diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index d9e60a520837a0756b9fef1b41ed8efc7597dee5..12a496cc9f0ab8672f7b53f07f8a5f5afdfb3cda 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -17,6 +17,32 @@ file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp)
file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
+# Utility functions
+function(list_to_bulletpoints result)
+ list(REMOVE_AT ARGV 0)
+ set(temp "")
+ foreach(item ${ARGV})
+ set(temp "${temp}* ${item}\n")
+ endforeach()
+ set(${result} "${temp}" PARENT_SCOPE)
+endfunction(list_to_bulletpoints)
+
+function(validate_option name values)
+ string(TOLOWER ${${name}} needle_lower)
+ string(TOUPPER ${${name}} needle_upper)
+ list(FIND ${values} ${needle_lower} IDX_LOWER)
+ list(FIND ${values} ${needle_upper} IDX_UPPER)
+ if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
+ list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
+ message(FATAL_ERROR "\n########################################################################\n"
+ "Invalid value '${${name}}' for option ${name}\n"
+ "\n"
+ "Possible values are:\n"
+ "${POSSIBLE_VALUE_LIST}"
+ "########################################################################")
+ endif()
+endfunction(validate_option)
+
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
@@ -106,8 +132,6 @@ if(NOT BUILD_EXE AND NOT BUILD_LIB)
message(FATAL_ERROR "You need to at least enable one of two following options: BUILD_LIB or BUILD_EXE")
endif()
-option(DEVELOPER_MODE "Enable developer mode" OFF)
-mark_as_advanced(DEVELOPER_MODE)
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
include(GNUInstallDirs)
@@ -133,15 +157,21 @@ else()
list(APPEND LAMMPS_LINK_LIBS mpi_stubs)
endif()
-set(LAMMPS_SIZE_LIMIT "LAMMPS_SMALLBIG" CACHE STRING "Lammps size limit")
-set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIGBIG LAMMPS_SMALLSMALL)
-add_definitions(-D${LAMMPS_SIZE_LIMIT})
-set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${LAMMPS_SIZE_LIMIT}")
+
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS size limit")
+set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
+set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
+validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
+string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
+add_definitions(-DLAMMPS_${LAMMPS_SIZES})
+set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_${LAMMPS_SIZES}")
# posix_memalign is not available on Windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
- set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
- add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
+ set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
+ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
+ add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
+ endif()
endif()
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
@@ -216,10 +246,12 @@ if(PKG_KSPACE)
if(${FFTW}_FOUND)
set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package")
else()
- set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
+ set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
endif()
- set_property(CACHE FFT PROPERTY STRINGS KISSFFT ${FFTW} MKL)
- if(NOT FFT STREQUAL "KISSFFT")
+ set(FFT_VALUES KISS ${FFTW} MKL)
+ set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
+ validate_option(FFT FFT_VALUES)
+ if(NOT FFT STREQUAL "KISS")
find_package(${FFT} REQUIRED)
if(NOT FFT STREQUAL "FFTW3F")
add_definitions(-DFFT_FFTW)
@@ -228,11 +260,16 @@ if(PKG_KSPACE)
endif()
include_directories(${${FFT}_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
+ else()
+ add_definitions(-DFFT_KISS)
endif()
- set(PACK_OPTIMIZATION "PACK_ARRAY" CACHE STRING "Optimization for FFT")
- set_property(CACHE PACK_OPTIMIZATION PROPERTY STRINGS PACK_ARRAY PACK_POINTER PACK_MEMCPY)
- if(NOT PACK_OPTIMIZATION STREQUAL "PACK_ARRAY")
- add_definitions(-D${PACK_OPTIMIZATION})
+ set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
+ set(FFT_PACK_VALUES array pointer memcpy)
+ set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
+ validate_option(FFT_PACK FFT_PACK_VALUES)
+ if(NOT FFT_PACK STREQUAL "array")
+ string(TOUPPER ${FFT_PACK} FFT_PACK)
+ add_definitions(-DFFT_PACK_${FFT_PACK})
endif()
endif()
@@ -374,8 +411,8 @@ if(PKG_USER-NETCDF)
endif()
if(PKG_USER-SMD)
- option(DOWNLOAD_Eigen3 "Download Eigen3 (instead of using the system's one)" OFF)
- if(DOWNLOAD_Eigen3)
+ option(DOWNLOAD_EIGEN3 "Download Eigen3 (instead of using the system's one)" OFF)
+ if(DOWNLOAD_EIGEN3)
include(ExternalProject)
ExternalProject_Add(Eigen3_build
URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
@@ -388,7 +425,7 @@ if(PKG_USER-SMD)
else()
find_package(Eigen3)
if(NOT Eigen3_FOUND)
- message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_Eigen3=ON to download it")
+ message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
endif()
endif()
include_directories(${EIGEN3_INCLUDE_DIR})
@@ -499,12 +536,13 @@ include(CheckLibraryExists)
if (CMAKE_VERSION VERSION_LESS "3.4")
enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4
endif()
-foreach(FUNC sin cos)
- check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
- if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
- message(FATAL_ERROR "Could not find needed math function - ${FUNC}")
- endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
-endforeach(FUNC)
+# RB: disabled this check because it breaks with KOKKOS CUDA enabled
+#foreach(FUNC sin cos)
+# check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
+# if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
+# message(FATAL_ERROR "Could not find needed math function - ${FUNC}")
+# endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
+#endforeach(FUNC)
list(APPEND LAMMPS_LINK_LIBS ${MATH_LIBRARIES})
######################################
@@ -729,33 +767,54 @@ if(PKG_OPT)
endif()
if(PKG_USER-INTEL)
- if(NOT DEVELOPER_MODE)
- if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
- message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler")
- endif()
- if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
+ find_package(TBB REQUIRED)
+ find_package(MKL REQUIRED)
+
+ if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+ message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler")
+ endif()
+
+ if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
- endif()
endif()
- option(INJECT_KNL_FLAG "Inject flags for KNL build" OFF)
- if(INJECT_KNL_FLAG)
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xMIC-AVX512")
+
+ if(NOT BUILD_OMP)
+ message(FATAL_ERROR "USER-INTEL requires OpenMP")
endif()
- option(INJECT_INTEL_FLAG "Inject OMG fast flags for USER-INTEL" ON)
- if(INJECT_INTEL_FLAG AND CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+
+ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "64")
+ message(FATAL_ERROR "USER-INTEL is only useful with LAMMPS_MEMALIGN=64")
+ endif()
+
+ set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
+ set(INTEL_ARCH_VALUES cpu knl)
+ set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
+ validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
+
+ if(INTEL_ARCH STREQUAL "knl")
+ set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
+ set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
+ add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
+ add_definitions(-DLMP_INTEL_OFFLOAD)
+ else()
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost")
endif()
include(CheckCXXCompilerFlag)
- foreach(_FLAG -qopenmp -qno-offload -fno-alias -ansi-alias -restrict -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high)
+ foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_FLAG}")
+ add_compile_options(${_FLAG})
endif()
endforeach()
endif()
+
+ add_definitions(-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG)
+
+ list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES} ${MKL_LIBRARIES})
+
set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
${USER-INTEL_SOURCES_DIR}/intel_buffers.h
@@ -788,11 +847,25 @@ if(PKG_GPU)
${GPU_SOURCES_DIR}/fix_gpu.h
${GPU_SOURCES_DIR}/fix_gpu.cpp)
- set(GPU_API "OpenCL" CACHE STRING "API used by GPU package")
- set_property(CACHE GPU_API PROPERTY STRINGS OpenCL CUDA)
-
- set(GPU_PREC "SINGLE_DOUBLE" CACHE STRING "LAMMPS GPU precision size")
- set_property(CACHE GPU_PREC PROPERTY STRINGS SINGLE_DOUBLE SINGLE_SINGLE DOUBLE_DOUBLE)
+ set(GPU_API "opencl" CACHE STRING "API used by GPU package")
+ set(GPU_API_VALUES opencl cuda)
+ set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES})
+ validate_option(GPU_API GPU_API_VALUES)
+ string(TOUPPER ${GPU_API} GPU_API)
+
+ set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision")
+ set(GPU_PREC_VALUES double mixed single)
+ set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES})
+ validate_option(GPU_PREC GPU_PREC_VALUES)
+ string(TOUPPER ${GPU_PREC} GPU_PREC)
+
+ if(GPU_PREC STREQUAL "DOUBLE")
+ set(GPU_PREC_SETTING "DOUBLE_DOUBLE")
+ elseif(GPU_PREC STREQUAL "MIXED")
+ set(GPU_PREC_SETTING "SINGLE_DOUBLE")
+ elseif(GPU_PREC STREQUAL "SINGLE")
+ set(GPU_PREC_SETTING "SINGLE_SINGLE")
+ endif()
file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
@@ -805,7 +878,7 @@ if(PKG_GPU)
endif()
option(CUDPP_OPT "Enable CUDPP_OPT" ON)
- set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)")
+ set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)")
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
@@ -819,10 +892,10 @@ if(PKG_GPU)
endif()
cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
- -DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
+ -DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING})
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>
- -DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
+ -DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING})
foreach(CU_OBJ ${GPU_GEN_OBJS})
get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
@@ -839,7 +912,7 @@ if(PKG_GPU)
add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
- target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
+ target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
if(CUDPP_OPT)
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
@@ -853,10 +926,13 @@ if(PKG_GPU)
target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
- elseif(GPU_API STREQUAL "OpenCL")
+ elseif(GPU_API STREQUAL "OPENCL")
find_package(OpenCL REQUIRED)
- set(OCL_TUNE "GENERIC" CACHE STRING "OpenCL Device Tuning")
- set_property(CACHE OCL_TUNE PROPERTY STRINGS INTEL FERMI KEPLER CYPRESS GENERIC)
+ set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
+ set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
+ set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
+ validate_option(OCL_TUNE OCL_TUNE_VALUES)
+ string(TOUPPER ${OCL_TUNE} OCL_TUNE)
include(OpenCLUtils)
set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
@@ -878,7 +954,7 @@ if(PKG_GPU)
add_library(gpu STATIC ${GPU_LIB_SOURCES})
target_link_libraries(gpu ${OpenCL_LIBRARIES})
target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
- target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
+ target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
list(APPEND LAMMPS_LINK_LIBS gpu)
@@ -1131,7 +1207,7 @@ if(PKG_GPU)
message(STATUS "GPU Api: ${GPU_API}")
if(GPU_API STREQUAL "CUDA")
message(STATUS "GPU Arch: ${GPU_ARCH}")
- elseif(GPU_API STREQUAL "OpenCL")
+ elseif(GPU_API STREQUAL "OPENCL")
message(STATUS "OCL Tune: ${OCL_TUNE}")
endif()
message(STATUS "GPU Precision: ${GPU_PREC}")
diff --git a/cmake/Modules/FindQUIP.cmake b/cmake/Modules/FindQUIP.cmake
index 4ee1baf4f878e4a1c684d1a71d6a6a2074a92ca9..b6d87d11fa1cc82fd65452074a48e7469f5d39b4 100644
--- a/cmake/Modules/FindQUIP.cmake
+++ b/cmake/Modules/FindQUIP.cmake
@@ -1,8 +1,8 @@
# - Find quip
# Find the native QUIP libraries.
#
-# QUIP_LIBRARIES - List of libraries when using fftw3.
-# QUIP_FOUND - True if fftw3 found.
+# QUIP_LIBRARIES - List of libraries of the QUIP package
+# QUIP_FOUND - True if QUIP library was found.
#
find_library(QUIP_LIBRARY NAMES quip)
diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..8cc050817e6b919d3d77935afcd26f1fd4d1cce0
--- /dev/null
+++ b/cmake/Modules/FindTBB.cmake
@@ -0,0 +1,46 @@
+# - Find parts of TBB
+# Find the native TBB headers and libraries.
+#
+# TBB_INCLUDE_DIRS - where to find tbb.h, etc.
+# TBB_LIBRARIES - List of libraries when using tbb.
+# TBB_FOUND - True if tbb found.
+#
+
+########################################################
+# TBB
+
+# TODO use more generic FindTBB
+
+find_path(TBB_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
+find_library(TBB_LIBRARY NAMES tbb PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
+ $ENV{TBBROOT}/lib/intel64/gcc4.4
+ $ENV{TBBROOT}/lib/intel64/gcc4.1)
+set(TBB_LIBRARIES ${TBB_LIBRARY})
+set(TBB_INCLUDE_DIRS ${TBB_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set TBB_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(TBB DEFAULT_MSG TBB_LIBRARY TBB_INCLUDE_DIR)
+
+mark_as_advanced(TBB_INCLUDE_DIR TBB_LIBRARY )
+
+########################################################
+# TBB Malloc
+
+find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
+find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
+ $ENV{TBBROOT}/lib/intel64/gcc4.4
+ $ENV{TBBROOT}/lib/intel64/gcc4.1)
+
+set(TBB_MALLOC_LIBRARIES ${TBB_MALLOC_LIBRARY})
+set(TBB_MALLOC_INCLUDE_DIRS ${TBB_MALLOC_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set TBB_MALLOC_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(TBB_MALLOC DEFAULT_MSG TBB_MALLOC_LIBRARY TBB_MALLOC_INCLUDE_DIR)
+
+mark_as_advanced(TBB_MALLOC_INCLUDE_DIR TBB_MALLOC_LIBRARY )
diff --git a/cmake/README.md b/cmake/README.md
index b6644ffda959c45faec16e89e0a6a3275725c796..85375cd2aa49ca9ddb0bc97b0fa50d048a344f4a 100644
--- a/cmake/README.md
+++ b/cmake/README.md
@@ -62,7 +62,7 @@ should get you started.
git clone https://github.com/lammps/lammps.git
mkdir lammps/build
cd lammps/build
-cmake ../cmake [-DOPTION_A=VALUE_A -DOPTION_B=VALUE_B ...]
+cmake [-D OPTION_A=VALUE_A -D OPTION_B=VALUE_B ...] ../cmake
make
```
@@ -174,7 +174,7 @@ presets can be found in the `cmake/presets` folder.
# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package
mkdir build
cd build
-cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
+cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
```
# Reference
@@ -265,6 +265,16 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
</dl>
</td>
</tr>
+<tr>
+ <td><code>BUILD_LIB</code></td>
+ <td>control whether to build LAMMPS as a library</td>
+ <td>
+ <dl>
+ <dt><code>off</code> (default)</dt>
+ <dt><code>on</code></dt>
+ </dl>
+ </td>
+</tr>
<tr>
<td><code>BUILD_SHARED_LIBS</code></td>
<td>control whether to build LAMMPS as a shared-library</td>
@@ -315,8 +325,8 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
`mpicxx` in your path and use this MPI implementation.</td>
<td>
<dl>
- <dt><code>off</code> (default)</dt>
- <dt><code>on</code></dt>
+ <dt><code>on</code> (default, if found)</dt>
+ <dt><code>off</code></dt>
</dl>
</td>
</tr>
@@ -325,8 +335,8 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
<td>control whether to build LAMMPS with OpenMP support.</td>
<td>
<dl>
- <dt><code>off</code> (default)</dt>
- <dt><code>on</code></dt>
+ <dt><code>on</code> (default, if found)</dt>
+ <dt><code>off</code></dt>
</dl>
</td>
</tr>
@@ -1271,7 +1281,7 @@ providing the identical features and USER interface.</strong></p>
</td>
<td>
<dl>
- <dt><code>KISSFFT</code></dt>
+ <dt><code>KISS</code></dt>
<dt><code>FFTW3</code></dt>
<dt><code>FFTW2</code></dt>
<dt><code>MKL</code></dt>
@@ -1279,13 +1289,13 @@ providing the identical features and USER interface.</strong></p>
</td>
</tr>
<tr>
- <td><code>PACK_ARRAY</code></td>
+ <td><code>FFT_PACK</code></td>
<td>Optimization for FFT</td>
<td>
<dl>
- <dt><code>PACK_ARRAY</code></dt>
- <dt><code>PACK_POINTER</code></dt>
- <dt><code>PACK_MEMCPY</code></dt>
+ <dt><code>array (default)</code></dt>
+ <dt><code>pointer</code></dt>
+ <dt><code>memcpy</code></dt>
</dl>
</td>
</tr>
@@ -1377,6 +1387,29 @@ TODO
### PYTHON Package
+### USER-INTEL Package
+
+<table>
+<thead>
+<tr>
+ <th>Option</th>
+ <th>Description</th>
+ <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+ <td><code>INTEL_ARCH</code></td>
+ <td>Target architecture for USER-INTEL package</td>
+ <td>
+ <dl>
+ <dt><code>cpu</code> (default)</dt>
+ <dt><code>knl</code></dt>
+ </dl>
+ </td>
+</tr>
+</tbody>
+</table>
### GPU Package
The GPU package builds a support library which can either use OpenCL or CUDA as
@@ -1396,8 +1429,8 @@ target API.
<td>API used by GPU package</td>
<td>
<dl>
- <dt><code>OpenCL</code> (default)</dt>
- <dt><code>CUDA</code></dt>
+ <dt><code>opencl</code> (default)</dt>
+ <dt><code>cuda</code></dt>
</dl>
</td>
</tr>
@@ -1406,9 +1439,9 @@ target API.
<td>Precision size used by GPU package kernels</td>
<td>
<dl>
- <dt><code>SINGLE_DOUBLE</code></dt>
- <dt><code>SINGLE_SINGLE</code></dt>
- <dt><code>DOUBLE_DOUBLE</code></dt>
+ <dt><code>mixed</code> (default)</dt>
+ <dt><code>single</code></dt>
+ <dt><code>double</code></dt>
</dl>
</td>
</tr>
@@ -1417,12 +1450,12 @@ target API.
<td>Tuning target for OpenCL driver code</td>
<td>
<dl>
- <dt><code>GENERIC</code> (default)</dt>
- <dt><code>INTEL</code> (Intel CPU)</dt>
- <dt><code>PHI</code> (Intel Xeon Phi)</dt>
- <dt><code>FERMI</code> (NVIDIA)</dt>
- <dt><code>KEPLER</code> (NVIDIA)</dt>
- <dt><code>CYPRESS</code> (AMD)</dt>
+ <dt><code>generic</code> (default)</dt>
+ <dt><code>intel</code> (Intel CPU)</dt>
+ <dt><code>phi</code> (Intel Xeon Phi)</dt>
+ <dt><code>fermi</code> (NVIDIA)</dt>
+ <dt><code>kepler</code> (NVIDIA)</dt>
+ <dt><code>cypress</code> (AMD)</dt>
</dl>
</td>
</tr>
@@ -1517,6 +1550,16 @@ Requires a Eigen3 installation
</tr>
</thead>
<tbody>
+<tr>
+ <td><code>WITH_JPEG</code></td>
+ <td>Enables/Disable JPEG support in LAMMPS</td>
+ <td>
+ <dl>
+ <dt><code>yes</code> (default, if found)</dt>
+ <dt><code>no</code></dt>
+ </dl>
+ </td>
+</tr>
<tr>
<td><code>JPEG_INCLUDE_DIR</code></td>
<td></td>
@@ -1544,6 +1587,16 @@ Requires a Eigen3 installation
</tr>
</thead>
<tbody>
+<tr>
+ <td><code>WITH_PNG</code></td>
+ <td>Enables/Disable PNG support in LAMMPS</td>
+ <td>
+ <dl>
+ <dt><code>yes</code> (default, if found)</dt>
+ <dt><code>no</code></dt>
+ </dl>
+ </td>
+</tr>
<tr>
<td><code>PNG_INCLUDE_DIR</code></td>
<td></td>
@@ -1572,6 +1625,16 @@ requires `gzip` to be in your `PATH`
</tr>
</thead>
<tbody>
+<tr>
+ <td><code>WITH_GZIP</code></td>
+ <td>Enables/Disable GZIP support in LAMMPS</td>
+ <td>
+ <dl>
+ <dt><code>yes</code> (default, if found)</dt>
+ <dt><code>no</code></dt>
+ </dl>
+ </td>
+</tr>
<tr>
<td><code>GZIP_EXECUTABLE</code></td>
<td></td>
@@ -1594,6 +1657,16 @@ requires `ffmpeg` to be in your `PATH`
</tr>
</thead>
<tbody>
+<tr>
+ <td><code>WITH_FFMPEG</code></td>
+ <td>Enables/Disable FFMPEG support in LAMMPS</td>
+ <td>
+ <dl>
+ <dt><code>yes</code> (default, if found)</dt>
+ <dt><code>no</code></dt>
+ </dl>
+ </td>
+</tr>
<tr>
<td><code>FFMPEG_EXECUTABLE</code></td>
<td></td>
@@ -1606,8 +1679,13 @@ requires `ffmpeg` to be in your `PATH`
## Compilers
-By default, `cmake` will use your environment C/C++/Fortran compilers for a build. It uses the `CC`, `CXX` and `FC` environment variables to detect which compilers should be used. However, these values
-will be cached after the first run of `cmake`. Subsequent runs of `cmake` will ignore changes in these environment variables. To ensure the correct values are used you avoid the cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`, `CMAKE_Fortran_COMPILER` options directly.
+By default, `cmake` will use your environment C/C++/Fortran compilers for a
+build. It uses the `CC`, `CXX` and `FC` environment variables to detect which
+compilers should be used. However, these values will be cached after the first
+run of `cmake`. Subsequent runs of `cmake` will ignore changes in these
+environment variables. To ensure the correct values are used you avoid the
+cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`,
+`CMAKE_Fortran_COMPILER` options directly.
<table>
<thead>
@@ -1643,20 +1721,20 @@ will be cached after the first run of `cmake`. Subsequent runs of `cmake` will i
### Building with GNU Compilers
```bash
-cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
+cmake -D CMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++ -D CMAKE_Fortran_COMPILER=gfortran ../cmake
```
### Building with Intel Compilers
```bash
-cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+cmake -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icpc -D CMAKE_Fortran_COMPILER=ifort ../cmake
```
### Building with LLVM/Clang Compilers
```bash
-cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
+cmake -D CMAKE_C_COMPILER=clang -D CMAKE_CXX_COMPILER=clang++ -D CMAKE_Fortran_COMPILER=flang ../cmake
```
diff --git a/doc/src/Build.txt b/doc/src/Build.txt
new file mode 100644
index 0000000000000000000000000000000000000000..218664897f70d20893ccae5256b404c6af756d42
--- /dev/null
+++ b/doc/src/Build.txt
@@ -0,0 +1,58 @@
+"Previous Section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Build LAMMPS :h2
+
+LAMMPS can be built as an executable or library from source code via
+either traditional makefiles (which may require manual editing)
+for use with GNU make or gmake, or a build environment generated by CMake
+(Unix Makefiles, Xcode, Visual Studio, KDevelop or more). As an
+alternative you can download a package with pre-built executables
+as described on the "Install"_Install.html doc page.
+
+<!-- RST
+
+.. toctree::
+ :maxdepth: 1
+
+ Build_cmake
+ Build_make
+ Build_link
+
+.. toctree::
+ :maxdepth: 1
+
+ Build_basics
+ Build_settings
+ Build_package
+
+.. toctree::
+ :maxdepth: 1
+
+ Build_extras
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Build LAMMPS with CMake"_Build_cmake.html
+"Build LAMMPS with make"_Build_make.html
+"Link LAMMPS as a library to another code"_Build_link.html :all(b)
+
+Build options:
+
+"Basic build options: serial/parallel, compilers, executable/library"_Build_basics.html
+"Optional build settings"_Build_settings.html :all(b)
+"Include packages in build"_Build_package.html
+"Packages with extra build options"_Build_extras.html :all(b)
+
+If you have problems building LAMMPS, it is often due to software
+issues on your local machine. If you can, find a local expert to
+help. If you're still stuck, send an email to the "LAMMPS mail
+list"_http://lammps.sandia.gov/mail.html.
diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt
new file mode 100644
index 0000000000000000000000000000000000000000..425266a35fd8e40bf1e30831245101f2d0695b0b
--- /dev/null
+++ b/doc/src/Build_basics.txt
@@ -0,0 +1,315 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Basic build options :h3
+
+The following topics are covered on this page, for building both with
+CMake and make:
+
+"Serial vs parallel build"_#serial
+"Choice of compiler and compile/link options"_#compile
+"Build LAMMPS as an executable or a library"_#exe
+"Build the LAMMPS documentation"_#doc
+"Install LAMMPS after a build"_#install :ul
+
+:line
+
+Serial vs parallel build :h3,link(serial)
+
+LAMMPS can be built to run in parallel using the ubiquitous "MPI
+(message-passing
+interface)"_https://en.wikipedia.org/wiki/Message_Passing_Interface
+library. Or it can built to run on a single processor (serial)
+without MPI. It can also be built with support for OpenMP threading
+(see more discussion below).
+
+[CMake variables]:
+
+-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no
+-D BUILD_OMP=value # yes or no (default)
+-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc
+ # no default value :pre
+
+The executable created by CMake (after running make) is lmp_name. If
+the LAMMPS_MACHINE variable is not specified, the executable is just
+lmp. Using BUILD_MPI=no will produce a serial executable.
+
+[Traditional make]:
+
+cd lammps/src
+make mpi # parallel build, produces lmp_mpi using Makefile.mpi
+make serial # serial build, produces lmp_serial using Makefile/serial
+make mybox :pre # uses Makefile.mybox to produce lmp_mybox :pre
+
+Serial build (see src/MAKE/Makefile.serial):
+
+MPI_INC = -I../STUBS
+MPI_PATH = -L../STUBS
+MPI_LIB = -lmpi_stubs :pre
+
+For a parallel build, if MPI is installed on your system in the usual
+place (e.g. under /usr/local), you do not need to specify the 3
+variables MPI_INC, MPI_PATH, MPI_LIB. The MPI wrapper on the compiler
+(e.g. mpicxx, mpiCC) knows where to find the needed include and
+library files. Failing this, these 3 variables can be used to specify
+where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH)
+are found, and the name of the library files (MPI_LIB).
+
+For a serial build, you need to specify the 3 varaibles, as shown
+above.
+
+For a serial LAMMPS build, use the dummy MPI library provided in
+src/STUBS. You also need to build the STUBS library for your platform
+before making LAMMPS itself. A "make serial" build does this for.
+Otherwise, type "make mpi-stubs" from the src directory, or "make"
+from the src/STUBS dir. If the build fails, you will need to edit the
+STUBS/Makefile for your platform.
+
+The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
+that calls gettimeofday() . If your system doesn't support
+gettimeofday() , you'll need to insert code to call another timer.
+Note that the ANSI-standard function clock() rolls over after an hour
+or so, and is therefore insufficient for timing long LAMMPS
+simulations.
+
+[CMake and make info]:
+
+If you are installing MPI yourself, we recommend MPICH2 from Argonne
+National Laboratory or OpenMPI. MPICH can be downloaded from the
+"Argonne MPI site"_http://www.mcs.anl.gov/research/projects/mpich2/.
+OpenMPI can be downloaded from the "OpenMPI
+site"_http://www.open-mpi.org. Other MPI packages should also work.
+If you are running on a large parallel machine, your system admins or
+the vendor should have already installed a version of MPI, which is
+likely to be faster than a self-installed MPICH or OpenMPI, so find
+out how to build and link with it.
+
+The majority of OpenMP (threading) support in LAMMPS is provided by
+the USER-OMP package; see the "Speed omp"_Speed_omp.html doc page for
+details. The USER-INTEL package also provides OpenMP support (it is
+compatible with USER-OMP) and adds vectorization support when compiled
+with the Intel compilers on top of that. Also, the KOKKOS package can
+be compiled for using OpenMP threading.
+
+However, there are a few commands in LAMMPS that have native OpenMP
+support. These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
+USER-DPD packages. In addition some packages support OpenMP threading
+indirectly through the libraries they interface to: e.g. LATTE and
+USER-COLVARS. See the "Packages details"_Packages_details.html doc
+page for more info on these packages and the doc pages for their
+respective commands for OpenMP threading info.
+
+For CMake, if you use BUILD_OMP=yes, you can use these packages and
+turn on their native OpenMP support and turn on their native OpenMP
+support at run time, by setting the OMP_NUM_THREADS environment
+variable before you launch LAMMPS.
+
+For building via conventional make, the CCFLAGS and LINKFLAGS
+variables in Makefile.machine need to include the compiler flag that
+enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel
+compilers it is -qopenmp. If you are using a different compiler,
+please refer to its documentation.
+
+:line
+
+Choice of compiler and compile/link options :h3,link(compile)
+
+The choice of compiler and compiler flags can be important for
+performance. Vendor compilers can produce faster code than
+open-source compilers like GNU. On boxes with Intel CPUs, we suggest
+trying the "Intel C++ compiler"_intel.
+
+:link(intel,https://software.intel.com/en-us/intel-compilers)
+
+On parallel clusters or supercomputers which use "modules" for their
+compile/link environments, you can often access different compilers by
+simply loading the appropriate module before building LAMMPS.
+
+[CMake variables]:
+
+-D CMAKE_CXX_COMPILER=name # name of C++ compiler
+-D CMAKE_C_COMPILER=name # name of C compiler
+-D CMAKE_Fortran_COMPILER=name # name of Fortran compiler :pre
+
+-D CMAKE_CXX_FlAGS=string # flags to use with C++ compiler
+-D CMAKE_C_FlAGS=string # flags to use with C compiler
+-D CMAKE_Fortran_FlAGS=string # flags to use with Fortran compiler :pre
+
+By default CMake will use a compiler it finds and it will add
+optimization flags appropriate to that compiler and any "accelerator
+packages"_Speed_packages.html you have included in the build.
+
+You can tell CMake to look for a specific compiler with these varaible
+settings. Likewise you can specify the FLAGS variables if you want to
+experiment with alternate optimization flags. You should specify all
+3 compilers, so that the small number of LAMMPS source files written
+in C or Fortran are built with a compiler consistent with the one used
+for all the C++ files:
+
+Building with GNU Compilers:
+cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
+Building with Intel Compilers:
+cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+Building with LLVM/Clang Compilers:
+cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang :pre
+
+NOTE: When the cmake command completes, it prints info to the screen
+as to which compilers it is using, and what flags will be used in the
+compilation. Note that if the top-level compiler is mpicxx, it is
+simply a wrapper on a real compiler. The underlying compiler info is
+what will be listed in the CMake output. You should check to insure
+you are using the compiler and optimization flags are the ones you
+want.
+
+[Makefile.machine settings]:
+
+Parallel build (see src/MAKE/Makefile.mpi):
+
+CC = mpicxx
+CCFLAGS = -g -O3
+LINK = mpicxx
+LINKFLAGS = -g -O :pre
+
+Serial build (see src/MAKE/Makefile.serial):
+
+CC = g++
+CCFLAGS = -g -O3
+LINK = g++
+LINKFLAGS = -g -O :pre
+
+The "compiler/linker settings" section of a Makefile.machine lists
+compiler and linker settings for your C++ compiler, including
+optimization flags. You should always use mpicxx or mpiCC for
+a parallel build, since these compiler wrappers will include
+a variety of settings appropriate for your MPI installation.
+
+NOTE: If you build LAMMPS with any "accelerator
+packages"_Speed_packages.html included, they have specific
+optimization flags that are either required or recommended for optimal
+performance. You need to include these in the CCFLAGS and LINKFLAGS
+settings above. For details, see the individual package doc pages
+listed on the "Speed packages"_Speed_packages.html doc page. Or
+examine these files in the src/MAKE/OPTIONS directory. They
+correspond to each of the 5 accelerator packages and their hardware
+variants:
+
+Makefile.opt # OPT package
+Makefile.omp # USER-OMP package
+Makefile.intel_cpu # USER-INTEL package for CPUs
+Makefile.intel_coprocessor # USER-INTEL package for KNLs
+Makefile.gpu # GPU package
+Makefile.kokkos_cuda_mpi # KOKKOS package for GPUs
+Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP)
+Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP) :pre
+
+:line
+
+Build LAMMPS as an executable or a library :h3,link(exe)
+
+LAMMPS can be built as either an executable or as a static or shared
+library. The LAMMPS library can be called from another application or
+a scripting language. See the "Howto couple"_Howto_couple.html doc
+page for more info on coupling LAMMPS to other codes. See the
+"Python"_Python doc page for more info on wrapping and running LAMMPS
+from Python via its library interface.
+
+[CMake variables]:
+
+-D BUILD_EXE=value # yes (default) or no
+-D BUILD_LIB=value # yes or no (default)
+-D BUILD_SHARED_LIBS=value # yes or no (default) :pre
+
+Setting BUILD_EXE=no will not produce an executable. Setting
+BUILD_LIB=yes will produce a static library named liblammps.a.
+Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a
+shared library named liblammps.so.
+
+[Traditional make]:
+
+cd lammps/src
+make machine # build LAMMPS executable lmp_machine
+make mode=lib machine # build LAMMPS static lib liblammps_machine.a
+make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so :pre
+
+The two library builds also create generic soft links, named
+liblammps.a and liblammps.so, which point to the liblammps_machine
+files.
+
+[CMake and make info]:
+
+Note that for a shared library to be usable by a calling program, all
+the auxiliary libraries it depends on must also exist as shared
+libraries. This will be the case for libraries included with LAMMPS,
+such as the dummy MPI library in src/STUBS or any package libraries in
+the lib/packages directroy, since they are always built as shared
+libraries using the -fPIC switch. However, if a library like MPI or
+FFTW does not exist as a shared library, the shared library build will
+generate an error. This means you will need to install a shared
+library version of the auxiliary library. The build instructions for
+the library should tell you how to do this.
+
+As an example, here is how to build and install the "MPICH
+library"_mpich, a popular open-source version of MPI, distributed by
+Argonne National Lab, as a shared library in the default
+/usr/local/lib location:
+
+:link(mpich,http://www-unix.mcs.anl.gov/mpi)
+
+./configure --enable-shared
+make
+make install :pre
+
+You may need to use "sudo make install" in place of the last line if
+you do not have write privileges for /usr/local/lib. The end result
+should be the file /usr/local/lib/libmpich.so.
+
+:line
+
+Build the LAMMPS documentation :h3,link(doc)
+
+[CMake variable]:
+
+-D BUILD_DOC=value # yes or no (default) :pre
+
+This will create the HTML doc pages within the CMake build directory.
+The reason to do this is if you want to "install" LAMMPS on a system
+after the CMake build via "make install", and include the doc pages in
+the install.
+
+[Traditional make]:
+
+cd lammps/doc
+make html # html doc pages
+make pdf # single Manual.pdf file :pre
+
+This will create a lammps/doc/html dir with the HTML doc pages so that
+you can browse them locally on your system. Type "make" from the
+lammps/doc dir to see other options.
+
+:line
+
+Install LAMMPS after a build :h3,link(install)
+
+After building LAMMPS, you may wish to copy the LAMMPS executable of
+library, along with other LAMMPS files (library header, doc files) to
+a globally visible place on your system, for others to access. Note
+that you may need super-user priveleges (e.g. sudo) if the directory
+you want to copy files to is protected.
+
+[CMake variable]:
+
+cmake -D CMAKE_INSTALL_PREFIX=path \[options ...\] ../cmake
+make # perform make after CMake command
+make install # perform the installation into prefix :pre
+
+[Traditional make]:
+
+There is no "install" option in the src/Makefile for LAMMPS. If you
+wish to do this you will need to first build LAMMPS, then manually
+copy the desired LAMMPS files to the appropriate system directories.
diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c42bb21c7e129d2bca820515331f3c80f0bbbe5b
--- /dev/null
+++ b/doc/src/Build_cmake.txt
@@ -0,0 +1,197 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Build LAMMPS with CMake :h3
+
+This page is a short summary of how to use CMake to build LAMMPS.
+Details on CMake variables that enable specific LAMMPS build options
+are given on the pages linked to from the "Build"_Build.html doc page.
+
+Richard Berger (Temple U) has also written a more comprehensive guide
+for how to use CMake to build LAMMPS. If you are new to CMake it is a
+good place to start:
+
+"Bulding LAMMPS using
+CMake"_https://github.com/lammps/lammps/blob/master/cmake/README.md
+
+:line
+
+Building LAMMPS with CMake is a two-step process. First you use CMake
+to create a build environment in a new directory. On Linux systems,
+this will be based on makefiles for use with make. Then you use the
+make command to build LAMMPS, which uses the created
+Makefile(s). Example:
+
+cd lammps # change to the LAMMPS distribution directory
+mkdir build; cd build # create a new directory (folder) for build
+cmake ../cmake \[options ...\] # configuration with (command-line) cmake
+make # compilation :pre
+
+The cmake command will detect available features, enable selected
+packages and options, and will generate the build environment. The make
+command will then compile and link LAMMPS, producing (by default) an
+executable called "lmp" and a library called "liblammps.a" in the
+"build" folder.
+
+If your machine has multiple CPU cores (most do these days), using a
+command like "make -jN" (with N being the number of available local
+CPU cores) can be much faster. If you plan to do development on
+LAMMPS or need to recompile LAMMPS repeatedly, installation of the
+ccache (= Compiler Cache) software may speed up compilation even more.
+
+After compilation, you can optionally copy the LAMMPS executable and
+library into your system folders (by default under /usr/local) with:
+
+make install # optional, copy LAMMPS executable & library elsewhere :pre
+
+:line
+
+There are 3 variants of CMake: a command-line verison (cmake), a text mode
+UI version (ccmake), and a graphical GUI version (cmake-GUI). You can use
+any of them interchangeably to configure and create the LAMMPS build
+environment. On Linux all the versions produce a Makefile as their
+output. See more details on each below.
+
+You can specify a variety of options with any of the 3 versions, which
+affect how the build is performed and what is included in the LAMMPS
+executable. Links to pages explaining all the options are listed on
+the "Build"_Build.html doc page.
+
+You must perform the CMake build system generation and compilation in
+a new directory you create. It can be anywhere on your local machine.
+In these Build pages we assume that you are building in a directory
+called "lammps/build". You can perform separate builds independently
+with different options, so long as you perform each of them in a
+separate directory you create. All the auxiliary files created by one
+build process (executable, object files, log files, etc) are stored in
+this directory or sub-directories within it that CMake creates.
+
+NOTE: To perform a CMake build, no packages can be installed or a
+build been previously attempted in the LAMMPS src directory by using
+"make" commands to "perform a conventional LAMMPS
+build"_Build_make.html. CMake detects if this is the case and
+generates an error, telling you to type "make no-all purge" in the src
+directory to un-install all packages. The purge removes all the *.h
+files auto-generated by make.
+
+You must have CMake version 2.8 or later on your system to build
+LAMMPS. If you include the GPU or KOKKOS packages, CMake version 3.2
+or later is required. Installation instructions for CMake are below.
+
+After the initial build, if you edit LAMMPS source files, or add your
+own new files to the source directory, you can just re-type make from
+your build directory and it will re-compile only the files that have
+changed. If you want to change CMake options you can run cmake (or
+ccmake or cmake-gui) again from the same build directory and alter
+various options; see details below. Or you can remove the entire build
+folder, recreate the directory and start over.
+
+:line
+
+[Command-line version of CMake]:
+
+cmake \[options ...\] /path/to/lammps/cmake # build from any dir
+cmake \[options ...\] ../cmake # build from lammps/build :pre
+
+The cmake command takes one required argument, which is the LAMMPS
+cmake directory which contains the CMakeLists.txt file.
+
+The argument can be preceeded or followed by various CMake
+command-line options. Several useful ones are:
+
+-D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired
+-D CMAKE_BUILD_TYPE=type # type = Release or Debug
+-G output # style of output CMake generates
+-DVARIABLE=value # setting for a LAMMPS feature to enable
+-D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir :pre
+
+All the LAMMPS-specific -D variables that a LAMMPS build supports are
+described on the pages linked to from the "Build"_Build.html doc page.
+All of these variable names are upper-case and their values are
+lower-case, e.g. -D LAMMPS_SIZES=smallbig. For boolean values, any of
+these forms can be used: yes/no, on/off, 1/0.
+
+On Unix/Linux machines, CMake generates a Makefile by default to
+perform the LAMMPS build. Alternate forms of build info can be
+generated via the -G switch, e.g. Visual Studio on a Windows machine,
+Xcode on MacOS, or KDevelop on Linux. Type "cmake --help" to see the
+"Generator" styles of output your system supports.
+
+NOTE: When CMake runs, it prints configuration info to the screen.
+You should review this to verify all the features you requested were
+enabled, including packages. You can also see what compilers and
+compile options will be used for the build. Any errors in CMake
+variable syntax will also be flagged, e.g. mis-typed variable names or
+variable values.
+
+CMake creates a CMakeCache.txt file when it runs. This stores all the
+settings, so that when running CMake again you can use the current
+folder '.' instead of the path to the LAMMPS cmake folder as the
+required argument to the CMake command. Either way the existing
+settings will be inherited unless the CMakeCache.txt file is removed.
+
+If you later want to change a setting you can rerun cmake in the build
+directory with different setting. Please note that some automatically
+detected variables will not change their value when you rerun cmake.
+In these cases it is usually better to first remove all the
+files/directories in the build directory, or start with a fresh build
+directory.
+
+:line
+
+[Curses version (terminal-style menu) of CMake]:
+
+ccmake ../cmake :pre
+
+You initiate the configuration and build environment generation steps
+separately. For the first you have to type [c], for the second you
+have to type [g]. You may need to type [c] multiple times, and may be
+required to edit some of the entries of CMake configuration variables
+in between. Please see the "ccmake
+manual"_https://cmake.org/cmake/help/latest/manual/ccmake.1.html for
+more information.
+
+:line
+
+[GUI version of CMake]:
+
+cmake-gui ../cmake :pre
+
+You initiate the configuration and build environment generation steps
+separately. For the first you have to click on the [Configure] button,
+for the second you have to click on the [Generate] button. You may
+need to click on [Configure] multiple times, and may be required to
+edit some of the entries of CMake configuration variables in between.
+Please see the "cmake-gui
+manual"_https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html
+for more information.
+
+:line
+
+[Installing CMake]
+
+Check if your machine already has CMake installed:
+
+which cmake # do you have it?
+which cmake3 # version 3 may have this name
+cmake --version # what specific version you have :pre
+
+On clusters or supercomputers which use environment modules to manage
+software packages, do this:
+
+module list # is a cmake module already loaded?
+module avail # is a cmake module available?
+module load cmake3 # load cmake module with appropriate name :pre
+
+Most Linux distributions offer precompiled cmake packages through
+their package management system. If you do not have CMake or a new
+enough version, you can download the latest version at
+"https://cmake.org/download/"_https://cmake.org/download/.
+Instructions on how to install it on various platforms can be found
+"on this page"_https://cmake.org/install/.
diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3a05ed50ee8c2fbda866f9439ea3279d040c86e
--- /dev/null
+++ b/doc/src/Build_extras.txt
@@ -0,0 +1,923 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Packages with extra build options :h3
+
+When building with some packages, additional steps may be required,
+in addition to:
+
+-D PKG_NAME=yes # CMake
+make yes-name # make :pre
+
+as described on the "Build_package"_Build_package.html doc page.
+
+For a CMake build there may be additional optional or required
+variables to set. For a build with make, a provided library under the
+lammps/lib directory may need to be built first. Or an external
+library may need to exist on your system or be downloaded and built.
+You may need to tell LAMMPS where it is found on your system.
+
+This is the list of packages that may require additional steps.
+
+"GPU"_#gpu,
+"KIM"_#kim,
+"KOKKOS"_#kokkos,
+"LATTE"_#latte,
+"MEAM"_#meam,
+"MSCG"_#mscg,
+"OPT"_#opt,
+"POEMS"_#poems,
+"PYTHON"_#python,
+"REAX"_#reax,
+"VORONOI"_#voronoi,
+"USER-ATC"_#user-atc,
+"USER-AWPMD"_#user-awpmd,
+"USER-COLVARS"_#user-colvars,
+"USER-H5MD"_#user-h5md,
+"USER-INTEL"_#user-intel,
+"USER-MOLFILE"_#user-molfile,
+"USER-NETCDF"_#user-netcdf,
+"USER-OMP"_#user-omp,
+"USER-QMMM"_#user-qmmm,
+"USER-QUIP"_#user-quip,
+"USER-SMD"_#user-smd,
+"USER-VTK"_#user-vtk :tb(c=6,ea=c)
+
+:line
+
+COMPRESS package :h4,link(compress)
+
+To build with this package you must have the zlib compression library
+available on your system.
+
+[CMake build]:
+
+If CMake cannot find the library, you can set these variables:
+
+-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
+-D ZLIB_LIBRARIES=path # path to libz.a (.so) file :pre
+
+[Traditional make]:
+
+If make cannot find the library, you can edit the
+lib/compress/Makefile.lammps file to specify the paths and library
+name.
+
+:line
+
+GPU package :h4,link(gpu)
+
+To build with this package, you must choose options for precision and
+which GPU hardware to build for.
+
+[CMake build]:
+
+-D GPU_API=value # value = opencl (default) or cuda
+-D GPU_PREC=value # precision setting
+ # value = double or mixed (default) or single
+-D OCL_TUNE=value # hardware choice for GPU_API=opencl
+ # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
+-D GPU_ARCH=value # hardware choice for GPU_API=cuda
+ # value = sm_XX, see below
+ # default is Cuda-compiler dependent, but typically sm_20
+-D CUDPP_OPT=value # optimization setting for GPU_API=cudea
+ # enables CUDA Performance Primitives Optimizations
+ # yes (default) or no :pre
+
+GPU_ARCH settings for different GPU hardware is as follows:
+
+sm_20 for Fermi (C2050/C2070, deprecated as of CUDA 8.0) or GeForce GTX 580 or similar
+sm_30 for Kepler (K10)
+sm_35 for Kepler (K40) or GeForce GTX Titan or similar
+sm_37 for Kepler (dual K80)
+sm_50 for Maxwell
+sm_60 for Pascal (P100)
+sm_70 for Volta :ul
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the GPU library in lib/gpu.
+You can do this manually if you prefer; follow the instructions in
+lib/gpu/README. Note that the GPU library uses MPI calls, so you must
+use the same MPI library (or the STUBS library) settings as the main
+LAMMPS code. This also applies to the -DLAMMPS_BIGBIG,
+-DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL settings in whichever
+Makefile you use.
+
+You can also build the library 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="-b" # build GPU library with default Makefile.linux
+make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
+make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi :pre
+
+Note that this procedure starts with a Makefile.machine in lib/gpu, as
+specified by the "-m" switch. For your convenience, machine makefiles
+for "mpi" and "serial" are provided, which have the same settings as
+the corresponding machine makefiles in the main LAMMPS source
+folder. In addition you can alter 4 important settings in the
+Makefile.machine you start from via the corresponding -h, -a, -p, -e
+switches (as in the examples above), and also save a copy of the new
+Makefile if desired:
+
+CUDA_HOME = where NVIDIA CUDA software is installed on your system
+CUDA_ARCH = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above
+CUDA_PRECISION = precision (double, mixed, single)
+EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
+
+If the library build is successful, 3 files should be created:
+lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, 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, and
+lib/gpu/Makefile.lammps may need to be edited.
+
+NOTE: If you re-build the GPU library in lib/gpu, you should always
+un-install the GPU package in lammps/src, then re-install it and
+re-build LAMMPS. This is because the compilation of files in the GPU
+package uses the library settings from the lib/gpu/Makefile.machine
+used to build the GPU library.
+
+:line
+
+KIM package :h4,link(kim)
+
+To build with this package, the KIM library must be downloaded and
+built on your system. It must include the KIM models that you want to
+use with LAMMPS.
+
+Note that in LAMMPS lingo, a KIM model driver is a pair style
+(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
+element or alloy and set of parameters, e.g. EAM for Cu with a
+specific EAM potential file. Also note that installing the KIM API
+library with all its models, may take around 30 min to build. Of
+course you only need to do that once.
+
+See the list of KIM model drivers here:
+https://openkim.org/kim-items/model-drivers/alphabetical
+
+See the list of all KIM models here:
+https://openkim.org/kim-items/models/by-model-drivers
+
+See the list of example KIM models included by default here:
+https://openkim.org/kim-api on the "What is in the KIM API source
+package?" page.
+
+[CMake build]:
+
+-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes
+-D KIM_LIBRARY=path # path to KIM shared library (only needed if a custom location)
+-D KIM_INCLUDE_DIR=path # path to KIM include directory (only needed if a custom location) :pre
+
+[Traditional make]:
+
+You can download and build the KIM library manually if you prefer;
+follow the instructions in lib/kim/README. You can also do it in one
+step from the lammps/src dir, using a command like these, which simply
+invoke the lib/kim/Install.py script with the specified args.
+
+make lib-kim # print help message
+make lib-kim args="-b " # (re-)install KIM API lib with only example models
+make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
+make lib-kim args="-b -a everything" # install KIM API lib with all models
+make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
+make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
+make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
+
+:line
+
+KOKKOS package :h4,link(kokkos)
+
+To build with this package, you must choose which hardware you want to
+build for, either CPUs (multi-threading via OpenMP) or KNLs (OpenMP)
+or GPUs (NVIDIA Cuda).
+
+For a CMake or make build, these are the possible choices for the
+KOKKOS_ARCH settings described below. Note that for CMake, these are
+really Kokkos variables, not LAMMPS variables. Hence you must use
+case-sensitive values, e.g. BDW, not bdw.
+
+ARMv80 = ARMv8.0 Compatible CPU
+ARMv81 = ARMv8.1 Compatible CPU
+ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU
+BGQ = IBM Blue Gene/Q CPUs
+Power8 = IBM POWER8 CPUs
+Power9 = IBM POWER9 CPUs
+SNB = Intel Sandy/Ivy Bridge CPUs
+HSW = Intel Haswell CPUs
+BDW = Intel Broadwell Xeon E-class CPUs
+SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
+KNC = Intel Knights Corner Xeon Phi
+KNL = Intel Knights Landing Xeon Phi
+Kepler30 = NVIDIA Kepler generation CC 3.0
+Kepler32 = NVIDIA Kepler generation CC 3.2
+Kepler35 = NVIDIA Kepler generation CC 3.5
+Kepler37 = NVIDIA Kepler generation CC 3.7
+Maxwell50 = NVIDIA Maxwell generation CC 5.0
+Maxwell52 = NVIDIA Maxwell generation CC 5.2
+Maxwell53 = NVIDIA Maxwell generation CC 5.3
+Pascal60 = NVIDIA Pascal generation CC 6.0
+Pascal61 = NVIDIA Pascal generation CC 6.1 :ul
+
+[CMake build]:
+
+For multicore CPUs using OpenMP, set these 2 variables.
+
+-D KOKKOS_ARCH=archCPU # archCPU = CPU from list above :pre
+-D KOKKOS_ENABLE_OPENMP=yes :pre
+
+For Intel KNLs using OpenMP, set these 2 variables:
+
+-D KOKKOS_ARCH=KNL
+-D KOKKOS_ENABLE_OPENMP=yes :pre
+
+For NVIDIA GPUs using CUDA, set these 4 variables:
+
+-D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU
+ # archGPU = GPU from list above
+-D KOKKOS_ENABLE_CUDA=yes
+-D KOKKOS_ENABLE_OPENMP=yes
+-D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper :pre
+
+The wrapper value is the Cuda nvcc compiler wrapper provided in the
+Kokkos library: lib/kokkos/bin/nvcc_wrapper. The setting should
+include the full path name to the wrapper, e.g.
+
+-D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper :pre
+
+[Traditional make]:
+
+Choose which hardware to support in Makefile.machine via
+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 = archCPU # archCPU = CPU from list above :pre
+
+For Intel KNLs using OpenMP:
+
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = KNL :pre
+
+For NVIDIA GPUs using CUDA:
+
+KOKKOS_DEVICES = Cuda
+KOKKOS_ARCH = archCPU,archGPU # archCPU = CPU from list above that is hosting the GPU
+ # archGPU = GPU from list above :pre
+
+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 and use a C++ compiler for non-Kokkos, non-CUDA
+files.
+
+KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
+export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
+CC = mpicxx :pre
+
+:line
+
+LATTE package :h4,link(latte)
+
+To build with this package, you must download and build the LATTE
+library.
+
+[CMake build]:
+
+-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
+-D LATTE_LIBRARY=path # path to LATTE shared library (only needed if a custom location) :pre
+
+[Traditional make]:
+
+You can download and build the LATTE library manually if you prefer;
+follow the instructions in lib/latte/README. You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invokes the lib/latte/Install.py script with the specified
+args:
+
+make lib-latte # print help message
+make lib-latte args="-b" # download and build in lib/latte/LATTE-master
+make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
+make lib-latte args="-b -m gfortran" # download and build in lib/latte and
+ # copy Makefile.lammps.gfortran to Makefile.lammps
+:pre
+
+Note that 3 symbolic (soft) links, "includelink" and "liblink" and
+"filelink.o", are created in lib/latte to point into the LATTE home
+dir. When LAMMPS itself is built it will use these links. You should
+also check that the Makefile.lammps file you create is appropriate for
+the compiler you use on your system to build LATTE.
+
+:line
+
+MEAM package :h4,link(meam)
+
+NOTE: the use of the MEAM package is discouraged, as it has been
+superseded by the USER-MEAMC package, which is a direct translation of
+the Fortran code in the MEAM library to C++. The code in USER-MEAMC
+should be functionally equivalent to the MEAM package, fully supports
+use of "pair_style hybrid"_pair_hybrid.html (the MEAM packaged doesn
+not), and has optimizations that make it significantly faster than the
+MEAM package.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_MEAM=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the MEAM library in lib/meam.
+You can build the MEAM library 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 mpi" # build with default Fortran compiler compatible with your MPI library
+make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
+make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :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.
+
+:line
+
+MSCG package :h4,link(mscg)
+
+To build with this package, you must 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 the GSL (GNU Scientific Library)
+headers and libraries are installed on your machine. See the
+lib/mscg/README and MSCG/Install files for more details.
+
+[CMake build]:
+
+-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes
+-D MSCG_LIBRARY=path # path to MSCG shared library (only needed if a custom location)
+-D MSCG_INCLUDE_DIR=path # path to MSCG include directory (only needed if a custom location) :pre
+
+[Traditional make]:
+
+You can download and build the MS-CG library 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="-b -m serial" # download and build in lib/mscg/MSCG-release-master
+ # with the settings compatible with "make serial"
+make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
+ # with the settings compatible with "make mpi"
+make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink", will
+be created in lib/mscg to point to the MS-CG src/installation dir.
+When LAMMPS is built in src it will use these links. You should not
+need to edit the lib/mscg/Makefile.lammps file.
+
+:line
+
+OPT package :h4,link(opt)
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_OPT=yes".
+
+[Traditional make]:
+
+The compile flag "-restrict" must be used to build LAMMPS with the OPT
+package when using Intel compilers. It should be added to the CCFLAGS
+line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for
+an example.
+
+:line
+
+POEMS package :h4,link(poems)
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_OPT=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must 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 serial" # build with GNU g++ compiler (settings as with "make serial")
+make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
+make lib-poems args="-m icc" # build with Intel icc compiler :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.
+
+:line
+
+PYTHON package :h4,link(python)
+
+Building with the PYTHON package requires 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
+lib/python/README for more details.
+
+[CMake build]:
+
+-D PYTHON_EXECUTABLE=path # path to Python executable to use :pre
+
+Without this setting, CMake will ues the default Python on your
+system. To use a different Python version, you can either create a
+virtualenv, activate it and then run cmake. Or you can set the
+PYTHON_EXECUTABLE variable to specify which Python interpreter should
+be used. Note note that you will also need to have the development
+headers installed for this version, e.g. python2-devel.
+
+[Traditional make]:
+
+The build uses the lib/python/Makefile.lammps file in the compile/link
+process to find Python. You should only need to create a new
+Makefile.lammps.* file (and copy it to Makefile.lammps) if the LAMMPS
+build fails.
+
+:line
+
+REAX package :h4,link(reax)
+
+NOTE: the use of the REAX package and its "pair_style
+reax"_pair_reax.html command is discouraged, as it is no longer
+maintained. Please use the USER-REAXC package and its "pair_style
+reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
+enabled variant (pair_style reax/c/kk), which has a more robust memory
+management. See the "pair_style reax/c"_pair_reaxc.html doc page for
+details.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_REAX=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must 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 lib-reax # print help message
+make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
+make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
+
+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.
+
+:line
+
+VORONOI package :h4,link(voronoi)
+
+To build with this package, you must download and build the "Voro++
+library"_voro_home.
+
+:link(voro_home,http://math.lbl.gov/voro++)
+
+[CMake build]:
+
+-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
+-D VORO_LIBRARY=path # (only needed if at custom location) path to VORO shared library
+-D VORO_INCLUDE_DIR=path # (only needed if at custom location) path to VORO include directory :pre
+
+[Traditional make]:
+
+You can download and build the Voro++ library 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="-b" # download and build the default version in lib/voronoi/voro++-<version>
+make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
+make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink", are
+created in lib/voronoi to point to the Voro++ src dir. When LAMMPS
+builds in src it will use these links. You should not need to edit
+the lib/voronoi/Makefile.lammps file.
+
+:line
+
+USER-ATC package :h4,link(user-atc)
+
+The USER-ATC package requires the MANYBODY package also be installed.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_REAX=yes" and "-D
+PKG_MANYBODY=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must 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:
+
+make lib-atc # print help message
+make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
+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.
+
+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:
+
+make lib-linalg # print help message
+make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
+make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
+
+:line
+
+USER-AWPMD package :h4,link(user-awpmd)
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-AQPMD=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must 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 lib-awpmd # print help message
+make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
+make lib-awpmd args="-m icc" # build with Intel icc compiler :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.
+
+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 lib-linalg # print help message
+make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
+make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
+
+:line
+
+USER-COLVARS package :h4,link(user-colvars)
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-COLVARS=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must 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 serial" # build with GNU g++ compiler (settings as with "make serial")
+make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
+make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :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.
+
+:line
+
+USER-H5MD package :h4,link(user-h5md)
+
+To build with this package you must have the HDF5 software package
+installed on your system, which should include the h5cc compiler and
+the HDF5 library.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-H5MD=yes".
+
+This should autodetect the H5MD library on your system. Several
+advanced CMake H5MD options exist if you need to specify where it is
+installed. Use the ccmake (terminal window) or cmake-gui (graphical)
+tools to see these options and set them interactively from their user
+interfaces.
+
+[Traditional make]:
+
+Before building LAMMPS, you must 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:
+
+make lib-h5md # print help message
+make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre
+
+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.
+
+:line
+
+USER-INTEL package :h4,link(user-intel)
+
+To build with this package, you must choose which hardware you want to
+build for, either Intel CPUs or Intel KNLs. You should also typically
+"install the USER-OMP package"_#user-omp, as it can be used in tandem
+with the USER-INTEL package to good effect, as explained on the "Speed
+intel"_Speed_intel.html doc page.
+
+[CMake build]:
+
+-D INTEL_ARCH=value # value = cpu (default) or knl
+-D BUILD_OMP=yes # also required to build with the USER-INTEl package :pre
+
+Requires an Intel compiler as well as the Intel TBB and MKL libraries.
+
+[Traditional make]:
+
+Choose which hardware to compile for in Makefile.machine via the
+following settings. See src/MAKE/OPTIONS/Makefile.intel_cpu* and
+Makefile.knl files for examples.
+
+For CPUs:
+
+OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
+CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
+ -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+LINKFLAGS = -g -qopenmp $(OPTFLAGS)
+LIB = -ltbbmalloc :pre
+
+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 :pre
+
+:line
+
+USER-MOLFILE package :h4,link(user-molfile)
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-MOLFILE=yes".
+
+[Traditional make]:
+
+The lib/molfile/Makefile.lammps file has a setting for a dynamic
+loading library libdl.a that is typically present on all systems. It
+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.
+
+:line
+
+USER-NETCDF package :h4,link(user-netcdf)
+
+To build with this package you must have the NetCDF library installed
+on your system.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-NETCDF=yes".
+
+This should autodetect the NETCDF library if it is installed on your
+system at standard locations. Several advanced CMake NETCDF options
+exist if you need to specify where it was installed. Use the ccmake
+(terminal window) or cmake-gui (graphical) tools to see these options
+and set them interactively from their user interfaces.
+
+[Traditional make]:
+
+The lib/netcdf/Makefile.lammps file has settings for NetCDF include
+and library files which LAMMPS needs to build 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.
+
+:line
+
+USER-OMP package :h4,link(user-omp)
+
+[CMake build]:
+
+No additional settings are required besides "-D PKG_USER-OMP=yes". If
+CMake detects OpenMP support, the USER-OMP code will be compiled with
+multi-threading support enabled, otherwise as optimized serial code.
+
+[Traditional make]:
+
+To enable multi-threading support in the USER-OMP package (and other
+styles supporting OpenMP) the following compile and link flags must
+be added to your Makefile.machine file.
+See src/MAKE/OPTIONS/Makefile.omp for an example.
+
+CCFLAGS: -fopenmp # for GNU Compilers
+CCFLAGS: -qopenmp -restrict # for Intel compilers on Linux
+LINKFLAGS: -fopenmp # for GNU Compilers
+LINKFLAGS: -qopenmp # for Intel compilers on Linux :pre
+
+For other platforms and compilers, please consult the documentation
+about OpenMP support for your compiler.
+
+:line
+
+USER-QMMM package :h4,link(user-qmmm)
+
+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 (pwqmmm.x) which links LAMMPS and Quantum
+ESPRESSO together. These are steps 3 and 4 described in the
+lib/qmmm/README file. Unfortunately, the Quantum ESPRESSO developers
+have been breaking the interface that the QM/MM code in LAMMPS is using,
+so that currently (Summer 2018) using this feature requires either
+correcting the library interface feature in recent Quantum ESPRESSO
+releases, or using an outdated version of QE. The last version of
+Quantum ESPRESSO known to work with this QM/MM interface was version
+5.4.1 from 2016.
+
+[CMake build]:
+
+The CMake build system currently does not support building the full
+QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
+You must use the traditional make build for this package.
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the QMMM library in lib/qmmm.
+You can do this manually if you prefer; follow the first two steps
+explained in lib/qmmm/README. You can also do it in one step from the
+lammps/src dir, using a command like these, which simply invoke the
+lib/qmmm/Install.py script with the specified args:
+
+make lib-qmmm # print help message
+make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
+make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
+make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre
+
+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 QMMM package and build LAMMPS in the usual
+manner. After completing the LAMMPS build and compiling Quantum
+ESPRESSO with external library support, go back to the lib/qmmm folder
+and follow the instructions on the README file to build the combined
+LAMMPS/QE QM/MM executable (pwqmmm.x) in the lib/qmmm folder.
+
+:line
+
+USER-QUIP package :h4,link(user-quip)
+
+To build with this package, you must download and build the QUIP
+library. It can be obtained from GitHub. For support of GAP
+potentials, additional files with specific licensing conditions need
+to be downloaded and configured. See step 1 and step 1.1 in the
+lib/quip/README file for details on how to do this.
+
+[CMake build]:
+
+-D QUIP_LIBRARIES=path # path to libquip.a (only needed if a custom location)
+
+CMake will not download and build the QUIP library. But once you have
+done that, a CMake build of LAMMPS with "-D PKG_USER-QUIP=yes" should
+work. Set QUIP_LIBRARIES if CMake cannot find the QUIP library.
+
+[Traditional make]:
+
+The download/build procedure for the QUIP library, described in
+lib/quip/README file requires setting two environment variables,
+QUIP_ROOT and QUIP_ARCH. These are 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
+Makefile.lammps if the LAMMPS build can not use its settings to
+successfully build on your system.
+
+:line
+
+USER-SMD package :h4,link(user-smd)
+
+To build with this package, you must download the Eigen3 library.
+Eigen3 is a template library, so you do not need to build it.
+
+[CMake build]:
+
+-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
+-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) :pre
+
+Set EIGEN3_INCLUDE_DIR if CMake cannot find the Eigen3 library.
+
+[Traditional make]:
+
+You can download the Eigen3 library 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:
+
+make lib-smd # print help message
+make lib-smd args="-b" # download to lib/smd/eigen3
+make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre
+
+Note that a symbolic (soft) link named "includelink" is created 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.
+
+:line
+
+USER-VTK package :h4,link(user-vtk)
+
+To build with this package you must have the VTK library installed on
+your system.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-VTK=yes".
+
+This should autodetect the VTK library if it is installed on your
+system at standard locations. Several advanced VTK options exist if
+you need to specify where it was installed. Use the ccmake (terminal
+window) or cmake-gui (graphical) tools to see these options and set
+them interactively from their user interfaces.
+
+[Traditional make]:
+
+The lib/vtk/Makefile.lammps file has settings for accessing VTK files
+and its library, which LAMMPS needs to build 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. See lib/vtk/README for details.
diff --git a/doc/src/Build_link.txt b/doc/src/Build_link.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a1b387f3fd07dc2ad20433e840e4e3775b17bba
--- /dev/null
+++ b/doc/src/Build_link.txt
@@ -0,0 +1,85 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Link LAMMPS as a library to another code :h3
+
+LAMMPS can be used as a library by another application, including
+Python scripts. The files src/library.cpp and library.h define the
+C-style API for using LAMMPS as a library. See the "Howto
+library"_Howto_library.html doc page for a description of the
+interface and how to extend it for your needs.
+
+The "Build basics"_Build_basics.html doc page explains how to build
+LAMMPS as either a shared or static library. This results in one of
+these 2 files:
+
+liblammps.so # shared library
+liblammps.a # static library
+
+:line
+
+[Link with LAMMPS as a static library]:
+
+The calling application can link to LAMMPS as a static library with a
+link command like this:
+
+g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller
+
+The -L argument is the path to where the liblammps.a file is. The
+-llammps argument is shorthand for the file liblammps.a.
+
+:line
+
+[Link with LAMMPS as a shared library]:
+
+If you wish to link to liblammps.so, the operating system finds shared
+libraries to load at run-time using the environment variable
+LD_LIBRARY_PATH. To enable this you can do one of two things:
+
+(1) Copy the liblammps.so file to a location the system can find it,
+such as /usr/local/lib. I.e. a directory already listed in your
+LD_LIBRARY_PATH variable. You can type
+
+printenv LD_LIBRARY_PATH :pre
+
+to see what directories are in that list.
+
+(2) Add the LAMMPS src directory (or the directory you perform CMake
+build in) to your LD_LIBRARY_PATH, so that the current version of the
+shared library is always available to programs that use it.
+
+For the csh or tcsh shells, you would add something like this to your
+~/.cshrc file:
+
+setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
+
+:line
+
+[Calling the LAMMPS library]:
+
+Either flavor of library (static or shared) allows one or more LAMMPS
+objects to be instantiated from the calling program.
+
+When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
+namespace; you can safely use any of its classes and methods from
+within the calling code, as needed.
+
+When used from a C or Fortran program, the library has a simple
+C-style interface, provided in src/library.cpp and src/library.h.
+
+See the "Python library"_Python_library.html doc page for a
+description of the Python interface to LAMMPS, which wraps the C-style
+interface.
+
+See the sample codes in examples/COUPLE/simple for examples of C++ and
+C and Fortran codes that invoke LAMMPS thru its library interface.
+Other examples in the COUPLE directory use coupling ideas discussed on
+the "Howto couple"_Howto_couple.html doc page.
+
+
diff --git a/doc/src/Build_make.txt b/doc/src/Build_make.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c00ce1f4208ba04a8517b98a9128cb63e886ef8b
--- /dev/null
+++ b/doc/src/Build_make.txt
@@ -0,0 +1,85 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Build LAMMPS with make :h3
+
+Building LAMMPS with traditional makefiles requires that you have a
+Makefile."machine" file appropriate for your system in the src/MAKE,
+src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see
+below). It can include various options for customizing your LAMMPS
+build with a number of global compilation options and features.
+
+To include LAMMPS packages (i.e. optional commands and styles) you
+must install them first, as discussed on the "Build
+package"_Build_package.html doc page. If the packages require
+provided or external libraries, you must build those libraries before
+building LAMMPS. Building "LAMMPS with CMake"_Build_cmake.html can
+automate all of this for many types of machines, especially
+workstations, desktops and laptops, so we suggest you try it first.
+
+These commands perform a default LAMMPS build, producing the LAMMPS
+executable lmp_serial or lmp_mpi in lammps/src:
+
+cd lammps/src
+make serial # build a serial LAMMPS executable
+make mpi # build a parallel LAMMPS executable with MPI
+make # see a variety of make options :pre
+
+This initial compilation can take a long time, since LAMMPS is a large
+project with many features. If your machine has multiple CPU cores
+(most do these days), using a command like "make -jN mpi" (with N =
+the number of available CPU cores) can be much faster. If you plan to
+do development on LAMMPS or need to recompile LAMMPS repeatedly, the
+installation of the ccache (= Compiler Cache) software may speed up
+compilation even more.
