"""
This module handles visualization. Mostly powered by py3Dmol
"""
[docs]
def addBox(view, vecs, viewer=None):
pts = [
([0,0,0], vecs[0,:]),
([0,0,0], vecs[1,:]),
([0,0,0], vecs[2,:]),
(vecs[0,:], vecs[0,:]+vecs[1,:]),
(vecs[0,:], vecs[0,:]+vecs[2,:]),
(vecs[1,:], vecs[0,:]+vecs[1,:]),
(vecs[1,:], vecs[2,:]+vecs[1,:]),
(vecs[2,:], vecs[0,:]+vecs[2,:]),
(vecs[2,:], vecs[1,:]+vecs[2,:]),
(vecs[0,:]+vecs[1,:], vecs[0,:]+vecs[1,:]+vecs[2,:]),
(vecs[0,:]+vecs[2,:], vecs[0,:]+vecs[1,:]+vecs[2,:]),
(vecs[1,:]+vecs[2,:], vecs[0,:]+vecs[1,:]+vecs[2,:]),
]
for i, pt in enumerate(pts):
pt1, pt2 = pt
if viewer is None:
view.addLine({"start": {"x":pt1[0], "y": pt1[1], "z": pt1[2]},
"end": {"x":pt2[0], "y": pt2[1], "z": pt2[2]}})
else:
view.addLine({"start": {"x":pt1[0], "y": pt1[1], "z": pt1[2]},
"end": {"x":pt2[0], "y": pt2[1], "z": pt2[2]}},
viewer = viewer)
# add unitcell labels
labels = {"o": [0,0,0],
"a": vecs[0,:],
"b": vecs[1,:],
"c": vecs[2,:]}
for key in labels.keys():
text, pos = key, labels[key]
if viewer is None:
view.addLabel(text, {"position": {"x": pos[0], "y": pos[1], "z": pos[2]},
"fontColor":"black",
"backgroundColor": "white",
"fontsize": 12,
"backgroundOpacity": "0.1",
})
else:
view.addLabel(text, {"position": {"x": pos[0], "y": pos[1], "z": pos[2]},
"fontColor":"black",
"backgroundColor": "white",
"fontsize": 12,
"backgroundOpacity": "0.1",
},
viewer = viewer)
[docs]
def addlines(view, orig, axes, viewer=None):
for ax in axes:
ax += orig
if viewer is None:
view.addArrow({"start": {"x":orig[0], "y": orig[1], "z":orig[2]},
"end": {"x":ax[0], "y":ax[1], "z":ax[2]}})
else:
view.addArrow({"start": {"x":orig[0], "y": orig[1], "z":orig[2]},
"end": {"x":ax[0], "y":ax[1], "z":ax[2]}},
viewer=viewer)
[docs]
def display_atomic(struc, size=(600,300), scale=0.25, radius=0.10, supercell=(1,1,1), show_wp=False):
"""
display the molecular crystals generated from pyxtal. If the animation is False,
only dump the structure to cif and let py3Dmol display it. If animation is on,
show the generation of molecules in the crystal as an animation.
Args:
size: (width, height) in tuple
scale: the size of sphere
radius: the size of stick
supercell: replicate the crystal (valid only when animation is False)
show_wp: whether or not highlight the unique wyckoff site
Returns:
py3Dmol object
"""
import py3Dmol
(width, height) = size
view = py3Dmol.view(height=height, width=width)
if struc.dim == 0:
fmt = "xyz"
else:
fmt = "cif"
txt = struc.to_file(fmt=fmt)
view.addModel(txt, fmt, {'doAssembly':True,'duplicateAssemblyAtoms':True})
view.setStyle({'sphere':{'colorscheme':'Jmol','scale':scale},
'stick':{'colorscheme':'Jmol', 'radius':radius}})
if struc.dim != 0:
view.addUnitCell()
A, B, C = supercell
view.replicateUnitCell(A,B,C)
if show_wp:
view.setStyle({'sym':2},{'sphere':{'scale':scale*1.1,'color':'blue'}})
return view.zoomTo()
[docs]
def display_molecular(struc, size=(600, 300), supercell=(1,1,1), axis=None, animation=False, interval=2000):
"""
display the molecular crystals generated from pyxtal. If the animation is False,
only dump the structure to cif and let py3Dmol display it. If animation is on,
show the generation of molecules in the crystal as an animation.
