def showStructureWindow(self):
if self.swin is None:
self.swin = StructureWindow(title="p4vasp Structure",
atomtypes=getAtomtypes())
self.swin.structure_drawer.setRadiusFactor(0.5 *
self.radius_factor)
self.swin.show()
def showStructureWindow(self):
if self.swin is None:
l=[(0,0,0,0)]
for a in applets():
if isinstance(a,StructureWindowApplet):
if a.swin is not None:
w=a.swin.win
if w is not None:
l.append((w.x,w.y,w.w,w.h))
xx=max(map(lambda x:x[0]+x[2],l))
yy=max(map(lambda x:x[1]+x[3],l))
if yy<=600:
xx=0
else:
yy=0
self.swin=StructureWindow(x=xx,y=yy,w=500,h=400,title="p4vasp Structure",atomtypes=getAtomtypes())
self.swin.setRadiusFactor(0.5*self.radius_factor)
# self.swin.setBackground(1,1,1)
self.swin.show()
class StructureApplet(Applet, p4vasp.Selection.SelectionListener):
menupath = ["Structure", "Show (old)"]
def __init__(self):
Applet.__init__(self)
self.gladefile = "structureapplet.glade"
self.gladename = "applet_frame"
self.required = [
"NAME", "INITIAL_STRUCTURE", "FINAL_STRUCTURE",
"PRIMITIVE_STRUCTURE", "STRUCTURE_SEQUENCE_L"
]
self.swin = None
self.measure = None
self.radius_factor = 1.0
self.cell_centering = 0 #0:none, 1:to unit cel, 2:centered unit cel
self.visible_atoms = None
self.index = -1
self.hidden = []
self.arrows_sequence = []
self.view_iso = None
self.levelentry = None
self.subtrentry = None
self.subtr_density_fileselection = None
self.subtrchgcar = None
self.chgcar = None
def notifyAtomSelection(self, sel, origin):
# self.atom_selection.set_text(sel.encode(self.structure))
sel = p4vasp.Selection.selection()
self.swin.removeSelectedAll()
for i, nx, ny, nz in sel:
self.swin.selectAtom(i, nx, ny, nz)
def setSystem(self, s):
self.system = s
if s is not None:
self.system.require(self.required, self.updateSystem)
self.updateSystem()
def updateSystem(self, x=None):
s = self.system
if s is not None:
# structure=s.getCurrent("INITIAL_STRUCTURE")
structure = s.INITIAL_STRUCTURE
if structure is not None:
self.showStructureWindow()
self.setStructure(structure)
self.createStructureItems()
def setStructure(self, structure):
self.structure = structure
if self.cell_centering == 1:
self.structure.toCenteredUnitCell()
elif self.cell_centering == 2:
self.structure.toUnitCell()
self.swin.setStructure(structure)
self.swin.structure_drawer.setRadiusFactor(0.5 * self.radius_factor)
info = self.swin.structure_drawer.info
l = info.len()
for i in self.hidden:
if i >= 0 and i < l:
info.getRecord(i).hidden = 1
def showStructureWindow(self):
if self.swin is None:
self.swin = StructureWindow(title="p4vasp Structure",
atomtypes=getAtomtypes())
self.swin.structure_drawer.setRadiusFactor(0.5 *
self.radius_factor)
self.swin.show()
def createStructureItems(self):
omenu = self.xml.get_widget("structuremenu")
if omenu is None:
return None
menu = gtk.Menu()
omenu.set_menu(menu)
omenu.show()
if self.system is not None:
if self.system.current("INITIAL_STRUCTURE") is not None:
item = gtk.MenuItem("Initial positions")
item.connect("activate", self.on_structureitem_clicked_handler,
-1)
menu.append(item)
item.show()
