def test_o2_cc_pvtz_cart_num():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_cart")
fchk = FCHKFile(fn_fchk)
basis = GaussianBasis.from_fchk(fchk)
assert(basis.num_shells==20)
print basis.num_dof
assert(basis.num_dof==70)
def test_o2_cc_pvtz_cart_num():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_cart")
fchk = FCHKFile(fn_fchk)
basis = GaussianBasis.from_fchk(fchk)
assert (basis.num_shells == 20)
print basis.num_dof
assert (basis.num_dof == 70)
def test_orb0_hf_sto3g():
tmpdir, fn_fchk = setup_gaussian("hf_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
points = ref_data_hf_sto3g_orb0[:,:3]
fns = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1,-1)), points*angstrom, 1)[0]
assert(abs(fns-ref_data_hf_sto3g_orb0[:,3]).max() < 1e-10)
def test_orb0_o2_cc_pvtz_pure():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_pure")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
weights = weights[basis.g03_permutation]
points = ref_data_o2_cc_pvtz_pure_orb0[:,:3]
fns = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1,-1)), points*angstrom, 1)[0]
assert(abs(fns-ref_data_o2_cc_pvtz_pure_orb0[:,3]).max() < 1e-10)
def test_orb0_hf_sto3g():
tmpdir, fn_fchk = setup_gaussian("hf_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
points = ref_data_hf_sto3g_orb0[:, :3]
fns = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1, -1)),
points * angstrom, 1)[0]
assert (abs(fns - ref_data_hf_sto3g_orb0[:, 3]).max() < 1e-10)
def test_orb0_o2_cc_pvtz_pure():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_pure")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
weights = weights[basis.g03_permutation]
points = ref_data_o2_cc_pvtz_pure_orb0[:, :3]
fns = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1, -1)),
points * angstrom, 1)[0]
assert (abs(fns - ref_data_o2_cc_pvtz_pure_orb0[:, 3]).max() < 1e-10)
def test_orb0_h_sto3g():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
# real test for the output
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
points = ref_data_h_sto3g_orb0[:,:3]
fns = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1,-1)), points*angstrom, 1)[0]
assert(abs(fns-ref_data_h_sto3g_orb0[:,3]).max() < 1e-10)
# test error mechanism
basis.shell_types[0] = 102
assert_raises(ValueError, basis.call_gint_grid, gint1_fns_basis, weights.reshape((1,-1)), points*angstrom, 1)
basis.shell_types[0] = -763
assert_raises(ValueError, basis.call_gint_grid, gint1_fns_basis, weights.reshape((1,-1)), points*angstrom, 1)
def test_pot_h_sto3g():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
# real test for the output
dmat = fchk.fields["Total SCF Density"]
points = ref_data_h_sto3g_pot[:,:3]*angstrom
radius = numpy.sqrt((points**2).sum(axis=1))
ref_data_h_sto3g_pot[:,3] -= 1/radius
potential = -basis.call_gint_grid(gint2_nai_dmat, dmat, points)
assert(abs(potential-ref_data_h_sto3g_pot[:,3]).max() < 1e-8)
# test error mechanism
basis.shell_types[0] = 102
assert_raises(ValueError, basis.call_gint_grid, gint2_nai_dmat, dmat, points*angstrom)
basis.shell_types[0] = -763
assert_raises(ValueError, basis.call_gint_grid, gint2_nai_dmat, dmat, points*angstrom)
def test_dens_h_sto3g():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
weights = weights[basis.g03_permutation]
points = ref_data_h_sto3g_orb0[:,:3]
orb0 = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1,-1)), points*angstrom, 1)[0]
num_dmat = (basis.num_dof*(basis.num_dof+1))/2
dmat = fchk.fields["Total SCF Density"][:num_dmat]
density = basis.call_gint_grid(gint1_fn_dmat, dmat, points*angstrom)
assert(abs(orb0**2-density).max() < 1e-10)
# test error mechanism
basis.shell_types[0] = 102
assert_raises(ValueError, basis.call_gint_grid, gint1_fn_dmat, dmat, points*angstrom, 1)
basis.shell_types[0] = -763
assert_raises(ValueError, basis.call_gint_grid, gint1_fn_dmat, dmat, points*angstrom, 1)
def test_orb0_h_sto3g():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
# real test for the output
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
points = ref_data_h_sto3g_orb0[:, :3]
fns = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1, -1)),
points * angstrom, 1)[0]
assert (abs(fns - ref_data_h_sto3g_orb0[:, 3]).max() < 1e-10)
# test error mechanism
basis.shell_types[0] = 102
assert_raises(ValueError, basis.call_gint_grid, gint1_fns_basis,
weights.reshape((1, -1)), points * angstrom, 1)
basis.shell_types[0] = -763
assert_raises(ValueError, basis.call_gint_grid, gint1_fns_basis,
weights.reshape((1, -1)), points * angstrom, 1)
def test_pot_o2_cc_pvtz_pure():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_pure")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
