def _get_raw_pseudopotential_type(cls, calc, **kwargs): # pylint: disable=unused-argument
"""Return the raw pseudopotential type."""
from aiida.orm.nodes.data.upf import parse_upf
types = {}
for node in calc.get_incoming(node_class=UpfData).all_nodes():
element = node.element
parsed = parse_upf(node.get_file_abs_path())
if parsed['version'] != '2':
types[element] = None
continue
upf_type = None
with open(node.filename) as handle:
for line in handle:
match = cls._upf_type_v2_regexp.match(line.strip())
if match:
upf_type = match.group('upf_type')
break
types[element] = upf_type
return types
def test_invalid_element_upf_v1(self):
"""Test parsers exception on invalid element name in UPF v1."""
upf_filename = 'Ab.test_file_invalid_element_v1.UPF'
# upf file header contents
upf_contents = '\n'.join([
'<PP_INFO>'
'Human readable section is completely irrelevant for parsing!',
'<PP_HEADER',
'contents before element tag',
'Ab Element',
'contents following element tag',
'>',
])
path_to_upf = os.path.join(self.temp_dir, upf_filename)
with open(path_to_upf, 'w') as upf_file:
upf_file.write(upf_contents)
# Check if parser raises the desired ParsingError
with self.assertRaises(ParsingError):
_ = parse_upf(path_to_upf, check_filename=True)
def test_missing_element_upf_v2(self):
"""Test parsers exception on missing element name in UPF v2."""
upf_filename = 'Ab.test_file_missing_element_v2.UPF'
# upf file header contents
upf_contents = '\n'.join([
"<UPF version=\"2.0.1\">",
'Human readable section is completely irrelevant for parsing!',
'<PP_HEADER',
'contents before element tag',
'element should be here but is missing',
'contents following element tag',
'>',
])
path_to_upf = os.path.join(self.temp_dir, upf_filename)
with open(path_to_upf, 'w') as upf_file:
upf_file.write(upf_contents)
# Check if parser raises the desired ParsingError
with self.assertRaises(ParsingError):
_ = parse_upf(path_to_upf, check_filename=True)
def test_check_filename(self):
"""Test built-in check for if file name matches element"""
upf_filename = 'Al.test_file.UPF'
# upf file header contents
upf_contents = '\n'.join([
"<UPF version=\"2.0.1\">",
'Human readable section is completely irrelevant for parsing!',
'<PP_HEADER',
'contents before element tag',
"element=\"Pt\"",
'contents following element tag',
'>',
])
path_to_upf = os.path.join(self.temp_dir, upf_filename)
with open(path_to_upf, 'w') as upf_file:
upf_file.write(upf_contents)
# Check if parser raises the desired ParsingError
with self.assertRaises(ParsingError):
_ = parse_upf(path_to_upf, check_filename=True)
def test_upf_version_two(self):
"""Check if parsing for regular UPF file (version 2) succeeds."""
upf_filename = 'Al.test_file_v2.UPF'
# regular upf file version 2 header
upf_contents = '\n'.join([
"<UPF version=\"2.0.1\">",
'Human readable section is completely irrelevant for parsing!',
'<PP_HEADER',
'contents before element tag',
"element=\"Al\"",
'contents following element tag',
'>',
])
path_to_upf = os.path.join(self.temp_dir, upf_filename)
with open(path_to_upf, 'w') as upf_file:
upf_file.write(upf_contents)
# try to parse version / element name from UPF file contents
parsed_data = parse_upf(path_to_upf, check_filename=True)
# check that parsed data matches the expected one
self.assertEqual(parsed_data['version'], '2.0.1')
self.assertEqual(parsed_data['element'], 'Al')
def test_upf_version_one(self):
"""Check if parsing for regular UPF file (version 1) succeeds."""
upf_filename = 'O.test_file_v1.UPF'
# regular upf file version 1 header
upf_contents = u'\n'.join([
'<PP_INFO>'
'Human readable section is completely irrelevant for parsing!',
'<PP_HEADER',
'contents before element tag',
'O Element',
'contents following element tag',
'>',
])
path_to_upf = os.path.join(self.temp_dir, upf_filename)
with open(path_to_upf, 'w') as upf_file:
upf_file.write(upf_contents)
# try to parse version / element name from UPF file contents
parsed_data = parse_upf(path_to_upf, check_filename=True)
# check that parsed data matches the expected one
self.assertEqual(parsed_data['version'], '1')
self.assertEqual(parsed_data['element'], 'O')
def test_additional_header_line(self):
"""Regression #2228: check if parsing succeeds if additional header line is present."""
upf_filename = 'Pt.test_file.UPF'
# minimal contents required for parsing including additional header
# file
upf_contents = '\n'.join([
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>",
"<UPF version=\"2.0.1\">",
'Human readable section is completely irrelevant for parsing!',
'<PP_HEADER',
'contents before element tag',
"element=\"Pt\"",
'contents following element tag',
'>',
])
path_to_upf = os.path.join(self.temp_dir, upf_filename)
with open(path_to_upf, 'w') as upf_file:
upf_file.write(upf_contents)
# try to parse version / element name from UPF file contents
parsed_data = parse_upf(path_to_upf, check_filename=True)
# check that parsed data matches the expected one
self.assertEqual(parsed_data['version'], '2.0.1')
self.assertEqual(parsed_data['element'], 'Pt')
