diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index a6bc459530b15ee9750c1cc7a2c05e716f36e410..755bbe5e7e79f1eac661b6614b69efc1ed813c65 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -158,12 +158,11 @@ END_RST -->
2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
2.2 "Making LAMMPS"_start_2 :b
2.3 "Making LAMMPS with optional packages"_start_3 :b
- 2.4 "Building LAMMPS via the Make.py script"_start_4 :b
- 2.5 "Building LAMMPS as a library"_start_5 :b
- 2.6 "Running LAMMPS"_start_6 :b
- 2.7 "Command-line options"_start_7 :b
- 2.8 "Screen output"_start_8 :b
- 2.9 "Tips for users of previous versions"_start_9 :ule,b
+ 2.4 "Building LAMMPS as a library"_start_4 :b
+ 2.5 "Running LAMMPS"_start_5 :b
+ 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
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 3f1d6ff2039cd77b32b8bbb888422731c3e5c952..c71acfe06f2f081fbefacfb1d8bcf4564b74c8db 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -1052,7 +1052,7 @@ package"_Section_start.html#start_3.
"oxdna2/excv"_pair_oxdna2.html,
"oxdna2/stk"_pair_oxdna2.html,
"quip"_pair_quip.html,
-"reax/c (k)"_pair_reax_c.html,
+"reax/c (k)"_pair_reaxc.html,
"smd/hertz"_pair_smd_hertz.html,
"smd/tlsph"_pair_smd_tlsph.html,
"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt
index 0c438c6ce0bb9eae1ca22b1c6fbe5d9967eee967..bfb6ef390171f67cc4df16f5d1a4486d427cb469 100644
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@@ -249,8 +249,12 @@ Pizza.py WWW site"_pizza. :l
Specialized features :h5
-These are LAMMPS capabilities which you may not think of as typical
-molecular dynamics options:
+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
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index bd81361fa9aa0df743298292dbface81693a214a..2a0a8386e8886d18ff2c33161469de5c58682634 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -10,1897 +10,2592 @@ Section"_Section_accelerate.html :c
4. Packages :h3
-This section gives an overview of the add-on 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 granular systems are in packages. You can see the list of
-all packages by typing "make package" from within the src directory of
-the LAMMPS distribution.
-
-Here are links for two tables below, which list standard and user
-packages.
-
-4.1 "Standard packages"_#pkg_1
-4.2 "User packages"_#pkg_2 :all(b)
-
-"Section 2.3"_Section_start.html#start_3 of the manual describes
-the difference between standard packages and user packages. It also
-has general details on how to include/exclude specific packages as
-part of the LAMMPS build process, and on how to build auxiliary
-libraries or modify a machine Makefile if a package requires it.
-
-Following the two tables below, is a sub-section for each package. It
-has a summary of what the package contains. It has specific
-instructions on how to install it, build or obtain any auxiliary
-library it requires, and any Makefile.machine changes it requires. It
-also lists pointers to examples of its use or documentation provided
-in the LAMMPS distribution. If you want to know the complete list of
-commands that a package adds to LAMMPS, simply list the files in its
-directory, e.g. "ls src/GRANULAR". Source files with names that start
-with compute, fix, pair, bond, etc correspond to command styles with
-the same names.
-
-NOTE: The USER package sub-sections below are still being filled in,
-as of March 2016.
-
-Unless otherwise noted below, every package is independent of all the
-others. I.e. any package can be included or excluded in a LAMMPS
-build, independent of all other packages. However, note that some
-packages include commands derived from commands in other packages. If
-the other package is not installed, the derived command from the new
-package will also not be installed when you include the new one.
-E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
-will not be installed as part of the USER-OMP package if the KSPACE
-package is not also installed, since it contains the pair
-lj/cut/coul/long command. If you later install the KSPACE package and
-the USER-OMP package is already installed, both the pair
-lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
-
-:line
-
-4.1 Standard packages :h4,link(pkg_1)
-
-The current list of standard packages is as follows. Each package
-name links to a sub-section below with more details.
-
-Package, Description, Author(s), Doc page, Example, Library
-"ASPHERE"_#ASPHERE, aspherical particles, -, "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, Kumar (1), "atom_style colloid"_atom_style.html, colloid, -
-"COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
-"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "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, Mike Brown (ORNL), "Section 5.3.1"_accelerate_gpu.html, gpu, lib/gpu
-"GRANULAR"_#GRANULAR, granular systems, -, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
-"KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
-"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5.3.3"_accelerate_kokkos.html, kokkos, lib/kokkos
-"KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
-"MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
-"MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
-"MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
-"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
-"OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section 5.3.5"_accelerate_opt.html, -, -
-"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
-"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
-"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
-"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
-"REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
-"RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
-"SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
-"SNAP"_#SNAP, quantum-fit potential, Aidan Thompson (Sandia), "pair snap"_pair_snap.html, snap, -
-"SRD"_#SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
-"VORONOI"_#VORONOI, Voronoi tesselations, Daniel Schwen (LANL), "compute voronoi/atom"_compute_voronoi_atom.html, -, Voro++
-:tb(ea=c)
-
-The "Authors" column lists a name(s) if a specific person is
-responsible for creating and maintaining the package.
-
-(1) The COLLOID package includes Fast Lubrication Dynamics pair styles
-which were created by Amit Kumar and Michael Bybee from Jonathan
-Higdon's group at UIUC.
-
-(2) The OPT package was created by James Fischer (High Performance
-Technologies), David Richie, and Vincent Natoli (Stone Ridge
-Technolgy).
-
-(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
-and Ellad Tadmor (U Minn).
-
-(4) The KOKKOS package was created primarily by Christian Trott and
-Stan Moore (Sandia). It uses the Kokkos library which was developed
-by Carter Edwards, Christian Trott, and others at Sandia.
+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
+
+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. 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 "this section"_Section_modify.html#mod_15 of the
+manual.
+
+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.
+
+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
-The "Doc page" column links to either a sub-section of the
-"Section 6"_Section_howto.html of the manual, or an input script
-command implemented as part of the package, or to additional
-documentation provided within the package.
-
-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.
+:line
+:line
-The "Library" column lists an external library which must be built
-first and which LAMMPS links to when it is built. If it is listed as
-lib/package, then the code for the library is under the lib directory
-of the LAMMPS distribution. See the lib/package/README file for info
-on how to build the library. If it is not listed as lib/package, then
-it is a third-party library not included in the LAMMPS distribution.
-See details on all of this below for individual packages.
+[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, WWW bench, 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, WWW bench, -
+"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
+"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, WWW bench, -
+"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 snap"_pair_snap.html, snap, -
+"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-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, WWW bench, -
+"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-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-MOLFILE"_#USER-MOLFILE, "VMD"_VMD 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, WWW bench, -
+"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-VTK"_#USER-VTK, dump output via VTK, "compute custom/vtk"_dump_custom_vtk.html, -, ext
+:tb(ea=c,ca1=l)
:line
+:line
+
+ASPHERE package :link(ASPHERE),h4
-ASPHERE package :link(ASPHERE),h5
+[Contents:]
-Contents: Several computes, time-integration fixes, and pair styles
-for aspherical particle models: ellipsoids, 2d lines, 3d triangles.
+Computes, time-integration fixes, and pair styles for aspherical
+particle models including ellipsoids, 2d lines, and 3d triangles.
-To install via make or Make.py:
+[Install or un-install:]
make yes-asphere
make machine :pre
-Make.py -p asphere -a machine :pre
-
-To un-install via make or Make.py:
-
make no-asphere
make machine :pre
-Make.py -p ^asphere -a machine :pre
+[Supporting info:]
-Supporting info: "Section 6.14"_Section_howto.html#howto_14,
-"pair_style gayberne"_pair_gayberne.html, "pair_style
-resquared"_pair_resquared.html,
-"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf,
-"doc/PDF/pair_resquared_extra.pdf"_PDF/pair_resquared_extra.pdf,
-examples/ASPHERE, examples/ellipse
+src/ASPHERE: filenames -> commands
+"Section 6.14"_Section_howto.html#howto_14
+"pair_style gayberne"_pair_gayberne.html
+"pair_style resquared"_pair_resquared.html
+"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf
+"doc/PDF/pair_resquared_extra.pdf"_PDF/pair_resquared_extra.pdf
+examples/ASPHERE
+examples/ellipse
+http://lammps.sandia.gov/movies.html#line
+http://lammps.sandia.gov/movies.html#tri :ul
:line
-BODY package :link(BODY),h5
+BODY package :link(BODY),h4
+
+[Contents:]
-Contents: Support for body-style particles. Computes,
+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.
-To install via make or Make.py:
+[Install or un-install:]
make yes-body
make machine :pre
-Make.py -p body -a machine :pre
-
-To un-install via make or Make.py:
-
make no-body
make machine :pre
-Make.py -p ^body -a machine :pre
+[Supporting info:]
-Supporting info: "atom_style body"_atom_style.html, "body"_body.html,
-"pair_style body"_pair_body.html, examples/body
+src/BODY filenames -> commands
+"body"_body.html
+"atom_style body"_atom_style.html
+"fix nve/body"_fix_nve_body.html
+"pair_style body"_pair_body.html
+examples/body :ul
:line
-CLASS2 package :link(CLASS2),h5
+CLASS2 package :link(CLASS2),h4
-Contents: Bond, angle, dihedral, improper, and pair styles for the
-COMPASS CLASS2 molecular force field.
+[Contents:]
-To install via make or Make.py:
+Bond, angle, dihedral, improper, and pair styles for the COMPASS
+CLASS2 molecular force field.
+
+[Install or un-install:]
make yes-class2
make machine :pre
-Make.py -p class2 -a machine :pre
-
-To un-install via make or Make.py:
-
make no-class2
make machine :pre
-Make.py -p ^class2 -a machine :pre
+[Supporting info:]
-Supporting info: "bond_style class2"_bond_class2.html, "angle_style
-class2"_angle_class2.html, "dihedral_style
-class2"_dihedral_class2.html, "improper_style
-class2"_improper_class2.html, "pair_style lj/class2"_pair_class2.html
+src/CLASS2: filenames -> commands
+"bond_style class2"_bond_class2.html
+"angle_style class2"_angle_class2.html
+"dihedral_style class2"_dihedral_class2.html
+"improper_style class2"_improper_class2.html
+"pair_style lj/class2"_pair_class2.html :ul
:line
-COLLOID package :link(COLLOID),h5
+COLLOID package :link(COLLOID),h4
-Contents: Support for coarse-grained colloidal particles. Wall fix
-and pair styles that implement colloidal interaction models for
-finite-size particles. This includes the Fast Lubrication Dynamics
-method for hydrodynamic interactions, which is a simplified
-approximation to Stokesian dynamics.
+[Contents:]
-To install via make or Make.py:
+Coarse-grained finite-size colloidal particles. Pair stayle and fix
+wall styles for colloidal interactions. Includes the Fast Lubrication
+Dynamics (FLD) method for hydrodynamic interactions, which is a
+simplified approximation to Stokesian dynamics.
-make yes-colloid
-make machine :pre
+[Authors:] This package includes Fast Lubrication Dynamics pair styles
+which were created by Amit Kumar and Michael Bybee from Jonathan
+Higdon's group at UIUC.
-Make.py -p colloid -a machine :pre
+[Install or un-install:]
-To un-install via make or Make.py:
+make yes-colloid
+make machine :pre
make no-colloid
make machine :pre
-Make.py -p ^colloid -a machine :pre
+[Supporting info:]
-Supporting info: "fix wall/colloid"_fix_wall.html, "pair_style
-colloid"_pair_colloid.html, "pair_style
-yukawa/colloid"_pair_yukawa_colloid.html, "pair_style
-brownian"_pair_brownian.html, "pair_style
-lubricate"_pair_lubricate.html, "pair_style
-lubricateU"_pair_lubricateU.html, examples/colloid, examples/srd
+src/COLLOID: filenames -> commands
+"fix wall/colloid"_fix_wall.html
+"pair_style colloid"_pair_colloid.html
+"pair_style yukawa/colloid"_pair_yukawa_colloid.html
+"pair_style brownian"_pair_brownian.html
+"pair_style lubricate"_pair_lubricate.html
+"pair_style lubricateU"_pair_lubricateU.html
+examples/colloid
+examples/srd :ul
:line
-COMPRESS package :link(COMPRESS),h5
+COMPRESS package :link(COMPRESS),h4
-Contents: Support for compressed output of dump files via the zlib
-compression library, using dump styles with a "gz" in their style
-name.
+[Contents:]
-Building with the COMPRESS package assumes you have the zlib
-compression library available on your system. The build uses the
-lib/compress/Makefile.lammps file in the compile/link process. You
-should only need to edit this file if the LAMMPS build cannot find the
-zlib info it specifies.
+Compressed output of dump files via the zlib compression library,
+using dump styles with a "gz" in their style name.
-To install via make or Make.py:
+To use this package you must have the zlib compression library
+available on your system.
-make yes-compress
-make machine :pre
+[Author:] Axel Kohlmeyer (Temple U).
-Make.py -p compress -a machine :pre
+[Install or un-install:]
-To un-install via make or Make.py:
+Note that building with this package assumes you have the zlib
+compression library available on your system. The LAMMPS build uses
+the settings in the lib/compress/Makefile.lammps file in the
+compile/link process. You should only need to edit this file if the
+LAMMPS build fails on your system.
+
+make yes-compress
+make machine :pre
make no-compress
make machine :pre
-Make.py -p ^compress -a machine :pre
+[Supporting info:]
-Supporting info: src/COMPRESS/README, lib/compress/README, "dump
-atom/gz"_dump.html, "dump cfg/gz"_dump.html, "dump
-custom/gz"_dump.html, "dump xyz/gz"_dump.html
+src/COMPRESS: filenames -> commands
+src/COMPRESS/README
+lib/compress/README
+"dump atom/gz"_dump.html
+"dump cfg/gz"_dump.html
+"dump custom/gz"_dump.html
+"dump xyz/gz"_dump.html :ul
:line
-CORESHELL package :link(CORESHELL),h5
+CORESHELL package :link(CORESHELL),h4
-Contents: Compute and pair styles that implement the adiabatic
-core/shell model for polarizability. The compute temp/cs command
-measures the temperature of a system with core/shell particles. The
-pair styles augment Born, Buckingham, and Lennard-Jones styles with
-core/shell capabilities. See "Section 6.26"_Section_howto.html#howto_26
-for an overview of how to use the package.
+[Contents:]
-To install via make or Make.py:
+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.
-make yes-coreshell
-make machine :pre
+[Author:] Hendrik Heenen (Technical U of Munich).
-Make.py -p coreshell -a machine :pre
+[Install or un-install:]
-To un-install via make or Make.py:
+make yes-coreshell
+make machine :pre
make no-coreshell
make machine :pre
-Make.py -p ^coreshell -a machine :pre
+[Supporting info:]
-Supporting info: "Section 6.26"_Section_howto.html#howto_26,
-"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, pair_style
-lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell
+src/CORESHELL: filenames -> commands
+"Section 6.26"_Section_howto.html#howto_26
+"Section 6.25"_Section_howto.html#howto_25
+"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
+"pair_style lj/cut/coul/long/cs"_pair_lj.html
+examples/coreshell :ul
:line
-DIPOLE package :link(DIPOLE),h5
+DIPOLE package :link(DIPOLE),h4
-Contents: An atom style and several pair styles to support point
-dipole models with short-range or long-range interactions.
+[Contents:]
-To install via make or Make.py:
+An atom style and several pair styles for point dipole models with
+short-range or long-range interactions.
+
+[Install or un-install:]
make yes-dipole
make machine :pre
-Make.py -p dipole -a machine :pre
-
-To un-install via make or Make.py:
-
make no-dipole
make machine :pre
-Make.py -p ^dipole -a machine :pre
+[Supporting info:]
-Supporting info: "atom_style dipole"_atom_style.html, "pair_style
-lj/cut/dipole/cut"_pair_dipole.html, "pair_style
-lj/cut/dipole/long"_pair_dipole.html, "pair_style
-lj/long/dipole/long"_pair_dipole.html, examples/dipole
+src/DIPOLE: filenames -> commands
+"atom_style dipole"_atom_style.html
+"pair_style lj/cut/dipole/cut"_pair_dipole.html
+"pair_style lj/cut/dipole/long"_pair_dipole.html
+"pair_style lj/long/dipole/long"_pair_dipole.html
+examples/dipole :ul
:line
-GPU package :link(GPU),h5
+GPU package :link(GPU),h4
+
+[Contents:]
-Contents: Dozens of pair styles and a version of the PPPM long-range
-Coulombic solver for NVIDIA GPUs. All of them have a "gpu" in their
-style name. "Section 5.3.1"_accelerate_gpu.html gives
+Dozens of pair styles and a version of the PPPM long-range Coulombic
+solver optimized for NVIDIA GPUs. All such styles have a "gpu" as a
+suffix in their style name. "Section 5.3.1"_accelerate_gpu.html gives
details of what hardware and Cuda software is required on your system,
-and how to build and use this package. See the KOKKOS package, which
-also has GPU-enabled styles.
-
-Building LAMMPS with the GPU package requires first building the GPU
-library itself, which is a set of C and Cuda files in lib/gpu.
-Details of how to do this are in lib/gpu/README. As illustrated
-below, perform a "make" using one of the Makefile.machine files in
-lib/gpu which should create a lib/reax/libgpu.a file.
-Makefile.linux.* and Makefile.xk7 are examples for different
-platforms. There are 3 important settings in the Makefile.machine you
-use:
+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_7. See also the "KOKKOS"_#KOKKOS
+package, which has GPU-enabled styles.
+
+[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
+(Northwestern U) while at ORNL.
+
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first build the GPU
+library in lib/gpu from a set of provided C and Cuda files. You can
+do this manually if you prefer; follow the instructions in
+lib/gpu/README. You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/gpu/Install.py script with the specified args:
+
+make lib-gpu # print help message
+make lib-gpu args="-m" # build GPU library with default Makefile.linux
+make lib-gpu args="-i xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
+make lib-gpu args="-i xk7 -p single -o xk7.single -m" # ditto, also build GPU library
+
+Note that this procedure starts with one of the existing
+Makefile.machine files in lib/gpu. It allows you to alter 4 important
+settings in that Makefile, via the -h, -a, -p, -e switches,
+and save the new Makefile, if desired:
CUDA_HOME = where NVIDIA Cuda software is installed on your system
-CUDA_ARCH = appropriate to your GPU hardware
-CUDA_PREC = precision (double, mixed, single) you desire :ul
-
-See example Makefile.machine files in lib/gpu for the syntax of these
-settings. See lib/gpu/Makefile.linux.double for ARCH settings for
-various NVIDIA GPUs. The "make" also creates a
-lib/gpu/Makefile.lammps file. This file has settings that enable
-LAMMPS to link with Cuda libraries. If the settings in
-Makefile.lammps for your machine are not correct, the LAMMPS link will
-fail. Note that the Make.py script has a "-gpu" option to allow the
-GPU library (with several of its options) and LAMMPS to be built in
-one step, with Type "python src/Make.py -h -gpu" to see the details.
-
-To install via make or Make.py:
-
-cd ~/lammps/lib/gpu
-make -f Makefile.linux.mixed # for example
-cd ~/lammps/src
-make yes-gpu
-make machine :pre
+CUDA_ARCH = what GPU hardware you have (see help message for details)
+CUDA_PRECISION = precision (double, mixed, single)
+EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
+
+If the library build is successful, 2 files should be created:
+lib/gpu/libgpu.a and lib/gpu/Makefile.lammps. The latter has settings
+that enable LAMMPS to link with Cuda libraries. If the settings in
+Makefile.lammps for your machine are not correct, the LAMMPS build
+will fail.
-Make.py -p gpu -gpu mode=mixed arch=35 -a machine :pre
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
-To un-install via make or Make.py:
+make yes-gpu
+make machine :pre
make no-gpu
make machine :pre
-Make.py -p ^gpu -a machine :pre
+NOTE: If you re-build the GPU library in lib/gpu, you should always
+un-install the GPU package, then re-install it and re-build LAMMPS.
+This is because the compilation of files in the GPU package use the
+library settings from the lib/gpu/Makefile.machine used to build the
+GPU library.
-Supporting info: src/GPU/README, lib/gpu/README,
-"Section 5.3"_Section_accelerate.html#acc_3,
-"Section 5.3.1"_accelerate_gpu.html,
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
-for any pair style listed with a (g),
-"kspace_style"_kspace_style.html, "package gpu"_package.html,
-examples/accelerate, bench/FERMI, bench/KEPLER
+[Supporting info:]
+
+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
+"Section 2.7 -sf gpu"_Section_start.html#start_7
+"Section 2.7 -pk gpu"_Section_start.html#start_7
+"package gpu"_package.html
+Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g)
+"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-GRANULAR package :link(GRANULAR),h5
+GRANULAR package :link(GRANULAR),h4
-Contents: Fixes and pair styles that support models of finite-size
-granular particles, which interact with each other and boundaries via
-frictional and dissipative potentials.
+[Contents:]
-To install via make or Make.py:
+Pair styles and fixes for finite-size granular particles, which
+interact with each other and boundaries via frictional and dissipative
+potentials.
+
+[Install or un-install:]
make yes-granular
make machine :pre
-Make.py -p granular -a machine :pre
-
-To un-install via make or Make.py:
-
make no-granular
make machine :pre
-Make.py -p ^granular -a machine :pre
-
-Supporting info: "Section 6.6"_Section_howto.html#howto_6, "fix
-pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style
-gran/hooke"_pair_gran.html, "pair_style
-gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute
+[Supporting info:]
+
+src/GRANULAR: filenames -> commands
+"Section 6.6"_Section_howto.html#howto_6,
+"fix pour"_fix_pour.html
+"fix wall/gran"_fix_wall_gran.html
+"pair_style gran/hooke"_pair_gran.html
+"pair_style gran/hertz/history"_pair_gran.html
+examples/granregion
+examples/pour
+bench/in.chute
+http://lammps.sandia.gov/pictures.html#jamming
+http://lammps.sandia.gov/movies.html#hopper
+http://lammps.sandia.gov/movies.html#dem
+http://lammps.sandia.gov/movies.html#brazil
+http://lammps.sandia.gov/movies.html#granregion :ul
:line
-KIM package :link(KIM),h5
+KIM package :link(KIM),h4
-Contents: A pair style that interfaces to the Knowledge Base for
-Interatomic Models (KIM) repository of interatomic potentials, so that
-KIM potentials can be used in a LAMMPS simulation.
+[Contents:]
-To build LAMMPS with the KIM package you must have previously
-installed the KIM API (library) on your system. The lib/kim/README
-file explains how to download and install KIM. Building with the KIM
-package also uses the lib/kim/Makefile.lammps file in the compile/link
-process. You should not need to edit this file.
+A "pair_style kim"_pair_kim.html command which is a wrapper on the
+Knowledge Base for Interatomic Models (KIM) repository of interatomic
+potentials, enabling any of them to be used in LAMMPS simulations.
-To install via make or Make.py:
+To use this package you must have the KIM library available on your
+system.
-make yes-kim
-make machine :pre
+Information about the KIM project can be found at its website:
+https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan
+Elliott (U Minnesota) and James Sethna (Cornell U).
+
+[Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
+API which the "pair_style kim"_pair_kim.html command uses. He
+developed the pair style in collaboration with Valeriu Smirichinski (U
+Minnesota).
+
+[Install or un-install:]
-Make.py -p kim -a machine :pre
+Using this package requires the KIM library and its models
+(interatomic potentials) to be downloaded and installed on your
+system. The library can be downloaded and built in lib/kim or
+elsewhere on your system. Details of the download, build, and install
+process for KIM are given in the lib/kim/README file.
-To un-install via make or Make.py:
+Once that process is complete, you can then install/un-install the
+package and build LAMMPS in the usual manner:
+
+make yes-kim
+make machine :pre
make no-kim
make machine :pre
-Make.py -p ^kim -a machine :pre
+[Supporting info:]
-Supporting info: src/KIM/README, lib/kim/README, "pair_style
-kim"_pair_kim.html, examples/kim
+src/KIM: filenames -> commands
+src/KIM/README
+lib/kim/README
+"pair_style kim"_pair_kim.html
+examples/kim :ul
:line
-KOKKOS package :link(KOKKOS),h5
+KOKKOS package :link(KOKKOS),h4
-Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
-which run with the Kokkos library to provide optimization for
-multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in
-native mode). All of them have a "kk" 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. See the GPU, OPT, USER-INTEL, USER-OMP packages,
-which also provide optimizations for the same range of hardware.
+[Contents:]
-Building with the KOKKOS package requires choosing which of 3 hardware
-options you are optimizing for: CPU acceleration via OpenMP, GPU
-acceleration, or Intel Xeon Phi. (You can build multiple times to
-create LAMMPS executables for different hardware.) It also requires a
-C++11 compatible compiler. For GPUs, the NVIDIA "nvcc" compiler is
-used, and an appropriate KOKKOS_ARCH setting should be made in your
-Makefile.machine for your GPU hardware and NVIDIA software.
+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
+switches"_Section_start.html#start_7. 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.
-The simplest way to do this is to use Makefile.kokkos_cuda or
-Makefile.kokkos_omp or Makefile.kokkos_phi in src/MAKE/OPTIONS, via
-"make kokkos_cuda" or "make kokkos_omp" or "make kokkos_phi". (Check
-the KOKKOS_ARCH setting in Makefile.kokkos_cuda), Or, as illustrated
-below, you can use the Make.py script with its "-kokkos" option to
-choose which hardware to build for. Type "python src/Make.py -h
--kokkos" to see the details. If these methods do not work on your
-system, you will need to read the "Section 5.3.3"_accelerate_kokkos.html
-doc page for details of what Makefile.machine settings are needed.
+You must have a C++11 compatible compiler to use this package.
-To install via make or Make.py for each of 3 hardware options:
+[Authors:] The KOKKOS package was created primarily by Christian Trott
+and Stan Moore (Sandia), with contributions from other folks as well.
+It uses the open-source "Kokkos library"_https://github.com/kokkos
+which was developed by Carter Edwards, Christian Trott, and others at
+Sandia, and which is included in the LAMMPS distribution in
+lib/kokkos.
-make yes-kokkos
-make kokkos_omp # for CPUs with OpenMP
-make kokkos_cuda # for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda
-make kokkos_phi # for Xeon Phis :pre
+[Install or un-install:]
+
+For the KOKKOS package, you have 3 choices when building. You can
+build with either CPU or KNL or GPU support. Each choice requires
+additional settings in your Makefile.machine for the KOKKOS_DEVICES
+and KOKKOS_ARCH settings. See the src/MAKE/OPTIONS/Makefile.kokkos*
+files for examples.
+
+For multicore CPUs using OpenMP:
+
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc
+
+For Intel KNLs using OpenMP:
+
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = KNL
+
+For NVIDIA GPUs using Cuda:
+
+KOKKOS_DEVICES = Cuda
+KOKKOS_ARCH = Pascal60,Power8 # P100 hosted by an IBM Power8, etc
+KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc
+
+For GPUs, you also need these 2 lines in your Makefile.machine before
+the CC line is defined, in this case for use with OpenMPI mpicxx. The
+2 lines define a nvcc wrapper compiler, which will use nvcc for
+compiling Cuda files or use a C++ compiler for non-Kokkos, non-Cuda
+files.
-Make.py -p kokkos -kokkos omp -a machine # for CPUs with OpenMP
-Make.py -p kokkos -kokkos cuda arch=35 -a machine # for GPUs of style arch
-Make.py -p kokkos -kokkos phi -a machine # for Xeon Phis
+KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
+export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
+CC = mpicxx
-To un-install via make or Make.py:
+Once you have an appropriate Makefile.machine, you can
+install/un-install the package and build LAMMPS in the usual manner.
+Note that you cannot build one executable to run on multiple hardware
+targets (CPU or KNL or GPU). You need to build LAMMPS once for each
+hardware target, to produce a separate executable. Also note that we
+do not recommend building with other acceleration packages installed
+(GPU, OPT, USER-INTEL, USER-OMP) when also building with KOKKOS.
+make yes-kokkos
+make machine :pre
+
make no-kokkos
make machine :pre
-Make.py -p ^kokkos -a machine :pre
+[Supporting info:]
-Supporting info: src/KOKKOS/README, lib/kokkos/README,
-"Section 5.3"_Section_accelerate.html#acc_3,
-"Section 5.3.3"_accelerate_kokkos.html,
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
-for any pair style listed with a (k), "package kokkos"_package.html,
-examples/accelerate, bench/FERMI, bench/KEPLER
+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
+"Section 2.7 -k on ..."_Section_start.html#start_7
+"Section 2.7 -sf kk"_Section_start.html#start_7
+"Section 2.7 -pk kokkos"_Section_start.html#start_7
+"package kokkos"_package.html
+Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k)
+"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-KSPACE package :link(KSPACE),h5
+KSPACE package :link(KSPACE),h4
-Contents: A variety of long-range Coulombic solvers, and pair styles
-which compute the corresponding short-range portion of the pairwise
-Coulombic interactions. These include Ewald, particle-particle
-particle-mesh (PPPM), and multilevel summation method (MSM) solvers.
+[Contents:]
-Building with the KSPACE package requires a 1d FFT library be present
-on your system for use by the PPPM solvers. This can be the KISS FFT
-library provided with LAMMPS, or 3rd party libraries like FFTW or a
-vendor-supplied FFT library. See step 6 of "Section
-2.2.2"_Section_start.html#start_2_2 of the manual for details of how
-to select different FFT options in your machine Makefile. The Make.py
-tool has an "-fft" option which can insert these settings into your
-machine Makefile automatically. Type "python src/Make.py -h -fft" to
-see the details.
+A variety of long-range Coulombic solvers, as well as pair styles
+which compute the corresponding short-range pairwise Coulombic
+interactions. These include Ewald, particle-particle particle-mesh
+(PPPM), and multilevel summation method (MSM) solvers.
-To install via make or Make.py:
+[Install or un-install:]
+
+Building with this package requires a 1d FFT library be present on
+your system for use by the PPPM solvers. This can be the KISS FFT
+library provided with LAMMPS, 3rd party libraries like FFTW, or a
+vendor-supplied FFT library. See step 6 of "Section
+2.2.2"_Section_start.html#start_2_2 of the manual for details on how
+to select different FFT options in your machine Makefile.
make yes-kspace
make machine :pre
-Make.py -p kspace -a machine :pre
-
-To un-install via make or Make.py:
-
make no-kspace
make machine :pre
-Make.py -p ^kspace -a machine :pre
+[Supporting info:]
-Supporting info: "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,
-"pair_style coul"_pair_coul.html, other pair style command doc pages
-which have "long" or "msm" in their style name,
-examples/peptide, bench/in.rhodo
+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
+"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
+examples/peptide
+bench/in.rhodo :ul
:line
-MANYBODY package :link(MANYBODY),h5
+MANYBODY package :link(MANYBODY),h4
+
+[Contents:]
-Contents: A variety of many-body and bond-order potentials. These
-include (AI)REBO, EAM, EIM, BOP, Stillinger-Weber, and Tersoff
-potentials. Do a directory listing, "ls src/MANYBODY", to see
-the full list.
+A variety of manybody and bond-order potentials. These include
+(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
-To install via make or Make.py:
+[Install or un-install:]
make yes-manybody
make machine :pre
-Make.py -p manybody -a machine :pre
-
-To un-install via make or Make.py:
-
make no-manybody
make machine :pre
-Make.py -p ^manybody -a machine :pre
-
-Supporting info:
+[Supporting info:]
-Examples: Pair Styles section of "Section
-3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim,
-examples/nb3d, examples/vashishta
+src/MANYBODY: filenames -> commands
+Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
+examples/comb
+examples/eim
+examples/nb3d
+examples/shear
+examples/streitz
+examples/vashishta
+bench/in.eam :ul
:line
-MC package :link(MC),h5
+MC package :link(MC),h4
+
+[Contents:]
-Contents: Several fixes and a pair style that have Monte Carlo (MC) or
-MC-like attributes. These include fixes for creating, breaking, and
-swapping bonds, and for performing atomic swaps and grand-canonical MC
-in conjuction with dynamics.
+Several fixes and a pair style that have Monte Carlo (MC) or MC-like
+attributes. These include fixes for creating, breaking, and swapping
+bonds, for performing atomic swaps, and performing grand-canonical MC
+(GCMC) in conjuction with dynamics.
-To install via make or Make.py:
+[Install or un-install:]
make yes-mc
make machine :pre
-Make.py -p mc -a machine :pre
-
-To un-install via make or Make.py:
-
make no-mc
make machine :pre
-Make.py -p ^mc -a machine :pre
+[Supporting info:]
-Supporting info: "fix atom/swap"_fix_atom_swap.html, "fix
-bond/break"_fix_bond_break.html, "fix
-bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html,
-"fix gcmc"_fix_gcmc.html, "pair_style dsmc"_pair_dsmc.html
+src/MC: filenames -> commands
+"fix atom/swap"_fix_atom_swap.html
+"fix bond/break"_fix_bond_break.html
+"fix bond/create"_fix_bond_create.html
+"fix bond/swap"_fix_bond_swap.html
+"fix gcmc"_fix_gcmc.html
+"pair_style dsmc"_pair_dsmc.html
+http://lammps.sandia.gov/movies.html#gcmc :ul
:line
-MEAM package :link(MEAM),h5
+MEAM package :link(MEAM),h4
-Contents: A pair style for the modified embedded atom (MEAM)
-potential.
+[Contents:]
-Building LAMMPS with the MEAM package requires first building the MEAM
-library itself, which is a set of Fortran 95 files in lib/meam.
-Details of how to do this are in lib/meam/README. As illustrated
-below, perform a "make" using one of the Makefile.machine files in
-lib/meam which should create a lib/meam/libmeam.a file.
-Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran
-and Intel Fortran compilers. The "make" also copies a
-lib/meam/Makefile.lammps.machine file to lib/meam/Makefile.lammps.
-This file has settings that enable the C++ compiler used to build
-LAMMPS to link with a Fortran library (typically the 2 compilers to be
-consistent e.g. both Intel compilers, or both GNU compilers). If the
-settings in Makefile.lammps for your compilers and machine are not
-correct, the LAMMPS link will fail. Note that the Make.py script has
-a "-meam" option to allow the MEAM library and LAMMPS to be built in
-one step. Type "python src/Make.py -h -meam" to see the details.
+A pair style for the modified embedded atom (MEAM) potential.
-NOTE: The MEAM potential can run dramatically faster if built with the
-Intel Fortran compiler, rather than the GNU Fortran compiler.
+[Author:] Greg Wagner (Northwestern U) while at Sandia.
-To install via make or Make.py:
+[Install or un-install:]
-cd ~/lammps/lib/meam
-make -f Makefile.gfortran # for example
-cd ~/lammps/src
-make yes-meam
-make machine :pre
+Before building LAMMPS with this package, you must first build the
+MEAM library in lib/meam. You can do this manually if you prefer;
+follow the instructions in lib/meam/README. You can also do it in one
+step from the lammps/src dir, using a command like these, which simply
+invoke the lib/meam/Install.py script with the specified args:
+
+make lib-meam # print help message
+make lib-meam args="-m gfortran" # build with GNU Fortran compiler
+make lib-meam args="-m ifort" # build with Intel ifort compiler :pre
-Make.py -p meam -meam make=gfortran -a machine :pre
+The build should produce two files: lib/meam/libmeam.a and
+lib/meam/Makefile.lammps. The latter is copied from an existing
+Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
+Fortran (MEAM library). Typically the two compilers used for LAMMPS
+and the MEAM library need to be consistent (e.g. both Intel or both
+GNU compilers). If necessary, you can edit/create a new
+lib/meam/Makefile.machine file for your system, which should define an
+EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
+file.
-To un-install via make or Make.py:
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-meam
+make machine :pre
make no-meam
make machine :pre
-Make.py -p ^meam -a machine :pre
+NOTE: You should test building the MEAM library with both the Intel
+and GNU compilers to see if a simulation runs faster with one versus
+the other on your system.
+
+[Supporting info:]
-Supporting info: lib/meam/README, "pair_style meam"_pair_meam.html,
-examples/meam
+src/MEAM: filenames -> commands
+src/meam/README
+lib/meam/README
+"pair_style meam"_pair_meam.html
+examples/meam :ul
:line
-MISC package :link(MISC),h5
+MISC package :link(MISC),h4
-Contents: A variety of computes, fixes, and pair styles that are not
-commonly used, but don't align with other packages. Do a directory
+[Contents:]
+
+A variety of compute, fix, pair, dump styles with specialized
+capabilities that don't align with other packages. Do a directory
listing, "ls src/MISC", to see the list of commands.
-To install via make or Make.py:
+[Install or un-install:]
make yes-misc
make machine :pre
-Make.py -p misc -a machine :pre
-
-To un-install via make or Make.py:
-
make no-misc
make machine :pre
-Make.py -p ^misc -a machine :pre
+[Supporting info:]
-Supporting info: "compute ti"_compute_ti.html, "fix
-evaporate"_fix_evaporate.html, "fix tmm"_fix_ttm.html, "fix
-viscosity"_fix_viscosity.html, examples/misc
+src/MISC: filenames -> commands
+"compute ti"_compute_ti.html
+"fix evaporate"_fix_evaporate.html
+"fix orient/fcc"_fix_orient.html
+"fix ttm"_fix_ttm.html
+"fix thermal/conductivity"_fix_thermal_conductivity.html
+"fix viscosity"_fix_viscosity.html
+examples/KAPPA
+examples/VISCOSITY
+http://lammps.sandia.gov/pictures.html#ttm
+http://lammps.sandia.gov/movies.html#evaporation :ul
:line
-MOLECULE package :link(MOLECULE),h5
+MOLECULE package :link(MOLECULE),h4
-Contents: A large number of atom, pair, bond, angle, dihedral,
-improper styles that are used to model molecular systems with fixed
-covalent bonds. The pair styles include terms for the Dreiding
-(hydrogen-bonding) and CHARMM force fields, and TIP4P water model.
+[Contents:]
-To install via make or Make.py:
+A large number of atom, pair, bond, angle, dihedral, improper styles
+that are used to model molecular systems with fixed covalent bonds.
+The pair styles include the Dreiding (hydrogen-bonding) and CHARMM
+force fields, and a TIP4P water model.
+
+[Install or un-install:]
make yes-molecule
make machine :pre
-Make.py -p molecule -a machine :pre
-
-To un-install via make or Make.py:
-
make no-molecule
make machine :pre
-Make.py -p ^molecule -a machine :pre
-
-Supporting info:"atom_style"_atom_style.html,
-"bond_style"_bond_style.html, "angle_style"_angle_style.html,
-"dihedral_style"_dihedral_style.html,
-"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,
-examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo
+[Supporting info:]
+
+src/MOLECULE: filenames -> commands
+"atom_style"_atom_style.html
+"bond_style"_bond_style.html
+"angle_style"_angle_style.html
+"dihedral_style"_dihedral_style.html
+"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
+examples/cmap
+examples/dreiding
+examples/micelle,
+examples/peptide
+bench/in.chain
+bench/in.rhodo :ul
:line
-MPIIO package :link(MPIIO),h5
+MPIIO package :link(MPIIO),h4
+
+[Contents:]
-Contents: Support for parallel output/input of dump and restart files
-via the MPIIO library, which is part of the standard message-passing
-interface (MPI) library. It adds "dump styles"_dump.html with a
-"mpiio" in their style name. Restart files with an ".mpiio" suffix
-are also written and read in parallel.
+Support for parallel output/input of dump and restart files via the
+MPIIO library. It adds "dump styles"_dump.html with a "mpiio" in
+their style name. Restart files with an ".mpiio" suffix are also
+written and read in parallel.
-To install via make or Make.py:
+[Install or un-install:]
+Note that MPIIO is part of the standard message-passing interface
+(MPI) library, so you should not need any additional compiler or link
+settings, beyond what LAMMPS normally uses for MPI on your system.
+
make yes-mpiio
make machine :pre
+
+make no-mpiio
+make machine :pre
+
+[Supporting info:]
-Make.py -p mpiio -a machine :pre
+src/MPIIO: filenames -> commands
+"dump"_dump.html
+"restart"_restart.html
+"write_restart"_write_restart.html
+"read_restart"_read_restart.html :ul
-To un-install via make or Make.py:
+:line
+
+MSCG package :link(MSCG),h4
-make no-mpiio
+[Contents:]
+
+A "fix mscg"_fix_mscg.html command which can parameterize a
+Mulit-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
+library"_mscg.
+
+:link(mscg,https://github.com/uchicago-voth/MSCG-release)
+
+To use this package you must have the MS-CG library available on your
+system.
+
+[Authors:] The fix was written by Lauren Abbott (Sandia). The MS-CG
+library was developed by Jacob Wagner in Greg Voth's group at the
+University of Chicago.
+
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first download and
+build the MS-CG library. Building the MS-CG library and using it from
+LAMMPS requires a C++11 compatible compiler, and that LAPACK and GSL
+(GNU Scientific Library) libraries be installed on your machine. See
+the lib/mscg/README and MSCG/Install files for more details.
+
+Assuming these libraries are in place, you can do the download and
+build of MS-CG manually if you prefer; follow the instructions in
+lib/mscg/README. You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/mscg/Install.py script with the specified args:
+
+make lib-mscg # print help message
+make lib-mscg args="-g -b -l" # download and build in default lib/mscg/MSCG-release-master
+make lib-mscg args="-h . MSCG -g -b -l" # download and build in lib/mscg/MSCG
+make lib-mscg args="-h ~ MSCG -g -b -l" # download and build in ~/mscg :pre
+
+Note that the final -l switch is to create 2 symbolic (soft) links,
+"includelink" and "liblink", in lib/mscg to point to the MS-CG src
+dir. When LAMMPS builds it will use these links. You should not need
+to edit the lib/mscg/Makefile.lammps file.
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-mscg
+make machine :pre
+
+make no-mscg
make machine :pre
-Make.py -p ^mpiio -a machine :pre
+[Supporting info:]
-Supporting info: "dump"_dump.html, "restart"_restart.html,
-"write_restart"_write_restart.html, "read_restart"_read_restart.html
+src/MSCG: filenames -> commands
+src/MSCG/README
+lib/mscg/README
+examples/mscg :ul
:line
+
+OPT package :link(OPT),h4
-OPT package :link(OPT),h5
+[Contents:]
-Contents: A handful of pair styles with an "opt" in their style name
-which are optimized for improved CPU performance on single or multiple
-cores. These include EAM, LJ, CHARMM, and Morse potentials. "Section
-5.3.5"_accelerate_opt.html gives details of how to build and
-use this package. See the KOKKOS, USER-INTEL, and USER-OMP packages,
-which also have styles optimized for CPU performance.
+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
+switches"_Section_start.html#start_7. See also the "KOKKOS"_#KOKKOS,
+"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
+have styles optimized for CPU performance.
-Some C++ compilers, like the Intel compiler, require the compile flag
-"-restrict" to build LAMMPS with the OPT package. It should be added
-to the CCFLAGS line of your Makefile.machine. Or use Makefile.opt in
-src/MAKE/OPTIONS, via "make opt". For compilers that use the flag,
-the Make.py command adds it automatically to the Makefile.auto file it
-creates and uses.
+[Authors:] James Fischer (High Performance Technologies), David Richie,
+and Vincent Natoli (Stone Ridge Technolgy).
-To install via make or Make.py:
+[Install or un-install:]
make yes-opt
make machine :pre
-Make.py -p opt -a machine :pre
-
-To un-install via make or Make.py:
-
make no-opt
make machine :pre
-Make.py -p ^opt -a machine :pre
+NOTE: The compile flag "-restrict" must be used to build LAMMPS with
+the OPT package. It should be added to the CCFLAGS line of your
+Makefile.machine. See Makefile.opt in src/MAKE/OPTIONS for an
+example.
+
+CCFLAGS: add -restrict :ul
-Supporting info: "Section 5.3"_Section_accelerate.html#acc_3,
-"Section 5.3.5"_accelerate_opt.html, Pair Styles section of
-"Section 3.5"_Section_commands.html#cmd_5 for any pair style
-listed with an (t), examples/accelerate, bench/KEPLER
+[Supporting info:]
+
+src/OPT: filenames -> commands
+"Section 5.3"_Section_accelerate.html#acc_3
+"Section 5.3.5"_accelerate_opt.html
+"Section 2.7 -sf opt"_Section_start.html#start_7
+Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t)
+"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-PERI package :link(PERI),h5
+PERI package :link(PERI),h4
-Contents: Support for the Peridynamics method, a particle-based
-meshless continuum model. The package includes an atom style, several
-computes which calculate diagnostics, and several Peridynamic pair
-styles which implement different materials models.
+[Contents:]
-To install via make or Make.py:
+An atom style, several pair styles which implement different
+Peridynamics materials models, and several computes which calculate
+diagnostics. Peridynamics is a a particle-based meshless continuum
+model.
-make yes-peri
-make machine :pre
+[Authors:] The original package was created by Mike Parks (Sandia).
+Additional Peridynamics models were added by Rezwanur Rahman and John
+Foster (UTSA).
