def test_scripts():
# Generate some random system with random esp data
natom = 5
numbers = np.random.randint(1, 20, natom)
coordinates = np.random.uniform(0, 10, (natom, 3))
origin = np.zeros(3, float)
grid_rvecs = np.identity(3, float)*1.0
shape = np.array([10, 10, 10])
pbc = np.ones(3, int)
ugrid = UniformGrid(origin, grid_rvecs, shape, pbc)
esp_cube_data = np.random.uniform(-1, 1, shape)
rho_cube_data = np.random.uniform(-1, 1, shape)
mol_esp = IOData(coordinates=coordinates, numbers=numbers, grid=ugrid, cube_data=esp_cube_data)
mol_rho = mol_esp.copy()
mol_rho.cube_data = rho_cube_data
# Write the cube file to the tmpdir and run scripts (run 1)
with tmpdir('horton.scripts.test.test_espfit.test_scripts') as dn:
mol_esp.to_file(os.path.join(dn, 'esp.cube'))
check_script('horton-esp-cost.py esp.cube esp.h5 --wnear=0:1.0:0.5', dn)
check_script('horton-esp-fit.py esp.h5 other.h5', dn)
check_script('horton-esp-test.py esp.h5 other.h5:charges foo.h5', dn)
check_script('horton-esp-gen.py other.h5:charges esp.cube gen.h5', dn)
check_files(dn, ['esp.h5', 'other.h5', 'foo.h5', 'gen.h5'])
# Write the cube file to the tmpdir and run scripts (run 2)
with tmpdir('horton.scripts.test.test_espfit.test_scripts2') as dn:
mol_esp.to_file(os.path.join(dn, 'esp.cube'))
mol_rho.to_file(os.path.join(dn, 'rho.cube'))
check_script('horton-esp-cost.py esp.cube esp.h5 --wnear=0:1.0:0.5 --wdens=rho.cube --wsave=weight.cube', dn)
check_files(dn, ['esp.h5', 'weight.cube'])
check_script('horton-esp-fit.py esp.h5 other.h5', dn)
check_script('horton-esp-test.py esp.h5 other.h5:charges foo.h5', dn)
check_script('horton-esp-gen.py other.h5:charges esp.cube gen.h5', dn)
check_files(dn, ['esp.h5', 'other.h5', 'foo.h5', 'gen.h5'])
def test_dump_load_fcidimp_consistency_ao():
# Setup IOData
mol0 = IOData.from_file(context.get_fn('test/water.xyz'))
obasis = get_gobasis(mol0.coordinates, mol0.numbers, '3-21G')
lf = DenseLinalgFactory(obasis.nbasis)
# Compute stuff for fcidump file. test without transforming to mo basis
mol0.core_energy = compute_nucnuc(mol0.coordinates, mol0.pseudo_numbers)
mol0.nelec = 10
mol0.ms2 = 1
mol0.one_mo = lf.create_two_index()
obasis.compute_kinetic(mol0.one_mo)
obasis.compute_nuclear_attraction(mol0.coordinates, mol0.pseudo_numbers, mol0.one_mo)
mol0.two_mo = obasis.compute_electron_repulsion(lf)
# Dump to a file and load it again
with tmpdir('horton.io.test.test_molpro.test_dump_load_fcidump_consistency_ao') as dn:
mol0.to_file('%s/FCIDUMP' % dn)
mol1 = IOData.from_file('%s/FCIDUMP' % dn)
# Compare results
assert mol0.core_energy == mol1.core_energy
assert mol0.nelec == mol1.nelec
assert mol0.ms2 == mol1.ms2
assert mol0.one_mo == mol1.one_mo
assert mol0.two_mo == mol1.two_mo
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_water_sto3g(scheme, do_deriv=True):
with tmpdir('horton.scripts.test.test_wpart.test_script_water_sto3g_%s' % scheme) as dn:
fn_fchk = 'water_sto3g_hf_g03.fchk'
copy_files(dn, [fn_fchk])
if scheme == 'b':
check_script('horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart %s --debug' % (fn_fchk, scheme), dn)
else:
write_atomdb_sto3g(dn, do_deriv)
check_script('horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart %s atoms.h5 --slow' % (fn_fchk, scheme), dn)
fn_h5 = 'water_sto3g_hf_g03_wpart.h5'
check_files(dn, [fn_h5])
with h5.File(os.path.join(dn, fn_h5)) as f:
assert 'wpart' in f
assert abs(f['wpart/charges'][:].sum()) < 1e-2
assert 'wpart/spin_charges' not in f
assert 'atom_00000' in f['wpart']
for s in 'density_decomposition', 'hartree_decomposition':
assert s in f['wpart']['atom_00000']
assert 'spline_00000' in f['wpart']['atom_00000'][s]
assert 'rtransform' in f['wpart']['atom_00000'][s]['spline_00000'].attrs
assert 'extrapolation' in f['wpart']['atom_00000'][s]['spline_00000'].attrs
assert 'y' in f['wpart']['atom_00000'][s]['spline_00000']
assert 'd' in f['wpart']['atom_00000'][s]['spline_00000']
if scheme != 'b':
assert 'spline_prodensity' in f['wpart']['atom_00000']
assert 'spline_prohartree' in f['wpart']['atom_00000']
def test_dump_load_fcidimp_consistency_mo_active():
# Setup IOData
mol0 = IOData.from_file(context.get_fn('test/h2o_sto3g.fchk'))
lf = DenseLinalgFactory(mol0.obasis.nbasis)
