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bulk rename of remaining USER- packages

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This commit is contained in:
Axel Kohlmeyer
2021-06-29 19:49:18 -04:00
parent 2d4bb8f38c
commit 878795e64a
759 changed files with 878 additions and 878 deletions
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42
.github/CODEOWNERS vendored
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@ -22,33 +22,33 @@ src/MESSAGE/* @sjplimp
src/MLIAP/* @athomps
src/SNAP/* @athomps
src/SPIN/* @julient31
src/USER-BROWNIAN/* @samueljmcameron
src/BROWNIAN/* @samueljmcameron
src/CG-DNA/* @ohenrich
src/CG-SDK/* @akohlmey
src/USER-COLVARS/* @giacomofiorin
src/USER-DIELECTRIC/* @ndtrung81
src/USER-FEP/* @agiliopadua
src/COLVARS/* @giacomofiorin
src/DIELECTRIC/* @ndtrung81
src/FEP/* @agiliopadua
src/ML-HDNNP/* @singraber
src/USER-INTEL/* @wmbrownintel
src/USER-MANIFOLD/* @Pakketeretet2
src/USER-MDI/* @taylor-a-barnes
src/INTEL/* @wmbrownintel
src/MANIFOLD/* @Pakketeretet2
src/MDI/* @taylor-a-barnes
src/MEAM/* @martok
src/USER-MESONT/* @iafoss
src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
src/MESONT/* @iafoss
src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
src/ML-PACE/* @yury-lysogorskiy
src/USER-PLUMED/* @gtribello
src/USER-PHONON/* @lingtikong
src/USER-PTM/* @pmla
src/PLUMED/* @gtribello
src/PHONON/* @lingtikong
src/PTM/* @pmla
src/OPENMP/* @akohlmey
src/USER-QMMM/* @akohlmey
src/QMMM/* @akohlmey
src/REAXFF/* @hasanmetin
src/USER-REACTION/* @jrgissing
src/USER-SCAFACOS/* @rhalver
src/USER-TALLY/* @akohlmey
src/USER-UEF/* @danicholson
src/USER-VTK/* @rbberger
src/REACTION/* @jrgissing
src/SCAFACOS/* @rhalver
src/TALLY/* @akohlmey
src/UEF/* @danicholson
src/VTK/* @rbberger
# individual files in packages
@ -138,7 +138,7 @@ unittest/* @akohlmey @rbberger
# cmake
cmake/* @junghans @rbberger
cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
cmake/presets/*.cmake @akohlmey

6
.github/CONTRIBUTING.md vendored
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@ -74,13 +74,13 @@ Here is a checklist of steps you need to follow to submit a single file or user
* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no trailing whitespace, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'.
* If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this FOO directory.
* Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/PACKAGES for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
* For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree.
* When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.).
* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the <name>.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the <name>.cpp source file. See src/EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.

46
cmake/CMakeLists.txt
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@ -141,14 +141,14 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE PERI POEMS
PLUGIN QEQ REPLICA RIGID SHOCK SPIN ML-SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS CG-DNA DPD-MESO CG-SDK
USER-COLVARS USER-DIELECTRIC USER-DIFFRACTION DPD-REACT USER-DRUDE USER-EFF USER-FEP
USER-H5MD ML-HDNNP LATBOLTZ USER-MANIFOLD USER-MDI MEAM USER-MESONT USER-MGPT
USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
ML-RANN USER-REACTION REAXFF USER-SCAFACOS DPD-SMOOTH MACHDYN USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK ML-QUIP USER-QMMM USER-YAFF ML-PACE USER-BROWNIAN)
ADIOS ATC AWPMD BOCS CG-DNA DPD-MESO CG-SDK
COLVARS DIELECTRIC DIFFRACTION DPD-REACT DRUDE EFF FEP
H5MD ML-HDNNP LATBOLTZ MANIFOLD MDI MEAM MESONT MGPT
USER-MISC MOFFF MOLFILE NETCDF PHONON PLUMED PTM QTB
ML-RANN REACTION REAXFF SCAFACOS DPD-SMOOTH MACHDYN SMTBQ SPH
TALLY UEF VTK ML-QUIP QMMM YAFF ML-PACE BROWNIAN)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL OPENMP)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP)
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
@ -159,7 +159,7 @@ endforeach()
######################################################
target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}>)
if(PKG_USER-ADIOS)
if(PKG_ADIOS)
# The search for ADIOS2 must come before MPI because
# it includes its own MPI search with the latest FindMPI.cmake
# script that defines the MPI::MPI_C target
@ -231,11 +231,11 @@ endif()
# in an error instead of skipping over files
pkg_depends(ML-IAP ML-SNAP)
pkg_depends(MPIIO MPI)
pkg_depends(USER-ATC MANYBODY)
pkg_depends(ATC MANYBODY)
pkg_depends(LATBOLTZ MPI)
pkg_depends(USER-PHONON KSPACE)
pkg_depends(USER-SCAFACOS MPI)
pkg_depends(USER-DIELECTRIC KSPACE)
pkg_depends(PHONON KSPACE)
pkg_depends(SCAFACOS MPI)
pkg_depends(DIELECTRIC KSPACE)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
@ -271,7 +271,7 @@ if(BUILD_OMP)
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_ML-QUIP OR PKG_LATTE)
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE)
enable_language(C)
find_package(LAPACK)
find_package(BLAS)
@ -350,8 +350,8 @@ else()
set(CUDA_REQUEST_PIC)
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI USER-COLVARS ML-HDNNP USER-MDI USER-MOLFILE USER-NETCDF
USER-PLUMED USER-QMMM ML-QUIP USER-SCAFACOS MACHDYN USER-VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE)
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -444,9 +444,9 @@ endforeach()
##############################################
# add lib sources of (simple) enabled packages
############################################
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
foreach(SIMPLE_LIB POEMS ATC AWPMD H5MD MESONT)
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(REGEX REPLACE "^" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
if(PKG_LIB STREQUAL "mesont")
enable_language(Fortran)
@ -470,13 +470,13 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
endif()
endforeach()
if(PKG_USER-AWPMD)
if(PKG_AWPMD)
target_link_libraries(awpmd PRIVATE ${LAPACK_LIBRARIES})
endif()
if(PKG_USER-ATC)
if(PKG_ATC)
if(LAMMPS_SIZES STREQUAL "BIGBIG")
message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
message(FATAL_ERROR "The ATC Package is not compatible with -DLAMMPS_BIGBIG")
endif()
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
if(BUILD_MPI)
@ -488,15 +488,15 @@ if(PKG_USER-ATC)
target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
endif()
if(PKG_USER-H5MD)
include(Packages/USER-H5MD)
if(PKG_H5MD)
include(Packages/H5MD)
endif()
######################################################################
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT USER-INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()

0
cmake/Modules/Packages/USER-COLVARS.cmake → cmake/Modules/Packages/COLVARS.cmake
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0
cmake/Modules/Packages/USER-H5MD.cmake → cmake/Modules/Packages/H5MD.cmake
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46
cmake/Modules/Packages/USER-INTEL.cmake → cmake/Modules/Packages/INTEL.cmake
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@ -5,7 +5,7 @@ endif()
target_compile_definitions(lammps PRIVATE -DLMP_USER_INTEL)
set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by 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)
@ -40,10 +40,10 @@ endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
message(FATAL_ERROR "INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
endif()
else()
message(WARNING "USER-INTEL gives best performance with Intel compilers")
message(WARNING "INTEL gives best performance with Intel compilers")
endif()
find_package(TBB_MALLOC QUIET)
@ -52,7 +52,7 @@ if(TBB_MALLOC_FOUND)
else()
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_NO_TBB)
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
message(WARNING "INTEL with Intel compilers should use TBB malloc libraries")
endif()
endif()
@ -65,12 +65,12 @@ else()
endif()
if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
message(FATAL_ERROR "INTEL only supports memory alignment of 64, 128 or 256 on this platform")
endif()
if(INTEL_ARCH STREQUAL "KNL")
if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
message(FATAL_ERROR "Must use Intel compiler with INTEL for KNL architecture")
endif()
set(CMAKE_EXE_LINKER_FLAGS "${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\\\"\"")
@ -91,26 +91,26 @@ else()
endif()
# collect sources
set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
set(INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/INTEL)
set(INTEL_SOURCES ${INTEL_SOURCES_DIR}/fix_intel.cpp
${INTEL_SOURCES_DIR}/fix_nh_intel.cpp
${INTEL_SOURCES_DIR}/intel_buffers.cpp
${INTEL_SOURCES_DIR}/nbin_intel.cpp
${INTEL_SOURCES_DIR}/npair_intel.cpp)
set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
set_property(GLOBAL PROPERTY "INTEL_SOURCES" "${INTEL_SOURCES}")
# detect styles which have a USER-INTEL version
RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
# detect styles which have a INTEL version
RegisterStylesExt(${INTEL_SOURCES_DIR} intel INTEL_SOURCES)
RegisterNBinStyle(${INTEL_SOURCES_DIR}/nbin_intel.h)
RegisterNPairStyle(${INTEL_SOURCES_DIR}/npair_intel.h)
RegisterFixStyle(${INTEL_SOURCES_DIR}/fix_intel.h)
get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
get_property(INTEL_SOURCES GLOBAL PROPERTY INTEL_SOURCES)
if(PKG_KSPACE)
list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
endif()
target_sources(lammps PRIVATE ${USER-INTEL_SOURCES})
target_include_directories(lammps PRIVATE ${USER-INTEL_SOURCES_DIR})
target_sources(lammps PRIVATE ${INTEL_SOURCES})
target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

0
cmake/Modules/Packages/USER-MDI.cmake → cmake/Modules/Packages/MDI.cmake
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0
cmake/Modules/Packages/USER-MOLFILE.cmake → cmake/Modules/Packages/MOLFILE.cmake
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2
cmake/Modules/Packages/USER-NETCDF.cmake → cmake/Modules/Packages/NETCDF.cmake
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@ -1,4 +1,4 @@
# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
# NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
# NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
# may use NetCDF or PNetCDF with MPI, but must have NetCDF without

0
cmake/Modules/Packages/USER-PLUMED.cmake → cmake/Modules/Packages/PLUMED.cmake
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0
cmake/Modules/Packages/USER-QMMM.cmake → cmake/Modules/Packages/QMMM.cmake
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0
cmake/Modules/Packages/USER-SCAFACOS.cmake → cmake/Modules/Packages/SCAFACOS.cmake
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0
cmake/Modules/Packages/USER-SDPD.cmake → cmake/Modules/Packages/SDPD.cmake
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0
cmake/Modules/Packages/USER-VTK.cmake → cmake/Modules/Packages/VTK.cmake
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14
cmake/presets/all_off.cmake
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@ -5,13 +5,13 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS CG-DNA CG-SDK
USER-COLVARS USER-DIFFRACTION DPD-REACT USER-DRUDE USER-EFF USER-FEP USER-H5MD
ML-HDNNP USER-INTEL LATBOLTZ USER-MANIFOLD USER-MDI MEAM DPD-MESO
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF OPENMP
ML-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB ML-QUIP ML-RANN
USER-REACTION REAXFF USER-SCAFACOS DPD-SMOOTH MACHDYN USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC)
ADIOS ATC AWPMD BROWNIAN BOCS CG-DNA CG-SDK
COLVARS DIFFRACTION DPD-REACT DRUDE EFF FEP H5MD
ML-HDNNP INTEL LATBOLTZ MANIFOLD MDI MEAM DPD-MESO
MESONT MGPT USER-MISC MOFFF MOLFILE NETCDF OPENMP
ML-PACE PHONON PLUMED PTM QMMM QTB ML-QUIP ML-RANN
REACTION REAXFF SCAFACOS DPD-SMOOTH MACHDYN SMTBQ SPH
TALLY UEF VTK YAFF DIELECTRIC)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

14
cmake/presets/all_on.cmake
View File

@ -7,13 +7,13 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS CG-DNA CG-SDK
USER-COLVARS USER-DIFFRACTION DPD-REACT USER-DRUDE USER-EFF USER-FEP USER-H5MD
ML-HDNNP USER-INTEL LATBOLTZ USER-MANIFOLD USER-MDI MEAM DPD-MESO
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF OPENMP
ML-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB ML-QUIP ML-RANN
USER-REACTION REAXFF USER-SCAFACOS DPD-SMOOTH MACHDYN USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC)
ADIOS ATC AWPMD BROWNIAN BOCS CG-DNA CG-SDK
COLVARS DIFFRACTION DPD-REACT DRUDE EFF FEP H5MD
ML-HDNNP INTEL LATBOLTZ MANIFOLD MDI MEAM DPD-MESO
MESONT MGPT USER-MISC MOFFF MOLFILE NETCDF OPENMP
ML-PACE PHONON PLUMED PTM QMMM QTB ML-QUIP ML-RANN
REACTION REAXFF SCAFACOS DPD-SMOOTH MACHDYN SMTBQ SPH
TALLY UEF VTK YAFF DIELECTRIC)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

2
cmake/presets/download.cmake
View File

@ -1,7 +1,7 @@
# Preset that turns on packages with automatic downloads of sources or potentials.
# Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS MACHDYN USER-MESONT USER-MDI ML-PACE)
set(ALL_PACKAGES KIM LATTE MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

14
cmake/presets/mingw-cross.cmake
View File

@ -1,13 +1,13 @@
set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KSPACE LATTE MANYBODY MC MISC ML-IAP MOLECULE OPT
PERI POEMS QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI
USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN CG-DNA CG-SDK
USER-COLVARS USER-DIFFRACTION DPD-REACT USER-DRUDE USER-EFF USER-FEP
ML-HDNNP USER-INTEL USER-MANIFOLD USER-MDI MEAM DPD-MESO
USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE OPENMP
USER-PHONON USER-PTM USER-QTB USER-REACTION REAXFF
DPD-SMOOTH MACHDYN USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-YAFF USER-DIELECTRIC)
ATC AWPMD BOCS BROWNIAN CG-DNA CG-SDK
COLVARS DIFFRACTION DPD-REACT DRUDE EFF FEP
ML-HDNNP INTEL MANIFOLD MDI MEAM DPD-MESO
MESONT USER-MISC MGPT MOFFF MOLFILE OPENMP
PHONON PTM QTB REACTION REAXFF
DPD-SMOOTH MACHDYN SMTBQ SPH TALLY UEF
YAFF DIELECTRIC)
foreach(PKG ${WIN_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

8
cmake/presets/most.cmake
View File

@ -5,10 +5,10 @@
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
GRANULAR KSPACE MANYBODY MC MISC ML-IAP MOLECULE OPT PERI
PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI
USER-BROWNIAN USER-BOCS CG-DNA CG-SDK USER-COLVARS
USER-DIFFRACTION DPD-REACT USER-DRUDE USER-EFF USER-FEP MEAM
DPD-MESO USER-MISC USER-MOFFF OPENMP USER-PHONON USER-REACTION
REAXFF DPD-SMOOTH USER-SPH MACHDYN USER-UEF USER-YAFF USER-DIELECTRIC)
BROWNIAN BOCS CG-DNA CG-SDK COLVARS
DIFFRACTION DPD-REACT DRUDE EFF FEP MEAM
DPD-MESO USER-MISC MOFFF OPENMP PHONON REACTION
REAXFF DPD-SMOOTH SPH MACHDYN UEF YAFF DIELECTRIC)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

6
cmake/presets/nolib.cmake
View File

@ -3,9 +3,9 @@
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
PYTHON VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-H5MD ML-HDNNP LATBOLTZ USER-MOLFILE
USER-MESONT USER-MDI USER-NETCDF ML-PACE USER-PLUMED USER-QMMM ML-QUIP
USER-SCAFACOS MACHDYN USER-VTK)
ADIOS ATC AWPMD H5MD ML-HDNNP LATBOLTZ MOLFILE
MESONT MDI NETCDF ML-PACE PLUMED QMMM ML-QUIP
SCAFACOS MACHDYN VTK)
foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

2
doc/include-file-conventions.md
View File

@ -122,7 +122,7 @@ recorded compilation commands information when typing `make iwyu`.
A lot of code predates the application of the rules in this document
and the rules themselves are a moving target. So there are going to be
significant chunks of code that do not fully comply. This applies
for example to the REAXFF, or the USER-ATC package. The LAMMPS
for example to the REAXFF, or the ATC package. The LAMMPS
developers are dedicated to make an effort to improve the compliance
and welcome volunteers wanting to help with the process.

