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 status(self, atoms):
# use where here: XXX
natoms = len(atoms)
indices = np.arange(natoms)[self.images.selected[:natoms]]
ordered_indices = [
i for i in self.images.selected_ordered if i < len(atoms)
]
n = len(indices)
self.nselected = n
if n == 0:
self.window.update_status_line('')
return
Z = atoms.numbers[indices]
R = atoms.positions[indices]
if n == 1:
tag = atoms.get_tags()[indices[0]]
text = (u' #%d %s (%s): %.3f Å, %.3f Å, %.3f Å ' %
((indices[0], names[Z[0]], symbols[Z[0]]) + tuple(R[0])))
text += _(' tag=%(tag)s') % dict(tag=tag)
magmoms = get_magmoms(self.atoms)
if magmoms.any():
# TRANSLATORS: mom refers to magnetic moment
text += _(' mom={0:1.2f}'.format(magmoms[indices][0]))
charges = self.atoms.get_initial_charges()
if charges.any():
text += _(' q={0:1.2f}'.format(charges[indices][0]))
elif n == 2:
D = R[0] - R[1]
d = sqrt(np.dot(D, D))
text = u' %s-%s: %.3f Å' % (symbols[Z[0]], symbols[Z[1]], d)
elif n == 3:
d = []
for c in range(3):
D = R[c] - R[(c + 1) % 3]
d.append(np.dot(D, D))
a = []
for c in range(3):
t1 = 0.5 * (d[c] + d[(c + 1) % 3] - d[(c + 2) % 3])
t2 = sqrt(d[c] * d[(c + 1) % 3])
try:
t3 = acos(t1 / t2)
except ValueError:
if t1 > 0:
t3 = 0
else:
t3 = pi
a.append(t3 * 180 / pi)
text = (u' %s-%s-%s: %.1f°, %.1f°, %.1f°' %
tuple([symbols[z] for z in Z] + a))
elif len(ordered_indices) == 4:
angle = self.atoms.get_dihedral(*ordered_indices, mic=True)
text = (u'%s %s → %s → %s → %s: %.1f°' %
tuple([_('dihedral')] + [symbols[z] for z in Z] + [angle]))
else:
text = ' ' + formula(Z)
self.window.update_status_line(text)
def get_color_scalars(self, frame=None):
if self.colormode == 'tag':
return self.atoms.get_tags()
if self.colormode == 'force':
f = (self.get_forces()**2).sum(1)**0.5
return f * self.images.get_dynamic(self.atoms)
elif self.colormode == 'velocity':
return (self.atoms.get_velocities()**2).sum(1)**0.5
elif self.colormode == 'initial charge':
return self.atoms.get_initial_charges()
elif self.colormode == 'magmom':
return get_magmoms(self.atoms)
elif self.colormode == 'neighbors':
from ase.neighborlist import NeighborList
n = len(self.atoms)
nl = NeighborList(self.get_covalent_radii(self.atoms) * 1.5,
skin=0,
self_interaction=False,
bothways=True)
nl.update(self.atoms)
return [len(nl.get_neighbors(i)[0]) for i in range(n)]
else:
scalars = np.array(self.atoms.get_array(self.colormode),
dtype=float)
return np.ma.array(scalars, mask=np.isnan(scalars))
def update_labels(self):
index = self.window['show-labels']
if index == 0:
self.labels = None
elif index == 1:
self.labels = list(range(len(self.atoms)))
elif index == 2:
self.labels = list(get_magmoms(self.atoms))
else:
self.labels = self.atoms.get_chemical_symbols()
def get_color_scalars(self, frame=None):
if self.colormode == 'tag':
return self.atoms.get_tags()
if self.colormode == 'force':
f = (self.get_forces()**2).sum(1)**0.5
return f * self.images.get_dynamic(self.atoms)
elif self.colormode == 'velocity':
return (self.atoms.get_velocities()**2).sum(1)**0.5
elif self.colormode == 'charge':
return self.atoms.get_charges()
elif self.colormode == 'magmom':
return get_magmoms(self.atoms)
def get_color_scalars(self, frame=None):
if self.colormode == 'tag':
return self.atoms.get_tags()
if self.colormode == 'force':
f = (self.get_forces()**2).sum(1)**0.5
