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bond/react: custom group with stabilization option

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This commit is contained in:
jrgissing
2018-11-01 01:04:45 -06:00
parent 20b9c7fd79
commit 5821a5ecc8
3 changed files with 124 additions and 72 deletions
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161
src/USER-MISC/fix_bond_react.cpp
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@ -354,6 +354,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
id_fix1 = NULL;
id_fix2 = NULL;
id_fix3 = NULL;
statted_id = NULL;
custom_exclude_flag = 0;
}
/* ---------------------------------------------------------------------- */
@ -426,11 +429,17 @@ FixBondReact::~FixBondReact()
// check nfix in case all fixes have already been deleted
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_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2);
delete [] id_fix2;
delete [] statted_id;
delete [] guess_branch;
delete [] pioneer_count;
}
@ -461,21 +470,20 @@ void FixBondReact::post_constructor()
int ifix = modify->find_fix(id_fix2);
if (ifix == -1) {
char **newarg = new char*[8];
char **newarg = new char*[7];
newarg[0] = (char *) "bond_react_props_internal";
newarg[1] = (char *) "all"; // group ID is ignored
newarg[2] = (char *) "property/atom";
newarg[3] = (char *) "i_limit_tags";
newarg[4] = (char *) "i_statted_tags";
newarg[5] = (char *) "i_react_tags";
newarg[6] = (char *) "ghost";
newarg[7] = (char *) "yes";
modify->add_fix(8,newarg);
fix2 = modify->fix[modify->nfix-1];
newarg[4] = (char *) "i_react_tags";
newarg[5] = (char *) "ghost";
newarg[6] = (char *) "yes";
modify->add_fix(7,newarg);
delete [] newarg;
}
// create master_group if not already existing
// NOTE: limit_tags and react_tags automaticaly intitialized to zero (unless read from restart)
if (group->find(master_group) == -1) {
group->find_or_create(master_group);
char **newarg;
@ -489,33 +497,100 @@ void FixBondReact::post_constructor()
delete [] newarg;
}
// on to statted_tags (system-wide thermostat)
// intialize per-atom statted_flags to 1
// (only if not already initialized by restart)
// NOTE: limit_tags and react_tags automaticaly intitialized to zero (unless read from restart)
if (fix2->restart_reset != 1) {
int flag;
int index = atom->find_custom("statted_tags",flag);
int *i_statted_tags = atom->ivector[index];
for (int i = 0; i < atom->nlocal; i++)
i_statted_tags[i] = 1;
}
if (stabilization_flag == 1) {
// create exclude_group if not already existing
if (group->find(exclude_group) == -1) {
int igroup = group->find(exclude_group);
// create exclude_group if not already existing, or use as parent group if static
if (igroup == -1 || group->dynamic[igroup] == 0) {
// create stabilization per-atom property
len = strlen("bond_react_stabilization_internal") + 1;
id_fix3 = new char[len];
strcpy(id_fix3,"bond_react_stabilization_internal");
ifix = modify->find_fix(id_fix3);
if (ifix == -1) {
char **newarg = new char*[6];
newarg[0] = (char *) "bond_react_stabilization_internal";
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];
delete [] newarg;
}
len = strlen("statted_tags") + 1;
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;
}
group->find_or_create(exclude_group);
char **newarg;
newarg = new char*[5];
newarg[0] = exclude_group;
newarg[1] = (char *) "dynamic";
newarg[2] = (char *) "all";
if (igroup == -1) newarg[2] = (char *) "all";
else newarg[2] = (char *) "exclude_PARENT_group";
newarg[3] = (char *) "property";
newarg[4] = (char *) "statted_tags";
group->assign(5,newarg);
delete [] newarg;
}
// 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) {
int flag;
int index = atom->find_custom("statted_tags",flag);
int *i_statted_tags = atom->ivector[index];
for (int i = 0; i < atom->nlocal; i++)
i_statted_tags[i] = 1;
}
} else {
// sleeping code, for future capabilities
custom_exclude_flag = 1;
// first we have to find correct fix group reference
int n = strlen("GROUP_") + strlen(exclude_group) + 1;
char *fix_group = new char[n];
strcpy(fix_group,"GROUP_");
strcat(fix_group,exclude_group);
int ifix = modify->find_fix(fix_group);
Fix *fix = modify->fix[ifix];
delete [] fix_group;
// this returns names of corresponding property
int unused;
char * idprop;
idprop = (char *) fix->extract("property",unused);
if (idprop == NULL)
error->all(FLERR,"Exclude group must be a per-atom property group");
len = strlen(idprop) + 1;
statted_id = new char[len];
strcpy(statted_id,idprop);
// intialize per-atom statted_tags to 1
// need to correct for smooth restarts
//int flag;
//int index = atom->find_custom(statted_id,flag);
//int *i_statted_tags = atom->ivector[index];
//for (int i = 0; i < atom->nlocal; i++)
// i_statted_tags[i] = 1;
}
// let's create a new nve/limit fix to limit newly reacted atoms
len = strlen("bond_react_MASTER_nve_limit") + 1;
@ -534,40 +609,6 @@ void FixBondReact::post_constructor()
fix1 = modify->fix[modify->nfix-1];
delete [] newarg;
}
}
// currently must redefine dynamic groups so they are updated at proper time
// -> should double check as to why
int must_redefine_groups = 1;
if (must_redefine_groups) {
group->find_or_create(master_group);
char **newarg;
newarg = new char*[5];
newarg[0] = master_group;
newarg[1] = (char *) "dynamic";
newarg[2] = (char *) "all";
newarg[3] = (char *) "property";
newarg[4] = (char *) "limit_tags";
group->assign(5,newarg);
delete [] newarg;
}
if (stabilization_flag == 1) {
if (must_redefine_groups) {
group->find_or_create(exclude_group);
char **newarg;
newarg = new char*[5];
newarg[0] = exclude_group;
newarg[1] = (char *) "dynamic";
newarg[2] = (char *) "all";
newarg[3] = (char *) "property";
newarg[4] = (char *) "statted_tags";
group->assign(5,newarg);
delete [] newarg;
}
}
}
@ -1812,7 +1853,7 @@ void FixBondReact::limit_bond(int limit_bond_mode)
int index1 = atom->find_custom("limit_tags",flag);
int *i_limit_tags = atom->ivector[index1];
int index2 = atom->find_custom("statted_tags",flag);
int index2 = atom->find_custom(statted_id,flag);
int *i_statted_tags = atom->ivector[index2];
int index3 = atom->find_custom("react_tags",flag);
@ -1842,7 +1883,7 @@ void FixBondReact::unlimit_bond()
int index1 = atom->find_custom("limit_tags",flag);
int *i_limit_tags = atom->ivector[index1];
int index2 = atom->find_custom("statted_tags",flag);
int index2 = atom->find_custom(statted_id,flag);
int *i_statted_tags = atom->ivector[index2];
int index3 = atom->find_custom("react_tags",flag);