def showVAF(self):
if self.file1.isGoodFile():
try:
x = linspace(self.ni, self.nf, len(self.vacf))
self.GraphVAF = Graph.graphic(x,
self.vacf,
'step',
"VACF",
average=False,
name=self.file1.getNameFile() +
" VACF")
self.GraphVAF.show()
except:
self.vacf = Analysis.Correlation(
self.file1.getVel()).getCorrelationFunction(normalize=True)
x = linspace(self.ni, self.nf, len(self.vacf))
self.GraphVAF = Graph.graphic(x,
self.vacf,
'step',
"VACF",
average=False,
name=self.file1.getNameFile() +
" VACF")
self.GraphVAF.show()
else:
self.showError("Your NetCDF file is not correct")
def displayGraph(self):
res = self.sbres.value()
pdos = Analysis.DOS(self.VACF, res, self.dtion)
y = pdos.getDOS()
x = pdos.getFrequencies()
try:
self.GraphDOS.update(x,
y,
'E (meV)',
"Phonons DOS (1/meV)",
name=self.name,
adjust=True)
except:
self.GraphDOS = Graph.graphic(x,
y,
'E (meV)',
"Phonons DOS (1/meV)",
average=False,
adjust=True,
name=self.name)
self.connect(self.GraphDOS, QtCore.SIGNAL("myCustomizedSignal()"),
self.close)
self.GraphDOS.show()
if self.checkbox.isChecked():
self.addSprectum()
def GraphOutput(self):
#The purpose of this fonction is to create or update
#the graph of the output file
if self.checkbox1.isChecked():
boxData = self.getBoxData()
xlbl = boxData[0]
ylbl = boxData[1]
x = boxData[2]
y = boxData[3]
if (len(x) != len(y) or (len(x) == 0 or len(y) == 0)):
return
try:
self.graph.update(x,
y,
xlbl,
ylbl,
name=str(self.file2.getNameFile()) + ' ' +
ylbl)
except:
self.graph = Graph.graphic(x,
y,
xlbl,
ylbl,
average=False,
name=str(self.file2.getNameFile()) +
' ' + ylbl)
self.connect(self.graph, QtCore.SIGNAL("myCustomizedSignal()"),
self.closeGraph)
self.graph.show()
if self.birchCheckbox.isChecked():
self.showBirch()
else:
self.closeGraph()
def displayGraph(self):
atom = self.CBox1.currentIndex() + 1
self.MeanSquaredDeplacement = Analysis.MSD(self.file, atom)
x = self.MeanSquaredDeplacement.getX()
y = self.MeanSquaredDeplacement.getMSD()
try:
self.graphMSD.update(x,
y,
'step',
"Mean squared deplacement",
name=self.name)
self.graphMSD.addPlot(x, linspace(1, 1, len(x)))
self.graphMSD.show()
except:
self.graphMSD = Graph.graphic(x,
y,
'step',
"Mean squared deplacement",
average=False,
name=self.name)
self.connect(self.graphMSD, QtCore.SIGNAL("myCustomizedSignal()"),
self.close)
self.graphMSD.show()
def showVolume(self):
if self.file1.isGoodFile():
x = linspace(self.ni,self.nf-1,self.nf-self.ni)
vol = self.file1.getVol() * self.units['Volume'][1]
self.GraphVolume = Graph.graphic(x,vol,'Step',"Volume ("+str(self.units['Volume'][0])+")",\
name = self.file1.getNameFile() +" Volume")
self.GraphVolume.show()
else:
self.showError("Your NetCDF file is not correct")
def showStress(self):
if self.file1.isGoodFile():
x = linspace(self.ni,self.nf-1,self.nf-self.ni)# Temporarily !!!
st =self.file1.getStress()
self.GraphStress= Graph.graphic(x,st * self.units['Pressure'][1],'Step', "Stress ("+str(self.units['Pressure'][0])+")",\
average=False,name = self.file1.getNameFile() +" Stress")
self.GraphStress.addLegend([r'$\sigma_1$',r'$\sigma_2$',r'$\sigma_3$',r'$\sigma_4$',r'$\sigma_5$',r'$\sigma_6$'])
self.GraphStress.show()
def showPressure(self):
if self.file1.isGoodFile():
x = linspace(self.ni,self.nf-1,self.nf-self.ni)# Temporarily !!!
pressure = self.file1.getPress() * self.units['Pressure'][1]
self.GraphPressure = Graph.graphic(x,pressure,'Step',"Pressure ("+str(self.units['Pressure'][0])+")",\
name = self.file1.getNameFile() +" Pressure")
self.GraphPressure.show()
else:
self.showError("Your NetCDF file is not correct")
def showTemperature(self):
if self.file1.isGoodFile():
x = linspace(self.ni,self.nf-1,self.nf-self.ni)# Temporarily !!!
