def __init__(self, queue, signal_queue, vbox, window, rotations="", show_unit_cell=True, show_bonds=False):
threading.Thread.__init__(self)
self.image_queue = queue
self.signal_queue = signal_queue
self.configured = False
self.ui = FakeUI.__init__(self)
self.images = Images()
self.images.initialize([ase.atoms.Atoms()])
self.killed = False
self.paused = False
self.vbox = vbox
self.window = window
self.vbox.connect("scroll-event", self.scroll_event)
self.window.connect("key-press-event", self.on_key_press)
View.__init__(self, self.vbox, rotations)
Status.__init__(self, self.vbox)
self.vbox.show()
if os.name == "posix":
self.live_plot = True
else:
self.live_plot = False
self.drawing_area.realize()
self.scale = 10.0
self.center = np.array([8, 8, 8])
self.set_colors()
self.set_coordinates(0)
self.center = np.array([0, 0, 0])
self.tofs = get_tof_names()
# history tracking arrays
self.times = []
self.tof_hist = []
self.occupation_hist = []
# prepare diagrams
self.data_plot = plt.figure()
# plt.xlabel('$t$ in s')
self.tof_diagram = self.data_plot.add_subplot(211)
self.tof_diagram.set_yscale("log")
# self.tof_diagram.get_yaxis().get_major_formatter().set_powerlimits(
# (3, 3))
self.tof_plots = []
for tof in self.tofs:
self.tof_plots.append(self.tof_diagram.plot([], [], label=tof)[0])
self.tof_diagram.legend(loc="lower left")
self.tof_diagram.set_ylabel("TOF in $\mathrm{s}^{-1}\mathrm{site}^{-1}$")
self.occupation_plots = []
self.occupation_diagram = self.data_plot.add_subplot(212)
for species in sorted(settings.representations):
self.occupation_plots.append(self.occupation_diagram.plot([], [], label=species)[0])
self.occupation_diagram.legend(loc=2)
self.occupation_diagram.set_xlabel("$t$ in s")
self.occupation_diagram.set_ylabel("Coverage")
def __init__(self, images=None, rotations='', show_bonds=False, expr=None):
if not isinstance(images, Images):
images = Images(images)
self.images = images
self.observers = []
self.config = read_defaults()
if show_bonds:
self.config['show_bonds'] = True
menu = self.get_menu_data()
self.window = ui.ASEGUIWindow(close=self.exit,
menu=menu,
config=self.config,
scroll=self.scroll,
scroll_event=self.scroll_event,
press=self.press,
move=self.move,
release=self.release,
resize=self.resize)
View.__init__(self, rotations)
Status.__init__(self)
self.subprocesses = [] # list of external processes
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.
self.arrowkey_mode = self.ARROWKEY_SCAN
self.move_atoms_mask = None
self.set_frame(len(self.images) - 1, focus=True)
# Used to move the structure with the mouse
self.prev_pos = None
self.last_scroll_time = time()
self.orig_scale = self.scale
if len(self.images) > 1:
self.movie()
if expr is None:
expr = self.config['gui_graphs_string']
if expr is not None and expr != '' and len(self.images) > 1:
self.plot_graphs(expr=expr, ignore_if_nan=True)
def __init__(self,
images=None,
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
if not images:
images = Images()
images.initialize([Atoms()])
self.images = images
self.config = read_defaults()
menu = self.get_menu_data(show_unit_cell, show_bonds)
self.window = ui.ASEGUIWindow(close=self.exit,
menu=menu,
config=self.config,
scroll=self.scroll,
scroll_event=self.scroll_event,
press=self.press,
move=self.move,
release=self.release,
resize=self.resize)
View.__init__(self, rotations)
Status.__init__(self)
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.
self.arrowkey_mode = self.ARROWKEY_SCAN
self.move_atoms_mask = None
def __init__(self, images=None,
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
if not images:
images = Images()
images.initialize([Atoms()])
self.images = images
self.config = read_defaults()
menu = self.get_menu_data(show_unit_cell, show_bonds)
self.window = ui.ASEGUIWindow(self.exit, menu, self.config,
self.scroll,
self.scroll_event,
self.press, self.move, self.release,
self.resize)
View.__init__(self, rotations)
Status.__init__(self)
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.