-Make.py -p peri -a machine :pre
+[Install or un-install:]
-To un-install via make or Make.py:
+make yes-peri
+make machine :pre
make no-peri
make machine :pre
-Make.py -p ^peri -a machine :pre
+[Supporting info:]
-Supporting info:
-"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf,
-"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf,
-"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf, "atom_style
-peri"_atom_style.html, "compute damage/atom"_compute_damage_atom.html,
-"pair_style peri/pmb"_pair_peri.html, examples/peri
+src/PERI: filenames -> commands
+"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf
+"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf
+"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf
+"atom_style peri"_atom_style.html
+"pair_style peri/*"_pair_peri.html
+"compute damage/atom"_compute_damage_atom.html
+"compute plasticity/atom"_compute_plasticity_atom.html
+examples/peri
+http://lammps.sandia.gov/movies.html#peri :ul
:line
-POEMS package :link(POEMS),h5
+POEMS package :link(POEMS),h4
-Contents: A fix that wraps the Parallelizable Open source Efficient
-Multibody Software (POEMS) librar, which is able to simulate the
-dynamics of articulated body systems. These are systems with multiple
-rigid bodies (collections of atoms or particles) whose motion is
-coupled by connections at hinge points.
+[Contents:]
-Building LAMMPS with the POEMS package requires first building the
-POEMS library itself, which is a set of C++ files in lib/poems.
-Details of how to do this are in lib/poems/README. As illustrated
-below, perform a "make" using one of the Makefile.machine files in
-lib/poems which should create a lib/meam/libpoems.a file.
-Makefile.g++ and Makefile.icc are examples for the GNU and Intel C++
-compilers. The "make" also creates a lib/poems/Makefile.lammps file
-which you should not need to change. Note the Make.py script has a
-"-poems" option to allow the POEMS library and LAMMPS to be built in
-one step. Type "python src/Make.py -h -poems" to see the details.
+A fix that wraps the Parallelizable Open source Efficient Multibody
+Software (POEMS) library, which is able to simulate the dynamics of
+articulated body systems. These are systems with multiple rigid
+bodies (collections of particles) whose motion is coupled by
+connections at hinge points.
-To install via make or Make.py:
+[Author:] Rudra Mukherjee (JPL) while at RPI.
-cd ~/lammps/lib/poems
-make -f Makefile.g++ # for example
-cd ~/lammps/src
-make yes-poems
-make machine :pre
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first build the
+POEMS library in lib/poems. You can do this manually if you prefer;
+follow the instructions in lib/poems/README. You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invoke the lib/poems/Install.py script with the specified args:
+
+make lib-poems # print help message
+make lib-poems args="-m g++" # build with GNU g++ compiler
+make lib-poems args="-m icc" # build with Intel icc compiler :pre
-Make.py -p poems -poems make=g++ -a machine :pre
+The build should produce two files: lib/poems/libpoems.a and
+lib/poems/Makefile.lammps. The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the
+POEMS library (though typically the settings are just blank). If
+necessary, you can edit/create a new lib/poems/Makefile.machine file
+for your system, which should define an EXTRAMAKE variable to specify
+a corresponding Makefile.lammps.machine file.
-To un-install via make or Make.py:
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-poems
+make machine :pre
make no-meam
make machine :pre
-Make.py -p ^meam -a machine :pre
+[Supporting info:]
-Supporting info: src/POEMS/README, lib/poems/README,
-"fix poems"_fix_poems.html, examples/rigid
+src/POEMS: filenames -> commands
+src/POEMS/README
+lib/poems/README
+"fix poems"_fix_poems.html
+examples/rigid :ul
:line
-PYTHON package :link(PYTHON),h5
+PYTHON package :link(PYTHON),h4
-Contents: 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 "Section
-11.2"_Section_python.html#py_2 for an overview of using Python from
-LAMMPS and for other ways to use LAMMPS and Python together.
+[Contents:]
-Building with the PYTHON package assumes you have a Python shared
-library available on your system, which needs to be a Python 2
-version, 2.6 or later. Python 3 is not yet supported. The build uses
-the contents of the lib/python/Makefile.lammps file to find all the Python
-files required in the build/link process. See the lib/python/README
-file if the settings in that file do not work on your system. Note
-that the Make.py script has a "-python" option to allow an alternate
-lib/python/Makefile.lammps file to be specified and LAMMPS to be built
-in one step. Type "python src/Make.py -h -python" to see the details.
+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 "Section
+11.2"_Section_python.html#py_2 for an overview of using Python from
+LAMMPS in this manner and the entire section for other ways to use
+LAMMPS and Python together.
-To install via make or Make.py:
+[Install or un-install:]
make yes-python
make machine :pre
-Make.py -p python -a machine :pre
-
-To un-install via make or Make.py:
-
make no-python
make machine :pre
-Make.py -p ^python -a machine :pre
+NOTE: Building with the PYTHON package assumes you have a Python
+shared library available on your system, which needs to be a Python 2
+version, 2.6 or later. Python 3 is not yet supported. See the
+lib/python/README for more details. Note that the build uses the
+lib/python/Makefile.lammps file in the compile/link process. You
+should only need to create a new Makefile.lammps.* file (and copy it
+to Makefile.lammps) if the LAMMPS build fails.
-Supporting info: examples/python
+[Supporting info:]
+
+src/PYTHON: filenames -> commands
+"Section 11"_Section_python.html
+lib/python/README
+examples/python :ul
:line
-QEQ package :link(QEQ),h5
+QEQ package :link(QEQ),h4
+
+[Contents:]
-Contents: Several fixes for performing charge equilibration (QEq) via
-severeal different algorithms. These can be used with pair styles
-that use QEq as part of their formulation.
+Several fixes for performing charge equilibration (QEq) via different
+algorithms. These can be used with pair styles that perform QEq as
+part of their formulation.
-To install via make or Make.py:
+[Install or un-install:]
make yes-qeq
make machine :pre
-Make.py -p qeq -a machine :pre
-
-To un-install via make or Make.py:
-
make no-qeq
make machine :pre
-Make.py -p ^qeq -a machine :pre
+[Supporting info:]
-Supporting info: "fix qeq/*"_fix_qeq.html, examples/qeq
+src/QEQ: filenames -> commands
+"fix qeq/*"_fix_qeq.html
+examples/qeq
+examples/streitz :ul
:line
-REAX package :link(REAX),h5
+REAX package :link(REAX),h4
-Contents: A pair style for the ReaxFF potential, a universal reactive
-force field, as well as a "fix reax/bonds"_fix_reax_bonds.html command
-for monitoring molecules as bonds are created and destroyed.
+[Contents:]
-Building LAMMPS with the REAX package requires first building the REAX
-library itself, which is a set of Fortran 95 files in lib/reax.
-Details of how to do this are in lib/reax/README. As illustrated
-below, perform a "make" using one of the Makefile.machine files in
-lib/reax which should create a lib/reax/libreax.a file.
-Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran
-and Intel Fortran compilers. The "make" also copies a
-lib/reax/Makefile.lammps.machine file to lib/reax/Makefile.lammps.
-This file has settings that enable the C++ compiler used to build
-LAMMPS to link with a Fortran library (typically the 2 compilers to be
-consistent e.g. both Intel compilers, or both GNU compilers). If the
-settings in Makefile.lammps for your compilers and machine are not
-correct, the LAMMPS link will fail. Note that the Make.py script has
-a "-reax" option to allow the REAX library and LAMMPS to be built in
-one step. Type "python src/Make.py -h -reax" to see the details.
-
-To install via make or Make.py:
-
-cd ~/lammps/lib/reax
-make -f Makefile.gfortran # for example
-cd ~/lammps/src
-make yes-reax
-make machine :pre
+A pair style which wraps a Fortran library which implements the ReaxFF
+potential, which is a universal reactive force field. See the
+"USER-REAXC package"_#USER-REAXC for an alternate implementation in
+C/C++. Also a "fix reax/bonds"_fix_reax_bonds.html command for
+monitoring molecules as bonds are created and destroyed.
+
+[Author:] Aidan Thompson (Sandia).
+
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first build the
+REAX library in lib/reax. You can do this manually if you prefer;
+follow the instructions in lib/reax/README. You can also do it in one
+step from the lammps/src dir, using a command like these, which simply
+invoke the lib/reax/Install.py script with the specified args:
-Make.py -p reax -reax make=gfortran -a machine :pre
+make lib-reax # print help message
+make lib-reax args="-m gfortran" # build with GNU Fortran compiler
+make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
-To un-install via make or Make.py:
+The build should produce two files: lib/reax/libreax.a and
+lib/reax/Makefile.lammps. The latter is copied from an existing
+Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
+Fortran (REAX library). Typically the two compilers used for LAMMPS
+and the REAX library need to be consistent (e.g. both Intel or both
+GNU compilers). If necessary, you can edit/create a new
+lib/reax/Makefile.machine file for your system, which should define an
+EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
+file.
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-reax
+make machine :pre
make no-reax
make machine :pre
-Make.py -p ^reax -a machine :pre
+[Supporting info:]
-Supporting info: lib/reax/README, "pair_style reax"_pair_reax.html,
-"fix reax/bonds"_fix_reax_bonds.html, examples/reax
+src/REAX: filenames -> commands
+lib/reax/README
+"pair_style reax"_pair_reax.html
+"fix reax/bonds"_fix_reax_bonds.html
+examples/reax :ul
:line
-REPLICA package :link(REPLICA),h5
+REPLICA package :link(REPLICA),h4
-Contents: A collection of multi-replica methods that are used by
-invoking multiple instances (replicas) of LAMMPS
-simulations. Communication between individual replicas is performed in
-different ways by the different methods. See "Section
+[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
-multi-replica simulations in LAMMPS. Multi-replica methods included
-in the package are nudged elastic band (NEB), parallel replica
-dynamics (PRD), temperature accelerated dynamics (TAD), parallel
-tempering, and a verlet/split algorithm for performing long-range
-Coulombics on one set of processors, and the remainder of the force
-field calculation on another set.
+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
+verlet/split algorithm for performing long-range Coulombics on one set
+of processors, and the remainder of the force field calcalation on
+another set.
-To install via make or Make.py:
+[Install or un-install:]
make yes-replica
make machine :pre
-Make.py -p replica -a machine :pre
-
-To un-install via make or Make.py:
-
make no-replica
make machine :pre
-Make.py -p ^replica -a machine :pre
+[Supporting info:]
-Supporting info: "Section 6.5"_Section_howto.html#howto_5,
-"neb"_neb.html, "prd"_prd.html, "tad"_tad.html, "temper"_temper.html,
-"run_style verlet/split"_run_style.html, examples/neb, examples/prd,
-examples/tad
+src/REPLICA: filenames -> commands
+"Section 6.5"_Section_howto.html#howto_5
+"neb"_neb.html
+"prd"_prd.html
+"tad"_tad.html
+"temper"_temper.html,
+"run_style verlet/split"_run_style.html
+examples/neb
+examples/prd
+examples/tad :ul
:line
-RIGID package :link(RIGID),h5
+RIGID package :link(RIGID),h4
-Contents: A collection of computes and fixes which enforce rigid
-constraints on collections of atoms or particles. This includes SHAKE
-and RATTLE, as well as variants of rigid-body time integrators for a
-few large bodies or many small bodies.
+[Contents:]
-To install via make or Make.py:
+Fixes which enforce rigid constraints on collections of atoms or
+particles. This includes SHAKE and RATTLE, as well as varous
+rigid-body integrators for a few large bodies or many small bodies.
+Also several computes which calculate properties of rigid bodies.
+
+To install/build:
make yes-rigid
make machine :pre
-Make.py -p rigid -a machine :pre
-
-To un-install via make or Make.py:
+To un-install/re-build:
make no-rigid
make machine :pre
-Make.py -p ^rigid -a machine :pre
+[Supporting info:]
-Supporting info: "compute erotate/rigid"_compute_erotate_rigid.html,
-"fix shake"_fix_shake.html, "fix rattle"_fix_shake.html, "fix
-rigid/*"_fix_rigid.html, examples/ASPHERE, examples/rigid
+src/RIGID: filenames -> commands
+"compute erotate/rigid"_compute_erotate_rigid.html
+fix shake"_fix_shake.html
+"fix rattle"_fix_shake.html
+"fix rigid/*"_fix_rigid.html
+examples/ASPHERE
+examples/rigid
+bench/in.rhodo
+http://lammps.sandia.gov/movies.html#box
+http://lammps.sandia.gov/movies.html#star :ul
:line
-SHOCK package :link(SHOCK),h5
+SHOCK package :link(SHOCK),h4
-Contents: A small number of fixes useful for running impact
-simulations where a shock-wave passes through a material.
+[Contents:]
-To install via make or Make.py:
+Fixes for running impact simulations where a shock-wave passes through
+a material.
+
+[Install or un-install:]
make yes-shock
make machine :pre
-Make.py -p shock -a machine :pre
-
-To un-install via make or Make.py:
-
make no-shock
make machine :pre
-Make.py -p ^shock -a machine :pre
+[Supporting info:]
-Supporting info: "fix append/atoms"_fix_append_atoms.html, "fix
-msst"_fix_msst.html, "fix nphug"_fix_nphug.html, "fix
-wall/piston"_fix_wall_piston.html, examples/hugoniostat, examples/msst
+src/SHOCK: filenames -> commands
+"fix append/atoms"_fix_append_atoms.html
+"fix msst"_fix_msst.html
+"fix nphug"_fix_nphug.html
+"fix wall/piston"_fix_wall_piston.html
+examples/hugoniostat
+examples/msst :ul
:line
-SNAP package :link(SNAP),h5
+SNAP package :link(SNAP),h4
-Contents: A pair style for the spectral neighbor analysis potential
-(SNAP), which is an empirical potential which can be quantum accurate
-when fit to an archive of DFT data. Computes useful for analyzing
-properties of the potential are also included.
+[Contents:]
-To install via make or Make.py:
+A pair style for the spectral neighbor analysis potential (SNAP).
+SNAP is methodology for deriving a highly accurate classical potential
+fit to a large archive of quantum mechanical (DFT) data. Also several
+computes which analyze attributes of the potential.
-make yes-snap
-make machine :pre
+[Author:] Aidan Thompson (Sandia).
-Make.py -p snap -a machine :pre
+[Install or un-install:]
-To un-install via make or Make.py:
+make yes-snap
+make machine :pre
make no-snap
make machine :pre
-Make.py -p ^snap -a machine :pre
+[Supporting info:]
-Supporting info: "pair snap"_pair_snap.html, "compute
-sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna_atom.html,
-"compute snav/atom"_compute_sna_atom.html, examples/snap
+src/SNAP: filenames -> commands
+"pair snap"_pair_snap.html
+"compute sna/atom"_compute_sna_atom.html
+"compute snad/atom"_compute_sna_atom.html
+"compute snav/atom"_compute_sna_atom.html
+examples/snap :ul
:line
-SRD package :link(SRD),h5
+SRD package :link(SRD),h4
+
+[Contents:]
-Contents: Two fixes which implement the Stochastic Rotation Dynamics
-(SRD) method for coarse-graining of a solvent, typically around large
-colloidal-scale particles.
+A pair of fixes which implement the Stochastic Rotation Dynamics (SRD)
+method for coarse-graining of a solvent, typically around large
+colloidal particles.
-To install via make or Make.py:
+To install/build:
make yes-srd
make machine :pre
-Make.py -p srd -a machine :pre
-
-To un-install via make or Make.py:
+To un-install/re-build:
make no-srd
make machine :pre
-Make.py -p ^srd -a machine :pre
+[Supporting info:]
-Supporting info: "fix srd"_fix_srd.html, "fix
-wall/srd"_fix_wall_srd.html, examples/srd, examples/ASPHERE
+src/SRD: filenames -> commands
+"fix srd"_fix_srd.html
+"fix wall/srd"_fix_wall_srd.html
+examples/srd
+examples/ASPHERE
+http://lammps.sandia.gov/movies.html#tri
+http://lammps.sandia.gov/movies.html#line
+http://lammps.sandia.gov/movies.html#poly :ul
:line
-VORONOI package :link(VORONOI),h5
+VORONOI package :link(VORONOI),h4
-Contents: A "compute voronoi/atom"_compute_voronoi_atom.html command
-which computes the Voronoi tesselation of a collection of atoms or
-particles by wrapping the Voro++ lib
+[Contents:]
-To build LAMMPS with the KIM package you must have previously
-installed the KIM API (library) on your system. The lib/kim/README
-file explains how to download and install KIM. Building with the KIM
-package also uses the lib/kim/Makefile.lammps file in the compile/link
-process. You should not need to edit this file.
+A compute command which calculates the Voronoi tesselation of a
+collection of atoms by wrapping the "Voro++ library"_voronoi. This
+can be used to calculate the local volume or each atoms or its near
+neighbors.
+:link(voronoi,http://math.lbl.gov/voro++)
-To build LAMMPS with the VORONOI package you must have previously
-installed the Voro++ library on your system. The lib/voronoi/README
-file explains how to download and install Voro++. There is a
-lib/voronoi/install.py script which automates the process. Type
-"python install.py" to see instructions. The final step is to create
-soft links in the lib/voronoi directory for "includelink" and
-"liblink" which point to installed Voro++ directories. Building with
-the VORONOI package uses the contents of the
-lib/voronoi/Makefile.lammps file in the compile/link process. You
-should not need to edit this file. Note that the Make.py script has a
-"-voronoi" option to allow the Voro++ library to be downloaded and/or
-installed and LAMMPS to be built in one step. Type "python
-src/Make.py -h -voronoi" to see the details.
+To use this package you must have the Voro++ library available on your
+system.
-To install via make or Make.py:
+[Author:] Daniel Schwen (INL) while at LANL. The open-source Voro++
+library was written by Chris Rycroft (Harvard U) while at UC Berkeley
+and LBNL.
-cd ~/lammps/lib/voronoi
-python install.py -g -b -l # download Voro++, build in lib/voronoi, create links
-cd ~/lammps/src
-make yes-voronoi
-make machine :pre
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first download and
+build the Voro++ library. You can do this manually if you prefer;
+follow the instructions in lib/voronoi/README. You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invoke the lib/voronoi/Install.py script with the specified
+args:
+
+make lib-voronoi # print help message
+make lib-voronoi args="-g -b -l" # download and build in default lib/voronoi/voro++-0.4.6
+make lib-voronoi args="-h . voro++ -g -b -l" # download and build in lib/voronoi/voro++
+make lib-voronoi args="-h ~ voro++ -g -b -l" # download and build in ~/voro++ :pre
-Make.py -p voronoi -voronoi install="-g -b -l" -a machine :pre
+Note that the final -l switch is to create 2 symbolic (soft) links,
+"includelink" and "liblink", in lib/voronoi to point to the Voro++ src
+dir. When LAMMPS builds it will use these links. You should not need
+to edit the lib/voronoi/Makefile.lammps file.
-To un-install via make or Make.py:
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-voronoi
+make machine :pre
make no-voronoi
make machine :pre
-Make.py -p ^voronoi -a machine :pre
-
-Supporting info: src/VORONOI/README, lib/voronoi/README, "compute
-voronoi/atom"_compute_voronoi_atom.html, examples/voronoi
+[Supporting info:]
+
+src/VORONOI: filenames -> commands
+src/VORONOI/README
+lib/voronoi/README
+"compute voronoi/atom"_compute_voronoi_atom.html
+examples/voronoi :ul
+:line
:line
-4.2 User packages :h4,link(pkg_2)
+USER-ATC package :link(USER-ATC),h4
-The current list of user-contributed packages is as follows:
+[Contents:]
-Package, Description, Author(s), Doc page, Example, Pic/movie, Library
-"USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
-"USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
-"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Strathclyde Glasgow), src/USER-CGDNA/README, USER/cgdna, -, -
-"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, "cgsdk"_cgsdk, -
-"USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
-"USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
-"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
-"USER-DRUDE"_#USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
-"USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
-"USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
-"USER-H5MD"_#USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
-"USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section 5.3.2"_accelerate_intel.html, examples/intel, -, -
-"USER-LB"_#USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
-"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -
-"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
-"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
-"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
-"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc / dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
-"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
-"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
-"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
-"USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, -
-"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_style quip"_pair_quip.html, USER/quip, -, lib/quip
-"USER-REAXC"_#USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
-"USER-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, -
-"USER-SMTBQ"_#USER-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, -
-"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
-"USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute XXX/tally"_compute_tally.html, USER/tally, -, -
-"USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_dump_custom_vtk.html, -, -, lib/vtk
-:tb(ea=c)
+ATC stands for atoms-to-continuum. This package implements a "fix
+atc"_fix_atc.html command to either couple molecular dynamics with
+continuum finite element equations or perform on-the-fly conversion of
+atomic information to continuum fields.
-:link(atc,http://lammps.sandia.gov/pictures.html#atc)
-:link(cgsdk,http://lammps.sandia.gov/pictures.html#cg)
-:link(eff,http://lammps.sandia.gov/movies.html#eff)
-:link(manifold,http://lammps.sandia.gov/movies.html#manifold)
-:link(sph,http://lammps.sandia.gov/movies.html#sph)
-:link(VMD,http://www.ks.uiuc.edu/Research/vmd)
+[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
-The "Authors" column lists a name(s) if a specific person is
-responsible for creating and maintaining the package.
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first build the ATC
+library in lib/atc. You can do this manually if you prefer; follow
+the instructions in lib/atc/README. You can also do it in one step
+from the lammps/src dir, using a command like these, which simply
+invoke the lib/atc/Install.py script with the specified args:
-(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
-Jon Zimmerman (Sandia).
+make lib-atc # print help message
+make lib-atc args="-m g++" # build with GNU g++ compiler
+make lib-atc args="-m icc" # build with Intel icc compiler :pre
+
+The build should produce two files: lib/atc/libatc.a and
+lib/atc/Makefile.lammps. The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the ATC
+library. If necessary, you can edit/create a new
+lib/atc/Makefile.machine file for your system, which should define an
+EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
+file.
-(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
-the colvars module library written by Giacomo Fiorin (Temple U) and
-Jerome Henin (LISM, Marseille, France).
+Note that the Makefile.lammps file has settings for the BLAS and
+LAPACK linear algebra libraries. As explained in lib/atc/README these
+can either exist on your system, or you can use the files provided in
+lib/linalg. In the latter case you also need to build the library
+in lib/linalg with a command like these:
-(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
-Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
-(U Blaise Pascal).
+make lib-linalg # print help message
+make lib-atc args="-m gfortran" # build with GNU Fortran compiler
-(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
-Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
-(5) The USER-DPD package was created by James Larentzos (ARL), Timothy
-Mattox (Engility), and John Brennan (ARL).
+make yes-user-atc
+make machine :pre
+
+make no-user-atc
+make machine :pre
+
+[Supporting info:]
-(6) The USER-VTK package was created by Richard Berger (JKU) and
-Daniel Queteschiner (DCS Computing).
+src/USER-ATC: filenames -> commands
+src/USER-ATC/README
+"fix atc"_fix_atc.html
+examples/USER/atc
+http://lammps.sandia.gov/pictures.html#atc :ul
-The "Doc page" column links to either a sub-section of the
-"Section 6"_Section_howto.html of the manual, or an input script
-command implemented as part of the package, or to additional
-documentation provided within the package.
+:line
-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-AWPMD package :link(USER-AWPMD),h4
-The "Library" column lists an external library which must be built
-first and which LAMMPS links to when it is built. If it is listed as
-lib/package, then the code for the library is under the lib directory
-of the LAMMPS distribution. See the lib/package/README file for info
-on how to build the library. If it is not listed as lib/package, then
-it is a third-party library not included in the LAMMPS distribution.
-See details on all of this below for individual packages.
+[Contents:]
-:line
+AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This
+package implements an atom, pair, and fix style which allows electrons
+to be treated as explicit particles in a classical molecular dynamics
+model.
-USER-ATC package :link(USER-ATC),h5
+[Author:] Ilya Valuev (JIHT, Russia).
-Contents: ATC stands for atoms-to-continuum. This package implements
-a "fix atc"_fix_atc.html command to either couple MD with continuum
-finite element equations or perform on-the-fly post-processing of
-atomic information to continuum fields. See src/USER-ATC/README for
-more details.
-
-To build LAMMPS with this package ...
-
-To install via make or Make.py:
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first build the
+AWPMD library in lib/awpmd. You can do this manually if you prefer;
+follow the instructions in lib/awpmd/README. You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invoke the lib/awpmd/Install.py script with the specified args:
-make yes-user-atc
-make machine :pre
+make lib-awpmd # print help message
+make lib-awpmd args="-m g++" # build with GNU g++ compiler
+make lib-awpmd args="-m icc" # build with Intel icc compiler :pre
-Make.py -p atc -a machine :pre
+The build should produce two files: lib/awpmd/libawpmd.a and
+lib/awpmd/Makefile.lammps. The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the
+AWPMD library. If necessary, you can edit/create a new
+lib/awpmd/Makefile.machine file for your system, which should define
+an EXTRAMAKE variable to specify a corresponding
+Makefile.lammps.machine file.
-To un-install via make or Make.py:
+Note that the Makefile.lammps file has settings for the BLAS and
+LAPACK linear algebra libraries. As explained in lib/awpmd/README
+these can either exist on your system, or you can use the files
+provided in lib/linalg. In the latter case you also need to build the
+library in lib/linalg with a command like these:
-make no-user-atc
-make machine :pre
+make lib-linalg # print help message
+make lib-atc args="-m gfortran" # build with GNU Fortran compiler
-Make.py -p ^atc -a machine :pre
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
-Supporting info:src/USER-ATC/README, "fix atc"_fix_atc.html,
-examples/USER/atc
+make yes-user-awpmd
+make machine :pre
+
+make no-user-awpmd
+make machine :pre
+
+[Supporting info:]
-Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl
-at sandia.gov) and Jon Zimmerman (jzimmer at sandia.gov) at Sandia.
-Contact them directly if you have questions.
+src/USER-AWPMD: filenames -> commands
+src/USER-AWPMD/README
+"pair awpmd/cut"_pair_awpmd.html
+"fix nve/awpmd"_fix_nve_awpmd.html
+examples/USER/awpmd :ul
:line
-USER-AWPMD package :link(USER-AWPMD),h5
+USER-CGDNA package :link(USER-CGDNA),h4
-Contents: AWPMD stands for Antisymmetrized Wave Packet Molecular
-Dynamics. This package implements an atom, pair, and fix style which
-allows electrons to be treated as explicit particles in an MD
-calculation. See src/USER-AWPMD/README for more details.
+[Contents:]
-To build LAMMPS with this package ...
+Several pair styles, a bond style, and integration fixes for
+coarse-grained models of single- and double-stranded DNA based on the
+oxDNA model of Doye, Louis and Ouldridge at the University of Oxford.
+This includes Langevin-type rigid-body integrators with improved
+stability.
-Supporting info: src/USER-AWPMD/README, "fix
-awpmd/cut"_pair_awpmd.html, examples/USER/awpmd
+[Author:] Oliver Henrich (University of Edinburgh).
-Author: Ilya Valuev at the JIHT in Russia (valuev at
-physik.hu-berlin.de). Contact him directly if you have questions.
+[Install or un-install:]
+
+make yes-user-cgdna
+make machine :pre
+
+make no-user-cgdna
+make machine :pre
+
+[Supporting info:]
+
+src/USER-CGDNA: filenames -> commands
+/src/USER-CGDNA/README
+"pair_style oxdna/*"_pair_oxdna.html
+"pair_style oxdna2/*"_pair_oxdna2.html
+"bond_style oxdna/*"_bond_oxdna.html
+"bond_style oxdna2/*"_bond_oxdna2.html
+"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
:line
-USER-CGSDK package :link(USER-CGSDK),h5
-
-Contents: CGSDK stands for Shinoda-DeVane-Klein (SDK) coarse-grained
-molecular dynamics force field. This package implements several pair
-styles and an angle style using the coarse grained parametrization of
-Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007) (SDK), with extensions
-to simulate ionic liquids, electrolytes, lipids and charged amino acids.
-See src/USER-CGSDK/README for more details.
-
-Supporting info: src/USER-CGSDK/README, "pair lj/sdk"_pair_sdk.html,
-"pair lj/sdk/coul/long"_pair_sdk.html, "angle sdk"_angle_sdk.html,
-examples/USER/cgsdk
+USER-CGSDK package :link(USER-CGSDK),h4
-Author: Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact
-him directly if you have questions.
+[Contents:]
-:line
+Several pair styles and an angle style which implement the
+coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
+simulation of ionic liquids, electrolytes, lipids and charged amino
+acids.
-USER-CGDNA package :link(USER-CGDNA),h5
+[Author:] Axel Kohlmeyer (Temple U).
-Contents: The CGDNA package implements coarse-grained force fields for
-single- and double-stranded DNA. These are at the moment mainly the
-oxDNA and oxDNA2 models, developed by Doye, Louis and Ouldridge at the University
-of Oxford. The package also contains Langevin-type rigid-body
-integrators with improved stability.
+[Install or un-install:]
+
+make yes-user-cgsdk
+make machine :pre
+
+make no-user-cgsdk
+make machine :pre
+
+[Supporting info:]
-See these doc pages to get started:
+src/USER-CGSDK: filenames -> commands
+src/USER-CGSDK/README
+"pair_style lj/sdk/*"_pair_sdk.html
+"angle_style sdk"_angle_sdk.html
+examples/USER/cgsdk
+http://lammps.sandia.gov/pictures.html#cg :ul
-"bond_style oxdna/fene"_bond_oxdna.html
-"bond_style oxdna2/fene"_bond_oxdna.html
-"pair_style oxdna/..."_pair_oxdna.html
-"pair_style oxdna2/..."_pair_oxdna2.html
-"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
+:line
-Supporting info: /src/USER-CGDNA/README, "bond_style
-oxdna/fene"_bond_oxdna.html, "bond_style
-oxdna2/fene"_bond_oxdna.html, "pair_style
-oxdna/..."_pair_oxdna.html, "pair_style
-oxdna2/..."_pair_oxdna2.html, "fix
-nve/dotc/langevin"_fix_nve_dotc_langevin.html
+USER-COLVARS package :link(USER-COLVARS),h4
+
+[Contents:]
+
+COLVARS stands for collective variables, which can be used to
+implement various enhanced sampling methods, including Adaptive
+Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and
+Restraints. A "fix colvars"_fix_colvars.html command is implemented
+which wraps a COLVARS library, which implements these methods.
+simulations.
+
+[Authors:] Axel Kohlmeyer (Temple U). The COLVARS library was written
+by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
+Jerome Henin (LISM, CNRS, Marseille, France).
+
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first build the
+COLVARS library in lib/colvars. You can do this manually if you
+prefer; follow the instructions in lib/colvars/README. You can also
+do it in one step from the lammps/src dir, using a command like these,
+which simply invoke the lib/colvars/Install.py script with the
+specified args:
+
+make lib-colvars # print help message
+make lib-colvars args="-m g++" # build with GNU g++ compiler :pre
+
+The build should produce two files: lib/colvars/libcolvars.a and
+lib/colvars/Makefile.lammps. The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the
+COLVARS library (though typically the settings are just blank). If
+necessary, you can edit/create a new lib/colvars/Makefile.machine file
+for your system, which should define an EXTRAMAKE variable to specify
+a corresponding Makefile.lammps.machine file.
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-user-colvars
+make machine :pre
+
+make no-user-colvars
+make machine :pre
+
+[Supporting info:]
-Author: Oliver Henrich at the University of Strathclyde, Glasgow
-(oliver.henrich at strath.ac.uk, also ohenrich at ph.ed.ac.uk).
-Contact him directly if you have any questions.
+src/USER-COLVARS: filenames -> commands
+"doc/PDF/colvars-refman-lammps.pdf"_PDF/colvars-refman-lammps.pdf
+src/USER-COLVARS/README
+lib/colvars/README
+"fix colvars"_fix_colvars.html
+examples/USER/colvars :ul
:line
-USER-COLVARS package :link(USER-COLVARS),h5
+USER-DIFFRACTION package :link(USER-DIFFRACTION),h4
-Contents: COLVARS stands for collective variables which can be used to
-implement Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
-Sampling and Restraints. This package implements a "fix
-colvars"_fix_colvars.html command which wraps a COLVARS library which
-can perform those kinds of simulations. See src/USER-COLVARS/README
-for more details.
+[Contents:]
-Supporting info:
-"doc/PDF/colvars-refman-lammps.pdf"_PDF/colvars-refman-lammps.pdf,
-src/USER-COLVARS/README, lib/colvars/README, "fix
-colvars"_fix_colvars.html, examples/USER/colvars
+Two computes and a fix for calculating x-ray and electron diffraction
+intensities based on kinematic diffraction theory.
-Authors: Axel Kohlmeyer at Temple U (akohlmey at gmail.com) wrote the
-interface that integrates colvars into LAMMPS. The COLVARS library
-itself is written and maintained by Giacomo Fiorin (ICMS, Temple
-University, Philadelphia, PA, USA) and Jerome Henin (LISM, CNRS,
-Marseille, France). For more info, and to communicate with the COLVARS
-developers, please go to COLVARS home page at
-"http://colvars.github.io"_http://colvars.github.io/.
+[Author:] Shawn Coleman while at the U Arkansas.
-:line
+[Install or un-install:]
+
+make yes-user-diffraction
+make machine :pre
+
+make no-user-diffraction
+make machine :pre
+
+[Supporting info:]
-USER-DIFFRACTION package :link(USER-DIFFRACTION),h5
+src/USER-DIFFRACTION: filenames -> commands
+"compute saed"_compute_saed.html
+"compute xrd"_compute_xrd.html
+"fix saed/vtk"_fix_saed_vtk.html
+examples/USER/diffraction :ul
-Contents: This packages implements two computes and a fix for
-calculating x-ray and electron diffraction intensities based on
-kinematic diffraction theory. See src/USER-DIFFRACTION/README for
-more details.
+:line
-Supporting info: "compute saed"_compute_saed.html, "compute
-xrd"_compute_xrd.html, "fix saed/vtk"_fix_saed_vtk.html,
-examples/USER/diffraction
+USER-DPD package :link(USER-DPD),h4
-Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at
-the University of Arkansas. Contact him directly if you have
-questions.
+[Contents:]
-:line
+DPD stands for dissipative particle dynamics. This package implements
+coarse-grained DPD-based models for energetic, reactive molecular
+crystalline materials. It includes many pair styles specific to these
+systems, including for reactive DPD, where each particle has internal
+state for multiple species and a coupled set of chemical reaction ODEs
+are integrated each timestep. Highly accurate time intergrators for
+isothermal, isoenergetic, isobaric and isenthalpic conditions are
+included. These enable long timesteps via the Shardlow splitting
+algorithm.
-USER-DPD package :link(USER-DPD),h5
+[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John
+Brennan (ARL).
-Contents: DPD stands for dissipative particle dynamics, This package
-implements DPD for isothermal, isoenergetic, isobaric and isenthalpic
-conditions. It also has extensions for performing reactive DPD, where
-each particle has internal state for multiple species and a coupled
-set of chemical reaction ODEs are integrated each timestep. The DPD
-equations of motion are integrated efficiently through the Shardlow
-splitting algorithm. See src/USER-DPD/README for more details.
+[Install or un-install:]
+
+make yes-user-dpd
+make machine :pre
+
+make no-user-dpd
+make machine :pre
+
+[Supporting info:]
-Supporting info: /src/USER-DPD/README, "compute dpd"_compute_dpd.html
+src/USER-DPD: filenames -> commands
+/src/USER-DPD/README
+"compute dpd"_compute_dpd.html
"compute dpd/atom"_compute_dpd_atom.html
-"fix eos/cv"_fix_eos_table.html "fix eos/table"_fix_eos_table.html
-"fix eos/table/rx"_fix_eos_table_rx.html "fix shardlow"_fix_shardlow.html
-"fix rx"_fix_rx.html "pair table/rx"_pair_table_rx.html
-"pair dpd/fdt"_pair_dpd_fdt.html "pair dpd/fdt/energy"_pair_dpd_fdt.html
-"pair exp6/rx"_pair_exp6_rx.html "pair multi/lucy"_pair_multi_lucy.html
-"pair multi/lucy/rx"_pair_multi_lucy_rx.html, examples/USER/dpd
-
-Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil),
-Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com)
-and John Brennan (ARL) (john.k.brennan.civ at mail.mil). Contact them
-directly if you have questions.
+"fix eos/cv"_fix_eos_table.html
+"fix eos/table"_fix_eos_table.html
+"fix eos/table/rx"_fix_eos_table_rx.html
+"fix shardlow"_fix_shardlow.html
+"fix rx"_fix_rx.html
+"pair table/rx"_pair_table_rx.html
+"pair dpd/fdt"_pair_dpd_fdt.html
+"pair dpd/fdt/energy"_pair_dpd_fdt.html
+"pair exp6/rx"_pair_exp6_rx.html
+"pair multi/lucy"_pair_multi_lucy.html
+"pair multi/lucy/rx"_pair_multi_lucy_rx.html
+examples/USER/dpd :ul
:line
-USER-DRUDE package :link(USER-DRUDE),h5
+USER-DRUDE package :link(USER-DRUDE),h4
+
+[Contents:]
-Contents: This package contains methods for simulating polarizable
-systems using thermalized Drude oscillators. It has computes, fixes,
-and pair styles for this purpose. See "Section
+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. See src/USER-DRUDE/README for additional details. There are
-auxiliary tools for using this package in tools/drude.
+package. There are auxiliary tools for using this package in
+tools/drude.
-Supporting info: "Section 6.27"_Section_howto.html#howto_27,
-src/USER-DRUDE/README, "fix drude"_fix_drude.html, "fix
-drude/transform/*"_fix_drude_transform.html, "compute
-temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html,
-"pair lj/cut/thole/long"_pair_thole.html, examples/USER/drude,
-tools/drude
+[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
+Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
-Authors: Alain Dequidt at Universite Blaise Pascal Clermont-Ferrand
-(alain.dequidt at univ-bpclermont.fr); co-authors: Julien Devemy,
-Agilio Padua. Contact them directly if you have questions.
+[Install or un-install:]
+
+make yes-user-drude
+make machine :pre
+
+make no-user-drude
+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
+src/USER-DRUDE/README
+"fix drude"_fix_drude.html
+"fix drude/transform/*"_fix_drude_transform.html
+"compute temp/drude"_compute_temp_drude.html
+"pair thole"_pair_thole.html
+"pair lj/cut/thole/long"_pair_thole.html
+examples/USER/drude
+tools/drude :ul
:line
-USER-EFF package :link(USER-EFF),h5
+USER-EFF package :link(USER-EFF),h4
+
+[Contents:]
-Contents: EFF stands for electron force field. This package contains
-atom, pair, fix and compute styles which implement the eFF as
+EFF stands for electron force field which allows a classical MD code
+to model electrons as particles of variable radius. This package
+contains atom, pair, fix and compute styles which implement the eFF as
described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III,
-JCC, 2010. The eFF potential was first introduced by Su and Goddard,
-in 2007. See src/USER-EFF/README for more details. There are
-auxiliary tools for using this package in tools/eff; see its README
-file.
+JCC, 2010. The eFF potential was first introduced by Su and Goddard,
+in 2007. There are auxiliary tools for using this package in
+tools/eff; see its README file.
-Supporting info:
+[Author:] Andres Jaramillo-Botero (CalTech).
-Author: Andres Jaramillo-Botero at CalTech (ajaramil at
-wag.caltech.edu). Contact him directly if you have questions.
+[Install or un-install:]
+
+make yes-user-eff
+make machine :pre
+
+make no-user-eff
+make machine :pre
+
+[Supporting info:]
+
+src/USER-EFF: filenames -> commands
+src/USER-EFF/README
+"atom_style electron"_atom_style.html
+"fix nve/eff"_fix_nve_eff.html
+"fix nvt/eff"_fix_nvt_eff.html
+"fix npt/eff"_fix_npt_eff.html
+"fix langevin/eff"_fix_langevin_eff.html
+"compute temp/eff"_compute_temp_eff.html
+"pair eff/cut"_pair_eff.html
+"pair eff/inline"_pair_eff.html
+examples/USER/eff
+tools/eff/README
+tools/eff
+http://lammps.sandia.gov/movies.html#eff :ul
:line
-USER-FEP package :link(USER-FEP),h5
+USER-FEP package :link(USER-FEP),h4
-Contents: FEP stands for free energy perturbation. This package
-provides methods for performing FEP simulations by using a "fix
+[Contents:]
+
+FEP stands for free energy perturbation. This package provides
+methods for performing FEP simulations by using a "fix
adapt/fep"_fix_adapt_fep.html command with soft-core pair potentials,
-which have a "soft" in their style name. See src/USER-FEP/README for
-more details. There are auxiliary tools for using this package in
-tools/fep; see its README file.
+which have a "soft" in their style name. There are auxiliary tools
+for using this package in tools/fep; see its README file.
-Supporting info: src/USER-FEP/README, "fix
-adapt/fep"_fix_adapt_fep.html, "compute fep"_compute_fep.html,
-"pair_style */soft"_pair_lj_soft.html, examples/USER/fep
+[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
-Author: Agilio Padua at Universite Blaise Pascal Clermont-Ferrand
-(agilio.padua at univ-bpclermont.fr). Contact him directly if you have
-questions.
+[Install or un-install:]
+
+make yes-user-fep
+make machine :pre
+
+make no-user-fep
+make machine :pre
+
+[Supporting info:]
+
+src/USER-FEP: filenames -> commands
+src/USER-FEP/README
+"fix adapt/fep"_fix_adapt_fep.html
+"compute fep"_compute_fep.html
+"pair_style */soft"_pair_lj_soft.html
+examples/USER/fep
+tools/fep/README
+tools/fep :ul
:line
-USER-H5MD package :link(USER-H5MD),h5
-
-Contents: H5MD stands for HDF5 for MD. "HDF5"_HDF5 is a binary,
-portable, self-describing file format, used by many scientific
-simulations. H5MD is a format for molecular simulations, built on top
-of HDF5. This package implements a "dump h5md"_dump_h5md.html command
-to output LAMMPS snapshots in this format. See src/USER-H5MD/README
-for more details.
+USER-H5MD package :link(USER-H5MD),h4
-:link(HDF5,http://www.hdfgroup.org/HDF5/)
+[Contents:]
-Supporting info: src/USER-H5MD/README, lib/h5md/README, "dump
-h5md"_dump_h5md.html
+H5MD stands for HDF5 for MD. "HDF5"_HDF5 is a portable, binary,
+self-describing file format, used by many scientific simulations.
+H5MD is a format for molecular simulations, built on top of HDF5.
+This package implements a "dump h5md"_dump_h5md.html command to output
+LAMMPS snapshots in this format.
-Author: Pierre de Buyl at KU Leuven (see http://pdebuyl.be) created
-this package as well as the H5MD format and library. Contact him
-directly if you have questions.
+:link(HDF5,http://www.hdfgroup.org/HDF5)
-:line
+To use this package you must have the HDF5 library available on your
+system.
-USER-INTEL package :link(USER-INTEL),h5
+[Author:] Pierre de Buyl (KU Leuven) created both the package and the
+H5MD format.
-Contents: Dozens of pair, bond, angle, dihedral, and improper styles
-that are optimized for Intel CPUs and the Intel Xeon Phi (in offload
-mode). All of them have an "intel" in their style name. "Section
-5.3.2"_accelerate_intel.html gives details of what hardware
-and compilers are required on your system, and how to build and use
-this package. Also see src/USER-INTEL/README for more details. See
-the KOKKOS, OPT, and USER-OMP packages, which also have CPU and
-Phi-enabled styles.
+[Install or un-install:]
-Supporting info: examples/accelerate, src/USER-INTEL/TEST
-
-"Section 5.3"_Section_accelerate.html#acc_3
+Note that to follow these steps to compile and link to the CH5MD
+library, you need the standard HDF5 software package installed on your
+system, which should include the h5cc compiler and the HDF5 library.
-Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact
-him directly if you have questions.
+Before building LAMMPS with this package, you must first build the
+CH5MD library in lib/h5md. You can do this manually if you prefer;
+follow the instructions in lib/h5md/README. You can also do it in one
+step from the lammps/src dir, using a command like these, which simply
+invoke the lib/h5md/Install.py script with the specified args:
-For the USER-INTEL package, you have 2 choices when building. You can
-build with CPU or Phi support. The latter uses Xeon Phi chips in
-"offload" mode. Each of these modes requires additional settings in
-your Makefile.machine for CCFLAGS and LINKFLAGS.
+make lib-h5md # print help message
+make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre
-For CPU mode (if using an Intel compiler):
+The build should produce two files: lib/h5md/libch5md.a and
+lib/h5md/Makefile.lammps. The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the
+system HDF5 library. If necessary, you can edit/create a new
+lib/h5md/Makefile.machine file for your system, which should define an
+EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
+file.
-CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
-LINKFLAGS: add -fopenmp :ul
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-user-h5md
+make machine :pre
+
+make no-user-h5md
+make machine :pre
+
+[Supporting info:]
-For Phi mode add the following in addition to the CPU mode flags:
+src/USER-H5MD: filenames -> commands
+src/USER-H5MD/README
+lib/h5md/README
+"dump h5md"_dump_h5md.html :ul
-CCFLAGS: add -DLMP_INTEL_OFFLOAD and
-LINKFLAGS: add -offload :ul
+:line
-And also add this to CCFLAGS:
+USER-INTEL package :link(USER-INTEL),h4
--offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" :pre
+[Contents:]
-Examples:
+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
+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_7.
+Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
+packages, which have styles optimized for CPUs and KNLs.
-:line
+You need to have an Intel compiler, version 14 or higher to take full
+advantage of this package.
-USER-LB package :link(USER-LB),h5
+[Author:] Mike Brown (Intel).
-Supporting info:
+[Install or un-install:]
-This package contains a LAMMPS implementation of a background
-Lattice-Boltzmann fluid, which can be used to model MD particles
-influenced by hydrodynamic forces.
+For the USER-INTEL package, you have 2 choices when building. You can
+build with either CPU or KNL support. Each choice requires additional
+settings in your Makefile.machine for CCFLAGS and LINKFLAGS and
+optimized malloc libraries. See the
+src/MAKE/OPTIONS/Makefile.intel_cpu and src/MAKE/OPTIONS/Makefile.knl
+files for examples.
