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Merge branch 'fix-mdi-aimd-enhance' of github.com:lammps/lammps into fix-mdi-aimd-enhance

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This commit is contained in:
Steve Plimpton
2022-06-30 11:17:19 -06:00
parent aebf53679e 373c719f4f
commit 8f524cde33
147 changed files with 3889 additions and 1233 deletions
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6
.github/dependabot.yml vendored Normal file
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@ -0,0 +1,6 @@
version: 2
updates:
- package-ecosystem: "github-actions"
directory: "/"
schedule:
interval: "weekly"

13
.github/workflows/codeql-analysis.yml vendored
View File

@ -13,6 +13,11 @@ jobs:
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
permissions:
security-events: write
actions: read
contents: read
strategy:
fail-fast: false
matrix:
@ -20,17 +25,17 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
fetch-depth: 2
- name: Setup Python
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: '3.x'
- name: Initialize CodeQL
uses: github/codeql-action/init@v1
uses: github/codeql-action/init@v2
with:
languages: ${{ matrix.language }}
config-file: ./.github/codeql/${{ matrix.language }}.yml
@ -48,4 +53,4 @@ jobs:
cmake --build . --parallel 2
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v1
uses: github/codeql-action/analyze@v2

4
.github/workflows/compile-msvc.yml vendored
View File

@ -15,12 +15,12 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
fetch-depth: 2
- name: Select Python version
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: '3.10'

4
.github/workflows/unittest-macos.yml vendored
View File

@ -17,7 +17,7 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
fetch-depth: 2
@ -28,7 +28,7 @@ jobs:
run: mkdir build
- name: Set up ccache
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ${{ env.CCACHE_DIR }}
key: macos-ccache-${{ github.sha }}

20
cmake/CMakeLists.txt
View File

@ -135,11 +135,13 @@ set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
endif()
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
@ -784,14 +786,16 @@ if(BUILD_SHARED_LIBS)
find_package(Python COMPONENTS Interpreter)
endif()
if(BUILD_IS_MULTI_CONFIG)
set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/$<CONFIG>/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)
else()
set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
set(MY_BUILD_DIR ${CMAKE_BINARY_DIR})
endif()
set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
if(Python_EXECUTABLE)
add_custom_target(
install-python ${CMAKE_COMMAND} -E remove_directory build
COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps -l ${LIBLAMMPS_SHARED_BINARY}
COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
-l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR}
COMMENT "Installing LAMMPS Python module")
else()
add_custom_target(

197
cmake/Modules/LAMMPSInterfacePlugin.cmake Normal file
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@ -0,0 +1,197 @@
# CMake script code to define LAMMPS settings required for building LAMMPS plugins
# enforce out-of-source build
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
"Please remove CMakeCache.txt and CMakeFiles first.")
endif()
# global LAMMPS/plugin build settings
set(LAMMPS_SOURCE_DIR "" CACHE PATH "Location of LAMMPS sources folder")
if(NOT LAMMPS_SOURCE_DIR)
message(FATAL_ERROR "Must set LAMMPS_SOURCE_DIR")
endif()
# by default, install into $HOME/.local (not /usr/local),
# so that no root access (and sudo) is needed
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
endif()
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
endif()
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# C++11 is required
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# Need -restrict with Intel compilers
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif()
set(CMAKE_POSITION_INDEPENDENT_CODE TRUE)
#######
# helper functions from LAMMPSUtils.cmake
function(validate_option name values)
string(TOLOWER ${${name}} needle_lower)
string(TOUPPER ${${name}} needle_upper)
list(FIND ${values} ${needle_lower} IDX_LOWER)
list(FIND ${values} ${needle_upper} IDX_UPPER)
if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
message(FATAL_ERROR "\n########################################################################\n"
"Invalid value '${${name}}' for option ${name}\n"
"\n"
"Possible values are:\n"
"${POSSIBLE_VALUE_LIST}"
"########################################################################")
endif()
endfunction(validate_option)
# helper function for getting the most recently modified file or folder from a glob pattern
function(get_newest_file path variable)
file(GLOB _dirs ${path})
set(_besttime 2000-01-01T00:00:00)
set(_bestfile "<unknown>")
foreach(_dir ${_dirs})
file(TIMESTAMP ${_dir} _newtime)
if(_newtime IS_NEWER_THAN _besttime)
set(_bestfile ${_dir})
set(_besttime ${_newtime})
endif()
endforeach()
if(_bestfile STREQUAL "<unknown>")
message(FATAL_ERROR "Could not find valid path at: ${path}")
endif()
set(${variable} ${_bestfile} PARENT_SCOPE)
endfunction()
#################################################################################
# LAMMPS C++ interface. We only need the header related parts except on windows.
add_library(lammps INTERFACE)
target_include_directories(lammps INTERFACE ${LAMMPS_SOURCE_DIR})
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
target_link_libraries(lammps INTERFACE ${CMAKE_BINARY_DIR}/../liblammps.dll.a)
endif()
################################################################################
# MPI configuration
if(NOT CMAKE_CROSSCOMPILING)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
option(BUILD_MPI "Build MPI version" OFF)
endif()
if(BUILD_MPI)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${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)
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")
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)
if(LAMMPS_LONGLONG_TO_LONG)
target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
endif()
endif()
target_link_libraries(lammps INTERFACE MPI::MPI_CXX)
else()
add_library(mpi_stubs INTERFACE)
target_include_directories(mpi_stubs INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_link_libraries(lammps INTERFACE mpi_stubs)
endif()
################################################################################
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
find_package(OpenMP QUIET)
if(OpenMP_FOUND)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
if(HAVE_OMP_H_INCLUDE)
set(BUILD_OMP_DEFAULT ON)
endif()
endif()
option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
if(BUILD_OMP)
find_package(OpenMP REQUIRED)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
if(NOT HAVE_OMP_H_INCLUDE)
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif()
if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
(CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4)
else()
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3)
endif()
target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX)
endif()
################
# integer size selection
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES})

4
cmake/Modules/Packages/MDI.cmake
View File

@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.3.2.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "836f5da400d8cff0f0e4435640f9454f" CACHE STRING "MD5 checksum for MDI tarball")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.1.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "f9505fccd4c79301a619f6452dad4ad9" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
enable_language(C)

5
cmake/Modules/Packages/ML-PACE.cmake
View File

@ -32,5 +32,6 @@ target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_
target_link_libraries(pace PRIVATE yaml-cpp-pace)
target_link_libraries(lammps PRIVATE pace)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE pace)
endif()

3
cmake/presets/mingw-cross.cmake
View File

@ -46,8 +46,8 @@ set(WIN_PACKAGES
MISC
ML-HDNNP
ML-IAP
ML-SNAP
ML-RANN
ML-SNAP
MOFFF
MOLECULE
MOLFILE
@ -56,6 +56,7 @@ set(WIN_PACKAGES
ORIENT
PERI
PHONON
PLUGIN
POEMS
PTM
QEQ

2
doc/Makefile
View File

@ -13,7 +13,7 @@ VENV = $(BUILDDIR)/docenv
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
MATHJAX = $(SPHINXCONFIG)/_static/mathjax
MATHJAXTAG = 3.2.1
MATHJAXTAG = 3.2.2
PYTHON = $(word 3,$(shell type python3))
DOXYGEN = $(word 3,$(shell type doxygen))

4
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "2 June 2022" "2022-6-2"
.TH LAMMPS "1" "23 June 2022" "2022-6-23"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 2 June 2022
\- Molecular Dynamics Simulator. Version 23 June 2022
.SH SYNOPSIS
.B lmp

2
doc/src/Commands_compute.rst
View File

@ -138,6 +138,8 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`smd/vol <compute_smd_vol>`
* :doc:`snap <compute_sna_atom>`
* :doc:`sna/atom <compute_sna_atom>`
* :doc:`sna/grid <compute_sna_atom>`
* :doc:`sna/grid/local <compute_sna_atom>`
* :doc:`snad/atom <compute_sna_atom>`
* :doc:`snav/atom <compute_sna_atom>`
* :doc:`sph/e/atom <compute_sph_e_atom>`

29
doc/src/Developer_plugins.rst
View File

@ -276,10 +276,27 @@ Compilation of the plugin can be managed via both, CMake or traditional
GNU makefiles. Some examples that can be used as a template are in the
``examples/plugins`` folder. The CMake script code has some small
adjustments to allow building the plugins for running unit tests with
them. Another example that converts the KIM package into a plugin can be
found in the ``examples/kim/plugin`` folder. No changes to the sources
of the KIM package themselves are needed; only the plugin interface and
loader code needs to be added. This example only supports building with
CMake, but is probably a more typical example. To compile you need to
run CMake with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>. Other
them.
Another example that converts the KIM package into a plugin can be found
in the ``examples/kim/plugin`` folder. No changes to the sources of the
KIM package themselves are needed; only the plugin interface and loader
code needs to be added. This example only supports building with CMake,
but is probably a more typical example. To compile you need to run CMake
with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>. Other
configuration setting are identical to those for compiling LAMMPS.
A second example for a plugin from a package is in the
``examples/PACKAGES/pace/plugin`` folder that will create a plugin from
the ML-PACE package. In this case the bulk of the code is in a static
external library that is being downloaded and compiled first and then
combined with the pair style wrapper and the plugin loader. This
example also contains a NSIS script that can be used to create an
Installer package for Windows (the mutual licensing terms of the
external library and LAMMPS conflict when distributing binaries, so the
ML-PACE package cannot be linked statically, but the LAMMPS headers
required to build the plugin are also available under a less restrictive
license). This will automatically set the required environment variable
and launching a (compatible) LAMMPS binary will load and register the
plugin and the ML-PACE package can then be used as it was linked into
LAMMPS.

6
doc/src/Errors_warnings.rst
View File

@ -470,6 +470,12 @@ This will most likely cause errors in kinetic fluctuations.
*More than one compute sna/atom*
Self-explanatory.
*More than one compute sna/grid*
Self-explanatory.
*More than one compute sna/grid/local*
Self-explanatory.
*More than one compute snad/atom*
Self-explanatory.

2
doc/src/Howto_mdi.rst
View File

@ -72,7 +72,7 @@ either a stand-alone code or a plugin library.
As explained on the `fix mdi/qm <fix_mdi_qm>` command doc page, it can
be used to perform *ab initio* MD simulations or energy minimizations,
or to evalute the quantum energy and forces for a series of
or to evaluate the quantum energy and forces for a series of
independent systems. The examples/mdi directory has example input
scripts for all of these use cases.

4
doc/src/Howto_structured_data.rst
View File

@ -184,7 +184,7 @@ frame.
.. code-block:: python
import re, yaml
import yaml
import pandas as pd
try:
@ -193,7 +193,7 @@ frame.
from yaml import SafeLoader as Loader
with open("ave.yaml") as f:
ave = yaml.load(docs, Loader=Loader)
ave = yaml.load(f, Loader=Loader)
keys = ave['keywords']
df = {}

6
doc/src/Packages_details.rst
View File

@ -657,7 +657,7 @@ advection-diffusion-reaction systems. The equations of motion of these
DPD extensions are integrated through a modified velocity-Verlet (MVV)
algorithm.
**Author:** Zhen Li (Division of Applied Mathematics, Brown University)
**Author:** Zhen Li (Department of Mechanical Engineering, Clemson University)
**Supporting info:**
@ -1479,7 +1479,7 @@ the :doc:`Build extras <Build_extras>` page.
* lib/mdi/README
* :doc:`Howto MDI <Howto_mdi>`
* :doc:`mdi <mdi>`
* :doc:`fix mdi/aimd <fix_mdi_aimd>`
* :doc:`fix mdi/qm <fix_mdi_qm>`
* examples/PACKAGES/mdi
----------
@ -1801,6 +1801,8 @@ computes which analyze attributes of the potential.
* src/ML-SNAP: filenames -> commands
* :doc:`pair_style snap <pair_snap>`
* :doc:`compute sna/atom <compute_sna_atom>`
* :doc:`compute sna/grid <compute_sna_atom>`
* :doc:`compute sna/grid/local <compute_sna_atom>`
* :doc:`compute snad/atom <compute_sna_atom>`
* :doc:`compute snav/atom <compute_sna_atom>`
* examples/snap

3
doc/src/Speed_measure.rst
View File

@ -42,5 +42,4 @@ inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile
LAMMPS, to obtain synchronized timings.
use the :doc:`timer sync <timer>` command to obtain synchronized timings.

17
doc/src/Tools.rst
View File

@ -95,7 +95,7 @@ Miscellaneous tools
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
* :ref:`Offline build tool <offline>`
* :ref:`singularity <singularity_tool>`
* :ref:`singularity/apptainer <singularity_tool>`
* :ref:`SWIG interface <swig>`
* :ref:`vim <vim>`
@ -1007,14 +1007,15 @@ Ivanov, at University of Iceland (ali5 at hi.is).
.. _singularity_tool:
singularity tool
----------------------------------------
singularity/apptainer tool
--------------------------
The singularity sub-directory contains container definitions files
that can be used to build container images for building and testing
LAMMPS on specific OS variants using the `Singularity <https://sylabs.io>`_
container software. Contributions for additional variants are welcome.
For more details please see the README.md file in that folder.
The singularity sub-directory contains container definitions files that
can be used to build container images for building and testing LAMMPS on
specific OS variants using the `Apptainer <https://apptainer.org>`_ or
`Singularity <https://sylabs.io>`_ container software. Contributions for
additional variants are welcome. For more details please see the
README.md file in that folder.
----------

2
doc/src/compute.rst
View File

@ -284,6 +284,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
* :doc:`snap <compute_sna_atom>` - gradients of SNAP energy and forces w.r.t. linear coefficients and related quantities for fitting SNAP potentials
* :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
* :doc:`sna/grid <compute_sna_atom>` - global array of bispectrum components on a regular grid
* :doc:`sna/grid/local <compute_sna_atom>` - local array of bispectrum components on a regular grid
* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum components for each atom
* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum components for each atom
* :doc:`sph/e/atom <compute_sph_e_atom>` - per-atom internal energy of Smooth-Particle Hydrodynamics atoms

