def test_load_wfn_lif_fci():
fn_wfn = context.get_fn('test/lif_fci.wfn')
sys = System.from_file(fn_wfn)
assert isinstance(sys.wfn, RestrictedWFN)
assert sys.natom == 2
assert sys.obasis.nbasis == 44
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5) #Check normalization
assert sys.wfn.exp_alpha.occupations.shape == (18,)
assert abs(sys.wfn.exp_alpha.occupations.sum() - 6.0) < 1.e-6
assert sys.wfn.exp_alpha.occupations[0] == 2.00000000/2
assert sys.wfn.exp_alpha.occupations[10] == 0.00128021/2
assert sys.wfn.exp_alpha.occupations[-1] == 0.00000054/2
assert sys.wfn.exp_alpha.energies.shape == (18,)
assert sys.wfn.exp_alpha.energies[0] == -26.09321253
assert sys.wfn.exp_alpha.energies[15] == 1.70096290
assert sys.wfn.exp_alpha.energies[-1] == 2.17434072
assert sys.wfn.exp_alpha.coeffs.shape == (44, 18)
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute() #cannot be compared!
kin = sys.extra['energy_kin']
nn = sys.extra['energy_nn']
expected_kin = 106.9326884815 #FCI kinetic energy
expected_nn = 9.1130265227
assert (kin - expected_kin) < 1.e-6
assert (nn - expected_nn) < 1.e-6
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([-0.645282, 0.645282])
assert (abs(charges - expected_charge) < 1e-5).all()
points = np.array([[0.0, 0.0,-0.17008], [0.0, 0.0, 0.0], [0.0, 0.0, 0.03779]])
density = sys.compute_grid_density(points)
assert (abs(density - [0.492787, 0.784545, 0.867723]) < 1.e-4).all()
def test_load_wfn_li_sp_virtual():
fn_wfn = context.get_fn('test/li_sp_virtual.wfn')
sys = System.from_file(fn_wfn)
assert isinstance(sys.wfn, UnrestrictedWFN)
assert sys.obasis.nbasis == 8
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(),
1e-5) #Check normalization
sys.wfn.exp_beta.check_normalization(sys.get_overlap(),
1e-5) #Check normalization
assert abs(sys.wfn.exp_alpha.occupations.sum() - 2.0) < 1.e-6
assert abs(sys.wfn.exp_beta.occupations.sum() - 1.0) < 1.e-6
assert (sys.wfn.exp_alpha.occupations == [
1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
]).all()
assert (sys.wfn.exp_beta.occupations == [
1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
]).all()
assert (abs(sys.wfn.exp_alpha.energies - [
-0.087492, -0.080310, 0.158784, 0.158784, 1.078773, 1.090891, 1.090891,
49.643670
]) < 1.e-6).all()
assert (abs(sys.wfn.exp_beta.energies - [
-0.079905, 0.176681, 0.176681, 0.212494, 1.096631, 1.096631, 1.122821,
49.643827
]) < 1.e-6).all()
assert sys.wfn.exp_alpha.coeffs.shape == (8, 8)
assert sys.wfn.exp_beta.coeffs.shape == (8, 8)
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute()
assert abs(energy - (
-3.712905542719)) < 1.e-6 #Compare to the energy printed in wfn file
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([0.0, 0.0])
assert (abs(charges - expected_charge) < 1e-5).all()
def test_load_wfn_lif_fci():
fn_wfn = context.get_fn('test/lif_fci.wfn')
sys = System.from_file(fn_wfn)
assert isinstance(sys.wfn, RestrictedWFN)
assert sys.natom == 2
assert sys.obasis.nbasis == 44
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(),
1e-5) #Check normalization
assert sys.wfn.exp_alpha.occupations.shape == (18, )
assert abs(sys.wfn.exp_alpha.occupations.sum() - 6.0) < 1.e-6
assert sys.wfn.exp_alpha.occupations[0] == 2.00000000 / 2
assert sys.wfn.exp_alpha.occupations[10] == 0.00128021 / 2
assert sys.wfn.exp_alpha.occupations[-1] == 0.00000054 / 2
assert sys.wfn.exp_alpha.energies.shape == (18, )
assert sys.wfn.exp_alpha.energies[0] == -26.09321253
assert sys.wfn.exp_alpha.energies[15] == 1.70096290
assert sys.wfn.exp_alpha.energies[-1] == 2.17434072
assert sys.wfn.exp_alpha.coeffs.shape == (44, 18)
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute() #cannot be compared!