dmat = fchk.fields["Total SCF Density"]
reorder_dmat(dmat, basis.g03_permutation)
points = ref_data_o2_cc_pvtz_pure_pot[:, :3] * angstrom
ref_potential = ref_data_o2_cc_pvtz_pure_pot[:, 3]
nuc_potential = 0.0
for i in xrange(fchk.molecule.size):
center = fchk.molecule.coordinates[i]
Z = fchk.molecule.numbers[i]
radius = numpy.sqrt(((points - center)**2).sum(axis=1))
nuc_potential += Z / radius
ref_potential -= nuc_potential
potential = -basis.call_gint_grid(gint2_nai_dmat, dmat, points)
assert (abs(potential - ref_potential).max() < 1e-6)
def test_pot_o2_cc_pvtz_pure():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_pure")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
dmat = fchk.fields["Total SCF Density"]
reorder_dmat(dmat, basis.g03_permutation)
points = ref_data_o2_cc_pvtz_pure_pot[:,:3]*angstrom
ref_potential = ref_data_o2_cc_pvtz_pure_pot[:,3]
nuc_potential = 0.0
for i in xrange(fchk.molecule.size):
center = fchk.molecule.coordinates[i]
Z = fchk.molecule.numbers[i]
radius = numpy.sqrt(((points-center)**2).sum(axis=1))
nuc_potential += Z/radius
ref_potential -= nuc_potential
potential = -basis.call_gint_grid(gint2_nai_dmat, dmat, points)
assert(abs(potential-ref_potential).max() < 1e-6)
def test_pot_h_sto3g():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
# real test for the output
dmat = fchk.fields["Total SCF Density"]
points = ref_data_h_sto3g_pot[:, :3] * angstrom
radius = numpy.sqrt((points**2).sum(axis=1))
ref_data_h_sto3g_pot[:, 3] -= 1 / radius
potential = -basis.call_gint_grid(gint2_nai_dmat, dmat, points)
assert (abs(potential - ref_data_h_sto3g_pot[:, 3]).max() < 1e-8)
# test error mechanism
basis.shell_types[0] = 102
assert_raises(ValueError, basis.call_gint_grid, gint2_nai_dmat, dmat,
points * angstrom)
basis.shell_types[0] = -763
assert_raises(ValueError, basis.call_gint_grid, gint2_nai_dmat, dmat,
points * angstrom)
def test_dens_h_sto3g():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
weights = weights[basis.g03_permutation]
points = ref_data_h_sto3g_orb0[:, :3]
orb0 = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1, -1)),
points * angstrom, 1)[0]
num_dmat = (basis.num_dof * (basis.num_dof + 1)) / 2
dmat = fchk.fields["Total SCF Density"][:num_dmat]
density = basis.call_gint_grid(gint1_fn_dmat, dmat, points * angstrom)
assert (abs(orb0**2 - density).max() < 1e-10)
# test error mechanism
basis.shell_types[0] = 102
assert_raises(ValueError, basis.call_gint_grid, gint1_fn_dmat, dmat,
points * angstrom, 1)
basis.shell_types[0] = -763
assert_raises(ValueError, basis.call_gint_grid, gint1_fn_dmat, dmat,
points * angstrom, 1)
def test_dens_o2_cc_pvtz_pure():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_pure")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
num_dmat = (basis.num_dof*(basis.num_dof+1))/2
points = ref_data_o2_cc_pvtz_pure_orb0[:,:3]
dmat = fchk.fields["Total SCF Density"][:num_dmat]
reorder_dmat(dmat, basis.g03_permutation)
density = basis.call_gint_grid(gint1_fn_dmat, dmat, points*angstrom)
num_alpha = fchk.fields["Number of alpha electrons"]
weights = fchk.fields["Alpha MO coefficients"][:num_alpha*basis.num_dof]
weights = weights.reshape((num_alpha, basis.num_dof))
weights = weights[:,basis.g03_permutation]
orbitals = basis.call_gint_grid(gint1_fns_basis, weights, points*angstrom, num_alpha)
assert(orbitals.shape == (num_alpha, len(points)))
expected_density = 2*(orbitals**2).sum(axis=0)
assert(abs(density-expected_density).max() < 1e-6)
def test_dens_o2_cc_pvtz_pure():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_pure")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
num_dmat = (basis.num_dof * (basis.num_dof + 1)) / 2
points = ref_data_o2_cc_pvtz_pure_orb0[:, :3]
dmat = fchk.fields["Total SCF Density"][:num_dmat]
reorder_dmat(dmat, basis.g03_permutation)
density = basis.call_gint_grid(gint1_fn_dmat, dmat, points * angstrom)
num_alpha = fchk.fields["Number of alpha electrons"]
weights = fchk.fields["Alpha MO coefficients"][:num_alpha * basis.num_dof]
weights = weights.reshape((num_alpha, basis.num_dof))
weights = weights[:, basis.g03_permutation]
orbitals = basis.call_gint_grid(gint1_fns_basis, weights,
points * angstrom, num_alpha)
assert (orbitals.shape == (num_alpha, len(points)))
expected_density = 2 * (orbitals**2).sum(axis=0)
assert (abs(density - expected_density).max() < 1e-6)
def test_h_sto3g_num():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
basis = GaussianBasis.from_fchk(fchk)
assert(basis.num_shells==1)
assert(basis.num_dof==1)
def test_h_sto3g_num():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
basis = GaussianBasis.from_fchk(fchk)
assert (basis.num_shells == 1)
assert (basis.num_dof == 1)