# Compute stuff for fcidump file.
one = lf.create_two_index()
mol0.obasis.compute_kinetic(one)
mol0.obasis.compute_nuclear_attraction(mol0.coordinates, mol0.pseudo_numbers, one)
two = mol0.obasis.compute_electron_repulsion(lf)
# transform to mo basis and use only active space
enn = compute_nucnuc(mol0.coordinates, mol0.pseudo_numbers)
mol0.one_mo, mol0.two_mo, mol0.core_energy = split_core_active(one, two, enn, mol0.exp_alpha, 2, 4)
mol0.one_mo.symmetrize()
mol0.two_mo.symmetrize()
mol0.nelec = 10
mol0.ms2 = 0
# Dump to a file and load it again
with tmpdir('horton.io.test.test_molpro.test_dump_load_fcidump_consistency_mo_active') as dn:
mol0.to_file('%s/FCIDUMP' % dn)
mol1 = IOData.from_file('%s/FCIDUMP' % dn)
# Compare results
assert mol0.core_energy == mol1.core_energy
assert mol0.nelec == mol1.nelec
assert mol0.ms2 == mol1.ms2
assert mol0.one_mo == mol1.one_mo
assert mol0.two_mo == mol1.two_mo
def test_dump_load_fcidimp_consistency_mo_active():
# Setup IOData
mol0 = IOData.from_file(context.get_fn('test/h2o_sto3g.fchk'))
# Compute stuff for fcidump file.
one = mol0.obasis.compute_kinetic()
mol0.obasis.compute_nuclear_attraction(mol0.coordinates, mol0.pseudo_numbers, one)
two = mol0.obasis.compute_electron_repulsion()
# transform to mo basis and use only active space
enn = compute_nucnuc(mol0.coordinates, mol0.pseudo_numbers)
mol0.one_mo, mol0.two_mo, mol0.core_energy = split_core_active(one, two, enn, mol0.orb_alpha, 2, 4)
mol0.nelec = 10
mol0.ms2 = 0
# Dump to a file and load it again
with tmpdir('horton.io.test.test_molpro.test_dump_load_fcidump_consistency_mo_active') as dn:
mol0.to_file('%s/FCIDUMP' % dn)
mol1 = IOData.from_file('%s/FCIDUMP' % dn)
# Compare results
np.testing.assert_equal(mol0.core_energy, mol1.core_energy)
np.testing.assert_equal(mol0.nelec, mol1.nelec)
np.testing.assert_equal(mol0.ms2, mol1.ms2)
np.testing.assert_almost_equal(mol0.one_mo, mol1.one_mo)
np.testing.assert_almost_equal(mol0.two_mo, mol1.two_mo)
def check_load_dump_consistency(fn):
sys1 = System.from_file(context.get_fn(os.path.join('test', fn)))
with tmpdir('horton.io.test.test_molden.check_load_dump_consistency.%s' % fn) as dn:
fn_tmp = os.path.join(dn, 'foo.molden.input')
sys1.to_file(fn_tmp)
sys2 = System.from_file(fn_tmp)
compare_systems(sys1, sys2)
def test_write_script_output():
class Foo:
pass
def test_h5(fn_h5):
with h5.File(fn_h5, "r") as f:
assert sorted(f.keys()) == ["a", "c"]
assert f["a"].keys() == ["b"]
assert (f["a/b"][:] == np.array([1, 2, 3])).all()
assert (f["c"][:] == np.array([0.1, 0.2, 0.3])).all()
assert len(f.attrs) == 5
with tmpdir("horton.scripts.test.test_common.test_write_script_output") as dn:
fn_h5 = "%s/foo.h5" % dn
results = {"a": {"b": np.array([1, 2, 3])}, "c": np.array([0.1, 0.2, 0.3])}
args = Foo()
args.bar = "egg"
args.bork = "kwak"
write_script_output(fn_h5, "/", results, args)
test_h5(fn_h5)
write_script_output(fn_h5, "/", results, args)
test_h5(fn_h5)
with h5.File(fn_h5) as f:
f["d"] = 5
write_script_output(fn_h5, "/", results, args)
test_h5(fn_h5)
with h5.File(fn_h5) as f:
for key in f.keys():
del f[key]
write_script_output(fn_h5, "/", results, args)
test_h5(fn_h5)
def check_dump_load_fcidimp_consistency_mo(fn):
# Setup IOData
mol0 = IOData.from_file(fn)
lf = DenseLinalgFactory(mol0.obasis.nbasis)
