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|
from __future__ import print_function
# husk:
# DFT
# ADOS
# grey-out stuff after one second: vmd, rasmol, ...
# Show with ....
# rasmol: set same rotation as ag
# Graphs: save, Python, 3D
# start from python (interactive mode?)
# surfacebuilder
# screen-dump
# icon
# translate option: record all translations,
# and check for missing translations.
# TODO: Add possible way of choosing orinetations. \
# TODO: Two atoms defines a direction, three atoms their normal does
# TODO: Align orientations chosen in Rot_selected v unselcted
# TODO: Get the atoms_rotate_0 thing string
# TODO: Use set atoms instead og the get atoms
# TODO: Arrow keys will decide how the orientation changes
# TODO: Undo redo que should be implemented
# TODO: Update should have possibility to change positions
# TODO: Window for rotation modes and move moves which can be chosen
# TODO: WHen rotate and move / hide the movie menu
import os
import sys
import weakref
import pickle
import subprocess
from gettext import gettext as _
from gettext import ngettext
import numpy as np
import pygtk
pygtk.require("2.0")
import gtk
from ase.gui.view import View
from ase.gui.status import Status
from ase.gui.widgets import pack, oops
from ase.gui.settings import Settings
from ase.gui.crystal import SetupBulkCrystal
from ase.gui.surfaceslab import SetupSurfaceSlab
from ase.gui.nanoparticle import SetupNanoparticle
from ase.gui.nanotube import SetupNanotube
from ase.gui.graphene import SetupGraphene
from ase.gui.calculator import SetCalculator
from ase.gui.energyforces import EnergyForces
from ase.gui.minimize import Minimize
from ase.gui.scaling import HomogeneousDeformation
from ase.gui.quickinfo import QuickInfo
from ase.gui.save import save_dialog
from ase import __version__
ui_info = """\
<ui>
<menubar name='MenuBar'>
<menu action='FileMenu'>
<menuitem action='Open'/>
<menuitem action='New'/>
<menuitem action='Save'/>
<separator/>
<menuitem action='Quit'/>
</menu>
<menu action='EditMenu'>
<menuitem action='SelectAll'/>
<menuitem action='Invert'/>
<menuitem action='SelectConstrained'/>
<menuitem action='SelectImmobile'/>
<separator/>
<menuitem action='Copy'/>
<menuitem action='Paste'/>
<separator/>
<menuitem action='HideAtoms'/>
<menuitem action='ShowAtoms'/>
<separator/>
<menuitem action='Modify'/>
<menuitem action='AddAtoms'/>
<menuitem action='DeleteAtoms'/>
<separator/>
<menuitem action='First'/>
<menuitem action='Previous'/>
<menuitem action='Next'/>
<menuitem action='Last'/>
</menu>
<menu action='ViewMenu'>
<menuitem action='ShowUnitCell'/>
<menuitem action='ShowAxes'/>
<menuitem action='ShowBonds'/>
<menuitem action='ShowVelocities'/>
<menuitem action='ShowForces'/>
<menu action='ShowLabels'>
<menuitem action='NoLabel'/>
<menuitem action='AtomIndex'/>
<menuitem action='MagMom'/>
<menuitem action='Element'/>
</menu>
<separator/>
<menuitem action='QuickInfo'/>
<menuitem action='Repeat'/>
<menuitem action='Rotate'/>
<menuitem action='Colors'/>
<menuitem action='Focus'/>
<menuitem action='ZoomIn'/>
<menuitem action='ZoomOut'/>
<menu action='ChangeView'>
<menuitem action='ResetView'/>
<menuitem action='xyPlane'/>
<menuitem action='yzPlane'/>
<menuitem action='zxPlane'/>
<menuitem action='yxPlane'/>
<menuitem action='zyPlane'/>
<menuitem action='xzPlane'/>
<menuitem action='a2a3Plane'/>
<menuitem action='a3a1Plane'/>
<menuitem action='a1a2Plane'/>
<menuitem action='a3a2Plane'/>
<menuitem action='a2a1Plane'/>
<menuitem action='a1a3Plane'/>
</menu>
<menuitem action='Settings'/>
<menuitem action='VMD'/>
<menuitem action='RasMol'/>
<menuitem action='XMakeMol'/>
<menuitem action='Avogadro'/>
</menu>
<menu action='ToolsMenu'>
<menuitem action='Graphs'/>
<menuitem action='Movie'/>
<menuitem action='EModify'/>
<menuitem action='Constraints'/>
<menuitem action='RenderScene'/>
<menuitem action='MoveAtoms'/>
<menuitem action='RotateAtoms'/>
<menuitem action='OrientAtoms'/>
<menuitem action='NEB'/>
<menuitem action='BulkModulus'/>
</menu>
<menu action='SetupMenu'>
<menuitem action='Bulk'/>
<menuitem action='Surface'/>
<menuitem action='Nanoparticle'/>
<menuitem action='Graphene'/>
<menuitem action='Nanotube'/>
</menu>
<menu action='CalculateMenu'>
<menuitem action='SetCalculator'/>
<separator/>
<menuitem action='EnergyForces'/>
<menuitem action='Minimize'/>
<menuitem action='Scaling'/>
</menu>
<menu action='HelpMenu'>
<menuitem action='About'/>
<menuitem action='Webpage'/>
<menuitem action='Debug'/>
</menu>
</menubar>
</ui>"""
class GUI(View, Status):
def __init__(self, images,
rotations='',
show_unit_cell=True,
show_bonds=False):
# Try to change into directory of file you are viewing
try:
os.chdir(os.path.split(sys.argv[1])[0])
# This will fail sometimes (e.g. for starting a new session)
except:
pass
self.images = images
self.window = gtk.Window(gtk.WINDOW_TOPLEVEL)
# self.window.set_icon(gtk.gdk.pixbuf_new_from_file('guiase.png'))
self.window.set_position(gtk.WIN_POS_CENTER)
# self.window.connect("destroy", lambda w: gtk.main_quit())
self.window.connect('delete_event', self.exit)
vbox = gtk.VBox()
self.window.add(vbox)
if gtk.pygtk_version < (2, 12):
self.set_tip = gtk.Tooltips().set_tip
actions = gtk.ActionGroup("Actions")
actions.add_actions([
('FileMenu', None, _('_File')),
('EditMenu', None, _('_Edit')),
('ViewMenu', None, _('_View')),
('ToolsMenu', None, _('_Tools')),
# TRANSLATORS: Set up (i.e. build) surfaces, nanoparticles, ...
('SetupMenu', None, _('_Setup')),
('CalculateMenu', None, _('_Calculate')),
('HelpMenu', None, _('_Help')),
('Open', gtk.STOCK_OPEN, _('_Open'), '<control>O',
_('Create a new file'), self.open),
('New', gtk.STOCK_NEW, _('_New'), '<control>N',
_('New ase.gui window'), lambda widget: os.system('ase-gui &')),
('Save', gtk.STOCK_SAVE, _('_Save'), '<control>S',
_('Save current file'), lambda x: save_dialog(self)),
('Quit', gtk.STOCK_QUIT, _('_Quit'), '<control>Q', _('Quit'),
self.exit),
('SelectAll', None, _('Select _all'), None, '', self.select_all),
('Invert', None, _('_Invert selection'), None, '',
self.invert_selection),
('SelectConstrained', None, _('Select _constrained atoms'), None,
'', self.select_constrained_atoms),
('SelectImmobile', None, _('Select _immobile atoms'), '<control>I',
'', self.select_immobile_atoms),
('Copy', None, _('_Copy'), '<control>C',
_('Copy current selection and its orientation to clipboard'),
self.copy_atoms),
('Paste', None, _('_Paste'), '<control>V',
_('Insert current clipboard selection'), self.paste_atoms),
('Modify', None, _('_Modify'), '<control>Y',
_('Change tags, moments and atom types of the selected atoms'),
self.modify_atoms),
('AddAtoms', None, _('_Add atoms'), '<control>A',
_('Insert or import atoms and molecules'), self.add_atoms),
('DeleteAtoms', None, _('_Delete selected atoms'), 'BackSpace',
_('Delete the selected atoms'), self.delete_selected_atoms),
('First', gtk.STOCK_GOTO_FIRST, _('_First image'), 'Home', '',
self.step),
('Previous', gtk.STOCK_GO_BACK, _('_Previous image'), 'Page_Up',
'', self.step),
('Next', gtk.STOCK_GO_FORWARD, _('_Next image'), 'Page_Down', '',
self.step),
('Last', gtk.STOCK_GOTO_LAST, _('_Last image'), 'End', '',
self.step),
('ShowLabels', None, _('Show _Labels')),
('HideAtoms', None, _('Hide selected atoms'), None, '',
self.hide_selected),
('ShowAtoms', None, _('Show selected atoms'), None, '',
self.show_selected),
('QuickInfo', None, _('Quick Info ...'), None, '',
self.quick_info_window),
('Repeat', None, _('Repeat ...'), None, '', self.repeat_window),
('Rotate', None, _('Rotate ...'), None, '', self.rotate_window),
('Colors', None, _('Colors ...'), 'C', '', self.colors_window),
# TRANSLATORS: verb
('Focus', gtk.STOCK_ZOOM_FIT, _('Focus'), 'F', '', self.focus),
('ZoomIn', gtk.STOCK_ZOOM_IN, _('Zoom in'), 'plus', '', self.zoom),
('ZoomOut', gtk.STOCK_ZOOM_OUT, _('Zoom out'), 'minus', '',
self.zoom),
('ChangeView', None, _('Change View')),
('ResetView', None, _('Reset View'), 'equal', '', self.reset_view),
('xyPlane', None, _('\'xy\' Plane'), 'z', '', self.set_view),
('yzPlane', None, _('\'yz\' Plane'), 'x', '', self.set_view),
('zxPlane', None, _('\'zx\' Plane'), 'y', '', self.set_view),
('yxPlane', None, _('\'yx\' Plane'), '<alt>z', '', self.set_view),
('zyPlane', None, _('\'zy\' Plane'), '<alt>x', '', self.set_view),
('xzPlane', None, _('\'xz\' Plane'), '<alt>y', '', self.set_view),
