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update communicated rxn instances to doubles

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This commit is contained in:
jrgissing
2023-06-11 19:27:58 -04:00
parent 23552d4b7a
commit c214f654b6
2 changed files with 36 additions and 32 deletions
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60
src/REACTION/fix_bond_react.cpp
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@ -1340,9 +1340,9 @@ void FixBondReact::superimpose_algorithm()
status = REJECT;
} else {
status = ACCEPT;
my_mega_glove[0][my_num_mega] = rxnID;
my_mega_glove[0][my_num_mega] = (double) rxnID;
for (int i = 0; i < onemol->natoms; i++) {
my_mega_glove[i+cuff][my_num_mega] = glove[i][1];
my_mega_glove[i+cuff][my_num_mega] = (double) glove[i][1];
}
my_num_mega++;
}
@ -1388,9 +1388,9 @@ void FixBondReact::superimpose_algorithm()
if (fraction[rxnID] < 1.0 &&
random[rxnID]->uniform() >= fraction[rxnID]) status = REJECT;
else {
my_mega_glove[0][my_num_mega] = rxnID;
my_mega_glove[0][my_num_mega] = (double) rxnID;
for (int i = 0; i < onemol->natoms; i++) {
my_mega_glove[i+cuff][my_num_mega] = glove[i][1];
my_mega_glove[i+cuff][my_num_mega] = (double) glove[i][1];
}
my_num_mega++;
}
@ -2677,7 +2677,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
dedup_size = global_megasize;
}
tagint **dedup_glove;
double **dedup_glove;
memory->create(dedup_glove,max_natoms+cuff,dedup_size,"bond/react:dedup_glove");
if (dedup_mode == LOCAL) {
@ -2704,7 +2704,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
// let's randomly mix up our reaction instances first
// then we can feel okay about ignoring ones we've already deleted (or accepted)
// based off std::shuffle
int *temp_rxn = new int[max_natoms+cuff];
double *temp_rxn = new double[max_natoms+cuff];
for (int i = dedup_size-1; i > 0; --i) { //dedup_size
// choose random entry to swap current one with
int k = floor(random[0]->uniform()*(i+1));
@ -2764,7 +2764,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
int new_global_megasize = 0;
for (int i = 0; i < global_megasize; i++) {
if (dedup_mask[i] == 0) {
ghostly_rxn_count[dedup_glove[0][i]]++;
ghostly_rxn_count[(int) dedup_glove[0][i]]++;
for (int j = 0; j < max_natoms + cuff; j++) {
global_mega_glove[j][new_global_megasize] = dedup_glove[j][i];
}
@ -2834,7 +2834,7 @@ void FixBondReact::glove_ghostcheck()
local_rxn_count[i] = 0;
for (int i = 0; i < my_num_mega; i++) {
rxnID = my_mega_glove[0][i];
rxnID = (int) my_mega_glove[0][i];
onemol = atom->molecules[unreacted_mol[rxnID]];
int ghostly = 0;
#if !defined(MPI_STUBS)
@ -2843,7 +2843,7 @@ void FixBondReact::glove_ghostcheck()
ghostly = 1;
} else {
for (int j = 0; j < onemol->natoms; j++) {
int ilocal = atom->map(my_mega_glove[j+cuff][i]);
int ilocal = atom->map((tagint) my_mega_glove[j+cuff][i]);
if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
ghostly = 1;
break;
@ -2905,8 +2905,8 @@ void FixBondReact::ghost_glovecast()
int subsizes[2] = {max_natoms+cuff, 1};
int starts[2] = {0,0};
MPI_Type_create_subarray (2, sizes, subsizes, starts, MPI_ORDER_C,
MPI_LMP_TAGINT, &columnunsized);
MPI_Type_create_resized (columnunsized, 0, sizeof(tagint), &column);
MPI_DOUBLE, &columnunsized);
MPI_Type_create_resized (columnunsized, 0, sizeof(double), &column);
MPI_Type_commit(&column);
memory->destroy(global_mega_glove);
@ -3017,15 +3017,20 @@ void FixBondReact::update_everything()
for (int i = 0; i < nreacts; i++) iskip[i] = 0;
if (pass == 0) {
for (int i = 0; i < local_num_mega; i++) {
rxnID = local_mega_glove[0][i];
rxnID = (int) local_mega_glove[0][i];
// reactions already shuffled from dedup procedure, so can skip first N
if (iskip[rxnID]++ < nlocalskips[rxnID]) continue;
// this will be overwritten if reaction skipped by create_atoms below
update_mega_glove[0][update_num_mega] = (tagint) local_mega_glove[0][i];
for (int j = 0; j < max_natoms; j++)
update_mega_glove[j+1][update_num_mega] = (tagint) local_mega_glove[j+cuff][i];
// atoms inserted here for serial MPI_STUBS build only
if (create_atoms_flag[rxnID] == 1) {
onemol = atom->molecules[unreacted_mol[rxnID]];
twomol = atom->molecules[reacted_mol[rxnID]];
if (insert_atoms(local_mega_glove,i)) {
