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bond/react:add-modify-create-keyword

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This commit is contained in:
Jacob Gissinger
2020-09-21 10:29:42 -04:00
parent db8767ee63
commit 0236cabce9
2 changed files with 20 additions and 3 deletions
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22
src/USER-REACTION/fix_bond_react.cpp
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@ -205,6 +205,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(limit_duration,nreacts,"bond/react:limit_duration");
memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
memory->create(custom_charges_fragid,nreacts,"bond/react:custom_charges_fragid");
memory->create(modify_create_fragid,nreacts,"bond/react:modify_create_fragid");
memory->create(constraints,1,MAXCONARGS,"bond/react:constraints");
memory->create(var_flag,NUMVARVALS,nreacts,"bond/react:var_flag");
memory->create(var_id,NUMVARVALS,nreacts,"bond/react:var_id");
@ -225,6 +226,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
max_rxn[i] = INT_MAX;
stabilize_steps_flag[i] = 0;
custom_charges_fragid[i] = -1;
modify_create_fragid[i] = -1;
// set default limit duration to 60 timesteps
limit_duration[i] = 60;
reaction_count[i] = 0;
@ -380,6 +382,16 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
"'custom_charges' keyword does not exist");
}
iarg += 2;
} else if (strcmp(arg[iarg],"modify_create") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
"'modify_create' has too few arguments");
if (strcmp(arg[iarg+1],"no") == 0) modify_create_fragid[rxn] = -1; //default
else {
modify_create_fragid[rxn] = atom->molecules[unreacted_mol[rxn]]->findfragment(arg[iarg+1]);
if (modify_create_fragid[rxn] < 0) error->one(FLERR,"Bond/react: Molecule fragment for "
"'modify_create' keyword does not exist");
}
iarg += 2;
} else error->all(FLERR,"Illegal fix bond/react command: unknown keyword");
}
}
@ -561,6 +573,7 @@ FixBondReact::~FixBondReact()
memory->destroy(var_id);
memory->destroy(stabilize_steps_flag);
memory->destroy(custom_charges_fragid);
memory->destroy(modify_create_fragid);
memory->destroy(iatomtype);
memory->destroy(jatomtype);
@ -2605,8 +2618,7 @@ void FixBondReact::update_everything()
// used when deleting atoms
int ndel,ndelone;
int *mark = new int[nlocal];
for (int i = 0; i < nlocal; i++) mark[i] = 0;
int *mark;
tagint *tag = atom->tag;
AtomVec *avec = atom->avec;
@ -2653,6 +2665,8 @@ void FixBondReact::update_everything()
delete [] iskip;
// mark to-delete atoms
mark = new int[nlocal];
for (int i = 0; i < nlocal; i++) mark[i] = 0;
for (int i = 0; i < update_num_mega; i++) {
rxnID = update_mega_glove[0][i];
onemol = atom->molecules[unreacted_mol[rxnID]];
@ -3150,6 +3164,8 @@ void FixBondReact::update_everything()
atom->nimpropers += Tdelta_imprp;
}
/* ----------------------------------------------------------------------
read superimpose file
------------------------------------------------------------------------- */
@ -3258,7 +3274,7 @@ void FixBondReact::Equivalences(char *line, int myrxn)
for (int i = 0; i < nequivalent; i++) {
readline(line);
sscanf(line,"%d %d",&tmp1,&tmp2);
if (tmp1 > onemol->natoms || tmp2 > onemol->natoms)
if (tmp1 > onemol->natoms || tmp2 > twomol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
//equivalences is-> clmn 1: post-reacted, clmn 2: pre-reacted
equivalences[tmp2-1][0][myrxn] = tmp2;

1
src/USER-REACTION/fix_bond_react.h
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@ -65,6 +65,7 @@ class FixBondReact : public Fix {
int custom_exclude_flag;
int *stabilize_steps_flag;
int *custom_charges_fragid;
int *modify_create_fragid;
int nconstraints;
int narrhenius;
double **constraints;