def updateSystem(self,x=None):
s=self.getCurrentStructure()
s.updateRecipBasis()
self.b11.set_text(str(s.rbasis[0][0]))
self.b12.set_text(str(s.rbasis[0][1]))
self.b13.set_text(str(s.rbasis[0][2]))
self.b21.set_text(str(s.rbasis[1][0]))
self.b22.set_text(str(s.rbasis[1][1]))
self.b23.set_text(str(s.rbasis[1][2]))
self.b31.set_text(str(s.rbasis[2][0]))
self.b32.set_text(str(s.rbasis[2][1]))
self.b33.set_text(str(s.rbasis[2][2]))
s=getCurrentSystemPM()
primitive_cell = s.PRIMITIVE_STRUCTURE
dyna=s.DYNA
if dyna is None:
dyna=Dyna()
dyna.addSegment()
if primitive_cell is not None:
dyna=dyna.withBasis(primitive_cell.basis).reciprocal()
self.model = KPathTreeModel(dyna)
self.stepsPerSegment.set_text(str(dyna.size))
dynaPublisher().updateDyna(dyna)
self.treeview.set_model(self.model)
def __init__(self):
GraphWindowApplet.__init__(self)
# self.gladefile="graphapplet.glade"
# self.gladename="applet_frame"
self.world_name = "phonondispersion"
self.required = ["NAME"]
dynaPublisher().addListener(self)
def on_add_clicked_handler(self,w,*arg):
if self.selected is not None:
self.model.dyna.insertSegment(self.selected)
p=str(self.selected)
self.model.row_inserted(p,self.model.get_iter(p))
else:
self.model.dyna.addSegment()
p=str(len(self.model.dyna.segments)-1)
self.model.row_inserted(p,self.model.get_iter(p))
dynaPublisher().updateDyna(self.model.dyna)
def edited_h(self,renderer,path,txt,model,column):
value = txt
row=int(path)
if column==0:
self.model.dyna.labels[row][0]=value
if column==4:
self.model.dyna.labels[row][1]=value
if column in (1,2,3):
value= float(value.replace(",","."))
newpoint=Vector(self.model.dyna.segments[row][0])
newpoint[column-1]=float(str(value).replace(",","."))
newsegment=(newpoint,self.model.dyna.segments[row][1])
self.model.dyna.segments[row]=newsegment
if column in (5,6,7):
value= float(value.replace(",","."))
newpoint=Vector(self.model.dyna.segments[row][1])
newpoint[column-5]=float(str(value).replace(",","."))
newsegment=(self.model.dyna.segments[row][0],newpoint)
self.model.dyna.segments[row]=newsegment
dynaPublisher().updateDyna(self.model.dyna)
def __init__(self):
Applet.__init__(self)
self.celltype=self.PRIMITIVE_CELL
self.dyna=None
dynaPublisher().addListener(self)
def on_delete_clicked_handler(self,w,*arg):
if self.selected is not None:
self.model.dyna.deleteSegment(self.selected)
self.model.row_deleted(str(self.selected))
dynaPublisher().updateDyna(self.model.dyna)
def on_stepsPerSegment_activate_handler(self,w,*arg):
self.model.dyna.size=int(self.stepsPerSegment.get_text())
dynaPublisher().updateDyna(self.model.dyna)
def updateSystemGen(self, x=None):
msg().status("Update System in Energy Convergence applet")
system = self.system
self.world[0].subtitle = ""
# self.window_world[0].subtitle=""
self.setGraphData([[]])
self.update()
yield 1
if system is not None:
name = system.current("NAME")
if name is not None:
self.world[0].subtitle = "(%s)" % name
super_cell = system.INITIAL_STRUCTURE
system.scheduleFirst("FORCE_CONSTANTS")
force_const_mat = system.FORCE_CONSTANTS
primitive_cell = system.PRIMITIVE_STRUCTURE
if primitive_cell is None:
return
basis_masses = [
primitive_cell.getRecordForAtom(x)["mass"]
for x in range(len(primitive_cell))
]
yield 1
msg().status("Reading DYNA")
dyna = dynaPublisher().dyna
if dyna is None:
dyna = system.DYNA
if dyna is None:
msg().error("DYNA file not found, k-point path not specified.")
self.setGraphData([[]])
yield 1
else:
print "Dyna in dispersion:"
print dyna.toString()
dyna = dyna.withBasis(primitive_cell.basis).reciprocal()
steps = dyna.size
if len(dyna.segments) < 1:
msg().error(
"At least one segment is necessary for a k-point path")
return
msg().status("Generating k-point path")
yield 1
k_path = list(dyna.pointsAlongPath(steps))
k_path_ext = list(
dyna.pointsAlongPathWithDistanceAndLabel(steps))
msg().status("Start phonon calculation")
yield 1
p_calc = PhononsCalculation(primitive_cell, super_cell,
force_const_mat, basis_masses)
omega = []
for i, x in enumerate(p_calc.calcPhononFrequencies(k_path)):
msg().step(i, len(k_path_ext))
msg().status("Calculation k-point %s" % str(k_path[i]))
omega.append(x)
if (i % 5 == 0):
yield 1
msg().step(0, 1)
msg().status("OK")
yield 1
msg().status("Filling in graph")
yield 1
if omega is not None:
assert (len(omega) == len(k_path_ext))
g = []
for i in range(len(omega[0])):
gd = []
for j in range(len(omega)):
point, distance, label = k_path_ext[j]
gd.append((distance, omega[j][i]))
g.append(gd)
self.setGraphData([g])
# Create lines
self.viewAll()
self.update()
w = self.canvas.world
wg = w[0]
x1 = wg.world_xmin
x2 = wg.world_xmax
y1 = wg.world_ymin
y2 = wg.world_ymax
wg.graph_lines = [
GraphLine(distance, y1, distance, y2, 7)
for point, distance, label in k_path_ext if
label is not None and distance > x1 and distance < x2
]
self.viewAll()
self.update()
else:
self.setGraphData([[]])
wg.graph_lines = []
self.update()
self.viewAll()
msg().step(0, 1)
msg().status("OK")
def destroy(self):
GraphWindowApplet.destroy(self)
dynaPublisher().removeListener(self)