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pair_kim.cpp
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pair_kim.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Ryan S. Elliott,
Valeriu Smirichinski,
Ellad Tadmor
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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>
#include <cstdlib>
// includes from LAMMPS
#include "pair_kim.h"
#include "pair_kim_version.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "memory.h"
#include "domain.h"
#include "error.h"
// includes from KIM
#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_PATCH 0
#endif
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),
lmps_num_unique_elements(0),
lmps_units(METAL),
pkim(0),
kim_ind_coordinates(-1),
kim_ind_numberOfParticles(-1),
kim_ind_numberContributingParticles(-1),
kim_ind_numberOfSpecies(-1),
kim_ind_particleSpecies(-1),
kim_ind_get_neigh(-1),
kim_ind_neighObject(-1),
kim_ind_cutoff(-1),
kim_ind_energy(-1),
kim_ind_particleEnergy(-1),
kim_ind_forces(-1),
kim_ind_virial(-1),
kim_ind_particleVirial(-1),
kim_particle_codes(0),
lmps_local_tot_num_atoms(0),
kim_global_cutoff(0.0),
lmps_maxalloc(0),
kim_particleSpecies(0),
lmps_force_tmp(0),
lmps_stripped_neigh_list(0),
kim_iterator_position(0),
Rij(0)
{
// Initialize Pair data members to appropriate values
single_enable = 0; // We do not provide the Single() function
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
// (used by kim_free(), etc.)
kim_model_init_ok = false;
kim_init_ok = false;
// END
return;
}
/* ---------------------------------------------------------------------- */
PairKIM::~PairKIM()
{
// clean up kim_modelname
if (kim_modelname != 0) delete [] kim_modelname;
// 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++)
delete [] lmps_unique_elements[i];
delete [] lmps_unique_elements;
// clean up local memory used to support KIM interface
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_species_to_uniuqe in the allocate() function
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] lmps_map_species_to_unique;
}
// clean up Rij array
memory->destroy(Rij);
// clean up KIM interface (if necessary)
kim_free();
return;
}
/* ---------------------------------------------------------------------- */
void PairKIM::compute(int eflag , int vflag)
{
int kimerror;
if (eflag || vflag)
ev_setup(eflag,vflag);
else
ev_unset();
// grow kim_particleSpecies array if necessary
// needs to be atom->nmax in length
if (atom->nmax > lmps_maxalloc) {
memory->destroy(kim_particleSpecies);
memory->destroy(lmps_force_tmp);
lmps_maxalloc = atom->nmax;
memory->create(kim_particleSpecies,lmps_maxalloc,"pair:kim_particleSpecies");
memory->create(lmps_force_tmp,lmps_maxalloc,3,"pair:lmps_force_tmp");
}
// 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 *species = atom->type;
int nall = atom->nlocal + atom->nghost;
int ielement;
for (int i = 0; i < nall; i++) {
ielement = lmps_map_species_to_unique[species[i]];
ielement = MAX(ielement,0);
// @@ 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_particleSpecies[i] = kim_particle_codes[ielement];
}
// pass current atom pointers to KIM
set_volatiles();
pkim->setm_compute_by_index(&kimerror,3*3,
kim_ind_particleEnergy, eflag_atom,
(int) kim_model_has_particleEnergy,
kim_ind_particleVirial, vflag_atom,
(int) kim_model_has_particleVirial,
kim_ind_virial, vflag_global!=0,
no_virial_fdotr_compute);
kim_error(__LINE__,"setm_compute_by_index",kimerror);
