def test_Crystal(self):
''' Make a Crystal and check some stuff '''
from analyseClusters import getSpeciesListCIF, Crystal, splitASEAtomsToMols
structures = list(getSpeciesListCIF('CSPPCM_example.cif'))
#take the z'=2 one
myCrystal = Crystal(splitASEAtomsToMols(structures[-2]))
self.assertEqual(len(myCrystal.asymmetricMolecules), 2)
self.assertEqual(len(myCrystal.asymmetricMolecules[-1].aseAtoms), 33)
myCrystal.generateNeighbouringAtoms(nMolecules=16)
self.assertEqual(len(myCrystal.asymmetricMolecules[0].listNeighbours),
16)
self.assertEqual(len(myCrystal.asymmetricMolecules[1].listNeighbours),
16)
myCrystal.calculateClusterInformation([1, 0, 2], [6, 15, 7, 8],
groupLabels=groupLabels['MFA'])
self.assertEqual(
myCrystal.asymmetricMolecules[1].environment['v(com)'].shape,
(16, 3))
self.assertEqual(
myCrystal.asymmetricMolecules[0].environment['r(com)'].shape,
(16, ))
def test_printStuff(self):
from analyseClusters import getSpeciesListCIF, Surface, splitASEAtomsToMols
return
# mySurface = Surface(splitASEAtomsToMols(structures[-2]), millerIndex = np.array([1,1,1]))
structures = list(getSpeciesListCIF('CSPPCM_example.cif'))
#take the z'=2 one - but hack it to make one atom per mol
hackMols = splitASEAtomsToMols(structures[-2])
from ase import Atoms
#draw the cell (for some reason, it may help to see it)
mySurface.asymmetricMolecules = mySurface.filledUnitCellMolecules()
mySurface.writeASEAtoms('originalSetting.cif')
_cifName = 'exampleSurface.cif'
if os.path.isfile(_cifName):
os.remove(_cifName)
mySurface.writeASEAtoms(_cifName, pbc=False)
self.assertTrue(os.path.isfile(_cifName))
def test_makeSurface(self):
from analyseClusters import getSpeciesListCIF, Surface, splitASEAtomsToMols
structures = list(getSpeciesListCIF('CSPPCM_example.cif'))
#take the z'=2 one - but hack it to make one atom per mol
hackMols = splitASEAtomsToMols(structures[-2])
from ase import Atoms
mySurface = Surface(hackMols)
#try simple cells and cell returning sensible cells
_oldCell = mySurface.aseCell
mySurface = Surface(hackMols, millerIndex=np.array([0, 1, 0]))
np.testing.assert_array_almost_equal(
np.dot(np.array([[0., 0., 1.], [1., 0., 0.], [0., 1., 0.]]),
_oldCell), mySurface.aseCell)
mySurface = Surface(hackMols, millerIndex=np.array([1, 0, 0]))
np.testing.assert_array_almost_equal(
np.dot(
np.array([[0., 0., 1.], [1., 0., 0.], [0., 1., 0.]]).T,
_oldCell), mySurface.aseCell)
#this needs a cubic cell otherwise becomes big
hackMols = [
Atoms(symbols=['C'],
positions=[hackMols[0].get_center_of_mass()],
cell=hackMols[0].cell,
info=hackMols[0].info),
Atoms(symbols=['Xe'],
positions=[hackMols[1].get_center_of_mass()],
cell=hackMols[1].cell,
info=hackMols[1].info)
]
hackMols = [
Atoms(symbols=['Xe', 'C'],
positions=[[0.25, 0.5, 0.75], [0.75, 1., 1.]],
cell=[[1., 0., 0.], [0., 2., 0.], [0., 0., 3]],
info=hackMols[0].info)
]
mySurface = Surface(hackMols, millerIndex=np.array([0, 0, 1]))
np.testing.assert_array_almost_equal(np.diag([1., 2., 3.]),
mySurface.aseCell)
#try other cuts
mySurface.writeASEAtoms('hack001.cif')
mySurface = Surface(hackMols, millerIndex=np.array([0, 1, 1]))
mySurface.writeASEAtoms('hack011.cif')
def test_CrystalSubroutines(self):
from analyseClusters import getSpeciesListCIF, Crystal, splitASEAtomsToMols
structures = list(getSpeciesListCIF('CSPPCM_example.cif'))
#take the z'=2 one
myCrystal = Crystal(splitASEAtomsToMols(structures[-2]))
#spacegroup 7, z'2 = 4
self.assertTrue(len(myCrystal.filledUnitCellMolecules()), 4)
#check that in ase the convention is cartVec = fracVec.Cell
np.testing.assert_array_almost_equal(
myCrystal.asymmetricMolecules[0].aseAtoms.get_center_of_mass(),
np.dot(
myCrystal.asymmetricMolecules[0].aseAtoms.get_center_of_mass(
scaled=True), myCrystal.aseCell))
#check that in ase the convention is fracVec = cartVec.(Cell^-1)
np.testing.assert_array_almost_equal(
myCrystal.asymmetricMolecules[0].aseAtoms.get_center_of_mass(
scaled=True),
np.dot(
myCrystal.asymmetricMolecules[0].aseAtoms.get_center_of_mass(),
np.linalg.inv(myCrystal.aseCell)))
def test_readCIFAndManipulate(self):
#check can split up a 'molecule' into molecules
from analyseClusters import getSpeciesListCIF
# structs = ASERead('CSPPCM_example.cif', index=':') #old way - dont do this
structures = list(getSpeciesListCIF('CSPPCM_example.cif'))
self.assertEqual(len(structures), 7)
from analyseClusters import splitASEAtomsToMols
self.assertEqual(len(structures[-2]), 66)
self.assertEqual([len(x) for x in splitASEAtomsToMols(structures[-2])],
[33, 33])
#demonstrate that positions can be retrieved to full accuracy
splitStructure = splitASEAtomsToMols(structures[-2],
useOriginalPositions=False)
np.testing.assert_array_almost_equal(
np.array([x.position for x in structures[-2]]),
np.array(np.vstack([x.get_positions() for x in splitStructure])),
decimal=2)
splitStructure = splitASEAtomsToMols(structures[-2])
np.testing.assert_array_almost_equal(
np.array([x.position for x in structures[-2]]),
np.array(np.vstack([x.get_positions() for x in splitStructure])))