if self.system.current("FINAL_STRUCTURE") is not None:
item = gtk.MenuItem("Final positions")
item.connect("activate", self.on_structureitem_clicked_handler,
-2)
menu.append(item)
item.show()
if self.system.current("PRIMITIVE_STRUCTURE") is not None:
item = gtk.MenuItem("Primitive cell")
item.connect("activate", self.on_structureitem_clicked_handler,
-2)
menu.append(item)
item.show()
seq = self.system.current("STRUCTURE_SEQUENCE_L")
if seq is not None:
for i in range(len(seq)):
item = gtk.MenuItem("step %3d" % (i + 1))
item.connect("activate",
self.on_structureitem_clicked_handler, i)
menu.append(item)
item.show()
def initUI(self):
self.xml.get_widget("toolbar1").set_style(gtk.TOOLBAR_ICONS)
self.xml.get_widget("toolbar2").set_style(gtk.TOOLBAR_ICONS)
cs1 = self.xml.get_widget("cell_scale1")
cs2 = self.xml.get_widget("cell_scale2")
cs3 = self.xml.get_widget("cell_scale3")
self.csadj1 = gtk.Adjustment(1, 1, 10, 1, 0, 0)
self.csadj2 = gtk.Adjustment(1, 1, 10, 1, 0, 0)
self.csadj3 = gtk.Adjustment(1, 1, 10, 1, 0, 0)
cs1.set_adjustment(self.csadj1)
cs2.set_adjustment(self.csadj2)
cs3.set_adjustment(self.csadj3)
self.csadj1.connect("value-changed", self.on_cell_scale_changed)
self.csadj2.connect("value-changed", self.on_cell_scale_changed)
self.csadj3.connect("value-changed", self.on_cell_scale_changed)
self.sss_adj = gtk.Adjustment(1.0, 0.1, 5.0, 0.1, 0, 0)
sss = self.xml.get_widget("sphere_size_scale")
self.levelentry = self.xml.get_widget("levelentry")
self.subtrentry = self.xml.get_widget("subtrentry")
sss.set_adjustment(self.sss_adj)
self.sss_adj.connect("value-changed",
self.on_sphere_size_scale_changed)
self.ass_adj = gtk.Adjustment(1.0, 0.1, 20.0, 0.1, 0, 0)
ass = self.xml.get_widget("arrows_size_scale")
ass.set_adjustment(self.ass_adj)
self.ass_adj.connect("value-changed",
self.on_arrows_size_scale_changed)
# self.atom_selection=self.xml.get_widget("atom_selection")
self.createStructureItems()
amenu = self.xml.get_widget("arrowstypemenu")
if amenu is not None:
menu = gtk.Menu()
amenu.set_menu(menu)
amenu.show()
item = gtk.MenuItem("None")
item.connect("activate", self.on_none_arrows_clicked_handler, -1)
menu.append(item)
item.show()
item = gtk.MenuItem("Forces")
item.connect("activate", self.on_forces_arrows_clicked_handler, -1)
menu.append(item)
item.show()
item = gtk.MenuItem("Step - Initial")
item.connect("activate", self.on_SMI_arrows_clicked_handler, -1)
menu.append(item)
item.show()
item = gtk.MenuItem("Final - Step")
item.connect("activate", self.on_SMF_arrows_clicked_handler, -1)
menu.append(item)
item.show()
isomenu = self.xml.get_widget("isomenu")
if isomenu is not None:
menu = gtk.Menu()
isomenu.set_menu(menu)
isomenu.show()
item = gtk.MenuItem("None")
item.connect("activate", self.on_iso_clicked_handler, None)
menu.append(item)
item.show()
item = gtk.MenuItem("Charge density (CHG)")
item.connect("activate", self.on_iso_clicked_handler, "CHG")
menu.append(item)
item.show()
item = gtk.MenuItem("Charge density (CHGCAR)")
item.connect("activate", self.on_iso_clicked_handler, "CHGCAR")
