def icosahedron_grid(element, lattice_constant, size):
atoms = Icosahedron(symbol=element,
noshells=size,
latticeconstant=lattice_constant)
atoms.set_pbc(True)
atoms.center(vacuum=5.)
return atoms
atoms = ase.Atoms('NH2CH3')
# Define connectivity.
atoms_bonds = [ [0,1], [0,2], [0,3], [3,4], [3,5], [3,6] ]
# Displace atoms so that they aren't on top of each other.
atoms.rattle(0.001)
# Construct VSEPR calculator.
calculator = VSEPR(atoms, atoms_bonds)
atoms.set_calculator(calculator)
atoms.center()
# Run optimization.
opt = FIRE(atoms)
opt.run()
return atoms
ligand = make_methylamine()
nanoparticle = Icosahedron(symbol='Au', noshells=4)
nanoparticle.center(20)
atoms = add_ligands(nanoparticle,
ligand,
corner_sites=True,
edge_sites=[.5],
facet_111_sites=[])
write('POSCAR_Ih', atoms)
from ase.io import write
from ase.cluster.icosahedron import Icosahedron
import matplotlib.cm as cmx
import os
system = Icosahedron('Ag', 3)
for j in range(3):
d = max(system.positions[:, j]) - min(system.positions[:, j])
system.cell[j, j] = d + 15.
system.center()
center = (system.cell[0, 0] / 2., system.cell[1, 1] / 2.,
system.cell[2, 2] / 2.)
width = max(system.positions[:, 0]) - min(system.positions[:, 0])
height = max(system.positions[:, 1]) - min(system.positions[:, 1])
xmin = min(system.positions[:, 0])
xmax = max(system.positions[:, 0])
colors = []
map = cmx.rainbow
for i, at in enumerate(system):
code = int((at.position[0] - xmin) / width * 255)
color_ = map(code)
color = (color_[0], color_[1], color_[2], 0.5)
colors.append(color)
pad = 3
xmin = center[0] - width / 2. - pad
ymin = center[1] - height / 2. - pad
xmax = center[0] + width / 2. + pad