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($\AA$)'))
scatter.set_data(time[selectedTimeSteps[i]], light[selectedTimeSteps[i],
2])
setProperty(
axs[1],
**getPropertyFromPosition(1,
xlabel=r'time(fs)',
ylabel=r'E-Field(a.u.)'))
plt.tight_layout()
def case(indexCase, folderCase):
data = scanFolder(getTime)
selectedProcesses = ['evolve','DHSCF','PostSCF','siesta'] #,'TDbuildD'
explainations = ['Propagation', 'Build H', 'Postprocess','Total'] #,'Build DM'
image = data[-1][-1]['Prg.tot']
pieData = image[selectedProcesses[:-1]]
other = image[selectedProcesses[-1]] - np.sum(pieData.values)
ax = axsall[1][indexCase]
explode = np.zeros(len(pieData)) + 0.04
explode[0] = 0.07
patches, texts, autotexts = ax.pie(pieData.values, explode=explode, labels=explainations[:-1],
labeldistance = 0.2, autopct='%.0f%%',pctdistance = 0.7,
shadow=True, textprops={'fontsize':'xx-large','color':'gold'})
for text in texts:
text.set_fontsize(0)
kargs=ma.getPropertyFromPosition(indexCase + 3, title='')
ma.setProperty(ax,**kargs)
for key,label in zip(selectedProcesses,explainations):
totalTimes = np.array([time['Prg.tot'][key] for index, folder, time in data])/60.0
situations = np.array([int(folder) for index, folder, time in data])
ax = axsall[0][indexCase]
ax.semilogy(situations, totalTimes,'-o', mew = 3, alpha=0.8 ,ms=12, label = label)
# from scipy.optimize import curve_fit
# popt, pcov = curve_fit(errorFunc, situations, totalTimes)
# xfit = np.linspace(2,25,1000)
# ax.semilogy(xfit, errorFunc(xfit,*popt),'--',lw=3, )
ax.grid(which='major',axis=u'both')
kargs=ma.getPropertyFromPosition(indexCase, ylabel=r'Clock Time (Mimute)',title=folderCase,
#xlimits = [0,10]
)
ma.setProperty(ax,**kargs)
def case(indexCase, folderCase):
data = scanFolder(getTime)
selectedProcesses = ['evolve', 'DHSCF', 'PostSCF', 'siesta'] #,'TDbuildD'
explainations = ['Propagation', 'Build H', 'Postprocess',
'Total'] #,'Build DM'
image = data[-1][-1]['Prg.tot']
pieData = image[selectedProcesses[:-1]]
other = image[selectedProcesses[-1]] - np.sum(pieData.values)
ax = axsall[1][indexCase]
explode = np.zeros(len(pieData)) + 0.04
explode[0] = 0.07
patches, texts, autotexts = ax.pie(pieData.values,
explode=explode,
labels=explainations[:-1],
labeldistance=0.2,
autopct='%.0f%%',
pctdistance=0.7,
shadow=True,
textprops={
'fontsize': 'xx-large',
'color': 'gold'
})
for text in texts:
text.set_fontsize(0)
kargs = ma.getPropertyFromPosition(indexCase + 3, title='')
ma.setProperty(ax, **kargs)
for key, label in zip(selectedProcesses, explainations):
totalTimes = np.array(
[time['Prg.tot'][key] for index, folder, time in data]) / 60.0
situations = np.array([int(folder) for index, folder, time in data])
ax = axsall[0][indexCase]
ax.semilogy(situations,
totalTimes,
'-o',
mew=3,
alpha=0.8,
ms=12,
label=label)
# from scipy.optimize import curve_fit
# popt, pcov = curve_fit(errorFunc, situations, totalTimes)
# xfit = np.linspace(2,25,1000)
# ax.semilogy(xfit, errorFunc(xfit,*popt),'--',lw=3, )
ax.grid(which='major', axis=u'both')
kargs = ma.getPropertyFromPosition(
indexCase,
ylabel=r'Clock Time (Mimute)',
title=folderCase,
#xlimits = [0,10]
)
ma.setProperty(ax, **kargs)
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($\AA$)'))
scatter.set_data(time[selectedTimeSteps[i]],light[selectedTimeSteps[i],2])
setProperty(axs[1],**getPropertyFromPosition(1,
xlabel = r'time(fs)',ylabel = r'E-Field(a.u.)'))
plt.tight_layout()
def drawEnergy(ax, relative = False, divided = 1.0, popFirstStep = True, label = ''):
"""
Draw the KS Energy and Total Energy in the ax
"""
X, temp, E_KS, Etot, volume, pressure = tdp.getEnergyTemperaturePressure()
refEnergy=E_KS[0]
if relative:
E_KS = E_KS - refEnergy
Etot = Etot - refEnergy
if popFirstStep:
ax.plot(X[1:],E_KS[1:]/divided,'-',linewidth=3.0,label = 'KS'+ label)#,color=ma.colors[0]
ax.plot(X[1:],Etot[1:]/divided,'--',linewidth=3.0,label = 'Total'+ label)#,color=ma.colors[2]
else:
ax.plot(X,E_KS/divided,'-',linewidth=3.0,label = 'KS' + label)#,color=ma.colors[0]
ax.plot(X,Etot/divided,'--',linewidth=3.0,label = 'Total' + label)#,color=ma.colors[2]
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'Time(fs)',ylabel=r'Energy(eV)',title='',
xticks=None, yticks=None,
xticklabels=None, yticklabels=None,
xlimits=None, ylimits=None)
ma.setProperty(ax, **kargs)
def drawBands(ax, bandType='e', label=''):
"""
Draw the KS Energy and Total Energy in the ax
"""
X, Ek, xticks, xticklabels = tdp.getBands()
if bandType == 'e':
eFermi = tdp.getFermiEnergy()
Ek = Ek - eFermi
ylabel = 'Energy(eV)'
else:
ylabel = r'$\omega$(cm$^{-1}$)'
alpha = 1.0
color = 'b'
for ispin in range(Ek.shape[2]):
for iband in range(1, Ek.shape[1]):
ax[0].plot(X,
Ek[:, iband, ispin],
lw=3.0,
ls='-',
color=color,
alpha=alpha,