61
doc/src/compute_ave_sphere_atom.rst
View File

@ -35,16 +35,24 @@ Examples
Description
"""""""""""
Define a computation that calculates the local density and temperature
for each atom and neighbors inside a spherical cutoff.
Define a computation that calculates the local mass density and
temperature for each atom based on its neighbors inside a spherical
cutoff. If an atom has M neighbors, then its local mass density is
calculated as the sum of its mass and its M neighbor masses, divided
by the volume of the cutoff sphere (or circle in 2d). The local
temperature of the atom is calculated as the temperature of the
collection of M+1 atoms, after subtracting the center-of-mass velocity
of the M+1 atoms from each of the M+1 atom's velocities. This is
effectively the thermal velocity of the neighborhood of the central
atom, similar to :doc:`compute temp/com <compute_temp_com>`.
The optional keyword *cutoff* defines the distance cutoff
used when searching for neighbors. The default value is the cutoff
specified by the pair style. If no pair style is defined, then a cutoff
must be defined using this keyword. If the specified cutoff is larger than
that of the pair_style plus neighbor skin (or no pair style is defined),
the *comm_modify cutoff* option must also be set to match that of the
*cutoff* keyword.
The optional keyword *cutoff* defines the distance cutoff used when
searching for neighbors. The default value is the cutoff specified by
the pair style. If no pair style is defined, then a cutoff must be
defined using this keyword. If the specified cutoff is larger than
that of the pair_style plus neighbor skin (or no pair style is
defined), the *comm_modify cutoff* option must also be set to match
that of the *cutoff* keyword.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
@ -55,16 +63,16 @@ too frequently.
If you have a bonded system, then the settings of
:doc:`special_bonds <special_bonds>` command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the :doc:`special_bonds <special_bonds>`
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the order parameter. This
difficulty can be circumvented by writing a dump file, and using the
:doc:`rerun <rerun>` command to compute the order parameter for
snapshots in the dump file. The rerun script can use a
:doc:`special_bonds <special_bonds>` command that includes all pairs in
the neighbor list.
interactions between atoms in the same bond, angle, or dihedral.
This is the default setting for the :doc:`special_bonds
<special_bonds>` command, and means those pairwise interactions do
not appear in the neighbor list. Because this compute uses the
neighbor list, it also means those pairs will not be included in
the order parameter. This difficulty can be circumvented by
writing a dump file, and using the :doc:`rerun <rerun>` command to
compute the order parameter for snapshots in the dump file. The
rerun script can use a :doc:`special_bonds <special_bonds>` command
that includes all pairs in the neighbor list.
----------
@ -77,17 +85,20 @@ too frequently.
Output info
"""""""""""
This compute calculates a per-atom array with two columns: density and temperature.
This compute calculates a per-atom array with two columns: mass
density in density :doc:`units <units>` and temperature in temperature
:doc:`units <units>`.
These values can be accessed by any command that uses per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
from a compute as input. See the :doc:`Howto output <Howto_output>`
doc page for an overview of LAMMPS output options.
Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This compute is part of the EXTRA-COMPUTE 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
""""""""""""""""
@ -97,5 +108,5 @@ Related commands
Default
"""""""
The option defaults are *cutoff* = pair style cutoff
The option defaults are *cutoff* = pair style cutoff.

77
doc/src/compute_sna_atom.rst
View File

@ -2,6 +2,8 @@
.. index:: compute snad/atom
.. index:: compute snav/atom
.. index:: compute snap
.. index:: compute sna/grid
.. index:: compute sna/grid/local
compute sna/atom command
========================
@ -15,6 +17,12 @@ compute snav/atom command
compute snap command
====================
compute sna/grid command
========================
compute sna/grid/local command
==============================
Syntax
""""""
@ -24,6 +32,9 @@ Syntax
compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID sna/grid nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID sna/grid/local nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* sna/atom = style name of this compute command
@ -32,6 +43,7 @@ Syntax
* twojmax = band limit for bispectrum components (non-negative integer)
* R_1, R_2,... = list of cutoff radii, one for each type (distance units)
* w_1, w_2,... = list of neighbor weights, one for each type
* nx, ny, nz = number of grid points in x, y, and z directions (positive integer)
* zero or more keyword/value pairs may be appended
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner*
@ -78,6 +90,7 @@ Examples
compute snap all snap 1.4 0.95 6 2.0 1.0
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1 sinner 1.35 1.6 dinner 0.25 0.3
compute bgrid all sna/grid/local 200 200 200 1.4 0.95 6 2.0 1.0
Description
"""""""""""
@ -212,6 +225,46 @@ command:
See section below on output for a detailed explanation of the data
layout in the global array.
The compute *sna/grid* and *sna/grid/local* commands calculate
bispectrum components for a regular grid of points.
These are calculated from the local density of nearby atoms *i'*
around each grid point, as if there was a central atom *i*
at the grid point. This is useful for characterizing fine-scale
structure in a configuration of atoms, and it is used
in the `MALA package <https://github.com/casus/mala>`_
to build machine-learning surrogates for finite-temperature Kohn-Sham
density functional theory (:ref:`Ellis et al. <Ellis2021>`)
Neighbor atoms not in the group do not contribute to the
bispectrum components of the grid points. The distance cutoff :math:`R_{ii'}`
assumes that *i* has the same type as the neighbor atom *i'*.
Compute *sna/grid* calculates a global array containing bispectrum
components for a regular grid of points.
The grid is aligned with the current box dimensions, with the
first point at the box origin, and forming a regular 3d array with
*nx*, *ny*, and *nz* points in the x, y, and z directions. For triclinic
boxes, the array is congruent with the periodic lattice vectors
a, b, and c. The array contains one row for each of the
:math:`nx \times ny \times nz` grid points, looping over the index for *ix* fastest,
then *iy*, and *iz* slowest. Each row of the array contains the *x*, *y*,
and *z* coordinates of the grid point, followed by the bispectrum
components. See section below on output for a detailed explanation of the data
layout in the global array.
Compute *sna/grid/local* calculates bispectrum components of a regular
grid of points similarly to compute *sna/grid* described above.
However, because the array is local, it contains only rows for grid points
that are local to the processor sub-domain. The global grid
of :math:`nx \times ny \times nz` points is still laid out in space the same as for *sna/grid*,
but grid points are strictly partitioned, so that every grid point appears in
one and only one local array. The array contains one row for each of the
local grid points, looping over the global index *ix* fastest,
then *iy*, and *iz* slowest. Each row of the array contains
the global indexes *ix*, *iy*, and *iz* first, followed by the *x*, *y*,
and *z* coordinates of the grid point, followed by the bispectrum
components. See section below on output for a detailed explanation of the data
layout in the global array.
The value of all bispectrum components will be zero for atoms not in
the group. Neighbor atoms not in the group do not contribute to the
bispectrum of atoms in the group.
@ -414,6 +467,21 @@ number of columns in the global array generated by *snap* are 31, and
931, respectively, while the number of rows is 1+3\*\ *N*\ +6, where *N*
is the total number of atoms.
Compute *sna/grid* evaluates a global array.
The array contains one row for each of the
:math:`nx \times ny \times nz` grid points, looping over the index for *ix* fastest,
then *iy*, and *iz* slowest. Each row of the array contains the *x*, *y*,
and *z* coordinates of the grid point, followed by the bispectrum
components.
Compute *sna/grid/local* evaluates a local array.
The array contains one row for each of the
local grid points, looping over the global index *ix* fastest,
then *iy*, and *iz* slowest. Each row of the array contains
the global indexes *ix*, *iy*, and *iz* first, followed by the *x*, *y*,
and *z* coordinates of the grid point, followed by the bispectrum
components.
If the *quadratic* keyword value is set to 1, then additional columns
are generated, corresponding to the products of all distinct pairs of
bispectrum components. If the number of bispectrum components is *K*,
@ -464,8 +532,7 @@ The optional keyword defaults are *rmin0* = 0,
.. _Thompson20141:
**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
available at `arXiv:1409.3880 <http://arxiv.org/abs/1409.3880>`_
**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316, (2015).
.. _Bartok20101:
@ -486,4 +553,8 @@ of Angular Momentum, World Scientific, Singapore (1987).
.. _Cusentino2020:
**(Cusentino)** Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
**(Cusentino)** Cusentino, Wood, Thompson, J Phys Chem A, 124, 5456, (2020)
.. _Ellis2021:
**(Ellis)** Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, Phys Rev B, 104, 035120, (2021)

16
doc/src/fix_mdi_qm.rst
View File

@ -57,9 +57,9 @@ explained below.
These are example use cases for this fix, discussed further below:
* perform an ab intitio MD (AIMD) simulation with quantum forces
* perform an energy minimziation with quantum forces
* perform a nudged elatic band (NEB) calculation with quantum forces
* perform an ab initio MD (AIMD) simulation with quantum forces
* perform an energy minimization with quantum forces
* perform a nudged elastic band (NEB) calculation with quantum forces
* perform a QM calculation for a series of independent systems which LAMMPS reads or generates
The code coupling performed by this command is done via the `MDI
@ -71,7 +71,7 @@ information about how LAMMPS can operate as either an MDI driver or
engine.
The examples/mdi directory contains input scripts using this fix in
the various use cases dicussed below. In each case, two instances of
the various use cases discussed below. In each case, two instances of
LAMMPS are used, once as an MDI driver, once as an MDI engine
(surrogate for a QM code). The examples/mdi/README file explains how
to launch two codes so that they communicate via the MDI library using
@ -141,7 +141,7 @@ directory. See its README file for more details.
(1) To run an ab initio MD (AIMD) dynamics simulation, or an energy
minimization with QM forces, or a multi-replica NEB calculation, use
*add yes* and *every 1* (the defaults). This is so that every time
LAMMPS needs energy and forces, the QM code will be invoked.
LAMMPS needs energy and forces, the QM code will be invoked.
Both LAMMPS and the QM code should define the same system (simulation
box, atoms and their types) in their respective input scripts. Note
@ -157,7 +157,7 @@ atom coordinates. The engine code computes quantum forces on each
atom and the total energy of the system and returns them to LAMMPS.
Note that if the AIMD simulation is an NPT or NPH model, or the energy
minimization includesf :doc:`fix box relax <fix_box_relaxq>` to
minimization includes :doc:`fix box relax <fix_box_relax>` to
equilibrate the box size/shape, then LAMMPS computes a pressure. This
means the *virial* keyword should be set to *yes* so that the QM
contribution to the pressure can be included.
@ -172,7 +172,7 @@ atom coordinates and QM forces to a file. Likewise the QM energy and
virial could be output with the :doc:`thermo_style custom
<thermo_style>` command.
(3) To do a QM evaulation of energy and forces for a series of *N*
(3) To do a QM evaluation of energy and forces for a series of *N*
independent systems (simulation box and atoms), use *add no* and
*every 1*. Write a LAMMPS input script which loops over the *N*
systems. See the :doc:`Howto multiple <Howto_multiple>` doc page for
@ -180,7 +180,7 @@ details on looping and removing old systems. The series of systems
could be initialized by reading them from data files with
:doc:`read_data <read_data>` commands. Or, for example, by using the
:doc:`lattice <lattice>` , :doc:`create_atoms <create_atoms>`,
:doc:`delete_atoms <deletea_atoms>`, and/or :doc:`displace_atoms
:doc:`delete_atoms <delete_atoms>`, and/or :doc:`displace_atoms
random <displace_atoms>` commands to generate a series of different
systems. At the end of the loop perform :doc:`run 0 <run>` and
:doc:`write_dump <write_dump>` commands to invoke the QM code and

4
doc/src/kspace_style.rst
View File

@ -129,8 +129,8 @@ Examples
kspace_style pppm 1.0e-4
kspace_style pppm/cg 1.0e-5 1.0e-6
kspace style msm 1.0e-4
kspace style scafacos fmm 1.0e-4
kspace_style msm 1.0e-4
kspace_style scafacos fmm 1.0e-4
kspace_style none
Used in input scripts:

8
doc/src/mdi.rst
View File

@ -326,15 +326,15 @@ able to initiate and terminate the connection to the engine code.
The only current MDI driver command in LAMMPS is the :doc:`fix mdi/qm
<fix_mdi_qm>` command. If it is only used once in an input script
then it can initiate and terminate the connection. But if it is being
issuedd multiple times, e.g. in a loop that issues a :doc:`clear
<clear>` command, then it cannot initiate/terminate the connection
issued multiple times, e.g. in a loop that issues a :doc:`clear
<clear>` command, then it cannot initiate or terminate the connection
multiple times. Instead, the *mdi connect* and *mdi exit* commands
should be used outside the loop to intiate/terminate the connection.
should be used outside the loop to initiate or terminate the connection.
See the examples/mdi/in.series.driver script for an example of how
this is done. The LOOP in that script is reading a series of data
file configurations and passing them to an MDI engine (e.g. quantum
code) for enery and force evaluation. A *clear* command inside the
code) for energy and force evaluation. A *clear* command inside the
loop wipes out the current system so a new one can be defined. This
operation also destroys all fixes. So the :doc:`fix mdi/qm
<fix_mdi_qm>` command is issued once per loop iteration. Note that it

