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rename USER-QUIP to ML-QUIP

This commit is contained in:
Axel Kohlmeyer 2021-06-29 15:55:41 -04:00
parent fd24820603
commit d52cd88492
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GPG Key ID: D9B44E93BF0C375A
18 changed files with 32 additions and 28 deletions
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6
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 ML-PACE USER-BROWNIAN)
USER-TALLY USER-UEF USER-VTK ML-QUIP USER-QMMM USER-YAFF ML-PACE USER-BROWNIAN)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
@ -271,7 +271,7 @@ if(BUILD_OMP)
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_ML-QUIP OR PKG_LATTE)
enable_language(C)
find_package(LAPACK)
find_package(BLAS)
@ -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 ML-PACE)
USER-PLUMED USER-QMMM ML-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()

0
cmake/Modules/Packages/USER-QUIP.cmake → cmake/Modules/Packages/ML-QUIP.cmake
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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
ML-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 ML-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
ML-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 ML-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/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 ML-PACE USER-PLUMED USER-QMMM USER-QUIP
USER-MESONT USER-MDI USER-NETCDF ML-PACE USER-PLUMED USER-QMMM ML-QUIP
USER-SCAFACOS USER-SMD USER-VTK)
foreach(PKG ${PACKAGES_WITH_LIB})

8
doc/src/Build_extras.rst
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@ -58,7 +58,7 @@ This is the list of packages that may require additional steps.
* :ref:`USER-PLUMED <user-plumed>`
* :ref:`USER-OMP <user-omp>`
* :ref:`USER-QMMM <user-qmmm>`
* :ref:`USER-QUIP <user-quip>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`USER-SCAFACOS <user-scafacos>`
* :ref:`USER-SMD <user-smd>`
* :ref:`USER-VTK <user-vtk>`
@ -1848,9 +1848,9 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
----------
.. _user-quip:
.. _ml-quip:
USER-QUIP package
ML-QUIP package
---------------------------------
To build with this package, you must download and build the QUIP
@ -1868,7 +1868,7 @@ to be downloaded and configured. See step 1 and step 1.1 in the
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
CMake will **not** download and build the QUIP library. But once you have
done that, a CMake build of LAMMPS with ``-D PKG_USER-QUIP=yes`` should
done that, a CMake build of LAMMPS with ``-D PKG_ML-QUIP=yes`` should
work. Set the ``QUIP_LIBRARY`` variable if CMake cannot find the QUIP library.
.. tab:: Traditional make

2
doc/src/Build_package.rst
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@ -39,7 +39,7 @@ packages:
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :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>` | | |
| :ref:`ML-QUIP <ml-quip>` | :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
The mechanism for including packages is simple but different for CMake

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

16
doc/src/Packages_details.rst
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@ -100,7 +100,7 @@ page gives those details.
* :ref:`USER-PTM <PKG-USER-PTM>`
* :ref:`USER-QMMM <PKG-USER-QMMM>`
* :ref:`USER-QTB <PKG-USER-QTB>`
* :ref:`USER-QUIP <PKG-USER-QUIP>`
* :ref:`ML-QUIP <PKG-ML-QUIP>`
* :ref:`USER-RANN <PKG-USER-RANN>`
* :ref:`USER-REACTION <PKG-USER-REACTION>`
* :ref:`USER-REAXC <PKG-USER-REAXC>`
@ -2268,14 +2268,15 @@ simulation.
----------
.. _PKG-USER-QUIP:
.. _PKG-ML-QUIP:
USER-QUIP package
ML-QUIP package
-----------------
**Contents:**
A :doc:`pair_style quip <pair_quip>` command which wraps the `QUIP libAtoms library <quip_>`_, which includes a variety of interatomic
A :doc:`pair_style quip <pair_quip>` command which wraps the `QUIP
libAtoms library <quip_>`_, which includes a variety of interatomic
potentials, including Gaussian Approximation Potential (GAP) models
developed by the Cambridge University group.
@ -2288,12 +2289,13 @@ on your system.
**Install:**
This package has :ref:`specific installation instructions <user-quip>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <ml-quip>` on the
:doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-QUIP: filenames -> commands
* src/USER-QUIP/README
* src/ML-QUIP: filenames -> commands
* src/ML-QUIP/README
* :doc:`pair_style quip <pair_quip>`
* examples/PACKAGES/quip

2
doc/src/Packages_user.rst
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@ -101,7 +101,7 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-QTB <PKG-USER-QTB>` | quantum nuclear effects | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
| :ref:`ML-QUIP <PKG-ML-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-RANN <PKG-USER-RANN>` | rapid atomistic neural network (RANN) potentials | :doc:`pair rann <pair_rann>` | USER/rann | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+

2
doc/src/pair_quip.rst
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@ -75,7 +75,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
This pair style is part of the USER-QUIP package. It is only enabled
This pair style is part of the ML-QUIP package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
QUIP potentials are parameterized in electron-volts and Angstroms and

2
lib/README
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@ -51,7 +51,7 @@ python hooks to the system Python library, used by the PYTHON package
from the LAMMPS development team
qmmm quantum mechanics/molecular mechanics coupling interface
from Axel Kohlmeyer (Temple U)
quip interface to QUIP/libAtoms framework, USER-QUIP package
quip interface to QUIP/libAtoms framework, ML-QUIP package
from Albert Bartok-Partay and Gabor Csanyi (U Cambridge)
smd hooks to Eigen library, used by USER-SMD package
from Georg Ganzenmueller (Ernst Mach Institute, Germany)

8
lib/quip/README
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@ -76,11 +76,13 @@ and QUIP_ARCH should be autodetected, even without having to set
the environment variables. Otherwise export the environment variables
as shown above or edit Makefile.lammps
LAMMPS ships with a user package containing the interface necessary
LAMMPS ships with a package containing the interface necessary
to use QUIP potentials, but it needs to be added to the compilation
first. To do that, enter the LAMMPS source directory and type:
first. To do that, either enter the LAMMPS source directory and type:
$ make yes-user-quip
$ make yes-ml-quip
or use -DPKG_ML-QUIP=yes when configuring LAMMPS for compilation with CMake.
2.2) Build LAMMPS according to the instructions on the LAMMPS website.

0
src/USER-QUIP/Install.sh → src/ML-QUIP/Install.sh
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0
src/USER-QUIP/README → src/ML-QUIP/README
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0
src/USER-QUIP/pair_quip.cpp → src/ML-QUIP/pair_quip.cpp
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0
src/USER-QUIP/pair_quip.h → src/ML-QUIP/pair_quip.h
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6
src/Makefile
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@ -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 \
ml-pace user-plumed user-ptm user-qmmm user-qtb user-quip \
ml-pace user-plumed user-ptm user-qmmm user-qtb ml-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 ml-pace user-plumed user-qmmm user-quip \
user-mesont user-molfile user-netcdf ml-pace user-plumed user-qmmm ml-quip \
user-scafacos user-smd user-vtk
PACKSYS = compress mpiio python user-lb
@ -72,7 +72,7 @@ PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont
PACKEXT = kim latte mscg voronoi \
user-adios user-h5md ml-hdnnp user-molfile user-netcdf ml-pace user-plumed \
user-qmmm user-quip user-scafacos user-smd user-vtk
user-qmmm ml-quip user-scafacos user-smd user-vtk
PACKALL = $(PACKAGE) $(PACKUSER)