diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index 37e9f96882..7e2a228992 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -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); } diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h index 74d53b8f21..36fc13ae21 100644 --- a/src/USER-MISC/fix_bond_react.h +++ b/src/USER-MISC/fix_bond_react.h @@ -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. - -E: Cannot use fix bond/react with non-molecular systems - -Only systems with bonds that can be changed can be used. Atom_style +Only systems with bonds that can be changed can be used. Atom_style template does not qualify. -E: Fix bond/react cutoff is longer than pairwise cutoff +E: Bond/react: Rmax cutoff is longer than pairwise cutoff -This is not allowed because bond creation is done using the -pairwise neighbor list. +This is not allowed because bond creation is done using the pairwise +neighbor list. -E: Molecule template ID for fix bond/react does not exist +E: Bond/react: Molecule template ID for fix bond/react does not exist -A valid molecule template must have been created with the molecule command. +A valid molecule template must have been created with the molecule +command. -E: Superimpose file errors: +E: Bond/react: Reaction templates must contain the same number of atoms -Please ensure superimpose file is properly formatted. +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: Atom affected by reaction too close to template edge +E: Bond/react: Unknown section in map file + +Please ensure reaction map files are properly formatted. + +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: Excessive iteration of superimpose algorithm +E: Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted -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. +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: Bond/react topology/atom exceed system topology/atom + +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. */