ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

allow '#' character in type labels. support also when reading Atoms section

Browse Source
This commit is contained in:
Axel Kohlmeyer
2022-09-03 16:48:39 -04:00
parent 8d9adeef16
commit d43051d07c
3 changed files with 20 additions and 7 deletions
Download Patch File Download Diff File Expand all files Collapse all files

17
src/atom.cpp
View File

@ -1057,7 +1057,14 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
next = strchr(buf,'\n'); next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Atoms section of data file"); if (!next) error->all(FLERR, "Missing data in Atoms section of data file");
*next = '\0'; *next = '\0';
int nwords = utils::trim_and_count_words(buf); auto values = Tokenizer(buf).as_vector();
int nwords = 0;
for (std::size_t i = 0; i < values.size(); ++i) {
if (utils::strmatch(values[i], "^#")) {
nwords = i;
break;
}
}
*next = '\n'; *next = '\n';
if ((nwords != avec->size_data_atom) && (nwords != avec->size_data_atom + 3)) if ((nwords != avec->size_data_atom) && (nwords != avec->size_data_atom + 3))
@ -1135,10 +1142,12 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
next = strchr(buf,'\n'); next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Atoms section of data file"); if (!next) error->all(FLERR, "Missing data in Atoms section of data file");
*next = '\0'; *next = '\0';
auto values = Tokenizer(utils::trim_comment(buf)).as_vector(); auto values = Tokenizer(buf).as_vector();
if (values.size() == 0) { int nvalues = values.size();
if ((nvalues == 0) || (utils::strmatch(values[0],"^#.*"))) {
// skip over empty or comment lines // skip over empty or comment lines
} else if ((int)values.size() != nwords) { } else if ((nvalues < nwords) ||
((nvalues > nwords) && (!utils::strmatch(values[nwords],"^#")))) {
error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf)); error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
} else { } else {
int imx = 0, imy = 0, imz = 0; int imx = 0, imy = 0, imz = 0;

6
src/label_map.cpp
View File

@ -138,9 +138,9 @@ void LabelMap::modify_lmap(int narg, char **arg)
if ((itype < 1) || (itype > ntypes)) if ((itype < 1) || (itype > ntypes))
error->all(FLERR, "Labelmap {} type {} must be within 1-{}", tlabel, itype, ntypes); error->all(FLERR, "Labelmap {} type {} must be within 1-{}", tlabel, itype, ntypes);
std::string slabel(arg[iarg++]); std::string slabel(arg[iarg++]);
if (isdigit(slabel[0])) if (isdigit(slabel[0]) || (slabel[0] == '#') || (slabel[0] == '*'))
error->all(FLERR, "Label {} for {} type {} must not start with a number", slabel, tlabel, error->all(FLERR, "Label {} for {} type {} must not start with a number, a '#', or a '*'",
itype); slabel, tlabel, itype);
int found = search(slabel, (*labels_map)); int found = search(slabel, (*labels_map));
if ((found != -1) && (found != itype)) if ((found != -1) && (found != itype))
error->all(FLERR, "The {} type label {} is already in use for type {}", tlabel, slabel, error->all(FLERR, "The {} type label {} is already in use for type {}", tlabel, slabel,

4
unittest/commands/test_labelmap.cpp
View File

@ -119,6 +119,10 @@ TEST_F(SetTest, NoBoxAtoms)
command("labelmap atom 5 C1");); command("labelmap atom 5 C1"););
TEST_FAILURE(".*ERROR: Label 1C for atom type 1 must not start with a number.*", TEST_FAILURE(".*ERROR: Label 1C for atom type 1 must not start with a number.*",
command("labelmap atom 1 1C");); command("labelmap atom 1 1C"););
TEST_FAILURE(".*ERROR: Label #C for atom type 1 must not start with a number, a '#', or.*",
command("labelmap atom 1 '#C'"););
TEST_FAILURE(".*ERROR: Label \\*C for atom type 1 must not start with a number, a '#', or.*",
command("labelmap atom 1 *C"););
TEST_FAILURE(".*ERROR: The atom type label N2 is already in use for type 2.*", TEST_FAILURE(".*ERROR: The atom type label N2 is already in use for type 2.*",
command("labelmap atom 1 N2");); command("labelmap atom 1 N2"););