def create_cp2k_settings(mol: Molecule) -> Settings:
"""Create CP2K general settings."""
# Set path for basis set
path_basis = pkg_resources.resource_filename("nanoqm",
"basis/BASIS_MOLOPT")
path_potential = pkg_resources.resource_filename("nanoqm",
"basis/GTH_POTENTIALS")
# Settings specifics
s = Settings()
s.basis = "DZVP-MOLOPT-SR-GTH"
s.potential = "GTH-PBE"
s.cell_parameters = 25
s.specific.cp2k.force_eval.subsys.cell.periodic = 'none'
s.specific.cp2k.force_eval.dft.basis_set_file_name = path_basis
s.specific.cp2k.force_eval.dft.potential_file_name = path_potential
# functional
s.specific.cp2k.force_eval.dft.xc["xc_functional pbe"] = {}
# Generate kinds for the atom types
elements = [x.symbol for x in mol.atoms]
kinds = generate_kinds(elements, s.basis, s.potential)
# Update the setting with the kinds
s.specific = s.specific + kinds
return s
def test_c2pk_cell_opt() -> None:
"""Test CP2K cell optimization calculations with the :class:`CP2K_MM` class."""
mol = Molecule(PATH / 'cspbbr3_3d.xyz')
s = Settings()
s.specific.cp2k += cell_opt.specific.cp2k_mm.copy()
s.specific.cp2k.motion.cell_opt.max_iter = 10
s.specific.cp2k.motion.print['forces low'].filename = ''
s.gmax = [22, 22, 22]
s.cell_parameters = [25.452, 35.995, 24.452]
s.charge = {
'param': 'charge',
'Cs': 0.2,
'Pb': 0.4,
'Br': -0.2,
}
s.lennard_jones = {
'param': ('sigma', 'epsilon'),
'unit': ('nm', 'kjmol'),
'Cs Cs': (0.585, 1),
'Cs Pb': (0.510, 1),
'Br Se': (0.385, 1),
'Pb Pb': (0.598, 1),
'Br Pb': (0.290, 1),
'Br Br': (0.426, 1),
}
job = cp2k_mm(settings=s, mol=mol, job_name='cp2k_mm_cell_opt')
result = run(job, path=PATH)
assertion.eq(result.status, 'successful')
def test_cp2k_cell_parameters():
"""Test the translation from settings to CP2K specific cell parameters keywords."""
ETHYLENE = Molecule(PATH_MOLECULES / "ethylene.xyz")
# List of parameters
s = Settings()
abc = [5.958, 7.596, 15.610]
s.cell_parameters = abc
# apply transformations
CP2K.handle_special_keywords(s, "cell_parameters", abc, ETHYLENE)
# compare with the reference
ref = Settings()
ref.specific.cp2k.force_eval.subsys.cell.ABC = " [angstrom] 5.958 7.596 15.61"
assertion.eq(s.specific, ref.specific)
# cubic cell
s = Settings()
abc = 10
s.cell_parameters = abc
# apply transformations
CP2K.handle_special_keywords(s, "cell_parameters", abc, ETHYLENE)
# compare with the reference
ref = Settings()
ref.specific.cp2k.force_eval.subsys.cell.ABC = " [angstrom] 10.0 10.0 10.0"
assertion.eq(s.specific, ref.specific)
# Matrix
s = Settings()
abc = [[16.12, 0.078, -0.70], [-0.22, 4.39, 1.41], [-0.22, 1.73, 9.75]]
s.cell_parameters = abc
# apply transformations
CP2K.handle_special_keywords(s, "cell_parameters", abc, ETHYLENE)
# compare with the reference
ref = Settings()
ref.specific.cp2k.force_eval.subsys.cell.A = '{:} {:} {:}'.format(*abc[0])
ref.specific.cp2k.force_eval.subsys.cell.B = '{:} {:} {:}'.format(*abc[1])
ref.specific.cp2k.force_eval.subsys.cell.C = '{:} {:} {:}'.format(*abc[2])
assertion.eq(s.specific, ref.specific)
def prepare_cp2k_settings(geometry, work_dir):
"""
Fills in the parameters for running a single job in CP2K.
:param geometry: Molecular geometry stored as String
:type geometry: plams.Molecule
:param files: Tuple containing the IO files to run the calculations
:type files: nameTuple
:parameter settings: Dictionary contaning the data to
fill in the template
:type settings: ~qmflows.Settings
:parameter work_dir: Name of the Working folder
:type work_dir: String
:param wfn_restart_job: Path to *.wfn cp2k file use as restart file.
:type wfn_restart_job: String
:param cp2k_config: Parameters required by cp2k.
