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 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 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 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 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)
#!/usr/bin/python
import numpy as np
from matplotlib import pyplot as plt
import pyramids.io.result as dp
import pyramids.plot.setting as ma
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]