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re-indent code to better match LAMMPS conventions

This commit is contained in:
Axel Kohlmeyer 2020-04-26 23:25:52 -04:00
parent 8fec14f593
commit d946c61789
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GPG Key ID: D9B44E93BF0C375A
1 changed files with 62 additions and 61 deletions
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123
src/USER-REACTION/fix_bond_react.cpp
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@ -267,7 +267,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
} else { } else {
double cutoff = force->numeric(FLERR,arg[iarg]); double cutoff = force->numeric(FLERR,arg[iarg]);
if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command: " if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command: "
"'Rmin' cannot be negative"); "'Rmin' cannot be negative");
cutsq[rxn][0] = cutoff*cutoff; cutsq[rxn][0] = cutoff*cutoff;
} }
iarg++; iarg++;
@ -335,10 +335,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
iarg += 3; iarg += 3;
} else if (strcmp(arg[iarg],"max_rxn") == 0) { } else if (strcmp(arg[iarg],"max_rxn") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
"'max_rxn' has too few arguments"); "'max_rxn' has too few arguments");
max_rxn[rxn] = force->inumeric(FLERR,arg[iarg+1]); max_rxn[rxn] = force->inumeric(FLERR,arg[iarg+1]);
if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: " if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: "
"'max_rxn' cannot be negative"); "'max_rxn' cannot be negative");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"stabilize_steps") == 0) { } else if (strcmp(arg[iarg],"stabilize_steps") == 0) {
if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword " if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword "
@ -704,36 +704,36 @@ void FixBondReact::post_constructor()
i_statted_tags[i] = 1; i_statted_tags[i] = 1;
} }
} else { } else {
// sleeping code, for future capabilities // sleeping code, for future capabilities
custom_exclude_flag = 1; custom_exclude_flag = 1;
// first we have to find correct fix group reference // first we have to find correct fix group reference
int n = strlen("GROUP_") + strlen(exclude_group) + 1; int n = strlen("GROUP_") + strlen(exclude_group) + 1;
char *fix_group = new char[n]; char *fix_group = new char[n];
strcpy(fix_group,"GROUP_"); strcpy(fix_group,"GROUP_");
strcat(fix_group,exclude_group); strcat(fix_group,exclude_group);
int ifix = modify->find_fix(fix_group); int ifix = modify->find_fix(fix_group);
Fix *fix = modify->fix[ifix]; Fix *fix = modify->fix[ifix];
delete [] fix_group; delete [] fix_group;
// this returns names of corresponding property // this returns names of corresponding property
int unused; int unused;
char * idprop; char * idprop;
idprop = (char *) fix->extract("property",unused); idprop = (char *) fix->extract("property",unused);
if (idprop == NULL) if (idprop == NULL)
error->all(FLERR,"Exclude group must be a per-atom property group"); error->all(FLERR,"Exclude group must be a per-atom property group");
len = strlen(idprop) + 1; len = strlen(idprop) + 1;
statted_id = new char[len]; statted_id = new char[len];
strcpy(statted_id,idprop); strcpy(statted_id,idprop);
// initialize per-atom statted_tags to 1 // initialize per-atom statted_tags to 1
// need to correct for smooth restarts // need to correct for smooth restarts
//int flag; //int flag;
//int index = atom->find_custom(statted_id,flag); //int index = atom->find_custom(statted_id,flag);
//int *i_statted_tags = atom->ivector[index]; //int *i_statted_tags = atom->ivector[index];
//for (int i = 0; i < atom->nlocal; i++) //for (int i = 0; i < atom->nlocal; i++)
// i_statted_tags[i] = 1; // i_statted_tags[i] = 1;
} }
// let's create a new nve/limit fix to limit newly reacted atoms // let's create a new nve/limit fix to limit newly reacted atoms
@ -800,7 +800,7 @@ void FixBondReact::post_integrate()
nevery[i] = ceil(input->variable->compute_equal(var_id[NEVERY][i])); nevery[i] = ceil(input->variable->compute_equal(var_id[NEVERY][i]));