:type cp2k_config: Dict
:returns: ~qmflows.Settings
"""
# Input/Output Files
file_MO = join(work_dir, 'mo_coeffs.out')
# create Settings for the Cp2K Jobs
cp2k_args = Settings()
cp2k_args.basis = "DZVP-MOLOPT-SR-GTH"
cp2k_args.potential = "GTH-PBE"
cp2k_args.cell_parameters = [12.74] * 3
dft = cp2k_args.specific.cp2k.force_eval.dft
dft.scf.added_mos = 20
dft.scf.eps_scf = 1e-3
dft["print"]["mo"]["mo_index_range"] = "7 46"
dft.scf.diagonalization.jacobi_threshold = 1e-5
# Atom basis
cp2k_args.specific.cp2k.force_eval.subsys.kind["C"]["BASIS_SET"] = "DZVP-MOLOPT-SR-GTH-q4"
cp2k_args.specific.cp2k.force_eval.subsys.kind["C"]["POTENTIAL"] = "GTH-PBE-q4"
cp2k_args.specific.cp2k.force_eval.subsys.kind["H"]["BASIS_SET"] = "DZVP-MOLOPT-SR-GTH-q1"
cp2k_args.specific.cp2k.force_eval.subsys.kind["H"]["POTENTIAL"] = "GTH-PBE-q1"
# Functional
# cp2k_args.specific.cp2k.force_eval.dft.xc["xc_functional"]["pbe"]["scale_x"] = 0.75
# cp2k_args.specific.cp2k.force_eval.dft.xc["xc_functional"]["pbe"]["scale_c"] = 1.0
# copy the basis and potential to a tmp file
for f in ['BASIS_MOLOPT', 'GTH_POTENTIALS', 'BASIS_ADMM_MOLOPT']:
shutil.copy(join('test/test_files', f), work_dir)
# Cp2k configuration files
force = cp2k_args.specific.cp2k.force_eval
force.dft.basis_set_file_name = join(work_dir, 'BASIS_MOLOPT')
force.dft.Basis_set_file_name = join(work_dir, 'BASIS_ADMM_MOLOPT')
force.dft.potential_file_name = join(work_dir, 'GTH_POTENTIALS')
force.dft['print']['mo']['filename'] = file_MO
cp2k_args.specific.cp2k['global']['project'] = 'ethylene'
return templates.singlepoint.overlay(cp2k_args)
def cp2k_input(
range_orbitals, cell_parameters, cell_angles, added_mos,
basis="DZVP-MOLOPT-SR-GTH", potential="GTH-PBE"):
"""
# create ``Settings`` for the Cp2K Jobs.
"""
# Main Cp2k Jobs
cp2k_args = Settings()
cp2k_args.basis = fun_format(basis)
cp2k_args.potential = fun_format(potential)
cp2k_args.cell_parameters = cell_parameters
cp2k_args.cell_angles = cell_angles
main_dft = cp2k_args.specific.cp2k.force_eval.dft
main_dft.scf.added_mos = added_mos
main_dft.scf.max_scf = 40
main_dft.scf.eps_scf = 5e-4
main_dft['print']['mo']['mo_index_range'] = '"{} {}"'.format(*range_orbitals)
cp2k_args.specific.cp2k.force_eval.subsys.cell.periodic = fun_format('None')
# Setting to calculate the wave function used as guess
cp2k_OT = Settings()
cp2k_OT.basis = fun_format(basis)
cp2k_OT.potential = fun_format(potential)
cp2k_OT.cell_parameters = cell_parameters
cp2k_OT.cell_angles = cell_angles
ot_dft = cp2k_OT.specific.cp2k.force_eval.dft
ot_dft.scf.scf_guess = fun_format('atomic')
ot_dft.scf.ot.minimizer = fun_format('DIIS')
ot_dft.scf.ot.n_diis = 7
ot_dft.scf.ot.preconditioner = fun_format('FULL_SINGLE_INVERSE')
ot_dft.scf.added_mos = 0
ot_dft.scf.eps_scf = 1e-06
ot_dft.scf.scf_guess = fun_format('restart')
cp2k_OT.specific.cp2k.force_eval.subsys.cell.periodic = fun_format('None')
return cp2k_args, cp2k_OT
def test_c2pk_cell_opt_mock(mocker: MockFixture) -> None:
"""Mock a call to CP2K."""
mol = Molecule(PATH / 'cspbbr3_3d.xyz')
s = Settings()
s.specific.cp2k += cell_opt.specific.cp2k_mm.copy()
s.specific.cp2k.motion.cell_opt.max_iter = 10
s.specific.cp2k.motion.print['forces low'].filename = ''
s.gmax = [22, 22, 22]
s.cell_parameters = [25.452, 35.995, 24.452]
s.charge = {
'param': 'charge',
'Cs': 0.2,
'Pb': 0.4,
'Br': -0.2,
}
s.lennard_jones = {
'param': ('sigma', 'epsilon'),
'unit': ('nm', 'kjmol'),
'Cs Cs': (0.585, 1),
'Cs Pb': (0.510, 1),
'Br Se': (0.385, 1),
'Pb Pb': (0.598, 1),
'Br Pb': (0.290, 1),
'Br Br': (0.426, 1),
}
job = cp2k_mm(s, mol)
run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_cell_opt")
result = run_mocked(job)
assertion.eq(result.status, 'successful')
ref_volume = np.load(PATH / 'volume.npy')
ref_coordinates = np.load(PATH / 'coordinates.npy')
ref_forces = np.load(PATH / 'forces.npy')
ref_lattice = np.load(PATH / 'lattice.npy')
np.testing.assert_allclose(result.volume, ref_volume)
np.testing.assert_allclose(result.coordinates, ref_coordinates)
np.testing.assert_allclose(result.forces, ref_forces)
np.testing.assert_allclose(result.lattice, ref_lattice)