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 __init__(self, gui):
self.element = Element('', self.apply)
self.structure = ui.ComboBox(structures, structures,
self.structure_changed)
self.structure_warn = ui.Label('', 'red')
self.orthogonal = ui.CheckButton('', True, self.make)
self.lattice_a = ui.SpinBox(3.2, 0.0, 10.0, 0.001, self.make)
self.retrieve = ui.Button(_('Get from database'),
self.structure_changed)
self.lattice_c = ui.SpinBox(None, 0.0, 10.0, 0.001, self.make)
self.x = ui.SpinBox(1, 1, 30, 1, self.make)
self.x_warn = ui.Label('', 'red')
self.y = ui.SpinBox(1, 1, 30, 1, self.make)
self.y_warn = ui.Label('', 'red')
self.z = ui.SpinBox(1, 1, 30, 1, self.make)
self.vacuum_check = ui.CheckButton('', False, self.vacuum_checked)
self.vacuum = ui.SpinBox(5, 0, 40, 0.01, self.make)
self.description = ui.Label('')
win = self.win = ui.Window(_('Surface'))
win.add(ui.Text(introtext))
win.add(self.element)
win.add([_('Structure:'), self.structure, self.structure_warn])
win.add([_('Orthogonal cell:'), self.orthogonal])
win.add([_('Lattice constant:')])
win.add([_('\ta'), self.lattice_a, (u'Å'), self.retrieve])
win.add([_('\tc'), self.lattice_c, (u'Å')])
win.add([_('Size:')])
win.add([_('\tx: '), self.x, _(' unit cells'), self.x_warn])
win.add([_('\ty: '), self.y, _(' unit cells'), self.y_warn])
win.add([_('\tz: '), self.z, _(' unit cells')])
win.add([_('Vacuum: '), self.vacuum_check, self.vacuum, (u'Å')])
win.add(self.description)
# TRANSLATORS: This is a title of a window.
win.add([
pybutton(_('Creating a surface.'), self.make),
ui.Button(_('Apply'), self.apply),
ui.Button(_('OK'), self.ok)
])
self.element.grab_focus()
self.gui = gui
self.atoms = None
self.lattice_c.active = False
self.vacuum.active = False
self.structure_changed()
def __init__(self, gui):
# XXXXXXXXXXX still array based, not Atoms-based. Will crash
win = ui.Window(_('Add atoms'))
self.element = Element()
win.add(self.element)
self.absolute_position = ui.Entry('0,0,0')
self.relative_position = ui.Entry('1.5,0,0')
win.add([_('Absolute position:'),
self.absolute_position,
ui.Button(_('Add'), self.add_absolute)])
win.add([_('Relative to average position (of selection):'),
self.relative_position,
ui.Button(_('Add'), self.add_relative)])
self.gui = gui
def __init__(self, gui):
self.element = Element('C', self.make)
self.bondlength = ui.SpinBox(1.42, 0.0, 10.0, 0.01, self.make)
self.n = ui.SpinBox(5, 1, 100, 1, self.make)
self.m = ui.SpinBox(5, 0, 100, 1, self.make)
self.length = ui.SpinBox(1, 1, 100, 1, self.make)
self.description = ui.Label('')
win = self.win = ui.Window(_('Nanotube'))
win.add(ui.Text(introtext))
win.add(self.element)
win.add([_('Bond length: '), self.bondlength, _(u'Å')])
win.add(_('Select roll-up vector (n,m) and tube length:'))
win.add(['n:', self.n, 'm:', self.m, _('Length:'), self.length])
win.add(self.description)
win.add([
pybutton(_('Creating a nanoparticle.'), self.make),
ui.Button(_('Apply'), self.apply),
ui.Button(_('OK'), self.ok)
])
self.gui = gui
self.atoms = None
class SetupNanoparticle:
"Window for setting up a nanoparticle."
# Structures: Abbreviation, name,
# 4-index (boolean), two lattice const (bool), factory
structure_data = (('fcc', _('Face centered cubic (fcc)'), False, False,
FaceCenteredCubic),
('bcc', _('Body centered cubic (bcc)'), False, False,
BodyCenteredCubic), ('sc', _('Simple cubic (sc)'),
False, False, SimpleCubic),
('hcp', _('Hexagonal closed-packed (hcp)'), True, True,
HexagonalClosedPacked), ('graphite', _('Graphite'),
True, True, Graphite))
