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start adding tests for JSON format molecule files

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This commit is contained in:
Axel Kohlmeyer
2025-06-15 00:00:59 -04:00
parent 72538fbb84
commit 7fb930daed
1 changed files with 283 additions and 15 deletions
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298
unittest/formats/test_molecule_file.cpp
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@ -51,7 +51,7 @@ static void create_molecule_files(const std::string &h2o_filename, const std::st
"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"
const char co2_file[] = "# CO2 molecule file. TraPPE model. units = real\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 1\n2 2\n3 2\n\n"
@ -76,20 +76,21 @@ 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 HO\n3 HO\n\n"
"Charges\n\n1 -0.8472\n2 0.4236\n3 0.4236\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 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"
const char h2o_file[] =
"# Water molecule. SPC/E model. units = real\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 HO\n3 HO\n\n"
"Charges\n\n1 -0.8472\n2 0.4236\n3 0.4236\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 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. units = metal\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"
@ -111,6 +112,219 @@ static void create_labelmap_files(const std::string &h2o_filename, const std::st
}
}
static void create_molecule_json(const std::string &h2o_filename, const std::string &co2_filename)
{
// create molecule files
const char h2o_file[] =
"{\n"
"\"application\": \"LAMMPS\",\n"
"\"format\": \"molecule\",\n"
"\"revision\": 1,\n"
"\"scheme\": \"https://download.lammps.org/json/molecule-schema.json\",\n"
"\"title\": \"Water molecule. SPC/E model\",\n"
"\"types\": {\n"
" \"format\": [\"atom-id\", \"type\"],\n"
" \"data\": [\n"
" [1, 1],\n"
" [2, 2],\n"
" [3, 2],\n"
" ]\n"
"},\n"
"\"coords\": {\n"
" \"format\": [\"atom-id\", \"x\", \"y\", \"z\"],\n"
" \"data\": [\n"
" [1, 1.12456, 0.09298, 1.27452],\n"
" [2, 1.53683, 0.75606, 1.89928],\n"
" [3, 0.49482, 0.56390, 0.65678]\n"
" ]\n"
"},\n"
"\"charges\": {\n"
" \"format\": [\"atom-id\", \"charge\"],\n"
" \"data\": [\n"
" [1, -0.8472],\n"
" [2, 0.4236],\n"
" [3, 0.4236]\n"
" ]\n"
"},\n"
"\"bonds\": {\n"
" \"format\": [\"bond-type\", \"atom1\", \"atom2\"],\n"
" \"data\": [\n"
" [1, 1, 2],\n"
" [1, 1, 3]\n"
" ]\n"
"},\n"
"\"angles\": {\n"
" \"format\": [\"angle-type\", \"atom1\", \"atom2\", \"atom3\"],\n"
" \"data\": [\n"
" [1, 2, 1, 3]\n"
" ]\n"
"}\n";
const char co2_file[] =
"{\n"
"\"application\": \"LAMMPS\",\n"
"\"format\": \"molecule\",\n"
"\"revision\": 1,\n"
"\"scheme\": \"https://download.lammps.org/json/molecule-schema.json\",\n"
"\"title\": \"CO2 molecule file. TraPPE model.\",\n"
"\"units\": \"real\",\n"
"\"types\": {\n"
" \"format\": [\"atom-id\", \"type\"],\n"
" \"data\": [\n"
" [1, 1],\n"
