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Merge branch 'develop' into pod-updates

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This commit is contained in:
Axel Kohlmeyer
2022-11-22 18:32:20 -05:00
parent e5ac673e2b 94cc3f6590
commit e2d6bb0c31
44 changed files with 1082 additions and 517 deletions
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60
.github/CODEOWNERS vendored
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@ -13,40 +13,44 @@ lib/kim/* @ellio167
lib/mesont/* @iafoss
# whole packages
src/ADIOS/* @pnorbert
src/AMOEBA/* @sjplimp
src/COMPRESS/* @rbberger
src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
src/MLIAP/* @athomps
src/SNAP/* @athomps
src/SPIN/* @julient31
src/BPM/* @jtclemm
src/BROWNIAN/* @samueljmcameron
src/CG-DNA/* @ohenrich
src/CG-SPICA/* @yskmiyazaki
src/COLVARS/* @giacomofiorin
src/COMPRESS/* @rbberger
src/DIELECTRIC/* @ndtrung81
src/ELECTRODE/* @ludwig-ahrens
src/FEP/* @agiliopadua
src/ML-HDNNP/* @singraber
src/GPU/* @ndtrung81
src/GRANULAR/* @jtclemm @dsbolin
src/INTEL/* @wmbrownintel
src/KIM/* @ellio167
src/KOKKOS/* @stanmoore1
src/LATTE/* @cnegre
src/MANIFOLD/* @Pakketeretet2
src/MDI/* @taylor-a-barnes
src/MDI/* @taylor-a-barnes @sjplimp
src/MEAM/* @martok
src/MESONT/* @iafoss
src/ML-HDNNP/* @singraber
src/ML-IAP/* @athomps
src/ML-PACE/* @yury-lysogorskiy
src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
src/ML-PACE/* @yury-lysogorskiy
src/PLUMED/* @gtribello
src/PHONON/* @lingtikong
src/PTM/* @pmla
src/OPENMP/* @akohlmey
src/PHONON/* @lingtikong
src/PLUGIN/* @akohlmey
src/PLUMED/* @gtribello
src/PTM/* @pmla
src/QMMM/* @akohlmey
src/REAXFF/* @hasanmetin @stanmoore1
src/REACTION/* @jrgissing
src/REAXFF/* @hasanmetin @stanmoore1
src/SCAFACOS/* @rhalver
src/SNAP/* @athomps
src/SPIN/* @julient31
src/TALLY/* @akohlmey
src/UEF/* @danicholson
src/VTK/* @rbberger
@ -120,27 +124,32 @@ src/dump_movie.* @akohlmey
src/exceptions.h @rbberger
src/fix_nh.* @athomps
src/info.* @akohlmey @rbberger
src/timer.* @akohlmey
src/min* @sjplimp @stanmoore1
src/platform.* @akohlmey
src/timer.* @akohlmey
src/utils.* @akohlmey @rbberger
src/verlet.* @sjplimp @stanmoore1
src/math_eigen_impl.h @jewettaij
# tools
tools/msi2lmp/* @akohlmey
tools/coding_standard/* @akohlmey @rbberger
tools/emacs/* @HaoZeke
tools/singularity/* @akohlmey @rbberger
tools/coding_standard/* @rbberger
tools/valgrind/* @akohlmey
tools/swig/* @akohlmey
tools/lammps-shell/* @akohlmey
tools/msi2lmp/* @akohlmey
tools/offline/* @rbberger
tools/singularity/* @akohlmey @rbberger
tools/swig/* @akohlmey
tools/valgrind/* @akohlmey
tools/vim/* @hammondkd
# tests
unittest/* @akohlmey @rbberger
unittest/* @akohlmey
# cmake
cmake/* @junghans @rbberger
cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
cmake/Modules/MPI4WIN.cmake @akohlmey
cmake/Modules/OpenCLLoader.cmake @akohlmey
cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
cmake/presets/*.cmake @akohlmey
@ -149,13 +158,12 @@ cmake/presets/*.cmake @akohlmey
python/* @rbberger
# fortran
fortran/* @akohlmey
fortran/* @akohlmey @hammondkd
# docs
doc/utils/*/* @rbberger
doc/Makefile @rbberger
doc/README @rbberger
doc/* @akohlmey
examples/plugin/* @akohlmey
examples/PACKAGES/pace/plugin/* @akohlmey
# for releases
src/version.h @sjplimp

2
.github/workflows/compile-msvc.yml vendored
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@ -33,6 +33,8 @@ jobs:
run: |
python3 -m pip install numpy
python3 -m pip install pyyaml
nuget install MSMPIsdk
nuget install MSMPIDIST
cmake -C cmake/presets/windows.cmake \
-D PKG_PYTHON=on \
-S cmake -B build \

9
cmake/CMakeLists.txt
View File

@ -317,6 +317,15 @@ if(PKG_ADIOS)
# script that defines the MPI::MPI_C target
enable_language(C)
find_package(ADIOS2 REQUIRED)
if(BUILD_MPI)
if(NOT ADIOS2_HAVE_MPI)
message(FATAL_ERROR "ADIOS2 must be built with MPI support when LAMMPS has MPI enabled")
endif()
else()
if(ADIOS2_HAVE_MPI)
message(FATAL_ERROR "ADIOS2 must be built without MPI support when LAMMPS has MPI disabled")
endif()
endif()
target_link_libraries(lammps PRIVATE adios2::adios2)
endif()

19
cmake/Modules/FindZMQ.cmake
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@ -1,19 +0,0 @@
find_path(ZMQ_INCLUDE_DIR zmq.h)
find_library(ZMQ_LIBRARY NAMES zmq)
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
# Copy the results to the output variables and target.
if(ZMQ_FOUND)
set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
if(NOT TARGET ZMQ::ZMQ)
add_library(ZMQ::ZMQ UNKNOWN IMPORTED)
set_target_properties(ZMQ::ZMQ PROPERTIES
IMPORTED_LINK_INTERFACE_LANGUAGES "C"
IMPORTED_LOCATION "${ZMQ_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${ZMQ_INCLUDE_DIR}")
endif()
endif()

103
cmake/Modules/LAMMPSInterfacePlugin.cmake
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@ -112,45 +112,76 @@ if(BUILD_MPI)
set(MPI_CXX_SKIP_MPICXX TRUE)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
# Download and configure MinGW compatible MPICH development files for Windows
option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
if(USE_MSMPI)
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
else()
message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
else()
find_package(MPI REQUIRED)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)

107
cmake/Modules/MPI4WIN.cmake
View File

@ -1,39 +1,74 @@
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
# Download and configure MinGW compatible MPICH development files for Windows
option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
if(USE_MSMPI)
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
else()
message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
message(STATUS "Downloading and configuring MPICH2-1.4.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")

8
doc/src/bond_bpm_rotational.rst
View File

@ -45,6 +45,8 @@ Examples
Description
"""""""""""
.. versionadded:: 4May2022
The *bpm/rotational* bond style computes forces and torques based on
deviations from the initial reference state of the two atoms. The
reference state is stored by each bond when it is first computed in
@ -211,9 +213,9 @@ command, as *b1*, *b2*, ..., *b7*\ .
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the BPM
package. See the :doc:`Build package <Build_package>` doc page for
more info.
This bond style is part of the BPM package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
By default if pair interactions are to be disabled, this bond style
requires setting

8
doc/src/bond_bpm_spring.rst
View File

@ -45,6 +45,8 @@ Examples
Description
"""""""""""
.. versionadded:: 4May2022
The *bpm/spring* bond style computes forces and torques based on
deviations from the initial reference state of the two atoms. The
reference state is stored by each bond when it is first computed in
@ -167,9 +169,9 @@ extra quantity can be accessed by the
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the BPM
package. See the :doc:`Build package <Build_package>` doc page for
more info.
This bond style is part of the BPM package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
By default if pair interactions are to be disabled, this bond style
requires setting

7
doc/src/compute_nbond_atom.rst
View File

@ -23,6 +23,8 @@ Examples
Description
"""""""""""
.. versionadded:: 4May2022
Define a computation that computes the number of bonds each atom is
part of. Bonds which are broken are not counted in the tally. See
the :doc:`Howto broken bonds <Howto_bpm>` page for more information.
@ -40,8 +42,9 @@ LAMMPS output options.
Restrictions
""""""""""""
This fix can only be used if LAMMPS was built with the BPM package.
See the :doc:`Build package <Build_package>` doc page for more info.
This compute is part of the BPM package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
page for more info.
Related commands
""""""""""""""""

101
doc/src/fix_bond_react.rst
View File

@ -42,13 +42,16 @@ Syntax
* template-ID(post-reacted) = ID of a molecule template containing post-reaction topology
* map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
* zero or more individual keyword/value pairs may be appended to each react argument
* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *molecule* or *modify_create*
* individual_keyword = *prob* or *rate_limit* or *max_rxn* or *stabilize_steps* or *custom_charges* or *rescale_charges* or *molecule* or *modify_create*
.. parsed-literal::
*prob* values = fraction seed
fraction = initiate reaction with this probability if otherwise eligible
seed = random number seed (positive integer)
*rate_limit* = Nlimit Nsteps
Nlimit = maximum number of reactions allowed to occur within interval
Nsteps = the interval (number of timesteps) over which to count reactions
*max_rxn* value = N
N = maximum number of reactions allowed to occur
*stabilize_steps* value = timesteps
@ -56,6 +59,9 @@ Syntax
*custom_charges* value = *no* or fragment-ID
*no* = update all atomic charges (default)
fragment-ID = ID of molecule fragment whose charges are updated
*rescale_charges* value = *no* or *yes*
*no* = do not rescale atomic charges (default)
*yes* = rescale charges such that total charge does not change during reaction
*molecule* value = *off* or *inter* or *intra*
*off* = allow both inter- and intramolecular reactions (default)
*inter* = search for reactions between molecules with different IDs
@ -514,28 +520,40 @@ example, the molecule fragment could consist of only the backbone
atoms of a polymer chain. This constraint can be used to enforce a
specific relative position and orientation between reacting molecules.
.. versionchanged:: TBD
The constraint of type "custom" has the following syntax:
.. parsed-literal::
custom *varstring*
where "custom" is the required keyword, and *varstring* is a
variable expression. The expression must be a valid equal-style
variable formula that can be read by the :doc:`variable <variable>` command,
where 'custom' is the required keyword, and *varstring* is a variable
expression. The expression must be a valid equal-style variable
formula that can be read by the :doc:`variable <variable>` command,
after any special reaction functions are evaluated. If the resulting
expression is zero, the reaction is prevented from occurring;
otherwise, it is permitted to occur. There are two special reaction
functions available, "rxnsum" and "rxnave". These functions operate
over the atoms in a given reaction site, and have one mandatory
argument and one optional argument. The mandatory argument is the
identifier for an atom-style variable. The second, optional argument
is the name of a molecule fragment in the pre-reaction template, and
can be used to operate over a subset of atoms in the reaction site.
The "rxnsum" function sums the atom-style variable over the reaction
site, while the "rxnave" returns the average value. For example, a
constraint on the total potential energy of atoms involved in the
reaction can be imposed as follows:
otherwise, it is permitted to occur. There are three special reaction
functions available, 'rxnbond', 'rxnsum', and 'rxnave'. The 'rxnbond'
function allows per-bond values to be included in the variable strings
of the custom constraint. The 'rxnbond' function has two mandatory
arguments. The first argument is the ID of a previously defined
'compute bond/local' command. This 'compute bond/local' must compute
only one value, e.g. bond force. This value is returned by the
'rxnbond' function. The second argument is the name of a molecule
fragment in the pre-reaction template. The fragment must contain
exactly two atoms, corresponding to the atoms involved in the bond
whose value should be calculated. An example of a constraint that uses
the force experienced by a bond is provided below. The 'rxnsum' and
'rxnave' functions operate over the atoms in a given reaction site,
and have one mandatory argument and one optional argument. The
mandatory argument is the identifier for an atom-style variable. The
second, optional argument is the name of a molecule fragment in the
pre-reaction template, and can be used to operate over a subset of
atoms in the reaction site. The 'rxnsum' function sums the atom-style
variable over the reaction site, while the 'rxnave' returns the
average value. For example, a constraint on the total potential energy
of atoms involved in the reaction can be imposed as follows:
.. code-block:: LAMMPS
@ -547,11 +565,32 @@ reaction can be imposed as follows:
custom "rxnsum(v_my_pe) > 100" # in Constraints section of map file
The above example prevents the reaction from occurring unless the
total potential energy of the reaction site is above 100. The variable
expression can be interpreted as the probability of the reaction
occurring by using an inequality and the :doc:`random(x,y,z) <variable>`
function available for equal-style variables, similar to the 'arrhenius'
constraint above.
total potential energy of the reaction site is above 100. As a second
example, this time using the 'rxnbond' function, consider a modified
Arrhenius constraint that depends on the bond force of a specific bond:
.. code-block:: LAMMPS
# in LAMMPS input script
compute bondforce all bond/local force
compute ke_atom all ke/atom
variable ke atom c_ke_atom
variable E_a equal 100.0 # activation energy
variable l0 equal 1.0 # characteristic length
.. code-block:: LAMMPS
# in Constraints section of map file
custom "exp(-(v_E_a-rxnbond(c_bondforce,bond1frag)*v_l0)/(2/3*rxnave(v_ke))) < random(0,1,12345)"
By using an inequality and the 'random(x,y,z)' function, the left-hand
side can be interpreted as the probability of the reaction occurring,
similar to the 'arrhenius' constraint above.
By default, all constraints must be satisfied for the reaction to
occur. In other words, constraints are evaluated as a series of
@ -598,6 +637,15 @@ eligible reaction only occurs if the random number is less than the
fraction. Up to :math:`N` reactions are permitted to occur, as optionally
specified by the *max_rxn* keyword.
.. versionadded:: TBD
The *rate_limit* keyword can enforce an upper limit on the overall
rate of the reaction. The number of reaction occurences is limited to
Nlimit within an interval of Nsteps timesteps. No reactions are
permitted to occur within the first Nsteps timesteps of the first run
after reading a data file. Nlimit can be specified with an equal-style
:doc:`variable <variable>`.
The *stabilize_steps* keyword allows for the specification of how many
time steps a reaction site is stabilized before being returned to the
overall system thermostat. In order to produce the most physical
@ -616,6 +664,19 @@ charges are updated to those specified by the post-reaction template
fragment defined in the pre-reaction molecule template. In this case,
only the atomic charges of atoms in the molecule fragment are updated.
.. versionadded:: TBD
The *rescale_charges* keyword can be used to ensure the total charge
of the system does not change as reactions occur. When the argument is
set to *yes*\ , a fixed value is added to the charges of post-reaction
atoms such that their total charge equals that of the pre-reaction
site. If only a subset of atomic charges are updated via the
*custom_charges* keyword, this rescaling is applied to the subset.
This keyword could be useful for systems that contain different
molecules with the same reactive site, if the partial charges on the
reaction site vary from molecule to molecule, or when removing
reaction by-products.
The *molecule* keyword can be used to force the reaction to be
intermolecular, intramolecular or either. When the value is set to
*off*\ , molecule IDs are not considered when searching for reactions

