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bond/react: update error messages

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This commit is contained in:
jrgissing
2019-05-30 23:27:23 -06:00
parent e3e5a962b0
commit 80d906d445
2 changed files with 72 additions and 55 deletions
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57
src/USER-MISC/fix_bond_react.cpp
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@ -308,8 +308,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
onemol->check_attributes(0);
twomol->check_attributes(0);
if (onemol->natoms != twomol->natoms)
error->all(FLERR,"Post-reacted template must contain the same "
"number of atoms as the pre-reacted template");
error->all(FLERR,"Bond/react: Reaction templates must contain the same number of atoms");
get_molxspecials();
read(i);
fclose(fp);
@ -324,7 +323,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
delete [] files;
if (atom->molecular != 1)
error->all(FLERR,"Cannot use fix bond/react with non-molecular systems");
error->all(FLERR,"Bond/react: Cannot use fix bond/react with non-molecular systems");
// check if bonding atoms are 1-2, 1-3, or 1-4 bonded neighbors
// if so, we don't need non-bonded neighbor list
@ -665,7 +664,7 @@ void FixBondReact::init()
// check cutoff for iatomtype,jatomtype
for (int i = 0; i < nreacts; i++) {
if (force->pair == NULL || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
error->all(FLERR,"Fix bond/react cutoff is longer than pairwise cutoff");
error->all(FLERR,"Bond/react: Fix bond/react cutoff is longer than pairwise cutoff");
}
// need a half neighbor list, built every Nevery steps
@ -1174,7 +1173,7 @@ void FixBondReact::superimpose_algorithm()
// let's go ahead and catch the simplest of hangs
//if (hang_catch > onemol->natoms*4)
if (hang_catch > atom->nlocal*30) {
error->one(FLERR,"Excessive iteration of superimpose algorithm");
error->one(FLERR,"Bond/react: Excessive iteration of superimpose algorithm");
}
}
}
@ -1287,7 +1286,7 @@ void FixBondReact::make_a_guess()
for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) {
if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) {
error->all(FLERR,"Fix bond/react needs ghost atoms from further away1"); // parallel issues.
error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away1"); // parallel issues.
}
if (i_limit_tags[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] != 0) {
status = GUESSFAIL;
@ -1398,7 +1397,7 @@ void FixBondReact::check_a_neighbor()
//another check for ghost atoms. perhaps remove the one in make_a_guess
if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
error->all(FLERR,"Fix bond/react needs ghost atoms from further away2");
error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away2");
}
for (int j = 0; j < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; j++) {
@ -1450,7 +1449,7 @@ void FixBondReact::check_a_neighbor()
//another check for ghost atoms. perhaps remove the one in make_a_guess
if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
error->all(FLERR,"Fix bond/react needs ghost atoms from further away3");
error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away3");
}
for (int ii = 0; ii < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; ii++) {
@ -1492,7 +1491,7 @@ void FixBondReact::crosscheck_the_neighbor()
glove[onemol_xspecial[pion][trace]-1][0] == 0) {
if (avail_guesses == MAXGUESS) {
error->warning(FLERR,"Fix bond/react failed because MAXGUESS set too small. ask developer for info");
error->warning(FLERR,"Bond/react: Fix bond/react failed because MAXGUESS set too small. ask developer for info");
status = GUESSFAIL;
return;
}
@ -1561,7 +1560,7 @@ void FixBondReact::inner_crosscheck_loop()
//another check for ghost atoms. perhaps remove the one in make_a_guess
if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
error->all(FLERR,"Fix bond/react needs ghost atoms from further away4");
error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away4");
}
if (guess_branch[avail_guesses-1] == 0) avail_guesses--;
@ -1722,7 +1721,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
// if atoms change types, but aren't landlocked, that's bad
for (int i = 0; i < twomol->natoms; i++) {
if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0)
error->one(FLERR,"Atom affected by reaction too close to template edge");
error->one(FLERR,"Bond/react: Atom affected by reaction too close to template edge");
}
// additionally, if a bond changes type, but neither involved atom is landlocked, bad
@ -1738,7 +1737,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
error->one(FLERR,"Bond type affected by reaction too close to template edge");
error->one(FLERR,"Bond/react: Bond type affected by reaction too close to template edge");
}
}
}
@ -1748,7 +1747,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
if (onemol_batom == equivalences[i][1][myrxn]) {
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
error->one(FLERR,"Bond type affected by reaction too close to template edge");
error->one(FLERR,"Bond/react: Bond type affected by reaction too close to template edge");
}
}
}
@ -1764,7 +1763,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
int ii = reverse_equiv[i][1][myrxn] - 1;
for (int j = 0; j < twomol_nxspecial[ii][0]; j++) {
if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) {
