class TestHartreeFockHighLevelFrontend(HartreeFockTestCase):
@unittest.skipUnless(
"sturmian/atomic/cs_static14" in molsturm.available_basis_types,
"Required basis type sturmian/atomic/cs_static14 is not "
"available")
def test_sturmian_basis_on_the_fly(self):
case = testdata.test_cases_by_name("be_cs32")[0]
try:
params = molsturm.ScfParameters.from_dict(case["input_parameters"])
params.normalise()
except (ValueError, KeyError, TypeError) as e:
raise unittest.SkipTest(
"Skipped subtest " + case["testing"]["name"] +
", since construction of ScfParameters failed: " + str(e))
system = params.system
discretisation = params["discretisation"]
scf = params["scf"]
hfres = molsturm.hartree_fock(system,
basis_type=discretisation["basis_type"],
conv_tol=scf["max_error_norm"],
max_iter=scf["max_iter"],
n_eigenpairs=scf["n_eigenpairs"],
restricted=(scf["kind"] == "restricted"),
guess=params["guess/method"],
eigensolver=scf["eigensolver/method"],
print_iterations=scf["print_iterations"],
k_exp=discretisation["k_exp"],
n_max=discretisation["n_max"],
l_max=discretisation["l_max"],
m_max=discretisation["m_max"])
# TODO test guess from previous via this interface, too
self.compare_hf_results_small(case, hfres)
def run_hf(xyz,
basis,
charge=0,
multiplicity=1,
conv_tol=1e-12,
conv_tol_grad=1e-8,
max_iter=150):
import molsturm
# Quick-and-dirty xyz parser:
geom = xyz.split()
n_atom = len(geom) // 4
assert n_atom * 4 == len(geom)
atoms = [geom[i * 4] for i in range(n_atom)]
coords = [[
float(geom[i * 4 + 1]),
float(geom[i * 4 + 2]),
float(geom[i * 4 + 3])
] for i in range(n_atom)]
mol = molsturm.System(atoms, coords)
mol.charge = charge
mol.multiplicity = multiplicity
return molsturm.hartree_fock(mol,
basis_type="gaussian",
basis_set_name=basis_remap.get(basis, basis),
conv_tol=conv_tol_grad,
max_iter=max_iter)
def objective_function(args):
nonlocal recent_hf_res
nonlocal recent_hf_res_for_args
# Update geometry and run calculation:
system = geometryfctn(args)
res = molsturm.hartree_fock(system,
conv_tol=conv_tol / 10,
guess=recent_hf_res,
**params)
print("arguments: ", args, "niter:", res["n_iter"])
# Update the stored recent_hf_res but only if it differs enough
# from the one we currently have stored
if recent_hf_res_for_args is None or \
np.max(np.abs(np.array(recent_hf_res_for_args) - np.array(args))) > conv_tol:
recent_hf_res_for_args = args
recent_hf_res = res
print(" -> guess update")
if level == "hf":
return res["energy_ground_state"]
elif level == "mp2":
res = molsturm.posthf.mp2(res)
return res["energy_ground_state"]
else:
raise NotImplementedError("Level of theory not yet implemented")
def run(**extra):
res = molsturm.hartree_fock(water,
basis_type="gaussian/libint",
basis_set_name="def2-svp",
**extra)
molsturm.print_convergence_summary(res)
molsturm.print_energies(res)
molsturm.print_mo_occupation(res)
molsturm.print_quote(res)
return res
def compute_curve(atom,
basis_set="sto-3g",
conv_tol=1e-6,
zrange=(0.5, 8.0),
n_points=25,
restricted=False,
verbose=False,
method="hf"):
if method not in ["hf", "mp2", "fci"]:
raise ValueError("Only implemented for hf and mp2")
z = np.linspace(zrange[0], zrange[1], n_points)
f = np.empty_like(z)
previous_hf = None
idcs = np.argsort(z)[::-1]
for i in idcs:
sys = molsturm.MolecularSystem(atoms=[atom, atom],
coords=[(0, 0, 0), (0, 0, z[i])])
guess = previous_hf if previous_hf is not None else "random"
try:
hf = molsturm.hartree_fock(sys,
basis_type="gaussian",
conv_tol=conv_tol,
basis_set_name=basis_set,
guess=guess,
restricted=restricted,
print_iterations=verbose,
max_iter=100)
if previous_hf is None:
previous_hf = hf
if method == "hf":
f[i] = hf["energy_ground_state"]
elif method == "mp2":
mp2 = molsturm.posthf.mp2(hf)
f[i] = mp2["energy_ground_state"]
elif method == "fci":
fci = molsturm.posthf.fci(hf, n_roots=1)
f[i] = fci["states"][0]["energy"]
except RuntimeError as e:
print("Caught error for z=", z[i])
print(str(e))
print()
f[i] = np.nan
return z, f
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with molsturm. If not, see <http://www.gnu.org/licenses/>.
