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update: revert to using JSON for gr/ni interface
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@VsevolodX
VsevolodX committed Sep 11, 2024
1 parent 37257b5 commit 5b9d32c
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222 changes: 162 additions & 60 deletions tests/py/unit/fixtures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,14 +9,6 @@
from pymatgen.analysis.elasticity.strain import Strain
from pymatgen.core.interface import Interface

from mat3ra.made.tools.build.interface import (
create_interface,
InterfaceConfiguration,
ZSLStrainMatchingInterfaceBuilder,
ZSLStrainMatchingInterfaceBuilderParameters,
)

from mat3ra.made.tools.build.interface import ZSLStrainMatchingParameters
from .utils import atoms_to_interface_structure

# ASE Atoms fixtures
Expand Down Expand Up @@ -516,67 +508,177 @@
"isUpdated": True,
}

NICKEL = {
"name": "Ni, Nickel, FCC (Fm-3m) 3D (Bulk), mp-23",

GRAPHENE_NICKEL_INTERFACE = {
"name": "C2(001)-Ni4(111), Interface, Strain 0.105pct",
"basis": {
"elements": [
{"id": 0, "value": "Ni"},
{"id": 1, "value": "Ni"},
{"id": 2, "value": "Ni"},
{"id": 3, "value": "C"},
{"id": 4, "value": "C"},
],
"coordinates": [
{"id": 0, "value": [0.666666667, 0.666666667, 0.350869517]},
{"id": 1, "value": [1.0, 0.0, 0.425701769]},
{"id": 2, "value": [0.333333333, 0.333333333, 0.500534021]},
{"id": 3, "value": [0.333333333, 0.333333333, 0.611447347]},
{"id": 4, "value": [0.666666667, 0.666666667, 0.611447347]},
],
"units": "crystal",
"cell": [[2.478974, 0.0, 0.0], [1.239487, 2.14685446, 0.0], [0.0, 0.0, 27.048147591]],
"constraints": [],
"labels": [
{"id": 0, "value": 0},
{"id": 1, "value": 0},
{"id": 2, "value": 0},
{"id": 3, "value": 1},
{"id": 4, "value": 1},
],
},
"lattice": {
"a": 2.478974,
"b": 2.478974,
"c": 2.478974,
"alpha": 60,
"beta": 60,
"gamma": 60,
"c": 27.048147591,
"alpha": 90.0,
"beta": 90.0,
"gamma": 60.0,
"units": {"length": "angstrom", "angle": "degree"},
"type": "FCC",
"type": "TRI",
"vectors": {
"a": [2.146854, 0, 1.239487],
"b": [0.7156182, 2.024074, 1.239487],
"c": [0, 0, 2.478974],
"a": [2.478974, 0.0, 0.0],
"b": [1.239487, 2.14685446, 0.0],
"c": [0.0, 0.0, 27.048147591],
"alat": 1,
"units": "angstrom",
},
},
"basis": {
"elements": [{"id": 0, "value": "Ni"}],
"coordinates": [{"id": 0, "value": [0, 0, 0]}],
"units": "crystal",
"cell": [[2.146854, 0, 1.239487], [0.7156182, 2.024074, 1.239487], [0, 0, 2.478974]],
"constraints": [],
},
"isNonPeriodic": False,
"_id": "",
"metadata": {
"interface_properties": {
"film_sl_vectors": [[2.467291, 0.0, 0.0], [1.2336455, -2.136736685, -0.0]],
"substrate_sl_vectors": [[-1.752899326, 1.752899326, 0.0], [-1.752899326, 0.0, 1.752899326]],
"film_vectors": [[2.467291, 0.0, 0.0], [-1.2336455, 2.136736685, 0.0]],
"substrate_vectors": [[-1.752899326, 1.752899326, 0.0], [-1.752899326, 0.0, 1.752899326]],
"film_transformation": [[1.0, 0.0], [0.0, 1.0]],
"substrate_transformation": [[1.0, 0.0], [0.0, 1.0]],
"strain": [[0.004746364, -0.0, -0.0], [-0.0, 0.004746364, -0.0], [-0.0, -0.0, 0.0]],
"von_mises_strain": 0.003164242537164297,
"termination": "('C_P6/mmm_2', 'Ni_R-3m_1')",
"film_thickness": 1,
"substrate_thickness": 3,
"mean_abs_strain": 0.0010500000000000002,
},
"boundaryConditions": {"type": "pbc", "offset": 0},
"mean_abs_strain": 0.0010500000000000002,
"build": {
"configuration": {
"type": "InterfaceConfiguration",
"film_configuration": {
"type": "SlabConfiguration",
"bulk": {
"name": "C2",
"basis": {
"elements": [{"id": 0, "value": "C"}, {"id": 1, "value": "C"}],
"coordinates": [
{"id": 0, "value": [0.333333333, 0.666666667, 0.0]},
{"id": 1, "value": [0.666666667, 0.333333333, 0.0]},
],
"units": "crystal",
"cell": [[1.2336455, -2.136736685, 0.0], [1.2336455, 2.136736685, 0.0], [0.0, 0.0, 20.0]],
"constraints": [],
"labels": [],
},
"lattice": {
"a": 2.467291,
"b": 2.467291,
"c": 20.0,
"alpha": 90.0,
"beta": 90.0,
"gamma": 120.0,
"units": {"length": "angstrom", "angle": "degree"},
"type": "TRI",
"vectors": {
"a": [1.2336455, -2.136736685, 0.0],
"b": [1.2336455, 2.136736685, 0.0],
"c": [0.0, 0.0, 20.0],
"alat": 1,
"units": "angstrom",
},
},
"isNonPeriodic": False,
"_id": "",
"metadata": {"boundaryConditions": {"type": "pbc", "offset": 0}},
"isUpdated": True,
},
"miller_indices": [0, 0, 1],
"thickness": 1,
"vacuum": 0,
"xy_supercell_matrix": [[1, 0], [0, 1]],
"use_conventional_cell": True,
"use_orthogonal_z": True,
"make_primitive": False,
},
"substrate_configuration": {
"type": "SlabConfiguration",
"bulk": {
"name": "Ni4",
"basis": {
"elements": [
{"id": 0, "value": "Ni"},
{"id": 1, "value": "Ni"},
{"id": 2, "value": "Ni"},
{"id": 3, "value": "Ni"},
],
"coordinates": [
{"id": 0, "value": [0.0, 0.0, 0.0]},
{"id": 1, "value": [0.0, 0.5, 0.5]},
{"id": 2, "value": [0.5, 0.0, 0.5]},
{"id": 3, "value": [0.5, 0.5, 0.0]},
],
"units": "crystal",
"cell": [[3.505798652, 0.0, 0.0], [-0.0, 3.505798652, 0.0], [0.0, 0.0, 3.505798652]],
"constraints": [],
"labels": [],
},
"lattice": {
"a": 3.505798652,
"b": 3.505798652,
"c": 3.505798652,
"alpha": 90.0,
"beta": 90.0,
"gamma": 90.0,
"units": {"length": "angstrom", "angle": "degree"},
"type": "TRI",
"vectors": {
"a": [3.505798652, 0.0, 0.0],
"b": [-0.0, 3.505798652, 0.0],
"c": [0.0, 0.0, 3.505798652],
"alat": 1,
"units": "angstrom",
},
},
"isNonPeriodic": False,
"_id": "",
"metadata": {"boundaryConditions": {"type": "pbc", "offset": 0}},
"isUpdated": True,
},
"miller_indices": [1, 1, 1],
"thickness": 3,
"vacuum": 3,
"xy_supercell_matrix": [[1, 0], [0, 1]],
"use_conventional_cell": True,
"use_orthogonal_z": True,
"make_primitive": False,
},
"film_termination": "C_P6/mmm_2",
"substrate_termination": "Ni_P6/mmm_4",
"distance_z": 3.0,
"vacuum": 20.0,
}
},
},
"isUpdated": True,
}


