def test_pw_document_init(self):
document = PwDocument()
self.assertIsInstance(PwDocument(), PwDocument)
self.assertTrue(
document.schema.url.endswith("qeschema/schemas/qes.xsd"))
source = os.path.join(self.test_dir,
'resources/pw/Al001_relax_bfgs.xml')
document = PwDocument(source)
if platform.system() == 'Linux':
self.assertEqual(document.filename, source)
else:
self.assertTrue(document.filename.endswith('Al001_relax_bfgs.xml'))
self.assertTrue(
document.schema.url.endswith(
"qeschema/schemas/releases/qes_190719.xsd"))
document = PwDocument(source, schema='qes.xsd')
if platform.system() == 'Linux':
self.assertEqual(document.filename, source)
else:
self.assertTrue(document.filename.endswith('Al001_relax_bfgs.xml'))
self.assertTrue(
document.schema.url.endswith("qeschema/schemas/qes.xsd"))
source = os.path.join(self.test_dir, 'resources/pw/Al001_rlx_damp.xml')
document = PwDocument(source)
if platform.system() == 'Linux':
self.assertEqual(document.filename, source)
else:
self.assertTrue(document.filename.endswith('Al001_rlx_damp.xml'))
self.assertTrue(
document.schema.url.endswith("qeschema/schemas/qes.xsd"))
def test_document_init(self):
schema = os.path.join(self.schemas_dir, 'qes.xsd')
document = XmlDocument(schema)
self.assertIsInstance(document, XmlDocument)
self.assertIsNone(document.root)
self.assertIsNone(document.filename)
self.assertIsNone(document.format)
self.assertTrue(document.schema.url.endswith(schema))
self.assertIsInstance(document.schema, XMLSchema)
document = XmlDocument(schema=XMLSchema(schema))
self.assertTrue(document.schema.url.endswith(schema))
self.assertIsInstance(document.schema, XMLSchema)
self.assertIsInstance(PwDocument(), PwDocument)
self.assertIsInstance(PwDocument(schema=schema), PwDocument)
schema = os.path.join(self.schemas_dir, 'ph_temp.xsd')
self.assertIsInstance(PhononDocument(), PhononDocument)
self.assertIsInstance(PhononDocument(schema=schema), PhononDocument)
schema = os.path.join(self.schemas_dir, 'qes_neb.xsd')
self.assertIsInstance(NebDocument(), NebDocument)
self.assertIsInstance(NebDocument(schema=schema), NebDocument)
schema = os.path.join(self.schemas_dir, 'tddfpt.xsd')
self.assertIsInstance(TdDocument(), TdDocument)
self.assertIsInstance(TdDocument(schema=schema), TdDocument)
schema = os.path.join(self.schemas_dir, 'qes_spectrum.xsd')
self.assertIsInstance(TdSpectrumDocument(), TdSpectrumDocument)
self.assertIsInstance(TdSpectrumDocument(schema=schema),
TdSpectrumDocument)
def test_pw_output_get_ks_eigenvalues(self):
xml_filename = os.path.join(self.test_dir, 'resources/pw/Ni.xml')
document = PwDocument(source=xml_filename)
ks_eigenvalues = document.get_ks_eigenvalues()
self.assertEqual(len(ks_eigenvalues), 6)
for row in ks_eigenvalues:
self.assertEqual(len(row), 18)
for value in row:
self.assertIsInstance(value, float)
def test_pw_document(self):
xml_filename = os.path.join(self.test_dir,
'examples/pw/Al001_relax_bfgs.xml')
document = PwDocument()
document.read(xml_filename)
self.assertTrue(hasattr(document.root, 'tag'))
self.assertEqual(
document.root.tag,
'{http://www.quantum-espresso.org/ns/qes/qes-1.0}espresso')
self.assertEqual(document.filename, xml_filename)
self.assertEqual(document.format, 'xml')
self.assertEqual(document.input_path, 'input')
self.assertEqual(document.output_path, 'output')
def test_pw_output_get_k_points(self):
xml_filename = os.path.join(self.test_dir, 'resources/pw/Ni.xml')
document = PwDocument(source=xml_filename)
k_points = document.get_k_points()
expected = [
[-0.1666666666666667, 0.1666666666666667, 0.1666666666666667],
[0.5, -0.5, 0.8333333333333333],
[0.1666666666666667, -0.1666666666666667, 0.5],
[-0.1666666666666666, -1.166666666666667, 0.1666666666666666],
[-0.4999999999999999, -0.8333333333333334, -0.1666666666666666],
[0.5, -0.5, -0.5]
]
self.assertListEqual(k_points, expected)
def test_exception_class(self):
document = PwDocument()
with self.assertRaises(XmlDocumentError):
document.get_fortran_input()
schema = os.path.join(self.schemas_dir, 'qes.xsd')
document = TdSpectrumDocument(schema=schema)
document.read(
os.path.join(self.test_dir, 'resources/pw/Al001_relax_bfgs.xml'))
with self.assertRaises(XmlDocumentError):
document.get_fortran_input()
def test_init_with_schema_only(self):
schema = os.path.join(self.schemas_dir, 'qes.xsd')
document = PwDocument(schema=schema)
self.assertIsInstance(document, PwDocument)
self.assertTrue(
document.schema.url.endswith("qeschema/schemas/qes.xsd"))
document = PwDocument(schema='qes.xsd')
self.assertIsInstance(document, PwDocument)
self.assertTrue(
