@Test
public void testGaussianCollections() {
try {
// GAUSSIAN collections
for (int c = 0; c < collectionNames.length; c++) {
String inputDir = TestCommon.TEST_DATA_DIR + "/gaussian/" + collectionNames[c];
System.out.println("Parsing GAUSSIAN experiment " + inputDir);
ExperimentFactory factory = new ExperimentFactory(inputDir);
LocalDirectory coll = factory.parseDirectoryForMetadata(Software.GAUSSIAN, null, null);
MetadataAVUList md1 = coll.getMetadata();
logger.debug(md1.toString());
Assert.assertTrue(
TestCommon.compareMetadataToExpected(
md1,
TestCommon.TEST_DATA_DIR
+ "/expected_metadata/gaussian/"
+ collectionNames[c]
+ ".metadata"));
}
} catch (Exception e) {
e.printStackTrace();
assert (false);
}
}
@Test
public void testGaussianOutputs() {
try {
LocalFileFactory ffactory = LocalFileFactory.instance();
// GAUSSIAN output files
for (int f = 0; f < outputFileNames.length; f++) {
String outputFile = TestCommon.TEST_DATA_DIR + "/gaussian/" + outputFileNames[f];
System.out.println("Parsing GAUSSIAN output file " + outputFile);
GaussianOutputFile out = new GaussianOutputFile(outputFile);
MetadataAVUList md1 = out.getMetadata();
logger.debug(md1.toString());
// extract SCF energy values and store to CSV
GaussianUtils.extractEnergyFromLogFile(
out, TestCommon.TEST_DATA_DIR + "/output/" + out.getName() + ".csv");
LocalFile inpGen = ffactory.getFile(outputFile, Software.GAUSSIAN);
MetadataAVUList md2 = inpGen.getMetadata();
logger.debug(md2.toString());
Assert.assertTrue(TestCommon.compareMetadata(md1, md2));
Assert.assertTrue(
TestCommon.compareMetadataToExpected(
md1,
TestCommon.TEST_DATA_DIR
+ "/expected_metadata/gaussian/"
+ outputFileNames[f]
+ ".metadata"));
logger.debug("----------------------------------------");
}
} catch (IllegalAccessException e) {
e.printStackTrace();
assert (false);
} catch (SecurityException e) {
e.printStackTrace();
assert (false);
} catch (IllegalArgumentException e) {
e.printStackTrace();
assert (false);
} catch (NoSuchFieldException e) {
e.printStackTrace();
assert (false);
} catch (IOException e) {
e.printStackTrace();
assert (false);
} catch (Exception e) {
e.printStackTrace();
assert (false);
}
}
@Test
public void testGaussianInputs() {
try {
LocalFileFactory ffactory = LocalFileFactory.instance();
// GAUSSIAN input files
for (int f = 0; f < inputFileNames.length; f++) {
String inputFile = TestCommon.TEST_DATA_DIR + "/gaussian/" + inputFileNames[f];
System.out.println("Parsing GAUSSIAN input file " + inputFile);
GaussianInputFile inp = new GaussianInputFile(inputFile);
MetadataAVUList md1 = inp.getMetadata();
logger.debug(md1.toString());
LocalFile inpGen = ffactory.getFile(inputFile, Software.GAUSSIAN);
MetadataAVUList md2 = inpGen.getMetadata();
logger.debug(md2.toString());
Assert.assertTrue(TestCommon.compareMetadata(md1, md2));
// TestCommon.compareMetadataToExpected(md1, TestCommon.TEST_DATA_DIR +
// "/expected_metadata/gaussian/" + inputFileNames[f] + ".metadata");
Assert.assertTrue(
TestCommon.compareMetadataToExpected(
md1,
TestCommon.TEST_DATA_DIR
+ "/expected_metadata/gaussian/"
+ inputFileNames[f]
+ ".metadata"));
logger.debug("----------------------------------------");
}
} catch (IllegalAccessException e) {
e.printStackTrace();
assert (false);
} catch (SecurityException e) {
e.printStackTrace();
assert (false);
} catch (IllegalArgumentException e) {
e.printStackTrace();
assert (false);
} catch (NoSuchFieldException e) {
e.printStackTrace();
assert (false);
} catch (IOException e) {
e.printStackTrace();
assert (false);
} catch (Exception e) {
e.printStackTrace();
assert (false);
}
}
/**
* Get Gromacs collection metadata
*
* @throws Exception
*/
@Override
public MetadataAVUList getMetadata() throws Exception {
MetadataAVUList metadata = super.getMetadata();
// add aggregated metadata
SummaryExperimentTasks tasksSummary = this.getExperimentTasksSummary();
if (tasksSummary != null) {
metadata.addAll(tasksSummary.getMetadata());
}
// default to MD if no method found
if (!metadata.containsAttribute(MethodMetadata.COMPUTATIONAL_METHOD_NAME)) {
metadata.add(
new MetadataAVU(MethodMetadata.COMPUTATIONAL_METHOD_NAME, ParameterSet.METHOD_MD));
}
// if no task found, default software name to AMBER
if (!metadata.containsAttribute(PlatformMetadata.SOFTWARE_NAME))
metadata.add(new MetadataAVU(PlatformMetadata.SOFTWARE_NAME, Software.GROMACS));
// add topology info
if (mainTopologyFile != null
&& mainTopologyFile.getMolecularSystems() != null
&& mainTopologyFile.getMolecularSystems().size() > 0) {
MolecularSystem system = mainTopologyFile.getMolecularSystems().get(0);
metadata.addAll(system.getMetadata());
if (!metadata.containsAttribute(MethodMetadata.SOLVENT_TYPE)) {
// if water or ions are present, assume solvated system
if (system.getIonCount() > 0 || system.getSolventMoleculeCount() > 0)
metadata.updatePair(MethodMetadata.SOLVENT_TYPE, ParameterSet.SOLVENT_EXPLICIT);
else
metadata.add(new MetadataAVU(MethodMetadata.SOLVENT_TYPE, ParameterSet.SOLVENT_IN_VACUO));
}
}
return metadata;
}