# NB: HCP is broken!
# A list of import statements for the Python window.
import_names = {
'fcc': 'from ase.cluster.cubic import FaceCenteredCubic',
'bcc': 'from ase.cluster.cubic import BodyCenteredCubic',
'sc': 'from ase.cluster.cubic import SimpleCubic',
'hcp': 'from ase.cluster.hexagonal import HexagonalClosedPacked',
'graphite': 'from ase.cluster.hexagonal import Graphite'
}
# Default layer specifications for the different structures.
default_layers = {
'fcc': [((1, 0, 0), 6), ((1, 1, 0), 9), ((1, 1, 1), 5)],
'bcc': [((1, 0, 0), 6), ((1, 1, 0), 9), ((1, 1, 1), 5)],
'sc': [((1, 0, 0), 6), ((1, 1, 0), 9), ((1, 1, 1), 5)],
'hcp': [((0, 0, 0, 1), 5), ((1, 0, -1, 0), 5)],
'graphite': [((0, 0, 0, 1), 5), ((1, 0, -1, 0), 5)]
}
def __init__(self, gui):
self.atoms = None
self.no_update = True
self.old_structure = 'undefined'
win = self.win = ui.Window(_('Nanoparticle'))
win.add(ui.Text(introtext))
self.element = Element('', self.apply)
lattice_button = ui.Button(_('Get structure'), self.set_structure_data)
self.elementinfo = ui.Label(' ')
win.add(self.element)
win.add(self.elementinfo)
win.add(lattice_button)
# The structure and lattice constant
labels = []
values = []
self.needs_4index = {}
self.needs_2lat = {}
self.factory = {}
for abbrev, name, n4, c, factory in self.structure_data:
labels.append(name)
values.append(abbrev)
self.needs_4index[abbrev] = n4
self.needs_2lat[abbrev] = c
self.factory[abbrev] = factory
self.structure = ui.ComboBox(labels, values, self.update_structure)
win.add([_('Structure:'), self.structure])
self.fourindex = self.needs_4index[values[0]]
self.a = ui.SpinBox(3.0, 0.0, 1000.0, 0.01, self.update)
self.c = ui.SpinBox(3.0, 0.0, 1000.0, 0.01, self.update)
win.add([_('Lattice constant: a ='), self.a, ' c =', self.c])
# Choose specification method
self.method = ui.ComboBox(
[_('Layer specification'),
_('Wulff construction')], ['layers', 'wulff'],
self.update_gui_method)
win.add([_('Method: '), self.method])
self.layerlabel = ui.Label('Missing text') # Filled in later
win.add(self.layerlabel)
self.direction_table_rows = ui.Rows()
win.add(self.direction_table_rows)
self.default_direction_table()
win.add(_('Add new direction:'))
self.new_direction_and_size_rows = ui.Rows()
win.add(self.new_direction_and_size_rows)
self.update_new_direction_and_size_stuff()
# Information
win.add(_('Information about the created cluster:'))
self.info = [
_('Number of atoms: '),
ui.Label('-'),
_(' Approx. diameter: '),
ui.Label('-')
]
win.add(self.info)
# Finalize setup
self.update_structure('fcc')
self.update_gui_method()
self.no_update = False
self.auto = ui.CheckButton(_('Automatic Apply'))
win.add(self.auto)
win.add([
pybutton(_('Creating a nanoparticle.'), self.makeatoms),
ui.helpbutton(helptext),
ui.Button(_('Apply'), self.apply),
ui.Button(_('OK'), self.ok)
])
self.gui = gui
self.smaller_button = None
self.largeer_button = None
self.element.grab_focus()
def default_direction_table(self):
'Set default directions and values for the current crystal structure.'
self.direction_table = []
struct = self.structure.value
for direction, layers in self.default_layers[struct]:
self.direction_table.append((direction, layers, 1.0))
def update_direction_table(self):
self.direction_table_rows.clear()
for direction, layers, energy in self.direction_table:
self.add_direction(direction, layers, energy)
self.update()
def add_direction(self, direction, layers, energy):
i = len(self.direction_table_rows)
if self.method.value == 'wulff':
spin = ui.SpinBox(energy, 0.0, 1000.0, 0.1, self.update)
else:
spin = ui.SpinBox(layers, 1, 100, 1, self.update)
up = ui.Button(_('Up'), self.row_swap_next, i - 1)
down = ui.Button(_('Down'), self.row_swap_next, i)
delete = ui.Button(_('Delete'), self.row_delete, i)
self.direction_table_rows.add(
[str(direction) + ':', spin, up, down, delete])
up.active = i > 0
down.active = False
delete.active = i > 0
if i > 0:
down, delete = self.direction_table_rows[-2][3:]
down.active = True
delete.active = True
def update_new_direction_and_size_stuff(self):
if self.needs_4index[self.structure.value]:
n = 4
else:
n = 3
rows = self.new_direction_and_size_rows
rows.clear()
self.new_direction = row = ['(']
for i in range(n):
if i > 0:
row.append(',')
row.append(ui.SpinBox(0, -100, 100, 1))
row.append('):')
if self.method.value == 'wulff':
row.append(ui.SpinBox(1.0, 0.0, 1000.0, 0.1))
else:
row.append(ui.SpinBox(5, 1, 100, 1))
row.append(ui.Button(_('Add'), self.row_add))
rows.add(row)
if self.method.value == 'wulff':
# Extra widgets for the Wulff construction
self.size_radio = ui.RadioButtons(
[_('Number of atoms'), _('Diameter')], ['natoms', 'diameter'],
self.update_gui_size)
self.size_natoms = ui.SpinBox(100, 1, 100000, 1,
self.update_size_natoms)
self.size_diameter = ui.SpinBox(5.0, 0, 100.0, 0.1,
self.update_size_diameter)
self.round_radio = ui.RadioButtons(
[_('above '), _('below '),
_('closest ')], ['above', 'below', 'closest'],
callback=self.update)
self.smaller_button = ui.Button(_('Smaller'), self.wulff_smaller)
self.larger_button = ui.Button(_('Larger'), self.wulff_larger)
rows.add(_('Choose size using:'))
rows.add(self.size_radio)
rows.add(
[_('atoms'), self.size_natoms,
_(u'ų'), self.size_diameter])
rows.add(
_('Rounding: If exact size is not possible, choose the size:'))
rows.add(self.round_radio)
rows.add([self.smaller_button, self.larger_button])
self.update_gui_size()
else:
self.smaller_button = None
self.larger_button = None
def update_structure(self, s):
'Called when the user changes the structure.'