6
doc/src/fix_nve_bpm_sphere.rst
View File

@ -30,6 +30,8 @@ Examples
Description
"""""""""""
.. versionadded:: 4May2022
Perform constant NVE integration to update position, velocity, angular
velocity, and quaternion orientation for finite-size spherical
particles in the group each timestep. V is volume; E is energy. This
@ -65,6 +67,10 @@ the :doc:`run <run>` command. This fix is not invoked during
Restrictions
""""""""""""
This fix is part of the BPM package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
page for more info.
This fix requires that atoms store torque, angular velocity (omega), a
radius, and a quaternion as defined by the :doc:`atom_style bpm/sphere
<atom_style>` command.

8
doc/src/pair_bpm_spring.rst
View File

@ -22,6 +22,8 @@ Examples
Description
"""""""""""
.. versionadded:: 4May2022
Style *bpm/spring* computes pairwise forces with the formula
.. math::
@ -101,7 +103,11 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
none
This pair style is part of the BPM package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""

345
doc/src/python.rst
View File

@ -8,14 +8,25 @@ Syntax
.. parsed-literal::
python func keyword args ...
python mode keyword args ...
* func = name of Python function
* one or more keyword/args pairs must be appended
* mode = *source* or name of Python function
if mode is *source*:
.. parsed-literal::
keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists* or *source*
keyword = *here* or name of a *Python file*
*here* arg = inline
inline = one or more lines of Python code which defines func
must be a single argument, typically enclosed between triple quotes
*Python file* = name of a file with Python code which will be executed immediately
* if *mode* is the name of a Python function, one or more keywords with/without arguments must be appended
.. parsed-literal::
keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists*
*invoke* arg = none = invoke the previously defined Python function
*input* args = N i1 i2 ... iN
N = # of inputs to function
@ -24,7 +35,7 @@ Syntax
SELF = reference to LAMMPS itself which can be accessed by Python function
variable = v_name, where name = name of LAMMPS variable, e.g. v_abc
*return* arg = varReturn
varReturn = v_name = LAMMPS variable name which return value of function will be assigned to
varReturn = v_name = LAMMPS variable name which the return value of the Python function will be assigned to
*format* arg = fstring with M characters
M = N if no return value, where N = # of inputs
M = N+1 if there is a return value
@ -38,10 +49,6 @@ Syntax
inline = one or more lines of Python code which defines func
must be a single argument, typically enclosed between triple quotes
*exists* arg = none = Python code has been loaded by previous python command
*source* arg = *filename* or *inline*
filename = file of Python code which will be executed immediately
inline = one or more lines of Python code which will be executed immediately
must be a single argument, typically enclosed between triple quotes
Examples
""""""""
@ -70,80 +77,103 @@ Examples
lmp.command("pair_style lj/cut ${cut}") # LAMMPS commands
lmp.command("pair_coeff * * 1.0 1.0")
lmp.command("run 100")
"""
"""
python source funcdef.py
python source here "from lammps import lammps"
Description
"""""""""""
Define a Python function or execute a previously defined function or
execute some arbitrary python code.
The *python* command allows interfacing LAMMPS with an embedded Python
interpreter and enables either executing arbitrary python code in that
interpreter, registering a Python function for future execution (as a
python style variable, from a fix interfaced with python, or for direct
invocation), or invoking such a previously registered function.
Arguments, including LAMMPS variables, can be passed to the function
from the LAMMPS input script and a value returned by the Python
function to a LAMMPS variable. The Python code for the function can
be included directly in the input script or in a separate Python file.
The function can be standard Python code or it can make "callbacks" to
LAMMPS through its library interface to query or set internal values
within LAMMPS. This is a powerful mechanism for performing complex
operations in a LAMMPS input script that are not possible with the
simple input script and variable syntax which LAMMPS defines. Thus
your input script can operate more like a true programming language.
from the LAMMPS input script and a value returned by the Python function
assigned to a LAMMPS variable. The Python code for the function can be included
directly in the input script or in a separate Python file. The function
can be standard Python code or it can make "callbacks" to LAMMPS through
its library interface to query or set internal values within LAMMPS.
This is a powerful mechanism for performing complex operations in a
LAMMPS input script that are not possible with the simple input script
and variable syntax which LAMMPS defines. Thus your input script can
operate more like a true programming language.
Use of this command requires building LAMMPS with the PYTHON package
which links to the Python library so that the Python interpreter is
embedded in LAMMPS. More details about this process are given below.
There are two ways to invoke a Python function once it has been
defined. One is using the *invoke* keyword. The other is to assign
registered. One is using the *invoke* keyword. The other is to assign
the function to a :doc:`python-style variable <variable>` defined in
your input script. Whenever the variable is evaluated, it will
execute the Python function to assign a value to the variable. Note
that variables can be evaluated in many different ways within LAMMPS.
They can be substituted for directly in an input script. Or they can
be passed to various commands as arguments, so that the variable is
evaluated during a simulation run.
your input script. Whenever the variable is evaluated, it will execute
the Python function to assign a value to the variable. Note that
variables can be evaluated in many different ways within LAMMPS. They
can be substituted with their result directly in an input script, or
they can be passed to various commands as arguments, so that the
variable is evaluated during a simulation run.
A broader overview of how Python can be used with LAMMPS is given on
the :doc:`Python <Python_head>` doc page. There is an examples/python
directory which illustrates use of the python command.
A broader overview of how Python can be used with LAMMPS is given in the
:doc:`Use Python with LAMMPS <Python_head>` section of the
documentation. There also is an ``examples/python`` directory which
illustrates use of the python command.
----------
The *func* setting specifies the name of the Python function. The
code for the function is defined using the *file* or *here* keywords
as explained below. In case of the *source* keyword, the name of
the function is ignored.
The first argument of the *python* command is either the *source*
keyword or the name of a Python function. This defines the mode
of the python command.
If the *source* keyword is used, it is followed by either a file name or
the *here* keyword. No other keywords can be used. The *here* keyword
is followed by a string with python commands, either on a single line
enclosed in quotes, or as multiple lines enclosed in triple quotes.
These Python commands will be passed to the python interpreter and
executed immediately without registering a Python function for future
execution. The code will be loaded into and run in the "main" module of
the Python interpreter. This allows running arbitrary Python code at
any time while processing the LAMMPS input file. This can be used to
pre-load Python modules, initialize global variables, define functions
or classes, or perform operations using the python programming language.
The Python code will be executed in parallel on all MPI processes. No
arguments can be passed.
In all other cases, the first argument is the name of a Python function
that will be registered with LAMMPS for future execution. The function
may already be defined (see *exists* keyword) or must be defined using
the *file* or *here* keywords as explained below.
If the *invoke* keyword is used, no other keywords can be used, and a
previous python command must have defined the Python function
previous *python* command must have registered the Python function
referenced by this command. This invokes the Python function with the
previously defined arguments and return value processed as explained
below. You can invoke the function as many times as you wish in your
input script.
If the *source* keyword is used, no other keywords can be used.
The argument can be a filename or a string with python commands,
either on a single line enclosed in quotes, or as multiple lines
enclosed in triple quotes. These python commands will be passed
to the python interpreter and executed immediately without registering
a python function for future execution.
previously defined arguments and the return value is processed as
explained below. You can invoke the function as many times as you wish
in your input script.
The *input* keyword defines how many arguments *N* the Python function
expects. If it takes no arguments, then the *input* keyword should
not be used. Each argument can be specified directly as a value,
e.g. 6 or 3.14159 or abc (a string of characters). The type of each
expects. If it takes no arguments, then the *input* keyword should not
be used. Each argument can be specified directly as a value, e.g. '6'
or '3.14159' or 'abc' (a string of characters). The type of each
argument is specified by the *format* keyword as explained below, so
that Python will know how to interpret the value. If the word SELF is
used for an argument it has a special meaning. A pointer is passed to
the Python function which it converts into a reference to LAMMPS
itself. This enables the function to call back to LAMMPS through its
library interface as explained below. This allows the Python function
to query or set values internal to LAMMPS which can affect the
subsequent execution of the input script. A LAMMPS variable can also
be used as an argument, specified as v_name, where "name" is the name
of the variable. Any style of LAMMPS variable can be used, as defined
by the :doc:`variable <variable>` command. Each time the Python
function is invoked, the LAMMPS variable is evaluated and its value is
passed to the Python function.
the Python function which it can convert into a reference to LAMMPS
itself using the :doc:`LAMMPS Python module <Python_module>`. This
enables the function to call back to LAMMPS through its library
interface as explained below. This allows the Python function to query
or set values internal to LAMMPS which can affect the subsequent
execution of the input script. A LAMMPS variable can also be used as an
argument, specified as v_name, where "name" is the name of the variable.
Any style of LAMMPS variable returning a scalar or a string can be used,
as defined by the :doc:`variable <variable>` command. The *format*
keyword must be used to set the type of data that is passed to Python.
Each time the Python function is invoked, the LAMMPS variable is
evaluated and its value is passed to the Python function.
The *return* keyword is only needed if the Python function returns a
value. The specified *varReturn* must be of the form v_name, where
@ -153,8 +183,9 @@ numeric or string value, as specified by the *format* keyword.
As explained on the :doc:`variable <variable>` doc page, the definition
of a python-style variable associates a Python function name with the
variable. This must match the *func* setting for this command. For
example these two commands would be self-consistent:
variable. This must match the *Python function name* first argument of
the *python* command. For example these two commands would be
consistent:
.. code-block:: LAMMPS
@ -163,21 +194,22 @@ example these two commands would be self-consistent:
The two commands can appear in either order in the input script so
long as both are specified before the Python function is invoked for
the first time.
the first time. Afterwards, the variable 'foo' is associated with
the Python function 'myMultiply'.
The *format* keyword must be used if the *input* or *return* keyword
is used. It defines an *fstring* with M characters, where M = sum of
The *format* keyword must be used if the *input* or *return* keywords
are used. It defines an *fstring* with M characters, where M = sum of
number of inputs and outputs. The order of characters corresponds to
the N inputs, followed by the return value (if it exists). Each
character must be one of the following: "i" for integer, "f" for
floating point, "s" for string, or "p" for SELF. Each character
defines the type of the corresponding input or output value of the
Python function and affects the type conversion that is performed
internally as data is passed back and forth between LAMMPS and Python.
Note that it is permissible to use a :doc:`python-style variable <variable>` in a LAMMPS command that allows for an
equal-style variable as an argument, but only if the output of the
Python function is flagged as a numeric value ("i" or "f") via the
