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Merge branch 'collected-small-changes' into reset-command

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This commit is contained in:
Axel Kohlmeyer
2022-11-23 13:38:40 -05:00
parent 13e6c82273 7f4ebaf672
commit 4ba604fd37
58 changed files with 651 additions and 602 deletions
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42
src/REACTION/fix_bond_react.cpp
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@ -22,6 +22,7 @@ Contributing Author: Jacob Gissinger (jacob.r.gissinger@gmail.com)
#include "atom_vec.h"
#include "citeme.h"
#include "comm.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "fix_bond_history.h"
@ -118,10 +119,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
fix3 = nullptr;
reset_mol_ids = nullptr;
if (narg < 8) error->all(FLERR,"Illegal fix bond/react command: " "too few arguments");
if (narg < 8) utils::missing_cmd_args(FLERR,"fix bond/react", error);
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
newton_bond = force->newton_bond;
restart_global = 1;
@ -494,7 +493,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
for (int i = 0; i < nreacts; i++) {
for (int j = 0; j < nconstraints[i]; j++) {
if (constraints[j][i].type == ARRHENIUS) {
rrhandom[tmp++] = new RanMars(lmp,(int) constraints[j][i].par[4] + me);
rrhandom[tmp++] = new RanMars(lmp,(int) constraints[j][i].par[4] + comm->me);
}
}
}
@ -529,7 +528,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
random = new RanMars*[nreacts];
for (int i = 0; i < nreacts; i++) {
random[i] = new RanMars(lmp,seed[i] + me);
random[i] = new RanMars(lmp,seed[i] + comm->me);
}
// set comm sizes needed by this fix
@ -1251,6 +1250,7 @@ void FixBondReact::close_partner()
void FixBondReact::superimpose_algorithm()
{
const int nprocs = comm->nprocs;
local_num_mega = 0;
ghostly_num_mega = 0;
@ -1400,7 +1400,7 @@ void FixBondReact::superimpose_algorithm()
MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world);
int rxnflag = 0;
if (me == 0)
if (comm->me == 0)
for (int i = 0; i < nreacts; i++) {
reaction_count_total[i] += reaction_count[i] + ghostly_rxn_count[i];
rxnflag += reaction_count[i] + ghostly_rxn_count[i];
@ -1440,7 +1440,7 @@ void FixBondReact::superimpose_algorithm()
memory->create(local_rxncounts,nprocs,"bond/react:local_rxncounts");
memory->create(all_localskips,nprocs,"bond/react:all_localskips");
MPI_Gather(&local_rxn_count[i],1,MPI_INT,local_rxncounts,1,MPI_INT,0,world);
if (me == 0) {
if (comm->me == 0) {
int delta_rxn = reaction_count[i] + ghostly_rxn_count[i];
// when using variable input for rate_limit, rate_limit_overstep could be > delta_rxn (below)
// we need to limit overstep to the number of reactions on this timestep
@ -2615,7 +2615,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
}
// also, if atoms change number of bonds, but aren't landlocked, that could be bad
if (me == 0)
if (comm->me == 0)
for (int i = 0; i < twomol->natoms; i++) {
if ((create_atoms[i][myrxn] == 0) &&
(twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0]) &&
@ -2947,6 +2947,7 @@ broadcast entries of mega_glove which contain nonlocal atoms for perusal by all
void FixBondReact::ghost_glovecast()
{
#if !defined(MPI_STUBS)
const int nprocs = comm->nprocs;
global_megasize = 0;
@ -2965,7 +2966,7 @@ void FixBondReact::ghost_glovecast()
int *allstarts = new int[nprocs];
int start = 0;
for (int i = 0; i < me; i++) {
for (int i = 0; i < comm->me; i++) {
start += allncols[i];
}
MPI_Allgather(&start, 1, MPI_INT, allstarts, 1, MPI_INT, world);
