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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7613 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-01-31 00:13:02 +00:00
parent 80e8507fd9
commit 17f864c481
3 changed files with 85 additions and 113 deletions
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2
src/GPU/Install.sh
View File

@ -15,7 +15,7 @@ if (test $1 = 1) then
if (test -e ../Makefile.package.settings) then
sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings
sed -i '4 i include ..\/..\/lib\/gpu\/Makefile.lammps' ../Makefile.package.settings
sed -i -e '4 i include ..\/..\/lib\/gpu\/Makefile.lammps' ../Makefile.package.settings
fi
if (test -e ../pair_yukawa.cpp) then

190
src/KIM/pair_kim.cpp
View File

@ -31,11 +31,13 @@
#include "memory.h"
#include "error.h"
#include <iostream>
#include "KIMservice.h"
using namespace LAMMPS_NS;
using namespace std;
// allocate space for static class variable
PairKIM *PairKIM::self;
/* ---------------------------------------------------------------------- */
@ -51,6 +53,8 @@ PairKIM::PairKIM(LAMMPS *lmp) : Pair(lmp)
modelname = NULL;
testname = NULL;
self = this;
// reverse comm even if newton off
comm_reverse_off = 9;
@ -80,19 +84,13 @@ PairKIM::~PairKIM()
void PairKIM::compute(int eflag , int vflag)
{
if (eflag || vflag) {
if (vflag) ev_setup(eflag,5);
else ev_setup(eflag,vflag);
}
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom =
vflag_global = vflag_atom = 0;
set_volatiles();
long long nall = (long long) (atom->nghost + atom->nlocal);
int energyPerAtom_flag =0, virialPerAtom_flag=0,
process_d1Edr_flag=0, virialGlobal_flag=0;
int energyPerAtom_flag,virialPerAtom_flag,virialGlobal_flag;
int kimerr;
if (eflag_atom==1) energyPerAtom_flag=1;
@ -104,42 +102,32 @@ void PairKIM::compute(int eflag , int vflag)
if (vflag_global ==1) virialGlobal_flag =1;
else virialGlobal_flag =0;
if (process_d1Edr_ind >=0) if (vflag_atom==1 || vflag_global==1) {
process_d1Edr_flag =1;
}else {
process_d1Edr_flag=0;
int process_d1Edr_flag=0;
if (process_d1Edr_ind >= 0) {
if (vflag_atom==1 || vflag_global==1) process_d1Edr_flag =1;
else process_d1Edr_flag=0;
}
pkim->set_compute_byI_multiple(&kimerr,12, energyPerAtom_ind,
energyPerAtom_flag,1,
virialPerAtom_ind,virialPerAtom_flag,1,
virialPerAtom_ind,virialPerAtom_flag,1,
virialGlobal_ind,virialGlobal_flag,1,
process_d1Edr_ind,process_d1Edr_flag,1);
err_treat(__LINE__,"set_compute_byI_multiple",kimerr);
kim_error(__LINE__,"set_compute_byI_multiple",kimerr);
init2zero(pkim,&kimerr);
err_treat(__LINE__,"PairKIM::init2zero(..)",kimerr);
kim_error(__LINE__,"PairKIM::init2zero(..)",kimerr);
pkim->model_compute(&kimerr);
kim_error(__LINE__,"PairKIM::pkim->model_compute() error",kimerr);
err_treat(__LINE__,"PairKIM::pkim->model_compute() error",kimerr);
static int runs=0;
if (runs < 1) {
runs++;
cout<<"nghost = "<<atom->nghost<<", nlocals = "<<atom->nlocal<<endl;
cout<<"NBC method: "<<(char *) pkim->get_NBC_method(&kimerr)<<endl;
}
comm->reverse_comm_pair(this);
if(virialGlobal_flag==1 && !pkim->virialGlobal_need2add ){
for(int i=0; i<6;i++) virial[i]=-1.0*virial[i];
}
if(virialPerAtom_flag==1 && !pkim->virialPerAtom_need2add ){
for(int i=0; i<atom->nlocal;i++)
for(int j=0; j<6;j++) vatom[i][j]=-1.0*vatom[i][j];
}
if (virialGlobal_flag==1 && !pkim->virialGlobal_need2add)
for(int i=0; i<6;i++) virial[i]=-1.0*virial[i];
if (virialPerAtom_flag==1 && !pkim->virialPerAtom_need2add)
for(int i = 0; i < atom->nlocal; i++)
