parsing is done on all MPI ranks, so we better use error->all() instead of error->one()
This commit is contained in:
Axel Kohlmeyer
156
src/molecule.cpp
156
src/molecule.cpp
@ -691,12 +691,12 @@ void Molecule::coords(char *line)
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ValueTokenizer values(utils::trim_comment(line));
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if (values.count() != 4)
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error->one(FLERR,fmt::format("Invalid line in Coords section of "
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error->all(FLERR,fmt::format("Invalid line in Coords section of "
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"molecule file: {}",line));
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int iatom = values.next_int() - 1;
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if (iatom < 0 || iatom >= natoms)
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error->one(FLERR,"Invalid atom index in Coords section of molecule file");
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error->all(FLERR,"Invalid atom index in Coords section of molecule file");
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count[iatom]++;
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x[iatom][0] = values.next_double();
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x[iatom][1] = values.next_double();
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@ -707,8 +707,8 @@ void Molecule::coords(char *line)
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x[iatom][2] *= sizescale;
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}
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} catch (TokenizerException &e) {
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error->one(FLERR,fmt::format("Invalid line in Coords section of "
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"molecule file: {}.\n {}",e.what(),line));
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error->all(FLERR,fmt::format("Invalid line in Coords section of "
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"molecule file: {}\n{}",e.what(),line));
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}
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for (int i = 0; i < natoms; i++)
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@ -737,19 +737,19 @@ void Molecule::types(char *line)
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ValueTokenizer values(utils::trim_comment(line));
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if (values.count() != 2)
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error->one(FLERR,fmt::format("Invalid line in Types section of "
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error->all(FLERR,fmt::format("Invalid line in Types section of "
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"molecule file: {}",line));
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int iatom = values.next_int() - 1;
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if (iatom < 0 || iatom >= natoms)
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error->one(FLERR,"Invalid atom index in Types section of molecule file");
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error->all(FLERR,"Invalid atom index in Types section of molecule file");
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count[iatom]++;
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type[iatom] = values.next_int();
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type[iatom] += toffset;
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}
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid line in Types section of "
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"molecule file: {}.\n {}", e.what(),line));
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error->all(FLERR, fmt::format("Invalid line in Types section of "
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"molecule file: {}\n{}", e.what(),line));
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}
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for (int i = 0; i < natoms; i++) {
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@ -777,19 +777,19 @@ void Molecule::molecules(char *line)
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readline(line);
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ValueTokenizer values(utils::trim_comment(line));
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if (values.count() != 2)
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error->one(FLERR,fmt::format("Invalid line in Molecules section of "
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error->all(FLERR,fmt::format("Invalid line in Molecules section of "
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"molecule file: {}",line));
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int iatom = values.next_int() - 1;
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if (iatom < 0 || iatom >= natoms)
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error->one(FLERR,"Invalid atom index in Molecules section of molecule file");
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error->all(FLERR,"Invalid atom index in Molecules section of molecule file");
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count[iatom]++;
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molecule[iatom] = values.next_tagint();
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// molecule[iatom] += moffset; // placeholder for possible molecule offset
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}
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid line in Molecules section of "
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"molecule file: {}.\n {}", e.what(), line));
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error->all(FLERR, fmt::format("Invalid line in Molecules section of "
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"molecule file: {}\n{}",e.what(),line));
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}
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for (int i = 0; i < natoms; i++)
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@ -818,7 +818,7 @@ void Molecule::fragments(char *line)
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ValueTokenizer values(utils::trim_comment(line));
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if ((int)values.count() > natoms+1)
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error->one(FLERR,"Too many atoms per fragment in Fragments "
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error->all(FLERR,"Too many atoms per fragment in Fragments "
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"section of molecule file");
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fragmentnames[i] = values.next_string();
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@ -826,15 +826,15 @@ void Molecule::fragments(char *line)
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while (values.has_next()) {
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int iatom = values.next_int()-1;
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if (iatom < 0 || iatom >= natoms)