('a2a3Plane', None, _('\'a2 a3\' Plane'), '1', '', self.set_view),
('a3a1Plane', None, _('\'a3 a1\' Plane'), '2', '', self.set_view),
('a1a2Plane', None, _('\'a1 a2\' Plane'), '3', '', self.set_view),
('a3a2Plane', None, _('\'a3 a2\' Plane'), '<alt>1', '',
self.set_view),
('a1a3Plane', None, _('\'a1 a3\' Plane'), '<alt>2', '',
self.set_view),
('a2a1Plane', None, _('\'a2 a1\' Plane'), '<alt>3', '',
self.set_view),
('Settings', gtk.STOCK_PREFERENCES, _('Settings ...'), None, '',
self.settings),
('VMD', None, _('VMD'), None, '', self.external_viewer),
('RasMol', None, _('RasMol'), None, '', self.external_viewer),
('XMakeMol', None, _('xmakemol'), None, '', self.external_viewer),
('Avogadro', None, _('avogadro'), None, '', self.external_viewer),
('Graphs', None, _('Graphs ...'), None, '', self.plot_graphs),
('Movie', None, _('Movie ...'), None, '', self.movie),
('EModify', None, _('Expert mode ...'), '<control>E', '',
self.execute),
('Constraints', None, _('Constraints ...'), None, '',
self.constraints_window),
('RenderScene', None, _('Render scene ...'), None, '',
self.render_window),
('NEB', None, _('NE_B'), None, '', self.NEB),
('BulkModulus', None, _('B_ulk Modulus'), None, '',
self.bulk_modulus),
('Bulk', None, _('_Bulk Crystal'), None,
_("Create a bulk crystal with arbitrary orientation"),
self.bulk_window),
('Surface', None, _('_Surface slab'), None,
_("Create the most common surfaces"), self.surface_window),
('Nanoparticle', None, _('_Nanoparticle'), None,
_("Create a crystalline nanoparticle"), self.nanoparticle_window),
('Nanotube', None, _('Nano_tube'), None, _("Create a nanotube"),
self.nanotube_window),
('Graphene', None, _('Graphene'), None,
_("Create a graphene sheet or nanoribbon"), self.graphene_window),
('SetCalculator', None, _('Set _Calculator'), None,
_("Set a calculator used in all calculation modules"),
self.calculator_window),
('EnergyForces', None, _('_Energy and Forces'), None,
_("Calculate energy and forces"), self.energy_window),
('Minimize', None, _('Energy _Minimization'), None,
_("Minimize the energy"), self.energy_minimize_window),
('Scaling', None, _('Scale system'), None,
_("Deform system by scaling it"), self.scaling_window),
('About', None, _('_About'), None, None, self.about),
('Webpage', gtk.STOCK_HELP, _('Webpage ...'), None, None, webpage),
('Debug', None, _('Debug ...'), None, None, self.debug)
])
actions.add_toggle_actions([
('ShowUnitCell', None, _('Show _unit cell'), '<control>U', 'Bold',
self.toggle_show_unit_cell,
show_unit_cell > 0), ('ShowAxes', None, _('Show _axes'), None,
'Bold', self.toggle_show_axes, True),
('ShowBonds', None, _('Show _bonds'), '<control>B', 'Bold',
self.toggle_show_bonds,
show_bonds), ('ShowVelocities', None, _('Show _velocities'),
'<control>G', 'Bold', self.toggle_show_velocities,
False), ('ShowForces', None, _('Show _forces'),
'<control>F', 'Bold',
self.toggle_show_forces, False),
('MoveAtoms', None, _('_Move atoms'), '<control>M', 'Bold',
self.toggle_move_mode,
False), ('RotateAtoms', None, _('_Rotate atoms'), '<control>R',
'Bold', self.toggle_rotate_mode,
False), ('OrientAtoms', None, _('Orien_t atoms'),
'<control>T', 'Bold', self.toggle_orient_mode,
False)
])
actions.add_radio_actions(
(('NoLabel', None, _('_None'), None, None, 0),
('AtomIndex', None, _('Atom _Index'), None, None, 1),
('MagMom', None, _('_Magnetic Moments'), None, None, 2),
('Element', None, _('_Element Symbol'), None, None, 3)), 0,
self.show_labels)
self.ui = ui = gtk.UIManager()
ui.insert_action_group(actions, 0)
self.window.add_accel_group(ui.get_accel_group())
ui.add_ui_from_string(ui_info)
vbox.pack_start(ui.get_widget('/MenuBar'), False, False, 0)
View.__init__(self, vbox, rotations)
Status.__init__(self, vbox)
vbox.show()
# self.window.set_events(gtk.gdk.BUTTON_PRESS_MASK)
self.window.connect('key-press-event', self.scroll)
self.window.connect('scroll_event', self.scroll_event)
self.window.show()
self.graphs = [] # list of matplotlib processes
self.graph_wref = [] # list of weakrefs to Graph objects
self.movie_window = None
self.vulnerable_windows = []
self.simulation = {} # Used by modules on Calculate menu.