menu.append(item)
item.show()
item = gtk.MenuItem("ELF (ELFCAR)")
item.connect("activate", self.on_iso_clicked_handler, "ELFCAR")
menu.append(item)
item.show()
item = gtk.MenuItem("Local potential (LOCPOT)")
item.connect("activate", self.on_iso_clicked_handler, "LOCPOT")
menu.append(item)
item.show()
item = gtk.MenuItem("Partial charge (PARCHG)")
item.connect("activate", self.on_iso_clicked_handler, "PARCHG")
menu.append(item)
item.show()
def on_measure_button_clicked_handler(self, *arg):
if self.measure is None:
self.measure = Measure(self)
else:
self.measure.show()
def on_front_button_clicked_handler(self, *arg):
self.swin.navigator.setFrontView()
def on_back_button_clicked_handler(self, *arg):
self.swin.navigator.setBackView()
def on_left_button_clicked_handler(self, *arg):
self.swin.navigator.setLeftView()
def on_right_button_clicked_handler(self, *arg):
self.swin.navigator.setRightView()
def on_top_button_clicked_handler(self, *arg):
self.swin.navigator.setTopView()
def on_bottom_button_clicked_handler(self, *arg):
self.swin.navigator.setBottomView()
def on_home_button_clicked_handler(self, *arg):
self.swin.navigator.setHome()
def on_zoom_11_button_clicked_handler(self, *arg):
self.swin.navigator.setZoom(1.0)
def on_zoom_in_button_clicked_handler(self, *arg):
self.swin.navigator.mulZoom(1.1)
def on_zoom_out_button_clicked_handler(self, *arg):
self.swin.navigator.mulZoom(1.0 / 1.1)
def on_ortho_button_clicked_handler(self, *arg):
self.swin.navigator.setPerspective(0)
def on_persp_button_clicked_handler(self, *arg):
self.swin.navigator.setPerspective(1)
def on_cuc_button_clicked_handler(self, *arg):
self.cell_centering = 1
if self.structure is not None:
self.setStructure(self.structure)
def on_tuc_button_clicked_handler(self, *arg):
self.cell_centering = 2
if self.structure is not None:
self.setStructure(self.structure)
def on_cell_scale_changed(self, *arg):
self.swin.setMultiple(self.csadj1.value, self.csadj2.value,
self.csadj3.value)
def on_sphere_size_scale_changed(self, *arg):
self.radius_factor = self.sss_adj.value
self.swin.structure_drawer.setRadiusFactor(0.5 * self.radius_factor)
def on_arrows_size_scale_changed(self, *arg):
self.swin.setArrowsScale(self.ass_adj.value)
def on_show_button_clicked_handler(self, *arg):
if self.system is not None:
a = p4vasp.Selection.selection().getAtoms()
info = self.swin.structure_drawer.info
l = info.len()
for i in a:
if i >= 0 and i < l:
info.getRecord(i).hidden = 0
self.hidden = filter(lambda i, f=info.getRecord: f(i).hidden,
range(l))
self.swin.updateStructure()
def on_hide_button_clicked_handler(self, *arg):
if self.system is not None:
a = p4vasp.Selection.selection().getAtoms()
info = self.swin.structure_drawer.info
l = info.len()
for i in a:
if i >= 0 and i < l:
info.getRecord(i).hidden = 1
self.hidden = filter(lambda i, f=info.getRecord: f(i).hidden,
range(l))
self.swin.updateStructure()
def on_showonly_button_clicked_handler(self, *arg):
if self.system is not None:
a = p4vasp.Selection.selection().getAtoms()
info = self.swin.structure_drawer.info
