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Merge branch 'develop' into improve_type_label_support

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This commit is contained in:
Axel Kohlmeyer
2024-06-20 08:56:02 -04:00
parent 11ef510a93 71c5e04121
commit 2dc7de417a
127 changed files with 11675 additions and 485 deletions
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3
.github/CODEOWNERS vendored
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@ -38,6 +38,7 @@ src/ML-HDNNP/* @singraber
src/ML-IAP/* @athomps
src/ML-PACE/* @yury-lysogorskiy
src/ML-POD/* @exapde
src/ML-UF3/* @monk-04
src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
@ -72,6 +73,8 @@ src/MC/fix_sgcmc.* @athomps
src/REAXFF/compute_reaxff_atom.* @rbberger
src/KOKKOS/compute_reaxff_atom_kokkos.* @rbberger
src/REPLICA/fix_pimd_langevin.* @Yi-FanLi
src/DPD-BASIC/pair_dpd_coul_slater_long.* @Eddy-Barraud
src/GPU/pair_dpd_coul_slater_long.* @Eddy-Barraud
# core LAMMPS classes
src/lammps.* @sjplimp

4
cmake/CMakeLists.txt
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@ -256,6 +256,7 @@ set(STANDARD_PACKAGES
DRUDE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -285,6 +286,7 @@ set(STANDARD_PACKAGES
ML-RANN
ML-SNAP
ML-POD
ML-UF3
MOFFF
MOLECULE
MOLFILE
@ -689,7 +691,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()

9
cmake/Modules/Packages/DPD-BASIC.cmake Normal file
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@ -0,0 +1,9 @@
# pair style dpd/coul/slater/long may only be installed if also KSPACE is installed
if(NOT PKG_KSPACE)
get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.h)
set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

20
cmake/Modules/Packages/PLUMED.cmake
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@ -1,5 +1,9 @@
# Plumed2 support for PLUMED package
# for supporting multiple concurrent plumed2 installations for debugging and testing
set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
mark_as_advanced(PLUMED_SUFFIX)
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
@ -21,9 +25,11 @@ else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.3/plumed-src-2.8.3.tgz"
# Note: must also adjust check for supported API versions in
# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.1/plumed-src-2.9.1.tgz"
CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "76d23cd394eba9e6530316ed1184e219" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
@ -151,15 +157,15 @@ else()
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed)
pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
if(PLUMED_MODE STREQUAL "STATIC")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static)
elseif(PLUMED_MODE STREQUAL "SHARED")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.shared)
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${PLUMED_SUFFIX}Kernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.runtime)
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")

2
cmake/packaging/build_linux_tgz.sh
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@ -59,12 +59,14 @@ done
echo "Set up wrapper script"
MYDIR=$(dirname "$0")
cp ${MYDIR}/xdg-open ${DESTDIR}/bin
cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
for s in ${DESTDIR}/bin/*
do \
EXE=$(basename $s)
test ${EXE} = linux_wrapper.sh && continue
test ${EXE} = qt.conf && continue
test ${EXE} = xdg-open && continue
ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
done

14
cmake/packaging/linux_wrapper.sh
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@ -4,15 +4,17 @@
# reset locale to avoid problems with decimal numbers
export LC_ALL=C
BASEDIR=$(dirname "$0")
EXENAME=$(basename "$0")
BASEDIR="$(dirname "$0")"
EXENAME="$(basename "$0")"
PATH="${BASEDIR}/bin:${PATH}"
# append to LD_LIBRARY_PATH to prefer local (newer) libs
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib
LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BASEDIR}/lib"
# set some environment variables for LAMMPS etc.
LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials
MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files
export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY
LAMMPS_POTENTIALS="${BASEDIR}/share/lammps/potentials"
MSI2LMP_LIBRARY="${BASEDIR}/share/lammps/frc_files"
export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH
exec "${BASEDIR}/bin/${EXENAME}" "$@"

1074
cmake/packaging/xdg-open Executable file
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File diff suppressed because it is too large Load Diff

2
cmake/presets/all_off.cmake
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@ -28,6 +28,7 @@ set(ALL_PACKAGES
DRUDE
ELECTRODE
EFF
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -60,6 +61,7 @@ set(ALL_PACKAGES
ML-QUIP
ML-RANN
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE

2
cmake/presets/all_on.cmake
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@ -30,6 +30,7 @@ set(ALL_PACKAGES
DRUDE
ELECTRODE
EFF
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -62,6 +63,7 @@ set(ALL_PACKAGES
ML-QUIP
ML-RANN
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE

2
cmake/presets/mingw-cross.cmake
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@ -24,6 +24,7 @@ set(WIN_PACKAGES
DRUDE
ELECTRODE
EFF
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -50,6 +51,7 @@ set(WIN_PACKAGES
ML-POD
ML-RANN
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE

2
cmake/presets/most.cmake
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@ -26,6 +26,7 @@ set(ALL_PACKAGES
DRUDE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -45,6 +46,7 @@ set(ALL_PACKAGES
ML-IAP
ML-POD
ML-SNAP
ML-UF3
MOFFF
MOLECULE
OPENMP

2
cmake/presets/windows.cmake
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@ -22,6 +22,7 @@ set(WIN_PACKAGES
DRUDE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -42,6 +43,7 @@ set(WIN_PACKAGES
ML-IAP
ML-POD
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE

4
doc/src/Commands_bond.rst
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@ -27,7 +27,7 @@ OPT.
* :doc:`none <bond_none>`
* :doc:`zero <bond_zero>`
* :doc:`hybrid <bond_hybrid>`
* :doc:`hybrid (k) <bond_hybrid>`
*
*
*
@ -72,7 +72,7 @@ OPT.
* :doc:`none <angle_none>`
* :doc:`zero <angle_zero>`
* :doc:`hybrid (k) <angle_hybrid>`
* :doc:`hybrid <angle_hybrid>`
*
*
*

14
doc/src/Commands_pair.rst
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@ -25,16 +25,16 @@ OPT.
* :doc:`none <pair_none>`
* :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>`
* :doc:`hybrid/scaled <pair_hybrid>`
* :doc:`hybrid (ko) <pair_hybrid>`
* :doc:`hybrid/molecular (o) <pair_hybrid>`
* :doc:`hybrid/overlay (ko) <pair_hybrid>`
* :doc:`hybrid/scaled (o) <pair_hybrid>`
* :doc:`kim <pair_kim>`
* :doc:`list <pair_list>`
* :doc:`tracker <pair_tracker>`
*
*
*
*
* :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@ -94,9 +94,10 @@ OPT.
* :doc:`coul/wolf (ko) <pair_coul>`
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (giko) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
* :doc:`dpd/ext (ko) <pair_dpd_ext>`
* :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (gko) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>`
@ -269,7 +270,7 @@ OPT.
* :doc:`smd/ulsph <pair_smd_ulsph>`
* :doc:`smtbq <pair_smtbq>`
* :doc:`snap (ik) <pair_snap>`
* :doc:`soft (go) <pair_soft>`
* :doc:`soft (gko) <pair_soft>`
* :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
* :doc:`sph/idealgas <pair_sph_idealgas>`
* :doc:`sph/lj (g) <pair_sph_lj>`
@ -303,6 +304,7 @@ OPT.
* :doc:`tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`tri/lj <pair_tri_lj>`
* :doc:`ufm (got) <pair_ufm>`
* :doc:`uf3 (k) <pair_uf3>`
* :doc:`vashishta (gko) <pair_vashishta>`
* :doc:`vashishta/table (o) <pair_vashishta>`
* :doc:`wf/cut <pair_wf_cut>`

51
doc/src/Packages_details.rst
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@ -52,6 +52,7 @@ page gives those details.
* :ref:`DRUDE <PKG-DRUDE>`
* :ref:`EFF <PKG-EFF>`
* :ref:`ELECTRODE <PKG-ELECTRODE>`
* :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
* :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
* :ref:`EXTRA-DUMP <PKG-EXTRA-DUMP>`
* :ref:`EXTRA-FIX <PKG-EXTRA-FIX>`
@ -84,6 +85,7 @@ page gives those details.
* :ref:`ML-QUIP <PKG-ML-QUIP>`
* :ref:`ML-RANN <PKG-ML-RANN>`
* :ref:`ML-SNAP <PKG-ML-SNAP>`
* :ref:`ML-UF3 <PKG-ML-UF3>`
* :ref:`MOFFF <PKG-MOFFF>`
* :ref:`MOLECULE <PKG-MOLECULE>`
* :ref:`MOLFILE <PKG-MOLFILE>`
@ -676,7 +678,12 @@ DPD-BASIC package
Pair styles for the basic dissipative particle dynamics (DPD) method
and DPD thermostatting.
**Author:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP)
Pair style :doc:`dpd/coul/slater/long <pair_dpd_coul_slater_long>` also
includes smeared charges for coulomb interactions and thus requires the
:ref:`KSPACE <PKG-KSPACE>` package to be installed to handle the long-range
Coulomb part of the interactions.
**Authors:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP), Eddy Barraud (IFPEN)
**Supporting info:**
@ -685,6 +692,7 @@ and DPD thermostatting.
* :doc:`pair_style dpd/tstat <pair_dpd>`
* :doc:`pair_style dpd/ext <pair_dpd_ext>`
* :doc:`pair_style dpd/ext/tstat <pair_dpd_ext>`
* :doc:`pair_style dpd/coul/slater/long <pair_dpd_coul_slater_long>`
* examples/PACKAGES/dpd-basic
----------
@ -886,6 +894,22 @@ This package has :ref:`specific installation instructions <electrode>` on the
----------
.. _PKG-EXTRA-COMMAND:
EXTRA-COMMAND package
---------------------
**Contents:**
Additional command styles that are less commonly used.
**Supporting info:**
* src/EXTRA-COMMAND: filenames -> commands
* :doc:`general commands <Commands_all>`
----------
.. _PKG-EXTRA-COMPUTE:
EXTRA-COMPUTE package
@ -1925,6 +1949,31 @@ computes which analyze attributes of the potential.
----------
.. _PKG-ML-UF3:
ML-UF3 package
--------------
**Contents:**
A pair style for the ultra-fast force field potentials (UF3). UF3 is a
methodology for deriving a highly accurate classical potential which is
fast to evaluate and is fitted to a large archives of quantum mechanical
(DFT) data. The use of b-spline basis set in UF3 enables the rapid
evaluation of 2-body and 3-body interactions.
**Authors:** Ajinkya C Hire (University of Florida),
Hendrik Krass (University of Constance),
Matthias Rupp (Luxembourg Institute of Science and Technology),
Richard Hennig (University of Florida)
**Supporting info:**
* src/ML-UF3: filenames -> commands
* :doc:`pair_style uf3 <pair_uf3>`
* examples/uf3
* https://github.com/uf3/uf3
.. _PKG-MOFFF:
MOFFF package

10
doc/src/Packages_list.rst
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@ -158,6 +158,11 @@ whether an extra library is needed to build and use the package:
- :doc:`fix electrode/conp <fix_electrode>`
- PACKAGES/electrode
- no
* - :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
- additional command styles
- :doc:`general commands <Commands_all>`
- n/a
- no
* - :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
- additional compute styles
- :doc:`compute <compute>`
@ -318,6 +323,11 @@ whether an extra library is needed to build and use the package:
- :doc:`pair_style snap <pair_snap>`
- snap
- no
* - :ref:`ML-UF3 <PKG-ML-UF3>`
- quantum-fitted ultra fast potentials
- :doc:`pair_style uf3 <pair_uf3>`
- PACKAGES/uf3
- no
* - :ref:`MOFFF <PKG-MOFFF>`
- styles for `MOF-FF <MOFplus_>`_ force field
- :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>`

33
doc/src/Tools.rst
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@ -728,8 +728,8 @@ CMake is required.
The LAMMPS GUI has been successfully compiled and tested on:
- Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
- Fedora Linux 38 x86\_64 using GCC 13 and Clang 16, Qt version 5.15LTS
- Fedora Linux 38 x86\_64 using GCC 13, Qt version 6.5LTS
- Fedora Linux 40 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.5LTS
- Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
@ -771,22 +771,23 @@ if necessary. When both, Qt5 and Qt6 are available, Qt6 will be preferred
unless ``-D LAMMPS_GUI_USE_QT5=yes`` is set.
It should be possible to build the LAMMPS GUI as a standalone
compilation (e.g. when LAMMPS has been compiled with traditional make),
then the CMake configuration needs to be told where to find the LAMMPS
compilation (e.g. when LAMMPS has been compiled with traditional make).
Then the CMake configuration needs to be told where to find the LAMMPS
headers and the LAMMPS library, via ``-D
LAMMPS_SOURCE_DIR=/path/to/lammps/src``. CMake will try to guess a
build folder with the LAMMPS library from that path, but it can also be
set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
Rather than linking to the LAMMPS library during compilation, it is also
possible to compile the GUI with a plugin loader library that will load
possible to compile the GUI with a plugin loader that will load
the LAMMPS library dynamically at runtime during the start of the GUI
from a shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or
``liblammps.dll`` (depending on the operating system). This has the
advantage that the LAMMPS library can be updated LAMMPS without having
to recompile the GUI. The ABI of the LAMMPS C-library interface is very
stable and generally backward compatible. This feature is enabled by
setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
advantage that the LAMMPS library can be built from updated or modified
LAMMPS source without having to recompile the GUI. The ABI of the
LAMMPS C-library interface is very stable and generally backward
compatible. This feature is enabled by setting
``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
would be the ``examples/COUPLE/plugin`` folder of the LAMMPS
distribution.
@ -798,8 +799,8 @@ macOS
"""""
When building on macOS, the build procedure will try to manufacture a
drag-n-drop installer, LAMMPS-macOS-multiarch.dmg, when using the 'dmg'
target (i.e. ``cmake --build <build dir> --target dmg`` or ``make dmg``.
drag-n-drop installer, ``LAMMPS-macOS-multiarch.dmg``, when using the
'dmg' target (i.e. ``cmake --build <build dir> --target dmg`` or ``make dmg``.
To build multi-arch executables that will run on both, arm64 and x86_64
architectures natively, it is necessary to set the CMake variable ``-D
@ -839,11 +840,11 @@ and LAMMPS GUI can be launched from anywhere from the command line.
The standard CMake build procedure can be applied and the
``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake
command will automatically include a suitable CMake toolset file (the
regular cmake command can be used after that). After building the
libraries and executables, you can build the target 'zip'
(i.e. ``cmake --build <build dir> --target zip`` or ``make zip``
to stage all installed files into a LAMMPS_GUI folder and then
run a script to copy all required dependencies, some other files,
regular cmake command can be used after that to modify the configuration
settings, if needed). After building the libraries and executables,
you can build the target 'zip' (i.e. ``cmake --build <build dir> --target zip``
or ``make zip`` to stage all installed files into a LAMMPS_GUI folder
and then run a script to copy all required dependencies, some other files,
and create a zip file from it.
Linux

2
doc/src/fix_deform.rst
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@ -64,6 +64,8 @@ Syntax
effectively an engineering shear strain rate
*erate* value = R
R = engineering shear strain rate (1/time units)
*erate/rescale* value = R (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
R = engineering shear strain rate (1/time units)
*trate* value = R
R = true shear strain rate (1/time units)
*wiggle* values = A Tp

31
doc/src/fix_sgcmc.rst
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@ -15,7 +15,7 @@ Syntax
* every_nsteps = number of MD steps between MC cycles
* swap_fraction = fraction of a full MC cycle carried out at each call (a value of 1.0 will perform as many trial moves as there are atoms)
* temperature = temperature that enters Boltzmann factor in Metropolis criterion (usually the same as MD temperature)
* deltamu = chemical potential difference(s) (`N-1` values must be provided, with `N` being the number of elements)
* deltamu = `N-1` chemical potential differences :math:`\mu_1-\mu_2, \ldots, \mu_1-\mu_N` (`N` is the number of atom types)
* Zero or more keyword/value pairs may be appended to fix definition line:
.. parsed-literal::
@ -23,7 +23,7 @@ Syntax
keyword = *variance* or *randseed* or *window_moves* or *window_size*
*variance* kappa conc1 [conc2] ... [concN]
kappa = variance constraint parameter
conc1,conc2,... = target concentration(s) in the range 0.0-1.0 (*N-1* values must be provided, with *N* being the number of elements)
`c_2`, `c_3`,..., `c_N` = `N-1` target concentration fractions
*randseed* N
N = seed for pseudo random number generator
*window_moves* N
@ -90,11 +90,10 @@ the simulation, e.g., to speed up equilibration at low temperatures.
------------
The parameter *deltamu* is used to set the chemical potential difference
in the SGC MC algorithm (see Eq. 16 in :ref:`Sadigh1 <Sadigh1>`). By
convention it is the difference of the chemical potentials of elements
`B`, `C` ..., with respect to element A. When the simulation includes
`N` elements, `N-1` values must be specified.
The parameter *deltamu* is used to set the chemical potential differences
in the SGC MC algorithm (see Eq. 16 in :ref:`Sadigh1 <Sadigh1>`).
The `N-1` differences are defined as :math:`\mu_1-\mu_2, \ldots, \mu_1-\mu_N`,
where `N` is the number of atom types.
------------
@ -104,12 +103,12 @@ the effective average constraint in the parallel VC-SGC MC algorithm
(parameter :math:`\delta\mu_0` in Eq. (20) of :ref:`Sadigh1
<Sadigh1>`). The parameter *kappa* specifies the variance constraint
(see Eqs. (20-21) in :ref:`Sadigh1 <Sadigh1>`).
The parameter *conc* sets the target concentration (parameter
:math:`c_0` in Eqs. (20-21) of :ref:`Sadigh1 <Sadigh1>`). The atomic
concentrations refer to components `B`, `C` ..., with `A` being set
automatically. When the simulation includes `N` elements, `N-1`
concentration values must be specified.
The parameter *conc* sets the `N-1` target atomic concentration
fractions (parameter :math:`c_0` in Eqs. (20-21) of :ref:`Sadigh1 <Sadigh1>`)
:math:`0 \le c_2, \ldots, c_N \le 1`, with
:math:`c_1 = 1 - \Sigma_{i=2}^N c_i`.
When the simulation includes `N` atom types (elements),
`N-1` concentration values must be specified.
------------
@ -143,10 +142,10 @@ components of the vector represent the following quantities:
* 1 = The absolute number of accepted trial swaps during the last MC step
* 2 = The absolute number of rejected trial swaps during the last MC step
* 3 = The current global concentration of species *A* (= number of atoms of type 1 / total number of atoms)
* 4 = The current global concentration of species *B* (= number of atoms of type 2 / total number of atoms)
* 3 = Current global concentration `c_1` (= number of atoms of type 1 / total number of atoms)
* 4 = Current global concentration `c_2` (= number of atoms of type 2 / total number of atoms)
* ...
* N+2: The current global concentration of species *X* (= number of atoms of type *N* / total number of atoms)
* N+2: Current global concentration `c_N` (= number of atoms of type *N* / total number of atoms)
The vector values calculated by this fix are "intensive".

12
doc/src/fix_wall_gran.rst
View File

@ -115,6 +115,18 @@ friction and twisting friction supported by the :doc:`pair_style granular <pair_
supported for walls. These are discussed in greater detail on the doc
page for :doc:`pair_style granular <pair_granular>`.
.. note::
When *fstyle* *granular* is specified, the associated *fstyle_params* are taken as
those for a wall/particle interaction. For example, for the *hertz/material* normal
contact model with :math:`E = 960` and :math:`\nu = 0.2`, the effective Young's
modulus for a wall/particle interaction is computed as
:math:`E_{eff} = \frac{960}{2(1-0.2^2)} = 500`. Any pair coefficients defined by
:doc:`pair_style granular <pair_granular>` are not taken into consideration. To
model different wall/particle interactions for particles of different material
types, the user may define multiple fix wall/gran commands operating on separate
groups (e.g. based on particle type) each with a different wall/particle effective
Young's modulus.
Note that you can choose a different force styles and/or different
values for the wall/particle coefficients than for particle/particle
interactions. E.g. if you wish to model the wall as a different

64
doc/src/group2ndx.rst
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@ -34,32 +34,66 @@ Description
Write or read a Gromacs style index file in text format that associates
atom IDs with the corresponding group definitions. This index file can be
used with in combination with Gromacs analysis tools or to import group
definitions into the :doc:`fix colvars <fix_colvars>` input file. It can
also be used to save and restore group definitions for static groups.
definitions into the :doc:`fix colvars <fix_colvars>` input file.
It can also be used to save and restore group definitions for static groups
using the individual atom IDs. This may be important if the original
group definition depends on a region or otherwise on the geometry and thus
cannot be easily recreated.
Another application would be to import atom groups defined for Gromacs
simulation into LAMMPS. When translating Gromacs topology and geometry
data to LAMMPS.
The *group2ndx* command will write group definitions to an index file.
Without specifying any group IDs, all groups will be written to the index
file. When specifying group IDs, only those groups will be written to the
index file. In order to follow the Gromacs conventions, the group *all*
will be renamed to *System* in the index file.
Without specifying any group IDs, all groups will be written to the
index file. When specifying group IDs, only those groups will be
written to the index file. In order to follow the Gromacs conventions,
the group *all* will be renamed to *System* in the index file.
The *ndx2group* command will create of update group definitions from those
stored in an index file. Without specifying any group IDs, all groups except
*System* will be read from the index file and the corresponding groups
recreated. If a group of the same name already exists, it will be completely
reset. When specifying group IDs, those groups, if present, will be read
from the index file and restored.
The *ndx2group* command will create of update group definitions from
those stored in an index file. Without specifying any group IDs, all
groups except *System* will be read from the index file and the
corresponding groups recreated. If a group of the same name already
exists, it will be completely reset. When specifying group IDs, those
groups, if present, will be read from the index file and restored.
File Format
"""""""""""
The file format is equivalent and compatible with what is produced by
the `Gromacs make_ndx command <https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html>`_.
and follows the `Gromacs definition of an ndx file <https://manual.gromacs.org/current/reference-manual/file-formats.html#ndx>`_
Each group definition begins with the group name in square brackets with
blanks, e.g. \[ water \] and is then followed by the list of atom
indices, which may be spread over multiple lines. Here is a small
example file:
.. code-block:: ini
[ Oxygen ]
1 4 7
[ Hydrogen ]
2 3 5 6
8 9
[ Water ]
1 2 3 4 5 6 7 8 9
The index file defines 3 groups: Oxygen, Hydrogen, and Water and the
latter happens to be the union of the first two.
----------
Restrictions
""""""""""""
This command requires that atoms have atom IDs, since this is the
These commands require that atoms have atom IDs, since this is the
information that is written to the index file.
These commands are part of the COLVARS package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
These commands are part of the EXTRA-COMMAND package. They are only
enabled if LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""

179
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@ -0,0 +1,179 @@
.. index:: pair_style dpd/coul/slater/long
.. index:: pair_style dpd/coul/slater/long/gpu
pair_style dpd/coul/slater/long command
=======================================
Accelerator Variants: *dpd/coul/slater/long/gpu*
Syntax
""""""
.. code-block:: LAMMPS
pair_style dpd/coul/slater/long T cutoff_DPD seed lambda cutoff_coul
pair_coeff I J a_IJ Gamma is_charged
* T = temperature (temperature units) (dpd only)
* cutoff_DPD = global cutoff for DPD interactions (distance units)
* seed = random # seed (positive integer)
* lambda = decay length of the charge (distance units)
* cutoff_coul = real part cutoff for Coulombic interactions (distance units)
* I,J = numeric atom types, or type labels
* Gamma = DPD Gamma coefficient
* is_charged (boolean) set to yes if I and J are charged beads
Examples
""""""""
.. code-block:: LAMMPS
pair_style dpd/coul/slater/long 1.0 2.5 34387 0.25 3.0
pair_coeff 1 1 78.0 4.5 # not charged by default
pair_coeff 2 2 78.0 4.5 yes
Description
"""""""""""
.. versionadded:: TBD
Style *dpd/coul/slater/long* computes a force field for dissipative particle dynamics
(DPD) following the exposition in :ref:`(Groot) <Groot5>` with the addition of
electrostatic interactions. The coulombic forces in mesoscopic models
employ potentials without explicit excluded-volume interactions.
The goal is to prevent artificial ionic pair formation by including a charge
distribution in the Coulomb potential, following the formulation of
:ref:`(Melchor) <Melchor1>`:
The force on bead I due to bead J is given as a sum
of 4 terms
.. math::
\vec{f} = & (F^C + F^D + F^R + F^E) \hat{r_{ij}} \\
F^C = & A w(r) \qquad \qquad \qquad \qquad \qquad r < r_c \\
F^D = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v}_{ij}) \qquad \qquad r < r_c \\
F^R = & \sigma w(r) \alpha (\Delta t)^{-1/2} \qquad \qquad \qquad r < r_c \\
w(r) = & 1 - \frac{r}{r_c} \\
F^E = & \frac{Cq_iq_j}{\epsilon r^2} \left( 1- exp\left( \frac{2r_{ij}}{\lambda} \right) \left( 1 + \frac{2r_{ij}}{\lambda} \left( 1 + \frac{r_{ij}}{\lambda} \right)\right) \right)
where :math:`F^C` is a conservative force, :math:`F^D` is a dissipative
force, :math:`F^R` is a random force, and :math:`F^E` is an electrostatic force.
:math:`\hat{r_{ij}}` is a unit vector in the direction
:math:`r_i - r_j`, :math:`\vec{v}_{ij}` is
the vector difference in velocities of the two atoms :math:`\vec{v}_i -
\vec{v}_j`, :math:`\alpha` is a Gaussian random number with zero mean
and unit variance, *dt* is the timestep size, and :math:`w(r)` is a
weighting factor that varies between 0 and 1. :math:`r_c` is the
pairwise cutoff. :math:`\sigma` is set equal to :math:`\sqrt{2 k_B T
\gamma}`, where :math:`k_B` is the Boltzmann constant and *T* is the
temperature parameter in the pair_style command.
C is the same Coulomb conversion factor as in the pair_styles
coul/cut and coul/long. In this way the Coulomb
interaction between ions is corrected at small distances r, and
the long-range interactions are computed either by the Ewald or the PPPM technique.
The following parameters must be defined for each
pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in
the examples above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* A (force units)
* :math:`\gamma` (force/velocity units)
* is_charged (boolean)
.. note::
This style is the combination of :doc:`pair_style dpd <pair_dpd>` and :doc:`pair_style coul/slater/long <pair_coul_slater>`.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift option for the energy of the pair interaction.
The :doc:`pair_modify <pair_modify>` table option is not relevant
for this pair style.
This pair style does not support the :doc:`pair_modify <pair_modify>`
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to :doc:`binary restart files
<restart>`, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file. Note that the
user-specified random number seed is stored in the restart file, so when
a simulation is restarted, each processor will re-initialize its random
number generator the same way it did initially. This means the random
forces will be random, but will not be the same as they would have been
if the original simulation had continued past the restart time.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*, *middle*, *outer* keywords.
----------
Restrictions
""""""""""""
This style is part of the DPD-BASIC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
The default frequency for rebuilding neighbor lists is every 10 steps
(see the :doc:`neigh_modify <neigh_modify>` command). This may be too
infrequent since particles move rapidly and
can overlap by large amounts. If this setting yields a non-zero number
of "dangerous" reneighborings (printed at the end of a simulation), you
should experiment with forcing reneighboring more often and see if
system energies/trajectories change.
This pair style requires you to use the :doc:`comm_modify vel yes
<comm_modify>` command so that velocities are stored by ghost atoms.
This pair style also requires the long-range solvers included in the KSPACE package.
This pair style will not restart exactly when using the
:doc:`read_restart <read_restart>` command, though they should provide
statistically similar results. This is because the forces they compute
depend on atom velocities. See the :doc:`read_restart <read_restart>`
command for more details.
Related commands
""""""""""""""""
:doc:`pair_style dpd <pair_dpd>`, :doc:`pair_style coul/slater/long <pair_coul_slater>`,
:doc:`pair_coeff <pair_coeff>`, :doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`,
:doc:`pair_style srp <pair_srp>`, :doc:`fix mvv/dpd <fix_mvv_dpd>`.
Default
"""""""
is_charged = no
----------
.. _Groot5:
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
.. _Melchor1:
**(Melchor)** Gonzalez-Melchor, Mayoral, Velazquez, and Alejandre, J Chem Phys, 125, 224107 (2006).

