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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13501 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -1,9 +1,14 @@
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-*- fill-column: 70; -*-
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This package provides a pair_style kim command which is a wrapper on
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the Knowledge Base for Interatomic Models (KIM) repository of
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interatomic potentials, so that they can be used by LAMMPS scripts.
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Information about the KIM project can be found at https://openkim.org.
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It's PIs are Ellad Tadmor and Ryan Elliott (U Minn).
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The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn) and
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James Sethna (Cornell U). Ryan Elliott is the main developer for the
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KIM API and he also maintains the code that implements the pair_style
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kim command.
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Using this package requires the KIM library and its models
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(interatomic potentials) to be downloaded and installed on your
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@ -15,6 +20,8 @@ soon be provided to help automate the process. Also see the LAMMPS
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manual for general information on building LAMMPS with external
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libraries. The settings in the Makefile.lammps file in lib/kim must
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be correct for LAMMPS to build correctly with this package installed.
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However, the default settings should be correct in most cases and the
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Makefile.lammps file usually will not need to be changed.
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Once you have successfully built LAMMPS with this package and the KIM
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library you can test it using an input file from the examples dir:
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@ -27,6 +27,7 @@
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// includes from LAMMPS
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#include "pair_kim.h"
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#include "pair_kim_version.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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@ -46,7 +47,7 @@
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// support v1.5.0
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#define KIM_API_VERSION_MAJOR 1
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#define KIM_API_VERSION_MINOR 5
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#define KIM_API_VERSION_PATHC 0
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#define KIM_API_VERSION_PATCH 0
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#endif
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using namespace LAMMPS_NS;
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@ -55,6 +56,8 @@ using namespace LAMMPS_NS;
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PairKIM::PairKIM(LAMMPS *lmp) :
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Pair(lmp),
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settings_call_count(0),
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init_style_call_count(0),
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kim_modelname(0),
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lmps_map_species_to_unique(0),
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lmps_unique_elements(0),
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@ -258,10 +261,13 @@ void PairKIM::settings(int narg, char **arg)
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{
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// This is called when "pair_style kim ..." is read from input
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// may be called multiple times
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++settings_call_count;
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init_style_call_count = 0;
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if (narg != 2) error->all(FLERR,"Illegal pair_style command");
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if (narg < 2) error->all(FLERR,"Illegal pair_style command");
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// arg[0] is the virial handling option: "LAMMPSvirial" or "KIMvirial"
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// arg[1] is the KIM Model name
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// arg[2] is the print-kim-file flag: 0/1 do-not/do print (default 0)
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// ensure we are in a clean state for KIM (needed on repeated call)
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// first time called will do nothing...
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@ -300,6 +306,16 @@ void PairKIM::settings(int narg, char **arg)
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kim_modelname = new char[nmlen+1];
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strcpy(kim_modelname, arg[1]);
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// set print_kim_file
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if ((2 == narg) || ('0' == *(arg[2])))
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{
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print_kim_file = false;
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}
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else
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{
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print_kim_file = true;
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}
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return;
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}
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@ -385,6 +401,7 @@ void PairKIM::coeff(int narg, char **arg)
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void PairKIM::init_style()
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{
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// This is called for each "run ...", "minimize ...", etc. read from input
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++init_style_call_count;
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if (domain->dimension != 3)
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error->all(FLERR,"PairKIM only works with 3D problems");
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@ -770,6 +787,8 @@ void PairKIM::kim_init()
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{
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int kimerror;
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//
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// determine KIM Model capabilities (used in this function below)
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set_kim_model_has_flags();
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@ -777,6 +796,11 @@ void PairKIM::kim_init()
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char* test_descriptor_string = 0;
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// allocate memory for test_descriptor_string and write descriptor file
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write_descriptor(&test_descriptor_string);
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// print descriptor
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if (print_kim_file)
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{
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error->message(FLERR, test_descriptor_string);
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}
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// initialize KIM model
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pkim = new KIM_API_model();
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@ -1051,10 +1075,33 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
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// Write Test name and units
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strcat(*test_descriptor_string,
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"#\n"
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"# BEGINNING OF KIM DESCRIPTOR FILE\n"
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"#\n"
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"# This file is automatically generated from LAMMPS pair_style "
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"PairKIM command\n"
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"kim command\n");
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char tmp_version[100];
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sprintf(tmp_version,"# This is pair-kim-v%i.%i.%i",
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PAIR_KIM_VERSION_MAJOR, PAIR_KIM_VERSION_MINOR,
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PAIR_KIM_VERSION_PATCH);
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strcat(*test_descriptor_string, tmp_version);
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#ifdef PAIR_KIM_VERSION_PRERELEASE
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sprintf(tmp_version,"-%s", PAIR_KIM_VERSION_PRERELEASE);
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strcat(*test_descriptor_string, tmp_version);
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#endif
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#ifdef PAIR_KIM_VERSION_BUILD_METADATA
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sprintf(tmp_version,"+%s", PAIR_KIM_VERSION_BUILD_METADATA);