l = info.len()
for i in range(l):
info.getRecord(i).hidden = 1
for i in a:
if i >= 0 and i < l:
info.getRecord(i).hidden = 0
self.hidden = filter(lambda i, f=info.getRecord: f(i).hidden,
range(l))
self.swin.updateStructure()
def on_hideonly_button_clicked_handler(self, *arg):
if self.system is not None:
a = p4vasp.Selection.selection().getAtoms()
info = self.swin.structure_drawer.info
l = info.len()
for i in range(l):
info.getRecord(i).hidden = 0
for i in a:
if i >= 0 and i < l:
info.getRecord(i).hidden = 1
self.hidden = filter(lambda i, f=info.getRecord: f(i).hidden,
range(l))
self.swin.updateStructure()
# def on_put_selection_button_clicked_handler(self,*arg):
# if self.system is not None:
# sel=self.atom_selection.get_text()
# a=p4vasp.sellang.decode(sel,self.system.INITIAL_STRUCTURE)
# self.swin.removeSelectedAll()
# for i in a:
# self.swin.selectAtom(i)
# #self.swin.updateStructure()
#
# def on_get_selection_button_clicked_handler(self,*arg):
# if self.system is not None:
# sel=[]
# for i in range(self.swin.getSelectedCount()):
# sel.append(self.swin.getSelected(i).atom)
# a=p4vasp.sellang.encode(sel,self.system.INITIAL_STRUCTURE)
# sel=self.atom_selection.set_text(a)
# #self.swin.updateStructure()
def destroy(self):
print "destroy"
if self.swin is not None:
# print "hide"
# self.swin.hide()
# print "<-None"
self.swin = None
print "done"
def hide(self):
if self.swin is not None:
self.swin.hide()
def show(self):
if self.swin is not None:
self.swin.show()
self.updateSystem()
def setSeqIndex(self, index):
if index < -2:
index = -1
else:
if self.system.current("STRUCTURE_SEQUENCE_L") is not None:
if index >= len(self.system.STRUCTURE_SEQUENCE_L):
index = -2
self.index = index
try:
if index == -1:
self.setStructure(self.system.INITIAL_STRUCTURE)
self.swin.setArrows([])
elif index == -2:
self.setStructure(self.system.FINAL_STRUCTURE)
self.swin.setArrows([])
else:
self.setStructure(self.system.STRUCTURE_SEQUENCE_L[index])
if index < len(self.arrows_sequence):
self.swin.setArrows(self.arrows_sequence[index])
else:
self.swin.setArrows([])
error = 0
except:
msg().exception()
error = 1
entry = self.xml.get_widget("seq_entry")
if entry is not None:
if index == -1:
if error:
entry.set_text("ERR (Init. pos.)")
else:
entry.set_text("Initial pos.")
elif index == -2:
if error:
entry.set_text("ERR (Final pos.)")
else:
entry.set_text("Final pos.")
else:
if error:
entry.set_text("ERR " + str(index))
else:
entry.set_text(str(index))
def on_seq_first_clicked_handler(self, w):
self.setSeqIndex(-1)
def on_seq_last_clicked_handler(self, w):
self.setSeqIndex(-2)
def on_seq_back_clicked_handler(self, w):
if self.index == -2:
self.setSeqIndex(len(self.system.STRUCTURE_SEQUENCE_L) - 1)
else:
self.setSeqIndex(self.index - 1)
def on_seq_forward_clicked_handler(self, w):
self.setSeqIndex(self.index + 1)
def on_structureitem_clicked_handler(self, w, index):
self.setSeqIndex(index)
def on_none_arrows_clicked_handler(self, *arg):
self.arrows_sequence = []
self.setSeqIndex(self.index)
def on_forces_arrows_clicked_handler(self, *arg):
