def action(index, folder): timeEf, eField = dP.getEField() timeEl, exe = dP.getExcitedElectrons() exe -= exe[0] timeEn, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure() deltaE = E_ks[start:,] - E_ks[2] return [(index, folder), (timeEf, eField), (timeEl, exe), (timeEn,deltaE)]
def action(index, folder):
timeEf, eField = dP.getEField()
timeEl, exe = dP.getExcitedElectrons()
exe -= exe[0]
timeEn, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure()
deltaE = E_ks[start:, ] - E_ks[2]
return [(index, folder), (timeEf, eField), (timeEl, exe), (timeEn, deltaE)]
def action(index, folder): #------------------------------------------------------------------------------ timeEf, eField = dP.getEField() timeEl, exe, exe1 = dP.getExcitedElectrons( comp = True) timeEn, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure(ave=True) deltaE = (E_ks[2:,] - E_ks[2]) return [(index, folder), (timeEf, eField), (timeEl, exe, exe1), (timeEn,deltaE)]
def action(index, folder):
#------------------------------------------------------------------------------
timeEf, eField = dP.getEField()
timeEl, exe, exe1 = dP.getExcitedElectrons(comp=True)
timeEn, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure(ave=True)
deltaE = (E_ks[2:, ] - E_ks[2])
return [(index, folder), (timeEf, eField), (timeEl, exe, exe1),
(timeEn, deltaE)]
def action(index, folder):
import os
os.chdir('1')
timeEf, eField = dP.getEField()
timeEl, exe = dP.getExcitedElectrons()
exe -= exe[0]
timeEn, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure()
deltaE = (E_tot[2:, ] - E_tot[2])
os.chdir('..')
return [(index, folder), (timeEf, eField), (timeEl, exe), (timeEn, deltaE)]
def plotEField(ax, label=''):
time, Efield = dp.getEField()
directions = ['x', 'y', 'z']
for direct in range(3):
if max(Efield[:,direct]) > 1E-10:
ax.plot(time,Efield[:,direct],
label=directions[direct], lw=2, alpha=1.0)
kargs=ma.getPropertyFromPosition(ylabel=r'$\varepsilon$ (a.u.)',xlabel='Time(fs)',
title='Electric Field')
ma.setProperty(ax,**kargs)
def plotEField(ax, label=''):
time, Efield = dp.getEField()
directions = ['x', 'y', 'z']
for direct in range(3):
if max(Efield[:, direct]) > 1E-10:
ax.plot(time,
Efield[:, direct],
label=directions[direct],
lw=2,
alpha=1.0)
kargs = ma.getPropertyFromPosition(ylabel=r'$\varepsilon$ (a.u.)',
xlabel='Time(fs)',
title='Electric Field')
ma.setProperty(ax, **kargs)
def action(index,folder):
ls = ['-','-','-','-']
ax = axs[0]
time, Efield = dP.getEField()
#directions = ['x', 'y', 'z']
for direct in range(3):
if max(Efield[:,direct]) > 1E-10:
ax.plot(time,Efield[:,direct],
label=folder,lw=2,alpha=0.5)
kargs=ma.getPropertyFromPosition(ylabel=r'$\varepsilon$(a.u.)',xlabel='Time(fs)',
title='Electric Field')
ma.setProperty(ax,**kargs)
ax.ticklabel_format(style='sci',axis='y',scilimits=[0,0])
#------------------------------------------------------------------------------
ax = axs[1]
time, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure(ave=True)
# for i in range(2,E_ks.shape[0]-1):
# if E_ks[i+1] - (E_ks[i] + E_ks[i-1])*0.5 > 2.0:
# E_ks[i+1] = (E_ks[i] + E_ks[i-1])*0.5
ax.plot(time[2:], E_ks[2:] - E_ks[2],'-', lw=1, alpha=1, label=folder)
kargs=ma.getPropertyFromPosition(ylabel=r'E(eV)',title='Excitation Energy')
ma.setProperty(ax,**kargs)
