ase traj to pov input

traj2pov.py

import os
import sys
from glob import glob
from ase.io import read, write
from ase import Atoms
import numpy as np
from ase.utils import natural_cutoffs
from ase.build import molecule
import matplotlib.pyplot as plt


def attachbonds(atoms):
    bondatoms = []
    symbols = atoms.get_chemical_symbols()
    cutoffs = np.array(natural_cutoffs(atoms)) + 0.15
    num = len(symbols)
    for i in range(num):
        for j in range(i):
            ni = cutoffs[i]
            nj = cutoffs[j]
            disij = atoms.get_distance(i, j)
            if ni + nj > disij:
                bondatoms.append((i, j))
    return bondatoms


rot = '-90x'  # found using ag: 'view -> rotate'
kwargs = {
    'rotation'      : rot, # text string with rotation (default='' )
    "radii": .85,  # float, or a list with one float per atom
    'colors': None,  # List: one (r, g, b) tuple per atom
    'show_unit_cell': 2,   # 0, 1, or 2 to not show, show, and show all of cell
}

kwargs.update({
    'run_povray': True,  # Run povray or just write .pov + .ini files
    'display': False,  # Display while rendering
    'pause': True,  # Pause when done rendering (only if display)
    'transparent': False,  # Transparent background
    'canvas_width': None,  # Width of canvas in pixels
    'canvas_height': None,  # Height of canvas in pixels
    'camera_dist': 20.,  # Distance from camera to front atom
    'image_plane': None,  # Distance from front atom to image plane
    'camera_type': 'perspective',  # perspective, ultra_wide_angle
    'point_lights': [],             # [[loc1, color1], [loc2, color2],...]
    'area_light': [(2., 3., 40.),  # location
                   'White',       # color
                   .7, .7, 3, 3],  # width, height, Nlamps_x, Nlamps_y
    'background': 'White',        # color
    'textures': None,  # Length of atoms list of texture names
    'celllinewidth': 0.03,  # Radius of the cylinders representing the cell})


tj = sys.argv[1]   # traj file
atoms = read(tj)
bondatoms = attachbonds(atoms)
cell = atoms.get_cell()
ads = 'test.pov'
kwargs.update(
    {
        'bondatoms': bondatoms,
        'bondlinewidth': 0.2,
    })

write(ads, atoms, **kwargs)