def test_scripts_symmetry():
# Write the cube file to the tmpdir and run scripts
with tmpdir('horton.scripts.test.test_espfit.test_scripts_symmetry') as dn:
# prepare files
write_random_lta_cube(dn, 'esp.cube')
copy_files(dn, ['lta_gulp.cif'])
# run scripts
check_script('horton-esp-cost.py esp.cube esp.h5 --wnear=0:1.0:0.5 --rcut=4 --alpha-scale=0.1', dn)
check_files(dn, ['esp.h5'])
check_script('horton-esp-fit.py esp.h5 other.h5 --symmetry esp.cube lta_gulp.cif', dn)
mol_sym = IOData.from_file('%s/lta_gulp.cif' % dn)
with h5.File(os.path.join(dn, 'other.h5')) as f:
assert 'symmetry' in f
assert f['symmetry/charges'].shape == (mol_sym.symmetry.natom, 2)
def check_script_lta(fn_sym, suffix):
with tmpdir('horton.scripts.test.test_cpart.test_script_lta_coarse_h_%s' % suffix) as dn:
# prepare files
if fn_sym is not None:
copy_files(dn, [fn_sym])
write_atomdb_refatoms(dn)
# write a random cube file
fn_cube = 'dens.cube'
sys = write_random_lta_cube(dn, fn_cube)
# run the script
fn_h5 = '%s_cpart.h5' % fn_cube[:-5]
if fn_sym is None:
check_script('horton-cpart.py %s %s:cpart/h_r1 h atoms.h5' % (fn_cube, fn_h5), dn)
else:
check_script('horton-cpart.py %s %s:cpart/h_r1 h atoms.h5 --symmetry=%s' % (fn_cube, fn_h5, fn_sym), dn)
# check the output
check_files(dn, [fn_h5])
with h5.File(os.path.join(dn, fn_h5)) as f:
assert 'cpart' in f
assert 'h_r1' in f['cpart']
if fn_sym is not None:
assert 'symmetry' in f['cpart/h_r1']
assert 'charges' in f['cpart/h_r1/symmetry']
assert 'cartesian_multipoles' in f['cpart/h_r1/symmetry']
for name, ds in f['cpart/h_r1/symmetry'].iteritems():
assert ds.shape[0] == sys.extra['symmetry'].natom
assert ds.shape[1] == 2
def check_script_lta(fn_sym, suffix):
with tmpdir('horton.scripts.test.test_cpart.test_script_lta_coarse_h_%s' % suffix) as dn:
# prepare files
if fn_sym is not None:
copy_files(dn, [fn_sym])
write_atomdb_refatoms(dn)
# write a random cube file
fn_cube = 'dens.cube'
sys = write_random_lta_cube(dn, fn_cube)
# run the script
fn_h5 = '%s_cpart.h5' % fn_cube[:-5]
if fn_sym is None:
check_script('horton-cpart.py %s %s:cpart/h_r1 h atoms.h5' % (fn_cube, fn_h5), dn)
else:
check_script('horton-cpart.py %s %s:cpart/h_r1 h atoms.h5 --symmetry=%s' % (fn_cube, fn_h5, fn_sym), dn)
# check the output
check_files(dn, [fn_h5])
with h5.File(os.path.join(dn, fn_h5)) as f:
assert 'cpart' in f
assert 'h_r1' in f['cpart']
if fn_sym is not None:
assert 'symmetry' in f['cpart/h_r1']
assert 'charges' in f['cpart/h_r1/symmetry']
assert 'cartesian_multipoles' in f['cpart/h_r1/symmetry']
for name, ds in f['cpart/h_r1/symmetry'].iteritems():
assert ds.shape[0] == sys.extra['symmetry'].natom
assert ds.shape[1] == 2
def check_script_lta(fn_sym, suffix, do_spin=False):
with tmpdir('horton.scripts.test.test_cpart.test_script_lta_coarse_h_%s' %
suffix) as dn:
# prepare files
if fn_sym is not None:
copy_files(dn, [fn_sym])
write_atomdb_refatoms(dn)
# write a random cube file
fn_cube = 'dens.cube'