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error->one(FLERR,fmt::format("Invalid atom ID {} for fragment {} in "
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error->all(FLERR,fmt::format("Invalid atom ID {} for fragment {} in "
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"Fragments section of molecule file",
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iatom+1, fragmentnames[i]));
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fragmentmask[i][iatom] = 1;
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}
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}
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid atom ID in Fragments section of "
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"molecule file: {}.\n {}", e.what(),line));
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error->all(FLERR, fmt::format("Invalid atom ID in Fragments section of "
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"molecule file: {}\n{}", e.what(),line));
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}
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}
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@ -850,20 +850,25 @@ void Molecule::charges(char *line)
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readline(line);
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ValueTokenizer values(utils::trim_comment(line));
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if ((int)values.count() != 2) error->one(FLERR,"Invalid Charges section in molecule file");
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if ((int)values.count() != 2)
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error->all(FLERR,fmt::format("Invalid line in Charges section of "
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"molecule file: {}",line));
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int iatom = values.next_int() - 1;
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if (iatom < 0 || iatom >= natoms) error->one(FLERR,"Invalid Charges section in molecule file");
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if (iatom < 0 || iatom >= natoms)
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error->all(FLERR,"Invalid atom index in Charges section of molecule file");
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count[iatom]++;
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q[iatom] = values.next_double();
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}
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid Charges section in molecule file\n"
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"{}", e.what()));
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error->all(FLERR, fmt::format("Invalid line in Charges section of "
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"molecule file: {}.\n{}",e.what(),line));
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}
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for (int i = 0; i < natoms; i++)
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if (count[i] == 0) error->all(FLERR,"Invalid Charges section in molecule file");
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if (count[i] == 0) error->all(FLERR,fmt::format("Atom {} missing in Charges "
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"section of molecule file",i+1));
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}
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/* ----------------------------------------------------------------------
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@ -879,10 +884,14 @@ void Molecule::diameters(char *line)
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readline(line);
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ValueTokenizer values(utils::trim_comment(line));
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if (values.count() != 2) error->one(FLERR,"Invalid Diameters section in molecule file");
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if (values.count() != 2)
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error->all(FLERR,fmt::format("Invalid line in Diameters section of "
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"molecule file: {}",line));
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int iatom = values.next_int() - 1;
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if (iatom < 0 || iatom >= natoms) error->one(FLERR,"Invalid Diameters section in molecule file");
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if (iatom < 0 || iatom >= natoms)
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error->all(FLERR,"Invalid atom index in Diameters section of molecule file");
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count[iatom]++;
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radius[iatom] = values.next_double();
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radius[iatom] *= sizescale;
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@ -890,16 +899,17 @@ void Molecule::diameters(char *line)
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maxradius = MAX(maxradius,radius[iatom]);
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}
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid Diameters section in molecule file\n"
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"{}", e.what()));
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error->all(FLERR, fmt::format("Invalid line in Diameters section of "
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"molecule file: {}\n{}",e.what(),line));
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}
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for (int i = 0; i < natoms; i++)
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if (count[i] == 0) error->all(FLERR,"Invalid Diameters section in molecule file");
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for (int i = 0; i < natoms; i++)
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for (int i = 0; i < natoms; i++) {
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if (count[i] == 0) error->all(FLERR,fmt::format("Atom {} missing in Diameters "
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"section of molecule file",i+1));
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if (radius[i] < 0.0)
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error->all(FLERR,"Invalid atom diameter in molecule file");
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error->all(FLERR,fmt::format("Invalid atom diameter {} for atom {} "
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"in molecule file", radius[i], i+1));
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}
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}
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/* ----------------------------------------------------------------------
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@ -914,16 +924,16 @@ void Molecule::masses(char *line)
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readline(line);
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ValueTokenizer values(utils::trim_comment(line));