2
doc/lammps.1
View File

@ -135,7 +135,7 @@ For example "-pk gpu 2" is the same as "package gpu 2" in the input
script. The possible styles and options are discussed in the
.B LAMMPS
manual for the "package" command. This switch can be used multiple
times, e.g. to set options for the USER-INTEL and OPENMP packages
times, e.g. to set options for the INTEL and OPENMP packages
when used together. Along with the "-sf" or "-suffix" switch, this
is a convenient mechanism for invoking accelerator packages and their
options without having to edit an input script.

14
doc/src/Build_basics.rst
View File

@ -121,18 +121,18 @@ documentation to find out how to build and link with it.
The majority of OpenMP (threading) support in LAMMPS is provided by the
``OPENMP`` package; see the :doc:`Speed_omp`
page for details. The ``USER-INTEL`` package also includes OpenMP
page for details. The ``INTEL`` package also includes OpenMP
threading (it is compatible with ``OPENMP`` and will usually fall
back on styles from that package, if a ``USER-INTEL`` does not exist)
back on styles from that package, if a ``INTEL`` does not exist)
and adds vectorization support when compiled with compatible compilers,
in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
package can be compiled to include OpenMP threading.
In addition, there are a few commands in LAMMPS that have native OpenMP
support included as well. These are commands in the ``MPIIO``,
``ML-SNAP``, ``USER-DIFFRACTION``, and ``DPD-REACT`` packages. In addition
``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages. In addition
some packages support OpenMP threading indirectly through the libraries
they interface to: e.g. ``LATTE``, ``KSPACE``, and ``USER-COLVARS``.
they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.
See the :doc:`Packages details <Packages_details>` page for more
info on these packages and the pages for their respective commands
for OpenMP threading info.
@ -176,7 +176,7 @@ performance. Vendor provided compilers for a specific hardware can
produce faster code than open-source compilers like the GNU compilers.
On the most common x86 hardware most popular C++ compilers are quite
similar in performance of C/C++ code at high optimization levels. When
using the ``USER-INTEL`` package, there is a distinct advantage in using
using the ``INTEL`` package, there is a distinct advantage in using
the `Intel C++ compiler <intel_>`_ due to much improved vectorization
through SSE and AVX instructions on compatible hardware as the source
code includes changes and Intel compiler specific directives to enable
@ -326,8 +326,8 @@ LAMMPS.
Makefile.opt # OPT package
Makefile.omp # OPENMP package
Makefile.intel_cpu # USER-INTEL package for CPUs
Makefile.intel_coprocessor # USER-INTEL package for KNLs
Makefile.intel_cpu # INTEL package for CPUs
Makefile.intel_coprocessor # INTEL package for KNLs
Makefile.gpu # GPU package
Makefile.kokkos_cuda_mpi # KOKKOS package for GPUs
Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP)

2
doc/src/Build_development.rst
View File

@ -310,7 +310,7 @@ and working.
parameter needs to be adjusted. Typically a value around 1.0e-13
can be used, but it may need to be as large as 1.0e-8 in some
cases.
- The tests for pair styles from OPT, OPENMP and USER-INTEL are
- The tests for pair styles from OPT, OPENMP and INTEL are
performed with automatically rescaled epsilon to account for
additional loss of precision from code optimizations and different
summation orders.

112
doc/src/Build_extras.rst
View File

@ -43,25 +43,25 @@ This is the list of packages that may require additional steps.
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`VORONOI <voronoi>`
* :ref:`USER-ADIOS <user-adios>`
* :ref:`USER-ATC <user-atc>`
* :ref:`USER-AWPMD <user-awpmd>`
* :ref:`USER-COLVARS <user-colvars>`
* :ref:`USER-H5MD <user-h5md>`
* :ref:`ADIOS <adios>`
* :ref:`ATC <atc>`
* :ref:`AWPMD <awpmd>`
* :ref:`COLVARS <colvars>`
* :ref:`H5MD <h5md>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`USER-INTEL <user-intel>`
* :ref:`USER-MDI <user-mdi>`
* :ref:`USER-MESONT <user-mesont>`
* :ref:`USER-MOLFILE <user-molfile>`
* :ref:`USER-NETCDF <user-netcdf>`
* :ref:`INTEL <intel>`
* :ref:`MDI <mdi>`
* :ref:`MESONT <mesont>`
* :ref:`MOLFILE <molfile>`
* :ref:`NETCDF <netcdf>`
* :ref:`ML-PACE <ml-pace>`
* :ref:`USER-PLUMED <user-plumed>`
* :ref:`PLUMED <plumed>`
* :ref:`OPENMP <openmp>`
* :ref:`USER-QMMM <user-qmmm>`
* :ref:`QMMM <qmmm>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`USER-SCAFACOS <user-scafacos>`
* :ref:`SCAFACOS <scafacos>`
* :ref:`MACHDYN <machdyn>`
* :ref:`USER-VTK <user-vtk>`
* :ref:`VTK <vtk>`
----------
@ -1058,10 +1058,10 @@ binary package provided by your operating system.
.. _user-adios:
USER-ADIOS package
ADIOS package
-----------------------------------
The USER-ADIOS package requires the `ADIOS I/O library
The ADIOS package requires the `ADIOS I/O library
<https://github.com/ornladios/ADIOS2>`_, version 2.3.1 or newer. Make
sure that you have ADIOS built either with or without MPI to match if
you build LAMMPS with or without MPI. ADIOS compilation settings for
@ -1077,38 +1077,38 @@ systems.
.. code-block:: bash
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
-D PKG_USER-ADIOS=yes
-D PKG_ADIOS=yes
.. tab:: Traditional make
Turn on the USER-ADIOS package before building LAMMPS. If the
Turn on the ADIOS package before building LAMMPS. If the
ADIOS 2.x software is installed in PATH, there is nothing else to
do:
.. code-block:: bash
$ make yes-user-adios
$ make yes-adios
otherwise, set ADIOS2_DIR environment variable when turning on the package:
.. code-block:: bash
$ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed
$ ADIOS2_DIR=path make yes-adios # path is where ADIOS 2.x is installed
----------
.. _user-atc:
USER-ATC package
ATC package
-------------------------------
The USER-ATC package requires the MANYBODY package also be installed.
The ATC package requires the MANYBODY package also be installed.
.. tabs::
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-ATC=yes``
No additional settings are needed besides ``-D PKG_ATC=yes``
and ``-D PKG_MANYBODY=yes``.
.. tab:: Traditional make
@ -1153,14 +1153,14 @@ The USER-ATC package requires the MANYBODY package also be installed.
.. _user-awpmd:
USER-AWPMD package
AWPMD package
------------------
.. tabs::
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``.
No additional settings are needed besides ``-D PKG_AQPMD=yes``.
.. tab:: Traditional make
@ -1204,7 +1204,7 @@ USER-AWPMD package
.. _user-colvars:
USER-COLVARS package
COLVARS package
---------------------------------------
This package includes the `Colvars library
@ -1218,7 +1218,7 @@ be built for the most part with all major versions of the C++ language.
This is the recommended build procedure for using Colvars in
LAMMPS. No additional settings are normally needed besides
``-D PKG_USER-COLVARS=yes``.
``-D PKG_COLVARS=yes``.
.. tab:: Traditional make
@ -1303,7 +1303,7 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
.. _user-plumed:
USER-PLUMED package
PLUMED package
-------------------------------------
.. _plumedinstall: https://plumed.github.io/doc-master/user-doc/html/_installation.html
@ -1311,7 +1311,7 @@ USER-PLUMED package
Before building LAMMPS with this package, you must first build PLUMED.
PLUMED can be built as part of the LAMMPS build or installed separately
from LAMMPS using the generic `PLUMED installation instructions <plumedinstall_>`_.
The USER-PLUMED package has been tested to work with Plumed versions
The PLUMED package has been tested to work with Plumed versions
2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
with a different version of the Plumed kernel.
@ -1347,7 +1347,7 @@ LAMMPS build.
.. tab:: CMake build
When the ``-D PKG_USER-PLUMED=yes`` flag is included in the cmake
When the ``-D PKG_PLUMED=yes`` flag is included in the cmake
command you must ensure that GSL is installed in locations that
are specified in your environment. There are then two additional
variables that control the manner in which PLUMED is obtained and
@ -1380,7 +1380,7 @@ LAMMPS build.
.. tab:: Traditional make
PLUMED needs to be installed before the USER-PLUMED package is
PLUMED needs to be installed before the PLUMED package is
installed so that LAMMPS can find the right settings when
compiling and linking the LAMMPS executable. You can either
download and build PLUMED inside the LAMMPS plumed library folder
@ -1405,12 +1405,12 @@ LAMMPS build.
build to use. A new file ``lib/plumed/Makefile.lammps`` is also
created with settings suitable for LAMMPS to compile and link
PLUMED using the desired linkage mode. After this step is
completed, you can install the USER-PLUMED package and compile
completed, you can install the PLUMED package and compile
LAMMPS in the usual manner:
.. code-block:: bash
$ make yes-user-plumed
$ make yes-plumed
$ make machine
Once this compilation completes you should be able to run LAMMPS
@ -1425,7 +1425,7 @@ LAMMPS build.
If you want to change the linkage mode, you have to re-run "make
lib-plumed" with the desired settings **and** do a re-install if
the USER-PLUMED package with "make yes-user-plumed" to update the
the PLUMED package with "make yes-plumed" to update the
required makefile settings with the changes in the lib/plumed
folder.
@ -1433,7 +1433,7 @@ LAMMPS build.
.. _user-h5md:
USER-H5MD package
H5MD package
---------------------------------
To build with this package you must have the HDF5 software package
@ -1444,7 +1444,7 @@ the HDF5 library.
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-H5MD=yes``.
No additional settings are needed besides ``-D PKG_H5MD=yes``.
This should auto-detect the H5MD library on your system. Several
advanced CMake H5MD options exist if you need to specify where it
@ -1530,15 +1530,15 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
----------
.. _user-intel:
.. _intel:
USER-INTEL package
INTEL package
-----------------------------------
To build with this package, you must choose which hardware you want to
build for, either x86 CPUs or Intel KNLs in offload mode. You should
also typically :ref:`install the OPENMP package <openmp>`, as it can be
used in tandem with the USER-INTEL package to good effect, as explained
used in tandem with the INTEL package to good effect, as explained
on the :doc:`Speed_intel` page.
When using Intel compilers version 16.0 or later is required. You can
@ -1547,7 +1547,7 @@ improvements over regular styles and OPENMP styles, but less so than
with the Intel compilers. Please also note, that some compilers have
been found to apply memory alignment constraints incompletely or
incorrectly and thus can cause segmentation faults in otherwise correct
code when using features from the USER-INTEL package.
code when using features from the INTEL package.
.. tabs::
@ -1564,7 +1564,7 @@ code when using features from the USER-INTEL package.
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. and
``src/USER-INTEL/README`` for additional information.
``src/INTEL/README`` for additional information.
For CPUs:
@ -1602,7 +1602,7 @@ TBB and MKL.
.. _user-mdi:
USER-MDI package
MDI package
-----------------------------
.. tabs::
@ -1631,7 +1631,7 @@ USER-MDI package
.. _user-mesont:
USER-MESONT package
MESONT package
-------------------------
This package includes a library written in Fortran 90 in the
@ -1644,7 +1644,7 @@ they will be downloaded the first time this package is installed.
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-MESONT=yes``
No additional settings are needed besides ``-D PKG_MESONT=yes``
.. tab:: Traditional make
@ -1673,7 +1673,7 @@ they will be downloaded the first time this package is installed.
.. _user-molfile:
USER-MOLFILE package
MOLFILE package
---------------------------------------
.. tabs::
@ -1683,9 +1683,9 @@ USER-MOLFILE package
.. code-block:: bash
-D MOLFILE_INCLUDE_DIR=path # (optional) path where VMD molfile plugin headers are installed
-D PKG_USER-MOLFILE=yes
-D PKG_MOLFILE=yes
Using ``-D PKG_USER-MOLFILE=yes`` enables the package, and setting
Using ``-D PKG_MOLFILE=yes`` enables the package, and setting
``-D MOLFILE_INCLUDE_DIR`` allows to provide a custom location for
the molfile plugin header files. These should match the ABI of the
plugin files used, and thus one typically sets them to include
@ -1711,7 +1711,7 @@ USER-MOLFILE package
.. _user-netcdf:
USER-NETCDF package
NETCDF package
-------------------------------------
To build with this package you must have the NetCDF library installed
@ -1721,7 +1721,7 @@ on your system.
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-NETCDF=yes``.
No additional settings are needed besides ``-D PKG_NETCDF=yes``.
This should auto-detect the NETCDF library if it is installed on
your system at standard locations. Several advanced CMake NETCDF
@ -1775,10 +1775,10 @@ OPENMP package
.. _user-qmmm:
USER-QMMM package
QMMM package
---------------------------------
For using LAMMPS to do QM/MM simulations via the USER-QMMM package you
For using LAMMPS to do QM/MM simulations via the QMMM package you
need to build LAMMPS as a library. A LAMMPS executable with :doc:`fix
qmmm <fix_qmmm>` included can be built, but will not be able to do a
QM/MM simulation on as such. You must also build a QM code - currently
@ -1801,11 +1801,11 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
libqmmm.a) are not included in the static LAMMPS library and
(currently) not installed, while their code is included in the
shared LAMMPS library. Thus a typical command line to configure
building LAMMPS for USER-QMMM would be:
building LAMMPS for QMMM would be:
.. code-block:: bash
cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \
cmake -C ../cmake/presets/minimal.cmake -D PKG_QMMM=yes \
-D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake
After completing the LAMMPS build and also configuring and
@ -1885,7 +1885,7 @@ to be downloaded and configured. See step 1 and step 1.1 in the
.. _user-scafacos:
USER-SCAFACOS package
SCAFACOS package
-----------------------------------------
To build with this package, you must download and build the
@ -1976,7 +1976,7 @@ Eigen3 is a template library, so you do not need to build it.
.. _user-vtk:
USER-VTK package
VTK package
-------------------------------
To build with this package you must have the VTK library installed on
@ -1986,7 +1986,7 @@ your system.
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-VTK=yes``.
No additional settings are needed besides ``-D PKG_VTK=yes``.
This should auto-detect the VTK library if it is installed on your
system at standard locations. Several advanced VTK options exist