30
doc/src/pair_granular.rst
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@ -111,7 +111,7 @@ For the *hertz* model, the normal component of force is given by:
\mathbf{F}_{ne, Hertz} = k_n R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n}
Here, :math:`R_{eff} = \frac{R_i R_j}{R_i + R_j}` is the effective
Here, :math:`R_{eff} = R = \frac{R_i R_j}{R_i + R_j}` is the effective
radius, denoted for simplicity as *R* from here on. For *hertz*, the
units of the spring constant :math:`k_n` are *force*\ /\ *length*\ \^2, or
equivalently *pressure*\ .
@ -120,13 +120,14 @@ For the *hertz/material* model, the force is given by:
.. math::
\mathbf{F}_{ne, Hertz/material} = \frac{4}{3} E_{eff} R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n}
\mathbf{F}_{ne, Hertz/material} = \frac{4}{3} E_{eff} R^{1/2}\delta_{ij}^{3/2} \mathbf{n}
Here, :math:`E_{eff} = E = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\right)^{-1}` is the effective Young's
modulus, with :math:`\nu_i, \nu_j` the Poisson ratios of the particles of
types *i* and *j*\ . Note that if the elastic modulus and the shear
modulus of the two particles are the same, the *hertz/material* model
is equivalent to the *hertz* model with :math:`k_n = 4/3 E_{eff}`
Here, :math:`E_{eff} = E = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\right)^{-1}`
is the effective Young's modulus, with :math:`\nu_i, \nu_j` the Poisson ratios
of the particles of types *i* and *j*. :math:`E_{eff}` is denoted as *E* from here on.
Note that if the elastic modulus and the shear modulus of the two particles are the
same, the *hertz/material* model is equivalent to the *hertz* model with
:math:`k_n = 4/3 E`
The *dmt* model corresponds to the
:ref:`(Derjaguin-Muller-Toporov) <DMT1975>` cohesive model, where the force
@ -270,7 +271,8 @@ where :math:`k_n = \frac{4}{3} E_{eff}` for the *hertz/material* model. Since
*coeff_restitution* accounts for the effective mass, effective radius, and
pairwise overlaps (except when used with the *hooke* normal model) when calculating
the damping coefficient, it accurately reproduces the specified coefficient of
restitution for both monodisperse and polydisperse particle pairs.
restitution for both monodisperse and polydisperse particle pairs. This damping
model is not compatible with cohesive normal models such as *JKR* or *DMT*.
The total normal force is computed as the sum of the elastic and
damping components:
@ -441,11 +443,11 @@ discussion above. To match the Mindlin solution, one should set
G_{eff} = \left(\frac{2-\nu_i}{G_i} + \frac{2-\nu_j}{G_j}\right)^{-1}
where :math:`G` is the shear modulus, related to Young's modulus :math:`E`
and Poisson's ratio :math:`\nu` by :math:`G = E/(2(1+\nu))`. This can also be
achieved by specifying *NULL* for :math:`k_t`, in which case a
normal contact model that specifies material parameters :math:`E` and
:math:`\nu` is required (e.g. *hertz/material*, *dmt* or *jkr*\ ). In this
where :math:`G_i` is the shear modulus of a particle of type :math:`i`, related to Young's
modulus :math:`E_i` and Poisson's ratio :math:`\nu_i` by :math:`G_i = E_i/(2(1+\nu_i))`.
This can also be achieved by specifying *NULL* for :math:`k_t`, in which case a
normal contact model that specifies material parameters :math:`E_i` and
:math:`\nu_i` is required (e.g. *hertz/material*, *dmt* or *jkr*\ ). In this
case, mixing of the shear modulus for different particle types *i* and
*j* is done according to the formula above.
@ -575,7 +577,7 @@ opposite torque on each particle, according to:
.. math::
\tau_{roll,i} = R_{eff} \mathbf{n} \times \mathbf{F}_{roll}
\tau_{roll,i} = R \mathbf{n} \times \mathbf{F}_{roll}
.. math::

54
doc/src/pair_hybrid.rst
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@ -1,28 +1,41 @@
.. index:: pair_style hybrid
.. index:: pair_style hybrid/kk
.. index:: pair_style hybrid/omp
.. index:: pair_style hybrid/molecular
.. index:: pair_style hybrid/molecular/omp
.. index:: pair_style hybrid/overlay
.. index:: pair_style hybrid/overlay/omp
.. index:: pair_style hybrid/overlay/kk
.. index:: pair_style hybrid/scaled
.. index:: pair_style hybrid/scaled/omp
pair_style hybrid command
=========================
Accelerator Variants: *hybrid/kk*
Accelerator Variants: *hybrid/kk*, *hybrid/omp*
pair_style hybrid/molecular command
===================================
Accelerator Variant: *hybrid/molecular/omp*
pair_style hybrid/overlay command
=================================
Accelerator Variants: *hybrid/overlay/kk*
Accelerator Variants: *hybrid/overlay/kk*, *hybrid/overlay/omp*
pair_style hybrid/scaled command
==================================
Accelerator Variant: *hybrid/scaled/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style hybrid style1 args style2 args ...
pair_style hybrid/molecular factor1 style1 args factor2 style 2 args
pair_style hybrid/overlay style1 args style2 args ...
pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ...
@ -47,6 +60,10 @@ Examples
pair_coeff * * tersoff Si.tersoff Si
pair_coeff * * sw Si.sw Si
pair_style hybrid/molecular lj/cut 2.5 lj/cut 2.5
pair_coeff * * lj/cut 1 1.0 1.0
pair_coeff * * lj/cut 2 1.5 1.0
variable one equal ramp(1.0,0.0)
variable two equal 1.0-v_one
pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5
@ -56,17 +73,26 @@ Examples
Description
"""""""""""
The *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles enable the
use of multiple pair styles in one simulation. With the *hybrid* style,
exactly one pair style is assigned to each pair of atom types. With the
*hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can
be assigned to each pair of atom types. The assignment of pair styles
to type pairs is made via the :doc:`pair_coeff <pair_coeff>` command.
The major difference between the *hybrid/overlay* and *hybrid/scaled*
styles is that the *hybrid/scaled* adds a scale factor for each
sub-style contribution to forces, energies and stresses. Because of the
added complexity, the *hybrid/scaled* style has more overhead and thus
may be slower than *hybrid/overlay*.
The *hybrid*, *hybrid/overlay*, *hybrid/molecular*, and *hybrid/scaled*
styles enable the use of multiple pair styles in one simulation. With
the *hybrid* style, exactly one pair style is assigned to each pair of
atom types. With the *hybrid/overlay* and *hybrid/scaled* styles, one
or more pair styles can be assigned to each pair of atom types. With
the hybrid/molecular style, pair styles are assigned to either intra-
or inter-molecular interactions.
The assignment of pair styles to type pairs is made via the
:doc:`pair_coeff <pair_coeff>` command. The major difference between
the *hybrid/overlay* and *hybrid/scaled* styles is that the
*hybrid/scaled* adds a scale factor for each sub-style contribution to
forces, energies and stresses. Because of the added complexity, the
*hybrid/scaled* style has more overhead and thus may be slower than
*hybrid/overlay*.
The *hybrid/molecular* pair style accepts *only* two sub-styles: the
first is assigned to intra-molecular interactions (i.e. both atoms
have the same molecule ID), the second to inter-molecular interactions
(i.e. interacting atoms have different molecule IDs).
Here are two examples of hybrid simulations. The *hybrid* style could
be used for a simulation of a metal droplet on a LJ surface. The metal
@ -476,6 +502,8 @@ the same or else LAMMPS will generate an error.
Pair style *hybrid/scaled* currently only works for non-accelerated
pair styles and pair styles from the OPT package.
Pair style *hybrid/molecular* is not compatible with manybody potentials.
When using pair styles from the GPU package they must not be listed
multiple times. LAMMPS will detect this and abort.

3
doc/src/pair_soft.rst
View File

@ -1,11 +1,12 @@
.. index:: pair_style soft
.. index:: pair_style soft/gpu
.. index:: pair_style soft/kk
.. index:: pair_style soft/omp
pair_style soft command
=======================
Accelerator Variants: *soft/gpu*, *soft/omp*
Accelerator Variants: *soft/gpu*, *soft/kk*, *soft/omp*
Syntax
""""""

3
doc/src/pair_style.rst
View File

@ -108,6 +108,7 @@ accelerated styles exist.
* :doc:`none <pair_none>` - turn off pairwise interactions
* :doc:`hybrid <pair_hybrid>` - multiple styles of pairwise interactions
* :doc:`hybrid/molecular <pair_hybrid>` - different pair styles for intra- and inter-molecular interactions
* :doc:`hybrid/overlay <pair_hybrid>` - multiple styles of superposed pairwise interactions
* :doc:`hybrid/scaled <pair_hybrid>` - multiple styles of scaled superposed pairwise interactions
* :doc:`zero <pair_zero>` - neighbor list but no interactions
@ -171,6 +172,7 @@ accelerated styles exist.
* :doc:`coul/wolf <pair_coul>` - Coulomb via Wolf potential
* :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
* :doc:`dpd/coul/slater/long <pair_dpd_coul_slater_long>` - dissipative particle dynamics (DPD) with electrostatic interactions
* :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pairwise DPD thermostatting with generalized force field
* :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure
@ -382,6 +384,7 @@ accelerated styles exist.
* :doc:`tracker <pair_tracker>` - monitor information about pairwise interactions
* :doc:`tri/lj <pair_tri_lj>` - LJ potential between triangles
* :doc:`ufm <pair_ufm>` -
* :doc:`uf3 <pair_uf3>` - UF3 machine-learning potential
* :doc:`vashishta <pair_vashishta>` - Vashishta 2-body and 3-body potential
* :doc:`vashishta/table <pair_vashishta>` -
* :doc:`wf/cut <pair_wf_cut>` - Wang-Frenkel Potential for short-ranged interactions

213
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@ -0,0 +1,213 @@
.. index:: pair_style uf3
.. index:: pair_style uf3/kk
pair_style uf3 command
======================
Accelerator Variants: *uf3/kk*
Syntax
""""""
.. code-block:: LAMMPS
pair_style style BodyFlag
* style = *uf3* or *uf3/kk*
.. parsed-literal::
BodyFlag = Indicates whether to calculate only 2-body or 2 and 3-body interactions. Possible values: 2 or 3
Examples
""""""""
.. code-block:: LAMMPS
pair_style uf3 3
pair_coeff * * Nb.uf3 Nb
pair_style uf3 2
pair_coeff * * NbSn.uf3 Nb Sn
pair_style uf3 3
pair_coeff * * NbSn.uf3 Nb Sn
Description
"""""""""""
.. versionadded:: TBD
The *uf3* style computes the :ref:`Ultra-Fast Force Fields (UF3)
<Xie23>` potential, a machine-learning interatomic potential. In UF3,
the total energy of the system is defined via two- and three-body
interactions:
.. math::
E & = \sum_{i,j} V_2(r_{ij}) + \sum_{i,j,k} V_3 (r_{ij},r_{ik},r_{jk}) \\
V_2(r_{ij}) & = \sum_{n=0}^N c_n B_n(r_{ij}) \\
V_3 (r_{ij},r_{ik},r_{jk}) & = \sum_{l=0}^{N_l} \sum_{m=0}^{N_m} \sum_{n=0}^{N_n} c_{l,m,n} B_l(r_{ij}) B_m(r_{ik}) B_n(r_{jk})
where :math:`V_2(r_{ij})` and :math:`V_3 (r_{ij},r_{ik},r_{jk})` are the
two- and three-body interactions, respectively. For the two-body the
summation is over all neighbors J and for the three-body the summation
is over all neighbors J and K of atom I within a cutoff distance
determined from the potential files. :math:`B_n(r_{ij})` are the cubic
b-spline basis, :math:`c_n` and :math:`c_{l,m,n}` are the machine-learned
interaction parameters and :math:`N`, :math:`N_l`, :math:`N_m`, and
:math:`N_n` denote the number of basis functions per spline or tensor
spline dimension.
With *uf3* style only a single pair_coeff command is used to indicate the
UF3 LAMMPS potential file containing all the two- and three-body interactions
followed by N additional arguments specifying the mapping of UF3 elements to
LAMMPS atom types, where N is the number of LAMMPS atom types:
* UF3 LAMMPS potential file
* N elements names = mapping of UF3 elements to atom types
As an example, if a LAMMPS simulation contains 2 atom types (elements
'A' and 'B'), the pair_coeff command will be:
.. code-block:: LAMMPS
pair_style uf3 3
pair_coeff * * AB.uf3 A B
The AB.uf3 file should contain all two-body (A-A, A-B, B-B) and three-body
(A-A-A, A-A-B, A-B-B, B-A-A, B-A-B, B-B-B).
If a value of "2" is specified in the :code:`pair_style uf3` command,
only the two-body potentials are needed. For 3-body interaction the
first atom type is the central atom. We recommend using the
:code:`generate_uf3_lammps_pots.py` script (found `here
<https://github.com/uf3/uf3/tree/develop/lammps_plugin/scripts>`_) for
generating the UF3 LAMMPS potential file from the UF3 JSON potentials.
----------
UF3 LAMMPS potential file in the *potentials* directory of the LAMMPS
distribution have a ".uf3" suffix. The interaction block in UF3 LAMMPS potential
file should start with :code:`#UF3 POT` and end with :code:`#` characters.
Following shows the format of a generic 2-body and 3-body potential block in
UF3 LAMMPS potential file-
.. code-block:: LAMMPS
#UF3 POT UNITS: units DATE: POT_GEN_DATE AUTHOR: AUTHOR_NAME CITATION: CITE
2B ELEMENT1 ELEMENT2 LEADING_TRIM TRAILING_TRIM
Rij_CUTOFF NUM_OF_KNOTS
BSPLINE_KNOTS
NUM_OF_COEFF
COEFF
#
#UF3 POT UNITS: units DATE: POT_GEN_DATE AUTHOR: AUTHOR_NAME CITATION: CITE
3B ELEMENT1 ELEMENT2 ELEMENT3 LEADING_TRIM TRAILING_TRIM
Rjk_CUTOFF Rik_CUTOFF Rij_CUTOFF NUM_OF_KNOTS_JK NUM_OF_KNOTS_IK NUM_OF_KNOTS_IJ
BSPLINE_KNOTS_FOR_JK
BSPLINE_KNOTS_FOR_IK
BSPLINE_KNOTS_FOR_IJ
SHAPE_OF_COEFF_MATRIX[I][J][K]
COEFF_MATRIX[0][0][K]
COEFF_MATRIX[0][1][K]
COEFF_MATRIX[0][2][K]
.
.
.
COEFF_MATRIX[1][0][K]
COEFF_MATRIX[1][1][K]
COEFF_MATRIX[1][2][K]
.
.
.
#
The second line indicates whether the block contains data for 2-body
(:code:`2B`) or 3-body (:code:`3B`) interaction. This is followed by element
combination interaction, :code:`LEADING_TRIM` and :code:`TRAILING_TRIM`
number on the same line. The current implementation is only tested for
:code:`LEADING_TRIM=0` and :code:`TRAILING_TRIM=3`.
If other values are used LAMMPS is terminated after issuing an error message.
The :code:`Rij_CUTOFF` sets the 2-body cutoff for the interaction described
by the potential block. :code:`NUM_OF_KNOTS` is the number of knots
(or the length of the knot vector) present on the very next line. The
:code:`BSPLINE_KNOTS` line should contain all the knots in ascending order.
:code:`NUM_OF_COEFF` is the number of coefficients in the :code:`COEFF` line.
All the numbers in the BSPLINE_KNOTS and COEFF line should be space-separated.
Similar to the 2-body potential block, the third line sets the cutoffs and
length of the knots. The cutoff distance between atom-type I and J is
:code:`Rij_CUTOFF`, atom-type I and K is :code:`Rik_CUTOFF` and between
J and K is :code:`Rjk_CUTOFF`.
.. note::
The current implementation only works for UF3 potentials with cutoff
distances for 3-body interactions that follows
:code:`2Rij_CUTOFF=2Rik_CUTOFF=Rjk_CUTOFF` relation.
The :code:`BSPLINE_KNOTS_FOR_JK`, :code:`BSPLINE_KNOTS_FOR_IK`, and
:code:`BSPLINE_KNOTS_FOR_IJ` lines (note the order) contain the knots in
increasing order for atoms J and K, I and K, and atoms I and J
respectively. The number of knots is defined by the
:code:`NUM_OF_KNOTS_*` characters in the previous line. The shape of
the coefficient matrix is defined on the
:code:`SHAPE_OF_COEFF_MATRIX[I][J][K]` line followed by the columns of
the coefficient matrix, one per line, as shown above. For example, if
the coefficient matrix has the shape of 8x8x13, then
:code:`SHAPE_OF_COEFF_MATRIX[I][J][K]` will be :code:`8 8 13` followed
by 64 (8x8) lines each containing 13 coefficients separated by space.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as described
above from values in the potential file.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style does not write its information to :doc:`binary restart
files <restart>`, since it is stored in potential file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*, *middle*, *outer* keywords.
Restrictions
""""""""""""
The 'uf3' pair style is part of the ML-UF3 package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This pair style requires the :doc:`newton <newton>` setting to be "on".
The UF3 LAMMPS potential file provided with LAMMPS (see the potentials
directory) are parameterized for metal :doc:`units <units>`.
The single() function of 'uf3' pair style only return the 2-body
interaction energy.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
Default
"""""""
none
----------
.. _Xie23:
**(Xie23)** Xie, S.R., Rupp, M. & Hennig, R.G. Ultra-fast interpretable machine-learning potentials. npj Comput Mater 9, 162 (2023). https://doi.org/10.1038/s41524-023-01092-7

8
doc/src/run_style.rst
View File

@ -327,10 +327,12 @@ Restrictions
""""""""""""
The *verlet/split* style can only be used if LAMMPS was built with the
REPLICA package. Correspondingly the *respa/omp* style is available
REPLICA package. Correspondingly the *respa/omp* style is available
only if the OPENMP package was included. See the :doc:`Build package
<Build_package>` page for more info. It is not compatible with
kspace styles from the INTEL package.
<Build_package>` page for more info.
Run style *verlet/split* is not compatible with kspace styles from
the INTEL package and it is not compatible with any TIP4P styles.
Whenever using rRESPA, the user should experiment with trade-offs in
speed and accuracy for their system, and verify that they are

2
doc/utils/requirements.txt
View File

@ -1,4 +1,4 @@
Sphinx >= 5.3.0, <7.3
Sphinx >= 5.3.0, <8.0
sphinxcontrib-spelling
sphinxcontrib-jquery
git+https://github.com/akohlmey/sphinx-fortran@parallel-read

7
doc/utils/sphinx-config/false_positives.txt
View File

@ -1434,6 +1434,7 @@ Hendrik
Henin
Henkelman
Henkes
Hennig
henrich
Henrich
Hermitian
@ -1595,6 +1596,7 @@ interlayer
intermolecular
interoperable
Interparticle
interpretable
interstitials
intertube
Intr
@ -1817,6 +1819,7 @@ Koziol
Kp
kradius
Kraker
Krass
Kraus
Kremer
Kress
@ -2959,6 +2962,7 @@ Priya
proc
Proc
procs
proggrid
progguide
Prony
ps
@ -3271,6 +3275,7 @@ Rudranarayan
Rudzinski
Runge
runtime
Rupp
Rutuparna
rx
rxd
@ -3820,6 +3825,8 @@ uChem
uCond
uef
UEF
uf
uf3
ufm
Uhlenbeck
Ui

2
examples/PACKAGES/dpd-basic/README
View File

@ -14,3 +14,5 @@ pair styles from the DPD-BASIC package.
4) 'dpdext_tstat' - coarse-grained SPC/E water example for 'dpd/ext/tstat' pair style
(in.dpdext_tstat), an initial configuration (dpdext.data) and tabulated potential
(cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water.
5) 'dpd_coul_slater_long' - simple example (DPD ionic fluid) for 'dpd/coul/slater/long' pair style (in.dpd_coul_slater_long).

779
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/data.dpd_coul_slater_long Normal file
View File

