def getEigAndPar(timeSteps=None, forceReread=False):
"""
return the Times, Eigvalues and Partitions at selected timeSteps
write two files EIG and PAR
"""
options = tdapOptions()
systemLabel = options.label
timestep = options.tdTimeStep[0]
if timeSteps == None:
timeSteps = getEIGSteps()
time = np.array(timeSteps) * timestep
eig = loadSaved('EIG')
par = loadSaved('PAR')
saved = ((len(eig)) != 0 and (len(par)) != 0)
if (not saved) or forceReread:
eig = []
par = []
for i in timeSteps:
eig.append(readEigFile(systemLabel + str(i) + '.EIG'))
par.append(readEigFile(systemLabel + str(i) + 'q.EIG'))
eig = np.array(eig)
par = np.array(par)
np.save('EIG', eig)
np.save('PAR', par)
return time, eig, par
def getImagElectricFunction(direction, dumping=0.00):
from scipy.fftpack import fft
timeArray, efield = getEField()
timeArray, dipole = getDipolePython()
option = tdapOptions()
lengthTime = option.tdTimeStep[0]
timeArray = timeArray[2:] / option.tdTimeStep[0]
numStep = len(timeArray)
dipole = dipole[2:, direction]
dipole *= np.exp(-dumping * timeArray)
freqResolution = 1.0 / (lengthTime * numStep)
freqArray = (timeArray - (numStep / 2.0)) * freqResolution
energyArray = freqArray * 4.1356
energyArray = energyArray[numStep / 2:]
epsilon = fft(dipole)[:numStep / 2]
epsilon = (np.real(epsilon), np.imag(epsilon))
import pandas as pd
df = pd.DataFrame({
'x-energy': energyArray,
'y1-Im(alpha)': np.abs(epsilon[0] * energyArray / 4.1356),
'y2-Re(alpha)': np.abs(epsilon[1] * energyArray / 4.1356)
})
#print df
df.to_csv('DielectricFunction.csv', sep=',')
return energyArray, np.abs(epsilon[0] * energyArray / 4.1356), np.abs(
epsilon[1] * energyArray / 4.1356)
def getBerrySteps():
options = tdapOptions()
stepLines = os.popen('ls ' + options.label + '*.Berry').readlines()
steps = [
int(step.split('.')[0].replace(options.label, ''))
for step in stepLines
]
return np.sort(steps)
def getBerry():
options = tdapOptions()
selectStep = getBerrySteps()
#print selectStep
timestep = options.tdTimeStep[0]
selectTime = selectStep * timestep
berry = np.array([readBerryFile(str(step)) for step in selectStep])
return selectTime, berry
def getDipole():
options = tdapOptions()
lines = os.popen('grep -n "Electric dipole (a.u.)" result').readlines()
dipole = [(float(line.split()[-3]), float(line.split()[-2]),
float(line.split()[-1])) for line in lines]
timestep = options.tdTimeStep[0]
dipole = np.array(dipole[:-1])
time = np.arange(len(dipole)) * timestep
return time, dipole
def readBerryFile(step=''):
"""
return the Eigenvalues read from systemLabel.EIG
"""
options = tdapOptions()
systemLabel = options.label
BerryFile = open(systemLabel + step + '.Berry')
Berry = [[float(value) for value in line.split()]
for line in BerryFile.readlines()]
return np.array(Berry)
def getFermiEnergy():
"""
return the Fermi Energy read from systemLabel.EIG
if failed, return 0 rather than raise an exception
"""
options = tdapOptions()
systemLabel = options.label
if os.path.exists(systemLabel + '.EIG'):
Efermi = float(open(systemLabel + '.EIG').readline().split()[0])
else:
Efermi = 0.0
return Efermi
def getHomo():
"""
return the index of the highest occupied molecular orbital (H**O)
"""
options = tdapOptions()
#NumElectron=float(os.popen('grep "Total number of electrons:" result').readline().split()[-1])
NumElectron = float(
pythonGrep("Total number of electrons:", 'result')[0].split()[-1])
readFile = os.popen('grep -i "SpinPolarized" ' + options.inputFile)
line = readFile.readline()
if line == '':
nspin = 2
else:
nspin = 1
h**o = int(NumElectron) / nspin
return h**o
def getBands(bandType='e'):
"""
return the bands read from systemLabel.bands as the dimension numKpoint x numBand x numSpin
returns: X, Ek, xticks, xticklabels
"""
import math
options = tdapOptions()
systemLabel = options.label
band_file = open(systemLabel + '.bands')
if bandType == 'e':
FermiEnergy = float(band_file.readline().split()[0])
else:
band_file.readline()
FermiEnergy = 0.0
kmin, kmax = (float(i) for i in band_file.readline().split())