// compute via KIM model
kimerror = pkim->model_compute();
kim_error(__LINE__,"PairKIM::pkim->model_compute() error",kimerror);
// assemble force and particleVirial if needed
if (!lmps_using_newton) comm->reverse_comm_pair(this);
// sum lmps_force_tmp to f if running in hybrid mode
if (lmps_hybrid) {
double **f = atom->f;
for (int i = 0; i < nall; i++) {
f[i][0] += lmps_force_tmp[i][0];
f[i][1] += lmps_force_tmp[i][1];
f[i][2] += lmps_force_tmp[i][2];
}
}
if ((no_virial_fdotr_compute == 1) && (vflag_global))
{ // flip sign and order of virial if KIM is computing it
for (int i = 0; i < 3; ++i) virial[i] = -1.0*virial[i];
double tmp = virial[3];
virial[3] = -virial[5];
virial[4] = -virial[4];
virial[5] = -tmp;
}
else
{ // compute virial via LAMMPS fdotr mechanism
if (vflag_fdotr) virial_fdotr_compute();
}
if ((kim_model_has_particleVirial) && (vflag_atom))
{ // flip sign and order of virial if KIM is computing it
double tmp;
for (int i = 0; i < nall; ++i)
{
for (int j = 0; j < 3; ++j) vatom[i][j] = -1.0*vatom[i][j];
tmp = vatom[i][3];
vatom[i][3] = -vatom[i][5];
vatom[i][4] = -vatom[i][4];
vatom[i][5] = -tmp;
}
}
return;
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairKIM::allocate()
{
int n = atom->ntypes;
// allocate standard Pair class arrays
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
// allocate mapping array
lmps_map_species_to_unique = new int[n+1];
allocated = 1;
return;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
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");
// 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...
kim_free();
// make sure things are allocated
if (allocated != 1) allocate();
// clear setflag to ensure coeff() is called after settings()
int n = atom->ntypes;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set lmps_* bool flags
set_lmps_flags();
// set virial handling
if (strcmp(arg[0],"LAMMPSvirial") == 0)
{
no_virial_fdotr_compute = 0;
}
else if (strcmp(arg[0],"KIMvirial") == 0)
{
no_virial_fdotr_compute = 1;
}
else
{
error->all(FLERR,"Unrecognized virial argument in pair_style command");
}
// set KIM Model name
int nmlen = strlen(arg[1]);
if (kim_modelname != 0)
{
delete [] kim_modelname;
kim_modelname = 0;
}
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;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
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();
if (narg != 2 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
// 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++)
delete [] lmps_unique_elements[i];
delete [] lmps_unique_elements;
}
lmps_unique_elements = new char*[atom->ntypes];
for (i = 0; i < atom->ntypes; i++) lmps_unique_elements[i] = 0;
lmps_num_unique_elements = 0;
for (i = 2; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
if (!lmps_hybrid)
error->all(FLERR,"Invalid args for non-hybrid pair coefficients");
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_species_to_unique[i-1] = j;
if (j == lmps_num_unique_elements) {
n = strlen(arg[i]) + 1;
lmps_unique_elements[j] = new char[n];
strcpy(lmps_unique_elements[j],arg[i]);
lmps_num_unique_elements++;
}
}
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
if (lmps_map_species_to_unique[i] >= 0 &&
lmps_map_species_to_unique[j] >= 0) {
setflag[i][j] = 1;
count++;
}
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
return;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
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");
int kimerror;