label=label)
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'',
ylabel=ylabel,
title='',
xticks=xticks,
yticks=None,
xticklabels=xticklabels,
yticklabels=None,
xlimits=None,
ylimits=None)
ma.setProperty(ax, **kargs)
def drawRDF(ax, step=None, label=''):
"""
Draw the KS Energy and Total Energy in the ax
"""
if step == None:
step = tdp.getNumStep()
systemLabel, timestep = tdp.getSystemLabelTimpstep()
tdp.splitMDCAR()
hist, bin_edges = tdp.calculateRDF(step - 1)
ax.plot(bin_edges[:-1],
hist,
linewidth=3.0,
label='RDF ' + str(
(step) * timestep) + ' fs' + label) #,color=ma.colors[0]
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'Radius($\AA$)',
ylabel=r'RDF(a.u.)',
title='',
xticks=None,
yticks=None,
xticklabels=None,
yticklabels=None,
xlimits=None,
ylimits=None)
ma.setProperty(ax, **kargs)
def drawRMSD(ax, selected=None, label='', init=0):
"""
Draw the KS Energy and Total Energy in the ax
"""
systemLabel, timestep = tdp.getSystemLabelTimpstep()
if selected == None:
selected = range(0, tdp.getNumStep(), int(1.0 / timestep))
tdp.splitMDCAR()
time, distance, velocity = tdp.calculateRMSD(selected, init=init)
#os.remove('POSCAR')
ax.plot(time, distance, linewidth=3.0,
label='RMSD' + label) #,color=ma.colors[0])
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'Time(fs)',
ylabel=r'RMSD($\AA$)',
title='',
xticks=None,
yticks=None,
xticklabels=None,
yticklabels=None,
xlimits=None,
ylimits=None)
ma.setProperty(ax, **kargs)
def plotDistribution(ax,
step,
bins=100,
intepNum=2000,
ylimits=[0, 1],
**kargs):
xlabel = 'Energy (eV)'
ylabel = 'FD'
yticklabels = []
eDos, dos, par = dp.calculateDOS(step, ref=False, interp=False, bins=bins)
distribution = (np.abs(par)) / ((dos) + 1E-10)
def interp(xin, yin, xout):
from scipy.interpolate import interp1d
spline = interp1d(xin, yin, kind='cubic')
return spline(xout)
x = np.linspace(eDos[0], eDos[-1], intepNum)
y = interp(eDos, distribution, x)
#print (np.abs(yDosInterp)+0.001).min()
ax.fill_between(x, y, color='b')
#print yDosInterp.min()
kargs = ma.getPropertyFromPosition(xlabel=xlabel,
ylabel=ylabel,
ylimits=ylimits,
**kargs)
ma.setProperty(ax, **kargs)
def plotTotalEnergy(ax, label=''):
time, T, E_ks, E_tot, Vol, P = dp.getEnergyTemperaturePressure()
ax.plot(time, E_tot - E_tot[0], '-', lw=2, alpha=1, label=label)
kargs = ma.getPropertyFromPosition(ylabel=r'E (eV)',
xlabel='T (fs)',
title='Excitation Energy')
ma.setProperty(ax, **kargs)
def plotTemperature(ax, label=''):
time, T, E_ks, E_tot, Vol, P = dp.getEnergyTemperaturePressure()
ax.plot(time, T, lw=3, label=label)
kargs = ma.getPropertyFromPosition(xlabel='Time (fs)',
ylabel=r'T (K)',
title='Temperature')
ma.setProperty(ax, **kargs)
def plotRMSD(ax, label=''):
dp.getTrajactory()
import pyramids.process.struct as pps
time, distance = pps.calculateRMSD()
ax.plot(time, distance, lw=2, label=label)
kargs=ma.getPropertyFromPosition(xlabel='Time (fs)', ylabel=r'$\langle u \rangle^\frac{1}{2}$ ($\AA$)',
title='RMSD')
ma.setProperty(ax,**kargs)
def plotExcitation(ax, label=''):
time, exe = dp.getExcitedElectrons()
ax.plot(time, exe - exe[0],'-', lw=2)
kargs=ma.getPropertyFromPosition(ylabel=r'n(e)', xlabel='Time (fs)',
title='Excited Electrons')
print exe[-1] - exe[0]
ma.setProperty(ax,**kargs)
def plotExcitation(ax, label=''):
time, exe = dp.getExcitedElectrons()
ax.plot(time, exe - exe[0], '-', lw=2)
kargs = ma.getPropertyFromPosition(ylabel=r'n(e)',
xlabel='Time (fs)',
title='Excited Electrons')
#print exe[-1] - exe[0]
ma.setProperty(ax, **kargs)
def plotAField(ax, label=''):
time, Afield = dp.getAField()
#directions = ['x', 'y', 'z']
for direct in range(3):
if max(Afield[:, direct]) > 1E-10:
ax.plot(time, Afield[:, direct], label=label, lw=2, alpha=1.0)
kargs = ma.getPropertyFromPosition(ylabel=r'$\varepsilon$(a.u.)',
xlabel='Time(fs)',
title='vector Field')
ma.setProperty(ax, **kargs)
def plotRMSD(ax, label=''):
dp.getTrajactory()
import pyramids.process.struct as pps
time, distance = pps.calculateRMSD()
ax.plot(time, distance, lw=2, label=label)
kargs = ma.getPropertyFromPosition(
xlabel='Time (fs)',
ylabel=r'$\langle u \rangle^\frac{1}{2}$ ($\AA$)',
title='RMSD')
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 plotKpoints(kpts):
#Plot the K points
from pyramids.plot.setting import setProperty, getPropertyFromPosition
fig, ax = plt.subplots(1,1)
ax.plot(kpts[:,0],kpts[:,1],'o')
setProperty(ax,**getPropertyFromPosition(title='K points',xlabel=r'$k_x(1/\AA)$',ylabel=r'$k_y(1/\AA)$'))
plt.axis('equal')
plt.tight_layout()
plt.savefig('Kpoints.pdf',dpi=600)
plt.show()
#plt.close()
#unit = reciprocal_vectors/grid
#KIndex = np.dot(kpts,np.linalg.inv(unit)) + [nkx/2, nky/2, nkz/2]
#kIndex = np.array(KIndex, dtype=int)
#skpts = np.array([kpts + np.dot([i,j,k],reciprocal_vectors)
