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)
timeEl, exe = dP.getExcitedElectrons()
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,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,
import pyramids.plot.setting as ma
from pyramids.plot.PlotUtility import scanFolder
def getTime(index, folder):
#------------------------------------------------------------------------------
time = dP.getTime()
return index, folder,time
def getEnergy(index,folder):
time, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure(ave=True)
return index, folder, E_ks
#------------------------------------------------------------------------------
fig, axs = plt.subplots(1,2,sharex=False,sharey=False,figsize=(10,6))
SaveName = __file__.split('/')[-1].split('.')[0]
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 = 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')
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('.')
for ufolder in os.listdir('.'):
if os.path.isdir(ufolder):
os.chdir(ufolder)
ax = ax
data = scanFolder(getEnergy)
ref = np.load('ref.npy')
deltaEnergy = np.array([
np.average(np.abs(energy - ref)) for index, folder, energy in data
])
#xticks = [ for index, folder, energy in data]
xdata = np.array([int(folder) for index, folder, energy in data])
ax.semilogy(xdata,
deltaEnergy,
'o-',
ms=10,
lw=3,
label=ufolder,
alpha=0.8,
mew=3)
#from scipy.optimize import curve_fit
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]
#!/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
#-----------------------------------------------------------------------------
def action(index, folder):
ls = ['-', '--', '-.', '-:']
pu.plotExcitation(axs[0])
pu.plotTotalEnergy(axs[1])
#------------------------------------------------------------------------------
if __name__ == '__main__':
fig, axs = plt.subplots(1, 2, sharex=True, sharey=False, figsize=(10, 6))
#axs = axs.flatten()
SaveName = __file__.split('/')[-1].split('.')[0]
c = ['b', 'r', 'g', 'y']
plt.style.use('ggplot')
#action(1,'')
from pyramids.plot.PlotUtility import scanFolder
scanFolder(action)
plt.tight_layout()
if False:
for save_type in ['.pdf', '.png']:
filename = SaveName + save_type
plt.savefig(filename, dpi=600)
#--------------------------------------------------------------------------------------------
def action(index, folder):
dataCurFolder = []
dataCurFolder.append([index, folder])
dp.getTrajactory()
dataCurFolder.append(pps.calculateRMSD())
dataCurFolder.append(dp.getEnergyTemperaturePressure())
return dataCurFolder
M = 28.08
R = 8.3144598
#--------------------------------------------------------------------------------------------
fig, axs = plt.subplots(2, 1, sharex=True, sharey=False, figsize=(6, 8)) #
data = scanFolder(action,
folders=['0.0025', '0.0035', '0.0045', '0.0055', '0.0065'])
c = ma.getColors(len(data))
melt_v = []
for line in data:
index, folder = line[0]
ax = axs[0]
ax.plot(line[1][0], line[1][1], lw=3, label=folder, c=c[index])
selectedstep = 5000
t, v = float(folder) / 2.0, line[1][1][selectedstep] / line[1][0][
selectedstep] * 1E3
#melt_v.append(t, v)
if index == 0:
vt = np.sqrt(3 * R * 300 / (M * 1E-3)) * 1E-2
ax.plot(line[1][0], line[1][0] * vt / 1E3)
#!/usr/bin/python
import numpy as np
import matplotlib.pyplot as plt
import pyramids.io.result as dP
import pyramids.plot.setting as ma
#-----------------------------------------------------------------------------
def getEnergy(index,folder):
time, T, E_ks, E_tot, Vol, P = dP.getEnergyTemperaturePressure(ave=True)
return index, folder, E_ks
from pyramids.plot.PlotUtility import scanFolder
data = scanFolder(getEnergy)
ref = np.load('ref.npy')
deltaEnergy = np.array([np.average(np.abs(energy - ref)) for index, folder, energy in data])
xticks = [float(folder) for index, folder, energy in data]
import pandas as pd
data = pd.DataFrame(data={'x':xticks, 'y':deltaEnergy})
SaveName = __file__.split('/')[-1].split('.')[0]
data.to_csv(SaveName+'.csv')
from pyramids.io.result import getHomo
eigenvalues = dp.readEigFile()
x = float(folder)
y = eigenvalues
plotedBand = getHomo()
return x, y, plotedBand
import pyramids.plot.setting as ma
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,
#!/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
#-----------------------------------------------------------------------------
def action(index,folder):
ls = ['-','--','-.','-:']
import pyramids.plot.PlotUtility as pu
pu.plotEField(axs[0][0],label=folder)
pu.plotTotalEnergy(axs[1][0],label=folder)
pu.plotRMSD(axs[0][1],label=folder)
pu.plotTemperature(axs[1][1],label=folder)
#------------------------------------------------------------------------------
if __name__ == '__main__':
fig, axs = plt.subplots(2,2,sharex=True,sharey=False,figsize=(10,6))
#axs = axs.flatten()
SaveName = __file__.split('/')[-1].split('.')[0]
c = ['b','r','g','y']
plt.style.use('ggplot')
#action(1,'')
from pyramids.plot.PlotUtility import scanFolder
scanFolder(action)
plt.tight_layout()
if False:
for save_type in ['.pdf','.png']:
filename = SaveName + save_type
plt.savefig(filename,dpi=600)
import pyramids.io.result as dp
from pyramids.io.result import getHomo
eigenvalues = dp.readEigFile()
x = float(folder)
y = eigenvalues
plotedBand = getHomo()
return x,y,plotedBand
import pyramids.plot.setting as ma
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]))
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)
fig, axsall = plt.subplots(2,3,sharex='row',sharey='row',figsize=(15,10))
print axsall
SaveName = __file__.split('/')[-1].split('.')[0]
scanFolder(case)
plt.tight_layout()
for save_type in ['.pdf','.eps']:
filename = SaveName + save_type
plt.savefig(filename,dpi=800)