// KIM and Model initialization (only once)
// also sets kim_ind_* and kim_* bool flags
if (!kim_init_ok)
{
kim_init();
kimerror = pkim->model_init();
if (kimerror != KIM_STATUS_OK)
kim_error(__LINE__, "KIM API:model_init() failed", kimerror);
else
{
kim_model_init_ok = true;
// allocate enough memory to ensure we are safe
// (by using neighbor->oneatom)
if (kim_model_using_Rij)
memory->create(Rij,3*(neighbor->oneatom),"pair:Rij");
}
}
// request none, half, or full neighbor list
// depending on KIM model requirement
int irequest = neighbor->request(this,instance_me);
if (kim_model_using_cluster)
{
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 0;
}
else
{
// make sure comm_reverse expects (at most) 9 values when newton is off
if (!lmps_using_newton) comm_reverse_off = 9;
if (kim_model_using_half)
{
neighbor->requests[irequest]->half = 1;
neighbor->requests[irequest]->full = 0;
// make sure half lists also include local-ghost pairs
if (lmps_using_newton) neighbor->requests[irequest]->newton = 2;
}
else
{
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
// make sure full lists also include local-ghost pairs
if (lmps_using_newton) neighbor->requests[irequest]->newton = 0;
}
}
return;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairKIM::init_one(int i, int j)
{
// This is called once of each (unordered) i,j pair for each
// "run ...", "minimize ...", etc. read from input
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
return kim_global_cutoff;
}
/* ---------------------------------------------------------------------- */
void PairKIM::reinit()
{
// This is called by fix-adapt
// Call parent class implementation
Pair::reinit();
// Then reinit KIM model
int kimerror;
kimerror = pkim->model_reinit();
kim_error(__LINE__,"model_reinit unsuccessful", kimerror);
}
/* ---------------------------------------------------------------------- */
int PairKIM::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
double *fp;
if (lmps_hybrid) fp = &(lmps_force_tmp[0][0]);
else fp = &(atom->f[0][0]);
m = 0;
last = first + n;
if ((kim_model_has_forces) && ((vflag_atom == 0) ||
(!kim_model_has_particleVirial)))
{
for (i = first; i < last; i++)
{
buf[m++] = fp[3*i+0];
buf[m++] = fp[3*i+1];
buf[m++] = fp[3*i+2];
}
return m;
}
else if ((kim_model_has_forces) && (vflag_atom == 1) &&
(kim_model_has_particleVirial))
{
double *va=&(vatom[0][0]);
for (i = first; i < last; i++)
{
buf[m++] = fp[3*i+0];
buf[m++] = fp[3*i+1];
buf[m++] = fp[3*i+2];
buf[m++] = va[6*i+0];
buf[m++] = va[6*i+1];
buf[m++] = va[6*i+2];
buf[m++] = va[6*i+3];
buf[m++] = va[6*i+4];
buf[m++] = va[6*i+5];
}
return m;
}
else if ((!kim_model_has_forces) && (vflag_atom == 1) &&
(kim_model_has_particleVirial))
{
double *va=&(vatom[0][0]);
for (i = first; i < last; i++)
{
buf[m++] = va[6*i+0];
buf[m++] = va[6*i+1];
buf[m++] = va[6*i+2];
buf[m++] = va[6*i+3];
buf[m++] = va[6*i+4];
buf[m++] = va[6*i+5];
}
return m;
}
else
return 0;
}
/* ---------------------------------------------------------------------- */
void PairKIM::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
double *fp;
if (lmps_hybrid) fp = &(lmps_force_tmp[0][0]);
else fp = &(atom->f[0][0]);
m = 0;
if ((kim_model_has_forces) && ((vflag_atom == 0) ||
(!kim_model_has_particleVirial)))
{
for (i = 0; i < n; i++)
{
j = list[i];
fp[3*j+0]+= buf[m++];
fp[3*j+1]+= buf[m++];
fp[3*j+2]+= buf[m++];
}
}
else if ((kim_model_has_forces) && (vflag_atom == 1) &&
(kim_model_has_particleVirial))
{
double *va=&(vatom[0][0]);