temp = self.file1.getTemp() - self.units['Temperature'][1]
self.GraphTemperature = Graph.graphic(x,temp,'Step',"Temperature ("+str(self.units['Temperature'][0])+")",\
name = self.file1.getNameFile() +" Temperature")
self.GraphTemperature.show()
else:
self.showError("Your NetCDF file is not correct")
def showKineticEnergy(self):
if self.file1.isGoodFile():
x = linspace(self.ni,self.nf-1,self.nf-self.ni)# Temporarily !!!
eKin = self.file1.getE_kin() * self.units['Energy'][1]
self.GraphKineticEnergy = Graph.graphic(x,eKin,'Step',"Kinetic Energy ("+str(self.units['Energy'][0])+")",\
name = self.file1.getNameFile() +" kinetic Energy")
self.GraphKineticEnergy.show()
else:
self.showError("Your NetCDF file is not correct")
def showAngles(self):
if self.file1.isGoodFile():
x = linspace(self.ni,self.nf-1,self.nf-self.ni)
angles = self.file1.getAngles() * self.units['Angle'][1]
self.GraphAngles = Graph.graphic(x,angles,'Step',"Angles ("+str(self.units['Angle'][0])+")",\
average=False,name = self.file1.getNameFile() +" Angles")
self.GraphAngles.addLegend([r'$\alpha$',r'$\beta$',r'$\gamma$'])
self.GraphAngles.show()
else:
self.showError("Your NetCDF file is not correct")
def showAcell(self):
if self.file1.isGoodFile():
x = linspace(self.ni,self.nf-1,self.nf-self.ni)
acell = self.file1.getAcell() * self.units['Distance'][1]
self.GraphAcell = Graph.graphic(x,acell,'Step',"Acell ("+str(self.units['Distance'][0])+")",\
average=False,name = self.file1.getNameFile() +" Distance")
self.GraphAcell.addLegend([r'$a$',r'$b$',r'$c$'])
self.GraphAcell.show()
else:
self.showError("Your NetCDF file is not correct")
def showPotentialEnergy(self):
if self.file1.isGoodFile():
x = linspace(self.ni,self.nf-1,self.nf-self.ni)# Temporarily !!!
epot = self.file1.getE_pot() * self.units['Energy'][1]
self.file1.getNameFile()
self.GraphPotentialEnergy = Graph.graphic(x,epot,'Step',"Potential Energy ("+str(self.units['Energy'][0])+")",\
name = self.file1.getNameFile()+" Potential Energy")
self.GraphPotentialEnergy.show()
else:
self.showError("Your NetCDF file is not correct")
def Graphics(self):
mode1 = self.sbm.currentText()
if mode1 == 'RDF':
typat = self.file.getTypat()
ntypat = max(typat)
if ntypat == 1:
atom1 = 1
atom2 = 1
elif ntypat >= 2:
atom1 = self.CBox1.currentIndex()
atom2 = self.CBox2.currentIndex()
box = self.sbrm.value()
dr = self.sbdr.value()
step = self.sbStep.value()
if self.sbdec.isChecked():
self.RadialDistrib = Analysis.RDF(self.file, 1, atom1, atom2,
box, dr, step)
data = self.RadialDistrib.getDATA()
x = self.RadialDistrib.getR()
for i in range(1, len(typat) - 1):
self.Deconvolution = Analysis.DEC(self.file, i, atom1,
atom2, data, box, dr,
step)
y = self.Deconvolution.getNEI()
try:
self.GraphDEC.addGraph(x, y, False)
except:
self.GraphDEC = Graph.graphic(x,
y,
'R (Bohr)',
"Radial Distribution",
average=False,
name=self.name)
self.GraphDEC.show()
else:
self.RadialDistrib = Analysis.RDF(self.file, 0, atom1, atom2,
box, dr, step)
x = self.RadialDistrib.getR()
y = self.RadialDistrib.getRDF()
try:
self.GraphRDF.update(x,
y,
'R (Bohr)',
"Radial Distribution",
name=self.name)
self.GraphRDF.addPlot(x, linspace(1, 1, len(x)))
except:
self.GraphRDF = Graph.graphic(x,
y,
'R (Bohr)',
"Radial Distribution",
average=False,
name=self.name)
self.GraphRDF.addPlot(x, linspace(1, 1, len(x)))
#self.connect(self.GraphRDF, QtCore.SIGNAL("myCustomizedSignal()"), self.close)
self.GraphRDF.show()
def close(self):
self.hide()
try:
del self.GraphRDF
except:
pass
y = self.RadialDistrib.getINT()
try:
self.GraphINT.update(x,
y,
'R (Bohr)',
"Integral of the Radial Distribution",
name=self.name)
except:
self.GraphINT = Graph.graphic(
x,
y,
'R (Bohr)',
"Integral of the Radial Distribution",
average=False,
name=self.name)
#self.connect(self.GraphRDF, QtCore.SIGNAL("myCustomizedSignal()"), self.close)
self.GraphINT.show()
def close(self):
self.hide()
try:
del self.GraphINT
except:
pass
elif mode1 == 'ADF':
neib = self.sbn.value()
