def test_potcar_spec_raises_valueerror_if_md5sum_not_matched( self ):
mock_potcar_filename = 'POTCAR'
md5sum_return_values = ( '12', '56', '90' )
with patch('builtins.open', return_value=io.StringIO(mock_potcar_string)) as mock_open:
with patch('vasppy.summary.md5sum', side_effect=md5sum_return_values ) as mock_md5sum:
with patch.dict('vasppy.data.potcar_data.potcar_md5sum_data', mock_potcar_data, clear=True ):
with self.assertRaises( ValueError ):
potcar_spec( mock_potcar_filename )
def main():
args = parse_command_line_arguments()
if args.hash:
hashes = {}
for p, md5hash in potcar_spec(args.potcar, return_hashes=True).items():
hashes[p] = md5hash
for p, ps in potcar_spec(args.potcar).items():
if args.hash:
print(p, ps, hashes[p])
else:
print(p, ps, hashes[p])
def test_potcar_spec_raises_valueerror_if_md5sum_not_matched(self):
mock_potcar_filename = 'POTCAR'
md5sum_return_values = ('12', '56', '90')
with patch('builtins.open',
return_value=io.StringIO(mock_potcar_string)) as mock_open:
with patch('vasppy.summary.md5sum',
side_effect=md5sum_return_values) as mock_md5sum:
with patch.dict('vasppy.data.potcar_data.potcar_md5sum_data',
mock_potcar_data,
clear=True):
with self.assertRaises(ValueError):
potcar_spec(mock_potcar_filename)
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 test_potcar_spec( self ):
mock_potcar_filename = 'POTCAR'
md5sum_return_values = ( '12', '56', '23' )
with patch('builtins.open', return_value=io.StringIO(mock_potcar_string)) as mock_open:
with patch('vasppy.summary.md5sum', side_effect=md5sum_return_values ) as mock_md5sum:
with patch.dict('vasppy.data.potcar_data.potcar_md5sum_data', mock_potcar_data, clear=True ):
p_spec = potcar_spec( mock_potcar_filename )
mock_open.assert_called_with( mock_potcar_filename, 'r' )
mock_md5sum.assert_has_calls( [ call('foo\nEnd of Dataset\n'),
call('bar\nEnd of Dataset\n'),
call('sds\nEnd of Dataset\n') ] )
self.assertEqual( p_spec, {'A': 'PBE', 'E': 'PBE_54', 'D': 'PBE_52'} )
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 test_potcar_spec(self):
mock_potcar_filename = 'POTCAR'
md5sum_return_values = ('12', '56', '23')
with patch('builtins.open',
return_value=io.StringIO(mock_potcar_string)) as mock_open:
with patch('vasppy.summary.md5sum',
side_effect=md5sum_return_values) as mock_md5sum:
with patch.dict('vasppy.data.potcar_data.potcar_md5sum_data',
mock_potcar_data,
clear=True):
p_spec = potcar_spec(mock_potcar_filename)
mock_open.assert_called_with(mock_potcar_filename, 'r')
mock_md5sum.assert_has_calls([
call('foo\nEnd of Dataset\n'),
call('bar\nEnd of Dataset\n'),
call('sds\nEnd of Dataset\n')
])
self.assertEqual(p_spec, {'A': 'PBE', 'E': 'PBE_54', 'D': 'PBE_52'})
def main():
args = parse_command_line_arguments()
for p, ps in potcar_spec(args.potcar).items():
print(p, ps)
def main():
args = parse_command_line_arguments()
for p, ps in potcar_spec( args.potcar ).items():
print( p, ps )
#! /usr/bin/env python3
from vasppy.summary import potcar_spec
import argparse
def parse_command_line_arguments():
parser = argparse.ArgumentParser( description='Generate POTCAR specification based on hashing individual pseudopotential strings' )
parser.add_argument( 'potcar', help="filename of the VASP POTCAR to be processed", nargs='?', default='POTCAR' )
args = parser.parse_args()
return args
if __name__ == '__main__':
args = parse_command_line_arguments()
for p, ps in potcar_spec( args.potcar ).items():
print( p, ps )