*format* keyword.
floating point, "s" for string, or "p" for SELF. Each character defines
the type of the corresponding input or output value of the Python
function and affects the type conversion that is performed internally as
data is passed back and forth between LAMMPS and Python. Note that it
is permissible to use a :doc:`python-style variable <variable>` in a
LAMMPS command that allows for an equal-style variable as an argument,
but only if the output of the Python function is flagged as a numeric
value ("i" or "f") via the *format* keyword.
If the *return* keyword is used and the *format* keyword specifies the
output as a string, then the default maximum length of that string is
@ -192,12 +224,13 @@ truncated.
Either the *file*, *here*, or *exists* keyword must be used, but only
one of them. These keywords specify what Python code to load into the
Python interpreter. The *file* keyword gives the name of a file,
which should end with a ".py" suffix, which contains Python code. The
code will be immediately loaded into and run in the "main" module of
the Python interpreter. Note that Python code which contains a
function definition does not "execute" the function when it is run; it
simply defines the function so that it can be invoked later.
Python interpreter. The *file* keyword gives the name of a file
containing Python code, which should end with a ".py" suffix. The code
will be immediately loaded into and run in the "main" module of the
Python interpreter. The Python code will be executed in parallel on all
MPI processes. Note that Python code which contains a function
definition does not "execute" the function when it is run; it simply
defines the function so that it can be invoked later.
The *here* keyword does the same thing, except that the Python code
follows as a single argument to the *here* keyword. This can be done
@ -208,14 +241,15 @@ proper indentation, blank lines, and comments, as desired. See the
how triple quotes can be used as part of input script syntax.
The *exists* keyword takes no argument. It means that Python code
containing the required Python function defined by the *func* setting,
is assumed to have been previously loaded by another python command.
containing the required Python function with the given name has already
been executed, for example by a *python source* command or in the same
file that was used previously with the *file* keyword.
Note that the Python code that is loaded and run must contain a
function with the specified *func* name. To operate properly when
later invoked, the function code must match the *input* and
*return* and *format* keywords specified by the python command.
Otherwise Python will generate an error.
Note that the Python code that is loaded and run must contain a function
with the specified function name. To operate properly when later
invoked, the function code must match the *input* and *return* and
*format* keywords specified by the python command. Otherwise Python
will generate an error.
----------
@ -225,19 +259,19 @@ LAMMPS.
Whether you load Python code from a file or directly from your input
script, via the *file* and *here* keywords, the code can be identical.
It must be indented properly as Python requires. It can contain
comments or blank lines. If the code is in your input script, it
cannot however contain triple-quoted Python strings, since that will
conflict with the triple-quote parsing that the LAMMPS input script
performs.
comments or blank lines. If the code is in your input script, it cannot
however contain triple-quoted Python strings, since that will conflict
with the triple-quote parsing that the LAMMPS input script performs.
All the Python code you specify via one or more python commands is
loaded into the Python "main" module, i.e. __main__. The code can
define global variables or statements that are outside of function
definitions. It can contain multiple functions, only one of which
matches the *func* setting in the python command. This means you can
use the *file* keyword once to load several functions, and the
*exists* keyword thereafter in subsequent python commands to access
the other functions previously loaded.
loaded into the Python "main" module, i.e. ``__name__ == '__main__'``.
The code can define global variables, define global functions, define
classes or execute statements that are outside of function definitions.
It can contain multiple functions, only one of which matches the *func*
setting in the python command. This means you can use the *file*
keyword once to load several functions, and the *exists* keyword
thereafter in subsequent python commands to register the other functions
that were previously loaded with LAMMPS.
A Python function you define (or more generally, the code you load)
can import other Python modules or classes, it can make calls to other
@ -264,12 +298,13 @@ outside the function:
nvaluelast = nvalue
return nvalue
Nsteplast stores the previous timestep the function was invoked
(passed as an argument to the function). Nvaluelast stores the return
value computed on the last function invocation. If the function is
invoked again on the same timestep, the previous value is simply
returned, without re-computing it. The "global" statement inside the
Python function allows it to overwrite the global variables.
The variable 'nsteplast' stores the previous timestep the function was
invoked (passed as an argument to the function). The variable
'nvaluelast' stores the return value computed on the last function
invocation. If the function is invoked again on the same timestep, the
previous value is simply returned, without re-computing it. The
"global" statement inside the Python function allows it to overwrite the
global variables from within the local context of the function.
Note that if you load Python code multiple times (via multiple python
commands), you can overwrite previously loaded variables and functions
@ -285,19 +320,39 @@ copy of the Python function(s) you define. There is no connection
between the Python interpreters running on different processors.
This implies three important things.
First, if you put a print statement in your Python function, you will
see P copies of the output, when running on P processors. If the
prints occur at (nearly) the same time, the P copies of the output may
be mixed together. Welcome to the world of parallel programming and
debugging.
First, if you put a print or other statement creating output to the
screen in your Python function, you will see P copies of the output,
when running on P processors. If the prints occur at (nearly) the same
time, the P copies of the output may be mixed together. When loading
the LAMMPS Python module into the embedded Python interpreter, it is
possible to pass the pointer to the current LAMMPS class instance and
via the Python interface to the LAMMPS library interface, it is possible
to determine the MPI rank of the current process and thus adapt the
Python code so that output will only appear on MPI rank 0. The
following LAMMPS input demonstrates how this could be done. The text
'Hello, LAMMPS!' should be printed only once, even when running LAMMPS
in parallel.
Second, if your Python code loads modules that are not pre-loaded by
the Python library, then it will load the module from disk. This may
be a bottleneck if 1000s of processors try to load a module at the
same time. On some large supercomputers, loading of modules from disk
by Python may be disabled. In this case you would need to pre-build a
Python library that has the required modules pre-loaded and link
LAMMPS with that library.
.. code-block:: LAMMPS
python python_hello input 1 SELF format p here """
def python_hello(handle):
from lammps import lammps
lmp = lammps(ptr=handle)
me = lmp.extract_setting('world_rank')
if me == 0:
print('Hello, LAMMPS!')
"""
python python_hello invoke
If your Python code loads Python modules that are not pre-loaded by the
Python library, then it will load the module from disk. This may be a
bottleneck if 1000s of processors try to load a module at the same time.
On some large supercomputers, loading of modules from disk by Python may
be disabled. In this case you would need to pre-build a Python library
that has the required modules pre-loaded and link LAMMPS with that
library.
Third, if your Python code calls back to LAMMPS (discussed in the
next section) and causes LAMMPS to perform an MPI operation requires
@ -315,22 +370,21 @@ Python function is as follows:
.. code-block:: python
def foo(lmpptr,...):
def foo(handle,...):
from lammps import lammps
lmp = lammps(ptr=lmpptr)
lmp = lammps(ptr=handle)
lmp.command('print "Hello from inside Python"')
...
The function definition must include a variable (lmpptr in this case)
which corresponds to SELF in the python command. The first line of the
function imports the :doc:`"lammps" Python module <Python_module>`.
The second line creates a Python object ``lmp`` which
wraps the instance of LAMMPS that called the function. The "ptr=lmpptr"
argument is what makes that happen. The third line invokes the
command() function in the LAMMPS library interface. It takes a single
string argument which is a LAMMPS input script command for LAMMPS to
execute, the same as if it appeared in your input script. In this case,
LAMMPS should output
The function definition must include a variable ('handle' in this case)
which corresponds to SELF in the *python* command. The first line of
the function imports the :doc:`"lammps" Python module <Python_module>`.
The second line creates a Python object ``lmp`` which wraps the instance
of LAMMPS that called the function. The 'ptr=handle' argument is what
makes that happen. The third line invokes the command() function in the
LAMMPS library interface. It takes a single string argument which is a
LAMMPS input script command for LAMMPS to execute, the same as if it
appeared in your input script. In this case, LAMMPS should output
.. parsed-literal::
@ -344,8 +398,8 @@ The :doc:`Python_head` page describes the syntax
for how Python wraps the various functions included in the LAMMPS
library interface.
A more interesting example is in the examples/python/in.python script
which loads and runs the following function from examples/python/funcs.py:
A more interesting example is in the ``examples/python/in.python`` script
which loads and runs the following function from ``examples/python/funcs.py``:
.. code-block:: python
@ -495,24 +549,35 @@ Restrictions
""""""""""""
This command is part of the PYTHON package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Building LAMMPS with the PYTHON package will link LAMMPS with the
Python library on your system. Settings to enable this are in the
Building LAMMPS with the PYTHON package will link LAMMPS with the Python
library on your system. Settings to enable this are in the
lib/python/Makefile.lammps file. See the lib/python/README file for
information on those settings.
If you use Python code which calls back to LAMMPS, via the SELF input argument
explained above, there is an extra step required when building LAMMPS. LAMMPS
must also be built as a shared library and your Python function must be able to
load the :doc:`"lammps" Python module <Python_module>` that wraps the LAMMPS
library interface. These are the same steps required to use Python by itself
to wrap LAMMPS. Details on these steps are explained on the :doc:`Python
<Python_head>` doc page. Note that it is important that the stand-alone LAMMPS
executable and the LAMMPS shared library be consistent (built from the same
source code files) in order for this to work. If the two have been built at
If you use Python code which calls back to LAMMPS, via the SELF input
argument explained above, there is an extra step required when building
LAMMPS. LAMMPS must also be built as a shared library and your Python
function must be able to load the :doc:`"lammps" Python module
<Python_module>` that wraps the LAMMPS library interface. These are the
same steps required to use Python by itself to wrap LAMMPS. Details on
these steps are explained on the :doc:`Python <Python_head>` doc page.
Note that it is important that the stand-alone LAMMPS executable and the
LAMMPS shared library be consistent (built from the same source code
files) in order for this to work. If the two have been built at
different times using different source files, problems may occur.
Another limitation of calling back to Python from the LAMMPS module
using the *python* command in a LAMMPS input is that both, the Python
interpreter and LAMMPS, must be linked to the same Python runtime as a
shared library. If the Python interpreter is linked to Python
statically (which seems to happen with Conda) then loading the shared
LAMMPS library will create a second python "main" module that hides the
one from the Python interpreter and all previous defined function and
global variables will become invisible.
Related commands
""""""""""""""""

5
doc/utils/sphinx-config/false_positives.txt
View File

@ -2248,6 +2248,7 @@ MxN
myCompute
myIndex
mylammps
myMultiply
MyPool
mysocket
mySpin
@ -2473,7 +2474,7 @@ nsq
Nstart
nstats
Nstep
Nsteplast
nsteplast
Nstop
nsub
Nsw
@ -2503,7 +2504,7 @@ numpy
Numpy
Nurdin
Nvalue
Nvaluelast
nvaluelast
Nvalues
nvc
nvcc

