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_summary_is_initialised(self, mock_parse_vasprun, MockVASPMeta):
MockVASPMeta.from_file = Mock(return_value='foo')
summary = Summary()
self.assertEqual(mock_parse_vasprun.call_count, 1)
expected_print_methods = [
'title', 'type', 'status', 'stoichiometry', 'potcar', 'eatom',
'energy', 'k-points', 'functional', 'encut', 'plus_u', 'ediffg',
'ibrion', 'converged', 'version', 'md5', 'directory', 'lreal',
'vbm', 'cbm'
]
for key in expected_print_methods:
self.assertTrue(key in summary.print_methods)
self.assertTrue(inspect.ismethod(summary.print_methods[key]))
def setUp(self, mock_parse_vaspun, MockVASPMeta):
MockVASPMeta.from_file = Mock(return_value='foo')
self.summary = Summary()
self.summary.vasprun = Mock(spec=Vasprun)
self.summary.meta = Mock(spec=VASPMeta)
class SummaryTestCase(unittest.TestCase):
@patch('vasppy.summary.VASPMeta')
@patch('vasppy.summary.Summary.parse_vasprun')
def setUp(self, mock_parse_vaspun, MockVASPMeta):
MockVASPMeta.from_file = Mock(return_value='foo')
self.summary = Summary()
self.summary.vasprun = Mock(spec=Vasprun)
self.summary.meta = Mock(spec=VASPMeta)
def test_functional_not_PBE(self):
self.summary.potcars_are_pbe = Mock(return_value=False)
self.assertEqual(self.summary.functional, 'not recognised')
def test_functional_is_PBE(self):
self.summary.potcars_are_pbe = Mock(return_value=True)
self.summary.vasprun.parameters = {'GGA': 'PE'}
self.assertEqual(self.summary.functional, 'PBE')
def test_functional_is_PBEsol(self):
self.summary.potcars_are_pbe = Mock(return_value=True)
self.summary.vasprun.parameters = {'GGA': 'PS'}
self.assertEqual(self.summary.functional, 'PBEsol')
def test_functional_is_PW91(self):
self.summary.potcars_are_pbe = Mock(return_value=True)
self.summary.vasprun.parameters = {'GGA': '91'}
self.assertEqual(self.summary.functional, 'PW91')
def test_functional_is_rPBE(self):
self.summary.potcars_are_pbe = Mock(return_value=True)
self.summary.vasprun.parameters = {'GGA': 'RP'}
self.assertEqual(self.summary.functional, 'rPBE')
def test_functional_is_AM05(self):
self.summary.potcars_are_pbe = Mock(return_value=True)
self.summary.vasprun.parameters = {'GGA': 'AM'}
self.assertEqual(self.summary.functional, 'AM05')
def test_functional_is_PBE0(self):
self.summary.potcars_are_pbe = Mock(return_value=True)
self.summary.vasprun.parameters = {
'GGA': 'AM',
'LHFCALC': 'True',
'AEXX': '0.25'
}
self.assertEqual(self.summary.functional, 'PBE0')
def test_functional_is_HSE06(self):
self.summary.potcars_are_pbe = Mock(return_value=True)
self.summary.vasprun.parameters = {
'GGA': 'AM',
'LHFCALC': 'True',
'AEXX': '0.25',
'HFSCREEN': '0.2'
}
self.assertEqual(self.summary.functional, 'HSE06')
def test_functional_is_a_PBE_hybrid(self):
self.summary.potcars_are_pbe = Mock(return_value=True)
self.summary.vasprun.parameters = {
'GGA': 'AM',
'LHFCALC': 'True',
'AEXX': '0.19'
}
self.assertEqual(self.summary.functional, 'hybrid. alpha=0.19')
def test_functional_is_a_screened_PBE_hybrid(self):
self.summary.potcars_are_pbe = Mock(return_value=True)
self.summary.vasprun.parameters = {
'GGA': 'AM',
'LHFCALC': 'True',
'AEXX': '0.19',
'HFSCREEN': '0.34'
}
self.assertEqual(self.summary.functional,
'screened hybrid. alpha=0.19, mu=0.34')
def test_functional_raises_KeyError_if_PBE_tag_is_invalid(self):
self.summary.potcars_are_pbe = Mock(return_value=True)
self.summary.vasprun.parameters = {'GGA': 'foo'}
with self.assertRaises(KeyError):
self.summary.functional
@patch('sys.stdout', new_callable=StringIO)
