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rename USER-PACE to ML-PACE

This commit is contained in:
Axel Kohlmeyer 2021-06-29 15:45:50 -04:00
parent 031e537d3f
commit fd24820603
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GPG Key ID: D9B44E93BF0C375A
20 changed files with 46 additions and 49 deletions
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2
.github/CODEOWNERS vendored
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@ -37,7 +37,7 @@ src/USER-MESONT/* @iafoss
src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
src/USER-PACE/* @yury-lysogorskiy
src/ML-PACE/* @yury-lysogorskiy
src/USER-PLUMED/* @gtribello
src/USER-PHONON/* @lingtikong
src/USER-PTM/* @pmla

4
cmake/CMakeLists.txt
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@ -146,7 +146,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
USER-H5MD ML-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT
USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF ML-PACE USER-BROWNIAN)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
@ -351,7 +351,7 @@ else()
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI USER-COLVARS ML-HDNNP USER-MDI USER-MOLFILE USER-NETCDF
USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()

4
cmake/Modules/Packages/USER-PACE.cmake → cmake/Modules/Packages/ML-PACE.cmake
View File

@ -14,8 +14,8 @@ execute_process(
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/ML-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/ML-PACE/*.cpp)
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})

2
cmake/presets/all_off.cmake
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@ -9,7 +9,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
ML-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
ML-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC)

2
cmake/presets/all_on.cmake
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@ -11,7 +11,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
ML-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
ML-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC)

2
cmake/presets/download.cmake
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@ -1,7 +1,7 @@
# Preset that turns on packages with automatic downloads of sources or potentials.
# Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI USER-PACE)
set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI ML-PACE)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

2
cmake/presets/nolib.cmake
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@ -4,7 +4,7 @@
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
PYTHON VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-H5MD ML-HDNNP USER-LB USER-MOLFILE
USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP
USER-MESONT USER-MDI USER-NETCDF ML-PACE USER-PLUMED USER-QMMM USER-QUIP
USER-SCAFACOS USER-SMD USER-VTK)
foreach(PKG ${PACKAGES_WITH_LIB})

12
doc/src/Build_extras.rst
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@ -54,7 +54,7 @@ This is the list of packages that may require additional steps.
* :ref:`USER-MESONT <user-mesont>`
* :ref:`USER-MOLFILE <user-molfile>`
* :ref:`USER-NETCDF <user-netcdf>`
* :ref:`USER-PACE <user-pace>`
* :ref:`ML-PACE <ml-pace>`
* :ref:`USER-PLUMED <user-plumed>`
* :ref:`USER-OMP <user-omp>`
* :ref:`USER-QMMM <user-qmmm>`
@ -1261,9 +1261,9 @@ be built for the most part with all major versions of the C++ language.
----------
.. _user-pace:
.. _ml-pace:
USER-PACE package
ML-PACE package
-----------------------------
This package requires a library that can be downloaded and built
@ -1276,8 +1276,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
.. tab:: CMake build
By default the library will be downloaded from the git repository
and built automatically when the USER-PACE package is enabled with
``-D PKG_USER-PACE=yes``. The location for the sources may be
and built automatically when the ML-PACE package is enabled with
``-D PKG_ML-PACE=yes``. The location for the sources may be
customized by setting the variable ``PACELIB_URL`` when
configuring with CMake (e.g. to use a local archive on machines
without internet access). Since CMake checks the validity of the
@ -1288,7 +1288,7 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
.. tab:: Traditional make
You can download and build the USER-PACE library
You can download and build the ML-PACE library
in one step from the ``lammps/src`` dir, using these commands,
which invoke the ``lib/pace/Install.py`` script.

2
doc/src/Build_package.rst
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@ -37,7 +37,7 @@ packages:
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`ML-HDNNP <ml-hdnnp>` | :ref:`USER-INTEL <user-intel>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`USER-MOLFILE <user-molfile>` | :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PACE <user-pace>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` |
| :ref:`USER-MOLFILE <user-molfile>` | :ref:`USER-NETCDF <user-netcdf>` | :ref:`ML-PACE <ml-pace>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`USER-QUIP <user-quip>` | :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+

13
doc/src/Packages_details.rst
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@ -94,7 +94,7 @@ page gives those details.
* :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
* :ref:`USER-NETCDF <PKG-USER-NETCDF>`
* :ref:`USER-OMP <PKG-USER-OMP>`
* :ref:`USER-PACE <PKG-USER-PACE>`
* :ref:`ML-PACE <PKG-ML-PACE>`
* :ref:`USER-PHONON <PKG-USER-PHONON>`
* :ref:`USER-PLUMED <PKG-USER-PLUMED>`
* :ref:`USER-PTM <PKG-USER-PTM>`
@ -2075,16 +2075,16 @@ This package has :ref:`specific installation instructions <user-omp>` on the :do
----------
.. _PKG-USER-PACE:
.. _PKG-ML-PACE:
USER-PACE package
ML-PACE package
-------------------
**Contents:**
A pair style for the Atomic Cluster Expansion potential (ACE).
ACE is a methodology for deriving a highly accurate classical potential
fit to a large archive of quantum mechanical (DFT) data. The USER-PACE
fit to a large archive of quantum mechanical (DFT) data. The ML-PACE
package provides an efficient implementation for running simulations
with ACE potentials.
@ -2105,11 +2105,12 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
**Install:**
This package has :ref:`specific installation instructions <user-pace>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <ml-pace>` on the
:doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-PACE: filenames -> commands
* src/ML-PACE: filenames -> commands
* :doc:`pair_style pace <pair_pace>`
* examples/PACKAGES/pace

2
doc/src/Packages_user.rst
View File

@ -89,7 +89,7 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PACE <PKG-USER-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext |
| :ref:`ML-PACE <PKG-ML-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PHONON <PKG-USER-PHONON>` | phonon dynamical matrix | :doc:`fix phonon <fix_phonon>` | USER/phonon | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+

2
doc/src/pair_pace.rst
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@ -91,7 +91,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
This pair style is part of the USER-PACE package. It is only enabled if LAMMPS
This pair style is part of the ML-PACE package. It is only enabled if LAMMPS
was built with that package.
See the :doc:`Build package <Build_package>` doc page for more info.