@ -0,0 +1,779 @@
LAMMPS data file via write_data, version 17 Apr 2024, timestep = 1394, units = lj
375 atoms
3 atom types
0 5 xlo xhi
0 5 ylo yhi
0 5 zlo zhi
Masses
1 1
2 1
3 1
PairIJ Coeffs # dpd/coul/slater/long
1 1 78 4.5 yes 1
1 2 78 4.5 yes 1
1 3 78 4.5 yes 1
2 2 78 4.5 no 1
2 3 78 4.5 no 1
3 3 78 4.5 no 1
Atoms # full
189 0 1 0 0.8621554018960034 1.5213257556560191 0.4064444607843129 0 1 0
107 0 1 0 2.040249318291146 0.3862591116608294 1.8661957131854634 0 0 0
253 0 1 0 3.511834308089607 0.7338273870464224 0.801173549802059 0 1 1
163 0 1 0 2.303289649738226 0.6809493239075631 0.7383435796468727 0 1 0
26 0 1 0 0.03534770106704549 1.4889933012536283 1.4815498922617432 0 0 0
27 0 1 0 4.170525658289272 1.8438490221677797 2.1918634082517614 -1 0 0
56 0 1 0 2.9501314702448633 2.322938987390429 0.6158870411938201 0 0 0
167 0 1 0 1.948558457807243 0.1261294591496785 0.039492485708843984 0 1 0
364 0 3 -1 4.538825953029656 0.2655458359259118 2.131668601530241 0 1 0
61 0 1 0 4.645784299395809 0.3574274125207269 1.7056474795918568 -1 0 0
222 0 1 0 4.41481966340897 2.262979887349817 1.1679075968940398 0 0 0
332 0 2 1 3.853874714249102 0.1758912358513287 0.8799773810713412 0 1 0
1 0 1 0 4.608301143657016 1.4090100132224024 1.218887039455649 -1 0 0
319 0 2 1 3.732213186171727 0.981827023519373 2.3857377768158727 -1 0 0
53 0 1 0 2.380311878254328 0.953677113042391 1.8268738776443192 0 0 0
68 0 1 0 0.33279009298924916 1.0106375746131884 0.7038515854567269 0 0 0
220 0 1 0 1.1094848303775686 2.378414106514282 1.4793246435196352 1 0 0
44 0 1 0 0.12449238274832848 1.7475396894040345 0.5495194876290164 0 0 0
55 0 1 0 0.1451415441609303 2.337329820574407 0.940744164662616 0 0 0
362 0 3 -1 1.2987762452744613 1.8352325797868587 1.1809674941775483 0 0 0
165 0 1 0 0.6610209400465688 2.22554349560855 1.971912177574677 0 0 0
60 0 1 0 1.8643313870571518 0.6352678895179578 1.4416996493100478 0 0 0
202 0 1 0 0.007896731087640774 1.5385720917803027 0.18965671583085075 0 1 0
85 0 1 0 1.5630176980330266 1.1482985441214197 2.019916217302335 1 0 0
73 0 1 0 0.5556133646182337 1.6170466333456652 2.101792903006452 0 0 0
96 0 1 0 1.6611967219346682 0.07688637034882238 0.46572063062814617 0 0 1
30 0 1 0 0.46644353751713447 1.8254820637852556 1.2380479793915407 1 0 0
67 0 1 0 3.4270812515248483 2.350996339385886 1.77527952461483 0 0 0
349 0 3 -1 1.7935506583370944 1.7235931740659332 0.4478371869612185 1 0 0
132 0 1 0 4.951074988035153 1.5039089286454406 2.4219801232797398 -1 0 0
328 0 2 1 0.8958492991096989 1.2809413147557527 1.0440931858570435 0 0 1
161 0 1 0 4.798276598985588 0.9882558902185279 2.462987088497934 0 1 0
185 0 1 0 0.6126520391294695 0.04940161418784647 0.6135262263024062 0 1 0
219 0 1 0 1.647872968759676 2.305100092833184 2.0217182617222096 0 0 0
8 0 1 0 2.8077478718165207 0.7661158156519451 1.3602857540877684 0 0 0
69 0 1 0 2.8568644931819835 0.13340029053585767 2.106212637519767 0 0 0
3 0 1 0 1.908450187819087 2.298808713848062 0.4221817812562634 0 0 0
7 0 1 0 1.8799145446976495 0.9814789886011673 0.955308672406064 0 0 0
329 0 2 1 0.9727877144189607 0.8906662949552561 1.4472553696387669 0 1 0
174 0 1 0 3.9905681672951636 0.6401683928312465 1.0284041192891435 -1 1 0
20 0 1 0 3.392515194191721 2.0774851454870427 0.8812446323305514 0 0 0
57 0 1 0 4.874212056539195 0.13899230379169403 0.7199140773346149 0 0 0
325 0 2 1 1.362093021934204 2.3422237404192465 0.6655225660551776 0 0 1
40 0 1 0 4.306473534903154 1.7047871476017826 0.8560715024613603 0 0 0
51 0 1 0 2.297377802384159 0.11499650506694176 1.4731005354419167 0 0 0
54 0 1 0 2.971300335884777 1.8792385205105047 1.3973014092900102 0 0 0
186 0 1 0 3.583414064904102 1.7542346893771112 0.35130247738019466 0 0 0
289 0 1 0 2.5651653875350906 1.4858962835620086 0.6587351599193196 0 0 1
75 0 1 0 3.132107705055228 0.19794042232605677 0.44488993973642094 0 0 1
48 0 1 0 3.4384178020381717 0.7217742755424055 1.7304812232062636 0 0 0
66 0 1 0 3.191389133037332 1.1674191637093172 1.7413707516914332 0 0 0
52 0 1 0 1.856006413772654 1.871405713016935 1.5164995404363106 0 0 0
158 0 1 0 3.725559226243618 1.2320067990055215 0.4240371305587515 -1 1 0
330 0 2 1 0.4226192821951129 0.22648053650193767 0.04025715930862768 1 1 0
359 0 3 -1 4.4476116877707925 0.8271711042623823 1.1688054720798116 0 1 0
366 0 3 -1 0.13989896192253948 0.6502137062351493 0.845841913773404 1 1 0
196 0 1 0 0.21878194805964699 2.4139077401885523 1.602735237996178 1 0 0
128 0 1 0 2.474112780481313 1.5036993910540244 1.234391076605564 0 0 1
118 0 1 0 0.1703454662324439 0.9401878407982331 0.17224714060344348 0 0 1
43 0 1 0 3.708324777814944 2.4767443359210524 0.5791362456922102 0 0 0
184 0 1 0 0.4061592126934206 0.22209165285150972 1.3598048859115588 0 1 0
360 0 3 -1 1.225690366400486 0.4472136514952278 1.0864811555493794 0 1 0
64 0 1 0 2.6116937036965266 1.793563094424563 2.091822223631947 0 0 0
285 0 1 0 0.7747031518566616 0.24118573693540882 2.1434463705260494 0 1 0
58 0 1 0 1.598997109049339 1.2355543729347458 1.1437352681100093 0 0 0
257 0 1 0 0.02882436640692898 0.8179392413775496 1.6880006059524528 1 1 0
356 0 3 -1 2.0441963785801733 1.236982129976697 2.2147135788798726 0 0 0
100 0 1 0 3.653446945164378 0.3462603812889145 1.6428480228892703 0 0 0
121 0 1 0 3.3427026587713 1.3818800793465942 1.0715223415915789 0 0 1
130 0 1 0 3.3647959804349648 1.6468424783155522 2.142743574286686 0 0 1
238 0 1 0 1.3459228411155364 0.633596613028775 2.1301210835283637 0 1 0
211 0 1 0 0.6615598402766512 2.33271179551025 0.47581804017205676 1 0 0
208 0 1 0 2.962020456626749 0.2159270527386094 1.30534135402314 0 1 0
63 0 1 0 1.3612122125160733 0.010635376740000254 1.5982897032081793 0 0 0
22 0 1 0 4.210300352056279 0.36529901441609736 0.22595511161653342 0 0 0
355 0 3 -1 1.2042503283777344 1.597276477439138 1.9589099368399292 0 0 0
70 0 1 0 4.378695647703822 2.2211752925991073 0.5054248018357668 0 0 0
65 0 1 0 4.730200694542147 1.8860651406962996 1.9541188923646609 0 0 0
182 0 1 0 0.6006579892093956 1.0766698682185656 1.8982320873119558 0 1 0
188 0 1 0 3.968278800401347 2.2778420975676017 1.5855956915283134 -1 0 0
35 0 1 0 2.223480574739111 2.044750380955685 1.1501174861326973 0 0 0
6 0 1 0 4.393818207857278 0.9691596735067866 0.4973738964333318 0 0 0
346 0 3 -1 1.799292171051204 0.9378491451956622 0.32819450450408366 0 0 0
14 0 1 0 4.116276227278533 0.9144868046413738 1.9001996318293624 0 0 0
15 0 1 0 4.057083687324151 1.5512296337030849 1.8388944544921122 0 0 0
16 0 1 0 3.82411370026405 1.5506478336832812 1.2725337401183239 0 0 0
287 0 1 0 2.6387027215894454 1.893079917045916 0.49300315071401646 0 0 1
81 0 1 0 0.23374890251430025 0.34479122000015083 2.377074044522331 1 0 0
114 0 1 0 2.97788308248854 0.8029642133737654 0.43679357743492564 0 0 1
232 0 1 0 1.1637120121074183 0.7914170906883582 0.5169414304881136 1 1 1
50 0 1 0 1.3582030484899448 1.733969902734067 2.475757370252963 0 0 -1
79 0 1 0 4.002398001699839 2.453310546669259 2.3569732163529196 0 0 0
74 0 1 0 2.5693171940612936 0.3236751012125613 0.052755933881527994 0 0 1
194 0 1 0 2.8970695996535842 1.3203227830648074 2.4866087995688972 0 0 0
133 0 1 0 2.6178632265286743 1.0115830273791913 0.19081692003348572 0 0 1
311 0 1 0 3.3683313684704523 1.1471203834722834 0.04523595785096113 0 1 1
115 0 1 0 0.43505007353257874 2.385803272207332 0.02841287624716582 0 0 1
4 0 1 0 4.3073950086925725 2.400627067573385 4.56127636601268 -1 0 -1
151 0 1 0 0.6919123879927325 2.1849820555988084 3.5078472275384267 0 0 0
306 0 1 0 0.5589151617318056 0.058029533314856774 4.427085995859885 0 1 0
138 0 1 0 1.7147207261520883 1.4323880737092538 3.757478681577442 0 0 0
110 0 1 0 1.3876397037618702 1.3714565550984217 4.5219172301432895 0 0 0
251 0 1 0 2.788428291071368 2.3409448558940977 3.4381375025566263 0 0 0
331 0 2 1 2.838525921735314 0.09442598845901452 3.3146265769160324 0 1 0
243 0 1 0 4.489290143790526 2.26853729359999 3.7839844553823094 0 0 0
156 0 1 0 0.23302160032454478 1.3603287603692662 4.342729568698205 1 1 -1
32 0 1 0 2.081389395149717 0.4938421510915584 2.707994013583073 0 0 0
205 0 1 0 0.09940021857353744 2.408012210772126 3.2074615425616426 0 0 0
41 0 1 0 4.323708181823033 0.4958928465474822 2.525689303250374 0 0 0
28 0 1 0 4.717322170568759 1.0215969335342936 3.32138298357052 -1 0 -1
322 0 2 1 2.2029274368349303 2.0230576314539634 3.254975041225457 0 0 0
103 0 1 0 3.4039994449255992 0.5284405133705601 4.809880920488395 0 0 0
353 0 3 -1 1.1636351711418296 1.6849823280188108 3.628904996363181 0 0 0
295 0 1 0 2.015582444660267 2.152457218882018 4.802270482662931 0 0 0
365 0 3 -1 0.1355221924615853 0.6843479265638512 3.832358314244189 0 0 0
98 0 1 0 2.5146420394624114 1.4050031824562241 2.965312255745623 0 0 0
33 0 1 0 2.3626541269063335 0.301607887792709 4.126675184172655 0 0 0
39 0 1 0 1.0864796756700101 0.14884263883618853 3.538403788545902 0 0 -1
343 0 2 1 1.4514575528852092 0.7274022675751877 4.022000140293159 0 1 0
259 0 1 0 3.655779855306037 1.3576945405765304 3.834017837247726 0 0 0
77 0 1 0 0.8784812240014032 1.3079405939838267 3.865082861143354 1 0 0
140 0 1 0 0.8162940643502995 1.1305386542609035 4.8092097458556715 0 0 0
111 0 1 0 4.795245146003238 1.9956723305718642 3.9129401250192046 0 0 0
129 0 1 0 0.34843108982968385 0.5298485948666217 2.8292148084141364 0 0 0
317 0 2 1 4.124560425539725 0.9992026808502931 4.821938521772994 0 0 -1
25 0 1 0 2.8922318837378698 0.9335539802277806 4.287158919025898 -1 0 -1
21 0 1 0 4.585171090824654 1.3705322366558885 4.19496485298651 0 0 -1
276 0 1 0 2.403137350597824 1.5009012449757657 3.808385508050605 0 0 0
160 0 1 0 2.937633869764959 0.00248285164262807 4.155863012635541 0 1 -1
308 0 1 0 2.007117640798801 0.07533937286437335 3.949461187876648 0 1 0
313 0 1 0 3.138628385914381 0.06932121228333508 4.61254641181726 0 1 0
71 0 1 0 0.7604830442534299 1.8783527414570997 4.529066129071014 0 0 -1
42 0 1 0 0.8786351691021071 1.5220089570408293 2.909825736835378 0 0 0
83 0 1 0 2.268823589694475 0.8105925806076607 3.3728322715236114 0 0 0
123 0 1 0 1.7884920869805707 1.339956019375266 2.861286357841185 0 0 0
29 0 1 0 4.460413120634612 1.661186434187469 2.731131826280074 0 0 0
291 0 1 0 0.0035749317593865015 0.21166749654426853 3.275077495308186 1 1 0
299 0 1 0 0.6601895850752213 0.7060682406274252 3.722602054061811 0 1 0
87 0 1 0 3.635932620062484 1.4708618427874118 4.477899978536171 0 0 0
78 0 1 0 1.5540100281849198 2.289959113070306 3.8245622090496108 0 0 0
5 0 1 0 2.937548438619819 2.211877405174181 2.85571535820357 0 0 0
95 0 1 0 3.105981604150784 2.188298914603185 4.094702761761116 0 0 0
352 0 3 -1 0.11773003147587424 1.9458234584845089 4.811739126011424 0 0 0
281 0 1 0 1.1502488869841234 0.20873030537461357 4.295523149721441 1 1 0
206 0 1 0 3.330001486381421 1.53529174323865 3.1417824971878447 0 0 0
241 0 1 0 3.878317992103332 2.023909280872213 4.783549131197242 0 0 0
109 0 1 0 2.580544454574246 2.2025316047831676 4.264813345165653 0 0 0
126 0 1 0 2.6463397268489866 0.7745950386723881 3.699331340328284 0 0 0
62 0 1 0 0.10088965537315422 1.464964032622401 3.4200098453857786 0 0 -1
145 0 1 0 4.7108240170803874 2.1614660538205466 3.070399886653731 -1 0 0
354 0 3 -1 1.610893620580725 0.7512309895438358 3.571881076052697 0 0 0
248 0 1 0 2.3260578668858516 2.409053529199307 3.878500098271755 0 0 0
278 0 1 0 1.0565916295142963 0.21636101668521504 2.9280061580151355 1 1 0
334 0 2 1 3.3217760513533556 0.20221074730138347 3.857259461716569 0 0 0
344 0 2 1 2.145759202198284 0.8646312386735645 4.34482845102358 0 0 0
84 0 1 0 3.310133712882211 0.8325063678401754 3.1928917336760043 0 0 0
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124 0 1 0 1.5924837125088054 2.3295502621690507 3.1555629363203055 0 0 0
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189 -0.32037987935911505 -1.8545793275796412 -0.3389478887810303
107 0.3468735347167663 -0.2955882500703209 0.7493971092549213
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89 0.30853654184225165 1.4220670510027051 -2.1642949762748867
191 0.20906754014854564 0.026904283363689382 0.39272994979179504
237 0.8114113274128864 -1.2134195876500447 -1.2542604312044792
226 0.05086738376609842 1.9155895254467763 0.5909889856323195
231 0.12002855122048815 0.02004736909508279 0.11081960871345642
49 0.03966621608393742 -0.8770492944397817 0.8690111691798925
375 0.9491508595606913 0.58883338187899 -0.3157968091718698
265 -1.202404469596496 -1.5086124324682335 0.25807518315254696
193 0.4146818842856516 0.2647601963673656 0.730972113530503
318 -1.8694737066425302 -0.761959044368273 -0.7096835210855107
38 1.4229802153283508 -1.36140802862721 -0.8467736118278119
195 -0.8905011743693773 0.7285788649892662 -1.1668737157134021
224 0.27425001045805447 -1.4123472657200646 -1.3276958804580687
139 0.17701044314199935 1.2384991288614933 0.707649077312958
102 -0.49170524562266826 0.9342585115109375 0.4160956308860243
263 -0.7682667946507794 0.5411620297128601 -0.14243425461628567
361 0.4874350807265555 -1.118941056651683 0.4602449779293269
298 0.04321754250044474 -0.15386666534573679 -1.0460367336946477
106 -0.3645858676063196 -0.008671871254614383 -1.0359720474498813
288 -1.275865518017513 -1.0371041509619956 2.212604082967035
320 -0.377092487120416 -0.5974519455300853 -0.22840203412473642
12 -0.24251540706937524 -0.1402656612039157 0.2434885714233267
350 1.1678886543574276 -0.45657425471012764 -0.2662438133234255
255 0.5964565878330671 -1.3463852257768025 1.2786356338266742
264 1.6104915551559742 1.8273229008351088 -0.9803231882687425
131 -0.8634566501958852 -0.3775110787982123 -0.4297068950811986
271 0.022978578950211624 0.1537857816854949 0.41326352661226756
239 1.1101812509452746 -1.0996094771595475 -0.5405483522697302
247 0.366683557977341 -0.40591154743605157 0.3199408653703203
336 -0.4204708954513029 1.1245949705896916 0.14059678344621293
80 0.7468471903560799 0.16912425014962304 0.9566573830732898
351 0.07048942766011615 -1.3084119272893855 -1.2549170044600249
345 0.7055909005169286 1.5707280888607302 2.170499205441559
23 -1.331563904677986 0.7554001948296128 0.6695113635015243
372 -1.4331361061806305 -0.7926393821400735 0.5238882724688806
374 -0.825494743089428 1.5035094266963547 1.4373542115371403
99 0.27578368704586625 -0.6711803184635016 0.5730720207589178
134 -1.1904489259413122 1.5650039062713583 -0.4846706283407857
94 0.9633444927305759 0.47059281614148496 0.1502870940642896
108 0.26924336654778097 -0.21911864351862886 0.3263366196031549
116 0.6191352094412962 -0.7085456797691245 -0.2795453344586494
47 -0.81507518857967 0.5002361185490026 0.1633824556071923
177 0.9242227597235199 -0.9239301127385003 -0.6516754024576575
154 0.36428957391605954 1.0522574437068934 0.47589301799726774
272 -1.0875391115124131 -0.5442742977183277 0.6272696858994802
292 -2.3018786976959547 -0.719034234609397 -0.3976068240680647
348 -0.7074103387842228 -0.0767390137549914 -0.963801034994381
113 0.0030054733602942266 -1.3950743743038958 1.867999225141668
76 1.5225615991122337 -0.6220818112064357 -0.15128024907071225
178 -0.9036534708064256 0.27189024225898883 -1.310213331624685
82 -0.42289693438412584 -0.022877233686993723 0.16757191063647395
358 -1.084491323240786 0.309617438081422 0.19221704824216043
302 -1.0553000696338095 -0.7753368184729383 -1.6522442141368283
13 0.845507404222631 -1.1655430839109384 1.5339500987877546
72 0.41215075448394733 -1.3387634915542448 -1.701720507581037
245 -0.34884333851309834 -1.599607748547356 -0.08374549876035683
234 -1.8167563819027162 -1.1826697278339255 1.1323923705559067
300 -1.1492146391765459 0.2483076272654141 -0.7388669957162219
105 1.860014533900312 0.7148855192575438 0.950732381457607
254 -0.6941521238655652 1.3286658685743733 -0.09912945530019143
371 -0.03007825734775041 0.17488055593531995 -0.5660994145015367
262 1.1816791457721831 -0.2527818393194355 0.49550489641014006
266 0.7025922230527104 -1.3294406800025553 -0.610134301603067
31 -1.015719812353546 0.699060801172419 0.9860089149766915
267 0.38654355926704703 -0.1264135931208901 0.1337359898717711
290 1.0106897270034887 -0.6174340186836875 0.17719301929654596
324 1.5906920275906873 -1.4359983538965082 -0.8582706716695392
293 0.9982234808302441 0.543717193528767 -2.062895773562878
323 0.17420566156018166 -0.8499393438675438 -0.22821645799213797
335 -1.4047556653990858 0.2558049214304259 -0.20559797586706147
270 -0.6321821769779428 -0.4192527616747393 -0.8336466516152516
173 -1.454149943391539 -0.7091620301715705 0.1032726804162123
2 -0.13160744352132697 -0.8530661810441926 -1.4081064081887786
210 0.005780708280217166 -0.1314037001754253 -0.2650271980684433
125 -0.09249384396894937 -1.1079543363063478 0.5855224371258938
214 0.5201018860617912 1.5761782081656692 0.035238788848664875
258 0.029258855657727026 0.9978609610551674 -0.14936661862149073
93 1.3599706012850858 0.5138196159795498 -0.5479657931310508
24 -0.36848780789234786 0.5502667846431184 -0.8219909931831206
152 1.443106679308555 -1.5881504830897177 0.5251248932583428
367 -0.8318296913109121 -1.0659118655536617 1.4652035277005255
249 -0.7272493937720567 -1.0554246074355031 1.9106526180491246
252 0.15824074140715003 1.3574893627297528 0.849299710142209
227 -1.8919742394027095 0.35022746838873914 -0.8716265785931281
120 -0.571575152303992 -1.2924338935753592 1.6398975078681308
342 0.04170661506757478 -0.2554943852733288 1.2031995777997446
370 -0.3474083481747786 -0.8268210706239789 0.11710668216712806
283 0.34259631654561 -0.638600994930959 0.021713727624721322
279 -2.1091380649692364 0.5683510572154551 -0.9091778578938636
314 -0.43834173946024524 -1.6956466398316619 -1.741986521654538
297 0.9805330343066516 1.9653989039948883 -0.06267823210622318
341 0.6436707559323198 0.17740641651830055 0.7923601196148916
312 -1.4662653378890305 0.8912504951091632 -3.2848373130153616
373 -0.3818721621040007 1.1303100555115857 1.117083484179991
91 -1.0354512700928402 0.7952901789933705 -1.3376868649958413
260 -0.7142984506137289 0.4503083150384257 0.7493938136595016
286 0.12497815933423412 -1.4185031297528174 -0.7147963619923647
277 -0.04273979718334558 0.6681668442079539 -1.627755052910915
162 0.6571166297602984 0.4444526727563672 1.4878784469904562
148 0.3177520883327088 1.0855120103126268 -0.6584725796441712
199 -1.2545559409413416 -0.5694770345954823 0.33932040400166985
59 -0.6235113592986508 -0.2086994539745325 1.6873018374682558
240 0.705376364763962 -0.6227531276788822 1.6071635134558022

58
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/in.dpd_coul_slater_long Normal file
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# DPD Ionic Fluid
variable T equal 1.0
variable cut_DPD equal 1.0
variable seed equal 165412
variable lambda equal 0.25
variable cut_coul equal 2.0
#-------------------------------------------------------------------------------
# Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
bond_style none
angle_style none
dihedral_style none
improper_style none
newton on
comm_modify vel yes # store info of ghost atoms btw processors
#-------------------------------------------------------------------------------
# Box creation and configuration
#-------------------------------------------------------------------------------
# Define pair style and coefficients
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
read_data data.dpd_coul_slater_long
# Enable long range electrostatics solver
kspace_style pppm 1e-04
# Construct neighbors every steps
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
#-------------------------------------------------------------------------------
# Run the simulation
#-------------------------------------------------------------------------------
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
timestep 0.01
run_style verlet
fix 1 all nve
run 1000
unfix 1

147
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.1 Normal file
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LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# DPD Ionic Fluid
variable T equal 1.0
variable cut_DPD equal 1.0
variable seed equal 165412
variable lambda equal 0.25
variable cut_coul equal 2.0
#-------------------------------------------------------------------------------
# Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
bond_style none
angle_style none
dihedral_style none
improper_style none
newton on
comm_modify vel yes # store info of ghost atoms btw processors
#-------------------------------------------------------------------------------
# Box creation and configuration
#-------------------------------------------------------------------------------
# Define pair style and coefficients
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
read_data data.dpd_coul_slater_long
Reading data file ...
orthogonal box = (0 0 0) to (5 5 5)
1 by 1 by 1 MPI processor grid
reading atoms ...
375 atoms
reading velocities ...
375 velocities
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
# Enable long range electrostatics solver
kspace_style pppm 1e-04
# Construct neighbors every steps
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
#-------------------------------------------------------------------------------
# Run the simulation
#-------------------------------------------------------------------------------
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
timestep 0.01
run_style verlet
fix 1 all nve
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 1.4828454
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 7.7240141e-05
estimated relative force accuracy = 7.7240141e-05
using double precision FFTW3
3d grid and FFT values/proc = 24389 8000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd/coul/slater/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
0 0.9849949 69.271905 125 4673.0443 0 -30.365103 4642.6792 552.58214 646.76798 65.851035
100 1.0614027 69.794624 125 4659.0139 0 -31.906319 4627.1075 595.44692 612.94396 60.338653
200 0.9422517 68.721098 125 4687.8862 0 -33.81531 4654.0709 528.6032 620.25627 62.726994
300 0.8956649 69.323482 125 4721.0824 0 -33.854275 4687.2281 502.46801 670.22699 73.087908
400 0.99584547 69.670416 125 4713.9086 0 -30.783633 4683.125 558.66931 607.65881 59.224652
500 1.0565931 69.497816 125 4701.2584 0 -26.80545 4674.4529 592.74873 646.18907 71.398122
600 1.0071523 70.26222 125 4659.2061 0 -29.98909 4629.217 565.01243 630.00244 58.264115
700 1.0507355 67.920078 125 4695.255 0 -32.649209 4662.6058 589.46259 651.80459 70.573524
800 0.98561942 68.279591 125 4745.7603 0 -28.98491 4716.7754 552.9325 627.14371 67.196483
900 0.96470105 70.742864 125 4706.3605 0 -30.271633 4676.0889 541.19729 644.43036 79.474998
1000 1.0204819 70.164419 125 4654.6077 0 -27.797433 4626.8103 572.49035 624.19728 71.825307
Loop time of 2.10153 on 1 procs for 1000 steps with 375 atoms
Performance: 411128.483 tau/day, 475.843 timesteps/s, 178.441 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1779 | 1.1779 | 1.1779 | 0.0 | 56.05
Bond | 6.507e-05 | 6.507e-05 | 6.507e-05 | 0.0 | 0.00
Kspace | 0.74636 | 0.74636 | 0.74636 | 0.0 | 35.51
Neigh | 0.12903 | 0.12903 | 0.12903 | 0.0 | 6.14
Comm | 0.039726 | 0.039726 | 0.039726 | 0.0 | 1.89
Output | 0.00027587 | 0.00027587 | 0.00027587 | 0.0 | 0.01
Modify | 0.0037596 | 0.0037596 | 0.0037596 | 0.0 | 0.18
Other | | 0.004451 | | | 0.21
Nlocal: 375 ave 375 max 375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3613 ave 3613 max 3613 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 62354 ave 62354 max 62354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 62354
Ave neighs/atom = 166.27733
Ave special neighs/atom = 0
Neighbor list builds = 65
Dangerous builds = 0
unfix 1
Total wall time: 0:00:02

147
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.4 Normal file
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LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# DPD Ionic Fluid
variable T equal 1.0
variable cut_DPD equal 1.0
variable seed equal 165412
variable lambda equal 0.25
variable cut_coul equal 2.0
#-------------------------------------------------------------------------------
# Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
bond_style none
angle_style none
dihedral_style none
improper_style none
newton on
comm_modify vel yes # store info of ghost atoms btw processors
#-------------------------------------------------------------------------------
# Box creation and configuration
#-------------------------------------------------------------------------------
# Define pair style and coefficients
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
read_data data.dpd_coul_slater_long
Reading data file ...
orthogonal box = (0 0 0) to (5 5 5)
1 by 2 by 2 MPI processor grid
reading atoms ...
375 atoms
reading velocities ...
375 velocities
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
# Enable long range electrostatics solver
kspace_style pppm 1e-04
# Construct neighbors every steps
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
#-------------------------------------------------------------------------------
# Run the simulation
#-------------------------------------------------------------------------------
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
timestep 0.01
run_style verlet
fix 1 all nve
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 1.4828454
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 7.7240141e-05
estimated relative force accuracy = 7.7240141e-05
using double precision FFTW3
3d grid and FFT values/proc = 10469 2000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd/coul/slater/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
0 0.9849949 69.076433 125 4673.0443 0 -30.365103 4642.6792 552.58214 613.18374 70.700582
100 0.95374867 69.110009 125 4681.1097 0 -31.260804 4649.8489 535.053 629.95109 62.05418
200 1.0076152 69.824904 125 4670.7458 0 -28.382203 4642.3636 565.27213 656.8501 72.049813
300 1.0014752 69.666331 125 4696.454 0 -26.943577 4669.5105 561.8276 631.49861 74.737274
400 0.98863876 69.731774 125 4700.7552 0 -23.816077 4676.9391 554.62634 637.74742 68.928573
500 0.95782852 68.588075 125 4698.588 0 -29.249543 4669.3385 537.3418 646.31897 68.800569
600 0.97443232 70.864079 125 4674.8821 0 -26.415644 4648.4664 546.65653 606.50755 78.664429
700 0.98783988 68.908299 125 4692.5536 0 -28.092022 4664.4616 554.17817 638.98401 69.691814
800 0.98000145 69.83977 125 4706.6365 0 -29.648365 4676.9881 549.78082 626.84362 73.133934
900 1.0526251 69.466078 125 4671.9648 0 -30.941117 4641.0237 590.52269 618.1049 62.333546
1000 0.98340746 69.527121 125 4728.2894 0 -31.869907 4696.4195 551.69159 630.14208 61.392611
Loop time of 0.928543 on 4 procs for 1000 steps with 375 atoms
Performance: 930490.137 tau/day, 1076.956 timesteps/s, 403.859 katom-step/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.30761 | 0.34974 | 0.38864 | 4.9 | 37.67
Bond | 8.4633e-05 | 9.0539e-05 | 9.9184e-05 | 0.0 | 0.01
Kspace | 0.39038 | 0.42976 | 0.47215 | 4.4 | 46.28
Neigh | 0.033986 | 0.035576 | 0.036791 | 0.5 | 3.83
Comm | 0.10247 | 0.10324 | 0.10481 | 0.3 | 11.12
Output | 0.00024145 | 0.00027404 | 0.00036867 | 0.0 | 0.03
Modify | 0.0022402 | 0.0025068 | 0.0026343 | 0.3 | 0.27
Other | | 0.007356 | | | 0.79
Nlocal: 93.75 ave 96 max 93 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 2289.75 ave 2317 max 2271 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 15590.2 ave 16765 max 14540 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 62361
Ave neighs/atom = 166.296
Ave special neighs/atom = 0
Neighbor list builds = 64
Dangerous builds = 0
unfix 1
Total wall time: 0:00:00