for(int j=0; j<6;j++) vatom[i][j] = -1.0*vatom[i][j];
}
/* ----------------------------------------------------------------------
@ -230,7 +218,7 @@ void PairKIM::coeff(int narg, char **arg)
my_init();
if (!pkim->model_init())
err_treat(__LINE__,"KIM API:model_init() failed",-1);
kim_error(__LINE__,"KIM API:model_init() failed",-1);
// clear setflag since coeff() called once with I,J = * *
@ -353,6 +341,16 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf)
KIM-specific interface
------------------------------------------------------------------------- */
void PairKIM::kim_error(int ln, const char* msg, int errcode)
{
if (errcode == 1) return;
KIM_API_model::report_error(ln,(char *) __FILE__,
(char *) msg,errcode);
error->all(__FILE__,ln,"Internal KIM error");
}
/* ---------------------------------------------------------------------- */
int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
int *atom, int *numnei, int **nei1atom, double **pRij)
{
@ -369,19 +367,17 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
int kimerr;
neighObject_ind = pkim->get_index((char*) "neighObject",&kimerr);
err_treat(__LINE__,"get_neigh:get_index of : neighObject",kimerr);
self->kim_error(__LINE__,"get_neigh:get_index of : neighObject",kimerr);
NeighList * neiobj = (NeighList * ) (*pkim)[neighObject_ind].data;
cout<<"inum="<<neiobj->inum;
cout<<", ghostflag ="<<neiobj->ghostflag<<" requires full neighbor? :"<<pkim->requiresFullNeighbors()<<endl;
numberOfAtoms_ind= pkim->get_index((char *) "numberOfAtoms",&kimerr);
err_treat(__LINE__,"get_neigh:get_index of : neighObject",kimerr);
self->kim_error(__LINE__,"get_neigh:get_index of : neighObject",kimerr);
key1strun=false;
coordinates_ind= pkim->get_index((char *) "coordinates",&kimerr);
err_treat(__LINE__,"get_neigh:get_index of : coordinates",kimerr);
self->kim_error(__LINE__,"get_neigh:get_index of : coordinates",kimerr);
key1strun=false;
}
@ -404,9 +400,7 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
return KIM_STATUS_NEIGH_ITER_INIT_OK; //succsesful restart
} else if(*request==1){//increment iterator
if (pointsto > inum || inum <0){
printf("pair_KIM: iterator is >= then numnei or < 0\n");
cout<<" pointsto ="<<pointsto<<" inum="<<inum<<endl;
exit (237);
self->error->one(FLERR,"KIM neighbor iterator exceeded range");
}else if(pointsto == inum) {
pointsto ==0;
*numnei=0;
@ -425,7 +419,6 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
Rij[jj*3 +0] = -x[i*3+0] + x[j*3+0];
Rij[jj*3 +1] = -x[i*3+1] + x[j*3+1];
Rij[jj*3 +2] = -x[i*3+2] + x[j*3+2];
}
}
return KIM_STATUS_OK;//successful increment
@ -442,7 +435,8 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
*atom=ilist[*request];
*numnei=numneigh[*request];
*nei1atom = firstneigh[*request];
if(*numnei > KIM_API_MAX_NEIGHBORS) return KIM_STATUS_NEIGH_TOO_MANY_NEIGHBORS;
if (*numnei > KIM_API_MAX_NEIGHBORS)
return KIM_STATUS_NEIGH_TOO_MANY_NEIGHBORS;
if (pkim->support_Rij){
for(int jj=0; jj < *numnei; jj++){
int i = *atom;
@ -467,7 +461,6 @@ void PairKIM::my_free(){
pkim->model_destroy(&kimerr);
pkim->free();
// cout<<(*pkim);
delete pkim;
if (atypeMapKIM != NULL) delete [] atypeMapKIM;
@ -490,32 +483,34 @@ void PairKIM::my_init()
char * kim_models_dir = getenv("KIM_MODELS_DIR");
char * current_path = getenv("PWD");
if (kim_dir == NULL)
cout<<"pair_KIM: error in initialization: env KIM_DIR is not set"<<endl;
error->all(FLERR,"KIM_DIR environement variable is unset");
if (current_path == NULL)
error->all(FLERR,"PWD environement variable is unset");
