def getcurrentfft(direction, dumping=0.00):
from scipy.fftpack import fft
timeArray,afield =getAField()
current =getCurrentPython()
option = tdapOptions()
lengthTime = option.tdTimeStep[0]
timeArray = timeArray[2:]/option.tdTimeStep[0]
numStep = len(timeArray)
current = current[:,1] #perform FFT for current in different directions,eg:the second line is y direction
current *= np.exp(-dumping*timeArray)
freqResolution =1.0/(lengthTime*numStep)
freqArray = (timeArray-(numStep/2.0))*freqResolution
energyArray = freqArray*4.1356
energyArray = energyArray[numStep/2:]
epsilon_current = fft(current)[:numStep/2]
epsilon_current = (np.real(epsilon_current),np.imag(epsilon_current))
current_fft_mode=np.power(epsilon_current[0],2)+np.power(epsilon_current[1],2)
import pandas as pd
df = pd.DataFrame({'x-energy':energyArray,
'y1-Im(current)':np.abs(epsilon_current[0]*energyArray/4.1356),
'y2-Re(current)':np.abs(epsilon_current[1]*energyArray/4.1356)})
#print df
df.to_csv('current_fft.csv',sep=',')
return current,energyArray[10:],current_fft_mode[10:]#current,energyArray[76:],current_fft_mode[76:]#to ensure that the nth order is the maximum
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 calculateRMSD(selectedStep=None,atomsOrigin=None,init=0, selectedAtoms=None):
"""
return the radius mean square displacements of the selected steps
compared with the init step
"""
from ase.io.trajectory import Trajectory
traj = Trajectory("Trajectory")
options = tdapOptions()
timestep = options.mdTimeStep[0]
if atomsOrigin is None:
atomsOrigin = traj[0]
#print 'no'
if selectedStep == None:
selectedStep = range(len(traj))
#print selectedStep, timestep
time = np.array(selectedStep) * timestep
SaveName = 'RMSD'
distance = loadSaved(SaveName)
if len(distance) != len(selectedStep):
#print 'Calculation'
distance = np.array([np.mean(calculateDisplacement(traj[step],atomsOrigin,selectedAtoms)**2)**0.5
for step in selectedStep])
np.save(SaveName,distance)
return time,distance
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 getExcitedElectrons(selectK=None, comp=False):
"""
"""
h**o = getHomo()
kpoint, kweight = readKpoints()
options = tdapOptions()
selectStep = getEIGSteps()
#print selectStep
timestep = options.tdTimeStep[0]
selectTime = selectStep * timestep
SaveName = 'ExcitedElectrons'
SaveName1 = 'ExcitedElectrons1'
exe = loadSaved(SaveName)
exe1 = loadSaved(SaveName)
if len(exe) != len(selectStep):
exe = np.zeros([len(selectStep)])
exe1 = np.zeros([len(selectStep)])
for index, step in enumerate(selectStep):
partition = readEigFile(options.label + str(step) + 'q.EIG')
for i in range(partition.shape[0]):
partition[i, :] *= kweight[i]
if selectK is not None:
exe[index] = np.sum(partition[selectK, h**o:])
else:
exe[index] = h**o * 2 - np.sum(partition[:, :h**o])
exe1[index] = np.sum(partition[:, h**o:])
np.save(SaveName, exe)
np.save(SaveName1, exe1)
if comp:
return selectTime, exe, exe1
else:
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:,2:3] /= 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 getExcitedElectrons(selectK=None, comp = False):
"""
"""
h**o = getHomo()
kpoint,kweight = readKpoints()
options = tdapOptions()
selectStep = getEIGSteps()
#print selectStep
timestep = options.tdTimeStep[0]
selectTime = selectStep*timestep
SaveName = 'ExcitedElectrons'
SaveName1 = 'ExcitedElectrons1'
exe = loadSaved(SaveName)
exe1 = loadSaved(SaveName)
if len(exe) != len(selectStep):
exe = np.zeros([len(selectStep)])
exe1 = np.zeros([len(selectStep)])
for index,step in enumerate(selectStep):
partition = readEigFile(options.label+str(step)+'q.EIG')
for i in range(partition.shape[0]):
partition[i,:] *= kweight[i]
if selectK is not None:
exe[index] = np.sum(partition[selectK,h**o:])
else:
exe[index] = h**o*2 - np.sum(partition[:,:h**o])
exe1[index] = np.sum(partition[:,h**o:])
np.save(SaveName,exe)
np.save(SaveName1,exe1)
if comp:
return selectTime, exe, exe1
else:
return selectTime, exe
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 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 calculateRMSD(selectedStep=None,atomsOrigin=None,init=0, selectedAtoms=None):
