def getAtomName(self):
#return array with the name of the atom
PTOE = Analysis.PeriodicTableElement()
znucl = self.getZnucl()
name = []
for i in range(len(znucl)):
name.append(PTOE.getName(znucl[i]))
return name
def xyzFormat(self,pos,acell,typat,znucl):
PTOE = Analysis.PeriodicTableElement()
file_out = open( self.namefile ,"w")
for t in range(len(pos)):
file_out.write(str(len(pos[0]))+'\n')
file_out.write('acell ' + str(acell[t][0])+' '+str(acell[t][1])+' '+str(acell[t][2])+' '+'\n')
for i in range(len(pos[0])):
typeofatom = PTOE.getName(znucl[typat[i] - 1 ])
file_out.write(str(typeofatom) +' '+ str(pos[t][i][0]) +' '+ str(pos[t][i][1]) +' '+ str(pos[t][i][2]) + '\n')
def __init__(self, file, punits, parent=None, name=''):
self.file = file
self.name = name
self.units = punits #Dictionary with the units ans the conversion
self.x = []
self.y = []
self.legend_x = ""
self.legend_y = ""
self.typat = self.file.getTypat()
self.ntypat = max(self.typat)
self.PTOE = Analysis.PeriodicTableElement()
self.initUI(parent) #Creation of postion windows
self.changeMode() #Generation of graphic of position
self.raise_()
class winMSD(QtGui.QWidget):
PTOE = Analysis.PeriodicTableElement()
def __init__(self, file, parent = None,name =''):
self.file = file
self.name = name
self.initUI(parent)
self.displayGraph()
self.raise_()
def initUI(self, parent):
#-----------------Creation of the windows----------------------------#
QtGui.QWidget.__init__(self, parent)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.setWindowTitle(self.name + ' MSD option')
self.setFixedSize(200, 150)
self.center()
self.layout = QtGui.QGridLayout()
self.setLayout(self.layout)
self.lbl1 = QtGui.QLabel(" Atom type 1 :", self)
self.lbl1.setFixedWidth(95)
self.CBox1 = QtGui.QComboBox()
self.CBox1.setFixedWidth(70)
for i in range(len(self.file.getZnucl())):
self.CBox1.addItem(str(self.PTOE.getName(self.file.getZnucl()[i])))
self.connect(self.CBox1,QtCore.SIGNAL('currentIndexChanged(const QString&)'),self.displayGraph)
self.pbClose = QtGui.QPushButton("close")
self.pbClose.setFixedSize(70,20)
self.connect(self.pbClose,QtCore.SIGNAL("clicked()"),QtCore.SLOT('close()'))
self.layout.addWidget(self.lbl1 , 1, 0, 1, 1, QtCore.Qt.AlignRight)
self.layout.addWidget(self.CBox1 , 1, 1, 1, 1, QtCore.Qt.AlignCenter)
self.layout.addWidget(self.pbClose , 7, 0, 1, 2, QtCore.Qt.AlignCenter)
self.show()
#------------------------------------------------------------------------#
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 update(self,pfile):
self.file = pfile
atom = self.CBox1.currentIndex() + 1
try:
self.MeanSquaredDeplacement = Analysis.MSD(self.file,atom)
x = self.MeanSquaredDeplacement.getX()
y = self.MeanSquaredDeplacement.getMSD()
self.graphMSD.update(x,y,'step', "Mean squared deplacement",name = self.name)
self.graphMSD.addPlot(x,linspace(1,1,len(x)))
except:
pass
def close(self):
del self.graphMSD
del self
def closeEvent(self, event):
try:
del self.graphMSD
except:
pass
try:
del self
except:
pass
def center(self):
screen = QtGui.QDesktopWidget().screenGeometry()
size = self.geometry()
self.move((screen.width()-size.width())/2, (screen.height()-size.height())/2)
if choiceformat == 1 or choiceformat == 3:
fname = saveFile('dat',name_quantitie)
Write.SaveFile(fname).saveGraph(x,y,'E (meV)',"Phonons DOS (nm^2/ps)")
print fname
print 'File save sucessful!'