6
lib/pace/Makefile
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@ -2,8 +2,8 @@ SHELL = /bin/sh
# ------ FILES ------
SRC_FILES = $(wildcard src/USER-PACE/*.cpp)
SRC = $(filter-out src/USER-PACE/pair_pace.cpp, $(SRC_FILES))
SRC_FILES = $(wildcard src/ML-PACE/*.cpp)
SRC = $(filter-out src/ML-PACE/pair_pace.cpp, $(SRC_FILES))
# ------ DEFINITIONS ------
@ -12,7 +12,7 @@ OBJ = $(SRC:.cpp=.o)
# ------ SETTINGS ------
CXXFLAGS = -O3 -fPIC -Isrc/USER-PACE
CXXFLAGS = -O3 -fPIC -Isrc/ML-PACE
ARCHIVE = ar
ARCHFLAG = -rc

2
lib/pace/Makefile.lammps
View File

@ -1,3 +1,3 @@
pace_SYSINC =-I../../lib/pace/src/USER-PACE
pace_SYSINC =-I../../lib/pace/src/ML-PACE
pace_SYSLIB = -L../../lib/pace/ -lpace
pace_SYSPATH =

28
lib/pace/README
View File

@ -1,18 +1,14 @@
This directory contains files required to use the USER-PACE package,
which provides the pace pair style, an efficient implementation of
the Atomic Cluster Expansion potential (ACE).
ACE is a methodology for deriving a highly accurate classical potential
fit to a large archive of quantum mechanical (DFT) data.
This package was written by Yury Lysogorskiy and others
at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation,
Ruhr University Bochum, Germany, http://www.icams.de
This directory contains files required to use the ML-PACE package, which
provides the pace pair style, an efficient implementation of the Atomic
Cluster Expansion potential (ACE). ACE is a methodology for deriving a
highly accurate classical potential fit to a large archive of quantum
mechanical (DFT) data. This package was written by Yury Lysogorskiy and
others at ICAMS, the Interdisciplinary Centre for Advanced Materials
Simulation, Ruhr University Bochum, Germany, http://www.icams.de
You can type "make lib-pace" from the src directory to see help on
how to download and build this library via make commands, or you can
do the same thing by typing "python Install.py" from within this
directory.
You can type "make lib-pace" from the src directory to see help on how
to download and build this library via make commands, or you can do the
same thing by typing "python Install.py" from within this directory.
More information about the USER-PACE implementation of ACE
is available here:
https://github.com/ICAMS/lammps-user-pace
More information about the ML-PACE implementation of ACE is available
here: https://github.com/ICAMS/lammps-user-pace

0
src/USER-PACE/Install.sh → src/ML-PACE/Install.sh
View File

4
src/USER-PACE/README → src/ML-PACE/README
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@ -1,4 +1,4 @@
The USER-PACE package provides the pace pair style,
The ML-PACE package provides the pace pair style,
an efficient implementation of the Atomic Cluster Expansion
potential (ACE).
@ -17,7 +17,7 @@ provided to help automate the process. Also see the LAMMPS manual for
general information on building LAMMPS with external libraries
using either traditional make or CMake.
More information about the USER-PACE implementation of ACE
More information about the ML-PACE implementation of ACE
is available here:
https://github.com/ICAMS/lammps-user-pace

0
src/USER-PACE/pair_pace.cpp → src/ML-PACE/pair_pace.cpp
View File

0
src/USER-PACE/pair_pace.h → src/ML-PACE/pair_pace.h
View File

6
src/Makefile
View File

@ -56,13 +56,13 @@ PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs cg-dna \
user-eff user-fep user-h5md ml-hdnnp user-intel user-lb user-manifold \
user-mdi user-meamc user-mesodpd user-mesont user-mgpt user-misc \
user-mofff user-molfile user-netcdf user-omp user-phonon \
user-pace user-plumed user-ptm user-qmmm user-qtb user-quip \
ml-pace user-plumed user-ptm user-qmmm user-qtb user-quip \
user-rann user-reaction user-reaxc user-scafacos user-smd user-smtbq \
user-sdpd user-sph user-tally user-uef user-vtk user-yaff
PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \
user-adios user-atc user-awpmd user-colvars user-h5md ml-hdnnp user-lb user-mdi \
user-mesont user-molfile user-netcdf user-pace user-plumed user-qmmm user-quip \
user-mesont user-molfile user-netcdf ml-pace user-plumed user-qmmm user-quip \
user-scafacos user-smd user-vtk
PACKSYS = compress mpiio python user-lb
@ -71,7 +71,7 @@ PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont
user-mdi
PACKEXT = kim latte mscg voronoi \
user-adios user-h5md ml-hdnnp user-molfile user-netcdf user-pace user-plumed \
user-adios user-h5md ml-hdnnp user-molfile user-netcdf ml-pace user-plumed \
user-qmmm user-quip user-scafacos user-smd user-vtk
PACKALL = $(PACKAGE) $(PACKUSER)