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update whitespace and argument formats for longer source lines

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This commit is contained in:
Axel Kohlmeyer
2022-01-16 15:36:01 -05:00
parent aa71ea6c40
commit 943fe487b5
1 changed files with 81 additions and 141 deletions
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214
src/molecule.cpp
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@ -57,8 +57,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
id = utils::strdup(arg[0]); id = utils::strdup(arg[0]);
if (!utils::is_id(id)) if (!utils::is_id(id))
error->all(FLERR,"Molecule template ID must have only " error->all(FLERR,"Molecule template ID must have only alphanumeric or underscore characters");
"alphanumeric or underscore characters");
// parse args until reach unknown arg (next file) // parse args until reach unknown arg (next file)
@ -130,8 +129,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
if (me == 0) { if (me == 0) {
fp = fopen(arg[ifile],"r"); fp = fopen(arg[ifile],"r");
if (fp == nullptr) if (fp == nullptr)
error->one(FLERR,"Cannot open molecule file {}: {}", error->one(FLERR,"Cannot open molecule file {}: {}",arg[ifile], utils::getsyserror());
arg[ifile], utils::getsyserror());
} }
read(0); read(0);
if (me == 0) fclose(fp); if (me == 0) fclose(fp);
@ -496,8 +494,7 @@ void Molecule::read(int flag)
if (nmatch != nwant) if (nmatch != nwant)
error->one(FLERR,"Invalid header line format in molecule file"); error->one(FLERR,"Invalid header line format in molecule file");
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->one(FLERR, "Invalid header in molecule file\n" error->one(FLERR,"Invalid header in molecule file: {}", e.what());
"{}", e.what());
} }
} }
@ -618,11 +615,9 @@ void Molecule::read(int flag)
// Error: Either a too long/short section or a typo in the keyword // Error: Either a too long/short section or a typo in the keyword
if (utils::strmatch(keyword,"^[A-Za-z ]+$")) if (utils::strmatch(keyword,"^[A-Za-z ]+$"))
error->one(FLERR,"Unknown section '{}' in molecule " error->one(FLERR,"Unknown section '{}' in molecule file\n",keyword);
"file\n",keyword);
else error->one(FLERR,"Unexpected line in molecule file " else error->one(FLERR,"Unexpected line in molecule file "
"while looking for the next " "while looking for the next section:\n{}",line);
"section:\n{}",line);
} }
keyword = parse_keyword(1,line); keyword = parse_keyword(1,line);
} }
@ -648,8 +643,7 @@ void Molecule::read(int flag)
if (bondflag && specialflag == 0) { if (bondflag && specialflag == 0) {
if (domain->box_exist == 0) if (domain->box_exist == 0)
error->all(FLERR,"Cannot auto-generate special bonds before " error->all(FLERR,"Cannot auto-generate special bonds before simulation box is defined");
"simulation box is defined");
if (flag) { if (flag) {
special_generate(); special_generate();
@ -691,8 +685,7 @@ void Molecule::coords(char *line)
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 4) if (values.count() != 4)
error->all(FLERR,"Invalid line in Coords section of " error->all(FLERR,"Invalid line in Coords section of molecule file: {}",line);
"molecule file: {}",line);
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
if (iatom < 0 || iatom >= natoms) if (iatom < 0 || iatom >= natoms)
@ -707,19 +700,16 @@ void Molecule::coords(char *line)
x[iatom][2] *= sizescale; x[iatom][2] *= sizescale;
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR,"Invalid line in Coords section of " error->all(FLERR,"Invalid line in Coords section of molecule file: {}\n{}",e.what(),line);
"molecule file: {}\n{}",e.what(),line);
} }
for (int i = 0; i < natoms; i++) for (int i = 0; i < natoms; i++)
if (count[i] == 0) error->all(FLERR,"Atom {} missing in Coords " if (count[i] == 0) error->all(FLERR,"Atom {} missing in Coords section of molecule file",i+1);
"section of molecule file",i+1);
if (domain->dimension == 2) { if (domain->dimension == 2) {
