root / ase / gui / gui.py @ 20
Historique | Voir | Annoter | Télécharger (41,34 ko)
| 1 |
# husk:
|
|---|---|
| 2 |
# Exit*2? remove pylab.show()
|
| 3 |
# close button
|
| 4 |
# DFT
|
| 5 |
# ADOS
|
| 6 |
# grey-out stuff after one second: vmd, rasmol, ...
|
| 7 |
# Show with ....
|
| 8 |
# rasmol: set same rotation as ag
|
| 9 |
# Graphs: save, Python, 3D
|
| 10 |
# start from python (interactive mode?)
|
| 11 |
# ascii-art option (colored)|
|
| 12 |
# option -o (output) and -f (force overwrite)
|
| 13 |
# surfacebuilder
|
| 14 |
# screen-dump
|
| 15 |
# icon
|
| 16 |
# ag-community-server
|
| 17 |
# translate option: record all translations,
|
| 18 |
# and check for missing translations.
|
| 19 |
|
| 20 |
#TODO: Add possible way of choosing orinetations. \
|
| 21 |
#TODO: Two atoms defines a direction, three atoms their normal does
|
| 22 |
#TODO: Align orientations chosen in Rot_selected v unselcted
|
| 23 |
#TODO: Get the atoms_rotate_0 thing string
|
| 24 |
#TODO: Use set atoms instead og the get atoms
|
| 25 |
#TODO: Arrow keys will decide how the orientation changes
|
| 26 |
#TODO: Undo redo que should be implemented
|
| 27 |
#TODO: Update should have possibility to change positions
|
| 28 |
#TODO: Window for rotation modes and move moves which can be chosen
|
| 29 |
#TODO: WHen rotate and move / hide the movie menu
|
| 30 |
|
| 31 |
import os |
| 32 |
import weakref |
| 33 |
import numpy as np |
| 34 |
|
| 35 |
import gtk |
| 36 |
from ase.gui.view import View |
| 37 |
from ase.gui.status import Status |
| 38 |
from ase.gui.widgets import pack, help, Help, oops |
| 39 |
from ase.gui.languages import translate as _ |
| 40 |
|
| 41 |
from ase.gui.settings import Settings |
| 42 |
from ase.gui.surfaceslab import SetupSurfaceSlab |
| 43 |
from ase.gui.nanoparticle import SetupNanoparticle |
| 44 |
from ase.gui.nanotube import SetupNanotube |
| 45 |
from ase.gui.graphene import SetupGraphene |
| 46 |
from ase.gui.calculator import SetCalculator |
| 47 |
from ase.gui.energyforces import EnergyForces |
| 48 |
from ase.gui.minimize import Minimize |
| 49 |
from ase.gui.scaling import HomogeneousDeformation |
| 50 |
|
| 51 |
ui_info = """\
|
| 52 |
<ui>
|
| 53 |
<menubar name='MenuBar'>
|
| 54 |
<menu action='FileMenu'>
|
| 55 |
<menuitem action='Open'/>
|
| 56 |
<menuitem action='New'/>
|
| 57 |
<menuitem action='Save'/>
|
| 58 |
<separator/>
|
| 59 |
<menuitem action='Quit'/>
|
| 60 |
</menu>
|
| 61 |
<menu action='EditMenu'>
|
| 62 |
<menuitem action='SelectAll'/>
|
| 63 |
<menuitem action='Invert'/>
|
| 64 |
<menuitem action='SelectConstrained'/>
|
| 65 |
<separator/>
|
| 66 |
<menuitem action='Modify'/>
|
| 67 |
<menuitem action='AddAtoms'/>
|
| 68 |
<menuitem action='DeleteAtoms'/>
|
| 69 |
<separator/>
|
| 70 |
<menuitem action='First'/>
|
| 71 |
<menuitem action='Previous'/>
|
| 72 |
<menuitem action='Next'/>
|
| 73 |
<menuitem action='Last'/>
|
| 74 |
</menu>
|
| 75 |
<menu action='ViewMenu'>
|
| 76 |
<menuitem action='ShowUnitCell'/>
|
| 77 |
<menuitem action='ShowAxes'/>
|
| 78 |
<menuitem action='ShowBonds'/>
|
| 79 |
<separator/>
|
| 80 |
<menuitem action='Repeat'/>
|
| 81 |
<menuitem action='Rotate'/>
|
| 82 |
<menuitem action='Focus'/>
|
| 83 |
<menuitem action='ZoomIn'/>
|
| 84 |
<menuitem action='ZoomOut'/>
|
| 85 |
<menuitem action='Settings'/>
|
| 86 |
<menuitem action='VMD'/>
|
| 87 |
<menuitem action='RasMol'/>
|
| 88 |
<menuitem action='XMakeMol'/>
|
| 89 |
<menuitem action='Avogadro'/>
|
| 90 |
</menu>
|
| 91 |
<menu action='ToolsMenu'>
|
| 92 |
<menuitem action='Graphs'/>
|
| 93 |
<menuitem action='Movie'/>
|
| 94 |
<menuitem action='EModify'/>
|
| 95 |
<menuitem action='Constraints'/>
|
| 96 |
<menuitem action='MoveAtoms'/>
|
| 97 |
<menuitem action='RotateAtoms'/>
|
| 98 |
<menuitem action='OrientAtoms'/>
|
| 99 |
<menuitem action='DFT'/>
|
| 100 |
<menuitem action='NEB'/>
|
| 101 |
<menuitem action='BulkModulus'/>
|
| 102 |
</menu>
|
| 103 |
<menu action='SetupMenu'>
|
| 104 |
<menuitem action='Surface'/>
|
| 105 |
<menuitem action='Nanoparticle'/>
|
| 106 |
<menuitem action='Graphene'/>
|
| 107 |
<menuitem action='Nanotube'/>
|
| 108 |
</menu>
|
| 109 |
<menu action='CalculateMenu'>
|
| 110 |
<menuitem action='SetCalculator'/>
|
| 111 |
<separator/>
|
| 112 |
<menuitem action='EnergyForces'/>
|
| 113 |
<menuitem action='Minimize'/>
|
| 114 |
<menuitem action='Scaling'/>
|
| 115 |
</menu>
|
| 116 |
<menu action='HelpMenu'>
|
| 117 |
<menuitem action='About'/>
|
| 118 |
<menuitem action='Webpage'/>
|
| 119 |
<menuitem action='Debug'/>
|
| 120 |
</menu>
|
| 121 |
</menubar>
|
| 122 |
</ui>"""
|
| 123 |
|
| 124 |
class GUI(View, Status): |
| 125 |
def __init__(self, images, rotations='', show_unit_cell=True, |
| 126 |
show_bonds=False):
|
| 127 |
self.images = images
|
| 128 |
self.window = gtk.Window(gtk.WINDOW_TOPLEVEL)
|
| 129 |
#self.window.set_icon(gtk.gdk.pixbuf_new_from_file('guiase.png'))