12
examples/PACKAGES/pace/plugin/CMakeLists.txt
View File

@ -38,9 +38,15 @@ elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/lammps.ico
${CMAKE_SOURCE_DIR}/lammps-text-logo-wide.bmp ${CMAKE_SOURCE_DIR}/paceplugin.nsis ${CMAKE_BINARY_DIR})
if(BUILD_MPI)
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI paceplugin.nsis
DEPENDS paceplugin
BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}-MPI.exe)
if(USE_MSMPI)
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MSMPI paceplugin.nsis
DEPENDS paceplugin
BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}-MSMPI.exe)
else()
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI paceplugin.nsis
DEPENDS paceplugin
BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}-MPI.exe)
endif()
else()
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} paceplugin.nsis
COMMAND ${CMAKE_COMMAND} -E echo ${PWD}

107
examples/plugins/LAMMPSInterfaceCXX.cmake
View File

@ -45,45 +45,80 @@ if(BUILD_MPI)
set(MPI_CXX_SKIP_MPICXX TRUE)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
# Download and configure MinGW compatible MPICH development files for Windows
option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
if(USE_MSMPI)
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
else()
message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
else()
find_package(MPI REQUIRED)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)

108
src/ADIOS/dump_atom_adios.cpp
View File

@ -62,7 +62,11 @@ DumpAtomADIOS::DumpAtomADIOS(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp,
internal = new DumpAtomADIOSInternal();
try {
#if defined(MPI_STUBS)
internal->ad = new adios2::ADIOS("adios2_config.xml", adios2::DebugON);
#else
internal->ad = new adios2::ADIOS("adios2_config.xml", world, adios2::DebugON);
#endif
} catch (std::ios_base::failure &e) {
error->all(FLERR, "ADIOS initialization failed with error: {}", e.what());
}
@ -84,11 +88,19 @@ void DumpAtomADIOS::openfile()
if (multifile) {
// if one file per timestep, replace '*' with current timestep
auto filecurrent = utils::star_subst(filename, update->ntimestep, padflag);
#if defined(MPI_STUBS)
internal->fh = internal->io.Open(filecurrent, adios2::Mode::Write);
#else
internal->fh = internal->io.Open(filecurrent, adios2::Mode::Write, world);
#endif
if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filecurrent);
} else {
if (!singlefile_opened) {
#if defined(MPI_STUBS)
internal->fh = internal->io.Open(filename, adios2::Mode::Write);
#else
internal->fh = internal->io.Open(filename, adios2::Mode::Write, world);
#endif
if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filename);
singlefile_opened = 1;
}
@ -256,61 +268,63 @@ void DumpAtomADIOS::init_style()
else if (scale_flag == 0 && image_flag == 1)
pack_choice = &DumpAtomADIOS::pack_noscale_image;
/* Define the group of variables for the atom style here since it's a fixed
* set */
internal->io = internal->ad->DeclareIO(internal->ioName);
if (!internal->io.InConfigFile()) {
// if not defined by user, we can change the default settings
// BPFile is the default writer
internal->io.SetEngine("BPFile");
int num_aggregators = multiproc;
if (num_aggregators == 0) num_aggregators = 1;
auto nstreams = std::to_string(num_aggregators);
internal->io.SetParameters({{"substreams", nstreams}});
if (me == 0)
utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename,
nstreams);
}
/* Define the group of variables for the atom style here since it's a fixed set */
internal->io.DefineVariable<uint64_t>("ntimestep");
internal->io.DefineVariable<uint64_t>("natoms");
if (!internal->io) {
internal->io = internal->ad->DeclareIO(internal->ioName);
if (!internal->io.InConfigFile()) {
// if not defined by user, we can change the default settings
// BPFile is the default writer
internal->io.SetEngine("BPFile");
int num_aggregators = multiproc;
if (num_aggregators == 0) num_aggregators = 1;
auto nstreams = std::to_string(num_aggregators);
internal->io.SetParameters({{"substreams", nstreams}});
if (me == 0)
utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename,
nstreams);
}
internal->io.DefineVariable<int>("nprocs");
internal->io.DefineVariable<int>("ncolumns");
internal->io.DefineVariable<uint64_t>("ntimestep");
internal->io.DefineVariable<uint64_t>("natoms");
internal->io.DefineVariable<double>("boxxlo");
internal->io.DefineVariable<double>("boxxhi");
internal->io.DefineVariable<double>("boxylo");
internal->io.DefineVariable<double>("boxyhi");
internal->io.DefineVariable<double>("boxzlo");
internal->io.DefineVariable<double>("boxzhi");
internal->io.DefineVariable<int>("nprocs");
internal->io.DefineVariable<int>("ncolumns");
internal->io.DefineVariable<double>("boxxy");
internal->io.DefineVariable<double>("boxxz");
internal->io.DefineVariable<double>("boxyz");
internal->io.DefineVariable<double>("boxxlo");
internal->io.DefineVariable<double>("boxxhi");
internal->io.DefineVariable<double>("boxylo");
internal->io.DefineVariable<double>("boxyhi");
internal->io.DefineVariable<double>("boxzlo");
internal->io.DefineVariable<double>("boxzhi");
internal->io.DefineAttribute<int>("triclinic", domain->triclinic);
internal->io.DefineAttribute<int>("scaled", scale_flag);
internal->io.DefineAttribute<int>("image", image_flag);
internal->io.DefineVariable<double>("boxxy");
internal->io.DefineVariable<double>("boxxz");
internal->io.DefineVariable<double>("boxyz");
int *boundaryptr = reinterpret_cast<int *>(domain->boundary);
internal->io.DefineAttribute<int>("boundary", boundaryptr, 6);
internal->io.DefineAttribute<int>("triclinic", domain->triclinic);
internal->io.DefineAttribute<int>("scaled", scale_flag);
internal->io.DefineAttribute<int>("image", image_flag);
auto nColumns = static_cast<size_t>(size_one);
internal->io.DefineAttribute<std::string>("columns", columnNames.data(), nColumns);
internal->io.DefineAttribute<std::string>("columnstr", columns);
internal->io.DefineAttribute<std::string>("boundarystr", boundstr);
internal->io.DefineAttribute<std::string>("LAMMPS/dump_style", "atom");
internal->io.DefineAttribute<std::string>("LAMMPS/version", lmp->version);
internal->io.DefineAttribute<std::string>("LAMMPS/num_ver", std::to_string(lmp->num_ver));
int *boundaryptr = reinterpret_cast<int *>(domain->boundary);
internal->io.DefineAttribute<int>("boundary", boundaryptr, 6);
// local dimension variables
internal->io.DefineVariable<uint64_t>("nme", {adios2::LocalValueDim});
internal->io.DefineVariable<uint64_t>("offset", {adios2::LocalValueDim});
auto nColumns = static_cast<size_t>(size_one);
internal->io.DefineAttribute<std::string>("columns", columnNames.data(), nColumns);
internal->io.DefineAttribute<std::string>("columnstr", columns);
internal->io.DefineAttribute<std::string>("boundarystr", boundstr);
internal->io.DefineAttribute<std::string>("LAMMPS/dump_style", "atom");
internal->io.DefineAttribute<std::string>("LAMMPS/version", lmp->version);
internal->io.DefineAttribute<std::string>("LAMMPS/num_ver", std::to_string(lmp->num_ver));
// atom table size is not known at the moment
// it will be correctly defined at the moment of write
size_t UnknownSizeYet = 1;
internal->varAtoms = internal->io.DefineVariable<double>(
// local dimension variables
internal->io.DefineVariable<uint64_t>("nme", {adios2::LocalValueDim});
internal->io.DefineVariable<uint64_t>("offset", {adios2::LocalValueDim});
// atom table size is not known at the moment
// it will be correctly defined at the moment of write
size_t UnknownSizeYet = 1;
internal->varAtoms = internal->io.DefineVariable<double>(
"atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns});
}
}

12
src/ADIOS/dump_custom_adios.cpp
View File

@ -70,7 +70,11 @@ DumpCustomADIOS::DumpCustomADIOS(LAMMPS *lmp, int narg, char **arg) : DumpCustom
internal = new DumpCustomADIOSInternal();
try {
#if defined(MPI_STUBS)
internal->ad = new adios2::ADIOS("adios2_config.xml", adios2::DebugON);
#else
internal->ad = new adios2::ADIOS("adios2_config.xml", world, adios2::DebugON);
#endif
} catch (std::ios_base::failure &e) {
error->all(FLERR, "ADIOS initialization failed with error: {}", e.what());
}
@ -96,11 +100,19 @@ void DumpCustomADIOS::openfile()
if (multifile) {
// if one file per timestep, replace '*' with current timestep
auto filecurrent = utils::star_subst(filename, update->ntimestep, padflag);
#if defined(MPI_STUBS)
internal->fh = internal->io.Open(filecurrent, adios2::Mode::Write);
#else
internal->fh = internal->io.Open(filecurrent, adios2::Mode::Write, world);
#endif
if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filecurrent);
} else {
if (!singlefile_opened) {
#if defined(MPI_STUBS)
internal->fh = internal->io.Open(filename, adios2::Mode::Write);
#else
internal->fh = internal->io.Open(filename, adios2::Mode::Write, world);
#endif
if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filename);
singlefile_opened = 1;
}

8
src/ADIOS/reader_adios.cpp
View File

@ -82,7 +82,11 @@ ReaderADIOS::ReaderADIOS(LAMMPS *lmp) : Reader(lmp)
internal = new ReadADIOSInternal();
try {
#if defined(MPI_STUBS)
internal->ad = new adios2::ADIOS("adios2_config.xml", adios2::DebugON);
#else
internal->ad = new adios2::ADIOS("adios2_config.xml", world, adios2::DebugON);
#endif
} catch (std::ios_base::failure &e) {
error->one(FLERR, "ADIOS initialization failed with error: {}", e.what());
}
@ -134,7 +138,11 @@ void ReaderADIOS::open_file(const std::string &file)
if (internal->fh) internal->fh.Close();
try {
#if defined(MPI_STUBS)
internal->fh = internal->io.Open(file, adios2::Mode::Read);
#else
internal->fh = internal->io.Open(file, adios2::Mode::Read, world);
#endif
} catch (std::ios_base::failure &e) {
error->one(FLERR, "Error opening file {}: {}", file, e.what());
}

11
src/AMOEBA/amoeba_polar.cpp
View File

@ -250,10 +250,12 @@ void PairAmoeba::polar_real()
double drc3[3],drc5[3],drc7[3];
double urc3[3],urc5[3],tep[3];
double fix[3],fiy[3],fiz[3];
#if 0 // for poltyp TCG which is currently not supported
double uax[3],uay[3],uaz[3];
double ubx[3],uby[3],ubz[3];
double uaxp[3],uayp[3],uazp[3];
double ubxp[3],ubyp[3],ubzp[3];
#endif
double dmpi[9],dmpk[9];
double dmpik[9];
double bn[5];
@ -320,6 +322,7 @@ void PairAmoeba::polar_real()
uixp = uinp[i][0];
uiyp = uinp[i][1];
uizp = uinp[i][2];
#if 0 // for poltyp TCG which is currently not supported
for (m = 0; m < tcgnab; m++) {
uax[m] = uad[m][i][0];
uay[m] = uad[m][i][1];
@ -334,7 +337,7 @@ void PairAmoeba::polar_real()
ubyp[m] = ubp[m][i][1];
ubzp[m] = ubp[m][i][2];
}
#endif
if (amoeba) {
pdi = pdamp[itype];
pti = thole[itype];
@ -1030,7 +1033,8 @@ void PairAmoeba::polar_real()
// get the dtau/dr terms used for TCG polarization force
} else if (poltyp == TCG) {
/*
#if 0
// poltyp TCG not yet supported for AMOEBA/HIPPO
for (m = 0; m < tcgnab; m++) {
ukx = ubd[m][j][0];
uky = ubd[m][j][1];
@ -1131,8 +1135,7 @@ void PairAmoeba::polar_real()
frcx += depx;
frcy += depy;
frcz += depz;
}
*/
#endif
}
// increment force-based gradient on the interaction sites

2
src/ASPHERE/pair_ylz.cpp
View File

@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mehdi Baghaee (SUSTech)
Contributing author: Hongyan Yuan (SUSTech)
------------------------------------------------------------------------- */
#include "pair_ylz.h"

