def test_readingCIFs(self):
from analyseClusters import Crystal
#arbitrarily divide in 2 parts
myCrystal = Crystal.fromZp1Cif('mfa_tfa_tfa_pcm_f16_translated.cif',
nAtomsPerMol=15)
self.assertEqual(
[len(m.aseAtoms) for m in myCrystal.asymmetricMolecules], [15, 15])
#P-1 structure with z'=1
myCrystal = Crystal.fromCif('mfa_tfa_tfa_pcm_f16_translated.cif')
self.assertTrue(len(myCrystal.asymmetricMolecules), 2)
self.assertEqual(
[len(x.aseAtoms) for x in myCrystal.asymmetricMolecules], [30, 30])
#Originally P1 with z'=4 (already expanded the symmetry and reduced to P1)
myCrystal = Crystal.fromCif('tfa_ffa_tfa_pcm_p21c.cif')
self.assertTrue(len(myCrystal.asymmetricMolecules), 4)
self.assertEqual(
[len(x.aseAtoms) for x in myCrystal.asymmetricMolecules], [30] * 4)
def calculatePerfectSurfaceAngles(surfaceCif, nanocrystalCif):
''' look at bottom molecule surface and return angle such that nanocrystal will match this '''
from analyseClusters import Crystal
from listMathsSlow import overlay_points_RMSD
from quaternions import zyz_angles
surfaceCrystal = Crystal.fromCif(surfaceCif)
nanoCrystal = Crystal.fromCif(nanocrystalCif)
#nanoCrystal is lowest along c axis
nanoCrystal.asymmetricMolecules = [
sorted(
nanoCrystal.asymmetricMolecules,
key=lambda x: np.dot(x.aseAtoms.get_center_of_mass(scaled=False),
nanoCrystal.aseCell[2]))[0]
]
#surfaceCrystal is just lowest along c axis (dont need any more at this stage - just want to make 'perfect' cut)
surfaceCrystal.asymmetricMolecules = [
sorted(
surfaceCrystal.asymmetricMolecules,
key=lambda x: np.dot(x.aseAtoms.get_center_of_mass(scaled=False),
surfaceCrystal.aseCell[2]))[0]
]
#should assert that both are in a unit cell 0,1
#
nanoAtoms = nanoCrystal.asymmetricMolecules[0].aseAtoms.get_positions()[
7:13, :]
surfaceAtoms = surfaceCrystal.asymmetricMolecules[
0].aseAtoms.get_positions()[7:13, :]
# print nanoCrystal.asymmetricMolecules[0].aseAtoms.get_chemical_symbols(), surfaceCrystal.asymmetricMolecules[0].aseAtoms.get_chemical_symbols()
print 'assuming numbering system such that ring of atoms is 2nd ring ->7-12', nanoAtoms.shape, surfaceAtoms.shape
_rmsd, _qRot = overlay_points_RMSD(
surfaceAtoms - np.mean(surfaceAtoms, axis=0),
nanoAtoms - np.mean(nanoAtoms, axis=0))
assert (_rmsd < 0.1)
return zyz_angles(_qRot)
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_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_changingCellParams(self):
from analyseClusters import latticeParameters, Crystal
myCrystal = Crystal.fromZp1Cif('expStructuresTFA.cif')
np.testing.assert_array_almost_equal(
np.array(latticeParameters(myCrystal.aseCell)),
np.array([6.9136, 7.2915, 14.1096, 78.1106, 80.0763, 64.8556]))
#swap (a,b,c) -> (c,a,b)
np.testing.assert_array_almost_equal(
latticeParameters(
np.dot(np.array([[0., 0., 1.], [1., 0., 0.], [0., 1., 0.]]),
myCrystal.aseCell)),
np.array([14.1096, 6.9136, 7.2915, 64.8556, 78.1106, 80.0763]))
newCrystal = myCrystal.clone(
np.array([[0., 0., 1.], [1., 0., 0.], [0., 1., 0.]]))