if choiceformat == 2 or choiceformat == 3:
fname = saveFile('pdf',name_quantitie)
pdf = Canvas.Canvas(width=10, height=8, dpi=100,x=x,y=y,pxlbl='E (meV)',pylbl= "Phonons DOS (nm^2/ps)",adjust=True)
pdf.print_figure(str(fname))
print fname
print 'File save sucessful!'
elif choiceQuantitie == 9:
PTOE = Analysis.PeriodicTableElement()
nameAtom = MD_file.getAtomName()
if len(nameAtom) == 1:
atom0 = 1
atom1 = 1
else:
for i in range(2):
stringChoice = 'Choose the atom' + str(i+1)+' ( '
for k in range(len(nameAtom)):
stringChoice += str(nameAtom[k])
if k != len(nameAtom)-1:
stringChoice += ' or '
else:
stringChoice+= ' ):'
while True:
class winNetcdf(QtGui.QWidget):
PTOE = Analysis.PeriodicTableElement()
def __init__(self, file, parent=None, name=''):
self.file = file
self.name = name
self.ni = 1
self.nf = 2
self.initUI(parent)
self.raise_()
def initUI(self, parent):
#-----------------Creation of the windows----------------------------#
QtGui.QWidget.__init__(self, parent)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.setWindowTitle(self.name + ' Save Netcdf')
self.setFixedSize(600, 450)
self.center()
self.layout = QtGui.QGridLayout()
self.setLayout(self.layout)
self.lbl1 = QtGui.QLabel(" Name :", self)
self.lbl1.setFixedWidth(95)
self.lname = QtGui.QLineEdit()
self.lname.setFixedWidth(200)
self.pbClose = QtGui.QPushButton("Close")
self.pbClose.setFixedSize(70, 20)
self.connect(self.pbClose, QtCore.SIGNAL("clicked()"),
QtCore.SLOT('close()'))
self.pbSave = QtGui.QPushButton("Save")
self.pbSave.setFixedSize(70, 20)
self.connect(self.pbSave, QtCore.SIGNAL("clicked()"), self.save)
self.layout.addWidget(self.lbl1, 1, 0, 1, 1, QtCore.Qt.AlignRight)
self.layout.addWidget(self.lname, 1, 1, 1, 1, QtCore.Qt.AlignCenter)
self.layout.addWidget(self.pbClose, 7, 0, 1, 2, QtCore.Qt.AlignCenter)
self.layout.addWidget(self.pbSave, 7, 1, 1, 4, QtCore.Qt.AlignCenter)
self.show()
#------------------------------------------------------------------------#
def save(self):
Write.writeHIST(self.file, self.name, self.ni, self.nf)
def close(self):
del self.graphMSD
del self
def closeEvent(self, event):
try:
del self.graphMSD
except:
pass
try:
del self
except:
pass
def center(self):
screen = QtGui.QDesktopWidget().screenGeometry()
size = self.geometry()
self.move((screen.width() - size.width()) / 2,
(screen.height() - size.height()) / 2)
class winRDF(QtGui.QWidget):
PTOE = Analysis.PeriodicTableElement()
def __init__(self, file, parent=None, name=''):
self.file = file
self.name = name
self.initUI(parent)
self.raise_()
#-----------------Creation of the windows----------------------------#
def initUI(self, parent):
QtGui.QWidget.__init__(self, parent)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.setWindowTitle(self.name + ' RDF option')
typat = self.file.getTypat()
ntypat = max(typat)
nat = 0
for i in enumerate(typat):
nat = nat + 1
self.center()
self.layout = QtGui.QGridLayout()
self.setLayout(self.layout)
self.mode = QtGui.QLabel("Calculation :", self)
self.mode.setFixedWidth(85)
self.sbm = QtGui.QComboBox()
self.sbm.setFixedWidth(70)
self.sbm.addItem(str('RDF'))
self.sbm.addItem(str('ADF'))
self.sbm.addItem(str('NDF'))
self.sbm.addItem(str('Proba'))
if ntypat == 1:
self.lbl1 = QtGui.QLabel(" Atom type :", self)
self.lbl1.setFixedWidth(80)
self.CBox1 = QtGui.QComboBox()
self.CBox1.setFixedWidth(70)
for i in range(len(self.file.getZnucl())):
self.CBox1.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
elif ntypat >= 2:
self.lbl1 = QtGui.QLabel(" Atom type 1 :", self)
self.lbl1.setFixedWidth(85)
self.lbl2 = QtGui.QLabel(" Atom type 2 :", self)
self.lbl2.setFixedWidth(85)
self.CBox1 = QtGui.QComboBox()
self.CBox1.setFixedWidth(70)
self.CBox2 = QtGui.QComboBox()
self.CBox2.setFixedWidth(70)
self.CBox1.addItem(str('all'))