"""
return the radius mean square displacements of the selected steps
compared with the init step
"""
from ase.io.trajectory import Trajectory
traj = Trajectory("Trajectory")
options = tdapOptions()
timestep = options.mdTimeStep[0]
if atomsOrigin is None:
atomsOrigin = traj[init]
#print 'no'
if selectedStep == None:
selectedStep = range(len(traj))
#print selectedStep, timestep
time = np.array(selectedStep) * timestep
SaveName = 'RMSD'
distance = loadSaved(SaveName)
if len(distance) != len(selectedStep):
#print 'Calculation'
distance = np.array([np.mean(calculateDisplacement(traj[step],atomsOrigin,selectedAtoms)**2)**0.5
for step in selectedStep])
np.save(SaveName,distance)
return time,distance
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 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 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 getEIGSteps():
options = tdapOptions()
steps = []
for i in os.listdir('.'):
if i[:6] == 'siesta' and i[-5:] == 'q.EIG':
steps.append(int(i[6:-5]))
a = np.array(np.sort(steps),dtype=int)
#print a
return a
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 getEIGSteps():
options = tdapOptions()
steps = []
for i in os.listdir('.'):
if i[:6] == 'siesta' and i[-5:] == 'q.EIG':
steps.append(int(i[6:-5]))
a = np.array(np.sort(steps), dtype=int)
#print a
return a
def getAField():
if os.path.exists('TDAFIELD'):
Afield = [[float(i) for i in line.split()] for line in open('TDAFIELD')]
Afield = np.array(Afield)/1E5
options = tdapOptions()
timestep = options.tdTimeStep[0]
time = np.arange(len(Afield))*timestep
else:
time = np.zeros(2)
Afield = np.zeros([2,3])
return time, Afield
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 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 getCurrent():
#bug
if os.path.exists('TDEFIELD'):
Efield = [[float(i) for i in line.split()] for line in open('TDEFIELD')]
Efield = np.array(Efield)/1E5
options = tdapOptions()
timestep = options.tdTimeStep[0]
time = np.arange(len(Efield))*timestep
else:
time = np.zeros(2)
Efield = np.zeros([2,3])
return time, Efield
def getCurrent():
#bug
if os.path.exists('TDEFIELD'):
Efield = [[float(i) for i in line.split()]
for line in open('TDEFIELD')]
Efield = np.array(Efield) / 1E5
options = tdapOptions()
timestep = options.tdTimeStep[0]
time = np.arange(len(Efield)) * timestep
else:
time = np.zeros(2)
Efield = np.zeros([2, 3])
return time, Efield
def getEField():
if os.path.exists('TDEFIELD'):
Efield = [[float(i) for i in line.split()] for line in open('TDEFIELD')]
Efield = np.array(Efield)/1E5
if os.path.exists('input.fdf'):
options = tdapOptions()
timestep = options.tdTimeStep[0]
time = np.arange(len(Efield))*timestep
else:
time, msd = readMSD()
else:
time = np.zeros(2)
Efield = np.zeros([2,3])
return time, Efield
def readKpoints():
options = tdapOptions()
systemLabel = options.label
bohr=0.52917721
filename = systemLabel+'.KP'
f=open(filename,'r')
nkpts = int(f.readline().split()[0])
kcood = [] ; kweight = []
for i in range(nkpts):
index, kx, ky, kz, wk = [float(value) for value in f.readline().split()]
kcood.append((kx,ky,kz))
kweight.append(wk)
return np.array(kcood)/bohr, np.array(kweight)
#getTrajactory()
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 getCurrentPython():
options = tdapOptions()
context = []
for line in open('result').readlines():
if len(line) == 1:
continue
if 'Current' in line.split() :
context.append(line[:-1])
#print context
current = [[float(line.split()[-4]),float(line.split()[-3]),float(line.split()[-2])] for line in context]
#print current
data = np.array(current)
#time = np.arange(len(current))*timestep
# print data
return data
def getEField():
if os.path.exists('TDEFIELD'):
Efield = [[float(i) for i in line.split()]
for line in open('TDEFIELD')]
Efield = np.array(Efield) / 1E5
if os.path.exists('input.fdf'):
options = tdapOptions()
timestep = options.tdTimeStep[0]
time = np.arange(len(Efield)) * timestep
else:
time, msd = readMSD()
else:
time = np.zeros(2)
Efield = np.zeros([2, 3])
return time, Efield
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 getTrajactory():
