/usr/share/pyshared/ase/gui/surfaceslab.py is in python-ase 3.6.0.2515-1.
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"""surfaceslab.py - Window for setting up surfaces
"""
import gtk
from gettext import gettext as _
from ase.gui.widgets import pack, cancel_apply_ok, oops
from ase.gui.pybutton import PyButton
from ase.gui.setupwindow import SetupWindow
import ase.lattice.surface as _surf
import ase
import numpy as np
introtext = _("""\
Use this dialog to create surface slabs. Select the element by
writing the chemical symbol or the atomic number in the box. Then
select the desired surface structure. Note that some structures can
be created with an othogonal or a non-orthogonal unit cell, in these
cases the non-orthogonal unit cell will contain fewer atoms.
If the structure matches the experimental crystal structure, you can
look up the lattice constant, otherwise you have to specify it
yourself.""")
# Name, structure, orthogonal, support-nonorthogonal, function
surfaces = [(_('FCC(100)'), _('fcc'), True, False, _surf.fcc100),
(_('FCC(110)'), _('fcc'), True, False, _surf.fcc110),
(_('FCC(111) non-orthogonal'), _('fcc'), False, True,
_surf.fcc111),
(_('FCC(111) orthogonal'), _('fcc'), True, True, _surf.fcc111),
(_('BCC(100)'), _('bcc'), True, False, _surf.bcc100),
(_('BCC(110) non-orthogonal'), _('bcc'), False, True,
_surf.bcc110),
(_('BCC(110) orthogonal'), _('bcc'), True, True, _surf.bcc110),
(_('BCC(111) non-orthogonal'), _('bcc'), False, True,
_surf.bcc111),
(_('BCC(111) orthogonal'), _('bcc'), True, True, _surf.bcc111),
(_('HCP(0001) non-orthogonal'), _('hcp'), False, True,
_surf.hcp0001),
(_('HCP(0001) orthogonal'), _('hcp'), True, True, _surf.hcp0001),
(_('HCP(10-10) orthogonal'), _('hcp'), True, False,
_surf.hcp10m10),
(_('DIAMOND(100) orthogonal'), _('diamond'), True, False,
_surf.diamond100),
(_('DIAMOND(111) non-orthogonal'), _('diamond'), False, True,
_surf.diamond111),
]
py_template = """
from ase.lattice.surface import %(func)s
atoms = %(func)s(symbol='%(symbol)s', size=%(size)s,
a=%(a).3f, vacuum=%(vacuum).3f%(orthoarg)s)
"""
class SetupSurfaceSlab(SetupWindow):
"""Window for setting up a surface."""
def __init__(self, gui):
SetupWindow.__init__(self)
self.set_title(_("Surface"))
self.atoms = None
vbox = gtk.VBox()
# Intoductory text
self.packtext(vbox, introtext)
# Choose the element
label = gtk.Label(_("Element: "))
element = gtk.Entry(max=3)
self.element = element
self.elementinfo = gtk.Label("")
pack(vbox, [label, element, self.elementinfo])
self.element.connect('activate', self.update)
self.legal_element = False
# Choose the surface structure
label = gtk.Label(_("Structure: "))
self.structchoice = gtk.combo_box_new_text()
self.surfinfo = {}
for s in surfaces:
assert len(s) == 5
self.structchoice.append_text(s[0])
self.surfinfo[s[0]] = s
pack(vbox, [label, self.structchoice])
self.structchoice.connect('changed', self.update)
# Choose the lattice constant
tbl = gtk.Table(2, 3)
label = gtk.Label(_("Lattice constant: "))
tbl.attach(label, 0, 1, 0, 1)
vbox2 = gtk.VBox() # For the non-HCP stuff
self.vbox_hcp = gtk.VBox() # For the HCP stuff.
