1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
|
# encoding: utf-8
"""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.status import formula
from ase.build 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.build import nanotube
atoms = nanotube(%(n)i, %(m)i, length=%(length)i, bond=%(bl).3f, symbol=%(symb)s)
"""
label_template = _(""" %(natoms)i atoms: %(symbols)s, Volume: %(volume).3f A<sup>3</sup>""")
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)
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)
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.bondlength = gtk.Adjustment(1.42, 0.0, 1000.0, 0.01)
label2 = gtk.Label(_(" Bond length: "))
label3 = gtk.Label(_(u"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.bondlength2 = gtk.Adjustment(1.12, 0.0, 1000.0, 0.01)
self.sat_label2 = gtk.Label(_(" Bond length: "))
self.sat_label3 = gtk.Label(_(u"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(_(u"Å"))
vac_box = gtk.SpinButton(self.vacuum, 10.0, 2)
pack(vbox, [label1, vac_box, label2])
pack(vbox, gtk.Label(""))
self.status = gtk.Label("")
pack(vbox,[self.status])
pack(vbox,[gtk.Label("")])
# Buttons
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.makeatoms()
self.struct.connect('changed', self.makeatoms)
self.orient.connect('changed', self.makeatoms)
self.element.connect('activate', self.makeatoms)
self.bondlength.connect('value-changed', self.makeatoms)
self.element2.connect('activate', self.makeatoms)
self.bondlength2.connect('value-changed', self.makeatoms)
self.n.connect('value-changed', self.makeatoms)
self.m.connect('value-changed', self.makeatoms)
self.vacuum.connect('value-changed', self.makeatoms)
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()
self.update_gui()
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
self.status.set_markup(_("Please specify a consistent set of atoms. "))
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]])
# 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]))
label = label_template % {'natoms' : len(self.atoms),
'symbols' : formula(self.atoms.get_atomic_numbers()),
'volume' : self.atoms.get_volume()}
self.status.set_markup(label)
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()
|
