"_#variable
+"Summary table of output options and data flow between commands"_#table :ul
+
+Global/per-atom/local data :h4,link(global)
+
+Various output-related commands work with three different styles of
+data: global, per-atom, or local. A global datum is one or more
+system-wide values, e.g. the temperature of the system. A per-atom
+datum is one or more values per atom, e.g. the kinetic energy of each
+atom. Local datums are calculated by each processor based on the
+atoms it owns, but there may be zero or more per atom, e.g. a list of
+bond distances.
+
+Scalar/vector/array data :h4,link(scalar)
+
+Global, per-atom, and local datums can each come in three kinds: a
+single scalar value, a vector of values, or a 2d array of values. The
+doc page for a "compute" or "fix" or "variable" that generates data
+will specify both the style and kind of data it produces, e.g. a
+per-atom vector.
+
+When a quantity is accessed, as in many of the output commands
+discussed below, it can be referenced via the following bracket
+notation, where ID in this case is the ID of a compute. The leading
+"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
+
+c_ID | entire scalar, vector, or array
+c_ID\[I\] | one element of vector, one column of array
+c_ID\[I\]\[J\] | one element of array :tb(s=|)
+
+In other words, using one bracket reduces the dimension of the data
+once (vector -> scalar, array -> vector). Using two brackets reduces
+the dimension twice (array -> scalar). Thus a command that uses
+scalar values as input can typically also process elements of a vector
+or array.
+
+Thermodynamic output :h4,link(thermo)
+
+The frequency and format of thermodynamic output is set by the
+"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
+"thermo_modify"_thermo_modify.html commands. The
+"thermo_style"_thermo_style.html command also specifies what values
+are calculated and written out. Pre-defined keywords can be specified
+(e.g. press, etotal, etc). Three additional kinds of keywords can
+also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html
+or "fix"_fix.html or "variable"_variable.html provides the value to be
+output. In each case, the compute, fix, or variable must generate
+global values for input to the "thermo_style custom"_dump.html
+command.
+
+Note that thermodynamic output values can be "extensive" or
+"intensive". The former scale with the number of atoms in the system
+(e.g. total energy), the latter do not (e.g. temperature). The
+setting for "thermo_modify norm"_thermo_modify.html determines whether
+extensive quantities are normalized or not. Computes and fixes
+produce either extensive or intensive values; see their individual doc
+pages for details. "Equal-style variables"_variable.html produce only
+intensive values; you can include a division by "natoms" in the
+formula if desired, to make an extensive calculation produce an
+intensive result.
+
+Dump file output :h4,link(dump)
+
+Dump file output is specified by the "dump"_dump.html and
+"dump_modify"_dump_modify.html commands. There are several
+pre-defined formats (dump atom, dump xtc, etc).
+
+There is also a "dump custom"_dump.html format where the user
+specifies what values are output with each atom. Pre-defined atom
+attributes can be specified (id, x, fx, etc). Three additional kinds
+of keywords can also be specified (c_ID, f_ID, v_name), where a
+"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
+provides the values to be output. In each case, the compute, fix, or
+variable must generate per-atom values for input to the "dump
+custom"_dump.html command.
+
+There is also a "dump local"_dump.html format where the user specifies
+what local values to output. A pre-defined index keyword can be
+specified to enumerate the local values. Two additional kinds of
+keywords can also be specified (c_ID, f_ID), where a
+"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
+provides the values to be output. In each case, the compute or fix
+must generate local values for input to the "dump local"_dump.html
+command.
+
+Fixes that write output files :h4,link(fixoutput)
+
+Several fixes take various quantities as input and can write output
+files: "fix ave/time"_fix_ave_time.html, "fix
+ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html,
+"fix ave/correlate"_fix_ave_correlate.html, and "fix
+print"_fix_print.html.
+
+The "fix ave/time"_fix_ave_time.html command enables direct output to
+a file and/or time-averaging of global scalars or vectors. The user
+specifies one or more quantities as input. These can be global
+"compute"_compute.html values, global "fix"_fix.html values, or
+"variables"_variable.html of any style except the atom style which
+produces per-atom values. Since a variable can refer to keywords used
+by the "thermo_style custom"_thermo_style.html command (like temp or
+press) and individual per-atom values, a wide variety of quantities
+can be time averaged and/or output in this way. If the inputs are one
+or more scalar values, then the fix generate a global scalar or vector
+of output. If the inputs are one or more vector values, then the fix
+generates a global vector or array of output. The time-averaged
+output of this fix can also be used as input to other output commands.
+
+The "fix ave/chunk"_fix_ave_chunk.html command enables direct output
+to a file of chunk-averaged per-atom quantities like those output in
+dump files. Chunks can represent spatial bins or other collections of
+atoms, e.g. individual molecules. The per-atom quantities can be atom
+density (mass or number) or atom attributes such as position,
+velocity, force. They can also be per-atom quantities calculated by a
+"compute"_compute.html, by a "fix"_fix.html, or by an atom-style
+"variable"_variable.html. The chunk-averaged output of this fix can
+also be used as input to other output commands.
+
+The "fix ave/histo"_fix_ave_histo.html command enables direct output
+to a file of histogrammed quantities, which can be global or per-atom
+or local quantities. The histogram output of this fix can also be
+used as input to other output commands.
+
+The "fix ave/correlate"_fix_ave_correlate.html command enables direct
+output to a file of time-correlated quantities, which can be global
+values. The correlation matrix output of this fix can also be used as
+input to other output commands.
+
+The "fix print"_fix_print.html command can generate a line of output
+written to the screen and log file or to a separate file, periodically
+during a running simulation. The line can contain one or more
+"variable"_variable.html values for any style variable except the
+vector or atom styles). As explained above, variables themselves can
+contain references to global values generated by "thermodynamic
+keywords"_thermo_style.html, "computes"_compute.html,
+"fixes"_fix.html, or other "variables"_variable.html, or to per-atom
+values for a specific atom. Thus the "fix print"_fix_print.html
+command is a means to output a wide variety of quantities separate
+from normal thermodynamic or dump file output.
+
+Computes that process output quantities :h4,link(computeoutput)
+
+The "compute reduce"_compute_reduce.html and "compute
+reduce/region"_compute_reduce.html commands take one or more per-atom
+or local vector quantities as inputs and "reduce" them (sum, min, max,
+ave) to scalar quantities. These are produced as output values which
+can be used as input to other output commands.
+
+The "compute slice"_compute_slice.html command take one or more global
+vector or array quantities as inputs and extracts a subset of their
+values to create a new vector or array. These are produced as output
+values which can be used as input to other output commands.
+
+The "compute property/atom"_compute_property_atom.html command takes a
+list of one or more pre-defined atom attributes (id, x, fx, etc) and
+stores the values in a per-atom vector or array. These are produced
+as output values which can be used as input to other output commands.
+The list of atom attributes is the same as for the "dump
+custom"_dump.html command.
+
+The "compute property/local"_compute_property_local.html command takes
+a list of one or more pre-defined local attributes (bond info, angle
+info, etc) and stores the values in a local vector or array. These
+are produced as output values which can be used as input to other
+output commands.
+
+Fixes that process output quantities :h4,link(fixprocoutput)
+
+The "fix vector"_fix_vector.html command can create global vectors as
+output from global scalars as input, accumulating them one element at
+a time.
+
+The "fix ave/atom"_fix_ave_atom.html command performs time-averaging
+of per-atom vectors. The per-atom quantities can be atom attributes
+such as position, velocity, force. They can also be per-atom
+quantities calculated by a "compute"_compute.html, by a
+"fix"_fix.html, or by an atom-style "variable"_variable.html. The
+time-averaged per-atom output of this fix can be used as input to
+other output commands.
+
+The "fix store/state"_fix_store_state.html command can archive one or
+more per-atom attributes at a particular time, so that the old values
+can be used in a future calculation or output. The list of atom
+attributes is the same as for the "dump custom"_dump.html command,
+including per-atom quantities calculated by a "compute"_compute.html,
+by a "fix"_fix.html, or by an atom-style "variable"_variable.html.
+The output of this fix can be used as input to other output commands.
+
+Computes that generate values to output :h4,link(compute)
+
+Every "compute"_compute.html in LAMMPS produces either global or
+per-atom or local values. The values can be scalars or vectors or
+arrays of data. These values can be output using the other commands
+described in this section. The doc page for each compute command
+describes what it produces. Computes that produce per-atom or local
+values have the word "atom" or "local" in their style name. Computes
+without the word "atom" or "local" produce global values.
+
+Fixes that generate values to output :h4,link(fix)
+
+Some "fixes"_fix.html in LAMMPS produces either global or per-atom or
+local values which can be accessed by other commands. The values can
+be scalars or vectors or arrays of data. These values can be output
+using the other commands described in this section. The doc page for
+each fix command tells whether it produces any output quantities and
+describes them.
+
+Variables that generate values to output :h4,link(variable)
+
+"Variables"_variable.html defined in an input script can store one or
+more strings. But equal-style, vector-style, and atom-style or
+atomfile-style variables generate a global scalar value, global vector
+or values, or a per-atom vector, respectively, when accessed. The
+formulas used to define these variables can contain references to the
+thermodynamic keywords and to global and per-atom data generated by
+computes, fixes, and other variables. The values generated by
+variables can be used as input to and thus output by the other
+commands described in this section.
+
+Summary table of output options and data flow between commands :h4,link(table)
+
+This table summarizes the various commands that can be used for
+generating output from LAMMPS. Each command produces output data of
+some kind and/or writes data to a file. Most of the commands can take
+data from other commands as input. Thus you can link many of these
+commands together in pipeline form, where data produced by one command
+is used as input to another command and eventually written to the
+screen or to a file. Note that to hook two commands together the
+output and input data types must match, e.g. global/per-atom/local
+data and scalar/vector/array data.
+
+Also note that, as described above, when a command takes a scalar as
+input, that could be an element of a vector or array. Likewise a
+vector input could be a column of an array.
+
+Command: Input: Output:
+"thermo_style custom"_thermo_style.html: global scalars: screen, log file:
+"dump custom"_dump.html: per-atom vectors: dump file:
+"dump local"_dump.html: local vectors: dump file:
+"fix print"_fix_print.html: global scalar from variable: screen, file:
+"print"_print.html: global scalar from variable: screen:
+"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array:
+"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array:
+"variables"_variable.html: global scalars and vectors, per-atom vectors: global scalar and vector, per-atom vector:
+"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector:
+"compute slice"_compute_slice.html: global vectors/arrays: global vector/array:
+"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array:
+"compute property/local"_compute_property_local.html: local vectors: local vector/array:
+"fix vector"_fix_vector.html: global scalars: global vector:
+"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array:
+"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file:
+"fix ave/chunk"_fix_ave_chunk.html: per-atom vectors: global array, file:
+"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file:
+"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file:
+"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array :tb(c=3,s=:)
diff --git a/doc/src/Howto_polarizable.txt b/doc/src/Howto_polarizable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2653b117e9caed203f1a9127575278f1747fcb4
--- /dev/null
+++ b/doc/src/Howto_polarizable.txt
@@ -0,0 +1,81 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Polarizable models :h3
+
+In polarizable force fields the charge distributions in molecules and
+materials respond to their electrostatic environments. Polarizable
+systems can be simulated in LAMMPS using three methods:
+
+the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html
+package, :ulb,l
+the adiabatic core-shell method, implemented in the
+"CORESHELL"_Howto_coreshell.html package, :l
+the thermalized Drude dipole method, implemented in the
+"USER-DRUDE"_Howto_drude.html package. :l,ule
+
+The fluctuating charge method calculates instantaneous charges on
+interacting atoms based on the electronegativity equalization
+principle. It is implemented in the "fix qeq"_fix_qeq.html which is
+available in several variants. It is a relatively efficient technique
+since no additional particles are introduced. This method allows for
+charge transfer between molecules or atom groups. However, because the
+charges are located at the interaction sites, off-plane components of
+polarization cannot be represented in planar molecules or atom groups.
+
+The two other methods share the same basic idea: polarizable atoms are
+split into one core atom and one satellite particle (called shell or
+Drude particle) attached to it by a harmonic spring. Both atoms bear
+a charge and they represent collectively an induced electric dipole.
+These techniques are computationally more expensive than the QEq
+method because of additional particles and bonds. These two
+charge-on-spring methods differ in certain features, with the
+core-shell model being normally used for ionic/crystalline materials,
+whereas the so-called Drude model is normally used for molecular
+systems and fluid states.
+
+The core-shell model is applicable to crystalline materials where the
+high symmetry around each site leads to stable trajectories of the
+core-shell pairs. However, bonded atoms in molecules can be so close
+that a core would interact too strongly or even capture the Drude
+particle of a neighbor. The Drude dipole model is relatively more
+complex in order to remediate this and other issues. Specifically, the
+Drude model includes specific thermostating of the core-Drude pairs
+and short-range damping of the induced dipoles.
+
+The three polarization methods can be implemented through a
+self-consistent calculation of charges or induced dipoles at each
+timestep. In the fluctuating charge scheme this is done by the matrix
+inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell
+or Drude-dipoles the relaxed-dipoles technique would require an slow
+iterative procedure. These self-consistent solutions yield accurate
+trajectories since the additional degrees of freedom representing
+polarization are massless. An alternative is to attribute a mass to
+the additional degrees of freedom and perform time integration using
+an extended Lagrangian technique. For the fluctuating charge scheme
+this is done by "fix qeq/dynamic"_fix_qeq.html, and for the
+charge-on-spring models by the methods outlined in the next two
+sections. The assignment of masses to the additional degrees of
+freedom can lead to unphysical trajectories if care is not exerted in
+choosing the parameters of the polarizable models and the simulation
+conditions.
+
+In the core-shell model the vibration of the shells is kept faster
+than the ionic vibrations to mimic the fast response of the
+polarizable electrons. But in molecular systems thermalizing the
+core-Drude pairs at temperatures comparable to the rest of the
+simulation leads to several problems (kinetic energy transfer, too
+short a timestep, etc.) In order to avoid these problems the relative
+motion of the Drude particles with respect to their cores is kept
+"cold" so the vibration of the core-Drude pairs is very slow,
+approaching the self-consistent regime. In both models the
+temperature is regulated using the velocities of the center of mass of
+core+shell (or Drude) pairs, but in the Drude model the actual
+relative core-Drude particle motion is thermostated separately as
+well.
diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/Howto_pylammps.txt
similarity index 95%
rename from doc/src/tutorial_pylammps.txt
rename to doc/src/Howto_pylammps.txt
index 11cddb3cbf3fa7abc4350c9fe0cfb685f19b7b47..8be4b66e78a511b404987929d247ce3836a40086 100644
--- a/doc/src/tutorial_pylammps.txt
+++ b/doc/src/Howto_pylammps.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -15,13 +15,19 @@ END_RST -->
Overview :h4
-PyLammps is a Python wrapper class which can be created on its own or use an
-existing lammps Python object. It creates a simpler, Python-like interface to
-common LAMMPS functionality. Unlike the original flat C-types interface, it
-exposes a discoverable API. It no longer requires knowledge of the underlying
-C++ code implementation. Finally, the IPyLammps wrapper builds on top of
-PyLammps and adds some additional features for IPython integration into IPython
-notebooks, e.g. for embedded visualization output from dump/image.
+PyLammps is a Python wrapper class which can be created on its own or
+use an existing lammps Python object. It creates a simpler,
+Python-like interface to common LAMMPS functionality, in contrast to
+the lammps.py wrapper on the C-style LAMMPS library interface which is
+written using Python ctypes. The lammps.py wrapper is discussed on
+the "Python library"_Python_library.html doc page.
+
+Unlike the flat ctypes interface, PyLammps exposes a discoverable API.
+It no longer requires knowledge of the underlying C++ code
+implementation. Finally, the IPyLammps wrapper builds on top of
+PyLammps and adds some additional features for IPython integration
+into IPython notebooks, e.g. for embedded visualization output from
+dump/image.
Comparison of lammps and PyLammps interfaces :h5
@@ -40,7 +46,6 @@ communication with LAMMPS is hidden from API user
shorter, more concise Python
better IPython integration, designed for quick prototyping :ul
-
Quick Start :h4
System-wide Installation :h5
diff --git a/doc/src/Howto_replica.txt b/doc/src/Howto_replica.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b44fe53748d4dc1adf35aebe333b97bea4c33ac
--- /dev/null
+++ b/doc/src/Howto_replica.txt
@@ -0,0 +1,61 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Multi-replica simulations :h3
+
+Several commands in LAMMPS run mutli-replica simulations, meaning
+that multiple instances (replicas) of your simulation are run
+simultaneously, with small amounts of data exchanged between replicas
+periodically.
+
+These are the relevant commands:
+
+"neb"_neb.html for nudged elastic band calculations
+"prd"_prd.html for parallel replica dynamics
+"tad"_tad.html for temperature accelerated dynamics
+"temper"_temper.html for parallel tempering
+"fix pimd"_fix_pimd.html for path-integral molecular dynamics (PIMD) :ul
+
+NEB is a method for finding transition states and barrier energies.
+PRD and TAD are methods for performing accelerated dynamics to find
+and perform infrequent events. Parallel tempering or replica exchange
+runs different replicas at a series of temperature to facilitate
+rare-event sampling.
+
+These commands can only be used if LAMMPS was built with the REPLICA
+package. See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info on packages.
+
+PIMD runs different replicas whose individual particles are coupled
+together by springs to model a system or ring-polymers.
+
+This commands can only be used if LAMMPS was built with the USER-MISC
+package. See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info on packages.
+
+In all these cases, you must run with one or more processors per
+replica. The processors assigned to each replica are determined at
+run-time by using the "-partition command-line
+switch"_Section_start.html#start_6 to launch LAMMPS on multiple
+partitions, which in this context are the same as replicas. E.g.
+these commands:
+
+mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
+mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
+
+would each run 8 replicas, on either 16 or 8 processors. Note the use
+of the "-in command-line switch"_Section_start.html#start_6 to specify
+the input script which is required when running in multi-replica mode.
+
+Also note that with MPI installed on a machine (e.g. your desktop),
+you can run on more (virtual) processors than you have physical
+processors. Thus the above commands could be run on a
+single-processor (or few-processor) desktop so that you can run
+a multi-replica simulation on more replicas than you have
+physical processors.
diff --git a/doc/src/Howto_restart.txt b/doc/src/Howto_restart.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b211775479bfc367301a408ef15e45f8bd46cca0
--- /dev/null
+++ b/doc/src/Howto_restart.txt
@@ -0,0 +1,97 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Restart a simulation :h3
+
+There are 3 ways to continue a long LAMMPS simulation. Multiple
+"run"_run.html commands can be used in the same input script. Each
+run will continue from where the previous run left off. Or binary
+restart files can be saved to disk using the "restart"_restart.html
+command. At a later time, these binary files can be read via a
+"read_restart"_read_restart.html command in a new script. Or they can
+be converted to text data files using the "-r command-line
+switch"_Section_start.html#start_6 and read by a
+"read_data"_read_data.html command in a new script.
+
+Here we give examples of 2 scripts that read either a binary restart
+file or a converted data file and then issue a new run command to
+continue where the previous run left off. They illustrate what
+settings must be made in the new script. Details are discussed in the
+documentation for the "read_restart"_read_restart.html and
+"read_data"_read_data.html commands.
+
+Look at the {in.chain} input script provided in the {bench} directory
+of the LAMMPS distribution to see the original script that these 2
+scripts are based on. If that script had the line
+
+restart 50 tmp.restart :pre
+
+added to it, it would produce 2 binary restart files (tmp.restart.50
+and tmp.restart.100) as it ran.
+
+This script could be used to read the 1st restart file and re-run the
+last 50 timesteps:
+
+read_restart tmp.restart.50 :pre
+
+neighbor 0.4 bin
+neigh_modify every 1 delay 1 :pre
+
+fix 1 all nve
+fix 2 all langevin 1.0 1.0 10.0 904297 :pre
+
+timestep 0.012 :pre
+
+run 50 :pre
+
+Note that the following commands do not need to be repeated because
+their settings are included in the restart file: {units, atom_style,
+special_bonds, pair_style, bond_style}. However these commands do
+need to be used, since their settings are not in the restart file:
+{neighbor, fix, timestep}.
+
+If you actually use this script to perform a restarted run, you will
+notice that the thermodynamic data match at step 50 (if you also put a
+"thermo 50" command in the original script), but do not match at step
+100. This is because the "fix langevin"_fix_langevin.html command
+uses random numbers in a way that does not allow for perfect restarts.
+
+As an alternate approach, the restart file could be converted to a data
+file as follows:
+
+lmp_g++ -r tmp.restart.50 tmp.restart.data :pre
+
+Then, this script could be used to re-run the last 50 steps:
+
+units lj
+atom_style bond
+pair_style lj/cut 1.12
+pair_modify shift yes
+bond_style fene
+special_bonds 0.0 1.0 1.0 :pre
+
+read_data tmp.restart.data :pre
+
+neighbor 0.4 bin
+neigh_modify every 1 delay 1 :pre
+
+fix 1 all nve
+fix 2 all langevin 1.0 1.0 10.0 904297 :pre
+
+timestep 0.012 :pre
+
+reset_timestep 50
+run 50 :pre
+
+Note that nearly all the settings specified in the original {in.chain}
+script must be repeated, except the {pair_coeff} and {bond_coeff}
+commands since the new data file lists the force field coefficients.
+Also, the "reset_timestep"_reset_timestep.html command is used to tell
+LAMMPS the current timestep. This value is stored in restart files,
+but not in data files.
diff --git a/doc/src/Howto_spc.txt b/doc/src/Howto_spc.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cbf16547be6f318794d837d832d3651edd072be
--- /dev/null
+++ b/doc/src/Howto_spc.txt
@@ -0,0 +1,54 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+SPC water model :h3
+
+The SPC water model specifies a 3-site rigid water molecule with
+charges and Lennard-Jones parameters assigned to each of the 3 atoms.
+In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
+the two O-H bonds and the H-O-H angle rigid. A bond style of
+{harmonic} and an angle style of {harmonic} or {charmm} should also be
+used.
+
+These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid SPC model.
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -0.820
+H charge = 0.410
+LJ epsilon of OO = 0.1553
+LJ sigma of OO = 3.166
+LJ epsilon, sigma of OH, HH = 0.0
+r0 of OH bond = 1.0
+theta of HOH angle = 109.47 :all(b),p
+
+Note that as originally proposed, the SPC model was run with a 9
+Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
+with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
+any of the parameters above, though it becomes a different model in
+that mode of usage.
+
+The SPC/E (extended) water model is the same, except
+the partial charge assignments change:
+
+O charge = -0.8476
+H charge = 0.4238 :all(b),p
+
+See the "(Berendsen)"_#howto-Berendsen reference for more details on both
+the SPC and SPC/E models.
+
+Wikipedia also has a nice article on "water
+models"_http://en.wikipedia.org/wiki/Water_model.
+
+:line
+
+:link(howto-Berendsen)
+[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91,
+6269-6271 (1987).
diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e737df655462c2fc0e1059ac7bc56ecdb120287
--- /dev/null
+++ b/doc/src/Howto_spherical.txt
@@ -0,0 +1,243 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Finite-size spherical and aspherical particles :h3
+
+Typical MD models treat atoms or particles as point masses. Sometimes
+it is desirable to have a model with finite-size particles such as
+spheroids or ellipsoids or generalized aspherical bodies. The
+difference is that such particles have a moment of inertia, rotational
+energy, and angular momentum. Rotation is induced by torque coming
+from interactions with other particles.
+
+LAMMPS has several options for running simulations with these kinds of
+particles. The following aspects are discussed in turn:
+
+atom styles
+pair potentials
+time integration
+computes, thermodynamics, and dump output
+rigid bodies composed of finite-size particles :ul
+
+Example input scripts for these kinds of models are in the body,
+colloid, dipole, ellipse, line, peri, pour, and tri directories of the
+"examples directory"_Examples.html in the LAMMPS distribution.
+
+Atom styles :h4
+
+There are several "atom styles"_atom_style.html that allow for
+definition of finite-size particles: sphere, dipole, ellipsoid, line,
+tri, peri, and body.
+
+The sphere style defines particles that are spheriods and each
+particle can have a unique diameter and mass (or density). These
+particles store an angular velocity (omega) and can be acted upon by
+torque. The "set" command can be used to modify the diameter and mass
+of individual particles, after then are created.
+
+The dipole style does not actually define finite-size particles, but
+is often used in conjunction with spherical particles, via a command
+like
+
+atom_style hybrid sphere dipole :pre
+
+This is because when dipoles interact with each other, they induce
+torques, and a particle must be finite-size (i.e. have a moment of
+inertia) in order to respond and rotate. See the "atom_style
+dipole"_atom_style.html command for details. The "set" command can be
+used to modify the orientation and length of the dipole moment of
+individual particles, after then are created.
+
+The ellipsoid style defines particles that are ellipsoids and thus can
+be aspherical. Each particle has a shape, specified by 3 diameters,
+and mass (or density). These particles store an angular momentum and
+their orientation (quaternion), and can be acted upon by torque. They
+do not store an angular velocity (omega), which can be in a different
+direction than angular momentum, rather they compute it as needed.
+The "set" command can be used to modify the diameter, orientation, and
+mass of individual particles, after then are created. It also has a
+brief explanation of what quaternions are.
+
+The line style defines line segment particles with two end points and
+a mass (or density). They can be used in 2d simulations, and they can
+be joined together to form rigid bodies which represent arbitrary
+polygons.
+
+The tri style defines triangular particles with three corner points
+and a mass (or density). They can be used in 3d simulations, and they
+can be joined together to form rigid bodies which represent arbitrary
+particles with a triangulated surface.
+
+The peri style is used with "Peridynamic models"_pair_peri.html and
+defines particles as having a volume, that is used internally in the
+"pair_style peri"_pair_peri.html potentials.
+
+The body style allows for definition of particles which can represent
+complex entities, such as surface meshes of discrete points,
+collections of sub-particles, deformable objects, etc. The body style
+is discussed in more detail on the "Howto body"_Howto_body.html doc
+page.
+
+Note that if one of these atom styles is used (or multiple styles via
+the "atom_style hybrid"_atom_style.html command), not all particles in
+the system are required to be finite-size or aspherical.
+
+For example, in the ellipsoid style, if the 3 shape parameters are set
+to the same value, the particle will be a sphere rather than an
+ellipsoid. If the 3 shape parameters are all set to 0.0 or if the
+diameter is set to 0.0, it will be a point particle. In the line or
+tri style, if the lineflag or triflag is specified as 0, then it
+will be a point particle.
+
+Some of the pair styles used to compute pairwise interactions between
+finite-size particles also compute the correct interaction with point
+particles as well, e.g. the interaction between a point particle and a
+finite-size particle or between two point particles. If necessary,
+"pair_style hybrid"_pair_hybrid.html can be used to insure the correct
+interactions are computed for the appropriate style of interactions.
+Likewise, using groups to partition particles (ellipsoids versus
+spheres versus point particles) will allow you to use the appropriate
+time integrators and temperature computations for each class of
+particles. See the doc pages for various commands for details.
+
+Also note that for "2d simulations"_dimension.html, atom styles sphere
+and ellipsoid still use 3d particles, rather than as circular disks or
+ellipses. This means they have the same moment of inertia as the 3d
+object. When temperature is computed, the correct degrees of freedom
+are used for rotation in a 2d versus 3d system.
+
+Pair potentials :h4
+
+When a system with finite-size particles is defined, the particles
+will only rotate and experience torque if the force field computes
+such interactions. These are the various "pair
+styles"_pair_style.html that generate torque:
+
+"pair_style gran/history"_pair_gran.html
+"pair_style gran/hertzian"_pair_gran.html
+"pair_style gran/no_history"_pair_gran.html
+"pair_style dipole/cut"_pair_dipole.html
+"pair_style gayberne"_pair_gayberne.html
+"pair_style resquared"_pair_resquared.html
+"pair_style brownian"_pair_brownian.html
+"pair_style lubricate"_pair_lubricate.html
+"pair_style line/lj"_pair_line_lj.html
+"pair_style tri/lj"_pair_tri_lj.html
+"pair_style body/nparticle"_pair_body_nparticle.html :ul
+
+The granular pair styles are used with spherical particles. The
+dipole pair style is used with the dipole atom style, which could be
+applied to spherical or ellipsoidal particles. The GayBerne and
+REsquared potentials require ellipsoidal particles, though they will
+also work if the 3 shape parameters are the same (a sphere). The
+Brownian and lubrication potentials are used with spherical particles.
+The line, tri, and body potentials are used with line segment,
+triangular, and body particles respectively.
+
+Time integration :h4
+
+There are several fixes that perform time integration on finite-size
+spherical particles, meaning the integrators update the rotational
+orientation and angular velocity or angular momentum of the particles:
+
+"fix nve/sphere"_fix_nve_sphere.html
+"fix nvt/sphere"_fix_nvt_sphere.html
+"fix npt/sphere"_fix_npt_sphere.html :ul
+
+Likewise, there are 3 fixes that perform time integration on
+ellipsoidal particles:
+
+"fix nve/asphere"_fix_nve_asphere.html
+"fix nvt/asphere"_fix_nvt_asphere.html
+"fix npt/asphere"_fix_npt_asphere.html :ul
+
+The advantage of these fixes is that those which thermostat the
+particles include the rotational degrees of freedom in the temperature
+calculation and thermostatting. The "fix langevin"_fix_langevin
+command can also be used with its {omgea} or {angmom} options to
+thermostat the rotational degrees of freedom for spherical or
+ellipsoidal particles. Other thermostatting fixes only operate on the
+translational kinetic energy of finite-size particles.
+
+These fixes perform constant NVE time integration on line segment,
+triangular, and body particles:
+
+"fix nve/line"_fix_nve_line.html
+"fix nve/tri"_fix_nve_tri.html
+"fix nve/body"_fix_nve_body.html :ul
+
+Note that for mixtures of point and finite-size particles, these
+integration fixes can only be used with "groups"_group.html which
+contain finite-size particles.
+
+Computes, thermodynamics, and dump output :h4
+
+There are several computes that calculate the temperature or
+rotational energy of spherical or ellipsoidal particles:
+
+"compute temp/sphere"_compute_temp_sphere.html
+"compute temp/asphere"_compute_temp_asphere.html
+"compute erotate/sphere"_compute_erotate_sphere.html
+"compute erotate/asphere"_compute_erotate_asphere.html :ul
+
+These include rotational degrees of freedom in their computation. If
+you wish the thermodynamic output of temperature or pressure to use
+one of these computes (e.g. for a system entirely composed of
+finite-size particles), then the compute can be defined and the
+"thermo_modify"_thermo_modify.html command used. Note that by default
+thermodynamic quantities will be calculated with a temperature that
+only includes translational degrees of freedom. See the
+"thermo_style"_thermo_style.html command for details.
+
+These commands can be used to output various attributes of finite-size
+particles:
+
+"dump custom"_dump.html
+"compute property/atom"_compute_property_atom.html
+"dump local"_dump.html
+"compute body/local"_compute_body_local.html :ul
+
+Attributes include the dipole moment, the angular velocity, the
+angular momentum, the quaternion, the torque, the end-point and
+corner-point coordinates (for line and tri particles), and
+sub-particle attributes of body particles.
+
+Rigid bodies composed of finite-size particles :h4
+
+The "fix rigid"_fix_rigid.html command treats a collection of
+particles as a rigid body, computes its inertia tensor, sums the total
+force and torque on the rigid body each timestep due to forces on its
+constituent particles, and integrates the motion of the rigid body.
+
+If any of the constituent particles of a rigid body are finite-size
+particles (spheres or ellipsoids or line segments or triangles), then
+their contribution to the inertia tensor of the body is different than
+if they were point particles. This means the rotational dynamics of
+the rigid body will be different. Thus a model of a dimer is
+different if the dimer consists of two point masses versus two
+spheroids, even if the two particles have the same mass. Finite-size
+particles that experience torque due to their interaction with other
+particles will also impart that torque to a rigid body they are part
+of.
+
+See the "fix rigid" command for example of complex rigid-body models
+it is possible to define in LAMMPS.
+
+Note that the "fix shake"_fix_shake.html command can also be used to
+treat 2, 3, or 4 particles as a rigid body, but it always assumes the
+particles are point masses.
+
+Also note that body particles cannot be modeled with the "fix
+rigid"_fix_rigid.html command. Body particles are treated by LAMMPS
+as single particles, though they can store internal state, such as a
+list of sub-particles. Individual body partices are typically treated
+as rigid bodies, and their motion integrated with a command like "fix
+nve/body"_fix_nve_body.html. Interactions between pairs of body
+particles are computed via a command like "pair_style
+body/nparticle"_pair_body_nparticle.html.
diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b9adb49a5701789dafc9f86cebc23a87623411c
--- /dev/null
+++ b/doc/src/Howto_spins.txt
@@ -0,0 +1,59 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Magnetic spins :h3
+
+The magnetic spin simualtions are enabled by the SPIN package, whose
+implementation is detailed in "Tranchida"_#Tranchida7.
+
+The model representents the simulation of atomic magnetic spins coupled
+to lattice vibrations. The dynamics of those magnetic spins can be used
+to simulate a broad range a phenomena related to magneto-elasticity, or
+or to study the influence of defects on the magnetic properties of
+materials.
+
+The magnetic spins are interacting with each others and with the
+lattice via pair interactions. Typically, the magnetic exchange
+interaction can be defined using the
+"pair/spin/exchange"_pair_spin_exchange.html command. This exchange
+applies a magnetic torque to a given spin, considering the orientation
+of its neighboring spins and their relative distances.
+It also applies a force on the atoms as a function of the spin
+orientations and their associated inter-atomic distances.
+
+The command "fix precession/spin"_fix_precession_spin.html allows to
+apply a constant magnetic torque on all the spins in the system. This
+torque can be an external magnetic field (Zeeman interaction), or an
+uniaxial magnetic anisotropy.
+
+A Langevin thermostat can be applied to those magnetic spins using
+"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
+can be coupled to another Langevin thermostat applied to the atoms
+using "fix langevin"_fix_langevin.html in order to simulate
+thermostated spin-lattice system.
+
+The magnetic Gilbert damping can also be applied using "fix
+langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
+the thermal energy of the Langevin thermostat, or to perform a
+relaxation of the magnetic configuration toward an equilibrium state.
+
+All the computed magnetic properties can be outputed by two main
+commands. The first one is "compute spin"_compute_spin.html, that
+enables to evaluate magnetic averaged quantities, such as the total
+magnetization of the system along x, y, or z, the spin temperature, or
+the magnetic energy. The second command is "compute
+property/atom"_compute_property_atom.html. It enables to output all the
+per atom magnetic quantities. Typically, the orientation of a given
+magnetic spin, or the magnetic force acting on this spin.
+
+:line
+
+:link(Tranchida7)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
+arXiv preprint arXiv:1801.10233, (2018).
diff --git a/doc/src/Howto_temperature.txt b/doc/src/Howto_temperature.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a318250cffa956692693e601638e749cc4d6df4
--- /dev/null
+++ b/doc/src/Howto_temperature.txt
@@ -0,0 +1,40 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Calcalate temperature :h3
+
+Temperature is computed as kinetic energy divided by some number of
+degrees of freedom (and the Boltzmann constant). Since kinetic energy
+is a function of particle velocity, there is often a need to
+distinguish between a particle's advection velocity (due to some
+aggregate motion of particles) and its thermal velocity. The sum of
+the two is the particle's total velocity, but the latter is often what
+is wanted to compute a temperature.
+
+LAMMPS has several options for computing temperatures, any of which can be used in "thermostatting"_Howto_thermostat.html and "barostatting"_Howto_barostat.html. These "compute commands"_compute.html calculate temperature:
+
+"compute temp"_compute_temp.html
+"compute temp/sphere"_compute_temp_sphere.html
+"compute temp/asphere"_compute_temp_asphere.html
+"compute temp/com"_compute_temp_com.html
+"compute temp/deform"_compute_temp_deform.html
+"compute temp/partial"_compute_temp_partial.html
+"compute temp/profile"_compute_temp_profile.html
+"compute temp/ramp"_compute_temp_ramp.html
+"compute temp/region"_compute_temp_region.html :ul
+
+All but the first 3 calculate velocity biases directly (e.g. advection
+velocities) that are removed when computing the thermal temperature.
+"Compute temp/sphere"_compute_temp_sphere.html and "compute
+temp/asphere"_compute_temp_asphere.html compute kinetic energy for
+finite-size particles that includes rotational degrees of freedom.
+They both allow for velocity biases indirectly, via an optional extra
+argument which is another temperature compute that subtracts a velocity bias.
+This allows the translational velocity of spherical or aspherical
+particles to be adjusted in prescribed ways.
diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e2feb18699cd993abf78df4542b599431d8512a
--- /dev/null
+++ b/doc/src/Howto_thermostat.txt
@@ -0,0 +1,89 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Thermostats :h3
+
+Thermostatting means controlling the temperature of particles in an MD
+simulation. "Barostatting"_Howto_barostat.html means controlling the
+pressure. Since the pressure includes a kinetic component due to
+particle velocities, both these operations require calculation of the
+temperature. Typically a target temperature (T) and/or pressure (P)
+is specified by the user, and the thermostat or barostat attempts to
+equilibrate the system to the requested T and/or P.
+
+Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one
+case by a pair style. Several thermostatting fixes are available:
+Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
+(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
+can be invoked via the {dpd/tstat} pair style:
+
+"fix nvt"_fix_nh.html
+"fix nvt/sphere"_fix_nvt_sphere.html
+"fix nvt/asphere"_fix_nvt_asphere.html
+"fix nvt/sllod"_fix_nvt_sllod.html
+"fix temp/berendsen"_fix_temp_berendsen.html
+"fix temp/csvr"_fix_temp_csvr.html
+"fix langevin"_fix_langevin.html
+"fix temp/rescale"_fix_temp_rescale.html
+"pair_style dpd/tstat"_pair_dpd.html :ul
+
+"Fix nvt"_fix_nh.html only thermostats the translational velocity of
+particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except
+that it subtracts out a velocity bias due to a deforming box and
+integrates the SLLOD equations of motion. See the "Howto
+nemd"_Howto_nemd.html doc page for further details. "Fix
+nvt/sphere"_fix_nvt_sphere.html and "fix
+nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
+velocities but also rotational velocities for spherical and aspherical
+particles.
+
+DPD thermostatting alters pairwise interactions in a manner analogous
+to the per-particle thermostatting of "fix
+langevin"_fix_langevin.html.
+
+Any of the thermostatting fixes can use "temperature
+computes"_Howto_thermostat.html that remove bias which has two
+effects. First, the current calculated temperature, which is compared
+to the requested target temperature, is calculated with the velocity
+bias removed. Second, the thermostat adjusts only the thermal
+temperature component of the particle's velocities, which are the
+velocities with the bias removed. The removed bias is then added back
+to the adjusted velocities. See the doc pages for the individual
+fixes and for the "fix_modify"_fix_modify.html command for
+instructions on how to assign a temperature compute to a
+thermostatting fix. For example, you can apply a thermostat to only
+the x and z components of velocity by using it in conjunction with
+"compute temp/partial"_compute_temp_partial.html. Of you could
+thermostat only the thermal temperature of a streaming flow of
+particles without affecting the streaming velocity, by using "compute
+temp/profile"_compute_temp_profile.html.
+
+NOTE: Only the nvt fixes perform time integration, meaning they update
+the velocities and positions of particles due to forces and velocities
+respectively. The other thermostat fixes only adjust velocities; they
+do NOT perform time integration updates. Thus they should be used in
+conjunction with a constant NVE integration fix such as these:
+
+"fix nve"_fix_nve.html
+"fix nve/sphere"_fix_nve_sphere.html
+"fix nve/asphere"_fix_nve_asphere.html :ul
+
+Thermodynamic output, which can be setup via the
+"thermo_style"_thermo_style.html command, often includes temperature
+values. As explained on the doc page for the
+"thermo_style"_thermo_style.html command, the default temperature is
+setup by the thermo command itself. It is NOT the temperature
+associated with any thermostatting fix you have defined or with any
+compute you have defined that calculates a temperature. The doc pages
+for the thermostatting fixes explain the ID of the temperature compute
+they create. Thus if you want to view these temperatures, you need to
+specify them explicitly via the "thermo_style
+custom"_thermo_style.html command. Or you can use the
+"thermo_modify"_thermo_modify.html command to re-define what
+temperature compute is used for default thermodynamic output.
diff --git a/doc/src/Howto_tip3p.txt b/doc/src/Howto_tip3p.txt
new file mode 100644
index 0000000000000000000000000000000000000000..942b42aea16ea63d2541ca839646f4b77dc9c079
--- /dev/null
+++ b/doc/src/Howto_tip3p.txt
@@ -0,0 +1,69 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+TIP3P water model :h3
+
+The TIP3P water model as implemented in CHARMM
+"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
+charges and Lennard-Jones parameters assigned to each of the 3 atoms.
+In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
+the two O-H bonds and the H-O-H angle rigid. A bond style of
+{harmonic} and an angle style of {harmonic} or {charmm} should also be
+used.
+
+These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
+cutoff. The K values can be used if a flexible TIP3P model (without
+fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
+set to 0.0, it corresponds to the original 1983 TIP3P model
+"(Jorgensen)"_#Jorgensen1.
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -0.834
+H charge = 0.417
+LJ epsilon of OO = 0.1521
+LJ sigma of OO = 3.1507
+LJ epsilon of HH = 0.0460
+LJ sigma of HH = 0.4000
+LJ epsilon of OH = 0.0836
+LJ sigma of OH = 1.7753
+K of OH bond = 450
+r0 of OH bond = 0.9572
+K of HOH angle = 55
+theta of HOH angle = 104.52 :all(b),p
+
+These are the parameters to use for TIP3P with a long-range Coulombic
+solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for
+details:
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -0.830
+H charge = 0.415
+LJ epsilon of OO = 0.102
+LJ sigma of OO = 3.188
+LJ epsilon, sigma of OH, HH = 0.0
+K of OH bond = 450
+r0 of OH bond = 0.9572
+K of HOH angle = 55
+theta of HOH angle = 104.52 :all(b),p
+
+Wikipedia also has a nice article on "water
+models"_http://en.wikipedia.org/wiki/Water_model.
+
+:line
+
+:link(Jorgensen1)
+[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
+
+:link(Price1)
+[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004).
+
diff --git a/doc/src/Howto_tip4p.txt b/doc/src/Howto_tip4p.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9e548e26896c1143f1cead59e3c0a1effb015c3
--- /dev/null
+++ b/doc/src/Howto_tip4p.txt
@@ -0,0 +1,112 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+TIP4P water model :h3
+
+The four-point TIP4P rigid water model extends the traditional
+three-point TIP3P model by adding an additional site, usually
+massless, where the charge associated with the oxygen atom is placed.
+This site M is located at a fixed distance away from the oxygen along
+the bisector of the HOH bond angle. A bond style of {harmonic} and an
+angle style of {harmonic} or {charmm} should also be used.
+
+A TIP4P model is run with LAMMPS using either this command
+for a cutoff model:
+
+"pair_style lj/cut/tip4p/cut"_pair_lj.html
+
+or these two commands for a long-range model:
+
+"pair_style lj/cut/tip4p/long"_pair_lj.html
+"kspace_style pppm/tip4p"_kspace_style.html :ul
+
+For both models, the bond lengths and bond angles should be held fixed
+using the "fix shake"_fix_shake.html command.
+
+These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid TIP4P model with a cutoff
+"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in
+the "pair_style"_pair_style.html command, not as part of the pair
+coefficients.
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -1.040
+H charge = 0.520
+r0 of OH bond = 0.9572
+theta of HOH angle = 104.52
+OM distance = 0.15
+LJ epsilon of O-O = 0.1550
+LJ sigma of O-O = 3.1536
+LJ epsilon, sigma of OH, HH = 0.0
+Coulombic cutoff = 8.5 :all(b),p
+
+For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
+http://dx.doi.org/10.1063/1.1931662) these values can be used:
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -1.1794
+H charge = 0.5897
+r0 of OH bond = 0.9572
+theta of HOH angle = 104.52
+OM distance = 0.1577
+LJ epsilon of O-O = 0.21084
+LJ sigma of O-O = 3.1668
+LJ epsilon, sigma of OH, HH = 0.0
+Coulombic cutoff = 8.5 :all(b),p
+
+For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
+http://dx.doi.org/10.1063/1.2121687), these values can be used:
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -1.1128
+H charge = 0.5564
+r0 of OH bond = 0.9572
+theta of HOH angle = 104.52
+OM distance = 0.1546
+LJ epsilon of O-O = 0.1852
+LJ sigma of O-O = 3.1589
+LJ epsilon, sigma of OH, HH = 0.0
+Coulombic cutoff = 8.5 :all(b),p
+
+These are the parameters to use for TIP4P with a long-range Coulombic
+solver (e.g. Ewald or PPPM in LAMMPS):
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -1.0484
+H charge = 0.5242
+r0 of OH bond = 0.9572
+theta of HOH angle = 104.52
+OM distance = 0.1250
+LJ epsilon of O-O = 0.16275
+LJ sigma of O-O = 3.16435
+LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
+
+Note that the when using the TIP4P pair style, the neighbor list
+cutoff for Coulomb interactions is effectively extended by a distance
+2 * (OM distance), to account for the offset distance of the
+fictitious charges on O atoms in water molecules. Thus it is
+typically best in an efficiency sense to use a LJ cutoff >= Coulomb
+cutoff + 2*(OM distance), to shrink the size of the neighbor list.
+This leads to slightly larger cost for the long-range calculation, so
+you can test the trade-off for your model. The OM distance and the LJ
+and Coulombic cutoffs are set in the "pair_style
+lj/cut/tip4p/long"_pair_lj.html command.
+
+Wikipedia also has a nice article on "water
+models"_http://en.wikipedia.org/wiki/Water_model.
+
+:line
+
+:link(Jorgensen1)
+[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
diff --git a/doc/src/Howto_triclinic.txt b/doc/src/Howto_triclinic.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b299e5ae1ecc024c3be42bbc019bc8d9550c54d
--- /dev/null
+++ b/doc/src/Howto_triclinic.txt
@@ -0,0 +1,213 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+Triclinic (non-orthogonal) simulation boxes :h3
+
+By default, LAMMPS uses an orthogonal simulation box to encompass the
+particles. The "boundary"_boundary.html command sets the boundary
+conditions of the box (periodic, non-periodic, etc). The orthogonal
+box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
+starting from the origin given by [a] = (xhi-xlo,0,0); [b] =
+(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters
+(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
+is created, e.g. by the "create_box"_create_box.html or
+"read_data"_read_data.html or "read_restart"_read_restart.html
+commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
+where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
+parameters, as well as lx,ly,lz, can be output via the "thermo_style
+custom"_thermo_style.html command.
+
+LAMMPS also allows simulations to be performed in triclinic
+(non-orthogonal) simulation boxes shaped as a parallelepiped with
+triclinic symmetry. The parallelepiped has its "origin" at
+(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
+origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] =
+(xz,yz,zhi-zlo). {xy,xz,yz} can be 0.0 or positive or negative values
+and are called "tilt factors" because they are the amount of
+displacement applied to faces of an originally orthogonal box to
+transform it into the parallelepiped. In LAMMPS the triclinic
+simulation box edge vectors [a], [b], and [c] cannot be arbitrary
+vectors. As indicated, [a] must lie on the positive x axis. [b] must
+lie in the xy plane, with strictly positive y component. [c] may have
+any orientation with strictly positive z component. The requirement
+that [a], [b], and [c] have strictly positive x, y, and z components,
+respectively, ensures that [a], [b], and [c] form a complete
+right-handed basis. These restrictions impose no loss of generality,
+since it is possible to rotate/invert any set of 3 crystal basis
+vectors so that they conform to the restrictions.
+
+For example, assume that the 3 vectors [A],[B],[C] are the edge
+vectors of a general parallelepiped, where there is no restriction on
+[A],[B],[C] other than they form a complete right-handed basis i.e.
+[A] x [B] . [C] > 0. The equivalent LAMMPS [a],[b],[c] are a linear
+rotation of [A], [B], and [C] and can be computed as follows:
+
+:c,image(Eqs/transform.jpg)
+
+where A = | [A] | indicates the scalar length of [A]. The hat symbol (^)
+indicates the corresponding unit vector. {beta} and {gamma} are angles
+between the vectors described below. Note that by construction,
+[a], [b], and [c] have strictly positive x, y, and z components, respectively.
+If it should happen that
+[A], [B], and [C] form a left-handed basis, then the above equations
+are not valid for [c]. In this case, it is necessary
+to first apply an inversion. This can be achieved
+by interchanging two basis vectors or by changing the sign of one of them.
+
+For consistency, the same rotation/inversion applied to the basis vectors
+must also be applied to atom positions, velocities,
+and any other vector quantities.
+This can be conveniently achieved by first converting to
+fractional coordinates in the
+old basis and then converting to distance coordinates in the new basis.
+The transformation is given by the following equation:
+
+:c,image(Eqs/rotate.jpg)
+
+where {V} is the volume of the box, [X] is the original vector quantity and
+[x] is the vector in the LAMMPS basis.
+
+There is no requirement that a triclinic box be periodic in any
+dimension, though it typically should be in at least the 2nd dimension
+of the tilt (y in xy) if you want to enforce a shift in periodic
+boundary conditions across that boundary. Some commands that work
+with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix
+npt"_fix_nh.html commands, require periodicity or non-shrink-wrap
+boundary conditions in specific dimensions. See the command doc pages
+for details.
+
+The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
+time the simulation box is created. This happens in one of 3 ways.
+If the "create_box"_create_box.html command is used with a region of
+style {prism}, then a triclinic box is setup. See the
+"region"_region.html command for details. If the
+"read_data"_read_data.html command is used to define the simulation
+box, and the header of the data file contains a line with the "xy xz
+yz" keyword, then a triclinic box is setup. See the
+"read_data"_read_data.html command for details. Finally, if the
+"read_restart"_read_restart.html command reads a restart file which
+was written from a simulation using a triclinic box, then a triclinic
+box will be setup for the restarted simulation.
+
+Note that you can define a triclinic box with all 3 tilt factors =
+0.0, so that it is initially orthogonal. This is necessary if the box
+will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or
+"fix deform"_fix_deform.html commands. Alternatively, you can use the
+"change_box"_change_box.html command to convert a simulation box from
+orthogonal to triclinic and vice versa.
+
+As with orthogonal boxes, LAMMPS defines triclinic box size parameters
+lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
+The 9 parameters, as well as lx,ly,lz, can be output via the
+"thermo_style custom"_thermo_style.html command.
+
+To avoid extremely tilted boxes (which would be computationally
+inefficient), LAMMPS normally requires that no tilt factor can skew
+the box more than half the distance of the parallel box length, which
+is the 1st dimension in the tilt factor (x for xz). This is required
+both when the simulation box is created, e.g. via the
+"create_box"_create_box.html or "read_data"_read_data.html commands,
+as well as when the box shape changes dynamically during a simulation,
+e.g. via the "fix deform"_fix_deform.html or "fix npt"_fix_nh.html
+commands.
+
+For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
+the xy tilt factor must be between -5 and 5. Similarly, both xz and
+yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
+not a limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are geometrically all equivalent. If the box tilt exceeds this
+limit during a dynamics run (e.g. via the "fix deform"_fix_deform.html
+command), then the box is "flipped" to an equivalent shape with a tilt
+factor within the bounds, so the run can continue. See the "fix
+deform"_fix_deform.html doc page for further details.
+
+One exception to this rule is if the 1st dimension in the tilt
+factor (x for xy) is non-periodic. In that case, the limits on the
+tilt factor are not enforced, since flipping the box in that dimension
+does not change the atom positions due to non-periodicity. In this
+mode, if you tilt the system to extreme angles, the simulation will
+simply become inefficient, due to the highly skewed simulation box.
+
+The limitation on not creating a simulation box with a tilt factor
+skewing the box more than half the distance of the parallel box length
+can be overridden via the "box"_box.html command. Setting the {tilt}
+keyword to {large} allows any tilt factors to be specified.
+
+Box flips that may occur using the "fix deform"_fix_deform.html or
+"fix npt"_fix_nh.html commands can be turned off using the {flip no}
+option with either of the commands.
+
+Note that if a simulation box has a large tilt factor, LAMMPS will run
+less efficiently, due to the large volume of communication needed to
+acquire ghost atoms around a processor's irregular-shaped sub-domain.
+For extreme values of tilt, LAMMPS may also lose atoms and generate an
+error.
+
+Triclinic crystal structures are often defined using three lattice
+constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and
+{gamma}. Note that in this nomenclature, the a, b, and c lattice
+constants are the scalar lengths of the edge vectors [a], [b], and [c]
+defined above. The relationship between these 6 quantities
+(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
+(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
+
+:c,image(Eqs/box.jpg)
+
+The inverse relationship can be written as follows:
+
+:c,image(Eqs/box_inverse.jpg)
+
+The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
+out or accessed by computes using the
+"thermo_style custom"_thermo_style.html keywords
+{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma},
+respectively.
+
+As discussed on the "dump"_dump.html command doc page, when the BOX
+BOUNDS for a snapshot is written to a dump file for a triclinic box,
+an orthogonal bounding box which encloses the triclinic simulation box
+is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
+box, formatted as follows:
+
+ITEM: BOX BOUNDS xy xz yz
+xlo_bound xhi_bound xy
+ylo_bound yhi_bound xz
+zlo_bound zhi_bound yz :pre
+
+This bounding box is convenient for many visualization programs and is
+calculated from the 9 triclinic box parameters
+(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
+
+xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
+xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
+ylo_bound = ylo + MIN(0.0,yz)
+yhi_bound = yhi + MAX(0.0,yz)
+zlo_bound = zlo
+zhi_bound = zhi :pre
+
+These formulas can be inverted if you need to convert the bounding box
+back into the triclinic box parameters, e.g. xlo = xlo_bound -
+MIN(0.0,xy,xz,xy+xz).
+
+One use of triclinic simulation boxes is to model solid-state crystals
+with triclinic symmetry. The "lattice"_lattice.html command can be
+used with non-orthogonal basis vectors to define a lattice that will
+tile a triclinic simulation box via the
+"create_atoms"_create_atoms.html command.
+
+A second use is to run Parinello-Rahman dynamics via the "fix
+npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
+factors to compensate for off-diagonal components of the pressure
+tensor. The analog for an "energy minimization"_minimize.html is
+the "fix box/relax"_fix_box_relax.html command.
+
+A third use is to shear a bulk solid to study the response of the
+material. The "fix deform"_fix_deform.html command can be used for
+this purpose. It allows dynamic control of the xy, xz, yz tilt
+factors as a simulation runs. This is discussed in the next section
+on non-equilibrium MD (NEMD) simulations.
diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8bcab6dd247f02de5dbb3135e67fe76cc32efb01
--- /dev/null
+++ b/doc/src/Howto_viscosity.txt
@@ -0,0 +1,133 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Calculate viscosity :h3
+
+The shear viscosity eta of a fluid can be measured in at least 5 ways
+using various options in LAMMPS. See the examples/VISCOSITY directory
+for scripts that implement the 5 methods discussed here for a simple
+Lennard-Jones fluid model. Also, see the "Howto
+kappa"_Howto_kappa.html doc page for an analogous discussion for
+thermal conductivity.
+
+Eta is a measure of the propensity of a fluid to transmit momentum in
+a direction perpendicular to the direction of velocity or momentum
+flow. Alternatively it is the resistance the fluid has to being
+sheared. It is given by
+
+J = -eta grad(Vstream)
+
+where J is the momentum flux in units of momentum per area per time.
+and grad(Vstream) is the spatial gradient of the velocity of the fluid
+moving in another direction, normal to the area through which the
+momentum flows. Viscosity thus has units of pressure-time.
+
+The first method is to perform a non-equilibrium MD (NEMD) simulation
+by shearing the simulation box via the "fix deform"_fix_deform.html
+command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to
+thermostat the fluid via the SLLOD equations of motion.
+Alternatively, as a second method, one or more moving walls can be
+used to shear the fluid in between them, again with some kind of
+thermostat that modifies only the thermal (non-shearing) components of
+velocity to prevent the fluid from heating up.
+
+In both cases, the velocity profile setup in the fluid by this
+procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html
+command, which determines grad(Vstream) in the equation above.
+E.g. the derivative in the y-direction of the Vx component of fluid
+motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of
+the pressure or stress tensor, as calculated by the "compute
+pressure"_compute_pressure.html command, can also be monitored, which
+is the J term in the equation above. See the "Howto
+nemd"_Howto_nemd.html doc page for details on NEMD simulations.
+
+The third method is to perform a reverse non-equilibrium MD simulation
+using the "fix viscosity"_fix_viscosity.html command which implements
+the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
+swapped between atoms in two different layers of the simulation box in
+a different dimension. This induces a velocity gradient which can be
+monitored with the "fix ave/chunk"_fix_ave_chunk.html command.
+The fix tallies the cumulative momentum transfer that it performs.
+See the "fix viscosity"_fix_viscosity.html command for details.
+
+The fourth method is based on the Green-Kubo (GK) formula which
+relates the ensemble average of the auto-correlation of the
+stress/pressure tensor to eta. This can be done in a fully
+equilibrated simulation which is in contrast to the two preceding
+non-equilibrium methods, where momentum flows continuously through the
+simulation box.
+
+Here is an example input script that calculates the viscosity of
+liquid Ar via the GK formalism:
+
+# Sample LAMMPS input script for viscosity of liquid Ar :pre
+
+units real
+variable T equal 86.4956
+variable V equal vol
+variable dt equal 4.0
+variable p equal 400 # correlation length
+variable s equal 5 # sample interval
+variable d equal $p*$s # dump interval :pre
+
+# convert from LAMMPS real units to SI :pre
+
+variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann
+variable atm2Pa equal 101325.0
+variable A2m equal 1.0e-10
+variable fs2s equal 1.0e-15
+variable convert equal $\{atm2Pa\}*$\{atm2Pa\}*$\{fs2s\}*$\{A2m\}*$\{A2m\}*$\{A2m\} :pre
+
+# setup problem :pre
+
+dimension 3
+boundary p p p
+lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
+region box block 0 4 0 4 0 4
+create_box 1 box
+create_atoms 1 box
+mass 1 39.948
+pair_style lj/cut 13.0
+pair_coeff * * 0.2381 3.405
+timestep $\{dt\}
+thermo $d :pre
+
+# equilibration and thermalization :pre
+
+velocity all create $T 102486 mom yes rot yes dist gaussian
+fix NVT all nvt temp $T $T 10 drag 0.2
+run 8000 :pre
+
+# viscosity calculation, switch to NVE if desired :pre
+
+#unfix NVT
+#fix NVE all nve :pre
+
+reset_timestep 0
+variable pxy equal pxy
+variable pxz equal pxz
+variable pyz equal pyz
+fix SS all ave/correlate $s $p $d &
+ v_pxy v_pxz v_pyz type auto file S0St.dat ave running
+variable scale equal $\{convert\}/($\{kB\}*$T)*$V*$s*$\{dt\}
+variable v11 equal trap(f_SS\[3\])*$\{scale\}
+variable v22 equal trap(f_SS\[4\])*$\{scale\}
+variable v33 equal trap(f_SS\[5\])*$\{scale\}
+thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
+run 100000
+variable v equal (v_v11+v_v22+v_v33)/3.0
+variable ndens equal count(all)/vol
+print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre
+
+The fifth method is related to the above Green-Kubo method,
+but uses the Einstein formulation, analogous to the Einstein
+mean-square-displacement formulation for self-diffusivity. The
+time-integrated momentum fluxes play the role of Cartesian
+coordinates, whose mean-square displacement increases linearly
+with time at sufficiently long times.
diff --git a/doc/src/Howto_viz.txt b/doc/src/Howto_viz.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00c329c50b1a7f5685d31b4f9a59b3affa2dcb4f
--- /dev/null
+++ b/doc/src/Howto_viz.txt
@@ -0,0 +1,40 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Visualize LAMMPS snapshots :h3
+
+LAMMPS itself does not do visualization, but snapshots from LAMMPS
+simulations can be visualized (and analyzed) in a variety of ways.
+
+Mention dump image and dump movie.
+
+LAMMPS snapshots are created by the "dump"_dump.html command which can
+create files in several formats. The native LAMMPS dump format is a
+text file (see "dump atom" or "dump custom") which can be visualized
+by several popular visualization tools. The "dump
+image"_dump_image.html and "dump movie"_dump_image.html styles can
+output internally rendered images and convert a sequence of them to a
+movie during the MD run. Several programs included with LAMMPS as
+auxiliary tools can convert between LAMMPS format files and other
+formats. See the "Tools"_Tools.html doc page for details.
+
+A Python-based toolkit distributed by our group can read native LAMMPS
+dump files, including custom dump files with additional columns of
+user-specified atom information, and convert them to various formats
+or pipe them into visualization software directly. See the "Pizza.py
+WWW site"_pizza for details. Specifically, Pizza.py can convert
+LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats.
+Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
+RasMol visualization programs. Pizza.py has tools that do interactive
+3d OpenGL visualization and one that creates SVG images of dump file
+snapshots.
+
+:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
+:link(ensight,http://www.ensight.com)
+:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
diff --git a/doc/src/Howto_walls.txt b/doc/src/Howto_walls.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75221185829cfbb3c6b4f9489ee1a3cd47764b43
--- /dev/null
+++ b/doc/src/Howto_walls.txt
@@ -0,0 +1,80 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Walls :h3
+
+Walls in an MD simulation are typically used to bound particle motion,
+i.e. to serve as a boundary condition.
+
+Walls in LAMMPS can be of rough (made of particles) or idealized
+surfaces. Ideal walls can be smooth, generating forces only in the
+normal direction, or frictional, generating forces also in the
+tangential direction.
+
+Rough walls, built of particles, can be created in various ways. The
+particles themselves can be generated like any other particle, via the
+"lattice"_lattice.html and "create_atoms"_create_atoms.html commands,
+or read in via the "read_data"_read_data.html command.
+
+Their motion can be constrained by many different commands, so that
+they do not move at all, move together as a group at constant velocity
+or in response to a net force acting on them, move in a prescribed
+fashion (e.g. rotate around a point), etc. Note that if a time
+integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html
+is not used with the group that contains wall particles, their
+positions and velocities will not be updated.
+
+"fix aveforce"_fix_aveforce.html - set force on particles to average value, so they move together
+"fix setforce"_fix_setforce.html - set force on particles to a value, e.g. 0.0
+"fix freeze"_fix_freeze.html - freeze particles for use as granular walls
+"fix nve/noforce"_fix_nve_noforce.html - advect particles by their velocity, but without force
+"fix move"_fix_move.html - prescribe motion of particles by a linear velocity, oscillation, rotation, variable :ul
+
+The "fix move"_fix_move.html command offers the most generality, since
+the motion of individual particles can be specified with
+"variable"_variable.html formula which depends on time and/or the
+particle position.
+
+For rough walls, it may be useful to turn off pairwise interactions
+between wall particles via the "neigh_modify
+exclude"_neigh_modify.html command.
+
+Rough walls can also be created by specifying frozen particles that do
+not move and do not interact with mobile particles, and then tethering
+other particles to the fixed particles, via a "bond"_bond_style.html.
+The bonded particles do interact with other mobile particles.
+
+Idealized walls can be specified via several fix commands. "Fix
+wall/gran"_fix_wall_gran.html creates frictional walls for use with
+granular particles; all the other commands create smooth walls.
+
+"fix wall/reflect"_fix_wall_reflect.html - reflective flat walls
+"fix wall/lj93"_fix_wall.html - flat walls, with Lennard-Jones 9/3 potential
+"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential
+"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential
+"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential
+"fix wall/region"_fix_wall_region.html - use region surface as wall
+"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul
+
+The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the
+flat walls to move with a constant velocity, or oscillate in time.
+The "fix wall/region"_fix_wall_region.html command offers the most
+generality, since the region surface is treated as a wall, and the
+geometry of the region can be a simple primitive volume (e.g. a
+sphere, or cube, or plane), or a complex volume made from the union
+and intersection of primitive volumes. "Regions"_region.html can also
+specify a volume "interior" or "exterior" to the specified primitive
+shape or {union} or {intersection}. "Regions"_region.html can also be
+"dynamic" meaning they move with constant velocity, oscillate, or
+rotate.
+
+The only frictional idealized walls currently in LAMMPS are flat or
+curved surfaces specified by the "fix wall/gran"_fix_wall_gran.html
+command. At some point we plan to allow regoin surfaces to be used as
+frictional walls, as well as triangulated surfaces.
diff --git a/doc/src/Intro.txt b/doc/src/Intro.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3eaa404376015a1bec4d63d34397456b9c425dd
--- /dev/null
+++ b/doc/src/Intro.txt
@@ -0,0 +1,37 @@
+"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Install.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html#comm)
+
+:line
+
+Introduction :h2
+
+These pages provide a brief introduction to LAMMPS.
+
+<!-- RST
+
+.. toctree::
+
+ Intro_overview
+ Intro_features
+ Intro_nonfeatures
+ Intro_opensource
+ Intro_authors
+ Intro_website
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Overview of LAMMPS"_Intro_overview.html
+"LAMMPS features"_Intro_features.html
+"LAMMPS non-features"_Intro_nonfeatures.html
+"LAMMPS open-source license"_Intro_license.html
+"LAMMPS authors"_Intro_authors.html
+"Additional website links"_Intro_website.html :all(b)
+
+<!-- END_HTML_ONLY -->
diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce418d0ce1cfc4463581ceadc5057cb4556ecc65
--- /dev/null
+++ b/doc/src/Intro_authors.txt
@@ -0,0 +1,379 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+LAMMPS authors :h3
+
+The primary LAMMPS developers are at Sandia National Labs and Temple
+University:
+
+"Steve Plimpton"_sjp, sjplimp at sandia.gov
+Aidan Thompson, athomps at sandia.gov
+Stan Moore, stamoor at sandia.gov
+Axel Kohlmeyer, akohlmey at gmail.com :ul
+
+:link(sjp,http://www.cs.sandia.gov/~sjplimp)
+
+Past developers include Paul Crozier and Mark Stevens, both at Sandia,
+and Ray Shan, now at Materials Design.
+
+:line
+
+The following folks are responsible for significant contributions to
+the code, or other aspects of the LAMMPS development effort. Many of
+the packages they have written are somewhat unique to LAMMPS and the
+code would not be as general-purpose as it is without their expertise
+and efforts.
+
+Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM packages
+Roy Pollock (LLNL), Ewald and PPPM solvers
+Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages
+Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
+Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
+Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
+Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
+Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
+Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages
+Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
+Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
+Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
+Georg Gunzenmueller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
+Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
+
+:line
+
+As discussed on the "History
+page"_http://lammps.sandia.gov/history.html of the website, LAMMPS
+originated as a cooperative project between DOE labs and industrial
+partners. Folks involved in the design and testing of the original
+version of LAMMPS were the following:
+
+John Carpenter (Mayo Clinic, formerly at Cray Research)
+Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
+Steve Lustig (Dupont)
+Jim Belak and Roy Pollock (LLNL) :ul
+
+:line
+:line
+
+Here is a timeline for when various individuals contributed to a new
+feature or command or tool added to LAMMPS:
+
+Jul18 : DEM polygonal and polyhedron particles : Trung Nguyen (Northwestern U)
+Jun18 : SPIN package : Julien Tranchida (Sandia and CEA)
+Jun18 : compute entropy/atom : Pablo Piaggi (EPLF, Switzerland)
+May18 : fix bond/react : Jake Gissinger (CU Boulder)
+Apr18 : USER-BOCS package : Nicholas Dunn and Michael DeLyser (Penn State U)
+Mar18: pair coul/shield, kolmogorov/crespi/full, ilp/graphene/hbn : Wengen Ouyang (Tel Aviv U)
+Feb18 : pair lj/cut/coul/wolf : Vishal Boddu (U of Erlangen-Nuremberg)
+Feb18 : USER-MOFFF package : Hendrik Heenen (Technical U of Munich) and Rochus Schmid (Ruhr-University Bochum)
+Feb18 : pair ufm : Rodolfo Paula Leite and Maurice de Koning (Unicamp/Brazil)
+Dec17 : fix python/move : Richard Berger (Temple U)
+Nov17 : pair extep : Jaap Kroes (Radboud U)
+Oct17 : USER-UEF package : David Nicholson (MIT)
+Oct17 : fix rhok : Ulf Pederson (Roskilde U)
+Oct17 : bond gromos : Axel Kohlmeyer (Temple U)
+Oct17 : pair born/coul/wolf/cs and coul/wolf/cs : Vishal Boddu
+Sep17 : fix latte : Christian Negre (LANL)
+Sep17 : temper_npt : Amulya Pervaje and Cody Addington (NCSU)
+Aug17 : USER-MESO package : Zhen Li (Brown University)
+Aug17 : compute aggregate/atom & fragment/atom : Axel Kohlmeyer (Temple U)
+Jul17 : pair meam/c : Sebastian Hutter (Otto-von-Guericke University)
+Jun17 : pair reaxc/omp : Metin Aktulga (MSU) and Axel Kohlmeyer (Temple U)
+Jun17 : pair vashishita/gpu : Anders Hafreager (UiO)
+Jun17 : kspace pppm/disp/intel and pair lj/long/coul/long/intel : Mike Brown (Intel) and William McDoniel (RWTH Aachen U)
+Jun17 : compute cnp/atom : Paulo Branicio (USC)
+May17 : fix python and pair python : Richard Berger (Temple U)
+May17 : pair edip/multi : Chao Jiang (U Wisconsin)
+May17 : pair gw and gw/zbl : German Samolyuk (ORNL)
+Mar17 : pair charmm fsw and fsh : Robert Meissner & Lucio Colombi Ciacchi (Bremen U), Robert Latour (Clemson U)
+Mar17 : pair momb : Ya Zhou, Kristen Fichthorn, and Tonnam Balankura (PSU)
+Mar17 : fix filter/corotate : Lukas Fath (KIT)
+Mar17 : pair kolmogorov/crespi/z : Jaap Kroes (Radboud Universiteit)
+Feb17 : Kokkos versions of the class2 bond/angle/dihedral/improper : Ray Shan (Materials Design)
+Jan17 : USER-CGDNA package : Oliver Henrich (U Edinburgh)
+Jan17 : fix mscg : Lauren Abbott (Sandia)
+Nov16 : temper/grem and fix grem : David Stelter (BU), Edyta Malolepsza (Broad Institute), Tom Keyes (BU)
+Nov16 : pair agni : Axel Kohlmeyer (Temple U) and Venkatesh Botu
+Nov16 : pair tersoff/mod.c : Ganga P Purja Pun (George Mason University)
+Nov16 : pair born/coul/dsf and pair born/coul/dsf/cs : Ariel Lozano
+Nov16 : fix reaxc/species/kk & fix reaxc/bonds/kk : Stan Moore (Sandia)
+Oct16 : fix wall/gran/region : Dan Bolintineanu (Sandia)
+Sep16 : weight options for balance & fix balance : Axel Kohlmeyer (Temple U) & Iain Bethune (EPCC)
+Sep16 : fix cmap : Xiaohu Hu (ORNL), David Hyde-Volpe & Tigran Abramyan & Robert Latour (Clemson U), Chris Lorenz (Kings College, London)
+Sep16 : pair vashishta/table : Anders Hafreager (U Oslo)
+Sep16 : kspace pppm/kk : Stan Moore (Sandia)
+Aug16 : fix flow/gauss : Steve Strong and Joel Eaves (U Colorado)
+Aug16 : fix controller : Aidan Thompson (Sandia)
+Jul16 : dipole integration by DLM method : Iain Bethune (EPCC)
+Jul16 : dihedral spherical : Andrew Jewett
+Jun16 : pair reax/c/kk : Ray Shan (Materials Design), Stan Moore (Sandia)
+Jun16 : fix orient/bcc : Tegar Wicaksono (UBC)
+Jun16 : fix ehex : Peter Wirnsberger (University of Cambridge)
+Jun16 : reactive DPD extensions to USER-DPD : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL), Christopher Stone (Computational Science & Engineering, LLC)
+May16 : USER-MANIFOLD package : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
+Apr16 : write_coeff : Axel Kohlmeyer (Temple U)
+Apr16 : pair morse/soft : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
+Apr16 : compute dipole/chunk : Axel Kohlmeyer (Temple U)
+Apr16 : bond write : Axel Kohlmeyer (Temple U)
+Mar16 : pair morse/smooth/linear : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
+Feb16 : pair/bond/angle/dihedral/improper zero : Carsten Svaneborg (SDU)
+Feb16 : dump custom/vtk : Richard Berger (JKU) and Daniel Queteschiner (DCS Computing)
+Feb16 : fix (nvt/npt/nph)/body and compute temp/body : Trung Nguyen
+Feb16 : USER-DPD package : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL)
+Dec15 : fix qeq/fire : Ray Shan (Sandia)
+Dec15 : pair lj/mdf, pair lennard/mdf, pair buck/mdf, improper distance : Paolo Raiteri (Curtin University)
+Nov15 : compute orientorder/atom : Aidan Thompson (Sandia) and Axel Kohlmeyer (U Temple)
+Nov15 : compute hexorder/atom : Aidan Thompson (Sandia)
+Oct15 : displace_atoms variable option : Reese Jones (Sandia)
+Oct15 : pair mgpt & USER-MGPT package : Tomas Oppelstrup and John Moriarty (LLNL)
+Oct15 : pair smtbq & USER-SMTBQ package : Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS)
+Oct15 : fix ave/correlate/long command : Jorge Ramirez (UPM) and Alexei Likhtman (U Reading)
+Oct15 : pair vashishta command : Aidan Thompson (Sandia) and Yongnan Xiong (HNU)
+Aug15 : USER-TALLY package : Axel Kohlmeyer (Temple U)
+Aug15 : timer command : Axel Kohlmeyer (Temple U)
+Aug15 : USER-H5MD package : Pierre de Buyl (KU Leuven)
+Aug15 : COMPRESS package : Axel Kohlmeyer (Temple U)
+Aug15 : USER-SMD package : Georg Gunzenmueller (EMI)
+Jul15 : new HTML format for "doc pages"_Manual.html with search option : Richard Berger (JKU)
+Jul15 : rRESPA with pair hybrid : Sam Genheden (U of Southampton)
+Jul15 : pair_modify special : Axel Kohlmeyer (Temple U)
+Jul15 : pair polymorphic : Xiaowang Zhou and Reese Jones (Sandia)
+Jul15 : USER-DRUDE package : Alain Dequidt and Agilio Padua (U Blaise Pascal Clermont-Ferrand) and Julien Devemy (CNRS)
+Jul15 : USER-QTB package : Yuan Shen, Tingting Qi, and Evan Reed (Stanford U)
+Jul15 : USER-DIFFRACTION package : Shawn Coleman (ARL)
+Mar15 : fix temp/csld : Axel Kohlmeyer (Temple U)
+Mar15 : CORESHELL package : Hendrik Heenen (Technical University of Munich)
+Feb15 : pair quip for GAP and other potentials : Albert Bartok-Partay (U Cambridge)
+Feb15 : pair coul/streitz for Streitz-Mintmire potential : Ray Shan (Sandia)
+Feb15 : fix tfmc : Kristof Bal (U of Antwerp)
+Feb15 : fix ttm/mod : Sergey Starikov and Vasily Pisarev (JIHT of RAS)
+Jan15 : fix atom/swap for MC swaps of atom types/charge : Paul Crozier (Sandia)
+Nov14 : fix pimd for path-integral MD : Chris Knight and Yuxing Peng (U Chicago)
+Nov14 : fix gle and fix ipi for path-integral MD : Michele Ceriotti (EPFL)
+Nov14 : pair style srp : Tim Sirk (ARL) and Pieter in 't Veld (BASF)
+Nov14 : fix ave/spatial/sphere : Niall Jackson (Imperial College)
+Sep14 : QEQ package and several fix qeq/variant styles : Ray Shan (Sandia)
+Sep14 : SNAP package and pair style : Aidan Thompson (Sandia) and collaborators
+Aug14 : USER-INTEL package : Mike Brown (Intel)
+May14 : KOKKOS pacakge : Christian Trott and Carter Edwards (Sandia)
+May14 : USER-FEP pacakge : Agilio Padua (U Blaise Pascal Clermont-Ferrand)
+Apr14 : fix rigid/small NVE/NVT/NPH/NPT : Trung Nguyen (ORNL)
+Apr14 : fix qmmm for QM/MM coupling : Axel Kohlmeyer (Temple U)
+Mar14 : kspace_modify collective for faster FFTs on BG/Q : Paul Coffman (IBM)
+Mar14 : fix temp/csvr and fix oneway : Axel Kohlmeyer (Temple U)
+Feb14 : pair peri/eps, compute dilatation/atom, compute plasticity/atom : Rezwanur Rahman and John Foster (UTSA)
+Jan14 : MPI-IO options for dump and restart files : Paul Coffman (IBM)
+Nov13 : USER-LB package for Lattice Boltzmann : Francis Mackay and Colin Denniston (U Western Ontario)
+Nov13 : fix ti/rs and ti/spring : Rodrigo Freitas (UC Berkeley)
+Nov13 : pair comb3 : Ray Shan (Sandia), Tao Liang and Dundar Yilmaz (U Florida)
+Nov13 : write_dump and dump movie : Axel Kohlmeyer (Temple U)
+Sep13 : xmgrace tool : Vikas Varshney
+Sep13 : pair zbl : Aidan Thompson and Stephen Foiles (Sandia)
+Aug13 : pair nm and variants : Julien Devemy (ICCF)
+Aug13 : fix wall/lj1043 : Jonathan Lee (Sandia)
+Jul13 : pair peri/ves : Rezwan Rahman, JT Foster (U Texas San Antonio)
+Jul13 : pair tersoff/mod : Vitaly Dozhdikov (JIHT of RAS)
+Jul13 : compute basal/atom : Christopher Barrett,(Mississippi State)
+Jul13 : polybond tool : Zachary Kraus (Georgia Tech)
+Jul13 : fix gld : Stephen Bond and Andrew Baczewski (Sandia)
+Jun13 : pair nb3b/harmonic : Todd Zeitler (Sandia)
+Jun13 : kspace_style pppm/stagger : Stan Moore (Sandia)
+Jun13 : fix tune/kspace : Paul Crozier (Sandia)
+Jun13 : long-range point dipoles : Stan Moore (Sandia) and Pieter in 't Veld (BASF)
+May13 : compute msd/nongauss : Rob Hoy
+May13 : pair list : Axel Kohlmeyer (Temple U)
+May13 : triclinic support for long-range solvers : Stan Moore (Sandia)
+Apr13 : dump_modify nfile and fileper : Christopher Knight
+Mar13 : fix phonon : Ling-Ti Kong (Shanghai Jiao Tong University)
+Mar13 : pair_style lj/cut/tip4p/cut : Pavel Elkind (Gothenburg University)
+Feb13 : immediate variables in input script : Daniel Moller (Autonomous University of Barcelona)
+Feb13 : fix species : Ray Shan (Sandia)
+Jan13 : compute voronoi/atom : Daniel Schwen
+Nov12 : pair_style mie/cut : Cassiano Aimoli Petrobras (U Notre Dame)
+Oct12 : pair_style meam/sw/spline : Robert Rudd (LLNL)
+Oct12 : angle_style fourier and fourier/simple and quartic : Loukas Peristeras (Scienomics)
+Oct12 : dihedral_style fourier and nharmonic and quadratic : Loukas Peristeras (Scienomics)
+Oct12 : improper_style fourier : Loukas Peristeras (Scienomics)
+Oct12 : kspace_style pppm/disp for 1/r^6 : Rolf Isele-Holder (Aachen University)
+Oct12 : moltemplate molecular builder tool : Andrew Jewett (UCSB)
+Sep12 : pair_style lj/cut/coul/dsf and coul/dsf : Trung Nguyen (ORNL)
+Sep12 : multi-level summation long-range solver : Stan Moore, Stephen Bond, and Paul Crozier (Sandia)
+Aug12 : fix rigid/npt and fix rigid/nph : Trung Nguyen (ORNL)
+Aug12 : Fortran wrapper on lib interface : Karl Hammond (UT, Knoxville)
+Aug12 : kspace_modify diff for 2-FFT PPPM : Rolf Isele-Holder (Aachen University), Stan Moore (BYU), Paul Crozier (Sandia)
+Jun12 : pair_style bop : Don Ward and Xiaowang Zhou (Sandia)
+Jun12 : USER-MOLFILE package : Axel Kohlmeyer (U Temple)
+Jun12 : USER-COLVARS package : Axel Kohlmeyer (U Temple)
+May12 : read_dump : Tim Sirk (ARL)
+May12 : improper_style cossq and ring : Georgios Vogiatzis (CoMSE, NTU Athens)
+May12 : pair_style lcbop : Dominik Wojt (Wroclaw University of Technology)
+Feb12 : PPPM per-atom energy/virial : Stan Moore (BYU)
+Feb12 : Ewald per-atom energy/virial : German Samolyuk (ORNL), Stan Moore (BYU)
+Feb12 : minimize forcezero linesearch : Asad Hasan (CMU)
+Feb12 : pair_style beck : Jon Zimmerman (Sandia)
+Feb12 : pair_style meam/spline : Alex Stukowski (LLNL)
+Jan12 : pair_style kim : Valeriu Smirichinski, Ryan Elliott, Ellad Tadmor (U Minn)
+Jan12 : dihedral_style table : Andrew Jewett (UCSB)
+Jan12 : angle_style dipole : Mario Orsi
+Jan12 : pair_style lj/smooth/linear : Jon Zimmerman (Sandia)
+Jan12 : fix reax/c/bond : Tzu-Ray Shan (Sandia)
+Dec11 : pair_style coul/wolf : Yongfeng Zhang (INL)
+Dec11 : run_style verlet/split : Yuxing Peng and Chris Knight (U Chicago)
+Dec11 : pair_style tersoff/table : Luca Ferraro (CASPUR)
+Nov11 : per-atom energy/stress for reax/c : Tzu-Ray Shan (Sandia)
+Oct11 : Fast Lubrication Dynamics (FLD) package: Amit Kumar, Michael Bybee, Jonathan Higdon (UIUC)
+Oct11 : USER-OMP package : Axel Kohlmeyer (Temple U)
+Sep11 : pair_style edip : Luca Ferraro (CASPUR)
+Aug11 : USER-SPH package : Georg Ganzenmuller (FIHSD, EMI, Germany)
+Aug11 : fix restrain : Craig Tenney (Sandia)
+Aug11 : USER-CUDA package : Christian Trott (U Tech Ilmenau)
+Aug11 : pair_style lj/sf : Laurent Joly (U Lyon)
+Aug11 : bond_style harmonic/shift and harmonic/shift/cut : Carsten Svaneborg
+Aug11 : angle_style cosine/shift and cosine/shift/exp : Carsten Svaneborg
+Aug11 : dihedral_style cosine/shift/exp : Carsten Svaneborg
+Aug11 : pair_style dipole/sf : Mario Orsi
+Aug11 : fix addtorque and compute temp/rotate : Laurent Joly (U Lyon)
+Aug11 : FFT support via FFTW3, MKL, ACML, KISSFFT libraries : \
+ Axel Kohlmeyer (Temple U)
+Jun11 : pair_style adp : Chris Weinberger (Sandia), Stephen Foiles (Sandia), \
+ Chandra Veer Singh (Cornell)
+Jun11 : Windows build option via Microsoft Visual Studio : \
+ Ilya Valuev (JIHT, Moscow, Russia)
+Jun11 : antisymmetrized wave packet MD : Ilya Valuev (JIHT, Moscow, Russia)
+Jun11 : dump image : Nathan Fabian (Sandia)
+May11 : pppm GPU single and double : Mike Brown (ORNL)
+May11 : pair_style lj/expand/gpu : Inderaj Bains (NVIDIA)
+2010 : pair_style reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL)
+- : DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (Caltech)
+- : fix adapt and compute ti for thermodynamic integration for \
+ free energies : Sai Jayaraman (Sandia)
+- : pair_style born and gauss : Sai Jayaraman (Sandia)
+- : stochastic rotation dynamics (SRD) via fix srd : \
+ Jeremy Lechman (Sandia) and Pieter in 't Veld (BASF)
+- : ipp Perl script tool : Reese Jones (Sandia)
+- : eam_database and createatoms tools : Xiaowang Zhou (Sandia)
+- : electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
+- : embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
+- : COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
+- : fix ave/correlate : Benoit Leblanc, Dave Rigby, \
+ Paul Saxe (Materials Design) and Reese Jones (Sandia)
+- : pair_style peri/lps : Mike Parks (Sandia)
+- : fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
+- : thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U)
+- : fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
+- : public SVN & Git repositories for LAMMPS : \
+ Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
+- : compute heat/flux : German Samolyuk (ORNL) and \
+ Mario Pinto (Computational Research Lab, Pune, India)
+- : pair_style yukawa/colloid : Randy Schunk (Sandia)
+- : fix wall/colloid : Jeremy Lechman (Sandia)
+2009 : fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ)
+- : concentration-dependent EAM potential : \
+ Alexander Stukowski (Technical University of Darmstadt)
+- : parallel replica dymamics (PRD) : Mike Brown (Sandia)
+- : min_style hftn : Todd Plantenga (Sandia)
+- : fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)
+- : dump cfg : Liang Wan (Chinese Academy of Sciences)
+- : fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland)
+- : pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia)
+- : pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo
+- : fix langevin tally : Carolyn Phillips (U Michigan)
+- : compute heat/flux for Green-Kubo : Reese Jones (Sandia), \
+ Philip Howell (Siemens), Vikas Varsney (AFRL)
+- : region cone : Pim Schravendijk
+- : pair_style born/coul/long : Ahmed Ismail (Sandia)
+- : fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
+- : fix box/relax : Aidan Thompson and David Olmsted (Sandia)
+- : ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
+- : compute cna/atom : Liang Wan (Chinese Academy of Sciences)
+2008 : Tersoff/ZBL potential : Dave Farrell (Northwestern U)
+- : peridynamics : Mike Parks (Sandia)
+- : fix smd for steered MD : Axel Kohlmeyer (U Penn)
+- : GROMACS pair potentials : Mark Stevens (Sandia)
+- : lmp2vmd tool : Axel Kohlmeyer (U Penn)
+- : compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U)
+- : USER-CG-CMM package for coarse-graining : Axel Kohlmeyer (U Penn)
+- : cosine/delta angle potential : Axel Kohlmeyer (U Penn)
+- : VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain
+- : pair_style lubricate : Randy Schunk (Sandia)
+- : compute ackland/atom : Gerolf Ziegenhain
+- : kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \
+ Pieter in 't Veld (Sandia)
+- : AI-REBO bond-order potential : Ase Henry (MIT)
+- : making LAMMPS a true "object" that can be instantiated \
+ multiple times, e.g. as a library : Ben FrantzDale (RPI)
+- : pymol_asphere viz tool : Mike Brown (Sandia)
+2007 : NEMD SLLOD integration : Pieter in 't Veld (Sandia)
+- : tensile and shear deformations : Pieter in 't Veld (Sandia)
+- : GayBerne potential : Mike Brown (Sandia)
+- : ellipsoidal particles : Mike Brown (Sandia)
+- : colloid potentials : Pieter in 't Veld (Sandia)
+- : fix heat : Paul Crozier and Ed Webb (Sandia)
+- : neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
+- : MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
+- : triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
+- : thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
+- : fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
+- : MEAM potential : Greg Wagner (Sandia)
+- : optimized pair potentials for lj/cut, charmm/long, eam, morse : \
+ James Fischer (High Performance Technologies), \
+ David Richie and Vincent Natoli (Stone Ridge Technologies)
+2006 : fix wall/lj126 : Mark Stevens (Sandia)
+- : Stillinger-Weber and Tersoff potentials : \
+ Aidan Thompson and Xiaowang Zhou (Sandia)
+- : region prism : Pieter in 't Veld (Sandia)
+- : fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U)
+- : multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U)
+- : OPLS dihedral potential: Mark Stevens (Sandia)
+- : POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI)
+- : faster pair hybrid potential: James Fischer \
+ (High Performance Technologies, Inc), Vincent Natoli and \
+ David Richie (Stone Ridge Technology)
+- : breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia)
+- : DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U)
+- : grain boundary orientation fix : Koenraad Janssens and \
+ David Olmsted (Sandia)
+- : pair_style lj/smooth potential : Craig Maloney (UCSB)
+- : radius-of-gyration spring fix : Naveen Michaud-Agrawal \
+ (Johns Hopkins U) and Paul Crozier (Sandia)
+- : self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U)
+- : EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea)
+- : cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U)
+- : helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \
+ Mark Stevens (Sandia)
+- : Finnis/Sinclair EAM: Tim Lau (MIT)
+- : dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \
+ Frank van Swol (Sandia)
+- : TIP4P potential (4-site water): Ahmed Ismail and \
+ Amalie Frischknecht (Sandia)
+2005 : uniaxial strain fix: Carsten Svaneborg (Max Planck Institute)
+- : compressed dump files: Erik Luijten (U Illinois)
+- : cylindrical indenter fix: Ravi Agrawal (Northwestern U)
+- : electric field fix: Christina Payne (Vanderbilt U)
+- : AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \
+ Vikas Varshney (U Akron)
+- : CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia)
+- : Morse bond potential: Jeff Greathouse (Sandia)
+- : radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
+- : force tables for long-range Coulombics: Paul Crozier (Sandia)
+2004 : targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
+ Christian Burisch (Bochum University, Germany)
+- : FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech)
+- : lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
+ Andrey Kalinichev (Sandia)
+- : parallel tempering: Mark Sears (Sandia)
+earlier : granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
+- : multi-harmonic dihedral potential: Mathias Putz (Sandia)
+- : embedded atom method (EAM) potential: Stephen Foiles (Sandia)
+- : msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)
+- : HTFN energy minimizer: Todd Plantenga (Sandia)
+- : class 2 force fields: Eric Simon (Cray)
+- : NVT/NPT integrators: Mark Stevens (Sandia)
+- : rRESPA: Mark Stevens & Paul Crozier (Sandia)
+- : Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:,ca1=c)
diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2bb7e25683be9bd90610193a3b265729b1eb9afa
--- /dev/null
+++ b/doc/src/Intro_features.txt
@@ -0,0 +1,202 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+LAMMPS features :h3
+
+LAMMPS is a classical molecular dynamics (MD) code with these general
+classes of functionality:
+
+"General features"_#general
+"Particle and model types"_#particle
+"Interatomic potentials (force fields)"_#ff
+"Atom creation"_#create
+"Ensembles, constraints, and boundary conditions"_#ensemble
+"Integrators"_#integrate
+"Diagnostics"_#diag
+"Output"_#output
+"Multi-replica models"_#replica
+"Pre- and post-processing"_#prepost
+"Specialized features (beyond MD itself)"_#special :ul
+
+:line
+
+General features :h4,link(general)
+
+ runs on a single processor or in parallel
+ distributed-memory message-passing parallelism (MPI)
+ spatial-decomposition of simulation domain for parallelism
+ open-source distribution
+ highly portable C++
+ optional libraries used: MPI and single-processor FFT
+ GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features
+ easy to extend with new features and functionality
+ runs from an input script
+ syntax for defining and using variables and formulas
+ syntax for looping over runs and breaking out of loops
+ run one or multiple simulations simultaneously (in parallel) from one script
+ build as library, invoke LAMMPS thru library interface or provided Python wrapper
+ couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
+
+Particle and model types :h4,link(particle)
+("atom style"_atom_style.html command)
+
+ atoms
+ coarse-grained particles (e.g. bead-spring polymers)
+ united-atom polymers or organic molecules
+ all-atom polymers, organic molecules, proteins, DNA
+ metals
+ granular materials
+ coarse-grained mesoscale models
+ finite-size spherical and ellipsoidal particles
+ finite-size line segment (2d) and triangle (3d) particles
+ point dipole particles
+ rigid collections of particles
+ hybrid combinations of these :ul
+
+Interatomic potentials (force fields) :h4,link(ff)
+("pair style"_pair_style.html, "bond style"_bond_style.html,
+"angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
+"improper style"_improper_style.html, "kspace style"_kspace_style.html
+commands)
+
+ pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
+ Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
+ charged pairwise potentials: Coulombic, point-dipole
+ manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
+ embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
+ REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
+ long-range interactions for charge, point-dipoles, and LJ dispersion: \
+ Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
+ polarization models: "QEq"_fix_qeq.html, \
+ "core/shell model"_Howto_coreshell.html, \
+ "Drude dipole model"_Howto_drude.html
+ charge equilibration (QEq via dynamic, point, shielded, Slater methods)
+ coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
+ mesoscopic potentials: granular, Peridynamics, SPH
+ electron force field (eFF, AWPMD)
+ bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
+ quartic (breakable)
+ angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \
+ class 2 (COMPASS)
+ dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
+ class 2 (COMPASS), OPLS
+ improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
+ polymer potentials: all-atom, united-atom, bead-spring, breakable
+ water potentials: TIP3P, TIP4P, SPC
+ implicit solvent potentials: hydrodynamic lubrication, Debye
+ force-field compatibility with common CHARMM, AMBER, DREIDING, \
+ OPLS, GROMACS, COMPASS options
+ access to "KIM archive"_http://openkim.org of potentials via \
+ "pair kim"_pair_kim.html
+ hybrid potentials: multiple pair, bond, angle, dihedral, improper \
+ potentials can be used in one simulation
+ overlaid potentials: superposition of multiple pair potentials :ul
+
+Atom creation :h4,link(create)
+("read_data"_read_data.html, "lattice"_lattice.html,
+"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
+"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
+
+ read in atom coords from files
+ create atoms on one or more lattices (e.g. grain boundaries)
+ delete geometric or logical groups of atoms (e.g. voids)
+ replicate existing atoms multiple times
+ displace atoms :ul
+
+Ensembles, constraints, and boundary conditions :h4,link(ensemble)
+("fix"_fix.html command)
+
+ 2d or 3d systems
+ orthogonal or non-orthogonal (triclinic symmetry) simulation domains
+ constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
+ thermostatting options for groups and geometric regions of atoms
+ pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
+ simulation box deformation (tensile and shear)
+ harmonic (umbrella) constraint forces
+ rigid body constraints
+ SHAKE bond and angle constraints
+ Monte Carlo bond breaking, formation, swapping
+ atom/molecule insertion and deletion
+ walls of various kinds
+ non-equilibrium molecular dynamics (NEMD)
+ variety of additional boundary conditions and constraints :ul
+
+Integrators :h4,link(integrate)
+("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
+
+ velocity-Verlet integrator
+ Brownian dynamics
+ rigid body integration
+ energy minimization via conjugate gradient or steepest descent relaxation
+ rRESPA hierarchical timestepping
+ rerun command for post-processing of dump files :ul
+
+Diagnostics :h4,link(diag)
+
+ see various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
+
+Output :h4,link(output)
+("dump"_dump.html, "restart"_restart.html commands)
+
+ log file of thermodynamic info
+ text dump files of atom coords, velocities, other per-atom quantities
+ binary restart files
+ parallel I/O of dump and restart files
+ per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
+ user-defined system-wide (log file) or per-atom (dump file) calculations
+ spatial and time averaging of per-atom quantities
+ time averaging of system-wide quantities
+ atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
+
+Multi-replica models :h4,link(replica)
+
+"nudged elastic band"_neb.html
+"parallel replica dynamics"_prd.html
+"temperature accelerated dynamics"_tad.html
+"parallel tempering"_temper.html :ul
+
+Pre- and post-processing :h4,link(prepost)
+
+A handful of pre- and post-processing tools are packaged with LAMMPS,
+some of which can convert input and output files to/from formats used
+by other codes; see the "Toos"_Tools.html doc page. :ulb,l
+
+Our group has also written and released a separate toolkit called
+"Pizza.py"_pizza which provides tools for doing setup, analysis,
+plotting, and visualization for LAMMPS simulations. Pizza.py is
+written in "Python"_python and is available for download from "the
+Pizza.py WWW site"_pizza. :l,ule
+
+:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
+:link(python,http://www.python.org)
+
+Specialized features :h4,link(special)
+
+LAMMPS can be built with optional packages which implement a variety
+of additional capabilities. See the "Packages"_Packages.html doc
+page for details.
+
+These are LAMMPS capabilities which you may not think of as typical
+classical MD options:
+
+"static"_balance.html and "dynamic load-balancing"_fix_balance.html
+"generalized aspherical particles"_Howto_body.html
+"stochastic rotation dynamics (SRD)"_fix_srd.html
+"real-time visualization and interactive MD"_fix_imd.html
+calculate "virtual diffraction patterns"_compute_xrd.html
+"atom-to-continuum coupling"_fix_atc.html with finite elements
+coupled rigid body integration via the "POEMS"_fix_poems.html library
+"QM/MM coupling"_fix_qmmm.html
+Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_atom_swap.html
+"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
+"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
+"Peridynamics mesoscale modeling"_pair_peri.html
+"Lattice Boltzmann fluid"_fix_lb_fluid.html
+"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
+"two-temperature electron model"_fix_ttm.html :ul
diff --git a/doc/src/Intro_nonfeatures.txt b/doc/src/Intro_nonfeatures.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41f001fc8b675de6c1e3624b1695dd3bfc5ca96c
--- /dev/null
+++ b/doc/src/Intro_nonfeatures.txt
@@ -0,0 +1,83 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+LAMMPS non-features :h3
+
+LAMMPS is designed to be a fast, parallel engine for molecular
+dynamics (MD) simulations. It provides only a modest amount of
+functionality for setting up simulations and analyzing their output.
+
+Specifically, LAMMPS does not:
+
+run thru a GUI
+build molecular systems
+assign force-field coefficients automagically
+perform sophisticated analyses of your MD simulation
+visualize your MD simulation interactively
+plot your output data :ul
+
+Here are suggestions on how to perform these tasks:
+
+GUI: LAMMPS can be built as a library and a Python wrapper that wraps
+the library interface is provided. Thus, GUI interfaces can be
+written in Python (or C or C++ if desired) that run LAMMPS and
+visualize or plot its output. Examples of this are provided in the
+python directory and described on the "Python"_Python.html doc
+page. :ulb,l
+
+Builder: Several pre-processing tools are packaged with LAMMPS. Some
+of them convert input files in formats produced by other MD codes such
+as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them
+are simple programs that will build simple molecular systems, such as
+linear bead-spring polymer chains. The moltemplate program is a true
+molecular builder that will generate complex molecular models. See
+the "Tools"_Tools.html doc page for details on tools packaged with
+LAMMPS. The "Pre/post processing
+page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
+describes a variety of 3rd party tools for this task. :l
+
+Force-field assignment: The conversion tools described in the previous
+bullet for CHARMM, AMBER, and Insight will also assign force field
+coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
+or Accelerys force field files. :l
+
+Simulation analyses: If you want to perform analyses on-the-fly as
+your simulation runs, see the "compute"_compute.html and
+"fix"_fix.html doc pages, which list commands that can be used in a
+LAMMPS input script. Also see the "Modify"_Modify.html doc page for
+info on how to add your own analysis code or algorithms to LAMMPS.
+For post-processing, LAMMPS output such as "dump file
+snapshots"_dump.html can be converted into formats used by other MD or
+post-processing codes. Some post-processing tools packaged with
+LAMMPS will do these conversions. Scripts provided with the {python}
+tool in the tools directory can extract and massage data in dump files
+to make it easier to import into other programs. See the
+"Tools"_Tools.html doc page for details on these various options. :l
+
+Visualization: LAMMPS can produce JPG or PNG snapshot images
+on-the-fly via its "dump image"_dump_image.html command. For
+high-quality, interactive visualization there are many excellent and
+free tools available. See the "Other Codes
+page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
+visualization packages that can use LAMMPS output data. :l
+
+Plotting: See the next bullet about Pizza.py as well as the
+"Python"_Python.html doc page for examples of plotting LAMMPS output.
+Scripts provided with the {python} tool in the tools directory will
+extract and massage data in log and dump files to make it easier to
+analyze and plot. See the "Tools"_Tools.html doc page for more
+discussion of the various tools. :l
+
+Pizza.py: Our group has also written a separate toolkit called
+"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
+setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
+simulations. It thus provides some functionality for several of the
+above bullets. Pizza.py is written in "Python"_http://www.python.org
+and is available for download from "this
+page"_http://www.cs.sandia.gov/~sjplimp/download.html. :l,ule
diff --git a/doc/src/Intro_opensource.txt b/doc/src/Intro_opensource.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0d57f7ce199b35ffa8abab06e9e0217b3a54304
--- /dev/null
+++ b/doc/src/Intro_opensource.txt
@@ -0,0 +1,44 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+LAMMPS open-source license :h3
+
+LAMMPS is a freely-available open-source code, distributed under the
+terms of the "GNU Public License"_gnu, which means you can use or
+modify the code however you wish.
+
+LAMMPS comes with no warranty of any kind. As each source file states
+in its header, it is a copyrighted code that is distributed free-of-
+charge, under the terms of the "GNU Public License"_gnu (GPL). This
+is often referred to as open-source distribution - see
+"www.gnu.org"_gnuorg or "www.opensource.org"_opensource. The legal
+text of the GPL is in the LICENSE file included in the LAMMPS
+distribution.
+
+:link(gnu,http://www.gnu.org/copyleft/gpl.html)
+:link(gnuorg,http://www.gnu.org)
+:link(opensource,http://www.opensource.org)
+
+Here is a summary of what the GPL means for LAMMPS users:
+
+(1) Anyone is free to use, modify, or extend LAMMPS in any way they
+choose, including for commercial purposes.
+
+(2) If you distribute a modified version of LAMMPS, it must remain
+open-source, meaning you distribute it under the terms of the GPL.
+You should clearly annotate such a code as a derivative version of
+LAMMPS.
+
+(3) If you release any code that includes LAMMPS source code, then it
+must also be open-sourced, meaning you distribute it under the terms
+of the GPL.
+
+(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
+source file headers (including the copyright and GPL notices) should
+remain part of the code.
diff --git a/doc/src/Intro_overview.txt b/doc/src/Intro_overview.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49c14bc5f06d463037d294d28873b43fdf6c7f14
--- /dev/null
+++ b/doc/src/Intro_overview.txt
@@ -0,0 +1,58 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Overview of LAMMPS :h3
+
+LAMMPS is a classical molecular dynamics (MD) code that models
+ensembles of particles in a liquid, solid, or gaseous state. It can
+model atomic, polymeric, biological, solid-state (metals, ceramics,
+oxides), granular, coarse-grained, or macroscopic systems using a
+variety of interatomic potentials (force fields) and boundary
+conditions. It can model 2d or 3d systems with only a few particles
+up to millions or billions.
+
+LAMMPS can be built and run on a laptop or destop machine, but is
+designed for parallel computers. It will run on any parallel machine
+that supports the "MPI"_mpi message-passing library. This includes
+shared-memory boxes and distributed-memory clusters and
+supercomputers.
+
+:link(mpi,http://www-unix.mcs.anl.gov/mpi)
+
+LAMMPS is written in C++. Earlier versions were written in F77 and
+F90. See the "History page"_http://lammps.sandia.gov/history.html of
+the website for details. All versions can be downloaded from the
+"LAMMPS website"_lws.
+
+LAMMPS is designed to be easy to modify or extend with new
+capabilities, such as new force fields, atom types, boundary
+conditions, or diagnostics. See the "Modify"_Modify.html doc page for
+more details.
+
+In the most general sense, LAMMPS integrates Newton's equations of
+motion for a collection of interacting particles. A single particle
+can be an atom or molecule or electron, a coarse-grained cluster of
+atoms, or a mesoscopic or macroscopic clump of material. The
+interaction models that LAMMPS includes are mostly short-range in
+nature; some long-range models are included as well.
+
+LAMMPS uses neighbor lists to keep track of nearby particles. The
+lists are optimized for systems with particles that are repulsive at
+short distances, so that the local density of particles never becomes
+too large. This is in contrast to methods used for modeling plasmas
+or gravitational bodies (e.g. galaxy formation).
+
+On parallel machines, LAMMPS uses spatial-decomposition techniques to
+partition the simulation domain into small sub-domains of equal
+computational cost, one of which is assigned to each processor.
+Processors communicate and store "ghost" atom information for atoms
+that border their sub-domain.
+
+
+
diff --git a/doc/src/Intro_website.txt b/doc/src/Intro_website.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8af94157ceb9545be2c6ddd22bcb928115b63d8
--- /dev/null
+++ b/doc/src/Intro_website.txt
@@ -0,0 +1,42 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Additional website links :h3
+
+The "LAMMPS website"_lws has a variety of additional info about
+LAMMPS, beyond what is in this manual. Some of the other pages in
+this Intr are included in this list.