|
| 130 |
self.window.set_position(gtk.WIN_POS_CENTER)
|
| 131 |
#self.window.connect("destroy", lambda w: gtk.main_quit())
|
| 132 |
self.window.connect('delete_event', self.exit) |
| 133 |
vbox = gtk.VBox() |
| 134 |
self.window.add(vbox)
|
| 135 |
if gtk.pygtk_version < (2, 12): |
| 136 |
self.set_tip = gtk.Tooltips().set_tip
|
| 137 |
|
| 138 |
actions = gtk.ActionGroup("Actions")
|
| 139 |
actions.add_actions([ |
| 140 |
('FileMenu', None, '_File'), |
| 141 |
('EditMenu', None, '_Edit'), |
| 142 |
('ViewMenu', None, '_View' ), |
| 143 |
('ToolsMenu', None, '_Tools'), |
| 144 |
('SetupMenu', None, '_Setup'), |
| 145 |
('CalculateMenu', None, '_Calculate'), |
| 146 |
('HelpMenu', None, '_Help'), |
| 147 |
('Open', gtk.STOCK_OPEN, '_Open', '<control>O', |
| 148 |
'Create a new file',
|
| 149 |
self.open),
|
| 150 |
('New', gtk.STOCK_NEW, '_New', '<control>N', |
| 151 |
'New ase.gui window',
|
| 152 |
lambda widget: os.system('ag &')), |
| 153 |
('Save', gtk.STOCK_SAVE, '_Save', '<control>S', |
| 154 |
'Save current file',
|
| 155 |
self.save),
|
| 156 |
('Quit', gtk.STOCK_QUIT, '_Quit', '<control>Q', |
| 157 |
'Quit',
|
| 158 |
self.exit),
|
| 159 |
('SelectAll', None, 'Select _all', None, |
| 160 |
'',
|
| 161 |
self.select_all),
|
| 162 |
('Invert', None, '_Invert selection', None, |
| 163 |
'',
|
| 164 |
self.invert_selection),
|
| 165 |
('SelectConstrained', None, 'Select _constrained atoms', None, |
| 166 |
'',
|
| 167 |
self.select_constrained_atoms),
|
| 168 |
('Modify', None, '_Modify', '<control>Y', |
| 169 |
'Change tags, moments and atom types of the selected atoms',
|
| 170 |
self.modify_atoms),
|
| 171 |
('AddAtoms', None, '_Add atoms', '<control>A', |
| 172 |
'Insert or import atoms and molecules',
|
| 173 |
self.add_atoms),
|
| 174 |
('DeleteAtoms', None, '_Delete selected atoms', 'BackSpace', |
| 175 |
'Deletes the selected atoms',
|
| 176 |
self.delete_selected_atoms),
|
| 177 |
('First', gtk.STOCK_GOTO_FIRST, '_First image', 'Home', |
| 178 |
'',
|
| 179 |
self.step),
|
| 180 |
('Previous', gtk.STOCK_GO_BACK, '_Previous image', 'Page_Up', |
| 181 |
'',
|
| 182 |
self.step),
|
| 183 |
('Next', gtk.STOCK_GO_FORWARD, '_Next image', 'Page_Down', |
| 184 |
'',
|
| 185 |
self.step),
|
| 186 |
('Last', gtk.STOCK_GOTO_LAST, '_Last image', 'End', |
| 187 |
'',
|
| 188 |
self.step),
|
| 189 |
('Repeat', None, 'Repeat ...', None, |
| 190 |
'',
|
| 191 |
self.repeat_window),
|
| 192 |
('Rotate', None, 'Rotate ...', None, |
| 193 |
'',
|
| 194 |
self.rotate_window),
|
| 195 |
('Focus', gtk.STOCK_ZOOM_FIT, 'Focus', 'F', |
| 196 |
'',
|
| 197 |
self.focus),
|
| 198 |
('ZoomIn', gtk.STOCK_ZOOM_IN, 'Zoom in', 'plus', |
| 199 |
'',
|
| 200 |
self.zoom),
|
| 201 |
('ZoomOut', gtk.STOCK_ZOOM_OUT, 'Zoom out', 'minus', |
| 202 |
'',
|
| 203 |
self.zoom),
|
| 204 |
('Settings', gtk.STOCK_PREFERENCES, 'Settings ...', None, |
| 205 |
'',
|
| 206 |
self.settings),
|
| 207 |
('VMD', None, 'VMD', None, |
| 208 |
'',
|
| 209 |
self.external_viewer),
|
| 210 |
('RasMol', None, 'RasMol', None, |
| 211 |
'',
|
| 212 |
self.external_viewer),
|
| 213 |
('XMakeMol', None, 'xmakemol', None, |
| 214 |
'',
|
| 215 |
self.external_viewer),
|
| 216 |
('Avogadro', None, 'avogadro', None, |
| 217 |
'',
|
| 218 |
self.external_viewer),
|
| 219 |
('Graphs', None, 'Graphs ...', None, |
| 220 |
'',
|
| 221 |
self.plot_graphs),
|
| 222 |
('Movie', None, 'Movie ...', None, |
| 223 |
'',
|
| 224 |
self.movie),
|
| 225 |
('EModify', None, 'Expert modify ...', None, |
| 226 |
'',
|
| 227 |
self.execute),
|
| 228 |
('Constraints', None, 'Constraints ...', None, |
| 229 |
'',
|
| 230 |
self.constraints_window),
|
| 231 |
('DFT', None, 'DFT ...', None, |
| 232 |
'',
|
| 233 |
self.dft_window),
|
| 234 |
('NEB', None, 'NE_B', None, |
| 235 |
'',
|
| 236 |
self.NEB),
|
| 237 |
('BulkModulus', None, 'B_ulk Modulus', None, |
| 238 |
'',
|
| 239 |
self.bulk_modulus),
|
| 240 |
('Bulk', None, '_Bulk Crystal', None, |
| 241 |
"Create a bulk crystal with arbitrary orientation",
|
| 242 |
self.bulk_window),
|
| 243 |
('Surface', None, '_Surface slab', None, |
| 244 |
"Create the most common surfaces",
|
| 245 |
self.surface_window),
|
| 246 |
('Nanoparticle', None, '_Nanoparticle', None, |
| 247 |
"Create a crystalline nanoparticle",
|
| 248 |
self.nanoparticle_window),
|
| 249 |
('Nanotube', None, 'Nano_tube', None, |
| 250 |
"Create a nanotube",
|
| 251 |
self.nanotube_window),
|
| 252 |
('Graphene', None, 'Graphene', None, |
| 253 |
"Create a graphene sheet or nanoribbon",
|
| 254 |
self.graphene_window),
|
| 255 |
('SetCalculator', None, 'Set _Calculator', None, |
| 256 |
"Set a calculator used in all calculation modules",
|
| 257 |
self.calculator_window),
|
| 258 |
('EnergyForces', None, '_Energy and Forces', None, |
| 259 |
"Calculate energy and forces",
|
| 260 |
self.energy_window),
|
| 261 |
('Minimize', None, 'Energy _Minimization', None, |