if (nevery[i] <= 0) if (nevery[i] <= 0)
error->all(FLERR,"Illegal fix bond/react command: " error->all(FLERR,"Illegal fix bond/react command: "
"'Nevery' must be a positive integer"); "'Nevery' must be a positive integer");
if (!(update->ntimestep % nevery[i])) { if (!(update->ntimestep % nevery[i])) {
nevery_check = 0; nevery_check = 0;
break; break;
@ -915,7 +915,7 @@ void FixBondReact::post_integrate()
if (fraction[rxnID] < 1.0) { if (fraction[rxnID] < 1.0) {
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (partner[i]) probability[i] = random[rxnID]->uniform(); if (partner[i]) probability[i] = random[rxnID]->uniform();
} }
commflag = 2; commflag = 2;
@ -1872,7 +1872,7 @@ int FixBondReact::check_constraints()
} else if (constraints[i][1] == ARRHENIUS) { } else if (constraints[i][1] == ARRHENIUS) {
t = get_temperature(); t = get_temperature();
prrhob = constraints[i][3]*pow(t,constraints[i][4])* prrhob = constraints[i][3]*pow(t,constraints[i][4])*
exp(-constraints[i][5]/(force->boltz*t)); exp(-constraints[i][5]/(force->boltz*t));
if (prrhob < rrhandom[(int) constraints[i][2]]->uniform()) return 0; if (prrhob < rrhandom[(int) constraints[i][2]]->uniform()) return 0;
} }
} }
@ -1924,13 +1924,13 @@ double FixBondReact::get_temperature()
for (i = 0; i < onemol->natoms; i++) { for (i = 0; i < onemol->natoms; i++) {
ilocal = atom->map(glove[i][1]); ilocal = atom->map(glove[i][1]);
t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] + t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] +
v[ilocal][2]*v[ilocal][2]) * rmass[ilocal]; v[ilocal][2]*v[ilocal][2]) * rmass[ilocal];
} }
} else { } else {
for (i = 0; i < onemol->natoms; i++) { for (i = 0; i < onemol->natoms; i++) {
ilocal = atom->map(glove[i][1]); ilocal = atom->map(glove[i][1]);
t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] + t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] +
v[ilocal][2]*v[ilocal][2]) * mass[type[ilocal]]; v[ilocal][2]*v[ilocal][2]) * mass[type[ilocal]];
} }
} }
@ -1959,7 +1959,7 @@ int FixBondReact::get_chirality(double four_coords[12])
for (int i = 0; i < 3; i++) { for (int i = 0; i < 3; i++) {
mean3[i] = (four_coords[i] + four_coords[i+3] + mean3[i] = (four_coords[i] + four_coords[i+3] +
four_coords[i+6])/3; four_coords[i+6])/3;
vec4[i] = four_coords[i+9] - mean3[i]; vec4[i] = four_coords[i+9] - mean3[i];
} }
@ -2107,7 +2107,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
int ii = reverse_equiv[i][1][myrxn] - 1; int ii = reverse_equiv[i][1][myrxn] - 1;
for (int j = 0; j < twomol_nxspecial[ii][0]; j++) { for (int j = 0; j < twomol_nxspecial[ii][0]; j++) {
if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) { if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) {
error->all(FLERR,"Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted"); error->all(FLERR,"Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted");
} }
} }
} }
@ -2394,19 +2394,19 @@ void FixBondReact::glove_ghostcheck()
// 'ghosts of another' indication taken from comm->sendlist // 'ghosts of another' indication taken from comm->sendlist
int ghostly = 0; int ghostly = 0;
#if !defined(MPI_STUBS) #if !defined(MPI_STUBS)
if (comm->style == 0) { if (comm->style == 0) {
for (int i = 0; i < onemol->natoms; i++) { for (int i = 0; i < onemol->natoms; i++) {
int ilocal = atom->map(glove[i][1]); int ilocal = atom->map(glove[i][1]);
if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) { if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
ghostly = 1; ghostly = 1;
break; break;
}
} }
} else {
ghostly = 1;
} }
#endif } else {
ghostly = 1;
}
#endif
if (ghostly == 1) { if (ghostly == 1) {
ghostly_mega_glove[0][ghostly_num_mega] = rxnID; ghostly_mega_glove[0][ghostly_num_mega] = rxnID;
@ -2480,12 +2480,12 @@ void FixBondReact::ghost_glovecast()
// let's send to root, dedup, then broadcast // let's send to root, dedup, then broadcast
if (me == 0) { if (me == 0) {
