Update docs for KIM
This commit is contained in:
Ryan S. Elliott
@ -63,7 +63,7 @@ available on your system.
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If CMake cannot find the library, you can set these variables:
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-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
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-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
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-D ZLIB_LIBRARIES=path # path to libz.a (.so) file :pre
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[Traditional make]:
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@ -150,7 +150,7 @@ package uses the library settings from the lib/gpu/Makefile.machine
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used to build the GPU library.
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:line
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KIM package :h4,link(kim)
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To build with this package, the KIM library must be downloaded and
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@ -176,16 +176,12 @@ package?" page.
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[CMake build]:
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-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes
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-D KIM_LIBRARY=path # KIM library file (only needed if a custom location)
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-D KIM_INCLUDE_DIR=path # KIM include directory (only needed if a custom location) :pre
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-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes :pre
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If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
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inside the CMake build directory. If the KIM library is already on
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your system (in a location CMake cannot find it), KIM_LIBRARY is the
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filename (plus path) of the KIM library file, not the directory the
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library file is in. KIM_INCLUDE_DIR is the directory the KIM include
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file is in.
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your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
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environment variable so that libkim-api-v2 can be found.
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[Traditional make]:
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@ -199,8 +195,8 @@ make lib-kim args="-b " # (re-)install KIM API lib with only example models
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make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
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make lib-kim args="-b -a everything" # install KIM API lib with all models
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make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
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make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
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make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
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make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
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make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
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:line
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@ -254,7 +250,7 @@ For NVIDIA GPUs using CUDA, set these 4 variables:
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-D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU
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# archGPU = GPU from list above
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-D KOKKOS_ENABLE_CUDA=yes
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-D KOKKOS_ENABLE_OPENMP=yes
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-D KOKKOS_ENABLE_OPENMP=yes
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-D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper :pre
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The wrapper value is the Cuda nvcc compiler wrapper provided in the
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@ -296,7 +292,7 @@ export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
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CC = mpicxx :pre
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:line
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LATTE package :h4,link(latte)
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To build with this package, you must download and build the LATTE
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@ -324,7 +320,7 @@ args:
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make lib-latte # print help message
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make lib-latte args="-b" # download and build in lib/latte/LATTE-master
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make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
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make lib-latte args="-b -m gfortran" # download and build in lib/latte and
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make lib-latte args="-b -m gfortran" # download and build in lib/latte and
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# copy Makefile.lammps.gfortran to Makefile.lammps
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:pre
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@ -335,7 +331,7 @@ also check that the Makefile.lammps file you create is appropriate for
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the compiler you use on your system to build LATTE.
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:line
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MEAM package :h4,link(meam)
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NOTE: the use of the MEAM package is discouraged, as it has been
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@ -378,7 +374,7 @@ EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
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file.
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:line
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MESSAGE package :h4,link(message)
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This package can optionally include support for messaging via sockets,
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@ -407,7 +403,7 @@ existing Makefile.lammps.* and has settings to link with the ZeroMQ
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library if requested in the build.
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:line
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MSCG package :h4,link(mscg)
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To build with this package, you must download and build the MS-CG
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@ -419,7 +415,7 @@ lib/mscg/README and MSCG/Install files for more details.
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[CMake build]:
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-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes
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-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
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-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
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-D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location) :pre
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If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built
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@ -464,7 +460,7 @@ line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for
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an example.
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:line
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POEMS package :h4,link(poems)
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[CMake build]:
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@ -493,7 +489,7 @@ for your system, which should define an EXTRAMAKE variable to specify
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a corresponding Makefile.lammps.machine file.
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:line
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PYTHON package :h4,link(python)
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Building with the PYTHON package requires you have a Python shared
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@ -520,7 +516,7 @@ Makefile.lammps.* file (and copy it to Makefile.lammps) if the LAMMPS
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build fails.
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:line
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REAX package :h4,link(reax)
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NOTE: the use of the REAX package and its "pair_style
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@ -570,7 +566,7 @@ library"_voro-home.
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[CMake build]:
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-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
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-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
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-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
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-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) :pre
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If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and
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@ -869,7 +865,7 @@ Quantum ESPRESSO known to work with this QM/MM interface was version
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[CMake build]:
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The CMake build system currently does not support building the full
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QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
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QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
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You must use the traditional make build for this package.
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[Traditional make]:
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@ -939,7 +935,7 @@ Coulomb solver library"_scafacos-home
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[CMake build]:
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-D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes
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-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location)
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-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location)
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-D SCAFACOS_INCLUDE_DIR=path # ScaFaCoS include directory (only needed if at custom location) :pre
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If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded
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@ -6994,12 +6994,6 @@ The atom style defined does not have this attribute. :dd
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The atom style defined does not have these attributes. :dd
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{KIM neighbor iterator exceeded range} :dt
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This should not happen. It likely indicates a bug
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in the KIM implementation of the interatomic potential
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where it is requesting neighbors incorrectly. :dd
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{KOKKOS package does not yet support comm_style tiled} :dt
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Self-explanatory. :dd
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@ -10193,8 +10187,6 @@ Self-explanatory. :dd
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{Unrecognized virial argument in pair_style command} :dt
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Only two options are supported: LAMMPSvirial and KIMvirial :dd
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{Unsupported mixing rule in kspace_style ewald/disp} :dt
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Only geometric mixing is supported. :dd
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@ -203,7 +203,7 @@ available on your system.
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[Author:] Axel Kohlmeyer (Temple U).
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -284,7 +284,7 @@ also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles.