4
doc/src/Build_make.rst
View File

@ -117,8 +117,8 @@ 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 intel_cpu # build with the INTEL package optimized for CPUs
make knl # build with the INTEL package optimized for KNLs
make opt # build with the OPT package optimized for CPUs
make omp # build with the OPENMP package optimized for OpenMP
make kokkos_omp # build with the KOKKOS package for OpenMP

14
doc/src/Build_package.rst
View File

@ -33,13 +33,13 @@ packages:
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` |
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`ADIOS <adios>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`ML-HDNNP <ml-hdnnp>` | :ref:`USER-INTEL <user-intel>` |
| :ref:`ATC <atc>` | :ref:`AWPMD <awpmd>` | :ref:`COLVARS <colvars>` | :ref:`H5MD <h5md>` | :ref:`ML-HDNNP <ml-hdnnp>` | :ref:`INTEL <intel>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`USER-MOLFILE <user-molfile>` | :ref:`USER-NETCDF <user-netcdf>` | :ref:`ML-PACE <ml-pace>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`OPENMP <openmp>` | :ref:`USER-QMMM <user-qmmm>` |
| :ref:`MOLFILE <molfile>` | :ref:`NETCDF <netcdf>` | :ref:`ML-PACE <ml-pace>` | :ref:`PLUMED <plumed>` | :ref:`OPENMP <openmp>` | :ref:`QMMM <qmmm>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`ML-QUIP <ml-quip>` | :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`MACHDYN <machdyn>` | :ref:`USER-VTK <user-vtk>` | | |
| :ref:`ML-QUIP <ml-quip>` | :ref:`SCAFACOS <scafacos>` | :ref:`MACHDYN <machdyn>` | :ref:`VTK <vtk>` | | |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
The mechanism for including packages is simple but different for CMake
@ -58,7 +58,7 @@ versus make.
.. code-block:: csh
-D PKG_MANYBODY=yes
-D PKG_USER-INTEL=yes
-D PKG_INTEL=yes
All standard and user packages are included the same way. Note
that USER packages have a hyphen between USER and the rest of the
@ -89,7 +89,7 @@ versus make.
.. code-block:: bash
make no-rigid
make yes-user-intel
make yes-intel
All standard and user packages are included the same way.
@ -225,7 +225,7 @@ package`` will list all the these commands.
Installing or un-installing a package for the make based build process
works by simply copying files back and forth between the main source
directory src and the sub-directories with the package name (e.g.
src/KSPACE, src/USER-ATC), so that the files are included or excluded
src/KSPACE, src/ATC), so that the files are included or excluded
when LAMMPS is built. Only source files in the src folder will be
compiled.

4
doc/src/Build_settings.rst
View File

@ -242,8 +242,8 @@ does not support 64-bit integers or incurs performance penalties when
using them.
These are limits for the core of the LAMMPS code, specific features or
some styles may impose additional limits. The :ref:`USER-ATC
<PKG-USER-ATC>` package cannot be compiled with the "bigbig" setting.
some styles may impose additional limits. The :ref:`ATC
<PKG-ATC>` package cannot be compiled with the "bigbig" setting.
Also, there are limitations when using the library interface where some
functions with known issues have been replaced by dummy calls printing a
corresponding error message rather than crashing randomly or corrupting

8
doc/src/Commands_bond.rst
View File

@ -18,7 +18,7 @@ Bond_style potentials
All LAMMPS :doc:`bond_style <bond_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = OPENMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
@ -57,7 +57,7 @@ Angle_style potentials
All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = OPENMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
@ -99,7 +99,7 @@ Dihedral_style potentials
All LAMMPS :doc:`dihedral_style <dihedral_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = OPENMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
@ -135,7 +135,7 @@ Improper_style potentials
All LAMMPS :doc:`improper_style <improper_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = OPENMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::

2
doc/src/Commands_compute.rst
View File

@ -16,7 +16,7 @@ Compute commands
An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
Some styles have accelerated versions. This is indicated by
additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
additional letters in parenthesis: g = GPU, i = INTEL, k =
KOKKOS, o = OPENMP, t = OPT.
.. table_from_list::

2
doc/src/Commands_fix.rst
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@ -16,7 +16,7 @@ Fix commands
An alphabetic list of all LAMMPS :doc:`fix <fix>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = OPENMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::

2
doc/src/Commands_kspace.rst
View File

@ -16,7 +16,7 @@ KSpace solvers
All LAMMPS :doc:`kspace_style <kspace_style>` solvers. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = OPENMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::

2
doc/src/Commands_pair.rst
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@ -16,7 +16,7 @@ Pair_style potentials
All LAMMPS :doc:`pair_style <pair_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = OPENMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::

2
doc/src/Developer_unittest.rst
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@ -405,7 +405,7 @@ compare with the reference and also start from the data file. A final
check will use multi-cutoff r-RESPA (if supported by the pair style) at
a 1:1 split and compare to the Verlet results. These sets of tests are
run with multiple test fixtures for accelerated styles (OPT, OPENMP,
USER-INTEL) and for the latter two with 4 OpenMP threads enabled. For
INTEL) and for the latter two with 4 OpenMP threads enabled. For
these tests the relative error (epsilon) is lowered by a common factor
due to the additional numerical noise, but the tests are still comparing
to the same reference data.

6
doc/src/Errors_messages.rst
View File

@ -6344,8 +6344,8 @@ keyword to allow for additional bonds to be formed
The GPU package must be installed via "make yes-gpu" before LAMMPS is
built.
*Package intel command without USER-INTEL package installed*
The USER-INTEL package must be installed via "make yes-user-intel"
*Package intel command without INTEL package installed*
The INTEL package must be installed via "make yes-intel"
before LAMMPS is built.
*Package kokkos command without KOKKOS package enabled*
@ -8064,7 +8064,7 @@ keyword to allow for additional bonds to be formed
*Using suffix gpu without GPU package installed*
Self-explanatory.
*Using suffix intel without USER-INTEL package installed*
*Using suffix intel without INTEL package installed*
Self-explanatory.
*Using suffix kk without KOKKOS package enabled*

6
doc/src/Howto_drude2.rst
View File

@ -2,10 +2,10 @@ Tutorial for Thermalized Drude oscillators in LAMMPS
====================================================
This tutorial explains how to use Drude oscillators in LAMMPS to
simulate polarizable systems using the USER-DRUDE package. As an
simulate polarizable systems using the DRUDE package. As an
illustration, the input files for a simulation of 250 phenol molecules
are documented. First of all, LAMMPS has to be compiled with the
USER-DRUDE package activated. Then, the data file and input scripts
DRUDE package activated. Then, the data file and input scripts
have to be modified to include the Drude dipoles and how to handle
them.
@ -82,7 +82,7 @@ The data file is similar to a standard LAMMPS data file for
to their DC should appear in the data file as normal atoms and bonds.
You can use the *polarizer* tool (Python script distributed with the
USER-DRUDE package) to convert a non-polarizable data file (here
DRUDE package) to convert a non-polarizable data file (here
*data.102494.lmp*\ ) to a polarizable data file (\ *data-p.lmp*\ )
.. code-block:: bash

6
doc/src/Howto_manifold.rst
View File

@ -5,11 +5,11 @@ Manifolds (surfaces)
This doc page is not about a LAMMPS input script command, but about
manifolds, which are generalized surfaces, as defined and used by the
USER-MANIFOLD package, to track particle motion on the manifolds. See
the src/USER-MANIFOLD/README file for more details about the package
MANIFOLD package, to track particle motion on the manifolds. See
the src/MANIFOLD/README file for more details about the package
and its commands.
Below is a list of currently supported manifolds by the USER-MANIFOLD
Below is a list of currently supported manifolds by the MANIFOLD
package, their parameters and a short description of them. The
parameters listed here are in the same order as they should be passed
to the relevant fixes.

2
doc/src/Howto_polarizable.rst
View File

@ -10,7 +10,7 @@ systems can be simulated in LAMMPS using three methods:
* the adiabatic core-shell method, implemented in the
:doc:`CORESHELL <Howto_coreshell>` package,
* the thermalized Drude dipole method, implemented in the
:doc:`USER-DRUDE <Howto_drude>` package.
:doc:`DRUDE <Howto_drude>` package.
The fluctuating charge method calculates instantaneous charges on
interacting atoms based on the electronegativity equalization

2
doc/src/Install_windows.rst
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@ -18,7 +18,7 @@ needed to run in parallel with MPI.
The LAMMPS binaries contain *all* :doc:`optional packages <Packages>`
included in the source distribution except: KIM, KOKKOS, MSCG, PYTHON,
USER-ADIOS, USER-H5MD, USER-NETCDF, USER-QMMM, ML-QUIP, and USER-VTK.
ADIOS, H5MD, NETCDF, QMMM, ML-QUIP, and VTK.
The serial version also does not include the MPIIO and
LATBOLTZ packages. The GPU package is compiled for OpenCL with
mixed precision kernels.

12
doc/src/Intro_authors.rst
View File

@ -30,18 +30,18 @@ they have written are unique for an MD code and LAMMPS would not be as
general-purpose as it is without their expertise and efforts.
* Metin Aktulga (MSU), REAXFF package for C version of ReaxFF
* Mike Brown (Intel), GPU and USER-INTEL packages
* Mike Brown (Intel), GPU and INTEL packages
* Colin Denniston (U Western Ontario), LATBOLTZ package
* Georg Ganzenmuller (EMI), MACHDYN and USER-SPH packages
* Andres Jaramillo-Botero (Caltech), USER-EFF package for electron force field
* Reese Jones (Sandia) and colleagues, USER-ATC package for atom/continuum coupling
* Georg Ganzenmuller (EMI), MACHDYN and SPH packages
* Andres Jaramillo-Botero (Caltech), EFF package for electron force field
* Reese Jones (Sandia) and colleagues, ATC package for atom/continuum coupling
* Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS
* Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion
* Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages
* Mike Parks (Sandia), PERI package for Peridynamics
* Roy Pollock (LLNL), Ewald and PPPM solvers
* Christian Trott (Sandia), USER-CUDA and KOKKOS packages
* Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD
* Christian Trott (Sandia), CUDA and KOKKOS packages
* Ilya Valuev (JIHT), AWPMD package for wave packet MD
* Greg Wagner (Northwestern U), MEAM package for MEAM potential
----------

2
doc/src/Library.rst
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@ -31,7 +31,7 @@ that are not possible with existing input script commands.
applies to the core LAMMPS code and less so on add-on packages,
especially when those packages require additional code in the *lib*
folder, interface LAMMPS to Fortran libraries, or the code uses
static variables (like the USER-COLVARS package).
static variables (like the COLVARS package).
Another major issue to deal with is to correctly handle MPI.
Creating a LAMMPS instance requires passing an MPI communicator, or

2
doc/src/Modify_compute.rst
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@ -53,5 +53,5 @@ in two stages: the callback function is registered with the pair style
and then called from the Pair::ev_tally() function, which is called for
each pair after force and energy has been computed for this pair. Then
the tallied values are retrieved with the standard compute_scalar or
compute_vector or compute_peratom methods. The :doc:`compute styles in the USER-TALLY package <compute_tally>`
compute_vector or compute_peratom methods. The :doc:`compute styles in the TALLY package <compute_tally>`
provide *examples* for utilizing this mechanism.

