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