self.CBox2.addItem(str('all'))
for i in range(len(self.file.getZnucl())):
self.CBox1.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
self.CBox2.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
self.lbl3 = QtGui.QLabel("delta R :", self)
self.lbl3.setFixedWidth(55)
self.sbdr = QtGui.QDoubleSpinBox()
self.sbdr.setSingleStep(0.01)
self.sbdr.setValue(0.1)
self.sbdr.setMinimum(0.01)
self.sbdr.setMaximum(2)
self.sbdr.setFixedWidth(70)
self.lbl4 = QtGui.QLabel("Box wide :", self)
self.lbl4.setFixedWidth(68)
self.sbrm = QtGui.QDoubleSpinBox()
self.sbrm.setSingleStep(0.5)
self.sbrm.setMinimum(-0.5)
self.sbrm.setMaximum(2.0)
self.sbrm.setValue(0)
self.sbrm.setFixedWidth(70)
self.lbl5 = QtGui.QLabel("Step :", self)
self.lbl5.setFixedWidth(36)
self.sbStep = QtGui.QSpinBox()
self.sbStep.setMinimum(1)
self.sbStep.setMaximum(self.file.getNbTime())
self.sbStep.setFixedWidth(70)
self.sbStep.setValue(5)
self.lbl8 = QtGui.QLabel("Deconvolution :", self)
self.lbl8.setFixedWidth(105)
self.sbdec = QtGui.QCheckBox()
self.pbClose = QtGui.QPushButton("close")
self.pbClose.setFixedSize(70, 20)
self.connect(self.pbClose, QtCore.SIGNAL("clicked()"),
QtCore.SLOT('close()'))
self.pbDraw = QtGui.QPushButton("g(r)")
self.pbDraw.setFixedSize(70, 20)
self.connect(self.pbDraw, QtCore.SIGNAL("clicked()"), self.Graphics)
self.changeBox()
def changeBox(self):
mode = self.sbm.currentText()
typat = self.file.getTypat()
ntypat = max(typat)
nat = 0
if ntypat == 1:
s1 = 0
elif ntypat >= 2:
s1 = 50
if mode == 'RDF':
self.setFixedSize(200, 250 + s1)
if ntypat == 1:
self.layout.addWidget(self.mode, 1, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbm, 1, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl1, 2, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.CBox1, 2, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl3, 3, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbdr, 3, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl4, 4, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbrm, 4, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl5, 5, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbStep, 5, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl8, 6, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbdec, 6, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.pbClose, 8, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.pbDraw, 8, 1, 1, 1,
QtCore.Qt.AlignCenter)
else:
self.layout.addWidget(self.mode, 1, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbm, 1, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl1, 2, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.CBox1, 2, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl2, 3, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.CBox2, 3, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl3, 4, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbdr, 4, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl4, 5, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbrm, 5, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl5, 6, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbStep, 6, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl8, 7, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbdec, 7, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.pbClose, 9, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.pbDraw, 9, 1, 1, 1,
QtCore.Qt.AlignCenter)
elif mode == 'ADF':
self.setFixedSize(200, 200 + s1)
if ntypat == 1:
