def __init__(self, directory='.'):
self.directory = directory
with cd(directory):
try:
self.meta = VASPMeta.from_file('vaspmeta.yaml')
except FileNotFoundError as e:
raise type(e)(str(e) +
' in {}'.format(directory)).with_traceback(
sys.exc_info()[2])
self.parse_vasprun()
self.print_methods = {
'title': self.print_title,
'type': self.print_type,
'status': self.print_status,
'stoichiometry': self.print_stoichiometry,
'potcar': self.print_potcar,
'eatom': self.print_eatom,
'energy': self.print_energy,
'k-points': self.print_kpoints,
'functional': self.print_functional,
'encut': self.print_encut,
'plus_u': self.print_plus_u,
'ediffg': self.print_ediffg,
'ibrion': self.print_ibrion,
'converged': self.print_converged,
'version': self.print_version,
'md5': self.print_vasprun_md5,
'directory': self.print_directory,
'lreal': self.print_lreal,
'vbm': self.print_vbm,
'cbm': self.print_cbm
}
def test_init_vaspmeta_with_invalid_type_raises_valueerror(self):
title = 'title'
description = 'description'
status = 'finished'
type = 'invalid type'
with self.assertRaises(ValueError):
VASPMeta(title, description, status, type=type)
def test_init_vaspmeta_with_file_tracking(self):
title = 'title'
description = 'description'
status = 'finished'
track = {'DOSCAR': 'doscar', 'CHGCAR': 'chgcar'}
vaspmeta = VASPMeta(title, description, status, track=track)
self.assertEqual(vaspmeta.track, track)
def test_init_vaspmeta_with_valid_type(self):
title = 'title'
description = 'description'
status = 'finished'
valid_types = ['single-point', 'neb']
for t in valid_types:
vaspmeta = VASPMeta(title, description, status, type=t)
self.assertEqual(vaspmeta.type, t)
def test_init_vaspmeta(self):
title = 'title'
description = 'description'
notes = 'notes'
valid_status = ['to-run', 'incomplete', 'finished', 'dropped']
for s in valid_status:
vaspmeta = VASPMeta(title, description, status=s, notes=notes)
self.assertEqual(vaspmeta.title, title)
self.assertEqual(vaspmeta.description, description)
self.assertEqual(vaspmeta.status, s)
self.assertEqual(vaspmeta.notes, notes)
def test_from_file_with_type( self ):
example_file = """\
title: title
description: description
status: finished
type: single-point\
"""
with patch( 'vasppy.vaspmeta.VASPMeta' ) as mock_VASPMeta:
with patch( 'builtins.open', mock_open( read_data=example_file ), create=True ) as m:
vaspmeta = VASPMeta.from_file( example_file )
mock_VASPMeta.assert_called_with( 'title', 'description', 'finished', notes=None, type='single-point' )
self.assertEqual( vaspmeta, mock_VASPMeta.return_value )
def test_from_file( self ):
example_file = """\
title: title
description: description
notes: notes
status: finished\
"""
with patch( 'vasppy.vaspmeta.VASPMeta' ) as mock_VASPMeta:
mock_VASPMeta.return_value = 'my VASP metadata'
with patch( 'builtins.open', mock_open( read_data=example_file ), create=True ) as m:
vaspmeta = VASPMeta.from_file( example_file )
mock_VASPMeta.assert_called_with( 'title', 'description', 'finished', notes='notes', type=None )
self.assertEqual( vaspmeta, mock_VASPMeta.return_value )
def main():
supported_flags = Summary.supported_flags
to_print = [
'title', 'status', 'stoichiometry', 'potcar', 'plus_u', 'energy',
'lreal', 'k-points', 'functional', 'encut', 'ediffg', 'ibrion',
'converged', 'version', 'md5', 'directory'
]
titles = None
args = get_args()
if args.list:
for k, v, in supported_flags.items():
print("{}: {}".format(k.ljust(15), v))
sys.exit()
if args.file:
with open(args.file, 'r') as stream:
settings = yaml.load(stream)
if 'to_print' in settings:
to_print = settings['to_print']
if 'titles' in settings:
titles = settings['titles']
if args.print:
not_supported = [p for p in args.print if p not in supported_flags]
if not_supported:
raise ValueError(not_supported)
else:
to_print = args.print
if args.recursive:
path = sorted(find_vasp_calculations())
else:
path = ['.']
