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
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'))
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 __init__(self, gui):
self.gui = gui
self.win = win = ui.Window(_('Render current view in povray ... '))
win.add(ui.Label(_("Rendering %d atoms.") % len(self.gui.atoms)))
guiwidth, guiheight = self.get_guisize()
self.width_widget = ui.SpinBox(guiwidth, start=1, end=9999, step=1)
self.height_widget = ui.SpinBox(guiheight, start=1, end=9999, step=1)
win.add([ui.Label(_('Size')), self.width_widget,
ui.Label('⨯'), self.height_widget])
self.linewidth_widget = ui.SpinBox(0.07, start=0.01, end=9.99,
step=0.01)
win.add([ui.Label(_('Line width')), self.linewidth_widget,
ui.Label(_('Ångström'))])
self.constraints_widget = ui.CheckButton(_("Render constraints"))
self.cell_widget = ui.CheckButton(_("Render unit cell"), value=True)
win.add([self.cell_widget, self.constraints_widget])
formula = gui.atoms.get_chemical_formula(mode='hill')
self.basename_widget = ui.Entry(width=30, value=formula,
callback=self.update_outputname)
win.add([ui.Label(_('Output basename: ')), self.basename_widget])
self.povray_executable = ui.Entry(width=30,value='povray')
win.add([ui.Label(_('POVRAY executable')), self.povray_executable])
self.outputname_widget = ui.Label()
win.add([ui.Label(_('Output filename: ')), self.outputname_widget])
self.update_outputname()
self.texture_widget = ui.ComboBox(labels=self.texture_list,
values=self.texture_list)
win.add([ui.Label(_('Atomic texture set:')),
self.texture_widget])
# complicated texture stuff
self.camera_widget = ui.ComboBox(labels=self.cameras,
values=self.cameras)
self.camera_distance_widget = ui.SpinBox(50.0, -99.0, 99.0, 1.0)
win.add([ui.Label(_('Camera type: ')), self.camera_widget])
win.add([ui.Label(_('Camera distance')), self.camera_distance_widget])
# render current frame/all frames
self.frames_widget = ui.RadioButtons([_('Render current frame'),
_('Render all frames')])
win.add(self.frames_widget)
if len(gui.images) == 1:
self.frames_widget.buttons[1].widget.configure(state='disabled')
self.run_povray_widget = ui.CheckButton(_('Run povray'), True)
self.keep_files_widget = ui.CheckButton(_('Keep povray files'), False)
self.show_output_widget = ui.CheckButton(_('Show output window'), True)
self.transparent = ui.CheckButton(_("Transparent background"), True)
win.add(self.transparent)
win.add([self.run_povray_widget, self.keep_files_widget,
self.show_output_widget])
win.add(ui.Button(_('Render'), self.ok))
def toggle(self, value):
self.gui.colormode = value
if value == 'jmol' or value == 'neighbors':
if hasattr(self, 'mnmx'):
"delete the min max fields by creating a new window"
del self.mnmx
del self.cmaps
self.win.close()
self.reset(self.gui)
text = ''
else:
scalars = np.ma.array([self.gui.get_color_scalars(i)
for i in range(len(self.gui.images))])
mn = np.min(scalars)
mx = np.max(scalars)
self.gui.colormode_data = None, mn, mx
cmaps = ['default', 'old']
try:
import pylab as plt
cmaps += [m for m in plt.cm.datad if not m.endswith("_r")]
except ImportError:
pass
self.cmaps = [_('cmap:'),
ui.ComboBox(cmaps, cmaps, self.update_colormap),
_('N:'),
ui.SpinBox(26, 0, 100, 1, self.update_colormap)]
self.update_colormap('default')
try:
unit = {'tag': '',
'force': 'eV/Ang',
'velocity': '(eV/amu)^(1/2)',
'charge': '|e|',
'initial charge': '|e|',
u'magmom': 'μB'}[value]
except KeyError:
unit = ''
text = ''
rng = mx - mn # XXX what are optimal allowed range and steps ?
self.mnmx = [_('min:'),
ui.SpinBox(mn, mn - 10 * rng, mx + rng, rng / 10.,
self.change_mnmx),
_('max:'),
ui.SpinBox(mx, mn - 10 * rng, mx + rng, rng / 10.,
self.change_mnmx),
_(unit)]
self.win.close()
self.reset(self.gui)
self.label.text = text
self.radio.value = value
self.gui.draw()
return text # for testing
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 __init__(self, gui):
self.gui = gui
win = ui.Window(_('Settings'))
# Constraints
win.add(_('Constraints:'))
win.add([
ui.Button(_('Constrain'), self.constrain_selected), '/',
ui.Button(_('release'), self.release_selected),
_(' selected atoms')
])
win.add(ui.Button(_('Constrain immobile atoms'), self.immobile))
win.add(ui.Button(_('Clear all constraints'), self.clear_constraints))
# Visibility
win.add(_('Visibility:'))
win.add([
ui.Button(_('Hide'), self.hide_selected), '/',
ui.Button(_('show'), self.show_selected),
_(' selected atoms')
])
win.add(ui.Button(_('View all atoms'), self.view_all))
# Miscellaneous
win.add(_('Miscellaneous:'))
self.scale = ui.SpinBox(self.gui.images.atom_scale, 0.2, 2.0, 0.1,
self.scale_radii)
win.add([_('Scale atomic radii:'), self.scale])
def __init__(self, gui):
self.win = win = ui.Window(_('Movie'), self.close)
win.add(_('Image number:'))
self.frame_number = ui.Scale(gui.frame + 1,
1,
len(gui.images),
callback=self.new_frame)
win.add(self.frame_number)
win.add([
ui.Button(_('First'), self.click, -1, True),
ui.Button(_('Back'), self.click, -1),
ui.Button(_('Forward'), self.click, 1),
ui.Button(_('Last'), self.click, 1, True)
])
play = ui.Button(_('Play'), self.play)
stop = ui.Button(_('Stop'), self.stop)
# TRANSLATORS: This function plays an animation forwards and backwards
# alternatingly, e.g. for displaying vibrational movement
self.rock = ui.CheckButton(_('Rock'))
win.add([play, stop, self.rock])
if len(gui.images) > 150:
skipdefault = len(gui.images) // 150
tdefault = min(max(len(gui.images) / (skipdefault * 5.0), 1.0), 30)
else:
skipdefault = 0
tdefault = min(max(len(gui.images) / 5.0, 1.0), 30)
self.time = ui.SpinBox(tdefault, 1.0, 99, 0.1)
self.skip = ui.SpinBox(skipdefault, 0, 99, 1)
win.add(
[_(' Frame rate: '), self.time,
_(' Skip frames: '), self.skip])
self.gui = gui
self.direction = 1
self.timer = None
gui.register_vulnerable(self)
def __init__(self, gui):
self.gui = gui
win = ui.Window(_('Rotate'))
win.add(_('Rotation angles:'))
self.rotate = [ui.SpinBox(42.0, -360, 360, 1, self.change)
for i in '123']
win.add(self.rotate)
win.add(ui.Button(_('Update'), self.update_angles))
win.add(_('Note:\nYou can rotate freely\n'
'with the mouse, by holding\n'
'down mouse button 2.'))
self.update_angles()
def __init__(self, gui):
self.gui = gui
win = ui.Window(_('Settings'))
# Constraints
win.add(_('Constraints:'))
win.add([ui.Button(_('Fix'), self.constrain_selected),
'/',
ui.Button(_('release'), self.release_selected),
_(' selected atoms')])
win.add(ui.Button(_('Clear all constraints'), self.clear_constraints))
# Visibility
win.add(_('Visibility:'))
win.add([ui.Button(_('Hide'), self.hide_selected),
'/',
ui.Button(_('show'), self.show_selected),
_(' selected atoms')])
win.add(ui.Button(_('View all atoms'), self.view_all))
# Miscellaneous
win.add(_('Miscellaneous:'))
self.scale = ui.SpinBox(self.gui.images.atom_scale,
0.2, 2.0, 0.1, self.scale_radii)
win.add([_('Scale atomic radii:'), self.scale])
self.force_vector_scale = ui.SpinBox(
self.gui.force_vector_scale,
0.0, 1e32, 0.1,
rounding=2,
callback=self.scale_force_vectors
)
win.add([_('Scale force vectors:'), self.force_vector_scale])
self.velocity_vector_scale = ui.SpinBox(
self.gui.velocity_vector_scale,
0.0, 1e32, 0.1,
rounding=2,
callback=self.scale_velocity_vectors
)
win.add([_('Scale velocity vectors:'), self.velocity_vector_scale])
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 __init__(self, gui):
win = ui.Window(_('Repeat'))
win.add(_('Repeat atoms:'))
self.repeat = [ui.SpinBox(r, 1, 9, 1, self.change)
for r in gui.images.repeat]
win.add(self.repeat)
win.add(ui.Button(_('Set unit cell'), self.set_unit_cell))
for sb, vec in zip(self.repeat, gui.atoms.cell):
if not vec.any():
sb.active = False
self.gui = gui
def __init__(self, gui):
self.gui = gui
win = self.win = ui.Window(_('Add atoms'))
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 = list(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 __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
def __init__(self, gui):
self.gui = gui
win = self.win = ui.Window(_('Add atoms'))
win.add(_('Specify chemical symbol, formula, or filename.'))
def set_molecule(value):
self.entry.value = value
self.focus()
def choose_file():
chooser = ui.ASEFileChooser(self.win.win)
filename = chooser.go()
if filename is None: # No file selected
return
self.entry.value = filename
# Load the file immediately, so we can warn now in case of error
self.readfile(filename, format=chooser.format)
self.entry = ui.Entry('', callback=self.add)
win.add([
_('Add:'), self.entry,
ui.Button(_('File ...'), callback=choose_file)
])
self._filename = None
self._atoms_from_file = None
from ase.collections import g2
labels = list(sorted(g2.names))
values = labels
box = ui.ComboBox(labels, values, callback=set_molecule)
win.add([_('Get molecule:'), box])
box.value = 'H2'
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 __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):
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()