for (i = 0; i < n; i++)
{
j = list[i];
fp[3*j+0]+= buf[m++];
fp[3*j+1]+= buf[m++];
fp[3*j+2]+= buf[m++];
va[j*6+0]+=buf[m++];
va[j*6+1]+=buf[m++];
va[j*6+2]+=buf[m++];
va[j*6+3]+=buf[m++];
va[j*6+4]+=buf[m++];
va[j*6+5]+=buf[m++];
}
}
else if ((!kim_model_has_forces) && (vflag_atom == 1) &&
(kim_model_has_particleVirial))
{
double *va=&(vatom[0][0]);
for (i = 0; i < n; i++)
{
j = list[i];
va[j*6+0]+=buf[m++];
va[j*6+1]+=buf[m++];
va[j*6+2]+=buf[m++];
va[j*6+3]+=buf[m++];
va[j*6+4]+=buf[m++];
va[j*6+5]+=buf[m++];
}
}
else
;// do nothing
return;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairKIM::memory_usage()
{
double bytes = lmps_maxalloc * sizeof(int);
return bytes;
}
/* ----------------------------------------------------------------------
KIM-specific interface
------------------------------------------------------------------------- */
void PairKIM::kim_error(int ln, const char* msg, int errcode)
{
if (errcode == KIM_STATUS_OK) return;
KIM_API_model::report_error(ln,(char *) __FILE__, (char *) msg,errcode);
error->all(__FILE__,ln,"Internal KIM error");
return;
}
/* ---------------------------------------------------------------------- */
int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
int *atom, int *numnei, int **nei1atom, double **pRij)
{
KIM_API_model *pkim = (KIM_API_model *) *kimmdl;
int 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 * )
// (*pkim).get_data_by_index(self->kim_ind_neighObject, &kimerror);
NeighList * neiobj = self->list;
// subvert KIM api by using direct acces to self->lmps_local_tot_num_atoms
//
//int * pnAtoms = (int *)
// (*pkim).get_data_by_index(self->kim_ind_numberOfParticles, &kimerror);
//int nAtoms = *pnAtoms;
int nAtoms = self->lmps_local_tot_num_atoms;
int j, jj, inum, *ilist, *numneigh, **firstneigh;
inum = neiobj->inum; //# of I atoms neighbors are stored for
ilist = neiobj->ilist; //local indices of I atoms
numneigh = neiobj->numneigh; // # of J neighbors for each I atom
firstneigh = neiobj->firstneigh; // ptr to 1st J int value of each I atom
if (*mode==0){ //iterator mode
if (*request==1) { //increment iterator
if (self->kim_iterator_position < inum) {
*atom = ilist[self->kim_iterator_position];
*numnei = numneigh[*atom];
// strip off neighbor mask for molecular systems
if (!self->lmps_using_molecular)
*nei1atom = firstneigh[*atom];
else
{
int n = *numnei;
int *ptr = firstneigh[*atom];
int *lmps_stripped_neigh_list = self->lmps_stripped_neigh_list;
for (int i = 0; i < n; i++)
lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK;
*nei1atom = lmps_stripped_neigh_list;
}
// set Rij if needed
if (self->kim_model_using_Rij) {
double* x = (double *)
(*pkim).get_data_by_index(self->kim_ind_coordinates,
&kimerror);
for (jj=0; jj < *numnei; jj++) {
int i = *atom;
j = (*nei1atom)[jj];
self->Rij[jj*3 +0] = -x[i*3+0] + x[j*3+0];
self->Rij[jj*3 +1] = -x[i*3+1] + x[j*3+1];
self->Rij[jj*3 +2] = -x[i*3+2] + x[j*3+2];
}
}
// increment iterator
self->kim_iterator_position++;
return KIM_STATUS_OK; //successful increment
} else if (self->kim_iterator_position == inum) {
*numnei = 0;
return KIM_STATUS_NEIGH_ITER_PAST_END; //reached end by iterator
} else if (self->kim_iterator_position > inum || inum < 0){
self->error->one(FLERR, "KIM neighbor iterator exceeded range");
}
} else if (*request == 0){ //restart iterator
self->kim_iterator_position = 0;
*numnei = 0;
return KIM_STATUS_NEIGH_ITER_INIT_OK; //succsesful restart
}
} else if (*mode == 1){//locator mode
//...