1
examples/PACKAGES/uf3/Nb.uf3 Symbolic link
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../../../potentials/Nb.uf3

46
examples/PACKAGES/uf3/in.uf3.Nb Normal file
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# Demonstrate UF3 W potential
# # ============= Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.3005
units metal
# 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 bcc $a
region box block 0 ${nx} 0 ${ny} 0 ${nz}
create_box 1 box
create_atoms 1 box
mass 1 92.906
# # ============= set pair style
pair_style uf3 3
pair_coeff * * Nb.uf3 Nb
# # ============= Setup output
thermo 10
thermo_modify norm yes
# # ============= Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# # ============= Run MD
velocity all create 300.0 2367804 loop geom
fix 1 all nve
run ${nsteps}

118
examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.1 Normal file
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@ -0,0 +1,118 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Demonstrate UF3 W potential
# # ============= Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.3005
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice bcc $a
lattice bcc 3.3005
Lattice spacing in x,y,z = 3.3005 3.3005 3.3005
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (13.202 13.202 13.202)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
using lattice units in orthogonal box = (0 0 0) to (13.202 13.202 13.202)
create_atoms CPU = 0.000 seconds
mass 1 92.906
# # ============= set pair style
pair_style uf3 3
pair_coeff * * Nb.uf3 Nb
Reading potential file Nb.uf3 with DATE: 2024-04-02
# # ============= Setup output
thermo 10
thermo_modify norm yes
# # ============= Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# # ============= Run MD
velocity all create 300.0 2367804 loop geom
fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair uf3, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.376 | 3.376 | 3.376 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -4.4256832 0 -4.3872081 90756.437
10 294.36659 -4.4249607 0 -4.3872081 91006.427
20 277.9021 -4.422849 0 -4.387208 91716.126
30 251.88303 -4.4195119 0 -4.3872078 92789.12
40 218.42803 -4.4152211 0 -4.3872076 94118.45
50 180.40641 -4.4103445 0 -4.3872073 95579.009
60 141.2326 -4.4053202 0 -4.3872071 97031.816
70 104.54429 -4.4006146 0 -4.3872068 98332.882
80 73.787889 -4.3966699 0 -4.3872066 99351.332
90 51.759956 -4.3938446 0 -4.3872064 99992.934
100 40.209821 -4.3923633 0 -4.3872064 100211.98
Loop time of 0.385575 on 1 procs for 100 steps with 128 atoms
Performance: 11.204 ns/day, 2.142 hours/ns, 259.353 timesteps/s, 33.197 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38403 | 0.38403 | 0.38403 | 0.0 | 99.60
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00090609 | 0.00090609 | 0.00090609 | 0.0 | 0.23
Output | 0.00017626 | 0.00017626 | 0.00017626 | 0.0 | 0.05
Modify | 0.00018204 | 0.00018204 | 0.00018204 | 0.0 | 0.05
Other | | 0.0002795 | | | 0.07
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1601 ave 1601 max 1601 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 21504 ave 21504 max 21504 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21504
Ave neighs/atom = 168
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

118
examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.4 Normal file
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@ -0,0 +1,118 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Demonstrate UF3 W potential
# # ============= Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.3005
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice bcc $a
lattice bcc 3.3005
Lattice spacing in x,y,z = 3.3005 3.3005 3.3005
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (13.202 13.202 13.202)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
using lattice units in orthogonal box = (0 0 0) to (13.202 13.202 13.202)
create_atoms CPU = 0.001 seconds
mass 1 92.906
# # ============= set pair style
pair_style uf3 3
pair_coeff * * Nb.uf3 Nb
Reading potential file Nb.uf3 with DATE: 2024-04-02
# # ============= Setup output
thermo 10
thermo_modify norm yes
# # ============= Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# # ============= Run MD
velocity all create 300.0 2367804 loop geom
fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair uf3, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.351 | 3.351 | 3.351 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -4.4256832 0 -4.3872081 90756.437
10 294.36659 -4.4249607 0 -4.3872081 91006.427
20 277.9021 -4.422849 0 -4.387208 91716.126
30 251.88303 -4.4195119 0 -4.3872078 92789.12
40 218.42803 -4.4152211 0 -4.3872076 94118.45
50 180.40641 -4.4103445 0 -4.3872073 95579.009
60 141.2326 -4.4053202 0 -4.3872071 97031.816
70 104.54429 -4.4006146 0 -4.3872068 98332.882
80 73.787889 -4.3966699 0 -4.3872066 99351.332
90 51.759956 -4.3938446 0 -4.3872064 99992.934
100 40.209821 -4.3923633 0 -4.3872064 100211.98
Loop time of 0.11881 on 4 procs for 100 steps with 128 atoms
Performance: 36.361 ns/day, 0.660 hours/ns, 841.679 timesteps/s, 107.735 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10673 | 0.10875 | 0.11236 | 0.7 | 91.53
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0057324 | 0.0093477 | 0.011375 | 2.4 | 7.87
Output | 0.00016629 | 0.00018236 | 0.00022483 | 0.0 | 0.15
Modify | 9.4948e-05 | 0.00010621 | 0.00012066 | 0.0 | 0.09
Other | | 0.0004263 | | | 0.36
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1049 ave 1049 max 1049 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5376 ave 5376 max 5376 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21504
Ave neighs/atom = 168
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

4
lib/gpu/lal_base_dpd.cpp
View File

@ -57,7 +57,7 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
const double cell_size, const double gpu_split,
FILE *_screen, const void *pair_program,
const char *k_name, const int onetype,
const int extra_fields) {
const int extra_fields, bool need_charges) {
screen=_screen;
int gpu_nbor=0;
@ -73,7 +73,7 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
_threads_per_atom=device->threads_per_atom();
bool charge = false;
bool charge = need_charges;
bool rot = false;
bool vel = true;
_extra_fields = extra_fields;

3
lib/gpu/lal_base_dpd.h
View File

@ -53,7 +53,8 @@ class BaseDPD {
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen,
const void *pair_program, const char *k_name,
const int onetype=0, const int extra_fields=0);
const int onetype=0, const int extra_fields=0,
bool need_charges=false);
/// Estimate the overhead for GPU context changes and CPU driver
void estimate_gpu_overhead();

238
lib/gpu/lal_dpd_coul_slater_long.cpp Normal file
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@ -0,0 +1,238 @@
/***************************************************************************
lal_dpd_coul_slater_long.cpp
-------------------
Eddy BARRAUD (IFPEN/Sorbonne)
Class for acceleration of the dpd/coul/slater/long pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : May 28, 2024
email : eddy.barraud@outlook.fr
***************************************************************************/
#if defined(USE_OPENCL)
#include "dpd_coul_slater_long_cl.h"
#elif defined(USE_CUDART)
const char *dpd_coul_slater_long=0;
#else
#include "dpd_coul_slater_long_cubin.h"
#endif
#include "lal_dpd_coul_slater_long.h"
#include <cassert>
namespace LAMMPS_AL {
#define DPDCoulSlaterLongT DPDCoulSlaterLong<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
DPDCoulSlaterLongT::DPDCoulSlaterLong() : BaseDPD<numtyp,acctyp>(), _allocated(false) {
}
template <class numtyp, class acctyp>
DPDCoulSlaterLongT::~DPDCoulSlaterLong() {
clear();
}
template <class numtyp, class acctyp>
int DPDCoulSlaterLongT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int DPDCoulSlaterLongT::init(const int ntypes,
double **host_cutsq, double **host_a0,
double **host_gamma, double **host_sigma,
double **host_cut_dpd, double **host_cut_dpdsq,
double **host_cut_slatersq, double *host_special_lj,
const bool tstat_only,
const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size,
const double gpu_split, FILE *_screen, double *host_special_coul,
const double qqrd2e, const double g_ewald, double lamda) {
const int max_shared_types=this->device->max_shared_types();
int onetype=0;
#ifdef USE_OPENCL
if (maxspecial==0)
for (int i=1; i<ntypes; i++)
for (int j=i; j<ntypes; j++)
if (host_cutsq[i][j]>0) {
if (onetype>0)
onetype=-1;
else if (onetype==0)
onetype=i*max_shared_types+j;
}
if (onetype<0) onetype=0;
#endif
int extra_fields = 4; // round up to accomodate quadruples of numtyp values
// q
int success;
bool need_charges = true;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
gpu_split,_screen,dpd_coul_slater_long,"k_dpd_coul_slater_long",onetype, extra_fields, need_charges);
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
shared_types=false;
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write_coul(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
sp_cl.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
for (int i=0; i<4; i++) {
host_write_coul[i]=host_special_coul[i];
}
ucl_copy(sp_cl,host_write_coul,4,false);
_lj_types=lj_types;
_qqrd2e=qqrd2e;
_g_ewald=g_ewald;
_lamda=lamda;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
coeff.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_a0,host_gamma,
host_sigma,host_cut_dpd);
cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,cutsq,host_write,host_cutsq,
host_cut_dpdsq,host_cut_slatersq);
double special_sqrt[4];
special_sqrt[0] = sqrt(host_special_lj[0]);
special_sqrt[1] = sqrt(host_special_lj[1]);
special_sqrt[2] = sqrt(host_special_lj[2]);
special_sqrt[3] = sqrt(host_special_lj[3]);
UCL_H_Vec<double> dview;
sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(host_special_lj,4,*(this->ucl_device));
ucl_copy(sp_lj,dview,false);
sp_sqrt.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(special_sqrt,4,*(this->ucl_device));
ucl_copy(sp_sqrt,dview,false);
_tstat_only = 0;
if (tstat_only) _tstat_only=1;
_allocated=true;
this->_max_bytes=coeff.row_bytes()+cutsq.row_bytes()+sp_lj.row_bytes()+sp_sqrt.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void DPDCoulSlaterLongT::clear() {
if (!_allocated)
return;
_allocated=false;
coeff.clear();
cutsq.clear();
sp_lj.clear();
sp_sqrt.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double DPDCoulSlaterLongT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(DPDCoulSlaterLong<numtyp,acctyp>);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int DPDCoulSlaterLongT::loop(const int eflag, const int vflag) {
int nall = this->atom->nall();
// signal that we need to transfer extra data from the host
this->atom->extra_data_unavail();
numtyp4 *pextra=reinterpret_cast<numtyp4*>(&(this->atom->extra[0]));
int n = 0;
int nstride = 1;
for (int i = 0; i < nall; i++) {
int idx = n+i*nstride;
numtyp4 v;
v.x = q[i];
v.y = 0;
v.z = 0;
v.w = 0;
pextra[idx] = v;
}
this->atom->add_extra_data();
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &this->atom->extra, &coeff, &sp_lj, &sp_cl, &sp_sqrt,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag,
&vflag, &ainum, &nbor_pitch, &this->atom->v, &cutsq,
&this->_dtinvsqrt, &this->_seed, &this->_timestep,
&_qqrd2e, &_g_ewald, &_lamda,
&this->_tstat_only, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &this->atom->extra, &coeff, &_lj_types, &sp_lj, &sp_cl, &sp_sqrt,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &cutsq, &this->_dtinvsqrt,
&this->_seed, &this->_timestep,
&_qqrd2e, &_g_ewald, &_lamda,
&this->_tstat_only, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
template <class numtyp, class acctyp>
void DPDCoulSlaterLongT::update_coeff(int ntypes, double **host_a0, double **host_gamma,
double **host_sigma, double **host_cut_dpd)
{
UCL_H_Vec<numtyp> host_write(_lj_types*_lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
this->atom->type_pack4(ntypes,_lj_types,coeff,host_write,host_a0,host_gamma,
host_sigma,host_cut_dpd);
}
// ---------------------------------------------------------------------------
// Get the extra data pointers from host
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void DPDCoulSlaterLongT::get_extra_data(double *host_q) {
q = host_q;
}
template class DPDCoulSlaterLong<PRECISION,ACC_PRECISION>;
}

523
lib/gpu/lal_dpd_coul_slater_long.cu Normal file
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@ -0,0 +1,523 @@
// **************************************************************************
// dpd.cu
// -------------------
// Eddy BARRAUD (IFPEN/Sorbonne)
// Trung Dac Nguyen (U Chicago)
//
// Device code for acceleration of the dpd/coul/slater/long pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : May 28, 2024
// email : eddy.barraud@outlook.fr
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( vel_tex,float4);
#else
_texture_2d( pos_tex,int4);
_texture_2d( vel_tex,int4);
#endif
#else
#define pos_tex x_
#define vel_tex v_
#endif
#define EPSILON (numtyp)1.0e-10
//#define _USE_UNIFORM_SARU_LCG
//#define _USE_UNIFORM_SARU_TEA8
//#define _USE_GAUSSIAN_SARU_LCG
#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && !defined(_USE_GAUSSIAN_SARU_LCG)
#define _USE_UNIFORM_SARU_LCG
#endif
// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
#define LCGA 0x4beb5d59 /* Full period 32 bit LCG */
#define LCGC 0x2600e1f7
#define oWeylPeriod 0xda879add /* Prime period 3666320093 */
#define oWeylOffset 0x8009d14b
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0]
// using the inherent LCG, then multiply u with sqrt(3) to "match"
// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
#define SQRT3 (numtyp)1.7320508075688772935274463
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define SQRT3 (numtyp)1.7320508075688772935274463
#define k0 0xA341316C
#define k1 0xC8013EA4
#define k2 0xAD90777D
#define k3 0x7E95761E
#define delta 0x9e3779b9
#define rounds 8
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int sum = 0; \
for (int i=0; i < rounds; i++) { \
sum += delta; \
state += ((wstate<<4) + k0)^(wstate + sum)^((wstate>>5) + k1); \
wstate += ((state<<4) + k2)^(state + sum)^((state>>5) + k3); \
} \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state=0x12345678; \
unsigned int wstate=12345678; \
state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int v, s; \
numtyp r1, r2, rsq; \
while (1) { \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r1 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r2 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
rsq = r1 * r1 + r2 * r2; \
if (rsq < (numtyp)1.0) break; \
} \
numtyp fac = ucl_sqrt((numtyp)-2.0*log(rsq)/rsq); \
randnum = r2*fac; \
}
#endif
__kernel void k_dpd_coul_slater_long(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff,
const int lj_types,
const __global numtyp *restrict sp_lj,
const __global numtyp *restrict sp_cl_in,
const __global numtyp *restrict sp_sqrt,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp4 *restrict cutsq,
const numtyp dtinvsqrt, const int seed,
const int timestep, const numtyp qqrd2e,
const numtyp g_ewald, const numtyp lamda,
const int tstat_only,
const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp sp_cl[4];
///local_allocate_store_charge();
sp_cl[0]=sp_cl_in[0];
sp_cl[1]=sp_cl_in[1];
sp_cl[2]=sp_cl_in[2];
sp_cl[3]=sp_cl_in[3];
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp e_coul, energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
numtyp qtmp = extra[i].x; // q[i]
numtyp lamdainv = ucl_recip(lamda);
numtyp factor_dpd, factor_sqrt;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
factor_dpd = sp_lj[sbmask(j)];
factor_sqrt = sp_sqrt[sbmask(j)];
numtyp factor_coul;
factor_coul = (numtyp)1.0-sp_cl[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
// cutsq[mtype].x -> global squared cutoff
if (rsq<cutsq[mtype].x) {
numtyp r=ucl_sqrt(rsq);
numtyp force_dpd = (numtyp)0.0;
numtyp force_coul = (numtyp)0.0;
// apply DPD force if distance below DPD cutoff
// cutsq[mtype].y -> DPD squared cutoff
if (rsq < cutsq[mtype].y && r > EPSILON) {
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp wd = (numtyp)1.0 - r/coeff[mtype].w;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = a0 * wd, or 0 if tstat only
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
if (!tstat_only) force_dpd = coeff[mtype].x*wd;
force_dpd -= coeff[mtype].y*wd*wd*dot*rinv;
force_dpd *= factor_dpd;
force_dpd += factor_sqrt*coeff[mtype].z*wd*randnum*dtinvsqrt;
force_dpd *=rinv;
if (EVFLAG && eflag) {
// unshifted eng of conservative term:
// evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
// eng shifted to 0.0 at cutoff
numtyp e = (numtyp)0.5*coeff[mtype].x*coeff[mtype].w * wd*wd;
energy += factor_dpd*e;
}
}// if cut_dpdsq
// apply Slater electrostatic force if distance below Slater cutoff
// and the two species have a slater coeff
// cutsq[mtype].z -> Coulombic squared cutoff
if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){
numtyp r2inv=ucl_recip(rsq);
numtyp _erfc;
numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
numtyp prefactor = extra[j].x;
prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r;
numtyp rlamdainv = r * lamdainv;
numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv);
numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv)));
force_coul = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term);
if (factor_coul > (numtyp)0) force_coul -= factor_coul*prefactor*((numtyp)1.0-slater_term);
force_coul *= r2inv;
if (EVFLAG && eflag) {
numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv;
numtyp e = prefactor*(_erfc-e_slater);
if (factor_coul > (numtyp)0) e -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
e_coul += e;
}
} // if cut_coulsq
numtyp force = force_coul + force_dpd;
f.x += delx*force;
f.y += dely*force;
f.z += delz*force;
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
} // if cutsq
} // for nbor
} // if ii
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
}
__kernel void k_dpd_coul_slater_long_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff_in,
const __global numtyp *restrict sp_lj_in,
const __global numtyp *restrict sp_cl_in,
const __global numtyp *restrict sp_sqrt_in,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp4 *restrict cutsq_in,
const numtyp dtinvsqrt, const int seed,
const int timestep, const numtyp qqrd2e,
const numtyp g_ewald, const numtyp lamda,
const int tstat_only,
const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 cutsq[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[4];
__local numtyp sp_sqrt[4];
/// COUL Init
__local numtyp sp_cl[4];
if (tid<4) {
sp_lj[tid]=sp_lj_in[tid];
sp_sqrt[tid]=sp_sqrt_in[tid];
sp_cl[tid]=sp_cl_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
cutsq[tid]=cutsq_in[tid];
}
__syncthreads();
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp e_coul, energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int iw=ix.w;
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
numtyp qtmp = extra[i].x; // q[i]
numtyp lamdainv = ucl_recip(lamda);
numtyp factor_dpd, factor_sqrt;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
factor_dpd = sp_lj[sbmask(j)];
factor_sqrt = sp_sqrt[sbmask(j)];
numtyp factor_coul;
factor_coul = (numtyp)1.0-sp_cl[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype+jx.w;
/// cutsq.x = cutsq, cutsq.y = cut_dpdsq, cutsq.z = cut_slatersq
if (rsq<cutsq[mtype].x) {
numtyp r=ucl_sqrt(rsq);
numtyp force_dpd = (numtyp)0.0;
numtyp force_coul = (numtyp)0.0;
// apply DPD force if distance below DPD cutoff
// cutsq[mtype].y -> DPD squared cutoff
if (rsq < cutsq[mtype].y && r > EPSILON) {
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp wd = (numtyp)1.0 - r/coeff[mtype].w;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = a0 * wd, or 0 if tstat only
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
/// coeff.x = a0, coeff.y = gamma, coeff.z = sigma, coeff.w = cut_dpd
if (!tstat_only) force_dpd = coeff[mtype].x*wd;
force_dpd -= coeff[mtype].y*wd*wd*dot*rinv;
force_dpd *= factor_dpd;
force_dpd += factor_sqrt*coeff[mtype].z*wd*randnum*dtinvsqrt;
force_dpd *=rinv;
if (EVFLAG && eflag) {
// unshifted eng of conservative term:
// evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
// eng shifted to 0.0 at cutoff
numtyp e = (numtyp)0.5*coeff[mtype].x*coeff[mtype].w * wd*wd;
energy += factor_dpd*e;
}
}// if cut_dpdsq
// apply Slater electrostatic force if distance below Slater cutoff
// and the two species have a slater coeff
// cutsq[mtype].z -> Coulombic squared cutoff
if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){
numtyp r2inv=ucl_recip(rsq);
numtyp _erfc;
numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
numtyp prefactor = extra[j].x;
prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r;
numtyp rlamdainv = r * lamdainv;
numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv);
numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv)));
force_coul = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term);
if (factor_coul > (numtyp)0) force_coul -= factor_coul*prefactor*((numtyp)1.0-slater_term);
force_coul *= r2inv;
if (EVFLAG && eflag) {
numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv;
numtyp e_sf = prefactor*(_erfc-e_slater);
if (factor_coul > (numtyp)0) e_sf -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
e_coul += e_sf;
}
} // if cut_coulsq
numtyp force = force_coul + force_dpd;
f.x += delx*force;
f.y += dely*force;
f.z += delz*force;
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
} // if cutsq
} // for nbor
} // if ii
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
}

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/***************************************************************************
lal_dpd_coul_slater_long.h
-------------------
Eddy BARRAUD (IFPEN/Sorbonne)
Class for acceleration of the dpd/coul/slater/long pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : May 28, 2024
email : eddy.barraud@outlook.fr
***************************************************************************/
#ifndef LAL_DPD_CHARGED_H
#define LAL_DPD_CHARGED_H
#include "lal_base_dpd.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class DPDCoulSlaterLong : public BaseDPD<numtyp, acctyp> {
public:
DPDCoulSlaterLong();
~DPDCoulSlaterLong();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **host_cutsq, double **host_a0, double **host_gamma,
double **host_sigma, double **host_cut_dpd, double **host_cut_dpdsq,
double **host_cut_slatersq, double *host_special_lj, bool tstat_only, const int nlocal,
const int nall, const int max_nbors, const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen, double *host_special_coul, const double qqrd2e,
const double g_ewald, const double lamda);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
/// Update coeff if needed (tstat only)
void update_coeff(int ntypes, double **host_a0, double **host_gamma,
double **host_sigma, double **host_cut_dpd );
void get_extra_data(double *host_q);
// --------------------------- TYPE DATA --------------------------
/// coeff.x = a0, coeff.y = gamma, coeff.z = sigma, coeff.w = cut_dpd
UCL_D_Vec<numtyp4> coeff;
/// cutsq.x = cutsq, cutsq.y = cut_dpdsq, cutsq.w = cut_slatersq
UCL_D_Vec<numtyp4> cutsq;
/// Special LJ values
UCL_D_Vec<numtyp> sp_lj, sp_sqrt;
/// Special Coul values [0-3]
UCL_D_Vec<numtyp> sp_cl;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
/// Only used for thermostat
int _tstat_only;
/// Coulombic terms
numtyp _qqrd2e, _g_ewald, _lamda;
/// pointer to host data for atom charge
double *q;
private:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

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/***************************************************************************
lal_dpd_coul_slater_long_ext.cpp
-------------------
Eddy BARRAUD (IFPEN/Sorbonne)
Functions for LAMMPS access to dpd/coul/slater/long acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : May 28, 2024
email : eddy.barraud@outlook.fr
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_dpd_coul_slater_long.h"
using namespace std;
using namespace LAMMPS_AL;
static DPDCoulSlaterLong<PRECISION,ACC_PRECISION> DPDCMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int dpd_coul_slater_long_gpu_init(const int ntypes, double **host_cutsq, double **host_a0,
double **host_gamma, double **host_sigma, double **host_cut_dpd,
double **host_cut_dpdsq, double **host_cut_slatersq,
double *special_lj, const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double *host_special_coul, const double qqrd2e,
const double g_ewald, const double lamda) {
DPDCMF.clear();
gpu_mode=DPDCMF.device->gpu_mode();
double gpu_split=DPDCMF.device->particle_split();
int first_gpu=DPDCMF.device->first_device();
int last_gpu=DPDCMF.device->last_device();
int world_me=DPDCMF.device->world_me();
int gpu_rank=DPDCMF.device->gpu_rank();
int procs_per_gpu=DPDCMF.device->procs_per_gpu();
DPDCMF.device->init_message(screen,"dpd",first_gpu,last_gpu);
bool message=false;
if (DPDCMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=DPDCMF.init(ntypes, host_cutsq, host_a0, host_gamma, host_sigma, host_cut_dpd,
host_cut_dpdsq, host_cut_slatersq, special_lj, false, inum, nall,
max_nbors, maxspecial, cell_size, gpu_split, screen, host_special_coul,
qqrd2e, g_ewald, lamda);
DPDCMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=DPDCMF.init(ntypes, host_cutsq, host_a0, host_gamma, host_sigma, host_cut_dpd,
host_cut_dpdsq, host_cut_slatersq, special_lj, false, inum, nall,
max_nbors, maxspecial, cell_size, gpu_split, screen, host_special_coul,
qqrd2e, g_ewald, lamda);
DPDCMF.device->serialize_init();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
DPDCMF.estimate_gpu_overhead();
return init_ok;
}
void dpd_coul_slater_long_gpu_clear() {
DPDCMF.clear();
}
int ** dpd_coul_slater_long_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time, bool &success,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
double *boxlo, double *prd) {
return DPDCMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
host_v, dtinvsqrt, seed, timestep, boxlo, prd);
}
void dpd_coul_slater_long_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
const int nlocal, double *boxlo, double *prd) {
DPDCMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
tag, host_v, dtinvsqrt, seed, timestep, nlocal, boxlo, prd);
}
void dpd_coul_slater_long_gpu_update_coeff(int ntypes, double **host_a0, double **host_gamma,
double **host_sigma, double **host_cut_dpd)
{
DPDCMF.update_coeff(ntypes,host_a0,host_gamma,host_sigma, host_cut_dpd);
}
void dpd_coul_slater_long_gpu_get_extra_data(double *host_q) {
DPDCMF.get_extra_data(host_q);
}
double dpd_coul_slater_long_gpu_bytes() {
return DPDCMF.host_memory_usage();
}

