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import os
import numpy as np
import ase.gui.ui as ui
from ase import Atoms
from ase.data import atomic_numbers, chemical_symbols
from ase.gui.i18n import _
current_selection_string = _('(selection)')
class AddAtoms:
def __init__(self, gui):
self.gui = gui
win = self.win = ui.Window(_('Add atoms'), wmtype='utility')
win.add(_('Specify chemical symbol, formula, or filename.'))
def choose_file():
chooser = ui.ASEFileChooser(self.win.win)
filename = chooser.go()
if filename is None: # No file selected
return
self.combobox.value = filename
# Load the file immediately, so we can warn now in case of error
self.readfile(filename, format=chooser.format)
if self.gui.images.selected.any():
default = current_selection_string
else:
default = 'H2'
self._filename = None
self._atoms_from_file = None
from ase.collections import g2
labels = sorted(name for name in g2.names
if len(g2[name]) > 1)
values = labels
combobox = ui.ComboBox(labels, values)
win.add([_('Add:'), combobox,
ui.Button(_('File ...'), callback=choose_file)])
combobox.widget.bind('<Return>', lambda e: self.add())
combobox.value = default
self.combobox = combobox
spinners = [ui.SpinBox(0.0, -1e3, 1e3, 0.1, rounding=2, width=3)
for __ in range(3)]
win.add([_('Coordinates:')] + spinners)
self.spinners = spinners
win.add(_('Coordinates are relative to the center of the selection, '
'if any, else absolute.'))
self.picky = ui.CheckButton(_('Check positions'), True)
win.add([ui.Button(_('Add'), self.add),
self.picky])
self.focus()
def readfile(self, filename, format=None):
if filename == self._filename:
# We have this file already
return self._atoms_from_file
from ase.io import read
try:
atoms = read(filename)
except Exception as err:
ui.show_io_error(filename, err)
atoms = None
filename = None
# Cache selected Atoms/filename (or None) for future calls
self._atoms_from_file = atoms
self._filename = filename
return atoms
def get_atoms(self):
# Get the text, whether it's a combobox item or not
val = self.combobox.widget.get()
if val == current_selection_string:
selection = self.gui.images.selected.copy()
if selection.any():
atoms = self.gui.atoms.copy()
return atoms[selection[:len(self.gui.atoms)]]
if val in atomic_numbers: # Note: This means val is a symbol!
return Atoms(val)
if val.isdigit() and int(val) < len(chemical_symbols):
return Atoms(numbers=[int(val)])
from ase.collections import g2
if val in g2.names:
return g2[val]
if os.path.exists(val):
return self.readfile(val) # May show UI error
ui.showerror(_('Cannot add atoms'),
_('{} is neither atom, molecule, nor file')
.format(val))
return None
def getcoords(self):
addcoords = np.array([spinner.value for spinner in self.spinners])
pos = self.gui.atoms.positions
if self.gui.images.selected[:len(pos)].any():
pos = pos[self.gui.images.selected[:len(pos)]]
center = pos.mean(0)
addcoords += center
return addcoords
def focus(self):
self.combobox.widget.focus_set()
def add(self):
newatoms = self.get_atoms()
if newatoms is None: # Error dialog was shown
return
newcenter = self.getcoords()
# Not newatoms.center() because we want the same centering method
# used for adding atoms relative to selections (mean).
previous_center = newatoms.positions.mean(0)
newatoms.positions += newcenter - previous_center
atoms = self.gui.atoms
if len(atoms) and self.picky.value:
from ase.geometry import get_distances
_disps, dists = get_distances(atoms.positions,
newatoms.positions)
mindist = dists.min()
if mindist < 0.5:
ui.showerror(_('Bad positions'),
_('Atom would be less than 0.5 Å from '
'an existing atom. To override, '
'uncheck the check positions option.'))
return
self.gui.add_atoms_and_select(newatoms)
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