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if (values.count() != 2) error->one(FLERR,"Invalid Masses section in molecule file");
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if (values.count() != 2) error->all(FLERR,"Invalid Masses section in molecule file");
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int iatom = values.next_int() - 1;
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if (iatom < 0 || iatom >= natoms) error->one(FLERR,"Invalid Masses section in molecule file");
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if (iatom < 0 || iatom >= natoms) error->all(FLERR,"Invalid Masses section in molecule file");
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count[iatom]++;
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rmass[iatom] = values.next_double();
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rmass[iatom] *= sizescale*sizescale*sizescale;
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}
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid Masses section in molecule file\n"
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error->all(FLERR, fmt::format("Invalid Masses section in molecule file\n"
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"{}", e.what()));
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}
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@ -958,13 +968,13 @@ void Molecule::bonds(int flag, char *line)
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try {
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ValueTokenizer values(utils::trim_comment(line));
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if (values.count() != 4) error->one(FLERR,"Invalid Bonds section in molecule file");
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if (values.count() != 4) error->all(FLERR,"Invalid Bonds section in molecule file");
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values.next_int();
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itype = values.next_int();
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atom1 = values.next_tagint();
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atom2 = values.next_tagint();
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid Bonds section in molecule file\n"
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error->all(FLERR, fmt::format("Invalid Bonds section in molecule file\n"
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"{}", e.what()));
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}
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@ -972,9 +982,9 @@ void Molecule::bonds(int flag, char *line)
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if ((atom1 <= 0) || (atom1 > natoms) ||
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(atom2 <= 0) || (atom2 > natoms) || (atom1 == atom2))
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error->one(FLERR,"Invalid atom ID in Bonds section of molecule file");
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error->all(FLERR,"Invalid atom ID in Bonds section of molecule file");
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if ((itype <= 0) || (domain->box_exist && (itype > atom->nbondtypes)))
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error->one(FLERR,"Invalid bond type in Bonds section of molecule file");
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error->all(FLERR,"Invalid bond type in Bonds section of molecule file");
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if (flag) {
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m = atom1-1;
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@ -1026,14 +1036,14 @@ void Molecule::angles(int flag, char *line)
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try {
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ValueTokenizer values(utils::trim_comment(line));
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if (values.count() != 5) error->one(FLERR,"Invalid Angles section in molecule file");
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if (values.count() != 5) error->all(FLERR,"Invalid Angles section in molecule file");
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values.next_int();
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itype = values.next_int();
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atom1 = values.next_tagint();
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atom2 = values.next_tagint();
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atom3 = values.next_tagint();
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid Angles section in molecule file\n"
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error->all(FLERR, fmt::format("Invalid Angles section in molecule file\n"
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"{}", e.what()));
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}
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@ -1043,9 +1053,9 @@ void Molecule::angles(int flag, char *line)
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(atom2 <= 0) || (atom2 > natoms) ||
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(atom3 <= 0) || (atom3 > natoms) ||
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(atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3))
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error->one(FLERR,"Invalid atom ID in Angles section of molecule file");
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error->all(FLERR,"Invalid atom ID in Angles section of molecule file");
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if ((itype <= 0) || (domain->box_exist && (itype > atom->nangletypes)))
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error->one(FLERR,"Invalid angle type in Angles section of molecule file");
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error->all(FLERR,"Invalid angle type in Angles section of molecule file");
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if (flag) {
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m = atom2-1;
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@ -1110,7 +1120,7 @@ void Molecule::dihedrals(int flag, char *line)
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try {
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ValueTokenizer values(utils::trim_comment(line));
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if (values.count() != 6) error->one(FLERR,"Invalid Dihedrals section in molecule file");
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if (values.count() != 6) error->all(FLERR,"Invalid Dihedrals section in molecule file");
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values.next_int();
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itype = values.next_int();
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atom1 = values.next_tagint();
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@ -1118,7 +1128,7 @@ void Molecule::dihedrals(int flag, char *line)
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atom3 = values.next_tagint();
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atom4 = values.next_tagint();
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid Dihedrals section in molecule file\n"
