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need to update exclusions with the new atom IDs in case of molecular systems

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This commit is contained in:
Axel Kohlmeyer
2018-07-11 07:22:47 -04:00
parent 1ed25d195b
commit 1f1447c3ac
1 changed files with 12 additions and 4 deletions
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16
src/reset_ids.cpp
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@ -16,6 +16,7 @@
#include "atom_vec.h" #include "atom_vec.h"
#include "domain.h" #include "domain.h"
#include "comm.h" #include "comm.h"
#include "special.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
@ -44,7 +45,7 @@ void ResetIDs::command(int narg, char **arg)
} }
// create an atom map if one doesn't exist already // create an atom map if one doesn't exist already
int mapflag = 0; int mapflag = 0;
if (atom->map_style == 0) { if (atom->map_style == 0) {
mapflag = 1; mapflag = 1;
@ -93,7 +94,7 @@ void ResetIDs::command(int narg, char **arg)
// forward_comm_array acquires new IDs for ghost atoms // forward_comm_array acquires new IDs for ghost atoms
double **newIDs; double **newIDs;
memory->create(newIDs,nall,1,"reset_ids:newIDs"); memory->create(newIDs,nall,1,"reset_ids:newIDs");
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
newIDs[i][0] = tag[i]; newIDs[i][0] = tag[i];
@ -105,7 +106,7 @@ void ResetIDs::command(int narg, char **arg)
// loop over bonds, angles, etc and reset IDs in stored topology arrays // loop over bonds, angles, etc and reset IDs in stored topology arrays
// only necessary for molecular = 1, not molecular = 2 // only necessary for molecular = 1, not molecular = 2
// badcount = atom IDs that could not be found // badcount = atom IDs that could not be found
int badcount = 0; int badcount = 0;
if (atom->molecular == 1) { if (atom->molecular == 1) {
@ -232,8 +233,15 @@ void ResetIDs::command(int narg, char **arg)
atom->map_init(); atom->map_init();
atom->map_set(); atom->map_set();
// need to update exclusions with new atom IDs
if (atom->molecular == 1) {
Special special(lmp);
special.build();
}
// delete temporary atom map // delete temporary atom map
if (mapflag) { if (mapflag) {
atom->map_delete(); atom->map_delete();
atom->map_style = 0; atom->map_style = 0;