+
+For CPUs:
+
+OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
+CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
+ -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+LINKFLAGS = -g -qopenmp $(OPTFLAGS)
+LIB = -ltbbmalloc -ltbbmalloc_proxy
+
+For KNLs:
+
+OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
+CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
+ -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+LINKFLAGS = -g -qopenmp $(OPTFLAGS)
+LIB = -ltbbmalloc
+
+Once you have an appropriate Makefile.machine, you can
+install/un-install the package and build LAMMPS in the usual manner.
+Note that you cannot build one executable to run on multiple hardware
+targets (Intel CPUs or KNL). You need to build LAMMPS once for each
+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.
+
+make yes-user-intel yes-user-omp
+make machine :pre
+
+make no-user-intel no-user-omp
+make machine :pre
-See this doc page and its related commands to get started:
+[Supporting info:]
-"fix lb/fluid"_fix_lb_fluid.html
+src/USER-INTEL: filenames -> commands
+src/USER-INTEL/README
+"Section 5.3"_Section_accelerate.html#acc_3
+"Section 5.3.2"_accelerate_gpu.html
+"Section 2.7 -sf intel"_Section_start.html#start_7
+"Section 2.7 -pk intel"_Section_start.html#start_7
+"package intel"_package.html
+Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i)
+src/USER-INTEL/TEST
+"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
-The people who created this package are Frances Mackay (fmackay at
-uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
-Western Ontario. Contact them directly if you have questions.
+:line
-Examples: examples/USER/lb
+USER-LB package :link(USER-LB),h4
-:line
+[Contents:]
-USER-MGPT package :link(USER-MGPT),h5
+Fixes which implement a background Lattice-Boltzmann (LB) fluid, which
+can be used to model MD particles influenced by hydrodynamic forces.
-Supporting info:
+[Authors:] Frances Mackay and Colin Denniston (University of Western
+Ontario).
-This package contains a fast implementation for LAMMPS of
-quantum-based MGPT multi-ion potentials. The MGPT or model GPT method
-derives from first-principles DFT-based generalized pseudopotential
-theory (GPT) through a series of systematic approximations valid for
-mid-period transition metals with nearly half-filled d bands. The
-MGPT method was originally developed by John Moriarty at Lawrence
-Livermore National Lab (LLNL).
+[Install or un-install:]
+
+make yes-user-lb
+make machine :pre
+
+make no-user-lb
+make machine :pre
+
+[Supporting info:]
-In the general matrix representation of MGPT, which can also be
-applied to f-band actinide metals, the multi-ion potentials are
-evaluated on the fly during a simulation through d- or f-state matrix
-multiplication, and the forces that move the ions are determined
-analytically. The {mgpt} pair style in this package calculates forces
-and energies using an optimized matrix-MGPT algorithm due to Tomas
-Oppelstrup at LLNL.
+src/USER-LB: filenames -> commands
+src/USER-LB/README
+"fix lb/fluid"_fix_lb_fluid.html
+"fix lb/momentum"_fix_lb_momentum.html
+"fix lb/viscous"_fix_lb_viscous.html
+examples/USER/lb :ul
-See this doc page to get started:
+:line
-"pair_style mgpt"_pair_mgpt.html
+USER-MGPT package :link(USER-MGPT),h4
-The persons who created the USER-MGPT package are Tomas Oppelstrup
-(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov)
-Contact them directly if you have any questions.
+[Contents:]
-Examples: examples/USER/mgpt
+A pair style which provides a fast implementation of the quantum-based
+MGPT multi-ion potentials. The MGPT or model GPT method derives from
+first-principles DFT-based generalized pseudopotential theory (GPT)
+through a series of systematic approximations valid for mid-period
+transition metals with nearly half-filled d bands. The MGPT method
+was originally developed by John Moriarty at LLNL. The pair style in
+this package calculates forces and energies using an optimized
+matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
-:line
+[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
-USER-MISC package :link(USER-MISC),h5
+[Install or un-install:]
+
+make yes-user-mgpt
+make machine :pre
+
+make no-user-mgpt
+make machine :pre
+
+[Supporting info:]
-Supporting info:
+src/USER-MGPT: filenames -> commands
+src/USER-MGPT/README
+"pair_style mgpt"_pair_mgpt.html
+examples/USER/mgpt :ul
-The files in this package are a potpourri of (mostly) unrelated
-features contributed to LAMMPS by users. Each feature is a single
-pair of files (*.cpp and *.h).
+:line
-More information about each feature can be found by reading its doc
-page in the LAMMPS doc directory. The doc page which lists all LAMMPS
-input script commands is as follows:
+USER-MISC package :link(USER-MISC),h4
-"Section 3.5"_Section_commands.html#cmd_5
+[Contents:]
-User-contributed features are listed at the bottom of the fix,
-compute, pair, etc sections.
+A potpourri of (mostly) unrelated features contributed to LAMMPS by
+users. Each feature is a single fix, compute, pair, bond, angle,
+dihedral, improper, or command style.
-The list of features and author of each is given in the
+[Authors:] The author for each style in the package is listed in the
src/USER-MISC/README file.
-You should contact the author directly if you have specific questions
-about the feature or its coding.
+[Install or un-install:]
+
+make yes-user-misc
+make machine :pre
+
+make no-user-misc
+make machine :pre
+
+[Supporting info:]
-Examples: examples/USER/misc
+src/USER-MISC: filenames -> commands
+src/USER-MISC/README
+one doc page per individual command listed in src/USER-MISC/README
+examples/USER/misc :ul
:line
-USER-MANIFOLD package :link(USER-MANIFOLD),h5
+USER-MANIFOLD package :link(USER-MANIFOLD),h4
-Supporting info:
+[Contents:]
-This package contains a dump molfile command which uses molfile
-plugins that are bundled with the
-"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
-analysis program, to enable LAMMPS to dump its information in formats
-compatible with various molecular simulation tools.
+Several fixes and a "manifold" class which enable simulations of
+particles constrained to a manifold (a 2D surface within the 3D
+simulation box). This is done by applying the RATTLE constraint
+algorithm to formulate single-particle constraint functions
+g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
+n = grad(g).
-This package allows LAMMPS to perform MD simulations of particles
-constrained on a manifold (i.e., a 2D subspace of the 3D simulation
-box). It achieves this using the RATTLE constraint algorithm applied
-to single-particle constraint functions g(xi,yi,zi) = 0 and their
-derivative (i.e. the normal of the manifold) n = grad(g).
+[Author:] Stefan Paquay (Eindhoven University of Technology (TU/e), The
+Netherlands)
-See this doc page to get started:
+[Install or un-install:]
+
+make yes-user-manifold
+make machine :pre
+
+make no-user-manifold
+make machine :pre
+
+[Supporting info:]
+src/USER-MANIFOLD: filenames -> commands
+src/USER-MANIFOLD/README
+"doc/manifolds"_manifolds.html
"fix manifoldforce"_fix_manifoldforce.html
-
-The person who created this package is Stefan Paquay, at the Eindhoven
-University of Technology (TU/e), The Netherlands (s.paquay at tue.nl).
-Contact him directly if you have questions.
+"fix nve/manifold/rattle"_fix_nve_manifold/rattle.html
+"fix nvt/manifold/rattle"_fix_nvt_manifold/rattle.html
+examples/USER/manifold
+http://lammps.sandia.gov/movies.html#manifold :ul
:line
-USER-MOLFILE package :link(USER-MOLFILE),h5
+USER-MOLFILE package :link(USER-MOLFILE),h4
+
+[Contents:]
+
+A "dump molfile"_dump_molfile.html command which uses molfile plugins
+that are bundled with the "VMD"_http://www.ks.uiuc.edu/Research/vmd
+molecular visualization and analysis program, to enable LAMMPS to dump
+snapshots in formats compatible with various molecular simulation
+tools.
+
+To use this package you must have the desired VMD plugins available on
+your system.
+
+Note that this package only provides the interface code, not the
+plugins themselves, which will be accessed when requesting a specific
+plugin via the "dump molfile"_dump_molfile.html command. Plugins can
+be obtained from a VMD installation which has to match the platform
+that you are using to compile LAMMPS for. By adding plugins to VMD,
+support for new file formats can be added to LAMMPS (or VMD or other
+programs that use them) without having to recompile the application
+itself. More information about the VMD molfile plugins can be found
+at
+"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.
+
+[Author:] Axel Kohlmeyer (Temple U).
+
+[Install or un-install:]
+
+Note that the lib/molfile/Makefile.lammps file has a setting for a
+dynamic loading library libdl.a that should is typically present on
+all systems, which is required for LAMMPS to link with this package.
+If the setting is not valid for your system, you will need to edit the
+Makefile.lammps file. See lib/molfile/README and
+lib/molfile/Makefile.lammps for details.
+
+make yes-user-molfile
+make machine :pre
+
+make no-user-molfile
+make machine :pre
+
+[Supporting info:]
+
+src/USER-MOLFILE: filenames -> commands
+src/USER-MOLFILE/README
+lib/molfile/README
+"dump molfile"_dump_molfile.html :ul
-Supporting info:
+:line
-This package contains a dump molfile command which uses molfile
-plugins that are bundled with the
-"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
-analysis program, to enable LAMMPS to dump its information in formats
-compatible with various molecular simulation tools.
+USER-NETCDF package :link(USER-NETCDF),h4
-The package only provides the interface code, not the plugins. These
-can be obtained from a VMD installation which has to match the
-platform that you are using to compile LAMMPS for. By adding plugins
-to VMD, support for new file formats can be added to LAMMPS (or VMD or
-other programs that use them) without having to recompile the
-application itself.
+[Contents:]
-See this doc page to get started:
+Dump styles for writing NetCDF formatted dump files. NetCDF is a
+portable, binary, self-describing file format developed on top of
+HDF5. The file contents follow the AMBER NetCDF trajectory conventions
+(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
-"dump molfile"_dump_molfile.html
+To use this package you must have the NetCDF library available on your
+system.
-The person who created this package is Axel Kohlmeyer at Temple U
-(akohlmey at gmail.com). Contact him directly if you have questions.
+Note that NetCDF files can be directly visualized with the following
+tools:
-:line
+"Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above)
+"VMD"_vmd
+"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
+
+:link(ovito,http://www.ovito.org)
+:link(atomeye,http://www.libatoms.org)
-USER-NC-DUMP package :link(USER-NC-DUMP),h5
+[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
-Contents: Dump styles for writing NetCDF format files. NetCDF is a binary,
-portable, self-describing file format on top of HDF5. The file format
-contents follow the AMBER NetCDF trajectory conventions
-(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions to this
-convention. This package implements a "dump nc"_dump_nc.html command
-and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
-in this format. See src/USER-NC-DUMP/README for more details.
+[Install or un-install:]
+
+Note that to follow these steps, you need the standard NetCDF software
+package installed on your system. The lib/netcdf/Makefile.lammps file
+has settings for NetCDF include and library files that LAMMPS needs to
+compile and linkk with this package. If the settings are not valid
+for your system, you will need to edit the Makefile.lammps file. See
+lib/netcdf/README for details.
-NetCDF files can be directly visualized with the following tools:
+make yes-user-netcdf
+make machine :pre
+
+make no-user-netcdf
+make machine :pre
-Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
-and all of the above extensions. :ulb,l
-VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
-AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
-a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+[Supporting info:]
-The person who created these files is Lars Pastewka at
-Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
-Contact him directly if you have questions.
+src/USER-NETCDF: filenames -> commands
+src/USER-NETCDF/README
+lib/netcdf/README
+"dump netcdf"_dump_netcdf.html :ul
:line
-USER-OMP package :link(USER-OMP),h5
+USER-OMP package :link(USER-OMP),h4
-Supporting info:
+[Contents:]
-This package provides OpenMP multi-threading support and
-other optimizations of various LAMMPS pair styles, dihedral
-styles, and fix styles.
+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_7.
+Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
+"USER-INTEL"_#USER-INTEL packages, which have styles optimized for
+CPUs.
-See this section of the manual to get started:
+[Author:] Axel Kohlmeyer (Temple U).
-"Section 5.3"_Section_accelerate.html#acc_3
+NOTE: The compile flags "-restrict" and "-fopenmp" must be used to
+build LAMMPS with the USER-OMP package, as well as the link flag
+"-fopenmp". They should be added to the CCFLAGS and LINKFLAGS lines
+of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.omp for an
+example.
-The person who created this package is Axel Kohlmeyer at Temple U
-(akohlmey at gmail.com). Contact him directly if you have questions.
+Once you have an appropriate Makefile.machine, you can
+install/un-install the package and build LAMMPS in the usual manner:
-For the USER-OMP package, your Makefile.machine needs additional
-settings for CCFLAGS and LINKFLAGS.
+[Install or un-install:]
+
+make yes-user-omp
+make machine :pre
+
+make no-user-omp
+make machine :pre
CCFLAGS: add -fopenmp and -restrict
LINKFLAGS: add -fopenmp :ul
-Examples: examples/accelerate, bench/KEPLER
+[Supporting info:]
+
+src/USER-OMP: filenames -> commands
+src/USER-OMP/README
+"Section 5.3"_Section_accelerate.html#acc_3
+"Section 5.3.4"_accelerate_omp.html
+"Section 2.7 -sf omp"_Section_start.html#start_7
+"Section 2.7 -pk omp"_Section_start.html#start_7
+"package omp"_package.html
+Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o)
+"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-USER-PHONON package :link(USER-PHONON),h5
+USER-PHONON package :link(USER-PHONON),h4
+
+[Contents:]
-This package contains a fix phonon command that calculates dynamical
+A "fix phonon"_fix_phonon.html command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.
-See this doc page to get started:
-
-"fix phonon"_fix_phonon.html
+[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
-The person who created this package is Ling-Ti Kong (konglt at
-sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
-if you have questions.
+[Install or un-install:]
+
+make yes-user-phonon
+make machine :pre
+
+make no-user-phonon
+make machine :pre
+
+[Supporting info:]
-Examples: examples/USER/phonon
+src/USER-PHONON: filenames -> commands
+src/USER-PHONON/README
+"fix phonon"_fix_phonon.html
+examples/USER/phonon :ul
:line
-USER-QMMM package :link(USER-QMMM),h5
+USER-QMMM package :link(USER-QMMM),h4
-Supporting info:
+[Contents:]
-This package provides a fix qmmm command which allows LAMMPS to be
-used in a QM/MM simulation, currently only in combination with pw.x
-code from the "Quantum ESPRESSO"_espresso package.
+A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a
+QM/MM simulation, currently only in combination with the "Quantum
+ESPRESSO"_espresso package.
:link(espresso,http://www.quantum-espresso.org)
+To use this package you must have Quantum ESPRESSO available on your
+system.
+
The current implementation only supports an ONIOM style mechanical
coupling to the Quantum ESPRESSO plane wave DFT package.
Electrostatic coupling is in preparation and the interface has been
written in a manner that coupling to other QM codes should be possible
without changes to LAMMPS itself.
-See this doc page to get started:
+[Author:] Axel Kohlmeyer (Temple U).
+
+[Install or un-install:]
-"fix qmmm"_fix_qmmm.html
+Before building LAMMPS with this package, you must first build the
+QMMM library in lib/qmmm. You can do this manually if you prefer;
+follow the first two steps explained in lib/colvars/README. You can
+also do it in one step from the lammps/src dir, using a command like
+these, which simply invoke the lib/colvars/Install.py script with the
+specified args:
-as well as the lib/qmmm/README file.
+make lib-qmmm # print help message
+make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre
-The person who created this package is Axel Kohlmeyer at Temple U
-(akohlmey at gmail.com). Contact him directly if you have questions.
+The build should produce two files: lib/qmmm/libqmmm.a and
+lib/qmmm/Makefile.lammps. The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the
+QMMM library (though typically the settings are just blank). If
+necessary, you can edit/create a new lib/qmmm/Makefile.machine file
+for your system, which should define an EXTRAMAKE variable to specify
+a corresponding Makefile.lammps.machine file.
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-user-qmmm
+make machine :pre
+
+make no-user-qmmm
+make machine :pre
+
+NOTE: The LAMMPS executable these steps produce is not yet functional
+for a QM/MM simulation. You must also build Quantum ESPRESSO and
+create a new executable which links LAMMPS and Quanutm ESPRESSO
+together. These are steps 3 and 4 described in the lib/qmmm/README
+file.
+
+[Supporting info:]
+
+src/USER-QMMM: filenames -> commands
+src/USER-QMMM/README
+lib/qmmm/README
+"fix phonon"_fix_phonon.html
+lib/qmmm/example-ec/README
+lib/qmmm/example-mc/README :ul
:line
-USER-QTB package :link(USER-QTB),h5
+USER-QTB package :link(USER-QTB),h4
-Supporting info:
+[Contents:]
-This package provides a self-consistent quantum treatment of the
+Two fixes which provide a self-consistent quantum treatment of
vibrational modes in a classical molecular dynamics simulation. By
coupling the MD simulation to a colored thermostat, it introduces zero
-point energy into the system, alter the energy power spectrum and the
-heat capacity towards their quantum nature. This package could be of
-interest if one wants to model systems at temperatures lower than
-their classical limits or when temperatures ramp up across the
-classical limits in the simulation.
+point energy into the system, altering the energy power spectrum and
+the heat capacity to account for their quantum nature. This is useful
+when modeling systems at temperatures lower than their classical
+limits or when temperatures ramp across the classical limits in a
+simulation.
-See these two doc pages to get started:
+[Author:] Yuan Shen (Stanford U).
+
+[Install or un-install:]
+
+make yes-user-qtb
+make machine :pre
+
+make no-user-qtb
+make machine :pre
+
+[Supporting info:]
-"fix qtb"_fix_qtb.html provides quantum nulcear correction through a
-colored thermostat and can be used with other time integration schemes
-like "fix nve"_fix_nve.html or "fix nph"_fix_nh.html.
+src/USER-QTB: filenames -> commands
+src/USER-QTB/README
+"fix qtb"_fix_qtb.html
+"fix qbmsst"_fix_qbmsst.html
+examples/USER/qtb :ul
-"fix qbmsst"_fix_qbmsst.html enables quantum nuclear correction of a
-multi-scale shock technique simulation by coupling the quantum thermal
-bath with the shocked system.
+:line
-The person who created this package is Yuan Shen (sy0302 at
-stanford.edu) at Stanford University. Contact him directly if you
-have questions.
+USER-QUIP package :link(USER-QUIP),h4
-Examples: examples/USER/qtb
+[Contents:]
-:line
+A "pair_style quip"_pair_quip.html command which wraps the "QUIP
+libAtoms library"_quip, which includes a variety of interatomic
+potentials, including Gaussian Approximation Potential (GAP) models
+developed by the Cambridge University group.
-USER-QUIP package :link(USER-QUIP),h5
+:link(quip,https://github.com/libAtoms/QUIP)
-Supporting info:
+To use this package you must have the QUIP libAatoms library available
+on your system.
-Examples: examples/USER/quip
+[Author:] Albert Bartok (Cambridge University)
-:line
+[Install or un-install:]
-USER-REAXC package :link(USER-REAXC),h5
+Note that to follow these steps to compile and link to the QUIP
+library, you must first download and build QUIP on your systems. It
+can be obtained from GitHub. See step 1 and step 1.1 in the
+lib/quip/README file for details on how to do this. Note that it
+requires setting two environment variables, QUIP_ROOT and QUIP_ARCH,
+which will be accessed by the lib/quip/Makefile.lammps file which is
+used when you compile and link LAMMPS with this package. You should
+only need to edit this file if the LAMMPS build can not use its
+settings to successfully build on your system.
-Supporting info:
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
-This package contains a implementation for LAMMPS of the ReaxFF force
-field. ReaxFF uses distance-dependent bond-order functions to
-represent the contributions of chemical bonding to the potential
-energy. It was originally developed by Adri van Duin and the Goddard
-group at CalTech.
+make yes-user-quip
+make machine :pre
+
+make no-user-quip
+make machine :pre
+
+[Supporting info:]
-The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
-C, should give identical or very similar results to pair_style reax,
-which is a ReaxFF implementation on top of a Fortran library, a
-version of which library was originally authored by Adri van Duin.
+src/USER-QUIP: filenames -> commands
+src/USER-QUIP/README
+"pair_style quip"_pair_quip.html
+examples/USER/quip :ul
-The reax/c version should be somewhat faster and more scalable,
-particularly with respect to the charge equilibration calculation. It
-should also be easier to build and use since there are no complicating
-issues with Fortran memory allocation or linking to a Fortran library.
+:line
-For technical details about this implementation of ReaxFF, see
-this paper:
+USER-REAXC package :link(USER-REAXC),h4
-Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
-and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
-S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).
+[Contents:]
-See the doc page for the pair_style reax/c command for details
-of how to use it in LAMMPS.
+A pair style which implements the ReaxFF potential in C/C++ (in
+contrast to the "REAX package"_#REAX and its Fortran library). ReaxFF
+is universal reactive force field. See the src/USER-REAXC/README file
+for more info on differences between the two packages. Also two fixes
+for monitoring molecules as bonds are created and destroyed.
-The person who created this package is Hasan Metin Aktulga (hmaktulga
-at lbl.gov), while at Purdue University. Contact him directly, or
-Aidan Thompson at Sandia (athomps at sandia.gov), if you have
-questions.
+[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
-Examples: examples/reax
+[Install or un-install:]
+
+make yes-user-reaxc
+make machine :pre
+
+make no-user-reaxc
+make machine :pre
+
+[Supporting info:]
+
+src/USER-REAXC: filenames -> commands
+src/USER-REAXC/README
+"pair_style reax/c"_pair_reaxc.html
+"fix reax/c/bonds"_fix_reax_bonds.html
+"fix reax/c/species"_fix_reaxc_species.html
+examples/reax :ul
:line
-USER-SMD package :link(USER-SMD),h5
+USER-SMD package :link(USER-SMD),h4
-Supporting info:
+[Contents:]
-This package implements smoothed Mach dynamics (SMD) in
-LAMMPS. Currently, the package has the following features:
+An atom style, fixes, computes, and several pair styles which
+implements smoothed Mach dynamics (SMD) for solids, which is a model
+related to smoothed particle hydrodynamics (SPH) for liquids (see the
+"USER-SPH package"_#USER-SPH).
-* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)
+This package solves solids mechanics problems via a state of the art
+stabilized meshless method with hourglass control. It can specify
+hydrostatic interactions independently from material strength models,
+i.e. pressure and deviatoric stresses are separated. It provides many
+material models (Johnson-Cook, plasticity with hardening,
+Mie-Grueneisen, Polynomial EOS) and allows new material models to be
+added. It implements rigid boundary conditions (walls) which can be
+specified as surface geometries from *.STL files.
-* Also solves solids mechanics problems via a state of the art
- stabilized meshless method with hourglass control.
+[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
+Dynamics, Ernst Mach Institute, Germany).
-* Can specify hydrostatic interactions independently from material
- strength models, i.e. pressure and deviatoric stresses are separated.
+[Install or un-install:]
-* Many material models available (Johnson-Cook, plasticity with
- hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
- material models.
+Before building LAMMPS with this package, you must first download the
+Eigen library. Eigen is a template library, so you do not need to
+build it, just download it. You can do this manually if you prefer;
+follow the instructions in lib/smd/README. You can also do it in one
+step from the lammps/src dir, using a command like these, which simply
+invoke the lib/smd/Install.py script with the specified args:
-* Rigid boundary conditions (walls) can be loaded as surface geometries
- from *.STL files.
+make lib-smd # print help message
+make lib-smd args="-g -l" # download in default lib/smd/eigen-eigen-*
+make lib-smd args="-h . eigen -g -l" # download in lib/smd/eigen
+make lib-smd args="-h ~ eigen -g -l" # download and build in ~/eigen :pre
-See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.
+Note that the final -l switch is to create a symbolic (soft) link
+named "includelink" in lib/smd to point to the Eigen dir. When LAMMPS
+builds it will use this link. You should not need to edit the
+lib/smd/Makefile.lammps file.
-There are example scripts for using this package in examples/USER/smd.
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
-The person who created this package is Georg Ganzenmuller at the
-Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
-Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
-you have questions.
+make yes-user-smd
+make machine :pre
+
+make no-user-smd
+make machine :pre
+
+[Supporting info:]
-Examples: examples/USER/smd
+src/USER-SMD: filenames -> commands
+src/USER-SMD/README
+doc/PDF/SMD_LAMMPS_userguide.pdf
+examples/USER/smd
+http://lammps.sandia.gov/movies.html#smd :ul
:line
-USER-SMTBQ package :link(USER-SMTBQ),h5
+USER-SMTBQ package :link(USER-SMTBQ),h4
-Supporting info:
+[Contents:]
-This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
-potential for the description of ionocovalent bonds in oxides.
+A pair style which implements a Second Moment Tight Binding model with
+QEq charge equilibration (SMTBQ) potential for the description of
+ionocovalent bonds in oxides.
-There are example scripts for using this package in
-examples/USER/smtbq.
+[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert
+Tetot (LAAS-CNRS, France).
-See this doc page to get started:
+[Install or un-install:]
+
+make yes-user-smtbq
+make machine :pre
+
+make no-user-smtbq
+make machine :pre
+
+[Supporting info:]
+src/USER-SMTBQ: filenames -> commands
+src/USER-SMTBQ/README
"pair_style smtbq"_pair_smtbq.html
+examples/USER/smtbq :ul
-The persons who created the USER-SMTBQ package are Nicolas Salles,
-Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
-these email addresses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact
-them directly if you have any questions.
+:line
-Examples: examples/USER/smtbq
+USER-SPH package :link(USER-SPH),h4
-:line
+[Contents:]
-USER-SPH package :link(USER-SPH),h5
+An atom style, fixes, computes, and several pair styles which
+implements smoothed particle hydrodynamics (SPH) for liquids. See the
+related "USER-SMD package"_#USER-SMD package for smooth Mach dynamics
+(SMD) for solids.
-Supporting info:
+This package contains ideal gas, Lennard-Jones equation of states,
+Tait, and full support for complete (i.e. internal-energy dependent)
+equations of state. It allows for plain or Monaghans XSPH integration
+of the equations of motion. It has options for density continuity or
+density summation to propagate the density field. It has
+"set"_set.html command options to set the internal energy and density
+of particles from the input script and allows the same quantities to
+be output with thermodynamic output or to dump files via the "compute
+property/atom"_compute_property_atom.html command.
-This package implements smoothed particle hydrodynamics (SPH) in
-LAMMPS. Currently, the package has the following features:
+[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
+Dynamics, Ernst Mach Institute, Germany).
-* Tait, ideal gas, Lennard-Jones equation of states, full support for
- complete (i.e. internal-energy dependent) equations of state
+[Install or un-install:]
+
+make yes-user-sph
+make machine :pre
+
+make no-user-sph
+make machine :pre
+
+[Supporting info:]
-* Plain or Monaghans XSPH integration of the equations of motion
+src/USER-SPH: filenames -> commands
+src/USER-SPH/README
+doc/PDF/SPH_LAMMPS_userguide.pdf
+examples/USER/sph
+http://lammps.sandia.gov/movies.html#sph :ul
-* Density continuity or density summation to propagate the density field
+:line
-* Commands to set internal energy and density of particles from the
- input script
+USER-TALLY package :link(USER-TALLY),h4
-* Output commands to access internal energy and density for dumping and
- thermo output
+[Contents:]
-See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.
+Several compute styles that can be called when pairwise interactions
+are calculated to tally information (forces, heat flux, energy,
+stress, etc) about individual interactions.
-There are example scripts for using this package in examples/USER/sph.
+[Author:] Axel Kohlmeyer (Temple U).
-The person who created this package is Georg Ganzenmuller at the
-Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
-Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
-you have questions.
+[Install or un-install:]
+
+make yes-user-tally
+make machine :pre
+
+make no-user-tally
+make machine :pre
+
+[Supporting info:]
-Examples: examples/USER/sph
+src/USER-TALLY: filenames -> commands
+src/USER-TALLY/README
+"compute */tally"_compute_tally.html
+examples/USER/tally :ul
:line
-USER-TALLY package :link(USER-TALLY),h5
+USER-VTK package :link(USER-VTK),h4
-Supporting info:
+[Contents:]
-Examples: examples/USER/tally
+A "dump custom/vtk"_dump_custom_vtk.html command which outputs
+snapshot info in the "VTK format"_vtk, enabling visualization by
+"Paraview"_paraview or other visuzlization packages.
-:line
+:link(vtk,http://www.vtk.org)
+:link(paraview,http://www.paraview.org)
+
+To use this package you must have VTK library available on your
+system.
+
+[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
-USER-VTK package :link(USER-VTK),h5
+[Install or un-install:]
+
+The lib/vtk/Makefile.lammps file has settings for accessing VTK files
+and its library, which are required for LAMMPS to build and link with
+this package. If the settings are not valid for your system, check if
+one of the other lib/vtk/Makefile.lammps.* files is compatible and
+copy it to Makefile.lammps. If none of the provided files work, you
+will need to edit the Makefile.lammps file.
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-user-vtk
+make machine :pre
+
+make no-user-vtk
+make machine :pre
+
+[Supporting info:]
+src/USER-VTK: filenames -> commands
+src/USER-VTK/README
+lib/vtk/README
+"dump custom/vtk"_dump_custom_vtk.html :ul
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index 5a5de9ac9bb8d09d6a84ea42efab7d4059f4b21a..0a7209765e6f9bc2e62d14b020337bae35f72d4e 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -14,12 +14,11 @@ experienced users.
2.1 "What's in the LAMMPS distribution"_#start_1
2.2 "Making LAMMPS"_#start_2
2.3 "Making LAMMPS with optional packages"_#start_3
-2.4 "Building LAMMPS via the Make.py script"_#start_4
-2.5 "Building LAMMPS as a library"_#start_5
-2.6 "Running LAMMPS"_#start_6
-2.7 "Command-line options"_#start_7
-2.8 "Screen output"_#start_8
-2.9 "Tips for users of previous versions"_#start_9 :all(b)
+2.5 "Building LAMMPS as a library"_#start_4
+2.6 "Running LAMMPS"_#start_5
+2.7 "Command-line options"_#start_6
+2.8 "Screen output"_#start_7
+2.9 "Tips for users of previous versions"_#start_8 :all(b)
:line
@@ -80,7 +79,7 @@ This section has the following sub-sections:
Read this first :h5,link(start_2_1)
-If you want to avoid building LAMMPS yourself, read the preceding
+If you want to avoid building LAMMPS yourself, read the preceeding
section about options available for downloading and installing
executables. Details are discussed on the "download"_download page.
@@ -96,7 +95,7 @@ make serial :pre
Note that on a facility supercomputer, there are often "modules"
loaded in your environment that provide the compilers and MPI you
should use. In this case, the "mpicxx" compile/link command in
-Makefile.mpi should just work by accessing those modules.
+Makefile.mpi should simply work by accessing those modules.
It may be the case that one of the other Makefile.machine files in the
src/MAKE sub-directories is a better match to your system (type "make"
@@ -107,33 +106,35 @@ make stampede :pre
If any of these builds (with an existing Makefile.machine) works on
your system, then you're done!
+If you need to install an optional package with a LAMMPS command you
+want to use, and the package does not depend on an extra library, you
+can simply type
+
+make name :pre
+
+before invoking (or re-invoking) the above steps. "Name" is the
+lower-case name of the package, e.g. replica or user-misc.
+
If you want to do one of the following:
-use optional LAMMPS features that require additional libraries
-use optional packages that require additional libraries
-use optional accelerator packages that require special compiler/linker settings
-run on a specialized platform that has its own compilers, settings, or other libs to use :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
-auxiliary libraries exist on your machine or install them if they
-don't. You may need to build additional libraries that are part of
-the LAMMPS package, before building LAMMPS. You may need to edit a
+extra libraries exist on your machine or install them if they don't.
+You may need to build extra libraries that are included in the LAMMPS
+distribution, before building LAMMPS itself. You may need to edit a
Makefile.machine file to make it compatible with your system.
-Note that there is a Make.py tool in the src directory that automates
-several of these steps, but you still have to know what you are doing.
-"Section 2.4"_#start_4 below describes the tool. It is a convenient
-way to work with installing/un-installing various packages, the
-Makefile.machine changes required by some packages, and the auxiliary
-libraries some of them use.
-
Please read the following sections carefully. If you are not
comfortable with makefiles, or building codes on a Unix platform, or
running an MPI job on your machine, please find a local expert to help
-you. Many compilation, linking, and run problems that users have are
-often not really LAMMPS issues - they are peculiar to the user's
-system, compilers, libraries, etc. Such questions are better answered
-by a local expert.
+you. Many compilation, linking, and run problems users experience are
+often not LAMMPS issues - they are peculiar to the user's system,
+compilers, libraries, etc. Such questions are better answered by a
+local expert.
If you have a build problem that you are convinced is a LAMMPS issue
(e.g. the compiler complains about a line of LAMMPS source code), then
@@ -251,7 +252,7 @@ re-compile, after typing "make clean" (which will describe different
clean options).
The LMP_INC variable is used to include options that turn on ifdefs
-within the LAMMPS code. The options that are currently recognized are:
+within the LAMMPS code. The options that are currently recogized are:
-DLAMMPS_GZIP
-DLAMMPS_JPEG
@@ -362,7 +363,7 @@ installed on your platform. If MPI is installed on your system in the
usual place (under /usr/local), you also may not need to specify these
3 variables, assuming /usr/local is in your path. On some large
parallel machines which use "modules" for their compile/link
-environments, you may simply need to include the correct module in
+environements, you may simply need to include the correct module in
your build environment, before building LAMMPS. Or the parallel
machine may have a vendor-provided MPI which the compiler has no
trouble finding.
@@ -430,7 +431,7 @@ use the KISS library described above.
You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
so the compiler and linker can find the needed FFT header and library
files. Note that on some large parallel machines which use "modules"
-for their compile/link environments, you may simply need to include
+for their compile/link environements, you may simply need to include
the correct module in your build environment. Or the parallel machine
may have a vendor-provided FFT library which the compiler has no
trouble finding.
@@ -450,12 +451,13 @@ you must also manually specify the correct library, namely -lsfftw or
The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
use single-precision FFTs with PPPM, which can speed-up long-range
-calculations, particularly in parallel or on GPUs. Fourier transform
+calulations, particularly in parallel or on GPUs. Fourier transform
and related PPPM operations are somewhat insensitive to floating point
truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little
accuracy for reduced memory use and parallel communication costs for
-transposing 3d FFT data.
+transposing 3d FFT data. Note that single precision FFTs have only
+been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
Step 7 :h6
@@ -507,13 +509,13 @@ You should get the executable lmp_foo when the build is complete.
Errors that can occur when making LAMMPS: h5 :link(start_2_3)
-NOTE: If an error occurs when building LAMMPS, the compiler or linker
-will state very explicitly what the problem is. The error message
-should give you a hint as to which of the steps above has failed, and
-what you need to do in order to fix it. Building a code with a
-Makefile is a very logical process. The compiler and linker need to
-find the appropriate files and those files need to be compatible with
-LAMMPS source files. When a make fails, there is usually a very
+If an error occurs when building LAMMPS, the compiler or linker will
+state very explicitly what the problem is. The error message should
+give you a hint as to which of the steps above has failed, and what
+you need to do in order to fix it. Building a code with a Makefile is
+a very logical process. The compiler and linker need to find the
+appropriate files and those files need to be compatible with LAMMPS
+settings and source files. When a make fails, there is usually a very
simple reason, which you or a local expert will need to fix.
Here are two non-obvious errors that can occur:
@@ -556,7 +558,8 @@ Typing "make clean-all" or "make clean-machine" will delete *.o object
files created when LAMMPS is built, for either all builds or for a
particular machine.
-Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
+Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
+-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
As explained above, any of these 3 settings can be specified on the
LMP_INC line in your low-level src/MAKE/Makefile.foo.
@@ -655,11 +658,6 @@ This section has the following sub-sections:
2.3.3 "Packages that require extra libraries"_#start_3_3
2.3.4 "Packages that require Makefile.machine settings"_#start_3_4 :all(b)
-Note that the following "Section 2.4"_#start_4 describes the Make.py
-tool which can be used to install/un-install packages and build the
-auxiliary libraries which some of them use. It can also auto-edit a
-Makefile.machine to add settings needed by some packages.
-
:line
Package basics: :h5,link(start_3_1)
@@ -669,235 +667,221 @@ 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, including specific instructions for building
-LAMMPS with each package, which are covered in a more general manner
+"Section 4"_Section_packages.html in the manual 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.
You can see the list of all packages by typing "make package" from
-within the src directory of the LAMMPS distribution. This also lists
-various make commands that can be used to manipulate packages.
+within the src directory of the LAMMPS distribution. It will also
+list various make commands that can be used to manage packages.
If you use a command in a LAMMPS input script that is part of a
package, you must have built LAMMPS with that package, else you will
get an error that the style is invalid or the command is unknown.
-Every command's doc page specifies if it is part of a package. You can
-also type
+Every command's doc page specfies if it is part of a package. You can
+type
lmp_machine -h :pre
to run your executable with the optional "-h command-line
-switch"_#start_7 for "help", which will simply list the styles and
-commands known to your executable, and immediately exit.
-
-There are two kinds of packages in LAMMPS, standard and user packages.
-More information about the contents of standard and user packages is
-given in "Section 4"_Section_packages.html of the manual. The
-difference between standard and user packages is as follows:
-
-Standard packages, such as molecule or kspace, are supported by the
-LAMMPS developers and are written in a syntax and style consistent
-with the rest of LAMMPS. This means we will answer questions about
-them, debug and fix them if necessary, and keep them compatible with
-future changes to LAMMPS.
-
-User packages, such as user-atc or user-omp, have been contributed by
-users, and always begin with the user prefix. If they are a single
-command (single file), they are typically in the user-misc package.
-Otherwise, they are a set of files grouped together which add a
-specific functionality to the code.
-
-User packages don't necessarily meet the requirements of the standard
-packages. 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 either a standard or user-contributed package are given in
-"this section"_Section_modify.html#mod_15 of the documentation.
+switch"_#start_7 for "help", which will list the styles and commands
+known to your executable, and immediately exit.
:line
Including/excluding packages :h5,link(start_3_2)
-To use (or not use) a package you must include it (or exclude it)
-before building LAMMPS. From the src directory, this is typically as
-simple as:
+To use (or not use) a package you must install it (or un-install it)
+before building LAMMPS. From the src directory, this is as simple as:
make yes-colloid
make mpi :pre
or
-make no-manybody
+make no-user-omp
make mpi :pre
-NOTE: You should NOT include/exclude packages and build LAMMPS in a
+NOTE: You should NOT install/un-install packages and build LAMMPS in a
single make command using multiple targets, e.g. make yes-colloid mpi.
This is because the make procedure creates a list of source files that
will be out-of-date for the build if the package configuration changes
within the same command.
-Some packages have individual files that depend on other packages
-being included. LAMMPS checks for this and does the right thing.
-I.e. individual files are only included if their dependencies are
-already included. Likewise, if a package is excluded, other files
+Any package can be installed or not in a LAMMPS build, independent of
+all other packages. However, some packages include files derived from
+files in other packages. LAMMPS checks for this and does the right
+thing. I.e. individual files are only included if their dependencies
+are already included. Likewise, if a package is excluded, other files
dependent on that package are also excluded.
+NOTE: The one exception is that we do not recommend building with both
+the KOKKOS package installed and any of the other acceleration
+packages (GPU, OPT, USER-INTEL, USER-OMP) also installed. This is
+because of how Kokkos sometimes builds using a wrapper compiler which
+can make it difficult to invoke all the compile/link flags correctly
+for both Kokkos and non-Kokkos files.
+
If you will never run simulations that use the features in a
particular packages, there is no reason to include it in your build.
-For some packages, this will keep you from having to build auxiliary
-libraries (see below), and will also produce a smaller executable
-which may run a bit faster.
-
-When you download a LAMMPS tarball, these packages are pre-installed
-in the src directory: KSPACE, MANYBODY,MOLECULE, because they are so
-commonly used. When you download LAMMPS source files from the SVN or
-Git repositories, no packages are pre-installed.
-
-Packages are included or excluded by typing "make yes-name" or "make
-no-name", where "name" is the name of the package in lower-case, e.g.
-name = kspace for the KSPACE package or name = user-atc for the
-USER-ATC package. You can also type "make yes-standard", "make
-no-standard", "make yes-std", "make no-std", "make yes-user", "make
-no-user", "make yes-lib", "make no-lib", "make yes-all", or "make
-no-all" to include/exclude various sets of packages. Type "make
-package" to see all of the package-related make options.
-
-NOTE: Inclusion/exclusion of a package works by simply moving files
-back and forth between the main src directory and sub-directories with
-the package name (e.g. src/KSPACE, src/USER-ATC), so that the files
-are seen or not seen when LAMMPS is built. After you have included or
-excluded a package, you must re-build LAMMPS.
-
-Additional package-related make options exist to help manage LAMMPS
-files that exist in both the src directory and in package
-sub-directories. You do not normally need to use these commands
-unless you are editing LAMMPS files or have downloaded a patch from
-the LAMMPS WWW site.
-
-Typing "make package-update" or "make pu" will overwrite src files
-with files from the package sub-directories if the package has been
-included. It should be used after a patch is installed, since patches
-only update the files in the package sub-directory, but not the src
-files. Typing "make package-overwrite" will overwrite files in the
-package sub-directories with src files.
+For some packages, this will keep you from having to build extra
+libraries, and will also produce a smaller executable which may run a
+bit faster.
+
+When you download a LAMMPS tarball, three packages are pre-installed
+in the src directory -- KSPACE, MANYBODY, MOLECULE -- because they are
+so commonly used. When you download LAMMPS source files from the SVN
+or Git repositories, no packages are pre-installed.
+
+Packages are installed or un-installed by typing
+
+make yes-name
+make no-name :pre
+
+where "name" is the name of the package in lower-case, e.g. name =
+kspace for the KSPACE package or name = user-atc for the USER-ATC
+package. You can also type any of these commands:
+
+make yes-all | install all packages
+make no-all | un-install all packages
+make yes-standard or make yes-std | install standard packages
+make no-standard or make no-std| un-install standard packages
+make yes-user | install user packages
+make no-user | un-install user packages
+make yes-lib | install packages that require extra libraries
+make no-lib | un-install packages that require extra libraries
+make yes-ext | install packages that require external libraries
+make no-ext | un-install packages that require external libraries :tb(s=|)
+
+which install/un-install various sets of packages. Typing "make
+package" will list all the these commands.
+
+NOTE: Installing or un-installing a package works by simply moving
+files back and forth between the main src directory and
+sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
+so that the files are included or excluded when LAMMPS is built.
+After you have installed or un-installed a package, you must re-build
+LAMMPS for the action to take effect.
+
+The following make commands help manage files that exist in both the
+src directory and in package sub-directories. You do not normally
+need to use these commands unless you are editing LAMMPS files or have
+downloaded a patch from the LAMMPS web site.
Typing "make package-status" or "make ps" will show which packages are
-currently included. For those that are included, it will list any
+currently installed. For those that are installed, it will list any
files that are different in the src directory and package
-sub-directory. Typing "make package-diff" lists all differences
-between these files. Again, type "make package" to see all of the
-package-related make options.
+sub-directory.
-:line
+Typing "make package-update" or "make pu" will overwrite src files
+with files from the package sub-directories if the package is
+installed. It should be used after a patch has been applied, since
+patches only update the files in the package sub-directory, but not
+the src files.
-Packages that require extra libraries :h5,link(start_3_3)
+Typing "make package-overwrite" will overwrite files in the package
+sub-directories with src files.
-A few of the standard and user packages require additional auxiliary
-libraries. Many of them are provided with LAMMPS, in which case they
-must be compiled first, before LAMMPS is built, if you wish to include
-that package. If you get a LAMMPS build error about a missing
-library, this is likely the reason. See the
-"Section 4"_Section_packages.html doc page for a list of
-packages that have these kinds of auxiliary libraries.
-
-The lib directory in the distribution has sub-directories with package
-names that correspond to the needed auxiliary libs, e.g. lib/gpu.
-Each sub-directory has a README file that gives more details. Code
-for most of the auxiliary libraries is included in that directory.
-Examples are the USER-ATC and MEAM packages.
-
-A few of the lib sub-directories do not include code, but do include
-instructions (and sometimes scripts) that automate the process of
-downloading the auxiliary library and installing it so LAMMPS can link
-to it. Examples are the KIM, VORONOI, USER-MOLFILE, and USER-SMD
-packages.
-
-The lib/python directory (for the PYTHON package) contains only a
-choice of Makefile.lammps.* files. This is because no auxiliary code
-or libraries are needed, only the Python library and other system libs
-that should already available on your system. However, the
-Makefile.lammps file is needed to tell LAMMPS which libs to use and
-where to find them.
-
-For libraries with provided code, the sub-directory README file
-(e.g. lib/atc/README) has instructions on how to build that library.
-This information is also summarized in "Section
-4"_Section_packages.html. Typically this is done by typing
-something like:
+Typing "make package-diff" lists all differences between these files.
-make -f Makefile.g++ :pre
-
-If one of the provided Makefiles is not appropriate for your system
-you will need to edit or add one. Note that all the Makefiles have a
-setting for EXTRAMAKE at the top that specifies a Makefile.lammps.*
-file.
-
-If the library build is successful, it will produce 2 files in the lib
-directory:
-
-libpackage.a
-Makefile.lammps :pre
-
-The Makefile.lammps file will typically be a copy of one of the
-Makefile.lammps.* files in the library directory.
-
-Note that you must insure that the settings in Makefile.lammps are
-appropriate for your system. If they are not, the LAMMPS build may
-fail. To fix this, you can edit or create a new Makefile.lammps.*
-file for your system, and copy it to Makefile.lammps.
