def test_custom_grid():
s = pyopencap.System(sys_dict)
pc = pyopencap.CAP(s, cap_dict, 5)
pc.read_data(es_dict)
pc.compute_projected_cap()
e1 = get_corrected_energy(pc)
pc = pyopencap.CAP(s, cap_dict, 5)
pc.read_data(es_dict)
import numgrid
for center_index in range(len(center_coordinates_bohr)):
coordinates, w = numgrid.atom_grid_bse(
"aug-cc-pvtz",
1.0e-12,
590,
590,
proton_charges,
center_index,
center_coordinates_bohr,
hardness=3,
)
coordinates = np.array(coordinates)
x = np.array(coordinates[:, 0])
y = np.array(coordinates[:, 1])
z = np.array(coordinates[:, 2])
w = np.array(w)
pc.compute_cap_on_grid(x, y, z, w)
pc.compute_projected_cap()
e2 = get_corrected_energy(pc)
assert np.isclose(e1, e2)
def test_heff():
sys = pyopencap.System(sys_dict)
pc = pyopencap.CAP(sys, cap_dict, 10)
pc.read_data(es_dict2)
h0 = pc.get_H()
print(h0[0][0])
assert np.isclose(h0[0][0], -109.312105)
def test_molcas():
sys = pyopencap.System(sys_dict)
pc = pyopencap.CAP(sys, cap_dict, 10)
pc.read_data(es_dict)
pc.compute_ao_cap(cap_dict)
pc.compute_projected_cap()
CAPH = CAPHamiltonian(pc=pc)
def test_numerical_integration():
s = pyopencap.System(sys_dict)
pc = pyopencap.CAP(s, cap_dict, 5)
pc.read_data(es_dict)
pc.compute_projected_cap()
e1 = get_corrected_energy(pc)
pc.compute_ao_cap(cap_dict_numerical)
e2 = get_corrected_energy(pc)
assert np.isclose(e1, e2)
def test_custom_cap():
s = pyopencap.System(sys_dict)
pc = pyopencap.CAP(s, {"cap_type": "custom"}, 5, box_cap)
pc.read_data(es_dict)
pc.compute_projected_cap()
e1 = get_corrected_energy(pc)
pc.compute_ao_cap(cap_dict)
pc.compute_projected_cap()
e2 = get_corrected_energy(pc)
assert np.isclose(e1, e2)
def test_qchem():
sys = pyopencap.System(sys_dict)
pc = pyopencap.CAP(sys, cap_dict, 5)
pc.read_data(es_dict)
pc.compute_ao_cap(cap_dict)
pc.compute_projected_cap()
W = pc.get_projected_cap()
pc.compute_ao_cap(cap_dict2)
pc.compute_projected_cap()
W2 = pc.get_projected_cap()
assert not W[0][0] == W2[0][0]
CAPH = CAPHamiltonian(pc=pc)
def test_pyscf():
mol, myhf = get_hf()
tools.molden.from_scf(myhf, "molden_file.molden")
s = pyopencap.System(sys_dict)
pc = pyopencap.CAP(s, cap_dict, 3)
fs = fci.FCI(mol, myhf.mo_coeff)
fs.nroots = 3
e, c = fs.kernel()
for i in range(0, len(fs.ci)):
for j in range(0, len(fs.ci)):
dm1 = fs.trans_rdm1(fs.ci[i], fs.ci[j], myhf.mo_coeff.shape[1],
mol.nelec)
dm1_ao = np.einsum('pi,ij,qj->pq', myhf.mo_coeff, dm1,
myhf.mo_coeff.conj())
pc.add_tdm(dm1_ao, i, j, "pyscf")
pc.compute_projected_cap()
os.remove("molden_file.molden")
def test_psi4():
ci_wfn, mints = get_ci_wfn()
write_molden(ci_wfn)
s = pyopencap.System(molden_dict)
pc = pyopencap.CAP(s, cap_dict, nstates)
mo_coeff = ci_wfn.Ca()
S_mat = np.asarray(mints.ao_overlap())
n_bas = S_mat.shape[0]