if (insert_atoms(update_mega_glove,update_num_mega)) {
inserted_atoms_flag = 1;
} else { // create aborted
reaction_count_total[rxnID]--;
@ -3033,24 +3038,26 @@ void FixBondReact::update_everything()
}
}
update_mega_glove[0][update_num_mega] = local_mega_glove[0][i];
for (int j = 0; j < max_natoms; j++)
update_mega_glove[j+1][update_num_mega] = local_mega_glove[j+cuff][i];
update_num_mega++;
}
} else if (pass == 1) {
for (int i = 0; i < global_megasize; i++) {
rxnID = global_mega_glove[0][i];
rxnID = (int) global_mega_glove[0][i];
// reactions already shuffled from dedup procedure, so can skip first N
if (iskip[rxnID]++ < nghostlyskips[rxnID]) continue;
// this will be overwritten if reaction skipped by create_atoms below
update_mega_glove[0][update_num_mega] = (tagint) global_mega_glove[0][i];
for (int j = 0; j < max_natoms; j++)
update_mega_glove[j+1][update_num_mega] = (tagint) global_mega_glove[j+cuff][i];
// we can insert atoms here, now that reactions are finalized
// can't do it any earlier, due to skipped reactions (max_rxn)
// for MPI build, reactions that create atoms are always treated as 'global'
if (create_atoms_flag[rxnID] == 1) {
onemol = atom->molecules[unreacted_mol[rxnID]];
twomol = atom->molecules[reacted_mol[rxnID]];
if (insert_atoms(global_mega_glove,i)) {
if (insert_atoms(update_mega_glove,update_num_mega)) {
inserted_atoms_flag = 1;
} else { // create aborted
reaction_count_total[rxnID]--;
@ -3058,9 +3065,6 @@ void FixBondReact::update_everything()
}
}
update_mega_glove[0][update_num_mega] = global_mega_glove[0][i];
for (int j = 0; j < max_natoms; j++)
update_mega_glove[j+1][update_num_mega] = global_mega_glove[j+cuff][i];
update_num_mega++;
}
}
@ -3648,7 +3652,7 @@ void FixBondReact::update_everything()
insert created atoms
------------------------------------------------------------------------- */
int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate)
{
// inserting atoms based off fix_deposit->pre_exchange
int flag;
@ -3697,14 +3701,14 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
n2superpose++;
}
int ifit = atom->map(my_mega_glove[ibonding[rxnID]+cuff][iupdate]); // use this local ID to find fitting proc
int ifit = atom->map(my_update_mega_glove[ibonding[rxnID]+1][iupdate]); // use this local ID to find fitting proc
Superpose3D<double, double **> superposer(n2superpose);
int fitroot = 0;
if (ifit >= 0 && ifit < atom->nlocal) {
fitroot = comm->me;
// get 'temperatere' averaged over site, used for created atoms' vels
t = get_temperature(my_mega_glove,1,iupdate);
t = get_temperature(my_update_mega_glove,1,iupdate);
double **xfrozen; // coordinates for the "frozen" target molecule
double **xmobile; // coordinates for the "mobile" molecule
@ -3718,12 +3722,12 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
if (!twomol->fragmentmask[modify_create_fragid[rxnID]][j]) continue;
int ipre = equivalences[j][1][rxnID]-1; // equiv pre-reaction template index
if (!create_atoms[j][rxnID] && !delete_atoms[ipre][rxnID]) {
if (atom->map(my_mega_glove[ipre+cuff][iupdate]) < 0) {
if (atom->map(my_update_mega_glove[ipre+1][iupdate]) < 0) {
error->warning(FLERR," eligible atoms skipped for created-atoms fit on rank {}\n",
comm->me);
continue;
}
iatom = atom->map(my_mega_glove[ipre+cuff][iupdate]);
iatom = atom->map(my_update_mega_glove[ipre+1][iupdate]);
if (iref == -1) iref = iatom;
iatom = domain->closest_image(iref,iatom);
for (int k = 0; k < 3; k++) {
@ -3843,7 +3847,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
atom->tag[n] = maxtag_all + add_count;
// locally update mega_glove
my_mega_glove[preID+cuff-1][iupdate] = atom->tag[n];
my_update_mega_glove[preID][iupdate] = atom->tag[n];
if (atom->molecule_flag) {
if (twomol->moleculeflag) {
@ -3871,7 +3875,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
}
// globally update mega_glove and equivalences
MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world);
MPI_Bcast(&my_mega_glove[preID+cuff-1][iupdate],1,MPI_LMP_TAGINT,root,world);
MPI_Bcast(&my_update_mega_glove[preID][iupdate],1,MPI_LMP_TAGINT,root,world);
equivalences[m][0][rxnID] = m+1;
equivalences[m][1][rxnID] = preID;
reverse_equiv[preID-1][0][rxnID] = preID;