-
-As explained in the lib/package/README files, the settings in
-Makefile.lammps are used to specify additional system libraries and
-their locations so that LAMMPS can build with the auxiliary library.
-For example, if the MEAM package is used, the auxiliary library
-consists of F90 code, built with a Fortran complier. To link that
-library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS is
-built with, typically requires additional Fortran-to-C libraries be
-included in the link. Another example are the BLAS and LAPACK
-libraries needed to use the USER-ATC or USER-AWPMD packages.
-
-For libraries without provided code, the sub-directory README file has
-information on where to download the library and how to build it,
-e.g. lib/voronoi/README and lib/smd/README. The README files also
-describe how you must either (a) create soft links, via the "ln"
-command, in those directories to point to where you built or installed
-the packages, or (b) check or edit the Makefile.lammps file in the
-same directory to provide that information.
-
-Some of the sub-directories, e.g. lib/voronoi, also have an install.py
-script which can be used to automate the process of
-downloading/building/installing the auxiliary library, and setting the
-needed soft links. Type "python install.py" for further instructions.
-
-As with the sub-directories containing library code, if the soft links
-or settings in the lib/package/Makefile.lammps files are not correct,
-the LAMMPS build will typically fail.
+Again, just type "make package" to see all of the package-related make
+options.
:line
-Packages that require Makefile.machine settings :h5,link(start_3_4)
-
-A few packages require specific settings in Makefile.machine, to
-either build or use the package effectively. These are the
-USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
-code performance on CPUs or other hardware, as discussed in "Section
-5.3"_Section_accelerate.html#acc_3.
+Packages that require extra libraries :h5,link(start_3_3)
-A summary of what Makefile.machine changes are needed for each of
-these packages is given in "Section 4"_Section_packages.html.
-The details are given on the doc pages that describe each of these
-accelerator packages in detail:
+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.
+
+[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.
+
+[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.
+
+[External libraries:]
+
+Packages in the tables "Section 4"_Section_packages.html with an "ext"
+in the last column link to exernal 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"_voronoi. 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.
+
+:link(voronoi,http://math.lbl.gov/voro++)
+
+[Possible errors:]
+
+There are various common errors which can occur when building extra
+libraries or when building LAMMPS with packages that require the extra
+libraries.
+
+If you cannot build the extra library itself successfully, you may
+need to edit or create an appropriate Makefile for your machine, e.g.
+with appropriate compiler or system settings. Provided makefiles are
+typically in the lib/name directory. E.g. see the Makefile.* files in
+lib/gpu.
+
+The LAMMPS build often uses settings in a lib/name/Makefile.lammps
+file which either exists in the LAMMPS distribution or is created or
+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.
+
+[Compiler options needed for accelerator packages:]
+
+Several packages contain code that is optimized for specific hardware,
+e.g. CPU, KNL, or GPU. These are the OPT, GPU, KOKKOS, USER-INTEL,
+and USER-OMP packages. Compiling and linking the source files in
+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:
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)
-You can also look at the following machine Makefiles in
-src/MAKE/OPTIONS, which include the changes. Note that the USER-INTEL
-and KOKKOS packages allow for settings that build LAMMPS for different
-hardware. The USER-INTEL package builds for CPU and the Xeon Phi, the
-KOKKOS package builds for OpenMP, GPUs (Cuda), and the Xeon Phi.
+You can also use or examine the following machine Makefiles in
+src/MAKE/OPTIONS, which include the settings. Note that the
+USER-INTEL and KOKKOS packages can use settings that build LAMMPS for
+different hardware. The USER-INTEL package can be compiled for Intel
+CPUs and KNLs; the KOKKOS package builds for CPUs (OpenMP), GPUs
+(Cuda), and Intel KNLs.
Makefile.intel_cpu
Makefile.intel_phi
@@ -907,127 +891,9 @@ Makefile.kokkos_phi
Makefile.omp
Makefile.opt :ul
-Also note that the Make.py tool, described in the next "Section
-2.4"_#start_4 can automatically add the needed info to an existing
-machine Makefile, using simple command-line arguments.
-
-:line
-
-2.4 Building LAMMPS via the Make.py tool :h4,link(start_4)
-
-The src directory includes a Make.py script, written in Python, which
-can be used to automate various steps of the build process. It is
-particularly useful for working with the accelerator packages, as well
-as other packages which require auxiliary libraries to be built.
-
-The goal of the Make.py tool is to allow any complex multi-step LAMMPS
-build to be performed as a single Make.py command. And you can
-archive the commands, so they can be re-invoked later via the -r
-(redo) switch. If you find some LAMMPS build procedure that can't be
-done in a single Make.py command, let the developers know, and we'll
-see if we can augment the tool.
-
-You can run Make.py from the src directory by typing either:
-
-Make.py -h
-python Make.py -h :pre
-
-which will give you help info about the tool. For the former to work,
-you may need to edit the first line of Make.py to point to your local
-Python. And you may need to insure the script is executable:
-
-chmod +x Make.py :pre
-
-Here are examples of build tasks you can perform with Make.py:
-
-Install/uninstall packages: Make.py -p no-lib kokkos omp intel
-Build specific auxiliary libs: Make.py -a lib-atc lib-meam
-Build libs for all installed packages: Make.py -p cuda gpu -gpu mode=double arch=31 -a lib-all
-Create a Makefile from scratch with compiler and MPI settings: Make.py -m none -cc g++ -mpi mpich -a file
-Augment Makefile.serial with settings for installed packages: Make.py -p intel -intel cpu -m serial -a file
-Add JPG and FFTW support to Makefile.mpi: Make.py -m mpi -jpg -fft fftw -a file
-Build LAMMPS with a parallel make using Makefile.mpi: Make.py -j 16 -m mpi -a exe
-Build LAMMPS and libs it needs using Makefile.serial with accelerator settings: Make.py -p gpu intel -intel cpu -a lib-all file serial :tb(s=:)
-
-The bench and examples directories give Make.py commands that can be
-used to build LAMMPS with the various packages and options needed to
-run all the benchmark and example input scripts. See these files for
-more details:
-
-bench/README
-bench/FERMI/README
-bench/KEPLER/README
-bench/PHI/README
-examples/README
-examples/accelerate/README
-examples/accelerate/make.list :ul
-
-All of the Make.py options and syntax help can be accessed by using
-the "-h" switch.
-
-E.g. typing "Make.py -h" gives
-
-Syntax: Make.py switch args ...
- switches can be listed in any order
- help switch:
- -h prints help and syntax for all other specified switches
- switch for actions:
- -a lib-all, lib-dir, clean, file, exe or machine
- list one or more actions, in any order
- machine is a Makefile.machine suffix, must be last if used
- one-letter switches:
- -d (dir), -j (jmake), -m (makefile), -o (output),
- -p (packages), -r (redo), -s (settings), -v (verbose)
- switches for libs:
- -atc, -awpmd, -colvars, -cuda
- -gpu, -meam, -poems, -qmmm, -reax
- switches for build and makefile options:
- -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png :pre
-
-Using the "-h" switch with other switches and actions gives additional
-info on all the other specified switches or actions. The "-h" can be
-anywhere in the command-line and the other switches do not need their
-arguments. E.g. type "Make.py -h -d -atc -intel" will print:
-
--d dir
- dir = LAMMPS home dir
- if -d not specified, working dir must be lammps/src :pre
-
--atc make=suffix lammps=suffix2
- all args are optional and can be in any order
- make = use Makefile.suffix (def = g++)
- lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile) :pre
-
--intel mode
- mode = cpu or phi (def = cpu)
- build Intel package for CPU or Xeon Phi :pre
-
-Note that Make.py never overwrites an existing Makefile.machine.
-Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
-rename if desired. Likewise it creates an executable named
-src/lmp_auto, which you can rename using the -o switch if desired.
-
-The most recently executed Make.py command is saved in
-src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke
-the last command, or you can save a sequence of one or more Make.py
-commands to a file and invoke the file of commands using "-r". You
-can also label the commands in the file and invoke one or more of them
-by name.
-
-A typical use of Make.py is to start with a valid Makefile.machine for
-your system, that works for a vanilla LAMMPS build, i.e. when optional
-packages are not installed. You can then use Make.py to add various
-settings (FFT, JPG, PNG) to the Makefile.machine as well as change its
-compiler and MPI options. You can also add additional packages to the
-build, as well as build the needed supporting libraries.
-
-You can also use Make.py to create a new Makefile.machine from
-scratch, using the "-m none" switch, if you also specify what compiler
-and MPI options to use, via the "-cc" and "-mpi" switches.
-
:line
-2.5 Building LAMMPS as a library :h4,link(start_5)
+2.4 Building LAMMPS as a library :h4,link(start_4)
LAMMPS can be built as either a static or shared library, which can
then be called from another application or a scripting language. See
@@ -1063,7 +929,7 @@ src/MAKE/Makefile.foo and perform the build in the directory
Obj_shared_foo. This is so that each file can be compiled with the
-fPIC flag which is required for inclusion in a shared library. The
build will create the file liblammps_foo.so which another application
-can link to dynamically. It will also create a soft link liblammps.so,
+can link to dyamically. It will also create a soft link liblammps.so,
which will point to the most recently built shared library. This is
the file the Python wrapper loads by default.
@@ -1149,7 +1015,7 @@ interface and how to extend it for your needs.
:line
-2.6 Running LAMMPS :h4,link(start_6)
+2.5 Running LAMMPS :h4,link(start_5)
By default, LAMMPS runs by reading commands from standard input. Thus
if you run the LAMMPS executable by itself, e.g.
@@ -1281,7 +1147,7 @@ more processors or setup a smaller problem.
:line
-2.7 Command-line options :h4,link(start_7)
+2.6 Command-line options :h4,link(start_6)
At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or a one-or-two
@@ -1415,8 +1281,8 @@ LAMMPS is compiled with CUDA=yes.
numa Nm :pre
This option is only relevant when using pthreads with hwloc support.
-In this case Nm defines the number of NUMA regions (typically sockets)
-on a node which will be utilized by a single MPI rank. By default Nm
+In this case Nm defines the number of NUMA regions (typicaly sockets)
+on a node which will be utilizied by a single MPI rank. By default Nm
= 1. If this option is used the total number of worker-threads per
MPI rank is threads*numa. Currently it is always almost better to
assign at least one MPI rank per NUMA region, and leave numa set to
@@ -1480,7 +1346,7 @@ 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
+To run multiple independent simulatoins 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.
@@ -1711,7 +1577,7 @@ negative numeric value. It is OK if the first value1 starts with a
:line
-2.8 LAMMPS screen output :h4,link(start_8)
+2.7 LAMMPS screen output :h4,link(start_7)
As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
@@ -1759,7 +1625,7 @@ The first section provides a global loop timing summary. The {loop time}
is the total wall time for the section. The {Performance} line is
provided for convenience to help predicting the number of loop
continuations required and for comparing performance with other,
-similar MD codes. The {CPU use} line provides the CPU utilization per
+similar MD codes. The {CPU use} line provides the CPU utilzation per
MPI task; it should be close to 100% times the number of OpenMP
threads (or 1 of no OpenMP). Lower numbers correspond to delays due
to file I/O or insufficient thread utilization.
@@ -1867,7 +1733,7 @@ communication, roughly 75% in the example above.
:line
-2.9 Tips for users of previous LAMMPS versions :h4,link(start_9)
+2.8 Tips for users of previous LAMMPS versions :h4,link(start_8)
The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed
diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt
index e2df706473e178202b1fbb10985cade08dce831f..f82df0d81601eb16d6f0ba578ab6783cc735f7a5 100644
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@@ -24,7 +24,7 @@ twojmax = band limit for bispectrum components (non-negative integer) :l
R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l
w_1, w_2,... = list of neighbor weights, one for each type :l
zero or more keyword/value pairs may be appended :l
-keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} :l
+keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag}:l
{diagonal} value = {0} or {1} or {2} or {3}
{0} = all j1, j2, j <= twojmax, j2 <= j1
{1} = subset satisfying j1 == j2
@@ -36,7 +36,10 @@ keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} :l
{1} = use switching function
{bzeroflag} value = {0} or {1}
{0} = do not subtract B0
- {1} = subtract B0 :pre
+ {1} = subtract B0
+ {quadraticflag} value = {0} or {1}
+ {0} = do not generate quadratic terms
+ {1} = generate quadratic terms :pre
:ule
[Examples:]
@@ -151,7 +154,7 @@ linear mapping from radial distance to polar angle {theta0} on the
The argument {twojmax} and the keyword {diagonal} define which
bispectrum components are generated. See section below on output for a
detailed explanation of the number of bispectrum components and the
-ordered in which they are listed
+ordered in which they are listed.
The keyword {switchflag} can be used to turn off the switching
function.
@@ -162,6 +165,14 @@ the calculated bispectrum components. This optional keyword is only
available for compute {sna/atom}, as {snad/atom} and {snav/atom}
are unaffected by the removal of constant terms.
+The keyword {quadraticflag} determines whether or not the
+quadratic analogs to the bispectrum quantities are generated.
+These are formed by taking the outer product of the vector
+of bispectrum components with itself.
+See section below on output for a
+detailed explanation of the number of quadratic terms and the
+ordered in which they are listed.
+
NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
@@ -180,7 +191,7 @@ command that includes all pairs in the neighbor list.
Compute {sna/atom} calculates a per-atom array, each column
corresponding to a particular bispectrum component. The total number
-of columns and the identities of the bispectrum component contained in
+of columns and the identity of the bispectrum component contained in
each column depend on the values of {twojmax} and {diagonal}, as
described by the following piece of python code:
@@ -213,6 +224,19 @@ block contains six sub-blocks corresponding to the {xx}, {yy}, {zz},
notation. Each of these sub-blocks contains one column for each
bispectrum component, the same as for compute {sna/atom}
+For example, if {K}=30 and ntypes=1, the number of columns in the per-atom
+arrays generated by {sna/atom}, {snad/atom}, and {snav/atom}
+are 30, 90, and 180, respectively. With {quadratic} value=1,
+the numbers of columns are 930, 2790, and 5580, respectively.
+
+If the {quadratic} keyword value is set to 1, then additional
+columns are appended to each per-atom array, corresponding to
+a matrix of quantities that are products of two bispectrum components. If the
+number of bispectrum components is {K}, then the number of matrix elements
+is {K}^2. These are output in subblocks of {K}^2 columns, using the same
+ordering of columns and sub-blocks as was used for the bispectrum
+components.
+
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
@@ -231,7 +255,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Default:]
The optional keyword defaults are {diagonal} = 0, {rmin0} = 0,
-{switchflag} = 1, {bzeroflag} = 0.
+{switchflag} = 1, {bzeroflag} = 1, {quadraticflag} = 0,
:line
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index cb9a5ba74112849fb220344a720ea5e66015fe75..69a00eb473735f9115bae72efb682095675ff4e6 100644
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@@ -7,12 +7,12 @@
:line
dump command :h3
-"dump custom/vtk"_dump_custom_vtk.html command :h3
+"dump vtk"_dump_vtk.html command :h3
"dump h5md"_dump_h5md.html command :h3
+"dump molfile"_dump_molfile.html command :h3
+"dump netcdf"_dump_netcdf.html command :h3
"dump image"_dump_image.html command :h3
"dump movie"_dump_image.html command :h3
-"dump molfile"_dump_molfile.html command :h3
-"dump nc"_dump_nc.html command :h3
[Syntax:]
@@ -20,7 +20,7 @@ dump ID group-ID style N file args :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be dumped :l
-style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {dcd} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} or {h5md} or {image} or {movie} or {molfile} or {local} or {custom} or {custom/gz} or {custom/mpiio} :l
+style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
N = dump every this many timesteps :l
file = name of file to write dump info to :l
args = list of arguments for a particular style :l
@@ -30,33 +30,22 @@ args = list of arguments for a particular style :l
{cfg} args = same as {custom} args, see below
{cfg/gz} args = same as {custom} args, see below
{cfg/mpiio} args = same as {custom} args, see below
+ {custom}, {custom/gz}, {custom/mpiio} args = see below
{dcd} args = none
+ {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page
+ {image} args = discussed on "dump image"_dump_image.html doc page
+ {local} args = see below
+ {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page
+ {movie} args = discussed on "dump image"_dump_image.html doc page
+ {netcdf} args = discussed on "dump netcdf"_dump_netcdf.html doc page
+ {netcdf/mpiio} args = discussed on "dump netcdf"_dump_netcdf.html doc page
+ {vtk} args = same as {custom} args, see below, also "dump vtk"_dump_vtk.html doc page
{xtc} args = none
- {xyz} args = none :pre
- {xyz/gz} args = none :pre
+ {xyz} args = none
+ {xyz/gz} args = none
{xyz/mpiio} args = none :pre
- {custom/vtk} args = similar to custom args below, discussed on "dump custom/vtk"_dump_custom_vtk.html doc page :pre
-
- {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page :pre
-
- {image} args = discussed on "dump image"_dump_image.html doc page :pre
-
- {movie} args = discussed on "dump image"_dump_image.html doc page :pre
-
- {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page
-
- {nc} args = discussed on "dump nc"_dump_nc.html doc page :pre
-
- {local} args = list of local attributes
- possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\]
- index = enumeration of local values
- c_ID = local vector calculated by a compute with ID
- c_ID\[I\] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below)
- f_ID = local vector calculated by a fix with ID
- f_ID\[I\] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below) :pre
-
- {custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes
+{custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes :l
possible attributes = id, mol, proc, procp1, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
@@ -94,6 +83,15 @@ args = list of arguments for a particular style :l
v_name = per-atom vector calculated by an atom-style variable with name
d_name = per-atom floating point vector with name, managed by fix property/atom
i_name = per-atom integer vector with name, managed by fix property/atom :pre
+
+{local} args = list of local attributes :l
+ possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\]
+ index = enumeration of local values
+ c_ID = local vector calculated by a compute with ID
+ c_ID\[I\] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below)
+ f_ID = local vector calculated by a fix with ID
+ f_ID\[I\] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below) :pre
+
:ule
[Examples:]
diff --git a/doc/src/dump_custom_vtk.txt b/doc/src/dump_custom_vtk.txt
deleted file mode 100644
index d4c16193d89f22eb956f0bdcc99b64c6b72ba8b5..0000000000000000000000000000000000000000
--- a/doc/src/dump_custom_vtk.txt
+++ /dev/null
@@ -1,347 +0,0 @@
- "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
-
-dump custom/vtk command :h3
-
-[Syntax:]
-
-dump ID group-ID style N file args :pre
-
-ID = user-assigned name for the dump :ulb,l
-group-ID = ID of the group of atoms to be dumped :l
-style = {custom/vtk} :l
-N = dump every this many timesteps :l
-file = name of file to write dump info to :l
-args = list of arguments for a particular style :l
- {custom/vtk} args = list of atom attributes
- possible attributes = id, mol, proc, procp1, type, element, mass,
- x, y, z, xs, ys, zs, xu, yu, zu,
- xsu, ysu, zsu, ix, iy, iz,
- vx, vy, vz, fx, fy, fz,
- q, mux, muy, muz, mu,
- radius, diameter, omegax, omegay, omegaz,
- angmomx, angmomy, angmomz, tqx, tqy, tqz,
- c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
-
- id = atom ID
- mol = molecule ID
- proc = ID of processor that owns atom
- procp1 = ID+1 of processor that owns atom
- type = atom type
- element = name of atom element, as defined by "dump_modify"_dump_modify.html command
- mass = atom mass
- x,y,z = unscaled atom coordinates
- xs,ys,zs = scaled atom coordinates
- xu,yu,zu = unwrapped atom coordinates
- xsu,ysu,zsu = scaled unwrapped atom coordinates
- ix,iy,iz = box image that the atom is in
- vx,vy,vz = atom velocities
- fx,fy,fz = forces on atoms
- q = atom charge
- mux,muy,muz = orientation of dipole moment of atom
- mu = magnitude of dipole moment of atom
- radius,diameter = radius,diameter of spherical particle
- omegax,omegay,omegaz = angular velocity of spherical particle
- angmomx,angmomy,angmomz = angular momentum of aspherical particle
- tqx,tqy,tqz = torque on finite-size particles
- c_ID = per-atom vector calculated by a compute with ID
- c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
- f_ID = per-atom vector calculated by a fix with ID
- f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
- v_name = per-atom vector calculated by an atom-style variable with name
- d_name = per-atom floating point vector with name, managed by fix property/atom
- i_name = per-atom integer vector with name, managed by fix property/atom :pre
-:ule
-
-[Examples:]
-
-dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
-dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke :pre
-
-The style {custom/vtk} is similar to the "custom"_dump.html style but
-uses the VTK library to write data to VTK simple legacy or XML format
-depending on the filename extension specified. This can be either
-{*.vtk} for the legacy format or {*.vtp} and {*.vtu}, respectively,
-for the XML format; see the "VTK
-homepage"_http://www.vtk.org/VTK/img/file-formats.pdf for a detailed
-description of these formats. Since this naming convention conflicts
-with the way binary output is usually specified (see below),
-"dump_modify binary"_dump_modify.html allows to set the binary
-flag for this dump style explicitly.
-
-[Description:]
-
-Dump a snapshot of atom quantities to one or more files every N
-timesteps in a format readable by the "VTK visualization
-toolkit"_http://www.vtk.org or other visualization tools that use it,
-e.g. "ParaView"_http://www.paraview.org. The timesteps on which dump
-output is written can also be controlled by a variable; see the
-"dump_modify every"_dump_modify.html command for details.
-
-Only information for atoms in the specified group is dumped. The
-"dump_modify thresh and region"_dump_modify.html commands can also
-alter what atoms are included; see details below.
-
-As described below, special characters ("*", "%") in the filename
-determine the kind of output.
-
-IMPORTANT NOTE: Because periodic boundary conditions are enforced only
-on timesteps when neighbor lists are rebuilt, the coordinates of an
-atom written to a dump file may be slightly outside the simulation
-box.
-
-IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html
-option is invoked, the lines of atom information written to dump files
-will be in an indeterminate order for each snapshot. This is even
-true when running on a single processor, if the "atom_modify
-sort"_atom_modify.html option is on, which it is by default. In this
-case atoms are re-ordered periodically during a simulation, due to
-spatial sorting. It is also true when running in parallel, because
-data for a single snapshot is collected from multiple processors, each
-of which owns a subset of the atoms.
-
-For the {custom/vtk} style, sorting is off by default. See the
-"dump_modify"_dump_modify.html doc page for details.
-
-:line
-
-The dimensions of the simulation box are written to a separate file
-for each snapshot (either in legacy VTK or XML format depending on
-the format of the main dump file) with the suffix {_boundingBox}
-appended to the given dump filename.
-
-For an orthogonal simulation box this information is saved as a
-rectilinear grid (legacy .vtk or .vtr XML format).
-
-Triclinic simulation boxes (non-orthogonal) are saved as
-hexahedrons in either legacy .vtk or .vtu XML format.
-
-Style {custom/vtk} allows you to specify a list of atom attributes
-to be written to the dump file for each atom. Possible attributes
-are listed above. In contrast to the {custom} style, the attributes
-are rearranged to ensure correct ordering of vector components
-(except for computes and fixes - these have to be given in the right
-order) and duplicate entries are removed.
-
-You cannot specify a quantity that is not defined for a particular
-simulation - such as {q} for atom style {bond}, since that atom style
-doesn't assign charges. Dumps occur at the very end of a timestep,
-so atom attributes will include effects due to fixes that are applied
-during the timestep. An explanation of the possible dump custom/vtk attributes
-is given below. Since position data is required to write VTK files "x y z"
-do not have to be specified explicitly.
-
-The VTK format uses a single snapshot of the system per file, thus
-a wildcard "*" must be included in the filename, as discussed below.
-Otherwise the dump files will get overwritten with the new snapshot
-each time.
-
-:line
-
-Dumps are performed on timesteps that are a multiple of N (including
-timestep 0) and on the last timestep of a minimization if the
-minimization converges. Note that this means a dump will not be
-performed on the initial timestep after the dump command is invoked,
-if the current timestep is not a multiple of N. This behavior can be
-changed via the "dump_modify first"_dump_modify.html command, which
-can also be useful if the dump command is invoked after a minimization
-ended on an arbitrary timestep. N can be changed between runs by
-using the "dump_modify every"_dump_modify.html command.
-The "dump_modify every"_dump_modify.html command
-also allows a variable to be used to determine the sequence of
-timesteps on which dump files are written. In this mode a dump on the
-first timestep of a run will also not be written unless the
-"dump_modify first"_dump_modify.html command is used.
-
-Dump filenames can contain two wildcard characters. If a "*"
-character appears in the filename, then one file per snapshot is
-written and the "*" character is replaced with the timestep value.
-For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
-tmp.dump20000.vtk, etc. Note that the "dump_modify pad"_dump_modify.html
-command can be used to insure all timestep numbers are the same length
-(e.g. 00010), which can make it easier to read a series of dump files
-in order with some post-processing tools.
-
-If a "%" character appears in the filename, then each of P processors
-writes a portion of the dump file, and the "%" character is replaced
-with the processor ID from 0 to P-1 preceded by an underscore character.
-For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ...
-tmp.dump_P-1.vtp, etc. This creates smaller files and can be a fast
-mode of output on parallel machines that support parallel I/O for output.
-
-By default, P = the number of processors meaning one file per
-processor, but P can be set to a smaller value via the {nfile} or
-{fileper} keywords of the "dump_modify"_dump_modify.html command.
-These options can be the most efficient way of writing out dump files
-when running on large numbers of processors.
-
-For the legacy VTK format "%" is ignored and P = 1, i.e., only
-processor 0 does write files.
-
-Note that using the "*" and "%" characters together can produce a
-large number of small dump files!
-
-If {dump_modify binary} is used, the dump file (or files, if "*" or
-"%" is also used) is written in binary format. A binary dump file
-will be about the same size as a text version, but will typically
-write out much faster.
-
-:line
-
-This section explains the atom attributes that can be specified as
-part of the {custom/vtk} style.
-
-The {id}, {mol}, {proc}, {procp1}, {type}, {element}, {mass}, {vx},
-{vy}, {vz}, {fx}, {fy}, {fz}, {q} attributes are self-explanatory.
-
-{Id} is the atom ID. {Mol} is the molecule ID, included in the data
-file for molecular systems. {Proc} is the ID of the processor (0 to
-Nprocs-1) that currently owns the atom. {Procp1} is the proc ID+1,
-which can be convenient in place of a {type} attribute (1 to Ntypes)
-for coloring atoms in a visualization program. {Type} is the atom
-type (1 to Ntypes). {Element} is typically the chemical name of an
-element, which you must assign to each type via the "dump_modify
-element"_dump_modify.html command. More generally, it can be any
-string you wish to associated with an atom type. {Mass} is the atom
-mass. {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components of
-atom velocity and force and atomic charge.
-
-There are several options for outputting atom coordinates. The {x},
-{y}, {z} attributes write atom coordinates "unscaled", in the
-appropriate distance "units"_units.html (Angstroms, sigma, etc). Use
-{xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size,
-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.
-
-Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
-image flags for each atom. Unwrapped means that if the atom has
-passed thru a periodic boundary one or more times, the value is
-printed for what the coordinate would be if it had not been wrapped
-back into the periodic box. Note that using {xu}, {yu}, {zu} means
-that the coordinate values may be far outside the box bounds printed
-with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using
-{xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by
-the box size. Atoms that have passed through a periodic boundary will
-have the corresponding coordinate increased or decreased by 1.0.
-
-The image flags can be printed directly using the {ix}, {iy}, {iz}
-attributes. For periodic dimensions, they specify which image of the
-simulation box the atom is considered to be in. An image of 0 means
-it is inside the box as defined. A value of 2 means add 2 box lengths
-to get the true value. A value of -1 means subtract 1 box length to
-get the true value. LAMMPS updates these flags as atoms cross
-periodic boundaries during the simulation.
-
-The {mux}, {muy}, {muz} attributes are specific to dipolar systems
-defined with an atom style of {dipole}. They give the orientation of
-the atom's point dipole moment. The {mu} attribute gives the
-magnitude of the atom's dipole moment.
-
-The {radius} and {diameter} attributes are specific to spherical
-particles that have a finite size, such as those defined with an atom
-style of {sphere}.
-
-The {omegax}, {omegay}, and {omegaz} attributes are specific to
-finite-size spherical particles that have an angular velocity. Only
-certain atom styles, such as {sphere} define this quantity.
-
-The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
-finite-size aspherical particles that have an angular momentum. Only
-the {ellipsoid} atom style defines this quantity.
-
-The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that
-can sustain a rotational torque due to interactions with other
-particles.
-
-The {c_ID} and {c_ID\[I\]} attributes allow per-atom vectors or arrays
-calculated by a "compute"_compute.html to be output. The ID in the
-attribute should be replaced by the actual ID of the compute that has
-been defined previously in the input script. See the
-"compute"_compute.html command for details. There are computes for
-calculating the per-atom energy, stress, centro-symmetry parameter,
-and coordination number of individual atoms.
-
-Note that computes which calculate global or local quantities, as
-opposed to per-atom quantities, cannot be output in a dump custom/vtk
-command. Instead, global quantities can be output by the
-"thermo_style custom"_thermo_style.html command, and local quantities
-can be output by the dump local command.
-
-If {c_ID} is used as a attribute, then the per-atom vector calculated
-by the compute is printed. If {c_ID\[I\]} is used, then I must be in
-the range from 1-M, which will print the Ith column of the per-atom
-array with M columns calculated by the compute. See the discussion
-above for how I can be specified with a wildcard asterisk to
-effectively specify multiple values.
-
-The {f_ID} and {f_ID\[I\]} attributes allow vector or array per-atom
-quantities calculated by a "fix"_fix.html to be output. The ID in the
-attribute should be replaced by the actual ID of the fix that has been
-defined previously in the input script. The "fix
-ave/atom"_fix_ave_atom.html command is one that calculates per-atom
-quantities. Since it can time-average per-atom quantities produced by
-any "compute"_compute.html, "fix"_fix.html, or atom-style
-"variable"_variable.html, this allows those time-averaged results to
-be written to a dump file.
-
-If {f_ID} is used as a attribute, then the per-atom vector calculated
-by the fix is printed. If {f_ID\[I\]} is used, then I must be in the
-range from 1-M, which will print the Ith column of the per-atom array
-with M columns calculated by the fix. See the discussion above for
-how I can be specified with a wildcard asterisk to effectively specify
-multiple values.
-
-The {v_name} attribute allows per-atom vectors calculated by a
-"variable"_variable.html to be output. The name in the attribute
-should be replaced by the actual name of the variable that has been
-defined previously in the input script. Only an atom-style variable
-can be referenced, since it is the only style that generates per-atom
-values. Variables of style {atom} can reference individual atom
-attributes, per-atom atom attributes, thermodynamic keywords, or
-invoke other computes, fixes, or variables when they are evaluated, so
-this is a very general means of creating quantities to output to a
-dump file.
-
-The {d_name} and {i_name} attributes allow to output custom per atom
-floating point or integer properties that are managed by
-"fix property/atom"_fix_property_atom.html.
-
-See "Section 10"_Section_modify.html of the manual for information
-on how to add new compute and fix styles to LAMMPS to calculate
-per-atom quantities which could then be output into dump files.
-
-:line
-
-[Restrictions:]
-
-The {custom/vtk} style does not support writing of gzipped dump files.
-
-The {custom/vtk} dump style is part of the USER-VTK package. It is
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
-
-To use this dump style, you also must link to the VTK library. See
-the info in lib/vtk/README and insure the Makefile.lammps file in that
-directory is appropriate for your machine.
-
-The {custom/vtk} dump style neither supports buffering nor custom
-format strings.
-
-[Related commands:]
-
-"dump"_dump.html, "dump image"_dump_image.html,
-"dump_modify"_dump_modify.html, "undump"_undump.html
-
-[Default:]
-
-By default, files are written in ASCII format. If the file extension
-is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.
-
diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt
index d797e633e63adb884ada2147bfdf2e00ac081a92..93c87d85b7a6064140b6cf320199d3cd99114e10 100644
--- a/doc/src/dump_h5md.txt
+++ b/doc/src/dump_h5md.txt
@@ -17,9 +17,7 @@ group-ID = ID of the group of atoms to be imaged :l
h5md = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
N = dump every this many timesteps :l
file.h5 = name of file to write to :l
-args = list of data elements to dump, with their dump "subintervals".
-At least one element must be given and image may only be present if
-position is specified first. :l
+args = list of data elements to dump, with their dump "subintervals"
position options
image
velocity options
@@ -29,15 +27,17 @@ position is specified first. :l
box value = {yes} or {no}
create_group value = {yes} or {no}
author value = quoted string :pre
+:ule
-For the elements {position}, {velocity}, {force} and {species}, one
-may specify a sub-interval to write the data only every N_element
-iterations of the dump (i.e. every N*N_element time steps). This is
-specified by the option
+Note that at least one element must be specified and image may only be
+present if position is specified first.
- every N_element :pre
+For the elements {position}, {velocity}, {force} and {species}, a
+sub-interval may be specified to write the data only every N_element
+iterations of the dump (i.e. every N*N_element time steps). This is
+specified by this option directly following the element declaration:
-that follows directly the element declaration.
+every N_element :pre
:ule
diff --git a/doc/src/dump_nc.txt b/doc/src/dump_nc.txt
deleted file mode 100644
index 0b81ee6a32bdd884ccc15ee4e6d1624bee72ad13..0000000000000000000000000000000000000000
--- a/doc/src/dump_nc.txt
+++ /dev/null
@@ -1,66 +0,0 @@
-"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
-
-dump nc command :h3
-dump nc/mpiio command :h3
-
-[Syntax:]
-
-dump ID group-ID nc N file.nc args
-dump ID group-ID nc/mpiio N file.nc args :pre
-
-ID = user-assigned name for the dump :ulb,l
-group-ID = ID of the group of atoms to be imaged :l
-{nc} or {nc/mpiio} = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
-N = dump every this many timesteps :l
-file.nc = name of file to write to :l
-args = list of per atom data elements to dump, same as for the 'custom' dump style. :l,ule
-
-[Examples:]
-
-dump 1 all nc 100 traj.nc type x y z vx vy vz
-dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press :pre
-
-dump 1 all nc/mpiio 1000 traj.nc id type x y z :pre
-
-[Description:]
-
-Dump a snapshot of atom coordinates every N timesteps in Amber-style
-NetCDF file format. NetCDF files are binary, portable and
-self-describing. This dump style will write only one file on the root
-node. The dump style {nc} uses the "standard NetCDF
-library"_netcdf-home all data is collected on one processor and then
-written to the dump file. Dump style {nc/mpiio} used the "parallel
-NetCDF library"_pnetcdf-home and MPI-IO; it has better performance on
-a larger number of processors. Note that 'nc' outputs all atoms sorted
-by atom tag while 'nc/mpiio' outputs in order of the MPI rank.
-
-In addition to per-atom data, also global (i.e. not per atom, but per
-frame) quantities can be included in the dump file. This can be
-variables, output from computes or fixes data prefixed with v_, c_ and
-f_, respectively. These properties are included via
-"dump_modify"_dump_modify.html {global}.
-
-:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
-:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
-
-:line
-
-[Restrictions:]
-
-The {nc} and {nc/mpiio} dump styles are part of the USER-NC-DUMP
-package. It is only enabled if LAMMPS was built with that
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
-
-:line
-
-[Related commands:]
-
-"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
-
diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e82656698a61860a9b376e2eac19e11f05ec1c8
--- /dev/null
+++ b/doc/src/dump_netcdf.txt
@@ -0,0 +1,82 @@
+"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
+
+dump netcdf command :h3
+dump netcdf/mpiio command :h3
+
+[Syntax:]
+
+dump ID group-ID netcdf N file args
+dump ID group-ID netcdf/mpiio N file args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be imaged :l
+{netcdf} or {netcdf/mpiio} = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
+N = dump every this many timesteps :l
+file = name of file to write dump info to :l
+args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule
+
+[Examples:]
+
+dump 1 all netcdf 100 traj.nc type x y z vx vy vz
+dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press
+dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre
+
+[Description:]
+
+Dump a snapshot of atom coordinates every N timesteps in Amber-style
+NetCDF file format. NetCDF files are binary, portable and
+self-describing. This dump style will write only one file on the root
+node. The dump style {netcdf} uses the "standard NetCDF
+library"_netcdf-home. All data is collected on one processor and then
+written to the dump file. Dump style {netcdf/mpiio} uses the
+"parallel NetCDF library"_pnetcdf-home and MPI-IO to write to the dump
+file in parallel; it has better performance on a larger number of
+processors. Note that style {netcdf} outputs all atoms sorted by atom
+tag while style {netcdf/mpiio} outputs atoms in order of their MPI
+rank.
+
+NetCDF files can be directly visualized via the following tools:
+
+Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and
+all of the above extensions. :ule,b
+
+VMD (http://www.ks.uiuc.edu/Research/vmd/). :l
+
+AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye
+contains a NetCDF reader that is not present in the standard
+distribution of AtomEye. :l,ule
+
+In addition to per-atom data, global data can be included in the dump
+file, which are the kinds of values output by the
+"thermo_style"_thermo_style.html command . See "Section howto
+6.15"_Section_howto.html#howto_15 for an explanation of per-atom
+versus global data. The global output written into the dump file can
+be from computes, fixes, or variables, by prefixing the compute/fix ID
+or variable name with "c_" or "f_" or "v_" respectively, as in the
+example above. These global values are specified via the "dump_modify
+global"_dump_modify.html command.
+
+:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
+:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
+
+:line
+
+[Restrictions:]
+
+The {netcdf} and {netcdf/mpiio} dump styles are part of the
+USER-NETCDF 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.
+
+:line
+
+[Related commands:]
+
+"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
+
diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21502e7f491dd32a774509644ee4b6267f14d259
--- /dev/null
+++ b/doc/src/dump_vtk.txt
@@ -0,0 +1,179 @@
+ "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
+
+dump vtk command :h3
+
+[Syntax:]
+
+dump ID group-ID vtk N file args :pre
+
+ID = user-assigned name for the dump
+group-ID = ID of the group of atoms to be dumped
+vtk = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page)
+N = dump every this many timesteps
+file = name of file to write dump info to
+args = same as arguments for "dump_style custom"_dump.html :ul
+
+[Examples:]
+
+dump dmpvtk all vtk 100 dump*.myforce.vtk id type vx fx
+dump dmpvtp flow vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke :pre
+
+[Description:]
+
+Dump a snapshot of atom quantities to one or more files every N
+timesteps in a format readable by the "VTK visualization
+toolkit"_http://www.vtk.org or other visualization tools that use it,
+e.g. "ParaView"_http://www.paraview.org. The timesteps on which dump
+output is written can also be controlled by a variable; see the
+"dump_modify every"_dump_modify.html command for details.
+
+This dump style is similar to "dump_style custom"_dump.html but uses
+the VTK library to write data to VTK simple legacy or XML format
+depending on the filename extension specified for the dump file. This
+can be either {*.vtk} for the legacy format or {*.vtp} and {*.vtu},
+respectively, for XML format; see the "VTK
+homepage"_http://www.vtk.org/VTK/img/file-formats.pdf for a detailed
+description of these formats. Since this naming convention conflicts
+with the way binary output is usually specified (see below), the
+"dump_modify binary"_dump_modify.html command allows setting of a
+binary option for this dump style explicitly.
+
+Only information for atoms in the specified group is dumped. The
+"dump_modify thresh and region"_dump_modify.html commands can also
+alter what atoms are included; see details below.
+
+As described below, special characters ("*", "%") in the filename
+determine the kind of output.
+
+IMPORTANT NOTE: Because periodic boundary conditions are enforced only
+on timesteps when neighbor lists are rebuilt, the coordinates of an
+atom written to a dump file may be slightly outside the simulation
+box.
+
+IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html option
+is invoked, the lines of atom information written to dump files will
+be in an indeterminate order for each snapshot. This is even true
+when running on a single processor, if the "atom_modify
+sort"_atom_modify.html option is on, which it is by default. In this
+case atoms are re-ordered periodically during a simulation, due to
+spatial sorting. It is also true when running in parallel, because
+data for a single snapshot is collected from multiple processors, each
+of which owns a subset of the atoms.
+
+For the {vtk} style, sorting is off by default. See the
+"dump_modify"_dump_modify.html doc page for details.
+
+:line
+
+The dimensions of the simulation box are written to a separate file
+for each snapshot (either in legacy VTK or XML format depending on the
+format of the main dump file) with the suffix {_boundingBox} appended
+to the given dump filename.
+
+For an orthogonal simulation box this information is saved as a
+rectilinear grid (legacy .vtk or .vtr XML format).
+
+Triclinic simulation boxes (non-orthogonal) are saved as
+hexahedrons in either legacy .vtk or .vtu XML format.
+
+Style {vtk} allows you to specify a list of atom attributes to be
+written to the dump file for each atom. The list of possible attributes
+is the same as for the "dump_style custom"_dump.html command; see
+its doc page for a listing and an explanation of each attribute.
+
+NOTE: Since position data is required to write VTK files the atom
+attributes "x y z" do not have to be specified explicitly; they will
+be included in the dump file regardless. Also, in contrast to the
+{custom} style, the specified {vtk} attributes are rearranged to
+ensure correct ordering of vector components (except for computes and
+fixes - these have to be given in the right order) and duplicate
+entries are removed.
+
+The VTK format uses a single snapshot of the system per file, thus
+a wildcard "*" must be included in the filename, as discussed below.
+Otherwise the dump files will get overwritten with the new snapshot
+each time.
+
+:line
+
+Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges. Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N. This behavior can be
+changed via the "dump_modify first"_dump_modify.html command, which
+can also be useful if the dump command is invoked after a minimization
+ended on an arbitrary timestep. N can be changed between runs by
+using the "dump_modify every"_dump_modify.html command.
+The "dump_modify every"_dump_modify.html command
+also allows a variable to be used to determine the sequence of
+timesteps on which dump files are written. In this mode a dump on the
+first timestep of a run will also not be written unless the
+"dump_modify first"_dump_modify.html command is used.
+
+Dump filenames can contain two wildcard characters. If a "*"
+character appears in the filename, then one file per snapshot is
+written and the "*" character is replaced with the timestep value.
+For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
+tmp.dump20000.vtk, etc. Note that the "dump_modify pad"_dump_modify.html
+command can be used to insure all timestep numbers are the same length
+(e.g. 00010), which can make it easier to read a series of dump files
+in order with some post-processing tools.
+
+If a "%" character appears in the filename, then each of P processors
+writes a portion of the dump file, and the "%" character is replaced
+with the processor ID from 0 to P-1 preceded by an underscore character.
+For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ...
+tmp.dump_P-1.vtp, etc. This creates smaller files and can be a fast
+mode of output on parallel machines that support parallel I/O for output.
+
+By default, P = the number of processors meaning one file per
+processor, but P can be set to a smaller value via the {nfile} or
+{fileper} keywords of the "dump_modify"_dump_modify.html command.
+These options can be the most efficient way of writing out dump files
+when running on large numbers of processors.
+
+For the legacy VTK format "%" is ignored and P = 1, i.e., only
+processor 0 does write files.
+
+Note that using the "*" and "%" characters together can produce a
+large number of small dump files!
+
+If {dump_modify binary} is used, the dump file (or files, if "*" or
+"%" is also used) is written in binary format. A binary dump file
+will be about the same size as a text version, but will typically
+write out much faster.
+
+:line
+
+[Restrictions:]
+
+The {vtk} style does not support writing of gzipped dump files.
+
+The {vtk} dump style is part of the USER-VTK package. It is
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+To use this dump style, you also must link to the VTK library. See
+the info in lib/vtk/README and insure the Makefile.lammps file in that
+directory is appropriate for your machine.
+
+The {vtk} dump style supports neither buffering or custom format
+strings.
+
+[Related commands:]
+
+"dump"_dump.html, "dump image"_dump_image.html,
+"dump_modify"_dump_modify.html, "undump"_undump.html
+
+[Default:]
+
+By default, files are written in ASCII format. If the file extension
+is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.
+
diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt
index 5fcac589bef767f74140feb3bcd0a3503aad9f37..2b14a20c1d062b01fab0d267ac04a6e1524b5e6d 100644
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@@ -87,8 +87,11 @@ the note below about how to include the CMAP energy when performing an
[Restart, fix_modify, output, run start/stop, minimize info:]
-No information about this fix is written to "binary restart
-files"_restart.html.
+This fix writes the list of CMAP crossterms to "binary restart
+files"_restart.html. See the "read_restart"_read_restart.html 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.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the potential "energy" of the CMAP interactions system's
diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt
index 53973cdfb816b78bc86e4c16d6bf5d2ff4fa7074..7ac607a2f1e146e1f24e68cf69797402dbda4044 100644
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@@ -317,7 +317,7 @@ solution is to start a new simulation after the equilibrium density
has been reached.
With some pair_styles, such as "Buckingham"_pair_buck.html,
-"Born-Mayer-Huggins"_pair_born.html and "ReaxFF"_pair_reax_c.html, two
+"Born-Mayer-Huggins"_pair_born.html and "ReaxFF"_pair_reaxc.html, two
atoms placed close to each other may have an arbitrary large, negative
potential energy due to the functional form of the potential. While
these unphysical configurations are inaccessible to typical dynamical
diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt
index f9c8ecde63f64dd3c7ef566445b28c3569edfcf9..22f47668965c0958a3c23172bd09b90ededc0c3c 100644
--- a/doc/src/fix_qeq.txt
+++ b/doc/src/fix_qeq.txt
@@ -74,7 +74,7 @@ NOTE: The "fix qeq/comb"_fix_qeq_comb.html command must still be used
to perform charge equilibration with the "COMB
potential"_pair_comb.html. The "fix qeq/reax"_fix_qeq_reax.html
command can be used to perform charge equilibration with the "ReaxFF
-force field"_pair_reax_c.html, although fix qeq/shielded yields the
+force field"_pair_reaxc.html, although fix qeq/shielded yields the
same results as fix qeq/reax if {Nevery}, {cutoff}, and {tolerance}
are the same. Eventually the fix qeq/reax command will be deprecated.