kin = sys.extra['energy_kin']
nn = sys.extra['energy_nn']
expected_kin = 106.9326884815 #FCI kinetic energy
expected_nn = 9.1130265227
assert (kin - expected_kin) < 1.e-6
assert (nn - expected_nn) < 1.e-6
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([-0.645282, 0.645282])
assert (abs(charges - expected_charge) < 1e-5).all()
points = np.array([[0.0, 0.0, -0.17008], [0.0, 0.0, 0.0],
[0.0, 0.0, 0.03779]])
density = sys.compute_grid_density(points)
assert (abs(density - [0.492787, 0.784545, 0.867723]) < 1.e-4).all()
def test_load_wfn_h2_ccpvqz_virtual():
fn_wfn = context.get_fn('test/h2_ccpvqz.wfn')
sys = System.from_file(fn_wfn)
assert isinstance(sys.wfn, RestrictedWFN)
assert sys.obasis.nbasis == 74
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(),
1e-5) #Chech normalization
assert (abs(sys.obasis.alphas[:5] -
[82.64000, 12.41000, 2.824000, 0.7977000, 0.2581000]) <
1.e-5).all()
assert (sys.wfn.exp_alpha.energies[:5] == [
-0.596838, 0.144565, 0.209605, 0.460401, 0.460401
]).all()
assert (sys.wfn.exp_alpha.energies[-5:] == [
12.859067, 13.017471, 16.405834, 25.824716, 26.100443
]).all()
assert (sys.wfn.exp_alpha.occupations[:5] == [1.0, 0.0, 0.0, 0.0,
0.0]).all()
assert abs(sys.wfn.exp_alpha.occupations.sum() - 1.0) < 1.e-6
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute()
assert abs(energy - (
-1.133504568400)) < 1.e-5 #Compare to the energy printed in wfn file
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([0.0, 0.0])
assert (abs(charges - expected_charge) < 1e-5).all()
def test_load_wfn_he_spd():
sys, energy = check_load_wfn('he_spd_orbital')
assert isinstance(sys.wfn, RestrictedWFN)
assert abs(energy - (-2.855319016184)) < 1.e-6 #Compare to the energy printed in wfn file
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([0.0])
assert (abs(charges - expected_charge) < 1e-5).all()
def test_load_wfn_he_spdfgh_virtual():
sys, energy = check_load_wfn('he_spdfgh_virtual')
assert isinstance(sys.wfn, RestrictedWFN)
assert abs(energy - (-1.048675168346)) < 1.e-6 #Compare to the energy printed in wfn file
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([0.0])
assert (abs(charges - expected_charge) < 1e-5).all()
def check_load_wfn(name):
# system out of *.wfn file
mol1 = IOData.from_file(context.get_fn('test/%s.wfn' % name))
# system out of *.fchk file
mol2 = IOData.from_file(context.get_fn('test/%s.fchk' % name))
# Coordinates check:
assert (abs(mol1.coordinates - mol2.coordinates) < 1e-6).all()
# Numbers check
numbers1 = mol1.numbers
numbers2 = mol2.numbers
assert (numbers1 == numbers2).all()
# Basis Set check:
obasis1 = mol1.obasis
obasis2 = mol2.obasis
assert obasis1.nbasis == obasis2.nbasis
assert (obasis1.shell_map == obasis2.shell_map).all()
assert (obasis1.shell_types == obasis2.shell_types).all()
assert (obasis1.nprims == obasis2.nprims).all()
assert (abs(obasis1.alphas - obasis2.alphas) < 1.e-4).all()
# Comparing MOs (*.wfn might not contain virtual orbitals):
n_mo = mol1.orb_alpha.nfn
assert (abs(mol1.orb_alpha.energies - mol2.orb_alpha.energies[:n_mo]) <
1.e-5).all()
assert (
mol1.orb_alpha.occupations == mol2.orb_alpha.occupations[:n_mo]).all()
assert (abs(mol1.orb_alpha.coeffs - mol2.orb_alpha.coeffs[:, :n_mo]) <
1.e-7).all()
# Check overlap
olp1 = obasis1.compute_overlap()
olp2 = obasis2.compute_overlap()
obasis2.compute_overlap(olp2)
assert (abs(olp1 - olp2) < 1e-6).all()
# Check normalization
mol1.orb_alpha.check_normalization(olp1, 1e-5)
# Check charges
dm_full1 = mol1.get_dm_full()
charges1 = compute_mulliken_charges(obasis1, numbers1, dm_full1)
dm_full2 = mol2.get_dm_full()
charges2 = compute_mulliken_charges(obasis2, numbers2, dm_full2)
assert (abs(charges1 - charges2) < 1e-6).all()
# Check energy
energy1 = compute_hf_energy(mol1)
energy2 = compute_hf_energy(mol2)
# check loaded & computed energy from wfn file
assert abs(energy1 - mol1.energy) < 1.e-5
assert abs(energy1 - energy2) < 1e-5
return energy1, charges1
def test_load_molden_neon_turbomole():
# The file tested here is created with Turbomole 7.1.
fn_molden = context.get_fn('test/neon_turbomole_def2-qzvp.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.pseudo_numbers, dm_full)
assert abs(charges).max() < 1e-3
def test_load_wfn_he_spd():
sys, energy = check_load_wfn('he_spd_orbital')
assert isinstance(sys.wfn, RestrictedWFN)
assert abs(energy - (
-2.855319016184)) < 1.e-6 #Compare to the energy printed in wfn file
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([0.0])
assert (abs(charges - expected_charge) < 1e-5).all()
def test_load_wfn_he_spdfgh_virtual():
sys, energy = check_load_wfn('he_spdfgh_virtual')
assert isinstance(sys.wfn, RestrictedWFN)
assert abs(energy - (
-1.048675168346)) < 1.e-6 #Compare to the energy printed in wfn file
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([0.0])
assert (abs(charges - expected_charge) < 1e-5).all()
def test_load_molden_neon_turbomole():
