root / ase / gui / graphene.py @ 13
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| 1 | 1 | tkerber | # encoding: utf-8
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| 2 | 1 | tkerber | """nanotube.py - Window for setting up Graphene sheets and ribbons.
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| 3 | 1 | tkerber | """
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| 4 | 1 | tkerber | |
| 5 | 1 | tkerber | |
| 6 | 1 | tkerber | import gtk |
| 7 | 1 | tkerber | from ase.gui.widgets import pack, cancel_apply_ok, oops |
| 8 | 1 | tkerber | from ase.gui.setupwindow import SetupWindow |
| 9 | 1 | tkerber | from ase.gui.pybutton import PyButton |
| 10 | 1 | tkerber | from ase.structure import graphene_nanoribbon |
| 11 | 1 | tkerber | import ase |
| 12 | 1 | tkerber | import numpy as np |
| 13 | 1 | tkerber | |
| 14 | 1 | tkerber | introtext = """\
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| 15 | 1 | tkerber | Set up a graphene sheet or a graphene nanoribbon. A nanoribbon may
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| 16 | 1 | tkerber | optionally be saturated with hydrogen (or another element).\
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| 17 | 1 | tkerber | """
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| 18 | 1 | tkerber | |
| 19 | 1 | tkerber | py_template = """
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| 20 | 1 | tkerber | from ase.structure import nanotube
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| 21 | 1 | tkerber |
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| 22 | 1 | tkerber | atoms = nanotube(%(n)i, %(m)i, length=%(length)i, bond=%(bl).3f, symbol=%(symb)s)
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| 23 | 1 | tkerber | """
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| 24 | 1 | tkerber | |
| 25 | 1 | tkerber | class SetupGraphene(SetupWindow): |
| 26 | 1 | tkerber | "Window for setting up a graphene sheet or nanoribbon."
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| 27 | 1 | tkerber | def __init__(self, gui): |
| 28 | 1 | tkerber | SetupWindow.__init__(self)
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| 29 | 1 | tkerber | self.set_title("Nanotube") |
| 30 | 1 | tkerber | vbox = gtk.VBox() |
| 31 | 1 | tkerber | |
| 32 | 1 | tkerber | # Intoductory text
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| 33 | 1 | tkerber | self.packtext(vbox, introtext)
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| 34 | 1 | tkerber | |
| 35 | 1 | tkerber | # Choose structure
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| 36 | 1 | tkerber | label = gtk.Label("Structure: ")
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| 37 | 1 | tkerber | self.struct = gtk.combo_box_new_text()
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| 38 | 1 | tkerber | for s in ("Infinite sheet", "Unsaturated ribbon", "Saturated ribbon"): |
| 39 | 1 | tkerber | self.struct.append_text(s)
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| 40 | 1 | tkerber | self.struct.set_active(0) |
| 41 | 1 | tkerber | self.struct.connect('changed', self.update_gui) |
| 42 | 1 | tkerber | pack(vbox, [label, self.struct])
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| 43 | 1 | tkerber | |
| 44 | 1 | tkerber | # Orientation
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| 45 | 1 | tkerber | label = gtk.Label("Orientation: ")
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| 46 | 1 | tkerber | self.orient = gtk.combo_box_new_text()
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| 47 | 1 | tkerber | self.orient_text = []
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| 48 | 1 | tkerber | for s in ("zigzag", "armchair"): |
| 49 | 1 | tkerber | self.orient.append_text(s)
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| 50 | 1 | tkerber | self.orient_text.append(s)
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| 51 | 1 | tkerber | self.orient.set_active(0) |
| 52 | 1 | tkerber | self.orient.connect('changed', self.update_gui) |
| 53 | 1 | tkerber | pack(vbox, [label, self.orient])