" [2, 2],\n"
" [3, 2]\n"
" ]\n"
"},\n"
"\"coords\": {\n"
" \"format\": [\"atom-id\", \"x\", \"y\", \"z\"],\n"
" \"data\": [\n"
" [1, 0.00, 0.0, 0.0],\n"
" [2, -1.16, 0.0, 0.0],\n"
" [3, 1.16, 0.0, 0.0]\n"
" ]\n"
"},\n"
"\"charges\": {\n"
" \"format\": [\"atom-id\", \"charge\"],\n"
" \"data\": [\n"
" [1, 0.7],\n"
" [2, -0.35],\n"
" [3, -0.35]\n"
" ]\n"
"},\n"
"\"bonds\": {\n"
" \"format\": [\"bond-type\", \"atom1\", \"atom2\"],\n"
" \"data\": [\n"
" [1, 1, 2],\n"
" [1, 1, 3]\n"
" ]\n"
"},\n"
"\"angles\": {\n"
" \"format\": [\"angle-type\", \"atom1\", \"atom2\", \"atom3\"],\n"
" \"data\": [\n"
" [1, 2, 1, 3]\n"
" ]\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);
}
}
static void create_labelmap_json(const std::string &h2o_filename, const std::string &co2_filename)
{
// create molecule files
const char h2o_file[] =
"{\n"
"\"application\": \"LAMMPS\",\n"
"\"format\": \"molecule\",\n"
"\"revision\": 1,\n"
"\"scheme\": \"https://download.lammps.org/json/molecule-schema.json\",\n"
"\"title\": \"Water molecule. SPC/E model\",\n"
"\"units\": \"real\",\n"
"\"types\": {\n"
" \"format\": [\"atom-id\", \"type\"],\n"
" \"data\": [\n"
" [\"OW\", 1],\n"
" [\"HO\", 2],\n"
" [\"HO\", 2],\n"
" ]\n"
"},\n"
"\"coords\": {\n"
" \"format\": [\"atom-id\", \"x\", \"y\", \"z\"],\n"
" \"data\": [\n"
" [1, 1.12456, 0.09298, 1.27452],\n"
" [2, 1.53683, 0.75606, 1.89928],\n"
" [3, 0.49482, 0.56390, 0.65678]\n"
" ]\n"
"},\n"
"\"charges\": {\n"
" \"format\": [\"atom-id\", \"charge\"],\n"
" \"data\": [\n"
" [1, -0.8472],\n"
" [2, 0.4236],\n"
" [3, 0.4236]\n"
" ]\n"
"},\n"
"\"bonds\": {\n"
" \"format\": [\"bond-type\", \"atom1\", \"atom2\"],\n"
" \"data\": [\n"
" [\"OW-HO\", 1, 2],\n"
" [\"OW-HO\", 1, 3]\n"
" ]\n"
"},\n"
"\"angles\": {\n"
" \"format\": [\"angle-type\", \"atom1\", \"atom2\", \"atom3\"],\n"
" \"data\": [\n"
" [\"HO-OW-HO\", 2, 1, 3]\n"
" ]\n"
"}\n";
const char co2_file[] =
"{\n"
"\"application\": \"LAMMPS\",\n"
"\"format\": \"molecule\",\n"
"\"revision\": 1,\n"
"\"scheme\": \"https://download.lammps.org/json/molecule-schema.json\",\n"
"\"title\": \"CO2 molecule file. TraPPE model.\",\n"
"\"units\": \"metal\",\n"
"\"types\": {\n"
" \"format\": [\"atom-id\", \"type\"],\n"
" \"data\": [\n"
" [\"C\", 1],\n"
" [\"O\", 2],\n"
" [\"O\", 2]\n"
" ]\n"
"},\n"
"\"coords\": {\n"
" \"format\": [\"atom-id\", \"x\", \"y\", \"z\"],\n"
" \"data\": [\n"
" [1, 0.00, 0.0, 0.0],\n"
" [2, -1.16, 0.0, 0.0],\n"
" [3, 1.16, 0.0, 0.0]\n"
" ]\n"
"},\n"
"\"charges\": {\n"
" \"format\": [\"atom-id\", \"charge\"],\n"
" \"data\": [\n"
" [1, 0.7],\n"
" [2, -0.35],\n"
" [3, -0.35]\n"
" ]\n"
"},\n"
"\"bonds\": {\n"
" \"format\": [\"bond-type\", \"atom1\", \"atom2\"],\n"
" \"data\": [\n"
" [\"C=O\", 1, 2],\n"
" [\"C=O\", 1, 3]\n"
" ]\n"
"},\n"
"\"angles\": {\n"
" \"format\": [\"angle-type\", \"atom1\", \"atom2\", \"atom3\"],\n"
" \"data\": [\n"
" [\"O=C=O\", 2, 1, 3]\n"
" ]\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;