# The file tested here is created with Turbomole 7.1.
fn_molden = context.get_fn('test/neon_turbomole_def2-qzvp.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, mol.pseudo_numbers, dm_full)
assert abs(charges).max() < 1e-3
def test_load_molden_nh3_molpro2012():
# The file tested here is created with MOLPRO2012.
fn_molden = context.get_fn('test/nh3_molpro2012.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges. Comparison with numbers from the Molden program output.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, mol.pseudo_numbers, dm_full)
molden_charges = np.array([0.0381, -0.2742, 0.0121, 0.2242])
assert abs(charges - molden_charges).max() < 1e-3
def test_load_molden_nh3_molpro2012():
# The file tested here is created with MOLPRO2012.
fn_molden = context.get_fn('test/nh3_molpro2012.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges. Comparison with numbers from the Molden program output.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.pseudo_numbers, dm_full)
molden_charges = np.array([0.0381, -0.2742, 0.0121, 0.2242])
assert abs(charges - molden_charges).max() < 1e-3
def check_load_wfn(name):
# system out of *.wfn file
mol1 = IOData.from_file(context.get_fn('test/%s.wfn' % name))
# system out of *.fchk file
mol2 = IOData.from_file(context.get_fn('test/%s.fchk' % name))
# Coordinates check:
assert (abs(mol1.coordinates - mol2.coordinates) < 1e-6).all()
# Numbers check
numbers1 = mol1.numbers
numbers2 = mol2.numbers
assert (numbers1 == numbers2).all()
# Basis Set check:
obasis1 = mol1.obasis
obasis2 = mol2.obasis
assert obasis1.nbasis == obasis2.nbasis
assert (obasis1.shell_map == obasis2.shell_map).all()
assert (obasis1.shell_types == obasis2.shell_types).all()
assert (obasis1.nprims == obasis2.nprims).all()
assert (abs(obasis1.alphas - obasis2.alphas) < 1.e-4).all()
# Comparing MOs (*.wfn might not contain virtual orbitals):
n_mo = mol1.orb_alpha.nfn
assert (abs(mol1.orb_alpha.energies - mol2.orb_alpha.energies[:n_mo]) < 1.e-5).all()
assert (mol1.orb_alpha.occupations == mol2.orb_alpha.occupations[:n_mo]).all()
assert (abs(mol1.orb_alpha.coeffs - mol2.orb_alpha.coeffs[:, :n_mo]) < 1.e-7).all()
# Check overlap
olp1 = obasis1.compute_overlap()
olp2 = obasis2.compute_overlap()
obasis2.compute_overlap(olp2)
assert (abs(olp1 - olp2) < 1e-6).all()
# Check normalization
mol1.orb_alpha.check_normalization(olp1, 1e-5)
# Check charges
dm_full1 = mol1.get_dm_full()
charges1 = compute_mulliken_charges(obasis1, numbers1, dm_full1)
dm_full2 = mol2.get_dm_full()
charges2 = compute_mulliken_charges(obasis2, numbers2, dm_full2)
assert (abs(charges1 - charges2) < 1e-6).all()
# Check energy
energy1 = compute_hf_energy(mol1)
energy2 = compute_hf_energy(mol2)
# check loaded & computed energy from wfn file
assert abs(energy1 - mol1.energy) < 1.e-5
assert abs(energy1 - energy2) < 1e-5
return energy1, charges1
def test_load_molden_nh3_psi4_1():
# The file tested here is created with PSI4 (version 1.0). It should be read in
# properly by renormalizing the contractions.
fn_molden = context.get_fn('test/nh3_psi4_1.0.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges. Comparison with numbers from the Molden program output.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, mol.pseudo_numbers, dm_full)
molden_charges = np.array([0.0381, -0.2742, 0.0121, 0.2242])
assert abs(charges - molden_charges).max() < 1e-3
def test_load_molden_nh3_psi4_1():
# The file tested here is created with PSI4 (version 1.0). It should be read in
# properly by renormalizing the contractions.
fn_molden = context.get_fn('test/nh3_psi4_1.0.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges. Comparison with numbers from the Molden program output.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.pseudo_numbers, dm_full)
molden_charges = np.array([0.0381, -0.2742, 0.0121, 0.2242])
assert abs(charges - molden_charges).max() < 1e-3
def test_load_molden_nh3_orca():
# The file tested here is created with ORCA. It should be read in
# properly by altering normalization and sign conventions.
fn_molden = context.get_fn('test/nh3_orca.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges. Comparison with numbers from the Molden program output.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, mol.pseudo_numbers, dm_full)
molden_charges = np.array([0.0381, -0.2742, 0.0121, 0.2242])
assert abs(charges - molden_charges).max() < 1e-3
def test_load_molden_nh3_orca():
