def setUp(self):
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 6
system_1 = dpdata.LabeledSystem('gaussian/methane.gaussianlog',
fmt='gaussian/log')
system_2 = dpdata.LabeledSystem(
'gaussian/methane_reordered.gaussianlog', fmt='gaussian/log')
system_3 = dpdata.LabeledSystem('gaussian/methane_sub.gaussianlog',
fmt='gaussian/log')
system_4 = dpdata.LabeledSystem('gaussian/noncoveraged.gaussianlog',
fmt='gaussian/log')
systems = dpdata.MultiSystems(system_1, system_2, system_3, system_4)
path = "tmp.deepmd.multi"
systems.to_deepmd_raw(path)
self.system_1 = dpdata.LabeledSystem(os.path.join(path, 'C1H3'),
fmt='deepmd/raw',
type_map=['C', 'H'])
self.system_2 = system_3
def setUp(self):
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 6
system_1 = dpdata.LabeledSystem('gaussian/methane.gaussianlog',
fmt='gaussian/log')
system_2 = dpdata.LabeledSystem(
'gaussian/methane_reordered.gaussianlog', fmt='gaussian/log')
system_3 = dpdata.LabeledSystem('gaussian/methane_sub.gaussianlog',
fmt='gaussian/log')
system_4 = dpdata.LabeledSystem('gaussian/noncoveraged.gaussianlog',
fmt='gaussian/log')
self.systems = dpdata.MultiSystems(system_1, system_3, system_4)
self.systems.append(system_2)
self.system_1 = self.systems['C1H3']
self.system_2 = system_3
self.system_names = ['C1H4', 'C1H3']
self.system_sizes = {'C1H4': 2, 'C1H3': 1}
self.atom_names = ['C', 'H']
def test_npy_type_map(self):
system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md',
fmt='vasp/outcar')
system_1.to_deepmd_npy('tmp.deepmd')
with open(os.path.join('tmp.deepmd', 'type_map.raw')) as fp:
tm = fp.read().split()
self.assertEqual(tm, ['O', 'H'])
self.assertEqual(system_1['atom_names'], ['O', 'H'])
self.assertEqual(system_1['atom_types'][0], 0)
self.assertEqual(system_1['atom_types'][1], 0)
self.assertEqual(system_1['atom_types'][2], 1)
self.assertEqual(system_1['atom_types'][3], 1)
self.assertEqual(system_1['atom_types'][4], 1)
self.assertEqual(system_1['atom_types'][5], 1)
def setUp(self):
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 6
system_1 = dpdata.LabeledSystem('gaussian/methane.gaussianlog', fmt='gaussian/log')
system_2 = dpdata.LabeledSystem('gaussian/methane_reordered.gaussianlog', fmt='gaussian/log')
system_3 = dpdata.LabeledSystem('gaussian/methane_sub.gaussianlog', fmt='gaussian/log')
system_4 = dpdata.LabeledSystem('gaussian/noncoveraged.gaussianlog', fmt='gaussian/log')
self.systems = dpdata.MultiSystems(system_1)
self.systems += system_2
self.systems += system_3
self.systems += system_4
for s in self.systems:
if s.formula == 'C1H3':
self.system_1 = s
self.system_2 = system_3
self.system_names = ['C1H4', 'C1H3']
self.system_sizes = {'C1H4':2, 'C1H3':1}
self.atom_names = ['C', 'H']
def test_data_empty(self):
data = {
'atom_names': ['A', 'B'],
'atom_numbs': [0, 0],
'atom_types': np.array([], dtype=int),
'orig': np.array([0, 0, 0]),
'cells': np.array([]),
'coords': np.array([]),
}
sys1 = dpdata.System(data=data)
data = {
'atom_names': ['A', 'B'],
'atom_numbs': [0, 0],
'atom_types': np.array([], dtype=int),
'orig': np.array([0, 0, 0]),
'cells': np.array([]),
'coords': np.array([]),
'forces': np.array([]),
'energies': np.array([]),
'virials': np.array([]),
}
