/usr/share/pyshared/ase/io/eps.py is in python-ase 3.6.0.2515-1.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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from math import sqrt
import numpy as np
from ase.utils import rotate
from ase.data import covalent_radii
from ase.data.colors import jmol_colors
class EPS:
def __init__(self, atoms,
rotation='', show_unit_cell=False, radii=None,
bbox=None, colors=None, scale=20):
self.numbers = atoms.get_atomic_numbers()
self.colors = colors
if colors is None:
self.colors = jmol_colors[self.numbers]
if radii is None:
radii = covalent_radii[self.numbers]
elif type(radii) is float:
radii = covalent_radii[self.numbers] * radii
else:
radii = np.array(radii)
natoms = len(atoms)
if isinstance(rotation, str):
rotation = rotate(rotation)
A = atoms.get_cell()
if show_unit_cell > 0:
L, T, D = self.cell_to_lines(A)
C = np.empty((2, 2, 2, 3))
for c1 in range(2):
for c2 in range(2):
for c3 in range(2):
C[c1, c2, c3] = np.dot([c1, c2, c3], A)
C.shape = (8, 3)
C = np.dot(C, rotation) # Unit cell vertices
else:
L = np.empty((0, 3))
T = None
D = None
C = None
nlines = len(L)
X = np.empty((natoms + nlines, 3))
R = atoms.get_positions()
X[:natoms] = R
X[natoms:] = L
r2 = radii**2
for n in range(nlines):
d = D[T[n]]
if ((((R - L[n] - d)**2).sum(1) < r2) &
(((R - L[n] + d)**2).sum(1) < r2)).any():
T[n] = -1
X = np.dot(X, rotation)
R = X[:natoms]
if bbox is None:
X1 = (R - radii[:, None]).min(0)
X2 = (R + radii[:, None]).max(0)
if show_unit_cell == 2:
X1 = np.minimum(X1, C.min(0))
X2 = np.maximum(X2, C.max(0))
M = (X1 + X2) / 2
S = 1.05 * (X2 - X1)
w = scale * S[0]
if w > 500:
w = 500
scale = w / S[0]
h = scale * S[1]
offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])
else:
w = (bbox[2] - bbox[0]) * scale
h = (bbox[3] - bbox[1]) * scale
offset = np.array([bbox[0], bbox[1], 0]) * scale
self.w = w
self.h = h
X *= scale
X -= offset
if nlines > 0:
D = np.dot(D, rotation)[:, :2] * scale
if C is not None:
C *= scale
C -= offset
A = np.dot(A, rotation)
A *= scale
self.A = A
self.X = X
self.D = D
self.T = T
self.C = C
self.natoms = natoms
self.d = 2 * scale * radii
def cell_to_lines(self, A):
nlines = 0
nn = []
for c in range(3):
d = sqrt((A[c]**2).sum())
n = max(2, int(d / 0.3))
nn.append(n)
nlines += 4 * n
X = np.empty((nlines, 3))
T = np.empty(nlines, int)
D = np.zeros((3, 3))
n1 = 0
for c in range(3):
n = nn[c]
dd = A[c] / (4 * n - 2)
D[c] = dd
P = np.arange(1, 4 * n + 1, 4)[:, None] * dd
T[n1:] = c
for i, j in [(0, 0), (0, 1), (1, 0), (1, 1)]:
n2 = n1 + n
X[n1:n2] = P + i * A[(c + 1) % 3] + j * A[(c + 2) % 3]
n1 = n2
return X, T, D
def write(self, filename):
self.filename = filename
self.write_header()
self.write_body()
self.write_trailer()
def write_header(self):
import matplotlib
if matplotlib.__version__ <= '0.8':
raise RuntimeError('Your version of matplotlib (%s) is too old' %
matplotlib.__version__)
from matplotlib.backends.backend_ps import RendererPS, \
GraphicsContextPS, psDefs
self.fd = open(self.filename, 'w')
self.fd.write('%!PS-Adobe-3.0 EPSF-3.0\n')
self.fd.write('%%Creator: G2\n')
self.fd.write('%%CreationDate: %s\n' % time.ctime(time.time()))
self.fd.write('%%Orientation: portrait\n')
bbox = (0, 0, self.w, self.h)
self.fd.write('%%%%BoundingBox: %d %d %d %d\n' % bbox)
self.fd.write('%%EndComments\n')
Ndict = len(psDefs)
self.fd.write('%%BeginProlog\n')
self.fd.write('/mpldict %d dict def\n' % Ndict)
self.fd.write('mpldict begin\n')
for d in psDefs:
d = d.strip()
for l in d.split('\n'):
self.fd.write(l.strip() + '\n')
self.fd.write('%%EndProlog\n')
self.fd.write('mpldict begin\n')
self.fd.write('%d %d 0 0 clipbox\n' % (self.w, self.h))
self.renderer = RendererPS(self.w, self.h, self.fd)
def write_body(self):
try:
from matplotlib.path import Path
except ImportError:
Path = None
from matplotlib.patches import Circle, Polygon
else:
from matplotlib.patches import Circle, PathPatch
indices = self.X[:, 2].argsort()
for a in indices:
xy = self.X[a, :2]
if a < self.natoms:
r = self.d[a] / 2
if ((xy[1] + r > 0) and (xy[1] - r < self.h) and
(xy[0] + r > 0) and (xy[0] - r < self.w)):
circle = Circle(xy, r, facecolor=self.colors[a])
circle.draw(self.renderer)
else:
a -= self.natoms
c = self.T[a]
if c != -1:
hxy = self.D[c]
if Path is None:
line = Polygon((xy + hxy, xy - hxy))
else:
line = PathPatch(Path((xy + hxy, xy - hxy)))
line.draw(self.renderer)
def write_trailer(self):
self.fd.write('end\n')
self.fd.write('showpage\n')
self.fd.close()
def write_eps(filename, atoms, **parameters):
if isinstance(atoms, list):
assert len(atoms) == 1
atoms = atoms[0]
EPS(atoms, **parameters).write(filename)
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