ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7639 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2012-02-01 15:32:01 +00:00
parent 385e3c6576
commit 44b7f26dd7
2 changed files with 34 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files

41
src/KIM/pair_kim.cpp
View File

@ -46,6 +46,11 @@ PairKIM::PairKIM(LAMMPS *lmp) : Pair(lmp)
nelements = 0;
elements = NULL;
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
no_virial_fdotr_compute = 1;
virialGlobal_ind = -1;
virialPerAtom_ind = -1;
process_d1Edr_ind = -1;
@ -55,6 +60,7 @@ PairKIM::PairKIM(LAMMPS *lmp) : Pair(lmp)
maxall = 0;
kimtype = NULL;
onebuf = NULL;
// static pointer that static callbacks can use to access class variables
@ -77,6 +83,7 @@ PairKIM::~PairKIM()
delete [] testname;
memory->destroy(kimtype);
memory->destroy(onebuf);
if (allocated) {
memory->destroy(setflag);
@ -277,6 +284,14 @@ void PairKIM::init_style()
if (force->newton_pair != 0)
error->all(FLERR,"Pair style pair_KIM requires newton pair Off");
// setup onebuf for neighbors of one atom if needed
molecular = atom->molecular;
if (molecular) {
memory->destroy(onebuf);
memory->create(onebuf,neighbor->oneatom,"pair:onebuf");
}
// request half or full neighbor list depending on KIM model requirement
int irequest = neighbor->request(this);
@ -446,17 +461,17 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
*numnei=0;
return KIM_STATUS_NEIGH_ITER_PAST_END; //reached end by iterator
}else{
*numnei = numneigh[pointsto] ;
*atom =ilist[pointsto];
*numnei = numneigh[pointsto];
*atom = ilist[pointsto];
// strip off neighbor mask for molecular systems
if (atom->molecular) {
if (self->molecular) {
int n = *numnei;
for (int i = 0; i < n; i++) {
onebuf[i] = *neiatom & NEIGHMASK;
neiatom++;
}
int *ptr = firstneigh[pointsto];
int *onebuf = self->onebuf;
for (int i = 0; i < n; i++)
onebuf[i] = *(ptr++) & NEIGHMASK;
*nei1atom = onebuf;
} else *nei1atom = firstneigh[pointsto];
@ -487,9 +502,15 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
*numnei=numneigh[*request];
// strip off neighbor mask for molecular systems
if (atom->molecular) {
} else *nei1atom = firstneigh[*request];
if (self->molecular) {
int n = *numnei;
int *ptr = firstneigh[pointsto];
int *onebuf = self->onebuf;
for (int i = 0; i < n; i++)
onebuf[i] = *(ptr++) & NEIGHMASK;
*nei1atom = onebuf;
} else *nei1atom = firstneigh[pointsto];
if (*numnei > KIM_API_MAX_NEIGHBORS)
return KIM_STATUS_NEIGH_TOO_MANY_NEIGHBORS;

3
src/KIM/pair_kim.h
View File

@ -49,6 +49,9 @@ class PairKIM : public Pair {
int maxall;
int *kimtype; // KIM atom types for each LAMMPS atom
int *onebuf; // neighbors of one atom
int molecular;
void allocate();
// KIM data