def testSetRelaxed(self):
crystal = self._crystal.copy()
surface = Surface3D(crystal=self._crystal,
miller_indices=(0,0,1),
surface_cell=((1, 0), (0, 1)),
extra_atoms=Atoms('H', [[0.2, 0.3, 0.7]]),
)
surface_parameters1 = surface.defaultParameters().copy(
free_layers=2,
bound_layers=1,
vectors=((2, 0),(0, 2)),
cell_size=50,
)
surface_parameters2 = surface_parameters1.copy(
free_layers=2,
bound_layers=1,
vectors=((2, 0),(0, 3)),
cell_size=50,
)
surface_atoms = surface.atoms(parameters=surface_parameters1)
atoms = crystal.atoms()
atoms.cell *= 1.1
new_crystal = TestRelaxationSystem(crystal, atoms)
surface = surface.setSubSystems([new_crystal])
new_surface_atoms = surface.atoms(parameters=surface_parameters1)
self.assertArraysEqual(new_surface_atoms.cell[:2, :2], surface_atoms.cell[:2,:2]*1.1)
surface_atoms = new_surface_atoms.copy()
surface_atoms.rattle(0.2)
new_surface = TestRelaxationSystem(surface, surface_atoms)
self.assertTrue(new_surface.isRelaxed())
atoms = new_surface.atoms(parameters=surface_parameters2)
positions = [[ -1.38723744e+00 ,-4.16171232e+00 ,-1.96185000e+00],
[ 1.38723744e+00 ,-4.16171232e+00 ,-1.96185000e+00],
[ -1.38723744e+00 ,-1.38723744e+00 ,-1.96185000e+00],
[ 1.38723744e+00 ,-1.38723744e+00 ,-1.96185000e+00],
[ -1.38723744e+00 , 1.38723744e+00 ,-1.96185000e+00],
[ 1.38723744e+00 , 1.38723744e+00 ,-1.96185000e+00],
[ -1.33884498e+00 ,-3.15713093e+00 ,-1.32590857e+00],
[ 1.27477993e+00 ,-2.97704110e+00 ,-9.18075533e-01],
[ -1.56884225e+00 ,-2.82460740e-01 ,-6.87795246e-01],
[ 1.34208218e+00 , 1.35056409e-02 ,-1.26587464e+00],
[ -1.33884498e+00 , 2.39181883e+00 ,-1.32590857e+00],
[ 1.27477993e+00 , 2.57190865e+00 ,-9.18075533e-01],
[ -2.88335142e+00 ,-2.75229036e+00 ,-2.30198715e-01],
[ 7.51396037e-02 ,-2.89460262e+00 ,-5.83387500e-02],
[ -2.89481620e+00 , 3.70455637e-01 ,-2.69944495e-03],
[ -2.11542186e-01 , 1.64508982e-01 ,-2.44168730e-01],
[ -2.88335142e+00 , 2.79665940e+00 ,-2.30198715e-01],
[ 7.51396037e-02 , 2.65434714e+00 ,-5.83387500e-02],
[ -1.27164335e+00 ,-3.80576182e+00 , 1.07759060e+00],
[ 1.38199234e+00 ,-3.83766884e+00 , 1.58471945e+00],
[ -1.20674098e+00 ,-1.36300023e+00 , 1.10765779e+00],
[ 1.56533343e+00 ,-8.23372891e-01 , 1.40756866e+00],
[ -1.27164335e+00 , 1.74318793e+00 , 1.07759060e+00],
[ 1.38199234e+00 , 1.71128092e+00 , 1.58471945e+00]]
exp_atoms = Atoms('C18H6', positions)
self.assertAtomsEqual(exp_atoms, atoms)
def testCalculate(self):
crystal = SiAlpha
atoms = crystal.atoms()
atoms.cell *= 1.5
store = atoms.copy()
new_crystal = TestRelaxationSystem(crystal, atoms)
atoms = new_crystal.atoms()
self.assertArraysEqual(store.cell, atoms.cell)
def testCopy(self):
crystal = SiAlpha
atoms = crystal.atoms()
atoms.cell *= 1.5
store = atoms.copy()
crystal = TestRelaxationSystem(crystal, atoms)
new_crystal = crystal.copy()
self.assertIsInstance(new_crystal, DiamondStructure)
self.assertEqual(new_crystal.symbol(), 'Si')
atoms = new_crystal.atoms()
self.assertArraysEqual(store.cell, atoms.cell, 5)
def testRelaxation(self):
defect = Cross2DBDefect('Si', initial_state=AFM)
defect_parameters = defect.defaultParameters().copy(
free_layers=0,
bound_layers=1,
vectors=((2,0),(0,3)),