91
doc/src/pair_e3b.rst
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@ -50,6 +50,12 @@ Examples
pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5
pair_coeff * * e3b preset 2011
Used in example input script:
.. parsed-literal::
examples/PACKAGES/e3b/in.e3b-tip4p2005
Description
"""""""""""
@ -68,21 +74,27 @@ The *e3b* style computes an \"explicit three-body\" (E3B) potential for water :r
0 & r>R_f\\
\end{cases}
This potential was developed as a water model that includes the three-body cooperativity of hydrogen bonding explicitly.
To use it in this way, it must be applied in conjunction with a conventional two-body water model, through *pair_style hybrid/overlay*.
The three body interactions are split into three types: A, B, and C.
Type A corresponds to anti-cooperative double hydrogen bond donor interactions.
Type B corresponds to the cooperative interaction of molecules that both donate and accept a hydrogen bond.
Type C corresponds to anti-cooperative double hydrogen bond acceptor interactions.
The three-body interactions are smoothly cutoff by the switching function s(r) between Rs and Rc3.
The two-body interactions are designed to correct for the effective many-body interactions implicitly included in the conventional two-body potential.
The two-body interactions are cut off sharply at Rc2, because K3 is typically significantly smaller than K2.
See :ref:`(Kumar 2008) <Kumar>` for more details.
This potential was developed as a water model that includes the
three-body cooperativity of hydrogen bonding explicitly. To use it in
this way, it must be applied in conjunction with a conventional two-body
water model, through pair style :doc:`hybrid/overlay <pair_hybrid>`. The
three body interactions are split into three types: A, B, and C. Type A
corresponds to anti-cooperative double hydrogen bond donor interactions.
Type B corresponds to the cooperative interaction of molecules that both
donate and accept a hydrogen bond. Type C corresponds to
anti-cooperative double hydrogen bond acceptor interactions. The
three-body interactions are smoothly cutoff by the switching function
s(r) between Rs and Rc3. The two-body interactions are designed to
correct for the effective many-body interactions implicitly included in
the conventional two-body potential. The two-body interactions are cut
off sharply at Rc2, because K3 is typically significantly smaller than
K2. See :ref:`(Kumar 2008) <Kumar>` for more details.
Only a single *pair_coeff* command is used with the *e3b* style.
The first two arguments must be \* \*.
The oxygen atom type for the pair style is passed as the only argument to the *pair_style* command, not in the *pair_coeff* command.
The hydrogen atom type is inferred by the ordering of the atoms.
Only a single :doc:`pair_coeff <pair_coeff>` command is used with the
*e3b* style and the first two arguments must be \* \*. The oxygen atom
type for the pair style is passed as the only argument to the
*pair_style* command, not in the *pair_coeff* command. The hydrogen
atom type is inferred from the ordering of the atoms.
.. note::
@ -90,26 +102,41 @@ The hydrogen atom type is inferred by the ordering of the atoms.
Each water molecule must have consecutive IDs with the oxygen first.
This pair style does not test that this criteria is met.
The *pair_coeff* command must have at least one keyword/value pair, as described above.
The *preset* keyword sets the potential parameters to the values used in :ref:`(Tainter 2011) <Tainter2011>` or :ref:`(Tainter 2015) <Tainter2015>`.
To use the water models defined in those references, the *e3b* style should always be used in conjunction with an *lj/cut/tip4p/long* style through *pair_style hybrid/overlay*, as demonstrated in the second example above.
The *preset 2011* option should be used with the :doc:`TIP4P water model <Howto_tip4p>`.
The *preset 2015* option should be used with the :doc:`TIP4P/2005 water model <Howto_tip4p>`.
If the *preset* keyword is used, no other keyword is needed.
Changes to the preset parameters can be made by specifying the *preset* keyword followed by the specific parameter to change, like *Ea*\ .
Note that the other keywords must come after *preset* in the pair_style command.
The *e3b* style can also be used to implement any three-body potential of the same form by specifying all the keywords except *neigh*\ : *Ea*, *Eb*, *Ec*, *E2*, *K3*, *K2*, *Rc3*, *Rc2*, *Rs*, and *bondL*\ .
The keyword *bondL* specifies the intramolecular OH bond length of the water model being used.
This is needed to include H atoms that are within the cutoff even when the attached oxygen atom is not.
The *pair_coeff* command must have at least one keyword/value pair, as
described above. The *preset* keyword sets the potential parameters to
the values used in :ref:`(Tainter 2011) <Tainter2011>` or
:ref:`(Tainter 2015) <Tainter2015>`. To use the water models defined in
those references, the *e3b* style should always be used in conjunction
with an *lj/cut/tip4p/long* style through *pair_style hybrid/overlay*,
as demonstrated in the second example above. The *preset 2011* option
should be used with the :doc:`TIP4P water model <Howto_tip4p>`. The
*preset 2015* option should be used with the :doc:`TIP4P/2005 water
model <Howto_tip4p>`. If the *preset* keyword is used, no other keyword
is needed. Changes to the preset parameters can be made by specifying
the *preset* keyword followed by the specific parameter to change, like
*Ea*\ . Note that the other keywords must come after *preset* in the
pair_style command. The *e3b* style can also be used to implement any
three-body potential of the same form by specifying all the keywords
except *neigh*\ : *Ea*, *Eb*, *Ec*, *E2*, *K3*, *K2*, *Rc3*, *Rc2*,
*Rs*, and *bondL*\ . The keyword *bondL* specifies the intramolecular
OH bond length of the water model being used. This is needed to include
H atoms that are within the cutoff even when the attached oxygen atom is
not.
This pair style allocates arrays sized according to the number of pairwise interactions within Rc3.
To do this it needs an estimate for the number of water molecules within Rc3 of an oxygen atom.
This estimate defaults to 10 and can be changed using the *neigh* keyword, which takes an integer as an argument.
If the neigh setting is too small, the simulation will fail with the error "neigh is too small".
If the neigh setting is too large, the pair style will use more memory than necessary.
This pair style allocates arrays sized according to the number of
pairwise interactions within Rc3. To do this it needs an estimate for
the number of water molecules within Rc3 of an oxygen atom. This
estimate defaults to 10 and can be changed using the *neigh* keyword,
which takes an integer as an argument. If the neigh setting is too
small, the simulation will fail with the error "neigh is too small". If
the neigh setting is too large, the pair style will use more memory than
necessary.
This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 4.
The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term.
This pair style tallies a breakdown of the total E3B potential energy
into sub-categories, which can be accessed via the :doc:`compute pair
<compute_pair>` command as a vector of values of length 4. The 4 values
correspond to the terms in the first equation above: the E2 term, the Ea
term, the Eb term, and the Ec term.
See the examples/PACKAGES/e3b directory for a complete example script.

4
doc/src/pair_sw_angle_table.rst
View File

@ -23,9 +23,9 @@ Examples
Used in example input script:
.. parsed-literal::
.. parsed-literal::
examples/PACKAGES/manybody_table/in.spce_sw
examples/PACKAGES/manybody_table/in.spce_sw
Description

6
doc/src/pair_threebody_table.rst
View File

@ -27,10 +27,10 @@ Examples
Used in example input scripts:
.. parsed-literal::
.. parsed-literal::
examples/PACKAGES/manybody_table/in.spce
examples/PACKAGES/manybody_table/in.spce2
examples/PACKAGES/manybody_table/in.spce
examples/PACKAGES/manybody_table/in.spce2
Description
"""""""""""

4
doc/src/read_data.rst
View File

@ -56,7 +56,7 @@ Examples
read_data ../run7/data.polymer.gz
read_data data.protein fix mycmap crossterm CMAP
read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
read_data data.water add merge 1 group solvent
read_data data.water add merge group solvent
Description
"""""""""""
@ -622,6 +622,8 @@ of analysis.
- atom-ID molecule-ID atom-type x y z
* - charge
- atom-ID atom-type q x y z
* - dielectric
- atom-ID atom-type q x y z normx normy normz area ed em epsilon curvature
* - dipole
- atom-ID atom-type q x y z mux muy muz
* - dpd

102
doc/src/read_restart.rst
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@ -11,7 +11,6 @@ Syntax
read_restart file flag
* file = name of binary restart file to read in
* flag = remap (optional)
Examples
""""""""
@ -19,44 +18,40 @@ Examples
.. code-block:: LAMMPS
read_restart save.10000
read_restart save.10000 remap
read_restart restart.*
read_restart restart.*.mpiio
read_restart poly.*.% remap
Description
"""""""""""
Read in a previously saved system configuration from a restart file.
This allows continuation of a previous run. Details about what
information is stored (and not stored) in a restart file is given
below. Basically this operation will re-create the simulation box
with all its atoms and their attributes as well as some related global
settings, at the point in time it was written to the restart file by a
previous simulation. The simulation box will be partitioned into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors in the current simulation and the settings of the
information is stored (and not stored) in a restart file is given below.
Basically this operation will re-create the simulation box with all its
atoms and their attributes as well as some related global settings, at
the point in time it was written to the restart file by a previous
simulation. The simulation box will be partitioned into a regular 3d
grid of rectangular bricks, one per processor, based on the number of
processors in the current simulation and the settings of the
:doc:`processors <processors>` command. The partitioning can later be
changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
.. note::
Normally, restart files are written by the
:doc:`restart <restart>` or :doc:`write_restart <write_restart>` commands
so that all atoms in the restart file are inside the simulation box.
If this is not the case, the read_restart command will print an error
that atoms were "lost" when the file is read. This error should be
reported to the LAMMPS developers so the invalid writing of the
restart file can be fixed. If you still wish to use the restart file,
the optional *remap* flag can be appended to the read_restart command.
This should avoid the error, by explicitly remapping each atom back
into the simulation box, updating image flags for the atom
appropriately.
changed by the :doc:`balance <balance>` or :doc:`fix balance
<fix_balance>` commands.
Restart files are saved in binary format to enable exact restarts,
meaning that the trajectories of a restarted run will precisely match
those produced by the original run had it continued on.
The binary restart file format was not designed with backward, forward,
or cross-platform compatibility in mind, so the files are only expected
to be read correctly by the same LAMMPS executable on the same platform.
Changes to the architecture, compilation settings, or LAMMPS version can
render a restart file unreadable or it may read the data incorrectly.
If you want a more portable format, you can use the data file format as
created by the :doc:`write_data <write_data>` command. Binary restart
files can also be converted into a data file from the command line by
the LAMMPS executable that wrote them using the :ref:`-restart2data
<restart2data>` command line flag.
Several things can prevent exact restarts due to round-off effects, in
which case the trajectories in the 2 runs will slowly diverge. These
include running on a different number of processors or changing
@ -65,7 +60,8 @@ certain settings such as those set by the :doc:`newton <newton>` or
these cases.
Certain fixes will not restart exactly, though they should provide
statistically similar results. These include :doc:`fix shake <fix_shake>` and :doc:`fix langevin <fix_langevin>`.
statistically similar results. These include :doc:`fix shake
<fix_shake>` and :doc:`fix langevin <fix_langevin>`.
Certain pair styles will not restart exactly, though they should
provide statistically similar results. This is because the forces
@ -81,18 +77,19 @@ produced the restart file, it could be a LAMMPS bug, so consider
:doc:`reporting it <Errors_bugs>` if you think the behavior is a bug.
Because restart files are binary, they may not be portable to other
machines. In this case, you can use the :doc:`-restart command-line switch <Run_options>` to convert a restart file to a data file.
machines. In this case, you can use the :doc:`-restart command-line
switch <Run_options>` to convert a restart file to a data file.
Similar to how restart files are written (see the
:doc:`write_restart <write_restart>` and :doc:`restart <restart>`
commands), the restart filename can contain two wild-card characters.
If a "\*" appears in the filename, the directory is searched for all
filenames that match the pattern where "\*" is replaced with a timestep
value. The file with the largest timestep value is read in. Thus,
this effectively means, read the latest restart file. It's useful if
you want your script to continue a run from where it left off. See
the :doc:`run <run>` command and its "upto" option for how to specify
the run command so it does not need to be changed either.
Similar to how restart files are written (see the :doc:`write_restart
<write_restart>` and :doc:`restart <restart>` commands), the restart
filename can contain two wild-card characters. If a "\*" appears in the
filename, the directory is searched for all filenames that match the
pattern where "\*" is replaced with a timestep value. The file with the
largest timestep value is read in. Thus, this effectively means, read
the latest restart file. It's useful if you want your script to
continue a run from where it left off. See the :doc:`run <run>` command
and its "upto" option for how to specify the run command so it does not
need to be changed either.
If a "%" character appears in the restart filename, LAMMPS expects a
set of multiple files to exist. The :doc:`restart <restart>` and
@ -222,17 +219,17 @@ its calculations in a consistent manner.
.. note::
There are a handful of commands which can be used before or
between runs which may require a system initialization. Examples
include the "balance", "displace_atoms", "delete_atoms", "set" (some
options), and "velocity" (some options) commands. This is because
they can migrate atoms to new processors. Thus they will also discard
unused "state" information from fixes. You will know the discard has
There are a handful of commands which can be used before or between
runs which may require a system initialization. Examples include the
"balance", "displace_atoms", "delete_atoms", "set" (some options),
and "velocity" (some options) commands. This is because they can
migrate atoms to new processors. Thus they will also discard unused
"state" information from fixes. You will know the discard has
occurred because a list of discarded fixes will be printed to the
screen and log file, as explained above. This means that if you wish
to retain that info in a restarted run, you must re-specify the
relevant fixes and computes (which create fixes) before those commands
are used.
relevant fixes and computes (which create fixes) before those
commands are used.
Some pair styles, like the :doc:`granular pair styles <pair_gran>`, also
use a fix to store "state" information that persists from timestep to
@ -245,18 +242,19 @@ LAMMPS allows bond interactions (angle, etc) to be turned off or
deleted in various ways, which can affect how their info is stored in
a restart file.
If bonds (angles, etc) have been turned off by the :doc:`fix shake <fix_shake>` or :doc:`delete_bonds <delete_bonds>` command,
their info will be written to a restart file as if they are turned on.
This means they will need to be turned off again in a new run after
the restart file is read.
If bonds (angles, etc) have been turned off by the :doc:`fix shake
<fix_shake>` or :doc:`delete_bonds <delete_bonds>` command, their info
will be written to a restart file as if they are turned on. This means
they will need to be turned off again in a new run after the restart
file is read.
Bonds that are broken (e.g. by a bond-breaking potential) are written
to the restart file as broken bonds with a type of 0. Thus these
bonds will still be broken when the restart file is read.
Bonds that have been broken by the :doc:`fix bond/break <fix_bond_break>` command have disappeared from the
system. No information about these bonds is written to the restart
file.
Bonds that have been broken by the :doc:`fix bond/break
<fix_bond_break>` command have disappeared from the system. No
information about these bonds is written to the restart file.
----------

14
doc/utils/sphinx-config/false_positives.txt
View File

@ -120,6 +120,7 @@ Antonelli
api
Apoorva
Appl
apptainer
Apu
arallel
arccos
@ -372,6 +373,7 @@ Caltech
Camilloni
Camiloni
Campana
Cangi
Cao
Capolungo
Caro
@ -2368,7 +2370,11 @@ nopreliminary
Nord
norder
Nordlund
noremap
normals
normx
normy
normz
Noskov
noslip
noticable
@ -2676,6 +2682,7 @@ polyhedra
Polym
polymorphism
popen
Popoola
Popov
popstore
Poresag
@ -2819,6 +2826,7 @@ radians
Rafferty
rahman
Rahman
Rajamanickam
Ralf
Raman
ramped
@ -3671,13 +3679,19 @@ vx
Vx
vxcm
vxmu
vxx
vxy
vxz
vy
Vy
vycm
vyy
vyz
vz
Vz
vzcm
vzi
vzz
Waals
Wadley
wallstyle

182
examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
View File

@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
Contributing author: Karl D. Hammond <hammondkd@missouri.edu>
University of Missouri (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
@ -23,6 +23,7 @@
#include <mpi.h>
#include "LAMMPS-wrapper.h"
#define LAMMPS_LIB_MPI 1
#include <library.h>
#include <lammps.h>
#include <atom.h>
@ -56,181 +57,40 @@ void lammps_error_all (void *ptr, const char *file, int line, const char *str)
int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 ) return 0;
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->vector_flag )
return 0;
else
return compute->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !compute->local_flag )
return 0;
else
return compute->size_local_rows;
}
else
return 0;
int *size;
size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR);
if (size) return *size;
return 0;
}
void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_array_rows;
*ncols = compute->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !compute->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = compute->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !compute->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_local_rows;
*ncols = compute->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
int *tmp;
tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS);
if (tmp) *nrows = *tmp;
tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS);
if (tmp) *ncols = *tmp;
return;
}
int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 ) return 0;
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->vector_flag )
return 0;
else
return fix->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !fix->local_flag )
return 0;
else
return fix->size_local_rows;
}
else
return 0;
int *size;
size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0);
if (size) return *size;
return 0;
}
void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_array_rows;
*ncols = fix->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !fix->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = fix->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !fix->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_local_rows;
*ncols = fix->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
int *tmp;
tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0);
if (tmp) *nrows = *tmp;
tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0);
if (tmp) *ncols = *tmp;
return;
}
/* vim: set ts=3 sts=3 expandtab: */

