def getStress(self):
stress = [None] * 9
for i in range(0, self.pwFile.lineCount):
if 'total stress ' in self.pwFile.fileData[i]:
i = i + 1
fileRow = oStrings.removeDouble(self.pwFile.fileData[i], " ")
fileRow = oStrings.trimEnds(fileRow)
stressArr = fileRow.split(" ")
stress[0] = float(stressArr[0])
stress[1] = float(stressArr[1])
stress[2] = float(stressArr[2])
i = i + 1
fileRow = oStrings.removeDouble(self.pwFile.fileData[i], " ")
fileRow = oStrings.trimEnds(fileRow)
stressArr = fileRow.split(" ")
stress[3] = float(stressArr[0])
stress[4] = float(stressArr[1])
stress[5] = float(stressArr[2])
i = i + 1
fileRow = oStrings.removeDouble(self.pwFile.fileData[i], " ")
fileRow = oStrings.trimEnds(fileRow)
stressArr = fileRow.split(" ")
stress[6] = float(stressArr[0])
stress[7] = float(stressArr[1])
stress[8] = float(stressArr[2])
return stress
def getCell_Relaxed(self):
cell = [[0 for x in range(3)] for y in range(3)]
inRelaxed = False
for i in range(0, self.pwFile.lineCount):
if 'A final scf calculation' in self.pwFile.fileData[i]:
inRelaxed = True
if (inRelaxed):
if 'crystal axes:' in self.pwFile.fileData[i]:
i = i + 1
dataRow = oStrings.removeDouble(self.pwFile.fileData[i],
" ")
dataRow = oStrings.trimEnds(dataRow)
dataArr = dataRow.split(" ")
cell[0][0] = float(dataArr[3])
cell[0][1] = float(dataArr[4])
cell[0][2] = float(dataArr[5])
i = i + 1
dataRow = oStrings.removeDouble(self.pwFile.fileData[i],
" ")
dataRow = oStrings.trimEnds(dataRow)
dataArr = dataRow.split(" ")
cell[1][0] = float(dataArr[3])
cell[1][1] = float(dataArr[4])
cell[1][2] = float(dataArr[5])
i = i + 1
dataRow = oStrings.removeDouble(self.pwFile.fileData[i],
" ")
dataRow = oStrings.trimEnds(dataRow)
dataArr = dataRow.split(" ")
cell[2][0] = float(dataArr[3])
cell[2][1] = float(dataArr[4])
cell[2][2] = float(dataArr[5])
return cell
def normaliseParameters(self):
# Set the cell_parameter matrix such that (1,1) = 1.0 and adjust aLat accordingly
aLat = 0.0e0
cellParameters = [[0 for x in range(3)] for y in range(3)]
for i in range(0, self.pwFile.lineCount):
if 'celldm(1)' in self.pwFile.fileData[i]:
aLat = self.getInput(self.pwFile.fileData[i])
if 'CELL_PARAMETERS' in self.pwFile.fileData[i]:
for j in range(0, 3):
i = i + 1
fileRow = oStrings.removeDouble(self.pwFile.fileData[i],
" ")
fileRow = fileRow.split(" ")
for k in range(0, 3):
cellParameters[j][k] = float(fileRow[k])
topVal = cellParameters[0][0]
# Change aLat
aLat = aLat * topVal
# Change cell
for j in range(0, 3):
for k in range(0, 3):
if (j == 0 and k == 0):
cellParameters[j][k] = 1.0
else:
cellParameters[j][k] = cellParameters[j][k] / topVal
self.changeAlat(aLat)
self.changeCellParameters(cellParameters)
def increaseSize(self, copyX, copyY=None, copyZ=None):
label = []
x = []
y = []
z = []
fileTemp = []
fileBottom = []
if (copyY == None):
copyY = copyX
if (copyZ == None):
copyZ = copyX
nat = self.getNAT()
aLat = self.getAlat()
nat_New = 0
aLat_New = aLat * copyX