| 262 |
"Minimize the energy",
|
| 263 |
self.energy_minimize_window),
|
| 264 |
('Scaling', None, 'Scale system', None, |
| 265 |
"Deform system by scaling it",
|
| 266 |
self.scaling_window),
|
| 267 |
('About', None, '_About', None, |
| 268 |
None,
|
| 269 |
self.about),
|
| 270 |
('Webpage', gtk.STOCK_HELP, 'Webpage ...', None, None, webpage), |
| 271 |
('Debug', None, 'Debug ...', None, None, self.debug)]) |
| 272 |
actions.add_toggle_actions([ |
| 273 |
('ShowUnitCell', None, 'Show _unit cell', '<control>U', |
| 274 |
'Bold',
|
| 275 |
self.toggle_show_unit_cell,
|
| 276 |
show_unit_cell > 0),
|
| 277 |
('ShowAxes', None, 'Show _axes', None, |
| 278 |
'Bold',
|
| 279 |
self.toggle_show_axes,
|
| 280 |
True),
|
| 281 |
('ShowBonds', None, 'Show _bonds', '<control>B', |
| 282 |
'Bold',
|
| 283 |
self.toggle_show_bonds,
|
| 284 |
show_bonds), |
| 285 |
('MoveAtoms', None, '_Move atoms', '<control>M', |
| 286 |
'Bold',
|
| 287 |
self.toggle_move_mode,
|
| 288 |
False),
|
| 289 |
('RotateAtoms', None, '_Rotate atoms', '<control>R', |
| 290 |
'Bold',
|
| 291 |
self.toggle_rotate_mode,
|
| 292 |
False),
|
| 293 |
('OrientAtoms', None, 'Orien_t atoms', '<control>T', |
| 294 |
'Bold',
|
| 295 |
self.toggle_orient_mode,
|
| 296 |
False)
|
| 297 |
]) |
| 298 |
self.ui = ui = gtk.UIManager()
|
| 299 |
ui.insert_action_group(actions, 0)
|
| 300 |
self.window.add_accel_group(ui.get_accel_group())
|
| 301 |
|
| 302 |
try:
|
| 303 |
mergeid = ui.add_ui_from_string(ui_info) |
| 304 |
except gobject.GError, msg:
|
| 305 |
print 'building menus failed: %s' % msg |
| 306 |
|
| 307 |
vbox.pack_start(ui.get_widget('/MenuBar'), False, False, 0) |
| 308 |
|
| 309 |
View.__init__(self, vbox, rotations)
|
| 310 |
Status.__init__(self, vbox)
|
| 311 |
vbox.show() |
| 312 |
#self.window.set_events(gtk.gdk.BUTTON_PRESS_MASK)
|
| 313 |
self.window.connect('key-press-event', self.scroll) |
| 314 |
self.window.connect('scroll_event', self.scroll_event) |
| 315 |
self.window.show()
|
| 316 |
self.graphs = [] # List of open pylab windows |
| 317 |
self.graph_wref = [] # List of weakrefs to Graph objects |
| 318 |
self.movie_window = None |
| 319 |
self.vulnerable_windows = []
|
| 320 |
self.simulation = {} # Used by modules on Calculate menu. |
| 321 |
self.module_state = {} # Used by modules to store their state. |
| 322 |
|
| 323 |
def run(self, expr=None): |
| 324 |
self.set_colors()
|
| 325 |
self.set_coordinates(self.images.nimages - 1, focus=True) |
| 326 |
|
| 327 |
if self.images.nimages > 1: |
| 328 |
self.movie()
|
| 329 |
|
| 330 |
if expr is None and not np.isnan(self.images.E[0]): |
| 331 |
expr = 'i, e - E[-1]'
|
| 332 |
|
| 333 |
if expr is not None and expr != '' and self.images.nimages > 1: |
| 334 |
self.plot_graphs(expr=expr)
|
| 335 |
|
| 336 |
gtk.main() |
| 337 |
|
| 338 |
|
| 339 |
def step(self, action): |
| 340 |
d = {'First': -10000000,
|
| 341 |
'Previous': -1, |
| 342 |
'Next': 1, |
| 343 |
'Last': 10000000}[action.get_name()] |
| 344 |
i = max(0, min(self.images.nimages - 1, self.frame + d)) |
| 345 |
self.set_frame(i)
|
| 346 |
if self.movie_window is not None: |
| 347 |
self.movie_window.frame_number.value = i
|
| 348 |
|
| 349 |
def _do_zoom(self, x): |
| 350 |
"""Utility method for zooming"""
|
| 351 |
self.scale *= x
|
| 352 |
self.draw()
|
| 353 |
|
| 354 |
def zoom(self, action): |
| 355 |
"""Zoom in/out on keypress or clicking menu item"""
|
| 356 |
x = {'ZoomIn': 1.2, 'ZoomOut':1 / 1.2}[action.get_name()]
|
| 357 |
self._do_zoom(x)
|
| 358 |
|
| 359 |
def scroll_event(self, window, event): |
| 360 |
"""Zoom in/out when using mouse wheel"""
|
| 361 |
x = 1.0
|
| 362 |
if event.direction == gtk.gdk.SCROLL_UP:
|
| 363 |
x = 1.2
|
| 364 |
elif event.direction == gtk.gdk.SCROLL_DOWN:
|
| 365 |
x = 1.0 / 1.2 |
| 366 |
self._do_zoom(x)
|
| 367 |
|
| 368 |
def settings(self, menuitem): |
| 369 |
Settings(self)
|
| 370 |
|
| 371 |
def scroll(self, window, event): |
| 372 |
from copy import copy |
| 373 |
CTRL = event.state == gtk.gdk.CONTROL_MASK |
| 374 |
SHIFT = event.state == gtk.gdk.SHIFT_MASK |
| 375 |
dxdydz = {gtk.keysyms.KP_Add: ('zoom', 1.2, 0),
|
| 376 |
gtk.keysyms.KP_Subtract: ('zoom', 1 / 1.2, 0), |
| 377 |
gtk.keysyms.Up: ( 0, +1 - CTRL, +CTRL), |
| 378 |
gtk.keysyms.Down: ( 0, -1 + CTRL, -CTRL), |
| 379 |
gtk.keysyms.Right: (+1, 0, 0), |
| 380 |
gtk.keysyms.Left: (-1, 0, 0)}.get(event.keyval, None) |
| 381 |
try:
|
| 382 |
inch = chr(event.keyval)
|
| 383 |
except:
|
| 384 |
inch = None
|
| 385 |
|
| 386 |
sel = [] |
| 387 |
|
| 388 |
atom_move = self.ui.get_widget('/MenuBar/ToolsMenu/MoveAtoms' |
| 389 |
).get_active() |
| 390 |
atom_rotate = self.ui.get_widget('/MenuBar/ToolsMenu/RotateAtoms' |
| 391 |
).get_active() |
| 392 |
atom_orient = self.ui.get_widget('/MenuBar/ToolsMenu/OrientAtoms' |
| 393 |
).get_active() |
| 394 |
if dxdydz is None: |
| 395 |
return
|
| 396 |