4
examples/COUPLE/fortran2/LAMMPS-wrapper.h
View File

@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
Contributing author: Karl D. Hammond <hammondkd@missouri.edu>
University of Missouri (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

4
examples/COUPLE/fortran2/LAMMPS.F90
View File

@ -1292,7 +1292,7 @@ contains !! Wrapper functions local to this module {{{1
Cname = string2Cstring (name)
Ccount = size(data) / natoms
if ( Ccount /= 1 .and. Ccount /= 3 ) &
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires&
& count to be either 1 or 3')
Fdata = data
Cdata = C_loc (Fdata(1))
@ -1355,7 +1355,7 @@ contains !! Wrapper functions local to this module {{{1
Cname = string2Cstring (name)
Ccount = size(data) / ndata
if ( Ccount /= 1 .and. Ccount /= 3 ) &
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires&
& count to be either 1 or 3')
Fdata = data
Cdata = C_loc (Fdata(1))

2
examples/COUPLE/fortran2/Makefile
View File

@ -14,7 +14,7 @@ CXXLIB = -lstdc++ # replace with your C++ runtime libs
# Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
FFLAGS = -O2 -fPIC
CXXFLAGS = -O2 -fPIC
CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX -DLAMMPS_LIB_MPI
CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
all : liblammps_fortran.a liblammps_fortran.so

5
examples/COUPLE/fortran2/README
View File

@ -11,9 +11,8 @@ This interface was created by Karl Hammond who you can contact with
questions:
Karl D. Hammond
University of Tennessee, Knoxville
karlh at ugcs.caltech.edu
karlh at utk.edu
University of Missouri
hammondkd at missouri.edu
-------------------------------------

182
examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp
View File

@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
Contributing author: Karl D. Hammond <hammondkd@missouri.edu>
University of Missouri (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
@ -23,6 +23,7 @@
#include <mpi.h>
#include "LAMMPS-wrapper.h"
#define LAMMPS_LIB_MPI 1
#include <library.h>
#include <lammps.h>
#include <atom.h>
@ -56,181 +57,40 @@ void lammps_error_all (void *ptr, const char *file, int line, const char *str)
int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 ) return 0;
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->vector_flag )
return 0;
else
return compute->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !compute->local_flag )
return 0;
else
return compute->size_local_rows;
}
else
return 0;
int *size;
size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR);
if (size) return *size;
return 0;
}
void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_array_rows;
*ncols = compute->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !compute->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = compute->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !compute->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_local_rows;
*ncols = compute->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
int *tmp;
tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS);
if (tmp) *nrows = *tmp;
tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS);
if (tmp) *ncols = *tmp;
return;
}
int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 ) return 0;
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->vector_flag )
return 0;
else
return fix->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !fix->local_flag )
return 0;
else
return fix->size_local_rows;
}
else
return 0;
int *size;
size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0);
if (size) return *size;
return 0;
}
void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_array_rows;
*ncols = fix->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !fix->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = fix->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !fix->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_local_rows;
*ncols = fix->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
int *tmp;
tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0);
if (tmp) *nrows = *tmp;
tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0);
if (tmp) *ncols = *tmp;
return;
}
/* vim: set ts=3 sts=3 expandtab: */

4
examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h
View File

@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
Contributing author: Karl D. Hammond <hammondkd@missouri.edu>
University of Missouri (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

3
examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
View File

@ -12,8 +12,7 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
Contributing author: Nir Goldman, LLNL <ngoldman@llnl.gov>, 2016
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

2
examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h
View File

@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Nir Goldman, ngoldman@llnl.gov, Oct. 19th, 2016
Contributing author: Nir Goldman, LLNL <ngoldman@llnl.gov>, 2016
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

4
examples/COUPLE/fortran_dftb/LAMMPS.F90
View File

@ -12,8 +12,8 @@
!--------------------------------------------------------------------------
!! ------------------------------------------------------------------------
! Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
! University of Tennessee, Knoxville (USA), 2012
! Contributing author: Karl D. Hammond <hammondkd@missouri.edu>
! University of Missouri (USA), 2012
!--------------------------------------------------------------------------
!! LAMMPS, a Fortran 2003 module containing an interface between Fortran

1
examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py
View File

@ -1,7 +1,6 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import sys
import numpy as np
def reduce_Born(Cf):

1
examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py
View File

@ -1,7 +1,6 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import sys
import numpy as np
def reduce_Born(Cf):

2
examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic_utils.py
View File

@ -1,5 +1,5 @@
import numpy as np
from lammps import lammps, LAMMPS_INT, LMP_STYLE_GLOBAL, LMP_VAR_EQUAL, LMP_VAR_ATOM
from lammps import lammps, LMP_VAR_EQUAL
# method for rotating elastic constants

36
examples/PACKAGES/pace/plugin/CMakeLists.txt Normal file
View File

@ -0,0 +1,36 @@
##########################################
# CMake build system for plugin examples.
# The is meant to be used as a template for plugins that are
# distributed independent from the LAMMPS package.
##########################################
cmake_minimum_required(VERSION 3.10)
project(paceplugin VERSION 1.0 LANGUAGES CXX)
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
include(CheckIncludeFileCXX)
include(LAMMPSInterfacePlugin)
include(ML-PACE)
##########################
# building the plugins
add_library(paceplugin MODULE paceplugin.cpp ${LAMMPS_SOURCE_DIR}/ML-PACE/pair_pace.cpp)
target_link_libraries(paceplugin PRIVATE pace)
target_link_libraries(paceplugin PRIVATE lammps)
target_include_directories(paceplugin PRIVATE ${LAMMPS_SOURCE_DIR}/ML-PACE)
set_target_properties(paceplugin PROPERTIES PREFIX "" SUFFIX ".so")
# MacOS seems to need this
if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers
set_target_properties(paceplugin PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
if(CMAKE_CROSSCOMPILING)
set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
endif()
else()
set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-rdynamic")
endif()

1
examples/PACKAGES/pace/plugin/LAMMPSInterfacePlugin.cmake Symbolic link
View File

@ -0,0 +1 @@
../../../../cmake/Modules/LAMMPSInterfacePlugin.cmake

1
examples/PACKAGES/pace/plugin/ML-PACE.cmake Symbolic link
View File

@ -0,0 +1 @@
../../../../cmake/Modules/Packages/ML-PACE.cmake

2
examples/PACKAGES/pace/plugin/README.txt Normal file
View File

@ -0,0 +1,2 @@
This folder contains a loader and support files to build the ML-PACE package as plugin.
For more information please see: https://docs.lammps.org/Developer_plugins.html

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28
examples/PACKAGES/pace/plugin/paceplugin.cpp Normal file
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@ -0,0 +1,28 @@
#include "lammpsplugin.h"
#include "version.h"
#include "pair_pace.h"
using namespace LAMMPS_NS;
static Pair *pair_pace_creator(LAMMPS *lmp)
{
return new PairPACE(lmp);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_t plugin;
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
// register pace pair style
plugin.version = LAMMPS_VERSION;
plugin.style = "pair";
plugin.name = "pace";
plugin.info = "PACE plugin pair style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_pace_creator;
plugin.handle = handle;
(*register_plugin)(&plugin, lmp);
}

157
examples/PACKAGES/pace/plugin/paceplugin.nsis Normal file
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@ -0,0 +1,157 @@
#!Nsis Installer Command Script
#
# The following external defines are recognized:
# ${VERSION} = YYYYMMDD
!include "MUI2.nsh"
!include "FileFunc.nsh"
!define MUI_ICON "lammps.ico"
!define MUI_UNICON "lammps.ico"
!define MUI_HEADERIMAGE
!define MUI_HEADERIMAGE_BITMAP "lammps-text-logo-wide.bmp"
!define MUI_HEADERIMAGE_RIGHT
Unicode true
XPStyle on
!include "LogicLib.nsh"
!addplugindir "envvar/Plugins/x86-unicode"
!include "x64.nsh"
RequestExecutionLevel user
!macro VerifyUserIsAdmin
UserInfo::GetAccountType
pop $0
${If} $0 != "admin"
messageBox mb_iconstop "Administrator rights required!"
setErrorLevel 740 ;ERROR_ELEVATION_REQUIRED
quit
${EndIf}
!macroend
!define PACEPLUGIN "LAMMPS ML-PACE Plugin ${VERSION}"
OutFile "LAMMPS-ML-PACE-plugin-${VERSION}.exe"
Name "${PACEPLUGIN}"
InstallDir "$LOCALAPPDATA\${PACEPLUGIN}"
ShowInstDetails show
ShowUninstDetails show
SetCompressor lzma
!define MUI_ABORTWARNING
!insertmacro MUI_PAGE_DIRECTORY
!insertmacro MUI_PAGE_INSTFILES
!insertmacro MUI_UNPAGE_CONFIRM
!insertmacro MUI_UNPAGE_INSTFILES
!insertmacro MUI_LANGUAGE "English"
function .onInit
# Determine if LAMMPS was already installed and check whether it was in 32-bit
# or 64-bit. Then look up path to uninstaller and offer to uninstall or quit
SetRegView 32
ReadRegDWORD $0 HKCU "Software\LAMMPS-ML-PACE" "Bits"
SetRegView LastUsed
${If} $0 == "32"
SetRegView 32
${ElseIf} $0 == "64"
SetRegView 64
${Else}
SetRegView 64
${EndIf}
ClearErrors
ReadRegStr $R0 HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" "UninstallString"
SetRegView LastUsed
${If} ${Errors}
DetailPrint "LAMMPS ML-PACE plugin not (yet) installed"
${Else}
MessageBox MB_YESNO "LAMMPS ML-PACE plugin ($0 bit) is already installed. Uninstall existing version?" /SD IDYES IDNO Quit
Pop $R1
StrCmp $R1 2 Quit +1
Exec $R0
Quit:
Quit
${EndIf}
setShellVarContext all
functionEnd
Section "${PACEPLUGIN}" SecPaceplugin
SectionIn RO
# Write LAMMPS installation bitness marker. Always use 32-bit registry view
SetRegView 32
IntFmt $0 "0x%08X" 64
WriteRegDWORD HKCU "Software\LAMMPS-ML-PACE" "Bits" $0
# Switch to "native" registry view
SetRegView 64
SetShellVarContext current
SetOutPath "$INSTDIR"
File lammps.ico
File paceplugin.so
# Register Application and its uninstaller
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \
"DisplayName" "${PACEPLUGIN}"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \
"Publisher" "The LAMMPS and PACE Developers"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \
"URLInfoAbout" "lammps.org"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \
"DisplayIcon" "$INSTDIR\lammps.ico"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \
"DisplayVersion" "${VERSION}"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \
"InstallLocation" "$INSTDIR"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \
"UninstallString" "$\"$INSTDIR\uninstall.exe$\""
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \
"QuietUninstallString" "$\"$INSTDIR\uninstall.exe$\" /S"
${GetSize} "$INSTDIR" "/S=0K" $0 $1 $2
IntFmt $0 "0x%08X" $0
WriteRegDWORD HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \
"EstimatedSize" "$0"
# update path variables
EnVar::SetHKCU
# add to LAMMPS plugin search path
EnVar::AddValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
WriteUninstaller "$INSTDIR\Uninstall.exe"
SectionEnd
function un.onInit
SetShellVarContext current
functionEnd
Section "Uninstall"
# remove LAMMPS bitness/installation indicator always in 32-bit registry view
SetRegView 32
DeleteRegKey HKCU "Software\LAMMPS-ML-PACE"
# unregister extension, and uninstall info
SetRegView 64
SetShellVarContext current
# unregister installation
DeleteRegKey HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE"
# update path variables
EnVar::SetHKCU
# remove entry from LAMMPS plugin search path
EnVar::DeleteValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
Delete /REBOOTOK "$INSTDIR\paceplugin.so"
Delete /REBOOTOK "$INSTDIR\Uninstall.exe"
Delete /REBOOTOK "$INSTDIR\lammps.ico"
RMDir /REBOOTOK "$INSTDIR"
SectionEnd
# Local Variables:
# mode: sh
# End:

41
examples/kim/plugin/CMakeLists.txt
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@ -6,46 +6,11 @@
cmake_minimum_required(VERSION 3.10)
# enforce out-of-source build
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
"Please remove CMakeCache.txt and CMakeFiles first.")
endif()
project(kimplugin VERSION 1.0 LANGUAGES CXX)
set(LAMMPS_SOURCE_DIR "" CACHE PATH "Location of LAMMPS sources folder")
if(NOT LAMMPS_SOURCE_DIR)
message(FATAL_ERROR "Must set LAMMPS_SOURCE_DIR")
endif()
# by default, install into $HOME/.local (not /usr/local),
# so that no root access (and sudo) is needed
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
endif()
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# C++11 is required
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# Need -restrict with Intel compilers
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif()
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
include(CheckIncludeFileCXX)
include(LAMMPSInterfaceCXX)
include(LAMMPSInterfacePlugin)
##########################
# building the plugins
@ -90,9 +55,9 @@ if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers
set_target_properties(kimplugin.so PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
set_target_properties(kimplugin PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
if(CMAKE_CROSSCOMPILING)
set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
endif()
else()
set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-rdynamic")