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error->all(FLERR, fmt::format("Invalid Dihedrals section in molecule file\n"
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"{}", e.what()));
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}
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@ -1130,10 +1140,10 @@ void Molecule::dihedrals(int flag, char *line)
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(atom4 <= 0) || (atom4 > natoms) ||
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(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
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(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
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error->one(FLERR,
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error->all(FLERR,
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"Invalid atom ID in dihedrals section of molecule file");
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if ((itype <= 0) || (domain->box_exist && (itype > atom->ndihedraltypes)))
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error->one(FLERR,"Invalid dihedral type in Dihedrals section of molecule file");
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error->all(FLERR,"Invalid dihedral type in Dihedrals section of molecule file");
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if (flag) {
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m = atom2-1;
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@ -1209,7 +1219,7 @@ void Molecule::impropers(int flag, char *line)
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try {
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ValueTokenizer values(utils::trim_comment(line));
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if (values.count() != 6) error->one(FLERR,"Invalid Impropers section in molecule file");
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if (values.count() != 6) error->all(FLERR,"Invalid Impropers section in molecule file");
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values.next_int();
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itype = values.next_int();
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atom1 = values.next_tagint();
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@ -1217,7 +1227,7 @@ void Molecule::impropers(int flag, char *line)
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atom3 = values.next_tagint();
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atom4 = values.next_tagint();
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid Impropers section in molecule file\n"
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error->all(FLERR, fmt::format("Invalid Impropers section in molecule file\n"
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"{}", e.what()));
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}
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@ -1229,10 +1239,10 @@ void Molecule::impropers(int flag, char *line)
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(atom4 <= 0) || (atom4 > natoms) ||
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(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
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(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
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error->one(FLERR,
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error->all(FLERR,
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"Invalid atom ID in impropers section of molecule file");
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if ((itype <= 0) || (domain->box_exist && (itype > atom->nimpropertypes)))
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error->one(FLERR,"Invalid improper type in Impropers section of molecule file");
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error->all(FLERR,"Invalid improper type in Impropers section of molecule file");
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if (flag) {
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m = atom2-1;
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@ -1302,13 +1312,13 @@ void Molecule::nspecial_read(int flag, char *line)
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try {
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ValueTokenizer values(utils::trim_comment(line));
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if (values.count() != 4) error->one(FLERR,"Invalid Special Bond Counts section in molecule file");
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if (values.count() != 4) error->all(FLERR,"Invalid Special Bond Counts section in molecule file");
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values.next_int();
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c1 = values.next_tagint();
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c2 = values.next_tagint();
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c3 = values.next_tagint();
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid Special Bond Counts section in molecule file\n"
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error->all(FLERR, fmt::format("Invalid Special Bond Counts section in molecule file\n"
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"{}", e.what()));
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}
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@ -1334,7 +1344,7 @@ void Molecule::special_read(char *line)
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int nwords = values.count();
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if (nwords != nspecial[i][2]+1)
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error->one(FLERR,"Molecule file special list "
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error->all(FLERR,"Molecule file special list "
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"does not match special count");
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values.next_int(); // ignore
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@ -1343,11 +1353,11 @@ void Molecule::special_read(char *line)
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special[i][m-1] = values.next_tagint();
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if (special[i][m-1] <= 0 || special[i][m-1] > natoms ||
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special[i][m-1] == i+1)
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error->one(FLERR,"Invalid special atom index in molecule file");
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error->all(FLERR,"Invalid special atom index in molecule file");
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}
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}
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} catch (TokenizerException &e) {
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error->one(FLERR, fmt::format("Invalid Molecule file special list\n"
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error->all(FLERR, fmt::format("Invalid Molecule file special list\n"
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"{}", e.what()));
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}
