feature/SOF 7397 #151

VsevolodX · 2024-07-25T21:07:39Z

feat: add first implementations of perturbation

timurbazhirov · 2024-07-31T03:32:57Z

src/py/mat3ra/made/tools/build/deformation/builders.py

+
+    @staticmethod
+    def deform_slab(configuration):
+        new_material = configuration.slab.clone()


The logic is ambiguous - why is there slab in configuration for deformation?

Changed to SlabDeformationBuilder

timurbazhirov · 2024-07-31T03:33:14Z

src/py/mat3ra/made/tools/build/deformation/builders.py

+
+
+class ContinuousDeformationBuilder(DeformationBuilder):
+    def deform_slab_isometrically(self, configuration):


Same as above

timurbazhirov · 2024-07-31T03:33:35Z

src/py/mat3ra/made/tools/build/deformation/builders.py

+        new_basis.to_crystal()
+        new_material.basis = new_basis
+
+        # TODO: adjust the lattice parameters with the same coordinates transformation


Remove or implement

timurbazhirov · 2024-07-31T03:34:13Z

src/py/mat3ra/made/tools/build/deformation/configuration.py

+from ...utils import DeformationFunctionBuilder
+
+
+class DeformationConfiguration(BaseModel, InMemoryEntity):


DeformationConfiguration with deformation_function

SlabDeformationConfiguration inheriting from it and adding slab

Same for builders

timurbazhirov · 2024-07-31T03:35:49Z

src/py/mat3ra/made/tools/utils.py

+    ]
+
+
+class DeformationFunctionBuilder:


Builder -> Holder for this and above class

timurbazhirov · 2024-07-31T03:37:14Z

src/py/mat3ra/made/tools/utils.py

+        return coordinate
+
+
+def solve_sine_wave_coordinate_prime(


timurbazhirov · 2024-07-31T03:41:07Z

src/py/mat3ra/made/tools/utils.py

+    return sine_wave(coordinate_prime, amplitude, wavelength, phase, axis="x")
+
+
+def sine_wave_radial(


The coordinate functions need to be better organized

timurbazhirov · 2024-07-31T03:41:41Z

src/py/mat3ra/made/tools/build/deformation/builders.py

@@ -0,0 +1,63 @@
+from typing import List


Let's use perturbation

timurbazhirov · 2024-08-07T00:47:15Z

src/py/mat3ra/made/tools/build/perturbation/builders.py

+        return new_material
+
+    @staticmethod
+    def _set_new_coordinates(new_material, new_coordinates):


This can be inside material class or basis class

timurbazhirov · 2024-08-07T00:48:57Z

src/py/mat3ra/made/tools/build/perturbation/builders.py

+
+
+class SlabPerturbationBuilder(PerturbationBuilder):
+    def create_perturbed_slab(self, configuration):


Here and elsewhere - type hints

timurbazhirov · 2024-08-07T00:49:20Z

src/py/mat3ra/made/tools/build/perturbation/builders.py

+
+
+class CellMatchingDistancePreservingSlabPerturbationBuilder(DistancePreservingSlabPerturbationBuilder):
+    def _transform_cell_vectors(self, configuration: PerturbationConfiguration) -> List[List[float]]:


_transform_lattice_vectors or _transform_cell

timurbazhirov · 2024-08-07T00:51:45Z

src/py/mat3ra/made/tools/build/perturbation/configuration.py

+
+class PerturbationConfiguration(BaseModel, InMemoryEntity):
+    material: Material
+    perturbation_function: Tuple[Callable, Dict] = PerturbationFunctionHolder.sine_wave()


We need to call things for what they are if this is a tuple, we should call it a tuple, or object, or function_config_tuple

I restructured instead

timurbazhirov · 2024-08-07T00:55:06Z

src/py/mat3ra/made/tools/utils/__init__.py

+    return converted_array.tolist()
+
+
+class CoordinateConditionBuilder:


Should go to coordinate

timurbazhirov · 2024-08-07T00:55:37Z

src/py/mat3ra/made/tools/utils/__init__.py

+        )
+
+
+class PerturbationFunctionHolder:


Should be inside perturbation subfolder

timurbazhirov · 2024-08-07T01:05:30Z

src/py/mat3ra/made/tools/utils/helpers.py

+        raise NotImplementedError
+
+
+class SineWave(FunctionHolder):


SineWaveFunctionHolder

timurbazhirov · 2024-08-07T01:07:14Z

src/py/mat3ra/made/tools/utils/helpers.py

+    ) -> Callable[[List[float]], List[float]]:
+        index = AXIS_TO_INDEX_MAP[axis]
+
+        def coordinate_transformation(coordinate: List[float]):


We should avoid nested defs

timurbazhirov · 2024-08-07T01:08:11Z

src/py/mat3ra/made/tools/utils/factories.py

+from mat3ra.utils.factory import BaseFactory
+
+
+class PerturbationFunctionHelperFactory(BaseFactory):