# Compute stuff for fcidump file.
one = lf.create_two_index()
mol0.obasis.compute_kinetic(one)
mol0.obasis.compute_nuclear_attraction(mol0.coordinates, mol0.pseudo_numbers, one)
two = mol0.obasis.compute_electron_repulsion(lf)
# transform to mo basis, skip core energy
(mol0.one_mo,), (mol0.two_mo,) = transform_integrals(one, two, 'tensordot', mol0.exp_alpha)
mol0.one_mo.symmetrize()
mol0.two_mo.symmetrize()
# Dump to a file and load it again
with tmpdir('horton.io.test.test_molpro.test_dump_load_fcidump_consistency_mo_%s' % os.path.basename(fn)) as dn:
fn = '%s/FCIDUMP' % dn
mol0.to_file(fn)
mol1 = IOData.from_file(fn)
# Compare results
assert mol1.core_energy == 0.0
assert mol1.nelec == 0
assert mol1.ms2 == 0
assert mol0.one_mo == mol1.one_mo
assert mol0.two_mo == mol1.two_mo
def test_script_convert_g03():
with tmpdir("horton.scripts.test.test_atomdb.test_script_convert_g03") as dn:
copy_atom_output("atom_001_001_hf_sto3g.fchk", 1, 0, 2, dn, "atom.fchk")
copy_atom_output("atom_001_002_hf_sto3g.fchk", 1, -1, 1, dn, "atom.fchk")
copy_atom_output("atom_008_007_hf_sto3g.fchk", 8, +1, 4, dn, "atom.fchk")
copy_atom_output("atom_008_008_hf_sto3g.fchk", 8, 0, 3, dn, "atom.fchk")
copy_atom_output("atom_008_009_hf_sto3g.fchk", 8, -1, 2, dn, "atom.fchk")
make_fake_run_script("g03", dn)
check_script("horton-atomdb.py convert", dn)
# check presence of files
fns = [
"atoms.h5",
"dens_001__h.png",
"rdens_001__h.png",
"fukui_001__h.png",
"rfukui_001__h.png",
"dens_008__o.png",
"rdens_008__o.png",
"fukui_008__o.png",
"rfukui_008__o.png",
]
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, "atoms.h5"))
assert padb.get_numbers() == [1, 8]
assert padb.get_charges(1) == [0, -1]
assert padb.get_charges(8) == [+1, 0, -1]
def test_write_script_output():
class Foo:
pass
def test_h5(fn_h5):
with h5.File(fn_h5, 'r') as f:
assert sorted(f.keys()) == ['a', 'c']
assert f['a'].keys() == ['b']
assert (f['a/b'][:] == np.array([1, 2, 3])).all()
assert (f['c'][:] == np.array([0.1, 0.2, 0.3])).all()
assert len(f.attrs) == 5
with tmpdir('horton.scripts.test.test_common.test_write_script_output') as dn:
fn_h5 = '%s/foo.h5' % dn
results = {'a': {'b': np.array([1, 2, 3])}, 'c': np.array([0.1, 0.2, 0.3])}
args = Foo()
args.bar = 'egg'
args.bork = 'kwak'
write_script_output(fn_h5, '/', results, args)
test_h5(fn_h5)
write_script_output(fn_h5, '/', results, args)
test_h5(fn_h5)
with h5.File(fn_h5) as f:
f['d'] = 5
write_script_output(fn_h5, '/', results, args)
test_h5(fn_h5)
with h5.File(fn_h5) as f:
for key in f.keys():
del f[key]
write_script_output(fn_h5, '/', results, args)
test_h5(fn_h5)
def check_load_dump_consistency(fn):
mol1 = IOData.from_file(context.get_fn(os.path.join('test', fn)))
with tmpdir('horton.io.test.test_molden.check_load_dump_consistency.%s' % fn) as dn:
fn_tmp = os.path.join(dn, 'foo.molden')
mol1.to_file(fn_tmp)
mol2 = IOData.from_file(fn_tmp)
compare_mols(mol1, mol2)
def test_script_input_orca():
with tmpdir("horton.scripts.test.test_atomdb.test_script_input_orca") as dn:
fn_template = "template_atomdb_orca.in"
copy_files(dn, [fn_template])
check_script("horton-atomdb.py input orca H,13 %s --no-hund" % fn_template, dn)
fns = [
"001__h_003_q-02/mult02/atom.in",
"001__h_003_q-02/mult04/atom.in",
"001__h_002_q-01/mult01/atom.in",
"001__h_002_q-01/mult03/atom.in",
"001__h_001_q+00/mult02/atom.in",
"013_al_015_q-02/mult04/atom.in",
"013_al_015_q-02/mult02/atom.in",
"013_al_014_q-01/mult03/atom.in",
"013_al_014_q-01/mult05/atom.in",
"013_al_014_q-01/mult01/atom.in",
"013_al_013_q+00/mult02/atom.in",
"013_al_013_q+00/mult04/atom.in",
"013_al_012_q+01/mult01/atom.in",
"013_al_012_q+01/mult03/atom.in",
"013_al_011_q+02/mult02/atom.in",
"013_al_010_q+03/mult01/atom.in",
"run_orca.sh",
]
check_files(dn, fns)
def test_dump_load_fcidimp_consistency_ao():
# Setup IOData
mol0 = IOData.from_file(context.get_fn('test/water.xyz'))
obasis = get_gobasis(mol0.coordinates, mol0.numbers, '3-21G')
# Compute stuff for fcidump file. test without transforming to mo basis
mol0.core_energy = compute_nucnuc(mol0.coordinates, mol0.pseudo_numbers)
mol0.nelec = 10
mol0.ms2 = 1
mol0.one_mo = (
obasis.compute_kinetic() +
obasis.compute_nuclear_attraction(mol0.coordinates, mol0.pseudo_numbers))
mol0.two_mo = obasis.compute_electron_repulsion()
# Dump to a file and load it again
with tmpdir('horton.io.test.test_molpro.test_dump_load_fcidump_consistency_ao') as dn:
