# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.
import numpy as np
from pyiron.atomistics.structure.atoms import Atoms
from pyiron.atomistics.job.interactive import GenericInteractive
__author__ = "Jan Janssen"
__copyright__ = "Copyright 2020, Max-Planck-Institut für Eisenforschung GmbH " \
"- Computational Materials Design (CM) Department"
__version__ = "1.0"
__maintainer__ = "Jan Janssen"
__email__ = "janssen@mpie.de"
__status__ = "development"
__date__ = "Feb 20, 2020"
[docs]class HessianJob(GenericInteractive):
def __init__(self, project, job_name):
super(GenericInteractive, self).__init__(project, job_name)
self.__version__ = "0.0.1"
self.__name__ = "HessianJob"
self.interactive_cache = {
"forces": [],
"positions": [],
"energy_pot": []
}
self._force_constants = None
self._reference_structure = None
self._next_positions = None
[docs] def set_force_constants(self, force_constants):
force_shape = np.shape(force_constants)
force_reshape = force_shape[0] * force_shape[2]
self._force_constants = np.transpose(force_constants, (0, 2, 1, 3)).reshape((force_reshape, force_reshape))
[docs] def set_reference_structure(self, structure):
self._reference_structure = structure
self.structure = structure
[docs] def interactive_position_setter(self, positions):
positions -= self._reference_structure.positions
positions[positions > self._reference_structure.cell[0, 0] / 2] -= self._reference_structure.cell[0, 0]
self._next_positions = positions
[docs] def calculate_forces(self):
self.interactive_cache["positions"].append(self._next_positions)
position_transformed = self._next_positions.reshape(
self._next_positions.shape[0] * self._next_positions.shape[1])
forces_transformed = -np.dot(self._force_constants, position_transformed)
self.interactive_cache["forces"].append(forces_transformed.reshape(self._next_positions.shape))
self.interactive_cache["energy_pot"].append(-1 / 2 * np.dot(position_transformed, forces_transformed))
self._next_positions = None
[docs] def run_if_interactive(self):
"""
Run the job as Python library and store the result in the HDF5 File.
Returns:
int: job ID
"""
self._interactive_library = True
self.status.running = True
self.interactive_position_setter(positions=self.structure.positions)
self.calculate_forces()
[docs] def to_hdf(self, hdf=None, group_name=None):
"""
Store the ExampleJob object in the HDF5 File
Args:
hdf (ProjectHDFio): HDF5 group object - optional
group_name (str): HDF5 subgroup name - optional
"""
super(HessianJob, self).to_hdf(hdf=hdf, group_name=group_name)
with self.project_hdf5.open("input") as hdf5_input:
if self._force_constants is not None:
hdf5_input["force_constants"] = self._force_constants
if self._reference_structure is not None:
self._reference_structure.to_hdf(hdf5_input)
[docs] def from_hdf(self, hdf=None, group_name=None):
"""
Restore the ExampleJob object in the HDF5 File
Args:
hdf (ProjectHDFio): HDF5 group object - optional
group_name (str): HDF5 subgroup name - optional
"""
super(HessianJob, self).from_hdf(hdf=hdf, group_name=group_name)
with self.project_hdf5.open("input") as hdf5_input:
if "structure" in hdf5_input.list_groups():
self._reference_structure = Atoms().from_hdf(hdf5_input)
if "force_constants" in hdf5_input.list_nodes():
self._force_constants = hdf5_input["force_constants"]
[docs] def interactive_close(self):
self._interactive_library = False
self.to_hdf()
with self.project_hdf5.open("output") as h5:
h5["generic/forces"] = np.array(self.interactive_cache["forces"])
h5["generic/energy_pot"] = np.array(self.interactive_cache["energy_pot"])
h5["generic/positions"] = np.array(self.interactive_cache["positions"])
self.project.db.item_update(self._runtime(), self._job_id)
self.status.finished = True