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from pathlib import Path
import numpy as np
from ase.io import read, write
# This reads and writes XSF examples taken from the
# specification of the XSF format:
#
# http://www.xcrysden.org/doc/XSF.html
#
# See the data below
def check(name, xsf_text, check_data):
fname = '%s.xsf' % name
with open(fname, 'w') as fd:
fd.write(xsf_text)
print('Read: %s' % fname)
images = read(fname, index=':', read_data=check_data)
if check_data:
array, images = images
assert isinstance(images, list)
print(' Images: %s' % len(images))
for image in images:
print(' %s' % image)
# Now write the same system back out:
outfname = 'out.%s' % fname
if check_data:
write(outfname, images, data=array)
else:
write(outfname, images)
# ...and read it back in:
images2 = read(outfname, index=':', read_data=check_data)
if check_data:
array2, images2 = images2
# It should be the same as the original file.
assert images == images2
if check_data:
print(array)
print(array2)
assert np.abs(array - array2).max() < 1e-13
# In fact, if we write it back out again, it should be
# byte-wise identical to the other file that we just wrote.
# So do that:
outfname2 = 'doubleout.%s' % fname
if check_data:
write(outfname2, images2, data=array2)
else:
write(outfname2, images2)
assert Path(outfname).read_text() == Path(outfname2).read_text()
def test_xsf_spec():
files = {'01-comments': f1,
'02-atoms': f2,
'03-periodic': f3,
'04-forces-atoms': f4,
'05-forces-slab': f5,
'06-anim-atoms': f6,
'07-anim-crystal-fixcell': f7,
'08-anim-crystal-varcell': f8}
names = list(sorted(files.keys()))
for name in names:
check(name, files[name], check_data=False)
check('%s-ignore-datagrid' % name, files[name] + datagrid,
check_data=False)
check('%s-read-datagrid' % name, files[name] + datagrid,
check_data=True)
f1 = """
# this is a specification
# of ZnS crystal structure
CRYSTAL
# these are primitive lattice vectors (in Angstroms)
PRIMVEC
2.7100000000 2.7100000000 0.0000000000
2.7100000000 0.0000000000 2.7100000000
0.0000000000 2.7100000000 2.7100000000
# these are convetional lattice vectors (in Angstroms)
CONVVEC
5.4200000000 0.0000000000 0.0000000000
0.0000000000 5.4200000000 0.0000000000
0.0000000000 0.0000000000 5.4200000000
# these are atomic coordinates in a primitive unit cell
# (in Angstroms)
PRIMCOORD
2 1
16 0.0000000000 0.0000000000 0.0000000000
30 1.3550000000 -1.3550000000 -1.3550000000
"""
f2 = """
ATOMS
6 2.325243 -0.115261 0.031711
1 2.344577 -0.363301 1.077589
9 3.131708 -0.909527 -0.638930
9 2.736189 1.130568 -0.134093
8 1.079338 -0.265162 -0.526351
6 0.007719 -0.041269 0.244204
9 0.064656 1.154700 0.824420
9 -0.042641 -0.911850 1.255074
8 -1.071578 -0.152842 -0.539134
6 -2.310374 0.036537 0.022189
1 -2.267004 0.230694 1.077874
9 -2.890949 1.048938 -0.593940
9 -3.029540 -1.046542 -0.203665
"""
f3 = """
CRYSTAL
PRIMVEC
0.0000000 2.7100000 2.7100000
2.7100000 0.0000000 2.7100000
2.7100000 2.7100000 0.0000000
CONVVEC
5.4200000 0.0000000 0.0000000
0.0000000 5.4200000 0.0000000
0.0000000 0.0000000 5.4200000
PRIMCOORD
2 1
16 0.0000000 0.0000000 0.0000000
30 1.3550000 -1.3550000 -1.3550000
"""
f4 = """
ATOMS
8 0.00000 0.00000 0.00000 -.05164 .00000 -.03999
1 0.00000 0.00000 1.00000 .01769 .00000 .03049
1 0.96814 0.00000 -0.25038 .03395 .00000 .00949
"""
f5 = """
SLAB
PRIMVEC