88
examples/kim/plugin/LAMMPSInterfaceCXX.cmake
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@ -1,88 +0,0 @@
# Cmake script code to define the LAMMPS C++ interface
# settings required for building LAMMPS plugins
################################################################################
# helper function
function(validate_option name values)
string(TOLOWER ${${name}} needle_lower)
string(TOUPPER ${${name}} needle_upper)
list(FIND ${values} ${needle_lower} IDX_LOWER)
list(FIND ${values} ${needle_upper} IDX_UPPER)
if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
message(FATAL_ERROR "\n########################################################################\n"
"Invalid value '${${name}}' for option ${name}\n"
"\n"
"Possible values are:\n"
"${POSSIBLE_VALUE_LIST}"
"########################################################################")
endif()
endfunction(validate_option)
#################################################################################
# LAMMPS C++ interface. We only need the header related parts.
add_library(lammps INTERFACE)
target_include_directories(lammps INTERFACE ${LAMMPS_SOURCE_DIR})
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
target_link_libraries(lammps INTERFACE ${CMAKE_BINARY_DIR}/../liblammps.dll.a)
endif()
################################################################################
# MPI configuration
if(NOT CMAKE_CROSSCOMPILING)
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
option(BUILD_MPI "Build MPI version" OFF)
endif()
if(BUILD_MPI)
find_package(MPI REQUIRED)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
endif()
target_link_libraries(lammps INTERFACE MPI::MPI_CXX)
else()
target_include_directories(lammps INTERFACE "${LAMMPS_SOURCE_DIR}/STUBS")
endif()
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES})
################################################################################
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
find_package(OpenMP QUIET)
if(OpenMP_FOUND)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
if(HAVE_OMP_H_INCLUDE)
set(BUILD_OMP_DEFAULT ON)
endif()
endif()
option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
if(BUILD_OMP)
find_package(OpenMP REQUIRED)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
if(NOT HAVE_OMP_H_INCLUDE)
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif()
if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
(CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4)
else()
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3)
endif()
target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX)
endif()

1
examples/kim/plugin/LAMMPSInterfacePlugin.cmake Symbolic link
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@ -0,0 +1 @@
../../../cmake/Modules/LAMMPSInterfacePlugin.cmake

2
examples/kim/plugin/README.txt Normal file
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@ -0,0 +1,2 @@
This folder contains a loader and support files to build the KIM package as plugin.
For more information please see: https://docs.lammps.org/Developer_plugins.html

5
examples/mdi/aimd_driver.py
View File

@ -26,7 +26,7 @@
# -nsteps 10
# number of timesteps, default = 10
import sys,math,random
import sys
import mdi
import numpy as np
from mpi4py import MPI
@ -42,10 +42,9 @@ def error(txt=None):
def perform_aimd(world,mm_comm,qm_comm):
me = world.Get_rank()
nprocs = world.Get_size()
# receive number of atoms from the MM engine
mdi.MDI_Send_command("<NATOMS",mm_comm)
natoms = mdi.MDI_Recv(1,mdi.MDI_INT,mm_comm)
natoms = world.bcast(natoms,root=0)

11
examples/plugins/CMakeLists.txt
View File

@ -32,9 +32,14 @@ else()
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
endif()
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
endif()

94
examples/snap/in.grid.snap Normal file
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@ -0,0 +1,94 @@
# Demonstrate calculation of SNAP bispectrum descriptors on a grid
# CORRECTNESS: The two atom positions coincide with two of
# the gridpoints, so c_b[2][1-5] should match c_mygrid[8][4-8].
# The same is true for compute grid/local c_mygridlocal[8][4-11].
# Local arrays can not be access directly in the script,
# but they are printed out to file dump.blocal
variable nrep index 1
variable a index 3.316
variable ngrid index 2
units metal
atom_modify map hash
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable ny equal ${nrep}
variable nz equal ${nrep}
boundary p p p
lattice custom $a &
a1 1 0 0 &
a2 0 1 0 &
a3 0 0 1 &
basis 0 0 0 &
basis 0.5 0.5 0.5 &
region box block 0 ${nx} 0 ${ny} 0 ${nz}
create_box 1 box
create_atoms 1 box
mass 1 180.88
# define atom compute and grid compute
group snapgroup type 1
variable twojmax equal 2
variable rcutfac equal 4.67637
variable rfac0 equal 0.99363
variable rmin0 equal 0
variable wj equal 1
variable radelem equal 0.5
variable bzero equal 0
variable quadratic equal 0
variable switch equal 1
variable snap_options string &
"${rcutfac} ${rfac0} ${twojmax} ${radelem} &
${wj} rmin0 ${rmin0} quadraticflag ${quadratic} &
bzeroflag ${bzero} switchflag ${switch}"
# build zero potential to satisfy compute sna/atom
pair_style zero ${rcutfac}
pair_coeff * *
# define atom and grid computes
compute b all sna/atom ${snap_options}
compute mygrid all sna/grid grid ${ngrid} ${ngrid} ${ngrid} &
${snap_options}
compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} &
${snap_options}
# define output
variable B5atom equal c_b[2][5]
variable B5grid equal c_mygrid[8][8]
variable rmse_global equal "sqrt( &
(c_mygrid[8][1] - x[2])^2 + &
(c_mygrid[8][2] - y[2])^2 + &
(c_mygrid[8][3] - z[2])^2 + &
(c_mygrid[8][4] - c_b[2][1])^2 + &
(c_mygrid[8][5] - c_b[2][2])^2 + &
(c_mygrid[8][6] - c_b[2][3])^2 + &
(c_mygrid[8][7] - c_b[2][4])^2 + &
(c_mygrid[8][8] - c_b[2][5])^2 &
)"
thermo_style custom step v_B5atom v_B5grid v_rmse_global
# this is the only way to view the local grid
dump 1 all local 1000 dump.blocal c_mygridlocal[*]
dump 2 all custom 1000 dump.batom id x y z c_b[*]
# run
run 0

114
examples/snap/in.grid.tri Normal file
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@ -0,0 +1,114 @@
# Demonstrate calculation of SNAP bispectrum
# descriptors on a grid for triclinic cell
# This triclinic cell has 6 times the volume of the single
# unit cell used by in.grid
# and contains 12 atoms. It is a 3x2x1 supercell
# with each unit cell containing 2 atoms and the
# reduced lattice vectors are [1 0 0], [1 1 0], and [1 1 1].
# The grid is listed in x-fastest order
# CORRECTNESS: The atom positions coincide with certain
# gridpoints, so c_b[1][1-5] should match c_mygrid[1][4-8]
# and c_b[7][1-5] should match c_mygrid[13][4-8].
# Local arrays can not be access directly in the script,
# but they are printed out to file dump.blocal.tri
# Initialize simulation
variable nrep index 1
variable a index 3.316
variable ngrid index 2
variable nrepx equal 3*${nrep}
variable nrepy equal 2*${nrep}
variable nrepz equal 1*${nrep}
variable ngridx equal 3*${ngrid}
variable ngridy equal 2*${ngrid}
variable ngridz equal 1*${ngrid}
units metal
atom_modify map hash sort 0 0
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrepx}
variable ny equal ${nrepy}
variable nz equal ${nrepz}
boundary p p p
lattice custom $a &
a1 1 0 0 &
a2 1 1 0 &
a3 1 1 1 &
basis 0 0 0 &
basis 0.0 0.0 0.5 &
spacing 1 1 1
box tilt large
region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
create_box 1 box
create_atoms 1 box
mass 1 180.88
# define atom compute and grid compute
group snapgroup type 1
variable twojmax equal 2
variable rcutfac equal 4.67637
variable rfac0 equal 0.99363
variable rmin0 equal 0
variable wj equal 1
variable radelem equal 0.5
variable bzero equal 0
variable quadratic equal 0
variable switch equal 1
variable snap_options string &
"${rcutfac} ${rfac0} ${twojmax} ${radelem} &
${wj} rmin0 ${rmin0} quadraticflag ${quadratic} &
bzeroflag ${bzero} switchflag ${switch}"
# build zero potential to satisfy compute sna/atom
pair_style zero ${rcutfac}
pair_coeff * *
# define atom and grid computes
compute b all sna/atom ${snap_options}
compute mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} &
${snap_options}
compute mygridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} &
${snap_options}
# define output
variable B5atom equal c_b[7][5]
variable B5grid equal c_mygrid[13][8]
# do not compare x,y,z because assignment of ids
# to atoms is not unnique for different processor grids
variable rmse_global equal "sqrt( &
(c_mygrid[13][4] - c_b[7][1])^2 + &
(c_mygrid[13][5] - c_b[7][2])^2 + &
(c_mygrid[13][6] - c_b[7][3])^2 + &
(c_mygrid[13][7] - c_b[7][4])^2 + &
(c_mygrid[13][8] - c_b[7][5])^2 &
)"
thermo_style custom step v_B5atom v_B5grid v_rmse_global
# this is the only way to view the local grid
dump 1 all local 1000 dump.blocal.tri c_mygridlocal[*]
dump 2 all custom 1000 dump.batom.tri id x y z c_b[*]
# run
run 0

159
examples/snap/log.15Jun22.grid.snap.g++.1 Normal file
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@ -0,0 +1,159 @@
LAMMPS (2 Jun 2022)
using 1 OpenMP thread(s) per MPI task
# Demonstrate calculation of SNAP bispectrum descriptors on a grid
# CORRECTNESS: The two atom positions coincide with two of
# the gridpoints, so c_b[2][1-5] should match c_mygrid[8][4-8].
# The same is true for compute grid/local c_mygridlocal[8][4-11].
# Local arrays can not be access directly in the script,
# but they are printed out to file dump.blocal
variable nrep index 1
variable a index 3.316
variable ngrid index 2
units metal
atom_modify map hash
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 1
variable ny equal ${nrep}
variable ny equal 1
variable nz equal ${nrep}
variable nz equal 1
boundary p p p
lattice custom $a a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
lattice custom 3.316 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
Lattice spacing in x,y,z = 3.316 3.316 3.316
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 1 0 ${ny} 0 ${nz}
region box block 0 1 0 1 0 ${nz}
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (3.316 3.316 3.316)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 2 atoms
using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316)
create_atoms CPU = 0.000 seconds
mass 1 180.88
# define atom compute and grid compute
group snapgroup type 1
2 atoms in group snapgroup
variable twojmax equal 2
variable rcutfac equal 4.67637
variable rfac0 equal 0.99363
variable rmin0 equal 0
variable wj equal 1
variable radelem equal 0.5
variable bzero equal 0
variable quadratic equal 0
variable switch equal 1
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
4.67637 ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
# build zero potential to satisfy compute sna/atom
pair_style zero ${rcutfac}
pair_style zero 4.67637
pair_coeff * *
# define atom and grid computes
compute b all sna/atom ${snap_options}
compute b all sna/atom 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
compute mygrid all sna/grid grid ${ngrid} ${ngrid} ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 ${ngrid} ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 2 ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 2 2 ${snap_options}
compute mygrid all sna/grid grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 ${ngrid} ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 2 ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
# define output
variable B5atom equal c_b[2][5]
variable B5grid equal c_mygrid[8][8]
variable rmse_global equal "sqrt( (c_mygrid[8][1] - x[2])^2 + (c_mygrid[8][2] - y[2])^2 + (c_mygrid[8][3] - z[2])^2 + (c_mygrid[8][4] - c_b[2][1])^2 + (c_mygrid[8][5] - c_b[2][2])^2 + (c_mygrid[8][6] - c_b[2][3])^2 + (c_mygrid[8][7] - c_b[2][4])^2 + (c_mygrid[8][8] - c_b[2][5])^2 )"
thermo_style custom step v_B5atom v_B5grid v_rmse_global
# this is the only way to view the local grid
dump 1 all local 1000 dump.blocal c_mygridlocal[*]
dump 2 all custom 1000 dump.batom id x y z c_b[*]
# run
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.67637
ghost atom cutoff = 6.67637
binsize = 3.338185, bins = 1 1 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.127 | 7.127 | 7.127 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 9.1551336e-16
Loop time of 1.43e-06 on 1 procs for 0 steps with 2 atoms
139.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.43e-06 | | |100.00
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 339 ave 339 max 339 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 64 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 128
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (2 Jun 2022)
using 1 OpenMP thread(s) per MPI task
# Demonstrate calculation of SNAP bispectrum descriptors on a grid
# CORRECTNESS: The two atom positions coincide with two of
# the gridpoints, so c_b[2][1-5] should match c_mygrid[8][4-8].
# The same is true for compute grid/local c_mygridlocal[8][4-11].
# Local arrays can not be access directly in the script,
# but they are printed out to file dump.blocal
variable nrep index 1
variable a index 3.316
variable ngrid index 2
units metal
atom_modify map hash
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 1
variable ny equal ${nrep}
variable ny equal 1
variable nz equal ${nrep}
variable nz equal 1
boundary p p p
lattice custom $a a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
lattice custom 3.316 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
Lattice spacing in x,y,z = 3.316 3.316 3.316
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 1 0 ${ny} 0 ${nz}
region box block 0 1 0 1 0 ${nz}
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (3.316 3.316 3.316)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 2 atoms
using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316)
create_atoms CPU = 0.001 seconds
mass 1 180.88
# define atom compute and grid compute
group snapgroup type 1
2 atoms in group snapgroup
variable twojmax equal 2
variable rcutfac equal 4.67637
variable rfac0 equal 0.99363
variable rmin0 equal 0
variable wj equal 1
variable radelem equal 0.5
variable bzero equal 0
variable quadratic equal 0
variable switch equal 1
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
4.67637 ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
# build zero potential to satisfy compute sna/atom
pair_style zero ${rcutfac}
pair_style zero 4.67637
pair_coeff * *
# define atom and grid computes
compute b all sna/atom ${snap_options}
compute b all sna/atom 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
compute mygrid all sna/grid grid ${ngrid} ${ngrid} ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 ${ngrid} ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 2 ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 2 2 ${snap_options}
compute mygrid all sna/grid grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 ${ngrid} ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 2 ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
# define output
variable B5atom equal c_b[2][5]
variable B5grid equal c_mygrid[8][8]
variable rmse_global equal "sqrt( (c_mygrid[8][1] - x[2])^2 + (c_mygrid[8][2] - y[2])^2 + (c_mygrid[8][3] - z[2])^2 + (c_mygrid[8][4] - c_b[2][1])^2 + (c_mygrid[8][5] - c_b[2][2])^2 + (c_mygrid[8][6] - c_b[2][3])^2 + (c_mygrid[8][7] - c_b[2][4])^2 + (c_mygrid[8][8] - c_b[2][5])^2 )"
thermo_style custom step v_B5atom v_B5grid v_rmse_global
# this is the only way to view the local grid
dump 1 all local 1000 dump.blocal c_mygridlocal[*]
dump 2 all custom 1000 dump.batom id x y z c_b[*]
# run
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.67637
ghost atom cutoff = 6.67637
binsize = 3.338185, bins = 1 1 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
Per MPI rank memory allocation (min/avg/max) = 6.123 | 6.631 | 7.139 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 1.6316879e-15
Loop time of 2.57125e-06 on 4 procs for 0 steps with 2 atoms
107.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.571e-06 | | |100.00
Nlocal: 0.5 ave 1 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 274.5 ave 275 max 274 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 16 ave 40 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
FullNghs: 32 ave 64 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 128
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (2 Jun 2022)
using 1 OpenMP thread(s) per MPI task
# Demonstrate calculation of SNAP bispectrum
# descriptors on a grid for triclinic cell
# This triclinic cell has 6 times the volume of the single
# unit cell used by in.grid
# and contains 12 atoms. It is a 3x2x1 supercell
# with each unit cell containing 2 atoms and the
# reduced lattice vectors are [1 0 0], [1 1 0], and [1 1 1].
# The grid is listed in x-fastest order
# CORRECTNESS: The atom positions coincide with certain
# gridpoints, so c_b[1][1-5] should match c_mygrid[1][4-8]
# and c_b[7][1-5] should match c_mygrid[13][4-8].
# Local arrays can not be access directly in the script,
# but they are printed out to file dump.blocal.tri
# Initialize simulation
variable nrep index 1
variable a index 3.316
variable ngrid index 2
variable nrepx equal 3*${nrep}
variable nrepx equal 3*1
variable nrepy equal 2*${nrep}
variable nrepy equal 2*1
variable nrepz equal 1*${nrep}
variable nrepz equal 1*1
variable ngridx equal 3*${ngrid}
variable ngridx equal 3*2
variable ngridy equal 2*${ngrid}
variable ngridy equal 2*2
variable ngridz equal 1*${ngrid}
variable ngridz equal 1*2
units metal
atom_modify map hash sort 0 0
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrepx}
variable nx equal 3
variable ny equal ${nrepy}
variable ny equal 2
variable nz equal ${nrepz}
variable nz equal 1
boundary p p p
lattice custom $a a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1
lattice custom 3.316 a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1
Lattice spacing in x,y,z = 3.316 3.316 3.316
box tilt large
region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
region box prism 0 3 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
region box prism 0 3 0 2 0 ${nz} ${ny} ${nz} ${nz}
region box prism 0 3 0 2 0 1 ${ny} ${nz} ${nz}
region box prism 0 3 0 2 0 1 2 ${nz} ${nz}
region box prism 0 3 0 2 0 1 2 1 ${nz}
region box prism 0 3 0 2 0 1 2 1 1
create_box 1 box
Created triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
WARNING: Triclinic box skew is large (src/domain.cpp:224)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 12 atoms
using lattice units in triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
create_atoms CPU = 0.000 seconds
mass 1 180.88
# define atom compute and grid compute
group snapgroup type 1
12 atoms in group snapgroup
variable twojmax equal 2
variable rcutfac equal 4.67637
variable rfac0 equal 0.99363
variable rmin0 equal 0
variable wj equal 1
variable radelem equal 0.5
variable bzero equal 0
variable quadratic equal 0
variable switch equal 1
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
4.67637 ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
# build zero potential to satisfy compute sna/atom
pair_style zero ${rcutfac}
pair_style zero 4.67637
pair_coeff * *
# define atom and grid computes
compute b all sna/atom ${snap_options}
compute b all sna/atom 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
compute mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} ${snap_options}
compute mygrid all sna/grid grid 6 ${ngridy} ${ngridz} ${snap_options}
compute mygrid all sna/grid grid 6 4 ${ngridz} ${snap_options}
compute mygrid all sna/grid grid 6 4 2 ${snap_options}
compute mygrid all sna/grid grid 6 4 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
compute mygridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} ${snap_options}
compute mygridlocal all sna/grid/local grid 6 ${ngridy} ${ngridz} ${snap_options}
compute mygridlocal all sna/grid/local grid 6 4 ${ngridz} ${snap_options}
compute mygridlocal all sna/grid/local grid 6 4 2 ${snap_options}
compute mygridlocal all sna/grid/local grid 6 4 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
# define output
variable B5atom equal c_b[7][5]
variable B5grid equal c_mygrid[13][8]
# do not compare x,y,z because assignment of ids
# to atoms is not unnique for different processor grids
variable rmse_global equal "sqrt( (c_mygrid[13][4] - c_b[7][1])^2 + (c_mygrid[13][5] - c_b[7][2])^2 + (c_mygrid[13][6] - c_b[7][3])^2 + (c_mygrid[13][7] - c_b[7][4])^2 + (c_mygrid[13][8] - c_b[7][5])^2 )"
thermo_style custom step v_B5atom v_B5grid v_rmse_global
# this is the only way to view the local grid
dump 1 all local 1000 dump.blocal.tri c_mygridlocal[*]
dump 2 all custom 1000 dump.batom.tri id x y z c_b[*]
# run
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.67637
ghost atom cutoff = 6.67637
binsize = 3.338185, bins = 6 3 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
(2) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.183 | 7.183 | 7.183 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 7.2262471e-14
Loop time of 1.414e-06 on 1 procs for 0 steps with 12 atoms
70.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.414e-06 | | |100.00
Nlocal: 12 ave 12 max 12 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 604 ave 604 max 604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 768 ave 768 max 768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 768
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

