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 action(index, folder):
dataCurFolder = []
dataCurFolder.append([index, folder])
dp.getTrajactory()
dataCurFolder.append(pps.calculateRMSD())
dataCurFolder.append(dp.getEnergyTemperaturePressure())
return dataCurFolder
def action(index,folder): dataCurFolder = [] dataCurFolder.append([index, folder]) dp.getTrajactory() dataCurFolder.append(pps.calculateRMSD()) dataCurFolder.append(dp.getEnergyTemperaturePressure()) return dataCurFolder
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 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 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 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)
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)
omega = np.linspace(0, 70, 1000)
absorbance = np.abs([
np.imag(io * np.sum(
np.exp(1j * io * np.arange(N) * timeStep) * dipoles[:, idir]))
import pyramids.process.struct as pps
fig, axs = plt.subplots(2,1,sharex=True,sharey=False,figsize=(8,6))#
#--------------------------------------------------------------------------------------------
ax = axs[0]
dp.getTrajactory()
time, distance = pps.calculateRMSD()
ax.plot(time, distance, lw=3)
kargs=ma.getPropertyFromPosition(xlabel='Time (fs)', ylabel=r'$\langle u \rangle^\frac{1}{2}$ ($\AA$)',
title='RMSD')
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()
ax.plot(time, T, lw=3)
kargs=ma.getPropertyFromPosition(xlabel='Time (fs)', ylabel='T (K)',
title='Temperature')
ma.setProperty(ax,**kargs)
#ax.ticklabel_format(style='sci',axis='y',scilimits=[0,0])
#--------------------------------------------------------------------------------------------
#plt.style.use('ggplot')
plt.tight_layout()
SaveName = __file__.split('/')[-1].split('.')[0]
for save_type in ['.pdf','.png']:
filename = SaveName + save_type
plt.savefig(filename,dpi=800)
# -*- coding: utf-8 -*-
"""
Created on Thu Dec 22 08:43:43 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
from pyramids.plot.PlotUtility import scanFolder
import os
os.chdir('Demo/Comp')
time, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure(ave=True)
ref = np.load('ref.npy')
fig, ax = plt.subplots(1, 1, sharex=False, sharey=False, figsize=(8, 6))
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
axin = inset_axes(ax, width=2.5, height=2, loc=1)
axin.plot(
time,
E_ks,
'-',
lw=3,
)
axin.plot(
time,
ref,
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:])]
# -*- coding: utf-8 -*-
"""
Created on Thu Dec 22 08:43:43 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
from pyramids.plot.PlotUtility import scanFolder
import os
os.chdir('Demo/Comp')
time, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure(ave=True)
ref = np.load('ref.npy')
fig, ax = plt.subplots(1,1,sharex=False,sharey=False,figsize=(8,6))
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
axin = inset_axes(ax, width=2.5, height=2, loc=1)
axin.plot(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)
ax =axs[0]
for eFieldType in ('ExternalElectricField','TD.GaugeField'):
print eFieldType
os.chdir(eFieldType)
efields = os.popen('ls -d [0-9]*').readlines()
nDir = len(efields)
Efield = np.zeros([nDir])
energy = np.zeros([nDir])
dipoles = np.zeros([nDir,3])
dipolesIon = np.zeros([nDir,3])
for index, efield in enumerate(efields):
os.chdir(efield[:-1])
Efield[index] = float(efield[:-1])*VA
energy[index] = dp.getEnergyTemperaturePressure()[3][-1]
if eFieldType == 'TD.GaugeField':
dipolesIon[index,:] = dp.getIonicPolarization()[-1]
dipoles[index,:] = dp.getElectronPolarization()[-1]
else:
dipoles[index,:] = dp.getDipole()[1][-1]
os.chdir('..')
print dipoles
print dipolesIon
print dipoles + dipolesIon
#print (energy[-1]-energy[0])/(Efield[-1]-Efield[0])
axs[0].plot(Efield,energy ,'-o',label=eFieldType)
for i, direction in enumerate(('x','y','z')):
axs[1].plot(Efield,(dipoles + dipolesIon)[:,i] ,'-o',label=eFieldType+' '+direction)
os.chdir('..')
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 plotAllEnergies(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) ax.plot(time, E_ks - E_ks[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 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
def getEnergy(index,folder): time, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure(ave=True) return index, folder, E_ks
def action(index, folder):
timeEn, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure()
deltaE = E_ks[start:,] - E_ks[2]
atoms = xv_to_atoms('siesta.XV')
return index, folder, timeEn, deltaE, atoms