+
+"Brief intro and recently added significant features"_lws
+"List of features"_http://lammps.sandia.gov/features.html
+"List of non-features"_http://lammps.sandia.gov/non_features.html
+"Recent bug fixes and new features"_http://lammps.sandia.gov/bug.html :ul
+
+"Download info"_http://lammps.sandia.gov/download.html
+"GitHub site"_https://github.com/lammps/lammps
+"SourceForge site"_https://sourceforge.net/projects/lammps
+"LAMMPS open-source license"_http://lammps.sandia.gov/open_source.html :ul
+
+"Glossary of MD terms relevant to LAMMPS"_http://lammps.sandia.gov/glossary.html
+"LAMMPS highlights with images"_http://lammps.sandia.gov/pictures.html
+"LAMMPS highlights with movies"_http://lammps.sandia.gov/movies.html
+"Mail list"_http://lammps.sandia.gov/mail.html
+"Workshops"_http://lammps.sandia.gov/workshops.html
+"Tutorials"_http://lammps.sandia.gov/tutorials.html
+"Developer guide"_http://lammps.sandia.gov/Developer.pdf :ul
+
+"Pre- and post-processing tools for LAMMPS"_http://lammps.sandia.gov/prepost.html
+"Other software usable with LAMMPS"_http://lammps.sandia.gov/offsite.html
+"Viz tools usable with LAMMPS"_http://lammps.sandia.gov/viz.html :ul
+
+"Benchmark performance"_http://lammps.sandia.gov/bench.html
+"Publications that have cited LAMMPS"_http://lammps.sandia.gov/papers.html
+"Authors of LAMMPS"_http://lammps.sandia.gov/authors.html
+"History of LAMMPS development"_http://lammps.sandia.gov/history.html
+"Funding for LAMMPS"_http://lammps.sandia.gov/funding.html :ul
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 4481c911a009feee3e7babc29ab47cad43a03df7..a5e8b63640be29f7212d66e1d6b42ceb66747a41 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
-<
+<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="16 Jul 2018 version">
+<META NAME="docnumber" CONTENT="2 Aug 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -14,90 +14,53 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html#comm)
:line
-LAMMPS Documentation :c,h1
-16 Jul 2018 version :c,h2
-
-Version info: :h3
-
-The LAMMPS "version" is the date when it was released, such as 1 May
-2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
-feature, we release it immediately, and post a notice on "this page of
-the WWW site"_bug. Every 2-4 months one of the incremental releases
-is subjected to more thorough testing and labeled as a {stable} version.
-
-Each dated copy of LAMMPS contains all the
-features and bug-fixes up to and including that version date. The
-version date is printed to the screen and logfile every time you run
-LAMMPS. It is also in the file src/version.h and in the LAMMPS
-directory name created when you unpack a tarball, and at the top of
-the first page of the manual (this page).
-
-If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current [development] version of LAMMPS. :ulb,l
+<H1></H1>
-If you browse the HTML doc pages included in your tarball, they
-describe the version you have. :l
-
-The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
-about once per month. This is because it is large, and we don't want
-it to be part of every patch. :l
+LAMMPS Documentation :c,h1
+2 Aug 2018 version :c,h2
-There is also a "Developer.pdf"_Developer.pdf file in the doc
-directory, which describes the internal structure and algorithms of
-LAMMPS. :l
-:ule
+"What is a LAMMPS version?"_Manual_version.html
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
-LAMMPS is a classical molecular dynamics simulation code designed to
-run efficiently on parallel computers. It was developed at Sandia
-National Laboratories, a US Department of Energy facility, with
-funding from the DOE. It is an open-source code, distributed freely
-under the terms of the GNU Public License (GPL).
+LAMMPS is a classical molecular dynamics simulation code with a focus
+on materials modeling. It was designed to run efficiently on parallel
+computers. It was developed originally at Sandia National
+Laboratories, a US Department of Energy facility. The majority of
+funding for LAMMPS has come from the US Department of Energy (DOE).
+LAMMPS is an open-source code, distributed freely under the terms of
+the GNU Public License (GPL).
-The current core group of LAMMPS developers is at Sandia National
-Labs and Temple University:
+The "LAMMPS website"_lws has a variety of information about the code.
+It includes links to an on-line version of this manual, a "mail
+list"_http://lammps.sandia.gov/mail.html where users can post
+questions, and a "GitHub site"https://github.com/lammps/lammps where
+all LAMMPS development is coordinated.
-"Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l
-Aidan Thompson, athomps at sandia.gov :l
-Stan Moore, stamoor at sandia.gov :l
-"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l
-:ule
+:line
-Past core developers include Paul Crozier, Ray Shan and Mark Stevens,
-all at Sandia. The [LAMMPS home page] at
-"http://lammps.sandia.gov"_http://lammps.sandia.gov has more information
-about the code and its uses. Interaction with external LAMMPS developers,
-bug reports and feature requests are mainly coordinated through the
-"LAMMPS project on GitHub."_https://github.com/lammps/lammps
-The lammps.org domain, currently hosting "public continuous integration
-testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux
-RPM and Windows installer packages"_http://packages.lammps.org is located
-at Temple University and managed by Richard Berger,
-richard.berger at temple.edu.
+"PDF file"_Manual.pdf of the entire manual, generated by
+"htmldoc"_http://freecode.com/projects/htmldoc
-:link(bug,http://lammps.sandia.gov/bug.html)
-:link(sjp,http://www.sandia.gov/~sjplimp)
-:link(ako,http://goo.gl/1wk0)
+The content for this manual is part of the LAMMPS distribution.
+You can build a local copy of the Manual as HTML pages or a PDF file,
+by following the steps on the "this page"_Build_manual.html.
+
+There is also a "Developer.pdf"_Developer.pdf document which gives
+a brief description of the basic code structure of LAMMPS.
:line
-The LAMMPS documentation is organized into the following sections. If
-you find errors or omissions in this manual or have suggestions for
-useful information to add, please send an email to the developers so
-we can improve the LAMMPS documentation.
+This manual is organized into the following sections.
Once you are familiar with LAMMPS, you may want to bookmark "this
-page"_Section_commands.html#comm at Section_commands.html#comm since
-it gives quick access to documentation for all LAMMPS commands.
-
-"PDF file"_Manual.pdf of the entire manual, generated by
-"htmldoc"_http://freecode.com/projects/htmldoc
+page"_Commands.html since it gives quick access to a doc page for
+every LAMMPS command.
<!-- RST
@@ -108,26 +71,23 @@ it gives quick access to documentation for all LAMMPS commands.
:name: userdoc
:includehidden:
- Section_intro
+ Intro
Section_start
- Section_commands
- Section_packages
- Section_accelerate
- Section_howto
+ Commands
+ Packages
+ Speed
+ Howto
Examples
- Section_perf
Tools
Modify
Python
Errors
- Section_history
.. toctree::
:caption: Index
:name: index
:hidden:
- tutorials
commands
fixes
computes
@@ -146,12 +106,7 @@ Indices and tables
END_RST -->
<!-- HTML_ONLY -->
-"Introduction"_Section_intro.html :olb,l
- 1.1 "What is LAMMPS"_intro_1 :ulb,b
- 1.2 "LAMMPS features"_intro_2 :b
- 1.3 "LAMMPS non-features"_intro_3 :b
- 1.4 "Open source distribution"_intro_4 :b
- 1.5 "Acknowledgments and citations"_intro_5 :ule,b
+"Introduction"_Intro.html :olb,l
"Getting started"_Section_start.html :l
2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
2.2 "Making LAMMPS"_start_2 :b
@@ -161,70 +116,17 @@ END_RST -->
2.6 "Command-line options"_start_6 :b
2.7 "Screen output"_start_7 :b
2.8 "Tips for users of previous versions"_start_8 :ule,b
-"Commands"_Section_commands.html :l
- 3.1 "LAMMPS input script"_cmd_1 :ulb,b
- 3.2 "Parsing rules"_cmd_2 :b
- 3.3 "Input script structure"_cmd_3 :b
- 3.4 "Commands listed by category"_cmd_4 :b
- 3.5 "Commands listed alphabetically"_cmd_5 :ule,b
-"Packages"_Section_packages.html :l
- 4.1 "Standard packages"_pkg_1 :ulb,b
- 4.2 "User packages"_pkg_2 :ule,b
-"Accelerating LAMMPS performance"_Section_accelerate.html :l
- 5.1 "Measuring performance"_acc_1 :ulb,b
- 5.2 "Algorithms and code options to boost performace"_acc_2 :b
- 5.3 "Accelerator packages with optimized styles"_acc_3 :b
- 5.3.1 "GPU package"_accelerate_gpu.html :b
- 5.3.2 "USER-INTEL package"_accelerate_intel.html :b
- 5.3.3 "KOKKOS package"_accelerate_kokkos.html :b
- 5.3.4 "USER-OMP package"_accelerate_omp.html :b
- 5.3.5 "OPT package"_accelerate_opt.html :b
- 5.4 "Comparison of various accelerator packages"_acc_4 :ule,b
-"How-to discussions"_Section_howto.html :l
- 6.1 "Restarting a simulation"_howto_1 :ulb,b
- 6.2 "2d simulations"_howto_2 :b
- 6.3 "CHARMM and AMBER force fields"_howto_3 :b
- 6.4 "Running multiple simulations from one input script"_howto_4 :b
- 6.5 "Multi-replica simulations"_howto_5 :b
- 6.6 "Granular models"_howto_6 :b
- 6.7 "TIP3P water model"_howto_7 :b
- 6.8 "TIP4P water model"_howto_8 :b
- 6.9 "SPC water model"_howto_9 :b
- 6.10 "Coupling LAMMPS to other codes"_howto_10 :b
- 6.11 "Visualizing LAMMPS snapshots"_howto_11 :b
- 6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b
- 6.13 "NEMD simulations"_howto_13 :b
- 6.14 "Finite-size spherical and aspherical particles"_howto_14 :b
- 6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b
- 6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b
- 6.17 "Walls"_howto_17 :b
- 6.18 "Elastic constants"_howto_18 :b
- 6.19 "Library interface to LAMMPS"_howto_19 :b
- 6.20 "Calculating thermal conductivity"_howto_20 :b
- 6.21 "Calculating viscosity"_howto_21 :b
- 6.22 "Calculating a diffusion coefficient"_howto_22 :b
- 6.23 "Using chunks to calculate system properties"_howto_23 :b
- 6.24 "Setting parameters for pppm/disp"_howto_24 :b
- 6.25 "Polarizable models"_howto_25 :b
- 6.26 "Adiabatic core/shell model"_howto_26 :b
- 6.27 "Drude induced dipoles"_howto_27 :ule,b
+"Commands"_Commands.html :l
+"Optional packages"_Packages.html :l
+"Accelerate performance"_Speed.html :l
+"How-to discussions"_Howto.html :l
"Example scripts"_Examples.html :l
-"Performance & scalability"_Section_perf.html :l
"Auxiliary tools"_Tools.html :l
"Modify & extend LAMMPS"_Modify.html :l
"Use Python with LAMMPS"_Python.html :l
"Errors"_Errors.html :l
-"Future and history"_Section_history.html :l
- 13.1 "Coming attractions"_hist_1 :ulb,b
- 13.2 "Past versions"_hist_2 :ule,b
:ole
-:link(intro_1,Section_intro.html#intro_1)
-:link(intro_2,Section_intro.html#intro_2)
-:link(intro_3,Section_intro.html#intro_3)
-:link(intro_4,Section_intro.html#intro_4)
-:link(intro_5,Section_intro.html#intro_5)
-
:link(start_1,Section_start.html#start_1)
:link(start_2,Section_start.html#start_2)
:link(start_3,Section_start.html#start_3)
@@ -234,50 +136,6 @@ END_RST -->
:link(start_7,Section_start.html#start_7)
:link(start_8,Section_start.html#start_8)
-:link(cmd_1,Section_commands.html#cmd_1)
-:link(cmd_2,Section_commands.html#cmd_2)
-:link(cmd_3,Section_commands.html#cmd_3)
-:link(cmd_4,Section_commands.html#cmd_4)
-:link(cmd_5,Section_commands.html#cmd_5)
-
-:link(pkg_1,Section_packages.html#pkg_1)
-:link(pkg_2,Section_packages.html#pkg_2)
-
-:link(acc_1,Section_accelerate.html#acc_1)
-:link(acc_2,Section_accelerate.html#acc_2)
-:link(acc_3,Section_accelerate.html#acc_3)
-:link(acc_4,Section_accelerate.html#acc_4)
-
-:link(howto_1,Section_howto.html#howto_1)
-:link(howto_2,Section_howto.html#howto_2)
-:link(howto_3,Section_howto.html#howto_3)
-:link(howto_4,Section_howto.html#howto_4)
-:link(howto_5,Section_howto.html#howto_5)
-:link(howto_6,Section_howto.html#howto_6)
-:link(howto_7,Section_howto.html#howto_7)
-:link(howto_8,Section_howto.html#howto_8)
-:link(howto_9,Section_howto.html#howto_9)
-:link(howto_10,Section_howto.html#howto_10)
-:link(howto_11,Section_howto.html#howto_11)
-:link(howto_12,Section_howto.html#howto_12)
-:link(howto_13,Section_howto.html#howto_13)
-:link(howto_14,Section_howto.html#howto_14)
-:link(howto_15,Section_howto.html#howto_15)
-:link(howto_16,Section_howto.html#howto_16)
-:link(howto_17,Section_howto.html#howto_17)
-:link(howto_18,Section_howto.html#howto_18)
-:link(howto_19,Section_howto.html#howto_19)
-:link(howto_20,Section_howto.html#howto_20)
-:link(howto_21,Section_howto.html#howto_21)
-:link(howto_22,Section_howto.html#howto_22)
-:link(howto_23,Section_howto.html#howto_23)
-:link(howto_24,Section_howto.html#howto_24)
-:link(howto_25,Section_howto.html#howto_25)
-:link(howto_26,Section_howto.html#howto_26)
-:link(howto_27,Section_howto.html#howto_27)
-
-:link(hist_1,Section_history.html#hist_1)
-:link(hist_2,Section_history.html#hist_2)
<!-- END_HTML_ONLY -->
</BODY>
diff --git a/doc/src/Manual_version.txt b/doc/src/Manual_version.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8583eabf865afc3b9b9aeaae76d3acb34028fc85
--- /dev/null
+++ b/doc/src/Manual_version.txt
@@ -0,0 +1,33 @@
+"Higher level section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+What does a LAMMPS version mean: :h3
+
+The LAMMPS "version" is the date when it was released, such as 1 May
+2014. LAMMPS is updated continuously. Whenever we fix a bug or add a
+feature, we release it in the next {patch} release, which are
+typically made every couple of weeks. Info on patch releases are on
+"this website page"_http://lammps.sandia.gov/bug.html. Every few
+months, the latest patch release is subjected to more thorough testing
+and labeled as a {stable} version.
+
+Each version of LAMMPS contains all the features and bug-fixes up to
+and including its version date.
+
+The version date is printed to the screen and logfile every time you
+run LAMMPS. It is also in the file src/version.h and in the LAMMPS
+directory name created when you unpack a tarball. And it is on the
+first page of the "manual"_Manual.html.
+
+If you browse the HTML doc pages on the LAMMPS WWW site, they always
+describe the most current patch release of LAMMPS. :ulb,l
+
+If you browse the HTML doc pages included in your tarball, they
+describe the version you have, which may be older. :l,ule
+
diff --git a/doc/src/Modify.txt b/doc/src/Modify.txt
index ae0b0dc6bdf2371f9a205c39fbc267b91ecd11b3..f828bd5d74db99ceb5c0dfffd93062d93228ef4c 100644
--- a/doc/src/Modify.txt
+++ b/doc/src/Modify.txt
@@ -4,7 +4,7 @@ Section"_Python.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_atom.txt b/doc/src/Modify_atom.txt
index afa1c319d25539594bb65f9dcb1f146023623ff8..60c7dccb29a38e4c628752f87c58a84532eb7c24 100644
--- a/doc/src/Modify_atom.txt
+++ b/doc/src/Modify_atom.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_body.txt b/doc/src/Modify_body.txt
index b1dc8130cd6ad46318fe7a9c336b7e8978cbdbe5..0114ae10c885c2cbd78cd1d2067ad2751ac997fd 100644
--- a/doc/src/Modify_body.txt
+++ b/doc/src/Modify_body.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -14,10 +14,9 @@ Body particles can represent complex entities, such as surface meshes
of discrete points, collections of sub-particles, deformable objects,
etc.
-See "Section 6.14"_Section_howto.html#howto_14 of the manual for
-an overview of using body particles and the "body"_body.html doc page
-for details on the various body styles LAMMPS supports. New styles
-can be created to add new kinds of body particles to LAMMPS.
+See the "Howto body"_Howto_body.html doc page for an overview of using
+body particles and the various body styles LAMMPS supports. New
+styles can be created to add new kinds of body particles to LAMMPS.
Body_nparticle.cpp is an example of a body particle that is treated as
a rigid body containing N sub-particles.
diff --git a/doc/src/Modify_bond.txt b/doc/src/Modify_bond.txt
index f0828a0c3b8544c84fa8539c7eb9f30e63489cfb..7ceea3f910121c4191b27cd0aaa8256e421281e3 100644
--- a/doc/src/Modify_bond.txt
+++ b/doc/src/Modify_bond.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_command.txt b/doc/src/Modify_command.txt
index 6fc9aad1fc55174fa3be29eda559966b34db2259..4576f6c8067684ca95b94b7ae022ec0df6166f76 100644
--- a/doc/src/Modify_command.txt
+++ b/doc/src/Modify_command.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_compute.txt b/doc/src/Modify_compute.txt
index b02b8a983ec4c32f0935c7b00b1c3c3dd59e7f5d..2f6481dbd5be934fd8dcfa7f1abed50bd57cc3c3 100644
--- a/doc/src/Modify_compute.txt
+++ b/doc/src/Modify_compute.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt
index 80795b5e205332fdfac501c74bee8153706ad33e..ef9fe6a7174eed7d41a74908b49b21e8ecfa6f6d 100644
--- a/doc/src/Modify_contribute.txt
+++ b/doc/src/Modify_contribute.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,14 +32,14 @@ How quickly your contribution will be integrated depends largely on
how much effort it will cause to integrate and test it, how much it
requires changes to the core codebase, and of how much interest it is
to the larger LAMMPS community. Please see below for a checklist of
-typical requirements. Once you have prepared everything, see "this
-tutorial"_tutorial_github.html for instructions on how to submit your
-changes or new files through a GitHub pull request. If you prefer to
-submit patches or full files, you should first make certain, that your
-code works correctly with the latest patch-level version of LAMMPS and
-contains all bugfixes from it. Then create a gzipped tar file of all
-changed or added files or a corresponding patch file using 'diff -u'
-or 'diff -c' and compress it with gzip. Please only use gzip
+typical requirements. Once you have prepared everything, see the
+"Howto github"_Howto_github.html doc page for instructions on how to
+submit your changes or new files through a GitHub pull request. If you
+prefer to submit patches or full files, you should first make certain,
+that your code works correctly with the latest patch-level version of
+LAMMPS and contains all bugfixes from it. Then create a gzipped tar
+file of all changed or added files or a corresponding patch file using
+'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip
compression, as this works well on all platforms.
If the new features/files are broadly useful we may add them as core
@@ -54,8 +54,9 @@ packages by typing "make package" in the LAMMPS src directory.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
-used as a license for the rest of LAMMPS. See "Section
-1.4"_Section_intro.html#intro_4 for details.
+used as a license for the rest of LAMMPS. See the "Open
+source"_http://lammps.sandia.gov/open_source.html page on the LAMMPS
+website for details.
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
diff --git a/doc/src/Modify_dump.txt b/doc/src/Modify_dump.txt
index 81af54e0039a3ad9f95f34f7f0498457914a6f6d..cfe96f5d3d0bc25402b73beef55261f8e7679eb1 100644
--- a/doc/src/Modify_dump.txt
+++ b/doc/src/Modify_dump.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_fix.txt b/doc/src/Modify_fix.txt
index ba985475cc9e72721b7dd50bf3bc9268f97f60c0..b095ebc4b5fa8b549fbfb411c2558e5c6bb14c4d 100644
--- a/doc/src/Modify_fix.txt
+++ b/doc/src/Modify_fix.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_kspace.txt b/doc/src/Modify_kspace.txt
index 21407bf2e9af32f5aa836889ca40824845eb5b98..d5f018411d8d280d679b7a7940403b1658a20726 100644
--- a/doc/src/Modify_kspace.txt
+++ b/doc/src/Modify_kspace.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_min.txt b/doc/src/Modify_min.txt
index 5dcf0f1e6751899be88458220e188dde5e6f716a..8252a576f3b01b7d58461a5bf200c0ddc1405c19 100644
--- a/doc/src/Modify_min.txt
+++ b/doc/src/Modify_min.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_overview.txt b/doc/src/Modify_overview.txt
index f9964d964b14d0ae81d219aab6891278e37a3f36..cf94b40281417805515700d697dc84cbd476fc38 100644
--- a/doc/src/Modify_overview.txt
+++ b/doc/src/Modify_overview.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_pair.txt b/doc/src/Modify_pair.txt
index 8c234dc62135f635bccc3e96ce93179cb901c569..0ebf2daa30baab30e377cb5df9cae40d5e0f5a36 100644
--- a/doc/src/Modify_pair.txt
+++ b/doc/src/Modify_pair.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_region.txt b/doc/src/Modify_region.txt
index 9fbf359292b3e2edd95a3e1b6bd616c4336831a2..cdf192323ac50a8f5d771a4ea80822ec2bc6d3bf 100644
--- a/doc/src/Modify_region.txt
+++ b/doc/src/Modify_region.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_thermo.txt b/doc/src/Modify_thermo.txt
index 001a9f99e108e2fb26285ee8a672f0a54d9f0097..1772bae87a185846f941e0b540d8df2a904a1208 100644
--- a/doc/src/Modify_thermo.txt
+++ b/doc/src/Modify_thermo.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_variable.txt b/doc/src/Modify_variable.txt
index 3c5b29cd1af5d234dd76b2d573bcc07d2eb8087f..b163272f3ebc225522467d08fe144b725dc22a27 100644
--- a/doc/src/Modify_variable.txt
+++ b/doc/src/Modify_variable.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Packages.txt b/doc/src/Packages.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7f45a99b7fa8f3d33e3c8d2e771f069139a0249
--- /dev/null
+++ b/doc/src/Packages.txt
@@ -0,0 +1,39 @@
+"Previous Section"_Commands.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Speed.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Optional packages :h2
+
+This section gives an overview of the optional packages that extend
+LAMMPS functionality. Packages are groups of files that enable a
+specific set of features. For example, force fields for molecular
+systems or rigid-body constraint are in packages. You can see the
+list of all packages and "make" commands to manage them by typing
+"make package" from within the src directory of the LAMMPS
+distribution. "Section 2.3"_Section_start.html#start_3 gives general
+info on how to install and un-install packages as part of the LAMMPS
+build process.
+
+<!-- RST
+
+.. toctree::
+
+ Packages_standard
+ Packages_user
+ Packages_details
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Standard packages"_Packages_standard.html
+"User packages"_Packages_user.html
+"Details on each package"_Packages_details.html :ul
+
+<!-- END_HTML_ONLY -->
diff --git a/doc/src/Section_packages.txt b/doc/src/Packages_details.txt
similarity index 85%
rename from doc/src/Section_packages.txt
rename to doc/src/Packages_details.txt
index 340a77310d81837fa170a21fea14be888b859bc1..eb92fe4dc4c27506cf41b250f7a3dce49e159941 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Packages_details.txt
@@ -1,159 +1,96 @@
-"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_accelerate.html :c
+"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-4. Packages :h2
-
-This section gives an overview of the optional packages that extend
-LAMMPS functionality with instructions on how to build LAMMPS with
-each of them. Packages are groups of files that enable a specific set
-of features. For example, force fields for molecular systems or
-granular systems are in packages. You can see the list of all
-packages and "make" commands to manage them by typing "make package"
-from within the src directory of the LAMMPS distribution. "Section
-2.3"_Section_start.html#start_3 gives general info on how to install
-and un-install packages as part of the LAMMPS build process.
-
-There are two kinds of packages in LAMMPS, standard and user packages:
-
-"Table of standard packages"_#table_standard
-"Table of user packages"_#table_user :ul
-
-Either of these kinds of packages may work as is, may require some
-additional code compiled located in the lib folder, or may require
-an external library to be downloaded, compiled, installed, and LAMMPS
-configured to know about its location and additional compiler flags.
-You can often do the build of the internal or external libraries
-in one step by typing "make lib-name args='...'" from the src dir,
-with appropriate arguments included in args='...'. If you just type
-"make lib-name" you should see a help message about supported flags
-and some examples. For more details about this, please study the
-tables below and the sections about the individual packages.
-
-Standard packages are supported by the LAMMPS developers and are
-written in a syntax and style consistent with the rest of LAMMPS.
-This means the developers will answer questions about them, debug and
-fix them if necessary, and keep them compatible with future changes to
-LAMMPS.
-
-User packages have been contributed by users, and begin with the
-"user" prefix. If they are a single command (single file), they are
-typically in the user-misc package. User packages don't necessarily
-meet the requirements of the standard packages. This means the
-developers will try to keep things working and usually can answer
-technical questions about compiling the package. If you have problems
-using a feature provided in a user package, you may need to contact
-the contributor directly to get help. Information on how to submit
-additions you make to LAMMPS as single files or as a standard or user
-package are given in the "Modify contribute"_Modify.html doc page.
-
-Following the next two tables is a sub-section for each package. It
-lists authors (if applicable) and summarizes the package contents. It
-has specific instructions on how to install the package, including (if
-necessary) downloading or building any extra library it requires. It
-also gives links to documentation, example scripts, and
-pictures/movies (if available) that illustrate use of the package.
+:link(lc,Commands_all.html)
+
+:line
+
+Package details :h3
+
+Here is a brief description of all the standard and user packages in
+LAMMPS. It lists authors (if applicable) and summarizes the package
+contents. It has specific instructions on how to install the package,
+including, if necessary, info on how to download or build any extra
+library it requires. It also gives links to documentation, example
+scripts, and pictures/movies (if available) that illustrate use of the
+package.
NOTE: To see the complete list of commands a package adds to LAMMPS,
-just look at the files in its src directory, e.g. "ls src/GRANULAR".
-Files with names that start with fix, compute, atom, pair, bond,
-angle, etc correspond to commands with the same style names.
-
-In these two tables, the "Example" column is a sub-directory in the
-examples directory of the distribution which has an input script that
-uses the package. E.g. "peptide" refers to the examples/peptide
-directory; USER/atc refers to the examples/USER/atc directory. The
-"Library" column indicates whether an extra library is needed to build
-and use the package:
-
-dash = no library
-sys = system library: you likely have it on your machine
-int = internal library: provided with LAMMPS, but you may need to build it
-ext = external library: you will need to download and install it on your machine :ul
-
-:line
-:line
-
-[Standard packages] :link(table_standard),p
-
-Package, Description, Doc page, Example, Library
-"ASPHERE"_#ASPHERE, aspherical particle models, "Section 6.6.14"_Section_howto.html#howto_14, ellipse, -
-"BODY"_#BODY, body-style particles, "body"_body.html, body, -
-"CLASS2"_#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
-"COLLOID"_#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
-"COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
-"CORESHELL"_#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
-"DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
-"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
-"GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
-"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
-"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
-"LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
-"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
-"MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
-"MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
-"MISC"_#MISC, miscellanous single-file commands, -, -, -
-"MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
-"MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
-"MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
-"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
-"POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
-"PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
-"QEQ"_#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
-"REAX"_#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
-"REPLICA"_#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
-"RIGID"_#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
-"SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
-"SNAP"_#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
-"SPIN"_#SPIN, magnetic atomic spin dynamics, "Section 6.6.28"_Section_howto.html#howto_28, SPIN, -
-"SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
-"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
-
-[USER packages] :link(table_user),p
-
-Package, Description, Doc page, Example, Library
-"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
-"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
-"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
-"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
-"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
-"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
-"USER-DIFFRACTION"_#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
-"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
-"USER-DRUDE"_#USER-DRUDE, Drude oscillators, "tutorial"_tutorial_drude.html, USER/drude, -
-"USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
-"USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
-"USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
-"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
-"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
-"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
-"USER-MESO"_#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
-"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
-"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
-"USER-MOFFF"_#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
-"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
-"USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
-"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
-"USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
-"USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
-"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
-"USER-REAXC"_#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
-"USER-SMD"_#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
-"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
-"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
-"USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
-"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
-"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
+you can examine the files in its src directory, e.g. "ls
+src/GRANULAR". Files with names that start with fix, compute, atom,
+pair, bond, angle, etc correspond to commands with the same style name
+as contained in the file name.
+
+"ASPHERE"_#ASPHERE,
+"BODY"_#BODY,
+"CLASS2"_#CLASS2,
+"COLLOID"_#COLLOID,
+"COMPRESS"_#COMPRESS,
+"CORESHELL"_#CORESHELL,
+"DIPOLE"_#DIPOLE,
+"GPU"_#GPU,
+"GRANULAR"_#GRANULAR,
+"KIM"_#KIM,
+"KOKKOS"_#KOKKOS,
+"KSPACE"_#KSPACE,
+"LATTE"_#LATTE,
+"MANYBODY"_#MANYBODY,
+"MC"_#MC,
+"MEAM"_#MEAM,
+"MISC"_#MISC,
+"MOLECULE"_#MOLECULE,
+"MPIIO"_#MPIIO,
+"MSCG"_#MSCG,
+"OPT"_#OPT,
+"PERI"_#PERI,
+"POEMS"_#POEMS,
+"PYTHON"_#PYTHON,
+"QEQ"_#QEQ,
+"REAX"_#REAX,
+"REPLICA"_#REPLICA,
+"RIGID"_#RIGID,
+"SHOCK"_#SHOCK,
+"SNAP"_#SNAP,
+"SPIN"_#SPIN,
+"SRD"_#SRD,
+"VORONOI"_#VORONOI :tb(c=6,ea=c)
+
+"USER-ATC"_#USER-ATC,
+"USER-AWPMD"_#USER-AWPMD,
+"USER-BOCS"_#USER-BOCS,
+"USER-CGDNA"_#USER-CGDNA,
+"USER-CGSDK"_#USER-CGSDK,
+"USER-COLVARS"_#USER-COLVARS,
+"USER-DIFFRACTION"_#USER-DIFFRACTION,
+"USER-DPD"_#USER-DPD,
+"USER-DRUDE"_#USER-DRUDE,
+"USER-EFF"_#USER-EFF,
+"USER-FEP"_#USER-FEP,
+"USER-H5MD"_#USER-H5MD,
+"USER-INTEL"_#USER-INTEL,
+"USER-LB"_#USER-LB,
+"USER-MANIFOLD"_#USER-MANIFOLD,
+"USER-MEAMC"_#USER-MEAMC,
+"USER-MESO"_#USER-MESO,
+"USER-MGPT"_#USER-MGPT,
+"USER-MISC"_#USER-MISC,
+"USER-MOFFF"_#USER-MOFFF,
+"USER-MOLFILE"_#USER-MOLFILE,
+"USER-NETCDF"_#USER-NETCDF,
+"USER-OMP"_#USER-OMP,
+"USER-PHONON"_#USER-PHONON,
+"USER-QMMM"_#USER-QMMM,
+"USER-QTB"_#USER-QTB,
+"USER-QUIP"_#USER-QUIP,
+"USER-REAXC"_#USER-REAXC,
+"USER-SMD"_#USER-SMD,
+"USER-SMTBQ"_#USER-SMTBQ,
+"USER-SPH"_#USER-SPH,
+"USER-TALLY"_#USER-TALLY,
+"USER-UEF"_#USER-UEF,
+"USER-VTK"_#USER-VTK :tb(c=6,ea=c)
:line
:line
@@ -176,7 +113,7 @@ make machine :pre
[Supporting info:]
src/ASPHERE: filenames -> commands
-"Section 6.14"_Section_howto.html#howto_14
+"Howto spherical"_Howto_spherical.html
"pair_style gayberne"_pair_gayberne.html
"pair_style resquared"_pair_resquared.html
"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf
@@ -194,7 +131,8 @@ BODY package :link(BODY),h4
Body-style particles with internal structure. Computes,
time-integration fixes, pair styles, as well as the body styles
-themselves. See the "body"_body.html doc page for an overview.
+themselves. See the "Howto body"_Howto_body.html doc page for an
+overview.
[Install or un-install:]
@@ -207,10 +145,10 @@ make machine :pre
[Supporting info:]
src/BODY filenames -> commands
-"body"_body.html
+"Howto_body"_Howto_body.html
"atom_style body"_atom_style.html
"fix nve/body"_fix_nve_body.html
-"pair_style body"_pair_body.html
+"pair_style body/nparticle"_pair_body_nparticle.html
examples/body :ul
:line
@@ -322,9 +260,9 @@ Compute and pair styles that implement the adiabatic core/shell model
for polarizability. The pair styles augment Born, Buckingham, and
Lennard-Jones styles with core/shell capabilities. The "compute
temp/cs"_compute_temp_cs.html command calculates the temperature of a
-system with core/shell particles. See "Section
-6.26"_Section_howto.html#howto_26 for an overview of how to use this
-package.
+system with core/shell particles. See the "Howto
+coreshell"_Howto_coreshell.html doc page for an overview of how to use
+this package.
[Author:] Hendrik Heenen (Technical U of Munich).
@@ -339,8 +277,8 @@ make machine :pre
[Supporting info:]
src/CORESHELL: filenames -> commands
-"Section 6.26"_Section_howto.html#howto_26
-"Section 6.25"_Section_howto.html#howto_25
+"Howto coreshell"_Howto_coreshell.html
+"Howto polarizable"_Howto_polarizable.html
"compute temp/cs"_compute_temp_cs.html
"pair_style born/coul/long/cs"_pair_cs.html
"pair_style buck/coul/long/cs"_pair_cs.html
@@ -380,14 +318,14 @@ GPU package :link(GPU),h4
[Contents:]
Dozens of pair styles and a version of the PPPM long-range Coulombic
-solver optimized for GPUs. All such styles have a "gpu" as a
-suffix in their style name. The GPU code can be compiled with either
-CUDA or OpenCL, however the OpenCL variants are no longer actively
-maintained and only the CUDA versions are regularly tested.
-"Section 5.3.1"_accelerate_gpu.html gives details of what
-hardware and GPU software is required on your system,
-and details on how to build and use this package. Its styles can be
-invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line
+solver optimized for GPUs. All such styles have a "gpu" as a suffix
+in their style name. The GPU code can be compiled with either CUDA or
+OpenCL, however the OpenCL variants are no longer actively maintained
+and only the CUDA versions are regularly tested. The "Speed
+gpu"_Speed_gpu.html doc page gives details of what hardware and GPU
+software is required on your system, and details on how to build and
+use this package. Its styles can be invoked at run time via the "-sf
+gpu" or "-suffix gpu" "command-line
switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS
package, which has GPU-enabled styles.
@@ -453,12 +391,12 @@ GPU library.
src/GPU: filenames -> commands
src/GPU/README
lib/gpu/README
-"Section 5.3"_Section_accelerate.html#acc_3
-"Section 5.3.1"_accelerate_gpu.html
+"Speed packages"_Speed_packages.html
+"Speed gpu"_Speed_gpu.html.html
"Section 2.6 -sf gpu"_Section_start.html#start_6
"Section 2.6 -pk gpu"_Section_start.html#start_6
"package gpu"_package.html
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g)
+"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@@ -482,7 +420,7 @@ make machine :pre
[Supporting info:]
src/GRANULAR: filenames -> commands
-"Section 6.6"_Section_howto.html#howto_6,
+"Howto granular"_Howto_granular.html
"fix pour"_fix_pour.html
"fix wall/gran"_fix_wall_gran.html
"pair_style gran/hooke"_pair_gran.html
@@ -549,8 +487,8 @@ See the list of all KIM models here:
https://openkim.org/kim-items/models/by-model-drivers
See the list of example KIM models included by default here:
-https://openkim.org/kim-api in the "What is in the KIM API source
-package?" section
+https://openkim.org/kim-api on the "What is in the KIM API source
+package?" page.
You can then install/un-install the package and build LAMMPS in the
usual manner:
@@ -579,10 +517,10 @@ Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
styles adapted to compile using the Kokkos library which can convert
them to OpenMP or CUDA code so that they run efficiently on multicore
CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their
-style name. "Section 5.3.3"_accelerate_kokkos.html gives details of
-what hardware and software is required on your system, and how to
-build and use this package. Its styles can be invoked at run time via
-the "-sf kk" or "-suffix kk" "command-line
+style name. The "Speed kokkos"_Speed_kokkos.html doc page gives
+details of what hardware and software is required on your system, and
+how to build and use this package. Its styles can be invoked at run
+time via the "-sf kk" or "-suffix kk" "command-line
switches"_Section_start.html#start_6. Also see the "GPU"_#GPU,
"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
packages, which have styles optimized for CPUs, KNLs, and GPUs.
@@ -649,13 +587,13 @@ make machine :pre
src/KOKKOS: filenames -> commands
src/KOKKOS/README
lib/kokkos/README
-"Section 5.3"_Section_accelerate.html#acc_3
-"Section 5.3.3"_accelerate_kokkos.html
+"Speed packages"_Speed_packages.html
+"Speed kokkos"_Speed_kokkos.html
"Section 2.6 -k on ..."_Section_start.html#start_6
"Section 2.6 -sf kk"_Section_start.html#start_6
"Section 2.6 -pk kokkos"_Section_start.html#start_6
"package kokkos"_package.html
-Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k)
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@@ -689,11 +627,11 @@ make machine :pre
src/KSPACE: filenames -> commands
"kspace_style"_kspace_style.html
"doc/PDF/kspace.pdf"_PDF/kspace.pdf
-"Section 6.7"_Section_howto.html#howto_7
-"Section 6.8"_Section_howto.html#howto_8
-"Section 6.9"_Section_howto.html#howto_9
+"Howto tip3p"_Howto_tip3p.html
+"Howto tip4p"_Howto_tip4p.html
+"Howto spc"_Howto_spc.html
"pair_style coul"_pair_coul.html
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 with "long" or "msm" in pair style name
+"Commands pair"_Commands_pair.html page for styles with "long" or "msm" in name
examples/peptide
bench/in.rhodo :ul
@@ -777,7 +715,7 @@ make machine :pre
[Supporting info:]
src/MANYBODY: filenames -> commands
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
+"Commands pair"_Commands_pair.html page
examples/comb
examples/eim
examples/nb3d
@@ -940,7 +878,7 @@ src/MOLECULE: filenames -> commands
"improper_style"_improper_style.html
"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html
"pair_style lj/charmm/coul/charmm"_pair_charmm.html
-"Section 6.3"_Section_howto.html#howto_3
+"Howto bioFF"_Howto_bioFF.html
examples/cmap
examples/dreiding
examples/micelle,
@@ -1048,9 +986,9 @@ OPT package :link(OPT),h4
A handful of pair styles which are optimized for improved CPU
performance on single or multiple cores. These include EAM, LJ,
CHARMM, and Morse potentials. The styles have an "opt" suffix in
-their style name. "Section 5.3.5"_accelerate_opt.html gives details
-of how to build and use this package. Its styles can be invoked at
-run time via the "-sf opt" or "-suffix opt" "command-line
+their style name. The "Speed opt"_Speed_opt.html doc page gives
+details of how to build and use this package. Its styles can be
+invoked at run time via the "-sf opt" or "-suffix opt" "command-line
switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS,
"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
have styles optimized for CPU performance.
@@ -1076,10 +1014,10 @@ CCFLAGS: add -restrict for Intel compilers :ul
[Supporting info:]
src/OPT: filenames -> commands
-"Section 5.3"_Section_accelerate.html#acc_3
-"Section 5.3.5"_accelerate_opt.html
+"Speed packages"_Speed_packages.html
+"Speed opt"_Speed_opt.html
"Section 2.6 -sf opt"_Section_start.html#start_6
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t)
+"Commands pair"_Commands_pair.html for styles followed by (t)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@@ -1180,8 +1118,8 @@ A "python"_python.html command which allow you to execute Python code
from a LAMMPS input script. The code can be in a separate file or
embedded in the input script itself. See the "Python
call"_Python_call.html doc page for an overview of using Python from
-LAMMPS in this manner and the "Python"_Python.html doc page for other
-ways to use LAMMPS and Python together.
+LAMMPS in this manner and all the "Python"_Python.html doc pages for
+other ways to use LAMMPS and Python together.
[Install or un-install:]
@@ -1202,7 +1140,7 @@ to Makefile.lammps) if the LAMMPS build fails.
[Supporting info:]
src/PYTHON: filenames -> commands
-"Python call"_Python_call.html
+"Python call"_Python.html
lib/python/README
examples/python :ul
@@ -1292,8 +1230,8 @@ REPLICA package :link(REPLICA),h4
[Contents:]
A collection of multi-replica methods which can be used when running
-multiple LAMMPS simulations (replicas). See "Section
-6.5"_Section_howto.html#howto_5 for an overview of how to run
+multiple LAMMPS simulations (replicas). See the "Howto
+replica"_Howto_replica.html doc page for an overview of how to run
multi-replica simulations in LAMMPS. Methods in the package include
nudged elastic band (NEB), parallel replica dynamics (PRD),
temperature accelerated dynamics (TAD), parallel tempering, and a
@@ -1312,7 +1250,7 @@ make machine :pre
[Supporting info:]
src/REPLICA: filenames -> commands
-"Section 6.5"_Section_howto.html#howto_5
+"Howto replica"_Howto_replica.html
"neb"_neb.html
"prd"_prd.html
"tad"_tad.html
@@ -1435,7 +1373,7 @@ make machine :pre
[Supporting info:]
src/SPIN: filenames -> commands
-"Section 6.28"_Section_howto.html#howto_28
+"Howto spin"_Howto_spin.html
"pair_style spin/dmi"_pair_spin_dmi.html
"pair_style spin/exchange"_pair_spin_exchange.html
"pair_style spin/magelec"_pair_spin_magelec.html
@@ -1894,10 +1832,10 @@ USER-DRUDE package :link(USER-DRUDE),h4
[Contents:]
Fixes, pair styles, and a compute to simulate thermalized Drude
-oscillators as a model of polarization. See "Section
-6.27"_Section_howto.html#howto_27 for an overview of how to use the
-package. There are auxiliary tools for using this package in
-tools/drude.
+oscillators as a model of polarization. See the "Howto
+drude"_Howto_drude.html and "Howto drude2"_Howto_drude2.html doc pages
+for an overview of how to use the package. There are auxiliary tools
+for using this package in tools/drude.
[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
@@ -1913,8 +1851,9 @@ make machine :pre
[Supporting info:]
src/USER-DRUDE: filenames -> commands
-"Section 6.27"_Section_howto.html#howto_27
-"Section 6.25"_Section_howto.html#howto_25
+"Howto drude"_Howto_drude.html
+"Howto drude2"_Howto_drude2.html
+"Howto polarizable"_Howto_polarizable.html
src/USER-DRUDE/README
"fix drude"_fix_drude.html
"fix drude/transform/*"_fix_drude_transform.html
@@ -2065,8 +2004,8 @@ USER-INTEL package :link(USER-INTEL),h4
Dozens of pair, fix, bond, angle, dihedral, improper, and kspace
styles which are optimized for Intel CPUs and KNLs (Knights Landing).
-All of them have an "intel" in their style name. "Section
-5.3.2"_accelerate_intel.html gives details of what hardware and
+All of them have an "intel" in their style name. The "Speed
+intel"_Speed_intel.html doc page gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf intel" or
"-suffix intel" "command-line switches"_Section_start.html#start_6.
@@ -2116,7 +2055,7 @@ hardware target, to produce a separate executable.
You should also typically install the USER-OMP package, as it can be
used in tandem with the USER-INTEL package to good effect, as
-explained in "Section 5.3.2"_accelerate_intel.html.
+explained on the "Speed intel"_Speed_intel.html doc page.
make yes-user-intel yes-user-omp
make machine :pre
@@ -2128,12 +2067,12 @@ make machine :pre
src/USER-INTEL: filenames -> commands
src/USER-INTEL/README
-"Section 5.3"_Section_accelerate.html#acc_3
-"Section 5.3.2"_accelerate_gpu.html
+"Speed packages"_Speed_packages.html
+"Speed intel"_Speed_intel.html
"Section 2.6 -sf intel"_Section_start.html#start_6
"Section 2.6 -pk intel"_Section_start.html#start_6
"package intel"_package.html
-Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i)
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
src/USER-INTEL/TEST
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -2254,7 +2193,7 @@ make machine :pre
src/USER-MANIFOLD: filenames -> commands
src/USER-MANIFOLD/README
-"doc/manifolds"_manifolds.html
+"Howto manifold"_Howto_manifold.html
"fix manifoldforce"_fix_manifoldforce.html
"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
@@ -2475,10 +2414,10 @@ USER-OMP package :link(USER-OMP),h4
Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and
kspace styles which are altered to enable threading on many-core CPUs
via OpenMP directives. All of them have an "omp" in their style name.
-"Section 5.3.4"_accelerate_omp.html gives details of what hardware and
-compilers are required on your system, and how to build and use this
-package. Its styles can be invoked at run time via the "-sf omp" or
-"-suffix omp" "command-line switches"_Section_start.html#start_6.
+The "Speed omp"_Speed_omp.html doc page gives details of what hardware
+and compilers are required on your system, and how to build and use
+this package. Its styles can be invoked at run time via the "-sf omp"
+or "-suffix omp" "command-line switches"_Section_start.html#start_6.
Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
"USER-INTEL"_#USER-INTEL packages, which have styles optimized for
CPUs.
@@ -2513,12 +2452,12 @@ LINKFLAGS: add -fopenmp :ul
src/USER-OMP: filenames -> commands
src/USER-OMP/README
-"Section 5.3"_Section_accelerate.html#acc_3
-"Section 5.3.4"_accelerate_omp.html
+"Speed packages"_Speed_packages.html
+"Speed omp"_Speed_omp.html
"Section 2.6 -sf omp"_Section_start.html#start_6
"Section 2.6 -pk omp"_Section_start.html#start_6
"package omp"_package.html
-Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o)
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e6434560244abfce710c182af2c4fb6cad31da6
--- /dev/null
+++ b/doc/src/Packages_standard.txt
@@ -0,0 +1,65 @@
+"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Standard packages :h3
+
+This is the list of standard packages in LAMMPS. The link for each
+package name gives more details.
+
+Standard packages are supported by the LAMMPS developers and are
+written in a syntax and style consistent with the rest of LAMMPS.
+This means the developers will answer questions about them, debug and
+fix them if necessary, and keep them compatible with future changes to
+LAMMPS.
+
+The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory; USER/atc
+refers to the examples/USER/atc directory. The "Library" column
+indicates whether an extra library is needed to build and use the
+package:
+
+dash = no library
+sys = system library: you likely have it on your machine
+int = internal library: provided with LAMMPS, but you may need to build it
+ext = external library: you will need to download and install it on your machine :ul
+
+Package, Description, Doc page, Example, Library
+"ASPHERE"_Packages_details.html#ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, -
+"BODY"_Packages_details.html#BODY, body-style particles, "Howto body"_Howto_body.html, body, -
+"CLASS2"_Packages_details.html#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
+"COLLOID"_Packages_details.html#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
+"COMPRESS"_Packages_details.html#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
+"CORESHELL"_Packages_details.html#CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, -
+"DIPOLE"_Packages_details.html#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
+"GPU"_Packages_details.html#GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
+"GRANULAR"_Packages_details.html#GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, -
+"KIM"_Packages_details.html#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
+"KOKKOS"_Packages_details.html#KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"KSPACE"_Packages_details.html#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
+"LATTE"_Packages_details.html#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
+"MANYBODY"_Packages_details.html#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
+"MC"_Packages_details.html#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
+"MEAM"_Packages_details.html#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
+"MISC"_Packages_details.html#MISC, miscellanous single-file commands, -, -, -
+"MOLECULE"_Packages_details.html#MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, -
+"MPIIO"_Packages_details.html#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
+"MSCG"_Packages_details.html#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
+"OPT"_Packages_details.html#OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"PERI"_Packages_details.html#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
+"POEMS"_Packages_details.html#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
+"PYTHON"_Packages_details.html#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
+"QEQ"_Packages_details.html#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
+"REAX"_Packages_details.html#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
+"REPLICA"_Packages_details.html#REPLICA, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
+"RIGID"_Packages_details.html#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
+"SHOCK"_Packages_details.html#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
+"SNAP"_Packages_details.html#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
+"SPIN"_#SPIN, magnetic atomic spin dynamics, "Howto spin"_Howto_spin.html, SPIN, -"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
+"VORONOI"_Packages_details.html#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8728148f9c1a83f0c900524e3b49bc586101aa6
--- /dev/null
+++ b/doc/src/Packages_user.txt
@@ -0,0 +1,74 @@
+"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+User packages :h3
+
+This is a list of user packages in LAMMPS. The link for each package
+name gives more details.
+
+User packages have been contributed by users, and begin with the
+"user" prefix. If a contribution is a single command (single file),
+it is typically in the user-misc package. User packages don't
+necessarily meet the requirements of the "standard
+packages"_Packages_standard.html. This means the developers will try
+to keep things working and usually can answer technical questions
+about compiling the package. If you have problems using a specific
+feature provided in a user package, you may need to contact the
+contributor directly to get help. Information on how to submit
+additions you make to LAMMPS as single files or as a standard or user
+package is explained on the "Modify contribute"_Modify_contribute.html
+doc page.
+
+The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory; USER/atc
+refers to the examples/USER/atc directory. The "Library" column
+indicates whether an extra library is needed to build and use the
+package:
+
+dash = no library
+sys = system library: you likely have it on your machine
+int = internal library: provided with LAMMPS, but you may need to build it
+ext = external library: you will need to download and install it on your machine :ul
+
+Package, Description, Doc page, Example, Library
+"USER-ATC"_Packages_details.html#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
+"USER-AWPMD"_Packages_details.html#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
+"USER-BOCS"_Packages_details.html#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
+"USER-CGDNA"_Packages_details.html#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
+"USER-CGSDK"_Packages_details.html#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
+"USER-COLVARS"_Packages_details.html#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
+"USER-DIFFRACTION"_Packages_details.html#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
+"USER-DPD"_Packages_details.html#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
+"USER-DRUDE"_Packages_details.html#USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, -
+"USER-EFF"_Packages_details.html#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
+"USER-FEP"_Packages_details.html#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
+"USER-H5MD"_Packages_details.html#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
+"USER-INTEL"_Packages_details.html#USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"USER-LB"_Packages_details.html#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
+"USER-MANIFOLD"_Packages_details.html#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
+"USER-MEAMC"_Packages_details.html#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
+"USER-MESO"_Packages_details.html#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
+"USER-MGPT"_Packages_details.html#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
+"USER-MISC"_Packages_details.html#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
+"USER-MOFFF"_Packages_details.html#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
+"USER-MOLFILE"_Packages_details.html#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
+"USER-NETCDF"_Packages_details.html#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
+"USER-OMP"_Packages_details.html#USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"USER-PHONON"_Packages_details.html#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
+"USER-QMMM"_Packages_details.html#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
+"USER-QTB"_Packages_details.html#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
+"USER-QUIP"_Packages_details.html#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
+"USER-REAXC"_Packages_details.html#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
+"USER-SMD"_Packages_details.html#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
+"USER-SMTBQ"_Packages_details.html#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
+"USER-SPH"_Packages_details.html#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
+"USER-TALLY"_Packages_details.html#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
+"USER-UEF"_Packages_details.html#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
+"USER-VTK"_Packages_details.html#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
diff --git a/doc/src/Python.txt b/doc/src/Python.txt
index 169670d669da6bbfcbdcb9adb491276819685f9f..2c9c6872bbf21e5704088b46752603f7349cd3e6 100644
--- a/doc/src/Python.txt
+++ b/doc/src/Python.txt
@@ -4,7 +4,7 @@ Section"_Errors.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt
index 3e30a5a7c7e7d831413c1e532de421d40555fdd0..621f1fe2410f7f7d58e193466481cc3cd19a4578 100644
--- a/doc/src/Python_call.txt
+++ b/doc/src/Python_call.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_examples.txt b/doc/src/Python_examples.txt
index fbca381e8b0f1cc4084e491162f2dad6dd7ddb36..46e5fee2b97da5d4f46644883434729c6e5406ad 100644
--- a/doc/src/Python_examples.txt
+++ b/doc/src/Python_examples.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_install.txt b/doc/src/Python_install.txt
index 631f6c4a7f1a3a40245e3d7ab98b7b195bb4fefc..6591360ae2535935f0c9e88e8bf6bc2c830f6cb0 100644
--- a/doc/src/Python_install.txt
+++ b/doc/src/Python_install.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt
index 4babbb746cc3c1753f85ef6f5146dfdc51e8ee9a..8d0c724a45992294f7860612e5042387efc150ec 100644
--- a/doc/src/Python_library.txt
+++ b/doc/src/Python_library.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -21,8 +21,8 @@ from lammps import lammps :pre
These are the methods defined by the lammps module. If you look at
the files src/library.cpp and src/library.h you will see they
correspond one-to-one with calls you can make to the LAMMPS library
-from a C++ or C or Fortran program, and which are described in
-"Section 6.19"_Section_howto.html#howto_19 of the manual.
+from a C++ or C or Fortran program, and which are described on the
+"Howto library"_Howto_library.html doc page.
The python/examples directory has Python scripts which show how Python
can run LAMMPS, grab data, change it, and put it back into LAMMPS.
@@ -165,11 +165,11 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
-See "Section 6.15"_Section_howto.html#howto_15 of the manual for a
-discussion of global, per-atom, and local data, and of scalar, vector,
-and array data types. See the doc pages for individual
-"computes"_compute.html and "fixes"_fix.html for a description of what
-they calculate and store.
+See the "Howto output"_Howto_output.html doc page for a discussion of
+global, per-atom, and local data, and of scalar, vector, and array
+data types. See the doc pages for individual "computes"_compute.html
+and "fixes"_fix.html for a description of what they calculate and
+store.
For extract_variable(), an "equal-style or atom-style
variable"_variable.html is evaluated and its result returned.
diff --git a/doc/src/Python_mpi.txt b/doc/src/Python_mpi.txt
index 8377bbb3d0a0ac058c1f97274ba7fe7ba054b648..6e0a2ce3198fd79bb98d1bf24fe0e60675de72ce 100644
--- a/doc/src/Python_mpi.txt
+++ b/doc/src/Python_mpi.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_pylammps.txt b/doc/src/Python_pylammps.txt
index ad5ed192ee669f0b14fcaa10ccd9097391e74f54..d7baa93e2e69154b20fdc2f7f4666f500f2d6a02 100644
--- a/doc/src/Python_pylammps.txt
+++ b/doc/src/Python_pylammps.txt
@@ -3,12 +3,12 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
PyLammps interface :h3
PyLammps is a Python wrapper class which can be created on its own or
-use an existing lammps Python object. It has its own "PyLammps
-Tutorial"_tutorial_pylammps.html doc page.
+use an existing lammps Python object. It has its own "Howto
+pylammps"_Howto_pylammps.html doc page.
diff --git a/doc/src/Python_run.txt b/doc/src/Python_run.txt
index 03ab2ed3d7dc3e6b4703c78950978323835c394d..a94dc07f2d7368ec8086fc1535337ed3c245f82f 100644
--- a/doc/src/Python_run.txt
+++ b/doc/src/Python_run.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_shlib.txt b/doc/src/Python_shlib.txt
index 1aafbe2e847e3b486f10b7991b85bbea9009d45b..1a921e4025cde5cc1376c603a4beb2cf5c4c58fb 100644
--- a/doc/src/Python_shlib.txt
+++ b/doc/src/Python_shlib.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_test.txt b/doc/src/Python_test.txt
index 5f361a500b6c8ba12748fed18b61af3c81d9028b..4a05d5c4680df053cd563f5e09d017e64fe4bb1f 100644
--- a/doc/src/Python_test.txt
+++ b/doc/src/Python_test.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt
deleted file mode 100644
index d5cbf77a84e2881a7cfd2f23d6cd94d98031cfec..0000000000000000000000000000000000000000
--- a/doc/src/Section_accelerate.txt
+++ /dev/null
@@ -1,391 +0,0 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_howto.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-5. Accelerating LAMMPS performance :h2
-
-This section describes various methods for improving LAMMPS
-performance for different classes of problems running on different
-kinds of machines.
-
-There are two thrusts to the discussion that follows. The
-first is using code options that implement alternate algorithms
-that can speed-up a simulation. The second is to use one
-of the several accelerator packages provided with LAMMPS that
-contain code optimized for certain kinds of hardware, including
-multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
-
-5.1 "Measuring performance"_#acc_1 :ulb,l
-5.2 "Algorithms and code options to boost performace"_#acc_2 :l
-5.3 "Accelerator packages with optimized styles"_#acc_3 :l
- 5.3.1 "GPU package"_accelerate_gpu.html :l
- 5.3.2 "USER-INTEL package"_accelerate_intel.html :l
- 5.3.3 "KOKKOS package"_accelerate_kokkos.html :l
- 5.3.4 "USER-OMP package"_accelerate_omp.html :l
- 5.3.5 "OPT package"_accelerate_opt.html :l
-5.4 "Comparison of various accelerator packages"_#acc_4 :l
-:ule
-
-The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
-web site gives performance results for the various accelerator
-packages discussed in Section 5.2, for several of the standard LAMMPS
-benchmark problems, as a function of problem size and number of
-compute nodes, on different hardware platforms.
-
-:line
-:line
-
-5.1 Measuring performance :h3,link(acc_1)
-
-Before trying to make your simulation run faster, you should
-understand how it currently performs and where the bottlenecks are.
-
-The best way to do this is run the your system (actual number of
-atoms) for a modest number of timesteps (say 100 steps) on several
-different processor counts, including a single processor if possible.
-Do this for an equilibrium version of your system, so that the
-100-step timings are representative of a much longer run. There is
-typically no need to run for 1000s of timesteps to get accurate
-timings; you can simply extrapolate from short runs.
-
-For the set of runs, look at the timing data printed to the screen and
-log file at the end of each LAMMPS run. "This
-section"_Section_start.html#start_7 of the manual has an overview.
-
-Running on one (or a few processors) should give a good estimate of
-the serial performance and what portions of the timestep are taking
-the most time. Running the same problem on a few different processor
-counts should give an estimate of parallel scalability. I.e. if the
-simulation runs 16x faster on 16 processors, its 100% parallel
-efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
-
-The most important data to look at in the timing info is the timing
-breakdown and relative percentages. For example, trying different
-options for speeding up the long-range solvers will have little impact
-if they only consume 10% of the run time. If the pairwise time is
-dominating, you may want to look at GPU or OMP versions of the pair
-style, as discussed below. Comparing how the percentages change as
-you increase the processor count gives you a sense of how different
-operations within the timestep are scaling. Note that if you are
-running with a Kspace solver, there is additional output on the
-breakdown of the Kspace time. For PPPM, this includes the fraction
-spent on FFTs, which can be communication intensive.
-
-Another important detail in the timing info are the histograms of
-atoms counts and neighbor counts. If these vary widely across
-processors, you have a load-imbalance issue. This often results in
-inaccurate relative timing data, because processors have to wait when
-communication occurs for other processors to catch up. Thus the
-reported times for "Communication" or "Other" may be higher than they
-really are, due to load-imbalance. If this is an issue, you can
-uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
-LAMMPS, to obtain synchronized timings.
-
-:line
-
-5.2 General strategies :h3,link(acc_2)
-
-NOTE: this section 5.2 is still a work in progress
-
-Here is a list of general ideas for improving simulation performance.
-Most of them are only applicable to certain models and certain
-bottlenecks in the current performance, so let the timing data you
-generate be your guide. It is hard, if not impossible, to predict how
-much difference these options will make, since it is a function of
-problem size, number of processors used, and your machine. There is
-no substitute for identifying performance bottlenecks, and trying out
-various options.
-
-rRESPA
-2-FFT PPPM
-Staggered PPPM
-single vs double PPPM
-partial charge PPPM
-verlet/split run style
-processor command for proc layout and numa layout
-load-balancing: balance and fix balance :ul
-
-2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses
-2 FFTs instead of the 4 FFTs used by the default {ik differentiation}
-PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
-achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
-cost is the performance bottleneck (typically large problems running
-on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
-
-Staggered PPPM performs calculations using two different meshes, one
-shifted slightly with respect to the other. This can reduce force
-aliasing errors and increase the accuracy of the method, but also
-doubles the amount of work required. For high relative accuracy, using
-staggered PPPM allows one to half the mesh size in each dimension as
-compared to regular PPPM, which can give around a 4x speedup in the
-kspace time. However, for low relative accuracy, using staggered PPPM
-gives little benefit and can be up to 2x slower in the kspace
-time. For example, the rhodopsin benchmark was run on a single
-processor, and results for kspace time vs. relative accuracy for the
-different methods are shown in the figure below. For this system,
-staggered PPPM (using ik differentiation) becomes useful when using a
-relative accuracy of slightly greater than 1e-5 and above.
-
-:c,image(JPG/rhodo_staggered.jpg)
-
-NOTE: Using staggered PPPM may not give the same increase in accuracy
-of energy and pressure as it does in forces, so some caution must be
-used if energy and/or pressure are quantities of interest, such as
-when using a barostat.
-
-:line
-
-5.3 Packages with optimized styles :h3,link(acc_3)
-
-Accelerated versions of various "pair_style"_pair_style.html,
-"fixes"_fix.html, "computes"_compute.html, and other commands have
-been added to LAMMPS, which will typically run faster than the
-standard non-accelerated versions. Some require appropriate hardware
-to be present on your system, e.g. GPUs or Intel Xeon Phi
-coprocessors.
-
-All of these commands are in packages provided with LAMMPS. An
-overview of packages is give in "Section
-packages"_Section_packages.html.
-
-These are the accelerator packages
-currently in LAMMPS, either as standard or user packages:
-
-"GPU Package"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support
-"USER-INTEL Package"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi
-"KOKKOS Package"_accelerate_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading
-"USER-OMP Package"_accelerate_omp.html : for OpenMP threading and generic CPU optimizations
-"OPT Package"_accelerate_opt.html : generic CPU optimizations :tb(s=:)
-
-<!-- RST
-
-.. toctree::
- :maxdepth: 1
- :hidden:
-
- accelerate_gpu
- accelerate_intel
- accelerate_kokkos
- accelerate_omp
- accelerate_opt
-
-END_RST -->
-
-Inverting this list, LAMMPS currently has acceleration support for
-three kinds of hardware, via the listed packages:
-
-Many-core CPUs : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html, "USER-OMP"_accelerate_omp.html, "OPT"_accelerate_opt.html packages
-NVIDIA GPUs : "GPU"_accelerate_gpu.html, "KOKKOS"_accelerate_kokkos.html packages
-Intel Phi : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html packages :tb(s=:)
-
-Which package is fastest for your hardware may depend on the size
-problem you are running and what commands (accelerated and
-non-accelerated) are invoked by your input script. While these doc
-pages include performance guidelines, there is no substitute for
-trying out the different packages appropriate to your hardware.
-
-Any accelerated style has the same name as the corresponding standard
-style, except that a suffix is appended. Otherwise, the syntax for
-the command that uses the style is identical, their functionality is
-the same, and the numerical results it produces should also be the
-same, except for precision and round-off effects.
-
-For example, all of these styles are accelerated variants of the
-Lennard-Jones "pair_style lj/cut"_pair_lj.html:
-
-"pair_style lj/cut/gpu"_pair_lj.html
-"pair_style lj/cut/intel"_pair_lj.html
-"pair_style lj/cut/kk"_pair_lj.html
-"pair_style lj/cut/omp"_pair_lj.html
-"pair_style lj/cut/opt"_pair_lj.html :ul
-
-To see what accelerate styles are currently available, see
-"Section 3.5"_Section_commands.html#cmd_5 of the manual. The
-doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or
-"fix nve"_fix_nve.html) also list any accelerated variants available
-for that style.
-
-To use an accelerator package in LAMMPS, and one or more of the styles
-it provides, follow these general steps. Details vary from package to
-package and are explained in the individual accelerator doc pages,
-listed above:
-
-build the accelerator library |
- only for GPU package |
-install the accelerator package |
- make yes-opt, make yes-user-intel, etc |
-add compile/link flags to Makefile.machine in src/MAKE |
- only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |
-re-build LAMMPS |
- make machine |
-prepare and test a regular LAMMPS simulation |
- lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
-enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
- only needed for KOKKOS package |
-set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
- only if defaults need to be changed |
-use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
-:tb(c=2,s=|)
-
-Note that the first 4 steps can be done as a single command with
-suitable make command invocations. This is discussed in "Section
-4"_Section_packages.html of the manual, and its use is
-illustrated in the individual accelerator sections. Typically these
-steps only need to be done once, to create an executable that uses one
-or more accelerator packages.
-
-The last 4 steps can all be done from the command-line when LAMMPS is
-launched, without changing your input script, as illustrated in the
-individual accelerator sections. Or you can add
-"package"_package.html and "suffix"_suffix.html commands to your input
-script.
-
-NOTE: With a few exceptions, you can build a single LAMMPS executable
-with all its accelerator packages installed. Note however that the
-USER-INTEL and KOKKOS packages require you to choose one of their
-hardware options when building for a specific platform. I.e. CPU or
-Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
-option for the KOKKOS package.
-
-These are the exceptions. You cannot build a single executable with:
-
-both the USER-INTEL Phi and KOKKOS Phi options
-the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul
-
-See the examples/accelerate/README and make.list files for sample
-Make.py commands that build LAMMPS with any or all of the accelerator
-packages. As an example, here is a command that builds with all the
-GPU related packages installed (GPU, KOKKOS with Cuda), including
-settings to build the needed auxiliary GPU libraries for Kepler GPUs:
-
-Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \
- -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre
-
-The examples/accelerate directory also has input scripts that can be
-used with all of the accelerator packages. See its README file for
-details.
-
-Likewise, the bench directory has FERMI and KEPLER and PHI
-sub-directories with Make.py commands and input scripts for using all
-the accelerator packages on various machines. See the README files in
-those dirs.
-
-As mentioned above, the "Benchmark
-page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives
-performance results for the various accelerator packages for several
-of the standard LAMMPS benchmark problems, as a function of problem
-size and number of compute nodes, on different hardware platforms.
-
-Here is a brief summary of what the various packages provide. Details
-are in the individual accelerator sections.
-
-Styles with a "gpu" suffix are part of the GPU package, and can be run
-on NVIDIA GPUs. The speed-up on a GPU depends on a variety of
-factors, discussed in the accelerator sections. :ulb,l
-
-Styles with an "intel" suffix are part of the USER-INTEL
-package. These styles support vectorized single and mixed precision
-calculations, in addition to full double precision. In extreme cases,
-this can provide speedups over 3.5x on CPUs. The package also
-supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
-coprocessors. This can result in additional speedup over 2x depending
-on the hardware configuration. :l
-
-Styles with a "kk" suffix are part of the KOKKOS package, and can be
-run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
-Xeon Phi in "native" mode. The speed-up depends on a variety of
-factors, as discussed on the KOKKOS accelerator page. :l
-
-Styles with an "omp" suffix are part of the USER-OMP package and allow
-a pair-style to be run in multi-threaded mode using OpenMP. This can
-be useful on nodes with high-core counts when using less MPI processes
-than cores is advantageous, e.g. when running with PPPM so that FFTs
-are run on fewer MPI processors or when the many MPI tasks would
-overload the available bandwidth for communication. :l
-
-Styles with an "opt" suffix are part of the OPT package and typically
-speed-up the pairwise calculations of your simulation by 5-25% on a
-CPU. :l
-:ule
-
-The individual accelerator package doc pages explain:
-
-what hardware and software the accelerated package requires
-how to build LAMMPS with the accelerated package
-how to run with the accelerated package either via command-line switches or modifying the input script
-speed-ups to expect
-guidelines for best performance
-restrictions :ul
-
-:line
-
-5.4 Comparison of various accelerator packages :h3,link(acc_4)
-
-NOTE: this section still needs to be re-worked with additional KOKKOS
-and USER-INTEL information.
-
-The next section compares and contrasts the various accelerator
-options, since there are multiple ways to perform OpenMP threading,
-run on GPUs, and run on Intel Xeon Phi coprocessors.
-
-All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
-hardware, but they do it in different ways.
-
-As a consequence, for a particular simulation on specific hardware,
-one package may be faster than the other. We give guidelines below,
-but the best way to determine which package is faster for your input
-script is to try both of them on your machine. See the benchmarking
-section below for examples where this has been done.
-
-[Guidelines for using each package optimally:]
-
-The GPU package allows you to assign multiple CPUs (cores) to a single
-GPU (a common configuration for "hybrid" nodes that contain multicore
-CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l
-
-The GPU package moves per-atom data (coordinates, forces)
-back-and-forth between the CPU and GPU every timestep. The
-KOKKOS/CUDA package only does this on timesteps when a CPU calculation
-is required (e.g. to invoke a fix or compute that is non-GPU-ized).
-Hence, if you can formulate your input script to only use GPU-ized
-fixes and computes, and avoid doing I/O too often (thermo output, dump
-file snapshots, restart files), then the data transfer cost of the
-KOKKOS/CUDA package can be very low, causing it to run faster than the
-GPU package. :l
-
-The GPU package is often faster than the KOKKOS/CUDA package, if the
-number of atoms per GPU is smaller. The crossover point, in terms of
-atoms/GPU at which the KOKKOS/CUDA package becomes faster depends
-strongly on the pair style. For example, for a simple Lennard Jones
-system the crossover (in single precision) is often about 50K-100K
-atoms per GPU. When performing double precision calculations the
-crossover point can be significantly smaller. :l
-
-Both packages compute bonded interactions (bonds, angles, etc) on the
-CPU. If the GPU package is running with several MPI processes
-assigned to one GPU, the cost of computing the bonded interactions is
-spread across more CPUs and hence the GPU package can run faster. :l
-
-When using the GPU package with multiple CPUs assigned to one GPU, its
-performance depends to some extent on high bandwidth between the CPUs
-and the GPU. Hence its performance is affected if full 16 PCIe lanes
-are not available for each GPU. In HPC environments this can be the
-case if S2050/70 servers are used, where two devices generally share
-one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
-full 16 lanes to each of the PCIe 2.0 16x slots. :l
-:ule
-
-[Differences between the two packages:]
-
-The GPU package accelerates only pair force, neighbor list, and PPPM
-calculations. :ulb,l
-
-The GPU package requires neighbor lists to be built on the CPU when using
-exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
-:ule
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
deleted file mode 100644
index 19301e9d01fb4afc1b1a3ca52f474443ad9d50f1..0000000000000000000000000000000000000000
--- a/doc/src/Section_commands.txt
+++ /dev/null
@@ -1,1293 +0,0 @@
-"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-3. Commands :h2
-
-This section describes how a LAMMPS input script is formatted and the
-input script commands used to define a LAMMPS simulation.
-
-3.1 "LAMMPS input script"_#cmd_1
-3.2 "Parsing rules"_#cmd_2
-3.3 "Input script structure"_#cmd_3
-3.4 "Commands listed by category"_#cmd_4
-3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
-
-:line
-:line
-
-3.1 LAMMPS input script :link(cmd_1),h4
-
-LAMMPS executes by reading commands from a input script (text file),
-one line at a time. When the input script ends, LAMMPS exits. Each
-command causes LAMMPS to take some action. It may set an internal
-variable, read in a file, or run a simulation. Most commands have
-default settings, which means you only need to use the command if you
-wish to change the default.
-
-In many cases, the ordering of commands in an input script is not
-important. However the following rules apply:
-
-(1) LAMMPS does not read your entire input script and then perform a
-simulation with all the settings. Rather, the input script is read
-one line at a time and each command takes effect when it is read.
-Thus this sequence of commands:
-
-timestep 0.5
-run 100
-run 100 :pre
-
-does something different than this sequence:
-
-run 100
-timestep 0.5
-run 100 :pre
-
-In the first case, the specified timestep (0.5 fmsec) is used for two
-simulations of 100 timesteps each. In the 2nd case, the default
-timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
-fmsec timestep is used for the 2nd one.
-
-(2) Some commands are only valid when they follow other commands. For
-example you cannot set the temperature of a group of atoms until atoms
-have been defined and a group command is used to define which atoms
-belong to the group.
-
-(3) Sometimes command B will use values that can be set by command A.
-This means command A must precede command B in the input script if it
-is to have the desired effect. For example, the
-"read_data"_read_data.html command initializes the system by setting
-up the simulation box and assigning atoms to processors. If default
-values are not desired, the "processors"_processors.html and
-"boundary"_boundary.html commands need to be used before read_data to
-tell LAMMPS how to map processors to the simulation box.
-
-Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed. The "Errors"_Errors.html doc page gives
-more information on what errors mean. The documentation for each
-command lists restrictions on how the command can be used.
-
-:line
-
-3.2 Parsing rules :link(cmd_2),h4
-
-Each non-blank line in the input script is treated as a command.
-LAMMPS commands are case sensitive. Command names are lower-case, as
-are specified command arguments. Upper case letters may be used in
-file names or user-chosen ID strings.
-
-Here is how each line in the input script is parsed by LAMMPS:
-
-(1) If the last printable character on the line is a "&" character,
-the command is assumed to continue on the next line. The next line is
-concatenated to the previous line by removing the "&" character and
-line break. This allows long commands to be continued across two or
-more lines. See the discussion of triple quotes in (6) for how to
-continue a command across multiple line without using "&" characters.
-
-(2) All characters from the first "#" character onward are treated as
-comment and discarded. See an exception in (6). Note that a
-comment after a trailing "&" character will prevent the command from
-continuing on the next line. Also note that for multi-line commands a
-single leading "#" will comment out the entire command.
-
-(3) The line is searched repeatedly for $ characters, which indicate
-variables that are replaced with a text string. See an exception in
-(6).
-
-If the $ is followed by curly brackets, then the variable name is the
-text inside the curly brackets. If no curly brackets follow the $,
-then the variable name is the single character immediately following
-the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and
-"x".
-
-How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable.html doc page for details.
-It can be a variable that stores multiple text strings, and return one
-of them. The returned text string can be multiple "words" (space
-separated) which will then be interpreted as multiple arguments in the
-input command. The variable can also store a numeric formula which
-will be evaluated and its numeric result returned as a string.
-
-As a special case, if the $ is followed by parenthesis, then the text
-inside the parenthesis is treated as an "immediate" variable and
-evaluated as an "equal-style variable"_variable.html. This is a way
-to use numeric formulas in an input script without having to assign
-them to variable names. For example, these 3 input script lines:
-
-variable X equal (xlo+xhi)/2+sqrt(v_area)
-region 1 block $X 2 INF INF EDGE EDGE
-variable X delete :pre
-
-can be replaced by
-
-region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
-
-so that you do not have to define (or discard) a temporary variable X.
-
-Additionally, the "immediate" variable expression may be followed by a
-colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
-The format string must be appropriate for a double-precision
-floating-point value. The format string is used to output the result
-of the variable expression evaluation. If a format string is not
-specified a high-precision "%.20g" is used as the default.
-
-This can be useful for formatting print output to a desired precion:
-
-print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
-
-Note that neither the curly-bracket or immediate form of variables can
-contain nested $ characters for other variables to substitute for.
-Thus you cannot do this:
-
-variable a equal 2
-variable b2 equal 4
-print "B2 = $\{b$a\}" :pre
-
-Nor can you specify this $($x-1.0) for an immediate variable, but
-you could use $(v_x-1.0), since the latter is valid syntax for an
-"equal-style variable"_variable.html.
-
-See the "variable"_variable.html command for more details of how
-strings are assigned to variables and evaluated, and how they can be
-used in input script commands.
-
-(4) The line is broken into "words" separated by whitespace (tabs,
-spaces). Note that words can thus contain letters, digits,
-underscores, or punctuation characters.
-
-(5) The first word is the command name. All successive words in the
-line are arguments.
-
-(6) If you want text with spaces to be treated as a single argument,
-it can be enclosed in either single or double or triple quotes. A
-long single argument enclosed in single or double quotes can span
-multiple lines if the "&" character is used, as described above. When
-the lines are concatenated together (and the "&" characters and line
-breaks removed), the text will become a single line. If you want
-multiple lines of an argument to retain their line breaks, the text
-can be enclosed in triple quotes, in which case "&" characters are not
-needed. For example:
-
-print "Volume = $v"
-print 'Volume = $v'
-if "$\{steps\} > 1000" then quit
-variable a string "red green blue &
- purple orange cyan"
-print """
-System volume = $v
-System temperature = $t
-""" :pre
-
-In each case, the single, double, or triple quotes are removed when
-the single argument they enclose is stored internally.
-
-See the "dump modify format"_dump_modify.html, "print"_print.html,
-"if"_if.html, and "python"_python.html commands for examples.
-
-A "#" or "$" character that is between quotes will not be treated as a
-comment indicator in (2) or substituted for as a variable in (3).
-
-NOTE: If the argument is itself a command that requires a quoted
-argument (e.g. using a "print"_print.html command as part of an
-"if"_if.html or "run every"_run.html command), then single, double, or
-triple quotes can be nested in the usual manner. See the doc pages
-for those commands for examples. Only one of level of nesting is
-allowed, but that should be sufficient for most use cases.
-
-:line
-
-3.3 Input script structure :h3,link(cmd_3)
-
-This section describes the structure of a typical LAMMPS input script.
-The examples directory in the LAMMPS distribution contains many sample
-input scripts; the corresponding problems are discussed on the
-"Examples"_Examples.html doc page, and animated on the "LAMMPS WWW
-Site"_lws.
-
-A LAMMPS input script typically has 4 parts:
-
-Initialization
-Atom definition
-Settings
-Run a simulation :ol
-
-The last 2 parts can be repeated as many times as desired. I.e. run a
-simulation, change some settings, run some more, etc. Each of the 4
-parts is now described in more detail. Remember that almost all the
-commands need only be used if a non-default value is desired.
-
-(1) Initialization
-
-Set parameters that need to be defined before atoms are created or
-read-in from a file.
-
-The relevant commands are "units"_units.html,
-"dimension"_dimension.html, "newton"_newton.html,
-"processors"_processors.html, "boundary"_boundary.html,
-"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
-
-If force-field parameters appear in the files that will be read, these
-commands tell LAMMPS what kinds of force fields are being used:
-"pair_style"_pair_style.html, "bond_style"_bond_style.html,
-"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
-"improper_style"_improper_style.html.
-
-(2) Atom definition
-
-There are 3 ways to define atoms in LAMMPS. Read them in from a data
-or restart file via the "read_data"_read_data.html or
-"read_restart"_read_restart.html commands. These files can contain
-molecular topology information. Or create atoms on a lattice (with no
-molecular topology), using these commands: "lattice"_lattice.html,
-"region"_region.html, "create_box"_create_box.html,
-"create_atoms"_create_atoms.html. The entire set of atoms can be
-duplicated to make a larger simulation using the
-"replicate"_replicate.html command.
-
-(3) Settings
-
-Once atoms and molecular topology are defined, a variety of settings
-can be specified: force field coefficients, simulation parameters,
-output options, etc.
-
-Force field coefficients are set by these commands (they can also be
-set in the read-in files): "pair_coeff"_pair_coeff.html,
-"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"improper_coeff"_improper_coeff.html,
-"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
-"special_bonds"_special_bonds.html.
-
-Various simulation parameters are set by these commands:
-"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
-"group"_group.html, "timestep"_timestep.html,
-"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
-"min_style"_min_style.html, "min_modify"_min_modify.html.
-
-Fixes impose a variety of boundary conditions, time integration, and
-diagnostic options. The "fix"_fix.html command comes in many flavors.
-
-Various computations can be specified for execution during a
-simulation using the "compute"_compute.html,
-"compute_modify"_compute_modify.html, and "variable"_variable.html
-commands.
-
-Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
-and "restart"_restart.html commands.
-
-(4) Run a simulation
-
-A molecular dynamics simulation is run using the "run"_run.html
-command. Energy minimization (molecular statics) is performed using
-the "minimize"_minimize.html command. A parallel tempering
-(replica-exchange) simulation can be run using the
-"temper"_temper.html command.
-
-:line
-
-3.4 Commands listed by category :link(cmd_4),h4
-
-This section lists core LAMMPS commands, grouped by category.
-The "next section"_#cmd_5 lists all commands alphabetically. The
-next section also includes (long) lists of style options for entries
-that appear in the following categories as a single command (fix,
-compute, pair, etc). Commands that are added by user packages are not
-included in the categories here, but they are in the next section.
-
-Initialization:
-
-"newton"_newton.html,
-"package"_package.html,
-"processors"_processors.html,
-"suffix"_suffix.html,
-"units"_units.html
-
-Setup simulation box:
-
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"create_box"_create_box.html,
-"dimension"_dimension.html,
-"lattice"_lattice.html,
-"region"_region.html
-
-Setup atoms:
-
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"displace_atoms"_displace_atoms.html,
-"group"_group.html,
-"mass"_mass.html,
-"molecule"_molecule.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"replicate"_replicate.html,
-"set"_set.html,
-"velocity"_velocity.html
-
-Force fields:
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"bond_write"_bond_write.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"special_bonds"_special_bonds.html
-
-Settings:
-
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"info"_info.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"partition"_partition.html,
-"reset_timestep"_reset_timestep.html,
-"run_style"_run_style.html,
-"timer"_timer.html,
-"timestep"_timestep.html
-
-Operations within timestepping (fixes) and diagnostics (computes):
-
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"uncompute"_uncompute.html,
-"unfix"_unfix.html
-
-Output:
-
-"dump image"_dump_image.html,
-"dump movie"_dump_image.html,
-"dump"_dump.html,
-"dump_modify"_dump_modify.html,
-"restart"_restart.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"undump"_undump.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html
-
-Actions:
-
-"minimize"_minimize.html,
-"neb"_neb.html,
-"prd"_prd.html,
-"rerun"_rerun.html,
-"run"_run.html,
-"tad"_tad.html,
-"temper"_temper.html
-
-Input script control:
-
-"clear"_clear.html,
-"echo"_echo.html,
-"if"_if.html,
-"include"_include.html,
-"jump"_jump.html,
-"label"_label.html,
-"log"_log.html,
-"next"_next.html,
-"print"_print.html,
-"python"_python.html,
-"quit"_quit.html,
-"shell"_shell.html,
-"variable"_variable.html
-
-:line
-
-3.5 Individual commands :h3,link(cmd_5),link(comm)
-
-This section lists all LAMMPS commands alphabetically, with a separate
-listing below of styles within certain commands. The "previous
-section"_#cmd_4 lists the same commands, grouped by category. Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built. Not all packages are included in a
-default LAMMPS build. These dependencies are listed as Restrictions
-in the command's documentation.
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"bond_write"_bond_write.html,
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"clear"_clear.html,
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.html,
-"create_box"_create_box.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"dimension"_dimension.html,
-"displace_atoms"_displace_atoms.html,
-"dump"_dump.html,
-"dump image"_dump_image.html,
-"dump_modify"_dump_modify.html,
-"dump movie"_dump_image.html,
-"echo"_echo.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"group"_group.html,
-"if"_if.html,
-"info"_info.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"include"_include.html,
-"jump"_jump.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"label"_label.html,
-"lattice"_lattice.html,
-"log"_log.html,
-"mass"_mass.html,
-"minimize"_minimize.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"molecule"_molecule.html,
-"neb"_neb.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"newton"_newton.html,
-"next"_next.html,
-"package"_package.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"partition"_partition.html,
-"prd"_prd.html,
-"print"_print.html,
-"processors"_processors.html,
-"python"_python.html,
-"quit"_quit.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"region"_region.html,
-"replicate"_replicate.html,
-"rerun"_rerun.html,
-"reset_ids"_reset_ids.html,
-"reset_timestep"_reset_timestep.html,
-"restart"_restart.html,
-"run"_run.html,
-"run_style"_run_style.html,
-"set"_set.html,
-"shell"_shell.html,
-"special_bonds"_special_bonds.html,
-"suffix"_suffix.html,
-"tad"_tad.html,
-"temper"_temper.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"timer"_timer.html,
-"timestep"_timestep.html,
-"uncompute"_uncompute.html,
-"undump"_undump.html,
-"unfix"_unfix.html,
-"units"_units.html,
-"variable"_variable.html,
-"velocity"_velocity.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html :tb(c=6,ea=c)
-
-These are additional commands in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"dump netcdf"_dump_netcdf.html,
-"dump netcdf/mpiio"_dump_netcdf.html,
-"dump vtk"_dump_vtk.html,
-"group2ndx"_group2ndx.html,
-"ndx2group"_group2ndx.html,
-"temper/grem"_temper_grem.html,
-"temper/npt"_temper_npt.html :tb(c=3,ea=c)
-
-:line
-
-Fix styles :h3
-
-See the "fix"_fix.html command for one-line descriptions of each style
-or click on the style itself for a full description. Some of the
-styles have accelerated versions, which can be used if LAMMPS is built
-with the "appropriate accelerated package"_Section_accelerate.html.
-This is indicated by additional letters in parenthesis: g = GPU, i =
-USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
-
-"adapt"_fix_adapt.html,
-"addforce"_fix_addforce.html,
-"append/atoms"_fix_append_atoms.html,
-"atom/swap"_fix_atom_swap.html,
-"aveforce"_fix_aveforce.html,
-"ave/atom"_fix_ave_atom.html,
-"ave/chunk"_fix_ave_chunk.html,
-"ave/correlate"_fix_ave_correlate.html,
-"ave/histo"_fix_ave_histo.html,
-"ave/histo/weight"_fix_ave_histo.html,
-"ave/time"_fix_ave_time.html,
-"balance"_fix_balance.html,
-"bond/break"_fix_bond_break.html,
-"bond/create"_fix_bond_create.html,
-"bond/swap"_fix_bond_swap.html,
-"box/relax"_fix_box_relax.html,
-"cmap"_fix_cmap.html,
-"controller"_fix_controller.html,
-"deform (k)"_fix_deform.html,
-"deposit"_fix_deposit.html,
-"drag"_fix_drag.html,
-"dt/reset"_fix_dt_reset.html,
-"efield"_fix_efield.html,
-"ehex"_fix_ehex.html,
-"enforce2d (k)"_fix_enforce2d.html,
-"evaporate"_fix_evaporate.html,
-"external"_fix_external.html,
-"freeze"_fix_freeze.html,
-"gcmc"_fix_gcmc.html,
-"gld"_fix_gld.html,
-"gravity (o)"_fix_gravity.html,
-"halt"_fix_halt.html,
-"heat"_fix_heat.html,
-"indent"_fix_indent.html,
-"latte"_fix_latte.html,
-"langevin (k)"_fix_langevin.html,
-"langevin/spin"_fix_langevin_spin.hmtl,
-"lineforce"_fix_lineforce.html,
-"momentum (k)"_fix_momentum.html,
-"move"_fix_move.html,
-"mscg"_fix_mscg.html,
-"msst"_fix_msst.html,
-"neb"_fix_neb.html,
-"nph (ko)"_fix_nh.html,
-"nphug (o)"_fix_nphug.html,
-"nph/asphere (o)"_fix_nph_asphere.html,
-"nph/body"_fix_nph_body.html,
-"nph/sphere (o)"_fix_nph_sphere.html,
-"npt (kio)"_fix_nh.html,
-"npt/asphere (o)"_fix_npt_asphere.html,
-"npt/body"_fix_npt_body.html,
-"npt/sphere (o)"_fix_npt_sphere.html,
-"nve (kio)"_fix_nve.html,
-"nve/asphere (i)"_fix_nve_asphere.html,
-"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
-"nve/body"_fix_nve_body.html,
-"nve/limit"_fix_nve_limit.html,
-"nve/line"_fix_nve_line.html,
-"nve/noforce"_fix_nve_noforce.html,
-"nve/sphere (o)"_fix_nve_sphere.html,
-"nve/spin"_fix_nve_spin.html,
-"nve/tri"_fix_nve_tri.html,
-"nvt (iko)"_fix_nh.html,
-"nvt/asphere (o)"_fix_nvt_asphere.html,
-"nvt/body"_fix_nvt_body.html,
-"nvt/sllod (io)"_fix_nvt_sllod.html,
-"nvt/sphere (o)"_fix_nvt_sphere.html,
-"oneway"_fix_oneway.html,
-"orient/bcc"_fix_orient.html,
-"orient/fcc"_fix_orient.html,
-"planeforce"_fix_planeforce.html,
-"poems"_fix_poems.html,
-"pour"_fix_pour.html,
-"precession/spin"_fix_precession_spin.html,
-"press/berendsen"_fix_press_berendsen.html,
-"print"_fix_print.html,
-"property/atom (k)"_fix_property_atom.html,
-"python/invoke"_fix_python_invoke.html,
-"python/move"_fix_python_move.html,
-"qeq/comb (o)"_fix_qeq_comb.html,
-"qeq/dynamic"_fix_qeq.html,
-"qeq/fire"_fix_qeq.html,
-"qeq/point"_fix_qeq.html,
-"qeq/shielded"_fix_qeq.html,
-"qeq/slater"_fix_qeq.html,
-"rattle"_fix_shake.html,
-"reax/bonds"_fix_reax_bonds.html,
-"recenter"_fix_recenter.html,
-"restrain"_fix_restrain.html,
-"rigid (o)"_fix_rigid.html,
-"rigid/nph (o)"_fix_rigid.html,
-"rigid/npt (o)"_fix_rigid.html,
-"rigid/nve (o)"_fix_rigid.html,
-"rigid/nvt (o)"_fix_rigid.html,
-"rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
-"setforce (k)"_fix_setforce.html,
-"shake"_fix_shake.html,
-"spring"_fix_spring.html,
-"spring/chunk"_fix_spring_chunk.html,
-"spring/rg"_fix_spring_rg.html,
-"spring/self"_fix_spring_self.html,
-"srd"_fix_srd.html,
-"store/force"_fix_store_force.html,
-"store/state"_fix_store_state.html,
-"temp/berendsen"_fix_temp_berendsen.html,
-"temp/csld"_fix_temp_csvr.html,
-"temp/csvr"_fix_temp_csvr.html,
-"temp/rescale"_fix_temp_rescale.html,
-"tfmc"_fix_tfmc.html,
-"thermal/conductivity"_fix_thermal_conductivity.html,
-"tmd"_fix_tmd.html,
-"ttm"_fix_ttm.html,
-"tune/kspace"_fix_tune_kspace.html,
-"vector"_fix_vector.html,
-"viscosity"_fix_viscosity.html,
-"viscous"_fix_viscous.html,
-"wall/body/polygon"_fix_wall_body_polygon.html,
-"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
-"wall/colloid"_fix_wall.html,
-"wall/gran"_fix_wall_gran.html,
-"wall/gran/region"_fix_wall_gran_region.html,
-"wall/harmonic"_fix_wall.html,
-"wall/lj1043"_fix_wall.html,
-"wall/lj126"_fix_wall.html,
-"wall/lj93 (k)"_fix_wall.html,
-"wall/piston"_fix_wall_piston.html,
-"wall/reflect (k)"_fix_wall_reflect.html,
-"wall/region"_fix_wall_region.html,
-"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
-
-These are additional fix styles in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"adapt/fep"_fix_adapt_fep.html,
-"addtorque"_fix_addtorque.html,
-"atc"_fix_atc.html,
-"ave/correlate/long"_fix_ave_correlate_long.html,
-"bond/react"_fix_bond_react.html,
-"colvars"_fix_colvars.html,
-"dpd/energy (k)"_fix_dpd_energy.html,
-"drude"_fix_drude.html,
-"drude/transform/direct"_fix_drude_transform.html,
-"drude/transform/reverse"_fix_drude_transform.html,
-"edpd/source"_fix_dpd_source.html,
-"eos/cv"_fix_eos_cv.html,
-"eos/table"_fix_eos_table.html,
-"eos/table/rx (k)"_fix_eos_table_rx.html,
-"filter/corotate"_fix_filter_corotate.html,
-"flow/gauss"_fix_flow_gauss.html,
-"gle"_fix_gle.html,
-"grem"_fix_grem.html,
-"imd"_fix_imd.html,
-"ipi"_fix_ipi.html,
-"langevin/drude"_fix_langevin_drude.html,
-"langevin/eff"_fix_langevin_eff.html,
-"lb/fluid"_fix_lb_fluid.html,
-"lb/momentum"_fix_lb_momentum.html,
-"lb/pc"_fix_lb_pc.html,
-"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
-"lb/viscous"_fix_lb_viscous.html,
-"meso"_fix_meso.html,
-"manifoldforce"_fix_manifoldforce.html,
-"meso/stationary"_fix_meso_stationary.html,
-"mvv/dpd"_fix_mvv_dpd.html,
-"mvv/edpd"_fix_mvv_dpd.html,
-"mvv/tdpd"_fix_mvv_dpd.html,
-"nph/eff"_fix_nh_eff.html,
-"npt/eff"_fix_nh_eff.html,
-"npt/uef"_fix_nh_uef.html,
-"nve/dot"_fix_nve_dot.html,
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
-"nve/eff"_fix_nve_eff.html,
-"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
-"nvk"_fix_nvk.html,
-"nvt/eff"_fix_nh_eff.html,
-"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
-"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
-"nvt/uef"_fix_nh_uef.html,
-"phonon"_fix_phonon.html,
-"pimd"_fix_pimd.html,
-"qbmsst"_fix_qbmsst.html,
-"qeq/reax (ko)"_fix_qeq_reax.html,
-"qmmm"_fix_qmmm.html,
-"qtb"_fix_qtb.html,
-"reax/c/bonds (k)"_fix_reax_bonds.html,
-"reax/c/species (k)"_fix_reaxc_species.html,
-"rhok"_fix_rhok.html,
-"rx (k)"_fix_rx.html,
-"saed/vtk"_fix_saed_vtk.html,
-"shardlow (k)"_fix_shardlow.html,
-"smd"_fix_smd.html,
-"smd/adjust/dt"_fix_smd_adjust_dt.html,
-"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
-"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
-"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
-"smd/setvel"_fix_smd_setvel.html,
-"smd/wall/surface"_fix_smd_wall_surface.html,
-"tdpd/source"_fix_dpd_source.html,
-"temp/rescale/eff"_fix_temp_rescale_eff.html,
-"ti/spring"_fix_ti_spring.html,
-"ttm/mod"_fix_ttm.html,
-"wall/ees"_fix_wall_ees.html,
-"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)
-
-:line
-
-Compute styles :h3
-
-See the "compute"_compute.html command for one-line descriptions of
-each style or click on the style itself for a full description. Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"aggregate/atom"_compute_cluster_atom.html,
-"angle"_compute_angle.html,
-"angle/local"_compute_angle_local.html,
-"angmom/chunk"_compute_angmom_chunk.html,
-"body/local"_compute_body_local.html,
-"bond"_compute_bond.html,
-"bond/local"_compute_bond_local.html,
-"centro/atom"_compute_centro_atom.html,
-"chunk/atom"_compute_chunk_atom.html,
-"cluster/atom"_compute_cluster_atom.html,
-"cna/atom"_compute_cna_atom.html,
-"com"_compute_com.html,
-"com/chunk"_compute_com_chunk.html,
-"contact/atom"_compute_contact_atom.html,
-"coord/atom"_compute_coord_atom.html,
-"damage/atom"_compute_damage_atom.html,
-"dihedral"_compute_dihedral.html,
-"dihedral/local"_compute_dihedral_local.html,
-"dilatation/atom"_compute_dilatation_atom.html,
-"dipole/chunk"_compute_dipole_chunk.html,
-"displace/atom"_compute_displace_atom.html,
-"erotate/asphere"_compute_erotate_asphere.html,
-"erotate/rigid"_compute_erotate_rigid.html,
-"erotate/sphere"_compute_erotate_sphere.html,
-"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
-"event/displace"_compute_event_displace.html,
-"fragment/atom"_compute_cluster_atom.html,
-"global/atom"_compute_global_atom.html,
-"group/group"_compute_group_group.html,
-"gyration"_compute_gyration.html,
-"gyration/chunk"_compute_gyration_chunk.html,
-"heat/flux"_compute_heat_flux.html,
-"hexorder/atom"_compute_hexorder_atom.html,
-"improper"_compute_improper.html,
-"improper/local"_compute_improper_local.html,
-"inertia/chunk"_compute_inertia_chunk.html,
-"ke"_compute_ke.html,
-"ke/atom"_compute_ke_atom.html,
-"ke/rigid"_compute_ke_rigid.html,
-"msd"_compute_msd.html,
-"msd/chunk"_compute_msd_chunk.html,
-"msd/nongauss"_compute_msd_nongauss.html,
-"omega/chunk"_compute_omega_chunk.html,
-"orientorder/atom"_compute_orientorder_atom.html,
-"pair"_compute_pair.html,
-"pair/local"_compute_pair_local.html,
-"pe"_compute_pe.html,
-"pe/atom"_compute_pe_atom.html,
-"plasticity/atom"_compute_plasticity_atom.html,
-"pressure"_compute_pressure.html,
-"property/atom"_compute_property_atom.html,
-"property/local"_compute_property_local.html,
-"property/chunk"_compute_property_chunk.html,
-"rdf"_compute_rdf.html,
-"reduce"_compute_reduce.html,
-"reduce/region"_compute_reduce.html,
-"rigid/local"_compute_rigid_local.html,
-"slice"_compute_slice.html,
-"sna/atom"_compute_sna_atom.html,
-"snad/atom"_compute_sna_atom.html,
-"snav/atom"_compute_sna_atom.html,
-"spin"_compute_spin.html,
-"stress/atom"_compute_stress_atom.html,
-"temp (k)"_compute_temp.html,
-"temp/asphere"_compute_temp_asphere.html,
-"temp/body"_compute_temp_body.html,
-"temp/chunk"_compute_temp_chunk.html,
-"temp/com"_compute_temp_com.html,
-"temp/deform"_compute_temp_deform.html,
-"temp/partial"_compute_temp_partial.html,
-"temp/profile"_compute_temp_profile.html,
-"temp/ramp"_compute_temp_ramp.html,
-"temp/region"_compute_temp_region.html,
-"temp/sphere"_compute_temp_sphere.html,
-"ti"_compute_ti.html,
-"torque/chunk"_compute_torque_chunk.html,
-"vacf"_compute_vacf.html,
-"vcm/chunk"_compute_vcm_chunk.html,
-"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c)
-
-These are additional compute styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"ackland/atom"_compute_ackland_atom.html,
-"basal/atom"_compute_basal_atom.html,
-"cnp/atom"_compute_cnp_atom.html,
-"dpd"_compute_dpd.html,
-"dpd/atom"_compute_dpd_atom.html,
-"edpd/temp/atom"_compute_edpd_temp_atom.html,
-"entropy/atom"_compute_entropy_atom.html,
-"fep"_compute_fep.html,
-"force/tally"_compute_tally.html,
-"heat/flux/tally"_compute_tally.html,
-"ke/eff"_compute_ke_eff.html,
-"ke/atom/eff"_compute_ke_atom_eff.html,
-"meso/e/atom"_compute_meso_e_atom.html,
-"meso/rho/atom"_compute_meso_rho_atom.html,
-"meso/t/atom"_compute_meso_t_atom.html,
-"pe/tally"_compute_tally.html,
-"pe/mol/tally"_compute_tally.html,
-"pressure/uef"_compute_pressure_uef.html,
-"saed"_compute_saed.html,
-"smd/contact/radius"_compute_smd_contact_radius.html,
-"smd/damage"_compute_smd_damage.html,
-"smd/hourglass/error"_compute_smd_hourglass_error.html,
-"smd/internal/energy"_compute_smd_internal_energy.html,
-"smd/plastic/strain"_compute_smd_plastic_strain.html,
-"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
-"smd/rho"_compute_smd_rho.html,
-"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
-"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
-"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
-"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
-"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
-"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
-"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
-"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
-"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
-"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
-"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
-"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
-"smd/vol"_compute_smd_vol.html,
-"stress/tally"_compute_tally.html,
-"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
-"temp/drude"_compute_temp_drude.html,
-"temp/eff"_compute_temp_eff.html,
-"temp/deform/eff"_compute_temp_deform_eff.html,
-"temp/region/eff"_compute_temp_region_eff.html,
-"temp/rotate"_compute_temp_rotate.html,
-"temp/uef"_compute_temp_uef.html,
-"xrd"_compute_xrd.html :tb(c=6,ea=c)
-
-:line
-
-Pair_style potentials :h3
-
-See the "pair_style"_pair_style.html command for an overview of pair
-potentials. Click on the style itself for a full description. Many
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_pair_none.html,
-"zero"_pair_zero.html,
-"hybrid"_pair_hybrid.html,
-"hybrid/overlay (k)"_pair_hybrid.html,
-"adp (o)"_pair_adp.html,
-"airebo (oi)"_pair_airebo.html,
-"airebo/morse (oi)"_pair_airebo.html,
-"atm"_pair_atm.html,
-"beck (go)"_pair_beck.html,
-"body/nparticle"_pair_body_nparticle.html,
-"body/rounded/polygon"_pair_body_rounded/polygon.html,
-"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html,
-"bop"_pair_bop.html,
-"born (go)"_pair_born.html,
-"born/coul/dsf"_pair_born.html,
-"born/coul/dsf/cs"_pair_born.html,
-"born/coul/long (go)"_pair_born.html,
-"born/coul/long/cs"_pair_born.html,
-"born/coul/msm (o)"_pair_born.html,
-"born/coul/wolf (go)"_pair_born.html,
-"born/coul/wolf/cs"_pair_born.html,
-"brownian (o)"_pair_brownian.html,
-"brownian/poly (o)"_pair_brownian.html,
-"buck (giko)"_pair_buck.html,
-"buck/coul/cut (giko)"_pair_buck.html,
-"buck/coul/long (giko)"_pair_buck.html,
-"buck/coul/long/cs"_pair_buck.html,
-"buck/coul/msm (o)"_pair_buck.html,
-"buck/long/coul/long (o)"_pair_buck_long.html,
-"colloid (go)"_pair_colloid.html,
-"comb (o)"_pair_comb.html,
-"comb3"_pair_comb.html,
-"coul/cut (gko)"_pair_coul.html,
-"coul/debye (gko)"_pair_coul.html,
-"coul/dsf (gko)"_pair_coul.html,
-"coul/long (gko)"_pair_coul.html,
-"coul/long/cs"_pair_coul.html,
-"coul/msm"_pair_coul.html,
-"coul/streitz"_pair_coul.html,
-"coul/wolf (ko)"_pair_coul.html,
-"coul/wolf/cs"_pair_coul.html,
-"dpd (gio)"_pair_dpd.html,
-"dpd/tstat (go)"_pair_dpd.html,
-"dsmc"_pair_dsmc.html,
-"eam (gikot)"_pair_eam.html,
-"eam/alloy (gikot)"_pair_eam.html,
-"eam/fs (gikot)"_pair_eam.html,
-"eim (o)"_pair_eim.html,
-"gauss (go)"_pair_gauss.html,
-"gayberne (gio)"_pair_gayberne.html,
-"gran/hertz/history (o)"_pair_gran.html,
-"gran/hooke (o)"_pair_gran.html,
-"gran/hooke/history (o)"_pair_gran.html,
-"gw"_pair_gw.html,
-"gw/zbl"_pair_gw.html,
-"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
-"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
-"kim"_pair_kim.html,
-"lcbop"_pair_lcbop.html,
-"line/lj"_pair_line_lj.html,
-"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
-"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (giko)"_pair_charmm.html,
-"lj/charmm/coul/msm"_pair_charmm.html,
-"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
-"lj/charmmfsw/coul/long"_pair_charmm.html,
-"lj/class2 (gko)"_pair_class2.html,
-"lj/class2/coul/cut (ko)"_pair_class2.html,
-"lj/class2/coul/long (gko)"_pair_class2.html,
-"lj/cubic (go)"_pair_lj_cubic.html,
-"lj/cut (gikot)"_pair_lj.html,
-"lj/cut/coul/cut (gko)"_pair_lj.html,
-"lj/cut/coul/debye (gko)"_pair_lj.html,
-"lj/cut/coul/dsf (gko)"_pair_lj.html,
-"lj/cut/coul/long (gikot)"_pair_lj.html,
-"lj/cut/coul/long/cs"_pair_lj.html,
-"lj/cut/coul/msm (go)"_pair_lj.html,
-"lj/cut/coul/wolf (o)"_pair_lj.html,
-"lj/cut/dipole/cut (go)"_pair_dipole.html,
-"lj/cut/dipole/long"_pair_dipole.html,
-"lj/cut/tip4p/cut (o)"_pair_lj.html,
-"lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/expand (gko)"_pair_lj_expand.html,
-"lj/gromacs (gko)"_pair_gromacs.html,
-"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (io)"_pair_lj_long.html,
-"lj/long/dipole/long"_pair_dipole.html,
-"lj/long/tip4p/long"_pair_lj_long.html,
-"lj/smooth (o)"_pair_lj_smooth.html,
-"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
-"lj96/cut (go)"_pair_lj96.html,
-"lubricate (o)"_pair_lubricate.html,
-"lubricate/poly (o)"_pair_lubricate.html,
-"lubricateU"_pair_lubricateU.html,
-"lubricateU/poly"_pair_lubricateU.html,
-"meam"_pair_meam.html,
-"mie/cut (o)"_pair_mie.html,
-"morse (gkot)"_pair_morse.html,
-"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
-"nm/cut (o)"_pair_nm.html,
-"nm/cut/coul/cut (o)"_pair_nm.html,
-"nm/cut/coul/long (o)"_pair_nm.html,
-"peri/eps"_pair_peri.html,
-"peri/lps (o)"_pair_peri.html,
-"peri/pmb (o)"_pair_peri.html,
-"peri/ves"_pair_peri.html,
-"polymorphic"_pair_polymorphic.html,
-"python"_pair_python.html,
-"reax"_pair_reax.html,
-"rebo (oi)"_pair_airebo.html,
-"resquared (go)"_pair_resquared.html,
-"snap (k)"_pair_snap.html,
-"soft (go)"_pair_soft.html,
-"sw (giko)"_pair_sw.html,
-"spin/dmi"_pair_spin_dmi.html,
-"spin/exchange"_pair_spin_exchange.html,
-"spin/magelec"_pair_spin_magelec.html,
-"spin/neel"_pair_spin_neel.html,
-"table (gko)"_pair_table.html,
-"tersoff (giko)"_pair_tersoff.html,
-"tersoff/mod (gko)"_pair_tersoff_mod.html,
-"tersoff/mod/c (o)"_pair_tersoff_mod.html,
-"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
-"tip4p/cut (o)"_pair_coul.html,
-"tip4p/long (o)"_pair_coul.html,
-"tri/lj"_pair_tri_lj.html,
-"ufm (got)"_pair_ufm.html,
-"vashishta (ko)"_pair_vashishta.html,
-"vashishta/table (o)"_pair_vashishta.html,
-"yukawa (gok)"_pair_yukawa.html,
-"yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
-
-These are additional pair styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"agni (o)"_pair_agni.html,
-"awpmd/cut"_pair_awpmd.html,
-"buck/mdf"_pair_mdf.html,
-"coul/cut/soft (o)"_pair_lj_soft.html,
-"coul/diel (o)"_pair_coul_diel.html,
-"coul/long/soft (o)"_pair_lj_soft.html,
-"coul/shield"_pair_coul_shield.html,
-"dpd/fdt"_pair_dpd_fdt.html,
-"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
-"eam/cd (o)"_pair_eam.html,
-"edip (o)"_pair_edip.html,
-"edip/multi"_pair_edip.html,
-"edpd"_pair_meso.html,
-"eff/cut"_pair_eff.html,
-"exp6/rx (k)"_pair_exp6_rx.html,
-"extep"_pair_extep.html,
-"gauss/cut"_pair_gauss.html,
-"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
-"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
-"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
-"lennard/mdf"_pair_mdf.html,
-"list"_pair_list.html,
-"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
-"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
-"lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/thole/long (o)"_pair_thole.html,
-"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
-"lj/mdf"_pair_mdf.html,
-"lj/sdk (gko)"_pair_sdk.html,
-"lj/sdk/coul/long (go)"_pair_sdk.html,
-"lj/sdk/coul/msm (o)"_pair_sdk.html,
-"mdpd"_pair_meso.html,
-"mdpd/rhosum"_pair_meso.html,
-"meam/c"_pair_meam.html,
-"meam/spline (o)"_pair_meam_spline.html,
-"meam/sw/spline"_pair_meam_sw_spline.html,
-"mgpt"_pair_mgpt.html,
-"momb"_pair_momb.html,
-"morse/smooth/linear"_pair_morse.html,
-"morse/soft"_pair_morse.html,
-"multi/lucy"_pair_multi_lucy.html,
-"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
-"oxdna/coaxstk"_pair_oxdna.html,
-"oxdna/excv"_pair_oxdna.html,
-"oxdna/hbond"_pair_oxdna.html,
-"oxdna/stk"_pair_oxdna.html,
-"oxdna/xstk"_pair_oxdna.html,
-"oxdna2/coaxstk"_pair_oxdna2.html,
-"oxdna2/dh"_pair_oxdna2.html,
-"oxdna2/excv"_pair_oxdna2.html,
-"oxdna2/stk"_pair_oxdna2.html,
-"quip"_pair_quip.html,
-"reax/c (ko)"_pair_reaxc.html,
-"smd/hertz"_pair_smd_hertz.html,
-"smd/tlsph"_pair_smd_tlsph.html,
-"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
-"smd/ulsph"_pair_smd_ulsph.html,
-"smtbq"_pair_smtbq.html,
-"snap (k)"_pair_snap.html,
-"sph/heatconduction"_pair_sph_heatconduction.html,
-"sph/idealgas"_pair_sph_idealgas.html,
-"sph/lj"_pair_sph_lj.html,
-"sph/rhosum"_pair_sph_rhosum.html,
-"sph/taitwater"_pair_sph_taitwater.html,
-"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
-"srp"_pair_srp.html,
-"table/rx (k)"_pair_table_rx.html,
-"tdpd"_pair_meso.html,
-"tersoff/table (o)"_pair_tersoff.html,
-"thole"_pair_thole.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
-
-:line
-
-Bond_style potentials :h3
-
-See the "bond_style"_bond_style.html command for an overview of bond
-potentials. Click on the style itself for a full description. Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_bond_none.html,
-"zero"_bond_zero.html,
-"hybrid"_bond_hybrid.html,
-"class2 (ko)"_bond_class2.html,
-"fene (iko)"_bond_fene.html,
-"fene/expand (o)"_bond_fene_expand.html,
-"gromos (o)"_bond_gromos.html,
-"harmonic (ko)"_bond_harmonic.html,
-"morse (o)"_bond_morse.html,
-"nonlinear (o)"_bond_nonlinear.html,
-"quartic (o)"_bond_quartic.html,
-"table (o)"_bond_table.html :tb(c=4,ea=c)
-
-These are additional bond styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"oxdna/fene"_bond_oxdna.html,
-"oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c)
-
-:line
-
-Angle_style potentials :h3
-
-See the "angle_style"_angle_style.html command for an overview of
-angle potentials. Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"none"_angle_none.html,
-"zero"_angle_zero.html,
-"hybrid"_angle_hybrid.html,
-"charmm (ko)"_angle_charmm.html,
-"class2 (ko)"_angle_class2.html,
-"cosine (o)"_angle_cosine.html,
-"cosine/delta (o)"_angle_cosine_delta.html,
-"cosine/periodic (o)"_angle_cosine_periodic.html,
-"cosine/squared (o)"_angle_cosine_squared.html,
-"harmonic (iko)"_angle_harmonic.html,
-"table (o)"_angle_table.html :tb(c=4,ea=c)
-
-These are additional angle styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift (o)"_angle_cosine_shift.html,
-"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
-"dipole (o)"_angle_dipole.html,
-"fourier (o)"_angle_fourier.html,
-"fourier/simple (o)"_angle_fourier_simple.html,
-"quartic (o)"_angle_quartic.html,
-"sdk"_angle_sdk.html :tb(c=4,ea=c)
-
-:line
-
-Dihedral_style potentials :h3
-
-See the "dihedral_style"_dihedral_style.html command for an overview
-of dihedral potentials. Click on the style itself for a full
-description. Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"none"_dihedral_none.html,
-"zero"_dihedral_zero.html,
-"hybrid"_dihedral_hybrid.html,
-"charmm (iko)"_dihedral_charmm.html,
-"charmmfsw"_dihedral_charmm.html,
-"class2 (ko)"_dihedral_class2.html,
-"harmonic (io)"_dihedral_harmonic.html,
-"helix (o)"_dihedral_helix.html,
-"multi/harmonic (o)"_dihedral_multi_harmonic.html,
-"opls (iko)"_dihedral_opls.html :tb(c=4,ea=c)
-
-These are additional dihedral styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (io)"_dihedral_fourier.html,
-"nharmonic (o)"_dihedral_nharmonic.html,
-"quadratic (o)"_dihedral_quadratic.html,
-"spherical (o)"_dihedral_spherical.html,
-"table (o)"_dihedral_table.html,
-"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
-
-:line
-
-Improper_style potentials :h3
-
-See the "improper_style"_improper_style.html command for an overview
-of improper potentials. Click on the style itself for a full
-description. Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"none"_improper_none.html,
-"zero"_improper_zero.html,
-"hybrid"_improper_hybrid.html,
-"class2 (ko)"_improper_class2.html,
-"cvff (io)"_improper_cvff.html,
-"harmonic (iko)"_improper_harmonic.html,
-"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
-
-These are additional improper styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cossq (o)"_improper_cossq.html,
-"distance"_improper_distance.html,
-"fourier (o)"_improper_fourier.html,
-"ring (o)"_improper_ring.html :tb(c=4,ea=c)
-
-:line
-
-Kspace solvers :h3
-
-See the "kspace_style"_kspace_style.html command for an overview of
-Kspace solvers. Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"ewald (o)"_kspace_style.html,
-"ewald/disp"_kspace_style.html,
-"msm (o)"_kspace_style.html,
-"msm/cg (o)"_kspace_style.html,
-"pppm (gok)"_kspace_style.html,
-"pppm/cg (o)"_kspace_style.html,
-"pppm/disp (i)"_kspace_style.html,
-"pppm/disp/tip4p"_kspace_style.html,
-"pppm/stagger"_kspace_style.html,
-"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/src/Section_history.txt b/doc/src/Section_history.txt
deleted file mode 100644
index 6bbd1e4d99a8d02e89147b5a240f1479252c2940..0000000000000000000000000000000000000000
--- a/doc/src/Section_history.txt
+++ /dev/null
@@ -1,135 +0,0 @@
-"Previous Section"_Errors.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Manual.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-13. Future and history :h2
-
-This section lists features we plan to add to LAMMPS, features of
-previous versions of LAMMPS, and features of other parallel molecular
-dynamics codes our group has distributed.