np.testing.assert_array_almost_equal(
latticeParameters(newCrystal.aseCell),
np.array([14.1096, 6.9136, 7.2915, 64.8556, 78.1106, 80.0763]))
def makeFilesSingleMolSurface(surfaceCif,
nanocrystalCif,
surfaceDMA,
nanocrystalDMA,
nanocrystalAngles=[0., 0., 0.],
nanocrystalSize=[1, 1, 1],
freezeRotations=False,
manuallyRotateNanocrystal=False,
rotateAllAngles=False):
''' Writes the files needed to run orient (.in is the input)
Also can write other things to visualize components or composite - may be useful as check '''
from analyseClusters import getSpeciesListCIF, Surface, splitASEAtomsToMols, Crystal
from orientIO import NanocrystalOnSurfaceInput
#from ccdc.io import CrystalReader
from ioAndInterfaces import ccdcCrystalToASE
from multipoleFile import MultipoleFile, BOHRTOANGSTROM
from copy import deepcopy
#variables
# nanocrystalAngles = [0., 0., 0.]
#reading filenames
moleculeFilename = 'nanoCryst.punch'
#writing filenames
cellFilename = 'surface.cell'
inputFilename = 'surfaceCalc.in'
#other filenams
potentialFilename = 'fit4orient.pots'
surfaceCrystal = Crystal.fromCif(surfaceCif)
nanoCrystal = Crystal.fromCif(nanocrystalCif)
#keep only lowest molecule along c axis
print "%s mols in nanocrystal %s in surface" % (
len(nanoCrystal.asymmetricMolecules),
len(surfaceCrystal.asymmetricMolecules))
nanoCrystal.asymmetricMolecules = [
sorted(
nanoCrystal.asymmetricMolecules,
key=lambda x: np.dot(x.aseAtoms.get_center_of_mass(scaled=False),
nanoCrystal.aseCell[2]))[0]
]
print 'MASSIVE HACK - KEEPING BUT A SINGLE MOL'
surfaceCrystal.asymmetricMolecules = [
sorted(
surfaceCrystal.asymmetricMolecules,
key=lambda x: np.dot(x.aseAtoms.get_center_of_mass(scaled=False),
surfaceCrystal.aseCell[2]))[0]
]
# If doing this, rotate the nanocrystal so that the bottom molecule of surface is same orientation as it
if manuallyRotateNanocrystal:
from listMathsSlow import overlay_points_RMSD
from quaternions import quaternion_rotatn
targetAtomPositions = sorted(
surfaceCrystal.asymmetricMolecules,
key=lambda x: np.dot(x.aseAtoms.get_center_of_mass(
scaled=False), surfaceCrystal.aseCell[2]
))[0].aseAtoms.get_positions()[7:13, :]
nanoAtoms = nanoCrystal.asymmetricMolecules[0].aseAtoms.get_positions(
)[7:13, :]
print 'assuming numbering system such that ring of atoms is 2nd ring ->7-12', nanoAtoms.shape, targetAtomPositions.shape
if rotateAllAngles:
print 'dont do this - rotating all angles prevents coplanar surfaces'
exit()
_rmsd, _qRot = overlay_points_RMSD(
nanoAtoms - np.mean(nanoAtoms, axis=0),
targetAtomPositions - np.mean(targetAtomPositions, axis=0))
assert (_rmsd < 0.1)
else:
#just rotate around z axis - the allowRMSDNoRestriction should not be used- just make sure atomic numbering consistent
from listMathsSlow import optimalZRotation
_rmsd, _qRot = optimalZRotation(
nanoAtoms - np.mean(nanoAtoms, axis=0),
targetAtomPositions - np.mean(targetAtomPositions, axis=0),
allowRMSDNoRestriction=False)
def tempDistPrint(x):
print[np.linalg.norm(x[i + 1] - x[i]) for i in range(5)]
# tempDistPrint(targetAtomPositions - np.mean(targetAtomPositions, axis=0))
# tempDistPrint(np.array([quaternion_rotatn(x, _qRot) for x in nanoAtoms - np.mean(nanoAtoms, axis=0)]))
#rotate nanocrystal atoms and cell
nanoCrystal.asymmetricMolecules[0].rotateASEAtomsAroundCentroidQuat(
_qRot)
nanoCrystal.aseCell = np.array(
[quaternion_rotatn(x, _qRot) for x in nanoCrystal.aseCell])
print "%s mols in nanocrystal %s in surface" % (
len(nanoCrystal.asymmetricMolecules),