5.8859828533 0.0000000000 0.0000000000
0.0000000000 5.8859828533 0.0000000000
0.0000000000 0.0000000000 1.0000000000
PRIMCOORD
11 1
6 3.674759 2.942992 -3.493103 -0.021668 0.000000 -0.057324
1 4.121990 3.816734 -4.007689 -0.000478 0.001204 0.006657
1 4.121990 2.069250 -4.007689 -0.000478 -0.001204 0.006657
6 2.211226 2.942992 -3.493103 0.021668 0.000000 -0.057324
1 1.763995 3.816734 -4.007689 0.000478 0.001204 0.006657
1 1.763995 2.069250 -4.007689 0.000478 -0.001204 0.006657
8 0.000000 0.000000 -2.719012 0.000000 0.000000 -0.050242
47 4.448147 4.449892 -1.919011 -0.022812 -0.029123 0.007553
47 4.448147 1.436093 -1.919011 -0.022812 0.029123 0.007553
47 1.437838 4.449892 -1.919011 0.022812 -0.029123 0.007553
47 1.437838 1.436093 -1.919011 0.022812 0.029123 0.007553
"""
f6 = """
ANIMSTEPS 4
ATOMS 1
8 0.0000 0.0000 0.0000 -0.0516 0.0000 -0.0399
1 0.0000 0.0000 1.0000 0.0176 0.0000 0.0304
1 0.9681 0.0000 -0.2503 0.0339 0.0000 0.0094
ATOMS 2
8 -0.1480 0.0000 -0.1146 0.0020 0.0000 0.0015
1 -0.0468 0.0000 0.9134 -0.0069 0.0000 0.0069
1 0.8726 0.0000 -0.2740 0.0049 0.0000 -0.0084
ATOMS 3
8 -0.1032 0.0000 -0.0799 0.0013 0.0000 0.0010
1 -0.0319 0.0000 0.9591 0.0011 0.0000 -0.0028
1 0.9205 0.0000 -0.2710 -0.0025 0.0000 0.0018
ATOMS 4
8 -0.1102 0.0000 -0.0853 0.0001 0.0000 0.0000
1 -0.0345 0.0000 0.9503 -0.0000 0.0000 -0.0000
1 0.9114 0.0000 -0.2714 -0.0000 0.0000 -0.0000
"""
f7 = """
ANIMSTEPS 2
CRYSTAL
PRIMVEC
0.0000000 2.7100000 2.7100000
2.7100000 0.0000000 2.7100000
2.7100000 2.7100000 0.0000000
PRIMCOORD 1
2 1
16 0.0000000 0.0000000 0.0000000
30 1.3550000 -1.3550000 -1.3550000
PRIMCOORD 2
2 1
16 0.0000000 0.0000000 0.0000000
30 1.2550000 -1.2550000 -1.2550000
"""
f8 = """
ANIMSTEPS 2
CRYSTAL
PRIMVEC 1
2.7100000 2.7100000 0.00000000
2.7100000 0.0000000 2.71000000
0.0000000 2.7100000 2.71000000
CONVVEC 1
5.4200000 0.0000000 0.00000000
0.0000000 5.4200000 0.00000000
0.0000000 0.0000000 5.42000000
PRIMCOORD 1
2 1
16 0.0000000 0.0000000 0.00000000
30 1.3550000 -1.3550000 -1.35500000
PRIMVEC 2
2.9810000 2.9810000 0.00000000
2.9810000 0.0000000 2.98100000
0.0000000 2.9810000 2.98100000
CONVVEC 2
5.9620000 0.0000000 0.00000000
0.0000000 5.9620000 0.00000000
0.0000000 0.0000000 5.96200000
PRIMCOORD 2
2 1
16 0.0000000 0.0000000 0.00000000
30 1.5905000 -1.5905000 -1.59050000
"""
datagrid = """BEGIN_BLOCK_DATAGRID_3D
my_first_example_of_3D_datagrid
BEGIN_DATAGRID_3D_this_is_3Dgrid#1
5 5 5
0.0 0.0 0.0
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
0.000 1.000 2.000 5.196 8.000
1.000 1.414 2.236 5.292 8.062
2.000 2.236 2.828 5.568 8.246
3.000 3.162 3.606 6.000 8.544
4.000 4.123 4.472 6.557 8.944
1.000 1.414 2.236 5.292 8.062
1.414 1.732 2.449 5.385 8.124
2.236 2.449 3.000 5.657 8.307
3.162 3.317 3.742 6.083 8.602
4.123 4.243 4.583 6.633 9.000
2.000 2.236 2.828 5.568 8.246
2.236 2.449 3.000 5.657 8.307
2.828 3.000 3.464 5.916 8.485
3.606 3.742 4.123 6.325 8.775
4.472 4.583 4.899 6.856 9.165
3.000 3.162 3.606 6.000 8.544
3.162 3.317 3.742 6.083 8.602
3.606 3.742 4.123 6.325 8.775
4.243 4.359 4.690 6.708 9.055
5.000 5.099 5.385 7.211 9.434
4.000 4.123 4.472 6.557 8.944
4.123 4.243 4.583 6.633 9.000
4.472 4.583 4.899 6.856 9.165
5.000 5.099 5.385 7.211 9.434
5.657 5.745 6.000 7.681 9.798
END_DATAGRID_3D
END_BLOCK_DATAGRID_3D
"""
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