Commit 65f55e70 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13501 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent a67cb068

src/KIM/README

+8 −1
Original line number Diff line number Diff line 
-*- fill-column: 70; -*-



This package provides a pair_style kim command which is a wrapper on

the Knowledge Base for Interatomic Models (KIM) repository of

interatomic potentials, so that they can be used by LAMMPS scripts.



Information about the KIM project can be found at https://openkim.org.

It's PIs are Ellad Tadmor and Ryan Elliott (U Minn).

The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn) and

James Sethna (Cornell U).  Ryan Elliott is the main developer for the

KIM API and he also maintains the code that implements the pair_style

kim command.



Using this package requires the KIM library and its models

(interatomic potentials) to be downloaded and installed on your
@@ -15,6 +20,8 @@ soon be provided to help automate the process. Also see the LAMMPS 
manual for general information on building LAMMPS with external

libraries.  The settings in the Makefile.lammps file in lib/kim must

be correct for LAMMPS to build correctly with this package installed.

However, the default settings should be correct in most cases and the

Makefile.lammps file usually will not need to be changed.



Once you have successfully built LAMMPS with this package and the KIM

library you can test it using an input file from the examples dir:

src/KIM/pair_kim.cpp

+86 −29
Original line number Diff line number Diff line
@@ -27,6 +27,7 @@ 


// includes from LAMMPS

#include "pair_kim.h"

#include "pair_kim_version.h"

#include "atom.h"

#include "comm.h"

#include "force.h"
@@ -46,7 +47,7 @@ 
// support v1.5.0

#define KIM_API_VERSION_MAJOR 1

#define KIM_API_VERSION_MINOR 5

#define KIM_API_VERSION_PATHC 0

#define KIM_API_VERSION_PATCH 0

#endif



using namespace LAMMPS_NS;
@@ -55,6 +56,8 @@ using namespace LAMMPS_NS; 


PairKIM::PairKIM(LAMMPS *lmp) :

   Pair(lmp),

   settings_call_count(0),

   init_style_call_count(0),

   kim_modelname(0),

   lmps_map_species_to_unique(0),

   lmps_unique_elements(0),
@@ -258,10 +261,13 @@ void PairKIM::settings(int narg, char **arg) 
{

   // This is called when "pair_style kim ..." is read from input

   // may be called multiple times

   ++settings_call_count;

   init_style_call_count = 0;



   if (narg != 2) error->all(FLERR,"Illegal pair_style command");

   if (narg < 2) error->all(FLERR,"Illegal pair_style command");

   // arg[0] is the virial handling option: "LAMMPSvirial" or "KIMvirial"

   // arg[1] is the KIM Model name

   // arg[2] is the print-kim-file flag: 0/1 do-not/do print (default 0)



   // ensure we are in a clean state for KIM (needed on repeated call)

   // first time called will do nothing...
@@ -300,6 +306,16 @@ void PairKIM::settings(int narg, char **arg) 
   kim_modelname = new char[nmlen+1];

   strcpy(kim_modelname, arg[1]);



   // set print_kim_file

   if ((2 == narg) || ('0' == *(arg[2])))

   {

     print_kim_file = false;

   }

   else

   {

     print_kim_file = true;

   }



   return;

}
@@ -385,6 +401,7 @@ void PairKIM::coeff(int narg, char **arg) 
void PairKIM::init_style()

{

   // This is called for each "run ...", "minimize ...", etc. read from input

   ++init_style_call_count;



   if (domain->dimension != 3)

      error->all(FLERR,"PairKIM only works with 3D problems");
@@ -770,6 +787,8 @@ void PairKIM::kim_init() 
{

   int kimerror;



   //



   // determine KIM Model capabilities (used in this function below)

   set_kim_model_has_flags();
@@ -777,6 +796,11 @@ void PairKIM::kim_init() 
   char* test_descriptor_string = 0;

   // allocate memory for test_descriptor_string and write descriptor file

   write_descriptor(&test_descriptor_string);

   // print descriptor

   if (print_kim_file)

   {

      error->message(FLERR, test_descriptor_string);

   }



   // initialize KIM model

   pkim = new KIM_API_model();
@@ -1051,10 +1075,33 @@ void PairKIM::write_descriptor(char** test_descriptor_string) 


   // Write Test name and units

   strcat(*test_descriptor_string,

      "#\n"

      "# BEGINNING OF KIM DESCRIPTOR FILE\n"

      "#\n"

      "# This file is automatically generated from LAMMPS pair_style "

      "PairKIM command\n"

          "kim command\n");

   char tmp_version[100];

   sprintf(tmp_version,"# This is pair-kim-v%i.%i.%i",

           PAIR_KIM_VERSION_MAJOR, PAIR_KIM_VERSION_MINOR,

           PAIR_KIM_VERSION_PATCH);

   strcat(*test_descriptor_string, tmp_version);

#ifdef PAIR_KIM_VERSION_PRERELEASE

   sprintf(tmp_version,"-%s", PAIR_KIM_VERSION_PRERELEASE);

   strcat(*test_descriptor_string, tmp_version);

#endif

#ifdef PAIR_KIM_VERSION_BUILD_METADATA

   sprintf(tmp_version,"+%s", PAIR_KIM_VERSION_BUILD_METADATA);