-
-13.1 "Coming attractions"_#hist_1
-13.2 "Past versions"_#hist_2 :all(b)
-
-:line
-:line
-
-13.1 Coming attractions :h3,link(hist_1)
-
-As of summer 2016 we are using the "LAMMPS project issue tracker
-on GitHub"_https://github.com/lammps/lammps/issues for keeping
-track of suggested, planned or pending new features. This includes
-discussions of how to best implement them, or why they would be
-useful. Especially if a planned or proposed feature is non-trivial
-to add, e.g. because it requires changes to some of the core
-classes of LAMMPS, people planning to contribute a new feature to
-LAMMS are encouraged to submit an issue about their planned
-implementation this way in order to receive feedback from the
-LAMMPS core developers. They will provide suggestions about
-the validity of the proposed approach and possible improvements,
-pitfalls or alternatives.
-
-Please see some of the closed issues for examples of how to
-suggest code enhancements, submit proposed changes, or report
-possible bugs and how they are resolved.
-
-As an alternative to using GitHub, you may e-mail the
-"core developers"_http://lammps.sandia.gov/authors.html or send
-an e-mail to the "LAMMPS Mail list"_http://lammps.sandia.gov/mail.html
-if you want to have your suggestion added to the list.
-
-:line
-
-13.2 Past versions :h3,link(hist_2)
-
-LAMMPS development began in the mid 1990s under a cooperative research
-& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
-and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
-to develop a large-scale parallel classical MD code; the coding effort
-was led by Steve Plimpton at Sandia.
-
-After the CRADA ended, a final F77 version, LAMMPS 99, was
-released. As development of LAMMPS continued at Sandia, its memory
-management was converted to F90; a final F90 version was released as
-LAMMPS 2001.
-
-The current LAMMPS is a rewrite in C++ and was first publicly released
-as an open source code in 2004. It includes many new features beyond
-those in LAMMPS 99 or 2001. It also includes features from older
-parallel MD codes written at Sandia, namely ParaDyn, Warp, and
-GranFlow (see below).
-
-In late 2006 we began merging new capabilities into LAMMPS that were
-developed by Aidan Thompson at Sandia for his MD code GRASP, which has
-a parallel framework similar to LAMMPS. Most notably, these have
-included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
-and the associated charge-equilibration routines needed for ReaxFF.
-
-The "History link"_http://lammps.sandia.gov/history.html on the
-LAMMPS WWW page gives a timeline of features added to the
-C++ open-source version of LAMMPS over the last several years.
-
-These older codes are available for download from the "LAMMPS WWW
-site"_lws, except for Warp & GranFlow which were primarily used
-internally. A brief listing of their features is given here.
-
-LAMMPS 2001
-
- F90 + MPI
- dynamic memory
- spatial-decomposition parallelism
- NVE, NVT, NPT, NPH, rRESPA integrators
- LJ and Coulombic pairwise force fields
- all-atom, united-atom, bead-spring polymer force fields
- CHARMM-compatible force fields
- class 2 force fields
- 3d/2d Ewald & PPPM
- various force and temperature constraints
- SHAKE
- Hessian-free truncated-Newton minimizer
- user-defined diagnostics :ul
-
-LAMMPS 99
-
- F77 + MPI
- static memory allocation
- spatial-decomposition parallelism
- most of the LAMMPS 2001 features with a few exceptions
- no 2d Ewald & PPPM
- molecular force fields are missing a few CHARMM terms
- no SHAKE :ul
-
-Warp
-
- F90 + MPI
- spatial-decomposition parallelism
- embedded atom method (EAM) metal potentials + LJ
- lattice and grain-boundary atom creation
- NVE, NVT integrators
- boundary conditions for applying shear stresses
- temperature controls for actively sheared systems
- per-atom energy and centro-symmetry computation and output :ul
-
-ParaDyn
-
- F77 + MPI
- atom- and force-decomposition parallelism
- embedded atom method (EAM) metal potentials
- lattice atom creation
- NVE, NVT, NPT integrators
- all serial DYNAMO features for controls and constraints :ul
-
-GranFlow
-
- F90 + MPI
- spatial-decomposition parallelism
- frictional granular potentials
- NVE integrator
- boundary conditions for granular flow and packing and walls
- particle insertion :ul
diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
deleted file mode 100644
index 3c5fe47057d3cbca85e60f0ffe7aab4fd0ecee56..0000000000000000000000000000000000000000
--- a/doc/src/Section_howto.txt
+++ /dev/null
@@ -1,3011 +0,0 @@
-"Previous Section"_Section_accelerate.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Examples.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-6. How-to discussions :h2
-
-This section describes how to perform common tasks using LAMMPS.
-
-6.1 "Restarting a simulation"_#howto_1
-6.2 "2d simulations"_#howto_2
-6.3 "CHARMM, AMBER, and DREIDING force fields"_#howto_3
-6.4 "Running multiple simulations from one input script"_#howto_4
-6.5 "Multi-replica simulations"_#howto_5
-6.6 "Granular models"_#howto_6
-6.7 "TIP3P water model"_#howto_7
-6.8 "TIP4P water model"_#howto_8
-6.9 "SPC water model"_#howto_9
-6.10 "Coupling LAMMPS to other codes"_#howto_10
-6.11 "Visualizing LAMMPS snapshots"_#howto_11
-6.12 "Triclinic (non-orthogonal) simulation boxes"_#howto_12
-6.13 "NEMD simulations"_#howto_13
-6.14 "Finite-size spherical and aspherical particles"_#howto_14
-6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#howto_15
-6.16 "Thermostatting, barostatting and computing temperature"_#howto_16
-6.17 "Walls"_#howto_17
-6.18 "Elastic constants"_#howto_18
-6.19 "Library interface to LAMMPS"_#howto_19
-6.20 "Calculating thermal conductivity"_#howto_20
-6.21 "Calculating viscosity"_#howto_21
-6.22 "Calculating a diffusion coefficient"_#howto_22
-6.23 "Using chunks to calculate system properties"_#howto_23
-6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24
-6.25 "Polarizable models"_#howto_25
-6.26 "Adiabatic core/shell model"_#howto_26
-6.27 "Drude induced dipoles"_#howto_27
-6.28 "Magnetic spins"_#howto_28 :all(b)
-
-The example input scripts included in the LAMMPS distribution and
-highlighted on the "Examples"_Examples.html doc page also show how to
-setup and run various kinds of simulations.
-
-:line
-:line
-
-6.1 Restarting a simulation :link(howto_1),h4
-
-There are 3 ways to continue a long LAMMPS simulation. Multiple
-"run"_run.html commands can be used in the same input script. Each
-run will continue from where the previous run left off. Or binary
-restart files can be saved to disk using the "restart"_restart.html
-command. At a later time, these binary files can be read via a
-"read_restart"_read_restart.html command in a new script. Or they can
-be converted to text data files using the "-r command-line
-switch"_Section_start.html#start_6 and read by a
-"read_data"_read_data.html command in a new script.
-
-Here we give examples of 2 scripts that read either a binary restart
-file or a converted data file and then issue a new run command to
-continue where the previous run left off. They illustrate what
-settings must be made in the new script. Details are discussed in the
-documentation for the "read_restart"_read_restart.html and
-"read_data"_read_data.html commands.
-
-Look at the {in.chain} input script provided in the {bench} directory
-of the LAMMPS distribution to see the original script that these 2
-scripts are based on. If that script had the line
-
-restart 50 tmp.restart :pre
-
-added to it, it would produce 2 binary restart files (tmp.restart.50
-and tmp.restart.100) as it ran.
-
-This script could be used to read the 1st restart file and re-run the
-last 50 timesteps:
-
-read_restart tmp.restart.50 :pre
-
-neighbor 0.4 bin
-neigh_modify every 1 delay 1 :pre
-
-fix 1 all nve
-fix 2 all langevin 1.0 1.0 10.0 904297 :pre
-
-timestep 0.012 :pre
-
-run 50 :pre
-
-Note that the following commands do not need to be repeated because
-their settings are included in the restart file: {units, atom_style,
-special_bonds, pair_style, bond_style}. However these commands do
-need to be used, since their settings are not in the restart file:
-{neighbor, fix, timestep}.
-
-If you actually use this script to perform a restarted run, you will
-notice that the thermodynamic data match at step 50 (if you also put a
-"thermo 50" command in the original script), but do not match at step
-100. This is because the "fix langevin"_fix_langevin.html command
-uses random numbers in a way that does not allow for perfect restarts.
-
-As an alternate approach, the restart file could be converted to a data
-file as follows:
-
-lmp_g++ -r tmp.restart.50 tmp.restart.data :pre
-
-Then, this script could be used to re-run the last 50 steps:
-
-units lj
-atom_style bond
-pair_style lj/cut 1.12
-pair_modify shift yes
-bond_style fene
-special_bonds 0.0 1.0 1.0 :pre
-
-read_data tmp.restart.data :pre
-
-neighbor 0.4 bin
-neigh_modify every 1 delay 1 :pre
-
-fix 1 all nve
-fix 2 all langevin 1.0 1.0 10.0 904297 :pre
-
-timestep 0.012 :pre
-
-reset_timestep 50
-run 50 :pre
-
-Note that nearly all the settings specified in the original {in.chain}
-script must be repeated, except the {pair_coeff} and {bond_coeff}
-commands since the new data file lists the force field coefficients.
-Also, the "reset_timestep"_reset_timestep.html command is used to tell
-LAMMPS the current timestep. This value is stored in restart files,
-but not in data files.
-
-:line
-
-6.2 2d simulations :link(howto_2),h4
-
-Use the "dimension"_dimension.html command to specify a 2d simulation.
-
-Make the simulation box periodic in z via the "boundary"_boundary.html
-command. This is the default.
-
-If using the "create box"_create_box.html command to define a
-simulation box, set the z dimensions narrow, but finite, so that the
-create_atoms command will tile the 3d simulation box with a single z
-plane of atoms - e.g.
-
-"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre
-
-If using the "read data"_read_data.html command to read in a file of
-atom coordinates, set the "zlo zhi" values to be finite but narrow,
-similar to the create_box command settings just described. For each
-atom in the file, assign a z coordinate so it falls inside the
-z-boundaries of the box - e.g. 0.0.
-
-Use the "fix enforce2d"_fix_enforce2d.html command as the last
-defined fix to insure that the z-components of velocities and forces
-are zeroed out every timestep. The reason to make it the last fix is
-so that any forces induced by other fixes will be zeroed out.
-
-Many of the example input scripts included in the LAMMPS distribution
-are for 2d models.
-
-NOTE: Some models in LAMMPS treat particles as finite-size spheres, as
-opposed to point particles. See the "atom_style
-sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html
-commands for details. By default, for 2d simulations, such particles
-will still be modeled as 3d spheres, not 2d discs (circles), meaning
-their moment of inertia will be that of a sphere. If you wish to
-model them as 2d discs, see the "set density/disc"_set.html command
-and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html,
-"fix nvt/sphere"_fix_nvt_sphere.html, "fix
-nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html
-commands.
-
-:line
-
-6.3 CHARMM, AMBER, and DREIDING force fields :link(howto_3),h4
-
-A force field has 2 parts: the formulas that define it and the
-coefficients used for a particular system. Here we only discuss
-formulas implemented in LAMMPS that correspond to formulas commonly
-used in the CHARMM, AMBER, and DREIDING force fields. Setting
-coefficients is done in the input data file via the
-"read_data"_read_data.html command or in the input script with
-commands like "pair_coeff"_pair_coeff.html or
-"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for
-additional tools that can use CHARMM or AMBER to assign force field
-coefficients and convert their output into LAMMPS input.
-
-See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
-field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force
-field.
-
-:link(charmm,http://www.scripps.edu/brooks)
-:link(amber,http://amber.scripps.edu)
-
-These style choices compute force field formulas that are consistent
-with common options in CHARMM or AMBER. See each command's
-documentation for the formula it computes.
-
-"bond_style"_bond_harmonic.html harmonic
-"angle_style"_angle_charmm.html charmm
-"dihedral_style"_dihedral_charmm.html charmmfsh
-"dihedral_style"_dihedral_charmm.html charmm
-"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh
-"pair_style"_pair_charmm.html lj/charmmfsw/coul/long
-"pair_style"_pair_charmm.html lj/charmm/coul/charmm
-"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
-"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
-
-"special_bonds"_special_bonds.html charmm
-"special_bonds"_special_bonds.html amber :ul
-
-NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
-released in March 2017. We recommend they be used instead of the
-older {charmm} styles. See discussion of the differences on the "pair
-charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
-doc pages.
-
-DREIDING is a generic force field developed by the "Goddard
-group"_http://www.wag.caltech.edu at Caltech and is useful for
-predicting structures and dynamics of organic, biological and
-main-group inorganic molecules. The philosophy in DREIDING is to use
-general force constants and geometry parameters based on simple
-hybridization considerations, rather than individual force constants
-and geometric parameters that depend on the particular combinations of
-atoms involved in the bond, angle, or torsion terms. DREIDING has an
-"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
-interactions involving a hydrogen atom on very electronegative atoms
-(N, O, F).
-
-See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
-
-These style choices compute force field formulas that are consistent
-with the DREIDING force field. See each command's
-documentation for the formula it computes.
-
-"bond_style"_bond_harmonic.html harmonic
-"bond_style"_bond_morse.html morse :ul
-
-"angle_style"_angle_harmonic.html harmonic
-"angle_style"_angle_cosine.html cosine
-"angle_style"_angle_cosine_periodic.html cosine/periodic :ul
-
-"dihedral_style"_dihedral_charmm.html charmm
-"improper_style"_improper_umbrella.html umbrella :ul
-
-"pair_style"_pair_buck.html buck
-"pair_style"_pair_buck.html buck/coul/cut
-"pair_style"_pair_buck.html buck/coul/long
-"pair_style"_pair_lj.html lj/cut
-"pair_style"_pair_lj.html lj/cut/coul/cut
-"pair_style"_pair_lj.html lj/cut/coul/long :ul
-
-"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj
-"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul
-
-"special_bonds"_special_bonds.html dreiding :ul
-
-:line
-
-6.4 Running multiple simulations from one input script :link(howto_4),h4
-
-This can be done in several ways. See the documentation for
-individual commands for more details on how these examples work.
-
-If "multiple simulations" means continue a previous simulation for
-more timesteps, then you simply use the "run"_run.html command
-multiple times. For example, this script
-
-units lj
-atom_style atomic
-read_data data.lj
-run 10000
-run 10000
-run 10000
-run 10000
-run 10000 :pre
-
-would run 5 successive simulations of the same system for a total of
-50,000 timesteps.
-
-If you wish to run totally different simulations, one after the other,
-the "clear"_clear.html command can be used in between them to
-re-initialize LAMMPS. For example, this script
-
-units lj
-atom_style atomic
-read_data data.lj
-run 10000
-clear
-units lj
-atom_style atomic
-read_data data.lj.new
-run 10000 :pre
-
-would run 2 independent simulations, one after the other.
-
-For large numbers of independent simulations, you can use
-"variables"_variable.html and the "next"_next.html and
-"jump"_jump.html commands to loop over the same input script
-multiple times with different settings. For example, this
-script, named in.polymer
-
-variable d index run1 run2 run3 run4 run5 run6 run7 run8
-shell cd $d
-read_data data.polymer
-run 10000
-shell cd ..
-clear
-next d
-jump in.polymer :pre
-
-would run 8 simulations in different directories, using a data.polymer
-file in each directory. The same concept could be used to run the
-same system at 8 different temperatures, using a temperature variable
-and storing the output in different log and dump files, for example
-
-variable a loop 8
-variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
-log log.$a
-read data.polymer
-velocity all create $t 352839
-fix 1 all nvt $t $t 100.0
-dump 1 all atom 1000 dump.$a
-run 100000
-clear
-next t
-next a
-jump in.polymer :pre
-
-All of the above examples work whether you are running on 1 or
-multiple processors, but assumed you are running LAMMPS on a single
-partition of processors. LAMMPS can be run on multiple partitions via
-the "-partition" command-line switch as described in "this
-section"_Section_start.html#start_6 of the manual.
-
-In the last 2 examples, if LAMMPS were run on 3 partitions, the same
-scripts could be used if the "index" and "loop" variables were
-replaced with {universe}-style variables, as described in the
-"variable"_variable.html command. Also, the "next t" and "next a"
-commands would need to be replaced with a single "next a t" command.
-With these modifications, the 8 simulations of each script would run
-on the 3 partitions one after the other until all were finished.
-Initially, 3 simulations would be started simultaneously, one on each
-partition. When one finished, that partition would then start
-the 4th simulation, and so forth, until all 8 were completed.
-
-:line
-
-6.5 Multi-replica simulations :link(howto_5),h4
-
-Several commands in LAMMPS run mutli-replica simulations, meaning
-that multiple instances (replicas) of your simulation are run
-simultaneously, with small amounts of data exchanged between replicas
-periodically.
-
-These are the relevant commands:
-
-"neb"_neb.html for nudged elastic band calculations
-"prd"_prd.html for parallel replica dynamics
-"tad"_tad.html for temperature accelerated dynamics
-"temper"_temper.html for parallel tempering
-"fix pimd"_fix_pimd.html for path-integral molecular dynamics (PIMD) :ul
-
-NEB is a method for finding transition states and barrier energies.
-PRD and TAD are methods for performing accelerated dynamics to find
-and perform infrequent events. Parallel tempering or replica exchange
-runs different replicas at a series of temperature to facilitate
-rare-event sampling.
-
-These commands can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
-
-PIMD runs different replicas whose individual particles are coupled
-together by springs to model a system or ring-polymers.
-
-This commands can only be used if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
-
-In all these cases, you must run with one or more processors per
-replica. The processors assigned to each replica are determined at
-run-time by using the "-partition command-line
-switch"_Section_start.html#start_6 to launch LAMMPS on multiple
-partitions, which in this context are the same as replicas. E.g.
-these commands:
-
-mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
-mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
-
-would each run 8 replicas, on either 16 or 8 processors. Note the use
-of the "-in command-line switch"_Section_start.html#start_6 to specify
-the input script which is required when running in multi-replica mode.
-
-Also note that with MPI installed on a machine (e.g. your desktop),
-you can run on more (virtual) processors than you have physical
-processors. Thus the above commands could be run on a
-single-processor (or few-processor) desktop so that you can run
-a multi-replica simulation on more replicas than you have
-physical processors.
-
-:line
-
-6.6 Granular models :link(howto_6),h4
-
-Granular system are composed of spherical particles with a diameter,
-as opposed to point particles. This means they have an angular
-velocity and torque can be imparted to them to cause them to rotate.
-
-To run a simulation of a granular model, you will want to use
-the following commands:
-
-"atom_style sphere"_atom_style.html
-"fix nve/sphere"_fix_nve_sphere.html
-"fix gravity"_fix_gravity.html :ul
-
-This compute
-
-"compute erotate/sphere"_compute_erotate_sphere.html :ul
-
-calculates rotational kinetic energy which can be "output with
-thermodynamic info"_Section_howto.html#howto_15.
-
-Use one of these 3 pair potentials, which compute forces and torques
-between interacting pairs of particles:
-
-"pair_style"_pair_style.html gran/history
-"pair_style"_pair_style.html gran/no_history
-"pair_style"_pair_style.html gran/hertzian :ul
-
-These commands implement fix options specific to granular systems:
-
-"fix freeze"_fix_freeze.html
-"fix pour"_fix_pour.html
-"fix viscous"_fix_viscous.html
-"fix wall/gran"_fix_wall_gran.html :ul
-
-The fix style {freeze} zeroes both the force and torque of frozen
-atoms, and should be used for granular system instead of the fix style
-{setforce}.
-
-For computational efficiency, you can eliminate needless pairwise
-computations between frozen atoms by using this command:
-
-"neigh_modify"_neigh_modify.html exclude :ul
-
-NOTE: By default, for 2d systems, granular particles are still modeled
-as 3d spheres, not 2d discs (circles), meaning their moment of inertia
-will be the same as in 3d. If you wish to model granular particles in
-2d as 2d discs, see the note on this topic in "Section
-6.2"_Section_howto.html#howto_2, where 2d simulations are discussed.
-
-:line
-
-6.7 TIP3P water model :link(howto_7),h4
-
-The TIP3P water model as implemented in CHARMM
-"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
-charges and Lennard-Jones parameters assigned to each of the 3 atoms.
-In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
-the two O-H bonds and the H-O-H angle rigid. A bond style of
-{harmonic} and an angle style of {harmonic} or {charmm} should also be
-used.
-
-These are the additional parameters (in real units) to set for O and H
-atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
-cutoff. The K values can be used if a flexible TIP3P model (without
-fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
-set to 0.0, it corresponds to the original 1983 TIP3P model
-"(Jorgensen)"_#Jorgensen1.
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -0.834
-H charge = 0.417
-LJ epsilon of OO = 0.1521
-LJ sigma of OO = 3.1507
-LJ epsilon of HH = 0.0460
-LJ sigma of HH = 0.4000
-LJ epsilon of OH = 0.0836
-LJ sigma of OH = 1.7753
-K of OH bond = 450
-r0 of OH bond = 0.9572
-K of HOH angle = 55
-theta of HOH angle = 104.52 :all(b),p
-
-These are the parameters to use for TIP3P with a long-range Coulombic
-solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for
-details:
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -0.830
-H charge = 0.415
-LJ epsilon of OO = 0.102
-LJ sigma of OO = 3.188
-LJ epsilon, sigma of OH, HH = 0.0
-K of OH bond = 450
-r0 of OH bond = 0.9572
-K of HOH angle = 55
-theta of HOH angle = 104.52 :all(b),p
-
-Wikipedia also has a nice article on "water
-models"_http://en.wikipedia.org/wiki/Water_model.
-
-:line
-
-6.8 TIP4P water model :link(howto_8),h4
-
-The four-point TIP4P rigid water model extends the traditional
-three-point TIP3P model by adding an additional site, usually
-massless, where the charge associated with the oxygen atom is placed.
-This site M is located at a fixed distance away from the oxygen along
-the bisector of the HOH bond angle. A bond style of {harmonic} and an
-angle style of {harmonic} or {charmm} should also be used.
-
-A TIP4P model is run with LAMMPS using either this command
-for a cutoff model:
-
-"pair_style lj/cut/tip4p/cut"_pair_lj.html
-
-or these two commands for a long-range model:
-
-"pair_style lj/cut/tip4p/long"_pair_lj.html
-"kspace_style pppm/tip4p"_kspace_style.html :ul
-
-For both models, the bond lengths and bond angles should be held fixed
-using the "fix shake"_fix_shake.html command.
-
-These are the additional parameters (in real units) to set for O and H
-atoms and the water molecule to run a rigid TIP4P model with a cutoff
-"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in
-the "pair_style"_pair_style.html command, not as part of the pair
-coefficients.
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -1.040
-H charge = 0.520
-r0 of OH bond = 0.9572
-theta of HOH angle = 104.52
-OM distance = 0.15
-LJ epsilon of O-O = 0.1550
-LJ sigma of O-O = 3.1536
-LJ epsilon, sigma of OH, HH = 0.0
-Coulombic cutoff = 8.5 :all(b),p
-
-For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
-http://dx.doi.org/10.1063/1.1931662) these values can be used:
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -1.1794
-H charge = 0.5897
-r0 of OH bond = 0.9572
-theta of HOH angle = 104.52
-OM distance = 0.1577
-LJ epsilon of O-O = 0.21084
-LJ sigma of O-O = 3.1668
-LJ epsilon, sigma of OH, HH = 0.0
-Coulombic cutoff = 8.5 :all(b),p
-
-For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
-http://dx.doi.org/10.1063/1.2121687), these values can be used:
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -1.1128
-H charge = 0.5564
-r0 of OH bond = 0.9572
-theta of HOH angle = 104.52
-OM distance = 0.1546
-LJ epsilon of O-O = 0.1852
-LJ sigma of O-O = 3.1589
-LJ epsilon, sigma of OH, HH = 0.0
-Coulombic cutoff = 8.5 :all(b),p
-
-These are the parameters to use for TIP4P with a long-range Coulombic
-solver (e.g. Ewald or PPPM in LAMMPS):
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -1.0484
-H charge = 0.5242
-r0 of OH bond = 0.9572
-theta of HOH angle = 104.52
-OM distance = 0.1250
-LJ epsilon of O-O = 0.16275
-LJ sigma of O-O = 3.16435
-LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
-
-Note that the when using the TIP4P pair style, the neighbor list
-cutoff for Coulomb interactions is effectively extended by a distance
-2 * (OM distance), to account for the offset distance of the
-fictitious charges on O atoms in water molecules. Thus it is
-typically best in an efficiency sense to use a LJ cutoff >= Coulomb
-cutoff + 2*(OM distance), to shrink the size of the neighbor list.
-This leads to slightly larger cost for the long-range calculation, so
-you can test the trade-off for your model. The OM distance and the LJ
-and Coulombic cutoffs are set in the "pair_style
-lj/cut/tip4p/long"_pair_lj.html command.
-
-Wikipedia also has a nice article on "water
-models"_http://en.wikipedia.org/wiki/Water_model.
-
-:line
-
-6.9 SPC water model :link(howto_9),h4
-
-The SPC water model specifies a 3-site rigid water molecule with
-charges and Lennard-Jones parameters assigned to each of the 3 atoms.
-In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
-the two O-H bonds and the H-O-H angle rigid. A bond style of
-{harmonic} and an angle style of {harmonic} or {charmm} should also be
-used.
-
-These are the additional parameters (in real units) to set for O and H
-atoms and the water molecule to run a rigid SPC model.
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -0.820
-H charge = 0.410
-LJ epsilon of OO = 0.1553
-LJ sigma of OO = 3.166
-LJ epsilon, sigma of OH, HH = 0.0
-r0 of OH bond = 1.0
-theta of HOH angle = 109.47 :all(b),p
-
-Note that as originally proposed, the SPC model was run with a 9
-Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
-with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
-any of the parameters above, though it becomes a different model in
-that mode of usage.
-
-The SPC/E (extended) water model is the same, except
-the partial charge assignments change:
-
-O charge = -0.8476
-H charge = 0.4238 :all(b),p
-
-See the "(Berendsen)"_#howto-Berendsen reference for more details on both
-the SPC and SPC/E models.
-
-Wikipedia also has a nice article on "water
-models"_http://en.wikipedia.org/wiki/Water_model.
-
-:line
-
-6.10 Coupling LAMMPS to other codes :link(howto_10),h4
-
-LAMMPS is designed to allow it to be coupled to other codes. For
-example, a quantum mechanics code might compute forces on a subset of
-atoms and pass those forces to LAMMPS. Or a continuum finite element
-(FE) simulation might use atom positions as boundary conditions on FE
-nodal points, compute a FE solution, and return interpolated forces on
-MD atoms.
-
-LAMMPS can be coupled to other codes in at least 3 ways. Each has
-advantages and disadvantages, which you'll have to think about in the
-context of your application.
-
-(1) Define a new "fix"_fix.html command that calls the other code. In
-this scenario, LAMMPS is the driver code. During its timestepping,
-the fix is invoked, and can make library calls to the other code,
-which has been linked to LAMMPS as a library. This is the way the
-"POEMS"_poems package that performs constrained rigid-body motion on
-groups of atoms is hooked to LAMMPS. See the "fix
-poems"_fix_poems.html command for more details. See the
-"Modify"_Modify.html doc page for info on how to add a new fix to
-LAMMPS.
-
-:link(poems,http://www.rpi.edu/~anderk5/lab)
-
-(2) Define a new LAMMPS command that calls the other code. This is
-conceptually similar to method (1), but in this case LAMMPS and the
-other code are on a more equal footing. Note that now the other code
-is not called during the timestepping of a LAMMPS run, but between
-runs. The LAMMPS input script can be used to alternate LAMMPS runs
-with calls to the other code, invoked via the new command. The
-"run"_run.html command facilitates this with its {every} option, which
-makes it easy to run a few steps, invoke the command, run a few steps,
-invoke the command, etc.
-
-In this scenario, the other code can be called as a library, as in
-(1), or it could be a stand-alone code, invoked by a system() call
-made by the command (assuming your parallel machine allows one or more
-processors to start up another program). In the latter case the
-stand-alone code could communicate with LAMMPS thru files that the
-command writes and reads.
-
-See the "Modify"_Modify.html doc page for how to add a new command to
-LAMMPS.
-
-(3) Use LAMMPS as a library called by another code. In this case the
-other code is the driver and calls LAMMPS as needed. Or a wrapper
-code could link and call both LAMMPS and another code as libraries.
-Again, the "run"_run.html command has options that allow it to be
-invoked with minimal overhead (no setup or clean-up) if you wish to do
-multiple short runs, driven by another program.
-
-Examples of driver codes that call LAMMPS as a library are included in
-the examples/COUPLE directory of the LAMMPS distribution; see
-examples/COUPLE/README for more details:
-
-simple: simple driver programs in C++ and C which invoke LAMMPS as a
-library :ulb,l
-
-lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical
-MD with quantum forces calculated by a density functional code :l
-
-lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple
-a kinetic Monte Carlo model for grain growth using MD to calculate
-strain induced across grain boundaries :l
-:ule
-
-:link(quest,http://dft.sandia.gov/Quest)
-:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
-
-"This section"_Section_start.html#start_5 of the documentation
-describes how to build LAMMPS as a library. Once this is done, you
-can interface with LAMMPS either via C++, C, Fortran, or Python (or
-any other language that supports a vanilla C-like interface). For
-example, from C++ you could create one (or more) "instances" of
-LAMMPS, pass it an input script to process, or execute individual
-commands, all by invoking the correct class methods in LAMMPS. From C
-or Fortran you can make function calls to do the same things. See the
-"Python"_Python.html doc page for a description of the Python wrapper
-provided with LAMMPS that operates through the LAMMPS library
-interface.
-
-The files src/library.cpp and library.h contain the C-style interface
-to LAMMPS. See "Section 6.19"_Section_howto.html#howto_19 of the
-manual for a description of the interface and how to extend it for
-your needs.
-
-Note that the lammps_open() function that creates an instance of
-LAMMPS takes an MPI communicator as an argument. This means that
-instance of LAMMPS will run on the set of processors in the
-communicator. Thus the calling code can run LAMMPS on all or a subset
-of processors. For example, a wrapper script might decide to
-alternate between LAMMPS and another code, allowing them both to run
-on all the processors. Or it might allocate half the processors to
-LAMMPS and half to the other code and run both codes simultaneously
-before syncing them up periodically. Or it might instantiate multiple
-instances of LAMMPS to perform different calculations.
-
-:line
-
-6.11 Visualizing LAMMPS snapshots :link(howto_11),h4
-
-LAMMPS itself does not do visualization, but snapshots from LAMMPS
-simulations can be visualized (and analyzed) in a variety of ways.
-
-LAMMPS snapshots are created by the "dump"_dump.html command which can
-create files in several formats. The native LAMMPS dump format is a
-text file (see "dump atom" or "dump custom") which can be visualized
-by several popular visualization tools. The "dump
-image"_dump_image.html and "dump movie"_dump_image.html styles can
-output internally rendered images and convert a sequence of them to a
-movie during the MD run. Several programs included with LAMMPS as
-auxiliary tools can convert between LAMMPS format files and other
-formats. See the "Tools"_Tools.html doc page for details.
-
-A Python-based toolkit distributed by our group can read native LAMMPS
-dump files, including custom dump files with additional columns of
-user-specified atom information, and convert them to various formats
-or pipe them into visualization software directly. See the "Pizza.py
-WWW site"_pizza for details. Specifically, Pizza.py can convert
-LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats.
-Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
-RasMol visualization programs. Pizza.py has tools that do interactive
-3d OpenGL visualization and one that creates SVG images of dump file
-snapshots.
-
-:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
-:link(ensight,http://www.ensight.com)
-:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
-
-:line
-
-6.12 Triclinic (non-orthogonal) simulation boxes :link(howto_12),h4
-
-By default, LAMMPS uses an orthogonal simulation box to encompass the
-particles. The "boundary"_boundary.html command sets the boundary
-conditions of the box (periodic, non-periodic, etc). The orthogonal
-box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
-starting from the origin given by [a] = (xhi-xlo,0,0); [b] =
-(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters
-(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
-is created, e.g. by the "create_box"_create_box.html or
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
-where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
-parameters, as well as lx,ly,lz, can be output via the "thermo_style
-custom"_thermo_style.html command.
-
-LAMMPS also allows simulations to be performed in triclinic
-(non-orthogonal) simulation boxes shaped as a parallelepiped with
-triclinic symmetry. The parallelepiped has its "origin" at
-(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
-origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] =
-(xz,yz,zhi-zlo). {xy,xz,yz} can be 0.0 or positive or negative values
-and are called "tilt factors" because they are the amount of
-displacement applied to faces of an originally orthogonal box to
-transform it into the parallelepiped. In LAMMPS the triclinic
-simulation box edge vectors [a], [b], and [c] cannot be arbitrary
-vectors. As indicated, [a] must lie on the positive x axis. [b] must
-lie in the xy plane, with strictly positive y component. [c] may have
-any orientation with strictly positive z component. The requirement
-that [a], [b], and [c] have strictly positive x, y, and z components,
-respectively, ensures that [a], [b], and [c] form a complete
-right-handed basis. These restrictions impose no loss of generality,
-since it is possible to rotate/invert any set of 3 crystal basis
-vectors so that they conform to the restrictions.
-
-For example, assume that the 3 vectors [A],[B],[C] are the edge
-vectors of a general parallelepiped, where there is no restriction on
-[A],[B],[C] other than they form a complete right-handed basis i.e.
-[A] x [B] . [C] > 0. The equivalent LAMMPS [a],[b],[c] are a linear
-rotation of [A], [B], and [C] and can be computed as follows:
-
-:c,image(Eqs/transform.jpg)
-
-where A = | [A] | indicates the scalar length of [A]. The hat symbol (^)
-indicates the corresponding unit vector. {beta} and {gamma} are angles
-between the vectors described below. Note that by construction,
-[a], [b], and [c] have strictly positive x, y, and z components, respectively.
-If it should happen that
-[A], [B], and [C] form a left-handed basis, then the above equations
-are not valid for [c]. In this case, it is necessary
-to first apply an inversion. This can be achieved
-by interchanging two basis vectors or by changing the sign of one of them.
-
-For consistency, the same rotation/inversion applied to the basis vectors
-must also be applied to atom positions, velocities,
-and any other vector quantities.
-This can be conveniently achieved by first converting to
-fractional coordinates in the
-old basis and then converting to distance coordinates in the new basis.
-The transformation is given by the following equation:
-
-:c,image(Eqs/rotate.jpg)
-
-where {V} is the volume of the box, [X] is the original vector quantity and
-[x] is the vector in the LAMMPS basis.
-
-There is no requirement that a triclinic box be periodic in any
-dimension, though it typically should be in at least the 2nd dimension
-of the tilt (y in xy) if you want to enforce a shift in periodic
-boundary conditions across that boundary. Some commands that work
-with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix
-npt"_fix_nh.html commands, require periodicity or non-shrink-wrap
-boundary conditions in specific dimensions. See the command doc pages
-for details.
-
-The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
-time the simulation box is created. This happens in one of 3 ways.
-If the "create_box"_create_box.html command is used with a region of
-style {prism}, then a triclinic box is setup. See the
-"region"_region.html command for details. If the
-"read_data"_read_data.html command is used to define the simulation
-box, and the header of the data file contains a line with the "xy xz
-yz" keyword, then a triclinic box is setup. See the
-"read_data"_read_data.html command for details. Finally, if the
-"read_restart"_read_restart.html command reads a restart file which
-was written from a simulation using a triclinic box, then a triclinic
-box will be setup for the restarted simulation.
-
-Note that you can define a triclinic box with all 3 tilt factors =
-0.0, so that it is initially orthogonal. This is necessary if the box
-will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or
-"fix deform"_fix_deform.html commands. Alternatively, you can use the
-"change_box"_change_box.html command to convert a simulation box from
-orthogonal to triclinic and vice versa.
-
-As with orthogonal boxes, LAMMPS defines triclinic box size parameters
-lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
-The 9 parameters, as well as lx,ly,lz, can be output via the
-"thermo_style custom"_thermo_style.html command.
-
-To avoid extremely tilted boxes (which would be computationally
-inefficient), LAMMPS normally requires that no tilt factor can skew
-the box more than half the distance of the parallel box length, which
-is the 1st dimension in the tilt factor (x for xz). This is required
-both when the simulation box is created, e.g. via the
-"create_box"_create_box.html or "read_data"_read_data.html commands,
-as well as when the box shape changes dynamically during a simulation,
-e.g. via the "fix deform"_fix_deform.html or "fix npt"_fix_nh.html
-commands.
-
-For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
-the xy tilt factor must be between -5 and 5. Similarly, both xz and
-yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
-not a limitation, since if the maximum tilt factor is 5 (as in this
-example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
-... are geometrically all equivalent. If the box tilt exceeds this
-limit during a dynamics run (e.g. via the "fix deform"_fix_deform.html
-command), then the box is "flipped" to an equivalent shape with a tilt
-factor within the bounds, so the run can continue. See the "fix
-deform"_fix_deform.html doc page for further details.
-
-One exception to this rule is if the 1st dimension in the tilt
-factor (x for xy) is non-periodic. In that case, the limits on the
-tilt factor are not enforced, since flipping the box in that dimension
-does not change the atom positions due to non-periodicity. In this
-mode, if you tilt the system to extreme angles, the simulation will
-simply become inefficient, due to the highly skewed simulation box.
-
-The limitation on not creating a simulation box with a tilt factor
-skewing the box more than half the distance of the parallel box length
-can be overridden via the "box"_box.html command. Setting the {tilt}
-keyword to {large} allows any tilt factors to be specified.
-
-Box flips that may occur using the "fix deform"_fix_deform.html or
-"fix npt"_fix_nh.html commands can be turned off using the {flip no}
-option with either of the commands.
-
-Note that if a simulation box has a large tilt factor, LAMMPS will run
-less efficiently, due to the large volume of communication needed to
-acquire ghost atoms around a processor's irregular-shaped sub-domain.
-For extreme values of tilt, LAMMPS may also lose atoms and generate an
-error.
-
-Triclinic crystal structures are often defined using three lattice
-constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and
-{gamma}. Note that in this nomenclature, the a, b, and c lattice
-constants are the scalar lengths of the edge vectors [a], [b], and [c]
-defined above. The relationship between these 6 quantities
-(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
-(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
-
-:c,image(Eqs/box.jpg)
-
-The inverse relationship can be written as follows:
-
-:c,image(Eqs/box_inverse.jpg)
-
-The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
-out or accessed by computes using the
-"thermo_style custom"_thermo_style.html keywords
-{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma},
-respectively.
-
-As discussed on the "dump"_dump.html command doc page, when the BOX
-BOUNDS for a snapshot is written to a dump file for a triclinic box,
-an orthogonal bounding box which encloses the triclinic simulation box
-is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
-box, formatted as follows:
-
-ITEM: BOX BOUNDS xy xz yz
-xlo_bound xhi_bound xy
-ylo_bound yhi_bound xz
-zlo_bound zhi_bound yz :pre
-
-This bounding box is convenient for many visualization programs and is
-calculated from the 9 triclinic box parameters
-(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
-
-xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
-xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
-ylo_bound = ylo + MIN(0.0,yz)
-yhi_bound = yhi + MAX(0.0,yz)
-zlo_bound = zlo
-zhi_bound = zhi :pre
-
-These formulas can be inverted if you need to convert the bounding box
-back into the triclinic box parameters, e.g. xlo = xlo_bound -
-MIN(0.0,xy,xz,xy+xz).
-
-One use of triclinic simulation boxes is to model solid-state crystals
-with triclinic symmetry. The "lattice"_lattice.html command can be
-used with non-orthogonal basis vectors to define a lattice that will
-tile a triclinic simulation box via the
-"create_atoms"_create_atoms.html command.
-
-A second use is to run Parinello-Rahman dynamics via the "fix
-npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
-factors to compensate for off-diagonal components of the pressure
-tensor. The analog for an "energy minimization"_minimize.html is
-the "fix box/relax"_fix_box_relax.html command.
-
-A third use is to shear a bulk solid to study the response of the
-material. The "fix deform"_fix_deform.html command can be used for
-this purpose. It allows dynamic control of the xy, xz, yz tilt
-factors as a simulation runs. This is discussed in the next section
-on non-equilibrium MD (NEMD) simulations.
-
-:line
-
-6.13 NEMD simulations :link(howto_13),h4
-
-Non-equilibrium molecular dynamics or NEMD simulations are typically
-used to measure a fluid's rheological properties such as viscosity.
-In LAMMPS, such simulations can be performed by first setting up a
-non-orthogonal simulation box (see the preceding Howto section).
-
-A shear strain can be applied to the simulation box at a desired
-strain rate by using the "fix deform"_fix_deform.html command. The
-"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
-the sheared fluid and integrate the SLLOD equations of motion for the
-system. Fix nvt/sllod uses "compute
-temp/deform"_compute_temp_deform.html to compute a thermal temperature
-by subtracting out the streaming velocity of the shearing atoms. The
-velocity profile or other properties of the fluid can be monitored via
-the "fix ave/chunk"_fix_ave_chunk.html command.
-
-As discussed in the previous section on non-orthogonal simulation
-boxes, the amount of tilt or skew that can be applied is limited by
-LAMMPS for computational efficiency to be 1/2 of the parallel box
-length. However, "fix deform"_fix_deform.html can continuously strain
-a box by an arbitrary amount. As discussed in the "fix
-deform"_fix_deform.html command, when the tilt value reaches a limit,
-the box is flipped to the opposite limit which is an equivalent tiling
-of periodic space. The strain rate can then continue to change as
-before. In a long NEMD simulation these box re-shaping events may
-occur many times.
-
-In a NEMD simulation, the "remap" option of "fix
-deform"_fix_deform.html should be set to "remap v", since that is what
-"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity
-profile consistent with the applied shear strain rate.
-
-An alternative method for calculating viscosities is provided via the
-"fix viscosity"_fix_viscosity.html command.
-
-NEMD simulations can also be used to measure transport properties of a fluid
-through a pore or channel. Simulations of steady-state flow can be performed
-using the "fix flow/gauss"_fix_flow_gauss.html command.
-
-:line
-
-6.14 Finite-size spherical and aspherical particles :link(howto_14),h4
-
-Typical MD models treat atoms or particles as point masses. Sometimes
-it is desirable to have a model with finite-size particles such as
-spheroids or ellipsoids or generalized aspherical bodies. The
-difference is that such particles have a moment of inertia, rotational
-energy, and angular momentum. Rotation is induced by torque coming
-from interactions with other particles.
-
-LAMMPS has several options for running simulations with these kinds of
-particles. The following aspects are discussed in turn:
-
-atom styles
-pair potentials
-time integration
-computes, thermodynamics, and dump output
-rigid bodies composed of finite-size particles :ul
-
-Example input scripts for these kinds of models are in the body,
-colloid, dipole, ellipse, line, peri, pour, and tri directories of the
-"examples directory"_Examples.html in the LAMMPS distribution.
-
-Atom styles :h4
-
-There are several "atom styles"_atom_style.html that allow for
-definition of finite-size particles: sphere, dipole, ellipsoid, line,
-tri, peri, and body.
-
-The sphere style defines particles that are spheriods and each
-particle can have a unique diameter and mass (or density). These
-particles store an angular velocity (omega) and can be acted upon by
-torque. The "set" command can be used to modify the diameter and mass
-of individual particles, after then are created.
-
-The dipole style does not actually define finite-size particles, but
-is often used in conjunction with spherical particles, via a command
-like
-
-atom_style hybrid sphere dipole :pre
-
-This is because when dipoles interact with each other, they induce
-torques, and a particle must be finite-size (i.e. have a moment of
-inertia) in order to respond and rotate. See the "atom_style
-dipole"_atom_style.html command for details. The "set" command can be
-used to modify the orientation and length of the dipole moment of
-individual particles, after then are created.
-
-The ellipsoid style defines particles that are ellipsoids and thus can
-be aspherical. Each particle has a shape, specified by 3 diameters,
-and mass (or density). These particles store an angular momentum and
-their orientation (quaternion), and can be acted upon by torque. They
-do not store an angular velocity (omega), which can be in a different
-direction than angular momentum, rather they compute it as needed.
-The "set" command can be used to modify the diameter, orientation, and
-mass of individual particles, after then are created. It also has a
-brief explanation of what quaternions are.
-
-The line style defines line segment particles with two end points and
-a mass (or density). They can be used in 2d simulations, and they can
-be joined together to form rigid bodies which represent arbitrary
-polygons.
-
-The tri style defines triangular particles with three corner points
-and a mass (or density). They can be used in 3d simulations, and they
-can be joined together to form rigid bodies which represent arbitrary
-particles with a triangulated surface.
-
-The peri style is used with "Peridynamic models"_pair_peri.html and
-defines particles as having a volume, that is used internally in the
-"pair_style peri"_pair_peri.html potentials.
-
-The body style allows for definition of particles which can represent
-complex entities, such as surface meshes of discrete points,
-collections of sub-particles, deformable objects, etc. The body style
-is discussed in more detail on the "body"_body.html doc page.
-
-Note that if one of these atom styles is used (or multiple styles via
-the "atom_style hybrid"_atom_style.html command), not all particles in
-the system are required to be finite-size or aspherical.
-
-For example, in the ellipsoid style, if the 3 shape parameters are set
-to the same value, the particle will be a sphere rather than an
-ellipsoid. If the 3 shape parameters are all set to 0.0 or if the
-diameter is set to 0.0, it will be a point particle. In the line or
-tri style, if the lineflag or triflag is specified as 0, then it
-will be a point particle.
-
-Some of the pair styles used to compute pairwise interactions between
-finite-size particles also compute the correct interaction with point
-particles as well, e.g. the interaction between a point particle and a
-finite-size particle or between two point particles. If necessary,
-"pair_style hybrid"_pair_hybrid.html can be used to insure the correct
-interactions are computed for the appropriate style of interactions.
-Likewise, using groups to partition particles (ellipsoids versus
-spheres versus point particles) will allow you to use the appropriate
-time integrators and temperature computations for each class of
-particles. See the doc pages for various commands for details.
-
-Also note that for "2d simulations"_dimension.html, atom styles sphere
-and ellipsoid still use 3d particles, rather than as circular disks or
-ellipses. This means they have the same moment of inertia as the 3d
-object. When temperature is computed, the correct degrees of freedom
-are used for rotation in a 2d versus 3d system.
-
-Pair potentials :h4
-
-When a system with finite-size particles is defined, the particles
-will only rotate and experience torque if the force field computes
-such interactions. These are the various "pair
-styles"_pair_style.html that generate torque:
-
-"pair_style gran/history"_pair_gran.html
-"pair_style gran/hertzian"_pair_gran.html
-"pair_style gran/no_history"_pair_gran.html
-"pair_style dipole/cut"_pair_dipole.html
-"pair_style gayberne"_pair_gayberne.html
-"pair_style resquared"_pair_resquared.html
-"pair_style brownian"_pair_brownian.html
-"pair_style lubricate"_pair_lubricate.html
-"pair_style line/lj"_pair_line_lj.html
-"pair_style tri/lj"_pair_tri_lj.html
-"pair_style body"_pair_body.html :ul
-
-The granular pair styles are used with spherical particles. The
-dipole pair style is used with the dipole atom style, which could be
-applied to spherical or ellipsoidal particles. The GayBerne and
-REsquared potentials require ellipsoidal particles, though they will
-also work if the 3 shape parameters are the same (a sphere). The
-Brownian and lubrication potentials are used with spherical particles.
-The line, tri, and body potentials are used with line segment,
-triangular, and body particles respectively.
-
-Time integration :h4
-
-There are several fixes that perform time integration on finite-size
-spherical particles, meaning the integrators update the rotational
-orientation and angular velocity or angular momentum of the particles:
-
-"fix nve/sphere"_fix_nve_sphere.html
-"fix nvt/sphere"_fix_nvt_sphere.html
-"fix npt/sphere"_fix_npt_sphere.html :ul
-
-Likewise, there are 3 fixes that perform time integration on
-ellipsoidal particles:
-
-"fix nve/asphere"_fix_nve_asphere.html
-"fix nvt/asphere"_fix_nvt_asphere.html
-"fix npt/asphere"_fix_npt_asphere.html :ul
-
-The advantage of these fixes is that those which thermostat the
-particles include the rotational degrees of freedom in the temperature
-calculation and thermostatting. The "fix langevin"_fix_langevin
-command can also be used with its {omgea} or {angmom} options to
-thermostat the rotational degrees of freedom for spherical or
-ellipsoidal particles. Other thermostatting fixes only operate on the
-translational kinetic energy of finite-size particles.
-
-These fixes perform constant NVE time integration on line segment,
-triangular, and body particles:
-
-"fix nve/line"_fix_nve_line.html
-"fix nve/tri"_fix_nve_tri.html
-"fix nve/body"_fix_nve_body.html :ul
-
-Note that for mixtures of point and finite-size particles, these
-integration fixes can only be used with "groups"_group.html which
-contain finite-size particles.
-
-Computes, thermodynamics, and dump output :h4
-
-There are several computes that calculate the temperature or
-rotational energy of spherical or ellipsoidal particles:
-
-"compute temp/sphere"_compute_temp_sphere.html
-"compute temp/asphere"_compute_temp_asphere.html
-"compute erotate/sphere"_compute_erotate_sphere.html
-"compute erotate/asphere"_compute_erotate_asphere.html :ul
-
-These include rotational degrees of freedom in their computation. If
-you wish the thermodynamic output of temperature or pressure to use
-one of these computes (e.g. for a system entirely composed of
-finite-size particles), then the compute can be defined and the
-"thermo_modify"_thermo_modify.html command used. Note that by default
-thermodynamic quantities will be calculated with a temperature that
-only includes translational degrees of freedom. See the
-"thermo_style"_thermo_style.html command for details.
-
-These commands can be used to output various attributes of finite-size
-particles:
-
-"dump custom"_dump.html
-"compute property/atom"_compute_property_atom.html
-"dump local"_dump.html
-"compute body/local"_compute_body_local.html :ul
-
-Attributes include the dipole moment, the angular velocity, the
-angular momentum, the quaternion, the torque, the end-point and
-corner-point coordinates (for line and tri particles), and
-sub-particle attributes of body particles.
-
-Rigid bodies composed of finite-size particles :h4
-
-The "fix rigid"_fix_rigid.html command treats a collection of
-particles as a rigid body, computes its inertia tensor, sums the total
-force and torque on the rigid body each timestep due to forces on its
-constituent particles, and integrates the motion of the rigid body.
-
-If any of the constituent particles of a rigid body are finite-size
-particles (spheres or ellipsoids or line segments or triangles), then
-their contribution to the inertia tensor of the body is different than
-if they were point particles. This means the rotational dynamics of
-the rigid body will be different. Thus a model of a dimer is
-different if the dimer consists of two point masses versus two
-spheroids, even if the two particles have the same mass. Finite-size
-particles that experience torque due to their interaction with other
-particles will also impart that torque to a rigid body they are part
-of.
-
-See the "fix rigid" command for example of complex rigid-body models
-it is possible to define in LAMMPS.
-
-Note that the "fix shake"_fix_shake.html command can also be used to
-treat 2, 3, or 4 particles as a rigid body, but it always assumes the
-particles are point masses.
-
-Also note that body particles cannot be modeled with the "fix
-rigid"_fix_rigid.html command. Body particles are treated by LAMMPS
-as single particles, though they can store internal state, such as a
-list of sub-particles. Individual body partices are typically treated
-as rigid bodies, and their motion integrated with a command like "fix
-nve/body"_fix_nve_body.html. Interactions between pairs of body
-particles are computed via a command like "pair_style
-body"_pair_body.html.
-
-:line
-
-6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(howto_15),h4
-
-There are four basic kinds of LAMMPS output:
-
-"Thermodynamic output"_thermo_style.html, which is a list
-of quantities printed every few timesteps to the screen and logfile. :ulb,l
-
-"Dump files"_dump.html, which contain snapshots of atoms and various
-per-atom values and are written at a specified frequency. :l
-
-Certain fixes can output user-specified quantities to files: "fix
-ave/time"_fix_ave_time.html for time averaging, "fix
-ave/chunk"_fix_ave_chunk.html for spatial or other averaging, and "fix
-print"_fix_print.html for single-line output of
-"variables"_variable.html. Fix print can also output to the
-screen. :l
-
-"Restart files"_restart.html. :l
-:ule
-
-A simulation prints one set of thermodynamic output and (optionally)
-restart files. It can generate any number of dump files and fix
-output files, depending on what "dump"_dump.html and "fix"_fix.html
-commands you specify.
-
-As discussed below, LAMMPS gives you a variety of ways to determine
-what quantities are computed and printed when the thermodynamics,
-dump, or fix commands listed above perform output. Throughout this
-discussion, note that users can also "add their own computes and fixes
-to LAMMPS"_Modify.html which can then generate values that can then be
-output with these commands.
-
-The following sub-sections discuss different LAMMPS command related
-to output and the kind of data they operate on and produce:
-
-"Global/per-atom/local data"_#global
-"Scalar/vector/array data"_#scalar
-"Thermodynamic output"_#thermo
-"Dump file output"_#dump
-"Fixes that write output files"_#fixoutput
-"Computes that process output quantities"_#computeoutput
-"Fixes that process output quantities"_#fixprocoutput
-"Computes that generate values to output"_#compute
-"Fixes that generate values to output"_#fix
-"Variables that generate values to output"_#variable
-"Summary table of output options and data flow between commands"_#table :ul
-
-Global/per-atom/local data :h4,link(global)
-
-Various output-related commands work with three different styles of
-data: global, per-atom, or local. A global datum is one or more
-system-wide values, e.g. the temperature of the system. A per-atom
-datum is one or more values per atom, e.g. the kinetic energy of each
-atom. Local datums are calculated by each processor based on the
-atoms it owns, but there may be zero or more per atom, e.g. a list of
-bond distances.
-
-Scalar/vector/array data :h4,link(scalar)
-
-Global, per-atom, and local datums can each come in three kinds: a
-single scalar value, a vector of values, or a 2d array of values. The
-doc page for a "compute" or "fix" or "variable" that generates data
-will specify both the style and kind of data it produces, e.g. a
-per-atom vector.
-
-When a quantity is accessed, as in many of the output commands
-discussed below, it can be referenced via the following bracket
-notation, where ID in this case is the ID of a compute. The leading
-"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
-
-c_ID | entire scalar, vector, or array
-c_ID\[I\] | one element of vector, one column of array
-c_ID\[I\]\[J\] | one element of array :tb(s=|)
-
-In other words, using one bracket reduces the dimension of the data
-once (vector -> scalar, array -> vector). Using two brackets reduces
-the dimension twice (array -> scalar). Thus a command that uses
-scalar values as input can typically also process elements of a vector
-or array.
-
-Thermodynamic output :h4,link(thermo)
-
-The frequency and format of thermodynamic output is set by the
-"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
-"thermo_modify"_thermo_modify.html commands. The
-"thermo_style"_thermo_style.html command also specifies what values
-are calculated and written out. Pre-defined keywords can be specified
-(e.g. press, etotal, etc). Three additional kinds of keywords can
-also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html
-or "fix"_fix.html or "variable"_variable.html provides the value to be
-output. In each case, the compute, fix, or variable must generate
-global values for input to the "thermo_style custom"_dump.html
-command.
-
-Note that thermodynamic output values can be "extensive" or
-"intensive". The former scale with the number of atoms in the system
-(e.g. total energy), the latter do not (e.g. temperature). The
-setting for "thermo_modify norm"_thermo_modify.html determines whether
-extensive quantities are normalized or not. Computes and fixes
-produce either extensive or intensive values; see their individual doc
-pages for details. "Equal-style variables"_variable.html produce only
-intensive values; you can include a division by "natoms" in the
-formula if desired, to make an extensive calculation produce an
-intensive result.
-
-Dump file output :h4,link(dump)
-
-Dump file output is specified by the "dump"_dump.html and
-"dump_modify"_dump_modify.html commands. There are several
-pre-defined formats (dump atom, dump xtc, etc).
-
-There is also a "dump custom"_dump.html format where the user
-specifies what values are output with each atom. Pre-defined atom
-attributes can be specified (id, x, fx, etc). Three additional kinds
-of keywords can also be specified (c_ID, f_ID, v_name), where a
-"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
-provides the values to be output. In each case, the compute, fix, or
-variable must generate per-atom values for input to the "dump
-custom"_dump.html command.
-
-There is also a "dump local"_dump.html format where the user specifies
-what local values to output. A pre-defined index keyword can be
-specified to enumerate the local values. Two additional kinds of
-keywords can also be specified (c_ID, f_ID), where a
-"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
-provides the values to be output. In each case, the compute or fix
-must generate local values for input to the "dump local"_dump.html
-command.
-
-Fixes that write output files :h4,link(fixoutput)
-
-Several fixes take various quantities as input and can write output
-files: "fix ave/time"_fix_ave_time.html, "fix
-ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html,
-"fix ave/correlate"_fix_ave_correlate.html, and "fix
-print"_fix_print.html.
-
-The "fix ave/time"_fix_ave_time.html command enables direct output to
-a file and/or time-averaging of global scalars or vectors. The user
-specifies one or more quantities as input. These can be global
-"compute"_compute.html values, global "fix"_fix.html values, or
-"variables"_variable.html of any style except the atom style which
-produces per-atom values. Since a variable can refer to keywords used
-by the "thermo_style custom"_thermo_style.html command (like temp or
-press) and individual per-atom values, a wide variety of quantities
-can be time averaged and/or output in this way. If the inputs are one
-or more scalar values, then the fix generate a global scalar or vector
-of output. If the inputs are one or more vector values, then the fix
-generates a global vector or array of output. The time-averaged
-output of this fix can also be used as input to other output commands.
-
-The "fix ave/chunk"_fix_ave_chunk.html command enables direct output
-to a file of chunk-averaged per-atom quantities like those output in
-dump files. Chunks can represent spatial bins or other collections of
-atoms, e.g. individual molecules. The per-atom quantities can be atom
-density (mass or number) or atom attributes such as position,
-velocity, force. They can also be per-atom quantities calculated by a
-"compute"_compute.html, by a "fix"_fix.html, or by an atom-style
-"variable"_variable.html. The chunk-averaged output of this fix can
-also be used as input to other output commands.
-
-The "fix ave/histo"_fix_ave_histo.html command enables direct output
-to a file of histogrammed quantities, which can be global or per-atom
-or local quantities. The histogram output of this fix can also be
-used as input to other output commands.
-
-The "fix ave/correlate"_fix_ave_correlate.html command enables direct
-output to a file of time-correlated quantities, which can be global
-values. The correlation matrix output of this fix can also be used as
-input to other output commands.
-
-The "fix print"_fix_print.html command can generate a line of output
-written to the screen and log file or to a separate file, periodically
-during a running simulation. The line can contain one or more
-"variable"_variable.html values for any style variable except the
-vector or atom styles). As explained above, variables themselves can
-contain references to global values generated by "thermodynamic
-keywords"_thermo_style.html, "computes"_compute.html,
-"fixes"_fix.html, or other "variables"_variable.html, or to per-atom
-values for a specific atom. Thus the "fix print"_fix_print.html
-command is a means to output a wide variety of quantities separate
-from normal thermodynamic or dump file output.
-
-Computes that process output quantities :h4,link(computeoutput)
-
-The "compute reduce"_compute_reduce.html and "compute
-reduce/region"_compute_reduce.html commands take one or more per-atom
-or local vector quantities as inputs and "reduce" them (sum, min, max,
-ave) to scalar quantities. These are produced as output values which
-can be used as input to other output commands.
-
-The "compute slice"_compute_slice.html command take one or more global
-vector or array quantities as inputs and extracts a subset of their
-values to create a new vector or array. These are produced as output
-values which can be used as input to other output commands.
-
-The "compute property/atom"_compute_property_atom.html command takes a
-list of one or more pre-defined atom attributes (id, x, fx, etc) and
-stores the values in a per-atom vector or array. These are produced
-as output values which can be used as input to other output commands.
-The list of atom attributes is the same as for the "dump
-custom"_dump.html command.
-
-The "compute property/local"_compute_property_local.html command takes
-a list of one or more pre-defined local attributes (bond info, angle
-info, etc) and stores the values in a local vector or array. These
-are produced as output values which can be used as input to other
-output commands.
-
-Fixes that process output quantities :h4,link(fixprocoutput)
-
-The "fix vector"_fix_vector.html command can create global vectors as
-output from global scalars as input, accumulating them one element at
-a time.
-
-The "fix ave/atom"_fix_ave_atom.html command performs time-averaging
-of per-atom vectors. The per-atom quantities can be atom attributes
-such as position, velocity, force. They can also be per-atom
-quantities calculated by a "compute"_compute.html, by a
-"fix"_fix.html, or by an atom-style "variable"_variable.html. The
-time-averaged per-atom output of this fix can be used as input to
-other output commands.
-
-The "fix store/state"_fix_store_state.html command can archive one or
-more per-atom attributes at a particular time, so that the old values
-can be used in a future calculation or output. The list of atom
-attributes is the same as for the "dump custom"_dump.html command,
-including per-atom quantities calculated by a "compute"_compute.html,
-by a "fix"_fix.html, or by an atom-style "variable"_variable.html.
-The output of this fix can be used as input to other output commands.
-
-Computes that generate values to output :h4,link(compute)
-
-Every "compute"_compute.html in LAMMPS produces either global or
-per-atom or local values. The values can be scalars or vectors or
-arrays of data. These values can be output using the other commands
-described in this section. The doc page for each compute command
-describes what it produces. Computes that produce per-atom or local
-values have the word "atom" or "local" in their style name. Computes
-without the word "atom" or "local" produce global values.
-
-Fixes that generate values to output :h4,link(fix)
-
-Some "fixes"_fix.html in LAMMPS produces either global or per-atom or
-local values which can be accessed by other commands. The values can
-be scalars or vectors or arrays of data. These values can be output
-using the other commands described in this section. The doc page for
-each fix command tells whether it produces any output quantities and
-describes them.
-
-Variables that generate values to output :h4,link(variable)
-
-"Variables"_variable.html defined in an input script can store one or
-more strings. But equal-style, vector-style, and atom-style or
-atomfile-style variables generate a global scalar value, global vector
-or values, or a per-atom vector, respectively, when accessed. The
-formulas used to define these variables can contain references to the
-thermodynamic keywords and to global and per-atom data generated by
-computes, fixes, and other variables. The values generated by
-variables can be used as input to and thus output by the other
-commands described in this section.
-
-Summary table of output options and data flow between commands :h4,link(table)
-
-This table summarizes the various commands that can be used for
-generating output from LAMMPS. Each command produces output data of
-some kind and/or writes data to a file. Most of the commands can take
-data from other commands as input. Thus you can link many of these
-commands together in pipeline form, where data produced by one command
-is used as input to another command and eventually written to the
-screen or to a file. Note that to hook two commands together the
-output and input data types must match, e.g. global/per-atom/local
-data and scalar/vector/array data.
-
-Also note that, as described above, when a command takes a scalar as
-input, that could be an element of a vector or array. Likewise a
-vector input could be a column of an array.
-
-Command: Input: Output:
-"thermo_style custom"_thermo_style.html: global scalars: screen, log file:
-"dump custom"_dump.html: per-atom vectors: dump file:
-"dump local"_dump.html: local vectors: dump file:
-"fix print"_fix_print.html: global scalar from variable: screen, file:
-"print"_print.html: global scalar from variable: screen:
-"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array:
-"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array:
-"variables"_variable.html: global scalars and vectors, per-atom vectors: global scalar and vector, per-atom vector:
-"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector:
-"compute slice"_compute_slice.html: global vectors/arrays: global vector/array:
-"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array:
-"compute property/local"_compute_property_local.html: local vectors: local vector/array:
-"fix vector"_fix_vector.html: global scalars: global vector:
-"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array:
-"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file:
-"fix ave/chunk"_fix_ave_chunk.html: per-atom vectors: global array, file:
-"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file:
-"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file:
-"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array :tb(c=3,s=:)
-
-:line
-
-6.16 Thermostatting, barostatting, and computing temperature :link(howto_16),h4
-
-Thermostatting means controlling the temperature of particles in an MD
-simulation. Barostatting means controlling the pressure. Since the
-pressure includes a kinetic component due to particle velocities, both
-these operations require calculation of the temperature. Typically a
-target temperature (T) and/or pressure (P) is specified by the user,
-and the thermostat or barostat attempts to equilibrate the system to
-the requested T and/or P.
-
-Temperature is computed as kinetic energy divided by some number of
-degrees of freedom (and the Boltzmann constant). Since kinetic energy
-is a function of particle velocity, there is often a need to
-distinguish between a particle's advection velocity (due to some
-aggregate motion of particles) and its thermal velocity. The sum of
-the two is the particle's total velocity, but the latter is often what
-is wanted to compute a temperature.
-
-LAMMPS has several options for computing temperatures, any of which
-can be used in thermostatting and barostatting. These "compute
-commands"_compute.html calculate temperature, and the "compute
-pressure"_compute_pressure.html command calculates pressure.
-
-"compute temp"_compute_temp.html
-"compute temp/sphere"_compute_temp_sphere.html
-"compute temp/asphere"_compute_temp_asphere.html
-"compute temp/com"_compute_temp_com.html
-"compute temp/deform"_compute_temp_deform.html
-"compute temp/partial"_compute_temp_partial.html
-"compute temp/profile"_compute_temp_profile.html
-"compute temp/ramp"_compute_temp_ramp.html
-"compute temp/region"_compute_temp_region.html :ul
-
-All but the first 3 calculate velocity biases directly (e.g. advection
-velocities) that are removed when computing the thermal temperature.
-"Compute temp/sphere"_compute_temp_sphere.html and "compute
-temp/asphere"_compute_temp_asphere.html compute kinetic energy for
-finite-size particles that includes rotational degrees of freedom.
-They both allow for velocity biases indirectly, via an optional extra
-argument, another temperature compute that subtracts a velocity bias.
-This allows the translational velocity of spherical or aspherical
-particles to be adjusted in prescribed ways.
-
-Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one
-case by a pair style. Several thermostatting fixes are available:
-Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
-(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
-can be invoked via the {dpd/tstat} pair style:
-
-"fix nvt"_fix_nh.html
-"fix nvt/sphere"_fix_nvt_sphere.html
-"fix nvt/asphere"_fix_nvt_asphere.html
-"fix nvt/sllod"_fix_nvt_sllod.html
-"fix temp/berendsen"_fix_temp_berendsen.html
-"fix temp/csvr"_fix_temp_csvr.html
-"fix langevin"_fix_langevin.html
-"fix temp/rescale"_fix_temp_rescale.html
-"pair_style dpd/tstat"_pair_dpd.html :ul
-
-"Fix nvt"_fix_nh.html only thermostats the translational velocity of
-particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except
-that it subtracts out a velocity bias due to a deforming box and
-integrates the SLLOD equations of motion. See the "NEMD
-simulations"_#howto_13 section of this page for further details. "Fix
-nvt/sphere"_fix_nvt_sphere.html and "fix
-nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
-velocities but also rotational velocities for spherical and aspherical
-particles.
-
-DPD thermostatting alters pairwise interactions in a manner analogous
-to the per-particle thermostatting of "fix
-langevin"_fix_langevin.html.
-
-Any of the thermostatting fixes can use temperature computes that
-remove bias which has two effects. First, the current calculated
-temperature, which is compared to the requested target temperature, is
-calculated with the velocity bias removed. Second, the thermostat
-adjusts only the thermal temperature component of the particle's
-velocities, which are the velocities with the bias removed. The
-removed bias is then added back to the adjusted velocities. See the
-doc pages for the individual fixes and for the
-"fix_modify"_fix_modify.html command for instructions on how to assign
-a temperature compute to a thermostatting fix. For example, you can
-apply a thermostat to only the x and z components of velocity by using
-it in conjunction with "compute
-temp/partial"_compute_temp_partial.html. Of you could thermostat only
-the thermal temperature of a streaming flow of particles without
-affecting the streaming velocity, by using "compute
-temp/profile"_compute_temp_profile.html.
-
-NOTE: Only the nvt fixes perform time integration, meaning they update
-the velocities and positions of particles due to forces and velocities
-respectively. The other thermostat fixes only adjust velocities; they
-do NOT perform time integration updates. Thus they should be used in
-conjunction with a constant NVE integration fix such as these:
-
-"fix nve"_fix_nve.html
-"fix nve/sphere"_fix_nve_sphere.html
-"fix nve/asphere"_fix_nve_asphere.html :ul
-
-Barostatting in LAMMPS is also performed by "fixes"_fix.html. Two
-barosttating methods are currently available: Nose-Hoover (npt and
-nph) and Berendsen:
-
-"fix npt"_fix_nh.html
-"fix npt/sphere"_fix_npt_sphere.html
-"fix npt/asphere"_fix_npt_asphere.html
-"fix nph"_fix_nh.html
-"fix press/berendsen"_fix_press_berendsen.html :ul
-
-The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat
-and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;
-it does no thermostatting. Both "fix nph"_fix_nh.html and "fix
-press/berendsen"_fix_press_berendsen.html can be used in conjunction
-with any of the thermostatting fixes.
-
-As with the thermostats, "fix npt"_fix_nh.html and "fix
-nph"_fix_nh.html only use translational motion of the particles in
-computing T and P and performing thermo/barostatting. "Fix
-npt/sphere"_fix_npt_sphere.html and "fix
-npt/asphere"_fix_npt_asphere.html thermo/barostat using not only
-translation velocities but also rotational velocities for spherical
-and aspherical particles.
-
-All of the barostatting fixes use the "compute
-pressure"_compute_pressure.html compute to calculate a current
-pressure. By default, this compute is created with a simple "compute
-temp"_compute_temp.html (see the last argument of the "compute
-pressure"_compute_pressure.html command), which is used to calculated
-the kinetic component of the pressure. The barostatting fixes can
-also use temperature computes that remove bias for the purpose of
-computing the kinetic component which contributes to the current
-pressure. See the doc pages for the individual fixes and for the
-"fix_modify"_fix_modify.html command for instructions on how to assign
-a temperature or pressure compute to a barostatting fix.
-
-NOTE: As with the thermostats, the Nose/Hoover methods ("fix
-npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration.
-"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should
-be used with one of the constant NVE fixes or with one of the NVT
-fixes.
-
-Finally, thermodynamic output, which can be setup via the
-"thermo_style"_thermo_style.html command, often includes temperature
-and pressure values. As explained on the doc page for the
-"thermo_style"_thermo_style.html command, the default T and P are
-setup by the thermo command itself. They are NOT the ones associated
-with any thermostatting or barostatting fix you have defined or with
-any compute that calculates a temperature or pressure. Thus if you
-want to view these values of T and P, you need to specify them
-explicitly via a "thermo_style custom"_thermo_style.html command. Or
-you can use the "thermo_modify"_thermo_modify.html command to
-re-define what temperature or pressure compute is used for default
-thermodynamic output.
-
-:line
-
-6.17 Walls :link(howto_17),h4
-
-Walls in an MD simulation are typically used to bound particle motion,
-i.e. to serve as a boundary condition.
-
-Walls in LAMMPS can be of rough (made of particles) or idealized
-surfaces. Ideal walls can be smooth, generating forces only in the
-normal direction, or frictional, generating forces also in the
-tangential direction.
-
-Rough walls, built of particles, can be created in various ways. The
-particles themselves can be generated like any other particle, via the
-"lattice"_lattice.html and "create_atoms"_create_atoms.html commands,
-or read in via the "read_data"_read_data.html command.
-
-Their motion can be constrained by many different commands, so that
-they do not move at all, move together as a group at constant velocity
-or in response to a net force acting on them, move in a prescribed
-fashion (e.g. rotate around a point), etc. Note that if a time
-integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html
-is not used with the group that contains wall particles, their
-positions and velocities will not be updated.
-
-"fix aveforce"_fix_aveforce.html - set force on particles to average value, so they move together
-"fix setforce"_fix_setforce.html - set force on particles to a value, e.g. 0.0
-"fix freeze"_fix_freeze.html - freeze particles for use as granular walls
-"fix nve/noforce"_fix_nve_noforce.html - advect particles by their velocity, but without force
-"fix move"_fix_move.html - prescribe motion of particles by a linear velocity, oscillation, rotation, variable :ul
-
-The "fix move"_fix_move.html command offers the most generality, since
-the motion of individual particles can be specified with
-"variable"_variable.html formula which depends on time and/or the
-particle position.
-
-For rough walls, it may be useful to turn off pairwise interactions
-between wall particles via the "neigh_modify
-exclude"_neigh_modify.html command.
-
-Rough walls can also be created by specifying frozen particles that do
-not move and do not interact with mobile particles, and then tethering
-other particles to the fixed particles, via a "bond"_bond_style.html.
-The bonded particles do interact with other mobile particles.
-
-Idealized walls can be specified via several fix commands. "Fix
-wall/gran"_fix_wall_gran.html creates frictional walls for use with
-granular particles; all the other commands create smooth walls.
-
-"fix wall/reflect"_fix_wall_reflect.html - reflective flat walls
-"fix wall/lj93"_fix_wall.html - flat walls, with Lennard-Jones 9/3 potential
-"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential
-"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential
-"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential
-"fix wall/region"_fix_wall_region.html - use region surface as wall
-"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul
-
-The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the
-flat walls to move with a constant velocity, or oscillate in time.
-The "fix wall/region"_fix_wall_region.html command offers the most
-generality, since the region surface is treated as a wall, and the
-geometry of the region can be a simple primitive volume (e.g. a
-sphere, or cube, or plane), or a complex volume made from the union
-and intersection of primitive volumes. "Regions"_region.html can also
-specify a volume "interior" or "exterior" to the specified primitive
-shape or {union} or {intersection}. "Regions"_region.html can also be
-"dynamic" meaning they move with constant velocity, oscillate, or
-rotate.
-
-The only frictional idealized walls currently in LAMMPS are flat or
-curved surfaces specified by the "fix wall/gran"_fix_wall_gran.html
-command. At some point we plan to allow regoin surfaces to be used as
-frictional walls, as well as triangulated surfaces.
-
-:line
-
-6.18 Elastic constants :link(howto_18),h4
-
-Elastic constants characterize the stiffness of a material. The formal
-definition is provided by the linear relation that holds between the
-stress and strain tensors in the limit of infinitesimal deformation.
-In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where
-the repeated indices imply summation. s_ij are the elements of the
-symmetric stress tensor. e_kl are the elements of the symmetric strain
-tensor. C_ijkl are the elements of the fourth rank tensor of elastic
-constants. In three dimensions, this tensor has 3^4=81 elements. Using
-Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
-is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
-derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
-most 7*6/2 = 21 distinct elements.
-
-At zero temperature, it is easy to estimate these derivatives by
-deforming the simulation box in one of the six directions using the
-"change_box"_change_box.html command and measuring the change in the
-stress tensor. A general-purpose script that does this is given in the
-examples/elastic directory described on the "Examples"_Examples.html
-doc page.
-
-Calculating elastic constants at finite temperature is more
-challenging, because it is necessary to run a simulation that perfoms
-time averages of differential properties. One way to do this is to
-measure the change in average stress tensor in an NVT simulations when
-the cell volume undergoes a finite deformation. In order to balance
-the systematic and statistical errors in this method, the magnitude of
-the deformation must be chosen judiciously, and care must be taken to
-fully equilibrate the deformed cell before sampling the stress
-tensor. Another approach is to sample the triclinic cell fluctuations
-that occur in an NPT simulation. This method can also be slow to
-converge and requires careful post-processing "(Shinoda)"_#Shinoda1
-
-:line
-
-6.19 Library interface to LAMMPS :link(howto_19),h4
-
-As described in "Section 2.5"_Section_start.html#start_5, LAMMPS can
-be built as a library, so that it can be called by another code, used
-in a "coupled manner"_Section_howto.html#howto_10 with other codes, or
-driven through a "Python interface"_Python.html.
-
-All of these methodologies use a C-style interface to LAMMPS that is
-provided in the files src/library.cpp and src/library.h. The
-functions therein have a C-style argument list, but contain C++ code
-you could write yourself in a C++ application that was invoking LAMMPS
-directly. The C++ code in the functions illustrates how to invoke
-internal LAMMPS operations. Note that LAMMPS classes are defined
-within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
-application.
-
-The examples/COUPLE and python/examples directories have example C++
-and C and Python codes which show how a driver code can link to LAMMPS
-as a library, run LAMMPS on a subset of processors, grab data from
-LAMMPS, change it, and put it back into LAMMPS.
-
-The file src/library.cpp contains the following functions for creating
-and destroying an instance of LAMMPS and sending it commands to
-execute. See the documentation in the src/library.cpp file for
-details.
-
-NOTE: You can write code for additional functions as needed to define
-how your code talks to LAMMPS and add them to src/library.cpp and
-src/library.h, as well as to the "Python interface"_Python.html. The
-added functions can access or change any internal LAMMPS data you
-wish.
-
-void lammps_open(int, char **, MPI_Comm, void **)
-void lammps_open_no_mpi(int, char **, void **)
-void lammps_close(void *)
-int lammps_version(void *)
-void lammps_file(void *, char *)
-char *lammps_command(void *, char *)
-void lammps_commands_list(void *, int, char **)
-void lammps_commands_string(void *, char *)
-void lammps_free(void *) :pre
-
-The lammps_open() function is used to initialize LAMMPS, passing in a
-list of strings as if they were "command-line
-arguments"_Section_start.html#start_6 when LAMMPS is run in
-stand-alone mode from the command line, and a MPI communicator for
-LAMMPS to run under. It returns a ptr to the LAMMPS object that is
-created, and which is used in subsequent library calls. The
-lammps_open() function can be called multiple times, to create
-multiple instances of LAMMPS.
-
-LAMMPS will run on the set of processors in the communicator. This
-means the calling code can run LAMMPS on all or a subset of
-processors. For example, a wrapper script might decide to alternate
-between LAMMPS and another code, allowing them both to run on all the
-processors. Or it might allocate half the processors to LAMMPS and
-half to the other code and run both codes simultaneously before
-syncing them up periodically. Or it might instantiate multiple
-instances of LAMMPS to perform different calculations.
-
-The lammps_open_no_mpi() function is similar except that no MPI
-communicator is passed from the caller. Instead, MPI_COMM_WORLD is
-used to instantiate LAMMPS, and MPI is initialized if necessary.
-
-The lammps_close() function is used to shut down an instance of LAMMPS
-and free all its memory.
-
-The lammps_version() function can be used to determined the specific
-version of the underlying LAMMPS code. This is particularly useful
-when loading LAMMPS as a shared library via dlopen(). The code using
-the library interface can than use this information to adapt to
-changes to the LAMMPS command syntax between versions. The returned
-LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
-20150902) that grows with every new LAMMPS version.
-
-The lammps_file(), lammps_command(), lammps_commands_list(), and
-lammps_commands_string() functions are used to pass one or more
-commands to LAMMPS to execute, the same as if they were coming from an
-input script.
-
-Via these functions, the calling code can read or generate a series of
-LAMMPS commands one or multiple at a time and pass it thru the library
-interface to setup a problem and then run it in stages. The caller
-can interleave the command function calls with operations it performs,
-calls to extract information from or set information within LAMMPS, or
-calls to another code's library.
-
-The lammps_file() function passes the filename of an input script.
-The lammps_command() function passes a single command as a string.
-The lammps_commands_list() function passes multiple commands in a
-char** list. In both lammps_command() and lammps_commands_list(),
-individual commands may or may not have a trailing newline. The
-lammps_commands_string() function passes multiple commands
-concatenated into one long string, separated by newline characters.
-In both lammps_commands_list() and lammps_commands_string(), a single
-command can be spread across multiple lines, if the last printable
-character of all but the last line is "&", the same as if the lines
-appeared in an input script.
-
-The lammps_free() function is a clean-up function to free memory that
-the library allocated previously via other function calls. See
-comments in src/library.cpp file for which other functions need this
-clean-up.
-
-The file src/library.cpp also contains these functions for extracting
-information from LAMMPS and setting value within LAMMPS. Again, see
-the documentation in the src/library.cpp file for details, including
-which quantities can be queried by name:
-
-int lammps_extract_setting(void *, char *)
-void *lammps_extract_global(void *, char *)
-void lammps_extract_box(void *, double *, double *,
- double *, double *, double *, int *, int *)
-void *lammps_extract_atom(void *, char *)
-void *lammps_extract_compute(void *, char *, int, int)
-void *lammps_extract_fix(void *, char *, int, int, int, int)
-void *lammps_extract_variable(void *, char *, char *) :pre
-
-The extract_setting() function returns info on the size
-of data types (e.g. 32-bit or 64-bit atom IDs) used
-by the LAMMPS executable (a compile-time choice).
-
-The other extract functions return a pointer to various global or
-per-atom quantities stored in LAMMPS or to values calculated by a
-compute, fix, or variable. The pointer returned by the
-extract_global() function can be used as a permanent reference to a
-value which may change. For the extract_atom() method, see the
-extract() method in the src/atom.cpp file for a list of valid per-atom
-properties. New names could easily be added if the property you want
-is not listed. For the other extract functions, the underlying
-storage may be reallocated as LAMMPS runs, so you need to re-call the
-function to assure a current pointer or returned value(s).
-
-double lammps_get_thermo(void *, char *)
-int lammps_get_natoms(void *) :pre
-
-int lammps_set_variable(void *, char *, char *)
-void lammps_reset_box(void *, double *, double *, double, double, double) :pre
-
-The lammps_get_thermo() function returns the current value of a thermo
-keyword as a double precision value.
-
-The lammps_get_natoms() function returns the total number of atoms in
-the system and can be used by the caller to allocate memory for the
-lammps_gather_atoms() and lammps_scatter_atoms() functions.
-
-The lammps_set_variable() function can set an existing string-style
-variable to a new string value, so that subsequent LAMMPS commands can
-access the variable.
-
-The lammps_reset_box() function resets the size and shape of the
-simulation box, e.g. as part of restoring a previously extracted and
-saved state of a simulation.
-
-void lammps_gather_atoms(void *, char *, int, int, void *)
-void lammps_gather_atoms_concat(void *, char *, int, int, void *)
-void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *)
-void lammps_scatter_atoms(void *, char *, int, int, void *)
-void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre
-
-void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
- imageint *, int) :pre
-
-The gather functions collect peratom info of the requested type (atom
-coords, atom types, forces, etc) from all processors, and returns the
-same vector of values to each callling processor. The scatter
-functions do the inverse. They distribute a vector of peratom values,
-passed by all calling processors, to invididual atoms, which may be
-owned by different processos.
-
-The lammps_gather_atoms() function does this for all N atoms in the
-system, ordered by atom ID, from 1 to N. The
-lammps_gather_atoms_concat() function does it for all N atoms, but
-simply concatenates the subset of atoms owned by each processor. The
-resulting vector is not ordered by atom ID. Atom IDs can be requetsed
-by the same function if the caller needs to know the ordering. The
-lammps_gather_subset() function allows the caller to request values
-for only a subset of atoms (identified by ID).
-For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
-If the count is specified as 1, they are returned
-in a packed format with all three image flags stored in a single integer.
-If the count is specified as 3, the values are unpacked into xyz flags
-by the library before returning them.
-
-The lammps_scatter_atoms() function takes a list of values for all N
-atoms in the system, ordered by atom ID, from 1 to N, and assigns
-those values to each atom in the system. The
-lammps_scatter_atoms_subset() function takes a subset of IDs as an
-argument and only scatters those values to the owning atoms.
-
-The lammps_create_atoms() function takes a list of N atoms as input
-with atom types and coords (required), an optionally atom IDs and
-velocities and image flags. It uses the coords of each atom to assign
-it as a new atom to the processor that owns it. This function is
-useful to add atoms to a simulation or (in tandem with
-lammps_reset_box()) to restore a previously extracted and saved state
-of a simulation. Additional properties for the new atoms can then be
-assigned via the lammps_scatter_atoms() or lammps_extract_atom()
-functions.
-
-:line
-
-6.20 Calculating thermal conductivity :link(howto_20),h4
-
-The thermal conductivity kappa of a material can be measured in at
-least 4 ways using various options in LAMMPS. See the examples/KAPPA
-directory for scripts that implement the 4 methods discussed here for
-a simple Lennard-Jones fluid model. Also, see "this
-section"_Section_howto.html#howto_21 of the manual for an analogous
-discussion for viscosity.
-
-The thermal conductivity tensor kappa is a measure of the propensity
-of a material to transmit heat energy in a diffusive manner as given
-by Fourier's law
-
-J = -kappa grad(T)
-
-where J is the heat flux in units of energy per area per time and
-grad(T) is the spatial gradient of temperature. The thermal
-conductivity thus has units of energy per distance per time per degree
-K and is often approximated as an isotropic quantity, i.e. as a
-scalar.
-
-The first method is to setup two thermostatted regions at opposite
-ends of a simulation box, or one in the middle and one at the end of a
-periodic box. By holding the two regions at different temperatures
-with a "thermostatting fix"_Section_howto.html#howto_13, the energy
-added to the hot region should equal the energy subtracted from the
-cold region and be proportional to the heat flux moving between the
-regions. See the papers by "Ikeshoji and Hafskjold"_#howto-Ikeshoji
-and "Wirnsberger et al"_#howto-Wirnsberger for details of this idea.
-Note that thermostatting fixes such as "fix nvt"_fix_nh.html, "fix
-langevin"_fix_langevin.html, and "fix
-temp/rescale"_fix_temp_rescale.html store the cumulative energy they
-add/subtract.
-
-Alternatively, as a second method, the "fix heat"_fix_heat.html or
-"fix ehex"_fix_ehex.html commands can be used in place of thermostats
-on each of two regions to add/subtract specified amounts of energy to
-both regions. In both cases, the resulting temperatures of the two
-regions can be monitored with the "compute temp/region" command and
-the temperature profile of the intermediate region can be monitored
-with the "fix ave/chunk"_fix_ave_chunk.html and "compute
-ke/atom"_compute_ke_atom.html commands.
-
-The third method is to perform a reverse non-equilibrium MD simulation
-using the "fix thermal/conductivity"_fix_thermal_conductivity.html
-command which implements the rNEMD algorithm of Muller-Plathe.
-Kinetic energy is swapped between atoms in two different layers of the
-simulation box. This induces a temperature gradient between the two
-layers which can be monitored with the "fix
-ave/chunk"_fix_ave_chunk.html and "compute
-ke/atom"_compute_ke_atom.html commands. The fix tallies the
-cumulative energy transfer that it performs. See the "fix
-thermal/conductivity"_fix_thermal_conductivity.html command for
-details.
-
-The fourth method is based on the Green-Kubo (GK) formula which
-relates the ensemble average of the auto-correlation of the heat flux
-to kappa. The heat flux can be calculated from the fluctuations of
-per-atom potential and kinetic energies and per-atom stress tensor in
-a steady-state equilibrated simulation. This is in contrast to the
-two preceding non-equilibrium methods, where energy flows continuously
-between hot and cold regions of the simulation box.
-
-The "compute heat/flux"_compute_heat_flux.html command can calculate
-the needed heat flux and describes how to implement the Green_Kubo
-formalism using additional LAMMPS commands, such as the "fix
-ave/correlate"_fix_ave_correlate.html command to calculate the needed
-auto-correlation. See the doc page for the "compute
-heat/flux"_compute_heat_flux.html command for an example input script
-that calculates the thermal conductivity of solid Ar via the GK
-formalism.
-
-:line
-
-6.21 Calculating viscosity :link(howto_21),h4
-
-The shear viscosity eta of a fluid can be measured in at least 5 ways
-using various options in LAMMPS. See the examples/VISCOSITY directory
-for scripts that implement the 5 methods discussed here for a simple
-Lennard-Jones fluid model. Also, see "this
-section"_Section_howto.html#howto_20 of the manual for an analogous
-discussion for thermal conductivity.
-
-Eta is a measure of the propensity of a fluid to transmit momentum in
-a direction perpendicular to the direction of velocity or momentum
-flow. Alternatively it is the resistance the fluid has to being
-sheared. It is given by
-
-J = -eta grad(Vstream)
-
-where J is the momentum flux in units of momentum per area per time.
-and grad(Vstream) is the spatial gradient of the velocity of the fluid
-moving in another direction, normal to the area through which the
-momentum flows. Viscosity thus has units of pressure-time.
-
-The first method is to perform a non-equilibrium MD (NEMD) simulation
-by shearing the simulation box via the "fix deform"_fix_deform.html
-command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to
-thermostat the fluid via the SLLOD equations of motion.
-Alternatively, as a second method, one or more moving walls can be
-used to shear the fluid in between them, again with some kind of
-thermostat that modifies only the thermal (non-shearing) components of
-velocity to prevent the fluid from heating up.
-
-In both cases, the velocity profile setup in the fluid by this
-procedure can be monitored by the "fix
-ave/chunk"_fix_ave_chunk.html command, which determines
-grad(Vstream) in the equation above. E.g. the derivative in the
-y-direction of the Vx component of fluid motion or grad(Vstream) =
-dVx/dy. The Pxy off-diagonal component of the pressure or stress
-tensor, as calculated by the "compute pressure"_compute_pressure.html
-command, can also be monitored, which is the J term in the equation
-above. See "this section"_Section_howto.html#howto_13 of the manual
-for details on NEMD simulations.
-
-The third method is to perform a reverse non-equilibrium MD simulation
-using the "fix viscosity"_fix_viscosity.html command which implements
-the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
-swapped between atoms in two different layers of the simulation box in
-a different dimension. This induces a velocity gradient which can be
-monitored with the "fix ave/chunk"_fix_ave_chunk.html command.
-The fix tallies the cumulative momentum transfer that it performs.
-See the "fix viscosity"_fix_viscosity.html command for details.
-
-The fourth method is based on the Green-Kubo (GK) formula which
-relates the ensemble average of the auto-correlation of the
-stress/pressure tensor to eta. This can be done in a fully
-equilibrated simulation which is in contrast to the two preceding
-non-equilibrium methods, where momentum flows continuously through the
-simulation box.
-
-Here is an example input script that calculates the viscosity of
-liquid Ar via the GK formalism:
-
-# Sample LAMMPS input script for viscosity of liquid Ar :pre
-
-units real
-variable T equal 86.4956
-variable V equal vol
-variable dt equal 4.0
-variable p equal 400 # correlation length
-variable s equal 5 # sample interval
-variable d equal $p*$s # dump interval :pre
-
-# convert from LAMMPS real units to SI :pre
-
-variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann
-variable atm2Pa equal 101325.0
-variable A2m equal 1.0e-10
-variable fs2s equal 1.0e-15
-variable convert equal $\{atm2Pa\}*$\{atm2Pa\}*$\{fs2s\}*$\{A2m\}*$\{A2m\}*$\{A2m\} :pre
-
-# setup problem :pre
-
-dimension 3
-boundary p p p
-lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
-region box block 0 4 0 4 0 4
-create_box 1 box
-create_atoms 1 box
-mass 1 39.948
-pair_style lj/cut 13.0
-pair_coeff * * 0.2381 3.405
-timestep $\{dt\}
-thermo $d :pre
-
-# equilibration and thermalization :pre
-
-velocity all create $T 102486 mom yes rot yes dist gaussian
-fix NVT all nvt temp $T $T 10 drag 0.2
-run 8000 :pre
-
-# viscosity calculation, switch to NVE if desired :pre
-
-#unfix NVT
-#fix NVE all nve :pre
-
-reset_timestep 0
-variable pxy equal pxy
-variable pxz equal pxz
-variable pyz equal pyz
-fix SS all ave/correlate $s $p $d &
- v_pxy v_pxz v_pyz type auto file S0St.dat ave running
-variable scale equal $\{convert\}/($\{kB\}*$T)*$V*$s*$\{dt\}
-variable v11 equal trap(f_SS\[3\])*$\{scale\}
-variable v22 equal trap(f_SS\[4\])*$\{scale\}
-variable v33 equal trap(f_SS\[5\])*$\{scale\}
-thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
-run 100000
-variable v equal (v_v11+v_v22+v_v33)/3.0
-variable ndens equal count(all)/vol
-print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre
-
-The fifth method is related to the above Green-Kubo method,
-but uses the Einstein formulation, analogous to the Einstein
-mean-square-displacement formulation for self-diffusivity. The
-time-integrated momentum fluxes play the role of Cartesian
-coordinates, whose mean-square displacement increases linearly
-with time at sufficiently long times.
-
-:line
-
-6.22 Calculating a diffusion coefficient :link(howto_22),h4
-
-The diffusion coefficient D of a material can be measured in at least
-2 ways using various options in LAMMPS. See the examples/DIFFUSE
-directory for scripts that implement the 2 methods discussed here for
-a simple Lennard-Jones fluid model.
-
-The first method is to measure the mean-squared displacement (MSD) of
-the system, via the "compute msd"_compute_msd.html command. The slope
-of the MSD versus time is proportional to the diffusion coefficient.
-The instantaneous MSD values can be accumulated in a vector via the
-"fix vector"_fix_vector.html command, and a line fit to the vector to
-compute its slope via the "variable slope"_variable.html function, and
-thus extract D.
-
-The second method is to measure the velocity auto-correlation function
-(VACF) of the system, via the "compute vacf"_compute_vacf.html
-command. The time-integral of the VACF is proportional to the
-diffusion coefficient. The instantaneous VACF values can be
-accumulated in a vector via the "fix vector"_fix_vector.html command,
-and time integrated via the "variable trap"_variable.html function,
-and thus extract D.
-
-:line
-
-6.23 Using chunks to calculate system properties :link(howto_23),h4
-
-In LAMMS, "chunks" are collections of atoms, as defined by the
-"compute chunk/atom"_compute_chunk_atom.html command, which assigns
-each atom to a chunk ID (or to no chunk at all). The number of chunks
-and the assignment of chunk IDs to atoms can be static or change over
-time. Examples of "chunks" are molecules or spatial bins or atoms
-with similar values (e.g. coordination number or potential energy).
-
-The per-atom chunk IDs can be used as input to two other kinds of
-commands, to calculate various properties of a system:
-
-"fix ave/chunk"_fix_ave_chunk.html
-any of the "compute */chunk"_compute.html commands :ul
-
-Here, each of the 3 kinds of chunk-related commands is briefly
-overviewed. Then some examples are given of how to compute different
-properties with chunk commands.
-
-Compute chunk/atom command: :h4
-
-This compute can assign atoms to chunks of various styles. Only atoms
-in the specified group and optional specified region are assigned to a
-chunk. Here are some possible chunk definitions:
-
-atoms in same molecule | chunk ID = molecule ID |
-atoms of same atom type | chunk ID = atom type |
-all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom |
-atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command |
-atoms in same spatial bin | chunk ID = bin ID |
-atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies |
-atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html |
-atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2)
-
-Note that chunk IDs are integer values, so for atom properties or
-computes that produce a floating point value, they will be truncated
-to an integer. You could also use the compute in a variable that
-scales the floating point value to spread it across multiple integers.
-
-Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
-pencils, 3d bins = boxes, spherical bins, cylindrical bins.
-
-This compute also calculates the number of chunks {Nchunk}, which is
-used by other commands to tally per-chunk data. {Nchunk} can be a
-static value or change over time (e.g. the number of clusters). The
-chunk ID for an individual atom can also be static (e.g. a molecule
-ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
-
-Note that this compute allows the per-atom output of other
-"computes"_compute.html, "fixes"_fix.html, and
-"variables"_variable.html to be used to define chunk IDs for each
-atom. This means you can write your own compute or fix to output a
-per-atom quantity to use as chunk ID. See the "Modify"_Modify.html
-doc page for how to do this. You can also define a "per-atom
-variable"_variable.html in the input script that uses a formula to
-generate a chunk ID for each atom.
-
-Fix ave/chunk command: :h4
-
-This fix takes the ID of a "compute
-chunk/atom"_compute_chunk_atom.html command as input. For each chunk,
-it then sums one or more specified per-atom values over the atoms in
-each chunk. The per-atom values can be any atom property, such as
-velocity, force, charge, potential energy, kinetic energy, stress,
-etc. Additional keywords are defined for per-chunk properties like
-density and temperature. More generally any per-atom value generated
-by other "computes"_compute.html, "fixes"_fix.html, and "per-atom
-variables"_variable.html, can be summed over atoms in each chunk.
-
-Similar to other averaging fixes, this fix allows the summed per-chunk
-values to be time-averaged in various ways, and output to a file. The
-fix produces a global array as output with one row of values per
-chunk.
-
-Compute */chunk commands: :h4
-
-Currently the following computes operate on chunks of atoms to produce
-per-chunk values.
-
-"compute com/chunk"_compute_com_chunk.html
-"compute gyration/chunk"_compute_gyration_chunk.html
-"compute inertia/chunk"_compute_inertia_chunk.html
-"compute msd/chunk"_compute_msd_chunk.html
-"compute property/chunk"_compute_property_chunk.html
-"compute temp/chunk"_compute_temp_chunk.html
-"compute torque/chunk"_compute_vcm_chunk.html
-"compute vcm/chunk"_compute_vcm_chunk.html :ul
-
-They each take the ID of a "compute
-chunk/atom"_compute_chunk_atom.html command as input. As their names
-indicate, they calculate the center-of-mass, radius of gyration,
-moments of inertia, mean-squared displacement, temperature, torque,
-and velocity of center-of-mass for each chunk of atoms. The "compute
-property/chunk"_compute_property_chunk.html command can tally the
-count of atoms in each chunk and extract other per-chunk properties.
-
-The reason these various calculations are not part of the "fix
-ave/chunk command"_fix_ave_chunk.html, is that each requires a more
-complicated operation than simply summing and averaging over per-atom
-values in each chunk. For example, many of them require calculation
-of a center of mass, which requires summing mass*position over the
-atoms and then dividing by summed mass.