# The file tested here is created with ORCA. It should be read in
# properly by altering normalization and sign conventions.
fn_molden = context.get_fn('test/nh3_orca.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges. Comparison with numbers from the Molden program output.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.pseudo_numbers, dm_full)
molden_charges = np.array([0.0381, -0.2742, 0.0121, 0.2242])
assert abs(charges - molden_charges).max() < 1e-3
def test_load_mkl_ethanol():
fn_mkl = context.get_fn('test/ethanol.mkl')
mol = IOData.from_file(fn_mkl)
# Direct checks with mkl file
assert mol.numbers.shape == (9, )
assert mol.numbers[0] == 1
assert mol.numbers[4] == 6
assert mol.coordinates.shape == (9, 3)
assert abs(mol.coordinates[2, 1] / angstrom - 2.239037) < 1e-5
assert abs(mol.coordinates[5, 2] / angstrom - 0.948420) < 1e-5
assert mol.obasis.nbasis == 39
assert mol.obasis.alphas[0] == 18.731137000
assert mol.obasis.alphas[10] == 7.868272400
assert mol.obasis.alphas[-3] == 2.825393700
#assert mol.obasis.con_coeffs[5] == 0.989450608
#assert mol.obasis.con_coeffs[7] == 2.079187061
#assert mol.obasis.con_coeffs[-1] == 0.181380684
assert (mol.obasis.shell_map[:5] == [0, 0, 1, 1, 1]).all()
assert (mol.obasis.shell_types[:5] == [0, 0, 0, 0, 1]).all()
assert (mol.obasis.nprims[-5:] == [3, 1, 1, 3, 1]).all()
assert mol.exp_alpha.coeffs.shape == (39, 39)
assert mol.exp_alpha.energies.shape == (39, )
assert mol.exp_alpha.occupations.shape == (39, )
assert (mol.exp_alpha.occupations[:13] == 1.0).all()
assert (mol.exp_alpha.occupations[13:] == 0.0).all()
assert mol.exp_alpha.energies[4] == -1.0206976
assert mol.exp_alpha.energies[-1] == 2.0748685
assert mol.exp_alpha.coeffs[0, 0] == 0.0000119
assert mol.exp_alpha.coeffs[1, 0] == -0.0003216
assert mol.exp_alpha.coeffs[-1, -1] == -0.1424743
# Comparison of derived properties with ORCA output file
# nuclear-nuclear repulsion
assert abs(
compute_nucnuc(mol.coordinates, mol.pseudo_numbers) -
81.87080034) < 1e-5
# Check normalization
olp = mol.obasis.compute_overlap(mol.lf)
mol.exp_alpha.check_normalization(olp, 1e-5)
# Mulliken charges
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, mol.numbers,
dm_full)
expected_charges = np.array([
0.143316, -0.445861, 0.173045, 0.173021, 0.024542, 0.143066, 0.143080,
-0.754230, 0.400021
])
assert abs(charges - expected_charges).max() < 1e-5
# Compute HF energy
assert abs(compute_hf_energy(mol) - -154.01322894) < 1e-4
def test_load_wfn_h2o_sto3g():
fn_wfn = context.get_fn('test/h2o_sto3g.wfn')
sys = System.from_file(fn_wfn)
assert isinstance(sys.wfn, RestrictedWFN)
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5) #Check normalization
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute()
assert abs(energy - (-74.965901217080)) < 1.e-5 #Compare to the energy printed in wfn file
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([-0.330532, 0.165266, 0.165266])
assert (abs(charges - expected_charge) < 1e-5).all()
def test_load_molden_h2o():
fn_mkl = context.get_fn('test/h2o.molden.input')
sys = System.from_file(fn_mkl)
# Check normalization
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5)
# Check charges
charges = compute_mulliken_charges(sys)
expected_charges = np.array([-0.816308, 0.408154, 0.408154])
assert abs(charges - expected_charges).max() < 1e-5
def test_load_molden_he2_ghost_psi4_1():
# The file tested here is created with PSI4 (version 1.0). It should be read in
# properly by ignoring the ghost atoms.
fn_molden = context.get_fn('test/he2_ghost_psi4_1.0.molden')
mol = IOData.from_file(fn_molden)
np.testing.assert_equal(mol.pseudo_numbers, np.array([2.0]))
# Check Mulliken charges. Comparison with numbers from the Molden program output.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, np.array([0.0, 2.0]), dm_full)
molden_charges = np.array([-0.0041, 0.0041])
assert abs(charges - molden_charges).max() < 5e-4
def test_load_molden_nh3_turbomole():
# The file tested here is created with Turbomole 7.1
fn_molden = context.get_fn('test/nh3_turbomole.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges. Comparison with numbers from the Turbomole output. These
# are slightly different than in the other tests because we are using Cartesian
# functions.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, mol.pseudo_numbers, dm_full)
molden_charges = np.array([0.03801, -0.27428, 0.01206, 0.22421])
assert abs(charges - molden_charges).max() < 1e-3
def test_load_molden_nh3_molden_cart():
# The file tested here is created with molden. It should be read in
# properly without altering normalization and sign conventions.
fn_molden = context.get_fn('test/nh3_molden_cart.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges. Comparison with numbers from the Molden program output.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, mol.pseudo_numbers, dm_full)
print charges
molden_charges = np.array([0.3138, -0.4300, -0.0667, 0.1829])
assert abs(charges - molden_charges).max() < 1e-3
def test_load_molden_nh3_molden_cart():