#endif

   strcat(*test_descriptor_string,

      "\n"

#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSON_MINOR == 5

      "# The call number is (pair_style).(init_style): ");

   char tmp_num[100];

   sprintf(tmp_num, "%i.%i\n", settings_call_count, init_style_call_count);

   strcat(*test_descriptor_string, tmp_num);

   strcat(*test_descriptor_string,

      "#\n"

      "\n"

#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSION_MINOR == 5

#else

      "KIM_API_Version := 1.6.0\n\n"

#endif
@@ -1111,7 +1158,7 @@ void PairKIM::write_descriptor(char** test_descriptor_string) 
#else

      "PARTICLE_SPECIES:\n"

#endif

      "# Symbol/name           Type            code\n\n");

      "# Symbol/name           Type            code\n");

   int code=1;

   char* tmp_line = 0;

   tmp_line = new char[100];
@@ -1128,7 +1175,7 @@ void PairKIM::write_descriptor(char** test_descriptor_string) 
   strcat(*test_descriptor_string,

      "\n"

      "CONVENTIONS:\n"

      "# Name                  Type\n\n"

      "# Name                  Type\n"

      "ZeroBasedLists          flag\n");

   // can use iterator or locator neighbor mode, unless in hybrid mode

   if (lmps_hybrid)
@@ -1158,43 +1205,53 @@ void PairKIM::write_descriptor(char** test_descriptor_string) 
   strcat(*test_descriptor_string,

      "\n"

      "MODEL_INPUT:\n"

      "# Name                         Type         Unit    Shape\n\n"

      "numberOfParticles              integer      none    []\n\n"

      "numberContributingParticles    integer      none    []\n\n"

      "# Name                         Type         Unit    Shape\n"

      "numberOfParticles              integer      none    []\n"

      "numberContributingParticles    integer      none    []\n"

#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSON_MINOR == 5

      "numberParticleTypes            integer      none    []\n\n"

      "numberParticleTypes            integer      none    []\n"

      "particleTypes                  integer      none    "

#else

      "numberOfSpecies                integer      none    []\n\n"

      "numberOfSpecies                integer      none    []\n"

      "particleSpecies                integer      none    "

#endif

      "[numberOfParticles]\n\n"

      "[numberOfParticles]\n"

      "coordinates                    double       length  "

      "[numberOfParticles,3]\n\n"

      "neighObject                    pointer      none    []\n\n"

      "get_neigh                      method       none    []\n\n");

      "[numberOfParticles,3]\n"

      "neighObject                    pointer      none    []\n"

      "get_neigh                      method       none    []\n");



   // Write output section

   strcat(*test_descriptor_string,

      "\n"

      "MODEL_OUPUT:\n"

      "# Name                         Type         Unit    Shape\n\n"

      "compute                        method       none    []\n\n"

      "destroy                        method       none    []\n\n"

      "cutoff                         double       length  []\n\n");

   if (kim_model_has_energy) strcat(*test_descriptor_string,

      "energy                         double       energy  []\n\n");

   if (kim_model_has_forces) strcat(*test_descriptor_string,

      "# Name                         Type         Unit    Shape\n"

      "compute                        method       none    []\n"

      "destroy                        method       none    []\n"

      "cutoff                         double       length  []\n");

   if (!kim_model_has_energy) strcat(*test_descriptor_string,"# ");

   strcat(*test_descriptor_string,

      "energy                         double       energy  []\n");

   if (!kim_model_has_forces) strcat(*test_descriptor_string, "# ");

   strcat(*test_descriptor_string,

      "forces                         double       force   "

       "[numberOfParticles,3]\n\n");

   if (kim_model_has_particleEnergy) strcat(*test_descriptor_string,

      "[numberOfParticles,3]\n");

   if (!kim_model_has_particleEnergy) strcat(*test_descriptor_string, "# ");

   strcat(*test_descriptor_string,

      "particleEnergy                 double       energy  "

       "[numberOfParticles]\n\n");

   if (no_virial_fdotr_compute == 1) strcat(*test_descriptor_string,

      "virial                         double       energy  [6] \n\n");

   if (kim_model_has_particleVirial) strcat(*test_descriptor_string,

      "[numberOfParticles]\n");

   if (no_virial_fdotr_compute != 1) strcat(*test_descriptor_string, "# ");

   strcat(*test_descriptor_string,

      "virial                         double       energy  [6]\n");

   if (!kim_model_has_particleVirial) strcat(*test_descriptor_string, "# ");

   strcat(*test_descriptor_string,

      "particleVirial                 double       energy  "

       "[numberOfParticles,6] \n\n");

      "[numberOfParticles,6]\n"

      "\n");

   strcat(*test_descriptor_string,

      "#\n"

      "# END OF KIM DESCRIPTOR FILE\n"

      "#\n");



   return;

}

src/KIM/pair_kim.h

+3 −0
Original line number Diff line number Diff line
@@ -57,9 +57,12 @@ namespace LAMMPS_NS { 
      // (nearly) all bool flags are not initialized in constructor, but set

      // explicitly in the indicated function.  All other data members are

      // initialized in constructor

      int settings_call_count;

      int init_style_call_count;



      // values set in settings()

      char* kim_modelname;

      bool print_kim_file;



      // values set in coeff()

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