options = tdapOptions()
#print(options.laserParam)
systemLabel = options.label
NumBlocks = int(
os.popen('grep -i %s %s.MD_CAR | wc -l' %
(systemLabel, systemLabel)).readline().split()[0])
position_file = open(systemLabel + '.MD_CAR')
atomNumList = [
int(i)
for i in os.popen('head -6 siesta.MD_CAR |tail -1').readline().split()
]
numAtomPositionLine = sum(atomNumList)
totalNumLine = numAtomPositionLine + 7
context = position_file.readlines()
#import ase.calculators.vasp as vinter
#from ase.visualize import view
atoms = xv_to_atoms(systemLabel + '.XV')
atoms.pbc = [True, True, True]
filename = 'Trajectory'
from ase.io.trajectory import Trajectory
if not os.path.exists(filename) or os.path.getmtime(
filename) < os.path.getmtime(systemLabel + '.MD_CAR'):
atomsList = []
for index in range(NumBlocks):
output = context[index * totalNumLine:(index + 1) * totalNumLine]
coodinates = np.array(
[[float(value.replace('\n', '')) for value in line.split()]
for line in output[7:]])
atomsCurrent = atoms.copy()
atomsCurrent.set_scaled_positions(coodinates)
atomsList.append(atomsCurrent)
#poscarFileName = "POSCAR"+str(index)
#poscarFile=open(poscarFileName,'w')
#poscarFile.writelines(output)
from ase.io import write
write(filename, atomsList, 'traj')
atomsList = Trajectory(filename)
#print atomsList
return atomsList
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 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 getcurrentfft_angle(angle, dumping=0.00):
from scipy.fftpack import fft
timeArray, afield = getAField()
current = getCurrentPython()
option = tdapOptions()
lengthTime = option.tdTimeStep[0]
timeArray = timeArray[2:] / option.tdTimeStep[0]
numStep = len(timeArray)
freqResolution = 1.0 / (lengthTime * numStep)
freqArray = (timeArray - (numStep / 2.0)) * freqResolution
energyArray = freqArray * 4.1356
energyArray = energyArray[numStep / 2:]
angle = angle * np.pi / 180.0
# print current[:,0] , current[:,1]
current_x = current[:,
0] #perform FFT for current in different directions,eg:the second line is y direction
current_y = current[:, 1]
current_x *= np.exp(-dumping * timeArray)
current_y *= np.exp(-dumping * timeArray)
current_par = np.cos(angle) * current_y + np.sin(angle) * current_x
current_per = np.sin(angle) * current_y + np.cos(angle) * current_x
epsilon_currentpar = fft(current_par)[:numStep / 2]
epsilon_currentpar = (np.real(epsilon_currentpar),
np.imag(epsilon_currentpar))
currentpar_fft_mode = np.power(epsilon_currentpar[0], 2) + np.power(
epsilon_currentpar[1], 2)
epsilon_currentper = fft(current_per)[:numStep / 2]
epsilon_currentper = (np.real(epsilon_currentper),
np.imag(epsilon_currentper))
currentper_fft_mode = np.power(epsilon_currentper[0], 2) + np.power(
epsilon_currentper[1], 2)
return energyArray[20:], currentpar_fft_mode[20:], currentper_fft_mode[
20:] #to ensure that the nth order is the maximum
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 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 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 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)
def readKpoints():
options = tdapOptions()
systemLabel = options.label
bohr = 0.52917721
filename = systemLabel + '.KP'
f = open(filename, 'r')
nkpts = int(f.readline().split()[0])
kcood = []
kweight = []
for i in range(nkpts):
index, kx, ky, kz, wk = [
float(value) for value in f.readline().split()
]
kcood.append((kx, ky, kz))
kweight.append(wk)
return np.array(kcood) / bohr, np.array(kweight)
#getTrajactory()
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 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 getTrajactory():
options = tdapOptions()
systemLabel = options.label
NumBlocks=int(os.popen('grep -i '+systemLabel+' '+systemLabel+'.MD_CAR | wc -l').readline().split()[0])
position_file = open(systemLabel+'.MD_CAR')
atomNumList = [int(i) for i in os.popen('head -6 siesta.MD_CAR |tail -1').readline().split()]
numAtomPositionLine = sum(atomNumList)
totalNumLine = numAtomPositionLine + 7
context = position_file.readlines()
