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Deduplicate elastic #166

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Deduplicate elastic #166

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4425fcf
Condense three classes into one
liamhuber Jan 2, 2024
c73180e
:bug: fix the fields
liamhuber Jan 2, 2024
760b3a4
Make the elastic_matrix_inverse public
liamhuber Jan 2, 2024
6daf367
Black suggestion
liamhuber Jan 2, 2024
9ebe6be
Use the public variable
liamhuber Jan 2, 2024
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20 changes: 0 additions & 20 deletions atomistics/shared/output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,26 +77,6 @@ class OutputEnergyVolumeCurve(
volume: callable


@dataclasses.dataclass
class OutputElastic(Output):
elastic_matrix: callable
elastic_matrix_inverse: callable
bulkmodul_voigt: callable
bulkmodul_reuss: callable
bulkmodul_hill: callable
shearmodul_voigt: callable
shearmodul_reuss: callable
shearmodul_hill: callable
youngsmodul_voigt: callable
youngsmodul_reuss: callable
youngsmodul_hill: callable
poissonsratio_voigt: callable
poissonsratio_reuss: callable
poissonsratio_hill: callable
AVR: callable
elastic_matrix_eigval: callable
Comment on lines -80 to -97
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While currently only the ElasticMatrix implements the calculation of the elastic moduli, @samwaseda developed the ElasticTensor class which can also calculate the elastic moduli. https://github.com/pyiron/pyiron_atomistics/blob/main/pyiron_atomistics/atomistics/master/elastic.py So I would prefer to have a reference interface for the elastic moduli defined in shared/output and a specific implementation in the workflows/elastic/workflow.py module.

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I would suggest to make it specific now anyhow, then introduce a shared parent if and when failing to do so would result in code duplication or a lack of clarity about the relationship between the two approaches.



@dataclasses.dataclass
class OutputPhonons(Output):
mesh_dict: callable
Expand Down
178 changes: 87 additions & 91 deletions atomistics/workflows/elastic/elastic_moduli.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,11 @@
from functools import cached_property

import numpy as np

from atomistics.shared.output import Output


def get_bulkmodul_voigt(elastic_matrix):
def get_bulkmodul_voigt(elastic_matrix) -> float:
return (
elastic_matrix[0, 0]
+ elastic_matrix[1, 1]
Expand All @@ -10,27 +14,27 @@ def get_bulkmodul_voigt(elastic_matrix):
) / 9


def get_shearmodul_voigt(elastic_matrix):
def get_shearmodul_voigt(elastic_matrix) -> float:
return (
(elastic_matrix[0, 0] + elastic_matrix[1, 1] + elastic_matrix[2, 2])
- (elastic_matrix[0, 1] + elastic_matrix[0, 2] + elastic_matrix[1, 2])
+ 3 * (elastic_matrix[3, 3] + elastic_matrix[4, 4] + elastic_matrix[5, 5])
) / 15


def get_youngsmodul_voigt(bulkmodul_voigt, shearmodul_voigt):
def get_youngsmodul_voigt(bulkmodul_voigt, shearmodul_voigt) -> float:
return (9 * bulkmodul_voigt * shearmodul_voigt) / (
3 * bulkmodul_voigt + shearmodul_voigt
)


def get_poissonsratio_voigt(bulkmodul_voigt, shearmodul_voigt):
def get_poissonsratio_voigt(bulkmodul_voigt, shearmodul_voigt) -> float:
return (1.5 * bulkmodul_voigt - shearmodul_voigt) / (
3 * bulkmodul_voigt + shearmodul_voigt
)


def get_bulkmodul_reuss(elastic_matrix_inverse):
def get_bulkmodul_reuss(elastic_matrix_inverse) -> float:
return 1 / (
elastic_matrix_inverse[0, 0]
+ elastic_matrix_inverse[1, 1]
Expand All @@ -44,7 +48,7 @@ def get_bulkmodul_reuss(elastic_matrix_inverse):
)