mol0.to_file('%s/FCIDUMP' % dn)
mol1 = IOData.from_file('%s/FCIDUMP' % dn)
# Compare results
np.testing.assert_equal(mol0.core_energy, mol1.core_energy)
np.testing.assert_equal(mol0.nelec, mol1.nelec)
np.testing.assert_equal(mol0.ms2, mol1.ms2)
np.testing.assert_almost_equal(mol0.one_mo, mol1.one_mo)
np.testing.assert_almost_equal(mol0.two_mo, mol1.two_mo)
def test_ap1rog_cs_scf_restart():
lf, occ_model, one, er, external, exp_alpha, olp = prepare_hf('6-31G')
# Do AP1roG optimization:
geminal_solver = RAp1rog(lf, occ_model)
guess = np.array([-0.1, -0.05, -0.02])
with tmpdir('horton.correlatedwfn.test.test_geminals.test_ap1rog_cs_scf_restart') as dn:
checkpoint_fn = '%s/checkpoint.h5' % dn
energy, g, l = geminal_solver(one, er, external['nn'], exp_alpha, olp,
True, guess={'geminal': guess},
checkpoint_fn=checkpoint_fn)
assert (abs(energy - -1.151686291339) < 1e-6)
old = IOData.from_file(checkpoint_fn)
assert hasattr(old, 'olp')
assert hasattr(old, 'exp_alpha')
# Update to slightly stretch geometry of H2
mol1, lf, olp1, one1, er1 = prepare_mol('6-31G', 1.05)
# re-orthogonalize orbitals
project_orbitals_ortho(old.olp, olp1, old.exp_alpha, exp_alpha)
# recompute
energy, c, l = geminal_solver(one1, er1, external['nn'], exp_alpha, olp1,
True, guess={'geminal': guess},
checkpoint=-1)
assert (abs(energy - -1.11221603918) < 1e-6)
def test_agspec_local_file():
with tmpdir('horton.scripts.test.test_espfit.test_scripts_symmetry') as dn:
fn_dest = os.path.join(dn, 'mygrid.txt')
shutil.copy(context.get_fn('grids/tv-13.7-4.txt'), fn_dest)
agspec = AtomicGridSpec(fn_dest)
rgrid, nlls = agspec.get(1, 1)
assert rgrid.rtransform.to_string() == 'PowerRTransform 3.69705074304963e-06 19.279558946793685 24'
assert (nlls == np.array([6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 26, 38, 50, 86, 110, 110, 110, 110, 86, 50, 50, 14, 6, 6])).all()
def test_consistency_file():
with tmpdir('horton.io.test.test_chk.test_consistency_file') as dn:
fn_h5 = '%s/foo.h5' % dn
fn_fchk = context.get_fn('test/water_sto3g_hf_g03.fchk')
fn_log = context.get_fn('test/water_sto3g_hf_g03.log')
mol1 = IOData.from_file(fn_fchk, fn_log)
mol1.to_file(fn_h5)
mol2 = IOData.from_file(fn_h5)
compare_mols(mol1, mol2)
def test_consistency_file():
with tmpdir('horton.io.test.test_chk.test_consistency_file') as dn:
fn_chk = '%s/chk.h5' % dn
fn_fchk = context.get_fn('test/water_sto3g_hf_g03.fchk')
fn_log = context.get_fn('test/water_sto3g_hf_g03.log')
sys1 = System.from_file(fn_fchk, fn_log, chk=None)
sys1.to_file(fn_chk)
sys2 = System.from_file(fn_chk, chk=None)
compare_systems(sys1, sys2)
def test_load_dump_consistency():
mol0 = IOData.from_file(context.get_fn('test/ch3_hf_sto3g.fchk'))
with tmpdir('horton.io.test.test_xyz.test_load_dump_consistency') as dn:
mol0.to_file('%s/test.xyz' % dn)
mol1 = IOData.from_file('%s/test.xyz' % dn)
assert mol0.title == mol1.title
assert (mol0.numbers == mol1.numbers).all()
assert abs(mol0.coordinates - mol1.coordinates).max() < 1e-5
def test_io_filename():
padb1 = ProAtomDB.from_refatoms(numbers=[1, 6], max_kation=1, max_anion=0)
keys = sorted(padb1._map.keys())
assert keys == [(1, 0), (6, 0), (6, 1)]
with tmpdir('horton.dpart.test.test_proatomdb.test_io_filename') as dn:
filename = '%s/test.h5' % dn
padb1.to_file(filename)
padb2 = ProAtomDB.from_file(filename)
compare_padbs(padb1, padb2)
def check_script_jbw_coarse(scheme):
with tmpdir("horton.scripts.test.test_cpart.test_script_jbw_coarse_%s" % scheme) as dn:
fn_cube = "jbw_coarse_aedens.cube"
copy_files(dn, [fn_cube])
write_atomdb_refatoms(dn)
fn_h5 = "foobar.h5"
check_script("horton-cpart.py %s foobar.h5:cpart/%s_r1 %s atoms.h5" % (fn_cube, scheme, scheme), dn)
check_files(dn, [fn_h5])
with h5.File(os.path.join(dn, fn_h5)) as f:
assert "cpart" in f
assert scheme + "_r1" in f["cpart"]
def check_script_jbw_coarse(scheme):
with tmpdir('horton.scripts.test.test_cpart.test_script_jbw_coarse_%s' % scheme) as dn:
fn_cube = 'jbw_coarse_aedens.cube'
copy_files(dn, [fn_cube])
write_atomdb_refatoms(dn)
fn_h5 = 'foobar.h5'
check_script('horton-cpart.py %s foobar.h5:cpart/%s_r1 %s atoms.h5' % (fn_cube, scheme, scheme), dn)
check_files(dn, [fn_h5])
with h5.File(os.path.join(dn, fn_h5)) as f:
assert 'cpart' in f
assert scheme + '_r1' in f['cpart']
def test_script_convert_g09():
with tmpdir("horton.scripts.test.test_atomdb.test_script_convert_g09") as dn:
