#/usr/bin/python """ Created on Fri Jul 22 09:54:42 2016 @author: Chao (Charles) Lian @email: [email protected] """ import matplotlib.pyplot as plt from pyramids.io.result import getTDEig from pyramids.plot.setting import getPropertyFromPosition from pyramids.plot.setting import setProperty from pyramids.plot.setting import getColors import numpy as np from mpl_toolkits.mplot3d import Axes3D import os colors = getColors(5) #ti = 3; tf = 1000; #selectTime =range(ti,tf) # initial timestep and final timestep #selectBand = [0]# initial band and final band selectKpts = [0]#[0,1,4,6,7]# initial band and final band numK = len(selectKpts) fig, axs = plt.subplots(1,len(selectKpts),sharex=True,figsize=(8,6)) #print eig.shape, time.shape, #for diri, directory in enumerate(['TDDFT','BOMD']): #os.chdir(directory) time, eig = getTDEig() #print time.shape
"""
Created on Thu Sep 22 15:36:43 2016
@author: moomin
"""
import numpy as np
from scipy.fftpack import fft, ifft
import pyramids.plot.PlotUtility as pu
from pyramids.plot.setting import getPropertyFromPosition, setProperty, getColors
from pyramids.io.fdf import tdapOptions
import pyramids.io.result as dp
import matplotlib.pyplot as plt
import os
from scipy.interpolate import interp1d
fig, ax = plt.subplots(1,1,sharey=True,sharex=True,figsize=(7,15))
colors = getColors(7)
dumping = 0.01
width = 186.0
fieldE = 0.01
xlimits = [0,30]
ylimits = None
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()
timeEn, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure()
deltaE = (E_tot[2:,] - E_tot[2])
return [(index, folder), (timeEf, eField), (timeEl, exe), (timeEn,deltaE)]
#------------------------------------------------------------------------------
fig, axs = plt.subplots(2,2,sharex=True,sharey=False,figsize=(8,6))
axs = axs.flatten()
SaveName = __file__.split('/')[-1].split('.')[0]
pimdData = getPIMDdata()
axs[ipiTemp].plot(pimdData[:,0],pimdData[:,2])
data = scanFolder(action)
#print data[-1][0][0]
c = ma.getColors(data[-1][0][0]+1)
maxElectrons = []
maxEnergies = []
minEnergies = []
for [(index, folder), (timeEf, eField), (timeEl, exe), (timeEn,deltaE)] in data:
#ax = axs[efield]
#ax.plot(timeEf,eField[:,2], c=c[index],
# label=folder,lw=2,alpha=0.8)
#eField = float(folder) * 13.6/0.529
ax = axs[exElectron]
ax.plot(timeEl,exe,'-',alpha=0.8,
#label=r'%5.2f $V/\AA$' % eField,c=c[index],
markerfacecolor='w',lw=2)
"""
Created on Thu Sep 22 15:36:43 2016
@author: moomin
"""
import numpy as np
from scipy.fftpack import fft, ifft
import pyramids.plot.PlotUtility as pu
from pyramids.plot.setting import getPropertyFromPosition, setProperty, getColors
from pyramids.io.fdf import tdapOptions
import pyramids.io.result as dp
import matplotlib.pyplot as plt
import os
from scipy.interpolate import interp1d
fig, ax = plt.subplots(1, 1, sharey=True, sharex=True, figsize=(7, 15))
colors = getColors(7)
dumping = 0.01
width = 186.0
fieldE = 0.01
xlimits = [0, 30]
ylimits = None
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)
#!/usr/bin/python
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
