moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fix illegal accesses due to invalid type of ghost atoms

Browse Source 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2021-10-26 12:34:35 +02:00
parent 99d6a4bdd8
commit d7056f09f4
2 changed files with 13 additions and 13 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
src/force_eam.c
View File

@ -44,7 +44,7 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz; MD_FLOAT* fp = eam->fp; MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz; MD_FLOAT* fp = eam->fp;
MD_FLOAT* rhor_spline = eam->rhor_spline; MD_FLOAT* frho_spline = eam->frho_spline; MD_FLOAT* z2r_spline = eam->z2r_spline; MD_FLOAT* rhor_spline = eam->rhor_spline; MD_FLOAT* frho_spline = eam->frho_spline; MD_FLOAT* z2r_spline = eam->z2r_spline;
int rdr = eam->rdr; int nr = eam->nr; int nr_tot = eam->nr_tot; int rdrho = eam->rdrho; int rdr = eam->rdr; int nr = eam->nr; int nr_tot = eam->nr_tot; int rdrho = eam->rdrho;
int nrho = eam->nrho; int nrho_tot = eam->nrho_tot; int nrho = eam->nrho; int nrho_tot = eam->nrho_tot; int ntypes = eam->ntypes;
double S = getTimeStamp(); double S = getTimeStamp();
LIKWID_MARKER_START("force_eam_fp"); LIKWID_MARKER_START("force_eam_fp");
@ -66,8 +66,8 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i
MD_FLOAT delz = ztmp - atom_z(j); MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz; MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
const int type_j = atom->type[j]; const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j; const int type_ij = type_i * ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij]; const MD_FLOAT cutforcesq = eam->cutforcesq[type_ij];
if(rsq < cutforcesq) { if(rsq < cutforcesq) {
MD_FLOAT p = sqrt(rsq) * rdr + 1.0; MD_FLOAT p = sqrt(rsq) * rdr + 1.0;
@ -75,7 +75,6 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i
m = m < nr - 1 ? m : nr - 1; m = m < nr - 1 ? m : nr - 1;
p -= m; p -= m;
p = p < 1.0 ? p : 1.0; p = p < 1.0 ? p : 1.0;
rhoi += ((rhor_spline[type_ij * nr_tot + m * 7 + 3] * p + rhoi += ((rhor_spline[type_ij * nr_tot + m * 7 + 3] * p +
rhor_spline[type_ij * nr_tot + m * 7 + 4]) * p + rhor_spline[type_ij * nr_tot + m * 7 + 4]) * p +
rhor_spline[type_ij * nr_tot + m * 7 + 5]) * p + rhor_spline[type_ij * nr_tot + m * 7 + 5]) * p +
@ -93,7 +92,6 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i
frho_spline[type_ii * nrho_tot + m * 7 + 1]) * p + frho_spline[type_ii * nrho_tot + m * 7 + 1]) * p +
frho_spline[type_ii * nrho_tot + m * 7 + 2]; frho_spline[type_ii * nrho_tot + m * 7 + 2];
} }
LIKWID_MARKER_STOP("force_eam_fp"); LIKWID_MARKER_STOP("force_eam_fp");
LIKWID_MARKER_START("force_eam"); LIKWID_MARKER_START("force_eam");
@ -116,8 +114,8 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i
MD_FLOAT delz = ztmp - atom_z(j); MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz; MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
const int type_j = atom->type[j]; const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j; const int type_ij = type_i * ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij]; const MD_FLOAT cutforcesq = eam->cutforcesq[type_ij];
if(rsq < cutforcesq) { if(rsq < cutforcesq) {
MD_FLOAT r = sqrt(rsq); MD_FLOAT r = sqrt(rsq);

14
src/pbc.c
View File

@ -93,12 +93,14 @@ void updateAtomsPbc(Atom *atom, Parameter *param)
* defining ghost atoms around domain * defining ghost atoms around domain
* only creates mapping and coordinate corrections * only creates mapping and coordinate corrections
* that are then enforced in updatePbc */ * that are then enforced in updatePbc */
#define ADDGHOST(dx,dy,dz) \ #define ADDGHOST(dx,dy,dz) \
Nghost++; \ Nghost++; \
BorderMap[Nghost] = i; \ BorderMap[Nghost] = i; \
PBCx[Nghost] = dx; \ PBCx[Nghost] = dx; \
PBCy[Nghost] = dy; \ PBCy[Nghost] = dy; \
PBCz[Nghost] = dz; PBCz[Nghost] = dz; \
atom->type[atom->Nlocal + Nghost] = atom->type[i]
void setupPbc(Atom *atom, Parameter *param) void setupPbc(Atom *atom, Parameter *param)
{ {
MD_FLOAT xprd = param->xprd; MD_FLOAT xprd = param->xprd;