error->one(FLERR,"A deleted atom cannot remain bonded to an atom that is not deleted");
error->one(FLERR,"Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted");
}
}
}
@ -1775,7 +1774,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
for (int i = 0; i < twomol->natoms; i++) {
if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) {
char str[128];
sprintf(str,"An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
sprintf(str,"Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
error->warning(FLERR,str);
break;
}
@ -2263,7 +2262,7 @@ void FixBondReact::update_everything()
if (landlocked_atoms[j][rxnID] == 1) {
for (int k = 0; k < nspecial[atom->map(update_mega_glove[jj+1][i])][2]; k++) {
if (atom->map(special[atom->map(update_mega_glove[jj+1][i])][k]) < 0) {
error->all(FLERR,"Fix bond/react needs ghost atoms from further away - most likely too many processors");
error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away - most likely too many processors");
}
}
}
@ -2388,7 +2387,7 @@ void FixBondReact::update_everything()
bond_atom[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i];
num_bond[atom->map(update_mega_glove[jj+1][i])]++;
if (num_bond[atom->map(update_mega_glove[jj+1][i])] > atom->bond_per_atom)
error->one(FLERR,"Bond/react bonds/atom exceed system bonds/atom");
error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
delta_bonds++;
}
}
@ -2464,7 +2463,7 @@ void FixBondReact::update_everything()
angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i];
num_angle[atom->map(update_mega_glove[jj+1][i])]++;
if (num_angle[atom->map(update_mega_glove[jj+1][i])] > atom->angle_per_atom)
error->one(FLERR,"Bond/react angles/atom exceed system angles/atom");
error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
delta_angle++;
}
}
@ -2547,7 +2546,7 @@ void FixBondReact::update_everything()
dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i];
num_dihedral[atom->map(update_mega_glove[jj+1][i])]++;
if (num_dihedral[atom->map(update_mega_glove[jj+1][i])] > atom->dihedral_per_atom)
error->one(FLERR,"Bond/react dihedrals/atom exceed system dihedrals/atom");
error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
delta_dihed++;
}
}
@ -2630,7 +2629,7 @@ void FixBondReact::update_everything()
improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i];
num_improper[atom->map(update_mega_glove[jj+1][i])]++;
if (num_improper[atom->map(update_mega_glove[jj+1][i])] > atom->improper_per_atom)
error->one(FLERR,"Bond/react impropers/atom exceed system impropers/atom");
error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
delta_imprp++;
}
}
@ -2728,7 +2727,7 @@ void FixBondReact::read(int myrxn)
// skip 1st line of file
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of superimpose file");
if (eof == NULL) error->one(FLERR,"Bond/react: Unexpected end of superimpose file");
// read header lines
// skip blank lines or lines that start with "#"
@ -2782,7 +2781,7 @@ void FixBondReact::read(int myrxn)
DeleteAtoms(line, myrxn);
} else if (strcmp(keyword,"Constraints") == 0) {
Constraints(line, myrxn);
} else error->one(FLERR,"Unknown section in superimpose file");
} else error->one(FLERR,"Bond/react: Unknown section in map file");
parse_keyword(1,line,keyword);
@ -2790,13 +2789,13 @@ void FixBondReact::read(int myrxn)
// error check
if (bondflag == 0 || equivflag == 0)
error->all(FLERR,"Superimpose file missing BondingIDs or Equivalences section\n");
error->all(FLERR,"Bond/react: Map file missing BondingIDs or Equivalences section\n");
if (update_edges_flag[myrxn] == 2 && customedgesflag == 0)
error->all(FLERR,"Map file must have a Custom Edges section when using 'update_edges custom'\n");
error->all(FLERR,"Bond/react: Map file must have a Custom Edges section when using 'update_edges custom'\n");
if (update_edges_flag[myrxn] != 2 && customedgesflag == 1)
error->all(FLERR,"Specify 'update_edges custom' to include Custom Edges section in map file\n");
error->all(FLERR,"Bond/react: Specify 'update_edges custom' to include Custom Edges section in map file\n");
}
void FixBondReact::EdgeIDs(char *line, int myrxn)
@ -2842,7 +2841,7 @@ void FixBondReact::CustomEdges(char *line, int myrxn)
else if (strcmp(edgemode,"charges") == 0)
custom_edges[tmp-1][myrxn] = 1;
else
error->one(FLERR,"Illegal value in 'Custom Edges' section of map file");
error->one(FLERR,"Bond/react: Illegal value in 'Custom Edges' section of map file");
}
delete [] edgemode;
}
@ -2873,7 +2872,7 @@ void FixBondReact::Constraints(char *line, int myrxn)
constraints[myrxn][3] = tmp[2]*tmp[2]; // using square of distance
constraints[myrxn][4] = tmp[3]*tmp[3];
} else
error->one(FLERR,"Illegal constraint type in 'Constraints' section of map file");
error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file");
}
delete [] constraint_type;
}
@ -2883,7 +2882,7 @@ void FixBondReact::open(char *file)
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open superimpose file %s",file);
snprintf(str,128,"Bond/react: Cannot open map file %s",file);
error->one(FLERR,str);
}
}
@ -2896,7 +2895,7 @@ void FixBondReact::readline(char *line)
else n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
if (n == 0) error->all(FLERR,"Unexpected end of superimpose file");
if (n == 0) error->all(FLERR,"Bond/react: Unexpected end of map file");
MPI_Bcast(line,n,MPI_CHAR,0,world);
}