if (*request < inum) {
*atom = *request;
*numnei = numneigh[*atom];
// strip off neighbor mask for molecular systems
if (!self->lmps_using_molecular)
*nei1atom = firstneigh[*atom];
else
{
int n = *numnei;
int *ptr = firstneigh[*atom];
int *lmps_stripped_neigh_list = self->lmps_stripped_neigh_list;
for (int i = 0; i < n; i++)
lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK;
*nei1atom = lmps_stripped_neigh_list;
}
// set Rij if needed
if (self->kim_model_using_Rij){
double* x = (double *)
(*pkim).get_data_by_index(self->kim_ind_coordinates, &kimerror);
for(int jj=0; jj < *numnei; jj++){
int i = *atom;
int j = (*nei1atom)[jj];
self->Rij[jj*3 +0] = -x[i*3+0] + x[j*3+0];
self->Rij[jj*3 +1] = -x[i*3+1] + x[j*3+1];
self->Rij[jj*3 +2] = -x[i*3+2] + x[j*3+2];
}
}
return KIM_STATUS_OK; //successful end
}
else if (*request >= nAtoms || inum < 0)
return KIM_STATUS_NEIGH_INVALID_REQUEST;
else if (*request >= inum) {
*atom = *request;
*numnei = 0;
return KIM_STATUS_OK; //successfull but no neighbors in the list
}
} else return KIM_STATUS_NEIGH_INVALID_MODE; //invalid mode
return -16; //should not get here: unspecified error
}
/* ---------------------------------------------------------------------- */
void PairKIM::kim_free()
{
int kimerror;
if (kim_model_init_ok)
{
kimerror = pkim->model_destroy();
kim_model_init_ok = false;
}
if (kim_init_ok)
{
pkim->free(&kimerror);
kim_init_ok = false;
}
if (pkim != 0)
{
delete pkim;
pkim = 0;
}
if (kim_particle_codes_ok)
{
delete [] kim_particle_codes;
kim_particle_codes = 0;
kim_particle_codes_ok = false;
}
return;
}
/* ---------------------------------------------------------------------- */
void PairKIM::kim_init()
{
int kimerror;
//
// determine KIM Model capabilities (used in this function below)
set_kim_model_has_flags();
// create appropriate KIM descriptor file
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();
kimerror = pkim->string_init(test_descriptor_string, kim_modelname);
if (kimerror != KIM_STATUS_OK)
kim_error(__LINE__,"KIM initialization failed", kimerror);
else
{
kim_init_ok = true;
delete [] test_descriptor_string;
test_descriptor_string = 0;
}
// determine kim_model_using_* true/false values
//
// check for half or full list
kim_model_using_half = (pkim->is_half_neighbors(&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));
// 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,
#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,
(int) kim_model_has_particleEnergy,
"energy", &kim_ind_energy, (int) kim_model_has_energy,
"forces", &kim_ind_forces, (int) kim_model_has_forces,
"neighObject", &kim_ind_neighObject, (int) !kim_model_using_cluster,
"get_neigh", &kim_ind_get_neigh, (int) !kim_model_using_cluster,
"particleVirial", &kim_ind_particleVirial,
(int) kim_model_has_particleVirial,
"virial", &kim_ind_virial, no_virial_fdotr_compute);
kim_error(__LINE__,"getm_index",kimerror);
// 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_species_code(lmps_unique_elements[i], &kimerror);
kim_error(__LINE__, "create_kim_particle_codes: symbol not found ",
kimerror);
}
// set pointer values in KIM API object that will not change during run
set_statics();
return;
}
/* ---------------------------------------------------------------------- */
void PairKIM::set_statics()
{
// set total number of atoms
lmps_local_tot_num_atoms = (int) (atom->nghost + atom->nlocal);
int kimerror;
pkim->setm_data_by_index(&kimerror, 4*6,
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),
(int) kim_model_using_half,
kim_ind_energy, 1, (void *) &(eng_vdwl), (int) kim_model_has_energy,
kim_ind_virial, 1, (void *) &(virial[0]), no_virial_fdotr_compute);
kim_error(__LINE__, "setm_data_by_index", kimerror);