#------------------------------------------------------------------------------
time, exe = dP.getProjectedPartition()
time, eigen = dP.getAdiabaticEigenvalue()
#print eigen[:,1,:]
#h**o = dP.getHomo()
#print h**o
print exe.shape, eigen.shape
c = ma.getColors(exe.shape[2], cmap='brg')
norm = 50.0 #/np.max(exe[:,:,:] - exe[0,:,:])
#print norm
kpts = [0]
for kpt in kpts:
fig, ax = plt.subplots(1, 1, sharex=True, sharey=False, figsize=(8, 6))
SaveName = __file__.split('/')[-1].split('.')[0] + str(kpt)
h**o = 0
for i, band in enumerate(eigen[0, kpt, :]):
#print band
if band < 0:
h**o = i
evolvingBands = range(0, h**o + 40)
X, Y = np.meshgrid(time, eigen[0, kpt, evolvingBands])
Z = np.transpose(exe[0, kpt, evolvingBands] - exe[:, kpt, evolvingBands])
Created on Wed Jun 29 12:59:03 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
import os
fig, axs = plt.subplots(2, 1, sharex=False, sharey=False, figsize=(6, 8))
SaveName = __file__.split('/')[-1].split('.')[0]
startStep = 10
c = ma.getColors(4)
scandir = ('x', 'y')
for idir, direct in enumerate(scandir):
os.chdir(direct)
ax = axs[0]
time, T, E_ks, E_tot, Vol, P = dp.getEnergyTemperaturePressure()
dipoles = dp.getDipole()
dipoles[:, idir] = (dipoles[:, idir] - dipoles[0, idir]
) #* np.exp(-0.01*time)
ax.plot(time, dipoles[:, idir], label=direct)
ax.grid(which=u'major', axis='x')
ax.grid(which=u'major', axis='y')
ax = axs[1]
N = dipoles.shape[0]
#!/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=(8, 6))
SaveName = __file__.split('/')[-1].split('.')[0]
c = ma.getColors(2, cmap='brg')
#------------------------------------------------------------------------------
Time, exe = dP.getExcitedElectrons()
ax = axs[0]
ax.plot(Time,
exe - exe[0],
'.',
alpha=0.8,
c='b',
markerfacecolor='w',
lw=2,
label='Excited Electrons')
kargs = ma.getPropertyFromPosition(
ylabel=r'n(e)',
title='',
xlimits=None,
)
ma.setProperty(ax, **kargs)
#------------------------------------------------------------------------------
ax = axs[1]
time, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure()
deltaE = (E_ks[2:] - E_ks[2])
cut = [0]
specialKPoints = [r'$M$',r'$\Gamma$',r'$K$',r'$\Gamma$']
for i in range(667,38,-37):
kpath.append(i)
cut.append(len(kpath))
for i in range(36,421,35):
kpath.append(i+1)
kpath.append(i)
cut.append(len(kpath))
for i in range(421,649,38):
kpath.append(i)
kpath.append(i+1)
cut.append(len(kpath))
kpath = np.array(kpath) - 1
c = ma.getColors(exe.shape[2] - h**o + 1,cmap='brg')
evolvingBands = range(0, h**o + 9)
x = np.arange(kpath.shape[0])
excited = np.abs(exe[1,kpath,:] - exe[0,kpath,:])
norm = 2.0/np.max(exe[:,kpath,:] - exe[0,kpath,:])
eigenvalue = eigen[0,kpath,:]
print eigenvalue.shape, excited.shape, x.shape
line = []
scatter = []
for band in evolvingBands:
if band < h**o:
part = excited[:,band]
s = ax.fill_between(x, eigenvalue[:,band] - norm*part,
exe -= exe[0]
timeEn, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure()
deltaE = (E_tot[2:,] - E_tot[2])
return [(index, folder), (timeEf, eField), (timeEl, exe), (timeEn[2:],deltaE)]
#------------------------------------------------------------------------------