8
doc/src/Modify_contribute.rst
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@ -169,7 +169,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
* If you want your contribution to be added as a user-contribution and
it is several related features, it is probably best to make it a user
package directory with a name like USER-FOO. In addition to your new
package directory with a name like FOO. In addition to your new
files, the directory should contain a README text file. The README
should contain your name and contact information and a brief
description of what your new package does. If your files depend on
@ -177,7 +177,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
is a derived class from the other LAMMPS class), then an Install.sh
file is also needed to check for those dependencies. See other README
and Install.sh files in other USER directories as examples. Send us a
tarball of this USER-FOO directory.
tarball of this FOO directory.
* Your new source files need to have the LAMMPS copyright, GPL notice,
and your name and email address at the top, like other
@ -212,7 +212,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
cite itself. Citation labels must be unique across all .rst files.
The "Restrictions" section of the doc page should indicate if your
command is only available if LAMMPS is built with the appropriate
USER-MISC or USER-FOO package. See other user package doc files for
USER-MISC or FOO package. See other user package doc files for
examples of how to do this. Please run at least "make html" and "make
spelling" and carefully inspect and proofread the resulting HTML
format doc page before submitting your code. Upon submission of a
@ -234,7 +234,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
* If there is a paper of yours describing your feature (either the
algorithm/science behind the feature itself, or its initial usage, or
its implementation in LAMMPS), you can add the citation to the \*.cpp
source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
source file. See src/EFF/atom_vec_electron.cpp for an example.
A LaTeX citation is stored in a variable at the top of the file and
a single line of code registering this variable is added to the
constructor of the class. If there is additional functionality (which

360
doc/src/Packages_details.rst
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@ -65,54 +65,54 @@ page gives those details.
.. table_from_list::
:columns: 6
* :ref:`USER-ADIOS <PKG-USER-ADIOS>`
* :ref:`USER-ATC <PKG-USER-ATC>`
* :ref:`USER-AWPMD <PKG-USER-AWPMD>`
* :ref:`USER-BOCS <PKG-USER-BOCS>`
* :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>`
* :ref:`ADIOS <PKG-ADIOS>`
* :ref:`ATC <PKG-ATC>`
* :ref:`AWPMD <PKG-AWPMD>`
* :ref:`BOCS <PKG-BOCS>`
* :ref:`BROWNIAN <PKG-BROWNIAN>`
* :ref:`CG-DNA <PKG-CG-DNA>`
* :ref:`CG-SDK <PKG-CG-SDK>`
* :ref:`USER-COLVARS <PKG-USER-COLVARS>`
* :ref:`USER-DIELECTRIC <PKG-USER-DIELECTRIC>`
* :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>`
* :ref:`COLVARS <PKG-COLVARS>`
* :ref:`DIELECTRIC <PKG-DIELECTRIC>`
* :ref:`DIFFRACTION <PKG-DIFFRACTION>`
* :ref:`DPD-REACT <PKG-DPD-REACT>`
* :ref:`USER-DRUDE <PKG-USER-DRUDE>`
* :ref:`USER-EFF <PKG-USER-EFF>`
* :ref:`USER-FEP <PKG-USER-FEP>`
* :ref:`USER-H5MD <PKG-USER-H5MD>`
* :ref:`DRUDE <PKG-DRUDE>`
* :ref:`EFF <PKG-EFF>`
* :ref:`FEP <PKG-FEP>`
* :ref:`H5MD <PKG-H5MD>`
* :ref:`ML-HDNNP <PKG-ML-HDNNP>`
* :ref:`USER-INTEL <PKG-USER-INTEL>`
* :ref:`INTEL <PKG-INTEL>`
* :ref:`LATBOLTZ <PKG-LATBOLTZ>`
* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
* :ref:`USER-MDI <PKG-USER-MDI>`
* :ref:`MANIFOLD <PKG-MANIFOLD>`
* :ref:`MDI <PKG-MDI>`
* :ref:`MEAM <PKG-MEAM>`
* :ref:`DPD-MESO <PKG-DPD-MESO>`
* :ref:`USER-MESONT <PKG-USER-MESONT>`
* :ref:`USER-MGPT <PKG-USER-MGPT>`
* :ref:`MESONT <PKG-MESONT>`
* :ref:`MGPT <PKG-MGPT>`
* :ref:`USER-MISC <PKG-USER-MISC>`
* :ref:`USER-MOFFF <PKG-USER-MOFFF>`
* :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
* :ref:`USER-NETCDF <PKG-USER-NETCDF>`
* :ref:`MOFFF <PKG-MOFFF>`
* :ref:`MOLFILE <PKG-MOLFILE>`
* :ref:`NETCDF <PKG-NETCDF>`
* :ref:`OPENMP <PKG-OPENMP>`
* :ref:`ML-PACE <PKG-ML-PACE>`
* :ref:`USER-PHONON <PKG-USER-PHONON>`
* :ref:`USER-PLUMED <PKG-USER-PLUMED>`
* :ref:`USER-PTM <PKG-USER-PTM>`
* :ref:`USER-QMMM <PKG-USER-QMMM>`
* :ref:`USER-QTB <PKG-USER-QTB>`
* :ref:`PHONON <PKG-PHONON>`
* :ref:`PLUMED <PKG-PLUMED>`
* :ref:`PTM <PKG-PTM>`
* :ref:`QMMM <PKG-QMMM>`
* :ref:`QTB <PKG-QTB>`
* :ref:`ML-QUIP <PKG-ML-QUIP>`
* :ref:`ML-RANN <PKG-ML-RANN>`
* :ref:`USER-REACTION <PKG-USER-REACTION>`
* :ref:`REACTION <PKG-REACTION>`
* :ref:`REAXFF <PKG-REAXFF>`
* :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>`
* :ref:`SCAFACOS <PKG-SCAFACOS>`
* :ref:`DPD-SMOOTH <PKG-DPD-SMOOTH>`
* :ref:`MACHDYN <PKG-MACHDYN>`
* :ref:`USER-SMTBQ <PKG-USER-SMTBQ>`
* :ref:`USER-SPH <PKG-USER-SPH>`
* :ref:`USER-TALLY <PKG-USER-TALLY>`
* :ref:`USER-UEF <PKG-USER-UEF>`
* :ref:`USER-VTK <PKG-USER-VTK>`
* :ref:`USER-YAFF <PKG-USER-YAFF>`
* :ref:`SMTBQ <PKG-SMTBQ>`
* :ref:`SPH <PKG-SPH>`
* :ref:`TALLY <PKG-TALLY>`
* :ref:`UEF <PKG-UEF>`
* :ref:`VTK <PKG-VTK>`
* :ref:`YAFF <PKG-YAFF>`
----------
@ -447,7 +447,7 @@ style name. The :doc:`KOKKOS package <Speed_kokkos>` 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" :doc:`command-line switches <Run_options>`. Also see the :ref:`GPU <PKG-GPU>`, :ref:`OPT <PKG-OPT>`,
:ref:`USER-INTEL <PKG-USER-INTEL>`, and :ref:`OPENMP <PKG-OPENMP>` packages, which
:ref:`INTEL <PKG-INTEL>`, and :ref:`OPENMP <PKG-OPENMP>` packages, which
have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++14 compatible compiler to use this package.
@ -802,7 +802,7 @@ CHARMM, and Morse potentials. The styles have an "opt" suffix in
their style name. The :doc:`OPT package <Speed_opt>` 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" :doc:`command-line switches <Run_options>`. See also the :ref:`KOKKOS <PKG-KOKKOS>`,
:ref:`USER-INTEL <PKG-USER-INTEL>`, and :ref:`OPENMP <PKG-OPENMP>` packages, which
:ref:`INTEL <PKG-INTEL>`, and :ref:`OPENMP <PKG-OPENMP>` packages, which
have styles optimized for CPU performance.
**Authors:** James Fischer (High Performance Technologies), David Richie,
@ -1154,9 +1154,9 @@ This package has :ref:`specific installation instructions <voronoi>` on the :doc
----------
.. _PKG-USER-ADIOS:
.. _PKG-ADIOS:
USER-ADIOS package
ADIOS package
------------------
**Contents:**
@ -1170,12 +1170,12 @@ commands to write and read data using the ADIOS library.
**Install:**
This package has :ref:`specific installation instructions <user-adios>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <adios>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-ADIOS: filenames -> commands
* src/USER-ADIOS/README
* src/ADIOS: filenames -> commands
* src/ADIOS/README
* examples/PACKAGES/adios
* https://github.com/ornladios/ADIOS2
* :doc:`dump atom/adios <dump_adios>`
@ -1184,9 +1184,9 @@ This package has :ref:`specific installation instructions <user-adios>` on the :
----------
.. _PKG-USER-ATC:
.. _PKG-ATC:
USER-ATC package
ATC package
----------------
**Contents:**
@ -1199,21 +1199,21 @@ atomic information to continuum fields.
**Install:**
This package has :ref:`specific installation instructions <user-atc>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <atc>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-ATC: filenames -> commands
* src/USER-ATC/README
* src/ATC: filenames -> commands
* src/ATC/README
* :doc:`fix atc <fix_atc>`
* examples/PACKAGES/atc
* https://www.lammps.org/pictures.html#atc
----------
.. _PKG-USER-AWPMD:
.. _PKG-AWPMD:
USER-AWPMD package
AWPMD package
------------------
**Contents:**
@ -1227,20 +1227,20 @@ model.
**Install:**
This package has :ref:`specific installation instructions <user-awpmd>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <awpmd>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-AWPMD: filenames -> commands
* src/USER-AWPMD/README
* src/AWPMD: filenames -> commands
* src/AWPMD/README
* :doc:`pair_style awpmd/cut <pair_awpmd>`
* examples/PACKAGES/awpmd
----------
.. _PKG-USER-BOCS:
.. _PKG-BOCS:
USER-BOCS package
BOCS package
-----------------
**Contents:**
@ -1258,7 +1258,7 @@ Pennsylvania State University)
**Supporting info:**
The USER-BOCS user package for LAMMPS is part of the BOCS software package:
The BOCS user package for LAMMPS is part of the BOCS software package:
`https://github.com/noid-group/BOCS <https://github.com/noid-group/BOCS>`_
See the following reference for information about the entire package:
@ -1271,9 +1271,9 @@ Example inputs are in the examples/PACKAGES/bocs folder.
----------
.. _PKG-USER-BROWNIAN:
.. _PKG-BROWNIAN:
USER-BROWNIAN package
BROWNIAN package
---------------------
**Contents:**
@ -1344,9 +1344,9 @@ acids.
----------
.. _PKG-USER-COLVARS:
.. _PKG-COLVARS:
USER-COLVARS package
COLVARS package
--------------------
**Contents:**
@ -1366,22 +1366,22 @@ the NAMD MD code, but with portability in mind. Axel Kohlmeyer
**Install:**
This package has :ref:`specific installation instructions <user-colvars>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <colvars>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-COLVARS: filenames -> commands
* src/COLVARS: filenames -> commands
* `doc/PDF/colvars-refman-lammps.pdf <PDF/colvars-refman-lammps.pdf>`_
* src/USER-COLVARS/README
* src/COLVARS/README
* lib/colvars/README
* :doc:`fix colvars <fix_colvars>`
* examples/PACKAGES/colvars
----------
.. _PKG-USER-DIELECTRIC:
.. _PKG-DIELECTRIC:
USER-DIELECTRIC package
DIELECTRIC package
------------------------
**Contents:**
@ -1395,16 +1395,16 @@ different dielectric constants.
**Supporting info:**
* src/USER-DIELECTRIC: filenames -> commands
* src/DIELECTRIC: filenames -> commands
* :doc:`compute efield/atom <compute_efield_atom>`
* TODO: add all styles
* examples/PACKAGES/dielectric
----------
.. _PKG-USER-DIFFRACTION:
.. _PKG-DIFFRACTION:
USER-DIFFRACTION package
DIFFRACTION package
------------------------
**Contents:**
@ -1416,7 +1416,7 @@ intensities based on kinematic diffraction theory.
**Supporting info:**
* src/USER-DIFFRACTION: filenames -> commands
* src/DIFFRACTION: filenames -> commands
* :doc:`compute saed <compute_saed>`
* :doc:`compute xrd <compute_xrd>`
* :doc:`fix saed/vtk <fix_saed_vtk>`
@ -1465,9 +1465,9 @@ Brennan (ARL).
----------
.. _PKG-USER-DRUDE:
.. _PKG-DRUDE:
USER-DRUDE package
DRUDE package
------------------
**Contents:**
@ -1482,11 +1482,11 @@ Devemy (CNRS), and Agilio Padua (ENS de Lyon).
**Supporting info:**
* src/USER-DRUDE: filenames -> commands
* src/DRUDE: filenames -> commands
* :doc:`Howto drude <Howto_drude>`
* :doc:`Howto drude2 <Howto_drude2>`
* :doc:`Howto polarizable <Howto_polarizable>`
* src/USER-DRUDE/README
* src/DRUDE/README
* :doc:`fix drude <fix_drude>`
* :doc:`fix drude/transform/\* <fix_drude_transform>`
* :doc:`compute temp/drude <compute_temp_drude>`
@ -1497,9 +1497,9 @@ Devemy (CNRS), and Agilio Padua (ENS de Lyon).
----------
.. _PKG-USER-EFF:
.. _PKG-EFF:
USER-EFF package
EFF package
----------------
**Contents:**
@ -1516,8 +1516,8 @@ tools/eff; see its README file.
**Supporting info:**
* src/USER-EFF: filenames -> commands
* src/USER-EFF/README
* src/EFF: filenames -> commands
* src/EFF/README
* :doc:`atom_style electron <atom_style>`
* :doc:`fix nve/eff <fix_nve_eff>`
* :doc:`fix nvt/eff <fix_nh_eff>`
@ -1533,9 +1533,9 @@ tools/eff; see its README file.
----------
.. _PKG-USER-FEP:
.. _PKG-FEP:
USER-FEP package
FEP package
----------------
**Contents:**
@ -1549,8 +1549,8 @@ for using this package in tools/fep; see its README file.
**Supporting info:**
* src/USER-FEP: filenames -> commands
* src/USER-FEP/README
* src/FEP: filenames -> commands
* src/FEP/README
* :doc:`fix adapt/fep <fix_adapt_fep>`
* :doc:`compute fep <compute_fep>`
* :doc:`pair_style \*/soft <pair_fep_soft>`
@ -1560,9 +1560,9 @@ for using this package in tools/fep; see its README file.
----------
.. _PKG-USER-H5MD:
.. _PKG-H5MD:
USER-H5MD package
H5MD package
-----------------
**Contents:**
@ -1583,12 +1583,12 @@ H5MD format.
**Install:**
This package has :ref:`specific installation instructions <user-h5md>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <h5md>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-H5MD: filenames -> commands
* src/USER-H5MD/README
* src/H5MD: filenames -> commands
* src/H5MD/README
* lib/h5md/README
* :doc:`dump h5md <dump_h5md>`
@ -1628,9 +1628,9 @@ This package has :ref:`specific installation instructions <ml-hdnnp>` on the
----------
.. _PKG-USER-INTEL:
.. _PKG-INTEL:
USER-INTEL package
INTEL package
------------------
**Contents:**
@ -1638,7 +1638,7 @@ USER-INTEL package
Dozens of pair, fix, bond, angle, dihedral, improper, and kspace
styles which are optimized for Intel CPUs and KNLs (Knights Landing).
All of them have an "intel" in their style name. The
:doc:`USER-INTEL package <Speed_intel>` page gives details of what hardware and
:doc:`INTEL package <Speed_intel>` 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" :doc:`command-line switches <Run_options>`. Also see
@ -1651,27 +1651,27 @@ supported, performance will be sub-optimal.
.. note::
the USER-INTEL package contains styles that require using the
the INTEL package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
**Author:** Mike Brown (Intel).
**Install:**
This package has :ref:`specific installation instructions <user-intel>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <intel>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-INTEL: filenames -> commands
* src/USER-INTEL/README
* src/INTEL: filenames -> commands
* src/INTEL/README
* :doc:`Accelerator packages <Speed_packages>`
* :doc:`USER-INTEL package <Speed_intel>`
* :doc:`INTEL package <Speed_intel>`
* :doc:`Section 2.6 -sf intel <Run_options>`
* :doc:`Section 2.6 -pk intel <Run_options>`
* :doc:`package intel <package>`
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`kspace <Commands_kspace>`) for styles followed by (i)
* src/USER-INTEL/TEST
* src/INTEL/TEST
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -1700,9 +1700,9 @@ Ontario).
----------
.. _PKG-USER-MGPT:
.. _PKG-MGPT:
USER-MGPT package
MGPT package
-----------------
**Contents:**
@ -1720,8 +1720,8 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
**Supporting info:**
* src/USER-MGPT: filenames -> commands
* src/USER-MGPT/README
* src/MGPT: filenames -> commands
* src/MGPT/README
* :doc:`pair_style mgpt <pair_mgpt>`
* examples/PACKAGES/mgpt
@ -1750,9 +1750,9 @@ src/USER-MISC/README file.
----------
.. _PKG-USER-MANIFOLD:
.. _PKG-MANIFOLD:
USER-MANIFOLD package
MANIFOLD package
---------------------
**Contents:**
@ -1770,8 +1770,8 @@ Waltham, MA, USA)
**Supporting info:**
* src/USER-MANIFOLD: filenames -> commands
* src/USER-MANIFOLD/README
* src/MANIFOLD: filenames -> commands
* src/MANIFOLD/README
* :doc:`Howto manifold <Howto_manifold>`
* :doc:`fix manifoldforce <fix_manifoldforce>`
* :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
@ -1781,9 +1781,9 @@ Waltham, MA, USA)
----------
.. _PKG-USER-MDI:
.. _PKG-MDI:
USER-MDI package
MDI package
----------------
**Contents:**
@ -1796,7 +1796,7 @@ other atomic or molecular simulation codes via the `MolSSI Driver Interface
**Supporting info:**
* src/USER-MDI/README
* src/MDI/README
* :doc:`mdi/engine <mdi_engine>`
* :doc:`fix mdi/engine <fix_mdi_engine>`
* examples/PACKAGES/mdi
@ -1859,14 +1859,14 @@ algorithm.
----------
.. _PKG-USER-MESONT:
.. _PKG-MESONT:
USER-MESONT package
MESONT package
-------------------
**Contents:**
USER-MESONT is a LAMMPS package for simulation of nanomechanics of
MESONT is a LAMMPS package for simulation of nanomechanics of
nanotubes (NTs). The model is based on a coarse-grained representation
of NTs as "flexible cylinders" consisting of a variable number of
segments. Internal interactions within a NT and the van der Waals
@ -1895,8 +1895,8 @@ Philipp Kloza (U Cambridge)
**Supporting info:**
* src/USER-MESONT: filenames -> commands
* src/USER-MESONT/README
* src/MESONT: filenames -> commands
* src/MESONT/README
* :doc:`atom_style mesont <atom_style>`
* :doc:`pair_style mesont/tpm <pair_mesont_tpm>`
* :doc:`compute mesont <compute_mesont>`
@ -1906,9 +1906,9 @@ Philipp Kloza (U Cambridge)
----------
.. _PKG-USER-MOFFF:
.. _PKG-MOFFF:
USER-MOFFF package
MOFFF package
------------------
**Contents:**
@ -1929,8 +1929,8 @@ Rochus Schmid (Ruhr-University Bochum).
**Supporting info:**
* src/USER-MOFFF: filenames -> commands
* src/USER-MOFFF/README
* src/MOFFF: filenames -> commands
* src/MOFFF/README
* :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>`
* :doc:`angle_style class2 <angle_class2>`
* :doc:`angle_style cosine/buck6d <angle_cosine_buck6d>`
@ -1939,9 +1939,9 @@ Rochus Schmid (Ruhr-University Bochum).
----------
.. _PKG-USER-MOLFILE:
.. _PKG-MOLFILE:
USER-MOLFILE package
MOLFILE package
--------------------
**Contents:**
@ -1970,20 +1970,20 @@ at
**Install:**
This package has :ref:`specific installation instructions <user-molfile>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <molfile>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-MOLFILE: filenames -> commands
* src/USER-MOLFILE/README
* src/MOLFILE: filenames -> commands
* src/MOLFILE/README
* lib/molfile/README
* :doc:`dump molfile <dump_molfile>`
----------
.. _PKG-USER-NETCDF:
.. _PKG-NETCDF:
USER-NETCDF package
NETCDF package
-------------------
**Contents:**
@ -2010,12 +2010,12 @@ tools:
**Install:**
This package has :ref:`specific installation instructions <user-netcdf>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <netcdf>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-NETCDF: filenames -> commands
* src/USER-NETCDF/README
* src/NETCDF: filenames -> commands
* src/NETCDF/README
* lib/netcdf/README
* :doc:`dump netcdf <dump_netcdf>`
@ -2035,7 +2035,7 @@ The :doc:`OPENMP package <Speed_omp>` 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" :doc:`command-line switches <Run_options>`. Also see
the :ref:`KOKKOS <PKG-KOKKOS>`, :ref:`OPT <PKG-OPT>`, and :ref:`USER-INTEL <PKG-USER-INTEL>`
the :ref:`KOKKOS <PKG-KOKKOS>`, :ref:`OPT <PKG-OPT>`, and :ref:`INTEL <PKG-INTEL>`
packages, which have styles optimized for CPUs.
**Author:** Axel Kohlmeyer (Temple U).
@ -2117,9 +2117,9 @@ This package has :ref:`specific installation instructions <ml-pace>` on the
----------
.. _PKG-USER-PHONON:
.. _PKG-PHONON:
USER-PHONON package
PHONON package
-------------------
**Contents:**
@ -2136,8 +2136,8 @@ and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order"
**Supporting info:**
* src/USER-PHONON: filenames -> commands
* src/USER-PHONON/README
* src/PHONON: filenames -> commands
* src/PHONON/README
* :doc:`fix phonon <fix_phonon>`
* :doc:`dynamical_matrix <dynamical_matrix>`
* :doc:`third_order <third_order>`
@ -2145,9 +2145,9 @@ and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order"
----------
.. _PKG-USER-PLUMED:
.. _PKG-PLUMED:
USER-PLUMED package
PLUMED package
-------------------
**Contents:**
@ -2163,20 +2163,20 @@ and Gareth Tribello.
**Install:**
This package has :ref:`specific installation instructions <user-plumed>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <plumed>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-PLUMED/README
* src/PLUMED/README
* lib/plumed/README
* :doc:`fix plumed <fix_plumed>`
* examples/PACKAGES/plumed
----------
.. _PKG-USER-PTM:
.. _PKG-PTM:
USER-PTM package
PTM package
----------------
**Contents:**
@ -2189,16 +2189,16 @@ Matching methodology.
**Supporting info:**
* src/USER-PTM: filenames not starting with ptm\_ -> commands
* src/USER-PTM: filenames starting with ptm\_ -> supporting code
* src/USER-PTM/LICENSE
* src/PTM: filenames not starting with ptm\_ -> commands
* src/PTM: filenames starting with ptm\_ -> supporting code
* src/PTM/LICENSE
* :doc:`compute ptm/atom <compute_ptm_atom>`
----------
.. _PKG-USER-QMMM:
.. _PKG-QMMM:
USER-QMMM package
QMMM package
-----------------
**Contents:**
@ -2227,13 +2227,13 @@ changes to LAMMPS itself.
**Install:**
This package has :ref:`specific installation instructions <user-qmmm>`
This package has :ref:`specific installation instructions <qmmm>`
on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-QMMM: filenames -> commands
* src/USER-QMMM/README
* src/QMMM: filenames -> commands
* src/QMMM/README
* lib/qmmm/README
* :doc:`fix phonon <fix_phonon>`
* lib/qmmm/example-ec/README
@ -2241,9 +2241,9 @@ on the :doc:`Build extras <Build_extras>` page.
----------
.. _PKG-USER-QTB:
.. _PKG-QTB:
USER-QTB package
QTB package
----------------
**Contents:**
@ -2261,8 +2261,8 @@ simulation.
**Supporting info:**
* src/USER-QTB: filenames -> commands
* src/USER-QTB/README
* src/QTB: filenames -> commands
* src/QTB/README
* :doc:`fix qtb <fix_qtb>`
* :doc:`fix qbmsst <fix_qbmsst>`
* examples/PACKAGES/qtb
@ -2327,9 +2327,9 @@ with contributions by Doyl Dickel, Mississippi State University.
----------
.. _PKG-USER-REACTION:
.. _PKG-REACTION:
USER-REACTION package
REACTION package
---------------------
**Contents:**
@ -2348,8 +2348,8 @@ molecules, and chiral-sensitive reactions.
**Supporting info:**
* src/USER-REACTION: filenames -> commands
* src/USER-REACTION/README
* src/REACTION: filenames -> commands
* src/REACTION/README
* :doc:`fix bond/react <fix_bond_react>`
* examples/PACKAGES/reaction
* `2017 LAMMPS Workshop <https://www.lammps.org/workshops/Aug17/pdf/gissinger.pdf>`_
@ -2383,9 +2383,9 @@ for monitoring molecules as bonds are created and destroyed.
----------
.. _PKG-USER-SCAFACOS:
.. _PKG-SCAFACOS:
USER-SCAFACOS package
SCAFACOS package
---------------------
**Contents:**
@ -2406,12 +2406,12 @@ the Forschungszentrum Juelich.
**Install:**
This package has :ref:`specific installation instructions <user-scafacos>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <scafacos>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-SCAFACOS: filenames -> commands
* src/USER-SCAFACOS/README
* src/SCAFACOS: filenames -> commands
* src/SCAFACOS/README
* :doc:`kspace_style scafacos <kspace_style>`
* :doc:`kspace_modify <kspace_modify>`
* examples/PACKAGES/scafacos
@ -2428,7 +2428,7 @@ DPD-SMOOTH package
A pair style for smoothed dissipative particle dynamics (SDPD), which
is an extension of smoothed particle hydrodynamics (SPH) to mesoscale
where thermal fluctuations are important (see the
:ref:`USER-SPH package <PKG-USER-SPH>`).
:ref:`SPH package <PKG-SPH>`).
Also two fixes for moving and rigid body integration of SPH/SDPD particles
(particles of atom_style meso).
@ -2456,7 +2456,7 @@ MACHDYN package
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
:ref:`USER-SPH package <PKG-USER-SPH>`).
:ref:`SPH package <PKG-SPH>`).
This package solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control. It can specify
@ -2484,9 +2484,9 @@ This package has :ref:`specific installation instructions <machdyn>` on the :doc
----------
.. _PKG-USER-SMTBQ:
.. _PKG-SMTBQ:
USER-SMTBQ package
SMTBQ package
------------------
**Contents:**
@ -2500,16 +2500,16 @@ Tetot (LAAS-CNRS, France).
**Supporting info:**
* src/USER-SMTBQ: filenames -> commands
* src/USER-SMTBQ/README
* src/SMTBQ: filenames -> commands
* src/SMTBQ/README
* :doc:`pair_style smtbq <pair_smtbq>`
* examples/PACKAGES/smtbq
----------
.. _PKG-USER-SPH:
.. _PKG-SPH:
USER-SPH package
SPH package
----------------
**Contents:**
@ -2533,17 +2533,17 @@ Dynamics, Ernst Mach Institute, Germany).
**Supporting info:**
* src/USER-SPH: filenames -> commands
* src/USER-SPH/README
* src/SPH: filenames -> commands
* src/SPH/README
* doc/PDF/SPH_LAMMPS_userguide.pdf
* examples/PACKAGES/sph
* https://www.lammps.org/movies.html#sph
----------
.. _PKG-USER-TALLY:
.. _PKG-TALLY:
USER-TALLY package
TALLY package
------------------
**Contents:**
@ -2556,16 +2556,16 @@ stress, etc) about individual interactions.
**Supporting info:**
* src/USER-TALLY: filenames -> commands
* src/USER-TALLY/README
* src/TALLY: filenames -> commands
* src/TALLY/README
* :doc:`compute \*/tally <compute_tally>`
* examples/PACKAGES/tally
----------
.. _PKG-USER-UEF:
.. _PKG-UEF:
USER-UEF package
UEF package
----------------
**Contents:**
@ -2578,8 +2578,8 @@ supporting compute styles and an output option.
**Supporting info:**
* src/USER-UEF: filenames -> commands
* src/USER-UEF/README
* src/UEF: filenames -> commands
* src/UEF/README
* :doc:`fix nvt/uef <fix_nh_uef>`
* :doc:`fix npt/uef <fix_nh_uef>`
* :doc:`compute pressure/uef <compute_pressure_uef>`
@ -2589,9 +2589,9 @@ supporting compute styles and an output option.
----------
.. _PKG-USER-VTK:
.. _PKG-VTK:
USER-VTK package
VTK package
----------------
**Contents:**
@ -2611,20 +2611,20 @@ system.
**Install:**
This package has :ref:`specific installation instructions <user-vtk>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <vtk>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-VTK: filenames -> commands
* src/USER-VTK/README
* src/VTK: filenames -> commands
* src/VTK/README
* lib/vtk/README
* :doc:`dump vtk <dump_vtk>`
----------
.. _PKG-USER-YAFF:
.. _PKG-YAFF:
USER-YAFF package
YAFF package
-----------------
**Contents:**
@ -2646,7 +2646,7 @@ which discuss the `QuickFF <quickff_>`_ methodology.
**Supporting info:**
* src/USER-YAFF/README
* src/YAFF/README
* :doc:`angle_style cross <angle_cross>`
* :doc:`angle_style mm3 <angle_mm3>`
* :doc:`bond_style mm3 <bond_mm3>`

