File size: 4,055 Bytes
b78a213 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 | """
Script to generate gifs from traj
Note:
This is just a quick way to generate gifs and visalizations from traj, there are many parameters and settings in the code that people can vary to make visualizations better. We have chosen these settings as this seem to work fine for most of our systems.
Requirements:
povray
ffmpeg
ase==3.21
"""
import argparse
import copy
import multiprocessing as mp
import os
import ase.io
import numpy as np
from ase.data import covalent_radii
from ase.io.pov import get_bondpairs
def pov_from_atoms(mp_args):
atoms, idx, out_path = mp_args
# how many extra repeats to generate on either side to look infinite
extra_cells = 2
# try and guess which atoms are adsorbates since the tags aren't correct after running in vasp
# ideally this would be fixed by getting the right adsorbate atoms from the initial configurations
atoms_organic = np.array(
[atom.symbol in set(["C", "H", "O", "N"]) for atom in atoms]
)
# get the bare surface (note: this will not behave correctly for nitrides/hydrides/carbides/etc)
atoms_surface = atoms[~atoms_organic].copy()
# replicate the bare surface
atoms_surface = atoms_surface.repeat(
(extra_cells * 2 + 1, extra_cells * 2 + 1, 1)
)
# make an image of the adsorbate in the center of the slab
atoms_adsorbate = atoms[atoms_organic]
atoms_adsorbate.positions += extra_cells * (
atoms.cell[0, :] + atoms.cell[1, :]
)
# add the adsorbate to the replicated surface, then center the positions on the adsorbate
num_surface_atoms = len(atoms_surface)
atoms_surface += atoms_adsorbate
atoms_surface.positions -= atoms_adsorbate.positions.mean(axis=0)
# only include bonds for the adsorbate atoms
bondpairs = get_bondpairs(atoms_surface)
bondpairs = [
bond
for bond in bondpairs
if bond[0] >= num_surface_atoms and bond[1] >= num_surface_atoms
]
# write the image with povray
bbox = (-6.4, -4, 6.4, 4) # clip to a small region around the adsorbate
os.chdir(f"{out_path}")
renderer = ase.io.write(
"snapshot_%04i.pov" % idx,
atoms_surface,
povray_settings={
"celllinewidth": 0,
"canvas_height": 300,
"textures": ["intermediate"] * len(atoms_surface),
"bondatoms": bondpairs,
},
bbox=bbox,
rotation="-40x",
radii=covalent_radii[atoms_surface.numbers],
)
renderer.render()
print(f"image {idx} completed!")
def parallelize_generation(traj_path, out_path, n_procs):
# make the covalent radii for O/C/N a little smaller to make bonds visible
covalent_radii[6] = covalent_radii[6] * 0.7
covalent_radii[7] = covalent_radii[7] * 0.7
covalent_radii[8] = covalent_radii[8] * 0.7
# name of the folder containing images and gif
file_name = os.path.basename(traj_path).split(".")[0]
out_path = os.path.join(out_path, file_name)
out_path = os.path.abspath(out_path)
os.makedirs(out_path, exist_ok=True)
atoms_list = ase.io.read(traj_path, ":")
# parallelizing image generation
mp_args_list = [
(atoms, idx, out_path) for idx, atoms in enumerate(atoms_list)
]
pool = mp.Pool(processes=n_procs)
pool.map(pov_from_atoms, mp_args_list)
# creating gif
os.system(
f"ffmpeg -pattern_type glob -i '{out_path}/*.png' {out_path}/{file_name}.gif"
)
def get_parser():
parser = argparse.ArgumentParser()
parser.add_argument("--traj-path", required=True, help="Path to traj file")
parser.add_argument(
"--out-path",
required=True,
help="Directory to save generated images and gif",
)
parser.add_argument(
"--num-workers",
type=int,
default=1,
help="Number of processes to be used",
)
return parser
if __name__ == "__main__":
parser = get_parser()
args = parser.parse_args()
parallelize_generation(args.traj_path, args.out_path, args.num_workers)
|