fig, axs = plt.subplots(2,1,sharex=True,sharey=False,figsize=(6,8))
SaveName = __file__.split('/')[-1].split('.')[0]
#pimdData = getPIMDdata()
#axs[-1].plot(pimdData[:,0],pimdData[:,4])
data = scanFolder(action)
rows = data[-1][0][0]+1
c = ma.getColors(rows)
exSteps = min([line[2][0].shape[0] for line in data])
exAve = np.zeros(exSteps)
enSteps = min([line[3][0].shape[0] for line in data])
enAve = np.zeros(enSteps)
for [(index, folder), (timeEf, eField), (timeEl, exe), (timeEn,deltaE)] in data:
exAve += exe[:exSteps]/rows
enAve += deltaE[:enSteps]/rows
axs[0].plot(timeEl[:exSteps],exAve,label='4 Beads')
axs[1].plot(timeEn[:enSteps],enAve,label='4 Beads')
@author: cl-iop
"""
from graphene import *
import pyramids.plot.setting as ma
import matplotlib.pyplot as plt
fig, axs = plt.subplots(2,1,sharex=False,sharey=False,figsize=(12,10))
#k = (0.0,1.0) #(np.sqrt(0.5),np.sqrt(0.5))
numSample = 20
args={'t0':20.0,'sigma': 8.0, 'omega':2.0, 'phi':0.0, 'parity':1, 'vFermi' : 1}
args['times'] = np.linspace(0.0, 50.0, 500.0)
args['A'] = 0.2
thetas = np.linspace(0,np.pi/2,numSample)
colors = ma.getColors(numSample)
function = []
for index, theta in enumerate(thetas):
args['kpoint'] = (np.cos(theta), np.sin(theta))
ax = axs[1]
#label = r'$A = $ %2.1f eV'% (A)
ax.plot(args['times'], HCoeff(args['times'],args), color=colors[index])
result, proj0, proj1 = excitation(args)
ax = axs[0]
#title = r'k$_x$ = %2.1f, k$_y$ = %2.1f'% (k[0],k[1])
ax.plot(result.times, proj1, '-', color=colors[index])
function.append(proj1[-1])
cut = [0]
specialKPoints = [r'$M$', r'$\Gamma$', r'$K$', r'$\Gamma$']
for i in range(667, 38, -37):
kpath.append(i)
cut.append(len(kpath))
for i in range(36, 421, 35):
kpath.append(i + 1)
kpath.append(i)
cut.append(len(kpath))
for i in range(421, 649, 38):
kpath.append(i)
kpath.append(i + 1)
cut.append(len(kpath))
kpath = np.array(kpath) - 1
c = ma.getColors(exe.shape[2] - h**o + 1, cmap='brg')
evolvingBands = range(0, h**o + 9)
x = np.arange(kpath.shape[0])
excited = np.abs(exe[1, kpath, :] - exe[0, kpath, :])
norm = 2.0 / np.max(exe[:, kpath, :] - exe[0, kpath, :])
eigenvalue = eigen[0, kpath, :]
print eigenvalue.shape, excited.shape, x.shape
line = []
scatter = []
for band in evolvingBands:
if band < h**o:
part = excited[:, band]
s = ax.fill_between(x,
@author: cl-iop
"""
import numpy as np
import matplotlib.pyplot as plt
import pyramids.io.result as dp
import pyramids.plot.setting as ma
import os
fig, axs = plt.subplots(2,1,sharex=False,sharey=False,figsize=(6,8))
SaveName = __file__.split('/')[-1].split('.')[0]
startStep = 10
c = ma.getColors(4)
scandir = ('x','y')
for idir, direct in enumerate(scandir):
os.chdir(direct)
ax = axs[0]
time, T, E_ks, E_tot, Vol, P = dp.getEnergyTemperaturePressure()
dipoles = dp.getDipole()
dipoles[:,idir] = (dipoles[:,idir] - dipoles[0,idir]) #* np.exp(-0.01*time)
ax.plot(time,dipoles[:,idir],label=direct)
ax.grid(which=u'major',axis='x')
ax.grid(which=u'major',axis='y')
ax = axs[1]
N = dipoles.shape[0]
timeStep = (time[-1] - time[0]) / (N-1)
SaveName = __file__.split('/')[-1].split('.')[0]
