def __init__(self, gui):
self.gui = gui
selected = self.selection()
if not selected.any():
ui.error(_('No atoms selected!'))
return
win = ui.Window(_('Modify'))
element = Element(callback=self.set_element)
win.add(element)
win.add(ui.Button(_('Change element'),
partial(self.set_element, element)))
self.tag = ui.SpinBox(0, -1000, 1000, 1, self.set_tag)
win.add([_('Tag'), self.tag])
self.magmom = ui.SpinBox(0.0, -10, 10, 0.1, self.set_magmom)
win.add([_('Moment'), self.magmom])
atoms = self.gui.atoms
Z = atoms.numbers
if Z.ptp() == 0:
element.Z = Z[0]
tags = atoms.get_tags()[selected]
if tags.ptp() == 0:
self.tag.value = tags[0]
magmoms = get_magmoms(atoms)[selected]
if magmoms.round(2).ptp() == 0.0:
self.magmom.value = round(magmoms[0], 2)
def __init__(self, gui):
self.gui = gui
selected = self.selection()
if not selected.any():
ui.error(_('No atoms selected!'))
return
win = ui.Window(_('Modify'))
element = Element(callback=self.set_element)
win.add(element)
win.add(
ui.Button(_('Change element'), partial(self.set_element, element)))
self.tag = ui.SpinBox(0, -1000, 1000, 1, self.set_tag)
win.add([_('Tag'), self.tag])
self.magmom = ui.SpinBox(0.0, -10, 10, 0.1, self.set_magmom)
win.add([_('Moment'), self.magmom])
atoms = self.gui.atoms
Z = atoms.numbers
if Z.ptp() == 0:
element.Z = Z[0]
tags = atoms.get_tags()[selected]
if tags.ptp() == 0:
self.tag.value = tags[0]
magmoms = get_magmoms(atoms)[selected]
if magmoms.round(2).ptp() == 0.0:
self.magmom.value = round(magmoms[0], 2)
def set_structure_data(self, *args):
'Called when the user presses [Get structure].'
if not self.element.check():
return
z = self.element.Z
ref = ase.data.reference_states[z]
if ref is None:
structure = None
else:
structure = ref['symmetry']
if ref is None or structure not in [s[0]
for s in self.structure_data]:
ui.error(_('Unsupported or unknown structure'),
_('Element = {0}, structure = {1}')
.format(self.element.symbol, structure))
return
self.structure.value = structure
a = ref['a']
self.a.value = a
self.fourindex = self.needs_4index[structure]
if self.fourindex:
try:
c = ref['c']
except KeyError:
c = ref['c/a'] * a
self.c.value = c
def txt2pos(txt):
try:
x, y, z = (float(x) for x in txt.split(','))
except ValueError as ex:
ui.error(_('Bad position'), ex)
else:
return x, y, z
def set_structure_data(self, *args):
'Called when the user presses [Get structure].'
z = self.element.Z
if z is None:
return
ref = ase.data.reference_states[z]
if ref is None:
structure = None
else:
structure = ref['symmetry']
if ref is None or structure not in [s[0] for s in self.structure_data]:
ui.error(
_('Unsupported or unknown structure'),
_('Element = {0}, structure = {1}').format(
self.element.symbol, structure))
return
self.structure.value = structure
a = ref['a']
self.a.value = a
self.fourindex = self.needs_4index[structure]
if self.fourindex:
try:
c = ref['c']
except KeyError:
c = ref['c/a'] * a
self.c.value = c
def pywindow(title, callback):
code = callback()
if code is None:
ui.error(
_('No Python code'),
_('You have not (yet) specified a consistent set of parameters.'))
else:
win = ui.Window(title)
win.add(ui.Text(code))
def pywindow(title, callback):
code = callback()
if code is None:
ui.error(
_('No Python code'),
_('You have not (yet) specified a consistent set of parameters.'))