6
src/FEP/compute_fep.cpp
View File

@ -198,8 +198,12 @@ void ComputeFEP::init()
if (pert->which == PAIR) {
pairflag = 1;
Pair *pair = nullptr;
Pair *pair = force->pair_match(pert->pstyle, 1);
if (lmp->suffix_enable)
pair = force->pair_match(std::string(pert->pstyle)+"/"+lmp->suffix,1);
if (pair == nullptr) pair = force->pair_match(pert->pstyle,1);
if (pair == nullptr)
error->all(FLERR,
"compute fep pair style "

109
src/PYTHON/python_impl.cpp
View File

@ -112,37 +112,42 @@ PythonImpl::~PythonImpl()
void PythonImpl::command(int narg, char **arg)
{
if (narg < 2) error->all(FLERR, "Invalid python command");
if (narg < 2) utils::missing_cmd_args(FLERR, "python", error);
// if invoke is only keyword, invoke the previously defined function
if (narg == 2 && strcmp(arg[1], "invoke") == 0) {
int ifunc = find(arg[0]);
if (ifunc < 0) error->all(FLERR, "Python invoke of undefined function");
if (ifunc < 0) error->all(FLERR, "Python invoke of unknown function: {}", arg[0]);
char *str = nullptr;
if (pfuncs[ifunc].noutput) {
str = input->variable->pythonstyle(pfuncs[ifunc].ovarname, pfuncs[ifunc].name);
if (!str) error->all(FLERR, "Python variable does not match Python function");
if (!str)
error->all(FLERR,
"Python variable {} does not match variable {} "
"registered with Python function {}",
arg[0], pfuncs[ifunc].ovarname, pfuncs[ifunc].name);
}
invoke_function(ifunc, str);
return;
}
// if source is only keyword, execute the python code
// if source is only keyword, execute the python code in file
if (narg == 3 && strcmp(arg[1], "source") == 0) {
int err;
if ((narg > 1) && (strcmp(arg[0], "source") == 0)) {
int err = -1;
FILE *fp = fopen(arg[2], "r");
if (fp == nullptr)
if ((narg > 2) && (strcmp(arg[1], "here") == 0)) {
err = execute_string(arg[2]);
else
err = execute_file(arg[2]);
if (fp) fclose(fp);
if (err) error->all(FLERR, "Could not process Python source command");
} else {
if (platform::file_is_readable(arg[1]))
err = execute_file(arg[1]);
else
error->all(FLERR, "Could not open python source file {} for processing", arg[1]);
}
if (err) error->all(FLERR, "Failure in python source command");
return;
}
@ -162,48 +167,51 @@ void PythonImpl::command(int narg, char **arg)
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg], "input") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python input", error);
ninput = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (ninput < 0) error->all(FLERR, "Invalid python command");
if (ninput < 0) error->all(FLERR, "Invalid number of python input arguments: {}", ninput);
iarg += 2;
delete[] istr;
istr = new char *[ninput];
if (iarg + ninput > narg) error->all(FLERR, "Invalid python command");
if (iarg + ninput > narg) utils::missing_cmd_args(FLERR, "python input", error);
for (int i = 0; i < ninput; i++) istr[i] = arg[iarg + i];
iarg += ninput;
} else if (strcmp(arg[iarg], "return") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python return", error);
noutput = 1;
ostr = arg[iarg + 1];
iarg += 2;
} else if (strcmp(arg[iarg], "format") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python format", error);
format = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else if (strcmp(arg[iarg], "length") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python length", error);
length_longstr = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (length_longstr <= 0) error->all(FLERR, "Invalid python command");
if (length_longstr <= 0) error->all(FLERR, "Invalid python return value length");
iarg += 2;
} else if (strcmp(arg[iarg], "file") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python file", error);
delete[] pyfile;
pyfile = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else if (strcmp(arg[iarg], "here") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python here", error);
herestr = arg[iarg + 1];
iarg += 2;
} else if (strcmp(arg[iarg], "exists") == 0) {
existflag = 1;
iarg++;
} else
error->all(FLERR, "Invalid python command");
error->all(FLERR, "Unknown python command keyword: {}", arg[iarg]);
}
if (pyfile && herestr) error->all(FLERR, "Invalid python command");
if (pyfile && existflag) error->all(FLERR, "Invalid python command");
if (herestr && existflag) error->all(FLERR, "Invalid python command");
if (pyfile && herestr)
error->all(FLERR, "Must not use python 'file' and 'here' keywords at the same time");
if (pyfile && existflag)
error->all(FLERR, "Must not use python 'file' and 'exists' keywords at the same time");
if (herestr && existflag)
error->all(FLERR, "Must not use python 'here' and 'exists' keywords at the same time");
// create or overwrite entry in pfuncs vector with name = arg[0]
@ -221,23 +229,21 @@ void PythonImpl::command(int narg, char **arg)
if (fp == nullptr) {
PyUtils::Print_Errors();
error->all(FLERR, "Could not open Python file");
error->all(FLERR, "Could not open Python file: {}", pyfile);
}
int err = PyRun_SimpleFile(fp, pyfile);
if (err) {
PyUtils::Print_Errors();
error->all(FLERR, "Could not process Python file");
error->all(FLERR, "Could not process Python file: {}", pyfile);
}
fclose(fp);
} else if (herestr) {
int err = PyRun_SimpleString(herestr);
if (err) {
PyUtils::Print_Errors();
error->all(FLERR, "Could not process Python string");
error->all(FLERR, "Could not process Python string: {}", herestr);
}
}
@ -280,14 +286,17 @@ void PythonImpl::invoke_function(int ifunc, char *result)
int ninput = pfuncs[ifunc].ninput;
PyObject *pArgs = PyTuple_New(ninput);
if (!pArgs) { error->all(FLERR, "Could not create Python function arguments"); }
if (!pArgs)
error->all(FLERR, "Could not prepare arguments for Python function {}", pfuncs[ifunc].name);
for (int i = 0; i < ninput; i++) {
int itype = pfuncs[ifunc].itype[i];
if (itype == INT) {
if (pfuncs[ifunc].ivarflag[i]) {
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
if (!str) { error->all(FLERR, "Could not evaluate Python function input variable"); }
if (!str)
error->all(FLERR, "Could not evaluate Python function {} input variable: {}",
pfuncs[ifunc].name, pfuncs[ifunc].svalue[i]);
pValue = PY_INT_FROM_LONG(atoi(str));
} else {
pValue = PY_INT_FROM_LONG(pfuncs[ifunc].ivalue[i]);
@ -295,7 +304,9 @@ void PythonImpl::invoke_function(int ifunc, char *result)
} else if (itype == DOUBLE) {
if (pfuncs[ifunc].ivarflag[i]) {
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
if (!str) { error->all(FLERR, "Could not evaluate Python function input variable"); }
if (!str)
error->all(FLERR, "Could not evaluate Python function {} input variable: {}",
pfuncs[ifunc].name, pfuncs[ifunc].svalue[i]);
pValue = PyFloat_FromDouble(atof(str));
} else {
pValue = PyFloat_FromDouble(pfuncs[ifunc].dvalue[i]);
@ -303,7 +314,9 @@ void PythonImpl::invoke_function(int ifunc, char *result)
} else if (itype == STRING) {
if (pfuncs[ifunc].ivarflag[i]) {
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
if (!str) { error->all(FLERR, "Could not evaluate Python function input variable"); }
if (!str)
error->all(FLERR, "Could not evaluate Python function {} input variable: {}",
pfuncs[ifunc].name, pfuncs[ifunc].svalue[i]);
pValue = PY_STRING_FROM_STRING(str);
} else {
pValue = PY_STRING_FROM_STRING(pfuncs[ifunc].svalue[i]);
@ -311,7 +324,7 @@ void PythonImpl::invoke_function(int ifunc, char *result)
} else if (itype == PTR) {
pValue = PY_VOID_POINTER(lmp);
} else {
error->all(FLERR, "Unsupported variable type");
error->all(FLERR, "Unsupported variable type: {}", itype);
}
PyTuple_SetItem(pArgs, i, pValue);
}
@ -324,7 +337,7 @@ void PythonImpl::invoke_function(int ifunc, char *result)
if (!pValue) {
PyUtils::Print_Errors();
error->one(FLERR, "Python function evaluation failed");
error->one(FLERR, "Python evaluation of function {} failed", pfuncs[ifunc].name);
}
// function returned a value
@ -365,9 +378,9 @@ int PythonImpl::variable_match(const char *name, const char *varname, int numeri
{
int ifunc = find(name);
if (ifunc < 0) return -1;
if (pfuncs[ifunc].noutput == 0) return -1;
if (strcmp(pfuncs[ifunc].ovarname, varname) != 0) return -1;
if (numeric && pfuncs[ifunc].otype == STRING) return -1;
if (pfuncs[ifunc].noutput == 0) return -2;
if (strcmp(pfuncs[ifunc].ovarname, varname) != 0) return -3;
if (numeric && pfuncs[ifunc].otype == STRING) return -4;
return ifunc;
}
@ -400,9 +413,10 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon
pfuncs[ifunc].noutput = noutput;
if (!format && ninput + noutput)
error->all(FLERR, "Invalid python command");
error->all(FLERR, "Missing python format keyword");
else if (format && ((int) strlen(format) != ninput + noutput))
error->all(FLERR, "Invalid python command");
error->all(FLERR, "Input/output arguments ({}) and format characters ({}) are inconsistent",
(ninput + noutput), strlen(format));
// process inputs as values or variables
@ -448,7 +462,7 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon
if (strcmp(istr[i], "SELF") != 0) error->all(FLERR, "Invalid python command");
} else
error->all(FLERR, "Invalid python command");
error->all(FLERR, "Invalid python format character: {}", type);
}
// process output as value or variable
@ -465,7 +479,7 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon
else if (type == 's')
pfuncs[ifunc].otype = STRING;
else
error->all(FLERR, "Invalid python command");
error->all(FLERR, "Invalid python return format character: {}", type);
if (length_longstr) {
if (pfuncs[ifunc].otype != STRING)
@ -486,7 +500,9 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon
int PythonImpl::execute_string(char *cmd)
{
PyUtils::GIL lock;
return PyRun_SimpleString(cmd);
int err = PyRun_SimpleString(cmd);
if (err) PyUtils::Print_Errors();
return err;
}
/* ---------------------------------------------------------------------- */
@ -498,6 +514,7 @@ int PythonImpl::execute_file(char *fname)
PyUtils::GIL lock;
int err = PyRun_SimpleFile(fp, fname);
if (err) PyUtils::Print_Errors();
if (fp) fclose(fp);
return err;