from matplotlib import pyplot as plt
import numpy as np
fig, ax = plt.subplots(1,1,sharex=True,sharey=False,figsize=(8,6))
from pyramids.plot.PlotUtility import scanFolder
data = scanFolder(plotEigenvalues)
y0 = data[0][1].flatten()
numBand = y0.shape[0]
x = []
y = []
for x1,y1,h**o in data:
x.append(x1)
y.append(y1.flatten()-y0)
y = np.array(y)
plotedBand = h**o + 0
colors = ma.getColors(plotedBand)
for i in range(plotedBand):
ax.plot(x,y[:,i],'-o',color=colors[i],label=str(i)+' + '+str(y0[i]))
args = ma.getPropertyFromPosition(xlabel=r'$\varepsilon(a.u.)$',
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)
#
#Excitation
TotalStep,nkstot,npol,nbnd,wk,norm = qeout.Readnorm()
h**o=qeout.GetHomo()
time=np.arange(TotalStep)*edt
#画哪些k点的激发
ksample=np.arange(nkstot)
Nksample=ksample.shape[0]
exciteelectron=np.zeros((TotalStep,Nksample))
hole=np.zeros((TotalStep,Nksample)) #if only "=", change hole will chenge exciteelectron
#目前程序还未只是SOC，所以npol=1，不用考虑太多
colors = setfig.getColors(Nksample)
for ik in ksample:
exciteelectron[:,ik]=norm[:,ik,h**o:nbnd].sum(axis=1) #*wk[ik]
#py index from 0, for ik ,so sum(axis=1 not 2)
#h**o:nbnd
hole[:,ik]=(norm[0,ik,0:h**o]-norm[:,ik,0:h**o]).sum(axis=1) #*wk[ik] #py index from 0
axs[1,0].plot(time,exciteelectron[:,ik],label='Kpoint'+str(ksample[ik]),color=colors[ik])
#axs[1].plot(time,hole[:,ik])
axs[1,0].legend()
kargs=setfig.getPropertyFromPosition(ylabel=r'Excitation',
xlabel='Time(fs)',
title='(c) Excitation at each kpoint',
#hline=[0.0],
xlimits=[0,None],
"""
Created on Mon Dec 19 11:58:44 2016
@author: cl-iop
"""
from graphene import *
import pyramids.plot.setting as ma
import matplotlib.pyplot as plt
fig, axs = plt.subplots(2,1,sharex=False,sharey=False,figsize=(12,10))
k = (0.0,1.0) #(np.sqrt(0.5),np.sqrt(0.5))
numSample = 20
thetas = np.linspace(0,np.pi/2,numSample)
intensities = 0.2*np.sin(thetas)
colors = ma.getColors(intensities.shape[0])
args={'t0':20.0,'sigma': 8.0, 'omega':2.0, 'phi':0.0, 'parity':1, 'vFermi' : 1}
args['times'] = np.linspace(0.0, 50.0, 500.0)
args['kpoint'] = k
function = []
for index, A in enumerate(intensities):
ax = axs[1]
args['A'] = A
#label = r'$A = $ %2.1f eV'% (A)
ax.plot(args['times'], HCoeff(args['times'],args), color=colors[index])
result, proj0, proj1 = excitation(args)
ax = axs[0]
zoomV = EELS.zoomV if zoomX is not None: zoomX[0] = Q[0] v = [mainV, zoomV] x = [mainX, zoomX] y = [mainY, zoomY] nContour = 400 #Q.shape[0] * 5 cmap = 'jet' ax = axs[0] ax1 = axs[1] c = ma.getColors(Q.shape[0]) #print np.sqrt(np.abs(np.log(Q))) print atoms.cell #Q = np.array(Q) latticeVector = np.linalg.norm(atoms.cell[0,:])/(2*np.pi) print latticeVector dispersion = Q*np.sqrt(np.abs(np.log(Q*latticeVector))) print dispersion maxE = np.ones(Q.shape[0])*3.5*dispersion + 0.3 def d1dispersion(q,A,a=1): return A*q*np.sqrt(np.abs(np.log(q*a)))
fig, ax = plt.subplots(1,1,sharex=False,sharey=True,figsize=(8,6))
SaveName = __file__.split('/')[-1].split('.')[0]
kpath = ls.kpath
cut = ls.cut
print kpath
specialKPoints = ls.specialKPoints
x = ls.x
h**o = dP.getHomo()
evolvingBands = range(0, h**o + 7)