if (!kim_model_using_cluster)
{
kimerror = pkim->set_method_by_index(kim_ind_get_neigh, 1,
(func_ptr) &get_neigh);
kim_error(__LINE__, "set_method_by_index", kimerror);
}
pkim->set_sim_buffer((void *)this, &kimerror);
kim_error(__LINE__, "set_sim_buffer", kimerror);
return;
}
/* ---------------------------------------------------------------------- */
void PairKIM::set_volatiles()
{
int kimerror;
lmps_local_tot_num_atoms = (int) (atom->nghost + atom->nlocal);
intptr_t nall = (intptr_t) lmps_local_tot_num_atoms;
pkim->setm_data_by_index(&kimerror, 4*2,
kim_ind_coordinates, 3*nall, (void*) &(atom->x[0][0]), 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))
{
kimerror = pkim->set_data_by_index(kim_ind_particleEnergy, nall,
(void*) eatom);
kim_error(__LINE__, "set_data_by_index", kimerror);
}
if (kim_model_has_particleVirial && (vflag_atom == 1))
{
kimerror = pkim->set_data_by_index(kim_ind_particleVirial, 6*nall,
(void*) &(vatom[0][0]));
kim_error(__LINE__, "set_data_by_index", kimerror);
}
if (kim_model_has_forces)
{
if (lmps_hybrid)
kimerror = pkim->set_data_by_index(kim_ind_forces, nall*3,
(void*) &(lmps_force_tmp[0][0]));
else
kimerror = pkim->set_data_by_index(kim_ind_forces, nall*3,
(void*) &(atom->f[0][0]));
kim_error(__LINE__, "setm_data_by_index", kimerror);
}
// subvert the KIM api by direct access to this->list in get_neigh
//
//if (!kim_model_using_cluster)
// kimerror = pkim->set_data_by_index(kim_ind_neighObject, 1,
// (void*) this->list);
if (kim_model_has_particleVirial)
{
if(vflag_atom != 1) {
pkim->set_compute_by_index(kim_ind_particleVirial, KIM_COMPUTE_FALSE,
&kimerror);
} else {
pkim->set_compute_by_index(kim_ind_particleVirial, KIM_COMPUTE_TRUE,
&kimerror);
}
}
if (no_virial_fdotr_compute == 1)
{
pkim->set_compute_by_index(kim_ind_virial,
((vflag_global != 1) ? KIM_COMPUTE_FALSE : KIM_COMPUTE_TRUE),
&kimerror);
}
return;
}
/* ---------------------------------------------------------------------- */
void PairKIM::set_lmps_flags()
{
// determint if newton is on or off
lmps_using_newton = (force->newton_pair == 1);
// setup lmps_stripped_neigh_list for neighbors of one atom, if needed
lmps_using_molecular = (atom->molecular > 0);
if (lmps_using_molecular) {
memory->destroy(lmps_stripped_neigh_list);
memory->create(lmps_stripped_neigh_list,neighbor->oneatom,
"pair:lmps_stripped_neigh_list");
}
// determine if running with pair hybrid
lmps_hybrid = (force->pair_match("hybrid",0));
// support cluster mode if everything is just right
lmps_support_cluster = ((domain->xperiodic == 0 &&
domain->yperiodic == 0 &&
domain->zperiodic == 0
)
&&
(comm->nprocs == 1)
);
// determine unit system and set lmps_units flag
if ((strcmp(update->unit_style,"real")==0))
lmps_units = REAL;
else if ((strcmp(update->unit_style,"metal")==0))
lmps_units = METAL;
else if ((strcmp(update->unit_style,"si")==0))
lmps_units = SI;
else if ((strcmp(update->unit_style,"cgs")==0))
lmps_units = CGS;
else if ((strcmp(update->unit_style,"electron")==0))
lmps_units = ELECTRON;
else if ((strcmp(update->unit_style,"lj")==0))
error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models");
else
error->all(FLERR,"Unknown unit_style");
return;
}
/* ---------------------------------------------------------------------- */
void PairKIM::set_kim_model_has_flags()
{
KIM_API_model mdl;
int kimerror;
// get KIM API object representing the KIM Model only
kimerror = mdl.model_info(kim_modelname);
kim_error(__LINE__,"KIM initialization failed", kimerror);
// 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)
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)
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)
error->warning(FLERR,"KIM Model does not provide `particleEnergy'; "