+
+After the initial build, whenever you edit LAMMPS source files, or add
+or remove new files to the source directory (e.g. by installing or
+uninstalling packages), you must recompile and relink the LAMMPS
+executable with the same "make" command. This makefiles dependencies
+should insure that only the subset of files that need to be are
+recompiled.
+
+NOTE: When you build LAMMPS for the first time, a long list of *.d
+files will be printed out rapidly. This is not an error; it is the
+Makefile doing its normal creation of dependencies.
+
+:line
+
+The lammps/src/MAKE tree contains all the Makefile.machine files
+included in the LAMMPS distribution. Typing "make machine" uses
+Makefile.machine. Thus the "make serial" or "make mpi" lines above
+use Makefile.serial and Makefile.mpi. Others are in these dirs:
+
+OPTIONS # Makefiles which enable specific options
+MACHINES # Makefiles for specific machines
+MINE # customized Makefiles you create (you may need to create this folder) :pre
+
+Typing "make" lists all the available Makefile.machine files. A file
+with the same name can appear in multiple folders (not a good idea).
+The order the dirs are searched is as follows: src/MAKE/MINE,
+src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES. This gives preference
+to a customized file you put in src/MAKE/MINE.
+
+Makefiles you may wish to try include these (some require a package
+first be installed). Many of these include specific compiler flags
+for optimized performance. Please note, however, that some of these
+customized machine Makefile are contributed by users. Since both
+compilers, OS configs, and LAMMPS itself keep changing, their settings
+may become outdated:
+
+make mac # build serial LAMMPS on a Mac
+make mac_mpi # build parallel LAMMPS on a Mac
+make intel_cpu # build with the USER-INTEL package optimized for CPUs
+make knl # build with the USER-INTEL package optimized for KNLs
+make opt # build with the OPT package optimized for CPUs
+make omp # build with the USER-OMP package optimized for OpenMP
+make kokkos_omp # build with the KOKKOS package for OpenMP
+make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
+make kokkos_phi # build with the KOKKOS package for KNLs :pre
diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc8918c884a860674b461e98992c56ae58a6376d
--- /dev/null
+++ b/doc/src/Build_package.txt
@@ -0,0 +1,222 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Include packages in build :h3
+
+In LAMMPS, a package is a group of files that enable a specific set of
+features. For example, force fields for molecular systems or
+rigid-body constraints are in packages. In the src directory, each
+package is a sub-directory with the package name in capital letters.
+
+An overview of packages is given on the "Packages"_Packages.html doc
+page. Brief overviews of each package are on the "Packages
+details"_Packages_details.html doc page.
+
+When building LAMMPS, you can choose to include or exclude each
+package. In general there is no need to include a package if you
+never plan to use its features.
+
+If you get a run-time error that a LAMMPS command or style is
+"Unknown", it is often because the command is contained in a package,
+and your build did not include that package. Running LAMMPS with the
+"-h command-line switch"_Run_options.html will print all the included
+packages and commands for that executable.
+
+For the majority of packages, if you follow the single step below to
+include it, you can then build LAMMPS exactly the same as you would
+without any packages installed. A few packages may require additional
+steps, as explained on the "Build extras"_Build_extras.html doc page.
+
+These links take you to the extra instructions for those select
+packages:
+
+"GPU"_Build_extras.html#gpu,
+"KIM"_Build_extras.html#kim,
+"KOKKOS"_Build_extras.html#kokkos,
+"LATTE"_Build_extras.html#latte,
+"MEAM"_Build_extras.html#meam,
+"MSCG"_Build_extras.html#mscg,
+"OPT"_Build_extras.html#opt,
+"POEMS"_Build_extras.html#poems,
+"PYTHON"_Build_extras.html#python,
+"REAX"_Build_extras.html#reax,
+"VORONOI"_Build_extras.html#voronoi,
+"USER-ATC"_Build_extras.html#user-atc,
+"USER-AWPMD"_Build_extras.html#user-awpmd,
+"USER-COLVARS"_Build_extras.html#user-colvars,
+"USER-H5MD"_Build_extras.html#user-h5md,
+"USER-INTEL"_Build_extras.html#user-intel,
+"USER-MOLFILE"_Build_extras.html#user-molfile,
+"USER-NETCDF"_Build_extras.html#user-netcdf,
+"USER-OMP"_Build_extras.html#user-omp,
+"USER-QMMM"_Build_extras.html#user-qmmm,
+"USER-QUIP"_Build_extras.html#user-quip,
+"USER-SMD"_Build_extras.html#user-smd,
+"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c)
+
+The mechanism for including packages is simple but different for CMake
+versus make.
+
+[CMake variables]:
+
+-D PKG_NAME=value # yes or no (default) :pre
+
+Examples:
+
+-D PKG_MANYBODY=yes
+-D PKG_USER-INTEL=yes :pre
+
+All standard and user packages are included the same way. Note that
+USER packages have a hyphen between USER and the rest of the package
+name, not an underscore.
+
+See the shortcut section below for how to install many packages at
+once with CMake.
+
+NOTE: If you toggle back and forth between building with CMake vs
+make, no packages in the src directory can be installed when you
+invoke cmake. CMake will give an error if that is not the case,
+indicating how you can un-install all packages in the src dir.
+
+[Traditional make]:
+
+cd lammps/src
+make ps # check which packages are currently installed
+make yes-name # install a package with name
+make no-name # un-install a package with name
+make mpi # build LAMMPS with whatever packages are now installed :pre
+
+Examples:
+
+make no-rigid
+make yes-user-intel :pre
+
+All standard and user packages are included the same way.
+
+See the shortcut section below for how to install many packages at
+once with make.
+
+NOTE: You must always re-build LAMMPS (via make) after installing or
+un-installing a package, for the action to take effect.
+
+NOTE: You cannot install or un-install packages and build LAMMPS in a
+single make command with 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. You can include or exclude multiple packages
+in a single make command, e.g. make yes-colloid no-manybody.
+
+[CMake and make info]:
+
+Any package can be included or excluded 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. 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.
+
+When you download a LAMMPS tarball or download LAMMPS source files
+from the Git or SVN repositories, no packages are pre-installed in the
+src directory.
+
+NOTE: Prior to Aug 2018, if you downloaded a tarball, 3 packages
+(KSPACE, MANYBODY, MOLECULE) were pre-installed in the src directory.
+That is no longer the case, so that CMake will build as-is without the
+need to un-install those packages.
+
+:line
+
+[CMake shortcuts for installing many packages]:
+
+Instead of specifying all the CMake options via the command-line,
+CMake allows initializing the variable cache using script files. These
+are regular CMake files which can manipulate and set variables, and
+can also contain control flow constructs.
+
+LAMMPS includes several of these files to define configuration
+"presets", similar to the options that exist for the Make based
+system. Using these files you can enable/disable portions of the
+available packages in LAMMPS. If you need a custom preset you can take
+one of them as a starting point and customize it to your needs.
+
+cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake | enable all packages
+cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake | disable all packages
+cmake -C ../cmake/presets/std.cmake \[OPTIONS\] ../cmake | enable standard packages
+cmake -C ../cmake/presets/user.cmake \[OPTIONS\] ../cmake | enable user packages
+cmake -C ../cmake/presets/std_nolib.cmake \[OPTIONS\] ../cmake | enable standard packages that do not require extra libraries
+cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | disable all packages that do not require extra libraries
+cmake -C ../cmake/presets/manual_selection.cmake \[OPTIONS\] ../cmake | example of how to create a manual selection of packages :tb(s=|,a=l)
+
+NOTE: Running cmake this way manipulates the variable cache in your
+current build directory. You can combine presets and options with
+multiple cmake runs.
+
+[Example:]
+
+# build LAMMPS with all "standard" packages which don't
+# use libraries and enable GPU package
+mkdir build
+cd build
+cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake :pre
+
+:line
+
+[Make shortcuts for installing many packages]:
+
+The following commands are useful for managing package source files
+and their installation when building LAMMPS via traditional make.
+Just type "make" in lammps/src to see a one-line summary.
+
+These commands install/un-install sets of packages:
+
+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=|,a=l)
+
+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 copying
+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.
+
+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 are
+"installing a patch"_Install_patch.html downloaded from the LAMMPS web
+site.
+
+Type "make package-status" or "make ps" to show which packages are
+currently installed. For those that are installed, it will list any
+files that are different in the src directory and package
+sub-directory.
+
+Type "make package-installed" or "make pi" to show which packages are
+currently installed, without listing the status of packages that are
+not installed.
+
+Type "make package-update" or "make pu" to 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"_Install_patch.html,
+since patches only update the files in the package sub-directory, but
+not the src files.
+
+Type "make package-overwrite" to overwrite files in the package
+sub-directories with src files.
+
+Type "make package-diff" to list all differences between pairs of
+files in both the src dir and a package dir.
diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db281c0857d6d10a5167ec1e13bbed4ef178af23
--- /dev/null
+++ b/doc/src/Build_settings.txt
@@ -0,0 +1,341 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Optional build settings :h3
+
+LAMMPS can be built with several optional settings. Each sub-section
+explain how to do this for building both with CMake and make.
+
+"FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command
+"Size of LAMMPS data types"_#size
+"Read or write compressed files"_#gzip
+"Output of JPG and PNG files"_#graphics via the "dump image"_dump_image.html command
+"Output of movie files"_#graphics via the "dump_movie"_dump_image.html command
+"Memory allocation alignment"_#align
+"Workaround for long long integers"_#longlong
+"Error handling exceptions"_#exceptions when using LAMMPS as a library :all(b)
+
+:line
+
+FFT library :h3,link(fft)
+
+When the KSPACE package is included in a LAMMPS build, the
+"kspace_style pppm"_kspace_style.html command performs 3d FFTs which
+require use of an FFT library to compute 1d FFTs. The KISS FFT
+library is included with LAMMPS but other libraries can be faster.
+LAMMPS can use them if they are available on your system.
+
+[CMake variables]:
+
+-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
+-D FFT_SINGLE=value # yes or no (default), no = double precision
+-D FFT_PACK=value # array (default) or pointer or memcpy :pre
+
+NOTE: The values for the FFT variable must be in upper-case. This is
+an exception to the rule that all CMake variables can be specified
+with lower-case values.
+
+Usually these settings are all that is needed. If CMake cannot find
+the FFT library, you can set these variables:
+
+-D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files
+-D FFTW3_LIBRARIES=path # path to FFTW3 libraries
+-D MKL_INCLUDE_DIRS=path # ditto for Intel MKL library
+-D MKL_LIBRARIES=path :pre
+
+[Makefile.machine settings]:
+
+FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
+ # default is KISS if not specified
+FFT_INC = -DFFT_SINGLE # do not specify for double precision
+FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY :pre
+ # default is FFT_PACK_ARRAY if not specified
+
+FFT_INC = -I/usr/local/include
+FFT_PATH = -L/usr/local/lib
+FFT_LIB = -lfftw3 # FFTW3 double precision
+FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
+FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler
+FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compier :pre
+
+As with CMake, you do not need to set paths in FFT_INC or FFT_PATH, if
+make can find the FFT header and library files. You must specify
+FFT_LIB with the appropriate FFT libraries to include in the link.
+
+[CMake and make info]:
+
+The "KISS FFT library"_http://kissfft.sf.net is included in the LAMMPS
+distribution. It is portable across all platforms. Depending on the
+size of the FFTs and the number of processors used, the other
+libraries listed here can be faster.
+
+However, note that long-range Coulombics are only a portion of the
+per-timestep CPU cost, FFTs are only a portion of long-range
+Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
+communication can be costly). A breakdown of these timings is printed
+to the screen at the end of a run using the "kspace_style
+pppm"_kspace_style.html command. The "Run output"_doc page gives more
+details.
+
+FFTW is a fast, portable FFT library that should also work on any
+platform and can be faster than the KISS FFT library. You can
+download it from "www.fftw.org"_http://www.fftw.org. LAMMPS requires
+version 3.X; the legacy version 2.1.X is no longer supported.
+
+Building FFTW for your box should be as simple as ./configure; make;
+make install. The install command typically requires root privileges
+(e.g. invoke it via sudo), unless you specify a local directory with
+the "--prefix" option of configure. Type "./configure --help" to see
+various options.
+
+The Intel MKL math library is part of the Intel compiler suite. It
+can be used with the Intel or GNU compiler (see FFT_LIB setting above).
+
+Performing 3d FFTs in parallel can be time consuming due to data
+access and required communication. This cost can be reduced by
+performing single-precision FFTs instead of double precision. Single
+precision means the real and imaginary parts of a complex datum are
+4-byte floats. Double precesion means they are 8-byte doubles. Note
+that Fourier transform and related PPPM operations are somewhat less
+sensitive to floating point truncation errors and thus the resulting
+error is less than the difference in precision. Using the -DFFT_SINGLE
+setting trades off a little accuracy for reduced memory use and
+parallel communication costs for transposing 3d FFT data.
+
+When using -DFFT_SINGLE with FFTW3 you may need to build the FFTW
+library a second time with support for single-precision.
+
+For FFTW3, do the following, which should produce the additional
+library libfftw3f.a
+
+make clean
+./configure --enable-single; make; make install :pre
+
+Performing 3d FFTs requires communication to transpose the 3d FFT
+grid. The data packing/unpacking for this can be done in one of 3
+modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
+Depending on the machine, the size of the FFT grid, the number of
+processors used, one option may be slightly faster. The default is
+ARRAY mode.
+
+:line
+
+Size of LAMMPS data types :h3,link(size)
+
+LAMMPS has a few integer data types which can be defined as 4-byte or
+8-byte integers. The default setting of "smallbig" is almost always
+adequate.
+
+[CMake variable]:
+
+-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre
+ # default is LAMMMPS_SMALLBIG if not specified
+[CMake and make info]:
+
+The default "smallbig" setting allows for simulations with:
+
+total atom count = 2^63 atoms (about 9e18)
+total timesteps = 2^63 (about 9e18)
+atom IDs = 2^31 (about 2 billion)
+image flags = roll over at 512 :ul
+
+The "bigbig" setting increases the latter two limits. It allows for:
+
+total atom count = 2^63 atoms (about 9e18)
+total timesteps = 2^63 (about 9e18)
+atom IDs = 2^63 (about 9e18)
+image flags = roll over at about 1 million (2^20) :ul
+
+The "smallsmall" setting is only needed if your machine does not
+support 8-byte integers. It allows for:
+
+total atom count = 2^31 atoms (about 2 billion)
+total timesteps = 2^31 (about 2 billion)
+atom IDs = 2^31 (about 2 billion)
+image flags = roll over at 512 (2^9) :ul
+
+Atom IDs are not required for atomic systems which do not store bond
+topology information, though IDs are enabled by default. The
+"atom_modify id no"_atom_modify.html command will turn them off. Atom
+IDs are required for molecular systems with bond topology (bonds,
+angles, dihedrals, etc). Thus if you model a molecular system with
+more than 2 billion atoms, you need the "bigbig" setting.
+
+Image flags store 3 values per atom which count the number of times an
+atom has moved through the periodic box in each dimension. See the
+"dump"_dump.html doc page for a discussion. If an atom moves through
+the periodic box more than this limit, the value will "roll over",
+e.g. from 511 to -512, which can cause diagnostics like the
+mean-squared displacement, as calculated by the "compute
+msd"_compute_msd.html command, to be faulty.
+
+Note that the USER-ATC package is not currently compatible with the
+"bigbig" setting.
+
+Also note that the GPU package requires its lib/gpu library to be
+compiled with the same size setting, or the link will fail. A CMake
+build does this automatically. When building with make, the setting
+in whichever lib/gpu/Makefile is used must be the same as above.
+
+:line
+
+Output of JPG, PNG, and movie files :h3,link(graphics)
+
+The "dump image"_dump_image.html command has options to output JPEG or
+PNG image files. Likewise the "dump movie"_dump_image.html command
+ouputs movie files in MPEG format. Using these options requires the
+following settings:
+
+[CMake variables]:
+
+-D WITH_JPEG=value # yes or no
+ # default = yes if CMake finds JPEG files, else no
+-D WITH_PNG=value # yes or no
+ # default = yes if CMake finds PNG and ZLIB files, else no
+-D WITH_FFMPEG=value # yes or no
+ # default = yes if CMake can find ffmpeg, else no :pre
+
+Usually these settings are all that is needed. If CMake cannot find
+the graphics header, library, executuable files, you can set these
+variables:
+
+-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
+-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file
+-D PNG_INCLUDE_DIR=path # path to png.h header file
+-D PNG_LIBRARIES=path # path to libpng.a (.so) file
+-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
+-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
+-D FFMPEG_EXECUTABLE=path # path to ffmpeg executable :pre
+
+[Makefile.machine settings]:
+
+LMP_INC = -DLAMMPS_JPEG
+LMP_INC = -DLAMMPS_PNG
+LMP_INC = -DLAMMPS_FFMPEG :pre
+
+JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
+JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
+JPG_LIB = -ljpeg -lpng -lz # library names :pre
+
+As with CMake, you do not need to set JPG_INC or JPG_PATH, if make can
+find the graphics header and library files. You must specify JPG_LIB
+with a list of graphics libraries to include in the link. You must
+insure ffmpeg is in a directory where LAMMPS can find it at runtime,
+i.e. a dir in your PATH environment variable.
+
+[CMake and make info]:
+
+Using ffmpeg to output movie files requires that your machine
+supports the "popen" function in the standard runtime library.
+
+NOTE: On some clusters with high-speed networks, using the fork()
+library calls (required by popen()) can interfere with the fast
+communication library and lead to simulations using ffmpeg to hang or
+crash.
+
+:line
+
+Read or write compressed files :h3,link(gzip)
+
+If this option is enabled, large files can be read or written with
+gzip compression by several LAMMPS commands, including
+"read_data"_read_data.html, "rerun"_rerun.html, and "dump"_dump.html.
+
+[CMake variables]:
+
+-D WITH_GZIP=value # yes or no
+ # default is yes if CMake can find gzip, else no
+-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_GZIP :pre
+
+[CMake and make info]:
+
+This option requires that your machine supports the "popen()" function
+in the standard runtime library and that a gzip executable can be
+found by LAMMPS during a run.
+
+NOTE: On some clusters with high-speed networks, using the fork()
+library calls (required by popen()) can interfere with the fast
+communication library and lead to simulations using compressed output
+or input to hang or crash. For selected operations, compressed file
+I/O is also available using a compression library instead, which is
+what the "COMPRESS package"_Packages_details.html#PKG-COMPRESS enables.
+
+:line
+
+Memory allocation alignment :h3,link(align)
+
+This setting enables the use of the posix_memalign() call instead of
+malloc() when LAMMPS allocates large chunks or memory. This can make
+vector instructions on CPUs more efficient, if dynamically allocated
+memory is aligned on larger-than-default byte boundaries.
+On most current systems, the malloc() implementation returns
+pointers that are aligned to 16-byte boundaries. Using SSE vector
+instructions efficiently, however, requires memory blocks being
+aligned on 64-byte boundaries.
+
+[CMake variable]:
+
+-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default) :pre
+
+Use a LAMMPS_MEMALIGN value of 0 to disable using posix_memalign()
+and revert to using the malloc() C-library function instead. When
+compiling LAMMPS for Windows systems, malloc() will always be used
+and this setting ignored.
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64 :pre
+
+Do not set -DLAMMPS_MEMALIGN, if you want to have memory allocated
+with the malloc() function call instead. -DLAMMPS_MEMALIGN [cannot]
+be used on Windows, as it does use different function calls for
+allocating aligned memory, that are not compatible with how LAMMPS
+manages its dynamical memory.
+
+:line
+
+Workaround for long long integers :h3,link(longlong)
+
+If your system or MPI version does not recognize "long long" data
+types, the following setting will be needed. It converts "long long"
+to a "long" data type, which should be the desired 8-byte integer on
+those systems:
+
+[CMake variable]:
+
+-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default) :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_LONGLONG_TO_LONG :pre
+
+:line
+
+Exception handling when using LAMMPS as a library :h3,link(exceptions)
+
+This setting is useful when external codes drive LAMMPS as a library.
+With this option enabled LAMMPS errors do not kill the caller.
+Instead, the call stack is unwound and control returns to the caller,
+e.g. to Python.
+
+[CMake variable]:
+
+-D LAMMPS_EXCEPTIONS=value # yes or no (default) :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_EXCEPTIONS :pre
diff --git a/doc/src/Commands.txt b/doc/src/Commands.txt
index 30e3343bd21c1203b8182f5f42dbab92a15c723b..84eac285f73387fa6046c5e1fe26de0ffac66489 100644
--- a/doc/src/Commands.txt
+++ b/doc/src/Commands.txt
@@ -16,6 +16,7 @@ commands in it are used to define a LAMMPS simulation.
<!-- RST
.. toctree::
+ :maxdepth: 1
Commands_input
Commands_parse
@@ -23,6 +24,7 @@ commands in it are used to define a LAMMPS simulation.
Commands_category
.. toctree::
+ :maxdepth: 1
Commands_all
Commands_fix
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
index 314260cb14bc582a5791912ac055ec50260878f1..48069d3120048e9d59ead6a3f2959be296d078de 100644
--- a/doc/src/Commands_bond.txt
+++ b/doc/src/Commands_bond.txt
@@ -9,7 +9,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
+"Bond styles"_Commands_bond.html#bond,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
diff --git a/doc/src/Errors.txt b/doc/src/Errors.txt
index 1b6206c780e7a8e02ea5303ad09889dd070e44a0..10f84874a32a6b187aa11e306f698695f0e607bd 100644
--- a/doc/src/Errors.txt
+++ b/doc/src/Errors.txt
@@ -1,4 +1,4 @@
-"Previous Section"_Python.html - "LAMMPS WWW Site"_lws -
+"Previous Section"_Python_head.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Manual.html :c
@@ -19,6 +19,7 @@ additional details for many of them.
<!-- RST
.. toctree::
+ :maxdepth: 1
Errors_common
Errors_bugs
diff --git a/doc/src/Errors_common.txt b/doc/src/Errors_common.txt
index 43d1a85a7bd0ff2772c5dfeb690073d93d50bb10..651040ebc9e7b2bae23fc4cfc8df0d975295d6aa 100644
--- a/doc/src/Errors_common.txt
+++ b/doc/src/Errors_common.txt
@@ -58,9 +58,9 @@ style", with ... being fix, compute, pair, etc, it means that you
mistyped the style name or that the command is part of an optional
package which was not compiled into your executable. The list of
available styles in your executable can be listed by using "the -h
-command-line argument"_Section_start.html#start_6. The installation
-and compilation of optional packages is explained in the "installation
-instructions"_Section_start.html#start_3.
+command-line swith"_Run_options.html. The installation and
+compilation of optional packages is explained on the "Build
+packages"_Build_package.html doc page.
For a given command, LAMMPS expects certain arguments in a specified
order. If you mess this up, LAMMPS will often flag the error, but it
@@ -93,7 +93,7 @@ decide if the WARNING is important or not. A WARNING message that is
generated in the middle of a run is only printed to the screen, not to
the logfile, to avoid cluttering up thermodynamic output. If LAMMPS
crashes or hangs without spitting out an error message first then it
-could be a bug (see "this section"_#err_2) or one of the following
+could be a bug (see "this section"_Errors_bugs.html) or one of the following
cases:
LAMMPS runs in the available memory a processor allows to be
diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt
index 03fc25b5618c3b6803c719cdbb5473edad5cbf6a..d279b5e9758c0366169abb962e3d27b9fddaa56e 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -7911,8 +7911,8 @@ Atom IDs must be positive integers. :dd
{One or more atom IDs is too big} :dt
The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
-setting in your Makefile. See Section_start 2.2 of the manual for
-more details. :dd
+setting in your LAMMPS build. See the "Build
+settings"_Build_settings.html doc page for more info. :dd
{One or more atom IDs is zero} :dt
diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt
index 5bd8da2409185873b745cc87b1ae95b5a0b6ac1b..4b6db8a047f64b5ab204750c8bf0a88da9d45140 100644
--- a/doc/src/Examples.txt
+++ b/doc/src/Examples.txt
@@ -112,10 +112,10 @@ web site.
If you uncomment the "dump image"_dump_image.html line(s) in the input
script a series of JPG images will be produced by the run (assuming
-you built LAMMPS with JPG support; see "Section
-2.2"_Section_start.html#start_2 for details). These can be viewed
-individually or turned into a movie or animated by tools like
-ImageMagick or QuickTime or various Windows-based tools. See the
+you built LAMMPS with JPG support; see the
+"Build_settings"_Build_settings.html doc page for details). These can
+be viewed individually or turned into a movie or animated by tools
+like ImageMagick or QuickTime or various Windows-based tools. See the
"dump image"_dump_image.html doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.
diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt
index d9a60d1ef4b8e8365683794e5bfc96d5fc325b32..fc7329aad5846382382bf1e112bece67570c45d6 100644
--- a/doc/src/Howto.txt
+++ b/doc/src/Howto.txt
@@ -22,12 +22,14 @@ also show how to setup and run various kinds of simulations.
<!-- RST
.. toctree::
+ :maxdepth: 1
Howto_github
Howto_pylammps
Howto_bash
.. toctree::
+ :maxdepth: 1
Howto_restart
Howto_viz
@@ -37,11 +39,13 @@ also show how to setup and run various kinds of simulations.
Howto_couple
.. toctree::
+ :maxdepth: 1
Howto_output
Howto_chunk
.. toctree::
+ :maxdepth: 1
Howto_2d
Howto_triclinic
@@ -52,6 +56,7 @@ also show how to setup and run various kinds of simulations.
Howto_dispersion
.. toctree::
+ :maxdepth: 1
Howto_temperature
Howto_thermostat
@@ -62,6 +67,7 @@ also show how to setup and run various kinds of simulations.
Howto_diffusion
.. toctree::
+ :maxdepth: 1
Howto_bioFF
Howto_tip3p
@@ -69,6 +75,7 @@ also show how to setup and run various kinds of simulations.
Howto_spc
.. toctree::
+ :maxdepth: 1
Howto_body
Howto_polarizable
@@ -84,7 +91,7 @@ END_RST -->
"Using GitHub with LAMMPS"_Howto_github.html
"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
-"Using LAMMPS with bash on Windows"_Howto_bash.html
+"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
"Restart a simulation"_Howto_restart.html
"Visualize LAMMPS snapshots"_Howto_viz.html
@@ -121,8 +128,8 @@ END_RST -->
"Polarizable models"_Howto_polarizable.html
"Adiabatic core/shell model"_Howto_coreshell.html
"Drude induced dipoles"_Howto_drude.html
-"Drude induced dipoles (extended)"_Howto_drude2.html :all(b)
+"Drude induced dipoles (extended)"_Howto_drude2.html
"Manifolds (surfaces)"_Howto_manifold.html
-"Magnetic spins"_Howto_spins.html
+"Magnetic spins"_Howto_spins.html :all(b)
<!-- END_HTML_ONLY -->
diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt
index afb8a84f2e32ac4397054054c4032ab339629290..deb5b31441918e8646b29c74740fc16ed0ed4b52 100644
--- a/doc/src/Howto_bioFF.txt
+++ b/doc/src/Howto_bioFF.txt
@@ -96,6 +96,10 @@ documentation for the formula it computes.
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+:link(howto-Cornell)
+[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
+Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+
:link(howto-Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
diff --git a/doc/src/Howto_coreshell.txt b/doc/src/Howto_coreshell.txt
index 4f1cd64384e696dbf00eccf023a3a10be8f40cc9..7503fa1ebe4a2f2dcbf8eace63fce07ee0b155a7 100644
--- a/doc/src/Howto_coreshell.txt
+++ b/doc/src/Howto_coreshell.txt
@@ -119,7 +119,7 @@ the core/shell pair, which is an imaginary degree of freedom, from the
real physical system. To do that, the "compute
temp/cs"_compute_temp_cs.html command can be used, in conjunction with
any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
-langevin"_fix_langevin. This compute uses the center-of-mass velocity
+langevin"_fix_langevin.html. This compute uses the center-of-mass velocity
of the core/shell pairs to calculate a temperature, and insures that
velocity is what is rescaled for thermostatting purposes. This
compute also works for a system with both core/shell pairs and
@@ -150,9 +150,9 @@ The pressure for the core/shell system is computed via the regular
LAMMPS convention by "treating the cores and shells as individual
particles"_#MitchellFincham2. For the thermo output of the pressure
as well as for the application of a barostat, it is necessary to
-use an additional "pressure"_compute_pressure compute based on the
-default "temperature"_compute_temp and specifying it as a second
-argument in "fix modify"_fix_modify.html and
+use an additional "pressure"_compute_pressure.html compute based on
+the default "temperature"_compute_temp.html and specifying it as a
+second argument in "fix modify"_fix_modify.html and
"thermo_modify"_thermo_modify.html resulting in:
(...)
diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt
index 38595a9d1641ddb869cf5606ce003c2189690813..d7b4924d8cda690ef5204f6adabab34f2fff0a7d 100644
--- a/doc/src/Howto_couple.txt
+++ b/doc/src/Howto_couple.txt
@@ -77,17 +77,16 @@ strain induced across grain boundaries :l
:link(quest,http://dft.sandia.gov/Quest)
:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
-"This section"_Section_start.html#start_5 of the documentation
-describes how to build LAMMPS as a library. Once this is done, you
-can interface with LAMMPS either via C++, C, Fortran, or Python (or
-any other language that supports a vanilla C-like interface). For
-example, from C++ you could create one (or more) "instances" of
-LAMMPS, pass it an input script to process, or execute individual
-commands, all by invoking the correct class methods in LAMMPS. From C
-or Fortran you can make function calls to do the same things. See the
-"Python"_Python.html doc pages for a description of the Python wrapper
-provided with LAMMPS that operates through the LAMMPS library
-interface.
+The "Build basics"_Build_basics.html doc page describes how to build
+LAMMPS as a library. Once this is done, you can interface with LAMMPS
+either via C++, C, Fortran, or Python (or any other language that
+supports a vanilla C-like interface). For example, from C++ you could
+create one (or more) "instances" of LAMMPS, pass it an input script to
+process, or execute individual commands, all by invoking the correct
+class methods in LAMMPS. From C or Fortran you can make function
+calls to do the same things. See the "Python"_Python_head.html doc
+pages for a description of the Python wrapper provided with LAMMPS
+that operates through the LAMMPS library interface.
The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See the "Howto library"_Howto_library.html doc page for a
diff --git a/doc/src/Howto_granular.txt b/doc/src/Howto_granular.txt
index 8027369501eb0730dd4008b56503d95642ee9380..758b1cebee76645f7e5c6d023cbab045269875de 100644
--- a/doc/src/Howto_granular.txt
+++ b/doc/src/Howto_granular.txt
@@ -53,5 +53,5 @@ computations between frozen atoms by using this command:
NOTE: By default, for 2d systems, granular particles are still modeled
as 3d spheres, not 2d discs (circles), meaning their moment of inertia
will be the same as in 3d. If you wish to model granular particles in
-2d as 2d discs, see the note on this topic on the "Howto 2d"_Howto_2d
+2d as 2d discs, see the note on this topic on the "Howto 2d"_Howto_2d.html
doc page, where 2d simulations are discussed.
diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt
index 0d4852fbf247adee92be56045d7b98af7e5a3542..741078e7eb7cb74a574c0e0bada4cca4414cce89 100644
--- a/doc/src/Howto_library.txt
+++ b/doc/src/Howto_library.txt
@@ -9,10 +9,10 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Library interface to LAMMPS :h3
-As described in "Section 2.5"_Section_start.html#start_5, LAMMPS can
-be built as a library, so that it can be called by another code, used
-in a "coupled manner"_Howto_couple.html with other codes, or driven
-through a "Python interface"_Python.html.
+As described on the "Build basics"_Build_basics.html doc page, LAMMPS
+can be built as a library, so that it can be called by another code,
+used in a "coupled manner"_Howto_couple.html with other codes, or
+driven through a "Python interface"_Python_head.html.
All of these methodologies use a C-style interface to LAMMPS that is
provided in the files src/library.cpp and src/library.h. The
@@ -35,8 +35,8 @@ details.
NOTE: You can write code for additional functions as needed to define
how your code talks to LAMMPS and add them to src/library.cpp and
-src/library.h, as well as to the "Python interface"_Python.html. The
-added functions can access or change any internal LAMMPS data you
+src/library.h, as well as to the "Python interface"_Python_head.html.
+The added functions can access or change any internal LAMMPS data you
wish.
void lammps_open(int, char **, MPI_Comm, void **)
@@ -51,12 +51,11 @@ void lammps_free(void *) :pre
The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were "command-line
-arguments"_Section_start.html#start_6 when LAMMPS is run in
-stand-alone mode from the command line, and a MPI communicator for
-LAMMPS to run under. It returns a ptr to the LAMMPS object that is
-created, and which is used in subsequent library calls. The
-lammps_open() function can be called multiple times, to create
-multiple instances of LAMMPS.
+arguments"_Run_options.html when LAMMPS is run in stand-alone mode
+from the command line, and a MPI communicator for LAMMPS to run under.
+It returns a ptr to the LAMMPS object that is created, and which is
+used in subsequent library calls. The lammps_open() function can be
+called multiple times, to create multiple instances of LAMMPS.
LAMMPS will run on the set of processors in the communicator. This
means the calling code can run LAMMPS on all or a subset of
diff --git a/doc/src/Howto_multiple.txt b/doc/src/Howto_multiple.txt
index edcb8196cf015543db85b6ab83411d4d13373758..9ad872fedc1890c9fc166b884a3585f56dd3a329 100644
--- a/doc/src/Howto_multiple.txt
+++ b/doc/src/Howto_multiple.txt
@@ -80,8 +80,7 @@ jump in.polymer :pre
All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
-the "-partition" command-line switch as described in "this
-section"_Section_start.html#start_6 of the manual.
+the "-partition command-line switch"_Run_options.html.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
diff --git a/doc/src/Howto_replica.txt b/doc/src/Howto_replica.txt
index 1b44fe53748d4dc1adf35aebe333b97bea4c33ac..2135e52e0e360c7b62f052b58763262d6d0d651e 100644
--- a/doc/src/Howto_replica.txt
+++ b/doc/src/Howto_replica.txt
@@ -29,29 +29,28 @@ runs different replicas at a series of temperature to facilitate
rare-event sampling.
These commands can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
PIMD runs different replicas whose individual particles are coupled
together by springs to model a system or ring-polymers.
This commands can only be used if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the "-partition command-line
-switch"_Section_start.html#start_6 to launch LAMMPS on multiple
-partitions, which in this context are the same as replicas. E.g.
-these commands:
+switch"_Run_options.html to launch LAMMPS on multiple partitions,
+which in this context are the same as replicas. E.g. these commands:
mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
would each run 8 replicas, on either 16 or 8 processors. Note the use
-of the "-in command-line switch"_Section_start.html#start_6 to specify
-the input script which is required when running in multi-replica mode.
+of the "-in command-line switch"_Run_options.html to specify the input
+script which is required when running in multi-replica mode.
Also note that with MPI installed on a machine (e.g. your desktop),
you can run on more (virtual) processors than you have physical
diff --git a/doc/src/Howto_restart.txt b/doc/src/Howto_restart.txt
index b211775479bfc367301a408ef15e45f8bd46cca0..bc67daa78e3b9a3c2e866b8d9a748753300e6ffe 100644
--- a/doc/src/Howto_restart.txt
+++ b/doc/src/Howto_restart.txt
@@ -16,8 +16,8 @@ restart files can be saved to disk using the "restart"_restart.html
command. At a later time, these binary files can be read via a
"read_restart"_read_restart.html command in a new script. Or they can
be converted to text data files using the "-r command-line
-switch"_Section_start.html#start_6 and read by a
-"read_data"_read_data.html command in a new script.
+switch"_Run_options.html and read by a "read_data"_read_data.html
+command in a new script.
Here we give examples of 2 scripts that read either a binary restart
file or a converted data file and then issue a new run command to
diff --git a/doc/src/Howto_temperature.txt b/doc/src/Howto_temperature.txt
index 7a318250cffa956692693e601638e749cc4d6df4..8a9e262da1b071abde5ab8b6957addba8444b718 100644
--- a/doc/src/Howto_temperature.txt
+++ b/doc/src/Howto_temperature.txt
@@ -17,7 +17,10 @@ aggregate motion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
-LAMMPS has several options for computing temperatures, any of which can be used in "thermostatting"_Howto_thermostat.html and "barostatting"_Howto_barostat.html. These "compute commands"_compute.html calculate temperature:
+LAMMPS has several options for computing temperatures, any of which
+can be used in "thermostatting"_Howto_thermostat.html and
+"barostatting"_Howto_barostat.html. These "compute
+commands"_compute.html calculate temperature:
"compute temp"_compute_temp.html
"compute temp/sphere"_compute_temp_sphere.html
@@ -35,6 +38,6 @@ velocities) that are removed when computing the thermal temperature.
temp/asphere"_compute_temp_asphere.html compute kinetic energy for
finite-size particles that includes rotational degrees of freedom.
They both allow for velocity biases indirectly, via an optional extra
-argument which is another temperature compute that subtracts a velocity bias.
-This allows the translational velocity of spherical or aspherical
-particles to be adjusted in prescribed ways.
+argument which is another temperature compute that subtracts a
+velocity bias. This allows the translational velocity of spherical or
+aspherical particles to be adjusted in prescribed ways.
diff --git a/doc/src/Howto_tip4p.txt b/doc/src/Howto_tip4p.txt
index f9e548e26896c1143f1cead59e3c0a1effb015c3..9f7f1413147e9f13e9ce21b44457502d1d95fa87 100644
--- a/doc/src/Howto_tip4p.txt
+++ b/doc/src/Howto_tip4p.txt
@@ -31,7 +31,7 @@ using the "fix shake"_fix_shake.html command.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
-"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in
+"(Jorgensen)"_#Jorgensen5. Note that the OM distance is specified in
the "pair_style"_pair_style.html command, not as part of the pair
coefficients.
@@ -107,6 +107,6 @@ models"_http://en.wikipedia.org/wiki/Water_model.
:line
-:link(Jorgensen1)
+:link(Jorgensen5)
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
diff --git a/doc/src/Install.txt b/doc/src/Install.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a2e870a5d7ec5762337bc4c6b30dc5f419f9481
--- /dev/null
+++ b/doc/src/Install.txt
@@ -0,0 +1,65 @@
+"Previous Section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Build.html
+:c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Install LAMMPS :h2
+
+You can download LAMMPS as an executable or as source code.
+
+With source code, you also have to "build LAMMPS"_Build.html. But you
+have more flexibility as to what features to include or exclude in the
+build. If you plan to "modify or extend LAMMPS"_Modify.html, then you
+need the source code.
+
+<!-- RST
+
+.. toctree::
+ :maxdepth: 1
+
+ Install_linux
+ Install_mac
+ Install_windows
+
+ Install_tarball
+ Install_git
+ Install_svn
+ Install_patch
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Download an executable for Linux"_Install_linux.html
+"Download an executable for Mac"_Install_mac.html
+"Download an executable for Windows"_Install_windows.html :all(b)
+
+"Download source as a tarball"_Install_tarball.html
+"Donwload source via Git"_Install_git.html
+"Donwload source via SVN"_Install_svn.html
+"Install patch files"_Install_patch.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+These are the files and sub-directories in the LAMMPS distribution:
+
+README: text file
+LICENSE: GNU General Public License (GPL)
+bench: benchmark problems
+cmake: CMake build files
+doc: documentation
+examples: simple test problems
+lib: additional provided or external libraries
+potentials: interatomic potential files
+python: Python wrapper on LAMMPS
+src: source files
+tools: pre- and post-processing tools :tb(s=:,a=l)
+
+You will have all of these if you download source. You will only have
+some of them if you download executables, as explained on the pages
+listed above.
diff --git a/doc/src/Install_git.txt b/doc/src/Install_git.txt
new file mode 100644
index 0000000000000000000000000000000000000000..538fa8aff80c43c890e9dca75bcfe2adce443390
--- /dev/null
+++ b/doc/src/Install_git.txt
@@ -0,0 +1,120 @@
+"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Download source via Git :h3
+
+All LAMMPS development is coordinated through the "LAMMPS GitHub
+site". If you clone the LAMMPS repository onto your local machine, it
+has several advantages:
+
+You can stay current with changes to LAMMPS with a single git
+command. :ulb,l
+
+You can create your own development branches to add code to LAMMPS. :l
+
+You can submit your new features back to GitHub for inclusion in
+LAMMPS. :l,ule
+
+You must have "Git"_git installed on your system to communicate with
+the public Git server for LAMMPS.
+
+IMPORTANT NOTE: As of Oct 2016, the official home of public LAMMPS
+development is on GitHub. The previously advertised LAMMPS git
+repositories on git.lammps.org and bitbucket.org are now deprecated,
+may not be up-to-date, and may go away at any time.
+
+:link(git,http://git-scm.com)
+
+You can follow LAMMPS development on 3 different Git branches:
+
+[stable] : this branch is updated with every stable release
+[unstable] : this branch is updated with every patch release
+[master] : this branch continuously follows ongoing development :ul
+
+To access the Git repositories on your box, use the clone command to
+create a local copy of the LAMMPS repository with a command like:
+
+git clone -b unstable https://github.com/lammps/lammps.git mylammps :pre
+
+where "mylammps" is the name of the directory you wish to create on
+your machine and "unstable" is one of the 3 branches listed above.
+(Note that you actually download all 3 branches; you can switch
+between them at any time using "git checkout <branchname>".)
+
+Once the command completes, your directory will contain the same files
+as if you unpacked a current LAMMPS tarball, with two exceptions:
+
+1) No LAMMPS packages are initially installed in the src dir (a few
+packages are installed by default in the tarball src dir). You can
+install whichever packages you wish before building LAMMPS; type "make
+package" from the src dir to see the options, and the
+"Packages"_Packages.html doc page for a discussion of packages.
+
+2) The HTML documentation files are not included. They can be fetched
+from the LAMMPS website by typing "make fetch" in the doc directory.
+Or they can be generated from the content provided in doc/src by
+typing "make html" from the the doc directory.
+
+After initial cloning, as bug fixes and new features are added to
+LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay
+up-to-date by typing the following Git commands from within the
+"mylammps" directory:
+
+git checkout unstable # not needed if you always stay in this branch
+git checkout stable # use one of the 3 checkout commands
+git checkout master
+git pull :pre
+
+Doing a "pull" will not change any files you have added to the LAMMPS
+directory structure. It will also not change any existing LAMMPS
+files you have edited, unless those files have changed in the
+repository. In that case, Git will attempt to merge the new
+repository file with your version of the file and tell you if there
+are any conflicts. See the Git documentation for details.
+
+If you want to access a particular previous release version of LAMMPS,
+you can instead "checkout" any version with a published tag. See the
+output of "git tag -l" for the list of tags. The Git command to do
+this is as follows.
+
+git checkout tagID :pre
+
+Stable versions and what tagID to use for a particular stable version
+are discussed on "this page"_Errors_bugs.html. Note that this command
+will print some warnings, because in order to get back to the latest
+revision and to be able to update with "git pull" again, you first
+will need to first type "git checkout unstable" (or check out any
+other desired branch).
+
+Once you have updated your local files with a "git pull" (or "git
+checkout"), you still need to re-build LAMMPS if any source files have
+changed. To do this, you should cd to the src directory and type:
+
+make purge # remove any deprecated src files
+make package-update # sync package files with src files
+make foo # re-build for your machine (mpi, serial, etc) :pre
+
+just as described on the "Install patch"_Install_patch.html doc page,
+after a patch has been installed.
+
+IMPORTANT NOTE: If you wish to edit/change a src file that is from a
+package, you should edit the version of the file inside the package
+sub-directory with src, then re-install the package. The version in
+the src dir is merely a copy and will be wiped out if you type "make
+package-update".
+
+IMPORTANT NOTE: The GitHub servers support both the "git://" and
+"https://" access protocols for anonymous read-only access. If you
+have a correspondingly configured GitHub account, you may also use SSH
+with "git@github.com:/lammps/lammps.git".
+
+The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
+junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
+gmail.com) and Richard Berger (Temple U, richard.berger at
+temple.edu).
diff --git a/doc/src/Install_linux.txt b/doc/src/Install_linux.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc15ac0ae0f6f4ef43f9b9fbfd0372eeae28e8e4
--- /dev/null
+++ b/doc/src/Install_linux.txt
@@ -0,0 +1,119 @@
+"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Download an executable for Linux :h3
+
+Binaries are available for many different versions of Linux:
+
+"Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE"_#rpm
+"Pre-built Ubuntu Linux executables"_#ubuntu
+"Pre-built Gentoo Linux executable"_#gentoo :all(b)
+
+:line
+
+Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE :h4,link(rpm)
+
+Pre-built LAMMPS executables for various Linux distributions
+can be downloaded as binary RPM files from this site:
+
+"http://rpm.lammps.org"_http://rpm.lammps.org
+
+There are multiple package variants supporting serial, parallel and
+Python wrapper versions. The LAMMPS binaries contain all optional
+packages included in the source distribution except: GPU, KIM, REAX,
+and USER-INTEL.
+
+Installation instructions for the various versions are here:
+
+"http://rpm.lammps.org/install.html"_http://rpm.lammps.org/install.html
+
+The instructions show how to enable the repository in the respective
+system's package management system. Installing and updating are then
+straightforward and automatic.
+
+Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting
+up this RPM capability.
+
+:line
+
+Pre-built Ubuntu Linux executables :h4,link(ubuntu)
+
+A pre-built LAMMPS executable suitable for running on the latest
+Ubuntu Linux versions, can be downloaded as a Debian package. This
+allows you to install LAMMPS with a single command, and stay
+up-to-date with the current version of LAMMPS by simply updating your
+operating system.
+
+To install the appropriate personal-package archive (PPA), do the
+following once:
+
+sudo add-apt-repository ppa:gladky-anton/lammps
+sudo apt-get update :pre
+
+To install LAMMPS do the following once:
+
+sudo apt-get install lammps-daily :pre
+
+This downloads an executable named "lammps-daily" to your box, which
+can then be used in the usual way to run input scripts:
+
+lammps-daily < in.lj :pre
+
+To update LAMMPS to the most current version, do the following:
+
+sudo apt-get update :pre
+
+which will also update other packages on your system.
+
+To get a copy of the current documentation and examples:
+
+sudo apt-get install lammps-daily-doc :pre
+
+which will download the doc files in
+/usr/share/doc/lammps-daily-doc/doc and example problems in
+/usr/share/doc/lammps-doc/examples.
+
+Note that you may still wish to download the tarball to get potential
+files and auxiliary tools.
+
+To un-install LAMMPS, do the following:
+
+sudo apt-get remove lammps-daily :pre
+
+Note that the lammps-daily executable is built with the following
+sequence of make commands, as if you had done the same with the
+unpacked tarball files in the src directory:
+
+make yes-all; make no-lib; make openmpi
+
+Thus it builds with FFTW3 and OpenMPI.
+
+Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this
+Ubuntu package capability.
+
+:line
+
+Pre-built Gentoo Linux executable :h4,link(gentoo)
+
+LAMMPS is part of Gentoo's main package tree and can be installed by
+typing:
+
+% emerge --ask lammps :pre
+
+Note that in Gentoo the LAMMPS source is downloaded and the package is
+built on the your machine.
+
+Certain LAMMPS packages can be enable via USE flags, type
+
+% equery uses lammps :pre
+
+for details.
+
+Thanks to Nicolas Bock and Christoph Junghans (LANL) for setting up
+this Gentoo capability.
diff --git a/doc/src/Install_mac.txt b/doc/src/Install_mac.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3fcc55b8abb8ac08bda46f06e0bad0f1445e9cc9
--- /dev/null
+++ b/doc/src/Install_mac.txt
@@ -0,0 +1,55 @@
+"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Download an executable for Mac :h3
+
+LAMMPS can be downloaded, built, and configured for OS X on a Mac with
+"Homebrew"_homebrew. Only four of the LAMMPS packages are unavailable
+at this time because of additional needs not yet met: KIM, GPU,
+USER-INTEL, USER-ATC.
+
+After installing Homebrew, you can install LAMMPS on your system with
+the following commands:
+
+% brew tap homebrew/science
+% brew install lammps # serial version
+% brew install lammps --with-mpi # mpi support :pre
+
+This will install the executable "lammps", a python module named
+"lammps", and additional resources with all the standard packages. To
+get the location of the additional resources type this:
+
+% brew info lammps :pre
+
+This command also tells you additional installation options available.
+The user-packages are available as options, just install them like
+this example for the USER-OMP package:
+
+% brew install lammps --enable-user-omp :pre
+
+It is usually best to install LAMMPS with the most up to date source
+files, which can be done with the "--HEAD" option:
+
+% brew install lammps --HEAD :pre
+
+To re-install the LAMMPS HEAD, run this command occasionally (make sure
+to use the desired options).
+
+% brew install --force lammps --HEAD $\{options\} :pre
+
+Once LAMMPS is installed, you can test the installation with the
+Lennard-Jones benchmark file:
+
+% brew test lammps -v :pre
+
+If you have problems with the installation you can post issues to
+"this link"_https://github.com/Homebrew/homebrew-science/issues.
+
+Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
+up the Homebrew capability.
diff --git a/doc/src/Install_patch.txt b/doc/src/Install_patch.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d0b27370e1285e293f247e02c7a4fac0c24c630
--- /dev/null
+++ b/doc/src/Install_patch.txt
@@ -0,0 +1,67 @@
+"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Applying patches :h3
+
+It is easy to stay current with the most recent LAMMPS patch releases
+if you use Git or SVN to track LAMMPS development. Instructions for
+how to stay current are on the "Install git"_Install_git.html and
+"Install svn"_Install_svn.html doc pages.
+
+If you prefer to download a tarball, as described on the "Install
+git"_Install_tarball.html doc page, you can stay current by
+downloading "patch files" when new patch releases are made. A link to
+a patch file is posted on the "bug and feature page"_bug of the
+website, along with a list of changed files and details about what is
+in the new patch release. This page explains how to apply the patch
+file to your local LAMMPS directory.
+
+NOTE: You should not apply patch files to a local Git or SVN repo of
+LAMMPS, only to an unpacked tarball. Use Git and SVN commands to
+update repo versions of LAMMPS.
+
+Here are the steps to apply a patch file. Note that if your version
+of LAMMPS is several patch releases behind, you need to apply all the
+intervening patch files in succession to bring your version of LAMMPS
+up to date.
+
+Download the patch file. You may have to shift-click in your browser
+to download the file instead of display it. Patch files have names
+like patch.12Dec16. :ulb,l
+
+Put the patch file in your top-level LAMMPS directory, where the
+LICENSE and README files are. :l
+
+Apply the patch by typing the following command from your top-level
+LAMMPS directory, where the redirected file is the name of the patch
+file. :l
+
+patch -bp1 < patch.12Dec16 :pre
+
+A list of updated files print out to the screen. The -b switch
+creates backup files of your originals (e.g. src/force.cpp.orig), so
+you can manually undo the patch if something goes wrong. :l
+
+Type the following from the src directory, to enforce consistency
+between the src and package directories. This is OK to do even if you
+don't use one or more packages. If you are applying several patches
+successively, you only need to type this once at the end. The purge
+command removes deprecated src files if any were removed by the patch
+from package sub-directories. :l
+
+make purge
+make package-update :pre
+
+Re-build LAMMPS via the "make" command. :l,ule
+
+IMPORTANT NOTE: If you wish to edit/change a src file that is from a
+package, you should edit the version of the file inside the package
+sub-dir of src, then re-install the package. The version in the src
+dir is merely a copy and will be wiped out if you type "make
+package-update".
diff --git a/doc/src/Install_svn.txt b/doc/src/Install_svn.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a0211ab65fa39a41985e74198f7a7cdd145b0b2
--- /dev/null
+++ b/doc/src/Install_svn.txt
@@ -0,0 +1,95 @@
+"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Download source via SVN :h3
+
+IMPORTANT NOTE: As of Oct 2016, SVN support is now implemented via a
+git-to-subversion interface service on GitHub and no longer through a
+mirror of the internal SVN repository at Sandia.
+
+You must have the "Subversion (SVN) client software"_svn installed on
+your system to communicate with the Git server in this mode.
+
+:link(svn,http://subversion.apache.org)
+
+You can follow LAMMPS development on 3 different SVN branches:
+
+[stable] : this branch is updated with every stable release
+[unstable] : this branch is updated with every patch release
+[master] : this branch continuously follows ongoing development :ul
+
+The corresponding command lines to do an initial checkout are as
+follows. (Note that unlike Git, you must perform a separate checkout
+into a unique directory for each of the 3 branches.)
+
+svn checkout https://github.com/lammps/lammps.git/branches/unstable mylammps
+svn checkout https://github.com/lammps/lammps.git/branches/stable mylammps
+svn checkout https://github.com/lammps/lammps.git/trunk mylammps :pre
+
+where "mylammps" is the name of the directory you wish to create on
+your machine.
+
+Once the command completes, your directory will contain the same files
+as if you unpacked a current LAMMPS tarball, with two exceptions:
+
+1) No LAMMPS packages are initially installed in the src dir (a few
+packages are installed by default in the tarball src dir). You can
+install whichever packages you wish before building LAMMPS; type "make
+package" from the src dir to see the options, and the
+"Packages"_Packages.html doc page for a discussion of packages.
+
+2) The HTML documentation files are not included. They can be fetched
+from the LAMMPS website by typing "make fetch" in the doc directory.
+Or they can be generated from the content provided in doc/src by
+typing "make html" from the the doc directory.
+
+After initial checkout, as bug fixes and new features are added to
+LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay
+up-to-date by typing the following SVN commands from within the
+"mylammps" directory:
+
+svn update :pre
+
+You can also check if there are any updates by typing:
+
+svn -qu status :pre
+
+Doing an "update" will not change any files you have added to the
+LAMMPS directory structure. It will also not change any existing
+LAMMPS files you have edited, unless those files have changed in the
+repository. In that case, SVN will attempt to merge the new
+repository file with your version of the file and tell you if there
+are any conflicts. See the SVN documentation for details.
+
+Please refer to the "subversion client support help pages on
+GitHub"_https://help.github.com/articles/support-for-subversion-clients
+if you want to use advanced features like accessing particular
+previous release versions via tags.
+
+Once you have updated your local files with an "svn update" (or "svn
+co"), you still need to re-build LAMMPS if any source files have
+changed. To do this, you should cd to the src directory and type:
+
+make purge # remove any deprecated src files
+make package-update # sync package files with src files
+make foo # re-build for your machine (mpi, serial, etc) :pre
+
+just as described on the "Install patch"_Install_patch.html doc page,
+after a patch has been installed.
+
+IMPORTANT NOTE: If you wish to edit/change a src file that is from a
+package, you should edit the version of the file inside the package
+sub-directory with src, then re-install the package. The version in
+the src dir is merely a copy and will be wiped out if you type "make
+package-update".
+
+The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
+junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
+gmail.com) and Richard Berger (Temple U, richard.berger at
+temple.edu).
diff --git a/doc/src/Install_tarball.txt b/doc/src/Install_tarball.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b672c5ff252143a0484cd60025549c64878b127f
--- /dev/null
+++ b/doc/src/Install_tarball.txt
@@ -0,0 +1,64 @@
+"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Download source as a tarball :h3
+
+You can download a current LAMMPS tarball from the "download page"_download
+of the "LAMMPS website"_lws.
+
+:link(download,http://lammps.sandia.gov/download.html)
+:link(bug,http://lammps.sandia.gov/bug.html)
+:link(older,http://lammps.sandia.gov/tars)
+
+You have two choices of tarballs, either the most recent stable
+release or the most current patch release. Stable releases occur a
+few times per year, and undergo more testing before release. Patch
+releases occur a couple times per month. The new contents in all
+releases are listed on the "bug and feature page"_bug of the website.
+
+Older versions of LAMMPS can also be downloaded from "this
+page"_older.
+
+Once you have a tarball, unzip and untar it with the following
+command:
+
+tar -xzvf lammps*.tar.gz :pre
+
+This will create a LAMMPS directory with the version date
+in its name, e.g. lammps-23Jun18.
+
+:line
+
+You can also download a zip file via the "Clone or download" button on
+the "LAMMPS GitHub site"_git. The file name will be lammps-master.zip
+which can be unzipped with the following command, to create
+a lammps-master dir:
+
+unzip lammps*.zip :pre
+
+This version is the most up-to-date LAMMPS development version. It
+will have the date of the most recent patch release (see the file
+src/version.h). But it will also include any new bug-fixes or
+features added since the last patch release. They will be included in
+the next patch release tarball.
+
+:link(git,https://github.com/lammps/lammps)
+
+:line
+
+If you download a current LAMMPS tarball, one way to stay current as
+new patch tarballs are released, is to download a patch file which you
+can apply to your local directory to update it for each new patch
+release. (Or of course you could just download the newest tarball
+periodically.)
+
+The patch files are posted on the "bug and feature page"_bug of the
+website, along with a list of changed files and details about what is
+in the new patch release. Instructions for applying a patch file are
+on the "Install patch"_Install_patch.html doc page.
diff --git a/doc/src/Install_windows.txt b/doc/src/Install_windows.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df87754c5fcfc84bf9f55bc99679ffe8e4b793dd
--- /dev/null
+++ b/doc/src/Install_windows.txt
@@ -0,0 +1,52 @@
+"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Download an executable for Windows :h3
+
+Pre-compiled Windows installers which install LAMMPS executables on a
+Windows system can be downloaded from this site:
+
+"http://rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html
+
+Note that each installer package has a date in its name, which
+corresponds to the LAMMPS version of the same date. Installers for
+current and older versions of LAMMPS are available. 32-bit and 64-bit
+installers are available, and each installer contains both a serial
+and parallel executable. The installer site also explains how to
+install the Windows MPI package (MPICH2 from Argonne National Labs),
+needed to run in parallel.
+
+The LAMMPS binaries contain all optional packages included in the
+source distribution except: KIM, REAX, KOKKOS, USER-INTEL,
+and USER-QMMM. The serial version also does not include the MPIIO and
+USER-LB packages. GPU support is provided for OpenCL.
+
+The installer site also has instructions on how to run LAMMPS under
+Windows, once it is installed, in both serial and parallel.
+
+When you download the installer package, you run it on your Windows
+machine. It will then prompt you with a dialog, where you can choose
+the installation directory, unpack and copy several executables,
+potential files, documentation pdfs, selected example files, etc. It
+will then update a few system settings (e.g. PATH, LAMMPS_POTENTIALS)
+and add an entry into the Start Menu (with references to the
+documentation, LAMMPS homepage and more). From that menu, there is
+also a link to an uninstaller that removes the files and undoes the
+environment manipulations.
+
+Note that to update to a newer version of LAMMPS, you should typically
+uninstall the version you currently have, download a new installer,
+and go thru the install procedure described above. I.e. the same
+procedure for installing/updating most Windows programs. You can
+install multiple versions of LAMMPS (in different directories), but
+only the executable for the last-installed package will be found
+automatically, so this should only be done for debugging purposes.
+
+Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting
+up this Windows capability.
diff --git a/doc/src/Intro.txt b/doc/src/Intro.txt
index e3eaa404376015a1bec4d63d34397456b9c425dd..c8725e0085edde75afcc8afd1ab2bd50da8b17a1 100644
--- a/doc/src/Intro.txt
+++ b/doc/src/Intro.txt
@@ -15,8 +15,10 @@ These pages provide a brief introduction to LAMMPS.
<!-- RST
.. toctree::
+ :maxdepth: 1
Intro_overview
+ Manual_version
Intro_features
Intro_nonfeatures
Intro_opensource
diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt
index ce418d0ce1cfc4463581ceadc5057cb4556ecc65..06c86f6e3cd6539307cf7b6305c4d7ce6e678ccc 100644
--- a/doc/src/Intro_authors.txt
+++ b/doc/src/Intro_authors.txt
@@ -58,12 +58,12 @@ Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
Steve Lustig (Dupont)
Jim Belak and Roy Pollock (LLNL) :ul
-:line
:line
Here is a timeline for when various individuals contributed to a new
feature or command or tool added to LAMMPS:
+Aug18 : CMake build option for LAMMPS : Christoph Junghans (LANL), Richard Berger, and Axel Kohlmeyer (Temple U)
Jul18 : DEM polygonal and polyhedron particles : Trung Nguyen (Northwestern U)
Jun18 : SPIN package : Julien Tranchida (Sandia and CEA)
Jun18 : compute entropy/atom : Pablo Piaggi (EPLF, Switzerland)
@@ -239,7 +239,7 @@ Aug11 : angle_style cosine/shift and cosine/shift/exp : Carsten Svaneborg
Aug11 : dihedral_style cosine/shift/exp : Carsten Svaneborg
Aug11 : pair_style dipole/sf : Mario Orsi
Aug11 : fix addtorque and compute temp/rotate : Laurent Joly (U Lyon)
-Aug11 : FFT support via FFTW3, MKL, ACML, KISSFFT libraries : \
+Aug11 : FFT support via FFTW3, MKL, ACML, KISS FFT libraries : \
Axel Kohlmeyer (Temple U)
Jun11 : pair_style adp : Chris Weinberger (Sandia), Stephen Foiles (Sandia), \
Chandra Veer Singh (Cornell)
diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt
index 2bb7e25683be9bd90610193a3b265729b1eb9afa..07c549c1566a73c09d66b92b590c87d5654773d5 100644
--- a/doc/src/Intro_features.txt
+++ b/doc/src/Intro_features.txt
@@ -20,7 +20,7 @@ classes of functionality:
"Integrators"_#integrate
"Diagnostics"_#diag
"Output"_#output
-"Multi-replica models"_#replica
+"Multi-replica models"_#replica1
"Pre- and post-processing"_#prepost
"Specialized features (beyond MD itself)"_#special :ul
@@ -154,7 +154,7 @@ Output :h4,link(output)
time averaging of system-wide quantities
atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
-Multi-replica models :h4,link(replica)
+Multi-replica models :h4,link(replica1)
"nudged elastic band"_neb.html
"parallel replica dynamics"_prd.html
diff --git a/doc/src/Intro_nonfeatures.txt b/doc/src/Intro_nonfeatures.txt
index 41f001fc8b675de6c1e3624b1695dd3bfc5ca96c..2acf6db71f5ccfeea1db3609ba47b2673d00c86d 100644
--- a/doc/src/Intro_nonfeatures.txt
+++ b/doc/src/Intro_nonfeatures.txt
@@ -28,7 +28,7 @@ GUI: LAMMPS can be built as a library and a Python wrapper that wraps
the library interface is provided. Thus, GUI interfaces can be
written in Python (or C or C++ if desired) that run LAMMPS and
visualize or plot its output. Examples of this are provided in the
-python directory and described on the "Python"_Python.html doc
+python directory and described on the "Python"_Python_head.html doc
page. :ulb,l
Builder: Several pre-processing tools are packaged with LAMMPS. Some
@@ -55,9 +55,9 @@ info on how to add your own analysis code or algorithms to LAMMPS.
For post-processing, LAMMPS output such as "dump file
snapshots"_dump.html can be converted into formats used by other MD or
post-processing codes. Some post-processing tools packaged with
-LAMMPS will do these conversions. Scripts provided with the {python}
-tool in the tools directory can extract and massage data in dump files
-to make it easier to import into other programs. See the
+LAMMPS will do these conversions. Scripts provided in the
+tools/python directory can extract and massage data in dump files to
+make it easier to import into other programs. See the
"Tools"_Tools.html doc page for details on these various options. :l
Visualization: LAMMPS can produce JPG or PNG snapshot images
@@ -68,11 +68,11 @@ page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
visualization packages that can use LAMMPS output data. :l
Plotting: See the next bullet about Pizza.py as well as the
-"Python"_Python.html doc page for examples of plotting LAMMPS output.
-Scripts provided with the {python} tool in the tools directory will
-extract and massage data in log and dump files to make it easier to
-analyze and plot. See the "Tools"_Tools.html doc page for more
-discussion of the various tools. :l
+"Python"_Python_head.html doc page for examples of plotting LAMMPS
+output. Scripts provided with the {python} tool in the tools
+directory will extract and massage data in log and dump files to make
+it easier to analyze and plot. See the "Tools"_Tools.html doc page
+for more discussion of the various tools. :l
Pizza.py: Our group has also written a separate toolkit called
"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index a5e8b63640be29f7212d66e1d6b42ceb66747a41..c4dbf0415ee1a59672bf383d1f84c7cbd3558375 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -8,6 +8,8 @@
<BODY>
+<H1></H1>
+
<!-- END_HTML_ONLY -->
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
@@ -18,8 +20,6 @@
:line
-<H1></H1>
-
LAMMPS Documentation :c,h1
2 Aug 2018 version :c,h2
@@ -47,9 +47,9 @@ all LAMMPS development is coordinated.
"PDF file"_Manual.pdf of the entire manual, generated by
"htmldoc"_http://freecode.com/projects/htmldoc
-The content for this manual is part of the LAMMPS distribution.
-You can build a local copy of the Manual as HTML pages or a PDF file,
-by following the steps on the "this page"_Build_manual.html.
+The content for this manual is part of the LAMMPS distribution. You
+can build a local copy of the Manual as HTML pages or a PDF file, by
+following the steps on the "Manual build"_Manual_build.html doc page.
There is also a "Developer.pdf"_Developer.pdf document which gives
a brief description of the basic code structure of LAMMPS.
@@ -72,7 +72,9 @@ every LAMMPS command.
:includehidden:
Intro
- Section_start
+ Install
+ Build
+ Run
Commands
Packages
Speed
@@ -80,15 +82,16 @@ every LAMMPS command.
Examples
Tools
Modify
- Python
+ Python_head
Errors
+ Manual_build
.. toctree::
:caption: Index
:name: index
:hidden:
- commands
+ commands_list
fixes
computes
pairs
@@ -107,15 +110,9 @@ END_RST -->
<!-- HTML_ONLY -->
"Introduction"_Intro.html :olb,l
-"Getting started"_Section_start.html :l
- 2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
- 2.2 "Making LAMMPS"_start_2 :b
- 2.3 "Making LAMMPS with optional packages"_start_3 :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
+"Install LAMMPS"_Install.html :l
+"Build LAMMPS"_Build.html :l
+"Run LAMMPS"_Run.html :l
"Commands"_Commands.html :l
"Optional packages"_Packages.html :l
"Accelerate performance"_Speed.html :l
@@ -123,19 +120,11 @@ END_RST -->
"Example scripts"_Examples.html :l
"Auxiliary tools"_Tools.html :l
"Modify & extend LAMMPS"_Modify.html :l
-"Use Python with LAMMPS"_Python.html :l
+"Use Python with LAMMPS"_Python_head.html :l
"Errors"_Errors.html :l
+"Building the LAMMPS manual"_Manual_build.html :l
:ole
-:link(start_1,Section_start.html#start_1)
-:link(start_2,Section_start.html#start_2)
-:link(start_3,Section_start.html#start_3)
-:link(start_4,Section_start.html#start_4)
-:link(start_5,Section_start.html#start_5)
-:link(start_6,Section_start.html#start_6)
-:link(start_7,Section_start.html#start_7)
-:link(start_8,Section_start.html#start_8)
-
<!-- END_HTML_ONLY -->
</BODY>
diff --git a/doc/src/Manual_build.txt b/doc/src/Manual_build.txt
new file mode 100644
index 0000000000000000000000000000000000000000..747a55a7296d0ab206c0119ecb7a85dd5e8e7a36
--- /dev/null
+++ b/doc/src/Manual_build.txt
@@ -0,0 +1,124 @@
+"Previous Section"_Errors.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Manual.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Building the LAMMPS manual :h2
+
+Depending on how you obtained LAMMPS, the doc directory has
+2 or 3 sub-directories and optionally 2 PDF files and an ePUB file:
+
+src # content files for LAMMPS documentation
+html # HTML version of the LAMMPS manual (see html/Manual.html)
+tools # tools and settings for building the documentation
+Manual.pdf # large PDF version of entire manual
+Developer.pdf # small PDF with info about how LAMMPS is structured
+LAMMPS.epub # Manual in ePUB format :pre
+
+If you downloaded LAMMPS as a tarball from the web site, all these
+directories and files should be included.
+
+If you downloaded LAMMPS from the public SVN or Git repositories, then
+the HTML and PDF files are not included. Instead you need to create
+them, in one of three ways:
+
+(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
+site. Just type "make fetch". This should create a html_www dir and
+Manual_www.pdf/Developer_www.pdf files. Note that if new LAMMPS
+features have been added more recently than the date of your version,
+the fetched documentation will include those changes (but your source
+code will not, unless you update your local repository).
+
+(b) You can build the HTML and PDF files yourself, by typing "make
+html" followed by "make pdf". Note that the PDF make requires the
+HTML files already exist. This requires various tools including
+Sphinx, which the build process will attempt to download and install
+on your system, if not already available. See more details below.
