def parse_vasprun(self):
"""
Read in `vasprun.xml` as a pymatgen Vasprun object.
Args:
None
Returns:
None
None:
If the vasprun.xml is not well formed this method will catch the ParseError
and set self.vasprun = None.
"""
self.vasprun_filename = match_filename('vasprun.xml')
if not self.vasprun_filename:
raise FileNotFoundError(
'Could not find vasprun.xml or vasprun.xml.gz file')
try:
self.vasprun = Vasprun(self.vasprun_filename,
parse_potcar_file=False,
parse_dos=False)
except ET.ParseError:
self.vasprun = None
except:
raise
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 print_file_tracking(self):
if self.meta.track:
print("file tracking:")
for f, new_filename in self.meta.track.items():
print(" {}:".format(f))
if not new_filename:
new_filename = f
print(" filename: {}".format(new_filename))
filename = match_filename(self.directory + f)
if filename:
md5 = file_md5(filename)
else:
md5 = 'null'
print(" md5: {}".format(md5))
def print_file_tracking( self ):
if self.meta.track:
print( "file tracking:" )
for f, new_filename in self.meta.track.items():
print( " {}:".format( f ) )
if not new_filename:
new_filename = f
print( " filename: {}".format( new_filename ) )
filename = match_filename( self.directory + f )
if filename:
md5 = file_md5( filename )
else:
md5 = 'null'
print( " md5: {}".format( md5 ) )
def parse_vasprun( self ):
"""
Read in `vasprun.xml` as a pymatgen Vasprun object.
Args:
None
Returns:
None
None:
If the vasprun.xml is not well formed this method will catch the ParseError
and set self.vasprun = None.
"""
self.vasprun_filename = match_filename( 'vasprun.xml' )
if not self.vasprun_filename:
raise FileNotFoundError( 'Could not find vasprun.xml or vasprun.xml.gz file' )
try:
self.vasprun = Vasprun( self.vasprun_filename, parse_potcar_file=False )
except ET.ParseError:
self.vasprun = None
except:
raise