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bond/react: update error messages
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@jrgissing
jrgissing committed May 31, 2019
1 parent e3e5a96 commit 80d906d
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Showing 2 changed files with 71 additions and 54 deletions.
57 changes: 28 additions & 29 deletions src/USER-MISC/fix_bond_react.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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");
}
}
}
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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++) {
Expand Down Expand Up @@ -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++) {
Expand Down Expand Up @@ -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;
}
Expand Down Expand Up @@ -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--;
Expand Down Expand Up @@ -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
Expand All @@ -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");
}
}
}
Expand All @@ -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");
}
}
}
Expand All @@ -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");
}
}
}
Expand All @@ -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;
}
Expand Down Expand Up @@ -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");
}
}
}
Expand Down Expand Up @@ -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++;
}
}
Expand Down Expand Up @@ -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++;
}
}
Expand Down Expand Up @@ -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++;
}
}
Expand Down Expand Up @@ -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++;
}
}
Expand Down Expand Up @@ -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 "#"
Expand Down Expand Up @@ -2782,21 +2781,21 @@ 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);

}

// 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)
Expand Down Expand Up @@ -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;
}
Expand Down Expand Up @@ -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;
}
Expand All @@ -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);
}
}
Expand All @@ -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);
}

Expand Down
68 changes: 43 additions & 25 deletions src/USER-MISC/fix_bond_react.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -189,47 +189,65 @@ Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Invalid exclude group name
E: Bond/react: Cannot use fix bond/react with non-molecular systems
Exclude group name should not previously be defined.
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
E: Cannot use fix bond/react with non-molecular systems
E: Bond/react: Rmax cutoff is longer than pairwise cutoff
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
This is not allowed because bond creation is done using the pairwise
neighbor list.
E: Fix bond/react cutoff is longer than pairwise cutoff
E: Bond/react: Molecule template ID for fix bond/react does not exist
This is not allowed because bond creation is done using the
pairwise neighbor list.
A valid molecule template must have been created with the molecule
command.
E: Molecule template ID for fix bond/react does not exist
E: Bond/react: Reaction templates must contain the same number of atoms
A valid molecule template must have been created with the molecule command.
There should be a one-to-one correspondence between atoms in the
pre-reacted and post-reacted templates, as specified by the map file.
E: Superimpose file errors:
E: Bond/react: Unknown section in map file
Please ensure superimpose file is properly formatted.
Please ensure reaction map files are properly formatted.
E: Atom affected by reaction too close to template edge
E: Bond/react: Atom affected by reaction too close to template edge
This means an atom which changes type during the reaction is too close
to an 'edge' atom defined in the superimpose file. This could cause incorrect
assignment of bonds, angle, etc. Generally, this means you must include
more atoms in your templates, such that there are at least two atoms
between each atom involved in the reaction and an edge atom.
to an 'edge' atom defined in the superimpose file. This could cause
incorrect assignment of bonds, angle, etc. Generally, this means you
must include more atoms in your templates, such that there are at
least two atoms between each atom involved in the reaction and an edge
atom.
E: Fix bond/react needs ghost atoms from farther away
E: Bond/react: Fix bond/react needs ghost atoms from farther away
This is because a processor needs to superimpose the entire unreacted
molecule template onto simulation atoms it can 'see.' The comm_modify cutoff
command can be used to extend the communication range.
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range.
E: Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted
Self-explanatory.
W: Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type
You may want to double-check that all atom types are properly assigned
in the post-reaction template.
E: Bond/react special bond generation overflow
The number of special bonds per-atom created by a reaction exceeds the
system setting. See the read_data or create_box command for how to
specify this value.
E: Excessive iteration of superimpose algorithm
E: Bond/react topology/atom exceed system topology/atom
You may have discovered a bug! But first, please double check that your
molecule template atom types, bond types, etc. are consistent with your simulation,
and that all atoms affected by a reaction are sufficently separated from edge atoms.
If this issue persists, please contact the developer.
The number of bonds, angles etc per-atom created by a reaction exceeds
the system setting. See the read_data or create_box command for how to
specify this value.
*/

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