@ -120,6 +334,8 @@ protected:
{
create_molecule_files("moltest.h2o.mol", "moltest.co2.mol");
create_labelmap_files("labelmap.h2o.mol", "labelmap.co2.mol");
create_molecule_json("moltest.h2o.json", "moltest.co2.json");
create_labelmap_json("labelmap.h2o.json", "labelmap.co2.json");
}
static void TearDownTestSuite()
@ -128,12 +344,17 @@ protected:
platform::unlink("moltest.co2.mol");
platform::unlink("labelmap.h2o.mol");
platform::unlink("labelmap.co2.mol");
platform::unlink("moltest.h2o.json");
platform::unlink("moltest.co2.json");
platform::unlink("labelmap.h2o.json");
platform::unlink("labelmap.co2.json");
}
void SetUp() override
{
testbinary = "MoleculeFileTest";
LAMMPSTest::SetUp();
command("units real");
ASSERT_NE(lmp, nullptr);
}
@ -149,6 +370,17 @@ protected:
command(fmt::format("molecule {} {} {}", name, file, args));
platform::unlink(file);
}
void run_json_cmd(const std::string &name, const std::string &args, const std::string &content)
{
std::string file = fmt::format("moltest_{}.json", name);
FILE *fp = fopen(file.c_str(), "w");
fputs(content.c_str(), fp);
fclose(fp);
command(fmt::format("molecule {} {} {}", name, file, args));
platform::unlink(file);
}
};
TEST_F(MoleculeFileTest, nofile)
@ -197,6 +429,29 @@ TEST_F(MoleculeFileTest, noatom)
platform::unlink("moltest_noatom.mol");
}
TEST_F(MoleculeFileTest, nojson)
{
TEST_FAILURE(
".*Molecule template nojson: No types entries in JSON data for molecule.*",
run_json_cmd(test_name, "",
"{\"application\":\"LAMMPS\",\"format\":\"molecule\",\"revision\": 1,"
"\"types\":{\"format\": [\"atom-id\",\"type\"],\"data\": [ ]},"
"\"coords\":{\"format\":[\"atom-id\",\"x\",\"y\",\"z\"],\"data\": [ ]}}"););
platform::unlink("moltest_noatom.json");
}
TEST_F(MoleculeFileTest, jsonunits)
{
TEST_FAILURE(
".*Molecule template jsonunits: Incompatible units in JSON molecule data: current = real, "
"JSON = lj.*",
run_json_cmd(test_name, "",
"{\"application\":\"LAMMPS\",\"units\":\"lj\",\"format\":\"molecule\","
"\"revision\": 1,\"types\":{\"format\": [\"atom-id\",\"type\"],\"data\": [ ]},"
"\"coords\":{\"format\":[\"atom-id\",\"x\",\"y\",\"z\"],\"data\": [ ]}}"););
platform::unlink("moltest_jsonunits.json");
}
TEST_F(MoleculeFileTest, empty)
{
TEST_FAILURE(".*Unexpected end of molecule file.*", run_mol_cmd(test_name, "", "Comment\n\n"););
@ -222,6 +477,19 @@ TEST_F(MoleculeFileTest, minimal)
".*0 fragments.*\n.*1 atoms.*\n.*0 bonds.*"));
}
TEST_F(MoleculeFileTest, minjson)
{
BEGIN_CAPTURE_OUTPUT();
run_mol_cmd(
test_name, "",
"{\"application\":\"LAMMPS\",\"format\":\"molecule\",\"revision\": 1,"
"\"types\":{\"format\": [\"atom-id\",\"type\"],\"data\": [[1,1]]},"
"\"coords\":{\"format\":[\"atom-id\",\"x\",\"y\",\"z\"],\"data\": [[1,0.0,0.0,0.0]]}}");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template minjson:\n.no title.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*1 atoms.*\n.*0 bonds.*"));
}
TEST_F(MoleculeFileTest, notype)
{
BEGIN_CAPTURE_OUTPUT();