"energy per atom will be zero");
// determine if the KIM Model can compute the particleVerial
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 ||
(kimerror == KIM_STATUS_OK);
if (!kim_model_has_particleVirial)
error->warning(FLERR,"KIM Model does not provide `particleVirial'; "
"virial per atom will be zero");
// tear down KIM API object
mdl.free(&kimerror);
// now destructor will do the remaining tear down for mdl
return;
}
/* ---------------------------------------------------------------------- */
void PairKIM::write_descriptor(char** test_descriptor_string)
{
// allocate memory
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];
// initialize
strcpy(*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 "
"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"
"# 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
"# Base units\n");
switch (lmps_units)
{
case REAL:
strcat(*test_descriptor_string,
"Unit_length := A\n"
"Unit_energy := kcal/mol\n"
"Unit_charge := e\n"
"Unit_temperature := K\n"
"Unit_time := fs\n\n");
break;
case METAL:
strcat(*test_descriptor_string,
"Unit_length := A\n"
"Unit_energy := eV\n"
"Unit_charge := e\n"
"Unit_temperature := K\n"
"Unit_time := ps\n\n");
break;
case SI:
strcat(*test_descriptor_string,
"Unit_length := m\n"
"Unit_energy := J\n"
"Unit_charge := C\n"
"Unit_temperature := K\n"
"Unit_time := s\n\n");
break;
case CGS:
strcat(*test_descriptor_string,
"Unit_length := cm\n"
"Unit_energy := erg\n"
"Unit_charge := statC\n"
"Unit_temperature := K\n"
"Unit_time := s\n\n");
break;
case ELECTRON:
strcat(*test_descriptor_string,
"Unit_length := Bohr\n"
"Unit_energy := Hartree\n"
"Unit_charge := e\n"
"Unit_temperature := K\n"
"Unit_time := fs\n\n");
break;
}
// 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");
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],
"spec", code++);
strcat(*test_descriptor_string, tmp_line);
}
delete [] tmp_line;
tmp_line = 0;
strcat(*test_descriptor_string, "\n");
// Write conventions section
strcat(*test_descriptor_string,
"\n"
"CONVENTIONS:\n"
"# Name Type\n"
"ZeroBasedLists flag\n");
// can use iterator or locator neighbor mode, unless in hybrid mode
if (lmps_hybrid)
strcat(*test_descriptor_string,
"Neigh_IterAccess flag\n");
else
strcat(*test_descriptor_string,
"Neigh_BothAccess flag\n\n");
strcat(*test_descriptor_string,
"NEIGH_PURE_H flag\n"
"NEIGH_PURE_F flag\n"
"NEIGH_RVEC_H flag\n"
"NEIGH_RVEC_F flag\n");
// @@ add code for MI_OPBC_? support ????
if (lmps_support_cluster)
{
strcat(*test_descriptor_string,
"CLUSTER flag\n\n");
}
else
{
strcat(*test_descriptor_string, "\n");
}
// Write input section
strcat(*test_descriptor_string,
"\n"
"MODEL_INPUT:\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"
"particleTypes integer none "
#else
"numberOfSpecies integer none []\n"
"particleSpecies integer none "
#endif
"[numberOfParticles]\n"
"coordinates double length "
"[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"
"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");
if (!kim_model_has_particleEnergy) strcat(*test_descriptor_string, "# ");
strcat(*test_descriptor_string,
"particleEnergy double energy "
"[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");
strcat(*test_descriptor_string,
"#\n"
"# END OF KIM DESCRIPTOR FILE\n"
"#\n");
return;
}
void *PairKIM::extract(const char *str, int &dim)
{
void *paramData;
int kimerror=0;
int ier;
int dummyint;
int isIndexed = 0;
int maxLine = 1024;
int rank;
int validParam = 0;
int numParams;
int *speciesIndex = new int[maxLine];
char *paramStr = new char[maxLine];
char *paramName;
char *indexStr;
char message[maxLine];
int offset;
double* paramPtr;