len(surfaceCrystal.asymmetricMolecules))
print "Atoms in nanoCrystal moleucules " + " ".join(
[str(len(x.aseAtoms)) for x in nanoCrystal.asymmetricMolecules])
print "Atoms in surface moleucules " + " ".join(
[str(len(x.aseAtoms)) for x in surfaceCrystal.asymmetricMolecules])
punchSurface = MultipoleFile(fileName=surfaceDMA)
punchNanocrystal = MultipoleFile(fileName=nanocrystalDMA)
print "%s atoms in surfaceDMA" % (len(punchSurface.aseAtoms()))
print "%s atoms in nanocrystalDMA" % (len(punchNanocrystal.aseAtoms()))
# punchSurface.writeFile('dummyPunchSurf.cif')
# punchNanocrystal.writeFile('dummyPunchNano.cif')
uniqueAtomTypes = list(set(list(surfaceCrystal.uniqueElements()) +\
list(nanoCrystal.uniqueElements())))
#print 'using same atoms for surface and nanocrystal'
print 'automatically setting all H bonded to O or N to Hn type'
inputHandler = NanocrystalOnSurfaceInput()
#displace by c of surfaceCrystal - and add a bit
displacementBohr = (surfaceCrystal.aseCell[2] +
np.array([0., 0., 3.5])) / BOHRTOANGSTROM
variables = [['x1', displacementBohr[0], 'Bohr'],
['y1', displacementBohr[1], 'Bohr'],
['z1', displacementBohr[2], 'Bohr'],
['alpha1', nanocrystalAngles[0], 'Degree'],
['beta1', nanocrystalAngles[1], 'Degree'],
['gamma1', nanocrystalAngles[2], 'Degree']]
atomsInCell = [
punchSurface.newPositions(m.aseAtoms.positions)
for m in surfaceCrystal.asymmetricMolecules
]
atomsInNanocrystal = [
punchNanocrystal.newPositions(m.aseAtoms.positions)
for m in nanoCrystal.asymmetricMolecules
]
with open(moleculeFilename, 'w') as outf:
#acidic hydrogens
for im, m in enumerate(atomsInNanocrystal):
m.setAtomTypes(
dict([(x, 'Hn') for x in nanoCrystal.asymmetricMolecules[im].
indicesAcidicHydrogens()]))
outf.write('\n'.join([
x.stringFormat(header='', printTypes=True)
for x in atomsInNanocrystal
]))
print 'passing one molecule in nanocrystal as only needs cell -- clear up later'
aseAtomsNanocrystal = nanoCrystal.asymmetricMolecules[0].aseAtoms
with open(cellFilename, 'w') as outf:
#acidic hydrogens
for im, m in enumerate(atomsInCell):
m.setAtomTypes(
dict([(x, 'Hn') for x in surfaceCrystal.
asymmetricMolecules[im].indicesAcidicHydrogens()]))
outf.write(
inputHandler.cellAndSitesString(surfaceCrystal.aseCell,
atomsInCell))
with open(inputFilename, 'w') as outf:
outf.write(
inputHandler.inputString(variables=variables,
moleculeFilename=moleculeFilename,
potentialFile=potentialFilename,
cellFile=cellFilename,
nanocrystal=aseAtomsNanocrystal,
surfaceCrystal=surfaceCrystal,
nanocrystalSize=nanocrystalSize,
atomTypes=uniqueAtomTypes,
freezeRotations=freezeRotations))
#
# EVERYTHING BELOW HERE IS FOR MY (DHC) DEBUGGING AND LOOKING AT FILES TO CHECK THINGS - NOT USED
#
#write temp.xyz with all atoms
print 'writing temporary xyz file to temp.xyz - note that this used only by DHC, not ORIENT itself'
try:
from ase import Atoms
except ImportError:
print 'Need ASE to print out temp.xyz but not important for ORIENT - ignore this'
return
# superSurface = deepcopy(surfaceCrystal)
# superSurface.filledUnitCellMolecules(superCell=np.array([3,3,2]))
# print [x[1] for x in variables[3:6]]
nanocrystalSize = [1, 1, 1]
print 'hack small nano'
surfaceBounds = inputHandler.boundsShowSurface(
nanocrystalSize, nanoCrystal.aseCell, surfaceCrystal.aseCell,
[x[1] for x in variables[3:6]])
print nanocrystalSize