351
src/REACTION/fix_bond_react.cpp
View File

@ -80,7 +80,7 @@ static const char cite_fix_bond_react[] =
#define DELTA 16
#define MAXGUESS 20 // max # of guesses allowed by superimpose algorithm
#define MAXCONARGS 14 // max # of arguments for any type of constraint + rxnID
#define NUMVARVALS 4 // max # of keyword values that have variables as input
#define NUMVARVALS 5 // max # of keyword values that have variables as input
// various statuses of superimpose algorithm:
// ACCEPT: site successfully matched to pre-reacted template
@ -98,7 +98,7 @@ enum{DISTANCE,ANGLE,DIHEDRAL,ARRHENIUS,RMSD,CUSTOM};
enum{ATOM,FRAG};
// keyword values that accept variables as input
enum{NEVERY,RMIN,RMAX,PROB};
enum{NEVERY,RMIN,RMAX,PROB,NRATE};
// flag for one-proc vs shared reaction sites
enum{LOCAL,GLOBAL};
@ -138,10 +138,15 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
status = PROCEED;
// reaction functions used by 'custom' constraint
nrxnfunction = 2;
nrxnfunction = 3;
rxnfunclist.resize(nrxnfunction);
peratomflag.resize(nrxnfunction);
rxnfunclist[0] = "rxnsum";
peratomflag[0] = 1;
rxnfunclist[1] = "rxnave";
peratomflag[1] = 1;
rxnfunclist[2] = "rxnbond";
peratomflag[2] = 0;
nvvec = 0;
ncustomvars = 0;
vvec = nullptr;
@ -224,8 +229,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(nghostlyskips,nreacts,"bond/react:nghostlyskips");
memory->create(seed,nreacts,"bond/react:seed");
memory->create(limit_duration,nreacts,"bond/react:limit_duration");
memory->create(rate_limit,3,nreacts,"bond/react:rate_limit");
memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
memory->create(custom_charges_fragid,nreacts,"bond/react:custom_charges_fragid");
memory->create(rescale_charges_flag,nreacts,"bond/react:rescale_charges_flag");
memory->create(create_atoms_flag,nreacts,"bond/react:create_atoms_flag");
memory->create(modify_create_fragid,nreacts,"bond/react:modify_create_fragid");
memory->create(overlapsq,nreacts,"bond/react:overlapsq");
@ -249,8 +256,11 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
fraction[i] = 1;
seed[i] = 12345;
max_rxn[i] = INT_MAX;
for (int j = 0; j < 3; j++)
rate_limit[j][i] = 0;
stabilize_steps_flag[i] = 0;
custom_charges_fragid[i] = -1;
rescale_charges_flag[i] = 0;
create_atoms_flag[i] = 0;
modify_create_fragid[i] = -1;
overlapsq[i] = 0;
@ -286,55 +296,31 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
if (groupid == -1) error->all(FLERR,"Could not find fix group ID");
groupbits[rxn] = group->bitmask[groupid];
if (strncmp(arg[iarg],"v_",2) == 0) {
const char *str = &arg[iarg][2];
var_id[NEVERY][rxn] = input->variable->find(str);
if (var_id[NEVERY][rxn] < 0)
error->all(FLERR,"Fix bond/react: Variable name {} does not exist", str);
if (!input->variable->equalstyle(var_id[NEVERY][rxn]))
error->all(FLERR,"Fix bond/react: Variable {} is not equal-style", str);
var_flag[NEVERY][rxn] = 1;
} else {
if (strncmp(arg[iarg],"v_",2) == 0) read_variable_keyword(&arg[iarg][2],NEVERY,rxn);
else {
nevery[rxn] = utils::inumeric(FLERR,arg[iarg],false,lmp);
if (nevery[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command: "
"'Nevery' must be a positive integer");
}
iarg++;
double cutoff;
if (strncmp(arg[iarg],"v_",2) == 0) {
const char *str = &arg[iarg][2];
var_id[RMIN][rxn] = input->variable->find(str);
if (var_id[RMIN][rxn] < 0)
error->all(FLERR,"Fix bond/react: Variable name {} does not exist", str);
if (!input->variable->equalstyle(var_id[RMIN][rxn]))
error->all(FLERR,"Fix bond/react: Variable {} is not equal-style", str);
double cutoff = input->variable->compute_equal(var_id[RMIN][rxn]);
cutsq[rxn][0] = cutoff*cutoff;
var_flag[RMIN][rxn] = 1;
} else {
double cutoff = utils::numeric(FLERR,arg[iarg],false,lmp);
read_variable_keyword(&arg[iarg][2],RMIN,rxn);
cutoff = input->variable->compute_equal(var_id[RMIN][rxn]);
} else cutoff = utils::numeric(FLERR,arg[iarg],false,lmp);
if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command: "
"'Rmin' cannot be negative");
cutsq[rxn][0] = cutoff*cutoff;
}
iarg++;
if (strncmp(arg[iarg],"v_",2) == 0) {
const char *str = &arg[iarg][2];
var_id[RMAX][rxn] = input->variable->find(str);
if (var_id[RMAX][rxn] < 0)
error->all(FLERR,"Fix bond/react: Variable name {} does not exist", str);
if (!input->variable->equalstyle(var_id[RMAX][rxn]))
error->all(FLERR,"Fix bond/react: Variable is {} not equal-style", str);
double cutoff = input->variable->compute_equal(var_id[RMAX][rxn]);
cutsq[rxn][1] = cutoff*cutoff;
var_flag[RMAX][rxn] = 1;
} else {
double cutoff = utils::numeric(FLERR,arg[iarg],false,lmp);
read_variable_keyword(&arg[iarg][2],RMAX,rxn);
cutoff = input->variable->compute_equal(var_id[RMAX][rxn]);
} else cutoff = utils::numeric(FLERR,arg[iarg],false,lmp);
if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command:"
"'Rmax' cannot be negative");
cutsq[rxn][1] = cutoff*cutoff;
}
iarg++;
unreacted_mol[rxn] = atom->find_molecule(arg[iarg++]);
@ -344,7 +330,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
if (reacted_mol[rxn] == -1) error->all(FLERR,"Reacted molecule template ID for "
"fix bond/react does not exist");
// read superimpose file
//read map file
files[rxn] = utils::strdup(arg[iarg]);
iarg++;
@ -354,14 +340,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
"'prob' keyword has too few arguments");
// check if probability is a variable
if (strncmp(arg[iarg+1],"v_",2) == 0) {
const char *str = &arg[iarg+1][2];
var_id[PROB][rxn] = input->variable->find(str);
if (var_id[PROB][rxn] < 0)
error->all(FLERR,"Fix bond/react: Variable name {} does not exist", str);
if (!input->variable->equalstyle(var_id[PROB][rxn]))
error->all(FLERR,"Fix bond/react: Variable {} is not equal-style", str);
read_variable_keyword(&arg[iarg+1][2],PROB,rxn);
fraction[rxn] = input->variable->compute_equal(var_id[PROB][rxn]);
var_flag[PROB][rxn] = 1;
} else {
// otherwise probability should be a number
fraction[rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
@ -380,6 +360,14 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: "
"'max_rxn' cannot be negative");
iarg += 2;
} else if (strcmp(arg[iarg],"rate_limit") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/react command: "
"'rate_limit' has too few arguments");
rate_limit[0][rxn] = 1; // serves as flag for rate_limit keyword
if (strncmp(arg[iarg+1],"v_",2) == 0) read_variable_keyword(&arg[iarg+1][2],NRATE,rxn);
else rate_limit[1][rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
rate_limit[2][rxn] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
iarg += 3;
} else if (strcmp(arg[iarg],"stabilize_steps") == 0) {
if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword "
"used without stabilization keyword");
@ -398,6 +386,13 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
"'custom_charges' keyword does not exist");
}
iarg += 2;
} else if (strcmp(arg[iarg],"rescale_charges") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
"'rescale_charges' has too few arguments");
if (strcmp(arg[iarg+1],"no") == 0) rescale_charges_flag[rxn] = 0; //default
else if (strcmp(arg[iarg+1],"yes") == 0) rescale_charges_flag[rxn] = 1;
else error->one(FLERR,"Bond/react: Illegal option for 'rescale_charges' keyword");
iarg += 2;
} else if (strcmp(arg[iarg],"molecule") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
"'molecule' has too few arguments");
@ -433,21 +428,24 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
}
max_natoms = 0; // the number of atoms in largest molecule template
max_rate_limit_steps = 0;
for (int myrxn = 0; myrxn < nreacts; myrxn++) {
twomol = atom->molecules[reacted_mol[myrxn]];
max_natoms = MAX(max_natoms,twomol->natoms);
max_rate_limit_steps = MAX(max_rate_limit_steps,rate_limit[2][myrxn]);
}
memory->create(equivalences,max_natoms,2,nreacts,"bond/react:equivalences");
memory->create(reverse_equiv,max_natoms,2,nreacts,"bond/react:reverse_equiv");
memory->create(edge,max_natoms,nreacts,"bond/react:edge");
memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
memory->create(store_rxn_count,max_rate_limit_steps,nreacts,"bond/react:store_rxn_count");
memory->create(custom_charges,max_natoms,nreacts,"bond/react:custom_charges");
memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms");
memory->create(create_atoms,max_natoms,nreacts,"bond/react:create_atoms");
memory->create(chiral_atoms,max_natoms,6,nreacts,"bond/react:chiral_atoms");
for (int j = 0; j < nreacts; j++)
for (int j = 0; j < nreacts; j++) {
for (int i = 0; i < max_natoms; i++) {
edge[i][j] = 0;
custom_charges[i][j] = 1; // update all partial charges by default
@ -462,6 +460,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
equivalences[i][m][j] = i+1;
}
}
for (int i = 0; i < max_rate_limit_steps; i++) {
store_rxn_count[i][j] = -1;
}
}
// read all map files afterward
for (int i = 0; i < nreacts; i++) {
@ -471,7 +473,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
onemol->check_attributes();
twomol->check_attributes();
get_molxspecials();
read(i);
read_map_file(i);
fclose(fp);
if (ncreate == 0 && onemol->natoms != twomol->natoms)
error->all(FLERR,"Fix bond/react: Reaction templates must contain the same number of atoms");
@ -598,6 +600,7 @@ FixBondReact::~FixBondReact()
memory->destroy(equivalences);
memory->destroy(reverse_equiv);
memory->destroy(landlocked_atoms);
memory->destroy(store_rxn_count);
memory->destroy(custom_charges);
memory->destroy(delete_atoms);
memory->destroy(create_atoms);
@ -617,8 +620,10 @@ FixBondReact::~FixBondReact()
memory->destroy(limit_duration);
memory->destroy(var_flag);
memory->destroy(var_id);
memory->destroy(rate_limit);
memory->destroy(stabilize_steps_flag);
memory->destroy(custom_charges_fragid);
memory->destroy(rescale_charges_flag);
memory->destroy(molecule_keyword);
memory->destroy(nconstraints);
memory->destroy(constraintstr);
@ -819,6 +824,16 @@ void FixBondReact::init_list(int /*id*/, NeighList *ptr)
void FixBondReact::post_integrate()
{
// update store_rxn_count on every step
for (int myrxn = 0; myrxn < nreacts; myrxn++) {
if (rate_limit[0][myrxn] == 1) {
for (int i = rate_limit[2][myrxn]-1; i > 0; i--) {
store_rxn_count[i][myrxn] = store_rxn_count[i-1][myrxn];
}
store_rxn_count[0][myrxn] = reaction_count_total[myrxn];
}
}
// check if any reactions could occur on this timestep
int nevery_check = 1;
for (int i = 0; i < nreacts; i++) {
@ -873,6 +888,8 @@ void FixBondReact::post_integrate()
for (int i = 0; i < nreacts; i++) {
nattempt[i] = 0;
}
// reset per-bond compute map flag
atoms2bondflag = 0;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
@ -911,8 +928,22 @@ void FixBondReact::post_integrate()
int j;
for (rxnID = 0; rxnID < nreacts; rxnID++) {
int rate_limit_flag = 1;
if (rate_limit[0][rxnID] == 1) {
int myrxn_count = store_rxn_count[rate_limit[2][rxnID]-1][rxnID];
if (myrxn_count == -1) rate_limit_flag = 0;
else {
int nrxns_delta = reaction_count_total[rxnID] - myrxn_count;
int my_nrate;
if (var_flag[NRATE][rxnID] == 1) {
my_nrate = input->variable->compute_equal(var_id[NRATE][rxnID]);
} else my_nrate = rate_limit[1][rxnID];
if (nrxns_delta > my_nrate) rate_limit_flag = 0;
}
}
if ((update->ntimestep % nevery[rxnID]) ||
(max_rxn[rxnID] <= reaction_count_total[rxnID])) continue;
(max_rxn[rxnID] <= reaction_count_total[rxnID]) ||
(rate_limit_flag == 0)) continue;
for (int ii = 0; ii < nall; ii++) {
partner[ii] = 0;
finalpartner[ii] = 0;
@ -1385,9 +1416,25 @@ void FixBondReact::superimpose_algorithm()
std::random_device rnd;
std::minstd_rand park_rng(rnd());
// check if we overstepped our reaction limit
// check if we overstepped our reaction limit, via either max_rxn or rate_limit
for (int i = 0; i < nreacts; i++) {
if (reaction_count_total[i] > max_rxn[i]) {
int overstep = 0;
int max_rxn_overstep = reaction_count_total[i] - max_rxn[i];
overstep = MAX(overstep,max_rxn_overstep);
if (rate_limit[0][i] == 1) {
