def read_data( verbose=True ):
dir_list = find_vasp_calculations()
if not dir_list:
raise ValueError( 'Did not find any subdirectories containing vasprun.xml or vasprun.xml.gz files' )
data = []
for d in dir_list:
converged = True
try:
with warnings.catch_warnings(record=True) as w:
vasprun = read_vasprun( match_filename( d + 'vasprun.xml' ) )
for warning in w:
if isinstance( warning.message, UnconvergedVASPWarning ):
converged = False
else:
print( warning.message )
except:
continue
poscar = Poscar.from_file( d + 'POSCAR' )
data.append( [ poscar.scaling,
vasprun.final_structure.volume,
vasprun.final_energy,
converged ] )
column_titles = [ 'scaling', 'volume', 'energy', 'converged' ]
df = pd.DataFrame( data, columns=column_titles ).sort_values( by='scaling' )
df = df.reset_index( drop=True )
df['scaling_factor'] = df.volume / df.scaling**3
scaling_factor_round = 4
if verbose:
print( df.to_string(index=False) )
if len( set( df.scaling_factor.round( scaling_factor_round ) ) ) != 1:
raise ValueError( "POSCAR scaling factors and volumes are inconsistent" )
return df
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 main():
parser = argparse.ArgumentParser()
parser.add_argument('-d',
'--directories',
default='all',
help='directories (containing INCARs) to edit')
args = parser.parse_args()
directories = args.directories
parameters_to_update = {
"GGA": "PE",
"ISYM": 3,
"PRECFOCK": "Fast",
"LMAXFOCK": 4,
"TIME": 0.30,
"LHFCALC": True,
"AEXX": 0.25,
"HFSCREEN": 0.2
}
if directories == 'all':
directories = find_vasp_calculations()
for directory in directories:
incar = Incar.from_file(f"{directory}/INCAR").as_dict()
incar = deepcopy(incar)
to_del = [i for i in incar.keys() if "LDA" in i]
for d in to_del:
incar.pop(d)
new_incar = Incar.from_dict(incar | parameters_to_update)
os.mkdir(f"{directory}/hygam")
new_incar.write_file(f"{directory}/hygam/INCAR")
structure = Poscar.from_file(f"{directory}/CONTCAR").structure
structure.to(filename=f"{directory}/hygam/POSCAR")
os.system(f"cp {directory}/POTCAR {directory}/hygam/POTCAR")
Kpoints().write_file(f"{directory}/hygam/KPOINTS")
def parse_calcs():
"""
find all vasp caluclations in directories "below" current directory and generate a ".csv"
summarising the status of these calculations ("calc_data.csv")
args:
- None
returns:
- None
"""
calculation_status = {}
home = os.getcwd()
entries = []
calculations = find_vasp_calculations()
for calc_dir in tqdm(calculations):
calc_status = {
'converged': assess_vasprun(f'{home}/{calc_dir}'),
'errors': assess_stdout(f'{home}/{calc_dir}'),
'contcar': assess_CONTCAR(f'{home}/{calc_dir}'),
'ionic_steps': assess_XDATCAR(f'{home}/{calc_dir}'),
'last_updated': assess_OUTCAR(f'{home}/{calc_dir}')
}
calculation_status.update({calc_dir: calc_status})
df = pd.DataFrame.from_dict(calculation_status, orient='index')
df.to_csv('calc_data.csv')
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_find_vasp_calculations(self):
mock_glob_output = ['dir_A/vasprun.xml', 'dir_B/dir_C/vasprun.xml']
with patch('glob.iglob', return_value=mock_glob_output) as mock_glob:
v = find_vasp_calculations()
self.assertEqual(v, ['./dir_A/', './dir_B/dir_C/'])
def test_find_vasp_calculations( self ):
mock_glob_output = [ 'dir_A/vasprun.xml', 'dir_B/dir_C/vasprun.xml' ]
with patch('glob.iglob', side_effect=[mock_glob_output, []]) as mock_glob:
v = find_vasp_calculations()
self.assertEqual( v, [ './dir_A/', './dir_B/dir_C/' ] )
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: