@mat3ra/made 2026.7.4-0 → 2026.7.8-0

package/src/js/tools/surface.ts

@@ -1,21 +1,21 @@
-import { math } from "@mat3ra/code/dist/js/math";
 import {
     Coordinate3DSchema,
     MaterialSchema,
     Matrix3X3Schema,
     Vector3DSchema,
 } from "@mat3ra/esse/dist/js/types";
+import { Utils } from "@mat3ra/utils";
 
 import { Cell } from "../cell/cell";
 import { Lattice } from "../lattice/lattice";
 import { Material } from "../material";
 import SupercellTools from "./supercell";
 
-const MULT = math.multiply;
-const ADD = math.add;
-const DOT = math.product;
+const MULT = Utils.math.multiply;
+const ADD = Utils.math.add;
+const DOT = Utils.math.product;
 const getMatrixInLeftHandedRepresentation = (matrix: Matrix3X3Schema) => {
-    return math.det(matrix) < 0 ? MULT(matrix, -1) : matrix;
+    return Utils.math.det(matrix) < 0 ? MULT(matrix, -1) : matrix;
 };
 
 /**
@@ -27,10 +27,10 @@ const getMatrixInLeftHandedRepresentation = (matrix: Matrix3X3Schema) => {
  */
 function extGCD(a: number, b: number): [number, number] {
     if (b === 0) return [1, 0];
-    if (math.mod(a, b) === 0) return [0, 1];
+    if (Utils.math.mod(a, b) === 0) return [0, 1];
 
-    const [x, y] = extGCD(b, math.mod(a, b));
-    return [y, x - y * math.floor(a / b)];
+    const [x, y] = extGCD(b, Utils.math.mod(a, b));
+    return [y, x - y * Utils.math.floor(a / b)];
 }
 
 /**
@@ -46,7 +46,7 @@ function getMillerScalingMatrix(
     millerIndices: Coordinate3DSchema,
     tol = 1e-8,
 ): Matrix3X3Schema {
-    if (!millerIndices.reduce((a, b) => math.abs(a) + math.abs(b)))
+    if (!millerIndices.reduce((a, b) => Utils.math.abs(a) + Utils.math.abs(b)))
         throw new Error("Miller indices are zeros.");
 
     let scalingMatrix;
@@ -94,20 +94,26 @@ function getMillerScalingMatrix(
         // @ts-ignore
         const k2 = DOT(ADD(MULT(l, z1), -MULT(k, z2)), z3);
 
-        if (math.abs(k2) > tol) {
+        // @ts-ignore
+        if (Utils.math.abs(k2) > tol) {
             // For mathjs version 3.20: round(-0.5) = -0
             // For mathjs version 5.10: round(-0.5) = -1
             // Here we specify rounding method to Bankers
             // For Python 3.11: round(-0.5) = 0
+            // @ts-ignore - mathjs v12 dot return type
             const value = k1 / k2;
-            const roundedValue = math.roundCustom(value, 0, math.RoundingMethod.Bankers);
+            const roundedValue = Utils.math.roundCustom(
+                value,
+                0,
+                Utils.math.RoundingMethod.Bankers,
+            );
             const i = -roundedValue;
             [p, q] = [p + i * l, q - i * k];
         }
 
         const [a, b] = extGCD(p * k + q * l, h);
         const c1 = [p * k + q * l, -p * h, -q * h];
-        const c2 = [0, l, -k].map((c) => math.trunc(c / math.gcd(l, k))); // floor division
+        const c2 = [0, l, -k].map((c) => Utils.math.trunc(c / Utils.math.gcd(l, k))); // floor division
         const c3 = [b, a * p, a * q];
 
         scalingMatrix = [c1, c2, c3];

package/tests/fixtures/hashes.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:823cf1e89c00beb0df0799a86573d038f725f7d7612bab4e9e40df5dab3330d8
+size 132

package/tests/js/cell/cell.ts

@@ -41,7 +41,7 @@ const VECTORS_EQUAL_UP_TO_PRECISION_4: Matrix3X3Schema = [
     [0.0, 0.0, 3.00001],
 ];
 
-const VECTORS_EQUAL_UP_TO_PRECISION_4_VOLUME = 6.000110000600002;
+const VECTORS_EQUAL_UP_TO_PRECISION_4_VOLUME = 6.000110000600001;
 const VECTORS_EQUAL_UP_TO_PRECISION_4_VOLUME_ROUNDED_TO_PRECISION_4 = 6.0001;
 const VECTORS_EQUAL_UP_TO_PRECISION_4_VOLUME_ROUNDED_TO_PRECISION_5 = 6.00011;
 

package/tests/js/fixtures.ts

@@ -1,14 +1,15 @@
 import { AtomicConstraintsSchema, BasisSchema, MaterialSchema } from "@mat3ra/esse/dist/js/types";
+import { MaterialStandata } from "@mat3ra/standata";
 import fs from "fs";
 import path from "path";
 
