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'''celleditor.py - Window for editing the cell of an atoms object
'''
import numpy as np
import ase.gui.ui as ui
from ase.cell import Cell
from ase.gui.i18n import _
class CellEditor:
'''Window for editing the cell of an atoms object.'''
def __init__(self, gui):
self.gui = gui
self.gui.register_vulnerable(self)
# Create grid control for cells
# xx xy xz ||x|| pbc
# yx yy yz ||y|| pbc
# zx zy zz ||z|| pbc
self.cell_grid = []
self.pbc = []
self.angles = []
atoms = self.gui.atoms
cell = atoms.cell
mags = cell.lengths()
angles = cell.angles()
pbc = atoms.pbc
for i in [0, 1, 2]: # x_ y_ z_
row = []
for j in [0, 1, 2]: # _x _y _z
row.append(ui.SpinBox(cell[i][j], -30, 30, 0.1,
self.apply_vectors, rounding=7, width=9))
row.append(ui.SpinBox(mags[i], -30, 30, 0.1, self.apply_magnitudes,
rounding=7, width=9))
self.cell_grid.append(row)
self.pbc.append(ui.CheckButton('', bool(pbc[i]), self.apply_pbc))
self.angles.append(ui.SpinBox(angles[i], -360, 360, 15,
self.apply_angles,
rounding=7, width=9))
self.scale_atoms = ui.CheckButton('', False)
self.vacuum = ui.SpinBox(5, 0, 15, 0.1, self.apply_vacuum)
# TRANSLATORS: This is a title of a window.
win = self.win = ui.Window(_('Cell Editor'), wmtype='utility')
x, y, z = self.cell_grid
win.add([_('A:'), x[0], x[1], x[2], _('||A||:'), x[3],
_('periodic:'), self.pbc[0]])
win.add([_('B:'), y[0], y[1], y[2], _('||B||:'), y[3],
_('periodic:'), self.pbc[1]])
win.add([_('C:'), z[0], z[1], z[2], _('||C||:'), z[3],
_('periodic:'), self.pbc[2]])
win.add([_('∠BC:'), self.angles[0], _('∠AC:'), self.angles[1],
_('∠AB:'), self.angles[2]])
win.add([_('Scale atoms with cell:'), self.scale_atoms])
win.add([ui.Button(_('Apply Vectors'), self.apply_vectors),
ui.Button(_('Apply Magnitudes'), self.apply_magnitudes),
ui.Button(_('Apply Angles'), self.apply_angles)])
win.add([_('Pressing 〈Enter〉 as you enter values will '
'automatically apply correctly')])
# TRANSLATORS: verb
win.add([ui.Button(_('Center'), self.apply_center),
ui.Button(_('Wrap'), self.apply_wrap),
_('Vacuum:'), self.vacuum,
ui.Button(_('Apply Vacuum'), self.apply_vacuum)])
def apply_center(self, *args):
atoms = self.gui.atoms.copy()
atoms.center()
self.gui.new_atoms(atoms)
def apply_wrap(self, *args):
atoms = self.gui.atoms.copy()
atoms.wrap()
self.gui.new_atoms(atoms)
def apply_vacuum(self, *args):
atoms = self.gui.atoms.copy()
axis = []
for index, pbc in enumerate(atoms.pbc):
if not pbc:
axis.append(index)
atoms.center(vacuum=self.vacuum.value, axis=axis)
self.gui.new_atoms(atoms)
def apply_vectors(self, *args):
atoms = self.gui.atoms.copy()
atoms.set_cell(self.get_vectors(),
scale_atoms=self.scale_atoms.var.get())
self.gui.new_atoms(atoms)
def get_vectors(self):
x, y, z = self.cell_grid
cell = np.array(
[[x[0].value, x[1].value, x[2].value],
[y[0].value, y[1].value, y[2].value],
[z[0].value, z[1].value, z[2].value]]
)
return Cell(cell)
def get_magnitudes(self):
x, y, z = self.cell_grid
return np.array([x[3].value, y[3].value, z[3].value])
def apply_magnitudes(self, *args):
atoms = self.gui.atoms.copy()
old_mags = atoms.cell.lengths()
new_mags = self.get_magnitudes()
newcell = atoms.cell.copy()
for i in range(3):
newcell[i] *= new_mags[i] / old_mags[i]
atoms.set_cell(newcell,
scale_atoms=self.scale_atoms.var.get())
self.gui.new_atoms(atoms)
def apply_angles(self, *args):
atoms = self.gui.atoms.copy()
cell_data = atoms.cell.cellpar()
cell_data[3:7] = [self.angles[0].value, self.angles[1].value,
self.angles[2].value]
atoms.set_cell(cell_data, scale_atoms=self.scale_atoms.var.get())
self.gui.new_atoms(atoms)
def apply_pbc(self, *args):
atoms = self.gui.atoms.copy()
pbc = [pbc.var.get() for pbc in self.pbc]
atoms.set_pbc(pbc)
self.gui.new_atoms(atoms)
def notify_atoms_changed(self):
atoms = self.gui.atoms
self.update(atoms.cell, atoms.pbc)
def update(self, cell, pbc):
cell = Cell(cell)
mags = cell.lengths()
angles = cell.angles()
for i in range(3):
for j in range(3):
if np.isnan(cell[i][j]):
cell[i][j] = 0
self.cell_grid[i][j].value = cell[i][j]
if np.isnan(mags[i]):
mags[i] = 0
self.cell_grid[i][3].value = mags[i]
if np.isnan(angles[i]):
angles[i] = 0
self.angles[i].value = angles[i]
self.pbc[i].var.set(bool(pbc[i]))
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