def main(file_xyz, cell, restart, basis, basis_folder):
"""Define which systems need to be calculated."""
system = Molecule(file_xyz)
# Set path for basis set
basisCP2K = join(basis_folder, "BASIS_MOLOPT")
potCP2K = join(basis_folder, "GTH_POTENTIALS")
# Settings specifics
s = templates.geometry
s.basis = basis
s.potential = "GTH-PBE"
s.cell_parameters = cell
s.specific.cp2k.force_eval.dft.basis_set_file_name = basisCP2K
s.specific.cp2k.force_eval.dft.potential_file_name = potCP2K
s.specific.cp2k.force_eval.dft.uks = ''
s.specific.cp2k.force_eval.dft.charge = '-1'
s.specific.cp2k.force_eval.dft.multiplicity = '2'
s.specific.cp2k.force_eval.dft.wfn_restart_file_name = f'{restart}'
# =======================
# Compute OPT files with CP2k
# =======================
result = run(cp2k(s, system))
# ======================
# Output the results
# ======================
print(result.energy)
def prepare_job_cp2k(settings: Settings, dict_input: Dict[str, Any],
guess_job: PromisedObject) -> CP2K:
"""Generate a :class:`qmflows.packages.cp2k_packages.CP2K` job.
Parameters
----------
settings
Input for CP2K
dict_input
Input for the current molecular geometry
guess_job
Previous job to read the guess wave function
Returns
-------
:class:`qmflows.packages.cp2k_package.CP2K`
job to run
"""
job_settings = prepare_cp2k_settings(settings, dict_input, guess_job)
# remove keywords not use on the next translation phase
for x in ('basis', 'potential'):
if x in job_settings:
del job_settings[x]
return cp2k(job_settings,
string_to_plams_Molecule(dict_input["geometry"]),
work_dir=dict_input['point_dir'])
def main(file_xyz, cell, restart, basis, basis_folder):
# Define which systems need to be calculated
system = Molecule(file_xyz)
# Set path for basis set
basisCP2K = join(basis_folder, "BASIS_MOLOPT")
potCP2K = join(basis_folder, "GTH_POTENTIALS")
# Settings specifics
s = templates.geometry
s.basis = basis
s.potential = "GTH-PBE"
s.cell_parameters = cell
s.specific.cp2k.force_eval.dft.basis_set_file_name = basisCP2K
s.specific.cp2k.force_eval.dft.potential_file_name = potCP2K
# s.specific.cp2k.force_eval.dft.uks = ''
# s.specific.cp2k.force_eval.dft.charge = '1'
# s.specific.cp2k.force_eval.dft.multiplicity = '2'
s.specific.cp2k.force_eval.dft.wfn_restart_file_name = '{}'.format(restart)
# =======================
# Compute OPT files with CP2k
# =======================
result = run(cp2k(s, system))
# ======================
# Output the results
# ======================
print(result.energy)
def test_cp2k_singlepoint_mock(mocker: MockFixture):
"""Mock a call to CP2K."""
# single point calculation
s = fill_cp2k_defaults(templates.singlepoint)
# print orbitals
s.specific.cp2k.force_eval.dft.print.mo.filename = (
PATH / "orbitals.out").as_posix()
s.specific.cp2k.force_eval.dft.print.mo.mo_index_range = "7 46"
s.specific.cp2k.force_eval.dft.scf.added_mos = 20
# Construct a result objects
job = cp2k(s, ETHYLENE)
jobname = "cp2k_job"
run_mocked = mock_runner(mocker, jobname)
rs = run_mocked(job)
# electronic energy
assertion.isfinite(rs.energy)
# Molecular orbitals
orbs = rs.orbitals
assertion.assert_(np.isfinite, orbs.eigenvectors,
post_process=np.all) # eigenvalues
assertion.shape_eq(orbs.eigenvectors, (46, 40))
def test_c2pk_freq_mock(mocker: MockFixture):
"""Mock a call to CP2K."""
# Frequency calculation
s = fill_cp2k_defaults(templates.singlepoint)
s.specific.cp2k.vibrational_analysis.thermochemistry = ".TRUE."
s.specific.cp2k["global"]["run_type"] = "VIBRATIONAL_ANALYSIS"
jobname = "cp2k_freq"
run_mocked = mock_runner(mocker, jobname)
job = cp2k(s, ETHYLENE, job_name=jobname)
rs = run_mocked(job)
# check properties
assertion.isfinite(rs.enthalpy)
assertion.isfinite(rs.free_energy)
def test_cp2k_opt(tmp_path: PathLike):
"""Run a simple molecular optimization."""
s = fill_cp2k_defaults(templates.geometry)
# Do a single step
s.specific.cp2k.motion.geo_opt.max_iter = 1
s.specific.cp2k.force_eval.dft.scf.eps_scf = 1e-1
water = Molecule(PATH_MOLECULES / "h2o.xyz",
'xyz',
charge=0,
multiplicity=1)
job = cp2k(s, water)
mol = run(job, folder=tmp_path)
assertion.isinstance(mol.molecule, Molecule)
def test_c2pk_opt_mock(mocker: MockFixture):
"""Mock a call to CP2K."""