self.layout.addWidget(self.mode, 1, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbm, 1, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl1, 2, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.CBox1, 2, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl6, 3, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbdt, 3, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl7, 4, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbn, 4, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl5, 5, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbStep, 5, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.pbClose, 7, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.pbDraw, 7, 1, 1, 1,
QtCore.Qt.AlignCenter)
else:
self.layout.addWidget(self.mode, 1, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbm, 1, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl1, 2, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.CBox1, 2, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl2, 3, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.CBox2, 3, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl6, 4, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbdt, 4, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl7, 5, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbn, 5, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl5, 6, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbStep, 6, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.pbClose, 8, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.pbDraw, 8, 1, 1, 1,
QtCore.Qt.AlignCenter)
elif mode == 'NDF':
self.setFixedSize(200, 200 + s1)
if ntypat == 1:
self.layout.addWidget(self.mode, 1, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbm, 1, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl1, 2, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.CBox1, 2, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl3, 3, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbdr, 3, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl7, 4, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbn, 4, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl5, 5, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbStep, 5, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.pbClose, 7, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.pbDraw, 7, 1, 1, 1,
QtCore.Qt.AlignCenter)
else:
self.layout.addWidget(self.mode, 1, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbm, 1, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl1, 2, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.CBox1, 2, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl2, 3, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.CBox2, 3, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl3, 4, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbdr, 4, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl7, 5, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbn, 5, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl5, 6, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbStep, 6, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.pbClose, 8, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.pbDraw, 8, 1, 1, 1,
QtCore.Qt.AlignCenter)
elif mode == 'Proba':
self.setFixedSize(200, 170)
self.layout.addWidget(self.mode, 1, 0, 1, 1, QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbm, 1, 1, 1, 1, QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl1, 2, 0, 1, 1, QtCore.Qt.AlignRight)
self.layout.addWidget(self.CBox1, 2, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.layout.addWidget(self.lbl7, 3, 0, 1, 1, QtCore.Qt.AlignRight)
self.layout.addWidget(self.sbn, 3, 1, 1, 1, QtCore.Qt.AlignCenter)
self.layout.addWidget(self.pbClose, 5, 0, 1, 1,
QtCore.Qt.AlignRight)
self.layout.addWidget(self.pbDraw, 5, 1, 1, 1,
QtCore.Qt.AlignCenter)
self.show()
self.connect(self.sbm,
QtCore.SIGNAL('currentIndexChanged(const QString&)'),
self.changeMode)
def changeMode(self):
mode = self.sbm.currentText()