copy_atom_output("atom_014_013_hf_lan.fchk", 14, +1, 2, dn, "atom.fchk")
make_fake_run_script("g09", dn)
check_script("horton-atomdb.py convert --grid medium", dn)
# check presence of files
fns = ["atoms.h5", "dens_014_si.png", "rdens_014_si.png", "fukui_014_si.png", "rfukui_014_si.png"]
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, "atoms.h5"))
assert padb.get_numbers() == [14]
assert padb.get_charges(14) == [+1]
assert padb.get_rgrid(14).size == 49
def test_load_dump_consistency():
sys0 = System.from_file(context.get_fn('test/water_element.xyz'))
sys0._cell = get_random_cell(5.0, 3)
with tmpdir('horton.io.test.test_vasp.test_load_dump_consistency') as dn:
sys0.to_file('%s/POSCAR' % dn)
sys1 = System.from_file('%s/POSCAR' % dn)
assert (sys1.numbers == [8, 1, 1]).all()
assert abs(sys0.coordinates[1] - sys1.coordinates[0]).max() < 1e-10
assert abs(sys0.coordinates[0] - sys1.coordinates[1]).max() < 1e-10
assert abs(sys0.coordinates[2] - sys1.coordinates[2]).max() < 1e-10
assert abs(sys0.cell.rvecs - sys1.cell.rvecs).max() < 1e-10
def test_script_convert_g09():
with tmpdir('horton.scripts.test.test_atomdb.test_script_convert_g09') as dn:
copy_atom_output('atom_014_013_hf_lan.fchk', 14, +1, 2, dn, 'atom.fchk')
make_fake_run_script('g09', dn)
check_script('horton-atomdb.py convert --grid medium', dn)
# check presence of files
fns = ['atoms.h5', 'dens_014_si.png', 'rdens_014_si.png', 'fukui_014_si.png', 'rfukui_014_si.png']
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, 'atoms.h5'))
assert padb.get_numbers() == [14]
assert padb.get_charges(14) == [+1]
assert padb.get_rgrid(14).size == 49
def test_script():
with tmpdir('horton.scripts.test.test_hdf2csv.test_script') as dn:
with h5.File('%s/test.h5' % dn) as f:
fill_hdf5(f)
check_script('horton-hdf2csv.py test.h5:/ test.csv', dn)
check_files(dn, ['test.h5', 'test.csv'])
with open('%s/test.csv' % dn) as f:
r = csv.reader(f)
rows = [row for row in r]
with h5.File('%s/test.h5' % dn) as f:
assert rows[0][0] == 'Converted data from test.h5:/'
assert len(rows[1]) == 0
assert len(rows[2]) == 2
assert rows[2][0] == 'Dataset'
assert rows[2][1] == 'bar/foo'
assert len(rows[3]) == 3
assert rows[3][0] == 'Shape'
assert rows[3][1] == '5'
assert rows[3][2] == '2'
assert float(rows[4][0]) == f['bar/foo'][0,0]
assert float(rows[8][1]) == f['bar/foo'][4,1]
assert len(rows[9]) == 0
assert len(rows[22]) == 2
assert rows[22][0] == 'Dataset'
assert rows[22][1] == 'test2'
assert len(rows[23]) == 3
assert rows[23][0] == 'Shape'
assert rows[23][1] == '5'
assert rows[23][2] == '2'
assert float(rows[24][0]) == f['test2'][0,0]
assert float(rows[28][1]) == f['test2'][4,1]
assert rows[29] == []
assert len(rows[30]) == 2
assert rows[30][0] == 'Dataset'
assert rows[30][1] == 'zzz'
assert len(rows[31]) == 4
assert rows[31][0] == 'Shape'
assert rows[31][1] == '5'
assert rows[31][2] == '2'
assert rows[31][3] == '5'
assert float(rows[32][0]) == f['zzz'][0,0,0]
assert float(rows[32][1]) == f['zzz'][0,1,0]
assert rows[32][2] == ''
assert float(rows[32][3]) == f['zzz'][0,0,1]
assert float(rows[32][4]) == f['zzz'][0,1,1]
assert rows[32][5] == ''
assert len(rows[32]) == 3*5-1
assert float(rows[36][1]) == f['zzz'][4,1,0]
assert float(rows[36][3*5-2]) == f['zzz'][4,1,4]
assert rows[-1] == []
def test_load_dump_consistency():
mol0 = IOData.from_file(context.get_fn('test/water_element.xyz'))
mol0.cell = get_random_cell(5.0, 3)
with tmpdir('horton.io.test.test_vasp.test_load_dump_consistency') as dn:
mol0.to_file('%s/POSCAR' % dn)
mol1 = IOData.from_file('%s/POSCAR' % dn)
assert mol0.title == mol1.title
assert (mol1.numbers == [8, 1, 1]).all()
assert abs(mol0.coordinates[1] - mol1.coordinates[0]).max() < 1e-10
assert abs(mol0.coordinates[0] - mol1.coordinates[1]).max() < 1e-10
assert abs(mol0.coordinates[2] - mol1.coordinates[2]).max() < 1e-10
assert abs(mol0.cell.rvecs - mol1.cell.rvecs).max() < 1e-10
def check_script_water_sto3g(scheme, do_deriv=True):
with tmpdir('horton.scripts.test.test_wpart.test_script_water_sto3g_%s' % scheme) as dn:
fn_fchk = 'water_sto3g_hf_g03.fchk'
copy_files(dn, [fn_fchk])
if scheme == 'b':
check_script('horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart/%s %s --debug' % (fn_fchk, scheme, scheme), dn)
else:
write_atomdb_sto3g(dn, do_deriv)
check_script('horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart/%s %s atoms.h5' % (fn_fchk, scheme, scheme), dn)
