/usr/share/pyshared/ase/gui/graphene.py is in python-ase 3.6.0.2515-1.
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"""nanotube.py - Window for setting up Graphene sheets and ribbons.
"""
import gtk
from gettext import gettext as _
from ase.gui.widgets import pack, cancel_apply_ok, oops
from ase.gui.setupwindow import SetupWindow
from ase.gui.pybutton import PyButton
from ase.structure import graphene_nanoribbon
import ase
import numpy as np
introtext = _("""\
Set up a graphene sheet or a graphene nanoribbon. A nanoribbon may
optionally be saturated with hydrogen (or another element).\
""")
py_template = """
from ase.structure import nanotube
atoms = nanotube(%(n)i, %(m)i, length=%(length)i, bond=%(bl).3f, symbol=%(symb)s)
"""
class SetupGraphene(SetupWindow):
"Window for setting up a graphene sheet or nanoribbon."
def __init__(self, gui):
SetupWindow.__init__(self)
self.set_title(_("Graphene"))
vbox = gtk.VBox()
# Intoductory text
self.packtext(vbox, introtext)
# Choose structure
label = gtk.Label(_("Structure: "))
self.struct = gtk.combo_box_new_text()
for s in (_("Infinite sheet"), _("Unsaturated ribbon"),
_("Saturated ribbon")):
self.struct.append_text(s)
self.struct.set_active(0)
self.struct.connect('changed', self.update_gui)
pack(vbox, [label, self.struct])
# Orientation
label = gtk.Label(_("Orientation: "))
self.orient = gtk.combo_box_new_text()
self.orient_text = []
for s in (_("zigzag"), _("armchair")):
self.orient.append_text(s)
self.orient_text.append(s)
self.orient.set_active(0)
self.orient.connect('changed', self.update_gui)
pack(vbox, [label, self.orient])
pack(vbox, gtk.Label(""))
# Choose the element and bond length
label1 = gtk.Label("Element: ")
#label.set_alignment(0.0, 0.2)
self.element = gtk.Entry(max=3)
self.element.set_text("C")
self.element.connect('activate', self.update_element)
self.bondlength = gtk.Adjustment(1.42, 0.0, 1000.0, 0.01)
label2 = gtk.Label(_(" Bond length: "))
label3 = gtk.Label(_("Å"))
bond_box = gtk.SpinButton(self.bondlength, 10.0, 3)
pack(vbox, [label1, self.element, label2, bond_box, label3])
# Choose the saturation element and bond length
self.sat_label1 = gtk.Label(_("Saturation: "))
#label.set_alignment(0.0, 0.2)
self.element2 = gtk.Entry(max=3)
self.element2.set_text(_("H"))
self.element2.connect('activate', self.update_element)
self.bondlength2 = gtk.Adjustment(1.12, 0.0, 1000.0, 0.01)
self.sat_label2 = gtk.Label(_(" Bond length: "))
self.sat_label3 = gtk.Label(_("Å"))
self.bond_box = gtk.SpinButton(self.bondlength2, 10.0, 3)
pack(vbox, [self.sat_label1, self.element2, self.sat_label2,
self.bond_box, self.sat_label3])
self.elementinfo = gtk.Label("")
self.elementinfo.modify_fg(gtk.STATE_NORMAL,
gtk.gdk.color_parse('#FF0000'))
pack(vbox, [self.elementinfo])
pack(vbox, gtk.Label(""))
# Size
label1 = gtk.Label(_("Width: "))
label2 = gtk.Label(_(" Length: "))
self.n = gtk.Adjustment(1, 1, 100, 1)
self.m = gtk.Adjustment(1, 1, 100, 1)
spinn = gtk.SpinButton(self.n, 0, 0)
spinm = gtk.SpinButton(self.m, 0, 0)
pack(vbox, [label1, spinn, label2, spinm])
# Vacuum
label1 = gtk.Label(_("Vacuum: "))
self.vacuum = gtk.Adjustment(5.0, 0.0, 1000.0, 0.1)
label2 = gtk.Label(_("Å"))
vac_box = gtk.SpinButton(self.vacuum, 10.0, 2)
pack(vbox, [label1, vac_box, label2])
pack(vbox, gtk.Label(""))
# Buttons
#self.pybut = PyButton("Creating a nanoparticle.")
