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update error handling for read_data command

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This commit is contained in:
Axel Kohlmeyer
2022-09-04 16:15:13 -04:00
parent 14871facf2
commit a7d4d819ef
1 changed files with 75 additions and 67 deletions
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142
src/read_data.cpp
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@ -135,7 +135,7 @@ ReadData::~ReadData()
void ReadData::command(int narg, char **arg)
{
if (narg < 1) error->all(FLERR, "Illegal read_data command");
if (narg < 1) utils::missing_cmd_args(FLERR, "read_data", error);
MPI_Barrier(world);
double time1 = platform::walltime();
@ -162,29 +162,31 @@ void ReadData::command(int narg, char **arg)
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg], "add") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data add", error);
if (strcmp(arg[iarg + 1], "append") == 0)
addflag = APPEND;
else if (strcmp(arg[iarg + 1], "merge") == 0)
addflag = MERGE;
else {
if (atom->molecule_flag && (iarg + 3 > narg))
error->all(FLERR, "Illegal read_data command");
utils::missing_cmd_args(FLERR, "read_data add", error);
addflag = VALUE;
bigint offset = utils::bnumeric(FLERR, arg[iarg + 1], false, lmp);
if (offset > MAXTAGINT) error->all(FLERR, "Read data add atomID offset is too big");
if (offset > MAXTAGINT)
error->all(FLERR, "Read data add atomID offset {} is too big", offset);
id_offset = offset;
if (atom->molecule_flag) {
offset = utils::bnumeric(FLERR, arg[iarg + 2], false, lmp);
if (offset > MAXTAGINT) error->all(FLERR, "Read data add molID offset is too big");
if (offset > MAXTAGINT)
error->all(FLERR, "Read data add molID offset {} is too big", offset);
mol_offset = offset;
iarg++;
}
}
iarg += 2;
} else if (strcmp(arg[iarg], "offset") == 0) {
if (iarg + 6 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 6 > narg) utils::missing_cmd_args(FLERR, "read_data offset", error);
offsetflag = 1;
toffset = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
boffset = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
@ -192,93 +194,109 @@ void ReadData::command(int narg, char **arg)
doffset = utils::inumeric(FLERR, arg[iarg + 4], false, lmp);
ioffset = utils::inumeric(FLERR, arg[iarg + 5], false, lmp);
if (toffset < 0 || boffset < 0 || aoffset < 0 || doffset < 0 || ioffset < 0)
error->all(FLERR, "Illegal read_data command");
error->all(FLERR, "Illegal read_data offset value(s)");
iarg += 6;
} else if (strcmp(arg[iarg], "shift") == 0) {
if (iarg + 4 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 4 > narg) utils::missing_cmd_args(FLERR, "read_data shift", error);
shiftflag = 1;
shift[0] = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
shift[1] = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
shift[2] = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
if (domain->dimension == 2 && shift[2] != 0.0)
error->all(FLERR, "Non-zero read_data shift z value for 2d simulation");
error->all(FLERR, "Non-zero read_data shift z value for 2d simulation not allowed");
iarg += 4;
} else if (strcmp(arg[iarg], "nocoeff") == 0) {
coeffflag = 0;
iarg++;
} else if (strcmp(arg[iarg], "extra/atom/types") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data extra/atom/types", error);
extra_atom_types = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (extra_atom_types < 0) error->all(FLERR, "Illegal read_data command");
if (extra_atom_types < 0)
error->all(FLERR, "Illegal read_data extra/atom/types value {}", extra_atom_types);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/bond/types") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (!atom->avec->bonds_allow) error->all(FLERR, "No bonds allowed with this atom style");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data extra/bond/types", error);
if (!atom->avec->bonds_allow)
error->all(FLERR, "No bonds allowed with atom style {}", atom->get_style());
extra_bond_types = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (extra_bond_types < 0) error->all(FLERR, "Illegal read_data command");
if (extra_bond_types < 0)
error->all(FLERR, "Illegal read_data extra/bond/types value {}", extra_bond_types);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/angle/types") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (!atom->avec->angles_allow) error->all(FLERR, "No angles allowed with this atom style");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data extra/angle/types", error);
if (!atom->avec->angles_allow)
error->all(FLERR, "No angles allowed with atom style {}", atom->get_style());
extra_angle_types = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (extra_angle_types < 0) error->all(FLERR, "Illegal read_data command");
if (extra_angle_types < 0)
error->all(FLERR, "Illegal read_data extra/angle/types value {}", extra_angle_types);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/dihedral/types") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data extra/dihedral/types", error);
if (!atom->avec->dihedrals_allow)
error->all(FLERR, "No dihedrals allowed with this atom style");