# for i in [0,-1,1] for j in [0,-1,1] for k in [0,-1,1]])
#skIndex = np.array(np.dot(skpts,np.linalg.inv(unit)) + [0.5,0.5,0], dtype=int)
#print kIndex.shape, #skIndex.shape
#print kIndex
#Ef = 6.0
#T = 300
#qOrder = 2
#susp = np.zeros([qOrder,qOrder,qOrder],dtype=float)
#
#
#for ik, ikpt in enumerate(kpts):
# kxy = kIndex[ik]
# for i in range(-qOrder,qOrder):
# for j in range(-qOrder,qOrder):
# for k in range(-qOrder,qOrder):
# qxy = (kxy + np.array([i,j,k])) % np.array([nkx,nky,nkz])
# iq = qxy[0]*nky*nkz + qxy[1]*nkz + qxy[2]
# #susp[i,j,k] = susFunc(eigValueAllK,ik,iq,Ef,T)
# pass
#print susp
#if __name__ == "__main__":
# nkx = 12
# nky = 12
# nkz = 1
# # Read the structure information from POSCAR
# from ase.io import read
# atoms = read('POSCAR')
# # Generate K points,
# # Selection: Monkhorst-Pack or Line-Mode
# grid = np.array([nkx,nky,nkz],dtype=int)
# kpts = getMPKpts(atoms,grid)
# #kpts = getBandKpoints(atoms,npoints=50)
# x, v, u = calculateEigenPairs(kpts)
# plotBands(x, v)
# plotKpoints(kpts)
def drawPartition(ax, label = ''):
"""
Draw the KS Energy and Total Energy in the ax
"""
X,qo = tdp.getPartition()
ax.plot(X,qo,'-',linewidth=3.0,label = 'Partitions '+ label)#,color=ma.colors[0]
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'Time(fs)',ylabel=r'Partition',title='',
xticks=None, yticks=None,
xticklabels=None, yticklabels=None,
xlimits=None, ylimits=None)
ma.setProperty(ax, **kargs)
def plotBands(xall,eigValueAllK):
from pyramids.plot.setting import setProperty, getPropertyFromPosition
fig, ax = plt.subplots(1,1)
#Plot the eigenvalues
for index in range(eigValueAllK.shape[0]):
ax.plot(xall[index,:],eigValueAllK[index,:],'ob',lw=1)
setProperty(ax,**getPropertyFromPosition(title='Energy Bands',xlabel=r'',ylabel=r'Energy(eV)',xticklabels=[]))
#Set tight layout and output
plt.axis('tight')
plt.tight_layout()
plt.savefig('Bands.pdf',dpi=600)
plt.show()
def drawPressure(ax, label = ''):
"""
Draw the KS Energy and Total Energy in the ax
"""
X, temp, E_KS, Etot, volume, pressure = tdp.getEnergyTemperaturePressure()
ax.plot(X,pressure,'-',linewidth=3.0,label = 'Pressure '+ label)#,color=ma.colors[0]
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'Time(fs)',ylabel=r'Pressure(KBar)',title='',
xticks=None, yticks=None,
xticklabels=None, yticklabels=None,
xlimits=None, ylimits=None)
ma.setProperty(ax, **kargs)
def plotDOS(ax, step, ylimits=[0,None], bins=100, **kargs):
xlabel = 'Energy (eV)'
ylabel = 'DOS'
eDosInterp, yDosInterp, yParInterp = dp.calculateDOS(step,bins=bins)
ax.fill_between(eDosInterp, yParInterp, color='b')
ax.fill_between(eDosInterp,-yParInterp, color='r')
ax.fill_between(eDosInterp, yDosInterp, lw=3, color='g',alpha=0.2)
kargs = ma.getPropertyFromPosition(xlabel=xlabel, ylabel=ylabel,
ylimits=ylimits, yticklabels=[],
**kargs)
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)
def plotDOS(ax, step, ylimits=[0, None], bins=100, **kargs):
xlabel = 'Energy (eV)'
ylabel = 'DOS'
eDosInterp, yDosInterp, yParInterp = dp.calculateDOS(step, bins=bins)
ax.fill_between(eDosInterp, yParInterp, color='b')
ax.fill_between(eDosInterp, -yParInterp, color='r')
ax.fill_between(eDosInterp, yDosInterp, lw=3, color='g', alpha=0.2)
kargs = ma.getPropertyFromPosition(xlabel=xlabel,
ylabel=ylabel,
ylimits=ylimits,
yticklabels=[],
**kargs)
ma.setProperty(ax, **kargs)
def drawRDF(ax,step=None, label = ''):
"""
Draw the KS Energy and Total Energy in the ax
"""
if step == None:
step = tdp.getNumStep()
systemLabel,timestep = tdp.getSystemLabelTimpstep()
tdp.splitMDCAR()
hist,bin_edges = tdp.calculateRDF(step-1)
ax.plot(bin_edges[:-1],hist,linewidth=3.0,label='RDF '+str((step)*timestep)+' fs'+ label) #,color=ma.colors[0]
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'Radius($\AA$)',ylabel=r'RDF(a.u.)',title='',
xticks=None, yticks=None,
xticklabels=None, yticklabels=None,
xlimits=None, ylimits=None)
ma.setProperty(ax, **kargs)
def drawPartition(ax, label=''):
"""
Draw the KS Energy and Total Energy in the ax
"""
X, qo = tdp.getPartition()
ax.plot(X, qo, '-', linewidth=3.0,
label='Partitions ' + label) #,color=ma.colors[0]
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'Time(fs)',
ylabel=r'Partition',
title='',
xticks=None,
yticks=None,
xticklabels=None,
yticklabels=None,
xlimits=None,
ylimits=None)
ma.setProperty(ax, **kargs)
def drawPressure(ax, label=''):
"""
Draw the KS Energy and Total Energy in the ax
"""
X, temp, E_KS, Etot, volume, pressure = tdp.getEnergyTemperaturePressure()
ax.plot(X, pressure, '-', linewidth=3.0,
label='Pressure ' + label) #,color=ma.colors[0]
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'Time(fs)',
ylabel=r'Pressure(KBar)',
title='',
xticks=None,
yticks=None,
xticklabels=None,