if (current_path == NULL)
cout<<"pair_KIM: error in initialization: env PWD is not supported on OS system"<<endl;
if (kim_models_dir == NULL) {
strcat(modelfile,kim_dir);strcat(modelfile,"MODELs/");
strcat(modelfile,modelname); strcat(modelfile,"/");
strcat(modelfile,modelname); strcat(modelfile,".kim");
}else{
strcat(modelfile,kim_models_dir);strcat(modelfile,modelname);
strcat(modelfile,"/");
strcat(modelfile,modelname);
strcat(modelfile,".kim");
}
strcat(testfile,current_path); strcat(testfile,"/");
strcat(testfile,testname);strcat(testfile,".kim");
if (kim_models_dir == NULL) {
strcat(modelfile,kim_dir);strcat(modelfile,"MODELs/");
strcat(modelfile,modelname); strcat(modelfile,"/");
strcat(modelfile,modelname); strcat(modelfile,".kim");
}else{
strcat(modelfile,kim_models_dir);strcat(modelfile,modelname);
strcat(modelfile,"/");
strcat(modelfile,modelname);
strcat(modelfile,".kim");
}
strcat(testfile,current_path); strcat(testfile,"/");
strcat(testfile,testname);strcat(testfile,".kim");
// now testfile and modelfile are set
// now testfile and modelfile are set
int kimerr;
int kimerr;
if (!(strcmp(update->unit_style,"metal")==0))
err_treat(__LINE__,"LAMMPS unit_style must be metal to work with KIM models",-12);
if (!(strcmp(update->unit_style,"metal")==0))
self->kim_error(__LINE__,
"LAMMPS unit_style must be metal to "
"work with KIM models",-12);
// create temporary kim file
test_descriptor_string = new char[80*60];
for(int i=50;i<80*60;i++) test_descriptor_string[i]='\0';
@ -661,7 +656,7 @@ void PairKIM::my_init()
//check if Rij needed for get_neigh
char * NBC_method =(char *) pkim->get_NBC_method(&kimerr);
err_treat(__LINE__,"NBC method not set",kimerr);
self->kim_error(__LINE__,"NBC method not set",kimerr);
support_Rij=false;
if (strcmp(NBC_method,"NEIGH-RVEC-F")==0) support_Rij=true;
delete [] NBC_method;
@ -672,10 +667,8 @@ void PairKIM::my_init()
void PairKIM::my_init2()
{
pkim = new KIM_API_model();
if(!pkim->init_str_testname(test_descriptor_string,modelname)){
cout<<"pkim: error in initialization "<<endl;
exit (357);
}
if (!pkim->init_str_testname(test_descriptor_string,modelname))
error->all(FLERR,"KIM initialization failed");
delete [] test_descriptor_string;
@ -696,13 +689,13 @@ void PairKIM::my_init2()
"virialPerAtom", &virialPerAtom_ind,1,
"virialGlobal", &virialGlobal_ind,1,
"process_d1Edr",&process_d1Edr_ind,1 );
err_treat(__LINE__,"get_index_multiple",kimerr);
self->kim_error(__LINE__,"get_index_multiple",kimerr);
if(support_atypes){
numberAtomTypes_ind = pkim->get_index((char *) "numberAtomTypes",&kimerr);
err_treat(__LINE__,"numberAtomTypes",kimerr);
self->kim_error(__LINE__,"numberAtomTypes",kimerr);
atomTypes_ind = pkim->get_index((char *) "atomTypes",&kimerr);
err_treat(__LINE__,"atomTypes",kimerr);
self->kim_error(__LINE__,"atomTypes",kimerr);
}
set_statics();
@ -717,20 +710,21 @@ void PairKIM:: create_atypeMapKIM()
atypeMapKIM[i*2 + 0] = i;
int kimerr;
atypeMapKIM[i*2 + 1] = pkim->get_aTypeCode(elements[i],&kimerr);
err_treat(__LINE__,"create_atypeMapKIM: symbol not found ",kimerr);
self->kim_error(__LINE__,"create_atypeMapKIM: symbol not found ",kimerr);
}
atomTypes=NULL;
}
/* ---------------------------------------------------------------------- */
void PairKIM::atypeMap2KIM(){
static long long n=0;
if (n!= (long long)localnall) {
n=(long long)localnall;
if (atomTypes != NULL) delete [] atomTypes;
atomTypes = new int[n];
}
void PairKIM::atypeMap2KIM()
{
static long long n=0;