for (int i = 0; i < natoms; i++) for (int i = 0; i < natoms; i++)
if (x[i][2] != 0.0) if (x[i][2] != 0.0)
error->all(FLERR,"Z coord in molecule file for atom {} " error->all(FLERR,"Z coord in molecule file for atom {} must be 0.0 for 2d-simulation",i+1);
"must be 0.0 for 2d-simulation.",i+1);
} }
} }
@ -737,8 +727,7 @@ void Molecule::types(char *line)
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 2) if (values.count() != 2)
error->all(FLERR,"Invalid line in Types section of " error->all(FLERR,"Invalid line in Types section of molecule file: {}",line);
"molecule file: {}",line);
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
if (iatom < 0 || iatom >= natoms) if (iatom < 0 || iatom >= natoms)
@ -748,17 +737,14 @@ void Molecule::types(char *line)
type[iatom] += toffset; type[iatom] += toffset;
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Types section of " error->all(FLERR,"Invalid line in Types section of molecule file: {}\n{}",e.what(),line);
"molecule file: {}\n{}", e.what(),line);
} }
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
if (count[i] == 0) error->all(FLERR,"Atom {} missing in Types " if (count[i] == 0) error->all(FLERR,"Atom {} missing in Types section of molecule file",i+1);
"section of molecule file",i+1);
if ((type[i] <= 0) || (domain->box_exist && (type[i] > atom->ntypes))) if ((type[i] <= 0) || (domain->box_exist && (type[i] > atom->ntypes)))
error->all(FLERR,"Invalid atom type {} for atom {} " error->all(FLERR,"Invalid atom type {} for atom {} in molecule file",type[i],i+1);
"in molecule file",type[i],i+1);
ntypes = MAX(ntypes,type[i]); ntypes = MAX(ntypes,type[i]);
} }
@ -777,8 +763,7 @@ void Molecule::molecules(char *line)
readline(line); readline(line);
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 2) if (values.count() != 2)
error->all(FLERR,"Invalid line in Molecules section of " error->all(FLERR,"Invalid line in Molecules section of molecule file: {}",line);
"molecule file: {}",line);
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
if (iatom < 0 || iatom >= natoms) if (iatom < 0 || iatom >= natoms)
@ -788,19 +773,17 @@ void Molecule::molecules(char *line)
// molecule[iatom] += moffset; // placeholder for possible molecule offset // molecule[iatom] += moffset; // placeholder for possible molecule offset
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Molecules section of " error->all(FLERR,"Invalid line in Molecules section of molecule file: {}\n{}",e.what(),line);
"molecule file: {}\n{}",e.what(),line);
} }
for (int i = 0; i < natoms; i++) for (int i = 0; i < natoms; i++) {
if (count[i] == 0) error->all(FLERR,"Atom {} missing in Molecules " if (count[i] == 0)
"section of molecule file",i+1); error->all(FLERR,"Atom {} missing in Molecules section of molecule file",i+1);
}
for (int i = 0; i < natoms; i++) for (int i = 0; i < natoms; i++) {
if (molecule[i] < 0) if (molecule[i] < 0)
error->all(FLERR,"Invalid molecule ID {} for atom {} " error->all(FLERR,"Invalid molecule ID {} for atom {} in molecule file",molecule[i],i+1);
"in molecule file",molecule[i],i+1); }
for (int i = 0; i < natoms; i++) for (int i = 0; i < natoms; i++)
nmolecules = MAX(nmolecules,molecule[i]); nmolecules = MAX(nmolecules,molecule[i]);
} }
@ -818,22 +801,20 @@ void Molecule::fragments(char *line)
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if ((int)values.count() > natoms+1) if ((int)values.count() > natoms+1)
error->all(FLERR,"Too many atoms per fragment in Fragments " error->all(FLERR,"Too many atoms per fragment in Fragments section of molecule file");
"section of molecule file");
fragmentnames[i] = values.next_string(); fragmentnames[i] = values.next_string();
while (values.has_next()) { while (values.has_next()) {
int iatom = values.next_int()-1; int iatom = values.next_int()-1;
if (iatom < 0 || iatom >= natoms) if (iatom < 0 || iatom >= natoms)
error->all(FLERR,"Invalid atom ID {} for fragment {} in " error->all(FLERR,"Invalid atom ID {} for fragment {} in Fragments section of "
