From 29ae88e309fd02a3b4fbb3f882f498258096a794 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Mon, 5 Nov 2018 09:37:35 -0600 Subject: [PATCH] Update docs for KIM --- doc/src/Build_extras.txt | 44 ++++++++++++------------- doc/src/Errors_messages.txt | 8 ----- doc/src/Packages_details.txt | 63 +++++++++++++++++------------------- doc/src/pair_kim.txt | 2 +- 4 files changed, 51 insertions(+), 66 deletions(-) diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index d256a1afc8..5f4ad6ee69 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -63,7 +63,7 @@ available on your system. If CMake cannot find the library, you can set these variables: --D ZLIB_INCLUDE_DIR=path # path to zlib.h header file +-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file -D ZLIB_LIBRARIES=path # path to libz.a (.so) file :pre [Traditional make]: @@ -150,7 +150,7 @@ package uses the library settings from the lib/gpu/Makefile.machine used to build the GPU library. :line - + KIM package :h4,link(kim) To build with this package, the KIM library must be downloaded and @@ -176,16 +176,12 @@ package?" page. [CMake build]: --D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes --D KIM_LIBRARY=path # KIM library file (only needed if a custom location) --D KIM_INCLUDE_DIR=path # KIM include directory (only needed if a custom location) :pre +-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes :pre If DOWNLOAD_KIM is set, the KIM library will be downloaded and built inside the CMake build directory. If the KIM library is already on -your system (in a location CMake cannot find it), KIM_LIBRARY is the -filename (plus path) of the KIM library file, not the directory the -library file is in. KIM_INCLUDE_DIR is the directory the KIM include -file is in. +your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH +environment variable so that libkim-api-v2 can be found. [Traditional make]: @@ -199,8 +195,8 @@ make lib-kim args="-b " # (re-)install KIM API lib with only example models make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model make lib-kim args="-b -a everything" # install KIM API lib with all models make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver -make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location -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 +make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location +make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre :line @@ -254,7 +250,7 @@ For NVIDIA GPUs using CUDA, set these 4 variables: -D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU # archGPU = GPU from list above -D KOKKOS_ENABLE_CUDA=yes --D KOKKOS_ENABLE_OPENMP=yes +-D KOKKOS_ENABLE_OPENMP=yes -D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper :pre The wrapper value is the Cuda nvcc compiler wrapper provided in the @@ -296,7 +292,7 @@ export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper CC = mpicxx :pre :line - + LATTE package :h4,link(latte) To build with this package, you must download and build the LATTE @@ -324,7 +320,7 @@ args: make lib-latte # print help message make lib-latte args="-b" # download and build in lib/latte/LATTE-master make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte -make lib-latte args="-b -m gfortran" # download and build in lib/latte and +make lib-latte args="-b -m gfortran" # download and build in lib/latte and # copy Makefile.lammps.gfortran to Makefile.lammps :pre @@ -335,7 +331,7 @@ also check that the Makefile.lammps file you create is appropriate for the compiler you use on your system to build LATTE. :line - + MEAM package :h4,link(meam) NOTE: the use of the MEAM package is discouraged, as it has been @@ -378,7 +374,7 @@ EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine file. :line - + MESSAGE package :h4,link(message) This package can optionally include support for messaging via sockets, @@ -407,7 +403,7 @@ existing Makefile.lammps.* and has settings to link with the ZeroMQ library if requested in the build. :line - + MSCG package :h4,link(mscg) To build with this package, you must download and build the MS-CG @@ -419,7 +415,7 @@ lib/mscg/README and MSCG/Install files for more details. [CMake build]: -D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes --D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location) +-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location) -D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location) :pre If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built @@ -464,7 +460,7 @@ line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for an example. :line - + POEMS package :h4,link(poems) [CMake build]: @@ -493,7 +489,7 @@ for your system, which should define an EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine file. :line - + PYTHON package :h4,link(python) Building with the PYTHON package requires you have a Python shared @@ -520,7 +516,7 @@ Makefile.lammps.* file (and copy it to Makefile.lammps) if the LAMMPS build fails. :line - + REAX package :h4,link(reax) NOTE: the use of the REAX package and its "pair_style @@ -570,7 +566,7 @@ library"_voro-home. [CMake build]: -D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes --D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location) +-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location) -D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) :pre If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and @@ -869,7 +865,7 @@ Quantum ESPRESSO known to work with this QM/MM interface was version [CMake build]: The CMake build system currently does not support building the full -QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x. +QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x. You must use the traditional make build for this package. [Traditional make]: @@ -939,7 +935,7 @@ Coulomb solver library"_scafacos-home [CMake build]: -D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes --D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location) +-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location) -D SCAFACOS_INCLUDE_DIR=path # ScaFaCoS include directory (only needed if at custom location) :pre If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index 695b949f7e..3dc93044c8 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -6994,12 +6994,6 @@ The atom style defined does not have this attribute. :dd The atom style defined does not have these attributes. :dd -{KIM neighbor iterator exceeded range} :dt - -This should not happen. It likely indicates a bug -in the KIM implementation of the interatomic potential -where it is requesting neighbors incorrectly. :dd - {KOKKOS package does not yet support comm_style tiled} :dt Self-explanatory. :dd @@ -10193,8 +10187,6 @@ Self-explanatory. :dd {Unrecognized virial argument in pair_style command} :dt -Only two options are supported: LAMMPSvirial and KIMvirial :dd - {Unsupported mixing rule in kspace_style ewald/disp} :dt Only geometric mixing is supported. :dd diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 031858e846..7365e986e5 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -203,7 +203,7 @@ available on your system. [Author:] Axel Kohlmeyer (Temple U). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -284,7 +284,7 @@ also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles. [Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen (Northwestern U) while at ORNL. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -345,14 +345,13 @@ system. Information about the KIM project can be found at its website: https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan -Elliott (U Minnesota) and James Sethna (Cornell U). +Elliott (U Minnesota). [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM API which the "pair_style kim"_pair_kim.html command uses. He -developed the pair style in collaboration with Valeriu Smirichinski (U -Minnesota). +developed the pair style. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -398,7 +397,7 @@ which was developed by Carter Edwards, Christian Trott, and others at Sandia, and which is included in the LAMMPS distribution in lib/kokkos. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -546,7 +545,7 @@ and user interface. [Author:] Greg Wagner (Northwestern U) while at Sandia. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -679,7 +678,7 @@ system. library was developed by Jacob Wagner in Greg Voth's group at the University of Chicago. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -711,7 +710,7 @@ have styles optimized for CPU performance. [Authors:] James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge Technolgy). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -768,7 +767,7 @@ connections at hinge points. [Author:] Rudra Mukherjee (JPL) while at RPI. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -800,7 +799,7 @@ shared library available on your system, which needs to be a Python 2 version, 2.6 or later. Python 3 is not yet supported. See the lib/python/README for more details. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -848,7 +847,7 @@ as bonds are created and destroyed. [Author:] Aidan Thompson (Sandia). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1021,7 +1020,7 @@ system. library was written by Chris Rycroft (Harvard U) while at UC Berkeley and LBNL. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1048,7 +1047,7 @@ atomic information to continuum fields. [Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1075,7 +1074,7 @@ model. [Author:] Ilya Valuev (JIHT, Russia). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1098,7 +1097,7 @@ This package provides "fix bocs"_fix_bocs.html, a modified version of "fix npt"_fix_nh.html which includes the pressure correction to the barostat as outlined in: -N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that +N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids," J. Chem. Phys. 143, 243148 (2015). @@ -1183,7 +1182,7 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for the NAMD MD code, but with portability in mind. Axel Kohlmeyer (Temple U) provided the interface to LAMMPS. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1363,7 +1362,7 @@ system. [Author:] Pierre de Buyl (KU Leuven) created both the package and the H5MD format. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1401,7 +1400,7 @@ NOTE: the USER-INTEL package contains styles that require using the [Author:] Mike Brown (Intel). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1571,17 +1570,17 @@ USER-MOFFF package :link(PKG-USER-MOFFF),h4 [Contents:] Pair, angle and improper styles needed to employ the MOF-FF -force field by Schmid and coworkers with LAMMPS. +force field by Schmid and coworkers with LAMMPS. MOF-FF is a first principles derived force field with the primary aim -to simulate MOFs and related porous framework materials, using spherical +to simulate MOFs and related porous framework materials, using spherical Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B 2013, 250, 1128-1141. -For the usage of MOF-FF see the example in the example directory as +For the usage of MOF-FF see the example in the example directory as well as the "MOF+"_MOFplus website. :link(MOFplus,https://www.mofplus.org/content/show/MOF-FF) -[Author:] Hendrik Heenen (Technical U of Munich), +[Author:] Hendrik Heenen (Technical U of Munich), Rochus Schmid (Ruhr-University Bochum). [Supporting info:] @@ -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. 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. [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 - - diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index 8bd6aa9937..0c05913117 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -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:]