##
## ---------------------------------------------------------------------
## vi: tabstop=2 shiftwidth=2 softtabstop=2 expandtab
import molsturm
import molsturm.posthf
sys = molsturm.System(["beryllium"], [[0, 0, 0]])
bas = molsturm.construct_basis("sturmian/atomic",
sys,
k_exp=2.1,
n_max=11,
l_max=0,
backend="cs_reference_pc")
res = molsturm.hartree_fock(sys, bas, conv_tol=1e-10, print_iterations=True)
molsturm.print_convergence_summary(res)
molsturm.print_energies(res)
molsturm.print_mo_occupation(res)
print()
res_adc = molsturm.posthf.mp2(res)
print("MP2 energy", res_adc["energy_mp2"])
print("tot energy", res_adc["energy_ground_state"])
molsturm.print_quote(res)
residual_norm = np.max(np.max(residual))
print(fmt.format(n_iter, corr, residual_norm))
# Quasi-Newton update step
n_iter += 1
t2 -= residual / ccd_approx_jacobian(t2, state.fock, eri_asym)
if n_iter > 100:
raise RuntimeError("CCD not converged after 100 iterations.")
return corr, t2
if __name__ == "__main__":
sys = molsturm.System(
atoms=["O", "O"],
coords=[(0, 0, 0), (0, 0, 2.8535)],
)
sys.multiplicity = 3
state = molsturm.hartree_fock(sys, basis_type="gaussian",
basis_set_name="6-31g", conv_tol=5e-7)
corr, t2 = ccd(state)
maxamp = np.max(np.abs(t2))
print("CCD correlation energy: ", corr)
print("Largest t2 amplitude: ", maxamp)
print()
hf = state.energy_ground_state
print("HF energy: ", hf)
print("CCD total energy: ", corr + hf)
def run_molsturm(x):
res = molsturm.hartree_fock(system, basis, eigensolver="lapack", max_iter=200,
conv_tol=error, guess="random")
return (res["n_iter"], res["energy_ground_state"])
#!/usr/bin/env python3
## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab
import adcc
import molsturm
# Run SCF in molsturm
atoms = ["O", "H", "H"]
coords = [[0, 0, 0],
[0, 0, 1.795239827225189],
[1.693194615993441, 0, -0.599043184453037]]
system = molsturm.System(atoms, coords)
hfres = molsturm.hartree_fock(system, basis_type="gaussian",
basis_set_name="sto-3g",
conv_tol=1e-12, print_iterations=True)
# Run an adc2 calculation:
singlets = adcc.adc2(hfres, n_singlets=5, conv_tol=1e-9)
triplets = adcc.adc2(singlets.matrix, n_triplets=3, conv_tol=1e-9)
print(singlets.describe())
print(triplets.describe())
## it under the terms of the GNU General Public License as published
## by the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.
##
## molsturm is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with molsturm. If not, see <http://www.gnu.org/licenses/>.
##
## ---------------------------------------------------------------------
## vi: tabstop=2 shiftwidth=2 softtabstop=2 expandtab
import molsturm
import molsturm.posthf
sys = molsturm.System([4], [[0, 0, 0]])
res = molsturm.hartree_fock(sys, basis_type="gaussian", basis_set_name="cc-pvdz",
print_iterations=True, conv_tol=1e-10)
molsturm.print_convergence_summary(res)
molsturm.print_energies(res)
molsturm.print_mo_occupation(res)
res_adc = molsturm.posthf.mp2(res)
print("MP2 energy", res_adc["energy_mp2"])
print("tot energy", res_adc["energy_ground_state"])
molsturm.print_quote(res)
"Required basis type gaussian/libint is not available"
)
def test_gaussian_basis_on_the_flay(self):
case = testdata.test_cases_by_name("c_321g")[0]
try:
params = molsturm.ScfParameters.from_dict(case["input_parameters"])
params.normalise()
except (ValueError, KeyError, TypeError) as e:
raise unittest.SkipTest(
"Skipped subtest " + case["testing"]["name"] +
", since construction of ScfParameters failed: " + str(e))
system = params.system
discretisation = params["discretisation"]
scf = params["scf"]
hfres = molsturm.hartree_fock(
system,
basis_type=discretisation["basis_type"],
conv_tol=scf["max_error_norm"],
max_iter=scf["max_iter"],
n_eigenpairs=scf["n_eigenpairs"],
restricted=(scf["kind"] == "restricted"),
guess=params["guess/method"],
eigensolver=scf["eigensolver/method"],
print_iterations=scf["print_iterations"],
basis_set_name=discretisation["basis_set_name"])
# TODO test guess from previous via this interface, too
self.compare_hf_results_small(case, hfres)