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}
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@ -1379,7 +1389,7 @@ void Molecule::special_generate()
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nspecial[i][0]++;
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nspecial[atom2][0]++;
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if (count[i] >= atom->maxspecial || count[atom2] >= atom->maxspecial)
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error->one(FLERR,"Molecule auto special bond generation overflow");
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error->all(FLERR,"Molecule auto special bond generation overflow");
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tmpspecial[i][count[i]++] = atom2 + 1;
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tmpspecial[atom2][count[atom2]++] = i + 1;
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}
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@ -1391,7 +1401,7 @@ void Molecule::special_generate()
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atom1 = i;
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atom2 = bond_atom[i][j];
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if (count[atom1] >= atom->maxspecial)
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error->one(FLERR,"Molecule auto special bond generation overflow");
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error->all(FLERR,"Molecule auto special bond generation overflow");
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tmpspecial[i][count[atom1]++] = atom2;
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}
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}
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@ -1414,7 +1424,7 @@ void Molecule::special_generate()
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}
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if (!dedup) {
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if (count[i] >= atom->maxspecial)
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error->one(FLERR,"Molecule auto special bond generation overflow");
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error->all(FLERR,"Molecule auto special bond generation overflow");
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tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m]-1][j];
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nspecial[i][1]++;
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}
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@ -1438,7 +1448,7 @@ void Molecule::special_generate()
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}
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if (!dedup) {
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if (count[i] >= atom->maxspecial)
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error->one(FLERR,"Molecule auto special bond generation overflow");
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error->all(FLERR,"Molecule auto special bond generation overflow");
|
||||
tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m]-1][j];
|
||||
nspecial[i][2]++;
|
||||
}
|
||||
@ -1471,19 +1481,19 @@ void Molecule::shakeflag_read(char *line)
|
||||
ValueTokenizer values(utils::trim_comment(line));
|
||||
|
||||
if (values.count() != 2)
|
||||
error->one(FLERR,"Invalid Shake Flags section in molecule file");
|
||||
error->all(FLERR,"Invalid Shake Flags section in molecule file");
|
||||
|
||||
values.next_int();
|
||||
shake_flag[i] = values.next_int();
|
||||
}
|
||||
} catch (TokenizerException &e) {
|
||||
error->one(FLERR, fmt::format("Invalid Shake Flags section in molecule file\n"
|
||||
error->all(FLERR, fmt::format("Invalid Shake Flags section in molecule file\n"
|
||||
"{}", e.what()));
|
||||
}
|
||||
|
||||
for (int i = 0; i < natoms; i++)
|
||||
if (shake_flag[i] < 0 || shake_flag[i] > 4)
|
||||
error->one(FLERR,"Invalid shake flag in molecule file");
|
||||
error->all(FLERR,"Invalid shake flag in molecule file");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -1539,15 +1549,15 @@ void Molecule::shakeatom_read(char *line)
|
||||
break;
|
||||
|
||||
default:
|
||||
error->one(FLERR,"Invalid shake atom in molecule file");
|
||||
error->all(FLERR,"Invalid shake atom in molecule file");
|
||||
}
|
||||
|
||||
if (nmatch != nwant)
|
||||
error->one(FLERR,"Invalid shake atom in molecule file");
|
||||
error->all(FLERR,"Invalid shake atom in molecule file");
|
||||
}
|
||||
|
||||
} catch (TokenizerException &e) {
|
||||
error->one(FLERR,fmt::format("Invalid shake atom in molecule file\n"
|
||||
error->all(FLERR,fmt::format("Invalid shake atom in molecule file\n"
|
||||
"{}", e.what()));
|
||||
}
|
||||
|
||||
@ -1556,7 +1566,7 @@ void Molecule::shakeatom_read(char *line)
|
||||
if (m == 1) m = 3;
|
||||
for (int j = 0; j < m; j++)
|
||||
if (shake_atom[i][j] <= 0 || shake_atom[i][j] > natoms)
|
||||
error->one(FLERR,"Invalid shake atom in molecule file");
|
||||
error->all(FLERR,"Invalid shake atom in molecule file");
|
||||
}
|
||||
}
|
||||
|
||||
@ -1610,14 +1620,14 @@ void Molecule::shaketype_read(char *line)
|
||||
break;
|
||||
|
||||
default:
|
||||
error->one(FLERR,"Invalid shake type data in molecule file");
|
||||
error->all(FLERR,"Invalid shake type data in molecule file");
|
||||
}
|
||||
|
||||
if (nmatch != nwant)
|
||||
error->one(FLERR,"Invalid shake type data in molecule file");
|
||||
error->all(FLERR,"Invalid shake type data in molecule file");
|
||||
}
|
||||
} catch (TokenizerException &e) {
|
||||
error->one(FLERR, fmt::format("Invalid shake type data in molecule file\n",
|
||||
error->all(FLERR, fmt::format("Invalid shake type data in molecule file\n",
|
||||
"{}", e.what()));
|
||||
}
|
||||
|
||||
@ -1626,10 +1636,10 @@ void Molecule::shaketype_read(char *line)
|
||||
if (m == 1) m = 3;
|
||||
for (int j = 0; j < m-1; j++)
|
||||
if (shake_type[i][j] <= 0)
|
||||
error->one(FLERR,"Invalid shake bond type in molecule file");
|
||||
error->all(FLERR,"Invalid shake bond type in molecule file");
|
||||
if (shake_flag[i] == 1)
|
||||
if (shake_type[i][2] <= 0)
|
||||
error->one(FLERR,"Invalid shake angle type in molecule file");
|
||||
error->all(FLERR,"Invalid shake angle type in molecule file");
|
||||
}
|
||||
}
|
||||
|
||||
@ -1653,9 +1663,9 @@ void Molecule::body(int flag, int pflag, char *line)
|
||||
int ncount = values.count();
|
||||
|
||||
if (ncount == 0)
|
||||
error->one(FLERR,"Too few values in body section of molecule file");
|
||||
error->all(FLERR,"Too few values in body section of molecule file");
|
||||
if (nword+ncount > nparam)
|
||||
error->one(FLERR,"Too many values in body section of molecule file");
|
||||
error->all(FLERR,"Too many values in body section of molecule file");
|
||||
|
||||
if (flag) {
|
||||
if (pflag == 0) {
|
||||
@ -1670,7 +1680,7 @@ void Molecule::body(int flag, int pflag, char *line)
|
||||
} else nword += ncount;
|
||||
}
|
||||
} catch (TokenizerException &e) {
|
||||
error->one(FLERR, fmt::format("Invalid body params in molecule file\n",
|
||||
error->all(FLERR, fmt::format("Invalid body params in molecule file\n",
|
||||
"{}", e.what()));
|
||||
}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user