Args:
size: (width, height) in tuple
supercell: replicate the crystal (valid only when animation is False)
axis: 3-vector to reprent the rotational axis
animation: whether or not display the animation
Returns:
py3Dmol object
"""
import py3Dmol
(width, height) = size
view = py3Dmol.view(height=height, width=width)
if not animation:
cif = struc.to_file()
view.addModel(cif,'cif',{'doAssembly':True,
'duplicateAssemblyAtoms':True,
'normalizeAssembly':True})
view.setStyle({'stick':{'colorscheme':'greenCarbon'}})
view.addUnitCell()
if axis is not None:
site = struc.mol_sites[0]
for id in range(len(site.wp)):
mol = site.get_mol_object(id)
addlines(view, mol.cart_coords.mean(axis=0), [axis.copy()])
A, B, C = supercell
view.replicateUnitCell(A,B,C)
else:
cifs = ""
for i in range(len(struc.mol_sites[0].wp)):
cifs += struc.to_file(sym_num=i+1)
view.addModelsAsFrames(cifs, 'cif')
view.animate({'loop': 'forward', 'interval': interval})
view.addUnitCell()
view.setStyle({'model':0},{'stick':{'colorscheme':'greenCarbon'}})
return view.zoomTo()
[docs]
def display_molecular_site(site, id=None, size=(400, 300), axis=True, ax_id=range(3), box=False):
"""
display the Wyckoff site in the molecular crystals generated from pyxtal.
Args:
site: pyxtal.wyckoff_site.mol_site object
id: list of molecules to display. If None, display all molecules in this site
size: (width, height) in tuple
axis: boolean, whether or not display the rotational axis
axis_label: whether or not display the unitcell axis labels
Returns:
py3Dmol object
"""
import py3Dmol
(width, height) = size
view = py3Dmol.view(height=height, width=width)
if id is None:
ids = range(site.wp.multiplicity)
else:
ids = [id]
for i in ids:
mol = site.get_mol_object(i)
cell, _, center = site.molecule.get_box_coordinates(mol.cart_coords)
view.addModel(mol.to(fmt='xyz'), 'xyz')
if axis:
axes = site.molecule.get_principle_axes(mol.cart_coords)
addlines(view, mol.cart_coords.mean(axis=0), axes.T[ax_id]*5, viewer=(0,1))
if box:
center_spec = {'x':center[0], 'y':center[1], 'z': center[2]}
w_spec = {'x':cell[0,0], 'y': cell[0,1], 'z': cell[0,2]}
h_spec = {'x':cell[1,0], 'y': cell[1,1], 'z': cell[1,2]}
d_spec = {'x':cell[2,0], 'y': cell[2,1], 'z': cell[2,2]}
view.addBox({'center': center_spec,
'dimensions': {'w': w_spec, 'h': h_spec, 'd': d_spec},
'color':'magenta',
'alpha': 0.5,
})
addBox(view, site.lattice.matrix, viewer=(0,1))
view.setStyle({'stick':{'colorscheme':'greenCarbon'}})
return view.zoomTo()
[docs]
def display_molecules(molecules, size=(400,300), animation=False, center=False):
"""
display the molecules in Pymatgen object.
Args:
molecules: a list of pymatgen molecules
size: (width, height) in tuple
animation: whether or not display animation
center: highlight center or not
Returns:
py3Dmol object
"""
import py3Dmol
(width, height) = size
view = py3Dmol.view(height=height, width=width)
mol_strs = ""
for mol in molecules:
mol_strs += mol.to(fmt='xyz') + '\n'
if animation:
view.addModelsasFrames(mol_strs, 'xyz')
view.animate({'loop': 'forward'})
else:
view.addModels(mol_strs, 'xyz')
view.setStyle({'stick':{'colorscheme':'greenCarbon'}})
return view.zoomTo()
[docs]
def display_molecule(molecule, center, cell, size=(400,300)):
"""
display the molecules in Pymatgen object.