def test_print_cbm(self, mock_stdout):
summary = self.summary
summary.vasprun.eigenvalue_band_properties = ['null', 'CBM', 'VBM']
summary.print_cbm()
self.assertEqual(mock_stdout.getvalue(), 'cbm: CBM\n')
@patch('sys.stdout', new_callable=StringIO)
def test_print_vbm(self, mock_stdout):
self.summary.vasprun.eigenvalue_band_properties = [
'null', 'CBM', 'VBM'
]
self.summary.print_vbm()
self.assertEqual(mock_stdout.getvalue(), 'vbm: VBM\n')
@patch('sys.stdout', new_callable=StringIO)
def test_print_converged(self, mock_stdout):
self.summary.vasprun.converged = 'conv'
self.summary.print_converged()
self.assertEqual(mock_stdout.getvalue(), 'converged: conv\n')
def test_potcars_are_pbe_if_true(self):
self.summary.vasprun.potcar_symbols = [
'PAW_PBE Fe_pv 06Sep2000', 'PAW_PBE O 08Apr2002'
]
self.assertTrue(self.summary.potcars_are_pbe())
def test_potcars_are_pbe_if_false(self):
self.summary.vasprun.potcar_symbols = ['foo', 'PAW_PBE O 08Apr2002']
self.assertFalse(self.summary.potcars_are_pbe())
@patch('sys.stdout', new_callable=StringIO)
def test_print_type(self, mock_stdout):
self.summary.meta.type = 'TYPE'
self.summary.print_type()
self.assertEqual(mock_stdout.getvalue(), 'type: TYPE\n')
@patch('sys.stdout', new_callable=StringIO)
def test_print_type_if_type_is_not_set(self, mock_stdout):
self.summary.meta.type = None
self.summary.print_type()
self.assertEqual(mock_stdout.getvalue(), '')
@patch('sys.stdout', new_callable=StringIO)
def test_print_title(self, mock_stdout):
self.summary.meta.title = 'TITLE'
self.summary.print_title()
self.assertEqual(mock_stdout.getvalue(), 'title: TITLE\n')
def test_summary_init_raises_filenotfounderror_if_file_is_not_found(
self, mock_parse_vasprun, MockVASPMeta):
MockVASPMeta.from_file = Mock(side_effect=FileNotFoundError)
with self.assertRaises(FileNotFoundError):
summary = Summary()
def get_summary(p):
return Summary(p)
def setUp( self, mock_parse_vaspun, MockVASPMeta ):
MockVASPMeta.from_file = Mock( return_value='foo' )
self.summary = Summary()
self.summary.vasprun = Mock( spec=Vasprun )
self.summary.meta = Mock( spec=VASPMeta )
self.summary.meta.notes = None
class SummaryTestCase( unittest.TestCase ):
@patch('vasppy.summary.VASPMeta')
@patch('vasppy.summary.Summary.parse_vasprun')
def setUp( self, mock_parse_vaspun, MockVASPMeta ):
MockVASPMeta.from_file = Mock( return_value='foo' )
self.summary = Summary()
self.summary.vasprun = Mock( spec=Vasprun )
self.summary.meta = Mock( spec=VASPMeta )
self.summary.meta.notes = None
def test_functional_not_PBE( self ):
self.summary.potcars_are_pbe = Mock( return_value=False )
self.assertEqual( self.summary.functional, 'not recognised' )
def test_functional_is_PBE( self ):
self.summary.potcars_are_pbe = Mock( return_value=True )
self.summary.vasprun.parameters = { 'GGA': 'PE' }
self.assertEqual( self.summary.functional, 'PBE' )
def test_functional_is_PBEsol( self ):
self.summary.potcars_are_pbe = Mock( return_value=True )
self.summary.vasprun.parameters = { 'GGA': 'PS' }
self.assertEqual( self.summary.functional, 'PBEsol' )
def test_functional_is_PW91( self ):
self.summary.potcars_are_pbe = Mock( return_value=True )
self.summary.vasprun.parameters = { 'GGA': '91' }
self.assertEqual( self.summary.functional, 'PW91' )
def test_functional_is_rPBE( self ):
self.summary.potcars_are_pbe = Mock( return_value=True )
self.summary.vasprun.parameters = { 'GGA': 'RP' }
self.assertEqual( self.summary.functional, 'rPBE' )
def test_functional_is_AM05( self ):
self.summary.potcars_are_pbe = Mock( return_value=True )
