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')