6
lib/plumed/Install.py
View File

@ -16,8 +16,10 @@ parser = ArgumentParser(prog='Install.py',
description="LAMMPS library build wrapper script")
# settings
# Note: must also adjust check for supported API versions in
# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
version = "2.8.3"
version = "2.9.1"
mode = "static"
# help message
@ -46,7 +48,9 @@ checksums = { \
'2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \
'2.8.2' : '599092b6a0aa6fff992612537ad98994', \
'2.8.3' : '76d23cd394eba9e6530316ed1184e219', \
'2.8.4' : '9f59c4f9bda86fe5bef19543c295a981', \
'2.9.0' : '661eabeebee05cf84bbf9dc23d7d5f46', \
'2.9.1' : 'c3b2d31479c1e9ce211719d40e9efbd7', \
}
# parse and process arguments

136
potentials/Nb.uf3 Normal file
View File

@ -0,0 +1,136 @@
#UF3 POT UNITS: metal DATE: 2024-04-02 12:18:15.359106 AUTHOR: Ajinkya_Hire CITATION:
2B Nb Nb 0 3 nk
8.0 31
0.001 0.001 0.001 0.001 0.33429166666666665 0.66758333333333331 1.000875 1.3341666666666665 1.6674583333333333 2.00075 2.3340416666666663 2.6673333333333331 3.0006249999999999 3.3339166666666666 3.667208333333333 4.0004999999999997 4.3337916666666665 4.6670833333333333 5.000375 5.3336666666666668 5.6669583333333335 6.0002500000000003 6.3335416666666671 6.6668333333333338 7.0001249999999997 7.3334166666666665 7.6667083333333332 8 8 8 8
27
79.140244588519465 79.140244588519465 55.85833391113556 36.597903318706138 21.358952811231141 12.290000872768841 1.9593931914091953 -0.65697974623243804 -0.85177956270573463 -0.68929688239869991 -0.46787243412973262 -0.27624655899523165 -0.11912921944351409 -0.056302369393035338 -0.0049812809608429064 0.0085637634684603507 0.0034716161454604712 -0.0058751075573311978 -0.005453415412748467 -0.0015123194244718201 0.0011577919587182201 0.001583772506713282 -0.00049823976100720228 -0.0013902809146717273 0 0 0
#
#UF3 POT UNITS: metal DATE: 2024-04-02 12:18:15.359106 AUTHOR: Ajinkya_Hire CITATION:
3B Nb Nb Nb 0 3 nk
8.0 4.0 4.0 23 15 15
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#

1
potentials/README
View File

@ -118,4 +118,5 @@ sw Stillinger-Weber potential
tersoff Tersoff potential
tersoff.mod modified Tersoff potential
tersoff.zbl Tersoff with ZBL core
uf3 UF3 potential
vashishta Vashishta 2-body and 3-body potential

2
python/lammps/core.py
View File

@ -891,7 +891,7 @@ class lammps(object):
# set length of vector for items that are not a scalar
vec_dict = { 'boxlo':3, 'boxhi':3, 'sublo':3, 'subhi':3,
'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3,
'special_lj':4, 'special_coul':4 }
'special_lj':4, 'special_coul':4, 'procgrid':3 }
if name in vec_dict:
veclen = vec_dict[name]
elif name == 'respa_dt':

14
python/lammps/pylammps.py
View File

@ -796,18 +796,16 @@ class PyLammps(object):
comm = {}
comm['nprocs'] = self.lmp.extract_setting("world_size")
comm['nthreads'] = self.lmp.extract_setting("nthreads")
comm['proc_grid'] = comm['procgrid'] = self.lmp.extract_global("procgrid")
idx = self.lmp.extract_setting("comm_style")
comm['comm_style'] = ('brick', 'tiled')[idx]
idx = self.lmp.extract_setting("comm_style")
comm['comm_layout'] = ('uniform', 'nonuniform', 'irregular')[idx]
comm['ghost_velocity'] = self.lmp.extract_setting("ghost_velocity") == 1
for line in output:
if line.startswith("MPI library"):
comm['mpi_version'] = line.split(':')[1].strip()
elif line.startswith("Comm style"):
parts = self._split_values(line)
comm['comm_style'] = self._get_pair(parts[0])[1]
comm['comm_layout'] = self._get_pair(parts[1])[1]
elif line.startswith("Processor grid"):
comm['proc_grid'] = [int(x) for x in self._get_pair(line)[1].split('x')]
elif line.startswith("Communicate velocities for ghost atoms"):
comm['ghost_velocity'] = (self._get_pair(line)[1] == "yes")
return comm
def _parse_element_list(self, output):

13
src/.gitignore vendored
View File

@ -169,6 +169,17 @@
/rann_*.cpp
/rann_*.h
/pair_uf3.cpp
/pair_uf3.h
/uf3_bspline_basis2.cpp
/uf3_bspline_basis2.h
/uf3_bspline_basis3.cpp
/uf3_bspline_basis3.h
/uf3_pair_bspline.cpp
/uf3_pair_bspline.h
/uf3_triplet_bspline.cpp
/uf3_triplet_bspline.h
/compute_test_nbl.cpp
/compute_test_nbl.h
/pair_multi_lucy.cpp
@ -1704,6 +1715,8 @@
/pair_dpd.h
/pair_dpd_tstat.cpp
/pair_dpd_tstat.h
/pair_dpd_coul_slater_long.cpp
/pair_dpd_coul_slater_long.h
/pair_dpd_ext.cpp
/pair_dpd_ext.h
/pair_dpd_ext_tstat.cpp

25
src/BPM/bond_bpm.cpp
View File

@ -352,19 +352,32 @@ void BondBPM::process_broken(int i, int j)
{
if (!break_flag)
error->one(FLERR, "BPM bond broke with break no option");
if (fix_store_local) {
for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j);
fix_store_local->add_data(output_data, i, j);
int nlocal = atom->nlocal;
if (fix_store_local) {
// If newton off, bond can break on two procs so only record if proc owns lower tag
// (BPM bond styles should sort so i -> atom with lower tag)
if (force->newton_bond || (i < nlocal)) {
for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j);
fix_store_local->add_data(output_data, i, j);
}
}
if (fix_update_special_bonds) fix_update_special_bonds->add_broken_bond(i, j);
if (fix_update_special_bonds) {
// If this processor owns two copies of the bond (i.e. if the domain is periodic and 1 proc thick),
// skip instance where larger tag (j) owned
int check = 1;
if (i >= nlocal) {
int imap = atom->map(atom->tag[i]);
if (imap < nlocal) check = 0;
}
if (check) fix_update_special_bonds->add_broken_bond(i, j);
}
// Manually search and remove from atom arrays
// need to remove in case special bonds arrays rebuilt
int m, n;
int nlocal = atom->nlocal;
int m, n;
tagint *tag = atom->tag;
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;

7
src/BPM/compute_nbond_atom.cpp
View File

@ -65,14 +65,13 @@ void ComputeNBondAtom::compute_peratom()
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int ntotal = nlocal;
if (force->newton) ntotal += atom->nghost;
// set local nbond array
int i, j, k;
int *num_bond = atom->num_bond;
int newton_bond = force->newton_bond;
int ntotal = nlocal;
if (newton_bond) ntotal += atom->nghost;
for (i = 0; i < ntotal; i++) nbond[i] = 0;
for (i = 0; i < nlocal; i++) {
@ -88,7 +87,7 @@ void ComputeNBondAtom::compute_peratom()
}
// communicate ghost nbond between neighbor procs
if (force->newton) comm->reverse_comm(this);
if (newton_bond) comm->reverse_comm(this);
// zero nbond of atoms not in group
// only do this after comm since ghost contributions must be included

2
src/BPM/fix_update_special_bonds.cpp
View File

@ -100,6 +100,7 @@ void FixUpdateSpecialBonds::pre_exchange()
n1 = nspecial[i][0];
for (m = 0; m < n1; m++)
if (slist[m] == tagj) break;
if (m == n1) error->one(FLERR, "Special bond {} {} not found", tagi, tagj);
for (; m < n1 - 1; m++) slist[m] = slist[m + 1];
nspecial[i][0]--;
nspecial[i][1] = nspecial[i][2] = nspecial[i][0];
@ -110,6 +111,7 @@ void FixUpdateSpecialBonds::pre_exchange()
n1 = nspecial[j][0];
for (m = 0; m < n1; m++)
if (slist[m] == tagi) break;
if (m == n1) error->one(FLERR, "Special bond {} {} not found", tagi, tagj);
for (; m < n1 - 1; m++) slist[m] = slist[m + 1];
nspecial[j][0]--;
nspecial[j][1] = nspecial[j][2] = nspecial[j][0];

199
src/COLVARS/ndx_group.cpp
View File

@ -1,199 +0,0 @@
// clang-format off
// -*- c++ -*-
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "ndx_group.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "group.h"
#include "tokenizer.h"
using namespace LAMMPS_NS;
static constexpr int BUFLEN = 4096;
// read file until next section "name" or any next section if name == ""
static std::string find_section(FILE *fp, const std::string &name)
{
char linebuf[BUFLEN];
std::string pattern = "^\\s*\\[\\s+\\S+\\s+\\]\\s*$";
if (!name.empty())
pattern = fmt::format("^\\s*\\[\\s+{}\\s+\\]\\s*$",name);
fgets(linebuf,BUFLEN,fp);
while (!feof(fp)) {
if (utils::strmatch(linebuf,pattern))
return Tokenizer(linebuf).as_vector()[1];
fgets(linebuf,BUFLEN,fp);
}
return "";
}
static std::vector<tagint> read_section(FILE *fp, std::string &name)
{
char linebuf[BUFLEN];
std::vector<tagint> tagbuf;
std::string pattern = "^\\s*\\[\\s+\\S+\\s+\\]\\s*$";
while (fgets(linebuf,BUFLEN,fp)) {
// start of new section. we are done, update "name"
if (utils::strmatch(linebuf,pattern)) {
name = Tokenizer(linebuf).as_vector()[1];
return tagbuf;
}
ValueTokenizer values(linebuf);
while (values.has_next())
tagbuf.push_back(values.next_tagint());
}
// set empty name to indicate end of file
name = "";
return tagbuf;
}
/* ---------------------------------------------------------------------- */
void Ndx2Group::command(int narg, char **arg)
{
int len;
bigint num;
FILE *fp;
std::string name, next;
if (narg < 1) error->all(FLERR,"Illegal ndx2group command");
if (atom->tag_enable == 0)
error->all(FLERR,"Must have atom IDs for ndx2group command");
if (atom->map_style == Atom::MAP_NONE)
error->all(FLERR,"Must have an atom map for ndx2group command");
if (comm->me == 0) {
fp = fopen(arg[0], "r");
if (fp == nullptr)
error->one(FLERR,"Cannot open index file for reading: {}",
utils::getsyserror());
utils::logmesg(lmp,"Reading groups from index file {}:\n",arg[0]);
}
if (narg == 1) { // restore all groups
if (comm->me == 0) {
name = find_section(fp,"");
while (!name.empty()) {
// skip over group "all", which is called "System" in gromacs
if (name == "System") {
name = find_section(fp,"");
continue;
}
utils::logmesg(lmp," Processing group '{}'\n",name);
len = name.size()+1;
MPI_Bcast(&len,1,MPI_INT,0,world);
if (len > 1) {
MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world);
// read tags for atoms in group and broadcast
std::vector<tagint> tags = read_section(fp,next);
num = tags.size();
MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world);
create(name,tags);
name = next;
}
}
len = -1;
MPI_Bcast(&len,1,MPI_INT,0,world);
} else {
while (true) {
MPI_Bcast(&len,1,MPI_INT,0,world);
if (len < 0) break;
if (len > 1) {
char *buf = new char[len];
MPI_Bcast(buf,len,MPI_CHAR,0,world);
MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
tagint *tbuf = new tagint[num];
MPI_Bcast(tbuf,num,MPI_LMP_TAGINT,0,world);
create(buf,std::vector<tagint>(tbuf,tbuf+num));
delete[] buf;
delete[] tbuf;
}
}
}
} else { // restore selected groups
for (int idx=1; idx < narg; ++idx) {
if (comm->me == 0) {
// find named section, search from beginning of file
rewind(fp);
name = find_section(fp,arg[idx]);
utils::logmesg(lmp," {} group '{}'\n", name.size()
? "Processing" : "Skipping",arg[idx]);
len = name.size()+1;
MPI_Bcast(&len,1,MPI_INT,0,world);
if (len > 1) {
MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world);
// read tags for atoms in group and broadcast
std::vector<tagint> tags = read_section(fp,next);
num = tags.size();
MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world);
create(name,tags);
name = next;
}
} else {
MPI_Bcast(&len,1,MPI_INT,0,world);
if (len > 1) {
char *buf = new char[len];
MPI_Bcast(buf,len,MPI_CHAR,0,world);
MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
tagint *tbuf = new tagint[num];
MPI_Bcast(tbuf,num,MPI_LMP_TAGINT,0,world);
create(buf,std::vector<tagint>(tbuf,tbuf+num));
delete[] buf;
delete[] tbuf;
}
}
}
}
if (comm->me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
void Ndx2Group::create(const std::string &name, const std::vector<tagint> &tags)
{
// wipe out all members if the group exists. gid==0 is group "all"
int gid = group->find(name);
if (gid > 0) group->assign(name + " clear");
// map from global to local
const int nlocal = atom->nlocal;
int *flags = (int *)calloc(nlocal,sizeof(int));
for (bigint i=0; i < (int)tags.size(); ++i) {
const int id = atom->map(tags[i]);
if (id < nlocal && id >= 0) flags[id] = 1;
}
group->create(name,flags);
free(flags);
}

39
src/DPD-BASIC/Install.sh Executable file
View File

@ -0,0 +1,39 @@
# Install/unInstall package files in LAMMPS
# mode = 0/1/2 for uninstall/install/update
mode=$1
# enforce using portable C locale
LC_ALL=C
export LC_ALL
# arg1 = file, arg2 = file it depends on
action () {
if (test $mode = 0) then
rm -f ../$1
elif (! cmp -s $1 ../$1) then
if (test -z "$2" || test -e ../$2) then
cp $1 ..
if (test $mode = 2) then
echo " updating src/$1"
fi
fi
elif (test -n "$2") then
if (test ! -e ../$2) then
rm -f ../$1
fi
fi
}
# list of files with optional dependcies
action pair_dpd_coul_slater_long.cpp pppm.cpp
action pair_dpd_coul_slater_long.h pppm.h
action pair_dpd.cpp
action pair_dpd_ext.cpp
action pair_dpd_ext.h
action pair_dpd_ext_tstat.cpp
action pair_dpd_ext_tstat.h
action pair_dpd.h
action pair_dpd_tstat.cpp
action pair_dpd_tstat.h

544
src/DPD-BASIC/pair_dpd_coul_slater_long.cpp Normal file
View File

@ -0,0 +1,544 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Eddy BARRAUD (IFPEN/Sorbonne)
------------------------------------------------------------------------- */
#include "pair_dpd_coul_slater_long.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "random_mars.h"
#include "update.h"
#include "ewald_const.h"
#include "kspace.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace EwaldConst;
static constexpr double EPSILON = 1.0e-10;
/* ---------------------------------------------------------------------- */
PairDPDCoulSlaterLong::PairDPDCoulSlaterLong(LAMMPS *lmp) :
Pair(lmp), cut_dpd(nullptr), cut_dpdsq(nullptr), cut_slatersq(nullptr),
a0(nullptr), gamma(nullptr), sigma(nullptr), random(nullptr)
{
writedata = 1;
ewaldflag = pppmflag = 1;
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
PairDPDCoulSlaterLong::~PairDPDCoulSlaterLong()
{
if (copymode) return;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut_dpd);
memory->destroy(cut_dpdsq);
memory->destroy(cut_slatersq);
memory->destroy(cut);
memory->destroy(a0);
memory->destroy(gamma);
memory->destroy(sigma);
}
if (random) delete random;
}
/* ---------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double vxtmp,vytmp,vztmp,delvx,delvy,delvz;
double r2inv,forcedpd,forcecoul,factor_coul;
double grij,expm2,prefactor,t,erfc;
double rsq,r,rinv,dot,wd,randnum,factor_dpd,factor_sqrt;
int *ilist,*jlist,*numneigh,**firstneigh;
double slater_term;
evdwl = ecoul = 0.0;
ev_init(eflag,vflag);
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double dtinvsqrt = 1.0/sqrt(update->dt);
double *q = atom->q;
double *special_coul = force->special_coul;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
vxtmp = v[i][0];
vytmp = v[i][1];
vztmp = v[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_dpd = special_lj[sbmask(j)];
factor_sqrt = special_sqrt[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
// forces if below maximum cutoff
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
if (evflag) evdwl = ecoul = 0.0;
// apply DPD force if distance below DPD cutoff
if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON) {
rinv = 1.0/r;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
dot = delx*delvx + dely*delvy + delz*delvz;
wd = 1.0 - r/cut_dpd[itype][jtype];
randnum = random->gaussian();
// conservative force = a0 * wd
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
// random force must be scaled by sqrt(factor_dpd)
forcedpd = a0[itype][jtype]*wd;
forcedpd -= gamma[itype][jtype]*wd*wd*dot*rinv;
forcedpd *= factor_dpd;
forcedpd += factor_sqrt*sigma[itype][jtype]*wd*randnum*dtinvsqrt;
forcedpd *= rinv;
if (eflag) {
// eng shifted to 0.0 at cutoff
evdwl = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd;
evdwl *= factor_dpd;
}
} else forcedpd = 0.0;
// apply Slater electrostatic force if distance below Slater cutoff
// and the two species are charged
if (rsq < cut_slatersq[itype][jtype]){
r2inv = 1.0/rsq;
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*(1-slater_term);
forcecoul *= r2inv;
if (eflag) {
ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor*(1.0-(1 + r/lamda)*exp(-2*r/lamda));
}
} else forcecoul = 0.0;
fpair = forcedpd + forcecoul;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::allocate()
{
int i,j;
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (i = 1; i <= n; i++)
for (j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(cut_dpd,n+1,n+1,"pair:cut_dpd");
memory->create(cut_dpdsq,n+1,n+1,"pair:cut_dpdsq");
memory->create(cut_slatersq,n+1,n+1,"pair:cut_slatersq");
memory->create(a0,n+1,n+1,"pair:a0");
memory->create(gamma,n+1,n+1,"pair:gamma");
memory->create(sigma,n+1,n+1,"pair:sigma");
for (i = 0; i <= atom->ntypes; i++)
for (j = 0; j <= atom->ntypes; j++)
sigma[i][j] = gamma[i][j] = 0.0;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::settings(int narg, char **arg)
{
// params : T cut_dpd seed lambda cut_coul
if (narg != 5) error->all(FLERR,"Illegal pair_style command");
temperature = utils::numeric(FLERR,arg[0],false,lmp);
cut_global = utils::numeric(FLERR,arg[1],false,lmp);
seed = utils::inumeric(FLERR,arg[2],false,lmp);
lamda = utils::numeric(FLERR,arg[3],false,lmp);
cut_coul = utils::numeric(FLERR,arg[4],false,lmp);
// initialize Marsaglia RNG with processor-unique seed
if (seed <= 0)
error->all(FLERR,"Invalid random seed {} for pair_style dpd/coul/slater/long command", seed);
delete random;
random = new RanMars(lmp,seed + comm->me);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
if (setflag[i][j]) cut_dpd[i][j] = MAX(cut_global,cut_coul);
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
double a0_one = utils::numeric(FLERR,arg[2],false,lmp);
double gamma_one = utils::numeric(FLERR,arg[3],false,lmp);
double cut_one = cut_global;
double cut_two = 0.0;
if (narg > 4) {
bool do_slater = utils::logical(FLERR,arg[4],false,lmp);
if (do_slater) cut_two = cut_coul;
}
if (narg > 5) cut_one = utils::numeric(FLERR,arg[5],false,lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
a0[i][j] = a0_one;
gamma[i][j] = gamma_one;
cut_dpd[i][j] = cut_one;
cut_slatersq[i][j] = cut_two * cut_two;
cut[i][j] = MAX(cut_one, cut_two);
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::init_style()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair dpd requires ghost atoms store velocity");
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/slater/long requires atom attribute q");
// if newton off, forces between atoms ij will be double computed
// using different random numbers
if (force->newton_pair == 0 && comm->me == 0)
error->warning(FLERR, "Pair dpd needs newton pair on for momentum conservation");
neighbor->add_request(this);
// precompute random force scaling factors
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
// ensure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr)
error->all(FLERR,"Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
return the maximum cutoff between Slater or DPD cutoff if charged
return the DPD cutoff for uncharged
------------------------------------------------------------------------- */
double PairDPDCoulSlaterLong::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]);
cut_dpdsq[i][j] = cut_dpd[i][j] * cut_dpd[i][j];
a0[j][i] = a0[i][j];
gamma[j][i] = gamma[i][j];
sigma[j][i] = sigma[i][j];
cut_dpd[j][i] = cut_dpd[i][j];
cut[j][i] = cut[i][j];
cut_dpdsq[j][i] = cut_dpdsq[i][j];
cut_slatersq[j][i] = cut_slatersq[i][j];
return MAX(cut_dpd[i][j], sqrt(cut_slatersq[i][j]));
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&a0[i][j],sizeof(double),1,fp);
fwrite(&gamma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&cut_dpd[i][j],sizeof(double),1,fp);
fwrite(&cut_slatersq[i][j],sizeof(double),1,fp);
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_dpd[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_slatersq[i][j],sizeof(double),1,fp,nullptr,error);
}
MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_dpd[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_slatersq[i][j],1,MPI_DOUBLE,0,world);
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::write_restart_settings(FILE *fp)
{
fwrite(&temperature,sizeof(double),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&seed,sizeof(int),1,fp);
fwrite(&lamda,sizeof(double),1,fp);
fwrite(&cut_coul,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
utils::sfread(FLERR,&temperature,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&seed,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR,&lamda,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,nullptr,error);
}
MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&seed,1,MPI_INT,0,world);
MPI_Bcast(&lamda,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
// initialize Marsaglia RNG with processor-unique seed
// same seed that pair_style command initially specified
if (random) delete random;
random = new RanMars(lmp,seed + comm->me);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,a0[i][i],gamma[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g %s %g\n",i,j,a0[i][j],gamma[i][j],
(cut_slatersq[i][j] == 0.0) ? "yes" : "no", cut_dpd[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairDPDCoulSlaterLong::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_dpd, double &fforce)
{
double r,rinv,wd,phi;
double r2inv,grij,expm2,t,erfc,prefactor;
double slater_term;
double forcecoul,phicoul;
double energy = 0.0;
fforce = 0.0;
r = sqrt(rsq);
// compute DPD force and energy
if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON) {
rinv = 1.0/r;
wd = 1.0 - r/cut_dpd[itype][jtype];
fforce += a0[itype][jtype]*wd * factor_dpd*rinv;
phi = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd;
energy += factor_dpd*phi;
}
// compute Slater coulombic force and energy
if (atom->q[i]*atom->q[j] != 0.0 && rsq < cut_slatersq[itype][jtype]) {
r2inv = 1.0/rsq;
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
fforce += forcecoul * r2inv;
phicoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
energy += phicoul;
}
return energy;
}
void *PairDPDCoulSlaterLong::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
if (strcmp(str,"lamda") == 0) return (void *) &lamda;
dim = 2;
if (strcmp(str,"a0") == 0) return (void *) a0;
if (strcmp(str,"gamma") == 0) return (void *) gamma;
return nullptr;
}

64
src/DPD-BASIC/pair_dpd_coul_slater_long.h Normal file
View File

@ -0,0 +1,64 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(dpd/coul/slater/long,PairDPDCoulSlaterLong);
// clang-format on
#else
#ifndef LMP_PAIR_DPD_COUL_SLATER_LONG_H
#define LMP_PAIR_DPD_COUL_SLATER_LONG_H
#include "pair.h"
namespace LAMMPS_NS {
class PairDPDCoulSlaterLong : public Pair {
public:
PairDPDCoulSlaterLong(class LAMMPS *);
~PairDPDCoulSlaterLong() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_restart_settings(FILE *) override;
void read_restart_settings(FILE *) override;
void write_data(FILE *) override;
void write_data_all(FILE *) override;
double single(int, int, int, int, double, double, double, double &) override;
void *extract(const char *, int &) override;
protected:
double cut_global, temperature;
double special_sqrt[4];
int seed;
double **cut;
double **cut_dpd, **cut_dpdsq, **cut_slatersq;
double **a0, **gamma;
double **sigma;
class RanMars *random;
double cut_coul, qdist;
double lamda;
double g_ewald;
virtual void allocate();
};
} // namespace LAMMPS_NS
#endif
#endif

1
src/Depend.sh
View File

@ -116,6 +116,7 @@ if (test $1 = "KSPACE") then
depend CG-SPICA
depend CORESHELL
depend DIELECTRIC
depend DPD-BASIC
depend GPU
depend KOKKOS
depend OPT