self.lattice_const = gtk.Adjustment(3.0, 0.0, 1000.0, 0.01)
lattice_box = gtk.SpinButton(self.lattice_const, 10.0, 3)
lattice_box.numeric = True
pack(vbox2, [gtk.Label(_("a:")), lattice_box, gtk.Label(_("Å"))])
tbl.attach(vbox2, 1, 2, 0, 1)
lattice_button = gtk.Button(_("Get from database"))
tbl.attach(lattice_button, 2, 3, 0, 1)
# HCP stuff
self.hcp_ideal = (8.0/3)**(1.0/3)
self.lattice_const_c = gtk.Adjustment(self.lattice_const.value * self.hcp_ideal,
0.0, 1000.0, 0.01)
lattice_box_c = gtk.SpinButton(self.lattice_const_c, 10.0, 3)
lattice_box_c.numeric = True
pack(self.vbox_hcp, [gtk.Label("c:"),
lattice_box_c, gtk.Label("Å")])
self.hcp_c_over_a_format = "c/a: %.3f " + _("(%.1f %% of ideal)")
self.hcp_c_over_a_label = gtk.Label(self.hcp_c_over_a_format % \
(self.hcp_ideal, 100.0))
pack(self.vbox_hcp, [self.hcp_c_over_a_label])
tbl.attach(self.vbox_hcp, 1, 2, 1, 2)
tbl.show_all()
pack(vbox, [tbl])
self.lattice_const.connect('value-changed', self.update)
self.lattice_const_c.connect('value-changed', self.update)
lattice_button.connect('clicked', self.get_lattice_const)
pack(vbox, gtk.Label(""))
# System size
self.size = [gtk.Adjustment(1, 1, 100, 1) for i in range(3)]
buttons = [gtk.SpinButton(s, 0, 0) for s in self.size]
self.vacuum = gtk.Adjustment(10.0, 0, 100.0, 0.1)
vacuum_box = gtk.SpinButton(self.vacuum, 0.0, 1)
pack(vbox, [gtk.Label(_("Size: \tx: ")), buttons[0],
gtk.Label(_(" unit cells"))])
pack(vbox, [gtk.Label(_("\t\ty: ")), buttons[1],
gtk.Label(_(" unit cells"))])
pack(vbox, [gtk.Label(_(" \t\tz: ")), buttons[2],
gtk.Label(_(" layers, ")),
vacuum_box, gtk.Label(_(" Å vacuum"))])
self.nosize = _("\t\tNo size information yet.")
self.sizelabel = gtk.Label(self.nosize)
pack(vbox, [self.sizelabel])
for s in self.size:
s.connect('value-changed', self.update)
self.vacuum.connect('value-changed', self.update)
pack(vbox, gtk.Label(""))
# Buttons
self.pybut = PyButton(_("Creating a surface slab."))
self.pybut.connect('clicked', self.update)
buts = cancel_apply_ok(cancel=lambda widget: self.destroy(),
apply=self.apply,
ok=self.ok)
pack(vbox, [self.pybut, buts], end=True, bottom=True)
self.add(vbox)
vbox.show()
self.show()
self.gui = gui
# Hide the HCP stuff to begin with.
self.vbox_hcp.hide_all()
# update_element inherited from SetupWindow
def update(self, *args):
"Called when something has changed."
struct = self.structchoice.get_active_text()
if struct:
structinfo = self.surfinfo[struct]
if structinfo[1] == 'hcp':
self.vbox_hcp.show_all()
ca = self.lattice_const_c.value / self.lattice_const.value
self.hcp_c_over_a_label.set_text(self.hcp_c_over_a_format %
(ca, 100 * ca / self.hcp_ideal))
else:
self.vbox_hcp.hide_all()
# Abort if element or structure is invalid
if not (self.update_element() and struct):
self.sizelabel.set_text(self.nosize)
self.atoms = None
self.pybut.python = None
return False
# Make the atoms
assert self.legal_element
kw = {}
kw2 = {}
if structinfo[3]: # Support othogonal keyword?
kw['orthogonal'] = structinfo[2]
kw2['orthoarg'] = ', orthogonal=' + str(kw['orthogonal'])
else:
kw2['orthoarg'] = ''
kw2['func'] = structinfo[4].__name__
kw['symbol'] = self.legal_element
kw['size'] = [int(s.value) for s in self.size]
kw['a'] = self.lattice_const.value
kw['vacuum'] = self.vacuum.value
# Now create the atoms
try:
self.atoms = structinfo[4](**kw)
except ValueError, e:
# The values were illegal - for example some size
# constants must be even for some structures.
self.pybut.python = None
self.atoms = None
self.sizelabel.set_text(str(e).replace(". ", ".\n"))
return False
kw2.update(kw)
self.pybut.python = py_template % kw2
# Find the heights of the unit cell
h = np.zeros(3)
uc = self.atoms.get_cell()
for i in range(3):
norm = np.cross(uc[i-1], uc[i-2])
norm /= np.sqrt(np.dot(norm, norm))
h[i] = np.abs(np.dot(norm, uc[i]))
natoms = len(self.atoms)
txt = ("\t\t%.2f Å x %.2f Å x %.2f Å, %s"
% (h[0], h[1], h[2], _('%i atoms.') % natoms))
self.sizelabel.set_text(txt)
return True
def get_lattice_const(self, *args):
if not self.update_element():
oops(_("Invalid element."))
return
z = ase.atomic_numbers[self.legal_element]
ref = ase.data.reference_states[z]
surface = self.structchoice.get_active_text()
if not surface:
oops(_("No structure specified!"))
return
struct = self.surfinfo[surface][1]
if ref is None or ref['symmetry'] != struct:
from ase.data.alternatives import alternative_structures
alt = alternative_structures[z]
if alt and alt['symmetry'] == struct:
ref = alt
else:
oops(_('%(struct)s lattice constant unknown for %(element)s.')
% dict(struct=struct.upper(), element=self.legal_element))
a = ref['a']
self.lattice_const.set_value(a)
if struct == 'hcp':
c = ref['c/a'] * a
self.lattice_const_c.set_value(c)
def apply(self, *args):
self.update()
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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