66
doc/src/Packages_user.rst
View File

@ -31,101 +31,101 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| Package | Description | Doc page | Example | Library |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-ADIOS <PKG-USER-ADIOS>` | dump output via ADIOS | :doc:`dump adios <dump_adios>` | USER/adios | ext |
| :ref:`ADIOS <PKG-ADIOS>` | dump output via ADIOS | :doc:`dump adios <dump_adios>` | USER/adios | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-ATC <PKG-USER-ATC>` | Atom-to-Continuum coupling | :doc:`fix atc <fix_atc>` | USER/atc | int |
| :ref:`ATC <PKG-ATC>` | Atom-to-Continuum coupling | :doc:`fix atc <fix_atc>` | USER/atc | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-AWPMD <PKG-USER-AWPMD>` | wave packet MD | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | int |
| :ref:`AWPMD <PKG-AWPMD>` | wave packet MD | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-BOCS <PKG-USER-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
| :ref:`BOCS <PKG-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>` | Brownian dynamics and self-propelled particles | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>` | USER/brownian | no |
| :ref:`BROWNIAN <PKG-BROWNIAN>` | Brownian dynamics and self-propelled particles | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>` | USER/brownian | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`CG-DNA <PKG-CG-DNA>` | coarse-grained DNA force fields | src/CG-DNA/README | USER/cgdna | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`CG-SDK <PKG-CG-SDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-COLVARS <PKG-USER-COLVARS>` | collective variables library | :doc:`fix colvars <fix_colvars>` | USER/colvars | int |
| :ref:`COLVARS <PKG-COLVARS>` | collective variables library | :doc:`fix colvars <fix_colvars>` | USER/colvars | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-DIELECTRIC <PKG-USER-DIELECTRIC>` | dielectric boundary solvers and force styles | :doc:`compute efield/atom <compute_efield_atom>` | USER/dielectric | no |
| :ref:`DIELECTRIC <PKG-DIELECTRIC>` | dielectric boundary solvers and force styles | :doc:`compute efield/atom <compute_efield_atom>` | USER/dielectric | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>` | virtual x-ray and electron diffraction | :doc:`compute xrd <compute_xrd>` | USER/diffraction | no |
| :ref:`DIFFRACTION <PKG-DIFFRACTION>` | virtual x-ray and electron diffraction | :doc:`compute xrd <compute_xrd>` | USER/diffraction | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DPD-REACT <PKG-DPD-REACT>` | reactive dissipative particle dynamics | src/DPD-REACT/README | USER/dpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-DRUDE <PKG-USER-DRUDE>` | Drude oscillators | :doc:`Howto drude <Howto_drude>` | USER/drude | no |
| :ref:`DRUDE <PKG-DRUDE>` | Drude oscillators | :doc:`Howto drude <Howto_drude>` | USER/drude | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-EFF <PKG-USER-EFF>` | electron force field | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | no |
| :ref:`EFF <PKG-EFF>` | electron force field | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-FEP <PKG-USER-FEP>` | free energy perturbation | :doc:`compute fep <compute_fep>` | USER/fep | no |
| :ref:`FEP <PKG-FEP>` | free energy perturbation | :doc:`compute fep <compute_fep>` | USER/fep | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-H5MD <PKG-USER-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | ext |
| :ref:`H5MD <PKG-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-HDNNP <PKG-ML-HDNNP>` | High-dimensional neural network potentials | :doc:`pair_style hdnnp <pair_hdnnp>` | USER/hdnnp | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-INTEL <PKG-USER-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
| :ref:`INTEL <PKG-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`LATBOLTZ <PKG-LATBOLTZ>` | Lattice Boltzmann fluid | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
| :ref:`MANIFOLD <PKG-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MDI <PKG-USER-MDI>` | client-server coupling | :doc:`MDI Howto <Howto_mdi>` | USER/mdi | ext |
| :ref:`MDI <PKG-MDI>` | client-server coupling | :doc:`MDI Howto <Howto_mdi>` | USER/mdi | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MEAM <PKG-MEAM>` | modified EAM potential (C++) | :doc:`pair_style meam <pair_meam>` | meam | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DPD-MESO <PKG-DPD-MESO>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | USER/mesodpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MESONT <PKG-USER-MESONT>` | mesoscopic tubular potential model for nanotubes | pair style :doc:`mesont/tpm <pair_mesont_tpm>`, :doc:`mesocnt <pair_mesocnt>` | USER/mesont | int |
| :ref:`MESONT <PKG-MESONT>` | mesoscopic tubular potential model for nanotubes | pair style :doc:`mesont/tpm <pair_mesont_tpm>`, :doc:`mesocnt <pair_mesocnt>` | USER/mesont | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MGPT <PKG-USER-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | no |
| :ref:`MGPT <PKG-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MISC <PKG-USER-MISC>` | single-file contributions | USER-MISC/README | USER/misc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MOFFF <PKG-USER-MOFFF>` | styles for `MOF-FF <MOFplus_>`_ force field | :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` | USER/mofff | no |
| :ref:`MOFFF <PKG-MOFFF>` | styles for `MOF-FF <MOFplus_>`_ force field | :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` | USER/mofff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MOLFILE <PKG-USER-MOLFILE>` | `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_ molfile plug-ins | :doc:`dump molfile <dump_molfile>` | n/a | ext |
| :ref:`MOLFILE <PKG-MOLFILE>` | `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_ molfile plug-ins | :doc:`dump molfile <dump_molfile>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-NETCDF <PKG-USER-NETCDF>` | dump output via NetCDF | :doc:`dump netcdf <dump_netcdf>` | n/a | ext |
| :ref:`NETCDF <PKG-NETCDF>` | dump output via NetCDF | :doc:`dump netcdf <dump_netcdf>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`OPENMP <PKG-OPENMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-PACE <PKG-ML-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PHONON <PKG-USER-PHONON>` | phonon dynamical matrix | :doc:`fix phonon <fix_phonon>` | USER/phonon | no |
| :ref:`PHONON <PKG-PHONON>` | phonon dynamical matrix | :doc:`fix phonon <fix_phonon>` | USER/phonon | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PLUMED <PKG-USER-PLUMED>` | :ref:`PLUMED <PLUMED>` free energy library | :doc:`fix plumed <fix_plumed>` | USER/plumed | ext |
| :ref:`PLUMED <PKG-PLUMED>` | :ref:`PLUMED <PLUMED>` free energy library | :doc:`fix plumed <fix_plumed>` | USER/plumed | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PTM <PKG-USER-PTM>` | Polyhedral Template Matching | :doc:`compute ptm/atom <compute_ptm_atom>` | n/a | no |
| :ref:`PTM <PKG-PTM>` | Polyhedral Template Matching | :doc:`compute ptm/atom <compute_ptm_atom>` | n/a | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-QMMM <PKG-USER-QMMM>` | QM/MM coupling | :doc:`fix qmmm <fix_qmmm>` | USER/qmmm | ext |
| :ref:`QMMM <PKG-QMMM>` | QM/MM coupling | :doc:`fix qmmm <fix_qmmm>` | USER/qmmm | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-QTB <PKG-USER-QTB>` | quantum nuclear effects | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | no |
| :ref:`QTB <PKG-QTB>` | quantum nuclear effects | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-QUIP <PKG-ML-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-RANN <PKG-ML-RANN>` | rapid atomistic neural network (RANN) potentials | :doc:`pair rann <pair_rann>` | USER/rann | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-REACTION <PKG-USER-REACTION>` | chemical reactions in classical MD | :doc:`fix bond/react <fix_bond_react>` | USER/reaction | no |
| :ref:`REACTION <PKG-REACTION>` | chemical reactions in classical MD | :doc:`fix bond/react <fix_bond_react>` | USER/reaction | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`REAXFF <PKG-REAXFF>` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc <pair_reaxc>` | reax | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos <kspace_style>` | USER/scafacos | ext |
| :ref:`SCAFACOS <PKG-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos <kspace_style>` | USER/scafacos | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DPD-SMOOTH <PKG-DPD-SMOOTH>` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | USER/sdpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MACHDYN <PKG-MACHDYN>` | smoothed Mach dynamics | `SMD User Guide <PDF/SMD_LAMMPS_userguide.pdf>`_ | USER/smd | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | second moment tight binding QEq potential | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | no |
| :ref:`SMTBQ <PKG-SMTBQ>` | second moment tight binding QEq potential | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-SPH <PKG-USER-SPH>` | smoothed particle hydrodynamics | `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_ | USER/sph | no |
| :ref:`SPH <PKG-SPH>` | smoothed particle hydrodynamics | `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_ | USER/sph | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-TALLY <PKG-USER-TALLY>` | pairwise tally computes | :doc:`compute XXX/tally <compute_tally>` | USER/tally | no |
| :ref:`TALLY <PKG-TALLY>` | pairwise tally computes | :doc:`compute XXX/tally <compute_tally>` | USER/tally | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-UEF <PKG-USER-UEF>` | extensional flow | :doc:`fix nvt/uef <fix_nh_uef>` | USER/uef | no |
| :ref:`UEF <PKG-UEF>` | extensional flow | :doc:`fix nvt/uef <fix_nh_uef>` | USER/uef | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-VTK <PKG-USER-VTK>` | dump output via VTK | :doc:`compute vtk <dump_vtk>` | n/a | ext |
| :ref:`VTK <PKG-VTK>` | dump output via VTK | :doc:`compute vtk <dump_vtk>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-YAFF <PKG-USER-YAFF>` | additional styles implemented in YAFF | :doc:`angle_style cross <angle_cross>` | USER/yaff | no |
| :ref:`YAFF <PKG-YAFF>` | additional styles implemented in YAFF | :doc:`angle_style cross <angle_cross>` | USER/yaff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF

14
doc/src/Run_options.rst
View File

@ -202,7 +202,7 @@ Option -plog will override the name of the partition log files file.N.
**-mdi 'multiple flags'**
This flag is only recognized and used when LAMMPS has support for the MolSSI
Driver Interface (MDI) included as part of the :ref:`USER-MDI <PKG-USER-MDI>`
Driver Interface (MDI) included as part of the :ref:`MDI <PKG-MDI>`
package. This flag is specific to the MDI library and controls how LAMMPS
interacts with MDI. There are usually multiple flags that have to follow it
and those have to be placed in quotation marks. For more information about
@ -274,7 +274,7 @@ script. For example "-package gpu 2" or "-pk gpu 2" is the same as
:doc:`package gpu 2 <package>` in the input script. The possible styles
and args are documented on the :doc:`package <package>` doc page. This
switch can be used multiple times, e.g. to set options for the
USER-INTEL and OPENMP packages which can be used together.
INTEL and OPENMP 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
@ -540,7 +540,7 @@ Use variants of various styles if they exist. 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 :doc:`Accelerate performance <Speed>`. The "gpu" style corresponds to the
GPU package, the "intel" style to the USER-INTEL package, the "kk"
GPU package, the "intel" style to the INTEL package, the "kk"
style to the KOKKOS package, the "opt" style to the OPT package, and
the "omp" style to the OPENMP package. The hybrid style is the only
style that accepts arguments. It allows for two packages to be
@ -548,7 +548,7 @@ 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
INTEL package if they are installed and available, but styles for
the OPENMP package otherwise.
Along with the "-package" command-line switch, this is a convenient
@ -570,14 +570,14 @@ 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 :doc:`package gpu <package>` 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
For the INTEL package, using this command-line switch also
invokes the default 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 :doc:`package intel <package>` command in your script. If the
OPENMP 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
requested style is not available in the INTEL package. It will
also invoke the default OPENMP 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

4
doc/src/Speed_compare.rst
View File

@ -72,7 +72,7 @@ section below for examples where this has been done.
small number of threads with increasing overhead as the number of threads
per MPI rank grows. The KOKKOS/OpenMP kernels have less overhead in that
case, but have lower performance with few threads.
* The USER-INTEL package contains many options and settings for achieving
* The INTEL package contains many options and settings for achieving
additional performance on Intel hardware (CPU and accelerator cards), but
to unlock this potential, an Intel compiler is required. The package code
will compile with GNU gcc, but it will not be as efficient.
@ -90,5 +90,5 @@ section below for examples where this has been done.
both, NVIDIA and AMD GPUs well. On NVIDIA hardware, using CUDA is typically
resulting in equal or better performance over OpenCL.
* OpenCL in the GPU package does theoretically also support Intel CPUs or
Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL)
Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL)
is superior.

2
doc/src/Speed_gpu.rst
View File

@ -150,7 +150,7 @@ hardware, which pair style is used, the number of atoms/GPU, and the
precision used on the GPU (double, single, mixed). Using the GPU package
in OpenCL mode on CPUs (which uses vectorization and multithreading) is
usually resulting in inferior performance compared to using LAMMPS' native
threading and vectorization support in the OPENMP and USER-INTEL packages.
threading and vectorization support in the OPENMP and INTEL packages.
See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
LAMMPS web site for performance of the GPU package on various