cell_size=50,
)
surface_parameters = defect.surface().defaultParameters().copy(
free_layers=0,
bound_layers=1,
vectors=((2, 0),(0, 2)),
cell_size=50,
)
self.assertFalse(defect.isRelaxed())
surface = defect.surface()
crystal = surface.crystal()
atoms = crystal.atoms()
atoms.cell *= 1.1
relaxation = atoms
rcrystal = TestRelaxationSystem(crystal, relaxation)
surface = surface.setSubSystems([rcrystal])
atoms = surface.atoms(parameters=defect_parameters)
atoms.rattle(0.2)
rsurface = TestRelaxationSystem(surface, relaxation)
atoms = surface.atoms(parameters=surface_parameters)
defect = defect.setSubSystems([rsurface])
self.assertTrue(defect.hasRelaxedSubsystems())
self.assertTrue(defect.surface().isRelaxed())
self.assertFalse(defect.isRelaxed())
self.assertTrue(defect.hasRelaxedSubsystems())
atoms3 = defect.atoms(parameters=defect_parameters)
atoms3.rattle(0.1)
relaxed_defect = TestRelaxationSystem(defect, atoms3)
atoms4 = relaxed_defect.atoms(parameters=defect_parameters)
expected = [[-7.85928, -4.43554, -4.23354],
[-5.23613, -4.43554, -4.23354],
[-3.63496, -4.43554, -4.23354],
[-1.0118 , -4.43554, -4.23354],
[0.58937 , -4.43554, -4.23354],
[3.21253 , -4.43554, -4.23354],
[4.8137 , -4.43554, -4.23354],
[7.43685 , -4.43554, -4.23354],
[-7.85928, -0.21122, -4.23354],
[-5.23613, -0.21122, -4.23354],
[-3.63496, -0.21122, -4.23354],
[-1.0118 , -0.21122, -4.23354],
[0.58937 , -0.21122, -4.23354],
[3.21253 , -0.21122, -4.23354],
[4.8137 , -0.21122, -4.23354],
[7.43685 , -0.21122, -4.23354],
[-7.85928, 4.01311 , -4.23354],
[-5.23613, 4.01311 , -4.23354],
[-3.63496, 4.01311 , -4.23354],
[-1.0118 , 4.01311 , -4.23354],
[0.58937 , 4.01311 , -4.23354],
[3.21253 , 4.01311 , -4.23354],
[4.8137 , 4.01311 , -4.23354],
[7.43685 , 4.01311 , -4.23354],
[-6.54771, -4.43554, -3.21618],
[-2.32338, -4.43554, -3.21618],
[1.90095 , -4.43554, -3.21618],
[6.12527 , -4.43554, -3.21618],
[-6.54771, -0.21122, -3.21618],
[-2.32338, -0.21122, -3.21618],
[1.90095 , -0.21122, -3.21618],
[6.12527 , -0.21122, -3.21618],
[-6.54771, 4.01311 , -3.21618],
[-2.32338, 4.01311 , -3.21618],
[1.90095 , 4.01311 , -3.21618],
[6.63777 , 4.52561 , -3.21618],
[-7.29651, -6.55515, -2.05506],
[-1.55147, -6.54168, -1.61686],
[1.10715 , -6.51755, -1.86665],
[6.78297 , -6.43342, -1.78799],
[-6.86063, -3.16873, -1.71815],
[-1.10581, -3.01911, -1.63938],
[1.02733 , -2.38001, -1.85321],
[6.84949 , -2.47845, -1.85632],
[-7.4285 , 1.94831 , -1.95512],
[-1.39382, 1.82262 , -1.89539],
[1.20774 , 1.77786 , -1.84043],
[7.03055 , 1.7402 , -1.84472],
[-6.69238, -6.46952, -0.41608],
[-2.28476, -6.49551, -0.26268],
[1.75533 , -6.51306, -0.36038],
[6.31916 , -6.5184 , -0.36382],
[-6.53179, -2.276 , -0.41151],
[-2.08706, -2.42085, -0.21367],
[6.4118 , -2.40545, -0.19604],
[-6.67709, 1.98315 , -0.1027 ],
[1.70574 , 1.82557 , -0.38133],
[6.21436 , 1.89324 , -0.25826]]
self.assertArraysEqual(expected, atoms4.positions)
def testRelaxation(self):
surface = Si001
surface_parameters1 = surface.defaultParameters().copy(
free_layers=0,
bound_layers=1,
vectors=((2, 0),(0, 2)),
cell_size=50,
)
surface_parameters2 = surface_parameters1.copy(
free_layers=0,
bound_layers=1,
vectors=((2, 0),(0, 4)),
