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Merge pull request #914 from jrgissing/bond-react-restart 

smooth restarts with bond/react
This commit is contained in:
Steve Plimpton 2018-05-14 16:16:58 -06:00 committed by GitHub
parent f5d66e74c5 8303d1a375
commit 307e471456
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GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 13 additions and 24 deletions
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37
src/USER-MISC/fix_bond_react.cpp
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@ -430,16 +430,6 @@ void FixBondReact::post_constructor()
delete [] newarg;
}
// limit_tags: these are recently reacted atoms being relaxed
// per-atom properties already initialized to zero (not in group)
// let's do it anyway for clarity
int flag;
int index = atom->find_custom("limit_tags",flag); //here's where error would happen
int *i_limit_tags = atom->ivector[index];
for (int i = 0; i < atom->nlocal; i++)
i_limit_tags[i] = 0;
// create master_group if not already existing
if (group->find(master_group) == -1) {
group->find_or_create(master_group);
@ -456,11 +446,16 @@ void FixBondReact::post_constructor()
// on to statted_tags (system-wide thermostat)
// intialize per-atom statted_flags to 1
index = atom->find_custom("statted_tags",flag);
int *i_statted_tags = atom->ivector[index];
// (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;
for (int i = 0; i < atom->nlocal; i++)
i_statted_tags[i] = 1;
}
if (stabilization_flag == 1) {
// create exclude_group if not already existing
@ -497,16 +492,6 @@ void FixBondReact::post_constructor()
}
//react_tags: this per-atom property is the ID of the 'react' argument which recently caused atom to react
//so that atoms which wander between processors may be released to global thermostat at the proper time
//per-atom values initalized to 0
index = atom->find_custom("react_tags",flag);
int *i_react_tags = atom->ivector[index];
for (int i = 0; i < atom->nlocal; i++)
i_react_tags[i] = 0;
// currently must redefine dynamic groups so they are updated at proper time
// -> should double check as to why
@ -553,6 +538,10 @@ void FixBondReact::init()
if (strcmp(modify->fix[i]->style,"bond/react") == 0) count++;
if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix bond/react");
if (force->newton_bond == 0 && comm->me == 0) error->warning(FLERR,"Fewer reactions may occur in some cases "
"when 'newton off' is set for bonded interactions. "
"The reccomended setting is 'newton on'.");
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;