self.module_state = {} # Used by modules to store their state.
def run(self, expr=None):
self.set_colors()
self.set_coordinates(self.images.nimages - 1, focus=True)
if self.images.nimages > 1:
self.movie()
if expr is None and not np.isnan(self.images.E[0]):
expr = self.config['gui_graphs_string']
if expr is not None and expr != '' and self.images.nimages > 1:
self.plot_graphs(expr=expr)
gtk.main()
def step(self, action):
d = {'First': -10000000,
'Previous': -1,
'Next': 1,
'Last': 10000000}[action.get_name()]
i = max(0, min(self.images.nimages - 1, self.frame + d))
self.set_frame(i)
if self.movie_window is not None:
self.movie_window.frame_number.value = i
def _do_zoom(self, x):
"""Utility method for zooming"""
self.scale *= x
self.draw()
def zoom(self, action):
"""Zoom in/out on keypress or clicking menu item"""
x = {'ZoomIn': 1.2, 'ZoomOut': 1 / 1.2}[action.get_name()]
self._do_zoom(x)
def scroll_event(self, window, event):
"""Zoom in/out when using mouse wheel"""
SHIFT = event.state == gtk.gdk.SHIFT_MASK
x = 1.0
if event.direction == gtk.gdk.SCROLL_UP:
x = 1.0 + (1 - SHIFT) * 0.2 + SHIFT * 0.01
elif event.direction == gtk.gdk.SCROLL_DOWN:
x = 1.0 / (1.0 + (1 - SHIFT) * 0.2 + SHIFT * 0.01)
self._do_zoom(x)
def settings(self, menuitem):
Settings(self)
def scroll(self, window, event):
from copy import copy
CTRL = event.state == gtk.gdk.CONTROL_MASK
SHIFT = event.state == gtk.gdk.SHIFT_MASK
dxdydz = {
gtk.keysyms.KP_Add: ('zoom', 1.0 +
(1 - SHIFT) * 0.2 + SHIFT * 0.01, 0),
gtk.keysyms.KP_Subtract: ('zoom', 1 /
(1.0 +
(1 - SHIFT) * 0.2 + SHIFT * 0.01), 0),
gtk.keysyms.Up: (0, +1 - CTRL, +CTRL),
gtk.keysyms.Down: (0, -1 + CTRL, -CTRL),
gtk.keysyms.Right: (+1, 0, 0),
gtk.keysyms.Left: (-1, 0, 0)
}.get(event.keyval, None)
sel = []
atom_move = self.ui.get_widget(
'/MenuBar/ToolsMenu/MoveAtoms').get_active()
atom_rotate = self.ui.get_widget(
'/MenuBar/ToolsMenu/RotateAtoms').get_active()
atom_orient = self.ui.get_widget(
'/MenuBar/ToolsMenu/OrientAtoms').get_active()
if dxdydz is None:
return
dx, dy, dz = dxdydz
if dx == 'zoom':
self._do_zoom(dy)
return
tvec = np.array([dx, dy, dz])
dir_vec = np.dot(self.axes, tvec)
if (atom_move):
rotmat = self.axes
s = 0.1
if SHIFT:
s = 0.01
add = s * dir_vec
for i in range(len(self.R)):
if self.atoms_to_rotate_0[i]:
self.R[i] += add
for jx in range(self.images.nimages):
self.images.P[jx][i] += add
elif atom_rotate:
from .rot_tools import rotate_about_vec, rotate_vec
sel = self.images.selected
if sum(sel) == 0:
sel = self.atoms_to_rotate_0
nsel = sum(sel)
# this is the first one to get instatiated
if nsel != 2:
self.rot_vec = dir_vec
change = False
z_axis = np.dot(self.axes, np.array([0, 0, 1]))
if self.atoms_to_rotate is None:
change = True
self.z_axis_old = z_axis.copy()
self.dx_change = [0, 0]
self.atoms_to_rotate = self.atoms_to_rotate_0.copy()
self.atoms_selected = sel.copy()
self.rot_vec = dir_vec
if nsel != 2 or sum(self.atoms_to_rotate) == 2:
self.dx_change = [0, 0]
for i in range(len(sel)):
if sel[i] != self.atoms_selected[i]:
change = True
cz = [dx, dy + dz]
if cz[0] or cz[1]:
change = False
if not (cz[0] * (self.dx_change[1])):
change = True
for i in range(2):
if cz[i] and self.dx_change[i]:
self.rot_vec = self.rot_vec * cz[i] * self.dx_change[i]
if cz[1]:
change = False
if np.prod(self.z_axis_old != z_axis):
change = True
self.z_axis_old = z_axis.copy()
self.dx_change = copy(cz)
dihedral_rotation = len(self.images.selected_ordered) == 4
if change:
self.atoms_selected = sel.copy()
if nsel == 2 and sum(self.atoms_to_rotate) != 2:
asel = []
for i, j in enumerate(sel):
if j:
asel.append(i)
a1, a2 = asel
rvx = (self.images.P[self.frame][a1] -
self.images.P[self.frame][a2])
rvy = np.cross(rvx, np.dot(self.axes, np.array([0, 0, 1])))
self.rot_vec = rvx * dx + rvy * (dy + dz)
self.dx_change = [dx, dy + dz]
# dihedral rotation?
if dihedral_rotation:
sel = self.images.selected_ordered
self.rot_vec = (dx + dy + dz) * (
self.R[sel[2]] - self.R[sel[1]])
rot_cen = np.array([0.0, 0.0, 0.0])
if dihedral_rotation:
sel = self.images.selected_ordered
rot_cen = self.R[sel[1]].copy()
elif nsel:
for i, b in enumerate(sel):
if b:
rot_cen += self.R[i]
rot_cen /= float(nsel)
degrees = 5 * (1 - SHIFT) + SHIFT
degrees = abs(sum(dxdydz)) * 3.1415 / 360.0 * degrees
rotmat = rotate_about_vec(self.rot_vec, degrees)
# now rotate the atoms that are to be rotated
for i in range(len(self.R)):
if self.atoms_to_rotate[i]:
self.R[i] -= rot_cen
for jx in range(self.images.nimages):
self.images.P[jx][i] -= rot_cen
self.R[i] = rotate_vec(rotmat, self.R[i])
for jx in range(self.images.nimages):
self.images.P[jx][i] = rotate_vec(rotmat,
self.images.P[jx][i])
self.R[i] += rot_cen
for jx in range(self.images.nimages):
self.images.P[jx][i] += rot_cen
elif atom_orient:
to_vec = np.array([dx, dy, dz])
from .rot_tools import rotate_vec_into_newvec
rot_mat = rotate_vec_into_newvec(self.orient_normal, to_vec)
self.axes = rot_mat
self.set_coordinates()
else:
self.center -= (
dx * 0.1 * self.axes[:, 0] - dy * 0.1 * self.axes[:, 1]
)
self.draw()
def copy_atoms(self, widget):
"Copies selected atoms to a clipboard."
clip = gtk.clipboard_get(gtk.gdk.SELECTION_CLIPBOARD)
if self.images.selected.any():
atoms = self.images.get_atoms(self.frame)
lena = len(atoms)
for i in range(len(atoms)):
li = lena - 1 - i
if not self.images.selected[li]:
del (atoms[li])
for i in atoms:
i.position = np.dot(self.axes.T, i.position)
ref = atoms[0].position
for i in atoms:
if i.position[2] < ref[2]:
ref = i.position
atoms.reference_position = ref
clip.set_text(pickle.dumps(atoms, 0))
def paste_atoms(self, widget):
"""Inserts clipboard selection into the current frame using the
add_atoms window."""
clip = gtk.clipboard_get(gtk.gdk.SELECTION_CLIPBOARD)
try:
atoms = pickle.loads(clip.wait_for_text())
except TypeError:
pass
else:
self.add_atoms(widget, data='Paste', paste=atoms)
def add_atoms(self, widget, data=None, paste=None):
"""Presents a dialogbox to the user, that allows him to add
atoms/molecule to the current slab or to paste the clipboard.
The molecule/atom is rotated using the current rotation of the
coordinate system.
The molecule/atom can be added at a specified position - if the
keyword auto+Z is used, the COM of the selected atoms will be used
as COM for the moleculed. The COM is furthermore
translated Z ang towards the user.
If no molecules are selected, the COM of all the atoms will be used
for the x-y components of the active coordinate system, while the
z-direction will be chosen from the nearest atom position
along this direction.
Note: If this option is used, all frames except the active one are
deleted.
