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bond/react: convert group-ID to group-ID-prefix

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enables consistent syntax when using custom groups
This commit is contained in:
jrgissing
2018-11-03 11:57:46 -06:00
parent 0c7c344e19
commit f7aa01d74a
3 changed files with 40 additions and 38 deletions
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38
src/USER-MISC/fix_bond_react.cpp
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@ -78,6 +78,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
fix1 = NULL;
fix2 = NULL;
fix3 = NULL;
if (narg < 8) error->all(FLERR,"Illegal fix bond/react command: "
"too few arguments");
@ -433,10 +434,8 @@ FixBondReact::~FixBondReact()
if (id_fix1 == NULL && modify->nfix) modify->delete_fix(id_fix1);
delete [] id_fix1;
if (custom_exclude_flag == 0) {
if (id_fix3 == NULL && modify->nfix) modify->delete_fix(id_fix3);
delete [] id_fix3;
}
if (id_fix3 == NULL && modify->nfix) modify->delete_fix(id_fix3);
delete [] id_fix3;
}
if (id_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2);
@ -512,14 +511,14 @@ void FixBondReact::post_constructor()
ifix = modify->find_fix(id_fix3);
if (ifix == -1) {
char **newarg = new char*[6];
newarg[0] = (char *) "bond_react_stabilization_internal";
newarg[0] = (char *) id_fix3;
newarg[1] = (char *) "all"; // group ID is ignored
newarg[2] = (char *) "property/atom";
newarg[3] = (char *) "i_statted_tags";
newarg[4] = (char *) "ghost";
newarg[5] = (char *) "yes";
modify->add_fix(6,newarg);
fix2 = modify->fix[modify->nfix-1];
fix3 = modify->fix[modify->nfix-1];
delete [] newarg;
}
@ -527,17 +526,17 @@ void FixBondReact::post_constructor()
statted_id = new char[len];
strcpy(statted_id,"statted_tags");
// if static group exists, duplicate it, use duplicate as parent group
// original will be converted into dynamic per-atom property group
if (igroup != -1) {
char **newarg;
newarg = new char*[3];
newarg[0] = (char *) "exclude_PARENT_group";
newarg[1] = (char *) "union";
newarg[2] = exclude_group;
group->assign(3,newarg);
delete [] newarg;
}
// if static group exists, use as parent group
// also, rename dynamic exclude_group by appending '_REACT'
char *exclude_PARENT_group;
int n = strlen(exclude_group) + 1;
exclude_PARENT_group = new char[n];
strcpy(exclude_PARENT_group,exclude_group);
n += strlen("_REACT");
delete [] exclude_group;
exclude_group = new char[n];
strcpy(exclude_group,exclude_PARENT_group);
strcat(exclude_group,"_REACT");
group->find_or_create(exclude_group);
char **newarg;
@ -545,16 +544,17 @@ void FixBondReact::post_constructor()
newarg[0] = exclude_group;
newarg[1] = (char *) "dynamic";
if (igroup == -1) newarg[2] = (char *) "all";
else newarg[2] = (char *) "exclude_PARENT_group";
else newarg[2] = (char *) exclude_PARENT_group;
newarg[3] = (char *) "property";
newarg[4] = (char *) "statted_tags";
group->assign(5,newarg);
delete [] newarg;
delete [] exclude_PARENT_group;
// on to statted_tags (system-wide thermostat)
// intialize per-atom statted_flags to 1
// (only if not already initialized by restart)
if (fix2->restart_reset != 1) {
if (fix3->restart_reset != 1) {
int flag;
int index = atom->find_custom("statted_tags",flag);
int *i_statted_tags = atom->ivector[index];