dx, dy, dz = dxdydz |
| 397 |
if dx == 'zoom': |
| 398 |
self._do_zoom(dy)
|
| 399 |
return
|
| 400 |
if dx == 'zoom': |
| 401 |
self._do_zoom(dy)
|
| 402 |
return
|
| 403 |
d = self.scale * 0.1 |
| 404 |
tvec = np.array([dx, dy, dz]) |
| 405 |
|
| 406 |
dir_vec = np.dot(self.axes, tvec)
|
| 407 |
if (atom_move):
|
| 408 |
rotmat = self.axes
|
| 409 |
s = 0.1
|
| 410 |
if SHIFT:
|
| 411 |
s = 0.01
|
| 412 |
add = s * dir_vec |
| 413 |
for i in range(len(self.R)): |
| 414 |
if self.atoms_to_rotate_0[i]: |
| 415 |
self.R[i] += add
|
| 416 |
for jx in range(self.images.nimages): |
| 417 |
self.images.P[jx][i] += add
|
| 418 |
elif atom_rotate:
|
| 419 |
from rot_tools import rotate_about_vec, \ |
| 420 |
rotate_vec
|
| 421 |
sel = self.images.selected
|
| 422 |
if sum(sel) == 0: |
| 423 |
sel = self.atoms_to_rotate_0
|
| 424 |
nsel = sum(sel)
|
| 425 |
# this is the first one to get instatiated
|
| 426 |
if nsel != 2: |
| 427 |
self.rot_vec = dir_vec
|
| 428 |
|
| 429 |
change = False
|
| 430 |
z_axis = np.dot(self.axes, np.array([0, 0, 1])) |
| 431 |
if self.atoms_to_rotate == None: |
| 432 |
change = True
|
| 433 |
self.z_axis_old = z_axis.copy()
|
| 434 |
self.dx_change = [0, 0] |
| 435 |
self.atoms_to_rotate = self.atoms_to_rotate_0.copy() |
| 436 |
self.atoms_selected = sel.copy()
|
| 437 |
self.rot_vec = dir_vec
|
| 438 |
|
| 439 |
if nsel != 2 or sum(self.atoms_to_rotate) == 2: |
| 440 |
self.dx_change = [0, 0] |
| 441 |
|
| 442 |
for i in range(len(sel)): |
| 443 |
if sel[i] != self.atoms_selected[i]: |
| 444 |
change = True
|
| 445 |
cz = [dx, dy+dz] |
| 446 |
|
| 447 |
if cz[0] or cz[1]: |
| 448 |
change = False
|
| 449 |
if not(cz[0] * (self.dx_change[1])): |
| 450 |
change = True
|
| 451 |
for i in range(2): |
| 452 |
if cz[i] and self.dx_change[i]: |
| 453 |
self.rot_vec = self.rot_vec * cz[i] * self.dx_change[i] |
| 454 |
if cz[1]: |
| 455 |
change = False
|
| 456 |
|
| 457 |
if np.prod(self.z_axis_old != z_axis): |
| 458 |
change = True
|
| 459 |
self.z_axis_old = z_axis.copy()
|
| 460 |
self.dx_change = copy(cz)
|
| 461 |
dihedral_rotation = len(self.images.selected_ordered) == 4 |
| 462 |
|
| 463 |
if change:
|
| 464 |
self.atoms_selected = sel.copy()
|
| 465 |
|
| 466 |
if nsel == 2 and sum(self.atoms_to_rotate) != 2: |
| 467 |
asel = [] |
| 468 |
for i, j in enumerate(sel): |
| 469 |
if j:
|
| 470 |
asel.append(i) |
| 471 |
a1, a2 = asel |
| 472 |
|
| 473 |
rvx = self.images.P[self.frame][a1] - \ |
| 474 |
self.images.P[self.frame][a2] |
| 475 |
|
| 476 |
rvy = np.cross(rvx, |
| 477 |
np.dot(self.axes,
|
| 478 |
np.array([0, 0, 1]))) |
| 479 |
self.rot_vec = rvx * dx + rvy * (dy + dz)
|
| 480 |
self.dx_change = [dx, dy+dz]
|
| 481 |
|
| 482 |
# dihedral rotation?
|
| 483 |
if dihedral_rotation:
|
| 484 |
sel = self.images.selected_ordered
|
| 485 |
self.rot_vec = (dx+dy+dz)*(self.R[sel[2]]-self.R[sel[1]]) |
| 486 |
|
| 487 |
rot_cen = np.array([0.0, 0.0, 0.0]) |
| 488 |
if dihedral_rotation:
|
| 489 |
sel = self.images.selected_ordered
|
| 490 |
rot_cen = self.R[sel[1]].copy() |
| 491 |
elif nsel:
|
| 492 |
for i, b in enumerate( sel): |
| 493 |
if b:
|
| 494 |
rot_cen += self.R[i]
|
| 495 |
rot_cen /= float(nsel)
|
| 496 |
|
| 497 |
degrees = 5 * (1 - SHIFT) + SHIFT |
| 498 |
degrees = abs(sum(dxdydz)) * 3.1415 / 360.0 * degrees |
| 499 |
rotmat = rotate_about_vec(self.rot_vec, degrees)
|
| 500 |
|
| 501 |
# now rotate the atoms that are to be rotated
|
| 502 |
for i in range(len(self.R)): |
| 503 |
if self.atoms_to_rotate[i]: |
| 504 |
self.R[i] -= rot_cen
|
| 505 |
for jx in range(self.images.nimages): |
| 506 |
self.images.P[jx][i] -= rot_cen
|
| 507 |
|
| 508 |
self.R[i] = rotate_vec(rotmat, self.R[i]) |
| 509 |
for jx in range(self.images.nimages): |
| 510 |
self.images.P[jx][i] = rotate_vec(rotmat, self.images.P[jx][i]) |
| 511 |
|
| 512 |
self.R[i] += rot_cen
|
| 513 |
for jx in range(self.images.nimages): |
| 514 |
self.images.P[jx][i] += rot_cen
|
| 515 |
elif atom_orient:
|
| 516 |
to_vec = np.array([dx, dy, dz]) |
| 517 |
|
| 518 |
from rot_tools import rotate_vec_into_newvec |
| 519 |
rot_mat = rotate_vec_into_newvec(self.orient_normal, to_vec)
|
| 520 |
self.axes = rot_mat
|
| 521 |
|
| 522 |
self.set_coordinates()
|
| 523 |
else:
|
| 524 |
self.center -= (dx * 0.1 * self.axes[:, 0] - |
| 525 |
dy * 0.1 * self.axes[:, 1]) |
| 526 |
self.draw()
|
| 527 |
|
| 528 |
|
| 529 |
def add_atoms(self, widget, data=None): |
| 530 |
"""
|
| 531 |
Presents a dialogbox to the user, that allows him to add atoms/molecule to the current slab.
|
| 532 |
|
| 533 |
The molecule/atom is rotated using the current rotation of the coordinate system.
|
| 534 |
|
| 535 |
The molecule/atom can be added at a specified position - if the keyword auto+Z is used,
|
| 536 |
the COM of the selected atoms will be used as COM for the moleculed. The COM is furthermore
|
| 537 |
translated Z ang towards the user.