cell_size=50,
)
atoms = surface.atoms(parameters=surface_parameters1)
crystal = surface.crystal()
atoms = crystal.atoms()
atoms.cell *= 1.1
relaxation = atoms
rcrystal = TestRelaxationSystem(crystal, relaxation)
atoms = surface.atoms(parameters=surface_parameters1)
surface = surface.setSubSystems([rcrystal])
self.assertTrue(surface.hasRelaxedSubsystems())
self.assertFalse(surface.isRelaxed())
atoms = surface.atoms(parameters=surface_parameters1)
atoms.rattle(0.2)
surface = TestRelaxationSystem(surface, atoms)
atoms2 = surface.atoms(parameters=surface_parameters1)
self.assertAtomsEqual(atoms, atoms2)
atoms3 = surface.atoms(parameters=surface_parameters2)
expected = [[-7.24595, -8.42647, -1.24756],
[-5.46077, -8.56878, -1.0757 ],
[-3.03309, -8.0782 , -1.02006],
[-1.52312, -8.28414, -1.26153],
[1.35335 , -8.84059, -1.283 ],
[2.95212 , -8.30096, -0.98309],
[5.51278 , -8.50887, -1.31307],
[6.99311 , -8.54078, -0.80594],
[-7.03773, -4.25198, -0.88783],
[-5.2313 , -4.27116, -1.06419],
[-2.59691, -4.07084, -1.11126],
[-1.20307, -4.31701, -1.11051],
[1.35997 , -4.60698, -1.36235],
[2.80029 , -4.42689, -0.95451],
[5.3543 , -4.50679, -0.72423],
[7.09192 , -4.21082, -1.30231],
[-7.24595, 0.02218 , -1.24756],
[-5.46077, -0.12013, -1.0757 ],
[-3.03309, 0.37046 , -1.02006],
[-1.52312, 0.16451 , -1.26153],
[1.35335 , -0.39193, -1.283 ],
[2.95212 , 0.14769 , -0.98309],
[5.51278 , -0.06022, -1.31307],
[6.99311 , -0.09213, -0.80594],
[-7.03773, 4.19667 , -0.88783],
[-5.2313 , 4.1775 , -1.06419],
[-2.59691, 4.37781 , -1.11126],
[-1.20307, 4.13164 , -1.11051],
[1.35997 , 3.84167 , -1.36235],
[2.80029 , 4.02176 , -0.95451],
[5.3543 , 3.94187 , -0.72423],
[7.09192 , 4.23783 , -1.30231],
[-8.44865, -8.44865, 0.0 ],
[-4.22433, -8.44865, 0.0 ],
[0.0 , -8.44865, 0.0 ],
[4.22433 , -8.44865, 0.0 ],
[-8.44865, -4.22433, 0.0 ],
[-4.22433, -4.22433, 0.0 ],
[0.0 , -4.22433, 0.0 ],
[4.22433 , -4.22433, 0.0 ],
[-8.44865, 0.0 , 0.0 ],
[-4.22433, 0.0 , 0.0 ],
[0.0 , 0.0 , 0.0 ],
[4.22433 , 0.0 , 0.0 ],
[-8.44865, 4.22433 , 0.0 ],
[-4.22433, 4.22433 , 0.0 ],
[0.0 , 4.22433 , 0.0 ],
[4.22433 , 4.22433 , 0.0 ],
[-7.83579, -6.43684, 1.53608 ],
[-4.93314, -6.44244, 1.45565 ],
[0.79398 , -6.14276, 1.21259 ],
[3.38423 , -6.41491, 1.0603 ],
[-7.68126, -1.79923, 0.82905 ],
[-4.83451, -2.09475, 1.2932 ],
[0.79292 , -2.50968, 1.30907 ],
[3.52119 , -1.81658, 1.24935 ],
[-7.83579, 2.01181 , 1.53608 ],
[-4.93314, 2.00621 , 1.45565 ],
[0.79398 , 2.30589 , 1.21259 ],
[3.38423 , 2.03374 , 1.0603 ],
[-7.68126, 6.64942 , 0.82905 ],
[-4.83451, 6.3539 , 1.2932 ],
[0.79292 , 5.93898 , 1.30907 ],
[3.52119 , 6.63207 , 1.24935 ],
[-8.22648, -6.35138, 2.54005 ],
[-4.40029, -6.32444, 3.41645 ],
[0.13219 , -6.27618, 2.91686 ],
[3.81993 , -6.10793, 3.07419 ],
[-8.21877, -2.05995, 2.92482 ],
[-4.44191, -2.39524, 2.83967 ],
[0.10212 , -2.27262, 2.89154 ],
[4.13447 , -1.73493, 2.95872 ],
[-8.22648, 2.09727 , 2.54005 ],
[-4.40029, 2.12421 , 3.41645 ],
[0.13219 , 2.17247 , 2.91686 ],
[3.81993 , 2.34073 , 3.07419 ],
[-8.21877, 6.3887 , 2.92482 ],
[-4.44191, 6.05342 , 2.83967 ],
[0.10212 , 6.17603 , 2.89154 ],
[4.13447 , 6.71373 , 2.95872 ]]
self.assertArraysEqual(expected, atoms3.positions)