omega = np.zeros( (numFreq) ) omega = np.arange(numFreq) * (freqMax / numFreq) ## Create lammps position file ## mylamp = lt.Lammps(inPosName) myBox = lt.Block([ljLat, ljLat, ljLat], latType, dim, atom_mass = [ljMass]) mylamp.buildLammps([myBox]) latPos = lt.buildNumpy([myBox]) ## Lattice properties numAtomsUC = myBox.numAtomsUcell() numUcell = myBox.numUcell() numAtoms = myBox.numAtoms() Lx = myBox.Lx() Ly = myBox.Ly() Lz = myBox.Lz() numModes = 3 * numAtomsUC ## Create kpoints kpt = lt.kpt(dim, conv=True) kptIndex = np.zeros( (kpt[:,0].size) ) kptIndex = range(kpt[:,0].size) # Other kpoint parameters numKpts = kpt[:,0].size sliceLength = kpt[:,0].size / numKslice # Create the irreducible k-point list irrKpt, irrKptCnt, degen = lt.cubicKptSym(kpt)
# # Create volume
latType = "fcc"
ljLat = ((lj.value("lat" + str(rTemps[itemp])) / lj.value("sigma")) * 1e-10) * (1.0 + sNum)
myBox = lt.Block([ljLat, ljLat, ljLat], latType, [zNum, zNum, zNum])
Lx = myBox.Lx()
Ly = myBox.Ly()
Lz = myBox.Lz()
numAtomsUC = myBox.numAtomsUcell()
numModes = 3 * numAtomsUC
V = (Lx * Ly * Lz) * (1.0 * lj.value("sigma") ** 3)
# # Extract Data
pathName = basePathName + tStr + "/" + sStr + "/" + zStr + "/"
jobName = pathName + fileData
kpt, freq, freqShiftQ, lifeQ, freqShiftC, lifeC, vg = aldLife(jobName)
rKpt = lt.kpt([zNum, zNum, zNum], conv=True)
# EigenVectors
jobName = pathName + fileEigVec
eigVec = aldEigVec(jobName)
newKpt, newFreq, newLife, newVel, newEigVec = joeTrans(kpt, rKpt * zNum, freq, lifeC, vg, eigVec, numModes)
# # Extract Conductivity
pathName = basePathName + tStr + "/" + sStr + "/" + zStr + "/"
jobName = pathName + fileCond
qCond, cCond = aldThermCond(jobName)
tmpKappa[itemp, istrain, isize] = cCond[0]
# # Save Data