if args.check:
for p in path:
vaspmeta = Path('{}/vaspmeta.yaml'.format(p))
if not vaspmeta.is_file():
print('{} is missing vaspmeta.yaml'.format(p))
vasprun = Path('{}/vasprun.xml'.format(p))
if not vasprun.is_file():
print('{} is missing vasprun.xml'.format(p))
else:
if titles:
# Only parse directories with matching vasp_meta titles
matching_path = []
for p in path:
vm = VASPMeta.from_file('{}/vaspmeta.yaml'.format(p))
if vm.title in titles:
matching_path.append(p)
path = matching_path
for p in path:
s = Summary(p)
s.output(to_print=to_print)
def main():
supported_flags = Summary.supported_flags
to_print=[ 'title', 'status', 'stoichiometry', 'potcar', 'plus_u', 'energy', 'lreal', 'k-points', 'functional', 'encut', 'ediffg', 'ibrion', 'converged', 'version', 'md5', 'directory' ]
titles = None
args = get_args()
if args.list:
for k, v, in supported_flags.items():
print( "{}: {}".format( k.ljust(15), v ) )
sys.exit()
if args.file:
with open( args.file, 'r' ) as stream:
settings = yaml.load( stream, Loader=yaml.SafeLoader )
if 'to_print' in settings:
to_print = settings['to_print']
if 'titles' in settings:
titles = settings['titles']
if args.print:
not_supported = [ p for p in args.print if p not in supported_flags ]
if not_supported:
raise ValueError( not_supported )
else:
to_print = args.print
if args.recursive:
path = sorted( find_vasp_calculations() )
else:
path = [ '.' ]
if args.check:
for p in path:
vaspmeta = Path( '{}/vaspmeta.yaml'.format( p ) )
if not vaspmeta.is_file():
print( '{} is missing vaspmeta.yaml'.format( p ) )
vasprun = Path( '{}/vasprun.xml'.format( p ) )
if not vasprun.is_file():
print( '{} is missing vasprun.xml'.format( p ) )
else:
if titles:
# Only parse directories with matching vasp_meta titles
matching_path = []
for p in path:
vm = VASPMeta.from_file( '{}/vaspmeta.yaml'.format(p) )
if vm.title in titles:
matching_path.append( p )
path = matching_path
for p in path:
s = Summary( p )
s.output( to_print=to_print )
def test_from_file_with_no_notes_entry(self):
example_file = """\
title: title
description: description
status: finished\
"""
with patch('vasppy.vaspmeta.VASPMeta') as mock_VASPMeta:
mock_VASPMeta.return_value = 'my VASP metadata'
with patch('builtins.open',
mock_open(read_data=example_file),
create=True) as m:
vaspmeta = VASPMeta.from_file(example_file)
mock_VASPMeta.assert_called_with('title',
'description',
'finished',
notes=None,
type=None)
self.assertEqual(vaspmeta, mock_VASPMeta.return_value)
def __init__(self, directory='.'):
self.directory = directory
with cd(directory):
try:
self.meta = VASPMeta.from_file('vaspmeta.yaml')
except FileNotFoundError as e:
raise FileNotFoundError(
f'vaspmeta.yaml not found in {directory}')
self.parse_vasprun()
self.print_methods = {
'title': self.print_title,
'description': self.print_description,
'notes': self.print_notes,
'type': self.print_type,
'status': self.print_status,
'stoichiometry': self.print_stoichiometry,
'potcar': self.print_potcar,
'eatom': self.print_eatom,
'energy': self.print_energy,
'k-points': self.print_kpoints,
'functional': self.print_functional,
'encut': self.print_encut,
'plus_u': self.print_plus_u,
'ediffg': self.print_ediffg,
'ibrion': self.print_ibrion,
'converged': self.print_converged,
'version': self.print_version,
'md5': self.print_vasprun_md5,
'directory': self.print_directory,
'lreal': self.print_lreal,
'vbm': self.print_vbm,
'cbm': self.print_cbm,
'track': self.print_file_tracking,
'nelect': self.print_nelect
}
if not set(self.print_methods.keys()) == set(self.supported_flags):
print(set(self.print_methods.keys()))
print('--------------')
print(set(self.supported_flags.keys()))
raise (ValueError)
def __init__( self, directory='.' ):
self.directory = directory
with cd( directory ):
try:
self.meta = VASPMeta.from_file( 'vaspmeta.yaml' )
except FileNotFoundError as e:
raise type(e)( str(e) + ' in {}'.format( directory )).with_traceback( sys.exc_info()[2] )
self.parse_vasprun()