self.summary.vasprun.parameters = { 'GGA': 'AM' }
self.assertEqual( self.summary.functional, 'AM05' )
def test_functional_is_PBE0( self ):
self.summary.potcars_are_pbe = Mock( return_value=True )
self.summary.vasprun.parameters = { 'GGA': 'AM', 'LHFCALC': 'True', 'AEXX': '0.25' }
self.assertEqual( self.summary.functional, 'PBE0' )
def test_functional_is_HSE06( self ):
self.summary.potcars_are_pbe = Mock( return_value=True )
self.summary.vasprun.parameters = { 'GGA': 'AM', 'LHFCALC': 'True', 'AEXX': '0.25', 'HFSCREEN': '0.2' }
self.assertEqual( self.summary.functional, 'HSE06' )
def test_functional_is_a_PBE_hybrid( self ):
self.summary.potcars_are_pbe = Mock( return_value=True )
self.summary.vasprun.parameters = { 'GGA': 'AM', 'LHFCALC': 'True', 'AEXX': '0.19' }
self.assertEqual( self.summary.functional, 'hybrid. alpha=0.19' )
def test_functional_is_a_screened_PBE_hybrid( self ):
self.summary.potcars_are_pbe = Mock( return_value=True )
self.summary.vasprun.parameters = { 'GGA': 'AM', 'LHFCALC': 'True', 'AEXX': '0.19', 'HFSCREEN': '0.34' }
self.assertEqual( self.summary.functional, 'screened hybrid. alpha=0.19, mu=0.34' )
def test_functional_raises_KeyError_if_PBE_tag_is_invalid( self ):
self.summary.potcars_are_pbe = Mock( return_value=True )
self.summary.vasprun.parameters = { 'GGA': 'foo' }
with self.assertRaises( KeyError ):
self.summary.functional
@patch('sys.stdout', new_callable=StringIO)
def test_print_cbm( self, mock_stdout ):
summary = self.summary
summary.vasprun.eigenvalue_band_properties = [ 'null', 'CBM', 'VBM' ]
summary.print_cbm()
self.assertEqual( mock_stdout.getvalue(), 'cbm: CBM\n' )
@patch('sys.stdout', new_callable=StringIO)
def test_print_vbm( self, mock_stdout ):
self.summary.vasprun.eigenvalue_band_properties = [ 'null', 'CBM', 'VBM' ]
self.summary.print_vbm()
self.assertEqual( mock_stdout.getvalue(), 'vbm: VBM\n' )
@patch('sys.stdout', new_callable=StringIO)
def test_print_converged( self, mock_stdout ):
self.summary.vasprun.converged = 'conv'
self.summary.print_converged()
self.assertEqual( mock_stdout.getvalue(), 'converged: conv\n' )
def test_potcars_are_pbe_if_true( self ):
self.summary.vasprun.potcar_symbols = [ 'PAW_PBE Fe_pv 06Sep2000', 'PAW_PBE O 08Apr2002' ]
self.assertTrue( self.summary.potcars_are_pbe() )
def test_potcars_are_pbe_if_false( self ):
self.summary.vasprun.potcar_symbols = [ 'foo', 'PAW_PBE O 08Apr2002' ]
self.assertFalse( self.summary.potcars_are_pbe() )
@patch('sys.stdout', new_callable=StringIO)
def test_print_type( self, mock_stdout ):
self.summary.meta.type = 'TYPE'
self.summary.print_type()
self.assertEqual( mock_stdout.getvalue(), 'type: TYPE\n' )
@patch('sys.stdout', new_callable=StringIO)
def test_print_type_if_type_is_not_set( self, mock_stdout ):
self.summary.meta.type = None
self.summary.print_type()
self.assertEqual( mock_stdout.getvalue(), '' )
@patch('sys.stdout', new_callable=StringIO)
def test_print_title( self, mock_stdout ):
self.summary.meta.title = 'TITLE'
self.summary.print_title()
self.assertEqual( mock_stdout.getvalue(), 'title: TITLE\n' )
@patch('sys.stdout', new_callable=StringIO)
def test_print_notes( self, mock_stdout ):
self.summary.meta.notes = 'NOTES'
self.summary.print_notes()
self.assertEqual( mock_stdout.getvalue(), 'notes: NOTES\n' )
@patch('sys.stdout', new_callable=StringIO)
def test_print_notes_handles_empty_notes_attribute( self, mock_stdout ):
self.summary.print_notes()
self.assertEqual( mock_stdout.getvalue(), 'notes: ~\n' )
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)