time, exe = dP.getProjectedPartition()
time, eigen = dP.getAdiabaticEigenvalue()
colors = ma.getColors(5,cmap='gnuplot')
#for index, step in enumerate(ls.selectedTimeStep):
excited = np.abs(exe[0,kpath,:] - exe[0,kpath,:])
norm = ls.norm/np.max(exe[:,kpath,:] - exe[0,kpath,:])
eigenvalue = eigen[0,kpath,:]
line = []
scatter = []
for i in evolvingBands:
if i < h**o:
part = excited[:,i]
if ls.drawfill:
s = ax.fill_between(x, eigenvalue[:,i] - norm*part,
eigenvalue[:,i] + norm*part,
lw=0.0,color='b',alpha=0.7)
else:
from pyramids.plot.PlotUtility import scanFolder
import pyramids.plot.setting as ma
import pyramids.process.struct as pps
#--------------------------------------------------------------------------------------------
def action(index,folder):
dataCurFolder = []
dataCurFolder.append([index, folder])
dataCurFolder.append(dp.getEnergyTemperaturePressure(ave=True))
dataCurFolder.append(dp.getEField())
return dataCurFolder
#--------------------------------------------------------------------------------------------
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)
#--------------------------------------------------------------------------------------------
#/usr/bin/python """ Created on Fri Jul 22 09:54:42 2016 @author: Chao (Charles) Lian @email: [email protected] """ import matplotlib.pyplot as plt from pyramids.io.result import getTDEig from pyramids.plot.setting import getPropertyFromPosition from pyramids.plot.setting import setProperty from pyramids.plot.setting import getColors import numpy as np from mpl_toolkits.mplot3d import Axes3D import os colors = getColors(5) #ti = 3; tf = 1000; #selectTime =range(ti,tf) # initial timestep and final timestep #selectBand = [0]# initial band and final band selectKpts = [0] #[0,1,4,6,7]# initial band and final band numK = len(selectKpts) fig, axs = plt.subplots(1, len(selectKpts), sharex=True, figsize=(8, 6)) #print eig.shape, time.shape, #for diri, directory in enumerate(['TDDFT','BOMD']): #os.chdir(directory) time, eig = getTDEig() #print time.shape print eig for k in selectKpts:
from pyramids.plot.PlotUtility import scanFolder
data = scanFolder(plotEigenvalues)
y0 = data[0][1].flatten()
numBand = y0.shape[0]
x = []
y = []
for x1, y1, h**o in data:
x.append(x1)
y.append(y1.flatten() - y0)
y = np.array(y)
plotedBand = h**o + 0
colors = ma.getColors(plotedBand)
for i in range(plotedBand):
ax.plot(x,
y[:, i],
'-o',
color=colors[i],
label=str(i) + ' + ' + str(y0[i]))
args = ma.getPropertyFromPosition(xlabel=r'$\varepsilon(a.u.)$',
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)
exEnergy = 1
def action(index, folder):
#------------------------------------------------------------------------------
timeEn, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure()
deltaE = (E_tot[2:,] - E_tot[2])
return [(index, folder), (timeEn[2:], deltaE, T[2:])]
#------------------------------------------------------------------------------
fig, axs = plt.subplots(2,1,sharex=True,sharey=False,figsize=(6,8))
SaveName = __file__.split('/')[-1].split('.')[0]
data = scanFolder(action)
#print data[-1][0][0]
chenc = ma.getColors(5)[1:-1]