from ase.calculators.siesta.import_functions import xv_to_atoms
#import ase.calculators.vasp as vinter
#from ase.visualize import view
atoms = xv_to_atoms(systemLabel+'.XV')
atoms.pbc = [True,True,True]
filename = 'Trajectory'
from ase.io.trajectory import Trajectory
if not os.path.exists(filename) or os.path.getmtime(filename) < os.path.getmtime(systemLabel+'.MD_CAR'):
atomsList = []
for index in range(NumBlocks):
output=context[index*totalNumLine:(index+1)*totalNumLine]
coodinates=np.array([[float(value.replace('\n',''))
for value in line.split()]
for line in output[7:]])
atomsCurrent = atoms.copy()
atomsCurrent.set_scaled_positions(coodinates)
atomsList.append(atomsCurrent)
#poscarFileName = "POSCAR"+str(index)
#poscarFile=open(poscarFileName,'w')
#poscarFile.writelines(output)
from ase.io import write
write(filename,atomsList,'traj')
atomsList = Trajectory(filename)
#print atomsList
return atomsList
def getcurrentfft_angle(angle, dumping=0.00):
from scipy.fftpack import fft
timeArray,afield =getAField()
current =getCurrentPython()
option = tdapOptions()
lengthTime = option.tdTimeStep[0]
timeArray = timeArray[2:]/option.tdTimeStep[0]
numStep = len(timeArray)
freqResolution =1.0/(lengthTime*numStep)
freqArray = (timeArray-(numStep/2.0))*freqResolution
energyArray = freqArray*4.1356
energyArray = energyArray[numStep/2:]
angle =angle*np.pi/180.0
# print current[:,0] , current[:,1]
current_x = current[:,0] #perform FFT for current in different directions,eg:the second line is y direction
current_y = current[:,1]
current_x *= np.exp(-dumping*timeArray)
current_y *= np.exp(-dumping*timeArray)
current_par=np.cos(angle)*current_y+np.sin(angle)*current_x
current_per=np.sin(angle)*current_y+np.cos(angle)*current_x
epsilon_currentpar = fft(current_par)[:numStep/2]
epsilon_currentpar = (np.real(epsilon_currentpar),np.imag(epsilon_currentpar))
currentpar_fft_mode=np.power(epsilon_currentpar[0],2)+np.power(epsilon_currentpar[1],2)
epsilon_currentper= fft(current_per)[:numStep/2]
epsilon_currentper = (np.real(epsilon_currentper),np.imag(epsilon_currentper))
currentper_fft_mode=np.power(epsilon_currentper[0],2)+np.power(epsilon_currentper[1],2)
return energyArray[20:],currentpar_fft_mode[20:],currentper_fft_mode[20:]#to ensure that the nth order is the maximum
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)
for i, direct in enumerate(['x','y','z']):
if not os.path.exists(direct):
continue
#
os.chdir(direct)
# import pyramids.plot.PlotUtility as pu
# rotation = [0,0,0]
# rotation[i] = 90
# pu.insertStruct(axs, width="50%", height=1.5, loc=2,
# rotation=rotation,
# camera='perspective', cell=False)
timeArray, efield = dp.getEField()
option = tdapOptions()
lengthTime = option.tdTimeStep[0]
numStep = option.tdFinalStep - 2
timeArray = timeArray[2:]/option.tdTimeStep[0]
time, dipole = dp.getDipolePython()
dipole = dipole[2:,i]
freqResolution = 1.0/(lengthTime*numStep)
freqArray = (timeArray-(numStep/2.0))*freqResolution
energyArray = freqArray*4.1356
energyArray = energyArray[numStep/2:]
epsilon = fft(dipole)[:numStep/2]
import numpy as np
import matplotlib.pyplot as plt
import pyramids.io.result as dp
from pyramids.io.fdf import tdapOptions
import pyramids.plot.setting as ma
#------------------------------------------------------------------------------
fig, axs = plt.subplots(1, 2, sharex=False, sharey=False, figsize=(8, 6))
SaveName = __file__.split('/')[-1].split('.')[0]
h**o = dp.getHomo()
time, exe = dp.getProjectedPartition()
time, eigen = dp.getAdiabaticEigenvalue()
print eigen.shape
option = tdapOptions()
import numpy as np
import matplotlib.pyplot as plt
import pyramids.io.result as dp
import pyramids.plot.setting as ma
import pyramids.plot.PlotUtility as pu
import os
from ase.dft.kpoints import special_paths, special_points
ax = axs[1]
import pyramids.plot.PlotUtility as pu
pu.plotEField(ax)
timeE, Efield = dp.getEField()
lightScat, = ax.plot(0, Efield[0, 0], 'o')
kargs = ma.getPropertyFromPosition(xlabel=r'Time', ylabel=r'EField')
def huskyOnTheFly(index, folder):
count = 0
for i, direct in enumerate(['x', 'y', 'z']):
#print os.listdir('.')