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| 54 | 1 | tkerber | pack(vbox, gtk.Label(""))
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| 55 | 1 | tkerber | |
| 56 | 1 | tkerber | |
| 57 | 1 | tkerber | # Choose the element and bond length
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| 58 | 1 | tkerber | label1 = gtk.Label("Element: ")
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| 59 | 1 | tkerber | #label.set_alignment(0.0, 0.2)
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| 60 | 1 | tkerber | self.element = gtk.Entry(max=3) |
| 61 | 1 | tkerber | self.element.set_text("C") |
| 62 | 1 | tkerber | self.element.connect('activate', self.update_element) |
| 63 | 1 | tkerber | self.bondlength = gtk.Adjustment(1.42, 0.0, 1000.0, 0.01) |
| 64 | 1 | tkerber | label2 = gtk.Label(" Bond length: ")
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| 65 | 1 | tkerber | label3 = gtk.Label("Å")
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| 66 | 1 | tkerber | bond_box = gtk.SpinButton(self.bondlength, 10.0, 3) |
| 67 | 1 | tkerber | pack(vbox, [label1, self.element, label2, bond_box, label3])
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| 68 | 1 | tkerber | |
| 69 | 1 | tkerber | # Choose the saturation element and bond length
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| 70 | 1 | tkerber | self.sat_label1 = gtk.Label("Saturation: ") |
| 71 | 1 | tkerber | #label.set_alignment(0.0, 0.2)
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| 72 | 1 | tkerber | self.element2 = gtk.Entry(max=3) |
| 73 | 1 | tkerber | self.element2.set_text("H") |
| 74 | 1 | tkerber | self.element2.connect('activate', self.update_element) |
| 75 | 1 | tkerber | self.bondlength2 = gtk.Adjustment(1.12, 0.0, 1000.0, 0.01) |
| 76 | 1 | tkerber | self.sat_label2 = gtk.Label(" Bond length: ") |
| 77 | 1 | tkerber | self.sat_label3 = gtk.Label("Å") |
| 78 | 1 | tkerber | self.bond_box = gtk.SpinButton(self.bondlength2, 10.0, 3) |
| 79 | 1 | tkerber | pack(vbox, [self.sat_label1, self.element2, self.sat_label2, |
| 80 | 1 | tkerber | self.bond_box, self.sat_label3]) |
| 81 | 1 | tkerber | |
| 82 | 1 | tkerber | self.elementinfo = gtk.Label("") |
| 83 | 1 | tkerber | self.elementinfo.modify_fg(gtk.STATE_NORMAL,
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| 84 | 1 | tkerber | gtk.gdk.color_parse('#FF0000'))
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| 85 | 1 | tkerber | pack(vbox, [self.elementinfo])
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| 86 | 1 | tkerber | pack(vbox, gtk.Label(""))
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| 87 | 1 | tkerber | |
| 88 | 1 | tkerber | # Size
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| 89 | 1 | tkerber | label1 = gtk.Label("Width: ")
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| 90 | 1 | tkerber | label2 = gtk.Label(" Length: ")
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| 91 | 1 | tkerber | self.n = gtk.Adjustment(1, 1, 100, 1) |
| 92 | 1 | tkerber | self.m = gtk.Adjustment(1, 1, 100, 1) |
| 93 | 1 | tkerber | spinn = gtk.SpinButton(self.n, 0, 0) |
| 94 | 1 | tkerber | spinm = gtk.SpinButton(self.m, 0, 0) |
| 95 | 1 | tkerber | pack(vbox, [label1, spinn, label2, spinm]) |
| 96 | 1 | tkerber | |
| 97 | 1 | tkerber | # Vacuum
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| 98 | 1 | tkerber | label1 = gtk.Label("Vacuum: ")
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| 99 | 1 | tkerber | self.vacuum = gtk.Adjustment(5.0, 0.0, 1000.0, 0.1) |
| 100 | 1 | tkerber | label2 = gtk.Label("Å")
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| 101 | 1 | tkerber | vac_box = gtk.SpinButton(self.vacuum, 10.0, 2) |
| 102 | 1 | tkerber | pack(vbox, [label1, vac_box, label2]) |
| 103 | 1 | tkerber | pack(vbox, gtk.Label(""))
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| 104 | 1 | tkerber | |
| 105 | 1 | tkerber | |
| 106 | 1 | tkerber | # Buttons
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| 107 | 1 | tkerber | #self.pybut = PyButton("Creating a nanoparticle.")
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| 108 | 1 | tkerber | #self.pybut.connect('clicked', self.makeatoms)
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| 109 | 1 | tkerber | buts = cancel_apply_ok(cancel=lambda widget: self.destroy(), |
| 110 | 1 | tkerber | apply=self.apply,
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| 111 | 1 | tkerber | ok=self.ok)
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| 112 | 1 | tkerber | pack(vbox, [buts], end=True, bottom=True) |
| 113 | 1 | tkerber | |
| 114 | 1 | tkerber | # Finalize setup
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| 115 | 1 | tkerber | self.update_gui()
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| 116 | 1 | tkerber | self.add(vbox)
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| 117 | 1 | tkerber | vbox.show() |
| 118 | 1 | tkerber | self.show()
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| 119 | 1 | tkerber | self.gui = gui
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| 120 | 1 | tkerber | |
| 121 | 1 | tkerber | def update_element(self, *args): |
| 122 | 1 | tkerber | "Called when a new element may have been entered."
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| 123 | 1 | tkerber | # Assumes the element widget is self.element and that a label
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| 124 | 1 | tkerber | # for errors is self.elementinfo. The chemical symbol is
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| 125 | 1 | tkerber | # placed in self.legalelement - or None if the element is
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| 126 | 1 | tkerber | # invalid.
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| 127 | 1 | tkerber | symb = [] |
| 128 | 1 | tkerber | if self.struct.get_active() == 2: |
| 129 | 1 | tkerber | # Saturated nanoribbon
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| 130 | 1 | tkerber | elements = (self.element.get_text(), self.element2.get_text()) |
| 131 | 1 | tkerber | else:
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| 132 | 1 | tkerber | elements = (self.element.get_text(), )
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| 133 | 1 | tkerber | |
| 134 | 1 | tkerber | for elem in elements: |
| 135 | 1 | tkerber | if not elem: |
| 136 | 1 | tkerber | self.invalid_element(" No element specified!") |
| 137 | 1 | tkerber | return False |
| 138 | 1 | tkerber | try:
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| 139 | 1 | tkerber | z = int(elem)
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| 140 | 1 | tkerber | except ValueError: |
| 141 | 1 | tkerber | # Probably a symbol
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| 142 | 1 | tkerber | try:
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| 143 | 1 | tkerber | z = ase.data.atomic_numbers[elem] |
| 144 | 1 | tkerber | except KeyError: |
| 145 | 1 | tkerber | self.invalid_element()
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| 146 | 1 | tkerber | return False |
| 147 | 1 | tkerber | try:
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| 148 | 1 | tkerber | symb.append(ase.data.chemical_symbols[z]) |
| 149 | 1 | tkerber | except KeyError: |
| 150 | 1 | tkerber | self.invalid_element()
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| 151 | 1 | tkerber | return False |
| 152 | 1 | tkerber | self.elementinfo.set_text("") |
| 153 | 1 | tkerber | self.legal_element = symb[0] |
| 154 | 1 | tkerber | if len(symb) == 2: |
| 155 | 1 | tkerber | self.legal_element2 = symb[1] |
| 156 | 1 | tkerber | else:
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| 157 | 1 | tkerber | self.legal_element2 = None |
| 158 | 1 | tkerber | return True |
| 159 | 1 | tkerber | |
| 160 | 1 | tkerber | def update_gui(self, *args): |
| 161 | 1 | tkerber | # Saturation element is only relevant for saturated nanoribbons
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| 162 | 1 | tkerber | satur = self.struct.get_active() == 2 |
| 163 | 1 | tkerber | for w in (self.element2, self.bond_box): |
| 164 | 1 | tkerber | w.set_sensitive(satur) |
| 165 | 1 | tkerber | # Infinite zigzag sheets must have even width
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| 166 | 1 | tkerber | if self.struct.get_active() == 0 and self.orient.get_active() == 0: |
| 167 | 1 | tkerber | if self.n.value % 2 == 1: |
| 168 | 1 | tkerber | self.n.value += 1 |
| 169 | 1 | tkerber | self.n.lower = 2 |
| 170 | 1 | tkerber | self.n.step_increment = 2 |
| 171 | 1 | tkerber | else:
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| 172 | 1 | tkerber | self.n.lower = 1 |
| 173 | 1 | tkerber | self.n.step_increment = 1 |
| 174 | 1 | tkerber | |
| 175 | 1 | tkerber | def makeatoms(self, *args): |
| 176 | 1 | tkerber | self.update_element()
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| 177 | 1 | tkerber | if self.legal_element is None or (self.struct.get_active() == 2 and |
| 178 | 1 | tkerber | self.legal_element2 is None): |
| 179 | 1 | tkerber | self.atoms = None |
| 180 | 1 | tkerber | self.pybut.python = None |
| 181 | 1 | tkerber | else:
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| 182 | 1 | tkerber | n = int(self.n.value) |
| 183 | 1 | tkerber | m = int(self.m.value) |
| 184 | 1 | tkerber | CC = self.bondlength.value
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| 185 | 1 | tkerber | vacuum = self.vacuum.value
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| 186 | 1 | tkerber | orient = self.orient_text[self.orient.get_active()] |
| 187 | 1 | tkerber | elem = self.legal_element
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| 188 | 1 | tkerber | if self.struct.get_active() == 0: |
| 189 | 1 | tkerber | # Extended sheet
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| 190 | 1 | tkerber | self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
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| 191 | 1 | tkerber | vacc=vacuum, sheet=True,
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| 192 | 1 | tkerber | main_element=elem) |
| 193 | 1 | tkerber | elif self.struct.get_active() == 1: |
| 194 | 1 | tkerber | # Unsaturated nanoribbon
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| 195 | 1 | tkerber | self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
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| 196 | 1 | tkerber | vacc=vacuum, |
| 197 | 1 | tkerber | main_element=elem) |
| 198 | 1 | tkerber | elif self.struct.get_active() == 2: |
| 199 | 1 | tkerber | # Saturated nanoribbon
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| 200 | 1 | tkerber | elem2 = self.legal_element2
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| 201 | 1 | tkerber | self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
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| 202 | 1 | tkerber | C_H=self.bondlength2.value,
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| 203 | 1 | tkerber | vacc=vacuum, |
| 204 | 1 | tkerber | saturated=True,
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| 205 | 1 | tkerber | main_element=elem, |
| 206 | 1 | tkerber | satur_element=elem2) |
| 207 | 1 | tkerber | else:
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| 208 | 1 | tkerber | raise RuntimeError("Unknown structure in SetupGraphene!") |
| 209 | 1 | tkerber | # Now, rotate into the xy plane (ase.gui's default view plane)
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| 210 | 1 | tkerber | pos = self.atoms.get_positions()
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| 211 | 1 | tkerber | cell = self.atoms.get_cell()
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| 212 | 1 | tkerber | pbc = self.atoms.get_pbc()
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| 213 | 1 | tkerber | cell[1,1], cell[2,2] = cell[2,2], cell[1,1] |
| 214 | 1 | tkerber | x = pos[:,1].copy()
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| 215 | 1 | tkerber | z = pos[:,2].copy()
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| 216 | 1 | tkerber | pos[:,1] = z
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| 217 | 1 | tkerber | pos[:,2] = x
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| 218 | 1 | tkerber | self.atoms.set_cell(cell)
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| 219 | 1 | tkerber | self.atoms.set_positions(pos)
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| 220 | 1 | tkerber | self.atoms.set_pbc([pbc[0], pbc[2], pbc[1]]) |
| 221 | 1 | tkerber | |
| 222 | 1 | tkerber | def apply(self, *args): |
| 223 | 1 | tkerber | self.makeatoms()
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| 224 | 1 | tkerber | if self.atoms is not None: |
| 225 | 1 | tkerber | self.gui.new_atoms(self.atoms) |
| 226 | 1 | tkerber | return True |
| 227 | 1 | tkerber | else:
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| 228 | 1 | tkerber | oops("No valid atoms.",
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| 229 | 1 | tkerber | "You have not (yet) specified a consistent set of parameters.")
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| 230 | 1 | tkerber | return False |
| 231 | 1 | tkerber | |
| 232 | 1 | tkerber | def ok(self, *args): |
| 233 | 1 | tkerber | if self.apply(): |
| 234 | 1 | tkerber | self.destroy()
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| 235 | 1 | tkerber | |
| 236 | 1 | tkerber |