# geometry optimization input
s = fill_cp2k_defaults(templates.geometry)
jobname = "cp2k_opt"
run_mocked = mock_runner(mocker, jobname)
job = cp2k(s, ETHYLENE, job_name=jobname)
rs = run_mocked(job)
# check the optimized geometry
mol = rs.geometry
assertion.len_eq(mol, 6)
atom = mol[1]
assertion.len_eq(atom.coords, 3)
assertion.eq(atom.symbol, 'C')
def compute_geo_opt(mol: Molecule, name: str, workdir: str,
path_results: str) -> Molecule:
"""Perform the geometry optimization of **mol**."""
# Get cp2k settings
s = create_cp2k_settings(mol)
# Update the setting with the geometry optimization template
sett_geo_opt = templates.geometry.overlay(s)
# Create the cp2k job
opt_job = cp2k(sett_geo_opt, mol, job_name="cp2k_opt")
# Run the cp2k job
optimized_geometry = run(opt_job.geometry, path=workdir, folder=name)
store_optimized_molecule(optimized_geometry, name, path_results)
logger.info(f"{name} has been optimized with CP2K")
return optimized_geometry
def run_plams(path_input):
"""
Call Plams to run a CP2K job
"""
# create settings
dict_input = process_input(path_input, "derivative_couplings")
sett = dict_input['cp2k_general_settings']['cp2k_settings_guess']
# adjust the cell parameters
file_cell_parameters = dict_input['cp2k_general_settings'].get("file_cell_parameters")
if file_cell_parameters is not None:
array_cell_parameters = read_cell_parameters_as_array(file_cell_parameters)[1]
sett.cell_parameters = array_cell_parameters[0, 2:11].reshape(3, 3).tolist()
# Run the job
job = cp2k(sett, plams.Molecule("test/test_files/C.xyz"))
print("sett: ", sett)
return run(job.energy)
def run_plams(path_input: PathLike) -> float:
"""Call Plams to run a CP2K job."""
# create settings
dict_input = process_input(path_input, "derivative_couplings")
sett = dict_input['cp2k_general_settings']['cp2k_settings_guess']
# adjust the cell parameters
file_cell_parameters = dict_input['cp2k_general_settings'].get(
"file_cell_parameters")
if file_cell_parameters is not None:
array_cell_parameters = read_cell_parameters_as_array(
file_cell_parameters)[1]
sett.cell_parameters = array_cell_parameters[0,
2:11].reshape(3,
3).tolist()
# Run the job
job = cp2k(sett, plams.Molecule(PATH_TEST / "C.xyz"))
return run(job.energy)
def compute_ldos(mol: Molecule, coord: NestedDict, name: str, workdir: str,
path_results: str) -> None:
"""Compute the DOS projected on subsets of atoms given through lists.
These lists are divided by atom type and coordination number.
"""
# Get cp2k settings
s = create_cp2k_settings(mol)
# Get the cp2k ldos setting containing the lists
ldos = create_ldos_lists(coord)
# Join settings and update with the single point template
s.specific = s.specific + ldos
sett_ldos = templates.singlepoint.overlay(s)
# Create the cp2k job
dos_job = cp2k(sett_ldos, mol, job_name="cp2k_ldos")
# Run the cp2k job
run(dos_job, path=workdir, folder=name)
store_coordination(coord, name, path_results)
logger.info(f"{name} LDOS has been printed with CP2K")
def main(file_xyz, cell, restart, basis, basis_folder):
"""
Define which systems need to be calculated
"""
system = Molecule(file_xyz)
# Set path for basis set
basisCP2K = join(basis_folder, "BASIS_MOLOPT")
potCP2K = join(basis_folder, "GTH_POTENTIALS")
# Settings specifics
s = templates.singlepoint
del s.specific.cp2k.force_eval.dft.print.mo
s.basis = basis
s.potential = "GTH-PBE"
s.cell_parameters = cell
s.specific.cp2k.force_eval.dft.basis_set_file_name = basisCP2K
s.specific.cp2k.force_eval.dft.potential_file_name = potCP2K
s.specific.cp2k.force_eval.dft.print.pdos.nlumo = '1000'
s.specific.cp2k.force_eval.dft.wfn_restart_file_name = '{}'.format(restart)
s.specific.cp2k.force_eval.dft.scf.ot.minimizer = 'DIIS'
s.specific.cp2k.force_eval.dft.scf.ot.n_diis = 7
s.specific.cp2k.force_eval.dft.scf.ot.preconditioner = 'FULL_SINGLE_INVERSE'
s.specific.cp2k['global']['run_type'] = 'energy'
# =======================
# Compute OPT files with CP2k
# =======================
result = run(cp2k(s, system))
# ======================
# Output the results
# ======================
print(result.energy)