"Fragments section of molecule file", "molecule file", iatom+1, fragmentnames[i]);
iatom+1, fragmentnames[i]);
fragmentmask[i][iatom] = 1; fragmentmask[i][iatom] = 1;
} }
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid atom ID in Fragments section of " error->all(FLERR,"Invalid atom ID in Fragments section of "
"molecule file: {}\n{}", e.what(),line); "molecule file: {}\n{}", e.what(),line);
} }
} }
@ -851,8 +832,7 @@ void Molecule::charges(char *line)
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if ((int)values.count() != 2) if ((int)values.count() != 2)
error->all(FLERR,"Invalid line in Charges section of " error->all(FLERR,"Invalid line in Charges section of molecule file: {}",line);
"molecule file: {}",line);
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
if (iatom < 0 || iatom >= natoms) if (iatom < 0 || iatom >= natoms)
@ -862,13 +842,13 @@ void Molecule::charges(char *line)
q[iatom] = values.next_double(); q[iatom] = values.next_double();
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Charges section of " error->all(FLERR,"Invalid line in Charges section of molecule file: {}\n{}",e.what(),line);
"molecule file: {}.\n{}",e.what(),line);
} }
for (int i = 0; i < natoms; i++) for (int i = 0; i < natoms; i++) {
if (count[i] == 0) error->all(FLERR,"Atom {} missing in Charges " if (count[i] == 0)
"section of molecule file",i+1); error->all(FLERR,"Atom {} missing in Charges section of molecule file",i+1);
}
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -885,8 +865,7 @@ void Molecule::diameters(char *line)
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 2) if (values.count() != 2)
error->all(FLERR,"Invalid line in Diameters section of " error->all(FLERR,"Invalid line in Diameters section of molecule file: {}",line);
"molecule file: {}",line);
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
if (iatom < 0 || iatom >= natoms) if (iatom < 0 || iatom >= natoms)
error->all(FLERR,"Invalid atom index in Diameters section of molecule file"); error->all(FLERR,"Invalid atom index in Diameters section of molecule file");
@ -897,16 +876,14 @@ void Molecule::diameters(char *line)
maxradius = MAX(maxradius,radius[iatom]); maxradius = MAX(maxradius,radius[iatom]);
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Diameters section of " error->all(FLERR,"Invalid line in Diameters section of molecule file: {}\n{}",e.what(),line);
"molecule file: {}\n{}",e.what(),line);
} }
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
if (count[i] == 0) error->all(FLERR,"Atom {} missing in Diameters " if (count[i] == 0)
"section of molecule file",i+1); error->all(FLERR,"Atom {} missing in Diameters section of molecule file",i+1);
if (radius[i] < 0.0) if (radius[i] < 0.0)
error->all(FLERR,"Invalid atom diameter {} for atom {} " error->all(FLERR,"Invalid atom diameter {} for atom {} in molecule file", radius[i], i+1);
"in molecule file", radius[i], i+1);
} }
} }
@ -923,8 +900,7 @@ void Molecule::masses(char *line)
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 2) if (values.count() != 2)
error->all(FLERR,"Invalid line in Masses section of " error->all(FLERR,"Invalid line in Masses section of molecule file: {}",line);
"molecule file: {}",line);
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
if (iatom < 0 || iatom >= natoms) if (iatom < 0 || iatom >= natoms)
@ -934,8 +910,7 @@ void Molecule::masses(char *line)
rmass[iatom] *= sizescale*sizescale*sizescale; rmass[iatom] *= sizescale*sizescale*sizescale;
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Masses section of " error->all(FLERR,"Invalid line in Masses section of molecule file: {}\n{}",e.what(),line);
"molecule file: {}\n{}",e.what(),line);
} }
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
@ -972,15 +947,13 @@ void Molecule::bonds(int flag, char *line)
try { try {
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 4) if (values.count() != 4)