document.schema.url.endswith("qeschema/schemas/qes.xsd"))
document = PwDocument(schema='qes-20180511.xsd')
self.assertIsInstance(document, PwDocument)
self.assertTrue(
document.schema.url.endswith(
"qeschema/schemas/releases/qes-20180511.xsd"))
def test_init_from_xml_resource(self):
xml_file = os.path.join(self.test_dir,
'resources/pw/CO_bgfs_relax.xml')
document = PwDocument(source=XMLResource(xml_file))
if platform.system() == 'Linux':
self.assertEqual(document.filename, xml_file)
else:
self.assertTrue(document.filename.endswith('CO_bgfs_relax.xml'))
self.assertTrue(
document.schema.url.endswith("qeschema/schemas/qes.xsd"))
def test_pw_get_atomic_positions(self):
source = os.path.join(self.test_dir,
'resources/pw/Al001_relax_bfgs.xml')
document = PwDocument(source)
positions = document.get_atomic_positions()
self.assertIsNone(positions)
source = os.path.join(self.test_dir, 'resources/pw/Ni.xml')
document = PwDocument(source)
positions = document.get_atomic_positions()
self.assertEqual(positions, (['Ni'], [[0.0, 0.0, 0.0]]))
def test_incomplete_schema(self):
schema_path = os.path.join(self.test_dir,
'resources/dummy/incomplete.xsd')
document = PwDocument(schema=schema_path)
xml_filename = os.path.join(self.test_dir,
'resources/dummy/incomplete.xml')
document.read(xml_filename)
with self.assertRaises(XmlDocumentError) as ctx:
document.get_fortran_input()
self.assertEqual(str(ctx.exception),
"Missing input './input' in XML data!")
document.root.append(ElementTree.Element('input'))
with self.assertRaises(XmlDocumentError) as ctx:
document.get_fortran_input()
self.assertEqual(str(ctx.exception),
"Missing input element in XSD schema!")
def test_pw_document(self):
xml_filename = os.path.join(self.test_dir,
'resources/pw/Al001_relax_bfgs.xml')
document = PwDocument(source=xml_filename)
self.assertTrue(hasattr(document.root, 'tag'))
self.assertEqual(
document.root.tag,
'{http://www.quantum-espresso.org/ns/qes/qes-1.0}espresso')
if platform.system() == 'Linux':
self.assertEqual(document.filename, xml_filename)
else:
self.assertTrue(document.filename.endswith('Al001_relax_bfgs.xml'))
self.assertEqual(document.format, 'xml')
self.assertEqual(document.input_path, 'input')
self.assertEqual(document.output_path, 'output')
def test_pw_get_cell_parameters(self):
source = os.path.join(self.test_dir,
'resources/pw/Al001_relax_bfgs.xml')
document = PwDocument(source)
cells = document.get_cell_parameters()
self.assertIsNone(cells)
source = os.path.join(self.test_dir, 'resources/pw/Ni.xml')
document = PwDocument(source)
cells = document.get_cell_parameters()
self.assertListEqual(
cells,
[[-3.325, 0.0, 3.325], [0.0, 3.325, 3.325], [-3.325, 3.325, 0.0]])
def test_fortran_input_generator(self):
xml_filename = os.path.join(self.test_dir,
'resources/pw/Al001_relax_bfgs.xml')
document = PwDocument()
document.read(xml_filename)
self.assertFalse(os.path.isfile(self.output_file))
document.write_fortran_input(self.output_file)
with open(self.output_file) as f:
fortran_input = f.read()
if os.path.isfile(self.output_file):
os.unlink(self.output_file)
self.assertFalse(os.path.isfile(self.output_file))
self.assertEqual(fortran_input[:9], '&CONTROL\n')
self.assertEqual(fortran_input, document.get_fortran_input())
def test_pw_get_stress(self):
source = os.path.join(self.test_dir,
'resources/pw/Al001_relax_bfgs.xml')
document = PwDocument(source)
stress = document.get_stress()
self.assertIsNone(stress)
source = os.path.join(self.test_dir, 'resources/pw/Si.xml')
document = PwDocument(source)
stress = document.get_stress()
self.assertListEqual(
stress, [[
-1.825058728527109e-06, 1.058791184067875e-22,
-1.058791184067875e-22
], [1.058791184067875e-22, -1.825058728527109e-06, 0.0],
[
-1.058791184067875e-22, 1.058791184067875e-22,
-1.825058728527109e-06
]])
def test_pw_output_get_forces(self):
xml_filename = os.path.join(self.test_dir, 'resources/pw/Si.xml')
document = PwDocument(source=xml_filename)
self.assertIsNone(document.get_forces())
def test_pw_output_get_total_energy(self):
xml_filename = os.path.join(self.test_dir, 'resources/pw/Ni.xml')
document = PwDocument(source=xml_filename)
total_energy = document.get_total_energy()
self.assertEqual(total_energy, -30.44558256272531)
def test_unsupported_schema(self):
with self.assertRaises(NotImplementedError):
PwDocument(schema=os.path.join(self.test_dir,
'resources/dummy/schema.xsd'))
def test_init_with_schema_as_text(self):
with open(os.path.join(self.schemas_dir, 'qes.xsd')) as fp:
schema = fp.read()
document = PwDocument(schema=schema)
self.assertIsNone(document.schema.url)
