Blase

Python module for drawing and rendering ASE (Atomic Simulation Environment) atoms and molecules objects using blender.

For the introduction of ASE , please visit https://wiki.fysik.dtu.dk/ase/index.html

• Support all file-formats using by ASE, including cif, xyz, cube, pdb, json, VASP-out and so on.
• Ball & stick
• Polyhedral
• Meta ball
• GPU rendering and HPC jobs

Deploying

wget https://www.blender.org/download/Blender2.91/blender-2.91.2-linux64.tar.xz/

tar -xf blender-2.91.2-linux64.tar.xz

mv ./blender-2.91.2-linux64/2.91/python ./blender-2.91.2-linux64/2.91/python_bak

conda create -n py37 python=3.7.7 -y
conda activate py37

pip install ase spglib
conda install -c conda-forge scikit-image numpy scipy matplotlib seaborn jupyter ipython scikit-learn tqdm jupyter_contrib_nbextensions -y

cd ~/git/test/blase
export BLASE_PATH=/home/felix/git/test/blase
export BLENDER_COMMAND="/home/felix/source/blender-2.91.2-linux64/blender"

python examples/c2h6so.py

Notebook installation of blender

git clone https://github.com/felixmusil/blender_notebook.git
cd blender_notebook
pip install -e .
blender_notebook install --blender-exec="/home/felix/source/blender-2.91.2-linux64/blender" --blender-external-python

Author

• Xing Wang [email protected]

Dependencies

• Python
• Blender
• ASE
• Skimage

Installation

Clone this repo. Add it to your PYTHONPATH and PATH. On windows, you can edit the system environment variables.

export PYTHONPATH=~/apps/blase:$PYTHONPATH
export PATH=~/apps/blase/bin:$PATH
export BLASE_PATH="~/apps/blase/"

You can specify the location of blender by sh export BLENDER_COMMAND="~/bin/blender" , otherwise blase will use the default blender command in the system.

How to use

• Run from command line directly, supporting functions from build inside blase. blase_gui h2o.xyz

• Run from python code directly, supporting functions from build inside blase. python examples/c2h6so.py

• Run from blender, supporting full functions from blender. blender -b -P examples/b-c2h6so.py

Examples

Draw molecule with bonds

A example of C₂H₆SO molecule. See examples/c2h6so.py

from ase.build import molecule
from blase.tools import get_bondpairs, write_blender

atoms = molecule('C2H6SO')
atoms.center(vacuum  = 1.0)

camera_loc = atoms[3].position + [30, 0, 10]

kwargs = {'show_unit_cell': 0,
          'engine': 'CYCLES', #'BLENDER_EEVEE' #'BLENDER_WORKBENCH'
          'camera_loc': camera_loc,  # distance from camera to front atom
          'camera_type': 'PERSP',  #  ['PERSP', 'ORTHO', 'PANO']
          'camera_lens': 100,  #
          'camera_target': atoms[3].position, #
          'ortho_scale': None, #
          'radii': 0.6,
          'bonds': 'all',
        'functions': [['add_light', {'loc': [10, 0, 10], 'light_type': 'POINT'}],
                      ['draw_plane', {'size': 100, 'loc': (0, 0, -0.0), 'color': (0, 0, 0, 1.0), 'material_style': 'mirror'}]],
          'outfile': 'c2h6so-cycles'}
write_blender(atoms, **kwargs)

PDB file

A example to read atoms from exist PDB file.

from ase.build import molecule
from ase.io import read
from blase.tools import get_bondpairs, write_blender

atoms = read('ATP.pdb')
atoms.positions[:, 2] -= min(atoms.positions[:, 2]) - 2
camera_loc = atoms[3].position + [50, 0, 20]

kwargs = {'show_unit_cell': 0,
          'engine': 'CYCLES', #'BLENDER_EEVEE' #'BLENDER_WORKBENCH'
          'camera_loc': camera_loc,  # distance from camera to front atom
          'camera_type': 'PERSP',  #  ['PERSP', 'ORTHO', 'PANO']
          'camera_lens': 100,  #
          'camera_target': atoms[3].position, #
          'ortho_scale': None, #
          'radii': 0.6,
          'bonds': 'all',
          'functions': [['draw_plane', {'size': 1000, 'loc': (0, 0, -1.0)}]],
          # 'resolution_x': 2000,
          'outfile': 'atp-cycles'}
write_blender(atoms, **kwargs)

Draw molecule on nanoparticle surface

A example of molecules adsorbed on nanoparticle.

Draw oxide monolayer on metal (111) surface

Animation

Cut stepped surface from ceria oxide

![]

Draw isosurface for electron density

Read cube files, then draw atoms and isosurface. Here is a example of isosurface of Pt/Ti₂O₃ interface.

from ase.io.cube import read_cube_data
from blase.tools import write_blender

data, atoms = read_cube_data('test.cube')
kwargs = {'show_unit_cell': 1,
          'radii': 0.4,
          'functions': [['draw_isosurface', {'density_grid': data, 'cut_off': -0.002}],
                        ['draw_isosurface', {'density_grid': data, 'cut_off': 0.002, 'color': (0.0, 0.0, 1.0)}]],
          'rotations': [[90, '-x'], [30, 'y']],
          'outfile': 'testcube'}

write_blender(atoms, display=False, **kwargs)

Polyhedra

A example to draw polyhedra.

from ase.io import read, write
from blase.tools import write_blender

atoms = read('tio2.cif')
kwargs = {'show_unit_cell': 1,
          'engine': 'BLENDER_WORKBENCH',
          'radii': 0.6,
          'bond_cutoff': 1.0,
          'search_pbc': {'search_dict': {'Ti': ['O']}},
          'polyhedra_dict': {'Ti': ['O']},
          'outfile': 'figs/test-search-bonds',
          }
write_blender(atoms, **kwargs)

Search molecule bonds out of unit cell

from ase.io import read, write
from blase.tools import write_blender, get_polyhedra_kinds, get_bondpairs
atoms = read('anthraquinone.cif')
kwargs = {'show_unit_cell': 1,
          'engine': 'BLENDER_WORKBENCH', #'BLENDER_EEVEE' #'BLENDER_WORKBENCH', CYCLES
          'radii': 0.6,
          'bond_cutoff': 1.0,
          'search_pbc': {'molecule_list':[['C', 'C'], ['C', 'O']]},
          'outfile': 'figs/test-search-molecule',
          }
write_blender(atoms, **kwargs)

Cut surface

A example to cut (110) surface, with distance from origin to be d.

from ase.build import bulk
from blase.tools import write_blender

atoms = bulk('Pt', cubic = True)
atoms = atoms*[6, 6, 6]

kwargs = {'show_unit_cell': 1,
          'engine': 'BLENDER_WORKBENCH', #'BLENDER_EEVEE' #'BLENDER_WORKBENCH', CYCLES
          'radii': 1.0,
          # 'display': True,
          'boundary_list': [{'d': 10.0, 'index': [1, 1, 0]}],
          'outfile': 'figs/test-boundary',
          }
write_blender(atoms, **kwargs)

Set different kind of atoms for the same element

#!/usr/bin/env python
from ase.build import surface, fcc111
from ase.visualize import view
from blase.tools import get_bondpairs, write_blender
#============================================================
atoms = fcc111('Pt', (7, 7, 3), vacuum=0.0)
kinds = []
kind_props = {
'Pt_0': {'color': [208/255.0, 208/255.0, 224/255.0]},
'Pt_1': {'color': [225/255.0, 128/255.0, 0/255.0]},
'Pt_2': {'color': [0/255.0, 191/255.0, 56/255.0]},
}
for i in range(len(atoms)):
     ind = int((atoms[i].x/5))
     kind = atoms[i].symbol + '_{0}'.format(ind)
     kinds.append(kind)
atoms.kinds = kinds

camera_loc = atoms.get_center_of_mass() + [0, -60, 30]

kwargs = {'show_unit_cell': 0,
          'camera_loc': camera_loc,  # distance from camera to front atom
          'camera_type': 'PERSP',  #  ['PERSP', 'ORTHO', 'PANO']
          'camera_lens': 100,  #
          'camera_target': atoms.get_center_of_mass(), #
          'ortho_scale': None, #
          'kind_props': kind_props,
          'resolution_x': 1000,
          'outfile': 'test-kinds',
          }
write_blender(atoms, **kwargs)

Running on HPC using multi-process

Set up a bash file, and run the python script directly.

#!/bin/bash -l
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=36
#========================================

python h2o.py > blase.out

The performance is show below. The speed scales well with number of cpu.

Number of CPU	Times (s)
1	512
12	24
36	15

Set materials type for atoms

Select materials type from ['blase', 'glass', 'ceramic', 'plastic'].

bobj.draw_atoms(material_type = 'blase')

Or set your own materials by setting the bsdf_inputs dict.

bsdf_inputs = {'Metallic': 1.0, 'Specular': 1.0, 'Roughness': 0.01, }
bobj.draw_atoms(bsdf_inputs = bsdf_inputs)

To do

• cut boundary for isosurface
• add panel to manipulate the atoms interactively
• add animation