-
-All of these computes produce a global vector or global array as
-output, wih one or more values per chunk. They can be used
-in various ways:
-
-As input to the "fix ave/time"_fix_ave_time.html command, which can
-write the values to a file and optionally time average them. :ulb,l
-
-As input to the "fix ave/histo"_fix_ave_histo.html command to
-histogram values across chunks. E.g. a histogram of cluster sizes or
-molecule diffusion rates. :l
-
-As input to special functions of "equal-style
-variables"_variable.html, like sum() and max(). E.g. to find the
-largest cluster or fastest diffusing molecule. :l
-:ule
-
-Example calculations with chunks :h4
-
-Here are examples using chunk commands to calculate various
-properties:
-
-(1) Average velocity in each of 1000 2d spatial bins:
-
-compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
-fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre
-
-(2) Temperature in each spatial bin, after subtracting a flow
-velocity:
-
-compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
-compute vbias all temp/profile 1 0 0 y 10
-fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre
-
-(3) Center of mass of each molecule:
-
-compute cc1 all chunk/atom molecule
-compute myChunk all com/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre
-
-(4) Total force on each molecule and ave/max across all molecules:
-
-compute cc1 all chunk/atom molecule
-fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
-variable xave equal ave(f_1\[2\])
-variable xmax equal max(f_1\[2\])
-thermo 1000
-thermo_style custom step temp v_xave v_xmax :pre
-
-(5) Histogram of cluster sizes:
-
-compute cluster all cluster/atom 1.0
-compute cc1 all chunk/atom c_cluster compress yes
-compute size all property/chunk cc1 count
-fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
-
-:line
-
-6.24 Setting parameters for the "kspace_style pppm/disp"_kspace_style.html command :link(howto_24),h4
-
-The PPPM method computes interactions by splitting the pair potential
-into two parts, one of which is computed in a normal pairwise fashion,
-the so-called real-space part, and one of which is computed using the
-Fourier transform, the so called reciprocal-space or kspace part. For
-both parts, the potential is not computed exactly but is approximated.
-Thus, there is an error in both parts of the computation, the
-real-space and the kspace error. The just mentioned facts are true
-both for the PPPM for Coulomb as well as dispersion interactions. The
-deciding difference - and also the reason why the parameters for
-pppm/disp have to be selected with more care - is the impact of the
-errors on the results: The kspace error of the PPPM for Coulomb and
-dispersion interaction and the real-space error of the PPPM for
-Coulomb interaction have the character of noise. In contrast, the
-real-space error of the PPPM for dispersion has a clear physical
-interpretation: the underprediction of cohesion. As a consequence, the
-real-space error has a much stronger effect than the kspace error on
-simulation results for pppm/disp. Parameters must thus be chosen in a
-way that this error is much smaller than the kspace error.
-
-When using pppm/disp and not making any specifications on the PPPM
-parameters via the kspace modify command, parameters will be tuned
-such that the real-space error and the kspace error are equal. This
-will result in simulations that are either inaccurate or slow, both of
-which is not desirable. For selecting parameters for the pppm/disp
-that provide fast and accurate simulations, there are two approaches,
-which both have their up- and downsides.
-
-The first approach is to set desired real-space an kspace accuracies
-via the {kspace_modify force/disp/real} and {kspace_modify
-force/disp/kspace} commands. Note that the accuracies have to be
-specified in force units and are thus dependent on the chosen unit
-settings. For real units, 0.0001 and 0.002 seem to provide reasonable
-accurate and efficient computations for the real-space and kspace
-accuracies. 0.002 and 0.05 work well for most systems using lj
-units. PPPM parameters will be generated based on the desired
-accuracies. The upside of this approach is that it usually provides a
-good set of parameters and will work for both the {kspace_modify diff
-ad} and {kspace_modify diff ik} options. The downside of the method
-is that setting the PPPM parameters will take some time during the
-initialization of the simulation.
-
-The second approach is to set the parameters for the pppm/disp
-explicitly using the {kspace_modify mesh/disp}, {kspace_modify
-order/disp}, and {kspace_modify gewald/disp} commands. This approach
-requires a more experienced user who understands well the impact of
-the choice of parameters on the simulation accuracy and
-performance. This approach provides a fast initialization of the
-simulation. However, it is sensitive to errors: A combination of
-parameters that will perform well for one system might result in
-far-from-optimal conditions for other simulations. For example,
-parameters that provide accurate and fast computations for
-all-atomistic force fields can provide insufficient accuracy or
-united-atomistic force fields (which is related to that the latter
-typically have larger dispersion coefficients).
-
-To avoid inaccurate or inefficient simulations, the pppm/disp stops
-simulations with an error message if no action is taken to control the
-PPPM parameters. If the automatic parameter generation is desired and
-real-space and kspace accuracies are desired to be equal, this error
-message can be suppressed using the {kspace_modify disp/auto yes}
-command.
-
-A reasonable approach that combines the upsides of both methods is to
-make the first run using the {kspace_modify force/disp/real} and
-{kspace_modify force/disp/kspace} commands, write down the PPPM
-parameters from the outut, and specify these parameters using the
-second approach in subsequent runs (which have the same composition,
-force field, and approximately the same volume).
-
-Concerning the performance of the pppm/disp there are two more things
-to consider. The first is that when using the pppm/disp, the cutoff
-parameter does no longer affect the accuracy of the simulation
-(subject to that gewald/disp is adjusted when changing the cutoff).
-The performance can thus be increased by examining different values
-for the cutoff parameter. A lower bound for the cutoff is only set by
-the truncation error of the repulsive term of pair potentials.
-
-The second is that the mixing rule of the pair style has an impact on
-the computation time when using the pppm/disp. Fastest computations
-are achieved when using the geometric mixing rule. Using the
-arithmetic mixing rule substantially increases the computational cost.
-The computational overhead can be reduced using the {kspace_modify
-mix/disp geom} and {kspace_modify splittol} commands. The first
-command simply enforces geometric mixing of the dispersion
-coefficients in kspace computations. This introduces some error in
-the computations but will also significantly speed-up the
-simulations. The second keyword sets the accuracy with which the
-dispersion coefficients are approximated using a matrix factorization
-approach. This may result in better accuracy then using the first
-command, but will usually also not provide an equally good increase of
-efficiency.
-
-Finally, pppm/disp can also be used when no mixing rules apply.
-This can be achieved using the {kspace_modify mix/disp none} command.
-Note that the code does not check automatically whether any mixing
-rule is fulfilled. If mixing rules do not apply, the user will have
-to specify this command explicitly.
-
-:line
-
-6.25 Polarizable models :link(howto_25),h4
-
-In polarizable force fields the charge distributions in molecules and
-materials respond to their electrostatic environments. Polarizable
-systems can be simulated in LAMMPS using three methods:
-
-the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html
-package, :ulb,l
-the adiabatic core-shell method, implemented in the
-"CORESHELL"_#howto_26 package, :l
-the thermalized Drude dipole method, implemented in the
-"USER-DRUDE"_#howto_27 package. :l
-:ule
-
-The fluctuating charge method calculates instantaneous charges on
-interacting atoms based on the electronegativity equalization
-principle. It is implemented in the "fix qeq"_fix_qeq.html which is
-available in several variants. It is a relatively efficient technique
-since no additional particles are introduced. This method allows for
-charge transfer between molecules or atom groups. However, because the
-charges are located at the interaction sites, off-plane components of
-polarization cannot be represented in planar molecules or atom groups.
-
-The two other methods share the same basic idea: polarizable atoms are
-split into one core atom and one satellite particle (called shell or
-Drude particle) attached to it by a harmonic spring. Both atoms bear
-a charge and they represent collectively an induced electric dipole.
-These techniques are computationally more expensive than the QEq
-method because of additional particles and bonds. These two
-charge-on-spring methods differ in certain features, with the
-core-shell model being normally used for ionic/crystalline materials,
-whereas the so-called Drude model is normally used for molecular
-systems and fluid states.
-
-The core-shell model is applicable to crystalline materials where the
-high symmetry around each site leads to stable trajectories of the
-core-shell pairs. However, bonded atoms in molecules can be so close
-that a core would interact too strongly or even capture the Drude
-particle of a neighbor. The Drude dipole model is relatively more
-complex in order to remediate this and other issues. Specifically, the
-Drude model includes specific thermostating of the core-Drude pairs
-and short-range damping of the induced dipoles.
-
-The three polarization methods can be implemented through a
-self-consistent calculation of charges or induced dipoles at each
-timestep. In the fluctuating charge scheme this is done by the matrix
-inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell
-or Drude-dipoles the relaxed-dipoles technique would require an slow
-iterative procedure. These self-consistent solutions yield accurate
-trajectories since the additional degrees of freedom representing
-polarization are massless. An alternative is to attribute a mass to
-the additional degrees of freedom and perform time integration using
-an extended Lagrangian technique. For the fluctuating charge scheme
-this is done by "fix qeq/dynamic"_fix_qeq.html, and for the
-charge-on-spring models by the methods outlined in the next two
-sections. The assignment of masses to the additional degrees of
-freedom can lead to unphysical trajectories if care is not exerted in
-choosing the parameters of the polarizable models and the simulation
-conditions.
-
-In the core-shell model the vibration of the shells is kept faster
-than the ionic vibrations to mimic the fast response of the
-polarizable electrons. But in molecular systems thermalizing the
-core-Drude pairs at temperatures comparable to the rest of the
-simulation leads to several problems (kinetic energy transfer, too
-short a timestep, etc.) In order to avoid these problems the relative
-motion of the Drude particles with respect to their cores is kept
-"cold" so the vibration of the core-Drude pairs is very slow,
-approaching the self-consistent regime. In both models the
-temperature is regulated using the velocities of the center of mass of
-core+shell (or Drude) pairs, but in the Drude model the actual
-relative core-Drude particle motion is thermostated separately as
-well.
-
-:line
-
-6.26 Adiabatic core/shell model :link(howto_26),h4
-
-The adiabatic core-shell model by "Mitchell and
-Fincham"_#MitchellFincham is a simple method for adding
-polarizability to a system. In order to mimic the electron shell of
-an ion, a satellite particle is attached to it. This way the ions are
-split into a core and a shell where the latter is meant to react to
-the electrostatic environment inducing polarizability.
-
-Technically, shells are attached to the cores by a spring force f =
-k*r where k is a parametrized spring constant and r is the distance
-between the core and the shell. The charges of the core and the shell
-add up to the ion charge, thus q(ion) = q(core) + q(shell). This
-setup introduces the ion polarizability (alpha) given by
-alpha = q(shell)^2 / k. In a
-similar fashion the mass of the ion is distributed on the core and the
-shell with the core having the larger mass.
-
-To run this model in LAMMPS, "atom_style"_atom_style.html {full} can
-be used since atom charge and bonds are needed. Each kind of
-core/shell pair requires two atom types and a bond type. The core and
-shell of a core/shell pair should be bonded to each other with a
-harmonic bond that provides the spring force. For example, a data file
-for NaCl, as found in examples/coreshell, has this format:
-
-432 atoms # core and shell atoms
-216 bonds # number of core/shell springs :pre
-
-4 atom types # 2 cores and 2 shells for Na and Cl
-2 bond types :pre
-
-0.0 24.09597 xlo xhi
-0.0 24.09597 ylo yhi
-0.0 24.09597 zlo zhi :pre
-
-Masses # core/shell mass ratio = 0.1 :pre
-
-1 20.690784 # Na core
-2 31.90500 # Cl core
-3 2.298976 # Na shell
-4 3.54500 # Cl shell :pre
-
-Atoms :pre
-
-1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
-2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
-3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
-4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
-(...) :pre
-
-Bonds # Bond topology for spring forces :pre
-
-1 2 1 2 # spring for core/shell pair 1
-2 2 3 4 # spring for core/shell pair 2
-(...) :pre
-
-Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
-defined between the shells. Coulombic interactions are defined
-between all cores and shells. If desired, additional bonds can be
-specified between cores.
-
-The "special_bonds"_special_bonds.html command should be used to
-turn-off the Coulombic interaction within core/shell pairs, since that
-interaction is set by the bond spring. This is done using the
-"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0,
-which is the default value. It needs to be considered whether one has
-to adjust the "special_bonds"_special_bonds.html weighting according
-to the molecular topology since the interactions of the shells are
-bypassed over an extra bond.
-
-Note that this core/shell implementation does not require all ions to
-be polarized. One can mix core/shell pairs and ions without a
-satellite particle if desired.
-
-Since the core/shell model permits distances of r = 0.0 between the
-core and shell, a pair style with a "cs" suffix needs to be used to
-implement a valid long-range Coulombic correction. Several such pair
-styles are provided in the CORESHELL package. See "this doc
-page"_pair_cs.html for details. All of the core/shell enabled pair
-styles require the use of a long-range Coulombic solver, as specified
-by the "kspace_style"_kspace_style.html command. Either the PPPM or
-Ewald solvers can be used.
-
-For the NaCL example problem, these pair style and bond style settings
-are used:
-
-pair_style born/coul/long/cs 20.0 20.0
-pair_coeff * * 0.0 1.000 0.00 0.00 0.00
-pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
-pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
-pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre
-
-bond_style harmonic
-bond_coeff 1 63.014 0.0
-bond_coeff 2 25.724 0.0 :pre
-
-When running dynamics with the adiabatic core/shell model, the
-following issues should be considered. The relative motion of
-the core and shell particles corresponds to the polarization,
-hereby an instantaneous relaxation of the shells is approximated
-and a fast core/shell spring frequency ensures a nearly constant
-internal kinetic energy during the simulation.
-Thermostats can alter this polarization behaviour, by scaling the
-internal kinetic energy, meaning the shell will not react freely to
-its electrostatic environment.
-Therefore it is typically desirable to decouple the relative motion of
-the core/shell pair, which is an imaginary degree of freedom, from the
-real physical system. To do that, the "compute
-temp/cs"_compute_temp_cs.html command can be used, in conjunction with
-any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
-langevin"_fix_langevin. This compute uses the center-of-mass velocity
-of the core/shell pairs to calculate a temperature, and insures that
-velocity is what is rescaled for thermostatting purposes. This
-compute also works for a system with both core/shell pairs and
-non-polarized ions (ions without an attached satellite particle). The
-"compute temp/cs"_compute_temp_cs.html command requires input of two
-groups, one for the core atoms, another for the shell atoms.
-Non-polarized ions which might also be included in the treated system
-should not be included into either of these groups, they are taken
-into account by the {group-ID} (2nd argument) of the compute. The
-groups can be defined using the "group {type}"_group.html command.
-Note that to perform thermostatting using this definition of
-temperature, the "fix modify temp"_fix_modify.html command should be
-used to assign the compute to the thermostat fix. Likewise the
-"thermo_modify temp"_thermo_modify.html command can be used to make
-this temperature be output for the overall system.
-
-For the NaCl example, this can be done as follows:
-
-group cores type 1 2
-group shells type 3 4
-compute CSequ all temp/cs cores shells
-fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
-fix thermostatequ all nve # integrator as needed for the berendsen thermostat
-fix_modify thermoberendsen temp CSequ
-thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
-
-The pressure for the core/shell system is computed via the regular
-LAMMPS convention by "treating the cores and shells as individual
-particles"_#MitchellFincham2. For the thermo output of the pressure
-as well as for the application of a barostat, it is necessary to
-use an additional "pressure"_compute_pressure compute based on the
-default "temperature"_compute_temp and specifying it as a second
-argument in "fix modify"_fix_modify.html and
-"thermo_modify"_thermo_modify.html resulting in:
-
-(...)
-compute CSequ all temp/cs cores shells
-compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles
-thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure
-fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
-fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre
-
-If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
-relative motion of the core and the shell should in theory be
-stable. However numerical fluctuation can introduce a small
-momentum to the system, which is noticable over long trajectories.
-Therefore it is recommendable to use the "fix
-momentum"_fix_momentum.html command in combination with "compute
-temp/cs"_compute_temp_cs.html when equilibrating the system to
-prevent any drift.
-
-When initializing the velocities of a system with core/shell pairs, it
-is also desirable to not introduce energy into the relative motion of
-the core/shell particles, but only assign a center-of-mass velocity to
-the pairs. This can be done by using the {bias} keyword of the
-"velocity create"_velocity.html command and assigning the "compute
-temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
-"velocity"_velocity.html command, e.g.
-
-velocity all create 1427 134 bias yes temp CSequ
-velocity all scale 1427 temp CSequ :pre
-
-To maintain the correct polarizability of the core/shell pairs, the
-kinetic energy of the internal motion shall remain nearly constant.
-Therefore the choice of spring force and mass ratio need to ensure
-much faster relative motion of the 2 atoms within the core/shell pair
-than their center-of-mass velocity. This allows the shells to
-effectively react instantaneously to the electrostatic environment and
-limits energy transfer to or from the core/shell oscillators.
-This fast movement also dictates the timestep that can be used.
-
-The primary literature of the adiabatic core/shell model suggests that
-the fast relative motion of the core/shell pairs only allows negligible
-energy transfer to the environment.
-The mentioned energy transfer will typically lead to a small drift
-in total energy over time. This internal energy can be monitored
-using the "compute chunk/atom"_compute_chunk_atom.html and "compute
-temp/chunk"_compute_temp_chunk.html commands. The internal kinetic
-energies of each core/shell pair can then be summed using the sum()
-special function of the "variable"_variable.html command. Or they can
-be time/averaged and output using the "fix ave/time"_fix_ave_time.html
-command. To use these commands, each core/shell pair must be defined
-as a "chunk". If each core/shell pair is defined as its own molecule,
-the molecule ID can be used to define the chunks. If cores are bonded
-to each other to form larger molecules, the chunks can be identified
-by the "fix property/atom"_fix_property_atom.html via assigning a
-core/shell ID to each atom using a special field in the data file read
-by the "read_data"_read_data.html command. This field can then be
-accessed by the "compute property/atom"_compute_property_atom.html
-command, to use as input to the "compute
-chunk/atom"_compute_chunk_atom.html command to define the core/shell
-pairs as chunks.
-
-For example if core/shell pairs are the only molecules:
-
-read_data NaCl_CS_x0.1_prop.data
-compute prop all property/atom molecule
-compute cs_chunk all chunk/atom c_prop
-compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
-fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
-
-For example if core/shell pairs and other molecules are present:
-
-fix csinfo all property/atom i_CSID # property/atom command
-read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
-compute prop all property/atom i_CSID
-(...) :pre
-
-The additional section in the date file would be formatted like this:
-
-CS-Info # header of additional section :pre
-
-1 1 # column 1 = atom ID, column 2 = core/shell ID
-2 1
-3 2
-4 2
-5 3
-6 3
-7 4
-8 4
-(...) :pre
-
-:line
-
-6.27 Drude induced dipoles :link(howto_27),h4
-
-The thermalized Drude model, similarly to the "core-shell"_#howto_26
-model, represents induced dipoles by a pair of charges (the core atom
-and the Drude particle) connected by a harmonic spring. The Drude
-model has a number of features aimed at its use in molecular systems
-("Lamoureux and Roux"_#howto-Lamoureux):
-
-Thermostating of the additional degrees of freedom associated with the
-induced dipoles at very low temperature, in terms of the reduced
-coordinates of the Drude particles with respect to their cores. This
-makes the trajectory close to that of relaxed induced dipoles. :ulb,l
-
-Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
-pair represents a single (polarizable) atom, so the special screening
-factors in a covalent structure should be the same for the core and
-the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
-special neighbor relations from their respective cores. :l
-
-Stabilization of the interactions between induced dipoles. Drude
-dipoles on covalently bonded atoms interact too strongly due to the
-short distances, so an atom may capture the Drude particle of a
-neighbor, or the induced dipoles within the same molecule may align
-too much. To avoid this, damping at short range can be done by Thole
-functions (for which there are physical grounds). This Thole damping
-is applied to the point charges composing the induced dipole (the
-charge of the Drude particle and the opposite charge on the core, not
-to the total charge of the core atom). :l
-:ule
-
-A detailed tutorial covering the usage of Drude induced dipoles in
-LAMMPS is "available here"_tutorial_drude.html.
-
-As with the core-shell model, the cores and Drude particles should
-appear in the data file as standard atoms. The same holds for the
-springs between them, which are described by standard harmonic bonds.
-The nature of the atoms (core, Drude particle or non-polarizable) is
-specified via the "fix drude"_fix_drude.html command. The special
-list of neighbors is automatically refactored to account for the
-equivalence of core and Drude particles as regards special 1-2 to 1-4
-screening. It may be necessary to use the {extra/special/per/atom}
-keyword of the "read_data"_read_data.html command. If using "fix
-shake"_fix_shake.html, make sure no Drude particle is in this fix
-group.
-
-There are two ways to thermostat the Drude particles at a low
-temperature: use either "fix langevin/drude"_fix_langevin_drude.html
-for a Langevin thermostat, or "fix
-drude/transform/*"_fix_drude_transform.html for a Nose-Hoover
-thermostat. The former requires use of the command "comm_modify vel
-yes"_comm_modify.html. The latter requires two separate integration
-fixes like {nvt} or {npt}. The correct temperatures of the reduced
-degrees of freedom can be calculated using the "compute
-temp/drude"_compute_temp_drude.html. This requires also to use the
-command {comm_modify vel yes}.
-
-Short-range damping of the induced dipole interactions can be achieved
-using Thole functions through the "pair style
-thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
-with a Coulomb pair style. It may be useful to use {coul/long/cs} or
-similar from the CORESHELL package if the core and Drude particle come
-too close, which can cause numerical issues.
-
-:line
-
-6.28 Magnetic spins :link(howto_28),h4
-
-Classical magnetic spin simualtions can be performed via the SPIN
-package. The algrorithmic and implementation details are described in
-"Tranchida"_#Tranchida7.
-
-The model representents the simulation of atomic magnetic spins
-coupled to lattice vibrations. The dynamics of those magnetic spins
-can be used to simulate a broad range a phenomena related to
-magneto-elasticity, or or to study the influence of defects on the
-magnetic properties of materials.
-
-The magnetic spins are interacting with each others and with the
-lattice via pair interactions. Typically, the magnetic exchange
-interaction can be defined using the
-"pair/spin/exchange"_pair_spin_exchange.html command. This exchange
-applies a magnetic torque to a given spin, considering the orientation
-of its neighboring spins and their relative distances.
-It also applies a force on the atoms as a function of the spin
-orientations and their associated inter-atomic distances.
-
-The command "fix precession/spin"_fix_precession_spin.html allows to
-apply a constant magnetic torque on all the spins in the system. This
-torque can be an external magnetic field (Zeeman interaction), or an
-uniaxial magnetic anisotropy.
-
-A Langevin thermostat can be applied to those magnetic spins using
-"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
-can be coupled to another Langevin thermostat applied to the atoms
-using "fix langevin"_fix_langevin.html in order to simulate
-thermostated spin-lattice system.
-
-The magnetic Gilbert damping can also be applied using "fix
-langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
-the thermal energy of the Langevin thermostat, or to perform a
-relaxation of the magnetic configuration toward an equilibrium state.
-
-All the computed magnetic properties can be outputed by two main
-commands. The first one is "compute spin"_compute_spin.html, that
-enables to evaluate magnetic averaged quantities, such as the total
-magnetization of the system along x, y, or z, the spin temperature, or
-the magnetic energy. The second command is "compute
-property/atom"_compute_property_atom.html. It enables to output all the
-per atom magnetic quantities. Typically, the orientation of a given
-magnetic spin, or the magnetic force acting on this spin.
-
-:line
-:line
-
-:link(howto-Berendsen)
-[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91,
-6269-6271 (1987).
-
-:link(howto-Cornell)
-[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
-Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
-
-:link(Horn)
-[(Horn)] Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
-J Chem Phys, 120, 9665 (2004).
-
-:link(howto-Ikeshoji)
-[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
-(1994).
-
-:link(howto-Wirnsberger)
-[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
-(2015).
-
-:link(howto-MacKerell)
-[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
-Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
-
-:link(howto-Mayo)
-[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
-(1990).
-
-:link(Jorgensen1)
-[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
-Phys, 79, 926 (1983).
-
-:link(Price1)
-[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004).
-
-:link(Shinoda1)
-[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
-
-:link(MitchellFincham)
-[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter,
-5, 1031-1038 (1993).
-
-:link(MitchellFincham2)
-[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
-6, 393-404 (1994).
-
-:link(howto-Lamoureux)
-[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
-
-:link(Tranchida7)
-[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt
deleted file mode 100644
index c7cf5bf8d29bdb5e76b426ee16d9391f33684b14..0000000000000000000000000000000000000000
--- a/doc/src/Section_intro.txt
+++ /dev/null
@@ -1,550 +0,0 @@
-"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_start.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-1. Introduction :h2
-
-This section provides an overview of what LAMMPS can and can't do,
-describes what it means for LAMMPS to be an open-source code, and
-acknowledges the funding and people who have contributed to LAMMPS
-over the years.
-
-1.1 "What is LAMMPS"_#intro_1
-1.2 "LAMMPS features"_#intro_2
-1.3 "LAMMPS non-features"_#intro_3
-1.4 "Open source distribution"_#intro_4
-1.5 "Acknowledgments and citations"_#intro_5 :all(b)
-
-:line
-:line
-
-1.1 What is LAMMPS :link(intro_1),h4
-
-LAMMPS is a classical molecular dynamics code that models an ensemble
-of particles in a liquid, solid, or gaseous state. It can model
-atomic, polymeric, biological, metallic, granular, and coarse-grained
-systems using a variety of force fields and boundary conditions.
-
-For examples of LAMMPS simulations, see the Publications page of the
-"LAMMPS WWW Site"_lws.
-
-LAMMPS runs efficiently on single-processor desktop or laptop
-machines, but is designed for parallel computers. It will run on any
-parallel machine that compiles C++ and supports the "MPI"_mpi
-message-passing library. This includes distributed- or shared-memory
-parallel machines and Beowulf-style clusters.
-
-:link(mpi,http://www-unix.mcs.anl.gov/mpi)
-
-LAMMPS can model systems with only a few particles up to millions or
-billions. See "Section 8"_Section_perf.html for information on
-LAMMPS performance and scalability, or the Benchmarks section of the
-"LAMMPS WWW Site"_lws.
-
-LAMMPS is a freely-available open-source code, distributed under the
-terms of the "GNU Public License"_gnu, which means you can use or
-modify the code however you wish. See "this section"_#intro_4 for a
-brief discussion of the open-source philosophy.
-
-:link(gnu,http://www.gnu.org/copyleft/gpl.html)
-
-LAMMPS is designed to be easy to modify or extend with new
-capabilities, such as new force fields, atom types, boundary
-conditions, or diagnostics. See the "Modify"_Modify.html doc page for
-more details.
-
-The current version of LAMMPS is written in C++. Earlier versions
-were written in F77 and F90. See
-"Section 13"_Section_history.html for more information on
-different versions. All versions can be downloaded from the "LAMMPS
-WWW Site"_lws.
-
-LAMMPS was originally developed under a US Department of Energy CRADA
-(Cooperative Research and Development Agreement) between two DOE labs
-and 3 companies. It is distributed by "Sandia National Labs"_snl.
-See "this section"_#intro_5 for more information on LAMMPS funding and
-individuals who have contributed to LAMMPS.
-
-:link(snl,http://www.sandia.gov)
-
-In the most general sense, LAMMPS integrates Newton's equations of
-motion for collections of atoms, molecules, or macroscopic particles
-that interact via short- or long-range forces with a variety of
-initial and/or boundary conditions. For computational efficiency
-LAMMPS uses neighbor lists to keep track of nearby particles. The
-lists are optimized for systems with particles that are repulsive at
-short distances, so that the local density of particles never becomes
-too large. On parallel machines, LAMMPS uses spatial-decomposition
-techniques to partition the simulation domain into small 3d
-sub-domains, one of which is assigned to each processor. Processors
-communicate and store "ghost" atom information for atoms that border
-their sub-domain. LAMMPS is most efficient (in a parallel sense) for
-systems whose particles fill a 3d rectangular box with roughly uniform
-density. Papers with technical details of the algorithms used in
-LAMMPS are listed in "this section"_#intro_5.
-
-:line
-
-1.2 LAMMPS features :link(intro_2),h4
-
-This section highlights LAMMPS features, with pointers to specific
-commands which give more details. If LAMMPS doesn't have your
-favorite interatomic potential, boundary condition, or atom type, see
-the "Modify"_Modify.html doc page, which describes how you can add it
-to LAMMPS.
-
-General features :h4
-
- runs on a single processor or in parallel
- distributed-memory message-passing parallelism (MPI)
- spatial-decomposition of simulation domain for parallelism
- open-source distribution
- highly portable C++
- optional libraries used: MPI and single-processor FFT
- GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features
- easy to extend with new features and functionality
- runs from an input script
- syntax for defining and using variables and formulas
- syntax for looping over runs and breaking out of loops
- run one or multiple simulations simultaneously (in parallel) from one script
- build as library, invoke LAMMPS thru library interface or provided Python wrapper
- couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
-
-Particle and model types :h4
-("atom style"_atom_style.html command)
-
- atoms
- coarse-grained particles (e.g. bead-spring polymers)
- united-atom polymers or organic molecules
- all-atom polymers, organic molecules, proteins, DNA
- metals
- granular materials
- coarse-grained mesoscale models
- finite-size spherical and ellipsoidal particles
- finite-size line segment (2d) and triangle (3d) particles
- point dipole particles
- rigid collections of particles
- hybrid combinations of these :ul
-
-Force fields :h4
-("pair style"_pair_style.html, "bond style"_bond_style.html,
-"angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
-"improper style"_improper_style.html, "kspace style"_kspace_style.html
-commands)
-
- pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
- Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
- charged pairwise potentials: Coulombic, point-dipole
- manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
- embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
- REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
- long-range interactions for charge, point-dipoles, and LJ dispersion: \
- Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
- polarization models: "QEq"_fix_qeq.html, \
- "core/shell model"_Section_howto.html#howto_26, \
- "Drude dipole model"_Section_howto.html#howto_27
- charge equilibration (QEq via dynamic, point, shielded, Slater methods)
- coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
- mesoscopic potentials: granular, Peridynamics, SPH
- electron force field (eFF, AWPMD)
- bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
- quartic (breakable)
- angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \
- class 2 (COMPASS)
- dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
- class 2 (COMPASS), OPLS
- improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
- polymer potentials: all-atom, united-atom, bead-spring, breakable
- water potentials: TIP3P, TIP4P, SPC
- implicit solvent potentials: hydrodynamic lubrication, Debye
- force-field compatibility with common CHARMM, AMBER, DREIDING, \
- OPLS, GROMACS, COMPASS options
- access to "KIM archive"_http://openkim.org of potentials via \
- "pair kim"_pair_kim.html
- hybrid potentials: multiple pair, bond, angle, dihedral, improper \
- potentials can be used in one simulation
- overlaid potentials: superposition of multiple pair potentials :ul
-
-Atom creation :h4
-("read_data"_read_data.html, "lattice"_lattice.html,
-"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
-"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
-
- read in atom coords from files
- create atoms on one or more lattices (e.g. grain boundaries)
- delete geometric or logical groups of atoms (e.g. voids)
- replicate existing atoms multiple times
- displace atoms :ul
-
-Ensembles, constraints, and boundary conditions :h4
-("fix"_fix.html command)
-
- 2d or 3d systems
- orthogonal or non-orthogonal (triclinic symmetry) simulation domains
- constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
- thermostatting options for groups and geometric regions of atoms
- pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
- simulation box deformation (tensile and shear)
- harmonic (umbrella) constraint forces
- rigid body constraints
- SHAKE bond and angle constraints
- Monte Carlo bond breaking, formation, swapping
- atom/molecule insertion and deletion
- walls of various kinds
- non-equilibrium molecular dynamics (NEMD)
- variety of additional boundary conditions and constraints :ul
-
-Integrators :h4
-("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
-
- velocity-Verlet integrator
- Brownian dynamics
- rigid body integration
- energy minimization via conjugate gradient or steepest descent relaxation
- rRESPA hierarchical timestepping
- rerun command for post-processing of dump files :ul
-
-Diagnostics :h4
-
- see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
-
-Output :h4
-("dump"_dump.html, "restart"_restart.html commands)
-
- log file of thermodynamic info
- text dump files of atom coords, velocities, other per-atom quantities
- binary restart files
- parallel I/O of dump and restart files
- per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
- user-defined system-wide (log file) or per-atom (dump file) calculations
- spatial and time averaging of per-atom quantities
- time averaging of system-wide quantities
- atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
-
-Multi-replica models :h4
-
-"nudged elastic band"_neb.html
-"parallel replica dynamics"_prd.html
-"temperature accelerated dynamics"_tad.html
-"parallel tempering"_temper.html
-
-Pre- and post-processing :h4
-
-Various pre- and post-processing serial tools are packaged with
-LAMMPS; see the "Tools"_Tools.html doc page for details. :ulb,l
-
-Our group has also written and released a separate toolkit called
-"Pizza.py"_pizza which provides tools for doing setup, analysis,
-plotting, and visualization for LAMMPS simulations. Pizza.py is
-written in "Python"_python and is available for download from "the
-Pizza.py WWW site"_pizza. :l
-:ule
-
-:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
-:link(python,http://www.python.org)
-
-Specialized features :h4
-
-LAMMPS can be built with optional packages which implement a variety
-of additional capabilities. An overview of all the packages is "given
-here"_Section_packages.html.
-
-These are some LAMMPS capabilities which you may not think of as
-typical classical molecular dynamics options:
-
-"static"_balance.html and "dynamic load-balancing"_fix_balance.html
-"generalized aspherical particles"_body.html
-"stochastic rotation dynamics (SRD)"_fix_srd.html
-"real-time visualization and interactive MD"_fix_imd.html
-calculate "virtual diffraction patterns"_compute_xrd.html
-"atom-to-continuum coupling"_fix_atc.html with finite elements
-coupled rigid body integration via the "POEMS"_fix_poems.html library
-"QM/MM coupling"_fix_qmmm.html
-"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
-Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html "atom swapping"_fix_atom_swap.html and "bond swapping"_fix_bond_swap.html
-"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
-"Peridynamics mesoscale modeling"_pair_peri.html
-"Lattice Boltzmann fluid"_fix_lb_fluid.html
-"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
-"two-temperature electron model"_fix_ttm.html :ul
-
-:line
-
-1.3 LAMMPS non-features :link(intro_3),h4
-
-LAMMPS is designed to efficiently compute Newton's equations of motion
-for a system of interacting particles. Many of the tools needed to
-pre- and post-process the data for such simulations are not included
-in the LAMMPS kernel for several reasons:
-
-the desire to keep LAMMPS simple
-they are not parallel operations
-other codes already do them
-limited development resources :ul
-
-Specifically, LAMMPS itself does not:
-
-run thru a GUI
-build molecular systems
-assign force-field coefficients automagically
-perform sophisticated analyses of your MD simulation
-visualize your MD simulation
-plot your output data :ul
-
-A few tools for pre- and post-processing tasks are provided as part of
-the LAMMPS package; they are described on the "Tools"_Tools.html doc
-page. However, many people use other codes or write their own tools
-for these tasks.
-
-As noted above, our group has also written and released a separate
-toolkit called "Pizza.py"_pizza which addresses some of the listed
-bullets. It provides tools for doing setup, analysis, plotting, and
-visualization for LAMMPS simulations. Pizza.py is written in
-"Python"_python and is available for download from "the Pizza.py WWW
-site"_pizza.
-
-LAMMPS requires as input a list of initial atom coordinates and types,
-molecular topology information, and force-field coefficients assigned
-to all atoms and bonds. LAMMPS will not build molecular systems and
-assign force-field parameters for you.
-
-For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html
-command which places atoms on solid-state lattices (fcc, bcc,
-user-defined, etc). Assigning small numbers of force field
-coefficients can be done via the "pair coeff"_pair_coeff.html, "bond
-coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, etc commands.
-For molecular systems or more complicated simulation geometries, users
-typically use another code as a builder and convert its output to
-LAMMPS input format, or write their own code to generate atom
-coordinate and molecular topology for LAMMPS to read in.
-
-For complicated molecular systems (e.g. a protein), a multitude of
-topology information and hundreds of force-field coefficients must
-typically be specified. We suggest you use a program like
-"CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup
-such problems and dump its information to a file. You can then
-reformat the file as LAMMPS input. Some of the tools described on the
-"Tools"_Tools.html doc page can assist in this process.
-
-Similarly, LAMMPS creates output files in a simple format. Most users
-post-process these files with their own analysis tools or re-format
-them for input into other programs, including visualization packages.
-If you are convinced you need to compute something on-the-fly as
-LAMMPS runs, see the "Modify"_Modify.html doc page for a discussion of
-how you can use the "dump"_dump.html and "compute"_compute.html and
-"fix"_fix.html commands to print out data of your choosing. Keep in
-mind that complicated computations can slow down the molecular
-dynamics timestepping, particularly if the computations are not
-parallel, so it is often better to leave such analysis to
-post-processing codes.
-
-For high-quality visualization we recommend the
-following packages:
-
-"VMD"_http://www.ks.uiuc.edu/Research/vmd
-"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
-"OVITO"_http://www.ovito.org/
-"ParaView"_http://www.paraview.org/
-"PyMol"_http://www.pymol.org
-"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
-"RasMol"_http://www.openrasmol.org :ul
-
-Other features that LAMMPS does not yet (and may never) support are
-discussed in "Section 13"_Section_history.html.
-
-Finally, these are freely-available molecular dynamics codes, most of
-them parallel, which may be well-suited to the problems you want to
-model. They can also be used in conjunction with LAMMPS to perform
-complementary modeling tasks.
-
-"CHARMM"_charmm
-"AMBER"_amber
-"NAMD"_namd
-"NWCHEM"_nwchem
-"DL_POLY"_dlpoly
-"Tinker"_tinker :ul
-
-:link(charmm,http://www.charmm.org)
-:link(amber,http://ambermd.org)
-:link(namd,http://www.ks.uiuc.edu/Research/namd/)
-:link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
-:link(dlpoly,http://www.ccp5.ac.uk/DL_POLY_CLASSIC)
-:link(tinker,http://dasher.wustl.edu/tinker)
-
-CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
-modeling biological molecules. CHARMM and AMBER use
-atom-decomposition (replicated-data) strategies for parallelism; NAMD
-and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
-Tinker is a serial code. DL_POLY includes potentials for a variety of
-biological and non-biological materials; both a replicated-data and
-spatial-decomposition version exist.
-
-:line
-
-1.4 Open source distribution :link(intro_4),h4
-
-LAMMPS comes with no warranty of any kind. As each source file states
-in its header, it is a copyrighted code that is distributed free-of-
-charge, under the terms of the "GNU Public License"_gnu (GPL). This
-is often referred to as open-source distribution - see
-"www.gnu.org"_gnuorg or "www.opensource.org"_opensource for more
-details. The legal text of the GPL is in the LICENSE file that is
-included in the LAMMPS distribution.
-
-:link(gnuorg,http://www.gnu.org)
-:link(opensource,http://www.opensource.org)
-
-Here is a summary of what the GPL means for LAMMPS users:
-
-(1) Anyone is free to use, modify, or extend LAMMPS in any way they
-choose, including for commercial purposes.
-
-(2) If you distribute a modified version of LAMMPS, it must remain
-open-source, meaning you distribute it under the terms of the GPL.
-You should clearly annotate such a code as a derivative version of
-LAMMPS.
-
-(3) If you release any code that includes LAMMPS source code, then it
-must also be open-sourced, meaning you distribute it under the terms
-of the GPL.
-
-(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
-source file headers (including the copyright and GPL notices) should
-remain part of the code.
-
-In the spirit of an open-source code, these are various ways you can
-contribute to making LAMMPS better. You can send email to the
-"developers"_http://lammps.sandia.gov/authors.html on any of these
-items.
-
-Point prospective users to the "LAMMPS WWW Site"_lws. Mention it in
-talks or link to it from your WWW site. :ulb,l
-
-If you find an error or omission in this manual or on the "LAMMPS WWW
-Site"_lws, or have a suggestion for something to clarify or include,
-send an email to the
-"developers"_http://lammps.sandia.gov/authors.html. :l
-
-If you find a bug, the "Errors bugs"_Errors_bugs.html doc page
-describes how to report it. :l
-
-If you publish a paper using LAMMPS results, send the citation (and
-any cool pictures or movies if you like) to add to the Publications,
-Pictures, and Movies pages of the "LAMMPS WWW Site"_lws, with links
-and attributions back to you. :l
-
-Create a new Makefile.machine that can be added to the src/MAKE
-directory. :l
-
-The tools sub-directory of the LAMMPS distribution has various
-stand-alone codes for pre- and post-processing of LAMMPS data. More
-details are given on the "Tools"_Tools.html doc page. If you write a
-new tool that users will find useful, it can be added to the LAMMPS
-distribution. :l
-
-LAMMPS is designed to be easy to extend with new code for features
-like potentials, boundary conditions, diagnostic computations, etc.
-The "Modify"_Modify.html doc page gives details. If you add a feature
-of general interest, it can be added to the LAMMPS distribution. :l
-
-The Benchmark page of the "LAMMPS WWW Site"_lws lists LAMMPS
-performance on various platforms. The files needed to run the
-benchmarks are part of the LAMMPS distribution. If your machine is
-sufficiently different from those listed, your timing data can be
-added to the page. :l
-
-You can send feedback for the User Comments page of the "LAMMPS WWW
-Site"_lws. It might be added to the page. No promises. :l
-
-Cash. Small denominations, unmarked bills preferred. Paper sack OK.
-Leave on desk. VISA also accepted. Chocolate chip cookies
-encouraged. :l
-:ule
-
-:line
-
-1.5 Acknowledgments and citations :h3,link(intro_5)
-
-LAMMPS development has been funded by the "US Department of
-Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
-programs and its "OASCR"_oascr and "OBER"_ober offices.
-
-Specifically, work on the latest version was funded in part by the US
-Department of Energy's Genomics:GTL program
-("www.doegenomestolife.org"_gtl) under the "project"_ourgtl, "Carbon
-Sequestration in Synechococcus Sp.: From Molecular Machines to
-Hierarchical Modeling".
-
-:link(doe,http://www.doe.gov)
-:link(gtl,http://www.doegenomestolife.org)
-:link(ourgtl,http://www.genomes2life.org)
-:link(oascr,http://www.sc.doe.gov/ascr/home.html)
-:link(ober,http://www.er.doe.gov/production/ober/ober_top.html)
-
-The following paper describe the basic parallel algorithms used in
-LAMMPS. If you use LAMMPS results in your published work, please cite
-this paper and include a pointer to the "LAMMPS WWW Site"_lws
-(http://lammps.sandia.gov):
-
-S. Plimpton, [Fast Parallel Algorithms for Short-Range Molecular
-Dynamics], J Comp Phys, 117, 1-19 (1995).
-
-Other papers describing specific algorithms used in LAMMPS are listed
-under the "Citing LAMMPS link"_http://lammps.sandia.gov/cite.html of
-the LAMMPS WWW page.
-
-The "Publications link"_http://lammps.sandia.gov/papers.html on the
-LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is
-not listed there for some reason, feel free to send us the info. If
-the simulations in your paper produced cool pictures or animations,
-we'll be pleased to add them to the
-"Pictures"_http://lammps.sandia.gov/pictures.html or
-"Movies"_http://lammps.sandia.gov/movies.html pages of the LAMMPS WWW
-site.
-
-The primary LAMMPS developers are at Sandia National Labs and Temple University:
-
-Steve Plimpton, sjplimp at sandia.gov
-Aidan Thompson, athomps at sandia.gov
-Stan Moore, stamoor at sandia.gov
-Axel Kohlmeyer, akohlmey at gmail.com :ul
-
-Past primary developers include Paul Crozier and Mark Stevens,
-both at Sandia, and Ray Shan, now at Materials Design.
-
-The following folks are responsible for significant contributions to
-the code, or other aspects of the LAMMPS development effort. Many of
-the packages they have written are somewhat unique to LAMMPS and the
-code would not be as general-purpose as it is without their expertise
-and efforts.
-
-Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages
-Roy Pollock (LLNL), Ewald and PPPM solvers
-Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package
-Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential (superseded by USER-MEAMC)
-Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
-Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
-Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
-Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
-Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA (obsoleted by KOKKOS) and KOKKOS packages
-Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
-Christoph Kloss (JKU), Christoph.Kloss at jku.at, LIGGGHTS fork for granular models and granular/fluid coupling
-Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
-Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
-Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
-
-As discussed in "Section 13"_Section_history.html, LAMMPS
-originated as a cooperative project between DOE labs and industrial
-partners. Folks involved in the design and testing of the original
-version of LAMMPS were the following:
-
-John Carpenter (Mayo Clinic, formerly at Cray Research)
-Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
-Steve Lustig (Dupont)
-Jim Belak (LLNL) :ul
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index d8f340b17996c25d8e3b3aceb56002e80fc2861b..19a798d5dfddbbb14e2d9ccbf9e66b943392d920 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -1,10 +1,10 @@
-"Previous Section"_Section_intro.html - "LAMMPS WWW Site"_lws -
+"Previous Section"_Intro.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_commands.html :c
+Section"_Commands.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -119,10 +119,11 @@ lower-case name of the package, e.g. replica or user-misc.
If you want to do one of the following:
-use a LAMMPS command that requires an extra library (e.g. "dump image"_dump_image.html)
-build with a package that requires an extra library
-build with an accelerator package that requires special compiler/linker settings
-run on a machine that has its own compilers, settings, or libraries :ul
+use a LAMMPS command that requires an extra library (e.g. "dump
+image"_dump_image.html) build with a package that requires an extra
+library build with an accelerator package that requires special
+compiler/linker settings run on a machine that has its own compilers,
+settings, or libraries :ul
then building LAMMPS is more complicated. You may need to find where
extra libraries exist on your machine or install them if they don't.
@@ -697,8 +698,8 @@ are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages.
-"Section 4"_Section_packages.html in the manual has details about all
-the packages, which come in two flavors: [standard] and [user]
+The "Packages"_Packages.html doc pages has details about all the
+packages, which come in two flavors: [standard] and [user]
packages. It also has specific instructions for building LAMMPS with
any package which requires an extra library. General instructions are
below.
@@ -828,45 +829,47 @@ options.
Packages that require extra libraries :h4,link(start_3_3)
A few of the standard and user packages require extra libraries. See
-"Section 4"_Section_packages.html for two tables of packages which
-indicate which ones require libraries. For each such package, the
-Section 4 doc page gives details on how to build the extra library,
-including how to download it if necessary. The basic ideas are
-summarized here.
+the "Packages"_Packages.html doc pages for two tables of packages
+which indicate which ones require libraries. For each such package,
+the Section 4 doc page gives details on how to build the extra
+library, including how to download it if necessary. The basic ideas
+are summarized here.
[System libraries:]
-Packages in the tables "Section 4"_Section_packages.html with a "sys"
-in the last column link to system libraries that typically already
-exist on your machine. E.g. the python package links to a system
-Python library. If your machine does not have the required library,
-you will have to download and install it on your machine, in either
-the system or user space.
+Packages in the standard and user tables of the
+"Packages"_Packages.html doc pages with a "sys" in the last column
+link to system libraries that typically already exist on your machine.
+E.g. the python package links to a system Python library. If your
+machine does not have the required library, you will have to download
+and install it on your machine, in either the system or user space.
[Internal libraries:]
-Packages in the tables "Section 4"_Section_packages.html with an "int"
-in the last column link to internal libraries whose source code is
-included with LAMMPS, in the lib/name directory where name is the
-package name. You must first build the library in that directory
-before building LAMMPS with that package installed. E.g. the gpu
-package links to a library you build in the lib/gpu dir. You can
-often do the build in one step by typing "make lib-name args=..."
-from the src dir, with appropriate arguments. You can leave off the
-args to see a help message. See "Section 4"_Section_packages.html for
-details for each package.
+Packages in the standard and user tables of the
+"Packages"_Packages.html doc pages with an "int" in the last column
+link to internal libraries whose source code is included with LAMMPS,
+in the lib/name directory where name is the package name. You must
+first build the library in that directory before building LAMMPS with
+that package installed. E.g. the gpu package links to a library you
+build in the lib/gpu dir. You can often do the build in one step by
+typing "make lib-name args=..." from the src dir, with appropriate
+arguments. You can leave off the args to see a help message. See the
+"Packages details"_Packages_details.html doc page for details for each
+package.
[External libraries:]
-Packages in the tables "Section 4"_Section_packages.html with an "ext"
-in the last column link to external libraries whose source code is not
-included with LAMMPS. You must first download and install the library
-before building LAMMPS with that package installed. E.g. the voronoi
-package links to the freely available "Voro++ library"_voro_home2. You
-can often do the download/build in one step by typing "make lib-name
+Packages in the standard and user tables of the
+"Packages"_Packages.html doc pages with an "ext" in the last column
+link to external libraries whose source code is not included with
+LAMMPS. You must first download and install the library before
+building LAMMPS with that package installed. E.g. the voronoi package
+links to the freely available "Voro++ library"_voro_home2. You can
+often do the download/build in one step by typing "make lib-name
args=..." from the src dir, with appropriate arguments. You can leave
-off the args to see a help message. See "Section
-4"_Section_packages.html for details for each package.
+off the args to see a help message. See the "Packages
+details"_Packages_details.html doc page for details for each package.
:link(voro_home2,http://math.lbl.gov/voro++)
@@ -888,9 +891,9 @@ copied from a lib/name/Makefile.lammps.* file when the library is
built. If those settings are not correct for your machine you will
need to edit or create an appropriate Makefile.lammps file.
-Package-specific details for these steps are given in "Section
-4"_Section_packages.html an in README files in the lib/name
-directories.
+Package-specific details for these steps are given on the "Packages
+details"_Packages_details.html doc page and in README files in the
+lib/name directories.
[Compiler options needed for accelerator packages:]
@@ -901,14 +904,14 @@ these accelerator packages for optimal performance requires specific
settings in the Makefile.machine file you use.
A summary of the Makefile.machine settings needed for each of these
-packages is given in "Section 4"_Section_packages.html. More info is
-given on the doc pages that describe each package in detail:
+packages is given on the "Packages"_Packages.html doc pages. More
+info is given on the doc pages that describe each package in detail:
-5.3.1 "USER-INTEL package"_accelerate_intel.html
-5.3.2 "GPU package"_accelerate_intel.html
-5.3.3 "KOKKOS package"_accelerate_kokkos.html
-5.3.4 "USER-OMP package"_accelerate_omp.html
-5.3.5 "OPT package"_accelerate_opt.html :all(b)
+"USER-INTEL package"_Speed_intel.html
+"GPU package"_Speed_gpu.html
+"KOKKOS package"_Speed_kokkos.html
+"USER-OMP package"_Speed_omp.html
+"OPT package"_Speed_opt.html :all(b)
You can also use or examine the following machine Makefiles in
src/MAKE/OPTIONS, which include the settings. Note that the
@@ -931,9 +934,9 @@ Makefile.opt :ul
LAMMPS can be built as either a static or shared library, which can
then be called from another application or a scripting language. See
-"this section"_Section_howto.html#howto_10 for more info on coupling
-LAMMPS to other codes. See the "Python"_Python.html doc page for more
-info on wrapping and running LAMMPS from Python.
+the "Howto couple"_Howto_couple.html doc page for more info on
+coupling LAMMPS to other codes. See the "Python"_Python.html doc page
+for more info on wrapping and running LAMMPS from Python.
Static library :h4
@@ -1036,16 +1039,16 @@ src/library.cpp and src/library.h.
See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS thru its library interface.
-There are other examples as well in the COUPLE directory which are
-discussed in "Section 6.10"_Section_howto.html#howto_10 of the manual.
-See the "Python"_Python.html doc page for a description of the Python
-wrapper provided with LAMMPS that operates through the LAMMPS library
-interface.
+There are other examples as well in the COUPLE directory which use
+coupling ideas discussed on the "Howto couple"_Howto_couple.html doc
+page. See the "Python"_Python.html doc page for a description of the
+Python wrapper provided with LAMMPS that operates through the LAMMPS
+library interface.
The files src/library.cpp and library.h define the C-style API for
-using LAMMPS as a library. See "Section
-6.19"_Section_howto.html#howto_19 of the manual for a description of the
-interface and how to extend it for your needs.
+using LAMMPS as a library. See the "Howto library"_Howto_library.html
+doc page for a description of the interface and how to extend it for
+your needs.
:line
@@ -1067,7 +1070,7 @@ the '-in' command-line switch, e.g.
lmp_linux -in in.file :pre
-"This section"_Section_commands.html describes how input scripts are
+The "Commands"_Commands.html doc page describes how input scripts are
structured and what commands they contain.
You can test LAMMPS on any of the sample inputs provided in the
@@ -1276,8 +1279,8 @@ Either the full word or an abbreviation can be used for the keywords.
Note that the keywords do not use a leading minus sign. I.e. the
keyword is "t", not "-t". Also note that each of the keywords has a
default setting. Example of when to use these options and what
-settings to use on different platforms is given in "Section
-5.3"_Section_accelerate.html#acc_3.
+settings to use on different platforms is given on the "Speed
+kokkos"_Speed_kokkos.html doc page.
d or device
g or gpus
@@ -1388,16 +1391,16 @@ processors in all partitions must equal P. Thus the command
"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
processors.
-Running with multiple partitions can e useful for running
-"multi-replica simulations"_Section_howto.html#howto_5, where each
-replica runs on on one or a few processors. Note that with MPI
-installed on a machine (e.g. your desktop), you can run on more
-(virtual) processors than you have physical processors.
+Running with multiple partitions can be useful for running
+"multi-replica simulations"_Howto_replica.html, where each replica
+runs on on one or a few processors. Note that with MPI installed on a
+machine (e.g. your desktop), you can run on more (virtual) processors
+than you have physical processors.
To run multiple independent simulations from one input script, using
-multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
-of the manual. World- and universe-style "variables"_variable.html
-are useful in this context.
+multiple partitions, see the "Howto multiple"_Howto_multiple.html doc
+page. World- and universe-style "variables"_variable.html are useful
+in this context.
-plog file :pre
@@ -1461,8 +1464,7 @@ cores within each node are ranked in a desired order. Or when using
the "run_style verlet/split"_run_style.html command with 2 partitions
to insure that a specific Kspace processor (in the 2nd partition) is
matched up with a specific set of processors in the 1st partition.
-See the "Section 5"_Section_accelerate.html doc pages for
-more details.
+See the "Speed tips"_Speed_tips.html doc page for more details.
If the keyword {nth} is used with a setting {N}, then it means every
Nth processor will be moved to the end of the ranking. This is useful
@@ -1613,9 +1615,9 @@ value2 ..." at the beginning of the input script. Defining an index
variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined. See the "variable"_variable.html command for more info on
-defining index and other kinds of variables and "this
-section"_Section_commands.html#cmd_2 for more info on using variables
-in input scripts.
+defining index and other kinds of variables and the "Commands
+parse"_Commands_parse.html page for more info on using variables in
+input scripts.
NOTE: Currently, the command-line parser looks for arguments that
start with "-" to indicate new switches. Thus you cannot specify
@@ -1785,11 +1787,13 @@ communication, roughly 75% in the example above.
The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed
-in "Section 13"_Section_history.html. The F90 and F77 versions
-(2001 and 99) are also freely distributed as open-source codes; check
-the "LAMMPS WWW Site"_lws for distribution information if you prefer
-those versions. The 99 and 2001 versions are no longer under active
-development; they do not have all the features of C++ LAMMPS.
+on the "History page"_http://lammps.sandia.gov/history.html of the
+LAMMPS website. The F90 and F77 versions (2001 and 99) are also
+freely distributed as open-source codes; check the "History
+page"_http://lammps.sandia.gov/history.html of the LAMMPS website for
+info about those versions. The 99 and 2001 versions are no longer
+under active development; they do not have all the features of C++
+LAMMPS.
If you are a previous user of LAMMPS 2001, these are the most
significant changes you will notice in C++ LAMMPS:
diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt
new file mode 100644
index 0000000000000000000000000000000000000000..091657082ae75a48d53c433a8fd98428ba6180ff
--- /dev/null
+++ b/doc/src/Speed.txt
@@ -0,0 +1,64 @@
+"Previous Section"_Package.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Howto.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Accelerate performance :h2
+
+This section describes various methods for improving LAMMPS
+performance for different classes of problems running on different
+kinds of machines.
+
+There are two thrusts to the discussion that follows. The first is
+using code options that implement alternate algorithms that can
+speed-up a simulation. The second is to use one of the several
+accelerator packages provided with LAMMPS that contain code optimized
+for certain kinds of hardware, including multi-core CPUs, GPUs, and
+Intel Xeon Phi coprocessors.
+
+The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
+web site gives performance results for the various accelerator
+packages discussed on the "Speed packages"_Speed_packages.html doc
+page, for several of the standard LAMMPS benchmark problems, as a
+function of problem size and number of compute nodes, on different
+hardware platforms.
+
+<!-- RST
+
+.. toctree::
+
+ Speed_bench
+ Speed_measure
+
+.. toctree::
+
+ Speed_tips
+
+.. toctree::
+
+ Speed_packages
+ Speed_compare
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Benchmarks"_Speed_bench.html
+"Measuring performance"_Speed_measure.html :all(b)
+
+"General tips"_Speed_tips.html :all(b)
+
+"Accelerator packages"_Speed_packages.html
+"GPU package"_Speed_gpu.html
+"USER-INTEL package"_Speed_intel.html
+"KOKKOS package"_Speed_kokkos.html
+"USER-OMP package"_Speed_omp.html
+"OPT package"_Speed_opt.html
+"Comparison of accelerator packages"_Speed_compare.html :all(b)
+
+<!-- END_HTML_ONLY -->
diff --git a/doc/src/Section_perf.txt b/doc/src/Speed_bench.txt
similarity index 86%
rename from doc/src/Section_perf.txt
rename to doc/src/Speed_bench.txt
index f320780129a9fd67bb2dcccb28ef8a7cacfc92f6..8e407d14ea6bdb7428bff3818a670a9a84244f63 100644
--- a/doc/src/Section_perf.txt
+++ b/doc/src/Speed_bench.txt
@@ -1,19 +1,18 @@
-"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Tools.html
-:c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-8. Performance & scalability :h2
+Benchmarks :h3
-Current LAMMPS performance is discussed on the Benchmarks page of the
-"LAMMPS WWW Site"_lws where CPU timings and parallel efficiencies are
-listed. The page has several sections, which are briefly described
-below:
+Current LAMMPS performance is discussed on the "Benchmarks
+page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws
+where timings and parallel efficiencies are listed. The page has
+several sections, which are briefly described below:
CPU performance on 5 standard problems, strong and weak scaling
GPU and Xeon Phi performance on same and related problems
@@ -53,8 +52,8 @@ of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI
and bench/KEPLER dirs have input files and scripts and instructions
for running the same (or similar) problems using OpenMP or GPU or Xeon
Phi acceleration options. See the README files in those dirs and the
-"Section 5.3"_Section_accelerate.html#acc_3 doc pages for
-instructions on how to build LAMMPS and run on that kind of hardware.
+"Speed packages"_Speed_packages.html doc pages for instructions on how
+to build LAMMPS and run on that kind of hardware.
The bench/POTENTIALS directory has input files which correspond to the
table of results on the
diff --git a/doc/src/Speed_compare.txt b/doc/src/Speed_compare.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a17b39c79b672e43062770253ae5e82fc1f998d
--- /dev/null
+++ b/doc/src/Speed_compare.txt
@@ -0,0 +1,73 @@
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Comparison of various accelerator packages :h3
+
+NOTE: this section still needs to be re-worked with additional KOKKOS
+and USER-INTEL information.
+
+The next section compares and contrasts the various accelerator
+options, since there are multiple ways to perform OpenMP threading,
+run on GPUs, and run on Intel Xeon Phi coprocessors.
+
+All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
+hardware, but they do it in different ways.
+
+As a consequence, for a particular simulation on specific hardware,
+one package may be faster than the other. We give guidelines below,
+but the best way to determine which package is faster for your input
+script is to try both of them on your machine. See the benchmarking
+section below for examples where this has been done.
+
+[Guidelines for using each package optimally:]
+
+The GPU package allows you to assign multiple CPUs (cores) to a single
+GPU (a common configuration for "hybrid" nodes that contain multicore
+CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l
+
+The GPU package moves per-atom data (coordinates, forces)
+back-and-forth between the CPU and GPU every timestep. The
+KOKKOS/CUDA package only does this on timesteps when a CPU calculation
+is required (e.g. to invoke a fix or compute that is non-GPU-ized).
+Hence, if you can formulate your input script to only use GPU-ized
+fixes and computes, and avoid doing I/O too often (thermo output, dump
+file snapshots, restart files), then the data transfer cost of the
+KOKKOS/CUDA package can be very low, causing it to run faster than the
+GPU package. :l
+
+The GPU package is often faster than the KOKKOS/CUDA package, if the
+number of atoms per GPU is smaller. The crossover point, in terms of
+atoms/GPU at which the KOKKOS/CUDA package becomes faster depends
+strongly on the pair style. For example, for a simple Lennard Jones
+system the crossover (in single precision) is often about 50K-100K
+atoms per GPU. When performing double precision calculations the
+crossover point can be significantly smaller. :l
+
+Both packages compute bonded interactions (bonds, angles, etc) on the
+CPU. If the GPU package is running with several MPI processes
+assigned to one GPU, the cost of computing the bonded interactions is
+spread across more CPUs and hence the GPU package can run faster. :l
+
+When using the GPU package with multiple CPUs assigned to one GPU, its
+performance depends to some extent on high bandwidth between the CPUs
+and the GPU. Hence its performance is affected if full 16 PCIe lanes
+are not available for each GPU. In HPC environments this can be the
+case if S2050/70 servers are used, where two devices generally share
+one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
+full 16 lanes to each of the PCIe 2.0 16x slots. :l
+:ule
+
+[Differences between the two packages:]
+
+The GPU package accelerates only pair force, neighbor list, and PPPM
+calculations. :ulb,l
+
+The GPU package requires neighbor lists to be built on the CPU when using
+exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
+:ule
diff --git a/doc/src/accelerate_gpu.txt b/doc/src/Speed_gpu.txt
similarity index 96%
rename from doc/src/accelerate_gpu.txt
rename to doc/src/Speed_gpu.txt
index 816a31c788e99592a3f70af5e42c786c2ce75410..ab8ec7e9d164b64c269e729e77936cd92fd6dfc0 100644
--- a/doc/src/accelerate_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -1,15 +1,13 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-"Return to Section accelerate overview"_Section_accelerate.html
-
-5.3.1 GPU package :h5
+GPU package :h3
The GPU package was developed by Mike Brown at ORNL and his
collaborators, particularly Trung Nguyen (ORNL). It provides GPU
@@ -72,10 +70,9 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t
[Building LAMMPS with the GPU package:]
This requires two steps (a,b): build the GPU library, then build
-LAMMPS with the GPU package.
-
-You can do both these steps in one line as described in
-"Section 4"_Section_packages.html of the manual.
+LAMMPS with the GPU package. You can do both these steps in one line
+as described on the "Packages details"_Packages_details.html#GPU doc
+page.
Or you can follow these two (a,b) steps:
diff --git a/doc/src/accelerate_intel.txt b/doc/src/Speed_intel.txt
similarity index 97%
rename from doc/src/accelerate_intel.txt
rename to doc/src/Speed_intel.txt
index 71f5185b154f9f832d0ab5b92bd3d2e49f25df2f..20f49672e02849e2f0b544604bc6a88049eb0f05 100644
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/Speed_intel.txt
@@ -1,15 +1,13 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-"Return to Section accelerate overview"_Section_accelerate.html
-
-5.3.2 USER-INTEL package :h5
+USER-INTEL package :h3
The USER-INTEL package is maintained by Mike Brown at Intel
Corporation. It provides two methods for accelerating simulations,
@@ -188,8 +186,8 @@ can start running so that the CPU pipeline is still being used
efficiently. Although benefits can be seen by launching a MPI task
for every hardware thread, for multinode simulations, we recommend
that OpenMP threads are used for SMT instead, either with the
-USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or
-"KOKKOS package"_accelerate_kokkos.html. In the example above, up
+USER-INTEL package, "USER-OMP package"_Speed_omp.html, or
+"KOKKOS package"_Speed_kokkos.html. In the example above, up
to 36X speedups can be observed by using all 36 physical cores with
LAMMPS. By using all 72 hardware threads, an additional 10-30%
performance gain can be achieved.
@@ -233,9 +231,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
# or psxevars.csh for C-shell
make intel_cpu_intelmpi :pre
-Alternatively this can be done as a single command with
-suitable make command invocations. This is discussed in "Section
-4"_Section_packages.html of the manual.
+Alternatively this can be done as a single command with suitable make
+command invocations, as described on the "Packages
+details"_Packages_details.html#USER-INTEL doc page.
Note that if you build with support for a Phi coprocessor, the same
binary can be used on nodes with or without coprocessors installed.
@@ -391,8 +389,8 @@ performance and/or scalability for simple 2-body potentials such as
lj/cut or when using LRT mode on processors supporting AVX-512.
Not all styles are supported in the USER-INTEL package. You can mix
-the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
-package or the "USER-OMP package"_accelerate_omp.html. Of course,
+the USER-INTEL package with styles from the "OPT"_Speed_opt.html
+package or the "USER-OMP package"_Speed_omp.html. Of course,
this requires that these packages were installed at build time. This
can performed automatically by using "-sf hybrid intel opt" or
"-sf hybrid intel omp" command-line options. Alternatively, the "opt"
diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/Speed_kokkos.txt
similarity index 59%
rename from doc/src/accelerate_kokkos.txt
rename to doc/src/Speed_kokkos.txt
index 0c9178d6e4f42863003b0a2848f29cd42189620f..14f4103aed8d6df6e782eba0e63c196c2daf380d 100644
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -1,38 +1,41 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-"Return to Section accelerate overview"_Section_accelerate.html
-
-5.3.3 KOKKOS package :h5
+KOKKOS package :h3
Kokkos is a templated C++ library that provides abstractions to allow
-a single implementation of an application kernel (e.g. a pair style) to run efficiently on
-different kinds of hardware, such as GPUs, Intel Xeon Phis, or many-core
-CPUs. Kokkos maps the C++ kernel onto different backend languages such as CUDA, OpenMP, or Pthreads.
-The Kokkos library also provides data abstractions to adjust (at
-compile time) the memory layout of data structures like 2d and
-3d arrays to optimize performance on different hardware. For more information on Kokkos, see
-"Github"_https://github.com/kokkos/kokkos. Kokkos is part of
-"Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards,
-Christian Trott, and Dan Sunderland (all Sandia).
-
-The LAMMPS KOKKOS package contains versions of pair, fix, and atom styles
-that use data structures and macros provided by the Kokkos library,
-which is included with LAMMPS in /lib/kokkos. The KOKKOS package was developed primarily by Christian Trott (Sandia)
-and Stan Moore (Sandia) with contributions of various styles by others, including Sikandar
-Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions
+a single implementation of an application kernel (e.g. a pair style)
+to run efficiently on different kinds of hardware, such as GPUs, Intel
+Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto
+different backend languages such as CUDA, OpenMP, or Pthreads. The
+Kokkos library also provides data abstractions to adjust (at compile
+time) the memory layout of data structures like 2d and 3d arrays to
+optimize performance on different hardware. For more information on
+Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part
+of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos
+library was written primarily by Carter Edwards, Christian Trott, and
+Dan Sunderland (all Sandia).
+
+The LAMMPS KOKKOS package contains versions of pair, fix, and atom
+styles that use data structures and macros provided by the Kokkos
+library, which is included with LAMMPS in /lib/kokkos. The KOKKOS
+package was developed primarily by Christian Trott (Sandia) and Stan
+Moore (Sandia) with contributions of various styles by others,
+including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
+(Sandia). For more information on developing using Kokkos abstractions
see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf.
Kokkos currently provides support for 3 modes of execution (per MPI
-task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP (threading
-for many-core CPUs and Intel Phi), and CUDA (for NVIDIA GPUs). You choose the mode at build time to
-produce an executable compatible with specific hardware.
+task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
+(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA
+GPUs). You choose the mode at build time to produce an executable
+compatible with specific hardware.
[Building LAMMPS with the KOKKOS package:]
@@ -40,16 +43,18 @@ NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible
compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or
Clang 3.5.2 or later is required.
-The recommended method of building the KOKKOS package is to start with the provided Kokkos
-Makefiles in /src/MAKE/OPTIONS/. You may need to modify the KOKKOS_ARCH variable in the Makefile
-to match your specific hardware. For example:
+The recommended method of building the KOKKOS package is to start with
+the provided Kokkos Makefiles in /src/MAKE/OPTIONS/. You may need to
+modify the KOKKOS_ARCH variable in the Makefile to match your specific
+hardware. For example:
for Sandy Bridge CPUs, set KOKKOS_ARCH=SNB
for Broadwell CPUs, set KOKKOS_ARCH=BWD
for K80 GPUs, set KOKKOS_ARCH=Kepler37
for P100 GPUs and Power8 CPUs, set KOKKOS_ARCH=Pascal60,Power8 :ul
-See the [Advanced Kokkos Options] section below for a listing of all KOKKOS_ARCH options.
+See the [Advanced Kokkos Options] section below for a listing of all
+KOKKOS_ARCH options.
[Compile for CPU-only (MPI only, no threading):]
@@ -63,11 +68,12 @@ make kokkos_mpi_only :pre
[Compile for CPU-only (MPI plus OpenMP threading):]
-NOTE: To build with Kokkos support for OpenMP threading, your compiler must support the
-OpenMP interface. You should have one or more multi-core CPUs so that
-multiple threads can be launched by each MPI task running on a CPU.
+NOTE: To build with Kokkos support for OpenMP threading, your compiler
+must support the OpenMP interface. You should have one or more
+multi-core CPUs so that multiple threads can be launched by each MPI
+task running on a CPU.
-use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+Use a C++11 compatible compiler and set KOKKOS_ARCH variable in
/src/MAKE/OPTIONS/Makefile.kokkos_omp as described above. Then do the
following:
@@ -85,14 +91,14 @@ make kokkos_phi :pre
[Compile for CPUs and GPUs (with OpenMPI or MPICH):]
-NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
-version 7.5 or later must be installed on your system. See the
-discussion for the "GPU"_accelerate_gpu.html package for details of
-how to check and do this.
+NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA
+software version 7.5 or later must be installed on your system. See
+the discussion for the "GPU package"_Speed_gpu.html for details of how
+to check and do this.
-use a C++11 compatible compiler and set KOKKOS_ARCH variable in
-/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as described
-above. Then do the following:
+Use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as
+described above. Then do the following:
cd lammps/src
make yes-kokkos
@@ -106,24 +112,24 @@ on the make command line. For example:
make mpi KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=SNB # set the KOKKOS_DEVICES and KOKKOS_ARCH variable explicitly
make kokkos_cuda_mpi KOKKOS_ARCH=Pascal60,Power8 # set the KOKKOS_ARCH variable explicitly :pre
-Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the
-make command line requires a GNU-compatible make command. Try
-"gmake" if your system's standard make complains.
+Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the make
+command line requires a GNU-compatible make command. Try "gmake" if
+your system's standard make complains.
NOTE: If you build using make line variables and re-build LAMMPS twice
-with different KOKKOS options and the *same* target, then you *must* perform a "make clean-all"
-or "make clean-machine" before each build. This is to force all the
-KOKKOS-dependent files to be re-compiled with the new options.
+with different KOKKOS options and the *same* target, then you *must*
+perform a "make clean-all" or "make clean-machine" before each
+build. This is to force all the KOKKOS-dependent files to be
+re-compiled with the new options.
[Running LAMMPS with the KOKKOS package:]
-All Kokkos operations occur within the
-context of an individual MPI task running on a single node of the
-machine. The total number of MPI tasks used by LAMMPS (one or
-multiple per compute node) is set in the usual manner via the mpirun
-or mpiexec commands, and is independent of Kokkos. E.g. the mpirun
-command in OpenMPI does this via its
--np and -npernode switches. Ditto for MPICH via -np and -ppn.
+All Kokkos operations occur within the context of an individual MPI
+task running on a single node of the machine. The total number of MPI
+tasks used by LAMMPS (one or multiple per compute node) is set in the
+usual manner via the mpirun or mpiexec commands, and is independent of
+Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
+-npernode switches. Ditto for MPICH via -np and -ppn.
[Running on a multi-core CPU:]
@@ -135,8 +141,9 @@ mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI
mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
-To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk kokkos" "command-line switches"_Section_start.html#start_7 in your mpirun command.
-You must use the "-k on" "command-line
+To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk
+kokkos" "command-line switches"_Section_start.html#start_7 in your
+mpirun command. You must use the "-k on" "command-line
switch"_Section_start.html#start_7 to enable the KOKKOS package. It
takes additional arguments for hardware settings appropriate to your
system. Those arguments are "documented
@@ -144,32 +151,33 @@ here"_Section_start.html#start_7. For OpenMP use:
-k on t Nt :pre
-The "t Nt" option specifies how many OpenMP threads per MPI
-task to use with a node. The default is Nt = 1, which is MPI-only mode.
-Note that the product of MPI tasks * OpenMP
-threads/task should not exceed the physical number of cores (on a
-node), otherwise performance will suffer. If hyperthreading is enabled, then
-the product of MPI tasks * OpenMP threads/task should not exceed the
-physical number of cores * hardware threads.
-The "-k on" switch also issues a "package kokkos" command (with no
-additional arguments) which sets various KOKKOS options to default
-values, as discussed on the "package"_package.html command doc page.
-
-The "-sf kk" "command-line switch"_Section_start.html#start_7
-will automatically append the "/kk" suffix to styles that support it.
-In this manner no modification to the input script is needed. Alternatively,
-one can run with the KOKKOS package by editing the input script as described below.
-
-NOTE: The default for the "package kokkos"_package.html command is
-to use "full" neighbor lists and set the Newton flag to "off" for both
+The "t Nt" option specifies how many OpenMP threads per MPI task to
+use with a node. The default is Nt = 1, which is MPI-only mode. Note
+that the product of MPI tasks * OpenMP threads/task should not exceed
+the physical number of cores (on a node), otherwise performance will
+suffer. If hyperthreading is enabled, then the product of MPI tasks *
+OpenMP threads/task should not exceed the physical number of cores *
+hardware threads. The "-k on" switch also issues a "package kokkos"
+command (with no additional arguments) which sets various KOKKOS
+options to default values, as discussed on the "package"_package.html
+command doc page.
+
+The "-sf kk" "command-line switch"_Section_start.html#start_7 will
+automatically append the "/kk" suffix to styles that support it. In
+this manner no modification to the input script is
+needed. Alternatively, one can run with the KOKKOS package by editing
+the input script as described below.
+
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions. However, when running on CPUs, it
will typically be faster to use "half" neighbor lists and set the
Newton flag to "on", just as is the case for non-accelerated pair
-styles. It can also be faster to use non-threaded communication.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html
-options. See its doc page for details and default settings. Experimenting with
-its options can provide a speed-up for specific calculations. For example:
+styles. It can also be faster to use non-threaded communication. Use
+the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html options. See its doc
+page for details and default settings. Experimenting with its options
+can provide a speed-up for specific calculations. For example:
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre
@@ -178,9 +186,9 @@ script, it can also override the Newton flag defaults.
[Core and Thread Affinity:]
-When using multi-threading, it is important for
-performance to bind both MPI tasks to physical cores, and threads to
-physical cores, so they do not migrate during a simulation.
+When using multi-threading, it is important for performance to bind
+both MPI tasks to physical cores, and threads to physical cores, so
+they do not migrate during a simulation.
If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags:
@@ -191,24 +199,24 @@ Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... :
For binding threads with KOKKOS OpenMP, use thread affinity
environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
later, intel 12 or later) setting the environment variable
-OMP_PROC_BIND=true should be sufficient. In general, for best performance
-with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads.
-For binding threads with the
-KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
-as described below.
+OMP_PROC_BIND=true should be sufficient. In general, for best
+performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and
+OMP_PLACES=threads. For binding threads with the KOKKOS pthreads
+option, compile LAMMPS the KOKKOS HWLOC=yes option as described below.
[Running on Knight's Landing (KNL) Intel Xeon Phi:]
-Here is a quick overview of how to use the KOKKOS package
-for the Intel Knight's Landing (KNL) Xeon Phi:
+Here is a quick overview of how to use the KOKKOS package for the
+Intel Knight's Landing (KNL) Xeon Phi:
-KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores
-are reserved for the OS, and only 64 or 66 cores are used. Each core
-has 4 hyperthreads,so there are effectively N = 256 (4*64) or
-N = 264 (4*66) cores to run on. The product of MPI tasks * OpenMP threads/task should not exceed this limit,
-otherwise performance will suffer. Note that with the KOKKOS package you do not need to
-specify how many KNLs there are per node; each
-KNL is simply treated as running some number of MPI tasks.
+KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
+reserved for the OS, and only 64 or 66 cores are used. Each core has 4
+hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
+cores to run on. The product of MPI tasks * OpenMP threads/task should
+not exceed this limit, otherwise performance will suffer. Note that
+with the KOKKOS package you do not need to specify how many KNLs there
+are per node; each KNL is simply treated as running some number of MPI
+tasks.
Examples of mpirun commands that follow these rules are shown below.
@@ -223,57 +231,60 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of
threads/task as Nt. The product of these two values should be N, i.e.
256 or 264.
-NOTE: The default for the "package kokkos"_package.html command is
-to use "full" neighbor lists and set the Newton flag to "off" for both
-pairwise and bonded interactions. When running on KNL, this
-will typically be best for pair-wise potentials. For manybody potentials,
-using "half" neighbor lists and setting the
-Newton flag to "on" may be faster. It can also be faster to use non-threaded communication.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html
-options. See its doc page for details and default settings. Experimenting with
-its options can provide a speed-up for specific calculations. For example:
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions. When running on KNL, this will
+typically be best for pair-wise potentials. For manybody potentials,
+using "half" neighbor lists and setting the Newton flag to "on" may be
+faster. It can also be faster to use non-threaded communication. Use
+the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html options. See its doc
+page for details and default settings. Experimenting with its options
+can provide a speed-up for specific calculations. For example:
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj # Newton off, full neighbor list, non-threaded comm
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax # Newton on, half neighbor list, non-threaded comm :pre
-NOTE: MPI tasks and threads should be bound to cores as described above for CPUs.
+NOTE: MPI tasks and threads should be bound to cores as described
+above for CPUs.
-NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors such as Knight's Corner (KNC), your
-system must be configured to use them in "native" mode, not "offload"
-mode like the USER-INTEL package supports.
+NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors
+such as Knight's Corner (KNC), your system must be configured to use
+them in "native" mode, not "offload" mode like the USER-INTEL package
+supports.
[Running on GPUs:]
-Use the "-k" "command-line switch"_Section_commands.html#start_7 to
-specify the number of GPUs per node. Typically the -np setting
-of the mpirun command should set the number of MPI
-tasks/node to be equal to the # of physical GPUs on the node.
-You can assign multiple MPI tasks to the same GPU with the
-KOKKOS package, but this is usually only faster if significant portions
-of the input script have not been ported to use Kokkos. Using CUDA MPS
-is recommended in this scenario. As above for multi-core CPUs (and no GPU), if N is the number
-of physical cores/node, then the number of MPI tasks/node should not exceed N.
+Use the "-k" "command-line switch"_Section_start.html#start_7 to
+specify the number of GPUs per node. Typically the -np setting of the
+mpirun command should set the number of MPI tasks/node to be equal to
+the # of physical GPUs on the node. You can assign multiple MPI tasks
+to the same GPU with the KOKKOS package, but this is usually only
+faster if significant portions of the input script have not been
+ported to use Kokkos. Using CUDA MPS is recommended in this
+scenario. As above for multi-core CPUs (and no GPU), if N is the
+number of physical cores/node, then the number of MPI tasks/node
+should not exceed N.
-k on g Ng :pre
-Here are examples of how to use the KOKKOS package for GPUs,
-assuming one or more nodes, each with two GPUs:
+Here are examples of how to use the KOKKOS package for GPUs, assuming
+one or more nodes, each with two GPUs:
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node
mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
-NOTE: The default for the "package kokkos"_package.html command is
-to use "full" neighbor lists and set the Newton flag to "off" for both
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions, along with threaded communication.
-When running on Maxwell or Kepler GPUs, this will typically be best. For Pascal GPUs,
-using "half" neighbor lists and setting the
-Newton flag to "on" may be faster. For many pair styles, setting the neighbor binsize
-equal to the ghost atom cutoff will give speedup.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html
-options. See its doc page for details and default settings. Experimenting with
-its options can provide a speed-up for specific calculations. For example:
+When running on Maxwell or Kepler GPUs, this will typically be
+best. For Pascal GPUs, using "half" neighbor lists and setting the
+Newton flag to "on" may be faster. For many pair styles, setting the
+neighbor binsize equal to the ghost atom cutoff will give speedup.
+Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7
+to change the default "package kokkos"_package.html options. See its
+doc page for details and default settings. Experimenting with its
+options can provide a speed-up for specific calculations. For example:
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
@@ -301,8 +312,8 @@ Alternatively the effect of the "-sf" or "-pk" switches can be
duplicated by adding the "package kokkos"_package.html or "suffix
kk"_suffix.html commands to your input script.
-The discussion above for building LAMMPS with the KOKKOS package, the mpirun/mpiexec command, and setting
-appropriate thread are the same.
+The discussion above for building LAMMPS with the KOKKOS package, the
+mpirun/mpiexec command, and setting appropriate thread are the same.
You must still use the "-k on" "command-line
switch"_Section_start.html#start_7 to enable the KOKKOS package, and
@@ -320,17 +331,19 @@ wish to change any of its option defaults, as set by the "-k on"
[Using OpenMP threading and CUDA together (experimental):]
-With the KOKKOS package, both OpenMP multi-threading and GPUs can be used
-together in a few special cases. In the Makefile, the KOKKOS_DEVICES variable must
-include both "Cuda" and "OpenMP", as is the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
+With the KOKKOS package, both OpenMP multi-threading and GPUs can be
+used together in a few special cases. In the Makefile, the
+KOKKOS_DEVICES variable must include both "Cuda" and "OpenMP", as is
+the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
KOKKOS_DEVICES=Cuda,OpenMP :pre
The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
-using the "-sf kk" in the command line gives the default CUDA version everywhere.
-However, if the "/kk/host" suffix is added to a specific style in the input
-script, the Kokkos OpenMP (CPU) version of that specific style will be used instead.
-Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng"
+using the "-sf kk" in the command line gives the default CUDA version
+everywhere. However, if the "/kk/host" suffix is added to a specific
+style in the input script, the Kokkos OpenMP (CPU) version of that
+specific style will be used instead. Set the number of OpenMP threads
+as "t Nt" and the number of GPUs as "g Ng"
-k on t Nt g Ng :pre
@@ -338,18 +351,20 @@ For example, the command to run with 1 GPU and 8 OpenMP threads is then:
mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre
-Conversely, if the "-sf kk/host" is used in the command line and then the
-"/kk" or "/kk/device" suffix is added to a specific style in your input script,
-then only that specific style will run on the GPU while everything else will
-run on the CPU in OpenMP mode. Note that the execution of the CPU and GPU
-styles will NOT overlap, except for a special case:
-
-A kspace style and/or molecular topology (bonds, angles, etc.) running on
-the host CPU can overlap with a pair style running on the GPU. First compile
-with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile.
-Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc.
-in the input file and the "kk" suffix (equal to "kk/device") on the command line.
-Also make sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
+Conversely, if the "-sf kk/host" is used in the command line and then
+the "/kk" or "/kk/device" suffix is added to a specific style in your
+input script, then only that specific style will run on the GPU while
+everything else will run on the CPU in OpenMP mode. Note that the
+execution of the CPU and GPU styles will NOT overlap, except for a
+special case:
+
+A kspace style and/or molecular topology (bonds, angles, etc.) running
+on the host CPU can overlap with a pair style running on the
+GPU. First compile with "--default-stream per-thread" added to CCFLAGS
+in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host"
+suffix for kspace and bonds, angles, etc. in the input file and the
+"kk" suffix (equal to "kk/device") on the command line. Also make
+sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
so CPU/GPU overlap can occur.
[Speed-ups to expect:]
@@ -386,9 +401,8 @@ hardware.
There are other allowed options when building with the KOKKOS package.
As above, they can be set either as variables on the make command line
or in Makefile.machine. This is the full list of options, including
-those discussed above. Each takes a value shown below. The
-default value is listed, which is set in the
-/lib/kokkos/Makefile.kokkos file.
+those discussed above. Each takes a value shown below. The default
+value is listed, which is set in the /lib/kokkos/Makefile.kokkos file.
KOKKOS_DEVICES, values = {Serial}, {OpenMP}, {Pthreads}, {Cuda}, default = {OpenMP}
KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {Pascal60}, {Pascal61}, {ARMv80}, {ARMv81}, {ARMv81}, {ARMv8-ThunderX}, {BGQ}, {Power7}, {Power8}, {Power9}, {KNL}, {BDW}, {SKX}, default = {none}
@@ -434,8 +448,8 @@ migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding
-threads to hardware cores. More info on binding threads to cores is
-given in "Section 5.3"_Section_accelerate.html#acc_3.
+threads to hardware cores. More info on binding threads to cores is
+given on the "Speed omp"_Speed_omp.html doc page.
KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
on most Unix platforms. This library is not available on all
@@ -446,13 +460,14 @@ within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
debugging information that can be useful. It also enables runtime
bounds checking on Kokkos data structures.
-KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when building LAMMPS.
+KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when
+building LAMMPS.
-KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS package must be compiled
-with the {enable_lambda} option when using GPUs.
+KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS
+package must be compiled with the {enable_lambda} option when using
+GPUs.
[Restrictions:]
-Currently, there are no precision options with the KOKKOS
-package. All compilation and computation is performed in double
-precision.
+Currently, there are no precision options with the KOKKOS package. All
+compilation and computation is performed in double precision.
diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78dc220088d3873b241aae6237b84b8426f03776
--- /dev/null
+++ b/doc/src/Speed_measure.txt
@@ -0,0 +1,55 @@
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Measuring performance :h3
+
+Before trying to make your simulation run faster, you should
+understand how it currently performs and where the bottlenecks are.
+
+The best way to do this is run the your system (actual number of
+atoms) for a modest number of timesteps (say 100 steps) on several
+different processor counts, including a single processor if possible.
+Do this for an equilibrium version of your system, so that the
+100-step timings are representative of a much longer run. There is
+typically no need to run for 1000s of timesteps to get accurate
+timings; you can simply extrapolate from short runs.
+
+For the set of runs, look at the timing data printed to the screen and
+log file at the end of each LAMMPS run. "This
+section"_Section_start.html#start_7 of the manual has an overview.
+
+Running on one (or a few processors) should give a good estimate of
+the serial performance and what portions of the timestep are taking
+the most time. Running the same problem on a few different processor
+counts should give an estimate of parallel scalability. I.e. if the
+simulation runs 16x faster on 16 processors, its 100% parallel
+efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
+
+The most important data to look at in the timing info is the timing
+breakdown and relative percentages. For example, trying different
+options for speeding up the long-range solvers will have little impact
+if they only consume 10% of the run time. If the pairwise time is
+dominating, you may want to look at GPU or OMP versions of the pair
+style, as discussed below. Comparing how the percentages change as
+you increase the processor count gives you a sense of how different
+operations within the timestep are scaling. Note that if you are
+running with a Kspace solver, there is additional output on the
+breakdown of the Kspace time. For PPPM, this includes the fraction
+spent on FFTs, which can be communication intensive.
+
+Another important detail in the timing info are the histograms of
+atoms counts and neighbor counts. If these vary widely across
+processors, you have a load-imbalance issue. This often results in
+inaccurate relative timing data, because processors have to wait when
+communication occurs for other processors to catch up. Thus the
+reported times for "Communication" or "Other" may be higher than they
+really are, due to load-imbalance. If this is an issue, you can
+uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
+LAMMPS, to obtain synchronized timings.
+
diff --git a/doc/src/accelerate_omp.txt b/doc/src/Speed_omp.txt
similarity index 95%
rename from doc/src/accelerate_omp.txt
rename to doc/src/Speed_omp.txt
index fa7bef1a520bd867b4d3cf610d50b5ea8614c865..bcfc406902d0947e2c6d9e0426b2fe8d7406dda3 100644
--- a/doc/src/accelerate_omp.txt
+++ b/doc/src/Speed_omp.txt
@@ -1,15 +1,13 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-"Return to Section 5 overview"_Section_accelerate.html
-
-5.3.4 USER-OMP package :h5
+USER-OMP package :h3
The USER-OMP package was developed by Axel Kohlmeyer at Temple
University. It provides multi-threaded versions of most pair styles,
@@ -39,7 +37,8 @@ each MPI task running on a CPU.
The lines above illustrate how to include/build with the USER-OMP
package in two steps, using the "make" command. Or how to do it with
-one command as described in "Section 4"_Section_packages.html of the manual.
+one command as described on the "Packages
+details"_Packages_details.html#USER-OMP doc page.
Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
include "-fopenmp". Likewise, if you use an Intel compiler, the
@@ -100,7 +99,7 @@ task, versus running standard LAMMPS with its standard un-accelerated
styles (in serial or all-MPI parallelization with 1 task/core). This
is because many of the USER-OMP styles contain similar optimizations
to those used in the OPT package, described in "Section
-5.3.5"_accelerate_opt.html.
+5.3.5"_Speed_opt.html.
With multiple threads/task, the optimal choice of number of MPI
tasks/node and OpenMP threads/task can vary a lot and should always be
diff --git a/doc/src/accelerate_opt.txt b/doc/src/Speed_opt.txt
similarity index 85%
rename from doc/src/accelerate_opt.txt
rename to doc/src/Speed_opt.txt
index 845264b5227ca31493cb582eac91ab5c216427ae..676a5d84182e90ea4f832c3938bab51e5a3011dc 100644
--- a/doc/src/accelerate_opt.txt
+++ b/doc/src/Speed_opt.txt
@@ -1,15 +1,13 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-"Return to Section accelerate overview"_Section_accelerate.html
-
-5.3.5 OPT package :h5
+OPT package :h3
The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
@@ -34,7 +32,8 @@ None.
The lines above illustrate how to build LAMMPS with the OPT package in
two steps, using the "make" command. Or how to do it with one command
-as described in "Section 4"_Section_packages.html of the manual.
+as described on the "Packages details"_Packages_details.html#OPT doc
+page.
Note that if you use an Intel compiler to build with the OPT package,
the CCFLAGS setting in your Makefile.machine must include "-restrict".
diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f463ed91b85d28cf495db638a401f7c52a5326fe
--- /dev/null
+++ b/doc/src/Speed_packages.txt
@@ -0,0 +1,192 @@
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Accelerator packages :h3
+
+Accelerated versions of various "pair_style"_pair_style.html,
+"fixes"_fix.html, "computes"_compute.html, and other commands have
+been added to LAMMPS, which will typically run faster than the
+standard non-accelerated versions. Some require appropriate hardware
+to be present on your system, e.g. GPUs or Intel Xeon Phi
+coprocessors.
+
+All of these commands are in packages provided with LAMMPS. An
+overview of packages is give on the "Packages"_Packages.html doc
+pages.
+
+These are the accelerator packages currently in LAMMPS, either as
+standard or user packages:
+
+"GPU Package"_Speed_gpu.html : for NVIDIA GPUs as well as OpenCL support
+"USER-INTEL Package"_Speed_intel.html : for Intel CPUs and Intel Xeon Phi
+"KOKKOS Package"_Speed_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading
+"USER-OMP Package"_Speed_omp.html : for OpenMP threading and generic CPU optimizations
+"OPT Package"_Speed_opt.html : generic CPU optimizations :tb(s=:)
+
+<!-- RST
+
+.. toctree::
+ :maxdepth: 1
+ :hidden:
+
+ Speed_gpu
+ Speed_intel
+ Speed_kokkos
+ Speed_omp
+ Speed_opt
+
+END_RST -->
+
+Inverting this list, LAMMPS currently has acceleration support for
+three kinds of hardware, via the listed packages:
+
+Many-core CPUs : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html, "USER-OMP"_Speed_omp.html, "OPT"_Speed_opt.html packages
+NVIDIA GPUs : "GPU"_Speed_gpu.html, "KOKKOS"_Speed_kokkos.html packages
+Intel Phi : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html packages :tb(s=:)
+
+Which package is fastest for your hardware may depend on the size
+problem you are running and what commands (accelerated and
+non-accelerated) are invoked by your input script. While these doc
+pages include performance guidelines, there is no substitute for
+trying out the different packages appropriate to your hardware.
+
+Any accelerated style has the same name as the corresponding standard
+style, except that a suffix is appended. Otherwise, the syntax for
+the command that uses the style is identical, their functionality is
+the same, and the numerical results it produces should also be the
+same, except for precision and round-off effects.
+
+For example, all of these styles are accelerated variants of the
+Lennard-Jones "pair_style lj/cut"_pair_lj.html:
+
+"pair_style lj/cut/gpu"_pair_lj.html
+"pair_style lj/cut/intel"_pair_lj.html
+"pair_style lj/cut/kk"_pair_lj.html
+"pair_style lj/cut/omp"_pair_lj.html
+"pair_style lj/cut/opt"_pair_lj.html :ul
+
+To see what accelerate styles are currently available for a particular
+style, find the style name in the "Commands_all"_Commands_all.html
+style pages (fix,compute,pair,etc) and see what suffixes are listed
+(g,i,k,o,t) with it. The doc pages for individual commands
+(e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list
+any accelerated variants available for that style.
+
+To use an accelerator package in LAMMPS, and one or more of the styles
+it provides, follow these general steps. Details vary from package to
+package and are explained in the individual accelerator doc pages,
+listed above:
+
+build the accelerator library |
+ only for GPU package |
+install the accelerator package |
+ make yes-opt, make yes-user-intel, etc |
+add compile/link flags to Makefile.machine in src/MAKE |
+ only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |
+re-build LAMMPS |
+ make machine |
+prepare and test a regular LAMMPS simulation |
+ lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
+enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
+ only needed for KOKKOS package |
+set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
+ only if defaults need to be changed |
+use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
+:tb(c=2,s=|)
+
+Note that the first 4 steps can be done as a single command with
+suitable make command invocations. This is discussed on the
+"Packages"_Packages.html doc pages, and its use is illustrated in the
+individual accelerator sections. Typically these steps only need to
+be done once, to create an executable that uses one or more
+accelerator packages.
+
+The last 4 steps can all be done from the command-line when LAMMPS is
+launched, without changing your input script, as illustrated in the
+individual accelerator sections. Or you can add
+"package"_package.html and "suffix"_suffix.html commands to your input
+script.
+
+NOTE: With a few exceptions, you can build a single LAMMPS executable
+with all its accelerator packages installed. Note however that the
+USER-INTEL and KOKKOS packages require you to choose one of their
+hardware options when building for a specific platform. I.e. CPU or
+Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
+option for the KOKKOS package.
+
+These are the exceptions. You cannot build a single executable with:
+
+both the USER-INTEL Phi and KOKKOS Phi options
+the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul
+
+See the examples/accelerate/README and make.list files for sample
+Make.py commands that build LAMMPS with any or all of the accelerator
+packages. As an example, here is a command that builds with all the
+GPU related packages installed (GPU, KOKKOS with Cuda), including
+settings to build the needed auxiliary GPU libraries for Kepler GPUs:
+
+Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \
+ -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre
+
+The examples/accelerate directory also has input scripts that can be
+used with all of the accelerator packages. See its README file for
+details.
+
+Likewise, the bench directory has FERMI and KEPLER and PHI
+sub-directories with Make.py commands and input scripts for using all
+the accelerator packages on various machines. See the README files in
+those dirs.
+
+As mentioned above, the "Benchmark
+page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives
+performance results for the various accelerator packages for several
+of the standard LAMMPS benchmark problems, as a function of problem
+size and number of compute nodes, on different hardware platforms.
+
+Here is a brief summary of what the various packages provide. Details
+are in the individual accelerator sections.
+
+Styles with a "gpu" suffix are part of the GPU package, and can be run
+on NVIDIA GPUs. The speed-up on a GPU depends on a variety of
+factors, discussed in the accelerator sections. :ulb,l
+
+Styles with an "intel" suffix are part of the USER-INTEL
+package. These styles support vectorized single and mixed precision
+calculations, in addition to full double precision. In extreme cases,
+this can provide speedups over 3.5x on CPUs. The package also
+supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
+coprocessors. This can result in additional speedup over 2x depending
+on the hardware configuration. :l
+
+Styles with a "kk" suffix are part of the KOKKOS package, and can be
+run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
+Xeon Phi in "native" mode. The speed-up depends on a variety of
+factors, as discussed on the KOKKOS accelerator page. :l
+
+Styles with an "omp" suffix are part of the USER-OMP package and allow
+a pair-style to be run in multi-threaded mode using OpenMP. This can
+be useful on nodes with high-core counts when using less MPI processes
+than cores is advantageous, e.g. when running with PPPM so that FFTs
+are run on fewer MPI processors or when the many MPI tasks would
+overload the available bandwidth for communication. :l
+
+Styles with an "opt" suffix are part of the OPT package and typically
+speed-up the pairwise calculations of your simulation by 5-25% on a
+CPU. :l
+:ule
+
+The individual accelerator package doc pages explain:
+
+what hardware and software the accelerated package requires
+how to build LAMMPS with the accelerated package
+how to run with the accelerated package either via command-line switches or modifying the input script
+speed-ups to expect
+guidelines for best performance
+restrictions :ul
+
diff --git a/doc/src/Speed_tips.txt b/doc/src/Speed_tips.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c950779d5e4864db0802e90369c6acaaf8b6d36
--- /dev/null
+++ b/doc/src/Speed_tips.txt
@@ -0,0 +1,63 @@
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+General tips :h3
+
+NOTE: this section 5.2 is still a work in progress
+
+Here is a list of general ideas for improving simulation performance.
+Most of them are only applicable to certain models and certain
+bottlenecks in the current performance, so let the timing data you
+generate be your guide. It is hard, if not impossible, to predict how
+much difference these options will make, since it is a function of
+problem size, number of processors used, and your machine. There is
+no substitute for identifying performance bottlenecks, and trying out
+various options.
+
+make individual pages for these, or one for PPPM
+one for timestepping, etc
+one for balancing
+or proc layout
+
+rRESPA
+2-FFT PPPM
+Staggered PPPM
+single vs double PPPM
+partial charge PPPM
+verlet/split run style
+processor command for proc layout and numa layout
+load-balancing: balance and fix balance :ul
+
+2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses
+2 FFTs instead of the 4 FFTs used by the default {ik differentiation}
+PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
+achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
+cost is the performance bottleneck (typically large problems running
+on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
+
+Staggered PPPM performs calculations using two different meshes, one
+shifted slightly with respect to the other. This can reduce force
+aliasing errors and increase the accuracy of the method, but also
+doubles the amount of work required. For high relative accuracy, using
+staggered PPPM allows one to half the mesh size in each dimension as
+compared to regular PPPM, which can give around a 4x speedup in the
+kspace time. However, for low relative accuracy, using staggered PPPM
+gives little benefit and can be up to 2x slower in the kspace
+time. For example, the rhodopsin benchmark was run on a single
+processor, and results for kspace time vs. relative accuracy for the
+different methods are shown in the figure below. For this system,
+staggered PPPM (using ik differentiation) becomes useful when using a
+relative accuracy of slightly greater than 1e-5 and above.
+
+:c,image(JPG/rhodo_staggered.jpg)
+
+NOTE: Using staggered PPPM may not give the same increase in accuracy
+of energy and pressure as it does in forces, so some caution must be
+used if energy and/or pressure are quantities of interest, such as
+when using a barostat.
diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt
index 4c5fbbd45327f6e68d9ff29704add3ae4de96a12..85ee531cfd905371ebef6f17db26713c2a496d6c 100644
--- a/doc/src/Tools.txt
+++ b/doc/src/Tools.txt
@@ -1,10 +1,10 @@
-"Previous Section"_Section_perf.html - "LAMMPS WWW Site"_lws - "LAMMPS
+"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Modify.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -142,8 +142,8 @@ The syntax for running the tool is
chain < def.chain > data.file :pre
See the def.chain or def.chain.ab files in the tools directory for
-examples of definition files. This tool was used to create the
-system for the "chain benchmark"_Section_perf.html.
+examples of definition files. This tool was used to create the system
+for the "chain benchmark"_Speed_bench.html.
:line
@@ -249,9 +249,9 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
emacs tool :h4,link(emacs)
-The tools/emacs directory contains a Lips add-on file for Emacs that
-enables a lammps-mode for editing of input scripts when using Emacs,
-with various highlighting options setup.
+The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
+that enables a lammps-mode for editing input scripts when using GNU Emacs,
+with various highlighting options set up.
These tools were provided by Aidan Thompson at Sandia
(athomps at sandia.gov).
diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt
index 7ff7ef8fd417c1118951adcbc0f89b4c7d08540a..f72f0862348328bbd5c62a11d42274bb4f4c14d3 100644
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -51,10 +51,9 @@ internally; hence the units of K are in energy/radian^2.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt
index d4330139c963c12c53dc50aa2312eca93ce068e6..3e5445d3a3c17200bd5e548791bdbfbb31f4dcbe 100644
--- a/doc/src/angle_class2.txt
+++ b/doc/src/angle_class2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -83,10 +83,9 @@ same value from the Ea formula.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -98,8 +97,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_coeff.txt b/doc/src/angle_coeff.txt
index 37298ba14591ca28fe4a45952ec5ed80551a8178..4c217bae7d3905298202c2d48592e1bb045e49ef 100644
--- a/doc/src/angle_coeff.txt
+++ b/doc/src/angle_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,9 +65,9 @@ the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command.
Note that there are also additional angle styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the angle section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+angle styles is on the "Commands bond"_Commands_bond.html#angle doc
+page.
"angle_style none"_angle_none.html - turn off angle interactions
"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt
index c0ce3c9301f735fc69fb1b239d30ddce3150c3b0..5a1fe91c834271bfe883e1b2d5a410f3bb148a23 100644
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,10 +38,9 @@ K (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -53,8 +52,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt
index 7182ffecc849e1c581793add231af6ed1fa03d57..63a451b7631456aa21b870eadf5808e92b052ec9 100644
--- a/doc/src/angle_cosine_buck6d.txt
+++ b/doc/src/angle_cosine_buck6d.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt
index 830fd6db584a67bf7c93082b971e3abb383e69d2..b6ac0ed8181ad55b183ab59962e9502c2cd5ab93 100644
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,10 +43,9 @@ internally.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt
index b5c53b1b0fb5a81d8ab33d2ebbc8e2087fd26fab..c5b184e0b46b1e5b14efb8b1dd0477740c59ae19 100644
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -21,10 +21,10 @@ angle_coeff * 75.0 1 6 :pre
[Description:]
The {cosine/periodic} angle style uses the following potential, which
-is commonly used in the "DREIDING"_Section_howto.html#howto_4 force
-field, particularly for organometallic systems where {n} = 4 might be
-used for an octahedral complex and {n} = 3 might be used for a
-trigonal center:
+is commonly used in the "DREIDING"_Howto_bioFF.html force field,
+particularly for organometallic systems where {n} = 4 might be used
+for an octahedral complex and {n} = 3 might be used for a trigonal
+center:
:c,image(Eqs/angle_cosine_periodic.jpg)
@@ -51,10 +51,9 @@ geometry.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt
index 6ed9fe2150b7d7bdcda19e55bc7ca852ceed4a88..90ac61fe23c9d45f595c579e937d55bdea284909 100644
--- a/doc/src/angle_cosine_shift.txt
+++ b/doc/src/angle_cosine_shift.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,10 +41,9 @@ theta (angle) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt
index 44a68c1087582357c0d2b27a98ba21184a582531..f1c4c93c425e0ce8f51d12e39dd34c9493bf0426 100644
--- a/doc/src/angle_cosine_shift_exp.txt
+++ b/doc/src/angle_cosine_shift_exp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -53,10 +53,9 @@ A (real number) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt
index 065cdad5421bf816fd6cb600a023d265e4bbfff8..ba5fd9d4139a4f1142c287e121d3e3e7f002a6d4 100644
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,10 +43,9 @@ internally.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt
index 34cc8c153cf8037bde166eba3158e13dcea4654e..c001d9d9206c743222357f1cdcb345934f9a9ead 100644
--- a/doc/src/angle_dipole.txt
+++ b/doc/src/angle_dipole.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -71,10 +71,9 @@ gamma0 (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -86,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restrictions:]
diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt
index da39e7cf326b43afce171e0005c1ef93cde2d5c8..e0e32c1eed001fa0d6ecb70f2f2c69542d39d6c0 100644
--- a/doc/src/angle_fourier.txt
+++ b/doc/src/angle_fourier.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -39,10 +39,9 @@ C2 (real) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -54,8 +53,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt
index 5adda6cb32f85a00310f5dc62ada7838e84d5715..3c50536a2cbc0720ec69c4a4b02cdefa15bd48ff 100644
--- a/doc/src/angle_fourier_simple.txt
+++ b/doc/src/angle_fourier_simple.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,10 +38,9 @@ n (real) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -53,8 +52,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt
index 4c74763964832d98cfcae9443866e2db4293ca64..76c7a491e8943aa7cdd720750394818fc7460b9e 100644
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -45,10 +45,9 @@ internally; hence the units of K are in energy/radian^2.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt
index bdd3707ccb80130284817d86a3eec53a698c2a2a..26469034212fe359d66a965e216543404b2d1020 100644
--- a/doc/src/angle_hybrid.txt
+++ b/doc/src/angle_hybrid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/angle_none.txt b/doc/src/angle_none.txt
index a4a9b07c78e0bf7616ffe4d0ae0dc4ee8c4c9061..1eca5cbbeca786991139f7af6a44547f86d9d821 100644
--- a/doc/src/angle_none.txt
+++ b/doc/src/angle_none.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt
index f7640bdfbc0f75af1170cb551220d846df1529a0..294be330b1faab22d868d16b1a78edb048be928c 100644
--- a/doc/src/angle_quartic.txt
+++ b/doc/src/angle_quartic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -45,10 +45,9 @@ internally; hence the units of K are in energy/radian^2.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt
index 0cc535e543f878bba02b38b9a5fa18e65da0aea2..9c5630ef3adf62b7688dbbd021555283536b2cff 100644
--- a/doc/src/angle_sdk.txt
+++ b/doc/src/angle_sdk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt
index f687e9286c40ac37a84566a5ab904c65fb3d30bf..63295faf264d8fee8b2a75fb32143ae710d02586 100644
--- a/doc/src/angle_style.txt
+++ b/doc/src/angle_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -58,9 +58,9 @@ the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command.
