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Merge pull request #4046 from akohlmey/molecule-dipole

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Add support for Dipoles section to molecule files
This commit is contained in:
Axel Kohlmeyer
2024-01-18 14:57:01 -05:00
committed by GitHub
parent 14abc184f8 f23ba8fbad
commit fe1b568241
5 changed files with 268 additions and 57 deletions
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86
unittest/formats/test_molecule_file.cpp
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@ -32,6 +32,8 @@ using testing::StrEq;
using utils::split_words;
const double EPSILON = 5.0e-14;
#define test_name test_info_->name()
static void create_molecule_files(const std::string &h2o_filename, const std::string &co2_filename)
@ -145,7 +147,7 @@ protected:
fclose(fp);
command(fmt::format("molecule {} {} {}", name, file, args));
remove(file.c_str());
platform::unlink(file.c_str());
}
};
@ -184,7 +186,7 @@ TEST_F(MoleculeFileTest, badargs)
TEST_FAILURE(
".*Illegal molecule command.*",
run_mol_cmd(test_name, "scale", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
remove("badargs.mol");
platform::unlink("moltest_badargs.mol");
}
TEST_F(MoleculeFileTest, noatom)
@ -193,14 +195,14 @@ TEST_F(MoleculeFileTest, noatom)
run_mol_cmd(test_name, "",
"Comment\n0 atoms\n1 bonds\n\n"
" Coords\n\nBonds\n\n 1 1 2\n"););
remove("noatom.mol");
platform::unlink("moltest_noatom.mol");
}
TEST_F(MoleculeFileTest, empty)
{
TEST_FAILURE(".*ERROR: Unexpected end of molecule file.*",
run_mol_cmd(test_name, "", "Comment\n\n"););
remove("empty.mol");
platform::unlink("moltest_empty.mol");
}
TEST_F(MoleculeFileTest, nospecial)
@ -210,7 +212,7 @@ TEST_F(MoleculeFileTest, nospecial)
"Comment\n3 atoms\n\n2 bonds\n\n"
" Coords\n\n 1 1.0 1.0 1.0\n 2 1.0 1.0 0.0\n 3 1.0 0.0 1.0\n"
" Bonds\n\n 1 1 1 2\n 2 1 1 3\n"););
remove("nospecial.mol");
platform::unlink("moltest_nospecial.mol");
}
TEST_F(MoleculeFileTest, minimal)
@ -218,7 +220,7 @@ TEST_F(MoleculeFileTest, minimal)
BEGIN_CAPTURE_OUTPUT();
run_mol_cmd(test_name, "", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*1 molecules.*\n"
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*Comment.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*1 atoms.*\n.*0 bonds.*"));
}
@ -230,7 +232,7 @@ TEST_F(MoleculeFileTest, notype)
command("create_box 1 box");
run_mol_cmd(test_name, "", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*1 molecules.*\n"
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*Comment.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*1 atoms.*\n.*0 bonds.*"));
TEST_FAILURE(".*ERROR: Create_atoms molecule must have atom types.*",
command("create_atoms 0 single 0.0 0.0 0.0 mol notype 542465"););
@ -259,7 +261,7 @@ TEST_F(MoleculeFileTest, twomols)
" Coords\n\n 1 0.0 0.0 0.0\n 2 0.0 0.0 1.0\n"
" Molecules\n\n 1 1\n 2 2\n\n Types\n\n 1 1\n 2 2\n\n");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*2 molecules.*\n"
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*Comment.*\n.*2 molecules.*\n"
".*0 fragments.*\n.*2 atoms with max type 2.*\n.*0 bonds.*"));
ASSERT_EQ(lmp->atom->nmolecule, 1);
auto mols = lmp->atom->get_molecule_by_id(test_name);
@ -273,10 +275,10 @@ TEST_F(MoleculeFileTest, twofiles)
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(
output,
ContainsRegex(".*Read molecule template twomols:.*\n.*1 molecules.*\n"
ContainsRegex(".*Read molecule template twomols:.*\n.*Water.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 2.*\n.*2 bonds with max type 1.*\n"
".*1 angles with max type 1.*\n.*0 dihedrals.*\n.*0 impropers.*\n"
".*Read molecule template twomols:.*\n.*1 molecules.*\n"
".*Read molecule template twomols:.*\n.*CO2.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 4.*\n.*2 bonds with max type 2.*\n"
".*1 angles with max type 2.*\n.*0 dihedrals.*"));
BEGIN_CAPTURE_OUTPUT();
