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refactor how to insert atoms

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This commit is contained in:
Jacob Gissinger
2024-08-25 13:42:51 -04:00
parent 732be489a3
commit 6514dbb4b6
2 changed files with 79 additions and 50 deletions
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114
src/REACTION/fix_bond_react.cpp
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@ -2962,6 +2962,8 @@ void FixBondReact::update_everything()
int *type = atom->type;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
tagint *tag = atom->tag;
AtomVec *avec = atom->avec;
int **bond_type = atom->bond_type;
tagint **bond_atom = atom->bond_atom;
@ -2974,13 +2976,16 @@ void FixBondReact::update_everything()
memory->create(mark,nmark,"bond/react:mark");
for (int i = 0; i < nmark; i++) mark[i] = 0;
// used when creating atoms
addatomtag = 0;
for (int i = 0; i < nlocal; i++) addatomtag = MAX(addatomtag,tag[i]);
MPI_Allreduce(MPI_IN_PLACE,&addatomtag,1,MPI_LMP_TAGINT,MPI_MAX,world);
addatoms.clear();
// flag used to delete special interactions
int *delflag;
memory->create(delflag,atom->maxspecial,"bond/react:delflag");
tagint *tag = atom->tag;
AtomVec *avec = atom->avec;
// used when creating atoms
int inserted_atoms_flag = 0;
@ -3029,6 +3034,7 @@ void FixBondReact::update_everything()
for (int i = 0; i < local_num_mega; i++) {
rxnID = (int) local_mega_glove[0][i];
// reactions already shuffled from dedup procedure, so can skip first N
// wait, this check needs to be after add atoms, because they can also be 'skipped' due to overlap
if (iskip[rxnID]++ < nlocalskips[rxnID]) continue;
// this will be overwritten if reaction skipped by create_atoms below
@ -3040,7 +3046,7 @@ void FixBondReact::update_everything()
if (create_atoms_flag[rxnID] == 1) {
onemol = atom->molecules[unreacted_mol[rxnID]];
twomol = atom->molecules[reacted_mol[rxnID]];
if (insert_atoms(update_mega_glove,update_num_mega)) {
if (insert_atoms_setup(update_mega_glove,update_num_mega)) {
inserted_atoms_flag = 1;
} else { // create aborted
reaction_count_total[rxnID]--;
@ -3068,7 +3074,7 @@ void FixBondReact::update_everything()
if (create_atoms_flag[rxnID] == 1) {
onemol = atom->molecules[unreacted_mol[rxnID]];
twomol = atom->molecules[reacted_mol[rxnID]];
if (insert_atoms(update_mega_glove,update_num_mega)) {
if (insert_atoms_setup(update_mega_glove,update_num_mega)) {
inserted_atoms_flag = 1;
} else { // create aborted
reaction_count_total[rxnID]--;
@ -3084,14 +3090,32 @@ void FixBondReact::update_everything()
if (update_num_mega == 0) continue;
// if inserted atoms and global map exists, reset map now instead
// of waiting for comm since other pre-exchange fixes may use it
// invoke map_init() b/c atom count has grown
// do this once after all atom insertions
if (inserted_atoms_flag == 1 && atom->map_style != Atom::MAP_NONE) {
// insert all atoms for all rxns here
if (inserted_atoms_flag == 1) {
// clear to-be-overwritten ghost info
atom->nghost = 0;
atom->avec->clear_bonus();
for (auto & myaddatom : addatoms) {
atom->avec->create_atom(myaddatom.type,myaddatom.x);
int n = atom->nlocal - 1;
atom->tag[n] = myaddatom.tag;
atom->molecule[n] = myaddatom.molecule;
atom->mask[n] = myaddatom.mask;
atom->image[n] = myaddatom.image;
atom->v[n][0] = myaddatom.v[0];
atom->v[n][1] = myaddatom.v[1];
atom->v[n][2] = myaddatom.v[2];
if (atom->rmass) atom->rmass[n]= myaddatom.rmass;
modify->create_attribute(n);
}
// reset atom->map
if (atom->map_style != Atom::MAP_NONE) {
atom->map_init();
atom->map_set();
}
}
// mark to-delete atoms
nlocal = atom->nlocal;
@ -3644,10 +3668,11 @@ void FixBondReact::update_everything()
}
/* ----------------------------------------------------------------------
insert created atoms
setup for inserting created atoms
atoms for all rxns are actually created all at once in update_everything
------------------------------------------------------------------------- */
int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate)
int FixBondReact::insert_atoms_setup(tagint **my_update_mega_glove, int iupdate)
{
// inserting atoms based off fix_deposit->pre_exchange
int flag;
@ -3675,14 +3700,9 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate)
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
tagint maxtag_all,maxmol_all;
tagint max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
MPI_Allreduce(&max,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,molecule[i]);