error->all(FLERR,"Invalid line in Bonds section of " error->all(FLERR,"Invalid line in Bonds section of molecule file: {}",line);
"molecule file: {}",line);
values.next_int(); values.next_int();
itype = values.next_int(); itype = values.next_int();
atom1 = values.next_tagint(); atom1 = values.next_tagint();
atom2 = values.next_tagint(); atom2 = values.next_tagint();
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Bonds section of " error->all(FLERR,"Invalid line in Bonds section of molecule file: {}\n{}",e.what(),line);
"molecule file: {}\n{}",e.what(),line);
} }
itype += boffset; itype += boffset;
@ -1042,16 +1015,14 @@ void Molecule::angles(int flag, char *line)
try { try {
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 5) if (values.count() != 5)
error->all(FLERR,"Invalid line in Angles section of " error->all(FLERR,"Invalid line in Angles section of molecule file: {}",line);
"molecule file: {}",line);
values.next_int(); values.next_int();
itype = values.next_int(); itype = values.next_int();
atom1 = values.next_tagint(); atom1 = values.next_tagint();
atom2 = values.next_tagint(); atom2 = values.next_tagint();
atom3 = values.next_tagint(); atom3 = values.next_tagint();
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Angles section of " error->all(FLERR,"Invalid line in Angles section of molecule file: {}\n{}",e.what(),line);
"molecule file: {}\n{}",e.what(),line);
} }
itype += aoffset; itype += aoffset;
@ -1128,8 +1099,7 @@ void Molecule::dihedrals(int flag, char *line)
try { try {
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 6) if (values.count() != 6)
error->all(FLERR,"Invalid line in Dihedrals section of " error->all(FLERR,"Invalid line in Dihedrals section of molecule file: {}",line);
"molecule file: {}",line);
values.next_int(); values.next_int();
itype = values.next_int(); itype = values.next_int();
@ -1138,8 +1108,7 @@ void Molecule::dihedrals(int flag, char *line)
atom3 = values.next_tagint(); atom3 = values.next_tagint();
atom4 = values.next_tagint(); atom4 = values.next_tagint();
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Dihedrals section of " error->all(FLERR,"Invalid line in Dihedrals section of molecule file: {}\n{}",e.what(),line);
"molecule file: {}\n{}",e.what(),line);
} }
itype += doffset; itype += doffset;
@ -1150,8 +1119,7 @@ void Molecule::dihedrals(int flag, char *line)
(atom4 <= 0) || (atom4 > natoms) || (atom4 <= 0) || (atom4 > natoms) ||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) || (atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4)) (atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->all(FLERR, error->all(FLERR,"Invalid atom ID in dihedrals section of molecule file");
"Invalid atom ID in dihedrals section of molecule file");
if ((itype <= 0) || (domain->box_exist && (itype > atom->ndihedraltypes))) if ((itype <= 0) || (domain->box_exist && (itype > atom->ndihedraltypes)))
error->all(FLERR,"Invalid dihedral type in Dihedrals section of molecule file"); error->all(FLERR,"Invalid dihedral type in Dihedrals section of molecule file");
@ -1230,8 +1198,7 @@ void Molecule::impropers(int flag, char *line)
try { try {
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 6) if (values.count() != 6)
error->all(FLERR,"Invalid line in Impropers section of " error->all(FLERR,"Invalid line in Impropers section of molecule file: {}",line);
"molecule file: {}",line);
values.next_int(); values.next_int();
itype = values.next_int(); itype = values.next_int();
atom1 = values.next_tagint(); atom1 = values.next_tagint();
@ -1239,8 +1206,7 @@ void Molecule::impropers(int flag, char *line)
atom3 = values.next_tagint(); atom3 = values.next_tagint();
atom4 = values.next_tagint(); atom4 = values.next_tagint();
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Impropers section of " error->all(FLERR,"Invalid line in Impropers section of molecule file: {}\n{}",e.what(),line);
"molecule file: {}\n{}",e.what(),line);
} }
itype += ioffset; itype += ioffset;
@ -1251,8 +1217,7 @@ void Molecule::impropers(int flag, char *line)
