def test_optimisingOverlays(self):
pts1 = np.array([[-0.541357990208,0.840223963793,0.967951435],
[-0.507301547591,-0.542664198999,1.171816351],
[0.0255987444643,-1.38443421464,0.204678748],
[0.556845352422,-0.849058545788,-0.964797836],
[0.509212767371,0.526541086859,-1.159201955],
[-0.0429973264567,1.40939190877,-0.220446743]])
pts2 = np.array([[-0.452870161944,1.0471304112,0.822046103134],
[0.838143143533,0.525685681579,0.978663279603],
[1.28692322978,-0.496230348673,0.148563133317],
[0.457098160295,-1.03724996618,-0.829129779641],
[-0.837847702903,-0.538192702582,-0.964350371592],
[-1.29144666876,0.49885692466,-0.155792364821]])
np.testing.assert_array_almost_equal(np.mean(pts1, axis=0),
np.mean(pts2, axis=0))
from listMathsSlow import rmsd
print rmsd(pts1, pts2)
from listMathsSlow import overlay_points_RMSD
originalRMSD, qRot = overlay_points_RMSD(pts1, pts2)
# print originalRMSD
from quaternions import quaternion_rotatn
self.assertAlmostEqual(rmsd(pts2,
np.array([quaternion_rotatn(x, qRot) for x in pts1])),
originalRMSD)
from listMathsSlow import optimalZRotation
bestRMSDZ, bestQRotZ = optimalZRotation(pts1,
pts2)
from quaternions import make_quat_rot2
from listMathsSlow import rmsdNoRestriction
#check with a grid that optimal Z really is about the best
_nPts = 20
gridOptimisedPoints = np.array([rmsd(pts2,
np.array([quaternion_rotatn(x,
make_quat_rot2(float(i)/float(_nPts) * 2. * np.pi,
np.array([0., 0., 1.])))
for x in pts1])
)
for i in xrange(_nPts)])
self.assertTrue(all([x > bestRMSDZ for x in gridOptimisedPoints]))
self.assertTrue(bestRMSDZ + 1.e-3 > gridOptimisedPoints[3])
def functionOfOverlay(angle, pts1, pts2, allowRMSDNoRestriction):
_quat = make_quat_rot2(angle, np.array([0., 0., 1.]))
rotatedPts1 = np.array([quaternion_rotatn(x, _quat) for x in pts1])
if allowRMSDNoRestriction:
return rmsdNoRestriction(rotatedPts1, pts2)
else:
return rmsd(rotatedPts1, pts2)
def boundsShowSurface(self, nanocrystalSize, nanoCell, surfaceCell,
angleVariables):
''' estimate bounds for surface during plotting (wont effect calculation)
returns surfaceMinA, surfaceMaxA, surfaceMinB, surfaceMaxB
(status - run this and visually inspected things, but not extended to general angles, thoroughly tested) '''
cornersNanoCrystal = np.dot(
np.array([[nanocrystalSize[0], 0.,
0.], [0., nanocrystalSize[1], 0.],
[nanocrystalSize[0], nanocrystalSize[1], 0.],
[0., 0., 0.]]), nanoCell)
#zyz convention -- (after comparing to Stone's book) --
# assert(all([x==0. for x in angleVariables[1:]]))
from quaternions import zyz_quaternion, quaternion_rotatn
cornersNanoCrystal = np.array([
quaternion_rotatn(
x,
zyz_quaternion(
*map(lambda x: x * np.pi / 180., angleVariables)))
for x in cornersNanoCrystal
])
#find bounds in surface cell
boundsSurface = np.dot(cornersNanoCrystal, np.linalg.inv(surfaceCell))
boundsSurface = np.vstack(
[np.min(boundsSurface, axis=0),
np.max(boundsSurface, axis=0)])
return map(int, [
np.floor(boundsSurface[0, 0]),
np.ceil(boundsSurface[1, 0]),
np.floor(boundsSurface[0, 1]),
np.ceil(boundsSurface[1, 1])
])
def rotateASEAtomsAroundCentroidQuat(self, quat):
from quaternions import quaternion_rotatn
oldPositions = self.aseAtoms.get_positions()
_mean = np.mean(oldPositions, axis=0)
oldPositions -= _mean
newPositions = [quaternion_rotatn(x, quat) for x in oldPositions]
for i in xrange(len(self.aseAtoms)):
self.aseAtoms[i].position = newPositions[i] + _mean
def calculateAxisSystem(self, atom1, atom2, atom3):
''' atom1 (int) is (index for) pivot, to atom2 is x, 3 -> y . Make right handed frame '''
from quaternions import make_quat_rot2, quaternion_rotatn
internalX = (self.aseAtoms[atom2].position - self.aseAtoms[atom1].position) /\
np.linalg.norm(self.aseAtoms[atom1].position - self.aseAtoms[atom2].position)
internalY = (self.aseAtoms[atom3].position - self.aseAtoms[atom1].position) /\
np.linalg.norm(self.aseAtoms[atom3].position - self.aseAtoms[atom1].position)
internalZ = np.cross(internalX, internalY) / np.linalg.norm(
np.cross(internalX, internalY))
_angle = np.pi / 2. - vecAngle(internalX, internalY)
rotationQ = make_quat_rot2(_angle, internalZ)
internalY = quaternion_rotatn(internalY, rotationQ)
self.axisSystem = np.vstack([internalX, internalY, internalZ])
return self.axisSystem
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')