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add typelabel support for Shake Bond Types section in molecule files

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This commit is contained in:
Axel Kohlmeyer
2022-09-05 10:16:31 -04:00
parent 4f3f2412fb
commit 1a5a509c1d
2 changed files with 87 additions and 56 deletions
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79
src/molecule.cpp
View File

@ -1667,58 +1667,89 @@ void Molecule::shakeatom_read(char *line)
void Molecule::shaketype_read(char *line)
{
try {
int nmatch = 0, nwant = 0;
for (int i = 0; i < natoms; i++) {
readline(line);
ValueTokenizer values(utils::trim_comment(line));
nmatch = values.count();
auto values = Tokenizer(utils::trim(line)).as_vector();
nmatch = values.size();
for (std::size_t i = 0; i < values.size(); ++i) {
if (utils::strmatch(values[i], "^#")) {
nmatch = i;
break;
}
}
char *subst;
switch (shake_flag[i]) {
case 1:
values.next_int();
shake_type[i][0] = values.next_int();
shake_type[i][1] = values.next_int();
shake_type[i][2] = values.next_int();
subst = utils::expand_type(FLERR, values[1], Atom::BOND, lmp);
if (subst) values[1] = subst;
shake_type[i][0] = utils::inumeric(FLERR, values[1], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst;
subst = utils::expand_type(FLERR, values[2], Atom::BOND, lmp);
if (subst) values[2] = subst;
shake_type[i][1] = utils::inumeric(FLERR, values[2], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst;
subst = utils::expand_type(FLERR, values[3], Atom::ANGLE, lmp);
if (subst) values[3] = subst;
shake_type[i][2] = utils::inumeric(FLERR, values[3], false, lmp) + ((subst) ? 0 : aoffset);
delete[] subst;
nwant = 4;
break;
case 2:
values.next_int();
shake_type[i][0] = values.next_int();
subst = utils::expand_type(FLERR, values[1], Atom::BOND, lmp);
if (subst) values[1] = subst;
shake_type[i][0] = utils::inumeric(FLERR, values[1], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst;
nwant = 2;
break;
case 3:
values.next_int();
shake_type[i][0] = values.next_int();
shake_type[i][1] = values.next_int();
subst = utils::expand_type(FLERR, values[1], Atom::BOND, lmp);
if (subst) values[1] = subst;
shake_type[i][0] = utils::inumeric(FLERR, values[1], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst;
subst = utils::expand_type(FLERR, values[1], Atom::BOND, lmp);
if (subst) values[1] = subst;
shake_type[i][1] = utils::inumeric(FLERR, values[2], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst;
nwant = 3;
break;
case 4:
values.next_int();
shake_type[i][0] = values.next_int();
shake_type[i][1] = values.next_int();
shake_type[i][2] = values.next_int();
subst = utils::expand_type(FLERR, values[1], Atom::BOND, lmp);
if (subst) values[1] = subst;
shake_type[i][0] = utils::inumeric(FLERR, values[1], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst;
subst = utils::expand_type(FLERR, values[1], Atom::BOND, lmp);
if (subst) values[1] = subst;
shake_type[i][1] = utils::inumeric(FLERR, values[2], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst;
subst = utils::expand_type(FLERR, values[1], Atom::BOND, lmp);
if (subst) values[1] = subst;
shake_type[i][2] = utils::inumeric(FLERR, values[3], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst;
nwant = 4;
break;
case 0:
values.next_int();
nwant = 1;
break;
default:
error->all(FLERR, "Invalid shake type data in molecule file");
error->all(FLERR, "Invalid shake type values in molecule file");
}
if (nmatch != nwant) error->all(FLERR, "Invalid shake type data in molecule file");
}
} catch (TokenizerException &e) {
error->all(FLERR, "Invalid shake type data in molecule file: {}", e.what());
}
for (int i = 0; i < natoms; i++) {
int m = shake_flag[i];

14
unittest/formats/test_molecule_file.cpp
View File

@ -77,13 +77,13 @@ static void create_labelmap_files(const std::string &h2o_filename, const std::st
const char h2o_file[] = "# Water molecule. SPC/E model.\n\n3 atoms\n2 bonds\n1 angles\n\n"
"Coords\n\n1 1.12456 0.09298 1.27452\n"
"2 1.53683 0.75606 1.89928\n3 0.49482 0.56390 0.65678\n\n"
"Types\n\n1 OW\n2 HW\n3 HW\n\n"
"Types\n\n1 OW\n2 HO\n3 HO\n\n"
"Charges\n\n1 -0.8472\n2 0.4236\n3 0.4236\n\n"
"Bonds\n\n1 OW-HW 1 2\n2 OW-HW 1 3\n\n"
"Angles\n\n1 HW-OW-HW 2 1 3\n\n"
"Bonds\n\n1 OW-HO 1 2\n2 OW-HO 1 3\n\n"
"Angles\n\n1 HO-OW-HO 2 1 3\n\n"
"Shake Flags\n\n1 1\n2 1\n3 1\n\n"
"Shake Atoms\n\n1 1 2 3\n2 1 2 3\n3 1 2 3\n\n"
"Shake Bond Types\n\n1 1 1 1\n2 1 1 1\n3 1 1 1\n\n"
"Shake Bond Types\n\n1 OW-HO OW-HO HO-OW-HO\n2 OW-HO OW-HO HO-OW-HO\n3 OW-HO OW-HO HO-OW-HO\n\n"
"Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n"
"Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n";
const char co2_file[] = "# CO2 molecule file. TraPPE model.\n\n"
@ -298,9 +298,9 @@ TEST_F(MoleculeFileTest, labelmap)
command("atom_style full");
command("region box block 0 2 0 2 0 2");
command("create_box 4 box bond/types 2 angle/types 2");
command("labelmap atom 1 HW 2 OW 3 C 4 O");
command("labelmap bond 1 OW-HW 2 C=O");
command("labelmap angle 1 HW-OW-HW 2 O=C=O");
command("labelmap atom 1 HO 2 OW 3 C 4 O");
command("labelmap bond 1 OW-HO 2 C=O");
command("labelmap angle 1 HO-OW-HO 2 O=C=O");
command("molecule h2olabel labelmap.h2o.mol");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(