j = 0
rowCounter = 0
for i in range(0, self.pwFile.lineCount):
if (j == 0):
fileTemp.append(self.pwFile.fileData[i])
rowCounter = rowCounter + 1
if (j > nat):
fileTemp.append(self.pwFile.fileData[i])
rowCounter = rowCounter + 1
if (j > 0 and j <= nat):
fileRow = oStrings.removeDouble(self.pwFile.fileData[i], " ")
fileRowArr = fileRow.split(" ")
label.append(fileRowArr[0])
x.append(float(fileRowArr[1]))
y.append(float(fileRowArr[2]))
z.append(float(fileRowArr[3]))
j = j + 1
if (j == (nat + 1)):
j = j + 1
# Make structure
for xx in range(0, copyX):
for yy in range(0, copyY):
for zz in range(0, copyZ):
for n in range(0, nat):
nat_New = nat_New + 1
label_ext = str(label[n])
x_ext = str((xx + x[n]) / copyX)
y_ext = str((yy + y[n]) / copyY)
z_ext = str((zz + z[n]) / copyZ)
row = label_ext + " " + x_ext + " " + y_ext + " " + z_ext
rowCounter = rowCounter + 1
fileTemp.append(row)
if (self.checkString(self.pwFile.fileData[i], "ATOMIC_POSITIONS")):
j = j + 1
self.pwFile.fileData = fileTemp
self.pwFile.lineCount = rowCounter
self.changeNat(nat_New)
self.changeAlat(float(aLat_New))
def getAtomPP(self, atomID):
nType = self.getNType()
atomID = atomID % nType
for i in range(0, self.pwFile.lineCount):
if 'ATOMIC_SPECIES' in self.pwFile.fileData[i].upper():
for j in range(0, nType):
i = i + 1
fileRow = oStrings.removeDouble(self.pwFile.fileData[i],
" ")
fileRowArr = fileRow.split(" ")
if (j == atomID):
return fileRowArr[2]
break
def checkKeyword(lineIn, keyword, verbose=False):
result = None
if (lineIn != ""):
lineInArr = lineIn.split("#")
lineIn = lineInArr[0]
if (lineIn != ""):
lineInUC = lineIn.upper()
keywordUC = keyword.upper()
keywordLen = len(keywordUC)
if (lineInUC[0:keywordLen] == keywordUC):
result = oStrings.removeDouble(lineIn, " ")
if (verbose):
print(result)
return result
def readAtomSpecies(self):
self.atomSpecies_symbol = []
self.atomSpecies_mass = []
self.atomSpecies_pp = []
for i in range(0, self.pwFile.lineCount):
if 'ATOMIC_SPECIES' in self.pwFile.fileData[i].upper():
for j in range(0, self.ntype):
i = i + 1
fileRow = oStrings.removeDouble(self.pwFile.fileData[i],
" ")
fileRowArr = fileRow.split(" ")
self.atomSpecies_symbol.append(fileRowArr[0])
self.atomSpecies_mass.append(fileRowArr[1])
self.atomSpecies_pp.append(fileRowArr[2])
def extractData(self):
self.aLat = 0.0e0
self.cellParameters = [[0 for x in range(3)] for y in range(3)]
self.nat = 0
self.ntype = 0
self.atomSpecies_symbol = []
self.atomSpecies_mass = []
self.atomSpecies_pp = []
for i in range(0, self.pwFile.lineCount):
if 'CELLDM(1)' in self.pwFile.fileData[i].upper():
self.aLat = self.getInput(self.pwFile.fileData[i])
if 'CELL_PARAMETERS' in self.pwFile.fileData[i].upper():
for j in range(0, 3):
i = i + 1
fileRow = oStrings.removeDouble(self.pwFile.fileData[i],
" ")
fileRow = fileRow.split(" ")
for k in range(0, 3):
self.cellParameters[j][k] = float(fileRow[k])
if 'NTYP' in self.pwFile.fileData[i].upper():