+
+(c) You can genererate an older, simpler, less-fancy style of HTML
+documentation by typing "make old". This will create an "old"
+directory. This can be useful if (b) does not work on your box for
+some reason, or you want to quickly view the HTML version of a doc
+page you have created or edited yourself within the src directory.
+E.g. if you are planning to submit a new feature to LAMMPS.
+
+:line
+
+The generation of all documentation is managed by the Makefile in
+the doc dir.
+
+Documentation Build Options: :pre
+
+make html # generate HTML in html dir using Sphinx
+make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
+ # in doc dir via htmldoc and pdflatex
+make old # generate old-style HTML pages in old dir via txt2html
+make fetch # fetch HTML doc pages and 2 PDF files from web site
+ # as a tarball and unpack into html dir and 2 PDFs
+make epub # generate LAMMPS.epub in ePUB format using Sphinx
+make clean # remove intermediate RST files created by HTML build
+make clean-all # remove entire build folder and any cached data :pre
+
+:line
+
+Installing prerequisites for HTML build :h3
+
+To run the HTML documention build toolchain, Python 3 and virtualenv
+have to be installed. Here are instructions for common setups:
+
+Ubuntu :h4
+
+sudo apt-get install python-virtualenv :pre
+
+Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x) :h4
+
+sudo yum install python3-virtualenv :pre
+
+Fedora (since version 22) :h4
+
+sudo dnf install python3-virtualenv pre
+
+MacOS X :h4
+
+Python 3 :h5
+
+Download the latest Python 3 MacOS X package from
+"https://www.python.org"_https://www.python.org
+and install it. This will install both Python 3
+and pip3.
+
+virtualenv :h5
+
+Once Python 3 is installed, open a Terminal and type
+
+pip3 install virtualenv :pre
+
+This will install virtualenv from the Python Package Index.
+
+:line
+
+Installing prerequisites for PDF build
+
+[TBA]
+
+:line
+
+Installing prerequisites for epub build :h3
+
+ePUB :h4
+
+Same as for HTML. This uses the same tools and configuration
+files as the HTML tree.
+
+For converting the generated ePUB file to a mobi format file
+(for e-book readers like Kindle, that cannot read ePUB), you
+also need to have the 'ebook-convert' tool from the "calibre"
+software installed. "http://calibre-ebook.com/"_http://calibre-ebook.com/
+You first create the ePUB file with 'make epub' and then do:
+
+ebook-convert LAMMPS.epub LAMMPS.mobi :pre
diff --git a/doc/src/Manual_version.txt b/doc/src/Manual_version.txt
index 8583eabf865afc3b9b9aeaae76d3acb34028fc85..436e531246053144e26cff63e37920c7069fd7d6 100644
--- a/doc/src/Manual_version.txt
+++ b/doc/src/Manual_version.txt
@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
-What does a LAMMPS version mean: :h3
+What does a LAMMPS version mean :h3
The LAMMPS "version" is the date when it was released, such as 1 May
2014. LAMMPS is updated continuously. Whenever we fix a bug or add a
diff --git a/doc/src/Modify.txt b/doc/src/Modify.txt
index f828bd5d74db99ceb5c0dfffd93062d93228ef4c..666aaba8a77a4d69eccbe9fe8b381e5c1d494dc1 100644
--- a/doc/src/Modify.txt
+++ b/doc/src/Modify.txt
@@ -1,6 +1,6 @@
"Previous Section"_Tools.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Python.html :c
+Section"_Python_head.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@@ -24,11 +24,13 @@ contribute"_Modify_contribute.html doc page.
<!-- RST
.. toctree::
+ :maxdepth: 1
Modify_overview
Modify_contribute
.. toctree::
+ :maxdepth: 1
Modify_atom
Modify_pair
@@ -38,6 +40,7 @@ contribute"_Modify_contribute.html doc page.
Modify_command
.. toctree::
+ :maxdepth: 1
Modify_dump
Modify_kspace
@@ -46,6 +49,7 @@ contribute"_Modify_contribute.html doc page.
Modify_body
.. toctree::
+ :maxdepth: 1
Modify_thermo
Modify_variable
diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt
index ef9fe6a7174eed7d41a74908b49b21e8ecfa6f6d..8cbea8bb317f912a500857886b50a6f8a42e3c4d 100644
--- a/doc/src/Modify_contribute.txt
+++ b/doc/src/Modify_contribute.txt
@@ -44,13 +44,14 @@ compression, as this works well on all platforms.
If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a "standard
-package"_Section_start.html#start_3. Else we will add them as a
-user-contributed file or package. Examples of user packages are in
-src sub-directories that start with USER. The USER-MISC package is
-simply a collection of (mostly) unrelated single files, which is the
-simplest way to have your contribution quickly added to the LAMMPS
-distribution. You can see a list of the both standard and user
-packages by typing "make package" in the LAMMPS src directory.
+package"_Packages_standard.html. Else we will add them as a
+user-contributed file or "user package"_Packages_user.html. Examples
+of user packages are in src sub-directories that start with USER. The
+USER-MISC package is simply a collection of (mostly) unrelated single
+files, which is the simplest way to have your contribution quickly
+added to the LAMMPS distribution. All the standard and user packages
+are listed and described on the "Packages
+details"_Packages_details.html doc page.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
diff --git a/doc/src/Packages.txt b/doc/src/Packages.txt
index a7f45a99b7fa8f3d33e3c8d2e771f069139a0249..231c8528e90d57b7291297b40a7f8f0a19d0da75 100644
--- a/doc/src/Packages.txt
+++ b/doc/src/Packages.txt
@@ -13,16 +13,17 @@ Optional packages :h2
This section gives an overview of the optional packages that extend
LAMMPS functionality. Packages are groups of files that enable a
specific set of features. For example, force fields for molecular
-systems or rigid-body constraint are in packages. You can see the
+systems or rigid-body constraints 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.
+distribution. The "Build package"_Build_package.html doc page gives
+general info on how to install and un-install packages as part of the
+LAMMPS build process.
<!-- RST
.. toctree::
+ :maxdepth: 1
Packages_standard
Packages_user
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index eb92fe4dc4c27506cf41b250f7a3dce49e159941..5ab85a80c842c8a0a1672af8140e27e0be33d0e8 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -17,99 +17,97 @@ library it requires. It also gives links to documentation, example
scripts, and pictures/movies (if available) that illustrate use of the
package.
+The majority of packages can be included in a LAMMPS build with a
+single setting (-D PGK_NAME for CMake) or command ("make yes-name" for
+make). See the "Build package"_Build_package.html doc page for more
+info. A few packages may require additional steps; this is indicated
+in the descriptions below. The "Build extras"_Build_extras.html doc
+page gives those details.
+
NOTE: To see the complete list of commands a package adds to LAMMPS,
you can examine the files in its src directory, e.g. "ls
src/GRANULAR". Files with names that start with fix, compute, atom,
pair, bond, angle, etc correspond to commands with the same style name
as contained in the file name.
-"ASPHERE"_#ASPHERE,
-"BODY"_#BODY,
-"CLASS2"_#CLASS2,
-"COLLOID"_#COLLOID,
-"COMPRESS"_#COMPRESS,
-"CORESHELL"_#CORESHELL,
-"DIPOLE"_#DIPOLE,
-"GPU"_#GPU,
-"GRANULAR"_#GRANULAR,
-"KIM"_#KIM,
-"KOKKOS"_#KOKKOS,
-"KSPACE"_#KSPACE,
-"LATTE"_#LATTE,
-"MANYBODY"_#MANYBODY,
-"MC"_#MC,
-"MEAM"_#MEAM,
-"MISC"_#MISC,
-"MOLECULE"_#MOLECULE,
-"MPIIO"_#MPIIO,
-"MSCG"_#MSCG,
-"OPT"_#OPT,
-"PERI"_#PERI,
-"POEMS"_#POEMS,
-"PYTHON"_#PYTHON,
-"QEQ"_#QEQ,
-"REAX"_#REAX,
-"REPLICA"_#REPLICA,
-"RIGID"_#RIGID,
-"SHOCK"_#SHOCK,
-"SNAP"_#SNAP,
-"SPIN"_#SPIN,
-"SRD"_#SRD,
-"VORONOI"_#VORONOI :tb(c=6,ea=c)
-
-"USER-ATC"_#USER-ATC,
-"USER-AWPMD"_#USER-AWPMD,
-"USER-BOCS"_#USER-BOCS,
-"USER-CGDNA"_#USER-CGDNA,
-"USER-CGSDK"_#USER-CGSDK,
-"USER-COLVARS"_#USER-COLVARS,
-"USER-DIFFRACTION"_#USER-DIFFRACTION,
-"USER-DPD"_#USER-DPD,
-"USER-DRUDE"_#USER-DRUDE,
-"USER-EFF"_#USER-EFF,
-"USER-FEP"_#USER-FEP,
-"USER-H5MD"_#USER-H5MD,
-"USER-INTEL"_#USER-INTEL,
-"USER-LB"_#USER-LB,
-"USER-MANIFOLD"_#USER-MANIFOLD,
-"USER-MEAMC"_#USER-MEAMC,
-"USER-MESO"_#USER-MESO,
-"USER-MGPT"_#USER-MGPT,
-"USER-MISC"_#USER-MISC,
-"USER-MOFFF"_#USER-MOFFF,
-"USER-MOLFILE"_#USER-MOLFILE,
-"USER-NETCDF"_#USER-NETCDF,
-"USER-OMP"_#USER-OMP,
-"USER-PHONON"_#USER-PHONON,
-"USER-QMMM"_#USER-QMMM,
-"USER-QTB"_#USER-QTB,
-"USER-QUIP"_#USER-QUIP,
-"USER-REAXC"_#USER-REAXC,
-"USER-SMD"_#USER-SMD,
-"USER-SMTBQ"_#USER-SMTBQ,
-"USER-SPH"_#USER-SPH,
-"USER-TALLY"_#USER-TALLY,
-"USER-UEF"_#USER-UEF,
-"USER-VTK"_#USER-VTK :tb(c=6,ea=c)
-
-:line
-:line
-
-ASPHERE package :link(ASPHERE),h4
+"ASPHERE"_#PKG-ASPHERE,
+"BODY"_#PKG-BODY,
+"CLASS2"_#PKG-CLASS2,
+"COLLOID"_#PKG-COLLOID,
+"COMPRESS"_#PKG-COMPRESS,
+"CORESHELL"_#PKG-CORESHELL,
+"DIPOLE"_#PKG-DIPOLE,
+"GPU"_#PKG-GPU,
+"GRANULAR"_#PKG-GRANULAR,
+"KIM"_#PKG-KIM,
+"KOKKOS"_#PKG-KOKKOS,
+"KSPACE"_#PKG-KSPACE,
+"LATTE"_#PKG-LATTE,
+"MANYBODY"_#PKG-MANYBODY,
+"MC"_#PKG-MC,
+"MEAM"_#PKG-MEAM,
+"MISC"_#PKG-MISC,
+"MOLECULE"_#PKG-MOLECULE,
+"MPIIO"_#PKG-MPIIO,
+"MSCG"_#PKG-MSCG,
+"OPT"_#PKG-OPT,
+"PERI"_#PKG-PERI,
+"POEMS"_#PKG-POEMS,
+"PYTHON"_#PKG-PYTHON,
+"QEQ"_#PKG-QEQ,
+"REAX"_#PKG-REAX,
+"REPLICA"_#PKG-REPLICA2,
+"RIGID"_#PKG-RIGID,
+"SHOCK"_#PKG-SHOCK,
+"SNAP"_#PKG-SNAP,
+"SPIN"_#PKG-SPIN,
+"SRD"_#PKG-SRD,
+"VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
+
+"USER-ATC"_#PKG-USER-ATC,
+"USER-AWPMD"_#PKG-USER-AWPMD,
+"USER-BOCS"_#PKG-USER-BOCS,
+"USER-CGDNA"_#PKG-USER-CGDNA,
+"USER-CGSDK"_#PKG-USER-CGSDK,
+"USER-COLVARS"_#PKG-USER-COLVARS,
+"USER-DIFFRACTION"_#PKG-USER-DIFFRACTION,
+"USER-DPD"_#PKG-USER-DPD,
+"USER-DRUDE"_#PKG-USER-DRUDE,
+"USER-EFF"_#PKG-USER-EFF,
+"USER-FEP"_#PKG-USER-FEP,
+"USER-H5MD"_#PKG-USER-H5MD,
+"USER-INTEL"_#PKG-USER-INTEL,
+"USER-LB"_#PKG-USER-LB,
+"USER-MANIFOLD"_#PKG-USER-MANIFOLD,
+"USER-MEAMC"_#PKG-USER-MEAMC,
+"USER-MESO"_#PKG-USER-MESO,
+"USER-MGPT"_#PKG-USER-MGPT,
+"USER-MISC"_#PKG-USER-MISC,
+"USER-MOFFF"_#PKG-USER-MOFFF,
+"USER-MOLFILE"_#PKG-USER-MOLFILE,
+"USER-NETCDF"_#PKG-USER-NETCDF,
+"USER-OMP"_#PKG-USER-OMP,
+"USER-PHONON"_#PKG-USER-PHONON,
+"USER-QMMM"_#PKG-USER-QMMM,
+"USER-QTB"_#PKG-USER-QTB,
+"USER-QUIP"_#PKG-USER-QUIP,
+"USER-REAXC"_#PKG-USER-REAXC,
+"USER-SMD"_#PKG-USER-SMD,
+"USER-SMTBQ"_#PKG-USER-SMTBQ,
+"USER-SPH"_#PKG-USER-SPH,
+"USER-TALLY"_#PKG-USER-TALLY,
+"USER-UEF"_#PKG-USER-UEF,
+"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c)
+
+:line
+
+ASPHERE package :link(PKG-ASPHERE),h4
[Contents:]
Computes, time-integration fixes, and pair styles for aspherical
particle models including ellipsoids, 2d lines, and 3d triangles.
-[Install or un-install:]
-
-make yes-asphere
-make machine :pre
-
-make no-asphere
-make machine :pre
-
[Supporting info:]
src/ASPHERE: filenames -> commands
@@ -125,7 +123,7 @@ http://lammps.sandia.gov/movies.html#tri :ul
:line
-BODY package :link(BODY),h4
+BODY package :link(PKG-BODY),h4
[Contents:]
@@ -134,14 +132,6 @@ time-integration fixes, pair styles, as well as the body styles
themselves. See the "Howto body"_Howto_body.html doc page for an
overview.
-[Install or un-install:]
-
-make yes-body
-make machine :pre
-
-make no-body
-make machine :pre
-
[Supporting info:]
src/BODY filenames -> commands
@@ -153,21 +143,13 @@ examples/body :ul
:line
-CLASS2 package :link(CLASS2),h4
+CLASS2 package :link(PKG-CLASS2),h4
[Contents:]
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 no-class2
-make machine :pre
-
[Supporting info:]
src/CLASS2: filenames -> commands
@@ -179,7 +161,7 @@ src/CLASS2: filenames -> commands
:line
-COLLOID package :link(COLLOID),h4
+COLLOID package :link(PKG-COLLOID),h4
[Contents:]
@@ -192,14 +174,6 @@ simplified approximation to Stokesian dynamics.
which were created by Amit Kumar and Michael Bybee from Jonathan
Higdon's group at UIUC.
-[Install or un-install:]
-
-make yes-colloid
-make machine :pre
-
-make no-colloid
-make machine :pre
-
[Supporting info:]
src/COLLOID: filenames -> commands
@@ -214,7 +188,7 @@ examples/srd :ul
:line
-COMPRESS package :link(COMPRESS),h4
+COMPRESS package :link(PKG-COMPRESS),h4
[Contents:]
@@ -226,19 +200,11 @@ available on your system.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-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.
+[Install:]
-make yes-compress
-make machine :pre
-
-make no-compress
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -252,7 +218,7 @@ lib/compress/README
:line
-CORESHELL package :link(CORESHELL),h4
+CORESHELL package :link(PKG-CORESHELL),h4
[Contents:]
@@ -266,14 +232,6 @@ this package.
[Author:] Hendrik Heenen (Technical U of Munich).
-[Install or un-install:]
-
-make yes-coreshell
-make machine :pre
-
-make no-coreshell
-make machine :pre
-
[Supporting info:]
src/CORESHELL: filenames -> commands
@@ -287,21 +245,13 @@ examples/coreshell :ul
:line
-DIPOLE package :link(DIPOLE),h4
+DIPOLE package :link(PKG-DIPOLE),h4
[Contents:]
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 no-dipole
-make machine :pre
-
[Supporting info:]
src/DIPOLE: filenames -> commands
@@ -313,7 +263,7 @@ examples/dipole :ul
:line
-GPU package :link(GPU),h4
+GPU package :link(PKG-GPU),h4
[Contents:]
@@ -325,66 +275,17 @@ and only the CUDA versions are regularly tested. The "Speed
gpu"_Speed_gpu.html doc page gives details of what hardware and GPU
software is required on your system, and details on how to build and
use this package. Its styles can be invoked at run time via the "-sf
-gpu" or "-suffix gpu" "command-line
-switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS
-package, which has GPU-enabled styles.
+gpu" or "-suffix gpu" "command-line switches"_Run_options.html. See
+also the "KOKKOS"_#PKG-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. Please note, that the GPU library uses MPI calls, so
-you have to make certain to use the same MPI library (or the STUBS
-library) settings as the main LAMMPS code. That same applies to the
--DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define.
-
-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="-b" # build GPU library with default Makefile.linux
-make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
-make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre
+[Install:]
-Note that this procedure through the '-m machine' flag starts with one of
-the existing Makefile.machine files in lib/gpu. For your convenience,
-machine makefiles for "mpi" and "serial" are provided, which have the
-same settings as the corresponding machine makefiles in the main LAMMPS
-source folder. In addition you can alter 4 important settings in that
-Makefile, via the -h, -a, -p, -e switches, and also save a copy of the
-new Makefile, if desired:
-
-CUDA_HOME = where NVIDIA CUDA software is installed on your system
-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, at least 3 files should be created:
-lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, 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, and lib/gpu/Makefile.lammps may need to
-be edited.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-gpu
-make machine :pre
-
-make no-gpu
-make 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.
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -392,16 +293,16 @@ src/GPU: filenames -> commands
src/GPU/README
lib/gpu/README
"Speed packages"_Speed_packages.html
-"Speed gpu"_Speed_gpu.html.html
-"Section 2.6 -sf gpu"_Section_start.html#start_6
-"Section 2.6 -pk gpu"_Section_start.html#start_6
+"Speed gpu"_Speed_gpu.html
+"Section 2.6 -sf gpu"_Run_options.html
+"Section 2.6 -pk gpu"_Run_options.html
"package gpu"_package.html
"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-GRANULAR package :link(GRANULAR),h4
+GRANULAR package :link(PKG-GRANULAR),h4
[Contents:]
@@ -409,14 +310,6 @@ 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 no-granular
-make machine :pre
-
[Supporting info:]
src/GRANULAR: filenames -> commands
@@ -436,7 +329,7 @@ http://lammps.sandia.gov/movies.html#granregion :ul
:line
-KIM package :link(KIM),h4
+KIM package :link(PKG-KIM),h4
[Contents:]
@@ -456,48 +349,11 @@ 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:]
-
-Before building LAMMPS with this package, you must first download and
-build the KIM library and include the KIM models that you want to
-use. You can do this manually if you prefer; follow the instructions
-in lib/kim/README. You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/kim/Install.py script with the specified args.
-
-make lib-kim # print help message
-make lib-kim args="-b " # (re-)install KIM API lib with only example models
-make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
-make lib-kim args="-b -a everything" # install KIM API lib with all models
-make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
-make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
-make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
-
-Note that in LAMMPS lingo, a KIM model driver is a pair style
-(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
-element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file. Also note that installing the KIM API
-library with all its models, may take around 30 min to build. Of
-course you only need to do that once.
-
-See the list of KIM model drivers here:
-https://openkim.org/kim-items/model-drivers/alphabetical
-
-See the list of all KIM models here:
-https://openkim.org/kim-items/models/by-model-drivers
-
-See the list of example KIM models included by default here:
-https://openkim.org/kim-api on the "What is in the KIM API source
-package?" page.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-kim
-make machine :pre
-
-make no-kim
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -509,7 +365,7 @@ examples/kim :ul
:line
-KOKKOS package :link(KOKKOS),h4
+KOKKOS package :link(PKG-KOKKOS),h4
[Contents:]
@@ -521,9 +377,9 @@ style name. The "Speed kokkos"_Speed_kokkos.html doc page gives
details of what hardware and software is required on your system, and
how to build and use this package. Its styles can be invoked at run
time via the "-sf kk" or "-suffix kk" "command-line
-switches"_Section_start.html#start_6. Also see the "GPU"_#GPU,
-"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
-packages, which have styles optimized for CPUs, KNLs, and GPUs.
+switches"_Run_options.html. Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT,
+"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
+have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package.
@@ -534,53 +390,11 @@ which was developed by Carter Edwards, Christian Trott, and others at
Sandia, and which is included in the LAMMPS distribution in
lib/kokkos.
-[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 :pre
-
-For Intel KNLs using OpenMP:
-
-KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = KNL :pre
-
-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 :pre
+[Install:]
-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.
-
-KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
-export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
-CC = mpicxx :pre
-
-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
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -589,16 +403,16 @@ src/KOKKOS/README
lib/kokkos/README
"Speed packages"_Speed_packages.html
"Speed kokkos"_Speed_kokkos.html
-"Section 2.6 -k on ..."_Section_start.html#start_6
-"Section 2.6 -sf kk"_Section_start.html#start_6
-"Section 2.6 -pk kokkos"_Section_start.html#start_6
+"Section 2.6 -k on ..."_Run_options.html
+"Section 2.6 -sf kk"_Run_options.html
+"Section 2.6 -pk kokkos"_Run_options.html
"package kokkos"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-KSPACE package :link(KSPACE),h4
+KSPACE package :link(PKG-KSPACE),h4
[Contents:]
@@ -607,20 +421,14 @@ which compute the corresponding short-range pairwise Coulombic
interactions. These include Ewald, particle-particle particle-mesh
(PPPM), and multilevel summation method (MSM) solvers.
-[Install or un-install:]
+[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 no-kspace
-make machine :pre
+vendor-supplied FFT library. See the "Build
+settings"_Build_settings.html doc page for details on how to select
+different FFT options for your LAMPMS build.
[Supporting info:]
@@ -637,7 +445,7 @@ bench/in.rhodo :ul
:line
-LATTE package :link(LATTE),h4
+LATTE package :link(PKG-LATTE),h4
[Contents:]
@@ -655,36 +463,11 @@ description is given with the "fix latte"_fix_latte.html command.
itself is developed at Los Alamos National Laboratory by Marc
Cawkwell, Anders Niklasson, and Christian Negre.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the LATTE library. You can do this manually if you prefer;
-follow the instructions in lib/latte/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invokes the lib/latte/Install.py script with the specified
-args:
+[Install:]
-make lib-latte # print help message
-make lib-latte args="-b" # download and build in lib/latte/LATTE-master
-make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
-make lib-latte args="-b -m gfortran" # download and build in lib/latte and
- # copy Makefile.lammps.gfortran to Makefile.lammps
-:pre
-
-Note that 3 symbolic (soft) links, "includelink" and "liblink" and
-"filelink.o", are created in lib/latte to point into the LATTE home dir.
-When LAMMPS builds in src it will use these links. You should
-also check that the Makefile.lammps file you create is appropriate
-for the compiler you use on your system to build LATTE.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-latte
-make machine :pre
-
-make no-latte
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -697,21 +480,13 @@ examples/latte
:line
-MANYBODY package :link(MANYBODY),h4
+MANYBODY package :link(PKG-MANYBODY),h4
[Contents:]
A variety of manybody and bond-order potentials. These include
(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
-[Install or un-install:]
-
-make yes-manybody
-make machine :pre
-
-make no-manybody
-make machine :pre
-
[Supporting info:]
src/MANYBODY: filenames -> commands
@@ -726,7 +501,7 @@ bench/in.eam :ul
:line
-MC package :link(MC),h4
+MC package :link(PKG-MC),h4
[Contents:]
@@ -735,14 +510,6 @@ attributes. These include fixes for creating, breaking, and swapping
bonds, for performing atomic swaps, and performing grand-canonical MC
(GCMC) in conjuction with dynamics.
-[Install or un-install:]
-
-make yes-mc
-make machine :pre
-
-make no-mc
-make machine :pre
-
[Supporting info:]
src/MC: filenames -> commands
@@ -756,51 +523,26 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
:line
-MEAM package :link(MEAM),h4
+MEAM package :link(PKG-MEAM),h4
[Contents:]
A pair style for the modified embedded atom (MEAM) potential.
-Please note that the MEAM package has been superseded by the
-"USER-MEAMC"_#USER-MEAMC package, which is a direct translation
-of the MEAM package to C++. USER-MEAMC contains additional
-optimizations making it run faster than MEAM on most machines,
-while providing the identical features and USER interface.
+Please note that the use of the MEAM package is discouraged as
+it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
+which is a direct translation of the MEAM package to C++.
+USER-MEAMC contains additional optimizations making it run faster
+than MEAM on most machines, while providing the identical features
+and user interface.
[Author:] Greg Wagner (Northwestern U) while at Sandia.
-[Install or un-install:]
-
-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 mpi" # build with default Fortran compiler compatible with your MPI library
-make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
-make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre
+[Install:]
-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.
-
-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
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
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
@@ -816,7 +558,7 @@ examples/meam :ul
:line
-MISC package :link(MISC),h4
+MISC package :link(PKG-MISC),h4
[Contents:]
@@ -827,14 +569,6 @@ listing, "ls src/MISC", to see the list of commands.
NOTE: the MISC package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
-[Install or un-install:]
-
-make yes-misc
-make machine :pre
-
-make no-misc
-make machine :pre
-
[Supporting info:]
src/MISC: filenames -> commands
@@ -851,7 +585,7 @@ http://lammps.sandia.gov/movies.html#evaporation :ul
:line
-MOLECULE package :link(MOLECULE),h4
+MOLECULE package :link(PKG-MOLECULE),h4
[Contents:]
@@ -860,14 +594,6 @@ 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 no-molecule
-make machine :pre
-
[Supporting info:]
src/MOLECULE: filenames -> commands
@@ -888,7 +614,7 @@ bench/in.rhodo :ul
:line
-MPIIO package :link(MPIIO),h4
+MPIIO package :link(PKG-MPIIO),h4
[Contents:]
@@ -897,18 +623,6 @@ 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.
-[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:]
src/MPIIO: filenames -> commands
@@ -919,7 +633,7 @@ src/MPIIO: filenames -> commands
:line
-MSCG package :link(mscg),h4
+MSCG package :link(PKG-mscg),h4
[Contents:]
@@ -936,39 +650,11 @@ system.
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 the GSL
-(GNU Scientific Library) headers and libraries are 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="-b -m serial" # download and build in lib/mscg/MSCG-release-master
- # with the settings compatible with "make serial"
-make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
- # with the settings compatible with "make mpi"
-make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre
+[Install:]
-Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg
-to point to the MS-CG src/installation dir. When LAMMPS is built in src 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
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -979,7 +665,7 @@ examples/mscg :ul
:line
-OPT package :link(OPT),h4
+OPT package :link(PKG-OPT),h4
[Contents:]
@@ -989,40 +675,31 @@ CHARMM, and Morse potentials. The styles have an "opt" suffix in
their style name. The "Speed opt"_Speed_opt.html doc page gives
details of how to build and use this package. Its styles can be
invoked at run time via the "-sf opt" or "-suffix opt" "command-line
-switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS,
-"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
+switches"_Run_options.html. See also the "KOKKOS"_#PKG-KOKKOS,
+"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
have styles optimized for CPU performance.
[Authors:] James Fischer (High Performance Technologies), David Richie,
and Vincent Natoli (Stone Ridge Technolgy).
-[Install or un-install:]
-
-make yes-opt
-make machine :pre
+[Install:]
-make no-opt
-make machine :pre
-
-NOTE: The compile flag "-restrict" must be used to build LAMMPS with
-the OPT package when using Intel compilers. 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 for Intel compilers :ul
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
src/OPT: filenames -> commands
"Speed packages"_Speed_packages.html
"Speed opt"_Speed_opt.html
-"Section 2.6 -sf opt"_Section_start.html#start_6
+"Section 2.6 -sf opt"_Run_options.html
"Commands pair"_Commands_pair.html for styles followed by (t)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-PERI package :link(PERI),h4
+PERI package :link(PKG-PERI),h4
[Contents:]
@@ -1035,14 +712,6 @@ model.
Additional Peridynamics models were added by Rezwanur Rahman and John
Foster (UTSA).
-[Install or un-install:]
-
-make yes-peri
-make machine :pre
-
-make no-peri
-make machine :pre
-
[Supporting info:]
src/PERI: filenames -> commands
@@ -1058,7 +727,7 @@ http://lammps.sandia.gov/movies.html#peri :ul
:line
-POEMS package :link(POEMS),h4
+POEMS package :link(PKG-POEMS),h4
[Contents:]
@@ -1070,35 +739,11 @@ connections at hinge points.
[Author:] Rudra Mukherjee (JPL) while at RPI.
-[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 serial" # build with GNU g++ compiler (settings as with "make serial")
-make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
-make lib-poems args="-m icc" # build with Intel icc compiler :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.
+[Install:]
-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
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1110,7 +755,7 @@ examples/rigid :ul
:line
-PYTHON package :link(PYTHON),h4
+PYTHON package :link(PKG-PYTHON),h4
[Contents:]
@@ -1118,35 +763,30 @@ A "python"_python.html command which allow you to execute Python code
from a LAMMPS input script. The code can be in a separate file or
embedded in the input script itself. See the "Python
call"_Python_call.html doc page for an overview of using Python from
-LAMMPS in this manner and all the "Python"_Python.html doc pages for
-other ways to use LAMMPS and Python together.
-
-[Install or un-install:]
-
-make yes-python
-make machine :pre
-
-make no-python
-make machine :pre
+LAMMPS in this manner and all the "Python"_Python_head.html doc pages
+for other ways to use LAMMPS and Python together.
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.
+lib/python/README for more details.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
src/PYTHON: filenames -> commands
-"Python call"_Python.html
+"Python call"_Python_head.html
lib/python/README
examples/python :ul
:line
-QEQ package :link(QEQ),h4
+QEQ package :link(PKG-QEQ),h4
[Contents:]
@@ -1154,14 +794,6 @@ 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.
-[Install or un-install:]
-
-make yes-qeq
-make machine :pre
-
-make no-qeq
-make machine :pre
-
[Supporting info:]
src/QEQ: filenames -> commands
@@ -1171,49 +803,27 @@ examples/streitz :ul
:line
-REAX package :link(REAX),h4
+REAX package :link(PKG-REAX),h4
[Contents:]
+NOTE: the use of the REAX package is discouraged, as it is no longer
+maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
+and possibly the KOKKOS enabled variant of that, which has a more robust
+memory management.
+
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.
+potential, which is a universal reactive force field. Also included is
+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 lib-reax # print help message
-make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
-
-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
+[Install:]
-make no-reax
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1225,7 +835,7 @@ examples/reax :ul
:line
-REPLICA package :link(REPLICA),h4
+REPLICA package :link(PKG-REPLICA2),h4
[Contents:]
@@ -1239,14 +849,6 @@ verlet/split algorithm for performing long-range Coulombics on one set
of processors, and the remainder of the force field calcalation on
another set.
-[Install or un-install:]
-
-make yes-replica
-make machine :pre
-
-make no-replica
-make machine :pre
-
[Supporting info:]
src/REPLICA: filenames -> commands
@@ -1262,7 +864,7 @@ examples/tad :ul
:line
-RIGID package :link(RIGID),h4
+RIGID package :link(PKG-RIGID),h4
[Contents:]
@@ -1271,16 +873,6 @@ 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
-
-To un-install/re-build:
-
-make no-rigid
-make machine :pre
-
[Supporting info:]
src/RIGID: filenames -> commands
@@ -1296,21 +888,13 @@ http://lammps.sandia.gov/movies.html#star :ul
:line
-SHOCK package :link(SHOCK),h4
+SHOCK package :link(PKG-SHOCK),h4
[Contents:]
Fixes for running impact simulations where a shock-wave passes through
a material.
-[Install or un-install:]
-
-make yes-shock
-make machine :pre
-
-make no-shock
-make machine :pre
-
[Supporting info:]
src/SHOCK: filenames -> commands
@@ -1323,7 +907,7 @@ examples/msst :ul
:line
-SNAP package :link(SNAP),h4
+SNAP package :link(PKG-SNAP),h4
[Contents:]
@@ -1334,14 +918,6 @@ computes which analyze attributes of the potential.
[Author:] Aidan Thompson (Sandia).
-[Install or un-install:]
-
-make yes-snap
-make machine :pre
-
-make no-snap
-make machine :pre
-
[Supporting info:]
src/SNAP: filenames -> commands
@@ -1353,7 +929,7 @@ examples/snap :ul
:line
-SPIN package :link(SPIN),h4
+SPIN package :link(PKG-SPIN),h4
[Contents:]
@@ -1362,18 +938,10 @@ the usual manner via MD. Various pair, fix, and compute styles.
[Author:] Julian Tranchida (Sandia).
-[Install or un-install:]
-
-make yes-spin
-make machine :pre
-
-make no-spin
-make machine :pre
-
[Supporting info:]
src/SPIN: filenames -> commands
-"Howto spin"_Howto_spin.html
+"Howto spins"_Howto_spins.html
"pair_style spin/dmi"_pair_spin_dmi.html
"pair_style spin/exchange"_pair_spin_exchange.html
"pair_style spin/magelec"_pair_spin_magelec.html
@@ -1385,7 +953,7 @@ examples/SPIN :ul
:line
-SRD package :link(SRD),h4
+SRD package :link(PKG-SRD),h4
[Contents:]
@@ -1393,16 +961,6 @@ 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/build:
-
-make yes-srd
-make machine :pre
-
-To un-install/re-build:
-
-make no-srd
-make machine :pre
-
[Supporting info:]
src/SRD: filenames -> commands
@@ -1416,7 +974,7 @@ http://lammps.sandia.gov/movies.html#poly :ul
:line
-VORONOI package :link(VORONOI),h4
+VORONOI package :link(PKG-VORONOI),h4
[Contents:]
@@ -1434,33 +992,11 @@ system.
library was written by Chris Rycroft (Harvard U) while at UC Berkeley
and LBNL.
-[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="-b" # download and build the default version in lib/voronoi/voro++-<version>
-make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
-make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre
-
-Note that 2 symbolic (soft) links, "includelink" and "liblink", are
-created in lib/voronoi to point to the Voro++ src dir. When LAMMPS
-builds in src it will use these links. You should not need to edit
-the lib/voronoi/Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-voronoi
-make machine :pre
-
-make no-voronoi
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1470,10 +1006,9 @@ lib/voronoi/README
"compute voronoi/atom"_compute_voronoi_atom.html
examples/voronoi :ul
-:line
:line
-USER-ATC package :link(USER-ATC),h4
+USER-ATC package :link(PKG-USER-ATC),h4
[Contents:]
@@ -1484,46 +1019,11 @@ atomic information to continuum fields.
[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
-[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:
-
-make lib-atc # print help message
-make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-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.
-
-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:
-
-make lib-linalg # print help message
-make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-user-atc
-make machine :pre
-
-make no-user-atc
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1535,7 +1035,7 @@ http://lammps.sandia.gov/pictures.html#atc :ul
:line
-USER-AWPMD package :link(USER-AWPMD),h4
+USER-AWPMD package :link(PKG-USER-AWPMD),h4
[Contents:]
@@ -1546,46 +1046,11 @@ model.
[Author:] Ilya Valuev (JIHT, Russia).
-[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 lib-awpmd # print help message
-make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-make lib-awpmd args="-m icc" # build with Intel icc compiler :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.
-
-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 lib-linalg # print help message
-make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-awpmd
-make machine :pre
+[Install:]
-make no-user-awpmd
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1596,7 +1061,7 @@ examples/USER/awpmd :ul
:line
-USER-BOCS package :link(USER-BOCS),h4
+USER-BOCS package :link(PKG-USER-BOCS),h4
[Contents:]
@@ -1608,15 +1073,8 @@ N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
accurately describe the structure, pressure, and compressibility of
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
-[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
-
-[Install or un-install:]
-
-make yes-user-bocs
-make machine :pre
-
-make no-user-bocs
-make machine :pre
+[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The
+Pennsylvania State University)
[Supporting info:]
@@ -1633,7 +1091,7 @@ Example inputs are in the examples/USER/bocs folder.
:line
-USER-CGDNA package :link(USER-CGDNA),h4
+USER-CGDNA package :link(PKG-USER-CGDNA),h4
[Contents:]
@@ -1645,14 +1103,6 @@ stability.
[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
-[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
@@ -1665,7 +1115,7 @@ src/USER-CGDNA: filenames -> commands
:line
-USER-CGSDK package :link(USER-CGSDK),h4
+USER-CGSDK package :link(PKG-USER-CGSDK),h4
[Contents:]
@@ -1676,14 +1126,6 @@ acids.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-make yes-user-cgsdk
-make machine :pre
-
-make no-user-cgsdk
-make machine :pre
-
[Supporting info:]
src/USER-CGSDK: filenames -> commands
@@ -1695,7 +1137,7 @@ http://lammps.sandia.gov/pictures.html#cg :ul
:line
-USER-COLVARS package :link(USER-COLVARS),h4
+USER-COLVARS package :link(PKG-USER-COLVARS),h4
[Contents:]
@@ -1712,36 +1154,11 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for
the NAMD MD code, but with portability in mind. Axel Kohlmeyer
(Temple U) provided the interface to LAMMPS.
-[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 serial" # build with GNU g++ compiler (settings as with "make serial")
-make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :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.
+[Install:]
-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
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1754,7 +1171,7 @@ examples/USER/colvars :ul
:line
-USER-DIFFRACTION package :link(USER-DIFFRACTION),h4
+USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4
[Contents:]
@@ -1763,14 +1180,6 @@ intensities based on kinematic diffraction theory.
[Author:] Shawn Coleman while at the U Arkansas.
-[Install or un-install:]
-
-make yes-user-diffraction
-make machine :pre
-
-make no-user-diffraction
-make machine :pre
-
[Supporting info:]
src/USER-DIFFRACTION: filenames -> commands
@@ -1781,7 +1190,7 @@ examples/USER/diffraction :ul
:line
-USER-DPD package :link(USER-DPD),h4
+USER-DPD package :link(PKG-USER-DPD),h4
[Contents:]
@@ -1798,14 +1207,6 @@ algorithm.
[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John
Brennan (ARL).
-[Install or un-install:]
-
-make yes-user-dpd
-make machine :pre
-
-make no-user-dpd
-make machine :pre
-
[Supporting info:]
src/USER-DPD: filenames -> commands
@@ -1827,7 +1228,7 @@ examples/USER/dpd :ul
:line
-USER-DRUDE package :link(USER-DRUDE),h4
+USER-DRUDE package :link(PKG-USER-DRUDE),h4
[Contents:]
@@ -1840,14 +1241,6 @@ for using this package in tools/drude.
[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
-[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
@@ -1865,7 +1258,7 @@ tools/drude :ul
:line
-USER-EFF package :link(USER-EFF),h4
+USER-EFF package :link(PKG-USER-EFF),h4
[Contents:]
@@ -1879,14 +1272,6 @@ tools/eff; see its README file.
[Author:] Andres Jaramillo-Botero (CalTech).
-[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
@@ -1906,7 +1291,7 @@ http://lammps.sandia.gov/movies.html#eff :ul
:line
-USER-FEP package :link(USER-FEP),h4
+USER-FEP package :link(PKG-USER-FEP),h4
[Contents:]
@@ -1918,14 +1303,6 @@ for using this package in tools/fep; see its README file.
[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
-[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
@@ -1939,7 +1316,7 @@ tools/fep :ul
:line
-USER-H5MD package :link(USER-H5MD),h4
+USER-H5MD package :link(PKG-USER-H5MD),h4
[Contents:]
@@ -1957,37 +1334,11 @@ system.
[Author:] Pierre de Buyl (KU Leuven) created both the package and the
H5MD format.
-[Install or un-install:]
-
-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.
-
-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:
-
-make lib-h5md # print help message
-make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre
+[Install:]
-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.
-
-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
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1998,7 +1349,7 @@ lib/h5md/README
:line
-USER-INTEL package :link(USER-INTEL),h4
+USER-INTEL package :link(PKG-USER-INTEL),h4
[Contents:]
@@ -2008,9 +1359,9 @@ All of them have an "intel" in their style name. The "Speed
intel"_Speed_intel.html doc page gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf intel" or
-"-suffix intel" "command-line switches"_Section_start.html#start_6.
-Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
-packages, which have styles optimized for CPUs and KNLs.
+"-suffix intel" "command-line switches"_Run_options.html. Also see
+the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-OMP"_#PKG-USER-OMP packages,
+which have styles optimized for CPUs and KNLs.
You need to have an Intel compiler, version 14 or higher to take full
advantage of this package. While compilation with GNU compilers is
@@ -2019,49 +1370,13 @@ supported, performance will be suboptimal.
NOTE: the USER-INTEL package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
-
[Author:] Mike Brown (Intel).
-[Install or un-install:]
-
-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 :pre
-
-For KNLs:
+[Install:]
-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 :pre
-
-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 on the "Speed intel"_Speed_intel.html doc page.
-
-make yes-user-intel yes-user-omp
-make machine :pre
-
-make no-user-intel no-user-omp
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2069,8 +1384,8 @@ src/USER-INTEL: filenames -> commands
src/USER-INTEL/README
"Speed packages"_Speed_packages.html
"Speed intel"_Speed_intel.html
-"Section 2.6 -sf intel"_Section_start.html#start_6
-"Section 2.6 -pk intel"_Section_start.html#start_6
+"Section 2.6 -sf intel"_Run_options.html
+"Section 2.6 -pk intel"_Run_options.html
"package intel"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
src/USER-INTEL/TEST
@@ -2078,7 +1393,7 @@ src/USER-INTEL/TEST
:line
-USER-LB package :link(USER-LB),h4
+USER-LB package :link(PKG-USER-LB),h4
[Contents:]
@@ -2088,14 +1403,6 @@ can be used to model MD particles influenced by hydrodynamic forces.
[Authors:] Frances Mackay and Colin Denniston (University of Western
Ontario).
-[Install or un-install:]
-
-make yes-user-lb
-make machine :pre
-
-make no-user-lb
-make machine :pre
-
[Supporting info:]
src/USER-LB: filenames -> commands
@@ -2107,7 +1414,7 @@ examples/USER/lb :ul
:line
-USER-MGPT package :link(USER-MGPT),h4
+USER-MGPT package :link(PKG-USER-MGPT),h4
[Contents:]
@@ -2122,14 +1429,6 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
-[Install or un-install:]
-
-make yes-user-mgpt
-make machine :pre
-
-make no-user-mgpt
-make machine :pre
-
[Supporting info:]
src/USER-MGPT: filenames -> commands
@@ -2139,7 +1438,7 @@ examples/USER/mgpt :ul
:line
-USER-MISC package :link(USER-MISC),h4
+USER-MISC package :link(PKG-USER-MISC),h4
[Contents:]
@@ -2150,14 +1449,6 @@ dihedral, improper, or command style.
[Authors:] The author for each style in the package is listed in the
src/USER-MISC/README file.
-[Install or un-install:]
-
-make yes-user-misc
-make machine :pre
-
-make no-user-misc
-make machine :pre
-
[Supporting info:]
src/USER-MISC: filenames -> commands
@@ -2167,7 +1458,7 @@ examples/USER/misc :ul
:line
-USER-MANIFOLD package :link(USER-MANIFOLD),h4
+USER-MANIFOLD package :link(PKG-USER-MANIFOLD),h4
[Contents:]
@@ -2178,16 +1469,9 @@ 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).
-[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The
-Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
-
-[Install or un-install:]
-
-make yes-user-manifold
-make machine :pre
-
-make no-user-manifold
-make machine :pre
+[Author:] Stefan Paquay (until 2017: Eindhoven University of
+Technology (TU/e), The Netherlands; since 2017: Brandeis University,
+Waltham, MA, USA)
[Supporting info:]
@@ -2202,7 +1486,7 @@ http://lammps.sandia.gov/movies.html#manifold :ul
:line
-USER-MEAMC package :link(USER-MEAMC),h4
+USER-MEAMC package :link(PKG-USER-MEAMC),h4
[Contents:]
@@ -2216,14 +1500,6 @@ multiple times.
based on the Fortran version of Greg Wagner (Northwestern U) while at
Sandia.
-[Install or un-install:]
-
-make yes-user-meamc
-make machine :pre
-
-make no-user-meamc
-make machine :pre
-
[Supporting info:]
src/USER-MEAMC: filenames -> commands
@@ -2233,7 +1509,7 @@ examples/meam :ul
:line
-USER-MESO package :link(USER-MESO),h4
+USER-MESO package :link(PKG-USER-MESO),h4
[Contents:]
@@ -2247,14 +1523,6 @@ algorithm.
[Author:] Zhen Li (Division of Applied Mathematics, Brown University)
-[Install or un-install:]
-
-make yes-user-meso
-make machine :pre
-
-make no-user-meso
-make machine :pre
-
[Supporting info:]
src/USER-MESO: filenames -> commands
@@ -2269,7 +1537,7 @@ http://lammps.sandia.gov/movies.html#mesodpd :ul
:line
-USER-MOFFF package :link(USER-MOFFF),h4
+USER-MOFFF package :link(PKG-USER-MOFFF),h4
[Contents:]
@@ -2287,14 +1555,6 @@ well as the "MOF+"_MOFplus website.
[Author:] Hendrik Heenen (Technical U of Munich),
Rochus Schmid (Ruhr-University Bochum).
-[Install or un-install:]
-
-make yes-user-mofff
-make machine :pre
-
-make no-user-mofff
-make machine :pre
-
[Supporting info:]
src/USER-MOFFF: filenames -> commands
@@ -2307,7 +1567,7 @@ examples/USER/mofff :ul
:line
-USER-MOLFILE package :link(USER-MOLFILE),h4
+USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
[Contents:]
@@ -2335,20 +1595,11 @@ at
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
+[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
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2359,7 +1610,7 @@ lib/molfile/README
:line
-USER-NETCDF package :link(USER-NETCDF),h4
+USER-NETCDF package :link(PKG-USER-NETCDF),h4
[Contents:]
@@ -2383,20 +1634,11 @@ tools:
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
-[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.
-
-make yes-user-netcdf
-make machine :pre
+[Install:]
-make no-user-netcdf
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2407,7 +1649,7 @@ lib/netcdf/README
:line
-USER-OMP package :link(USER-OMP),h4
+USER-OMP package :link(PKG-USER-OMP),h4
[Contents:]
@@ -2417,10 +1659,9 @@ via OpenMP directives. All of them have an "omp" in their style name.
The "Speed omp"_Speed_omp.html doc page gives details of what hardware
and compilers are required on your system, and how to build and use
this package. Its styles can be invoked at run time via the "-sf omp"
-or "-suffix omp" "command-line switches"_Section_start.html#start_6.
-Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
-"USER-INTEL"_#USER-INTEL packages, which have styles optimized for
-CPUs.
+or "-suffix omp" "command-line switches"_Run_options.html. Also see
+the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-INTEL"_#PKG-USER-INTEL
+packages, which have styles optimized for CPUs.
[Author:] Axel Kohlmeyer (Temple U).
@@ -2437,16 +1678,11 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
Once you have an appropriate Makefile.machine, you can
install/un-install the package and build LAMMPS in the usual manner:
-[Install or un-install:]
+[Install:]
-make yes-user-omp
-make machine :pre
-
-make no-user-omp
-make machine :pre
-
-CCFLAGS: add -fopenmp (and -restrict when using Intel compilers)
-LINKFLAGS: add -fopenmp :ul
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2454,15 +1690,15 @@ src/USER-OMP: filenames -> commands
src/USER-OMP/README
"Speed packages"_Speed_packages.html
"Speed omp"_Speed_omp.html
-"Section 2.6 -sf omp"_Section_start.html#start_6
-"Section 2.6 -pk omp"_Section_start.html#start_6
+"Section 2.6 -sf omp"_Run_options.html
+"Section 2.6 -pk omp"_Run_options.html
"package omp"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-USER-PHONON package :link(USER-PHONON),h4
+USER-PHONON package :link(PKG-USER-PHONON),h4
[Contents:]
@@ -2472,14 +1708,6 @@ relations, directly from molecular dynamics simulations.
[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
-[Install or un-install:]
-
-make yes-user-phonon
-make machine :pre
-
-make no-user-phonon
-make machine :pre
-
[Supporting info:]
src/USER-PHONON: filenames -> commands
@@ -2489,7 +1717,7 @@ examples/USER/phonon :ul
:line
-USER-QMMM package :link(USER-QMMM),h4
+USER-QMMM package :link(PKG-USER-QMMM),h4
[Contents:]
@@ -2510,42 +1738,11 @@ without changes to LAMMPS itself.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-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/qmmm/README. You can
-also do it in one step from the lammps/src dir, using a command like
-these, which simply invoke the lib/qmmm/Install.py script with the
-specified args:
-
-make lib-qmmm # print help message
-make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
-make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
-make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre
-
-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.
+[Install:]
-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 Quantum ESPRESSO
-together. These are steps 3 and 4 described in the lib/qmmm/README
-file.
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2558,7 +1755,7 @@ lib/qmmm/example-mc/README :ul
:line
-USER-QTB package :link(USER-QTB),h4
+USER-QTB package :link(PKG-USER-QTB),h4
[Contents:]
@@ -2573,14 +1770,6 @@ simulation.
[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:]
src/USER-QTB: filenames -> commands
@@ -2591,7 +1780,7 @@ examples/USER/qtb :ul
:line
-USER-QUIP package :link(USER-QUIP),h4
+USER-QUIP package :link(PKG-USER-QUIP),h4
[Contents:]
@@ -2607,26 +1796,11 @@ on your system.
[Author:] Albert Bartok (Cambridge University)
-[Install or un-install:]
-
-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.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-user-quip
-make machine :pre
-
-make no-user-quip
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2637,26 +1811,18 @@ examples/USER/quip :ul
:line
-USER-REAXC package :link(USER-REAXC),h4
+USER-REAXC package :link(PKG-USER-REAXC),h4
[Contents:]
A pair style which implements the ReaxFF potential in C/C++ (in
-contrast to the "REAX package"_#REAX and its Fortran library). ReaxFF
+contrast to the "REAX package"_#PKG-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.
[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
-[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
@@ -2668,14 +1834,14 @@ examples/reax :ul
:line
-USER-SMD package :link(USER-SMD),h4
+USER-SMD package :link(PKG-USER-SMD),h4
[Contents:]
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).
+"USER-SPH package"_#PKG-USER-SPH).
This package solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control. It can specify
@@ -2689,31 +1855,11 @@ specified as surface geometries from *.STL files.
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
-[Install or un-install:]
-
-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:
-
-make lib-smd # print help message
-make lib-smd args="-b" # download and build in default lib/smd/eigen-eigen-...
-make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre
-
-Note that a symbolic (soft) link named "includelink" is created 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.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-user-smd
-make machine :pre
-
-make no-user-smd
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2725,7 +1871,7 @@ http://lammps.sandia.gov/movies.html#smd :ul
:line
-USER-SMTBQ package :link(USER-SMTBQ),h4
+USER-SMTBQ package :link(PKG-USER-SMTBQ),h4
[Contents:]
@@ -2736,14 +1882,6 @@ ionocovalent bonds in oxides.
[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert
Tetot (LAAS-CNRS, France).
-[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
@@ -2753,13 +1891,13 @@ examples/USER/smtbq :ul
:line
-USER-SPH package :link(USER-SPH),h4
+USER-SPH package :link(PKG-USER-SPH),h4
[Contents:]
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
+related "USER-SMD package"_#PKG-USER-SMD package for smooth Mach dynamics
(SMD) for solids.
This package contains ideal gas, Lennard-Jones equation of states,
@@ -2775,14 +1913,6 @@ property/atom"_compute_property_atom.html command.
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
-[Install or un-install:]
-
-make yes-user-sph
-make machine :pre
-
-make no-user-sph
-make machine :pre
-
[Supporting info:]
src/USER-SPH: filenames -> commands
@@ -2793,7 +1923,7 @@ http://lammps.sandia.gov/movies.html#sph :ul
:line
-USER-TALLY package :link(USER-TALLY),h4
+USER-TALLY package :link(PKG-USER-TALLY),h4
[Contents:]
@@ -2803,14 +1933,6 @@ stress, etc) about individual interactions.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-make yes-user-tally
-make machine :pre
-
-make no-user-tally
-make machine :pre
-
[Supporting info:]
src/USER-TALLY: filenames -> commands
@@ -2820,7 +1942,7 @@ examples/USER/tally :ul
:line
-USER-UEF package :link(USER-UEF),h4
+USER-UEF package :link(PKG-USER-UEF),h4
[Contents:]
@@ -2830,14 +1952,6 @@ supporting compute styles and an output option.
[Author:] David Nicholson (MIT).
-[Install or un-install:]
-
-make yes-user-uef
-make machine :pre
-
-make no-user-uef
-make machine :pre
-
[Supporting info:]
src/USER-UEF: filenames -> commands
@@ -2851,7 +1965,7 @@ examples/uef :ul
:line
-USER-VTK package :link(USER-VTK),h4
+USER-VTK package :link(PKG-USER-VTK),h4
[Contents:]
@@ -2867,23 +1981,11 @@ system.
[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
-[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
+[Install:]
-make no-user-vtk
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt
index 7e6434560244abfce710c182af2c4fb6cad31da6..a79caae141c68a4a0f5bcd6383658e20c3a307a9 100644
--- a/doc/src/Packages_standard.txt
+++ b/doc/src/Packages_standard.txt
@@ -31,35 +31,36 @@ int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
Package, Description, Doc page, Example, Library
-"ASPHERE"_Packages_details.html#ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, -
-"BODY"_Packages_details.html#BODY, body-style particles, "Howto body"_Howto_body.html, body, -
-"CLASS2"_Packages_details.html#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
-"COLLOID"_Packages_details.html#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
-"COMPRESS"_Packages_details.html#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
-"CORESHELL"_Packages_details.html#CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, -
-"DIPOLE"_Packages_details.html#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
-"GPU"_Packages_details.html#GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
-"GRANULAR"_Packages_details.html#GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, -
-"KIM"_Packages_details.html#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
-"KOKKOS"_Packages_details.html#KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"KSPACE"_Packages_details.html#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
-"LATTE"_Packages_details.html#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
-"MANYBODY"_Packages_details.html#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
-"MC"_Packages_details.html#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
-"MEAM"_Packages_details.html#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
-"MISC"_Packages_details.html#MISC, miscellanous single-file commands, -, -, -
-"MOLECULE"_Packages_details.html#MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, -
-"MPIIO"_Packages_details.html#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
-"MSCG"_Packages_details.html#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
-"OPT"_Packages_details.html#OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"PERI"_Packages_details.html#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
-"POEMS"_Packages_details.html#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
-"PYTHON"_Packages_details.html#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
-"QEQ"_Packages_details.html#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
-"REAX"_Packages_details.html#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
-"REPLICA"_Packages_details.html#REPLICA, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
-"RIGID"_Packages_details.html#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
-"SHOCK"_Packages_details.html#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
-"SNAP"_Packages_details.html#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
-"SPIN"_#SPIN, magnetic atomic spin dynamics, "Howto spin"_Howto_spin.html, SPIN, -"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
-"VORONOI"_Packages_details.html#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
+"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, -
+"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, -
+"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
+"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
+"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
+"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, -
+"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
+"GPU"_Packages_details.html#PKG-GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
+"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, -
+"KIM"_Packages_details.html#PKG-KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
+"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
+"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
+"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
+"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
+"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
+"MISC"_Packages_details.html#PKG-MISC, miscellanous single-file commands, -, -, -
+"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, -
+"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
+"MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
+"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
+"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
+"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
+"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
+"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
+"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
+"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
+"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
+"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
+"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, -
+"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
+"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index c8728148f9c1a83f0c900524e3b49bc586101aa6..7157ebead0ffaef0ec03508272f4a58b698719da 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -38,37 +38,37 @@ int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
Package, Description, Doc page, Example, Library
-"USER-ATC"_Packages_details.html#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
-"USER-AWPMD"_Packages_details.html#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
-"USER-BOCS"_Packages_details.html#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
-"USER-CGDNA"_Packages_details.html#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
-"USER-CGSDK"_Packages_details.html#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
-"USER-COLVARS"_Packages_details.html#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
-"USER-DIFFRACTION"_Packages_details.html#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
-"USER-DPD"_Packages_details.html#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
-"USER-DRUDE"_Packages_details.html#USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, -
-"USER-EFF"_Packages_details.html#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
-"USER-FEP"_Packages_details.html#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
-"USER-H5MD"_Packages_details.html#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
-"USER-INTEL"_Packages_details.html#USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-LB"_Packages_details.html#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
-"USER-MANIFOLD"_Packages_details.html#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
-"USER-MEAMC"_Packages_details.html#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
-"USER-MESO"_Packages_details.html#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
-"USER-MGPT"_Packages_details.html#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
-"USER-MISC"_Packages_details.html#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
-"USER-MOFFF"_Packages_details.html#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
-"USER-MOLFILE"_Packages_details.html#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
-"USER-NETCDF"_Packages_details.html#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
-"USER-OMP"_Packages_details.html#USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-PHONON"_Packages_details.html#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
-"USER-QMMM"_Packages_details.html#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
-"USER-QTB"_Packages_details.html#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
-"USER-QUIP"_Packages_details.html#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
-"USER-REAXC"_Packages_details.html#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
-"USER-SMD"_Packages_details.html#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
-"USER-SMTBQ"_Packages_details.html#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
-"USER-SPH"_Packages_details.html#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
-"USER-TALLY"_Packages_details.html#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
-"USER-UEF"_Packages_details.html#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
-"USER-VTK"_Packages_details.html#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
+"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
+"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
+"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
+"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
+"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
+"USER-COLVARS"_Packages_details.html#PKG-USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
+"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
+"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
+"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, -
+"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
+"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
+"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
+"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
+"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
+"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
+"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
+"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
+"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
+"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
+"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
+"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
+"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
+"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
+"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
+"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
+"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
+"USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
+"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
+"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
+"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
+"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
+"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt
index 621f1fe2410f7f7d58e193466481cc3cd19a4578..029c8f831cc537da73f898ac5ba3172036a54faf 100644
--- a/doc/src/Python_call.txt
+++ b/doc/src/Python_call.txt
@@ -1,5 +1,5 @@
-"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
diff --git a/doc/src/Python_examples.txt b/doc/src/Python_examples.txt
index 46e5fee2b97da5d4f46644883434729c6e5406ad..f4b2197464312286a4a5cacd7600ba4c5bc56007 100644
--- a/doc/src/Python_examples.txt
+++ b/doc/src/Python_examples.txt
@@ -1,5 +1,5 @@
-"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
diff --git a/doc/src/Python.txt b/doc/src/Python_head.txt
similarity index 98%
rename from doc/src/Python.txt
rename to doc/src/Python_head.txt
index 2c9c6872bbf21e5704088b46752603f7349cd3e6..b5d33c5daadce4144a3cf4da8783d093b87c36ff 100644
--- a/doc/src/Python.txt
+++ b/doc/src/Python_head.txt
@@ -16,10 +16,12 @@ used together.
<!-- RST
.. toctree::
+ :maxdepth: 1
Python_overview
.. toctree::
+ :maxdepth: 1
Python_run
Python_shlib
@@ -31,6 +33,7 @@ used together.
Python_examples
.. toctree::
+ :maxdepth: 1
Python_call
diff --git a/doc/src/Python_install.txt b/doc/src/Python_install.txt
index 6591360ae2535935f0c9e88e8bf6bc2c830f6cb0..97f6bf3c3a6ba5c21bb9f043d9d7313b769c7742 100644
--- a/doc/src/Python_install.txt
+++ b/doc/src/Python_install.txt
@@ -1,5 +1,5 @@
-"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@@ -68,7 +68,7 @@ need to prefix this with "sudo". In this mode you cannot control
which Python is invoked by root.
Note that if you want Python to be able to load different versions of
-the LAMMPS shared library (see "this section"_#py_5 below), you will
+the LAMMPS shared library (see "this section"_Python_shlib.html), you will
need to manually copy files like liblammps_g++.so into the appropriate
system directory. This is not needed if you set the LD_LIBRARY_PATH
environment variable as described above.
diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt
index 8d0c724a45992294f7860612e5042387efc150ec..9a3ea93fc30ee932cbc1a85e374f37fb41bddee9 100644
--- a/doc/src/Python_library.txt
+++ b/doc/src/Python_library.txt
@@ -1,5 +1,5 @@
-"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
diff --git a/doc/src/Python_mpi.txt b/doc/src/Python_mpi.txt
index 6e0a2ce3198fd79bb98d1bf24fe0e60675de72ce..96c42e0d0ff2a06ff889f3c5072047df6677632f 100644
--- a/doc/src/Python_mpi.txt
+++ b/doc/src/Python_mpi.txt
@@ -1,5 +1,5 @@
-"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
diff --git a/doc/src/Python_pylammps.txt b/doc/src/Python_pylammps.txt
index d7baa93e2e69154b20fdc2f7f4666f500f2d6a02..303ac21a276fcab9444a33686b2373ee79cfae53 100644
--- a/doc/src/Python_pylammps.txt
+++ b/doc/src/Python_pylammps.txt
@@ -1,5 +1,5 @@
-"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
diff --git a/doc/src/Python_run.txt b/doc/src/Python_run.txt
index a94dc07f2d7368ec8086fc1535337ed3c245f82f..963248efced3a9ce8a084cf3411f562e33f00138 100644
--- a/doc/src/Python_run.txt
+++ b/doc/src/Python_run.txt
@@ -1,5 +1,5 @@
-"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
diff --git a/doc/src/Python_shlib.txt b/doc/src/Python_shlib.txt
index 1a921e4025cde5cc1376c603a4beb2cf5c4c58fb..91c90d9a8f46628102a7ce200fb535e873a9061c 100644
--- a/doc/src/Python_shlib.txt
+++ b/doc/src/Python_shlib.txt
@@ -1,5 +1,5 @@
-"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@@ -9,10 +9,13 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Build LAMMPS as a shared library :h3
-Instructions on how to build LAMMPS as a shared library are given in
-"Section 2.4"_Section_start.html#start_4. A shared library is one
-that is dynamically loadable, which is what Python requires to wrap
-LAMMPS. On Linux this is a library file that ends in ".so", not ".a".
+Build LAMMPS as a shared library using make :h4
+
+Instructions on how to build LAMMPS as a shared library are given on
+the "Build_basics"_Build_basics.html doc page. A shared library is
+one that is dynamically loadable, which is what Python requires to
+wrap LAMMPS. On Linux this is a library file that ends in ".so", not
+".a".
From the src directory, type
@@ -29,6 +32,42 @@ NOTE: If you are building LAMMPS with an MPI or FFT library or other
auxiliary libraries (used by various packages), then all of these
extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
-"Section 2.4"_Section_start.html#start_4 for more details.
+the "Build_basics"_Build_basics.html doc page.
+
+Build LAMMPS as a shared library using CMake :h4
+
+When using CMake the following two options are necessary to generate the LAMMPS
+shared library:
+
+-D BUILD_LIB=on # enable building LAMMPS as a library
+-D BUILD_SHARED_LIBS=on # enable building of LAMMPS shared library (both options are needed!) :pre
+
+What this does is create a liblammps.so which contains the majority of LAMMPS
+code. The generated lmp binary also dynamically links to this library. This
+means that either this liblammps.so file has to be in the same directory, a system
+library path (e.g. /usr/lib64/) or in the LD_LIBRARY_PATH.
+
+If you want to use the shared library with Python the recommended way is to create a virtualenv and use it as
+CMAKE_INSTALL_PREFIX.
+
+# create virtualenv
+virtualenv --python=$(which python3) myenv3
+source myenv3/bin/activate :pre
+
+# build library
+mkdir build
+cd build
+cmake -D PKG_PYTHON=on -D BUILD_LIB=on -D BUILD_SHARED_LIBS=on -D CMAKE_INSTALL_PREFIX=$VIRTUAL_ENV ../cmake
+make -j 4 :pre
+
+# install into prefix
+make install :pre
+
+This will also install the Python module into your virtualenv. Since virtualenv
+doesn't change your LD_LIBRARY_PATH, you still need to add its lib64 folder to
+it, which contains the installed liblammps.so.
+
+export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib64:$LD_LIBRARY_PATH :pre
-Also include CMake info on this
+Starting Python outside (!) of your build directory, but with the virtualenv
+enabled and with the LD_LIBRARY_PATH set gives you access to LAMMPS via Python.
diff --git a/doc/src/Python_test.txt b/doc/src/Python_test.txt
index 4a05d5c4680df053cd563f5e09d017e64fe4bb1f..2bfec91bd60827dcfaab23ca389ea065cb92b846 100644
--- a/doc/src/Python_test.txt
+++ b/doc/src/Python_test.txt
@@ -1,5 +1,5 @@
-"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@@ -32,10 +32,10 @@ first importing from the lammps.py file:
>>> from ctypes import CDLL
>>> CDLL("liblammps.so") :pre
-If an error occurs, carefully go thru the steps in "Section
-2.4"_Section_start.html#start_4 and above about building a shared
-library and about insuring Python can find the necessary two files
-it needs.
+If an error occurs, carefully go thru the steps on the
+"Build_basics"_Build_basics.html doc page about building a shared
+library and the "Python_install"_Python_install.html doc page about
+insuring Python can find the necessary two files it needs.
[Test LAMMPS and Python in serial:] :h4
diff --git a/doc/src/Run.txt b/doc/src/Run.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e2c0fe23539eb3d513dd9b12699a7c78b09efc2
--- /dev/null
+++ b/doc/src/Run.txt
@@ -0,0 +1,38 @@
+"Previous Section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Commands.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Run LAMMPS :h2
+
+These pages explain how to run LAMMPS once you have "installed an
+executable"_Install.html or "downloaded the source code"_Install.html
+and "built an executable"_Build.html. The "Commands"_Commands.html
+doc page describes how input scripts are structured and the commands
+they can contain.
+
+<!-- RST
+
+.. toctree::
+ :maxdepth: 1
+
+ Run_basics
+ Run_options
+ Run_output
+ Run_windows
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Basics of running LAMMPS"_Run_basics.html
+"Command-line options"_Run_options.html
+"Screen and logfile output"_Run_output.html
+"Running LAMMPS on Windows"_Run_windows.html :all(b)
+
+<!-- END_HTML_ONLY -->
diff --git a/doc/src/Run_basics.txt b/doc/src/Run_basics.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c83d17d6a9d13afbd19bb5e271c8cd3763c17bd9
--- /dev/null
+++ b/doc/src/Run_basics.txt
@@ -0,0 +1,89 @@
+"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Basics of running LAMMPS :h3
+
+LAMMPS is run from the command line, reading commands from a
+file via the -in command line flag, or from standard input.
+Using the "-in in.file" variant is recommended:
+
+lmp_serial < in.file
+lmp_serial -in in.file
+/path/to/lammps/src/lmp_serial < in.file
+mpirun -np 4 lmp_mpi -in in.file
+mpirun -np 8 /path/to//lammps/src/lmp_mpi -in in.file
+mpirun -np 6 /usr/local/bin/lmp -in in.file :pre
+
+You normally run the LAMMPS command in the directory where your
+input script is located. That is also where output files are
+produced by default, unless you provide specific other paths in
+your input script or on the command line. As in some of the
+examples above, the LAMMPS executable itself can be placed elsewhere.
+
+NOTE: The redirection operator "<" will not always work when running
+in parallel with mpirun; for those systems the -in form is required.
+
+As LAMMPS runs it prints info to the screen and a logfile named
+log.lammps. More info about output is given on the "Run
+output"_Run_output.html doc page.
+
+If LAMMPS encounters errors in the input script or while running a
+simulation it will print an ERROR message and stop or a WARNING
+message and continue. See the "Errors"_Errors.html doc page for a
+discussion of the various kinds of errors LAMMPS can or can't detect,
+a list of all ERROR and WARNING messages, and what to do about them.
+
+:line
+
+LAMMPS can run the same problem on any number of processors, including
+a single processor. In theory you should get identical answers on any
+number of processors and on any machine. In practice, numerical
+round-off can cause slight differences and eventual divergence of
+molecular dynamics phase space trajectories. See the "Errors
+common"_Errors_common.html doc page for discussion of this.