# erase text on the window
try:
self.layout.removeWidget(self.lbl1)
except:
pass
try:
self.layout.removeWidget(self.lbl2)
except:
pass
try:
self.layout.removeWidget(self.lbl3)
except:
pass
try:
self.layout.removeWidget(self.lbl4)
except:
pass
try:
self.layout.removeWidget(self.lbl5)
except:
pass
try:
self.layout.removeWidget(self.lbl6)
except:
pass
try:
self.layout.removeWidget(self.lbl7)
except:
pass
try:
self.layout.removeWidget(self.lbl8)
except:
pass
try:
self.lbl1.setParent(None)
except:
pass
try:
self.lbl2.setParent(None)
except:
pass
try:
self.lbl3.setParent(None)
except:
pass
try:
self.lbl4.setParent(None)
except:
pass
try:
self.lbl5.setParent(None)
except:
pass
try:
self.lbl6.setParent(None)
except:
pass
try:
self.lbl7.setParent(None)
except:
pass
try:
self.lbl8.setParent(None)
except:
pass
try:
self.layout.removeWidget(self.CBox1)
except:
pass
try:
self.layout.removeWidget(self.CBox2)
except:
pass
try:
self.layout.removeWidget(sbdr)
except:
pass
try:
self.layout.removeWidget(sbrm)
except:
pass
try:
self.layout.removeWidget(sbstep)
except:
pass
try:
self.layout.removeWidget(sbdt)
except:
pass
try:
self.layout.removeWidget(sbn)
except:
pass
try:
self.layout.removeWidget(sdec)
except:
pass
try:
self.layout.removeWidget(pbClose)
except:
pass
try:
self.layout.removeWidget(pbDraw)
except:
pass
try:
self.CBox1.setParent(None)
except:
pass
try:
self.CBox2.setParent(None)
except:
pass
try:
self.sbdr.setParent(None)
except:
pass
try:
self.sbdm.setParent(None)
except:
pass
try:
self.sbstep.setParent(None)
except:
pass
try:
self.sbdt.setParent(None)
except:
pass
try:
self.sbn.setParent(None)
except:
pass
try:
self.sbdec.setParent(None)
except:
pass
try:
self.pbClose.setParent(None)
except:
pass
try:
self.pbDraw.setParent(None)
except:
pass
typat = self.file.getTypat()
ntypat = max(typat)
nat = 0
for i in enumerate(typat):
nat = nat + 1
#initialisation of texts
if mode == 'RDF':
if ntypat == 1:
self.lbl1 = QtGui.QLabel(" Atom type :", self)
self.lbl1.setFixedWidth(80)
self.CBox1 = QtGui.QComboBox()
self.CBox1.setFixedWidth(70)
for i in range(len(self.file.getZnucl())):
self.CBox1.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
elif ntypat >= 2:
self.lbl1 = QtGui.QLabel(" Atom type 1 :", self)
self.lbl1.setFixedWidth(85)
self.lbl2 = QtGui.QLabel(" Atom type 2 :", self)
self.lbl2.setFixedWidth(85)
self.CBox1 = QtGui.QComboBox()
self.CBox1.setFixedWidth(70)
self.CBox2 = QtGui.QComboBox()
self.CBox2.setFixedWidth(70)
self.CBox1.addItem(str('all'))
self.CBox2.addItem(str('all'))
for i in range(len(self.file.getZnucl())):
self.CBox1.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
self.CBox2.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
self.lbl3 = QtGui.QLabel("delta R :", self)
self.lbl3.setFixedWidth(55)
self.sbdr = QtGui.QDoubleSpinBox()
self.sbdr.setSingleStep(0.01)
self.sbdr.setValue(0.1)
self.sbdr.setMinimum(0.01)
self.sbdr.setMaximum(2)
self.sbdr.setFixedWidth(70)
self.lbl4 = QtGui.QLabel("Box wide :", self)
self.lbl4.setFixedWidth(68)
self.sbrm = QtGui.QDoubleSpinBox()
self.sbrm.setSingleStep(0.5)
self.sbrm.setMinimum(-0.5)
self.sbrm.setMaximum(2.0)
self.sbrm.setValue(0)
self.sbrm.setFixedWidth(70)
self.lbl5 = QtGui.QLabel("Step :", self)
self.lbl5.setFixedWidth(36)
self.sbStep = QtGui.QSpinBox()
self.sbStep.setMinimum(1)
self.sbStep.setMaximum(self.file.getNbTime())
self.sbStep.setFixedWidth(70)
self.sbStep.setValue(5)
self.lbl8 = QtGui.QLabel("Deconvolution :", self)
self.lbl8.setFixedWidth(105)
self.sbdec = QtGui.QCheckBox()
elif mode == 'ADF':
if ntypat == 1:
self.lbl1 = QtGui.QLabel(" Atom type :", self)
self.lbl1.setFixedWidth(80)
self.CBox1 = QtGui.QComboBox()
self.CBox1.setFixedWidth(70)
for i in range(len(self.file.getZnucl())):