if not os.path.exists(direct):
continue
os.chdir(direct)
timeArray, efield = dp.getEField()
option = tdapOptions()
lengthTime = option.tdTimeStep[0]
numStep = option.tdFinalStep - 2
timeArray = timeArray[2:] / option.tdTimeStep[0]
time, dipole = dp.getDipolePython()
dipole = dipole[2:, i]
dipole *= np.exp(-dumping * timeArray)
freqResolution = 1.0 / (lengthTime * numStep)
freqArray = (timeArray - (numStep / 2.0)) * freqResolution
energyArray0 = freqArray * 4.1356
energyArray = energyArray0[numStep / 2:]
# energyArray1 = list(energyArray0[numStep/2:])
# energyArray2 = list(energyArray0[:numStep/2])
# energyArray1 +=energyArray2
# energyArray = np.array(energyArray1)
epsilon = fft(dipole)[:numStep / 2]
epsilon = (np.real(epsilon), np.imag(epsilon))
# print (energyArray)
absorbanceimag = (epsilon[0] * energyArray * 0.0367 /
6.28) / (width * float(folder) * fieldE)
absorbancereal = (epsilon[1] * energyArray * 0.0367 /
6.28) / (width * float(folder) * fieldE)
# absorbanceimag = 3.334*(epsilon[0]*energyArray/4.1356)/0.25
# absorbancereal = 3.334*(epsilon[1]*energyArray/4.1356)/0.25
if count == 0:
count += 1
absorbanceSumimag = absorbanceimag
absorbanceSumreal = 0.25 / np.pi + absorbancereal
else:
absorbanceSumimag += absorbanceimag
absorbanceSumreal += absorbancereal
eels = absorbanceSumimag / (absorbanceSumimag**2 +
absorbanceSumreal**2)
os.chdir('..')
peaks = []
# for j in range(1,len(absorbanceSum)-1):
# if energyArray[j] > xlimits[0] and energyArray[j] < xlimits[1]:
# if absorbanceSum[j] >= absorbanceSum[j-1] and absorbanceSum[j] >= absorbanceSum[j+1]:
# if absorbanceSum[j] > 0.03 and energyArray[j] > 5 and energyArray[j] < 8: # energyArray[j] < 22.0 and
# peaks.append(energyArray[j])
# print peaks
return energyArray, absorbanceSumimag, folder, absorbanceSumreal, eels, peaks
@author: clian
"""
import numpy as np
from matplotlib import pyplot as plt
import pyramids.io.result as dp
import pyramids.plot.PlotUtility as ppu
import pyramids.plot.setting as ma
from pyramids.io.fdf import tdapOptions
numStep = 5
fig, axs = plt.subplots(numStep,1,sharex=True,sharey=True,figsize=(6,8))
timeStep = tdapOptions().tdTimeStep
steps = dp.getEIGSteps()
selectedSteps = range(0,len(steps),len(steps)/numStep)
print selectedSteps
for i in range(numStep):
ax = axs[i]
title = '$t = %3.2f$ %s' % (i*len(steps)/numStep*timeStep[0], timeStep[1])
ppu.plotDOS(ax, selectedSteps[i], bins=100, title = title, yticks=[])
plt.tight_layout()
SaveName = __file__.split('/')[-1].split('.')[0]
if True:
for save_type in ['.pdf','.png']:
filename = SaveName + save_type
Created on Thu Feb 2 09:55:49 2017
@author: clian
"""
import numpy as np
from matplotlib import pyplot as plt
import pyramids.io.result as dp
import pyramids.plot.PlotUtility as ppu
import pyramids.plot.setting as ma
from pyramids.io.fdf import tdapOptions
numStep = 5
fig, axs = plt.subplots(numStep, 1, sharex=True, sharey=True, figsize=(6, 8))
timeStep = tdapOptions().tdTimeStep
steps = dp.getEIGSteps()
selectedSteps = range(0, len(steps), len(steps) / numStep)
print selectedSteps
for i in range(numStep):
ax = axs[i]
title = '$t = %3.2f$ %s' % (i * len(steps) / numStep * timeStep[0],
timeStep[1])
ppu.plotDistribution(ax, selectedSteps[i], yticks=[0, 1], title=title)
plt.tight_layout()
SaveName = __file__.split('/')[-1].split('.')[0]