|
| 538 |
|
| 539 |
If no molecules are selected, the COM of all the atoms will be used for the x-y components of the
|
| 540 |
active coordinate system, while the z-direction will be chosen from the nearest atom position
|
| 541 |
along this direction.
|
| 542 |
|
| 543 |
Note: If this option is used, all frames except the active one are deleted.
|
| 544 |
"""
|
| 545 |
if data:
|
| 546 |
if data == 'load': |
| 547 |
chooser = gtk.FileChooserDialog( |
| 548 |
_('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN, |
| 549 |
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, |
| 550 |
gtk.STOCK_OPEN, gtk.RESPONSE_OK)) |
| 551 |
ok = chooser.run() |
| 552 |
if ok == gtk.RESPONSE_OK:
|
| 553 |
filename = chooser.get_filename() |
| 554 |
chooser.destroy() |
| 555 |
if not ok: |
| 556 |
return
|
| 557 |
|
| 558 |
if data == 'OK' or data == 'load': |
| 559 |
import ase |
| 560 |
if data == 'load': |
| 561 |
molecule = filename |
| 562 |
else:
|
| 563 |
molecule = self.add_entries[1].get_text() |
| 564 |
tag = self.add_entries[2].get_text() |
| 565 |
mom = self.add_entries[3].get_text() |
| 566 |
pos = self.add_entries[4].get_text().lower() |
| 567 |
|
| 568 |
a = None
|
| 569 |
try:
|
| 570 |
a = ase.Atoms([ase.Atom(molecule)]) |
| 571 |
except:
|
| 572 |
try:
|
| 573 |
a = ase.molecule(molecule) |
| 574 |
except:
|
| 575 |
try:
|
| 576 |
a = ase.read(molecule, -1)
|
| 577 |
except:
|
| 578 |
self.add_entries[1].set_text('?' + molecule) |
| 579 |
return ()
|
| 580 |
|
| 581 |
directions = np.transpose(self.axes)
|
| 582 |
if a != None: |
| 583 |
for i in a: |
| 584 |
try:
|
| 585 |
i.set_tag(int(tag))
|
| 586 |
except:
|
| 587 |
self.add_entries[2].set_text('?' + tag) |
| 588 |
return ()
|
| 589 |
try:
|
| 590 |
i.magmom = float(mom)
|
| 591 |
except:
|
| 592 |
self.add_entries[3].set_text('?' + mom) |
| 593 |
return ()
|
| 594 |
# apply the current rotation matrix to A
|
| 595 |
for i in a: |
| 596 |
i.position = np.dot(self.axes, i.position)
|
| 597 |
# find the extent of the molecule in the local coordinate system
|
| 598 |
a_cen_pos = np.array([0.0, 0.0, 0.0]) |
| 599 |
m_cen_pos = 0.0
|
| 600 |
for i in a.positions: |
| 601 |
a_cen_pos[0] += np.dot(directions[0], i) |
| 602 |
a_cen_pos[1] += np.dot(directions[1], i) |
| 603 |
a_cen_pos[2] += np.dot(directions[2], i) |
| 604 |
|
| 605 |
m_cen_pos = max(np.dot(-directions[2], i), m_cen_pos) |
| 606 |
a_cen_pos[0] /= len(a.positions) |
| 607 |
a_cen_pos[1] /= len(a.positions) |
| 608 |
a_cen_pos[2] /= len(a.positions) |
| 609 |
a_cen_pos[2] -= m_cen_pos
|
| 610 |
|
| 611 |
# now find the position
|
| 612 |
cen_pos = np.array([0.0, 0.0, 0.0]) |
| 613 |
if sum(self.images.selected) > 0: |
| 614 |
for i in range(len(self.R)): |
| 615 |
if self.images.selected[i]: |
| 616 |
cen_pos += self.R[i]
|
| 617 |
cen_pos /= sum(self.images.selected) |
| 618 |
elif len(self.R) > 0: |
| 619 |
px = 0.0
|
| 620 |
py = 0.0
|
| 621 |
pz = -1e6
|
| 622 |
|
| 623 |
for i in range(len(self.R)): |
| 624 |
px += np.dot(directions[0], self.R[i]) |
| 625 |
py += np.dot(directions[1], self.R[i]) |
| 626 |
pz = max(np.dot(directions[2], self.R[i]), pz) |
| 627 |
px = (px/float(len(self.R))) |
| 628 |
py = (py/float(len(self.R))) |
| 629 |
cen_pos = directions[0] * px + \
|
| 630 |
directions[1] * py + \
|
| 631 |
directions[2] * pz
|
| 632 |
|
| 633 |
if 'auto' in pos: |
| 634 |
pos = pos.replace('auto', '') |
| 635 |
import re |
| 636 |
pos = re.sub('\s', '', pos) |
| 637 |
if '(' in pos: |
| 638 |
sign = eval('%s1' % pos[0]) |
| 639 |
a_cen_pos -= sign * np.array(eval(pos[1:]), float) |
| 640 |
else:
|
| 641 |
a_cen_pos -= float(pos) * directions[2] |
| 642 |
else:
|
| 643 |
cen_pos = np.array(eval(pos))
|
| 644 |
for i in a: |
| 645 |
i.position += cen_pos - a_cen_pos |
| 646 |
|
| 647 |
# and them to the molecule
|
| 648 |
atoms = self.images.get_atoms(self.frame) |
| 649 |
atoms = atoms + a |
| 650 |
self.new_atoms(atoms, init_magmom=True) |
| 651 |
|
| 652 |
# and finally select the new molecule for easy moving and rotation
|
| 653 |
for i in range(len(a)): |
| 654 |
self.images.selected[len(atoms) - i - 1] = True |
| 655 |
|
| 656 |
self.draw()
|
| 657 |
self.add_entries[0].destroy() |
| 658 |
if data == None: |
| 659 |
molecule = ''
|
| 660 |
tag = '0'
|
| 661 |
mom = '0'
|
| 662 |
pos = 'auto+1'
|
| 663 |
self.add_entries = []
|
| 664 |
window = gtk.Window(gtk.WINDOW_TOPLEVEL) |
| 665 |
self.add_entries.append(window)
|
| 666 |
window.set_title('Add atoms')
|
| 667 |
|
| 668 |
vbox = gtk.VBox(False, 0) |
| 669 |
window.add(vbox) |
| 670 |
vbox.show() |
| 671 |
pack = False
|
| 672 |
for i, j in [['Insert atom or molecule', molecule], |
| 673 |
['Tag', tag],
|
| 674 |
['Moment', mom],
|
| 675 |
['Position', pos]]:
|
| 676 |
|
| 677 |
label = gtk.Label(i) |
| 678 |
if not pack: |
| 679 |
vbox.pack_start(label, True, True, 0) |
| 680 |
else:
|
| 681 |
pack = True
|
| 682 |
vbox.add(label) |
| 683 |
label.show() |
| 684 |
|
| 685 |
entry = gtk.Entry() |
| 686 |
entry.set_text(j) |
| 687 |
self.add_entries.append(entry)
|
| 688 |
entry.set_max_length(50)
|
| 689 |
entry.show() |
| 690 |
|
| 691 |
vbox.add(entry) |
| 692 |
|
| 693 |
button = gtk.Button('_Load molecule')
|
| 694 |
button.connect('clicked', self.add_atoms, 'load') |
| 695 |
button.show() |
| 696 |
vbox.add(button) |
| 697 |
button = gtk.Button('_OK')
|
| 698 |
button.connect('clicked', self.add_atoms, 'OK') |
| 699 |
button.show() |
| 700 |
vbox.add(button) |
| 701 |
button = gtk.Button('_Cancel')
|
| 702 |
button.connect('clicked', self.add_atoms, 'Cancel') |
| 703 |
button.show() |
| 704 |
vbox.add(button) |
| 705 |
|
| 706 |
window.show() |
| 707 |
|
| 708 |
def modify_atoms(self, widget, data=None): |
| 709 |
"""
|
| 710 |
Presents a dialog box where the user is able to change the atomic type, the magnetic
|
| 711 |
moment and tags of the selected atoms. An item marked with X will not be changed.