Args:
mol: pymatgen molecule
center: molecular
size: (width, height) in tuple
Returns:
py3Dmol object
"""
import py3Dmol
(width, height) = size
view = py3Dmol.view(height=height, width=width)
mol_strs = ""
mol_strs += molecule.to(fmt='xyz') + '\n'
view.addModels(mol_strs, 'xyz')
center_spec = {'x':center[0], 'y':center[1], 'z': center[2]}
w_spec = {'x':cell[0,0], 'y': cell[0,1], 'z': cell[0,2]}
h_spec = {'x':cell[1,0], 'y': cell[1,1], 'z': cell[1,2]}
d_spec = {'x':cell[2,0], 'y': cell[2,1], 'z': cell[2,2]}
view.addBox({'center': center_spec,
'dimensions': {'w': w_spec, 'h': h_spec, 'd': d_spec},
'color':'magenta',
'opacity': 0.4,
#'alpha': 0.6,
})
view.setStyle({'stick':{'colorscheme':'greenCarbon'}})
return view.zoomTo()
[docs]
def display_mol_crystals(strucs, size=(600, 300), supercell=(1,1,1), axis=None, animation='slider', interval=2000):
"""
display the molecular crystals generated from pyxtal.
two modes of animations are supported: slider or movie
Args:
size: (width, height) in tuple
supercell: replicate the crystal (valid only when animation is False)
animation: slider or movie
Returns:
py3Dmol object
"""
import py3Dmol
(width, height) = size
view = py3Dmol.view(height=height, width=width)
if animation=='slider':
from ipywidgets import interact, IntSlider
def conf_viewer(idx):
return strucs[idx].show(size=size, supercell=supercell, axis=axis)
interact(conf_viewer, idx=IntSlider(min=0, max=len(strucs)-1, description='id:'))
elif animation=='movie':
cifs = ""
for struc in strucs:
cifs += struc.to_file()
view.addModelsAsFrames(cifs, 'cif')
view.animate({'loop': 'forward', 'interval': interval})
view.addUnitCell()
view.setStyle({'model':0},{'stick':{'colorscheme':'greenCarbon'}})
return view.zoomTo()
else:
raise ValueError("only movie or slider is supported")
[docs]
def display_crystals(strucs, size=(600, 300), supercell=(1,1,1), labels=None):
"""
display the molecular crystals generated from pyxtal.
two modes of animations are supported: slider or movie
Args:
size: (width, height) in tuple
supercell: replicate the crystal (valid only when animation is False)
labels: labels for each structures
Returns:
py3Dmol object
"""
import py3Dmol
from ipywidgets import interact, IntSlider
(width, height) = size
view = py3Dmol.view(height=height, width=width)
if labels is None:
l_min, l_max = 0, len(strucs)-1
else:
l_min, l_max = labels[0], labels[-1]
def conf_viewer(idx):
return strucs[idx].show(size=size, supercell=supercell)
interact(conf_viewer, idx=IntSlider(min=0, max=len(strucs)-1, description='id:'))
[docs]
def display_cluster(molecules, cell, Ps, cmap='YlGn', s_opacity=0.5, size=(400,300), style='sphere'):
import py3Dmol
import numpy as np
from matplotlib import cm, colors
cmaps = getattr(cm, cmap)(Ps/np.mean(Ps))
models = {}
view = py3Dmol.view()
mol_str = ""
mol_str += molecules[0].to(fmt='xyz') + '\n'
view.addModel(mol_str, 'xyz')
model = view.getModel()
model.setStyle({}, {"sphere": {'colorscheme':'grayCarbon',
'scale':0.7}})
center = molecules[0].center_of_mass
center_spec = {'x':center[0], 'y':center[1], 'z': center[2]}
w_spec = {'x':cell[0,0], 'y': cell[0,1], 'z': cell[0,2]}
h_spec = {'x':cell[1,0], 'y': cell[1,1], 'z': cell[1,2]}
d_spec = {'x':cell[2,0], 'y': cell[2,1], 'z': cell[2,2]}
#view.addBox({'center': center_spec,
# 'dimensions': {'w': w_spec, 'h': h_spec, 'd': d_spec},
# 'color':'magenta',
# 'alpha': 0.5,
# #'opacity': 0.1,
# })
addBox(view, cell)
for i in range(1, len(molecules)):
mol = molecules[i]
mol_strs = ""
mol_strs += mol.to(fmt='xyz') + '\n'
view.addModel(mol_strs, 'xyz')
model = view.getModel()
color = 'greenCarbon'
opacity = 0.65
if style == 'sphere':
model.setStyle({}, {"sphere": {'colorscheme':color,
'scale':0.5,
'opacity': opacity}})
else:
model.setStyle({}, {"stick": {'colorscheme':color,
'radius': 0.1,
'opacity': opacity}})
view.addSurface(py3Dmol.VDW, {'opacity': s_opacity,
'color': colors.rgb2hex(cmaps[i-1])})
return view.zoomTo({"model": list(models.values())})