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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12267 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-08-06 23:30:26 +00:00
parent 1177fd9af3
commit f58ea4fdc0
3 changed files with 113 additions and 86 deletions
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6
src/KIM/Makefile.lammps
View File

@ -20,6 +20,6 @@
# Settings that the LAMMPS build will import when this package is installed
kim_SYSINC = -Iopenkim-api-vX.X.X/KIM_API
kim_SYSLIB = -lkim
kim_SYSPATH = -Lopenkim-api-vX.X.X/KIM_API
kim_SYSINC = $(shell kim-api-build-config --includes)
kim_SYSLIB = $(shell kim-api-build-config --ldlibs)
kim_SYSPATH = $(shell kim-api-build-config --ldflags)

166
src/KIM/pair_kim.cpp
View File

@ -18,7 +18,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Designed for use with the openkim-api-v1.2.0 (and newer) package
Designed for use with the openkim-api-v1.5.0 package and for use with
the kim-api-v1.6.0 (and newer) package
------------------------------------------------------------------------- */
#include <cstring>
@ -41,6 +42,13 @@
#include "KIM_API.h"
#include "KIM_API_status.h"
#ifndef KIM_API_VERSION_MAJOR
// support v1.5.0
#define KIM_API_VERSION_MAJOR 1
#define KIM_API_VERSION_MINOR 5
#define KIM_API_VERSION_PATHC 0
#endif
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -48,7 +56,7 @@ using namespace LAMMPS_NS;
PairKIM::PairKIM(LAMMPS *lmp) :
Pair(lmp),
kim_modelname(0),
lmps_map_types_to_unique(0),
lmps_map_species_to_unique(0),
lmps_unique_elements(0),
lmps_num_unique_elements(0),
lmps_units(METAL),
@ -56,8 +64,8 @@ PairKIM::PairKIM(LAMMPS *lmp) :
kim_ind_coordinates(-1),
kim_ind_numberOfParticles(-1),
kim_ind_numberContributingParticles(-1),
kim_ind_numberParticleTypes(-1),
kim_ind_particleTypes(-1),
kim_ind_numberOfSpecies(-1),
kim_ind_particleSpecies(-1),
kim_ind_get_neigh(-1),
kim_ind_neighObject(-1),
kim_ind_cutoff(-1),
@ -67,10 +75,10 @@ PairKIM::PairKIM(LAMMPS *lmp) :
kim_ind_virial(-1),
kim_ind_particleVirial(-1),
kim_particle_codes(0),
lmps_local_tot_num_atoms(0),
lmps_local_tot_num_atoms(0),
kim_global_cutoff(0.0),
lmps_maxalloc(0),
kim_particleTypes(0),
kim_particleSpecies(0),
lmps_force_tmp(0),
lmps_stripped_neigh_list(0),
kim_iterator_position(0),
@ -81,7 +89,7 @@ PairKIM::PairKIM(LAMMPS *lmp) :
restartinfo = 0; // We do not write any restart info
one_coeff = 1; // We only allow one coeff * * call
// BEGIN: initial values that determine the KIM state
// BEGIN: initial values that determine the KIM state
// (used by kim_free(), etc.)
kim_model_init_ok = false;
kim_init_ok = false;
@ -97,23 +105,23 @@ PairKIM::~PairKIM()
// clean up kim_modelname
if (kim_modelname != 0) delete [] kim_modelname;
// clean up lammps atom type number to unique particle names mapping
// clean up lammps atom species number to unique particle names mapping
if (lmps_unique_elements)
for (int i = 0; i < lmps_num_unique_elements; i++)
for (int i = 0; i < lmps_num_unique_elements; i++)
delete [] lmps_unique_elements[i];
delete [] lmps_unique_elements;
// clean up local memory used to support KIM interface
memory->destroy(kim_particleTypes);
memory->destroy(kim_particleSpecies);
memory->destroy(lmps_force_tmp);
memory->destroy(lmps_stripped_neigh_list);
// clean up allocated memory for standard Pair class usage
// also, we allocate lmps_map_types_to_uniuqe in the allocate() function
// also, we allocate lmps_map_species_to_uniuqe in the allocate() function
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] lmps_map_types_to_unique;
delete [] lmps_map_species_to_unique;
}
// clean up Rij array
@ -136,33 +144,33 @@ void PairKIM::compute(int eflag , int vflag)
else
ev_unset();
// grow kim_particleTypes array if necessary
// grow kim_particleSpecies array if necessary
// needs to be atom->nmax in length
if (atom->nmax > lmps_maxalloc) {
memory->destroy(kim_particleTypes);
memory->destroy(kim_particleSpecies);
memory->destroy(lmps_force_tmp);
lmps_maxalloc = atom->nmax;
memory->create(kim_particleTypes,lmps_maxalloc,"pair:kim_particleTypes");
memory->create(kim_particleSpecies,lmps_maxalloc,"pair:kim_particleSpecies");
memory->create(lmps_force_tmp,lmps_maxalloc,3,"pair:lmps_force_tmp");
}
// kim_particleTypes = KIM atom type for each LAMMPS atom
// set ielement to valid 0 if lmps_map_types_to_unique[] stores an un-used -1
// kim_particleSpecies = KIM atom species for each LAMMPS atom
// set ielement to valid 0 if lmps_map_species_to_unique[] stores an un-used -1
int *type = atom->type;
int *species = atom->type;
int nall = atom->nlocal + atom->nghost;
int ielement;
for (int i = 0; i < nall; i++) {
ielement = lmps_map_types_to_unique[type[i]];
ielement = lmps_map_species_to_unique[species[i]];
ielement = MAX(ielement,0);
// @@ this (above line) provides bogus info
// @@ (when lmps_map_types_to_unique[type[i]]==-1) to KIM, but I guess
// @@ this only happens when lmps_hybrid==true,
// @@ this (above line) provides bogus info
// @@ (when lmps_map_species_to_unique[species[i]]==-1) to KIM, but
// @@ I guess this only happens when lmps_hybrid==true,
// @@ and we are sure that iterator mode will
// @@ not use these atoms.... (?)
kim_particleTypes[i] = kim_particle_codes[ielement];
kim_particleSpecies[i] = kim_particle_codes[ielement];
}
// pass current atom pointers to KIM
@ -173,7 +181,7 @@ void PairKIM::compute(int eflag , int vflag)
(int) kim_model_has_particleEnergy,
kim_ind_particleVirial, vflag_atom,
(int) kim_model_has_particleVirial,
kim_ind_virial, vflag_global!=0,
kim_ind_virial, vflag_global!=0,
no_virial_fdotr_compute);
kim_error(__LINE__,"setm_compute_by_index",kimerror);
@ -229,13 +237,13 @@ void PairKIM::compute(int eflag , int vflag)
void PairKIM::allocate()
{
int n = atom->ntypes;
// allocate standard Pair class arrays
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
// allocate mapping array
lmps_map_types_to_unique = new int[n+1];
lmps_map_species_to_unique = new int[n+1];
allocated = 1;
