def computeACNA(inputState, settings):
"""
ACNA filter
"""
if len(inputState.cellDims) == 9:
cellDims = np.empty(3, np.float64)
cellDims[0] = inputState.cellDims[0]
cellDims[1] = inputState.cellDims[4]
cellDims[2] = inputState.cellDims[8]
else:
cellDims = inputState.cellDims
visibleAtoms = np.arange(inputState.NAtoms, dtype=np.int32)
scalars = np.zeros(inputState.NAtoms, dtype=np.float64)
NScalars = 0
fullScalars = np.empty(NScalars, np.float64)
NVectors = 0
fullVectors = np.empty(NVectors, np.float64)
pbc = np.ones(3, np.int32)
# counter array
counters = np.zeros(7, np.int32)
NVisible = acna.adaptiveCommonNeighbourAnalysis(visibleAtoms, inputState.pos, scalars, cellDims, pbc, NScalars, fullScalars,
settings.maxBondDistance, counters, settings.filteringEnabled, settings.structureVisibility,
1, NVectors, fullVectors)
# resize visible atoms
visibleAtoms.resize(NVisible, refcheck=False)
# store scalars
scalars.resize(NVisible, refcheck=False)
# store counters
d = {}
for i, structure in enumerate(filterer.Filterer.knownStructures):
if counters[i] > 0:
d[structure] = counters[i]
return scalars, d
def findDefects(inputLattice, refLattice, settings, acnaArray=None, pbc=np.ones(3, np.int32)):
"""
Point defects filter
"""
if len(refLattice.cellDims) == 9:
cellDims = np.empty(3, np.float64)
cellDims[0] = refLattice.cellDims[0]
cellDims[1] = refLattice.cellDims[4]
cellDims[2] = refLattice.cellDims[8]
else:
cellDims = refLattice.cellDims
if settings.useAcna:
logging.debug("Computing ACNA from point defects filter...")
# dummy visible atoms and scalars arrays
visAtoms = np.arange(inputLattice.NAtoms, dtype=np.int32)
acnaArray = np.empty(inputLattice.NAtoms, np.float64)
NScalars = 0
fullScalars = np.empty(NScalars, np.float64)
NVectors = 0
fullVectors = np.empty(NVectors, np.float64)
structVis = np.ones(len(filterer.Filterer.knownStructures), np.int32)
# counter array
counters = np.zeros(7, np.int32)
# number of threads
numThreads = 1
acna.adaptiveCommonNeighbourAnalysis(visAtoms, inputLattice.pos, acnaArray, cellDims, pbc, NScalars, fullScalars,
settings.acnaMaxBondDistance, counters, 0, structVis, numThreads, NVectors,
fullVectors)
# store counters
d = {}
for i, structure in enumerate(filterer.Filterer.knownStructures):
if counters[i] > 0:
d[structure] = counters[i]
logging.debug(" %r", d)
elif acnaArray is None or len(acnaArray) != inputLattice.NAtoms:
acnaArray = np.empty(0, np.float64)
if settings.driftCompensation:
driftVector = computeDriftVector(inputLattice, refLattice, cellDims, pbc)
else:
driftVector = np.zeros(3, np.float64)
# set up arrays
interstitials = np.empty(inputLattice.NAtoms, np.int32)
if settings.identifySplitInts:
splitInterstitials = np.empty(inputLattice.NAtoms, np.int32)
else:
splitInterstitials = np.empty(0, np.int32)
vacancies = np.empty(refLattice.NAtoms, np.int32)
antisites = np.empty(refLattice.NAtoms, np.int32)
onAntisites = np.empty(refLattice.NAtoms, np.int32)
# set up excluded specie arrays
if settings.allSpeciesSelected:
exclSpecsInput = np.zeros(0, np.int32)
exclSpecsRef = np.zeros(0, np.int32)
else:
exclSpecs = []
# for i in xrange(len(inputLattice.specieList)):
# spec = inputLattice.specieList[i]
# if spec not in settings.visibleSpecieList:
# exclSpecs.append(i)
exclSpecsInput = np.empty(len(exclSpecs), np.int32)
for i in xrange(len(exclSpecs)):
exclSpecsInput[i] = exclSpecs[i]
exclSpecs = []
# for i in xrange(len(refLattice.specieList)):
# spec = refLattice.specieList[i]
# if spec not in settings.visibleSpecieList:
# exclSpecs.append(i)
exclSpecsRef = np.empty(len(exclSpecs), np.int32)
for i in xrange(len(exclSpecs)):
exclSpecsRef[i] = exclSpecs[i]
# specie counter arrays
vacSpecCount = np.zeros( len(refLattice.specieList), np.int32 )
intSpecCount = np.zeros( len(inputLattice.specieList), np.int32 )
antSpecCount = np.zeros( len(refLattice.specieList), np.int32 )
onAntSpecCount = np.zeros( (len(refLattice.specieList), len(inputLattice.specieList)), np.int32 )
splitIntSpecCount = np.zeros( (len(inputLattice.specieList), len(inputLattice.specieList)), np.int32 )
NDefectsByType = np.zeros(6, np.int32)
if settings.findClusters:
defectCluster = np.empty(inputLattice.NAtoms + refLattice.NAtoms, np.int32)
else:
defectCluster = np.empty(0, np.int32)
# call C library
status = _defects.findDefects(settings.showVacancies, settings.showInterstitials, settings.showAntisites, NDefectsByType, vacancies,