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') ma.setProperty(ax, **kargs) ax = axs[0] kpath = np.arange(exe.shape[1]) x = kpath #print list(kpath+1) evolvingBands = range(exe.shape[2]) excited = np.abs(exe[1, kpath, :] - exe[0, kpath, :]) norm = 100.0 / np.max(exe[:, kpath, :] - exe[0, kpath, :]) eigenvalue = eigen[0, kpath, :] #print eigenvalue.shape, excited.shape, x.shape
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
colors = getColors(4)
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:]
slide = 27
dataAndAtoms = [
read_cube_data(str(i) + '/siesta.DRHO.cube') for i in selectedTimeSteps
]
fig, axs = plt.subplots(1, 2, figsize=(12, 6))
pho0, atoms = dataAndAtoms[0]
#atoms = xv_to_atoms('siesta.XV')
X = np.arange(pho0.shape[1]) * atoms.cell[1, 1] / pho0.shape[1]
Y = np.arange(pho0.shape[2]) * atoms.cell[2, 2] / pho0.shape[2]
x, y = np.meshgrid(X, Y)
import pyramids.io.result as dP
time, light = dP.getEField()
step = len(time) / len(dataAndAtoms)
#print light.shape
line, = axs[1].plot(time, light[:, 2])
scatter, = axs[1].plot(0, 0, 'o')
def animate(i):
i = i % len(dataAndAtoms)
z = (dataAndAtoms[i][0] - pho0)[slide, :, :]
atoms = dataAndAtoms[i][1]
print z.min(), z.max()
axs[0].contourf(x, y, z, 100, vmin=vmin, vmax=vmax, cmap=cm.jet)
for pos, Z in zip(atoms.positions, atoms.numbers):
axs[0].scatter(pos[2],
pos[1],
fig, axs = plt.subplots(2, 1, sharex=True, sharey=False, figsize=(6, 8))
SaveName = __file__.split('/')[-1].split('.')[0]
startStep = 10
c = ma.getColors(4)
ax = axs[0]
time, T, E_ks, E_tot, Vol, P = dp.getEnergyTemperaturePressure()
time, dipoles = dp.getDipolePython()
for i, direct in enumerate(('x', 'y', 'z')):
ax.plot(time[2:], dipoles[2:, i], label=direct)
ax.grid(which=u'major', axis='x')
ax.grid(which=u'major', axis='y')
kargs = ma.getPropertyFromPosition(ylabel=r'Dipole(a.u)', xlabel='Time(fs)')
ma.setProperty(ax, **kargs)
ax = axs[1]
time, dipoles = dp.getEField()
for i, direct in enumerate(('x', 'y', 'z')):
ax.plot(time, dipoles[:, i] - dipoles[0, i], label=direct)
ax.grid(which=u'major', axis='x')
ax.grid(which=u'major', axis='y')
kargs = ma.getPropertyFromPosition(ylabel=r'$\varepsilon$(a.u)',
xlabel='Time(fs)')
ma.setProperty(ax, **kargs)
plt.tight_layout()
#!/usr/bin/python
import numpy as np
import matplotlib.pyplot as plt
import pyramids.io.result as dP
import pyramids.plot.setting as ma
#------------------------------------------------------------------------------
fig, axs = plt.subplots(3, 1, sharex=True, sharey=False, figsize=(6, 8))
SaveName = __file__.split('/')[-1].split('.')[0]
c = ['b', 'r', 'g', 'y']
ax = axs[2]
time, Efield = dP.getEField()
directions = ['x', 'y', 'z']
for direct in range(3):
ax.plot(time,
Efield[:, direct],
c=c[direct],
label=directions[direct],
lw=2,
alpha=0.8)
kargs = ma.getPropertyFromPosition(ylabel=r'$\varepsilon$(a.u.)',
xlabel='Time(fs)',
title='Electric Field')
ma.setProperty(ax, **kargs)
ax.ticklabel_format(style='sci', axis='y', scilimits=[0, 0])
#------------------------------------------------------------------------------
ax = axs[0]
Time, exe, exe1 = dP.getExcitedElectrons(comp=True)
ax.plot(Time, exe - exe[0], '--', alpha=0.8, markerfacecolor='w', lw=2)
ax.plot(Time, exe1 - exe1[0], '-', alpha=0.8, markerfacecolor='w', lw=2)
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
