feature/SOF-7427 feat: ASE distance norm calculator #160

VsevolodX · 2024-09-02T21:21:09Z

feat: add ASE calculator
add docstrings explaining
add required forces defintions and calculations

timurbazhirov · 2024-09-13T03:35:02Z

src/py/mat3ra/made/tools/calculate.py

@@ -167,3 +167,100 @@ def calculate_norm_of_distances(material: Material, shadowing_radius: float = 2.
    substrate_coordinates_values = np.array(substrate_atoms_surface_coordinates.values)

    return get_norm_of_distances_between_coordinates(film_coordinates_values, substrate_coordinates_values)
+
+
+class SurfaceDistanceCalculator(ASECalculator):


Uhm, we pass this as a paramter: whether to fix_z, fix_substrate or not

FilmSubstrateDistanceCalculator

timurbazhirov · 2024-09-13T03:37:31Z

src/py/mat3ra/made/tools/calculate.py

+
+        ASECalculator.calculate(self, atoms, properties, system_changes)
+        material = Material(from_ase(atoms))
+        norm = calculate_norm_of_distances(material, self.shadowing_radius)


timurbazhirov · 2024-09-13T03:38:17Z

src/py/mat3ra/made/tools/calculate.py

+        atoms.set_constraint(constraints)
+        return atoms
+
+    def _calculate_forces(self, atoms: ASEAtoms, norm: float) -> np.ndarray:


Maybe we can remove this

timurbazhirov · 2024-09-14T01:24:25Z

src/py/mat3ra/made/tools/calculate.py

+    Args:
+        shadowing_radius (float): The radius for atom to shadow underlying from being considered surface, in Angstroms.
+        force_constant (float): The force constant for the finite difference approximation of the forces.
+        fix_substrate (bool): Whether to fix the substrate atoms.


is_substrate_fixed, is_z_axis_fixed

timurbazhirov · 2024-09-14T01:25:14Z

src/py/mat3ra/made/tools/calculate.py

+        force_constant (float): The force constant for the finite difference approximation of the forces.
+        fix_substrate (bool): Whether to fix the substrate atoms.
+        fix_z (bool): Whether to fix atoms movement in the z direction.
+        symprec (float): The symmetry precision for the ASE calculator.


What is that - let's put a link to the original explanation

timurbazhirov · 2024-09-14T01:26:16Z

src/py/mat3ra/made/tools/calculate.py

+
+        ASECalculator.calculate(self, atoms, properties, system_changes)
+        material = Material(from_ase(atoms))
+        energy = calculate_film_substrate_interaction_metric(material, self.shadowing_radius)


This should be MaterialCalculator.get_energy(material, calculator_parameters**)

timurbazhirov · 2024-09-14T02:38:58Z

src/py/mat3ra/made/tools/calculate.py

+        shadowing_radius (float): Radius for atoms shadowing underlying from being treated as a surface, in Angstroms.
+        force_constant (float): The force constant for the finite difference approximation of the
+    Note:
+        Built following: https://wiki.fysik.dtu.dk/ase/development/calculators.html


timurbazhirov · 2024-09-14T02:42:16Z

src/py/mat3ra/made/tools/calculate.py

+        atoms = self._add_constraints(atoms)
+        constraints = atoms.constraints
+
+        ASECalculator.calculate(self, atoms, properties, system_changes)


timurbazhirov · 2024-09-14T02:44:43Z

src/py/mat3ra/made/tools/calculate.py

+
+        return forces
+
+    @decorator_convert_material_args_kwargs_to_atoms


No point of having this

timurbazhirov · 2024-09-14T02:49:20Z

src/py/mat3ra/made/tools/calculate.py

+    implemented_properties = ["energy", "forces"]
+
+    def __init__(
+        self,


should have material_calculator as parameter

timurbazhirov · 2024-09-14T02:51:31Z

src/py/mat3ra/made/tools/calculate.py

+
+    Args:
+        shadowing_radius (float): The radius for atom to shadow underlying from being considered surface, in Angstroms.
+        force_constant (float): The force constant for the finite difference approximation of the forces.