else:
win = ui.Window(title)
win.add(ui.Text(code))
def add_relative(self):
rpos = txt2pos(self.relative_position.value)
pos = self.gui.atoms.positions
if self.gui.images.selected.any():
pos = pos[self.gui.images.selected[:len(pos)]]
if len(pos) == 0:
ui.error('No atoms present')
else:
center = pos.mean(0)
self.add(center + rpos)
def apply(self):
self.makeatoms()
if self.atoms is not None:
self.gui.new_atoms(self.atoms)
return True
else:
ui.error(_('No valid atoms.'),
_('You have not (yet) specified a consistent set of '
'parameters.'))
return False
def apply(self, callbackarg=None):
self.makeatoms()
if self.atoms is not None:
self.gui.new_atoms(self.atoms)
return True
else:
ui.error(
_('No valid atoms.'),
_('You have not (yet) specified a consistent set of '
'parameters.'))
return False
def apply(self):
self.make()
if self.atoms is not None:
self.gui.new_atoms(self.atoms)
return True
else:
ui.error(
_('No valid atoms.'),
_('You have not (yet) specified a consistent '
'set of parameters.'))
return False
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 plot(self, type=None, expr=None, ignore_if_nan=False):
if expr is None:
expr = self.expr.value
else:
self.expr.value = expr
try:
data = self.gui.images.graph(expr)
except Exception as ex:
ui.error(ex)
return
if ignore_if_nan and len(data) == 2 and np.isnan(data[1]).all():
return
pickledata = (data, self.gui.frame, expr, type)
self.gui.pipe('graph', pickledata)
def plot(self, type=None, expr=None):
if expr is None:
expr = self.expr.value
else:
self.expr.value = expr
try:
data = self.gui.images.graph(expr)
except (SyntaxError, NameError) as ex:
ui.error(ex)
return
process = subprocess.Popen([sys.executable, '-m', 'ase.gui.graphs'],
stdin=subprocess.PIPE)
pickle.dump((data, self.gui.frame, expr, type), process.stdin,
protocol=0)
process.stdin.close()
self.gui.graphs.append(process)
def plot(self, type=None, expr=None):
if expr is None:
expr = self.expr.value
else:
self.expr.value = expr
try:
data = self.gui.images.graph(expr)
except (SyntaxError, NameError) as ex:
ui.error(ex)
return
process = subprocess.Popen([sys.executable, '-m', 'ase.gui.graphs'],
stdin=subprocess.PIPE)
pickledata = (data, self.gui.frame, expr, type)
pickle.dump(pickledata, process.stdin, protocol=0)
process.stdin.close()
self.gui.graphs.append(process)
def row_add(self, widget=None):
'Add a row to the list of directions.'
if self.fourindex:
n = 4
else:
n = 3
idx = tuple(a.value for a in self.new_direction[1:1 + 2 * n:2])
if not any(idx):
ui.error(_('At least one index must be non-zero'), '')
return
if n == 4 and sum(idx) != 0:
ui.error(_('Invalid hexagonal indices',
'The sum of the first three numbers must be zero'))
return
new = [idx, 5, 1.0]
if self.method.value == 'wulff':
new[1] = self.new_direction[-2].value
else:
new[2] = self.new_direction[-2].value
self.direction_table.append(new)
self.add_direction(*new)
self.update()
def row_add(self, widget=None):
'Add a row to the list of directions.'
if self.fourindex:
n = 4
else:
n = 3
idx = tuple(a.value for a in self.new_direction[1:1 + 2 * n:2])
if not any(idx):
ui.error(_('At least one index must be non-zero'), '')
return
if n == 4 and sum(idx) != 0:
ui.error(
_('Invalid hexagonal indices',
'The sum of the first three numbers must be zero'))
return
new = [idx, 5, 1.0]
if self.method.value == 'wulff':
new[1] = self.new_direction[-2].value
else:
new[2] = self.new_direction[-2].value
self.direction_table.append(new)
self.add_direction(*new)
self.update()
def bad_plot(self, err, msg=''):
ui.error(_('Plotting failed'), '\n'.join([str(err), msg]).strip())