@@ -116,7 +116,7 @@ the shielded Coulomb is given by equation (13) of the "ReaxFF force
field"_#vanDuin paper. The shielding accounts for charge overlap
between charged particles at small separation. This style is the same
as "fix qeq/reax"_fix_qeq_reax.html, and can be used with "pair_style
-reax/c"_pair_reax_c.html. Only the {chi}, {eta}, and {gamma}
+reax/c"_pair_reaxc.html. Only the {chi}, {eta}, and {gamma}
parameters from the {qfile} file are used. This style solves partial
charges on atoms via the matrix inversion method. A tolerance of
1.0e-6 is usually a good number.
diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt
index 76c95e11173f9337e18c000b2591cda86c3e5fd0..aed043f6c0e93382bf377f07df855560e7da82ab 100644
--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@@ -30,7 +30,7 @@ fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq :pre
Perform the charge equilibration (QEq) method as described in "(Rappe
and Goddard)"_#Rappe2 and formulated in "(Nakano)"_#Nakano2. It is
typically used in conjunction with the ReaxFF force field model as
-implemented in the "pair_style reax/c"_pair_reax_c.html command, but
+implemented in the "pair_style reax/c"_pair_reaxc.html command, but
it can be used with any potential in LAMMPS, so long as it defines and
uses charges on each atom. The "fix qeq/comb"_fix_qeq_comb.html
command should be used to perform charge equilibration with the "COMB
@@ -42,7 +42,7 @@ The QEq method minimizes the electrostatic energy of the system by
adjusting the partial charge on individual atoms based on interactions
with their neighbors. It requires some parameters for each atom type.
If the {params} setting above is the word "reax/c", then these are
-extracted from the "pair_style reax/c"_pair_reax_c.html command and
+extracted from the "pair_style reax/c"_pair_reaxc.html command and
the ReaxFF force field file it reads in. If a file name is specified
for {params}, then the parameters are taken from the specified file
and the file must contain one line for each atom type. The latter
@@ -106,7 +106,7 @@ be used for periodic cell dimensions less than 10 angstroms.
[Related commands:]
-"pair_style reax/c"_pair_reax_c.html
+"pair_style reax/c"_pair_reaxc.html
[Default:] none
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt
index 1fd1b3ca5a18f2db3d1f6054f771ba52f8bdaf3a..d3f108709406fb57eaa263b0290f0cb8dd8a9725 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@@ -28,7 +28,7 @@ fix 1 all reax/c/bonds 100 bonds.reaxc :pre
Write out the bond information computed by the ReaxFF potential
specified by "pair_style reax"_pair_reax.html or "pair_style
-reax/c"_pair_reax_c.html in the exact same format as the original
+reax/c"_pair_reaxc.html in the exact same format as the original
stand-alone ReaxFF code of Adri van Duin. The bond information is
written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0. For time-averaged chemical species analysis,
@@ -80,7 +80,7 @@ reax"_pair_reax.html be invoked. This fix is part of the REAX
package. It is only enabled if LAMMPS was built with that package,
which also requires the REAX library be built and linked with LAMMPS.
The fix reax/c/bonds command requires that the "pair_style
-reax/c"_pair_reax_c.html be invoked. This fix is part of the
+reax/c"_pair_reaxc.html be invoked. This fix is part of the
USER-REAXC package. It is only enabled if LAMMPS was built with that
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info.
@@ -88,6 +88,6 @@ for more info.
[Related commands:]
"pair_style reax"_pair_reax.html, "pair_style
-reax/c"_pair_reax_c.html, "fix reax/c/species"_fix_reaxc_species.html
+reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
[Default:] none
diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt
index 00db91900e1dcb01a032413a742184374465f45a..d43a338a66e776f19b6098b439690b87f97946e1 100644
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@@ -41,7 +41,7 @@ fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH
[Description:]
Write out the chemical species information computed by the ReaxFF
-potential specified by "pair_style reax/c"_pair_reax_c.html.
+potential specified by "pair_style reax/c"_pair_reaxc.html.
Bond-order values (either averaged or instantaneous, depending on
value of {Nrepeat}) are used to determine chemical bonds. Every
{Nfreq} timesteps, chemical species information is written to
@@ -65,7 +65,7 @@ symbol printed for each LAMMPS atom type. The number of symbols must
match the number of LAMMPS atom types and each symbol must consist of
1 or 2 alphanumeric characters. Normally, these symbols should be
chosen to match the chemical identity of each LAMMPS atom type, as
-specified using the "reax/c pair_coeff"_pair_reax_c.html command and
+specified using the "reax/c pair_coeff"_pair_reaxc.html command and
the ReaxFF force field file.
The optional keyword {position} writes center-of-mass positions of
@@ -158,8 +158,8 @@ more instructions on how to use the accelerated styles effectively.
[Restrictions:]
The fix species currently only works with
-"pair_style reax/c"_pair_reax_c.html and it requires that the "pair_style
-reax/c"_pair_reax_c.html be invoked. This fix is part of the
+"pair_style reax/c"_pair_reaxc.html and it requires that the "pair_style
+reax/c"_pair_reaxc.html be invoked. This fix is part of the
USER-REAXC package. It is only enabled if LAMMPS was built with that
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info.
@@ -170,7 +170,7 @@ It should be possible to extend it to other reactive pair_styles (such as
[Related commands:]
-"pair_style reax/c"_pair_reax_c.html, "fix
+"pair_style reax/c"_pair_reaxc.html, "fix
reax/bonds"_fix_reax_bonds.html
[Default:]
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 6c68955bc9f8eeb646a88f7dfd617df4119c8146..b2b42aa7e65b53e842189410c95c2fceb1ad7364 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -469,7 +469,7 @@ pair_peri.html
pair_polymorphic.html
pair_quip.html
pair_reax.html
-pair_reax_c.html
+pair_reaxc.html
pair_resquared.html
pair_sdk.html
pair_smd_hertz.html
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index 7ef54e7f07fbb40222b450a1275884fffb1bbdd3..afef0c4c5f68319427783edee2997faebfd6e32d 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -73,7 +73,7 @@ pair_coeff command to assign parameters for the different type pairs.
NOTE: There are two exceptions to this option to list an individual
pair style multiple times. The first is for pair styles implemented
as Fortran libraries: "pair_style meam"_pair_meam.html and "pair_style
-reax"_pair_reax.html ("pair_style reax/c"_pair_reax_c.html is OK).
+reax"_pair_reax.html ("pair_style reax/c"_pair_reaxc.html is OK).
This is because unlike a C++ class, they can not be instantiated
multiple times, due to the manner in which they were coded in Fortran.
The second is for GPU-enabled pair styles in the GPU package. This is
diff --git a/doc/src/pair_reax.txt b/doc/src/pair_reax.txt
index 7215c12cee671fa775ed1b8d1ba2d8d66bfd112e..1d13f937061c95963165efc936a680ca14415147 100644
--- a/doc/src/pair_reax.txt
+++ b/doc/src/pair_reax.txt
@@ -36,7 +36,7 @@ supplemental information of the following paper:
the most up-to-date version of ReaxFF as of summer 2010.
WARNING: pair style reax is now deprecated and will soon be retired. Users
-should switch to "pair_style reax/c"_pair_reax_c.html. The {reax} style
+should switch to "pair_style reax/c"_pair_reaxc.html. The {reax} style
differs from the {reax/c} style in the lo-level implementation details.
The {reax} style is a
Fortran library, linked to LAMMPS. The {reax/c} style was initially
@@ -82,7 +82,7 @@ be specified.
Two examples using {pair_style reax} are provided in the examples/reax
sub-directory, along with corresponding examples for
-"pair_style reax/c"_pair_reax_c.html. Note that while the energy and force
+"pair_style reax/c"_pair_reaxc.html. Note that while the energy and force
calculated by both of these pair styles match very closely, the
contributions due to the valence angles differ slightly due to
the fact that with {pair_style reax/c} the default value of {thb_cutoff_sq}
@@ -201,7 +201,7 @@ appropriate units if your simulation doesn't use "real" units.
[Related commands:]
-"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reax_c.html,
+"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reaxc.html,
"fix_reax_bonds"_fix_reax_bonds.html
[Default:]
diff --git a/doc/src/pair_reax_c.txt b/doc/src/pair_reaxc.txt
similarity index 96%
rename from doc/src/pair_reax_c.txt
rename to doc/src/pair_reaxc.txt
index c1d719d22ef0276c119047e861ed08c2627356e0..76a8e6fd5c4a2b27e6352f9c6abb53d838bcfc6b 100644
--- a/doc/src/pair_reax_c.txt
+++ b/doc/src/pair_reaxc.txt
@@ -17,6 +17,7 @@ cfile = NULL or name of a control file :ulb,l
zero or more keyword/value pairs may be appended :l
keyword = {checkqeq} or {lgvdw} or {safezone} or {mincap}
{checkqeq} value = {yes} or {no} = whether or not to require qeq/reax fix
+ {enobonds} value = {yes} or {no} = whether or not to tally energy of atoms with no bonds
{lgvdw} value = {yes} or {no} = whether or not to use a low gradient vdW correction
{safezone} = factor used for array allocation
{mincap} = minimum size for array allocation :pre
@@ -127,6 +128,13 @@ recommended value for parameter {thb} is 0.01, which can be set in the
control file. Note: Force field files are different for the original
or lg corrected pair styles, using wrong ffield file generates an error message.
+Using the optional keyword {enobonds} with the value {yes}, the energy
+of atoms with no bonds (i.e. isolated atoms) is included in the total
+potential energy and the per-atom energy of that atom. If the value
+{no} is specified then the energy of atoms with no bonds is set to zero.
+The latter behavior is usual not desired, as it causes discontinuities
+in the potential energy when the bonding of an atom drops to zero.
+
Optional keywords {safezone} and {mincap} are used for allocating
reax/c arrays. Increasing these values can avoid memory problems, such
as segmentation faults and bondchk failed errors, that could occur under
@@ -331,7 +339,7 @@ reax"_pair_reax.html
[Default:]
-The keyword defaults are checkqeq = yes, lgvdw = no, safezone = 1.2,
+The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no, safezone = 1.2,
mincap = 50.
:line
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 8694747dad5d9a5a40a4ef74f9699d15abd7e4f2..0898906e7ce4c8156c8a0caaae5cb2f225c162b8 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -73,7 +73,7 @@ Pair Styles :h1
pair_polymorphic
pair_quip
pair_reax
- pair_reax_c
+ pair_reaxc
pair_resquared
pair_sdk
pair_smd_hertz
diff --git a/examples/USER/flow_gauss/README b/examples/USER/misc/flow_gauss/README
similarity index 100%
rename from examples/USER/flow_gauss/README
rename to examples/USER/misc/flow_gauss/README
diff --git a/examples/USER/flow_gauss/in.GD b/examples/USER/misc/flow_gauss/in.GD
similarity index 100%
rename from examples/USER/flow_gauss/in.GD
rename to examples/USER/misc/flow_gauss/in.GD
diff --git a/examples/mscg/log.31Mar17.g++.1 b/examples/mscg/log.31Mar17.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..c67bc483db3976b52b18c5f04fd129387d1cab11
--- /dev/null
+++ b/examples/mscg/log.31Mar17.g++.1
@@ -0,0 +1,145 @@
+LAMMPS (13 Apr 2017)
+units real
+atom_style full
+pair_style zero 10.0
+
+read_data data.meoh
+ orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+ 0 = max # of 1-2 neighbors
+ 0 = max # of 1-3 neighbors
+ 0 = max # of 1-4 neighbors
+ 1 = max # of special neighbors
+pair_coeff * *
+
+thermo 1
+thermo_style custom step
+
+# Test 1a: range finder functionality
+fix 1 all mscg 1 range on
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6, bins = 7 7 7
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.794 | 5.794 | 5.794 Mbytes
+Step
+ 0
+ 250
+ 500
+ 750
+ 1000
+ 1250
+ 1500
+ 1750
+ 2000
+ 2250
+ 2500
+ 2750
+ 3000
+ 3250
+ 3500
+ 3750
+ 4000
+ 4250
+ 4500
+Loop time of 0.581537 on 1 procs for 19 steps with 1000 atoms
+
+Performance: 2.823 ns/day, 8.502 hours/ns, 32.672 timesteps/s
+99.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Bond | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.5815 | | |100.00
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2934 ave 2934 max 2934 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 50654 ave 50654 max 50654 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 50654
+Ave neighs/atom = 50.654
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_1a mscg range finder"
+TEST_1a mscg range finder
+unfix 1
+
+# Test 1b: force matching functionality
+fix 1 all mscg 1
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+Per MPI rank memory allocation (min/avg/max) = 5.794 | 5.794 | 5.794 Mbytes
+Step
+ 0
+ 250
+ 500
+ 750
+ 1000
+ 1250
+ 1500
+ 1750
+ 2000
+ 2250
+ 2500
+ 2750
+ 3000
+ 3250
+ 3500
+ 3750
+ 4000
+ 4250
+ 4500
+Loop time of 0.841917 on 1 procs for 19 steps with 1000 atoms
+
+Performance: 1.950 ns/day, 12.309 hours/ns, 22.568 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Bond | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.8419 | | |100.00
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2934 ave 2934 max 2934 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 50654 ave 50654 max 50654 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 50654
+Ave neighs/atom = 50.654
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_1b mscg force matching"
+TEST_1b mscg force matching
+
+print TEST_DONE
+TEST_DONE
+Total wall time: 0:00:01
diff --git a/lib/Install.py b/lib/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..18b426f9282819ce196b6cf030aef477e3769d66
--- /dev/null
+++ b/lib/Install.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+# install.py tool to do a generic build of a library
+# soft linked to by many of the lib/Install.py files
+# used to automate the steps described in the corresponding lib/README
+
+import sys,commands,os
+
+# help message
+
+help = """
+Syntax: python Install.py -m machine -e suffix
+ specify -m and optionally -e, order does not matter
+ -m = peform a clean followed by "make -f Makefile.machine"
+ machine = suffix of a lib/Makefile.* file
+ -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
+ does not alter existing Makefile.machine
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+machine = None
+extraflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ if iarg+2 > nargs: error()
+ machine = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-e":
+ if iarg+2 > nargs: error()
+ extraflag = 1
+ suffix = args[iarg+1]
+ iarg += 2
+ else: error()
+
+# set lib from working dir
+
+cwd = os.getcwd()
+lib = os.path.basename(cwd)
+
+# create Makefile.auto as copy of Makefile.machine
+# reset EXTRAMAKE if requested
+
+if not os.path.exists("Makefile.%s" % machine):
+ error("lib/%s/Makefile.%s does not exist" % (lib,machine))
+
+lines = open("Makefile.%s" % machine,'r').readlines()
+fp = open("Makefile.auto",'w')
+
+for line in lines:
+ words = line.split()
+ if len(words) == 3 and extraflag and \
+ words[0] == "EXTRAMAKE" and words[1] == '=':
+ line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+ print >>fp,line,
+
+fp.close()
+
+# make the library via Makefile.auto
+
+print "Building lib%s.a ..." % lib
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+txt = commands.getoutput(cmd)
+print txt
+
+if os.path.exists("lib%s.a" % lib): print "Build was successful"
+else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
+if not os.path.exists("Makefile.lammps"):
+ print "lib/%s/Makefile.lammps was NOT created" % lib
diff --git a/lib/README b/lib/README
index 72ebb0a5f7543c1c3ec3ead1c601e6b9aec69262..3c8f46dd0a957162660045fc76caeafceb03adec 100644
--- a/lib/README
+++ b/lib/README
@@ -33,14 +33,16 @@ kokkos Kokkos package for GPU and many-core acceleration
from Kokkos development team (Sandia)
linalg set of BLAS and LAPACK routines needed by USER-ATC package
from Axel Kohlmeyer (Temple U)
-poems POEMS rigid-body integration package, POEMS package
- from Rudranarayan Mukherjee (RPI)
meam modified embedded atom method (MEAM) potential, MEAM package
from Greg Wagner (Sandia)
molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package
from Axel Kohlmeyer (Temple U) and the VMD development team
mscg hooks to the MSCG library, used by fix_mscg command
from Jacob Wagner and Greg Voth group (U Chicago)
+netcdf hooks to a NetCDF library installed on your system
+ from Lars Pastewka (Karlsruhe Institute of Technology)
+poems POEMS rigid-body integration package, POEMS package
+ from Rudranarayan Mukherjee (RPI)
python hooks to the system Python library, used by the PYTHON package
from the LAMMPS development team
qmmm quantum mechanics/molecular mechanics coupling interface
diff --git a/lib/atc/Install.py b/lib/atc/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..18b426f9282819ce196b6cf030aef477e3769d66
--- /dev/null
+++ b/lib/atc/Install.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+# install.py tool to do a generic build of a library
+# soft linked to by many of the lib/Install.py files
+# used to automate the steps described in the corresponding lib/README
+
+import sys,commands,os
+
+# help message
+
+help = """
+Syntax: python Install.py -m machine -e suffix
+ specify -m and optionally -e, order does not matter
+ -m = peform a clean followed by "make -f Makefile.machine"
+ machine = suffix of a lib/Makefile.* file
+ -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
+ does not alter existing Makefile.machine
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+machine = None
+extraflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ if iarg+2 > nargs: error()
+ machine = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-e":
+ if iarg+2 > nargs: error()
+ extraflag = 1
+ suffix = args[iarg+1]
+ iarg += 2
+ else: error()
+
+# set lib from working dir
+
+cwd = os.getcwd()
+lib = os.path.basename(cwd)
+
+# create Makefile.auto as copy of Makefile.machine
+# reset EXTRAMAKE if requested
+
+if not os.path.exists("Makefile.%s" % machine):
+ error("lib/%s/Makefile.%s does not exist" % (lib,machine))
+
+lines = open("Makefile.%s" % machine,'r').readlines()
+fp = open("Makefile.auto",'w')
+
+for line in lines:
+ words = line.split()
+ if len(words) == 3 and extraflag and \
+ words[0] == "EXTRAMAKE" and words[1] == '=':
+ line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+ print >>fp,line,
+
+fp.close()
+
+# make the library via Makefile.auto
+
+print "Building lib%s.a ..." % lib
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+txt = commands.getoutput(cmd)
+print txt
+
+if os.path.exists("lib%s.a" % lib): print "Build was successful"
+else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
+if not os.path.exists("Makefile.lammps"):
+ print "lib/%s/Makefile.lammps was NOT created" % lib
diff --git a/lib/atc/README b/lib/atc/README
index 106c303dd14fc8a2a3885de4688b3d390a4a1d17..d3adfdafe4493c8c443ad78d953d9fc2a2286299 100644
--- a/lib/atc/README
+++ b/lib/atc/README
@@ -15,6 +15,11 @@ links against when using the USER-ATC package.
This library must be built with a C++ compiler, before LAMMPS is
built, so LAMMPS can link against it.
+You can type "make lib-atc" from the src directory to see help on how
+to build this library via make commands, or you can do the same thing
+by typing "python Install.py" from within this directory, or you can
+do it manually by following the instructions below.
+
Build the library using one of the provided Makefile.* files or create
your own, specific to your compiler and system. For example:
@@ -44,16 +49,16 @@ user-atc_SYSINC = leave blank for this package
user-atc_SYSLIB = BLAS and LAPACK libraries needed by this package
user-atc_SYSPATH = path(s) to where those libraries are
-You have several choices for these settings:
+You have 3 choices for these settings:
-If the 2 libraries are already installed on your system, the settings
-in Makefile.lammps.installed should work.
+a) If the 2 libraries are already installed on your system, the
+settings in Makefile.lammps.installed should work.
-If they are not, you can install them yourself, and speficy the
-appropriate settings accordingly.
+b) If they are not, you can install them yourself, and specify the
+appropriate settings accordingly in a Makefile.lammps.* file
+and set the EXTRAMAKE setting in Makefile.* to that file.
-If you want to use the minimalist version of these libraries provided
-with LAMMPS in lib/linalg, then the settings in Makefile.lammps.linalg
-should work. Note that in this case you also need to build the
-linear-algebra in lib/linalg; see the lib/linalg/README for more
-details.
+c) Use the minimalist version of these libraries provided with LAMMPS
+in lib/linalg, by using Makefile.lammps.linalg. In this case you also
+need to build the library in lib/linalg; see the lib/linalg/README
+file for more details.
diff --git a/lib/awpmd/Install.py b/lib/awpmd/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..18b426f9282819ce196b6cf030aef477e3769d66
--- /dev/null
+++ b/lib/awpmd/Install.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+# install.py tool to do a generic build of a library
+# soft linked to by many of the lib/Install.py files
+# used to automate the steps described in the corresponding lib/README
+
+import sys,commands,os
+
+# help message
+
+help = """
+Syntax: python Install.py -m machine -e suffix
+ specify -m and optionally -e, order does not matter
+ -m = peform a clean followed by "make -f Makefile.machine"
+ machine = suffix of a lib/Makefile.* file
+ -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
+ does not alter existing Makefile.machine
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+machine = None
+extraflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ if iarg+2 > nargs: error()
+ machine = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-e":
+ if iarg+2 > nargs: error()
+ extraflag = 1
+ suffix = args[iarg+1]
+ iarg += 2
+ else: error()
+
+# set lib from working dir
+
+cwd = os.getcwd()
+lib = os.path.basename(cwd)
+
+# create Makefile.auto as copy of Makefile.machine
+# reset EXTRAMAKE if requested
+
+if not os.path.exists("Makefile.%s" % machine):
+ error("lib/%s/Makefile.%s does not exist" % (lib,machine))
+
+lines = open("Makefile.%s" % machine,'r').readlines()
+fp = open("Makefile.auto",'w')
+
+for line in lines:
+ words = line.split()
+ if len(words) == 3 and extraflag and \
+ words[0] == "EXTRAMAKE" and words[1] == '=':
+ line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+ print >>fp,line,
+
+fp.close()
+
+# make the library via Makefile.auto
+
+print "Building lib%s.a ..." % lib
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+txt = commands.getoutput(cmd)
+print txt
+
+if os.path.exists("lib%s.a" % lib): print "Build was successful"
+else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
+if not os.path.exists("Makefile.lammps"):
+ print "lib/%s/Makefile.lammps was NOT created" % lib
diff --git a/lib/awpmd/README b/lib/awpmd/README
index 3c02480419643f572700f2b54c66c3eeed33f6d2..20e142f74c0fe3bb7375225baeb91b21b0f3636a 100644
--- a/lib/awpmd/README
+++ b/lib/awpmd/README
@@ -19,6 +19,11 @@ links against when using the USER-AWPMD package.
This library must be built with a C++ compiler, before LAMMPS is
built, so LAMMPS can link against it.
+You can type "make lib-awpmd" from the src directory to see help on
+how to build this library via make commands, or you can do the same
+thing by typing "python Install.py" from within this directory, or you
+can do it manually by following the instructions below.
+
Build the library using one of the provided Makefile.* files or create
your own, specific to your compiler and system. For example:
@@ -47,16 +52,16 @@ user-awpmd_SYSINC = leave blank for this package
user-awpmd_SYSLIB = BLAS and LAPACK libraries needed by this package
user-awpmd_SYSPATH = path(s) to where those libraries are
-You have several choices for these settings:
+You have 3 choices for these settings:
-If the 2 libraries are already installed on your system, the settings
-in Makefile.lammps.installed should work.
+a) If the 2 libraries are already installed on your system, the
+settings in Makefile.lammps.installed should work.
-If they are not, you can install them yourself, and speficy the
-appropriate settings accordingly.
+b) If they are not, you can install them yourself, and specify the
+appropriate settings accordingly in a Makefile.lammps.* file
+and set the EXTRAMAKE setting in Makefile.* to that file.
-If you want to use the minimalist version of these libraries provided
-with LAMMPS in lib/linalg, then the settings in Makefile.lammps.linalg
-should work. Note that in this case you also need to build the
-linear-algebra in lib/linalg; see the lib/linalg/README for more
-details.
+c) Use the minimalist version of these libraries provided with LAMMPS
+in lib/linalg, by using Makefile.lammps.linalg. In this case you also
+need to build the library in lib/linalg; see the lib/linalg/README
+file for more details.
diff --git a/lib/colvars/Install.py b/lib/colvars/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..18b426f9282819ce196b6cf030aef477e3769d66
--- /dev/null
+++ b/lib/colvars/Install.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+# install.py tool to do a generic build of a library
+# soft linked to by many of the lib/Install.py files
+# used to automate the steps described in the corresponding lib/README
+
+import sys,commands,os
+
+# help message
+
+help = """
+Syntax: python Install.py -m machine -e suffix
+ specify -m and optionally -e, order does not matter
+ -m = peform a clean followed by "make -f Makefile.machine"
+ machine = suffix of a lib/Makefile.* file
+ -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
+ does not alter existing Makefile.machine
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+machine = None
+extraflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ if iarg+2 > nargs: error()
+ machine = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-e":
+ if iarg+2 > nargs: error()
+ extraflag = 1
+ suffix = args[iarg+1]
+ iarg += 2
+ else: error()
+
+# set lib from working dir
+
+cwd = os.getcwd()
+lib = os.path.basename(cwd)
+
+# create Makefile.auto as copy of Makefile.machine
+# reset EXTRAMAKE if requested
+
+if not os.path.exists("Makefile.%s" % machine):
+ error("lib/%s/Makefile.%s does not exist" % (lib,machine))
+
+lines = open("Makefile.%s" % machine,'r').readlines()
+fp = open("Makefile.auto",'w')
+
+for line in lines:
+ words = line.split()
+ if len(words) == 3 and extraflag and \
+ words[0] == "EXTRAMAKE" and words[1] == '=':
+ line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+ print >>fp,line,
+
+fp.close()
+
+# make the library via Makefile.auto
+
+print "Building lib%s.a ..." % lib
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+txt = commands.getoutput(cmd)
+print txt
+
+if os.path.exists("lib%s.a" % lib): print "Build was successful"
+else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
+if not os.path.exists("Makefile.lammps"):
+ print "lib/%s/Makefile.lammps was NOT created" % lib
diff --git a/lib/colvars/README b/lib/colvars/README
index d6efc333a59a55c04bbcdc0ee3829ed793cae442..a5e5938b20ea4c11f148a14a09d7557a8e3236f8 100644
--- a/lib/colvars/README
+++ b/lib/colvars/README
@@ -35,6 +35,11 @@ links against when using the USER-COLVARS package.
This library must be built with a C++ compiler, before LAMMPS is
built, so LAMMPS can link against it.
+You can type "make lib-colvars" from the src directory to see help on
+how to build this library via make commands, or you can do the same
+thing by typing "python Install.py" from within this directory, or you
+can do it manually by following the instructions below.
+
Build the library using one of the provided Makefile.* files or create
your own, specific to your compiler and system. For example:
diff --git a/lib/gpu/Install.py b/lib/gpu/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..d396be5e1a00fdbc296d711faaafbd46a3e3a811
--- /dev/null
+++ b/lib/gpu/Install.py
@@ -0,0 +1,146 @@
+#!/usr/bin/env python
+
+# Install.py tool to build the GPU library
+# used to automate the steps described in the README file in this dir
+
+import sys,os,re,commands
+
+# help message
+
+help = """
+Syntax: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix
+ specify one or more options, order does not matter
+ copies an existing Makefile.isuffix in lib/gpu to Makefile.auto
+ optionally edits these variables in Makefile.auto:
+ CUDA_HOME, CUDA_ARCH, CUDA_PRECISION, EXTRAMAKE
+ optionally uses Makefile.auto to build the GPU library -> libgpu.a
+ and to copy a Makefile.lammps.esuffix -> Makefile.lammps
+ optionally copies Makefile.auto to a new Makefile.osuffix
+
+ -i = use Makefile.isuffix as starting point, copy to Makefile.auto
+ default isuffix = linux
+ -h = set CUDA_HOME variable in Makefile.auto to hdir
+ hdir = path to NVIDIA Cuda software, e.g. /usr/local/cuda
+ -a = set CUDA_ARCH variable in Makefile.auto to arch
+ use arch = ?? for K40 (Tesla)
+ use arch = 37 for dual K80 (Tesla)
+ use arch = 60 for P100 (Pascal)
+ -p = set CUDA_PRECISION variable in Makefile.auto to precision
+ use precision = double or mixed or single
+ -e = set EXTRAMAKE variable in Makefile.auto to Makefile.lammps.esuffix
+ -m = make the GPU library using Makefile.auto
+ first performs a "make clean"
+ produces libgpu.a if successful
+ also copies EXTRAMAKE file -> Makefile.lammps
+ -e can set which Makefile.lammps.esuffix file is copied
+ -o = copy final Makefile.auto to Makefile.osuffix
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+isuffix = "linux"
+hflag = aflag = pflag = eflag = 0
+makeflag = 0
+outflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-i":
+ if iarg+2 > nargs: error()
+ isuffix = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-h":
+ if iarg+2 > nargs: error()
+ hflag = 1
+ hdir = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-a":
+ if iarg+2 > nargs: error()
+ aflag = 1
+ arch = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-p":
+ if iarg+2 > nargs: error()
+ pflag = 1
+ precision = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-e":
+ if iarg+2 > nargs: error()
+ eflag = 1
+ lmpsuffix = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-m":
+ makeflag = 1
+ iarg += 1
+ elif args[iarg] == "-o":
+ if iarg+2 > nargs: error()
+ outflag = 1
+ osuffix = args[iarg+1]
+ iarg += 2
+ else: error()
+
+if pflag:
+ if precision == "double": precstr = "-D_DOUBLE_DOUBLE"
+ elif precision == "mixed": precstr = "-D_SINGLE_DOUBLE"
+ elif precision == "single": precstr = "-D_SINGLE_SINGLE"
+ else: error("Invalid precision setting")
+
+# create Makefile.auto
+# reset EXTRAMAKE, CUDA_HOME, CUDA_ARCH, CUDA_PRECISION if requested
+
+if not os.path.exists("Makefile.%s" % isuffix):
+ error("lib/gpu/Makefile.%s does not exist" % isuffix)
+
+lines = open("Makefile.%s" % isuffix,'r').readlines()
+fp = open("Makefile.auto",'w')
+
+for line in lines:
+ words = line.split()
+ if len(words) != 3:
+ print >>fp,line,
+ continue
+
+ if hflag and words[0] == "CUDA_HOME" and words[1] == '=':
+ line = line.replace(words[2],hdir)
+ if aflag and words[0] == "CUDA_ARCH" and words[1] == '=':
+ line = line.replace(words[2],"-arch=sm_%s" % arch)
+ if pflag and words[0] == "CUDA_PRECISION" and words[1] == '=':
+ line = line.replace(words[2],precstr)
+ if eflag and words[0] == "EXTRAMAKE" and words[1] == '=':
+ line = line.replace(words[2],"Makefile.lammps.%s" % lmpsuffix)
+
+ print >>fp,line,
+
+fp.close()
+
+# perform make
+# make operations copies EXTRAMAKE file to Makefile.lammps
+
+if makeflag:
+ print "Building libgpu.a ..."
+ cmd = "rm -f libgpu.a"
+ commands.getoutput(cmd)
+ cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+ commands.getoutput(cmd)
+ if not os.path.exists("libgpu.a"):
+ error("Build of lib/gpu/libgpu.a was NOT successful")
+ if not os.path.exists("Makefile.lammps"):
+ error("lib/gpu/Makefile.lammps was NOT created")
+
+# copy new Makefile.auto to Makefile.osuffix
+
+if outflag:
+ print "Creating new Makefile.%s" % osuffix
+ cmd = "cp Makefile.auto Makefile.%s" % osuffix
+ commands.getoutput(cmd)
diff --git a/lib/gpu/README b/lib/gpu/README
index 45c8ce49ba675b92f1be2f804a72e218fc8cce2a..b26897e885379c95eb8cda4b69850dad70879dff 100644
--- a/lib/gpu/README
+++ b/lib/gpu/README
@@ -17,6 +17,11 @@ links against when using the GPU package.
This library must be built with a C++ compiler, before LAMMPS is
built, so LAMMPS can link against it.
+You can type "make lib-gpu" from the src directory to see help on how
+to build this library via make commands, or you can do the same thing
+by typing "python Install.py" from within this directory, or you can
+do it manually by following the instructions below.
+
Build the library using one of the provided Makefile.* files or create
your own, specific to your compiler and system. For example:
@@ -164,9 +169,9 @@ this directory).
The gpu library supports 3 precision modes as determined by
the CUDA_PRECISION variable:
- CUDA_PREC = -D_SINGLE_SINGLE # Single precision for all calculations
- CUDA_PREC = -D_DOUBLE_DOUBLE # Double precision for all calculations
- CUDA_PREC = -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
+ CUDA_PRECISION = -D_SINGLE_SINGLE # Single precision for all calculations
+ CUDA_PRECISION = -D_DOUBLE_DOUBLE # Double precision for all calculations
+ CUDA_PRECISION = -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
NOTE: PPPM acceleration can only be run on GPUs with compute capability>=1.1.
You will get the error "GPU library not compiled for this accelerator."
diff --git a/lib/h5md/Install.py b/lib/h5md/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..18b426f9282819ce196b6cf030aef477e3769d66
--- /dev/null
+++ b/lib/h5md/Install.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+# install.py tool to do a generic build of a library
+# soft linked to by many of the lib/Install.py files
+# used to automate the steps described in the corresponding lib/README
+
+import sys,commands,os
+
+# help message
+
+help = """
+Syntax: python Install.py -m machine -e suffix
+ specify -m and optionally -e, order does not matter
+ -m = peform a clean followed by "make -f Makefile.machine"
+ machine = suffix of a lib/Makefile.* file
+ -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
+ does not alter existing Makefile.machine
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+machine = None
+extraflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ if iarg+2 > nargs: error()
+ machine = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-e":
+ if iarg+2 > nargs: error()
+ extraflag = 1
+ suffix = args[iarg+1]
+ iarg += 2
+ else: error()
+
+# set lib from working dir
+
+cwd = os.getcwd()
+lib = os.path.basename(cwd)
+
+# create Makefile.auto as copy of Makefile.machine
+# reset EXTRAMAKE if requested
+
+if not os.path.exists("Makefile.%s" % machine):
+ error("lib/%s/Makefile.%s does not exist" % (lib,machine))
+
+lines = open("Makefile.%s" % machine,'r').readlines()
+fp = open("Makefile.auto",'w')
+
+for line in lines:
+ words = line.split()
+ if len(words) == 3 and extraflag and \
+ words[0] == "EXTRAMAKE" and words[1] == '=':
+ line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+ print >>fp,line,
+
+fp.close()
+
+# make the library via Makefile.auto
+
+print "Building lib%s.a ..." % lib
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+txt = commands.getoutput(cmd)
+print txt
+
+if os.path.exists("lib%s.a" % lib): print "Build was successful"
+else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
+if not os.path.exists("Makefile.lammps"):
+ print "lib/%s/Makefile.lammps was NOT created" % lib
diff --git a/lib/h5md/Makefile b/lib/h5md/Makefile.h5cc
similarity index 95%
rename from lib/h5md/Makefile
rename to lib/h5md/Makefile.h5cc
index 085d21ff69c4e4c0502361be2e716c4b5ed6db9d..bd3e8a978432448a446d415ccfc7a062e0390f22 100644
--- a/lib/h5md/Makefile
+++ b/lib/h5md/Makefile.h5cc
@@ -19,7 +19,7 @@ build/ch5md.o: src/ch5md.c | build
$(CC) $(INC) $(CFLAGS) -c $< -o $@
Makefile.lammps:
- cp Makefile.lammps.empty $@
+ cp $(EXTRAMAKE) $@
.PHONY: all lib clean
diff --git a/lib/h5md/README b/lib/h5md/README
index 62a4979cba6bc5b5853723481cfdb2ef19937791..fb7d82bfccc3dc993adb2cd39cae00cb52273944 100644
--- a/lib/h5md/README
+++ b/lib/h5md/README
@@ -3,6 +3,11 @@ LAMMPS under its own BSD license; see below. This library is used
when the USER-H5MD package is included in a LAMMPS build and the dump
h5md command is invoked in a LAMMPS input script.
+You can type "make lib-h5md" from the src directory to see help on how
+to build this library via make commands, or you can do the same thing
+by typing "python Install.py" from within this directory, or you can
+do it manually by following the instructions below.
+
---------------------
ch5md : Read and write H5MD files in C
@@ -17,8 +22,14 @@ molecular data, whose development is found at <http://nongnu.org/h5md/>.
ch5md is developped by Pierre de Buyl and is released under the 3-clause BSD
license that can be found in the file LICENSE.
-To use the h5md dump style in lammps, execute make in this directory then 'make
-yes-user-h5md' in the src directory of lammps. Rebuild lammps.
+To use the h5md dump style in lammps, execute
+make -f Makefile.h5cc
+in this directory then
+make yes-user-h5md
+in the src directory of LAMMPS to rebuild LAMMPS.
+
+Note that you must have the h5cc compiler installed to use
+Makefile.h5cc. It should be part
If HDF5 is not in a standard system location, edit Makefile.lammps accordingly.
diff --git a/lib/linalg/Install.py b/lib/linalg/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..c7076ca52f28dd63d09dae244f8491110d4a7891
--- /dev/null
+++ b/lib/linalg/Install.py
@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+
+# install.py tool to do build of the linear algebra library
+# used to automate the steps described in the README file in this dir
+
+import sys,commands,os
+
+# help message
+
+help = """
+Syntax: python Install.py -m machine
+ -m = peform a clean followed by "make -f Makefile.machine"
+ machine = suffix of a lib/Makefile.* file
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+machine = None
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ if iarg+2 > nargs: error()
+ machine = args[iarg+1]
+ iarg += 2
+ else: error()
+
+# set lib from working dir
+
+cwd = os.getcwd()
+lib = os.path.basename(cwd)
+
+# make the library
+
+print "Building lib%s.a ..." % lib
+cmd = "make -f Makefile.%s clean; make -f Makefile.%s" % (machine,machine)
+txt = commands.getoutput(cmd)
+print txt
+
+if os.path.exists("lib%s.a" % lib): print "Build was successful"
+else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
diff --git a/lib/linalg/README b/lib/linalg/README
index 20f3ff094d1c9a0f5a27a039d1a6b524427e8af9..725df86c4cc363b32436287efeb182390d39e683 100644
--- a/lib/linalg/README
+++ b/lib/linalg/README
@@ -3,11 +3,16 @@ USER-AWPMD packages, and possibly by other packages in the future.
Note that this is an *incomplete* subset of full BLAS/LAPACK.
-You should only need to build and use the resulting library in this
-directory if you want to build LAMMPS with the USER-ATC and/or
-USER-AWPMD packages AND you do not have any other suitable BLAS and
-LAPACK libraries installed on your system. E.g. ATLAS, GOTO-BLAS,
-OpenBLAS, ACML, or MKL.
+You should only need to build and use the library in this directory if
+you want to build LAMMPS with the USER-ATC and/or USER-AWPMD packages
+AND you do not have any other suitable BLAS and LAPACK libraries
+installed on your system. E.g. ATLAS, GOTO-BLAS, OpenBLAS, ACML, or
+MKL.
+
+You can type "make lib-linalg" from the src directory to see help on
+how to build this library via make commands, or you can do the same
+thing by typing "python Install.py" from within this directory, or you
+can do it manually by following the instructions below.
Build the library using one of the provided Makefile.* files or create
your own, specific to your compiler and system. For example:
@@ -20,4 +25,5 @@ directory:
liblinalg.a the library LAMMPS will link against
You can then include this library and its path in the Makefile.lammps
-file of any packages that need it, e.g. in lib/atc/Makefile.lammps.
+file of any packages that need it. As an example, see the
+lib/atc/Makefile.lammps.linalg file.
diff --git a/lib/meam/Install.py b/lib/meam/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..18b426f9282819ce196b6cf030aef477e3769d66
--- /dev/null
+++ b/lib/meam/Install.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+# install.py tool to do a generic build of a library
+# soft linked to by many of the lib/Install.py files
+# used to automate the steps described in the corresponding lib/README
+
+import sys,commands,os
+
+# help message
+
+help = """
+Syntax: python Install.py -m machine -e suffix
+ specify -m and optionally -e, order does not matter
+ -m = peform a clean followed by "make -f Makefile.machine"
+ machine = suffix of a lib/Makefile.* file
+ -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
+ does not alter existing Makefile.machine
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+machine = None
+extraflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ if iarg+2 > nargs: error()
+ machine = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-e":
+ if iarg+2 > nargs: error()
+ extraflag = 1
+ suffix = args[iarg+1]
+ iarg += 2
+ else: error()
+
+# set lib from working dir
+
+cwd = os.getcwd()
+lib = os.path.basename(cwd)
+
+# create Makefile.auto as copy of Makefile.machine
+# reset EXTRAMAKE if requested
+
+if not os.path.exists("Makefile.%s" % machine):
+ error("lib/%s/Makefile.%s does not exist" % (lib,machine))
+
+lines = open("Makefile.%s" % machine,'r').readlines()
+fp = open("Makefile.auto",'w')
+
+for line in lines:
+ words = line.split()
+ if len(words) == 3 and extraflag and \
+ words[0] == "EXTRAMAKE" and words[1] == '=':
+ line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+ print >>fp,line,
+
+fp.close()
+
+# make the library via Makefile.auto
+
+print "Building lib%s.a ..." % lib
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+txt = commands.getoutput(cmd)
+print txt
+
+if os.path.exists("lib%s.a" % lib): print "Build was successful"
+else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
+if not os.path.exists("Makefile.lammps"):
+ print "lib/%s/Makefile.lammps was NOT created" % lib
diff --git a/lib/meam/README b/lib/meam/README
index 436259ee8121238041fb956f981e20feb67fd47f..b3111c131745e4275fc819fd014f3ce40eb194fd 100644
--- a/lib/meam/README
+++ b/lib/meam/README
@@ -15,6 +15,11 @@ links against when using the MEAM package.
This library must be built with a F90 compiler, before LAMMPS is
built, so LAMMPS can link against it.
+You can type "make lib-meam" from the src directory to see help on how
+to build this library via make commands, or you can do the same thing
+by typing "python Install.py" from within this directory, or you can
+do it manually by following the instructions below.
+
Build the library using one of the provided Makefile.* files or create
your own, specific to your compiler and system. For example:
diff --git a/lib/mscg/Install.py b/lib/mscg/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..e54723261452d1af2ddf1c837985089fd71aa2cd
--- /dev/null
+++ b/lib/mscg/Install.py
@@ -0,0 +1,122 @@
+#!/usr/bin/env python
+
+# Install.py tool to download, unpack, build, and link to the MS-CG library
+# used to automate the steps described in the README file in this dir
+
+import sys,os,re,commands
+
+# help message
+
+help = """
+Syntax: python Install.py -h hpath hdir -g -b [suffix] -l
+ specify one or more options, order does not matter
+ -h = set home dir of MS-CG to be hpath/hdir
+ hpath can be full path, contain '~' or '.' chars
+ default hpath = . = lib/mscg
+ default hdir = MSCG-release-master = what GitHub zipfile unpacks to
+ -g = grab (download) zipfile from MS-CG GitHub website
+ unpack it to hpath/hdir
+ hpath must already exist
+ if hdir already exists, it will be deleted before unpack
+ -b = build MS-CG library in its src dir
+ optional suffix specifies which src/Make/Makefile.suffix to use
+ default suffix = g++_simple
+ -l = create 2 softlinks (includelink,liblink) in lib/mscg to MS-CG src dir
+"""
+
+# settings
+
+url = "https://github.com/uchicago-voth/MSCG-release/archive/master.zip"
+zipfile = "MS-CG-master.zip"
+zipdir = "MSCG-release-master"
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# expand to full path name
+# process leading '~' or relative path
+
+def fullpath(path):
+ return os.path.abspath(os.path.expanduser(path))
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+homepath = "."
+homedir = zipdir
+
+grabflag = 0
+buildflag = 0
+msuffix = "g++_simple"
+linkflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-h":
+ if iarg+3 > nargs: error()
+ homepath = args[iarg+1]
+ homedir = args[iarg+2]
+ iarg += 3
+ elif args[iarg] == "-g":
+ grabflag = 1
+ iarg += 1
+ elif args[iarg] == "-b":
+ buildflag = 1
+ if iarg+1 < nargs and args[iarg+1][0] != '-':
+ msuffix = args[iarg+1]
+ iarg += 1
+ iarg += 1
+ elif args[iarg] == "-l":
+ linkflag = 1
+ iarg += 1
+ else: error()
+
+homepath = fullpath(homepath)
+if not os.path.isdir(homepath): error("MS-CG path does not exist")
+homedir = "%s/%s" % (homepath,homedir)
+
+# download and unpack MS-CG zipfile
+
+if grabflag:
+ print "Downloading MS-CG ..."
+ cmd = "curl -L %s > %s/%s" % (url,homepath,zipfile)
+ print cmd
+ print commands.getoutput(cmd)
+
+ print "Unpacking MS-CG zipfile ..."