def get_shearmodul_reuss(elastic_matrix_inverse):
def get_shearmodul_reuss(elastic_matrix_inverse) -> float:
return 15 / (
4
* (
Expand All @@ -67,164 +71,156 @@ def get_shearmodul_reuss(elastic_matrix_inverse):
)


def get_youngsmodul_reuss(bulkmodul_reuss, shearmodul_reuss):
def get_youngsmodul_reuss(bulkmodul_reuss, shearmodul_reuss) -> float:
return (9 * bulkmodul_reuss * shearmodul_reuss) / (
3 * bulkmodul_reuss + shearmodul_reuss
)


def get_poissonsratio_reuss(bulkmodul_reuss, shearmodul_reuss):
def get_poissonsratio_reuss(bulkmodul_reuss, shearmodul_reuss) -> float:
return (1.5 * bulkmodul_reuss - shearmodul_reuss) / (
3 * bulkmodul_reuss + shearmodul_reuss
)


def get_bulkmodul_hill(bulkmodul_voigt, bulkmodul_reuss):
def get_bulkmodul_hill(bulkmodul_voigt, bulkmodul_reuss) -> float:
return _hill_approximation(voigt=bulkmodul_voigt, reuss=bulkmodul_reuss)


def get_shearmodul_hill(shearmodul_voigt, shearmodul_reuss):
def get_shearmodul_hill(shearmodul_voigt, shearmodul_reuss) -> float:
return _hill_approximation(voigt=shearmodul_voigt, reuss=shearmodul_reuss)


def get_youngsmodul_hill(bulkmodul_hill, shearmodul_hill):
def get_youngsmodul_hill(bulkmodul_hill, shearmodul_hill) -> float:
return (9.0 * bulkmodul_hill * shearmodul_hill) / (
3.0 * bulkmodul_hill + shearmodul_hill
)


def get_poissonsratio_hill(bulkmodul_hill, shearmodul_hill):
def get_poissonsratio_hill(bulkmodul_hill, shearmodul_hill) -> float:
return (1.5 * bulkmodul_hill - shearmodul_hill) / (
3.0 * bulkmodul_hill + shearmodul_hill
)


def get_AVR(shearmodul_voigt, shearmodul_reuss):
def get_AVR(shearmodul_voigt, shearmodul_reuss) -> float:
return (
100.0
* (shearmodul_voigt - shearmodul_reuss)
/ (shearmodul_voigt + shearmodul_reuss)
)


def get_elastic_matrix_eigval(elastic_matrix):
def get_elastic_matrix_eigval(elastic_matrix) -> tuple[np.ndarray, np.ndarray]:
return np.linalg.eig(elastic_matrix)


def get_elastic_matrix_inverse(elastic_matrix):
def get_elastic_matrix_inverse(elastic_matrix) -> np.ndarray:
return np.linalg.inv(elastic_matrix)


def _hill_approximation(voigt, reuss):
return 0.50 * (voigt + reuss)


class ElasticProperties:
def __init__(self, elastic_matrix):
class OutputElastic(Output):
def __init__(self, elastic_matrix: np.ndarray):
self._elastic_matrix = elastic_matrix
self._elastic_matrix_inverse = None
self._bulkmodul_voigt = None
self._shearmodul_voigt = None
self._bulkmodul_reuss = None
self._shearmodul_reuss = None
self._bulkmodul_hill = None
self._shearmodul_hill = None

def get_elastic_matrix(self):

@property
def elastic_matrix(self):
return self._elastic_matrix

def get_elastic_matrix_inverse(self):
if self._elastic_matrix_inverse is None:
self._elastic_matrix_inverse = get_elastic_matrix_inverse(
elastic_matrix=self._elastic_matrix
)
return self._elastic_matrix_inverse
@cached_property
def elastic_matrix_inverse(self):
return get_elastic_matrix_inverse(elastic_matrix=self.elastic_matrix)