self.arrows_sequence = self.system.FORCES_SEQUENCE_L
self.setSeqIndex(self.index)
def on_SMI_arrows_clicked_handler(self, *arg):
self.arrows_sequence = SubtrSequence(self, "INITIAL_STRUCTURE", 1)
self.setSeqIndex(self.index)
def on_SMF_arrows_clicked_handler(self, *arg):
self.arrows_sequence = SubtrSequence(self, "FINAL_STRUCTURE", -1)
self.setSeqIndex(self.index)
def updateIsosurface(self):
if self.view_iso is None:
self.swin.setChgcar(None)
else:
if self.system[self.view_iso] is not None:
c = self.system[self.view_iso].get().clone()
if self.subtrchgcar is None:
s = strip(self.subtrentry.get_text())
if len(s):
self.subtrchgcar = cp4vasp.Chgcar()
self.subtrchgcar.read(s)
if self.subtrchgcar is not None:
try:
c.subtractChgcar(self.subtrchgcar)
except:
self.subtrchgcar = None
self.swin.setChgcar(None)
try:
msg().message("Isosurface Level: %s" %
self.levelentry.get_text())
l = float(self.levelentry.get_text())
self.swin.setIsosurfaceLevel(l)
except:
pass
self.swin.setChgcar(c)
def updateIsosurfaceGen(self):
if self.view_iso is None:
self.swin.setChgcar(None)
msg().message("isosurface off")
else:
msg().message("view isosurface of %s" % self.view_iso)
if self.system[self.view_iso] is not None:
self.system.scheduleFirst(self.view_iso)
yield 1
c = self.system[self.view_iso].get().clone()
yield 1
if self.subtrchgcar is None:
s = strip(self.subtrentry.get_text())
if len(s):
msg().status("Read %s for subtraction" % s)
self.subtrchgcar = cp4vasp.Chgcar()
g = self.subtrchgcar.createReadProcess(s)
yield 1
while g.next():
st = g.error()
if st is not None:
msg().error(st)
st = g.status()
if s is not None:
msg().status(st)
msg().step(g.step(), g.total())
yield 1
s = g.error()
if s is not None:
msg().error(s)
s = g.status()
if s is not None:
msg().status(s)
msg().step(g.step(), g.total())
msg().step(0, 1)
if self.subtrchgcar is not None:
try:
msg().status("Chgcar subtraction")
yield 1
c.subtractChgcar(self.subtrchgcar)
yield 1
except:
self.subtrchgcar = None
self.swin.setChgcar(None)
try:
msg().message("Isosurface Level: %s" %
self.levelentry.get_text())
l = float(self.levelentry.get_text())
self.swin.setIsosurfaceLevel(l)
except:
pass
msg().status("Creating isosurface")
yield 1
self.swin.setChgcar(c)
msg().status("OK")
def on_iso_clicked_handler(self, w, iso):
self.view_iso = iso
# self.updateIsosurface()
schedule(self.updateIsosurfaceGen())
# def on_levelentry_changed(self,*arg):
# print "on_levelentry_changed"
def on_selectsubtr_clicked_handler(self, *arg):
if self.subtr_density_fileselection is None:
xml = p4vasp.util.loadGlade(self.gladefile,
"subtr_density_fileselection")
xml.signal_connect('hide_widget', self.hide_widget_handler)
xml.signal_connect('show_widget', self.show_widget_handler)
xml.signal_connect("on_subtr_density_ok_clicked",
self.on_subtr_density_ok_clicked_handler)
self.subtr_density_fileselection = xml.get_widget(
"subtr_density_fileselection")
self.subtr_density_fileselection.show()
# def on_subtrentry_changed(self,*arg):
# print "on_subtrentry_changed"
def on_updateisobutton_clicked_handler(self, *arg):
