# fmt: off
import pickle
import subprocess
import sys
from functools import partial
from time import time
import numpy as np
import ase.gui.ui as ui
from ase import Atoms, __version__
from ase.gui.defaults import read_defaults
from ase.gui.i18n import _
from ase.gui.images import Images
from ase.gui.nanoparticle import SetupNanoparticle
from ase.gui.nanotube import SetupNanotube
from ase.gui.observer import Observers
from ase.gui.save import save_dialog
from ase.gui.settings import Settings
from ase.gui.status import Status
from ase.gui.surfaceslab import SetupSurfaceSlab
from ase.gui.view import View
class GUIObservers:
def __init__(self):
self.new_atoms = Observers()
self.set_atoms = Observers()
self.change_atoms = Observers()
class GUI(View):
ARROWKEY_SCAN = 0
ARROWKEY_MOVE = 1
ARROWKEY_ROTATE = 2
def __init__(self, images=None,
rotations='',
show_bonds=False, expr=None):
if not isinstance(images, Images):
images = Images(images)
self.images = images
# Ordinary observers seem unused now, delete?
self.observers = []
self.obs = GUIObservers()
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)
super().__init__(rotations)
self.status = Status(self)
self.subprocesses = [] # list of external processes
self.movie_window = None
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)
@property
def moving(self):
return self.arrowkey_mode != self.ARROWKEY_SCAN
def run(self):
self.window.run()
def toggle_move_mode(self, key=None):
self.toggle_arrowkey_mode(self.ARROWKEY_MOVE)
def toggle_rotate_mode(self, key=None):
self.toggle_arrowkey_mode(self.ARROWKEY_ROTATE)
def toggle_arrowkey_mode(self, mode):
# If not currently in given mode, activate it.
# Else, deactivate it (go back to SCAN mode)
assert mode != self.ARROWKEY_SCAN
if self.arrowkey_mode == mode:
self.arrowkey_mode = self.ARROWKEY_SCAN
self.move_atoms_mask = None
else:
self.arrowkey_mode = mode
self.move_atoms_mask = self.images.selected.copy()
self.draw()
def step(self, key):
d = {'Home': -10000000,
'Page-Up': -1,
'Page-Down': 1,
'End': 10000000}[key]
i = max(0, min(len(self.images) - 1, self.frame + d))
self.set_frame(i)
if self.movie_window is not None:
self.movie_window.frame_number.value = i
def copy_image(self, key=None):
self.images._images.append(self.atoms.copy())
self.images.filenames.append(None)
if self.movie_window is not None:
self.movie_window.frame_number.scale.configure(to=len(self.images))
self.step('End')
def _do_zoom(self, x):
"""Utility method for zooming"""
self.scale *= x
self.draw()
def zoom(self, key):
"""Zoom in/out on keypress or clicking menu item"""
x = {'+': 1.2, '-': 1 / 1.2}[key]
self._do_zoom(x)
def scroll_event(self, event):
"""Zoom in/out when using mouse wheel"""
SHIFT = event.modifier == 'shift'
x = 1.0
if event.button == 4 or event.delta > 0:
x = 1.0 + (1 - SHIFT) * 0.2 + SHIFT * 0.01
elif event.button == 5 or event.delta < 0:
x = 1.0 / (1.0 + (1 - SHIFT) * 0.2 + SHIFT * 0.01)
self._do_zoom(x)
def settings(self):
return Settings(self)
def scroll(self, event):
shift = 0x1
ctrl = 0x4
alt_l = 0x8 # Also Mac Command Key
mac_option_key = 0x10
use_small_step = bool(event.state & shift)
rotate_into_plane = bool(event.state & (ctrl | alt_l | mac_option_key))
dxdydz = {'up': (0, 1 - rotate_into_plane, rotate_into_plane),
'down': (0, -1 + rotate_into_plane, -rotate_into_plane),
'right': (1, 0, 0),
'left': (-1, 0, 0)}.get(event.key, None)
# Get scroll direction using shift + right mouse button
# event.type == '6' is mouse motion, see:
# http://infohost.nmt.edu/tcc/help/pubs/tkinter/web/event-types.html
if event.type == '6':
cur_pos = np.array([event.x, -event.y])
# Continue scroll if button has not been released
if self.prev_pos is None or time() - self.last_scroll_time > .5:
self.prev_pos = cur_pos
self.last_scroll_time = time()
else:
dxdy = cur_pos - self.prev_pos
dxdydz = np.append(dxdy, [0])
self.prev_pos = cur_pos
self.last_scroll_time = time()
if dxdydz is None:
return
vec = 0.1 * np.dot(self.axes, dxdydz)
if use_small_step:
vec *= 0.1
if self.arrowkey_mode == self.ARROWKEY_MOVE:
self.atoms.positions[self.move_atoms_mask[:len(self.atoms)]] += vec
self.set_frame()
elif self.arrowkey_mode == self.ARROWKEY_ROTATE:
# For now we use atoms.rotate having the simplest interface.
# (Better to use something more minimalistic, obviously.)
mask = self.move_atoms_mask[:len(self.atoms)]
center = self.atoms.positions[mask].mean(axis=0)
tmp_atoms = self.atoms[mask]
tmp_atoms.positions -= center
tmp_atoms.rotate(50 * np.linalg.norm(vec), vec)
self.atoms.positions[mask] = tmp_atoms.positions + center
self.set_frame()
else:
# The displacement vector is scaled
# so that the cursor follows the structure
# Scale by a third works for some reason
scale = self.orig_scale / (3 * self.scale)
self.center -= vec * scale
# dx * 0.1 * self.axes[:, 0] - dy * 0.1 * self.axes[:, 1])
self.draw()
def delete_selected_atoms(self, widget=None, data=None):
import ase.gui.ui as ui
nselected = sum(self.images.selected)
if nselected and ui.ask_question(_('Delete atoms'),
_('Delete selected atoms?')):
self.really_delete_selected_atoms()
def really_delete_selected_atoms(self):
mask = self.images.selected[:len(self.atoms)]
del self.atoms[mask]
# Will remove selection in other images, too
self.images.selected[:] = False
self.set_frame()
self.draw()
def constraints_window(self):
from ase.gui.constraints import Constraints
return Constraints(self)
def set_selected_atoms(self, selected):
newmask = np.zeros(len(self.images.selected), bool)
newmask[selected] = True
if np.array_equal(newmask, self.images.selected):
return
# (By creating newmask, we can avoid resetting the selection in
# case the selected indices are invalid)
self.images.selected[:] = newmask
self.draw()
def select_all(self, key=None):
self.images.selected[:] = True
self.draw()
def invert_selection(self, key=None):
self.images.selected[:] = ~self.images.selected
self.draw()
def select_constrained_atoms(self, key=None):
self.images.selected[:] = ~self.images.get_dynamic(self.atoms)
self.draw()
def select_immobile_atoms(self, key=None):
if len(self.images) > 1:
R0 = self.images[0].positions
for atoms in self.images[1:]:
R = atoms.positions
self.images.selected[:] = ~(np.abs(R - R0) > 1.0e-10).any(1)
self.draw()
def movie(self):
from ase.gui.movie import Movie
self.movie_window = Movie(self)
def plot_graphs(self, key=None, expr=None, ignore_if_nan=False):
from ase.gui.graphs import Graphs
g = Graphs(self)
if expr is not None:
g.plot(expr=expr, ignore_if_nan=ignore_if_nan)
def pipe(self, task, data):
process = subprocess.Popen([sys.executable, '-m', 'ase.gui.pipe'],
stdout=subprocess.PIPE,
stdin=subprocess.PIPE)
pickle.dump((task, data), process.stdin)
process.stdin.close()
# Either process writes a line, or it crashes and line becomes ''
line = process.stdout.readline().decode('utf8').strip()
if line != 'GUI:OK':
if line == '': # Subprocess probably crashed
line = _('Failure in subprocess')
self.bad_plot(line)
else:
self.subprocesses.append(process)
return process
def bad_plot(self, err, msg=''):
ui.error(_('Plotting failed'), '\n'.join([str(err), msg]).strip())
def neb(self):
from ase.utils.forcecurve import fit_images
try:
forcefit = fit_images(self.images)
except Exception as err:
self.bad_plot(err, _('Images must have energies and forces, '
'and atoms must not be stationary.'))