typat = self.file.getTypat()
ntypat = max(typat)
if ntypat == 1:
atom1 = 1
atom2 = 1
elif ntypat >= 2:
atom1 = self.CBox1.currentIndex()
atom2 = self.CBox2.currentIndex()
dtheta = self.sbdt.value()
step = self.sbStep.value()
self.AngularDistrib = Analysis.ADF(neib, self.file, atom1, atom2,
dtheta, step)
x = self.AngularDistrib.getTheta()
y = self.AngularDistrib.getADF()
try:
self.GraphADF.update(x,
y,
'Theta (degres)',
"Angular Distribution",
name=self.name)
except:
self.GraphADF = Graph.graphic(x,
y,
'Theta (degres)',
"Angular Distribution",
average=False,
name=self.name)
#self.connect(self.GraphRDF, QtCore.SIGNAL("myCustomizedSignal()"), self.close)
self.GraphADF.show()
def close(self):
self.hide()
try:
del self.GraphADF
except:
pass
elif mode1 == 'NDF':
neib = self.sbn.value()
typat = self.file.getTypat()
ntypat = max(typat)
if ntypat == 1:
atom1 = 1
atom2 = 1
elif ntypat >= 2:
atom1 = self.CBox1.currentIndex()
atom2 = self.CBox2.currentIndex()
dr = self.sbdr.value()
step = self.sbStep.value()
self.NeighborDistrib = Analysis.NDF(neib, self.file, atom1, atom2,
dr, step)
x = self.NeighborDistrib.getR()
y = self.NeighborDistrib.getNDF()
try:
self.GraphNDF.update(x,
y,
'R (Bohr)',
"Neighbor distance",
name=self.name)
except:
self.GraphNDF = Graph.graphic(x,
y,
'R (Bohr)',
"Neighbor distance",
average=False,
name=self.name)
#self.connect(self.GraphRDF, QtCore.SIGNAL("myCustomizedSignal()"), self.close)
self.GraphNDF.show()
def close(self):
self.hide()
try:
del self.GraphNDF
except:
pass
elif mode1 == 'Proba':
neib = self.sbn.value()
typat = self.file.getTypat()
ntypat = max(typat)
if ntypat == 1:
atom1 = 1
elif ntypat >= 2:
atom1 = self.CBox1.currentIndex()
self.Probability = Analysis.Proba(neib, self.file, atom1)
x = self.Probability.getN()
y = self.Probability.getProba()
try:
self.GraphProba.update(x,
y,
'Neighbor',
"Probability",
name=self.name)
except:
self.GraphProba = Graph.graphic(x,
y,
'Neighbor',
"Probability",
average=False,
name=self.name)
#self.connect(self.GraphRDF, QtCore.SIGNAL("myCustomizedSignal()"), self.close)
self.GraphProba.show()
def changeMode(self):
mode1 = self.sbm1.currentText()
mode2 = self.sbm2.currentText()
self.marker_size = 2 #Set maker_size to 2 (except average)
self.markerscale = 5 #Set the relative size of legend marker vs original
if self.sbrel.isChecked():
reduced = True
unit = 1 # No Conversion
legend = ""
else:
reduced = False
unit = self.units['Distance'][1]
legend = " (" + str(self.units['Distance'][0]) + ")"
option = 0
if mode1 == 'Average':
option = 1
self.marker_size = 5 #set marker_size to 5 (better for visualization)
self.markerscale = 2
elif mode1 == 'PBC (cubic only)':
option = 2
for itype in range(1, self.ntypat + 1):
indexAtom = array(
[i for i, x in enumerate(self.typat) if x == itype], dtype=int)
self.pos_conv = Atom.convert_position(self.file,
indexAtom,
option=option,
reduced=reduced)
if mode2 == 'XY':
self.x = self.pos_conv.getX()
self.y = self.pos_conv.getY()
self.legend_x = "x" + legend
self.legend_y = "y" + legend
elif mode2 == 'XZ':
self.x = self.pos_conv.getX()
self.y = self.pos_conv.getZ()
self.legend_x = "x" + legend
self.legend_y = "z" + legend
else:
self.x = self.pos_conv.getY()
self.y = self.pos_conv.getZ()
self.legend_x = "y" + legend
self.legend_y = "z " + legend
if itype == 1:
try:
self.graphPosition.updatePos(self.x*unit,self.y*unit,\
self.legend_x,\
self.legend_y,\
marker_size=self.marker_size, name = self.name)
except:
self.graphPosition = Graph.graphic(self.x*unit,self.y*unit,\
self.legend_x,\
self.legend_y,\
average=False,point = True,marker='.',\
marker_size=self.marker_size,name = self.name)
else:
self.graphPosition.addPlot(self.x*unit,self.y*unit,\
point=True,marker_size=self.marker_size)
self.legend = []
for i in range(self.ntypat):
self.legend.append(str(self.PTOE.getName(self.file.getZnucl()[i])))
self.graphPosition.addLegend(self.legend, markerscale=self.markerscale)
self.graphPosition.show()