Remove, this can be in interaction_function

:

timurbazhirov · 2024-09-17T04:01:17Z

src/py/mat3ra/made/tools/calculate/calculators.py

@@ -120,3 +122,174 @@ def get_energy(
        substrate_coordinates_values = np.array(substrate_surface_atom_coordinates.values)

        return interaction_function(film_coordinates_values, substrate_coordinates_values)
+
+
+class FixFilmRigidXY(BaseModel):


class InterfaceConstraint

class RigidFilmXYConstraint(InterfaceConstraint)

timurbazhirov · 2024-09-19T00:03:25Z

src/py/mat3ra/made/tools/calculate/calculators.py

+    def _add_constraints(self, atoms: ASEAtoms) -> ASEAtoms:
+        constraints: List[Union[ASEFixAtoms, ASEFixedPlane, RigidFilmXYConstraint]] = []
+        if self.fix_substrate:
+            substrate_indices = [i for i, tag in enumerate(atoms.get_tags()) if tag == 0]


We should abstract this into get_interface_part_indices

Ok, but locally. Since it's ASE atoms, not Material

timurbazhirov · 2024-09-19T00:03:36Z

src/py/mat3ra/made/tools/calculate/calculators.py

+            all_indices = list(range(len(atoms)))
+            constraints.append(ASEFixedPlane(indices=all_indices, direction=[0, 0, 1]))
+
+        film_indices = [i for i, tag in enumerate(atoms.get_tags()) if tag == 1]


Same as above

timurbazhirov · 2024-09-19T00:07:45Z

src/py/mat3ra/made/tools/calculate/calculators.py

@@ -120,3 +123,112 @@ def get_energy(
        substrate_coordinates_values = np.array(substrate_surface_atom_coordinates.values)

        return interaction_function(film_coordinates_values, substrate_coordinates_values)
+
+
+class FilmSubstrateDistanceASECalculator(ASECalculator):


Let's put in ase subfolder for this and constraints into it

timurbazhirov · 2024-09-19T00:08:12Z

src/py/mat3ra/made/tools/calculate/constraints.py

+        raise NotImplementedError
+
+
+class RigidFilmXYConstraint(InterfaceConstraint):


InterfaceConstraint

feat: add ASE calculator with docstring and required forces

cf6244c

VsevolodX changed the base branch from main to feature/SOF-7426 September 2, 2024 21:22

VsevolodX added 5 commits September 2, 2024 16:54

Merge branch 'feature/SOF-7426' into feature/SOF-7427

51e3e87

update: add constraints

e695e33

update: optimize code

f1f4eaa

chore: import from 3rd party

db91642

Merge branch 'feature/SOF-7426' into feature/SOF-7427

65d5843

timurbazhirov reviewed Sep 13, 2024

View reviewed changes

VsevolodX added 4 commits September 13, 2024 12:25

Merge branch 'feature/SOF-7426' into feature/SOF-7427

7c2890f

Merge branch 'feature/SOF-7426' into feature/SOF-7427

fad3997

chore: docstring

ce42e81

chore: rename norm -> energy

c4daf74

timurbazhirov reviewed Sep 14, 2024

View reviewed changes

VsevolodX added 8 commits September 16, 2024 15:06

Merge branch 'feature/SOF-7426' into feature/SOF-7427

708ff39

update: use m calculator

0daf4ce

update: adjustemtns in calculator

81dd780

chore: small adjustmnets

4761da8

feat: add rigid xy constraints with help from o1

3617623

chore: remove unused imports

56b5bf9

chore: add types

4079d8a

:

chore: arbitrary types allowed

736be41

timurbazhirov reviewed Sep 17, 2024

View reviewed changes

Base automatically changed from feature/SOF-7426 to main September 17, 2024 04:19

VsevolodX added 3 commits September 17, 2024 09:50

Merge branch 'main' into feature/SOF-7427

9a8db13

update: inherit from constraint class

09b2acd

chore: move constraints to a separate file

aaf4946

timurbazhirov reviewed Sep 19, 2024

View reviewed changes

VsevolodX added 2 commits September 18, 2024 18:44

update: isolate ase-related calculator

da49cf4

update: isolate filtering

5aa6454

timurbazhirov approved these changes Sep 19, 2024

View reviewed changes

VsevolodX merged commit 7c090f6 into main Sep 19, 2024
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VsevolodX deleted the feature/SOF-7427 branch September 19, 2024 02:52

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feature/SOF-7427 feat: ASE distance norm calculator #160

feature/SOF-7427 feat: ASE distance norm calculator #160

VsevolodX commented Sep 2, 2024 •

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		return forces

		@decorator_convert_material_args_kwargs_to_atoms

		raise NotImplementedError


		class RigidFilmXYConstraint(InterfaceConstraint):

feature/SOF-7427 feat: ASE distance norm calculator #160

feature/SOF-7427 feat: ASE distance norm calculator #160

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VsevolodX commented Sep 2, 2024 •

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