diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index e48dad549d..0717b5098b 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -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() diff --git a/cmake/Modules/Packages/USER-QUIP.cmake b/cmake/Modules/Packages/ML-QUIP.cmake similarity index 100% rename from cmake/Modules/Packages/USER-QUIP.cmake rename to cmake/Modules/Packages/ML-QUIP.cmake diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 50ae9fbca1..75af24189a 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -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) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 807e48a26b..90ad9731d3 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -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) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index 667f22bfae..9dc6e01fb3 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -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}) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index f56dd724ce..9be7b931ef 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -58,7 +58,7 @@ This is the list of packages that may require additional steps. * :ref:`USER-PLUMED ` * :ref:`USER-OMP ` * :ref:`USER-QMMM ` - * :ref:`USER-QUIP ` + * :ref:`ML-QUIP ` * :ref:`USER-SCAFACOS ` * :ref:`USER-SMD ` * :ref:`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 diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index f97988f613..dbe303964e 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -39,7 +39,7 @@ packages: +--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ | :ref:`USER-MOLFILE ` | :ref:`USER-NETCDF ` | :ref:`ML-PACE ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | +--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`USER-QUIP ` | :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | +| :ref:`ML-QUIP ` | :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | +--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ The mechanism for including packages is simple but different for CMake diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst index 1df7ae7f3f..693c5244dc 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -18,7 +18,7 @@ needed to run in parallel with MPI. The LAMMPS binaries contain *all* :doc:`optional 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. diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 9c5f9961cd..69ad86a593 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -100,7 +100,7 @@ page gives those details. * :ref:`USER-PTM ` * :ref:`USER-QMMM ` * :ref:`USER-QTB ` - * :ref:`USER-QUIP ` + * :ref:`ML-QUIP ` * :ref:`USER-RANN ` * :ref:`USER-REACTION ` * :ref:`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 ` command which wraps the `QUIP libAtoms library `_, which includes a variety of interatomic +A :doc:`pair_style quip ` command which wraps the `QUIP +libAtoms library `_, 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 ` on the :doc:`Build extras ` page. +This package has :ref:`specific installation instructions ` on the +:doc:`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 ` * examples/PACKAGES/quip diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 4de8439ff3..4a75eb1206 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -101,7 +101,7 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-QTB ` | quantum nuclear effects | :doc:`fix qtb ` :doc:`fix qbmsst ` | qtb | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | +| :ref:`ML-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-RANN ` | rapid atomistic neural network (RANN) potentials | :doc:`pair rann ` | USER/rann | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst index c55792579a..5f520f3d03 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -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 ` doc page for more info. QUIP potentials are parameterized in electron-volts and Angstroms and diff --git a/lib/README b/lib/README index 794bf93d55..50af12543a 100644 --- a/lib/README +++ b/lib/README @@ -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) diff --git a/lib/quip/README b/lib/quip/README index 5e737db11d..6783430a42 100644 --- a/lib/quip/README +++ b/lib/quip/README @@ -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. diff --git a/src/USER-QUIP/Install.sh b/src/ML-QUIP/Install.sh similarity index 100% rename from src/USER-QUIP/Install.sh rename to src/ML-QUIP/Install.sh diff --git a/src/USER-QUIP/README b/src/ML-QUIP/README similarity index 100% rename from src/USER-QUIP/README rename to src/ML-QUIP/README diff --git a/src/USER-QUIP/pair_quip.cpp b/src/ML-QUIP/pair_quip.cpp similarity index 100% rename from src/USER-QUIP/pair_quip.cpp rename to src/ML-QUIP/pair_quip.cpp diff --git a/src/USER-QUIP/pair_quip.h b/src/ML-QUIP/pair_quip.h similarity index 100% rename from src/USER-QUIP/pair_quip.h rename to src/ML-QUIP/pair_quip.h diff --git a/src/Makefile b/src/Makefile index ecb0e0c797..bab09e9f1d 100644 --- a/src/Makefile +++ b/src/Makefile @@ -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)