+
+LAMMPS can run as large a problem as will fit in the physical memory
+of one or more processors. If you run out of memory, you must run on
+more processors or define a smaller problem.
+
+If you run LAMMPS in parallel via mpirun, you should be aware of the
+"processors"_processors.html command which controls how MPI tasks are
+mapped to the simulation box, as well as mpirun options that control
+how MPI tasks are assigned to physical cores of the node(s) of the
+machine you are running on. These settings can improve performance,
+though the defaults are often adequate.
+
+For example, it is often important to bind MPI tasks (processes) to
+physical cores (processor affinity), so that the operating system does
+not migrate them during a simulation. If this is not the default
+behavior on your machine, the mpirun option "--bind-to core" (OpenMPI)
+or "-bind-to core" (MPICH) can be used.
+
+If the LAMMPS command(s) you are using support multi-threading, you
+can set the number of threads per MPI task via the environment
+variable OMP_NUM_THREADS, before you launch LAMMPS:
+
+export OMP_NUM_THREADS=2 # bash
+setenv OMP_NUM_THREADS 2 # csh or tcsh :pre
+
+This can also be done via the "package"_package.html command or via
+the "-pk command-line switch"_Run_options.html which invokes the
+package command. See the "package"_package.html command or
+"Speed"_Speed.html doc pages for more details about which accerlarator
+packages and which commands support multi-threading.
+
+:line
+
+You can experiment with running LAMMPS using any of the input scripts
+provided in the examples or bench directory. Input scripts are named
+in.* and sample outputs are named log.*.P where P is the number of
+processors it was run on.
+
+Some of the examples or benchmarks require LAMMPS to be built with
+optional packages.
diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0704e3b619951bb24f2d4e63c1ad0a99e628316e
--- /dev/null
+++ b/doc/src/Run_options.txt
@@ -0,0 +1,469 @@
+"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Command-line options :h3
+
+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
+letter abbreviation can be used:
+
+"-e or -echo"_#echo
+"-h or -help"_#help
+"-i or -in"_#file
+"-k or -kokkos"_#run-kokkos
+"-l or -log"_#log
+"-nc or -nocite"_#nocite
+"-pk or -package"_#package
+"-p or -partition"_#partition
+"-pl or -plog"_#plog
+"-ps or -pscreen"_#pscreen
+"-r or -restart"_#restart
+"-ro or -reorder"_#reorder
+"-sc or -screen"_#screen
+"-sf or -suffix"_#suffix
+"-v or -var"_#var :ul
+
+For example, the lmp_mpi executable might be launched as follows:
+
+mpirun -np 16 lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
+mpirun -np 16 lmp_mpi -var f tmp.out -log my.log -screen none -in in.alloy :pre
+
+:line
+
+[-echo style] :link(echo)
+
+Set the style of command echoing. The style can be {none} or {screen}
+or {log} or {both}. Depending on the style, each command read from
+the input script will be echoed to the screen and/or logfile. This
+can be useful to figure out which line of your script is causing an
+input error. The default value is {log}. The echo style can also be
+set by using the "echo"_echo.html command in the input script itself.
+
+:line
+
+[-help] :link(help)
+
+Print a brief help summary and a list of options compiled into this
+executable for each LAMMPS style (atom_style, fix, compute,
+pair_style, bond_style, etc). This can tell you if the command you
+want to use was included via the appropriate package at compile time.
+LAMMPS will print the info and immediately exit if this switch is
+used.
+
+:line
+
+[-in file] :link(file)
+
+Specify a file to use as an input script. This is an optional switch
+when running LAMMPS in one-partition mode. If it is not specified,
+LAMMPS reads its script from standard input, typically from a script
+via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should
+also work in parallel, but if it does not (in the unlikely case that
+an MPI implementation does not support it), then use the -in flag.
+Note that this is a required switch when running LAMMPS in
+multi-partition mode, since multiple processors cannot all read from
+stdin.
+
+:line
+
+[-kokkos on/off keyword/value ...] :link(run-kokkos)
+
+Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
+package. Even if LAMMPS is built with this package, as described
+in "Speed kokkos"_Speed_kokkos.html, this switch must be set to enable
+running with the KOKKOS-enabled styles the package provides. If the
+switch is not set (the default), LAMMPS will operate as if the KOKKOS
+package were not installed; i.e. you can run standard LAMMPS or with
+the GPU or USER-OMP packages, for testing or benchmarking purposes.
+
+Additional optional keyword/value pairs can be specified which
+determine how Kokkos will use the underlying hardware on your
+platform. These settings apply to each MPI task you launch via the
+"mpirun" or "mpiexec" command. You may choose to run one or more MPI
+tasks per physical node. Note that if you are running on a desktop
+machine, you typically have one physical node. On a cluster or
+supercomputer there may be dozens or 1000s of physical nodes.
+
+Either the full word or an abbreviation can be used for the keywords.
+Note that the keywords do not use a leading minus sign. I.e. the
+keyword is "t", not "-t". Also note that each of the keywords has a
+default setting. Examples of when to use these options and what
+settings to use on different platforms is given on the "Speed
+kokkos"_Speed_kokkos.html doc page.
+
+d or device
+g or gpus
+t or threads
+n or numa :ul
+
+device Nd :pre
+
+This option is only relevant if you built LAMMPS with CUDA=yes, you
+have more than one GPU per node, and if you are running with only one
+MPI task per node. The Nd setting is the ID of the GPU on the node to
+run on. By default Nd = 0. If you have multiple GPUs per node, they
+have consecutive IDs numbered as 0,1,2,etc. This setting allows you
+to launch multiple independent jobs on the node, each with a single
+MPI task per node, and assign each job to run on a different GPU.
+
+gpus Ng Ns :pre
+
+This option is only relevant if you built LAMMPS with CUDA=yes, you
+have more than one GPU per node, and you are running with multiple MPI
+tasks per node (up to one per GPU). The Ng setting is how many GPUs
+you will use. The Ns setting is optional. If set, it is the ID of a
+GPU to skip when assigning MPI tasks to GPUs. This may be useful if
+your desktop system reserves one GPU to drive the screen and the rest
+are intended for computational work like running LAMMPS. By default
+Ng = 1 and Ns is not set.
+
+Depending on which flavor of MPI you are running, LAMMPS will look for
+one of these 3 environment variables
+
+SLURM_LOCALID (various MPI variants compiled with SLURM support)
+MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
+OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre
+
+which are initialized by the "srun", "mpirun" or "mpiexec" commands.
+The environment variable setting for each MPI rank is used to assign a
+unique GPU ID to the MPI task.
+
+threads Nt :pre
+
+This option assigns Nt number of threads to each MPI task for
+performing work when Kokkos is executing in OpenMP or pthreads mode.
+The default is Nt = 1, which essentially runs in MPI-only mode. If
+there are Np MPI tasks per physical node, you generally want Np*Nt =
+the number of physical cores per node, to use your available hardware
+optimally. This also sets the number of threads used by the host when
+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
+= 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
+its default value of 1. This is because letting a single process span
+multiple NUMA regions induces a significant amount of cross NUMA data
+traffic which is slow.
+
+:line
+
+[-log file] :link(log)
+
+Specify a log file for LAMMPS to write status information to. In
+one-partition mode, if the switch is not used, LAMMPS writes to the
+file log.lammps. If this switch is used, LAMMPS writes to the
+specified file. In multi-partition mode, if the switch is not used, a
+log.lammps file is created with hi-level status information. Each
+partition also writes to a log.lammps.N file where N is the partition
+ID. If the switch is specified in multi-partition mode, the hi-level
+logfile is named "file" and each partition also logs information to a
+file.N. For both one-partition and multi-partition mode, if the
+specified file is "none", then no log files are created. Using a
+"log"_log.html command in the input script will override this setting.
+Option -plog will override the name of the partition log files file.N.
+
+:line
+
+[-nocite] :link(nocite)
+
+Disable writing the log.cite file which is normally written to list
+references for specific cite-able features used during a LAMMPS run.
+See the "citation page"_http://lammps.sandia.gov/cite.html for more
+details.
+
+:line
+
+[-package style args ....] :link(package)
+
+Invoke the "package"_package.html command with style and args. The
+syntax is the same as if the command appeared at the top of the input
+script. For example "-package gpu 2" or "-pk gpu 2" is the same as
+"package gpu 2"_package.html in the input script. The possible styles
+and args are documented on the "package"_package.html doc page. This
+switch can be used multiple times, e.g. to set options for the
+USER-INTEL and USER-OMP packages which can be used together.
+
+Along with the "-suffix" command-line switch, this is a convenient
+mechanism for invoking accelerator packages and their options without
+having to edit an input script.
+
+:line
+
+[-partition 8x2 4 5 ...] :link(partition)
+
+Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
+processors and this switch is not used, LAMMPS runs in one partition,
+i.e. all P processors run a single simulation. If this switch is
+used, the P processors are split into separate partitions and each
+partition runs its own simulation. The arguments to the switch
+specify the number of processors in each partition. Arguments of the
+form MxN mean M partitions, each with N processors. Arguments of the
+form N mean a single partition with N processors. The sum of
+processors in all partitions must equal P. Thus the command
+"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
+processors.
+
+Running with multiple partitions can be useful for running
+"multi-replica simulations"_Howto_replica.html, where each replica
+runs on on one or a few processors. Note that with MPI installed on a
+machine (e.g. your desktop), you can run on more (virtual) processors
+than you have physical processors.
+
+To run multiple independent simulations from one input script, using
+multiple partitions, see the "Howto multiple"_Howto_multiple.html doc
+page. World- and universe-style "variables"_variable.html are useful
+in this context.
+
+:line
+
+[-plog file] :link(plog)
+
+Specify the base name for the partition log files, so partition N
+writes log information to file.N. If file is none, then no partition
+log files are created. This overrides the filename specified in the
+-log command-line option. This option is useful when working with
+large numbers of partitions, allowing the partition log files to be
+suppressed (-plog none) or placed in a sub-directory (-plog
+replica_files/log.lammps) If this option is not used the log file for
+partition N is log.lammps.N or whatever is specified by the -log
+command-line option.
+
+:line
+
+[-pscreen file] :link(pscreen)
+
+Specify the base name for the partition screen file, so partition N
+writes screen information to file.N. If file is none, then no
+partition screen files are created. This overrides the filename
+specified in the -screen command-line option. This option is useful
+when working with large numbers of partitions, allowing the partition
+screen files to be suppressed (-pscreen none) or placed in a
+sub-directory (-pscreen replica_files/screen). If this option is not
+used the screen file for partition N is screen.N or whatever is
+specified by the -screen command-line option.
+
+:line
+
+[-restart restartfile {remap} datafile keyword value ...] :link(restart)
+
+Convert the restart file into a data file and immediately exit. This
+is the same operation as if the following 2-line input script were
+run:
+
+read_restart restartfile {remap}
+write_data datafile keyword value ... :pre
+
+Note that the specified restartfile and datafile can have wild-card
+characters ("*",%") as described by the
+"read_restart"_read_restart.html and "write_data"_write_data.html
+commands. But a filename such as file.* will need to be enclosed in
+quotes to avoid shell expansion of the "*" character.
+
+Note that following restartfile, the optional flag {remap} can be
+used. This has the same effect as adding it to the
+"read_restart"_read_restart.html command, as explained on its doc
+page. This is only useful if the reading of the restart file triggers
+an error that atoms have been lost. In that case, use of the remap
+flag should allow the data file to still be produced.
+
+Also note that following datafile, the same optional keyword/value
+pairs can be listed as used by the "write_data"_write_data.html
+command.
+
+:line
+
+[-reorder] :link(reorder)
+
+This option has 2 forms:
+
+-reorder nth N
+-reorder custom filename :pre
+
+Reorder the processors in the MPI communicator used to instantiate
+LAMMPS, in one of several ways. The original MPI communicator ranks
+all P processors from 0 to P-1. The mapping of these ranks to
+physical processors is done by MPI before LAMMPS begins. It may be
+useful in some cases to alter the rank order. E.g. to insure that
+cores within each node are ranked in a desired order. Or when using
+the "run_style verlet/split"_run_style.html command with 2 partitions
+to insure that a specific Kspace processor (in the 2nd partition) is
+matched up with a specific set of processors in the 1st partition.
+See the "Speed tips"_Speed_tips.html doc page for more details.
+
+If the keyword {nth} is used with a setting {N}, then it means every
+Nth processor will be moved to the end of the ranking. This is useful
+when using the "run_style verlet/split"_run_style.html command with 2
+partitions via the -partition command-line switch. The first set of
+processors will be in the first partition, the 2nd set in the 2nd
+partition. The -reorder command-line switch can alter this so that
+the 1st N procs in the 1st partition and one proc in the 2nd partition
+will be ordered consecutively, e.g. as the cores on one physical node.
+This can boost performance. For example, if you use "-reorder nth 4"
+and "-partition 9 3" and you are running on 12 processors, the
+processors will be reordered from
+
+0 1 2 3 4 5 6 7 8 9 10 11 :pre
+
+to
+
+0 1 2 4 5 6 8 9 10 3 7 11 :pre
+
+so that the processors in each partition will be
+
+0 1 2 4 5 6 8 9 10
+3 7 11 :pre
+
+See the "processors" command for how to insure processors from each
+partition could then be grouped optimally for quad-core nodes.
+
+If the keyword is {custom}, then a file that specifies a permutation
+of the processor ranks is also specified. The format of the reorder
+file is as follows. Any number of initial blank or comment lines
+(starting with a "#" character) can be present. These should be
+followed by P lines of the form:
+
+I J :pre
+
+where P is the number of processors LAMMPS was launched with. Note
+that if running in multi-partition mode (see the -partition switch
+above) P is the total number of processors in all partitions. The I
+and J values describe a permutation of the P processors. Every I and
+J should be values from 0 to P-1 inclusive. In the set of P I values,
+every proc ID should appear exactly once. Ditto for the set of P J
+values. A single I,J pairing means that the physical processor with
+rank I in the original MPI communicator will have rank J in the
+reordered communicator.
+
+Note that rank ordering can also be specified by many MPI
+implementations, either by environment variables that specify how to
+order physical processors, or by config files that specify what
+physical processors to assign to each MPI rank. The -reorder switch
+simply gives you a portable way to do this without relying on MPI
+itself. See the "processors out"_processors.html command for how
+to output info on the final assignment of physical processors to
+the LAMMPS simulation domain.
+
+:line
+
+[-screen file] :link(screen)
+
+Specify a file for LAMMPS to write its screen information to. In
+one-partition mode, if the switch is not used, LAMMPS writes to the
+screen. If this switch is used, LAMMPS writes to the specified file
+instead and you will see no screen output. In multi-partition mode,
+if the switch is not used, hi-level status information is written to
+the screen. Each partition also writes to a screen.N file where N is
+the partition ID. If the switch is specified in multi-partition mode,
+the hi-level screen dump is named "file" and each partition also
+writes screen information to a file.N. For both one-partition and
+multi-partition mode, if the specified file is "none", then no screen
+output is performed. Option -pscreen will override the name of the
+partition screen files file.N.
+
+:line
+
+[-suffix style args] :link(suffix)
+
+Use variants of various styles if they exist. The specified style can
+be {cuda}, {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}. These
+refer to optional packages that LAMMPS can be built with, as described
+in "Accelerate performance"_Speed.html. The "gpu" style corresponds to the
+GPU package, the "intel" style to the USER-INTEL package, the "kk"
+style to the KOKKOS package, the "opt" style to the OPT package, and
+the "omp" style to the USER-OMP package. The hybrid style is the only
+style that accepts arguments. It allows for two packages to be
+specified. The first package specified is the default and will be used
+if it is available. If no style is available for the first package,
+the style for the second package will be used if available. For
+example, "-suffix hybrid intel omp" will use styles from the
+USER-INTEL package if they are installed and available, but styles for
+the USER-OMP package otherwise.
+
+Along with the "-package" command-line switch, this is a convenient
+mechanism for invoking accelerator packages and their options without
+having to edit an input script.
+
+As an example, all of the packages provide a "pair_style
+lj/cut"_pair_lj.html variant, with style names lj/cut/gpu,
+lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A variant style
+can be specified explicitly in your input script, e.g. pair_style
+lj/cut/gpu. If the -suffix switch is used the specified suffix
+(gpu,intel,kk,omp,opt) is automatically appended whenever your input
+script command creates a new "atom"_atom_style.html,
+"pair"_pair_style.html, "fix"_fix.html, "compute"_compute.html, or
+"run"_run_style.html style. If the variant version does not exist,
+the standard version is created.
+
+For the GPU package, using this command-line switch also invokes the
+default GPU settings, as if the command "package gpu 1" were used at
+the top of your input script. These settings can be changed by using
+the "-package gpu" command-line switch or the "package
+gpu"_package.html command in your script.
+
+For the USER-INTEL package, using this command-line switch also
+invokes the default USER-INTEL settings, as if the command "package
+intel 1" were used at the top of your input script. These settings
+can be changed by using the "-package intel" command-line switch or
+the "package intel"_package.html command in your script. If the
+USER-OMP package is also installed, the hybrid style with "intel omp"
+arguments can be used to make the omp suffix a second choice, if a
+requested style is not available in the USER-INTEL package. It will
+also invoke the default USER-OMP settings, as if the command "package
+omp 0" were used at the top of your input script. These settings can
+be changed by using the "-package omp" command-line switch or the
+"package omp"_package.html command in your script.
+
+For the KOKKOS package, using this command-line switch also invokes
+the default KOKKOS settings, as if the command "package kokkos" were
+used at the top of your input script. These settings can be changed
+by using the "-package kokkos" command-line switch or the "package
+kokkos"_package.html command in your script.
+
+For the OMP package, using this command-line switch also invokes the
+default OMP settings, as if the command "package omp 0" were used at
+the top of your input script. These settings can be changed by using
+the "-package omp" command-line switch or the "package
+omp"_package.html command in your script.
+
+The "suffix"_suffix.html command can also be used within an input
+script to set a suffix, or to turn off or back on any suffix setting
+made via the command line.
+
+:line
+
+[-var name value1 value2 ...] :link(var)
+
+Specify a variable that will be defined for substitution purposes when
+the input script is read. This switch can be used multiple times to
+define multiple variables. "Name" is the variable name which can be a
+single character (referenced as $x in the input script) or a full
+string (referenced as $\{abc\}). An "index-style
+variable"_variable.html will be created and populated with the
+subsequent values, e.g. a set of filenames. Using this command-line
+option is equivalent to putting the line "variable name index value1
+value2 ..." at the beginning of the input script. Defining an index
+variable as a command-line argument overrides any setting for the same
+index variable in the input script, since index variables cannot be
+re-defined.
+
+See the "variable"_variable.html command for more info on defining
+index and other kinds of variables and the "Commands
+parse"_Commands_parse.html page for more info on using variables in
+input scripts.
+
+NOTE: Currently, the command-line parser looks for arguments that
+start with "-" to indicate new switches. Thus you cannot specify
+multiple variable values if any of them start with a "-", e.g. a
+negative numeric value. It is OK if the first value1 starts with a
+"-", since it is automatically skipped.
diff --git a/doc/src/Run_output.txt b/doc/src/Run_output.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a534ae7c7b35bef9fc1ea41bdad87db9fabe43c2
--- /dev/null
+++ b/doc/src/Run_output.txt
@@ -0,0 +1,176 @@
+"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Screen and logfile output :h3
+
+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
+simulation. When the simulation is ready to begin, LAMMPS performs
+various initializations, and prints info about the run it is about to
+perform, including the amount of memory (in MBytes per processor) that
+the simulation requires. It also prints details of the initial
+thermodynamic state of the system. During the run itself,
+thermodynamic information is printed periodically, every few
+timesteps. When the run concludes, LAMMPS prints the final
+thermodynamic state and a total run time for the simulation. It also
+appends statistics about the CPU time and storage requirements for the
+simulation. An example set of statistics is shown here:
+
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre
+
+Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
+97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
+
+MPI task timings breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.9808 | 2.0134 | 2.0318 | 1.4 | 71.60
+Bond | 0.0021894 | 0.0060319 | 0.010058 | 4.7 | 0.21
+Kspace | 0.3207 | 0.3366 | 0.36616 | 3.1 | 11.97
+Neigh | 0.28411 | 0.28464 | 0.28516 | 0.1 | 10.12
+Comm | 0.075732 | 0.077018 | 0.07883 | 0.4 | 2.74
+Output | 0.00030518 | 0.00042665 | 0.00078821 | 1.0 | 0.02
+Modify | 0.086606 | 0.086631 | 0.086668 | 0.0 | 3.08
+Other | | 0.007178 | | | 0.26 :pre
+
+Nlocal: 501 ave 508 max 490 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Nghost: 6586.25 ave 6628 max 6548 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs: 177007 ave 180562 max 170212 min
+Histogram: 1 0 0 0 0 0 0 1 1 1 :pre
+
+Total # of neighbors = 708028
+Ave neighs/atom = 353.307
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 26
+Dangerous builds = 0 :pre
+
+:line
+
+The first section provides a global loop timing summary. The {loop
+time} is the total wall-clock time for the simulation to run. The
+{Performance} line is provided for convenience to help predict how
+long it will take to run a desired physical simulation. The {CPU use}
+line provides the CPU utilization per MPI task; it should be close to
+100% times the number of OpenMP threads (or 1 of not using OpenMP).
+Lower numbers correspond to delays due to file I/O or insufficient
+thread utilization.
+
+:line
+
+The {MPI task} section gives the breakdown of the CPU run time (in
+seconds) into major categories:
+
+{Pair} = non-bonded force computations
+{Bond} = bonded interactions: bonds, angles, dihedrals, impropers
+{Kspace} = long-range interactions: Ewald, PPPM, MSM
+{Neigh} = neighbor list construction
+{Comm} = inter-processor communication of atoms and their properties
+{Output} = output of thermodynamic info and dump files
+{Modify} = fixes and computes invoked by fixes
+{Other} = all the remaining time :ul
+
+For each category, there is a breakdown of the least, average and most
+amount of wall time any processor spent on this category of
+computation. The "%varavg" is the percentage by which the max or min
+varies from the average. This is an indication of load imbalance. A
+percentage close to 0 is perfect load balance. A large percentage is
+imbalance. The final "%total" column is the percentage of the total
+loop time is spent in this category.
+
+When using the "timer full"_timer.html setting, an additional column
+is added that also prints the CPU utilization in percent. In addition,
+when using {timer full} and the "package omp"_package.html command are
+active, a similar timing summary of time spent in threaded regions to
+monitor thread utilization and load balance is provided. A new {Thread
+timings} section is also added, which lists the time spent in reducing
+the per-thread data elements to the storage for non-threaded
+computation. These thread timings are measured for the first MPI rank
+only and and thus, because the breakdown for MPI tasks can change from
+MPI rank to MPI rank, this breakdown can be very different for
+individual ranks. Here is an example output for this section:
+
+Thread timings breakdown (MPI rank 0):
+Total threaded time 0.6846 / 90.6%
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18
+Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68
+Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89
+Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70
+Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55 :pre
+
+:line
+
+The third section above lists the number of owned atoms (Nlocal),
+ghost atoms (Nghost), and pair-wise neighbors stored per processor.
+The max and min values give the spread of these values across
+processors with a 10-bin histogram showing the distribution. The total
+number of histogram counts is equal to the number of processors.
+
+:line
+
+The last section gives aggregate statistics (across all processors)
+for pair-wise neighbors and special neighbors that LAMMPS keeps track
+of (see the "special_bonds"_special_bonds.html command). The number
+of times neighbor lists were rebuilt is tallied, as is the number of
+potentially {dangerous} rebuilds. If atom movement triggered neighbor
+list rebuilding (see the "neigh_modify"_neigh_modify.html command),
+then dangerous reneighborings are those that were triggered on the
+first timestep atom movement was checked for. If this count is
+non-zero you may wish to reduce the delay factor to insure no force
+interactions are missed by atoms moving beyond the neighbor skin
+distance before a rebuild takes place.
+
+:line
+
+If an energy minimization was performed via the
+"minimize"_minimize.html command, additional information is printed,
+e.g.
+
+Minimization stats:
+ Stopping criterion = linesearch alpha is zero
+ Energy initial, next-to-last, final =
+ -6372.3765206 -8328.46998942 -8328.46998942
+ Force two-norm initial, final = 1059.36 5.36874
+ Force max component initial, final = 58.6026 1.46872
+ Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
+ Iterations, force evaluations = 701 1516 :pre
+
+The first line prints the criterion that determined minimization was
+converged. The next line lists the initial and final energy, as well
+as the energy on the next-to-last iteration. The next 2 lines give a
+measure of the gradient of the energy (force on all atoms). The
+2-norm is the "length" of this 3N-component force vector; the largest
+component (x, y, or z) of force (infinity-norm) is also given. Then
+information is provided about the line search and statistics on how
+many iterations and force-evaluations the minimizer required.
+Multiple force evaluations are typically done at each iteration to
+perform a 1d line minimization in the search direction. See the
+"minimize"_minimize.html doc page for more details.
+
+:line
+
+If a "kspace_style"_kspace_style.html long-range Coulombics solver
+that performs FFTs was used during the run (PPPM, Ewald), then
+additional information is printed, e.g.
+
+FFT time (% of Kspce) = 0.200313 (8.34477)
+FFT Gflps 3d 1d-only = 2.31074 9.19989 :pre
+
+The first line is the time spent doing 3d FFTs (several per timestep)
+and the fraction it represents of the total KSpace time (listed
+above). Each 3d FFT requires computation (3 sets of 1d FFTs) and
+communication (transposes). The total flops performed is 5Nlog_2(N),
+where N is the number of points in the 3d grid. The FFTs are timed
+with and without the communication and a Gflop rate is computed. The
+3d rate is with communication; the 1d rate is without (just the 1d
+FFTs). Thus you can estimate what fraction of your FFT time was spent
+in communication, roughly 75% in the example above.
diff --git a/doc/src/Run_windows.txt b/doc/src/Run_windows.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1151a4a2bbdd0ed40b52ac4ad4367f036c3cd1b1
--- /dev/null
+++ b/doc/src/Run_windows.txt
@@ -0,0 +1,73 @@
+"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Running LAMMPS on Windows :h3
+
+To run a serial (non-MPI) executable, follow these steps:
+
+Get a command prompt by going to Start->Run... ,
+then typing "cmd". :ulb,l
+
+Move to the directory where you have your input script,
+(e.g. by typing: cd "Documents"). :l
+
+At the command prompt, type "lmp_serial -in in.file", where
+in.file is the name of your LAMMPS input script. :l,ule
+
+Note that the serial executable includes support for multi-threading
+parallelization from the styles in the USER-OMP packages. To run with
+4 threads, you can type this:
+
+lmp_serial -in in.lj -pk omp 4 -sf omp :pre
+
+:line
+
+For the MPI executable, which allows you to run LAMMPS under Windows
+in parallel, follow these steps.
+
+Download and install a compatible MPI library binary package:
+
+for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
+for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul
+
+The LAMMPS Windows installer packages will automatically adjust your
+path for the default location of this MPI package. After the
+installation of the MPICH2 software, it needs to be integrated into
+the system. For this you need to start a Command Prompt in
+{Administrator Mode} (right click on the icon and select it). Change
+into the MPICH2 installation directory, then into the subdirectory
+[bin] and execute [smpd.exe -install]. Exit the command window.
+
+Get a new, regular command prompt by going to Start->Run... ,
+then typing "cmd". :ulb,l
+
+Move to the directory where you have your input file
+(e.g. by typing: cd "Documents"). :l,ule
+
+Then type something like this:
+
+mpiexec -localonly 4 lmp_mpi -in in.file
+mpiexec -np 4 lmp_mpi -in in.file :pre
+
+where in.file is the name of your LAMMPS input script. For the latter
+case, you may be prompted to enter your password.
+
+In this mode, output may not immediately show up on the screen, so if
+your input script takes a long time to execute, you may need to be
+patient before the output shows up.
+
+The parallel executable can also run on a single processor by typing
+something like this:
+
+lmp_mpi -in in.lj :pre
+
+Note that the parallel executable also includes OpenMP
+multi-threading, which can be combined with MPI using something like:
+
+mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
deleted file mode 100644
index 19a798d5dfddbbb14e2d9ccbf9e66b943392d920..0000000000000000000000000000000000000000
--- a/doc/src/Section_start.txt
+++ /dev/null
@@ -1,1823 +0,0 @@
-"Previous Section"_Intro.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Commands.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-2. Getting Started :h2
-
-This section describes how to build and run LAMMPS, for both new and
-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 as a library"_#start_4
-2.5 "Running LAMMPS"_#start_5
-2.6 "Command-line options"_#start_6
-2.7 "Screen output"_#start_7
-2.8 "Tips for users of previous versions"_#start_8 :all(b)
-
-:line
-
-2.1 What's in the LAMMPS distribution :h3,link(start_1)
-
-When you download a LAMMPS tarball you will need to unzip and untar
-the downloaded file with the following commands, after placing the
-tarball in an appropriate directory.
-
-tar -xzvf lammps*.tar.gz :pre
-
-This will create a LAMMPS directory containing two files and several
-sub-directories:
-
-README: text file
-LICENSE: the GNU General Public License (GPL)
-bench: benchmark problems
-doc: documentation
-examples: simple test problems
-potentials: embedded atom method (EAM) potential files
-src: source files
-tools: pre- and post-processing tools :tb(s=:)
-
-Note that the "download page"_download also has links to download
-pre-build Windows installers, as well as pre-built packages for
-several widely used Linux distributions. It also has instructions
-for how to download/install LAMMPS for Macs (via Homebrew), and to
-download and update LAMMPS from SVN and Git repositories, which gives
-you access to the up-to-date sources that are used by the LAMMPS
-core developers.
-
-:link(download,http://lammps.sandia.gov/download.html)
-
-The Windows and Linux packages for serial or parallel include
-only selected packages and bug-fixes/upgrades listed on "this
-page"_http://lammps.sandia.gov/bug.html up to a certain date, as
-stated on the download page. If you want an executable with
-non-included packages or that is more current, then you'll need to
-build LAMMPS yourself, as discussed in the next section.
-
-Skip to the "Running LAMMPS"_#start_6 sections for info on how to
-launch a LAMMPS Windows executable on a Windows box.
-
-:line
-
-2.2 Making LAMMPS :h3,link(start_2)
-
-This section has the following sub-sections:
-
-2.2.1 "Read this first"_#start_2_1
-2.2.1 "Steps to build a LAMMPS executable"_#start_2_2
-2.2.3 "Common errors that can occur when making LAMMPS"_#start_2_3
-2.2.4 "Additional build tips"_#start_2_4
-2.2.5 "Building for a Mac"_#start_2_5
-2.2.6 "Building for Windows"_#start_2_6 :all(b)
-
-:line
-
-Read this first :h4,link(start_2_1)
-
-If you want to avoid building LAMMPS yourself, read the preceding
-section about options available for downloading and installing
-executables. Details are discussed on the "download"_download page.
-
-Building LAMMPS can be simple or not-so-simple. If all you need are
-the default packages installed in LAMMPS, and MPI is already installed
-on your machine, or you just want to run LAMMPS in serial, then you
-can typically use the Makefile.mpi or Makefile.serial files in
-src/MAKE by typing one of these lines (from the src dir):
-
-make mpi
-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 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"
-to see a list), you can use it as-is by typing (for example):
-
-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 a LAMMPS command that requires an extra library (e.g. "dump
-image"_dump_image.html) build with a package that requires an extra
-library build with an accelerator package that requires special
-compiler/linker settings run on a machine that has its own compilers,
-settings, or libraries :ul
-
-then building LAMMPS is more complicated. You may need to find where
-extra libraries exist on your machine or install them if they don't.
-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.
-
-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 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
-please post the issue to the "LAMMPS mail
-list"_http://lammps.sandia.gov/mail.html.
-
-If you succeed in building LAMMPS on a new kind of machine, for which
-there isn't a similar machine Makefile included in the
-src/MAKE/MACHINES directory, then send it to the developers and we can
-include it in the LAMMPS distribution.
-
-:line
-
-Steps to build a LAMMPS executable :h4,link(start_2_2)
-
-Step 0 :h5
-
-The src directory contains the C++ source and header files for LAMMPS.
-It also contains a top-level Makefile and a MAKE sub-directory with
-low-level Makefile.* files for many systems and machines. See the
-src/MAKE/README file for a quick overview of what files are available
-and what sub-directories they are in.
-
-The src/MAKE dir has a few files that should work as-is on many
-platforms. The src/MAKE/OPTIONS dir has more that invoke additional
-compiler, MPI, and other setting options commonly used by LAMMPS, to
-illustrate their syntax. The src/MAKE/MACHINES dir has many more that
-have been tweaked or optimized for specific machines. These files are
-all good starting points if you find you need to change them for your
-machine. Put any file you edit into the src/MAKE/MINE directory and
-it will be never be touched by any LAMMPS updates.
-
->From within the src directory, type "make" or "gmake". You should see
-a list of available choices from src/MAKE and all of its
-sub-directories. If one of those has the options you want or is the
-machine you want, you can type a command like:
-
-make mpi :pre
-or
-
-make serial :pre
-or
-
-gmake mac :pre
-
-Note that the corresponding Makefile.machine can exist in src/MAKE or
-any of its sub-directories. If a file with the same name appears in
-multiple places (not a good idea), the order they are used is as
-follows: src/MAKE/MINE, src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.
-This gives preference to a file you have created/edited and put in
-src/MAKE/MINE.
-
-Note that on a multi-processor or multi-core platform you can launch a
-parallel make, by using the "-j" switch with the make command, which
-will build LAMMPS more quickly.
-
-If you get no errors and an executable like [lmp_mpi] or [lmp_serial]
-or [lmp_mac] is produced, then you're done; it's your lucky day.
-
-Note that by default only a few of LAMMPS optional packages are
-installed. To build LAMMPS with optional packages, see "this
-section"_#start_3 below.
-
-Step 1 :h5
-
-If Step 0 did not work, you will need to create a low-level Makefile
-for your machine, like Makefile.foo. You should make a copy of an
-existing Makefile.* in src/MAKE or one of its sub-directories as a
-starting point. The only portions of the file you need to edit are
-the first line, the "compiler/linker settings" section, and the
-"LAMMPS-specific settings" section. When it works, put the edited
-file in src/MAKE/MINE and it will not be altered by any future LAMMPS
-updates.
-
-Step 2 :h5
-
-Change the first line of Makefile.foo to list the word "foo" after the
-"#", and whatever other options it will set. This is the line you
-will see if you just type "make".
-
-Step 3 :h5
-
-The "compiler/linker settings" section lists compiler and linker
-settings for your C++ compiler, including optimization flags. You can
-use g++, the open-source GNU compiler, which is available on all Unix
-systems. You can also use mpicxx which will typically be available if
-MPI is installed on your system, though you should check which actual
-compiler it wraps. Vendor compilers often produce faster code. On
-boxes with Intel CPUs, we suggest using the Intel icc compiler, which
-can be downloaded from "Intel's compiler site"_intel.
-
-:link(intel,http://www.intel.com/software/products/noncom)
-
-If building a C++ code on your machine requires additional libraries,
-then you should list them as part of the LIB variable. You should
-not need to do this if you use mpicxx.
-
-The DEPFLAGS setting is what triggers the C++ compiler to create a
-dependency list for a source file. This speeds re-compilation when
-source (*.cpp) or header (*.h) files are edited. Some compilers do
-not support dependency file creation, or may use a different switch
-than -D. GNU g++ and Intel icc works with -D. If your compiler can't
-create dependency files, then you'll need to create a Makefile.foo
-patterned after Makefile.storm, which uses different rules that do not
-involve dependency files. Note that when you build LAMMPS for the
-first time on a new platform, a long list of *.d files will be printed
-out rapidly. This is not an error; it is the Makefile doing its
-normal creation of dependencies.
-
-Step 4 :h5
-
-The "system-specific settings" section has several parts. Note that
-if you change any -D setting in this section, you should do a full
-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:
-
--DLAMMPS_GZIP
--DLAMMPS_JPEG
--DLAMMPS_PNG
--DLAMMPS_FFMPEG
--DLAMMPS_MEMALIGN
--DLAMMPS_SMALLBIG
--DLAMMPS_BIGBIG
--DLAMMPS_SMALLSMALL
--DLAMMPS_LONGLONG_TO_LONG
--DLAMMPS_EXCEPTIONS
--DPACK_ARRAY
--DPACK_POINTER
--DPACK_MEMCPY :ul
-
-The read_data and dump commands will read/write gzipped files if you
-compile with -DLAMMPS_GZIP. It requires that your machine supports
-the "popen()" function in the standard runtime library and that a gzip
-executable can be found by LAMMPS during a run.
-
-NOTE: on some clusters with high-speed networks, using the fork()
-library calls (required by popen()) can interfere with the fast
-communication library and lead to simulations using compressed output
-or input to hang or crash. For selected operations, compressed file
-I/O is also available using a compression library instead, which are
-provided in the COMPRESS package. From more details about compiling
-LAMMPS with packages, please see below.
-
-If you use -DLAMMPS_JPEG, the "dump image"_dump_image.html command
-will be able to write out JPEG image files. For JPEG files, you must
-also link LAMMPS with a JPEG library, as described below. If you use
--DLAMMPS_PNG, the "dump image"_dump.html command will be able to write
-out PNG image files. For PNG files, you must also link LAMMPS with a
-PNG library, as described below. If neither of those two defines are
-used, LAMMPS will only be able to write out uncompressed PPM image
-files.
-
-If you use -DLAMMPS_FFMPEG, the "dump movie"_dump_image.html command
-will be available to support on-the-fly generation of rendered movies
-the need to store intermediate image files. It requires that your
-machines supports the "popen" function in the standard runtime library
-and that an FFmpeg executable can be found by LAMMPS during the run.
-
-NOTE: Similar to the note above, this option can conflict with
-high-speed networks, because it uses popen().
-
-Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
-posix_memalign() call instead of malloc() when large chunks or memory
-are allocated by LAMMPS. This can help to make more efficient use of
-vector instructions of modern CPUS, since dynamically allocated memory
-has to be aligned on larger than default byte boundaries (e.g. 16
-bytes instead of 8 bytes on x86 type platforms) for optimal
-performance.
-
-Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG,
--DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These
-settings refer to use of 4-byte (small) vs 8-byte (big) integers
-within LAMMPS, as specified in src/lmptype.h. The only reason to use
-the BIGBIG setting is to enable simulation of huge molecular systems
-(which store bond topology info) with more than 2 billion atoms, or to
-track the image flags of moving atoms that wrap around a periodic box
-more than 512 times. Normally, the only reason to use SMALLSMALL is
-if your machine does not support 64-bit integers, though you can use
-SMALLSMALL setting if you are running in serial or on a desktop
-machine or small cluster where you will never run large systems or for
-long time (more than 2 billion atoms, more than 2 billion timesteps).
-See the "Additional build tips"_#start_2_4 section below for more
-details on these settings.
-
-Note that the USER-ATC package is not currently compatible with
--DLAMMPS_BIGBIG. Also the GPU package requires the lib/gpu library to
-be compiled with the same setting, or the link will fail.
-
-The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or
-MPI version does not recognize "long long" data types. In this case a
-"long" data type is likely already 64-bits, in which case this setting
-will convert to that data type.
-
-The -DLAMMPS_EXCEPTIONS setting can be used to activate alternative
-versions of error handling inside of LAMMPS. This is useful when
-external codes drive LAMMPS as a library. Using this option, LAMMPS
-errors do not kill the caller. Instead, the call stack is unwound and
-control returns to the caller. The library interface provides the
-lammps_has_error() and lammps_get_last_error_message() functions to
-detect and find out more about a LAMMPS error.
-
-Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY
-options can make for faster parallel FFTs (in the PPPM solver) on some
-platforms. The -DPACK_ARRAY setting is the default. See the
-"kspace_style"_kspace_style.html command for info about PPPM. See
-Step 6 below for info about building LAMMPS with an FFT library.
-
-Step 5 :h5
-
-The 3 MPI variables are used to specify an MPI library to build LAMMPS
-with. Note that you do not need to set these if you use the MPI
-compiler mpicxx for your CC and LINK setting in the section above.
-The MPI wrapper knows where to find the needed files.
-
-If you want LAMMPS to run in parallel, you must have an MPI library
-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
-your build environment, before building LAMMPS. Or the parallel
-machine may have a vendor-provided MPI which the compiler has no
-trouble finding.
-
-Failing this, these 3 variables can be used to specify where the mpi.h
-file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
-name of the library file (MPI_LIB).
-
-If you are installing MPI yourself, we recommend Argonne's MPICH2
-or OpenMPI. MPICH can be downloaded from the "Argonne MPI
-site"_http://www.mcs.anl.gov/research/projects/mpich2/. OpenMPI can
-be downloaded from the "OpenMPI site"_http://www.open-mpi.org.
-Other MPI packages should also work. If you are running on a big
-parallel platform, your system people or the vendor should have
-already installed a version of MPI, which is likely to be faster
-than a self-installed MPICH or OpenMPI, so find out how to build
-and link with it. If you use MPICH or OpenMPI, you will have to
-configure and build it for your platform. The MPI configure script
-should have compiler options to enable you to use the same compiler
-you are using for the LAMMPS build, which can avoid problems that can
-arise when linking LAMMPS to the MPI library.
-
-If you just want to run LAMMPS on a single processor, you can use the
-dummy MPI library provided in src/STUBS, since you don't need a true
-MPI library installed on your system. See src/MAKE/Makefile.serial
-for how to specify the 3 MPI variables in this case. You will also
-need to build the STUBS library for your platform before making LAMMPS
-itself. Note that if you are building with src/MAKE/Makefile.serial,
-e.g. by typing "make serial", then the STUBS library is built for you.
-
-To build the STUBS library from the src directory, type "make
-mpi-stubs", or from the src/STUBS dir, type "make". This should
-create a libmpi_stubs.a file suitable for linking to LAMMPS. If the
-build fails, you will need to edit the STUBS/Makefile for your
-platform.
-
-The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
-that calls gettimeofday() . If your system doesn't support
-gettimeofday() , you'll need to insert code to call another timer.
-Note that the ANSI-standard function clock() rolls over after an hour
-or so, and is therefore insufficient for timing long LAMMPS
-simulations.
-
-Step 6 :h5
-
-The 3 FFT variables allow you to specify an FFT library which LAMMPS
-uses (for performing 1d FFTs) when running the particle-particle
-particle-mesh (PPPM) option for long-range Coulombics via the
-"kspace_style"_kspace_style.html command.
-
-LAMMPS supports common open-source or vendor-supplied FFT libraries
-for this purpose. If you leave these 3 variables blank, LAMMPS will
-use the open-source "KISS FFT library"_http://kissfft.sf.net, which is
-included in the LAMMPS distribution. This library is portable to all
-platforms and for typical LAMMPS simulations is almost as fast as FFTW
-or vendor optimized libraries. If you are not including the KSPACE
-package in your build, you can also leave the 3 variables blank.
-
-Otherwise, select which kinds of FFTs to use as part of the FFT_INC
-setting by a switch of the form -DFFT_XXX. Recommended values for XXX
-are: MKL or FFTW3. FFTW2 and NONE are supported as legacy options.
-Selecting -DFFT_FFTW will use the FFTW3 library and -DFFT_NONE will
-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
-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. See the src/MAKE/OPTIONS/Makefile.fftw file for an
-example of how to specify these variables to use the FFTW3 library.
-
-FFTW is fast, portable library that should also work on any platform
-and typically be faster than KISS FFT. You can download it from
-"www.fftw.org"_http://www.fftw.org. Both the legacy version 2.1.X and
-the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3.
-Building FFTW for your box should be as simple as ./configure; make;
-make install. The install command typically requires root privileges
-(e.g. invoke it via sudo), unless you specify a local directory with
-the "--prefix" option of configure. Type "./configure --help" to see
-various options.
-
-If you wish to have FFTW support for single-precision FFTs (see below
-about -DFFT_SINGLE) in addition to the default double-precision FFTs,
-you will need to build FFTW a second time for single-precision. For
-FFTW3, do this via:
-
-make clean
-./configure --enable-single; make; make install :pre
-
-which should produce the additional library libfftw3f.a.
-
-For FFTW2, do this:
-
-make clean
-./configure --enable-float --enable-type-prefix; make; make install :pre
-
-which should produce the additional library libsfftw.a and additional
-include file sfttw.a. Note that on some platforms FFTW2 has been
-pre-installed for both single- and double-precision, and may already
-have these files as well as libdfftw.a and dfftw.h for double
-precision.
-
-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
-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. Note that single precision FFTs have only
-been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
-
-When using -DFFT_SINGLE with FFTW3 or FFTW2, you need to build FFTW
-with support for single-precision, as explained above. For FFTW3 you
-also need to include -lfftw3f with the FFT_LIB setting, in addition to
--lfftw3. For FFTW2, you also need to specify -DFFT_SIZE with the
-FFT_INC setting and -lsfftw with the FFT_LIB setting (in place of
--lfftw). Similarly, if FFTW2 has been pre-installed with an explicit
-double-precision library (libdfftw.a and not the default libfftw.a),
-then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify
--ldfftw to use double-precision FFTs.
-
-Step 7 :h5
-
-The 3 JPG variables allow you to specify a JPEG and/or PNG library
-which LAMMPS uses when writing out JPEG or PNG files via the "dump
-image"_dump_image.html command. These can be left blank if you do not
-use the -DLAMMPS_JPEG or -DLAMMPS_PNG switches discussed above in Step
-4, since in that case JPEG/PNG output will be disabled.
-
-A standard JPEG library usually goes by the name libjpeg.a or
-libjpeg.so and has an associated header file jpeglib.h. Whichever
-JPEG library you have on your platform, you'll need to set the
-appropriate JPG_INC, JPG_PATH, and JPG_LIB variables, so that the
-compiler and linker can find it.
-
-A standard PNG library usually goes by the name libpng.a or libpng.so
-and has an associated header file png.h. Whichever PNG library you
-have on your platform, you'll need to set the appropriate JPG_INC,
-JPG_PATH, and JPG_LIB variables, so that the compiler and linker can
-find it.
-
-As before, if these header and library files are in the usual place on
-your machine, you may not need to set these variables.
-
-Step 8 :h5
-
-Note that by default only a few of LAMMPS optional packages are
-installed. To build LAMMPS with optional packages, see "this
-section"_#start_3 below, before proceeding to Step 9.
-
-Step 9 :h5
-
-That's it. Once you have a correct Makefile.foo, and you have
-pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
-to do from the src directory is type something like this:
-
-make foo
-make -j N foo
-gmake foo
-gmake -j N foo :pre
-
-The -j or -j N switches perform a parallel build which can be much
-faster, depending on how many cores your compilation machine has. N
-is the number of cores the build runs on.
-
-You should get the executable lmp_foo when the build is complete.
-
-:line
-
-Errors that can occur when making LAMMPS :h4 :link(start_2_3)
-
-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:
-
-(1) If the make command breaks immediately with errors that indicate
-it can't find files with a "*" in their names, this can be because
-your machine's native make doesn't support wildcard expansion in a
-makefile. Try gmake instead of make. If that doesn't work, try using
-a -f switch with your make command to use a pre-generated
-Makefile.list which explicitly lists all the needed files, e.g.
-
-make makelist
-make -f Makefile.list linux
-gmake -f Makefile.list mac :pre
-
-The first "make" command will create a current Makefile.list with all
-the file names in your src dir. The 2nd "make" command (make or
-gmake) will use it to build LAMMPS. Note that you should
-include/exclude any desired optional packages before using the "make
-makelist" command.
-
-(2) If you get an error that says something like 'identifier "atoll"
-is undefined', then your machine does not support "long long"
-integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
-above in Step 4.
-
-:line
-
-Additional build tips :h4,link(start_2_4)
-
-Building LAMMPS for multiple platforms. :h5
-
-You can make LAMMPS for multiple platforms from the same src
-directory. Each target creates its own object sub-directory called
-Obj_target where it stores the system-specific *.o files.
-
-Cleaning up. :h5
-
-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 :h5
-
-As explained above, any of these 3 settings can be specified on the
-LMP_INC line in your low-level src/MAKE/Makefile.foo.
-
-The default is -DLAMMPS_SMALLBIG which allows for systems with up to
-2^63 atoms and 2^63 timesteps (about 9e18). The atom limit is for
-atomic systems which do not store bond topology info and thus do not
-require atom IDs. If you use atom IDs for atomic systems (which is
-the default) or if you use a molecular model, which stores bond
-topology info and thus requires atom IDs, the limit is 2^31 atoms
-(about 2 billion). This is because the IDs are stored in 32-bit
-integers.
-
-Likewise, with this setting, the 3 image flags for each atom (see the
-"dump"_dump.html doc page for a discussion) are stored in a 32-bit
-integer, which means the atoms can only wrap around a periodic box (in
-each dimension) at most 512 times. If atoms move through the periodic
-box more than this many times, the image flags will "roll over",
-e.g. from 511 to -512, which can cause diagnostics like the
-mean-squared displacement, as calculated by the "compute
-msd"_compute_msd.html command, to be faulty.
-
-To allow for larger atomic systems with atom IDs or larger molecular
-systems or larger image flags, compile with -DLAMMPS_BIGBIG. This
-stores atom IDs and image flags in 64-bit integers. This enables
-atomic or molecular systems with atom IDS of up to 2^63 atoms (about
-9e18). And image flags will not "roll over" until they reach 2^20 =
-1048576.
-
-If your system does not support 8-byte integers, you will need to
-compile with the -DLAMMPS_SMALLSMALL setting. This will restrict the
-total number of atoms (for atomic or molecular systems) and timesteps
-to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512.
-
-Note that in src/lmptype.h there are definitions of all these data
-types as well as the MPI data types associated with them. The MPI
-types need to be consistent with the associated C data types, or else
-LAMMPS will generate a run-time error. As far as we know, the
-settings defined in src/lmptype.h are portable and work on every
-current system.
-
-In all cases, the size of problem that can be run on a per-processor
-basis is limited by 4-byte integer storage to 2^31 atoms per processor
-(about 2 billion). This should not normally be a limitation since such
-a problem would have a huge per-processor memory footprint due to
-neighbor lists and would run very slowly in terms of CPU secs/timestep.
-
-:line
-
-Building for a Mac :h4,link(start_2_5)
-
-OS X is a derivative of BSD Unix, so it should just work. See the
-src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
-
-:line
-
-Building for Windows :h4,link(start_2_6)
-
-If you want to build a Windows version of LAMMPS, you can build it
-yourself, but it may require some effort. LAMMPS expects a Unix-like
-build environment for the default build procedure. This can be done
-using either Cygwin or MinGW; the latter also exists as a ready-to-use
-Linux-to-Windows cross-compiler in several Linux distributions. In
-these cases, you can do the installation after installing several
-unix-style commands like make, grep, sed and bash with some shell
-utilities.
-
-For Cygwin and the MinGW cross-compilers, suitable makefiles are
-provided in src/MAKE/MACHINES. When using other compilers, like
-Visual C++ or Intel compilers for Windows, you may have to implement
-your own build system. Due to differences between the Windows OS
-and Windows system libraries to Unix-like environments like Linux
-or MacOS, when compiling for Windows a few adjustments may be needed:
-
-Do [not] set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable)
-Add -lwsock32 -lpsapi to the linker flags (see LIB makefile variable)
-Try adding -static-libgcc or -static or both to the linker flags when your LAMMPS executable complains about missing .dll files :ul
-
-Since none of the current LAMMPS core developers has significant
-experience building executables on Windows, we are happy to distribute
-contributed instructions and modifications to improve the situation,
-but we cannot provide support for those.
-
-With the so-called "Anniversary Update" to Windows 10, there is a
-Ubuntu Linux subsystem available for Windows, that can be installed
-and then used to compile/install LAMMPS as if you are running on a
-Ubuntu Linux system instead of Windows.
-
-As an alternative, you can download pre-compiled installer packages from
-"packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html.
-These executables are built with most optional packages included and the
-download includes documentation, potential files, some tools and many
-examples, but no source code.
-
-:line
-
-2.3 Making LAMMPS with optional packages :h3,link(start_3)
-
-This section has the following sub-sections:
-
-2.3.1 "Package basics"_#start_3_1
-2.3.2 "Including/excluding packages"_#start_3_2
-2.3.3 "Packages that require extra libraries"_#start_3_3 :all(b)
-
-:line
-
-Package basics: :h4,link(start_3_1)
-
-The source code for LAMMPS is structured as a set of core files which
-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.
-
-The "Packages"_Packages.html doc pages has details about all the
-packages, which come in two flavors: [standard] and [user]
-packages. It also has specific instructions for building LAMMPS with
-any package which requires an extra library. General instructions are
-below.
-
-You can see the list of all packages by typing "make package" from
-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
-type
-
-lmp_machine -h :pre
-
-to run your executable with the optional "-h command-line
-switch"_#start_6 for "help", which will list the styles and commands
-known to your executable, and immediately exit.
-
-:line
-
-Including/excluding packages :h4,link(start_3_2)
-
-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-user-omp
-make mpi :pre
-
-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.
-
-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 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 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-installed" or "make pi" will list which packages are
-currently installed, without listing the status of packages that are not
-installed.
-
-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.
-
-Typing "make package-overwrite" will overwrite files in the package
-sub-directories with src files.
-
-Typing "make package-diff" lists all differences between these files.
-
-Again, just type "make package" to see all of the package-related make
-options.
-
-:line
-
-Packages that require extra libraries :h4,link(start_3_3)
-
-A few of the standard and user packages require extra libraries. See
-the "Packages"_Packages.html doc pages for two tables of packages
-which indicate which ones require libraries. For each such package,
-the Section 4 doc page gives details on how to build the extra
-library, including how to download it if necessary. The basic ideas
-are summarized here.
-
-[System libraries:]
-
-Packages in the standard and user tables of the
-"Packages"_Packages.html doc pages with a "sys" in the last column
-link to system libraries that typically already exist on your machine.
-E.g. the python package links to a system Python library. If your
-machine does not have the required library, you will have to download
-and install it on your machine, in either the system or user space.
-
-[Internal libraries:]
-
-Packages in the standard and user tables of the
-"Packages"_Packages.html doc pages with an "int" in the last column
-link to internal libraries whose source code is included with LAMMPS,
-in the lib/name directory where name is the package name. You must
-first build the library in that directory before building LAMMPS with
-that package installed. E.g. the gpu package links to a library you
-build in the lib/gpu dir. You can often do the build in one step by
-typing "make lib-name args=..." from the src dir, with appropriate
-arguments. You can leave off the args to see a help message. See the
-"Packages details"_Packages_details.html doc page for details for each
-package.
-
-[External libraries:]
-
-Packages in the standard and user tables of the
-"Packages"_Packages.html doc pages with an "ext" in the last column
-link to external libraries whose source code is not included with
-LAMMPS. You must first download and install the library before
-building LAMMPS with that package installed. E.g. the voronoi package
-links to the freely available "Voro++ library"_voro_home2. You can
-often do the download/build in one step by typing "make lib-name
-args=..." from the src dir, with appropriate arguments. You can leave
-off the args to see a help message. See the "Packages
-details"_Packages_details.html doc page for details for each package.
-
-:link(voro_home2,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 on the "Packages
-details"_Packages_details.html doc page and 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 on the "Packages"_Packages.html doc pages. More
-info is given on the doc pages that describe each package in detail:
-
-"USER-INTEL package"_Speed_intel.html
-"GPU package"_Speed_gpu.html
-"KOKKOS package"_Speed_kokkos.html
-"USER-OMP package"_Speed_omp.html
-"OPT package"_Speed_opt.html :all(b)
-
-You can also use or examine the following machine Makefiles in
-src/MAKE/OPTIONS, which include the settings. Note that the
-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
-Makefile.kokkos_omp
-Makefile.kokkos_cuda_mpi
-Makefile.kokkos_phi
-Makefile.omp
-Makefile.opt :ul
-
-:line
-
-2.4 Building LAMMPS as a library :h3,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
-the "Howto couple"_Howto_couple.html doc page for more info on
-coupling LAMMPS to other codes. See the "Python"_Python.html doc page
-for more info on wrapping and running LAMMPS from Python.
-
-Static library :h4
-
-To build LAMMPS as a static library (*.a file on Linux), type
-
-make foo mode=lib :pre
-
-where foo is the machine name. This kind of library is typically used
-to statically link a driver application to LAMMPS, so that you can
-insure all dependencies are satisfied at compile time. This will use
-the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build
-will create the file liblammps_foo.a which another application can
-link to. It will also create a soft link liblammps.a, which will
-point to the most recently built static library.
-
-Shared library :h4
-
-To build LAMMPS as a shared library (*.so file on Linux), which can be
-dynamically loaded, e.g. from Python, type
-
-make foo mode=shlib :pre
-
-where foo is the machine name. This kind of library is required when
-wrapping LAMMPS with Python; see the "Python"_Python.html doc page for
-details. This will use the SHFLAGS and SHLIBFLAGS settings in
-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, which will point to the most recently built shared
-library. This is the file the Python wrapper loads by default.
-
-Note that for a shared library to be usable by a calling program, all
-the auxiliary libraries it depends on must also exist as shared
-libraries. This will be the case for libraries included with LAMMPS,
-such as the dummy MPI library in src/STUBS or any package libraries in
-lib/packages, since they are always built as shared libraries using
-the -fPIC switch. However, if a library like MPI or FFTW does not
-exist as a shared library, the shared library build will generate an
-error. This means you will need to install a shared library version
-of the auxiliary library. The build instructions for the library
-should tell you how to do this.
-
-Here is an example of such errors when the system FFTW or provided
-lib/colvars library have not been built as shared libraries:
-
-/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
-R_X86_64_32 against '.rodata' can not be used when making a shared
-object; recompile with -fPIC
-/usr/local/lib/libfftw3.a: could not read symbols: Bad value :pre
-
-/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
-relocation R_X86_64_32 against '__pthread_key_create' can not be used
-when making a shared object; recompile with -fPIC
-../../lib/colvars/libcolvars.a: error adding symbols: Bad value :pre
-
-As an example, here is how to build and install the "MPICH
-library"_mpich, a popular open-source version of MPI, distributed by
-Argonne National Labs, as a shared library in the default
-/usr/local/lib location:
-
-:link(mpich,http://www-unix.mcs.anl.gov/mpi)
-
-./configure --enable-shared
-make
-make install :pre
-
-You may need to use "sudo make install" in place of the last line if
-you do not have write privileges for /usr/local/lib. The end result
-should be the file /usr/local/lib/libmpich.so.
-
-[Additional requirement for using a shared library:] :h4
-
-The operating system finds shared libraries to load at run-time using
-the environment variable LD_LIBRARY_PATH. So you may wish to copy the
-file src/liblammps.so or src/liblammps_g++.so (for example) to a place
-the system can find it by default, such as /usr/local/lib, or you may
-wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
-current version of the shared library is always available to programs
-that use it.
-
-For the csh or tcsh shells, you would add something like this to your
-~/.cshrc file:
-
-setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
-
-Calling the LAMMPS library :h4
-
-Either flavor of library (static or shared) allows one or more LAMMPS
-objects to be instantiated from the calling program.
-
-When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
-namespace; you can safely use any of its classes and methods from
-within the calling code, as needed.
-
-When used from a C or Fortran program or a scripting language like
-Python, the library has a simple function-style interface, provided in
-src/library.cpp and src/library.h.
-
-See the sample codes in examples/COUPLE/simple for examples of C++ and
-C and Fortran codes that invoke LAMMPS thru its library interface.
-There are other examples as well in the COUPLE directory which use
-coupling ideas discussed on the "Howto couple"_Howto_couple.html doc
-page. See the "Python"_Python.html doc page for a description of the
-Python wrapper provided with LAMMPS that operates through the LAMMPS
-library interface.
-
-The files src/library.cpp and library.h define the C-style API for
-using LAMMPS as a library. See the "Howto library"_Howto_library.html
-doc page for a description of the interface and how to extend it for
-your needs.
-
-:line
-
-2.5 Running LAMMPS :h3,link(start_5)
-
-By default, LAMMPS runs by reading commands from standard input. Thus
-if you run the LAMMPS executable by itself, e.g.
-
-lmp_linux :pre
-
-it will simply wait, expecting commands from the keyboard. Typically
-you should put commands in an input script and use I/O redirection,
-e.g.
-
-lmp_linux < in.file :pre
-
-For parallel environments this should also work. If it does not, use
-the '-in' command-line switch, e.g.
-
-lmp_linux -in in.file :pre
-
-The "Commands"_Commands.html doc page describes how input scripts are
-structured and what commands they contain.
-
-You can test LAMMPS on any of the sample inputs provided in the
-examples or bench directory. Input scripts are named in.* and sample
-outputs are named log.*.name.P where name is a machine and P is the
-number of processors it was run on.
-
-Here is how you might run a standard Lennard-Jones benchmark on a
-Linux box, using mpirun to launch a parallel job:
-
-cd src
-make linux
-cp lmp_linux ../bench
-cd ../bench
-mpirun -np 4 lmp_linux -in in.lj :pre
-
-See "this page"_bench for timings for this and the other benchmarks on
-various platforms. Note that some of the example scripts require
-LAMMPS to be built with one or more of its optional packages.
-
-:link(bench,http://lammps.sandia.gov/bench.html)
-
-:line
-
-On a Windows box, you can skip making LAMMPS and simply download an
-installer package from "here"_http://packages.lammps.org/windows.html
-
-For running the non-MPI executable, follow these steps:
-
-Get a command prompt by going to Start->Run... ,
-then typing "cmd". :ulb,l
-
-Move to the directory where you have your input, e.g. a copy of
-the [in.lj] input from the bench folder. (e.g. by typing: cd "Documents"). :l
-
-At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj]
-with the name of your LAMMPS input script. :l
-
-The serial executable includes support for multi-threading
-parallelization from the styles in the USER-OMP packages.
-
-To run with, e.g. 4 threads, type "lmp_serial -in in.lj -pk omp 4 -sf omp"
-:ule
-
-For the MPI version, which allows you to run LAMMPS under Windows with
-the more general message passing parallel library (LAMMPS has been
-designed from ground up to use MPI efficiently), follow these steps:
-
-Download and install a compatible MPI library binary package:
-for 32-bit Windows
-"mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
-and for 64-bit Windows
-"mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi
-:ulb,l
-
-The LAMMPS Windows installer packages will automatically adjust your
-path for the default location of this MPI package. After the installation
-of the MPICH2 software, it needs to be integrated into the system.
-For this you need to start a Command Prompt in {Administrator Mode}
-(right click on the icon and select it). Change into the MPICH2
-installation directory, then into the subdirectory [bin] and execute
-[smpd.exe -install]. Exit the command window.
-
-Get a new, regular command prompt by going to Start->Run... ,
-then typing "cmd". :l
-
-Move to the directory where you have your input file
-(e.g. by typing: cd "Documents"). :l
-
-Then type something like this:
-
-mpiexec -localonly 4 lmp_mpi -in in.lj :pre
-or
-
-mpiexec -np 4 lmp_mpi -in in.lj :pre
-
-replacing [in.lj] with the name of your LAMMPS input script. For the latter
-case, you may be prompted to enter your password. :l
-
-In this mode, output may not immediately show up on the screen, so if
-your input script takes a long time to execute, you may need to be
-patient before the output shows up. :l
-
-The parallel executable can also run on a single processor by typing
-something like:
-
-lmp_mpi -in in.lj :pre
-
-And the parallel executable also includes OpenMP multi-threading, which
-can be combined with MPI using something like:
-
-mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre
-
-:ule
-
-:line
-
-The screen output from LAMMPS is described in a section below. As it
-runs, LAMMPS also writes a log.lammps file with the same information.
-
-Note that this sequence of commands copies the LAMMPS executable
-(lmp_linux) to the directory with the input files. This may not be
-necessary, but some versions of MPI reset the working directory to
-where the executable is, rather than leave it as the directory where
-you launch mpirun from (if you launch lmp_linux on its own and not
-under mpirun). If that happens, LAMMPS will look for additional input
-files and write its output files to the executable directory, rather
-than your working directory, which is probably not what you want.
-
-If LAMMPS encounters errors in the input script or while running a
-simulation it will print an ERROR message and stop or a WARNING
-message and continue. See the "Errors"_Errors.html doc page for a
-discussion of the various kinds of errors LAMMPS can or can't detect,
-a list of all ERROR and WARNING messages, and what to do about them.
-
-LAMMPS can run a problem on any number of processors, including a
-single processor. In theory you should get identical answers on any
-number of processors and on any machine. In practice, numerical
-round-off can cause slight differences and eventual divergence of
-molecular dynamics phase space trajectories.
-
-LAMMPS can run as large a problem as will fit in the physical memory
-of one or more processors. If you run out of memory, you must run on
-more processors or setup a smaller problem.
-
-:line
-
-2.6 Command-line options :h3,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
-letter abbreviation can be used:
-
--e or -echo
--h or -help
--i or -in
--k or -kokkos
--l or -log
--nc or -nocite
--pk or -package
--p or -partition
--pl or -plog
--ps or -pscreen
--r or -restart
--ro or -reorder
--sc or -screen
--sf or -suffix
--v or -var :ul
-
-For example, lmp_ibm might be launched as follows:
-
-mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
-mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy :pre
-
-Here are the details on the options:
-
--echo style :pre
-
-Set the style of command echoing. The style can be {none} or {screen}
-or {log} or {both}. Depending on the style, each command read from
-the input script will be echoed to the screen and/or logfile. This
-can be useful to figure out which line of your script is causing an
-input error. The default value is {log}. The echo style can also be
-set by using the "echo"_echo.html command in the input script itself.
-
--help :pre
-
-Print a brief help summary and a list of options compiled into this
-executable for each LAMMPS style (atom_style, fix, compute,
-pair_style, bond_style, etc). This can tell you if the command you
-want to use was included via the appropriate package at compile time.
-LAMMPS will print the info and immediately exit if this switch is
-used.
-
--in file :pre
-
-Specify a file to use as an input script. This is an optional switch
-when running LAMMPS in one-partition mode. If it is not specified,
-LAMMPS reads its script from standard input, typically from a script
-via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should
-also work in parallel, but if it does not (in the unlikely case that
-an MPI implementation does not support it), then use the -in flag.
-Note that this is a required switch when running LAMMPS in
-multi-partition mode, since multiple processors cannot all read from
-stdin.
-
--kokkos on/off keyword/value ... :pre
-
-Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
-package. Even if LAMMPS is built with this package, as described
-above in "Section 2.3"_#start_3, this switch must be set to enable
-running with the KOKKOS-enabled styles the package provides. If the
-switch is not set (the default), LAMMPS will operate as if the KOKKOS
-package were not installed; i.e. you can run standard LAMMPS or with
-the GPU or USER-OMP packages, for testing or benchmarking purposes.
-
-Additional optional keyword/value pairs can be specified which
-determine how Kokkos will use the underlying hardware on your
-platform. These settings apply to each MPI task you launch via the
-"mpirun" or "mpiexec" command. You may choose to run one or more MPI
-tasks per physical node. Note that if you are running on a desktop
-machine, you typically have one physical node. On a cluster or
-supercomputer there may be dozens or 1000s of physical nodes.
-
-Either the full word or an abbreviation can be used for the keywords.
-Note that the keywords do not use a leading minus sign. I.e. the
-keyword is "t", not "-t". Also note that each of the keywords has a
-default setting. Example of when to use these options and what
-settings to use on different platforms is given on the "Speed
-kokkos"_Speed_kokkos.html doc page.
-
-d or device
-g or gpus
-t or threads
-n or numa :ul
-
-device Nd :pre
-
-This option is only relevant if you built LAMMPS with CUDA=yes, you
-have more than one GPU per node, and if you are running with only one
-MPI task per node. The Nd setting is the ID of the GPU on the node to
-run on. By default Nd = 0. If you have multiple GPUs per node, they
-have consecutive IDs numbered as 0,1,2,etc. This setting allows you
-to launch multiple independent jobs on the node, each with a single
-MPI task per node, and assign each job to run on a different GPU.
-
-gpus Ng Ns :pre
-
-This option is only relevant if you built LAMMPS with CUDA=yes, you
-have more than one GPU per node, and you are running with multiple MPI
-tasks per node (up to one per GPU). The Ng setting is how many GPUs
-you will use. The Ns setting is optional. If set, it is the ID of a
-GPU to skip when assigning MPI tasks to GPUs. This may be useful if
-your desktop system reserves one GPU to drive the screen and the rest
-are intended for computational work like running LAMMPS. By default
-Ng = 1 and Ns is not set.
-
-Depending on which flavor of MPI you are running, LAMMPS will look for
-one of these 3 environment variables
-
-SLURM_LOCALID (various MPI variants compiled with SLURM support)
-MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
-OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre
-
-which are initialized by the "srun", "mpirun" or "mpiexec" commands.