@ -303,7 +311,7 @@ void PairKIM::coeff(int narg, char **arg)
{
// This is called when "pair_coeff ..." is read from input
// may be called multiple times
int i,j,n;
if (!allocated) allocate();
@ -316,15 +324,15 @@ void PairKIM::coeff(int narg, char **arg)
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read args that map atom types to KIM elements
// lmps_map_types_to_unique[i] =
// read args that map atom species to KIM elements
// lmps_map_species_to_unique[i] =
// which element the Ith atom type is, -1 if NULL
// lmps_num_unique_elements = # of unique elements
// lmps_unique_elements = list of element names
// if called multiple times: update lmps_unique_elements
if (lmps_unique_elements) {
for (i = 0; i < lmps_num_unique_elements; i++)
for (i = 0; i < lmps_num_unique_elements; i++)
delete [] lmps_unique_elements[i];
delete [] lmps_unique_elements;
}
@ -334,14 +342,14 @@ void PairKIM::coeff(int narg, char **arg)
lmps_num_unique_elements = 0;
for (i = 2; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
if (!lmps_hybrid)
if (!lmps_hybrid)
error->all(FLERR,"Invalid args for non-hybrid pair coefficients");
lmps_map_types_to_unique[i-1] = -1;
lmps_map_species_to_unique[i-1] = -1;
continue;
}
for (j = 0; j < lmps_num_unique_elements; j++)
if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break;
lmps_map_types_to_unique[i-1] = j;
lmps_map_species_to_unique[i-1] = j;
if (j == lmps_num_unique_elements) {
n = strlen(arg[i]) + 1;
lmps_unique_elements[j] = new char[n];
@ -360,8 +368,8 @@ void PairKIM::coeff(int narg, char **arg)
int count = 0;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (lmps_map_types_to_unique[i] >= 0 &&
lmps_map_types_to_unique[j] >= 0) {
if (lmps_map_species_to_unique[i] >= 0 &&
lmps_map_species_to_unique[j] >= 0) {
setflag[i][j] = 1;
count++;
}
@ -383,7 +391,7 @@ void PairKIM::init_style()
// set lmps_* bool flags
set_lmps_flags();
int kimerror;
// KIM and Model initialization (only once)
// also sets kim_ind_* and kim_* bool flags
@ -462,7 +470,7 @@ int PairKIM::pack_reverse_comm(int n, int first, double *buf)
m = 0;
last = first + n;
if ((kim_model_has_forces) && ((vflag_atom == 0) ||
if ((kim_model_has_forces) && ((vflag_atom == 0) ||
(!kim_model_has_particleVirial)))
{
for (i = first; i < last; i++)
@ -473,7 +481,7 @@ int PairKIM::pack_reverse_comm(int n, int first, double *buf)
}
return 3;
}
else if ((kim_model_has_forces) && (vflag_atom == 1) &&
else if ((kim_model_has_forces) && (vflag_atom == 1) &&
(kim_model_has_particleVirial))
{
double *va=&(vatom[0][0]);
@ -492,7 +500,7 @@ int PairKIM::pack_reverse_comm(int n, int first, double *buf)
}
return 9;
}
else if ((!kim_model_has_forces) && (vflag_atom == 1) &&
else if ((!kim_model_has_forces) && (vflag_atom == 1) &&
(kim_model_has_particleVirial))
{
double *va=&(vatom[0][0]);
@ -521,7 +529,7 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf)
else fp = &(atom->f[0][0]);
m = 0;
if ((kim_model_has_forces) && ((vflag_atom == 0) ||
if ((kim_model_has_forces) && ((vflag_atom == 0) ||
(!kim_model_has_particleVirial)))
{
for (i = 0; i < n; i++)
@ -532,7 +540,7 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf)
fp[3*j+2]+= buf[m++];
}
}
else if ((kim_model_has_forces) && (vflag_atom == 1) &&
else if ((kim_model_has_forces) && (vflag_atom == 1) &&
(kim_model_has_particleVirial))
{
double *va=&(vatom[0][0]);
@ -551,7 +559,7 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf)
