def __run_find_kopt(self, case):
system = molsturm.System(case.atom)
system.multiplicity = case.multiplicity
scfparams = molsturm.ScfParameters()
scfparams.system = system
basis_type = "sturmian/atomic/cs_reference_pc"
if basis_type not in molsturm.available_basis_types:
raise unittest.SkipTest("Skipped subtest " + case.atom +
", since basis type not available: " +
basis_type)
scfparams.basis = molsturm.construct_basis(
basis_type,
scfparams.system,
k_exp=0.0, # dummy
n_max=case.n_max,
l_max=case.l_max)
scfparams["scf/eigensolver/method"] = "lapack"
scfparams["guess/eigensolver/method"] = "lapack"
conv_tol = 1e-3
best = molsturm.sturmian.cs.find_kopt(scfparams, conv_tol=conv_tol)
k = best["input_parameters"]["discretisation"]["k_exp"]
self.assertAlmostEqual(k,
case.ref_kexp,
tol=conv_tol,
prefix="optimal exponent kopt: ")
self.assertAlmostEqual(best["energy_ground_state"],
case.ref_energy,
tol=conv_tol / 100,
prefix="ground state energy: ")
def dump_integrals_gaussian(atoms,
coords,
electrons,
basis_set_name,
ifile=None):
system = molsturm.System(atoms, coords, electrons)
params = molsturm.ScfParameters()
params.system = system
params.basis = molsturm.construct_basis("gaussian",
params.system,
basis_set_name=basis_set_name)
if ifile is None:
latoms = [a.lower() for a in atoms]
ifile = "integrals_{}_{}.hdf5".format("".join(latoms), basis_set_name)
with h5py.File(ifile, "w") as h5f:
write_integrals_to_hdf5(params, h5f)
g_discr = h5f.create_group("discretisation")
g_discr.create_dataset("basis_type",
data="gaussian",
dtype=h5py.special_dtype(vlen=str))
g_discr.create_dataset("basis_set_name",
dtype=h5py.special_dtype(vlen=str),
data=basis_set_name)
g_discr.create_dataset("has_real_harmonics", data=1, dtype=np.uint8)
def run_matrix_free(system, basis, extra={}):
params = molsturm.ScfParameters()
params.system = system
params.basis = basis
params["guess/method"] = "random"
params["guess/eigensolver/method"] = "arpack"
params["scf/eigensolver/method"] = "arpack"
params["scf/n_eigenpairs"] = 2 * (basis.size // 2)
params.update(extra)
res = molsturm.self_consistent_field(params)
molsturm.print_convergence_summary(res)
molsturm.print_energies(res)
molsturm.print_mo_occupation(res)
molsturm.print_quote(res)
return res
def main():
carbon = molsturm.System("c")
carbon.multiplicity = 3
params = molsturm.ScfParameters()
params.system = carbon
params.basis = molsturm.construct_basis("sturmian/atomic/cs_reference_pc",
params.system, k_exp=3.3, n_max=4,
l_max=3)
params["scf/eigensolver/method"] = "lapack"
params["scf/print_iterations"] = True
params["guess/eigensolver/method"] = "lapack"
res = molsturm.self_consistent_field(params)
molsturm.print_convergence_summary(res)
molsturm.print_energies(res)
molsturm.print_mo_occupation(res)
molsturm.print_quote(res)
return res
def dump_integrals_sturmian(atoms,
coords,
electrons,
k_exp,
n_max,
l_max,
m_max,
ifile=None):
system = molsturm.System(atoms, coords, electrons)
params = molsturm.ScfParameters()
params.system = system
basis = molsturm.construct_basis("sturmian/atomic",
params.system,
k_exp=k_exp,
n_max=n_max,
l_max=l_max,
m_max=m_max)
basis.backend = "cs_reference"
params.basis = basis
if ifile is None:
latoms = [a.lower() for a in atoms]
ifile = ("integrals_{}_{:02d}{:02d}{:02d}_{:.4f}.hdf5"
"".format("".join(latoms), n_max, l_max, m_max, k_exp))
with h5py.File(ifile, "w") as h5f:
write_integrals_to_hdf5(params, h5f)
g_discr = h5f.create_group("discretisation")
g_discr.create_dataset("basis_type",
data="sturmian/atomic",
dtype=h5py.special_dtype(vlen=str))
g_discr.create_dataset("nlm_basis", data=basis.functions)
g_discr.create_dataset("k_exp", data=k_exp)
g_discr.create_dataset("n_max", data=n_max)
g_discr.create_dataset("l_max", data=l_max)
g_discr.create_dataset("m_max", data=m_max)
g_discr.create_dataset("has_real_harmonics",
data=basis.has_real_harmonics,
dtype=np.uint8)
## 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/>.
##
## ---------------------------------------------------------------------
import molsturm
import molsturm.gaussian
import numpy as np
import matplotlib.pyplot as plt
import warnings
params = molsturm.ScfParameters()
params.system = molsturm.MolecularSystem("Be")
params["scf/print_iterations"] = True
params.basis = molsturm.construct_basis("gaussian",
params.system,
basis_set_name="cc-pvdz")
print("Running fit, please wait")
with warnings.catch_warnings():
warnings.simplefilter("ignore")
res = molsturm.gaussian.extrapolate_cbs_limit(params)
# Print the result
cov = res.cov
print("Estimated parameters: value (stddev)")
print(" E(CBS) == {0:16.14G} ({1: >9.4G})".format(res.cbs,