-The environment variable setting for each MPI rank is used to assign a
-unique GPU ID to the MPI task.
-
-threads Nt :pre
-
-This option assigns Nt number of threads to each MPI task for
-performing work when Kokkos is executing in OpenMP or pthreads mode.
-The default is Nt = 1, which essentially runs in MPI-only mode. If
-there are Np MPI tasks per physical node, you generally want Np*Nt =
-the number of physical cores per node, to use your available hardware
-optimally. This also sets the number of threads used by the host when
-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
-= 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
-its default value of 1. This is because letting a single process span
-multiple NUMA regions induces a significant amount of cross NUMA data
-traffic which is slow.
-
--log file :pre
-
-Specify a log file for LAMMPS to write status information to. In
-one-partition mode, if the switch is not used, LAMMPS writes to the
-file log.lammps. If this switch is used, LAMMPS writes to the
-specified file. In multi-partition mode, if the switch is not used, a
-log.lammps file is created with hi-level status information. Each
-partition also writes to a log.lammps.N file where N is the partition
-ID. If the switch is specified in multi-partition mode, the hi-level
-logfile is named "file" and each partition also logs information to a
-file.N. For both one-partition and multi-partition mode, if the
-specified file is "none", then no log files are created. Using a
-"log"_log.html command in the input script will override this setting.
-Option -plog will override the name of the partition log files file.N.
-
--nocite :pre
-
-Disable writing the log.cite file which is normally written to list
-references for specific cite-able features used during a LAMMPS run.
-See the "citation page"_http://lammps.sandia.gov/cite.html for more
-details.
-
--package style args .... :pre
-
-Invoke the "package"_package.html command with style and args. The
-syntax is the same as if the command appeared at the top of the input
-script. For example "-package gpu 2" or "-pk gpu 2" is the same as
-"package gpu 2"_package.html in the input script. The possible styles
-and args are documented on the "package"_package.html doc page. This
-switch can be used multiple times, e.g. to set options for the
-USER-INTEL and USER-OMP packages which can be used together.
-
-Along with the "-suffix" command-line switch, this is a convenient
-mechanism for invoking accelerator packages and their options without
-having to edit an input script.
-
--partition 8x2 4 5 ... :pre
-
-Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
-processors and this switch is not used, LAMMPS runs in one partition,
-i.e. all P processors run a single simulation. If this switch is
-used, the P processors are split into separate partitions and each
-partition runs its own simulation. The arguments to the switch
-specify the number of processors in each partition. Arguments of the
-form MxN mean M partitions, each with N processors. Arguments of the
-form N mean a single partition with N processors. The sum of
-processors in all partitions must equal P. Thus the command
-"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
-processors.
-
-Running with multiple partitions can be useful for running
-"multi-replica simulations"_Howto_replica.html, where each replica
-runs on on one or a few processors. Note that with MPI installed on a
-machine (e.g. your desktop), you can run on more (virtual) processors
-than you have physical processors.
-
-To run multiple independent simulations from one input script, using
-multiple partitions, see the "Howto multiple"_Howto_multiple.html doc
-page. World- and universe-style "variables"_variable.html are useful
-in this context.
-
--plog file :pre
-
-Specify the base name for the partition log files, so partition N
-writes log information to file.N. If file is none, then no partition
-log files are created. This overrides the filename specified in the
--log command-line option. This option is useful when working with
-large numbers of partitions, allowing the partition log files to be
-suppressed (-plog none) or placed in a sub-directory (-plog
-replica_files/log.lammps) If this option is not used the log file for
-partition N is log.lammps.N or whatever is specified by the -log
-command-line option.
-
--pscreen file :pre
-
-Specify the base name for the partition screen file, so partition N
-writes screen information to file.N. If file is none, then no
-partition screen files are created. This overrides the filename
-specified in the -screen command-line option. This option is useful
-when working with large numbers of partitions, allowing the partition
-screen files to be suppressed (-pscreen none) or placed in a
-sub-directory (-pscreen replica_files/screen). If this option is not
-used the screen file for partition N is screen.N or whatever is
-specified by the -screen command-line option.
-
--restart restartfile {remap} datafile keyword value ... :pre
-
-Convert the restart file into a data file and immediately exit. This
-is the same operation as if the following 2-line input script were
-run:
-
-read_restart restartfile {remap}
-write_data datafile keyword value ... :pre
-
-Note that the specified restartfile and datafile can have wild-card
-characters ("*",%") as described by the
-"read_restart"_read_restart.html and "write_data"_write_data.html
-commands. But a filename such as file.* will need to be enclosed in
-quotes to avoid shell expansion of the "*" character.
-
-Note that following restartfile, the optional flag {remap} can be
-used. This has the same effect as adding it to the
-"read_restart"_read_restart.html command, as explained on its doc
-page. This is only useful if the reading of the restart file triggers
-an error that atoms have been lost. In that case, use of the remap
-flag should allow the data file to still be produced.
-
-Also note that following datafile, the same optional keyword/value
-pairs can be listed as used by the "write_data"_write_data.html
-command.
-
--reorder nth N
--reorder custom filename :pre
-
-Reorder the processors in the MPI communicator used to instantiate
-LAMMPS, in one of several ways. The original MPI communicator ranks
-all P processors from 0 to P-1. The mapping of these ranks to
-physical processors is done by MPI before LAMMPS begins. It may be
-useful in some cases to alter the rank order. E.g. to insure that
-cores within each node are ranked in a desired order. Or when using
-the "run_style verlet/split"_run_style.html command with 2 partitions
-to insure that a specific Kspace processor (in the 2nd partition) is
-matched up with a specific set of processors in the 1st partition.
-See the "Speed tips"_Speed_tips.html doc page for more details.
-
-If the keyword {nth} is used with a setting {N}, then it means every
-Nth processor will be moved to the end of the ranking. This is useful
-when using the "run_style verlet/split"_run_style.html command with 2
-partitions via the -partition command-line switch. The first set of
-processors will be in the first partition, the 2nd set in the 2nd
-partition. The -reorder command-line switch can alter this so that
-the 1st N procs in the 1st partition and one proc in the 2nd partition
-will be ordered consecutively, e.g. as the cores on one physical node.
-This can boost performance. For example, if you use "-reorder nth 4"
-and "-partition 9 3" and you are running on 12 processors, the
-processors will be reordered from
-
-0 1 2 3 4 5 6 7 8 9 10 11 :pre
-
-to
-
-0 1 2 4 5 6 8 9 10 3 7 11 :pre
-
-so that the processors in each partition will be
-
-0 1 2 4 5 6 8 9 10
-3 7 11 :pre
-
-See the "processors" command for how to insure processors from each
-partition could then be grouped optimally for quad-core nodes.
-
-If the keyword is {custom}, then a file that specifies a permutation
-of the processor ranks is also specified. The format of the reorder
-file is as follows. Any number of initial blank or comment lines
-(starting with a "#" character) can be present. These should be
-followed by P lines of the form:
-
-I J :pre
-
-where P is the number of processors LAMMPS was launched with. Note
-that if running in multi-partition mode (see the -partition switch
-above) P is the total number of processors in all partitions. The I
-and J values describe a permutation of the P processors. Every I and
-J should be values from 0 to P-1 inclusive. In the set of P I values,
-every proc ID should appear exactly once. Ditto for the set of P J
-values. A single I,J pairing means that the physical processor with
-rank I in the original MPI communicator will have rank J in the
-reordered communicator.
-
-Note that rank ordering can also be specified by many MPI
-implementations, either by environment variables that specify how to
-order physical processors, or by config files that specify what
-physical processors to assign to each MPI rank. The -reorder switch
-simply gives you a portable way to do this without relying on MPI
-itself. See the "processors out"_processors.html command for how
-to output info on the final assignment of physical processors to
-the LAMMPS simulation domain.
-
--screen file :pre
-
-Specify a file for LAMMPS to write its screen information to. In
-one-partition mode, if the switch is not used, LAMMPS writes to the
-screen. If this switch is used, LAMMPS writes to the specified file
-instead and you will see no screen output. In multi-partition mode,
-if the switch is not used, hi-level status information is written to
-the screen. Each partition also writes to a screen.N file where N is
-the partition ID. If the switch is specified in multi-partition mode,
-the hi-level screen dump is named "file" and each partition also
-writes screen information to a file.N. For both one-partition and
-multi-partition mode, if the specified file is "none", then no screen
-output is performed. Option -pscreen will override the name of the
-partition screen files file.N.
-
--suffix style args :pre
-
-Use variants of various styles if they exist. The specified style can
-be {cuda}, {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}. These
-refer to optional packages that LAMMPS can be built with, as described
-above in "Section 2.3"_#start_3. The "gpu" style corresponds to the
-GPU package, the "intel" style to the USER-INTEL package, the "kk"
-style to the KOKKOS package, the "opt" style to the OPT package, and
-the "omp" style to the USER-OMP package. The hybrid style is the only
-style that accepts arguments. It allows for two packages to be
-specified. The first package specified is the default and will be used
-if it is available. If no style is available for the first package,
-the style for the second package will be used if available. For
-example, "-suffix hybrid intel omp" will use styles from the
-USER-INTEL package if they are installed and available, but styles for
-the USER-OMP package otherwise.
-
-Along with the "-package" command-line switch, this is a convenient
-mechanism for invoking accelerator packages and their options without
-having to edit an input script.
-
-As an example, all of the packages provide a "pair_style
-lj/cut"_pair_lj.html variant, with style names lj/cut/gpu,
-lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A variant style
-can be specified explicitly in your input script, e.g. pair_style
-lj/cut/gpu. If the -suffix switch is used the specified suffix
-(gpu,intel,kk,omp,opt) is automatically appended whenever your input
-script command creates a new "atom"_atom_style.html,
-"pair"_pair_style.html, "fix"_fix.html, "compute"_compute.html, or
-"run"_run_style.html style. If the variant version does not exist,
-the standard version is created.
-
-For the GPU package, using this command-line switch also invokes the
-default GPU settings, as if the command "package gpu 1" were used at
-the top of your input script. These settings can be changed by using
-the "-package gpu" command-line switch or the "package
-gpu"_package.html command in your script.
-
-For the USER-INTEL package, using this command-line switch also
-invokes the default USER-INTEL settings, as if the command "package
-intel 1" were used at the top of your input script. These settings
-can be changed by using the "-package intel" command-line switch or
-the "package intel"_package.html command in your script. If the
-USER-OMP package is also installed, the hybrid style with "intel omp"
-arguments can be used to make the omp suffix a second choice, if a
-requested style is not available in the USER-INTEL package. It will
-also invoke the default USER-OMP settings, as if the command "package
-omp 0" were used at the top of your input script. These settings can
-be changed by using the "-package omp" command-line switch or the
-"package omp"_package.html command in your script.
-
-For the KOKKOS package, using this command-line switch also invokes
-the default KOKKOS settings, as if the command "package kokkos" were
-used at the top of your input script. These settings can be changed
-by using the "-package kokkos" command-line switch or the "package
-kokkos"_package.html command in your script.
-
-For the OMP package, using this command-line switch also invokes the
-default OMP settings, as if the command "package omp 0" were used at
-the top of your input script. These settings can be changed by using
-the "-package omp" command-line switch or the "package
-omp"_package.html command in your script.
-
-The "suffix"_suffix.html command can also be used within an input
-script to set a suffix, or to turn off or back on any suffix setting
-made via the command line.
-
--var name value1 value2 ... :pre
-
-Specify a variable that will be defined for substitution purposes when
-the input script is read. This switch can be used multiple times to
-define multiple variables. "Name" is the variable name which can be a
-single character (referenced as $x in the input script) or a full
-string (referenced as $\{abc\}). An "index-style
-variable"_variable.html will be created and populated with the
-subsequent values, e.g. a set of filenames. Using this command-line
-option is equivalent to putting the line "variable name index value1
-value2 ..." at the beginning of the input script. Defining an index
-variable as a command-line argument overrides any setting for the same
-index variable in the input script, since index variables cannot be
-re-defined. See the "variable"_variable.html command for more info on
-defining index and other kinds of variables and the "Commands
-parse"_Commands_parse.html page for more info on using variables in
-input scripts.
-
-NOTE: Currently, the command-line parser looks for arguments that
-start with "-" to indicate new switches. Thus you cannot specify
-multiple variable values if any of they start with a "-", e.g. a
-negative numeric value. It is OK if the first value1 starts with a
-"-", since it is automatically skipped.
-
-:line
-
-2.7 LAMMPS screen output :h3,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
-simulation. When the simulation is ready to begin, LAMMPS performs
-various initializations and prints the amount of memory (in MBytes per
-processor) that the simulation requires. It also prints details of
-the initial thermodynamic state of the system. During the run itself,
-thermodynamic information is printed periodically, every few
-timesteps. When the run concludes, LAMMPS prints the final
-thermodynamic state and a total run time for the simulation. It then
-appends statistics about the CPU time and storage requirements for the
-simulation. An example set of statistics is shown here:
-
-Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre
-
-Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
-97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
-
-MPI task timings breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.9808 | 2.0134 | 2.0318 | 1.4 | 71.60
-Bond | 0.0021894 | 0.0060319 | 0.010058 | 4.7 | 0.21
-Kspace | 0.3207 | 0.3366 | 0.36616 | 3.1 | 11.97
-Neigh | 0.28411 | 0.28464 | 0.28516 | 0.1 | 10.12
-Comm | 0.075732 | 0.077018 | 0.07883 | 0.4 | 2.74
-Output | 0.00030518 | 0.00042665 | 0.00078821 | 1.0 | 0.02
-Modify | 0.086606 | 0.086631 | 0.086668 | 0.0 | 3.08
-Other | | 0.007178 | | | 0.26 :pre
-
-Nlocal: 501 ave 508 max 490 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-Nghost: 6586.25 ave 6628 max 6548 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Neighs: 177007 ave 180562 max 170212 min
-Histogram: 1 0 0 0 0 0 0 1 1 1 :pre
-
-Total # of neighbors = 708028
-Ave neighs/atom = 353.307
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 26
-Dangerous builds = 0 :pre
-
-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
-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.
-
-The MPI task section gives the breakdown of the CPU run time (in
-seconds) into major categories:
-
-{Pair} stands for all non-bonded force computation
-{Bond} stands for bonded interactions: bonds, angles, dihedrals, impropers
-{Kspace} stands for reciprocal space interactions: Ewald, PPPM, MSM
-{Neigh} stands for neighbor list construction
-{Comm} stands for communicating atoms and their properties
-{Output} stands for writing dumps and thermo output
-{Modify} stands for fixes and computes called by them
-{Other} is the remaining time :ul
-
-For each category, there is a breakdown of the least, average and most
-amount of wall time a processor spent on this section. Also you have the
-variation from the average time. Together these numbers allow to gauge
-the amount of load imbalance in this segment of the calculation. Ideally
-the difference between minimum, maximum and average is small and thus
-the variation from the average close to zero. The final column shows
-the percentage of the total loop time is spent in this section.
-
-When using the "timer full"_timer.html setting, an additional column
-is present that also prints the CPU utilization in percent. In
-addition, when using {timer full} and the "package omp"_package.html
-command are active, a similar timing summary of time spent in threaded
-regions to monitor thread utilization and load balance is provided. A
-new entry is the {Reduce} section, which lists the time spent in
-reducing the per-thread data elements to the storage for non-threaded
-computation. These thread timings are taking from the first MPI rank
-only and and thus, as the breakdown for MPI tasks can change from MPI
-rank to MPI rank, this breakdown can be very different for individual
-ranks. Here is an example output for this section:
-
-Thread timings breakdown (MPI rank 0):
-Total threaded time 0.6846 / 90.6%
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18
-Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68
-Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89
-Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70
-Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55 :pre
-
-The third section lists the number of owned atoms (Nlocal), ghost atoms
-(Nghost), and pair-wise neighbors stored per processor. The max and min
-values give the spread of these values across processors with a 10-bin
-histogram showing the distribution. The total number of histogram counts
-is equal to the number of processors.
-
-The last section gives aggregate statistics for pair-wise neighbors
-and special neighbors that LAMMPS keeps track of (see the
-"special_bonds"_special_bonds.html command). The number of times
-neighbor lists were rebuilt during the run is given as well as the
-number of potentially "dangerous" rebuilds. If atom movement
-triggered neighbor list rebuilding (see the
-"neigh_modify"_neigh_modify.html command), then dangerous
-reneighborings are those that were triggered on the first timestep
-atom movement was checked for. If this count is non-zero you may wish
-to reduce the delay factor to insure no force interactions are missed
-by atoms moving beyond the neighbor skin distance before a rebuild
-takes place.
-
-If an energy minimization was performed via the
-"minimize"_minimize.html command, additional information is printed,
-e.g.
-
-Minimization stats:
- Stopping criterion = linesearch alpha is zero
- Energy initial, next-to-last, final =
- -6372.3765206 -8328.46998942 -8328.46998942
- Force two-norm initial, final = 1059.36 5.36874
- Force max component initial, final = 58.6026 1.46872
- Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
- Iterations, force evaluations = 701 1516 :pre
-
-The first line prints the criterion that determined the minimization
-to be completed. The third line lists the initial and final energy,
-as well as the energy on the next-to-last iteration. The next 2 lines
-give a measure of the gradient of the energy (force on all atoms).
-The 2-norm is the "length" of this force vector; the inf-norm is the
-largest component. Then some information about the line search and
-statistics on how many iterations and force-evaluations the minimizer
-required. Multiple force evaluations are typically done at each
-iteration to perform a 1d line minimization in the search direction.
-
-If a "kspace_style"_kspace_style.html long-range Coulombics solve was
-performed during the run (PPPM, Ewald), then additional information is
-printed, e.g.
-
-FFT time (% of Kspce) = 0.200313 (8.34477)
-FFT Gflps 3d 1d-only = 2.31074 9.19989 :pre
-
-The first line gives the time spent doing 3d FFTs (4 per timestep) and
-the fraction it represents of the total KSpace time (listed above).
-Each 3d FFT requires computation (3 sets of 1d FFTs) and communication
-(transposes). The total flops performed is 5Nlog_2(N), where N is the
-number of points in the 3d grid. The FFTs are timed with and without
-the communication and a Gflop rate is computed. The 3d rate is with
-communication; the 1d rate is without (just the 1d FFTs). Thus you
-can estimate what fraction of your FFT time was spent in
-communication, roughly 75% in the example above.
-
-:line
-
-2.8 Tips for users of previous LAMMPS versions :h3,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
-on the "History page"_http://lammps.sandia.gov/history.html of the
-LAMMPS website. The F90 and F77 versions (2001 and 99) are also
-freely distributed as open-source codes; check the "History
-page"_http://lammps.sandia.gov/history.html of the LAMMPS website for
-info about those versions. The 99 and 2001 versions are no longer
-under active development; they do not have all the features of C++
-LAMMPS.
-
-If you are a previous user of LAMMPS 2001, these are the most
-significant changes you will notice in C++ LAMMPS:
-
-(1) The names and arguments of many input script commands have
-changed. All commands are now a single word (e.g. read_data instead
-of read data).
-
-(2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS,
-but you may need to specify the relevant commands in different ways.
-
-(3) The format of the data file can be streamlined for some problems.
-See the "read_data"_read_data.html command for details. The data file
-section "Nonbond Coeff" has been renamed to "Pair Coeff" in C++ LAMMPS.
-
-(4) Binary restart files written by LAMMPS 2001 cannot be read by C++
-LAMMPS with a "read_restart"_read_restart.html command. This is
-because they were output by F90 which writes in a different binary
-format than C or C++ writes or reads. Use the {restart2data} tool
-provided with LAMMPS 2001 to convert the 2001 restart file to a text
-data file. Then edit the data file as necessary before using the C++
-LAMMPS "read_data"_read_data.html command to read it in.
-
-(5) There are numerous small numerical changes in C++ LAMMPS that mean
-you will not get identical answers when comparing to a 2001 run.
-However, your initial thermodynamic energy and MD trajectory should be
-close if you have setup the problem for both codes the same.
diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt
index 091657082ae75a48d53c433a8fd98428ba6180ff..7eac11ffa5ce39cf92a5786908ed4d337bcf947a 100644
--- a/doc/src/Speed.txt
+++ b/doc/src/Speed.txt
@@ -31,15 +31,18 @@ hardware platforms.
<!-- RST
.. toctree::
+ :maxdepth: 1
Speed_bench
Speed_measure
.. toctree::
+ :maxdepth: 1
Speed_tips
.. toctree::
+ :maxdepth: 1
Speed_packages
Speed_compare
diff --git a/doc/src/Speed_gpu.txt b/doc/src/Speed_gpu.txt
index ab8ec7e9d164b64c269e729e77936cd92fd6dfc0..3ae4639dc2391b492410a450c8f9b3ad56402684 100644
--- a/doc/src/Speed_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -43,89 +43,22 @@ same functionality can eventually be supported on a variety of GPU
hardware. :l
:ule
-Here is a quick overview of how to enable and use the GPU package:
-
-build the library in lib/gpu for your GPU hardware with the desired precision settings
-install the GPU package and build LAMMPS as usual
-use the mpirun command to set the number of MPI tasks/node which determines the number of MPI tasks/GPU
-specify the # of GPUs per node
-use GPU styles in your input script :ul
-
-The latter two steps can be done using the "-pk gpu" and "-sf gpu"
-"command-line switches"_Section_start.html#start_6 respectively. Or
-the effect of the "-pk" or "-sf" switches can be duplicated by adding
-the "package gpu"_package.html or "suffix gpu"_suffix.html commands
-respectively to your input script.
-
[Required hardware/software:]
To use this package, you currently need to have an NVIDIA GPU and
install the NVIDIA CUDA software on your system:
-Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information
-Go to http://www.nvidia.com/object/cuda_get.html
-Install a driver and toolkit appropriate for your system (SDK is not necessary)
-Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to list supported devices and properties :ul
+Check if you have an NVIDIA GPU: cat
+/proc/driver/nvidia/gpus/0/information Go to
+http://www.nvidia.com/object/cuda_get.html Install a driver and
+toolkit appropriate for your system (SDK is not necessary) Run
+lammps/lib/gpu/nvc_get_devices (after building the GPU library, see
+below) to list supported devices and properties :ul
[Building LAMMPS with the GPU package:]
-This requires two steps (a,b): build the GPU library, then build
-LAMMPS with the GPU package. You can do both these steps in one line
-as described on the "Packages details"_Packages_details.html#GPU doc
-page.
-
-Or you can follow these two (a,b) steps:
-
-(a) Build the GPU library
-
-The GPU library is in lammps/lib/gpu. Select a Makefile.machine (in
-lib/gpu) appropriate for your system. You should pay special
-attention to 3 settings in this makefile.
-
-CUDA_HOME = needs to be where NVIDIA CUDA software is installed on your system
-CUDA_ARCH = needs to be appropriate to your GPUs
-CUDA_PREC = precision (double, mixed, single) you desire :ul
-
-See lib/gpu/Makefile.linux.double for examples of the ARCH settings
-for different GPU choices, e.g. Fermi vs Kepler. It also lists the
-possible precision settings:
-
-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 :pre
-
-The last setting is the mixed mode referred to above. Note that your
-GPU must support double precision to use either the 2nd or 3rd of
-these settings.
-
-To build the library, type:
-
-make -f Makefile.machine :pre
-
-If successful, it will produce the files libgpu.a and Makefile.lammps.
-
-The latter file has 3 settings that need to be appropriate for the
-paths and settings for the CUDA system software on your machine.
-Makefile.lammps is a copy of the file specified by the EXTRAMAKE
-setting in Makefile.machine. You can change EXTRAMAKE or create your
-own Makefile.lammps.machine if needed.
-
-Note that to change the precision of the GPU library, you need to
-re-build the entire library. Do a "clean" first, e.g. "make -f
-Makefile.linux clean", followed by the make command above.
-
-(b) Build LAMMPS with the GPU package
-
-cd lammps/src
-make yes-gpu
-make machine :pre
-
-No additional compile/link flags are needed in Makefile.machine.
-
-Note that if you change the GPU library precision (discussed above)
-and rebuild the GPU library, then you also need to re-install the GPU
-package and re-build LAMMPS, so that all affected files are
-re-compiled and linked to the new GPU library.
+See the "Build extras"_Build_extras.html#gpu doc page for
+instructions.
[Run with the GPU package from the command line:]
@@ -143,10 +76,10 @@ automatically if you create more MPI tasks/node than there are
GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
shared by 4 MPI tasks.
-Use the "-sf gpu" "command-line switch"_Section_start.html#start_6,
-which will automatically append "gpu" to styles that support it. Use
-the "-pk gpu Ng" "command-line switch"_Section_start.html#start_6 to
-set Ng = # of GPUs/node to use.
+Use the "-sf gpu" "command-line switch"_Run_options.html, which will
+automatically append "gpu" to styles that support it. Use the "-pk
+gpu Ng" "command-line switch"_Run_options.html to set Ng = # of
+GPUs/node to use.
lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU
mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
@@ -180,8 +113,8 @@ pair_style lj/cut/gpu 2.5 :pre
You must also use the "package gpu"_package.html command to enable the
GPU package, unless the "-sf gpu" or "-pk gpu" "command-line
-switches"_Section_start.html#start_6 were used. It specifies the
-number of GPUs/node to use, as well as other options.
+switches"_Run_options.html were used. It specifies the number of
+GPUs/node to use, as well as other options.
[Speed-ups to expect:]
diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt
index 20f49672e02849e2f0b544604bc6a88049eb0f05..ef876a7d42108a3ae8aad4f6c2f65670f65e0223 100644
--- a/doc/src/Speed_intel.txt
+++ b/doc/src/Speed_intel.txt
@@ -203,16 +203,12 @@ cat /proc/cpuinfo :pre
[Building LAMMPS with the USER-INTEL package:]
-NOTE: See the src/USER-INTEL/README file for additional flags that
-might be needed for best performance on Intel server processors
-code-named "Skylake".
-
-The USER-INTEL package must be installed into the source directory:
-
-make yes-user-intel :pre
+See the "Build extras"_Build_extras.html#user-intel doc page for
+instructions. Some additional details are covered here.
-Several example Makefiles for building with the Intel compiler are
-included with LAMMPS in the src/MAKE/OPTIONS/ directory:
+For building with make, several example Makefiles for building with
+the Intel compiler are included with LAMMPS in the src/MAKE/OPTIONS/
+directory:
Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
Makefile.knl # Intel Compiler, Intel MPI, No Offload
@@ -221,20 +217,16 @@ Makefile.intel_cpu_openpmi # Intel Compiler, OpenMPI, No Offload
Makefile.intel_coprocessor # Intel Compiler, Intel MPI, Offload :pre
Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that
-it explicitly specifies that vectorization should be for Intel
-Xeon Phi x200 processors making it easier to cross-compile. For
-users with recent installations of Intel Parallel Studio, the
-process can be as simple as:
+it explicitly specifies that vectorization should be for Intel Xeon
+Phi x200 processors making it easier to cross-compile. For users with
+recent installations of Intel Parallel Studio, the process can be as
+simple as:
make yes-user-intel
source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
# or psxevars.csh for C-shell
make intel_cpu_intelmpi :pre
-Alternatively this can be done as a single command with suitable make
-command invocations, as described on the "Packages
-details"_Packages_details.html#USER-INTEL doc page.
-
Note that if you build with support for a Phi coprocessor, the same
binary can be used on nodes with or without coprocessors installed.
However, if you do not have coprocessors on your system, building
@@ -253,6 +245,10 @@ required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other
recommended CCFLAG options for best performance are "-O2 -fno-alias
-ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div".
+NOTE: See the src/USER-INTEL/README file for additional flags that
+might be needed for best performance on Intel server processors
+code-named "Skylake".
+
NOTE: The vectorization and math capabilities can differ depending on
the CPU. For Intel compilers, the "-x" flag specifies the type of
processor for which to optimize. "-xHost" specifies that the compiler
@@ -306,31 +302,31 @@ Hyper-Threading technology disabled.
[Run with the USER-INTEL package from the command line:]
To enable USER-INTEL optimizations for all available styles used in
-the input script, the "-sf intel"
-"command-line switch"_Section_start.html#start_6 can be used without
-any requirement for editing the input script. This switch will
-automatically append "intel" to styles that support it. It also
-invokes a default command: "package intel 1"_package.html. This
-package command is used to set options for the USER-INTEL package.
-The default package command will specify that USER-INTEL calculations
-are performed in mixed precision, that the number of OpenMP threads
-is specified by the OMP_NUM_THREADS environment variable, and that
-if coprocessors are present and the binary was built with offload
-support, that 1 coprocessor per node will be used with automatic
-balancing of work between the CPU and the coprocessor.
+the input script, the "-sf intel" "command-line
+switch"_Run_options.html can be used without any requirement for
+editing the input script. This switch will automatically append
+"intel" to styles that support it. It also invokes a default command:
+"package intel 1"_package.html. This package command is used to set
+options for the USER-INTEL package. The default package command will
+specify that USER-INTEL calculations are performed in mixed precision,
+that the number of OpenMP threads is specified by the OMP_NUM_THREADS
+environment variable, and that if coprocessors are present and the
+binary was built with offload support, that 1 coprocessor per node
+will be used with automatic balancing of work between the CPU and the
+coprocessor.
You can specify different options for the USER-INTEL package by using
-the "-pk intel Nphi" "command-line switch"_Section_start.html#start_6
-with keyword/value pairs as specified in the documentation. Here,
-Nphi = # of Xeon Phi coprocessors/node (ignored without offload
+the "-pk intel Nphi" "command-line switch"_Run_options.html with
+keyword/value pairs as specified in the documentation. Here, Nphi = #
+of Xeon Phi coprocessors/node (ignored without offload
support). Common options to the USER-INTEL package include {omp} to
override any OMP_NUM_THREADS setting and specify the number of OpenMP
-threads, {mode} to set the floating-point precision mode, and
-{lrt} to enable Long-Range Thread mode as described below. See the
-"package intel"_package.html command for details, including the
-default values used for all its options if not specified, and how to
-set the number of OpenMP threads via the OMP_NUM_THREADS environment
-variable if desired.
+threads, {mode} to set the floating-point precision mode, and {lrt} to
+enable Long-Range Thread mode as described below. See the "package
+intel"_package.html command for details, including the default values
+used for all its options if not specified, and how to set the number
+of OpenMP threads via the OMP_NUM_THREADS environment variable if
+desired.
Examples (see documentation for your MPI/Machine for differences in
launching MPI applications):
@@ -390,19 +386,18 @@ lj/cut or when using LRT mode on processors supporting AVX-512.
Not all styles are supported in the USER-INTEL package. You can mix
the USER-INTEL package with styles from the "OPT"_Speed_opt.html
-package or the "USER-OMP package"_Speed_omp.html. Of course,
-this requires that these packages were installed at build time. This
-can performed automatically by using "-sf hybrid intel opt" or
-"-sf hybrid intel omp" command-line options. Alternatively, the "opt"
-and "omp" suffixes can be appended manually in the input script. For
-the latter, the "package omp"_package.html command must be in the
-input script or the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_6 must be used where Nt is the
-number of OpenMP threads. The number of OpenMP threads should not be
-set differently for the different packages. Note that the "suffix
-hybrid intel omp"_suffix.html command can also be used within the
-input script to automatically append the "omp" suffix to styles when
-USER-INTEL styles are not available.
+package or the "USER-OMP package"_Speed_omp.html. Of course, this
+requires that these packages were installed at build time. This can
+performed automatically by using "-sf hybrid intel opt" or "-sf hybrid
+intel omp" command-line options. Alternatively, the "opt" and "omp"
+suffixes can be appended manually in the input script. For the latter,
+the "package omp"_package.html command must be in the input script or
+the "-pk omp Nt" "command-line switch"_Run_options.html must be used
+where Nt is the number of OpenMP threads. The number of OpenMP threads
+should not be set differently for the different packages. Note that
+the "suffix hybrid intel omp"_suffix.html command can also be used
+within the input script to automatically append the "omp" suffix to
+styles when USER-INTEL styles are not available.
NOTE: For simulations on higher node counts, add "processors * * *
grid numa"_processors.html" to the beginning of the input script for
@@ -496,8 +491,8 @@ sorting"_atom_modify.html is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists. All the
available coprocessor threads on each Phi will be divided among MPI
tasks, unless the {tptask} option of the "-pk intel" "command-line
-switch"_Section_start.html#start_6 is used to limit the coprocessor
-threads per MPI task.
+switch"_Run_options.html is used to limit the coprocessor threads per
+MPI task.
[Restrictions:]
diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt
index 597ed73e5316e6eb57d53d227798eeab2cb363ca..eb787df5d6ac8a1e97136453a8eda62f754bdc0b 100644
--- a/doc/src/Speed_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -37,100 +37,29 @@ task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
GPUs). You choose the mode at build time to produce an executable
compatible with specific hardware.
-[Building LAMMPS with the KOKKOS package:]
-
NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible
compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or
Clang 3.5.2 or later is required.
-The recommended method of building the KOKKOS package is to start with
-the provided Kokkos Makefiles in /src/MAKE/OPTIONS/. You may need to
-modify the KOKKOS_ARCH variable in the Makefile to match your specific
-hardware. For example:
-
-for Sandy Bridge CPUs, set KOKKOS_ARCH=SNB
-for Broadwell CPUs, set KOKKOS_ARCH=BWD
-for K80 GPUs, set KOKKOS_ARCH=Kepler37
-for P100 GPUs and Power8 CPUs, set KOKKOS_ARCH=Pascal60,Power8 :ul
-
-See the [Advanced Kokkos Options] section below for a listing of all
-KOKKOS_ARCH options.
-
-[Compile for CPU-only (MPI only, no threading):]
-
-use a C++11 compatible compiler and set KOKKOS_ARCH variable in
-/src/MAKE/OPTIONS/Makefile.kokkos_mpi_only as described above. Then do the
-following:
-
-cd lammps/src
-make yes-kokkos
-make kokkos_mpi_only :pre
-
-[Compile for CPU-only (MPI plus OpenMP threading):]
-
-NOTE: To build with Kokkos support for OpenMP threading, your compiler
-must support the OpenMP interface. You should have one or more
-multi-core CPUs so that multiple threads can be launched by each MPI
-task running on a CPU.
-
-Use a C++11 compatible compiler and set KOKKOS_ARCH variable in
-/src/MAKE/OPTIONS/Makefile.kokkos_omp as described above. Then do the
-following:
-
-cd lammps/src
-make yes-kokkos
-make kokkos_omp :pre
-
-[Compile for Intel KNL Xeon Phi (Intel Compiler, OpenMPI):]
-
-use a C++11 compatible compiler and do the following:
-
-cd lammps/src
-make yes-kokkos
-make kokkos_phi :pre
-
-[Compile for CPUs and GPUs (with OpenMPI or MPICH):]
-
NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA
software version 7.5 or later must be installed on your system. See
the discussion for the "GPU package"_Speed_gpu.html for details of how
to check and do this.
NOTE: Kokkos with CUDA currently implicitly assumes, that the MPI
-library is CUDA-aware and has support for GPU-direct. This is not always
-the case, especially when using pre-compiled MPI libraries provided by
-a Linux distribution. This is not a problem when using only a single
-GPU and a single MPI rank on a desktop. When running with multiple
-MPI ranks, you may see segmentation faults without GPU-direct support.
-These can be avoided by adding the flags '-pk kokkos gpu/direct off'
-to the LAMMPS command line or by using the command
-"package kokkos gpu/direct off"_package.html in the input file.
-
-Use a C++11 compatible compiler and set KOKKOS_ARCH variable in
-/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as
-described above. Then do the following:
-
-cd lammps/src
-make yes-kokkos
-make kokkos_cuda_mpi :pre
+library is CUDA-aware and has support for GPU-direct. This is not
+always the case, especially when using pre-compiled MPI libraries
+provided by a Linux distribution. This is not a problem when using
+only a single GPU and a single MPI rank on a desktop. When running
+with multiple MPI ranks, you may see segmentation faults without
+GPU-direct support. These can be avoided by adding the flags "-pk
+kokkos gpu/direct off"_Run_options.html to the LAMMPS command line or
+by using the command "package kokkos gpu/direct off"_package.html in
+the input file.
-[Alternative Methods of Compiling:]
-
-Alternatively, the KOKKOS package can be built by specifying Kokkos variables
-on the make command line. For example:
-
-make mpi KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=SNB # set the KOKKOS_DEVICES and KOKKOS_ARCH variable explicitly
-make kokkos_cuda_mpi KOKKOS_ARCH=Pascal60,Power8 # set the KOKKOS_ARCH variable explicitly :pre
-
-Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the make
-command line requires a GNU-compatible make command. Try "gmake" if
-your system's standard make complains.
+[Building LAMMPS with the KOKKOS package:]
-NOTE: If you build using make line variables and re-build LAMMPS twice
-with different KOKKOS options and the *same* target, then you *must*
-perform a "make clean-all" or "make clean-machine" before each
-build. This is to force all the KOKKOS-dependent files to be
-re-compiled with the new options.
+See the "Build extras"_Build_extras.html#kokkos doc page for instructions.
[Running LAMMPS with the KOKKOS package:]
@@ -152,12 +81,11 @@ mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI
mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk
-kokkos" "command-line switches"_Section_start.html#start_7 in your
-mpirun command. You must use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package. It
-takes additional arguments for hardware settings appropriate to your
-system. Those arguments are "documented
-here"_Section_start.html#start_7. For OpenMP use:
+kokkos" "command-line switches"_Run_options.html in your mpirun
+command. You must use the "-k on" "command-line
+switch"_Run_options.html to enable the KOKKOS package. It takes
+additional arguments for hardware settings appropriate to your system.
+For OpenMP use:
-k on t Nt :pre
@@ -172,11 +100,11 @@ command (with no additional arguments) which sets various KOKKOS
options to default values, as discussed on the "package"_package.html
command doc page.
-The "-sf kk" "command-line switch"_Section_start.html#start_7 will
-automatically append the "/kk" suffix to styles that support it. In
-this manner no modification to the input script is
-needed. Alternatively, one can run with the KOKKOS package by editing
-the input script as described below.
+The "-sf kk" "command-line switch"_Run_options.html will automatically
+append the "/kk" suffix to styles that support it. In this manner no
+modification to the input script is needed. Alternatively, one can run
+with the KOKKOS package by editing the input script as described
+below.
NOTE: The default for the "package kokkos"_package.html command is to
use "full" neighbor lists and set the Newton flag to "off" for both
@@ -184,10 +112,10 @@ pairwise and bonded interactions. However, when running on CPUs, it
will typically be faster to use "half" neighbor lists and set the
Newton flag to "on", just as is the case for non-accelerated pair
styles. It can also be faster to use non-threaded communication. Use
-the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html options. See its doc
-page for details and default settings. Experimenting with its options
-can provide a speed-up for specific calculations. For example:
+the "-pk kokkos" "command-line switch"_Run_options.html to change the
+default "package kokkos"_package.html options. See its doc page for
+details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre
@@ -247,10 +175,10 @@ pairwise and bonded interactions. When running on KNL, this will
typically be best for pair-wise potentials. For manybody potentials,
using "half" neighbor lists and setting the Newton flag to "on" may be
faster. It can also be faster to use non-threaded communication. Use
-the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html options. See its doc
-page for details and default settings. Experimenting with its options
-can provide a speed-up for specific calculations. For example:
+the "-pk kokkos" "command-line switch"_Run_options.html to change the
+default "package kokkos"_package.html options. See its doc page for
+details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj # Newton off, full neighbor list, non-threaded comm
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax # Newton on, half neighbor list, non-threaded comm :pre
@@ -265,15 +193,16 @@ supports.
[Running on GPUs:]
-Use the "-k" "command-line switch"_Section_start.html#start_7 to
+Use the "-k" "command-line switch"_Run_options.html to
specify the number of GPUs per node. Typically the -np setting of the
mpirun command should set the number of MPI tasks/node to be equal to
-the # of physical GPUs on the node. You can assign multiple MPI tasks
-to the same GPU with the KOKKOS package, but this is usually only
-faster if significant portions of the input script have not been
-ported to use Kokkos. Using CUDA MPS is recommended in this
+the number of physical GPUs on the node. You can assign multiple MPI
+tasks to the same GPU with the KOKKOS package, but this is usually
+only faster if significant portions of the input script have not
+been ported to use Kokkos. Using CUDA MPS is recommended in this
scenario. Using a CUDA-aware MPI library with support for GPU-direct
-is highly recommended. GPU-direct use can be avoided by using "-pk kokkos gpu/direct no".
+is highly recommended. GPU-direct use can be avoided by using
+"-pk kokkos gpu/direct no"_package.html.
As above for multi-core CPUs (and no GPU), if N is the number of
physical cores/node, then the number of MPI tasks/node should not
exceed N.
@@ -293,10 +222,10 @@ When running on Maxwell or Kepler GPUs, this will typically be
best. For Pascal GPUs, using "half" neighbor lists and setting the
Newton flag to "on" may be faster. For many pair styles, setting the
neighbor binsize equal to the ghost atom cutoff will give speedup.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7
-to change the default "package kokkos"_package.html options. See its
-doc page for details and default settings. Experimenting with its
-options can provide a speed-up for specific calculations. For example:
+Use the "-pk kokkos" "command-line switch"_Run_options.html to change
+the default "package kokkos"_package.html options. See its doc page
+for details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
@@ -327,10 +256,9 @@ kk"_suffix.html commands to your input script.
The discussion above for building LAMMPS with the KOKKOS package, the
mpirun/mpiexec command, and setting appropriate thread are the same.
-You must still use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package, and
-specify its additional arguments for hardware options appropriate to
-your system, as documented above.
+You must still use the "-k on" "command-line switch"_Run_options.html
+to enable the KOKKOS package, and specify its additional arguments for
+hardware options appropriate to your system, as documented above.
You can use the "suffix kk"_suffix.html command, or you can explicitly add a
"kk" suffix to individual styles in your input script, e.g.
@@ -339,7 +267,7 @@ pair_style lj/cut/kk 2.5 :pre
You only need to use the "package kokkos"_package.html command if you
wish to change any of its option defaults, as set by the "-k on"
-"command-line switch"_Section_start.html#start_7.
+"command-line switch"_Run_options.html.
[Using OpenMP threading and CUDA together (experimental):]
@@ -411,50 +339,18 @@ hardware.
[Advanced Kokkos options:]
There are other allowed options when building with the KOKKOS package.
-As above, they can be set either as variables on the make command line
-or in Makefile.machine. This is the full list of options, including
-those discussed above. Each takes a value shown below. The default
-value is listed, which is set in the /lib/kokkos/Makefile.kokkos file.
+As explained on the "Build extras"_Build_extras.html#kokkos doc page,
+they can be set either as variables on the make command line or in
+Makefile.machine, or they can be specified as CMake variables. Each
+takes a value shown below. The default value is listed, which is set
+in the lib/kokkos/Makefile.kokkos file.
-KOKKOS_DEVICES, values = {Serial}, {OpenMP}, {Pthreads}, {Cuda}, default = {OpenMP}
-KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {Pascal60}, {Pascal61}, {ARMv80}, {ARMv81}, {ARMv81}, {ARMv8-ThunderX}, {BGQ}, {Power7}, {Power8}, {Power9}, {KNL}, {BDW}, {SKX}, default = {none}
KOKKOS_DEBUG, values = {yes}, {no}, default = {no}
KOKKOS_USE_TPLS, values = {hwloc}, {librt}, {experimental_memkind}, default = {none}
KOKKOS_CXX_STANDARD, values = {c++11}, {c++1z}, default = {c++11}
KOKKOS_OPTIONS, values = {aggressive_vectorization}, {disable_profiling}, default = {none}
KOKKOS_CUDA_OPTIONS, values = {force_uvm}, {use_ldg}, {rdc}, {enable_lambda}, default = {enable_lambda} :ul
-KOKKOS_DEVICES sets the parallelization method used for Kokkos code
-(within LAMMPS). KOKKOS_DEVICES=Serial means that no threading will be used.
-KOKKOS_DEVICES=OpenMP means that OpenMP threading will be
-used. KOKKOS_DEVICES=Pthreads means that pthreads will be used.
-KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used.
-
-KOKKOS_ARCH enables compiler switches needed when compiling for a
-specific hardware:
-
-ARMv80 = ARMv8.0 Compatible CPU
-ARMv81 = ARMv8.1 Compatible CPU
-ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU
-SNB = Intel Sandy/Ivy Bridge CPUs
-HSW = Intel Haswell CPUs
-BDW = Intel Broadwell Xeon E-class CPUs
-SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
-KNC = Intel Knights Corner Xeon Phi
-KNL = Intel Knights Landing Xeon Phi
-Kepler30 = NVIDIA Kepler generation CC 3.0
-Kepler32 = NVIDIA Kepler generation CC 3.2
-Kepler35 = NVIDIA Kepler generation CC 3.5
-Kepler37 = NVIDIA Kepler generation CC 3.7
-Maxwell50 = NVIDIA Maxwell generation CC 5.0
-Maxwell52 = NVIDIA Maxwell generation CC 5.2
-Maxwell53 = NVIDIA Maxwell generation CC 5.3
-Pascal60 = NVIDIA Pascal generation CC 6.0
-Pascal61 = NVIDIA Pascal generation CC 6.1
-BGQ = IBM Blue Gene/Q CPUs
-Power8 = IBM POWER8 CPUs
-Power9 = IBM POWER9 CPUs :ul
-
KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt
index 78dc220088d3873b241aae6237b84b8426f03776..647ff71e36593f9a642c22360e74c36752e43e7d 100644
--- a/doc/src/Speed_measure.txt
+++ b/doc/src/Speed_measure.txt
@@ -21,8 +21,8 @@ typically no need to run for 1000s of timesteps to get accurate
timings; you can simply extrapolate from short runs.
For the set of runs, look at the timing data printed to the screen and
-log file at the end of each LAMMPS run. "This
-section"_Section_start.html#start_7 of the manual has an overview.
+log file at the end of each LAMMPS run. The
+"Run_output"_Run_output.html doc page gives an overview.
Running on one (or a few processors) should give a good estimate of
the serial performance and what portions of the timestep are taking
diff --git a/doc/src/Speed_omp.txt b/doc/src/Speed_omp.txt
index bcfc406902d0947e2c6d9e0426b2fe8d7406dda3..0abf54430ef042de4e04080cd741332cf5a7b85f 100644
--- a/doc/src/Speed_omp.txt
+++ b/doc/src/Speed_omp.txt
@@ -10,42 +10,32 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
USER-OMP package :h3
The USER-OMP package was developed by Axel Kohlmeyer at Temple
-University. It provides multi-threaded versions of most pair styles,
-nearly all bonded styles (bond, angle, dihedral, improper), several
-Kspace styles, and a few fix styles. The package currently uses the
-OpenMP interface for multi-threading.
-
-Here is a quick overview of how to use the USER-OMP package, assuming
-one or more 16-core nodes. More details follow.
-
-use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
-make yes-user-omp
-make mpi # build with USER-OMP package, if settings added to Makefile.mpi
-make omp # or Makefile.omp already has settings :pre
-
-lmp_mpi -sf omp -pk omp 16 < in.script # 1 MPI task, 16 threads
-mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
-mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
+University. It provides optimized and multi-threaded versions
+of many pair styles, nearly all bonded styles (bond, angle, dihedral,
+improper), several Kspace styles, and a few fix styles. It uses
+the OpenMP interface for multi-threading, but can also be compiled
+without OpenMP support, providing optimized serial styles in that case.
[Required hardware/software:]
-Your compiler must support the OpenMP interface. You should have one
-or more multi-core CPUs so that multiple threads can be launched by
-each MPI task running on a CPU.
+To enable multi-threading, your compiler must support the OpenMP interface.
+You should have one or more multi-core CPUs, as multiple threads can only be
+launched by each MPI task on the local node (using shared memory).
[Building LAMMPS with the USER-OMP package:]
-The lines above illustrate how to include/build with the USER-OMP
-package in two steps, using the "make" command. Or how to do it with
-one command as described on the "Packages
-details"_Packages_details.html#USER-OMP doc page.
-
-Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
-include "-fopenmp". Likewise, if you use an Intel compiler, the
-CCFLAGS setting must include "-restrict".
+See the "Build extras"_Build_extras.html#user-omp doc page for
+instructions.
[Run with the USER-OMP package from the command line:]
+These example asume one or more 16-core nodes.
+
+env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script # 1 MPI task, 16 threads according to OMP_NUM_THREADS
+lmp_mpi -sf omp -in in.script # 1 MPI task, no threads, optimized kernels
+mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
+mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
+
The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
@@ -57,19 +47,18 @@ threads/task should not exceed the physical number of cores (on a
node), otherwise performance will suffer.
As in the lines above, use the "-sf omp" "command-line
-switch"_Section_start.html#start_6, which will automatically append
-"omp" to styles that support it. The "-sf omp" switch also issues a
-default "package omp 0"_package.html command, which will set the
-number of threads per MPI task via the OMP_NUM_THREADS environment
-variable.
+switch"_Run_options.html, which will automatically append "omp" to
+styles that support it. The "-sf omp" switch also issues a default
+"package omp 0"_package.html command, which will set the number of
+threads per MPI task via the OMP_NUM_THREADS environment variable.
You can also use the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_6, to explicitly set Nt = # of OpenMP
-threads per MPI task to use, as well as additional options. Its
-syntax is the same as the "package omp"_package.html command whose doc
-page gives details, including the default values used if it is not
-specified. It also gives more details on how to set the number of
-threads via the OMP_NUM_THREADS environment variable.
+switch"_Run_options.html, to explicitly set Nt = # of OpenMP threads
+per MPI task to use, as well as additional options. Its syntax is the
+same as the "package omp"_package.html command whose doc page gives
+details, including the default values used if it is not specified. It
+also gives more details on how to set the number of threads via the
+OMP_NUM_THREADS environment variable.
[Or run with the USER-OMP package by editing an input script:]
diff --git a/doc/src/Speed_opt.txt b/doc/src/Speed_opt.txt
index 676a5d84182e90ea4f832c3938bab51e5a3011dc..7dd83a84bfb027d1a34cd4cda8285895fda53f76 100644
--- a/doc/src/Speed_opt.txt
+++ b/doc/src/Speed_opt.txt
@@ -15,34 +15,21 @@ Technologies). It contains a handful of pair styles whose compute()
methods were rewritten in C++ templated form to reduce the overhead
due to if tests and other conditional code.
-Here is a quick overview of how to use the OPT package. More details
-follow.
-
-make yes-opt
-make mpi # build with the OPT package :pre
-
-lmp_mpi -sf opt -in in.script # run in serial
-mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel :pre
-
[Required hardware/software:]
None.
[Building LAMMPS with the OPT package:]
-The lines above illustrate how to build LAMMPS with the OPT package in
-two steps, using the "make" command. Or how to do it with one command
-as described on the "Packages details"_Packages_details.html#OPT doc
-page.
-
-Note that if you use an Intel compiler to build with the OPT package,
-the CCFLAGS setting in your Makefile.machine must include "-restrict".
+See the "Build extras"_Build_extras.html#opt doc page for instructions.
[Run with the OPT package from the command line:]
-As in the lines above, use the "-sf opt" "command-line
-switch"_Section_start.html#start_6, which will automatically append
-"opt" to styles that support it.
+lmp_mpi -sf opt -in in.script # run in serial
+mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel :pre
+
+Use the "-sf opt" "command-line switch"_Run_options.html, which will
+automatically append "opt" to styles that support it.
[Or run with the OPT package by editing an input script:]
diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt
index f463ed91b85d28cf495db638a401f7c52a5326fe..6c837885cd4dd5272e9b7925d84aa01ee8f9ab79 100644
--- a/doc/src/Speed_packages.txt
+++ b/doc/src/Speed_packages.txt
@@ -93,11 +93,11 @@ re-build LAMMPS |
make machine |
prepare and test a regular LAMMPS simulation |
lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
-enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
+enable specific accelerator support via '-k on' "command-line switch"_Run_options.html, |
only needed for KOKKOS package |
-set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
+set any needed options for the package via "-pk" "command-line switch"_Run_options.html or "package"_package.html command, |
only if defaults need to be changed |
-use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
+use accelerated styles in your input via "-sf" "command-line switch"_Run_options.html or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
:tb(c=2,s=|)
Note that the first 4 steps can be done as a single command with
diff --git a/doc/src/Speed_tips.txt b/doc/src/Speed_tips.txt
index 7c950779d5e4864db0802e90369c6acaaf8b6d36..858b1d493fcbc9c54cc29ab6b23859a77df4677b 100644
--- a/doc/src/Speed_tips.txt
+++ b/doc/src/Speed_tips.txt
@@ -9,7 +9,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
General tips :h3
-NOTE: this section 5.2 is still a work in progress
+NOTE: this page is still a work in progress
Here is a list of general ideas for improving simulation performance.
Most of them are only applicable to certain models and certain
@@ -20,13 +20,8 @@ problem size, number of processors used, and your machine. There is
no substitute for identifying performance bottlenecks, and trying out
various options.
-make individual pages for these, or one for PPPM
-one for timestepping, etc
-one for balancing
-or proc layout
-
rRESPA
-2-FFT PPPM
+Two-FFT PPPM
Staggered PPPM
single vs double PPPM
partial charge PPPM
@@ -34,12 +29,13 @@ verlet/split run style
processor command for proc layout and numa layout
load-balancing: balance and fix balance :ul
-2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses
-2 FFTs instead of the 4 FFTs used by the default {ik differentiation}
-PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
-achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
-cost is the performance bottleneck (typically large problems running
-on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
+Two-FFT PPPM, also called {analytic differentiation} or {ad} PPPM,
+uses 2 FFTs instead of the 4 FFTs used by the default {ik
+differentiation} PPPM. However, 2-FFT PPPM also requires a slightly
+larger mesh size to achieve the same accuracy as 4-FFT PPPM. For
+problems where the FFT cost is the performance bottleneck (typically
+large problems running on many processors), 2-FFT PPPM may be faster
+than 4-FFT PPPM.
Staggered PPPM performs calculations using two different meshes, one
shifted slightly with respect to the other. This can reduce force
diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt
index 85ee531cfd905371ebef6f17db26713c2a496d6c..8b4e779cbe869ca7eda71988c841b41ea116f0a3 100644
--- a/doc/src/Tools.txt
+++ b/doc/src/Tools.txt
@@ -74,10 +74,9 @@ own sub-directories with their own Makefiles and/or README files.
"vim"_#vim
"xmgrace"_#xmgrace :ul
-:line
:line
-amber2lmp tool :h4,link(amber)
+amber2lmp tool :h3,link(amber)
The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
@@ -92,7 +91,7 @@ necessary modifications yourself.
:line
-binary2txt tool :h4,link(binary)
+binary2txt tool :h3,link(binary)
The file binary2txt.cpp converts one or more binary LAMMPS dump file
into ASCII text files. The syntax for running the tool is
@@ -105,7 +104,7 @@ since binary files are not compatible across all platforms.
:line
-ch2lmp tool :h4,link(charmm)
+ch2lmp tool :h3,link(charmm)
The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS.
@@ -130,7 +129,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
:line
-chain tool :h4,link(chain)
+chain tool :h3,link(chain)
The file chain.f creates a LAMMPS data file containing bead-spring
polymer chains and/or monomer solvent atoms. It uses a text file
@@ -147,7 +146,7 @@ for the "chain benchmark"_Speed_bench.html.
:line
-colvars tools :h4,link(colvars)
+colvars tools :h3,link(colvars)
The colvars directory contains a collection of tools for postprocessing
data produced by the colvars collective variable library.
@@ -169,7 +168,7 @@ gmail.com) at ICTP, Italy.
:line
-createatoms tool :h4,link(createatoms)
+createatoms tool :h3,link(createatoms)
The tools/createatoms directory contains a Fortran program called
createAtoms.f which can generate a variety of interesting crystal
@@ -182,7 +181,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
:line
-doxygen tool :h4,link(doxygen)
+doxygen tool :h3,link(doxygen)
The tools/doxygen directory contains a shell script called
doxygen.sh which can generate a call graph and API lists using
@@ -194,7 +193,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
:line
-drude tool :h4,link(drude)
+drude tool :h3,link(drude)
The tools/drude directory contains a Python script called
polarizer.py which can add Drude oscillators to a LAMMPS
@@ -207,7 +206,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
:line
-eam database tool :h4,link(eamdb)
+eam database tool :h3,link(eamdb)
The tools/eam_database directory contains a Fortran program that will
generate EAM alloy setfl potential files for any combination of 16
@@ -223,7 +222,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
:line
-eam generate tool :h4,link(eamgn)
+eam generate tool :h3,link(eamgn)
The tools/eam_generate directory contains several one-file C programs
that convert an analytic formula into a tabulated "embedded atom
@@ -236,7 +235,7 @@ The source files and potentials were provided by Gerolf Ziegenhain
:line
-eff tool :h4,link(eff)
+eff tool :h3,link(eff)
The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
@@ -247,7 +246,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
:line
-emacs tool :h4,link(emacs)
+emacs tool :h3,link(emacs)
The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
that enables a lammps-mode for editing input scripts when using GNU Emacs,
@@ -258,7 +257,7 @@ These tools were provided by Aidan Thompson at Sandia
:line
-fep tool :h4,link(fep)
+fep tool :h3,link(fep)
The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
@@ -271,7 +270,7 @@ See README file in the tools/fep directory.
:line
-i-pi tool :h4,link(ipi)
+i-pi tool :h3,link(ipi)
The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
@@ -288,7 +287,7 @@ calculations with LAMMPS.
:line
-ipp tool :h4,link(ipp)
+ipp tool :h3,link(ipp)
The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input
@@ -302,7 +301,7 @@ tools/createatoms tool's input file.
:line
-kate tool :h4,link(kate)
+kate tool :h3,link(kate)
The file in the tools/kate directory is an add-on to the Kate editor
in the KDE suite that allow syntax highlighting of LAMMPS input
@@ -313,7 +312,7 @@ The file was provided by Alessandro Luigi Sellerio
:line
-lmp2arc tool :h4,link(arc)
+lmp2arc tool :h3,link(arc)
The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys' Insight MD code (formerly
@@ -329,7 +328,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
:line
-lmp2cfg tool :h4,link(cfg)
+lmp2cfg tool :h3,link(cfg)
The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of *.cfg files which can be read into the
@@ -340,7 +339,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
:line
-matlab tool :h4,link(matlab)
+matlab tool :h3,link(matlab)
The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
post-processing LAMMPS output. The scripts include readers for log
@@ -358,7 +357,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
:line
-micelle2d tool :h4,link(micelle)
+micelle2d tool :h3,link(micelle)
The file micelle2d.f creates a LAMMPS data file containing short lipid
chains in a monomer solution. It uses a text file containing lipid
@@ -375,7 +374,7 @@ definition file. This tool was used to create the system for the
:line
-moltemplate tool :h4,link(moltemplate)
+moltemplate tool :h3,link(moltemplate)
The moltemplate sub-directory contains a Python-based tool for
building molecular systems based on a text-file description, and
@@ -389,7 +388,7 @@ supports it. It has its own WWW page at
:line
-msi2lmp tool :h4,link(msi)
+msi2lmp tool :h3,link(msi)
The msi2lmp sub-directory contains a tool for creating LAMMPS template
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
@@ -406,7 +405,7 @@ See the README file in the tools/msi2lmp folder for more information.
:line
-phonon tool :h4,link(phonon)
+phonon tool :h3,link(phonon)
The phonon sub-directory contains a post-processing tool useful for
analyzing the output of the "fix phonon"_fix_phonon.html command in
@@ -421,7 +420,7 @@ University.
:line
-polybond tool :h4,link(polybond)
+polybond tool :h3,link(polybond)
The polybond sub-directory contains a Python-based tool useful for
performing "programmable polymer bonding". The Python file
@@ -435,7 +434,7 @@ This tool was written by Zachary Kraus at Georgia Tech.
:line
-pymol_asphere tool :h4,link(pymol)
+pymol_asphere tool :h3,link(pymol)
The pymol_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
@@ -453,7 +452,7 @@ This tool was written by Mike Brown at Sandia.
:line
-python tool :h4,link(pythontools)
+python tool :h3,link(pythontools)
The python sub-directory contains several Python scripts
that perform common LAMMPS post-processing tasks, such as:
@@ -469,7 +468,7 @@ README for more info on Pizza.py and how to use these scripts.
:line
-reax tool :h4,link(reax_tool)
+reax tool :h3,link(reax_tool)
The reax sub-directory contains stand-alond codes that can
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
@@ -480,7 +479,7 @@ These tools were written by Aidan Thompson at Sandia.
:line
-smd tool :h4,link(smd)
+smd tool :h3,link(smd)
The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
Makefile which can be compiled and used to convert triangle output
@@ -496,7 +495,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
:line
-vim tool :h4,link(vim)
+vim tool :h3,link(vim)
The files in the tools/vim directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the README.txt
@@ -507,7 +506,7 @@ ziegenhain.com)
:line
-xmgrace tool :h4,link(xmgrace)
+xmgrace tool :h3,link(xmgrace)
The files in the tools/xmgrace directory can be used to plot the
thermodynamic data in LAMMPS log files via the xmgrace plotting
diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt
index f72f0862348328bbd5c62a11d42274bb4f4c14d3..8b0e298a43cccc82433505de4646f0cd254ffcb0 100644
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -73,8 +73,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt
index 3e5445d3a3c17200bd5e548791bdbfbb31f4dcbe..fa5e29582cf4762e2851ba82c69624076a09e705 100644
--- a/doc/src/angle_class2.txt
+++ b/doc/src/angle_class2.txt
@@ -89,13 +89,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -123,8 +123,8 @@ The bond-bond and bond-angle terms remain unchanged.
This angle style can only be used if LAMMPS was built with the CLASS2
package. For the {class2/p6} style LAMMPS needs to be built with the
-USER-MOFFF package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MOFFF package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt
index 5a1fe91c834271bfe883e1b2d5a410f3bb148a23..80cf8ae8f13ecee4bde4faf93ab923a153e61118 100644
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@@ -44,13 +44,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -60,8 +60,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt
index 63a451b7631456aa21b870eadf5808e92b052ec9..54709c1370f65d740f134a4e8d9bc80b8e106ca3 100644
--- a/doc/src/angle_cosine_buck6d.txt
+++ b/doc/src/angle_cosine_buck6d.txt
@@ -55,8 +55,8 @@ the "special_bonds"_special_bonds.html 1-3 interactions to be weighted
"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions.
This angle style can only be used if LAMMPS was built with the
-USER-MOFFF package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-MOFFF package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt
index b6ac0ed8181ad55b183ab59962e9502c2cd5ab93..1532e39b31007e149d964912a1fbde27fe4fe253 100644
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt
index c5b184e0b46b1e5b14efb8b1dd0477740c59ae19..039144797ff75badb1771d220720db471aebf6e6 100644
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -73,8 +73,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt
index 90ac61fe23c9d45f595c579e937d55bdea284909..3a4efad218bb204e5b23773725c3221a38ca47c8 100644
--- a/doc/src/angle_cosine_shift.txt
+++ b/doc/src/angle_cosine_shift.txt
@@ -47,13 +47,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -63,8 +63,7 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package.
[Related commands:]
diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt
index f1c4c93c425e0ce8f51d12e39dd34c9493bf0426..3091e838850742d8f1efdae6b1b921aa4afd6afd 100644
--- a/doc/src/angle_cosine_shift_exp.txt
+++ b/doc/src/angle_cosine_shift_exp.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -75,8 +75,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt
index ba5fd9d4139a4f1142c287e121d3e3e7f002a6d4..07fcb1ceb4cb731c89f1dc7eae7452fafe266c86 100644
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt
index c001d9d9206c743222357f1cdcb345934f9a9ead..cdb11972ecb01dc7d6c602c8444495fef8d46dba 100644
--- a/doc/src/angle_dipole.txt
+++ b/doc/src/angle_dipole.txt
@@ -77,13 +77,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -91,8 +91,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_2_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
NOTE: In the "Angles" section of the data file, the atom ID 'j'
defining the direction of the dipole vector to restrain must come
diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt
index e0e32c1eed001fa0d6ecb70f2f2c69542d39d6c0..7dc9975793353787e56cd677c25459744c0f2d87 100644
--- a/doc/src/angle_fourier.txt
+++ b/doc/src/angle_fourier.txt
@@ -45,13 +45,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -61,8 +61,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt
index 3c50536a2cbc0720ec69c4a4b02cdefa15bd48ff..ae5d30835387a071bf801c7f30af3b0f2cad6ce6 100644
--- a/doc/src/angle_fourier_simple.txt
+++ b/doc/src/angle_fourier_simple.txt
@@ -44,13 +44,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -60,8 +60,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt
index 76c7a491e8943aa7cdd720750394818fc7460b9e..b632f684786bc8c465bf350b270cd91388b4ef66 100644
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@@ -51,13 +51,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -67,8 +67,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt
index 26469034212fe359d66a965e216543404b2d1020..0046c161be6a30ea500e8b1a26b61b3145166f6a 100644
--- a/doc/src/angle_hybrid.txt
+++ b/doc/src/angle_hybrid.txt
@@ -76,8 +76,8 @@ for specific angle types.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a "binary restart
diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt
index 294be330b1faab22d868d16b1a78edb048be928c..b20a06eb8d681fd0f7987e9f686e4e247699ffa0 100644
--- a/doc/src/angle_quartic.txt
+++ b/doc/src/angle_quartic.txt
@@ -51,13 +51,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -67,8 +67,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt
index 9c5630ef3adf62b7688dbbd021555283536b2cff..4de1a6755d9eebf47045996fdad8b711367d9f6d 100644
--- a/doc/src/angle_sdk.txt
+++ b/doc/src/angle_sdk.txt
@@ -46,8 +46,8 @@ from the pair_style.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-CGSDK package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGSDK package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt
index 63295faf264d8fee8b2a75fb32143ae710d02586..756cfc0c6038d3d3a0e9dd7a12b229e2f8f11c09 100644
--- a/doc/src/angle_style.txt
+++ b/doc/src/angle_style.txt
@@ -83,10 +83,9 @@ Angle styles can only be set for atom_styles that allow angles to be
defined.
Most angle styles are part of the MOLECULE 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 on packages.
-The doc pages for individual bond potentials tell if it is part of a
-package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual bond potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt
index 31ab532be17c95598c2b54f3a34becbf3c966120..6b9187e512a355649ef7fffdaa87c3747d9a3010 100644
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@@ -130,13 +130,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -146,8 +146,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt
index c882d1b0ba0f43a916ee3a954a4b85e41d6c2007..4b4ac3862d102b54ed08cb0b2d8b63f84ec32f89 100644
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.txt
@@ -58,9 +58,9 @@ simulation so large that IDs cannot be uniquely assigned. For a
default LAMMPS build this limit is 2^31 or about 2 billion atoms.
However, even in this case, you can use 64-bit atom IDs, allowing 2^63
or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
-switch. This is described in "Section 2.2"_Section_start.html#start_2
-of the manual. If atom IDs are not used, they must be specified as 0
-for all atoms, e.g. in a data or restart file.
+switch. This is described on the "Build_settings"_Build_settings.html
+doc page. If atom IDs are not used, they must be specified as 0 for
+all atoms, e.g. in a data or restart file.
The {map} keyword determines how atoms with specific IDs are found
when required. An example are the bond (angle, etc) methods which
diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt
index abf05885a3ee3d96846af804d6ef1caaf42643c6..db2e285dc48fefb79709933d1230ed4a750f084d 100644
--- a/doc/src/atom_style.txt
+++ b/doc/src/atom_style.txt
@@ -272,13 +272,13 @@ USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
styles.
The accelerated styles are part of the KOKKOS package. They are only
-enabled if LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -289,8 +289,8 @@ This command cannot be used after the simulation box is defined by a
"read_data"_read_data.html or "create_box"_create_box.html command.
Many of the styles listed above are only enabled if LAMMPS was built
-with a specific package, as listed below. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with a specific package, as listed below. See the "Build
+package"_Build_package.html doc page for more info.
The {angle}, {bond}, {full}, {molecular}, and {template} styles are
part of the MOLECULE package.
diff --git a/doc/src/balance.txt b/doc/src/balance.txt
index 06c4eca491d1bd6cdb3c68a5caa2381718159ea7..26e146d89b3222fabdfdabe9daf4e6720d5f6750 100644
--- a/doc/src/balance.txt
+++ b/doc/src/balance.txt
@@ -394,11 +394,11 @@ weights. It assigns the same weight to each particle owned by a
processor based on the total computational time spent by that
processor. See details below on what time window is used. It uses
the same timing information as is used for the "MPI task timing
-breakdown"_Section_start.html#start_7, namely, for sections {Pair},
-{Bond}, {Kspace}, and {Neigh}. The time spent in those portions of
-the timestep are measured for each MPI rank, summed, then divided by
-the number of particles owned by that processor. I.e. the weight is
-an effective CPU time/particle averaged over the particles on that
+breakdown"_Run_output.html, namely, for sections {Pair}, {Bond},
+{Kspace}, and {Neigh}. The time spent in those portions of the
+timestep are measured for each MPI rank, summed, then divided by the
+number of particles owned by that processor. I.e. the weight is an
+effective CPU time/particle averaged over the particles on that
processor.