emin, emax = (float(i) for i in band_file.readline().split())
numBand, numSpin, numKpoint = (int(i)
for i in band_file.readline().split())
Ek = np.zeros([numKpoint, numBand, numSpin])
X = np.zeros(numKpoint)
for kpt in range(numKpoint):
eigen = []
for ispin in range(numSpin):
for iband in range(int(math.ceil(numBand / 10.0))):
line = band_file.readline()
eigen.extend([float(i) for i in line.split()])
X[kpt] = eigen[0]
eigen.pop()
Ek[kpt, :, :] = np.array(eigen).reshape(
numBand, numSpin) - FermiEnergy #.reshape(1,-1) - EFermi
numSpecK = int(band_file.readline().split()[0])
xticks = []
xticklabels = []
for i in range(numSpecK):
line = band_file.readline()
xticks.append(float(line.split()[0]))
xticklabels.append(r'$' + line.split()[1][1:-1] + '$')
return X, Ek, xticks, xticklabels
def getProjectedPartition(selectK=None):
"""
"""
options = tdapOptions()
selectStep = getEIGSteps()
#print selectStep
timestep = options.tdTimeStep[0]
selectTime = selectStep * timestep
SaveName = 'ProjectedPartition'
exe = []
if len(exe) != len(selectStep):
exe = []
for index, step in enumerate(selectStep):
partition = readEigFile(options.label + str(step) + 'q.EIG')
exe.append(partition)
exe = np.array(exe)
np.save(SaveName, exe)
return selectTime, exe
def getAdiabaticEigenvalue(selectK=None):
"""
"""
options = tdapOptions()
selectStep = getEIGSteps()
#print selectStep
timestep = options.tdTimeStep[0]
selectTime = selectStep * timestep
SaveName = 'AdiabaticEigenvalue'
exe = loadSaved(SaveName)
if len(exe) != len(selectStep):
exe = []
for index, step in enumerate(selectStep):
partition = readEigFile(options.label + str(step) + '.EIG')
exe.append(partition)
exe = np.array(exe)
np.save(SaveName, exe)
return selectTime, exe
def getEnergyTemperaturePressure(ave=False):
"""
return the Temperature, KS Energy and Total Energy as the dimension of Nstep
read from systemLabel.MDE
returns the Temperature, KS Energy, Total Energy, Volume, Pressure
"""
options = tdapOptions()
systemLabel = options.label
if options.mdTimeStep[0] < 1E-10:
timestep = options.tdTimeStep[0]
start = 2
else:
start = 0
timestep = options.mdTimeStep[0]
if (os.path.exists(systemLabel + '.MDE')):
energy_file = open(systemLabel + '.MDE')
data = []
for i in energy_file.readlines():
if i.split()[0] == '#': continue
data.append([float(j.replace('*', '0')) for j in i.split()])
data = np.array(data)
if ave:
numAtom = getNumOfAtoms()
#print numAtom
data[start:, 2:4] /= numAtom
#print data
X = data[:, 0] * timestep
return X[start:], data[start:,
1], data[start:,
2], data[start:,
3], data[start:,
4], data[start:, 5]
else:
time, msd = readMSD()
f = os.popen('grep "Ekin + Etot (const)" result')
energy = np.array([float(line.split()[-2])
for line in f.readlines()]) * 13.6
#data=np.array([energy,energy,energy,energy,energy]).T
return time, energy, energy, energy, energy, energy
def getTDEig(timeSteps=None, forceReread=False):
"""
return the Times, Eigvalues and Partitions at selected timeSteps
write two files EIG and PAR
"""
options = tdapOptions()
systemLabel = options.label
timestep = options.tdTimeStep[0]
steps = np.arange(3, options.mdFinalStep)
time = np.array(steps) * timestep
eig = loadSaved('TDEIG')
saved = ((len(eig)) != 0)
if (not saved) or forceReread:
eig = np.array([
readEigFile(systemLabel + str(i) + 'td.EIG', sep=False)
for i in steps
])
np.save('TDEIG', eig)
return time, eig
def getDipolePython():
options = tdapOptions()
context = []
for line in open('result').readlines():
if len(line) == 1:
continue
#print line,
if 'Electric' in line.split() and 'TDAP' in line.split():
context.append(line[:-1])
#for line in context:
# print line.split()[-3:]
dipole = [[
float(line.split()[-3]),
float(line.split()[-2]),
float(line.split()[-1])
] for line in context]
#print context
#dipole = [(float(line.split()[-3]),float(line.split()[-2]),float(line.split()[-1])) for line in lines]
timestep = options.tdTimeStep[0]
dipole = np.array(dipole)
time = np.arange(len(dipole)) * timestep
return np.array(time), np.array(dipole)