# s = self.structure.value
if s != self.old_structure:
old4 = self.fourindex
self.fourindex = self.needs_4index[s]
if self.fourindex != old4:
# The table of directions is invalid.
self.default_direction_table()
self.old_structure = s
self.c.active = self.needs_2lat[s]
self.update()
def update_gui_method(self, *args):
'Switch between layer specification and Wulff construction.'
self.update_direction_table()
self.update_new_direction_and_size_stuff()
if self.method.value == 'wulff':
self.layerlabel.text = _(
'Surface energies (as energy/area, NOT per atom):')
else:
self.layerlabel.text = _('Number of layers:')
self.update()
def wulff_smaller(self, widget=None):
'Make a smaller Wulff construction.'
n = len(self.atoms)
self.size_radio.value = 'natoms'
self.size_natoms.value = n - 1
self.round_radio.value = 'below'
self.apply()
def wulff_larger(self, widget=None):
'Make a larger Wulff construction.'
n = len(self.atoms)
self.size_radio.value = 'natoms'
self.size_natoms.value = n + 1
self.round_radio.value = 'above'
self.apply()
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_delete(self, row):
del self.direction_table[row]
self.update_direction_table()
def row_swap_next(self, row):
dt = self.direction_table
dt[row], dt[row + 1] = dt[row + 1], dt[row]
self.update_direction_table()
def update_gui_size(self, widget=None):
'Update gui when the cluster size specification changes.'
self.size_natoms.active = self.size_radio.value == 'natoms'
self.size_diameter.active = self.size_radio.value == 'diameter'
def update_size_natoms(self, widget=None):
at_vol = self.get_atomic_volume()
dia = 2.0 * (3 * self.size_natoms.value * at_vol /
(4 * np.pi))**(1 / 3)
self.size_diameter.value = dia
self.update()
def update_size_diameter(self, widget=None, update=True):
if self.size_diameter.active:
at_vol = self.get_atomic_volume()
n = round(np.pi / 6 * self.size_diameter.value**3 / at_vol)
self.size_natoms.value = int(n)
if update:
self.update()
def update(self, *args):
if self.no_update:
return
self.element.Z # Check
if self.auto.value:
self.makeatoms()
if self.atoms is not None:
self.gui.new_atoms(self.atoms)
else:
self.clearatoms()
self.makeinfo()
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 makeatoms(self, *args):
'Make the atoms according to the current specification.'
symbol = self.element.symbol
if symbol is None:
self.clearatoms()
self.makeinfo()
return False
struct = self.structure.value
if self.needs_2lat[struct]:
# a and c lattice constants
lc = {'a': self.a.value, 'c': self.c.value}
lc_str = str(lc)
else:
lc = self.a.value
lc_str = '%.5f' % (lc, )
if self.method.value == 'wulff':
# Wulff construction
surfaces = [x[0] for x in self.direction_table]
surfaceenergies = [
x[1].value for x in self.direction_table_rows.rows
]
self.update_size_diameter(update=False)
rounding = self.round_radio.value
self.atoms = wulff_construction(symbol, surfaces, surfaceenergies,
self.size_natoms.value,
self.factory[struct], rounding, lc)
python = py_template_wulff % {
'element': symbol,
'surfaces': str(surfaces),
'energies': str(surfaceenergies),
'latconst': lc_str,
'natoms': self.size_natoms.value,
'structure': struct,
'rounding': rounding
}
else:
# Layer-by-layer specification
surfaces = [x[0] for x in self.direction_table]
layers = [x[1].value for x in self.direction_table_rows.rows]
self.atoms = self.factory[struct](symbol,
copy(surfaces),
layers,
latticeconstant=lc)
imp = self.import_names[struct]
python = py_template_layers % {
'import': imp,
'element': symbol,
'surfaces': str(surfaces),
'layers': str(layers),
'latconst': lc_str,
'factory': imp.split()[-1]
}
self.makeinfo()
return python
def clearatoms(self):
self.atoms = None
def get_atomic_volume(self):
s = self.structure.value
a = self.a.value
c = self.c.value
if s == 'fcc':
return a**3 / 4
elif s == 'bcc':
return a**3 / 2
elif s == 'sc':
return a**3
elif s == 'hcp':
return np.sqrt(3.0) / 2 * a * a * c / 2
elif s == 'graphite':
return np.sqrt(3.0) / 2 * a * a * c / 4
def makeinfo(self):
"""Fill in information field about the atoms.