yticklabels=None,
xlimits=None,
ylimits=None)
ma.setProperty(ax, **kargs)
def drawRMSD(ax,selected=None, label = '', init = 0):
"""
Draw the KS Energy and Total Energy in the ax
"""
systemLabel,timestep = tdp.getSystemLabelTimpstep()
if selected == None:
selected = range(0,tdp.getNumStep(),int(1.0/timestep))
tdp.splitMDCAR()
time,distance,velocity = tdp.calculateRMSD(selected, init=init)
#os.remove('POSCAR')
ax.plot(time,distance,linewidth=3.0,label='RMSD'+ label)#,color=ma.colors[0])
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'Time(fs)',ylabel=r'RMSD($\AA$)',title='',
xticks=None, yticks=None,
xticklabels=None, yticklabels=None,
xlimits=None, ylimits=None)
ma.setProperty(ax, **kargs)
def plotDistribution(ax, step, bins=100, intepNum=2000, ylimits=[0,1], **kargs):
xlabel = 'Energy (eV)'
ylabel = 'FD'
yticklabels=[]
eDos, dos, par = dp.calculateDOS(step, ref=False, interp=False,bins=bins)
distribution = ((par))/((dos)+1E-10)
def interp(xin,yin,xout):
from scipy.interpolate import interp1d
spline = interp1d(xin, yin, kind='cubic')
return spline(xout)
x = np.linspace(eDos[0], eDos[-1], intepNum)
y = interp(eDos, distribution, x)
#print (np.abs(yDosInterp)+0.001).min()
ax.fill_between(x, y, color='b')
#print yDosInterp.min()
kargs = ma.getPropertyFromPosition(xlabel=xlabel, ylabel=ylabel, ylimits=ylimits, **kargs)
ma.setProperty(ax,**kargs)
def drawEnergy(ax, relative=False, divided=1.0, popFirstStep=True, label=''):
"""
Draw the KS Energy and Total Energy in the ax
"""
X, temp, E_KS, Etot, volume, pressure = tdp.getEnergyTemperaturePressure()
refEnergy = E_KS[0]
if relative:
E_KS = E_KS - refEnergy
Etot = Etot - refEnergy
if popFirstStep:
ax.plot(X[1:],
E_KS[1:] / divided,
'-',
linewidth=3.0,
label='KS' + label) #,color=ma.colors[0]
ax.plot(X[1:],
Etot[1:] / divided,
'--',
linewidth=3.0,
label='Total' + label) #,color=ma.colors[2]
else:
ax.plot(X, E_KS / divided, '-', linewidth=3.0,
label='KS' + label) #,color=ma.colors[0]
ax.plot(X, Etot / divided, '--', linewidth=3.0,
label='Total' + label) #,color=ma.colors[2]
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'Time(fs)',
ylabel=r'Energy(eV)',
title='',
xticks=None,
yticks=None,
xticklabels=None,
yticklabels=None,
xlimits=None,
ylimits=None)
ma.setProperty(ax, **kargs)
def drawEigenvalue(ax, label = ''):
"""
Draw the KS Energy and Total Energy in the ax
"""
X,eo = tdp.getEigenvalues()
X,qo = tdp.getPartition()
countEleState = 0
countHolState = 0
countNormalState = 0
for i in range(eo.shape[1]):
if eo[0,i] > 0.03 and qo[0,i] > 0.2:
if countEleState == 0:
ax.plot(X,eo[:,i],'-',linewidth=3.0,color=ma.colors[0],label='Electron'+ label)
else:
ax.plot(X,eo[:,i],'-',linewidth=3.0,color=ma.colors[0])
countEleState += 1
elif eo[0,i] < -0.03 and qo[0,i] < 1.8:
if countHolState == 0:
ax.plot(X,eo[:,i],'-',linewidth=3.0,color=ma.colors[1],label='Hole'+ label)
else:
ax.plot(X,eo[:,i],'-',linewidth=3.0,color=ma.colors[1])
countHolState +=1
else:
if countNormalState == 0:
ax.plot(X,eo[:,i],'--',linewidth=3.0,color='grey',alpha=0.7,label='Normal'+ label)
else:
ax.plot(X,eo[:,i],'--',linewidth=3.0,color='grey',alpha=0.7)
countNormalState +=1
#ax.plot(X,eo,'-',linewidth=qo,label = 'Eigenvalues')#,color=ma.colors[0]
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'Time(fs)',ylabel=r'Eigenvalues(eV)',title='',
xticks=None, yticks=None,
xticklabels=None, yticklabels=None,
xlimits=None, ylimits=None)
ma.setProperty(ax, **kargs)
def drawBands(ax,bandType='e', label = ''):
"""
Draw the KS Energy and Total Energy in the ax
"""
X, Ek, xticks, xticklabels = tdp.getBands()
if bandType == 'e':
eFermi = tdp.getFermiEnergy()
Ek = Ek - eFermi
ylabel = 'Energy(eV)'
else:
ylabel = r'$\omega$(cm$^{-1}$)'
alpha = 1.0
color = 'b'
for ispin in range(Ek.shape[2]):
for iband in range(1,Ek.shape[1]):
ax[0].plot(X,Ek[:,iband,ispin],lw=3.0,ls='-',color=color,alpha=alpha,label=label)
kargs = ma.getPropertyFromPosition(index=None,
xlabel=r'',ylabel=ylabel,title='',
xticks=xticks, yticks=None,
xticklabels=xticklabels, yticklabels=None,
xlimits=None, ylimits=None)
ma.setProperty(ax, **kargs)
#--------------------------------------------------------------------------------------------
fig, axs = plt.subplots(2, 1, sharex=True, sharey=False, figsize=(10, 8)) #
data = scanFolder(action)
c = ma.getColors(len(data))
for line in data:
index, folder = line[0]
ax = axs[1]
cts = ax.plot(line[1][0],
line[1][2] - line[1][2][0],
lw=3,
label=folder,
c=c[index])
kargs = ma.getPropertyFromPosition(xlabel='Time (fs)',
ylabel=r'E/atom (eV)',
title='Excitation Energy')
ma.setProperty(ax, **kargs)
ax = axs[0]
if index == 5:
cts = ax.plot(line[2][0],
line[2][1][:, 2],
lw=1,
c=c[index],
label='400 nm')
kargs = ma.getPropertyFromPosition(xlabel='Time (fs)',
