def test_potcar_from_node(potcar_family):
"""Create a PotcarIo instance from a PotcarData node."""
potcar_ga = get_data_class('vasp.potcar').find_one(element='Ga')
from_ctor = PotcarIo(potcar_node=potcar_ga)
verify_potcario(from_ctor)
from_from = PotcarIo.from_(potcar_ga)
assert from_ctor == from_from
def test_potcar_from_file_node(potcar_family):
"""Create a PotcarIo instance from a PotcarFileData node."""
potcar_file_in = get_data_class('vasp.potcar_file').find_one(element='In')
from_ctor = PotcarIo(potcar_file_node=potcar_file_in)
verify_potcario(from_ctor)
from_from = PotcarIo.from_(potcar_file_in)
assert from_ctor == from_from
def test_potcar_from_path(fresh_aiida_env):
"""Create a PotcarIo instance from a file path."""
potcar_path_as = data_path('potcar', 'As', 'POTCAR')
from_ctor = PotcarIo(path=potcar_path_as)
from_from = PotcarIo.from_(potcar_path_as)
verify_potcario(from_from)
assert from_ctor == from_from
def test_potcar_from_contents(potcar_family):
"""Create a PotcarIo from contents of a POTCAR file."""
contents_as = read_file('potcar', 'As', 'POTCAR')
from_ctor = PotcarIo(contents=contents_as.encode('utf-8'))
verify_potcario(from_ctor)
assert from_ctor.node.uuid == get_data_class('vasp.potcar').find_one(
element='As').uuid
from_from = PotcarIo.from_(contents_as)
assert from_ctor == from_from
def mock_vasp():
"""Verify input files are parseable and copy in output files."""
from aiida.manage.configuration.settings import AIIDA_CONFIG_FOLDER # pylint: disable=import-outside-toplevel
pwd = Path().absolute()
aiida_path = Path(AIIDA_CONFIG_FOLDER)
aiida_cfg = aiida_path / 'config.json'
click.echo('DEBUG: AIIDA_PATH = {}'.format(os.environ.get('AIIDA_PATH')))
click.echo('DEBUG: AIIDA_CONFIG_FOLDER = {}'.format(str(aiida_path)))
assert aiida_path.exists()
assert aiida_cfg.is_file()
click.echo(aiida_cfg.read_text())
incar = pwd / 'INCAR'
assert incar.is_file(), 'INCAR input file was not found.'
potcar = pwd / 'POTCAR'
assert potcar.is_file(), 'POTCAR input file not found.'
poscar = pwd / 'POSCAR'
assert poscar.is_file(), 'POSCAR input file not found.'
kpoints = pwd / 'KPOINTS'
assert kpoints.is_file(), 'KPOINTS input file not found.'
incar_parser = IncarParser(file_path=str(incar))
assert incar_parser, 'INCAR could not be parsed.'
assert PotcarIo(path=str(potcar)), 'POTCAR could not be parsed.'
assert PoscarParser(file_path=str(poscar)), 'POSCAR could not be parsed.'
assert KpointsParser(
file_path=str(kpoints)), 'KPOINTS could not be parsed.'
system = incar_parser.incar.get('system', '')
try:
test_case = system.strip().split(':')[1].strip()
except IndexError:
test_case = ''
if not test_case:
shutil.copy(output_file('outcar', 'OUTCAR'), pwd / 'OUTCAR')
shutil.copy(output_file('vasprun', 'vasprun.xml'), pwd / 'vasprun.xml')
shutil.copy(output_file('chgcar', 'CHGCAR'), pwd / 'CHGCAR')
shutil.copy(output_file('wavecar', 'WAVECAR'), pwd / 'WAVECAR')
shutil.copy(output_file('eigenval', 'EIGENVAL'), pwd / 'EIGENVAL')
shutil.copy(output_file('doscar', 'DOSCAR'), pwd / 'DOSCAR')
shutil.copy(output_file('basic_run', 'vasp_output'),
pwd / 'vasp_output')
shutil.copy(poscar, pwd / 'CONTCAR')
else:
test_data_path = data_path(test_case, 'out')
for out_file in Path(test_data_path).iterdir():
shutil.copy(out_file, pwd)
def mock_vasp():
"""Verify input files are parseable and copy in output files."""
from aiida.manage.configuration.settings import AIIDA_CONFIG_FOLDER # pylint: disable=import-outside-toplevel
pwd = py_path.local('.')
aiida_path = py_path.local(AIIDA_CONFIG_FOLDER)
aiida_cfg = aiida_path.join('config.json')
click.echo('DEBUG: AIIDA_PATH = {}'.format(os.environ.get('AIIDA_PATH')))
click.echo('DEBUG: AIIDA_CONFIG_FOLDER = {}'.format(aiida_path.strpath))
assert aiida_path.isdir()
assert aiida_cfg.isfile()
click.echo(aiida_cfg.read())
incar = pwd.join('INCAR')
assert incar.isfile(), 'INCAR input file was not found.'
potcar = pwd.join('POTCAR')
assert potcar.isfile(), 'POTCAR input file not found.'
poscar = pwd.join('POSCAR')
assert poscar.isfile(), 'POSCAR input file not found.'
kpoints = pwd.join('KPOINTS')
assert kpoints.isfile(), 'KPOINTS input file not found.'
incar_parser = IncarParser(file_path=incar.strpath)
assert incar_parser, 'INCAR could not be parsed.'
assert PotcarIo(path=potcar.strpath), 'POTCAR could not be parsed.'
assert PoscarParser(file_path=poscar.strpath), 'POSCAR could not be parsed.'
assert KpointsParser(file_path=kpoints.strpath), 'KPOINTS could not be parsed.'
system = incar_parser.incar.get('system', '')
try:
test_case = system.strip().split(':')[1].strip()
except IndexError:
test_case = ''
if not test_case:
output_file('outcar', 'OUTCAR').copy(pwd.join('OUTCAR'))
output_file('vasprun', 'vasprun.xml').copy(pwd.join('vasprun.xml'))
output_file('chgcar', 'CHGCAR').copy(pwd.join('CHGCAR'))
output_file('wavecar', 'WAVECAR').copy(pwd.join('WAVECAR'))
output_file('eigenval', 'EIGENVAL').copy(pwd.join('EIGENVAL'))
output_file('doscar', 'DOSCAR').copy(pwd.join('DOSCAR'))
poscar.copy(pwd.join('CONTCAR'))
else:
test_data_path = data_path(test_case, 'out')
for out_file in py_path.local(test_data_path).listdir():
out_file.copy(pwd)
def test_file_contents_equivalence(fresh_aiida_env):
potcar_path_as = ['potcar', 'As', 'POTCAR']
from_file = PotcarIo(path=data_path(*potcar_path_as))
from_contents = PotcarIo(contents=read_file(
*potcar_path_as).encode('utf-8'))
assert from_file.sha512 == from_contents.sha512