MPI_Allreduce(&max,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
tagint maxmol_all;
for (int i = 0; i < nlocal; i++) maxmol_all = MAX(maxmol_all,molecule[i]);
MPI_Allreduce(MPI_IN_PLACE,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
int dimension = domain->dimension;
@ -3776,6 +3796,7 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate)
break;
}
}
// !! need to add check against soon-to-added atoms
if (abortflag) break;
}
}
@ -3787,12 +3808,6 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate)
}
}
// clear ghost count and any ghost bonus data internal to AtomVec
// same logic as beginning of Comm::exchange()
// do it now b/c inserting atoms will overwrite ghost atoms
atom->nghost = 0;
atom->avec->clear_bonus();
// check if new atoms are in my sub-box or above it if I am highest proc
// if so, add atom to my list via create_atom()
// initialize additional info about the atoms
@ -3835,40 +3850,46 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate)
}
int root = 0;
addatomtag++;
if (flag) {
struct AddAtom myaddatom;
root = comm->me;
atom->avec->create_atom(twomol->type[m],coords[m]);
int n = atom->nlocal - 1;
atom->tag[n] = maxtag_all + add_count;
myaddatom.type = twomol->type[m];
myaddatom.x[0] = coords[m][0];
myaddatom.x[1] = coords[m][1];
myaddatom.x[2] = coords[m][2];
myaddatom.tag = addatomtag;
// locally update mega_glove
my_update_mega_glove[preID][iupdate] = atom->tag[n];
my_update_mega_glove[preID][iupdate] = myaddatom.tag;
// could do better job choosing mol ID for added atoms
if (atom->molecule_flag) {
if (twomol->moleculeflag) {
atom->molecule[n] = maxmol_all + twomol->molecule[m];
myaddatom.molecule = maxmol_all + twomol->molecule[m];
} else {
atom->molecule[n] = maxmol_all + 1;
myaddatom.molecule = maxmol_all + 1;
}
}
atom->mask[n] = 1 | groupbit;
atom->image[n] = imageflags[m];
myaddatom.mask = 1 | groupbit;
myaddatom.image = imageflags[m];
// guess a somewhat reasonable initial velocity based on reaction site
// further control is possible using bond_react_MASTER_group
// compute |velocity| corresponding to a given temperature t, using specific atom's mass
double mymass = atom->rmass ? atom->rmass[n] : atom->mass[twomol->type[m]];
double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / mymass);
v[n][0] = random[rxnID]->uniform();
v[n][1] = random[rxnID]->uniform();
v[n][2] = random[rxnID]->uniform();
double vnorm = sqrt(v[n][0]*v[n][0] + v[n][1]*v[n][1] + v[n][2]*v[n][2]);
v[n][0] = v[n][0]/vnorm*vtnorm;
v[n][1] = v[n][1]/vnorm*vtnorm;
v[n][2] = v[n][2]/vnorm*vtnorm;
modify->create_attribute(n);
myaddatom.rmass = atom->rmass ? twomol->rmass[m] : atom->mass[twomol->type[m]];
double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / myaddatom.rmass);
double myv[3];
myv[0] = random[rxnID]->uniform();
myv[1] = random[rxnID]->uniform();
myv[2] = random[rxnID]->uniform();
double vnorm = sqrt(myv[0]*myv[0] + myv[1]*myv[1] + myv[2]*myv[2]);
myaddatom.v[0] = myv[0]/vnorm*vtnorm;
myaddatom.v[1] = myv[1]/vnorm*vtnorm;
myaddatom.v[2] = myv[2]/vnorm*vtnorm;
addatoms.push_back(myaddatom);
}
// globally update mega_glove and equivalences
MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world);
@ -3881,12 +3902,11 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate)
}
// reset global natoms here
// reset atom map elsewhere, after all calls to 'insert_atoms'
// reset atom map elsewhere, after all calls to 'insert_atoms_setup'
atom->natoms += add_count;
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
maxtag_all += add_count;
if (maxtag_all >= MAXTAGINT)
if (addatomtag >= MAXTAGINT)
error->all(FLERR,"New atom IDs exceed maximum allowed ID");
// atom creation successful
memory->destroy(coords);

11
src/REACTION/fix_bond_react.h
View File

@ -216,7 +216,7 @@ class FixBondReact : public Fix {
void glove_ghostcheck();
void ghost_glovecast();
void update_everything();
int insert_atoms(tagint **, int);
int insert_atoms_setup(tagint **, int);
void unlimit_bond(); // removes atoms from stabilization, and other post-reaction every-step operations
void dedup_mega_gloves(int); //dedup global mega_glove
void write_restart(FILE *) override;
@ -246,6 +246,15 @@ class FixBondReact : public Fix {
std::map<std::set<tagint>, int> atoms2bond; // maps atom pair to index of local bond array
std::vector<std::vector<Constraint>> constraints;
tagint addatomtag;
struct AddAtom {
tagint tag, molecule;
int type, mask;
imageint image;
double rmass, x[3], v[3];
};
std::vector<AddAtom> addatoms;
// DEBUG
void print_bb();