48 lines
1.7 KiB
Python
48 lines
1.7 KiB
Python
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from util.colorschemes import hex_to_rgb_float
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def set_atom_color(symbol, hexcolor):
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from ase.data import atomic_numbers
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from ase.data.colors import jmol_colors, cpk_colors
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float_color = hex_to_rgb_float(hexcolor)
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n = atomic_numbers[symbol]
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jmol_colors[n] = float_color
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cpk_colors[n] = float_color
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from scipy.spatial.distance import pdist, squareform
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import numpy as np
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def get_bondatoms(atoms):
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site_positions = [site.position for site in atoms]
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pair_distances = squareform(pdist(np.stack(site_positions)))
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vs = pair_distances
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bondatoms = []
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for i in range(vs.shape[0]):
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for j in range(i):
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if vs[i, j] < 3: # up to 3 angstrom distance show a bond TODO
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bondatoms.append((i, j))
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return bondatoms
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# returns to many
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# from ase.io.pov import get_bondpairs
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# bondatoms=get_bondpairs(lat, 5)
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TARGET_DPI = 300
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# doc: https://github.com/WMD-group/ASE-Tutorials/blob/master/povray-tools/ase_povray.py
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def get_pov_settings(size, COLORSCHEME, bondatoms=None):
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white = hex_to_rgb_float(COLORSCHEME["bg0"])
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other = hex_to_rgb_float(COLORSCHEME["fg-yellow"])
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pixels = TARGET_DPI * size[0]
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pov_settings=dict(
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transparent=True,
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display=False,
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# camera_type='orthographic',
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camera_type='perspective',
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canvas_width=pixels,
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# point_lights : [], #[(18,20,40), 'White'],[(60,20,40),'White'], # [[loc1, color1], [loc2, color2],...]
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point_lights=[[(18,20,40), white],[(60,20,40),other]], # [[loc1, color1], [loc2, color2],...]
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background=(0, 0, 0, 1.,),
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bondlinewidth=0.07,
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bondatoms=bondatoms
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)
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return pov_settings
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