self.moving = False
self.move_atoms_mask = None
def __init__(self,
queue,
signal_queue,
vbox,
window,
rotations='',
show_unit_cell=True,
show_bonds=False):
threading.Thread.__init__(self)
self.image_queue = queue
self.signal_queue = signal_queue
self.configured = False
self.ui = FakeUI.__init__(self)
self.images = Images()
self.aseGui = GUI()
#self.aseGui.images.initialize([ase.atoms.Atoms()])
self.images.initialize([ase.atoms.Atoms()])
self.killed = False
self.paused = False
self.vbox = vbox
self.window = window
self.vbox.connect('scroll-event', self.scroll_event)
self.window.connect('key-press-event', self.on_key_press)
rotations = '0.0x,0.0y,0.0z' #[3,3,3]#np.zeros(3)
self.config = {
'force_vector_scale': None,
'velocity_vector_scale': None,
'swap_mouse': False
}
View.__init__(self, rotations)
Status.__init__(self)
self.vbox.show()
if os.name == 'posix':
self.live_plot = True
else:
self.live_plot = False
#self.drawing_area.realize()
self.scaleA = 3.0
self.center = np.array([8, 8, 8])
#self.set_colors()
#self.set_coordinates(0)
self.center = np.array([0, 0, 0])
self.tofs = get_tof_names()
# history tracking arrays
self.times = []
self.tof_hist = []
self.occupation_hist = []
# prepare diagrams
self.data_plot = plt.figure()
#plt.xlabel('$t$ in s')
self.tof_diagram = self.data_plot.add_subplot(211)
self.tof_diagram.set_yscale('log')
#self.tof_diagram.get_yaxis().get_major_formatter().set_powerlimits(
#(3, 3))
self.tof_plots = []
for tof in self.tofs:
self.tof_plots.append(self.tof_diagram.plot([], [], label=tof)[0])
self.tof_diagram.legend(loc='lower left')
self.tof_diagram.set_ylabel(
'TOF in $\mathrm{s}^{-1}\mathrm{site}^{-1}$')
self.occupation_plots = []
self.occupation_diagram = self.data_plot.add_subplot(212)
for species in sorted(settings.representations):
self.occupation_plots.append(
self.occupation_diagram.plot([], [], label=species)[0], )
self.occupation_diagram.legend(loc=2)
self.occupation_diagram.set_xlabel('$t$ in s')
self.occupation_diagram.set_ylabel('Coverage')
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 __init__(self, config, images=None, element_colors=None):
"""Initialise the GUI.
Parameters
----------
config: ViewConfig
initial configuration settings
images : ase.gui.images.Images
list of ase.Atoms, with some settings for visualisations (mainly radii)
element_colors: list[tuple]
hex colour for each atomic number (defaults to 'jmol' scheme)
"""
if not isinstance(images, Images):
images = Images(images)
self.images = images
self.observers = []
self.config = attr.asdict(config)
# aliases required by ui.ASEGUIWindow
self.config["gui_foreground_color"] = self.config["canvas_color_foreground"]
self.config["gui_background_color"] = self.config["canvas_color_background"]
self.config["swap_mouse"] = self.config["gui_swap_mouse"]
menu = self.get_menu_data()
self.window = ui.ASEGUIWindow(
close=self.exit,
menu=menu,
config=self.config,
scroll=self.scroll,
scroll_event=self.scroll_event,
press=self.press,
move=self.move,
release=self.release,
resize=self.resize,
)
# used by ``View.update_labels``
label_sites = {"index": 1, "magmom": 2, "element": 3, "charge": 4}.get(
self.config["atom_label_by"], 0
)
if not self.config["atom_show_label"]:
label_sites = 0
self.window["show-labels"] = label_sites
View.__init__(self, self.config["rotations"])
if element_colors:
self.colors = dict(enumerate(element_colors))
self.subprocesses = [] # list of external processes
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.
self.arrowkey_mode = self.ARROWKEY_SCAN
self.move_atoms_mask = None
self.set_frame(len(self.images) - 1, focus=True)
# Used to move the structure with the mouse
self.prev_pos = None
self.last_scroll_time = self.t0 = time()
self.orig_scale = self.scale
self.xy = None
if len(self.images) > 1:
self.movie()