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#endif
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strcat(*test_descriptor_string,
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"\n"
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#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSON_MINOR == 5
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"# The call number is (pair_style).(init_style): ");
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char tmp_num[100];
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sprintf(tmp_num, "%i.%i\n", settings_call_count, init_style_call_count);
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strcat(*test_descriptor_string, tmp_num);
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strcat(*test_descriptor_string,
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"#\n"
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"\n"
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#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSION_MINOR == 5
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#else
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"KIM_API_Version := 1.6.0\n\n"
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#endif
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@ -1111,7 +1158,7 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
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#else
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"PARTICLE_SPECIES:\n"
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#endif
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"# Symbol/name Type code\n\n");
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"# Symbol/name Type code\n");
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int code=1;
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char* tmp_line = 0;
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tmp_line = new char[100];
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@ -1128,7 +1175,7 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
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strcat(*test_descriptor_string,
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"\n"
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"CONVENTIONS:\n"
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"# Name Type\n\n"
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"# Name Type\n"
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"ZeroBasedLists flag\n");
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// can use iterator or locator neighbor mode, unless in hybrid mode
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if (lmps_hybrid)
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@ -1158,43 +1205,53 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
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strcat(*test_descriptor_string,
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"\n"
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"MODEL_INPUT:\n"
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"# Name Type Unit Shape\n\n"
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"numberOfParticles integer none []\n\n"
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"numberContributingParticles integer none []\n\n"
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"# Name Type Unit Shape\n"
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"numberOfParticles integer none []\n"
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"numberContributingParticles integer none []\n"
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#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSON_MINOR == 5
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"numberParticleTypes integer none []\n\n"
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"numberParticleTypes integer none []\n"
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"particleTypes integer none "
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#else
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"numberOfSpecies integer none []\n\n"
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"numberOfSpecies integer none []\n"
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"particleSpecies integer none "
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#endif
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"[numberOfParticles]\n\n"
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"[numberOfParticles]\n"
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"coordinates double length "
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"[numberOfParticles,3]\n\n"
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"neighObject pointer none []\n\n"
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"get_neigh method none []\n\n");
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"[numberOfParticles,3]\n"
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"neighObject pointer none []\n"
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"get_neigh method none []\n");
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// Write output section
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strcat(*test_descriptor_string,
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"\n"
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"MODEL_OUPUT:\n"
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"# Name Type Unit Shape\n\n"
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"compute method none []\n\n"
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"destroy method none []\n\n"
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"cutoff double length []\n\n");
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if (kim_model_has_energy) strcat(*test_descriptor_string,
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"energy double energy []\n\n");
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if (kim_model_has_forces) strcat(*test_descriptor_string,
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"# Name Type Unit Shape\n"
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"compute method none []\n"
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"destroy method none []\n"
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"cutoff double length []\n");
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if (!kim_model_has_energy) strcat(*test_descriptor_string,"# ");
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strcat(*test_descriptor_string,
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"energy double energy []\n");
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if (!kim_model_has_forces) strcat(*test_descriptor_string, "# ");
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strcat(*test_descriptor_string,
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"forces double force "
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"[numberOfParticles,3]\n\n");
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if (kim_model_has_particleEnergy) strcat(*test_descriptor_string,
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"[numberOfParticles,3]\n");
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if (!kim_model_has_particleEnergy) strcat(*test_descriptor_string, "# ");
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strcat(*test_descriptor_string,
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"particleEnergy double energy "
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"[numberOfParticles]\n\n");
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if (no_virial_fdotr_compute == 1) strcat(*test_descriptor_string,
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"virial double energy [6] \n\n");
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if (kim_model_has_particleVirial) strcat(*test_descriptor_string,
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"[numberOfParticles]\n");
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if (no_virial_fdotr_compute != 1) strcat(*test_descriptor_string, "# ");
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strcat(*test_descriptor_string,
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"virial double energy [6]\n");
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if (!kim_model_has_particleVirial) strcat(*test_descriptor_string, "# ");
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strcat(*test_descriptor_string,
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"particleVirial double energy "
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"[numberOfParticles,6] \n\n");
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"[numberOfParticles,6]\n"
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"\n");
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strcat(*test_descriptor_string,
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"#\n"
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"# END OF KIM DESCRIPTOR FILE\n"
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"#\n");
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return;
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}
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@ -57,9 +57,12 @@ namespace LAMMPS_NS {
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// (nearly) all bool flags are not initialized in constructor, but set
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// explicitly in the indicated function. All other data members are
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// initialized in constructor
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int settings_call_count;
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int init_style_call_count;
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// values set in settings()
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char* kim_modelname;
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bool print_kim_file;
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// values set in coeff()
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