ylabel=r'$\varepsilon$ (a.u.)',
title='Electric Field')
#plt.colorbar(cts,ax=ax)
ma.setProperty(ax, **kargs)
#--------------------------------------------------------------------------------------------
# interpXimge = np.linspace(data[0][xDownIndex], data[0][xUpIndex-1], 2000)
# splinesimge = interp1d(data[0][xDownIndex:xUpIndex], data[1][xDownIndex:xUpIndex],kind='cubic')
# overEimge = splinesimge(interpXimge)
#
# interpXreal = np.linspace(data[0][xDownIndex], data[0][xUpIndex-1], 2000)
# splinesreal = interp1d(data[0][xDownIndex:xUpIndex], data[3][xDownIndex:xUpIndex],kind='cubic')
# overEreal = splinesreal(interpXreal)
#
# interpXeels = np.linspace(data[0][xDownIndex], data[0][xUpIndex-1], 2000)
# splineseels = interp1d(data[0][xDownIndex:xUpIndex], data[4][xDownIndex:xUpIndex],kind='cubic')
# overEeels = splineseels(interpXeels)
# plt.plot(interpX,splines(interpX)/np.max(splines(interpX)),'-o',markersize=5.0,linewidth=4.0,color=colors[i],alpha=0.6,label=data[2])
plt.plot(data[0],i*3+data[1]/np.max(data[1]),'--',markersize=10.0,linewidth=3.0,color=colors[i+1],alpha=0.65)
plt.plot(data[0],i*3+data[3]/np.max(data[3]),'-',markersize=10.0,linewidth=3.0,color=colors[i+1],alpha=0.65)
# plt.plot(interpXreal,i*3+interpXreal-interpXreal,'-',markersize=10.0,linewidth=6.0,color=colors[i+1],alpha=0.65)
plt.fill_between(data[0],i*3+(data[4])/np.max(data[4]),i*3,linewidth=3.0,color=colors[i+1],alpha=0.5,)
# plt.plot(interpX,splines(interpX),'-o',markersize=5.0,linewidth=4.0,color=colors[i],alpha=0.6,label=data[2])
# plt.plot(data[0],data[1]/np.max(data[1]),'-o',linewidth=4.0,color=colors[i+1],alpha=0.6,label=data[2])
# plt.plot(data[0],data[1]/float(data[2]),'-o',linewidth=4.0,color=colors[i+1],alpha=0.6,label=data[2])
args = getPropertyFromPosition(xlimits=xlimits,ylimits=ylimits,
ylabel='EELs',xlabel='Energy(eV)')#,vline=data[3])
setProperty(ax,**args)
#plt.show()
plt.tight_layout()
#plt.savefig('dielectriFunctionVariable(without over E or maxabsorbance).pdf',dpi=600)
plt.savefig('EEls.eps',i=800)
plt.savefig('EEls.png',i=800)
#plt.savefig('dielectriFunctionVariable1-1.jpg',dpi=600)
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')
plt.tight_layout()
for save_type in ['.png']:
filename = SaveName + save_type
plt.savefig(filename,orientation='portrait',dpi=600)
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 line = []
deltaE[ie] = (deltaE[ie - 1] + deltaE[ie + 1])/2
ax.plot(timeEn[2:], deltaE,'-', c=c[index],
lw=2, alpha=1)
ax = axs[efield]
#print timeEf.shape, eField.shape
ax.plot(timeEf, eField*13.6/0.529)
maxElectrons.append(exe.max())
maxEnergies.append(deltaE.max())
minEnergies.append(deltaE.min())
kargs=ma.getPropertyFromPosition(exElectron, ylabel=r'n(e)',
title='Excited Electrons',
xlabel = 'Time (fs)', xlimits=[0,40],
#ylimits=[0,np.max(maxElectrons)],
)
ma.setProperty(axs[exElectron],**kargs)
kargs=ma.getPropertyFromPosition(exEnergy, ylabel=r'E (eV)', xlimits=[0,40],
#ylimits=[np.min(minEnergies),np.max(maxEnergies)],
title='Excitation Energy')
ma.setProperty(axs[exEnergy],**kargs)
kargs=ma.getPropertyFromPosition(efield, ylabel=r'E ($V/\AA$)',
xlabel = 'Time (fs)', xlimits=[0,40],
#ylimits=[np.min(minEnergies),np.max(maxEnergies)],
title='Electric Field')
ma.setProperty(axs[efield],**kargs)
kargs=ma.getPropertyFromPosition(ipiTemp, ylabel=r'T (K)',
xlabel = 'Time (fs)', xlimits=[0,40],
#ylimits=[np.min(minEnergies),np.max(maxEnergies)],
selectedProcesses = ['evolve','DHSCF','PostSCF','siesta'] #,'TDbuildD'
explainations = ['Propagation', 'Build H', 'Postprocess','Total'] #,'Build DM'
image = data[-1][-1]['Prg.tot']
pieData = image[selectedProcesses[:-1]]
other = image[selectedProcesses[-1]] - np.sum(pieData.values)
ax = axs[1]
explode = np.zeros(len(pieData)) + 0.04
explode[0] = 0.07
patches, texts, autotexts = ax.pie(pieData.values, explode=explode, labels=explainations[:-1],
labeldistance = 0.2, autopct='%.0f%%',pctdistance = 0.7,
shadow=True, textprops={'fontsize':'xx-large','color':'gold'})
for text in texts:
text.set_fontsize('xx-large')
plt.axis('tight')
for key,label in zip(selectedProcesses,explainations):
totalTimes = np.array([time['Prg.tot'][key] for index, folder, time in data])/3600.0
situations = [int(folder) for index, folder, time in data]
ax = axs[0]
ax.plot(situations, totalTimes,'-o', ms=12, label = label)
kargs=ma.getPropertyFromPosition(ylabel=r'Clock Time (hour)',title='Clock Time')
ma.setProperty(ax,**kargs)
plt.tight_layout()
for save_type in ['.pdf','.eps']:
filename = SaveName + save_type
plt.savefig(filename,dpi=800)
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Tue Dec 20 06:28:23 2016
@author: cl-iop
"""
import numpy as np
import matplotlib.pyplot as plt
import pyramids.io.result as dp