+ if os.path.exists("%s/%s" % (homepath,zipdir)):
+ commands.getoutput("rm -rf %s/%s" % (homepath,zipdir))
+ cmd = "cd %s; unzip %s" % (homepath,zipfile)
+ commands.getoutput(cmd)
+ if os.path.basename(homedir) != zipdir:
+ if os.path.exists(homedir): commands.getoutput("rm -rf %s" % homedir)
+ os.rename("%s/%s" % (homepath,zipdir),homedir)
+
+# build MS-CG
+
+if buildflag:
+ print "Building MS-CG ..."
+ cmd = "cd %s/src; cp Make/Makefile.%s .; make -f Makefile.%s" % \
+ (homedir,msuffix,msuffix)
+ txt = commands.getoutput(cmd)
+ print txt
+
+# create 2 links in lib/mscg to MS-CG src dir
+
+if linkflag:
+ print "Creating links to MS-CG include and lib files"
+ if os.path.isfile("includelink") or os.path.islink("includelink"):
+ os.remove("includelink")
+ if os.path.isfile("liblink") or os.path.islink("liblink"):
+ os.remove("liblink")
+ cmd = "ln -s %s/src includelink" % homedir
+ commands.getoutput(cmd)
+ cmd = "ln -s %s/src liblink" % homedir
+ commands.getoutput(cmd)
diff --git a/lib/mscg/Makefile.lammps b/lib/mscg/Makefile.lammps
index 0aa55b087dfc2ccd0fd22de84a82ee422f2b9178..f0d9a9b8a071b887115b46793514017fd11edf6f 100644
--- a/lib/mscg/Makefile.lammps
+++ b/lib/mscg/Makefile.lammps
@@ -1,5 +1,5 @@
# Settings that the LAMMPS build will import when this package library is used
-mscg_SYSINC =
-mscg_SYSLIB = -lm -lgsl -llapack -lcblas
+mscg_SYSINC = -std=c++11
+mscg_SYSLIB = -lm -lgsl -llapack -lgslcblas
mscg_SYSPATH =
diff --git a/lib/mscg/README b/lib/mscg/README
index cc4fc9a667bf1244d1975a4a2520fadbf7a388b3..b73c8563cd1bc4d76051fcff05acb6c9d4fbaee2 100755
--- a/lib/mscg/README
+++ b/lib/mscg/README
@@ -6,6 +6,15 @@ The MS-CG library is available at
https://github.com/uchicago-voth/MSCG-release and was developed by
Jacob Wagner in Greg Voth's group at the University of Chicago.
+This library requires a compiler with C++11 support (e.g., g++ v4.9+),
+LAPACK, and the GNU scientific library (GSL v 2.1+).
+
+You can type "make lib-mscg" from the src directory to see help on how
+to download and build this library via make commands, or you can do
+the same thing by typing "python Install.py" from within this
+directory, or you can do it manually by following the instructions
+below.
+
-----------------
You must perform the following steps yourself.
@@ -14,16 +23,21 @@ You must perform the following steps yourself.
either as a tarball or via SVN, and unpack the tarball either in
this /lib/mscg directory or somewhere else on your system.
-2. Compile MS-CG from within its home directory using your makefile choice:
+2. Ensure that you have LAPACK and GSL (or Intel MKL) as well as a compiler
+ with support for C++11.
+
+3. Compile MS-CG from within its home directory using your makefile of choice:
% make -f Makefile."name" libmscg.a
+ It is recommended that you start with Makefile.g++_simple
+ for most machines
-3. There is no need to install MS-CG if you only wish
+4. There is no need to install MS-CG if you only wish
to use it from LAMMPS.
-4. Create two soft links in this dir (lib/mscg) to the MS-CG src
+5. Create two soft links in this dir (lib/mscg) to the MS-CG src
directory. E.g if you built MS-CG in this dir:
- % ln -s mscgfm-master/src includelink
- % ln -s mscgfm-master/src liblink
+ % ln -s src includelink
+ % ln -s src liblink
These links could instead be set to the include and lib
directories created by a MS-CG install, e.g.
% ln -s /usr/local/include includelink
@@ -46,8 +60,8 @@ somewhere else, you will also need to repeat steps 1,2,3.
The Makefile.lammps file in this directory is there for compatibility
with the way other libraries under the lib dir are linked with by
-LAMMPS. MS-CG requires the GSL, LAPACK, and BLAS libraries as listed
-in Makefile.lammps. If they are not in default locations where your
+LAMMPS. MS-CG requires the GSL and LAPACK libraries as listed in
+Makefile.lammps. If they are not in default locations where your
LD_LIBRARY_PATH environment settings can find them, then you should
add the approrpriate -L paths to the mscg_SYSPATH variable in
Makefile.lammps.
diff --git a/lib/netcdf/README b/lib/netcdf/README
index 00db8df0012c2eec5d425db197cbb34f0c6c577e..b18ea1d276fdaf98a50bc882df31f7e006d04a6d 100644
--- a/lib/netcdf/README
+++ b/lib/netcdf/README
@@ -1,6 +1,9 @@
The Makefile.lammps file in this directory is used when building
LAMMPS with packages that make use of the NetCDF library or its
-parallel version. The file has several settings needed to compile
+parallel version. For example, the USER-NETCDF package which adds
+dump netcdf and dump netcdf/mpiio commands.
+
+The file has several settings needed to compile
and link LAMMPS with the NetCDF and parallel NetCDF support.
For any regular NetCDF installation, all required flags should be
autodetected. Please note that parallel NetCDF support is
diff --git a/lib/poems/Install.py b/lib/poems/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..18b426f9282819ce196b6cf030aef477e3769d66
--- /dev/null
+++ b/lib/poems/Install.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+# install.py tool to do a generic build of a library
+# soft linked to by many of the lib/Install.py files
+# used to automate the steps described in the corresponding lib/README
+
+import sys,commands,os
+
+# help message
+
+help = """
+Syntax: python Install.py -m machine -e suffix
+ specify -m and optionally -e, order does not matter
+ -m = peform a clean followed by "make -f Makefile.machine"
+ machine = suffix of a lib/Makefile.* file
+ -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
+ does not alter existing Makefile.machine
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+machine = None
+extraflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ if iarg+2 > nargs: error()
+ machine = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-e":
+ if iarg+2 > nargs: error()
+ extraflag = 1
+ suffix = args[iarg+1]
+ iarg += 2
+ else: error()
+
+# set lib from working dir
+
+cwd = os.getcwd()
+lib = os.path.basename(cwd)
+
+# create Makefile.auto as copy of Makefile.machine
+# reset EXTRAMAKE if requested
+
+if not os.path.exists("Makefile.%s" % machine):
+ error("lib/%s/Makefile.%s does not exist" % (lib,machine))
+
+lines = open("Makefile.%s" % machine,'r').readlines()
+fp = open("Makefile.auto",'w')
+
+for line in lines:
+ words = line.split()
+ if len(words) == 3 and extraflag and \
+ words[0] == "EXTRAMAKE" and words[1] == '=':
+ line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+ print >>fp,line,
+
+fp.close()
+
+# make the library via Makefile.auto
+
+print "Building lib%s.a ..." % lib
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+txt = commands.getoutput(cmd)
+print txt
+
+if os.path.exists("lib%s.a" % lib): print "Build was successful"
+else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
+if not os.path.exists("Makefile.lammps"):
+ print "lib/%s/Makefile.lammps was NOT created" % lib
diff --git a/lib/poems/README b/lib/poems/README
index 836595bdd1b06401e9d90ca735cbb1653403d2db..e0ded85e463ebb6528f79dfb7223f64900545458 100644
--- a/lib/poems/README
+++ b/lib/poems/README
@@ -40,6 +40,11 @@ links against when using the POEMA package.
This library must be built with a C++ compiler, before LAMMPS is
built, so LAMMPS can link against it.
+You can type "make lib-poems" from the src directory to see help on
+how to build this library via make commands, or you can do the same
+thing by typing "python Install.py" from within this directory, or you
+can do it manually by following the instructions below.
+
Build the library using one of the provided Makefile.* files or create
your own, specific to your compiler and system. For example:
diff --git a/lib/qmmm/Install.py b/lib/qmmm/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..18b426f9282819ce196b6cf030aef477e3769d66
--- /dev/null
+++ b/lib/qmmm/Install.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+# install.py tool to do a generic build of a library
+# soft linked to by many of the lib/Install.py files
+# used to automate the steps described in the corresponding lib/README
+
+import sys,commands,os
+
+# help message
+
+help = """
+Syntax: python Install.py -m machine -e suffix
+ specify -m and optionally -e, order does not matter
+ -m = peform a clean followed by "make -f Makefile.machine"
+ machine = suffix of a lib/Makefile.* file
+ -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
+ does not alter existing Makefile.machine
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+machine = None
+extraflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ if iarg+2 > nargs: error()
+ machine = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-e":
+ if iarg+2 > nargs: error()
+ extraflag = 1
+ suffix = args[iarg+1]
+ iarg += 2
+ else: error()
+
+# set lib from working dir
+
+cwd = os.getcwd()
+lib = os.path.basename(cwd)
+
+# create Makefile.auto as copy of Makefile.machine
+# reset EXTRAMAKE if requested
+
+if not os.path.exists("Makefile.%s" % machine):
+ error("lib/%s/Makefile.%s does not exist" % (lib,machine))
+
+lines = open("Makefile.%s" % machine,'r').readlines()
+fp = open("Makefile.auto",'w')
+
+for line in lines:
+ words = line.split()
+ if len(words) == 3 and extraflag and \
+ words[0] == "EXTRAMAKE" and words[1] == '=':
+ line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+ print >>fp,line,
+
+fp.close()
+
+# make the library via Makefile.auto
+
+print "Building lib%s.a ..." % lib
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+txt = commands.getoutput(cmd)
+print txt
+
+if os.path.exists("lib%s.a" % lib): print "Build was successful"
+else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
+if not os.path.exists("Makefile.lammps"):
+ print "lib/%s/Makefile.lammps was NOT created" % lib
diff --git a/lib/qmmm/README b/lib/qmmm/README
index b50f25ed695f5d52305253896f3b6f4976890cc7..2746c9e86e291e1c71253d1753326e6d7bfa7c06 100644
--- a/lib/qmmm/README
+++ b/lib/qmmm/README
@@ -18,6 +18,15 @@ the only option. Adding support for a different QM code will require
to write a new version of the top-level wrapper code, pwqmmm.c, and
also an interface layer into the QM code similar to the one in QE.
+You can type "make lib-qmmm" from the src directory to see help on how
+to build this library (steps 1 and 2 below) via make commands, or you
+can do the same thing by typing "python Install.py" from within this
+directory, or you can do it manually by following the instructions
+below.
+
+However you perform steps 1 and 2, you will need to perform steps 3
+and 4 manually, as outlined below.
+
-------------------------------------------------
WARNING: This is experimental code under developement and is provided
diff --git a/lib/reax/Install.py b/lib/reax/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..18b426f9282819ce196b6cf030aef477e3769d66
--- /dev/null
+++ b/lib/reax/Install.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+# install.py tool to do a generic build of a library
+# soft linked to by many of the lib/Install.py files
+# used to automate the steps described in the corresponding lib/README
+
+import sys,commands,os
+
+# help message
+
+help = """
+Syntax: python Install.py -m machine -e suffix
+ specify -m and optionally -e, order does not matter
+ -m = peform a clean followed by "make -f Makefile.machine"
+ machine = suffix of a lib/Makefile.* file
+ -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
+ does not alter existing Makefile.machine
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+machine = None
+extraflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ if iarg+2 > nargs: error()
+ machine = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-e":
+ if iarg+2 > nargs: error()
+ extraflag = 1
+ suffix = args[iarg+1]
+ iarg += 2
+ else: error()
+
+# set lib from working dir
+
+cwd = os.getcwd()
+lib = os.path.basename(cwd)
+
+# create Makefile.auto as copy of Makefile.machine
+# reset EXTRAMAKE if requested
+
+if not os.path.exists("Makefile.%s" % machine):
+ error("lib/%s/Makefile.%s does not exist" % (lib,machine))
+
+lines = open("Makefile.%s" % machine,'r').readlines()
+fp = open("Makefile.auto",'w')
+
+for line in lines:
+ words = line.split()
+ if len(words) == 3 and extraflag and \
+ words[0] == "EXTRAMAKE" and words[1] == '=':
+ line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+ print >>fp,line,
+
+fp.close()
+
+# make the library via Makefile.auto
+
+print "Building lib%s.a ..." % lib
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+txt = commands.getoutput(cmd)
+print txt
+
+if os.path.exists("lib%s.a" % lib): print "Build was successful"
+else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
+if not os.path.exists("Makefile.lammps"):
+ print "lib/%s/Makefile.lammps was NOT created" % lib
diff --git a/lib/reax/README b/lib/reax/README
index 2840a242a5fc5850154825dda8304e8a41aa8076..f21a47061827aab3c4c26fc8b3ccfbb5133b8fe4 100644
--- a/lib/reax/README
+++ b/lib/reax/README
@@ -17,6 +17,11 @@ links against when using the REAX package.
This library must be built with a F90 compiler, before LAMMPS is
built, so LAMMPS can link against it.
+You can type "make lib-reax" from the src directory to see help on how
+to build this library via make commands, or you can do the same thing
+by typing "python Install.py" from within this directory, or you can
+do it manually by following the instructions below.
+
Build the library using one of the provided Makefile.* files or create
your own, specific to your compiler and system. For example:
diff --git a/lib/smd/Install.py b/lib/smd/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..dc0a3187ce546e81176d780297588a91b04dccce
--- /dev/null
+++ b/lib/smd/Install.py
@@ -0,0 +1,103 @@
+#!/usr/bin/env python
+
+# Install.py tool to download, unpack, and point to the Eigen library
+# used to automate the steps described in the README file in this dir
+
+import sys,os,re,glob,commands
+
+# help message
+
+help = """
+Syntax: python Install.py -h hpath hdir -g -l
+ specify one or more options, order does not matter
+ -h = set home dir of Eigen to be hpath/hdir
+ hpath can be full path, contain '~' or '.' chars
+ default hpath = . = lib/smd
+ default hdir = "ee" = what tarball unpacks to (eigen-eigen-*)
+ -g = grab (download) tarball from http://eigen.tuxfamily.org website
+ unpack it to hpath/hdir
+ hpath must already exist
+ if hdir already exists, it will be deleted before unpack
+ -l = create softlink (includelink) in lib/smd to Eigen src dir
+"""
+
+# settings
+
+url = "http://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz"
+tarball = "eigen.tar.gz"
+
+# print error message or help
+
+def error(str=None):
+ if not str: print help
+ else: print "ERROR",str
+ sys.exit()
+
+# expand to full path name
+# process leading '~' or relative path
+
+def fullpath(path):
+ return os.path.abspath(os.path.expanduser(path))
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+homepath = "."
+homedir = "ee"
+
+grabflag = 0
+linkflag = 0
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-h":
+ if iarg+3 > nargs: error()
+ homepath = args[iarg+1]
+ homedir = args[iarg+2]
+ iarg += 3
+ elif args[iarg] == "-g":
+ grabflag = 1
+ iarg += 1
+ elif args[iarg] == "-l":
+ linkflag = 1
+ iarg += 1
+ else: error()
+
+homepath = fullpath(homepath)
+if not os.path.isdir(homepath): error("Eigen path does not exist")
+
+# download and unpack Eigen tarball
+# glob to find name of dir it unpacks to
+
+if grabflag:
+ print "Downloading Eigen ..."
+ cmd = "curl -L %s > %s/%s" % (url,homepath,tarball)
+ print cmd
+ print commands.getoutput(cmd)
+
+ print "Unpacking Eigen tarball ..."
+ edir = glob.glob("%s/eigen-eigen-*" % homepath)
+ for one in edir:
+ if os.path.isdir(one): commands.getoutput("rm -rf %s" % one)
+ cmd = "cd %s; tar zxvf %s" % (homepath,tarball)
+ commands.getoutput(cmd)
+ if homedir != "ee":
+ if os.path.exists(homedir): commands.getoutput("rm -rf %s" % homedir)
+ edir = glob.glob("%s/eigen-eigen-*" % homepath)
+ os.rename(edir[0],"%s/%s" % (homepath,homedir))
+
+# create link in lib/smd to Eigen src dir
+
+if linkflag:
+ print "Creating link to Eigen files"
+ if os.path.isfile("includelink") or os.path.islink("includelink"):
+ os.remove("includelink")
+ if homedir == "ee":
+ edir = glob.glob("%s/eigen-eigen-*" % homepath)
+ linkdir = edir[0]
+ else: linkdir = "%s/%s" % (homepath,homedir)
+ cmd = "ln -s %s includelink" % linkdir
+ commands.getoutput(cmd)
diff --git a/lib/smd/README b/lib/smd/README
index 846c440dae3c5fbb978e2edfbc8c6a88512509b7..1bd5902a1f4738e1e4caf1d886b1f39d8ef55761 100644
--- a/lib/smd/README
+++ b/lib/smd/README
@@ -4,9 +4,12 @@ to use the USER-SMD package in a LAMMPS input script.
The Eigen library is available at http://eigen.tuxfamily.org. It's
a general C++ template library for linear algebra.
-You must perform the following steps yourself, or you can use the
-install.py Python script to automate any or all steps of the process.
-Type "python install.py" for instructions.
+You can type "make lib-smd" from the src directory to see help on how
+to download build this library via make commands, or you can do the
+same thing by typing "python Install.py" from within this directory,
+or you can do it manually by following the instructions below.
+
+Instructions:
1. Download the Eigen tarball at http://eigen.tuxfamily.org and
unpack the tarball either in this /lib/smd directory or somewhere
diff --git a/lib/voronoi/Install.py b/lib/voronoi/Install.py
index 8ae08917e5bbde5c923617df136cd11e799ffbbc..7d847183b38fb3e0733df56f33a4ccffcf479bbc 100644
--- a/lib/voronoi/Install.py
+++ b/lib/voronoi/Install.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python
-# install.py tool to download, unpack, build, and link to the Voro++ library
+# Install.py tool to download, unpack, build, and link to the Voro++ library
# used to automate the steps described in the README file in this dir
import sys,os,re,urllib,commands
@@ -8,19 +8,20 @@ import sys,os,re,urllib,commands
# help message
help = """
-Syntax: install.py -v version -g gdir [gname] -b bdir -l ldir
+Syntax: python Install.py -v version -h hpath hdir -g -b -l
specify one or more options, order does not matter
- gdir,bdir,ldir can be paths relative to lib/latte, full paths, or contain ~
-v = version of Voro++ to download and build
- default = voro++-0.4.6 (current as of Jan 2015)
- -g = grab (download) from math.lbl.gov/voro++ website
- unpack tarfile in gdir to produce version dir (e.g. voro++-0.4.6)
- if optional gname specified, rename version dir to gname within gdir
- -b = build Voro++, bdir = Voro++ home directory
- note that bdir must include the version suffix unless renamed
- -l = create 2 softlinks (includelink,liblink)
- in lib/voronoi to src dir of ldir = Voro++ home directory
- note that ldir must include the version suffix unless renamed
+ default version = voro++-0.4.6 (current as of Jan 2015)
+ -h = set home dir of Voro++ to be hpath/hdir
+ hpath can be full path, contain '~' or '.' chars
+ default hpath = . = lib/voronoi
+ default hdir = voro++-0.4.6 = what tarball unpacks to
+ -g = grab (download) tarball from math.lbl.gov/voro++ website
+ unpack it to hpath/hdir
+ hpath must already exist
+ if hdir already exists, it will be deleted before unpack
+ -b = build Voro++ library in its src dir
+ -l = create 2 softlinks (includelink,liblink) in lib/voronoi to Voro++ src dir
"""
# settings
@@ -47,6 +48,9 @@ args = sys.argv[1:]
nargs = len(args)
if nargs == 0: error()
+homepath = "."
+homedir = version
+
grabflag = 0
buildflag = 0
linkflag = 0
@@ -56,49 +60,47 @@ while iarg < nargs:
if args[iarg] == "-v":
if iarg+2 > nargs: error()
version = args[iarg+1]
- iarg += 2
+ iarg += 2
+ elif args[iarg] == "-h":
+ if iarg+3 > nargs: error()
+ homepath = args[iarg+1]
+ homedir = args[iarg+2]
+ iarg += 3
elif args[iarg] == "-g":
- if iarg+2 > nargs: error()
grabflag = 1
- grabdir = args[iarg+1]
- grabname = None
- if iarg+2 < nargs and args[iarg+2][0] != '-':
- grabname = args[iarg+2]
- iarg += 1
- iarg += 2
+ iarg += 1
elif args[iarg] == "-b":
- if iarg+2 > nargs: error()
buildflag = 1
- builddir = args[iarg+1]
- iarg += 2
+ iarg += 1
elif args[iarg] == "-l":
- if iarg+2 > nargs: error()
linkflag = 1
- linkdir = args[iarg+1]
- iarg += 2
+ iarg += 1
else: error()
+homepath = fullpath(homepath)
+if not os.path.isdir(homepath): error("Voro++ path does not exist")
+homedir = "%s/%s" % (homepath,homedir)
+
# download and unpack Voro++ tarball
if grabflag:
print "Downloading Voro++ ..."
- grabdir = fullpath(grabdir)
- if not os.path.isdir(grabdir): error("Grab directory does not exist")
- urllib.urlretrieve(url,"%s/%s.tar.gz" % (grabdir,version))
+ urllib.urlretrieve(url,"%s/%s.tar.gz" % (homepath,version))
print "Unpacking Voro++ tarball ..."
- tardir = "%s/%s" % (grabdir,version)
- if os.path.exists(tardir): commands.getoutput("rm -rf %s" % tardir)
- cmd = "cd %s; tar zxvf %s.tar.gz" % (grabdir,version)
- txt = commands.getoutput(cmd)
- print tardir,grabdir,grabname
- if grabname: os.rename(tardir,"%s/%s" % (grabdir,grabname))
+ if os.path.exists("%s/%s" % (homepath,version)):
+ commands.getoutput("rm -rf %s/%s" % (homepath,version))
+ cmd = "cd %s; tar zxvf %s.tar.gz" % (homepath,version)
+ commands.getoutput(cmd)
+ if os.path.basename(homedir) != version:
+ if os.path.exists(homedir): commands.getoutput("rm -rf %s" % homedir)
+ os.rename("%s/%s" % (homepath,version),homedir)
# build Voro++
if buildflag:
print "Building Voro++ ..."
- cmd = "cd %s; make" % builddir
+ cmd = "cd %s; make" % homedir
txt = commands.getoutput(cmd)
print txt
@@ -110,7 +112,7 @@ if linkflag:
os.remove("includelink")
if os.path.isfile("liblink") or os.path.islink("liblink"):
os.remove("liblink")
- cmd = "ln -s %s/src includelink" % linkdir
+ cmd = "ln -s %s/src includelink" % homedir
commands.getoutput(cmd)
- cmd = "ln -s %s/src liblink" % linkdir
+ cmd = "ln -s %s/src liblink" % homedir
commands.getoutput(cmd)
diff --git a/lib/voronoi/README b/lib/voronoi/README
index 2507a9bae40d363380ce99404e12291e7986c933..9863632be0d1ea7e3f5c4158197291a5cd43ab30 100644
--- a/lib/voronoi/README
+++ b/lib/voronoi/README
@@ -6,11 +6,15 @@ The Voro++ library is available at http://math.lbl.gov/voro++ and was
developed by Chris H. Rycroft while at UC Berkeley / Lawrence Berkeley
Laboratory.
+You can type "make lib-voronoi" from the src directory to see help on
+how to download and build this library via make commands, or you can
+do the same thing by typing "python Install.py" from within this
+directory, or you can do it manually by following the instructions
+below.
+
-----------------
-You must perform the following steps yourself, or you can use the
-Install.py Python script to automate any or all steps of the process.
-Type "python Install.py" for instructions.
+Instructions:
1. Download Voro++ at http://math.lbl.gov/voro++/download
either as a tarball or via SVN, and unpack the
diff --git a/lib/vtk/Makefile.lammps b/lib/vtk/Makefile.lammps
index e3b28ed92828aaf5002b7147363914b2435751f9..b86856a9c615e552e0b41d27fa88bd85c8e52dd6 100644
--- a/lib/vtk/Makefile.lammps
+++ b/lib/vtk/Makefile.lammps
@@ -1,13 +1,12 @@
# Settings that the LAMMPS build will import when this package library is used
-#
+
# settings for VTK-5.8.0 on RHEL/CentOS 6.x
vtk_SYSINC = -I/usr/include/vtk
vtk_SYSLIB = -lvtkCommon -lvtkIO
vtk_SYSPATH = -L/usr/lib64/vtk
-#
+
# settings for VTK 6.2.0 on Fedora 23
#vtk_SYSINC = -I/usr/include/vtk
#vtk_SYSLIB = -lvtkCommonCore -lvtkIOCore -lvtkCommonDataModel -lvtkIOXML -lvtkIOLegacy -lvtkIOParallelXML
#vtk_SYSPATH = -L/usr/lib64/vtk
-#
diff --git a/lib/vtk/README b/lib/vtk/README
index 11add94f52bf7ba00c732a9c5897eecafc7645a8..61e2a40c23d0e56c94c9c2d5767138d2387c6d43 100644
--- a/lib/vtk/README
+++ b/lib/vtk/README
@@ -1,14 +1,15 @@
-The Makefile.lammps file in this directory is used when building LAMMPS with
-its USER-VTK package installed. The file has several settings needed to
-compile and link LAMMPS with the VTK library. You should choose a
-Makefile.lammps.* file compatible with your system and your version of VTK, and
-copy it to Makefile.lammps before building LAMMPS itself. You may need to edit
-one of the provided files to match your system.
+The Makefile.lammps file in this directory is used when building
+LAMMPS with its USER-VTK package installed. The file has several
+settings needed to compile and link LAMMPS with the VTK library. You
+should choose a Makefile.lammps.* file compatible with your system and
+your version of VTK, and copy it to Makefile.lammps before building
+LAMMPS itself. You may need to edit one of the provided files to
+match your system.
-If you create a new Makefile.lammps file suitable for some version of VTK on
-some system, that is not a match to one of the provided Makefile.lammps.*
-files, you can send it to the developers, and we can include it in the
-distribution for others to use.
+If you create a new Makefile.lammps file suitable for some version of
+VTK on some system, that is not a match to one of the provided
+Makefile.lammps.* files, you can send it to the developers, and we can
+include it in the distribution for others to use.
To illustrate, these are example settings from the
Makefile.lammps.ubuntu14.04_vtk6 file:
@@ -19,10 +20,11 @@ vtk_SYSPATH =
vtk_SYSINC refers to the include directory of the installed VTK library
-vtk_SYSLIB refers to the libraries needed to link to from an application
-(LAMMPS in this case) to "embed" VTK in the application. VTK consists of
-multiple shared libraries which are needed when using the USER-VTK package.
+vtk_SYSLIB refers to the libraries needed to link to from an
+application (LAMMPS in this case) to "embed" VTK in the
+application. VTK consists of multiple shared libraries which are
+needed when using the USER-VTK package.
-vtk_SYSPATH = refers to the path (e.g. -L/usr/local/lib) where the VTK library
-can be found. You may not need this setting if the path is already included in
-your LD_LIBRARY_PATH environment variable.
+vtk_SYSPATH = refers to the path (e.g. -L/usr/local/lib) where the VTK
+library can be found. You may not need this setting if the path is
+already included in your LD_LIBRARY_PATH environment variable.
diff --git a/src/KOKKOS/pair_reax_c_kokkos.cpp b/src/KOKKOS/pair_reax_c_kokkos.cpp
index acf9c754cdc70367e4f7bc96311291e92d6fe46a..a1f388b4f9e0b4dd22b89b2b89d992381aa8fae6 100644
--- a/src/KOKKOS/pair_reax_c_kokkos.cpp
+++ b/src/KOKKOS/pair_reax_c_kokkos.cpp
@@ -2294,12 +2294,12 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF
int numbonds = d_bo_num[i];
e_lp = 0.0;
- if (numbonds > 0)
+ if (numbonds > 0 || control->enobondsflag)
e_lp = p_lp2 * d_Delta_lp[i] * inv_expvd2;
const F_FLOAT dElp = p_lp2 * inv_expvd2 + 75.0 * p_lp2 * d_Delta_lp[i] * expvd2 * inv_expvd2*inv_expvd2;
const F_FLOAT CElp = dElp * d_dDelta_lp[i];
- if (numbonds > 0)
+ if (numbonds > 0 || control->enobondsflag)
a_CdDelta[i] += CElp;
if (eflag) ev.ereax[0] += e_lp;
@@ -2336,7 +2336,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF
const F_FLOAT inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8);
e_un = 0;
- if (numbonds > 0)
+ if (numbonds > 0 || control->enobondsflag)
e_un = -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
if (eflag) ev.ereax[2] += e_un;
@@ -2356,7 +2356,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF
// multibody forces
a_CdDelta[i] += CEover3;
- if (numbonds > 0)
+ if (numbonds > 0 || control->enobondsflag)
a_CdDelta[i] += CEunder3;
const int j_start = d_bo_first[i];
diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
index 11c7a147e76f41b005986a1685f8140d168ea426..6e17a9bbd7b0cc7fde788379910fea98979d7fa0 100644
--- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
@@ -57,6 +57,10 @@ PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(LAMMPS *lmp) : Pair(lmp)
implicit = 0;
mix_flag = ARITHMETIC;
writedata = 1;
+
+ // short-range/long-range flag accessed by DihedralCharmmfsw
+
+ dihedflag = 1;
}
/* ---------------------------------------------------------------------- */
@@ -669,10 +673,6 @@ void PairLJCharmmfswCoulLong::settings(int narg, char **arg)
cut_lj = force->numeric(FLERR,arg[1]);
if (narg == 2) cut_coul = cut_lj;
else cut_coul = force->numeric(FLERR,arg[2]);
-
- // indicates pair_style being used for dihedral_charmm
-
- dihedflag = 1;
}
/* ----------------------------------------------------------------------
diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
index c75da63caedcaf42d5fcc8b079cd2a0a457b57b6..af19f3eb3bedb8b7c137f410eadc4a440ad26e0c 100644
--- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
+++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
@@ -42,6 +42,10 @@ PairLJCharmmfswCoulCharmmfsh::PairLJCharmmfswCoulCharmmfsh(LAMMPS *lmp) :
implicit = 0;
mix_flag = ARITHMETIC;
writedata = 1;
+
+ // short-range/long-range flag accessed by DihedralCharmmfsw
+
+ dihedflag = 0;
}
/* ---------------------------------------------------------------------- */
@@ -235,10 +239,6 @@ void PairLJCharmmfswCoulCharmmfsh::settings(int narg, char **arg)
} else {
cut_coul = force->numeric(FLERR,arg[2]);
}
-
- // indicates pair_style being used for dihedral_charmm
-
- dihedflag = 0;
}
/* ----------------------------------------------------------------------
@@ -535,7 +535,7 @@ void *PairLJCharmmfswCoulCharmmfsh::extract(const char *str, int &dim)
dim = 0;
if (strcmp(str,"implicit") == 0) return (void *) &implicit;
- // info extracted by dihedral_charmmf
+ // info extracted by dihedral_charmmfsw
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
if (strcmp(str,"cut_lj_inner") == 0) return (void *) &cut_lj_inner;
diff --git a/src/Makefile b/src/Makefile
index 527e1979643243b3d9abdd1685a871dad22f6cdb..60c939bab2d9ab97aa88b1299d2962a3037ec016 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -46,39 +46,37 @@ endif
# PACKAGE = standard packages
# PACKUSER = user packagse
# PACKLIB = all packages that require an additional lib
+# should be PACKSYS + PACKINT + PACKEXT
# PACKSYS = subset that reqiure a common system library
+# include MPIIO and LB b/c require full MPI, not just STUBS
# PACKINT = subset that require an internal (provided) library
# PACKEXT = subset that require an external (downloaded) library
-# PACKLIB = PACKSYS + PACKING + PACKEXT
-# PACKSCRIPT = libs under lammps/lib that have an Install.py script
PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
granular kim kokkos kspace manybody mc meam misc molecule \
mpiio mscg opt peri poems \
python qeq reax replica rigid shock snap srd voronoi
-PACKUSER = user-atc user-awpmd user-cgsdk user-cgdna user-colvars \
+PACKUSER = user-atc user-awpmd user-cgdna user-cgsdk user-colvars \
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
user-intel user-lb user-manifold user-mgpt user-misc user-molfile \
- user-nc-dump user-omp user-phonon user-qmmm user-qtb \
+ user-netcdf user-omp user-phonon user-qmmm user-qtb \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-vtk
PACKLIB = compress gpu kim kokkos meam mpiio mscg poems \
python reax voronoi \
- user-atc user-awpmd user-colvars user-h5md user-molfile \
- user-nc-dump user-qmmm user-quip user-smd user-vtk
+ user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
+ user-netcdf user-qmmm user-quip user-smd user-vtk
-PACKSYS = compress mpiio python
+PACKSYS = compress mpiio python user-lb
PACKINT = gpu kokkos meam poems reax user-atc user-awpmd user-colvars
PACKEXT = kim mscg voronoi \
- user-h5md user-molfile user-nc-dump user-qmmm user-quip \
+ user-h5md user-molfile user-netcdf user-qmmm user-quip \
user-smd user-vtk
-PACKSCRIPT = voronoi
-
PACKALL = $(PACKAGE) $(PACKUSER)
PACKAGEUC = $(shell echo $(PACKAGE) | tr a-z A-Z)
@@ -87,6 +85,7 @@ PACKUSERUC = $(shell echo $(PACKUSER) | tr a-z A-Z)
YESDIR = $(shell echo $(@:yes-%=%) | tr a-z A-Z)
NODIR = $(shell echo $(@:no-%=%) | tr a-z A-Z)
LIBDIR = $(shell echo $(@:lib-%=%))
+LIBUSERDIR = $(shell echo $(@:lib-user-%=%))
# List of all targets
@@ -108,7 +107,7 @@ help:
@echo 'make no-standard (no-std) remove all standard pkgs'
@echo 'make yes-user install all user pkgs'
@echo 'make no-user remove all user pkgs'
- @echo 'make yes-lib install all pkgs with libs (incldued or ext)'
+ @echo 'make yes-lib install all pkgs with libs (included or ext)'
@echo 'make no-lib remove all pkgs with libs (included or ext)'
@echo 'make yes-ext install all pkgs with external libs'
@echo 'make no-ext remove all pkgs with external libs'
@@ -273,7 +272,7 @@ package:
@echo 'make package-overwrite replace package files with src files'
@echo 'make package-diff (pd) diff src files against package file'
@echo ''
- @echo 'make lib-package download/build/install a package library'
+ @echo 'make lib-package build and/or download a package library'
yes-all:
@for p in $(PACKALL); do $(MAKE) yes-$$p; done
@@ -338,11 +337,14 @@ no-%:
# download/build/install a package library
lib-%:
- @if [ ! -e ../lib/$(LIBDIR)/Install.py ]; then \
- echo "Install script for lib $(@:lib-%=%) does not exist"; \
- else \
- echo "Installing lib for package $(@:lib-%=%)"; \
+ @if [ -e ../lib/$(LIBDIR)/Install.py ]; then \
+ echo "Installing lib $(@:lib-%=%)"; \
cd ../lib/$(LIBDIR); python Install.py $(args); \
+ elif [ -e ../lib/$(LIBUSERDIR)/Install.py ]; then \
+ echo "Installing lib $(@:lib-user-%=%)"; \
+ cd ../lib/$(LIBUSERDIR); python Install.py $(args); \
+ else \
+ echo "Install script for lib $(@:lib-%=%) does not exist"; \
fi;
# status = list src files that differ from package files
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 1fe704efb0537e3f474a497c840de34c3c2520d1..5c993ee85933ff85b47710252be968e6e7905792 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -1419,12 +1419,14 @@ void FixShake::shake(int m)
domain->minimum_image(r01);
// s01 = distance vec after unconstrained update, with PBC
+ // use Domain::minimum_image_once(), not minimum_image()
+ // b/c xshake values might be huge, due to e.g. fix gcmc
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
- domain->minimum_image(s01);
+ domain->minimum_image_once(s01);
// scalar distances between atoms
@@ -1526,18 +1528,20 @@ void FixShake::shake3(int m)
domain->minimum_image(r02);
// s01,s02 = distance vec after unconstrained update, with PBC
+ // use Domain::minimum_image_once(), not minimum_image()
+ // b/c xshake values might be huge, due to e.g. fix gcmc
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
- domain->minimum_image(s01);
+ domain->minimum_image_once(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
- domain->minimum_image(s02);
+ domain->minimum_image_once(s02);
// scalar distances between atoms
@@ -1699,24 +1703,26 @@ void FixShake::shake4(int m)
domain->minimum_image(r03);
// s01,s02,s03 = distance vec after unconstrained update, with PBC
+ // use Domain::minimum_image_once(), not minimum_image()
+ // b/c xshake values might be huge, due to e.g. fix gcmc
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
- domain->minimum_image(s01);
+ domain->minimum_image_once(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
- domain->minimum_image(s02);
+ domain->minimum_image_once(s02);
double s03[3];
s03[0] = xshake[i0][0] - xshake[i3][0];
s03[1] = xshake[i0][1] - xshake[i3][1];
s03[2] = xshake[i0][2] - xshake[i3][2];
- domain->minimum_image(s03);
+ domain->minimum_image_once(s03);
// scalar distances between atoms
@@ -1941,24 +1947,26 @@ void FixShake::shake3angle(int m)
domain->minimum_image(r12);
// s01,s02,s12 = distance vec after unconstrained update, with PBC
+ // use Domain::minimum_image_once(), not minimum_image()
+ // b/c xshake values might be huge, due to e.g. fix gcmc
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
- domain->minimum_image(s01);
+ domain->minimum_image_once(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
- domain->minimum_image(s02);
+ domain->minimum_image_once(s02);
double s12[3];
s12[0] = xshake[i1][0] - xshake[i2][0];
s12[1] = xshake[i1][1] - xshake[i2][1];
s12[2] = xshake[i1][2] - xshake[i2][2];
- domain->minimum_image(s12);
+ domain->minimum_image_once(s12);
// scalar distances between atoms
@@ -2055,6 +2063,7 @@ void FixShake::shake3angle(int m)
double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda12_new;
while (!done && niter < max_iter) {
+
quad1 = quad1_0101 * lamda01*lamda01 +
quad1_0202 * lamda02*lamda02 +
quad1_1212 * lamda12*lamda12 +
diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp
index ad934535abd560c0b405109b17d4ce1d53a8c814..cba6fae9b75fcd51c3124ef39ff78d4e4b0849ce 100644
--- a/src/SNAP/compute_sna_atom.cpp
+++ b/src/SNAP/compute_sna_atom.cpp
@@ -48,7 +48,8 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
diagonalstyle = 0;
rmin0 = 0.0;
switchflag = 1;
- bzeroflag = 0;
+ bzeroflag = 1;
+ quadraticflag = 0;
// offset by 1 to match up with types
@@ -106,6 +107,11 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal compute sna/atom command");
bzeroflag = atoi(arg[iarg+1]);
iarg += 2;
+ } else if (strcmp(arg[iarg],"quadraticflag") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal compute sna/atom command");
+ quadraticflag = atoi(arg[iarg+1]);
+ iarg += 2;
} else error->all(FLERR,"Illegal compute sna/atom command");
}
@@ -122,8 +128,9 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
}
ncoeff = snaptr[0]->ncoeff;
- peratom_flag = 1;
size_peratom_cols = ncoeff;
+ if (quadraticflag) size_peratom_cols += ncoeff*ncoeff;
+ peratom_flag = 1;
nmax = 0;
njmax = 0;
@@ -264,8 +271,16 @@ void ComputeSNAAtom::compute_peratom()
snaptr[tid]->copy_bi2bvec();
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
sna[i][icoeff] = snaptr[tid]->bvec[icoeff];
+ if (quadraticflag) {
+ int ncount = ncoeff;
+ for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+ double bi = snaptr[tid]->bvec[icoeff];
+ for (int jcoeff = 0; jcoeff < ncoeff; jcoeff++)
+ sna[i][ncount++] = bi*snaptr[tid]->bvec[jcoeff];
+ }
+ }
} else {
- for (int icoeff = 0; icoeff < ncoeff; icoeff++)
+ for (int icoeff = 0; icoeff < size_peratom_cols; icoeff++)
sna[i][icoeff] = 0.0;
}
}
diff --git a/src/SNAP/compute_sna_atom.h b/src/SNAP/compute_sna_atom.h
index af62d7cf3b5caf9464da0370f4029021e14eefbf..b22eea71b5ae2b103a0fcaee2dadf1b1a1d835bb 100644
--- a/src/SNAP/compute_sna_atom.h
+++ b/src/SNAP/compute_sna_atom.h
@@ -44,7 +44,7 @@ class ComputeSNAAtom : public Compute {
double *wjelem;
class SNA** snaptr;
double cutmax;
-
+ int quadraticflag;
};
}
diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp
index 73452427bd48e42810f872eb6d4ba1c5aea4a696..39f34dd8cd50e8b15edace89accb10d8026e1178 100644
--- a/src/SNAP/compute_snad_atom.cpp
+++ b/src/SNAP/compute_snad_atom.cpp
@@ -48,9 +48,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
diagonalstyle = 0;
rmin0 = 0.0;
switchflag = 1;
- bzeroflag = 0;
+ bzeroflag = 1;
+ quadraticflag = 0;
// process required arguments
+
memory->create(radelem,ntypes+1,"sna/atom:radelem"); // offset by 1 to match up with types
memory->create(wjelem,ntypes+1,"sna/atom:wjelem");
rcutfac = atof(arg[3]);
@@ -60,11 +62,15 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
radelem[i+1] = atof(arg[6+i]);
for(int i = 0; i < ntypes; i++)
wjelem[i+1] = atof(arg[6+ntypes+i]);
+
// construct cutsq
+
double cut;
+ cutmax = 0.0;
memory->create(cutsq,ntypes+1,ntypes+1,"sna/atom:cutsq");
for(int i = 1; i <= ntypes; i++) {
cut = 2.0*radelem[i]*rcutfac;
+ if (cut > cutmax) cutmax = cut;
cutsq[i][i] = cut*cut;
for(int j = i+1; j <= ntypes; j++) {
cut = (radelem[i]+radelem[j])*rcutfac;
@@ -94,6 +100,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal compute snad/atom command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
+ } else if (strcmp(arg[iarg],"quadraticflag") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal compute snad/atom command");
+ quadraticflag = atoi(arg[iarg+1]);
+ iarg += 2;
} else error->all(FLERR,"Illegal compute snad/atom command");
}
@@ -110,9 +121,19 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
}
ncoeff = snaptr[0]->ncoeff;
- peratom_flag = 1;
- size_peratom_cols = 3*ncoeff*atom->ntypes;
+ twoncoeff = 2*ncoeff;
+ threencoeff = 3*ncoeff;
+ size_peratom_cols = threencoeff*atom->ntypes;
+ if (quadraticflag) {
+ ncoeffsq = ncoeff*ncoeff;
+ twoncoeffsq = 2*ncoeffsq;
+ threencoeffsq = 3*ncoeffsq;
+ size_peratom_cols +=
+ threencoeffsq*atom->ntypes;
+ }
comm_reverse = size_peratom_cols;
+ peratom_flag = 1;
+
nmax = 0;
njmax = 0;
snad = NULL;
@@ -136,10 +157,9 @@ void ComputeSNADAtom::init()
{
if (force->pair == NULL)
error->all(FLERR,"Compute snad/atom requires a pair style be defined");
- // TODO: Not sure what to do with this error check since cutoff radius is not
- // a single number
- //if (sqrt(cutsq) > force->pair->cutforce)
- //error->all(FLERR,"Compute snad/atom cutoff is longer than pairwise cutoff");
+
+ if (cutmax > force->pair->cutforce)
+ error->all(FLERR,"Compute sna/atom cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
@@ -228,7 +248,9 @@ void ComputeSNADAtom::compute_peratom()
const int* const jlist = firstneigh[i];
const int jnum = numneigh[i];
- const int typeoffset = 3*ncoeff*(atom->type[i]-1);
+ const int typeoffset = threencoeff*(atom->type[i]-1);
+ const int quadraticoffset = threencoeff*atom->ntypes +
+ threencoeffsq*(atom->type[i]-1);
// insure rij, inside, and typej are of size jnum
@@ -262,7 +284,11 @@ void ComputeSNADAtom::compute_peratom()
snaptr[tid]->compute_ui(ninside);
snaptr[tid]->compute_zi();
-
+ if (quadraticflag) {
+ snaptr[tid]->compute_bi();
+ snaptr[tid]->copy_bi2bvec();
+ }
+
for (int jj = 0; jj < ninside; jj++) {
const int j = snaptr[tid]->inside[jj];
snaptr[tid]->compute_duidrj(snaptr[tid]->rij[jj],
@@ -279,11 +305,38 @@ void ComputeSNADAtom::compute_peratom()
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
snadi[icoeff] += snaptr[tid]->dbvec[icoeff][0];
snadi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1];
- snadi[icoeff+2*ncoeff] += snaptr[tid]->dbvec[icoeff][2];
+ snadi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2];
snadj[icoeff] -= snaptr[tid]->dbvec[icoeff][0];
snadj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1];
- snadj[icoeff+2*ncoeff] -= snaptr[tid]->dbvec[icoeff][2];
+ snadj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2];
}
+
+ if (quadraticflag) {
+ double *snadi = snad[i]+quadraticoffset;
+ double *snadj = snad[j]+quadraticoffset;
+ int ncount = 0;
+ for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+ double bi = snaptr[tid]->bvec[icoeff];
+ double bix = snaptr[tid]->dbvec[icoeff][0];
+ double biy = snaptr[tid]->dbvec[icoeff][1];
+ double biz = snaptr[tid]->dbvec[icoeff][2];
+ for (int jcoeff = 0; jcoeff < ncoeff; jcoeff++) {
+ double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+ + bix*snaptr[tid]->bvec[jcoeff];
+ double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1]
+ + biy*snaptr[tid]->bvec[jcoeff];
+ double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2]
+ + biz*snaptr[tid]->bvec[jcoeff];
+ snadi[ncount] += dbxtmp;
+ snadi[ncount+ncoeffsq] += dbytmp;
+ snadi[ncount+twoncoeffsq] += dbztmp;
+ snadj[ncount] -= dbxtmp;
+ snadj[ncount+ncoeffsq] -= dbytmp;
+ snadj[ncount+twoncoeffsq] -= dbztmp;
+ ncount++;
+ }
+ }
+ }
}
}
}
@@ -331,7 +384,8 @@ double ComputeSNADAtom::memory_usage()
double bytes = nmax*size_peratom_cols * sizeof(double);
bytes += 3*njmax*sizeof(double);
bytes += njmax*sizeof(int);
- bytes += ncoeff*3;
+ bytes += threencoeff*atom->ntypes;
+ if (quadraticflag) bytes += threencoeffsq*atom->ntypes;
bytes += snaptr[0]->memory_usage()*comm->nthreads;
return bytes;
}
diff --git a/src/SNAP/compute_snad_atom.h b/src/SNAP/compute_snad_atom.h
index 31f5bf252d2ee8fde1739ea3e9b3e54a29e013ee..0d5a369ab6b9050bea1104c2d928bc55b388e886 100644
--- a/src/SNAP/compute_snad_atom.h
+++ b/src/SNAP/compute_snad_atom.h
@@ -37,7 +37,7 @@ class ComputeSNADAtom : public Compute {
private:
int nmax, njmax, diagonalstyle;
- int ncoeff;
+ int ncoeff, twoncoeff, threencoeff, ncoeffsq, twoncoeffsq, threencoeffsq;
double **cutsq;
class NeighList *list;
double **snad;
@@ -45,7 +45,8 @@ class ComputeSNADAtom : public Compute {
double *radelem;
double *wjelem;
class SNA** snaptr;
-
+ double cutmax;
+ int quadraticflag;
};
}
diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp
index f75b02fba72ea5f7fef25edc992c60c1cfc3ab4b..0d21d16561956cd1424c5b267067a471f93bd7bb 100644
--- a/src/SNAP/compute_snav_atom.cpp
+++ b/src/SNAP/compute_snav_atom.cpp
@@ -38,8 +38,6 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
radelem = NULL;
wjelem = NULL;
- nvirial = 6;
-
int ntypes = atom->ntypes;
int nargmin = 6+2*ntypes;
@@ -50,9 +48,11 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
diagonalstyle = 0;
rmin0 = 0.0;
switchflag = 1;
- bzeroflag = 0;
+ bzeroflag = 1;
+ quadraticflag = 0;
// process required arguments
+
memory->create(radelem,ntypes+1,"sna/atom:radelem"); // offset by 1 to match up with types
memory->create(wjelem,ntypes+1,"sna/atom:wjelem");
rcutfac = atof(arg[3]);
@@ -96,6 +96,11 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal compute snav/atom command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
+ } else if (strcmp(arg[iarg],"quadraticflag") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal compute snav/atom command");
+ quadraticflag = atoi(arg[iarg+1]);
+ iarg += 2;
} else error->all(FLERR,"Illegal compute snav/atom command");
}
@@ -112,9 +117,24 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
}
ncoeff = snaptr[0]->ncoeff;
- peratom_flag = 1;
- size_peratom_cols = nvirial*ncoeff*atom->ntypes;
+ twoncoeff = 2*ncoeff;
+ threencoeff = 3*ncoeff;
+ fourncoeff = 4*ncoeff;
+ fivencoeff = 5*ncoeff;
+ sixncoeff = 6*ncoeff;
+ size_peratom_cols = sixncoeff*atom->ntypes;
+ if (quadraticflag) {
+ ncoeffsq = ncoeff*ncoeff;
+ twoncoeffsq = 2*ncoeffsq;
+ threencoeffsq = 3*ncoeffsq;
+ fourncoeffsq = 4*ncoeffsq;
+ fivencoeffsq = 5*ncoeffsq;
+ sixncoeffsq = 6*ncoeffsq;
+ size_peratom_cols +=
+ sixncoeffsq*atom->ntypes;
+ }
comm_reverse = size_peratom_cols;
+ peratom_flag = 1;
nmax = 0;
njmax = 0;
@@ -231,7 +251,9 @@ void ComputeSNAVAtom::compute_peratom()
const int* const jlist = firstneigh[i];
const int jnum = numneigh[i];
- const int typeoffset = nvirial*ncoeff*(atom->type[i]-1);
+ const int typeoffset = sixncoeff*(atom->type[i]-1);
+ const int quadraticoffset = sixncoeff*atom->ntypes +
+ sixncoeffsq*(atom->type[i]-1);
// insure rij, inside, and typej are of size jnum
@@ -265,6 +287,10 @@ void ComputeSNAVAtom::compute_peratom()
snaptr[tid]->compute_ui(ninside);
snaptr[tid]->compute_zi();
+ if (quadraticflag) {
+ snaptr[tid]->compute_bi();
+ snaptr[tid]->copy_bi2bvec();
+ }
for (int jj = 0; jj < ninside; jj++) {
const int j = snaptr[tid]->inside[jj];
@@ -281,19 +307,52 @@ void ComputeSNAVAtom::compute_peratom()
double *snavj = snav[j]+typeoffset;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
- snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp;
- snavi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1]*ytmp;
- snavi[icoeff+2*ncoeff] += snaptr[tid]->dbvec[icoeff][2]*ztmp;
- snavi[icoeff+3*ncoeff] += snaptr[tid]->dbvec[icoeff][1]*ztmp;
- snavi[icoeff+4*ncoeff] += snaptr[tid]->dbvec[icoeff][0]*ztmp;
- snavi[icoeff+5*ncoeff] += snaptr[tid]->dbvec[icoeff][0]*ytmp;
- snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0];
- snavj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1];
- snavj[icoeff+2*ncoeff] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2];
- snavj[icoeff+3*ncoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2];
- snavj[icoeff+4*ncoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2];
- snavj[icoeff+5*ncoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1];
+ snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp;
+ snavi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1]*ytmp;
+ snavi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2]*ztmp;
+ snavi[icoeff+threencoeff] += snaptr[tid]->dbvec[icoeff][1]*ztmp;
+ snavi[icoeff+fourncoeff] += snaptr[tid]->dbvec[icoeff][0]*ztmp;
+ snavi[icoeff+fivencoeff] += snaptr[tid]->dbvec[icoeff][0]*ytmp;
+ snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0];
+ snavj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1];
+ snavj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2];
+ snavj[icoeff+threencoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2];
+ snavj[icoeff+fourncoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2];
+ snavj[icoeff+fivencoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1];
}
+
+ if (quadraticflag) {
+ double *snavi = snav[i]+quadraticoffset;
+ double *snavj = snav[j]+quadraticoffset;
+ int ncount = 0;
+ for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+ double bi = snaptr[tid]->bvec[icoeff];
+ double bix = snaptr[tid]->dbvec[icoeff][0];
+ double biy = snaptr[tid]->dbvec[icoeff][1];
+ double biz = snaptr[tid]->dbvec[icoeff][2];
+ for (int jcoeff = 0; jcoeff < ncoeff; jcoeff++) {
+ double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+ + bix*snaptr[tid]->bvec[jcoeff];
+ double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1]
+ + biy*snaptr[tid]->bvec[jcoeff];
+ double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2]
+ + biz*snaptr[tid]->bvec[jcoeff];
+ snavi[ncount] += dbxtmp*xtmp;
+ snavi[ncount+ncoeffsq] += dbytmp*ytmp;
+ snavi[ncount+twoncoeffsq] += dbztmp*ztmp;
+ snavi[ncount+threencoeffsq] += dbytmp*ztmp;
+ snavi[ncount+fourncoeffsq] += dbxtmp*ztmp;
+ snavi[ncount+fivencoeffsq] += dbxtmp*ytmp;
+ snavj[ncount] -= dbxtmp*x[j][0];
+ snavj[ncount+ncoeffsq] -= dbytmp*x[j][1];
+ snavj[ncount+twoncoeffsq] -= dbztmp*x[j][2];
+ snavj[ncount+threencoeffsq] -= dbytmp*x[j][2];
+ snavj[ncount+fourncoeffsq] -= dbxtmp*x[j][2];
+ snavj[ncount+fivencoeffsq] -= dbxtmp*x[j][1];
+ ncount++;
+ }
+ }
+ }
}
}
}
@@ -341,7 +400,8 @@ double ComputeSNAVAtom::memory_usage()
double bytes = nmax*size_peratom_cols * sizeof(double);
bytes += 3*njmax*sizeof(double);
bytes += njmax*sizeof(int);
- bytes += ncoeff*nvirial;
+ bytes += sixncoeff*atom->ntypes;
+ if (quadraticflag) bytes += sixncoeffsq*atom->ntypes;
bytes += snaptr[0]->memory_usage()*comm->nthreads;
return bytes;
}
diff --git a/src/SNAP/compute_snav_atom.h b/src/SNAP/compute_snav_atom.h
index 0252be705966e200a9e7e71e19d020e575ebfa68..33ae4f92173945c9754b0ef17b5a5b9e730d4a79 100644
--- a/src/SNAP/compute_snav_atom.h
+++ b/src/SNAP/compute_snav_atom.h
@@ -37,16 +37,17 @@ class ComputeSNAVAtom : public Compute {
private:
int nmax, njmax, diagonalstyle;
- int ncoeff,nvirial;
+ int ncoeff, twoncoeff, threencoeff, fourncoeff, fivencoeff, sixncoeff;
+ int ncoeffsq, twoncoeffsq, threencoeffsq, fourncoeffsq, fivencoeffsq, sixncoeffsq;
double **cutsq;
class NeighList *list;
double **snav;
double rcutfac;
double *radelem;
double *wjelem;
-
class SNA** snaptr;
-
+ double cutmax;
+ int quadraticflag;
};
}
diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp
index 06c2e48488e15d8ae072e5a7b16faafc0ed8a1e1..e4ed57b933cba2d65e310ff62238b6d9a92b1660 100644
--- a/src/SNAP/pair_snap.cpp
+++ b/src/SNAP/pair_snap.cpp
@@ -1635,7 +1635,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
rmin0 = 0.0;
diagonalstyle = 3;
switchflag = 1;
- bzeroflag = 0;
+ bzeroflag = 1;
+
// open SNAP parameter file on proc 0
FILE *fpparam;
diff --git a/src/USER-NC-DUMP/Install.sh b/src/USER-NETCDF/Install.sh
similarity index 100%
rename from src/USER-NC-DUMP/Install.sh
rename to src/USER-NETCDF/Install.sh
diff --git a/src/USER-NC-DUMP/README b/src/USER-NETCDF/README
similarity index 95%
rename from src/USER-NC-DUMP/README
rename to src/USER-NETCDF/README
index c02e879c61f369508bf87f5e5f546a688a10a512..57dec5e4c835fd41b4b5ac7a62ac8e96e75913e0 100644
--- a/src/USER-NC-DUMP/README
+++ b/src/USER-NETCDF/README
@@ -1,7 +1,7 @@
-USER-NC-DUMP
+USER-NETCDF
============
-This package provides the nc and (optionally) the nc/mpiio dump styles.