-// TODO: use @mat3ra/standata
 import AsGeBasis_JSON from "../fixtures/AsGe-basis.json";
 import atomicConstraints_JSON from "../fixtures/atomic-constraints.json";
 import C2H4_JSON from "../fixtures/C2H4.json";
 import C2H4Translated_JSON from "../fixtures/C2H4-translated.json";
 import FeLiSiBasis_JSON from "../fixtures/FeLiSi-basis.json";
 import FeO_JSON from "../fixtures/FeO.json";
+
 import Ge2Basis_JSON from "../fixtures/Ge2-basis.json";
 import Graphene_JSON from "../fixtures/Graphene.json";
 import H2HFinal_JSON from "../fixtures/H2+H-final.json";
@@ -27,6 +28,7 @@ import SiSlab111Gamma120_JSON from "../fixtures/si-slab-111-0.5-vacuum-gamma-120
 import SiSlab111_JSON from "../fixtures/si-slab-111-0.5-vacuum-ratio.json";
 import SiSlab111NoVacuum_JSON from "../fixtures/si-slab-111-0-vacuum.json";
 import Silicon_JSON from "../fixtures/si-standata.json";
+
 import SiSupercell_JSON from "../fixtures/Si-supercell.json";
 import Si2Basis_JSON from "../fixtures/Si2-basis.json";
 import Si2BasisRepeated_JSON from "../fixtures/Si2-basis-repeated.json";
@@ -41,6 +43,9 @@ const SiSlab111 = SiSlab111_JSON as unknown as MaterialSchema;
 const SiSlab111Gamma120 = SiSlab111Gamma120_JSON as unknown as MaterialSchema;
 const SiSlab111NoVacuum = SiSlab111NoVacuum_JSON as unknown as MaterialSchema;
 const FeO = FeO_JSON as unknown as MaterialSchema;
+const FeOStandata = MaterialStandata.getRuntimeDataConfigs().find(
+    (m: any) => m.name?.includes("FeO"),
+) as MaterialSchema;
 const Na4Cl4 = Na4Cl4_JSON as unknown as MaterialSchema;
 const Na4Cl4Cartesian = Na4Cl4Cartesian_JSON as unknown as MaterialSchema;
 const C2H4 = C2H4_JSON as unknown as MaterialSchema;
@@ -79,6 +84,7 @@ export {
     Si2BasisRepeated,
     // Other
     FeO,
+    FeOStandata,
     Na4Cl4,
     Na4Cl4Cartesian,
     C2H4,

package/tests/js/material.test.ts

@@ -1,7 +1,7 @@
 import { expect } from "chai";
 
 import { Material } from "../../src/js/material";
-import { Graphene, Na4Cl4, Silicon } from "./fixtures";
+import { FeOStandata, Graphene, Na4Cl4, Silicon } from "./fixtures";
 
 const newBasisXYZ = `Si     0.000000    0.000000    0.000000
 Ge     0.250000    0.250000    0.250000
@@ -31,5 +31,12 @@ describe("Material", () => {
                 expect(material.scaledHash).to.equal((fixture as any).scaledHash);
             });
         });
+
+        it("should match expected hash for FeO (standata)", () => {
+            const expectedHashes = require("../../fixtures/hashes.json");
+            const material = new Material(FeOStandata);
+            expect(material.calculateHash()).to.equal(expectedHashes.FeO.hash);
+            expect(material.scaledHash).to.equal(expectedHashes.FeO.scaledHash);
+        });
     });
 });

package/tests/py/unit/test_material.py

@@ -140,6 +140,16 @@ def test_calculate_hash(fixture_file):
     assert material.scaled_hash == fixture["scaledHash"]
 
 
+def test_calculate_hash_feo_standata():
+    from mat3ra.standata.materials import Materials
+
+    expected_hashes = load_fixture("hashes.json")["FeO"]
+    data = Materials.get_by_name_first_match("FeO")
+    material = Material.create(data)
+    assert material.hash == expected_hashes["hash"]
+    assert material.scaled_hash == expected_hashes["scaledHash"]
+
+
 def test_model_dump_includes_hashes():
     material = Material.create_default()
     serialized_material = material.model_dump()