import pyramids.plot.setting as ma
numSample = 20
thetas = np.linspace(0,np.pi/2.0,numSample)
x = 0.2*np.sin(thetas)
y1 = np.load('intense.npy')
y2 = np.load('angle.npy')
fig, ax = plt.subplots(1,1,sharex=False,sharey=False,figsize=(8,6))
ax.plot(x,y1,'-',label = 'intense')
ax.plot(x,y2,'o',label = 'angle')
kargs = ma.getPropertyFromPosition(ylabel=r'', xlabel=r'$A \sin\theta$',title='')
ma.setProperty(ax,**kargs)
plt.tight_layout()
SaveName = __file__.split('/')[-1].split('.')[0]
for save_type in ['.pdf']:
plt.savefig(SaveName+save_type,transparent=True,dpi=600)
import numpy as np
import matplotlib.pyplot as plt
from pyramids.plot.setting import getColors
from pyramids.plot.setting import A4_LANDSCAPE
from pyramids.plot.setting import getPropertyFromPosition
from pyramids.plot.setting import setProperty
import os
fig=plt.figure(figsize=A4_LANDSCAPE)#_LANDSCAPE
plt.subplots_adjust(left=0.1, bottom=0.10, right=0.95, top=0.95, wspace=0.3, hspace=0.05)
axs = [fig.add_subplot(2,1,1),
fig.add_subplot(2,1,2)]
colors = getColors(4)
chargeData=np.loadtxt('AECHARGE')
kargs=getPropertyFromPosition(1,'Charge(e)',r'r($\AA$)')
axs[0].plot(chargeData[:,0],chargeData[:,1],':',linewidth=3,label='Down',color=colors[1])
axs[0].plot(chargeData[:,0],chargeData[:,2],'--',linewidth=3,label='Up',color=colors[2])
axs[0].plot(chargeData[:,0],chargeData[:,3],'-',linewidth=3,label='Core',color=colors[0])
axs[0].legend(fontsize=16,loc=1)
kargs['xlimits'] = [0,6]
kargs['xticklabels'] = []
setProperty(axs[0],**kargs)
numWFfiles=int(os.popen('ls AEWFNR* |wc -l').readline())
print numWFfiles
waveData = []
lineTypes=['-','--',':']
orbitalType=['s','p','d','f']
for indexFile in range(min(numWFfiles,3)):
maxEnergies = []
minEnergies = []
for [(index, folder), (timeEn,deltaE, T)] in data:
eField = float(folder) * 13.6/0.529
ax = axs[exTemp]
ax.plot(timeEn, T,'-', c=c[index],
lw=2, alpha=1)
ax = axs[exEnergy]
ax.plot(timeEn, deltaE,'-', c=c[index],
label=r'%5.2f $V/\AA$' % eField,
lw=2, alpha=1)
kargs=ma.getPropertyFromPosition(exEnergy, ylabel=r'E(eV)',
title='Excitation Energy',
xlabel='Time (fs)',
#ylimits=[0,np.max(maxElectrons)],
xlimits=None,)
ma.setProperty(axs[exEnergy],**kargs)
kargs=ma.getPropertyFromPosition(exTemp, ylabel=r'T(K)',
#ylimits=[np.min(minEnergies),np.max(maxEnergies)],
title='Temperature')
ma.setProperty(axs[exTemp],**kargs)
plt.tight_layout()
for save_type in ['.pdf','.png']:
filename = SaveName + save_type
plt.savefig(filename,dpi=800)
time, msd = dp.readMSD()
nocc = int(float(os.popen('grep "starting charge" result').readline().split()[-1])/2.0)
fig, axs = plt.subplots(2,2,sharex=True,figsize=(8,5))
axs = axs.flatten()
norm, kweight = readData('pwscf.norm.dat')
excite = (norm - norm[0,:,:])
for ib in range(excite.shape[2]):
excite[:,:,ib] *= kweight
#pass
step = min(time.shape[0]-1, excite.shape[0])
axs[0].plot(time[1:step+1], (excite[:step,:,:nocc]).sum(axis=(1,2)))
axs[0].plot(time[1:step+1], (excite[:step,:,nocc:]).sum(axis=(1,2)))
args = ma.getPropertyFromPosition(0,title='Excited electrons',ylabel='n (e)')
ma.setProperty(axs[0],**args)
Efield = [[float(i) for i in line.split()] for line in open('TDEFIELD')]
Efield = np.array(Efield)/1E5
ppu.plotTotalEnergy(axs[2])
ppu.plotEField(axs[1])
f = os.popen('grep "first current is " result')
current = np.array([[float(i) for i in line.split()[-3:]] for line in f.readlines()])
for idir in range(3):
axs[3].plot(time[1:], current[:,idir],'-',label=['x','y','z'][idir])
args = ma.getPropertyFromPosition(3,title='Current',ylabel='j (a.u.)')
ma.setProperty(axs[3],**args)
# ,lw=0.0,color='b',alpha=0.7)
# else:
# part = abs(exe[0,kpt,i] - exe[:,kpt,i])
# s = ax.fill_between(time, eigen[:,kpt,i] - norm*part,
# eigen[:,kpt,i] + norm*part
# ,lw=0.0,color='r',alpha=0.7)
ax.plot(time, eigen[:, kpt, evolvingBands], '-', lw=0.2, c='k', alpha=0.8)
#print exe[-1,kpt,:]
# axin, imag = pu.insertStruct(ax, width="50%", height=1.5, loc=2,
# rotation=[0,0,0],
# camera='perspective', cell=True)
kargs = ma.getPropertyFromPosition(ylabel=r'Eigenvalues(eV)',
xlabel='Time(fs)',
title='Population',
hline=[0.0],
xlimits=[np.min(time),
np.max(time)],
ylimits=[
np.min(eigen[:, kpt,
evolvingBands]),
np.max(eigen[:, kpt, evolvingBands])
])
ma.setProperty(ax, **kargs)
#------------------------------------------------------------------------------
plt.tight_layout()
for save_type in ['.pdf']:
filename = SaveName + save_type
plt.savefig(filename, dpi=400)
epsilon = fft(dipole)[:numStep/2]
epsilon = (np.real(epsilon),np.imag(epsilon))
absorbance = epsilon[0]*energyArray/4.1356
if i == 0:
absorbanceSum = absorbance
else:
absorbanceSum += absorbance
axs.fill_between(energyArray,absorbance,linewidth=0.0,color=colors[i],label=direct,alpha=0.6)
os.chdir('..')
xlimits = [0,20]
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] > 0.5: # energyArray[j] < 22.0 and
peaks.append(energyArray[j])
#print energyArray[j], absorbanceSum[j]
print peaks
axs.plot(energyArray,absorbanceSum,'-',linewidth=1.5,color='black',label='Total')
args = getPropertyFromPosition(xlimits=xlimits,ylimits=[0,max(absorbanceSum)],ylabel='Absorbance',xlabel='Energy(eV)',vline=peaks)
setProperty(axs,**args)
plt.tight_layout()
plt.savefig('dielectriFunction.pdf',dpi=600)
#plt.plot(2*np.real(y))
ax = axs[exEnergy]
tolerance = 0.5
for ie, e in enumerate(deltaE[1:-2]):
if np.abs(deltaE[ie] - deltaE[ie - 1]) > tolerance and np.abs(
deltaE[ie] - deltaE[ie + 1]) > tolerance:
deltaE[ie] = (deltaE[ie - 1] + deltaE[ie + 1]) / 2
ax.plot(timeEn[2:], deltaE, '-', c=c[index], lw=2, alpha=1)
maxElectrons.append(exe.max())
maxEnergies.append(deltaE.max())
minEnergies.append(deltaE.min())
kargs = ma.getPropertyFromPosition(
exElectron,
ylabel=r'n(e)',
title='Excited Electrons',
ylimits=[0, np.max(maxElectrons)],
xlimits=None,
)
ma.setProperty(axs[exElectron], **kargs)
kargs = ma.getPropertyFromPosition(
exEnergy,
ylabel=r'E(eV)',
ylimits=[np.min(minEnergies), np.max(maxEnergies)],
title='Excitation Energy')
ma.setProperty(axs[exEnergy], **kargs)
plt.tight_layout()
for save_type in ['.pdf', '.png']:
filename = SaveName + save_type
plt.savefig(filename, dpi=800)
nocc = int(float(os.popen('grep "starting charge" result').readline().split()[-1])/2.0)
print nocc
fig, axs = plt.subplots(1,2,sharex=True,figsize=(8,5))
ax = axs[0]
norm, kweight = readData('pwscf.norm.dat')
excite = (norm - norm[0,:,:])
for ib in range(excite.shape[2]):
excite[:,:,ib] *= kweight
#pass
#print excite
time = np.arange(excite.shape[0]) * dt
ax.plot(time, (excite[:,:,:nocc]).sum(axis=(1,2)))
ax.plot(time, (excite[:,:,nocc:]).sum(axis=(1,2)))
args = ma.getPropertyFromPosition(0,title='Excited electrons',ylabel='n (e)')
ma.setProperty(ax,**args)
ax = axs[1]
value, kweight = readData('pwscf.value.dat')
#print norm
ax.plot(time, value[:,0,:],'-')
args = ma.getPropertyFromPosition(0,title='Excited electrons',ylabel='n (e)')
ma.setProperty(ax,**args)
plt.tight_layout()
time,
E_ks,
'-',
lw=3,
)
axin.plot(
time,
ref,
'-',
lw=3,
)
axin.fill_between(time, E_ks, ref, color='r', alpha=0.8, label=r'$\Delta$')
#axin.text(10.0,-0.10,r'$\Delta$',transform=axin.transAxes,fontsize=100)
#ax.annotate('eqweqweqeqw$\Delta$',(0,0.0),(0,0),fontsize=50,arrowprops={ 'arrowstyle': '->'}) #()
kargs = ma.getPropertyFromPosition(ylabel=r'Excitation enegy',
xlabel='Time',
xticklabels=[],
yticklabels=[])
ma.setProperty(axin, **kargs)
def getEnergy(index, folder):
time, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure(ave=True)
return index, folder, E_ks
def errorFunc(x, A, B):
return A * np.exp(B / x)
os.chdir('../../Data/')
print os.listdir('.')
maxPeak = energyArray[np.argmax(absorbanceSum)], np.max(absorbanceSum)
maxMinusPeak = energyArray[np.argmin(absorbanceSum)], np.min(absorbanceSum)
xlimits = [0, 8]#maxPeak[0]*1.5]
ylimits = None#[0, 50]#[0, maxPeak[1]]
from scipy.signal import argrelextrema
extrema = argrelextrema(absorbanceSum, np.greater)
maxPeakValue = max(absorbanceSum)
peaks = []
for extreme in extrema[0]:
peakPosition, peakValue = energyArray[extreme]/4.3, absorbanceSum[extreme]
if peakValue > 0.01 * maxPeakValue:
peaks.append((peakPosition,peakValue))
# axs.text(peakPosition, maxPeakValue*0.7,'%3.2f' % peakPosition, fontsize='large',rotation=90)
peaks = np.array(peaks)
axs[0].semilogy(energyArray/guassFieldEnergy,absorbanceSumHHG,'-',linewidth=2.,color='black',label='Total',alpha=0.5)
axs[1].plot(energyArray/guassFieldEnergy,absorbanceSumHHG,'-',linewidth=2.,color='red',label='Total')
args1 = getPropertyFromPosition(xlimits=xlimits,ylimits=ylimits,
ylabel='absorbance',xlabel='Order')
args2 = getPropertyFromPosition(xlimits=xlimits,ylimits=None,
ylabel='absorbance',xlabel='Order')
setProperty(axs[0],**args1)
setProperty(axs[1],**args2)
#plt.tight_layout()
plt.savefig('HHG.pdf',dpi=600)
color = 'r'
s = ax.fill_between(x,
eig[kpath, i] - norm * part,
eig[kpath, i] + norm * part,
lw=0.0,
color=color,
alpha=0.7)
ax.plot(x, eig[kpath, i], '--', lw=1.5, c='grey')
plt.axis('tight')
kargs = ma.getPropertyFromPosition(
ylabel=r'Eigenvalues(eV)',
xlabel='',
xticks=cut,
xticklabels=specialKPoints,
xlimits=[cut[0], cut[-1]],
vline=cut,
title='Population',
hline=[0.0],
)
#xlimits=[np.min(time),np.max(time)],
#ylimits=[np.min(eigen[:,kpt,evolvingBands]),
# np.max(eigen[:,kpt,evolvingBands])])
ma.setProperty(ax, **kargs)
#------------------------------------------------------------------------------
plt.tight_layout()
