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 """