Render Cube File

This is a Python script to render Gaussian cube files using the free, open-source 3D creation suite Blender.

A Gaussian cube file type described discrete volumetric data as well as atom positions. The file consists of a header which includes the atom information and the size of the volumetric data, which is followed by the volumetric data, one scalar per voxel element. It is a common output of multiple quantum chemistry programs. The cube files in this repository have been created via a time-dependent density functional theory calculation using Octopus Code.

The script works by providing a path to a cube file and an .json input file:

{
  "filterIterations": 0,
  "isosurfaceValue": 0.001,
  "deleteOBJFile": true,
  "pathToOBJFile": "/tmp/tmp.obj",
  "focalLenght": 70,
  "cameraLocation": "-x",
  "imagePath" : "README_files/cubeFileRender.png"
}

There are multiple ways to run this script, which are described below.

Run via python:

Install a virtual environment with python3.11 via:

make install

from renderCubeFile import RenderCubeFile

r = RenderCubeFile(pathToCubeFile='README_files/test.cube',pathToInputFile='README_files/testInputFile.json')
r.renderScene()

Jupyter environment detected. Enabling Open3D WebVisualizer.
[Open3D INFO] WebRTC GUI backend enabled.
[Open3D INFO] WebRTCWindowSystem: HTTP handshake server disabled.


2024-05-30 13:28:12,053 - INFO - Finished with reading input file README_files/testInputFile.json


2024-05-30 13:28:12,069 - INFO - Finished reading cube file README_files/test.cube


OBJ import of 'tmp.obj' took 1.61 ms
Fra:1 Mem:44.37M (Peak 45.43M) | Time:00:00.15 | Syncing New Light
Fra:1 Mem:44.37M (Peak 45.43M) | Time:00:00.15 | Syncing Camera
Fra:1 Mem:44.38M (Peak 45.43M) | Time:00:00.15 | Syncing tmp
Fra:1 Mem:44.93M (Peak 45.43M) | Time:00:00.17 | Syncing Sphere
Fra:1 Mem:45.06M (Peak 45.43M) | Time:00:00.18 | Syncing Sphere.001
Fra:1 Mem:45.16M (Peak 45.43M) | Time:00:00.19 | Syncing Sphere.002
Fra:1 Mem:45.25M (Peak 45.43M) | Time:00:00.19 | Syncing Cylinder
Fra:1 Mem:45.27M (Peak 45.43M) | Time:00:00.19 | Syncing Cylinder.001
Fra:1 Mem:45.27M (Peak 45.43M) | Time:00:00.19 | Rendering 1 / 65 samples
Fra:1 Mem:44.82M (Peak 45.43M) | Time:00:00.24 | Rendering 26 / 64 samples
Fra:1 Mem:44.82M (Peak 45.43M) | Time:00:00.24 | Rendering 51 / 64 samples
Fra:1 Mem:44.82M (Peak 45.43M) | Time:00:00.25 | Rendering 64 / 64 samples


Saved: 'README_files/cubeFileRender.png'
Time: 00:01.75 (Saving: 00:00.38)

If you have multiple cube files from a real-time time-dependent density functional theory calculation, you can make an simple animation form multiple cube files:

from renderCubeFile import RenderCubeFile
from os import walk, path
# get all cube files from the tddft simulation
pathToCubeFiles = []
for (root, _, filenames) in walk('README_files/collision/'):
    for filename in filenames:
        if filename.split('.')[1] == 'cube':
            pathToCubeFiles.append(path.join(root, filename))
pathToCubeFiles.sort()

# render the cube files to pngs
for cubeFile in pathToCubeFiles:
    print (cubeFile)
    r = RenderCubeFile(cubeFile, 'README_files/testInputFile.json')
    r.renderScene(f'{cubeFile.split(".")[0]}.png')

Render the .png files to a animation:

from os import walk, path
import contextlib
from PIL import Image

# get all pngs files
pngs = []
for (root, _, filenames) in walk('README_files/collision/'):
    for filename in filenames:
        if filename.split('.')[1] == 'png':
            pngs.append(path.join(root, filename))
pngs.sort()

# Render the pngs to an animation
with contextlib.ExitStack() as stack:
    imgs = (stack.enter_context(Image.open(f)) for f in pngs)
    img = next(imgs)
    img.save(fp='README_files/collision.gif', format='GIF', append_images=imgs,
             save_all=True, duration=8, loop=0)

Run via Blender:

You can also run the script via the command line using a blender installation downloaded here. This way, the internal Python installation Blender ships with is used, and the required modules are installed there.

<pathToBlenderExe> --background --python renderCubeFile.py  -- --cubeFile <pathToCubeFile> --inputFile <pathToInputFile>