Also turns the Wulff construction buttons [Larger] and
[Smaller] on and off.
"""
if self.atoms is None:
self.info[1].text = '-'
self.info[3].text = '-'
else:
at_vol = self.get_atomic_volume()
dia = 2 * (3 * len(self.atoms) * at_vol / (4 * np.pi))**(1 / 3)
self.info[1].text = str(len(self.atoms))
self.info[3].text = u'{0:.1f} Å'.format(dia)
if self.method.value == 'wulff':
if self.smaller_button is not None:
self.smaller_button.active = self.atoms is not None
self.larger_button.active = self.atoms is not None
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 ok(self):
if self.apply():
self.win.close()
def __init__(self, gui):
self.atoms = None
self.no_update = True
self.old_structure = 'undefined'
win = self.win = ui.Window(_('Nanoparticle'))
win.add(ui.Text(introtext))
self.element = Element('', self.apply)
lattice_button = ui.Button(_('Get structure'), self.set_structure_data)
self.elementinfo = ui.Label(' ')
win.add(self.element)
win.add(self.elementinfo)
win.add(lattice_button)
# The structure and lattice constant
labels = []
values = []
self.needs_4index = {}
self.needs_2lat = {}
self.factory = {}
for abbrev, name, n4, c, factory in self.structure_data:
labels.append(name)
values.append(abbrev)
self.needs_4index[abbrev] = n4
self.needs_2lat[abbrev] = c
self.factory[abbrev] = factory
self.structure = ui.ComboBox(labels, values, self.update_structure)
win.add([_('Structure:'), self.structure])
self.fourindex = self.needs_4index[values[0]]
self.a = ui.SpinBox(3.0, 0.0, 1000.0, 0.01, self.update)
self.c = ui.SpinBox(3.0, 0.0, 1000.0, 0.01, self.update)
win.add([_('Lattice constant: a ='), self.a, ' c =', self.c])
# Choose specification method
self.method = ui.ComboBox(
[_('Layer specification'),
_('Wulff construction')], ['layers', 'wulff'],
self.update_gui_method)
win.add([_('Method: '), self.method])
self.layerlabel = ui.Label('Missing text') # Filled in later
win.add(self.layerlabel)
self.direction_table_rows = ui.Rows()
win.add(self.direction_table_rows)
self.default_direction_table()
win.add(_('Add new direction:'))
self.new_direction_and_size_rows = ui.Rows()
win.add(self.new_direction_and_size_rows)
self.update_new_direction_and_size_stuff()
# Information
win.add(_('Information about the created cluster:'))
self.info = [
_('Number of atoms: '),
ui.Label('-'),
_(' Approx. diameter: '),
ui.Label('-')
]
win.add(self.info)
# Finalize setup
self.update_structure('fcc')
self.update_gui_method()
self.no_update = False
self.auto = ui.CheckButton(_('Automatic Apply'))
win.add(self.auto)
win.add([
pybutton(_('Creating a nanoparticle.'), self.makeatoms),
ui.helpbutton(helptext),
ui.Button(_('Apply'), self.apply),
ui.Button(_('OK'), self.ok)
])
self.gui = gui
self.smaller_button = None
self.largeer_button = None
self.element.grab_focus()
class SetupSurfaceSlab:
'''Window for setting up a surface.'''
def __init__(self, gui):
self.element = Element('', self.apply)
self.structure = ui.ComboBox(structures, structures,
self.structure_changed)
self.structure_warn = ui.Label('', 'red')
self.orthogonal = ui.CheckButton('', True, self.make)
self.lattice_a = ui.SpinBox(3.2, 0.0, 10.0, 0.001, self.make)
self.retrieve = ui.Button(_('Get from database'),
self.structure_changed)
self.lattice_c = ui.SpinBox(None, 0.0, 10.0, 0.001, self.make)
self.x = ui.SpinBox(1, 1, 30, 1, self.make)
self.x_warn = ui.Label('', 'red')
self.y = ui.SpinBox(1, 1, 30, 1, self.make)
self.y_warn = ui.Label('', 'red')
self.z = ui.SpinBox(1, 1, 30, 1, self.make)
self.vacuum_check = ui.CheckButton('', False, self.vacuum_checked)
self.vacuum = ui.SpinBox(5, 0, 40, 0.01, self.make)
self.description = ui.Label('')
win = self.win = ui.Window(_('Surface'))
win.add(ui.Text(introtext))
win.add(self.element)
win.add([_('Structure:'), self.structure, self.structure_warn])
win.add([_('Orthogonal cell:'), self.orthogonal])
win.add([_('Lattice constant:')])
win.add([_('\ta'), self.lattice_a, (u'Å'), self.retrieve])
win.add([_('\tc'), self.lattice_c, (u'Å')])
win.add([_('Size:')])
win.add([_('\tx: '), self.x, _(' unit cells'), self.x_warn])
win.add([_('\ty: '), self.y, _(' unit cells'), self.y_warn])
win.add([_('\tz: '), self.z, _(' unit cells')])
win.add([_('Vacuum: '), self.vacuum_check, self.vacuum, (u'Å')])
win.add(self.description)
