# -*- coding: utf-8 -*-
__copyright__ = """ This code is licensed under the 3-clause BSD license.
Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
See LICENSE.txt for details.
"""
from scine_puffin.config import Configuration
from .templates.job import calculation_context, job_configuration_wrapper
from .templates.scine_hessian_job import HessianJob
[docs]class ScineHessian(HessianJob):
"""
A job generating a Hessian and derived data for a single structure.
Derived data means the eigenvalues (frequencies) and eigenvectors
(normalmodes) as well as thermochemical data (Gibbs free energy).
**Order Name**
``scine_hessian``
**Optional Settings**
Optional settings are read from the ``settings`` field, which is part of
any ``Calculation`` stored in a SCINE Database.
Possible settings for this job are:
All settings recognized by ReaDuct's Hessian task. For a complete list see
the
`ReaDuct manual <https://scine.ethz.ch/static/download/readuct_manual.pdf>`_
All settings that are recognized by the SCF program chosen.
Common examples are:
max_scf_iterations :: int
The number of allowed SCF cycles until convergence.
**Required Packages**
- SCINE: Database (present by default)
- SCINE: Readuct (present by default)
- SCINE: Utils (present by default)
- A program implementing the SCINE Calculator interface, e.g. Sparrow
**Generated Data**
If successful the following data will be generated and added to the
database:
Properties
The ``hessian`` (``DenseMatrixProperty``), ``frequencies``
(``VectorProperty``), ``normal_modes`` (``DenseMatrixProperty``),
``gibbs_energy_correction`` (``NumberProperty``) and
``gibbs_free_energy` (``NumberProperty``) will be provided.
Optionally the ``electronic_energy`` associated with the structure if it
is present in the results of provided by the calculator interface.
"""
def __init__(self):
super().__init__()
self.name = "Scine Hessian Job"
@job_configuration_wrapper
def run(self, manager, calculation, config: Configuration) -> bool:
import scine_database as db
import scine_readuct as readuct
# preprocessing of structure
structure = db.Structure(calculation.get_structures()[0], self._structures)
settings_manager, program_helper = self.create_helpers(structure)
if len(structure.get_atoms()) < 2:
calculation.set_comment("No Hessian generated for a single atom.\n")
calculation.set_status(db.Status.FAILED)
return False
# actual calculation
with calculation_context(self):
systems, keys = settings_manager.prepare_readuct_task(
structure, calculation, calculation.get_settings(), config["resources"]
)
if program_helper is not None:
program_helper.calculation_preprocessing(systems[keys[0]], calculation.get_settings())
systems, success = readuct.run_hessian_task(systems, keys, **settings_manager.task_settings)
self.sp_postprocessing(success, systems, keys, structure, program_helper)
self.store_hessian_data(systems[keys[0]], structure)
return self.postprocess_calculation_context()