def get_bulkmodul_voigt(self):
if self._bulkmodul_voigt is None:
self._bulkmodul_voigt = get_bulkmodul_voigt(
elastic_matrix=self._elastic_matrix
)
return self._bulkmodul_voigt
@cached_property
def bulkmodul_voigt(self):
return get_bulkmodul_voigt(elastic_matrix=self.elastic_matrix)

def get_shearmodul_voigt(self):
if self._shearmodul_voigt is None:
self._shearmodul_voigt = get_shearmodul_voigt(
elastic_matrix=self._elastic_matrix
)
return self._shearmodul_voigt
@cached_property
def shearmodul_voigt(self):
return get_shearmodul_voigt(elastic_matrix=self.elastic_matrix)

def get_bulkmodul_reuss(self):
if self._bulkmodul_reuss is None:
self._bulkmodul_reuss = get_bulkmodul_reuss(
elastic_matrix_inverse=self.get_elastic_matrix_inverse()
)
return self._bulkmodul_reuss
@cached_property
def bulkmodul_reuss(self):
return get_bulkmodul_reuss(elastic_matrix_inverse=self.elastic_matrix_inverse)

def get_shearmodul_reuss(self):
if self._shearmodul_reuss is None:
self._shearmodul_reuss = get_shearmodul_reuss(
elastic_matrix_inverse=self.get_elastic_matrix_inverse()
)
return self._shearmodul_reuss
@cached_property
def shearmodul_reuss(self):
return get_shearmodul_reuss(elastic_matrix_inverse=self.elastic_matrix_inverse)

def get_bulkmodul_hill(self):
if self._bulkmodul_hill is None:
self._bulkmodul_hill = get_bulkmodul_hill(
bulkmodul_voigt=self.get_bulkmodul_voigt(),
bulkmodul_reuss=self.get_bulkmodul_reuss(),
@cached_property
def bulkmodul_hill(self):
return get_bulkmodul_hill(
bulkmodul_voigt=self.bulkmodul_voigt,
bulkmodul_reuss=self.bulkmodul_reuss,
)
return self._bulkmodul_hill

def get_shearmodul_hill(self):
if self._shearmodul_hill is None:
self._shearmodul_hill = get_shearmodul_hill(
shearmodul_voigt=self.get_shearmodul_voigt(),
shearmodul_reuss=self.get_shearmodul_reuss(),
@cached_property
def shearmodul_hill(self):
return get_shearmodul_hill(
shearmodul_voigt=self.shearmodul_voigt,
shearmodul_reuss=self.shearmodul_reuss,
)
return self._shearmodul_hill

def get_youngsmodul_voigt(self):
@cached_property
def youngsmodul_voigt(self):
return get_youngsmodul_voigt(
bulkmodul_voigt=self.get_bulkmodul_voigt(),
shearmodul_voigt=self.get_shearmodul_voigt(),
bulkmodul_voigt=self.bulkmodul_voigt,
shearmodul_voigt=self.shearmodul_voigt,
)

def get_poissonsratio_voigt(self):
@cached_property
def poissonsratio_voigt(self):
return get_poissonsratio_voigt(
bulkmodul_voigt=self.get_bulkmodul_voigt(),
shearmodul_voigt=self.get_shearmodul_voigt(),
bulkmodul_voigt=self.bulkmodul_voigt,
shearmodul_voigt=self.shearmodul_voigt,
)

def get_youngsmodul_reuss(self):
@cached_property
def youngsmodul_reuss(self):
return get_youngsmodul_reuss(
bulkmodul_reuss=self.get_bulkmodul_reuss(),
shearmodul_reuss=self.get_shearmodul_reuss(),
bulkmodul_reuss=self.bulkmodul_reuss,
shearmodul_reuss=self.shearmodul_reuss,
)

def get_poissonsratio_reuss(self):
@cached_property
def poissonsratio_reuss(self):
return get_poissonsratio_reuss(
bulkmodul_reuss=self.get_bulkmodul_reuss(),
shearmodul_reuss=self.get_shearmodul_reuss(),
bulkmodul_reuss=self.bulkmodul_reuss,
shearmodul_reuss=self.shearmodul_reuss,
)