# TRANSLATORS: This is a title of a window.
win.add([
pybutton(_('Creating a surface.'), self.make),
ui.Button(_('Apply'), self.apply),
ui.Button(_('OK'), self.ok)
])
self.element.grab_focus()
self.gui = gui
self.atoms = None
self.lattice_c.active = False
self.vacuum.active = False
self.structure_changed()
def vacuum_checked(self, *args):
if self.vacuum_check.var.get():
self.vacuum.active = True
else:
self.vacuum.active = False
self.make()
def get_lattice(self, *args):
if self.element.symbol is None:
return
ref = reference_states[self.element.Z]
symmetry = "unknown"
for struct in surfaces:
if struct[0] == self.structure.value:
symmetry = struct[1]
if ref['symmetry'] != symmetry:
# TRANSLATORS: E.g. "... assume fcc crystal structure for Au"
self.structure_warn.text = (_('Error: Reference values assume {} '
'crystal structure for {}!').format(
ref['symmetry'],
self.element.symbol))
else:
if symmetry == 'fcc' or symmetry == 'bcc' or symmetry == 'diamond':
self.lattice_a.value = ref['a']
elif symmetry == 'hcp':
self.lattice_a.value = ref['a']
self.lattice_c.value = ref['a'] * ref['c/a']
self.make()
def structure_changed(self, *args):
for surface in surfaces:
if surface[0] == self.structure.value:
if surface[2] == 'ortho':
self.orthogonal.var.set(True)
self.orthogonal.check['state'] = ['disabled']
elif surface[2] == 'non-ortho':
self.orthogonal.var.set(False)
self.orthogonal.check['state'] = ['disabled']
else:
self.orthogonal.check['state'] = ['normal']
if surface[1] == _('hcp'):
self.lattice_c.active = True
self.lattice_c.value = round(
self.lattice_a.value * ((8.0 / 3.0)**(0.5)), 3)
else:
self.lattice_c.active = False
self.lattice_c.value = 'None'
self.get_lattice()
def make(self, *args):
symbol = self.element.symbol
self.atoms = None
self.description.text = ''
self.python = None
self.x_warn.text = ''
self.y_warn.text = ''
if symbol is None:
return
x = self.x.value
y = self.y.value
z = self.z.value
size = (x, y, z)
a = self.lattice_a.value
c = self.lattice_c.value
vacuum = self.vacuum.value
if not self.vacuum_check.var.get():
vacuum = None
ortho = self.orthogonal.var.get()
ortho_warn_even = _('Please enter an even value for orthogonal cell')
struct = self.structure.value
if struct == _('BCC(111)') and (not (y % 2 == 0) and ortho):
self.y_warn.text = ortho_warn_even
return
if struct == _('BCC(110)') and (not (y % 2 == 0) and ortho):
self.y_warn.text = ortho_warn_even
return
if struct == _('FCC(111)') and (not (y % 2 == 0) and ortho):
self.y_warn.text = ortho_warn_even
return
if struct == _('FCC(211)') and (not (x % 3 == 0) and ortho):
self.x_warn.text = _('Please enter a value divisible by 3'
' for orthogonal cell')
return
if struct == _('HCP(0001)') and (not (y % 2 == 0) and ortho):
self.y_warn.text = ortho_warn_even
return
if struct == _('HCP(10-10)') and (not (y % 2 == 0) and ortho):
self.y_warn.text = ortho_warn_even
return
for surface in surfaces:
if surface[0] == struct:
c_py = ""
if surface[1] == _('hcp'):
self.atoms = surface[3](symbol, size, a, c, vacuum, ortho)
c_py = "{}, ".format(c)
else:
self.atoms = surface[3](symbol, size, a, vacuum, ortho)
if vacuum is not None:
vacuumtext = _(' Vacuum: {} Å.').format(vacuum)
else:
vacuumtext = ''
natoms = len(self.atoms)
label = ngettext(
# TRANSLATORS: e.g. "Au fcc100 surface with 2 atoms."
# or "Au fcc100 surface with 2 atoms. Vacuum: 5 Å."
'{symbol} {surf} surface with one atom.{vacuum}',
'{symbol} {surf} surface with {natoms} atoms.{vacuum}',
natoms).format(symbol=symbol,
surf=surface[3].__name__,
natoms=natoms,
vacuum=vacuumtext)
self.description.text = label
return py_template.format(func=surface[3].__name__,
a=a,
c=c_py,
symbol=symbol,
size=size,
ortho=ortho,
vacuum=vacuum)
def apply(self, *args):
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 ok(self, *args):
if self.apply():
self.win.close()
class SetupNanoparticle:
"Window for setting up a nanoparticle."