"""
if data == 'load':
chooser = gtk.FileChooserDialog(
_('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN,
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_OPEN,
gtk.RESPONSE_OK))
chooser.set_filename(_("<<filename>>"))
ok = chooser.run()
if ok == gtk.RESPONSE_OK:
filename = chooser.get_filename()
chooser.destroy()
else:
chooser.destroy()
return
if data == 'OK' or data == 'load':
import ase
if data == 'load':
molecule = filename
else:
molecule = self.add_entries[1].get_text()
tag = self.add_entries[2].get_text()
mom = self.add_entries[3].get_text()
pos = self.add_entries[4].get_text().lower()
if paste is not None:
a = paste.copy()
else:
a = None
if a is None:
try:
a = ase.Atoms([ase.Atom(molecule)])
except:
try:
import ase.build
a = ase.build.molecule(molecule)
except:
try:
a = ase.io.read(molecule, -1)
except:
self.add_entries[1].set_text('?' + molecule)
return ()
directions = np.transpose(self.axes)
if a is not None:
for i in a:
try:
i.set('tag', int(tag))
except:
self.add_entries[2].set_text('?' + tag)
return ()
try:
i.magmom = float(mom)
except:
self.add_entries[3].set_text('?' + mom)
return ()
if self.origin_radio.get_active() and paste:
a.translate(-paste.reference_position)
# apply the current rotation matrix to A
for i in a:
i.position = np.dot(self.axes, i.position)
# find the extent of the molecule in the local coordinate
# system
if self.centre_radio.get_active():
a_cen_pos = np.array([0.0, 0.0, 0.0])
m_cen_pos = 0.0
for i in a.positions:
a_cen_pos[0] += np.dot(directions[0], i)
a_cen_pos[1] += np.dot(directions[1], i)
a_cen_pos[2] += np.dot(directions[2], i)
m_cen_pos = max(np.dot(-directions[2], i), m_cen_pos)
a_cen_pos[0] /= len(a.positions)
a_cen_pos[1] /= len(a.positions)
a_cen_pos[2] /= len(a.positions)
a_cen_pos[2] -= m_cen_pos
else:
a_cen_pos = np.array([0.0, 0.0, 0.0])
# now find the position
cen_pos = np.array([0.0, 0.0, 0.0])
if sum(self.images.selected) > 0:
for i in range(len(self.R)):
if self.images.selected[i]:
cen_pos += self.R[i]
cen_pos /= sum(self.images.selected)
elif len(self.R) > 0:
px = 0.0
py = 0.0
pz = -1e6
for i in range(len(self.R)):
px += np.dot(directions[0], self.R[i])
py += np.dot(directions[1], self.R[i])
pz = max(np.dot(directions[2], self.R[i]), pz)
px = (px / float(len(self.R)))
py = (py / float(len(self.R)))
cen_pos = (directions[0] * px +
directions[1] * py +
directions[2] * pz)
if 'auto' in pos:
pos = pos.replace('auto', '')
import re
pos = re.sub('\s', '', pos)
if '(' in pos:
sign = eval('%s1' % pos[0])
a_cen_pos -= sign * np.array(eval(pos[1:]), float)
else:
a_cen_pos -= float(pos) * directions[2]
else:
cen_pos = np.array(eval(pos))
for i in a:
i.position += cen_pos - a_cen_pos
# and them to the molecule
atoms = self.images.get_atoms(self.frame)
atoms = atoms + a
self.new_atoms(atoms, init_magmom=True)
# and finally select the new molecule for easy moving and
# rotation
for i in range(len(a)):
self.images.selected[len(atoms) - i - 1] = True
self.draw()
self.add_entries[0].destroy()
if data == 'Cancel':
self.add_entries[0].destroy()
if data is None or data == 'Paste':
from ase.gui.widgets import pack
molecule = ''
tag = '0'
mom = '0'
pos = 'auto+1'
self.add_entries = []
window = gtk.Window(gtk.WINDOW_TOPLEVEL)
self.add_entries.append(window)
window.set_title(_('Add atoms'))
if data == 'Paste':
molecule = paste.get_chemical_formula()
window.set_title(_('Paste'))
vbox = gtk.VBox(False, 0)
window.add(vbox)
vbox.show()
packed = False
for i, j in [[_('Insert atom or molecule'), molecule],
[_('Tag'), tag], [_('Moment'), mom], [_('Position'),
pos]]:
label = gtk.Label(i)
if not packed:
vbox.pack_start(label, True, True, 0)
else:
packed = True
vbox.add(label)
label.show()
entry = gtk.Entry()
entry.set_text(j)
self.add_entries.append(entry)
entry.set_max_length(50)
entry.show()
vbox.add(entry)
pack(vbox, [gtk.Label('atom/molecule reference:')])
self.centre_radio = gtk.RadioButton(None, "centre ")
self.origin_radio = gtk.RadioButton(self.centre_radio, "origin")
pack(vbox, [self.centre_radio, self.origin_radio])
if data == 'Paste':
self.origin_radio.set_active(True)
self.add_entries[1].set_sensitive(False)
if data is None:
button = gtk.Button(_('_Load molecule'))
button.connect('clicked', self.add_atoms, 'load')
button.show()
vbox.add(button)
button = gtk.Button(_('_OK'))
button.connect('clicked', self.add_atoms, 'OK', paste)
button.show()
vbox.add(button)
button = gtk.Button(_('_Cancel'))
button.connect('clicked', self.add_atoms, 'Cancel')
button.show()
vbox.add(button)
window.show()
def modify_atoms(self, widget, data=None):
"""Presents a dialog box where the user is able to change the
atomic type, the magnetic moment and tags of the selected atoms.
An item marked with X will not be changed.