192
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LAMMPS (2 Jun 2022)
using 1 OpenMP thread(s) per MPI task
# Demonstrate calculation of SNAP bispectrum
# descriptors on a grid for triclinic cell
# This triclinic cell has 6 times the volume of the single
# unit cell used by in.grid
# and contains 12 atoms. It is a 3x2x1 supercell
# with each unit cell containing 2 atoms and the
# reduced lattice vectors are [1 0 0], [1 1 0], and [1 1 1].
# The grid is listed in x-fastest order
# CORRECTNESS: The atom positions coincide with certain
# gridpoints, so c_b[1][1-5] should match c_mygrid[1][4-8]
# and c_b[7][1-5] should match c_mygrid[13][4-8].
# Local arrays can not be access directly in the script,
# but they are printed out to file dump.blocal.tri
# Initialize simulation
variable nrep index 1
variable a index 3.316
variable ngrid index 2
variable nrepx equal 3*${nrep}
variable nrepx equal 3*1
variable nrepy equal 2*${nrep}
variable nrepy equal 2*1
variable nrepz equal 1*${nrep}
variable nrepz equal 1*1
variable ngridx equal 3*${ngrid}
variable ngridx equal 3*2
variable ngridy equal 2*${ngrid}
variable ngridy equal 2*2
variable ngridz equal 1*${ngrid}
variable ngridz equal 1*2
units metal
atom_modify map hash sort 0 0
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrepx}
variable nx equal 3
variable ny equal ${nrepy}
variable ny equal 2
variable nz equal ${nrepz}
variable nz equal 1
boundary p p p
lattice custom $a a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1
lattice custom 3.316 a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1
Lattice spacing in x,y,z = 3.316 3.316 3.316
box tilt large
region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
region box prism 0 3 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
region box prism 0 3 0 2 0 ${nz} ${ny} ${nz} ${nz}
region box prism 0 3 0 2 0 1 ${ny} ${nz} ${nz}
region box prism 0 3 0 2 0 1 2 ${nz} ${nz}
region box prism 0 3 0 2 0 1 2 1 ${nz}
region box prism 0 3 0 2 0 1 2 1 1
create_box 1 box
Created triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
WARNING: Triclinic box skew is large (src/domain.cpp:224)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 12 atoms
using lattice units in triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
create_atoms CPU = 0.000 seconds
mass 1 180.88
# define atom compute and grid compute
group snapgroup type 1
12 atoms in group snapgroup
variable twojmax equal 2
variable rcutfac equal 4.67637
variable rfac0 equal 0.99363
variable rmin0 equal 0
variable wj equal 1
variable radelem equal 0.5
variable bzero equal 0
variable quadratic equal 0
variable switch equal 1
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
4.67637 ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
# build zero potential to satisfy compute sna/atom
pair_style zero ${rcutfac}
pair_style zero 4.67637
pair_coeff * *
# define atom and grid computes
compute b all sna/atom ${snap_options}
compute b all sna/atom 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
compute mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} ${snap_options}
compute mygrid all sna/grid grid 6 ${ngridy} ${ngridz} ${snap_options}
compute mygrid all sna/grid grid 6 4 ${ngridz} ${snap_options}
compute mygrid all sna/grid grid 6 4 2 ${snap_options}
compute mygrid all sna/grid grid 6 4 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
compute mygridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} ${snap_options}
compute mygridlocal all sna/grid/local grid 6 ${ngridy} ${ngridz} ${snap_options}
compute mygridlocal all sna/grid/local grid 6 4 ${ngridz} ${snap_options}
compute mygridlocal all sna/grid/local grid 6 4 2 ${snap_options}
compute mygridlocal all sna/grid/local grid 6 4 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
# define output
variable B5atom equal c_b[7][5]
variable B5grid equal c_mygrid[13][8]
# do not compare x,y,z because assignment of ids
# to atoms is not unnique for different processor grids
variable rmse_global equal "sqrt( (c_mygrid[13][4] - c_b[7][1])^2 + (c_mygrid[13][5] - c_b[7][2])^2 + (c_mygrid[13][6] - c_b[7][3])^2 + (c_mygrid[13][7] - c_b[7][4])^2 + (c_mygrid[13][8] - c_b[7][5])^2 )"
thermo_style custom step v_B5atom v_B5grid v_rmse_global
# this is the only way to view the local grid
dump 1 all local 1000 dump.blocal.tri c_mygridlocal[*]
dump 2 all custom 1000 dump.batom.tri id x y z c_b[*]
# run
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.67637
ghost atom cutoff = 6.67637
binsize = 3.338185, bins = 6 3 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
(2) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.15 | 7.15 | 7.15 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 1.9367585e-14
Loop time of 2.65825e-06 on 4 procs for 0 steps with 12 atoms
84.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.658e-06 | | |100.00
Nlocal: 3 ave 4 max 2 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 459 ave 460 max 458 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 96 ave 128 max 64 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 192 ave 256 max 128 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 768
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

2
lib/install_helpers.py
View File

@ -1,4 +1,4 @@
import hashlib,os,subprocess,sys
import hashlib,os,subprocess
# try to auto-detect the maximum number of available CPUs
def get_cpus():

5
lib/latte/Install.py
View File

@ -71,7 +71,8 @@ buildflag = args.build
pathflag = args.path is not None
version = args.version
suffixflag = args.machine is not None
suffix = args.machine
if suffixflag:
suffix = args.machine
if pathflag:
lattedir = args.path
@ -132,8 +133,6 @@ os.symlink(os.path.join(lattedir, 'src', 'latte_c_bind.o'), 'filelink.o')
# copy Makefile.lammps.suffix to Makefile.lammps
if suffixflag or not os.path.exists("Makefile.lammps"):
if suffix is None:
suffix = 'gfortran'
print("Creating Makefile.lammps")
if os.path.exists("Makefile.lammps.%s" % suffix):
shutil.copyfile("Makefile.lammps.%s" % suffix, 'Makefile.lammps')

8
lib/mdi/Install.py
View File

@ -39,7 +39,7 @@ url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version
# known checksums for different MDI versions. used to validate the download.
checksums = { \
'1.3.2' : '836f5da400d8cff0f0e4435640f9454f', \
'1.4.1' : 'f9505fccd4c79301a619f6452dad4ad9', \
}
# print error message or help
@ -177,7 +177,7 @@ try:
except:
n_cpus = 1
print("Building lib%s.so ..." % lib)
print("Building lib%s.a ..." % lib)
cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT)
print(txt.decode('UTF-8'))
@ -201,10 +201,10 @@ makefile_lammps.write(str(rpath_option) + "\n")
makefile_lammps.close()
shared_files = glob.glob( os.path.join( homepath, "liblink", "lib%s.so*" % lib) )
shared_files = glob.glob( os.path.join( homepath, "liblink", "lib%s.a" % lib) )
if len(shared_files) > 0:
print("Build was successful")
else:
error("Build of lib/%s/lib%s.so was NOT successful" % (lib,lib))
error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
if has_extramake and not os.path.exists("Makefile.lammps"):
print("lib/%s/Makefile.lammps was NOT created" % lib)

2
lib/mdi/Makefile.g++
View File

@ -8,7 +8,7 @@ EXTRAMAKE = Makefile.lammps.empty
lib: $(OBJ)
mkdir -p build
cd build; cmake -Dlibtype=SHARED -Dlanguage=CXX -D CMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++ ../MDI_Library; make
cd build; cmake -Dlibtype=STATIC -Dlanguage=C -D CMAKE_POSITION_INDEPENDENT_CODE=yes -D CMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++ ../MDI_Library; make
@cp $(EXTRAMAKE) Makefile.lammps
# ------ CLEAN ------

2
lib/mdi/Makefile.gcc
View File

@ -8,7 +8,7 @@ EXTRAMAKE = Makefile.lammps.empty
lib: $(OBJ)
mkdir -p build
cd build; cmake -Dlibtype=SHARED -D CMAKE_C_COMPILER=gcc ../MDI_Library; make
cd build; cmake -Dlibtype=STATIC -Dlanguage=C -D CMAKE_POSITION_INDEPENDENT_CODE=yes -D CMAKE_C_COMPILER=gcc ../MDI_Library; make
@cp $(EXTRAMAKE) Makefile.lammps
# ------ CLEAN ------

2
lib/mdi/Makefile.icc
View File

@ -8,7 +8,7 @@ EXTRAMAKE = Makefile.lammps.empty
lib: $(OBJ)
mkdir -p build
cd build; cmake -Dlibtype=SHARED -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icc ../MDI_Library; make
cd build; cmake -Dlibtype=STATIC -Dlanguage=C -D CMAKE_POSITION_INDEPENDENT_CODE=yes -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icpc ../MDI_Library; make
@cp $(EXTRAMAKE) Makefile.lammps
# ------ CLEAN ------

2
lib/mdi/Makefile.mpi
View File

@ -8,7 +8,7 @@ EXTRAMAKE = Makefile.lammps.empty
lib: $(OBJ)
mkdir -p build
cd build; cmake -Dlibtype=SHARED -D CMAKE_C_COMPILER=mpicc -D CMAKE_CXX_COMPILER=mpicxx ../MDI_Library; make
cd build; cmake -Dlibtype=STATIC -Dlanguage=C -D CMAKE_POSITION_INDEPENDENT_CODE=yes -D CMAKE_C_COMPILER=mpicc -D CMAKE_CXX_COMPILER=mpicxx ../MDI_Library; make
@cp $(EXTRAMAKE) Makefile.lammps
# ------ CLEAN ------