// set dim to 0, we will always deal with scalars to circumvent lammps species
// indexing
dim = 0;
// copy the input str into paramStr for parsing
strcpy(paramStr, str);
// get the name of the parameter (whatever is before ":")
paramName = strtok(paramStr, ":");
if (0 == strcmp(paramName, str))
paramName = (char*) str;
else
isIndexed = 1;
// parse the rest of the string into tokens deliminated by "," and convert
// them to integers, saving them into speciesIndex
int count = -1;
if (isIndexed == 1)
{
while((indexStr = strtok(NULL, ",")) != NULL)
{
count++;
ier = sscanf(indexStr, "%d", &speciesIndex[count]);
if (ier != 1)
{
ier = -1;
break;
}
}
}
if (ier == -1)
{
delete [] speciesIndex, speciesIndex = 0;
delete [] paramStr, paramStr = 0;
kim_error(__LINE__,"error in PairKIM::extract(), invalid parameter-indicie format", KIM_STATUS_FAIL);
}
// check to make sure that the requested parameter is a valid free parameter
kimerror = pkim->get_num_params(&numParams, &dummyint);
kim_error(__LINE__, "get_num_free_params", kimerror);
char **freeParamNames = new char*[numParams];
for (int k = 0; k < numParams; k++)
{
kimerror = pkim->get_free_parameter(k, (const char**) &freeParamNames[k]);
kim_error(__LINE__, "get_free_parameter", kimerror);
if (0 == strcmp(paramName, freeParamNames[k]))
{
validParam = 1;
break;
}
}
delete [] freeParamNames, freeParamNames = 0;
if (validParam == 0)
{
sprintf(message, "Invalid parameter to adapt: \"%s\" is not a FREE_PARAM", paramName);
delete [] speciesIndex, speciesIndex = 0;
delete [] paramStr, paramStr = 0;
kim_error(__LINE__, message, KIM_STATUS_FAIL);
}
// get the parameter arry from pkim object
paramData = pkim->get_data(paramName, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
delete [] speciesIndex, speciesIndex = 0;
delete [] paramStr, paramStr = 0;
}
kim_error(__LINE__,"get_data",kimerror);
// get rank and shape of parameter
rank = (*pkim).get_rank(paramName, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
delete [] speciesIndex, speciesIndex = 0;
delete [] paramStr, paramStr = 0;
}
kim_error(__LINE__,"get_rank",kimerror);
int *shape = new int[maxLine];
dummyint = (*pkim).get_shape(paramName, shape, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
delete [] speciesIndex, speciesIndex = 0;
delete [] paramStr, paramStr = 0;
delete [] shape, shape = 0;
}
kim_error(__LINE__,"get_shape",kimerror);
delete [] paramStr, paramStr = 0;
// check that number of inputs is rank, and that input indicies are less than
// their respective dimensions in shape
if ((count+1) != rank)
{
sprintf(message, "Number of input indicies not equal to rank of specified parameter (%d)", rank);
kimerror = KIM_STATUS_FAIL;
delete [] speciesIndex, speciesIndex = 0;
delete [] shape, shape = 0;
kim_error(__LINE__,message, kimerror);
}
if (isIndexed == 1)
{
for (int i=0; i <= count; i++)
{
if (shape[i] <= speciesIndex[i] || speciesIndex[i] < 0)
{
kimerror = KIM_STATUS_FAIL;
break;
}
}
}
delete [] shape, shape = 0;
if (kimerror == KIM_STATUS_FAIL)
{
sprintf(message, "One or more parameter indicies out of bounds");
delete [] speciesIndex, speciesIndex = 0;
kim_error(__LINE__, message, kimerror);
}
// Cast it to a double
paramPtr = static_cast<double*>(paramData);
// If it is indexed (not just a scalar for the whole model), then get pointer
// corresponding to specified indicies by calculating the adress offset using
// specified indicies and the shape
if (isIndexed == 1)
{
offset = 0;
for (int i = 0; i < (rank-1); i++)
{
offset = (offset + speciesIndex[i]) * shape[i+1];
}
offset = offset + speciesIndex[(rank - 1)];
paramPtr = (paramPtr + offset);
}
delete [] speciesIndex, speciesIndex = 0;
return ((void*) paramPtr);
}

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