76
doc/src/Speed_intel.rst
View File

@ -1,7 +1,7 @@
USER-INTEL package
INTEL package
==================
The USER-INTEL package is maintained by Mike Brown at Intel
The INTEL package is maintained by Mike Brown at Intel
Corporation. It provides two methods for accelerating simulations,
depending on the hardware you have. The first is acceleration on
Intel CPUs by running in single, mixed, or double precision with
@ -12,7 +12,7 @@ When offloading to a co-processor from a CPU, the same routine is run
twice, once on the CPU and once with an offload flag. This allows
LAMMPS to run on the CPU cores and co-processor cores simultaneously.
Currently Available USER-INTEL Styles
Currently Available INTEL Styles
"""""""""""""""""""""""""""""""""""""
* Angle Styles: charmm, harmonic
@ -28,7 +28,7 @@ Currently Available USER-INTEL Styles
.. warning::
None of the styles in the USER-INTEL package currently
None of the styles in the INTEL package currently
support computing per-atom stress. If any compute or fix in your
input requires it, LAMMPS will abort with an error message.
@ -41,7 +41,7 @@ precision mode. Performance improvements are shown compared to
LAMMPS *without using other acceleration packages* as these are
under active development (and subject to performance changes). The
measurements were performed using the input files available in
the src/USER-INTEL/TEST directory with the provided run script.
the src/INTEL/TEST directory with the provided run script.
These are scalable in size; the results given are with 512K
particles (524K for Liquid Crystal). Most of the simulations are
standard LAMMPS benchmarks (indicated by the filename extension in
@ -56,7 +56,7 @@ Results are speedups obtained on Intel Xeon E5-2697v4 processors
Knights Landing), and Intel Xeon Gold 6148 processors (code-named
Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio
2017 update 2. Results are with 1 MPI task per physical core. See
*src/USER-INTEL/TEST/README* for the raw simulation rates and
*src/INTEL/TEST/README* for the raw simulation rates and
instructions to reproduce.
----------
@ -67,11 +67,11 @@ Accuracy and order of operations
In most molecular dynamics software, parallelization parameters
(# of MPI, OpenMP, and vectorization) can change the results due
to changing the order of operations with finite-precision
calculations. The USER-INTEL package is deterministic. This means
calculations. The INTEL package is deterministic. This means
that the results should be reproducible from run to run with the
*same* parallel configurations and when using deterministic
libraries or library settings (MPI, OpenMP, FFT). However, there
are differences in the USER-INTEL package that can change the
are differences in the INTEL package that can change the
order of operations compared to LAMMPS without acceleration:
* Neighbor lists can be created in a different order
@ -88,7 +88,7 @@ order of operations compared to LAMMPS without acceleration:
Twister generator included in the Intel MKL library (that should be
more robust than the default Masaglia random number generator)
The precision mode (described below) used with the USER-INTEL
The precision mode (described below) used with the INTEL
package can change the *accuracy* of the calculations. For the
default *mixed* precision option, calculations between pairs or
triplets of atoms are performed in single precision, intended to
@ -102,7 +102,7 @@ mode should not be used without appropriate validation.
Quick Start for Experienced Users
"""""""""""""""""""""""""""""""""
LAMMPS should be built with the USER-INTEL package installed.
LAMMPS should be built with the INTEL package installed.
Simulations should be run with 1 MPI task per physical *core*\ ,
not *hardware thread*\ .
@ -148,7 +148,7 @@ When using Intel compilers version 16.0 or later is required.
In order to use offload to co-processors, an Intel Xeon Phi
co-processor and an Intel compiler are required.
Although any compiler can be used with the USER-INTEL package,
Although any compiler can be used with the INTEL package,
currently, vectorization directives are disabled by default when
not using Intel compilers due to lack of standard support and
observations of decreased performance. The OpenMP standard now
@ -185,7 +185,7 @@ can start running so that the CPU pipeline is still being used
efficiently. Although benefits can be seen by launching a MPI task
for every hardware thread, for multinode simulations, we recommend
that OpenMP threads are used for SMT instead, either with the
USER-INTEL package, :doc:`OPENMP package <Speed_omp>`, or
INTEL package, :doc:`OPENMP package <Speed_omp>`, or
:doc:`KOKKOS package <Speed_kokkos>`. In the example above, up
to 36X speedups can be observed by using all 36 physical cores with
LAMMPS. By using all 72 hardware threads, an additional 10-30%
@ -202,10 +202,10 @@ this information can normally be obtained with:
cat /proc/cpuinfo
Building LAMMPS with the USER-INTEL package
Building LAMMPS with the INTEL package
"""""""""""""""""""""""""""""""""""""""""""
See the :ref:`Build extras <user-intel>` doc page for
See the :ref:`Build extras <intel>` doc page for
instructions. Some additional details are covered here.
For building with make, several example Makefiles for building with
@ -228,7 +228,7 @@ simple as:
.. code-block:: bash
make yes-user-intel
make yes-intel
source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
# or psxevars.csh for C-shell
make intel_cpu_intelmpi
@ -238,7 +238,7 @@ binary can be used on nodes with or without co-processors installed.
However, if you do not have co-processors on your system, building
without offload support will produce a smaller binary.
The general requirements for Makefiles with the USER-INTEL package
The general requirements for Makefiles with the INTEL package
are as follows. When using Intel compilers, "-restrict" is required
and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS.
CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads
@ -253,7 +253,7 @@ recommended CCFLAG options for best performance are "-O2 -fno-alias
.. note::
See the src/USER-INTEL/README file for additional flags that
See the src/INTEL/README file for additional flags that
might be needed for best performance on Intel server processors
code-named "Skylake".
@ -270,14 +270,14 @@ recommended CCFLAG options for best performance are "-O2 -fno-alias
in most of the example Makefiles is to use "-xHost", however this
should not be used when cross-compiling.
Running LAMMPS with the USER-INTEL package
Running LAMMPS with the INTEL package
""""""""""""""""""""""""""""""""""""""""""
Running LAMMPS with the USER-INTEL package is similar to normal use
Running LAMMPS with the INTEL package is similar to normal use
with the exceptions that one should 1) specify that LAMMPS should use
the USER-INTEL package, 2) specify the number of OpenMP threads, and
the INTEL package, 2) specify the number of OpenMP threads, and
3) optionally specify the specific LAMMPS styles that should use the
USER-INTEL package. 1) and 2) can be performed from the command-line
INTEL package. 1) and 2) can be performed from the command-line
or by editing the input script. 3) requires editing the input script.
Advanced performance tuning options are also described below to get
the best performance.
@ -312,27 +312,27 @@ almost all cases.
recommended, especially when running on a machine with Intel
Hyper-Threading technology disabled.
Run with the USER-INTEL package from the command line
Run with the INTEL package from the command line
"""""""""""""""""""""""""""""""""""""""""""""""""""""
To enable USER-INTEL optimizations for all available styles used in
To enable INTEL optimizations for all available styles used in
the input script, the "-sf intel" :doc:`command-line switch <Run_options>` 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:
:doc:`package intel 1 <package>`. 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,
options for the INTEL package. The default package command will
specify that 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 co-processors are present and the
binary was built with offload support, that 1 co-processor per node
will be used with automatic balancing of work between the CPU and the
co-processor.
You can specify different options for the USER-INTEL package by using
You can specify different options for the INTEL package by using
the "-pk intel Nphi" :doc:`command-line switch <Run_options>` with
keyword/value pairs as specified in the documentation. Here, Nphi = #
of Xeon Phi co-processors/node (ignored without offload
support). Common options to the USER-INTEL package include *omp* to
support). Common options to the 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 :doc:`package intel <package>` command for details, including the default values
@ -348,11 +348,11 @@ launching MPI applications):
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision
Or run with the USER-INTEL package by editing an input script
Or run with the INTEL package by editing an input script
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
As an alternative to adding command-line arguments, the input script
can be edited to enable the USER-INTEL package. This requires adding
can be edited to enable the INTEL package. This requires adding
the :doc:`package intel <package>` command to the top of the input
script. For the second example above, this would be:
@ -360,7 +360,7 @@ script. For the second example above, this would be:
package intel 0 omp 2 mode double
To enable the USER-INTEL package only for individual styles, you can
To enable the INTEL package only for individual styles, you can
add an "intel" suffix to the individual style, e.g.:
.. code-block:: LAMMPS
@ -368,7 +368,7 @@ add an "intel" suffix to the individual style, e.g.:
pair_style lj/cut/intel 2.5
Alternatively, the :doc:`suffix intel <suffix>` command can be added to
the input script to enable USER-INTEL styles for the commands that
the input script to enable INTEL styles for the commands that
follow in the input script.
Tuning for Performance
@ -376,7 +376,7 @@ Tuning for Performance
.. note::
The USER-INTEL package will perform better with modifications
The INTEL package will perform better with modifications
to the input script when :doc:`PPPM <kspace_style>` is used:
:doc:`kspace_modify diff ad <kspace_modify>` should be added to the
input script.
@ -388,7 +388,7 @@ is dedicated to performing some of the PPPM calculations and MPI
communications. This feature requires setting the pre-processor flag
-DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset
in the default makefiles (\ *Makefile.mpi* and *Makefile.serial*\ ) but
it is set in all makefiles tuned for the USER-INTEL package. On Intel
it is set in all makefiles tuned for the INTEL package. On Intel
Xeon Phi x200 series CPUs, the LRT feature will likely improve
performance, even on a single node. On Intel Xeon processors, using
this mode might result in better performance when using multiple nodes,
@ -407,8 +407,8 @@ when using offload.
performance and/or scalability for simple 2-body potentials such as
lj/cut or when using LRT mode on processors supporting AVX-512.
Not all styles are supported in the USER-INTEL package. You can mix
the USER-INTEL package with styles from the :doc:`OPT <Speed_opt>`
Not all styles are supported in the INTEL package. You can mix
the INTEL package with styles from the :doc:`OPT <Speed_opt>`
package or the :doc:`OPENMP package <Speed_omp>`. 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
@ -420,7 +420,7 @@ 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 :doc:`suffix hybrid intel omp <suffix>` command can also be used
within the input script to automatically append the "omp" suffix to
styles when USER-INTEL styles are not available.
styles when INTEL styles are not available.
.. note::
@ -492,7 +492,7 @@ tuning of the number of threads to use per MPI task or the number of
threads to use per core can be accomplished with keyword settings of
the :doc:`package intel <package>` command.
The USER-INTEL package has two modes for deciding which atoms will be
The INTEL package has two modes for deciding which atoms will be
handled by the co-processor. This choice is controlled with the *ghost*
keyword of the :doc:`package intel <package>` command. When set to 0,
ghost atoms (atoms at the borders between MPI tasks) are not offloaded
@ -528,7 +528,7 @@ accelerated style may be used with hybrid styles when offloading.
:doc:`Special_bonds <special_bonds>` exclusion lists are not currently
supported with offload, however, the same effect can often be
accomplished by setting cutoffs for excluded atom types to 0. None of
the pair styles in the USER-INTEL package currently support the
the pair styles in the INTEL package currently support the
"inner", "middle", "outer" options for rRESPA integration via the
:doc:`run_style respa <run_style>` command; only the "pair" option is
supported.

6
doc/src/Speed_kokkos.rst
View File

@ -235,7 +235,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
To build with Kokkos support for Intel Xeon Phi co-processors
such as Knight's Corner (KNC), your system must be configured to use
them in "native" mode, not "offload" mode like the USER-INTEL package
them in "native" mode, not "offload" mode like the INTEL package
supports.
Running on GPUs
@ -401,8 +401,8 @@ Generally speaking, the following rules of thumb apply:
significantly on the hardware in use and the simulated system and pair
style.
* When running on Intel hardware, KOKKOS is not as fast as
the USER-INTEL package, which is optimized for x86 hardware (not just
from Intel) and compilation with the Intel compilers. The USER-INTEL
the INTEL package, which is optimized for x86 hardware (not just
from Intel) and compilation with the Intel compilers. The INTEL
package also can increase the vector length of vector instructions
by switching to single or mixed precision mode.

20
doc/src/Speed_packages.rst
View File

@ -18,7 +18,7 @@ standard or user packages:
+-----------------------------------------+-------------------------------------------------------+
| :doc:`GPU Package <Speed_gpu>` | for GPUs via CUDA, OpenCL, or ROCm HIP |
+-----------------------------------------+-------------------------------------------------------+
| :doc:`USER-INTEL Package <Speed_intel>` | for Intel CPUs and Intel Xeon Phi |
| :doc:`INTEL Package <Speed_intel>` | for Intel CPUs and Intel Xeon Phi |
+-----------------------------------------+-------------------------------------------------------+
| :doc:`KOKKOS Package <Speed_kokkos>` | for NVIDIA GPUs, Intel Xeon Phi, and OpenMP threading |
+-----------------------------------------+-------------------------------------------------------+
@ -41,11 +41,11 @@ Inverting this list, LAMMPS currently has acceleration support for
three kinds of hardware, via the listed packages:
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Many-core CPUs | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>`, :doc:`OPENMP <Speed_omp>`, :doc:`OPT <Speed_opt>` packages |
| Many-core CPUs | :doc:`INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>`, :doc:`OPENMP <Speed_omp>`, :doc:`OPT <Speed_opt>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| GPUs | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Intel Phi/AVX | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>` packages |
| Intel Phi/AVX | :doc:`INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
Which package is fastest for your hardware may depend on the size
@ -84,9 +84,9 @@ listed above:
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
| build the accelerator library | only for GPU package |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
| install the accelerator package | make yes-opt, make yes-user-intel, etc |
| install the accelerator package | make yes-opt, make yes-intel, etc |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
| add compile/link flags to Makefile.machine in src/MAKE | only for USER-INTEL, KOKKOS, OPENMP, OPT packages |
| add compile/link flags to Makefile.machine in src/MAKE | only for INTEL, KOKKOS, OPENMP, OPT packages |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
| re-build LAMMPS | make machine |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
@ -116,15 +116,15 @@ script.
With a few exceptions, you can build a single LAMMPS executable
with all its accelerator packages installed. Note however that the
USER-INTEL and KOKKOS packages require you to choose one of their
INTEL and KOKKOS packages require you to choose one of their
hardware options when building for a specific platform. I.e. CPU or
Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
Phi option for the INTEL package. Or the OpenMP, Cuda, or Phi
option for the KOKKOS package.
These are the exceptions. You cannot build a single executable with:
* both the USER-INTEL Phi and KOKKOS Phi options
* the USER-INTEL Phi or Kokkos Phi option, and the GPU package
* both the INTEL Phi and KOKKOS Phi options
* the INTEL Phi or Kokkos Phi option, and the GPU package
See the examples/accelerate/README and make.list files for sample
Make.py commands that build LAMMPS with any or all of the accelerator
@ -156,7 +156,7 @@ are in the individual accelerator sections.
* Styles with a "gpu" suffix are part of the GPU package and can be run
on Intel, NVIDIA, or AMD GPUs. The speed-up on a GPU depends on a
variety of factors, discussed in the accelerator sections.
* Styles with an "intel" suffix are part of the USER-INTEL
* Styles with an "intel" suffix are part of the INTEL
package. These styles support vectorized single and mixed precision
calculations, in addition to full double precision. In extreme cases,
this can provide speedups over 3.5x on CPUs. The package also

4
doc/src/Tools.rst
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@ -341,7 +341,7 @@ fep tool
The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
simulations using the USER-FEP package.
simulations using the FEP package.
The scripts were contributed by Agilio Padua (ENS de Lyon), agilio.padua at ens-lyon.fr.
@ -861,7 +861,7 @@ phonon tool
The phonon sub-directory contains a post-processing tool useful for
analyzing the output of the :doc:`fix phonon <fix_phonon>` command in
the USER-PHONON package.
the PHONON package.
See the README file for instruction on building the tool and what
library it needs. And see the examples/PACKAGES/phonon directory

2
doc/src/accel_styles.rst
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@ -5,7 +5,7 @@ hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
These accelerated styles are part of the GPU, INTEL, KOKKOS,
OPENMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.

2
doc/src/angle_charmm.rst
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@ -63,7 +63,7 @@ hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
These accelerated styles are part of the GPU, INTEL, KOKKOS,
OPENMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.