fn_h5 = 'water_sto3g_hf_g03_wpart.h5'
check_files(dn, [fn_h5])
with h5.File(os.path.join(dn, fn_h5)) as f:
assert 'wpart' in f
assert scheme in f['wpart']
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 test_script():
with tmpdir("horton.scripts.test.test_hdf2csv.test_script") as dn:
with h5.File("%s/test.h5" % dn) as f:
fill_hdf5(f)
check_script("horton-hdf2csv.py test.h5:/ test.csv", dn)
check_files(dn, ["test.h5", "test.csv"])
with open("%s/test.csv" % dn) as f:
r = csv.reader(f)
rows = [row for row in r]
with h5.File("%s/test.h5" % dn) as f:
assert rows[0][0] == "Converted data from test.h5:/"
assert len(rows[1]) == 0
assert len(rows[2]) == 2
assert rows[2][0] == "Dataset"
assert rows[2][1] == "bar/foo"
assert len(rows[3]) == 3
assert rows[3][0] == "Shape"
assert rows[3][1] == "5"
assert rows[3][2] == "2"
assert float(rows[4][0]) == f["bar/foo"][0, 0]
assert float(rows[8][1]) == f["bar/foo"][4, 1]
assert len(rows[9]) == 0
assert len(rows[22]) == 2
assert rows[22][0] == "Dataset"
assert rows[22][1] == "test2"
assert len(rows[23]) == 3
assert rows[23][0] == "Shape"
assert rows[23][1] == "5"
assert rows[23][2] == "2"
assert float(rows[24][0]) == f["test2"][0, 0]
assert float(rows[28][1]) == f["test2"][4, 1]
assert rows[29] == []
assert len(rows[30]) == 2
assert rows[30][0] == "Dataset"
assert rows[30][1] == "zzz"
assert len(rows[31]) == 4
assert rows[31][0] == "Shape"
assert rows[31][1] == "5"
assert rows[31][2] == "2"
assert rows[31][3] == "5"
assert float(rows[32][0]) == f["zzz"][0, 0, 0]
assert float(rows[32][1]) == f["zzz"][0, 1, 0]
assert rows[32][2] == ""
assert float(rows[32][3]) == f["zzz"][0, 0, 1]
assert float(rows[32][4]) == f["zzz"][0, 1, 1]
assert rows[32][5] == ""
assert len(rows[32]) == 3 * 5 - 1
assert float(rows[36][1]) == f["zzz"][4, 1, 0]
assert float(rows[36][3 * 5 - 2]) == f["zzz"][4, 1, 4]
assert rows[-1] == []
def test_load_dump_load_aelta():
fn_cube1 = context.get_fn('test/aelta.cube')
mol1 = IOData.from_file(fn_cube1)
with tmpdir('horton.io.test.test_cube.test_load_dump_load_aelta') as dn:
fn_cube2 = '%s/%s' % (dn, 'aelta.cube')
mol1.to_file(fn_cube2)
mol2 = IOData.from_file(fn_cube2)
assert mol1.title == mol2.title
assert abs(mol1.coordinates - mol2.coordinates).max() < 1e-4
assert (mol1.numbers == mol2.numbers).all()
ugrid1 = mol1.grid
ugrid2 = mol2.grid
assert abs(ugrid1.grid_rvecs - ugrid2.grid_rvecs).max() < 1e-4
assert (ugrid1.shape == ugrid2.shape).all()
assert abs(mol1.cube_data - mol2.cube_data).max() < 1e-4
assert abs(mol1.pseudo_numbers - mol2.pseudo_numbers).max() < 1e-4
def test_script_convert_cp2k():
with tmpdir('horton.scripts.test.test_atomdb.test_script_convert_cp2k') as dn:
copy_atom_output('atom_op2.cp2k.out', 8, +2, 3, dn, 'atom.cp2k.out')
copy_atom_output('atom_op1.cp2k.out', 8, +1, 4, dn, 'atom.cp2k.out')
copy_atom_output('atom_o.cp2k.out', 8, 0, 2, dn, 'atom.cp2k.out')
copy_atom_output('atom_om1.cp2k.out', 8, -1, 1, dn, 'atom.cp2k.out')
copy_atom_output('atom_om2.cp2k.out', 8, -2, 0, dn, 'atom.cp2k.out')
make_fake_run_script('cp2k', dn)
check_script('horton-atomdb.py convert', dn)
# check presence of files
fns = ['atoms.h5', 'dens_008__o.png', 'rdens_008__o.png', 'fukui_008__o.png', 'rfukui_008__o.png']
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, 'atoms.h5'))
assert padb.get_numbers() == [8]
assert padb.get_charges(8) == [+2, +1, 0, -1, -2]
assert not padb.get_record(8, -2).safe
assert padb.get_rgrid(8).size == 71
def test_script_convert_g09():
with tmpdir(
'horton.scripts.test.test_atomdb.test_script_convert_g09') as dn:
copy_atom_output('atom_014_013_hf_lan.fchk', 14, +1, 2, dn,
'atom.fchk')
make_fake_run_script('g09', dn)
check_script('horton-atomdb.py convert --grid medium', dn)
# check presence of files
fns = [
'atoms.h5', 'dens_014_si.png', 'rdens_014_si.png',
'fukui_014_si.png', 'rfukui_014_si.png'
]
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, 'atoms.h5'))
assert padb.get_numbers() == [14]
assert padb.get_charges(14) == [+1]
assert padb.get_rgrid(14).size == 49
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 test_ap1rog_cs_scf_restart():
lf, occ_model, one, er, external, exp_alpha, olp = prepare_hf('6-31G')
# Do AP1roG optimization:
geminal_solver = RAp1rog(lf, occ_model)
guess = np.array([-0.1, -0.05, -0.02])
with tmpdir(
'horton.correlatedwfn.test.test_geminals.test_ap1rog_cs_scf_restart'