else:
self.pipe('neb', forcefit)
def bulk_modulus(self):
try:
v = [abs(np.linalg.det(atoms.cell)) for atoms in self.images]
e = [self.images.get_energy(a) for a in self.images]
from ase.eos import EquationOfState
eos = EquationOfState(v, e)
plotdata = eos.getplotdata()
except Exception as err:
self.bad_plot(err, _('Images must have energies '
'and varying cell.'))
else:
self.pipe('eos', plotdata)
def reciprocal(self):
if self.atoms.cell.rank != 3:
self.bad_plot(_('Requires 3D cell.'))
return None
cell = self.atoms.cell.uncomplete(self.atoms.pbc)
bandpath = cell.bandpath(npoints=0)
return self.pipe('reciprocal', bandpath)
def open(self, button=None, filename=None):
chooser = ui.ASEFileChooser(self.window.win)
filename = filename or chooser.go()
format = chooser.format
if filename:
try:
self.images.read([filename], slice(None), format)
except Exception as err:
ui.show_io_error(filename, err)
return # Hmm. Is self.images in a consistent state?
self.set_frame(len(self.images) - 1, focus=True)
def modify_atoms(self, key=None):
from ase.gui.modify import ModifyAtoms
return ModifyAtoms(self)
def add_atoms(self, key=None):
from ase.gui.add import AddAtoms
return AddAtoms(self)
def cell_editor(self, key=None):
from ase.gui.celleditor import CellEditor
return CellEditor(self)
def atoms_editor(self, key=None):
from ase.gui.atomseditor import AtomsEditor
return AtomsEditor(self)
def quick_info_window(self, key=None):
from ase.gui.quickinfo import info
info_win = ui.Window(_('Quick Info'), wmtype='utility')
info_win.add(info(self))
# Update quickinfo window when we change frame
def update(window):
exists = window.exists
if exists:
# Only update if we exist
window.things[0].text = info(self)
return exists
self.attach(update, info_win)
return info_win
def surface_window(self):
return SetupSurfaceSlab(self)
def nanoparticle_window(self):
return SetupNanoparticle(self)
def nanotube_window(self):
return SetupNanotube(self)
def new_atoms(self, atoms):
"Set a new atoms object."
rpt = getattr(self.images, 'repeat', None)
self.images.repeat_images(np.ones(3, int))
self.images.initialize([atoms])
self.frame = 0 # Prevent crashes
self.images.repeat_images(rpt)
self.set_frame(frame=0, focus=True)
self.obs.new_atoms.notify()
def exit(self, event=None):
for process in self.subprocesses:
process.terminate()
self.window.close()
def new(self, key=None):
subprocess.Popen([sys.executable, '-m', 'ase', 'gui'])
def save(self, key=None):
return save_dialog(self)
def external_viewer(self, name):
from ase.visualize import view
return view(list(self.images), viewer=name)
def selected_atoms(self):
selection_mask = self.images.selected[:len(self.atoms)]
return self.atoms[selection_mask]
def wrap_atoms(self, key=None):
"""Wrap atoms around the unit cell."""
for atoms in self.images:
atoms.wrap()
self.set_frame()
@property
def clipboard(self):
from ase.gui.clipboard import AtomsClipboard
return AtomsClipboard(self.window.win)
def cut_atoms_to_clipboard(self, event=None):
self.copy_atoms_to_clipboard(event)
self.really_delete_selected_atoms()
def copy_atoms_to_clipboard(self, event=None):
atoms = self.selected_atoms()
self.clipboard.set_atoms(atoms)
def paste_atoms_from_clipboard(self, event=None):
try:
atoms = self.clipboard.get_atoms()
except Exception as err:
ui.error(
'Cannot paste atoms',
'Pasting currently works only with the ASE JSON format.\n\n'
f'Original error:\n\n{err}')
return
if self.atoms == Atoms():
self.atoms.cell = atoms.cell
self.atoms.pbc = atoms.pbc
self.paste_atoms_onto_existing(atoms)
def paste_atoms_onto_existing(self, atoms):
selection = self.selected_atoms()
if len(selection):
paste_center = selection.positions.sum(axis=0) / len(selection)
# atoms.center() is a no-op in directions without a cell vector.
# But we actually want the thing centered nevertheless!
# Therefore we have to set the cell.
atoms = atoms.copy()
atoms.cell = (1, 1, 1) # arrrgh.