(atom4 <= 0) || (atom4 > natoms) || (atom4 <= 0) || (atom4 > natoms) ||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) || (atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4)) (atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->all(FLERR, error->all(FLERR,"Invalid atom ID in impropers section of molecule file");
"Invalid atom ID in impropers section of molecule file");
if ((itype <= 0) || (domain->box_exist && (itype > atom->nimpropertypes))) if ((itype <= 0) || (domain->box_exist && (itype > atom->nimpropertypes)))
error->all(FLERR,"Invalid improper type in Impropers section of molecule file"); error->all(FLERR,"Invalid improper type in Impropers section of molecule file");
@ -1325,14 +1290,13 @@ void Molecule::nspecial_read(int flag, char *line)
try { try {
ValueTokenizer values(utils::trim_comment(line)); ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 4) if (values.count() != 4)
error->all(FLERR,"Invalid line in Special Bond Counts section of " error->all(FLERR,"Invalid line in Special Bond Counts section of molecule file: {}",line);
"molecule file: {}",line);
values.next_int(); values.next_int();
c1 = values.next_tagint(); c1 = values.next_tagint();
c2 = values.next_tagint(); c2 = values.next_tagint();
c3 = values.next_tagint(); c3 = values.next_tagint();
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Special Bond Counts section of " error->all(FLERR,"Invalid line in Special Bond Counts section of "
"molecule file: {}\n{}",e.what(),line); "molecule file: {}\n{}",e.what(),line);
} }
@ -1358,8 +1322,7 @@ void Molecule::special_read(char *line)
int nwords = values.count(); int nwords = values.count();
if (nwords != nspecial[i][2]+1) if (nwords != nspecial[i][2]+1)
error->all(FLERR,"Molecule file special list " error->all(FLERR,"Molecule file special list does not match special count");
"does not match special count");
values.next_int(); // ignore values.next_int(); // ignore
@ -1367,12 +1330,11 @@ void Molecule::special_read(char *line)
special[i][m-1] = values.next_tagint(); special[i][m-1] = values.next_tagint();
if (special[i][m-1] <= 0 || special[i][m-1] > natoms || if (special[i][m-1] <= 0 || special[i][m-1] > natoms ||
special[i][m-1] == i+1) special[i][m-1] == i+1)
error->all(FLERR,"Invalid atom index in Special Bonds " error->all(FLERR,"Invalid atom index in Special Bonds section of molecule file");
"section of molecule file");
} }
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Special Bonds section of " error->all(FLERR,"Invalid line in Special Bonds section of "
"molecule file: {}\n{}",e.what(),line); "molecule file: {}\n{}",e.what(),line);
} }
} }
@ -1502,8 +1464,7 @@ void Molecule::shakeflag_read(char *line)
shake_flag[i] = values.next_int(); shake_flag[i] = values.next_int();
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid Shake Flags section in molecule file\n" error->all(FLERR,"Invalid Shake Flags section in molecule file: {}", e.what());
"{}", e.what());
} }
for (int i = 0; i < natoms; i++) for (int i = 0; i < natoms; i++)
@ -1572,8 +1533,7 @@ void Molecule::shakeatom_read(char *line)
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR,"Invalid shake atom in molecule file\n" error->all(FLERR,"Invalid shake atom in molecule file: {}", e.what());
"{}", e.what());
} }
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
@ -1642,8 +1602,7 @@ void Molecule::shaketype_read(char *line)
error->all(FLERR,"Invalid shake type data in molecule file"); error->all(FLERR,"Invalid shake type data in molecule file");
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid shake type data in molecule file\n", error->all(FLERR,"Invalid shake type data in molecule file: {}",e.what());
"{}", e.what());
} }
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
@ -1695,8 +1654,7 @@ void Molecule::body(int flag, int pflag, char *line)
} else nword += ncount; } else nword += ncount;