# Structures: Abbreviation, name,
# 4-index (boolean), two lattice const (bool), factory
structure_data = (('fcc', _('Face centered cubic (fcc)'),
False, False, FaceCenteredCubic),
('bcc', _('Body centered cubic (bcc)'),
False, False, BodyCenteredCubic),
('sc', _('Simple cubic (sc)'),
False, False, SimpleCubic),
('hcp', _('Hexagonal closed-packed (hcp)'),
True, True, HexagonalClosedPacked),
('graphite', _('Graphite'),
True, True, Graphite))
# NB: HCP is broken!
# A list of import statements for the Python window.
import_names = {
'fcc': 'from ase.cluster.cubic import FaceCenteredCubic',
'bcc': 'from ase.cluster.cubic import BodyCenteredCubic',
'sc': 'from ase.cluster.cubic import SimpleCubic',
'hcp': 'from ase.cluster.hexagonal import HexagonalClosedPacked',
'graphite': 'from ase.cluster.hexagonal import Graphite'}
# Default layer specifications for the different structures.
default_layers = {'fcc': [((1, 0, 0), 6),
((1, 1, 0), 9),
((1, 1, 1), 5)],
'bcc': [((1, 0, 0), 6),
((1, 1, 0), 9),
((1, 1, 1), 5)],
'sc': [((1, 0, 0), 6),
((1, 1, 0), 9),
((1, 1, 1), 5)],
'hcp': [((0, 0, 0, 1), 5),
((1, 0, -1, 0), 5)],
'graphite': [((0, 0, 0, 1), 5),
((1, 0, -1, 0), 5)]}
def __init__(self, gui):
self.atoms = None
self.no_update = True
self.old_structure = 'undefined'
win = self.win = ui.Window(_('Nanoparticle'))
win.add(ui.Text(introtext))
self.element = Element('', self.update)
lattice_button = ui.Button(_('Get structure'),
self.set_structure_data)
self.elementinfo = ui.Label(' ')
win.add(self.element)
win.add(self.elementinfo)
win.add(lattice_button)
# The structure and lattice constant
labels = []
values = []
self.needs_4index = {}
self.needs_2lat = {}
self.factory = {}
for abbrev, name, n4, c, factory in self.structure_data:
labels.append(name)
values.append(abbrev)
self.needs_4index[abbrev] = n4
self.needs_2lat[abbrev] = c
self.factory[abbrev] = factory
self.structure = ui.ComboBox(labels, values, self.update_structure)
win.add([_('Structure:'), self.structure])
self.fourindex = self.needs_4index[values[0]]
self.a = ui.SpinBox(3.0, 0.0, 1000.0, 0.01, self.update)
self.c = ui.SpinBox(3.0, 0.0, 1000.0, 0.01, self.update)
win.add([_('Lattice constant: a ='), self.a, ' c =', self.c])
# Choose specification method
self.method = ui.ComboBox(
[_('Layer specification'), _('Wulff construction')],
['layers', 'wulff'],
self.update_gui_method)
win.add([_('Method: '), self.method])
self.layerlabel = ui.Label('Missing text') # Filled in later
win.add(self.layerlabel)
self.direction_table_rows = ui.Rows()
win.add(self.direction_table_rows)
self.default_direction_table()
win.add(_('Add new direction:'))
self.new_direction_and_size_rows = ui.Rows()
win.add(self.new_direction_and_size_rows)
self.update_new_direction_and_size_stuff()
# Information
win.add(_('Information about the created cluster:'))
self.info = [_('Number of atoms: '),
ui.Label('-'),
_(' Approx. diameter: '),
ui.Label('-')]
win.add(self.info)
# Finalize setup
self.update_structure('fcc')
self.update_gui_method()
self.no_update = False
self.auto = ui.CheckButton(_('Automatic Apply'))
win.add(self.auto)
win.add([pybutton(_('Creating a nanoparticle.'), self.makeatoms),
ui.helpbutton(helptext),
ui.Button(_('Apply'), self.apply),
ui.Button(_('OK'), self.ok)])
self.gui = gui
self.smaller_button = None
self.largeer_button = None
def default_direction_table(self):
'Set default directions and values for the current crystal structure.'
