/usr/share/pyshared/ase/io/pov.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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Module for povray file format support.
See http://www.povray.org/ for details on the format.
"""
import os
import numpy as np
from ase.io.eps import EPS
from ase.data import chemical_symbols
from ase.constraints import FixAtoms
def pa(array):
"""Povray array syntax"""
return '<% 6.2f, % 6.2f, % 6.2f>' % tuple(array)
def pc(array):
"""Povray color syntax"""
if type(array) == str:
return 'color ' + array
if type(array) == float:
return 'rgb <%.2f>*3' % array
if len(array) == 3:
return 'rgb <%.2f, %.2f, %.2f>' % tuple(array)
if len(array) == 4: # filter
return 'rgbf <%.2f, %.2f, %.2f, %.2f>' % tuple(array)
if len(array) == 5: # filter and transmit
return 'rgbft <%.2f, %.2f, %.2f, %.2f, %.2f>' % tuple(array)
def get_bondpairs(atoms, radius=1.1):
"""Get all pairs of bonding atoms
Return all pairs of atoms which are closer than radius times the
sum of their respective covalent radii. The pairs are returned as
tuples::
(a, b, (i1, i2, i3))
so that atoms a bonds to atom b displaced by the vector::
_ _ _
i c + i c + i c ,
1 1 2 2 3 3
where c1, c2 and c3 are the unit cell vectors and i1, i2, i3 are
integers."""
from ase.data import covalent_radii
from ase.calculators.neighborlist import NeighborList
cutoffs = radius * covalent_radii[atoms.numbers]
nl = NeighborList(cutoffs=cutoffs, self_interaction=False)
nl.update(atoms)
bondpairs = []
for a in range(len(atoms)):
indices, offsets = nl.get_neighbors(a)
bondpairs.extend([(a, a2, offset)
for a2, offset in zip(indices, offsets)])
return bondpairs
class POVRAY(EPS):
default_settings = {
# x, y is the image plane, z is *out* of the screen
'display' : True, # Display while rendering
'pause' : True, # Pause when done rendering (only if display)
'transparent' : True, # Transparent background
'canvas_width' : None, # Width of canvas in pixels
'canvas_height' : None, # Height of canvas in pixels
'camera_dist' : 50., # Distance from camera to front atom
'image_plane' : None, # Distance from front atom to image plane
'camera_type' : 'orthographic', # perspective, ultra_wide_angle
'point_lights' : [], # [[loc1, color1], [loc2, color2],...]
'area_light' : [(2., 3., 40.), # location
'White', # color
.7, .7, 3, 3], # width, height, Nlamps_x, Nlamps_y
'background' : 'White', # color
'textures' : None, # Length of atoms list of texture names
'celllinewidth' : 0.05, # Radius of the cylinders representing the cell
'bondlinewidth' : 0.10, # Radius of the cylinders representing the bonds
'bondatoms' : [], # [[atom1, atom2], ... ] pairs of bonding atoms
'exportconstraints' : False} # honour FixAtom requests and mark relevant atoms?
def __init__(self, atoms, scale=1.0, **parameters):
for k, v in self.default_settings.items():
setattr(self, k, parameters.pop(k, v))
EPS.__init__(self, atoms, scale=scale, **parameters)
constr = atoms.constraints
self.constrainatoms = []
for c in constr:
if isinstance(c,FixAtoms):
for n,i in enumerate(c.index):
if i: self.constrainatoms += [n]
def cell_to_lines(self, A):
return np.empty((0, 3)), None, None
def write(self, filename, **settings):
# Determine canvas width and height
ratio = float(self.w) / self.h
if self.canvas_width is None:
if self.canvas_height is None:
self.canvas_width = min(self.w * 15, 640)
else:
self.canvas_width = self.canvas_height * ratio
elif self.canvas_height is not None:
raise RuntimeError, "Can't set *both* width and height!"
# Distance to image plane from camera
if self.image_plane is None:
if self.camera_type == 'orthographic':
self.image_plane = 1 - self.camera_dist
else:
self.image_plane = 0
self.image_plane += self.camera_dist
# Produce the .ini file
if filename.endswith('.pov'):
ini = open(filename[:-4] + '.ini', 'w').write
else:
ini = open(filename + '.ini', 'w').write
ini('Input_File_Name=%s\n' % filename)
ini('Output_to_File=True\n')
ini('Output_File_Type=N\n')
ini('Output_Alpha=%s\n' % self.transparent)
ini('; if you adjust Height, and width, you must preserve the ratio\n')
ini('; Width / Height = %s\n' % repr(ratio))
ini('Width=%s\n' % self.canvas_width)
ini('Height=%s\n' % (self.canvas_width / ratio))
ini('Antialias=True\n')
ini('Antialias_Threshold=0.1\n')
ini('Display=%s\n' % self.display)
ini('Pause_When_Done=%s\n' % self.pause)
ini('Verbose=False\n')
del ini
# Produce the .pov file
w = open(filename, 'w').write
w('#include "colors.inc"\n')
w('#include "finish.inc"\n')
w('\n')
w('global_settings {assumed_gamma 1 max_trace_level 6}\n')
w('background {%s}\n' % pc(self.background))
w('camera {%s\n' % self.camera_type)
w(' right -%.2f*x up %.2f*y\n' % (self.w, self.h))
w(' direction %.2f*z\n' % self.image_plane)
w(' location <0,0,%.2f> look_at <0,0,0>}\n' % self.camera_dist)
for loc, rgb in self.point_lights:
w('light_source {%s %s}\n' % (pa(loc), pc(rgb)))
if self.area_light is not None:
loc, color, width, height, nx, ny = self.area_light
w('light_source {%s %s\n' % (pa(loc), pc(color)))
w(' area_light <%.2f, 0, 0>, <0, %.2f, 0>, %i, %i\n' % (
width, height, nx, ny))
w(' adaptive 1 jitter}\n')
w('\n')
w('#declare simple = finish {phong 0.7}\n')
w('#declare pale = finish {'
'ambient .5 '
'diffuse .85 '
'roughness .001 '
'specular 0.200 }\n')
w('#declare intermediate = finish {'
'ambient 0.3 '
'diffuse 0.6 '
'specular 0.10 '
'roughness 0.04 }\n')
w('#declare vmd = finish {'
'ambient .0 '
'diffuse .65 '
'phong 0.1 '
'phong_size 40. '
'specular 0.500 }\n')
w('#declare jmol = finish {'
'ambient .2 '
'diffuse .6 '
'specular 1 '
'roughness .001 '
'metallic}\n')
w('#declare ase2 = finish {'
'ambient 0.05 '
'brilliance 3 '
'diffuse 0.6 '
'metallic '
'specular 0.70 '
'roughness 0.04 '
'reflection 0.15}\n')
w('#declare ase3 = finish {'
'ambient .15 '
'brilliance 2 '
'diffuse .6 '
'metallic '
'specular 1. '
'roughness .001 '
'reflection .0}\n')
w('#declare glass = finish {'
'ambient .05 '
'diffuse .3 '
'specular 1. '
'roughness .001}\n')
w('#declare Rcell = %.3f;\n' % self.celllinewidth)
w('#declare Rbond = %.3f;\n' % self.bondlinewidth)
w('\n')
w('#macro atom(LOC, R, COL, FIN)\n')
w(' sphere{LOC, R texture{pigment{COL} finish{FIN}}}\n')
w('#end\n')
w('#macro constrain(LOC, R, COL, FIN)\n')
w('union{torus{R, Rcell rotate 45*z texture{pigment{COL} finish{FIN}}}\n')
w(' torus{R, Rcell rotate -45*z texture{pigment{COL} finish{FIN}}}\n')
w(' translate LOC}\n')
w('#end\n')
w('\n')
z0 = self.X[:, 2].max()
self.X -= (self.w / 2, self.h / 2, z0)
# Draw unit cell
if self.C is not None:
self.C -= (self.w / 2, self.h / 2, z0)
self.C.shape = (2, 2, 2, 3)
for c in range(3):
for j in ([0, 0], [1, 0], [1, 1], [0, 1]):
w('cylinder {')
for i in range(2):
j.insert(c, i)
w(pa(self.C[tuple(j)]) + ', ')
del j[c]
w('Rcell pigment {Black}}\n')
# Draw atoms
a = 0
for loc, dia, color in zip(self.X, self.d, self.colors):
tex = 'ase3'
if self.textures is not None:
tex = self.textures[a]
w('atom(%s, %.2f, %s, %s) // #%i \n' % (
pa(loc), dia / 2., pc(color), tex, a))
a += 1
# Draw atom bonds
for pair in self.bondatoms:
if len(pair) == 2:
a, b = pair
offset = (0, 0, 0)
else:
a, b, offset = pair
R = np.dot(offset, self.A)
mida = 0.5 * (self.X[a] + self.X[b] + R)
midb = 0.5 * (self.X[a] + self.X[b] - R)
if self.textures is not None:
texa = self.textures[a]
texb = self.textures[b]
else:
texa = texb = 'ase3'
w('cylinder {%s, %s, Rbond texture{pigment {%s} finish{%s}}}\n' % (
pa(self.X[a]), pa(mida), pc(self.colors[a]), texa))
w('cylinder {%s, %s, Rbond texture{pigment {%s} finish{%s}}}\n' % (
pa(self.X[b]), pa(midb), pc(self.colors[b]), texb))
# Draw constraints if requested
if self.exportconstraints:
for a in self.constrainatoms:
dia = self.d[a]
loc = self.X[a]
w('constrain(%s, %.2f, Black, %s) // #%i \n' % (
pa(loc), dia / 2., tex, a))
def write_pov(filename, atoms, run_povray=False, **parameters):
if isinstance(atoms, list):
assert len(atoms) == 1
atoms = atoms[0]
assert 'scale' not in parameters
POVRAY(atoms, **parameters).write(filename)
if run_povray:
errcode = os.system('povray %s.ini 2> /dev/null' % filename[:-4])
if errcode != 0:
raise OSError('Povray failed with error code %d' % errcode)
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