#print data
maxElectrons = []
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],
"""
Created on Mon Dec 19 11:58:44 2016
@author: cl-iop
"""
from graphene import *
import pyramids.plot.setting as ma
import matplotlib.pyplot as plt
fig, axs = plt.subplots(2, 1, sharex=False, sharey=False, figsize=(12, 10))
k = (0.0, 1.0) #(np.sqrt(0.5),np.sqrt(0.5))
numSample = 20
thetas = np.linspace(0, np.pi / 2, numSample)
intensities = 0.2 * np.sin(thetas)
colors = ma.getColors(intensities.shape[0])
args = {
't0': 20.0,
'sigma': 8.0,
'omega': 2.0,
'phi': 0.0,
'parity': 1,
'vFermi': 1
}
args['times'] = np.linspace(0.0, 50.0, 500.0)
args['kpoint'] = k
function = []
for index, A in enumerate(intensities):
timeEl, exe = dP.getExcitedElectrons()
exe -= exe[0]
timeEn, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure()
deltaE = (E_ks[2:, ] - E_ks[2])
return [(index, folder), (timeEf, eField), (timeEl, exe), (timeEn, deltaE)]
#------------------------------------------------------------------------------
fig, axs = plt.subplots(1, 2, sharex=True, sharey=False, figsize=(10, 6))
SaveName = __file__.split('/')[-1].split('.')[0]
data = scanFolder(action)
#print data[-1][0][0]
c = ma.getColors(data[-1][0][0] + 1)
maxElectrons = []
maxEnergies = []
minEnergies = []
for [(index, folder), (timeEf, eField), (timeEl, exe),
(timeEn, deltaE)] in data:
#ax = axs[efield]
#ax.plot(timeEf,eField[:,2], c=c[index],
# label=folder,lw=2,alpha=0.8)
ax = axs[exElectron]
ax.plot(timeEl,
exe,
'-',
alpha=0.8,
#!/usr/bin/python
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
#------------------------------------------------------------------------------
time, exe = dP.getProjectedPartition()
time, eigen = dP.getAdiabaticEigenvalue()
#print eigen[:,1,:]
#h**o = dP.getHomo()
#print h**o
print exe.shape, eigen.shape
c = ma.getColors(exe.shape[2], cmap='brg')
norm = 50.0#/np.max(exe[:,:,:] - exe[0,:,:])
#print norm
kpts = [0]
for kpt in kpts:
fig, ax = plt.subplots(1,1,sharex=True,sharey=False,figsize=(8,6))
SaveName = __file__.split('/')[-1].split('.')[0] + str(kpt)
h**o = 0
for i, band in enumerate(eigen[0,kpt,:]):
#print band
if band < 0:
h**o = i
evolvingBands = range(0, h**o+40)
X, Y = np.meshgrid(time,eigen[0,kpt,evolvingBands])
Z = np.transpose(exe[0,kpt,evolvingBands] - exe[:,kpt,evolvingBands])
@author: cl-iop
"""
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=['-','--',':']
#!/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=(8,6))
SaveName = __file__.split('/')[-1].split('.')[0]
c = ma.getColors(2,cmap='brg')
#------------------------------------------------------------------------------
Time, exe = dP.getExcitedElectrons()
ax = axs[0]
ax.plot(Time,exe - exe[0],'.',alpha=0.8,c='b',markerfacecolor='w',lw=2,label='Excited Electrons')
kargs=ma.getPropertyFromPosition(ylabel=r'n(e)',
title='',
xlimits=None,)
ma.setProperty(ax,**kargs)
#------------------------------------------------------------------------------
ax = axs[1]
time, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure()
deltaE = (E_ks[2:] - E_ks[2])
deltaEt = (E_tot[2:] - E_tot[2])