error->all(FLERR, "No dihedrals allowed with atom style {}", atom->get_style());
extra_dihedral_types = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (extra_dihedral_types < 0) error->all(FLERR, "Illegal read_data command");
if (extra_dihedral_types < 0)
error->all(FLERR, "Illegal read_data extra/dihedral/types value {}", extra_dihedral_types);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/improper/types") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data extra/improper/types", error);
if (!atom->avec->impropers_allow)
error->all(FLERR, "No impropers allowed with this atom style");
error->all(FLERR, "No impropers allowed with atom style {}", atom->get_style());
extra_improper_types = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (extra_improper_types < 0) error->all(FLERR, "Illegal read_data command");
if (extra_improper_types < 0)
error->all(FLERR, "Illegal read_data extra/improper/types value {}", extra_improper_types);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/bond/per/atom") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data extra/bond/per/atom", error);
if (atom->molecular == Atom::ATOMIC)
error->all(FLERR, "No bonds allowed with this atom style");
error->all(FLERR, "No bonds allowed with atom style {}", atom->get_style());
atom->extra_bond_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (atom->extra_bond_per_atom < 0) error->all(FLERR, "Illegal read_data command");
if (atom->extra_bond_per_atom < 0)
error->all(FLERR, "Illegal read_data extra/bond/per/atom value {}",
atom->extra_bond_per_atom);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/angle/per/atom") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data extra/angle/per/atom", error);
if (atom->molecular == Atom::ATOMIC)
error->all(FLERR, "No angles allowed with this atom style");
error->all(FLERR, "No angles allowed with atom style {}", atom->get_style());
atom->extra_angle_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (atom->extra_angle_per_atom < 0) error->all(FLERR, "Illegal read_data command");
if (atom->extra_angle_per_atom < 0)
error->all(FLERR, "Illegal read_data extra/angle/per/atom value {}",
atom->extra_angle_per_atom);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/dihedral/per/atom") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data extra/dihedral/per/atom", error);
if (atom->molecular == Atom::ATOMIC)
error->all(FLERR, "No dihedrals allowed with this atom style");
error->all(FLERR, "No dihedrals allowed with atom style {}", atom->get_style());
atom->extra_dihedral_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (atom->extra_dihedral_per_atom < 0) error->all(FLERR, "Illegal read_data command");
if (atom->extra_dihedral_per_atom < 0)
error->all(FLERR, "Illegal read_data extra/dihedral/per/atom value {}",
atom->extra_dihedral_per_atom);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/improper/per/atom") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data extra/improper/per/atom", error);
if (atom->molecular == Atom::ATOMIC)
error->all(FLERR, "No impropers allowed with this atom style");
error->all(FLERR, "No impropers allowed with atom style {}", atom->get_style());
atom->extra_improper_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (atom->extra_improper_per_atom < 0) error->all(FLERR, "Illegal read_data command");
if (atom->extra_improper_per_atom < 0)
error->all(FLERR, "Illegal read_data extra/improper/per/atom value {}",
atom->extra_improper_per_atom);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/special/per/atom") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data extra/special/per/atom", error);
if (atom->molecular == Atom::ATOMIC)
error->all(FLERR, "No bonded interactions allowed with this atom style");
error->all(FLERR, "No bonded interactions allowed with atom style {}", atom->get_style());
force->special_extra = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (force->special_extra < 0) error->all(FLERR, "Illegal read_data command");
if (force->special_extra < 0)
error->all(FLERR, "Illegal read_data extra/special/per/atom value {}", force->special_extra);
iarg += 2;
} else if (strcmp(arg[iarg], "group") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "read_data group", error);
int igroup = group->find_or_create(arg[iarg + 1]);
groupbit = group->bitmask[igroup];
iarg += 2;
} else if (strcmp(arg[iarg], "fix") == 0) {
if (iarg + 4 > narg) error->all(FLERR, "Illegal read_data command");
if (iarg + 4 > narg) utils::missing_cmd_args(FLERR, "read_data fix", error);
fix_index =
(Fix **) memory->srealloc(fix_index, (nfix + 1) * sizeof(Fix *), "read_data:fix_index");
fix_header = (char **) memory->srealloc(fix_header, (nfix + 1) * sizeof(char *),
@ -304,7 +322,7 @@ void ReadData::command(int narg, char **arg)
iarg += 4;
} else
error->all(FLERR, "Illegal read_data command");
error->all(FLERR, "Unknown read_data keyword {}", arg[iarg]);
}
// error checks
@ -316,17 +334,17 @@ void ReadData::command(int narg, char **arg)
"Reading a data file with shrinkwrap boundaries is "