2
doc/src/angle_class2.rst
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@ -126,7 +126,7 @@ Restrictions
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 :doc:`Build package <Build_package>` doc
MOFFF package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands

2
doc/src/angle_cosine_buck6d.rst
View File

@ -60,7 +60,7 @@ Restrictions
:doc:`special_bonds <special_bonds>` 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 :doc:`Build package <Build_package>` doc
MOFFF package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands

10
doc/src/atom_style.rst
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@ -319,7 +319,7 @@ styles take the same arguments and should produce the same results,
except for round-off and precision issues.
Note that other acceleration packages in LAMMPS, specifically the GPU,
USER-INTEL, OPENMP, and OPT packages do not use accelerated atom
INTEL, OPENMP, and OPT packages do not use accelerated atom
styles.
The accelerated styles are part of the KOKKOS package. They are only
@ -352,7 +352,7 @@ The *dipole* style is part of the DIPOLE package.
The *peri* style is part of the PERI package for Peridynamics.
The *electron* style is part of the USER-EFF package for :doc:`electronic force fields <pair_eff>`.
The *electron* style is part of the EFF package for :doc:`electronic force fields <pair_eff>`.
The *dpd* style is part of the DPD-REACT package for dissipative
particle dynamics (DPD).
@ -362,14 +362,14 @@ for energy-conserving dissipative particle dynamics (eDPD), many-body
dissipative particle dynamics (mDPD), and transport dissipative particle
dynamics (tDPD), respectively.
The *sph* style is part of the USER-SPH package for smoothed particle
The *sph* style is part of the SPH package for smoothed particle
hydrodynamics (SPH). See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
The *mesont* style is part of the USER-MESONT package.
The *mesont* style is part of the MESONT package.
The *spin* style is part of the SPIN package.
The *wavepacket* style is part of the USER-AWPMD package for the
The *wavepacket* style is part of the AWPMD package for the
:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.
Related commands

4
doc/src/compute_efield_atom.rst
View File

@ -26,7 +26,7 @@ Description
Define a computation that calculates the electric field at each atom in a group.
The compute should only enabled with pair and kspace styles that are provided
by the USER-DIELECTRIC package because only these styles compute the per-atom
by the DIELECTRIC package because only these styles compute the per-atom
electric field at every time step.
The electric field is a 3-component vector. The value of the electric field
@ -52,7 +52,7 @@ The per-atom vector values will be in electric field :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the USER-DIELECTRIC package. It is only enabled if
This compute is part of the DIELECTRIC package. It is only enabled if
LAMMPS was built with that package.
Related commands

2
doc/src/compute_fep.rst
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@ -303,7 +303,7 @@ The values calculated by this compute are "extensive".
Restrictions
""""""""""""
This compute is distributed as the USER-FEP package. It is only
This compute is distributed as the FEP package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_ke_atom_eff.rst
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@ -73,7 +73,7 @@ The per-atom vector values will be in energy :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the USER-EFF package. It is only enabled if
This compute is part of the EFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_ke_eff.rst
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@ -78,7 +78,7 @@ scalar value will be in energy :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the USER-EFF package. It is only enabled if
This compute is part of the EFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_mesont.rst
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@ -43,7 +43,7 @@ The computed values are provided in energy :doc:`units <units>`.
Restrictions
""""""""""""
These computes are part of the USER-MESONT package. They are only enabled if
These computes are part of the MESONT package. They are only enabled if
LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
doc page for more info. In addition, :doc:`mesont pair_style <pair_style>`
must be used.

2
doc/src/compute_pressure_uef.rst
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@ -41,7 +41,7 @@ The keywords and output information are documented in
Restrictions
""""""""""""
This fix is part of the USER-UEF package. It is only enabled if LAMMPS
This fix is part of the UEF package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This command can only be used when :doc:`fix nvt/uef <fix_nh_uef>`

4
doc/src/compute_property_atom.rst
View File

@ -74,7 +74,7 @@ Syntax
.. parsed-literal::
USER-EFF and USER-AWPMD package per-atom properties:
EFF and AWPMD package per-atom properties:
spin = electron spin
eradius = electron radius
ervel = electron radial velocity
@ -82,7 +82,7 @@ Syntax
.. parsed-literal::
USER-SPH package per-atom properties:
SPH package per-atom properties:
rho = density of SPH particles
drho = change in density
e = energy

2
doc/src/compute_ptm_atom.rst
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@ -112,7 +112,7 @@ For atoms that are not within the compute group-ID, all values are set to zero.
Restrictions
""""""""""""
This fix is part of the USER-PTM package. It is only enabled if
This fix is part of the PTM package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_saed.rst
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@ -245,7 +245,7 @@ All array values calculated by this compute are "intensive".
Restrictions
""""""""""""
This compute is part of the USER-DIFFRACTION package. It is only
This compute is part of the DIFFRACTION package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
The compute_saed command does not work for triclinic cells.

2
doc/src/compute_sph_e_atom.rst
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@ -49,7 +49,7 @@ The per-atom vector values will be in energy :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the USER-SPH package. It is only enabled if
This compute is part of the SPH package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_sph_rho_atom.rst
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@ -48,7 +48,7 @@ The per-atom vector values will be in mass/volume :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the USER-SPH package. It is only enabled if
This compute is part of the SPH package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_sph_t_atom.rst
View File

@ -53,7 +53,7 @@ The per-atom vector values will be in temperature :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the USER-SPH package. It is only enabled if
This compute is part of the SPH package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_stress_atom.rst
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@ -233,7 +233,7 @@ since its computations are performed pairwise), nor granular pair
styles with pairwise forces which are not aligned with the vector
between the pair of particles. All bond styles are supported. All
angle, dihedral, improper styles are supported with the exception of
USER-INTEL and KOKKOS variants of specific styles. It also does not
INTEL and KOKKOS variants of specific styles. It also does not
support models with long-range Coulombic or dispersion forces,
i.e. the kspace_style command in LAMMPS. It also does not support the
following fixes which add rigid-body constraints: :doc:`fix shake

2
doc/src/compute_tally.rst
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@ -91,7 +91,7 @@ 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
This compute is part of the TALLY package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Not all pair styles can be evaluated in a pairwise mode as required by

2
doc/src/compute_temp_deform_eff.rst
View File

@ -61,7 +61,7 @@ vector values will be in energy :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the USER-EFF package. It is only enabled if
This compute is part of the EFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_temp_eff.rst
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@ -89,7 +89,7 @@ the simulation.
Restrictions
""""""""""""
This compute is part of the USER-EFF package. It is only enabled if
This compute is part of the EFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_temp_region_eff.rst
View File

@ -53,7 +53,7 @@ vector values will be in energy :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the USER-EFF package. It is only enabled if
This compute is part of the EFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_temp_uef.rst
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@ -38,7 +38,7 @@ documentation for :doc:`compute temp <compute_temp>`.
Restrictions
""""""""""""
This fix is part of the USER-UEF package. It is only enabled if LAMMPS
This fix is part of the UEF package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This command can only be used when :doc:`fix nvt/uef <fix_nh_uef>`

2
doc/src/compute_xrd.rst
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@ -223,7 +223,7 @@ All array values calculated by this compute are "intensive".
Restrictions
""""""""""""
This compute is part of the USER-DIFFRACTION package. It is only
This compute is part of the DIFFRACTION package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
The compute_xrd command does not work for triclinic cells.

2
doc/src/dump_adios.rst
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@ -64,7 +64,7 @@ When using the ADIOS tool 'bpls' to list the content of a .bp file,
bpls will print *__* for the size of the output table indicating that
its size is changing every step.
The *atom/adios* and *custom/adios* dump styles are part of the USER-ADIOS
The *atom/adios* and *custom/adios* dump styles are part of the ADIOS
package. They are only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` doc page for more info.

2
doc/src/dump_cfg_uef.rst
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@ -42,7 +42,7 @@ reference frame as the atomic positions.
Restrictions
""""""""""""
This fix is part of the USER-UEF package. It is only enabled if LAMMPS
This fix is part of the UEF package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This command can only be used when :doc:`fix nvt/uef <fix_nh_uef>`

2
doc/src/dump_h5md.rst
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@ -106,7 +106,7 @@ The position data is stored wrapped (box boundaries not enforced, see
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
The *h5md* dump style is part of the H5MD package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. It also requires
(i) building the ch5md library provided with LAMMPS (See the :doc:`Build package <Build_package>` doc page for more info.) and (ii) having
the `HDF5 <HDF5-ws_>`_ library installed (C bindings are sufficient) on

4
doc/src/dump_molfile.rst
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@ -92,12 +92,12 @@ 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
The *molfile* dump style is part of the MOLFILE package. It is
only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Molfile plugins provide a consistent programming interface to read and
write file formats commonly used in molecular simulations. The
USER-MOLFILE package only provides the interface code, not the plugins.
MOLFILE package only provides the interface code, not the plugins.
These can be obtained from a VMD installation which has to match the
platform that you are using to compile LAMMPS for. By adding plugins
to VMD, support for new file formats can be added to LAMMPS (or VMD

2
doc/src/dump_netcdf.rst
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@ -69,7 +69,7 @@ Restrictions
""""""""""""
The *netcdf* and *netcdf/mpiio* dump styles are part of the
USER-NETCDF package. They are only enabled if LAMMPS was built with
NETCDF package. They are only enabled if LAMMPS was built with
that package. See the :doc:`Build package <Build_package>` doc page for
more info.

2
doc/src/dump_vtk.rst
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@ -162,7 +162,7 @@ Restrictions
The *vtk* style does not support writing of gzipped dump files.
The *vtk* dump style is part of the USER-VTK package. It is only
The *vtk* dump style is part of the VTK package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
To use this dump style, you also must link to the VTK library. See

2
doc/src/dynamical_matrix.rst
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@ -63,7 +63,7 @@ The command collects an array of nine times the number of atoms in a group
on every single MPI rank, so the memory requirements can be very significant
for large systems.
This command is part of the USER-PHONON package. It is only enabled if
This command is part of the PHONON package. It is only enabled if
LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` doc page for more info.

2
doc/src/fix_bocs.rst
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@ -124,7 +124,7 @@ the examples. For the last argument in the command, you should put
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
This fix is part of the BOCS package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Further information

2
doc/src/fix_bond_react.rst
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@ -667,7 +667,7 @@ all other fixes that use any group created by fix bond/react.
Restrictions
""""""""""""
This fix is part of the USER-REACTION package. It is only enabled if
This fix is part of the REACTION package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` doc page for more info.

2
doc/src/fix_brownian.rst
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@ -185,7 +185,7 @@ as defined by the :doc:`atom_style ellipsoid <atom_style>` command.
If the *dipole* keyword is used, they must also store a dipole moment
as defined by the :doc:`atom_style dipole <atom_style>` command.
This fix is part of the USER-BROWNIAN package. It is only enabled if
This fix is part of the BROWNIAN package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.

2
doc/src/fix_colvars.rst
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@ -122,7 +122,7 @@ energy mentioned above. The scalar value calculated by this fix is
Restrictions
""""""""""""
This fix is part of the USER-COLVARS package. It is only enabled if
This fix is part of the COLVARS package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.

2
doc/src/fix_deform.rst
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@ -100,7 +100,7 @@ adjusted independently and simultaneously by this command.
This fix can be used to perform non-equilibrium MD (NEMD) simulations
of a continuously strained system. See the :doc:`fix nvt/sllod <fix_nvt_sllod>` and :doc:`compute temp/deform <compute_temp_deform>` commands for more details. Note
that simulation of a continuously extended system (extensional flow)
can be modeled using the :ref:`USER-UEF package <PKG-USER-UEF>` and its :doc:`fix commands <fix_nh_uef>`.
can be modeled using the :ref:`UEF package <PKG-UEF>` and its :doc:`fix commands <fix_nh_uef>`.
For the *x*\ , *y*\ , *z* parameters, the associated dimension cannot be
shrink-wrapped. For the *xy*\ , *yz*\ , *xz* parameters, the associated

2
doc/src/fix_langevin_eff.rst
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@ -104,7 +104,7 @@ Restrictions
""""""""""""
none
This fix is part of the USER-EFF package. It is only enabled if
This fix is part of the EFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/fix_manifoldforce.rst
View File

@ -48,7 +48,7 @@ the :doc:`run <run>` command. This fix is invoked during :doc:`energy minimizat
Restrictions
""""""""""""
This fix is part of the USER-MANIFOLD package. It is only enabled if
This fix is part of the MANIFOLD package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Only use this with *min_style hftn* or *min_style quickmin*. If not,

2
doc/src/fix_mdi_engine.rst
View File

@ -44,7 +44,7 @@ For more information about running LAMMPS as an MDI engine, see the
Restrictions
""""""""""""
This command is part of the USER-MDI package. It is only enabled if
This command is part of the MDI package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.

2
doc/src/fix_nh_eff.rst
View File

@ -116,7 +116,7 @@ for details.
Restrictions
""""""""""""
This fix is part of the USER-EFF package. It is only enabled if
This fix is part of the EFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Other restriction discussed on the doc page for the :doc:`fix nvt, npt, and nph <fix_nh>` commands also apply.

2
doc/src/fix_nh_uef.rst
View File

@ -199,7 +199,7 @@ The fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the USER-UEF package. It is only enabled if LAMMPS
This fix is part of the UEF package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Due to requirements of the boundary conditions, when the *strain*

2
doc/src/fix_nve_awpmd.rst
View File

@ -45,7 +45,7 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
This fix is part of the USER-AWPMD package. It is only enabled if
This fix is part of the AWPMD package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/fix_nve_eff.rst
View File

@ -42,7 +42,7 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
This fix is part of the USER-EFF package. It is only enabled if
This fix is part of the EFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/fix_nve_manifold_rattle.rst
View File

@ -83,7 +83,7 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
This fix is part of the USER-MANIFOLD package. It is only enabled if
This fix is part of the MANIFOLD package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
----------

2
doc/src/fix_nvt_manifold_rattle.rst
View File

@ -63,7 +63,7 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
This fix is part of the USER-MANIFOLD package. It is only enabled if
This fix is part of the MANIFOLD package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
----------

2
doc/src/fix_nvt_sllod_eff.rst
View File

@ -69,7 +69,7 @@ This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the USER-EFF package. It is only enabled if
This fix is part of the EFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This fix works best without Nose-Hoover chain thermostats, i.e. using

2
doc/src/fix_phonon.rst
View File

@ -181,7 +181,7 @@ This fix assumes a crystalline system with periodical lattice. The
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
This fix is part of the PHONON package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This fix requires LAMMPS be built with an FFT library. See the :doc:`Build settings <Build_settings>` doc page for details.

2
doc/src/fix_plumed.rst
View File

@ -113,7 +113,7 @@ are native to PLUMED.
Restrictions
""""""""""""
This fix is part of the USER-PLUMED package. It is only enabled if
This fix is part of the PLUMED package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.

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