@ -2993,7 +2994,7 @@ void FixBondReact::ghost_glovecast()
}
}
// let's send to root, dedup, then broadcast
if (me == 0) {
if (comm->me == 0) {
MPI_Gatherv(MPI_IN_PLACE, ghostly_num_mega, column, // Note: some values ignored for MPI_IN_PLACE
&(global_mega_glove[0][0]), allncols, allstarts,
column, 0, world);
@ -3003,7 +3004,7 @@ void FixBondReact::ghost_glovecast()
column, 0, world);
}
if (me == 0) dedup_mega_gloves(GLOBAL); // global_mega_glove mode
if (comm->me == 0) dedup_mega_gloves(GLOBAL); // global_mega_glove mode
MPI_Bcast(&global_megasize,1,MPI_INT,0,world);
MPI_Bcast(&(global_mega_glove[0][0]), global_megasize, column, 0, world);
@ -3745,7 +3746,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
Superpose3D<double, double **> superposer(n2superpose);
int fitroot = 0;
if (ifit >= 0 && ifit < atom->nlocal) {
fitroot = me;
fitroot = comm->me;
// get 'temperatere' averaged over site, used for created atoms' vels
t = get_temperature(my_mega_glove,1,iupdate);
@ -3763,7 +3764,8 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
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+1][iupdate]) < 0) {
error->warning(FLERR," eligible atoms skipped for created-atoms fit on rank {}\n",me);
error->warning(FLERR," eligible atoms skipped for created-atoms fit on rank {}\n",
comm->me);
continue;
}
iatom = atom->map(my_mega_glove[ipre+1][iupdate]);
@ -3791,7 +3793,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
if (create_atoms[m][rxnID] == 1) {
// apply optimal rotation/translation for created atom coords
// also map coords back into simulation box
if (fitroot == me) {
if (fitroot == comm->me) {
MathExtra::matvec(rotmat,twomol->x[m],coords[m]);
for (int i = 0; i < 3; i++) coords[m][i] += superposer.T[i];
imageflags[m] = atom->image[ifit];
@ -3879,7 +3881,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
int root = 0;
if (flag) {
root = me;
root = comm->me;
atom->avec->create_atom(twomol->type[m],coords[m]);
int n = atom->nlocal - 1;
@ -4025,7 +4027,7 @@ void FixBondReact::read_map_file(int myrxn)
while (strlen(keyword)) {
if (strcmp(keyword,"InitiatorIDs") == 0 || strcmp(keyword,"BondingIDs") == 0) {
if (strcmp(keyword,"BondingIDs") == 0)
if (me == 0) error->warning(FLERR,"Fix bond/react: The BondingIDs section title has been deprecated. Please use InitiatorIDs instead.");
if (comm->me == 0) error->warning(FLERR,"Fix bond/react: The BondingIDs section title has been deprecated. Please use InitiatorIDs instead.");
bondflag = 1;
readline(line);
sscanf(line,"%d",&ibonding[myrxn]);
@ -4291,7 +4293,7 @@ void FixBondReact::open(char *file)
void FixBondReact::readline(char *line)
{
int n;
if (me == 0) {
if (comm->me == 0) {
if (fgets(line,MAXLINE,fp) == nullptr) n = 0;
else n = strlen(line) + 1;
}
@ -4308,7 +4310,7 @@ void FixBondReact::parse_keyword(int flag, char *line, char *keyword)
// eof is set to 1 if any read hits end-of-file
int eof = 0;
if (me == 0) {
if (comm->me == 0) {
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) {
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
@ -4327,7 +4329,7 @@ void FixBondReact::parse_keyword(int flag, char *line, char *keyword)
// bcast keyword line to all procs
int n;
if (me == 0) n = strlen(line) + 1;
if (comm->me == 0) n = strlen(line) + 1;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
}
@ -4492,7 +4494,7 @@ void FixBondReact::write_restart(FILE *fp)
memcpy(rbuf,&store_rxn_count[0][0],sizeof(int)*rbufcount);
}
if (me == 0) {
if (comm->me == 0) {
int size = nreacts*sizeof(Set)+(rbufcount+1)*sizeof(int);
fwrite(&size,sizeof(int),1,fp);
fwrite(&revision,sizeof(int),1,fp);