# The file tested here is created with molden. It should be read in
# properly without altering normalization and sign conventions.
fn_molden = context.get_fn('test/nh3_molden_cart.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges. Comparison with numbers from the Molden program output.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.pseudo_numbers, dm_full)
print charges
molden_charges = np.array([0.3138, -0.4300, -0.0667, 0.1829])
assert abs(charges - molden_charges).max() < 1e-3
def test_load_molden_h2o():
fn_mkl = context.get_fn('test/h2o.molden.input')
sys = System.from_file(fn_mkl)
# Check normalization
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5)
# Check charges
charges = compute_mulliken_charges(sys)
expected_charges = np.array([-0.816308, 0.408154, 0.408154])
assert abs(charges - expected_charges).max() < 1e-5
def test_load_molden_nh3_turbomole():
# The file tested here is created with Turbomole 7.1
fn_molden = context.get_fn('test/nh3_turbomole.molden')
mol = IOData.from_file(fn_molden)
# Check Mulliken charges. Comparison with numbers from the Turbomole output. These
# are slightly different than in the other tests because we are using Cartesian
# functions.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.pseudo_numbers, dm_full)
molden_charges = np.array([0.03801, -0.27428, 0.01206, 0.22421])
assert abs(charges - molden_charges).max() < 1e-3
def test_load_wfn_h2o_sto3g_decontracted():
fn_wfn = context.get_fn('test/h2o_sto3g_decontracted.wfn')
sys = System.from_file(fn_wfn)
assert isinstance(sys.wfn, RestrictedWFN)
assert sys.obasis.nbasis == 21
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5) #Chech normalization
ham = Hamiltonian(sys, [HartreeFockExchange()]) #Compare to the energy printed in wfn file
energy = ham.compute()
assert abs(energy - (-75.162231674351)) < 1.e-5
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([-0.546656, 0.273328, 0.273328])
assert (abs(charges - expected_charge) < 1e-5).all()
def test_load_mkl_li2():
fn_mkl = context.get_fn('test/li2.mkl')
sys = System.from_file(fn_mkl)
# Check normalization
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5)
sys.wfn.exp_beta.check_normalization(sys.get_overlap(), 1e5)
# Check charges
charges = compute_mulliken_charges(sys)
expected_charges = np.array([0.5, 0.5])
assert abs(charges - expected_charges).max() < 1e-5
def test_load_molden_he2_ghost_psi4_1():
# The file tested here is created with PSI4 (version 1.0). It should be read in
# properly by ignoring the ghost atoms.
fn_molden = context.get_fn('test/he2_ghost_psi4_1.0.molden')
mol = IOData.from_file(fn_molden)
np.testing.assert_equal(mol.pseudo_numbers, np.array([2.0]))
# Check Mulliken charges. Comparison with numbers from the Molden program output.
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, np.array([0.0, 2.0]),
dm_full)
molden_charges = np.array([-0.0041, 0.0041])
assert abs(charges - molden_charges).max() < 5e-4
def test_load_mkl_li2():
fn_mkl = context.get_fn('test/li2.mkl')
sys = System.from_file(fn_mkl)
# Check normalization
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5)
sys.wfn.exp_beta.check_normalization(sys.get_overlap(), 1e5)
# Check charges
charges = compute_mulliken_charges(sys)
expected_charges = np.array([0.5, 0.5])
assert abs(charges - expected_charges).max() < 1e-5
def test_load_mkl_ethanol():
fn_mkl = context.get_fn('test/ethanol.mkl')
sys = System.from_file(fn_mkl)
# Direct checks with mkl file
assert sys.natom == 9
assert sys.coordinates.shape == (9,3)
assert sys.numbers[0] == 1
assert sys.numbers[4] == 6
assert abs(sys.coordinates[2,1]/angstrom - 2.239037) < 1e-5
assert abs(sys.coordinates[5,2]/angstrom - 0.948420) < 1e-5
assert sys.obasis.nbasis == 39
assert sys.obasis.alphas[0] == 18.731137000
assert sys.obasis.alphas[10] == 7.868272400
assert sys.obasis.alphas[-3] == 2.825393700
#assert sys.obasis.con_coeffs[5] == 0.989450608
#assert sys.obasis.con_coeffs[7] == 2.079187061
#assert sys.obasis.con_coeffs[-1] == 0.181380684
assert (sys.obasis.shell_map[:5] == [0, 0, 1, 1, 1]).all()
assert (sys.obasis.shell_types[:5] == [0, 0, 0, 0, 1]).all()
assert (sys.obasis.nprims[-5:] == [3, 1, 1, 3, 1]).all()
assert sys.wfn.exp_alpha.coeffs.shape == (39,39)
assert sys.wfn.exp_alpha.energies.shape == (39,)