sys2 = dpdata.LabeledSystem(data=data)
def setUp(self):
self.system_al = dpdata.LabeledSystem(['qe.scf/Al.in', 'qe.scf/Al.out'], fmt='qe/pw/scf')
def setUp(self):
self.system_ch4 = dpdata.LabeledSystem('pwscf.scf/01.out',
fmt='pwscf/scf')
self.system_h2o = dpdata.LabeledSystem('pwscf.scf/02.out',
fmt='pwscf/scf')
def setUp (self) :
self.system = dpdata.LabeledSystem('gaussian/noncoveraged.gaussianlog',
fmt = 'gaussian/log')
self.atom_names = []
self.atom_numbs = []
self.nframes = 0
def setUp(self):
self.system_ch4 = dpdata.LabeledSystem(['qe.scf/01.in', 'qe.scf/01.out'], fmt='qe/pw/scf')
self.system_h2o = dpdata.LabeledSystem(['qe.scf/02.in', 'qe.scf/02.out'], fmt='qe/pw/scf')
def setUp(self):
self.system = dpdata.LabeledSystem('pwscf.traj/oh-md',
fmt='pwscf/traj')
def setUp(self):
self.system_water = dpdata.LabeledSystem('abacus.md',fmt='abacus/md')
def setUp(self):
self.system = dpdata.LabeledSystem('fhi_aims/out_scf',
fmt='fhi_aims/scf')
def setUp (self) :
self.system_1 = dpdata.LabeledSystem('gaussian/methane.gaussianlog', fmt='gaussian/log')
self.system_2 = dpdata.LabeledSystem('gaussian/methane_reordered.gaussianlog', fmt='gaussian/log')
self.system_3 = dpdata.LabeledSystem('gaussian/methane_sub.gaussianlog', fmt='gaussian/log')
self.system_4 = dpdata.LabeledSystem('gaussian/noncoveraged.gaussianlog', fmt='gaussian/log')
def setUp(self):
self.system = dpdata.LabeledSystem('gaussian/noncoveraged.gaussianlog',
fmt='gaussian/log')
def setUp(self):
self.system = dpdata.LabeledSystem('cp2k/cp2k_output',
fmt='cp2k/output')
def setUp(self):
self.system = dpdata.LabeledSystem('gaussian/methane.gaussianlog',
fmt='gaussian/log')
def setUp(self):
self.system = dpdata.LabeledSystem('fhi_aims/output_multi_elements',
fmt='fhi_aims/md')
def setUp(self):
self.system = dpdata.LabeledSystem('siesta/aimd/output',
fmt='siesta/aiMD_output')
def setUp(self):
self.LabeledSystem1 = dpdata.LabeledSystem(os.path.join('poscars', 'OUTCAR.ch4.unconverged'),\
fmt='outcar' )
self.LabeledSystem2 = dpdata.LabeledSystem(os.path.join('poscars', 'OUTCAR.ch4.1step'),\
fmt='outcar' )
def test_empty(self):
sys1 = dpdata.System(type_map=['A', 'H', 'B', 'O', 'D'])
sys2 = dpdata.LabeledSystem(type_map=['A', 'H', 'B', 'O', 'D'])
def setUp(self):
self.system = dpdata.LabeledSystem('qe.traj/oh-md', fmt = 'qe/cp/traj')
def test(self):
system = dpdata.LabeledSystem('poscars/6362_OUTCAR', fmt='vasp/outcar')
expected_types = [0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1]
self.assertEqual(list(system['atom_types']), expected_types)
self.assertEqual(system['atom_names'], ['B', 'O'])
self.assertEqual(system['atom_numbs'], [8, 6])
def setUp (self) :
self.system_1 = dpdata.LabeledSystem('poscars/vasprun.h2o.md.10.xml')
self.system_types = np.array([0,0,1,1,1,1])
self.system_2 = self.system_1.set_atom_types(["H","C","O"])
self.system_3 = self.system_1.set_atom_types({"H":2,"C":1,"O":3})
def restart_error(self):
with self.assertRaises(AssertionError):
dpdata.LabeledSystem('cp2k/restart_aimd',
fmt='cp2k/aimd_output',
restart=False)
def setUp(self):
self.system = dpdata.LabeledSystem('siesta/scf/siesta_output',
fmt='siesta/output')
def setUp(self):
self.system_ch4 = dpdata.LabeledSystem('abacus.scf', fmt='abacus/scf')
