#thr_a2 = thr_a * thr_a
thr_b2 = thr_b * thr_b
dr2 = ((r_array[i] - r_array[j])**2).sum()
# print(dr2)
if dr2 < thr_b2:
bonds.append((i, j))
return np.array(bonds)
# END_PATCH ---
Si = Molecule([Atom('Si', [0.0, 0.0, 0.0])])
la = 0.5431
s = crystal([[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]], # Fractional Positions
[Si, Si], # Molecules
225, # Space Group
cellpar = [la,la,la, 90, 90, 90], # unit cell parameters
repetitions = [2, 2, 2]) # unit cell repetitions in each direction
bonds = guess_bonds(s.r_array, s.type_array, threshold=0.02)
#s.bonds = [[0,1], [1, 2]]
v = QtViewer()
v.add_renderer(BallAndStickRenderer, s.r_array, s.type_array,
bonds,shading='phong')
v.run()
# print(dr2)
if dr2 < thr_b2:
bonds.append((i, j))
return np.array(bonds)
# END_PATCH ---
Si = Molecule([Atom('Si', [0.0, 0.0, 0.0])])
la = 0.5431
s = crystal(
[[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]], # Fractional Positions
[Si, Si], # Molecules
225, # Space Group
cellpar=[la, la, la, 90, 90, 90], # unit cell parameters
repetitions=[2, 2, 2]) # unit cell repetitions in each direction
bonds = guess_bonds(s.r_array, s.type_array, threshold=0.02)
#s.bonds = [[0,1], [1, 2]]
v = QtViewer()
v.add_renderer(BallAndStickRenderer,
s.r_array,
s.type_array,
bonds,
shading='phong')
v.run()
import numpy as np
v1 = np.array([1.0, 0.0, -1.0/np.sqrt(2)])
v2 = np.array([-1.0, 0.0, -1.0/np.sqrt(2)])
v3 = np.array([0.0, 1.0, 1.0/np.sqrt(2)])
v4 = np.array([0.0, -1.0, 1.0/np.sqrt(2)])
from chemlab.graphics.qt import QtViewer
from chemlab.graphics.renderers import PointRenderer
from chemlab.graphics.colors import black, green, blue, red
colors = [black, green, blue, red]
v = QtViewer()
v.add_renderer(PointRenderer, np.array([v1, v2, v3, v4]), colors)
from chemlab.graphics.renderers import TriangleRenderer
vertices = np.array([
v1, v4, v3,
v3, v4, v2,
v1, v3, v2,
v2, v4, v1
])
colors = [green] * 12
# Normals: cross-product for each face
n1 = -np.cross(v4 - v1, v3 - v1)
n1 /= np.linalg.norm(n1)
n2 = -np.cross(v4 - v3, v2 - v3)
n2 /= np.linalg.norm(n2)
from chemlab.db import CirDB
from chemlab.graphics.qt import QtViewer
from chemlab.graphics.renderers import AtomRenderer
from chemlab.graphics.postprocessing import FXAAEffect, SSAOEffect
# A series of compounds to display
compounds = ["methane", "ethane", "propane", "butane"]
db = CirDB()
# Prepare the viewer
v = QtViewer()
v.widget.initializeGL()
v.add_post_processing(SSAOEffect, kernel_size=128, kernel_radius=1.0)
v.add_post_processing(FXAAEffect)
for compound in compounds:
mol = db.get("molecule", compound)
rend = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array)
v.widget.camera.autozoom(mol.r_array)
# Give some extra zoom
v.widget.camera.mouse_zoom(1.0)
v.widget.toimage(300, 300).save(compound + '.png')
# Cleanup
v.remove_renderer(rend)