"not compatible with a MSM KSpace style");
if (domain->box_exist && !addflag)
error->all(FLERR, "Cannot read_data without add keyword after simulation box is defined");
error->all(FLERR, "Cannot use read_data without add keyword after simulation box is defined");
if (!domain->box_exist && addflag)
error->all(FLERR, "Cannot use read_data add before simulation box is defined");
if (offsetflag && addflag == NONE)
error->all(FLERR, "Cannot use read_data offset without add flag");
error->all(FLERR, "Cannot use read_data offset without add keyword");
if (shiftflag && addflag == NONE)
error->all(FLERR, "Cannot use read_data shift without add flag");
error->all(FLERR, "Cannot use read_data shift without add keyword");
if (addflag != NONE &&
(extra_atom_types || extra_bond_types || extra_angle_types || extra_dihedral_types ||
extra_improper_types))
error->all(FLERR, "Cannot use read_data extra with add flag");
error->all(FLERR, "Cannot use any read_data extra/*/types keyword with add keyword");
// check if data file is available and readable
@ -554,8 +572,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (me == 0 && !style_match(style, atom->atom_style))
error->warning(FLERR,
"Atom style in data file differs "
"from currently defined atom style");
"Atom style in data file differs from currently defined atom style");
atoms();
} else
skip_lines(natoms);
@ -634,8 +651,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (me == 0 && !style_match(style, force->pair_style))
error->warning(FLERR,
"Pair style in data file differs "
"from currently defined pair style");
"Pair style in data file differs from currently defined pair style");
paircoeffs();
} else
skip_lines(ntypes);
@ -657,8 +673,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (me == 0 && !style_match(style, force->bond_style))
error->warning(FLERR,
"Bond style in data file differs "
"from currently defined bond style");
"Bond style in data file differs from currently defined bond style");
bondcoeffs();
} else
skip_lines(nbondtypes);
@ -670,8 +685,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (me == 0 && !style_match(style, force->angle_style))
error->warning(FLERR,
"Angle style in data file differs "
"from currently defined angle style");
"Angle style in data file differs from currently defined angle style");
anglecoeffs(0);
} else
skip_lines(nangletypes);
@ -864,7 +878,7 @@ void ReadData::command(int narg, char **arg)
// error if natoms > 0 yet no atoms were read
if (natoms > 0 && atomflag == 0) error->all(FLERR, "No atoms in data file");
if (natoms > 0 && atomflag == 0) error->all(FLERR, "No valid atoms found in data file");
// close file
@ -885,11 +899,11 @@ void ReadData::command(int narg, char **arg)
if ((nbonds && !bondflag) || (nangles && !angleflag) || (ndihedrals && !dihedralflag) ||
(nimpropers && !improperflag))
error->one(FLERR, "Needed molecular topology not in data file");
error->one(FLERR, "A required molecular topology section not found in data file");
if ((nellipsoids && !ellipsoidflag) || (nlines && !lineflag) || (ntris && !triflag) ||
(nbodies && !bodyflag))
error->one(FLERR, "Needed bonus data not in data file");
error->one(FLERR, "Required bonus data not found in data file");
// break out of loop if no molecular topology in file
// else make 2nd pass
@ -1706,9 +1720,7 @@ void ReadData::impropers(int firstpass)
if (addflag != NONE) {
if (maxall > atom->improper_per_atom)
error->all(FLERR,
"Subsequent read data induced "
"too many impropers per atom");
error->all(FLERR, "Subsequent read data induced too many impropers per atom");
} else
atom->improper_per_atom = maxall;
@ -1889,9 +1901,7 @@ void ReadData::mass()
int eof = utils::read_lines_from_file(fp, ntypes, MAXLINE, buf, me, world);
if (eof) error->all(FLERR, "Unexpected end of data file");
if (tlabelflag && !lmap->is_complete(Atom::ATOM))
error->all(FLERR,
"Label map is incomplete: "
"all types must be assigned a unique type label");
error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label");
char *original = buf;
for (int i = 0; i < ntypes; i++) {
@ -1914,9 +1924,7 @@ void ReadData::paircoeffs()
if (eof) error->all(FLERR, "Unexpected end of data file");
if (tlabelflag && !lmap->is_complete(Atom::ATOM))
error->all(FLERR,
"Label map is incomplete: "
"all types must be assigned a unique type label");
error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label");
char *original = buf;
for (int i = 0; i < ntypes; i++) {
@ -2152,7 +2160,7 @@ void ReadData::typelabels(int mode)
auto values = Tokenizer(buf).as_vector();
int nwords = values.size();
for (std::size_t ii = 0; ii < values.size(); ++ii) {
if (utils::strmatch(values[ii],"^#")) {
if (utils::strmatch(values[ii], "^#")) {
nwords = ii;
break;
}
@ -2175,7 +2183,7 @@ void ReadData::typelabels(int mode)
if ((*labels)[i].empty())
error->all(FLERR, "{} Type Labels map is incomplete", labeltypes[mode]);
}
if ((int)(*labels_map).size() != lntypes)
if ((int) (*labels_map).size() != lntypes)
error->all(FLERR, "{} Type Labels map is incomplete", labeltypes[mode]);
// merge this read_data label map to atom class