so2ao = mints.petite_list().sotoao()
for i in range(0, nstates):
for j in range(i, nstates):
opdm_mo = ci_wfn.get_opdm(i, j, "SUM", True)
opdm_so = psi4.core.triplet(ci_wfn.Ca(), opdm_mo, ci_wfn.Ca(),
False, False, True)
opdm_ao = psi4.core.Matrix(n_bas, n_bas)
opdm_ao.remove_symmetry(opdm_so, so2ao)
pc.add_tdm(opdm_ao.to_array(), i, j, "psi4")
if not i == j:
pc.add_tdm(opdm_ao.to_array(), j, i, "psi4")
pc.compute_projected_cap()
os.remove('h2.molden')
cap_dict = {
"cap_type": "voronoi",
"r_cut": "3.00",
"radial_precision": "14",
"angular_points": "590"
}
es_dict = {
"package": "qchem",
"method": "eom",
"qchem_output": "../../analysis/N2/ref_outputs/qc_inp.out",
"qchem_fchk": "../../analysis/N2/ref_outputs/qc_inp.fchk",
}
s = pyopencap.System(sys_dict)
pc = pyopencap.CAP(s, cap_dict, 5)
pc.read_data(es_dict)
pc.compute_projected_cap()
W = pc.get_projected_cap()
H0 = pc.get_H()
CAPH = CAPHamiltonian(pc=pc)
eta_list = np.linspace(0, 5000, 201)
eta_list = np.around(eta_list * 1E-5, decimals=5)
CAPH.run_trajectory(eta_list)
traj = CAPH.track_state(1, tracking="energy")
ref_energy = -109.36195558
# Find optimal value of eta
uc_energy, eta_opt = traj.find_eta_opt(start_idx=10,
ref_energy=ref_energy,
units="eV")
s = pyopencap.System(molden_dict)
pyscf_smat = scf.hf.get_ovlp(mol)
s.check_overlap_mat(pyscf_smat, "pyscf")
# run full ci
fs = fci.FCI(mol, myhf.mo_coeff)
fs.nroots = nstates
e, c = fs.kernel()
# fill density matrices
h0 = np.zeros((nstates, nstates))
for i in range(0, len(e)):
h0[i][i] = e[i]
# compute CAP
pc = pyopencap.CAP(s, cap_dict, nstates)
for i in range(0, len(fs.ci)):
for j in range(0, len(fs.ci)):
dm1 = fs.trans_rdm1(fs.ci[i], fs.ci[j], myhf.mo_coeff.shape[1],
mol.nelec)
dm1_ao = np.einsum('pi,ij,qj->pq', myhf.mo_coeff, dm1,
myhf.mo_coeff.conj())
pc.add_tdm(dm1_ao, i, j, "pyscf")
pc.compute_projected_cap()
W = pc.get_projected_cap()
from pyopencap.analysis import CAPHamiltonian as CAPH
my_CAPH = CAPH(H0=h0, W=W)
my_CAPH.export("H2_fci_opencap.out")
if np.abs(z[i]) > cap_z:
result += (np.abs(z[i]) - cap_z) * (np.abs(z[i]) - cap_z)
result = w[i] * result
cap_values.append(result)
return cap_values
radial_precision = 1.0e-12
min_num_angular_points = 590
max_num_angular_points = 590
proton_charges = [7, 7, 1]
center_coordinates_bohr = [(0.0, 0.0, 1.03699997), (0.0, 0.0, -1.03699997),
(0.0, 0.0, 0.0)]
s = pyopencap.System(sys_dict)
pc = pyopencap.CAP(s, cap_dict, 5, box_cap)
pc.read_data(es_dict)
# one can use the numgrid python API (https://github.com/dftlibs/numgrid) to allocate the grid
import numgrid
for center_index in range(len(center_coordinates_bohr)):
coordinates, w = numgrid.atom_grid_bse(
"aug-cc-pvtz",
1.0e-12,
590,
590,
proton_charges,
center_index,
center_coordinates_bohr,
hardness=3,
)
