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
- Xing Wang xingwang1991@gmail.com
- Python
- Blender
- ASE
- Skimage
Clone this repo. Add it to your PYTHONPATH. On windows, you can edit the system environment variables.
export PYTHONPATH=~/apps/blase:$PYTHONPATH
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.
-
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
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)
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)
A example of molecules adsorbed on nanoparticle.
Cut stepped surface from ceria oxide
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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)
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)
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)
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)
#!/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)
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.outThe performance is show below. The speed scales well with number of cpu.
| Number of CPU | Times (s) |
|---|---|
| 1 | 512 |
| 12 | 24 |
| 36 | 15 |
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)- cut boundary for isosurface
- add panel to manipulate the atoms interactively
- add animation