Note that there are also additional angle styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the angle section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+angle styles are is on the "Commands bond"_Commands_bond.html#angle
+doc page.
"angle_style none"_angle_none.html - turn off angle interactions
"angle_style zero"_angle_zero.html - topology but no interactions
diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt
index bd6e167bd8f4dfccc84412c6597e1d2568a1daec..31ab532be17c95598c2b54f3a34becbf3c966120 100644
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -124,10 +124,9 @@ one that matches the specified keyword.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -139,8 +138,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_zero.txt b/doc/src/angle_zero.txt
index b8e8ebf953c6b6ba40a583bef0508ab9992f3a6d..c6c1958ec8f35f7d1335b5a9cafaf36b96049c9a 100644
--- a/doc/src/angle_zero.txt
+++ b/doc/src/angle_zero.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt
index 1dc0fa6bfb6410df5eaef9abf35cebb3a66749fd..c882d1b0ba0f43a916ee3a954a4b85e41d6c2007 100644
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.txt
@@ -3,7 +3,7 @@ Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt
index 442bb5ac700c9dfe02b2f017cf2809348386c035..abf05885a3ee3d96846af804d6ef1caaf42643c6 100644
--- a/doc/src/atom_style.txt
+++ b/doc/src/atom_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -20,7 +20,7 @@ style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
{body} args = bstyle bstyle-args
bstyle = style of body particles
bstyle-args = additional arguments specific to the bstyle
- see the "body"_body.html doc page for details
+ see the "Howto body"_Howto_body.html doc page for details
{tdpd} arg = Nspecies
Nspecies = # of chemical species
{template} arg = template-ID
@@ -106,9 +106,9 @@ output the custom values.
All of the above styles define point particles, except the {sphere},
{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and
-{body} styles, which define finite-size particles. See "Section
-6.14"_Section_howto.html#howto_14 for an overview of using finite-size
-particle models with LAMMPS.
+{body} styles, which define finite-size particles. See the "Howto
+spherical"_Howto_spherical.html doc page for an overview of using
+finite-size particle models with LAMMPS.
All of the point-particle styles assign mass to particles on a
per-type basis, using the "mass"_mass.html command, The finite-size
@@ -224,15 +224,16 @@ the {bstyle} argument. Body particles can represent complex entities,
such as surface meshes of discrete points, collections of
sub-particles, deformable objects, etc.
-The "body"_body.html doc page describes the body styles LAMMPS
-currently supports, and provides more details as to the kind of body
-particles they represent. For all styles, each body particle stores
-moments of inertia and a quaternion 4-vector, so that its orientation
-and position can be time integrated due to forces and torques.
+The "Howto body"_Howto_body.html doc page describes the body styles
+LAMMPS currently supports, and provides more details as to the kind of
+body particles they represent. For all styles, each body particle
+stores moments of inertia and a quaternion 4-vector, so that its
+orientation and position can be time integrated due to forces and
+torques.
Note that there may be additional arguments required along with the
{bstyle} specification, in the atom_style body command. These
-arguments are described in the "body"_body.html doc page.
+arguments are described on the "Howto body"_Howto_body.html doc page.
:line
@@ -261,10 +262,10 @@ styles; see the "Modify"_Modify.html doc page.
Styles with a {kk} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
-run faster, depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+run faster, depending on your available hardware, as discussed in on
+the "Speed packages"_Speed_packages.html doc page. The accelerated
+styles take the same arguments and should produce the same results,
+except for round-off and precision issues.
Note that other acceleration packages in LAMMPS, specifically the GPU,
USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
@@ -279,8 +280,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restrictions:]
diff --git a/doc/src/balance.txt b/doc/src/balance.txt
index da6f59900d69fb784ee8cdf91cc3bef60921aaa8..06c4eca491d1bd6cdb3c68a5caa2381718159ea7 100644
--- a/doc/src/balance.txt
+++ b/doc/src/balance.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt
index 9687a6316805acb77298f74eeb84952e8f4243fe..3d8d5007bad145439de155227c8873fcfce616a9 100644
--- a/doc/src/bond_class2.txt
+++ b/doc/src/bond_class2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -44,10 +44,9 @@ K4 (energy/distance^4) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -59,8 +58,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_coeff.txt b/doc/src/bond_coeff.txt
index d93c0b223b84a0da9d6f171d9e222847d905ee69..7485fa3d8d1da5da832cc832f69f7ffd6d593696 100644
--- a/doc/src/bond_coeff.txt
+++ b/doc/src/bond_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -61,9 +61,8 @@ the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
Note that here are also additional bond styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the bond section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+bond styles is on the "Commands bond"_Commands_bond.html doc page.
"bond_style none"_bond_none.html - turn off bonded interactions
"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt
index 9050c3bf5ccecdd8701f414ef0caea5e39a19c2c..e16307a71076c6c2c2b6aecd5c660eb4acda8f2a 100644
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -47,10 +47,9 @@ sigma (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -62,8 +61,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt
index ff687444a97378373514442bda71a614b74bd821..8edd325885e457e039765074ce14be6fe5fe2764 100644
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -50,10 +50,9 @@ delta (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -65,8 +64,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt
index cc3ff75878f36dd27f2d85b61ae3bfb522f52583..275036a421f618085eb25625f87a716cb28876c5 100644
--- a/doc/src/bond_gromos.txt
+++ b/doc/src/bond_gromos.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,10 +40,9 @@ r0 (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt
index c18a7e0fd4d35a337a832255b64b4daf8f07392f..e4b2015fed2987dfe52a06e22021fff70bbb6ce6 100644
--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -42,10 +42,9 @@ r0 (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -57,8 +56,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt
index bf3b3c115adeb59fcbd0a7a51e36a4612e6c020d..b6dc18a5fd69453806968cebd189c4ca7c0d5dd3 100644
--- a/doc/src/bond_harmonic_shift.txt
+++ b/doc/src/bond_harmonic_shift.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,10 +43,9 @@ rc (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt
index 1918ce00b6210468a119d332762ed85f8f2bad0e..b3054437d8e8b4a4bda593bb756e7721ff7ebe26 100644
--- a/doc/src/bond_harmonic_shift_cut.txt
+++ b/doc/src/bond_harmonic_shift_cut.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,10 +43,9 @@ rc (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt
index 400c3e0be4c9e1b7fb1fd98936208ad19f384896..140fb723785476a1a09c67360b6865a898f8d1f5 100644
--- a/doc/src/bond_hybrid.txt
+++ b/doc/src/bond_hybrid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt
index 4f6a32e341b57a7977e4aaabc83d8dd1a1282137..9b64e8c5c1d2da41936def16578ba299160121a9 100644
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,10 +41,9 @@ r0 (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_none.txt b/doc/src/bond_none.txt
index 8cb262a50f939617011853d41fe416f1a6e3160a..cace1919e13ff668c51418063f6a2d4a30dbefbc 100644
--- a/doc/src/bond_none.txt
+++ b/doc/src/bond_none.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt
index 434af625061a45679e9f01630c3999743d6d77ee..08109bc699dfed95d7ad70cff09dbded043627f5 100644
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,10 +41,9 @@ lamda (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt
index 927fea64031d5422615d1251b9332e4e66120d3a..a0e14a123abed8da2728ed13d3ad3b836fc3414b 100644
--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt
index 4dc7ad4a3693e8d0ed492514fbaaf5f15deaecd0..87a21eff02ef4577638e44a5a6932ab181ec5a71 100644
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -76,10 +76,9 @@ delete_bonds all bond 0 remove :pre
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -91,8 +90,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt
index 3bd8afda196a642c883f7321d7998ed70f98f09c..41fa1cabb213847c51aef2b7acef0b1bb6bee00e 100644
--- a/doc/src/bond_style.txt
+++ b/doc/src/bond_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -66,9 +66,8 @@ the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
Note that there are also additional bond styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the bond section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+bond styles is on the "Commands bond"_Commands_bond.html doc page.
"bond_style none"_bond_none.html - turn off bonded interactions
"bond_style zero"_bond_zero.html - topology but no interactions
diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt
index 906d3e5d7639eb08e211554b2817195dd383bcf1..e53cbdfa9f626c0c36377d9ac56a8bea016f958b 100644
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -121,10 +121,9 @@ one that matches the specified keyword.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -136,8 +135,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_write.txt b/doc/src/bond_write.txt
index 4797d06cb1b5a164a47805840ce38824ea78b6ce..711bd2c2968b7119d80539027feb9deefe991a16 100644
--- a/doc/src/bond_write.txt
+++ b/doc/src/bond_write.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/bond_zero.txt b/doc/src/bond_zero.txt
index b599f291b4cc5fef8b4a77beb893c3b99026d893..554f26e7f00d5eeee62343792b1b3b351ec9f92f 100644
--- a/doc/src/bond_zero.txt
+++ b/doc/src/bond_zero.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/boundary.txt b/doc/src/boundary.txt
index ce638f11b3ffbe871d398762df4397114f147d76..f9685433b2c4ca35d6f5ebbdaf29b4071514a67f 100644
--- a/doc/src/boundary.txt
+++ b/doc/src/boundary.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -82,9 +82,9 @@ and xhi faces of the box are planes tilting in the +y direction as y
increases. These tilted planes are shrink-wrapped around the atoms to
determine the x extent of the box.
-See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
-for a geometric description of triclinic boxes, as defined by LAMMPS,
-and how to transform these parameters to and from other commonly used
+See the "Howto triclinic"_Howto_triclinic.html doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
triclinic representations.
[Restrictions:]
diff --git a/doc/src/box.txt b/doc/src/box.txt
index a6207ae9937e569277a9d5a9b001493297f991dc..38c874fb78bc68b93ddaf666c6f97c0c147794e4 100644
--- a/doc/src/box.txt
+++ b/doc/src/box.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,9 +30,9 @@ For triclinic (non-orthogonal) simulation boxes, the {tilt} keyword
allows simulation domains to be created with arbitrary tilt factors,
e.g. via the "create_box"_create_box.html or
"read_data"_read_data.html commands. Tilt factors determine how
-skewed the triclinic box is; see "this
-section"_Section_howto.html#howto_12 of the manual for a discussion of
-triclinic boxes in LAMMPS.
+skewed the triclinic box is; see the "Howto
+triclinic"_Howto_triclinic.html doc page for a discussion of triclinic
+boxes in LAMMPS.
LAMMPS normally requires that no tilt factor can skew the box more
than half the distance of the parallel box length, which is the 1st
diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt
index 2c7a890d4cfb406abf018fb4787917f797fcc963..adc5d6bdcb42ee3c8b814ad21480e2ef9496e8d5 100644
--- a/doc/src/change_box.txt
+++ b/doc/src/change_box.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -75,9 +75,9 @@ The "create_box"_create_box.html, "read data"_read_data.html, and
simulation box is orthogonal or triclinic and their doc pages explain
the meaning of the xy,xz,yz tilt factors.
-See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
-for a geometric description of triclinic boxes, as defined by LAMMPS,
-and how to transform these parameters to and from other commonly used
+See the "Howto triclinic"_Howto_triclinic.html doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
triclinic representations.
The keywords used in this command are applied sequentially to the
@@ -140,8 +140,8 @@ transformation in the sequence. If skew is exceeded before the final
transformation this can be avoided by changing the order of the
sequence, or breaking the transformation into two or more smaller
transformations. For more information on the allowed limits for box
-skew see the discussion on triclinic boxes on "this
-page"_Section_howto.html#howto_12.
+skew see the discussion on triclinic boxes on "Howto
+triclinic"_Howto_triclinic.html doc page.
:line
@@ -258,9 +258,7 @@ command.
:line
The {ortho} and {triclinic} keywords convert the simulation box to be
-orthogonal or triclinic (non-orthogonal). See "this
-section"_Section_howto#howto_13 for a discussion of how non-orthogonal
-boxes are represented in LAMMPS.
+orthogonal or triclinic (non-orthogonal).
The simulation box is defined as either orthogonal or triclinic when
it is created via the "create_box"_create_box.html,
@@ -271,8 +269,8 @@ These keywords allow you to toggle the existing simulation box from
orthogonal to triclinic and vice versa. For example, an initial
equilibration simulation can be run in an orthogonal box, the box can
be toggled to triclinic, and then a "non-equilibrium MD (NEMD)
-simulation"_Section_howto.html#howto_13 can be run with deformation
-via the "fix deform"_fix_deform.html command.
+simulation"_Howto_nemd.html can be run with deformation via the "fix
+deform"_fix_deform.html command.
If the simulation box is currently triclinic and has non-zero tilt in
xy, yz, or xz, then it cannot be converted to an orthogonal box.
diff --git a/doc/src/clear.txt b/doc/src/clear.txt
index 7ac4da5c8d93228e974c48d20b746a3abef2153c..c4ad4c4030ca601cc2c1fa9fde44ce71c21946d2 100644
--- a/doc/src/clear.txt
+++ b/doc/src/clear.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt
index 3e8d0eca4ffe2d8c55e0998dd26384619fc712d6..489278523bde3a605053c565405732c55c905825 100644
--- a/doc/src/comm_modify.txt
+++ b/doc/src/comm_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/comm_style.txt b/doc/src/comm_style.txt
index 8248d654d32265924b3e25734fb19d40d2c3b0f5..39eb1d4ef5aece3e2d77f2b6bbd8d16940700ccc 100644
--- a/doc/src/comm_style.txt
+++ b/doc/src/comm_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute.txt b/doc/src/compute.txt
index 532a5414e38a4f2d3fe7b70790d048703d8987b5..7d9e443e7da7455de147ca1531daab58887e65f8 100644
--- a/doc/src/compute.txt
+++ b/doc/src/compute.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -33,7 +33,7 @@ information about a previous state of the system. Defining a compute
does not perform a computation. Instead computes are invoked by other
LAMMPS commands as needed, e.g. to calculate a temperature needed for
a thermostat fix or to generate thermodynamic or dump file output.
-See this "howto section"_Section_howto.html#howto_15 for a summary of
+See the "Howto output"_Howto_output.html doc page for a summary of
various LAMMPS output options, many of which involve computes.
The ID of a compute can only contain alphanumeric characters and
@@ -161,13 +161,19 @@ calculations accessed in the various ways described above.
Each compute style has its own doc page which describes its arguments
and what it does. Here is an alphabetic list of compute styles
-available in LAMMPS. They are also given in more compact form in the
-Compute section of "this page"_Section_commands.html#cmd_5.
+available in LAMMPS. They are also listed in more compact form on the
+"Commands compute"_Commands_compute.html doc page.
There are also additional compute styles (not listed here) submitted
-by users which are included in the LAMMPS distribution. The list of
-these with links to the individual styles are given in the compute
-section of "this page"_Section_commands.html#cmd_5.
+by users which are included in the LAMMPS distribution. The full list
+of all compute styles is on the "Commands
+compute"_Commands_compute.html doc page.
+
+There are also additional accelerated compute styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the "Commands
+compute"_Commands_compute.html doc page are followed by one or more of
+(g,i,k,o,t) to indicate which accerlerated styles exist.
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
"angle/local"_compute_bond_local.html - theta and energy of each angle
@@ -243,16 +249,6 @@ section of "this page"_Section_commands.html#cmd_5.
"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul
-There are also additional compute styles submitted by users which are
-included in the LAMMPS distribution. The list of these with links to
-the individual styles are given in the compute section of "this
-page"_Section_commands.html#cmd_5.
-
-There are also additional accelerated compute styles included in the
-LAMMPS distribution for faster performance on CPUs and GPUs. The list
-of these with links to the individual styles are given in the pair
-section of "this page"_Section_commands.html#cmd_5.
-
[Restrictions:] none
[Related commands:]
diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt
index 3fd838d95775ae9e97f7ad8da792112b9890d80d..485c191313209e46eb2ac979d004f23314678190 100644
--- a/doc/src/compute_ackland_atom.txt
+++ b/doc/src/compute_ackland_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -60,7 +60,7 @@ which computes this quantity.-
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
[Restrictions:]
diff --git a/doc/src/compute_angle.txt b/doc/src/compute_angle.txt
index 2c363ce8f63fcb4f181814399b47b1cf5f558435..64eb2f4bb1262828736bb342d3f9fe145f6c4f7b 100644
--- a/doc/src/compute_angle.txt
+++ b/doc/src/compute_angle.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the
number of sub_styles defined by the "angle_style
hybrid"_angle_style.html command, which can be accessed by indices
1-N. These values can be used by any command that uses global scalar
-or vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+or vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector values are "extensive" and will be in energy
diff --git a/doc/src/compute_angle_local.txt b/doc/src/compute_angle_local.txt
index 0ee1d32d7dcf8e3611fb98a5b8f70774d8cb3334..3a321965ef71135104bdf12f8dc13111dd515564 100644
--- a/doc/src/compute_angle_local.txt
+++ b/doc/src/compute_angle_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -70,8 +70,8 @@ array is the number of angles. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {theta} will be in degrees. The output for {eng} will
diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt
index 813da15eeadeed76c43a5f933f52e272d9653cbc..7e49ff302480a753cc5aacefe28b609931d56b06 100644
--- a/doc/src/compute_angmom_chunk.txt
+++ b/doc/src/compute_angmom_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the 3 components of the angular momentum
vector for each chunk, due to the velocity/momentum of the individual
@@ -73,8 +72,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the 3 xyz components of the angular momentum for each chunk.
These values can be accessed by any command that uses global array
-values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt
index b59a3fd4c878789dfd13c3e60a40ef0fb682ec96..067a020c35ebec8da9acda96b21abb8c68724a30 100644
--- a/doc/src/compute_basal_atom.txt
+++ b/doc/src/compute_basal_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -46,9 +46,8 @@ in examples/USER/misc/basal.
This compute calculates a per-atom array with 3 columns, which can be
accessed by indices 1-3 by any command that uses per-atom values from
-a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
The per-atom vector values are unitless since the 3 columns represent
components of a unit vector.
diff --git a/doc/src/compute_body_local.txt b/doc/src/compute_body_local.txt
index 12ce21885356da3541d1d3f2c9a0fcf23f35f198..8ac3f00c559345d1de1547542296a9f7b0469c00 100644
--- a/doc/src/compute_body_local.txt
+++ b/doc/src/compute_body_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,9 +32,8 @@ Define a computation that calculates properties of individual body
sub-particles. The number of datums generated, aggregated across all
processors, equals the number of body sub-particles plus the number of
non-body particles in the system, modified by the group parameter as
-explained below. See "Section 6.14"_Section_howto.html#howto_14
-of the manual and the "body"_body.html doc page for more details on
-using body particles.
+explained below. See the "Howto body"_Howto_body.html doc page for
+more details on using body particles.
The local data stored by this command is generated by looping over all
the atoms. An atom will only be included if it is in the group. If
@@ -58,8 +57,8 @@ group.
For a body particle, the {integer} keywords refer to fields calculated
by the body style for each sub-particle. The body style, as specified
by the "atom_style body"_atom_style.html, determines how many fields
-exist and what they are. See the "body"_body.html doc page for
-details of the different styles.
+exist and what they are. See the "Howto_body"_Howto_body.html doc
+page for details of the different styles.
Here is an example of how to output body information using the "dump
local"_dump.html command with this compute. If fields 1,2,3 for the
@@ -78,9 +77,9 @@ array is the number of datums as described above. If a single keyword
is specified, a local vector is produced. If two or more keywords are
specified, a local array is produced where the number of columns = the
number of keywords. The vector or array can be accessed by any
-command that uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+command that uses local values from a compute as input. See the
+"Howto output"_Howto_output.html doc page for an overview of LAMMPS
+output options.
The "units"_units.html for output values depend on the body style.
diff --git a/doc/src/compute_bond.txt b/doc/src/compute_bond.txt
index 6c4384b0806c7436f9384fe9d043c3fd9cb33c51..a87c510538f6035bf90b75d61cbd886a78c19208 100644
--- a/doc/src/compute_bond.txt
+++ b/doc/src/compute_bond.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the
number of sub_styles defined by the "bond_style
hybrid"_bond_style.html command, which can be accessed by indices 1-N.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector values are "extensive" and will be in energy
diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt
index 58d96f9ee4951f4517809a2e49f2fd6171941a16..c3dc1cc4afe92ae09118e8f56c0e678a380cee71 100644
--- a/doc/src/compute_bond_local.txt
+++ b/doc/src/compute_bond_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,8 +116,8 @@ array is the number of bonds. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {dist} will be in distance "units"_units.html. The
diff --git a/doc/src/compute_centro_atom.txt b/doc/src/compute_centro_atom.txt
index 4e4b03d16762c97eb44fb010f131d63ab0d1fd4f..183537690f43f61a5c5099ac3c76c3dd37b8223c 100644
--- a/doc/src/compute_centro_atom.txt
+++ b/doc/src/compute_centro_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -97,8 +97,8 @@ too frequently or to have multiple compute/dump commands, each with a
By default, this compute calculates the centrosymmetry value for each
atom as a per-atom vector, which can be accessed by any command that
-uses per-atom values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses per-atom values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
If the {axes} keyword setting is {yes}, then a per-atom array is
diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt
index 00a75f50c439ad4f0896d9e654f332057eacdb02..95e6e6c0104a939af015cecc41a2c2ee3ea5c33c 100644
--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -101,14 +101,13 @@ msd/chunk"_compute_msd_chunk.html. Or they can be used by the "fix
ave/chunk"_fix_ave_chunk.html command to sum and time average a
variety of per-atom properties over the atoms in each chunk. Or they
can simply be accessed by any command that uses per-atom values from a
-compute as input, as discussed in "Section
-6.15"_Section_howto.html#howto_15.
+compute as input, as discussed on the "Howto output"_Howto_output.html
+doc page.
-See "Section 6.23"_Section_howto.html#howto_23 for an overview of
-how this compute can be used with a variety of other commands to
-tabulate properties of a simulation. The howto section gives several
-examples of input script commands that can be used to calculate
-interesting properties.
+See the "Howto chunk"_Howto_chunk.html doc page for an overview of how
+this compute can be used with a variety of other commands to tabulate
+properties of a simulation. The page gives several examples of input
+script commands that can be used to calculate interesting properties.
Conceptually it is important to realize that this compute does two
simple things. First, it sets the value of {Nchunk} = the number of
@@ -167,11 +166,11 @@ or the bounds specified by the optional {bounds} keyword.
For orthogonal simulation boxes, the bins are layers, pencils, or
boxes aligned with the xyz coordinate axes. For triclinic
(non-orthogonal) simulation boxes, the bin faces are parallel to the
-tilted faces of the simulation box. See "this
-section"_Section_howto.html#howto_12 of the manual for a discussion of
-the geometry of triclinic boxes in LAMMPS. As described there, a
-tilted simulation box has edge vectors a,b,c. In that nomenclature,
-bins in the x dimension have faces with normals in the "b" cross "c"
+tilted faces of the simulation box. See the "Howto
+triclinic"_Howto_triclinic.html doc page for a discussion of the
+geometry of triclinic boxes in LAMMPS. As described there, a tilted
+simulation box has edge vectors a,b,c. In that nomenclature, bins in
+the x dimension have faces with normals in the "b" cross "c"
direction. Bins in y have faces normal to the "a" cross "c"
direction. And bins in z have faces normal to the "a" cross "b"
direction. Note that in order to define the size and position of
@@ -626,7 +625,7 @@ cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values are unitless chunk IDs, ranging from 1 to
diff --git a/doc/src/compute_cluster_atom.txt b/doc/src/compute_cluster_atom.txt
index 94113de5f2422a2628acc9f5bcb22a4940eefe21..e6138fe1e8eb80256cdc317120bcedb8fb7326cb 100644
--- a/doc/src/compute_cluster_atom.txt
+++ b/doc/src/compute_cluster_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -84,7 +84,7 @@ the neighbor list.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be an ID > 0, as explained above.
diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt
index 23289b01325b4afac23c938788a8ef1e775ecc59..d69c5e9c467e626017381f6e96268c9ed8aa4b8f 100644
--- a/doc/src/compute_cna_atom.txt
+++ b/doc/src/compute_cna_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -74,7 +74,7 @@ too frequently or to have multiple compute/dump commands, each with a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be a number from 0 to 5, as explained
diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt
index 16a51f5241f16ee058553a6e4634ec578219712c..44a77d23ca0fedade05df5f523302bcdaaa6215a 100644
--- a/doc/src/compute_cnp_atom.txt
+++ b/doc/src/compute_cnp_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -78,7 +78,7 @@ too frequently or to have multiple compute/dump commands, each with a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be real positive numbers. Some typical CNP
diff --git a/doc/src/compute_com.txt b/doc/src/compute_com.txt
index b0e0c14e424ae0de3d043c2686bbc19be9e938f0..fdc631a263cb155e437a5f54aa368ffb40ee2d76 100644
--- a/doc/src/compute_com.txt
+++ b/doc/src/compute_com.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,9 +41,8 @@ image"_set.html command.
This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The vector values are "intensive". The vector values will be in
distance "units"_units.html.
diff --git a/doc/src/compute_com_chunk.txt b/doc/src/compute_com_chunk.txt
index d497585cb036455b2cf199b6bc1098e34077b16e..b982f0d9017f4a501d56a9d1696cf6d4a5e51486 100644
--- a/doc/src/compute_com_chunk.txt
+++ b/doc/src/compute_com_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the x,y,z coordinates of the center-of-mass
for each chunk, which includes all effects due to atoms passing thru
@@ -71,9 +70,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the x,y,z center-of-mass coordinates of each chunk. These
values can be accessed by any command that uses global array values
-from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The array values are "intensive". The array values will be in
distance "units"_units.html.
diff --git a/doc/src/compute_contact_atom.txt b/doc/src/compute_contact_atom.txt
index f0bd62f4e87b9b5b1bfc85693ba0a028f95435ff..efe524263aa8c399e8771dd7348b52c9ae5cd42c 100644
--- a/doc/src/compute_contact_atom.txt
+++ b/doc/src/compute_contact_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -36,7 +36,7 @@ specified compute group.
This compute calculates a per-atom vector, whose values can be
accessed by any command that uses per-atom values from a compute as
-input. See "Section 6.15"_Section_howto.html#howto_15 for an
+input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The per-atom vector values will be a number >= 0.0, as explained
diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt
index a88f7ec729298c45b534ff8799d6c58896fbb793..66eecd195da4fb19851d5d84349c72391e51add6 100644
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -109,9 +109,8 @@ array, with N columns.
For {cstyle} orientorder, this compute calculates a per-atom vector.
These values can be accessed by any command that uses per-atom values
-from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The per-atom vector or array values will be a number >= 0.0, as
explained above.
diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt
index 918fbf65eff0c4172e92a8d551ce74e1a9f59cd1..74939e22806077fe5fb274cd17a7630954db9017 100644
--- a/doc/src/compute_damage_atom.txt
+++ b/doc/src/compute_damage_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -44,7 +44,7 @@ group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values are unitless numbers (damage) >= 0.0.
diff --git a/doc/src/compute_dihedral.txt b/doc/src/compute_dihedral.txt
index a3c3dff8d68f0bb2c36d6461ceb42d6f85fd238d..aa25f9dd1029af8d7f23ffb938bd7fd6a70e08c8 100644
--- a/doc/src/compute_dihedral.txt
+++ b/doc/src/compute_dihedral.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the
number of sub_styles defined by the "dihedral_style
hybrid"_dihedral_style.html command. which can be accessed by indices
1-N. These values can be used by any command that uses global scalar
-or vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+or vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector values are "extensive" and will be in energy
diff --git a/doc/src/compute_dihedral_local.txt b/doc/src/compute_dihedral_local.txt
index 865e86fddb1483ccf7a3b1c3d79fec912b90ea04..77812699d35fc826c95a344ddc7bf0207caf2ec4 100644
--- a/doc/src/compute_dihedral_local.txt
+++ b/doc/src/compute_dihedral_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -62,8 +62,8 @@ array is the number of dihedrals. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {phi} will be in degrees.
diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt
index ce00f7f12a5b9daae8a2b9ce9ae07a03188c41b4..498110cf99338e56fb24a2b9a362438f03f5f9f3 100644
--- a/doc/src/compute_dilatation_atom.txt
+++ b/doc/src/compute_dilatation_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -47,8 +47,9 @@ compute group.
[Output info:]
This compute calculates a per-atom vector, which can be accessed by
-any command that uses per-atom values from a compute as input. See
-Section_howto 15 for an overview of LAMMPS output options.
+any command that uses per-atom values from a compute as input. See
+the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-atom vector values are unitless numbers (theta) >= 0.0.
diff --git a/doc/src/compute_dipole_chunk.txt b/doc/src/compute_dipole_chunk.txt
index 75131ffbb113ad75802e88afb59c36f07f160ab5..d45fde9af2dbdd86aedc30abaa55c4b62e82b648 100644
--- a/doc/src/compute_dipole_chunk.txt
+++ b/doc/src/compute_dipole_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,10 +32,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the x,y,z coordinates of the dipole vector
and the total dipole moment for each chunk, which includes all effects
@@ -76,8 +75,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
4 for the x,y,z dipole vector components and the total dipole of each
chunk. These values can be accessed by any command that uses global
-array values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+array values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt
index 00e5f696c118029431bf5a36395bcd906fe432ee..669ab9f7ca3ea74e4a3a8a0b5537c0b09cbd814d 100644
--- a/doc/src/compute_displace_atom.txt
+++ b/doc/src/compute_displace_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -118,9 +118,8 @@ would be empty.
This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 by any command that uses per-atom values from
-a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
The per-atom array values will be in distance "units"_units.html.
diff --git a/doc/src/compute_dpd.txt b/doc/src/compute_dpd.txt
index 0e43feb9d23195bced66f17990bd42022b86c1ee..1721456e35ab0da5a82d3965f676f35a3d4baa3b 100644
--- a/doc/src/compute_dpd.txt
+++ b/doc/src/compute_dpd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,9 +40,9 @@ where N is the number of particles in the system
[Output info:]
This compute calculates a global vector of length 5 (U_cond, U_mech,
-U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. See
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
-output options.
+U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The vector values will be in energy and temperature "units"_units.html.
diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt
index 0532fc60c64193f977ce7d74e84768709d6502cf..8e502d4a6060f297da9132013adf5e19d40b565a 100644
--- a/doc/src/compute_dpd_atom.txt
+++ b/doc/src/compute_dpd_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,9 +34,9 @@ particles.
[Output info:]
This compute calculates a per-particle array with 4 columns (u_cond,
-u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command
-that uses per-particle values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any
+command that uses per-particle values from a compute as input. See
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-particle array values will be in energy (u_cond, u_mech, u_chem)
diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt
index 5b8c8ebd67c371c20deb465941d4007008c60b35..f33398e03d68995dc18da4d73fd9537f5e75656d 100644
--- a/doc/src/compute_edpd_temp_atom.txt
+++ b/doc/src/compute_edpd_temp_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,9 +32,9 @@ For more details please see "(Espanol1997)"_#Espanol1997 and
[Output info:]
This compute calculates a per-atom vector, which can be accessed by
-any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
-LAMMPS output options.
+any command that uses per-atom values from a compute as input. See the
+"Howto output"_Howto_output.html doc page for an overview of LAMMPS
+output options.
The per-atom vector values will be in temperature "units"_units.html.
diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt
index f7e7b8a66764427cd117c4305920d457efbd7e2b..9c45fd287099ea6150621a177f55837bbc5855fb 100644
--- a/doc/src/compute_entropy_atom.txt
+++ b/doc/src/compute_entropy_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -98,8 +98,8 @@ compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 :pre
By default, this compute calculates the pair entropy value for each
atom as a per-atom vector, which can be accessed by any command that
-uses per-atom values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses per-atom values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The pair entropy values have units of the Boltzmann constant. They are
diff --git a/doc/src/compute_erotate_asphere.txt b/doc/src/compute_erotate_asphere.txt
index b9a486c32eab61c8399328e028d7eb6d59cdaa1c..5cdc0997826f3dfbfff0281e85efe3ebb4864bb0 100644
--- a/doc/src/compute_erotate_asphere.txt
+++ b/doc/src/compute_erotate_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,7 +40,7 @@ will be the same as in 3d.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
-input. See "Section 6.15"_Section_howto.html#howto_15 for an
+input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
diff --git a/doc/src/compute_erotate_rigid.txt b/doc/src/compute_erotate_rigid.txt
index dec0939a43375ebb3f082634f0d11e64b508b46c..5b9077870e1d25440827b5a6006b5c6e3233d830 100644
--- a/doc/src/compute_erotate_rigid.txt
+++ b/doc/src/compute_erotate_rigid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,9 +41,9 @@ calculation.
This compute calculates a global scalar (the summed rotational energy
of all the rigid bodies). This value can be used by any command that
-uses a global scalar value from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
-LAMMPS output options.
+uses a global scalar value from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
+options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.
diff --git a/doc/src/compute_erotate_sphere.txt b/doc/src/compute_erotate_sphere.txt
index 41e80b0154dad4d1a073b9fdb4674365e0fe1033..d0c176b50eb264ff3431b6bbcdd71ad578092b1a 100644
--- a/doc/src/compute_erotate_sphere.txt
+++ b/doc/src/compute_erotate_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,7 +35,7 @@ as in 3d.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
-input. See "Section 6.15"_Section_howto.html#howto_15 for an
+input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
diff --git a/doc/src/compute_erotate_sphere_atom.txt b/doc/src/compute_erotate_sphere_atom.txt
index a0081ff6a8cb8bc26106809817a108091026741e..fdd609a0e65ffd71a599a16310b9c1bacdd809b1 100644
--- a/doc/src/compute_erotate_sphere_atom.txt
+++ b/doc/src/compute_erotate_sphere_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -39,7 +39,7 @@ in the specified compute group or for point particles with a radius =
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.
diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt
index 5e3a0c8599d533af3313cbe711c5d64ab77c680d..561ded35c052ef3e99e53ea8cb0533e00d3f99e3 100644
--- a/doc/src/compute_event_displace.txt
+++ b/doc/src/compute_event_displace.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,7 +43,7 @@ local atom displacements and may generate "false positives."
This compute calculates a global scalar (the flag). This value can be
used by any command that uses a global scalar value from a compute as
-input. See "Section 6.15"_Section_howto.html#howto_15 for an
+input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt
index 9bbae7b20f1c835c67d7808867d4a398a79b4541..8b4a92e16ea3a0486ca2c7113bf0b1ac87a47399 100644
--- a/doc/src/compute_fep.txt
+++ b/doc/src/compute_fep.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -219,8 +219,8 @@ unperturbed parameters. The energies include kspace terms if these
are used in the simulation.
These output results can be used by any command that uses a global
-scalar or vector from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+scalar or vector from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options. For example, the computed values can be averaged using "fix
ave/time"_fix_ave_time.html.
diff --git a/doc/src/compute_global_atom.txt b/doc/src/compute_global_atom.txt
index 28b4aa2461b9be2841c5a8cb1253228ab922a5b3..a26dba72b008de7202aa880c2b6999be67dc56a8 100644
--- a/doc/src/compute_global_atom.txt
+++ b/doc/src/compute_global_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -67,7 +67,7 @@ this command. This command will then assign the global chunk value to
each atom in the chunk, producing a per-atom vector or per-atom array
as output. The per-atom values can then be output to a dump file or
used by any command that uses per-atom values from a compute as input,
-as discussed in "Section 6.15"_Section_howto.html#howto_15.
+as discussed on the "Howto output"_Howto_output.html doc page.
As a concrete example, these commands will calculate the displacement
of each atom from the center-of-mass of the molecule it is in, and
@@ -203,7 +203,7 @@ vector. If multiple inputs are specified, this compute produces a
per-atom array values, where the number of columns is equal to the
number of inputs specified. These values can be used by any command
that uses per-atom vector or array values from a compute as input.
-See "Section 6.15"_Section_howto.html#howto_15 for an overview of
+See the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector or array values will be in whatever units the
diff --git a/doc/src/compute_group_group.txt b/doc/src/compute_group_group.txt
index f10547339d476eb44866be4dd596fd67b4657520..cff3687354589ab402cbe03114425ec9baf04985 100644
--- a/doc/src/compute_group_group.txt
+++ b/doc/src/compute_group_group.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -123,8 +123,8 @@ group-group calculations are performed.
This compute calculates a global scalar (the energy) and a global
vector of length 3 (force), which can be accessed by indices 1-3.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
Both the scalar and vector values calculated by this compute are
diff --git a/doc/src/compute_gyration.txt b/doc/src/compute_gyration.txt
index dd71431527f6f985b4d0e64acb85d46881134390..4dc883ad0bd2f2737b4e547b05621da6f39a01d2 100644
--- a/doc/src/compute_gyration.txt
+++ b/doc/src/compute_gyration.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -55,8 +55,8 @@ using the "set image"_set.html command.
This compute calculates a global scalar (Rg) and a global vector of
length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These
values can be used by any command that uses a global scalar value or
-vector values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar and vector values calculated by this compute are
diff --git a/doc/src/compute_gyration_chunk.txt b/doc/src/compute_gyration_chunk.txt
index 3e338213cf579f317e773374183b115bd327d697..dcbfc653938f13b147d5cd58ec85fb3ca392f163 100644
--- a/doc/src/compute_gyration_chunk.txt
+++ b/doc/src/compute_gyration_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,10 +35,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the radius of gyration Rg for each chunk,
which includes all effects due to atoms passing thru periodic
@@ -93,8 +92,8 @@ calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. If the {tensor} keyword
is specified, the global array has 6 columns. The vector or array can
be accessed by any command that uses global values from a compute as
-input. See "this section"_Section_howto.html#howto_15 for an overview
-of LAMMPS output options.
+input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options.
All the vector or array values calculated by this compute are
"intensive". The vector or array values will be in distance
diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt
index 39a1470201fc3f6705ee222e9719261aeae5dd4f..81a2a3f51711dc56e4b763de70421fecab1e4a4c 100644
--- a/doc/src/compute_heat_flux.txt
+++ b/doc/src/compute_heat_flux.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,9 +32,9 @@ or to calculate a thermal conductivity using the equilibrium
Green-Kubo formalism.
For other non-equilibrium ways to compute a thermal conductivity, see
-"this section"_Section_howto.html#howto_20. These include use of the
-"fix thermal/conductivity"_fix_thermal_conductivity.html command for
-the Muller-Plathe method. Or the "fix heat"_fix_heat.html command
+the "Howto kappa"_Howto_kappa.html doc page.. These include use of
+the "fix thermal/conductivity"_fix_thermal_conductivity.html command
+for the Muller-Plathe method. Or the "fix heat"_fix_heat.html command
which can add or subtract heat from groups of atoms.
The compute takes three arguments which are IDs of other
@@ -99,8 +99,8 @@ result should be: average conductivity ~0.29 in W/mK.
This compute calculates a global vector of length 6 (total heat flux
vector, followed by convective heat flux vector), which can be
accessed by indices 1-6. These values can be used by any command that
-uses global vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses global vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector values calculated by this compute are "extensive", meaning
diff --git a/doc/src/compute_hexorder_atom.txt b/doc/src/compute_hexorder_atom.txt
index cdf47e0894aeffffb7d4a83da178ee328a8d1eb2..082a3cad7a0e62195fa333fd15f5071c2810000c 100644
--- a/doc/src/compute_hexorder_atom.txt
+++ b/doc/src/compute_hexorder_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -95,10 +95,9 @@ This compute calculates a per-atom array with 2 columns, giving the
real and imaginary parts {qn}, a complex number restricted to the
unit disk of the complex plane i.e. Re({qn})^2 + Im({qn})^2 <= 1 .
-These values can be accessed by any command that uses
-per-atom values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+These values can be accessed by any command that uses per-atom values
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
[Restrictions:] none
diff --git a/doc/src/compute_improper.txt b/doc/src/compute_improper.txt
index f0d2fa400e634ad40eccda5999f0bded55467eaf..867dd48cc16edc61f5b1cc8d64d4b80234120209 100644
--- a/doc/src/compute_improper.txt
+++ b/doc/src/compute_improper.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the
number of sub_styles defined by the "improper_style
hybrid"_improper_style.html command. which can be accessed by indices
1-N. These values can be used by any command that uses global scalar
-or vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+or vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector values are "extensive" and will be in energy
diff --git a/doc/src/compute_improper_local.txt b/doc/src/compute_improper_local.txt
index 0c289fbf0774fde0651d77d6a27b209621b5388e..f340d5a03fc472889b22f854480c0563eee0e6dc 100644
--- a/doc/src/compute_improper_local.txt
+++ b/doc/src/compute_improper_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,8 +63,8 @@ array is the number of impropers. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {chi} will be in degrees.
diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt
index b0dbb12aea8d5e7e1e5d982f0d4d656b9d0c2ffb..d6cdb3fe79eb950ce3aa3675c9a7d13986d1e957 100644
--- a/doc/src/compute_inertia_chunk.txt
+++ b/doc/src/compute_inertia_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the 6 components of the symmetric inertia
tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The
@@ -72,8 +71,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
6 for the 6 components of the inertia tensor for each chunk, ordered
as listed above. These values can be accessed by any command that
-uses global array values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses global array values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_ke.txt b/doc/src/compute_ke.txt
index caee8971627231b080a680612017df790ef292df..64ab83db48b792aa0bc26dbd60ca0de7800166ae 100644
--- a/doc/src/compute_ke.txt
+++ b/doc/src/compute_ke.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -44,7 +44,7 @@ include different degrees of freedom (translational, rotational, etc).
This compute calculates a global scalar (the summed KE). This value
can be used by any command that uses a global scalar value from a
-compute as input. See "Section 6.15"_Section_howto.html#howto_15
+compute as input. See the "Howto output"_Howto_output.html doc page
for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
diff --git a/doc/src/compute_ke_atom.txt b/doc/src/compute_ke_atom.txt
index f5431f0569fe48e82ec9ebbb48f77d3f9e1d7f17..d288ab0236d44a40c32805a94e8d1b04a181edd1 100644
--- a/doc/src/compute_ke_atom.txt
+++ b/doc/src/compute_ke_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,7 +34,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.
diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/src/compute_ke_atom_eff.txt
index 8228e13f07c697e32cf678c3e381082d21a653ea..f665f35055f36be914f26aa5c032b2b76233ccf2 100644
--- a/doc/src/compute_ke_atom_eff.txt
+++ b/doc/src/compute_ke_atom_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -57,9 +57,9 @@ electrons) not in the specified compute group.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
-LAMMPS output options.
+accessed by any command that uses per-atom computes as input. See the
+"Howto output"_Howto_output.html doc page for an overview of LAMMPS
+output options.
The per-atom vector values will be in energy "units"_units.html.
diff --git a/doc/src/compute_ke_eff.txt b/doc/src/compute_ke_eff.txt
index ac8d7e6c01d48b723484e9ff7ab7959e7b97b9e0..d6d7fdb10f5f3667a8443047505e80a775c3b1b6 100644
--- a/doc/src/compute_ke_eff.txt
+++ b/doc/src/compute_ke_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -61,7 +61,7 @@ See "compute temp/eff"_compute_temp_eff.html.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
-input. See "Section 6.15"_Section_howto.html#howto_15 for an
+input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
diff --git a/doc/src/compute_ke_rigid.txt b/doc/src/compute_ke_rigid.txt
index f79696a77a1fe3692fad26fadbca9f47f765612e..45ba2673b0283a8106d55ee621103a7f8eb3a7fa 100644
--- a/doc/src/compute_ke_rigid.txt
+++ b/doc/src/compute_ke_rigid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,8 +40,8 @@ calculation.
This compute calculates a global scalar (the summed KE of all the
rigid bodies). This value can be used by any command that uses a
-global scalar value from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+global scalar value from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "extensive". The
diff --git a/doc/src/compute_meso_e_atom.txt b/doc/src/compute_meso_e_atom.txt
index 4e621b43018137817134f567efc0c550574e5737..9a9c7fae118d4b6a84636b94a9f83d582c6331c8 100644
--- a/doc/src/compute_meso_e_atom.txt
+++ b/doc/src/compute_meso_e_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,7 +38,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.
diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/src/compute_meso_rho_atom.txt
index a017424dd01f0314e5155ac59e5b3dc50c652630..30b1142b6cdfef0afb329f7d3be5a360d9487465 100644
--- a/doc/src/compute_meso_rho_atom.txt
+++ b/doc/src/compute_meso_rho_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,7 +38,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in mass/volume "units"_units.html.
diff --git a/doc/src/compute_meso_t_atom.txt b/doc/src/compute_meso_t_atom.txt
index 9e81b038f452c901aeb5dc3d0747e4df6cafd215..ab92f05018a15b6f45edf30d4844b82b2c237493 100644
--- a/doc/src/compute_meso_t_atom.txt
+++ b/doc/src/compute_meso_t_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,7 +40,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in temperature "units"_units.html.
diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt
index 9a2480ec0ac7fd7b584216a74355ed9b707c877e..192ea0bc9ec96d6c7691214f78f7cf2c080f4ddd 100644
--- a/doc/src/compute_modify.txt
+++ b/doc/src/compute_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute_msd.txt b/doc/src/compute_msd.txt
index f806c5e29266752bae1859a33bcf8eb1101eb99c..b54e05bc6498ffd450ce91ff9f5b4c959f9790fd 100644
--- a/doc/src/compute_msd.txt
+++ b/doc/src/compute_msd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -93,9 +93,8 @@ instead of many, which will change the values of msd somewhat.
This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 by any command that uses global vector values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The vector values are "intensive". The vector values will be in
distance^2 "units"_units.html.
diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt
index 7f31b61ed0bda808a94a5a45e3c4d165f4e3c1cf..264f38d5fde4a6f587ff97f22ed797b07f3b50bc 100644
--- a/doc/src/compute_msd_chunk.txt
+++ b/doc/src/compute_msd_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
Four quantities are calculated by this compute for each chunk. The
first 3 quantities are the squared dx,dy,dz displacements of the
@@ -106,7 +105,7 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
4 for dx,dy,dz and the total displacement. These values can be
accessed by any command that uses global array values from a compute
-as input. See "this section"_Section_howto.html#howto_15 for an
+as input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt
index 198da999e0a3c36af28e45f173dc9683aca3aa50..814159121d11781bf29850db7c8787ab5644b807 100644
--- a/doc/src/compute_msd_nongauss.txt
+++ b/doc/src/compute_msd_nongauss.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -57,9 +57,8 @@ NOTEs, which also apply to this compute.
This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The vector values are "intensive". The first vector value will be in
distance^2 "units"_units.html, the second is in distance^4 units, and
diff --git a/doc/src/compute_omega_chunk.txt b/doc/src/compute_omega_chunk.txt
index 46c72d3dcb3d15aed65805003bd419b30d098fb2..84b25ac6f26e014a2258715bf2e7d847642854df 100644
--- a/doc/src/compute_omega_chunk.txt
+++ b/doc/src/compute_omega_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the 3 components of the angular velocity
vector for each chunk, via the formula L = Iw where L is the angular
@@ -73,8 +72,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the 3 xyz components of the angular velocity for each chunk.
These values can be accessed by any command that uses global array
-values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt
index adf11dcfcfa9822f4c736f1cb7203ca0e02c446c..7327a7b1d333a5375d033d5d8f88b9e74efc6237 100644
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -115,10 +115,9 @@ Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}). This
way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1)
columns.
-These values can be accessed by any command that uses
-per-atom values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+These values can be accessed by any command that uses per-atom values
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
[Restrictions:] none
diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt
index 0602dab81bd5902838a01d52432a881db684f710..a2c25fcc8dc0dbe737e3efb76fd1ef57197dd765 100644
--- a/doc/src/compute_pair.txt
+++ b/doc/src/compute_pair.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -62,9 +62,8 @@ This compute calculates a global scalar which is {epair} or {evdwl} or
{ecoul}. If the pair style supports it, it also calculates a global
vector of length >= 1, as determined by the pair style. These values
can be used by any command that uses global scalar or vector values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The scalar and vector values calculated by this compute are
"extensive".
diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt
index 16aaba4667396dfc038c9f7625fdca532a8cd04b..7588e92527aa5d32157f4f94207226597a9966f4 100644
--- a/doc/src/compute_pair_local.txt
+++ b/doc/src/compute_pair_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -119,8 +119,8 @@ array is the number of pairs. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {dist} will be in distance "units"_units.html. The
diff --git a/doc/src/compute_pe.txt b/doc/src/compute_pe.txt
index 15f27a8eff5f92cb97b215e8313b98429db8fef9..37655dfd480c8bb48b2b722436f5b6b0d15f5e6d 100644
--- a/doc/src/compute_pe.txt
+++ b/doc/src/compute_pe.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -64,9 +64,8 @@ See the "thermo_style" command for more details.
This compute calculates a global scalar (the potential energy). This
value can be used by any command that uses a global scalar value from
-a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.
diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt
index c312c886a692f5a0ffcbb277e432acb34bcc88aa..400621f8df1d50b921c2ad870df98b8cdf578784 100644
--- a/doc/src/compute_pe_atom.txt
+++ b/doc/src/compute_pe_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -81,7 +81,7 @@ global system energy.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.
diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt
index 788213fc65985cb86bee7a08b3e78f50adf423cc..50a51d99377899c3ed62a81059351ab494968567 100644
--- a/doc/src/compute_plasticity_atom.txt
+++ b/doc/src/compute_plasticity_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,8 +41,9 @@ compute group.
[Output info:]
This compute calculates a per-atom vector, which can be accessed by
-any command that uses per-atom values from a compute as input. See
-Section_howto 15 for an overview of LAMMPS output options.
+any command that uses per-atom values from a compute as input. See
+the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-atom vector values are unitless numbers (lambda) >= 0.0.
diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt
index f0691ad20762758234828f976e7519ef47568d57..dea0a7f05b7f03d209077628f19a07172eb93e0f 100644
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -105,10 +105,9 @@ where "thermo_temp" is the ID of a similarly defined compute of style
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -120,8 +119,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -130,8 +129,8 @@ more instructions on how to use the accelerated styles effectively.
This compute calculates a global scalar (the pressure) and a global
vector of length 6 (pressure tensor), which can be accessed by indices
1-6. These values can be used by any command that uses global scalar
-or vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+or vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar and vector values calculated by this compute are
diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt
index 5b252b369dd012691e62a3dcf267c6e00cca11c3..61cc85ad8097b3b43ac740cf186b7456f02db707 100644
--- a/doc/src/compute_pressure_uef.txt
+++ b/doc/src/compute_pressure_uef.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt
index c0970d5121cca49705fa5eb5eb02407f490a04e5..512009093c0e052e8e7b43f44455d1f61d7e6fb8 100644
--- a/doc/src/compute_property_atom.txt
+++ b/doc/src/compute_property_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -93,11 +93,11 @@ compute 3 all property/atom sp spx spy spz :pre
Define a computation that simply stores atom attributes for each atom
in the group. This is useful so that the values can be used by other
-"output commands"_Section_howto.html#howto_15 that take computes as
-inputs. See for example, the "compute reduce"_compute_reduce.html,
-"fix ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html,
-"fix ave/chunk"_fix_ave_chunk.html, and "atom-style
-variable"_variable.html commands.
+"output commands"_Howto_output.html that take computes as inputs. See
+for example, the "compute reduce"_compute_reduce.html, "fix
+ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html, "fix
+ave/chunk"_fix_ave_chunk.html, and "atom-style variable"_variable.html
+commands.
The list of possible attributes is the same as that used by the "dump
custom"_dump.html command, which describes their meaning, with some
@@ -149,8 +149,8 @@ on the number of input values. If a single input is specified, a
per-atom vector is produced. If two or more inputs are specified, a
per-atom array is produced where the number of columns = the number of
inputs. The vector or array can be accessed by any command that uses
-per-atom values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+per-atom values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector or array values will be in whatever "units"_units.html the
diff --git a/doc/src/compute_property_chunk.txt b/doc/src/compute_property_chunk.txt
index b9d4944b30740cfcb28313811a6885296c65acf4..a30b5a1f0a5526421610cc06946328874c762115 100644
--- a/doc/src/compute_property_chunk.txt
+++ b/doc/src/compute_property_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -36,15 +36,14 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates and stores the specified attributes of chunks
as global data so they can be accessed by other "output
-commands"_Section_howto.html#howto_15 and used in conjunction with
-other commands that generate per-chunk data, such as "compute
+commands"_Howto_output.html and used in conjunction with other
+commands that generate per-chunk data, such as "compute
com/chunk"_compute_com_chunk.html or "compute
msd/chunk"_compute_msd_chunk.html.
@@ -103,8 +102,8 @@ single input is specified, a global vector is produced. If two or
more inputs are specified, a global array is produced where the number
of columns = the number of inputs. The vector or array can be
accessed by any command that uses global values from a compute as
-input. See "this section"_Section_howto.html#howto_15 for an overview
-of LAMMPS output options.
+input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options.
The vector or array values are "intensive". The values will be
unitless or in the units discussed above.
diff --git a/doc/src/compute_property_local.txt b/doc/src/compute_property_local.txt
index 39106a39c890cae655d635216bbe93876f43fc74..b0ec088cf79d009e7c3062907d73dbfe3279e6da 100644
--- a/doc/src/compute_property_local.txt
+++ b/doc/src/compute_property_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -48,10 +48,10 @@ compute 1 all property/local atype aatom2 :pre
Define a computation that stores the specified attributes as local
data so it can be accessed by other "output
-commands"_Section_howto.html#howto_15. If the input attributes refer
-to bond information, then the number of datums generated, aggregated
-across all processors, equals the number of bonds in the system.
-Ditto for pairs, angles, etc.
+commands"_Howto_output.html. If the input attributes refer to bond
+information, then the number of datums generated, aggregated across
+all processors, equals the number of bonds in the system. Ditto for
+pairs, angles, etc.
If multiple attributes are specified then they must all generate the
same amount of information, so that the resulting local array has the
@@ -140,8 +140,8 @@ the array is the number of bonds, angles, etc. If a single input is
specified, a local vector is produced. If two or more inputs are
specified, a local array is produced where the number of columns = the
number of inputs. The vector or array can be accessed by any command
-that uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+that uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector or array values will be integers that correspond to the
diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt
index e462e85fc038a10dfe9de0c701fecb103002a731..04b38682cc4957ac67459b18652249b1dfb75f14 100644
--- a/doc/src/compute_rdf.txt
+++ b/doc/src/compute_rdf.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -152,7 +152,7 @@ coordinate (center of the bin), Each successive set of 2 columns has
the g(r) and coord(r) values for a specific set of {itypeN} versus
{jtypeN} interactions, as described above. These values can be used
by any command that uses a global values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The array values calculated by this compute are all "intensive".
diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt
index 48115a08861e6e272ea71cb86fdb0276c00aedee..ef3c7c6489e03ef3c1056edefd8d4dc419766cdf 100644
--- a/doc/src/compute_reduce.txt
+++ b/doc/src/compute_reduce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -192,7 +192,7 @@ This compute calculates a global scalar if a single input value is
specified or a global vector of length N where N is the number of
inputs, and which can be accessed by indices 1 to N. These values can
be used by any command that uses global scalar or vector values from a
-compute as input. See "Section 6.15"_Section_howto.html#howto_15
+compute as input. See the "Howto output"_Howto_output.html doc page
for an overview of LAMMPS output options.
All the scalar or vector values calculated by this compute are
diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt
index 077ad57d81b6bb1acd7d328e4e3f819867e71510..b5e6954ab99943f090a3153829ca08a6daa8f0b7 100644
--- a/doc/src/compute_rigid_local.txt
+++ b/doc/src/compute_rigid_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -49,8 +49,8 @@ Define a computation that simply stores rigid body attributes for
rigid bodies defined by the "fix rigid/small"_fix_rigid.html command
or one of its NVE, NVT, NPT, NPH variants. The data is stored as
local data so it can be accessed by other "output
-commands"_Section_howto.html#howto_15 that process local data, such as
-the "compute reduce"_compute_reduce.html or "dump local"_dump.html
+commands"_Howto_output.html that process local data, such as the
+"compute reduce"_compute_reduce.html or "dump local"_dump.html
commands.
Note that this command only works with the "fix
@@ -154,9 +154,9 @@ array is the number of rigid bodies. If a single keyword is
specified, a local vector is produced. If two or more keywords are
specified, a local array is produced where the number of columns = the
number of keywords. The vector or array can be accessed by any
-command that uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+command that uses local values from a compute as input. See the
+"Howto output"_Howto_output.html doc page for an overview of LAMMPS
+output options.
The vector or array values will be in whatever "units"_units.html the
corresponding attribute is in:
diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt
index 020f72f565c1009426ae22e891932aa648f6f1bd..8c17a30fcaf1acb403a936d4a15938206e89ad4d 100644
--- a/doc/src/compute_saed.txt
+++ b/doc/src/compute_saed.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -143,10 +143,9 @@ the number of reciprocal lattice nodes that are explored by the mesh.
The entries of the global vector are the computed diffraction
intensities as described above.
-The vector can be accessed by any command that uses global values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+The vector can be accessed by any command that uses global values from
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
All array values calculated by this compute are "intensive".
diff --git a/doc/src/compute_slice.txt b/doc/src/compute_slice.txt
index 13f40ecf9220c3245f6956c2c4d5908d974bb29e..51031aeab3017a4bbfee683c0055165d74fd8c03 100644
--- a/doc/src/compute_slice.txt
+++ b/doc/src/compute_slice.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -94,8 +94,8 @@ specified or a global array with N columns where N is the number of
inputs. The length of the vector or the number of rows in the array
is equal to the number of values extracted from each input vector.
These values can be used by any command that uses global vector or
-array values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+array values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector or array values calculated by this compute are simply
diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/src/compute_smd_contact_radius.txt
index 69fe45334398fb60c77b4582074d0b2309c4f6ff..cd1381604788bfcd42f00653d2c5e9b46f98d25f 100644
--- a/doc/src/compute_smd_contact_radius.txt
+++ b/doc/src/compute_smd_contact_radius.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,9 +35,9 @@ specified compute group.
[Output info:]
-This compute calculates a per-particle vector, which can be accessed by
-any command that uses per-particle values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-particle vector values will be in distance "units"_units.html.
diff --git a/doc/src/compute_smd_damage.txt b/doc/src/compute_smd_damage.txt
index b6c75a3b204532003231bad5f7a61089e9544199..afabe23d7cc1407496463c926ba8adcb9ddc7ff0 100644
--- a/doc/src/compute_smd_damage.txt
+++ b/doc/src/compute_smd_damage.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -28,10 +28,10 @@ See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in
[Output Info:]
-This compute calculates a per-particle vector, which can be accessed by
-any command that uses per-particle values from a compute as input. See
-"How-to discussions, section 6.15"_Section_howto.html#howto_15
-for an overview of LAMMPS output options.
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values are dimensionless an in the range of zero to one.
diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/src/compute_smd_hourglass_error.txt
index a15b79e64e4490e51a9321d06206757589a5c06a..13fd20a5891cab8bdeeabb570d8343c063a705af 100644
--- a/doc/src/compute_smd_hourglass_error.txt
+++ b/doc/src/compute_smd_hourglass_error.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,10 +37,10 @@ Mach Dynamics in LAMMPS.
[Output Info:]
-This compute calculates a per-particle vector, which can be accessed by
-any command that uses per-particle values from a compute as input. See
-"How-to discussions, section 6.15"_Section_howto.html#howto_15
-for an overview of LAMMPS output options.
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle vector values will are dimensionless. See
"units"_units.html.
diff --git a/doc/src/compute_smd_internal_energy.txt b/doc/src/compute_smd_internal_energy.txt
index bc6f9e0f2068b440c731bbaa6a5710daa8d2c446..6585c3429f27a9c97d17c66a15dff959ebbbe5be 100644
--- a/doc/src/compute_smd_internal_energy.txt
+++ b/doc/src/compute_smd_internal_energy.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,8 +31,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle vector values will be given in "units"_units.html of energy.
diff --git a/doc/src/compute_smd_plastic_strain.txt b/doc/src/compute_smd_plastic_strain.txt
index af5b1644534adcd3c624109aadf0f69205db78c6..fb3c5c9138cb5ae444320a5ff9f4a73878780a67 100644
--- a/doc/src/compute_smd_plastic_strain.txt
+++ b/doc/src/compute_smd_plastic_strain.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values will be given dimensionless. See "units"_units.html.
diff --git a/doc/src/compute_smd_plastic_strain_rate.txt b/doc/src/compute_smd_plastic_strain_rate.txt
index ba7b3176dbf538f25802ec53eb0e4a12b2db3cff..b913ae90976009a7caf916352cbfe9475577d9db 100644
--- a/doc/src/compute_smd_plastic_strain_rate.txt
+++ b/doc/src/compute_smd_plastic_strain_rate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values will be given in "units"_units.html of one over time.
diff --git a/doc/src/compute_smd_rho.txt b/doc/src/compute_smd_rho.txt
index ae50526725e091a21b80a1a1b0c8c39680fbf031..a1ee1d9c5b95a2971e64a52ad4416e74e54fc226 100644
--- a/doc/src/compute_smd_rho.txt
+++ b/doc/src/compute_smd_rho.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -33,8 +33,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values will be in "units"_units.html of mass over volume.
diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/src/compute_smd_tlsph_defgrad.txt
index 68b5dffa1cf558df517156e61bc604604bbfa113..1663c84f65fd3b3c59daf427d4b15fe6a5d27ea9 100644
--- a/doc/src/compute_smd_tlsph_defgrad.txt
+++ b/doc/src/compute_smd_tlsph_defgrad.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,9 +32,8 @@ Mach Dynamics in LAMMPS.
This compute outputss a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
-from a compute as input. See "How-to discussions, section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The per-particle vector values will be given dimensionless. See
"units"_units.html. The per-particle vector has 10 entries. The first
diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt
index 560a9b6fd878386ff140cba30ecf879a62cdc047..c714f3266bceaf96ea1b86d487cf653cdeeeb47e 100644
--- a/doc/src/compute_smd_tlsph_dt.txt
+++ b/doc/src/compute_smd_tlsph_dt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,8 +37,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values will be given in "units"_units.html of time.
diff --git a/doc/src/compute_smd_tlsph_num_neighs.txt b/doc/src/compute_smd_tlsph_num_neighs.txt
index 0420d1903d82c6d4af44e519b309e0da27813293..af5b0741db6c0c964ab4a73b21bdb928b663fe42 100644
--- a/doc/src/compute_smd_tlsph_num_neighs.txt
+++ b/doc/src/compute_smd_tlsph_num_neighs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values are dimensionless. See "units"_units.html.
diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/src/compute_smd_tlsph_shape.txt
index 02bd0c50ddb504d7effd71d7155e5cc39c7a4378..927cd7c7aecaa51cc45c095066586899bd37aefb 100644
--- a/doc/src/compute_smd_tlsph_shape.txt
+++ b/doc/src/compute_smd_tlsph_shape.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -33,9 +33,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors, which can be
accessed by any command that uses per-particle values from a compute
-as input. See "How-to discussions, section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+as input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options.
The per-particle vector has 7 entries. The first three entries
correspond to the lengths of the ellipsoid's axes and have units of
diff --git a/doc/src/compute_smd_tlsph_strain.txt b/doc/src/compute_smd_tlsph_strain.txt
index f25d1b77db2c32cc25a2d7a3dd64466db1370c20..4536f26c8ea364d40d306f1ac863f3fc4a278dff 100644
--- a/doc/src/compute_smd_tlsph_strain.txt
+++ b/doc/src/compute_smd_tlsph_strain.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,9 +31,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
-from a compute as input. See "How-to discussions, section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The per-particle tensor values will be given dimensionless. See
"units"_units.html.
diff --git a/doc/src/compute_smd_tlsph_strain_rate.txt b/doc/src/compute_smd_tlsph_strain_rate.txt
index 13ca57ac4df413e8348a37d34d49fa606239243e..ae2883e4bbedb0e698cac841601984de90af2031 100644
--- a/doc/src/compute_smd_tlsph_strain_rate.txt
+++ b/doc/src/compute_smd_tlsph_strain_rate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,9 +31,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
-from a compute as input. See "How-to discussions, section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The values will be given in "units"_units.html of one over time.
diff --git a/doc/src/compute_smd_tlsph_stress.txt b/doc/src/compute_smd_tlsph_stress.txt
index 5d707d4c2f6934cd0b630de1767a43f33b9de46c..50d6b7f4344ffb585cc27a00d644e803904e5fad 100644
--- a/doc/src/compute_smd_tlsph_stress.txt
+++ b/doc/src/compute_smd_tlsph_stress.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -29,11 +29,10 @@ Mach Dynamics in LAMMPS.
[Output info:]
-This compute calculates a per-particle vector of vectors (tensors), which can be
-accessed by any command that uses per-particle values from a compute
-as input. See
-"How-to discussions, section 6.15"_Section_howto.html#howto_15
-for an overview of LAMMPS output options.
+This compute calculates a per-particle vector of vectors (tensors),
+which can be accessed by any command that uses per-particle values
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The values will be given in "units"_units.html of pressure.
diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_mesh_vertices.txt
index 5b0f0afc4c84a93f0b1f31307da9d7a89197abbe..9e167924d1401fea40a6ac9b0d9bcc7d257d4355 100644
--- a/doc/src/compute_smd_triangle_mesh_vertices.txt
+++ b/doc/src/compute_smd_triangle_mesh_vertices.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,9 +31,9 @@ Mach Dynamics in LAMMPS.
[Output info:]
This compute returns a per-particle vector of vectors, which can be
-accessed by any command that uses per-particle values from a compute as
-input. See "How-to discussions, section 6.15"_Section_howto.html#howto_15
-for an overview of LAMMPS output options.
+accessed by any command that uses per-particle values from a compute
+as input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options.
The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and
(x3/y3/z3) corresponding to the first, second, and third vertex of
diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt
index adece9334361d154d3f7d7a62de19b0eaac01a93..202b8f15e1d95ec3441e272a23b618a0f57f443a 100644
--- a/doc/src/compute_smd_ulsph_num_neighs.txt
+++ b/doc/src/compute_smd_ulsph_num_neighs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,7 +32,7 @@ Mach Dynamics in LAMMPS.
This compute returns a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input.
-See "Section 6.15"_Section_howto.html#howto_15 for an overview of
+See the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-particle values will be given dimensionless, see "units"_units.html.
diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/src/compute_smd_ulsph_strain.txt
index b7d425b12b7e1b0146ba321986e56470719b115f..76c47162a5c85e0def8c8231224ccda416ea6360 100644
--- a/doc/src/compute_smd_ulsph_strain.txt
+++ b/doc/src/compute_smd_ulsph_strain.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,7 +31,7 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle tensor, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "Section 6.15"_Section_howto.html#howto_15 for an overview of
+See the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-particle vector has 6 entries, corresponding to the xx, yy,
diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/src/compute_smd_ulsph_strain_rate.txt
index e2c349c2656de89aaa53534f3980e235caa17901..c851e767b34a418a614cfeb537638ec294ae489f 100644
--- a/doc/src/compute_smd_ulsph_strain_rate.txt
+++ b/doc/src/compute_smd_ulsph_strain_rate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,9 +32,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
-from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The values will be given in "units"_units.html of one over time.
diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/src/compute_smd_ulsph_stress.txt
index 47f903d3b88effc7055084674b0866fe5ad4b596..a5692b2412ce589165a29514c6b199b7d0dd802d 100644
--- a/doc/src/compute_smd_ulsph_stress.txt
+++ b/doc/src/compute_smd_ulsph_stress.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,9 +30,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
-from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The values will be given in "units"_units.html of pressure.
diff --git a/doc/src/compute_smd_vol.txt b/doc/src/compute_smd_vol.txt
index fc736a5bf5c2fd0e9c6d89b749acb11d6d79d1e1..fc4871d6f301157c45fcaf88e99301f20cdff31c 100644
--- a/doc/src/compute_smd_vol.txt
+++ b/doc/src/compute_smd_vol.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,8 +31,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle vector values will be given in "units"_units.html of
volume.
diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt
index 268e23ac2808d82f8750b95bd652cd4d50f6b9d2..3b302a0a71c65de87fee8ae571e866b3cc19653c 100644
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -244,9 +244,8 @@ So the nesting order from inside to outside is bispectrum component,
linear then quadratic, vector/tensor component, type.
These values can be accessed by any command that uses per-atom values
-from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
[Restrictions:]
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
index fcc764c14cb0f7cc88869655bf8d2df1f745c777..792706ecdfae311acd293546d899b51b2bf28d73 100644
--- a/doc/src/compute_spin.txt
+++ b/doc/src/compute_spin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt
index 83b1df68e3555e4d74b4c0296845fc6a395148e7..222513da61d45e22238a38780c39977ec3900b68 100644
--- a/doc/src/compute_stress_atom.txt
+++ b/doc/src/compute_stress_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -142,9 +142,8 @@ global system pressure.
This compute calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 by any command that uses per-atom values from
-a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
The per-atom array values will be in pressure*volume
"units"_units.html as discussed above.
diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt
index 95ef4a553b8df78af94dd0d51a7fc48c12d313fb..23fac4309384bac044259f51d128726725fcd3f7 100644
--- a/doc/src/compute_tally.txt
+++ b/doc/src/compute_tally.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt
index a6a12dc52ccb31febe7a8bc5559b50913e0f242a..9ee4d3da3462fbed0bc3be6b66212d6988fd938d 100644
--- a/doc/src/compute_tdpd_cc_atom.txt
+++ b/doc/src/compute_tdpd_cc_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -33,9 +33,9 @@ details see "(Li2015)"_#Li2015a.
[Output info:]
This compute calculates a per-atom vector, which can be accessed by
-any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
-LAMMPS output options.
+any command that uses per-atom values from a compute as input. See the
+"Howto output"_Howto_output.html doc page for an overview of LAMMPS
+output options.
The per-atom vector values will be in the units of chemical species
per unit mass.
diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt
index b88be79e20704a41482ad444668ca8b81d0c4b32..9f3a1ca9061feeaab02ac197f5ab15c1844a709a 100644
--- a/doc/src/compute_temp.txt
+++ b/doc/src/compute_temp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -58,8 +58,8 @@ compute thermo_temp all temp :pre
See the "thermo_style" command for more details.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
:line
@@ -67,10 +67,9 @@ thermostatting.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -82,8 +81,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -92,8 +91,8 @@ more instructions on how to use the accelerated styles effectively.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt
index 495366b34501b65e785bff5ec6e442ff02e89b96..6766729ae0c463ce51c6470de27d6966102a0cff 100644
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -93,8 +93,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can
be altered using the {extra} option of the
"compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
:line
@@ -122,8 +122,8 @@ rotational degrees of freedom.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt
index f72b886cc47afa0b0f7badd75b39ef943375002d..4e3ce3e77f86db797f0222b62d403df6ef82c827 100644
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -75,8 +75,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can
be altered using the {extra} option of the
"compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
:line
@@ -104,8 +104,8 @@ rotational degrees of freedom.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt
index f877f6ece84b9a2429d64949eea298e20d98ef74..de8c850a7087329465e84544a2084309602a80d1 100644
--- a/doc/src/compute_temp_chunk.txt
+++ b/doc/src/compute_temp_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -52,10 +52,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
The temperature is calculated by the formula KE = DOF/2 k T, where KE =
total kinetic energy of all atoms assigned to chunks (sum of 1/2 m
@@ -200,8 +199,8 @@ molecule.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
This compute also optionally calculates a global array, if one or more
@@ -210,9 +209,8 @@ of the optional values are specified. The number of rows in the array
"compute chunk/atom"_compute_chunk_atom.html command. The number of
columns is the number of specified values (1 or more). These values
can be accessed by any command that uses global array values from a
-compute as input. Again, see "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+compute as input. Again, see the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive". The array values are "intensive".
diff --git a/doc/src/compute_temp_com.txt b/doc/src/compute_temp_com.txt
index c7cc5ec4e280db434892260b9b2d7d045515d765..12df694e382657c9424e8b0649a4dd677a2630d6 100644
--- a/doc/src/compute_temp_com.txt
+++ b/doc/src/compute_temp_com.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,8 +65,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
@@ -74,8 +74,8 @@ thermostatting.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_cs.txt b/doc/src/compute_temp_cs.txt
index 561b787df637b48a69173f2f863ccec871e4855b..0236319f547a2a71e5f533f797ffb191e6e8254d 100644
--- a/doc/src/compute_temp_cs.txt
+++ b/doc/src/compute_temp_cs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -28,9 +28,9 @@ Define a computation that calculates the temperature of a system based
on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham1. See
-"Section 6.25"_Section_howto.html#howto_25 of the manual for an
-overview of the model as implemented in LAMMPS. Specifically, this
-compute enables correct temperature calculation and thermostatting of
+the "Howto coreshell"_Howto_coreshell.html doc page for an overview of
+the model as implemented in LAMMPS. Specifically, this compute
+enables correct temperature calculation and thermostatting of
core/shell pairs where it is desirable for the internal degrees of
freedom of the core/shell pairs to not be influenced by a thermostat.
A compute of this style can be used by any command that computes a
@@ -83,8 +83,9 @@ langevin"_fix_langevin.html.
The internal energy of core/shell pairs can be calculated by the
"compute temp/chunk"_compute_temp_chunk.html command, if chunks are
-defined as core/shell pairs. See "Section
-6.25"_Section_howto.html#howto_25 for more discussion on how to do this.
+defined as core/shell pairs. See the "Howto
+coreshell"_Howto_coreshell.html doc page doc page for more discussion
+on how to do this.
[Output info:]
diff --git a/doc/src/compute_temp_deform.txt b/doc/src/compute_temp_deform.txt
index 168b0b3880b2ec25e2040b17d135d874709dc68a..26d322589ed70d49d23a0ac8948fc4524e04daef 100644
--- a/doc/src/compute_temp_deform.txt
+++ b/doc/src/compute_temp_deform.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -104,8 +104,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
@@ -113,8 +113,8 @@ thermostatting.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/src/compute_temp_deform_eff.txt
index d09a0ace2fbb449fd969dc63532402cfa2c3c06a..876d492f3446f7294ed295974e20c0f28a2369bd 100644
--- a/doc/src/compute_temp_deform_eff.txt
+++ b/doc/src/compute_temp_deform_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -48,8 +48,8 @@ component of the electrons is not affected.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_drude.txt b/doc/src/compute_temp_drude.txt
index 169b8d588086cefdac9aa0db42fc05ab95b18587..20d9a5c05670a66938a70bb85660cd6b79bc100a 100644
--- a/doc/src/compute_temp_drude.txt
+++ b/doc/src/compute_temp_drude.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -22,10 +22,10 @@ compute TDRUDE all temp/drude :pre
[Description:]
Define a computation that calculates the temperatures of core-Drude
-pairs. This compute is designed to be used with the
-"thermalized Drude oscillator model"_tutorial_drude.html. Polarizable
-models in LAMMPS are described in "this
-Section"_Section_howto.html#howto_25.
+pairs. This compute is designed to be used with the "thermalized Drude
+oscillator model"_Howto_drude.html. Polarizable models in LAMMPS
+are described on the "Howto polarizable"_Howto_polarizable.html doc
+page.
Drude oscillators consist of a core particle and a Drude particle
connected by a harmonic bond, and the relative motion of these Drude
@@ -57,8 +57,8 @@ kinetic energy of the centers of mass (energy units)
kinetic energy of the dipoles (energy units) :ol
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
Both the scalar value and the first two values of the vector
diff --git a/doc/src/compute_temp_eff.txt b/doc/src/compute_temp_eff.txt
index 409319edcb9f3a89ffc38d43892a8539073c13ba..35ddb75b12c30ffac0d1d5fc249f9abe33617a0a 100644
--- a/doc/src/compute_temp_eff.txt
+++ b/doc/src/compute_temp_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -69,8 +69,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt
index fe2420b4e40d8d28e0b824d8022b8322596877f6..2769246532fd55f8cf36df3c076d6d822609d765 100644
--- a/doc/src/compute_temp_partial.txt
+++ b/doc/src/compute_temp_partial.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,8 +65,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
:line
@@ -74,10 +74,9 @@ thermostatting.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -89,8 +88,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -99,8 +98,8 @@ more instructions on how to use the accelerated styles effectively.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_profile.txt b/doc/src/compute_temp_profile.txt
index 64a6abd283986747d01514a2e53d9fb3ca2cb1b3..4ed04ca67e0e0c07ebc3250829ad4f9486c791d2 100644
--- a/doc/src/compute_temp_profile.txt
+++ b/doc/src/compute_temp_profile.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -122,8 +122,8 @@ degrees-of-freedom adjustment described in the preceding paragraph,
for fixes that constrain molecular motion. It does include the
adjustment due to the {extra} option, which is applied to each bin.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting. Using this compute in conjunction with a
thermostatting fix, as explained there, will effectively implement a
profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans1.
@@ -145,8 +145,8 @@ indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10
indices are numbered from 1 to 10 in each dimension.
These values can be used by any command that uses global scalar or
-vector or array values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector or array values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_ramp.txt b/doc/src/compute_temp_ramp.txt
index bc9283469cf2bda9e55f2ee29f95e25d92f68c69..15cad9c0cb814ed464f5c9210499a333f6cf576d 100644
--- a/doc/src/compute_temp_ramp.txt
+++ b/doc/src/compute_temp_ramp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -83,8 +83,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
@@ -92,8 +92,8 @@ thermostatting.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_region.txt b/doc/src/compute_temp_region.txt
index 3e4a80db8dd1ff4cf2c0cee248754bf2f2721158..f23901af9861633b83b33d5c172b62f8fe3f681c 100644
--- a/doc/src/compute_temp_region.txt
+++ b/doc/src/compute_temp_region.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -81,8 +81,8 @@ If needed the number of subtracted degrees-of-freedom can be set
explicitly using the {extra} option of the
"compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
@@ -90,8 +90,8 @@ thermostatting.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_region_eff.txt b/doc/src/compute_temp_region_eff.txt
index 8baf2dd46cc01f57cbec0ede1d76265b3b8b113f..95892eb25778eac67c1042de5acf2ed97494c4f1 100644
--- a/doc/src/compute_temp_region_eff.txt
+++ b/doc/src/compute_temp_region_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -39,8 +39,8 @@ temp/eff"_compute_temp_eff.html command.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_rotate.txt b/doc/src/compute_temp_rotate.txt
index 34feca7b6fd014ee4792126aed5c9277e1b4c203..189246d3e47e734b00a63da770e83a0333c9c85e 100644
--- a/doc/src/compute_temp_rotate.txt
+++ b/doc/src/compute_temp_rotate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -64,8 +64,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
@@ -73,8 +73,8 @@ thermostatting.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_sphere.txt b/doc/src/compute_temp_sphere.txt
index 9e9dff2cb6dc149e5834043a7f420f968666f15a..5a55126d121755a60f9705e52189f28dbcca70cf 100644
--- a/doc/src/compute_temp_sphere.txt
+++ b/doc/src/compute_temp_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -79,8 +79,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can
be altered using the {extra} option of the
"compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
:line
@@ -108,8 +108,8 @@ rotational degrees of freedom.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt
index acd3a6218d9e39d25a73be4d7562ee8127ae9cfa..a94d5db8ed767604c3dd6edac9bf81723d02da1b 100644
--- a/doc/src/compute_temp_uef.txt
+++ b/doc/src/compute_temp_uef.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt
index 733954d146bc9ec9b90c821f45432115638db7fc..e79b594e3f32a252a1ea352a1b3fc113324ebb3d 100644
--- a/doc/src/compute_ti.txt
+++ b/doc/src/compute_ti.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -111,9 +111,8 @@ du/dl can be found in the paper by "Eike"_#Eike.
This compute calculates a global scalar, namely dUs/dlambda. This
value can be used by any command that uses a global scalar value from
-a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive".
diff --git a/doc/src/compute_torque_chunk.txt b/doc/src/compute_torque_chunk.txt
index b9f832dd03afe36960509535c348973a46e83e01..6484076b37619db625ea585480d1d00b73c455ed 100644
--- a/doc/src/compute_torque_chunk.txt
+++ b/doc/src/compute_torque_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the 3 components of the torque vector for eqch
chunk, due to the forces on the individual atoms in the chunk around
@@ -72,7 +71,7 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the 3 xyz components of the torque for each chunk. These values
can be accessed by any command that uses global array values from a
-compute as input. See "Section 6.15"_Section_howto.html#howto_15
+compute as input. See the "Howto output"_Howto_output.html doc page
for an overview of LAMMPS output options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_vacf.txt b/doc/src/compute_vacf.txt
index a0d9a3c5f702ea42c77d8a18f433743f73500f77..70f1e99490586badb949d7fe6bec0b791a0ebc1c 100644
--- a/doc/src/compute_vacf.txt
+++ b/doc/src/compute_vacf.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -55,9 +55,8 @@ correctly with time=0 atom velocities from the restart file.
This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 by any command that uses global vector values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The vector values are "intensive". The vector values will be in
velocity^2 "units"_units.html.
diff --git a/doc/src/compute_vcm_chunk.txt b/doc/src/compute_vcm_chunk.txt
index de02c586bf9d0d052f7e9421e4f52372b5b8e3c4..7e8ad712086fe17931a8676179865117aaf41c1f 100644
--- a/doc/src/compute_vcm_chunk.txt
+++ b/doc/src/compute_vcm_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the x,y,z components of the center-of-mass
velocity for each chunk. This is done by summing mass*velocity for
@@ -63,8 +62,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the x,y,z center-of-mass velocity coordinates of each chunk.
These values can be accessed by any command that uses global array
-values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt
index a280b2b151d7e7656a421e8007f04c1eed464c90..a8ce77882ad42069d32d51864cb06ce3566c8bba 100644
--- a/doc/src/compute_voronoi_atom.txt
+++ b/doc/src/compute_voronoi_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -122,18 +122,16 @@ to locate vacancies (the coordinates are given by the atom coordinates
at the time step when the compute was first invoked), while column two
data can be used to identify interstitial atoms.
-If the {neighbors} value is set to yes, then
-this compute creates a local array with 3 columns. There
-is one row for each face of each Voronoi cell. The
-3 columns are the atom ID of the atom that owns the cell,
-the atom ID of the atom in the neighboring cell
-(or zero if the face is external), and the area of the face.
-The array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options. More specifically, the array can be accessed by a
-"dump local"_dump.html command to write a file containing
-all the Voronoi neighbors in a system:
+If the {neighbors} value is set to yes, then this compute creates a
+local array with 3 columns. There is one row for each face of each
+Voronoi cell. The 3 columns are the atom ID of the atom that owns the
+cell, the atom ID of the atom in the neighboring cell (or zero if the
+face is external), and the area of the face. The array can be
+accessed by any command that uses local values from a compute as
+input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options. More specifically, the array can be
+accessed by a "dump local"_dump.html command to write a file
+containing all the Voronoi neighbors in a system:
compute 6 all voronoi/atom neighbors yes
dump d2 all local 1 dump.neighbors index c_6\[1\] c_6\[2\] c_6\[3\] :pre
@@ -186,8 +184,8 @@ columns. In regular dynamic tessellation mode the first column is the
Voronoi volume, the second is the neighbor count, as described above
(read above for the output data in case the {occupation} keyword is
specified). These values can be accessed by any command that uses
-per-atom values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+per-atom values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options. If the {peratom} keyword is set to "no", the per-atom array
is still created, but it is not accessible.
diff --git a/doc/src/compute_xrd.txt b/doc/src/compute_xrd.txt
index 1a151d63f9157380349a55d2f4a49d2ac806a4a2..609fde3582d9efd03bd9c0ae6fbb63ac3d54db20 100644
--- a/doc/src/compute_xrd.txt
+++ b/doc/src/compute_xrd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -162,7 +162,7 @@ or degrees) provided with the {2Theta} values. The second column contains
the computed diffraction intensities as described above.
The array can be accessed by any command that uses global values from
-a compute as input. See "this section"_Section_howto.html#howto_15
+a compute as input. See the "Howto output"_Howto_output.html doc page
for an overview of LAMMPS output options.
All array values calculated by this compute are "intensive".
diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt
index 5d824ae1ef2e57815bba64e8596d069048a46f12..d80e2d45f1473d2a4a084b35af0140e6a3e0605a 100644
--- a/doc/src/create_atoms.txt
+++ b/doc/src/create_atoms.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt
index 6700ed29d3f3f6d9b3c7d5094b182a1bf6235a82..8596cab51d24c6f0283d5d070192153d6d218534 100644
--- a/doc/src/create_bonds.txt
+++ b/doc/src/create_bonds.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/create_box.txt b/doc/src/create_box.txt
index f4ef13654c6eaf3f13a1795862879b6642e7734b..0993b4f927d49a02b8a93328f564c72e16e3fbdb 100644
--- a/doc/src/create_box.txt
+++ b/doc/src/create_box.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -73,9 +73,9 @@ factors that exceed these limits, you can use the "box tilt"_box.html
command, with a setting of {large}; a setting of {small} is the
default.
-See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
-for a geometric description of triclinic boxes, as defined by LAMMPS,
-and how to transform these parameters to and from other commonly used
+See the "Howto triclinic"_Howto_triclinic.html doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
triclinic representations.
When a prism region is used, the simulation domain should normally be
diff --git a/doc/src/delete_atoms.txt b/doc/src/delete_atoms.txt
index 1aa71d341f83a34a25017b4d123996f22a6fcd16..57faf97ad1bf1d213135707989985a1f866a8f8d 100644
--- a/doc/src/delete_atoms.txt
+++ b/doc/src/delete_atoms.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/delete_bonds.txt b/doc/src/delete_bonds.txt
index b1137a22881213506c8921b9e422d0d9f2e33253..b29fa82f2d0d16c9b1a252073080aba43332605c 100644
--- a/doc/src/delete_bonds.txt
+++ b/doc/src/delete_bonds.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dielectric.txt b/doc/src/dielectric.txt
index e98badf87b72c94b3a308c806044499966d76463..f93be8cc25823c691b108dce6d8e41b5d6367775 100644
--- a/doc/src/dielectric.txt
+++ b/doc/src/dielectric.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt
index 06abe054e4819e7c7e9ea9e248e7f2285e423572..8adef6cf4b5ed1ee5f25ab1d72c7fc12f43078fc 100644
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,10 +116,9 @@ computed.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -131,8 +130,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt
index cb9fc72c223b2293990764db4b0dffb59dc249b5..1a2f37abbbd0352fd04bc6e958912c0b17966627 100644
--- a/doc/src/dihedral_class2.txt
+++ b/doc/src/dihedral_class2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -141,10 +141,9 @@ r3 (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -156,8 +155,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_coeff.txt b/doc/src/dihedral_coeff.txt
index 5b43cbbe7f36d937fcb60334bde83a5911a2e61d..1db69e40d5739320b57139e56494749f6661e8d2 100644
--- a/doc/src/dihedral_coeff.txt
+++ b/doc/src/dihedral_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -74,9 +74,9 @@ the style to display the formula it computes and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html command.
Note that there are also additional dihedral styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the dihedral section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral
+doc page.
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt
index 715682affc010e657556ba9221ca68a093b5259a..7ef27e6bc966b129156159c9714e27a2cc050853 100644
--- a/doc/src/dihedral_cosine_shift_exp.txt
+++ b/doc/src/dihedral_cosine_shift_exp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -52,10 +52,9 @@ A (real number) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -67,8 +66,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt
index 0accbb22bf80bfb89e1b77bd7fa8760e56ad3e55..f51cbc9c8cd8e1aeed0248730d7b633a3d636f74 100644
--- a/doc/src/dihedral_fourier.txt
+++ b/doc/src/dihedral_fourier.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -44,10 +44,9 @@ dm (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -59,8 +58,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt
index d9a48ff384d9df3dd9228a05be3c523302b80362..1eda0c5d02b8f1a7bbba646ad26d684cff7e7806 100644
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -53,10 +53,9 @@ Some force fields let {n} be positive or negative which corresponds to
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt
index 1e907557b28564f74e3f080160997a107941d4b5..3af4b410bcd24e4469ccdc50e9576fb81cc9539c 100644
--- a/doc/src/dihedral_helix.txt
+++ b/doc/src/dihedral_helix.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -46,10 +46,9 @@ C (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -61,8 +60,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt
index 8cb40eff44a66189d2ff37aadbd0c25ccd5a00c3..c9ca86680c175aca2188891523265ca4d2203f81 100644
--- a/doc/src/dihedral_hybrid.txt
+++ b/doc/src/dihedral_hybrid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt
index 7d3c2ea083d0ef78b7e275caa9ca51e1305e8e49..7c22391923b37a065369b53c0871d20cd90710fe 100644
--- a/doc/src/dihedral_multi_harmonic.txt
+++ b/doc/src/dihedral_multi_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,10 +40,9 @@ A5 (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt
index 8392d83899de8c41cd855e6a038f3e7a585ec08a..aa8f1e0d7fdc646fa6c06009909b750294e06613 100644
--- a/doc/src/dihedral_nharmonic.txt
+++ b/doc/src/dihedral_nharmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,10 +40,9 @@ An (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_none.txt b/doc/src/dihedral_none.txt
index 3ce2aa1729c6dfb31ad8924b20554f974cbc73b5..4c1ff2ea5d30fadd25949e613b6ec29e4cfa3fdb 100644
--- a/doc/src/dihedral_none.txt
+++ b/doc/src/dihedral_none.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt
index d1a6ba3ff2865db905b97bf72b70d343f509e06e..f0cf91f30ad67fe914b376aef1c0c94ef5145955 100644
--- a/doc/src/dihedral_opls.txt
+++ b/doc/src/dihedral_opls.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -48,10 +48,9 @@ K4 (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -63,8 +62,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt
index ca2f5aed40f2f67512a255813689a50e35a4c7d7..e65cf2dee86a2b108513f1d83a5cbfe29c8a0034 100644
--- a/doc/src/dihedral_quadratic.txt
+++ b/doc/src/dihedral_quadratic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,10 +41,9 @@ phi0 (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt
index 7c17fbf5ef1c50aa939642c0eb224835c3721f0d..10a757e8986d6d9c5f450a84bfffc6be81221078 100644
--- a/doc/src/dihedral_spherical.txt
+++ b/doc/src/dihedral_spherical.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt
index ca592b29b55415fde7c4306fa231ea35e0c5f40a..6aff3f0994777390eba737e8273524f770fd5e8e 100644
--- a/doc/src/dihedral_style.txt
+++ b/doc/src/dihedral_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -81,9 +81,9 @@ the style to display the formula it computes and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html command.
Note that there are also additional dihedral styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the dihedral section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral
+doc page.
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
"dihedral_style zero"_dihedral_zero.html - topology but no interactions
diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt
index 0b88f26a61076c6b10750ea419b947fb88a0dd8f..d722ef7c82a76c67ac0353a02b1656b8a8de73c0 100644
--- a/doc/src/dihedral_table.txt
+++ b/doc/src/dihedral_table.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -174,10 +174,9 @@ that matches the specified keyword.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -189,8 +188,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restrictions:]
diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt
index 1c83d4ffa09f7221ac8c3859594abc754b9b28c4..cc7df8cdf9de397a6a91d9ec89bef542f5b5002a 100644
--- a/doc/src/dihedral_table_cut.txt
+++ b/doc/src/dihedral_table_cut.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dihedral_zero.txt b/doc/src/dihedral_zero.txt
index 4d33126eeb76330e830fced4f9c55d7b47c86fdf..0c9995a5637c84571297f7b6a28a7162dc75b2fd 100644
--- a/doc/src/dihedral_zero.txt
+++ b/doc/src/dihedral_zero.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dimension.txt b/doc/src/dimension.txt
index 0531e92acf60d439c22848fc3d2a94b653a1c52d..b7dde7652443a10a7199ddc46f9e7e70a21b3a09 100644
--- a/doc/src/dimension.txt
+++ b/doc/src/dimension.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -26,7 +26,7 @@ prior to setting up a simulation box via the
"create_box"_create_box.html or "read_data"_read_data.html commands.
Restart files also store this setting.
-See the discussion in "Section 6"_Section_howto.html for
+See the discussion on the "Howto 2d"_Howto_2d.html doc page for
additional instructions on how to run 2d simulations.
NOTE: Some models in LAMMPS treat particles as finite-size spheres or
diff --git a/doc/src/displace_atoms.txt b/doc/src/displace_atoms.txt
index 634add196b78fe249d4c42177482b69b05f5719e..b4afd5c3a9b9eb4af9666fc4b57f0b0df85810be 100644
--- a/doc/src/displace_atoms.txt
+++ b/doc/src/displace_atoms.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index ff1bf6424df10a43ffcefa95cae512ecfbf2f631..5b478b7301960bd536ef29158086c0c8b0f34023 100644
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -224,12 +224,12 @@ This bounding box is convenient for many visualization programs. The
meaning of the 6 character flags for "xx yy zz" is the same as above.
Note that the first two numbers on each line are now xlo_bound instead
-of xlo, etc, since they represent a bounding box. See "this
-section"_Section_howto.html#howto_12 of the doc pages for a geometric
-description of triclinic boxes, as defined by LAMMPS, simple formulas
-for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
-calculated from the triclinic parameters, and how to transform those
-parameters to and from other commonly used triclinic representations.
+of xlo, etc, since they represent a bounding box. See the "Howto
+triclinic"_Howto_triclinic.html doc page for a geometric description
+of triclinic boxes, as defined by LAMMPS, simple formulas for how the
+6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from
+the triclinic parameters, and how to transform those parameters to and
+from other commonly used triclinic representations.
The "ITEM: ATOMS" line in each snapshot lists column descriptors for
the per-atom lines that follow. For example, the descriptors would be
@@ -530,7 +530,7 @@ so that each value is 0.0 to 1.0. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0.
I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
the non-orthogonal vectors of the simulation box edges, as discussed
-in "Section 6.12"_Section_howto.html#howto_12.
+on the "Howto triclinic"_Howto_triclinic.html doc page.
Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
image flags for each atom. Unwrapped means that if the atom has
diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt
index e257f9c4f16d2f768ee4e688f3d71e0a0dd0c1cd..665be14be1330e0b902c73686d430f3ce904a315 100644
--- a/doc/src/dump_cfg_uef.txt
+++ b/doc/src/dump_cfg_uef.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt
index 93c87d85b7a6064140b6cf320199d3cd99114e10..fbd682dad9cac9c112fc10ee30c31c922e00f4a0 100644
--- a/doc/src/dump_h5md.txt
+++ b/doc/src/dump_h5md.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt
index c1732be972f6502111c71fbc411152e223c9053f..06332b5dcf92a593ba084c50f9daaacfd7fb4ae3 100644
--- a/doc/src/dump_image.txt
+++ b/doc/src/dump_image.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -356,16 +356,16 @@ is used to define body particles with internal state
body style. If this keyword is not used, such particles will be drawn
as spheres, the same as if they were regular atoms.
-The "body"_body.html doc page describes the body styles LAMMPS
-currently supports, and provides more details as to the kind of body
-particles they represent and how they are drawn by this dump image
-command. For all the body styles, individual atoms can be either a
-body particle or a usual point (non-body) particle. Non-body
+The "Howto body"_Howto_body.html doc page describes the body styles
+LAMMPS currently supports, and provides more details as to the kind of
+body particles they represent and how they are drawn by this dump
+image command. For all the body styles, individual atoms can be
+either a body particle or a usual point (non-body) particle. Non-body
particles will be drawn the same way they would be as a regular atom.
The {bflag1} and {bflag2} settings are numerical values which are
passed to the body style to affect how the drawing of a body particle
-is done. See the "body"_body.html doc page for a description of what
-these parameters mean for each body style.
+is done. See the "Howto body"_Howto_body.html doc page for a
+description of what these parameters mean for each body style.
The only setting currently allowed for the {color} value is {type},
which will color the body particles according to the atom type of the
diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt
index 5365610d640ab7598a11554d6c20bb47de8cf442..73107d07f786e40d60407423551ba839033d7948 100644
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt
index 7e68490a68e013c42f13883d9b7d1f9044929ce8..9fa04bd1aeed0de92d8fac59dfe3e8e0d83bee3e 100644
--- a/doc/src/dump_molfile.txt
+++ b/doc/src/dump_molfile.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt
index 70111a36a8b28d9654db6779426090b7e37b507d..b1c63736514d00e4c35e1056aebab49d18f1cc54 100644
--- a/doc/src/dump_netcdf.txt
+++ b/doc/src/dump_netcdf.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt
index d4d28c81fca69cea2fb65d72e940acf4de0fdcb0..afc6099534eb5c80ffb18461f0f8426ea50bcc67 100644
--- a/doc/src/dump_vtk.txt
+++ b/doc/src/dump_vtk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/echo.txt b/doc/src/echo.txt
index 3141c7a719bcb0de5d39366183a269f761bd0230..dc6918dc8981af7b971e3e3cd406d29c6aa2e8b7 100644
--- a/doc/src/echo.txt
+++ b/doc/src/echo.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index ba2088576f1b4137d61d89509d2e6089026864f4..fd966b5bd9916407648f6db1ea7f01d293faef10 100644
--- a/doc/src/fix.txt
+++ b/doc/src/fix.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -133,7 +133,7 @@ reduce"_compute_reduce.html command, or histogrammed by the "fix
ave/histo"_fix_ave_histo.html command. :l
:ule
-See this "howto section"_Section_howto.html#howto_15 for a summary of
+See the "Howto output"_Howto_output.html doc page for a summary of
various LAMMPS output options, many of which involve fixes.
The results of fixes that calculate global quantities can be either
@@ -151,16 +151,20 @@ for further info.
:line
-Each fix style has its own documentation page which describes its
-arguments and what it does, as listed below. Here is an alphabetic
-list of fix styles available in LAMMPS. They are also given in more
-compact form in the Fix section of "this
-page"_Section_commands.html#cmd_5.
+Each fix style has its own doc page which describes its arguments and
+what it does, as listed below. Here is an alphabetic list of fix
+styles available in LAMMPS. They are also listed in more compact form
+on the "Commands fix"_Commands_fix.html doc page.
There are also additional fix styles (not listed here) submitted by
-users which are included in the LAMMPS distribution. The list of
-these with links to the individual styles are given in the fix section
-of "this page"_Section_commands.html#cmd_5.
+users which are included in the LAMMPS distribution. The full list of
+all fix styles is on the "Commands fix"_Commands_fix.html doc page.
+
+There are also additional accelerated fix styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the "Commands fix"_Commands_fix.html doc
+page are followed by one or more of (g,i,k,o,t) to indicate which
+accerlerated styles exist.
"adapt"_fix_adapt.html - change a simulation parameter over time
"addforce"_fix_addforce.html - add a force to each atom
diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt
index 7a34f2ff4480004c3ff249957b2b36204a087035..0ca28fb8694c6c5c4d4c2d39ab649dc79a9152a3 100644
--- a/doc/src/fix_adapt.txt
+++ b/doc/src/fix_adapt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -270,10 +270,10 @@ fix 1 center adapt 10 atom diameter v_size :pre
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
For "rRESPA time integration"_run_style.html, this fix changes
parameters on the outermost rRESPA level.
diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt
index 5dd58bc39adb83c1994bf847bcaf4e878ea34fb4..7e30a1d29d5b4354b7fae0761f50fc7d8d6e8dd3 100644
--- a/doc/src/fix_adapt_fep.txt
+++ b/doc/src/fix_adapt_fep.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -243,10 +243,10 @@ parameters on the outermost rRESPA level.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt
index b2ac95eabb0f4e2e49e4af226ae6cc98ea0d0358..51be39fdb2b72156560b0d85c56b6fc1a517056f 100644
--- a/doc/src/fix_addforce.txt
+++ b/doc/src/fix_addforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -103,12 +103,12 @@ converge properly.
:line
-Styles with a suffix are functionally the same as the corresponding
-style without the suffix. They have been optimized to run faster,
-depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -120,8 +120,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -150,11 +150,11 @@ integrator the fix is adding its forces. Default is the outermost
level.
This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar is the potential
-energy discussed above. The vector is the total force on the group of
-atoms before the forces on individual atoms are changed by the fix.
-The scalar and vector values calculated by this fix are "extensive".
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar is the potential energy discussed above. The vector is the
+total force on the group of atoms before the forces on individual
+atoms are changed by the fix. The scalar and vector values calculated
+by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt
index 793ec0e0157121a404a6991a2e67d9c01444ae21..c80fad26da1c5e40d8a96f42c034f2f8b18cdb86 100644
--- a/doc/src/fix_addtorque.txt
+++ b/doc/src/fix_addtorque.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -70,11 +70,11 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its torque. Default is the outermost level.
This fix computes a global scalar and a global 3-vector, which can be
-accessed by various "output commands"_Section_howto.html#howto_15.
-The scalar is the potential energy discussed above. The vector is the
-total torque on the group of atoms before the forces on individual
-atoms are changed by the fix. The scalar and vector values calculated
-by this fix are "extensive".
+accessed by various "output commands"_Howto_output.html. The scalar
+is the potential energy discussed above. The vector is the total
+torque on the group of atoms before the forces on individual atoms are
+changed by the fix. The scalar and vector values calculated by this
+fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_append_atoms.txt b/doc/src/fix_append_atoms.txt
index 27070c9be53f3d725e5f4492a1d35ce1deffead2..c6af361afcfe24a5da8cc97c4e917238fe981ab0 100644
--- a/doc/src/fix_append_atoms.txt
+++ b/doc/src/fix_append_atoms.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -87,10 +87,10 @@ define the lattice spacings.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_atc.txt b/doc/src/fix_atc.txt
index 49014f0591ff08e6f6e636067eed11ee9c8aab43..6de917e5714e6b68537b1180a7f7c5b9769cec81 100644
--- a/doc/src/fix_atc.txt
+++ b/doc/src/fix_atc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -102,7 +102,13 @@ Note coupling and post-processing can be combined in the same simulations using
[Restart, fix_modify, output, run start/stop, minimize info:]
-No information about this fix is written to "binary restart files"_restart.html. The "fix_modify"_fix_modify.html options relevant to this fix are listed below. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output commands"_Section_howto.html#howto_15. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html.
+No information about this fix is written to "binary restart
+files"_restart.html. The "fix_modify"_fix_modify.html options
+relevant to this fix are listed below. No global scalar or vector or
+per-atom quantities are stored by this fix for access by various
+"output commands"_Howto_output.html. No parameter of this fix can be
+used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_atom_swap.txt b/doc/src/fix_atom_swap.txt
index bf56277214bf78ac10270d40ea2fcd56c1391aa7..c1d84dade1954b2a8d1ec15bb699cb99a5d1e1ae 100644
--- a/doc/src/fix_atom_swap.txt
+++ b/doc/src/fix_atom_swap.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -150,8 +150,8 @@ None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix computes a global vector of length 2, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. The vector
-values are the following global cumulative quantities:
+by various "output commands"_Howto_output.html. The vector values are
+the following global cumulative quantities:
1 = swap attempts
2 = swap successes :ul
diff --git a/doc/src/fix_ave_atom.txt b/doc/src/fix_ave_atom.txt
index 23e4ed235b2d21c3c9cde5df0207781b448d69c2..10deaf64cd2900ee76be741c7a835ed2d0e04175 100644
--- a/doc/src/fix_ave_atom.txt
+++ b/doc/src/fix_ave_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,7 +38,7 @@ fix 1 all ave/atom 10 20 1000 c_my_stress\[*\] :pre
Use one or more per-atom vectors as inputs every few timesteps, and
average them atom by atom over longer timescales. The resulting
per-atom averages can be used by other "output
-commands"_Section_howto.html#howto_15 such as the "fix
+commands"_Howto_output.html such as the "fix
ave/chunk"_fix_ave_chunk.html or "dump custom"_dump.html commands.
The group specified with the command means only atoms within the group
@@ -155,14 +155,14 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global scalar or vector quantities are
stored by this fix for access by various "output
-commands"_Section_howto.html#howto_15.
+commands"_Howto_output.html.
This fix produces a per-atom vector or array which can be accessed by
-various "output commands"_Section_howto.html#howto_15. A vector is
-produced if only a single quantity is averaged by this fix. If two or
-more quantities are averaged, then an array of values is produced.
-The per-atom values can only be accessed on timesteps that are
-multiples of {Nfreq} since that is when averaging is performed.
+various "output commands"_Howto_output.html. A vector is produced if
+only a single quantity is averaged by this fix. If two or more
+quantities are averaged, then an array of values is produced. The
+per-atom values can only be accessed on timesteps that are multiples
+of {Nfreq} since that is when averaging is performed.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt
index 8e2a09e33fb4a4da2872780fad28fb3f3dc54769..d331e512953b8c32817f0aef973ca99d4289216a 100644
--- a/doc/src/fix_ave_chunk.txt
+++ b/doc/src/fix_ave_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -85,17 +85,17 @@ fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile :pre
Use one or more per-atom vectors as inputs every few timesteps, sum
the values over the atoms in each chunk at each timestep, then average
the per-chunk values over longer timescales. The resulting chunk
-averages can be used by other "output
-commands"_Section_howto.html#howto_15 such as "thermo_style
-custom"_thermo_style.html, and can also be written to a file.
+averages can be used by other "output commands"_Howto_output.html such
+as "thermo_style custom"_thermo_style.html, and can also be written to
+a file.