va[j*6+5]+=buf[m++];
}
}
else if ((!kim_model_has_forces) && (vflag_atom == 1) &&
else if ((!kim_model_has_forces) && (vflag_atom == 1) &&
(kim_model_has_particleVirial))
{
double *va=&(vatom[0][0]);
@ -603,19 +611,19 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
KIM_API_model *pkim = (KIM_API_model *) *kimmdl;
int kimerror;
PairKIM *self = (PairKIM *) pkim->get_test_buffer(&kimerror);
PairKIM *self = (PairKIM *) pkim->get_sim_buffer(&kimerror);
if (self->kim_model_using_Rij) {
*pRij = &(self->Rij[0]);
} else {
*pRij = 0;
}
// subvert KIM api by using direct access to self->list
//
// get neighObj from KIM API obj
// NeighList * neiobj = (NeighList * )
// NeighList * neiobj = (NeighList * )
// (*pkim).get_data_by_index(self->kim_ind_neighObject, &kimerror);
NeighList * neiobj = self->list;
@ -653,8 +661,8 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
// set Rij if needed
if (self->kim_model_using_Rij) {
double* x = (double *)
(*pkim).get_data_by_index(self->kim_ind_coordinates,
double* x = (double *)
(*pkim).get_data_by_index(self->kim_ind_coordinates,
&kimerror);
for (jj=0; jj < *numnei; jj++) {
int i = *atom;
@ -701,7 +709,7 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
// set Rij if needed
if (self->kim_model_using_Rij){
double* x = (double *)
double* x = (double *)
(*pkim).get_data_by_index(self->kim_ind_coordinates, &kimerror);
for(int jj=0; jj < *numnei; jj++){
int i = *atom;
@ -787,22 +795,27 @@ void PairKIM::kim_init()
// check for half or full list
kim_model_using_half = (pkim->is_half_neighbors(&kimerror));
//
char * NBC_method =(char *) pkim->get_NBC_method(&kimerror);
const char* NBC_method;
kimerror = pkim->get_NBC_method(&NBC_method);
kim_error(__LINE__,"NBC method not set",kimerror);
// check for CLUSTER mode
kim_model_using_cluster = (strcmp(NBC_method,"CLUSTER")==0);
// check if Rij needed for get_neigh
kim_model_using_Rij = ((strcmp(NBC_method,"NEIGH_RVEC_H")==0) ||
(strcmp(NBC_method,"NEIGH_RVEC_F")==0));
free((void*)NBC_method);
// get correct index of each variable in kim_api object
pkim->getm_index(&kimerror, 3*13,
"coordinates", &kim_ind_coordinates, 1,
"cutoff", &kim_ind_cutoff, 1,
"numberOfParticles", &kim_ind_numberOfParticles, 1,
"numberParticleTypes", &kim_ind_numberParticleTypes, 1,
"particleTypes", &kim_ind_particleTypes, 1,
#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSON_MINOR == 5
"numberParticleTypes", &kim_ind_numberOfSpecies, 1,
"particleTypes", &kim_ind_particleSpecies, 1,
#else
"numberOfSpecies", &kim_ind_numberOfSpecies, 1,
"particleSpecies", &kim_ind_particleSpecies, 1,
#endif
"numberContributingParticles", &kim_ind_numberContributingParticles,
kim_model_using_half,
"particleEnergy", &kim_ind_particleEnergy,
@ -816,13 +829,13 @@ void PairKIM::kim_init()
"virial", &kim_ind_virial, no_virial_fdotr_compute);
kim_error(__LINE__,"getm_index",kimerror);
// setup mapping between LAMMPS unique elements and KIM particle type codes
// setup mapping between LAMMPS unique elements and KIM species codes
kim_particle_codes = new int[lmps_num_unique_elements];
kim_particle_codes_ok = true;
for(int i = 0; i < lmps_num_unique_elements; i++){
int kimerror;
kim_particle_codes[i]
= pkim->get_partcl_type_code(lmps_unique_elements[i], &kimerror);
= pkim->get_species_code(lmps_unique_elements[i], &kimerror);
kim_error(__LINE__, "create_kim_particle_codes: symbol not found ",
kimerror);
}