atoms.center(about=paste_center)
self.add_atoms_and_select(atoms)
self.move_atoms_mask = self.images.selected.copy()
self.arrowkey_mode = self.ARROWKEY_MOVE
self.draw()
def add_atoms_and_select(self, new_atoms):
atoms = self.atoms
atoms += new_atoms
if len(atoms) > self.images.maxnatoms:
self.images.initialize(list(self.images),
self.images.filenames)
selected = self.images.selected
selected[:] = False
# 'selected' array may be longer than current atoms
selected[len(atoms) - len(new_atoms):len(atoms)] = True
self.set_frame()
self.draw()
def get_menu_data(self):
M = ui.MenuItem
return [
(_('_File'),
[M(_('_Open'), self.open, 'Ctrl+O'),
M(_('_New'), self.new, 'Ctrl+N'),
M(_('_Save'), self.save, 'Ctrl+S'),
M('---'),
M(_('_Quit'), self.exit, 'Ctrl+Q')]),
(_('_Edit'),
[M(_('Select _all'), self.select_all),
M(_('_Invert selection'), self.invert_selection),
M(_('Select _constrained atoms'), self.select_constrained_atoms),
M(_('Select _immobile atoms'), self.select_immobile_atoms),
# M('---'),
M(_('_Cut'), self.cut_atoms_to_clipboard, 'Ctrl+X'),
M(_('_Copy'), self.copy_atoms_to_clipboard, 'Ctrl+C'),
M(_('_Paste'), self.paste_atoms_from_clipboard, 'Ctrl+V'),
M('---'),
M(_('Hide selected atoms'), self.hide_selected),
M(_('Show selected atoms'), self.show_selected),
M('---'),
M(_('_Modify'), self.modify_atoms, 'Ctrl+Y'),
M(_('_Add atoms'), self.add_atoms, 'Ctrl+A'),
M(_('_Delete selected atoms'), self.delete_selected_atoms,
'Backspace'),
M(_('Edit _cell …'), self.cell_editor, 'Ctrl+E'),
M(_('Edit _atoms …'), self.atoms_editor, 'A'),
M('---'),
M(_('_First image'), self.step, 'Home'),
M(_('_Previous image'), self.step, 'Page-Up'),
M(_('_Next image'), self.step, 'Page-Down'),
M(_('_Last image'), self.step, 'End'),
M(_('Append image copy'), self.copy_image)]),
(_('_View'),
[M(_('Show _unit cell'), self.toggle_show_unit_cell, 'Ctrl+U',
value=self.config['show_unit_cell']),
M(_('Show _axes'), self.toggle_show_axes,
value=self.config['show_axes']),
M(_('Show _bonds'), self.toggle_show_bonds, 'Ctrl+B',
value=self.config['show_bonds']),
M(_('Show _velocities'), self.toggle_show_velocities, 'Ctrl+G',
value=False),
M(_('Show _forces'), self.toggle_show_forces, 'Ctrl+F',
value=False),
M(_('Show _magmoms'), self.toggle_show_magmoms,
value=False),
M(_('Show _Labels'), self.show_labels,
choices=[_('_None'),
_('Atom _Index'),
_('_Magnetic Moments'), # XXX check if exist
_('_Element Symbol'),
_('_Initial Charges'), # XXX check if exist
]),
M('---'),
M(_('Quick Info ...'), self.quick_info_window, 'Ctrl+I'),
M(_('Repeat ...'), self.repeat_window, 'R'),
M(_('Rotate ...'), self.rotate_window),
M(_('Colors ...'), self.colors_window, 'C'),
# TRANSLATORS: verb
M(_('Focus'), self.focus, 'F'),
M(_('Zoom in'), self.zoom, '+'),
M(_('Zoom out'), self.zoom, '-'),
M(_('Change View'),
submenu=[
M(_('Reset View'), self.reset_view, '='),
M(_('xy-plane'), self.set_view, 'Z'),
M(_('yz-plane'), self.set_view, 'X'),
M(_('zx-plane'), self.set_view, 'Y'),
M(_('yx-plane'), self.set_view, 'Shift+Z'),
M(_('zy-plane'), self.set_view, 'Shift+X'),