assert sys.wfn.exp_alpha.occupations.shape == (39,)
assert (sys.wfn.exp_alpha.occupations[:13] == 1.0).all()
assert (sys.wfn.exp_alpha.occupations[13:] == 0.0).all()
assert sys.wfn.exp_alpha.energies[4] == -1.0206976
assert sys.wfn.exp_alpha.energies[-1] == 2.0748685
assert sys.wfn.exp_alpha.coeffs[0,0] == 0.0000119
assert sys.wfn.exp_alpha.coeffs[1,0] == -0.0003216
assert sys.wfn.exp_alpha.coeffs[-1,-1] == -0.1424743
# Comparison of derived properties with ORCA output file
# nuclear-nuclear repulsion
assert abs(sys.compute_nucnuc() - 81.87080034) < 1e-5
# Check normalization
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5)
# Mulliken charges
charges = compute_mulliken_charges(sys)
expected_charges = np.array([
0.143316, -0.445861, 0.173045, 0.173021, 0.024542, 0.143066, 0.143080,
-0.754230, 0.400021
])
assert abs(charges - expected_charges).max() < 1e-5
# Compute HF energy
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute()
assert abs(energy - -154.01322894) < 1e-4
def test_load_mkl_ethanol():
fn_mkl = context.get_fn('test/ethanol.mkl')
mol = IOData.from_file(fn_mkl)
# Direct checks with mkl file
assert mol.numbers.shape == (9,)
assert mol.numbers[0] == 1
assert mol.numbers[4] == 6
assert mol.coordinates.shape == (9,3)
assert abs(mol.coordinates[2,1]/angstrom - 2.239037) < 1e-5
assert abs(mol.coordinates[5,2]/angstrom - 0.948420) < 1e-5
assert mol.obasis.nbasis == 39
assert mol.obasis.alphas[0] == 18.731137000
assert mol.obasis.alphas[10] == 7.868272400
assert mol.obasis.alphas[-3] == 2.825393700
#assert mol.obasis.con_coeffs[5] == 0.989450608
#assert mol.obasis.con_coeffs[7] == 2.079187061
#assert mol.obasis.con_coeffs[-1] == 0.181380684
assert (mol.obasis.shell_map[:5] == [0, 0, 1, 1, 1]).all()
assert (mol.obasis.shell_types[:5] == [0, 0, 0, 0, 1]).all()
assert (mol.obasis.nprims[-5:] == [3, 1, 1, 3, 1]).all()
assert mol.exp_alpha.coeffs.shape == (39,39)
assert mol.exp_alpha.energies.shape == (39,)
assert mol.exp_alpha.occupations.shape == (39,)
assert (mol.exp_alpha.occupations[:13] == 1.0).all()
assert (mol.exp_alpha.occupations[13:] == 0.0).all()
assert mol.exp_alpha.energies[4] == -1.0206976
assert mol.exp_alpha.energies[-1] == 2.0748685
assert mol.exp_alpha.coeffs[0,0] == 0.0000119
assert mol.exp_alpha.coeffs[1,0] == -0.0003216
assert mol.exp_alpha.coeffs[-1,-1] == -0.1424743
# Comparison of derived properties with ORCA output file
# nuclear-nuclear repulsion
assert abs(compute_nucnuc(mol.coordinates, mol.pseudo_numbers) - 81.87080034) < 1e-5
# Check normalization
olp = mol.obasis.compute_overlap(mol.lf)
mol.exp_alpha.check_normalization(olp, 1e-5)
# Mulliken charges
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, mol.numbers, dm_full)
expected_charges = np.array([
0.143316, -0.445861, 0.173045, 0.173021, 0.024542, 0.143066, 0.143080,
-0.754230, 0.400021
])
assert abs(charges - expected_charges).max() < 1e-5
# Compute HF energy
assert abs(compute_hf_energy(mol) - -154.01322894) < 1e-4
def test_load_mkl_ethanol():
fn_mkl = context.get_fn('test/ethanol.mkl')
sys = System.from_file(fn_mkl)
# Direct checks with mkl file
assert sys.natom == 9
assert sys.coordinates.shape == (9, 3)
assert sys.numbers[0] == 1
assert sys.numbers[4] == 6
assert abs(sys.coordinates[2, 1] / angstrom - 2.239037) < 1e-5
assert abs(sys.coordinates[5, 2] / angstrom - 0.948420) < 1e-5
assert sys.obasis.nbasis == 39
assert sys.obasis.alphas[0] == 18.731137000
assert sys.obasis.alphas[10] == 7.868272400
assert sys.obasis.alphas[-3] == 2.825393700
#assert sys.obasis.con_coeffs[5] == 0.989450608
#assert sys.obasis.con_coeffs[7] == 2.079187061
#assert sys.obasis.con_coeffs[-1] == 0.181380684
assert (sys.obasis.shell_map[:5] == [0, 0, 1, 1, 1]).all()
assert (sys.obasis.shell_types[:5] == [0, 0, 0, 0, 1]).all()
assert (sys.obasis.nprims[-5:] == [3, 1, 1, 3, 1]).all()
assert sys.wfn.exp_alpha.coeffs.shape == (39, 39)
assert sys.wfn.exp_alpha.energies.shape == (39, )
assert sys.wfn.exp_alpha.occupations.shape == (39, )
assert (sys.wfn.exp_alpha.occupations[:13] == 1.0).all()
assert (sys.wfn.exp_alpha.occupations[13:] == 0.0).all()
assert sys.wfn.exp_alpha.energies[4] == -1.0206976
assert sys.wfn.exp_alpha.energies[-1] == 2.0748685
assert sys.wfn.exp_alpha.coeffs[0, 0] == 0.0000119
assert sys.wfn.exp_alpha.coeffs[1, 0] == -0.0003216
