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"""nanoparticle.py - Window for setting up crystalline nanoparticles.
"""
from copy import copy
from ase.gui.i18n import _
import numpy as np
import ase
import ase.data
import ase.gui.ui as ui
# Delayed imports:
# ase.cluster.data
from ase.cluster.cubic import FaceCenteredCubic, BodyCenteredCubic, SimpleCubic
from ase.cluster.hexagonal import HexagonalClosedPacked, Graphite
from ase.cluster import wulff_construction
from ase.gui.widgets import Element, pybutton
introtext = _("""\
Create a nanoparticle either by specifying the number of layers, or using the
Wulff construction. Please press the [Help] button for instructions on how to
specify the directions.
WARNING: The Wulff construction currently only works with cubic crystals!
""")
helptext = _("""
The nanoparticle module sets up a nano-particle or a cluster with a given
crystal structure.
1) Select the element, the crystal structure and the lattice constant(s).
The [Get structure] button will find the data for a given element.
2) Choose if you want to specify the number of layers in each direction, or if
you want to use the Wulff construction. In the latter case, you must
specify surface energies in each direction, and the size of the cluster.
How to specify the directions:
------------------------------
First time a direction appears, it is interpreted as the entire family of
directions, i.e. (0,0,1) also covers (1,0,0), (-1,0,0) etc. If one of these
directions is specified again, the second specification overrules that specific
direction. For this reason, the order matters and you can rearrange the
directions with the [Up] and [Down] keys. You can also add a new direction,
remember to press [Add] or it will not be included.
Example: (1,0,0) (1,1,1), (0,0,1) would specify the {100} family of directions,
the {111} family and then the (001) direction, overruling the value given for
the whole family of directions.
""")
py_template_layers = """
import ase
%(import)s
surfaces = %(surfaces)s
layers = %(layers)s
lc = %(latconst)s
atoms = %(factory)s('%(element)s', surfaces, layers, latticeconstant=lc)
# OPTIONAL: Cast to ase.Atoms object, discarding extra information:
# atoms = ase.Atoms(atoms)
"""
py_template_wulff = """
import ase
from ase.cluster import wulff_construction
surfaces = %(surfaces)s
esurf = %(energies)s
lc = %(latconst)s
size = %(natoms)s # Number of atoms
atoms = wulff_construction('%(element)s', surfaces, esurf,
size, '%(structure)s',
rounding='%(rounding)s', latticeconstant=lc)
# OPTIONAL: Cast to ase.Atoms object, discarding extra information:
# atoms = ase.Atoms(atoms)
"""
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()
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