#ax.plot(time[2:], deltaE,'.',c='r', lw=2, alpha=1,label='Excitation Energy')
ax.plot(time[2:], deltaEt,'.',c='g', lw=2, alpha=1,label='Excitation Energy')
kargs=ma.getPropertyFromPosition(ylabel=r'E(eV)',xlabel = r'Time(fs)',
title='')
ma.setProperty(ax,**kargs)
#------------------------------------------------------------------------------
import pyramids.process.struct as pps
#--------------------------------------------------------------------------------------------
def action(index, folder):
dataCurFolder = []
dataCurFolder.append([index, folder])
dataCurFolder.append(dp.getEnergyTemperaturePressure(ave=True))
dataCurFolder.append(dp.getEField())
return dataCurFolder
#--------------------------------------------------------------------------------------------
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:
return [(index, folder), (timeEf, eField), (timeEl, exe),
(timeEn[2:], deltaE)]
#------------------------------------------------------------------------------
fig, axs = plt.subplots(2, 1, sharex=True, sharey=False, figsize=(6, 8))
SaveName = __file__.split('/')[-1].split('.')[0]
#pimdData = getPIMDdata()
#axs[-1].plot(pimdData[:,0],pimdData[:,4])
data = scanFolder(action)
rows = data[-1][0][0] + 1
c = ma.getColors(rows)
exSteps = min([line[2][0].shape[0] for line in data])
exAve = np.zeros(exSteps)
enSteps = min([line[3][0].shape[0] for line in data])
enAve = np.zeros(enSteps)
for [(index, folder), (timeEf, eField), (timeEl, exe),
(timeEn, deltaE)] in data:
exAve += exe[:exSteps] / rows
enAve += deltaE[:enSteps] / rows
axs[0].plot(timeEl[:exSteps], exAve, label='4 Beads')
axs[1].plot(timeEn[:enSteps], enAve, label='4 Beads')
import os
print os.chdir('../../Beads=1/E=0.10/1')
zoomX = EELS.zoomX
zoomY = EELS.zoomY
zoomV = EELS.zoomV
if zoomX is not None:
zoomX[0] = Q[0]
v = [mainV, zoomV]
x = [mainX, zoomX]
y = [mainY, zoomY]
nContour = 400 #Q.shape[0] * 5
cmap = 'jet'
ax = axs[0]
ax1 = axs[1]
c = ma.getColors(Q.shape[0])
#print np.sqrt(np.abs(np.log(Q)))
print atoms.cell
#Q = np.array(Q)
latticeVector = np.linalg.norm(atoms.cell[0, :]) / (2 * np.pi)
print latticeVector
dispersion = Q * np.sqrt(np.abs(np.log(Q * latticeVector)))
print dispersion
maxE = np.ones(Q.shape[0]) * 3.5 * dispersion + 0.3
def d1dispersion(q, A, a=1):
return A * q * np.sqrt(np.abs(np.log(q * a)))
fig, ax = plt.subplots(1, 1, sharex=False, sharey=True, figsize=(8, 6))
SaveName = __file__.split('/')[-1].split('.')[0]
kpath = ls.kpath
cut = ls.cut
print kpath
specialKPoints = ls.specialKPoints
x = ls.x
h**o = dP.getHomo()
evolvingBands = range(0, h**o + 7)
time, exe = dP.getProjectedPartition()
time, eigen = dP.getAdiabaticEigenvalue()
colors = ma.getColors(5, cmap='gnuplot')
#for index, step in enumerate(ls.selectedTimeStep):
excited = np.abs(exe[0, kpath, :] - exe[0, kpath, :])
norm = ls.norm / np.max(exe[:, kpath, :] - exe[0, kpath, :])
eigenvalue = eigen[0, kpath, :]
line = []
scatter = []
for i in evolvingBands:
if i < h**o:
part = excited[:, i]
if ls.drawfill:
s = ax.fill_between(x,
eigenvalue[:, i] - norm * part,
eigenvalue[:, i] + norm * part,
lw=0.0,