int myrxn_count = store_rxn_count[rate_limit[2][i]-1][i];
if (myrxn_count != -1) {
int nrxn_delta = reaction_count_total[i] - myrxn_count;
int my_nrate;
if (var_flag[NRATE][i] == 1) {
my_nrate = input->variable->compute_equal(var_id[NRATE][i]);
} else my_nrate = rate_limit[1][i];
int rate_limit_overstep = nrxn_delta - my_nrate;
overstep = MAX(overstep,rate_limit_overstep);
}
}
if (overstep > 0) {
// let's randomly choose rxns to skip, unbiasedly from local and ghostly
int *local_rxncounts;
int *all_localskips;
@ -1395,8 +1442,11 @@ void FixBondReact::superimpose_algorithm()
memory->create(all_localskips,nprocs,"bond/react:all_localskips");
MPI_Gather(&local_rxn_count[i],1,MPI_INT,local_rxncounts,1,MPI_INT,0,world);
if (me == 0) {
int overstep = reaction_count_total[i] - max_rxn[i];
int delta_rxn = reaction_count[i] + ghostly_rxn_count[i];
// when using variable input for rate_limit, rate_limit_overstep could be > delta_rxn (below)
// we need to limit overstep to the number of reactions on this timestep
// essentially skipping all reactions, would be more efficient to use a skip_all flag
if (overstep > delta_rxn) overstep = delta_rxn;
int *rxn_by_proc;
memory->create(rxn_by_proc,delta_rxn,"bond/react:rxn_by_proc");
for (int j = 0; j < delta_rxn; j++)
@ -1414,14 +1464,15 @@ void FixBondReact::superimpose_algorithm()
else all_localskips[rxn_by_proc[j]]++;
}
memory->destroy(rxn_by_proc);
reaction_count_total[i] -= overstep;
}
reaction_count_total[i] = max_rxn[i];
MPI_Scatter(&all_localskips[0],1,MPI_INT,&nlocalskips[i],1,MPI_INT,0,world);
MPI_Bcast(&nghostlyskips[i],1,MPI_INT,0,world);
memory->destroy(local_rxncounts);
memory->destroy(all_localskips);
}
}
MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world);
// this updates topology next step
next_reneighbor = update->ntimestep;
@ -2118,7 +2169,7 @@ double FixBondReact::get_temperature(tagint **myglove, int row_offset, int col)
}
/* ----------------------------------------------------------------------
get per-atom variable names used by custom constraint
get per-atom variable names used by custom constraint
------------------------------------------------------------------------- */
void FixBondReact::customvarnames()
@ -2140,6 +2191,7 @@ void FixBondReact::customvarnames()
// find next reaction special function occurrence
pos1 = std::string::npos;
for (int i = 0; i < nrxnfunction; i++) {
if (peratomflag[i] == 0) continue;
pos = varstr.find(rxnfunclist[i],prev3+1);
if (pos == std::string::npos) continue;
if (pos < pos1) pos1 = pos;
@ -2261,12 +2313,67 @@ double FixBondReact::custom_constraint(const std::string& varstr)
}
/* ----------------------------------------------------------------------
currently two 'rxn' functions: rxnsum and rxnave
currently three 'rxn' functions: rxnsum, rxnave, and rxnbond
------------------------------------------------------------------------- */
double FixBondReact::rxnfunction(const std::string& rxnfunc, const std::string& varid,
const std::string& fragid)
{
int ifrag = -1;
if (fragid != "all") {
ifrag = onemol->findfragment(fragid.c_str());
if (ifrag < 0) error->one(FLERR,"Bond/react: Molecule fragment "
"in reaction special function does not exist");
}
// start with 'rxnbond' per-bond function
// for 'rxnbond', varid corresponds to 'compute bond/local' name,
// and fragid is a pre-reaction fragment containing the two atoms in the bond
if (rxnfunc == "rxnbond") {
int icompute,ibond,nsum;
double perbondval;
std::set<tagint> aset;
std::string computeid = varid;
std::map<std::set<tagint>,int>::iterator it;
if (computeid.substr(0,2) != "c_") error->one(FLERR,"Bond/react: Reaction special function compute "
"name should begin with 'c_'");
computeid = computeid.substr(2);
icompute = modify->find_compute(computeid);
if (icompute < 0) error->one(FLERR,"Bond/react: Reaction special function compute name does not exist");
cperbond = modify->compute[icompute];
std::string compute_style = cperbond->style;
if (compute_style != "bond/local") error->one(FLERR,"Bond/react: Compute used by reaction "
"special function 'rxnbond' must be of style 'bond/local'");
if (cperbond->size_local_cols > 0) error->one(FLERR,"Bond/react: 'Compute bond/local' used by reaction "
"special function 'rxnbond' must compute one value");
if (atoms2bondflag == 0) {
atoms2bondflag = 1;
get_atoms2bond(cperbond->groupbit);
}
nsum = 0;
for (int i = 0; i < onemol->natoms; i++) {
if (onemol->fragmentmask[ifrag][i]) {
aset.insert(glove[i][1]);
nsum++;
}
}
if (nsum != 2) error->one(FLERR,"Bond/react: Molecule fragment of reaction special function 'rxnbond' "
"must contain exactly two atoms");
if (cperbond->invoked_local != lmp->update->ntimestep)
cperbond->compute_local();
it = atoms2bond.find(aset);
if (it == atoms2bond.end()) error->one(FLERR,"Bond/react: Unable to locate bond referenced by "
"reaction special function 'rxnbond'");
ibond = it->second;
perbondval = cperbond->vector_local[ibond];
return perbondval;
}
int ivar = -1;
for (int i = 0; i < ncustomvars; i++) {
if (varid == customvarstrs[i]) {
@ -2280,13 +2387,6 @@ double FixBondReact::rxnfunction(const std::string& rxnfunc, const std::string&
error->one(FLERR,"Fix bond/react: Reaction special function variable "
"name does not exist");
int ifrag = -1;
if (fragid != "all") {
ifrag = onemol->findfragment(fragid.c_str());
if (ifrag < 0) error->one(FLERR,"Fix bond/react: Molecule fragment "
"in reaction special function does not exist");
}
int iatom;
int nsum = 0;
double sumvvec = 0;
@ -2313,6 +2413,39 @@ double FixBondReact::rxnfunction(const std::string& rxnfunc, const std::string&
return 0.0;
}
/* ----------------------------------------------------------------------
populate map to get bond index from atom IDs
------------------------------------------------------------------------- */
void FixBondReact::get_atoms2bond(int cgroupbit)
{
int i,m,atom1,atom2,btype,nb;
std::set<tagint> aset;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *mask = atom->mask;
m = 0;
atoms2bond.clear();
for (atom1 = 0; atom1 < nlocal; atom1++) {
if (!(mask[atom1] & cgroupbit)) continue;
nb = num_bond[atom1];
for (i = 0; i < nb; i++) {
btype = bond_type[atom1][i];
atom2 = atom->map(bond_atom[atom1][i]);
if (atom2 < 0 || !(mask[atom2] & cgroupbit)) continue;
if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
if (btype == 0) continue;
aset = {tag[atom1], tag[atom2]};
atoms2bond.insert(std::make_pair(aset,m++));
}
}
}
/* ----------------------------------------------------------------------
return handedness (1 or -1) of a chiral center, given ordered set of coordinates
------------------------------------------------------------------------- */
@ -2985,6 +3118,8 @@ void FixBondReact::update_everything()
}
delete [] iskip;
if (update_num_mega == 0) continue;
// if inserted atoms and global map exists, reset map now instead
// of waiting for comm since other pre-exchange fixes may use it
// invoke map_init() b/c atom count has grown
@ -3012,6 +3147,33 @@ void FixBondReact::update_everything()
}
}
// get charge rescale delta
double charge_rescale_addend = 0;
if (rescale_charges_flag[rxnID] == 1) {
double sim_total_charge = 0;
double mol_total_charge = 0;
int n_custom_charge = 0;
for (int i = 0; i < update_num_mega; i++) {
rxnID = update_mega_glove[0][i];
twomol = atom->molecules[reacted_mol[rxnID]];
for (int j = 0; j < twomol->natoms; j++) {
int jj = equivalences[j][1][rxnID]-1;
if (atom->map(update_mega_glove[jj+1][i]) >= 0 &&
atom->map(update_mega_glove[jj+1][i]) < nlocal) {
if (landlocked_atoms[j][rxnID] == 1)
type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j];
if (twomol->qflag && atom->q_flag && custom_charges[jj][rxnID] == 1) {
double *q = atom->q;
sim_total_charge += q[atom->map(update_mega_glove[jj+1][i])];
mol_total_charge += twomol->q[j];
n_custom_charge++;
}
}
}
}
charge_rescale_addend = (sim_total_charge-mol_total_charge)/n_custom_charge;
}
// update charges and types of landlocked atoms
for (int i = 0; i < update_num_mega; i++) {
rxnID = update_mega_glove[0][i];
@ -3024,7 +3186,7 @@ void FixBondReact::update_everything()
type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j];
if (twomol->qflag && atom->q_flag && custom_charges[jj][rxnID] == 1) {
double *q = atom->q;
q[atom->map(update_mega_glove[jj+1][i])] = twomol->q[j];
q[atom->map(update_mega_glove[jj+1][i])] = twomol->q[j]+charge_rescale_addend;
}
}
}
@ -3795,10 +3957,24 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
}
/* ----------------------------------------------------------------------
read superimpose file
add equal-style variable to keyword argument list
------------------------------------------------------------------------- */
void FixBondReact::read(int myrxn)
void FixBondReact::read_variable_keyword(const char *myarg, int keyword, int myrxn)
{
var_id[keyword][myrxn] = input->variable->find(myarg);
if (var_id[keyword][myrxn] < 0)
error->all(FLERR,"Fix bond/react: Variable name {} does not exist",myarg);
if (!input->variable->equalstyle(var_id[keyword][myrxn]))
error->all(FLERR,"Fix bond/react: Variable {} is not equal-style",myarg);
var_flag[keyword][myrxn] = 1;
}
/* ----------------------------------------------------------------------
read map file
------------------------------------------------------------------------- */
void FixBondReact::read_map_file(int myrxn)
{
char line[MAXLINE],keyword[MAXLINE];
char *eof,*ptr;
@ -4299,34 +4475,71 @@ void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf)
void FixBondReact::write_restart(FILE *fp)
{
int revision = 1;
set[0].nreacts = nreacts;
set[0].max_rate_limit_steps = max_rate_limit_steps;
for (int i = 0; i < nreacts; i++) {
set[i].reaction_count_total = reaction_count_total[i];
strncpy(set[i].rxn_name,rxn_name[i],MAXLINE-1);
set[i].rxn_name[MAXLINE-1] = '\0';
}
if (me == 0) {
int size = nreacts*sizeof(Set);
fwrite(&size,sizeof(int),1,fp);
fwrite(set,sizeof(Set),nreacts,fp);
int rbufcount = max_rate_limit_steps*nreacts;
int *rbuf;
if (rbufcount) {
memory->create(rbuf,rbufcount,"bond/react:rbuf");
memcpy(rbuf,&store_rxn_count[0][0],sizeof(int)*rbufcount);
}
if (me == 0) {
int size = nreacts*sizeof(Set)+(rbufcount+1)*sizeof(int);
fwrite(&size,sizeof(int),1,fp);
fwrite(&revision,sizeof(int),1,fp);
fwrite(set,sizeof(Set),nreacts,fp);
if (rbufcount) fwrite(rbuf,sizeof(int),rbufcount,fp);
}
if (rbufcount) memory->destroy(rbuf);
}
/* ----------------------------------------------------------------------
use selected state info from restart file to restart the Fix
bond/react restart revisions numbers added after LAMMPS version 3 Nov 2022
------------------------------------------------------------------------- */
void FixBondReact::restart(char *buf)
{
Set *set_restart = (Set *) buf;
for (int i = 0; i < set_restart[0].nreacts; i++) {
int n,revision,r_nreacts,r_max_rate_limit_steps,ibufcount,n2cpy;
int **ibuf;
n = 0;
if (lmp->restart_ver > utils::date2num("3 Nov 2022")) revision = buf[n++];
else revision = 0;
Set *set_restart = (Set *) &buf[n*sizeof(int)];
r_nreacts = set_restart[0].nreacts;
if (revision > 0) {
r_max_rate_limit_steps = set_restart[0].max_rate_limit_steps;
ibufcount = r_max_rate_limit_steps*r_nreacts;
memory->create(ibuf,r_max_rate_limit_steps,r_nreacts,"bond/react:ibuf");
memcpy(&ibuf[0][0],&buf[sizeof(int)+r_nreacts*sizeof(Set)],sizeof(int)*ibufcount);
n2cpy = r_max_rate_limit_steps;
} else n2cpy = 0;
if (max_rate_limit_steps < n2cpy) n2cpy = max_rate_limit_steps;
for (int i = 0; i < r_nreacts; i++) {
for (int j = 0; j < nreacts; j++) {
if (strcmp(set_restart[i].rxn_name,rxn_name[j]) == 0) {
reaction_count_total[j] = set_restart[i].reaction_count_total;
// read rate_limit restart information
for (int k = 0; k < n2cpy; k++)
store_rxn_count[k][j] = ibuf[k][i];
}
}
}
if (revision > 0) memory->destroy(ibuf);
}
/* ----------------------------------------------------------------------