mol = write_random_lta_cube(dn, fn_cube)
# if needed, write a random spin cube file
if do_spin:
fn_spin = 'spin.cube'
molspin = write_random_lta_cube(dn, fn_spin)
# run the script
fn_h5 = '%s_cpart.h5' % fn_cube[:-5]
opts = ''
if not (fn_sym is None):
opts += ' --symmetry=%s' % fn_sym
if do_spin:
opts += ' --spindens=%s' % fn_spin
check_script(
'horton-cpart.py %s %s:cpart/h_r1 h atoms.h5 %s' %
(fn_cube, fn_h5, opts), dn)
# check the output
check_files(dn, [fn_h5])
with h5.File(os.path.join(dn, fn_h5)) as f:
assert 'cpart' in f
assert 'h_r1' in f['cpart']
assert 'charges' in f['cpart/h_r1']
if do_spin:
assert 'spin_charges' in f['cpart/h_r1']
if fn_sym is not None:
assert 'symmetry' in f['cpart/h_r1']
assert 'charges' in f['cpart/h_r1/symmetry']
if do_spin:
assert 'spin_charges' in f['cpart/h_r1/symmetry']
assert 'cartesian_multipoles' in f['cpart/h_r1/symmetry']
for name, ds in f['cpart/h_r1/symmetry'].iteritems():
assert ds.shape[0] == mol.symmetry.natom
assert ds.shape[1] == 2
def test_scripts_symmetry():
# Write the cube file to the tmpdir and run scripts
with tmpdir('horton.scripts.test.test_espfit.test_scripts_symmetry') as dn:
# prepare files
write_random_lta_cube(dn, 'esp.cube')
copy_files(dn, ['lta_gulp.cif'])
# run scripts
check_script(
'horton-esp-cost.py esp.cube esp.h5 --wnear=0:1.0:0.5 --rcut=4 --alpha-scale=0.1',
dn)
check_files(dn, ['esp.h5'])
check_script(
'horton-esp-fit.py esp.h5 other.h5 --symmetry esp.cube lta_gulp.cif',
dn)
mol_sym = IOData.from_file('%s/lta_gulp.cif' % dn)
with h5.File(os.path.join(dn, 'other.h5')) as f:
assert 'symmetry' in f
assert f['symmetry/charges'].shape == (mol_sym.symmetry.natom, 2)
def check_script_lta(fn_sym, suffix, do_spin=False):
with tmpdir('horton.scripts.test.test_cpart.test_script_lta_coarse_h_%s' % suffix) as dn:
# prepare files
if fn_sym is not None:
copy_files(dn, [fn_sym])
write_atomdb_refatoms(dn)
# write a random cube file
fn_cube = 'dens.cube'
mol = write_random_lta_cube(dn, fn_cube)
# if needed, write a random spin cube file
if do_spin:
fn_spin = 'spin.cube'
molspin = write_random_lta_cube(dn, fn_spin)
# run the script
fn_h5 = '%s_cpart.h5' % fn_cube[:-5]
opts = ''
if not (fn_sym is None):
opts += ' --symmetry=%s' % fn_sym
if do_spin:
opts += ' --spindens=%s' % fn_spin
check_script('horton-cpart.py %s %s:cpart/h_r1 h atoms.h5 %s' % (fn_cube, fn_h5, opts), dn)
# check the output
check_files(dn, [fn_h5])
with h5.File(os.path.join(dn, fn_h5)) as f:
assert 'cpart' in f
assert 'h_r1' in f['cpart']
assert 'charges' in f['cpart/h_r1']
if do_spin:
assert 'spin_charges' in f['cpart/h_r1']
if fn_sym is not None:
assert 'symmetry' in f['cpart/h_r1']
assert 'charges' in f['cpart/h_r1/symmetry']
if do_spin:
assert 'spin_charges' in f['cpart/h_r1/symmetry']
assert 'cartesian_multipoles' in f['cpart/h_r1/symmetry']
for name, ds in f['cpart/h_r1/symmetry'].iteritems():
assert ds.shape[0] == mol.symmetry.natom
assert ds.shape[1] == 2