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']
