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

add molecule file tests with type labels

Browse Source
This commit is contained in:
Axel Kohlmeyer
2022-09-04 21:09:43 -04:00
parent c376d72158
commit 53d82056ce
2 changed files with 102 additions and 3 deletions
Download Patch File Download Diff File Expand all files Collapse all files

104
unittest/formats/test_molecule_file.cpp
View File

@ -17,6 +17,7 @@
#include "input.h"
#include "lammps.h"
#include "molecule.h"
#include "platform.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
@ -70,17 +71,60 @@ static void create_molecule_files(const std::string &h2o_filename, const std::st
}
}
static void create_labelmap_files(const std::string &h2o_filename, const std::string &co2_filename)
{
// create molecule files
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"
"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"
"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"
"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"
"3 atoms\n2 bonds\n1 angles\n\n"
"Coords\n\n1 0.0 0.0 0.0\n2 -1.16 0.0 0.0\n3 1.16 0.0 0.0\n\n"
"Types\n\n1 C\n2 O\n3 O\n\n"
"Charges\n\n1 0.7\n2 -0.35\n3 -0.35\n\n"
"Bonds\n\n1 C=O 1 2\n2 C=O 1 3\n\n"
"Angles\n\n1 O=C=O 2 1 3\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";
FILE *fp = fopen(h2o_filename.c_str(), "w");
if (fp) {
fputs(h2o_file, fp);
fclose(fp);
}
fp = fopen(co2_filename.c_str(), "w");
if (fp) {
fputs(co2_file, fp);
fclose(fp);
}
}
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
bool verbose = false;
class MoleculeFileTest : public LAMMPSTest {
protected:
static void SetUpTestSuite() { create_molecule_files("moltest.h2o.mol", "moltest.co2.mol"); }
static void SetUpTestSuite()
{
create_molecule_files("moltest.h2o.mol", "moltest.co2.mol");
create_labelmap_files("labelmap.h2o.mol", "labelmap.co2.mol");
}
static void TearDownTestSuite()
{
remove("moltest.h2o.mol");
remove("moltest.co2.mol");
platform::unlink("moltest.h2o.mol");
platform::unlink("moltest.co2.mol");
platform::unlink("labelmap.h2o.mol");
platform::unlink("labelmap.co2.mol");
}
void SetUp() override
@ -247,6 +291,60 @@ TEST_F(MoleculeFileTest, twofiles)
ASSERT_EQ(mols.size(), 1);
}
TEST_F(MoleculeFileTest, labelmap)
{
if (!info->has_style("atom", "full")) GTEST_SKIP();
BEGIN_CAPTURE_OUTPUT();
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("molecule h2olabel labelmap.h2o.mol");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(
output,
ContainsRegex(".*Read molecule template h2olabel:.*\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();
command("molecule co2label labelmap.co2.mol");
output = END_CAPTURE_OUTPUT();
ASSERT_THAT(
output,
ContainsRegex(".*Read molecule template co2label:.*\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();
command("molecule h2onum moltest.h2o.mol");
command("molecule co2num moltest.co2.mol offset 2 1 1 0 0");
output = END_CAPTURE_OUTPUT();
ASSERT_THAT(
output,
ContainsRegex(".*Read molecule template h2onum:.*\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 co2num:.*\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);
auto mols = lmp->atom->get_molecule_by_id("h2onum");
ASSERT_EQ(mols.size(), 1);
mols = lmp->atom->get_molecule_by_id("co2num");
ASSERT_EQ(mols.size(), 1);
mols = lmp->atom->get_molecule_by_id("h2olabel");
ASSERT_EQ(mols.size(), 1);
mols = lmp->atom->get_molecule_by_id("co2label");
ASSERT_EQ(mols.size(), 1);
BEGIN_CAPTURE_OUTPUT();
command("labelmap atom 1 A 2 B");
END_CAPTURE_OUTPUT();
TEST_FAILURE(".*ERROR: Unknown atom type OW in Types section of molecule file: 1 OW.*",
command("molecule fail labelmap.h2o.mol"););
}
TEST_F(MoleculeFileTest, bonds)
{
if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP();