# encoding: utf-8 """nanotube.py - Window for setting up Graphene sheets and ribbons. """ import gtk 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("Nanotube") 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, vacc=vacuum, saturated=True, main_element=elem, satur_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()