) as dn:
checkpoint_fn = '%s/checkpoint.h5' % dn
energy, g, l = geminal_solver(one,
er,
external['nn'],
exp_alpha,
olp,
True,
guess={'geminal': guess},
checkpoint_fn=checkpoint_fn)
assert (abs(energy - -1.151686291339) < 1e-6)
old = IOData.from_file(checkpoint_fn)
assert hasattr(old, 'olp')
assert hasattr(old, 'exp_alpha')
# Update to slightly stretch geometry of H2
mol1, lf, olp1, one1, er1 = prepare_mol('6-31G', 1.05)
# re-orthogonalize orbitals
project_orbitals_ortho(old.olp, olp1, old.exp_alpha, exp_alpha)
# recompute
energy, c, l = geminal_solver(one1,
er1,
external['nn'],
exp_alpha,
olp1,
True,
guess={'geminal': guess},
checkpoint=-1)
assert (abs(energy - -1.11221603918) < 1e-6)
def test_chk_initialization_override():
with tmpdir('horton.test.test_checkpoint.test_chk_override') as dn:
fn_chk1 = '%s/chk1.h5' % dn
fn_chk2 = '%s/chk2.h5' % dn
sys1 = System.from_file(context.get_fn('test/hf_sto3g.fchk'), chk=fn_chk1)
del sys1
sys1 = System.from_file(context.get_fn('test/hf_sto3g.fchk'))
sys2 = System.from_file(fn_chk1, chk=fn_chk2)
compare_systems(sys1, sys2)
assert os.path.isfile(fn_chk2)
sys3 = System.from_file(fn_chk2, chk=None)
compare_systems(sys1, sys3)
sys3.numbers[:] = 0
sys3.update_chk('numbers')
sys4 = System.from_file(fn_chk2, chk=None)
compare_systems(sys1, sys4)
def check_script_water_sto3g(scheme, do_deriv=True):
with tmpdir('horton.scripts.test.test_wpart.test_script_water_sto3g_%s' %
scheme) as dn:
fn_fchk = 'water_sto3g_hf_g03.fchk'
copy_files(dn, [fn_fchk])
if scheme == 'b':
check_script(
'horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart/%s %s --debug'
% (fn_fchk, scheme, scheme), dn)
else:
write_atomdb_sto3g(dn, do_deriv)
check_script(
'horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart/%s %s atoms.h5'
% (fn_fchk, scheme, scheme), dn)
fn_h5 = 'water_sto3g_hf_g03_wpart.h5'
check_files(dn, [fn_h5])
with h5.File(os.path.join(dn, fn_h5)) as f:
assert 'wpart' in f
assert scheme in f['wpart']
def test_load_dump_load_aelta():
fn_cube1 = context.get_fn('test/aelta.cube')
sys1 = System.from_file(fn_cube1)
with tmpdir('horton.io.test.test_cube.test_load_dump_load_aelta') as dn:
fn_cube2 = '%s/%s' % (dn, 'aelta.cube')
sys1.to_file(fn_cube2)
sys2 = System.from_file(fn_cube2)
assert sys1.natom == sys2.natom
assert abs(sys1.coordinates - sys2.coordinates).max() < 1e-4
assert (sys1.numbers == sys2.numbers).all()
ugrid1 = sys1.grid
ugrid2 = sys2.grid
assert abs(ugrid1.grid_rvecs - ugrid2.grid_rvecs).max() < 1e-4
assert (ugrid1.shape == ugrid2.shape).all()
assert abs(sys1.extra['cube_data'] -
sys2.extra['cube_data']).max() < 1e-4
assert abs(sys1.pseudo_numbers - sys2.pseudo_numbers).max() < 1e-4
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_script_convert_g03():
with tmpdir('horton.scripts.test.test_atomdb.test_script_convert_g03') as dn:
copy_atom_output('atom_001_001_hf_sto3g.fchk', 1, 0, 2, dn, 'atom.fchk')
copy_atom_output('atom_001_002_hf_sto3g.fchk', 1, -1, 1, dn, 'atom.fchk')
copy_atom_output('atom_008_007_hf_sto3g.fchk', 8, +1, 4, dn, 'atom.fchk')
copy_atom_output('atom_008_008_hf_sto3g.fchk', 8, 0, 3, dn, 'atom.fchk')
copy_atom_output('atom_008_009_hf_sto3g.fchk', 8, -1, 2, dn, 'atom.fchk')
make_fake_run_script('g03', dn)
check_script('horton-atomdb.py convert', dn)
# check presence of files
fns = [
'atoms.h5',
'dens_001__h.png', 'rdens_001__h.png', 'fukui_001__h.png', 'rfukui_001__h.png',
'dens_008__o.png', 'rdens_008__o.png', 'fukui_008__o.png', 'rfukui_008__o.png',
]
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, 'atoms.h5'))
assert padb.get_numbers() == [1, 8]
assert padb.get_charges(1) == [0, -1]
assert padb.get_charges(8) == [+1, 0, -1]
def test_dump_basis_atom_map_gbs():
sto3g = GOBasisFamily('original STO-3G',
filename=context.get_fn('basis/sto-3g.gbs'))
sto3g.load()
with tmpdir('horton.gbasis.test.test_iobas.test_dump_basis_atom_map_gbs'
) as tmp:
tmp_gbs = '{0}/test.gbs'.format(tmp)
dump_basis_atom_map_gbs(tmp_gbs, sto3g.name, sto3g.basis_atom_map)
new_sto3g = GOBasisFamily('new STO-3G', filename=tmp_gbs)
new_sto3g.load()
for atom, bca in new_sto3g.basis_atom_map.iteritems():
old_bca = sto3g.basis_atom_map[atom]
for i, contraction in enumerate(bca.bcs):
old_contraction = old_bca.bcs[i]
assert contraction.shell_type == old_contraction.shell_type
np.testing.assert_equal(contraction.alphas,
old_contraction.alphas)