self.direction_table = []
struct = self.structure.value
for direction, layers in self.default_layers[struct]:
self.direction_table.append((direction, layers, 1.0))
def update_direction_table(self):
self.direction_table_rows.clear()
for direction, layers, energy in self.direction_table:
self.add_direction(direction, layers, energy)
self.update()
def add_direction(self, direction, layers, energy):
i = len(self.direction_table_rows)
if self.method.value == 'wulff':
spin = ui.SpinBox(energy, 0.0, 1000.0, 0.1, self.update)
else:
spin = ui.SpinBox(layers, 1, 100, 1, self.update)
up = ui.Button(_('Up'), self.row_swap_next, i - 1)
down = ui.Button(_('Down'), self.row_swap_next, i)
delete = ui.Button(_('Delete'), self.row_delete, i)
self.direction_table_rows.add([str(direction) + ':',
spin, up, down, delete])
up.active = i > 0
down.active = False
delete.active = i > 0
if i > 0:
down, delete = self.direction_table_rows[-2][3:]
down.active = True
delete.active = True
def update_new_direction_and_size_stuff(self):
if self.needs_4index[self.structure.value]:
n = 4
else:
n = 3
rows = self.new_direction_and_size_rows
rows.clear()
self.new_direction = row = ['(']
for i in range(n):
if i > 0:
row.append(',')
row.append(ui.SpinBox(0, -100, 100, 1))
row.append('):')
if self.method.value == 'wulff':
row.append(ui.SpinBox(1.0, 0.0, 1000.0, 0.1))
else:
row.append(ui.SpinBox(5, 1, 100, 1))
row.append(ui.Button(_('Add'), self.row_add))
rows.add(row)
if self.method.value == 'wulff':
# Extra widgets for the Wulff construction
self.size_radio = ui.RadioButtons(
[_('Number of atoms'), _('Diameter')],
['natoms', 'diameter'],
self.update_gui_size)
self.size_natoms = ui.SpinBox(100, 1, 100000, 1,
self.update_size_natoms)
self.size_diameter = ui.SpinBox(5.0, 0, 100.0, 0.1,
self.update_size_diameter)
self.round_radio = ui.RadioButtons(
[_('above '), _('below '), _('closest ')],
['above', 'below', 'closest'],
callback=self.update)
self.smaller_button = ui.Button(_('Smaller'), self.wulff_smaller)
self.larger_button = ui.Button(_('Larger'), self.wulff_larger)
rows.add(_('Choose size using:'))
rows.add(self.size_radio)
rows.add([_('atoms'), self.size_natoms,
_(u'ų'), self.size_diameter])
rows.add(
_('Rounding: If exact size is not possible, choose the size:'))
rows.add(self.round_radio)
rows.add([self.smaller_button, self.larger_button])
self.update_gui_size()
else:
self.smaller_button = None
self.larger_button = None
def update_structure(self, s):
'Called when the user changes the structure.'
# s = self.structure.value
if s != self.old_structure:
old4 = self.fourindex
self.fourindex = self.needs_4index[s]
if self.fourindex != old4:
# The table of directions is invalid.
self.default_direction_table()
self.old_structure = s
self.c.active = self.needs_2lat[s]
self.update()
def update_gui_method(self, *args):
'Switch between layer specification and Wulff construction.'
self.update_direction_table()
self.update_new_direction_and_size_stuff()
if self.method.value == 'wulff':
self.layerlabel.text = _(
'Surface energies (as energy/area, NOT per atom):')
else:
self.layerlabel.text = _('Number of layers:')
self.update()
def wulff_smaller(self, widget=None):
'Make a smaller Wulff construction.'
n = len(self.atoms)
self.size_radio.value = 'natoms'
self.size_natoms.value = n - 1
self.round_radio.value = 'below'
self.apply()
def wulff_larger(self, widget=None):
'Make a larger Wulff construction.'
n = len(self.atoms)
self.size_radio.value = 'natoms'
self.size_natoms.value = n + 1
self.round_radio.value = 'above'
self.apply()
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_delete(self, row):
del self.direction_table[row]
self.update_direction_table()
def row_swap_next(self, row):
dt = self.direction_table
dt[row], dt[row + 1] = dt[row + 1], dt[row]
self.update_direction_table()
def update_gui_size(self, widget=None):
'Update gui when the cluster size specification changes.'
self.size_natoms.active = self.size_radio.value == 'natoms'
self.size_diameter.active = self.size_radio.value == 'diameter'
def update_size_natoms(self, widget=None):
at_vol = self.get_atomic_volume()
dia = 2.0 * (3 * self.size_natoms.value * at_vol /
(4 * np.pi))**(1 / 3)
self.size_diameter.value = dia
self.update()
def update_size_diameter(self, widget=None, update=True):
if self.size_diameter.active:
at_vol = self.get_atomic_volume()
n = round(np.pi / 6 * self.size_diameter.value**3 / at_vol)
self.size_natoms.value = int(n)
if update:
self.update()
def update(self, *args):
if self.no_update:
return
self.element.check()
if self.auto.value:
self.makeatoms()
if self.atoms is not None:
self.gui.new_atoms(self.atoms)
else:
self.clearatoms()
self.makeinfo()
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 makeatoms(self, *args):
'Make the atoms according to the current specification.'