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[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
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(Northwestern U) while at ORNL.
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -345,14 +345,13 @@ system.
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Information about the KIM project can be found at its website:
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https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan
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Elliott (U Minnesota) and James Sethna (Cornell U).
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Elliott (U Minnesota).
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[Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
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API which the "pair_style kim"_pair_kim.html command uses. He
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developed the pair style in collaboration with Valeriu Smirichinski (U
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Minnesota).
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developed the pair style.
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -398,7 +397,7 @@ which was developed by Carter Edwards, Christian Trott, and others at
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Sandia, and which is included in the LAMMPS distribution in
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lib/kokkos.
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -546,7 +545,7 @@ and user interface.
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[Author:] Greg Wagner (Northwestern U) while at Sandia.
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -679,7 +678,7 @@ system.
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library was developed by Jacob Wagner in Greg Voth's group at the
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University of Chicago.
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -711,7 +710,7 @@ have styles optimized for CPU performance.
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[Authors:] James Fischer (High Performance Technologies), David Richie,
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and Vincent Natoli (Stone Ridge Technolgy).
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -768,7 +767,7 @@ connections at hinge points.
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[Author:] Rudra Mukherjee (JPL) while at RPI.
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -800,7 +799,7 @@ shared library available on your system, which needs to be a Python 2
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version, 2.6 or later. Python 3 is not yet supported. See the
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lib/python/README for more details.
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -848,7 +847,7 @@ as bonds are created and destroyed.
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[Author:] Aidan Thompson (Sandia).
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -1021,7 +1020,7 @@ system.
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library was written by Chris Rycroft (Harvard U) while at UC Berkeley
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and LBNL.
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -1048,7 +1047,7 @@ atomic information to continuum fields.
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[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -1075,7 +1074,7 @@ model.
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[Author:] Ilya Valuev (JIHT, Russia).
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -1098,7 +1097,7 @@ This package provides "fix bocs"_fix_bocs.html, a modified version
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of "fix npt"_fix_nh.html which includes the pressure correction to
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the barostat as outlined in:
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N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
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N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
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accurately describe the structure, pressure, and compressibility of
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molecular liquids," J. Chem. Phys. 143, 243148 (2015).
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@ -1183,7 +1182,7 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for
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the NAMD MD code, but with portability in mind. Axel Kohlmeyer
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(Temple U) provided the interface to LAMMPS.
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -1363,7 +1362,7 @@ system.
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[Author:] Pierre de Buyl (KU Leuven) created both the package and the
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H5MD format.
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[Install:]
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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@ -1401,7 +1400,7 @@ NOTE: the USER-INTEL package contains styles that require using the
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[Author:] Mike Brown (Intel).
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[Install:]
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[Install:]
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||||
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This package has "specific installation
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||||
instructions"_Build_extras.html#gpu on the "Build
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@ -1571,17 +1570,17 @@ USER-MOFFF package :link(PKG-USER-MOFFF),h4
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[Contents:]
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Pair, angle and improper styles needed to employ the MOF-FF
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force field by Schmid and coworkers with LAMMPS.
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force field by Schmid and coworkers with LAMMPS.
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MOF-FF is a first principles derived force field with the primary aim
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to simulate MOFs and related porous framework materials, using spherical
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to simulate MOFs and related porous framework materials, using spherical
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Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
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2013, 250, 1128-1141.
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For the usage of MOF-FF see the example in the example directory as
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For the usage of MOF-FF see the example in the example directory as
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well as the "MOF+"_MOFplus website.
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:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
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[Author:] Hendrik Heenen (Technical U of Munich),
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[Author:] Hendrik Heenen (Technical U of Munich),
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Rochus Schmid (Ruhr-University Bochum).
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[Supporting info:]
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||||
@ -1622,7 +1621,7 @@ at
|
||||
|
||||
[Author:] Axel Kohlmeyer (Temple U).
|
||||
|
||||
[Install:]
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
@ -1662,7 +1661,7 @@ tools:
|
||||
|
||||
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
|
||||
|
||||
[Install:]
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
@ -1706,7 +1705,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
|
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Once you have an appropriate Makefile.machine, you can
|
||||
install/un-install the package and build LAMMPS in the usual manner:
|
||||
|
||||
[Install:]
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
@ -1785,7 +1784,7 @@ without changes to LAMMPS itself.
|
||||
|
||||
[Author:] Axel Kohlmeyer (Temple U).
|
||||
|
||||
[Install:]
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
@ -1843,7 +1842,7 @@ on your system.
|
||||
|
||||
[Author:] Albert Bartok (Cambridge University)
|
||||
|
||||
[Install:]
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
@ -1937,7 +1936,7 @@ specified as surface geometries from *.STL files.
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||||
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
|
||||
Dynamics, Ernst Mach Institute, Germany).
|
||||
|
||||
[Install:]
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
@ -2063,7 +2062,7 @@ system.
|
||||
|
||||
[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
|
||||
|
||||
[Install:]
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
@ -2075,5 +2074,3 @@ src/USER-VTK: filenames -> commands
|
||||
src/USER-VTK/README
|
||||
lib/vtk/README
|
||||
"dump vtk"_dump_vtk.html :ul
|
||||
|
||||
|
||||
|
||||
@ -115,7 +115,7 @@ LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
This current version of pair_style kim is compatible with the
|
||||
kim-api package version 2.0.0-beta.1 and higher.
|
||||
kim-api package version 2.0.0-beta.2 and higher.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
||||
Reference in New Issue
Block a user