83
src/COLVARS/group_ndx.cpp → src/EXTRA-COMMAND/group_ndx.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
// -*- c++ -*-
/* ----------------------------------------------------------------------
@ -34,12 +33,15 @@ using namespace LAMMPS_NS;
static int cmptagint(const void *p1, const void *p2)
{
const tagint i1 = * static_cast<const tagint *>(p1);
const tagint i2 = * static_cast<const tagint *>(p2);
if (i1 == i2) return 0;
const tagint i1 = *static_cast<const tagint *>(p1);
const tagint i2 = *static_cast<const tagint *>(p2);
if (i1 == i2)
return 0;
else {
if (i1 < i2) return -1;
else return 1;
if (i1 < i2)
return -1;
else
return 1;
}
}
@ -49,27 +51,24 @@ void Group2Ndx::command(int narg, char **arg)
{
FILE *fp = nullptr;
if (narg < 1) error->all(FLERR,"Illegal group2ndx command");
if (narg < 1) utils::missing_cmd_args(FLERR, "group2ndx", error);
if (atom->tag_enable == 0)
error->all(FLERR,"Must have atom IDs for group2ndx command");
if (atom->tag_enable == 0) error->all(FLERR, "Must have atom IDs for group2ndx command");
if (comm->me == 0) {
fp = fopen(arg[0], "w");
if (fp == nullptr)
error->one(FLERR,"Cannot open index file for writing: {}", utils::getsyserror());
utils::logmesg(lmp,"Writing groups to index file {}:\n",arg[0]);
error->one(FLERR, "Cannot open index file for writing: {}", utils::getsyserror());
utils::logmesg(lmp, "Writing groups to index file {}:\n", arg[0]);
}
if (narg == 1) { // write out all groups
for (int i=0; i < group->ngroup; ++i) {
write_group(fp,i);
}
} else { // write only selected groups
for (int i=1; i < narg; ++i) {
if (narg == 1) { // write out all groups
for (int i = 0; i < group->ngroup; ++i) { write_group(fp, i); }
} else { // write only selected groups
for (int i = 1; i < narg; ++i) {
int gid = group->find(arg[i]);
if (gid < 0) error->all(FLERR, "Non-existing group requested");
write_group(fp,gid);
write_group(fp, gid);
}
}
@ -85,22 +84,26 @@ void Group2Ndx::write_group(FILE *fp, int gid)
bigint gcount = group->count(gid);
int lnum, width, cols;
if (utils::strmatch(group->names[gid], "\\s+")) {
if (fp) utils::logmesg(lmp, " skipping group {}...done", group->names[gid]);
return;
}
if (fp) {
utils::logmesg(lmp," writing group {}...",group->names[gid]);
utils::logmesg(lmp, " writing group {}...", group->names[gid]);
// the "all" group in LAMMPS is called "System" in Gromacs
if (gid == 0) {
fputs("[ System ]\n", fp);
} else {
fmt::print(fp,"[ {} ]\n", group->names[gid]);
fmt::print(fp, "[ {} ]\n", group->names[gid]);
}
width = log10((double) atom->natoms)+2;
width = log10((double) atom->natoms) + 2;
cols = 80 / width;
}
if (gcount > 0) {
const int * const mask = atom->mask;
const tagint * const tag = atom->tag;
const int *const mask = atom->mask;
const tagint *const tag = atom->tag;
const int groupbit = group->bitmask[gid];
const int nlocal = atom->nlocal;
int i;
@ -111,45 +114,45 @@ void Group2Ndx::write_group(FILE *fp, int gid)
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) sendlist[lnum++] = tag[i];
int nrecv=0;
int nrecv = 0;
bigint allrecv;
if (comm->me == 0) {
MPI_Status status;
MPI_Request request;
for (i=0; i < lnum; i++)
recvlist[i] = sendlist[i];
for (i = 0; i < lnum; i++) recvlist[i] = sendlist[i];
allrecv = lnum;
for (i=1; i < comm->nprocs; ++i) {
MPI_Irecv(recvlist+allrecv,gcount-allrecv,MPI_LMP_TAGINT,i,0, world,&request);
MPI_Send(&nrecv,0,MPI_INT,i,0,world); // block rank "i" until we are ready to receive
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_LMP_TAGINT,&nrecv);
for (i = 1; i < comm->nprocs; ++i) {
MPI_Irecv(recvlist + allrecv, gcount - allrecv, MPI_LMP_TAGINT, i, 0, world, &request);
// block rank "i" until we are ready to receive
MPI_Send(&nrecv, 0, MPI_INT, i, 0, world);
MPI_Wait(&request, &status);
MPI_Get_count(&status, MPI_LMP_TAGINT, &nrecv);
allrecv += nrecv;
}
// sort received list
qsort((void *)recvlist, allrecv, sizeof(tagint), cmptagint);
qsort((void *) recvlist, allrecv, sizeof(tagint), cmptagint);
} else {
MPI_Recv(&nrecv,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(sendlist,lnum,MPI_LMP_TAGINT,0,0,world);
MPI_Recv(&nrecv, 0, MPI_INT, 0, 0, world, MPI_STATUS_IGNORE);
MPI_Rsend(sendlist, lnum, MPI_LMP_TAGINT, 0, 0, world);
}
delete [] sendlist;
delete[] sendlist;
}
if (fp) {
int i, j;
for (i=0, j=0; i < gcount; ++i) {
fmt::print(fp,"{:>{}}",recvlist[i],width);
for (i = 0, j = 0; i < gcount; ++i) {
fmt::print(fp, "{:>{}}", recvlist[i], width);
++j;
if (j == cols) {
fputs("\n",fp);
fputs("\n", fp);
j = 0;
}
}
if (j > 0) fputs("\n",fp);
utils::logmesg(lmp,"done\n");
if (j > 0) fputs("\n", fp);
utils::logmesg(lmp, "done\n");
}
if (gcount > 0) delete[] recvlist;
}

0
src/COLVARS/group_ndx.h → src/EXTRA-COMMAND/group_ndx.h
View File

220
src/EXTRA-COMMAND/ndx_group.cpp Normal file
View File

@ -0,0 +1,220 @@
// -*- c++ -*-
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "ndx_group.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "group.h"
#include "tokenizer.h"
using namespace LAMMPS_NS;
static constexpr int BUFLEN = 4096;
// read file until next section "name" or any next section if name == ""
static std::string find_section(FILE *fp, const std::string &name)
{
char linebuf[BUFLEN];
fgets(linebuf, BUFLEN, fp);
while (!feof(fp)) {
if (utils::strmatch(linebuf, "^\\s*\\[.*\\]\\s*$")) {
auto words = Tokenizer(linebuf).as_vector();
if (words.size() != 3)
throw TokenizerException("Invalid group name in index file",
utils::trim(utils::strfind(linebuf, "[^\\[^\\]]+")));
if (name.empty() || (name == words[1])) return words[1];
}
fgets(linebuf, BUFLEN, fp);
}
return "";
}
static std::vector<tagint> read_section(FILE *fp, std::string &name)
{
char linebuf[BUFLEN];
std::vector<tagint> tagbuf;
while (fgets(linebuf, BUFLEN, fp)) {
// start of new section. we are done, update "name"
if (utils::strmatch(linebuf, "^\\s*\\[.*\\]\\s*$")) {
auto words = Tokenizer(linebuf).as_vector();
if (words.size() != 3)
throw TokenizerException("Invalid group name in index file",
utils::trim(utils::strfind(linebuf, "[^\\[^\\]]+")));
name = words[1];
return tagbuf;
}
ValueTokenizer values(linebuf);
while (values.has_next()) tagbuf.push_back(values.next_tagint());
}
// set empty name to indicate end of file
name = "";
return tagbuf;
}
/* ---------------------------------------------------------------------- */
void Ndx2Group::command(int narg, char **arg)
{
int len;
bigint num;
FILE *fp;
std::string name, next;
if (narg < 1) utils::missing_cmd_args(FLERR, "ndx2group", error);
if (atom->tag_enable == 0) error->all(FLERR, "Must have atom IDs for ndx2group command");
if (atom->map_style == Atom::MAP_NONE)
error->all(FLERR, "Must have an atom map for ndx2group command");
if (comm->me == 0) {
fp = fopen(arg[0], "r");
if (fp == nullptr)
error->one(FLERR, "Cannot open index file for reading: {}", utils::getsyserror());
utils::logmesg(lmp, "Reading groups from index file {}:\n", arg[0]);
}
if (narg == 1) { // restore all groups
if (comm->me == 0) {
try {
name = find_section(fp, "");
} catch (std::exception &e) {
error->one(FLERR, e.what());
}
while (!name.empty()) {
// skip over group "all", which is called "System" in gromacs
if (name == "System") {
try {
name = find_section(fp, "");
} catch (std::exception &e) {
error->one(FLERR, e.what());
}
continue;
}
utils::logmesg(lmp, " Processing group '{}'\n", name);
len = name.size() + 1;
MPI_Bcast(&len, 1, MPI_INT, 0, world);
if (len > 1) {
MPI_Bcast((void *) name.c_str(), len, MPI_CHAR, 0, world);
// read tags for atoms in group and broadcast
std::vector<tagint> tags;
try {
tags = read_section(fp, next);
} catch (std::exception &e) {
error->one(FLERR, e.what());
}
num = tags.size();
MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
MPI_Bcast((void *) tags.data(), num, MPI_LMP_TAGINT, 0, world);
create(name, tags);
name = next;
}
}
len = -1;
MPI_Bcast(&len, 1, MPI_INT, 0, world);
} else {
while (true) {
MPI_Bcast(&len, 1, MPI_INT, 0, world);
if (len < 0) break;
if (len > 1) {
char *buf = new char[len];
MPI_Bcast(buf, len, MPI_CHAR, 0, world);
MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
tagint *tbuf = new tagint[num];
MPI_Bcast(tbuf, num, MPI_LMP_TAGINT, 0, world);
create(buf, std::vector<tagint>(tbuf, tbuf + num));
delete[] buf;
delete[] tbuf;
}
}
}
} else { // restore selected groups
for (int idx = 1; idx < narg; ++idx) {
if (comm->me == 0) {
// find named section, search from beginning of file
rewind(fp);
try {
name = find_section(fp, arg[idx]);
} catch (std::exception &e) {
error->one(FLERR, e.what());
}
utils::logmesg(lmp, " {} group '{}'\n", name.size() ? "Processing" : "Skipping", arg[idx]);
len = name.size() + 1;
MPI_Bcast(&len, 1, MPI_INT, 0, world);
if (len > 1) {
MPI_Bcast((void *) name.c_str(), len, MPI_CHAR, 0, world);
// read tags for atoms in group and broadcast
std::vector<tagint> tags;
try {
tags = read_section(fp, next);
} catch (std::exception &e) {
error->one(FLERR, e.what());
}
num = tags.size();
MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
MPI_Bcast((void *) tags.data(), num, MPI_LMP_TAGINT, 0, world);
create(name, tags);
name = next;
}
} else {
MPI_Bcast(&len, 1, MPI_INT, 0, world);
if (len > 1) {
char *buf = new char[len];
MPI_Bcast(buf, len, MPI_CHAR, 0, world);
MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
tagint *tbuf = new tagint[num];
MPI_Bcast(tbuf, num, MPI_LMP_TAGINT, 0, world);
create(buf, std::vector<tagint>(tbuf, tbuf + num));
delete[] buf;
delete[] tbuf;
}
}
}
}
if (comm->me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
void Ndx2Group::create(const std::string &name, const std::vector<tagint> &tags)
{
// wipe out all members if the group exists. gid==0 is group "all"
int gid = group->find(name);
if (gid > 0) group->assign(name + " clear");
// map from global to local
const int nlocal = atom->nlocal;
int *flags = (int *) calloc(nlocal, sizeof(int));
for (bigint i = 0; i < (int) tags.size(); ++i) {
const int id = atom->map(tags[i]);
if (id < nlocal && id >= 0) flags[id] = 1;
}
group->create(name, flags);
free(flags);
}

0
src/COLVARS/ndx_group.h → src/EXTRA-COMMAND/ndx_group.h
View File

3
src/EXTRA-PAIR/pair_coul_slater_long.cpp
View File

@ -39,7 +39,6 @@ using namespace EwaldConst;
PairCoulSlaterLong::PairCoulSlaterLong(LAMMPS *lmp) : Pair(lmp)
{
ewaldflag = pppmflag = 1;
qdist = 0.0;
}
/* ---------------------------------------------------------------------- */
@ -232,7 +231,7 @@ void PairCoulSlaterLong::init_style()
double PairCoulSlaterLong::init_one(int i, int j)
{
scale[j][i] = scale[i][j];
return cut_coul+2.0*qdist;
return cut_coul;
}
/* ----------------------------------------------------------------------

4
src/EXTRA-PAIR/pair_coul_slater_long.h
View File

@ -41,9 +41,7 @@ class PairCoulSlaterLong : public Pair {
void *extract(const char *, int &) override;
protected:
double cut_coul, cut_coulsq, qdist;
double lamda;
double g_ewald;
double cut_coul, cut_coulsq, lamda, g_ewald;
double **scale;
virtual void allocate();

474
src/GPU/pair_dpd_coul_slater_long_gpu.cpp Normal file
View File

@ -0,0 +1,474 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Eddy BARRAUD (IFPEN/Sorbonne)
------------------------------------------------------------------------- */
#include "pair_dpd_coul_slater_long_gpu.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include "update.h"
#include "ewald_const.h"
#include "kspace.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace EwaldConst;
// External functions from cuda library for atom decomposition
int dpd_coul_slater_long_gpu_init(const int ntypes, double **cutsq, double **host_a0,
double **host_gamma, double **host_sigma, double **host_cut_dpd,
double **host_cut_dpdsq, double **host_cut_slatersq,
double *special_lj, const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double *host_special_coul, const double qqrd2e,
const double g_ewald, const double lamda);
void dpd_coul_slater_long_gpu_clear();
int **dpd_coul_slater_long_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double **host_v, const double dtinvsqrt,
const int seed, const int timestep, double *boxlo,
double *prd);
void dpd_coul_slater_long_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
double **host_v, const double dtinvsqrt, const int seed,
const int timestep, const int nlocal, double *boxlo,
double *prd);
void dpd_coul_slater_long_gpu_get_extra_data(double *host_q);
double dpd_coul_slater_long_gpu_bytes();
static constexpr double EPSILON = 1.0e-10;
//#define _USE_UNIFORM_SARU_LCG
//#define _USE_UNIFORM_SARU_TEA8
//#define _USE_GAUSSIAN_SARU_LCG
#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && \
!defined(_USE_GAUSSIAN_SARU_LCG)
#define _USE_UNIFORM_SARU_LCG
#endif
// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
#define LCGA 0x4beb5d59 // Full period 32 bit LCG
#define LCGC 0x2600e1f7
#define oWeylPeriod 0xda879add // Prime period 3666320093
#define oWeylOffset 0x8009d14b
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0]
// using the inherent LCG, then multiply u with sqrt(3) to "match"
// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
#define numtyp double
#define SQRT3 (numtyp) 1.7320508075688772935274463
#define saru(seed1, seed2, seed, timestep, randnum) \
{ \
unsigned int seed3 = seed + timestep; \
seed3 ^= (seed1 << 7) ^ (seed2 >> 6); \
seed2 += (seed1 >> 4) ^ (seed3 >> 15); \
seed1 ^= (seed2 << 9) + (seed3 << 8); \
seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1)); \
seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16)); \
seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22)); \
seed2 += seed1 * seed3; \
seed1 += seed3 ^ (seed2 >> 2); \
seed2 ^= ((signed int) seed2) >> 17; \
unsigned int state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14)); \
unsigned int wstate = (state + seed2) ^ (((signed int) state) >> 8); \
state = state + (wstate * (wstate ^ 0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate >> 1); \
state = LCGA * state + LCGC; \
wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \
unsigned int v = (state ^ (state >> 26)) + wstate; \
unsigned int s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \
randnum = SQRT3 * (s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define numtyp double
#define SQRT3 (numtyp) 1.7320508075688772935274463
#define k0 0xA341316C
#define k1 0xC8013EA4
#define k2 0xAD90777D
#define k3 0x7E95761E
#define delta 0x9e3779b9
#define rounds 8
#define saru(seed1, seed2, seed, timestep, randnum) \
{ \
unsigned int seed3 = seed + timestep; \
seed3 ^= (seed1 << 7) ^ (seed2 >> 6); \
seed2 += (seed1 >> 4) ^ (seed3 >> 15); \
seed1 ^= (seed2 << 9) + (seed3 << 8); \
seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1)); \
seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16)); \
seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22)); \
seed2 += seed1 * seed3; \
seed1 += seed3 ^ (seed2 >> 2); \
seed2 ^= ((signed int) seed2) >> 17; \
unsigned int state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14)); \
unsigned int wstate = (state + seed2) ^ (((signed int) state) >> 8); \
state = state + (wstate * (wstate ^ 0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate >> 1); \
unsigned int sum = 0; \
for (int i = 0; i < rounds; i++) { \
sum += delta; \
state += ((wstate << 4) + k0) ^ (wstate + sum) ^ ((wstate >> 5) + k1); \
wstate += ((state << 4) + k2) ^ (state + sum) ^ ((state >> 5) + k3); \
} \
unsigned int v = (state ^ (state >> 26)) + wstate; \
unsigned int s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \
randnum = SQRT3 * (s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
#define numtyp double
#define saru(seed1, seed2, seed, timestep, randnum) \
{ \
unsigned int seed3 = seed + timestep; \
seed3 ^= (seed1 << 7) ^ (seed2 >> 6); \
seed2 += (seed1 >> 4) ^ (seed3 >> 15); \
seed1 ^= (seed2 << 9) + (seed3 << 8); \
seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1)); \
seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16)); \
seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22)); \
seed2 += seed1 * seed3; \
seed1 += seed3 ^ (seed2 >> 2); \
seed2 ^= ((signed int) seed2) >> 17; \
unsigned int state = 0x12345678; \
unsigned int wstate = 12345678; \
state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14)); \
wstate = (state + seed2) ^ (((signed int) state) >> 8); \
state = state + (wstate * (wstate ^ 0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate >> 1); \
unsigned int v, s; \
numtyp r1, r2, rsq; \
while (1) { \
state = LCGA * state + LCGC; \
wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \
v = (state ^ (state >> 26)) + wstate; \
s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \
r1 = s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0; \
state = LCGA * state + LCGC; \
wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \
v = (state ^ (state >> 26)) + wstate; \
s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \
r2 = s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0; \
rsq = r1 * r1 + r2 * r2; \
if (rsq < (numtyp) 1.0) break; \
} \
numtyp fac = sqrt((numtyp) -2.0 * log(rsq) / rsq); \
randnum = r2 * fac; \
}
#endif
/* ---------------------------------------------------------------------- */
PairDPDCoulSlaterLongGPU::PairDPDCoulSlaterLongGPU(LAMMPS *lmp) : PairDPDCoulSlaterLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairDPDCoulSlaterLongGPU::~PairDPDCoulSlaterLongGPU()
{
dpd_coul_slater_long_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairDPDCoulSlaterLongGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
double dtinvsqrt = 1.0 / sqrt(update->dt);
bool success = true;
int *ilist, *numneigh, **firstneigh;
double *q = atom->q;
dpd_coul_slater_long_gpu_get_extra_data(q);
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = dpd_coul_slater_long_gpu_compute_n(
neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh,
cpu_time, success, atom->v, dtinvsqrt, seed, update->ntimestep, domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
dpd_coul_slater_long_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, atom->tag,
atom->v, dtinvsqrt, seed, update->ntimestep, atom->nlocal, domain->boxlo,
domain->prd);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
if (host_start < inum) {
cpu_time = platform::walltime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = platform::walltime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLongGPU::init_style()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair dpd requires ghost atoms store velocity");
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/slater/long requires atom attribute q");
// ensure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
mcut = init_one(i, j);
mcut *= mcut;
if (mcut > maxcut) maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
dpd_coul_slater_long_gpu_init(atom->ntypes + 1, cutsq, a0, gamma, sigma,
cut_dpd, cut_dpdsq, cut_slatersq, force->special_lj, atom->nlocal,
atom->nlocal + atom->nghost, mnf, maxspecial, cell_size, gpu_mode, screen,
force->special_coul, force->qqrd2e, g_ewald, lamda);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairDPDCoulSlaterLongGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + dpd_coul_slater_long_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairDPDCoulSlaterLongGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i, j, ii, jj, jnum, itype, jtype;
double qtmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair;
double vxtmp, vytmp, vztmp, delvx, delvy, delvz;
double r2inv,forcedpd,forcecoul,factor_coul;
double grij,expm2,prefactor,t,erfc;
double rsq,r,rinv,dot,wd,randnum,factor_dpd,factor_sqrt;
int *jlist;
double slater_term;
tagint itag, jtag;
double *q = atom->q;
double *special_coul = force->special_coul;
double qqrd2e = force->qqrd2e;
evdwl = 0.0;
ecoul = 0.0;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
tagint *tag = atom->tag;
double *special_lj = force->special_lj;
double dtinvsqrt = 1.0 / sqrt(update->dt);
int timestep = (int) update->ntimestep;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
vxtmp = v[i][0];
vytmp = v[i][1];
vztmp = v[i][2];
itype = type[i];
itag = tag[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_dpd = special_lj[sbmask(j)];
factor_sqrt = special_sqrt[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
jtype = type[j];
jtag = tag[j];
// forces if below maximum cutoff
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
if (evflag) evdwl = ecoul = 0.0;
// apply DPD force if distance below DPD cutoff
if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON ) {
rinv = 1.0 / r;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
dot = delx * delvx + dely * delvy + delz * delvz;
wd = 1.0 - r / cut[itype][jtype];
unsigned int tag1 = itag, tag2 = jtag;
if (tag1 > tag2) {
tag1 = jtag;
tag2 = itag;
}
randnum = 0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = a0 * wd
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
forcedpd = a0[itype][jtype]*wd;
forcedpd -= gamma[itype][jtype]*wd*wd*dot*rinv;
forcedpd *= factor_dpd;
forcedpd += factor_sqrt*sigma[itype][jtype]*wd*randnum*dtinvsqrt;
forcedpd *= rinv;
if (eflag) {
// eng shifted to 0.0 at cutoff
evdwl = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd;
evdwl *= factor_dpd;
}
} else forcedpd = 0.0;
// apply Slater electrostatic force if distance below Slater cutoff
// and the two species are charged
if (rsq < cut_slatersq[itype][jtype]){
r2inv = 1.0/rsq;
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*(1-slater_term);
forcecoul *= r2inv;
if (eflag) {
ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor*(1.0-(1 + r/lamda)*exp(-2*r/lamda));
}
} else forcecoul = 0.0;
fpair = forcedpd + forcecoul;
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
if (evflag) ev_tally_full(i, evdwl, ecoul, fpair, delx, dely, delz);
}
}
}
}

45
src/GPU/pair_dpd_coul_slater_long_gpu.h Normal file
View File

@ -0,0 +1,45 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(dpd/coul/slater/long/gpu,PairDPDCoulSlaterLongGPU);
// clang-format on
#else
#ifndef LMP_PAIR_DPD_COUL_SLATER_LONG_GPU_H
#define LMP_PAIR_DPD_COUL_SLATER_LONG_GPU_H
#include "pair_dpd_coul_slater_long.h"
namespace LAMMPS_NS {
class PairDPDCoulSlaterLongGPU : public PairDPDCoulSlaterLong {
public:
PairDPDCoulSlaterLongGPU(LAMMPS *lmp);
~PairDPDCoulSlaterLongGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif

9
src/GRANULAR/gran_sub_mod_damping.cpp
View File

@ -156,6 +156,7 @@ double GranSubModDampingTsuji::calculate_forces()
GranSubModDampingCoeffRestitution::GranSubModDampingCoeffRestitution(GranularModel *gm, LAMMPS *lmp) :
GranSubModDamping(gm, lmp)
{
allow_cohesion = 0;
}
void GranSubModDampingCoeffRestitution::init()
@ -173,6 +174,12 @@ void GranSubModDampingCoeffRestitution::init()
double GranSubModDampingCoeffRestitution::calculate_forces()
{
damp_prefactor = damp * sqrt(gm->meff * gm->Fnormal / gm->delta);
// in case argument <= 0 due to precision issues
double sqrt1;
if (gm->delta > 0.0)
sqrt1 = MAX(0.0, gm->meff * gm->Fnormal / gm->delta);
else
sqrt1 = 0.0;
damp_prefactor = damp * sqrt(sqrt1);
return -damp_prefactor * gm->vnnr;
}

22
src/INTEL/npair_skip_intel.cpp
View File

@ -74,9 +74,13 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
const int nlocal = atom->nlocal;
const int e_nall = nlocal + atom->nghost;
const int * _noalias const type = atom->type;
const tagint * _noalias const molecule = atom->molecule;
int * _noalias const ilist = list->ilist;
int * _noalias const numneigh = list->numneigh;
int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT
const int molskip = list->molskip;
const int * _noalias const ilist_skip = list->listskip->ilist;
const int * _noalias const numneigh_skip = list->listskip->numneigh;
const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT
@ -110,7 +114,7 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
for (int ii = ifrom; ii < ito; ii++) {
const int i = ilist_skip[ii];
const int itype = type[i];
if (iskip[itype]) continue;
if (!molskip && iskip[itype]) continue;
int n = 0;
int *neighptr = ipage.vget();
@ -142,7 +146,11 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
for (int jj = 0; jj < jnum; jj++) {
const int joriginal = jlist[jj];
const int j = joriginal & NEIGHMASK;
if (!ijskip[itype][type[j]]) neighptr[n++] = joriginal;
if (!molskip && ijskip[itype][type[j]]) continue;
if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue;
if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue;
neighptr[n++] = joriginal;
}
}
@ -269,9 +277,13 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
const int e_nall = nlocal + atom->nghost;
const ATOM_T * _noalias const x = buffers->get_x();
const int * _noalias const type = atom->type;
const tagint * _noalias const molecule = atom->molecule;
int * _noalias const ilist = list->ilist;
int * _noalias const numneigh = list->numneigh;
int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT
const int molskip = list->molskip;
const int * _noalias const ilist_skip = list->listskip->ilist;
const int * _noalias const numneigh_skip = list->listskip->numneigh;
const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT
@ -306,7 +318,7 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
for (int ii = ifrom; ii < ito; ii++) {
const int i = ilist_skip[ii];
const int itype = type[i];
if (iskip[itype]) continue;
if (!molskip && iskip[itype]) continue;
const flt_t xtmp = x[i].x;
const flt_t ytmp = x[i].y;
@ -370,7 +382,9 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
const int j = joriginal & NEIGHMASK;
int addme = 1;
if (ijskip[itype][type[j]]) addme = 0;
if (!molskip && ijskip[itype][type[j]]) addme = 0;
if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) addme = 0;
if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) addme = 0;
// trim to shorter cutoff

2
src/KOKKOS/Install.sh
View File

@ -365,6 +365,8 @@ action pair_reaxff_kokkos.h pair_reaxff.h
action pair_snap_kokkos_impl.h pair_snap.cpp
action pair_snap_kokkos.cpp pair_snap.cpp
action pair_snap_kokkos.h pair_snap.h
action pair_soft_kokkos.cpp
action pair_soft_kokkos.h
action pair_sw_kokkos.cpp pair_sw.cpp
action pair_sw_kokkos.h pair_sw.h
action pair_table_kokkos.cpp