assert sys.wfn.exp_alpha.coeffs[-1, -1] == -0.1424743
# Comparison of derived properties with ORCA output file
# nuclear-nuclear repulsion
assert abs(sys.compute_nucnuc() - 81.87080034) < 1e-5
# Check normalization
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5)
# Mulliken charges
charges = compute_mulliken_charges(sys)
expected_charges = np.array([
0.143316, -0.445861, 0.173045, 0.173021, 0.024542, 0.143066, 0.143080,
-0.754230, 0.400021
])
assert abs(charges - expected_charges).max() < 1e-5
# Compute HF energy
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute()
assert abs(energy - -154.01322894) < 1e-4
def test_load_wfn_h2o_sto3g():
fn_wfn = context.get_fn('test/h2o_sto3g.wfn')
sys = System.from_file(fn_wfn)
assert isinstance(sys.wfn, RestrictedWFN)
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(),
1e-5) #Check normalization
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute()
assert abs(energy - (
-74.965901217080)) < 1.e-5 #Compare to the energy printed in wfn file
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([-0.330532, 0.165266, 0.165266])
assert (abs(charges - expected_charge) < 1e-5).all()
def test_load_mkl_li2():
fn_mkl = context.get_fn('test/li2.mkl')
mol = IOData.from_file(fn_mkl)
# Check normalization
olp = mol.obasis.compute_overlap(mol.lf)
mol.exp_alpha.check_normalization(olp, 1e-5)
mol.exp_beta.check_normalization(olp, 1e-5)
# Check charges
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, mol.numbers, dm_full)
expected_charges = np.array([0.5, 0.5])
assert abs(charges - expected_charges).max() < 1e-5
def test_load_wfn_h2o_sto3g_decontracted():
fn_wfn = context.get_fn('test/h2o_sto3g_decontracted.wfn')
sys = System.from_file(fn_wfn)
assert isinstance(sys.wfn, RestrictedWFN)
assert sys.obasis.nbasis == 21
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(),
1e-5) #Chech normalization
ham = Hamiltonian(
sys,
[HartreeFockExchange()]) #Compare to the energy printed in wfn file
energy = ham.compute()
assert abs(energy - (-75.162231674351)) < 1.e-5
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([-0.546656, 0.273328, 0.273328])
assert (abs(charges - expected_charge) < 1e-5).all()
def test_load_molden_h2o_orca():
fn_molden = context.get_fn('test/h2o.molden.input')
mol = IOData.from_file(fn_molden)
# Checkt title
assert mol.title == 'Molden file created by orca_2mkl for BaseName=h2o'
# Check normalization
olp = mol.obasis.compute_overlap()
mol.orb_alpha.check_normalization(olp, 1e-5)
# Check Mulliken charges
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.pseudo_numbers, dm_full)
expected_charges = np.array([-0.816308, 0.408154, 0.408154])
assert abs(charges - expected_charges).max() < 1e-5
def test_load_molden_h2o_orca():
fn_molden = context.get_fn('test/h2o.molden.input')
mol = IOData.from_file(fn_molden)
# Checkt title
assert mol.title == 'Molden file created by orca_2mkl for BaseName=h2o'
# Check normalization
olp = mol.obasis.compute_overlap(mol.lf)
mol.exp_alpha.check_normalization(olp, 1e-5)
# Check Mulliken charges
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, mol.pseudo_numbers, dm_full)
expected_charges = np.array([-0.816308, 0.408154, 0.408154])
assert abs(charges - expected_charges).max() < 1e-5
def test_load_wfn_h2_ccpvqz_virtual():
fn_wfn = context.get_fn('test/h2_ccpvqz.wfn')
sys = System.from_file(fn_wfn)
assert isinstance(sys.wfn, RestrictedWFN)
assert sys.obasis.nbasis == 74
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5) #Chech normalization
assert (abs(sys.obasis.alphas[:5] - [82.64000, 12.41000, 2.824000, 0.7977000, 0.2581000]) < 1.e-5).all()
assert (sys.wfn.exp_alpha.energies[:5] == [-0.596838, 0.144565, 0.209605, 0.460401, 0.460401]).all()
assert (sys.wfn.exp_alpha.energies[-5:] == [12.859067, 13.017471, 16.405834, 25.824716, 26.100443]).all()
assert (sys.wfn.exp_alpha.occupations[:5] == [1.0, 0.0, 0.0, 0.0, 0.0] ).all()
assert abs(sys.wfn.exp_alpha.occupations.sum() - 1.0) < 1.e-6
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute()
assert abs(energy - (-1.133504568400)) < 1.e-5 #Compare to the energy printed in wfn file
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([0.0, 0.0])
assert (abs(charges - expected_charge) < 1e-5).all()
def check_wfn(fn_wfn, restricted, nbasis, energy, charges):
fn_wfn = context.get_fn(fn_wfn)