|
| 712 |
"""
|
| 713 |
if data:
|
| 714 |
if data == 'OK': |
| 715 |
import ase |
| 716 |
symbol = self.add_entries[1].get_text() |
| 717 |
tag = self.add_entries[2].get_text() |
| 718 |
mom = self.add_entries[3].get_text() |
| 719 |
a = None
|
| 720 |
if symbol != 'X': |
| 721 |
try:
|
| 722 |
a = ase.Atoms([ase.Atom(symbol)]) |
| 723 |
except:
|
| 724 |
self.add_entries[1].set_text('?' + symbol) |
| 725 |
return ()
|
| 726 |
|
| 727 |
y = self.images.selected.copy()
|
| 728 |
# and them to the molecule
|
| 729 |
atoms = self.images.get_atoms(self.frame) |
| 730 |
for i in range(len(atoms)): |
| 731 |
if self.images.selected[i]: |
| 732 |
if a:
|
| 733 |
atoms[i].symbol = symbol |
| 734 |
try:
|
| 735 |
if tag != 'X': |
| 736 |
atoms[i].tag = int(tag)
|
| 737 |
except:
|
| 738 |
self.add_entries[2].set_text('?' + tag) |
| 739 |
return ()
|
| 740 |
try:
|
| 741 |
if mom != 'X': |
| 742 |
atoms[i].magmom = float(mom)
|
| 743 |
except:
|
| 744 |
self.add_entries[3].set_text('?' + mom) |
| 745 |
return ()
|
| 746 |
self.new_atoms(atoms, init_magmom=True) |
| 747 |
|
| 748 |
# and finally select the new molecule for easy moving and rotation
|
| 749 |
self.images.selected = y
|
| 750 |
self.draw()
|
| 751 |
|
| 752 |
self.add_entries[0].destroy() |
| 753 |
if data == None and sum(self.images.selected): |
| 754 |
atoms = self.images.get_atoms(self.frame) |
| 755 |
s_tag = ''
|
| 756 |
s_mom = ''
|
| 757 |
s_symbol = ''
|
| 758 |
# Get the tags, moments and symbols of the selected atomsa
|
| 759 |
for i in range(len(atoms)): |
| 760 |
if self.images.selected[i]: |
| 761 |
if not(s_tag): |
| 762 |
s_tag = str(atoms[i].tag)
|
| 763 |
elif s_tag != str(atoms[i].tag): |
| 764 |
s_tag = 'X'
|
| 765 |
if not(s_mom): |
| 766 |
s_mom = ("%2.2f" % (atoms[i].magmom))
|
| 767 |
elif s_mom != ("%2.2f" % (atoms[i].magmom)): |
| 768 |
s_mom = 'X'
|
| 769 |
if not(s_symbol): |
| 770 |
s_symbol = str(atoms[i].symbol)
|
| 771 |
elif s_symbol != str(atoms[i].symbol): |
| 772 |
s_symbol = 'X'
|
| 773 |
|
| 774 |
self.add_entries = []
|
| 775 |
window = gtk.Window(gtk.WINDOW_TOPLEVEL) |
| 776 |
self.add_entries.append(window)
|
| 777 |
window.set_title('Modify')
|
| 778 |
|
| 779 |
vbox = gtk.VBox(False, 0) |
| 780 |
window.add(vbox) |
| 781 |
vbox.show() |
| 782 |
pack = False
|
| 783 |
for i, j in [['Atom', s_symbol], |
| 784 |
['Tag', s_tag],
|
| 785 |
['Moment', s_mom]]:
|
| 786 |
label = gtk.Label(i) |
| 787 |
if not pack: |
| 788 |
vbox.pack_start(label, True, True, 0) |
| 789 |
else:
|
| 790 |
pack = True
|
| 791 |
vbox.add(label) |
| 792 |
label.show() |
| 793 |
|
| 794 |
entry = gtk.Entry() |
| 795 |
entry.set_text(j) |
| 796 |
self.add_entries.append(entry)
|
| 797 |
entry.set_max_length(50)
|
| 798 |
entry.show() |
| 799 |
vbox.add(entry) |
| 800 |
button = gtk.Button('_OK')
|
| 801 |
button.connect('clicked', self.modify_atoms, 'OK') |
| 802 |
button.show() |
| 803 |
vbox.add(button) |
| 804 |
button = gtk.Button('_Cancel')
|
| 805 |
button.connect('clicked', self.modify_atoms, 'Cancel') |
| 806 |
button.show() |
| 807 |
vbox.add(button) |
| 808 |
|
| 809 |
window.show() |
| 810 |
|
| 811 |
def delete_selected_atoms(self, widget, data=None): |
| 812 |
if data == 'OK': |
| 813 |
atoms = self.images.get_atoms(self.frame) |
| 814 |
lena = len(atoms)
|
| 815 |
for i in range(len(atoms)): |
| 816 |
li = lena-1-i
|
| 817 |
if self.images.selected[li]: |
| 818 |
del(atoms[li])
|
| 819 |
self.new_atoms(atoms)
|
| 820 |
|
| 821 |
self.draw()
|
| 822 |
if data:
|
| 823 |
self.window.destroy()
|
| 824 |
|
| 825 |
if not(data) and sum(self.images.selected): |
| 826 |
more = '' + (sum(self.images.selected) > 1) * 's' |
| 827 |
self.window = gtk.Window(gtk.WINDOW_TOPLEVEL)
|
| 828 |
self.window.set_title('Confirmation') |
| 829 |
self.window.set_border_width(10) |
| 830 |
self.box1 = gtk.HBox(False, 0) |
| 831 |
self.window.add(self.box1) |
| 832 |
self.button1 = gtk.Button('Delete selected atom%s?' % more) |
| 833 |
self.button1.connect("clicked", self.delete_selected_atoms, "OK") |
| 834 |
self.box1.pack_start(self.button1, True, True, 0) |
| 835 |
self.button1.show()
|
| 836 |
|
| 837 |
self.button2 = gtk.Button("Cancel") |
| 838 |
self.button2.connect("clicked", self.delete_selected_atoms, "Cancel") |
| 839 |
self.box1.pack_start(self.button2, True, True, 0) |
| 840 |
self.button2.show()
|
| 841 |
|
| 842 |
self.box1.show()
|
| 843 |
self.window.show()
|
| 844 |
|
| 845 |
def debug(self, x): |
| 846 |
from ase.gui.debug import Debug |
| 847 |
Debug(self)
|
| 848 |
|
| 849 |
def execute(self, widget=None): |
| 850 |
from ase.gui.execute import Execute |
| 851 |
Execute(self)
|
| 852 |
|
| 853 |
def constraints_window(self, widget=None): |
| 854 |
from ase.gui.constraints import Constraints |
| 855 |
Constraints(self)
|
| 856 |
|
| 857 |
def dft_window(self, widget=None): |
| 858 |
from ase.gui.dft import DFT |
| 859 |
DFT(self)
|
| 860 |
|
| 861 |
def select_all(self, widget): |
| 862 |
self.images.selected[:] = True |
| 863 |
self.draw()
|
| 864 |
|
| 865 |
def invert_selection(self, widget): |
| 866 |
self.images.selected[:] = ~self.images.selected |
| 867 |
self.draw()
|
| 868 |
|
| 869 |
def select_constrained_atoms(self, widget): |
| 870 |
self.images.selected[:] = ~self.images.dynamic |
| 871 |
self.draw()
|
| 872 |
|
| 873 |
def movie(self, widget=None): |
| 874 |
from ase.gui.movie import Movie |
| 875 |
self.movie_window = Movie(self) |
| 876 |
|
| 877 |
def plot_graphs(self, x=None, expr=None): |
| 878 |
from ase.gui.graphs import Graphs |
| 879 |
g = Graphs(self)
|
| 880 |
if expr is not None: |
| 881 |
g.plot(expr=expr) |
| 882 |
self.graph_wref.append(weakref.ref(g))
|
| 883 |
|
| 884 |
def plot_graphs_newatoms(self): |
| 885 |
"Notify any Graph objects that they should make new plots."