self.print_methods = { 'title': self.print_title,
'description': self.print_description,
'notes': self.print_notes,
'type': self.print_type,
'status': self.print_status,
'stoichiometry': self.print_stoichiometry,
'potcar': self.print_potcar,
'eatom': self.print_eatom,
'energy': self.print_energy,
'k-points': self.print_kpoints,
'functional': self.print_functional,
'encut': self.print_encut,
'plus_u': self.print_plus_u,
'ediffg': self.print_ediffg,
'ibrion': self.print_ibrion,
'converged': self.print_converged,
'version': self.print_version,
'md5': self.print_vasprun_md5,
'directory': self.print_directory,
'lreal': self.print_lreal,
'vbm': self.print_vbm,
'cbm': self.print_cbm,
'track': self.print_file_tracking,
'nelect': self.print_nelect }
if not set( self.print_methods.keys() ) == set( self.supported_flags ):
print( set( self.print_methods.keys() ) )
print( '--------------' )
print( set( self.supported_flags.keys() ) )
raise( ValueError )
def main():
supported_flags = Summary.supported_flags
to_print = [
'title', 'status', 'stoichiometry', 'potcar', 'plus_u', 'energy',
'lreal', 'k-points', 'functional', 'encut', 'ediffg', 'ibrion',
'converged', 'version', 'md5', 'directory'
]
titles = None
args = get_args()
if args.list:
for k, v, in supported_flags.items():
print("{}: {}".format(k.ljust(15), v))
sys.exit()
if args.file:
with open(args.file, 'r') as stream:
settings = yaml.load(stream, Loader=yaml.SafeLoader)
if 'to_print' in settings:
to_print = settings['to_print']
if 'titles' in settings:
titles = settings['titles']
if args.print:
not_supported = [p for p in args.print if p not in supported_flags]
if not_supported:
raise ValueError(not_supported)
else:
to_print = args.print
if args.recursive:
path = sorted(find_vasp_calculations())
else:
path = ['.']
if args.check:
for p in path:
vaspmeta = Path('{}/vaspmeta.yaml'.format(p))
if not vaspmeta.is_file():
print('{} is missing vaspmeta.yaml'.format(p))
vasprun = Path('{}/vasprun.xml'.format(p))
if not vasprun.is_file():
print('{} is missing vasprun.xml'.format(p))
else:
if titles:
# Only parse directories with matching vasp_meta titles
matching_path = []
for p in path:
vm = VASPMeta.from_file('{}/vaspmeta.yaml'.format(p))
if vm.title in titles:
matching_path.append(p)
path = matching_path
if args.maxjobs:
n = len(path)
with Pool(args.maxjobs) as p:
if args.progress_bar:
summaries = list(
tqdm.tqdm(p.imap(get_summary, path), total=len(path)))
else:
summaries = p.map(get_summary, path)
else:
if args.progress_bar:
path_iterator = tqdm.tqdm(path, unit='vasprun')
else:
path_iterator = path
summaries = [get_summary(p) for p in path_iterator]
if args.progress_bar:
iterable = tqdm.tqdm(summaries, unit='records')
else:
iterable = summaries
for s in iterable:
s.output(to_print=to_print)
def test_init_vaspmeta_with_no_file_tracking(self):
title = 'title'
description = 'description'
status = 'finished'
vaspmeta = VASPMeta(title, description, status)
self.assertEqual(vaspmeta.track, None)
def test_init_vaspmeta_with_invalid_status_raises_valueerror(self):
title = 'title'
description = 'description'
invalid_status = 'foo'
with self.assertRaises(ValueError):
VASPMeta(title, description, status=invalid_status)
if args.print:
not_supported = [p for p in args.print if p not in supported_flags]
if not_supported:
raise ValueError(not_supported)
else:
to_print = args.print
if args.recursive:
path = sorted(find_vasp_calculations())
else:
path = ['.']
if args.check:
for p in path:
vaspmeta = Path('{}/vaspmeta.yaml'.format(p))
if not vaspmeta.is_file():
print('{} is missing vaspmeta.yaml'.format(p))
vasprun = Path('{}/vasprun.xml'.format(p))
if not vasprun.is_file():
print('{} is missing vasprun.xml'.format(p))
else:
if titles:
# Only parse directories with matching vasp_meta titles
matching_path = []
for p in path:
vm = VASPMeta.from_file('{}/vaspmeta.yaml'.format(p))
if vm.title in titles:
matching_path.append(p)
path = matching_path
for p in path:
s = Summary(p)
s.output(to_print=to_print)