# -*- 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_optimization_job import OptimizationJob
[docs]class ScineGeometryOptimization(OptimizationJob):
"""
A job optimizing the geometry of a given structure, in search of a local
minimum on the potential energy surface.
Optimizing a given structure's geometry, generating a new minimum energy
structure, if successful.
**Order Name**
``scine_geometry_optimization``
**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 geometry optimization task.
Common examples are:
optimizer :: str
The name of the optimizer to be used, e.g. 'bfgs', 'lbfgs', 'nr' or
'sd'.
convergence_max_iterations :: int
The maximum number of geometry optimization cycles.
convergence_delta_value :: float
The convergence criterion for the electronic energy difference between
two steps.
convergence_gradient_max_coefficient :: float
The convergence criterion for the maximum absolute gradient.
contribution.
convergence_step_rms :: float
The convergence criterion for root mean square of the geometric
gradient.
convergence_step_max_coefficient :: float
The convergence criterion for the maximum absolute coefficient in the
last step taken in the geometry optimization.
convergence_gradient_rms :: float
The convergence criterion for root mean square of the last step taken
in the geometry optimization.
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:
Structures
A new minimum energy structure.
Properties
The ``electronic_energy`` associated with the new structure.
"""
def __init__(self):
super().__init__()
self.name = "Scine Geometry Optimization"
@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)
try:
new_label = self.determine_new_label(structure)
except Exception:
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_opt_task(systems, keys, **settings_manager.task_settings)
self.optimization_postprocessing(
success, systems, keys, structure, new_label, program_helper
)
return self.postprocess_calculation_context()