|
| 886 |
new_wref = [] |
| 887 |
found = 0
|
| 888 |
for wref in self.graph_wref: |
| 889 |
ref = wref() |
| 890 |
if ref is not None: |
| 891 |
ref.plot() |
| 892 |
new_wref.append(wref) # Preserve weakrefs that still work.
|
| 893 |
found += 1
|
| 894 |
self.graph_wref = new_wref
|
| 895 |
return found
|
| 896 |
|
| 897 |
def NEB(self, action): |
| 898 |
from ase.gui.neb import NudgedElasticBand |
| 899 |
NudgedElasticBand(self.images)
|
| 900 |
|
| 901 |
def bulk_modulus(self, action): |
| 902 |
from ase.gui.bulk_modulus import BulkModulus |
| 903 |
BulkModulus(self.images)
|
| 904 |
|
| 905 |
def open(self, button=None, filenames=None): |
| 906 |
if filenames == None: |
| 907 |
chooser = gtk.FileChooserDialog( |
| 908 |
_('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN, |
| 909 |
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, |
| 910 |
gtk.STOCK_OPEN, gtk.RESPONSE_OK)) |
| 911 |
ok = chooser.run() == gtk.RESPONSE_OK |
| 912 |
if ok:
|
| 913 |
filenames = [chooser.get_filename()] |
| 914 |
chooser.destroy() |
| 915 |
|
| 916 |
if not ok: |
| 917 |
return
|
| 918 |
|
| 919 |
self.reset_tools_modes()
|
| 920 |
self.images.read(filenames, slice(None)) |
| 921 |
self.set_colors()
|
| 922 |
self.set_coordinates(self.images.nimages - 1, focus=True) |
| 923 |
|
| 924 |
def import_atoms (self, button=None, filenames=None): |
| 925 |
if filenames == None: |
| 926 |
chooser = gtk.FileChooserDialog( |
| 927 |
_('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN, |
| 928 |
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, |
| 929 |
gtk.STOCK_OPEN, gtk.RESPONSE_OK)) |
| 930 |
ok = chooser.run() |
| 931 |
if ok == gtk.RESPONSE_OK:
|
| 932 |
filenames = [chooser.get_filename()] |
| 933 |
chooser.destroy() |
| 934 |
|
| 935 |
if not ok: |
| 936 |
return
|
| 937 |
|
| 938 |
|
| 939 |
self.images.import_atoms(filenames, self.frame) |
| 940 |
self.set_colors()
|
| 941 |
self.set_coordinates(self.images.nimages - 1, focus=True) |
| 942 |
|
| 943 |
def save(self, action): |
| 944 |
chooser = gtk.FileChooserDialog( |
| 945 |
_('Save ...'), None, gtk.FILE_CHOOSER_ACTION_SAVE, |
| 946 |
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, |
| 947 |
gtk.STOCK_SAVE, gtk.RESPONSE_OK)) |
| 948 |
|
| 949 |
# Add a file type filter
|
| 950 |
types = [] |
| 951 |
name_to_suffix = {}
|
| 952 |
for name, suffix in [('Automatic', None), |
| 953 |
('XYZ file', 'xyz'), |
| 954 |
('ASE trajectory', 'traj'), |
| 955 |
('PDB file', 'pdb'), |
| 956 |
('Gaussian cube file', 'cube'), |
| 957 |
('Python script', 'py'), |
| 958 |
('VNL file', 'vnl'), |
| 959 |
('Portable Network Graphics', 'png'), |
| 960 |
('Persistance of Vision', 'pov'), |
| 961 |
('Encapsulated PostScript', 'eps'), |
| 962 |
('FHI-aims geometry input', 'in'), |
| 963 |
('VASP geometry input', 'POSCAR')]: |
| 964 |
if suffix is None: |
| 965 |
name = _(name) |
| 966 |
else:
|
| 967 |
name = '%s (%s)' % (_(name), suffix)
|
| 968 |
filt = gtk.FileFilter() |
| 969 |
filt.set_name(name) |
| 970 |
if suffix is None: |
| 971 |
filt.add_pattern('*')
|
| 972 |
elif suffix == 'POSCAR': |
| 973 |
filt.add_pattern('*POSCAR*')
|
| 974 |
else:
|
| 975 |
filt.add_pattern('*.'+suffix)
|
| 976 |
if suffix is not None: |
| 977 |
types.append(suffix) |
| 978 |
name_to_suffix[name] = suffix |
| 979 |
|
| 980 |
chooser.add_filter(filt) |
| 981 |
|
| 982 |
if self.images.nimages > 1: |
| 983 |
img_vbox = gtk.VBox() |
| 984 |
button = gtk.CheckButton('Save current image only (#%d)' %
|
| 985 |
self.frame)
|
| 986 |
pack(img_vbox, button) |
| 987 |
entry = gtk.Entry(10)
|
| 988 |
pack(img_vbox, [gtk.Label(_('Slice: ')), entry,
|
| 989 |
help('Help for slice ...')])