if True:
for save_type in ['.pdf']:
filename = SaveName + save_type
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)
import numpy as np
def readCurrent():
import os
lines = os.popen('grep "TDAP: Afield: Current" result').readlines()
data = []
for line in lines:
#print line.split()
data.append([float(i) for i in line.split()[4:7]])
data = np.array(data)
return data
data = readCurrent()
from pyramids.io.fdf import tdapOptions
options = tdapOptions()
timestep = options.tdTimeStep[0]
fig, axs = plt.subplots(2,1,sharex=True,sharey=False)#,figsize=(10,6)
ax = axs[0]
for i in range(3):
ax.plot(np.arange(data.shape[0])*timestep,data[:,i],
label=['x','y','z'][i],lw=2, alpha=1.0)
args = ma.getPropertyFromPosition()
ma.setProperty(ax,**args)
ax = axs[1]
ppu.plotEField(ax,label='efield')
def huskyOnTheFly(index,folder):
count = 0
for i, direct in enumerate(['x','y','z']):
#print os.listdir('.')
if not os.path.exists(direct):
continue
os.chdir(direct)
timeArray, efield = dp.getEField()
option = tdapOptions()
lengthTime = option.tdTimeStep[0]
numStep = option.tdFinalStep - 2
timeArray = timeArray[2:]/option.tdTimeStep[0]
time, dipole = dp.getDipolePython()
dipole = dipole[2:,i]
dipole *= np.exp(-dumping*timeArray)
freqResolution = 1.0/(lengthTime*numStep)
freqArray = (timeArray-(numStep/2.0))*freqResolution
energyArray0 = freqArray*4.1356
energyArray = energyArray0[numStep/2:]
# energyArray1 = list(energyArray0[numStep/2:])
# energyArray2 = list(energyArray0[:numStep/2])
# energyArray1 +=energyArray2
# energyArray = np.array(energyArray1)
epsilon = fft(dipole)[:numStep/2]
epsilon = (np.real(epsilon),np.imag(epsilon))
# print (energyArray)
absorbanceimag = (epsilon[0]*energyArray*0.0367/6.28)/(width*float(folder)*fieldE)
absorbancereal = (epsilon[1]*energyArray*0.0367/6.28)/(width*float(folder)*fieldE)
# absorbanceimag = 3.334*(epsilon[0]*energyArray/4.1356)/0.25
# absorbancereal = 3.334*(epsilon[1]*energyArray/4.1356)/0.25
if count == 0:
count += 1
absorbanceSumimag = absorbanceimag
absorbanceSumreal = 0.25/np.pi+absorbancereal
else:
absorbanceSumimag += absorbanceimag
absorbanceSumreal += absorbancereal
eels = absorbanceSumimag / (absorbanceSumimag**2 + absorbanceSumreal**2)
os.chdir('..')
peaks = []
# for j in range(1,len(absorbanceSum)-1):
# if energyArray[j] > xlimits[0] and energyArray[j] < xlimits[1]:
# if absorbanceSum[j] >= absorbanceSum[j-1] and absorbanceSum[j] >= absorbanceSum[j+1]:
# if absorbanceSum[j] > 0.03 and energyArray[j] > 5 and energyArray[j] < 8: # energyArray[j] < 22.0 and
# peaks.append(energyArray[j])
# print peaks
return energyArray, absorbanceSumimag, folder, absorbanceSumreal, eels, peaks
def readCurrent():
import os
lines = os.popen('grep "TDAP: Afield: Current" result').readlines()
data = []
for line in lines:
#print line.split()
data.append([float(i) for i in line.split()[4:7]])
data = np.array(data)
return data
data = readCurrent()
from pyramids.io.fdf import tdapOptions
options = tdapOptions()
timestep = options.tdTimeStep[0]
fig, axs = plt.subplots(2, 1, sharex=True, sharey=False) #,figsize=(10,6)
ax = axs[0]
for i in range(3):
ax.plot(np.arange(data.shape[0]) * timestep,
data[:, i],
label=['x', 'y', 'z'][i],
lw=2,
alpha=1.0)
args = ma.getPropertyFromPosition()
ma.setProperty(ax, **args)
ax = axs[1]