50
python/install.py
View File

@ -11,7 +11,7 @@ independently and used to build the wheel without installing it.
"""
from __future__ import print_function
import sys,os,shutil,time,glob,subprocess
import sys,os,shutil,glob,subprocess
from argparse import ArgumentParser
parser = ArgumentParser(prog='install.py',
@ -23,6 +23,8 @@ parser.add_argument("-l", "--lib", required=True,
help="path to the compiled LAMMPS shared library")
parser.add_argument("-n", "--noinstall", action="store_true", default=False,
help="only build a binary wheel. Don't attempt to install it")
parser.add_argument("-w", "--wheeldir", required=False,
help="path to a directory where the created wheel will be stored")
args = parser.parse_args()
@ -30,7 +32,7 @@ args = parser.parse_args()
if args.package:
if not os.path.exists(args.package):
print( "ERROR: LAMMPS package %s does not exist" % args.package)
print("ERROR: LAMMPS package %s does not exist" % args.package)
parser.print_help()
sys.exit(1)
else:
@ -38,12 +40,20 @@ if args.package:
if args.lib:
if not os.path.exists(args.lib):
print( "ERROR: LAMMPS shared library %s does not exist" % args.lib)
print("ERROR: LAMMPS shared library %s does not exist" % args.lib)
parser.print_help()
sys.exit(1)
else:
args.lib = os.path.abspath(args.lib)
if args.wheeldir:
if not os.path.exists(args.wheeldir):
print("ERROR: directory %s to store the wheel does not exist" % args.wheeldir)
parser.print_help()
sys.exit(1)
else:
args.wheeldir = os.path.abspath(args.wheeldir)
# we need to switch to the folder of the python package
olddir = os.path.abspath('.')
os.chdir(os.path.dirname(args.package))
@ -80,10 +90,18 @@ os.remove(os.path.join('lammps',os.path.basename(args.lib)))
# stop here if we were asked not to install the wheel we created
if args.noinstall:
exit(0)
if args.wheeldir:
for wheel in glob.glob('lammps-*.whl'):
shutil.copy(wheel, args.wheeldir)
os.remove(wheel)
exit(0)
# install the wheel with pip. first try to install in the default environment.
# that will be a virtual environment, if active, or the system folder.
# if in a virtual environment, we must not use the python executable
# that is running this script (configured by cmake), but use "python"
# from the regular system path. The user may have changed to the virtual
# environment *after* running cmake.
# recent versions of pip will automatically drop to use the user folder
# in case the system folder is not writable.
@ -93,21 +111,35 @@ if args.noinstall:
# must be uninstalled manually. We must not ignore this and drop
# back to install into a (forced) user folder.
print("Installing wheel")
if "VIRTUAL_ENV" in os.environ:
print("Installing wheel into virtual environment")
py_exe = 'python'
else:
print("Installing wheel into system site-packages folder")
py_exe = sys.executable
for wheel in glob.glob('lammps-*.whl'):
try:
txt = subprocess.check_output([sys.executable, '-m', 'pip', 'install', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False)
txt = subprocess.check_output([py_exe, '-m', 'pip', 'install', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False)
print(txt.decode('UTF-8'))
if args.wheeldir:
shutil.copy(wheel, args.wheeldir)
else:
shutil.copy(wheel, olddir)
os.remove(wheel)
continue
except subprocess.CalledProcessError as err:
errmsg = err.output.decode('UTF-8')
if errmsg.find("distutils installed"):
sys.exit(errmsg + "You need to uninstall the LAMMPS python module manually first.\n")
try:
print('Installing wheel into standard site-packages folder failed. Trying user folder now')
print('Installing wheel into system site-packages folder failed. Trying user folder now')
txt = subprocess.check_output([sys.executable, '-m', 'pip', 'install', '--user', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False)
print(txt.decode('UTF-8'))
if args.wheeldir:
shutil.copy(wheel, args.wheeldir)
else:
shutil.copy(wheel, olddir)
os.remove(wheel)
except:
sys.exit('Failed to install wheel ' + wheel)
shutil.copy(wheel, olddir)
os.remove(wheel)

37
python/lammps/core.py
View File

@ -188,20 +188,17 @@ class lammps(object):
[c_void_p,POINTER(c_double),POINTER(c_double),c_double,c_double,c_double]
self.lib.lammps_reset_box.restype = None
self.lib.lammps_gather_atoms.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms.restype = None
self.lib.lammps_gather_atoms_concat.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms_concat.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms_concat.restype = None
self.lib.lammps_gather_atoms_subset.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_gather_atoms_subset.restype = None
self.lib.lammps_scatter_atoms.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter_atoms.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter_atoms.restype = None
self.lib.lammps_scatter_atoms_subset.argtypes = \
@ -211,20 +208,17 @@ class lammps(object):
self.lib.lammps_gather_bonds.argtypes = [c_void_p,c_void_p]
self.lib.lammps_gather_bonds.restype = None
self.lib.lammps_gather.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather.restype = None
self.lib.lammps_gather_concat.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_concat.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_concat.restype = None
self.lib.lammps_gather_subset.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_gather_subset.restype = None
self.lib.lammps_scatter.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter.restype = None
self.lib.lammps_scatter_subset.argtypes = \
@ -244,7 +238,8 @@ class lammps(object):
self.lib.lammps_neighlist_num_elements.argtypes = [c_void_p, c_int]
self.lib.lammps_neighlist_num_elements.restype = c_int
self.lib.lammps_neighlist_element_neighbors.argtypes = [c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))]
self.lib.lammps_neighlist_element_neighbors.argtypes = \
[c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))]
self.lib.lammps_neighlist_element_neighbors.restype = None
self.lib.lammps_is_running.argtypes = [c_void_p]
@ -368,11 +363,9 @@ class lammps(object):
if type(cmdargs[i]) is str:
cmdargs[i] = cmdargs[i].encode()
cargs = (c_char_p*narg)(*cmdargs)
self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, \
MPI_Comm, c_void_p]
self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, MPI_Comm, c_void_p]
else:
self.lib.lammps_open.argtypes = [c_int, c_char_p, \
MPI_Comm, c_void_p]
self.lib.lammps_open.argtypes = [c_int, c_char_p, MPI_Comm, c_void_p]
self.opened = 1
comm_ptr = self.MPI._addressof(comm)
@ -390,8 +383,7 @@ class lammps(object):
if type(cmdargs[i]) is str:
cmdargs[i] = cmdargs[i].encode()
cargs = (c_char_p*narg)(*cmdargs)
self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*narg, \
c_void_p]
self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*narg, c_void_p]
self.lmp = c_void_p(self.lib.lammps_open_no_mpi(narg,cargs,None))
else:
self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p, c_void_p]
@ -963,17 +955,14 @@ class lammps(object):
return ptr
elif ctype == LMP_SIZE_COLS:
if cstyle == LMP_STYLE_GLOBAL \
or cstyle == LMP_STYLE_ATOM \
or cstyle == LMP_STYLE_LOCAL:
if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_ATOM or cstyle == LMP_STYLE_LOCAL:
self.lib.lammps_extract_compute.restype = POINTER(c_int)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
return ptr[0]
elif ctype == LMP_SIZE_VECTOR or ctype == LMP_SIZE_ROWS:
if cstyle == LMP_STYLE_GLOBAL \
or cstyle == LMP_STYLE_LOCAL:
if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_LOCAL:
self.lib.lammps_extract_compute.restype = POINTER(c_int)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)

9
python/lammps/numpy_wrapper.py
View File

@ -165,7 +165,7 @@ class numpy_wrapper:
"""
value = self.lmp.extract_compute(cid, cstyle, ctype)
if cstyle in (LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL):
if cstyle == LMP_STYLE_GLOBAL:
if ctype == LMP_TYPE_VECTOR:
nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_VECTOR)
return self.darray(value, nrows)
@ -173,6 +173,13 @@ class numpy_wrapper:
nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_ROWS)
ncols = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_COLS)
return self.darray(value, nrows, ncols)
elif cstyle == LMP_STYLE_LOCAL:
nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_ROWS)
ncols = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_COLS)
if ncols == 0:
return self.darray(value, nrows)
else:
return self.darray(value, nrows, ncols)
elif cstyle == LMP_STYLE_ATOM:
if ctype == LMP_TYPE_VECTOR:
nlocal = self.lmp.extract_global("nlocal")

22
python/makewheel.py
View File

@ -1,14 +1,26 @@
#!/usr/bin/env python
import sys,os,shutil
import sys,os,site
# find python script to activate the virtual environment and source it
base = os.path.abspath('buildwheel')
if sys.platform == 'win32':
virtenv=os.path.join('buildwheel','Scripts','activate_this.py')
bin_dir=os.path.join(base,'Scripts')
else:
virtenv=os.path.join('buildwheel','bin','activate_this.py')
bin_dir=os.path.join(base,'bin')
exec(open(virtenv).read(), {'__file__': virtenv})
# prepend bin to PATH, set venv path
os.environ["PATH"] = os.pathsep.join([bin_dir] + os.environ.get("PATH", "").split(os.pathsep))
os.environ["VIRTUAL_ENV"] = base
# add the virtual environments libraries to the host python import mechanism
prev_length = len(sys.path)
for lib in "__LIB_FOLDERS__".split(os.pathsep):
path = os.path.realpath(os.path.join(bin_dir, lib))
site.addsitedir(path)
sys.path[:] = sys.path[prev_length:] + sys.path[0:prev_length]
sys.real_prefix = sys.prefix
sys.prefix = base
# update pip and install all requirements to build the wheel
os.system('python -m pip install --upgrade pip')

4
python/setup.py
View File

@ -3,7 +3,7 @@
from setuptools import setup
from setuptools.dist import Distribution
from sys import version_info
import os,time,shutil
import os,time
LAMMPS_PYTHON_DIR = os.path.dirname(os.path.realpath(__file__))
LAMMPS_DIR = os.path.dirname(LAMMPS_PYTHON_DIR)
LAMMPS_SOURCE_DIR = os.path.join(LAMMPS_DIR, 'src')
@ -24,7 +24,7 @@ def get_lammps_version():
class BinaryDistribution(Distribution):
"""Wrapper to enforce creating a binary package"""
def has_ext_modules(foo):
def has_ext_modules(self):
return True
if version_info.major >= 3:

16
src/.gitignore vendored
View File

@ -173,12 +173,20 @@
/pair_tdpd.cpp
/pair_tdpd.h
/compute_grid.cpp
/compute_grid.h
/compute_grid_local.cpp
/compute_grid_local.h
/compute_sna_atom.cpp
/compute_sna_atom.h
/compute_snad_atom.cpp
/compute_snad_atom.h
/compute_snav_atom.cpp
/compute_snav_atom.h
/compute_sna_grid.cpp
/compute_sna_grid.h
/compute_sna_grid_local.cpp
/compute_sna_grid_local.h
/compute_snap.cpp
/compute_snap.h
/openmp_snap.h
@ -997,8 +1005,8 @@
/neb.h
/netcdf_units.cpp
/netcdf_units.h
/pair_3b_table.cpp
/pair_3b_table.h
/pair_threebody_table.cpp
/pair_threebody_table.h
/pair_adp.cpp
/pair_adp.h
/pair_agni.cpp
@ -1293,8 +1301,8 @@
/pair_sph_taitwater_morris.h
/pair_sw.cpp
/pair_sw.h
/pair_sw_3b_table.cpp
/pair_sw_3b_table.h
/pair_sw_angle_table.cpp
/pair_sw_angle_table.h
/pair_sw_mod.cpp
/pair_sw_mod.h
/pair_tersoff.cpp

2
src/ATC/fix_atc.cpp
View File

@ -284,7 +284,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
int me = ATC::LammpsInterface::instance()->comm_rank();
string groupName(arg[1]);
int igroup = group->find(groupName.c_str());
int igroup = group->find(groupName);
int atomCount = group->count(igroup);
try {

4
src/DIELECTRIC/atom_vec_dielectric.cpp
View File

@ -78,9 +78,9 @@ AtomVecDielectric::AtomVecDielectric(LAMMPS *_lmp) : AtomVec(_lmp)
"mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_create = {"q", "molecule", "num_bond", "num_angle", "num_dihedral", "num_improper",
"nspecial", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_data_atom = { "id", "molecule", "type", "q", "x", "mu3", "area", "ed", "em", "epsilon",
fields_data_atom = {"id", "molecule", "type", "q", "x", "mu3", "area", "ed", "em", "epsilon",
"curvature"};
fields_data_vel = {"id v"};
fields_data_vel = {"id", "v"};
// clang-format on
setup_fields();

4
src/DPD-MESO/fix_mvv_dpd.cpp
View File

@ -17,8 +17,8 @@
modified velocity-Verlet (MVV) algorithm.
Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm.
Contributing author: Zhen Li (Brown University)
Email: zhen_li@brown.edu
Contributing author: Zhen Li (Clemson University)
Email: zli7@clemson.edu
------------------------------------------------------------------------- */
#include "fix_mvv_dpd.h"

4
src/DPD-MESO/fix_mvv_edpd.cpp
View File

@ -17,8 +17,8 @@
v and edpd_T) using the modified velocity-Verlet (MVV) algorithm.
Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm.
Contributing author: Zhen Li (Brown University)
Email: zhen_li@brown.edu
Contributing author: Zhen Li (Clemson University)
Email: zli7@clemson.edu
Please cite the related publication:
Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. "Energy-

4
src/DPD-MESO/fix_mvv_tdpd.cpp
View File

@ -17,8 +17,8 @@
v and cc) using the modified velocity-Verlet (MVV) algorithm.
Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm.
Contributing author: Zhen Li (Brown University)
Email: zhen_li@brown.edu
Contributing author: Zhen Li (Clemson University)
Email: zli7@clemson.edu
Please cite the related publication:
Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. "Transport

4
src/DPD-MESO/pair_edpd.cpp
View File

@ -13,8 +13,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Zhen Li (Brown University)
Email: zhen_li@brown.edu
Contributing author: Zhen Li (Clemson University)
Email: zli7@clemson.edu
------------------------------------------------------------------------- */
#include "pair_edpd.h"

4
src/DPD-MESO/pair_mdpd.cpp
View File

@ -13,8 +13,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Zhen Li (Brown University)
Email: zhen_li@brown.edu
Contributing author: Zhen Li (Clemson University)
Email: zli7@clemson.edu
------------------------------------------------------------------------- */
#include "pair_mdpd.h"

2
src/DPD-MESO/pair_mdpd_rhosum.cpp
View File

@ -17,7 +17,7 @@
before the force calculation.
The code uses 3D Lucy kernel, it can be modified for other kernels.
Contributing author: Zhen Li (Brown University)
Contributing author: Zhen Li (Clemson University)
------------------------------------------------------------------------- */
#include "pair_mdpd_rhosum.h"

4
src/DPD-MESO/pair_tdpd.cpp
View File

@ -13,8 +13,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Zhen Li (Brown University)
Email: zhen_li@brown.edu
Contributing author: Zhen Li (Clemson University)
Email: zli7@clemson.edu
------------------------------------------------------------------------- */
#include "pair_tdpd.h"