# self.updateIsosurface()
schedule(self.updateIsosurfaceGen())
def on_minlevelbutton_clicked_handler(self, *arg):
c = self.swin.chgcar
self.levelentry.set_text(str(c.getMinimum()))
# self.updateIsosurface()
schedule(self.updateIsosurfaceGen())
def on_maxlevelbutton_clicked_handler(self, *arg):
c = self.swin.chgcar
self.levelentry.set_text(str(c.getMaximum()))
# self.updateIsosurface()
schedule(self.updateIsosurfaceGen())
def on_avglevelbutton_clicked_handler(self, *arg):
c = self.swin.chgcar
self.levelentry.set_text(str(c.getAverage()))
# self.updateIsosurface()
schedule(self.updateIsosurfaceGen())
def hide_widget_handler(self, widget):
widget.hide()
def show_widget_handler(self, widget):
widget.show()
def on_subtr_density_ok_clicked_handler(self, *arg):
self.subtrentry.set_text(
self.subtr_density_fileselection.get_filename())
self.subtr_density_fileselection.hide()
self.subtrchgcar = None
# self.updateIsosurface()
schedule(self.updateIsosurfaceGen())
def on_foto_button_clicked_handler(self, *arg):
import os.path
i = 1
while os.path.exists("p4vasp%04d.tga" % i):
i += 1
self.swin.win.saveScreenshot("p4vasp%04d.tga" % i)
def saveanim(self):
import cp4vasp
seq = self.system.STRUCTURE_SEQUENCE_L
index = self.index
msg().status("Save picture of the initial structure")
yield 1
self.setSeqIndex(-1)
cp4vasp.VisCheck()
self.swin.win.saveScreenshot("p4vasp_initial.tga")
msg().status("Save picture of the final structure")
yield 1
self.setSeqIndex(-2)
cp4vasp.VisCheck()
self.swin.win.saveScreenshot("p4vasp_final.tga")
for i in range(len(seq)):
msg().step(i + 1, len(seq))
msg().status("Save step %d" % i)
yield 1
self.setSeqIndex(i)
cp4vasp.VisCheck()
self.swin.win.saveScreenshot("p4vasp_step%03d.tga" % (i + 1))
self.setSeqIndex(index)
msg().status("OK")
msg().step(0, 1)
def on_anim_button_clicked_handler(self, *arg):
schedule(self.saveanim())
class StructureWindowApplet(Applet, p4vasp.Selection.SelectionListener):
menupath = ["Structure", "Window"]
showmode = Applet.EXTERNAL_ONLY_MODE
NONE_SEQUENCE = 0
INITIAL_SEQUENCE = 1
FINAL_SEQUENCE = 2
PRIMITIVE_SEQUENCE = 3
UNDEFINED_SEQUENCE = 4
RELAXATION_SEQUENCE = 5
MD_SEQUENCE = 6
NONE_ARROWS = 0
FORCES_ARROWS = 1
DIFF_INITIAL_ARROWS = 2
DIFF_FINAL_ARROWS = 3
DIFF_PREVIOUS_ARROWS = 4
DIFF_NEXT_ARROWS = 5
PHONON_ARROWS = 6
CELL_CENTERING_NONE = 0
CELL_CENTERING_INSIDE = 1
CELL_CENTERING_ZERO = 2
def notifyAtomSelection(self, sel, origin):
# self.atom_selection.set_text(sel.encode(self.structure))
sel = p4vasp.Selection.selection()
self.swin.removeSelectedAll()
for i, nx, ny, nz in sel:
self.swin.selectAtom(i, nx, ny, nz)
def __init__(self):
Applet.__init__(self)
self.swin = None
self.radius_factor = 1.0
self.index = 0
self.sequencetype = self.INITIAL_SEQUENCE
self.arrowstype = 0
self.cell_centering = 0
def initUI(self):
self.showStructureWindow()
def setExternalMode(self):
pass
def setEmbeddedMode(self):
# msg().error("StructureWindowApplet.setEmbeddedMode() not supported.")
raise "StructureWindowApplet.setEmbeddedMode() not supported."