+This package provides the netcf and netcdf/mpiio dump styles.
See the doc page for dump nc or dump nc/mpiio command for how to use them.
Compiling these dump styles requires having the netCDF library installed
on your system. See lib/netcdf/README for additional details.
diff --git a/src/USER-NC-DUMP/dump_nc.cpp b/src/USER-NETCDF/dump_netcdf.cpp
similarity index 97%
rename from src/USER-NC-DUMP/dump_nc.cpp
rename to src/USER-NETCDF/dump_netcdf.cpp
index 7a66eb022429da91a6491051ac79d42973cd181c..bad90bdef3d1affe541a93c27e69856a66c3f700 100644
--- a/src/USER-NC-DUMP/dump_nc.cpp
+++ b/src/USER-NETCDF/dump_netcdf.cpp
@@ -32,14 +32,14 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+
#if defined(LMP_HAS_NETCDF)
#include <unistd.h>
#include <stdlib.h>
#include <string.h>
-
#include <netcdf.h>
-
+#include "dump_netcdf.h"
#include "atom.h"
#include "comm.h"
#include "compute.h"
@@ -56,8 +56,6 @@
#include "variable.h"
#include "force.h"
-#include "dump_nc.h"
-
using namespace LAMMPS_NS;
using namespace MathConst;
@@ -91,7 +89,7 @@ const int THIS_IS_A_BIGINT = -4;
/* ---------------------------------------------------------------------- */
-DumpNC::DumpNC(LAMMPS *lmp, int narg, char **arg) :
+DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
{
// arrays for data rearrangement
@@ -224,7 +222,7 @@ DumpNC::DumpNC(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
-DumpNC::~DumpNC()
+DumpNetCDF::~DumpNetCDF()
{
closefile();
@@ -238,7 +236,7 @@ DumpNC::~DumpNC()
/* ---------------------------------------------------------------------- */
-void DumpNC::openfile()
+void DumpNetCDF::openfile()
{
// now the computes and fixes have been initialized, so we can query
// for the size of vector quantities
@@ -594,12 +592,12 @@ void DumpNC::openfile()
/* ---------------------------------------------------------------------- */
-void DumpNC::closefile()
+void DumpNetCDF::closefile()
{
if (filewriter && singlefile_opened) {
NCERR( nc_close(ncid) );
singlefile_opened = 0;
- // append next time DumpNC::openfile is called
+ // append next time DumpNetCDF::openfile is called
append_flag = 1;
// write to next frame upon next open
framei++;
@@ -608,7 +606,7 @@ void DumpNC::closefile()
/* ---------------------------------------------------------------------- */
-void DumpNC::write()
+void DumpNetCDF::write()
{
// open file
@@ -678,7 +676,7 @@ void DumpNC::write()
/* ---------------------------------------------------------------------- */
-void DumpNC::write_header(bigint n)
+void DumpNetCDF::write_header(bigint n)
{
size_t start[2];
@@ -753,7 +751,7 @@ void DumpNC::write_header(bigint n)
write head of block (mass & element name) only if has atoms of the type
------------------------------------------------------------------------- */
-void DumpNC::write_data(int n, double *mybuf)
+void DumpNetCDF::write_data(int n, double *mybuf)
{
size_t start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
ptrdiff_t stride[NC_MAX_VAR_DIMS];
@@ -761,18 +759,17 @@ void DumpNC::write_data(int n, double *mybuf)
if (!int_buffer) {
n_buffer = n;
int_buffer = (int *)
- memory->smalloc(n*sizeof(int), "DumpNC::int_buffer");
+ memory->smalloc(n*sizeof(int),"dump::int_buffer");
double_buffer = (double *)
- memory->smalloc(n*sizeof(double), "DumpNC::double_buffer");
+ memory->smalloc(n*sizeof(double),"dump::double_buffer");
}
if (n > n_buffer) {
n_buffer = n;
int_buffer = (int *)
- memory->srealloc(int_buffer, n*sizeof(int), "DumpNC::int_buffer");
+ memory->srealloc(int_buffer, n*sizeof(int),"dump::int_buffer");
double_buffer = (double *)
- memory->srealloc(double_buffer, n*sizeof(double),
- "DumpNC::double_buffer");
+ memory->srealloc(double_buffer, n*sizeof(double),"dump::double_buffer");
}
start[0] = framei-1;
@@ -887,7 +884,7 @@ void DumpNC::write_data(int n, double *mybuf)
/* ---------------------------------------------------------------------- */
-int DumpNC::modify_param(int narg, char **arg)
+int DumpNetCDF::modify_param(int narg, char **arg)
{
int iarg = 0;
if (strcmp(arg[iarg],"double") == 0) {
@@ -925,17 +922,17 @@ int DumpNC::modify_param(int narg, char **arg)
if (!strcmp(arg[iarg],"step")) {
perframe[i].type = THIS_IS_A_BIGINT;
- perframe[i].compute = &DumpNC::compute_step;
+ perframe[i].compute = &DumpNetCDF::compute_step;
strcpy(perframe[i].name, arg[iarg]);
}
else if (!strcmp(arg[iarg],"elapsed")) {
perframe[i].type = THIS_IS_A_BIGINT;
- perframe[i].compute = &DumpNC::compute_elapsed;
+ perframe[i].compute = &DumpNetCDF::compute_elapsed;
strcpy(perframe[i].name, arg[iarg]);
}
else if (!strcmp(arg[iarg],"elaplong")) {
perframe[i].type = THIS_IS_A_BIGINT;
- perframe[i].compute = &DumpNC::compute_elapsed_long;
+ perframe[i].compute = &DumpNetCDF::compute_elapsed_long;
strcpy(perframe[i].name, arg[iarg]);
}
else {
@@ -1036,7 +1033,7 @@ int DumpNC::modify_param(int narg, char **arg)
/* ---------------------------------------------------------------------- */
-void DumpNC::write_prmtop()
+void DumpNetCDF::write_prmtop()
{
char fn[1024];
char tmp[81];
@@ -1098,7 +1095,7 @@ void DumpNC::write_prmtop()
/* ---------------------------------------------------------------------- */
-void DumpNC::ncerr(int err, const char *descr, int line)
+void DumpNetCDF::ncerr(int err, const char *descr, int line)
{
if (err != NC_NOERR) {
char errstr[1024];
@@ -1122,21 +1119,21 @@ void DumpNC::ncerr(int err, const char *descr, int line)
customize a new keyword by adding a method
------------------------------------------------------------------------- */
-void DumpNC::compute_step(void *r)
+void DumpNetCDF::compute_step(void *r)
{
*((bigint *) r) = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
-void DumpNC::compute_elapsed(void *r)
+void DumpNetCDF::compute_elapsed(void *r)
{
*((bigint *) r) = update->ntimestep - update->firststep;
}
/* ---------------------------------------------------------------------- */
-void DumpNC::compute_elapsed_long(void *r)
+void DumpNetCDF::compute_elapsed_long(void *r)
{
*((bigint *) r) = update->ntimestep - update->beginstep;
}
diff --git a/src/USER-NC-DUMP/dump_nc.h b/src/USER-NETCDF/dump_netcdf.h
similarity index 94%
rename from src/USER-NC-DUMP/dump_nc.h
rename to src/USER-NETCDF/dump_netcdf.h
index 788a9368f928d30c19a866b518815dd0ddeefd22..daf4e9d0de2d94151c6f0bad6b9e348171e48b82 100644
--- a/src/USER-NC-DUMP/dump_nc.h
+++ b/src/USER-NETCDF/dump_netcdf.h
@@ -32,16 +32,17 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+
#if defined(LMP_HAS_NETCDF)
#ifdef DUMP_CLASS
-DumpStyle(nc,DumpNC)
+DumpStyle(netcdf,DumpNetCDF)
#else
-#ifndef LMP_DUMP_NC_H
-#define LMP_DUMP_NC_H
+#ifndef LMP_DUMP_NETCDF_H
+#define LMP_DUMP_NETCDFC_H
#include "dump_custom.h"
@@ -50,10 +51,10 @@ namespace LAMMPS_NS {
const int NC_FIELD_NAME_MAX = 100;
const int DUMP_NC_MAX_DIMS = 100;
-class DumpNC : public DumpCustom {
+class DumpNetCDF : public DumpCustom {
public:
- DumpNC(class LAMMPS *, int, char **);
- virtual ~DumpNC();
+ DumpNetCDF(class LAMMPS *, int, char **);
+ virtual ~DumpNetCDF();
virtual void write();
private:
@@ -68,7 +69,7 @@ class DumpNC : public DumpCustom {
int ndumped; // number of enties written for this prop.
};
- typedef void (DumpNC::*funcptr_t)(void *);
+ typedef void (DumpNetCDF::*funcptr_t)(void *);
// per-frame quantities (variables, fixes or computes)
struct nc_perframe_t {
diff --git a/src/USER-NC-DUMP/dump_nc_mpiio.cpp b/src/USER-NETCDF/dump_netcdf_mpiio.cpp
similarity index 96%
rename from src/USER-NC-DUMP/dump_nc_mpiio.cpp
rename to src/USER-NETCDF/dump_netcdf_mpiio.cpp
index 6b26014030b2a509ea28f09af1a21a9af8ba09f0..2e9ec274a5e07cc04bddb7644aa87d54353b09c6 100644
--- a/src/USER-NC-DUMP/dump_nc_mpiio.cpp
+++ b/src/USER-NETCDF/dump_netcdf_mpiio.cpp
@@ -32,14 +32,14 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+
#if defined(LMP_HAS_PNETCDF)
#include <unistd.h>
#include <stdlib.h>
#include <string.h>
-
#include <pnetcdf.h>
-
+#include "dump_netcdf_mpiio.h"
#include "atom.h"
#include "comm.h"
#include "compute.h"
@@ -56,8 +56,6 @@
#include "variable.h"
#include "force.h"
-#include "dump_nc_mpiio.h"
-
using namespace LAMMPS_NS;
using namespace MathConst;
@@ -91,7 +89,7 @@ const int THIS_IS_A_BIGINT = -4;
/* ---------------------------------------------------------------------- */
-DumpNCMPIIO::DumpNCMPIIO(LAMMPS *lmp, int narg, char **arg) :
+DumpNetCDFMPIIO::DumpNetCDFMPIIO(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
{
// arrays for data rearrangement
@@ -217,7 +215,7 @@ DumpNCMPIIO::DumpNCMPIIO(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
-DumpNCMPIIO::~DumpNCMPIIO()
+DumpNetCDFMPIIO::~DumpNetCDFMPIIO()
{
closefile();
@@ -231,7 +229,7 @@ DumpNCMPIIO::~DumpNCMPIIO()
/* ---------------------------------------------------------------------- */
-void DumpNCMPIIO::openfile()
+void DumpNetCDFMPIIO::openfile()
{
// now the computes and fixes have been initialized, so we can query
// for the size of vector quantities
@@ -570,12 +568,12 @@ void DumpNCMPIIO::openfile()
/* ---------------------------------------------------------------------- */
-void DumpNCMPIIO::closefile()
+void DumpNetCDFMPIIO::closefile()
{
if (singlefile_opened) {
NCERR( ncmpi_close(ncid) );
singlefile_opened = 0;
- // append next time DumpNCMPIIO::openfile is called
+ // append next time DumpNetCDFMPIIO::openfile is called
append_flag = 1;
// write to next frame upon next open
framei++;
@@ -584,7 +582,7 @@ void DumpNCMPIIO::closefile()
/* ---------------------------------------------------------------------- */
-void DumpNCMPIIO::write()
+void DumpNetCDFMPIIO::write()
{
// open file
@@ -687,7 +685,7 @@ void DumpNCMPIIO::write()
/* ---------------------------------------------------------------------- */
-void DumpNCMPIIO::write_time_and_cell()
+void DumpNetCDFMPIIO::write_time_and_cell()
{
MPI_Offset start[2];
@@ -759,7 +757,7 @@ void DumpNCMPIIO::write_time_and_cell()
write head of block (mass & element name) only if has atoms of the type
------------------------------------------------------------------------- */
-void DumpNCMPIIO::write_data(int n, double *mybuf)
+void DumpNetCDFMPIIO::write_data(int n, double *mybuf)
{
MPI_Offset start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
MPI_Offset stride[NC_MAX_VAR_DIMS];
@@ -767,19 +765,18 @@ void DumpNCMPIIO::write_data(int n, double *mybuf)
if (!int_buffer) {
n_buffer = std::max(1, n);
int_buffer = (int *)
- memory->smalloc(n_buffer*sizeof(int), "DumpNCMPIIO::int_buffer");
+ memory->smalloc(n_buffer*sizeof(int),"dump::int_buffer");
double_buffer = (double *)
- memory->smalloc(n_buffer*sizeof(double), "DumpNCMPIIO::double_buffer");
+ memory->smalloc(n_buffer*sizeof(double),"dump::double_buffer");
}
if (n > n_buffer) {
n_buffer = std::max(1, n);
int_buffer = (int *)
- memory->srealloc(int_buffer, n_buffer*sizeof(int),
- "DumpNCMPIIO::int_buffer");
+ memory->srealloc(int_buffer, n_buffer*sizeof(int),"dump::int_buffer");
double_buffer = (double *)
memory->srealloc(double_buffer, n_buffer*sizeof(double),
- "DumpNCMPIIO::double_buffer");
+ "dump::double_buffer");
}
start[0] = framei-1;
@@ -882,7 +879,7 @@ void DumpNCMPIIO::write_data(int n, double *mybuf)
/* ---------------------------------------------------------------------- */
-int DumpNCMPIIO::modify_param(int narg, char **arg)
+int DumpNetCDFMPIIO::modify_param(int narg, char **arg)
{
int iarg = 0;
if (strcmp(arg[iarg],"double") == 0) {
@@ -920,17 +917,17 @@ int DumpNCMPIIO::modify_param(int narg, char **arg)
if (!strcmp(arg[iarg],"step")) {
perframe[i].type = THIS_IS_A_BIGINT;
- perframe[i].compute = &DumpNCMPIIO::compute_step;
+ perframe[i].compute = &DumpNetCDFMPIIO::compute_step;
strcpy(perframe[i].name, arg[iarg]);
}
else if (!strcmp(arg[iarg],"elapsed")) {
perframe[i].type = THIS_IS_A_BIGINT;
- perframe[i].compute = &DumpNCMPIIO::compute_elapsed;
+ perframe[i].compute = &DumpNetCDFMPIIO::compute_elapsed;
strcpy(perframe[i].name, arg[iarg]);
}
else if (!strcmp(arg[iarg],"elaplong")) {
perframe[i].type = THIS_IS_A_BIGINT;
- perframe[i].compute = &DumpNCMPIIO::compute_elapsed_long;
+ perframe[i].compute = &DumpNetCDFMPIIO::compute_elapsed_long;
strcpy(perframe[i].name, arg[iarg]);
}
else {
@@ -1031,7 +1028,7 @@ int DumpNCMPIIO::modify_param(int narg, char **arg)
/* ---------------------------------------------------------------------- */
-void DumpNCMPIIO::ncerr(int err, const char *descr, int line)
+void DumpNetCDFMPIIO::ncerr(int err, const char *descr, int line)
{
if (err != NC_NOERR) {
char errstr[1024];
@@ -1055,21 +1052,21 @@ void DumpNCMPIIO::ncerr(int err, const char *descr, int line)
customize a new keyword by adding a method
------------------------------------------------------------------------- */
-void DumpNCMPIIO::compute_step(void *r)
+void DumpNetCDFMPIIO::compute_step(void *r)
{
*((bigint *) r) = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
-void DumpNCMPIIO::compute_elapsed(void *r)
+void DumpNetCDFMPIIO::compute_elapsed(void *r)
{
*((bigint *) r) = update->ntimestep - update->firststep;
}
/* ---------------------------------------------------------------------- */
-void DumpNCMPIIO::compute_elapsed_long(void *r)
+void DumpNetCDFMPIIO::compute_elapsed_long(void *r)
{
*((bigint *) r) = update->ntimestep - update->beginstep;
}
diff --git a/src/USER-NC-DUMP/dump_nc_mpiio.h b/src/USER-NETCDF/dump_netcdf_mpiio.h
similarity index 95%
rename from src/USER-NC-DUMP/dump_nc_mpiio.h
rename to src/USER-NETCDF/dump_netcdf_mpiio.h
index 5e36335e648978c2e5e5dc40486487b066c7888c..6f5b00b03350f6a08c9c603a01cbae8c49f90e7b 100644
--- a/src/USER-NC-DUMP/dump_nc_mpiio.h
+++ b/src/USER-NETCDF/dump_netcdf_mpiio.h
@@ -32,16 +32,17 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+
#if defined(LMP_HAS_PNETCDF)
#ifdef DUMP_CLASS
-DumpStyle(nc/mpiio,DumpNCMPIIO)
+DumpStyle(netcdf/mpiio,DumpNetCDFMPIIO)
#else
-#ifndef LMP_DUMP_NC_MPIIO_H
-#define LMP_DUMP_NC_MPIIO_H
+#ifndef LMP_DUMP_NETCDF_MPIIO_H
+#define LMP_DUMP_NETCDF_MPIIO_H
#include "dump_custom.h"
@@ -50,10 +51,10 @@ namespace LAMMPS_NS {
const int NC_MPIIO_FIELD_NAME_MAX = 100;
const int DUMP_NC_MPIIO_MAX_DIMS = 100;
-class DumpNCMPIIO : public DumpCustom {
+class DumpNetCDFMPIIO : public DumpCustom {
public:
- DumpNCMPIIO(class LAMMPS *, int, char **);
- virtual ~DumpNCMPIIO();
+ DumpNetCDFMPIIO(class LAMMPS *, int, char **);
+ virtual ~DumpNetCDFMPIIO();
virtual void write();
private:
diff --git a/src/USER-REAXC/compute_spec_atom.cpp b/src/USER-REAXC/compute_spec_atom.cpp
index 4af8efcae71b324da7d5b8a872f13e5e491dae59..164ce87205a15854d0a2fe1079d41d3f6af9818e 100644
--- a/src/USER-REAXC/compute_spec_atom.cpp
+++ b/src/USER-REAXC/compute_spec_atom.cpp
@@ -24,7 +24,7 @@
#include "reaxc_defs.h"
#include "reaxc_types.h"
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
using namespace LAMMPS_NS;
@@ -71,7 +71,7 @@ ComputeSpecAtom::ComputeSpecAtom(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"vz") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_vz;
- // from pair_reax_c
+ // from pair_reaxc
} else if (strcmp(arg[iarg],"abo01") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo01;
} else if (strcmp(arg[iarg],"abo02") == 0) {
diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index 26cf03f60a838477d6fec05da6b58457c3f63895..ed057dfe7aee6c04e2955d945688c7a308a11902 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -23,7 +23,7 @@
#include <stdlib.h>
#include <string.h>
#include "fix_qeq_reax.h"
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
diff --git a/src/USER-REAXC/fix_reax_c.cpp b/src/USER-REAXC/fix_reaxc.cpp
similarity index 99%
rename from src/USER-REAXC/fix_reax_c.cpp
rename to src/USER-REAXC/fix_reaxc.cpp
index e1cc4e340ef57efd2e68cd28a226d14c79b4bb33..df06217993da53bc31492e1ea85957883a4ef475 100644
--- a/src/USER-REAXC/fix_reax_c.cpp
+++ b/src/USER-REAXC/fix_reaxc.cpp
@@ -21,7 +21,7 @@
Algorithmic Techniques", Parallel Computing, in press.
------------------------------------------------------------------------- */
-#include "fix_reax_c.h"
+#include "fix_reaxc.h"
#include "atom.h"
#include "pair.h"
#include "comm.h"
diff --git a/src/USER-REAXC/fix_reax_c.h b/src/USER-REAXC/fix_reaxc.h
similarity index 100%
rename from src/USER-REAXC/fix_reax_c.h
rename to src/USER-REAXC/fix_reaxc.h
diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp
index 543669de766cce7c3a1466988623af1f564b2dd0..cf9e4789c1342f232ffabc68eb5206a7cc24b149 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.cpp
+++ b/src/USER-REAXC/fix_reaxc_bonds.cpp
@@ -21,7 +21,7 @@
#include "fix_reaxc_bonds.h"
#include "atom.h"
#include "update.h"
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index ead73f02a1328cef35a4af076ee8e1f0818aa490..d291903fa8fb9ece2b071cf871f94e80104eb6ee 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -24,7 +24,7 @@
#include "fix_reaxc_species.h"
#include "domain.h"
#include "update.h"
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
diff --git a/src/USER-REAXC/fix_reaxc_species.h b/src/USER-REAXC/fix_reaxc_species.h
index 872ea2528f06df00cd27ee0e76fd19fa66fdad51..563a10f39db3913a49abbf97cb28b63975b64d51 100644
--- a/src/USER-REAXC/fix_reaxc_species.h
+++ b/src/USER-REAXC/fix_reaxc_species.h
@@ -23,7 +23,7 @@ FixStyle(reax/c/species,FixReaxCSpecies)
#include "fix.h"
#include "pointers.h"
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_types.h"
#include "reaxc_defs.h"
diff --git a/src/USER-REAXC/pair_reax_c.cpp b/src/USER-REAXC/pair_reaxc.cpp
similarity index 97%
rename from src/USER-REAXC/pair_reax_c.cpp
rename to src/USER-REAXC/pair_reaxc.cpp
index 4933c90f01d8273f38566fa456dc3da2e43aa91b..d51b0fc2f8bb28b9516218daf1bb433948ef7b9b 100644
--- a/src/USER-REAXC/pair_reax_c.cpp
+++ b/src/USER-REAXC/pair_reaxc.cpp
@@ -20,7 +20,7 @@
Hybrid and hybrid/overlay compatibility added by Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "atom.h"
#include "update.h"
#include "force.h"
@@ -30,7 +30,7 @@
#include "neigh_request.h"
#include "modify.h"
#include "fix.h"
-#include "fix_reax_c.h"
+#include "fix_reaxc.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
@@ -223,10 +223,11 @@ void PairReaxC::settings(int narg, char **arg)
qeqflag = 1;
control->lgflag = 0;
+ control->enobondsflag = 1;
system->mincap = MIN_CAP;
system->safezone = SAFE_ZONE;
system->saferzone = SAFER_ZONE;
-
+
// process optional keywords
int iarg = 1;
@@ -238,7 +239,13 @@ void PairReaxC::settings(int narg, char **arg)
else if (strcmp(arg[iarg+1],"no") == 0) qeqflag = 0;
else error->all(FLERR,"Illegal pair_style reax/c command");
iarg += 2;
- } else if (strcmp(arg[iarg],"lgvdw") == 0) {
+ } else if (strcmp(arg[iarg],"enobonds") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command");
+ if (strcmp(arg[iarg+1],"yes") == 0) control->enobondsflag = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) control->enobondsflag = 0;
+ else error->all(FLERR,"Illegal pair_style reax/c command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"lgvdw") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command");
if (strcmp(arg[iarg+1],"yes") == 0) control->lgflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) control->lgflag = 0;
diff --git a/src/USER-REAXC/pair_reax_c.h b/src/USER-REAXC/pair_reaxc.h
similarity index 100%
rename from src/USER-REAXC/pair_reax_c.h
rename to src/USER-REAXC/pair_reaxc.h
diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp
index dc8545e0069f0deafb38dac5484379e40a386915..969912e082ed8e7419ded19ee33c0ded09587c80 100644
--- a/src/USER-REAXC/reaxc_allocate.cpp
+++ b/src/USER-REAXC/reaxc_allocate.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_allocate.h"
#include "reaxc_list.h"
#include "reaxc_reset_tools.h"
diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp
index 0b4ca21adf4e128e21d9701486f8127e3f0d28d2..04cedf18a8e5d7c49699e48a1595fdc220503ed5 100644
--- a/src/USER-REAXC/reaxc_bond_orders.cpp
+++ b/src/USER-REAXC/reaxc_bond_orders.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_types.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp
index e0ef38ba0f2788fa739b1ed53e701f234721ac2d..a8a1298166e239c173d559616f568847c137fdc2 100644
--- a/src/USER-REAXC/reaxc_bonds.cpp
+++ b/src/USER-REAXC/reaxc_bonds.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_bonds.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp
index 3753360c68593c1f704ad9bf137839e95aa061c0..4def41bc8c7c309f1f3c4c0a47e1d74a54f8a758 100644
--- a/src/USER-REAXC/reaxc_control.cpp
+++ b/src/USER-REAXC/reaxc_control.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_control.h"
#include "reaxc_tool_box.h"
diff --git a/src/USER-REAXC/reaxc_defs.h b/src/USER-REAXC/reaxc_defs.h
index d0a75d431baa506cbe7a2b9d584b68542d8f5010..101b554fb23fe5247c7256dd4622f0974596339f 100644
--- a/src/USER-REAXC/reaxc_defs.h
+++ b/src/USER-REAXC/reaxc_defs.h
@@ -116,8 +116,8 @@
#define MAX_BOND 20
-#define MAXREAXBOND 24 /* used in fix_reaxc_bonds.cpp and pair_reax_c.cpp */
-#define MAXSPECBOND 24 /* used in fix_reaxc_species.cpp and pair_reax_c.cpp */
+#define MAXREAXBOND 24 /* used in fix_reaxc_bonds.cpp and pair_reaxc.cpp */
+#define MAXSPECBOND 24 /* used in fix_reaxc_species.cpp and pair_reaxc.cpp */
/******************* ENUMERATIONS *************************/
enum geo_formats { CUSTOM, PDB, ASCII_RESTART, BINARY_RESTART, GF_N };
diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp
index fda284140349885e083c50fe17e79f4d86489ec9..58a347ebf781daf0ffe4e3a1596cc28b944c2362 100644
--- a/src/USER-REAXC/reaxc_ffield.cpp
+++ b/src/USER-REAXC/reaxc_ffield.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "error.h"
#include "reaxc_ffield.h"
#include "reaxc_tool_box.h"
diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp
index 7f11f5565febf8fbeb2f3604c6976a1b259588b5..215ded6e5d0b2bbec7353c0a30b5ed632e32c69c 100644
--- a/src/USER-REAXC/reaxc_forces.cpp
+++ b/src/USER-REAXC/reaxc_forces.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_forces.h"
#include "reaxc_bond_orders.h"
#include "reaxc_bonds.h"
diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
index 8d7b3b381997575806e38f71df9f195c10ff4d33..ff771ad65bc96f6e987a2707863c93fcfa712607 100644
--- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
+++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_hydrogen_bonds.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp
index f912c95ea5b8ba13a99352dad21e180b1dc31a66..b11cdd2fbcddb8bd235bf410ac349a1e39328b47 100644
--- a/src/USER-REAXC/reaxc_init_md.cpp
+++ b/src/USER-REAXC/reaxc_init_md.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_init_md.h"
#include "reaxc_allocate.h"
#include "reaxc_forces.h"
diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp
index 0c14dad5d43a0300b4ce3e3c049960c3acc5c476..4d58f7514de5eefc6910fb9e345e9fb16ad64459 100644
--- a/src/USER-REAXC/reaxc_io_tools.cpp
+++ b/src/USER-REAXC/reaxc_io_tools.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "update.h"
#include "reaxc_io_tools.h"
#include "reaxc_list.h"
diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/USER-REAXC/reaxc_list.cpp
index d22ac4ca7f7d5a5b3b1cc628e945638bb702a13f..2755d5506e7b78c456dabe06cb9caab72021594f 100644
--- a/src/USER-REAXC/reaxc_list.cpp
+++ b/src/USER-REAXC/reaxc_list.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_list.h"
#include "reaxc_tool_box.h"
diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp
index 903e54962dcc9f39a285982ed0999e31597b00cd..9db8b7b9f650105c9c6c9d5bed90634a49b2e29f 100644
--- a/src/USER-REAXC/reaxc_lookup.cpp
+++ b/src/USER-REAXC/reaxc_lookup.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_lookup.h"
#include "reaxc_nonbonded.h"
#include "reaxc_tool_box.h"
diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp
index 1923668e89bf08160750eb78c0083e5c18b78b1d..ecfd3ad04d7fc179cf7a1806036ae8c7d58b7c29 100644
--- a/src/USER-REAXC/reaxc_multi_body.cpp
+++ b/src/USER-REAXC/reaxc_multi_body.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_multi_body.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
@@ -79,7 +79,7 @@ void Atom_Energy( reax_system *system, control_params *control,
numbonds ++;
/* calculate the energy */
- if (numbonds > 0)
+ if (numbonds > 0 || control->enobondsflag)
data->my_en.e_lp += e_lp =
p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
@@ -87,7 +87,8 @@ void Atom_Energy( reax_system *system, control_params *control,
75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2);
CElp = dElp * workspace->dDelta_lp[i];
- if (numbonds > 0) workspace->CdDelta[i] += CElp; // lp - 1st term
+ if (numbonds > 0 || control->enobondsflag)
+ workspace->CdDelta[i] += CElp; // lp - 1st term
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
@@ -187,7 +188,7 @@ void Atom_Energy( reax_system *system, control_params *control,
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
numbonds ++;
- if (numbonds > 0)
+ if (numbonds > 0 || control->enobondsflag)
data->my_en.e_un += e_un =
-p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
@@ -202,13 +203,15 @@ void Atom_Energy( reax_system *system, control_params *control,
/* tally into per-atom energy */
if( system->pair_ptr->evflag) {
eng_tmp = e_ov;
- if (numbonds > 0) eng_tmp += e_un;
+ if (numbonds > 0 || control->enobondsflag)
+ eng_tmp += e_un;
system->pair_ptr->ev_tally(i,i,system->n,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
}
/* forces */
workspace->CdDelta[i] += CEover3; // OvCoor - 2nd term
- if (numbonds > 0) workspace->CdDelta[i] += CEunder3; // UnCoor - 1st term
+ if (numbonds > 0 || control->enobondsflag)
+ workspace->CdDelta[i] += CEunder3; // UnCoor - 1st term
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
pbond = &(bonds->select.bond_list[pj]);
diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp
index cb24e2dc3704f8fa28008e336224b6352b185ecc..9c223428a68dfe386c52345a3a89193b2d2161f1 100644
--- a/src/USER-REAXC/reaxc_nonbonded.cpp
+++ b/src/USER-REAXC/reaxc_nonbonded.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_types.h"
#include "reaxc_nonbonded.h"
#include "reaxc_bond_orders.h"
diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp
index 1e6aeab4753148247f5182b545d2f62afe3c10cc..4ec744e7b1c0a9ff1f823951690d6f86de0b4cc4 100644
--- a/src/USER-REAXC/reaxc_reset_tools.cpp
+++ b/src/USER-REAXC/reaxc_reset_tools.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_reset_tools.h"
#include "reaxc_list.h"
#include "reaxc_tool_box.h"
diff --git a/src/USER-REAXC/reaxc_system_props.cpp b/src/USER-REAXC/reaxc_system_props.cpp
index 6b4551a03f7c4f810ece3d0366fdc99c3ac4794b..54eeb6da1e863108148a11c169f20311288355c7 100644
--- a/src/USER-REAXC/reaxc_system_props.cpp
+++ b/src/USER-REAXC/reaxc_system_props.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_system_props.h"
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp
index 22576e9f3bba5d7eb4bf04cfcb88a9105b31ca85..4fc6796efe0cc67c2c874b7180a1df58b90b7323 100644
--- a/src/USER-REAXC/reaxc_tool_box.cpp
+++ b/src/USER-REAXC/reaxc_tool_box.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_tool_box.h"
struct timeval tim;
diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp
index 2cfe3297657a7e48f920fac2c014cafdaaca8cad..74d5b04f20b7ce2ac9a846c4e3716dfd1edd0a5e 100644
--- a/src/USER-REAXC/reaxc_torsion_angles.cpp
+++ b/src/USER-REAXC/reaxc_torsion_angles.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_torsion_angles.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp
index 9d4fa73524078599bed83aa80642d0507fbbcfc8..ae2bba2150673f13cf3523fcb4ca1e78ab8d81e4 100644
--- a/src/USER-REAXC/reaxc_traj.cpp
+++ b/src/USER-REAXC/reaxc_traj.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_traj.h"
#include "reaxc_list.h"
#include "reaxc_tool_box.h"
diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h
index db4cf04178f4c722da766c980555b06b14705444..b3e2f40f02d1dceb06b0434b84c55f8f052a5efd 100644
--- a/src/USER-REAXC/reaxc_types.h
+++ b/src/USER-REAXC/reaxc_types.h
@@ -61,13 +61,12 @@
#define MAX_BOND 20 // same as reaxc_defs.h
/********************** TYPE DEFINITIONS ********************/
-typedef int ivec[3];
+typedef int ivec[3];
typedef double rvec[3];
typedef double rtensor[3][3];
typedef double rvec2[2];
typedef double rvec4[4];
-
// import LAMMPS' definition of tagint and bigint
typedef LAMMPS_NS::tagint rc_tagint;
typedef LAMMPS_NS::bigint rc_bigint;
@@ -79,7 +78,6 @@ typedef struct
void *out_atoms;
} mpi_out_data;
-
typedef struct
{
MPI_Comm world;
@@ -107,7 +105,6 @@ typedef struct
void *in2_buffer;
} mpi_datatypes;
-
typedef struct
{
int n_global;
@@ -115,8 +112,6 @@ typedef struct
int vdw_type;
} global_parameters;
-
-
typedef struct
{
/* Line one in field file */
@@ -163,8 +158,6 @@ typedef struct
} single_body_parameters;
-
-
/* Two Body Parameters */
typedef struct {
/* Bond Order parameters */
@@ -193,8 +186,6 @@ typedef struct {
double v13cor, ovc;
} two_body_parameters;
-
-
/* 3-body parameters */
typedef struct {
/* valence angle */
@@ -214,15 +205,11 @@ typedef struct{
three_body_parameters prm[REAX_MAX_3BODY_PARAM];
} three_body_header;
-
-
/* hydrogen-bond parameters */
typedef struct{
double r0_hb, p_hb1, p_hb2, p_hb3;
} hbond_parameters;
-
-
/* 4-body parameters */
typedef struct {
double V1, V2, V3;
@@ -234,14 +221,12 @@ typedef struct {
double p_cot1;
} four_body_parameters;
-
typedef struct
{
int cnt;
four_body_parameters prm[REAX_MAX_4BODY_PARAM];
} four_body_header;
-
typedef struct
{
int num_atom_types;
@@ -253,8 +238,6 @@ typedef struct
four_body_header ****fbp;
} reax_interaction;
-
-
struct _reax_atom
{
rc_tagint orig_id;
@@ -283,8 +266,6 @@ struct _reax_atom
};
typedef _reax_atom reax_atom;
-
-
typedef struct
{
double V;
@@ -295,8 +276,6 @@ typedef struct
rtensor g;
} simulation_box;
-
-
struct grid_cell
{
double cutoff;
@@ -471,7 +450,8 @@ typedef struct
int restrict_type;
int lgflag;
-
+ int enobondsflag;
+
} control_params;
diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp
index c2b3287be5fe71bb68f8a328ca463e4c678fed7f..c92996e56b9a776735bbe2eab7fa06819ef18eb2 100644
--- a/src/USER-REAXC/reaxc_valence_angles.cpp
+++ b/src/USER-REAXC/reaxc_valence_angles.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_valence_angles.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
diff --git a/src/USER-REAXC/reaxc_vector.cpp b/src/USER-REAXC/reaxc_vector.cpp
index ee63e94280844fc07b050ad131a7681f12a5cb54..977b17a6dc2eb70a9910eb1d12a87f3cbd04b93b 100644
--- a/src/USER-REAXC/reaxc_vector.cpp
+++ b/src/USER-REAXC/reaxc_vector.cpp
@@ -24,7 +24,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
#include "reaxc_vector.h"
diff --git a/src/USER-VTK/README b/src/USER-VTK/README
index 86ef56a7408eb2c1d0d49ae986e45734e7345566..3429c96b7282f2caa886ab707442e7b3fd0013bf 100644
--- a/src/USER-VTK/README
+++ b/src/USER-VTK/README
@@ -1,17 +1,17 @@
-This package implements the "dump custom/vtk" command which can be used in a
+This package implements the "dump vtk" command which can be used in a
LAMMPS input script.
