def setUp(self): # CH4 and O2 system_1 = dpdata.LabeledSystem('gaussian/methane.gaussianlog', fmt='gaussian/log') system_2 = dpdata.LabeledSystem('gaussian/oxygen.gaussianlog', fmt='gaussian/log') systems1 = dpdata.MultiSystems(system_1, system_2) systems1.to_deepmd_npy("tmp.multi.to") self.systems = dpdata.MultiSystems().from_deepmd_npy("tmp.multi.to") self.system_names = ['C1H4O0', 'C0H0O2'] self.system_sizes = {'C1H4O0': 1, 'C0H0O2': 1} self.atom_names = ['C', 'H', 'O']
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_type_map(self): for type_map in permutations(['C', 'H', 'O', 'N'], 4): systems = dpdata.MultiSystems(self.system_1, self.system_2, self.system_3, self.system_4, type_map=type_map) self.assertEqual(type_map, systems.atom_names)
def setUp (self) : self.system_temp0 = dpdata.MultiSystems.from_file(file_name='xyz/xyz_unittest.xyz', fmt='quip/gap/xyz') self.system_1 = self.system_temp0.systems['B5C7'] # .sort_atom_types() self.system_temp1 = dpdata.LabeledSystem('xyz/B1C9', fmt='deepmd') self.system_temp2 = dpdata.LabeledSystem('xyz/B5C7', fmt='deepmd') self.system_temp3 = dpdata.MultiSystems(self.system_temp2, self.system_temp1) self.system_2 = self.system_temp3.systems['B5C7'] self.places = 6 self.e_places = 6 self.f_places = 6 self.v_places = 4
def setUp(self): self.system_temp0 = dpdata.MultiSystems.from_file( file_name='ase/HeAlO.traj', fmt='ase/structure') self.system_1 = self.system_temp0.systems[ 'Al2He1O3'] # .sort_atom_types() self.system_temp1 = dpdata.LabeledSystem('ase/Al2He1O3', fmt='deepmd') self.system_temp2 = dpdata.LabeledSystem('ase/Al4He4O6', fmt='deepmd') self.system_temp3 = dpdata.MultiSystems(self.system_temp2, self.system_temp1) self.system_2 = self.system_temp3.systems['Al2He1O3'] self.places = 6 self.e_places = 6 self.f_places = 6 self.v_places = 4
def setUp (self) : self.places = 6 self.e_places = 4 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.npy.multi" systems.to_deepmd_npy(path) self.system_1 = dpdata.LabeledSystem(os.path.join(path, 'C1H3'), fmt='deepmd/npy', 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']