|
| 990 |
entry.set_text('0:%d' % self.images.nimages) |
| 991 |
img_vbox.show() |
| 992 |
chooser.set_extra_widget(img_vbox) |
| 993 |
|
| 994 |
while True: |
| 995 |
# Loop until the user selects a proper file name, or cancels.
|
| 996 |
response = chooser.run() |
| 997 |
if response == gtk.RESPONSE_CANCEL:
|
| 998 |
chooser.destroy() |
| 999 |
return
|
| 1000 |
elif response != gtk.RESPONSE_OK:
|
| 1001 |
print >>sys.stderr, "AG INTERNAL ERROR: strange response in Save,", response |
| 1002 |
chooser.destroy() |
| 1003 |
return
|
| 1004 |
|
| 1005 |
filename = chooser.get_filename() |
| 1006 |
|
| 1007 |
suffix = os.path.splitext(filename)[1][1:] |
| 1008 |
if 'POSCAR' in filename: |
| 1009 |
suffix = 'POSCAR'
|
| 1010 |
if suffix == '': |
| 1011 |
# No suffix given. If the user has chosen a special
|
| 1012 |
# file type, use the corresponding suffix.
|
| 1013 |
filt = chooser.get_filter().get_name() |
| 1014 |
suffix = name_to_suffix[filt] |
| 1015 |
filename = filename + '.' + suffix
|
| 1016 |
|
| 1017 |
if suffix not in types: |
| 1018 |
oops(message='Unknown output format!',
|
| 1019 |
message2='Use one of: ' + ', '.join(types[1:])) |
| 1020 |
continue
|
| 1021 |
|
| 1022 |
if self.images.nimages > 1: |
| 1023 |
if button.get_active():
|
| 1024 |
filename += '@%d' % self.frame |
| 1025 |
else:
|
| 1026 |
filename += '@' + entry.get_text()
|
| 1027 |
|
| 1028 |
break
|
| 1029 |
|
| 1030 |
chooser.destroy() |
| 1031 |
|
| 1032 |
bbox = np.empty(4)
|
| 1033 |
size = np.array([self.width, self.height]) / self.scale |
| 1034 |
bbox[0:2] = np.dot(self.center, self.axes[:, :2]) - size / 2 |
| 1035 |
bbox[2:] = bbox[:2] + size |
| 1036 |
suc = self.ui.get_widget('/MenuBar/ViewMenu/ShowUnitCell').get_active() |
| 1037 |
self.images.write(filename, self.axes, show_unit_cell=suc, bbox=bbox) |
| 1038 |
|
| 1039 |
def bulk_window(self, menuitem): |
| 1040 |
SetupBulkCrystal(self)
|
| 1041 |
|
| 1042 |
def surface_window(self, menuitem): |
| 1043 |
SetupSurfaceSlab(self)
|
| 1044 |
|
| 1045 |
def nanoparticle_window(self, menuitem): |
| 1046 |
SetupNanoparticle(self)
|
| 1047 |
|
| 1048 |
def graphene_window(self, menuitem): |
| 1049 |
SetupGraphene(self)
|
| 1050 |
|
| 1051 |
def nanotube_window(self, menuitem): |
| 1052 |
SetupNanotube(self)
|
| 1053 |
|
| 1054 |
def calculator_window(self, menuitem): |
| 1055 |
SetCalculator(self)
|
| 1056 |
|
| 1057 |
def energy_window(self, menuitem): |
| 1058 |
EnergyForces(self)
|
| 1059 |
|
| 1060 |
def energy_minimize_window(self, menuitem): |
| 1061 |
Minimize(self)
|
| 1062 |
|
| 1063 |
def scaling_window(self, menuitem): |
| 1064 |
HomogeneousDeformation(self)
|
| 1065 |
|
| 1066 |
def new_atoms(self, atoms, init_magmom=False): |
| 1067 |
"Set a new atoms object."
|
| 1068 |
self.notify_vulnerable()
|
| 1069 |
self.reset_tools_modes()
|
| 1070 |
|
| 1071 |
rpt = getattr(self.images, 'repeat', None) |
| 1072 |
self.images.repeat_images(np.ones(3, int)) |
| 1073 |
self.images.initialize([atoms], init_magmom=init_magmom)
|
| 1074 |
self.frame = 0 # Prevent crashes |
| 1075 |
self.images.repeat_images(rpt)
|
| 1076 |
self.set_colors()
|
| 1077 |
self.set_coordinates(frame=0, focus=True) |
| 1078 |
|
| 1079 |
def prepare_new_atoms(self): |
| 1080 |
"Marks that the next call to append_atoms should clear the images."
|
| 1081 |
self.images.prepare_new_atoms()
|
| 1082 |
|
| 1083 |
def append_atoms(self, atoms): |
| 1084 |
"Set a new atoms object."
|
| 1085 |
#self.notify_vulnerable() # Do this manually after last frame.
|
| 1086 |
frame = self.images.append_atoms(atoms)
|
| 1087 |
self.set_coordinates(frame=frame-1, focus=True) |
| 1088 |
|
| 1089 |
def notify_vulnerable(self): |
| 1090 |
"""Notify windows that would break when new_atoms is called.
|
| 1091 |
|
| 1092 |
The notified windows may adapt to the new atoms. If that is not
|
| 1093 |
possible, they should delete themselves.
|
| 1094 |
"""
|
| 1095 |
new_vul = [] # Keep weakrefs to objects that still exist.
|
| 1096 |
for wref in self.vulnerable_windows: |
| 1097 |
ref = wref() |
| 1098 |
if ref is not None: |
| 1099 |
new_vul.append(wref) |
| 1100 |
ref.notify_atoms_changed() |
| 1101 |
self.vulnerable_windows = new_vul
|
| 1102 |
|
| 1103 |
def register_vulnerable(self, obj): |
| 1104 |
"""Register windows that are vulnerable to changing the images.
|
| 1105 |
|
| 1106 |
Some windows will break if the atoms (and in particular the
|
| 1107 |
number of images) are changed. They can register themselves
|
| 1108 |
and be closed when that happens.
|
| 1109 |
"""
|
| 1110 |
self.vulnerable_windows.append(weakref.ref(obj))
|
| 1111 |
|
| 1112 |
def exit(self, button, event=None): |
| 1113 |
gtk.main_quit() |
| 1114 |
return True |
| 1115 |
|
| 1116 |
def xxx(self, x=None, |
| 1117 |
message1='Not implemented!',
|
| 1118 |
message2='do you really need it?'):
|
| 1119 |
oops(message1, message2) |
| 1120 |
|
| 1121 |
def about(self, action): |
| 1122 |
try:
|
| 1123 |
dialog = gtk.AboutDialog() |
| 1124 |
except AttributeError: |
| 1125 |
self.xxx()
|
| 1126 |
else:
|
| 1127 |
dialog.run() |
| 1128 |
|
| 1129 |
def webpage(widget): |
| 1130 |
import webbrowser |
| 1131 |
webbrowser.open('https://wiki.fysik.dtu.dk/ase/ase/gui.html')
|
| 1132 |
|