PerturbationFunctionHolderFactory

timurbazhirov · 2024-08-07T01:08:36Z

src/py/mat3ra/made/tools/utils/helpers.py

@@ -0,0 +1,84 @@
+from typing import Callable, List, Literal


file should be called functions

timurbazhirov · 2024-08-11T19:54:33Z

src/py/mat3ra/made/tools/utils/functions.py

+        """
+        raise NotImplementedError
+
+    def apply_derivative(self, coordinate: List[float]) -> float:


calculate_derivative

timurbazhirov · 2024-08-11T19:55:09Z

src/py/mat3ra/made/tools/utils/functions.py

+        """
+        raise NotImplementedError
+
+    def get_arc_length(self, a: float, b: float) -> float:


calculate_arc_length

timurbazhirov · 2024-08-11T19:55:50Z

src/py/mat3ra/made/tools/utils/functions.py

+        raise NotImplementedError
+
+
+class PerturbationFunctionHolder(FunctionHolder):


Should be in perturbation folder

timurbazhirov · 2024-08-11T19:58:11Z

src/py/mat3ra/made/tools/utils/functions.py

+        """
+        raise NotImplementedError
+
+    def get_json(self) -> dict:


Let's check for this to be used instead of the tuple logic in all the previously written code also

VsevolodX added 6 commits July 25, 2024 14:07

feat: add first implementations of perturbation

4f049c6

update: rename to deformation

af0f656

update: rename to deformation

15a99d0

feat: add deformation function builder

20b79c3

update: prepare for continuos deformation

7279daa

feat: working implementation

6939b39

VsevolodX changed the base branch from main to feature/SOF-7395 July 27, 2024 02:20

VsevolodX added 8 commits July 26, 2024 19:24

update: add sine and radial sine

95337d6

update: add sine helpers

b53ce87

update: use sine helpers

50658ad

update: helps with second time interface creation

b90b7ab

Merge branch 'feature/SOF-7395' into feature/SOF-7397

71987fb

update: simply use continuous deformations

11db833

update: optimize

b49ca69

update: types, cleanup

f304dcb

VsevolodX marked this pull request as ready for review July 31, 2024 03:23

timurbazhirov requested changes Jul 31, 2024

View reviewed changes

Base automatically changed from feature/SOF-7395 to main July 31, 2024 23:25

VsevolodX added 12 commits July 31, 2024 16:25

Merge branch 'main' into feature/SOF-7397

a97b7c3

update: fix and wrap

9e98b26

update: move functions to holder

425892d

update: OOP inheritance

c7f8d53

update: rename slab -> material

3861d28

update: rename deformation -> perturbation

83325e3

update: make work with distinct builders

e512d29

update: use OOP and cleanup

678eda1

update: small adjustments

a879f52

chore: add docstring

7cb6053

update: even more optimization

07cf54c

update: fix a mistake

2b0805a

timurbazhirov reviewed Aug 7, 2024

View reviewed changes

VsevolodX added 10 commits August 6, 2024 18:24

update: add json as method:

ccf9702

chore: add types

ae3cdcb

chore: remove duplicated method

5fca5dc

update: change folders and import

e8a22a1

update: renames

98a4358

chore: run lint fix

3697be4

update: optimize ann OOP

a42ebbd

chore: add a todo memo

e8f4947

update: optimize with OOP

f84e873

update: add set coordintes as a method

963822a

timurbazhirov reviewed Aug 11, 2024

View reviewed changes

timurbazhirov approved these changes Aug 11, 2024

View reviewed changes

VsevolodX added 3 commits August 11, 2024 15:55

update: rearrange

5f2dcf4

update: remove tuples

8ce0856

update: rename

4c6a391

VsevolodX merged commit 361e423 into main Aug 12, 2024
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VsevolodX deleted the feature/SOF-7397 branch August 12, 2024 17:48

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feature/SOF 7397 #151

feature/SOF 7397 #151

VsevolodX commented Jul 25, 2024 •

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		class ContinuousDeformationBuilder(DeformationBuilder):
		def deform_slab_isometrically(self, configuration):

		from ...utils import DeformationFunctionBuilder


		class DeformationConfiguration(BaseModel, InMemoryEntity):

		return sine_wave(coordinate_prime, amplitude, wavelength, phase, axis="x")


		def sine_wave_radial(



		class SlabPerturbationBuilder(PerturbationBuilder):
		def create_perturbed_slab(self, configuration):



		class CellMatchingDistancePreservingSlabPerturbationBuilder(DistancePreservingSlabPerturbationBuilder):
		def _transform_cell_vectors(self, configuration: PerturbationConfiguration) -> List[List[float]]:

		return converted_array.tolist()


		class CoordinateConditionBuilder:

		from mat3ra.utils.factory import BaseFactory


		class PerturbationFunctionHelperFactory(BaseFactory):

		raise NotImplementedError


		class PerturbationFunctionHolder(FunctionHolder):

feature/SOF 7397 #151

feature/SOF 7397 #151

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VsevolodX commented Jul 25, 2024 • edited Loading

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VsevolodX commented Jul 25, 2024 •

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