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
}