@ -306,7 +308,7 @@ TEST_F(MoleculeFileTest, labelmap)
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(
output,
ContainsRegex(".*Read molecule template h2olabel:.*\n.*1 molecules.*\n"
ContainsRegex(".*Read molecule template h2olabel:.*\n.*Water.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 2.*\n.*2 bonds with max type 1.*\n"
".*1 angles with max type 1.*\n.*0 dihedrals.*\n.*0 impropers.*"));
BEGIN_CAPTURE_OUTPUT();
@ -314,7 +316,7 @@ TEST_F(MoleculeFileTest, labelmap)
output = END_CAPTURE_OUTPUT();
ASSERT_THAT(
output,
ContainsRegex(".*Read molecule template co2label:.*\n.*1 molecules.*\n"
ContainsRegex(".*Read molecule template co2label:.*\n.*CO2.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 4.*\n.*2 bonds with max type 2.*\n"
".*1 angles with max type 2.*\n.*0 dihedrals.*"));
BEGIN_CAPTURE_OUTPUT();
@ -328,12 +330,12 @@ TEST_F(MoleculeFileTest, labelmap)
auto second = output.substr(mark);
ASSERT_THAT(
first,
ContainsRegex(".*Read molecule template h2onum:.*\n.*1 molecules.*\n"
ContainsRegex(".*Read molecule template h2onum:.*\n.*Water.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 2.*\n.*2 bonds with max type 1.*\n"
".*1 angles with max type 1.*\n.*0 dihedrals.*\n.*0 impropers.*\n"));
ASSERT_THAT(
second,
ContainsRegex(".*Read molecule template co2num:.*\n.*1 molecules.*\n"
ContainsRegex(".*Read molecule template co2num:.*\n.*CO2.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 4.*\n.*2 bonds with max type 2.*\n"
".*1 angles with max type 2.*\n.*0 dihedrals.*"));
ASSERT_EQ(lmp->atom->nmolecule, 4);
@ -379,7 +381,7 @@ TEST_F(MoleculeFileTest, bonds)
" 1 1 1 2\n"
" 2 2 1 3\n\n");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*1 molecules.*\n"
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*Comment.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*4 atoms.*type.*2.*\n"
".*2 bonds.*type.*2.*\n.*0 angles.*"));
@ -404,6 +406,60 @@ TEST_F(MoleculeFileTest, bonds)
END_HIDE_OUTPUT();
}
TEST_F(MoleculeFileTest, dipoles)
{
if (!LAMMPS::is_installed_pkg("DIPOLE")) GTEST_SKIP();
BEGIN_CAPTURE_OUTPUT();
command("atom_style dipole");
command("region box block 0 1 0 1 0 1");
command("create_box 2 box");
run_mol_cmd(test_name, "",
"# Dumbbell with dipole molecule file.\n\n"
"2 atoms\n\n"
"Coords\n\n1 -1.0 0.0 0.0\n2 1.0 0.0 0.0\n\n"
"Types\n\n1 1\n2 2\n\n"
"Dipoles\n\n1 1.0 0.0 0.0\n2 1.0 1.0 0.0\n\n");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*Dumbbell.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*2 atoms.*type.*2.*\n"));
BEGIN_CAPTURE_OUTPUT();
command("mass * 1.0");
command("create_atoms 0 single 0.5 0.5 0.5 mol dipoles 67235 rotate 90.0 0.0 0.0 1.0");
output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Created 2 atoms.*"));
Molecule *mol = lmp->atom->molecules[0];
ASSERT_EQ(mol->natoms, 2);
ASSERT_EQ(lmp->atom->natoms, 2);
mol->compute_mass();
mol->compute_com();
EXPECT_NEAR(mol->masstotal, 2.0, EPSILON);
EXPECT_NEAR(mol->com[0], 0.0, EPSILON);
EXPECT_NEAR(mol->com[1], 0.0, EPSILON);
EXPECT_NEAR(mol->com[2], 0.0, EPSILON);
EXPECT_EQ(mol->comatom, 1);
ASSERT_NE(mol->mu, nullptr);
EXPECT_NEAR(mol->mu[0][0], 1.0, EPSILON);
EXPECT_NEAR(mol->mu[0][1], 0.0, EPSILON);
EXPECT_NEAR(mol->mu[0][2], 0.0, EPSILON);
EXPECT_NEAR(mol->mu[1][0], 1.0, EPSILON);
EXPECT_NEAR(mol->mu[1][1], 1.0, EPSILON);
EXPECT_NEAR(mol->mu[1][2], 0.0, EPSILON);
EXPECT_NEAR(mol->maxextent, 2.0, EPSILON);
// dipoles should be rotated by 90 degrees clockwise around the z axis
double **mu = lmp->atom->mu;
ASSERT_NE(mu, nullptr);
EXPECT_NEAR(mu[0][0], 0.0, EPSILON);
EXPECT_NEAR(mu[0][1], 1.0, EPSILON);
EXPECT_NEAR(mu[0][2], 0.0, EPSILON);
EXPECT_NEAR(mu[0][3], 1.0, EPSILON);
EXPECT_NEAR(mu[1][0], -1.0, EPSILON);
EXPECT_NEAR(mu[1][1], 1.0, EPSILON);
EXPECT_NEAR(mu[1][2], 0.0, EPSILON);
EXPECT_NEAR(mu[1][3], sqrt(2.0), EPSILON);
}
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);