interstitials, antisites, onAntisites, exclSpecsInput, exclSpecsRef, inputLattice.NAtoms, inputLattice.specieList,
inputLattice.specie, inputLattice.pos, refLattice.NAtoms, refLattice.specieList, refLattice.specie,
refLattice.pos, cellDims, pbc, settings.vacancyRadius,
settings.findClusters, settings.neighbourRadius, defectCluster, vacSpecCount, intSpecCount, antSpecCount,
onAntSpecCount, splitIntSpecCount, settings.minClusterSize, settings.maxClusterSize, splitInterstitials,
settings.identifySplitInts, settings.driftCompensation, driftVector, acnaArray, settings.acnaStructureType)
# summarise
NDef = NDefectsByType[0]
NVac = NDefectsByType[1]
NInt = NDefectsByType[2]
NAnt = NDefectsByType[3]
NSplit = NDefectsByType[5]
vacancies.resize(NVac)
interstitials.resize(NInt)
antisites.resize(NAnt)
onAntisites.resize(NAnt)
splitInterstitials.resize(NSplit*3)
# report counters
logging.info("Found %d defects", NDef)
if settings.showVacancies:
logging.debug(" %d vacancies", NVac)
for i in xrange(len(refLattice.specieList)):
logging.debug(" %d %s vacancies", vacSpecCount[i], refLattice.specieList[i])
if settings.showInterstitials:
logging.debug(" %d interstitials", NInt + NSplit)
for i in xrange(len(inputLattice.specieList)):
logging.debug(" %d %s interstitials", intSpecCount[i], inputLattice.specieList[i])
if settings.identifySplitInts:
logging.debug(" %d split interstitials", NSplit)
for i in xrange(len(inputLattice.specieList)):
for j in xrange(i, len(inputLattice.specieList)):
if j == i:
N = splitIntSpecCount[i][j]
else:
N = splitIntSpecCount[i][j] + splitIntSpecCount[j][i]
logging.debug(" %d %s - %s split interstitials", N, inputLattice.specieList[i], inputLattice.specieList[j])
if settings.showAntisites:
logging.debug(" %d antisites", NAnt)
for i in xrange(len(refLattice.specieList)):
for j in xrange(len(inputLattice.specieList)):
if inputLattice.specieList[j] == refLattice.specieList[i]:
continue
logging.debug(" %d %s on %s antisites", onAntSpecCount[i][j], inputLattice.specieList[j], refLattice.specieList[i])
if settings.identifySplitInts:
logging.debug("Split interstitial analysis")
PBC = pbc
for i in xrange(NSplit):
ind1 = splitInterstitials[3*i+1]
ind2 = splitInterstitials[3*i+2]
pos1 = inputLattice.pos[3*ind1:3*ind1+3]
pos2 = inputLattice.pos[3*ind2:3*ind2+3]
sepVec = vectors.separationVector(pos1, pos2, cellDims, PBC)
norm = vectors.normalise(sepVec)
logging.debug(" Orientation of split int %d: (%.3f %.3f %.3f)", i, norm[0], norm[1], norm[2])
# sort clusters here
clusterList = []
if settings.findClusters:
NClusters = NDefectsByType[4]
defectCluster.resize(NDef)
# build cluster lists
for i in xrange(NClusters):
clusterList.append(clusters.DefectCluster())
# add atoms to cluster lists
clusterIndexMapper = {}
count = 0
for i in xrange(NVac):
atomIndex = vacancies[i]
clusterIndex = defectCluster[i]
if clusterIndex not in clusterIndexMapper:
clusterIndexMapper[clusterIndex] = count
count += 1
clusterListIndex = clusterIndexMapper[clusterIndex]
clusterList[clusterListIndex].vacancies.append(atomIndex)
clusterList[clusterListIndex].vacAsIndex.append(i)
for i in xrange(NInt):
atomIndex = interstitials[i]
clusterIndex = defectCluster[NVac + i]
if clusterIndex not in clusterIndexMapper:
clusterIndexMapper[clusterIndex] = count
count += 1
clusterListIndex = clusterIndexMapper[clusterIndex]
clusterList[clusterListIndex].interstitials.append(atomIndex)
for i in xrange(NAnt):
atomIndex = antisites[i]
atomIndex2 = onAntisites[i]
clusterIndex = defectCluster[NVac + NInt + i]
if clusterIndex not in clusterIndexMapper:
clusterIndexMapper[clusterIndex] = count
count += 1
clusterListIndex = clusterIndexMapper[clusterIndex]
clusterList[clusterListIndex].antisites.append(atomIndex)
clusterList[clusterListIndex].onAntisites.append(atomIndex2)
for i in xrange(NSplit):
clusterIndex = defectCluster[NVac + NInt + NAnt + i]
if clusterIndex not in clusterIndexMapper:
clusterIndexMapper[clusterIndex] = count
count += 1
clusterListIndex = clusterIndexMapper[clusterIndex]
atomIndex = splitInterstitials[3*i]
clusterList[clusterListIndex].splitInterstitials.append(atomIndex)
atomIndex = splitInterstitials[3*i+1]
clusterList[clusterListIndex].splitInterstitials.append(atomIndex)
atomIndex = splitInterstitials[3*i+2]
clusterList[clusterListIndex].splitInterstitials.append(atomIndex)
return NDef, interstitials, vacancies, antisites, onAntisites, splitInterstitials, vacSpecCount, intSpecCount, splitIntSpecCount, clusterList
