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from ase.gui.i18n import _
from math import sqrt, pi, acos
import numpy as np
from ase.data import chemical_symbols as symbols
from ase.data import atomic_names as names
from ase.gui.utils import get_magmoms
def formula(Z):
hist = {}
for z in Z:
if z in hist:
hist[z] += 1
else:
hist[z] = 1
Z = sorted(hist.keys())
strings = []
for z in Z:
n = hist[z]
s = ('' if n == 1 else str(n)) + symbols[z]
strings.append(s)
return '+'.join(strings)
class Status: # Status is used as a mixin in GUI
def __init__(self):
self.ordered_indices = []
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)
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]))
haveit = ['numbers', 'positions', 'forces', 'momenta',
'initial_charges', 'initial_magmoms']
for key in atoms.arrays:
if key not in haveit:
val = atoms.get_array(key)[indices[0]]
if val is not None:
text += ' {0}={1:g}'.format(key, val)
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)
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