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->all(FLERR, "Invalid body params in molecule file\n", error->all(FLERR,"Invalid body params in molecule file: {}", e.what());
"{}", e.what());
} }
} }
@ -1735,8 +1693,7 @@ void Molecule::check_attributes(int flag)
if (onemol->rmassflag && !atom->rmass_flag) mismatch = 1; if (onemol->rmassflag && !atom->rmass_flag) mismatch = 1;
if (mismatch && me == 0) if (mismatch && me == 0)
error->warning(FLERR, error->warning(FLERR,"Molecule attributes do not match system attributes");
"Molecule attributes do not match system attributes");
// for all atom styles, check nbondtype,etc // for all atom styles, check nbondtype,etc
@ -1770,8 +1727,7 @@ void Molecule::check_attributes(int flag)
// warn if molecule topology defined but no special settings // warn if molecule topology defined but no special settings
if (onemol->bondflag && !onemol->specialflag) if (onemol->bondflag && !onemol->specialflag)
if (me == 0) error->warning(FLERR,"Molecule has bond topology " if (me == 0) error->warning(FLERR,"Molecule has bond topology but no special bond settings");
"but no special bond settings");
} }
} }
@ -1878,47 +1834,31 @@ void Molecule::allocate()
memory->create(special,natoms,maxspecial,"molecule:special"); memory->create(special,natoms,maxspecial,"molecule:special");
if (bondflag) { if (bondflag) {
memory->create(bond_type,natoms,bond_per_atom, memory->create(bond_type,natoms,bond_per_atom,"molecule:bond_type");
"molecule:bond_type"); memory->create(bond_atom,natoms,bond_per_atom,"molecule:bond_atom");
memory->create(bond_atom,natoms,bond_per_atom,
"molecule:bond_atom");
} }
if (angleflag) { if (angleflag) {
memory->create(angle_type,natoms,angle_per_atom, memory->create(angle_type,natoms,angle_per_atom,"molecule:angle_type");
"molecule:angle_type"); memory->create(angle_atom1,natoms,angle_per_atom,"molecule:angle_atom1");
memory->create(angle_atom1,natoms,angle_per_atom, memory->create(angle_atom2,natoms,angle_per_atom,"molecule:angle_atom2");
"molecule:angle_atom1"); memory->create(angle_atom3,natoms,angle_per_atom,"molecule:angle_atom3");
memory->create(angle_atom2,natoms,angle_per_atom,
"molecule:angle_atom2");
memory->create(angle_atom3,natoms,angle_per_atom,
"molecule:angle_atom3");
} }
if (dihedralflag) { if (dihedralflag) {
memory->create(dihedral_type,natoms,dihedral_per_atom, memory->create(dihedral_type,natoms,dihedral_per_atom,"molecule:dihedral_type");
"molecule:dihedral_type"); memory->create(dihedral_atom1,natoms,dihedral_per_atom,"molecule:dihedral_atom1");
memory->create(dihedral_atom1,natoms,dihedral_per_atom, memory->create(dihedral_atom2,natoms,dihedral_per_atom,"molecule:dihedral_atom2");
"molecule:dihedral_atom1"); memory->create(dihedral_atom3,natoms,dihedral_per_atom,"molecule:dihedral_atom3");
memory->create(dihedral_atom2,natoms,dihedral_per_atom, memory->create(dihedral_atom4,natoms,dihedral_per_atom,"molecule:dihedral_atom4");
"molecule:dihedral_atom2");
memory->create(dihedral_atom3,natoms,dihedral_per_atom,
"molecule:dihedral_atom3");
memory->create(dihedral_atom4,natoms,dihedral_per_atom,
"molecule:dihedral_atom4");
} }
if (improperflag) { if (improperflag) {
memory->create(improper_type,natoms,improper_per_atom, memory->create(improper_type,natoms,improper_per_atom,"molecule:improper_type");
"molecule:improper_type"); memory->create(improper_atom1,natoms,improper_per_atom,"molecule:improper_atom1");
memory->create(improper_atom1,natoms,improper_per_atom, memory->create(improper_atom2,natoms,improper_per_atom,"molecule:improper_atom2");
"molecule:improper_atom1"); memory->create(improper_atom3,natoms,improper_per_atom,"molecule:improper_atom3");
memory->create(improper_atom2,natoms,improper_per_atom, memory->create(improper_atom4,natoms,improper_per_atom,"molecule:improper_atom4");
"molecule:improper_atom2");
memory->create(improper_atom3,natoms,improper_per_atom,
"molecule:improper_atom3");
memory->create(improper_atom4,natoms,improper_per_atom,
"molecule:improper_atom4");
} }
if (shakeflag) { if (shakeflag) {