# print len(superSurface.asymmetricMolecules)
# totalAtoms = Atoms(symbols = [x.symbol for m in superSurface.asymmetricMolecules for x in m.aseAtoms] +\
# [x.symbol for m in nanoCrystal.asymmetricMolecules for x in m.aseAtoms],
# positions = np.vstack([np.array([x.position for m in superSurface.asymmetricMolecules for x in m.aseAtoms]),
# displacementBohr * BOHRTOANGSTROM +\
# np.array([x.position for m in nanoCrystal.asymmetricMolecules for x in m.aseAtoms])])
# )
# checkSurfPunch = MultipoleFile()
# checkSurfPunch.initFromFile('surface.cell', _fileFormat='punch')
# checkSurfPunch.initFromFile('dummySurface.punch', _fileFormat='punch')
# checkNanoPunch = MultipoleFile()
# checkNanoPunch.initFromFile('nanoCryst.punch')
# print checkNanoPunch.atomPositions()[0]
# print nanoCrystal.asymmetricMolecules[0].aseAtoms[0].position
# print checkSurfPunch.atomPositions()[0]#
# print surfaceCrystal.asymmetricMolecules[0].aseAtoms[0].position
# tempASE = checkNanoPunch.aseAtoms()
# tempASE.write('nanoCheck.xyz')
# checkNanoPunch.writeFile('nanoCheck.xyz')
# tempASE = checkNanoPunch.aseAtoms()
# checkSurfPunch.writeFile('surfCheck.xyz')
# exit()
# print 'adding big gap'
totalAtoms = Atoms(symbols = [x.symbol for m in surfaceCrystal.asymmetricMolecules for x in m.aseAtoms
for a in xrange(surfaceBounds[0], surfaceBounds[1] + 1)
for b in xrange(surfaceBounds[2], surfaceBounds[3] + 1)] +\
[x.symbol for m in nanoCrystal.asymmetricMolecules for x in m.aseAtoms
for a in xrange(0, nanocrystalSize[0])
for b in xrange(0, nanocrystalSize[1])],
positions = np.vstack([np.array([x.position + np.dot(np.array([a, b, 1]), surfaceCrystal.aseCell)
for m in surfaceCrystal.asymmetricMolecules for x in m.aseAtoms
for a in xrange(surfaceBounds[0], surfaceBounds[1] + 1)
for b in xrange(surfaceBounds[2], surfaceBounds[3] + 1)]),
displacementBohr * BOHRTOANGSTROM +\
# np.array([0., 0., 50.]) + displacementBohr * BOHRTOANGSTROM +\
np.array([x.position + np.dot(np.array([a, b, 1]), nanoCrystal.aseCell)
for m in nanoCrystal.asymmetricMolecules for x in m.aseAtoms
for a in xrange(0, nanocrystalSize[0])
for b in xrange(0, nanocrystalSize[1])])])
)
# print np.min(np.array([x.position + np.dot(np.array([a, b, 1]), surfaceCrystal.aseCell)
# for m in surfaceCrystal.asymmetricMolecules for x in m.aseAtoms
# for a in xrange(surfaceBounds[0], surfaceBounds[1] + 1)
# for b in xrange(surfaceBounds[2], surfaceBounds[3] + 1)]), axis=0)
# print np.max(np.array([x.position + np.dot(np.array([a, b, 1]), surfaceCrystal.aseCell)
# for m in surfaceCrystal.asymmetricMolecules for x in m.aseAtoms
# for a in xrange(surfaceBounds[0], surfaceBounds[1] + 1)
# for b in xrange(surfaceBounds[2], surfaceBounds[3] + 1)]), axis=0)
# print np.min( displacementBohr * BOHRTOANGSTROM +\
# np.array([x.position + np.dot(np.array([a, b, 1]), nanoCrystal.aseCell)
# for m in nanoCrystal.asymmetricMolecules for x in m.aseAtoms
# for a in xrange(0, nanocrystalSize[0])
# for b in xrange(0, nanocrystalSize[1])]), axis=0)
# print np.max( displacementBohr * BOHRTOANGSTROM +\
# np.array([x.position + np.dot(np.array([a, b, 1]), nanoCrystal.aseCell)
# for m in nanoCrystal.asymmetricMolecules for x in m.aseAtoms
# for a in xrange(0, nanocrystalSize[0])
# for b in xrange(0, nanocrystalSize[1])]), axis=0)
# print displacementBohr * BOHRTOANGSTROM
# print surfaceCrystal.aseCell[2]
totalAtoms.write('temp.xyz')
def test_indicesAcidicHydrogens(self):
from analyseClusters import Crystal
myCrystal = Crystal.fromZp1Cif('mfa_tfa_tfa_pcm_f16_translated.cif')
self.assertTrue(myCrystal.asymmetricMolecules[0].
indicesAcidicHydrogens() == [18, 23])