@ -842,7 +855,7 @@ void PairKIM::set_statics()
int kimerror;
pkim->setm_data_by_index(&kimerror, 4*6,
kim_ind_numberParticleTypes, 1, (void *) &(atom->ntypes), 1,
kim_ind_numberOfSpecies, 1, (void *) &(atom->ntypes), 1,
kim_ind_cutoff, 1, (void *) &(kim_global_cutoff), 1,
kim_ind_numberOfParticles, 1, (void *) &lmps_local_tot_num_atoms, 1,
kim_ind_numberContributingParticles, 1, (void *) &(atom->nlocal),
@ -857,8 +870,8 @@ void PairKIM::set_statics()
kim_error(__LINE__, "set_method_by_index", kimerror);
}
pkim->set_test_buffer((void *)this, &kimerror);
kim_error(__LINE__, "set_test_buffer", kimerror);
pkim->set_sim_buffer((void *)this, &kimerror);
kim_error(__LINE__, "set_sim_buffer", kimerror);
return;
}
@ -873,7 +886,7 @@ void PairKIM::set_volatiles()
pkim->setm_data_by_index(&kimerror, 4*2,
kim_ind_coordinates, 3*nall, (void*) &(atom->x[0][0]), 1,
kim_ind_particleTypes, nall, (void*) kim_particleTypes, 1);
kim_ind_particleSpecies, nall, (void*) kim_particleSpecies, 1);
kim_error(__LINE__, "setm_data_by_index", kimerror);
if (kim_model_has_particleEnergy && (eflag_atom == 1))
@ -989,21 +1002,21 @@ void PairKIM::set_kim_model_has_flags()
// determine if the KIM Model can compute the total energy
mdl.get_index((char*) "energy", &kimerror);
kim_model_has_energy = (kimerror == KIM_STATUS_OK);
if (!kim_model_has_energy)
if (!kim_model_has_energy)
error->warning(FLERR,"KIM Model does not provide `energy'; "
"Potential energy will be zero");
// determine if the KIM Model can compute the forces
mdl.get_index((char*) "forces", &kimerror);
kim_model_has_forces = (kimerror == KIM_STATUS_OK);
if (!kim_model_has_forces)
if (!kim_model_has_forces)
error->warning(FLERR,"KIM Model does not provide `forces'; "
"Forces will be zero");
// determine if the KIM Model can compute the particleEnergy
mdl.get_index((char*) "particleEnergy", &kimerror);
kim_model_has_particleEnergy = (kimerror == KIM_STATUS_OK);
if (!kim_model_has_particleEnergy)
if (!kim_model_has_particleEnergy)
error->warning(FLERR,"KIM Model does not provide `particleEnergy'; "
"energy per atom will be zero");
@ -1011,9 +1024,9 @@ void PairKIM::set_kim_model_has_flags()
mdl.get_index((char*) "particleVirial", &kimerror);
kim_model_has_particleVirial = (kimerror == KIM_STATUS_OK);
mdl.get_index((char*) "process_dEdr", &kimerror);
kim_model_has_particleVirial = kim_model_has_particleVirial ||
kim_model_has_particleVirial = kim_model_has_particleVirial ||
(kimerror == KIM_STATUS_OK);
if (!kim_model_has_particleVirial)
if (!kim_model_has_particleVirial)
error->warning(FLERR,"KIM Model does not provide `particleVirial'; "
"virial per atom will be zero");
@ -1029,10 +1042,10 @@ void PairKIM::set_kim_model_has_flags()
void PairKIM::write_descriptor(char** test_descriptor_string)
{
// allocate memory
if (*test_descriptor_string != 0)
if (*test_descriptor_string != 0)
error->all(FLERR, "Test_descriptor_string already allocated");
// assuming 75 lines at 100 characters each (should be plenty)
*test_descriptor_string = new char[100*75];
*test_descriptor_string = new char[100*75];
// initialize
strcpy(*test_descriptor_string, "");
@ -1041,6 +1054,10 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
"# This file is automatically generated from LAMMPS pair_style "
"PairKIM command\n"
"\n"
#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSON_MINOR == 5
#else
"KIM_API_Version := 1.6.0\n\n"
#endif
"# Base units\n");