3
src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp
View File

@ -44,7 +44,7 @@ static const double sqrt_2_inv = std::sqrt(0.5);
/* ---------------------------------------------------------------------- */
PairSDPDTaitwaterIsothermal::PairSDPDTaitwaterIsothermal (LAMMPS *lmp)
: Pair (lmp) {
: Pair (lmp), random(nullptr) {
restartinfo = 0;
single_enable =0;
}
@ -61,6 +61,7 @@ PairSDPDTaitwaterIsothermal::~PairSDPDTaitwaterIsothermal () {
memory->destroy (soundspeed);
memory->destroy (B);
}
delete random;
}
/* ---------------------------------------------------------------------- */

76
src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp
View File

@ -11,10 +11,15 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
#include "compute_ave_sphere_atom.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
@ -98,7 +103,10 @@ void ComputeAveSphereAtom::init()
}
cutsq = cutoff * cutoff;
sphere_vol = 4.0 / 3.0 * MY_PI * cutsq * cutoff;
if (domain->dimension == 3)
volume = 4.0 / 3.0 * MY_PI * cutsq * cutoff;
else
volume = MY_PI * cutsq;
// need an occasional full neighbor list
@ -121,7 +129,7 @@ void ComputeAveSphereAtom::compute_peratom()
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
int *ilist, *jlist, *numneigh, **firstneigh;
int count;
double vsum[3], vavg[3], vnet[3];
double p[3], vcom[3], vnet[3];
invoked_peratom = update->ntimestep;
@ -152,12 +160,26 @@ void ComputeAveSphereAtom::compute_peratom()
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
double massone_i, massone_j, totalmass;
double adof = domain->dimension;
double mvv2e = force->mvv2e;
double mv2d = force->mv2d;
double boltz = force->boltz;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
if (rmass)
massone_i = rmass[i];
else
massone_i = mass[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
@ -167,13 +189,18 @@ void ComputeAveSphereAtom::compute_peratom()
// i atom contribution
count = 1;
vsum[0] = v[i][0];
vsum[1] = v[i][1];
vsum[2] = v[i][2];
totalmass = massone_i;
p[0] = v[i][0] * massone_i;
p[1] = v[i][1] * massone_i;
p[2] = v[i][2] * massone_i;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
if (rmass)
massone_j = rmass[j];
else
massone_j = mass[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -181,42 +208,45 @@ void ComputeAveSphereAtom::compute_peratom()
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq) {
count++;
vsum[0] += v[j][0];
vsum[1] += v[j][1];
vsum[2] += v[j][2];
totalmass += massone_j;
p[0] += v[j][0] * massone_j;
p[1] += v[j][1] * massone_j;
p[2] += v[j][2] * massone_j;
}
}
vavg[0] = vsum[0] / count;
vavg[1] = vsum[1] / count;
vavg[2] = vsum[2] / count;
vcom[0] = p[0] / totalmass;
vcom[1] = p[1] / totalmass;
vcom[2] = p[2] / totalmass;
// i atom contribution
count = 1;
vnet[0] = v[i][0] - vavg[0];
vnet[1] = v[i][1] - vavg[1];
vnet[2] = v[i][2] - vavg[2];
double ke_sum = vnet[0] * vnet[0] + vnet[1] * vnet[1] + vnet[2] * vnet[2];
vnet[0] = v[i][0] - vcom[0];
vnet[1] = v[i][1] - vcom[1];
vnet[2] = v[i][2] - vcom[2];
double ke_sum = massone_i * (vnet[0] * vnet[0] + vnet[1] * vnet[1] + vnet[2] * vnet[2]);
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
if (rmass)
massone_j = rmass[j];
else
massone_j = mass[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq) {
count++;
vnet[0] = v[j][0] - vavg[0];
vnet[1] = v[j][1] - vavg[1];
vnet[2] = v[j][2] - vavg[2];
ke_sum += vnet[0] * vnet[0] + vnet[1] * vnet[1] + vnet[2] * vnet[2];
vnet[0] = v[j][0] - vcom[0];
vnet[1] = v[j][1] - vcom[1];
vnet[2] = v[j][2] - vcom[2];
ke_sum += massone_j * (vnet[0] * vnet[0] + vnet[1] * vnet[1] + vnet[2] * vnet[2]);
}
}
double density = count / sphere_vol;
double temp = ke_sum / 3.0 / count;
double density = mv2d * totalmass / volume;
double temp = mvv2e * ke_sum / (adof * count * boltz);
result[i][0] = density;
result[i][1] = temp;
}

2
src/EXTRA-COMPUTE/compute_ave_sphere_atom.h
View File

@ -37,7 +37,7 @@ class ComputeAveSphereAtom : public Compute {
protected:
int nmax;
double cutoff, cutsq, sphere_vol;
double cutoff, cutsq, volume;
class NeighList *list;
double **result;

11
src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
View File

@ -266,7 +266,7 @@ void ComputeStressCartesian::compute_array()
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
double xi1, xi2, xj1, xj2;
double xi1, xi2;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@ -305,9 +305,6 @@ void ComputeStressCartesian::compute_array()
}
}
}
xj1 = x[j][dir1];
xj2 = x[j][dir2];
delx = x[j][0] - xtmp;
dely = x[j][1] - ytmp;
delz = x[j][2] - ztmp;
@ -318,7 +315,7 @@ void ComputeStressCartesian::compute_array()
// Check if inside cut-off
if (rsq >= cutsq[itype][jtype]) continue;
pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair);
compute_pressure(fpair, xi1, xi2, xj1, xj2, delx, dely, delz);
compute_pressure(fpair, xi1, xi2, delx, dely, delz);
}
}
@ -356,8 +353,8 @@ void ComputeStressCartesian::compute_array()
}
}
void ComputeStressCartesian::compute_pressure(double fpair, double xi, double yi, double xj,
double yj, double delx, double dely, double delz)
void ComputeStressCartesian::compute_pressure(double fpair, double xi, double yi, double delx,
double dely, double delz)
{
int bin1, bin2, next_bin1, next_bin2;
double la = 0.0, lb = 0.0, l_sum = 0.0;

2
src/EXTRA-COMPUTE/compute_stress_cartesian.h
View File

@ -41,7 +41,7 @@ class ComputeStressCartesian : public Compute {
double *dens, *pkxx, *pkyy, *pkzz, *pcxx, *pcyy, *pczz;
double *tdens, *tpkxx, *tpkyy, *tpkzz, *tpcxx, *tpcyy, *tpczz;
class NeighList *list;
void compute_pressure(double, double, double, double, double, double, double, double);
void compute_pressure(double, double, double, double, double, double);
};
} // namespace LAMMPS_NS

4
src/EXTRA-DUMP/dump_xtc.cpp
View File

@ -433,10 +433,10 @@ int xdropen(XDR *xdrs, const char *filename, const char *type)
return 0;
}
if (*type == 'w' || *type == 'W') {
type = (char *) "w+";
type = (char *) "wb+";
lmode = XDR_ENCODE;
} else {
type = (char *) "r";
type = (char *) "rb";
lmode = XDR_DECODE;
}
xdrfiles[xdrid] = fopen(filename, type);

6
src/EXTRA-DUMP/dump_yaml.cpp
View File

@ -124,6 +124,12 @@ void DumpYAML::write_data(int n, double *mybuf)
}
fputs("]\n", fp);
}
}
/* ---------------------------------------------------------------------- */
void DumpYAML::write_footer()
{
fputs("...\n", fp);
}

1
src/EXTRA-DUMP/dump_yaml.h
View File

@ -35,6 +35,7 @@ class DumpYAML : public DumpCustom {
void write() override;
void write_header(bigint) override;
void write_data(int, double *) override;
void write_footer() override;
int modify_param(int, char **) override;
};

2
src/INTERLAYER/pair_ilp_tmd.cpp
View File

@ -483,7 +483,7 @@ void PairILPTMD::calc_normal()
}
}
//############################ For the edge atoms of TMD ################################
else if (cont > 1 && cont < Nnei) {
else if (cont < Nnei) {
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0) {
// derivatives of Ni[l] respect to the cont neighbors

70
src/KOKKOS/compute_ave_sphere_atom_kokkos.cpp
View File

@ -11,11 +11,16 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
#include "compute_ave_sphere_atom_kokkos.h"
#include "atom_kokkos.h"
#include "atom_masks.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "memory_kokkos.h"
@ -105,11 +110,19 @@ void ComputeAveSphereAtomKokkos<DeviceType>::compute_peratom()
// compute properties for each atom in group
// use full neighbor list to count atoms less than cutoff
atomKK->sync(execution_space,X_MASK|V_MASK|TYPE_MASK|MASK_MASK);
atomKK->sync(execution_space,X_MASK|V_MASK|RMASS_MASK|TYPE_MASK|MASK_MASK);
x = atomKK->k_x.view<DeviceType>();
v = atomKK->k_v.view<DeviceType>();
rmass = atomKK->k_rmass.view<DeviceType>();
mass = atomKK->k_mass.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
adof = domain->dimension;
mvv2e = force->mvv2e;
mv2d = force->mv2d;
boltz = force->boltz;
Kokkos::deep_copy(d_result,0.0);
copymode = 1;
@ -125,8 +138,13 @@ template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void ComputeAveSphereAtomKokkos<DeviceType>::operator()(TagComputeAveSphereAtom, const int &ii) const
{
double massone_i,massone_j;
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
if (rmass.data()) massone_i = rmass[i];
else massone_i = mass[type[i]];
const X_FLOAT xtmp = x(i,0);
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
@ -135,14 +153,17 @@ void ComputeAveSphereAtomKokkos<DeviceType>::operator()(TagComputeAveSphereAtom,
// i atom contribution
int count = 1;
double vsum[3];
vsum[0] = v(i,0);
vsum[1] = v(i,1);
vsum[2] = v(i,2);
double totalmass = massone_i;
double p[3];
p[0] = v(i,0)*massone_i;
p[1] = v(i,1)*massone_i;
p[2] = v(i,2)*massone_i;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
if (rmass.data()) massone_j = rmass[j];
else massone_j = mass[type[j]];
const F_FLOAT delx = x(j,0) - xtmp;
const F_FLOAT dely = x(j,1) - ytmp;
@ -150,44 +171,45 @@ void ComputeAveSphereAtomKokkos<DeviceType>::operator()(TagComputeAveSphereAtom,
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
count++;
vsum[0] += v(j,0);
vsum[1] += v(j,1);
vsum[2] += v(j,2);
totalmass += massone_j;
p[0] += v(j,0)*massone_j;
p[1] += v(j,1)*massone_j;
p[2] += v(j,2)*massone_j;
}
}
double vavg[3];
vavg[0] = vsum[0]/count;
vavg[1] = vsum[1]/count;
vavg[2] = vsum[2]/count;
double vcom[3];
vcom[0] = p[0]/totalmass;
vcom[1] = p[1]/totalmass;
vcom[2] = p[2]/totalmass;
// i atom contribution
count = 1;
double vnet[3];
vnet[0] = v(i,0) - vavg[0];
vnet[1] = v(i,1) - vavg[1];
vnet[2] = v(i,2) - vavg[2];
double ke_sum = vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2];
vnet[0] = v(i,0) - vcom[0];
vnet[1] = v(i,1) - vcom[1];
vnet[2] = v(i,2) - vcom[2];
double ke_sum = massone_i * (vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2]);
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
if (rmass.data()) massone_j = rmass[j];
else massone_j = mass[type[j]];
const F_FLOAT delx = x(j,0) - xtmp;
const F_FLOAT dely = x(j,1) - ytmp;
const F_FLOAT delz = x(j,2) - ztmp;
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
count++;
vnet[0] = v(j,0) - vavg[0];
vnet[1] = v(j,1) - vavg[1];
vnet[2] = v(j,2) - vavg[2];
ke_sum += vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2];
vnet[0] = v(j,0) - vcom[0];
vnet[1] = v(j,1) - vcom[1];
vnet[2] = v(j,2) - vcom[2];
ke_sum += massone_j * (vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2]);
}
}
double density = count/sphere_vol;
double temp = ke_sum/3.0/count;
double density = mv2d*totalmass/volume;
double temp = mvv2e*ke_sum/(adof*count*boltz);
d_result(i,0) = density;
d_result(i,1) = temp;
}

13
src/KOKKOS/compute_ave_sphere_atom_kokkos.h
View File

@ -46,13 +46,18 @@ template <class DeviceType> class ComputeAveSphereAtomKokkos : public ComputeAve
void operator()(TagComputeAveSphereAtom, const int &) const;
private:
typename AT::t_x_array_randomread x;
typename AT::t_v_array_randomread v;
double adof,mvv2e,mv2d,boltz;
typename AT::t_x_array x;
typename AT::t_v_array v;
typename ArrayTypes<DeviceType>::t_float_1d rmass;
typename ArrayTypes<DeviceType>::t_float_1d mass;
typename ArrayTypes<DeviceType>::t_int_1d type;
typename ArrayTypes<DeviceType>::t_int_1d mask;
typename AT::t_neighbors_2d d_neighbors;
typename AT::t_int_1d_randomread d_ilist;
typename AT::t_int_1d_randomread d_numneigh;
typename AT::t_int_1d d_ilist;
typename AT::t_int_1d d_numneigh;
DAT::tdual_float_2d k_result;
typename AT::t_float_2d d_result;

3
src/KOKKOS/pair_pace_kokkos.cpp
View File

@ -534,8 +534,7 @@ void PairPACEKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
copymode = 1;
int newton_pair = force->newton_pair;
if (newton_pair == false)
if (!force->newton_pair)
error->all(FLERR,"PairPACEKokkos requires 'newton on'");
if (recursive)

2
src/KOKKOS/pair_reaxff_kokkos.cpp
View File

@ -2628,7 +2628,7 @@ int PairReaxFFKokkos<DeviceType>::preprocess_angular(int i, int itype, int j_sta
template<class DeviceType>
template<bool POPULATE>
KOKKOS_INLINE_FUNCTION
int PairReaxFFKokkos<DeviceType>::preprocess_torsion(int i, int /*itype*/, int itag,
int PairReaxFFKokkos<DeviceType>::preprocess_torsion(int i, int /*itype*/, tagint itag,
F_FLOAT xtmp, F_FLOAT ytmp, F_FLOAT ztmp, int j_start, int j_end, int location_torsion) const {
// in reaxff_torsion_angles: j = i, k = j, i = k;

2
src/KOKKOS/pair_reaxff_kokkos.h
View File

@ -257,7 +257,7 @@ class PairReaxFFKokkos : public PairReaxFF {
// Abstraction for counting and populating torsion intermediated
template<bool POPULATE>
KOKKOS_INLINE_FUNCTION
int preprocess_torsion(int, int, int, F_FLOAT, F_FLOAT, F_FLOAT, int, int, int) const;
int preprocess_torsion(int, int, tagint, F_FLOAT, F_FLOAT, F_FLOAT, int, int, int) const;
template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION

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