#self.pybut.connect('clicked', self.makeatoms)
buts = cancel_apply_ok(cancel=lambda widget: self.destroy(),
apply=self.apply,
ok=self.ok)
pack(vbox, [buts], end=True, bottom=True)
# Finalize setup
self.update_gui()
self.add(vbox)
vbox.show()
self.show()
self.gui = gui
def update_element(self, *args):
"Called when a new element may have been entered."
# Assumes the element widget is self.element and that a label
# for errors is self.elementinfo. The chemical symbol is
# placed in self.legalelement - or None if the element is
# invalid.
symb = []
if self.struct.get_active() == 2:
# Saturated nanoribbon
elements = (self.element.get_text(), self.element2.get_text())
else:
elements = (self.element.get_text(), )
for elem in elements:
if not elem:
self.invalid_element(_(" No element specified!"))
return False
try:
z = int(elem)
except ValueError:
# Probably a symbol
try:
z = ase.data.atomic_numbers[elem]
except KeyError:
self.invalid_element()
return False
try:
symb.append(ase.data.chemical_symbols[z])
except KeyError:
self.invalid_element()
return False
self.elementinfo.set_text("")
self.legal_element = symb[0]
if len(symb) == 2:
self.legal_element2 = symb[1]
else:
self.legal_element2 = None
return True
def update_gui(self, *args):
# Saturation element is only relevant for saturated nanoribbons
satur = self.struct.get_active() == 2
for w in (self.element2, self.bond_box):
w.set_sensitive(satur)
# Infinite zigzag sheets must have even width
if self.struct.get_active() == 0 and self.orient.get_active() == 0:
if self.n.value % 2 == 1:
self.n.value += 1
self.n.lower = 2
self.n.step_increment = 2
else:
self.n.lower = 1
self.n.step_increment = 1
def makeatoms(self, *args):
self.update_element()
if self.legal_element is None or (self.struct.get_active() == 2 and
self.legal_element2 is None):
self.atoms = None
self.pybut.python = None
else:
n = int(self.n.value)
m = int(self.m.value)
CC = self.bondlength.value
vacuum = self.vacuum.value
orient = self.orient_text[self.orient.get_active()]
elem = self.legal_element
if self.struct.get_active() == 0:
# Extended sheet
self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
vacc=vacuum, sheet=True,
main_element=elem)
elif self.struct.get_active() == 1:
# Unsaturated nanoribbon
self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
vacc=vacuum,
main_element=elem)
elif self.struct.get_active() == 2:
# Saturated nanoribbon
elem2 = self.legal_element2
self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
C_H=self.bondlength2.value,
vacuum=vacuum,
saturated=True,
main_element=elem,
saturate_element=elem2)
else:
raise RuntimeError("Unknown structure in SetupGraphene!")
# Now, rotate into the xy plane (ase.gui's default view plane)
pos = self.atoms.get_positions()
cell = self.atoms.get_cell()
pbc = self.atoms.get_pbc()
cell[1,1], cell[2,2] = cell[2,2], cell[1,1]
x = pos[:,1].copy()
z = pos[:,2].copy()
pos[:,1] = z
pos[:,2] = x
self.atoms.set_cell(cell)
self.atoms.set_positions(pos)
self.atoms.set_pbc([pbc[0], pbc[2], pbc[1]])
def apply(self, *args):
self.makeatoms()
if self.atoms is not None:
self.gui.new_atoms(self.atoms)
return True
else:
oops(_("No valid atoms."),
_("You have not (yet) specified a consistent set of "
"parameters."))
return False
def ok(self, *args):
if self.apply():
self.destroy()
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