# -*- coding: utf-8 -*-
from __future__ import annotations
__copyright__ = """ This code is licensed under the 3-clause BSD license.
Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
See LICENSE.txt for details.
"""
from typing import TYPE_CHECKING
from scine_puffin.config import Configuration
from .templates.job import calculation_context, job_configuration_wrapper
from .templates.scine_optimization_job import OptimizationJob
from scine_puffin.utilities.imports import module_exists, MissingDependency
if module_exists("scine_database") or TYPE_CHECKING:
import scine_database as db
else:
db = MissingDependency("scine_database")
[docs]class ScineTsOptimization(OptimizationJob):
"""
A job searching the nearest saddlepoint on the potential energy surface.
Optimizing a given structure's geometry, generating a new transition state
structure, if successful.
**Order Name**
``scine_ts_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 transition state search
Common examples are:
optimizer : str
The name of the optimizer to be used, e.g. 'bofill' or 'evf' or 'dimer'.
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/download/readuct>`_
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 transition state structure.
Properties
The ``electronic_energy`` associated with the new structure.
"""
def __init__(self) -> None:
super().__init__()
self.name = "Scine Transition State Optimization"
[docs] @job_configuration_wrapper
def run(self, manager: db.Manager, calculation: db.Calculation, config: Configuration) -> bool:
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)
# 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(self.get_calc(keys[0], systems), calculation.get_settings())
systems, success = readuct.run_tsopt_task(systems, keys, **settings_manager.task_settings)
self.optimization_postprocessing(
success, systems, keys, structure, db.Label.TS_OPTIMIZED, program_helper
)
return self.postprocess_calculation_context()