In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
+chunk/atom"_compute_chunk_atom.html doc page and the "Howto
+chunk"_Howto_chunk.html doc page for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
@@ -456,20 +456,19 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global array of values which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The values can
-only be accessed on timesteps that are multiples of {Nfreq} since that
-is when averaging is performed. The global array has # of rows =
-the number of chunks {Nchunk} as calculated by the specified "compute
+various "output commands"_Howto_output.html. The values can only be
+accessed on timesteps that are multiples of {Nfreq} since that is when
+averaging is performed. The global array has # of rows = the number
+of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The # of columns =
M+1+Nvalues, where M = 1 to 4, depending on whether the optional
-columns for OrigID and CoordN are used, as explained above.
-Following the optional columns, the next column contains the count of
-atoms in the chunk, and the remaining columns are the Nvalue
-quantities. When the array is accessed with a row I that exceeds the
-current number of chunks, than a 0.0 is returned by the fix instead of
-an error, since the number of chunks can vary as a simulation runs
-depending on how that value is computed by the compute chunk/atom
-command.
+columns for OrigID and CoordN are used, as explained above. Following
+the optional columns, the next column contains the count of atoms in
+the chunk, and the remaining columns are the Nvalue quantities. When
+the array is accessed with a row I that exceeds the current number of
+chunks, than a 0.0 is returned by the fix instead of an error, since
+the number of chunks can vary as a simulation runs depending on how
+that value is computed by the compute chunk/atom command.
The array values calculated by this fix are treated as "intensive",
since they are typically already normalized by the count of atoms in
diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt
index 98f352cb74ea0ed97e05324d2980c46bd7147ca1..22e8768f1d04444df665513b4d5651c1e31cdbde 100644
--- a/doc/src/fix_ave_correlate.txt
+++ b/doc/src/fix_ave_correlate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -68,7 +68,7 @@ calculate time correlations between them at varying time intervals,
and average the correlation data over longer timescales. The
resulting correlation values can be time integrated by
"variables"_variable.html or used by other "output
-commands"_Section_howto.html#howto_15 such as "thermo_style
+commands"_Howto_output.html such as "thermo_style
custom"_thermo_style.html, and can also be written to a file. See the
"fix ave/correlate/long"_fix_ave_correlate_long.html command for an
alternate method for computing correlation functions efficiently over
@@ -313,16 +313,15 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global array of values which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The values can
-only be accessed on timesteps that are multiples of {Nfreq} since that
-is when averaging is performed. The global array has # of rows =
-{Nrepeat} and # of columns = Npair+2. The first column has the time
-delta (in timesteps) between the pairs of input values used to
-calculate the correlation, as described above. The 2nd column has the
-number of samples contributing to the correlation average, as
-described above. The remaining Npair columns are for I,J pairs of the
-N input values, as determined by the {type} keyword, as described
-above.
+various "output commands"_Howto_output.html. The values can only be
+accessed on timesteps that are multiples of {Nfreq} since that is when
+averaging is performed. The global array has # of rows = {Nrepeat}
+and # of columns = Npair+2. The first column has the time delta (in
+timesteps) between the pairs of input values used to calculate the
+correlation, as described above. The 2nd column has the number of
+samples contributing to the correlation average, as described above.
+The remaining Npair columns are for I,J pairs of the N input values,
+as determined by the {type} keyword, as described above.
For {type} = {auto}, the Npair = N columns are ordered: C11, C22, ...,
CNN. :ulb,l
diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/src/fix_ave_correlate_long.txt
index 7b4bc53701cf9232ca87cd6cec1ceee38ac67690..ac0ef873aac6ae3cd90fca5077a3cc86e3160645 100644
--- a/doc/src/fix_ave_correlate_long.txt
+++ b/doc/src/fix_ave_correlate_long.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt
index 5155f42e7bca0335d29ac16566051255a2ff3a89..f1da130ff7e25c84528bda44cc2e582a8e910274 100644
--- a/doc/src/fix_ave_histo.txt
+++ b/doc/src/fix_ave_histo.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -69,10 +69,9 @@ fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD\[1\] c_XRD\[2\] :pre
Use one or more values as inputs every few timesteps to create a
single histogram. The histogram can then be averaged over longer
timescales. The resulting histogram can be used by other "output
-commands"_Section_howto.html#howto_15, and can also be written to a
-file. The fix ave/histo/weight command has identical syntax to fix
-ave/histo, except that exactly two values must be specified. See
-details below.
+commands"_Howto_output.html, and can also be written to a file. The
+fix ave/histo/weight command has identical syntax to fix ave/histo,
+except that exactly two values must be specified. See details below.
The group specified with this command is ignored for global and local
input values. For per-atom input values, only atoms in the group
@@ -320,10 +319,10 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix produces a global vector and global array which can be
-accessed by various "output commands"_Section_howto.html#howto_15.
-The values can only be accessed on timesteps that are multiples of
-{Nfreq} since that is when a histogram is generated. The global
-vector has 4 values:
+accessed by various "output commands"_Howto_output.html. The values
+can only be accessed on timesteps that are multiples of {Nfreq} since
+that is when a histogram is generated. The global vector has 4
+values:
1 = total counts in the histogram
2 = values that were not histogrammed (see {beyond} keyword)
diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt
index b61f56cf0274ef732216e2dcc1020a1bd8f4d4ee..a53e318d3fd83a3aab0382876b305681ed17ee0b 100644
--- a/doc/src/fix_ave_time.txt
+++ b/doc/src/fix_ave_time.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -64,7 +64,7 @@ fix 1 all ave/time 1 100 1000 f_indent f_indent\[1\] file temp.indent off 1 :pre
Use one or more global values as inputs every few timesteps, and
average them over longer timescales. The resulting averages can be
-used by other "output commands"_Section_howto.html#howto_15 such as
+used by other "output commands"_Howto_output.html such as
"thermo_style custom"_thermo_style.html, and can also be written to a
file. Note that if no time averaging is done, this command can be
used as a convenient way to simply output one or more global values to
@@ -305,10 +305,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix produces a global scalar or global vector or global array
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The values can only be
-accessed on timesteps that are multiples of {Nfreq} since that is when
-averaging is performed.
+which can be accessed by various "output commands"_Howto_output.html.
+The values can only be accessed on timesteps that are multiples of
+{Nfreq} since that is when averaging is performed.
A scalar is produced if only a single input value is averaged and
{mode} = scalar. A vector is produced if multiple input values are
diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt
index 5d7dec3e6aef7bb804f312546cb15bbe85b0e639..1fc7e4a18dd8f5efd1b84a21c0a785797be692a1 100644
--- a/doc/src/fix_aveforce.txt
+++ b/doc/src/fix_aveforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,12 +63,12 @@ to it.
:line
-Styles with a suffix are functionally the same as the corresponding
-style without the suffix. They have been optimized to run faster,
-depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -80,8 +80,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -95,10 +95,10 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global 3-vector of forces, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. This is the
-total force on the group of atoms before the forces on individual
-atoms are changed by the fix. The vector values calculated by this
-fix are "extensive".
+by various "output commands"_Howto_output.html. This is the total
+force on the group of atoms before the forces on individual atoms are
+changed by the fix. The vector values calculated by this fix are
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt
index f148e6f99663fe6028e83a246f334b5160ddb470..2de17cdd2a992344886a3eec4d92bc8e3d15b893 100644
--- a/doc/src/fix_balance.txt
+++ b/doc/src/fix_balance.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -357,8 +357,8 @@ number of particles (or total weight) on any processor to the average
number of particles (or total weight) per processor.
These quantities can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar and vector values
-calculated by this fix are "intensive".
+commands"_Howto_output.html. The scalar and vector values calculated
+by this fix are "intensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt
index f53b7c785c251240a0d325b820545f342ce21c06..f5bbc8a2519dcef980bdce8e3d08eb22a8789867 100644
--- a/doc/src/fix_bocs.txt
+++ b/doc/src/fix_bocs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt
index 83364b9efbbb0b6b9135707c15cae7353ca5b0da..bdb2f2a8624869a8552992b246a111cb3396e7c5 100644
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,8 +116,8 @@ are relevant to this fix.
This fix computes two statistics which it stores in a global vector of
length 2, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The vector values calculated
-by this fix are "intensive".
+commands"_Howto_output.html. The vector values calculated by this fix
+are "intensive".
These are the 2 quantities:
diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt
index c0045ac0f081e4df37c9fd6cf201d43238aea88f..ab34433cecf631fbb8b9cff9fb87d43b87d7c07d 100644
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -211,8 +211,8 @@ are relevant to this fix.
This fix computes two statistics which it stores in a global vector of
length 2, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The vector values calculated
-by this fix are "intensive".
+commands"_Howto_output.html. The vector values calculated by this fix
+are "intensive".
These are the 2 quantities:
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index f85ef9bc1aa6ea034364e5358ac1eafa2824f0d6..883968e012557e2ee8d13eddef15b8bc1f6873ef 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -298,9 +298,8 @@ relevant to this fix.
This fix computes one statistic for each {react} argument that it
stores in a global vector, of length 'number of react arguments', that
-can be accessed by various "output
-commands"_Section_howto.html#howto_15. The vector values calculated by
-this fix are "intensive".
+can be accessed by various "output commands"_Howto_output.html. The
+vector values calculated by this fix are "intensive".
These is 1 quantity for each react argument:
diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt
index ca7069e2478de279e063b5e43f1a82d29fe1f9b1..a829171f333aa3aa850fbc04c659eae6ac61ad40 100644
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -150,13 +150,13 @@ the Boltzmann criterion.
This fix computes two statistical quantities as a global 2-vector of
output, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The first component of the
-vector is the cumulative number of swaps performed by all processors.
-The second component of the vector is the cumulative number of swaps
-attempted (whether accepted or rejected). Note that a swap "attempt"
-only occurs when swap partners meeting the criteria described above
-are found on a particular timestep. The vector values calculated by
-this fix are "intensive".
+commands"_Howto_output.html. The first component of the vector is the
+cumulative number of swaps performed by all processors. The second
+component of the vector is the cumulative number of swaps attempted
+(whether accepted or rejected). Note that a swap "attempt" only
+occurs when swap partners meeting the criteria described above are
+found on a particular timestep. The vector values calculated by this
+fix are "intensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt
index e3d75ee858ea82013a59441cbc1fe016fcd19670..8e21ec2c748963302db1fd9876cc855d0d1e35d8 100644
--- a/doc/src/fix_box_relax.txt
+++ b/doc/src/fix_box_relax.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -315,17 +315,15 @@ specified by the {press} keyword will be unaffected by the {temp}
setting.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-pressure-volume energy, plus the strain energy, if it exists,
-as described above.
-The energy values reported at the
-end of a minimization run under "Minimization stats" include this
-energy, and so differ from what LAMMPS normally reports as potential
-energy. This fix does not support the "fix_modify"_fix_modify.html
-{energy} option, because that would result in double-counting of the
-fix energy in the minimization energy. Instead, the fix energy can be
-explicitly added to the potential energy using one of these two
-variants:
+"output commands"_Howto_output.html. The scalar is the pressure-volume
+energy, plus the strain energy, if it exists, as described above. The
+energy values reported at the end of a minimization run under
+"Minimization stats" include this energy, and so differ from what
+LAMMPS normally reports as potential energy. This fix does not support
+the "fix_modify"_fix_modify.html {energy} option, because that would
+result in double-counting of the fix energy in the minimization
+energy. Instead, the fix energy can be explicitly added to the
+potential energy using one of these two variants:
variable emin equal pe+f_1 :pre
diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt
index f8de2b4efec469736a067faa51fd4ac5a7d863eb..6f3769fafe6a634770dcdedb8908540972ee5d70 100644
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -103,9 +103,9 @@ the system's virial as part of "thermodynamic output"_thermo_style.html.
The default is {virial yes}
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-potential energy discussed above. The scalar value calculated by this
-fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the potential
+energy discussed above. The scalar value calculated by this fix is
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt
index e48dedacd9e17c54b7f4a28d588d173a821ad289..4a1d84de64a458dbc56999885ca8246a03ba21ed 100644
--- a/doc/src/fix_colvars.txt
+++ b/doc/src/fix_colvars.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -99,9 +99,9 @@ to the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
[Restrictions:]
diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt
index b8d2cb43be4b2fbc30d70034531969e4325a4709..7458f1bcfa015985158cbb3a1148fe625eb964e4 100644
--- a/doc/src/fix_controller.txt
+++ b/doc/src/fix_controller.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -180,9 +180,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix produces a global vector with 3 values which can be accessed
-by various "output commands"_Section_howto.html#howto_15. The values
-can be accessed on any timestep, though they are only updated on
-timesteps that are a multiple of {Nevery}.
+by various "output commands"_Howto_output.html. The values can be
+accessed on any timestep, though they are only updated on timesteps
+that are a multiple of {Nevery}.
The three values are the most recent updates made to the control
variable by each of the 3 terms in the PID equation above. The first
diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt
index c870c73bdccf918288589c5141ba4dbafcc60434..e92d1e6b19c5943d4de785c916738fdd10dc8ef0 100644
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -94,7 +94,7 @@ nvt/sllod"_fix_nvt_sllod.html and "compute
temp/deform"_compute_temp_deform.html commands for more details. Note
that simulation of a continuously extended system (extensional flow)
can be modeled using the "USER-UEF
-package"_Section_packages.html#USER-UEF and its "fix
+package"_Packages_details.html#USER-UEF and its "fix
commands"_fix_nh_uef.html.
For the {x}, {y}, {z} parameters, the associated dimension cannot be
@@ -550,10 +550,9 @@ command if you want to include lattice spacings in a variable formula.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -565,18 +564,17 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix will restore the initial box settings from "binary restart
files"_restart.html, which allows the fix to be properly continue
deformation, when using the start/stop options of the "run"_run.html
-command. None of the "fix_modify"_fix_modify.html options
-are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15.
+command. None of the "fix_modify"_fix_modify.html options are
+relevant to this fix. No global or per-atom quantities are stored by
+this fix for access by various "output commands"_Howto_output.html.
This fix can perform deformation over multiple runs, using the {start}
and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt
index 477c14ea8955ed45763bb1dd27d1242898e22ff5..277ca8777ad7409e586eb16344df34168786c165 100644
--- a/doc/src/fix_deposit.txt
+++ b/doc/src/fix_deposit.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,8 +116,8 @@ side = {in}.
NOTE: LAMMPS checks that the specified region is wholly inside the
simulation box. It can do this correctly for orthonormal simulation
-boxes. However for "triclinic boxes"_Section_howto.html#howto_12, it
-only tests against the larger orthonormal box that bounds the tilted
+boxes. However for "triclinic boxes"_Howto_triclinic.html, it only
+tests against the larger orthonormal box that bounds the tilted
simulation box. If the specified region includes volume outside the
tilted box, then an insertion will likely fail, leading to a "lost
atoms" error. Thus for triclinic boxes you should insure the
@@ -263,9 +263,9 @@ operation of the fix continues in an uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt
index 1c10d954d6eb910f5863120a405ace281b12e6da..f539bc534e76b7e667938ce4dcd78a2f9501ed4e 100644
--- a/doc/src/fix_dpd_energy.txt
+++ b/doc/src/fix_dpd_energy.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -50,10 +50,9 @@ examples/USER/dpd directory.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -65,8 +64,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_dpd_source.txt b/doc/src/fix_dpd_source.txt
index b6decc657cea412ac80a96ff4bcf7d8d84bb6348..04af9a28a184676e1ebc51f67dc13eb5340787a0 100644
--- a/doc/src/fix_dpd_source.txt
+++ b/doc/src/fix_dpd_source.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,10 +63,10 @@ cuboid domain to apply the source flux to.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_drag.txt b/doc/src/fix_drag.txt
index 235d3d38b5f97d91dae8a4fa3122e77486fbf7cd..92e68d13a447e07f9f83c4f5c2a1d1666cbdef53 100644
--- a/doc/src/fix_drag.txt
+++ b/doc/src/fix_drag.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -47,9 +47,9 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global 3-vector of forces, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. This is the
-total force on the group of atoms by the drag force. The vector
-values calculated by this fix are "extensive".
+by various "output commands"_Howto_output.html. This is the total
+force on the group of atoms by the drag force. The vector values
+calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_drude.txt b/doc/src/fix_drude.txt
index faa354b31439dbecf3dc8e04a3b31e47d1011757..80eb79201b2a8e5e0222337209bbacb074c6c78e 100644
--- a/doc/src/fix_drude.txt
+++ b/doc/src/fix_drude.txt
@@ -3,7 +3,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -25,10 +25,10 @@ fix 1 all drude C C N C N D D D :pre
[Description:]
Assign each atom type in the system to be one of 3 kinds of atoms
-within the Drude polarization model. This fix is designed to be
-used with the "thermalized Drude oscillator
-model"_tutorial_drude.html. Polarizable models in LAMMPS
-are described in "this Section"_Section_howto.html#howto_25.
+within the Drude polarization model. This fix is designed to be used
+with the "thermalized Drude oscillator model"_Howto_drude.html.
+Polarizable models in LAMMPS are described on the "Howto
+polarizable"_Howto_polarizable.html doc page.
The three possible types can be designated with an integer (0,1,2)
or capital letter (N,C,D):
diff --git a/doc/src/fix_drude_transform.txt b/doc/src/fix_drude_transform.txt
index 2e094d528c368ca35e59eb09d67abe2e2eb6198e..8864cc4eb66242f220bbc50a3e87e2e9abb5385a 100644
--- a/doc/src/fix_drude_transform.txt
+++ b/doc/src/fix_drude_transform.txt
@@ -9,7 +9,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,8 +34,8 @@ Transform the coordinates of Drude oscillators from real to reduced
and back for thermalizing the Drude oscillators as described in
"(Lamoureux)"_#Lamoureux1 using a Nose-Hoover thermostat. This fix is
designed to be used with the "thermalized Drude oscillator
-model"_tutorial_drude.html. Polarizable models in LAMMPS are
-described in "this Section"_Section_howto.html#howto_25.
+model"_Howto_drude.html. Polarizable models in LAMMPS are described
+on the "Howto polarizable"_Howto_polarizable.html doc page.
Drude oscillators are a pair of atoms representing a single
polarizable atom. Ideally, the mass of Drude particles would vanish
diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt
index 7605395ca05122bbde2a2600e2349b9026be4b56..be4fbd255b58983cd52ac8a9fbb1e4144b5a2f6c 100644
--- a/doc/src/fix_dt_reset.txt
+++ b/doc/src/fix_dt_reset.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -82,8 +82,8 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar stores
-the last timestep on which the timestep was reset to a new value.
+"output commands"_Howto_output.html. The scalar stores the last
+timestep on which the timestep was reset to a new value.
The scalar value calculated by this fix is "intensive".
diff --git a/doc/src/fix_efield.txt b/doc/src/fix_efield.txt
index 5d2b86fe4b9c1dcc3cc3b8ae5fd25802d5d1c1bd..b5a43f68aa76b5a205f50df3e6ff9325099711bb 100644
--- a/doc/src/fix_efield.txt
+++ b/doc/src/fix_efield.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -134,11 +134,10 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix adding its forces. Default is the outermost level.
This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar is the potential
-energy discussed above. The vector is the total force added to the
-group of atoms. The scalar and vector values calculated by this fix
-are "extensive".
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar is the potential energy discussed above. The vector is the
+total force added to the group of atoms. The scalar and vector values
+calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt
index 40752a811fdabe06285d0f980ee9cdd253ac10e6..cfcc917d012ba1dca5ff08afd75fb718bb101f82 100644
--- a/doc/src/fix_ehex.txt
+++ b/doc/src/fix_ehex.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt
index 4bbf41d25d13122c15f3da14ad8764e85d8346d9..2925e44bda17ef8cf023a9e41c0513694d4c50fa 100644
--- a/doc/src/fix_enforce2d.txt
+++ b/doc/src/fix_enforce2d.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,10 +31,9 @@ not move from their initial z coordinate.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -46,8 +45,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -56,9 +55,9 @@ more instructions on how to use the accelerated styles effectively.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
diff --git a/doc/src/fix_eos_cv.txt b/doc/src/fix_eos_cv.txt
index 4c973043353c307790aa15447d70ffe77f375e7d..b94e2c64a97ebd8373b3a3dafcee2ab9ecad6ed5 100644
--- a/doc/src/fix_eos_cv.txt
+++ b/doc/src/fix_eos_cv.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt
index 42778d79781c80ced6c90855f7fefe78f62d7207..743c51f4157cfeffc8c59840f9f95ab3132a3d74 100644
--- a/doc/src/fix_eos_table.txt
+++ b/doc/src/fix_eos_table.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt
index 0c878743471ae03c5bd76fec05f16dbc7631f01e..f9deab61c8acebfb5ffe69966b1880e7cacff369 100644
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -156,10 +156,9 @@ no 0.93 0.00 0.000 -1.76 :pre
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -171,8 +170,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt
index ed6c6d03775d5fe11195b3c3d6ccfc7eb365c909..6237a137fd0aa8c719d5f96f7791ebb176b669da 100644
--- a/doc/src/fix_evaporate.txt
+++ b/doc/src/fix_evaporate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -73,9 +73,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar, which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative number of deleted atoms. The scalar value calculated by
-this fix is "intensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+number of deleted atoms. The scalar value calculated by this fix is
+"intensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_external.txt b/doc/src/fix_external.txt
index 30e34b48587f2dd276dcd9bb50f398bc95f80a45..1dec226414c9f7e62b13b3d60a2f34efc6326ccd 100644
--- a/doc/src/fix_external.txt
+++ b/doc/src/fix_external.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,10 +31,10 @@ fix 1 all external pf/array 10 :pre
[Description:]
This fix allows external programs that are running LAMMPS through its
-"library interface"_Section_howto.html#howto_19 to modify certain
-LAMMPS properties on specific timesteps, similar to the way other
-fixes do. The external driver can be a "C/C++ or Fortran
-program"_Section_howto.html#howto_19 or a "Python script"_Python.html.
+"library interface"_Howto_library.html to modify certain LAMMPS
+properties on specific timesteps, similar to the way other fixes do.
+The external driver can be a "C/C++ or Fortran
+program"_Howto_library.html or a "Python script"_Python.html.
:line
@@ -136,9 +136,8 @@ external program to the system's virial as part of "thermodynamic
output"_thermo_style.html. The default is {virial yes}
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-potential energy discussed above. The scalar stored by this fix
-is "extensive".
+"output commands"_Howto_output.html. The scalar is the potential
+energy discussed above. The scalar stored by this fix is "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt
index b782d285c768ec6f4b25eaf29037cef6695e7613..d1e5e12f3ef1b764d4d2d9cc35a5d8f504c27a4e 100644
--- a/doc/src/fix_filter_corotate.txt
+++ b/doc/src/fix_filter_corotate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,10 +63,9 @@ No information about these fixes is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to these fixes. No global or per-atom quantities are
stored by these fixes for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of these fixes
-can be used with the {start/stop} keywords of the "run"_run.html
-command. These fixes are not invoked during "energy
-minimization"_minimize.html.
+commands"_Howto_output.html. No parameter of these fixes can be used
+with the {start/stop} keywords of the "run"_run.html command. These
+fixes are not invoked during "energy minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_flow_gauss.txt b/doc/src/fix_flow_gauss.txt
index efa58ea65fa8b71a940d707dbbabb5119ad90759..843c2a66a5505d5b3c7051fd9d84897a99ea4138 100644
--- a/doc/src/fix_flow_gauss.txt
+++ b/doc/src/fix_flow_gauss.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -128,11 +128,11 @@ integrator the fix computes and adds the external acceleration. Default is the
outermost level.
This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar is the negative of the
-work done on the system, see above discussion. The vector is the total force
-that this fix applied to the group of atoms on the current timestep.
-The scalar and vector values calculated by this fix are "extensive".
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar is the negative of the work done on the system, see above
+discussion. The vector is the total force that this fix applied to
+the group of atoms on the current timestep. The scalar and vector
+values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt
index a63ee4cb32688c286797292acbaa140fbed18101..76a9fd3b1a2d3f3ffc8372a2cebac2ac85f9fb6f 100644
--- a/doc/src/fix_freeze.txt
+++ b/doc/src/fix_freeze.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,12 +31,12 @@ using "fix setforce"_fix_setforce.html.
:line
-Styles with a suffix are functionally the same as the corresponding
-style without the suffix. They have been optimized to run faster,
-depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -48,8 +48,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -60,10 +60,10 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global 3-vector of forces, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. This is the
-total force on the group of atoms before the forces on individual
-atoms are changed by the fix. The vector values calculated by this
-fix are "extensive".
+by various "output commands"_Howto_output.html. This is the total
+force on the group of atoms before the forces on individual atoms are
+changed by the fix. The vector values calculated by this fix are
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt
index 191bc32b1499f1f4555330c8347bf49cb2472634..394690ea5d173b898b51acc6ee9b2094aa5d26b1 100644
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -382,8 +382,8 @@ None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix computes a global vector of length 8, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. The vector
-values are the following global cumulative quantities:
+by various "output commands"_Howto_output.html. The vector values are
+the following global cumulative quantities:
1 = translation attempts
2 = translation successes
diff --git a/doc/src/fix_gld.txt b/doc/src/fix_gld.txt
index 1425f62e13374d3c6f0feb14d624c63a1e2128cf..1c5db6157ddaca593ffc5fc70ebc59613038ae88 100644
--- a/doc/src/fix_gld.txt
+++ b/doc/src/fix_gld.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -126,7 +126,7 @@ sense, a restarted simulation should produce the same behavior.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15.
+access by various "output commands"_Howto_output.html.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt
index 6568060f0c2482c99607b1af93022a20ec0d6fe6..9fdc72bf9f206f9b5a6e55267638af159810beeb 100644
--- a/doc/src/fix_gle.txt
+++ b/doc/src/fix_gle.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,9 +116,9 @@ system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
[Restrictions:]
diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt
index dae8ac5ed0910fc2c91b776339de840707bf5500..832c677f81559e3893e643dc32330d0e9699a1f7 100644
--- a/doc/src/fix_gravity.txt
+++ b/doc/src/fix_gravity.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -90,10 +90,9 @@ field.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -105,8 +104,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -125,11 +124,11 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. This scalar is the
-gravitational potential energy of the particles in the defined field,
-namely mass * (g dot x) for each particles, where x and mass are the
-particles position and mass, and g is the gravitational field. The
-scalar value calculated by this fix is "extensive".
+"output commands"_Howto_output.html. This scalar is the gravitational
+potential energy of the particles in the defined field, namely mass *
+(g dot x) for each particles, where x and mass are the particles
+position and mass, and g is the gravitational field. The scalar value
+calculated by this fix is "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt
index 661f68ed99cf21d5c5a08514d78dff411a28880e..506e266505a54248fee381d4135802122fd86aba 100644
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt
index 08043eb5fb76659bf851d59444eeec56548b11cd..ec117518d285d488b28a78e552280f1ac7b81c17 100644
--- a/doc/src/fix_halt.txt
+++ b/doc/src/fix_halt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -133,10 +133,10 @@ files.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_heat.txt b/doc/src/fix_heat.txt
index 23db87dac27d8fc51d958bb1df857a0b6539e426..6db75926091bf4aac4e7fafa5679dab9e58231f4 100644
--- a/doc/src/fix_heat.txt
+++ b/doc/src/fix_heat.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -108,12 +108,11 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. This scalar is the
-most recent value by which velocites were scaled. The scalar value
-calculated by this fix is "intensive". If {eflux} is specified as
-an atom-style variable, this fix computes the average value by which
-the velocities were scaled for all of the atoms that had their
-velocities scaled.
+"output commands"_Howto_output.html. This scalar is the most recent
+value by which velocites were scaled. The scalar value calculated by
+this fix is "intensive". If {eflux} is specified as an atom-style
+variable, this fix computes the average value by which the velocities
+were scaled for all of the atoms that had their velocities scaled.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_imd.txt b/doc/src/fix_imd.txt
index b2756128191740d86ec6a9be5a18a831e48a0627..8e21a1619b8647b0ba6c497540ac2b7c4973b36a 100644
--- a/doc/src/fix_imd.txt
+++ b/doc/src/fix_imd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -136,9 +136,9 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+commands"_Howto_output.html. No parameter of this fix can be used
+with the {start/stop} keywords of the "run"_run.html command. This
+fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt
index c9a791ae4ece3069805ac86172ffae4805361076..9931793c0bffbc1398bee31bf7a5c87cda692d7d 100644
--- a/doc/src/fix_indent.txt
+++ b/doc/src/fix_indent.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -180,8 +180,8 @@ integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar energy and a global 3-vector of
forces (on the indenter), which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar and vector values
-calculated by this fix are "extensive".
+commands"_Howto_output.html. The scalar and vector values calculated
+by this fix are "extensive".
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command. Note that if you
diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt
index 07e8025d77061db6e41fd3c3e765898664f2ffcd..eba30ef08821d7c55ab06270d18a4300da293de5 100644
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt
index 93c73f5a5dd2390f93d80dfe7ce2d4efc7f53e69..4d7728cdba4b918d1cc8926f2aaef266bc20a42b 100644
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -101,7 +101,7 @@ should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix
temp/rescale"_fix_temp_rescale.html commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
+See the "Howto thermostat"_Howto_thermostat.html doc page for
a discussion of different ways to compute temperature and perform
thermostatting.
@@ -264,10 +264,9 @@ generates an average temperature of 220 K, instead of 300 K.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -279,8 +278,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -306,10 +305,10 @@ output"_thermo_style.html. Note that use of this option requires
setting the {tally} keyword to {yes}.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive". Note that calculation of this
-quantity requires setting the {tally} keyword to {yes}.
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive". Note that calculation of this quantity requires
+setting the {tally} keyword to {yes}.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt
index c85ff24c96d2982439d67c4ac52fd3bea5083044..19a3f87ffc0a20fb66038671e6a76529c5a1db6d 100644
--- a/doc/src/fix_langevin_drude.txt
+++ b/doc/src/fix_langevin_drude.txt
@@ -9,7 +9,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -44,8 +44,9 @@ fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes :pre
Apply two Langevin thermostats as described in "(Jiang)"_#Jiang1 for
thermalizing the reduced degrees of freedom of Drude oscillators.
This link describes how to use the "thermalized Drude oscillator
-model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS
-are discussed in "this Section"_Section_howto.html#howto_25.
+model"_Howto_drude.html in LAMMPS and polarizable models in LAMMPS
+are discussed on the "Howto polarizable"_Howto_polarizable.html doc
+page.
Drude oscillators are a way to simulate polarizables atoms, by
splitting them into a core and a Drude particle bound by a harmonic
@@ -99,8 +100,8 @@ Likewise, this fix should not normally be used on atoms that also have
their temperature controlled by another fix - e.g. by "fix
nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostating.
:line
diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt
index 4a50bfae54d1a058b3b31bf86159e838163ff87f..cf42f9c036b2dc4da5a9f2afb98296d8a78862d4 100644
--- a/doc/src/fix_langevin_eff.txt
+++ b/doc/src/fix_langevin_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -79,10 +79,10 @@ output"_thermo_style.html. Note that use of this option requires
setting the {tally} keyword to {yes}.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive". Note that calculation of this
-quantity requires setting the {tally} keyword to {yes}.
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive". Note that calculation of this quantity requires
+setting the {tally} keyword to {yes}.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt
index b089cd7f58148c74a805080cccde0ac2cb600143..1b1936376de0fe29450cf9b4c2db7e298e6d64ab 100644
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/src/fix_langevin_spin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt
index 4edd610546350ac082789fb517af918c7167c1f3..9bc589520bc3689a4ad4370f99e92b9977bb209c 100644
--- a/doc/src/fix_latte.txt
+++ b/doc/src/fix_latte.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -118,9 +118,9 @@ of "thermodynamic output"_thermo_style.html. The default is {virial
yes}
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-potential energy discussed above. The scalar value calculated by this
-fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the potential
+energy discussed above. The scalar value calculated by this fix is
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt
index fc6203b0f2c1967613e81b694977c9dd26accfcf..5347f0147f4be26b5e3b61877084925003c4fbf4 100644
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -299,9 +299,9 @@ is written to the main LAMMPS "binary restart files"_restart.html.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_lb_momentum.txt b/doc/src/fix_lb_momentum.txt
index 97965e870d95b70688428bd17304bdb83dce43e5..a58c5d257eabeb012284a3fd2dd3e2eecd20c1d7 100644
--- a/doc/src/fix_lb_momentum.txt
+++ b/doc/src/fix_lb_momentum.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -49,10 +49,10 @@ dimension.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can be
-used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt
index d2b6aafaab84a38d890abba5d5125ca5327f9687..bd121b7813253cb3b9e547235db88cdc85e5e472 100644
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,10 +34,10 @@ algorithm if the force coupling constant has been set by default.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can be
-used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/src/fix_lb_rigid_pc_sphere.txt
index 468ebe1ff5d31e8b224e6b864b3a8949eafd7c22..bc8fa2ea257212f588dabe01b824d98ff4289a1b 100644
--- a/doc/src/fix_lb_rigid_pc_sphere.txt
+++ b/doc/src/fix_lb_rigid_pc_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -80,12 +80,12 @@ assumes the constituent atoms are point particles); see
No information about the {rigid} and {rigid/nve} fixes are written to
"binary restart files"_restart.html.
-Similar to the "fix rigid"_fix_rigid.html command: The rigid
-fix computes a global scalar which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar value calculated by
-these fixes is "intensive". The scalar is the current temperature of
-the collection of rigid bodies. This is averaged over all rigid
-bodies and their translational and rotational degrees of freedom. The
+Similar to the "fix rigid"_fix_rigid.html command: The rigid fix
+computes a global scalar which can be accessed by various "output
+commands"_Howto_output.html. The scalar value calculated by these
+fixes is "intensive". The scalar is the current temperature of the
+collection of rigid bodies. This is averaged over all rigid bodies
+and their translational and rotational degrees of freedom. The
translational energy of a rigid body is 1/2 m v^2, where m = total
mass of the body and v = the velocity of its center of mass. The
rotational energy of a rigid body is 1/2 I w^2, where I = the moment
@@ -94,17 +94,17 @@ of freedom constrained by the {force} and {torque} keywords are
removed from this calculation.
All of these fixes compute a global array of values which can be
-accessed by various "output commands"_Section_howto.html#howto_15.
-The number of rows in the array is equal to the number of rigid
-bodies. The number of columns is 15. Thus for each rigid body, 15
-values are stored: the xyz coords of the center of mass (COM), the xyz
-components of the COM velocity, the xyz components of the force acting
-on the COM, the xyz components of the torque acting on the COM, and
-the xyz image flags of the COM, which have the same meaning as image
-flags for atom positions (see the "dump" command). The force and
-torque values in the array are not affected by the {force} and
-{torque} keywords in the fix rigid command; they reflect values before
-any changes are made by those keywords.
+accessed by various "output commands"_Howto_output.html. The number
+of rows in the array is equal to the number of rigid bodies. The
+number of columns is 15. Thus for each rigid body, 15 values are
+stored: the xyz coords of the center of mass (COM), the xyz components
+of the COM velocity, the xyz components of the force acting on the
+COM, the xyz components of the torque acting on the COM, and the xyz
+image flags of the COM, which have the same meaning as image flags for
+atom positions (see the "dump" command). The force and torque values
+in the array are not affected by the {force} and {torque} keywords in
+the fix rigid command; they reflect values before any changes are made
+by those keywords.
The ordering of the rigid bodies (by row in the array) is as follows.
For the {single} keyword there is just one rigid body. For the
diff --git a/doc/src/fix_lb_viscous.txt b/doc/src/fix_lb_viscous.txt
index fcc69d2b4315bd9a6695260efc0da5bafe27a0c2..7bbdd204e34d1a4fae91fcf2f4bb2aa4c32fefbf 100644
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -57,9 +57,9 @@ As described in the "fix viscous"_fix_viscous.html documentation:
"No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command. This fix should only
diff --git a/doc/src/fix_lineforce.txt b/doc/src/fix_lineforce.txt
index 65672fc5a5bdce5ca34fbff81f1c5fb0b94d6c07..3114ed62501e3c3c3581ae06a154c45de0d92996 100644
--- a/doc/src/fix_lineforce.txt
+++ b/doc/src/fix_lineforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,9 +35,9 @@ it should continue to move along the line thereafter.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
diff --git a/doc/src/fix_manifoldforce.txt b/doc/src/fix_manifoldforce.txt
index 5fc25167a7c7218097606cbbd77031a1cff0b709..aa32a875bfe2f77de00cdbee7f87085af8443a94 100644
--- a/doc/src/fix_manifoldforce.txt
+++ b/doc/src/fix_manifoldforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -36,10 +36,10 @@ I have found that only {hftn} and {quickmin} with a very small time step perform
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is invoked during "energy
+minimization"_minimize.html.
:line
diff --git a/doc/src/fix_meso.txt b/doc/src/fix_meso.txt
index 85f5838dd261fbd232a8fa570aaa20fc1391ef8a..8f5ad29929313fc6d1b31169b140b5dad0d46959 100644
--- a/doc/src/fix_meso.txt
+++ b/doc/src/fix_meso.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,10 +34,10 @@ LAMMPS.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_meso_stationary.txt b/doc/src/fix_meso_stationary.txt
index 5b83573bc8bcc58d2ad6aedc1d8b18c7d46f9368..38d26b34d67ad7d0a38eec70c7f28583394778eb 100644
--- a/doc/src/fix_meso_stationary.txt
+++ b/doc/src/fix_meso_stationary.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,10 +35,10 @@ LAMMPS.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt
index 308bba1ac31fdf9a7cbd45ec1da50122cd46bcb9..ddb5f9a4cd4346e6f0d3195a101445c15eaedfde 100644
--- a/doc/src/fix_modify.txt
+++ b/doc/src/fix_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt
index bcf4465fb8f5c9bc30626cc3275f422fd2158e9e..f7fe35be2a9fd3825b82db9a0cd3d3cca76dfb56 100644
--- a/doc/src/fix_momentum.txt
+++ b/doc/src/fix_momentum.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -61,10 +61,9 @@ initial velocities with zero aggregate linear and/or angular momentum.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -76,18 +75,18 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_move.txt b/doc/src/fix_move.txt
index 7cb40ad1320e365153d3d3165df06a8a1f064750..08f38d0ed65f2dec91bfec38fd572b8e82e75770 100644
--- a/doc/src/fix_move.txt
+++ b/doc/src/fix_move.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -203,10 +203,9 @@ None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix produces a per-atom array which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The number of columns
-for each atom is 3, and the columns store the original unwrapped x,y,z
-coords of each atom. The per-atom values can be accessed on any
-timestep.
+"output commands"_Howto_output.html. The number of columns for each
+atom is 3, and the columns store the original unwrapped x,y,z coords
+of each atom. The per-atom values can be accessed on any timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt
index 7d16967955d1d9988636092d721fe40902386054..aadc3caf5aa909c8ff32f23d51bcac2d3f0919ab 100644
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt
index 310692669abb39aaebb7e3596ee7f0b9e8cdf865..91ffbbb0fa147ea6e520ac75658d114198654da6 100644
--- a/doc/src/fix_msst.txt
+++ b/doc/src/fix_msst.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -156,8 +156,8 @@ thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_
These fixes compute a global scalar and a global vector of 4
quantities, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar values calculated
-by this fix are "extensive"; the vector values are "intensive".
+commands"_Howto_output.html. The scalar values calculated by this fix
+are "extensive"; the vector values are "intensive".
[Restrictions:]
diff --git a/doc/src/fix_mvv_dpd.txt b/doc/src/fix_mvv_dpd.txt
index fb3c6fe8885ce8a23b58897cd05a94269a20e5d7..1e9bf631fde813d95546bcc6638b3c24172a0e79 100644
--- a/doc/src/fix_mvv_dpd.txt
+++ b/doc/src/fix_mvv_dpd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -69,10 +69,10 @@ addition to position and velocity, and must be used with the
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt
index 5d18c39d994de3d58b752f7d595dfa4eb55e0019..5341d6999c4e6b0f5220af5d5d77ebd331176fbb 100644
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,9 +43,9 @@ Add nudging forces to atoms in the group for a multi-replica
simulation run via the "neb"_neb.html command to perform a nudged
elastic band (NEB) calculation for finding the transition state.
Hi-level explanations of NEB are given with the "neb"_neb.html command
-and in "Section_howto 5"_Section_howto.html#howto_5 of the manual.
-The fix neb command must be used with the "neb" command and defines
-how inter-replica nudging forces are computed. A NEB calculation is
+and on the "Howto replica"_Howto_replica.html doc page. The fix neb
+command must be used with the "neb" command and defines how
+inter-replica nudging forces are computed. A NEB calculation is
divided in two stages. In the first stage n replicas are relaxed
toward a MEP until convergence. In the second stage, the climbing
image scheme (see "(Henkelman2)"_#Henkelman2) is enabled, so that the
@@ -192,9 +192,9 @@ target energy.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
as invoked by the "minimize"_minimize.html command via the
diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt
index 41d0e6438fc9e05d08aa43d1548a98c0856ffd90..f6b155e2db2c66bad86e479a8d1ee67d86fd51a7 100644
--- a/doc/src/fix_nh.txt
+++ b/doc/src/fix_nh.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -386,9 +386,10 @@ have their temperature controlled by another fix - e.g. by "fix
langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html
commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
-thermostatting and barostatting.
+See the "Howto thermostat"_Howto_thermostat.html and "Howto
+barostat"_Howto_barostat.html doc pages for a discussion of different
+ways to compute temperature and perform thermostatting and
+barostatting.
:line
@@ -484,10 +485,9 @@ the various ways to do this.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -499,8 +499,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -538,9 +538,9 @@ and barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
These fixes compute a global scalar and a global vector of quantities,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar value calculated by
-these fixes is "extensive"; the vector values are "intensive".
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar value calculated by these fixes is "extensive"; the vector
+values are "intensive".
The scalar is the cumulative energy change due to the fix.
diff --git a/doc/src/fix_nh_eff.txt b/doc/src/fix_nh_eff.txt
index 1731f1f3317a6f982a564c256e593439a8f73423..afb319bfa51f6c518b213f63f75cbab14741e0bc 100644
--- a/doc/src/fix_nh_eff.txt
+++ b/doc/src/fix_nh_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt
index bde1818371f2c4bcab0bafe11e19c4b04df107b8..0e73c57e089b44643834f1b78fad2c1f046281f4 100644
--- a/doc/src/fix_nh_uef.txt
+++ b/doc/src/fix_nh_uef.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt
index 8c35b6a1a7a4b8bbd2fc98573764f99f0995249c..6bfd9d3fe26085cff9f1d3c5c0b32fbbd5c5948a 100644
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -81,10 +81,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -96,8 +95,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt
index 1e590f1cb3f3d5a46724d86e657d805a6a1906e3..377e1980eb3cf8c9c46b41baa6a14b2e379c7816 100644
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -80,10 +80,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt
index 62b45edfd7cd5ffbd8fe8ab48d5aefc29d3417ee..8b7639c4c6a7467e9107db127699efabea8a8993 100644
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -90,10 +90,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -105,8 +104,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt
index 292e46f94af6fcfe8e8c8b5b1e04908c2c55c9bc..0bd5153152b4afdcd8a0048b0472df81ad63ed08 100644
--- a/doc/src/fix_nphug.txt
+++ b/doc/src/fix_nphug.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -140,10 +140,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -155,8 +154,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -193,9 +192,9 @@ included in the definition of internal energy E when calculating the value
of Delta in the above equation.
These fixes compute a global scalar and a global vector of quantities,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar value calculated by
-these fixes is "extensive"; the vector values are "intensive".
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar value calculated by these fixes is "extensive"; the vector
+values are "intensive".
The scalar is the cumulative energy change due to the fix.
diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt
index 5f3979e36ed9e586f2eee15750364641348c040c..9c95a80d3310a08e3e8ddecd12af471419340773 100644
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -105,10 +105,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -120,8 +119,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt
index d89bf19db24fa7a988923a8cb5822cccc9641ed9..0d2b797299dd4d3c803e96cbfb1f4030ac13c032 100644
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -104,10 +104,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -119,8 +118,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt
index c4cf2cb08de85d8fe892f240473a0a90daa56de0..dcb25d1c737b39f3a2bcea9a4e01eb1a011fbb60 100644
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -115,10 +115,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -130,8 +129,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt
index c04c17858ebdf9b4166827a9cf5f52ed0f43e597..e446b273977b4dd05865de697b3d10af144bb149 100644
--- a/doc/src/fix_nve.txt
+++ b/doc/src/fix_nve.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,10 +34,9 @@ ensemble.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -49,8 +48,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -59,10 +58,10 @@ more instructions on how to use the accelerated styles effectively.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt
index 1f31fb96792239de806f99e78744106b0b08c1f7..b7fb3e922ce418d666b0cfe9b87170daa7c195ed 100644
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,20 +35,19 @@ assumes point particles and only updates their position and velocity.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt
index 5f1b2715464c01468494f8fb0da33bd46c1c5ec4..e57417bda5e1657ca69a621840ea82f2199b14b1 100644
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,10 +38,10 @@ Dynamics, since the velocity and angular momentum are updated by the
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt
index 604b5391cd180e064207ca3cd5a02d2335470ac7..d072bfa1611770921b5e97f7f1fb2bce2128c748 100644
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -24,9 +24,9 @@ fix 1 all nve/body :pre
Perform constant NVE integration to update position, velocity,
orientation, and angular velocity for body particles in the group each
timestep. V is volume; E is energy. This creates a system trajectory
-consistent with the microcanonical ensemble. See "Section
-6.14"_Section_howto.html#howto_14 of the manual and the "body"_body.html
-doc page for more details on using body particles.
+consistent with the microcanonical ensemble. See the "Howto
+body"_Howto_body.html doc page for more details on using body
+particles.
This fix differs from the "fix nve"_fix_nve.html command, which
assumes point particles and only updates their position and velocity.
@@ -36,10 +36,10 @@ assumes point particles and only updates their position and velocity.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt
index 0e0c8f8ecf5d9d02f3a6982ee1ae3e5cd8aa3746..1041a248d8784a0cfae575f1d5a515a4e2c76e35 100644
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt
index 93d875bca5436127526cdb5f1dad6b170d6c46b3..68c1b4232830fe1a2eaaadaf8ce832474a394f13 100644
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nve_eff.txt b/doc/src/fix_nve_eff.txt
index 156f184daceb6ee31c14168e65deecc43d7a9bc1..7343ddc4292df0f02e7eadef7829ec8041ccae5b 100644
--- a/doc/src/fix_nve_eff.txt
+++ b/doc/src/fix_nve_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,10 +35,10 @@ of electrons are also updated.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nve_limit.txt b/doc/src/fix_nve_limit.txt
index 2ecec83e9ce8bf5886a1d66dc4c50046a7f74882..8c8c66a0dac92424d08b577ee3957277e81e6ce2 100644
--- a/doc/src/fix_nve_limit.txt
+++ b/doc/src/fix_nve_limit.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,14 +63,14 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-count of how many updates of atom's velocity/position were limited by
-the maximum distance criterion. This should be roughly the number of
-atoms so affected, except that updates occur at both the beginning and
-end of a timestep in a velocity Verlet timestepping algorithm. This
-is a cumulative quantity for the current run, but is re-initialized to
-zero each time a run is performed. The scalar value calculated by
-this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the count of how
+many updates of atom's velocity/position were limited by the maximum
+distance criterion. This should be roughly the number of atoms so
+affected, except that updates occur at both the beginning and end of a
+timestep in a velocity Verlet timestepping algorithm. This is a
+cumulative quantity for the current run, but is re-initialized to zero
+each time a run is performed. The scalar value calculated by this fix
+is "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_nve_line.txt b/doc/src/fix_nve_line.txt
index ac5206aa5ce4ad1f9047bed437d96318498362d0..dd5101489b00d27a707ac4c044bed5f4a84be643 100644
--- a/doc/src/fix_nve_line.txt
+++ b/doc/src/fix_nve_line.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -24,9 +24,9 @@ fix 1 all nve/line :pre
Perform constant NVE integration to update position, velocity,
orientation, and angular velocity for line segment particles in the
group each timestep. V is volume; E is energy. This creates a system
-trajectory consistent with the microcanonical ensemble. See
-"Section 6.14"_Section_howto.html#howto_14 of the manual for an
-overview of using line segment particles.
+trajectory consistent with the microcanonical ensemble. See "Howto
+spherical"_Howto_spherical.html doc page for an overview of using line
+segment particles.
This fix differs from the "fix nve"_fix_nve.html command, which
assumes point particles and only updates their position and velocity.
@@ -36,10 +36,10 @@ assumes point particles and only updates their position and velocity.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt
index e032a7e1cc76408f8db42a9108662997a47e440d..b333d093fb8eec0ce08d16c8affb3a2cf481c802 100644
--- a/doc/src/fix_nve_manifold_rattle.txt
+++ b/doc/src/fix_nve_manifold_rattle.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,7 +40,7 @@ the dynamics of particles constrained to curved surfaces can be
studied. If combined with "fix langevin"_fix_langevin.html, this
generates Brownian motion of particles constrained to a curved
surface. For a list of currently supported manifolds and their
-parameters, see "manifolds"_manifolds.html.
+parameters, see the "Howto manifold"_Howto_manifold.html doc page.
Note that the particles must initially be close to the manifold in
question. If not, RATTLE will not be able to iterate until the
@@ -68,10 +68,10 @@ conserved.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
:line
diff --git a/doc/src/fix_nve_noforce.txt b/doc/src/fix_nve_noforce.txt
index a0dbcc80f18f0fc7d15f7b4503031fa80aaaa50c..da8d16bbb7c1c49bdee6af72dc4c1bcc2f355a1e 100644
--- a/doc/src/fix_nve_noforce.txt
+++ b/doc/src/fix_nve_noforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,10 +40,10 @@ fcm() group function to compute the total force on the group of atoms.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt
index 21dc6cba8a4aa7e067bcb9b0c066879e60b23479..6e259bdb8e7803482ee894d68d2a354dcefc0e6f 100644
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,10 +65,9 @@ moment of inertia, as used in the time integration.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -80,8 +79,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -90,10 +89,10 @@ more instructions on how to use the accelerated styles effectively.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt
index f4b38c270bc4b40b73c570ce590f39fc282bad1f..e31185bc889e785030dbef61a36019a7ba086af0 100644
--- a/doc/src/fix_nve_spin.txt
+++ b/doc/src/fix_nve_spin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nve_tri.txt b/doc/src/fix_nve_tri.txt
index cee27e2fa43087a2b6847a6f119fcb3792252259..ebdda19e36428828bdbeb6558b3202cc00982a80 100644
--- a/doc/src/fix_nve_tri.txt
+++ b/doc/src/fix_nve_tri.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -23,10 +23,10 @@ fix 1 all nve/tri :pre
Perform constant NVE integration to update position, velocity,
orientation, and angular momentum for triangular particles in the
-group each timestep. V is volume; E is energy. This creates a
-system trajectory consistent with the microcanonical ensemble. See
-"Section 6.14"_Section_howto.html#howto_14 of the manual for an
-overview of using triangular particles.
+group each timestep. V is volume; E is energy. This creates a system
+trajectory consistent with the microcanonical ensemble. See the
+"Howto spherical"_Howto_spherical.html doc page for an overview of
+using triangular particles.
This fix differs from the "fix nve"_fix_nve.html command, which
assumes point particles and only updates their position and velocity.
@@ -36,10 +36,10 @@ assumes point particles and only updates their position and velocity.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt
index 49fd8217ab7a88b90c23afc7ca56295e906ec245..e3189f8e8a3981b76f848f64080b6baa50500738 100644
--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -42,10 +42,10 @@ energy prior to this fix.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt
index 21b900f16ac69d3ef28b7b39fa90f232f43eb290..7b9763717574062e64b9e812bd201d8174cb4880 100644
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -86,10 +86,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -101,8 +100,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt
index 6a5e09ba7fb57ef45a91b9bf764e1f2e821fc34f..4493a892777221ee5c4375769438f8c02cfaf570 100644
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -85,10 +85,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -100,8 +99,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt
index a620648a460682c26780b67f9a4eddb3f21738ce..1b4ad7916626ea3550b69c4aef84514318acb30e 100644
--- a/doc/src/fix_nvt_manifold_rattle.txt
+++ b/doc/src/fix_nvt_manifold_rattle.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,9 +37,13 @@ fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0
[Description:]
-This fix combines the RATTLE-based "(Andersen)"_#Andersen2 time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the
-canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
-For a list of currently supported manifolds and their parameters, see "manifolds"_manifolds.html
+This fix combines the RATTLE-based "(Andersen)"_#Andersen2 time
+integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
+"(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the
+canonical ensemble of particles constrained to a curved surface
+(manifold). This sampling does suffer from discretization bias of
+O(dt). For a list of currently supported manifolds and their
+parameters, see the "Howto manifold"_Howto_manifold.html doc page.
:line
@@ -48,10 +52,10 @@ For a list of currently supported manifolds and their parameters, see "manifolds
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
:line
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index 392dbc281c6f5eee0fc164f4ed8eb6670bfbcbef..9eb506536910f574867121e26d6dee23ff8071a0 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -109,10 +109,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -124,8 +123,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt
index 408eb1da01f99bc026a4581bedbb4ecff2a91b6a..0200d5cb002312980fb21344687676dd06d74fee 100644
--- a/doc/src/fix_nvt_sllod_eff.txt
+++ b/doc/src/fix_nvt_sllod_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt
index ecf0922b7901a154f0728579b41d6e9502b2f3d0..a87e4abe677ed4c44d6b54470e5d2ee9539d8f7c 100644
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -96,10 +96,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -111,8 +110,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_oneway.txt b/doc/src/fix_oneway.txt
index 2d85c581ebd95ec5cfdf27129ee39ae1c73532d5..433ceb50f244e7570b83979dffed7c5b34d7a8ca 100644
--- a/doc/src/fix_oneway.txt
+++ b/doc/src/fix_oneway.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,10 +43,10 @@ membrane, or as an implementation of Maxwell's demon.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt
index 20ff94866ea3ad0c92fde75042cad455494bcc92..7552bea8c5bcfb73867322c90f502887276aacf9 100644
--- a/doc/src/fix_orient.txt
+++ b/doc/src/fix_orient.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -135,14 +135,14 @@ fixes. This allows to set at which level of the "r-RESPA"_run_style.html
integrator a fix is adding its forces. Default is the outermost level.
This fix calculates a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-potential energy change due to this fix. The scalar value calculated
-by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the potential
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
This fix also calculates a per-atom array which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The array
-stores the order parameter Xi and normalized order parameter (0 to 1)
-for each atom. The per-atom values can be accessed on any timestep.
+various "output commands"_Howto_output.html. The array stores the
+order parameter Xi and normalized order parameter (0 to 1) for each
+atom. The per-atom values can be accessed on any timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt
index aad6c2bfaa401bcb0af6e76851f849cb67c1af0c..30e5864e3d16af76cdc86ea021c0cf80fda6b2ff 100644
--- a/doc/src/fix_phonon.txt
+++ b/doc/src/fix_phonon.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -150,7 +150,7 @@ fix. You can use it to change the temperature compute from thermo_temp
to the one that reflects the true temperature of atoms in the group.
No global scalar or vector or per-atom quantities are stored by this
-fix for access by various "output commands"_Section_howto.html#howto_15.
+fix for access by various "output commands"_Howto_output.html.
Instead, this fix outputs its initialization information (including
mapping information) and the calculated dynamical matrices to the file
diff --git a/doc/src/fix_pimd.txt b/doc/src/fix_pimd.txt
index 38022e4c7dd3d6d2e2bb1b0a56177fae2918604c..b61b3f3065a7c0c57f5994a2a2a23d6ed8778407 100644
--- a/doc/src/fix_pimd.txt
+++ b/doc/src/fix_pimd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -103,14 +103,13 @@ is appropriate for most situations.
The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
as described in "(Calhoun)"_#Calhoun. In LAMMPS this is done by using
-"multi-replica feature"_Section_howto.html#howto_5 in LAMMPS, where
-each quasi-particle system is stored and simulated on a separate
-partition of processors. The following diagram illustrates this
-approach. The original system with 2 ring polymers is shown in red.
-Since each ring has 4 quasi-beads (imaginary time slices), there are 4
-replicas of the system, each running on one of the 4 partitions of
-processors. Each replica (shown in green) owns one quasi-bead in each
-ring.
+"multi-replica feature"_Howto_replica.html in LAMMPS, where each
+quasi-particle system is stored and simulated on a separate partition
+of processors. The following diagram illustrates this approach. The
+original system with 2 ring polymers is shown in red. Since each ring
+has 4 quasi-beads (imaginary time slices), there are 4 replicas of the
+system, each running on one of the 4 partitions of processors. Each
+replica (shown in green) owns one quasi-bead in each ring.
:c,image(JPG/pimd.jpg)
diff --git a/doc/src/fix_planeforce.txt b/doc/src/fix_planeforce.txt
index 67956c8b6ddfdcf7c3cfe0520f0fa888b4c9c87c..ffe1952e31a2f412ce23edf7b36a891b42f70f38 100644
--- a/doc/src/fix_planeforce.txt
+++ b/doc/src/fix_planeforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,9 +35,9 @@ should continue to move in the plane thereafter.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt
index 03abc058b8b0d6e982f6291e1fecbb887cf2ad9a..1a79c2a048fb75dc04935e978fdc50ae84ab9e69 100644
--- a/doc/src/fix_poems.txt
+++ b/doc/src/fix_poems.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -114,9 +114,9 @@ early or late in a timestep, i.e. at the post-force stage or at the
final-integrate stage, respectively.
No global or per-atom quantities are stored by this fix for access by
-various "output commands"_Section_howto.html#howto_15. No parameter
-of this fix can be used with the {start/stop} keywords of the
-"run"_run.html command. This fix is not invoked during "energy
+various "output commands"_Howto_output.html. No parameter of this fix
+can be used with the {start/stop} keywords of the "run"_run.html
+command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt
index 54f78287e01d98368f1938122b1c9317e8446659..e58d8ebc3ad90069a45cfd92ae504ce4656305dc 100644
--- a/doc/src/fix_pour.txt
+++ b/doc/src/fix_pour.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -237,9 +237,9 @@ appropriately.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt
index 4133d7dd57f42993ad8454d4d3e90973eccad34b..fafe78448be133680f5b22711403262f1f28086b 100644
--- a/doc/src/fix_precession_spin.txt
+++ b/doc/src/fix_precession_spin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -67,8 +67,8 @@ to add this magnetic potential energy to the potential energy of the system,
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix_modify 1 energy yes :pre
-This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15.
+This fix computes a global scalar which can be accessed by various
+"output commands"_Howto_output.html.
No information about this fix is written to "binary restart
files"_restart.html.
diff --git a/doc/src/fix_press_berendsen.txt b/doc/src/fix_press_berendsen.txt
index 9c9da8ec7b052f9e91651fa6adca5ee3ae675166..7f47a29ba35fa0a1ca9cc0c3aebd51917131564d 100644
--- a/doc/src/fix_press_berendsen.txt
+++ b/doc/src/fix_press_berendsen.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -58,9 +58,8 @@ to control the temperature, such as "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html or "fix
temp/berendsen"_fix_temp_berendsen.html.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
-thermostatting and barostatting.
+See the "Howto baroostat"_Howto_barostat.html doc page for a
+discussion of different ways to perform barostatting.
:line
@@ -196,7 +195,7 @@ pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
No global or per-atom quantities are stored by this fix for access by
-various "output commands"_Section_howto.html#howto_15.
+various "output commands"_Howto_output.html.
This fix can ramp its target pressure over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_print.txt b/doc/src/fix_print.txt
index cf3b542833b6d951e2b160797998e28406867758..d23c1103d3000963e8efcf4600080f79bf3eac20 100644
--- a/doc/src/fix_print.txt
+++ b/doc/src/fix_print.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -73,10 +73,10 @@ where ID is replaced with the fix-ID.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt
index 95fc2c424db6252553a8cd51583a8aa85bbe5d05..136ed6c15e6ecb9de65599eb41a821d6487bbf69 100644
--- a/doc/src/fix_property_atom.txt
+++ b/doc/src/fix_property_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -200,18 +200,17 @@ added classes.
:line
-:link(isotopes)
-Example for using per-atom masses with TIP4P water to study isotope
-effects. When setting up simulations with the "TIP4P pair
-styles"_Section_howto.html#howto_8 for water, you have to provide
-exactly one atom type each to identify the water oxygen and hydrogen
+:link(isotopes) Example for using per-atom masses with TIP4P water to
+study isotope effects. When setting up simulations with the "TIP4P
+pair styles"_Howto_tip4p.html for water, you have to provide exactly
+one atom type each to identify the water oxygen and hydrogen
atoms. Since the atom mass is normally tied to the atom type, this
makes it impossible to study multiple isotopes in the same simulation.
With {fix property/atom rmass} however, the per-type masses are
replaced by per-atom masses. Asumming you have a working input deck
-for regular TIP4P water, where water oxygen is atom type 1 and
-water hydrogen is atom type 2, the following lines of input script
-convert this to using per-atom masses:
+for regular TIP4P water, where water oxygen is atom type 1 and water
+hydrogen is atom type 2, the following lines of input script convert
+this to using per-atom masses:
fix Isotopes all property/atom rmass ghost yes
set type 1 mass 15.9994
@@ -247,12 +246,12 @@ command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
-None of the "fix_modify"_fix_modify.html options
-are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix. No global or per-atom quantities are stored by this fix for
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_python_invoke.txt b/doc/src/fix_python_invoke.txt
index 787940d9ebc4de8cd334a21454fe58dd6fa7b341..5e0c0369a54b62f81c5c14c6360d182c1f655df0 100644
--- a/doc/src/fix_python_invoke.txt
+++ b/doc/src/fix_python_invoke.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_python_move.txt b/doc/src/fix_python_move.txt
index f10f607a9bc29ca630445664b844d9c1fce36fe5..a4e0eb39376ea0945bd667ce6625c406b697534a 100644
--- a/doc/src/fix_python_move.txt
+++ b/doc/src/fix_python_move.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -83,10 +83,10 @@ Examples for how to do this are in the {examples/python} folder.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_qbmsst.txt b/doc/src/fix_qbmsst.txt
index 2c116fb0f8cf34f6e29143035d0c9cc7414e2750..e96bd97f4587cfa7446b5adc5606a6f4e13df09d 100644
--- a/doc/src/fix_qbmsst.txt
+++ b/doc/src/fix_qbmsst.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -179,10 +179,10 @@ thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_
The global scalar under the entry f_fix_id is the quantity of thermo
energy as an extra part of <i>etot</i>. This global scalar and the
vector of 5 quantities can be accessed by various "output
-commands"_Section_howto.html#howto_15. It is worth noting that the
-temp keyword under the "thermo_style"_thermo_style.html command print
-the instantaneous classical temperature <i>T</i><sup>cl</sup> as
-described in the command "fix qtb"_fix_qtb.html.
+commands"_Howto_output.html. It is worth noting that the temp keyword
+under the "thermo_style"_thermo_style.html command print the
+instantaneous classical temperature <i>T</i><sup>cl</sup> as described
+in the command "fix qtb"_fix_qtb.html.
:line
diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt
index 194361e990afdedbfccecf47be254c71df4623b7..27fb613ef957fc91f280f5eccf7328afcc1cdb35 100644
--- a/doc/src/fix_qeq.txt
+++ b/doc/src/fix_qeq.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -179,9 +179,8 @@ parameters. See the examples/qeq directory for some examples.
No information about these fixes is written to "binary restart
files"_restart.html. No global scalar or vector or per-atom
quantities are stored by these fixes for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of these fixes
-can be used with the {start/stop} keywords of the "run"_run.html
-command.
+commands"_Howto_output.html. No parameter of these fixes can be used
+with the {start/stop} keywords of the "run"_run.html command.
Thexe fixes are invoked during "energy minimization"_minimize.html.
diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt
index 7f82404127fc61f6c3225f1c0d9b960bad470e27..99e86df030fb80215b1dfceab6d521fd8f4167f8 100644
--- a/doc/src/fix_qeq_comb.txt
+++ b/doc/src/fix_qeq_comb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -62,10 +62,9 @@ equilibration calculation is written to the specified file.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -77,8 +76,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -93,9 +92,9 @@ integrator the fix is performing charge equilibration. Default is
the outermost level.
This fix produces a per-atom vector which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The vector stores the
-gradient of the charge on each atom. The per-atom values be accessed
-on any timestep.
+"output commands"_Howto_output.html. The vector stores the gradient
+of the charge on each atom. The per-atom values be accessed on any
+timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt
index 18450c7cd5c0852c30e2324f3c683d84a2b63479..cf16daf84731096ec617c9abce809de80764ee73 100644
--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -70,8 +70,8 @@ the {qeq/reax/omp} style. Otherwise they are processed separately.
No information about this fix is written to "binary restart
files"_restart.html. No global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+commands"_Howto_output.html. No parameter of this fix can be used
+with the {start/stop} keywords of the "run"_run.html command.
This fix is invoked during "energy minimization"_minimize.html.
@@ -80,10 +80,9 @@ This fix is invoked during "energy minimization"_minimize.html.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt
index 1b4a850a42f7740ba4649d0a5cd8e494537987b3..657ee841810a25338390cb7c14d6218691dfd6c1 100644
--- a/doc/src/fix_qmmm.txt
+++ b/doc/src/fix_qmmm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -46,9 +46,9 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+commands"_Howto_output.html. No parameter of this fix can be used
+with the {start/stop} keywords of the "run"_run.html command. This
+fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_qtb.txt b/doc/src/fix_qtb.txt
index 07a6af39ba2f81db6ed16cce0eb93d39ac98b65b..5b212934a94780b1d6e34c8c90873519b1bcc543 100644
--- a/doc/src/fix_qtb.txt
+++ b/doc/src/fix_qtb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt
index 3f8f237de1c7d574bfc214b9dfec2892e11b3793..49d61f4db80d45f1993bec664a07bc249f259ca1 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -62,17 +62,17 @@ version, but will also take longer to write.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section_accelerate"_Section_accelerate.html
+hardware, as discussed in "Speed"_Speed.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -87,7 +87,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section_accelerate"_Section_accelerate.html of the manual for
+See "Speed"_Speed.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt
index 7c920791f7b10bd923da0402c35a8215a15bf650..5be1c46230b477e62f07ff70c9dcf02c03ef7da3 100644
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,8 +116,8 @@ are relevant to this fix.
This fix computes both a global vector of length 2 and a per-atom
vector, either of which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The values in the global
-vector are "intensive".
+commands"_Howto_output.html. The values in the global vector are
+"intensive".
The 2 values in the global vector are as follows:
@@ -139,7 +139,7 @@ minimization"_minimize.html.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section_accelerate"_Section_accelerate.html
+hardware, as discussed in "Speed"_Speed.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -154,7 +154,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section_accelerate"_Section_accelerate.html of the manual for
+See "Speed"_Speed.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_recenter.txt b/doc/src/fix_recenter.txt
index 342bed42515f8b827cc18a1cd228480480bd70f0..cfac756cd1659f9d8e7fcc6abc2922104a6b7bb0 100644
--- a/doc/src/fix_recenter.txt
+++ b/doc/src/fix_recenter.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -94,13 +94,13 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-distance the group is moved by fix recenter.
+"output commands"_Howto_output.html. The scalar is the distance the
+group is moved by fix recenter.
This fix also computes global 3-vector which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The 3
-quantities in the vector are xyz components of displacement applied to
-the group of atoms by the fix.
+various "output commands"_Howto_output.html. The 3 quantities in the
+vector are xyz components of displacement applied to the group of
+atoms by the fix.
The scalar and vector values calculated by this fix are "extensive".
diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt
index 9de63defb700fb0f713187d87f4077fd35b86e0f..2edc7e32963bb94c3bd60158bd21f94ba123e0a4 100644
--- a/doc/src/fix_restrain.txt
+++ b/doc/src/fix_restrain.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -187,8 +187,8 @@ added forces to be included in the total potential energy of the
system (the quantity being minimized), you MUST enable the
"fix_modify"_fix_modify.html {energy} option for this fix.
-This fix computes a global scalar and a global vector of length 3, which
-can be accessed by various "output commands"_Section_howto.html#howto_15.
+This fix computes a global scalar and a global vector of length 3,
+which can be accessed by various "output commands"_Howto_output.html.
The scalar is the total potential energy for {all} the restraints as
discussed above. The vector values are the sum of contributions to the
following individual categories:
diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt
index 2db920ac4bef02c60f95604beb5e6feeb9cb7de6..68cce694e9b46eb71275eb61b5af3ad877eb1fa5 100644
--- a/doc/src/fix_rhok.txt
+++ b/doc/src/fix_rhok.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index 8d803ac6dacfcb4483fb4d66a204e8f3cba6989e..d5e3b0166810dd39613d4a9105d9ac0ed43e86b9 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -690,10 +690,9 @@ rigid/nvt.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -705,8 +704,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -746,29 +745,29 @@ computed early or late in a timestep, i.e. at the post-force stage or
at the final-integrate stage or the timestep, respectively.
The 2 NVE rigid fixes compute a global scalar which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The scalar
-value calculated by these fixes is "intensive". The scalar is the
-current temperature of the collection of rigid bodies. This is
-averaged over all rigid bodies and their translational and rotational
-degrees of freedom. The translational energy of a rigid body is 1/2 m
-v^2, where m = total mass of the body and v = the velocity of its
-center of mass. The rotational energy of a rigid body is 1/2 I w^2,
-where I = the moment of inertia tensor of the body and w = its angular
-velocity. Degrees of freedom constrained by the {force} and {torque}
-keywords are removed from this calculation, but only for the {rigid}
-and {rigid/nve} fixes.
+various "output commands"_Howto_output.html. The scalar value
+calculated by these fixes is "intensive". The scalar is the current
+temperature of the collection of rigid bodies. This is averaged over
+all rigid bodies and their translational and rotational degrees of
+freedom. The translational energy of a rigid body is 1/2 m v^2, where
+m = total mass of the body and v = the velocity of its center of mass.
+The rotational energy of a rigid body is 1/2 I w^2, where I = the
+moment of inertia tensor of the body and w = its angular velocity.
+Degrees of freedom constrained by the {force} and {torque} keywords
+are removed from this calculation, but only for the {rigid} and
+{rigid/nve} fixes.
The 6 NVT, NPT, NPH rigid fixes compute a global scalar which can be
-accessed by various "output commands"_Section_howto.html#howto_15.
-The scalar value calculated by these fixes is "extensive". The scalar
-is the cumulative energy change due to the thermostatting and
-barostatting the fix performs.
+accessed by various "output commands"_Howto_output.html. The scalar
+value calculated by these fixes is "extensive". The scalar is the
+cumulative energy change due to the thermostatting and barostatting
+the fix performs.
All of the {rigid} styles (not the {rigid/small} styles) compute a
global array of values which can be accessed by various "output
-commands"_Section_howto.html#howto_15. Similar information about the
-bodies defined by the {rigid/small} styles can be accessed via the
-"compute rigid/local"_compute_rigid_local.html command.
+commands"_Howto_output.html. Similar information about the bodies
+defined by the {rigid/small} styles can be accessed via the "compute
+rigid/local"_compute_rigid_local.html command.
The number of rows in the array is equal to the number of rigid
bodies. The number of columns is 15. Thus for each rigid body, 15
diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt
index 0810a347408f33cf20586448cf2141fb4c037275..d39e41e922d16158b2f643e4b0d4eb60e900493a 100644
--- a/doc/src/fix_rx.txt
+++ b/doc/src/fix_rx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -186,10 +186,9 @@ read_data data.dpd fix foo_SPECIES NULL Species
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -201,8 +200,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_saed_vtk.txt b/doc/src/fix_saed_vtk.txt
index 814e17b8e952ad71d3ffe918c99596a0d10dc575..60708cd6962cfa57823d1a3c3d33ba1b50a5f661 100644
--- a/doc/src/fix_saed_vtk.txt
+++ b/doc/src/fix_saed_vtk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt
index f5be0f93a54c459ead80c691dd4905df678760c4..14fceb7b49e87a01596f1e8f131c4aecd84d26de 100644
--- a/doc/src/fix_setforce.txt
+++ b/doc/src/fix_setforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,12 +65,12 @@ to it.
:line
-Styles with a r {kk} suffix are functionally the same as the
-corresponding style without the suffix. They have been optimized to
-run faster, depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
The region keyword is also supported by Kokkos, but a Kokkos-enabled
region must be used. See the region "region"_region.html command for
@@ -85,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -103,10 +103,10 @@ so that setforce values are not counted multiple times. Default is to
to override forces at the outermost level.
This fix computes a global 3-vector of forces, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. This is the
-total force on the group of atoms before the forces on individual
-atoms are changed by the fix. The vector values calculated by this
-fix are "extensive".
+by various "output commands"_Howto_output.html. This is the total
+force on the group of atoms before the forces on individual atoms are
+changed by the fix. The vector values calculated by this fix are
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index 46452a1f7e932eaf2531525f7ee6d557fceffb37..ea38de41cd1ba8b0ad9f2c759db429666798f524 100644
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -145,12 +145,12 @@ info of atoms in the molecule.
:line
-Styles with a suffix are functionally the same as the corresponding
-style without the suffix. They have been optimized to run faster,
-depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -162,8 +162,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -195,10 +195,9 @@ No information about these fixes is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to these fixes. No global or per-atom quantities are
stored by these fixes for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of these fixes
-can be used with the {start/stop} keywords of the "run"_run.html
-command. These fixes are not invoked during "energy
-minimization"_minimize.html.
+commands"_Howto_output.html. No parameter of these fixes can be used
+with the {start/stop} keywords of the "run"_run.html command. These
+fixes are not invoked during "energy minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt
index 24726d8610abf0a79db6e14b163731d61ff46404..33db2bf7cc9e25d81e6b842e6b8282d6ed5feb07 100644
--- a/doc/src/fix_shardlow.txt
+++ b/doc/src/fix_shardlow.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -56,10 +56,9 @@ examples/USER/dpd directory.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -71,8 +70,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt
index cb4a40f0fd0a3cbea0f95de29562e5e4faea110b..2f083dafc337f887ab75da54c4859dd901701844 100644
--- a/doc/src/fix_smd.txt
+++ b/doc/src/fix_smd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -111,12 +111,12 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a vector list of 7 quantities, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. The
-quantities in the vector are in this order: the x-, y-, and
-z-component of the pulling force, the total force in direction of the
-pull, the equilibrium distance of the spring, the distance between the
-two reference points, and finally the accumulated PMF (the sum of
-pulling forces times displacement).
+by various "output commands"_Howto_output.html. The quantities in the
+vector are in this order: the x-, y-, and z-component of the pulling
+force, the total force in direction of the pull, the equilibrium
+distance of the spring, the distance between the two reference points,
+and finally the accumulated PMF (the sum of pulling forces times
+displacement).
The force is the total force on the group of atoms by the spring. In
the case of the {couple} style, it is the force on the fix group
diff --git a/doc/src/fix_smd_adjust_dt.txt b/doc/src/fix_smd_adjust_dt.txt
index 86b7363300929bada7f049fae3f3c13cf3cec11f..740b10559d8aced34b4c1428bb355b20c144f325 100644
--- a/doc/src/fix_smd_adjust_dt.txt
+++ b/doc/src/fix_smd_adjust_dt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/src/fix_smd_integrate_tlsph.txt
index 17c9c0f400f4cdf5dfc67966d5b1f51d4d0f4672..cd676a51ce3cdc3eb1978e8d8d29ff7f3acc7832 100644
--- a/doc/src/fix_smd_integrate_tlsph.txt
+++ b/doc/src/fix_smd_integrate_tlsph.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/src/fix_smd_integrate_ulsph.txt
index 28e38c7f970a9d99a07294bd77f4fb66a54ced00..7f16b4b7ceabf7288252e5be36e84bda4c949465 100644
--- a/doc/src/fix_smd_integrate_ulsph.txt
+++ b/doc/src/fix_smd_integrate_ulsph.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt
index 2cba001267433e921d908bd9d344cb1152886fde..aeabf187686e105a9af292b6e5fd93ab01216095 100644
--- a/doc/src/fix_smd_move_triangulated_surface.txt
+++ b/doc/src/fix_smd_move_triangulated_surface.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_smd_setvel.txt b/doc/src/fix_smd_setvel.txt
index f93a7d0965b3eecb29dd130db7bbfbe0ae64bd63..6634751d6ad9e1ef17333982a7826b1c1e7d724b 100644
--- a/doc/src/fix_smd_setvel.txt
+++ b/doc/src/fix_smd_setvel.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -66,9 +66,9 @@ None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global 3-vector of forces, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. This is the
-total force on the group of atoms. The vector values calculated by this
-fix are "extensive".
+by various "output commands"_Howto_output.html. This is the total
+force on the group of atoms. The vector values calculated by this fix
+are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt
index feb65b2312823ece1b261e5349750500018b6ed7..a19b2c4cfb7eb2478ca21f684589491127b71eab 100644
--- a/doc/src/fix_smd_wall_surface.txt
+++ b/doc/src/fix_smd_wall_surface.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_spring.txt b/doc/src/fix_spring.txt
index 014a43aacc706e03b37ceb37ca906a1fb248f275..690fc3e67c381a9cddd7469e22d9a925f75e4c14 100644
--- a/doc/src/fix_spring.txt
+++ b/doc/src/fix_spring.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -105,19 +105,19 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-spring energy = 0.5 * K * r^2.
+"output commands"_Howto_output.html. The scalar is the spring energy
+= 0.5 * K * r^2.
This fix also computes global 4-vector which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The first 3
-quantities in the vector are xyz components of the total force added
-to the group of atoms by the spring. In the case of the {couple}
-style, it is the force on the fix group (group-ID) or the negative of
-the force on the 2nd group (group-ID2). The 4th quantity in the
-vector is the magnitude of the force added by the spring, as a
-positive value if (r-R0) > 0 and a negative value if (r-R0) < 0. This
-sign convention can be useful when using the spring force to compute a
-potential of mean force (PMF).
+various "output commands"_Howto_output.html. The first 3 quantities
+in the vector are xyz components of the total force added to the group
+of atoms by the spring. In the case of the {couple} style, it is the
+force on the fix group (group-ID) or the negative of the force on the
+2nd group (group-ID2). The 4th quantity in the vector is the
+magnitude of the force added by the spring, as a positive value if
+(r-R0) > 0 and a negative value if (r-R0) < 0. This sign convention
+can be useful when using the spring force to compute a potential of
+mean force (PMF).
The scalar and vector values calculated by this fix are "extensive".
diff --git a/doc/src/fix_spring_chunk.txt b/doc/src/fix_spring_chunk.txt
index 7630a009dd3bbfd9d087f5b57060f8f56c216227..9d4e8afd090e3a0ea9bc12af04cf1db4b53b6945 100644
--- a/doc/src/fix_spring_chunk.txt
+++ b/doc/src/fix_spring_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -60,8 +60,8 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-energy of all the springs, i.e. 0.5 * K * r^2 per-spring.
+"output commands"_Howto_output.html. The scalar is the energy of all
+the springs, i.e. 0.5 * K * r^2 per-spring.
The scalar value calculated by this fix is "extensive".
diff --git a/doc/src/fix_spring_rg.txt b/doc/src/fix_spring_rg.txt
index bff6b38e7e94c44477c07e94efb0b72f909dfc43..b252163958fe5b983faeb2fc25e976bcf602f211 100644
--- a/doc/src/fix_spring_rg.txt
+++ b/doc/src/fix_spring_rg.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -51,10 +51,10 @@ the time the fix is specified, and that value is used as the target.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
The "fix_modify"_fix_modify.html {respa} option is supported by this
fix. This allows to set at which level of the "r-RESPA"_run_style.html
diff --git a/doc/src/fix_spring_self.txt b/doc/src/fix_spring_self.txt
index 68961a1512d1ba80ddd72da8024333cc51180103..0ac1d5eecb627a363b900d5af01ebef318e200b0 100644
--- a/doc/src/fix_spring_self.txt
+++ b/doc/src/fix_spring_self.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -57,10 +57,10 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is an
-energy which is the sum of the spring energy for each atom, where the
-per-atom energy is 0.5 * K * r^2. The scalar value calculated by this
-fix is "extensive".
+"output commands"_Howto_output.html. The scalar is an energy which is
+the sum of the spring energy for each atom, where the per-atom energy
+is 0.5 * K * r^2. The scalar value calculated by this fix is
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt
index 4e190234fd2b873cb5592c9c335304b53245d5c1..893557b9acad71bd2f1be0690a3b0694b68022f6 100644
--- a/doc/src/fix_srd.txt
+++ b/doc/src/fix_srd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -341,11 +341,11 @@ are relevant to this fix.
This fix tabulates several SRD statistics which are stored in a vector
of length 12, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The vector values calculated
-by this fix are "intensive", meaning they do not scale with the size
-of the simulation. Technically, the first 8 do scale with the size of
-the simulation, but treating them as intensive means they are not
-scaled when printed as part of thermodynamic output.
+commands"_Howto_output.html. The vector values calculated by this fix
+are "intensive", meaning they do not scale with the size of the
+simulation. Technically, the first 8 do scale with the size of the
+simulation, but treating them as intensive means they are not scaled
+when printed as part of thermodynamic output.
These are the 12 quantities. All are values for the current timestep,
except for quantity 5 and the last three, each of which are
diff --git a/doc/src/fix_store_force.txt b/doc/src/fix_store_force.txt
index c988431f9de8dc47b85bfbce1d9cc82de1228270..33ebc962d5da9def4a817dbf6a1e9cdb78c5e4ad 100644
--- a/doc/src/fix_store_force.txt
+++ b/doc/src/fix_store_force.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -26,7 +26,7 @@ timestep when the fix is invoked, as described below. This is useful
for storing forces before constraints or other boundary conditions are
computed which modify the forces, so that unmodified forces can be
"written to a dump file"_dump.html or accessed by other "output
-commands"_Section_howto.html#howto_15 that use per-atom quantities.
+commands"_Howto_output.html that use per-atom quantities.
This fix is invoked at the point in the velocity-Verlet timestepping
immediately after "pair"_pair_style.html, "bond"_bond_style.html,
@@ -54,9 +54,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix produces a per-atom array which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The number of columns
-for each atom is 3, and the columns store the x,y,z forces on each
-atom. The per-atom values be accessed on any timestep.
+"output commands"_Howto_output.html. The number of columns for each
+atom is 3, and the columns store the x,y,z forces on each atom. The
+per-atom values be accessed on any timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_store_state.txt b/doc/src/fix_store_state.txt
index df694fb97b4e2dd037d41a21b1200b89d3c3594a..df05adc5b9ceb274061dab5bc7a0dbfc5cc395dd 100644
--- a/doc/src/fix_store_state.txt
+++ b/doc/src/fix_store_state.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -68,8 +68,7 @@ Define a fix that stores attributes for each atom in the group at the
time the fix is defined. If {N} is 0, then the values are never
updated, so this is a way of archiving an atom attribute at a given
time for future use in a calculation or output. See the discussion of
-"output commands"_Section_howto.html#howto_15 that take fixes as
-inputs.
+"output commands"_Howto_output.html that take fixes as inputs.
If {N} is not zero, then the attributes will be updated every {N}
steps.
@@ -108,9 +107,8 @@ fix.
If a single input is specified, this fix produces a per-atom vector.
If multiple inputs are specified, a per-atom array is produced where
the number of columns for each atom is the number of inputs. These
-can be accessed by various "output
-commands"_Section_howto.html#howto_15. The per-atom values be
-accessed on any timestep.
+can be accessed by various "output commands"_Howto_output.html. The
+per-atom values be accessed on any timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt
index b470babab72a14f2761805d4719d8bfc92165546..ade64d2056e0e23e58e3e762620077d6ada3f1f1 100644
--- a/doc/src/fix_surface_global.txt
+++ b/doc/src/fix_surface_global.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt
index 6944860e140d8ef9c5772a340007905086b86434..c1f1626782abffb6d380b0faae983b6642d67db0 100644
--- a/doc/src/fix_temp_berendsen.txt
+++ b/doc/src/fix_temp_berendsen.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -68,8 +68,8 @@ be used on atoms that also have their temperature controlled by
another fix - e.g. by "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
This fix computes a temperature each timestep. To do this, the fix
@@ -126,9 +126,9 @@ system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt
index 4129ad73c8fdbe514592b1a33d38e509c74f6f93..e50f821bfe9d55339164064ea18a515d4ac58967 100644
--- a/doc/src/fix_temp_csvr.txt
+++ b/doc/src/fix_temp_csvr.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -76,8 +76,8 @@ normally be used on atoms that also have their temperature controlled
by another fix - e.g. by "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
These fixes compute a temperature each timestep. To do this, the fix
@@ -135,9 +135,9 @@ the {start} and {stop} keywords of the "run"_run.html command. See the
These fixes are not invoked during "energy minimization"_minimize.html.
These fixes compute a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to the fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to the fix. The scalar value calculated by this fix
+is "extensive".
[Restrictions:]
diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt
index eff25297c1e295f6bcb775d65147dfac932ea956..5640317f1cf68ae357480d2b641441af9acf752a 100644
--- a/doc/src/fix_temp_rescale.txt
+++ b/doc/src/fix_temp_rescale.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -75,8 +75,8 @@ be used on atoms that also have their temperature controlled by
another fix - e.g. by "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
This fix computes a temperature each timestep. To do this, the fix
@@ -133,9 +133,9 @@ system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt
index f87c1a219249438c0864dba1f2880b0f1bfae9d8..0e08e4f1e81c9451e7c50742263f0b0b7b6988b9 100644
--- a/doc/src/fix_temp_rescale_eff.txt
+++ b/doc/src/fix_temp_rescale_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -51,9 +51,9 @@ system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt
index 3c81d62ee0aa7c136765e59267b0a9d85f1a8333..ddfa46261929de1fc4e1ab0c411537e6df97744d 100644
--- a/doc/src/fix_tfmc.txt
+++ b/doc/src/fix_tfmc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt
index 0353c095b29d60e4be37a581968a70d06f778492..86fc6f2c72feba87286126f2b48dacf0983bce69 100644
--- a/doc/src/fix_thermal_conductivity.txt
+++ b/doc/src/fix_thermal_conductivity.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -108,9 +108,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative kinetic energy transferred between the bottom and middle
-of the simulation box (in the {edim} direction) is stored as a scalar
+"output commands"_Howto_output.html. The scalar is the cumulative
+kinetic energy transferred between the bottom and middle of the
+simulation box (in the {edim} direction) is stored as a scalar
quantity by this fix. This quantity is zeroed when the fix is defined
and accumulates thereafter, once every N steps. The units of the
quantity are energy; see the "units"_units.html command for details.
diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt
index 191f9e7c6b8d8667b5baef112f20d16fb435a382..afe5373220095b949e9429f41e800f4e2fa6ad79 100644
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -121,13 +121,12 @@ fix to add the energy stored in the per-atom springs to the system's
potential energy as part of "thermodynamic output"_thermo_style.html.
This fix computes a global scalar and a global vector quantities which
-can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar is an energy which
-is the sum of the spring energy for each atom, where the per-atom
-energy is 0.5 * k * r^2. The vector has 2 positions, the first one is
-the coupling parameter lambda and the second one is the time
-derivative of lambda. The scalar and vector values calculated by this
-fix are "extensive".
+can be accessed by various "output commands"_Howto_output.html. The
+scalar is an energy which is the sum of the spring energy for each
+atom, where the per-atom energy is 0.5 * k * r^2. The vector has 2
+positions, the first one is the coupling parameter lambda and the
+second one is the time derivative of lambda. The scalar and vector
+values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_tmd.txt b/doc/src/fix_tmd.txt
index 71d8d2c7670a2956a091ed68d293064de4ffcb59..c2541692f5f4cb2667084e11c5f375132e99abf3 100644
--- a/doc/src/fix_tmd.txt
+++ b/doc/src/fix_tmd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -90,8 +90,7 @@ For more information about TMD, see "(Schlitter1)"_#Schlitter1 and
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15.
+by this fix for access by various "output commands"_Howto_output.html.
This fix can ramp its rho parameter over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt
index 48dfd254a00de377ddb027c8d8e1c77d54e209a3..6001def5817736192fd0f7ac357a63ce148ca3c1 100644
--- a/doc/src/fix_ttm.txt
+++ b/doc/src/fix_ttm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -272,18 +272,17 @@ None of the "fix_modify"_fix_modify.html options are relevant to these
fixes.
Both fixes compute 2 output quantities stored in a vector of length 2,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The first quantity is the
-total energy of the electronic subsystem. The second quantity is the
-energy transferred from the electronic to the atomic subsystem on that
-timestep. Note that the velocity verlet integrator applies the fix ttm
-forces to the atomic subsystem as two half-step velocity updates: one
-on the current timestep and one on the subsequent timestep.
-Consequently, the change in the atomic subsystem energy is lagged by
-half a timestep relative to the change in the electronic subsystem
-energy. As a result of this, users may notice slight fluctuations in
-the sum of the atomic and electronic subsystem energies reported at
-the end of the timestep.
+which can be accessed by various "output commands"_Howto_output.html.
+The first quantity is the total energy of the electronic
+subsystem. The second quantity is the energy transferred from the
+electronic to the atomic subsystem on that timestep. Note that the
+velocity verlet integrator applies the fix ttm forces to the atomic
+subsystem as two half-step velocity updates: one on the current
+timestep and one on the subsequent timestep. Consequently, the change
+in the atomic subsystem energy is lagged by half a timestep relative
+to the change in the electronic subsystem energy. As a result of this,
+users may notice slight fluctuations in the sum of the atomic and
+electronic subsystem energies reported at the end of the timestep.
The vector values calculated are "extensive".
diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt
index 60a34a26c9c671c291ff9ee77946e43e8c0a7c62..b4e8472591dee2164ddb4ef2550431ce0b575e4e 100644
--- a/doc/src/fix_tune_kspace.txt
+++ b/doc/src/fix_tune_kspace.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_vector.txt b/doc/src/fix_vector.txt
index 385d24cff19594096b6193443dd88fc8ad3a2f54..e1bfbe5738073e466f78f2742ed154e13884dc81 100644
--- a/doc/src/fix_vector.txt
+++ b/doc/src/fix_vector.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,7 +37,7 @@ simply store them. For a single specified value, the values are
stored as a global vector of growing length. For multiple specified
values, they are stored as rows in a global array, whose number of
rows is growing. The resulting vector or array can be used by other
-"output commands"_Section_howto.html#howto_15.
+"output commands"_Howto_output.html.
One way to to use this command is to accumulate a vector that is
time-integrated using the "variable trap()"_variable.html function.
@@ -127,9 +127,8 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix produces a global vector or global array which can be
-accessed by various "output commands"_Section_howto.html#howto_15.
-The values can only be accessed on timesteps that are multiples of
-{Nevery}.
+accessed by various "output commands"_Howto_output.html. The values
+can only be accessed on timesteps that are multiples of {Nevery}.
A vector is produced if only a single input value is specified.
An array is produced if multiple input values are specified.
diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt
index f6603be624da84ba7efa8de3c62a3ff9d5074e65..934da3efdd7820fff834d01e1daf8354e14c39c2 100644
--- a/doc/src/fix_viscosity.txt
+++ b/doc/src/fix_viscosity.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -100,13 +100,12 @@ accurately infer a viscosity and should try increasing the Nevery
parameter.
An alternative method for calculating a viscosity is to run a NEMD
-simulation, as described in "Section
-6.13"_Section_howto.html#howto_13 of the manual. NEMD simulations
-deform the simulation box via the "fix deform"_fix_deform.html
-command. Thus they cannot be run on a charged system using a "PPPM
-solver"_kspace_style.html since PPPM does not currently support
-non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
-thus it does not suffer from this limitation.
+simulation, as described on the "Howto nemd"_Howto_nemd.html doc page.
+NEMD simulations deform the simulation box via the "fix
+deform"_fix_deform.html command. Thus they cannot be run on a charged
+system using a "PPPM solver"_kspace_style.html since PPPM does not
+currently support non-orthogonal boxes. Using fix viscosity keeps the
+box orthogonal; thus it does not suffer from this limitation.
[Restart, fix_modify, output, run start/stop, minimize info:]
@@ -115,13 +114,13 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative momentum transferred between the bottom and middle of the
-simulation box (in the {pdim} direction) is stored as a scalar
-quantity by this fix. This quantity is zeroed when the fix is defined
-and accumulates thereafter, once every N steps. The units of the
-quantity are momentum = mass*velocity. The scalar value calculated by
-this fix is "intensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+momentum transferred between the bottom and middle of the simulation
+box (in the {pdim} direction) is stored as a scalar quantity by this
+fix. This quantity is zeroed when the fix is defined and accumulates
+thereafter, once every N steps. The units of the quantity are
+momentum = mass*velocity. The scalar value calculated by this fix is
+"intensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_viscous.txt b/doc/src/fix_viscous.txt
index 9c30e40249a4b4febdef4e17c508766ea8a619d7..c5a3ede0b24a908ffb9ed5652af2d179400a0dd0 100644
--- a/doc/src/fix_viscous.txt
+++ b/doc/src/fix_viscous.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -82,9 +82,9 @@ easily be used as a thermostat.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The "fix_modify"_fix_modify.html {respa} option is supported by this
fix. This allows to set at which level of the "r-RESPA"_run_style.html
diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt
index e814c89a0743af6b7d744ac71d62d71df5c3053d..2ac59d9588155915370d834c1eb2b0e7727602ca 100644
--- a/doc/src/fix_wall.txt
+++ b/doc/src/fix_wall.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -263,14 +263,14 @@ integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar energy and a global vector of
forces, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. Note that the scalar energy is
-the sum of interactions with all defined walls. If you want the
-energy on a per-wall basis, you need to use multiple fix wall
-commands. The length of the vector is equal to the number of walls
-defined by the fix. Each vector value is the normal force on a
-specific wall. Note that an outward force on a wall will be a
-negative value for {lo} walls and a positive value for {hi} walls.
-The scalar and vector values calculated by this fix are "extensive".
+commands"_Howto_output.html. Note that the scalar energy is the sum
+of interactions with all defined walls. If you want the energy on a
+per-wall basis, you need to use multiple fix wall commands. The
+length of the vector is equal to the number of walls defined by the
+fix. Each vector value is the normal force on a specific wall. Note
+that an outward force on a wall will be a negative value for {lo}
+walls and a positive value for {hi} walls. The scalar and vector
+values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
@@ -288,10 +288,9 @@ option for this fix.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -303,8 +302,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/src/fix_wall_body_polygon.txt
index 4ba16b56c79fab2c4cecf6798a71a895b862c5cf..0946a85131ae6c003daa63e7af939f9adf442227 100644
--- a/doc/src/fix_wall_body_polygon.txt
+++ b/doc/src/fix_wall_body_polygon.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,8 +43,8 @@ particles in the group interact with the wall when they are close
enough to touch it. The nature of the interaction between the wall
and the polygon particles is the same as that between the polygon
particles themselves, which is similar to a Hookean potential. See
-"Section 6.14"_Section_howto.html#howto_14 of the manual and the
-"body"_body.html doc page for more details on using body particles.
+the "Howto body"_Howto_body.html doc page for more details on using
+body particles.
The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as
those specified with the "pair_style
@@ -83,9 +83,9 @@ to the derivative of this expression.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/src/fix_wall_body_polyhedron.txt
index c937cbdbbc80a6c711c845212a0a47d85d0800be..407cf9fb339047e9b881c0e4df9b950280d5cbed 100644
--- a/doc/src/fix_wall_body_polyhedron.txt
+++ b/doc/src/fix_wall_body_polyhedron.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,8 +43,8 @@ All particles in the group interact with the wall when they are close
enough to touch it. The nature of the interaction between the wall
and the polygon particles is the same as that between the polygon
particles themselves, which is similar to a Hookean potential. See
-"Section 6.14"_Section_howto.html#howto_14 of the manual and the
-"body"_body.html doc page for more details on using body particles.
+the "Howto body"_Howto_body.html doc page for more details on using
+body particles.
The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as
those specified with the "pair_style
@@ -82,9 +82,9 @@ to the derivative of this expression.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_ees.txt b/doc/src/fix_wall_ees.txt
index f141a194057f30fbb940922bf04d18044c4937b4..ae16ca40d2ab731af1a4b77ac474d3dd8b00f841 100644
--- a/doc/src/fix_wall_ees.txt
+++ b/doc/src/fix_wall_ees.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt
index 5f1679604e365ae0c3c2b59db43331c4b4925b02..6c2769fc12840c85fdd60248009a45a851d8174a 100644
--- a/doc/src/fix_wall_gran.txt
+++ b/doc/src/fix_wall_gran.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -148,9 +148,9 @@ uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt
index 92fb042194db78bbf7d38794a4c49ee65dcbfa09..187214c1a36ca27c304d291150d16f56d440d204 100644
--- a/doc/src/fix_wall_gran_region.txt
+++ b/doc/src/fix_wall_gran_region.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -180,9 +180,9 @@ region with a different region ID.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt
index 4d7756c237d708840fc085a27b0540bdbe35c45d..eecf69ebf2b80164672bb2b21cdb48f3ce855a0d 100644
--- a/doc/src/fix_wall_piston.txt
+++ b/doc/src/fix_wall_piston.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -91,10 +91,10 @@ define the lattice spacings.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt
index 954ec65bf6a1c059226c1beac58bea86fab0fb84..78be84eb638224ec631841fabc022bf0700a5162 100644
--- a/doc/src/fix_wall_reflect.txt
+++ b/doc/src/fix_wall_reflect.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -130,10 +130,9 @@ position = c0 + A (1 - cos(omega*delta)) :pre
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -145,8 +144,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -155,10 +154,10 @@ more instructions on how to use the accelerated styles effectively.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt
index 9700545dc909c92f4327db4a155f0da789703b8a..559a2f0d89c0cd8c00cc49be87daf53f793cf6f9 100644
--- a/doc/src/fix_wall_region.txt
+++ b/doc/src/fix_wall_region.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -156,12 +156,11 @@ integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar energy and a global 3-length vector
of forces, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar energy is the sum
-of energy interactions for all particles interacting with the wall
-represented by the region surface. The 3 vector quantities are the
-x,y,z components of the total force acting on the wall due to the
-particles. The scalar and vector values calculated by this fix are
-"extensive".
+commands"_Howto_output.html. The scalar energy is the sum of energy
+interactions for all particles interacting with the wall represented
+by the region surface. The 3 vector quantities are the x,y,z
+components of the total force acting on the wall due to the particles.
+The scalar and vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_wall_srd.txt b/doc/src/fix_wall_srd.txt
index c465896d37578969cad9b33143d24260b097f525..3a50c45ab7592d0c7d3d16dc969423218eaee8b6 100644
--- a/doc/src/fix_wall_srd.txt
+++ b/doc/src/fix_wall_srd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -166,9 +166,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global array of values which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The number of
-rows in the array is equal to the number of walls defined by the fix.
-The number of columns is 3, for the x,y,z components of force on each
+various "output commands"_Howto_output.html. The number of rows in
+the array is equal to the number of walls defined by the fix. The
+number of columns is 3, for the x,y,z components of force on each
wall.
Note that an outward normal force on a wall will be a negative value
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index 9510217d029b79849ad03fc8092090472936e4fe..7a45ed8086a14cdc201eea9cce5f28f80b4df00e 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -168,6 +168,8 @@ Fixes :h1
fix_viscosity
fix_viscous
fix_wall
+ fix_wall_body_polygon
+ fix_wall_body_polyhedron
fix_wall_ees
fix_wall_gran
fix_wall_gran_region
diff --git a/doc/src/group.txt b/doc/src/group.txt
index dddb0459e3711e526e6077318aa6ae51922b0196..847267737286c79b0d99315d20b995907082cf81 100644
--- a/doc/src/group.txt
+++ b/doc/src/group.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/group2ndx.txt b/doc/src/group2ndx.txt
index 94d188399ba6937874f1d579eb4bdf66c840ea2d..242d6a69a4092798fb073f2f89a4c44957b46061 100644
--- a/doc/src/group2ndx.txt
+++ b/doc/src/group2ndx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/if.txt b/doc/src/if.txt
index 52fad5aea756031760c56e6e7ec4183266f9212c..513e451034da5f2752b96c4cdd81b3ec26ac58c4 100644
--- a/doc/src/if.txt
+++ b/doc/src/if.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,9 +65,9 @@ above.
NOTE: If a command itself requires a quoted argument (e.g. a
"print"_print.html command), then double and single quotes can be used
and nested in the usual manner, as in the examples above and below.
-See "Section 3.2"_Section_commands.html#cmd_2 of the manual for
-more details on using quotes in arguments. Only one of level of
-nesting is allowed, but that should be sufficient for most use cases.
+The "Commands parse"_Commands_parse.html doc page has more details on
+using quotes in arguments. Only one of level of nesting is allowed,
+but that should be sufficient for most use cases.
Note that by using the line continuation character "&", the if command
can be spread across many lines, though it is still a single command:
diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt
index 14ec6258de654a466ec429328014f420e81cb999..c38f73c64dc017d58ce25e86cb431d5c068e9b1e 100644
--- a/doc/src/improper_class2.txt
+++ b/doc/src/improper_class2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -87,10 +87,9 @@ radians internally; hence the units of M are in energy/radian^2.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -102,8 +101,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_coeff.txt b/doc/src/improper_coeff.txt
index 5c01a23ae9cda2b729894bb87a8b4108ff4a11b7..8ed65f95350a3a56eb776b5fe5ad67c3257d939d 100644
--- a/doc/src/improper_coeff.txt
+++ b/doc/src/improper_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -67,9 +67,9 @@ the style to display the formula it computes and coefficients
specified by the associated "improper_coeff"_improper_coeff.html command.
Note that there are also additional improper styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the improper section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+improper styles is on the "Commands bond"_Commands_bond.html#improper
+doc page.
"improper_style none"_improper_none.html - turn off improper interactions
"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt
index 138a6a16503b125003b15ec1ceb394f18963e1eb..04aa45255cb2faf860dcd0493b53e301c6a65bde 100644
--- a/doc/src/improper_cossq.txt
+++ b/doc/src/improper_cossq.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -53,10 +53,9 @@ X0 (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt
index 5f69eccc60a1d060b894c89f487d591fa1a8b0b8..d01faf288554e0281f1841e45c9f0c415083c547 100644
--- a/doc/src/improper_cvff.txt
+++ b/doc/src/improper_cvff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -54,10 +54,9 @@ n (0,1,2,3,4,6) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -69,8 +68,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_distance.txt b/doc/src/improper_distance.txt
index 7d49d17c976f262d39ff642380f23aadb0701595..93235fe60197f01fc50297ec4f8d0504c16c6b9a 100644
--- a/doc/src/improper_distance.txt
+++ b/doc/src/improper_distance.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt
index f9062da207b329cb7616ca38420e8878675252b4..78cc1b3f760fe81de8682983f11bc0f90615f9d4 100644
--- a/doc/src/improper_fourier.txt
+++ b/doc/src/improper_fourier.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -48,10 +48,9 @@ all (integer >= 0) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -63,8 +62,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt
index bb17e5a641e8da1b4b92f3e1b5ecfe8245fddf1a..f398dc425f935f605c3446075783df2b91d49c00 100644
--- a/doc/src/improper_harmonic.txt
+++ b/doc/src/improper_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -58,10 +58,9 @@ internally; hence the units of K are in energy/radian^2.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -73,8 +72,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt
index 0c2beaef18c07dc3cfcc8ad136a8940486bdeef8..42afbe8577dc30163dcc8e5053de9cc05022b6a2 100644
--- a/doc/src/improper_hybrid.txt
+++ b/doc/src/improper_hybrid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/src/improper_inversion_harmonic.txt
index 34683ca2bb0000db8f32f9e93838f344e0287b4c..2c0f2f0af84e1275c8511fc3d65f2508163a89cd 100644
--- a/doc/src/improper_inversion_harmonic.txt
+++ b/doc/src/improper_inversion_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/improper_none.txt b/doc/src/improper_none.txt
index af9964c7437af081e5a50ba8daf4359c94882593..f97af101fcffaf64ce4dacc34bc7824e4312d185 100644
--- a/doc/src/improper_none.txt
+++ b/doc/src/improper_none.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt
index c02d39247403622fe51e1ffbc4e47df43e11db77..60bbca170a9a3d06cc3d819d847fdf37370691d9 100644
--- a/doc/src/improper_ring.txt
+++ b/doc/src/improper_ring.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -57,10 +57,9 @@ theta0 (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -72,8 +71,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt
index 861701590fedcfce745e2542fd7c69c943e4e5a3..3d29b28ec4a69b2200db24e2fb742fdf1c7fabd4 100644
--- a/doc/src/improper_style.txt
+++ b/doc/src/improper_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -60,9 +60,9 @@ specified by the associated "improper_coeff"_improper_coeff.html
command.
Note that there are also additional improper styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the improper section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+improper styles is on the "Commands bond"_Commands_bond.html#improper
+doc page.