MPI_Gatherv(MPI_IN_PLACE, ghostly_num_mega, column, // Note: some values ignored for MPI_IN_PLACE MPI_Gatherv(MPI_IN_PLACE, ghostly_num_mega, column, // Note: some values ignored for MPI_IN_PLACE
&(global_mega_glove[0][0]), allncols, allstarts, &(global_mega_glove[0][0]), allncols, allstarts,
column, 0, world); column, 0, world);
} else { } else {
MPI_Gatherv(&(global_mega_glove[0][start]), ghostly_num_mega, column, MPI_Gatherv(&(global_mega_glove[0][start]), ghostly_num_mega, column,
&(global_mega_glove[0][0]), allncols, allstarts, &(global_mega_glove[0][0]), allncols, allstarts,
column, 0, world); column, 0, world);
} }
if (me == 0) dedup_mega_gloves(1); // global_mega_glove mode if (me == 0) dedup_mega_gloves(1); // global_mega_glove mode
@ -3092,7 +3092,7 @@ void FixBondReact::read(int myrxn)
sscanf(line,"%d",&nequivalent); sscanf(line,"%d",&nequivalent);
if (nequivalent != onemol->natoms) if (nequivalent != onemol->natoms)
error->one(FLERR,"Bond/react: Number of equivalences in map file must " error->one(FLERR,"Bond/react: Number of equivalences in map file must "
"equal number of atoms in reaction templates"); "equal number of atoms in reaction templates");
} }
else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom); else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom);
else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete); else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete);
@ -3285,7 +3285,7 @@ void FixBondReact::Constraints(char *line, int myrxn)
tmp[6] = 181.0; // impossible range tmp[6] = 181.0; // impossible range
tmp[7] = 182.0; tmp[7] = 182.0;
sscanf(line,"%*s %lg %lg %lg %lg %lg %lg %lg %lg",&tmp[0],&tmp[1], sscanf(line,"%*s %lg %lg %lg %lg %lg %lg %lg %lg",&tmp[0],&tmp[1],
&tmp[2],&tmp[3],&tmp[4],&tmp[5],&tmp[6],&tmp[7]); &tmp[2],&tmp[3],&tmp[4],&tmp[5],&tmp[6],&tmp[7]);
if (tmp[0] > onemol->natoms || tmp[1] > onemol->natoms || if (tmp[0] > onemol->natoms || tmp[1] > onemol->natoms ||
tmp[2] > onemol->natoms || tmp[3] > onemol->natoms) tmp[2] > onemol->natoms || tmp[3] > onemol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file"); error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
@ -3513,16 +3513,17 @@ void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf)
if (commflag != 1) { if (commflag != 1) {
for (i = 0; i < n; i++) { for (i = 0; i < n; i++) {
j = list[i]; j = list[i];
if (closeneigh[rxnID] != 0) if (closeneigh[rxnID] != 0) {
if (buf[m+1] < distsq[j][1]) { if (buf[m+1] < distsq[j][1]) {
partner[j] = (tagint) ubuf(buf[m++]).i; partner[j] = (tagint) ubuf(buf[m++]).i;
distsq[j][1] = buf[m++]; distsq[j][1] = buf[m++];
} else m += 2; } else m += 2;
else } else {
if (buf[m+1] > distsq[j][0]) { if (buf[m+1] > distsq[j][0]) {
partner[j] = (tagint) ubuf(buf[m++]).i; partner[j] = (tagint) ubuf(buf[m++]).i;
distsq[j][0] = buf[m++]; distsq[j][0] = buf[m++];
} else m += 2; } else m += 2;
}
} }
} }
} }
@ -3580,9 +3581,9 @@ double FixBondReact::memory_usage()
void FixBondReact::print_bb() void FixBondReact::print_bb()
{ {
#if 0
//fix bond/create cargo code. eg nbonds needs to be added //fix bond/create cargo code. eg nbonds needs to be added
/*
for (int i = 0; i < atom->nlocal; i++) { for (int i = 0; i < atom->nlocal; i++) {
// printf("TAG " TAGINT_FORMAT ": %d nbonds: ",atom->tag[i],atom->num_bond[i]); // printf("TAG " TAGINT_FORMAT ": %d nbonds: ",atom->tag[i],atom->num_bond[i]);
for (int j = 0; j < atom->num_bond[i]; j++) { for (int j = 0; j < atom->num_bond[i]; j++) {
@ -3615,9 +3616,9 @@ for (int i = 0; i < atom->nlocal; i++) {
// printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i], // printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i],
atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]); atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
for (int j = 0; j < atom->nspecial[i][2]; j++) { for (int j = 0; j < atom->nspecial[i][2]; j++) {
// printf(" " TAGINT_FORMAT,atom->special[i][j]); printf(" " TAGINT_FORMAT,atom->special[i][j]);
} }
// printf("\n"); // printf("\n");
} }
*/ #endif
} }