def createPanel(self):
return None
def setSystem(self, x=None):
if not self.pin_status:
self.system = x
self.updateSystem()
def updateSystem(self, x=None):
# self.swin.setStructure(self.system.INITIAL_STRUCTURE)
self.updateSeq()
def showStructureWindow(self):
if self.swin is None:
l = [(0, 0, 0, 0)]
for a in applets():
if isinstance(a, StructureWindowApplet):
if a.swin is not None:
w = a.swin.win
if w is not None:
l.append((w.x, w.y, w.w, w.h))
xx = max(map(lambda x: x[0] + x[2], l))
yy = max(map(lambda x: x[1] + x[3], l))
if yy <= 600:
xx = 0
else:
yy = 0
self.swin = StructureWindow(x=xx,
y=yy,
w=500,
h=400,
title="p4vasp Structure",
atomtypes=getAtomtypes())
self.swin.setRadiusFactor(0.5 * self.radius_factor)
# self.swin.setBackground(1,1,1)
self.swin.show()
def getSequence(self):
if self.sequencetype == self.NONE_SEQUENCE:
return None
if self.sequencetype == self.INITIAL_SEQUENCE:
s = self.system.INITIAL_STRUCTURE
if s is not None:
return [s]
else:
return None
if self.sequencetype == self.FINAL_SEQUENCE:
s = self.system.FINAL_STRUCTURE
if s is not None:
return [s]
else:
return None
if self.sequencetype == self.PRIMITIVE_SEQUENCE:
s = self.system.PRIMITIVE_STRUCTURE
if s is not None:
return [s]
else:
return None
if self.sequencetype == self.UNDEFINED_SEQUENCE:
return self.system.STRUCTURE_SEQUENCE_L
if self.sequencetype == self.RELAXATION_SEQUENCE:
return self.system.RELAXATION_SEQUENCE_L
if self.sequencetype == self.MD_SEQUENCE:
return self.system.MD_SEQUENCE_L
return None
def getArrows(self, index=None):
if index is None:
index = self.index
if self.system is None:
return None
if self.arrowstype == self.FORCES_ARROWS:
f = self.system.FORCES_SEQUENCE_L
if f is not None:
if index < len(f):
return f[index]
seq = self.getSequence()
if seq is not None:
if index < len(seq):
if len(seq[index]) == 0:
return None
si = p4vasp.cStructure.Structure(seq[index])
si.setCarthesian()
if self.arrowstype == self.DIFF_INITIAL_ARROWS:
rel = self.system.INITIAL_STRUCTURE
if rel is not None:
rel = p4vasp.cStructure.Structure(rel)
rel.setCarthesian()
l = []
for i in range(min(len(si), len(rel))):
l.append(si[i] - rel[i])
return l
if self.arrowstype == self.DIFF_FINAL_ARROWS:
rel = self.system.FINAL_STRUCTURE
if rel is not None:
rel = p4vasp.cStructure.Structure(rel)
rel.setCarthesian()
l = []
for i in range(min(len(si), len(rel))):
l.append(rel[i] - si[i])
return l
return None
def getArrowsSequence(self):
if self.arrowstype == self.NONE_ARROWS:
return None
sequence = self.getSequence()
if sequence is None:
return None
arrows_sequence = []
for i in range(len(sequence)):
arrows_sequence.append(self.getArrows(i))
return arrows_sequence
def setStructure(self, s):
if s is not None:
s = p4vasp.Structure.Structure(s)
if self.cell_centering == self.CELL_CENTERING_INSIDE:
s.toUnitCell()
elif self.cell_centering == self.CELL_CENTERING_ZERO:
s.toCenteredUnitCell()
self.swin.setStructure(s)
else:
self.swin.setStructure(None)
def updateSeq(self):
index = self.index
seq = self.getSequence()
# print "updateSeq",index,len(seq)
if seq is not None:
if index == "last":
index = len(seq) - 1
# print " a",index,len(seq)
if index < 0:
index = len(seq) + index
elif index >= len(seq):
index = len(seq) - 1
# print " b",index,len(seq)
if index < 0:
index = 0
# print " c",index,len(seq)
self.index = index
self.setStructure(seq[index])
else:
index = 0
self.index = 0
self.setStructure(None)
self.swin.setArrows(self.getArrows())
def setIndex(self, index):
self.index = index
self.updateSeq()
def setSequenceType(self, seqtype):
self.sequencetype = seqtype
self.updateSeq()
def setArrowsType(self, atype):
self.arrowstype = atype
self.updateSeq()
def getWindowPtr(self):
if self.swin is not None:
if self.swin.win is not None:
return self.swin.win.this
return None