return f * self.images.get_dynamic(self.atoms)
elif self.colormode == 'velocity':
return (self.atoms.get_velocities()**2).sum(1)**0.5
elif self.colormode == 'initial charge':
return self.atoms.get_initial_charges()
elif self.colormode == 'magmom':
return get_magmoms(self.atoms)
def activate(self):
images = self.gui.images
atoms = self.gui.atoms
radio = self.radio
radio['tag'].active = atoms.has('tags')
# XXX not sure how to deal with some images having forces,
# and other images not. Same goes for below quantities
F = images.get_forces(atoms)
radio['force'].active = F is not None
radio['velocity'].active = atoms.has('momenta')
radio['initial charge'].active = atoms.has('initial_charges')
radio['magmom'].active = get_magmoms(atoms).any()
def update_labels(self):
index = self.window['show-labels']
if index == 0:
self.labels = None
elif index == 1:
self.labels = list(range(len(self.atoms)))
elif index == 2:
self.labels = list(get_magmoms(self.atoms))
elif index == 4:
Q = self.atoms.get_initial_charges()
self.labels = ['{0:.4g}'.format(q) for q in Q]
else:
self.labels = self.atoms.get_chemical_symbols()
def activate(self):
images = self.gui.images
atoms = self.gui.atoms
radio = self.radio
radio['tag'].active = atoms.has('tags')
# XXX not sure how to deal with some images having forces,
# and other images not. Same goes for below quantities
F = images.get_forces(atoms)
radio['force'].active = F is not None
radio['velocity'].active = atoms.has('momenta')
radio['charge'].active = atoms.has('charges')
radio['magmom'].active = get_magmoms(atoms).any()
def get_color_scalars(self, frame=None):
if self.colormode == 'tag':
return self.atoms.get_tags()
if self.colormode == 'force':
f = (self.get_forces()**2).sum(1)**0.5
return f * self.images.get_dynamic(self.atoms)
elif self.colormode == 'atomic_energies': ## ssrokyz start
return self.atoms.get_atomic_energies() ## ssrokyz end
elif self.colormode == 'velocity':
return (self.atoms.get_velocities()**2).sum(1)**0.5
elif self.colormode == 'initial charge':
return self.atoms.get_initial_charges()
elif self.colormode == 'magmom':
return get_magmoms(self.atoms)
elif self.colormode == 'neighbors':
from ase.neighborlist import NeighborList
n = len(self.atoms)
nl = NeighborList(self.get_covalent_radii(self.atoms) * 1.5,
skin=0,
self_interaction=False,
bothways=True)
nl.update(self.atoms)
return [len(nl.get_neighbors(i)[0]) for i in range(n)]
def set_magmom(self):
magmoms = get_magmoms(self.gui.atoms)
magmoms[self.selection()] = self.magmom.value
self.gui.atoms.set_initial_magnetic_moments(magmoms)
self.gui.draw()
def set_magmom(self):
magmoms = get_magmoms(self.gui.atoms)
magmoms[self.selection()] = self.magmom.value
self.gui.atoms.set_initial_magnetic_moments(magmoms)
self.gui.draw()
def status(self, atoms):
# use where here: XXX
natoms = len(atoms)
indices = np.arange(natoms)[self.images.selected[:natoms]]
ordered_indices = [i for i in self.images.selected_ordered
if i < len(atoms)]
n = len(indices)
self.nselected = n
if n == 0:
self.window.update_status_line('')
return
Z = atoms.numbers[indices]
R = atoms.positions[indices]
if n == 1:
tag = atoms.get_tags()[indices[0]]
text = (u' #%d %s (%s): %.3f Å, %.3f Å, %.3f Å ' %
((indices[0], names[Z[0]], symbols[Z[0]]) + tuple(R[0])))
text += _(' tag=%(tag)s') % dict(tag=tag)