self.CBox1.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
elif ntypat >= 2:
self.lbl1 = QtGui.QLabel(" Atom type 1 :", self)
self.lbl1.setFixedWidth(85)
self.lbl2 = QtGui.QLabel(" Atom type 2 :", self)
self.lbl2.setFixedWidth(85)
self.CBox1 = QtGui.QComboBox()
self.CBox1.setFixedWidth(70)
self.CBox2 = QtGui.QComboBox()
self.CBox2.setFixedWidth(70)
self.CBox1.addItem(str('all'))
self.CBox2.addItem(str('all'))
for i in range(len(self.file.getZnucl())):
self.CBox1.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
self.CBox2.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
self.lbl5 = QtGui.QLabel("Step :", self)
self.lbl5.setFixedWidth(36)
self.sbStep = QtGui.QSpinBox()
self.sbStep.setMinimum(1)
self.sbStep.setMaximum(self.file.getNbTime())
self.sbStep.setFixedWidth(70)
self.sbStep.setValue(5)
self.lbl6 = QtGui.QLabel("delta theta :", self)
self.lbl6.setFixedWidth(80)
self.sbdt = QtGui.QDoubleSpinBox()
self.sbdt.setSingleStep(0.2)
self.sbdt.setValue(1)
self.sbdt.setMinimum(0.2)
self.sbdt.setMaximum(5)
self.sbdt.setFixedWidth(70)
self.lbl7 = QtGui.QLabel("cutoff :", self)
self.lbl7.setFixedWidth(60)
self.sbn = QtGui.QDoubleSpinBox()
self.sbn.setSingleStep(0.1)
self.sbn.setValue(4)
self.sbn.setMinimum(1)
self.sbn.setMaximum(20)
self.sbn.setFixedWidth(70)
elif mode == 'NDF':
if ntypat == 1:
self.lbl1 = QtGui.QLabel(" Atom type :", self)
self.lbl1.setFixedWidth(80)
self.CBox1 = QtGui.QComboBox()
self.CBox1.setFixedWidth(70)
for i in range(len(self.file.getZnucl())):
self.CBox1.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
elif ntypat >= 2:
self.lbl1 = QtGui.QLabel(" Atom type 1 :", self)
self.lbl1.setFixedWidth(85)
self.lbl2 = QtGui.QLabel(" Atom type 2 :", self)
self.lbl2.setFixedWidth(85)
self.CBox1 = QtGui.QComboBox()
self.CBox1.setFixedWidth(70)
self.CBox2 = QtGui.QComboBox()
self.CBox2.setFixedWidth(70)
self.CBox1.addItem(str('all'))
self.CBox2.addItem(str('all'))
for i in range(len(self.file.getZnucl())):
self.CBox1.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
self.CBox2.addItem(
str(self.PTOE.getName(self.file.getZnucl()[i])))
self.lbl3 = QtGui.QLabel("delta R :", self)
self.lbl3.setFixedWidth(55)
self.sbdr = QtGui.QDoubleSpinBox()
self.sbdr.setSingleStep(0.01)
self.sbdr.setValue(0.05)
self.sbdr.setMinimum(0.01)
self.sbdr.setMaximum(1)
self.sbdr.setFixedWidth(70)
self.lbl5 = QtGui.QLabel("Step :", self)
self.lbl5.setFixedWidth(36)
self.sbStep = QtGui.QSpinBox()
self.sbStep.setMinimum(1)
self.sbStep.setMaximum(self.file.getNbTime())
self.sbStep.setFixedWidth(70)
self.sbStep.setValue(5)
self.lbl7 = QtGui.QLabel("neighbors :", self)
self.lbl7.setFixedWidth(71)
self.sbn = QtGui.QSpinBox()
self.sbn.setSingleStep(1)
self.sbn.setValue(1)
self.sbn.setMinimum(1)
self.sbn.setMaximum(nat - 1)
self.sbn.setFixedWidth(70)
elif mode == 'Proba':
self.lbl7 = QtGui.QLabel("neighbors :", self)
self.lbl7.setFixedWidth(71)
self.sbn = QtGui.QSpinBox()
self.sbn.setSingleStep(1)
self.sbn.setValue(1)
self.sbn.setMinimum(1)
self.sbn.setMaximum(nat - 1)
self.sbn.setFixedWidth(70)
self.pbClose = QtGui.QPushButton("close")
self.pbClose.setFixedSize(70, 20)
self.connect(self.pbClose, QtCore.SIGNAL("clicked()"), self.close)
self.pbDraw = QtGui.QPushButton("g(r)")
self.pbDraw.setFixedSize(70, 20)
self.connect(self.pbDraw, QtCore.SIGNAL("clicked()"), self.Graphics)
self.changeBox()
#------------------------------------------------------------------------#
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 center(self):
screen = QtGui.QDesktopWidget().screenGeometry()
size = self.geometry()
self.move((screen.width() - size.width()) / 2,
(screen.height() - size.height()) / 2)
def close(self):
del self.graphPosition
del self
def closeEvent(self, event):
try:
del self.graphPosition
except:
pass
try:
del self
except:
pass