The {factor} setting is applied as an overall scale factor to the
diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt
index 3d8d5007bad145439de155227c8873fcfce616a9..4390e3613c001741ecc9a2203e6c3899402a8356 100644
--- a/doc/src/bond_class2.txt
+++ b/doc/src/bond_class2.txt
@@ -50,13 +50,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -66,8 +66,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the CLASS2
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt
index e16307a71076c6c2c2b6aecd5c660eb4acda8f2a..9ec4017d000a865108d08a209226283918b57c17 100644
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@@ -53,13 +53,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -68,9 +68,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
You typically should specify "special_bonds fene"_special_bonds.html
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt
index 8edd325885e457e039765074ce14be6fe5fe2764..4d7d2d54382e3afbfa74a4f25924052ed544b16a 100644
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@@ -56,13 +56,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -71,9 +71,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
You typically should specify "special_bonds fene"_special_bonds.html
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt
index 275036a421f618085eb25625f87a716cb28876c5..e039e6c4117ccbdabc132f24b723d4e5f2c8d1e2 100644
--- a/doc/src/bond_gromos.txt
+++ b/doc/src/bond_gromos.txt
@@ -46,13 +46,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -61,9 +61,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt
index e4b2015fed2987dfe52a06e22021fff70bbb6ce6..3afdf4ceba020fdd4f5e31d3a075da2b79b8712e 100644
--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@@ -48,13 +48,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -63,9 +63,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt
index b6dc18a5fd69453806968cebd189c4ca7c0d5dd3..23d3dcb5d509337005b973fd7610e59ab0ae81a1 100644
--- a/doc/src/bond_harmonic_shift.txt
+++ b/doc/src/bond_harmonic_shift.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt
index b3054437d8e8b4a4bda593bb756e7721ff7ebe26..13ccb5843b44b132789305b9779bccac6d08ed72 100644
--- a/doc/src/bond_harmonic_shift_cut.txt
+++ b/doc/src/bond_harmonic_shift_cut.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt
index 140fb723785476a1a09c67360b6865a898f8d1f5..0996f72ce3a4cbbf8f25869363f2b5072d790996 100644
--- a/doc/src/bond_hybrid.txt
+++ b/doc/src/bond_hybrid.txt
@@ -58,9 +58,9 @@ bond types.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a "binary restart
diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt
index 9b64e8c5c1d2da41936def16578ba299160121a9..60fd16e17a0894ef131bc9794354d645c067ac33 100644
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@@ -47,13 +47,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,9 +62,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt
index 08109bc699dfed95d7ad70cff09dbded043627f5..af51383213998faa6427bcb8b078b5c400127b6b 100644
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@@ -47,13 +47,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,9 +62,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt
index a0e14a123abed8da2728ed13d3ad3b836fc3414b..1944f7027a6573de91d6b490482931af332e0ed5 100644
--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@@ -62,8 +62,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGDNA package and the MOLECULE and ASPHERE package. See the
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt
index 87a21eff02ef4577638e44a5a6932ab181ec5a71..b7b1ee4ce61aac52c01b80a98acb9cd889e359bd 100644
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@@ -82,13 +82,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -97,9 +97,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
The {quartic} style requires that "special_bonds"_special_bonds.html
parameters be set to 1,1,1. Three- and four-body interactions (angle,
diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt
index 41fa1cabb213847c51aef2b7acef0b1bb6bee00e..22fae3e34698a7da47dd8d171fd2d996a682a01f 100644
--- a/doc/src/bond_style.txt
+++ b/doc/src/bond_style.txt
@@ -90,10 +90,9 @@ Bond styles can only be set for atom styles that allow bonds to be
defined.
Most bond styles are part of the MOLECULE 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 on packages.
-The doc pages for individual bond potentials tell if it is part of a
-package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual bond potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt
index e53cbdfa9f626c0c36377d9ac56a8bea016f958b..fbf6eb5815cc48661804af29a4e0e49543c75e70 100644
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@@ -127,13 +127,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -142,9 +142,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/commands.txt b/doc/src/commands_list.txt
similarity index 100%
rename from doc/src/commands.txt
rename to doc/src/commands_list.txt
diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt
index 485c191313209e46eb2ac979d004f23314678190..cda4a36b34d01c83a4977440adc94e747ea090df 100644
--- a/doc/src/compute_ackland_atom.txt
+++ b/doc/src/compute_ackland_atom.txt
@@ -66,8 +66,8 @@ LAMMPS output options.
[Restrictions:]
This compute is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The per-atom vector values will be unitless since they are the
integers defined above.
diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt
index 067a020c35ebec8da9acda96b21abb8c68724a30..5c28b8e378d6c3a0f6b3cc4d99b3f8b66b0572c7 100644
--- a/doc/src/compute_basal_atom.txt
+++ b/doc/src/compute_basal_atom.txt
@@ -55,8 +55,8 @@ components of a unit vector.
[Restrictions:]
This compute is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The output of this compute will be meaningless unless the atoms are on
(or near) hcp lattice sites, since the calculation assumes a
diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt
index 95e6e6c0104a939af015cecc41a2c2ee3ea5c33c..e76b51e6ec9df377f4e1354f0090c588f6dd4b53 100644
--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@@ -134,7 +134,6 @@ timesteps it specifies, while it accumulates per-chunk averages.
The details are described below.
-:line
:line
The different chunk styles operate as follows. For each style, how it
@@ -294,7 +293,6 @@ invoke other computes, fixes, or variables when they are evaluated, so
this is a very general means of generating per-atom quantities to
treat as a chunk ID.
-:line
:line
Normally, {Nchunk} = the number of chunks, is re-calculated every time
@@ -322,7 +320,6 @@ the same compute chunk/atom compute. However, the time windows they
induce for holding {Nchunk} constant must be identical, else an error
will be generated.
-:line
:line
The various optional keywords operate as follows. Note that some of
diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt
index 44a77d23ca0fedade05df5f523302bcdaaa6215a..95dd59089f60fb4fcccc1d4e79f1f0cb1e840639 100644
--- a/doc/src/compute_cnp_atom.txt
+++ b/doc/src/compute_cnp_atom.txt
@@ -95,8 +95,8 @@ FCC dislocation core ~ 11 :pre
[Restrictions:]
This compute is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt
index 74939e22806077fe5fb274cd17a7630954db9017..2594dfe3561e02bdcbbdbbfa0651d1f0db668d88 100644
--- a/doc/src/compute_damage_atom.txt
+++ b/doc/src/compute_damage_atom.txt
@@ -52,8 +52,8 @@ The per-atom vector values are unitless numbers (damage) >= 0.0.
[Restrictions:]
This compute is part of the PERI 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt
index 498110cf99338e56fb24a2b9a362438f03f5f9f3..292638bdf5e57f4fbe9cfc1079bb3ae64dec20fa 100644
--- a/doc/src/compute_dilatation_atom.txt
+++ b/doc/src/compute_dilatation_atom.txt
@@ -56,8 +56,8 @@ The per-atom vector values are unitless numbers (theta) >= 0.0.
[Restrictions:]
This compute is part of the PERI 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_dpd.txt b/doc/src/compute_dpd.txt
index 1721456e35ab0da5a82d3965f676f35a3d4baa3b..eccffee9b8fe85d02321ba85167a9b090c2b7972 100644
--- a/doc/src/compute_dpd.txt
+++ b/doc/src/compute_dpd.txt
@@ -49,8 +49,8 @@ The vector values will be in energy and temperature "units"_units.html.
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt
index 8e502d4a6060f297da9132013adf5e19d40b565a..2f9b4098cff988047b9a39f2926b3320b85e3aa3 100644
--- a/doc/src/compute_dpd_atom.txt
+++ b/doc/src/compute_dpd_atom.txt
@@ -45,8 +45,8 @@ and temperature (dpdTheta) "units"_units.html.
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt
index f33398e03d68995dc18da4d73fd9537f5e75656d..f3c1418d44c52c1d6678e32b568c3df389118fc0 100644
--- a/doc/src/compute_edpd_temp_atom.txt
+++ b/doc/src/compute_edpd_temp_atom.txt
@@ -41,8 +41,8 @@ The per-atom vector values will be in temperature "units"_units.html.
[Restrictions:]
This compute is part of the USER-MESO 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt
index 9c45fd287099ea6150621a177f55837bbc5855fb..b3891841b8ce04185b3f0705e877b8c34f87b34f 100644
--- a/doc/src/compute_entropy_atom.txt
+++ b/doc/src/compute_entropy_atom.txt
@@ -109,8 +109,8 @@ ordered environments.
[Restrictions:]
This compute is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_erotate_rigid.txt b/doc/src/compute_erotate_rigid.txt
index 5b9077870e1d25440827b5a6006b5c6e3233d830..fa433c1c97699957320110651323240b2cced994 100644
--- a/doc/src/compute_erotate_rigid.txt
+++ b/doc/src/compute_erotate_rigid.txt
@@ -51,8 +51,8 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the RIGID 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt
index 561ded35c052ef3e99e53ea8cb0533e00d3f99e3..a36cf2c9c49440c6428908915caa2f16ca58dab5 100644
--- a/doc/src/compute_event_displace.txt
+++ b/doc/src/compute_event_displace.txt
@@ -52,8 +52,8 @@ scalar value will be a 0 or 1 as explained above.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt
index 8b4a92e16ea3a0486ca2c7113bf0b1ac87a47399..5b3a6915dd4a6c3c442be5034caa03b7fb709602 100644
--- a/doc/src/compute_fep.txt
+++ b/doc/src/compute_fep.txt
@@ -230,8 +230,8 @@ The values calculated by this compute are "extensive".
[Restrictions:]
This compute is distributed as the USER-FEP 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.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/src/compute_ke_atom_eff.txt
index f665f35055f36be914f26aa5c032b2b76233ccf2..29905f81d6b624f119cfb05a8daebfb959971492 100644
--- a/doc/src/compute_ke_atom_eff.txt
+++ b/doc/src/compute_ke_atom_eff.txt
@@ -66,8 +66,8 @@ The per-atom vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_ke_eff.txt b/doc/src/compute_ke_eff.txt
index d6d7fdb10f5f3667a8443047505e80a775c3b1b6..fa2c51a032607c696bbb61c23abe489b189a3975 100644
--- a/doc/src/compute_ke_eff.txt
+++ b/doc/src/compute_ke_eff.txt
@@ -70,8 +70,8 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:] none
diff --git a/doc/src/compute_ke_rigid.txt b/doc/src/compute_ke_rigid.txt
index 45ba2673b0283a8106d55ee621103a7f8eb3a7fa..ad6baf567fa87e8e4be7e67d65f9fe5a7333ba40 100644
--- a/doc/src/compute_ke_rigid.txt
+++ b/doc/src/compute_ke_rigid.txt
@@ -50,8 +50,8 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the RIGID 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_meso_e_atom.txt b/doc/src/compute_meso_e_atom.txt
index 9a9c7fae118d4b6a84636b94a9f83d582c6331c8..0f0cfda2d1c8a9c01d367608e5e36d27f01de416 100644
--- a/doc/src/compute_meso_e_atom.txt
+++ b/doc/src/compute_meso_e_atom.txt
@@ -46,8 +46,8 @@ The per-atom vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-SPH 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/src/compute_meso_rho_atom.txt
index 30b1142b6cdfef0afb329f7d3be5a360d9487465..5127ad2c48f7a3f033957e800a7ba8303dfa0fe7 100644
--- a/doc/src/compute_meso_rho_atom.txt
+++ b/doc/src/compute_meso_rho_atom.txt
@@ -46,8 +46,8 @@ The per-atom vector values will be in mass/volume "units"_units.html.
[Restrictions:]
This compute is part of the USER-SPH 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_meso_t_atom.txt b/doc/src/compute_meso_t_atom.txt
index ab92f05018a15b6f45edf30d4844b82b2c237493..f4ab869ec27bd943dffcfe5b4df1dce358efa5cf 100644
--- a/doc/src/compute_meso_t_atom.txt
+++ b/doc/src/compute_meso_t_atom.txt
@@ -48,8 +48,8 @@ The per-atom vector values will be in temperature "units"_units.html.
[Restrictions:]
This compute is part of the USER-SPH 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt
index 814159121d11781bf29850db7c8787ab5644b807..c6e89a10615a191d4df77fd3e4d207d07ecb69a4 100644
--- a/doc/src/compute_msd_nongauss.txt
+++ b/doc/src/compute_msd_nongauss.txt
@@ -66,9 +66,9 @@ the 3rd is dimensionless.
[Restrictions:]
-This compute is part of the MISC 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.
+This compute is part of the MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt
index 7588e92527aa5d32157f4f94207226597a9966f4..1460ba18a5b1ffbadfce39cae346872c16866dd0 100644
--- a/doc/src/compute_pair_local.txt
+++ b/doc/src/compute_pair_local.txt
@@ -62,7 +62,7 @@ pair styles do not define any additional quantities, so N = 0. An
example of ones that do are the "granular pair styles"_pair_gran.html
which calculate the tangential force between two particles and return
its components and magnitude acting on atom I for N = 1,2,3,4. See
-individual pair styles for detils.
+individual pair styles for details.
The value {dist} will be in distance "units"_units.html. The value
{eng} will be in energy "units"_units.html. The values {force}, {fx},
@@ -76,7 +76,7 @@ command for the types of the two atoms is used. For the {radius}
setting, the sum of the radii of the two particles is used as a
cutoff. For example, this is appropriate for granular particles which
only interact when they are overlapping, as computed by "granular pair
-styles"_pair_gran.txt. Note that if a granular model defines atom
+styles"_pair_gran.html. Note that if a granular model defines atom
types such that all particles of a specific type are monodisperse
(same diameter), then the two settings are effectively identical.
diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt
index 50a51d99377899c3ed62a81059351ab494968567..b82179712abcd146420f0ac7b538f2c49b01f855 100644
--- a/doc/src/compute_plasticity_atom.txt
+++ b/doc/src/compute_plasticity_atom.txt
@@ -50,8 +50,8 @@ The per-atom vector values are unitless numbers (lambda) >= 0.0.
[Restrictions:]
This compute is part of the PERI 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt
index dea0a7f05b7f03d209077628f19a07172eb93e0f..6acbaf7d3d5619c4c08001bf712a606b911e280e 100644
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@@ -111,13 +111,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt
index 61cc85ad8097b3b43ac740cf186b7456f02db707..c4c0fc405ff563273c1d9b1ff72c51a638eedf02 100644
--- a/doc/src/compute_pressure_uef.txt
+++ b/doc/src/compute_pressure_uef.txt
@@ -38,9 +38,9 @@ The keywords and output information are documented in
[Restrictions:]
-This fix is part of the USER-UEF 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.
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt
index b5e6954ab99943f090a3153829ca08a6daa8f0b7..9b829a70fcb82a1de7defbafbce6b949ca833f20 100644
--- a/doc/src/compute_rigid_local.txt
+++ b/doc/src/compute_rigid_local.txt
@@ -175,8 +175,8 @@ inertiax,inertiay,inertiaz = mass*distance^2 units :ul
[Restrictions:]
This compute is part of the RIGID 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt
index 8c17a30fcaf1acb403a936d4a15938206e89ad4d..b27c36e318757159978998b723d2e3bc5b5c3924 100644
--- a/doc/src/compute_saed.txt
+++ b/doc/src/compute_saed.txt
@@ -152,8 +152,8 @@ All array values calculated by this compute are "intensive".
[Restrictions:]
This compute is part of the USER-DIFFRACTION 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.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The compute_saed command does not work for triclinic cells.
diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/src/compute_smd_contact_radius.txt
index cd1381604788bfcd42f00653d2c5e9b46f98d25f..4ab03e3738c4fcc60378ab988a60c33b1260ad41 100644
--- a/doc/src/compute_smd_contact_radius.txt
+++ b/doc/src/compute_smd_contact_radius.txt
@@ -45,8 +45,8 @@ The per-particle vector values will be in distance "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_smd_damage.txt b/doc/src/compute_smd_damage.txt
index afabe23d7cc1407496463c926ba8adcb9ddc7ff0..139fb3ec7bfb48e56b56e23af5cce1176f45cdbe 100644
--- a/doc/src/compute_smd_damage.txt
+++ b/doc/src/compute_smd_damage.txt
@@ -38,8 +38,8 @@ The per-particle values are dimensionless an in the range of zero to one.
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+
[Related commands:]
diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/src/compute_smd_hourglass_error.txt
index 13fd20a5891cab8bdeeabb570d8343c063a705af..5bc3e3a2decbefdcd3e026e12e1aae6ccf535758 100644
--- a/doc/src/compute_smd_hourglass_error.txt
+++ b/doc/src/compute_smd_hourglass_error.txt
@@ -48,8 +48,8 @@ The per-particle vector values will are dimensionless. See
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
tlsph pair style.
diff --git a/doc/src/compute_smd_internal_energy.txt b/doc/src/compute_smd_internal_energy.txt
index 6585c3429f27a9c97d17c66a15dff959ebbbe5be..b9d18ce933966e161c26a1ecc783e8a2bbc76abe 100644
--- a/doc/src/compute_smd_internal_energy.txt
+++ b/doc/src/compute_smd_internal_energy.txt
@@ -39,10 +39,10 @@ The per-particle vector values will be given in "units"_units.html of energy.
[Restrictions:]
This compute is part of the USER-SMD 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. This compute
-can only be used for particles which interact via the updated
-Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
[Related Commands:]
diff --git a/doc/src/compute_smd_plastic_strain.txt b/doc/src/compute_smd_plastic_strain.txt
index fb3c5c9138cb5ae444320a5ff9f4a73878780a67..d12be7222a23744d489b6a1153bae16fb91f6753 100644
--- a/doc/src/compute_smd_plastic_strain.txt
+++ b/doc/src/compute_smd_plastic_strain.txt
@@ -40,10 +40,10 @@ The per-particle values will be given dimensionless. See "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD 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. This compute
-can only be used for particles which interact via the updated
-Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
[Related commands:]
diff --git a/doc/src/compute_smd_plastic_strain_rate.txt b/doc/src/compute_smd_plastic_strain_rate.txt
index b913ae90976009a7caf916352cbfe9475577d9db..ffc009b2a70978a272f9184b71ca6b1828dc768a 100644
--- a/doc/src/compute_smd_plastic_strain_rate.txt
+++ b/doc/src/compute_smd_plastic_strain_rate.txt
@@ -40,10 +40,10 @@ The per-particle values will be given in "units"_units.html of one over time.
[Restrictions:]
This compute is part of the USER-SMD 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. This compute
-can only be used for particles which interact via the updated
-Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
[Related commands:]
diff --git a/doc/src/compute_smd_rho.txt b/doc/src/compute_smd_rho.txt
index a1ee1d9c5b95a2971e64a52ad4416e74e54fc226..31d7351c92e2aaeb55f53c71bd7fe75be82df9bc 100644
--- a/doc/src/compute_smd_rho.txt
+++ b/doc/src/compute_smd_rho.txt
@@ -41,8 +41,8 @@ The per-particle values will be in "units"_units.html of mass over volume.
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/src/compute_smd_tlsph_defgrad.txt
index 1663c84f65fd3b3c59daf427d4b15fe6a5d27ea9..a733a3d6a75f1394889be1c13eb402b146a1edc5 100644
--- a/doc/src/compute_smd_tlsph_defgrad.txt
+++ b/doc/src/compute_smd_tlsph_defgrad.txt
@@ -44,10 +44,10 @@ entry is the determinant of the deformation gradient.
[Restrictions:]
This compute is part of the USER-SMD 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. TThis
-compute can only be used for particles which interact via the total
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. TThis compute can
+only be used for particles which interact via the total Lagrangian SPH
+pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt
index c714f3266bceaf96ea1b86d487cf653cdeeeb47e..92f5923de05f735931aae9908844b197ad127fe3 100644
--- a/doc/src/compute_smd_tlsph_dt.txt
+++ b/doc/src/compute_smd_tlsph_dt.txt
@@ -45,8 +45,8 @@ The per-particle values will be given in "units"_units.html of time.
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This compute can only be used for particles interacting with the
Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_num_neighs.txt b/doc/src/compute_smd_tlsph_num_neighs.txt
index af5b0741db6c0c964ab4a73b21bdb928b663fe42..db977fe676b5185f39088c96e2a5157dda30a30f 100644
--- a/doc/src/compute_smd_tlsph_num_neighs.txt
+++ b/doc/src/compute_smd_tlsph_num_neighs.txt
@@ -40,8 +40,8 @@ The per-particle values are dimensionless. See "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian pair style.
diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/src/compute_smd_tlsph_shape.txt
index 927cd7c7aecaa51cc45c095066586899bd37aefb..9c17194ec18ed8c40fc775b4d68aa9ef54bf9e69 100644
--- a/doc/src/compute_smd_tlsph_shape.txt
+++ b/doc/src/compute_smd_tlsph_shape.txt
@@ -47,8 +47,8 @@ particle relative to its initial state.
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_strain.txt b/doc/src/compute_smd_tlsph_strain.txt
index 4536f26c8ea364d40d306f1ac863f3fc4a278dff..70f996e2064f0dc530844b825e8116f10b04b94b 100644
--- a/doc/src/compute_smd_tlsph_strain.txt
+++ b/doc/src/compute_smd_tlsph_strain.txt
@@ -43,8 +43,8 @@ zz, xy, xz, yz components of the symmetric strain tensor.
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_strain_rate.txt b/doc/src/compute_smd_tlsph_strain_rate.txt
index ae2883e4bbedb0e698cac841601984de90af2031..e6d968c523d62ce483b05a5a4522959bf4f6e2cb 100644
--- a/doc/src/compute_smd_tlsph_strain_rate.txt
+++ b/doc/src/compute_smd_tlsph_strain_rate.txt
@@ -42,8 +42,8 @@ zz, xy, xz, yz components of the symmetric strain rate tensor.
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_stress.txt b/doc/src/compute_smd_tlsph_stress.txt
index 50d6b7f4344ffb585cc27a00d644e803904e5fad..8340e885363c43c931f6734ffdbd2a415d74f74b 100644
--- a/doc/src/compute_smd_tlsph_stress.txt
+++ b/doc/src/compute_smd_tlsph_stress.txt
@@ -44,8 +44,8 @@ invariant of the stress tensor, i.e., the von Mises equivalent stress.
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_mesh_vertices.txt
index 9e167924d1401fea40a6ac9b0d9bcc7d257d4355..cd1f8fdd9b29b007ae0f3f0a28a491b7dee2fd7e 100644
--- a/doc/src/compute_smd_triangle_mesh_vertices.txt
+++ b/doc/src/compute_smd_triangle_mesh_vertices.txt
@@ -51,8 +51,8 @@ The values will be given in "units"_units.html of distance.
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt
index 202b8f15e1d95ec3441e272a23b618a0f57f443a..5157f17e578e80ec2a8799b63ea894c5ffc60ac5 100644
--- a/doc/src/compute_smd_ulsph_num_neighs.txt
+++ b/doc/src/compute_smd_ulsph_num_neighs.txt
@@ -40,10 +40,10 @@ The per-particle values will be given dimensionless, see "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2 section for more info. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/src/compute_smd_ulsph_strain.txt
index 76c47162a5c85e0def8c8231224ccda416ea6360..3dc6bd5249439a82cc76d12bd519f3f1803bbd27 100644
--- a/doc/src/compute_smd_ulsph_strain.txt
+++ b/doc/src/compute_smd_ulsph_strain.txt
@@ -43,10 +43,10 @@ The per-particle tensor values will be given dimensionless, see
[Restrictions:]
This compute is part of the USER-SMD 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. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/src/compute_smd_ulsph_strain_rate.txt
index c851e767b34a418a614cfeb537638ec294ae489f..1ade5ac2d5a8b77c950d4dfab582ad95aafa52e4 100644
--- a/doc/src/compute_smd_ulsph_strain_rate.txt
+++ b/doc/src/compute_smd_ulsph_strain_rate.txt
@@ -43,10 +43,11 @@ zz, xy, xz, yz components of the symmetric strain rate tensor.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2 section for more info. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+This compute can only be used for particles which interact with the
+updated Lagrangian SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/src/compute_smd_ulsph_stress.txt
index a5692b2412ce589165a29514c6b199b7d0dd802d..ff53e777c50615386d28db11a07a46ec682c0563 100644
--- a/doc/src/compute_smd_ulsph_stress.txt
+++ b/doc/src/compute_smd_ulsph_stress.txt
@@ -43,10 +43,10 @@ stress tensor, i.e., the von Mises equivalent stress.
[Restrictions:]
This compute is part of the USER-SMD 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. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_vol.txt b/doc/src/compute_smd_vol.txt
index fc4871d6f301157c45fcaf88e99301f20cdff31c..0edd61f624228972e7090aa15549b2361b24d0c8 100644
--- a/doc/src/compute_smd_vol.txt
+++ b/doc/src/compute_smd_vol.txt
@@ -43,8 +43,8 @@ per-particle volumes of the group for which the fix is defined.
[Restrictions:]
This compute is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt
index 3b302a0a71c65de87fee8ae571e866b3cc19653c..95d183937f8db2d79e202af0796c814b000b0ca2 100644
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@@ -250,8 +250,8 @@ page for an overview of LAMMPS output options.
[Restrictions:]
These computes are part of the SNAP 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
index 792706ecdfae311acd293546d899b51b2bf28d73..787ff8cdcfa822ba37c896d464e6c9655d5e543a 100644
--- a/doc/src/compute_spin.txt
+++ b/doc/src/compute_spin.txt
@@ -61,10 +61,10 @@ metal units ("units"_units.html).
[Restrictions:]
-The {spin} compute is part of the SPIN package.
-This compute is only enabled if LAMMPS was built with this package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
-The atom_style has to be "spin" for this compute to be valid.
+The {spin} compute is part of the SPIN package. This compute is only
+enabled if LAMMPS was built with this package. See the "Build
+package"_Build_package.html doc page for more info. The atom_style
+has to be "spin" for this compute to be valid.
[Related commands:] none
diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt
index 23fac4309384bac044259f51d128726725fcd3f7..a4a8441f9ec4e7555f977b454a56f3f8ffb137b0 100644
--- a/doc/src/compute_tally.txt
+++ b/doc/src/compute_tally.txt
@@ -76,9 +76,9 @@ Both the scalar and vector values calculated by this compute are
[Restrictions:]
-This compute is part of the USER-TALLY 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.
+This compute is part of the USER-TALLY package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Not all pair styles can be evaluated in a pairwise mode as required by
this compute. For example, 3-body and other many-body potentials,
diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt
index 9ee4d3da3462fbed0bc3be6b66212d6988fd938d..a385bef10b612c9e5a4a485570c82e406f83ff16 100644
--- a/doc/src/compute_tdpd_cc_atom.txt
+++ b/doc/src/compute_tdpd_cc_atom.txt
@@ -43,8 +43,8 @@ per unit mass.
[Restrictions:]
This compute is part of the USER-MESO 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt
index 9f3a1ca9061feeaab02ac197f5ab15c1844a709a..757e00c4d2f3e57ba70ccd180acc69099ee0e325 100644
--- a/doc/src/compute_temp.txt
+++ b/doc/src/compute_temp.txt
@@ -73,13 +73,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt
index 6766729ae0c463ce51c6470de27d6966102a0cff..eb73891e82572001a3834f292a373772edf9b396 100644
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
@@ -135,8 +135,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the ASPHERE 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This compute requires that atoms store angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt
index 4e3ce3e77f86db797f0222b62d403df6ef82c827..341d6d7f792c7815c540b03c25c480b212df9deb 100644
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
@@ -117,8 +117,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the BODY 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This compute requires that atoms store angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/src/compute_temp_deform_eff.txt
index 876d492f3446f7294ed295974e20c0f28a2369bd..4af61dc91867890533ea9a4f20606275bf4e3d07 100644
--- a/doc/src/compute_temp_deform_eff.txt
+++ b/doc/src/compute_temp_deform_eff.txt
@@ -61,8 +61,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_eff.txt b/doc/src/compute_temp_eff.txt
index 35ddb75b12c30ffac0d1d5fc249f9abe33617a0a..415cb775956ec3e759e0dfa6c2209c9e4b68520d 100644
--- a/doc/src/compute_temp_eff.txt
+++ b/doc/src/compute_temp_eff.txt
@@ -83,8 +83,8 @@ the simulation.
[Restrictions:]
This compute is part of the USER-EFF 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt
index 2769246532fd55f8cf36df3c076d6d822609d765..14294842a15b11c11461618224b663840b1dce0c 100644
--- a/doc/src/compute_temp_partial.txt
+++ b/doc/src/compute_temp_partial.txt
@@ -80,13 +80,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/compute_temp_region_eff.txt b/doc/src/compute_temp_region_eff.txt
index 95892eb25778eac67c1042de5acf2ed97494c4f1..f15f3155b08c51880ae3ae8fc9f6b255ff9b78fe 100644
--- a/doc/src/compute_temp_region_eff.txt
+++ b/doc/src/compute_temp_region_eff.txt
@@ -52,8 +52,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_rotate.txt b/doc/src/compute_temp_rotate.txt
index 189246d3e47e734b00a63da770e83a0333c9c85e..8dac0405b402efa55594068b1e7c57775ee47359 100644
--- a/doc/src/compute_temp_rotate.txt
+++ b/doc/src/compute_temp_rotate.txt
@@ -86,8 +86,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt
index a94d5db8ed767604c3dd6edac9bf81723d02da1b..9a509da4503db6cb3a9e03b0314de6300e28d36b 100644
--- a/doc/src/compute_temp_uef.txt
+++ b/doc/src/compute_temp_uef.txt
@@ -35,9 +35,9 @@ documentation for "compute temp"_compute_temp.html.
[Restrictions:]
-This fix is part of the USER-UEF 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.
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt
index e79b594e3f32a252a1ea352a1b3fc113324ebb3d..9057cab4769c5e201d1a30a7b47b8d1f6645d324 100644
--- a/doc/src/compute_ti.txt
+++ b/doc/src/compute_ti.txt
@@ -121,8 +121,8 @@ The scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt
index a8ce77882ad42069d32d51864cb06ce3566c8bba..d01f4df71217920649b688cb20562dab8396ac82 100644
--- a/doc/src/compute_voronoi_atom.txt
+++ b/doc/src/compute_voronoi_atom.txt
@@ -212,8 +212,8 @@ The Voronoi face area will be in distance "units"_units.html squared.
[Restrictions:]
This compute is part of the VORONOI 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
It also requires you have a copy of the Voro++ library built and
installed on your system. See instructions on obtaining and
diff --git a/doc/src/compute_xrd.txt b/doc/src/compute_xrd.txt
index 609fde3582d9efd03bd9c0ae6fbb63ac3d54db20..41523f25afa828f214491d7d3bdae2cf87172905 100644
--- a/doc/src/compute_xrd.txt
+++ b/doc/src/compute_xrd.txt
@@ -170,8 +170,8 @@ All array values calculated by this compute are "intensive".
[Restrictions:]
This compute is part of the USER-DIFFRACTION 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.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The compute_xrd command does not work for triclinic cells.
diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt
index 8596cab51d24c6f0283d5d070192153d6d218534..fbf741d914b4d1978d5179fffecb929a487fc099 100644
--- a/doc/src/create_bonds.txt
+++ b/doc/src/create_bonds.txt
@@ -132,7 +132,7 @@ between 1 and the number of bond types defined.
The {single/angle} style creates a single angle of type {atype}
between three atoms with IDs {aatom1}, {aatom2}, and {aatom3}. The
ordering of the atoms is the same as in the {Angles} section of a data
-file read by the "read_data"_read_data command. I.e. the 3 atoms are
+file read by the "read_data"_read_data.html command. I.e. the 3 atoms are
ordered linearly within the angle; the central atom is {aatom2}.
{Atype} must be a value between 1 and the number of angle types
defined.
@@ -140,7 +140,7 @@ defined.
The {single/dihedral} style creates a single dihedral of type {btype}
between two atoms with IDs {batom1} and {batom2}. The ordering of the
atoms is the same as in the {Dihedrals} section of a data file read by
-the "read_data"_read_data command. I.e. the 4 atoms are ordered
+the "read_data"_read_data.html command. I.e. the 4 atoms are ordered
linearly within the dihedral. {Dtype} must be a value between 1 and
the number of dihedral types defined.
diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt
index 8adef6cf4b5ed1ee5f25ab1d72c7fc12f43078fc..637a10102dc1f79c65995c9361731b00777bd1c9 100644
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@@ -122,13 +122,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -146,8 +146,8 @@ Otherwise non-bonded contributions for these 1-4 pairs will be
computed multiple times.
These dihedral styles can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt
index 1a2f37abbbd0352fd04bc6e958912c0b17966627..9936f3768df703d8b2e63072499c3d0c96d2c3f8 100644
--- a/doc/src/dihedral_class2.txt
+++ b/doc/src/dihedral_class2.txt
@@ -147,13 +147,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -163,8 +163,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-CLASS2 package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+CLASS2 package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt
index 7ef27e6bc966b129156159c9714e27a2cc050853..e2a46d28d8ad9f686f6221e2594a7f3b7a4392d3 100644
--- a/doc/src/dihedral_cosine_shift_exp.txt
+++ b/doc/src/dihedral_cosine_shift_exp.txt
@@ -58,13 +58,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -74,8 +74,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt
index f51cbc9c8cd8e1aeed0248730d7b633a3d636f74..3045f6824b1b27d393a720578193cca47627b160 100644
--- a/doc/src/dihedral_fourier.txt
+++ b/doc/src/dihedral_fourier.txt
@@ -50,13 +50,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -66,8 +66,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt
index 1eda0c5d02b8f1a7bbba646ad26d684cff7e7806..27bc04f9df6d05cf8774270a2900a5fb96cf1d4c 100644
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -75,8 +75,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt
index 3af4b410bcd24e4469ccdc50e9576fb81cc9539c..3b3607337b91bb056d3ea7f4227cc3cabb07c3d7 100644
--- a/doc/src/dihedral_helix.txt
+++ b/doc/src/dihedral_helix.txt
@@ -52,13 +52,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -68,8 +68,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt
index c9ca86680c175aca2188891523265ca4d2203f81..a4a2a2808eb1ca170a315708fa92c23326840aae 100644
--- a/doc/src/dihedral_hybrid.txt
+++ b/doc/src/dihedral_hybrid.txt
@@ -77,8 +77,8 @@ for specific dihedral types.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
Unlike other dihedral styles, the hybrid dihedral style does not store
dihedral coefficient info for individual sub-styles in a "binary
diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt
index 7c22391923b37a065369b53c0871d20cd90710fe..74f1f6abc69cc1e1dfbe009a5ef096de88a0110a 100644
--- a/doc/src/dihedral_multi_harmonic.txt
+++ b/doc/src/dihedral_multi_harmonic.txt
@@ -46,13 +46,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,8 +62,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt
index aa8f1e0d7fdc646fa6c06009909b750294e06613..7a8bf6cdb7c6ce73c0593896ace978cac62e044a 100644
--- a/doc/src/dihedral_nharmonic.txt
+++ b/doc/src/dihedral_nharmonic.txt
@@ -46,13 +46,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,8 +62,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt
index f0cf91f30ad67fe914b376aef1c0c94ef5145955..7fa5d81a14a778baf76815ad2cc8cede3a5ae4ce 100644
--- a/doc/src/dihedral_opls.txt
+++ b/doc/src/dihedral_opls.txt
@@ -54,13 +54,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -70,8 +70,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt
index e65cf2dee86a2b108513f1d83a5cbfe29c8a0034..dc951e4269fdbf3752dd7f36aa366b81a06389fd 100644
--- a/doc/src/dihedral_quadratic.txt
+++ b/doc/src/dihedral_quadratic.txt
@@ -47,13 +47,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -63,8 +63,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt
index 10a757e8986d6d9c5f450a84bfffc6be81221078..61949174df8d052740a1f0676a8c68e8b00606dd 100644
--- a/doc/src/dihedral_spherical.txt
+++ b/doc/src/dihedral_spherical.txt
@@ -78,8 +78,8 @@ wn (typically 0.0 or 1.0) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt
index 6aff3f0994777390eba737e8273524f770fd5e8e..749f74e399559570fc52f0c8fa65be30a9557a1d 100644
--- a/doc/src/dihedral_style.txt
+++ b/doc/src/dihedral_style.txt
@@ -104,10 +104,9 @@ Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
Most dihedral styles are part of the MOLECULE 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 on packages.
-The doc pages for individual dihedral potentials tell if it is part of
-a package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual dihedral potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt
index d722ef7c82a76c67ac0353a02b1656b8a8de73c0..3f679f57093c95954927fddbe73a3aa9beeb94bd 100644
--- a/doc/src/dihedral_table.txt
+++ b/doc/src/dihedral_table.txt
@@ -180,13 +180,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -194,8 +194,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt
index cc7df8cdf9de397a6a91d9ec89bef542f5b5002a..b8e0ec64c8863ac4b87db5b7433c84c3c4dbff55 100644
--- a/doc/src/dihedral_table_cut.txt
+++ b/doc/src/dihedral_table_cut.txt
@@ -192,8 +192,8 @@ that matches the specified keyword.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index 5b478b7301960bd536ef29158086c0c8b0f34023..8b630cc7069ccc949579c5cda38cc1834a4c0d54 100644
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@@ -634,23 +634,22 @@ which could then be output into dump files.
[Restrictions:]
To write gzipped dump files, you must either compile LAMMPS with the
--DLAMMPS_GZIP option or use the styles from the COMPRESS package
-- see the "Making LAMMPS"_Section_start.html#start_2 section of
-the documentation.
+-DLAMMPS_GZIP option or use the styles from the COMPRESS package.
+See the "Build settings"_Build_settings.html doc page for details.
-The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are part
-of the COMPRESS package. They are only enabled if LAMMPS was built
-with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are part of
+the COMPRESS package. They are only enabled if LAMMPS was built with
+that package. See the "Build package"_Build_package.html doc page for
+more info.
The {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and {xyz/mpiio} styles
are part of the MPIIO 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.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
The {xtc} style is part of the MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt
index 665be14be1330e0b902c73686d430f3ce904a315..16e4aba4c04fd6db18adfb622e670ba8448ddc10 100644
--- a/doc/src/dump_cfg_uef.txt
+++ b/doc/src/dump_cfg_uef.txt
@@ -38,9 +38,9 @@ reference frame as the atomic positions.
[Restrictions:]
-This fix is part of the USER-UEF 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.
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt
index fbd682dad9cac9c112fc10ee30c31c922e00f4a0..9065e8a648b4ae8f600e680bac713298d2043f37 100644
--- a/doc/src/dump_h5md.txt
+++ b/doc/src/dump_h5md.txt
@@ -98,13 +98,13 @@ note above). Only orthogonal domains are currently supported. This is
a limitation of the present dump h5md command and not of H5MD itself.
The {h5md} dump style is part of the USER-H5MD 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. It also
-requires (i) building the ch5md library provided with LAMMPS (See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.) and
-(ii) having the "HDF5"_HDF5_ws library installed (C bindings are
-sufficient) on your system. The library ch5md is compiled with the
-h5cc wrapper provided by the HDF5 library.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. It also requires
+(i) building the ch5md library provided with LAMMPS (See the "Build
+package"_Build_package.html doc page for more info.) and (ii) having
+the "HDF5"_HDF5_ws library installed (C bindings are sufficient) on
+your system. The library ch5md is compiled with the h5cc wrapper
+provided by the HDF5 library.
:link(HDF5_ws,http://www.hdfgroup.org/HDF5/)
diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt
index 06332b5dcf92a593ba084c50f9daaacfd7fb4ae3..9b56dd95a6006878dc9e865be9c148093e3f52a5 100644
--- a/doc/src/dump_image.txt
+++ b/doc/src/dump_image.txt
@@ -142,8 +142,8 @@ framerate can be set using the "dump_modify"_dump_modify.html command.
To write out JPEG and PNG format files, you must build LAMMPS with
support for the corresponding JPEG or PNG library. To convert images
into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG
-flag. See "this section"_Section_start.html#start_2_4 of the manual
-for instructions on how to do this.
+flag. See the "Build settings"_Build_settings.html doc page for
+details.
NOTE: Because periodic boundary conditions are enforced only on
timesteps when neighbor lists are rebuilt, the coordinates of an atom
@@ -624,8 +624,7 @@ building LAMMPS and have the FFmpeg executable available on the
machine where LAMMPS is being run. Typically it's name is lowercase,
i.e. ffmpeg.
-See the "Making LAMMPS"_Section_start.html#start_2_4 section of the
-documentation for details on how to compile with optional switches.
+See the "Build settings"_Build_settings.html doc page for details.
Note that since FFmpeg is run as an external program via a pipe,
LAMMPS has limited control over its execution and no knowledge about
diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt
index 73107d07f786e40d60407423551ba839033d7948..98bcbc5e551e85216732c74afebbc6c6b361a663 100644
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@@ -133,7 +133,6 @@ dump_modify option below is valid for the {atom} style, it is also
valid for the {atom/mpiio} style, and similarly for the other styles
which allow for use of MPI-IO.
-:line
:line
These keywords apply to various dump styles, including the "dump
@@ -629,7 +628,6 @@ the coordinate would be if it had not been wrapped back into the
periodic box. Note that these coordinates may thus be far outside the
box size stored with the snapshot.
-:line
:line
These keywords apply only to the "dump image"_dump_image.html and
@@ -894,7 +892,6 @@ frame rate higher than 24 is not recommended, as it will result in
simply dropping the rendered images. It is more efficient to dump
images less frequently.
-:line
:line
[Restrictions:] none
diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt
index 9fa04bd1aeed0de92d8fac59dfe3e8e0d83bee3e..dd2b212f0baafc6efd4200c42eb4439e1d6715e3 100644
--- a/doc/src/dump_molfile.txt
+++ b/doc/src/dump_molfile.txt
@@ -90,8 +90,8 @@ determine the sequence of timesteps on which dump files are written.
[Restrictions:]
The {molfile} dump style is part of the USER-MOLFILE 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.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Molfile plugins provide a consistent programming interface to read and
write file formats commonly used in molecular simulations. The
diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt
index b1c63736514d00e4c35e1056aebab49d18f1cc54..52d757eac562083eff17a2dc5ffebfc741b5b2f5 100644
--- a/doc/src/dump_netcdf.txt
+++ b/doc/src/dump_netcdf.txt
@@ -66,8 +66,8 @@ by "thermo_style"_thermo_style.html.
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.
+that package. See the "Build package"_Build_package.html doc page for
+more info.
:line
diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt
index afc6099534eb5c80ffb18461f0f8426ea50bcc67..7eaa59a79505a18318633a031cf4a64e8a3d4b43 100644
--- a/doc/src/dump_vtk.txt
+++ b/doc/src/dump_vtk.txt
@@ -156,9 +156,9 @@ write out much faster.
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.
+The {vtk} dump style is part of the USER-VTK package. It is only
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page 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
diff --git a/doc/src/echo.txt b/doc/src/echo.txt
index dc6918dc8981af7b971e3e3cd406d29c6aa2e8b7..3436737faaa6f364c520b62c713647a96e63d7d7 100644
--- a/doc/src/echo.txt
+++ b/doc/src/echo.txt
@@ -26,8 +26,8 @@ command to the screen and/or log file as it is read and processed. If
an input script has errors, it can be useful to look at echoed output
to see the last command processed.
-The "command-line switch"_Section_start.html#start_6 -echo can be used
-in place of this command.
+The "command-line switch"_Run_options.html -echo can be used in place
+of this command.
[Restrictions:] none
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index fd966b5bd9916407648f6db1ea7f01d293faef10..9c3a1d0349fd097eb9f5572b943872bce1254a4e 100644
--- a/doc/src/fix.txt
+++ b/doc/src/fix.txt
@@ -309,9 +309,9 @@ accerlerated styles exist.
[Restrictions:]
Some fix styles are part of specific packages. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual fixes tell if it is part of a package.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual fixes tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt
index 51be39fdb2b72156560b0d85c56b6fc1a517056f..4fdf9a41ddefb31f80e5d391aee7b2adc60c5a35 100644
--- a/doc/src/fix_addforce.txt
+++ b/doc/src/fix_addforce.txt
@@ -112,13 +112,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt
index c80fad26da1c5e40d8a96f42c034f2f8b18cdb86..0963915e7a38aabb9db22c12a7fcac6b918c35a9 100644
--- a/doc/src/fix_addtorque.txt
+++ b/doc/src/fix_addtorque.txt
@@ -88,8 +88,8 @@ the iteration count during the minimization.
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_append_atoms.txt b/doc/src/fix_append_atoms.txt
index c6af361afcfe24a5da8cc97c4e917238fe981ab0..d83f265982cdaadc3303c751779e1d7cf9112b18 100644
--- a/doc/src/fix_append_atoms.txt
+++ b/doc/src/fix_append_atoms.txt
@@ -95,8 +95,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix style is part of the SHOCK 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The boundary on which atoms are added with append/atoms must be
shrink/minimum. The opposite boundary may be any boundary type other
diff --git a/doc/src/fix_atom_swap.txt b/doc/src/fix_atom_swap.txt
index c1d84dade1954b2a8d1ec15bb699cb99a5d1e1ae..22091eca005540b5316aee0bccd2c3d4e77aa2ba 100644
--- a/doc/src/fix_atom_swap.txt
+++ b/doc/src/fix_atom_swap.txt
@@ -165,8 +165,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC 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.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/src/fix_ave_correlate_long.txt
index ac0ef873aac6ae3cd90fca5077a3cc86e3160645..d94bf8af7b08daf2767255ddeaaed993c2e1691a 100644
--- a/doc/src/fix_ave_correlate_long.txt
+++ b/doc/src/fix_ave_correlate_long.txt
@@ -120,8 +120,8 @@ the run command. This fix is not invoked during energy minimization.
[Restrictions:]
This compute is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt
index 1fc7e4a18dd8f5efd1b84a21c0a785797be692a1..8c759864c67eb60bf8583d3654c4f4d51a55fca1 100644
--- a/doc/src/fix_aveforce.txt
+++ b/doc/src/fix_aveforce.txt
@@ -72,13 +72,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt
index f5bbc8a2519dcef980bdce8e3d08eb22a8789867..7acc22d702e4b7cfd496df2865fdbdc0844bd276 100644
--- a/doc/src/fix_bocs.txt
+++ b/doc/src/fix_bocs.txt
@@ -85,8 +85,8 @@ XXXX_press, where XXXX is the ID given to the fix bocs command (in the
example, the ID of the fix bocs command is 1 ).
This fix is part of the USER-BOCS 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related:]
diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt
index bdb2f2a8624869a8552992b246a111cb3396e7c5..59fea8f45b846b3ad94f4d9b29f8617025d1bb4d 100644
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
@@ -131,8 +131,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC 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.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt
index ab34433cecf631fbb8b9cff9fb87d43b87d7c07d..02655577fdb2f9c6d712638ef4ed781ae0b1b6dc 100644
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
@@ -226,8 +226,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC 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.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index 883968e012557e2ee8d13eddef15b8bc1f6873ef..7317dd26bb3b9d4b563b0266364490fafc39d37c 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -312,8 +312,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt
index a829171f333aa3aa850fbc04c659eae6ac61ad40..3c90bb53f6d57606bf1f82870477de9055ff15db 100644
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
@@ -165,8 +165,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC 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.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
The settings of the "special_bond" command must be 0,1,1 in order to
use this fix, which is typical of bead-spring chains with FENE or
diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt
index 8e21ec2c748963302db1fd9876cc855d0d1e35d8..29ebeaeef391d370c5bb3f6659ccf73e68fe990b 100644
--- a/doc/src/fix_box_relax.txt
+++ b/doc/src/fix_box_relax.txt
@@ -126,8 +126,6 @@ minimizer from the new adjusted box size/shape, since that creates a
new objective function valid for the new box size/shape. Repeat as
necessary until the box size/shape has reached its new equilibrium.
-:line
-:line
:line
The {couple} keyword allows two or three of the diagonal components of
diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt
index 6f3769fafe6a634770dcdedb8908540972ee5d70..ef48e8b51c6c445f3ff1d0e365ec054392ee956f 100644
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@@ -125,8 +125,8 @@ To function as expected this fix command must be issued {before} a
"read_restart"_read_restart.html command.
This fix can only be used if LAMMPS was built with the MOLECULE
-package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt
index 4a1d84de64a458dbc56999885ca8246a03ba21ed..3a64840bdcc10620033873ce65a42900a7e1a866 100644
--- a/doc/src/fix_colvars.txt
+++ b/doc/src/fix_colvars.txt
@@ -106,8 +106,8 @@ fix is "extensive".
[Restrictions:]
This fix is part of the USER-COLVARS 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
There can only be one colvars fix active at a time. Since the interface
communicates only the minimum amount of information and colvars module
diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt
index e92d1e6b19c5943d4de785c916738fdd10dc8ef0..d35c3065a224ae25972e92bfb8b610fc47bdc2f2 100644
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@@ -94,7 +94,7 @@ nvt/sllod"_fix_nvt_sllod.html and "compute
temp/deform"_compute_temp_deform.html commands for more details. Note
that simulation of a continuously extended system (extensional flow)
can be modeled using the "USER-UEF
-package"_Packages_details.html#USER-UEF and its "fix
+package"_Packages_details.html#PKG-USER-UEF and its "fix
commands"_fix_nh_uef.html.
For the {x}, {y}, {z} parameters, the associated dimension cannot be
@@ -556,13 +556,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt
index 277ca8777ad7409e586eb16344df34168786c165..265f43bd4be218146ce5384c59b7d57b74ca3bda 100644
--- a/doc/src/fix_deposit.txt
+++ b/doc/src/fix_deposit.txt
@@ -271,8 +271,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The specified insertion region cannot be a "dynamic" region, as
defined by the "region"_region.html command.
diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt
index f539bc534e76b7e667938ce4dcd78a2f9501ed4e..5e8e295de915c91c4df76d59815f2f919f0f0190 100644
--- a/doc/src/fix_dpd_energy.txt
+++ b/doc/src/fix_dpd_energy.txt
@@ -56,13 +56,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -72,8 +72,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix must be used with an additional fix that specifies time
integration, e.g. "fix nve"_fix_nve.html.
diff --git a/doc/src/fix_dpd_source.txt b/doc/src/fix_dpd_source.txt
index 04af9a28a184676e1ebc51f67dc13eb5340787a0..691cfe86f15c1840f9fd0b6c2ef1baefa7bf54bb 100644
--- a/doc/src/fix_dpd_source.txt
+++ b/doc/src/fix_dpd_source.txt
@@ -71,8 +71,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MESO 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Fix {edpd/source} must be used with the "pair_style
edpd"_pair_meso.html command. Fix {tdpd/source} must be used with the
diff --git a/doc/src/fix_efield.txt b/doc/src/fix_efield.txt
index b5a43f68aa76b5a205f50df3e6ff9325099711bb..cecfb6e6a3ce804b958fd36b89b476e6d466cd2d 100644
--- a/doc/src/fix_efield.txt
+++ b/doc/src/fix_efield.txt
@@ -156,8 +156,8 @@ system (the quantity being minimized), you MUST enable the
[Restrictions:]
This fix is part of the MISC 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt
index cfcc917d012ba1dca5ff08afd75fb718bb101f82..75651e21a4c5812593699735b9eaf1bc2a549bc7 100644
--- a/doc/src/fix_ehex.txt
+++ b/doc/src/fix_ehex.txt
@@ -156,8 +156,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the RIGID 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt
index 2925e44bda17ef8cf023a9e41c0513694d4c50fa..17ac8146fd3242d531df02ba409dba553d946b9f 100644
--- a/doc/src/fix_enforce2d.txt
+++ b/doc/src/fix_enforce2d.txt
@@ -37,13 +37,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_eos_cv.txt b/doc/src/fix_eos_cv.txt
index b94e2c64a97ebd8373b3a3dafcee2ab9ecad6ed5..b2ac0eb6b932396ab229d8a14292d65cb1d99b39 100644
--- a/doc/src/fix_eos_cv.txt
+++ b/doc/src/fix_eos_cv.txt
@@ -39,8 +39,8 @@ possible.
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt
index 743c51f4157cfeffc8c59840f9f95ab3132a3d74..53b32043728d9213e15b2ff86d5b301e0dabf2c5 100644
--- a/doc/src/fix_eos_table.txt
+++ b/doc/src/fix_eos_table.txt
@@ -99,8 +99,8 @@ one that matches the specified keyword.
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt
index f9deab61c8acebfb5ffe69966b1880e7cacff369..1a2daa0bc646f19bec6032c43a2adfb28e4d5c36 100644
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@@ -162,13 +162,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -178,8 +178,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt
index 6237a137fd0aa8c719d5f96f7791ebb176b669da..59dab43d9a200465ba18e883cdb2e3a4dd80b23b 100644
--- a/doc/src/fix_evaporate.txt
+++ b/doc/src/fix_evaporate.txt
@@ -84,8 +84,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_external.txt b/doc/src/fix_external.txt
index 1dec226414c9f7e62b13b3d60a2f34efc6326ccd..dd7f7914e96f365db3d523578e88efa8068aee5d 100644
--- a/doc/src/fix_external.txt
+++ b/doc/src/fix_external.txt
@@ -34,7 +34,7 @@ This fix allows external programs that are running LAMMPS through its
"library interface"_Howto_library.html to modify certain LAMMPS
properties on specific timesteps, similar to the way other fixes do.
The external driver can be a "C/C++ or Fortran
-program"_Howto_library.html or a "Python script"_Python.html.
+program"_Howto_library.html or a "Python script"_Python_head.html.
:line
diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt
index d1e5e12f3ef1b764d4d2d9cc35a5d8f504c27a4e..b30966c2f941de518e42f4c90463f543a21fdad5 100644
--- a/doc/src/fix_filter_corotate.txt
+++ b/doc/src/fix_filter_corotate.txt
@@ -70,8 +70,8 @@ fixes are not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Currently, it does not support "molecule templates"_molecule.html.
diff --git a/doc/src/fix_flow_gauss.txt b/doc/src/fix_flow_gauss.txt
index 843c2a66a5505d5b3c7051fd9d84897a99ea4138..46a9477aa2184e4bb7699f8462db78aaf8316bbf 100644
--- a/doc/src/fix_flow_gauss.txt
+++ b/doc/src/fix_flow_gauss.txt
@@ -111,8 +111,8 @@ flow/gauss fixes, one that specifies {fix_modify respa 3} and one with
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
No information about this fix is written to "binary restart
files"_restart.html.
diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt
index 76a9fd3b1a2d3f3ffc8372a2cebac2ac85f9fb6f..89f2dd8179f9f6ab02cf054c24f790e9c10e7662 100644
--- a/doc/src/fix_freeze.txt
+++ b/doc/src/fix_freeze.txt
@@ -40,13 +40,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -72,8 +72,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
There can only be a single freeze fix defined. This is because other
the "granular pair styles"_pair_gran.html treat frozen particles
diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt
index 394690ea5d173b898b51acc6ee9b2094aa5d26b1..6b9a02eecada3fa7f2e8f2886b8ff6b88a106d7c 100644
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@@ -403,8 +403,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC 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.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
diff --git a/doc/src/fix_gld.txt b/doc/src/fix_gld.txt
index 1c5db6157ddaca593ffc5fc70ebc59613038ae88..97c3d0e408e9ea2d4eb675a994cb7c96a579b0e6 100644
--- a/doc/src/fix_gld.txt
+++ b/doc/src/fix_gld.txt
@@ -137,8 +137,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt
index 9fdc72bf9f206f9b5a6e55267638af159810beeb..70a8e7f34246b446d4b40456945c784b11c54665 100644
--- a/doc/src/fix_gle.txt
+++ b/doc/src/fix_gle.txt
@@ -132,9 +132,9 @@ In order to perform constant-pressure simulations please use
"fix npt"_fix_nh.html, to avoid duplicate integration of the
equations of motion.
-This fix is part of the USER-MISC 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.
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt
index 832c677f81559e3893e643dc32330d0e9699a1f7..ea596c866867e89f3c4b6b8a598ead8662976e57 100644
--- a/doc/src/fix_gravity.txt
+++ b/doc/src/fix_gravity.txt
@@ -96,13 +96,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt
index 506e266505a54248fee381d4135802122fd86aba..e096d4bd3cbe8ee0d461444985ac932f38bab787 100644
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@@ -91,8 +91,8 @@ by this fix to add the rescaled kinetic pressure as part of
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_imd.txt b/doc/src/fix_imd.txt
index 8e21a1619b8647b0ba6c497540ac2b7c4973b36a..a58cfdb3d396d7bec9ad67324bec3ba0bbe60fb1 100644
--- a/doc/src/fix_imd.txt
+++ b/doc/src/fix_imd.txt
@@ -143,8 +143,8 @@ fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
When used in combination with VMD, a topology or coordinate file has
to be loaded, which matches (in number and ordering of atoms) the
diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt
index eba30ef08821d7c55ab06270d18a4300da293de5..b115aba7dfa38d5a85a0aee82000d2e8bf568fcd 100644
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@@ -81,9 +81,9 @@ define an external potential acting on the atoms that are moved by
i-PI.
This fix is part of the USER-MISC 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. Because of
-the use of UNIX domain sockets, this fix will only work in a UNIX
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Because of the
+use of UNIX domain sockets, this fix will only work in a UNIX
environment.
[Related commands:]
diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt
index 4d7728cdba4b918d1cc8926f2aaef266bc20a42b..e97c7c3c3785011551f6c7b476c709acc2ec1925 100644
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@@ -270,13 +270,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt
index cf42f9c036b2dc4da5a9f2afb98296d8a78862d4..e55e40c6c80ea7e822222ffc84eedbbf9841d9e3 100644
--- a/doc/src/fix_langevin_eff.txt
+++ b/doc/src/fix_langevin_eff.txt
@@ -93,8 +93,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
This fix is part of the USER-EFF 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt
index 1b1936376de0fe29450cf9b4c2db7e298e6d64ab..7bb25e0a687af2c0af3f14a1ccd9d0c9a73e7257 100644
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/src/fix_langevin_spin.txt
@@ -76,9 +76,9 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-The {langevin/spin} fix is part of the SPIN package.
-This style is only enabled if LAMMPS was built with this package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+The {langevin/spin} fix is part of the SPIN package. This style is
+only enabled if LAMMPS was built with this package. See the "Build
+package"_Build_package.html doc page for more info.
The numerical integration has to be performed with {fix nve/spin}
when {fix langevin/spin} is enabled.
diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt
index 9bc589520bc3689a4ad4370f99e92b9977bb209c..bd61e29dcb66f9c19772345cbe3c19161143474e 100644
--- a/doc/src/fix_latte.txt
+++ b/doc/src/fix_latte.txt
@@ -136,11 +136,11 @@ quantity being minimized), you MUST enable the
[Restrictions:]
This fix is part of the LATTE 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
-You must use metal units, as set by the "units"_units command to use
-this fix.
+You must use metal units, as set by the "units"_units.html command to
+use this fix.
LATTE does not currently compute per-atom energy or per-atom virial
contributions. So they will not show up as part of the calculations
@@ -154,8 +154,8 @@ doing 99% or more of the work to compute quantum-accurate forces.
NOTE: NEB calculations can be done using this fix using multiple
replicas and running LAMMPS in parallel. However, each replica must
be run on a single MPI task. For details, see the "neb"_neb.html
-command and -partition command-line explained in "Section
-2.6"_Section_start.html#start_6 of the manual.
+command doc page and the "-partition command-line
+switch"_Run_options.html
[Related commands:] none
diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt
index 5347f0147f4be26b5e3b61877084925003c4fbf4..1a5239782268f34870cd3ec3faac1b560f7c451a 100644
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@@ -307,8 +307,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-LB 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix can only be used with an orthogonal simulation domain.
diff --git a/doc/src/fix_lb_momentum.txt b/doc/src/fix_lb_momentum.txt
index a58c5d257eabeb012284a3fd2dd3e2eecd20c1d7..408978f64c40cb1eff59995ed62481c1200b4960 100644
--- a/doc/src/fix_lb_momentum.txt
+++ b/doc/src/fix_lb_momentum.txt
@@ -61,8 +61,8 @@ Can only be used if a lattice-Boltzmann fluid has been created via the
command.
This fix is part of the USER-LB 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt
index bd121b7813253cb3b9e547235db88cdc85e5e472..05b5eb20a21ce268024eda47782fae035496efb2 100644
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
@@ -42,8 +42,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-LB 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
"fix lb/fluid"_fix_lb_fluid.html command, and must come after this
diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/src/fix_lb_rigid_pc_sphere.txt
index bc8fa2ea257212f588dabe01b824d98ff4289a1b..ddaa552ecc15165daa71f813b532e3737f5f6e80 100644
--- a/doc/src/fix_lb_rigid_pc_sphere.txt
+++ b/doc/src/fix_lb_rigid_pc_sphere.txt
@@ -122,8 +122,8 @@ of the "run"_run.html command. These fixes are not invoked during
[Restrictions:]
This fix is part of the USER-LB 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
"fix lb/fluid"_fix_lb_fluid.html command, and must come after this
diff --git a/doc/src/fix_lb_viscous.txt b/doc/src/fix_lb_viscous.txt
index 7bbdd204e34d1a4fae91fcf2f4bb2aa4c32fefbf..ba91a2cd541984096f79925097f2c38d9db17eee 100644
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
@@ -70,8 +70,8 @@ for details."
[Restrictions:]
This fix is part of the USER-LB 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
"fix lb/fluid"_fix_lb_fluid.html command, and must come after this
diff --git a/doc/src/fix_manifoldforce.txt b/doc/src/fix_manifoldforce.txt
index aa32a875bfe2f77de00cdbee7f87085af8443a94..a25b9f0b2e1c47d951d81906580dc6d011e32ea6 100644
--- a/doc/src/fix_manifoldforce.txt
+++ b/doc/src/fix_manifoldforce.txt
@@ -24,10 +24,14 @@ fix constrain all manifoldforce sphere 5.0
[Description:]
-This fix subtracts each time step from the force the component along the normal of the specified "manifold"_manifolds.html.
-This can be used in combination with "minimize"_minimize.html to remove overlap between particles while
-keeping them (roughly) constrained to the given manifold, e.g. to set up a run with "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html.
-I have found that only {hftn} and {quickmin} with a very small time step perform adequately though.
+This fix subtracts each time step from the force the component along
+the normal of the specified "manifold"_Howto_manifold.html. This can be
+used in combination with "minimize"_minimize.html to remove overlap
+between particles while keeping them (roughly) constrained to the
+given manifold, e.g. to set up a run with "fix
+nve/manifold/rattle"_fix_nve_manifold_rattle.html. I have found that
+only {hftn} and {quickmin} with a very small time step perform
+adequately though.
:line
@@ -45,17 +49,18 @@ minimization"_minimize.html.
[Restrictions:]
-This fix is part of the USER-MANIFOLD 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.
+This fix is part of the USER-MANIFOLD package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
-Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
-will not be satisfied very well at all. A warning is generated if the {min_style} is
-incompatible but no error.
+Only use this with {min_style hftn} or {min_style quickmin}. If not,
+the constraints will not be satisfied very well at all. A warning is
+generated if the {min_style} is incompatible but no error.
:line
[Related commands:]
-"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html, "fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
+"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html, "fix
+nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
diff --git a/doc/src/fix_meso.txt b/doc/src/fix_meso.txt
index 8f5ad29929313fc6d1b31169b140b5dad0d46959..8c0ce5a9b7b729b42ce2f13a3c612c1ea46cd096 100644
--- a/doc/src/fix_meso.txt
+++ b/doc/src/fix_meso.txt
@@ -42,8 +42,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-SPH 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_meso_stationary.txt b/doc/src/fix_meso_stationary.txt
index 38d26b34d67ad7d0a38eec70c7f28583394778eb..1a546efec06e64e6f125b53e006f78db7e2f5d69 100644
--- a/doc/src/fix_meso_stationary.txt
+++ b/doc/src/fix_meso_stationary.txt
@@ -43,8 +43,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-SPH 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt
index f7fe35be2a9fd3825b82db9a0cd3d3cca76dfb56..aeedad07197163423a2a3db32025095294fbf676 100644
--- a/doc/src/fix_momentum.txt
+++ b/doc/src/fix_momentum.txt
@@ -67,13 +67,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt
index aadc3caf5aa909c8ff32f23d51bcac2d3f0919ab..1ad780412756a117c28e8ac193295206e153c811 100644
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@@ -103,8 +103,8 @@ dihedrals a bead can have in the coarse-grained model.
[Restrictions:]
This fix is part of the MSCG 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.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
The MS-CG library uses C++11, which may not be supported by older
compilers. The MS-CG library also has some additional numeric library
diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt
index 91ffbbb0fa147ea6e520ac75658d114198654da6..e31f61e5f7c815c8a0253b3db69b6f8c8fcb6a35 100644
--- a/doc/src/fix_msst.txt
+++ b/doc/src/fix_msst.txt
@@ -162,8 +162,8 @@ are "extensive"; the vector values are "intensive".
[Restrictions:]
This fix style is part of the SHOCK 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The MSST fix has been tested only for the group-ID
diff --git a/doc/src/fix_mvv_dpd.txt b/doc/src/fix_mvv_dpd.txt
index 1e9bf631fde813d95546bcc6638b3c24172a0e79..507f271469df32842ba0dbd29630c513d79c8c3c 100644
--- a/doc/src/fix_mvv_dpd.txt
+++ b/doc/src/fix_mvv_dpd.txt
@@ -77,8 +77,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MESO 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt
index 5341d6999c4e6b0f5220af5d5d77ebd331176fbb..d331d9ad75fbf7c2a203bfe68bb1035abcfd410a 100644
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@@ -203,8 +203,8 @@ as invoked by the "minimize"_minimize.html command via the
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt
index f6b155e2db2c66bad86e479a8d1ee67d86fd51a7..644ced4bdc6c0aaba54d27dc59004aebb0f16022 100644
--- a/doc/src/fix_nh.txt
+++ b/doc/src/fix_nh.txt
@@ -491,13 +491,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nh_eff.txt b/doc/src/fix_nh_eff.txt
index afb319bfa51f6c518b213f63f75cbab14741e0bc..d7c045770860e1792dacb682170f6e64034282e6 100644
--- a/doc/src/fix_nh_eff.txt
+++ b/doc/src/fix_nh_eff.txt
@@ -101,8 +101,8 @@ for details.
[Restrictions:]
This fix is part of the USER-EFF 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Other restriction discussed on the doc page for the "fix nvt, npt, and
nph"_fix_nh.html commands also apply.
diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt
index 0e73c57e089b44643834f1b78fad2c1f046281f4..ae403cafd1d8ff7c5ee8f6e7fcc0589dd9437cb6 100644
--- a/doc/src/fix_nh_uef.txt
+++ b/doc/src/fix_nh_uef.txt
@@ -182,8 +182,8 @@ The fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-UEF 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Due to requirements of the boundary conditions, when the {strain}
keyword is set to zero (or unset), the initial simulation box must be
diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt
index 6bfd9d3fe26085cff9f1d3c5c0b32fbbd5c5948a..5cabf930e73b00b9eb2e46701c026b1f37397985 100644
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
@@ -87,13 +87,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -132,8 +132,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt
index 377e1980eb3cf8c9c46b41baa6a14b2e379c7816..e04c240de951965f94124617a1e88e658f5b8402 100644
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
@@ -86,13 +86,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -131,8 +131,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt
index 8b7639c4c6a7467e9107db127699efabea8a8993..f94c057c93f300a911b5f524087187038f58fc48 100644
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
@@ -96,13 +96,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt
index 0bd5153152b4afdcd8a0048b0472df81ad63ed08..855a4c9ae49fb49cf7929b59f796a8dc6dc89a30 100644
--- a/doc/src/fix_nphug.txt
+++ b/doc/src/fix_nphug.txt
@@ -146,13 +146,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -208,8 +208,8 @@ shock calculated from the RH conditions. They have units of distance/time.