-This dump allows to output atom data similar to dump custom, but directly into
-VTK files.
+This dump allows output of atom data similar to the dump custom
+command, but in VTK format.
-This package uses the VTK library (www.vtk.org) which must be installed on your
-system. See the lib/vtk/README file and the LAMMPS manual for information on
-building LAMMPS with external libraries. The settings in the Makefile.lammps
-file in that directory must be correct for LAMMPS to build correctly with this
-package installed.
+This package uses the VTK library (www.vtk.org) which must be
+installed on your system. See the lib/vtk/README file and the LAMMPS
+manual for information on building LAMMPS with external libraries.
+The settings in the Makefile.lammps file in that directory must be
+correct for LAMMPS to build correctly with this package installed.
-This code was initially developed for LIGGGHTS by Daniel Queteschiner at DCS
-Computing. This is an effort to integrate it back to LAMMPS.
+This code was initially developed for LIGGGHTS by Daniel Queteschiner
+at DCS Computing. This is an effort to integrate it back to LAMMPS.
The person who created this package is Richard Berger at JKU
(richard.berger@jku.at). Contact him directly if you have questions.
diff --git a/src/USER-VTK/dump_custom_vtk.cpp b/src/USER-VTK/dump_vtk.cpp
similarity index 91%
rename from src/USER-VTK/dump_custom_vtk.cpp
rename to src/USER-VTK/dump_vtk.cpp
index 0e4bc459766a69b8864724454b88a4f5997547ab..0aa749e73b18237f22b0b2afb8fc7b54f82ee588 100644
--- a/src/USER-VTK/dump_custom_vtk.cpp
+++ b/src/USER-VTK/dump_vtk.cpp
@@ -25,7 +25,7 @@
#include <math.h>
#include <stdlib.h>
#include <string.h>
-#include "dump_custom_vtk.h"
+#include "dump_vtk.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
@@ -39,12 +39,15 @@
#include "fix.h"
#include "memory.h"
#include "error.h"
+
#include <vector>
#include <sstream>
#include <vtkVersion.h>
+
#ifndef VTK_MAJOR_VERSION
#include <vtkConfigure.h>
#endif
+
#include <vtkPointData.h>
#include <vtkCellData.h>
#include <vtkDoubleArray.h>
@@ -93,10 +96,10 @@ enum{VTK,VTP,VTU,PVTP,PVTU}; // file formats
/* ---------------------------------------------------------------------- */
-DumpCustomVTK::DumpCustomVTK(LAMMPS *lmp, int narg, char **arg) :
+DumpVTK::DumpVTK(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
{
- if (narg == 5) error->all(FLERR,"No dump custom/vtk arguments specified");
+ if (narg == 5) error->all(FLERR,"No dump vtk arguments specified");
pack_choice.clear();
vtype.clear();
@@ -113,7 +116,7 @@ DumpCustomVTK::DumpCustomVTK(LAMMPS *lmp, int narg, char **arg) :
if (ioptional < narg &&
strcmp(style,"image") != 0 && strcmp(style,"movie") != 0)
- error->all(FLERR,"Invalid attribute in dump custom command");
+ error->all(FLERR,"Invalid attribute in dump vtk command");
size_one = pack_choice.size();
current_pack_choice_key = -1;
@@ -162,7 +165,7 @@ DumpCustomVTK::DumpCustomVTK(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
-DumpCustomVTK::~DumpCustomVTK()
+DumpVTK::~DumpVTK()
{
delete [] filecurrent;
delete [] domainfilecurrent;
@@ -173,7 +176,7 @@ DumpCustomVTK::~DumpCustomVTK()
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::init_style()
+void DumpVTK::init_style()
{
// default for element names = C
@@ -191,14 +194,14 @@ void DumpCustomVTK::init_style()
// setup function ptrs
- header_choice = &DumpCustomVTK::header_vtk;
+ header_choice = &DumpVTK::header_vtk;
if (vtk_file_format == VTP || vtk_file_format == PVTP)
- write_choice = &DumpCustomVTK::write_vtp;
+ write_choice = &DumpVTK::write_vtp;
else if (vtk_file_format == VTU || vtk_file_format == PVTU)
- write_choice = &DumpCustomVTK::write_vtu;
+ write_choice = &DumpVTK::write_vtu;
else
- write_choice = &DumpCustomVTK::write_vtk;
+ write_choice = &DumpVTK::write_vtk;
// find current ptr for each compute,fix,variable
// check that fix frequency is acceptable
@@ -206,24 +209,24 @@ void DumpCustomVTK::init_style()
int icompute;
for (int i = 0; i < ncompute; i++) {
icompute = modify->find_compute(id_compute[i]);
- if (icompute < 0) error->all(FLERR,"Could not find dump custom/vtk compute ID");
+ if (icompute < 0) error->all(FLERR,"Could not find dump vtk compute ID");
compute[i] = modify->compute[icompute];
}
int ifix;
for (int i = 0; i < nfix; i++) {
ifix = modify->find_fix(id_fix[i]);
- if (ifix < 0) error->all(FLERR,"Could not find dump custom/vtk fix ID");
+ if (ifix < 0) error->all(FLERR,"Could not find dump vtk fix ID");
fix[i] = modify->fix[ifix];
if (nevery % modify->fix[ifix]->peratom_freq)
- error->all(FLERR,"Dump custom/vtk and fix not computed at compatible times");
+ error->all(FLERR,"Dump vtk and fix not computed at compatible times");
}
int ivariable;
for (int i = 0; i < nvariable; i++) {
ivariable = input->variable->find(id_variable[i]);
if (ivariable < 0)
- error->all(FLERR,"Could not find dump custom/vtk variable name");
+ error->all(FLERR,"Could not find dump vtk variable name");
variable[i] = ivariable;
}
@@ -239,25 +242,25 @@ void DumpCustomVTK::init_style()
if (iregion >= 0) {
iregion = domain->find_region(idregion);
if (iregion == -1)
- error->all(FLERR,"Region ID for dump custom/vtk does not exist");
+ error->all(FLERR,"Region ID for dump vtk does not exist");
}
}
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::write_header(bigint)
+void DumpVTK::write_header(bigint)
{
}
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::header_vtk(bigint)
+void DumpVTK::header_vtk(bigint)
{
}
/* ---------------------------------------------------------------------- */
-int DumpCustomVTK::count()
+int DumpVTK::count()
{
n_calls_ = 0;
@@ -807,7 +810,7 @@ int DumpCustomVTK::count()
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::write()
+void DumpVTK::write()
{
// simulation box bounds
@@ -905,7 +908,7 @@ void DumpCustomVTK::write()
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::pack(tagint *ids)
+void DumpVTK::pack(tagint *ids)
{
int n = 0;
for (std::map<int,FnPtrPack>::iterator it=pack_choice.begin(); it!=pack_choice.end(); ++it, ++n) {
@@ -922,14 +925,14 @@ void DumpCustomVTK::pack(tagint *ids)
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::write_data(int n, double *mybuf)
+void DumpVTK::write_data(int n, double *mybuf)
{
(this->*write_choice)(n,mybuf);
}
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::setFileCurrent() {
+void DumpVTK::setFileCurrent() {
delete [] filecurrent;
filecurrent = NULL;
@@ -1064,7 +1067,7 @@ void DumpCustomVTK::setFileCurrent() {
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::buf2arrays(int n, double *mybuf)
+void DumpVTK::buf2arrays(int n, double *mybuf)
{
for (int iatom=0; iatom < n; ++iatom) {
vtkIdType pid[1];
@@ -1123,7 +1126,7 @@ void DumpCustomVTK::buf2arrays(int n, double *mybuf)
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::prepare_domain_data(vtkRectilinearGrid *rgrid)
+void DumpVTK::prepare_domain_data(vtkRectilinearGrid *rgrid)
{
vtkSmartPointer<vtkDoubleArray> xCoords = vtkSmartPointer<vtkDoubleArray>::New();
xCoords->InsertNextValue(boxxlo);
@@ -1143,7 +1146,7 @@ void DumpCustomVTK::prepare_domain_data(vtkRectilinearGrid *rgrid)
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::prepare_domain_data_triclinic(vtkUnstructuredGrid *hexahedronGrid)
+void DumpVTK::prepare_domain_data_triclinic(vtkUnstructuredGrid *hexahedronGrid)
{
vtkSmartPointer<vtkPoints> hexahedronPoints = vtkSmartPointer<vtkPoints>::New();
hexahedronPoints->SetNumberOfPoints(8);
@@ -1173,7 +1176,7 @@ void DumpCustomVTK::prepare_domain_data_triclinic(vtkUnstructuredGrid *hexahedro
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::write_domain_vtk()
+void DumpVTK::write_domain_vtk()
{
vtkSmartPointer<vtkRectilinearGrid> rgrid = vtkSmartPointer<vtkRectilinearGrid>::New();
prepare_domain_data(rgrid.GetPointer());
@@ -1197,7 +1200,7 @@ void DumpCustomVTK::write_domain_vtk()
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::write_domain_vtk_triclinic()
+void DumpVTK::write_domain_vtk_triclinic()
{
vtkSmartPointer<vtkUnstructuredGrid> hexahedronGrid = vtkSmartPointer<vtkUnstructuredGrid>::New();
prepare_domain_data_triclinic(hexahedronGrid.GetPointer());
@@ -1221,7 +1224,7 @@ void DumpCustomVTK::write_domain_vtk_triclinic()
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::write_domain_vtr()
+void DumpVTK::write_domain_vtr()
{
vtkSmartPointer<vtkRectilinearGrid> rgrid = vtkSmartPointer<vtkRectilinearGrid>::New();
prepare_domain_data(rgrid.GetPointer());
@@ -1242,7 +1245,7 @@ void DumpCustomVTK::write_domain_vtr()
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::write_domain_vtu_triclinic()
+void DumpVTK::write_domain_vtu_triclinic()
{
vtkSmartPointer<vtkUnstructuredGrid> hexahedronGrid = vtkSmartPointer<vtkUnstructuredGrid>::New();
prepare_domain_data_triclinic(hexahedronGrid.GetPointer());
@@ -1263,7 +1266,7 @@ void DumpCustomVTK::write_domain_vtu_triclinic()
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::write_vtk(int n, double *mybuf)
+void DumpVTK::write_vtk(int n, double *mybuf)
{
++n_calls_;
@@ -1330,7 +1333,7 @@ void DumpCustomVTK::write_vtk(int n, double *mybuf)
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::write_vtp(int n, double *mybuf)
+void DumpVTK::write_vtp(int n, double *mybuf)
{
++n_calls_;
@@ -1394,7 +1397,7 @@ void DumpCustomVTK::write_vtp(int n, double *mybuf)
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::write_vtu(int n, double *mybuf)
+void DumpVTK::write_vtu(int n, double *mybuf)
{
++n_calls_;
@@ -1457,7 +1460,7 @@ void DumpCustomVTK::write_vtu(int n, double *mybuf)
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::reset_vtk_data_containers()
+void DumpVTK::reset_vtk_data_containers()
{
points = vtkSmartPointer<vtkPoints>::New();
pointsCells = vtkSmartPointer<vtkCellArray>::New();
@@ -1489,16 +1492,16 @@ void DumpCustomVTK::reset_vtk_data_containers()
/* ---------------------------------------------------------------------- */
-int DumpCustomVTK::parse_fields(int narg, char **arg)
+int DumpVTK::parse_fields(int narg, char **arg)
{
- pack_choice[X] = &DumpCustomVTK::pack_x;
+ pack_choice[X] = &DumpVTK::pack_x;
vtype[X] = DOUBLE;
name[X] = "x";
- pack_choice[Y] = &DumpCustomVTK::pack_y;
+ pack_choice[Y] = &DumpVTK::pack_y;
vtype[Y] = DOUBLE;
name[Y] = "y";
- pack_choice[Z] = &DumpCustomVTK::pack_z;
+ pack_choice[Z] = &DumpVTK::pack_z;
vtype[Z] = DOUBLE;
name[Z] = "z";
@@ -1508,33 +1511,33 @@ int DumpCustomVTK::parse_fields(int narg, char **arg)
i = iarg-5;
if (strcmp(arg[iarg],"id") == 0) {
- pack_choice[ID] = &DumpCustomVTK::pack_id;
+ pack_choice[ID] = &DumpVTK::pack_id;
vtype[ID] = INT;
name[ID] = arg[iarg];
} else if (strcmp(arg[iarg],"mol") == 0) {
if (!atom->molecule_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[MOL] = &DumpCustomVTK::pack_molecule;
+ pack_choice[MOL] = &DumpVTK::pack_molecule;
vtype[MOL] = INT;
name[MOL] = arg[iarg];
} else if (strcmp(arg[iarg],"proc") == 0) {
- pack_choice[PROC] = &DumpCustomVTK::pack_proc;
+ pack_choice[PROC] = &DumpVTK::pack_proc;
vtype[PROC] = INT;
name[PROC] = arg[iarg];
} else if (strcmp(arg[iarg],"procp1") == 0) {
- pack_choice[PROCP1] = &DumpCustomVTK::pack_procp1;
+ pack_choice[PROCP1] = &DumpVTK::pack_procp1;
vtype[PROCP1] = INT;
name[PROCP1] = arg[iarg];
} else if (strcmp(arg[iarg],"type") == 0) {
- pack_choice[TYPE] = &DumpCustomVTK::pack_type;
+ pack_choice[TYPE] = &DumpVTK::pack_type;
vtype[TYPE] = INT;
name[TYPE] =arg[iarg];
} else if (strcmp(arg[iarg],"element") == 0) {
- pack_choice[ELEMENT] = &DumpCustomVTK::pack_type;
+ pack_choice[ELEMENT] = &DumpVTK::pack_type;
vtype[ELEMENT] = STRING;
name[ELEMENT] = arg[iarg];
} else if (strcmp(arg[iarg],"mass") == 0) {
- pack_choice[MASS] = &DumpCustomVTK::pack_mass;
+ pack_choice[MASS] = &DumpVTK::pack_mass;
vtype[MASS] = DOUBLE;
name[MASS] = arg[iarg];
@@ -1545,182 +1548,182 @@ int DumpCustomVTK::parse_fields(int narg, char **arg)
} else if (strcmp(arg[iarg],"z") == 0) {
// required property
} else if (strcmp(arg[iarg],"xs") == 0) {
- if (domain->triclinic) pack_choice[XS] = &DumpCustomVTK::pack_xs_triclinic;
- else pack_choice[XS] = &DumpCustomVTK::pack_xs;
+ if (domain->triclinic) pack_choice[XS] = &DumpVTK::pack_xs_triclinic;
+ else pack_choice[XS] = &DumpVTK::pack_xs;
vtype[XS] = DOUBLE;
name[XS] = arg[iarg];
} else if (strcmp(arg[iarg],"ys") == 0) {
- if (domain->triclinic) pack_choice[YS] = &DumpCustomVTK::pack_ys_triclinic;
- else pack_choice[YS] = &DumpCustomVTK::pack_ys;
+ if (domain->triclinic) pack_choice[YS] = &DumpVTK::pack_ys_triclinic;
+ else pack_choice[YS] = &DumpVTK::pack_ys;
vtype[YS] = DOUBLE;
name[YS] = arg[iarg];
} else if (strcmp(arg[iarg],"zs") == 0) {
- if (domain->triclinic) pack_choice[ZS] = &DumpCustomVTK::pack_zs_triclinic;
- else pack_choice[ZS] = &DumpCustomVTK::pack_zs;
+ if (domain->triclinic) pack_choice[ZS] = &DumpVTK::pack_zs_triclinic;
+ else pack_choice[ZS] = &DumpVTK::pack_zs;
vtype[ZS] = DOUBLE;
name[ZS] = arg[iarg];
} else if (strcmp(arg[iarg],"xu") == 0) {
- if (domain->triclinic) pack_choice[XU] = &DumpCustomVTK::pack_xu_triclinic;
- else pack_choice[XU] = &DumpCustomVTK::pack_xu;
+ if (domain->triclinic) pack_choice[XU] = &DumpVTK::pack_xu_triclinic;
+ else pack_choice[XU] = &DumpVTK::pack_xu;
vtype[XU] = DOUBLE;
name[XU] = arg[iarg];
} else if (strcmp(arg[iarg],"yu") == 0) {
- if (domain->triclinic) pack_choice[YU] = &DumpCustomVTK::pack_yu_triclinic;
- else pack_choice[YU] = &DumpCustomVTK::pack_yu;
+ if (domain->triclinic) pack_choice[YU] = &DumpVTK::pack_yu_triclinic;
+ else pack_choice[YU] = &DumpVTK::pack_yu;
vtype[YU] = DOUBLE;
name[YU] = arg[iarg];
} else if (strcmp(arg[iarg],"zu") == 0) {
- if (domain->triclinic) pack_choice[ZU] = &DumpCustomVTK::pack_zu_triclinic;
- else pack_choice[ZU] = &DumpCustomVTK::pack_zu;
+ if (domain->triclinic) pack_choice[ZU] = &DumpVTK::pack_zu_triclinic;
+ else pack_choice[ZU] = &DumpVTK::pack_zu;
vtype[ZU] = DOUBLE;
name[ZU] = arg[iarg];
} else if (strcmp(arg[iarg],"xsu") == 0) {
- if (domain->triclinic) pack_choice[XSU] = &DumpCustomVTK::pack_xsu_triclinic;
- else pack_choice[XSU] = &DumpCustomVTK::pack_xsu;
+ if (domain->triclinic) pack_choice[XSU] = &DumpVTK::pack_xsu_triclinic;
+ else pack_choice[XSU] = &DumpVTK::pack_xsu;
vtype[XSU] = DOUBLE;
name[XSU] = arg[iarg];
} else if (strcmp(arg[iarg],"ysu") == 0) {
- if (domain->triclinic) pack_choice[YSU] = &DumpCustomVTK::pack_ysu_triclinic;
- else pack_choice[YSU] = &DumpCustomVTK::pack_ysu;
+ if (domain->triclinic) pack_choice[YSU] = &DumpVTK::pack_ysu_triclinic;
+ else pack_choice[YSU] = &DumpVTK::pack_ysu;
vtype[YSU] = DOUBLE;
name[YSU] = arg[iarg];
} else if (strcmp(arg[iarg],"zsu") == 0) {
- if (domain->triclinic) pack_choice[ZSU] = &DumpCustomVTK::pack_zsu_triclinic;
- else pack_choice[ZSU] = &DumpCustomVTK::pack_zsu;
+ if (domain->triclinic) pack_choice[ZSU] = &DumpVTK::pack_zsu_triclinic;
+ else pack_choice[ZSU] = &DumpVTK::pack_zsu;
vtype[ZSU] = DOUBLE;
name[ZSU] = arg[iarg];
} else if (strcmp(arg[iarg],"ix") == 0) {
- pack_choice[IX] = &DumpCustomVTK::pack_ix;
+ pack_choice[IX] = &DumpVTK::pack_ix;
vtype[IX] = INT;
name[IX] = arg[iarg];
} else if (strcmp(arg[iarg],"iy") == 0) {
- pack_choice[IY] = &DumpCustomVTK::pack_iy;
+ pack_choice[IY] = &DumpVTK::pack_iy;
vtype[IY] = INT;
name[IY] = arg[iarg];
} else if (strcmp(arg[iarg],"iz") == 0) {
- pack_choice[IZ] = &DumpCustomVTK::pack_iz;
+ pack_choice[IZ] = &DumpVTK::pack_iz;
vtype[IZ] = INT;
name[IZ] = arg[iarg];
} else if (strcmp(arg[iarg],"vx") == 0) {
- pack_choice[VX] = &DumpCustomVTK::pack_vx;
+ pack_choice[VX] = &DumpVTK::pack_vx;
vtype[VX] = DOUBLE;
name[VX] = arg[iarg];
} else if (strcmp(arg[iarg],"vy") == 0) {
- pack_choice[VY] = &DumpCustomVTK::pack_vy;
+ pack_choice[VY] = &DumpVTK::pack_vy;
vtype[VY] = DOUBLE;
name[VY] = arg[iarg];
} else if (strcmp(arg[iarg],"vz") == 0) {
- pack_choice[VZ] = &DumpCustomVTK::pack_vz;
+ pack_choice[VZ] = &DumpVTK::pack_vz;
vtype[VZ] = DOUBLE;
name[VZ] = arg[iarg];
} else if (strcmp(arg[iarg],"fx") == 0) {
- pack_choice[FX] = &DumpCustomVTK::pack_fx;
+ pack_choice[FX] = &DumpVTK::pack_fx;
vtype[FX] = DOUBLE;
name[FX] = arg[iarg];
} else if (strcmp(arg[iarg],"fy") == 0) {
- pack_choice[FY] = &DumpCustomVTK::pack_fy;
+ pack_choice[FY] = &DumpVTK::pack_fy;
vtype[FY] = DOUBLE;
name[FY] = arg[iarg];
} else if (strcmp(arg[iarg],"fz") == 0) {
- pack_choice[FZ] = &DumpCustomVTK::pack_fz;
+ pack_choice[FZ] = &DumpVTK::pack_fz;
vtype[FZ] = DOUBLE;
name[FZ] = arg[iarg];
} else if (strcmp(arg[iarg],"q") == 0) {
if (!atom->q_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[Q] = &DumpCustomVTK::pack_q;
+ pack_choice[Q] = &DumpVTK::pack_q;
vtype[Q] = DOUBLE;
name[Q] = arg[iarg];
} else if (strcmp(arg[iarg],"mux") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[MUX] = &DumpCustomVTK::pack_mux;
+ pack_choice[MUX] = &DumpVTK::pack_mux;
vtype[MUX] = DOUBLE;
name[MUX] = arg[iarg];
} else if (strcmp(arg[iarg],"muy") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[MUY] = &DumpCustomVTK::pack_muy;
+ pack_choice[MUY] = &DumpVTK::pack_muy;
vtype[MUY] = DOUBLE;
name[MUY] = arg[iarg];
} else if (strcmp(arg[iarg],"muz") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[MUZ] = &DumpCustomVTK::pack_muz;
+ pack_choice[MUZ] = &DumpVTK::pack_muz;
vtype[MUZ] = DOUBLE;
name[MUZ] = arg[iarg];
} else if (strcmp(arg[iarg],"mu") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[MU] = &DumpCustomVTK::pack_mu;
+ pack_choice[MU] = &DumpVTK::pack_mu;
vtype[MU] = DOUBLE;
name[MU] = arg[iarg];
} else if (strcmp(arg[iarg],"radius") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[RADIUS] = &DumpCustomVTK::pack_radius;
+ pack_choice[RADIUS] = &DumpVTK::pack_radius;
vtype[RADIUS] = DOUBLE;
name[RADIUS] = arg[iarg];
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[DIAMETER] = &DumpCustomVTK::pack_diameter;
+ pack_choice[DIAMETER] = &DumpVTK::pack_diameter;
vtype[DIAMETER] = DOUBLE;
name[DIAMETER] = arg[iarg];
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[OMEGAX] = &DumpCustomVTK::pack_omegax;
+ pack_choice[OMEGAX] = &DumpVTK::pack_omegax;
vtype[OMEGAX] = DOUBLE;
name[OMEGAX] = arg[iarg];
} else if (strcmp(arg[iarg],"omegay") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[OMEGAY] = &DumpCustomVTK::pack_omegay;
+ pack_choice[OMEGAY] = &DumpVTK::pack_omegay;
vtype[OMEGAY] = DOUBLE;
name[OMEGAY] = arg[iarg];
} else if (strcmp(arg[iarg],"omegaz") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[OMEGAZ] = &DumpCustomVTK::pack_omegaz;
+ pack_choice[OMEGAZ] = &DumpVTK::pack_omegaz;
vtype[OMEGAZ] = DOUBLE;
name[OMEGAZ] = arg[iarg];
} else if (strcmp(arg[iarg],"angmomx") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[ANGMOMX] = &DumpCustomVTK::pack_angmomx;
+ pack_choice[ANGMOMX] = &DumpVTK::pack_angmomx;
vtype[ANGMOMX] = DOUBLE;
name[ANGMOMX] = arg[iarg];
} else if (strcmp(arg[iarg],"angmomy") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[ANGMOMY] = &DumpCustomVTK::pack_angmomy;
+ pack_choice[ANGMOMY] = &DumpVTK::pack_angmomy;
vtype[ANGMOMY] = DOUBLE;
name[ANGMOMY] = arg[iarg];
} else if (strcmp(arg[iarg],"angmomz") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[ANGMOMZ] = &DumpCustomVTK::pack_angmomz;
+ pack_choice[ANGMOMZ] = &DumpVTK::pack_angmomz;
vtype[ANGMOMZ] = DOUBLE;
name[ANGMOMZ] = arg[iarg];
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[TQX] = &DumpCustomVTK::pack_tqx;
+ pack_choice[TQX] = &DumpVTK::pack_tqx;
vtype[TQX] = DOUBLE;
name[TQX] = arg[iarg];
} else if (strcmp(arg[iarg],"tqy") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[TQY] = &DumpCustomVTK::pack_tqy;
+ pack_choice[TQY] = &DumpVTK::pack_tqy;
vtype[TQY] = DOUBLE;
name[TQY] = arg[iarg];
} else if (strcmp(arg[iarg],"tqz") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
- pack_choice[TQZ] = &DumpCustomVTK::pack_tqz;
+ pack_choice[TQZ] = &DumpVTK::pack_tqz;
vtype[TQZ] = DOUBLE;
name[TQZ] = arg[iarg];
@@ -1728,7 +1731,7 @@ int DumpCustomVTK::parse_fields(int narg, char **arg)
// if no trailing [], then arg is set to 0, else arg is int between []
} else if (strncmp(arg[iarg],"c_",2) == 0) {
- pack_choice[ATTRIBUTES+i] = &DumpCustomVTK::pack_compute;
+ pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_compute;
vtype[ATTRIBUTES+i] = DOUBLE;
int n = strlen(arg[iarg]);
@@ -1738,24 +1741,24 @@ int DumpCustomVTK::parse_fields(int narg, char **arg)
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Invalid attribute in dump custom/vtk command");
+ error->all(FLERR,"Invalid attribute in dump vtk command");
argindex[ATTRIBUTES+i] = atoi(ptr+1);
*ptr = '\0';
} else argindex[ATTRIBUTES+i] = 0;
n = modify->find_compute(suffix);
- if (n < 0) error->all(FLERR,"Could not find dump custom/vtk compute ID");
+ if (n < 0) error->all(FLERR,"Could not find dump vtk compute ID");
if (modify->compute[n]->peratom_flag == 0)
- error->all(FLERR,"Dump custom/vtk compute does not compute per-atom info");
+ error->all(FLERR,"Dump vtk compute does not compute per-atom info");
if (argindex[ATTRIBUTES+i] == 0 && modify->compute[n]->size_peratom_cols > 0)
error->all(FLERR,
- "Dump custom/vtk compute does not calculate per-atom vector");
+ "Dump vtk compute does not calculate per-atom vector");
if (argindex[ATTRIBUTES+i] > 0 && modify->compute[n]->size_peratom_cols == 0)
error->all(FLERR,\
- "Dump custom/vtk compute does not calculate per-atom array");
+ "Dump vtk compute does not calculate per-atom array");
if (argindex[ATTRIBUTES+i] > 0 &&
argindex[ATTRIBUTES+i] > modify->compute[n]->size_peratom_cols)
- error->all(FLERR,"Dump custom/vtk compute vector is accessed out-of-range");
+ error->all(FLERR,"Dump vtk compute vector is accessed out-of-range");
field2index[ATTRIBUTES+i] = add_compute(suffix);
name[ATTRIBUTES+i] = arg[iarg];
@@ -1765,7 +1768,7 @@ int DumpCustomVTK::parse_fields(int narg, char **arg)
// if no trailing [], then arg is set to 0, else arg is between []
} else if (strncmp(arg[iarg],"f_",2) == 0) {
- pack_choice[ATTRIBUTES+i] = &DumpCustomVTK::pack_fix;
+ pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_fix;
vtype[ATTRIBUTES+i] = DOUBLE;
int n = strlen(arg[iarg]);
@@ -1775,22 +1778,22 @@ int DumpCustomVTK::parse_fields(int narg, char **arg)
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Invalid attribute in dump custom/vtk command");
+ error->all(FLERR,"Invalid attribute in dump vtk command");
argindex[ATTRIBUTES+i] = atoi(ptr+1);
*ptr = '\0';
} else argindex[ATTRIBUTES+i] = 0;
n = modify->find_fix(suffix);
- if (n < 0) error->all(FLERR,"Could not find dump custom/vtk fix ID");
+ if (n < 0) error->all(FLERR,"Could not find dump vtk fix ID");
if (modify->fix[n]->peratom_flag == 0)
- error->all(FLERR,"Dump custom/vtk fix does not compute per-atom info");
+ error->all(FLERR,"Dump vtk fix does not compute per-atom info");
if (argindex[ATTRIBUTES+i] == 0 && modify->fix[n]->size_peratom_cols > 0)
- error->all(FLERR,"Dump custom/vtk fix does not compute per-atom vector");
+ error->all(FLERR,"Dump vtk fix does not compute per-atom vector");
if (argindex[ATTRIBUTES+i] > 0 && modify->fix[n]->size_peratom_cols == 0)
- error->all(FLERR,"Dump custom/vtk fix does not compute per-atom array");
+ error->all(FLERR,"Dump vtk fix does not compute per-atom array");
if (argindex[ATTRIBUTES+i] > 0 &&
argindex[ATTRIBUTES+i] > modify->fix[n]->size_peratom_cols)
- error->all(FLERR,"Dump custom/vtk fix vector is accessed out-of-range");
+ error->all(FLERR,"Dump vtk fix vector is accessed out-of-range");
field2index[ATTRIBUTES+i] = add_fix(suffix);
name[ATTRIBUTES+i] = arg[iarg];
@@ -1799,7 +1802,7 @@ int DumpCustomVTK::parse_fields(int narg, char **arg)
// variable value = v_name
} else if (strncmp(arg[iarg],"v_",2) == 0) {
- pack_choice[ATTRIBUTES+i] = &DumpCustomVTK::pack_variable;
+ pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_variable;
vtype[ATTRIBUTES+i] = DOUBLE;
int n = strlen(arg[iarg]);
@@ -1809,9 +1812,9 @@ int DumpCustomVTK::parse_fields(int narg, char **arg)
argindex[ATTRIBUTES+i] = 0;
n = input->variable->find(suffix);
- if (n < 0) error->all(FLERR,"Could not find dump custom/vtk variable name");
+ if (n < 0) error->all(FLERR,"Could not find dump vtk variable name");
if (input->variable->atomstyle(n) == 0)
- error->all(FLERR,"Dump custom/vtk variable is not atom-style variable");
+ error->all(FLERR,"Dump vtk variable is not atom-style variable");
field2index[ATTRIBUTES+i] = add_variable(suffix);
name[ATTRIBUTES+i] = suffix;
@@ -1820,7 +1823,7 @@ int DumpCustomVTK::parse_fields(int narg, char **arg)
// custom per-atom floating point value = d_ID
} else if (strncmp(arg[iarg],"d_",2) == 0) {
- pack_choice[ATTRIBUTES+i] = &DumpCustomVTK::pack_custom;
+ pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
vtype[ATTRIBUTES+i] = DOUBLE;
int n = strlen(arg[iarg]);
@@ -1843,7 +1846,7 @@ int DumpCustomVTK::parse_fields(int narg, char **arg)
// custom per-atom integer value = i_ID
} else if (strncmp(arg[iarg],"i_",2) == 0) {
- pack_choice[ATTRIBUTES+i] = &DumpCustomVTK::pack_custom;
+ pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
vtype[ATTRIBUTES+i] = INT;
int n = strlen(arg[iarg]);
@@ -1873,7 +1876,7 @@ int DumpCustomVTK::parse_fields(int narg, char **arg)
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::identify_vectors()
+void DumpVTK::identify_vectors()
{
// detect vectors
vector_set.insert(X); // required
@@ -1923,7 +1926,7 @@ void DumpCustomVTK::identify_vectors()
if already in list, do not add, just return index, else add to list
------------------------------------------------------------------------- */
-int DumpCustomVTK::add_compute(char *id)
+int DumpVTK::add_compute(char *id)
{
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
@@ -1948,7 +1951,7 @@ int DumpCustomVTK::add_compute(char *id)
if already in list, do not add, just return index, else add to list
------------------------------------------------------------------------- */
-int DumpCustomVTK::add_fix(char *id)
+int DumpVTK::add_fix(char *id)
{
int ifix;
for (ifix = 0; ifix < nfix; ifix++)
@@ -1973,7 +1976,7 @@ int DumpCustomVTK::add_fix(char *id)
if already in list, do not add, just return index, else add to list
------------------------------------------------------------------------- */
-int DumpCustomVTK::add_variable(char *id)
+int DumpVTK::add_variable(char *id)
{
int ivariable;
for (ivariable = 0; ivariable < nvariable; ivariable++)
@@ -2002,7 +2005,7 @@ int DumpCustomVTK::add_variable(char *id)
if already in list, do not add, just return index, else add to list
------------------------------------------------------------------------- */
-int DumpCustomVTK::add_custom(char *id, int flag)
+int DumpVTK::add_custom(char *id, int flag)
{
int icustom;
for (icustom = 0; icustom < ncustom; icustom++)
@@ -2026,7 +2029,7 @@ int DumpCustomVTK::add_custom(char *id, int flag)
/* ---------------------------------------------------------------------- */
-int DumpCustomVTK::modify_param(int narg, char **arg)
+int DumpVTK::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"region") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
@@ -2301,7 +2304,7 @@ int DumpCustomVTK::modify_param(int narg, char **arg)
return # of bytes of allocated memory in buf, choose, variable arrays
------------------------------------------------------------------------- */
-bigint DumpCustomVTK::memory_usage()
+bigint DumpVTK::memory_usage()
{
bigint bytes = Dump::memory_usage();
bytes += memory->usage(choose,maxlocal);
@@ -2315,7 +2318,7 @@ bigint DumpCustomVTK::memory_usage()
extraction of Compute, Fix, Variable results
------------------------------------------------------------------------- */
-void DumpCustomVTK::pack_compute(int n)
+void DumpVTK::pack_compute(int n)
{
double *vector = compute[field2index[current_pack_choice_key]]->vector_atom;
double **array = compute[field2index[current_pack_choice_key]]->array_atom;
@@ -2337,7 +2340,7 @@ void DumpCustomVTK::pack_compute(int n)
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::pack_fix(int n)
+void DumpVTK::pack_fix(int n)
{
double *vector = fix[field2index[current_pack_choice_key]]->vector_atom;
double **array = fix[field2index[current_pack_choice_key]]->array_atom;
@@ -2359,7 +2362,7 @@ void DumpCustomVTK::pack_fix(int n)
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::pack_variable(int n)
+void DumpVTK::pack_variable(int n)
{
double *vector = vbuf[field2index[current_pack_choice_key]];
@@ -2371,9 +2374,8 @@ void DumpCustomVTK::pack_variable(int n)
/* ---------------------------------------------------------------------- */
-void DumpCustomVTK::pack_custom(int n)
+void DumpVTK::pack_custom(int n)
{
-
int index = field2index[n];
if (flag_custom[index] == 0) { // integer
diff --git a/src/USER-VTK/dump_custom_vtk.h b/src/USER-VTK/dump_vtk.h
similarity index 95%
rename from src/USER-VTK/dump_custom_vtk.h
rename to src/USER-VTK/dump_vtk.h
index f3b4a8b63e63cad24849ed30ae8cfc7ccb24473e..603ca114ba6ddc33938b76d6c05cfb1aa9556056 100644
--- a/src/USER-VTK/dump_custom_vtk.h
+++ b/src/USER-VTK/dump_vtk.h
@@ -17,12 +17,12 @@
#ifdef DUMP_CLASS
-DumpStyle(custom/vtk,DumpCustomVTK)
+DumpStyle(vtk,DumpVTK)
#else
-#ifndef LMP_DUMP_CUSTOM_VTK_H
-#define LMP_DUMP_CUSTOM_VTK_H
+#ifndef LMP_DUMP_VTK_H
+#define LMP_DUMP_VTK_H
#include "dump_custom.h"
#include <map>
@@ -40,7 +40,7 @@ class vtkUnstructuredGrid;
namespace LAMMPS_NS {
/**
- * @brief DumpCustomVTK class
+ * @brief DumpVTK class
* write atom data to vtk files.
*
* Similar to the DumpCustom class but uses the vtk library to write data to vtk simple
@@ -54,10 +54,11 @@ namespace LAMMPS_NS {
* This dump command does not support compressed files, buffering or custom format strings,
* multiproc is only supported by the xml formats, multifile option has to be used.
*/
-class DumpCustomVTK : public DumpCustom {
+
+class DumpVTK : public DumpCustom {
public:
- DumpCustomVTK(class LAMMPS *, int, char **);
- virtual ~DumpCustomVTK();
+ DumpVTK(class LAMMPS *, int, char **);
+ virtual ~DumpVTK();
virtual void write();
protected:
@@ -86,11 +87,11 @@ class DumpCustomVTK : public DumpCustom {
int add_custom(char *, int);
virtual int modify_param(int, char **);
- typedef void (DumpCustomVTK::*FnPtrHeader)(bigint);
+ typedef void (DumpVTK::*FnPtrHeader)(bigint);
FnPtrHeader header_choice; // ptr to write header functions
void header_vtk(bigint);
- typedef void (DumpCustomVTK::*FnPtrWrite)(int, double *);
+ typedef void (DumpVTK::*FnPtrWrite)(int, double *);
FnPtrWrite write_choice; // ptr to write data functions
void write_vtk(int, double *);
void write_vtp(int, double *);
@@ -103,7 +104,7 @@ class DumpCustomVTK : public DumpCustom {
void write_domain_vtr();
void write_domain_vtu_triclinic();
- typedef void (DumpCustomVTK::*FnPtrPack)(int);
+ typedef void (DumpVTK::*FnPtrPack)(int);
std::map<int, FnPtrPack> pack_choice; // ptrs to pack functions
std::map<int, int> vtype; // data type
std::map<int, std::string> name; // attribute labels
diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp
index 74d66e7c1b5d03e673234cad9813f5aded6b9397..45389ee61418a425f082e8bb80ec6438a2f8f322 100644
--- a/src/compute_dipole_chunk.cpp
+++ b/src/compute_dipole_chunk.cpp
@@ -31,10 +31,12 @@ enum { MASSCENTER, GEOMCENTER };
ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- idchunk(NULL), massproc(NULL), masstotal(NULL), chrgproc(NULL), chrgtotal(NULL), com(NULL),
+ idchunk(NULL), massproc(NULL), masstotal(NULL), chrgproc(NULL),
+ chrgtotal(NULL), com(NULL),
comall(NULL), dipole(NULL), dipoleall(NULL)
{
- if ((narg != 4) && (narg != 5)) error->all(FLERR,"Illegal compute dipole/chunk command");
+ if ((narg != 4) && (narg != 5))
+ error->all(FLERR,"Illegal compute dipole/chunk command");
array_flag = 1;
size_array_cols = 4;
diff --git a/src/domain.cpp b/src/domain.cpp
index 31fb3b855955e15126bb2e881ac6cfa68872e1ca..8ead12cd4e2b0f6e1289dfaf17c1614e2e334b05 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -944,6 +944,10 @@ void Domain::subbox_too_small_check(double thresh)
changed "if" to "while" to enable distance to
far-away ghost atom returned by atom->map() to be wrapped back into box
could be problem for looking up atom IDs when cutoff > boxsize
+ this should not be used if atom has moved infinitely far outside box
+ b/c while could iterate forever
+ e.g. fix shake prediction of new position with highly overlapped atoms
+ use minimum_image_once() instead
------------------------------------------------------------------------- */
void Domain::minimum_image(double &dx, double &dy, double &dz)
@@ -1009,6 +1013,10 @@ void Domain::minimum_image(double &dx, double &dy, double &dz)
changed "if" to "while" to enable distance to
far-away ghost atom returned by atom->map() to be wrapped back into box
could be problem for looking up atom IDs when cutoff > boxsize
+ this should not be used if atom has moved infinitely far outside box
+ b/c while could iterate forever
+ e.g. fix shake prediction of new position with highly overlapped atoms
+ use minimum_image_once() instead
------------------------------------------------------------------------- */
void Domain::minimum_image(double *delta)
@@ -1067,6 +1075,70 @@ void Domain::minimum_image(double *delta)
}
}
+/* ----------------------------------------------------------------------
+ minimum image convention in periodic dimensions
+ use 1/2 of box size as test
+ for triclinic, also add/subtract tilt factors in other dims as needed
+ only shift by one box length in each direction
+ this should not be used if multiple box shifts are required
+------------------------------------------------------------------------- */
+
+void Domain::minimum_image_once(double *delta)
+{
+ if (triclinic == 0) {
+ if (xperiodic) {
+ if (fabs(delta[0]) > xprd_half) {
+ if (delta[0] < 0.0) delta[0] += xprd;
+ else delta[0] -= xprd;
+ }
+ }
+ if (yperiodic) {
+ if (fabs(delta[1]) > yprd_half) {
+ if (delta[1] < 0.0) delta[1] += yprd;
+ else delta[1] -= yprd;
+ }
+ }
+ if (zperiodic) {
+ if (fabs(delta[2]) > zprd_half) {
+ if (delta[2] < 0.0) delta[2] += zprd;
+ else delta[2] -= zprd;
+ }
+ }
+
+ } else {
+ if (zperiodic) {
+ if (fabs(delta[2]) > zprd_half) {
+ if (delta[2] < 0.0) {
+ delta[2] += zprd;
+ delta[1] += yz;
+ delta[0] += xz;
+ } else {
+ delta[2] -= zprd;
+ delta[1] -= yz;
+ delta[0] -= xz;
+ }
+ }
+ }
+ if (yperiodic) {
+ if (fabs(delta[1]) > yprd_half) {
+ if (delta[1] < 0.0) {
+ delta[1] += yprd;
+ delta[0] += xy;
+ } else {
+ delta[1] -= yprd;
+ delta[0] -= xy;
+ }
+ }
+ }
+ if (xperiodic) {
+ if (fabs(delta[0]) > xprd_half) {
+ if (delta[0] < 0.0) delta[0] += xprd;
+ else delta[0] -= xprd;
+ }
+ }
+ }
+}
+
/* ----------------------------------------------------------------------
return local index of atom J or any of its images that is closest to atom I
if J is not a valid index like -1, just return it
diff --git a/src/domain.h b/src/domain.h
index 22e3191231de93c6cd09dee8eafb92403716336a..0f47a3c2ca36e708efeea632b08b155d529c2a61 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -112,6 +112,7 @@ class Domain : protected Pointers {
void subbox_too_small_check(double);
void minimum_image(double &, double &, double &);
void minimum_image(double *);
+ void minimum_image_once(double *);
int closest_image(int, int);
int closest_image(double *, int);
void closest_image(const double * const, const double * const,
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 4cd99b41d7a3c6f24a3a39b0bf20edbc211e3cc3..1d12ef578e29c64bcfc8d638027f2ddca2f89df6 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -667,7 +667,7 @@ int Neighbor::init_pair()
// create new lists, one per request including added requests
// wait to allocate initial pages until copy lists are detected
- // NOTE: can I allocation now, instead of down below?
+ // NOTE: can I allocate now, instead of down below?
nlist = nrequest;
@@ -1216,7 +1216,7 @@ void Neighbor::morph_copy()
// check all other lists
- for (j = 0; j < i; j++) {
+ for (j = 0; j < nrequest; j++) {
if (i == j) continue;
jrq = requests[j];
@@ -1279,7 +1279,7 @@ void Neighbor::morph_copy()
// turn list I into a copy of list J
// do not copy a list from another copy list, but from its parent list
- if (j < i) {
+ if (j < nrequest) {
irq->copy = 1;
if (jrq->copy) irq->copylist = jrq->copylist;
else irq->copylist = j;