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():
args = parse_command_line_arguments()
poscar = Poscar.from_file( args.poscar )
potcars = potcar_spec( args.potcar )
for i, ( species, potcar ) in enumerate( zip( poscar.atoms, potcars ), 1 ):
matching_potcar = potcar.startswith( species )
if not matching_potcar:
raise AttributeError( 'Species {} mismatch:\nPOSCAR contains {}\nPOTCAR contains {}'.format( i, species, potcar ) )
if args.ppset:
this_ppset = potcars[potcar]
if args.ppset != this_ppset:
raise AttributeError( 'Pseudopotential set mismatch: {}'.format( potcars.values() ) )
def main():
args = parse_command_line_arguments()
poscar = Poscar.from_file(args.poscar)
potcars = potcar_spec(args.potcar)
for i, (species, potcar) in enumerate(zip(poscar.atoms, potcars), 1):
matching_potcar = potcar.startswith(species)
if not matching_potcar:
raise AttributeError(
'Species {} mismatch:\nPOSCAR contains {}\nPOTCAR contains {}'.
format(i, species, potcar))
if args.ppset:
this_ppset = potcars[potcar]
if args.ppset != this_ppset:
raise AttributeError('Pseudopotential set mismatch: {}'.format(
potcars.values()))
