def _on_change_structure(self, change):
"""Update viewer for new structure"""
self.reset()
if not change["new"].attributes.species:
return
self._current_view = self.viewer.add_structure(
nglview.ASEStructure(change["new"].convert("ase")))
self.viewer.add_representation("ball+stick", aspectRatio=4)
self.viewer.add_representation("unitcell")
def refresh_view(self):
viewer = self.viewer
# Note: viewer.clear() only removes the 1st component
# pylint: disable=protected-access
for comp_id in viewer._ngl_component_ids:
viewer.remove_component(comp_id)
viewer.add_component(nglview.ASEStructure(
self.structure_ase)) # adds ball+stick
viewer.add_unitcell()
def _update_structure_viewer(self, change):
"""Update the view if displayed_structure trait was modified."""
with self.hold_trait_notifications():
for comp_id in self._viewer._ngl_component_ids: # pylint: disable=protected-access
self._viewer.remove_component(comp_id)
self.selection = list()
if change['new'] is not None:
self._viewer.add_component(nglview.ASEStructure(change['new']))
self._viewer.clear()
self._viewer.add_ball_and_stick(aspectRatio=4) # pylint: disable=no-member
self._viewer.add_unitcell() # pylint: disable=no-member
def _update_structure_viewer(self, change):
"""Update the view if displayed_structure trait was modified."""
with self.hold_trait_notifications():
for (comp_id) in self._viewer._ngl_component_ids: # pylint: disable=protected-access
self._viewer.remove_component(comp_id)
self.selection = list()
if change["new"] is not None:
self._viewer.add_component(nglview.ASEStructure(change["new"]))
self._viewer.clear()
self._viewer.stage.set_parameters(clipDist=0)
self._viewer.add_representation("unitcell", diffuse="#df0587")
self._viewer.add_representation("ball+stick", aspectRatio=3.5)
def visualize_extra(self, vis_list):
"""
Two visualization options supported:
int - defines the atom index to highlight
xyz - defines a point in space
"""
if not hasattr(self.viewer, "component_0"):
return
self.reset()
if hasattr(self.viewer, "component_2"):
self.viewer.component_2.clear_representations()
self.viewer.component_2.remove_unitcell()
cid = self.viewer.component_2.id
self.viewer.remove_component(cid)
if len(vis_list) > 0:
vis_atoms = [x for x in vis_list if isinstance(x, int)]
vis_points = [x for x in vis_list if not isinstance(x, int)]
if len(vis_atoms) != 0:
self.highlight_atoms(vis_atoms,
color='red',
size=0.2,
opacity=0.6)
if len(vis_points) != 0:
fake_atoms = Atoms('Xe' * len(vis_points),
positions=vis_points)
self.viewer.add_component(nglview.ASEStructure(fake_atoms),
default_representation=False)
self.viewer.component_2.add_ball_and_stick(color='blue',
aspectRatio=3.1,
opacity=0.7)
def setup(self, atoms, details=None):
self.atoms = atoms
self.details = details
# delete all old components
while hasattr(self.viewer, "component_0"):
self.viewer.component_0.clear_representations()
cid = self.viewer.component_0.id
self.viewer.remove_component(cid)
if details is None:
self.mol_inds = [] #list(np.arange(0, len(atoms)))
if atoms is None:
return
else:
self.rest_inds = list(np.arange(
0, len(atoms))) # [] #default all big spheres
else:
if details['system_type'] == 'Bulk':
self.mol_inds = []
self.rest_inds = list(np.arange(0, len(atoms)))
elif details['system_type'] == 'Wire':
self.mol_inds = list(np.arange(0, len(atoms)))
self.rest_inds = []
else:
self.mol_inds = [
item for sublist in self.details['all_molecules']
for item in sublist
]
self.rest_inds = self.details['slabatoms'] + self.details[
'bottom_H'] + self.details['adatoms'] + self.details[
'unclassified']
self._gen_translation_indexes()
#print('in view mol ',self.mol_inds)
#print('in view rest ',self.rest_inds)
if len(self.mol_inds) > 0:
self.molecules_ase = self.atoms[self.mol_inds]
else:
self.molecules_ase = Atoms()
if len(self.rest_inds) > 0:
self.rest_ase = self.atoms[self.rest_inds]
else:
self.rest_ase = Atoms()
# component 0: Molecule
self.viewer.add_component(nglview.ASEStructure(self.molecules_ase),
default_representation=False)
self.viewer.add_ball_and_stick(aspectRatio=MOL_ASPECT,
opacity=1.0,
component=0)
# component 1: Everything else
self.viewer.add_component(nglview.ASEStructure(self.rest_ase),
default_representation=False)
self.viewer.add_ball_and_stick(aspectRatio=REST_ASPECT,
opacity=1.0,
component=1)
self.viewer.add_unitcell()
self.viewer.center()
#viewer.component_0.add_ball_and_stick(aspectRatio=10.0, opacity=1.0)
#for an in set(atoms.numbers):
# vdwr=vdw_radii[an]
# sel=[s[0] for s in np.argwhere(atoms.numbers==an)]
# viewer.add_ball_and_stick(selection=sel,aspectRatio=6.2*vdwr, opacity=1.0,component=0)
# Orient camera to look from positive z
cell_z = self.atoms.cell[2, 2]
com = self.atoms.get_center_of_mass()
def_orientation = self.viewer._camera_orientation
top_z_orientation = [
1.0, 0.0, 0.0, 0, 0.0, 1.0, 0.0, 0, 0.0, 0.0,
-np.max([cell_z, 30.0]), 0, -com[0], -com[1], -com[2], 1
]
self.viewer._set_camera_orientation(top_z_orientation)
self.viewer.observe(self._on_atom_click, names='picked')