GRAPHENE_FILM_CONFIGURATION = SlabConfiguration(
bulk=Material(GRAPHENE),
miller_indices=(0, 0, 1),
thickness=1,
use_orthogonal_z=True,
)

NICKEL_SLAB_CONFIGURATION = SlabConfiguration(
bulk=Material(NICKEL),
miller_indices=(1, 1, 1),
thickness=3,
vacuum=3,
use_orthogonal_z=True,
)

GRAPHENE_FILM_TERMINATION = get_terminations(GRAPHENE_FILM_CONFIGURATION)[0]
NICKEL_SLAB_TERMINATION = get_terminations(NICKEL_SLAB_CONFIGURATION)[0]
GRAPHENE_NICKEL_INTERFACE_CONFIGURATION = InterfaceConfiguration(
film_configuration=GRAPHENE_FILM_CONFIGURATION,
substrate_configuration=NICKEL_SLAB_CONFIGURATION,
film_termination=GRAPHENE_FILM_TERMINATION,
substrate_termination=NICKEL_SLAB_TERMINATION,
distance_z=3.0,
vacuum=5.0,
)

ZSL_BUILDER = ZSLStrainMatchingInterfaceBuilder(
build_parameters=ZSLStrainMatchingInterfaceBuilderParameters(
strain_matching_parameters=ZSLStrainMatchingParameters()
)
)

GRAPHENE_NICKEL_INTERFACE = create_interface(GRAPHENE_NICKEL_INTERFACE_CONFIGURATION, ZSL_BUILDER).to_json()
1 change: 0 additions & 1 deletion tests/py/unit/test_tools_modify.py
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Original file line number Diff line number Diff line change
Expand Up @@ -187,6 +187,5 @@ def test_displace_interface():
displaced_material = displace_interface(
material, [0.1, 0.2, 0.3], InterfacePartsEnum.FILM, use_cartesian_coordinates=False
)
print(displaced_material.to_json())
assertion_utils.assert_deep_almost_equal(expected_coordinates, displaced_material.basis.coordinates.to_dict())
assertion_utils.assert_deep_almost_equal(expected_labels, displaced_material.basis.labels.to_dict())

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