26
src/REACTION/fix_bond_react.h
View File

@ -25,6 +25,10 @@ FixStyle(bond/react,FixBondReact);
#define LMP_FIX_BOND_REACT_H
#include "fix.h"
#include "compute.h"
#include <map>
#include <set>
namespace LAMMPS_NS {
@ -64,8 +68,11 @@ class FixBondReact : public Fix {
int stabilization_flag;
int reset_mol_ids_flag;
int custom_exclude_flag;
int **rate_limit;
int **store_rxn_count;
int *stabilize_steps_flag;
int *custom_charges_fragid;
int *rescale_charges_flag;
int *create_atoms_flag;
int *modify_create_fragid;
double *overlapsq;
@ -74,9 +81,11 @@ class FixBondReact : public Fix {
int *nconstraints;
char **constraintstr;
int nrxnfunction;
std::vector<std::string> rxnfunclist;
std::vector<std::string> rxnfunclist; // lists current special rxn function
std::vector<int> peratomflag; // 1 if special rxn function uses per-atom variable (vs. per-bond)
int atoms2bondflag; // 1 if atoms2bond map has been populated on this timestep
int narrhenius;
int **var_flag, **var_id; // for keyword values with variable inputs
int **var_flag, **var_id; // for keyword values with variable inputs
int status;
int *groupbits;
@ -86,6 +95,7 @@ class FixBondReact : public Fix {
int *reaction_count_total;
int nmax; // max num local atoms
int max_natoms; // max natoms in a molecule template
int max_rate_limit_steps; // max rate limit interval
tagint *partner, *finalpartner;
double **distsq;
int *nattempt;
@ -160,7 +170,8 @@ class FixBondReact : public Fix {
// but whose first neighbors haven't
int glove_counter; // used to determine when to terminate Superimpose Algorithm
void read(int);
void read_variable_keyword(const char *, int, int);
void read_map_file(int);
void EdgeIDs(char *, int);
void Equivalences(char *, int);
void DeleteAtoms(char *, int);
@ -184,6 +195,7 @@ class FixBondReact : public Fix {
double custom_constraint(const std::string &); // evaulate expression for custom constraint
double rxnfunction(const std::string &, const std::string &,
const std::string &); // eval rxn_sum and rxn_ave
void get_atoms2bond(int);
int get_chirality(double[12]); // get handedness given an ordered set of coordinates
void open(char *);
@ -198,16 +210,18 @@ class FixBondReact : public Fix {
void ghost_glovecast();
void update_everything();
int insert_atoms(tagint **, int);
void unlimit_bond();
void unlimit_bond(); // removes atoms from stabilization, and other post-reaction every-step operations
void limit_bond(int);
void dedup_mega_gloves(int); //dedup global mega_glove
void write_restart(FILE *) override;
void restart(char *buf) override;
// store restart data
struct Set {
int nreacts;
char rxn_name[MAXLINE];
int reaction_count_total;
int max_rate_limit_steps;
};
Set *set;
@ -221,7 +235,9 @@ class FixBondReact : public Fix {
int ncustomvars;
std::vector<std::string> customvarstrs;
int nvvec;
double **vvec; // per-atom vector to store variable constraint atom-style variable values
double **vvec; // per-atom vector to store custom constraint atom-style variable values
Compute *cperbond; // pointer to 'compute bond/local' used by custom constraint ('rxnbond' function)
std::map<std::set<tagint>, int> atoms2bond; // maps atom pair to index of local bond array
std::vector<std::vector<Constraint>> constraints;
// DEBUG

3
src/lammps.cpp
View File

@ -130,6 +130,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
version = (const char *) LAMMPS_VERSION;
num_ver = utils::date2num(version);
restart_ver = -1;
external_comm = 0;
mdicomm = nullptr;
@ -993,6 +994,8 @@ void LAMMPS::destroy()
delete python;
python = nullptr;
restart_ver = -1; // reset last restart version id
}
/* ----------------------------------------------------------------------

2
src/lammps.h
View File

@ -49,6 +49,8 @@ class LAMMPS {
// that is constructed so that will be greater
// for newer versions in numeric or string
// value comparisons
int restart_ver; // -1 or numeric version id of LAMMPS version in restart
// file, in case LAMMPS was initialized from a restart
//
MPI_Comm world; // MPI communicator
FILE *infile; // infile

2
src/read_restart.cpp
View File

@ -599,6 +599,8 @@ void ReadRestart::header()
if (flag == VERSION) {
char *version = read_string();
lmp->restart_ver = utils::date2num(version);
if (me == 0)
utils::logmesg(lmp," restart file = {}, LAMMPS = {}\n", version, lmp->version);
delete[] version;

2
src/respa.cpp
View File

@ -372,7 +372,7 @@ void Respa::setup(int flag)
mesg += fmt::format(" {}:{}", ilevel + 1, step[ilevel]);
mesg += "\n r-RESPA fixes :";
for (int l = 0; l < modify->n_post_force_respa_any; ++l) {
for (int l = 0; l < modify->n_post_force_respa; ++l) {
Fix *f = modify->get_fix_by_index(modify->list_post_force_respa[l]);
if (f->respa_level >= 0)
mesg += fmt::format(" {}:{}[{}]", MIN(f->respa_level + 1, nlevels), f->style, f->id);

17
src/variable.cpp
View File

@ -985,8 +985,21 @@ char *Variable::retrieve(const char *name)
str = data[ivar][1] = utils::strdup(result);
} else if (style[ivar] == PYTHON) {
int ifunc = python->variable_match(data[ivar][0],name,0);
if (ifunc < 0)
error->all(FLERR,"Python variable {} does not match Python function {}", name, data[ivar][0]);
if (ifunc < 0) {
if (ifunc == -1) {
error->all(FLERR, "Could not find Python function {} linked to variable {}",
data[ivar][0], name);
} else if (ifunc == -2) {
error->all(FLERR, "Python function {} for variable {} does not have a return value",
data[ivar][0], name);
} else if (ifunc == -3) {
error->all(FLERR,"Python variable {} does not match variable name registered with "
"Python function {}", name, data[ivar][0]);
} else {
error->all(FLERR, "Unknown error verifying function {} linked to python style variable {}",
data[ivar][0],name);
}
}
python->invoke_function(ifunc,data[ivar][1]);
str = data[ivar][1];
// if Python func returns a string longer than VALUELENGTH

2
tools/singularity/ubuntu18.04.def
View File

@ -5,7 +5,7 @@ From: ubuntu:18.04
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \

2
tools/singularity/ubuntu18.04_amd_rocm.def
View File

@ -45,7 +45,7 @@ From: ubuntu:18.04
###########################################################################
# Common Software
###########################################################################
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get install --no-install-recommends -y \
bc \

2
tools/singularity/ubuntu18.04_gpu.def
View File

@ -48,7 +48,7 @@ From: ubuntu:18.04
###########################################################################
# Common Software
###########################################################################
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get install --no-install-recommends -y \
bc \

2
tools/singularity/ubuntu18.04_intel_opencl.def
View File

@ -5,7 +5,7 @@ From: ubuntu:18.04
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \

2
tools/singularity/ubuntu18.04_nvidia.def
View File

@ -5,7 +5,7 @@ From: nvidia/cuda:11.6.2-devel-ubuntu18.04
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \

2
tools/singularity/ubuntu20.04.def
View File

@ -5,7 +5,7 @@ From: ubuntu:20.04
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \

2
tools/singularity/ubuntu20.04_amd_rocm.def
View File

@ -36,7 +36,7 @@ From: ubuntu:20.04
###########################################################################
# Common Software
###########################################################################
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get install --no-install-recommends -y \
bc \

2
tools/singularity/ubuntu20.04_gpu.def
View File

@ -39,7 +39,7 @@ From: ubuntu:20.04
# Common Software
###########################################################################
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get install --no-install-recommends -y \
bc \

2
tools/singularity/ubuntu20.04_intel_opencl.def
View File

@ -5,7 +5,7 @@ From: ubuntu:20.04
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \

2
tools/singularity/ubuntu20.04_nvidia.def
View File

@ -5,7 +5,7 @@ From: nvidia/cuda:11.6.2-devel-ubuntu20.04
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \

2
tools/singularity/ubuntu20.04_oneapi.def
View File

@ -5,7 +5,7 @@ From: ubuntu:20.04
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \

2
tools/singularity/ubuntu22.04.def
View File

@ -5,7 +5,7 @@ From: ubuntu:22.04
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common gpg gpg-agent
add-apt-repository ppa:openkim/latest
add-apt-repository ppa:openkim/latest -y
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \

5
unittest/formats/test_file_operations.cpp
View File

@ -303,6 +303,7 @@ TEST_F(FileOperationsTest, error_all_one)
TEST_F(FileOperationsTest, write_restart)
{
ASSERT_EQ(lmp->restart_ver, -1);
BEGIN_HIDE_OUTPUT();
command("echo none");
END_HIDE_OUTPUT();
@ -356,6 +357,7 @@ TEST_F(FileOperationsTest, write_restart)
BEGIN_HIDE_OUTPUT();
command("clear");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->restart_ver, -1);
ASSERT_EQ(lmp->atom->natoms, 0);
ASSERT_EQ(lmp->update->ntimestep, 0);
ASSERT_EQ(lmp->domain->triclinic, 0);
@ -369,18 +371,21 @@ TEST_F(FileOperationsTest, write_restart)
command("change_box all triclinic");
command("write_restart triclinic.restart");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->restart_ver, lmp->num_ver);
ASSERT_EQ(lmp->atom->natoms, 1);
ASSERT_EQ(lmp->update->ntimestep, 333);
ASSERT_EQ(lmp->domain->triclinic, 1);
BEGIN_HIDE_OUTPUT();
command("clear");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->restart_ver, -1);
ASSERT_EQ(lmp->atom->natoms, 0);
ASSERT_EQ(lmp->update->ntimestep, 0);
ASSERT_EQ(lmp->domain->triclinic, 0);
BEGIN_HIDE_OUTPUT();
command("read_restart triclinic.restart");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->restart_ver, lmp->num_ver);
ASSERT_EQ(lmp->atom->natoms, 1);
ASSERT_EQ(lmp->update->ntimestep, 333);
ASSERT_EQ(lmp->domain->triclinic, 1);

4
unittest/python/test_python_package.cpp
View File

@ -276,7 +276,7 @@ TEST_F(PythonPackageTest, RunSource)
{
// execute python script from file
auto output = CAPTURE_OUTPUT([&] {
command("python xyz source ${input_dir}/run.py");
command("python source ${input_dir}/run.py");
});
ASSERT_THAT(output, HasSubstr(LOREM_IPSUM));
@ -286,7 +286,7 @@ TEST_F(PythonPackageTest, RunSourceInline)
{
// execute inline python script
auto output = CAPTURE_OUTPUT([&] {
command("python xyz source \"\"\"\n"
command("python source here \"\"\"\n"
"from __future__ import print_function\n"
"print(2+2)\n"
"\"\"\"");