fileRow = self.pwFile.fileData[i].replace(",", "")
fileRowArr = fileRow.split("=")
self.ntype = int(fileRowArr[1])
if 'NAT' in self.pwFile.fileData[i].upper():
fileRow = self.pwFile.fileData[i].replace(",", "")
fileRowArr = fileRow.split("=")
self.nat = int(fileRowArr[1])
if 'ATOMIC_SPECIES' in self.pwFile.fileData[i].upper():
for j in range(0, self.ntype):
i = i + 1
fileRow = oStrings.removeDouble(self.pwFile.fileData[i],
" ")
fileRowArr = fileRow.split(" ")
self.atomSpecies_symbol.append(fileRowArr[0])
self.atomSpecies_mass.append(fileRowArr[1])
self.atomSpecies_pp.append(fileRowArr[2])
def getAlat_RelaxedNormalised(self):
inRelaxed = False
for i in range(0, self.pwFile.lineCount):
if 'A final scf calculation' in self.pwFile.fileData[i]:
inRelaxed = True
if (inRelaxed):
if 'lattice parameter (alat) =' in self.pwFile.fileData[i]:
tString = self.pwFile.fileData[i].upper()
tString = tString.split("=")
tString = tString[1]
tString = tString.split("A.U.")
aLat = float(tString[0])
if 'crystal axes:' in self.pwFile.fileData[i]:
i = i + 1
dataRow = oStrings.removeDouble(self.pwFile.fileData[i],
" ")
dataRow = oStrings.trimEnds(dataRow)
dataArr = dataRow.split(" ")
aLat = aLat * float(dataArr[3])
return aLat
def changeKpoints(self, kpoints):
# Check input
kpoints = str(kpoints)
kpoints = oStrings.removeDouble(kpoints, " ")
kpoints = oStrings.trimEnds(kpoints)
kpoints = kpoints
kpointsArr = kpoints.split(" ")
print(len(kpointsArr))
if (len(kpointsArr) == 6):
kpoints_row = str(kpointsArr[0]) + " " + str(
kpointsArr[1]) + " " + str(kpointsArr[2]) + " " + " 1 1 1"
if (len(kpointsArr) == 3):
kpoints_row = str(kpointsArr[0]) + " " + str(
kpointsArr[1]) + " " + str(kpointsArr[2]) + " " + " 1 1 1"
if (len(kpointsArr) == 1):
kpoints_row = str(kpointsArr[0]) + " " + str(
kpointsArr[0]) + " " + str(kpointsArr[0]) + " 1 1 1"
for i in range(0, self.pwFile.lineCount):
if 'K_POINTS' in self.pwFile.fileData[i].upper():
self.pwFile.fileData[i] = 'K_POINTS automatic'
self.pwFile.fileData[i + 1] = kpoints_row
def heat(self, maxVariation):
# Set up random number
rd = RandDist()
rd.gheat(-1.0, 1.0, 1.0, 0.0, 1.0, 4.0)
# Get atom numbers
nAtoms = self.getNAT()
# Get lattice parameter
aLat = self.getAlat()
# Crystal variation
variation = maxVariation * (1.0 / aLat)
# Loop through rows
for i in range(0, self.pwFile.lineCount):
testStr = self.pwFile.fileData[i]
testStrU = testStr.upper()
# Update data file
if ('ATOMIC_POSITIONS' in testStrU):
for k in range(0, nAtoms):
i = i + 1
if (self.pwFile.fileData[i] == ""):
k = k - 1
else:
fileRow = oStrings.removeDouble(
self.pwFile.fileData[i], " ")
fileRow = fileRow.split(" ")
newRow = fileRow[0] + " "
x = float(fileRow[1])
x = x + variation * rd.rng()
x = x % 1
y = float(fileRow[2])
y = y + variation * rd.rng()
y = y % 1
z = float(fileRow[3])
z = z + variation * rd.rng()
z = z % 1
newRow = newRow + str(x) + " " + str(y) + " " + str(z)
self.pwFile.fileData[i] = newRow