colors = getColors(4)
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:]
#!/usr/bin/python
import numpy as np
import matplotlib.pyplot as plt
import pyramids.io.result as dp
import pyramids.plot.setting as ma
time, Efield = dp.getEField()
fig, axs = plt.subplots(1,1,sharex=True,sharey=True)
ax = axs
# print Efield
# Plot Block #
for i in range(3):
if np.max(np.abs(Efield[:,i])) > 1E-7:
ax.plot(time,Efield[:,i],label=i)
#ax.plot(time,Efield[:,1],label='y')
#ax.plot(time,Efield[:,2],label='z')
#ax.plot(Efield)
kargs=ma.getPropertyFromPosition(ylabel=r'E(a.u.)',xlabel='',title='',
xticks=None, yticks=None,
xticklabels=None, yticklabels=None,
xlimits=None, ylimits=None)
ma.setProperty(ax,**kargs)
plt.tight_layout()
SaveName = __file__.split('/')[-1].split('.')[0]
for save_type in ['.pdf']:
filename = SaveName + save_type
slide = 27
dataAndAtoms = [read_cube_data(str(i)+'/siesta.DRHO.cube') for i in selectedTimeSteps]
fig, axs = plt.subplots(1,2,figsize=(12,6))
pho0,atoms = dataAndAtoms[0]
#atoms = xv_to_atoms('siesta.XV')
X = np.arange(pho0.shape[1])*atoms.cell[1,1]/pho0.shape[1]
Y = np.arange(pho0.shape[2])*atoms.cell[2,2]/pho0.shape[2]
x, y = np.meshgrid(X, Y)
import pyramids.io.result as dP
time, light = dP.getEField()
step = len(time)/len(dataAndAtoms)
#print light.shape
line, = axs[1].plot(time,light[:,2])
scatter, = axs[1].plot(0,0,'o')
def animate(i):
i = i % len(dataAndAtoms)
z = (dataAndAtoms[i][0]-pho0)[slide,:,:]
atoms = dataAndAtoms[i][1]
print z.min(), z.max()
axs[0].contourf(x, y, z, 100,vmin = vmin,vmax =vmax, cmap = cm.jet)
for pos, Z in zip(atoms.positions, atoms.numbers):
axs[0].scatter(pos[2],pos[1],c=tuple(cpk_colors[Z]),s=400*covalent_radii[Z])
setProperty(axs[0],**getPropertyFromPosition(0,xlimits=[2,6],ylimits=[2,6],
xlabel = r'distance($\AA$)',ylabel = r'distance($\AA$)'))
def action(index,folder): dataCurFolder = [] dataCurFolder.append([index, folder]) dataCurFolder.append(dp.getEnergyTemperaturePressure(ave=True)) dataCurFolder.append(dp.getEField()) return dataCurFolder
def action(index, folder):
dataCurFolder = []
dataCurFolder.append([index, folder])
dataCurFolder.append(dp.getEnergyTemperaturePressure(ave=True))
dataCurFolder.append(dp.getEField())
return dataCurFolder
rotation=[-90,90,0],
camera='perspective', cell=False)
ma.setProperty(ax,**kargs)
#------------------------------------------------------------------------------
Time, exe = dP.getExcitedElectrons()
ax = axs[1]
ax.plot(Time,exe,'-',alpha=0.8,c=c[0],markerfacecolor='w',lw=2)
kargs=ma.getPropertyFromPosition(ylabel=r'n(e)',
title='Excited Electrons',
xlimits=None,)
#ylimits=[exe.min(),exe.max()])
print exe[-1]
ma.setProperty(ax,**kargs)
#------------------------------------------------------------------------------
ax = axs[2]
time, Efield = dP.getEField()
directions = ['x', 'y', 'z']
c = ma.getColors(3,cmap='brg')
for direct in range(3):
ax.plot(time,Efield[:,direct] ,c=c[direct],
label=directions[direct],lw=2,alpha=0.8)
kargs=ma.getPropertyFromPosition(ylabel=r'$\varepsilon$(Ry/Bohr)',
xlabel='Time(fs)',
title='Electric Field',
xlimits=[np.min(time),np.max(time)])
ma.setProperty(ax,**kargs)
#------------------------------------------------------------------------------
plt.tight_layout()
for save_type in ['.pdf','.png']: