Chimie Théorique » QMX

"""

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

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

        }

    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)

    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 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 {' # Use filter 0.7

          '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('\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))

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)