def get_youngsmodul_hill(self):
@cached_property
def youngsmodul_hill(self):
return get_youngsmodul_hill(
bulkmodul_hill=self.get_bulkmodul_hill(),
shearmodul_hill=self.get_shearmodul_hill(),
bulkmodul_hill=self.bulkmodul_hill,
shearmodul_hill=self.shearmodul_hill,
)

def get_poissonratio_hill(self):
@cached_property
def poissonsratio_hill(self):
return get_poissonsratio_hill(
bulkmodul_hill=self.get_bulkmodul_hill(),
shearmodul_hill=self.get_shearmodul_hill(),
bulkmodul_hill=self.bulkmodul_hill,
shearmodul_hill=self.shearmodul_hill,
)

def get_AVR(self):
@cached_property
def AVR(self):
return get_AVR(
shearmodul_voigt=self.get_shearmodul_voigt(),
shearmodul_reuss=self.get_shearmodul_reuss(),
shearmodul_voigt=self.shearmodul_voigt,
shearmodul_reuss=self.shearmodul_reuss,
)

def get_elastic_matrix_eigval(self):
return get_elastic_matrix_eigval(elastic_matrix=self._elastic_matrix)
@cached_property
def elastic_matrix_eigval(self):
return get_elastic_matrix_eigval(elastic_matrix=self.elastic_matrix)

def get(self, *output: str) -> dict:
return {q: getattr(self, q) for q in output}

@classmethod
def fields(cls):
return tuple(q for q in dir(cls) if not (q[0] == "_" or q in ["get", "fields"]))
27 changes: 2 additions & 25 deletions atomistics/workflows/elastic/workflow.py
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Original file line number Diff line number Diff line change
@@ -1,34 +1,13 @@
import numpy as np

from atomistics.shared.output import OutputElastic
from atomistics.workflows.interface import Workflow
from atomistics.workflows.elastic.elastic_moduli import ElasticProperties
from atomistics.workflows.elastic.elastic_moduli import OutputElastic
from atomistics.workflows.elastic.helper import (
generate_structures_helper,
analyse_structures_helper,
)


ElasticMatrixOutputElastic = OutputElastic(
elastic_matrix=ElasticProperties.get_elastic_matrix,
elastic_matrix_inverse=ElasticProperties.get_elastic_matrix_inverse,
bulkmodul_voigt=ElasticProperties.get_bulkmodul_voigt,
bulkmodul_reuss=ElasticProperties.get_bulkmodul_reuss,
bulkmodul_hill=ElasticProperties.get_bulkmodul_hill,
shearmodul_voigt=ElasticProperties.get_shearmodul_voigt,
shearmodul_reuss=ElasticProperties.get_shearmodul_reuss,
shearmodul_hill=ElasticProperties.get_shearmodul_hill,
youngsmodul_voigt=ElasticProperties.get_youngsmodul_voigt,
youngsmodul_reuss=ElasticProperties.get_youngsmodul_reuss,
youngsmodul_hill=ElasticProperties.get_youngsmodul_hill,
poissonsratio_voigt=ElasticProperties.get_poissonsratio_voigt,
poissonsratio_reuss=ElasticProperties.get_poissonsratio_reuss,
poissonsratio_hill=ElasticProperties.get_poissonratio_hill,
AVR=ElasticProperties.get_AVR,
elastic_matrix_eigval=ElasticProperties.get_elastic_matrix_eigval,
)


class ElasticMatrixWorkflow(Workflow):
def __init__(
self, structure, num_of_point=5, eps_range=0.005, sqrt_eta=True, fit_order=2
Expand Down Expand Up @@ -81,6 +60,4 @@ def analyse_structures(self, output_dict, output=OutputElastic.fields()):
self._data["strain_energy"] = strain_energy
self._data["e0"] = ene0
self._data["A2"] = A2
return ElasticMatrixOutputElastic.get(
ElasticProperties(elastic_matrix=elastic_matrix), *output
)
return OutputElastic(elastic_matrix).get(*output)
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