255
src/KOKKOS/pair_soft_kokkos.cpp Normal file
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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "pair_soft_kokkos.h"
#include "atom_kokkos.h"
#include "atom_masks.h"
#include "error.h"
#include "force.h"
#include "kokkos.h"
#include "math_const.h"
#include "memory_kokkos.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "respa.h"
#include "update.h"
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
template<class DeviceType>
PairSoftKokkos<DeviceType>::PairSoftKokkos(LAMMPS *lmp) : PairSoft(lmp)
{
respa_enable = 0;
kokkosable = 1;
atomKK = (AtomKokkos *) atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK;
datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
PairSoftKokkos<DeviceType>::~PairSoftKokkos()
{
if (copymode) return;
if (allocated) {
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_cutsq,cutsq);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairSoftKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
{
eflag = eflag_in;
vflag = vflag_in;
if (neighflag == FULL) no_virial_fdotr_compute = 1;
ev_init(eflag,vflag,0);
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
atomKK->sync(execution_space,datamask_read);
k_cutsq.template sync<DeviceType>();
k_params.template sync<DeviceType>();
if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
else atomKK->modified(execution_space,F_MASK);
x = atomKK->k_x.view<DeviceType>();
c_x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
nlocal = atom->nlocal;
nall = atom->nlocal + atom->nghost;
newton_pair = force->newton_pair;
special_lj[0] = force->special_lj[0];
special_lj[1] = force->special_lj[1];
special_lj[2] = force->special_lj[2];
special_lj[3] = force->special_lj[3];
// loop over neighbors of my atoms
copymode = 1;
EV_FLOAT ev = pair_compute<PairSoftKokkos<DeviceType>,void >(this,(NeighListKokkos<DeviceType>*)list);
if (eflag_global) eng_vdwl += ev.evdwl;
if (vflag_global) {
virial[0] += ev.v[0];
virial[1] += ev.v[1];
virial[2] += ev.v[2];
virial[3] += ev.v[3];
virial[4] += ev.v[4];
virial[5] += ev.v[5];
}
if (eflag_atom) {
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
if (vflag_fdotr) pair_virial_fdotr_compute(this);
copymode = 0;
}
template<class DeviceType>
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT PairSoftKokkos<DeviceType>::
compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
(void) i;
const F_FLOAT r = sqrt(rsq);
const F_FLOAT cut_ij = STACKPARAMS?m_params[itype][jtype].cut:params(itype,jtype).cut;
const F_FLOAT prefactor_ij = STACKPARAMS?m_params[itype][jtype].prefactor:params(itype,jtype).prefactor;
const F_FLOAT arg = MY_PI*r/cut_ij;
F_FLOAT fpair = 0.0;
if (r > 0.0) fpair = prefactor_ij *
sin(arg) * MY_PI/cut_ij/r;
return fpair;
}
template<class DeviceType>
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT PairSoftKokkos<DeviceType>::
compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
(void) i;
const F_FLOAT r = sqrt(rsq);
const F_FLOAT cut_ij = STACKPARAMS?m_params[itype][jtype].cut:params(itype,jtype).cut;
const F_FLOAT prefactor_ij = STACKPARAMS?m_params[itype][jtype].prefactor:params(itype,jtype).prefactor;
const F_FLOAT arg = MY_PI*r/cut_ij;
return prefactor_ij*(1.0+cos(arg));
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
template<class DeviceType>
void PairSoftKokkos<DeviceType>::allocate()
{
PairSoft::allocate();
int n = atom->ntypes;
memory->destroy(cutsq);
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_soft**,Kokkos::LayoutRight,DeviceType>("PairSoft::params",n+1,n+1);
params = k_params.template view<DeviceType>();
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
template<class DeviceType>
void PairSoftKokkos<DeviceType>::settings(int narg, char **arg)
{
if (narg > 2) error->all(FLERR,"Illegal pair_style command");
PairSoft::settings(1,arg);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
template<class DeviceType>
void PairSoftKokkos<DeviceType>::init_style()
{
PairSoft::init_style();
// error if rRESPA with inner levels
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
if (respa)
error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
}
// adjust neighbor list request for KOKKOS
neighflag = lmp->kokkos->neighflag;
auto request = neighbor->find_request(this);
request->set_kokkos_host(std::is_same_v<DeviceType,LMPHostType> &&
!std::is_same_v<DeviceType,LMPDeviceType>);
request->set_kokkos_device(std::is_same_v<DeviceType,LMPDeviceType>);
if (neighflag == FULL) request->enable_full();
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
template<class DeviceType>
double PairSoftKokkos<DeviceType>::init_one(int i, int j)
{
double cutone = PairSoft::init_one(i,j);
k_params.h_view(i,j).prefactor = prefactor[i][j];
k_params.h_view(i,j).cut = cutone;
k_params.h_view(i,j).cutsq = cutone*cutone;
k_params.h_view(j,i) = k_params.h_view(i,j);
if (i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
m_cutsq[j][i] = m_cutsq[i][j] = cutone*cutone;
}
k_cutsq.h_view(i,j) = k_cutsq.h_view(j,i) = cutone*cutone;
k_cutsq.template modify<LMPHostType>();
k_params.template modify<LMPHostType>();
return cutone;
}
namespace LAMMPS_NS {
template class PairSoftKokkos<LMPDeviceType>;
#ifdef LMP_KOKKOS_GPU
template class PairSoftKokkos<LMPHostType>;
#endif
}

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src/KOKKOS/pair_soft_kokkos.h Normal file
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(soft/kk,PairSoftKokkos<LMPDeviceType>);
PairStyle(soft/kk/device,PairSoftKokkos<LMPDeviceType>);
PairStyle(soft/kk/host,PairSoftKokkos<LMPHostType>);
// clang-format on
#else
// clang-format off
#ifndef LMP_PAIR_SOFT_KOKKOS_H
#define LMP_PAIR_SOFT_KOKKOS_H
#include "pair_kokkos.h"
#include "pair_soft.h"
#include "neigh_list_kokkos.h"
namespace LAMMPS_NS {
template<class DeviceType>
class PairSoftKokkos : public PairSoft {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
PairSoftKokkos(class LAMMPS *);
~PairSoftKokkos() override;
void compute(int, int) override;
void settings(int, char **) override;
void init_style() override;
double init_one(int, int) override;
struct params_soft{
KOKKOS_INLINE_FUNCTION
params_soft() {cutsq=0,cut=0,prefactor=0;};
KOKKOS_INLINE_FUNCTION
params_soft(int /*i*/) {cutsq=0,cut=0,prefactor=0;};
F_FLOAT cutsq,cut,prefactor;
};
protected:
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const;
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const;
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT compute_ecoul(const F_FLOAT& /*rsq*/, const int& /*i*/, const int& /*j*/,
const int& /*itype*/, const int& /*jtype*/) const { return 0; }
Kokkos::DualView<params_soft**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_soft**,Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
params_soft m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; // hardwired to space for 12 atom types
F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
typename AT::t_x_array_randomread x;
typename AT::t_x_array c_x;
typename AT::t_f_array f;
typename AT::t_int_1d_randomread type;
DAT::tdual_efloat_1d k_eatom;
DAT::tdual_virial_array k_vatom;
typename AT::t_efloat_1d d_eatom;
typename AT::t_virial_array d_vatom;
int newton_pair;
double special_lj[4];
typename AT::tdual_ffloat_2d k_cutsq;
typename AT::t_ffloat_2d d_cutsq;
int neighflag;
int nlocal,nall,eflag,vflag;
void allocate() override;
friend struct PairComputeFunctor<PairSoftKokkos,FULL,true,0>;
friend struct PairComputeFunctor<PairSoftKokkos,FULL,true,1>;
friend struct PairComputeFunctor<PairSoftKokkos,HALF,true>;
friend struct PairComputeFunctor<PairSoftKokkos,HALFTHREAD,true>;
friend struct PairComputeFunctor<PairSoftKokkos,FULL,false,0>;
friend struct PairComputeFunctor<PairSoftKokkos,FULL,false,1>;
friend struct PairComputeFunctor<PairSoftKokkos,HALF,false>;
friend struct PairComputeFunctor<PairSoftKokkos,HALFTHREAD,false>;
friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,FULL,0>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,FULL,1>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,HALF>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,HALFTHREAD>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute<PairSoftKokkos>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
friend void pair_virial_fdotr_compute<PairSoftKokkos>(PairSoftKokkos*);
};
}
#endif
#endif

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src/KOKKOS/pair_uf3_kokkos.cpp Normal file
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187
src/KOKKOS/pair_uf3_kokkos.h Normal file
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@ -0,0 +1,187 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ajinkya Hire (Univ. of Florida),
Hendrik Kraß (Univ. of Constance),
Matthias Rupp (Luxembourg Institute of Science and Technology),
Richard Hennig (Univ of Florida)
---------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(uf3/kk,PairUF3Kokkos<LMPDeviceType>)
PairStyle(uf3/kk/device,PairUF3Kokkos<LMPDeviceType>)
// clang-format on
#else
#ifndef LMP_PAIR_UF3_KOKKOS_H
#define LMP_PAIR_UF3_KOKKOS_H
#include "kokkos.h"
#include "pair_kokkos.h"
#include "pair_uf3.h"
template <int NEIGHFLAG, int EVFLAG> struct TagPairUF3ComputeFullA {};
struct TagPairUF3ComputeShortNeigh {};
namespace LAMMPS_NS {
template <class DeviceType> class PairUF3Kokkos : public PairUF3 {
public:
PairUF3Kokkos(class LAMMPS *);
~PairUF3Kokkos() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void allocate();
void init_style() override;
void init_list(int, class NeighList *) override; // needed for ptr to full neigh list
double init_one(int, int) override; // needed for cutoff radius for neighbour list
double single(int, int, int, int, double, double, double, double &) override;
template <typename T, typename V> void copy_2d(V &d, T **h, int m, int n);
template <typename T, typename V> void copy_3d(V &d, T ***h, int m, int n, int o);
template <int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION void operator()(TagPairUF3ComputeFullA<NEIGHFLAG, EVFLAG>, const int &,
EV_FLOAT &) const;
template <int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION void operator()(TagPairUF3ComputeFullA<NEIGHFLAG, EVFLAG>,
const int &) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagPairUF3ComputeShortNeigh, const int &) const;
enum { EnabledNeighFlags = FULL };
enum { COUL_FLAG = 0 };
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
typedef EV_FLOAT value_type;
protected:
typename AT::tdual_ffloat_2d k_cutsq;//Create a DualView, defination of tdual_ffloat_2d in kokkos_type.h
typename AT::t_ffloat_2d d_cutsq; //t_ffloat_2d = t_dev ==> Creates a new View d_cutsq
//the type of d_cutsq is decided by the Device(not host) type for the DualView k_cutsq
//Meaning the memory location of d_cutsq is the same as the Device(not host) memory location of
//k_cutsq
typedef Kokkos::DualView<F_FLOAT***, Kokkos::LayoutRight, DeviceType> tdual_ffloat_3d;
typedef Kokkos::DualView<F_FLOAT****, Kokkos::LayoutRight, DeviceType> tdual_ffloat_4d;
tdual_ffloat_3d k_cut_3b;
tdual_ffloat_4d k_min_cut_3b;
typename tdual_ffloat_3d::t_dev d_cut_3b;
typename tdual_ffloat_4d::t_dev d_min_cut_3b;
template <typename TYPE> void destroy_3d(TYPE data, typename TYPE::value_type*** &array);
template <typename TYPE> void destroy_4d(TYPE data, typename TYPE::value_type**** &array);
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> /*d_cutsq,*/ d_cut_3b_list;
//Kokkos::View<F_FLOAT ***, LMPDeviceType::array_layout, LMPDeviceType> d_cut_3b;
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_coefficients_2b;
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_dncoefficients_2b;
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_n2b_knot;
Kokkos::View<F_FLOAT *, LMPDeviceType::array_layout, LMPDeviceType> d_n2b_knot_spacings;
Kokkos::View<int **, LMPDeviceType::array_layout, LMPDeviceType> map2b;
Kokkos::View<F_FLOAT[4][4], LMPDeviceType::array_layout, LMPDeviceType> constants;
Kokkos::View<F_FLOAT[3][3], LMPDeviceType::array_layout, LMPDeviceType> dnconstants;
Kokkos::View<F_FLOAT ***, LMPDeviceType::array_layout, LMPDeviceType> d_n3b_knot_matrix;
Kokkos::View<F_FLOAT ****, LMPDeviceType::array_layout, LMPDeviceType> d_coefficients_3b;
Kokkos::View<F_FLOAT *****, LMPDeviceType::array_layout, LMPDeviceType> d_dncoefficients_3b;
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_n3b_knot_spacings;
Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_n3b_knot_matrix_spacings;
Kokkos::View<int ***, LMPDeviceType::array_layout, LMPDeviceType> map3b;
Kokkos::View<F_FLOAT **[16], LMPDeviceType::array_layout, LMPDeviceType> constants_2b;
Kokkos::View<F_FLOAT **[9], LMPDeviceType::array_layout, LMPDeviceType> dnconstants_2b;
Kokkos::View<F_FLOAT ***[16], LMPDeviceType::array_layout, LMPDeviceType> constants_3b;
Kokkos::View<F_FLOAT ***[9], LMPDeviceType::array_layout, LMPDeviceType> dnconstants_3b;
std::vector<F_FLOAT> get_constants(double *knots, double coefficient);
std::vector<F_FLOAT> get_dnconstants(double *knots, double coefficient);
int coefficients_created = 0;
void create_coefficients();
void create_3b_coefficients();
void create_2b_coefficients();
std::vector<F_FLOAT> get_coefficients(const double *knots, const double coefficient) const;
std::vector<F_FLOAT> get_dncoefficients(const double *knots, const double coefficient) const;
template <int EVFLAG>
void twobody(const int itype, const int jtype, const F_FLOAT r, F_FLOAT &evdwl,
F_FLOAT &fpair) const;
template <int EVFLAG>
void threebody(const int itype, const int jtype, const int ktype, const F_FLOAT value_rij,
const F_FLOAT value_rik, const F_FLOAT value_rjk, F_FLOAT &evdwl3,
F_FLOAT (&fforce)[3]) const;
template <int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION void
ev_tally(EV_FLOAT &ev, const int &i, const int &j, const F_FLOAT &epair, const F_FLOAT &fpair,
const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const;
template <int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION void ev_tally3(EV_FLOAT &ev, const int &i, const int &j, int &k,
const F_FLOAT &evdwl, const F_FLOAT &ecoul, F_FLOAT *fj,
F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drki) const;
typename AT::t_x_array_randomread x;
typename AT::t_f_array f;
typename AT::t_tagint_1d tag;
typename AT::t_int_1d_randomread type;
DAT::tdual_efloat_1d k_eatom;
DAT::tdual_virial_array k_vatom;
typename AT::t_efloat_1d d_eatom;
typename AT::t_virial_array d_vatom;
using ScatterFType = Kokkos::Experimental::ScatterView<F_FLOAT *[3], Kokkos::LayoutRight,
typename DeviceType::memory_space>;
ScatterFType fscatter;
using ScatterVType = Kokkos::Experimental::ScatterView<F_FLOAT *[6], Kokkos::LayoutRight,
typename DeviceType::memory_space>;
ScatterVType vscatter;
using ScatterCVType = Kokkos::Experimental::ScatterView<F_FLOAT *[9], Kokkos::LayoutRight,
typename DeviceType::memory_space>;
ScatterCVType cvscatter;
using ScatterEType = Kokkos::Experimental::ScatterView<E_FLOAT *, LMPDeviceType::array_layout,
typename DeviceType::memory_space>;
ScatterEType escatter;
typename AT::t_neighbors_2d d_neighbors;
typename AT::t_int_1d_randomread d_ilist;
typename AT::t_int_1d_randomread d_numneigh;
int neighflag, newton_pair;
int nlocal, nall, eflag, vflag;
int inum;
Kokkos::View<int **, DeviceType> d_neighbors_short;
Kokkos::View<int *, DeviceType> d_numneigh_short;
friend void pair_virial_fdotr_compute<PairUF3Kokkos>(PairUF3Kokkos *);
};
KOKKOS_INLINE_FUNCTION int min(int i, int j)
{
return i < j ? i : j;
}
KOKKOS_INLINE_FUNCTION int max(int i, int j)
{
return i > j ? i : j;
}
} // namespace LAMMPS_NS
#endif
#endif

1
src/MANYBODY/pair_sw.cpp
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@ -250,6 +250,7 @@ void PairSW::settings(int narg, char ** arg)
// pair_coeff * * and can enable the single function.
one_coeff = skip_threebody_flag ? 0 : 1;
single_enable = skip_threebody_flag ? 1 : 0;
manybody_flag = skip_threebody_flag ? 0 : 1;
iarg += 2;
} else error->all(FLERR, "Illegal pair_style sw keyword: {}", arg[iarg]);
}

3
src/MC/fix_gcmc.cpp
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@ -2233,7 +2233,8 @@ void FixGCMC::attempt_molecule_insertion_full()
}
/* ----------------------------------------------------------------------
compute particle's interaction energy with the rest of the system
compute particle's interaction energy with the rest of the system by
looping over all atoms in the sub-domain including ghosts.
------------------------------------------------------------------------- */
double FixGCMC::energy(int i, int itype, tagint imolecule, double *coord)

3
src/MC/fix_widom.cpp
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@ -973,7 +973,8 @@ void FixWidom::attempt_molecule_insertion_full()
}
/* ----------------------------------------------------------------------
compute particle's interaction energy with the rest of the system
compute particle's interaction energy with the rest of the system by
looping over all atoms in the sub-domain including ghosts.
------------------------------------------------------------------------- */
double FixWidom::energy(int i, int itype, tagint imolecule, double *coord)

14
src/ML-IAP/mliap_descriptor_ace.cpp
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@ -136,7 +136,6 @@ void MLIAPDescriptorACE::compute_descriptors(class MLIAPData *data)
int nei = 0;
int jtmp = 0;
for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) {
int itmp = data->iatoms[iitmp];
jtmp = data->numneighs[iitmp];
nei = nei + jtmp;
if (jtmp > max_jnum) { max_jnum = jtmp; }
@ -144,7 +143,6 @@ void MLIAPDescriptorACE::compute_descriptors(class MLIAPData *data)
for (int ii = 0; ii < data->nlistatoms; ii++) {
const int i = data->iatoms[ii];
const int ielemx = data->ielems[ii];
const int jnum = data->numneighs[ii];
delete acemlimpl->ace;
@ -184,7 +182,6 @@ void MLIAPDescriptorACE::compute_forces(class MLIAPData *data)
int nei = 0;
int jtmp = 0;
for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) {
int itmp = data->iatoms[iitmp];
jtmp = data->numneighs[iitmp];
nei = nei + jtmp;
if (jtmp > max_jnum) { max_jnum = jtmp; }
@ -193,7 +190,6 @@ void MLIAPDescriptorACE::compute_forces(class MLIAPData *data)
// BEGIN force loop
for (int ii = 0; ii < data->nlistatoms; ii++) {
const int i = data->iatoms[ii];
const int ielem = data->ielems[ii];
delete acemlimpl->ace;
acemlimpl->ace = new ACECTildeEvaluator(*acemlimpl->basis_set);
acemlimpl->ace->compute_projections = 1;
@ -268,7 +264,6 @@ void MLIAPDescriptorACE::compute_force_gradients(class MLIAPData *data)
int nei = 0;
int jtmp = 0;
for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) {
int itmp = data->iatoms[iitmp];
jtmp = data->numneighs[iitmp];
nei = nei + jtmp;
if (jtmp > max_jnum) { max_jnum = jtmp; }
@ -276,7 +271,6 @@ void MLIAPDescriptorACE::compute_force_gradients(class MLIAPData *data)
for (int ii = 0; ii < data->nlistatoms; ii++) {
const int i = data->iatoms[ii];
const int ielem = data->ielems[ii];
delete acemlimpl->ace;
acemlimpl->ace = new ACECTildeEvaluator(*acemlimpl->basis_set);
acemlimpl->ace->compute_projections = 1;
@ -327,14 +321,12 @@ void MLIAPDescriptorACE::compute_descriptor_gradients(class MLIAPData *data)
int nei = 0;
int jtmp = 0;
for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) {
int itmp = data->iatoms[iitmp];
jtmp = data->numneighs[iitmp];
nei = nei + jtmp;
if (jtmp > max_jnum) { max_jnum = jtmp; }
}
for (int ii = 0; ii < data->nlistatoms; ii++) {
const int i = data->iatoms[ii];
const int ielem = data->ielems[ii];
delete acemlimpl->ace;
acemlimpl->ace = new ACECTildeEvaluator(*acemlimpl->basis_set);
acemlimpl->ace->compute_projections = 1;
@ -349,7 +341,6 @@ void MLIAPDescriptorACE::compute_descriptor_gradients(class MLIAPData *data)
}
}
const int *const jlist = data->lmp_firstneigh[ii];
const int jnum = data->numneighs[ii];
acemlimpl->ace->resize_neighbours_cache(jnum);
acemlimpl->ace->compute_atom(i, atom->x, atom->type, data->numneighs[ii],
@ -363,11 +354,6 @@ void MLIAPDescriptorACE::compute_descriptor_gradients(class MLIAPData *data)
ij = ij0;
for (int jj = 0; jj < data->numneighs[ii]; jj++) {
const int jt = data->jatoms[ij];
const int j = jlist[jj];
int yoffset = ndescriptors;
int zoffset = ndescriptors * 2;
for (int iicoeff = 0; iicoeff < ndescriptors; iicoeff++) {
DOUBLE_TYPE fx_dB = acemlimpl->ace->neighbours_dB(iicoeff, jj, 0);
DOUBLE_TYPE fy_dB = acemlimpl->ace->neighbours_dB(iicoeff, jj, 1);

1984
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ajinkya Hire (Univ. of Florida),
Hendrik Kraß (Univ. of Constance),
Matthias Rupp (Luxembourg Institute of Science and Technology),
Richard Hennig (Univ of Florida)
---------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(uf3,PairUF3);
// clang-format on
#else
#ifndef LMP_PAIR_UF3_H
#define LMP_PAIR_UF3_H
#include "pair.h"
namespace LAMMPS_NS {
class PairUF3 : public Pair {
public:
PairUF3(class LAMMPS *);
~PairUF3() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
void init_list(int, class NeighList *) override; // needed for ptr to full neigh list
double init_one(int, int) override; // needed for cutoff radius for neighbour list
double single(int, int, int, int, double, double, double, double &) override;
double memory_usage() override;
protected:
int ***setflag_3b, **knot_spacing_type_2b, ***knot_spacing_type_3b;
double **cut, ***cut_3b, **cut_3b_list, ****min_cut_3b;
double **knot_spacing_2b, ****knot_spacing_3b;
double ***n2b_knots_array, ***n2b_coeff_array;
int **n2b_knots_array_size, **n2b_coeff_array_size;
double ****cached_constants_2b, ****cached_constants_2b_deri;
int ***map_3b;
double ***n3b_knots_array, ****n3b_coeff_array;
int **n3b_knots_array_size, **n3b_coeff_array_size;
double ****coeff_for_der_jk, ****coeff_for_der_ik,****coeff_for_der_ij;
double ****cached_constants_3b, ****cached_constants_3b_deri;
int *neighshort, maxshort; // short neighbor list array for 3body interaction
void uf3_read_unified_pot_file(char *potf_name);
void communicate();
int bsplines_created;
bool pot_3b;
virtual void allocate();
void create_bsplines();
void create_cached_constants_2b();
void create_cached_constants_3b();
int get_starting_index_uniform_2b(int i, int j, double r);
int get_starting_index_uniform_3b(int i, int j, int k, double r, int knot_dim);
int get_starting_index_nonuniform_2b(int i, int j, double r);
int get_starting_index_nonuniform_3b(int i, int j, int k, double r, int knot_dim);
int (PairUF3::*get_starting_index_2b)(int i, int j, double r);
int (PairUF3::*get_starting_index_3b)(int i, int j, int k, double r, int knot_dim);
int nbody_flag = 3;
int max_num_knots_2b = 0;
int max_num_coeff_2b = 0;
int max_num_knots_3b = 0;
int max_num_coeff_3b = 0;
int tot_interaction_count_3b = 0;
};
} // namespace LAMMPS_NS
#endif
#endif

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// clang-format off
/* ----------------------------------------------------------------------
lammps - large-scale atomic/molecular massively parallel simulator
https://www.lammps.org/, sandia national laboratories
lammps development team: developers@lammps.org
copyright (2003) sandia corporation. under the terms of contract
de-ac04-94al85000 with sandia corporation, the u.s. government retains
certain rights in this software. this software is distributed under
the gnu general public license.
see the readme file in the top-level lammps directory.
------------------------------------------------------------------------- */
#include "uf3_bspline_basis2.h"
#include "math_special.h"
using namespace LAMMPS_NS;
using MathSpecial::square;
// Constructor
// Initializes coefficients and knots
// Requires [knots] to have length 4
uf3_bspline_basis2::uf3_bspline_basis2(LAMMPS *ulmp, const double *knots, double coefficient)
{
lmp = ulmp;
double c0, c1, c2;
c0 = coefficient
* (square(knots[0])
/ (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2]));
c1 = coefficient *
(-2.0 * knots[0] /
(square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2]));
c2 = coefficient *
(1.0 / (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2]));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
constants[0] = c0;
constants[1] = c1;
constants[2] = c2;
c0 = coefficient *
(-knots[1] * knots[3] /
(square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) -
knots[0] * knots[2] /
(knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])));
c1 = coefficient *
(knots[1] /
(square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) +
knots[3] /
(square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) +
knots[0] /
(knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])) +
knots[2] /
(knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])));
c2 = coefficient *
(-1.0 / (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) -
1.0 / (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
constants[3] = c0;
constants[4] = c1;
constants[5] = c2;
c0 = coefficient *
(square(knots[3]) /
(knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3])));
c1 = coefficient *
(-2.0 * knots[3] /
(knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3])));
c2 = coefficient *
(1.0 / (knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3])));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
constants[6] = c0;
constants[7] = c1;
constants[8] = c2;
}
uf3_bspline_basis2::~uf3_bspline_basis2() {}
// Evaluate outer-left part of spline
double uf3_bspline_basis2::eval0(double rsq, double r)
{
return rsq * constants[2] + r * constants[1] + constants[0];
}
// Evaluate center-left part of spline
double uf3_bspline_basis2::eval1(double rsq, double r)
{
return rsq * constants[5] + r * constants[4] + constants[3];
}
// Evaluate center-right part of spline
double uf3_bspline_basis2::eval2(double rsq, double r)
{
return rsq * constants[8] + r * constants[7] + constants[6];
}
double uf3_bspline_basis2::memory_usage()
{
double bytes = 0;
bytes += (double)9*sizeof(double);
return bytes;
}

