lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

avoid segfault in Special::angle_trim() if only angles or only dihedrals are defined

This commit is contained in:
Axel Kohlmeyer 2019-04-04 09:13:18 -04:00
parent 8c03f51020
commit 88d160f86e
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
1 changed files with 107 additions and 94 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

201
src/special.cpp
View File

@ -821,21 +821,26 @@ void Special::angle_trim()
int nsend = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
m = atom->map(angle_atom1[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(angle_atom3[i][j]);
if (m < 0 || m >= nlocal) nsend++;
if (num_angle) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
m = atom->map(angle_atom1[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(angle_atom3[i][j]);
if (m < 0 || m >= nlocal) nsend++;
}
}
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
m = atom->map(dihedral_atom1[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(dihedral_atom3[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(dihedral_atom4[i][j]);
if (m < 0 || m >= nlocal) nsend++;
if (num_dihedral) {
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
m = atom->map(dihedral_atom1[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(dihedral_atom3[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(dihedral_atom4[i][j]);
if (m < 0 || m >= nlocal) nsend++;
}
}
}
@ -852,51 +857,55 @@ void Special::angle_trim()
nsend = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
if (num_angle) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
m = atom->map(angle_atom1[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = angle_atom1[i][j] % nprocs;
inbuf[nsend].atomID = angle_atom1[i][j];
inbuf[nsend].partnerID = angle_atom3[i][j];
nsend++;
}
m = atom->map(angle_atom1[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = angle_atom1[i][j] % nprocs;
inbuf[nsend].atomID = angle_atom1[i][j];
inbuf[nsend].partnerID = angle_atom3[i][j];
nsend++;
}
m = atom->map(angle_atom3[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = angle_atom3[i][j] % nprocs;
inbuf[nsend].atomID = angle_atom3[i][j];
inbuf[nsend].partnerID = angle_atom1[i][j];
nsend++;
m = atom->map(angle_atom3[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = angle_atom3[i][j] % nprocs;
inbuf[nsend].atomID = angle_atom3[i][j];
inbuf[nsend].partnerID = angle_atom1[i][j];
nsend++;
}
}
}
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
if (num_dihedral) {
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
m = atom->map(dihedral_atom1[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom1[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom1[i][j];
inbuf[nsend].partnerID = dihedral_atom3[i][j];
nsend++;
}
m = atom->map(dihedral_atom1[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom1[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom1[i][j];
inbuf[nsend].partnerID = dihedral_atom3[i][j];
nsend++;
}
m = atom->map(dihedral_atom3[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom3[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom3[i][j];
inbuf[nsend].partnerID = dihedral_atom1[i][j];
nsend++;
}
m = atom->map(dihedral_atom3[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom3[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom3[i][j];
inbuf[nsend].partnerID = dihedral_atom1[i][j];
nsend++;
}
m = atom->map(dihedral_atom4[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom4[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom4[i][j];
inbuf[nsend].partnerID = dihedral_atom2[i][j];
nsend++;
m = atom->map(dihedral_atom4[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom4[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom4[i][j];
inbuf[nsend].partnerID = dihedral_atom2[i][j];
nsend++;
}
}
}
}
@ -932,56 +941,60 @@ void Special::angle_trim()
// output datums = pairs of atoms that are 1-3 neighbors
for (i = 0; i < nlocal; i++) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
if (num_angle) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
m = atom->map(angle_atom1[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == angle_atom3[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(angle_atom1[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == angle_atom3[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(angle_atom3[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == angle_atom1[i][j]) {
flag[m][k] = 1;
break;
}
m = atom->map(angle_atom3[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == angle_atom1[i][j]) {
flag[m][k] = 1;
break;
}
}
}
}
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
if (num_dihedral) {
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
m = atom->map(dihedral_atom1[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom3[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(dihedral_atom1[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom3[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(dihedral_atom3[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom1[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(dihedral_atom3[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom1[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(dihedral_atom4[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom2[i][j]) {
flag[m][k] = 1;
break;
}
m = atom->map(dihedral_atom4[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom2[i][j]) {
flag[m][k] = 1;
break;
}
}
}
}
}
@ -1012,7 +1025,7 @@ void Special::angle_trim()
memory->destroy(flag);
// if no angles or dihedrals are defined, delete all 1-3 neighs
// if no angles or dihedrals are defined, delete all 1-3 neighs
} else {
for (i = 0; i < nlocal; i++) nspecial[i][1] = 0;