"""
if data:
if data == 'OK':
import ase
symbol = self.add_entries[1].get_text()
tag = self.add_entries[2].get_text()
mom = self.add_entries[3].get_text()
a = None
if symbol != 'X':
try:
a = ase.Atoms([ase.Atom(symbol)])
except:
self.add_entries[1].set_text('?' + symbol)
return ()
y = self.images.selected.copy()
# and them to the molecule
atoms = self.images.get_atoms(self.frame)
for i in range(len(atoms)):
if self.images.selected[i]:
if a:
atoms[i].symbol = symbol
try:
if tag != 'X':
atoms[i].tag = int(tag)
except:
self.add_entries[2].set_text('?' + tag)
return ()
try:
if mom != 'X':
atoms[i].magmom = float(mom)
except:
self.add_entries[3].set_text('?' + mom)
return ()
self.new_atoms(atoms, init_magmom=True)
# Updates atomic labels
a = self.ui.get_action_groups()[0].get_action("NoLabel")
cv = a.get_current_value()
a.set_current_value(0)
a.set_current_value(cv)
# and finally select the new molecule for easy moving
# and rotation
self.images.selected = y
self.draw()
self.add_entries[0].destroy()
if data is None and sum(self.images.selected):
atoms = self.images.get_atoms(self.frame)
s_tag = ''
s_mom = ''
s_symbol = ''
# Get the tags, moments and symbols of the selected atomsa
for i in range(len(atoms)):
if self.images.selected[i]:
if not (s_tag):
s_tag = str(atoms[i].tag)
elif s_tag != str(atoms[i].tag):
s_tag = 'X'
if not (s_mom):
s_mom = ("%2.2f" % (atoms[i].magmom))
elif s_mom != ("%2.2f" % (atoms[i].magmom)):
s_mom = 'X'
if not (s_symbol):
s_symbol = str(atoms[i].symbol)
elif s_symbol != str(atoms[i].symbol):
s_symbol = 'X'
self.add_entries = []
window = gtk.Window(gtk.WINDOW_TOPLEVEL)
self.add_entries.append(window)
window.set_title(_('Modify'))
vbox = gtk.VBox(False, 0)
window.add(vbox)
vbox.show()
pack = False
for i, j in [[_('Atom'), s_symbol], [_('Tag'), s_tag],
[_('Moment'), s_mom]]:
label = gtk.Label(i)
if not pack:
vbox.pack_start(label, True, True, 0)
else:
pack = True
vbox.add(label)
label.show()
entry = gtk.Entry()
entry.set_text(j)
self.add_entries.append(entry)
entry.set_max_length(50)
entry.show()
vbox.add(entry)
button = gtk.Button(_('_OK'))
button.connect('clicked', self.modify_atoms, 'OK')
button.show()
vbox.add(button)
button = gtk.Button(_('_Cancel'))
button.connect('clicked', self.modify_atoms, 'Cancel')
button.show()
vbox.add(button)
window.show()
def delete_selected_atoms(self, widget=None, data=None):
if data == 'OK':
atoms = self.images.get_atoms(self.frame)
lena = len(atoms)
for i in range(len(atoms)):
li = lena - 1 - i
if self.images.selected[li]:
del (atoms[li])
self.new_atoms(atoms)
self.draw()
if data:
self.delete_window.destroy()
if not (data) and sum(self.images.selected):
nselected = sum(self.images.selected)
self.delete_window = gtk.Window(gtk.WINDOW_TOPLEVEL)
self.delete_window.set_title(_('Confirmation'))
self.delete_window.set_border_width(10)
self.box1 = gtk.HBox(False, 0)
self.delete_window.add(self.box1)
self.button1 = gtk.Button(ngettext('Delete selected atom?',
'Delete selected atoms?',
nselected))
self.button1.connect("clicked", self.delete_selected_atoms, "OK")
self.box1.pack_start(self.button1, True, True, 0)
self.button1.show()
self.button2 = gtk.Button(_("Cancel"))
self.button2.connect("clicked", self.delete_selected_atoms,
"Cancel")
self.box1.pack_start(self.button2, True, True, 0)
self.button2.show()
self.box1.show()
self.delete_window.show()
def debug(self, x):
from ase.gui.debug import Debug
Debug(self)
def execute(self, widget=None):
from ase.gui.execute import Execute
Execute(self)
def constraints_window(self, widget=None):
from ase.gui.constraints import Constraints
Constraints(self)
def select_all(self, widget):
self.images.selected[:] = True
self.draw()
def invert_selection(self, widget):
self.images.selected[:] = ~self.images.selected
self.draw()
def select_constrained_atoms(self, widget):
self.images.selected[:] = ~self.images.dynamic
self.draw()
def select_immobile_atoms(self, widget):
if self.images.nimages > 1:
R0 = self.images.P[0]
for R in self.images.P[1:]:
self.images.selected[:] = ~(np.abs(R - R0) > 1.0e-10).any(1)
self.draw()
def movie(self, widget=None):
from ase.gui.movie import Movie
self.movie_window = Movie(self)
def plot_graphs(self, x=None, expr=None):
from ase.gui.graphs import Graphs
g = Graphs(self)
if expr is not None:
g.plot(expr=expr)
self.graph_wref.append(weakref.ref(g))
def plot_graphs_newatoms(self):
"Notify any Graph objects that they should make new plots."
new_wref = []
found = 0
for wref in self.graph_wref:
ref = wref()
if ref is not None:
ref.plot()
new_wref.append(wref) # Preserve weakrefs that still work.