"improper_style none"_improper_none.html - turn off improper interactions
"improper_style zero"_improper_zero.html - topology but no interactions
diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt
index d6df9ee6cccc8ec2f391a2583ac495caa0ad07e9..b05cf4b181bfceaed1160cebb650d99922af039a 100644
--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -22,7 +22,7 @@ improper_coeff 1 100.0 180.0 :pre
The {umbrella} improper style uses the following potential, which is
commonly referred to as a classic inversion and used in the
-"DREIDING"_Section_howto.html#howto_4 force field:
+"DREIDING"_Howto_bioFF.html force field:
:c,image(Eqs/improper_umbrella.jpg)
@@ -51,10 +51,9 @@ omega0 (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_zero.txt b/doc/src/improper_zero.txt
index 2a298573d5e359ef1676519ef494526fa14a2bc7..f3f3485b57cf0c6daf81233f1432e9b43f2aeb42 100644
--- a/doc/src/improper_zero.txt
+++ b/doc/src/improper_zero.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/include.txt b/doc/src/include.txt
index 95d08db3522d8d291512e477801860f41f78004a..c11405631365e173f57589d3a11825884a4b0157 100644
--- a/doc/src/include.txt
+++ b/doc/src/include.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/info.txt b/doc/src/info.txt
index d5b5bd97b942842c03a26011d66ce7049b1c3a27..99211de4fb5745edccf401a78f2045c756dee695 100644
--- a/doc/src/info.txt
+++ b/doc/src/info.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/jump.txt b/doc/src/jump.txt
index 4e3799f7b1c48fafa179454b458c2eff588c4453..b5afeb6559f4c80629947cf9376ae455fdde1a63 100644
--- a/doc/src/jump.txt
+++ b/doc/src/jump.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index 6d27bb7076344adfd81ba2a0b7242c985a3eff02..dd7b1e8deadfdd3e6defeddaa0cc85d3e4467370 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -285,15 +285,15 @@ performance and accuracy in the results is obtained when these values
are different.
The {disp/auto} option controls whether the pppm/disp is allowed to
-generate PPPM parameters automatically. If set to {no}, parameters have
-to be specified using the {gewald/disp}, {mesh/disp},
-{force/disp/real} or {force/disp/kspace} keywords, or
-the code will stop with an error message. When this option is set to
-{yes}, the error message will not appear and the simulation will start.
-For a typical application, using the automatic parameter generation
-will provide simulations that are either inaccurate or slow. Using this
-option is thus not recommended. For guidelines on how to obtain good
-parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
+generate PPPM parameters automatically. If set to {no}, parameters
+have to be specified using the {gewald/disp}, {mesh/disp},
+{force/disp/real} or {force/disp/kspace} keywords, or the code will
+stop with an error message. When this option is set to {yes}, the
+error message will not appear and the simulation will start. For a
+typical application, using the automatic parameter generation will
+provide simulations that are either inaccurate or slow. Using this
+option is thus not recommended. For guidelines on how to obtain good
+parameters, see the "Howto dispersion"_Howto_dispersion.html doc page.
[Restrictions:] none
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index 4f27c9aa78e95cb2819b65d44be17acfb53e4a6f..55ad4ab6107b828fd74e5daa91025063d29c5115 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -145,8 +145,8 @@ speedup in the KSpace time (8x less mesh points, 2x more expensive).
However, for low relative accuracy, the staggered PPPM mesh size may
be essentially the same as for regular PPPM, which means the method
will be up to 2x slower in the KSpace time (simply 2x more expensive).
-For more details and timings, see
-"Section 5"_Section_accelerate.html.
+For more details and timings, see the "Speed tips"_Speed_tips.html doc
+page.
NOTE: Using {pppm/stagger} may not give the same increase in the
accuracy of energy and pressure as it does in forces, so some caution
@@ -161,15 +161,16 @@ similar to the {ewald/disp} style. The 1/r^6 capability means
that Lennard-Jones or Buckingham potentials can be used without a cutoff,
i.e. they become full long-range potentials.
-For these styles, you will possibly want to adjust the default choice of
-parameters by using the "kspace_modify"_kspace_modify.html command.
+For these styles, you will possibly want to adjust the default choice
+of parameters by using the "kspace_modify"_kspace_modify.html command.
This can be done by either choosing the Ewald and grid parameters, or
by specifying separate accuracies for the real and kspace
-calculations. When not making any settings, the simulation will stop with
-an error message. Further information on the influence of the parameters
-and how to choose them is described in "(Isele-Holder)"_#Isele-Holder2012,
-"(Isele-Holder2)"_#Isele-Holder2013 and the
-"How-To"_Section_howto.html#howto_24 discussion.
+calculations. When not making any settings, the simulation will stop
+with an error message. Further information on the influence of the
+parameters and how to choose them is described in
+"(Isele-Holder)"_#Isele-Holder2012,
+"(Isele-Holder2)"_#Isele-Holder2013 and the "Howto
+dispersion"_Howto_dispersion.html doc page.
:line
@@ -267,10 +268,9 @@ relative RMS error.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
More specifically, the {pppm/gpu} style performs charge assignment and
force interpolation calculations on the GPU. These processes are
@@ -291,8 +291,8 @@ KOKKOS, USER-OMP, and OPT packages respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/label.txt b/doc/src/label.txt
index c6a573141b205b7dea517f3d24881f84f06e3414..adab44188c8cc3a45cc49139e935c2e7c37a9606 100644
--- a/doc/src/label.txt
+++ b/doc/src/label.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 4274ef48b3be56e6171b48632247b1e4fd2ce415..c0ca357f211aa973f0c80f28155b2cc9b6e0ebcd 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -1,19 +1,78 @@
#HTMLDOC 1.8.28
-t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow
Manual.html
-Section_intro.html
+Intro.html
+Intro_overview.html
+Intro_features.html
+Intro_nonfeatures.html
+Intro_opensource.html
+Intro_authors.html
+Intro_website.html
Section_start.html
-Section_commands.html
-Section_packages.html
-Section_accelerate.html
-accelerate_gpu.html
-accelerate_intel.html
-accelerate_kokkos.html
-accelerate_omp.html
-accelerate_opt.html
-Section_howto.html
+Commands.html
+Commands_input.html
+Commands_parse.html
+Commands_structure.html
+Commands_category.html
+Commands_all.html
+Commands_fix.html
+Commands_compute.html
+Commands_pair.html
+Commands_bond.html
+Commands_kspace.html
+Packages.html
+Packages_standard.html
+Packages_user.html
+Packages_details.html
+Speed.html
+Speed_bench.html
+Speed_measure.html
+Speed_tips.html
+Speed_packages.html
+Speed_gpu.html
+Speed_intel.html
+Speed_kokkos.html
+Speed_omp.html
+Speed_opt.html
+Speed_compare.html
+Howto.html
+Howto_github.html
+Howto_pylammps.html
+Howto_bash.html
+Howto_restart.html
+Howto_viz.html
+Howto_multiple.html
+Howto_replica.html
+Howto_library.html
+Howto_couple.html
+Howto_output.html
+Howto_chunk.html
+Howto_2d.html
+Howto_triclinic.html
+Howto_walls.html
+Howto_nemd.html
+Howto_granular.html
+Howto_spherical.html
+Howto_dispersion.html
+Howto_temperature.html
+Howto_thermostat.html
+Howto_barostat.html
+Howto_elastic.html
+Howto_kappa.html
+Howto_viscosity.html
+Howto_diffusion.html
+Howto_bioFF.html
+Howto_tip3p.html
+Howto_tip4p.html
+Howto_spc.html
+Howto_body.html
+Howto_polarizable.html
+Howto_coreshell.html
+Howto_drude.html
+Howto_drude2.html
+Howto_manifold.html
+Howto_spins.html
Examples.html
-Section_perf.html
Tools.html
Modify.html
Modify_overview.html
@@ -47,17 +106,6 @@ Errors_common.html
Errors_bugs.html
Errors_messages.html
Errors_warnings.html
-Section_history.html
-
-lammps_tutorials.html
-tutorial_bash_on_windows.html
-tutorial_drude.html
-tutorial_github.html
-tutorial_pylammps.html
-
-lammps_support.html
-body.html
-manifolds.html
lammps_commands.html
atom_modify.html
diff --git a/doc/src/lammps_support.txt b/doc/src/lammps_support.txt
deleted file mode 100644
index fa460ce6c23054e8409ad9b6e5392173c0972995..0000000000000000000000000000000000000000
--- a/doc/src/lammps_support.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-
-Supporting Information :h1
-
-This section of the manual contains supporting information that
-is not documenting individual commands but general concepts and
-supporting information about entities like body particles or
-manifolds.
diff --git a/doc/src/lammps_tutorials.txt b/doc/src/lammps_tutorials.txt
deleted file mode 100644
index 5ceda65b600744e9133168348bcc55ea78629bfc..0000000000000000000000000000000000000000
--- a/doc/src/lammps_tutorials.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-
-Tutorials :h2
-
-The following pages contain some in-depth tutorials for
-selected topics, that did not fit into any other place
-in the manual.
diff --git a/doc/src/lattice.txt b/doc/src/lattice.txt
index 7a90df1f5d553697e7433d4b41cc4a2b241a4531..6f16dc54323ae72ec99eed888f2c1a953e124647 100644
--- a/doc/src/lattice.txt
+++ b/doc/src/lattice.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/log.txt b/doc/src/log.txt
index 92bb12e6dbccf42c9c8d1b80d587088e91bf88c7..76037685194b5ba9b324b02d35ffd0ed34ea26d3 100644
--- a/doc/src/log.txt
+++ b/doc/src/log.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/mass.txt b/doc/src/mass.txt
index 4b75132ccfb63a763cb6f238201e19216b736d0a..c6939630441165e80bd0bacb0007e56fedbec7af 100644
--- a/doc/src/mass.txt
+++ b/doc/src/mass.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/min_modify.txt b/doc/src/min_modify.txt
index 73d142f5fabe4556a91064f674e62a37bed26773..9408eea167bbc49274a203b0fe4586f724e8659a 100644
--- a/doc/src/min_modify.txt
+++ b/doc/src/min_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/min_style.txt b/doc/src/min_style.txt
index 245ac5864c1d41bdbce4a42568e5ee555a25bb3d..4948a34864a4424a031e86ab4ace7937c1fd09fe 100644
--- a/doc/src/min_style.txt
+++ b/doc/src/min_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
min_style command :h3
diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt
index a3f2c5d0bf5aaa430740076b09ea39fad0b35baa..910fc7f821051bee5f28753442d479e85f7f27e7 100644
--- a/doc/src/minimize.txt
+++ b/doc/src/minimize.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt
index cd9ecce42c8b8750e52389e6b48c08885a7cae3f..88c6292d8b6d3bc63f075917f38df9f9482fcbae 100644
--- a/doc/src/molecule.txt
+++ b/doc/src/molecule.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -176,9 +176,8 @@ LAMMPS uses this info to properly exclude or weight bonded pairwise
interactions between bonded atoms. See the
"special_bonds"_special_bonds.html command for more details. One
reason to list the special bond info explicitly is for the
-"thermalized Drude oscillator model"_tutorial_drude.html which treats
-the bonds between nuclear cores and Drude electrons in a different
-manner.
+"thermalized Drude oscillator model"_Howto_drude.html which treats the
+bonds between nuclear cores and Drude electrons in a different manner.
NOTE: Whether a section is required depends on how the molecule
template is used by other LAMMPS commands. For example, to add a
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index 56f075c301046d40a0e940045225d5c3019458e9..fbd77ee32903f1d99f4f63232538e0fd88cdde7d 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -56,9 +56,8 @@ Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on just one or two
processors. You will simply not get the performance speed-up you
-would see with one or more physical processors per replica. See
-"Section 6.5"_Section_howto.html#howto_5 of the manual for further
-discussion.
+would see with one or more physical processors per replica. See the
+"Howto replica"_Howto_replica.html doc page for further discussion.
NOTE: As explained below, a NEB calculation perfoms a damped dynamics
minimization across all the replicas. The minimizer uses whatever
diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt
index c4544cb29bde3ccf25b708e7d2ad552fc97e7eea..6c4218cff56589fca8b41d6c8c8ab2fa96ee2c5b 100644
--- a/doc/src/neigh_modify.txt
+++ b/doc/src/neigh_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt
index 062f79a5bbba0bc7e9042145dd03cebbf1ceebe3..7c7e7b05e5229b3d1144f251543d5b8ded341c60 100644
--- a/doc/src/neighbor.txt
+++ b/doc/src/neighbor.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/newton.txt b/doc/src/newton.txt
index a3e7f4fa91eec43b623a57f58be483f35ba982e1..fd7b5369203f25c957f62e34d9d68960fee87495 100644
--- a/doc/src/newton.txt
+++ b/doc/src/newton.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/next.txt b/doc/src/next.txt
index 08f73b896cb7ef13f74c5dd982f07d021fe44eea..5a0b30b2a7fe6ff0d824a066376404808702958f 100644
--- a/doc/src/next.txt
+++ b/doc/src/next.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/package.txt b/doc/src/package.txt
index 5fd42f67d3b91b1d67811201b13f5692b17f4761..c2e7345bb74c4e25a5dc4861194c704d3017232d 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -149,9 +149,9 @@ the style options are set, either to default values or to specified
settings. I.e. settings from previous invocations do not persist
across multiple invocations.
-See the "Section 5.3"_Section_accelerate.html#acc_3 section of the
-manual for more details about using the various accelerator packages
-for speeding up LAMMPS simulations.
+See the "Speed packages"_Speed_packages.html doc page for more details
+about using the various accelerator packages for speeding up LAMMPS
+simulations.
:line
diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt
index 9d2a48dcbca399bc00f09458c56941cf3f622b5e..382a97eceaf93bf844915871d3210a4bca0e7666 100644
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -125,10 +125,9 @@ array tabulated with a scaling by r.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -140,8 +139,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt
index 402e537dadf39bc5728d6001d32a0709d17e54c0..34f99001390ca24026f0ea3218316ab465d68ac0 100644
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -58,11 +58,11 @@ and input files are provided in the examples/USER/misc/agni directory.
:line
Styles with {omp} suffix is functionally the same as the corresponding
-style without the suffix. They have been optimized to run faster, depending
-on your available hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated style takes the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+style without the suffix. They have been optimized to run faster,
+depending on your available hardware, as discussed on the "Speed
+packages"_Speed_packages.html doc page. The accelerated style takes
+the same arguments and should produce the same results, except for
+round-off and precision issues.
The accelerated style is part of the USER-OMP. They are only enabled if
LAMMPS was built with those packages. See the "Making
@@ -73,8 +73,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt
index 1aa017f2786ac95e60556d84b5a900fcab5a1704..94a692226d608687a094d48455070c1084eed3f4 100644
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -176,10 +176,9 @@ thermo_style custom step temp epair v_REBO v_LJ v_TORSION :pre
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -191,8 +190,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index b798f7d128c1349bfb6cac164e74dd9f6d6a7ffe..2e961a13568d810dc3a2f75e95ba9071ae307e15 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -49,9 +49,8 @@ The {atm} potential is typically used in combination with a two-body
potential using the "pair_style hybrid/overlay"_pair_hybrid.html
command as in the example above.
-The potential is calculated if atoms J and K are in the
-"neighbor list"_neighbor.html of atom I
-and the distances between atoms satisfy rIJ rJK rKI > cutoff^3.
+The potential for a triplet of atom is calculated only if all 3
+distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
diff --git a/doc/src/pair_awpmd.txt b/doc/src/pair_awpmd.txt
index fe0e3c952a759234f79234c60d825524b8984023..ec87101d0dc2fa89ed9089e13b37ca061ed3a9d9 100644
--- a/doc/src/pair_awpmd.txt
+++ b/doc/src/pair_awpmd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt
index e160f09b3d6fc5764c24bdd367d284e93db55622..ca4186e27b102d8199327d87a3ca0cd9da09f92f 100644
--- a/doc/src/pair_beck.txt
+++ b/doc/src/pair_beck.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -51,10 +51,9 @@ Rc is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_body_nparticle.txt b/doc/src/pair_body_nparticle.txt
index 8c5b6e155d801729a72b99276373ef4b0f525185..9fb88102eb0aece7ace62e32360614fa3bdef106 100644
--- a/doc/src/pair_body_nparticle.txt
+++ b/doc/src/pair_body_nparticle.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -24,15 +24,14 @@ pair_coeff 1 1 1.0 1.5 2.5 :pre
Style {body/nparticle} is for use with body particles and calculates
pairwise body/body interactions as well as interactions between body
-and point-particles. See "Section 6.14"_Section_howto.html#howto_14
-of the manual and the "body"_body.html doc page for more details on
-using body particles.
+and point-particles. See the "Howto body"_Howto_body.html doc page
+for more details on using body particles.
This pair style is designed for use with the "nparticle" body style,
which is specified as an argument to the "atom-style body" command.
-See the "body"_body.html doc page for more details about the body
-styles LAMMPS supports. The "nparticle" style treats a body particle
-as a rigid body composed of N sub-particles.
+See the "Howto body"_Howto_body.html doc page for more details about
+the body styles LAMMPS supports. The "nparticle" style treats a body
+particle as a rigid body composed of N sub-particles.
The coordinates of a body particle are its center-of-mass (COM). If
the COMs of a pair of body particles are within the cutoff (global or
diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt
index 9daeb08e9a9e3310380c4b5e40534aecedd59b09..e724874032afffe0d59f1f6fe2622a1669797b35 100644
--- a/doc/src/pair_body_rounded_polygon.txt
+++ b/doc/src/pair_body_rounded_polygon.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -29,9 +29,8 @@ pair_coeff 1 1 100.0 1.0 :pre
Style {body/rounded/polygon} is for use with 2d models of body
particles of style {rounded/polygon}. It calculates pairwise
body/body interactions which can include body particles modeled as
-1-vertex circular disks with a specified diameter. See "Section
-6.14"_Section_howto.html#howto_14 of the manual and the
-"body"_body.html doc page for more details on using body
+1-vertex circular disks with a specified diameter. See the "Howto
+body"_Howto_body.html doc page for more details on using body
rounded/polygon particles.
This pairwise interaction between rounded polygons is described in
diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt
index dc559feaafb6715e7f4b06800103951725078964..0f8548d98eab86a6d5e3647f46119162764409cb 100644
--- a/doc/src/pair_body_rounded_polyhedron.txt
+++ b/doc/src/pair_body_rounded_polyhedron.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -29,9 +29,8 @@ pair_coeff 1 1 100.0 1.0 :pre
Style {body/rounded/polygon} is for use with 3d models of body
particles of style {rounded/polyhedron}. It calculates pairwise
body/body interactions which can include body particles modeled as
-1-vertex spheres with a specified diameter. See "Section
-6.14"_Section_howto.html#howto_14 of the manual and the
-"body"_body.html doc page for more details on using body
+1-vertex spheres with a specified diameter. See the "Howto
+body"_Howto_body.html doc page for more details on using body
rounded/polyhedron particles.
This pairwise interaction between the rounded polyhedra is described
diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt
index 2a611e4bd038a50685897244936677ba09311cb9..654a7eb0b332dd5efdd4a9ca41410fbf6bd131df 100644
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt
index f867107426b04b7c4f92ddafafe75ed3687b2c16..c408de6db6f23b579f2800d7865fdcd35649f9e6 100644
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@@ -3,7 +3,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -108,10 +108,10 @@ The {born/coul/dsf} style computes the Coulomb contribution with the
damped shifted force model as in the "coul/dsf"_pair_coul.html style.
Style {born/coul/long/cs} is identical to {born/coul/long} except that
-a term is added for the "core/shell model"_Section_howto.html#howto_25
-to allow charges on core and shell particles to be separated by r =
-0.0. The same correction is introduced for the {born/coul/dsf/cs}
-style which is identical to {born/coul/dsf}. And likewise for
+a term is added for the "core/shell model"_Howto_coreshell.html to
+allow charges on core and shell particles to be separated by r = 0.0.
+The same correction is introduced for the {born/coul/dsf/cs} style
+which is identical to {born/coul/dsf}. And likewise for
{born/coul/wolf/cs} style which is identical to {born/coul/wolf}.
Note that these potentials are related to the "Buckingham
@@ -145,10 +145,9 @@ pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -160,8 +159,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt
index 79b71e91c73e3d6a99b129472cea4831e6905324..eaff85cbbca374db982add0557f03b57dedceaaf 100644
--- a/doc/src/pair_brownian.txt
+++ b/doc/src/pair_brownian.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -74,7 +74,7 @@ must be specified.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "this section"_Section_accelerate.html of
+hardware, as discussed in "this section"_Speed.html of
the manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
@@ -88,7 +88,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "this section"_Section_accelerate.html of the manual for more
+See "this section"_Speed.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index d18b39d5d92b0bf7882f51a3a32149ed5d9e56d6..cc782c11cf3f551930264316b838c488de4ddb6e 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -93,9 +93,8 @@ used as the cutoff for the A,C terms, and the second is the cutoff for
the Coulombic term.
Style {buck/coul/long/cs} is identical to {buck/coul/long} except that
-a term is added for the "core/shell model"_Section_howto.html#howto_25
-to allow charges on core and shell particles to be separated by r =
-0.0.
+a term is added for the "core/shell model"_Howto_coreshell.html to
+allow charges on core and shell particles to be separated by r = 0.0.
Note that these potentials are related to the "Born-Mayer-Huggins
potential"_pair_born.html.
@@ -140,10 +139,9 @@ pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -155,8 +153,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt
index 879972772ba1aceed1ebe3992725373955840ef1..485c35c6b2fffb04c14fa04469bd33a6400c65d5 100644
--- a/doc/src/pair_buck6d_coul_gauss.txt
+++ b/doc/src/pair_buck6d_coul_gauss.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt
index 05e760e1b22b44c5901f9160b9fa4f3eaaa44c5c..551204f1a7fe97ea559e98c7cfd1ddd92370d328 100644
--- a/doc/src/pair_buck_long.txt
+++ b/doc/src/pair_buck_long.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -102,10 +102,9 @@ global Coulombic cutoff is allowed.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -117,8 +116,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index 75a8e4bff944f8b6786f61bb50aa7eefe1e082c7..39c6f29b047fdbf02017352a1e787cc60c79cb78 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -184,10 +184,9 @@ the pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -199,8 +198,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt
index 36fae5068b6e055adac9b7a2fb475e0df513968c..104c51474c25764c20a7b064dad9722e548e0809 100644
--- a/doc/src/pair_class2.txt
+++ b/doc/src/pair_class2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -102,10 +102,9 @@ cutoff distance.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -117,8 +116,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_coeff.txt b/doc/src/pair_coeff.txt
index fe9238f423d22af362c51940a639fbc32312fb7e..63f85f23d5e480a77ccc5f0c673cdde81d5a2d16 100644
--- a/doc/src/pair_coeff.txt
+++ b/doc/src/pair_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -111,9 +111,8 @@ Windows:
:line
The alphabetic list of pair styles defined in LAMMPS is given on the
-"pair_style"_pair_style.html doc page. They are also given in more
-compact form in the pair section of "this
-page"_Section_commands.html#cmd_5.
+"pair_style"_pair_style.html doc page. They are also listed in more
+compact form on the "Commands pair"_Commands_pair.html doc page.
Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
@@ -121,15 +120,15 @@ associated "pair_coeff"_pair_coeff.html command.
Note that there are also additional pair styles (not listed on the
"pair_style"_pair_style.html doc page) submitted by users which are
-included in the LAMMPS distribution. The list of these with links to
-the individual styles are given in the pair section of "this
-page"_Section_commands.html#cmd_5.
+included in the LAMMPS distribution. The full list of all pair styles
+is on the "Commands pair"_Commands_pair.html doc page.
There are also additional accelerated pair styles (not listed on the
"pair_style"_pair_style.html doc page) included in the LAMMPS
-distribution for faster performance on CPUs and GPUs. The list of
-these with links to the individual styles are given in the pair
-section of "this page"_Section_commands.html#cmd_5.
+distribution for faster performance on CPUs, GPUs, and KNLs. The
+individual style names on the "Commands pair"_Commands_pair.html doc
+page are followed by one or more of (g,i,k,o,t) to indicate which
+accerlerated styles exist.
:line
diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt
index 83b15b358bf532f6725853f8fc7e7b2329419ac5..08540cfee082c761259d3d8e3772015557c21210 100644
--- a/doc/src/pair_colloid.txt
+++ b/doc/src/pair_colloid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -127,10 +127,9 @@ commands for efficiency: "neighbor multi"_neighbor.html and
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -142,8 +141,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt
index f5461b1cbc208ca0c5cd01583416f1821b0a6ec8..fc4cddbbae1fefa91ce37e930e2a589279f42566 100644
--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -112,10 +112,9 @@ nor file {ffield.comb3} with style {comb}.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -127,8 +126,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt
index aa3a008bd36f2e4b4c0f51da19390d1c8a5bb80a..2fd9445785e26a44a3b1f7b070caa7531e61003d 100644
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -205,9 +205,9 @@ pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Style {coul/long/cs} is identical to {coul/long} except that a term is
-added for the "core/shell model"_Section_howto.html#howto_25 to allow
-charges on core and shell particles to be separated by r = 0.0. The
-same correction is introduced for the {coul/wolf/cs} style which is
+added for the "core/shell model"_Howto_coreshell.html to allow charges
+on core and shell particles to be separated by r = 0.0. The same
+correction is introduced for the {coul/wolf/cs} style which is
identical to {coul/wolf}.
Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of
@@ -226,16 +226,16 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
-See the "howto section"_Section_howto.html#howto_8 for more
-information on how to use the TIP4P pair styles and lists of
-parameters to set. Note that the neighbor list cutoff for Coulomb
-interactions is effectively extended by a distance 2*qdist when using
-the TIP4P pair style, to account for the offset distance of the
-fictitious charges on O atoms in water molecules. Thus it is
-typically best in an efficiency sense to use a LJ cutoff >= Coulomb
-cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
-to slightly larger cost for the long-range calculation, so you can
-test the trade-off for your model.
+See the "Howto tip4p"_Howto_tip4p.html doc page for more information
+on how to use the TIP4P pair styles and lists of parameters to set.
+Note that the neighbor list cutoff for Coulomb interactions is
+effectively extended by a distance 2*qdist when using the TIP4P pair
+style, to account for the offset distance of the fictitious charges on
+O atoms in water molecules. Thus it is typically best in an
+efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to
+shrink the size of the neighbor list. This leads to slightly larger
+cost for the long-range calculation, so you can test the trade-off for
+your model.
:line
@@ -268,10 +268,9 @@ command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -283,8 +282,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt
index f651cb4b5e4e927d6d9d230bcfe5e37d9260885f..14932c4835043aa7e93cf7b900672def64f10323 100644
--- a/doc/src/pair_coul_diel.txt
+++ b/doc/src/pair_coul_diel.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt
index 19f69688d5b6b1d3da1af094a81340cf8cab1b5d..029e6e5b3b3458ce3fdbab9daaecdad467061dce 100644
--- a/doc/src/pair_coul_shield.txt
+++ b/doc/src/pair_coul_shield.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt
index c1084c608797863a3ecc7528cdb457298d8c3512..6540c4b8f0d4dd72b704854146d50b4f74815720 100644
--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -54,8 +54,8 @@ pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
These pair styles are designed to be used with the adiabatic
core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham2. See
-"Section 6.25"_Section_howto.html#howto_25 of the manual for an
-overview of the model as implemented in LAMMPS.
+the "Howto coreshell"_Howto_coreshell.html doc page for an overview of
+the model as implemented in LAMMPS.
The styles with a {coul/long} term are identical to the "pair_style
born/coul/long"_pair_born.html and "pair_style
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index 2516e5eae4d00113892dd8e97558b59ca13b97e3..1d8abc4521d2b26d2152d2157081a9d718bc3b47 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -186,10 +186,9 @@ type pair.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -201,8 +200,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt
index 9e29e93430602fd485bef467602d7001c8534fab..1b636795d962254fed114fd7cad91b2b53fb8bac 100644
--- a/doc/src/pair_dpd.txt
+++ b/doc/src/pair_dpd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -110,10 +110,9 @@ random force.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -125,8 +124,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt
index 867f3f2315dcb9d908438f91710016abe4ccf9d8..0d180ba068ffdec47eb78bc7fc7fcdb458aab766 100644
--- a/doc/src/pair_dpd_fdt.txt
+++ b/doc/src/pair_dpd_fdt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -129,10 +129,9 @@ significantly larger timesteps to be taken.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -144,8 +143,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt
index 9e24100ab7cf4ce5d6676060370e75e3ef172aa1..2478a96d5ff183f52d21f817a1205eee6ce99855 100644
--- a/doc/src/pair_dsmc.txt
+++ b/doc/src/pair_dsmc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt
index 03e77f53ab0f291be3054b1464d1936b057e95e6..361dacb703d41a95c365abd2ce5101e915fe11d3 100644
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -371,10 +371,9 @@ are listed.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -386,7 +385,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for more
+See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
@@ -414,15 +413,10 @@ The eam pair styles can only be used via the {pair} keyword of the
[Restrictions:]
-All of these styles except the {eam/cd} style are part of the MANYBODY
-package. They are only enabled if LAMMPS was built with that package.
+All of these styles are part of the MANYBODY package. They are only
+enabled if LAMMPS was built with that package.
See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
-The {eam/cd} style is part of the USER-MISC package and also requires
-the MANYBODY package. It is only enabled if LAMMPS was built with
-those packages. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
-
[Related commands:]
"pair_coeff"_pair_coeff.html
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index e5b1420b5938eed1008b780fc226e1258d0c3fa5..cce564856e6c2c420771e4c070b23605e0cdafe8 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -109,10 +109,9 @@ the EDIP package.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -124,8 +123,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt
index ee7dc9993296b92e353961284670052624ce11b6..a55860297e609eb106b63cda6655babf3f696966 100644
--- a/doc/src/pair_eff.txt
+++ b/doc/src/pair_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt
index 75ad2d4683ee64716ebc003ca5267d5733302760..6490a859c16b361e217faaa3eb04e52386b87143 100644
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -136,10 +136,9 @@ needs.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -151,8 +150,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt
index 7eafa235434386bcfe3438367cee1cec1852e74b..08ab1cf3c9b64a40fe70b251500fcecfcd2994f6 100644
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -153,10 +153,9 @@ pair interaction.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -168,8 +167,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_extep.txt b/doc/src/pair_extep.txt
index 9a784e2501638ecda41031366b0777346115c94f..3acad1132d108f61a70bd4c336b63ee14a919601 100644
--- a/doc/src/pair_extep.txt
+++ b/doc/src/pair_extep.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt
index f6f46a2de8ace2a7f982d305728b77f42f350ded..9662a4f29c743fefb3bddc480b6f70f75045ff88 100644
--- a/doc/src/pair_gauss.txt
+++ b/doc/src/pair_gauss.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -84,10 +84,9 @@ is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -99,8 +98,8 @@ by including their suffix, or you can use the "-suffix command-line
switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt
index c9235785866f6856ad438fb934afdcc64d4ba781..af41f6879e80ed299050eb6822553e819e22607f 100644
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -133,10 +133,9 @@ pair_coeff sigma to 1.0 as well.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -148,8 +147,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index d7e87af013f002a6e6472a4ae45e3f5c27fd3de5..55b00a172f56c4063a20298509cc54856d9b276a 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -179,10 +179,9 @@ potential.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -194,8 +193,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt
index ec84a2d57a13d7066fb49624cba932a425447656..9f34ac8c43da024cd0123454dfdc2666116379f3 100644
--- a/doc/src/pair_gromacs.txt
+++ b/doc/src/pair_gromacs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -91,10 +91,9 @@ cutoff(s) specified in the pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -106,8 +105,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt
index 8f1251cf1f3a96aa50e8f9339a69f20b893336bb..809ff008bc86dbaa33e6f899c354957e09a65fef 100644
--- a/doc/src/pair_gw.txt
+++ b/doc/src/pair_gw.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt
index d3cf90ec14c2172faf4eec91a5247724acc3428a..60b0b021743374cc08cfdd5cdc58a8605f02c9b0 100644
--- a/doc/src/pair_hbond_dreiding.txt
+++ b/doc/src/pair_hbond_dreiding.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -33,8 +33,8 @@ pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 :pre
[Description:]
The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD)
-3-body hydrogen bond interaction for the
-"DREIDING"_Section_howto.html#howto_4 force field, given by:
+3-body hydrogen bond interaction for the "DREIDING"_Howto_bioFF.html
+force field, given by:
:c,image(Eqs/pair_hbond_dreiding.jpg)
@@ -65,8 +65,8 @@ potential for the Donor-Acceptor interactions. "(Liu)"_#Liu showed
that the Morse form gives improved results for Dendrimer simulations,
when n = 2.
-See this "howto section"_Section_howto.html#howto_4 of the manual for
-more information on the DREIDING forcefield.
+See the "Howto bioFF"_Howto_bioFF.html doc page for more information
+on the DREIDING forcefield.
NOTE: Because the Dreiding hydrogen bond potential is only one portion
of an overall force field which typically includes other pairwise
@@ -166,10 +166,9 @@ optional parameters.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -181,8 +180,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index d37dedc709b82c43e6c49701f3b7916db93ef6d8..9b36109c279e7381ba5a73aea7adad55dee2f3c7 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -315,8 +315,8 @@ off C/C interaction, i.e. by setting the appropriate coefficients to
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.
Since the {hybrid} and {hybrid/overlay} styles delegate computation to
the individual sub-styles, the suffix versions of the {hybrid} and
@@ -334,8 +334,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index dbc9c458e2997d372b58b7aae7a87cca389c2168..9c9304c4a73ba02e35d575331f135ad32187a81e 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt
index c5d910e27c841f9d71e5e6dfd160bfce0a949b46..889c1e892fe69202a92ca98b02650b982c68c849 100644
--- a/doc/src/pair_kim.txt
+++ b/doc/src/pair_kim.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -46,8 +46,8 @@ are included in the KIM library by default, in the "What is in the KIM
API source package?" section.
To use this pair style, you must first download and install the KIM
-API library from the "OpenKIM website"_https://openkim.org. The "KIM
-section of Section packages"_Section_packages.html#KIM has
+API library from the "OpenKIM website"_https://openkim.org. The KIM
+section of the "Packages details"_Packages_details.html doc page has
instructions on how to do this with a simple make command, when
building LAMMPS.
diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt
index a16d123b89abc938fe172a3a73d123c896687588..8fc6bbff4996ecaefa81e0257048a14c702a7e5d 100644
--- a/doc/src/pair_kolmogorov_crespi_full.txt
+++ b/doc/src/pair_kolmogorov_crespi_full.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index 97f132eacd41e00cd4318cfde24b09e29b4a6ae1..7dad2e3701b852d41a2856e785d80be041f2f5c6 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_lcbop.txt b/doc/src/pair_lcbop.txt
index 148a1d47a067c014d193b14eb3647bbe9c2cd3be..ddf8551d560ff042b8c3d64331db263e5c3d5289 100644
--- a/doc/src/pair_lcbop.txt
+++ b/doc/src/pair_lcbop.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt
index 44cfeb48e96ca4043c8e811d2950ae1243dc126a..c2c6beb97f5490ce4cc11ab6cb3c0634375afc0f 100644
--- a/doc/src/pair_line_lj.txt
+++ b/doc/src/pair_line_lj.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_list.txt b/doc/src/pair_list.txt
index 653e8b0c2d1635c4d10a43889af4b5bd5e99767d..023cc0be4f1c52404fe1f875bdfd86cf03b68e7d 100644
--- a/doc/src/pair_list.txt
+++ b/doc/src/pair_list.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index e297d479bc3ae16d3054130ba67d9bb7fe3a0a97..a55cb348d7568f14dd25c715adf8a7fe382f3a23 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -185,9 +185,9 @@ distance are computed directly; interactions outside that distance are
computed in reciprocal space.
Style {lj/cut/coul/long/cs} is identical to {lj/cut/coul/long} except
-that a term is added for the "core/shell
-model"_Section_howto.html#howto_25 to allow charges on core and shell
-particles to be separated by r = 0.0.
+that a term is added for the "core/shell model"_Howto_coreshell.html
+to allow charges on core and shell particles to be separated by r =
+0.0.
Style {coul/wolf} adds a Coulombic pairwise interaction via the Wolf
summation method, described in "Wolf"_#Wolf1, given by:
@@ -223,16 +223,16 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
-See the "howto section"_Section_howto.html#howto_8 for more
-information on how to use the TIP4P pair styles and lists of
-parameters to set. Note that the neighbor list cutoff for Coulomb
-interactions is effectively extended by a distance 2*qdist when using
-the TIP4P pair style, to account for the offset distance of the
-fictitious charges on O atoms in water molecules. Thus it is
-typically best in an efficiency sense to use a LJ cutoff >= Coulomb
-cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
-to slightly larger cost for the long-range calculation, so you can
-test the trade-off for your model.
+See the "Howto tip4p"_Howto_tip4p.html doc page for more information
+on how to use the TIP4P pair styles and lists of parameters to set.
+Note that the neighbor list cutoff for Coulomb interactions is
+effectively extended by a distance 2*qdist when using the TIP4P pair
+style, to account for the offset distance of the fictitious charges on
+O atoms in water molecules. Thus it is typically best in an
+efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to
+shrink the size of the neighbor list. This leads to slightly larger
+cost for the long-range calculation, so you can test the trade-off for
+your model.
For all of the {lj/cut} pair styles, the following coefficients must
be defined for each pair of atoms types via the
@@ -269,10 +269,9 @@ pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -284,8 +283,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt
index 83f6ec063d4dd6476555a068a7eac6374544a3be..7c68e26acef1c9cf8d21b47fc70ba1109296e502 100644
--- a/doc/src/pair_lj96.txt
+++ b/doc/src/pair_lj96.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -49,10 +49,9 @@ cutoff specified in the pair_style command is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt
index 4ca8c3c141c39c9c874902f96f5178a1b1941d7a..d04a3d8b9d1b6e021ea2df92d2ee16a74ba5e45d 100644
--- a/doc/src/pair_lj_cubic.txt
+++ b/doc/src/pair_lj_cubic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,10 +63,9 @@ located at rmin = 2^(1/6)*sigma. In the above example, sigma =
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -78,8 +77,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index e0838426f637da3e3669fc4c35a17afaa6d6083b..3e9996da4d5507158a37cca38cf1db68597dcfdb 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -53,10 +53,9 @@ optional. If not specified, the global LJ cutoff is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index 6be4562d18849130536383878ac5acc084b20f20..1ba3610f8621801864930acf73a20b4d16bd5a04 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -90,7 +90,7 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
-See the "howto section"_Section_howto.html#howto_8 for more
+See the the "Howto tip4p"_Howto_tip4p.html doc page for more
information on how to use the TIP4P pair style. Note that the
neighbor list cutoff for Coulomb interactions is effectively extended
by a distance 2*qdist when using the TIP4P pair style, to account for
@@ -156,10 +156,9 @@ specified in the pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -171,8 +170,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt
index b1678cad5862cf4670a80a68e7c2074337250ba9..575c023579b4cf5b91927dd241c65d3ee9365c83 100644
--- a/doc/src/pair_lj_smooth.txt
+++ b/doc/src/pair_lj_smooth.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -62,10 +62,9 @@ specified, the global values for Rin and Rc are used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -77,8 +76,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt
index 5f7c226cee3ccc7b83c6139bf2a6c25dd2c13468..0fab768b8fbd9eecc9c80d0760262f9d9ea6111b 100644
--- a/doc/src/pair_lj_smooth_linear.txt
+++ b/doc/src/pair_lj_smooth_linear.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -49,10 +49,9 @@ LJ cutoff specified in the pair_style command is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt
index 2ef133da554adf3d141e337e3c1b9f4139f72f35..d10fcd0472d24ebd91510e0c4793597292e31127 100644
--- a/doc/src/pair_lj_soft.txt
+++ b/doc/src/pair_lj_soft.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -207,10 +207,9 @@ directory tree, under examples/USER/fep.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -222,8 +221,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt
index b39c7545c7e2bdbc90f72631eaadeca06cfe40c5..e9a0a0d2910e5a6036f4993c23e59b0849b88d78 100644
--- a/doc/src/pair_lubricate.txt
+++ b/doc/src/pair_lubricate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -143,7 +143,7 @@ must be specified.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "this section"_Section_accelerate.html of
+hardware, as discussed in "this section"_Speed.html of
the manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
@@ -157,7 +157,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "this section"_Section_accelerate.html of the manual for more
+See "this section"_Speed.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lubricateU.txt b/doc/src/pair_lubricateU.txt
index 720a8539b890c917ab41aa1f0db151c0520a8280..6b74c208bf2c211ec71b9efff608c2345626505e 100644
--- a/doc/src/pair_lubricateU.txt
+++ b/doc/src/pair_lubricateU.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_mdf.txt b/doc/src/pair_mdf.txt
index ca06f1bf8eb12ad7b4050aaa79359f09a100e6fc..e5a8cac845effe56f019729b2660ad001226923d 100644
--- a/doc/src/pair_mdf.txt
+++ b/doc/src/pair_mdf.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt
index c7449428bd05aa010182dc17cb2f9206b69e5303..45f88f0bbec33570565284ab50945076acb85906 100644
--- a/doc/src/pair_meam.txt
+++ b/doc/src/pair_meam.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index 6653b397a0cd04e7dfb56aa1f4c8df9159a9e4a9..96155120419297e54de85192f772f8fcb05216d5 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -106,10 +106,9 @@ MEAM files.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -121,8 +120,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt
index fa731799ddd450445ee07d19f4b45c7cc44cc866..ba0953a17c3957825fac150f3b373c92a5df44b9 100644
--- a/doc/src/pair_meam_sw_spline.txt
+++ b/doc/src/pair_meam_sw_spline.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt
index bcdf717d68cb6d06e84422abffe278f6c382eb94..ad3880e642411c30179bb8a1e9d3b8451cc9c227 100644
--- a/doc/src/pair_meso.txt
+++ b/doc/src/pair_meso.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt
index f8b0c9f0713c99856cbce64bb199ee55068bebbf..09fe61168698455d05fef6b67ed6a80b1b43a962 100644
--- a/doc/src/pair_mgpt.txt
+++ b/doc/src/pair_mgpt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_mie.txt b/doc/src/pair_mie.txt
index ad602db9f1e02cb1792acb2d1711ad0e189eacdc..818e37272bdd28f962195de66868aee119637d79 100644
--- a/doc/src/pair_mie.txt
+++ b/doc/src/pair_mie.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt
index 34dbb5bc3de7acc4f89588d730dc76b407c07d8e..c043fde5a77f7bb68ed0b74dc52d516589ee88f8 100644
--- a/doc/src/pair_modify.txt
+++ b/doc/src/pair_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_momb.txt b/doc/src/pair_momb.txt
index 77c4f184d9380f11848bb7e0deedc719802d130d..545b650f75176e7a32d83ce85312e29720731f0c 100644
--- a/doc/src/pair_momb.txt
+++ b/doc/src/pair_momb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt
index 3eb5ac5afe5b8cb089d5dea24ed02cdea1ec0eec..85a42986ec87ed45e30fe3fc3120587b4d345492 100644
--- a/doc/src/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -101,10 +101,9 @@ cutoff is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -116,8 +115,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_multi_lucy.txt b/doc/src/pair_multi_lucy.txt
index 38fd1ede4aa2201cb8e2cb2733877272f4b91e5c..31d52a58c89386b5cca80afcd4b585c4e314fc15 100644
--- a/doc/src/pair_multi_lucy.txt
+++ b/doc/src/pair_multi_lucy.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt
index 57abcf4a4c30c904b55cd07464ca60118ca13d3c..e09dde3f8051128f22a0817f847b3238061f9ad6 100644
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -204,10 +204,9 @@ This pair style can only be used via the {pair} keyword of the
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -219,8 +218,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt
index 2395707fb45b63425456a1ca612895b90bc289c8..720b9ea2a1f903f42b54525f4481e63f071aa389 100644
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -92,10 +92,9 @@ a particular simulation; LAMMPS ignores those entries.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -107,8 +106,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt
index 81cea1a38d4a255b6fdd01d080cecc67602c3a89..355bfd5573e951c2f28effcc2e4e0aee5c351917 100644
--- a/doc/src/pair_nm.txt
+++ b/doc/src/pair_nm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -133,10 +133,9 @@ the "run_style respa"_run_style.html command. They do not support the
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -148,8 +147,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restrictions:]
diff --git a/doc/src/pair_none.txt b/doc/src/pair_none.txt
index f4e9525198413d49fe26c94ce2795ea12d826d9f..960dc05d97be7d7dda8889bb129d348c9578f374 100644
--- a/doc/src/pair_none.txt
+++ b/doc/src/pair_none.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt
index f272d15a8680d6499df5f7164186789426589413..5ec99152978f42f5f603a1c87329ad005093583f 100644
--- a/doc/src/pair_oxdna.txt
+++ b/doc/src/pair_oxdna.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt
index 1b55031b2c97dc8c935c0ddb83a567f24d64ab6f..a1d2cfdb7c862f96affbd60ec4d216baef0795bc 100644
--- a/doc/src/pair_oxdna2.txt
+++ b/doc/src/pair_oxdna2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt
index deca093e3bb1cebb7183f9bb7b8b0df866c09df8..14abd4541e4b3f33d1dac80119d894f8b758608e 100644
--- a/doc/src/pair_peri.txt
+++ b/doc/src/pair_peri.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -139,10 +139,9 @@ details please see the description in "(Mtchell2011a)".
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -154,8 +153,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt
index c088e8bb2242918fe221ab1241cba70129d6c5f7..eb0c30f249cff1b58a11e21dcb2ff5df14a599fb 100644
--- a/doc/src/pair_polymorphic.txt
+++ b/doc/src/pair_polymorphic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt
index 2f8ed7a27c6702b9e80a82d0a14201f714430bd7..1433557e0388e581c94b2668ecc2721fdeea1928 100644
--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt
index 9436b0c4ed1f71b78d18880d411e64855e727aca..3570a52801852be5207d72ef27a45438518ef6bb 100644
--- a/doc/src/pair_quip.txt
+++ b/doc/src/pair_quip.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_reax.txt b/doc/src/pair_reax.txt
index 1d13f937061c95963165efc936a680ca14415147..a3b84955cd058937fd28cb84732656e2f3f055ef 100644
--- a/doc/src/pair_reax.txt
+++ b/doc/src/pair_reax.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt
index 39759b3111825077e3ee0e4dffe54b2eeecd4915..ec575486404904c6b92dd165e4d6ae490e8a7303 100644
--- a/doc/src/pair_reaxc.txt
+++ b/doc/src/pair_reaxc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -50,11 +50,11 @@ as a package.
The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that
is derived from the {reax/c} style. The Kokkos version can run on GPUs
and can also use OpenMP multithreading. For more information about the
-Kokkos package, see "Section 4"_Section_packages.html#kokkos and
-"Section 5.3.3"_accelerate_kokkos.html. One important consideration
-when using the {reax/c/kk} style is the choice of either half or full
-neighbor lists. This setting can be changed using the Kokkos
-"package"_package.html command.
+Kokkos package, see "Packages details"_Packages_details.html and
+"Speed kokkos"_Speed_kokkos.html doc pages. One important
+consideration when using the {reax/c/kk} style is the choice of either
+half or full neighbor lists. This setting can be changed using the
+Kokkos "package"_package.html command.
The {reax/c} style differs from the "pair_style reax"_pair_reax.html
command in the lo-level implementation details. The {reax} style is a
@@ -303,10 +303,9 @@ This pair style can only be used via the {pair} keyword of the
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -318,8 +317,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt
index 9ad95eb5fc4e9ddc0bb3f9eda4a1751b0afba726..6e72408ebc1a7243f3d01aadaa79dd02afd66553 100644
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -145,10 +145,9 @@ specified in the pair_style command is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -160,8 +159,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt
index 360136a4eaef3df735b65cfc0f8e7ce5ca78dc16..ccf704b6f7f85b163fdcdd375b8821146ee37c37 100644
--- a/doc/src/pair_sdk.txt
+++ b/doc/src/pair_sdk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -85,10 +85,9 @@ pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp} or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP, and OPT packages respectively. They are only enabled if
@@ -100,8 +99,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_smd_hertz.txt b/doc/src/pair_smd_hertz.txt
index eeaa3387a44a834cfe4361a75e40d2610d29bdb6..f2d633903ab99a90ac5485e1f871c994b872f69a 100644
--- a/doc/src/pair_smd_hertz.txt
+++ b/doc/src/pair_smd_hertz.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_smd_tlsph.txt b/doc/src/pair_smd_tlsph.txt
index f73acf74ee5b1a842d2b8cd1a7ed7c632885dd75..3aeaa3155382ee4b0b0b34c0bc8beaa381c68bac 100644
--- a/doc/src/pair_smd_tlsph.txt
+++ b/doc/src/pair_smd_tlsph.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/src/pair_smd_triangulated_surface.txt
index c32bf3a22ea89c35efd3231b0ffbfdd72590a810..65526cfba8cc15a6be2d8dd22510106b5d6a40cf 100644
--- a/doc/src/pair_smd_triangulated_surface.txt
+++ b/doc/src/pair_smd_triangulated_surface.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt
index 268fe78d02294eca17134ff7fcffb276512db2be..a5bda54d5f0c46d792fc23bdbdba13f6168bbeee 100644
--- a/doc/src/pair_smd_ulsph.txt
+++ b/doc/src/pair_smd_ulsph.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt
index c8d6b21b3f1f024421dc56426aa32da817d887f7..c70202c2e13f536307ad84c1f50133490e8bff72 100644
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt
index 27dcf6082b892b5a5df64442f2045215c8d5dbd8..f9bd8910e49ddfe37a044cf9e801f937a1b0cd7e 100644
--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -175,10 +175,9 @@ This pair style can only be used via the {pair} keyword of the
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -190,8 +189,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt
index 08fa88c477961677b4aafd786e13ad1b89befed9..374711825b5d4bbf656d15fab9a3753c6f2239ce 100644
--- a/doc/src/pair_soft.txt
+++ b/doc/src/pair_soft.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -82,10 +82,9 @@ variables.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -97,8 +96,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt
index 2387056a1b7b4b06235c3d8d88ad5edec4bccbdf..d19c28a3cb5a0fec2f893d69fc23715abed8ae64 100644
--- a/doc/src/pair_sph_heatconduction.txt
+++ b/doc/src/pair_sph_heatconduction.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt
index 957f901425993d91b248c9a7172a45b0753abd44..a670949a892025d8d30ca9a5d63134020483ddc3 100644
--- a/doc/src/pair_sph_idealgas.txt
+++ b/doc/src/pair_sph_idealgas.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt
index ef89c4ad3eaf351d07dad07e953b6dc4ea3eb139..152e6cf8a292cd5b03f895ff84282b9ac6652d63 100644
--- a/doc/src/pair_sph_lj.txt
+++ b/doc/src/pair_sph_lj.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_sph_rhosum.txt b/doc/src/pair_sph_rhosum.txt
index 352e717f76484a2b3c2c993560646fd110869b60..3cd1c5abb2577e0d7c155d7d5cedd9ae1b768307 100644
--- a/doc/src/pair_sph_rhosum.txt
+++ b/doc/src/pair_sph_rhosum.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt
index 9177ca80b868e417e3bf8a23d30f267fd882f3ff..7b9a8188f28b36d30e7a71d64d8b49024ffadd1e 100644
--- a/doc/src/pair_sph_taitwater.txt
+++ b/doc/src/pair_sph_taitwater.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/src/pair_sph_taitwater_morris.txt
index e6c5a6bb20dc302fa3105af4c3c224d9e2411b98..02f16d8982f5af327d25e4ce43fbeb9fa877015b 100644
--- a/doc/src/pair_sph_taitwater_morris.txt
+++ b/doc/src/pair_sph_taitwater_morris.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt
index 24877906f3de032b60b88db2cdc11ca3d7140f49..375e59fe89486ebec90679a9a4c08b20f9655bb4 100644
--- a/doc/src/pair_spin_dmi.txt
+++ b/doc/src/pair_spin_dmi.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -25,24 +25,46 @@ pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre
[Description:]
Style {spin/dmi} computes the Dzyaloshinskii-Moriya (DM) interaction
-between pairs of magnetic spins:
+between pairs of magnetic spins.
+According to the expression reported in "(Rohart)"_#Rohart, one has
+the following DM energy:
:c,image(Eqs/pair_spin_dmi_interaction.jpg)
where si and sj are two neighboring magnetic spins of two particles,
-eij = (ri - rj)/|ri-rj| is the normalized separation vector between the
-two particles, and D is the DM vector defining the intensity and the
-sign of the interaction.
+eij = (ri - rj)/|ri-rj| is the unit vector between sites i and j,
+and D is the DM vector defining the intensity (in eV) and the direction
+of the interaction.
-Examples and more explanations about this interaction and its parametrization are
-reported in "(Tranchida)"_#Tranchida5.
+In "(Rohart)"_#Rohart, D is defined as the direction normal to the film oriented
+from the high spin-orbit layer to the magnetic ultrathin film.
-From this DM interaction, each spin i will be submitted to a magnetic torque
-omega and its associated atom to a force F (for spin-lattice calculations only).
+The application of a spin-lattice Poisson bracket to this energy (as described
+in "(Tranchida)"_#Tranchida5) allows to derive a magnetic torque omega, and a
+mechanical force F (for spin-lattice calculations only) for each magnetic
+particle i:
+
+:c,image(Eqs/pair_spin_dmi_forces.jpg)
More details about the derivation of these torques/forces are reported in
"(Tranchida)"_#Tranchida5.
+For the {spin/dmi} pair style, the following coefficients must be defined for
+each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in
+the examples above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html commands, and
+set in the following order:
+
+rc (distance units)
+|D| (energy units)
+Dx, Dy, Dz (direction of D) :ul
+
+Note that rc is the radius cutoff of the considered DM interaction, |D| is
+the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction.
+
+None of those coefficients is optional. If not specified, the {spin/dmi}
+pair style cannot be used.
+
:line
[Restrictions:]
@@ -61,6 +83,9 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
:line
+:link(Rohart)
+[(Rohart)] Rohart and Thiaville,
+Physical Review B, 88(18), 184422. (2013).
:link(Tranchida5)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, (2018).
diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt
index ad3357cb5eebcfab4c12567752fbf95711ecb6a1..24eb635b819cd1982c5bc4a37d3e48950e13c28c 100644
--- a/doc/src/pair_spin_exchange.txt
+++ b/doc/src/pair_spin_exchange.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,18 +32,15 @@ pairs of magnetic spins:
where si and sj are two neighboring magnetic spins of two particles,
rij = ri - rj is the inter-atomic distance between the two particles,
and J(rij) is a function defining the intensity and the sign of the exchange
-interaction.
-
-This function is defined as:
+interaction for different neighboring shells. This function is defined as:
:c,image(Eqs/pair_spin_exchange_function.jpg)
where a, b and d are the three constant coefficients defined in the associated
-"pair_coeff" command.
+"pair_coeff" command (see below for more explanations).
The coefficients a, b, and d need to be fitted so that the function above matches with
the value of the exchange interaction for the N neighbor shells taken into account.
-
Examples and more explanations about this function and its parametrization are reported
in "(Tranchida)"_#Tranchida3.
@@ -54,11 +51,30 @@ such as:
:c,image(Eqs/pair_spin_exchange_forces.jpg)
-with h the Planck constant (in metal units).
+with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit
+vector between sites i and j.
More details about the derivation of these torques/forces are reported in
"(Tranchida)"_#Tranchida3.
+For the {spin/exchange} pair style, the following coefficients must be defined
+for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in
+the examples above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html commands, and
+set in the following order:
+
+rc (distance units)
+a (energy units)
+b (adim parameter)
+d (distance units) :ul
+
+Note that rc is the radius cutoff of the considered exchange interaction,
+and a, b and d are the three coefficients performing the parametrization
+of the function J(rij) defined above.
+
+None of those coefficients is optional. If not specified, the
+{spin/exchange} pair style cannot be used.
+
:line
[Restrictions:]
diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt
index 8ba24c46af2b98102e872b16f4c423336410338a..b338fae5dcdc3597e16dda8df691a012025114c1 100644
--- a/doc/src/pair_spin_magelec.txt
+++ b/doc/src/pair_spin_magelec.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt
index 8551f8d63650f50fd355903028cefd64eb96ed4c..0967632ed2037ccac12228f089b56c31c8272ad1 100644
--- a/doc/src/pair_spin_neel.txt
+++ b/doc/src/pair_spin_neel.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_srp.txt b/doc/src/pair_srp.txt
index e7f1e00d1028635db3c8cce28097cf62d54fa7d3..e784ac3d17d5f8fc0415003a6a084560d3a6a3c3 100644
--- a/doc/src/pair_srp.txt
+++ b/doc/src/pair_srp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index 7e29544a70ac83cbd74cbd0811b6cab9c991d30b..b0872e6447618882acfba7ef05bf4b8adca48e59 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -78,22 +78,22 @@ previously specified pair_coeff values.
:line
Here is an alphabetic list of pair styles defined in LAMMPS. They are
-also given in more compact form in the pair section of "this
-page"_Section_commands.html#cmd_5.
+also listed in more compact form on the "Commands
+pair"_Commands_pair.html doc page.
Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
associated "pair_coeff"_pair_coeff.html command.
There are also additional pair styles (not listed here) submitted by
-users which are included in the LAMMPS distribution. The list of
-these with links to the individual styles are given in the pair
-section of "this page"_Section_commands.html#cmd_5.
+users which are included in the LAMMPS distribution. The full list of
+all pair styles is on the "Commands pair"_Commands_pair.html doc page.
There are also additional accelerated pair styles (not listed here)
-included in the LAMMPS distribution for faster performance on CPUs and
-GPUs. The list of these with links to the individual styles are given
-in the pair section of "this page"_Section_commands.html#cmd_5.
+included in the LAMMPS distribution for faster performance on CPUs,
+GPUs, and KNLs. The individual style names on the "Commands
+pair"_Commands_pair.html doc page are followed by one or more of
+(g,i,k,o,t) to indicate which accerlerated styles exist.
"pair_style none"_pair_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
@@ -105,7 +105,7 @@ in the pair section of "this page"_Section_commands.html#cmd_5.
"pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
"pair_style atm"_pair_atm.html - Axilrod-Teller-Muto potential
"pair_style beck"_pair_beck.html - Beck potential
-"pair_style body"_pair_body.html - interactions between body particles
+"pair_style body/nparticle"_pair_body_nparticle.html - interactions between body particles
"pair_style bop"_pair_bop.html - BOP potential of Pettifor
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics
diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt
index 4932fe55d335bb101db35e478f0681ffe416a69d..e6741791dfe8d103ded1dbcfc27a9bcaf70e9527 100644
--- a/doc/src/pair_sw.txt
+++ b/doc/src/pair_sw.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -144,10 +144,9 @@ taken from the ij and ik pairs (sigma, a, gamma)
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -164,8 +163,8 @@ additional 5 to 10 percent performance improvement when the
Stillinger-Weber parameters p and q are set to 4 and 0 respectively.
These parameters are common for modeling silicon and water.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt
index b99491b477224e621da4429d10c0b20b84c66c0d..5e3c1f5ff6f2e1bf58c27589afc653c71c569d18 100644
--- a/doc/src/pair_table.txt
+++ b/doc/src/pair_table.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -217,10 +217,9 @@ one that matches the specified keyword.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -232,8 +231,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt
index cd3a7ef31b87d15268cfe93050889b4699a4adc7..41be067bacfcc6eb60286b7f259926c2729e832b 100644
--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -227,10 +227,9 @@ This pair style can only be used via the {pair} keyword of the
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -242,8 +241,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index 918e88992440045bda099cb2ad9849ab4faeff14..821c38f3e4174310f43c6ee504ede9b194ebdab8 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -179,10 +179,9 @@ defined in various papers.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -194,8 +193,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt
index e0c2b5a5cbb07b7c525d58d48eab97cb763971ca..ac1f79a80b772f602f951ed34e373eb3b8bb0f0b 100644
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -131,10 +131,9 @@ for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -146,8 +145,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt
index 21d57e4e8841570f44f114961af653ad9dde93b4..a89d4e3ea1fbce4376fa787123d1a98bf25dbbb2 100644
--- a/doc/src/pair_tersoff_zbl.txt
+++ b/doc/src/pair_tersoff_zbl.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -189,10 +189,9 @@ providing the base ZBL implementation.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -204,8 +203,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt
index 41a4059cee8d4de828d136343a282310f493403d..7ce8b7cf4bed33dc699d8c08197b01392d1d6ac3 100644
--- a/doc/src/pair_thole.txt
+++ b/doc/src/pair_thole.txt
@@ -9,7 +9,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -45,8 +45,8 @@ pair_style lj/cut/thole/long 2.6 12.0 :pre
The {thole} pair styles are meant to be used with force fields that
include explicit polarization through Drude dipoles. This link
describes how to use the "thermalized Drude oscillator
-model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS
-are discussed in "this Section"_Section_howto.html#howto_25.
+model"_Howto_drude.html in LAMMPS and polarizable models in LAMMPS are
+discussed on the "Howto polarizable"_Howto_polarizable.html doc page.
The {thole} pair style should be used as a sub-style within in the
"pair_hybrid/overlay"_pair_hybrid.html command, in conjunction with a
@@ -130,10 +130,9 @@ the {pair_style} command line.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -145,8 +144,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Mixing]:
diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt
index 42a5bbdfe2285c61c67ad980eecca779666f553b..3915ffc2383c79220f2b403f7e2d43dc0041ab1e 100644
--- a/doc/src/pair_tri_lj.txt
+++ b/doc/src/pair_tri_lj.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt
index 88a22864ccaf960472dbe5ea3f985ea2d375ab23..dbc6fd0664b99572fd39dcab68c60003ceef722f 100644
--- a/doc/src/pair_ufm.txt
+++ b/doc/src/pair_ufm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -69,10 +69,9 @@ NOTE: The thermodynamic integration procedure can be performed with this potenti
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -84,8 +83,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt
index d9c66d45c0cae201fa12b3799bdf562dc9f55a91..2e404e8befcba50b462a0efbb61b48f0ba8cc82e 100644
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -171,10 +171,9 @@ two-body parameters from the CCC and CSiSi entries.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -186,8 +185,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_write.txt b/doc/src/pair_write.txt
index 9f5970fcbc6c8c406746d752ac281e2eec3ebc9e..48ad76e76eabf624459cb37139e77ef4a09385f0 100644
--- a/doc/src/pair_write.txt
+++ b/doc/src/pair_write.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt
index e7c063ded9f41227210e17970dc9fb7cc59ed757..5a8363260a5e31f507d279500ea9eb2c78199758 100644
--- a/doc/src/pair_yukawa.txt
+++ b/doc/src/pair_yukawa.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -49,10 +49,9 @@ cutoff is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt
index 2037a9451f9e77079971382afde16709657c88e7..515062d9eb679cefc969f91e41c376b265541bd4 100644
--- a/doc/src/pair_yukawa_colloid.txt
+++ b/doc/src/pair_yukawa_colloid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -80,10 +80,9 @@ yukawa/colloid cutoff is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt
index 1984cd831f6bf2fef81c9f2ef39c16b04284e309..1472c7b6726d970179eeacd97915edabdfcdd55c 100644
--- a/doc/src/pair_zbl.txt
+++ b/doc/src/pair_zbl.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -71,10 +71,9 @@ copper.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -86,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_zero.txt b/doc/src/pair_zero.txt
index e58b33c75f4d0261d43a6eafee975c470e79c627..b324003bd1ca252e6ecaa8a341219dfb11d521cd 100644
--- a/doc/src/pair_zero.txt
+++ b/doc/src/pair_zero.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 1a5e98a10964f63e7c2c3cfbf8a4faaef3967271..4c3eef2cd11c32ea4801ebb830a6a985cc5a734b 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -10,8 +10,9 @@ Pair Styles :h1
pair_airebo
pair_awpmd
pair_beck
- pair_body
+ pair_body_nparticle
pair_body_rounded_polygon
+ pair_body_rounded_polyhedron
pair_bop
pair_born
pair_brownian
diff --git a/doc/src/partition.txt b/doc/src/partition.txt
index 610eee99b300bd96486991c1841cfde1a2b1d8e5..d4fe06c098fd2de94520c38b96346407a0cbf3b9 100644
--- a/doc/src/partition.txt
+++ b/doc/src/partition.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/prd.txt b/doc/src/prd.txt
index 3c0305e316d4e5c8a321e27ad4662a5dc1807d40..b2145ebad1a43ac0037f484f030a945479dd0ecb 100644
--- a/doc/src/prd.txt
+++ b/doc/src/prd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -69,8 +69,8 @@ simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. However for PRD, this makes little sense, since running a
replica on virtual instead of physical processors,offers no effective
-parallel speed-up in searching for infrequent events. See "Section
-6.5"_Section_howto.html#howto_5 of the manual for further discussion.
+parallel speed-up in searching for infrequent events. See the "Howto
+replica"_Howto_replica.html doc page for further discussion.
When a PRD simulation is performed, it is assumed that each replica is
running the same model, though LAMMPS does not check for this.
diff --git a/doc/src/print.txt b/doc/src/print.txt
index 77e0c7cfd3d64ed7a6bfeb6dcd17b716f0b1e1f3..476d4104fab9bfcf41aa9ef7b7216523e6faf0d4 100644
--- a/doc/src/print.txt
+++ b/doc/src/print.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/processors.txt b/doc/src/processors.txt
index e54b2cede3b94e8bb13324c22f3352601b8b79d8..df13ae1f617fd9507bdbf7192b52d668c3ca44df 100644
--- a/doc/src/processors.txt
+++ b/doc/src/processors.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/python.txt b/doc/src/python.txt
index d670fcc77f8ef4377c829ae0fa486fa9ba8347a1..4f4faca8f43c5fc6ca5db28f748238798405b862 100644
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -199,9 +199,9 @@ The {here} keyword does the same thing, except that the Python code
follows as a single argument to the {here} keyword. This can be done
using triple quotes as delimiters, as in the examples above. This
allows Python code to be listed verbatim in your input script, with
-proper indentation, blank lines, and comments, as desired. See
-"Section 3.2"_Section_commands.html#cmd_2, for an explanation of how
-triple quotes can be used as part of input script syntax.
+proper indentation, blank lines, and comments, as desired. See the
+"Commands parse"_Commands_parse.html doc page, for an explanation of
+how triple quotes can be used as part of input script syntax.
The {exists} keyword takes no argument. It means that Python code
containing the required Python function defined by the {func} setting,
diff --git a/doc/src/quit.txt b/doc/src/quit.txt
index 843d3de7f3545dfd330f7e7624fe21a3c3c6e430..802df97711e5c4b38e816f12f18043440cb669f3 100644
--- a/doc/src/quit.txt
+++ b/doc/src/quit.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index fd297e36c121e1efb8f631c95c182a51587a60c0..ded51a4d99855abfd9abc4361c1f0f2b052729dd 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -322,9 +322,9 @@ with tilt factors that exceed these limits, you can use the "box
tilt"_box.html command, with a setting of {large}; a setting of
{small} is the default.
-See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
-for a geometric description of triclinic boxes, as defined by LAMMPS,
-and how to transform these parameters to and from other commonly used
+See the "Howto triclinic"_Howto_triclinic.html doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
triclinic representations.
When a triclinic system is used, the simulation domain should normally
@@ -772,9 +772,9 @@ the "bodies" keyword.
Each body can have a variable number of integer and/or floating-point
values. The number and meaning of the values is defined by the body
-style, as described in the "body"_body.html doc page. The body style
-is given as an argument to the "atom_style body"_atom_style.html
-command.
+style, as described in the "Howto body"_Howto_body.html doc page. The
+body style is given as an argument to the "atom_style
+body"_atom_style.html command.
The Ninteger and Ndouble values determine how many integer and
floating-point values are specified for this particle. Ninteger and
diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt
index 21c6df5017a50b8bf35ef43198c659f60ae4fb51..a3c0733e07369da85b63f222069ce12b224a3f13 100644
--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt
index 6f6a82822929d26afd5d0a10ad9c28aa3bd252f7..488c36f02081d5be3c3a9a9067ed2638e4738c63 100644
--- a/doc/src/read_restart.txt
+++ b/doc/src/read_restart.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/region.txt b/doc/src/region.txt
index 5039e4a51615164a410bd85ff6572ac41d3a8bf6..21396ae1fd2b6652fc6928d24f685cfc39bc7031 100644
--- a/doc/src/region.txt
+++ b/doc/src/region.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -186,9 +186,9 @@ functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent radius.
-See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
-for a geometric description of triclinic boxes, as defined by LAMMPS,
-and how to transform these parameters to and from other commonly used
+See the "Howto tricilinc"_Howto_triclinic.html doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
triclinic representations.
The {union} style creates a region consisting of the volume of all the
@@ -358,12 +358,12 @@ sub-regions can be defined with the {open} keyword.
:line
-Styles with a {kk} suffix are functionally the same as the
-corresponding style without the suffix. They have been optimized to
-run faster, depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
The code using the region (such as a fix or compute) must also be supported
by Kokkos or no acceleration will occur. Currently, only {block} style
@@ -378,8 +378,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt
index 08523ecdd848a58ff04b8b63747fcd6c5c388914..0195dce9114f4a3d0bf30a805a1c0f0e31a70be7 100644
--- a/doc/src/replicate.txt
+++ b/doc/src/replicate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt
index edf94cc711c2e5a1ff7b34efed059b7e77327981..8eb3ebd5a19458aec21e3c799ef80cacf936e998 100644
--- a/doc/src/rerun.txt
+++ b/doc/src/rerun.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/reset_ids.txt b/doc/src/reset_ids.txt
index 8655a9d54f3c5b0f7e97512f6553dd6246bfa321..391b51fde99e167d813bef98b3a62f96786ed1de 100644
--- a/doc/src/reset_ids.txt
+++ b/doc/src/reset_ids.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/reset_timestep.txt b/doc/src/reset_timestep.txt
index 79a5812ca1f2a569c23d71e48a6dc8ffcc89d002..0d518655fb774108eb95da66297d854300d945b5 100644
--- a/doc/src/reset_timestep.txt
+++ b/doc/src/reset_timestep.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 7c39ae1404eebb9c70d1c7a99730d00200a25af2..6f2dc5ca467c354a9c576d467af4c5d49c1e9301 100644
--- a/doc/src/restart.txt
+++ b/doc/src/restart.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/run.txt b/doc/src/run.txt
index 913d81bb4d05c46274d5127bed7e6fb483732507..c7c73463d92d49bb8e72ca9b549e38d50960f67a 100644
--- a/doc/src/run.txt
+++ b/doc/src/run.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -127,9 +127,9 @@ be redefined, e.g. to reset a thermostat temperature. Or this could
be useful for invoking a command you have added to LAMMPS that wraps
some other code (e.g. as a library) to perform a computation
periodically during a long LAMMPS run. See the "Modify"_Modify.html
-doc page for info about how to add new commands to LAMMPS. See "this
-section"_Section_howto.html#howto_10 of the documentation for ideas
-about how to couple LAMMPS to other codes.
+doc page for info about how to add new commands to LAMMPS. See the
+"Howto couple"_Howto_couple.html doc page for ideas about how to
+couple LAMMPS to other codes.
With the {every} option, N total steps are simulated, in shorter runs
of M steps each. After each M-length run, the specified commands are
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index 7717ede86f085b3433234ee3b9f0c95596fd5b8d..deee51cfd3d6fc0857ea99b5b169d323cbc323c7 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -119,13 +119,13 @@ switches"_Section_start.html#start_6 to change this. The log and
screen file for the 2nd partition will not contain thermodynamic
output beyond the 1st timestep of the run.
-See "Section 5"_Section_accelerate.html of the manual for
-performance details of the speed-up offered by the {verlet/split}
-style. One important performance consideration is the assignment of
-logical processors in the 2 partitions to the physical cores of a
-parallel machine. The "processors"_processors.html command has
-options to support this, and strategies are discussed in
-"Section 5"_Section_accelerate.html of the manual.
+See the "Speed packages"_Speed_packages.html doc page for performance
+details of the speed-up offered by the {verlet/split} style. One
+important performance consideration is the assignment of logical
+processors in the 2 partitions to the physical cores of a parallel
+machine. The "processors"_processors.html command has options to
+support this, and strategies are discussed in "Section
+5"_Speed.html of the manual.
:line
@@ -274,21 +274,21 @@ run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre
:line
-The {respa/omp} styles is a variant of {respa} adapted for use with
+The {respa/omp} style is a variant of {respa} adapted for use with
pair, bond, angle, dihedral, improper, or kspace styles with an {omp}
-suffix. It is functionally equivalent to {respa} but performs additional
-operations required for managing {omp} styles. For more on {omp} styles
-see the "Section 5"_Section_accelerate.html of the manual.
-Accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+suffix. It is functionally equivalent to {respa} but performs
+additional operations required for managing {omp} styles. For more on
+{omp} styles see the "Speed omp"_Speed_omp.html doc page. Accelerated
+styles take the same arguments and should produce the same results,
+except for round-off and precision issues.
You can specify {respa/omp} explicitly in your input script, or
you can use the "-suffix command-line switch"_Section_start.html#start_6
when you invoke LAMMPS, or you can use the "suffix"_suffix.html
command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/set.txt b/doc/src/set.txt
index d2235d5c32bc03426c8f7c584c10c5fc2b6a7f1c..b83ad54f4e5fbef3b26a01372e0f3d959db90c9a 100644
--- a/doc/src/set.txt
+++ b/doc/src/set.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/shell.txt b/doc/src/shell.txt
index 205164f874173abd4de45b045e91ec741092acb9..d274f498e595c5abcfca59c182bd36c827016c90 100644
--- a/doc/src/shell.txt
+++ b/doc/src/shell.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt
index 1021c4856b02cc7cb91901d429eb8c1fc2ca22c4..a57b61664d56e76b28d3aad9f2059bdbb24a9c31 100644
--- a/doc/src/special_bonds.txt
+++ b/doc/src/special_bonds.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt
index 74f69b6dfe96296259f536c80e621b23b89edef1..bb0619f1e04af5ab1bafc7772c2e40f09e1f3767 100644
--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/tad.txt b/doc/src/tad.txt
index f5e7c6d6537cc50d6e3905249b847cca20cc7eed..a26ff79318ceed4f91cd402bb095a08c546baea5 100644
--- a/doc/src/tad.txt
+++ b/doc/src/tad.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -92,9 +92,8 @@ restricts you to having exactly one processor per replica. For more
information, see the documentation for the "neb"_neb.html command. In
the current LAMMPS implementation of TAD, all the non-NEB TAD
operations are performed on the first partition, while the other
-partitions remain idle. See "Section
-6.5"_Section_howto.html#howto_5 of the manual for further discussion of
-multi-replica simulations.
+partitions remain idle. See the "Howto replica"_Howto_replica.html doc
+page for further discussion of multi-replica simulations.
A TAD run has several stages, which are repeated each time an event is
performed. The logic for a TAD run is as follows:
diff --git a/doc/src/temper.txt b/doc/src/temper.txt
index b1c47c8076e1affde9b4c4ecc45c89148ddbd412..c7b482acc6467948a15321a363e138f5fb1962ae 100644
--- a/doc/src/temper.txt
+++ b/doc/src/temper.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,14 +32,13 @@ replicas (ensembles) of a system. Two or more replicas must be used.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
-switch; see "Section 2.6"_Section_start.html#start_6 of the
-manual. Note that if you have MPI installed, you can run a
-multi-replica simulation with more replicas (partitions) than you have
-physical processors, e.g you can run a 10-replica simulation on one or
-two processors. You will simply not get the performance speed-up you
-would see with one or more physical processors per replica. See "this
-section"_Section_howto.html#howto_5 of the manual for further
-discussion.
+switch; see "Section 2.6"_Section_start.html#start_6 of the manual.
+Note that if you have MPI installed, you can run a multi-replica
+simulation with more replicas (partitions) than you have physical
+processors, e.g you can run a 10-replica simulation on one or two
+processors. You will simply not get the performance speed-up you
+would see with one or more physical processors per replica. See the
+"Howto replica"_Howto_replica.html doc page for further discussion.
Each replica's temperature is controlled at a different value by a fix
with {fix-ID} that controls temperature. Most thermostat fix styles
diff --git a/doc/src/temper_grem.txt b/doc/src/temper_grem.txt
index 6145c8704cc131b96d21464031c9697733be02d1..9cb1bab78465c890c0f6377d9c5fb45d0803b145 100644
--- a/doc/src/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt
index 4ad49f9e3327ded89da41c2fd405929175990a67..4eee225de73cfd0e3ea3b4354a293d902fa8250c 100644
--- a/doc/src/temper_npt.txt
+++ b/doc/src/temper_npt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
temper/npt command :h3
diff --git a/doc/src/thermo.txt b/doc/src/thermo.txt
index 1d5d34995cd3cc979f3537b529950032be2ea4ba..5f12f987076bc54f50df9cbd5f37aa9c2be40b7e 100644
--- a/doc/src/thermo.txt
+++ b/doc/src/thermo.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/thermo_modify.txt b/doc/src/thermo_modify.txt
index e9aca0f20a1b2ed5c2d90ec3a70714c2dea25bf4..ca2957de776a5d3054da85a0eddfbcaad25bedf9 100644
--- a/doc/src/thermo_modify.txt
+++ b/doc/src/thermo_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt
index 18c5ad5ba1ce9ecedf74156c8f78a073101e8374..cbc2612f28c69a49bcd4dcb28b3b1c7a132fd85c 100644
--- a/doc/src/thermo_style.txt
+++ b/doc/src/thermo_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -286,11 +286,11 @@ takes place.
The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta},
{cellgamma}, correspond to the usual crystallographic quantities that
-define the periodic unit cell of a crystal. See "this
-section"_Section_howto.html#howto_12 of the doc pages for a geometric
-description of triclinic periodic cells, including a precise definition
-of these quantities in terms of the internal LAMMPS cell dimensions
-{lx}, {ly}, {lz}, {yz}, {xz}, {xy}.
+define the periodic unit cell of a crystal. See the "Howto
+triclinic"_Howto_triclinic.html doc page for a geometric description
+of triclinic periodic cells, including a precise definition of these
+quantities in terms of the internal LAMMPS cell dimensions {lx}, {ly},
+{lz}, {yz}, {xz}, {xy}.
:line
diff --git a/doc/src/timer.txt b/doc/src/timer.txt
index 768c3e1353fb3e6495f63f2d84830c060b4bf74a..10737dbda0cebfea9b99582c28327168aa55faa6 100644
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/timestep.txt b/doc/src/timestep.txt
index 639ad6f31136ff9a34f085b8d254b983a9e1ba4d..ee0ace05b9cf7397539cf615e4a87217270f4949 100644
--- a/doc/src/timestep.txt
+++ b/doc/src/timestep.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/tutorials.txt b/doc/src/tutorials.txt
deleted file mode 100644
index 338439ac8e9387c080e8bfd32bf237e85984ec0e..0000000000000000000000000000000000000000
--- a/doc/src/tutorials.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-Tutorials :h1
-
-<!-- RST
-
-.. toctree::
- :maxdepth: 1
-
- tutorial_drude
- tutorial_github
- tutorial_pylammps
- tutorial_bash_on_windows
- body
- manifolds
-
-END_RST -->
diff --git a/doc/src/uncompute.txt b/doc/src/uncompute.txt
index 49b46781d7ac363156674ef935881dacab2e048f..4c788d472207b302a51f73abddaf34803cae5062 100644
--- a/doc/src/uncompute.txt
+++ b/doc/src/uncompute.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/undump.txt b/doc/src/undump.txt
index a2a371aca5187a9248e8e33e33792087040a66e7..cc3d8b9103ffd2d9eff33bf3dbaefda820c29903 100644
--- a/doc/src/undump.txt
+++ b/doc/src/undump.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/unfix.txt b/doc/src/unfix.txt
index dcc4499b20b4b784779f9038b30c541a5585335e..9608b39c7e2c2056023b9da6607b8e280ed52a11 100644
--- a/doc/src/unfix.txt
+++ b/doc/src/unfix.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/units.txt b/doc/src/units.txt
index 0b856dcc68b67a9f7df9f159e779f8fb5a097379..8df8fe6810ec1163f366a7e53ad4f019418425da 100644
--- a/doc/src/units.txt
+++ b/doc/src/units.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/variable.txt b/doc/src/variable.txt
index 717c77c07908099a76f4f32991697bfcb8294bc6..c6598ccb514d2855259038e99d1560488f7cdff9 100644
--- a/doc/src/variable.txt
+++ b/doc/src/variable.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -124,8 +124,8 @@ provide, so that the variable gets its value from the evaluation of
the Python code. Variables of style {internal} are used by a few
commands which set their value directly.
-NOTE: As discussed in "Section 3.2"_Section_commands.html#cmd_2 of the
-manual, an input script can use "immediate" variables, specified as
+NOTE: As discussed on the "Commands parse"_Commands_parse.html doc
+page, an input script can use "immediate" variables, specified as
$(formula) with parenthesis, where the formula has the same syntax as
equal-style variables described on this page. This is a convenient
way to evaluate a formula immediately without using the variable
@@ -198,7 +198,7 @@ the same thing.
:line
-"This section"_Section_commands.html#cmd_2 of the manual explains how
+The "Commands parse"_Commands_parse.html doc page explains how
occurrences of a variable name in an input script line are replaced by
the variable's string. The variable name can be referenced as $x if
the name "x" is a single character, or as $\{LoopVar\} if the name
@@ -312,8 +312,8 @@ If you simply wish to print a variable value with desired precision to
the screen or logfile via the "print"_print.html or "fix
print"_fix_print.html commands, you can also do this by specifying an
"immediate" variable with a trailing colon and format string, as part
-of the string argument of those commands. This is explained in
-"Section 3.2"_Section_commands.html#cmd_2.
+of the string argument of those commands. This is explained on the
+"Commands parse"_Commands_parse.html doc page.
For the {getenv} style, a single string is assigned to the variable
which should be the name of an environment variable. When the
@@ -1119,24 +1119,23 @@ Vectors" discussion above.
If you want an equal-style variable to be evaluated immediately, it
may be the case that you do not need to define a variable at all. See
-"Section 3.2"_Section_commands.html#cmd_2 of the manual, which
-describes the use of "immediate" variables in an input script,
-specified as $(formula) with parenthesis, where the formula has the
-same syntax as equal-style variables described on this page. This
-effectively evaluates a formula immediately without using the variable
-command to define a named variable.
+the "Commands parse"_Commands_parse.html doc page for info on how to
+use "immediate" variables in an input script, specified as $(formula)
+with parenthesis, where the formula has the same syntax as equal-style
+variables described on this page. This effectively evaluates a
+formula immediately without using the variable command to define a
+named variable.
More generally, there is a difference between referencing a variable
with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_"
(e.g. v_x or v_abc). The former can be used in any input script
command, including a variable command. The input script parser
evaluates the reference variable immediately and substitutes its value
-into the command. As explained in "Section
-3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use
-un-named "immediate" variables for this purpose. For example, a
-string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
-command evaluates the string between the parenthesis as an equal-style
-variable formula.
+into the command. As explained on the "Commands
+parse"_Commands_parse.html doc page, you can also use un-named
+"immediate" variables for this purpose. For example, a string like
+this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates
+the string between the parenthesis as an equal-style variable formula.
Referencing a variable with a leading "v_" is an optional or required
kind of argument for some commands (e.g. the "fix
@@ -1180,10 +1179,9 @@ quotes if it contains variables preceded by $ signs. For example,
variable vratio equal "$\{vfinal\}/$\{v0\}" :pre
-This is because the quotes prevent variable substitution (see "this
-section"_Section_commands.html#cmd_2 on parsing input script
-commands), and thus an error will occur when the formula for "vratio"
-is evaluated later.
+This is because the quotes prevent variable substitution (explained on
+the "Commands parse"_Commands_parse.html doc page), and thus an error
+will occur when the formula for "vratio" is evaluated later.
:line
diff --git a/doc/src/velocity.txt b/doc/src/velocity.txt
index b8299a5acfc1576484c8f3683eba5eb9e947e4d0..96d3fa6dc4fa53e1b7d399fc2d774afbff682de5 100644
--- a/doc/src/velocity.txt
+++ b/doc/src/velocity.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -139,10 +139,9 @@ if rot = yes, the angular momentum is zeroed.
If specified, the {temp} keyword is used by {create} and {scale} to
specify a "compute"_compute.html that calculates temperature in a
desired way, e.g. by first subtracting out a velocity bias, as
-discussed in "Section 6.16"_Section_howto.html#howto_16 of the doc
-pages. If this keyword is not specified, {create} and {scale}
-calculate temperature using a compute that is defined internally as
-follows:
+discussed on the "Howto thermostat"_Howto_thermostat.html doc page.
+If this keyword is not specified, {create} and {scale} calculate
+temperature using a compute that is defined internally as follows:
compute velocity_temp group-ID temp :pre
@@ -161,11 +160,11 @@ The {bias} keyword with a {yes} setting is used by {create} and
If the temperature compute also calculates a velocity bias, the the
bias is subtracted from atom velocities before the {create} and
{scale} operations are performed. After the operations, the bias is
-added back to the atom velocities. See "Section
-6.16"_Section_howto.html#howto_16 of the doc pages for more discussion
-of temperature computes with biases. Note that the velocity bias is
-only applied to atoms in the temperature compute specified with the
-{temp} keyword.
+added back to the atom velocities. See the "Howto
+thermostat"_Howto_thermostat.html doc page for more discussion of
+temperature computes with biases. Note that the velocity bias is only
+applied to atoms in the temperature compute specified with the {temp}
+keyword.
As an example, assume atoms are currently streaming in a flow
direction (which could be separately initialized with the {ramp}
diff --git a/doc/src/write_coeff.txt b/doc/src/write_coeff.txt
index 764e119a9d1d310ae5f969a9163d1ec5753ebe1d..5dc4b331dedbe2940286af653c81a76654cb1347 100644
--- a/doc/src/write_coeff.txt
+++ b/doc/src/write_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt
index c76f20319c3182a2d9298d8aada887cb806878f3..d8a33f457f2ab15cb38d6922ec54c5b5b8d5d202 100644
--- a/doc/src/write_data.txt
+++ b/doc/src/write_data.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt
index 840716085feff0aaf6b7790befc98b902be87ea3..e67697900129a153801eb53f454641075955189d 100644
--- a/doc/src/write_dump.txt
+++ b/doc/src/write_dump.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/write_restart.txt b/doc/src/write_restart.txt
index ff3b652dba75feefdb3841bf764f885cc0b3a9d1..3935a5d5387bfd6118134c605058a146fbc81a43 100644
--- a/doc/src/write_restart.txt
+++ b/doc/src/write_restart.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/utils/converters/lammpsdoc/txt2html.py b/doc/utils/converters/lammpsdoc/txt2html.py
index 79a75d72f6e4be7796e685e7025adbef0d9eb5ff..ed9f47a4e4ae3cfe4c6363a34ab9b7deb42b8c0c 100755
--- a/doc/utils/converters/lammpsdoc/txt2html.py
+++ b/doc/utils/converters/lammpsdoc/txt2html.py
@@ -662,14 +662,15 @@ class TxtConverter:
parser = self.get_argument_parser()
parsed_args = parser.parse_args(args)
- write_to_files = len(parsed_args.files) > 1
+ write_to_files = parsed_args.output_dir or (len(parsed_args.files) > 1)
for filename in parsed_args.files:
if parsed_args.skip_files and filename in parsed_args.skip_files:
continue
with open(filename, 'r') as f:
- print("Converting", filename, "...", file=err)
+ if parsed_args.verbose:
+ print("Converting", filename, "...", file=err)
content = f.read()
converter = self.create_converter(parsed_args)
@@ -683,7 +684,10 @@ class TxtConverter:
result = msg
if write_to_files:
- output_filename = self.get_output_filename(filename)
+ if parsed_args.output_dir:
+ output_filename = os.path.join(parsed_args.output_dir, os.path.basename(self.get_output_filename(filename)))
+ else:
+ output_filename = self.get_output_filename(filename)
with open(output_filename, "w+t") as outfile:
outfile.write(result)
else:
@@ -698,6 +702,8 @@ class Txt2HtmlConverter(TxtConverter):
'HTML file. useful when set of HTML files'
' will be converted to PDF')
parser.add_argument('-x', metavar='file-to-skip', dest='skip_files', action='append')
+ parser.add_argument('--verbose', '-v', dest='verbose', action='store_true')
+ parser.add_argument('--output-directory', '-o', dest='output_dir')
parser.add_argument('--generate-title', dest='create_title', action='store_true', help='add HTML head page'
'title based on first '
'h1,h2,h3,h4... element')
diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py
index 17d0916157a4f2d9b07ec655522ac6999b6978cb..8119ad3a7869c5345ffad166536f98ffa7bd20ba 100755
--- a/doc/utils/converters/lammpsdoc/txt2rst.py
+++ b/doc/utils/converters/lammpsdoc/txt2rst.py
@@ -395,6 +395,8 @@ class Txt2RstConverter(TxtConverter):
parser = argparse.ArgumentParser(description='converts a text file with simple formatting & markup into '
'Restructured Text for Sphinx.')
parser.add_argument('-x', metavar='file-to-skip', dest='skip_files', action='append')
+ parser.add_argument('--verbose', '-v', dest='verbose', action='store_true')
+ parser.add_argument('--output-directory', '-o', dest='output_dir')
parser.add_argument('files', metavar='file', nargs='+', help='one or more files to convert')
return parser
diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2806c164989aa9137a6c1860716ae9abccef75ad
--- /dev/null
+++ b/doc/utils/requirements.txt
@@ -0,0 +1 @@
+Sphinx
diff --git a/examples/DIFFUSE/README b/examples/DIFFUSE/README
index df2a675f73b778dd3d4fda1bafff791f2bebf4a6..e78ca2eacf1a109ec3aeb79b3b13e3444ed7d7a9 100644
--- a/examples/DIFFUSE/README
+++ b/examples/DIFFUSE/README
@@ -47,7 +47,7 @@ compute the diffusion coefficient. You can see that both measures
give roughly the same answer and rapidly become roughly constant for
the 100K step simulation.
-Dcoeff = 0.36
+Dcoeff = 0.33
(2) in.vacf.2d
@@ -58,4 +58,4 @@ that point in time, converted into the diffusion coefficient. You can
see the VACF approach gives a more noise, fluctuating value for the
diffusion coefficient, compared to the MSD approach.