magmoms = get_magmoms(self.atoms)
if magmoms.any():
# TRANSLATORS: mom refers to magnetic moment
text += _(' mom={0:1.2f}'.format(
magmoms[indices][0]))
charges = self.atoms.get_initial_charges()
if charges.any():
text += _(' q={0:1.2f}'.format(
charges[indices][0]))
elif n == 2:
D = R[0] - R[1]
d = sqrt(np.dot(D, D))
text = u' %s-%s: %.3f Å' % (symbols[Z[0]], symbols[Z[1]], d)
elif n == 3:
d = []
for c in range(3):
D = R[c] - R[(c + 1) % 3]
d.append(np.dot(D, D))
a = []
for c in range(3):
t1 = 0.5 * (d[c] + d[(c + 1) % 3] - d[(c + 2) % 3])
t2 = sqrt(d[c] * d[(c + 1) % 3])
try:
t3 = acos(t1 / t2)
except ValueError:
if t1 > 0:
t3 = 0
else:
t3 = pi
a.append(t3 * 180 / pi)
text = (u' %s-%s-%s: %.1f°, %.1f°, %.1f°' %
tuple([symbols[z] for z in Z] + a))
elif len(ordered_indices) == 4:
R = self.atoms.positions[ordered_indices]
Z = self.atoms.numbers[ordered_indices]
a = R[1] - R[0]
b = R[2] - R[1]
c = R[3] - R[2]
bxa = np.cross(b, a)
bxa /= np.sqrt(np.vdot(bxa, bxa))
cxb = np.cross(c, b)
cxb /= np.sqrt(np.vdot(cxb, cxb))
angle = np.vdot(bxa, cxb)
if angle < -1:
angle = -1
if angle > 1:
angle = 1
angle = np.arccos(angle)
if (np.vdot(bxa, c)) > 0:
angle = 2 * np.pi - angle
angle = angle * 180.0 / np.pi
text = (u'%s %s->%s->%s->%s: %.1f°' %
tuple([_('dihedral')] + [symbols[z] for z in Z] + [angle]))
else:
text = ' ' + formula(Z)
self.window.update_status_line(text)
def create_info_lines(atoms, indices, ordered_indices=None):
"""Create a string of information about the selected atom(s).
Return
------
list[str]
"""
ordered_indices = ordered_indices or indices
num_selected = len(indices)
if num_selected == 0:
return []
a_nums = atoms.numbers[indices]
symbols = [chemical_symbols[z] for z in a_nums]
positions = atoms.positions[indices]
if num_selected == 1:
x, y, z = positions[0]
name = atomic_names[a_nums[0]]
text = [
f"#{indices[0]} {name} ({symbols[0]})",
f"({x:.3f}, {y:.3f}, {z:.3f}) Å",
_(f"tag={atoms.get_tags()[indices[0]]}"),
]
magmoms = get_magmoms(atoms)
if magmoms.any():
text.append(_(f"mom={magmoms[indices][0]:1.2f}"))
charges = atoms.get_initial_charges()
if charges.any():
text.append(_(f"q={charges[indices][0]:1.2f}"))
known_arrays = [
"numbers",
"positions",
"forces",
"momenta",
"initial_charges",
"initial_magmoms",
]
for key in atoms.arrays:
if key not in known_arrays:
val = atoms.get_array(key)[indices[0]]
if val is not None:
try:
text.append("{0}={1:g}".format(key, val))
except ValueError:
text.append("{0}={1}".format(key, val))
return text
if num_selected == 2:
dist = np.linalg.norm(positions[0] - positions[1])
return [f"Bond Distance {symbols[0]}-{symbols[0]}: {dist:.3f} Å"]
if num_selected == 3:
distances = []
for c in range(3):
vector = positions[c] - positions[(c + 1) % 3]
distances.append(np.dot(vector, vector))
angles = []
for c in range(3):
t1 = 0.5 * (distances[c] + distances[(c + 1) % 3] -
distances[(c + 2) % 3])
t2 = sqrt(distances[c] * distances[(c + 1) % 3])
try:
t3 = acos(t1 / t2)
except ValueError:
if t1 > 0:
t3 = 0
else:
t3 = pi
angles.append(t3 * 180 / pi)
return [
"Valence Angle %s-%s-%s: %.1f°, %.1f°, %.1f°" %
tuple(symbols + angles)
]
if len(ordered_indices) == 4:
angle = atoms.get_dihedral(*ordered_indices, mic=True)
return [
"%s %s → %s → %s → %s: %.1f°" %
tuple([_("Dihedral")] + symbols + [angle])
]
return [f"Formula: {create_formula(a_nums)}"]