for save_type in ['.pdf']:
filename = SaveName + save_type
plt.savefig(filename, dpi=400)
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Tue Dec 20 06:28:23 2016
@author: cl-iop
"""
import numpy as np
import matplotlib.pyplot as plt
import pyramids.io.result as dp
import pyramids.plot.setting as ma
numSample = 20
thetas = np.linspace(0, np.pi / 2.0, numSample)
x = 0.2 * np.sin(thetas)
y1 = np.load('intense.npy')
y2 = np.load('angle.npy')
fig, ax = plt.subplots(1, 1, sharex=False, sharey=False, figsize=(8, 6))
ax.plot(x, y1, '-', label='intense')
ax.plot(x, y2, 'o', label='angle')
kargs = ma.getPropertyFromPosition(ylabel=r'',
xlabel=r'$A \sin\theta$',
title='')
ma.setProperty(ax, **kargs)
plt.tight_layout()
SaveName = __file__.split('/')[-1].split('.')[0]
for save_type in ['.pdf']:
plt.savefig(SaveName + save_type, transparent=True, dpi=600)
exY = np.array([Z[i][ext] for ext in extreme])
#miX = np.array([d[ext,0] for ext in extremM])
#miY = np.array([Z[i][ext] for ext in extremM])
ax1.scatter(q * np.ones(exY.shape[0]), exY, 30, lw=0.0)
#ax1.scatter(q*np.ones(miY.shape[0]),miY,miX*30,lw=0.0,color='r')
#print extreme
#ax.fill_between(E,C[i],color='r',zs=i*0.01, zdir='z')
shift = -i * 0.0
#ax.plot(E[selectIndex],Z[i][selectIndex], lw=1, color=c[i])
ax.fill_between(E[selectIndex],
Z[i][selectIndex] + shift,
shift,
lw=3,
color=c[i])
axs[2].plot(q * np.ones(exX.shape[0]), exX, 'or')
ax.plot(exX, exY, 'ob')
args = ma.getPropertyFromPosition( #ylimits=[None,0.2], xlimits=[None,5],
grid=False,
title='EELS spectra: $%s$' % label,
#ylabel=r'q($\AA^{-1}$)',
xlabel='Energy(eV)')
ma.setProperty(ax, **args)
#from mpl_toolkits.axes_grid1.inset_locator import mark_inset
#mark_inset(axs[0], axs[1], loc1=2, loc2=3, fc="none", ec="0.5",ls='--',lw=3,zorder=100)
plt.tight_layout()
for save_type in ['.png', '.pdf']:
filename = SaveName + save_type
plt.savefig(filename, orientation='portrait', dpi=600)
#from ase.calculators.siesta.import_functions import xv_to_atoms
#atoms = xv_to_atoms('siesta.XV')
import os
atoms = dp.getStructrue()
# --------------------------------------a----------------------------------
ax = axs[iStruct]
generateStructPNG(atoms,cell=True,repeat = [5,3,1])
insertImag(ax)
#confStructrueFigure(ax)
kargs = getPropertyFromPosition(iStruct,r'',"",title='Structure',)
setProperty(ax,**kargs)
# --------------------------------------b----------------------------------
ax = axs[iBZone]
reciprocal_vectors = 2*np.pi*atoms.get_reciprocal_cell()
#print reciprocal_vectors
points=np.array([(reciprocal_vectors[0,0:2]*i+
reciprocal_vectors[1,0:2]*j+
reciprocal_vectors[2,0:2]*k)
for i in range(-1,2)
for j in range(-1,2)
for k in range(-0,1)])
from scipy.spatial import Voronoi
from pyramids.plot.PlotUtility import voronoi_plot_2d
vor = Voronoi(points)
import os
import pyramids.io.result as dp
from pyramids.io.result import getHomo
SaveName = __file__.split('/')[-1].split('.')[0]
fig1, ax = plt.subplots(1,1,sharey=True,sharex=True,figsize=(8,6))
eigenvalues = dp.readEigFile()
k = np.arange(eigenvalues.shape[0])
print k
k = []
for i in range(120,785,95):
k.append(i)
k.append(i+47)
for i in range(785,746,-1):
k.append(i)
k = np.array(k) - 1
y = eigenvalues
#plotedBand = getHomo()
ax.plot(np.arange(k.shape[0]),eigenvalues[k,:],'-o')
args = ma.getPropertyFromPosition(xlabel=r'$n_k$', ylimits=[-2,2],
ylabel=r'Eigenvalues(eV)')
ma.setProperty(ax,**args)
plt.tight_layout()
for save_type in ['.pdf']:
filename = SaveName + save_type
plt.savefig(filename,orientation='portrait',dpi=600)
absorbanceSum += absorbance
axs.fill_between(energyArray/8.56,absorbance,0.0,color=colors[i],label=direct,alpha=0.6)
os.chdir('..')
maxPeak = energyArray[np.argmax(absorbanceSum)], np.max(absorbanceSum)
maxMinusPeak = energyArray[np.argmin(absorbanceSum)], np.min(absorbanceSum)
xlimits = [0.1, 8]#maxPeak[0]*1.5]
ylimits = [0, maxPeak[1]]
from scipy.signal import argrelextrema
extrema = argrelextrema(absorbanceSum, np.greater)
maxPeakValue = max(absorbanceSum)
peaks = []
for extreme in extrema[0]:
peakPosition, peakValue = energyArray[extreme], absorbanceSum[extreme]
if peakValue > 0.05 * maxPeakValue:
peaks.append((peakPosition,peakValue))
axs.text(peakPosition, maxPeakValue*0.7,'%3.2f' % peakPosition, fontsize='large',rotation=90)
peaks = np.array(peaks)
#axs.semilogy(energyArray/8.56,absorbanceSum,'-',linewidth=2.,color='black',label='Total',alpha=0.5)
axs.plot(energyArray/8.56,absorbanceSum,'-',linewidth=2.,color='black',label='Total')
args = getPropertyFromPosition(xlimits=xlimits,ylimits=ylimits,
ylabel='absorbance',xlabel='energy(eV)')
setProperty(axs,**args)
plt.tight_layout()
#plt.savefig('dielectriFunction.pdf',dpi=600)