41
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// clang-format off
/* ----------------------------------------------------------------------
lammps - large-scale atomic/molecular massively parallel simulator
https://www.lammps.org/, sandia national laboratories
lammps development team: developers@lammps.org
copyright (2003) sandia corporation. under the terms of contract
de-ac04-94al85000 with sandia corporation, the u.s. government retains
certain rights in this software. this software is distributed under
the gnu general public license.
see the readme file in the top-level lammps directory.
------------------------------------------------------------------------- */
#include "pointers.h"
#include <vector>
#ifndef UF3_BSPLINE_BASIS2_H
#define UF3_BSPLINE_BASIS2_H
namespace LAMMPS_NS {
class uf3_bspline_basis2 {
private:
LAMMPS *lmp;
//std::vector<double> constants;
public:
uf3_bspline_basis2(LAMMPS *ulmp, const double *knots, double coefficient);
~uf3_bspline_basis2();
//std::vector<double> constants;
double constants[9] = {};
double eval0(double, double);
double eval1(double, double);
double eval2(double, double);
double memory_usage();
};
} // namespace LAMMPS_NS
#endif

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// clang-format off
/* ----------------------------------------------------------------------
lammps - large-scale atomic/molecular massively parallel simulator
https://www.lammps.org/, sandia national laboratories
lammps development team: developers@lammps.org
copyright (2003) sandia corporation. under the terms of contract
de-ac04-94al85000 with sandia corporation, the u.s. government retains
certain rights in this software. this software is distributed under
the gnu general public license.
see the readme file in the top-level lammps directory.
------------------------------------------------------------------------- */
#include "uf3_bspline_basis3.h"
#include "math_special.h"
using namespace LAMMPS_NS;
using MathSpecial::cube;
using MathSpecial::square;
// Constructor
// Initializes coefficients and knots
// [knots] needs to have length 4
uf3_bspline_basis3::uf3_bspline_basis3(LAMMPS *ulmp, const double *knots, double coefficient)
{
lmp = ulmp;
double c0, c1, c2, c3;
c0 = coefficient *
(-cube(knots[0]) /
(-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[3]));
c1 = coefficient *
(3.0 * square(knots[0]) /
(-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[3]));
c2 = coefficient *
(-3.0 * knots[0] /
(-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[3]));
c3 = coefficient *
(1.0 /
(-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[3]));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
//constants.push_back(c3);
constants[0] = c0;
constants[1] = c1;
constants[2] = c2;
constants[3] = c3;
c0 = coefficient *
(square(knots[1]) * knots[4] /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) +
square(knots[0]) * knots[2] /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) +
knots[0] * knots[1] * knots[3] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
c1 = coefficient *
(-square(knots[1]) /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) -
2.0 * knots[1] * knots[4] /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) -
square(knots[0]) /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) -
2.0 * knots[0] * knots[2] /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) -
knots[0] * knots[1] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])) -
knots[0] * knots[3] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])) -
knots[1] * knots[3] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
c2 = coefficient *
(2.0 * knots[1] /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) +
knots[4] /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) +
2.0 * knots[0] /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) +
knots[2] /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) +
knots[0] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])) +
knots[1] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])) +
knots[3] /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
c3 = coefficient *
(-1.0 /
(-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
knots[2] * knots[3] * knots[4]) -
1.0 /
(-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) -
1.0 /
(-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
//constants.push_back(c3);
constants[4] = c0;
constants[5] = c1;
constants[6] = c2;
constants[7] = c3;
c0 = coefficient *
(-knots[0] * square(knots[3]) /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) -
knots[1] * knots[3] * knots[4] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
knots[2] * square(knots[4]) /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
c1 = coefficient *
(2.0 * knots[0] * knots[3] /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) +
square(knots[3]) /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) +
knots[1] * knots[3] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
knots[1] * knots[4] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
knots[3] * knots[4] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
2.0 * knots[2] * knots[4] /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])) +
square(knots[4]) /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
c2 = coefficient *
(-knots[0] /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) -
2.0 * knots[3] /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) -
knots[1] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
knots[3] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
knots[4] /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
knots[2] /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])) -
2.0 * knots[4] /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
c3 = coefficient *
(1.0 /
(-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
knots[2] * square(knots[3]) + cube(knots[3])) +
1.0 /
(-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
1.0 /
(-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
//constants.push_back(c3);
constants[8] = c0;
constants[9] = c1;
constants[10] = c2;
constants[11] = c3;
c0 = coefficient *
(cube(knots[4]) /
(-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
cube(knots[4])));
c1 = coefficient *
(-3.0 * square(knots[4]) /
(-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
cube(knots[4])));
c2 = coefficient *
(3.0 * knots[4] /
(-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
cube(knots[4])));
c3 = coefficient *
(-1.0 /
(-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
cube(knots[4])));
//constants.push_back(c0);
//constants.push_back(c1);
//constants.push_back(c2);
//constants.push_back(c3);
constants[12] = c0;
constants[13] = c1;
constants[14] = c2;
constants[15] = c3;
}
uf3_bspline_basis3::~uf3_bspline_basis3() {}
// Evaluate outer-left part of spline
double uf3_bspline_basis3::eval0(double rth, double rsq, double r)
{
return rth * constants[3] + rsq * constants[2] + r * constants[1] + constants[0];
}
// Evaluate center-left part of spline
double uf3_bspline_basis3::eval1(double rth, double rsq, double r)
{
return rth * constants[7] + rsq * constants[6] + r * constants[5] + constants[4];
}
// Evaluate center-right part of spline
double uf3_bspline_basis3::eval2(double rth, double rsq, double r)
{
return rth * constants[11] + rsq * constants[10] + r * constants[9] + constants[8];
}
// Evaluate outer-right part of spline
double uf3_bspline_basis3::eval3(double rth, double rsq, double r)
{
return rth * constants[15] + rsq * constants[14] + r * constants[13] + constants[12];
}
double uf3_bspline_basis3::memory_usage()
{
double bytes = 0;
bytes += (double)16*sizeof(double);
return bytes;
}

42
src/ML-UF3/uf3_bspline_basis3.h Normal file
View File

@ -0,0 +1,42 @@
// clang-format off
/* ----------------------------------------------------------------------
lammps - large-scale atomic/molecular massively parallel simulator
https://www.lammps.org/, sandia national laboratories
lammps development team: developers@lammps.org
copyright (2003) sandia corporation. under the terms of contract
de-ac04-94al85000 with sandia corporation, the u.s. government retains
certain rights in this software. this software is distributed under
the gnu general public license.
see the readme file in the top-level lammps directory.
------------------------------------------------------------------------- */
#include "pointers.h"
#include <vector>
#ifndef UF3_BSPLINE_BASIS3_H
#define UF3_BSPLINE_BASIS3_H
namespace LAMMPS_NS {
class uf3_bspline_basis3 {
private:
LAMMPS *lmp;
//std::vector<double> constants;
public:
uf3_bspline_basis3(LAMMPS *ulmp, const double *knots, double coefficient);
~uf3_bspline_basis3();
double constants[16] = {};
double eval0(double, double, double);
double eval1(double, double, double);
double eval2(double, double, double);
double eval3(double, double, double);
double memory_usage();
};
} // namespace LAMMPS_NS
#endif

3
src/Makefile
View File

@ -74,6 +74,7 @@ PACKAGE = \
dpd-smooth \
drude \
eff \
extra-command \
extra-compute \
extra-dump \
extra-fix \
@ -104,6 +105,7 @@ PACKAGE = \
ml-quip \
ml-rann \
ml-snap \
ml-uf3 \
mofff \
molfile \
netcdf \
@ -167,6 +169,7 @@ PACKMOST = \
dpd-smooth \
drude \
eff \
extra-command \
extra-compute \
extra-dump \
extra-fix \

8
src/OPENMP/fix_omp.cpp
View File

@ -229,7 +229,13 @@ void FixOMP::init()
check_hybrid = 0; \
if (force->name) { \
if ( (strcmp(force->name ## _style,"hybrid") == 0) || \
(strcmp(force->name ## _style,"hybrid/overlay") == 0) ) \
(strcmp(force->name ## _style,"hybrid/overlay") == 0) || \
(strcmp(force->name ## _style,"hybrid/scaled") == 0) || \
(strcmp(force->name ## _style,"hybrid/molecular") == 0) || \
(strcmp(force->name ## _style,"hybrid/omp") == 0) || \
(strcmp(force->name ## _style,"hybrid/overlay/omp") == 0) || \
(strcmp(force->name ## _style,"hybrid/scaled/omp") == 0) || \
(strcmp(force->name ## _style,"hybrid/molecular/omp") == 0) ) \
check_hybrid=1; \
if (force->name->suffix_flag & Suffix::OMP) { \
last_force_name = (const char *) #name; \

34
src/OPENMP/npair_skip_omp.h
View File

@ -19,14 +19,12 @@
NPairStyle(skip/omp,
NPairSkip,
NP_SKIP | NP_HALF | NP_FULL |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/half/respa/omp,
NPairSkipRespa,
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/half/size/omp,
@ -36,32 +34,27 @@ NPairStyle(skip/half/size/omp,
NPairStyle(skip/size/off2on/omp,
NPairSkipSizeOff2on,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD |
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/size/off2on/oneside/omp,
NPairSkipSizeOff2onOneside,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF |
NP_ORTHO | NP_TRI | NP_OMP);
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
NPairStyle(skip/ghost/omp,
NPairSkip,
NP_SKIP | NP_HALF | NP_FULL |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST);
NPairStyle(skip/trim/omp,
NPairSkipTrim,
NP_SKIP | NP_HALF | NP_FULL |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/half/respa/omp,
NPairSkipTrimRespa,
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/half/size/omp,
@ -71,20 +64,17 @@ NPairStyle(skip/trim/half/size/omp,
NPairStyle(skip/trim/size/off2on/omp,
NPairSkipTrimSizeOff2on,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD |
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/size/off2on/oneside/omp,
NPairSkipTrimSizeOff2onOneside,
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF |
NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
NPairStyle(skip/trim/ghost/omp,
NPairSkipTrim,
NP_SKIP | NP_HALF | NP_FULL |
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP | NP_GHOST);
// clang-format off
#endif

5
src/PLUMED/fix_plumed.cpp
View File

@ -77,9 +77,9 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
int api_version=0;
p->cmd("getApiVersion",&api_version);
if ((api_version < 5) || (api_version > 9))
if ((api_version < 5) || (api_version > 10))
error->all(FLERR,"Incompatible API version for PLUMED in fix plumed. "
"Only Plumed 2.4.x, 2.5.x, 2.6.x, 2.7.x, 2.8.x are tested and supported.");
"Only Plumed 2.4.x, 2.5.x, 2.6.x, 2.7.x, 2.8.x, 2.9.x are tested and supported.");
#if !defined(MPI_STUBS)
// If the -partition option is activated then enable
@ -205,6 +205,7 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
double dt=update->dt;
p->cmd("setTimestep",&dt);
extscalar = 1;
scalar_flag = 1;
energy_global_flag = virial_global_flag = 1;
thermo_energy = thermo_virial = 1;

42
src/QEQ/fix_qeq_shielded.cpp
View File

@ -55,29 +55,53 @@ void FixQEqShielded::init()
neighbor->add_request(this, NeighConst::REQ_FULL);
int ntypes = atom->ntypes;
const int ntypes = atom->ntypes;
memory->create(shld, ntypes + 1, ntypes + 1, "qeq:shielding");
init_shielding();
int i;
for (i = 1; i <= ntypes; i++) {
if (gamma[i] == 0.0) error->all(FLERR, "Invalid param file for fix qeq/shielded");
// check if valid parameters for all atom types in the fix group are provided
const int *type = atom->type;
const int *mask = atom->mask;
int tmp = 0, tmp_all = 0;
for (int i = 0; i < nlocal; ++i) {
if (mask[i] & groupbit) {
if (gamma[type[i]] == 0.0)
tmp = type[i];
}
}
MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world);
if (tmp_all)
error->all(FLERR, "Invalid QEq parameters for atom type {} provided", tmp_all);
}
/* ---------------------------------------------------------------------- */
void FixQEqShielded::extract_reax()
{
Pair *pair = force->pair_match("^reax..", 0);
if (pair == nullptr) error->all(FLERR, "No pair reaxff for fix qeq/shielded");
int tmp;
const int nlocal = atom->nlocal;
const int *mask = atom->mask;
const int *type = atom->type;
Pair *pair = force->pair_match("^reaxff", 0);
if (pair == nullptr) error->all(FLERR, "No reaxff pair style for fix qeq/shielded");
int tmp, tmp_all;
chi = (double *) pair->extract("chi", tmp);
eta = (double *) pair->extract("eta", tmp);
gamma = (double *) pair->extract("gamma", tmp);
if (chi == nullptr || eta == nullptr || gamma == nullptr)
error->all(FLERR, "Fix qeq/shielded could not extract params from pair reaxff");
if ((chi == nullptr) || (eta == nullptr) || (gamma == nullptr))
error->all(FLERR, "Fix qeq/shielded could not extract all QEq parameters from pair reaxff");
tmp = tmp_all = 0;
for (int i = 0; i < nlocal; ++i) {
if (mask[i] & groupbit) {
if ((chi[type[i]] == 0.0) && (eta[type[i]] == 0.0) && (gamma[type[i]] == 0.0))
tmp = type[i];
}
}
MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world);
if (tmp_all)
error->all(FLERR, "No QEq parameters for atom type {} provided by pair reaxff", tmp_all);
}
// clang-format off

24
src/REAXFF/fix_qeq_reaxff.cpp
View File

@ -205,25 +205,41 @@ int FixQEqReaxFF::setmask()
void FixQEqReaxFF::pertype_parameters(char *arg)
{
const int nlocal = atom->nlocal;
const int *mask = atom->mask;
const int *type = atom->type;
if (utils::strmatch(arg,"^reaxff")) {
reaxflag = 1;
Pair *pair = force->pair_match("^reaxff",0);
if (!pair) error->all(FLERR,"No reaxff pair style for fix qeq/reaxff");
int tmp;
int tmp, tmp_all;
chi = (double *) pair->extract("chi",tmp);
eta = (double *) pair->extract("eta",tmp);
gamma = (double *) pair->extract("gamma",tmp);
if (chi == nullptr || eta == nullptr || gamma == nullptr)
error->all(FLERR, "Fix qeq/reaxff could not extract params from pair reaxff");
if ((chi == nullptr) || (eta == nullptr) || (gamma == nullptr))
error->all(FLERR, "Fix qeq/reaxff could not extract all QEq parameters from pair reaxff");
tmp = tmp_all = 0;
for (int i = 0; i < nlocal; ++i) {
if (mask[i] & groupbit) {
if ((chi[type[i]] == 0.0) && (eta[type[i]] == 0.0) && (gamma[type[i]] == 0.0))
tmp = type[i];
}
}
MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world);
if (tmp_all)
error->all(FLERR, "No QEq parameters for atom type {} provided by pair reaxff", tmp_all);
return;
} else if (utils::strmatch(arg,"^reax/c")) {
error->all(FLERR, "Fix qeq/reaxff keyword 'reax/c' is obsolete; please use 'reaxff'");
} else {
error->all(FLERR, "Unknown fix qeq/reaxff keyword {}", arg);
}
reaxflag = 0;
const int ntypes = atom->ntypes;
const int ntypes = atom->ntypes;
memory->create(chi,ntypes+1,"qeq/reaxff:chi");
memory->create(eta,ntypes+1,"qeq/reaxff:eta");
memory->create(gamma,ntypes+1,"qeq/reaxff:gamma");

4
src/REAXFF/pair_reaxff.cpp
View File

@ -694,24 +694,28 @@ void *PairReaxFF::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str,"chi") == 0 && chi) {
chi[0] = 0.0;
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) chi[i] = api->system->reax_param.sbp[map[i]].chi;
else chi[i] = 0.0;
return (void *) chi;
}
if (strcmp(str,"eta") == 0 && eta) {
eta[0] = 0.0;
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) eta[i] = api->system->reax_param.sbp[map[i]].eta;
else eta[i] = 0.0;
return (void *) eta;
}
if (strcmp(str,"gamma") == 0 && gamma) {
gamma[0] = 0.0;
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) gamma[i] = api->system->reax_param.sbp[map[i]].gamma;
else gamma[i] = 0.0;
return (void *) gamma;
}
if (strcmp(str,"bcut_acks2") == 0 && bcut_acks2) {
bcut_acks2[0] = 0.0;
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) bcut_acks2[i] = api->system->reax_param.sbp[map[i]].bcut_acks2;
else bcut_acks2[i] = 0.0;

10
src/delete_atoms.cpp
View File

@ -22,6 +22,7 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_bond_history.h"
#include "force.h"
#include "group.h"
#include "input.h"
@ -754,6 +755,10 @@ void DeleteAtoms::bondring(int nbuf, char *cbuf, void *ptr)
int nlocal = daptr->atom->nlocal;
// find instances of bond history to delete data
auto histories = daptr->modify->get_fix_by_style("BOND_HISTORY");
int n_histories = histories.size();
// cbuf = list of N deleted atom IDs from other proc, put them in hash
hash->clear();
@ -771,6 +776,11 @@ void DeleteAtoms::bondring(int nbuf, char *cbuf, void *ptr)
if (hash->find(bond_atom[i][m]) != hash->end()) {
bond_type[i][m] = bond_type[i][n - 1];
bond_atom[i][m] = bond_atom[i][n - 1];
if (n_histories > 0)
for (auto &ihistory: histories) {
dynamic_cast<FixBondHistory *>(ihistory)->shift_history(i,m,n-1);
dynamic_cast<FixBondHistory *>(ihistory)->delete_history(i,n-1);
}
n--;
} else
m++;

1
src/fix_bond_history.h
View File

@ -44,6 +44,7 @@ class FixBondHistory : public Fix {
void update_atom_value(int, int, int, double);
double get_atom_value(int, int, int);
int get_ndata() const { return ndata; }
// methods to reorder/delete elements of atom->bond_atom
void delete_history(int, int);

1
src/input.cpp
View File

@ -888,6 +888,7 @@ void Input::clear()
lmp->destroy();
lmp->create();
lmp->post_create();
variable->clear_in_progress();
}
/* ---------------------------------------------------------------------- */

33
src/library.cpp
View File

@ -1198,14 +1198,31 @@ internally by the :doc:`Fortran interface <Fortran>` and are not likely to be us
* - triclinic
- 1 if the the simulation box is triclinic, 0 if orthogonal.
See :doc:`change_box`.
**Communication status**
.. list-table::
:header-rows: 1
:widths: auto
* - Keyword
- Description / Return value
* - universe_rank
- MPI rank on LAMMPS' universe communicator (0 <= universe_rank < universe_size)
* - universe_size
- Number of ranks on LAMMPS' universe communicator (world_size <= universe_size)
* - world_rank
- MPI rank on LAMMPS' world communicator (0 <= world_rank < world_size)
- MPI rank on LAMMPS' world communicator (0 <= world_rank < world_size, aka comm->me)
* - world_size
- Number of ranks on LAMMPS' world communicator
- Number of ranks on LAMMPS' world communicator (aka comm->nprocs)
* - comm_style
- communication style (0 = BRICK, 1 = TILED)
* - comm_layout
- communication layout (0 = LAYOUT_UNIFORM, 1 = LAYOUT_NONUNIFORM, 2 = LAYOUT_TILED)
* - comm_mode
- communication mode (0 = SINGLE, 1 = MULTI, 2 = MULTIOLD)
* - ghost_velocity
- whether velocities are communicated for ghost atoms (0 = no, 1 = yes)
.. _extract_system_sizes:
@ -1310,6 +1327,10 @@ int lammps_extract_setting(void *handle, const char *keyword)
if (strcmp(keyword,"world_rank") == 0) return lmp->comm->me;
if (strcmp(keyword,"world_size") == 0) return lmp->comm->nprocs;
if (strcmp(keyword,"nthreads") == 0) return lmp->comm->nthreads;
if (strcmp(keyword,"comm_style") == 0) return lmp->comm->style;
if (strcmp(keyword,"comm_layout") == 0) return lmp->comm->layout;
if (strcmp(keyword,"comm_mode") == 0) return lmp->comm->mode;
if (strcmp(keyword,"ghost_velocity") == 0) return lmp->comm->ghost_velocity;
if (strcmp(keyword,"nlocal") == 0) return lmp->atom->nlocal;
if (strcmp(keyword,"nghost") == 0) return lmp->atom->nghost;
@ -1386,6 +1407,7 @@ int lammps_extract_global_datatype(void * /*handle*/, const char *name)
if (strcmp(name,"xy") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"xz") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"yz") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"procgrid") == 0) return LAMMPS_INT;
if (strcmp(name,"natoms") == 0) return LAMMPS_BIGINT;
if (strcmp(name,"nbonds") == 0) return LAMMPS_BIGINT;
@ -1604,6 +1626,10 @@ report the "native" data type. The following tables are provided:
- double
- 1
- triclinic tilt factor. See :doc:`Howto_triclinic`.
* - procgrid
- int
- 3
- processor count assigned to each dimension of 3d grid. See :doc:`processors`.
.. _extract_system_settings:
@ -1861,6 +1887,9 @@ void *lammps_extract_global(void *handle, const char *name)
if (strcmp(name,"xy") == 0) return (void *) &lmp->domain->xy;
if (strcmp(name,"xz") == 0) return (void *) &lmp->domain->xz;
if (strcmp(name,"yz") == 0) return (void *) &lmp->domain->yz;
if (((lmp->comm->layout == Comm::LAYOUT_UNIFORM) ||
(lmp->comm->layout == Comm::LAYOUT_NONUNIFORM)) && (strcmp(name,"procgrid") == 0))
return (void *) &lmp->comm->procgrid;
if (strcmp(name,"natoms") == 0) return (void *) &lmp->atom->natoms;
if (strcmp(name,"ntypes") == 0) return (void *) &lmp->atom->ntypes;

19
src/neigh_list.cpp
View File

@ -148,6 +148,7 @@ void NeighList::post_constructor(NeighRequest *nq)
copy = nq->copy;
trim = nq->trim;
id = nq->id;
molskip = nq->molskip;
if (nq->copy) {
listcopy = neighbor->lists[nq->copylist];
@ -157,14 +158,16 @@ void NeighList::post_constructor(NeighRequest *nq)
if (nq->skip) {
listskip = neighbor->lists[nq->skiplist];
int ntypes = atom->ntypes;
iskip = new int[ntypes+1];
memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
int i,j;
for (i = 1; i <= ntypes; i++) iskip[i] = nq->iskip[i];
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
ijskip[i][j] = nq->ijskip[i][j];
if (!molskip) {
int ntypes = atom->ntypes;
iskip = new int[ntypes+1];
memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
int i,j;
for (i = 1; i <= ntypes; i++) iskip[i] = nq->iskip[i];
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
ijskip[i][j] = nq->ijskip[i][j];
}
}
if (nq->halffull)

1
src/neigh_list.h
View File

@ -46,6 +46,7 @@ class NeighList : protected Pointers {
int kk2cpu; // 1 if this list is copied from Kokkos to CPU
int copymode; // 1 if this is a Kokkos on-device copy
int id; // copied from neighbor list request
int molskip; // 1/2 if this is an intra-/inter-molecular skip list
// data structs to store neighbor pairs I,J and associated values

9
src/neigh_request.cpp
View File

@ -76,6 +76,7 @@ NeighRequest::NeighRequest(LAMMPS *_lmp) : Pointers(_lmp)
skip = 0;
iskip = nullptr;
ijskip = nullptr;
molskip = REGULAR;
// only set when command = 1;
@ -183,6 +184,8 @@ int NeighRequest::identical(NeighRequest *other)
int NeighRequest::same_skip(NeighRequest *other)
{
if (molskip != other->molskip) return 0;
const int ntypes = atom->ntypes;
int same = 1;
@ -307,6 +310,12 @@ void NeighRequest::set_skip(int *_iskip, int **_ijskip)
ijskip = _ijskip;
}
void NeighRequest::set_molskip(int _molskip)
{
skip = 1;
molskip = _molskip;
}
void NeighRequest::enable_full()
{
half = 0;

5
src/neigh_request.h
View File

@ -29,6 +29,9 @@ class NeighRequest : protected Pointers {
friend class NPairSkipTrimIntel;
friend class FixIntel;
public:
enum { REGULAR, INTRA, INTER };
protected:
void *requestor; // class that made request
int requestor_instance; // instance of that class (only Fix, Compute, Pair)
@ -88,6 +91,7 @@ class NeighRequest : protected Pointers {
int skip; // 1 if this list skips atom types from another list
int *iskip; // iskip[i] if atoms of type I are not in list
int **ijskip; // ijskip[i][j] if pairs of type I,J are not in list
int molskip; // 0 reqular list, 1 keep only intra-molecular entries, 2 keep inter-molecular
// command_style only set if command = 1
// allows print_pair_info() to access command name
@ -137,6 +141,7 @@ class NeighRequest : protected Pointers {
void set_kokkos_device(int);
void set_kokkos_host(int);
void set_skip(int *, int **);
void set_molskip(int);
void enable_full();
void enable_ghost();
void enable_intel();

15
src/neighbor.cpp
View File

@ -1800,10 +1800,17 @@ void Neighbor::print_pairwise_info()
else
out += fmt::format(", half/full from ({})",rq->halffulllist+1);
} else if (rq->skip) {
if (rq->trim)
out += fmt::format(", skip trim from ({})",rq->skiplist+1);
else
out += fmt::format(", skip from ({})",rq->skiplist+1);
if (rq->molskip) {
if (rq->trim)
out += fmt::format(", molskip trim from ({})",rq->skiplist+1);
else
out += fmt::format(", molskip from ({})",rq->skiplist+1);
} else {
if (rq->trim)
out += fmt::format(", skip trim from ({})",rq->skiplist+1);
else
out += fmt::format(", skip from ({})",rq->skiplist+1);
}
}
out += "\n";

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