[Restrictions:]
This fix style is part of the SHOCK 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
All the usual restrictions for "fix npt"_fix_nh.html apply,
plus the additional ones mentioned above.
diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt
index 9c95a80d3310a08e3e8ddecd12af471419340773..194f4ff499ea8763112456accddb26f308fb738e 100644
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
@@ -111,13 +111,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -157,8 +157,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt
index 0d2b797299dd4d3c803e96cbfb1f4030ac13c032..1d608137b619e5b989c212a8aad83d92753c0570 100644
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
@@ -110,13 +110,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -156,8 +156,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt
index dcb25d1c737b39f3a2bcea9a4e01eb1a011fbb60..6ebb68e176311fe1eda0c1d71a2c84a6861a8366 100644
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
@@ -121,13 +121,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt
index e446b273977b4dd05865de697b3d10af144bb149..2347f957aef8636dc1e8ab2261cee737c93de8e5 100644
--- a/doc/src/fix_nve.txt
+++ b/doc/src/fix_nve.txt
@@ -40,13 +40,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt
index b7fb3e922ce418d666b0cfe9b87170daa7c195ed..bd9e4ae8731b35fdc140063e6f76c80dea58ef61 100644
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
@@ -51,13 +51,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -67,8 +67,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This fix is part of the ASPHERE 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt
index e57417bda5e1657ca69a621840ea82f2199b14b1..c0598e8839090202cfb662cb75959a06debcc4e7 100644
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
@@ -29,7 +29,7 @@ angular momenta are used to update their positions and orientation.
This is useful as an implicit time integrator for Fast Lubrication
Dynamics, since the velocity and angular momentum are updated by the
-"pair_style lubricuteU"_pair_lubricateU.txt command.
+"pair_style lubricuteU"_pair_lubricateU.html command.
:line
@@ -46,8 +46,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt
index d072bfa1611770921b5e97f7f1fb2bce2128c748..1a9efb5e139f99efd1ed8008b6e4fdcb10c6b84e 100644
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
@@ -44,8 +44,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt
index 1041a248d8784a0cfae575f1d5a515a4e2c76e35..06140c2d37361b3017ac685df08536ea34d1ca6a 100644
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@@ -44,8 +44,8 @@ A technical report with more information on this integrator can be found
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt
index 68c1b4232830fe1a2eaaadaf8ce832474a394f13..7339f251ad1c3ebbd56d8e754e4ea336f2fd76f6 100644
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@@ -122,8 +122,8 @@ A technical report with more information on this integrator can be found
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_nve_eff.txt b/doc/src/fix_nve_eff.txt
index 7343ddc4292df0f02e7eadef7829ec8041ccae5b..556b95deba6d5400466d088c8b34c9bdf1d24e56 100644
--- a/doc/src/fix_nve_eff.txt
+++ b/doc/src/fix_nve_eff.txt
@@ -43,8 +43,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-EFF 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_nve_line.txt b/doc/src/fix_nve_line.txt
index dd5101489b00d27a707ac4c044bed5f4a84be643..896e3b810d83049198c1e0f7f630d545836698c7 100644
--- a/doc/src/fix_nve_line.txt
+++ b/doc/src/fix_nve_line.txt
@@ -44,8 +44,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that particles be line segments as defined by the
"atom_style line"_atom_style.html command.
diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt
index b333d093fb8eec0ce08d16c8affb3a2cf481c802..5301ea603ce65747344f68fe42bf93233ecccac7 100644
--- a/doc/src/fix_nve_manifold_rattle.txt
+++ b/doc/src/fix_nve_manifold_rattle.txt
@@ -78,8 +78,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MANIFOLD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
:line
diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt
index 6e259bdb8e7803482ee894d68d2a354dcefc0e6f..818940a9bd1ebda7b50c44120a209aaa4ef4e270 100644
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
@@ -71,13 +71,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt
index e31185bc889e785030dbef61a36019a7ba086af0..08f0eab61dcfd4f505d1c840f0a0fb434c336c18 100644
--- a/doc/src/fix_nve_spin.txt
+++ b/doc/src/fix_nve_spin.txt
@@ -47,9 +47,9 @@ in "(Tranchida)"_#Tranchida1.
[Restrictions:]
-This fix style can only be used if LAMMPS was built with the
-SPIN package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+This fix style can only be used if LAMMPS was built with the SPIN
+package. See the "Build package"_Build_package.html doc page for more
+info.
To use the spin algorithm, it is necessary to define a map with
the atom_modify command. Typically, by adding the command:
diff --git a/doc/src/fix_nve_tri.txt b/doc/src/fix_nve_tri.txt
index ebdda19e36428828bdbeb6558b3202cc00982a80..c14907ca02596e448a3ee9004574f93bd3fd2e35 100644
--- a/doc/src/fix_nve_tri.txt
+++ b/doc/src/fix_nve_tri.txt
@@ -44,8 +44,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that particles be triangles as defined by the
"atom_style tri"_atom_style.html command.
diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt
index e3189f8e8a3981b76f848f64080b6baa50500738..98f63487b73144d9cc155ffd937147d0358d618b 100644
--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@@ -54,9 +54,9 @@ the simulation box. Therefore, the group must be set to all.
This fix has not yet been implemented to work with the RESPA integrator.
-This fix is part of the USER-MISC 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.
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:] none
diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt
index 7b9763717574062e64b9e812bd201d8174cb4880..a2187f8495f63ddec697337b417a16f53348da5f 100644
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
@@ -92,13 +92,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -133,8 +133,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt
index 4493a892777221ee5c4375769438f8c02cfaf570..62c7cfecf822973c40c343c17eb2c3e54e3a6d74 100644
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
@@ -91,13 +91,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -132,8 +132,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt
index 1b4ad7916626ea3550b69c4aef84514318acb30e..0c4b81aa32d83fa348ec660116a0ce8b53b56a34 100644
--- a/doc/src/fix_nvt_manifold_rattle.txt
+++ b/doc/src/fix_nvt_manifold_rattle.txt
@@ -27,8 +27,6 @@ keyword = {temp} or {tchain} or {every}
N = length of thermostat chain (1 = single thermostat)
{every} value = N
N = print info about iteration every N steps. N = 0 means no output :pre
-
-
:ule
[Examples:]
@@ -59,20 +57,18 @@ minimization"_minimize.html.
:line
-
[Restrictions:]
-This fix is part of the USER-MANIFOLD 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.
+This fix is part of the USER-MANIFOLD package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
:line
-
[Related commands:]
-"fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html
-[Default:] every = 0
+"fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix
+manifoldforce"_fix_manifoldforce.html [Default:] every = 0
:line
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index 9eb506536910f574867121e26d6dee23ff8071a0..97a864a231d32cbc503031840d17384fcfa8e44f 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -115,13 +115,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt
index 0200d5cb002312980fb21344687676dd06d74fee..5cba15c8cf3f3af230263ba9215efca001144726 100644
--- a/doc/src/fix_nvt_sllod_eff.txt
+++ b/doc/src/fix_nvt_sllod_eff.txt
@@ -69,8 +69,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-EFF 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix works best without Nose-Hoover chain thermostats, i.e. using
tchain = 1. Setting tchain to larger values can result in poor
diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt
index a87e4abe677ed4c44d6b54470e5d2ee9539d8f7c..75222e0de81d09462d5b1465c3f232f2a4903c44 100644
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
@@ -102,13 +102,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt
index 7552bea8c5bcfb73867322c90f502887276aacf9..9d8e4e86282727eaa85292803f1095e2224596f8 100644
--- a/doc/src/fix_orient.txt
+++ b/doc/src/fix_orient.txt
@@ -151,8 +151,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix should only be used with fcc or bcc lattices.
diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt
index 30e5864e3d16af76cdc86ea021c0cf80fda6b2ff..0c449899df2a15965649820af6202e7f06bd702f 100644
--- a/doc/src/fix_phonon.txt
+++ b/doc/src/fix_phonon.txt
@@ -171,11 +171,11 @@ temperature of the system should not exceed the melting temperature to
keep the system in its solid state.
This fix is part of the USER-PHONON 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
-This fix requires LAMMPS be built with an FFT library. See the
-"Making LAMMPS"_Section_start.html#start_2 section for more info.
+This fix requires LAMMPS be built with an FFT library. See the "Build
+settings"_Build_settings.html doc page for details.
[Related commands:]
diff --git a/doc/src/fix_pimd.txt b/doc/src/fix_pimd.txt
index b61b3f3065a7c0c57f5994a2a2a23d6ed8778407..a82624497308567c3528413e6c052a63c693605c 100644
--- a/doc/src/fix_pimd.txt
+++ b/doc/src/fix_pimd.txt
@@ -136,8 +136,8 @@ read_restart system_$\{ibead\}.restart2 :pre
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
A PIMD simulation can be initialized with a single data file read via
the "read_data"_read_data.html command. However, this means all
diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt
index 1a79c2a048fb75dc04935e978fdc50ae84ab9e69..52ab0ca44d7a740113441c0dd9d9e9a55f9b84a3 100644
--- a/doc/src/fix_poems.txt
+++ b/doc/src/fix_poems.txt
@@ -123,8 +123,8 @@ minimization"_minimize.html.
This fix is part of the POEMS package. It is only enabled if LAMMPS
was built with that package, which also requires the POEMS library be
-built and linked with LAMMPS. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built and linked with LAMMPS. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt
index e58d8ebc3ad90069a45cfd92ae504ce4656305dc..65f01c00fb85d7335afa734263a4c7da0a71255a 100644
--- a/doc/src/fix_pour.txt
+++ b/doc/src/fix_pour.txt
@@ -245,8 +245,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
For 3d simulations, a gravity fix in the -z direction must be defined
for use in conjunction with this fix. For 2d simulations, gravity
diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt
index fafe78448be133680f5b22711403262f1f28086b..d58cd622b0913de70a3674396bc856771c1c9212 100644
--- a/doc/src/fix_precession_spin.txt
+++ b/doc/src/fix_precession_spin.txt
@@ -75,10 +75,10 @@ files"_restart.html.
[Restrictions:]
-The {precession/spin} style is part of the SPIN package.
-This style is only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+The {precession/spin} style is part of the SPIN package. This style
+is only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt
index 136ed6c15e6ecb9de65599eb41a821d6487bbf69..8a70cd8213ccc223c279e6961bf31b059c2dbf1d 100644
--- a/doc/src/fix_property_atom.txt
+++ b/doc/src/fix_property_atom.txt
@@ -200,7 +200,8 @@ added classes.
:line
-:link(isotopes) Example for using per-atom masses with TIP4P water to
+:link(isotopes)
+Example for using per-atom masses with TIP4P water to
study isotope effects. When setting up simulations with the "TIP4P
pair styles"_Howto_tip4p.html for water, you have to provide exactly
one atom type each to identify the water oxygen and hydrogen
diff --git a/doc/src/fix_python_invoke.txt b/doc/src/fix_python_invoke.txt
index 5e0c0369a54b62f81c5c14c6360d182c1f655df0..2a0124e6bfc0dd01d65f3b47d76df3a7de1bebc4 100644
--- a/doc/src/fix_python_invoke.txt
+++ b/doc/src/fix_python_invoke.txt
@@ -62,9 +62,9 @@ case not work or in the worst case result in undefined behavior.
[Restrictions:]
-This fix is part of the PYTHON 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.
+This fix is part of the PYTHON package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Building LAMMPS with the PYTHON package will link LAMMPS with the
Python library on your system. Settings to enable this are in the
diff --git a/doc/src/fix_python_move.txt b/doc/src/fix_python_move.txt
index a4e0eb39376ea0945bd667ce6625c406b697534a..c64ee788af9354955eb9fd2b63d07f8dcf773945 100644
--- a/doc/src/fix_python_move.txt
+++ b/doc/src/fix_python_move.txt
@@ -91,8 +91,8 @@ minimization"_minimize.html.
[Restrictions:]
This pair style is part of the PYTHON 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_qbmsst.txt b/doc/src/fix_qbmsst.txt
index e96bd97f4587cfa7446b5adc5606a6f4e13df09d..546d8c0813235c18868dfc47ad07b60d799e4d1d 100644
--- a/doc/src/fix_qbmsst.txt
+++ b/doc/src/fix_qbmsst.txt
@@ -189,8 +189,8 @@ in the command "fix qtb"_fix_qtb.html.
[Restrictions:]
This fix style is part of the USER-QTB 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The QBMSST fix has been tested only for the group-ID
diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt
index 27fb613ef957fc91f280f5eccf7328afcc1cdb35..46d2dd918cfc9f260a5307bdbd7657c8a671fa56 100644
--- a/doc/src/fix_qeq.txt
+++ b/doc/src/fix_qeq.txt
@@ -187,8 +187,8 @@ Thexe fixes are invoked during "energy minimization"_minimize.html.
[Restrictions:]
These fixes are part of the QEQ 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt
index 99e86df030fb80215b1dfceab6d521fd8f4167f8..714d03f6020f398d04fb3ee67d8f395c3f9a9a21 100644
--- a/doc/src/fix_qeq_comb.txt
+++ b/doc/src/fix_qeq_comb.txt
@@ -68,13 +68,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt
index cf16daf84731096ec617c9abce809de80764ee73..b62d46d9de3a21e76a4f9405cc8acabaaa7009a0 100644
--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@@ -86,13 +86,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -102,8 +102,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix does not correctly handle interactions
involving multiple periodic images of the same atom. Hence, it should not
diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt
index 657ee841810a25338390cb7c14d6218691dfd6c1..2dbf935f93d3e82d7db6cbf8488da63e9d57812d 100644
--- a/doc/src/fix_qmmm.txt
+++ b/doc/src/fix_qmmm.txt
@@ -54,8 +54,8 @@ fix is not invoked during "energy minimization"_minimize.html.
This fix is part of the USER-QMMM package. It is only enabled if
LAMMPS was built with that package. It also requires building a
-library provided with LAMMPS. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+library provided with LAMMPS. See the "Build
+package"_Build_package.html doc page for more info.
The fix is only functional when LAMMPS is built as a library and
linked with a compatible QM program and a QM/MM frontend into a QM/MM
diff --git a/doc/src/fix_qtb.txt b/doc/src/fix_qtb.txt
index 5b212934a94780b1d6e34c8c90873519b1bcc543..c412146604d49dd4bded74ee6e97b4e885256405 100644
--- a/doc/src/fix_qtb.txt
+++ b/doc/src/fix_qtb.txt
@@ -155,8 +155,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix style is part of the USER-QTB 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
:line
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt
index 49d61f4db80d45f1993bec664a07bc249f259ca1..06d30d871adbc423057799f1469aba3d50c505ff 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@@ -79,13 +79,13 @@ issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "Speed"_Speed.html of the manual for
more instructions on how to use the accelerated styles effectively.
@@ -101,8 +101,8 @@ 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_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.
+package. See the "Build package"_Build_package.html doc page for more
+info.
To write gzipped bond files, you must compile LAMMPS with the
-DLAMMPS_GZIP option.
diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt
index 5be1c46230b477e62f07ff70c9dcf02c03ef7da3..980384ff34c778e6ee3246c91762faff19b9e37e 100644
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@@ -146,13 +146,13 @@ issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "Speed"_Speed.html of the manual for
more instructions on how to use the accelerated styles effectively.
@@ -161,12 +161,12 @@ more instructions on how to use the accelerated styles effectively.
[Restrictions:]
-The fix species currently only works with
-"pair_style reax/c"_pair_reaxc.html and it requires that the "pair_style
+The fix species currently only works with "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.
+package. See the "Build package"_Build_package.html doc page for more
+info.
To write gzipped species files, you must compile LAMMPS with the
-DLAMMPS_GZIP option.
diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt
index 68cce694e9b46eb71275eb61b5af3ad877eb1fa5..a3d1ab702ebd6b28c55215a80d40d548017cc863 100644
--- a/doc/src/fix_rhok.txt
+++ b/doc/src/fix_rhok.txt
@@ -40,8 +40,8 @@ An example of using the interface pinning method is located in the
[Restrictions:]
This fix is part of the MISC 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index d5e3b0166810dd39613d4a9105d9ac0ed43e86b9..d489762e8022bdfe7f4d82af51a7642fe8fbd286 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -244,7 +244,7 @@ includes atoms you want to be part of rigid bodies.
Bodystyle {custom} is similar to bodystyle {molecule} except that it
is more flexible in using other per-atom properties to define the sets
of atoms that form rigid bodies. An integer vector defined by the
-"fix property/atom"_fix_property_atom.txt command can be used. Or an
+"fix property/atom"_fix_property_atom.html command can be used. Or an
"atom-style or atomfile-style variable"_variable.html can be used; the
floating-point value produced by the variable is rounded to an
integer. As with bondstyle {molecule}, each set of atoms in the fix
@@ -696,13 +696,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -806,8 +806,8 @@ of the "run"_run.html command. These fixes are not invoked during
[Restrictions:]
These fixes are all part of the RIGID 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Assigning a temperature via the "velocity create"_velocity.html
command to a system with "rigid bodies"_fix_rigid.html may not have
diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt
index d39e41e922d16158b2f643e4b0d4eb60e900493a..ad42c577aaf279c007a3aa6a55cceea0b382ed05 100644
--- a/doc/src/fix_rx.txt
+++ b/doc/src/fix_rx.txt
@@ -192,13 +192,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -208,8 +208,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt
index 14fceb7b49e87a01596f1e8f131c4aecd84d26de..4b9abba52ffee7bba246501c3fc77a8d5f495616 100644
--- a/doc/src/fix_setforce.txt
+++ b/doc/src/fix_setforce.txt
@@ -77,13 +77,13 @@ region must be used. See the region "region"_region.html command for
more information.
These accelerated styles are part of the r Kokkos 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.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index ea38de41cd1ba8b0ad9f2c759db429666798f524..77bb5794f6d8e91852c1eb1857357e25e13337a9 100644
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@@ -154,13 +154,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -202,8 +202,8 @@ fixes are not invoked during "energy minimization"_minimize.html.
[Restrictions:]
These fixes are part of the RIGID 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
For computational efficiency, there can only be one shake or rattle
fix defined in a simulation.
diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt
index 33db2bf7cc9e25d81e6b842e6b8282d6ed5feb07..c1be146fa6f7ed71dd7114b46f5f77d954f5b5e0 100644
--- a/doc/src/fix_shardlow.txt
+++ b/doc/src/fix_shardlow.txt
@@ -62,13 +62,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -78,8 +78,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix is currently limited to orthogonal simulation cell
geometries.
diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt
index 2f083dafc337f887ab75da54c4859dd901701844..644c04eadb9efe7e64d6f51f68893e8d9e59a1e7 100644
--- a/doc/src/fix_smd.txt
+++ b/doc/src/fix_smd.txt
@@ -130,8 +130,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_smd_adjust_dt.txt b/doc/src/fix_smd_adjust_dt.txt
index 740b10559d8aced34b4c1428bb355b20c144f325..3535ddfcc22edee05efdaf4d2c6ab932d683ef5d 100644
--- a/doc/src/fix_smd_adjust_dt.txt
+++ b/doc/src/fix_smd_adjust_dt.txt
@@ -25,18 +25,23 @@ fix 1 all smd/adjust_dt 0.1 :pre
[Description:]
-The fix calculates a new stable time increment for use with the SMD time integrators.
+The fix calculates a new stable time increment for use with the SMD
+time integrators.
-The stable time increment is based on multiple conditions. For the SPH pair styles, a
-CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the speed of
-sound cannot propagate further than a typical spacing between particles within a single time step to ensure
-no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a
-stable maximum time step.
+The stable time increment is based on multiple conditions. For the SPH
+pair styles, a CFL criterion (Courant, Friedrichs & Lewy, 1928) is
+evaluated, which determines the speed of sound cannot propagate
+further than a typical spacing between particles within a single time
+step to ensure no information is lost. For the contact pair styles, a
+linear analysis of the pair potential determines a stable maximum time
+step.
-This fix inquires the minimum stable time increment across all particles contained in the group for which this
-fix is defined. An additional safety factor {s_fact} is applied to the time increment.
+This fix inquires the minimum stable time increment across all
+particles contained in the group for which this fix is defined. An
+additional safety factor {s_fact} is applied to the time increment.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach
+Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]
@@ -45,8 +50,8 @@ Currently, no part of USER-SMD supports restarting nor minimization.
[Restrictions:]
This fix is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/src/fix_smd_integrate_tlsph.txt
index cd676a51ce3cdc3eb1978e8d8d29ff7f3acc7832..029605ff7f7b5143e1ad99d5f6161fd4718a0764 100644
--- a/doc/src/fix_smd_integrate_tlsph.txt
+++ b/doc/src/fix_smd_integrate_tlsph.txt
@@ -27,22 +27,26 @@ fix 1 all smd/integrate_tlsph limit_velocity 1000 :pre
[Description:]
-The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style.
+The fix performs explicit time integration for particles which
+interact according with the Total-Lagrangian SPH pair style.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach
+Dynamics in LAMMPS.
-The {limit_velocity} keyword will control the velocity, scaling the norm of
-the velocity vector to max_vel in case it exceeds this velocity limit.
+The {limit_velocity} keyword will control the velocity, scaling the
+norm of the velocity vector to max_vel in case it exceeds this
+velocity limit.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/src/fix_smd_integrate_ulsph.txt
index 7f16b4b7ceabf7288252e5be36e84bda4c949465..a99574cc85d75427a5507cc90d3c69e8aece085e 100644
--- a/doc/src/fix_smd_integrate_ulsph.txt
+++ b/doc/src/fix_smd_integrate_ulsph.txt
@@ -24,7 +24,6 @@ adjust_radius values = adjust_radius_factor min_nn max_nn
limit_velocity values = max_velocity
max_velocity = maximum allowed velocity.
-
[Examples:]
fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
@@ -32,28 +31,33 @@ fix 1 all smd/integrate_ulsph limit_velocity 1000 :pre
[Description:]
-The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+The fix performs explicit time integration for particles which
+interact with the updated Lagrangian SPH pair style.
+
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach
+Dynamics in LAMMPS.
-The {adjust_radius} keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
-within the interval {min_nn} to {max_nn}. The parameter {adjust_radius_factor} determines the amount of adjustment per timestep. Typical values are
-{adjust_radius_factor} =1.02, {min_nn} =15, and {max_nn} =20.
+The {adjust_radius} keyword activates dynamic adjustment of the
+per-particle SPH smoothing kernel radius such that the number of
+neighbors per particles remains within the interval {min_nn} to
+{max_nn}. The parameter {adjust_radius_factor} determines the amount
+of adjustment per timestep. Typical values are {adjust_radius_factor}
+=1.02, {min_nn} =15, and {max_nn} =20.
The {limit_velocity} keyword will control the velocity, scaling the norm of
the velocity vector to max_vel in case it exceeds this velocity limit.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD 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.
-
-[Related commands:]
-
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+[Related commands:] none
[Default:] none
diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt
index aeabf187686e105a9af292b6e5fd93ab01216095..2a998ba8c6128b86ebd42c9e9f80ad03d07caf50 100644
--- a/doc/src/fix_smd_move_triangulated_surface.txt
+++ b/doc/src/fix_smd_move_triangulated_surface.txt
@@ -25,7 +25,6 @@ keyword = {*LINEAR} or {*WIGGLE} or {*ROTATE} :l
Px,Py,Pz = origin point of axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
period = period of rotation (time units) :pre
-
:ule
[Examples:]
@@ -36,9 +35,11 @@ fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1 :pre
[Description:]
-This fix applies only to rigid surfaces read from .STL files via fix "smd/wall_surface"_fix_smd_wall_surface.html .
-It updates position and velocity for the particles in the group each timestep without regard to forces on the particles.
-The rigid surfaces can thus be moved along simple trajectories during the simulation.
+This fix applies only to rigid surfaces read from .STL files via fix
+"smd/wall_surface"_fix_smd_wall_surface.html . It updates position
+and velocity for the particles in the group each timestep without
+regard to forces on the particles. The rigid surfaces can thus be
+moved along simple trajectories during the simulation.
The {*LINEAR} style moves particles with the specified constant velocity
vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle
@@ -49,27 +50,30 @@ Particles are moved along (vx, vy, vz) with constant velocity until a
displacement of max_travel is reached. Then, the velocity vector is
reversed. This process is repeated.
-The {*ROTATE} style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
-goes through a point P = (Px,Py,Pz). The period of the rotation is also
-specified. This style also sets the velocity of each particle to (omega cross
-Rperp) where omega is its angular velocity around the rotation axis and
-Rperp is a perpendicular vector from the rotation axis to the particle.
+The {*ROTATE} style rotates particles around a rotation axis R =
+(Rx,Ry,Rz) that goes through a point P = (Px,Py,Pz). The period of the
+rotation is also specified. This style also sets the velocity of each
+particle to (omega cross Rperp) where omega is its angular velocity
+around the rotation axis and Rperp is a perpendicular vector from the
+rotation axis to the particle.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach
+Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD 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.
-
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
-"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, "smd/wall_surface"_fix_smd_wall_surface.html
+"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/wall_surface"_fix_smd_wall_surface.html
[Default:] none
diff --git a/doc/src/fix_smd_setvel.txt b/doc/src/fix_smd_setvel.txt
index 6634751d6ad9e1ef17333982a7826b1c1e7d724b..b170eff8608c4465c77d02a4ff5a0d726c8e110b 100644
--- a/doc/src/fix_smd_setvel.txt
+++ b/doc/src/fix_smd_setvel.txt
@@ -76,8 +76,8 @@ the "run"_run.html command.
[Restrictions:]
This fix is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:] none
diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt
index a19b2c4cfb7eb2478ca21f684589491127b71eab..dc3625e95ed18df89d863785613a5241d80ece76 100644
--- a/doc/src/fix_smd_wall_surface.txt
+++ b/doc/src/fix_smd_wall_surface.txt
@@ -17,9 +17,7 @@ smd/wall_surface = style name of this fix command :l
arg = {file} :l
{file} = file name of a triangular mesh in stl format :pre
type = particle type to be given to the new particles created by this fix :l
-mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) :l
-
-:ule
+mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) :l,ule
[Examples:]
@@ -27,32 +25,47 @@ fix stl_surf all smd/wall_surface tool.stl 2 65535 :pre
[Description:]
-This fix creates reads a triangulated surface from a file in .STL format.
-For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions.
-The radius of the new particle is that of the minimum circle which encompasses the triangle vertices.
+This fix creates reads a triangulated surface from a file in .STL
+format. For each triangle, a new particle is created which stores the
+barycenter of the triangle and the vertex positions. The radius of
+the new particle is that of the minimum circle which encompasses the
+triangle vertices.
-The triangulated surface can be used as a complex rigid wall via the "smd/tri_surface"_pair_smd_triangulated_surface.html pair style.
-It is possible to move the triangulated surface via the "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html fix style.
+The triangulated surface can be used as a complex rigid wall via the
+"smd/tri_surface"_pair_smd_triangulated_surface.html pair style. It
+is possible to move the triangulated surface via the
+"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html fix style.
-Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles
-in the system. See the "funnel_flow" example in the USER-SMD examples directory.
+Immediately after a .STL file has been read, the simulation needs to
+be run for 0 timesteps in order to properly register the new particles
+in the system. See the "funnel_flow" example in the USER-SMD examples
+directory.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach
+Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD 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. The molecule ID given to the particles created by this fix have to be equal to or larger than 65535.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+The molecule ID given to the particles created by this fix have to be
+equal to or larger than 65535.
-Within each .STL file, only a single triangulated object must be present, even though the STL format allows for the possibility of multiple objects in one file.
+Within each .STL file, only a single triangulated object must be
+present, even though the STL format allows for the possibility of
+multiple objects in one file.
[Related commands:]
-"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, "smd/tri_surface"_pair_smd_triangulated_surface.html
+"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
+"smd/tri_surface"_pair_smd_triangulated_surface.html
[Default:] none
diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt
index 893557b9acad71bd2f1be0690a3b0694b68022f6..557eee1cfc65738f56609a576882bd06c8b7224f 100644
--- a/doc/src/fix_srd.txt
+++ b/doc/src/fix_srd.txt
@@ -371,8 +371,8 @@ minimization"_minimize.html.
[Restrictions:]
This command can only be used if LAMMPS was built with the SRD
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt
index 0e08e4f1e81c9451e7c50742263f0b0b7b6988b9..83b360df858d61f1769e1f8f3e56fde72985b7ec 100644
--- a/doc/src/fix_temp_rescale_eff.txt
+++ b/doc/src/fix_temp_rescale_eff.txt
@@ -64,8 +64,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-EFF 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt
index ddfa46261929de1fc4e1ab0c411537e6df97744d..2d4f00360761be172621dd3a2ca20566778dbf48 100644
--- a/doc/src/fix_tfmc.txt
+++ b/doc/src/fix_tfmc.txt
@@ -125,8 +125,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC 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.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
This fix is not compatible with "fix shake"_fix_shake.html.
diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt
index 86fc6f2c72feba87286126f2b48dacf0983bce69..2ab32b25f071545cde44fc1afd97e3f2032a6486 100644
--- a/doc/src/fix_thermal_conductivity.txt
+++ b/doc/src/fix_thermal_conductivity.txt
@@ -123,8 +123,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Swaps conserve both momentum and kinetic energy, even if the masses of
the swapped atoms are not equal. Thus you should not need to
diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt
index afe5373220095b949e9429f41e800f4e2fa6ad79..290ee95b9aef0f7fefb60ad34d13519450dcf659 100644
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
@@ -146,8 +146,8 @@ this fix.
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Default:]
diff --git a/doc/src/fix_tmd.txt b/doc/src/fix_tmd.txt
index c2541692f5f4cb2667084e11c5f375132e99abf3..73e95ba9fe58783c8b25df7d8081ca2e8c3980f1 100644
--- a/doc/src/fix_tmd.txt
+++ b/doc/src/fix_tmd.txt
@@ -110,8 +110,8 @@ are not multiple competing holonomic constraints applied to the same
atoms.
To read gzipped target files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
[Related commands:] none
diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt
index 6001def5817736192fd0f7ac357a63ce148ca3c1..85407f2466cb9aaaae417174361fbd237d7481bf 100644
--- a/doc/src/fix_ttm.txt
+++ b/doc/src/fix_ttm.txt
@@ -295,8 +295,7 @@ of the "run"_run.html command. The fixes are not invoked during
Fix {ttm} is part of the MISC package. It is only enabled if LAMMPS
was built with that package. Fix {ttm/mod} is part of the USER-MISC
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.
+See the "Build package"_Build_package.html doc page for more info.
These fixes can only be used for 3d simulations and orthogonal
simulation boxes. You must also use periodic
diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt
index b4e8472591dee2164ddb4ef2550431ce0b575e4e..147bb1eb3dc71792c23078312db4f00eb3c3e412 100644
--- a/doc/src/fix_tune_kspace.txt
+++ b/doc/src/fix_tune_kspace.txt
@@ -79,9 +79,9 @@ minimization"_minimize.html.
[Restrictions:]
-This fix is part of the KSPACE 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.
+This fix is part of the KSPACE package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt
index 934da3efdd7820fff834d01e1daf8354e14c39c2..d86b13d0557f52e79685a06e3196333ae7147802 100644
--- a/doc/src/fix_viscosity.txt
+++ b/doc/src/fix_viscosity.txt
@@ -129,8 +129,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Swaps conserve both momentum and kinetic energy, even if the masses of
the swapped atoms are not equal. Thus you should not need to
diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt
index 2ac59d9588155915370d834c1eb2b0e7727602ca..162e32c68c8e84d0613f47312185fe58a13ec60c 100644
--- a/doc/src/fix_wall.txt
+++ b/doc/src/fix_wall.txt
@@ -294,13 +294,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/src/fix_wall_body_polygon.txt
index 0946a85131ae6c003daa63e7af939f9adf442227..45cbb2841db4e4bb8d74c24e1aa704b1a3f3da2a 100644
--- a/doc/src/fix_wall_body_polygon.txt
+++ b/doc/src/fix_wall_body_polygon.txt
@@ -91,8 +91,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Any dimension (xy) that has a wall must be non-periodic.
diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/src/fix_wall_body_polyhedron.txt
index 407cf9fb339047e9b881c0e4df9b950280d5cbed..231ab1f0fe7763ddbe0fa3339cc5c0e5de3813ab 100644
--- a/doc/src/fix_wall_body_polyhedron.txt
+++ b/doc/src/fix_wall_body_polyhedron.txt
@@ -89,9 +89,9 @@ minimization"_minimize.html.
[Restrictions:]
-This fix is part of the BODY 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.
+This fix is part of the BODY package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Any dimension (xyz) that has a wall must be non-periodic.
diff --git a/doc/src/fix_wall_ees.txt b/doc/src/fix_wall_ees.txt
index ae16ca40d2ab731af1a4b77ac474d3dd8b00f841..4cc91f52227ba759280c9a7db34ef706d0c45fbd 100644
--- a/doc/src/fix_wall_ees.txt
+++ b/doc/src/fix_wall_ees.txt
@@ -97,8 +97,8 @@ of using this fix in the examples/USER/misc/ees/ directory.
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms be ellipsoids as defined by the
"atom_style ellipsoid"_atom_style.html command.
diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt
index 6c2769fc12840c85fdd60248009a45a851d8174a..0ea5b194ebefe000653562444ba455793b0a5da4 100644
--- a/doc/src/fix_wall_gran.txt
+++ b/doc/src/fix_wall_gran.txt
@@ -156,8 +156,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Any dimension (xyz) that has a granular wall must be non-periodic.
diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt
index 187214c1a36ca27c304d291150d16f56d440d204..50d744b305040799044fc85f033e10078150b0f7 100644
--- a/doc/src/fix_wall_gran_region.txt
+++ b/doc/src/fix_wall_gran_region.txt
@@ -188,8 +188,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt
index eecf69ebf2b80164672bb2b21cdb48f3ce855a0d..b1968e0d490c1840005bae18e77f2589799adf4b 100644
--- a/doc/src/fix_wall_piston.txt
+++ b/doc/src/fix_wall_piston.txt
@@ -99,8 +99,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix style is part of the SHOCK 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The face that has the wall/piston must be boundary type 's'
(shrink-wrapped). The opposing face can be
diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt
index 78be84eb638224ec631841fabc022bf0700a5162..d43cafbf0949f2706b05b3ea06f0e137ff211f15 100644
--- a/doc/src/fix_wall_reflect.txt
+++ b/doc/src/fix_wall_reflect.txt
@@ -51,7 +51,7 @@ corresponding component of its velocity is flipped.
When used in conjunction with "fix nve"_fix_nve.html and "run_style
verlet"_run_style.html, the resultant time-integration algorithm is
equivalent to the primitive splitting algorithm (PSA) described by
-"Bond"_#Bond. Because each reflection event divides
+"Bond"_#Bond1. Because each reflection event divides
the corresponding timestep asymmetrically, energy conservation is only
satisfied to O(dt), rather than to O(dt^2) as it would be for
velocity-Verlet integration without reflective walls.
@@ -136,13 +136,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -179,5 +179,5 @@ error.
:line
-:link(Bond)
+:link(Bond1)
[(Bond)] Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).
diff --git a/doc/src/group2ndx.txt b/doc/src/group2ndx.txt
index 242d6a69a4092798fb073f2f89a4c44957b46061..ed9bcb003a6ec590c14b70eed2bc51073b16855d 100644
--- a/doc/src/group2ndx.txt
+++ b/doc/src/group2ndx.txt
@@ -54,8 +54,8 @@ This command requires that atoms have atom IDs, since this is the
information that is written to the index file.
These commands are part of the USER-COLVARS 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.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt
index c38f73c64dc017d58ce25e86cb431d5c068e9b1e..704944920eceaf00f67138723c017991e2fdd10d 100644
--- a/doc/src/improper_class2.txt
+++ b/doc/src/improper_class2.txt
@@ -93,13 +93,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -109,8 +109,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-CLASS2 package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+CLASS2 package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt
index 04aa45255cb2faf860dcd0493b53e301c6a65bde..8bd02afb84b4e27dbb31f4e3f9318c83dd6cf9d4 100644
--- a/doc/src/improper_cossq.txt
+++ b/doc/src/improper_cossq.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -75,8 +75,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt
index d01faf288554e0281f1841e45c9f0c415083c547..d57fddc5122c737c2c0835919b3d9dc67b147c3e 100644
--- a/doc/src/improper_cvff.txt
+++ b/doc/src/improper_cvff.txt
@@ -60,13 +60,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -76,8 +76,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/improper_distance.txt b/doc/src/improper_distance.txt
index 93235fe60197f01fc50297ec4f8d0504c16c6b9a..bfd92f57ec9261b94c5b23c045fb726139efdafa 100644
--- a/doc/src/improper_distance.txt
+++ b/doc/src/improper_distance.txt
@@ -48,8 +48,8 @@ K_4 (energy/distance^4) :ul
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt
index 78cc1b3f760fe81de8682983f11bc0f90615f9d4..8b2021dccd5ff156aaaaf671cf77b12af9f1d105 100644
--- a/doc/src/improper_fourier.txt
+++ b/doc/src/improper_fourier.txt
@@ -54,13 +54,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -70,8 +70,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt
index f398dc425f935f605c3446075783df2b91d49c00..1e9e7172f9ca5be5bdc0f83758b364997a370835 100644
--- a/doc/src/improper_harmonic.txt
+++ b/doc/src/improper_harmonic.txt
@@ -64,13 +64,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -80,8 +80,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt
index 42afbe8577dc30163dcc8e5053de9cc05022b6a2..929eec43e16e0f6fd1d4f3cb4f24097a4d672f6f 100644
--- a/doc/src/improper_hybrid.txt
+++ b/doc/src/improper_hybrid.txt
@@ -55,8 +55,8 @@ types.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
Unlike other improper styles, the hybrid improper style does not store
improper coefficient info for individual sub-styles in a "binary
diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/src/improper_inversion_harmonic.txt
index 2c0f2f0af84e1275c8511fc3d65f2508163a89cd..43ffdeb8e9fae741bfd2825e1a620b079c6fc39e 100644
--- a/doc/src/improper_inversion_harmonic.txt
+++ b/doc/src/improper_inversion_harmonic.txt
@@ -52,8 +52,8 @@ in between.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MOFFF package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-MOFFF package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt
index 60bbca170a9a3d06cc3d819d847fdf37370691d9..8a2ee29e17a9c6a694d8a8f6497e93f2a5f161c0 100644
--- a/doc/src/improper_ring.txt
+++ b/doc/src/improper_ring.txt
@@ -63,13 +63,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -79,8 +79,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt
index 3d29b28ec4a69b2200db24e2fb742fdf1c7fabd4..ef0c524d14086488d8f360b505bf640d09e9f3ff 100644
--- a/doc/src/improper_style.txt
+++ b/doc/src/improper_style.txt
@@ -81,10 +81,9 @@ Improper styles can only be set for atom_style choices that allow
impropers to be defined.
Most improper styles are part of the MOLECULE 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 on packages.
-The doc pages for individual improper potentials tell if it is part of
-a package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual improper potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt
index b05cf4b181bfceaed1160cebb650d99922af039a..6c29ec7ac5d879befb81202bbb6883b49c0b6599 100644
--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -73,8 +73,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/jump.txt b/doc/src/jump.txt
index b5afeb6559f4c80629947cf9376ae455fdde1a63..2e26d32c4047537c6ca208456636277612bed612 100644
--- a/doc/src/jump.txt
+++ b/doc/src/jump.txt
@@ -40,15 +40,14 @@ lmp_g++ < in.script :pre
since the SELF option invokes the C-library rewind() call, which may
not be supported for stdin on some systems or by some MPI
implementations. This can be worked around by using the "-in
-command-line argument"_Section_start.html#start_6, e.g.
+command-line switch"_Run_options.html, e.g.
lmp_g++ -in in.script :pre
-or by using the "-var command-line
-argument"_Section_start.html#start_6 to pass the script name as a
-variable to the input script. In the latter case, a
-"variable"_variable.html called "fname" could be used in place of
-SELF, e.g.
+or by using the "-var command-line switch"_Run_options.html to pass
+the script name as a variable to the input script. In the latter
+case, a "variable"_variable.html called "fname" could be used in place
+of SELF, e.g.
lmp_g++ -var fname in.script < in.script :pre
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index 55ad4ab6107b828fd74e5daa91025063d29c5115..7e479c76a64e69a1e8116712457779c0f67b43b6 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -180,9 +180,9 @@ lo-level Makefile. This setting also changes some of the PPPM
operations (e.g. mapping charge to mesh and interpolating electric
fields to particles) to be performed in single precision. This option
can speed-up long-range calculations, particularly in parallel or on
-GPUs. The use of the -DFFT_SINGLE flag is discussed in "this
-section"_Section_start.html#start_2_4 of the manual. MSM does not
-currently support the -DFFT_SINGLE compiler switch.
+GPUs. The use of the -DFFT_SINGLE flag is discussed on the "Build
+settings"_Build_settings.html doc page. MSM does not currently support
+the -DFFT_SINGLE compiler switch.
:line
@@ -286,10 +286,10 @@ The {pppm/kk} style also performs charge assignment and force
interpolation calculations on the GPU while the FFTs themselves are
calculated on the CPU in non-threaded mode.
-These accelerated styles are part of the GPU, USER-INTEL,
-KOKKOS, USER-OMP, and OPT packages respectively. They are only
-enabled if LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP, and OPT packages respectively. They are only enabled if
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -308,9 +308,9 @@ triclinic simulation cells may not yet be supported by suffix versions
of these styles.
All of the kspace styles are part of the KSPACE 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. Note that
-the KSPACE package is installed by default.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Note that the
+KSPACE package is installed by default.
For MSM, a simulation must be 3d and one can use any combination of
periodic, non-periodic, or shrink-wrapped boundaries (specified using
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index c0ca357f211aa973f0c80f28155b2cc9b6e0ebcd..c961004f83c4cc012e86e676c2f2a1b04e8c5c70 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -3,12 +3,33 @@
Manual.html
Intro.html
Intro_overview.html
+Manual_version.html
Intro_features.html
Intro_nonfeatures.html
Intro_opensource.html
Intro_authors.html
Intro_website.html
-Section_start.html
+Install.html
+Install_linux.html
+Install_mac.html
+Install_windows.html
+Install_tarball.html
+Install_git.html
+Install_svn.html
+Install_patch.html
+Build.html
+Build_cmake.html
+Build_make.html
+Build_link.html
+Build_basics.html
+Build_settings.html
+Build_package.html
+Build_extras.html
+Run.html
+Run_basics.html
+Run_options.html
+Run_output.html
+Run_windows.html
Commands.html
Commands_input.html
Commands_parse.html
@@ -90,7 +111,7 @@ Modify_region.html
Modify_body.html
Modify_thermo.html
Modify_variable.html
-Python.html
+Python_head.html
Python_overview.html
Python_run.html
Python_shlib.html
@@ -106,6 +127,7 @@ Errors_common.html
Errors_bugs.html
Errors_messages.html
Errors_warnings.html
+Manual_build.html
lammps_commands.html
atom_modify.html
diff --git a/doc/src/log.txt b/doc/src/log.txt
index 76037685194b5ba9b324b02d35ffd0ed34ea26d3..d526158a3c6a59919fe5a6fdfcba5e5adf3e3889 100644
--- a/doc/src/log.txt
+++ b/doc/src/log.txt
@@ -33,9 +33,8 @@ be a variable, so that different processors do not attempt to write to
the same log file.
The file "log.lammps" is the default log file for a LAMMPS run. The
-name of the initial log file can also be set by the command-line
-switch -log. See "Section 2.6"_Section_start.html#start_6 for
-details.
+name of the initial log file can also be set by the "-log command-line
+switch"_Run_options.html.
[Restrictions:] none
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index fbd77ee32903f1d99f4f63232538e0fd88cdde7d..57e122fdcd53cec635f42746fd23c475f8fca7fc 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -50,14 +50,14 @@ follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA,
"(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2.
Each replica runs on a partition of one or more processors. Processor
-partitions are defined at run-time using the -partition command-line
-switch; see "Section 2.6"_Section_start.html#start_6 of the manual.
-Note that if you have MPI installed, you can run a multi-replica
-simulation with more replicas (partitions) than you have physical
-processors, e.g you can run a 10-replica simulation on just one or two
-processors. You will simply not get the performance speed-up you
-would see with one or more physical processors per replica. See the
-"Howto replica"_Howto_replica.html doc page for further discussion.
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html. Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on just one or two processors. You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica. See the "Howto replica"_Howto_replica.html
+doc page for further discussion.
NOTE: As explained below, a NEB calculation perfoms a damped dynamics
minimization across all the replicas. The minimizer uses whatever
@@ -395,8 +395,8 @@ image.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
:line
diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt
index 7c7e7b05e5229b3d1144f251543d5b8ded341c60..3e590eaff109e524fc08986bd5275ff858a651e1 100644
--- a/doc/src/neighbor.txt
+++ b/doc/src/neighbor.txt
@@ -65,8 +65,8 @@ stored in the list.
When a run is finished, counts of the number of neighbors stored in
the pairwise list and the number of times neighbor lists were built
-are printed to the screen and log file. See "this
-section"_Section_start.html#start_7 for details.
+are printed to the screen and log file. See the "Run
+output"_Run_output.html doc page for details.
[Restrictions:] none
diff --git a/doc/src/next.txt b/doc/src/next.txt
index 5a0b30b2a7fe6ff0d824a066376404808702958f..aefb2ca5949f16001a1016ac94aa07984082c491 100644
--- a/doc/src/next.txt
+++ b/doc/src/next.txt
@@ -70,11 +70,11 @@ incrementing is done, using a single lock file for all variables. The
next value (for each variable) is assigned to whichever processor
partition executes the command first. All processors in the partition
are assigned the same value(s). Running LAMMPS on multiple partitions
-of processors via the "-partition" command-line switch is described in
-"this section"_Section_start.html#start_6 of the manual. {Universe}-
-and {uloop}-style variables are incremented using the files
-"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
-see in your directory during and after such a LAMMPS run.
+of processors via the "-partition command-line
+switch"_Run_options.html. {Universe}- and {uloop}-style variables are
+incremented using the files "tmp.lammps.variable" and
+"tmp.lammps.variable.lock" which you will see in your directory during
+and after such a LAMMPS run.
Here is an example of running a series of simulations using the next
command with an {index}-style variable. If this input script is named
diff --git a/doc/src/package.txt b/doc/src/package.txt
index 3d25a64d3174aacc9218ed4d26e96cae5355ddef..8b0581929ff10cffd2661b5268761e61a276e418 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -124,8 +124,8 @@ their initialization, before a simulation is defined.
This command can also be specified from the command-line when
launching LAMMPS, using the "-pk" "command-line
-switch"_Section_start.html#start_6. The syntax is exactly the same as
-when used in an input script.
+switch"_Run_options.html. The syntax is exactly the same as when used
+in an input script.
Note that all of the accelerator packages require the package command
to be specified (except the OPT package), if the package is to be used
@@ -135,22 +135,21 @@ a default version of the command is typically invoked by other
accelerator settings.
The KOKKOS package requires a "-k on" "command-line
-switch"_Section_start.html#start_6 respectively, which invokes a
-"package kokkos" command with default settings.
+switch"_Run_options.html respectively, which invokes a "package
+kokkos" command with default settings.
For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf
-intel" or "-sf omp" "command-line switch"_Section_start.html#start_6
-is used to auto-append accelerator suffixes to various styles in the
-input script, then those switches also invoke a "package gpu",
-"package intel", or "package omp" command with default settings.
+intel" or "-sf omp" "command-line switch"_Run_options.html is used to
+auto-append accelerator suffixes to various styles in the input
+script, then those switches also invoke a "package gpu", "package
+intel", or "package omp" command with default settings.
NOTE: A package command for a particular style can be invoked multiple
-times when a simulation is setup, e.g. by the "-c on", "-k on", "-sf",
-and "-pk" "command-line switches"_Section_start.html#start_6, and by
-using this command in an input script. Each time it is used all of
-the style options are set, either to default values or to specified
-settings. I.e. settings from previous invocations do not persist
-across multiple invocations.
+times when a simulation is setup, e.g. by the "-c on, -k on, -sf, and
+-pk command-line switches"_Run_options.html, and by using this command
+in an input script. Each time it is used all of the style options are
+set, either to default values or to specified settings. I.e. settings
+from previous invocations do not persist across multiple invocations.
See the "Speed packages"_Speed_packages.html doc page for more details
about using the various accelerator packages for speeding up LAMMPS
@@ -341,10 +340,10 @@ value via their package commands, but there is only a single global
{Nthreads} value used by OpenMP. Thus if both package commands are
invoked, you should insure the two values are consistent. If they are
not, the last one invoked will take precedence, for both packages.
-Also note that if the "-sf hybrid intel omp" "command-line
-switch"_"_Section_start.html#start_6 is used, it invokes a "package
-intel" command, followed by a "package omp" command, both with a
-setting of {Nthreads} = 0.
+Also note that if the "-sf hybrid intel omp command-line
+switch"_Run_options.html is used, it invokes a "package intel"
+command, followed by a "package omp" command, both with a setting of
+{Nthreads} = 0.
The {mode} keyword determines the precision mode to use for
computing pair style forces, either on the CPU or on the coprocessor,
@@ -583,60 +582,58 @@ This command cannot be used after the simulation box is defined by a
"read_data"_read_data.html or "create_box"_create_box.html command.
The gpu style of this command can only be invoked if LAMMPS was built
-with the GPU package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with the GPU package. See the "Build package"_Build_package.html doc
+page for more info.
The intel style of this command can only be invoked if LAMMPS was
-built with the USER-INTEL package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with the USER-INTEL package. See the "Build
+package"_Build_package.html doc page for more info.
The kk style of this command can only be invoked if LAMMPS was built
-with the KOKKOS package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with the KOKKOS package. See the "Build package"_Build_package.html
+doc page for more info.
The omp style of this command can only be invoked if LAMMPS was built
-with the USER-OMP package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with the USER-OMP package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
-"suffix"_suffix.html, "-pk" "command-line
-setting"_Section_start.html#start_6
+"suffix"_suffix.html, "-pk command-line switch"_Run_options.html
[Default:]
For the GPU package, the default is Ngpu = 1 and the option defaults
are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
to Ngpu-1, tpa = 1, and device = not used. These settings are made
-automatically if the "-sf gpu" "command-line
-switch"_Section_start.html#start_6 is used. If it is not used, you
-must invoke the package gpu command in your input script or via the
-"-pk gpu" "command-line switch"_Section_start.html#start_6.
+automatically if the "-sf gpu" "command-line switch"_Run_options.html
+is used. If it is not used, you must invoke the package gpu command
+in your input script or via the "-pk gpu" "command-line
+switch"_Run_options.html.
For the USER-INTEL package, the default is Nphi = 1 and the option
defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4,
tptask = 240. The default ghost option is determined by the pair
style being used. This value is output to the screen in the offload
report at the end of each run. Note that all of these settings,
-except "omp" and "mode", are ignored if LAMMPS was not built with
-Xeon Phi coprocessor support. These settings are made automatically
-if the "-sf intel" "command-line switch"_Section_start.html#start_6
-is used. If it is not used, you must invoke the package intel
-command in your input script or or via the "-pk intel" "command-line
-switch"_Section_start.html#start_6.
+except "omp" and "mode", are ignored if LAMMPS was not built with Xeon
+Phi coprocessor support. These settings are made automatically if the
+"-sf intel" "command-line switch"_Run_options.html is used. If it is
+not used, you must invoke the package intel command in your input
+script or or via the "-pk intel" "command-line
+switch"_Run_options.html.
For the KOKKOS package, the option defaults neigh = full, neigh/qeq =
full, newton = off, binsize = 0.0, and comm = device, gpu/direct = on.
When LAMMPS can safely detect, that GPU-direct is not available, the
default value of gpu/direct becomes "off".
These settings are made automatically by the required "-k on"
-"command-line switch"_Section_start.html#start_6. You can change them by
-using the package kokkos command in your input script or via the "-pk
-kokkos" "command-line switch"_Section_start.html#start_6.
+"command-line switch"_Run_options.html. You can change them by
+using the package kokkos command in your input script or via the
+"-pk kokkos command-line switch"_Run_options.html.
For the OMP package, the default is Nthreads = 0 and the option
defaults are neigh = yes. These settings are made automatically if
-the "-sf omp" "command-line switch"_Section_start.html#start_6 is
-used. If it is not used, you must invoke the package omp command in
-your input script or via the "-pk omp" "command-line
-switch"_Section_start.html#start_6.
+the "-sf omp" "command-line switch"_Run_options.html is used. If it
+is not used, you must invoke the package omp command in your input
+script or via the "-pk omp" "command-line switch"_Run_options.html.
diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt
index 382a97eceaf93bf844915871d3210a4bca0e7666..fc888ffbffa7b38779ddaa9730316c787445d3cc 100644
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@@ -131,13 +131,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt
index 34f99001390ca24026f0ea3218316ab465d68ac0..74aef4125575d02b79436b7e8c79b6c468757f0e 100644
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@@ -64,14 +64,14 @@ packages"_Speed_packages.html doc page. The accelerated style takes
the same arguments and should produce the same results, except for
round-off and precision issues.
-The accelerated style is part of the USER-OMP. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+The accelerated style is part of the USER-OMP. They are only enabled
+if LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated style explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -96,13 +96,14 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-Currently, only elemental systems are implemented. Also, the method only
-provides access to the forces and not energies or stresses. However, one
-can access the energy via thermodynamic integration of the forces as
-discussed in "(Botu3)"_#Botu2016construct. This pair style is part
-of the USER-MISC 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.
+Currently, only elemental systems are implemented. Also, the method
+only provides access to the forces and not energies or
+stresses. However, one can access the energy via thermodynamic
+integration of the forces as discussed in
+"(Botu3)"_#Botu2016construct. This pair style is part of the
+USER-MISC package. It is only enabled if LAMMPS was built with that
+package. See the "Build package"_Build_package.html doc page for more
+info.
The AGNI force field files provided with LAMMPS (see the
potentials directory) are parameterized for metal "units"_units.html.
diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt
index 94a692226d608687a094d48455070c1084eed3f4..c090a39af756189a63728c59b4c58e369c847111 100644
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@@ -182,13 +182,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -212,8 +212,8 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the MANYBODY package. They are only
-enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair potentials require the "newton"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt
index ca4186e27b102d8199327d87a3ca0cd9da09f92f..af60041ff98b6a14e0bc84117a14082691a071b0 100644
--- a/doc/src/pair_beck.txt
+++ b/doc/src/pair_beck.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_body_nparticle.txt b/doc/src/pair_body_nparticle.txt
index 9fb88102eb0aece7ace62e32360614fa3bdef106..158eb68ca8f4c8357167534d0e936db7c4de2cff 100644
--- a/doc/src/pair_body_nparticle.txt
+++ b/doc/src/pair_body_nparticle.txt
@@ -103,8 +103,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Defining particles to be bodies so they participate in body/body or
body/particle interactions requires the use of the "atom_style
diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt
index e724874032afffe0d59f1f6fe2622a1669797b35..fc07d8faddc61a91dcba3cbcf32eb36211df8cff 100644
--- a/doc/src/pair_body_rounded_polygon.txt
+++ b/doc/src/pair_body_rounded_polygon.txt
@@ -116,8 +116,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the BODY 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt
index 0f8548d98eab86a6d5e3647f46119162764409cb..e650e5138ac456a405448f1476e29ec5cf7e754a 100644
--- a/doc/src/pair_body_rounded_polyhedron.txt
+++ b/doc/src/pair_body_rounded_polyhedron.txt
@@ -111,8 +111,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the BODY 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt
index 654a7eb0b332dd5efdd4a9ca41410fbf6bd131df..f9b4262f0c5f9717854e7c0bfeedefe831eeed46 100644
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@@ -382,9 +382,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the MANYBODY package. They are only
-enabled if LAMMPS was built with that package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more
-info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair potentials require the "newtion"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt
index c408de6db6f23b579f2800d7865fdcd35649f9e6..195d3e666961c321638fe03c1cfc0c67cb2c6c96 100644
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@@ -151,13 +151,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -193,8 +193,8 @@ respa"_run_style.html command. They do not support the {inner},
[Restrictions:]
The {born/coul/long} style is part of the KSPACE 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.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt
index eaff85cbbca374db982add0557f03b57dedceaaf..52720daa23f4c67a88e7ce88b43fb23524a4eac5 100644
--- a/doc/src/pair_brownian.txt
+++ b/doc/src/pair_brownian.txt
@@ -80,13 +80,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "this section"_Speed.html of the manual for more
instructions on how to use the accelerated styles effectively.
@@ -122,8 +122,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These styles are part of the COLLOID 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Only spherical monodisperse particles are allowed for pair_style
brownian.
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index cc782c11cf3f551930264316b838c488de4ddb6e..5b1688e8687345464fb832161360f15700608320 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -145,13 +145,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -186,8 +186,8 @@ respa"_run_style.html command. They do not support the {inner},
The {buck/coul/long} style is part of the KSPACE package. The
{buck/coul/long/cs} style is part of the CORESHELL 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.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt
index 485c35c6b2fffb04c14fa04469bd33a6400c65d5..4c43978fe5a44eae7d15fc21aecf5e2d2c8f780c 100644
--- a/doc/src/pair_buck6d_coul_gauss.txt
+++ b/doc/src/pair_buck6d_coul_gauss.txt
@@ -122,9 +122,9 @@ to be specified in an input script that reads a restart file.
[Restrictions:]
-These styles are part of the USER-MOFFF 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.
+These styles are part of the USER-MOFFF package. They are only
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt
index 551204f1a7fe97ea559e98c7cfd1ddd92370d328..7f3a959ad620a39db19c466ad7012b6412740cc6 100644
--- a/doc/src/pair_buck_long.txt
+++ b/doc/src/pair_buck_long.txt
@@ -108,13 +108,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -153,9 +153,9 @@ details.
[Restrictions:]
This style is part of the KSPACE 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. Note that
-the KSPACE package is installed by default.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Note that the
+KSPACE package is installed by default.
[Related commands:]
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index 39c6f29b047fdbf02017352a1e787cc60c79cb78..dfc87e1bcebf2c650867f24436da365ce516a40a 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -190,13 +190,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -245,9 +245,9 @@ details.
All the styles with {coul/charmm} or {coul/charmmfsh} styles are part
of the MOLECULE package. All the styles with {coul/long} style are
part of the KSPACE package. They are only enabled if LAMMPS was built
-with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. Note that
-the MOLECULE and KSPACE packages are installed by default.
+with those packages. See the "Build package"_Build_package.html doc
+page for more info. Note that the MOLECULE and KSPACE packages are
+installed by default.
[Related commands:]
diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt
index 104c51474c25764c20a7b064dad9722e548e0809..5fc42e78f9f9b4a34d854e30d9bd96999177252b 100644
--- a/doc/src/pair_class2.txt
+++ b/doc/src/pair_class2.txt
@@ -108,13 +108,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -154,8 +154,8 @@ support the {inner}, {middle}, {outer} keywords.
[Restrictions:]
These styles are part of the CLASS2 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt
index 08540cfee082c761259d3d8e3772015557c21210..e8a44e1cba7ec053e09831ee1201d074f62db215 100644
--- a/doc/src/pair_colloid.txt
+++ b/doc/src/pair_colloid.txt
@@ -133,13 +133,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -177,8 +177,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the COLLOID 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Normally, this pair style should be used with finite-size particles
which have a diameter, e.g. see the "atom_style
diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt
index fc4cddbbae1fefa91ce37e930e2a589279f42566..45ce3a3b7611d0847ef3aa05886d0a6dd6fb20b4 100644
--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@@ -118,13 +118,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -154,9 +154,9 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
-These pair styles are part of the MANYBODY 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.
+These pair styles are part of the MANYBODY package. It is only
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair styles requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt
index 2fd9445785e26a44a3b1f7b070caa7531e61003d..bc0d76a071829dba2182fede5e1aadcc725a5759 100644
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@@ -274,13 +274,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -319,7 +319,7 @@ This pair style can only be used via the {pair} keyword of the
The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the
KSPACE package. The {coul/long/cs} style is part of the CORESHELL
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.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt
index 14932c4835043aa7e93cf7b900672def64f10323..7708287db9e476c18c13932906ba885aa2e94fa9 100644
--- a/doc/src/pair_coul_diel.txt
+++ b/doc/src/pair_coul_diel.txt
@@ -67,7 +67,8 @@ The global cutoff (r_c) specified in the pair_style command is used.
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs.
+This pair style does not support parameter mixing. Coefficients must
+be given explicitly for each type of particle pairs.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the Gauss-potential portion of the pair
@@ -86,9 +87,9 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-This style is part of the "user-misc" package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+This style is part of the "USER-MISC" package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt
index 029e6e5b3b3458ce3fdbab9daaecdad467061dce..62ac157e76cf4b78797dfc2a073d9007c7eee270 100644
--- a/doc/src/pair_coul_shield.txt
+++ b/doc/src/pair_coul_shield.txt
@@ -69,9 +69,9 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-This style is part of the USER-MISC package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+This style is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt
index 6540c4b8f0d4dd72b704854146d50b4f74815720..8bd4abed68bb8bac94116d77c575453eb0c6d717 100644
--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@@ -100,8 +100,8 @@ core/shell pair.
[Restrictions:]
These pair styles are part of the CORESHELL 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.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index 1d8abc4521d2b26d2152d2157081a9d718bc3b47..dcb2448949699655f3021a860ca3112ae398d542 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -192,13 +192,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -240,12 +240,12 @@ This pair style can only be used via the {pair} keyword of the
The {lj/cut/dipole/cut}, {lj/cut/dipole/long}, and
{lj/long/dipole/long} styles are part of the DIPOLE 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.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The {lj/sf/dipole/sf} style is part of the USER-MISC 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.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Using dipole pair styles with {electron} "units"_units.html is not
currently supported.
diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt
index 1b636795d962254fed114fd7cad91b2b53fb8bac..55ae2986824e0c8baf92c5bf8cd4ba555837fdb9 100644
--- a/doc/src/pair_dpd.txt
+++ b/doc/src/pair_dpd.txt
@@ -116,13 +116,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt
index 0d180ba068ffdec47eb78bc7fc7fcdb458aab766..4f2459588a9b317d3f92b3bc732536d10ec2dbc4 100644
--- a/doc/src/pair_dpd_fdt.txt
+++ b/doc/src/pair_dpd_fdt.txt
@@ -135,13 +135,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -151,8 +151,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
These commands are part of the USER-DPD 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.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the
"comm_modify vel yes"_comm_modify.html option so that velocites are
diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt
index 2478a96d5ff183f52d21f817a1205eee6ce99855..adaeeb8390e07f080259009962109f909857f56b 100644
--- a/doc/src/pair_dsmc.txt
+++ b/doc/src/pair_dsmc.txt
@@ -130,8 +130,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the MC 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.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt
index 361dacb703d41a95c365abd2ce5101e915fe11d3..6c3793cb61bc2ad74102e02f1f9b73c9dcf2be74 100644
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@@ -377,13 +377,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -414,8 +414,8 @@ The eam pair styles can only be used via the {pair} keyword of the
[Restrictions:]
All of these styles are part of the MANYBODY package. They are only
-enabled if LAMMPS was built with that package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index cce564856e6c2c420771e4c070b23605e0cdafe8..053d43b2baeed3cd87cfb17e57aabb60335ca7d8 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -115,13 +115,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -147,8 +147,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt
index a55860297e609eb106b63cda6655babf3f696966..a665654af090af278e348dbd35e763df430cf547 100644
--- a/doc/src/pair_eff.txt
+++ b/doc/src/pair_eff.txt
@@ -280,8 +280,8 @@ These pair styles can only be used via the {pair} keyword of the
These pair styles will only be enabled if LAMMPS is built with the
USER-EFF package. It will only be enabled if LAMMPS was built with
-that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+that package. See the "Build package"_Build_package.html doc page for
+more info.
These pair styles require that particles store electron attributes
such as radius, radial velocity, and radial force, as defined by the
diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt
index 6490a859c16b361e217faaa3eb04e52386b87143..5f9dcd4c5c349b5123a1539a8ee60db1a09d77b9 100644
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@@ -142,13 +142,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt
index 08ab1cf3c9b64a40fe70b251500fcecfcd2994f6..790674644d8223230329ce8c2387c9879e7670eb 100644
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@@ -159,13 +159,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -175,8 +175,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt
index 9662a4f29c743fefb3bddc480b6f70f75045ff88..ef924b1ef07bffe80ba266df8b111fe8395ddb97 100644
--- a/doc/src/pair_gauss.txt
+++ b/doc/src/pair_gauss.txt
@@ -90,13 +90,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -167,8 +167,8 @@ thermo_style custom step temp epair v_occ :pre
[Restrictions:]
The {gauss/cut} style is part of the "user-misc" package. It is only
-enabled if LAMMPS is build with that package. See the "Making of
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS is build with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt
index af41f6879e80ed299050eb6822553e819e22607f..426352dc4cebe292b969fbdd5a2b119827fd8f3c 100644
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
@@ -139,13 +139,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -184,8 +184,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
The {gayberne} style is part of the ASPHERE 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.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair style require that atoms store torque and a quaternion to
represent their orientation, as defined by the
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index 55b00a172f56c4063a20298509cc54856d9b276a..e06d4100849b339d78999bf3ae54c02cbe73ffd3 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -185,13 +185,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -232,8 +232,8 @@ pair/local"_compute_pair_local.html command, as {p1}, {p2}, ...,
[Restrictions:]
All the granular pair styles are part of the GRANULAR 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.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair styles require that atoms store torque and angular velocity
(omega) as defined by the "atom_style"_atom_style.html. They also
diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt
index 9f34ac8c43da024cd0123454dfdc2666116379f3..6a36a036c93b2a8af88ebb62bdfac7f53dc243aa 100644
--- a/doc/src/pair_gromacs.txt
+++ b/doc/src/pair_gromacs.txt
@@ -97,13 +97,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt
index 809ff008bc86dbaa33e6f899c354957e09a65fef..ff85955dc006e05da8cf6fb22a8ebe8859979c09 100644
--- a/doc/src/pair_gw.txt
+++ b/doc/src/pair_gw.txt
@@ -96,8 +96,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt
index 60b0b021743374cc08cfdd5cdc58a8605f02c9b0..d4bdcd9258750593512a9acf727f476d7e0321de 100644
--- a/doc/src/pair_hbond_dreiding.txt
+++ b/doc/src/pair_hbond_dreiding.txt
@@ -172,13 +172,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index 9b36109c279e7381ba5a73aea7adad55dee2f3c7..6e68e820a883184ac4c1927fd232a3ce05c048a4 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -324,15 +324,15 @@ the individual sub-styles, the suffix versions of the {hybrid} and
to all sub-styles, if those versions exist. Otherwise the
non-accelerated version will be used.
-The individual accelerated sub-styles are part of the GPU,
-USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+The individual accelerated sub-styles are part of the GPU, USER-OMP
+and OPT packages, respectively. They are only enabled if LAMMPS was
+built with those packages. See the "Build package"_Build_package.html
+doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index 9c9304c4a73ba02e35d575331f135ad32187a81e..02d0db7af25e6c86f6ece52e56623bf71825173a 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -87,8 +87,8 @@ that reads a restart file.
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the newton setting to be {on} for pair
interactions.
diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt
index 889c1e892fe69202a92ca98b02650b982c68c849..e1bde4f10e1b445e978185286c1fc7d0a906542d 100644
--- a/doc/src/pair_kim.txt
+++ b/doc/src/pair_kim.txt
@@ -126,8 +126,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the KIM 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This current version of pair_style kim is compatible with the
kim-api package version 1.6.0 and higher.
diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt
index 8fc6bbff4996ecaefa81e0257048a14c702a7e5d..358d2168df277c2ce74e00992dfb87fe403817e5 100644
--- a/doc/src/pair_kolmogorov_crespi_full.txt
+++ b/doc/src/pair_kolmogorov_crespi_full.txt
@@ -78,8 +78,8 @@ that reads a restart file.
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the newton setting to be {on} for pair
interactions.
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index 7dad2e3701b852d41a2856e785d80be041f2f5c6..f557e6c731db499de0820bbb39ef9aab1aa0f46a 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -51,8 +51,8 @@ Other interactions can be set to zero using pair_style {none}.
[Restrictions:]
This fix is part of the USER-MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_lcbop.txt b/doc/src/pair_lcbop.txt
index ddf8551d560ff042b8c3d64331db263e5c3d5289..21c809bf6a2f3a5b853b2dcbbde5296ca81008e1 100644
--- a/doc/src/pair_lcbop.txt
+++ b/doc/src/pair_lcbop.txt
@@ -72,8 +72,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair styles is part of the MANYBODY 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the "newton"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt
index c2c6beb97f5490ce4cc11ab6cb3c0634375afc0f..ca5ececa5697f6cd6d90bda77e9aa62497f90f0b 100644
--- a/doc/src/pair_line_lj.txt
+++ b/doc/src/pair_line_lj.txt
@@ -130,8 +130,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the ASPHERE 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Defining particles to be line segments so they participate in
line/line or line/particle interactions requires the use the
diff --git a/doc/src/pair_list.txt b/doc/src/pair_list.txt
index 023cc0be4f1c52404fe1f875bdfd86cf03b68e7d..9500a4c508ad061b585dd695b3fe02b7ad4324cb 100644
--- a/doc/src/pair_list.txt
+++ b/doc/src/pair_list.txt
@@ -130,8 +130,8 @@ atom J (assuming the images are within the cutoff distance), but only
with the nearest image.