found += 1
self.graph_wref = new_wref
return found
def NEB(self, action):
from ase.gui.neb import NudgedElasticBand
NudgedElasticBand(self.images)
def bulk_modulus(self, action):
process = subprocess.Popen([sys.executable, '-m', 'ase.eos',
'--plot', '-'],
stdin=subprocess.PIPE)
v = np.array([abs(np.linalg.det(A)) for A in self.images.A])
e = self.images.E
pickle.dump((v, e), process.stdin)
process.stdin.close()
self.graphs.append(process)
def open(self, button=None):
from ase.io.formats import all_formats, get_ioformat
formats = [(_('Automatic'), None)]
def key(item):
return item[1][0]
for format, (description, code) in sorted(all_formats.items(),
key=key):
io = get_ioformat(format)
if io.read and description != '?':
formats.append((_(description), format))
chooser = gtk.FileChooserDialog(
_('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN,
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_OPEN,
gtk.RESPONSE_OK))
chooser.set_filename(_("<<filename>>"))
# Add a file type filter
name_to_format = {}
types = gtk.combo_box_new_text()
for name, format in formats:
types.append_text(name)
name_to_format[name] = format
types.set_active(0)
img_vbox = gtk.VBox()
pack(img_vbox, [gtk.Label(_('File type:')), types])
img_vbox.show()
chooser.set_extra_widget(img_vbox)
ok = chooser.run() == gtk.RESPONSE_OK
if ok:
filenames = [chooser.get_filename()]
filetype = types.get_active_text()
chooser.destroy()
if not ok:
return
self.reset_tools_modes()
self.images.read(filenames, slice(None), name_to_format[filetype])
self.set_colors()
self.set_coordinates(self.images.nimages - 1, focus=True)
def import_atoms(self, button=None, filenames=None):
if filenames is None:
chooser = gtk.FileChooserDialog(
_('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN,
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_OPEN,
gtk.RESPONSE_OK))
ok = chooser.run()
if ok == gtk.RESPONSE_OK:
filenames = [chooser.get_filename()]
chooser.destroy()
if not ok:
return
self.images.import_atoms(filenames, self.frame)
self.set_colors()
self.set_coordinates(self.images.nimages - 1, focus=True)
def quick_info_window(self, menuitem):
QuickInfo(self)
def bulk_window(self, menuitem):
SetupBulkCrystal(self)
def surface_window(self, menuitem):
SetupSurfaceSlab(self)
def nanoparticle_window(self, menuitem):
SetupNanoparticle(self)
def graphene_window(self, menuitem):
SetupGraphene(self)
def nanotube_window(self, menuitem):
SetupNanotube(self)
def calculator_window(self, menuitem):
SetCalculator(self)
def energy_window(self, menuitem):
EnergyForces(self)
def energy_minimize_window(self, menuitem):
Minimize(self)
def scaling_window(self, menuitem):
HomogeneousDeformation(self)
def new_atoms(self, atoms, init_magmom=False):
"Set a new atoms object."
self.reset_tools_modes()
rpt = getattr(self.images, 'repeat', None)
self.images.repeat_images(np.ones(3, int))
self.images.initialize([atoms], init_magmom=init_magmom)
self.frame = 0 # Prevent crashes
self.images.repeat_images(rpt)
self.set_colors()
self.set_coordinates(frame=0, focus=True)
self.notify_vulnerable()
def prepare_new_atoms(self):
"Marks that the next call to append_atoms should clear the images."
self.images.prepare_new_atoms()
def append_atoms(self, atoms):
"Set a new atoms object."
# self.notify_vulnerable() # Do this manually after last frame.
frame = self.images.append_atoms(atoms)
self.set_coordinates(frame=frame - 1, focus=True)
def notify_vulnerable(self):
"""Notify windows that would break when new_atoms is called.
The notified windows may adapt to the new atoms. If that is not
possible, they should delete themselves.
"""
new_vul = [] # Keep weakrefs to objects that still exist.
for wref in self.vulnerable_windows:
ref = wref()
if ref is not None:
new_vul.append(wref)
ref.notify_atoms_changed()
self.vulnerable_windows = new_vul
def register_vulnerable(self, obj):
"""Register windows that are vulnerable to changing the images.
Some windows will break if the atoms (and in particular the
number of images) are changed. They can register themselves
and be closed when that happens.
"""
self.vulnerable_windows.append(weakref.ref(obj))
def exit(self, button, event=None):
for process in self.graphs:
process.terminate()
self.window.destroy()
gtk.main_quit()
return True
def xxx(self,
x=None,
message1=_('Not implemented!'),
message2=_('do you really need it?')):
oops(message1, message2)
def about(self, action):
try:
dialog = gtk.AboutDialog()
dialog.set_version(__version__)
dialog.set_website(
'https://wiki.fysik.dtu.dk/ase/ase/gui/gui.html')
except AttributeError:
self.xxx()
else:
dialog.run()
dialog.destroy()
def webpage(widget):
import webbrowser
webbrowser.open('https://wiki.fysik.dtu.dk/ase/ase/gui/gui.html')
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