mol = IOData.from_file(fn_wfn)
assert mol.obasis.nbasis == nbasis
olp = mol.obasis.compute_overlap(mol.lf)
if restricted:
mol.exp_alpha.check_normalization(olp, 1e-5)
assert not hasattr(mol, 'exp_beta')
else:
mol.exp_alpha.check_normalization(olp, 1e-5)
mol.exp_beta.check_normalization(olp, 1e-5)
if energy is not None:
myenergy = compute_hf_energy(mol)
assert abs(energy - myenergy) < 1e-5
dm_full = mol.get_dm_full()
mycharges = compute_mulliken_charges(mol.obasis, mol.lf, mol.numbers, dm_full)
assert (abs(charges - mycharges) < 1e-5).all()
return mol.obasis, mol.lf, mol.coordinates, mol.numbers, dm_full, mol.exp_alpha, getattr(mol, 'exp_beta', None)
def test_load_molden_li2_orca():
fn_molden = context.get_fn('test/li2.molden.input')
mol = IOData.from_file(fn_molden)
# Checkt title
assert mol.title == 'Molden file created by orca_2mkl for BaseName=li2'
# Check normalization
olp = mol.obasis.compute_overlap(mol.lf)
mol.exp_alpha.check_normalization(olp, 1e-5)
mol.exp_beta.check_normalization(olp, 1e-5)
# Check Mulliken charges
dm_full = mol.get_dm_full()
charges = compute_mulliken_charges(mol.obasis, mol.lf, mol.numbers,
dm_full)
expected_charges = np.array([0.5, 0.5])
assert abs(charges - expected_charges).max() < 1e-5
def test_load_wfn_lih_cation_fci():
fn_wfn = context.get_fn('test/lih_cation_fci.wfn')
sys = System.from_file(fn_wfn)
assert sys.natom == 2
assert sys.obasis.nbasis == 26
assert (sys.numbers == [3, 1]).all()
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5) #Check normalization
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute() #cannot be compared!
kin = sys.extra['energy_kin']
nn = sys.extra['energy_nn']
expected_kin = 7.7989675958 #FCI kinetic energy
expected_nn = 0.9766607347
assert (kin - expected_kin) < 1.e-6
assert (nn - expected_nn) < 1.e-6
assert sys.wfn.exp_alpha.occupations.shape == (11,)
assert abs(sys.wfn.exp_alpha.occupations.sum() - 1.5) < 1.e-6
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([0.913206, 0.086794])
assert (abs(charges - expected_charge) < 1e-5).all()
point = np.array([])
def test_load_wfn_li_sp_virtual():
fn_wfn = context.get_fn('test/li_sp_virtual.wfn')
sys = System.from_file(fn_wfn)
assert isinstance(sys.wfn, UnrestrictedWFN)
assert sys.obasis.nbasis == 8
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(), 1e-5) #Check normalization
sys.wfn.exp_beta.check_normalization(sys.get_overlap(), 1e-5) #Check normalization
assert abs(sys.wfn.exp_alpha.occupations.sum() - 2.0) < 1.e-6
assert abs(sys.wfn.exp_beta.occupations.sum() - 1.0) < 1.e-6
assert (sys.wfn.exp_alpha.occupations == [1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]).all()
assert (sys.wfn.exp_beta.occupations == [1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]).all()
assert (abs(sys.wfn.exp_alpha.energies - [-0.087492, -0.080310, 0.158784, 0.158784, 1.078773, 1.090891, 1.090891, 49.643670]) < 1.e-6).all()
assert (abs(sys.wfn.exp_beta.energies - [-0.079905, 0.176681, 0.176681, 0.212494, 1.096631, 1.096631, 1.122821, 49.643827]) < 1.e-6).all()
assert sys.wfn.exp_alpha.coeffs.shape == (8, 8)
assert sys.wfn.exp_beta.coeffs.shape == (8, 8)
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute()
assert abs(energy - (-3.712905542719)) < 1.e-6 #Compare to the energy printed in wfn file
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([0.0, 0.0])
assert (abs(charges - expected_charge) < 1e-5).all()
def test_load_wfn_lih_cation_fci():
fn_wfn = context.get_fn('test/lih_cation_fci.wfn')
sys = System.from_file(fn_wfn)
assert sys.natom == 2
assert sys.obasis.nbasis == 26
assert (sys.numbers == [3, 1]).all()
sys.wfn.exp_alpha.check_normalization(sys.get_overlap(),
1e-5) #Check normalization
ham = Hamiltonian(sys, [HartreeFockExchange()])
energy = ham.compute() #cannot be compared!
kin = sys.extra['energy_kin']
nn = sys.extra['energy_nn']
expected_kin = 7.7989675958 #FCI kinetic energy
expected_nn = 0.9766607347
assert (kin - expected_kin) < 1.e-6
assert (nn - expected_nn) < 1.e-6
assert sys.wfn.exp_alpha.occupations.shape == (11, )
assert abs(sys.wfn.exp_alpha.occupations.sum() - 1.5) < 1.e-6
charges = compute_mulliken_charges(sys) #Check charges
expected_charge = np.array([0.913206, 0.086794])
assert (abs(charges - expected_charge) < 1e-5).all()
point = np.array([])