M(_('xz-plane'), self.set_view, 'Shift+Y'),
M(_('a2,a3-plane'), self.set_view, 'I'),
M(_('a3,a1-plane'), self.set_view, 'J'),
M(_('a1,a2-plane'), self.set_view, 'K'),
M(_('a3,a2-plane'), self.set_view, 'Shift+I'),
M(_('a1,a3-plane'), self.set_view, 'Shift+J'),
M(_('a2,a1-plane'), self.set_view, 'Shift+K')]),
M(_('Settings ...'), self.settings),
M('---'),
M(_('VMD'), partial(self.external_viewer, 'vmd')),
M(_('RasMol'), partial(self.external_viewer, 'rasmol')),
M(_('xmakemol'), partial(self.external_viewer, 'xmakemol')),
M(_('avogadro'), partial(self.external_viewer, 'avogadro'))]),
(_('_Tools'),
[M(_('Graphs ...'), self.plot_graphs),
M(_('Movie ...'), self.movie),
M(_('Constraints ...'), self.constraints_window),
M(_('Render scene ...'), self.render_window),
M(_('_Move selected atoms'), self.toggle_move_mode, 'Ctrl+M'),
M(_('_Rotate selected atoms'), self.toggle_rotate_mode,
'Ctrl+R'),
M(_('NE_B plot'), self.neb),
M(_('B_ulk Modulus'), self.bulk_modulus),
M(_('Reciprocal space ...'), self.reciprocal),
M(_('Wrap atoms'), self.wrap_atoms, 'Ctrl+W')]),
# TRANSLATORS: Set up (i.e. build) surfaces, nanoparticles, ...
(_('_Setup'),
[M(_('_Surface slab'), self.surface_window, disabled=False),
M(_('_Nanoparticle'),
self.nanoparticle_window),
M(_('Nano_tube'), self.nanotube_window)]),
# (_('_Calculate'),
# [M(_('Set _Calculator'), self.calculator_window, disabled=True),
# M(_('_Energy and Forces'), self.energy_window, disabled=True),
# M(_('Energy Minimization'), self.energy_minimize_window,
# disabled=True)]),
(_('_Help'),
[M(_('_About'), partial(ui.about, 'ASE-GUI',
version=__version__,
webpage='https://wiki.fysik.dtu.dk/'
'ase/ase/gui/gui.html')),
M(_('Webpage ...'), webpage)])]
def attach(self, function, *args, **kwargs):
self.observers.append((function, args, kwargs))
def call_observers(self):
# Use function return value to determine if we keep observer
self.observers = [(function, args, kwargs) for (function, args, kwargs)
in self.observers if function(*args, **kwargs)]
[docs]
def repeat_poll(self, callback, ms, ensure_update=True):
"""Invoke callback(gui=self) every ms milliseconds.
This is useful for polling a resource for updates to load them
into the GUI. The GUI display will be hence be updated after
each call; pass ensure_update=False to circumvent this.
Polling stops if the callback function raises StopIteration.
Example to run a movie manually, then quit::
from ase.collections import g2
from ase.gui.gui import GUI
names = iter(g2.names)
def main(gui):
try:
name = next(names)
except StopIteration:
gui.window.win.quit()
else:
atoms = g2[name]
gui.images.initialize([atoms])
gui = GUI()
gui.repeat_poll(main, 30)
gui.run()"""
def callbackwrapper():
try:
callback(gui=self)
except StopIteration:
pass
finally:
# Reinsert self so we get called again:
self.window.win.after(ms, callbackwrapper)
if ensure_update:
self.set_frame()
self.draw()
self.window.win.after(ms, callbackwrapper)
def webpage():
import webbrowser
webbrowser.open('https://wiki.fysik.dtu.dk/ase/ase/gui/gui.html')