if (n!= (long long)localnall) {
n=(long long)localnall;
if (atomTypes != NULL) delete [] atomTypes;
atomTypes = new int[n];
}
int itype;
int *type = atom->type;
@ -743,9 +737,9 @@ void PairKIM::atypeMap2KIM(){
}
/* ---------------------------------------------------------------------- */
void PairKIM::set_statics(){ //set pointers that are fixed (never reallocated)
//set pointers that are fixed (never reallocated)
void PairKIM::set_statics()
{
if(support_atypes)
pkim->set_data_byi(numberAtomTypes_ind,1,(void *) &(atom->ntypes )) ;
if ( process_d1Edr_ind >= 0 )
@ -759,7 +753,7 @@ void PairKIM::set_statics(){ //set pointers that are fixed (never reallocated)
get_full_neigh_ind,1,(void *) &get_neigh,1,
numberOfAtoms_ind,1, (void *) &localnall,1,
virialGlobal_ind,1,(void *)&(virial[0]),1);
err_treat(__LINE__,"set_data_byI_multiple",kimerr);
self->kim_error(__LINE__,"set_data_byI_multiple",kimerr);
pkim->set_data((char *) "numberContributingAtoms",1,(void *)&(atom->nlocal));
}
@ -769,7 +763,7 @@ void PairKIM::set_statics(){ //set pointers that are fixed (never reallocated)
void PairKIM::set_volatiles()
{ //set pointers that might be reallocated
localnall = (int) (atom->nghost + atom->nlocal);
long long nall= (long long) localnall;
bigint nall = (bigint) localnall;
pkim->set_data_byi(coordinates_ind,nall*3,(void *) &(atom->x[0][0]) );
pkim->set_data_byi(forces_ind,nall*3,(void *) &(atom->f[0][0]) ) ;
@ -867,8 +861,6 @@ void PairKIM::process_d1Edr(KIM_API_model **ppkim,
v=-(*de)/(*r);
if (virialGlobal_flag ==1 && pkim->virialGlobal_need2add) {
static int numruns1 =0;
if (numruns1 <1) cout<<"*********** global virial computing from pair_KIM!!!*********"<<endl;numruns1++;
vir[0] = v * dx[0] * dx[0];
vir[1] = v * dx[1] * dx[1];
vir[2] = v * dx[2] * dx[2];
@ -884,8 +876,6 @@ void PairKIM::process_d1Edr(KIM_API_model **ppkim,
}
if (virialPerAtom_flag==1 && pkim->virialPerAtom_need2add ){
static int numruns =0;
if (numruns <1) cout<<"*********** virial computing from pair_KIM!!!*********"<<endl;numruns++;
vir[0] =0.5 * v * dx[0] * dx[0];
vir[1] =0.5 * v * dx[1] * dx[1];
vir[2] =0.5 * v * dx[2] * dx[2];
@ -909,21 +899,3 @@ void PairKIM::process_d1Edr(KIM_API_model **ppkim,
*ier = KIM_STATUS_OK;
}
/* ---------------------------------------------------------------------- */
void PairKIM::err_treat(const char* msg, int errcode)
{
if (KIM_API_model::report_error(__LINE__,(char *) __FILE__,
(char *) msg,errcode) < 1)
exit(327);
}
/* ---------------------------------------------------------------------- */
void PairKIM::err_treat(int ln, const char* msg, int errcode)
{
if (KIM_API_model::report_error(ln,(char *) __FILE__,
(char *) msg,errcode) < 1)
exit(327);
}

6
src/KIM/pair_kim.h
View File

@ -49,6 +49,8 @@ class PairKIM : public Pair {
// KIM data
static PairKIM *self;
KIM_API_model *pkim;
int coordinates_ind,numberOfAtoms_ind,numberAtomTypes_ind;
int atomTypes_ind,compute_ind;
@ -69,6 +71,7 @@ class PairKIM : public Pair {
int *atypeMapKIM;
int *atomTypes; // atom types converted to KIM indices
void kim_error(int, const char *, int);
void my_init();
void my_init2();
void my_free();
@ -88,11 +91,8 @@ class PairKIM : public Pair {
static void process_d1Edr_init(KIM_API_model **,
double *, double *, double **,
int *, int *, int *);
static void process_d1Edr_fast();
static void process_d1Edr(KIM_API_model **, double *, double *,
double **, int *, int *, int *);
static void err_treat(const char *, int);
static void err_treat(int, const char *, int);
};
}