switch (lmps_units)
{
@ -1086,16 +1103,20 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
break;
}
// Write Supported types section
// Write Supported species section
strcat(*test_descriptor_string,
"\n"
#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSON_MINOR == 5
"SUPPORTED_ATOM/PARTICLES_TYPES:\n"
#else
"PARTICLE_SPECIES:\n"
#endif
"# Symbol/name Type code\n\n");
int code=1;
char* tmp_line = 0;
tmp_line = new char[100];
for (int i=0; i < lmps_num_unique_elements; i++){
sprintf(tmp_line, "%-24s%-16s%-3i\n", lmps_unique_elements[i],
sprintf(tmp_line, "%-24s%-16s%-3i\n", lmps_unique_elements[i],
"spec", code++);
strcat(*test_descriptor_string, tmp_line);
}
@ -1140,11 +1161,16 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
"# Name Type Unit Shape\n\n"
"numberOfParticles integer none []\n\n"
"numberContributingParticles integer none []\n\n"
#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSON_MINOR == 5
"numberParticleTypes integer none []\n\n"
"particleTypes integer none "
"[numberOfParticles]\n\n"
#else
"numberOfSpecies integer none []\n\n"
"particleSpecies integer none "
#endif
"[numberOfParticles]\n\n"
"coordinates double length "
"[numberOfParticles,3]\n\n"
"[numberOfParticles,3]\n\n"
"neighObject pointer none []\n\n"
"get_neigh method none []\n\n");

27
src/KIM/pair_kim.h
View File

@ -18,7 +18,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Designed for use with the openkim-api-v1.2.0 (and newer) package
Designed for use with the openkim-api-v1.5.0 package and for use with
the kim-api-v1.6.0 (and newer) package
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
@ -64,7 +65,7 @@ namespace LAMMPS_NS {
// values set in allocate(), called by coeff()
void allocate();
int* lmps_map_types_to_unique;
int* lmps_map_species_to_unique;
// values set in coeff(), after calling allocate()
char** lmps_unique_elements; // names of unique elements given
@ -95,8 +96,8 @@ namespace LAMMPS_NS {
int kim_ind_coordinates;
int kim_ind_numberOfParticles;
int kim_ind_numberContributingParticles;
int kim_ind_numberParticleTypes;
int kim_ind_particleTypes;
int kim_ind_numberOfSpecies;
int kim_ind_particleSpecies;
int kim_ind_get_neigh;
int kim_ind_neighObject;
int kim_ind_cutoff;
@ -114,19 +115,19 @@ namespace LAMMPS_NS {
// values set in set_statics(), called at end of kim_init(),
// then again in set_volatiles(), called in compute()
int lmps_local_tot_num_atoms;
double kim_global_cutoff; // KIM Model cutoff value
double kim_global_cutoff; // KIM Model cutoff value
// values set in compute()
int lmps_maxalloc; // max allocated memory value
int* kim_particleTypes; // array of KIM particle types
double** lmps_force_tmp; // temp storage for f, when running in
// hybrid mode needed to avoid reseting
// f to zero in each object
int* lmps_stripped_neigh_list;// neighbors of one atom, used when LAMMPS
// is in molecular mode
int lmps_maxalloc; // max allocated memory value
int* kim_particleSpecies; // array of KIM particle species
double** lmps_force_tmp; // temp storage for f, when running in
// hybrid mode needed to avoid reseting
// f to zero in each object
int* lmps_stripped_neigh_list; // neighbors of one atom, used when LAMMPS
// is in molecular mode
// values used in get_neigh()
int kim_iterator_position; //get_neigh iterator current position
int kim_iterator_position; //get_neigh iterator current position
double *Rij;
// KIM specific helper functions