# Limited precision due to normalization of contractions after loading
# them from file.
np.testing.assert_almost_equal(contraction.con_coeffs,
old_contraction.con_coeffs)
def test_script_input_cp2k():
with tmpdir(
'horton.scripts.test.test_atomdb.test_script_input_cp2k') as dn:
fn_template = 'template_atomdb_cp2k.in'
fn_valence = 'include_atomdb_cp2k_valence.inc'
fn_ppot = 'include_atomdb_cp2k_ppot.inc'
copy_files(dn, [fn_template, fn_valence, fn_ppot])
check_script('horton-atomdb.py input cp2k Ca,F %s' % fn_template, dn)
fns = [
'020_ca_021_q-01/mult02/atom.in',
'020_ca_020_q+00/mult01/atom.in',
'020_ca_019_q+01/mult02/atom.in',
'020_ca_018_q+02/mult01/atom.in',
'020_ca_017_q+03/mult02/atom.in',
'009__f_010_q-01/mult01/atom.in',
'009__f_009_q+00/mult02/atom.in',
'009__f_008_q+01/mult03/atom.in',
'009__f_007_q+02/mult04/atom.in',
'run_cp2k.sh',
]
check_files(dn, fns)
def check_script_ch3_rohf_sto3g(scheme, do_deriv=True):
with tmpdir(
'horton.scripts.test.test_wpart.test_script_ch3_rohf_sto3g_%s' %
scheme) as dn:
fn_fchk = 'ch3_rohf_sto3g_g03.fchk'
copy_files(dn, [fn_fchk])
if scheme == 'b':
check_script(
'horton-wpart.py %s foo.h5:wpart %s --debug' %
(fn_fchk, scheme), dn)
else:
write_atomdb_sto3g(dn, do_deriv)
check_script(
'horton-wpart.py %s foo.h5:wpart %s atoms.h5' %
(fn_fchk, scheme), dn)
fn_h5 = 'foo.h5'
check_files(dn, [fn_h5])
with h5.File(os.path.join(dn, fn_h5)) as f:
assert 'wpart' in f
assert abs(f['wpart/charges'][:].sum()) < 1e-2
assert abs(f['wpart/spin_charges'][:].sum() - 1) < 1e-2
def check_script_input_gaussian(binary):
with tmpdir('horton.scripts.test.test_atomdb.test_script_input_%s' %
binary) as dn:
fn_template = 'template_atomdb_gaussian.in'
fn_basis1 = 'include_atomdb_gaussian_basis.001_000_00'
fn_basis8 = 'include_atomdb_gaussian_basis.008_000_00'
copy_files(dn, [fn_template, fn_basis1, fn_basis8])
check_script(
'horton-atomdb.py input %s 1,O %s' % (binary, fn_template), dn)
fns = [
'001__h_003_q-02/mult02/atom.in',
'001__h_002_q-01/mult01/atom.in',
'001__h_001_q+00/mult02/atom.in',
'008__o_010_q-02/mult01/atom.in',
'008__o_009_q-01/mult02/atom.in',
'008__o_008_q+00/mult03/atom.in',
'008__o_007_q+01/mult04/atom.in',
'008__o_006_q+02/mult03/atom.in',
'008__o_005_q+03/mult02/atom.in',
'run_%s.sh' % binary,
]
check_files(dn, fns)
def test_check_output():
with tmpdir('horton.scripts.test.test_common.test_check_output') as dn:
assert not check_output('%s/foo.h5' % dn, '/', True)
assert not check_output('%s/foo.h5' % dn, '/bar', True)
assert not check_output('%s/foo.h5' % dn, '/', False)
assert not check_output('%s/foo.h5' % dn, '/bar', False)
with h5.File('%s/foo.h5' % dn) as f:
f.create_group('bork')
assert not check_output('%s/foo.h5' % dn, '/', True)
assert not check_output('%s/foo.h5' % dn, '/bork', True)
assert not check_output('%s/foo.h5' % dn, '/bar', True)
assert check_output('%s/foo.h5' % dn, '/', False)
assert not check_output('%s/foo.h5' % dn, '/bork', False)
assert not check_output('%s/foo.h5' % dn, '/bar', False)
with h5.File('%s/foo.h5' % dn) as f:
f['bork']['a'] = np.array([1, 2, 3])
assert not check_output('%s/foo.h5' % dn, '/', True)
assert not check_output('%s/foo.h5' % dn, '/bork', True)
assert not check_output('%s/foo.h5' % dn, '/bar', True)
assert check_output('%s/foo.h5' % dn, '/', False)
assert check_output('%s/foo.h5' % dn, '/bork', False)
assert not check_output('%s/foo.h5' % dn, '/bar', False)
def test_write_script_output():
class Foo:
pass
def test_h5(fn_h5):
with h5.File(fn_h5, 'r') as f:
assert sorted(f.keys()) == ['a', 'c']
assert f['a'].keys() == ['b']
assert (f['a/b'][:] == np.array([1, 2, 3])).all()
assert (f['c'][:] == np.array([0.1, 0.2, 0.3])).all()
assert len(f.attrs) == 5
with tmpdir(
'horton.scripts.test.test_common.test_write_script_output') as dn:
fn_h5 = '%s/foo.h5' % dn
results = {
'a': {
'b': np.array([1, 2, 3])
},
'c': np.array([0.1, 0.2, 0.3])
}
args = Foo()
args.bar = 'egg'
args.bork = 'kwak'
write_script_output(fn_h5, '/', results, args)
test_h5(fn_h5)
write_script_output(fn_h5, '/', results, args)
test_h5(fn_h5)
with h5.File(fn_h5) as f:
f['d'] = 5
write_script_output(fn_h5, '/', results, args)
test_h5(fn_h5)
with h5.File(fn_h5) as f:
for key in f.keys():
del f[key]
write_script_output(fn_h5, '/', results, args)
test_h5(fn_h5)
def test_scripts():
with tmpdir('horton.scripts.test.test_convert.test_scripts') as dn:
fn_fchk = 'water_sto3g_hf_g03.fchk'
copy_files(dn, [fn_fchk])
check_script('horton-convert.py %s test.xyz' % fn_fchk, dn)
def test_locked1():
# just a silly test
with tmpdir('horton.scripts.test.test_common.test_locked1') as dn:
with LockedH5File('%s/foo.h5' % dn) as f:
pass
def test_script():
with tmpdir('horton.scripts.test.test_cubehead.test_script') as dn:
fn_fchk = 'water_sto3g_hf_g03.fchk'
copy_files(dn, [fn_fchk])
check_script('horton-cubehead.py %s cubehead.txt' % fn_fchk, dn)
check_files(dn, ['cubehead.txt'])
def test_locked2():
# test error handling in h5.File constructor
with assert_raises(IOError):
with tmpdir('horton.scripts.test.test_common.test_locked2') as dn:
with LockedH5File('%s/foo.h5' % dn, mode='r', wait=0.1, count=3) as f:
pass
def test_locked4():
# test error handling of wrong driver
with assert_raises(ValueError):
with tmpdir('horton.scripts.test.test_common.test_locked4') as dn:
with LockedH5File('%s/foo.h5' % dn, driver='core') as f:
pass
def test_locked5():
# test error handling in with clause
with assert_raises(RuntimeError):
with tmpdir('horton.scripts.test.test_common.test_locked5') as dn:
with LockedH5File('%s/foo.h5' % dn) as f:
raise RuntimeError