if not self.element.check():
self.clearatoms()
self.makeinfo()
return False
struct = self.structure.value
if self.needs_2lat[struct]:
# a and c lattice constants
lc = {'a': self.a.value,
'c': self.c.value}
lc_str = str(lc)
else:
lc = self.a.value
lc_str = '%.5f' % (lc,)
if self.method.value == 'wulff':
# Wulff construction
surfaces = [x[0] for x in self.direction_table]
surfaceenergies = [x[1].value
for x in self.direction_table_rows.rows]
self.update_size_diameter(update=False)
rounding = self.round_radio.value
self.atoms = wulff_construction(self.element.symbol,
surfaces,
surfaceenergies,
self.size_natoms.value,
self.factory[struct],
rounding, lc)
python = py_template_wulff % {'element': self.element.symbol,
'surfaces': str(surfaces),
'energies': str(surfaceenergies),
'latconst': lc_str,
'natoms': self.size_natoms.value,
'structure': struct,
'rounding': rounding}
else:
# Layer-by-layer specification
surfaces = [x[0] for x in self.direction_table]
layers = [x[1].value for x in self.direction_table_rows.rows]
self.atoms = self.factory[struct](self.element.symbol,
copy(surfaces),
layers, latticeconstant=lc)
imp = self.import_names[struct]
python = py_template_layers % {'import': imp,
'element': self.element.symbol,
'surfaces': str(surfaces),
'layers': str(layers),
'latconst': lc_str,
'factory': imp.split()[-1]}
self.makeinfo()
return python
def clearatoms(self):
self.atoms = None
def get_atomic_volume(self):
s = self.structure.value
a = self.a.value
c = self.c.value
if s == 'fcc':
return a**3 / 4
elif s == 'bcc':
return a**3 / 2
elif s == 'sc':
return a**3
elif s == 'hcp':
return np.sqrt(3.0) / 2 * a * a * c / 2
elif s == 'graphite':
return np.sqrt(3.0) / 2 * a * a * c / 4
def makeinfo(self):
"""Fill in information field about the atoms.
Also turns the Wulff construction buttons [Larger] and
[Smaller] on and off.
"""
if self.atoms is None:
self.info[1].text = '-'
self.info[3].text = '-'
else:
at_vol = self.get_atomic_volume()
dia = 2 * (3 * len(self.atoms) * at_vol / (4 * np.pi))**(1 / 3)
self.info[1].text = str(len(self.atoms))
self.info[3].text = u'{0:.1f} Å'.format(dia)
if self.method.value == 'wulff':
if self.smaller_button is not None:
self.smaller_button.active = self.atoms is not None
self.larger_button.active = self.atoms is not None
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 ok(self):
if self.apply():
self.win.close()
def __init__(self, gui):
self.atoms = None
self.no_update = True
self.old_structure = 'undefined'
win = self.win = ui.Window(_('Nanoparticle'))
win.add(ui.Text(introtext))
self.element = Element('', self.update)
lattice_button = ui.Button(_('Get structure'),
self.set_structure_data)
self.elementinfo = ui.Label(' ')
win.add(self.element)
win.add(self.elementinfo)
win.add(lattice_button)
# The structure and lattice constant
labels = []
values = []
self.needs_4index = {}
self.needs_2lat = {}
self.factory = {}
for abbrev, name, n4, c, factory in self.structure_data:
labels.append(name)
values.append(abbrev)
self.needs_4index[abbrev] = n4
self.needs_2lat[abbrev] = c
self.factory[abbrev] = factory
self.structure = ui.ComboBox(labels, values, self.update_structure)
win.add([_('Structure:'), self.structure])
self.fourindex = self.needs_4index[values[0]]
self.a = ui.SpinBox(3.0, 0.0, 1000.0, 0.01, self.update)
self.c = ui.SpinBox(3.0, 0.0, 1000.0, 0.01, self.update)
win.add([_('Lattice constant: a ='), self.a, ' c =', self.c])
# Choose specification method
self.method = ui.ComboBox(
[_('Layer specification'), _('Wulff construction')],
['layers', 'wulff'],
self.update_gui_method)
win.add([_('Method: '), self.method])
self.layerlabel = ui.Label('Missing text') # Filled in later
win.add(self.layerlabel)
self.direction_table_rows = ui.Rows()
win.add(self.direction_table_rows)
self.default_direction_table()
win.add(_('Add new direction:'))
self.new_direction_and_size_rows = ui.Rows()
win.add(self.new_direction_and_size_rows)
self.update_new_direction_and_size_stuff()
# Information
win.add(_('Information about the created cluster:'))
self.info = [_('Number of atoms: '),
ui.Label('-'),
_(' Approx. diameter: '),
ui.Label('-')]
win.add(self.info)
# Finalize setup
self.update_structure('fcc')
self.update_gui_method()
self.no_update = False
self.auto = ui.CheckButton(_('Automatic Apply'))
win.add(self.auto)
win.add([pybutton(_('Creating a nanoparticle.'), self.makeatoms),
ui.helpbutton(helptext),
ui.Button(_('Apply'), self.apply),
ui.Button(_('OK'), self.ok)])
self.gui = gui
self.smaller_button = None
self.largeer_button = None