This style is part of the USER-MISC package. It is only enabled if
-LAMMPS is build with that package. See the "Making of
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS is build with that package. See the "Build
+package"_Build_package.html doc page on for more info.
[Related commands:]
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index a55cb348d7568f14dd25c715adf8a7fe382f3a23..b5a572618228d0b8e514e8157ad0347fc2690481 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -275,13 +275,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -326,9 +326,9 @@ See the "run_style"_run_style.html command for details.
The {lj/cut/coul/long} and {lj/cut/tip4p/long} styles are part of the
KSPACE package. The {lj/cut/tip4p/cut} style is part of the MOLECULE
package. These styles are only enabled if LAMMPS was built with those
-packages. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info. Note that the KSPACE and MOLECULE packages are
-installed by default.
+packages. See the "Build package"_Build_package.html doc page for
+more info. Note that the KSPACE and MOLECULE packages are installed
+by default.
[Related commands:]
diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt
index 7c68e26acef1c9cf8d21b47fc70ba1109296e502..19369adc66d1074ce4b5410f8c634cee68860ea6 100644
--- a/doc/src/pair_lj96.txt
+++ b/doc/src/pair_lj96.txt
@@ -55,13 +55,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt
index d04a3d8b9d1b6e021ea2df92d2ee16a74ba5e45d..0a56672d2861ff2d7b8555a684141d58149524b6 100644
--- a/doc/src/pair_lj_cubic.txt
+++ b/doc/src/pair_lj_cubic.txt
@@ -69,13 +69,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index 3e9996da4d5507158a37cca38cf1db68597dcfdb..d26c88e4f76f50db857c8510be9e6c23fdd77beb 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index 1ba3610f8621801864930acf73a20b4d16bd5a04..2bc2b656ac7b95832c60e7304b5ccd254e04953c 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -162,13 +162,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -209,9 +209,9 @@ different levels of the rRESPA hierarchy. See the
[Restrictions:]
These styles are part of the KSPACE 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. Note that
-the KSPACE package is installed by default.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Note that the
+KSPACE package is installed by default.
[Related commands:]
diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt
index 575c023579b4cf5b91927dd241c65d3ee9365c83..0c66dd0f669f199f06bcb1d9878120bc1b44a070 100644
--- a/doc/src/pair_lj_smooth.txt
+++ b/doc/src/pair_lj_smooth.txt
@@ -68,13 +68,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt
index 0fab768b8fbd9eecc9c80d0760262f9d9ea6111b..9c509515c0d71d1f1788e49a24f9176340ff254c 100644
--- a/doc/src/pair_lj_smooth_linear.txt
+++ b/doc/src/pair_lj_smooth_linear.txt
@@ -55,13 +55,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt
index d10fcd0472d24ebd91510e0c4793597292e31127..9bcc83fa66fcdf39c81a0375bce48aa69bcf89d3 100644
--- a/doc/src/pair_lj_soft.txt
+++ b/doc/src/pair_lj_soft.txt
@@ -213,13 +213,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -261,7 +261,7 @@ similar substyle can be used via the
All of the plain {soft} pair styles are part of the USER-FEP package.
The {long} styles also requires the KSPACE package to be installed.
They are only enabled if LAMMPS was built with those packages. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt
index e9a0a0d2910e5a6036f4993c23e59b0849b88d78..83a67d03006390b7031a73d03d4c35d03adc8e1d 100644
--- a/doc/src/pair_lubricate.txt
+++ b/doc/src/pair_lubricate.txt
@@ -149,13 +149,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "this section"_Speed.html of the manual for more
instructions on how to use the accelerated styles effectively.
@@ -191,8 +191,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These styles are part of the COLLOID package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Only spherical monodisperse particles are allowed for pair_style
lubricate.
diff --git a/doc/src/pair_lubricateU.txt b/doc/src/pair_lubricateU.txt
index 6b74c208bf2c211ec71b9efff608c2345626505e..bfc7c36013d2c7060686a20ee99440712e66fca0 100644
--- a/doc/src/pair_lubricateU.txt
+++ b/doc/src/pair_lubricateU.txt
@@ -179,8 +179,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These styles are part of the COLLOID package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Currently, these pair styles assume that all other types of
forces/torques on the particles have been already been computed when
diff --git a/doc/src/pair_mdf.txt b/doc/src/pair_mdf.txt
index e5a8cac845effe56f019729b2660ad001226923d..8a1551ddedf3b3ba964691798e7844693cc719ba 100644
--- a/doc/src/pair_mdf.txt
+++ b/doc/src/pair_mdf.txt
@@ -148,8 +148,8 @@ See the "run_style"_run_style.html command for details.
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt
index 45f88f0bbec33570565284ab50945076acb85906..0b1c1ac767eb987adbc0af82adbf67633f4dfef7 100644
--- a/doc/src/pair_meam.txt
+++ b/doc/src/pair_meam.txt
@@ -352,14 +352,14 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-The {meam} style is part of the MEAM package. It is only enabled if LAMMPS
-was built with that package, which also requires the MEAM library be
-built and linked with LAMMPS.
-The {meam/c} style is provided in the USER-MEAMC package. It is only enabled
-if LAMMPS was built with that package. In contrast to the {meam} style,
-{meam/c} does not require a separate library to be compiled and it can be
+The {meam} style is part of the MEAM package. It is only enabled if
+LAMMPS was built with that package, which also requires the MEAM
+library be built and linked with LAMMPS. The {meam/c} style is
+provided in the USER-MEAMC package. It is only enabled if LAMMPS was
+built with that package. In contrast to the {meam} style, {meam/c}
+does not require a separate library to be compiled and it can be
instantiated multiple times in a "hybrid"_pair_hybrid.html pair style.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index 96155120419297e54de85192f772f8fcb05216d5..df5db812648a9c4ff87e1e723578118d3b5075db 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -112,13 +112,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -147,8 +147,8 @@ This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
This pair style is only enabled if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt
index ba0953a17c3957825fac150f3b373c92a5df44b9..2e8c26658aea1de5840ba254fbeb7029640f194a 100644
--- a/doc/src/pair_meam_sw_spline.txt
+++ b/doc/src/pair_meam_sw_spline.txt
@@ -111,8 +111,9 @@ support the {inner}, {middle}, {outer} keywords.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
-This pair style is only enabled if LAMMPS was built with the USER-MISC package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+This pair style is only enabled if LAMMPS was built with the USER-MISC
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt
index ad3880e642411c30179bb8a1e9d3b8451cc9c227..005498d8bfdd1f1080f1bc297d4b1b3f1513ba5c 100644
--- a/doc/src/pair_meso.txt
+++ b/doc/src/pair_meso.txt
@@ -245,8 +245,8 @@ that reads a restart file.
The pair styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} are part of
the USER-MESO 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.
+that package. See the "Build package"_Build_package.html doc page for
+more info.
[Related commands:]
diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt
index 09fe61168698455d05fef6b67ed6a80b1b43a962..bd55d529b8177f52e0589fbf0fafc19b0b82a72d 100644
--- a/doc/src/pair_mgpt.txt
+++ b/doc/src/pair_mgpt.txt
@@ -159,8 +159,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the USER-MGPT package and is only enabled
-if LAMMPS is built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS is built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The MGPT potentials require the "newtion"_newton.html setting to be
"on" for pair style interactions.
diff --git a/doc/src/pair_momb.txt b/doc/src/pair_momb.txt
index 545b650f75176e7a32d83ce85312e29720731f0c..f1989f56f49a39d66bf8242522cc07987984c9ce 100644
--- a/doc/src/pair_momb.txt
+++ b/doc/src/pair_momb.txt
@@ -50,8 +50,8 @@ Rr (distance units, typically sum of atomic vdW radii) :ul
[Restrictions:]
This style is part of the USER-MISC package. It is only enabled if
-LAMMPS is built with that package. See the "Making of
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS is built with that package. See the "Build
+package"_Build_package.html doc page on for more info.
[Related commands:]
diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt
index 85a42986ec87ed45e30fe3fc3120587b4d345492..68894f691384d7445196aa4783dbb882964d6b3f 100644
--- a/doc/src/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@@ -107,13 +107,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -148,12 +148,12 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
The {morse/smooth/linear} pair style is only enabled if LAMMPS was
-built with the USER-MISC package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with the USER-MISC package. See the "Build
+package"_Build_package.html doc page for more info.
The {morse/soft} pair style is only enabled if LAMMPS was built with
-the USER-FEP package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+the USER-FEP package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/pair_multi_lucy.txt b/doc/src/pair_multi_lucy.txt
index 31d52a58c89386b5cca80afcd4b585c4e314fc15..0b3a430417370765db40d4ef682f70040ddb1863 100644
--- a/doc/src/pair_multi_lucy.txt
+++ b/doc/src/pair_multi_lucy.txt
@@ -177,8 +177,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt
index e09dde3f8051128f22a0817f847b3238061f9ad6..819a15b6244bb557c3d1b2f43f19aac2d8c8ec51 100644
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@@ -210,13 +210,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -226,8 +226,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt
index 720b9ea2a1f903f42b54525f4481e63f071aa389..6a119d74e160da95d9a61e522e6c87d75ad1627d 100644
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@@ -98,13 +98,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -114,8 +114,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This pair style can only be used if LAMMPS was built with the MANYBODY
-package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt
index 355bfd5573e951c2f28effcc2e4e0aee5c351917..a42dfa3c98a632e2decfc4564940501957be9cf5 100644
--- a/doc/src/pair_nm.txt
+++ b/doc/src/pair_nm.txt
@@ -139,13 +139,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -153,8 +153,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
These pair styles are part of the MISC 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt
index 5ec99152978f42f5f603a1c87329ad005093583f..b24e3c07dfad96f51a4d74dccf885b525f502427 100644
--- a/doc/src/pair_oxdna.txt
+++ b/doc/src/pair_oxdna.txt
@@ -82,8 +82,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGDNA package and the MOLECULE and ASPHERE package. See the
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt
index a1d2cfdb7c862f96affbd60ec4d216baef0795bc..c5662abdeb9dbfc49959af673d3f54992c1d9b67 100644
--- a/doc/src/pair_oxdna2.txt
+++ b/doc/src/pair_oxdna2.txt
@@ -88,8 +88,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGDNA package and the MOLECULE and ASPHERE package. See the
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt
index 14abd4541e4b3f33d1dac80119d894f8b758608e..b6baa4edc5790ef45d0f56264b1d2d240b8c2b2a 100644
--- a/doc/src/pair_peri.txt
+++ b/doc/src/pair_peri.txt
@@ -145,13 +145,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -182,8 +182,8 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
All of these styles are part of the PERI 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.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt
index eb0c30f249cff1b58a11e21dcb2ff5df14a599fb..7460044043754ae55519a714cbb91396b1fbabc9 100644
--- a/doc/src/pair_polymorphic.txt
+++ b/doc/src/pair_polymorphic.txt
@@ -191,8 +191,8 @@ input script. If using read_data, atomic masses must be defined in the
atomic structure data file.
This pair style is part of the MANYBODY 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the "newtion"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt
index 1433557e0388e581c94b2668ecc2721fdeea1928..23da86fc495a6daabdee6048cc4d8dcb72525b6b 100644
--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@@ -204,8 +204,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the PYTHON 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt
index 3570a52801852be5207d72ef27a45438518ef6bb..1f794d0c84b87d72dbbcbed8603cdeca00c9e526 100644
--- a/doc/src/pair_quip.txt
+++ b/doc/src/pair_quip.txt
@@ -74,8 +74,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the USER-QUIP 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
QUIP potentials are parametrized in electron-volts and Angstroms and
therefore should be used with LAMMPS metal "units"_units.html.
diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt
index ec575486404904c6b92dd165e4d6ae490e8a7303..e63f4a90eef6a957787fabcfa43084c00d090ff7 100644
--- a/doc/src/pair_reaxc.txt
+++ b/doc/src/pair_reaxc.txt
@@ -309,13 +309,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -325,8 +325,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This pair style 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real "units"_units.html. You can use
diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt
index 6e72408ebc1a7243f3d01aadaa79dd02afd66553..5e760be495e0a52e9b7294ed73b1e756a403e2c9 100644
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
@@ -151,13 +151,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -203,8 +203,8 @@ command"_run_style.html.
[Restrictions:]
This style is part of the ASPHERE 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires that atoms be ellipsoids as defined by the
"atom_style ellipsoid"_atom_style.html command.
diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt
index ccf704b6f7f85b163fdcdd375b8821146ee37c37..b977aefe889c25f066e509efacba760ac71842a4 100644
--- a/doc/src/pair_sdk.txt
+++ b/doc/src/pair_sdk.txt
@@ -91,13 +91,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP, and OPT packages respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -133,11 +133,11 @@ respa"_run_style.html command.
[Restrictions:]
-All of the lj/sdk pair styles are part of the USER-CGSDK package.
-The {lj/sdk/coul/long} style also requires the KSPACE package to be
-built (which is enabled by default). They are only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+All of the lj/sdk pair styles are part of the USER-CGSDK package. The
+{lj/sdk/coul/long} style also requires the KSPACE package to be built
+(which is enabled by default). They are only enabled if LAMMPS was
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_hertz.txt b/doc/src/pair_smd_hertz.txt
index f2d633903ab99a90ac5485e1f871c994b872f69a..2581c84dc97d647ec69c67c6590c52a5b8cc6740 100644
--- a/doc/src/pair_smd_hertz.txt
+++ b/doc/src/pair_smd_hertz.txt
@@ -19,32 +19,36 @@ pair_coeff 1 1 <contact_stiffness>
[Description:]
-The {smd/hertz} style calculates contact forces between SPH particles belonging to different physical bodies.
+The {smd/hertz} style calculates contact forces between SPH particles
+belonging to different physical bodies.
-The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles
-(whose spatial extents are defined via its contact radius).
-The effect is that a particles cannot penetrate into each other.
-The parameter <contact_stiffness> has units of pressure and should equal roughly one half
-of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.
+The contact forces are calculated using a Hertz potential, which
+evaluates the overlap between two particles (whose spatial extents are
+defined via its contact radius). The effect is that a particles
+cannot penetrate into each other. The parameter <contact_stiffness>
+has units of pressure and should equal roughly one half of the Young's
+modulus (or bulk modulus in the case of fluids) of the material model
+associated with the SPH particles.
-The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
-particles can approach each other. Usually, {scale_factor} =1.0.
+The parameter {scale_factor} can be used to scale the particles'
+contact radii. This can be useful to control how close particles can
+approach each other. Usually, {scale_factor} =1.0.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-No mixing is performed automatically.
-Currently, no part of USER-SMD supports restarting nor minimization.
-rRESPA does not apply to this pair style.
+No mixing is performed automatically. Currently, no part of USER-SMD
+supports restarting nor minimization. rRESPA does not apply to this
+pair style.
:line
[Restrictions:]
This fix is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_tlsph.txt b/doc/src/pair_smd_tlsph.txt
index 3aeaa3155382ee4b0b0b34c0bc8beaa381c68bac..44b0c6cae81961bf6f08abf04815937ff694e78e 100644
--- a/doc/src/pair_smd_tlsph.txt
+++ b/doc/src/pair_smd_tlsph.txt
@@ -16,10 +16,11 @@ pair_style smd/tlsph args :pre
pair_style smd/tlsph
-
[Description:]
-The {smd/tlsph} style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm.
+The {smd/tlsph} style computes particle interactions according to
+continuum mechanics constitutive laws and a Total-Lagrangian
+Smooth-Particle Hydrodynamics algorithm.
This pair style is invoked with the following command:
@@ -27,35 +28,40 @@ pair_style smd/tlsph
pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
*END :pre
-Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is
-defined. Note that {i} and {j} must be equal, i.e., no {tlsph} cross interactions
-between different particle types are allowed.
-In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a
-number of floats and integers, the {tlsph} {pair coeff} definition is organised using
-keywords. These keywords mark the beginning of different sets of parameters for particle properties,
-material constitutive models, and damage models. The {pair coeff} line must be terminated with
-the {*END} keyword. The use the line continuation operator {&} is recommended. A typical
-invocation of the {tlsph} for a solid body would consist of an equation of state for computing
-the pressure (the diagonal components of the stress tensor), and a material model to compute shear
-stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added.
-
-Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
+Here, {i} and {j} denote the {LAMMPS} particle types for which this
+pair style is defined. Note that {i} and {j} must be equal, i.e., no
+{tlsph} cross interactions between different particle types are
+allowed. In contrast to the usual {LAMMPS} {pair coeff} definitions,
+which are given solely a number of floats and integers, the {tlsph}
+{pair coeff} definition is organised using keywords. These keywords
+mark the beginning of different sets of parameters for particle
+properties, material constitutive models, and damage models. The {pair
+coeff} line must be terminated with the {*END} keyword. The use the
+line continuation operator {&} is recommended. A typical invocation of
+the {tlsph} for a solid body would consist of an equation of state for
+computing the pressure (the diagonal components of the stress tensor),
+and a material model to compute shear stresses (the off-diagonal
+components of the stress tensor). Damage and failure models can also
+be added.
+
+Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a
+complete listing of the possible keywords and material models.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-No mixing is performed automatically.
-Currently, no part of USER-SMD supports restarting nor minimization.
-rRESPA does not apply to this pair style.
+No mixing is performed automatically. Currently, no part of USER-SMD
+supports restarting nor minimization. rRESPA does not apply to this
+pair style.
:line
[Restrictions:]
This fix is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/src/pair_smd_triangulated_surface.txt
index 65526cfba8cc15a6be2d8dd22510106b5d6a40cf..9eb5e311b8e20dec7a7f51756b02454260d7879e 100644
--- a/doc/src/pair_smd_triangulated_surface.txt
+++ b/doc/src/pair_smd_triangulated_surface.txt
@@ -19,17 +19,21 @@ pair_coeff 1 1 <contact_stiffness>
[Description:]
-The {smd/tri_surface} style calculates contact forces between SPH particles and a rigid wall boundary defined via the
+The {smd/tri_surface} style calculates contact forces between SPH
+particles and a rigid wall boundary defined via the
"smd/wall_surface"_fix_smd_wall_surface.html fix.
-The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle
-(whose spatial extents are defined via its contact radius) and the triangle.
-The effect is that a particle cannot penetrate into the triangular surface.
-The parameter <contact_stiffness> has units of pressure and should equal roughly one half
-of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle
+The contact forces are calculated using a Hertz potential, which
+evaluates the overlap between a particle (whose spatial extents are
+defined via its contact radius) and the triangle. The effect is that
+a particle cannot penetrate into the triangular surface. The
+parameter <contact_stiffness> has units of pressure and should equal
+roughly one half of the Young's modulus (or bulk modulus in the case
+of fluids) of the material model associated with the SPH particle
-The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
-particles can approach the triangulated surface. Usually, {scale_factor} =1.0.
+The parameter {scale_factor} can be used to scale the particles'
+contact radii. This can be useful to control how close particles can
+approach the triangulated surface. Usually, {scale_factor} =1.0.
:line
@@ -44,8 +48,8 @@ rRESPA does not apply to this pair style.
[Restrictions:]
This fix is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt
index a5bda54d5f0c46d792fc23bdbdba13f6168bbeee..f28dd9043cec1e504df6c89a28c1f2fd4dcbb4d6 100644
--- a/doc/src/pair_smd_ulsph.txt
+++ b/doc/src/pair_smd_ulsph.txt
@@ -17,11 +17,13 @@ keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT}
[Examples:]
-pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
+pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION :pre
[Description:]
-The {smd/ulsph} style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm.
+The {smd/ulsph} style computes particle interactions according to
+continuum mechanics constitutive laws and an updated Lagrangian
+Smooth-Particle Hydrodynamics algorithm.
This pair style is invoked similar to the following command:
@@ -29,37 +31,45 @@ pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECT
pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
*END :pre
-Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is
-defined. Note that {i} and {j} can be different, i.e., {ulsph} cross interactions
-between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to precede a cross interaction.
-In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a
-number of floats and integers, the {ulsph} {pair coeff} definition is organised using
-keywords. These keywords mark the beginning of different sets of parameters for particle properties,
-material constitutive models, and damage models. The {pair coeff} line must be terminated with
-the {*END} keyword. The use the line continuation operator {&} is recommended. A typical
-invocation of the {ulsph} for a solid body would consist of an equation of state for computing
-the pressure (the diagonal components of the stress tensor), and a material model to compute shear
-stresses (the off-diagonal components of the stress tensor).
-
-Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended.
-
-Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
+Here, {i} and {j} denote the {LAMMPS} particle types for which this
+pair style is defined. Note that {i} and {j} can be different, i.e.,
+{ulsph} cross interactions between different particle types are
+allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have
+to precede a cross interaction. In contrast to the usual {LAMMPS}
+{pair coeff} definitions, which are given solely a number of floats
+and integers, the {ulsph} {pair coeff} definition is organised using
+keywords. These keywords mark the beginning of different sets of
+parameters for particle properties, material constitutive models, and
+damage models. The {pair coeff} line must be terminated with the
+{*END} keyword. The use the line continuation operator {&} is
+recommended. A typical invocation of the {ulsph} for a solid body
+would consist of an equation of state for computing the pressure (the
+diagonal components of the stress tensor), and a material model to
+compute shear stresses (the off-diagonal components of the stress
+tensor).
+
+Note that the use of *GRADIENT_CORRECTION can lead to severe numerical
+instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION
+is recommended.
+
+Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a
+complete listing of the possible keywords and material models.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-No mixing is performed automatically.
-Currently, no part of USER-SMD supports restarting nor minimization.
-rRESPA does not apply to this pair style.
+No mixing is performed automatically. Currently, no part of USER-SMD
+supports restarting nor minimization. rRESPA does not apply to this
+pair style.
:line
[Restrictions:]
This fix is part of the USER-SMD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt
index c70202c2e13f536307ad84c1f50133490e8bff72..e81411678a71e9347811d0a3990b442db26d1fe8 100644
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
@@ -219,8 +219,8 @@ This pair style can only be used via the {pair} keyword of the
[Restriction:]
This pair style is part of the USER-SMTBQ package and is only enabled
-if LAMMPS is built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS is built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This potential requires using atom type 1 for oxygen and atom type
higher than 1 for metal atoms.
diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt
index f9bd8910e49ddfe37a044cf9e801f937a1b0cd7e..6f8cc3d8a8b9998f28775ad20fcbe920efdc5e52 100644
--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@@ -181,13 +181,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -196,9 +196,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This style is part of the SNAP 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.
+This style is part of the SNAP package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt
index 374711825b5d4bbf656d15fab9a3753c6f2239ce..ca0266f34a7842c8f273a076f087ce442a6b92d0 100644
--- a/doc/src/pair_soft.txt
+++ b/doc/src/pair_soft.txt
@@ -88,13 +88,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt
index d19c28a3cb5a0fec2f893d69fc23715abed8ae64..78a9cf2b63bc7906d737f0c81f78759082c0bea2 100644
--- a/doc/src/pair_sph_heatconduction.txt
+++ b/doc/src/pair_sph_heatconduction.txt
@@ -53,8 +53,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt
index a670949a892025d8d30ca9a5d63134020483ddc3..59513e7a7370845c3e3dd43f81cd4b90d5627a7d 100644
--- a/doc/src/pair_sph_idealgas.txt
+++ b/doc/src/pair_sph_idealgas.txt
@@ -60,8 +60,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt
index 152e6cf8a292cd5b03f895ff84282b9ac6652d63..43e77f1aae2d8cfbecd4539ce1b0b7ce35183937 100644
--- a/doc/src/pair_sph_lj.txt
+++ b/doc/src/pair_sph_lj.txt
@@ -60,8 +60,8 @@ As noted above, the Lennard-Jones parameters epsilon and sigma are set
to unity.
This pair style is part of the USER-SPH 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_rhosum.txt b/doc/src/pair_sph_rhosum.txt
index 3cd1c5abb2577e0d7c155d7d5cedd9ae1b768307..9069176f29388ea1a0a1f2e3b24283d183f91214 100644
--- a/doc/src/pair_sph_rhosum.txt
+++ b/doc/src/pair_sph_rhosum.txt
@@ -54,8 +54,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt
index 7b9a8188f28b36d30e7a71d64d8b49024ffadd1e..dcb9e39603ff0440d2beb97dafb847f4320df47f 100644
--- a/doc/src/pair_sph_taitwater.txt
+++ b/doc/src/pair_sph_taitwater.txt
@@ -63,8 +63,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/src/pair_sph_taitwater_morris.txt
index 02f16d8982f5af327d25e4ce43fbeb9fa877015b..b88707d1afa1e43a3fc2885993db6d544b86391b 100644
--- a/doc/src/pair_sph_taitwater_morris.txt
+++ b/doc/src/pair_sph_taitwater_morris.txt
@@ -62,8 +62,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt
index 375e59fe89486ebec90679a9a4c08b20f9655bb4..bd605bd064637191044f1cfbba122632d5cbb98a 100644
--- a/doc/src/pair_spin_dmi.txt
+++ b/doc/src/pair_spin_dmi.txt
@@ -69,10 +69,10 @@ pair style cannot be used.
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt
index 24eb635b819cd1982c5bc4a37d3e48950e13c28c..2f158704a98007ba083e4b3e90cf67dbb4c5e5bc 100644
--- a/doc/src/pair_spin_exchange.txt
+++ b/doc/src/pair_spin_exchange.txt
@@ -79,10 +79,10 @@ None of those coefficients is optional. If not specified, the
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt
index b338fae5dcdc3597e16dda8df691a012025114c1..f552c56a4bd34b93f68beb5b95f0146785908e3b 100644
--- a/doc/src/pair_spin_magelec.txt
+++ b/doc/src/pair_spin_magelec.txt
@@ -51,10 +51,10 @@ More details about the derivation of these torques/forces are reported in
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt
index 0967632ed2037ccac12228f089b56c31c8272ad1..fe3bb1ad14ea69240f6bd71b4f9bf06fd63278ef 100644
--- a/doc/src/pair_spin_neel.txt
+++ b/doc/src/pair_spin_neel.txt
@@ -62,10 +62,10 @@ More details about the derivation of these torques/forces are reported in
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index cd395133293545306ceb7824e6158b47b5a211fb..b33897c5aa506cd6be92ef275194ec2ceb83ce44 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -218,10 +218,9 @@ This command must be used before any coefficients are set by the
"read_restart"_read_restart.html commands.
Some pair styles are part of specific packages. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual pair potentials tell if it is part of a
-package.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual pair potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt
index e6741791dfe8d103ded1dbcfc27a9bcaf70e9527..ff83316419081f1e25b0778a66aaa00b78535819 100644
--- a/doc/src/pair_sw.txt
+++ b/doc/src/pair_sw.txt
@@ -150,13 +150,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
When using the USER-INTEL package with this style, there is an
additional 5 to 10 percent performance improvement when the
@@ -191,8 +191,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt
index 5e3c1f5ff6f2e1bf58c27589afc653c71c569d18..22c63a1f32b2d347884218f4cb449f95beb7e219 100644
--- a/doc/src/pair_table.txt
+++ b/doc/src/pair_table.txt
@@ -223,13 +223,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt
index 41be067bacfcc6eb60286b7f259926c2729e832b..9b9a6abff861daab0e499ee53e7276e138631e0e 100644
--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@@ -233,13 +233,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -249,8 +249,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index 821c38f3e4174310f43c6ee504ede9b194ebdab8..20744bc2a9ae3928a98f3d7dc23e361067d35b73 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -185,13 +185,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -221,8 +221,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt
index ac1f79a80b772f602f951ed34e373eb3b8bb0f0b..2df23045a397b16e56409ec506d8bfeeae85a1a1 100644
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@@ -137,13 +137,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -169,8 +169,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt
index a89d4e3ea1fbce4376fa787123d1a98bf25dbbb2..5f03ffd94eca4028b40283b554815d7e67c9198c 100644
--- a/doc/src/pair_tersoff_zbl.txt
+++ b/doc/src/pair_tersoff_zbl.txt
@@ -195,13 +195,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -231,8 +231,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY 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.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt
index 7ce8b7cf4bed33dc699d8c08197b01392d1d6ac3..c7a304ca41689df96344438eb094796a0108657c 100644
--- a/doc/src/pair_thole.txt
+++ b/doc/src/pair_thole.txt
@@ -136,13 +136,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -161,8 +161,8 @@ are defined using
[Restrictions:]
These pair styles are part of the USER-DRUDE 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.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair_style should currently not be used with the "charmm dihedral
style"_dihedral_charmm.html if the latter has non-zero 1-4 weighting
diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt
index 3915ffc2383c79220f2b403f7e2d43dc0041ab1e..98bb4e284efcad05315c08b7a0d542febf3e5d2d 100644
--- a/doc/src/pair_tri_lj.txt
+++ b/doc/src/pair_tri_lj.txt
@@ -101,8 +101,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the ASPHERE 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Defining particles to be triangles so they participate in tri/tri or
tri/particle interactions requires the use the "atom_style
diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt
index dbc6fd0664b99572fd39dcab68c60003ceef722f..787c60a1bd8a8565f880863178d2d959528bf5e5 100644
--- a/doc/src/pair_ufm.txt
+++ b/doc/src/pair_ufm.txt
@@ -75,13 +75,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt
index 2e404e8befcba50b462a0efbb61b48f0ba8cc82e..01d089b4de9b0727103d4b1fd653b2684cf711a5 100644
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@@ -177,13 +177,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -213,8 +213,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair style are part of the MANYBODY package. They is only
-enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair styles requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt
index 5a8363260a5e31f507d279500ea9eb2c78199758..154fd3e8367620af646bd283270f4d71ffafe507 100644
--- a/doc/src/pair_yukawa.txt
+++ b/doc/src/pair_yukawa.txt
@@ -55,13 +55,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt
index 515062d9eb679cefc969f91e41c376b265541bd4..b36c4c235c6cefef90ade34eaabf4b3fe7b08b36 100644
--- a/doc/src/pair_yukawa_colloid.txt
+++ b/doc/src/pair_yukawa_colloid.txt
@@ -86,13 +86,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -129,8 +129,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the COLLOID 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the "atom_style sphere"_atom_style.html
diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt
index 1472c7b6726d970179eeacd97915edabdfcdd55c..4c8dfb545526e07e11979d911856b1c3becdf341 100644
--- a/doc/src/pair_zbl.txt
+++ b/doc/src/pair_zbl.txt
@@ -77,13 +77,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/partition.txt b/doc/src/partition.txt
index d4fe06c098fd2de94520c38b96346407a0cbf3b9..86673c226bd5ef463e1723fb9f0fcdc023f4a678 100644
--- a/doc/src/partition.txt
+++ b/doc/src/partition.txt
@@ -26,9 +26,8 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1 :pre
[Description:]
This command invokes the specified command on a subset of the
-partitions of processors you have defined via the -partition
-command-line switch. See "Section 2.6"_Section_start.html#start_6
-for an explanation of the switch.
+partitions of processors you have defined via the "-partition
+command-line switch"_Run_options.html.
Normally, every input script command in your script is invoked by
every partition. This behavior can be modified by defining world- or
@@ -49,7 +48,7 @@ argument.
Partitions are numbered from 1 to Np, where Np is the number of
partitions specified by the "-partition command-line
-switch"_Section_start.html#start_6.
+switch"_Run_options.html.
{N} can be specified in one of two ways. An explicit numeric value
can be used, as in the 1st example above. Or a wild-card asterisk can
diff --git a/doc/src/prd.txt b/doc/src/prd.txt
index b2145ebad1a43ac0037f484f030a945479dd0ecb..f71f285336ff716db8af3da6f05b232932629ae2 100644
--- a/doc/src/prd.txt
+++ b/doc/src/prd.txt
@@ -62,15 +62,15 @@ timescale spanned by the multiple simulations, while waiting for an
event to occur.
Each replica runs on a partition of one or more processors. Processor
-partitions are defined at run-time using the -partition command-line
-switch; see "Section 2.6"_Section_start.html#start_6 of the manual.
-Note that if you have MPI installed, you can run a multi-replica
-simulation with more replicas (partitions) than you have physical
-processors, e.g you can run a 10-replica simulation on one or two
-processors. However for PRD, this makes little sense, since running a
-replica on virtual instead of physical processors,offers no effective
-parallel speed-up in searching for infrequent events. See the "Howto
-replica"_Howto_replica.html doc page for further discussion.
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html. Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on one or two processors. However for PRD, this makes
+little sense, since running a replica on virtual instead of physical
+processors,offers no effective parallel speed-up in searching for
+infrequent events. See the "Howto replica"_Howto_replica.html doc
+page for further discussion.
When a PRD simulation is performed, it is assumed that each replica is
running the same model, though LAMMPS does not check for this.
@@ -285,8 +285,8 @@ value for the first event in the new run will be slightly off.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
The {N} and {t_correlate} settings must be integer multiples of
{t_event}.
diff --git a/doc/src/processors.txt b/doc/src/processors.txt
index df13ae1f617fd9507bdbf7192b52d668c3ca44df..b9bd927f9688efbde7448eaa025bd111335eca4b 100644
--- a/doc/src/processors.txt
+++ b/doc/src/processors.txt
@@ -81,11 +81,11 @@ communication costs due to the high surface area of each processor's
sub-domain.
Also note that if multiple partitions are being used then P is the
-number of processors in this partition; see "this
-section"_Section_start.html#start_6 for an explanation of the
--partition command-line switch. Also note that you can prefix the
-processors command with the "partition"_partition.html command to
-easily specify different Px,Py,Pz values for different partitions.
+number of processors in this partition; see the "-partition
+command-line switch"_Run_options.html doc page for details. Also note
+that you can prefix the processors command with the
+"partition"_partition.html command to easily specify different
+Px,Py,Pz values for different partitions.
You can use the "partition"_partition.html command to specify
different processor grids for different partitions, e.g.
@@ -249,7 +249,7 @@ partition {Precv} which is enforced when each is setting up their own
mapping of their processors to the simulation box. Each of {Psend}
and {Precv} must be integers from 1 to Np, where Np is the number of
partitions you have defined via the "-partition command-line
-switch"_Section_start.html#start_6.
+switch"_Run_options.html.
A "dependency" means that the sending partition will create its
regular 3d grid as Px by Py by Pz and after it has done this, it will
@@ -286,8 +286,8 @@ processors and their mapping to the 3d grid to the specified file
processors in the manner you desired, which can be tricky to figure
out, especially when running on multiple partitions or on, a multicore
machine or when the processor ranks were reordered by use of the
-"-reorder command-line switch"_Section_start.html#start_6 or due to
-use of MPI-specific launch options such as a config file.
+"-reorder command-line switch"_Run_options.html or due to use of
+MPI-specific launch options such as a config file.
If you have multiple partitions you should insure that each one writes
to a different file, e.g. using a "world-style variable"_variable.html
@@ -300,11 +300,11 @@ The IDs are the processor's rank in this simulation (the world), the
universe (of multiple simulations), and the original MPI communicator
used to instantiate LAMMPS, respectively. The world and universe IDs
will only be different if you are running on more than one partition;
-see the "-partition command-line switch"_Section_start.html#start_6.
-The universe and original IDs will only be different if you used the
-"-reorder command-line switch"_Section_start.html#start_6 to reorder
-the processors differently than their rank in the original
-communicator LAMMPS was instantiated with.
+see the "-partition command-line switch"_Run_options.html. The
+universe and original IDs will only be different if you used the
+"-reorder command-line switch"_Run_options.html to reorder the
+processors differently than their rank in the original communicator
+LAMMPS was instantiated with.
I,J,K are the indices of the processor in the regular 3d grid, each
from 1 to Nd, where Nd is the number of processors in that dimension
@@ -332,7 +332,8 @@ The {part} keyword (for the receiving partition) only works with the
[Related commands:]
-"partition"_partition.html, "-reorder command-line switch"_Section_start.html#start_6
+"partition"_partition.html, "-reorder command-line
+switch"_Run_options.html
[Default:]
diff --git a/doc/src/python.txt b/doc/src/python.txt
index 4f4faca8f43c5fc6ca5db28f748238798405b862..54d18d2f6069c8e23400b9fd10be83083006c54a 100644
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@@ -100,7 +100,7 @@ be passed to various commands as arguments, so that the variable is
evaluated during a simulation run.
A broader overview of how Python can be used with LAMMPS is given on
-the "Python"_Python.html doc page. There is an examples/python
+the "Python"_Python_head.html doc page. There is an examples/python
directory which illustrates use of the python command.
:line
@@ -469,8 +469,8 @@ sys.exit() in the except clause).
[Restrictions:]
This command is part of the PYTHON 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.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Building LAMMPS with the PYTHON package will link LAMMPS with the
Python library on your system. Settings to enable this are in the
@@ -483,8 +483,8 @@ building LAMMPS. LAMMPS must also be built as a shared library and
your Python function must be able to to load the Python module in
python/lammps.py that wraps the LAMMPS library interface. These are
the same steps required to use Python by itself to wrap LAMMPS.
-Details on these steps are explained on the "Python"_Python.html doc
-page. Note that it is important that the stand-alone LAMMPS
+Details on these steps are explained on the "Python"_Python_head.html
+doc page. Note that it is important that the stand-alone LAMMPS
executable and the LAMMPS shared library be consistent (built from the
same source code files) in order for this to work. If the two have
been built at different times using different source files, problems
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index ded51a4d99855abfd9abc4361c1f0f2b052729dd..ef899a15b44b153621cc194d317c3a313bd9afac 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -63,8 +63,8 @@ simulation. The file can be ASCII text or a gzipped text file
atom coordinates; see the "read_restart"_read_restart.html and
"create_atoms"_create_atoms.html commands for alternative methods.
Also see the explanation of the "-restart command-line
-switch"_Section_start.html#start_6 which can convert a restart file to
-a data file.
+switch"_Run_options.html which can convert a restart file to a data
+file.
This command can be used multiple times to add new atoms and their
properties to an existing system by using the {add}, {offset}, and
@@ -1153,8 +1153,8 @@ Translational velocities can also be set by the
[Restrictions:]
To read gzipped data files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
[Related commands:]
diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt
index a3c0733e07369da85b63f222069ce12b224a3f13..db9cfca825b10f19a55292b8e78da88ce8a15950 100644
--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@@ -311,12 +311,12 @@ needed to generate absolute, unscaled coordinates.
[Restrictions:]
To read gzipped dump files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
The {molfile} dump file formats are part of the USER-MOLFILE package.
They are only enabled if LAMMPS was built with that packages. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt
index 488c36f02081d5be3c3a9a9067ed2638e4738c63..08cb6a2e6cc459351e5b7598c95bcbabe939e2b1 100644
--- a/doc/src/read_restart.txt
+++ b/doc/src/read_restart.txt
@@ -80,8 +80,7 @@ produced the restart file, it could be a LAMMPS bug, so consider
Because restart files are binary, they may not be portable to other
machines. In this case, you can use the "-restart command-line
-switch"_Section_start.html#start_6 to convert a restart file to a data
-file.
+switch"_Run_options.html to convert a restart file to a data file.
Similar to how restart files are written (see the
"write_restart"_write_restart.html and "restart"_restart.html
diff --git a/doc/src/region.txt b/doc/src/region.txt
index 21396ae1fd2b6652fc6928d24f685cfc39bc7031..acc85dcebbd89986d59da3f09a59ea45bf35ee29 100644
--- a/doc/src/region.txt
+++ b/doc/src/region.txt
@@ -370,13 +370,13 @@ by Kokkos or no acceleration will occur. Currently, only {block} style
regions are supported by Kokkos.
These accelerated styles are part of the Kokkos 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.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt
index 8eb3ebd5a19458aec21e3c799ef80cacf936e998..71ad464bb0015a109bca2f812ac8fe289d99c1b2 100644
--- a/doc/src/rerun.txt
+++ b/doc/src/rerun.txt
@@ -189,8 +189,8 @@ every 1000 steps, then you will only see thermodynamic output every
[Restrictions:]
To read gzipped dump files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
[Related commands:]
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 6f2dc5ca467c354a9c576d467af4c5d49c1e9301..7c034f36e0c6d002739c35362afca8440f9358a5 100644
--- a/doc/src/restart.txt
+++ b/doc/src/restart.txt
@@ -125,8 +125,7 @@ Restart files can be read by a "read_restart"_read_restart.html
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, you can use the "-r command-line
-switch"_Section_start.html#start_6 to convert a restart file to a data
-file.
+switch"_Run_options.html to convert a restart file to a data file.
NOTE: Although the purpose of restart files is to enable restarting a
simulation from where it left off, not all information about a
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index deee51cfd3d6fc0857ea99b5b169d323cbc323c7..6dd9b56908960bbbe820bcd7f2667a3faf158a73 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -69,8 +69,8 @@ The {verlet} style is a standard velocity-Verlet integrator.
The {verlet/split} style is also a velocity-Verlet integrator, but it
splits the force calculation within each timestep over 2 partitions of
-processors. See "Section 2.6"_Section_start.html#start_6 for an
-explanation of the -partition command-line switch.
+processors. See the "-partition command-line switch"_Run_options.html
+for info on how to run LAMMPS with multiple partitions.
Specifically, this style performs all computation except the
"kspace_style"_kspace_style.html portion of the force field on the 1st
@@ -115,9 +115,9 @@ When you run in 2-partition mode with the {verlet/split} style, the
thermodynamic data for the entire simulation will be output to the log
and screen file of the 1st partition, which are log.lammps.0 and
screen.0 by default; see the "-plog and -pscreen command-line
-switches"_Section_start.html#start_6 to change this. The log and
-screen file for the 2nd partition will not contain thermodynamic
-output beyond the 1st timestep of the run.
+switches"_Run_options.html to change this. The log and screen file
+for the 2nd partition will not contain thermodynamic output beyond the
+1st timestep of the run.
See the "Speed packages"_Speed_packages.html doc page for performance
details of the speed-up offered by the {verlet/split} style. One
@@ -282,10 +282,10 @@ additional operations required for managing {omp} styles. For more on
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-You can specify {respa/omp} explicitly in your input script, or
-you can use the "-suffix command-line switch"_Section_start.html#start_6
-when you invoke LAMMPS, or you can use the "suffix"_suffix.html
-command in your input script.
+You can specify {respa/omp} explicitly in your input script, or you
+can use the "-suffix command-line switch"_Run_options.html when you
+invoke LAMMPS, or you can use the "suffix"_suffix.html command in your
+input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -296,8 +296,8 @@ instructions on how to use the accelerated styles effectively.
The {verlet/split} style can only be used if LAMMPS was built with the
REPLICA package. Correspondingly the {respa/omp} style is available
-only if the USER-OMP package was included. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+only if the USER-OMP package was included. See the "Build
+package"_Build_package.html doc page for more info.
Whenever using rRESPA, the user should experiment with trade-offs in
speed and accuracy for their system, and verify that they are
diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt
index bb0619f1e04af5ab1bafc7772c2e40f09e1f3767..62e41ed29a10a1a7d077cbbbef7074fdb45412c5 100644
--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@@ -28,16 +28,16 @@ suffix kk :pre
This command allows you to use variants of various styles if they
exist. In that respect it operates the same as the "-suffix
-command-line switch"_Section_start.html#start_6. It also has options
-to turn off or back on any suffix setting made via the command line.
+command-line switch"_Run_options.html. It also has options to turn
+off or back on any suffix setting made via the command line.
The specified style can be {gpu}, {intel}, {kk}, {omp}, {opt} or
{hybrid}. These refer to optional packages that LAMMPS can be built
-with, as described in "this section of the
-manual"_Section_start.html#start_3. The "gpu" style corresponds to
-the GPU package, the "intel" style to the USER-INTEL package, the "kk"
-style to the KOKKOS package, the "omp" style to the USER-OMP package,
-and the "opt" style to the OPT package.
+with, as described on the "Build package"_Build_package.html doc page.
+The "gpu" style corresponds to the GPU package, the "intel" style to
+the USER-INTEL package, the "kk" style to the KOKKOS package, the
+"omp" style to the USER-OMP package, and the "opt" style to the OPT
+package.
These are the variants these packages provide:
@@ -105,6 +105,6 @@ input script.
[Related commands:]
-"Command-line switch -suffix"_Section_start.html#start_6
+"-suffix command-line switch"_Run_options.html
[Default:] none
diff --git a/doc/src/tad.txt b/doc/src/tad.txt
index a26ff79318ceed4f91cd402bb095a08c546baea5..9b34a68636c1eaa0b37ddbc9dce9ca6a5f61bd27 100644
--- a/doc/src/tad.txt
+++ b/doc/src/tad.txt
@@ -271,8 +271,8 @@ are always monotonically increasing.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
{N} setting must be integer multiple of {t_event}.
diff --git a/doc/src/temper.txt b/doc/src/temper.txt
index c7b482acc6467948a15321a363e138f5fb1962ae..edd578fbc93449e4d3eb3e0c4fb15dad6bad507f 100644
--- a/doc/src/temper.txt
+++ b/doc/src/temper.txt
@@ -31,14 +31,14 @@ Run a parallel tempering or replica exchange simulation using multiple
replicas (ensembles) of a system. Two or more replicas must be used.
Each replica runs on a partition of one or more processors. Processor
-partitions are defined at run-time using the -partition command-line
-switch; see "Section 2.6"_Section_start.html#start_6 of the manual.
-Note that if you have MPI installed, you can run a multi-replica
-simulation with more replicas (partitions) than you have physical
-processors, e.g you can run a 10-replica simulation on one or two
-processors. You will simply not get the performance speed-up you
-would see with one or more physical processors per replica. See the
-"Howto replica"_Howto_replica.html doc page for further discussion.
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html. Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on one or two processors. You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica. See the "Howto replica"_Howto_replica.html
+doc page for further discussion.
Each replica's temperature is controlled at a different value by a fix
with {fix-ID} that controls temperature. Most thermostat fix styles
@@ -68,9 +68,8 @@ rejected based on a Boltzmann-weighted Metropolis criterion which uses
As a tempering run proceeds, multiple log files and screen output
files are created, one per replica. By default these files are named
log.lammps.M and screen.M where M is the replica number from 0 to N-1,
-with N = # of replicas. See the "section on command-line
-switches"_Section_start.html#start_6 for info on how to change these
-names.
+with N = # of replicas. See the "-log and -screen command-line
+swiches"_Run_options.html for info on how to change these names.
The main screen and log file (log.lammps) will list information about
which temperature is assigned to each replica at each thermodynamic
@@ -138,8 +137,8 @@ example above with $w as the last argument.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/temper_grem.txt b/doc/src/temper_grem.txt
index 9cb1bab78465c890c0f6377d9c5fb45d0803b145..7d22e464032dc8dbf93580eb33779f16b068c37e 100644
--- a/doc/src/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@@ -94,8 +94,8 @@ identical to "temper"_temper.html.
[Restrictions:]
This command can only be used if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
This command must be used with "fix grem"_fix_grem.html.
diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt
index 4eee225de73cfd0e3ea3b4354a293d902fa8250c..50ac5615f69ad6ca5282fa959db24ad231612274 100644
--- a/doc/src/temper_npt.txt
+++ b/doc/src/temper_npt.txt
@@ -48,8 +48,8 @@ on how the parallel tempering is handled in general.
[Restrictions:]
This command can only be used if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
This command should be used with a fix that maintains the
isothermal-isobaric (NPT) ensemble.
diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt
index cbc2612f28c69a49bcd4dcb28b3b1c7a132fd85c..4d294c1df7b4c6d6a364448304c535ba7d44b950 100644
--- a/doc/src/thermo_style.txt
+++ b/doc/src/thermo_style.txt
@@ -253,9 +253,9 @@ proceed for the maximum number of allowed iterations.
The {part} keyword is useful for multi-replica or multi-partition
simulations to indicate which partition this output and this file
corresponds to, or for use in a "variable"_variable.html to append to
-a filename for output specific to this partition. See "Section
-2.6"_Section_start.html#start_6 of the manual for details on running
-in multi-partition mode.
+a filename for output specific to this partition. See discussion of
+the "-partition command-line switch"_Run_options.html for details on
+running in multi-partition mode.
The {timeremain} keyword returns the remaining seconds when a
timeout has been configured via the "timer timeout"_timer.html command.
diff --git a/doc/src/timer.txt b/doc/src/timer.txt
index 10737dbda0cebfea9b99582c28327168aa55faa6..4025af9ea623a0de7e9a13b5b7994387e76fb58d 100644
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@@ -39,8 +39,8 @@ During a simulation run LAMMPS collects information about how much
time is spent in different sections of the code and thus can provide
information for determining performance and load imbalance problems.
This can be done at different levels of detail and accuracy. For more
-information about the timing output, see this "discussion of screen
-output in Section 2.7"_Section_start.html#start_7.
+information about the timing output, see the "Run
+output"_Run_output.html doc page.
The {off} setting will turn all time measurements off. The {loop}
setting will only measure the total time for a run and not collect any
diff --git a/doc/src/variable.txt b/doc/src/variable.txt
index c6598ccb514d2855259038e99d1560488f7cdff9..a8d50503ac96bb6ea49041c6469449ae9438ee05 100644
--- a/doc/src/variable.txt
+++ b/doc/src/variable.txt
@@ -178,9 +178,8 @@ This means variables can NOT be re-defined in an input script (with
two exceptions, read further). This is to allow an input script to be
processed multiple times without resetting the variables; see the
"jump"_jump.html or "include"_include.html commands. It also means
-that using the "command-line switch"_Section_start.html#start_6 -var
-will override a corresponding index variable setting in the input
-script.
+that using the "command-line switch"_Run_options.html -var will
+override a corresponding index variable setting in the input script.
There are two exceptions to this rule. First, variables of style
{string}, {getenv}, {internal}, {equal}, {vector}, {atom}, and
@@ -247,8 +246,7 @@ string is assigned. All processors assign the same string to the
variable.
{Index} style variables with a single string value can also be set by
-using the command-line switch -var; see "this
-section"_Section_start.html#start_6 for details.
+using the "command-line switch -var"_Run_options.html.
The {loop} style is identical to the {index} style except that the
strings are the integers from 1 to N inclusive, if only one argument N
@@ -263,32 +261,31 @@ inclusive, and the string N1 is initially assigned to the variable.
N1 <= N2 and N2 >= 0 is required.
For the {world} style, one or more strings are specified. There must
-be one string for each processor partition or "world". See "this
-section"_Section_start.html#start_6 of the manual for information on
-running LAMMPS with multiple partitions via the "-partition"
-command-line switch. This variable command assigns one string to each
-world. All processors in the world are assigned the same string. The
-next command cannot be used with {equal} style variables, since there
-is only one value per world. This style of variable is useful when
-you wish to run different simulations on different partitions, or when
-performing a parallel tempering simulation (see the
+be one string for each processor partition or "world". LAMMPS can be
+run with multiple partitions via the "-partition command-line
+switch"_Run_options.html. This variable command assigns one string to
+each world. All processors in the world are assigned the same string.
+The next command cannot be used with {equal} style variables, since
+there is only one value per world. This style of variable is useful
+when you wish to run different simulations on different partitions, or
+when performing a parallel tempering simulation (see the
"temper"_temper.html command), to assign different temperatures to
different partitions.
For the {universe} style, one or more strings are specified. There
must be at least as many strings as there are processor partitions or
-"worlds". See "this page"_Section_start.html#start_6 for information
-on running LAMMPS with multiple partitions via the "-partition"
-command-line switch. This variable command initially assigns one
-string to each world. When a "next"_next.html command is encountered
-using this variable, the first processor partition to encounter it, is
-assigned the next available string. This continues until all the
-variable strings are consumed. Thus, this command can be used to run
-50 simulations on 8 processor partitions. The simulations will be run
-one after the other on whatever partition becomes available, until
-they are all finished. {Universe} style variables are incremented
-using the files "tmp.lammps.variable" and "tmp.lammps.variable.lock"
-which you will see in your directory during such a LAMMPS run.
+"worlds". LAMMPS can be run with multiple partitions via the
+"-partition command-line switch"_Run_options.html. This variable
+command initially assigns one string to each world. When a
+"next"_next.html command is encountered using this variable, the first
+processor partition to encounter it, is assigned the next available
+string. This continues until all the variable strings are consumed.
+Thus, this command can be used to run 50 simulations on 8 processor
+partitions. The simulations will be run one after the other on
+whatever partition becomes available, until they are all finished.
+{Universe} style variables are incremented using the files
+"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
+see in your directory during such a LAMMPS run.
The {uloop} style is identical to the {universe} style except that the
strings are the integers from 1 to N. This allows generation of long
diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt
index d8a33f457f2ab15cb38d6922ec54c5b5b8d5d202..b6002b52529a14621623a490316d751c0ad421bc 100644
--- a/doc/src/write_data.txt
+++ b/doc/src/write_data.txt
@@ -60,7 +60,7 @@ If you want to do more exact restarts, using binary files, see the
"restart"_restart.html, "write_restart"_write_restart.html, and
"read_restart"_read_restart.html commands. You can also convert
binary restart files to text data files, after a simulation has run,
-using the "-r command-line switch"_Section_start.html#start_6.
+using the "-r command-line switch"_Run_options.html.
NOTE: Only limited information about a simulation is stored in a data
file. For example, no information about atom "groups"_group.html and
diff --git a/doc/src/write_restart.txt b/doc/src/write_restart.txt
index 3935a5d5387bfd6118134c605058a146fbc81a43..c393c7f735ece6718966ad7bf37fd31194b0408c 100644
--- a/doc/src/write_restart.txt
+++ b/doc/src/write_restart.txt
@@ -66,8 +66,7 @@ Restart files can be read by a "read_restart"_read_restart.html
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, you can use the "-r command-line
-switch"_Section_start.html#start_6 to convert a restart file to a data
-file.
+switch"_Run_options.html to convert a restart file to a data file.
NOTE: Although the purpose of restart files is to enable restarting a
simulation from where it left off, not all information about a
diff --git a/lib/gpu/Install.py b/lib/gpu/Install.py
index 13d7ad157ef6435c5c6f03e743ccdd1bd2d6fa63..d1024c0085eb230a004efce14c6a38227a6221a6 100644
--- a/lib/gpu/Install.py
+++ b/lib/gpu/Install.py
@@ -23,15 +23,17 @@ optionally copies Makefile.auto to a new Makefile.osuffix
-m = use Makefile.machine as starting point, copy to Makefile.auto
default machine = linux
+ default for -h, -a, -p, -e settings are those in -m Makefile
-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 = 20 for Tesla C2050/C2070 (Fermi) (deprecated as of CUDA 8.0)
- or GeForce GTX 580 or similar
- use arch = 30 for Tesla K10 (Kepler)
- use arch = 35 for Tesla K40 (Kepler) or GeForce GTX Titan or similar
- use arch = 37 for Tesla dual K80 (Kepler)
- use arch = 60 for Tesla P100 (Pascal)
+ use arch = sm_20 for Fermi (C2050/C2070, deprecated as of CUDA 8.0)
+ or GeForce GTX 580 or similar
+ use arch = sm_30 for Kepler (K10)
+ use arch = sm_35 for Kepler (K40) or GeForce GTX Titan or similar
+ use arch = sm_37 for Kepler (dual K80)
+ use arch = sm_60 for Pascal (P100)
+ use arch = sm_70 for Volta
-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
@@ -46,7 +48,7 @@ Examples:
make lib-gpu args="-b" # build GPU lib with default Makefile.linux
make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
-make lib-gpu args="-m mpi -a 35 -p single -o mpi.mixed -b" # create new Makefile.mpi.mixed, also build GPU lib with these settings
+make lib-gpu args="-m mpi -a sm_35 -p single -o mpi.mixed -b" # create new Makefile.mpi.mixed, also build GPU lib with these settings
"""
# print error message or help
@@ -127,7 +129,7 @@ for line in lines:
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)
+ line = line.replace(words[2],"-arch=%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] == '=':
diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux
index ed5b6092d3fdbd0c710ee94fe9ca4138cb369e89..9580bfd4ae32cfe68d094e04ed9e6cbb995551b5 100644
--- a/lib/gpu/Makefile.linux
+++ b/lib/gpu/Makefile.linux
@@ -13,8 +13,8 @@ endif
NVCC = nvcc
-# Tesla CUDA
-CUDA_ARCH = -arch=sm_21
+# older CUDA
+#CUDA_ARCH = -arch=sm_21
# newer CUDA
#CUDA_ARCH = -arch=sm_13
# older CUDA
diff --git a/lib/kokkos/cmake/kokkos_settings.cmake b/lib/kokkos/cmake/kokkos_settings.cmake
index 21c9d75a96aa52fd349c751aa0c2fa0f12316c91..58b30ba24d7b3aa8324f26da07bcceb436c28bb2 100644
--- a/lib/kokkos/cmake/kokkos_settings.cmake
+++ b/lib/kokkos/cmake/kokkos_settings.cmake
@@ -158,7 +158,7 @@ if (NOT "${KOKKOS_INTERNAL_PATHS}" STREQUAL "")
set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} ${KOKKOS_INTERNAL_PATHS})
endif()
if (NOT "${KOKKOS_INTERNAL_ADDTOPATH}" STREQUAL "")
- set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} "PATH=\"${KOKKOS_INTERNAL_ADDTOPATH}:$ENV{PATH}\"")
+ set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} "PATH=${KOKKOS_INTERNAL_ADDTOPATH}:$ENV{PATH}")
endif()
if (CMAKE_CXX_STANDARD)
diff --git a/src/.gitignore b/src/.gitignore
index 058833ffb38dfca1ea188bebfe5522f943a1c6df..df3a22a5cd08b1a924aadde018674d972f340a5f 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -729,6 +729,8 @@
/pair_eam.h
/pair_eam_alloy.cpp
/pair_eam_alloy.h
+/pair_eam_cd.cpp
+/pair_eam_cd.h
/pair_eam_fs.cpp
/pair_eam_fs.h
/pair_edip.cpp
diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp
index 6da7f197ee7024bb3a6457f33a21138ad24d0a73..7d3c8c83f2a785e77fe84a10d0658bde2d7a53e6 100644
--- a/src/KSPACE/fft3d.cpp
+++ b/src/KSPACE/fft3d.cpp
@@ -14,7 +14,7 @@
/* ----------------------------------------------------------------------
Contributing authors: Jim Shepherd (GA Tech) added SGI SCSL support
Axel Kohlmeyer (Temple U) added support for
- FFTW3, KISSFFT, Dfti/MKL, and ACML.
+ FFTW3, KISS FFT, Dfti/MKL, and ACML.
Phil Blood (PSC) added single precision FFT.
Paul Coffman (IBM) added MPI collectives remap
------------------------------------------------------------------------- */
@@ -26,7 +26,7 @@
#include "fft3d.h"
#include "remap.h"
-#ifdef FFT_KISSFFT
+#ifdef FFT_KISS
/* include kissfft implementation */
#include "kissfft.h"
#endif
@@ -104,11 +104,13 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
DftiComputeForward(plan->handle_fast,data);
else
DftiComputeBackward(plan->handle_fast,data);
+ /*
#elif defined(FFT_FFTW2)
if (flag == -1)
fftw(plan->plan_fast_forward,total/length,data,1,length,NULL,0,0);
else
- fftw(plan->plan_fast_backward,total/length,data,1,length,NULL,0,0);
+ fftw(plan->plan_fast_backward,total/length,data,1,length,NULL,0,0);
+ */
#elif defined(FFT_FFTW3)
if (flag == -1)
theplan=plan->plan_fast_forward;
@@ -143,11 +145,13 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
DftiComputeForward(plan->handle_mid,data);
else
DftiComputeBackward(plan->handle_mid,data);
+ /*
#elif defined(FFT_FFTW2)
if (flag == -1)
fftw(plan->plan_mid_forward,total/length,data,1,length,NULL,0,0);
else
fftw(plan->plan_mid_backward,total/length,data,1,length,NULL,0,0);
+ */
#elif defined(FFT_FFTW3)
if (flag == -1)
theplan=plan->plan_mid_forward;
@@ -182,11 +186,13 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan)
DftiComputeForward(plan->handle_slow,data);
else
DftiComputeBackward(plan->handle_slow,data);
+ /*
#elif defined(FFT_FFTW2)
if (flag == -1)
fftw(plan->plan_slow_forward,total/length,data,1,length,NULL,0,0);
else
fftw(plan->plan_slow_backward,total/length,data,1,length,NULL,0,0);
+ */
#elif defined(FFT_FFTW3)
if (flag == -1)
theplan=plan->plan_slow_forward;
@@ -520,6 +526,7 @@ struct fft_plan_3d *fft_3d_create_plan(
(out_khi-out_klo+1);
}
+ /*
#elif defined(FFT_FFTW2)
plan->plan_fast_forward =
@@ -561,6 +568,7 @@ struct fft_plan_3d *fft_3d_create_plan(
plan->normnum = (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) *
(out_khi-out_klo+1);
}
+ */
#elif defined(FFT_FFTW3)
plan->plan_fast_forward =
@@ -660,6 +668,7 @@ void fft_3d_destroy_plan(struct fft_plan_3d *plan)
DftiFreeDescriptor(&(plan->handle_fast));
DftiFreeDescriptor(&(plan->handle_mid));
DftiFreeDescriptor(&(plan->handle_slow));
+ /*
#elif defined(FFT_FFTW2)
if (plan->plan_slow_forward != plan->plan_fast_forward &&
plan->plan_slow_forward != plan->plan_mid_forward) {
@@ -672,6 +681,7 @@ void fft_3d_destroy_plan(struct fft_plan_3d *plan)
}
fftw_destroy_plan(plan->plan_fast_forward);
fftw_destroy_plan(plan->plan_fast_backward);
+ */
#elif defined(FFT_FFTW3)
FFTW_API(destroy_plan)(plan->plan_slow_forward);
FFTW_API(destroy_plan)(plan->plan_slow_backward);
@@ -809,6 +819,7 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan)
DftiComputeBackward(plan->handle_mid,data);
DftiComputeBackward(plan->handle_slow,data);
}
+ /*
#elif defined(FFT_FFTW2)
if (flag == -1) {
fftw(plan->plan_fast_forward,total1/length1,data,1,0,NULL,0,0);
@@ -819,6 +830,7 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan)
fftw(plan->plan_mid_backward,total2/length2,data,1,0,NULL,0,0);
fftw(plan->plan_slow_backward,total3/length3,data,1,0,NULL,0,0);
}
+ */
#elif defined(FFT_FFTW3)
FFTW_API(plan) theplan;
if (flag == -1)
diff --git a/src/KSPACE/fft3d.h b/src/KSPACE/fft3d.h
index 9a9caaef2626b66d3a6666556d39a8ab7d9658b5..a51818d986f6f4b5a9e5c2e2ead828f04b7acb86 100644
--- a/src/KSPACE/fft3d.h
+++ b/src/KSPACE/fft3d.h
@@ -24,8 +24,8 @@ typedef float FFT_SCALAR;
typedef double FFT_SCALAR;
#endif
+// if user set FFTW, it means FFTW3
-// set default fftw library. switch to FFT_FFTW3 when convenient.
#ifdef FFT_FFTW
#define FFT_FFTW3
#endif
@@ -41,13 +41,13 @@ typedef double FFT_SCALAR;
typedef float _Complex FFT_DATA;
#define FFT_MKL_PREC DFTI_SINGLE
-#elif defined(FFT_FFTW2)
-#if defined(FFTW_SIZE)
-#include "sfftw.h"
-#else
-#include "fftw.h"
-#endif
-typedef FFTW_COMPLEX FFT_DATA;
+//#elif defined(FFT_FFTW2)
+//#if defined(FFTW_SIZE)
+//#include "sfftw.h"
+//#else
+//#include "fftw.h"
+//#endif
+//typedef FFTW_COMPLEX FFT_DATA;
#elif defined(FFT_FFTW3)
#include "fftw3.h"
@@ -57,8 +57,9 @@ typedef fftwf_complex FFT_DATA;
#else
/* use a stripped down version of kiss fft as default fft */
-#ifndef FFT_KISSFFT
-#define FFT_KISSFFT
+
+#ifndef FFT_KISS
+#define FFT_KISS
#endif
#define kiss_fft_scalar float
typedef struct {
@@ -81,13 +82,13 @@ typedef struct kiss_fft_state* kiss_fft_cfg;
typedef double _Complex FFT_DATA;
#define FFT_MKL_PREC DFTI_DOUBLE
-#elif defined(FFT_FFTW2)
-#if defined(FFTW_SIZE)
-#include "dfftw.h"
-#else
-#include "fftw.h"
-#endif
-typedef FFTW_COMPLEX FFT_DATA;
+//#elif defined(FFT_FFTW2)
+//#if defined(FFTW_SIZE)
+//#include "dfftw.h"
+//#else
+//#include "fftw.h"
+//#endif
+//typedef FFTW_COMPLEX FFT_DATA;
#elif defined(FFT_FFTW3)
#include "fftw3.h"
@@ -97,8 +98,8 @@ typedef fftw_complex FFT_DATA;
#else
/* use a stripped down version of kiss fft as default fft */
-#ifndef FFT_KISSFFT
-#define FFT_KISSFFT
+#ifndef FFT_KISS
+#define FFT_KISS
#endif
#define kiss_fft_scalar double
typedef struct {
@@ -138,13 +139,13 @@ struct fft_plan_3d {
DFTI_DESCRIPTOR *handle_fast;
DFTI_DESCRIPTOR *handle_mid;
DFTI_DESCRIPTOR *handle_slow;
-#elif defined(FFT_FFTW2)
- fftw_plan plan_fast_forward;
- fftw_plan plan_fast_backward;
- fftw_plan plan_mid_forward;
- fftw_plan plan_mid_backward;
- fftw_plan plan_slow_forward;
- fftw_plan plan_slow_backward;
+//#elif defined(FFT_FFTW2)
+// fftw_plan plan_fast_forward;
+// fftw_plan plan_fast_backward;
+// fftw_plan plan_mid_forward;
+// fftw_plan plan_mid_backward;
+//fftw_plan plan_slow_forward;
+//fftw_plan plan_slow_backward;
#elif defined(FFT_FFTW3)
FFTW_API(plan) plan_fast_forward;
FFTW_API(plan) plan_fast_backward;
@@ -152,7 +153,7 @@ struct fft_plan_3d {
FFTW_API(plan) plan_mid_backward;
FFTW_API(plan) plan_slow_forward;
FFTW_API(plan) plan_slow_backward;
-#elif defined(FFT_KISSFFT)
+#elif defined(FFT_KISS)
kiss_fft_cfg cfg_fast_forward;
kiss_fft_cfg cfg_fast_backward;
kiss_fft_cfg cfg_mid_forward;
diff --git a/src/KSPACE/kissfft.h b/src/KSPACE/kissfft.h
index 4e15f494a972f817a23208d53b6d5c80e1f121ad..c95b648dcb2213c100e8f82a06cdbaf676af0f7d 100644
--- a/src/KSPACE/kissfft.h
+++ b/src/KSPACE/kissfft.h
@@ -13,6 +13,7 @@
changes 2008-2011 by Axel Kohlmeyer <akohlmey@gmail.com>
*/
+
#ifndef LMP_FFT_KISSFFT
#define LMP_FFT_KISSFFT
diff --git a/src/pack.h b/src/pack.h
index 066535f5c9fc576094ef9a059e090a2d10393286..837c33d14bc4b284eb8df25585d6b8ae34181f44 100644
--- a/src/pack.h
+++ b/src/pack.h
@@ -22,9 +22,8 @@ struct pack_plan_3d {
int nqty; // # of values/element
};
-
-#if !defined(PACK_POINTER) && !defined(PACK_MEMCPY)
-#define PACK_ARRAY
+#if !defined(FFT_PACK_POINTER) && !defined(FFT_PACK_MEMCPY)
+#define FFT_PACK_ARRAY
#endif
#ifndef PACK_DATA
@@ -47,7 +46,7 @@ struct pack_plan_3d {
pack/unpack with array indices
------------------------------------------------------------------------- */
-#ifdef PACK_ARRAY
+#ifdef FFT_PACK_ARRAY
/* ----------------------------------------------------------------------
pack from data -> buf
@@ -274,7 +273,7 @@ static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
pack/unpack with pointers
------------------------------------------------------------------------- */
-#ifdef PACK_POINTER
+#ifdef FFT_PACK_POINTER
/* ----------------------------------------------------------------------
pack from data -> buf
@@ -523,7 +522,7 @@ static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl
just use PACK_POINTER versions
------------------------------------------------------------------------- */
-#ifdef PACK_MEMCPY
+#ifdef FFT_PACK_MEMCPY
/* ----------------------------------------------------------------------
pack from data -> buf