-Dcoeff = 0.25 to 0.45
+Dcoeff = ~0.25
diff --git a/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 b/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8
deleted file mode 100644
index 473aa565278ec6802b78373adcf4b510722c93da..0000000000000000000000000000000000000000
--- a/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8
+++ /dev/null
@@ -1,245 +0,0 @@
-LAMMPS (13 Oct 2016)
-# sample LAMMPS input script for diffusion of 2d LJ liquid
-# mean-squared displacement via compute msd
-
-# settings
-
-variable x equal 40
-variable y equal 40
-
-variable rho equal 0.6
-variable t equal 1.0
-variable rc equal 2.5
-
-# problem setup
-
-units lj
-dimension 2
-atom_style atomic
-neigh_modify delay 0 every 1
-
-lattice sq2 ${rho}
-lattice sq2 0.6
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region simbox block 0 $x 0 $y -0.1 0.1
-region simbox block 0 40 0 $y -0.1 0.1
-region simbox block 0 40 0 40 -0.1 0.1
-create_box 1 simbox
-Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
- 4 by 2 by 1 MPI processor grid
-create_atoms 1 box
-Created 3200 atoms
-
-pair_style lj/cut ${rc}
-pair_style lj/cut 2.5
-pair_coeff * * 1 1
-
-mass * 1.0
-velocity all create $t 97287
-velocity all create 1 97287
-
-fix 1 all nve
-fix 2 all langevin $t $t 0.1 498094
-fix 2 all langevin 1 $t 0.1 498094
-fix 2 all langevin 1 1 0.1 498094
-fix 3 all enforce2d
-
-# equilibration run
-
-thermo 1000
-run 5000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 53 53 1
-Memory usage per processor = 2.478 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1 -1.56492 0 -0.5652325 -1.5346995
- 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
- 2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
- 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
- 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
- 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
-Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms
-
-Performance: 3896017.421 tau/day, 9018.559 timesteps/s
-98.9% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.23992 | 0.24608 | 0.25161 | 0.7 | 44.39
-Neigh | 0.063106 | 0.064417 | 0.066279 | 0.4 | 11.62
-Comm | 0.072465 | 0.085066 | 0.094837 | 2.3 | 15.34
-Output | 0.00013208 | 0.00013691 | 0.00014591 | 0.0 | 0.02
-Modify | 0.11441 | 0.11621 | 0.11769 | 0.3 | 20.96
-Other | | 0.04251 | | | 7.67
-
-Nlocal: 400 ave 406 max 394 min
-Histogram: 1 1 0 1 0 2 1 0 1 1
-Nghost: 202.5 ave 212 max 191 min
-Histogram: 1 0 0 0 3 1 0 2 0 1
-Neighs: 2800.88 ave 2903 max 2690 min
-Histogram: 1 1 0 0 1 2 1 0 1 1
-
-Total # of neighbors = 22407
-Ave neighs/atom = 7.00219
-Neighbor list builds = 599
-Dangerous builds = 0
-
-unfix 2
-
-# data gathering run
-
-reset_timestep 0
-
-# factor of 4 in 2 variables is for 2d
-
-compute msd all msd com yes
-variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
-fix 9 all vector 10 c_msd[4]
-variable fitslope equal slope(f_9)/4/(10*dt)
-
-thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
-
-# only need to run for 10K steps to make a good 100-frame movie
-
-#dump 1 all custom 1 tmp.dump id type vx vy vz
-
-#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
-
-thermo 1000
-run 100000
-Memory usage per processor = 2.853 Mbytes
-Step Temp c_msd[4] v_twopoint v_fitslope
- 0 0.97069905 0 0 5e+20
- 1000 0.98138076 4.0484996 0.20242494 0.18046446
- 2000 0.97606079 9.2121392 0.23030346 0.2091528
- 3000 0.97924866 14.815034 0.24691721 0.22619184
- 4000 0.98568451 20.516817 0.25646019 0.23715506
- 5000 0.97551815 27.33922 0.27339219 0.24709999
- 6000 0.98482252 34.37734 0.28647782 0.25735178
- 7000 0.9672559 41.696689 0.29783348 0.26654059
- 8000 0.9836541 48.340277 0.30212673 0.27440308
- 9000 0.99087147 56.042692 0.31134828 0.28113047
- 10000 0.99663166 63.69663 0.31848314 0.28767921
- 11000 0.97776688 71.144109 0.32338231 0.29344527
- 12000 0.98246011 78.301774 0.32625739 0.29849471
- 13000 0.98788732 85.061923 0.32716124 0.3026655
- 14000 0.96872483 91.1658 0.32559214 0.30601023
- 15000 0.98955796 97.278388 0.32426129 0.3084275
- 16000 0.99855196 104.23997 0.3257499 0.31049883
- 17000 0.98600861 110.66055 0.3254722 0.31220348
- 18000 0.98696963 116.90111 0.32472531 0.31352676
- 19000 0.9881192 124.21305 0.32687644 0.31480062
- 20000 0.98527319 131.09874 0.32774685 0.31596198
- 21000 0.99015191 137.89263 0.32831579 0.31705324
- 22000 0.97972418 146.68982 0.33338595 0.31833889
- 23000 0.98911012 155.1264 0.33723129 0.31979515
- 24000 0.98810498 162.88634 0.33934653 0.32131187
- 25000 0.96961962 170.37907 0.34075814 0.32276215
- 26000 0.99118408 179.26511 0.34474059 0.32427111
- 27000 0.98515159 185.90764 0.3442734 0.32574529
- 28000 0.98951677 192.12183 0.34307469 0.32700292
- 29000 0.9832026 196.99457 0.33964581 0.32799023
- 30000 0.98449493 203.48475 0.33914124 0.3287171
- 31000 0.96585993 210.06193 0.33880956 0.32935775
- 32000 0.98758117 218.94174 0.34209646 0.33001591
- 33000 0.98875584 225.96489 0.34237104 0.33072947
- 34000 0.98007229 233.5792 0.34349882 0.3314385
- 35000 0.98415295 241.98148 0.34568783 0.33216634
- 36000 0.98101154 250.30876 0.34765106 0.33295272
- 37000 0.97606878 258.2127 0.34893608 0.33377673
- 38000 0.97220293 266.40464 0.35053242 0.33459273
- 39000 0.979783 272.8578 0.34981769 0.33539728
- 40000 0.98375673 279.87598 0.34984497 0.33609699
- 41000 0.97506523 288.07676 0.35131312 0.33677708
- 42000 0.97106749 296.11647 0.3525196 0.33751312
- 43000 0.97717259 304.46747 0.35403194 0.33823441
- 44000 0.98541435 312.57228 0.35519578 0.3389771
- 45000 0.97678287 321.82674 0.35758527 0.33973306
- 46000 0.98169719 329.78197 0.35845866 0.34051748
- 47000 0.99471466 337.11283 0.35863066 0.34127239
- 48000 0.98332437 346.0754 0.3604952 0.34202442
- 49000 0.98126947 356.11859 0.36338631 0.34282132
- 50000 0.98809751 365.65248 0.36565248 0.34368171
- 51000 0.95919516 373.91833 0.36658659 0.34454516
- 52000 0.98097913 381.26492 0.36660089 0.34538506
- 53000 0.97774072 388.81031 0.36680218 0.34618232
- 54000 0.99096915 395.56767 0.36626636 0.3469296
- 55000 0.97652739 401.72735 0.36520668 0.34760374
- 56000 0.99185306 407.28834 0.3636503 0.34819906
- 57000 0.96289342 414.75298 0.3638184 0.34871992
- 58000 0.97871716 424.69443 0.36611588 0.34927986
- 59000 0.98637393 433.14205 0.36706953 0.34986296
- 60000 0.98009845 438.14533 0.36512111 0.35040349
- 61000 0.99416712 446.08007 0.3656394 0.35088379
- 62000 0.97612483 450.90846 0.36363585 0.35132647
- 63000 0.97786531 455.36749 0.36140277 0.35167458
- 64000 0.99080668 458.04873 0.35785057 0.3519105
- 65000 0.97952497 461.31241 0.3548557 0.3520506
- 66000 0.98095955 463.91727 0.35145248 0.35207764
- 67000 0.98370788 468.93 0.34994776 0.35204043
- 68000 0.96931818 471.07765 0.34638063 0.35192685
- 69000 0.98512552 474.59146 0.34390685 0.35174053
- 70000 0.98065743 478.66071 0.3419005 0.35149002
- 71000 0.98971283 482.57357 0.33984054 0.35119434
- 72000 0.99890324 485.32018 0.3370279 0.35084345
- 73000 0.98649924 490.19497 0.33574998 0.35043722
- 74000 0.98723422 496.04991 0.33516886 0.35003351
- 75000 1.0025633 501.6313 0.33442087 0.34962094
- 76000 0.97859959 505.97813 0.33288035 0.34921013
- 77000 0.97973006 510.55334 0.33152814 0.3487692
- 78000 0.9903944 515.06966 0.33017286 0.34830833
- 79000 0.96847518 518.76483 0.32833217 0.3478214
- 80000 0.99171112 524.18127 0.32761329 0.34733349
- 81000 0.97202573 529.09959 0.32660468 0.3468315
- 82000 0.99368438 535.80271 0.32670897 0.34633058
- 83000 0.97932483 543.08233 0.32715803 0.34586259
- 84000 0.99078651 547.57861 0.32593965 0.34540839
- 85000 0.98973457 552.24581 0.32485048 0.34493584
- 86000 0.9835873 557.3493 0.32404029 0.34446152
- 87000 0.97180564 564.93434 0.32467491 0.34400358
- 88000 0.99743353 571.39837 0.32465817 0.3435667
- 89000 0.98993437 577.81703 0.32461631 0.3431411
- 90000 0.9926071 583.39378 0.32410765 0.342724
- 91000 0.98800458 591.08741 0.3247733 0.34232767
- 92000 0.98501879 596.10133 0.32396811 0.34193949
- 93000 0.98810082 604.02652 0.32474544 0.3415681
- 94000 0.97563748 609.43676 0.32416849 0.341209
- 95000 0.97283448 615.15754 0.32376713 0.34084828
- 96000 0.9883071 622.30912 0.32411933 0.34049871
- 97000 0.97717678 628.84457 0.32414669 0.34016355
- 98000 0.97190208 634.37377 0.32366009 0.3398341
- 99000 0.98687379 640.66666 0.32356902 0.33950845
- 100000 0.97559757 646.96406 0.32348203 0.33919036
-Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms
-
-Performance: 4505729.040 tau/day, 10429.928 timesteps/s
-99.4% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 4.8572 | 4.9363 | 4.9822 | 1.7 | 51.49
-Neigh | 1.3583 | 1.376 | 1.3991 | 1.2 | 14.35
-Comm | 1.5192 | 1.7079 | 1.8264 | 7.2 | 17.81
-Output | 0.0085125 | 0.0086059 | 0.0089455 | 0.1 | 0.09
-Modify | 0.77663 | 0.7903 | 0.81378 | 1.3 | 8.24
-Other | | 0.7686 | | | 8.02
-
-Nlocal: 400 ave 413 max 391 min
-Histogram: 2 1 0 2 0 0 1 1 0 1
-Nghost: 204.75 ave 213 max 197 min
-Histogram: 1 1 0 1 0 3 0 1 0 1
-Neighs: 2800.62 ave 2959 max 2661 min
-Histogram: 1 1 1 2 0 0 0 1 1 1
-
-Total # of neighbors = 22405
-Ave neighs/atom = 7.00156
-Neighbor list builds = 12728
-Dangerous builds = 0
-Total wall time: 0:00:10
diff --git a/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8 b/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8
new file mode 100644
index 0000000000000000000000000000000000000000..113da9040d8a8eb37b84a4245ce3d904e219db3c
--- /dev/null
+++ b/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8
@@ -0,0 +1,251 @@
+LAMMPS (2 Aug 2018)
+# sample LAMMPS input script for diffusion of 2d LJ liquid
+# mean-squared displacement via compute msd
+
+# settings
+
+variable x equal 40
+variable y equal 40
+
+variable rho equal 0.6
+variable t equal 1.0
+variable rc equal 2.5
+
+# problem setup
+
+units lj
+dimension 2
+atom_style atomic
+neigh_modify delay 0 every 1
+
+lattice sq2 ${rho}
+lattice sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region simbox block 0 $x 0 $y -0.1 0.1
+region simbox block 0 40 0 $y -0.1 0.1
+region simbox block 0 40 0 40 -0.1 0.1
+create_box 1 simbox
+Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
+ 4 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 3200 atoms
+ Time spent = 0.000706911 secs
+
+pair_style lj/cut ${rc}
+pair_style lj/cut 2.5
+pair_coeff * * 1 1
+
+mass * 1.0
+velocity all create $t 97287
+velocity all create 1 97287
+
+fix 1 all nve
+fix 2 all langevin $t $t 0.1 498094
+fix 2 all langevin 1 $t 0.1 498094
+fix 2 all langevin 1 1 0.1 498094
+fix 3 all enforce2d
+
+# equilibration run
+
+thermo 1000
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 53 53 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1 -1.56492 0 -0.5652325 -1.5346995
+ 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
+ 2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
+ 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
+ 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
+ 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
+Loop time of 0.667446 on 8 procs for 5000 steps with 3200 atoms
+
+Performance: 3236214.756 tau/day, 7491.238 timesteps/s
+99.9% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.22913 | 0.24877 | 0.28382 | 3.6 | 37.27
+Neigh | 0.064419 | 0.071256 | 0.080013 | 1.7 | 10.68
+Comm | 0.103 | 0.14054 | 0.17204 | 5.5 | 21.06
+Output | 0.00010705 | 0.00013995 | 0.00021911 | 0.0 | 0.02
+Modify | 0.13457 | 0.14973 | 0.16887 | 2.6 | 22.43
+Other | | 0.05701 | | | 8.54
+
+Nlocal: 400 ave 406 max 394 min
+Histogram: 1 1 0 1 0 2 1 0 1 1
+Nghost: 202.5 ave 212 max 191 min
+Histogram: 1 0 0 0 3 1 0 2 0 1
+Neighs: 2800.88 ave 2903 max 2690 min
+Histogram: 1 1 0 0 1 2 1 0 1 1
+
+Total # of neighbors = 22407
+Ave neighs/atom = 7.00219
+Neighbor list builds = 599
+Dangerous builds = 0
+
+unfix 2
+
+# data gathering run
+
+reset_timestep 0
+
+# factor of 4 in 2 variables is for 2d
+
+compute msd all msd com yes
+variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
+fix 9 all vector 10 c_msd[4]
+variable fitslope equal slope(f_9)/4/(10*dt)
+
+thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
+
+# only need to run for 10K steps to make a good 100-frame movie
+
+#dump 1 all custom 1 tmp.dump id type vx vy vz
+
+#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
+
+thermo 1000
+run 100000
+Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
+Step Temp c_msd[4] v_twopoint v_fitslope
+ 0 0.97069905 0 0 5e+20
+ 1000 0.98138076 4.0484996 0.20242494 0.20685564
+ 2000 0.97606079 9.2121392 0.23030346 0.23687918
+ 3000 0.97924866 14.815034 0.24691721 0.25405247
+ 4000 0.98568451 20.516817 0.25646019 0.26353644
+ 5000 0.97551815 27.33922 0.27339219 0.27544492
+ 6000 0.98482252 34.37734 0.28647782 0.28966619
+ 7000 0.9672559 41.696689 0.29783348 0.30165524
+ 8000 0.9836541 48.340277 0.30212673 0.31085371
+ 9000 0.99087147 56.042692 0.31134828 0.31811489
+ 10000 0.99663166 63.69663 0.31848314 0.32589374
+ 11000 0.97776688 71.144109 0.32338231 0.33219745
+ 12000 0.98246011 78.301774 0.32625739 0.33723
+ 13000 0.98788732 85.061923 0.32716124 0.34053027
+ 14000 0.96872483 91.1658 0.32559214 0.34231162
+ 15000 0.98955796 97.278388 0.32426129 0.34229511
+ 16000 0.99855196 104.23997 0.3257499 0.34217252
+ 17000 0.98600861 110.66055 0.3254722 0.34172446
+ 18000 0.98696963 116.90111 0.32472531 0.3408227
+ 19000 0.9881192 124.21305 0.32687644 0.34036538
+ 20000 0.98527319 131.09874 0.32774685 0.34003478
+ 21000 0.99015191 137.89263 0.32831579 0.33987868
+ 22000 0.97972418 146.68982 0.33338595 0.34060035
+ 23000 0.98911012 155.1264 0.33723129 0.34201036
+ 24000 0.98810498 162.88634 0.33934653 0.34371488
+ 25000 0.96961962 170.37907 0.34075814 0.34531409
+ 26000 0.99118408 179.26511 0.34474059 0.34717195
+ 27000 0.98515159 185.90764 0.3442734 0.34898035
+ 28000 0.98951677 192.12183 0.34307469 0.35021808
+ 29000 0.9832026 196.99457 0.33964581 0.35075459
+ 30000 0.98449493 203.48475 0.33914124 0.35066186
+ 31000 0.96585993 210.06193 0.33880956 0.35046715
+ 32000 0.98758117 218.94174 0.34209646 0.35046623
+ 33000 0.98875584 225.96489 0.34237104 0.35073944
+ 34000 0.98007229 233.5792 0.34349882 0.35109188
+ 35000 0.98415295 241.98148 0.34568783 0.35157879
+ 36000 0.98101154 250.30876 0.34765106 0.3523013
+ 37000 0.97606878 258.2127 0.34893608 0.35318097
+ 38000 0.97220293 266.40464 0.35053242 0.3540743
+ 39000 0.979783 272.8578 0.34981769 0.35496561
+ 40000 0.98375673 279.87598 0.34984497 0.35558182
+ 41000 0.97506523 288.07676 0.35131312 0.35618259
+ 42000 0.97106749 296.11647 0.3525196 0.35698571
+ 43000 0.97717259 304.46747 0.35403194 0.3577736
+ 44000 0.98541435 312.57228 0.35519578 0.35865003
+ 45000 0.97678287 321.82674 0.35758527 0.35958623
+ 46000 0.98169719 329.78197 0.35845866 0.36062236
+ 47000 0.99471466 337.11283 0.35863066 0.36158322
+ 48000 0.98332437 346.0754 0.3604952 0.36255042
+ 49000 0.98126947 356.11859 0.36338631 0.3636628
+ 50000 0.98809751 365.65248 0.36565248 0.36496809
+ 51000 0.95919516 373.91833 0.36658659 0.36628073
+ 52000 0.98097913 381.26492 0.36660089 0.36752237
+ 53000 0.97774072 388.81031 0.36680218 0.36863962
+ 54000 0.99096915 395.56767 0.36626636 0.36961521
+ 55000 0.97652739 401.72735 0.36520668 0.37038579
+ 56000 0.99185306 407.28834 0.3636503 0.37094092
+ 57000 0.96289342 414.75298 0.3638184 0.37130039
+ 58000 0.97871716 424.69443 0.36611588 0.37180428
+ 59000 0.98637393 433.14205 0.36706953 0.37239862
+ 60000 0.98009845 438.14533 0.36512111 0.37288487
+ 61000 0.99416712 446.08007 0.3656394 0.37321496
+ 62000 0.97612483 450.90846 0.36363585 0.37345792
+ 63000 0.97786531 455.36749 0.36140277 0.37344803
+ 64000 0.99080668 458.04873 0.35785057 0.37313914
+ 65000 0.97952497 461.31241 0.3548557 0.3725875
+ 66000 0.98095955 463.91727 0.35145248 0.37174735
+ 67000 0.98370788 468.93 0.34994776 0.37076942
+ 68000 0.96931818 471.07765 0.34638063 0.36961868
+ 69000 0.98512552 474.59146 0.34390685 0.36830908
+ 70000 0.98065743 478.66071 0.3419005 0.36686789
+ 71000 0.98971283 482.57357 0.33984054 0.36535224
+ 72000 0.99890324 485.32018 0.3370279 0.36373174
+ 73000 0.98649924 490.19497 0.33574998 0.36200692
+ 74000 0.98723422 496.04991 0.33516886 0.36034919
+ 75000 1.0025633 501.6313 0.33442087 0.35872052
+ 76000 0.97859959 505.97813 0.33288035 0.35714939
+ 77000 0.97973006 510.55334 0.33152814 0.35553808
+ 78000 0.9903944 515.06966 0.33017286 0.35391584
+ 79000 0.96847518 518.76483 0.32833217 0.35226287
+ 80000 0.99171112 524.18127 0.32761329 0.35065267
+ 81000 0.97202573 529.09959 0.32660468 0.34904364
+ 82000 0.99368438 535.80271 0.32670897 0.34747913
+ 83000 0.97932483 543.08233 0.32715803 0.34605097
+ 84000 0.99078651 547.57861 0.32593965 0.34469765
+ 85000 0.98973457 552.24581 0.32485048 0.34332115
+ 86000 0.9835873 557.3493 0.32404029 0.34197018
+ 87000 0.97180564 564.93434 0.32467491 0.34069702
+ 88000 0.99743353 571.39837 0.32465817 0.33951258
+ 89000 0.98993437 577.81703 0.32461631 0.33838511
+ 90000 0.9926071 583.39378 0.32410765 0.33730429
+ 91000 0.98800458 591.08741 0.3247733 0.33630505
+ 92000 0.98501879 596.10133 0.32396811 0.33534725
+ 93000 0.98810082 604.02652 0.32474544 0.33445545
+ 94000 0.97563748 609.43676 0.32416849 0.33361404
+ 95000 0.97283448 615.15754 0.32376713 0.33278044
+ 96000 0.9883071 622.30912 0.32411933 0.33199212
+ 97000 0.97717678 628.84457 0.32414669 0.33125729
+ 98000 0.97190208 634.37377 0.32366009 0.33054877
+ 99000 0.98687379 640.66666 0.32356902 0.32986014
+ 100000 0.97559757 646.96406 0.32348203 0.32920186
+Loop time of 7.61838 on 8 procs for 100000 steps with 3200 atoms
+
+Performance: 5670494.518 tau/day, 13126.145 timesteps/s
+100.0% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.5458 | 3.6709 | 3.8234 | 4.3 | 48.19
+Neigh | 1.1363 | 1.1513 | 1.1753 | 1.0 | 15.11
+Comm | 1.5901 | 1.7017 | 1.8664 | 6.9 | 22.34
+Output | 0.0041966 | 0.0043583 | 0.0050626 | 0.4 | 0.06
+Modify | 0.63816 | 0.65537 | 0.68918 | 2.0 | 8.60
+Other | | 0.4348 | | | 5.71
+
+Nlocal: 400 ave 413 max 391 min
+Histogram: 2 1 0 2 0 0 1 1 0 1
+Nghost: 204.75 ave 213 max 197 min
+Histogram: 1 1 0 1 0 3 0 1 0 1
+Neighs: 2800.62 ave 2959 max 2661 min
+Histogram: 1 1 1 2 0 0 0 1 1 1
+
+Total # of neighbors = 22405
+Ave neighs/atom = 7.00156
+Neighbor list builds = 12728
+Dangerous builds = 0
+Total wall time: 0:00:08
diff --git a/examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8 b/examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8
similarity index 84%
rename from examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8
rename to examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8
index 458315bc29de64e5a2102de7e98ed958e591252c..80c57ada9c31b8e299944689fd1cba2f6afb95f4 100644
--- a/examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8
+++ b/examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8
@@ -1,4 +1,4 @@
-LAMMPS (13 Oct 2016)
+LAMMPS (2 Aug 2018)
# sample LAMMPS input script for diffusion of 2d LJ liquid
# mean-squared displacement via compute msd
@@ -29,6 +29,7 @@ Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
4 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3200 atoms
+ Time spent = 0.000712872 secs
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
@@ -49,13 +50,18 @@ fix 3 all enforce2d
thermo 1000
run 5000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 53 53 1
-Memory usage per processor = 2.478 Mbytes
+ binsize = 1.4, bins = 53 53 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.5652325 -1.5346995
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
@@ -63,20 +69,20 @@ Step Temp E_pair E_mol TotEng Press
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
-Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms
+Loop time of 0.648098 on 8 procs for 5000 steps with 3200 atoms
-Performance: 3873826.669 tau/day, 8967.191 timesteps/s
-99.1% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 3332829.949 tau/day, 7714.884 timesteps/s
+99.9% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.23784 | 0.24683 | 0.25594 | 1.0 | 44.27
-Neigh | 0.062975 | 0.06439 | 0.0662 | 0.4 | 11.55
-Comm | 0.083826 | 0.092564 | 0.1035 | 2.1 | 16.60
-Output | 0.00011778 | 0.00012615 | 0.00014257 | 0.1 | 0.02
-Modify | 0.11466 | 0.11648 | 0.1187 | 0.4 | 20.89
-Other | | 0.0372 | | | 6.67
+Pair | 0.22614 | 0.24602 | 0.27481 | 2.8 | 37.96
+Neigh | 0.066875 | 0.07135 | 0.077825 | 1.2 | 11.01
+Comm | 0.098293 | 0.12744 | 0.1569 | 5.6 | 19.66
+Output | 0.0001049 | 0.00012228 | 0.00014496 | 0.0 | 0.02
+Modify | 0.13725 | 0.14919 | 0.16903 | 2.4 | 23.02
+Other | | 0.05398 | | | 8.33
Nlocal: 400 ave 406 max 394 min
Histogram: 1 1 0 1 0 2 1 0 1 1
@@ -114,7 +120,7 @@ thermo_style custom step temp c_vacf[4] v_vacf
thermo 1000
run 100000
-Memory usage per processor = 2.853 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
Step Temp c_vacf[4] v_vacf
0 0.97069905 1.9407914 0
1000 0.98138076 0.029239763 0.22157396
@@ -217,20 +223,20 @@ Step Temp c_vacf[4] v_vacf
98000 0.97190208 0.015065013 0.20906937
99000 0.98687379 -0.036869401 0.22993959
100000 0.97559757 0.045464091 0.23369283
-Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms
+Loop time of 8.16691 on 8 procs for 100000 steps with 3200 atoms
-Performance: 3987213.825 tau/day, 9229.662 timesteps/s
-99.5% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 5289636.190 tau/day, 12244.528 timesteps/s
+100.0% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 4.8486 | 4.9469 | 5.0248 | 2.8 | 45.66
-Neigh | 1.3613 | 1.374 | 1.3916 | 0.8 | 12.68
-Comm | 1.8181 | 1.9534 | 2.0665 | 5.7 | 18.03
-Output | 0.016565 | 0.016701 | 0.017039 | 0.1 | 0.15
-Modify | 1.8395 | 1.9053 | 1.9704 | 2.8 | 17.59
-Other | | 0.6383 | | | 5.89
+Pair | 3.5668 | 3.6612 | 3.7867 | 4.0 | 44.83
+Neigh | 1.1409 | 1.1555 | 1.1804 | 1.4 | 14.15
+Comm | 1.581 | 1.711 | 1.8239 | 7.1 | 20.95
+Output | 0.016626 | 0.016831 | 0.017569 | 0.2 | 0.21
+Modify | 1.225 | 1.2594 | 1.3008 | 2.0 | 15.42
+Other | | 0.363 | | | 4.45
Nlocal: 400 ave 413 max 391 min
Histogram: 2 1 0 2 0 0 1 1 0 1
@@ -243,4 +249,4 @@ Total # of neighbors = 22405
Ave neighs/atom = 7.00156
Neighbor list builds = 12728
Dangerous builds = 0
-Total wall time: 0:00:11
+Total wall time: 0:00:08
diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo
index 2442b12b72294d2b138831565a868a65c5395af5..de23ba87ba2b825c129b88fd55fcfcb33703eb01 100644
--- a/examples/SPIN/bfo/in.spin.bfo
+++ b/examples/SPIN/bfo/in.spin.bfo
@@ -21,9 +21,11 @@ mass 1 1.0
set group all spin/random 11 2.50
-pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
+#pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
+pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
@@ -44,10 +46,11 @@ variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
-thermo_style custom step time v_magnorm v_emag temp etotal
-thermo 50
+#thermo_style custom step time v_magnorm v_emag temp etotal
+thermo_style custom step time v_magnorm pe ke v_emag temp etotal
+thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-run 5000
+run 2000
diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
index 4a42ec419aeb1a02603d86cb748d8964b439ea06..35aa1df86c4a2c2bdfff40f3e35f032939311b90 100644
--- a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
+++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
@@ -19,8 +19,8 @@ create_atoms 1 box
mass 1 58.93
-#set group all spin/random 31 1.72
-set group all spin 1.72 0.0 0.0 1.0
+set group all spin/random 31 1.72
+#set group all spin 1.72 0.0 0.0 1.0
velocity all create 100 4928459 rot yes dist gaussian
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
@@ -29,11 +29,11 @@ pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
-
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
-fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+#fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
@@ -56,4 +56,4 @@ thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-run 2000
+run 20000
diff --git a/examples/USER/diffraction/BulkNi.in b/examples/USER/diffraction/BulkNi.in
index a18163175cf35f9d125307df4dc8c7534d5526a5..0fa9c1b74c2c41d9917d21b7167d4761403a2c2b 100644
--- a/examples/USER/diffraction/BulkNi.in
+++ b/examples/USER/diffraction/BulkNi.in
@@ -20,7 +20,7 @@ compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.05 echo manual
-fix 1 all ave/histo 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
+fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp
index 5ec5a7cca8eb30309294a14b13f8e2d10e56bd26..0e7aaea1e1a2a6c9ac0060c092eb703eaf90f2b6 100644
--- a/src/BODY/fix_wall_body_polygon.cpp
+++ b/src/BODY/fix_wall_body_polygon.cpp
@@ -641,18 +641,15 @@ int FixWallBodyPolygon::compute_distance_to_wall(double* x0, double rradi,
mode = VERTEX;
contact = 1;
} else {
+ mode = NONE;
if (side == XLO) {
if (x0[0] < wall_pos) mode = VERTEX;
- else mode = NONE;
} else if (side == XHI) {
if (x0[0] > wall_pos) mode = VERTEX;
- else mode = NONE;
} else if (side == YLO) {
if (x0[1] < wall_pos) mode = VERTEX;
- else mode = NONE;
} else if (side == YHI) {
if (x0[1] > wall_pos) mode = VERTEX;
- else mode = NONE;
}
}
diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp
index 2ff209d609bf1d5f31f82ddf0c6b3063949b5e2e..051be762e5a432193326596e6acbc3ad7bb9e616 100644
--- a/src/BODY/pair_body_rounded_polyhedron.cpp
+++ b/src/BODY/pair_body_rounded_polyhedron.cpp
@@ -685,7 +685,7 @@ void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody,
{
int ni,nei,ifirst,iefirst,npi1,npi2,ibonus;
double xi1[3],xi2[3],vti[3],h[3],fn[3],ft[3],d,t;
- double delx,dely,delz,rij,rsqinv,R,fx,fy,fz,fpair,shift,energy;
+ double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,shift,energy;
double rradi,rradj,contact_dist;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double *quat, *inertia;
@@ -749,7 +749,9 @@ void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody,
delx = h[0] - x[jbody][0];
dely = h[1] - x[jbody][1];
delz = h[2] - x[jbody][2];
- rij = sqrt(delx*delx + dely*dely + delz*delz);
+ rsq = delx*delx + dely*dely + delz*delz;
+ rsqinv = (rsq == 0.0) ? 0.0 : 1.0/rsq;
+ rij = sqrt(rsq);
R = rij - contact_dist;
energy = 0;
@@ -2077,6 +2079,7 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1,
double s1,s2,x13[3],x23[3],x13h[3];
double t13,t23,t31,t41,x31[3],x41[3];
+ t13=t23=t31=t41=0.0;
MathExtra::sub3(x1,x3,x13); // x13 = x1 - x3
MathExtra::sub3(x2,x3,x23); // x23 = x2 - x3
diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp
index 679690ea82215c9a389ff9b417c74385a35a163e..347177b7f454bc03abfd739e8d51f218065b24de 100644
--- a/src/KOKKOS/fix_nh_kokkos.cpp
+++ b/src/KOKKOS/fix_nh_kokkos.cpp
@@ -148,7 +148,7 @@ void FixNHKokkos<DeviceType>::setup(int vflag)
if (pstat_flag) {
double kt = boltz * t_target;
- double nkt = atom->natoms * kt;
+ double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index 92d9338dc8418ce5e99f1aaf0c23032c455b95d6..9afa36b3c06be149b6d7610491ca3d6defc18f82 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -78,7 +78,7 @@ void PairATM::compute(int eflag, int vflag)
{
int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
double xi,yi,zi,evdwl;
- double rij2,rik2,rjk2,r6;
+ double rij2,rik2,rjk2;
double rij[3],rik[3],rjk[3],fj[3],fk[3];
double nu_local;
int *ilist,*jlist,*numneigh,**firstneigh;
@@ -91,8 +91,7 @@ void PairATM::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
- double cutoff_sixth = cut_global*cut_global;
- cutoff_sixth = cutoff_sixth*cutoff_sixth*cutoff_sixth;
+ double cutoff_squared = cut_global*cut_global;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -118,6 +117,7 @@ void PairATM::compute(int eflag, int vflag)
rij[2] = x[j][2] - zi;
if (rij[0] == 0.0 and rij[1] == 0.0 and rij[2] < 0.0) continue;
rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ if (rij2 > cutoff_squared) continue;
for (kk = jj+1; kk < jnum; kk++) {
k = jlist[kk];
@@ -130,20 +130,19 @@ void PairATM::compute(int eflag, int vflag)
rjk[2] = x[k][2] - x[j][2];
if (rjk[0] == 0.0 and rjk[1] == 0.0 and rjk[2] < 0.0) continue;
rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
+ if (rjk2 > cutoff_squared) continue;
rik[0] = x[k][0] - xi;
rik[1] = x[k][1] - yi;
rik[2] = x[k][2] - zi;
rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
-
- r6 = rij2*rik2*rjk2;
- if (r6 > cutoff_sixth) continue;
+ if (rik2 > cutoff_squared) continue;
nu_local = nu[type[i]][type[j]][type[k]];
if (nu_local == 0.0) continue;
interaction_ddd(nu_local,
- r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
+ rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
f[i][0] -= fj[0] + fk[0];
f[i][1] -= fj[1] + fk[1];
@@ -330,11 +329,12 @@ void PairATM::read_restart_settings(FILE *fp)
------------------------------------------------------------------------- */
void PairATM::interaction_ddd(double nu,
- double r6, double rij2, double rik2, double rjk2,
+ double rij2, double rik2, double rjk2,
double *rij, double *rik, double *rjk,
double *fj, double *fk, int eflag, double &eng)
{
- double r5inv,rri,rrj,rrk,rrr;
+ double r6,r5inv,rri,rrj,rrk,rrr;
+ r6 = rij2*rik2*rjk2;
r5inv = nu / (r6*r6*sqrt(r6));
rri = rik[0]*rij[0] + rik[1]*rij[1] + rik[2]*rij[2];
rrj = rij[0]*rjk[0] + rij[1]*rjk[1] + rij[2]*rjk[2];
diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h
index 210351cfad5b771e21faf23d3c5092ad6b866b9d..60d22348c36107df103cc5212f7f216c2607120a 100644
--- a/src/MANYBODY/pair_atm.h
+++ b/src/MANYBODY/pair_atm.h
@@ -39,11 +39,11 @@ class PairATM : public Pair {
void read_restart_settings(FILE *);
protected:
- double cut_global, cut_sixth;
+ double cut_global, cutoff_squared;
double ***nu;
void allocate();
- void interaction_ddd(double, double, double, double, double, double *,
+ void interaction_ddd(double, double, double, double, double *,
double *, double *, double *, double *, int, double &);
};
diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..66ebad6244a9d16b939bfb61c63862742e709cc8
--- /dev/null
+++ b/src/MANYBODY/pair_eam_cd.cpp
@@ -0,0 +1,677 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Alexander Stukowski
+ Technical University of Darmstadt,
+ Germany Department of Materials Science
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "pair_eam_cd.h"
+#include "atom.h"
+#include "force.h"
+#include "comm.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define ASSERT(cond)
+#define MAXLINE 1024 // This sets the maximum line length in EAM input files.
+
+PairEAMCD::PairEAMCD(LAMMPS *lmp, int _cdeamVersion)
+ : PairEAM(lmp), PairEAMAlloy(lmp), cdeamVersion(_cdeamVersion)
+{
+ single_enable = 0;
+ restartinfo = 0;
+
+ rhoB = NULL;
+ D_values = NULL;
+ hcoeff = NULL;
+
+ // Set communication buffer sizes needed by this pair style.
+
+ if (cdeamVersion == 1) {
+ comm_forward = 4;
+ comm_reverse = 3;
+ } else if (cdeamVersion == 2) {
+ comm_forward = 3;
+ comm_reverse = 2;
+ } else {
+ error->all(FLERR,"Invalid eam/cd potential version.");
+ }
+}
+
+PairEAMCD::~PairEAMCD()
+{
+ memory->destroy(rhoB);
+ memory->destroy(D_values);
+ if (hcoeff) delete[] hcoeff;
+}
+
+void PairEAMCD::compute(int eflag, int vflag)
+{
+ int i,j,ii,jj,inum,jnum,itype,jtype;
+ double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+ double rsq,rhoip,rhojp,recip,phi;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
+
+ // Grow per-atom arrays if necessary
+
+ if (atom->nmax > nmax) {
+ memory->destroy(rho);
+ memory->destroy(fp);
+ memory->destroy(rhoB);
+ memory->destroy(D_values);
+ nmax = atom->nmax;
+ memory->create(rho,nmax,"pair:rho");
+ memory->create(rhoB,nmax,"pair:rhoB");
+ memory->create(fp,nmax,"pair:fp");
+ memory->create(D_values,nmax,"pair:D_values");
+ }
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // Zero out per-atom arrays.
+
+ int m = nlocal + atom->nghost;
+ for (i = 0; i < m; i++) {
+ rho[i] = 0.0;
+ rhoB[i] = 0.0;
+ D_values[i] = 0.0;
+ }
+
+ // Stage I
+
+ // Compute rho and rhoB at each local atom site.
+
+ // Additionally calculate the D_i values here if we are using the
+ // one-site formulation. For the two-site formulation we have to
+ // calculate the D values in an extra loop (Stage II).
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq < cutforcesq) {
+ jtype = type[j];
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
+ double localrho = RhoOfR(index, jtype, itype);
+ rho[i] += localrho;
+ if (jtype == speciesB) rhoB[i] += localrho;
+ if (newton_pair || j < nlocal) {
+ localrho = RhoOfR(index, itype, jtype);
+ rho[j] += localrho;
+ if (itype == speciesB) rhoB[j] += localrho;
+ }
+
+ if (cdeamVersion == 1 && itype != jtype) {
+
+ // Note: if the i-j interaction is not concentration dependent (because either
+ // i or j are not species A or B) then its contribution to D_i and D_j should
+ // be ignored.
+ // This if-clause is only required for a ternary.
+
+ if ((itype == speciesA && jtype == speciesB)
+ || (jtype == speciesA && itype == speciesB)) {
+ double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
+ D_values[i] += Phi_AB;
+ if (newton_pair || j < nlocal)
+ D_values[j] += Phi_AB;
+ }
+ }
+ }
+ }
+ }
+
+ // Communicate and sum densities.
+
+ if (newton_pair) {
+ communicationStage = 1;
+ comm->reverse_comm_pair(this);
+ }
+
+ // fp = derivative of embedding energy at each atom
+ // phi = embedding energy at each atom
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ EAMTableIndex index = rhoToTableIndex(rho[i]);
+ fp[i] = FPrimeOfRho(index, type[i]);
+ if (eflag) {
+ phi = FofRho(index, type[i]);
+ if (eflag_global) eng_vdwl += phi;
+ if (eflag_atom) eatom[i] += phi;
+ }
+ }
+
+ // Communicate derivative of embedding function and densities
+ // and D_values (this for one-site formulation only).
+
+ communicationStage = 2;
+ comm->forward_comm_pair(this);
+
+ // The electron densities may not drop to zero because then the
+ // concentration would no longer be defined. But the concentration
+ // is not needed anyway if there is no interaction with another atom,
+ // which is the case if the electron density is exactly zero.
+ // That's why the following lines have been commented out.
+ //
+ //for (i = 0; i < nlocal + atom->nghost; i++) {
+ // if (rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB))
+ // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density.");
+ //}
+
+ // Stage II
+ // This is only required for the original two-site formulation of the CD-EAM potential.
+
+ if (cdeamVersion == 2) {
+
+ // Compute intermediate value D_i for each atom.
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ // This code line is required for ternary alloys.
+
+ if (itype != speciesA && itype != speciesB) continue;
+
+ double x_i = rhoB[i] / rho[i]; // Concentration at atom i.
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ jtype = type[j];
+ if (itype == jtype) continue;
+
+ // This code line is required for ternary alloys.
+
+ if (jtype != speciesA && jtype != speciesB) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq < cutforcesq) {
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
+
+ // The concentration independent part of the cross pair potential.
+
+ double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
+
+ // Average concentration of two sites
+
+ double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]);
+
+ // Calculate derivative of h(x_ij) polynomial function.
+
+ double h_prime = evalHprime(x_ij);
+
+ D_values[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]);
+ if (newton_pair || j < nlocal)
+ D_values[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]);
+ }
+ }
+ }
+
+ // Communicate and sum D values.
+
+ if (newton_pair) {
+ communicationStage = 3;
+ comm->reverse_comm_pair(this);
+ }
+ communicationStage = 4;
+ comm->forward_comm_pair(this);
+ }
+
+ // Stage III
+
+ // Compute force acting on each atom.
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ // Concentration at site i
+ // The value -1 indicates: no concentration dependence for all interactions of atom i.
+ // It will be replaced by the concentration at site i if atom i is either A or B.
+
+ double x_i = -1.0;
+ double D_i, h_prime_i;
+
+ // This if-clause is only required for ternary alloys.
+
+ if ((itype == speciesA || itype == speciesB) && rho[i] != 0.0) {
+
+ // Compute local concentration at site i.
+
+ x_i = rhoB[i]/rho[i];
+ ASSERT(x_i >= 0 && x_i<=1.0);
+
+ if (cdeamVersion == 1) {
+
+ // Calculate derivative of h(x_i) polynomial function.
+
+ h_prime_i = evalHprime(x_i);
+ D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]);
+ } else if (cdeamVersion == 2) {
+ D_i = D_values[i];
+ } else {
+ ASSERT(false);
+ }
+ }
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq < cutforcesq) {
+ jtype = type[j];
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
+
+ // rhoip = derivative of (density at atom j due to atom i)
+ // rhojp = derivative of (density at atom i due to atom j)
+ // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+ // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+ // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+
+ rhoip = RhoPrimeOfR(index, itype, jtype);
+ rhojp = RhoPrimeOfR(index, jtype, itype);
+ fpair = fp[i]*rhojp + fp[j]*rhoip;
+ recip = 1.0/r;
+
+ // The value -1 indicates: no concentration dependence for this
+ // i-j pair because atom j is not of species A nor B.
+
+ double x_j = -1;
+
+ // This code line is required for ternary alloy.
+
+ if (jtype == speciesA || jtype == speciesB) {
+ ASSERT(rho[i] != 0.0);
+ ASSERT(rho[j] != 0.0);
+
+ // Compute local concentration at site j.
+
+ x_j = rhoB[j]/rho[j];
+ ASSERT(x_j >= 0 && x_j<=1.0);
+
+ double D_j=0.0;
+ if (cdeamVersion == 1) {
+
+ // Calculate derivative of h(x_j) polynomial function.
+
+ double h_prime_j = evalHprime(x_j);
+ D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]);
+ } else if (cdeamVersion == 2) {
+ D_j = D_values[j];
+ } else {
+ ASSERT(false);
+ }
+ double t2 = -rhoB[j];
+ if (itype == speciesB) t2 += rho[j];
+ fpair += D_j * rhoip * t2;
+ }
+
+ // This if-clause is only required for a ternary alloy.
+ // Actually we don't need it at all because D_i should be zero
+ // anyway if atom i has no concentration dependent interactions
+ // (because it is not species A or B).
+
+ if (x_i != -1.0) {
+ double t1 = -rhoB[i];
+ if (jtype == speciesB) t1 += rho[i];
+ fpair += D_i * rhojp * t1;
+ }
+
+ double phip;
+ double phi = PhiOfR(index, itype, jtype, recip, phip);
+ if (itype == jtype || x_i == -1.0 || x_j == -1.0) {
+
+ // Case of no concentration dependence.
+
+ fpair += phip;
+ } else {
+
+ // We have a concentration dependence for the i-j interaction.
+
+ double h=0.0;
+ if (cdeamVersion == 1) {
+
+ // Calculate h(x_i) polynomial function.
+
+ double h_i = evalH(x_i);
+
+ // Calculate h(x_j) polynomial function.
+
+ double h_j = evalH(x_j);
+ h = 0.5 * (h_i + h_j);
+ } else if (cdeamVersion == 2) {
+
+ // Average concentration.
+
+ double x_ij = 0.5 * (x_i + x_j);
+
+ // Calculate h(x_ij) polynomial function.
+
+ h = evalH(x_ij);
+ } else {
+ ASSERT(false);
+ }
+ fpair += h * phip;
+ phi *= h;
+ }
+
+ // Divide by r_ij and negate to get forces from gradient.
+
+ fpair /= -r;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) evdwl = phi;
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairEAMCD::coeff(int narg, char **arg)
+{
+ PairEAMAlloy::coeff(narg, arg);
+
+ // Make sure the EAM file is a CD-EAM binary alloy.
+
+ if (setfl->nelements < 2)
+ error->all(FLERR,"The EAM file must contain at least 2 elements to be used with the eam/cd pair style.");
+
+ // Read in the coefficients of the h polynomial from the end of the EAM file.
+
+ read_h_coeff(arg[2]);
+
+ // Determine which atom type is the A species and which is the B
+ // species in the alloy. By default take the first element (index 0)
+ // in the EAM file as the A species and the second element (index 1)
+ // in the EAM file as the B species.
+
+ speciesA = -1;
+ speciesB = -1;
+ for (int i = 1; i <= atom->ntypes; i++) {
+ if (map[i] == 0) {
+ if (speciesA >= 0)
+ error->all(FLERR,"The first element from the EAM file may only be mapped to a single atom type.");
+ speciesA = i;
+ }
+ if (map[i] == 1) {
+ if (speciesB >= 0)
+ error->all(FLERR,"The second element from the EAM file may only be mapped to a single atom type.");
+ speciesB = i;
+ }
+ }
+ if (speciesA < 0)
+ error->all(FLERR,"The first element from the EAM file must be mapped to exactly one atom type.");
+ if (speciesB < 0)
+ error->all(FLERR,"The second element from the EAM file must be mapped to exactly one atom type.");
+}
+
+/* ----------------------------------------------------------------------
+ Reads in the h(x) polynomial coefficients
+------------------------------------------------------------------------- */
+
+void PairEAMCD::read_h_coeff(char *filename)
+{
+ if (comm->me == 0) {
+
+ // Open potential file
+
+ FILE *fptr;
+ char line[MAXLINE];
+ char nextline[MAXLINE];
+ fptr = force->open_potential(filename);
+ if (fptr == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open EAM potential file %s", filename);
+ error->one(FLERR,str);
+ }
+
+ // h coefficients are stored at the end of the file.
+ // Skip to last line of file.
+
+ while(fgets(nextline, MAXLINE, fptr) != NULL) {
+ strcpy(line, nextline);
+ }
+ char* ptr = strtok(line, " \t\n\r\f");
+ int degree = atoi(ptr);
+ nhcoeff = degree+1;
+ hcoeff = new double[nhcoeff];
+ int i = 0;
+ while((ptr = strtok(NULL," \t\n\r\f")) != NULL && i < nhcoeff) {
+ hcoeff[i++] = atof(ptr);
+ }
+ if (i != nhcoeff || nhcoeff < 1)
+ error->one(FLERR,"Failed to read h(x) function coefficients from EAM file.");
+
+ // Close the potential file.
+
+ fclose(fptr);
+ }
+
+ MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world);
+ if (comm->me != 0) hcoeff = new double[nhcoeff];
+ MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world);
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+int PairEAMCD::pack_forward_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+
+ m = 0;
+ if (communicationStage == 2) {
+ if (cdeamVersion == 1) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = fp[j];
+ buf[m++] = rho[j];
+ buf[m++] = rhoB[j];
+ buf[m++] = D_values[j];
+ }
+ return m;
+ } else if (cdeamVersion == 2) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = fp[j];
+ buf[m++] = rho[j];
+ buf[m++] = rhoB[j];
+ }
+ return m;
+ } else { ASSERT(false); return 0; }
+ } else if (communicationStage == 4) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = D_values[j];
+ }
+ return m;
+ } else return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairEAMCD::unpack_forward_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ if (communicationStage == 2) {
+ if (cdeamVersion == 1) {
+ for (i = first; i < last; i++) {
+ fp[i] = buf[m++];
+ rho[i] = buf[m++];
+ rhoB[i] = buf[m++];
+ D_values[i] = buf[m++];
+ }
+ } else if (cdeamVersion == 2) {
+ for (i = first; i < last; i++) {
+ fp[i] = buf[m++];
+ rho[i] = buf[m++];
+ rhoB[i] = buf[m++];
+ }
+ } else {
+ ASSERT(false);
+ }
+ } else if (communicationStage == 4) {
+ for (i = first; i < last; i++) {
+ D_values[i] = buf[m++];
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+int PairEAMCD::pack_reverse_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+
+ if (communicationStage == 1) {
+ if (cdeamVersion == 1) {
+ for (i = first; i < last; i++) {
+ buf[m++] = rho[i];
+ buf[m++] = rhoB[i];
+ buf[m++] = D_values[i];
+ }
+ return m;
+ } else if (cdeamVersion == 2) {
+ for (i = first; i < last; i++) {
+ buf[m++] = rho[i];
+ buf[m++] = rhoB[i];
+ }
+ return m;
+ } else { ASSERT(false); return 0; }
+ } else if (communicationStage == 3) {
+ for (i = first; i < last; i++) {
+ buf[m++] = D_values[i];
+ }
+ return m;
+ } else return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairEAMCD::unpack_reverse_comm(int n, int *list, double *buf)
+{
+ int i,j,m;
+
+ m = 0;
+ if (communicationStage == 1) {
+ if (cdeamVersion == 1) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ rho[j] += buf[m++];
+ rhoB[j] += buf[m++];
+ D_values[j] += buf[m++];
+ }
+ } else if (cdeamVersion == 2) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ rho[j] += buf[m++];
+ rhoB[j] += buf[m++];
+ }
+ } else {
+ ASSERT(false);
+ }
+ } else if (communicationStage == 3) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ D_values[j] += buf[m++];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based arrays
+------------------------------------------------------------------------- */
+double PairEAMCD::memory_usage()
+{
+ double bytes = 2 * nmax * sizeof(double);
+ return PairEAMAlloy::memory_usage() + bytes;
+}
diff --git a/src/USER-MISC/pair_cdeam.h b/src/MANYBODY/pair_eam_cd.h
similarity index 93%
rename from src/USER-MISC/pair_cdeam.h
rename to src/MANYBODY/pair_eam_cd.h
index 934b7601a4bfac37bbad057f94ed8a373a6848fe..ee84fb09c53f9fed5c2808f8e784340b705b7679 100644
--- a/src/USER-MISC/pair_cdeam.h
+++ b/src/MANYBODY/pair_eam_cd.h
@@ -13,26 +13,26 @@
#ifdef PAIR_CLASS
-PairStyle(eam/cd,PairCDEAM_OneSite)
-PairStyle(eam/cd/old,PairCDEAM_TwoSite)
+PairStyle(eam/cd,PairEAMCD_OneSite)
+PairStyle(eam/cd/old,PairEAMCD_TwoSite)
#else
-#ifndef LMP_PAIR_CDEAM_H
-#define LMP_PAIR_CDEAM_H
+#ifndef LMP_PAIR_EAM_CD_H
+#define LMP_PAIR_EAM_CD_H
#include "pair_eam_alloy.h"
namespace LAMMPS_NS {
-class PairCDEAM : public PairEAMAlloy
+class PairEAMCD : public PairEAMAlloy
{
public:
/// Constructor.
- PairCDEAM(class LAMMPS*, int cdeamVersion);
+ PairEAMCD(class LAMMPS*, int cdeamVersion);
/// Destructor.
- virtual ~PairCDEAM();
+ virtual ~PairEAMCD();
/// Calculates the energies and forces for all atoms in the system.
virtual void compute(int, int);
@@ -211,19 +211,19 @@ public:
};
/// The one-site concentration formulation of CD-EAM.
- class PairCDEAM_OneSite : public PairCDEAM
+ class PairEAMCD_OneSite : public PairEAMCD
{
public:
/// Constructor.
- PairCDEAM_OneSite(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAM(lmp, 1) {}
+ PairEAMCD_OneSite(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCD(lmp, 1) {}
};
/// The two-site concentration formulation of CD-EAM.
- class PairCDEAM_TwoSite : public PairCDEAM
+ class PairEAMCD_TwoSite : public PairEAMCD
{
public:
/// Constructor.
- PairCDEAM_TwoSite(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAM(lmp, 2) {}
+ PairEAMCD_TwoSite(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCD(lmp, 2) {}
};
}
diff --git a/src/Purge.list b/src/Purge.list
index cd4eb17dab5d142b0fde5bb4673d3266271645fd..cb98636b1c17860fab98343824d10bf5f2063bbf 100644
--- a/src/Purge.list
+++ b/src/Purge.list
@@ -24,6 +24,9 @@ style_nstencil.h
style_ntopo.h
# other auto-generated files
lmpinstalledpkgs.h
+# renamed on 31 July 2018
+pair_cdeam.h
+pair_cdeam.cpp
# renamed on 20 July 2018
pair_body.h
pair_body.cpp
diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp
index 8b47eff624c27535f6d1cb297a792de3aadf99ea..6460a6185fb72d0635b623dbd7e8a2e7a2d27ba6 100644
--- a/src/SPIN/atom_vec_spin.cpp
+++ b/src/SPIN/atom_vec_spin.cpp
@@ -816,9 +816,9 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values)
x[nlocal][2] = coord[2];
sp[nlocal][3] = atof(values[2]);
- sp[nlocal][0] = atof(values[5]);
- sp[nlocal][1] = atof(values[6]);
- sp[nlocal][2] = atof(values[7]);
+ sp[nlocal][0] = atof(values[6]);
+ sp[nlocal][1] = atof(values[7]);
+ sp[nlocal][2] = atof(values[8]);
double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] +
sp[nlocal][1]*sp[nlocal][1] +
sp[nlocal][2]*sp[nlocal][2]);
diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp
index b67f62d53d61cdf8fce10d1a09a07bb59939aa92..dc16190c98763053d76fb84e5a423eca570f860d 100644
--- a/src/SPIN/compute_spin.cpp
+++ b/src/SPIN/compute_spin.cpp
@@ -105,16 +105,16 @@ void ComputeSpin::compute_vector()
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (atom->sp_flag) {
- mag[0] += sp[i][0];
- mag[1] += sp[i][1];
- mag[2] += sp[i][2];
- magenergy -= (sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]);
- tx = sp[i][1]*fm[i][2]-sp[i][2]*fm[i][1];
- ty = sp[i][2]*fm[i][0]-sp[i][0]*fm[i][2];
- tz = sp[i][0]*fm[i][1]-sp[i][1]*fm[i][0];
- tempnum += tx*tx+ty*ty+tz*tz;
- tempdenom += sp[i][0]*fm[i][0]+fm[i][1]*sp[i][1]+sp[i][2]*fm[i][2];
- countsp++;
+ mag[0] += sp[i][0];
+ mag[1] += sp[i][1];
+ mag[2] += sp[i][2];
+ magenergy -= (sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]);
+ tx = sp[i][1]*fm[i][2]-sp[i][2]*fm[i][1];
+ ty = sp[i][2]*fm[i][0]-sp[i][0]*fm[i][2];
+ tz = sp[i][0]*fm[i][1]-sp[i][1]*fm[i][0];
+ tempnum += tx*tx+ty*ty+tz*tz;
+ tempdenom += sp[i][0]*fm[i][0]+fm[i][1]*sp[i][1]+sp[i][2]*fm[i][2];
+ countsp++;
}
}
else error->all(FLERR,"Compute compute/spin requires atom/spin style");
diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp
index b792969c5dcd5bc4c5d238143de90455c8cf885d..08e2c63e7f6ba147c6062da17f92a68b2a5d090a 100644
--- a/src/SPIN/pair_spin_dmi.cpp
+++ b/src/SPIN/pair_spin_dmi.cpp
@@ -65,6 +65,9 @@ PairSpinDmi::~PairSpinDmi()
memory->destroy(v_dmx);
memory->destroy(v_dmy);
memory->destroy(v_dmz);
+ memory->destroy(vmech_dmx);
+ memory->destroy(vmech_dmy);
+ memory->destroy(vmech_dmz);
memory->destroy(cutsq);
}
}
@@ -118,7 +121,7 @@ void PairSpinDmi::coeff(int narg, char **arg)
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
const double rij = force->numeric(FLERR,arg[3]);
- const double dm = (force->numeric(FLERR,arg[4]))/hbar;
+ const double dm = (force->numeric(FLERR,arg[4]));
double dmx = force->numeric(FLERR,arg[5]);
double dmy = force->numeric(FLERR,arg[6]);
double dmz = force->numeric(FLERR,arg[7]);
@@ -133,9 +136,12 @@ void PairSpinDmi::coeff(int narg, char **arg)
for (int j = MAX(jlo,i); j <= jhi; j++) {
cut_spin_dmi[i][j] = rij;
DM[i][j] = dm;
- v_dmx[i][j] = dmx * dm;
- v_dmy[i][j] = dmy * dm;
- v_dmz[i][j] = dmz * dm;
+ v_dmx[i][j] = dmx * dm / hbar;
+ v_dmy[i][j] = dmy * dm / hbar;
+ v_dmz[i][j] = dmz * dm / hbar;
+ vmech_dmx[i][j] = dmx * dm;
+ vmech_dmy[i][j] = dmy * dm;
+ vmech_dmz[i][j] = dmz * dm;
setflag[i][j] = 1;
count++;
}
@@ -187,9 +193,17 @@ void PairSpinDmi::init_style()
double PairSpinDmi::init_one(int i, int j)
{
-
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+ DM[j][i] = DM[i][j];
+ v_dmx[j][i] = v_dmx[i][j];
+ v_dmy[j][i] = v_dmy[i][j];
+ v_dmz[j][i] = v_dmz[i][j];
+ vmech_dmx[j][i] = vmech_dmx[i][j];
+ vmech_dmy[j][i] = vmech_dmy[i][j];
+ vmech_dmz[j][i] = vmech_dmz[i][j];
+ cut_spin_dmi[j][i] = cut_spin_dmi[i][j];
+
return cut_spin_dmi_global;
}
@@ -210,7 +224,8 @@ void PairSpinDmi::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double evdwl, ecoul;
- double xi[3], rij[3], eij[3];
+ double xi[3], eij[3];
+ double delx,dely,delz;
double spi[3], spj[3];
double fi[3], fmi[3];
double local_cut2;
@@ -264,20 +279,17 @@ void PairSpinDmi::compute(int eflag, int vflag)
spj[2] = sp[j][2];
evdwl = 0.0;
-
fi[0] = fi[1] = fi[2] = 0.0;
fmi[0] = fmi[1] = fmi[2] = 0.0;
- rij[0] = rij[1] = rij[2] = 0.0;
- eij[0] = eij[1] = eij[2] = 0.0;
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
inorm = 1.0/sqrt(rsq);
- eij[0] = rij[0]*inorm;
- eij[1] = rij[1]*inorm;
- eij[2] = rij[2]*inorm;
+ eij[0] = -inorm*delx;
+ eij[1] = -inorm*dely;
+ eij[2] = -inorm*delz;
local_cut2 = cut_spin_dmi[itype][jtype]*cut_spin_dmi[itype][jtype];
@@ -286,7 +298,7 @@ void PairSpinDmi::compute(int eflag, int vflag)
if (rsq <= local_cut2) {
compute_dmi(i,j,eij,fmi,spj);
if (lattice_flag) {
- compute_dmi_mech(fi);
+ compute_dmi_mech(i,j,rsq,eij,fi,spi,spj);
}
}
@@ -309,7 +321,7 @@ void PairSpinDmi::compute(int eflag, int vflag)
} else evdwl = 0.0;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
+ evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz);
}
}
@@ -325,8 +337,8 @@ void PairSpinDmi::compute_single_pair(int ii, double fmi[3])
double **x = atom->x;
double **sp = atom->sp;
double local_cut2;
-
- double xi[3], rij[3], eij[3];
+ double xi[3], eij[3];
+ double delx,dely,delz;
double spj[3];
int i,j,jnum,itype,jtype;
@@ -358,14 +370,14 @@ void PairSpinDmi::compute_single_pair(int ii, double fmi[3])
spj[1] = sp[j][1];
spj[2] = sp[j][2];
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
inorm = 1.0/sqrt(rsq);
- eij[0] = rij[0]*inorm;
- eij[1] = rij[1]*inorm;
- eij[2] = rij[2]*inorm;
+ eij[0] = -inorm*delx;
+ eij[1] = -inorm*dely;
+ eij[2] = -inorm*delz;
local_cut2 = cut_spin_dmi[itype][jtype]*cut_spin_dmi[itype][jtype];
@@ -390,23 +402,45 @@ void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double
jtype = type[j];
dmix = eij[1]*v_dmz[itype][jtype] - eij[2]*v_dmy[itype][jtype];
- dmiy = eij[2]*v_dmx[itype][jtype] - eij[2]*v_dmz[itype][jtype];
+ dmiy = eij[2]*v_dmx[itype][jtype] - eij[0]*v_dmz[itype][jtype];
dmiz = eij[0]*v_dmy[itype][jtype] - eij[1]*v_dmx[itype][jtype];
- fmi[0] += (spj[1]*dmiz - spj[2]*dmiy);
- fmi[1] += (spj[2]*dmix - spj[0]*dmiz);
- fmi[2] += (spj[0]*dmiy - spj[1]*dmix);
+ fmi[0] -= (spj[1]*dmiz - spj[2]*dmiy);
+ fmi[1] -= (spj[2]*dmix - spj[0]*dmiz);
+ fmi[2] -= (spj[0]*dmiy - spj[1]*dmix);
}
/* ----------------------------------------------------------------------
compute the mechanical force due to the dmi interaction between atom i and atom j
------------------------------------------------------------------------- */
-void PairSpinDmi::compute_dmi_mech(double fi[3])
+void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double eij[3],
+ double fi[3], double spi[3], double spj[3])
{
- fi[0] += 0.0;
- fi[1] += 0.0;
- fi[2] += 0.0;
+ int *type = atom->type;
+ int itype, jtype;
+ double dmix,dmiy,dmiz;
+ itype = type[i];
+ jtype = type[j];
+ double csx,csy,csz,cdmx,cdmy,cdmz,irij;
+
+ irij = 1.0/sqrt(rsq);
+
+ dmix = vmech_dmx[itype][jtype];
+ dmiy = vmech_dmy[itype][jtype];
+ dmiz = vmech_dmz[itype][jtype];
+
+ csx = (spi[1]*spj[2] - spi[2]*spj[1]);
+ csy = (spi[2]*spj[0] - spi[0]*spj[2]);
+ csz = (spi[0]*spj[1] - spi[1]*spj[0]);
+
+ cdmx = (dmiy*csz - dmiz*csy);
+ cdmy = (dmiz*csx - dmix*csz);
+ cdmz = (dmix*csy - dmiy*csz);
+
+ fi[0] += irij*cdmx;
+ fi[1] += irij*cdmy;
+ fi[2] += irij*cdmz;
}
/* ----------------------------------------------------------------------
@@ -428,6 +462,9 @@ void PairSpinDmi::allocate()
memory->create(v_dmx,n+1,n+1,"pair:DM_vector_x");
memory->create(v_dmy,n+1,n+1,"pair:DM_vector_y");
memory->create(v_dmz,n+1,n+1,"pair:DM_vector_z");
+ memory->create(vmech_dmx,n+1,n+1,"pair:DMmech_vector_x");
+ memory->create(vmech_dmy,n+1,n+1,"pair:DMmech_vector_y");
+ memory->create(vmech_dmz,n+1,n+1,"pair:DMmech_vector_z");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
@@ -451,6 +488,9 @@ void PairSpinDmi::write_restart(FILE *fp)
fwrite(&v_dmx[i][j],sizeof(double),1,fp);
fwrite(&v_dmy[i][j],sizeof(double),1,fp);
fwrite(&v_dmz[i][j],sizeof(double),1,fp);
+ fwrite(&vmech_dmx[i][j],sizeof(double),1,fp);
+ fwrite(&vmech_dmy[i][j],sizeof(double),1,fp);
+ fwrite(&vmech_dmz[i][j],sizeof(double),1,fp);
fwrite(&cut_spin_dmi[i][j],sizeof(double),1,fp);
}
}
@@ -478,12 +518,18 @@ void PairSpinDmi::read_restart(FILE *fp)
fread(&v_dmx[i][j],sizeof(double),1,fp);
fread(&v_dmy[i][j],sizeof(double),1,fp);
fread(&v_dmz[i][j],sizeof(double),1,fp);
+ fread(&vmech_dmx[i][j],sizeof(double),1,fp);
+ fread(&vmech_dmy[i][j],sizeof(double),1,fp);
+ fread(&vmech_dmz[i][j],sizeof(double),1,fp);
fread(&cut_spin_dmi[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&DM[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&v_dmx[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&v_dmy[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&v_dmz[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&vmech_dmx[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&vmech_dmy[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&vmech_dmz[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_spin_dmi[i][j],1,MPI_DOUBLE,0,world);
}
}
diff --git a/src/SPIN/pair_spin_dmi.h b/src/SPIN/pair_spin_dmi.h
index a309f0c8d52ade48d42cffc26254e5a5c6839988..68e42e879dfe15577d6bf73fe8f80a5593530dfd 100644
--- a/src/SPIN/pair_spin_dmi.h
+++ b/src/SPIN/pair_spin_dmi.h
@@ -38,22 +38,23 @@ class PairSpinDmi : public PairSpin {
void compute_single_pair(int, double *);
void compute_dmi(int, int, double *, double *, double *);
- void compute_dmi_mech(double *);
+ void compute_dmi_mech(int, int, double, double *, double *, double *, double *);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
- double cut_spin_dmi_global; // short range pair cutoff
+ double cut_spin_dmi_global; // short range pair cutoff
protected:
- double **DM; // dmi coeff in eV
- double **v_dmx, **v_dmy, **v_dmz; // dmi direction
- double **cut_spin_dmi; // cutoff distance dmi
+ double **DM; // dmi coeff in eV
+ double **v_dmx, **v_dmy, **v_dmz; // dmi direction
+ double **vmech_dmx, **vmech_dmy, **vmech_dmz; // dmi mech direction
+ double **cut_spin_dmi; // cutoff distance dmi
- int lattice_flag; // flag for mech force computation
- class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups
+ int lattice_flag; // flag for mech force computation
+ class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups
void allocate();
};
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
index 1b7b36b6dbac6d6cb69ef566e1bd71132c3b4d3b..cc074bb97d9b9dd91d2bfcc8e378d7cd56a7ba5e 100644
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@@ -65,7 +65,7 @@ PairSpinExchange::~PairSpinExchange()
memory->destroy(J1_mech);
memory->destroy(J2);
memory->destroy(J3);
- memory->destroy(cutsq); // to be deleted
+ memory->destroy(cutsq); // to be implemented
}
}
@@ -134,8 +134,8 @@ void PairSpinExchange::coeff(int narg, char **arg)
count++;
}
}
- if (count == 0)
- error->all(FLERR,"Incorrect args in pair_style command");
+
+ if (count == 0) error->all(FLERR,"Incorrect args in pair_style command");
}
/* ----------------------------------------------------------------------
@@ -183,6 +183,12 @@ double PairSpinExchange::init_one(int i, int j)
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+ J1_mag[j][i] = J1_mag[i][j];
+ J1_mech[j][i] = J1_mech[i][j];
+ J2[j][i] = J2[i][j];
+ J3[j][i] = J3[i][j];
+ cut_spin_exchange[j][i] = cut_spin_exchange[i][j];
+
return cut_spin_exchange_global;
}
@@ -203,7 +209,8 @@ void PairSpinExchange::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double evdwl, ecoul;
- double xi[3], rij[3], eij[3];
+ double xi[3], eij[3];
+ double delx,dely,delz;
double spi[3], spj[3];
double fi[3], fmi[3];
double local_cut2;
@@ -255,18 +262,17 @@ void PairSpinExchange::compute(int eflag, int vflag)
spj[2] = sp[j][2];
evdwl = 0.0;
-
fi[0] = fi[1] = fi[2] = 0.0;
fmi[0] = fmi[1] = fmi[2] = 0.0;
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
inorm = 1.0/sqrt(rsq);
- eij[0] = inorm*rij[0];
- eij[1] = inorm*rij[1];
- eij[2] = inorm*rij[2];
+ eij[0] = -inorm*delx;
+ eij[1] = -inorm*dely;
+ eij[2] = -inorm*delz;
local_cut2 = cut_spin_exchange[itype][jtype]*cut_spin_exchange[itype][jtype];
@@ -298,7 +304,7 @@ void PairSpinExchange::compute(int eflag, int vflag)
} else evdwl = 0.0;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
+ evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz);
}
}
@@ -317,8 +323,8 @@ void PairSpinExchange::compute_single_pair(int ii, double fmi[3])
double **x = atom->x;
double **sp = atom->sp;
double local_cut2;
-
double xi[3], rij[3];
+ double delx,dely,delz;
double spj[3];
int i,j,jnum,itype,jtype;
@@ -351,15 +357,14 @@ void PairSpinExchange::compute_single_pair(int ii, double fmi[3])
spj[1] = sp[j][1];
spj[2] = sp[j][2];
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= local_cut2) {
compute_exchange(i,j,rsq,fmi,spj);
}
-
}
}
@@ -390,7 +395,8 @@ void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3],
compute the mechanical force due to the exchange interaction between atom i and atom j
------------------------------------------------------------------------- */
-void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double rij[3], double fi[3], double spi[3], double spj[3])
+void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double eij[3],
+ double fi[3], double spi[3], double spj[3])
{
int *type = atom->type;
int itype, jtype;
@@ -408,9 +414,9 @@ void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double ri
Jex_mech *= 8.0*Jex*rr*exp(-ra);
Jex_mech *= (spi[0]*spj[0]+spi[1]*spj[1]+spi[2]*spj[2]);
- fi[0] -= Jex_mech*rij[0];
- fi[1] -= Jex_mech*rij[1];
- fi[2] -= Jex_mech*rij[2];
+ fi[0] -= Jex_mech*eij[0];
+ fi[1] -= Jex_mech*eij[1];
+ fi[2] -= Jex_mech*eij[2];
}
/* ----------------------------------------------------------------------
diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp
index 315b691d17ea38a265a16587ee1191ef7ca0f7cd..6bc1f71947333ac405e29d6342696165b47379ab 100644
--- a/src/SPIN/pair_spin_magelec.cpp
+++ b/src/SPIN/pair_spin_magelec.cpp
@@ -187,8 +187,14 @@ void PairSpinMagelec::init_style()
double PairSpinMagelec::init_one(int i, int j)
{
+ if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
- if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+ ME[j][i] = ME[i][j];
+ ME_mech[j][i] = ME_mech[i][j];
+ v_mex[j][i] = v_mex[i][j];
+ v_mey[j][i] = v_mey[i][j];
+ v_mez[j][i] = v_mez[i][j];
+ cut_spin_magelec[j][i] = cut_spin_magelec[i][j];
return cut_spin_magelec_global;
}
@@ -211,7 +217,8 @@ void PairSpinMagelec::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double evdwl, ecoul;
- double xi[3], rij[3], eij[3];
+ double xi[3], eij[3];
+ double delx,dely,delz;
double spi[3], spj[3];
double fi[3], fmi[3];
double local_cut2;
@@ -263,18 +270,17 @@ void PairSpinMagelec::compute(int eflag, int vflag)
spj[2] = sp[j][2];
evdwl = 0.0;
-
fi[0] = fi[1] = fi[2] = 0.0;
fmi[0] = fmi[1] = fmi[2] = 0.0;
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
inorm = 1.0/sqrt(rsq);
- eij[0] = inorm*rij[0];
- eij[1] = inorm*rij[1];
- eij[2] = inorm*rij[2];
+ eij[0] = -inorm*delx;
+ eij[1] = -inorm*dely;
+ eij[2] = -inorm*delz;
local_cut2 = cut_spin_magelec[itype][jtype]*cut_spin_magelec[itype][jtype];
@@ -301,12 +307,12 @@ void PairSpinMagelec::compute(int eflag, int vflag)
}
if (eflag) {
- evdwl = (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
+ evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
evdwl *= hbar;
} else evdwl = 0.0;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
+ evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz);
}
}
@@ -322,8 +328,8 @@ void PairSpinMagelec::compute_single_pair(int ii, double fmi[3])
double **x = atom->x;
double **sp = atom->sp;
double local_cut2;
-
- double xi[3], rij[3], eij[3];
+ double xi[3], eij[3];
+ double delx,dely,delz;
double spj[3];
int i,j,jnum,itype,jtype;
@@ -342,8 +348,6 @@ void PairSpinMagelec::compute_single_pair(int ii, double fmi[3])
xi[1] = x[i][1];
xi[2] = x[i][2];
- eij[0] = eij[1] = eij[2] = 0.0;
-
jlist = firstneigh[i];
jnum = numneigh[i];
@@ -358,14 +362,14 @@ void PairSpinMagelec::compute_single_pair(int ii, double fmi[3])
spj[1] = sp[j][1];
spj[2] = sp[j][2];
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
inorm = 1.0/sqrt(rsq);
- eij[0] = inorm*rij[0];
- eij[1] = inorm*rij[1];
- eij[2] = inorm*rij[2];
+ eij[0] = -inorm*delx;
+ eij[1] = -inorm*dely;
+ eij[2] = -inorm*delz;
if (rsq <= local_cut2) {
compute_magelec(i,j,rsq,eij,fmi,spj);
@@ -380,36 +384,26 @@ void PairSpinMagelec::compute_magelec(int i, int j, double rsq, double eij[3], d
{
int *type = atom->type;
int itype, jtype;
+ double meix,meiy,meiz;
+ double vx,vy,vz;
itype = type[i];
jtype = type[j];
- double local_cut2 = cut_spin_magelec[itype][jtype]*cut_spin_magelec[itype][jtype];
-
- if (rsq <= local_cut2) {
- double meix,meiy,meiz;
- double rx, ry, rz;
- double vx, vy, vz;
-
- rx = eij[0];
- ry = eij[1];
- rz = eij[2];
-
- vx = v_mex[itype][jtype];
- vy = v_mey[itype][jtype];
- vz = v_mez[itype][jtype];
+ vx = v_mex[itype][jtype];
+ vy = v_mey[itype][jtype];
+ vz = v_mez[itype][jtype];
- meix = vy*rz - vz*ry;
- meiy = vz*rx - vx*rz;
- meiz = vx*ry - vy*rx;
+ meix = vy*eij[2] - vz*eij[1];
+ meiy = vz*eij[0] - vx*eij[2];
+ meiz = vx*eij[1] - vy*eij[0];
- meix *= ME[itype][jtype];
- meiy *= ME[itype][jtype];
- meiz *= ME[itype][jtype];
+ meix *= ME[itype][jtype];
+ meiy *= ME[itype][jtype];
+ meiz *= ME[itype][jtype];
- fmi[0] += spj[1]*meiz - spj[2]*meiy;
- fmi[1] += spj[2]*meix - spj[0]*meiz;
- fmi[2] += spj[0]*meiy - spj[1]*meix;
- }
+ fmi[0] += spj[1]*meiz - spj[2]*meiy;
+ fmi[1] += spj[2]*meix - spj[0]*meiz;
+ fmi[2] += spj[0]*meiy - spj[1]*meix;
}
/* ---------------------------------------------------------------------- */
diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp
index 0daafad7567d32ff841a2bfd5bf0a5e400d1eeeb..55f537cf4fe1c4b2af7de3dc3a1945cca14b4f0e 100644
--- a/src/SPIN/pair_spin_neel.cpp
+++ b/src/SPIN/pair_spin_neel.cpp
@@ -193,8 +193,16 @@ void PairSpinNeel::init_style()
double PairSpinNeel::init_one(int i, int j)
{
-
- if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+ if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
+ g1[j][i] = g1[i][j];
+ g1_mech[j][i] = g1_mech[i][j];
+ g2[j][i] = g2[i][j];
+ g3[j][i] = g3[i][j];
+ q1[j][i] = q1[i][j];
+ q1_mech[j][i] = q1_mech[i][j];
+ q2[j][i] = q2[i][j];
+ q3[j][i] = q3[i][j];
return cut_spin_neel_global;
}
diff --git a/src/SPIN/pair_spin_neel.h b/src/SPIN/pair_spin_neel.h
index 934d4a93ad5f2bdd37a53da2403d9c7d7c049c76..f60d7d2dca0e6ac72ea3c0111698f79d60ea2f37 100644
--- a/src/SPIN/pair_spin_neel.h
+++ b/src/SPIN/pair_spin_neel.h
@@ -51,9 +51,9 @@ class PairSpinNeel : public PairSpin {
// pseudo-dipolar and pseudo-quadrupolar coeff.
- double **g1, **g1_mech; // exchange coeffs gij
+ double **g1, **g1_mech; // neel coeffs gij
double **g2, **g3; // g1 in eV, g2 adim, g3 in Ang
- double **q1, **q1_mech; // exchange coeffs qij
+ double **q1, **q1_mech; // neel coeffs qij
double **q2, **q3; // q1 in eV, q2 adim, q3 in Ang
double **cut_spin_neel; // cutoff distance exchange
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
index 37e128f55662a6e6c9152abb518d3233845604fd..7fb8a27110ba2528bf81e53f4e6e9c78de23ee54 100644
--- a/src/USER-BOCS/fix_bocs.cpp
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -846,7 +846,7 @@ void FixBocs::setup(int vflag)
if (pstat_flag) {
double kt = boltz * t_target;
- double nkt = atom->natoms * kt;
+ double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
@@ -1508,7 +1508,7 @@ double FixBocs::compute_scalar()
double volume;
double energy;
double kt = boltz * t_target;
- double lkt_press = kt;
+ double lkt_press = 0.0;
int ich;
if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
else volume = domain->xprd * domain->yprd;
@@ -1539,15 +1539,21 @@ double FixBocs::compute_scalar()
// sum is over barostatted dimensions
if (pstat_flag) {
- for (i = 0; i < 3; i++)
- if (p_flag[i])
+ for (i = 0; i < 3; i++) {
+ if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
p_hydro*(volume-vol0) / (pdim*nktv2p);
+ lkt_press += kt;
+ }
+ }
if (pstyle == TRICLINIC) {
- for (i = 3; i < 6; i++)
- if (p_flag[i])
+ for (i = 3; i < 6; i++) {
+ if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
+ lkt_press += kt;
+ }
+ }
}
// extra contributions from thermostat chain for barostat
@@ -1880,15 +1886,14 @@ void FixBocs::nhc_temp_integrate()
void FixBocs::nhc_press_integrate()
{
- int ich,i;
+ int ich,i,pdof;
double expfac,factor_etap,kecurrent;
double kt = boltz * t_target;
- double lkt_press = kt;
// Update masses, to preserve initial freq, if flag set
if (omega_mass_flag) {
- double nkt = atom->natoms * kt;
+ double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
@@ -1912,14 +1917,24 @@ void FixBocs::nhc_press_integrate()
}
kecurrent = 0.0;
- for (i = 0; i < 3; i++)
- if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ pdof = 0;
+ for (i = 0; i < 3; i++) {
+ if (p_flag[i]) {
+ kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ pdof++;
+ }
+ }
if (pstyle == TRICLINIC) {
- for (i = 3; i < 6; i++)
- if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ for (i = 3; i < 6; i++) {
+ if (p_flag[i]) {
+ kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ pdof++;
+ }
+ }
}
+ double lkt_press = pdof * kt;
etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
double ncfac = 1.0/nc_pchain;
diff --git a/src/USER-MISC/Install.sh b/src/USER-MISC/Install.sh
deleted file mode 100755
index 2d42125ec3a79cdb00cc88cb31d12b8be3959f4d..0000000000000000000000000000000000000000
--- a/src/USER-MISC/Install.sh
+++ /dev/null
@@ -1,40 +0,0 @@
-# Install/unInstall package files in LAMMPS
-# mode = 0/1/2 for uninstall/install/update
-
-mode=$1
-
-# enforce using portable C locale
-LC_ALL=C
-export LC_ALL
-
-# arg1 = file, arg2 = file it depends on
-
-action () {
- if (test $mode = 0) then
- rm -f ../$1
- elif (! cmp -s $1 ../$1) then
- if (test -z "$2" || test -e ../$2) then
- cp $1 ..
- if (test $mode = 2) then
- echo " updating src/$1"
- fi
- fi
- elif (test ! -n "$2") then
- if (test ! -e ../$2) then
- rm -f ../$1
- fi
- fi
-}
-
-# all package files
-# only a few files have dependencies
-
-for file in *.cpp *.h; do
- if (test $file = "pair_cdeam.cpp") then
- action pair_cdeam.cpp pair_eam_alloy.cpp
- elif (test $file = "pair_cdeam.h") then
- action pair_cdeam.h pair_eam_alloy.cpp
- else
- test -f ${file} && action $file
- fi
-done
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 68a6252d8dc692285b5577c6281723c4515f8d54..0f9e7bf383bf3e005b828672ad24b360d6f9b440 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -65,7 +65,6 @@ pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11
-pair_style eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de, 7 Nov 09
pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17
pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
diff --git a/src/USER-MISC/pair_cdeam.cpp b/src/USER-MISC/pair_cdeam.cpp
deleted file mode 100644
index 53d9036a61d44da205f921c3272ccf41b9075cde..0000000000000000000000000000000000000000
--- a/src/USER-MISC/pair_cdeam.cpp
+++ /dev/null
@@ -1,644 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing author: Alexander Stukowski
- Technical University of Darmstadt,
- Germany Department of Materials Science
-------------------------------------------------------------------------- */
-
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include "pair_cdeam.h"
-#include "atom.h"
-#include "force.h"
-#include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-// This is for debugging purposes. The ASSERT() macro is used in the code to check
-// if everything runs as expected. Change this to #if 0 if you don't need the checking.
-#if 0
- #define ASSERT(cond) ((!(cond)) ? my_failure(error,__FILE__,__LINE__) : my_noop())
-
- inline void my_noop() {}
- inline void my_failure(Error* error, const char* file, int line) {
- char str[1024];
- sprintf(str,"Assertion failure: File %s, line %i", file, line);
- error->one(FLERR,str);
- }
-#else
- #define ASSERT(cond)
-#endif
-
-#define MAXLINE 1024 // This sets the maximum line length in EAM input files.
-
-PairCDEAM::PairCDEAM(LAMMPS *lmp, int _cdeamVersion) : PairEAM(lmp), PairEAMAlloy(lmp), cdeamVersion(_cdeamVersion)
-{
- single_enable = 0;
- restartinfo = 0;
-
- rhoB = NULL;
- D_values = NULL;
- hcoeff = NULL;
-
- // Set communication buffer sizes needed by this pair style.
- if(cdeamVersion == 1) {
- comm_forward = 4;
- comm_reverse = 3;
- }
- else if(cdeamVersion == 2) {
- comm_forward = 3;
- comm_reverse = 2;
- }
- else {
- error->all(FLERR,"Invalid CD-EAM potential version.");
- }
-}
-
-PairCDEAM::~PairCDEAM()
-{
- memory->destroy(rhoB);
- memory->destroy(D_values);
- if(hcoeff) delete[] hcoeff;
-}
-
-void PairCDEAM::compute(int eflag, int vflag)
-{
- int i,j,ii,jj,inum,jnum,itype,jtype;
- double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
- double rsq,rhoip,rhojp,recip,phi;
- int *ilist,*jlist,*numneigh,**firstneigh;
-
- evdwl = 0.0;
- if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
-
- // Grow per-atom arrays if necessary
- if(atom->nmax > nmax) {
- memory->destroy(rho);
- memory->destroy(fp);
- memory->destroy(rhoB);
- memory->destroy(D_values);
- nmax = atom->nmax;
- memory->create(rho,nmax,"pair:rho");
- memory->create(rhoB,nmax,"pair:rhoB");
- memory->create(fp,nmax,"pair:fp");
- memory->create(D_values,nmax,"pair:D_values");
- }
-
- double **x = atom->x;
- double **f = atom->f;
- int *type = atom->type;
- int nlocal = atom->nlocal;
- int newton_pair = force->newton_pair;
-
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- // Zero out per-atom arrays.
- int m = nlocal + atom->nghost;
- for(i = 0; i < m; i++) {
- rho[i] = 0.0;
- rhoB[i] = 0.0;
- D_values[i] = 0.0;
- }
-
- // Stage I
-
- // Compute rho and rhoB at each local atom site.
- // Additionally calculate the D_i values here if we are using the one-site formulation.
- // For the two-site formulation we have to calculate the D values in an extra loop (Stage II).
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for(jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if(rsq < cutforcesq) {
- jtype = type[j];
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
- double localrho = RhoOfR(index, jtype, itype);
- rho[i] += localrho;
- if(jtype == speciesB) rhoB[i] += localrho;
- if(newton_pair || j < nlocal) {
- localrho = RhoOfR(index, itype, jtype);
- rho[j] += localrho;
- if(itype == speciesB) rhoB[j] += localrho;
- }
-
- if(cdeamVersion == 1 && itype != jtype) {
- // Note: if the i-j interaction is not concentration dependent (because either
- // i or j are not species A or B) then its contribution to D_i and D_j should
- // be ignored.
- // This if-clause is only required for a ternary.
- if((itype == speciesA && jtype == speciesB) || (jtype == speciesA && itype == speciesB)) {
- double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
- D_values[i] += Phi_AB;
- if(newton_pair || j < nlocal)
- D_values[j] += Phi_AB;
- }
- }
- }
- }
- }
-
- // Communicate and sum densities.
- if(newton_pair) {
- communicationStage = 1;
- comm->reverse_comm_pair(this);
- }
-
- // fp = derivative of embedding energy at each atom
- // phi = embedding energy at each atom
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- EAMTableIndex index = rhoToTableIndex(rho[i]);
- fp[i] = FPrimeOfRho(index, type[i]);
- if(eflag) {
- phi = FofRho(index, type[i]);
- if (eflag_global) eng_vdwl += phi;
- if (eflag_atom) eatom[i] += phi;
- }
- }
-
- // Communicate derivative of embedding function and densities
- // and D_values (this for one-site formulation only).
- communicationStage = 2;
- comm->forward_comm_pair(this);
-
- // The electron densities may not drop to zero because then the concentration would no longer be defined.
- // But the concentration is not needed anyway if there is no interaction with another atom, which is the case
- // if the electron density is exactly zero. That's why the following lines have been commented out.
- //
- //for(i = 0; i < nlocal + atom->nghost; i++) {
- // if(rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB))
- // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density.");
- //}
-
- // Stage II
- // This is only required for the original two-site formulation of the CD-EAM potential.
-
- if(cdeamVersion == 2) {
- // Compute intermediate value D_i for each atom.
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- // This code line is required for ternary alloys.
- if(itype != speciesA && itype != speciesB) continue;
-
- double x_i = rhoB[i] / rho[i]; // Concentration at atom i.
-
- for(jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
- jtype = type[j];
- if(itype == jtype) continue;
-
- // This code line is required for ternary alloys.
- if(jtype != speciesA && jtype != speciesB) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if(rsq < cutforcesq) {
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
-
- // The concentration independent part of the cross pair potential.
- double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
-
- // Average concentration of two sites
- double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]);
-
- // Calculate derivative of h(x_ij) polynomial function.
- double h_prime = evalHprime(x_ij);
-
- D_values[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]);
- if(newton_pair || j < nlocal)
- D_values[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]);
- }
- }
- }
-
- // Communicate and sum D values.
- if(newton_pair) {
- communicationStage = 3;
- comm->reverse_comm_pair(this);
- }
- communicationStage = 4;
- comm->forward_comm_pair(this);
- }
-
- // Stage III
-
- // Compute force acting on each atom.
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- itype = type[i];
-
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- // Concentration at site i
- double x_i = -1.0; // The value -1 indicates: no concentration dependence for all interactions of atom i.
- // It will be replaced by the concentration at site i if atom i is either A or B.
-
- double D_i, h_prime_i;
-
- // This if-clause is only required for ternary alloys.
- if((itype == speciesA || itype == speciesB) && rho[i] != 0.0) {
-
- // Compute local concentration at site i.
- x_i = rhoB[i]/rho[i];
- ASSERT(x_i >= 0 && x_i<=1.0);
-
- if(cdeamVersion == 1) {
- // Calculate derivative of h(x_i) polynomial function.
- h_prime_i = evalHprime(x_i);
- D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]);
- } else if(cdeamVersion == 2) {
- D_i = D_values[i];
- } else {
- ASSERT(false);
- }
- }
-
- for(jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if(rsq < cutforcesq) {
- jtype = type[j];
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
-
- // rhoip = derivative of (density at atom j due to atom i)
- // rhojp = derivative of (density at atom i due to atom j)
- // psip needs both fp[i] and fp[j] terms since r_ij appears in two
- // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
- // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
- rhoip = RhoPrimeOfR(index, itype, jtype);
- rhojp = RhoPrimeOfR(index, jtype, itype);
- fpair = fp[i]*rhojp + fp[j]*rhoip;
- recip = 1.0/r;
-
- double x_j = -1; // The value -1 indicates: no concentration dependence for this i-j pair
- // because atom j is not of species A nor B.
-
- // This code line is required for ternary alloy.
- if(jtype == speciesA || jtype == speciesB) {
- ASSERT(rho[i] != 0.0);
- ASSERT(rho[j] != 0.0);
-
- // Compute local concentration at site j.
- x_j = rhoB[j]/rho[j];
- ASSERT(x_j >= 0 && x_j<=1.0);
-
- double D_j=0.0;
- if(cdeamVersion == 1) {
- // Calculate derivative of h(x_j) polynomial function.
- double h_prime_j = evalHprime(x_j);
- D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]);
- } else if(cdeamVersion == 2) {
- D_j = D_values[j];
- } else {
- ASSERT(false);
- }
- double t2 = -rhoB[j];
- if(itype == speciesB) t2 += rho[j];
- fpair += D_j * rhoip * t2;
- }
-
- // This if-clause is only required for a ternary alloy.
- // Actually we don't need it at all because D_i should be zero anyway if
- // atom i has no concentration dependent interactions (because it is not species A or B).
- if(x_i != -1.0) {
- double t1 = -rhoB[i];
- if(jtype == speciesB) t1 += rho[i];
- fpair += D_i * rhojp * t1;
- }
-
- double phip;
- double phi = PhiOfR(index, itype, jtype, recip, phip);
- if(itype == jtype || x_i == -1.0 || x_j == -1.0) {
- // Case of no concentration dependence.
- fpair += phip;
- } else {
- // We have a concentration dependence for the i-j interaction.
- double h=0.0;
- if(cdeamVersion == 1) {
- // Calculate h(x_i) polynomial function.
- double h_i = evalH(x_i);
- // Calculate h(x_j) polynomial function.
- double h_j = evalH(x_j);
- h = 0.5 * (h_i + h_j);
- } else if(cdeamVersion == 2) {
- // Average concentration.
- double x_ij = 0.5 * (x_i + x_j);
- // Calculate h(x_ij) polynomial function.
- h = evalH(x_ij);
- } else {
- ASSERT(false);
- }
- fpair += h * phip;
- phi *= h;
- }
-
- // Divide by r_ij and negate to get forces from gradient.
- fpair /= -r;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if(newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if(eflag) evdwl = phi;
- if(evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
- }
- }
- }
-
- if(vflag_fdotr) virial_fdotr_compute();
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairCDEAM::coeff(int narg, char **arg)
-{
- PairEAMAlloy::coeff(narg, arg);
-
- // Make sure the EAM file is a CD-EAM binary alloy.
- if(setfl->nelements < 2)
- error->all(FLERR,"The EAM file must contain at least 2 elements to be used with the eam/cd pair style.");
-
- // Read in the coefficients of the h polynomial from the end of the EAM file.
- read_h_coeff(arg[2]);
-
- // Determine which atom type is the A species and which is the B species in the alloy.
- // By default take the first element (index 0) in the EAM file as the A species
- // and the second element (index 1) in the EAM file as the B species.
- speciesA = -1;
- speciesB = -1;
- for(int i = 1; i <= atom->ntypes; i++) {
- if(map[i] == 0) {
- if(speciesA >= 0)
- error->all(FLERR,"The first element from the EAM file may only be mapped to a single atom type.");
- speciesA = i;
- }
- if(map[i] == 1) {
- if(speciesB >= 0)
- error->all(FLERR,"The second element from the EAM file may only be mapped to a single atom type.");
- speciesB = i;
- }
- }
- if(speciesA < 0)
- error->all(FLERR,"The first element from the EAM file must be mapped to exactly one atom type.");
- if(speciesB < 0)
- error->all(FLERR,"The second element from the EAM file must be mapped to exactly one atom type.");
-}
-
-/* ----------------------------------------------------------------------
- Reads in the h(x) polynomial coefficients
-------------------------------------------------------------------------- */
-void PairCDEAM::read_h_coeff(char *filename)
-{
- if(comm->me == 0) {
- // Open potential file
- FILE *fptr;
- char line[MAXLINE];
- char nextline[MAXLINE];
- fptr = force->open_potential(filename);
- if (fptr == NULL) {
- char str[128];
- sprintf(str,"Cannot open EAM potential file %s", filename);
- error->one(FLERR,str);
- }
-
- // h coefficients are stored at the end of the file.
- // Skip to last line of file.
- while(fgets(nextline, MAXLINE, fptr) != NULL) {
- strcpy(line, nextline);
- }
- char* ptr = strtok(line, " \t\n\r\f");
- int degree = atoi(ptr);
- nhcoeff = degree+1;
- hcoeff = new double[nhcoeff];
- int i = 0;
- while((ptr = strtok(NULL," \t\n\r\f")) != NULL && i < nhcoeff) {
- hcoeff[i++] = atof(ptr);
- }
- if(i != nhcoeff || nhcoeff < 1)
- error->one(FLERR,"Failed to read h(x) function coefficients from EAM file.");
-
- // Close the potential file.
- fclose(fptr);
- }
-
- MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world);
- if(comm->me != 0) hcoeff = new double[nhcoeff];
- MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world);
-}
-
-
-/* ---------------------------------------------------------------------- */
-
-int PairCDEAM::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
-{
- int i,j,m;
-
- m = 0;
- if(communicationStage == 2) {
- if(cdeamVersion == 1) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = fp[j];
- buf[m++] = rho[j];
- buf[m++] = rhoB[j];
- buf[m++] = D_values[j];
- }
- return m;
- }
- else if(cdeamVersion == 2) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = fp[j];
- buf[m++] = rho[j];
- buf[m++] = rhoB[j];
- }
- return m;
- }
- else { ASSERT(false); return 0; }
- }
- else if(communicationStage == 4) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = D_values[j];
- }
- return m;
- }
- else return 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairCDEAM::unpack_forward_comm(int n, int first, double *buf)
-{
- int i,m,last;
-
- m = 0;
- last = first + n;
- if(communicationStage == 2) {
- if(cdeamVersion == 1) {
- for(i = first; i < last; i++) {
- fp[i] = buf[m++];
- rho[i] = buf[m++];
- rhoB[i] = buf[m++];
- D_values[i] = buf[m++];
- }
- }
- else if(cdeamVersion == 2) {
- for(i = first; i < last; i++) {
- fp[i] = buf[m++];
- rho[i] = buf[m++];
- rhoB[i] = buf[m++];
- }
- } else {
- ASSERT(false);
- }
- }
- else if(communicationStage == 4) {
- for(i = first; i < last; i++) {
- D_values[i] = buf[m++];
- }
- }
-}
-
-/* ---------------------------------------------------------------------- */
-int PairCDEAM::pack_reverse_comm(int n, int first, double *buf)
-{
- int i,m,last;
-
- m = 0;
- last = first + n;
-
- if(communicationStage == 1) {
- if(cdeamVersion == 1) {
- for(i = first; i < last; i++) {
- buf[m++] = rho[i];
- buf[m++] = rhoB[i];
- buf[m++] = D_values[i];
- }
- return m;
- }
- else if(cdeamVersion == 2) {
- for(i = first; i < last; i++) {
- buf[m++] = rho[i];
- buf[m++] = rhoB[i];
- }
- return m;
- }
- else { ASSERT(false); return 0; }
- }
- else if(communicationStage == 3) {
- for(i = first; i < last; i++) {
- buf[m++] = D_values[i];
- }
- return m;
- }
- else return 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairCDEAM::unpack_reverse_comm(int n, int *list, double *buf)
-{
- int i,j,m;
-
- m = 0;
- if(communicationStage == 1) {
- if(cdeamVersion == 1) {
- for(i = 0; i < n; i++) {
- j = list[i];
- rho[j] += buf[m++];
- rhoB[j] += buf[m++];
- D_values[j] += buf[m++];
- }
- } else if(cdeamVersion == 2) {
- for(i = 0; i < n; i++) {
- j = list[i];
- rho[j] += buf[m++];
- rhoB[j] += buf[m++];
- }
- } else {
- ASSERT(false);
- }
- }
- else if(communicationStage == 3) {
- for(i = 0; i < n; i++) {
- j = list[i];
- D_values[j] += buf[m++];
- }
- }
-}
-
-/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
-------------------------------------------------------------------------- */
-double PairCDEAM::memory_usage()
-{
- double bytes = 2 * nmax * sizeof(double);
- return PairEAMAlloy::memory_usage() + bytes;
-}
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index 186376d95230bc8d2bbbf977c95fba8c5c16243f..73c70420c5bc84e001d448a5d580b1fe10ce9ece 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -798,7 +798,7 @@ void FixNH::setup(int vflag)
if (pstat_flag) {
double kt = boltz * t_target;
- double nkt = atom->natoms * kt;
+ double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
@@ -1446,7 +1446,7 @@ double FixNH::compute_scalar()
double volume;
double energy;
double kt = boltz * t_target;
- double lkt_press = kt;
+ double lkt_press = 0.0;
int ich;
if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
else volume = domain->xprd * domain->yprd;
@@ -1477,15 +1477,21 @@ double FixNH::compute_scalar()
// sum is over barostatted dimensions
if (pstat_flag) {
- for (i = 0; i < 3; i++)
- if (p_flag[i])
+ for (i = 0; i < 3; i++) {
+ if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
p_hydro*(volume-vol0) / (pdim*nktv2p);
+ lkt_press += kt;
+ }
+ }
if (pstyle == TRICLINIC) {
- for (i = 3; i < 6; i++)
- if (p_flag[i])
+ for (i = 3; i < 6; i++) {
+ if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
+ lkt_press += kt;
+ }
+ }
}
// extra contributions from thermostat chain for barostat
@@ -1818,15 +1824,15 @@ void FixNH::nhc_temp_integrate()
void FixNH::nhc_press_integrate()
{
- int ich,i;
+ int ich,i,pdof;
double expfac,factor_etap,kecurrent;
double kt = boltz * t_target;
- double lkt_press = kt;
+ double lkt_press;
// Update masses, to preserve initial freq, if flag set
if (omega_mass_flag) {
- double nkt = atom->natoms * kt;
+ double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
@@ -1850,14 +1856,22 @@ void FixNH::nhc_press_integrate()
}
kecurrent = 0.0;
+ pdof = 0;
for (i = 0; i < 3; i++)
- if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ if (p_flag[i]) {
+ kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ pdof++;
+ }
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
- if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ if (p_flag[i]) {
+ kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ pdof++;
+ }
}
+ lkt_press = pdof * kt;
etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
double ncfac = 1.0/nc_pchain;
diff --git a/src/variable.cpp b/src/variable.cpp
index 86296b4b402e4c066d2692d5362d579be635c54d..f005221400509f76fd5887f0323fa11cc8f30a32 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -1576,7 +1576,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
newtree->nextra = 0;
treestack[ntreestack++] = newtree;
- } else print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
+ } else print_var_error(FLERR,
+ "Mismatched compute in variable formula",ivar);
// ----------------
// fix
@@ -1584,7 +1585,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (strncmp(word,"f_",2) == 0 || strncmp(word,"F_",2) == 0) {
if (domain->box_exist == 0)
- print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
+ print_var_error(FLERR,"Variable evaluation before "
+ "simulation box is defined",ivar);
// uppercase used to force access of
// global vector vs global scalar, and global array vs global vector
@@ -1667,11 +1669,14 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (index1 > fix->size_array_rows &&
fix->size_array_rows_variable == 0)
- print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar);
+ print_var_error(FLERR,"Variable formula fix array is "
+ "accessed out-of-range",ivar);
if (index2 > fix->size_array_cols)
- print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar);
+ print_var_error(FLERR,"Variable formula fix array is "
+ "accessed out-of-range",ivar);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at a "
+ "compatible time",ivar);
value1 = fix->compute_array(index1-1,index2-1);
if (tree) {
@@ -1688,13 +1693,17 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket == 0 && fix->vector_flag) {
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
if (tree == NULL)
- print_var_error(FLERR,"Fix global vector in ""equal-style variable formula",ivar);
+ print_var_error(FLERR,"Fix global vector in "
+ "equal-style variable formula",ivar);
if (treetype == ATOM)
- print_var_error(FLERR,"Fix global vector in ""atom-style variable formula",ivar);
+ print_var_error(FLERR,"Fix global vector in "
+ "atom-style variable formula",ivar);
if (fix->size_vector == 0)
- print_var_error(FLERR,"Variable formula fix vector is zero length",ivar);
+ print_var_error(FLERR,"Variable formula "
+ "fix vector is zero length",ivar);
int nvec = fix->size_vector;
double *vec;
@@ -1726,7 +1735,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
print_var_error(FLERR,"Fix global vector in "
"atom-style variable formula",ivar);
if (fix->size_array_rows == 0)
- print_var_error(FLERR,"Variable formula fix array is zero length",ivar);
+ print_var_error(FLERR,"Variable formula fix array is "
+ "zero length",ivar);
int nvec = fix->size_array_rows;
double *vec;
@@ -1785,10 +1795,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
fix->size_peratom_cols == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Per-atom fix in "
+ "equal-style variable formula",ivar);
if (update->whichflag > 0 &&
update->ntimestep % fix->peratom_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
Tree *newtree = new Tree();
newtree->type = ATOMARRAY;
@@ -1805,13 +1817,15 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
fix->size_peratom_cols > 0) {
if (tree == NULL)
- print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Per-atom fix in "
+ "equal-style variable formula",ivar);
if (index1 > fix->size_peratom_cols)
print_var_error(FLERR,"Variable formula fix array "
"is accessed out-of-range",ivar);
if (update->whichflag > 0 &&
update->ntimestep % fix->peratom_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
Tree *newtree = new Tree();
newtree->type = ATOMARRAY;
@@ -1878,7 +1892,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
char *var = retrieve(word+2);
if (var == NULL)
- print_var_error(FLERR,"Invalid variable evaluation in variable formula",ivar);
+ print_var_error(FLERR,"Invalid variable evaluation in "
+ "variable formula",ivar);
if (tree) {
Tree *newtree = new Tree();
newtree->type = VALUE;
@@ -1977,7 +1992,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
double *vec;
int nvec = compute_vector(ivar,&vec);
if (index <= 0 || index > nvec)
- print_var_error(FLERR,"Invalid index into vector-style variable",ivar);
+ print_var_error(FLERR,"Invalid index into "
+ "vector-style variable",ivar);
int m = index; // convert from tagint to int
if (tree) {
@@ -1989,7 +2005,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = vec[m-1];
- } else print_var_error(FLERR,"Mismatched variable in variable formula",ivar);
+ } else print_var_error(FLERR,"Mismatched variable in "
+ "variable formula",ivar);
// ----------------
// math/group/special function or atom value/vector or
@@ -2194,7 +2211,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (value2 == 0.0)
argstack[nargstack++] = 1.0;
else if ((value1 == 0.0) && (value2 < 0.0))
- print_var_error(FLERR,"Invalid power expression in variable formula",ivar);
+ print_var_error(FLERR,"Invalid power expression in "
+ "variable formula",ivar);
else argstack[nargstack++] = pow(value1,value2);
} else if (opprevious == UNARY) {
argstack[nargstack++] = -value2;
@@ -3368,7 +3386,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (tree) newtree->type = LN;
else {
if (value1 <= 0.0)
- print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar);
+ print_var_error(FLERR,"Log of zero/negative value in "
+ "variable formula",ivar);
argstack[nargstack++] = log(value1);
}
} else if (strcmp(word,"log") == 0) {
@@ -3377,7 +3396,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (tree) newtree->type = LOG;
else {
if (value1 <= 0.0)
- print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar);
+ print_var_error(FLERR,"Log of zero/negative value in "
+ "variable formula",ivar);
argstack[nargstack++] = log10(value1);
}
} else if (strcmp(word,"abs") == 0) {
@@ -3482,7 +3502,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use ramp in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use ramp in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = RAMP;
else {
double delta = update->ntimestep - update->beginstep;
@@ -3617,7 +3638,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use vdisplace in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use vdisplace in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = VDISPLACE;
else {
double delta = update->ntimestep - update->beginstep;
@@ -3629,7 +3651,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use swiggle in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use swiggle in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = CWIGGLE;
else {
if (values[0] == 0.0)
@@ -3644,7 +3667,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use cwiggle in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use cwiggle in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = CWIGGLE;
else {
if (values[0] == 0.0)
@@ -3709,7 +3733,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
if (strcmp(word,"count") == 0) {
if (narg == 1) value = group->count(igroup);
- else if (narg == 2) value = group->count(igroup,region_function(args[1],ivar));
+ else if (narg == 2)
+ value = group->count(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
} else if (strcmp(word,"mass") == 0) {
@@ -3719,7 +3744,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"charge") == 0) {
if (narg == 1) value = group->charge(igroup);
- else if (narg == 2) value = group->charge(igroup,region_function(args[1],ivar));
+ else if (narg == 2)
+ value = group->charge(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
} else if (strcmp(word,"xcm") == 0) {
@@ -3732,7 +3758,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
int iregion = region_function(args[2],ivar);
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = xcm[0];
else if (strcmp(args[1],"y") == 0) value = xcm[1];
else if (strcmp(args[1],"z") == 0) value = xcm[2];
@@ -3748,7 +3775,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
int iregion = region_function(args[2],ivar);
double masstotal = group->mass(igroup,iregion);
group->vcm(igroup,masstotal,vcm,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = vcm[0];
else if (strcmp(args[1],"y") == 0) value = vcm[1];
else if (strcmp(args[1],"z") == 0) value = vcm[2];
@@ -3767,7 +3795,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"bound") == 0) {
double minmax[6];
if (narg == 2) group->bounds(igroup,minmax);
- else if (narg == 3) group->bounds(igroup,minmax,region_function(args[2],ivar));
+ else if (narg == 3)
+ group->bounds(igroup,minmax,region_function(args[2],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
if (strcmp(args[1],"xmin") == 0) value = minmax[0];
else if (strcmp(args[1],"xmax") == 0) value = minmax[1];
@@ -3789,7 +3818,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
value = group->gyration(igroup,masstotal,xcm,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
} else if (strcmp(word,"ke") == 0) {
if (narg == 1) value = group->ke(igroup);
@@ -3808,7 +3838,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->angmom(igroup,xcm,lmom,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = lmom[0];
else if (strcmp(args[1],"y") == 0) value = lmom[1];
else if (strcmp(args[1],"z") == 0) value = lmom[2];
@@ -3826,7 +3857,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->torque(igroup,xcm,tq,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = tq[0];
else if (strcmp(args[1],"y") == 0) value = tq[1];
else if (strcmp(args[1],"z") == 0) value = tq[2];
@@ -3844,7 +3876,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->inertia(igroup,xcm,inertia,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"xx") == 0) value = inertia[0][0];
else if (strcmp(args[1],"yy") == 0) value = inertia[1][1];
else if (strcmp(args[1],"zz") == 0) value = inertia[2][2];
@@ -3869,7 +3902,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
group->angmom(igroup,xcm,angmom,iregion);
group->inertia(igroup,xcm,inertia,iregion);
group->omega(angmom,inertia,omega);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = omega[0];
else if (strcmp(args[1],"y") == 0) value = omega[1];
else if (strcmp(args[1],"z") == 0) value = omega[2];
@@ -3924,7 +3958,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
Tree **treestack, int &ntreestack,
double *argstack, int &nargstack, int ivar)
{
- double value,xvalue,sx,sy,sxx,sxy;
+ bigint sx,sxx;
+ double value,xvalue,sy,sxy;
// word not a match to any special function
@@ -4020,11 +4055,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else index = 0;
int ifix = modify->find_fix(&args[0][2]);
- if (ifix < 0) print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
+ if (ifix < 0)
+ print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
fix = modify->fix[ifix];
if (index == 0 && fix->vector_flag) {
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
nvec = fix->size_vector;
nstride = 1;
} else if (index && fix->array_flag) {
@@ -4032,7 +4069,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
print_var_error(FLERR,"Variable formula fix array "
"is accessed out-of-range",ivar);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
nvec = fix->size_array_rows;
nstride = fix->size_array_cols;
} else print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
@@ -4048,10 +4086,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else index = 0;
if (index)
- print_var_error(FLERR,"Invalid special function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid special function in "
+ "variable formula",ivar);
ivar = find(&args[0][2]);
if (ivar < 0)
- print_var_error(FLERR,"Invalid special function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid special function in "
+ "variable formula",ivar);
if (style[ivar] != VECTOR)
print_var_error(FLERR,"Mis-matched special function variable "
"in variable formula",ivar);
@@ -4062,12 +4102,16 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
nvec = compute_vector(ivar,&vec);
nstride = 1;
- } else print_var_error(FLERR,"Invalid special function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid special function in "
+ "variable formula",ivar);
value = 0.0;
- if (method == SLOPE) sx = sy = sxx = sxy = 0.0;
- if (method == XMIN) value = BIG;
- if (method == XMAX) value = -BIG;
+ if (method == SLOPE) {
+ sx = sxx = 0;
+ sy = sxy = 0.0;
+ }
+ else if (method == XMIN) value = BIG;
+ else if (method == XMAX) value = -BIG;
if (compute) {
double *vec;
@@ -4084,12 +4128,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
else if (method == AVE) value += vec[j];
else if (method == TRAP) value += vec[j];
else if (method == SLOPE) {
- if (nvec > 1) xvalue = (double) i / (nvec-1);
- else xvalue = 0.0;
- sx += xvalue;
+ sx += i;
sy += vec[j];
- sxx += xvalue*xvalue;
- sxy += xvalue*vec[j];
+ sxx += i*i;
+ sxy += i*vec[j];
}
j += nstride;
}
@@ -4107,12 +4149,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
else if (method == AVE) value += one;
else if (method == TRAP) value += one;
else if (method == SLOPE) {
- if (nvec > 1) xvalue = (double) i / (nvec-1);
- else xvalue = 0.0;
- sx += xvalue;
+ sx += i;
sy += one;
- sxx += xvalue*xvalue;
- sxy += xvalue*one;
+ sxx += i*i;
+ sxy += i*one;
}
}
if (method == TRAP) {
@@ -4134,12 +4174,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
else if (method == AVE) value += one;
else if (method == TRAP) value += one;
else if (method == SLOPE) {
- if (nvec > 1) xvalue = (double) i / (nvec-1);
- else xvalue = 0.0;
- sx += xvalue;
+ sx += i;
sy += one;
- sxx += xvalue*xvalue;
- sxy += xvalue*one;
+ sxx += i*i;
+ sxy += i*one;
}
}
if (method == TRAP) value -= 0.5*vec[0] + 0.5*vec[nvec-1];
@@ -4148,9 +4186,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
if (method == AVE) value /= nvec;
if (method == SLOPE) {
- double numerator = sxy - sx*sy;
- double denominator = sxx - sx*sx;
- if (denominator != 0.0) value = numerator/denominator / nvec;
+ double numerator = nvec*sxy - sx*sy;
+ double denominator = nvec*sxx - sx*sx;
+ if (denominator != 0.0) value = numerator/denominator;
else value = BIG;
}
@@ -4169,7 +4207,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"gmask") == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Gmask function in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Gmask function in equal-style "
+ "variable formula",ivar);
if (narg != 1)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@@ -4186,7 +4225,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"rmask") == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Rmask function in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Rmask function in equal-style "
+ "variable formula",ivar);
if (narg != 1)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@@ -4202,7 +4242,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"grmask") == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Grmask function in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Grmask function in equal-style "
+ "variable formula",ivar);
if (narg != 2)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@@ -4228,7 +4269,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
int ivar = find(args[0]);
if (ivar < 0)
- print_var_error(FLERR,"Variable ID in variable formula does not exist",ivar);
+ print_var_error(FLERR,"Variable ID in "
+ "variable formula does not exist",ivar);
// SCALARFILE has single current value, read next one
// save value in tree or on argstack
@@ -4253,7 +4295,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (style[ivar] == ATOMFILE) {
if (tree == NULL)
- print_var_error(FLERR,"Atomfile variable in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Atomfile variable in "
+ "equal-style variable formula",ivar);
double *result;
memory->create(result,atom->nlocal,"variable:result");
@@ -4271,11 +4314,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
newtree->nextra = 0;
treestack[ntreestack++] = newtree;
- } else print_var_error(FLERR,"Invalid variable style in special function next",ivar);
+ } else print_var_error(FLERR,"Invalid variable style in "
+ "special function next",ivar);
} else if (strcmp(word,"is_active") == 0) {
if (narg != 2)
- print_var_error(FLERR,"Invalid is_active() function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid is_active() function in "
+ "variable formula",ivar);
Info info(lmp);
value = (info.is_active(args[0],args[1])) ? 1.0 : 0.0;
@@ -4293,7 +4338,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"is_available") == 0) {
if (narg != 2)
- print_var_error(FLERR,"Invalid is_available() function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid is_available() function in "
+ "variable formula",ivar);
Info info(lmp);
value = (info.is_available(args[0],args[1])) ? 1.0 : 0.0;
@@ -4311,7 +4357,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"is_defined") == 0) {
if (narg != 2)
- print_var_error(FLERR,"Invalid is_defined() function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid is_defined() function in "
+ "variable formula",ivar);
Info info(lmp);
value = (info.is_defined(args[0],args[1])) ? 1.0 : 0.0;
diff --git a/src/version.h b/src/version.h
index 90a21631d9f1f2d26b690c4e5a160a466fa13560..b95c259dd68c7322ff261a38a925d32eec0aa984 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "16 Jul 2018"
+#define LAMMPS_VERSION "2 Aug 2018"
diff --git a/tools/emacs/README.md b/tools/emacs/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..75504a7000a0dcb9b5876985fe9ae4fafb63a912
--- /dev/null
+++ b/tools/emacs/README.md
@@ -0,0 +1,82 @@
+# GNU Emacs Syntax Highlighting
+
+> Copyright (C) 2010-2018 Aidan Thompson <athomps at sandia.gov>
+> Copyright (C) 2018 Rohit Goswami <r95g10 at gmail.com>
+
+The `lammps-mode.el` file provided in this directory will enable syntax
+highlighting for the lammps script syntax in GNU Emacs. The groupings of
+commands were originally copied from `tools/vim`.
+
+## Installation
+**Requirements: GNU Emacs 24.\***
+
+### Obtaining the Package
+
+#### MELPA
+
+The easiest installation method is via MELPA and it is advisable to use one of
+the many [MELPA installation methods](https://melpa.org/#/getting-started).
+
+For example, with [use-package](https://github.com/jwiegley/use-package) one can
+simply use the following:
+
+``` emacs-lisp
+(use-package lammps-mode)
+```
+
+#### Manually
+
+Assuming for some reason you have downloaded the file to `~/.emacs.d/lisp` you
+would do the following (kanged [from here](http://ergoemacs.org/emacs/emacs_installing_packages.html)):
+
+``` emacs-lisp
+;; Tell emacs where is your personal elisp lib dir
+(add-to-list 'load-path "~/.emacs.d/lisp/")
+
+;; load the package.
+(load "lammps-mode")
+```
+
+### Autoloading \& Auto-recognition
+
+To automatically turn on the LAMMPS mode for editing your input scripts,
+use the following line as the **first** line of your script:
+```
+# -*- lammps -*-
+```
+
+For automatically switching on the LAMMPS mode based on filename patterns,
+e.g. for `in.*` and `*.lmp` files, add the following code to your `.emacs`:
+
+``` emacs-lisp
+(autoload 'lammps-mode "lammps-mode.el" "LAMMPS mode." t)
+(setq auto-mode-alist (append auto-mode-alist
+ '(("in\\." . lammps-mode))
+ '(("\\.lmp\\'" . lammps-mode))
+ ))
+```
+
+## Status
+
+By far not all commands are included in the syntax file (lammps-mode.el). You
+can easily add new ones to the existing classes.
+
+## Implementation Details
+
+`lammps-mode` is derived from `shell-script-mode` which provides some basic
+syntax highlighting of strings, comments, etc.
+
+The MELPA recipe used for this package is simply:
+
+``` emacs-lisp
+(lammps-mode :fetcher github :repo "HaoZeke/lammps-mode")
+```
+
+## Caveats
+
+* Does not work with Xemacs [See [this comment](https://github.com/lammps/lammps/pull/1022#issuecomment-408871233)]
+
+## License
+
+[GNU GPL v2](https://github.com/HaoZeke/lammps-mode/blob/master/LICENSE).
+Check the file for more details.
diff --git a/tools/emacs/README.txt b/tools/emacs/README.txt
deleted file mode 100644
index 8dfc37cb851d3100ec052a7550d9b839f856c146..0000000000000000000000000000000000000000
--- a/tools/emacs/README.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-=== Emacs Syntax Highlighting ===
-Created by Aidan Thompson 12/2010
-===============================
-
-The lammps.el file provided in this directory will enable syntax
-highlighting for the lammps script syntax in emacs. The groupings
-of commands were copied from tools/vim. The simulation scripts have to
-end on *.lmp or start with in.* (see lammps.el). By far not all
-commands are included in the syntax file (lammps.el).
-You can easily add new ones to the existing classes.
-'lammps-mode' is derived from 'shell-script-mode' which provides
-some basic syntax highlighting of strings, comments, etc.
-
-=To enable the highlighting:
-============================
-(0) Create/edit the emacs init file ~/.emacs to contain:
-
-(load "~/.emacs.d/lammps")
-
-This file may also be called ~/.emacs.el, or ~/.emacs.d/init.el
-
-(1) Copy lammps.el to the directory ~/.emacs.d
-
diff --git a/tools/emacs/lammps.el b/tools/emacs/lammps-mode.el
similarity index 73%
rename from tools/emacs/lammps.el
rename to tools/emacs/lammps-mode.el
index d1ebebbbbfe9e9e75ca9c8403f0e9e54719ed515..37e8a32116755ff967380b772c442ef436b88341 100644
--- a/tools/emacs/lammps.el
+++ b/tools/emacs/lammps-mode.el
@@ -1,7 +1,48 @@
-;; LAMMPS auto-mode
+;;; lammps-mode.el --- basic syntax highlighting for LAMMPS files
+
+;; Copyright (C) 2010-18 Aidan Thompson
+;; Copyright (C) 2018 Rohit Goswami
+
+;; Author: Aidan Thompson <athomps at sandia.gov>
+;; Maintainer: Rohit Goswami <r95g10 at gmail.com>
+;; Created: December 4, 2010
+;; Modified: July 30, 2018
+;; Version: 1.5.0
+;; Keywords: languages, faces
+;; Homepage: https://github.com/lammps/lammps/tree/master/tools/emacs
+;; Package-Requires: ((emacs "24.4"))
+
+;; This file is not part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 2 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License along
+;; with this program; if not, write to the Free Software Foundation, Inc.,
+;; 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+;;; Commentary:
;; translation of keyword classes from tools/vim
;; see http://xahlee.org/emacs/elisp_syntax_coloring.html
+;; Put this in your .emacs file to enable autoloading of lammps-mode
+;; and auto-recognition of "in.*" and "*.lmp" files:
+;;
+;; (autoload 'lammps-mode "lammps-mode.el" "LAMMPS mode." t)
+;; (setq auto-mode-alist (append auto-mode-alist
+;; '(("in\\." . lammps-mode))
+;; '(("\\.lmp\\'" . lammps-mode))
+;; ))
+;;
+
+;;; Code:
;; define several keyword classes
(defvar lammps-output
'("log"
@@ -136,6 +177,8 @@
(defvar lammps-variable-regexp
"\\$\\({[a-zA-Z0-9_]+}\\)\\|\\$[A-Za-z]")
+(defvar lammps-font-lock-keywords)
+
;; clear memory
(setq lammps-output nil)
(setq lammps-read nil)
@@ -151,8 +194,7 @@
;; create the list for font-lock.
;; each class of keyword is given a particular face
-(setq
- lammps-font-lock-keywords
+(setq lammps-font-lock-keywords
`((,lammps-output-regexp . font-lock-function-name-face)
(,lammps-read-regexp . font-lock-preprocessor-face)
(,lammps-lattice-regexp . font-lock-type-face)
@@ -199,12 +241,5 @@
(setq lammps-comment-regexp nil)
(setq lammps-variable-regexp nil))
-;; apply it to specified filename patterns
-(setq
- auto-mode-alist
- (append
- auto-mode-alist
- '(("in\\." . lammps-mode))
- '(("\\.lmp\\'" . lammps-mode))
- ))
-
+(provide 'lammps-mode)
+;;; lammps-mode.el ends here