@mat3ra/made 2025.4.14-0 → 2025.4.15-0

package/dist/js/tools/surface.js

@@ -82,7 +82,8 @@ function getMillerScalingMatrix(cell, millerIndices, tol = 1e-8) {
             // Here we specify rounding method to Bankers
             // For Python 3.11: round(-0.5) = 0
             const value = k1 / k2;
-            const i = math_1.default.roundCustom(value, 0, math_1.default.RoundingMethod.Bankers);
+            const roundedValue = math_1.default.roundCustom(value, 0, math_1.default.RoundingMethod.Bankers);
+            const i = -roundedValue;
             [p, q] = [p + i * l, q - i * k];
         }
         const [a, b] = extGCD(p * k + q * l, h);

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/made",
-    "version": "2025.4.14-0",
+    "version": "2025.4.15-0",
     "description": "MAterials DEsign library",
     "scripts": {
         "lint": "eslint --cache src/js tests/js && prettier --write src/js tests/js",

package/src/js/tools/surface.js

@@ -85,7 +85,8 @@ function getMillerScalingMatrix(cell, millerIndices, tol = 1e-8) {
             // Here we specify rounding method to Bankers
             // For Python 3.11: round(-0.5) = 0
             const value = k1 / k2;
-            const i = math.roundCustom(value, 0, math.RoundingMethod.Bankers);
+            const roundedValue = math.roundCustom(value, 0, math.RoundingMethod.Bankers);
+            const i = -roundedValue;
             [p, q] = [p + i * l, q - i * k];
         }
 

package/tests/fixtures/si-slab-111-0.5-vacuum-gamma-120.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9f5905448537352e0af199e5d1b66a2d51585b6fc91ad2078809fda097a428ab
+size 1894

package/tests/js/fixtures.ts

@@ -2,34 +2,33 @@ import fs from "fs";
 import path from "path";
 
 // TODO: use @mat3ra/standata
-
-import Silicon from "../fixtures/si-standata.json";
-import FeO from "../fixtures/FeO.json";
-import Na4Cl4 from "../fixtures/Na4Cl4.json";
-import Na4Cl4Cartesian from "../fixtures/Na4Cl4-cartesian.json";
-import SiSupercell from "../fixtures/Si-supercell.json";
+import AsGeBasis from "../fixtures/AsGe-basis.json";
+import atomicConstraints from "../fixtures/atomic-constraints.json";
 import C2H4 from "../fixtures/C2H4.json";
 import C2H4Translated from "../fixtures/C2H4-translated.json";
-import Na from "../fixtures/Na.json";
-import OSiBasis from "../fixtures/OSi-basis.json";
-import Si2Basis from "../fixtures/Si2-basis.json";
-import Ge2Basis from "../fixtures/Ge2-basis.json";
-import AsGeBasis from "../fixtures/AsGe-basis.json";
 import FeLiSiBasis from "../fixtures/FeLiSi-basis.json";
-import LiFeSiBasis from "../fixtures/LiFeSi-basis.json";
-import atomicConstraints from "../fixtures/atomic-constraints.json";
-import Si2BasisRepeated from "../fixtures/Si2-basis-repeated.json";
-import H2HInitial from "../fixtures/H2+H-initial.json";
+import FeO from "../fixtures/FeO.json";
+import Ge2Basis from "../fixtures/Ge2-basis.json";
+import Graphene from "../fixtures/Graphene.json";
 import H2HFinal from "../fixtures/H2+H-final.json";
 import H2HImage from "../fixtures/H2+H-image.json";
-import SiSlab from "../fixtures/Si-slab.json";
-import Zr1H23Zr1H1 from "../fixtures/Zr1H23Zr1H1.json";
-import Graphene from "../fixtures/Graphene.json";
+import H2HInitial from "../fixtures/H2+H-initial.json";
+import LiFeSiBasis from "../fixtures/LiFeSi-basis.json";
+import Na from "../fixtures/Na.json";
+import Na4Cl4 from "../fixtures/Na4Cl4.json";
+import Na4Cl4Cartesian from "../fixtures/Na4Cl4-cartesian.json";
 import NiHex from "../fixtures/Ni-hex.json";
+import OSiBasis from "../fixtures/OSi-basis.json";
+import SiSlab from "../fixtures/Si-slab.json";
 import SiSlab100 from "../fixtures/si-slab-100.json";
+import SiSlab111Gamma120 from "../fixtures/si-slab-111-0.5-vacuum-gamma-120.json";
 import SiSlab111 from "../fixtures/si-slab-111-0.5-vacuum-ratio.json";
 import SiSlab111NoVacuum from "../fixtures/si-slab-111-0-vacuum.json";
-
+import Silicon from "../fixtures/si-standata.json";
+import SiSupercell from "../fixtures/Si-supercell.json";
+import Si2Basis from "../fixtures/Si2-basis.json";
+import Si2BasisRepeated from "../fixtures/Si2-basis-repeated.json";
+import Zr1H23Zr1H1 from "../fixtures/Zr1H23Zr1H1.json";
 
 export {
     // Silicon
@@ -38,6 +37,7 @@ export {
     SiSlab,
     SiSlab100,
     SiSlab111,
+    SiSlab111Gamma120,
     SiSlab111NoVacuum,
     Si2Basis,
     Si2BasisRepeated,

package/tests/js/tools/surface.js

@@ -2,10 +2,23 @@ import { Utils } from "@mat3ra/utils";
 
 import { Material } from "../../../src/js/material";
 import tools from "../../../src/js/tools";
-import { Silicon, SiSlab100, SiSlab111, SiSlab111NoVacuum } from "../fixtures";
+import { Silicon, SiSlab100, SiSlab111, SiSlab111Gamma120, SiSlab111NoVacuum } from "../fixtures";
 
 const { assertDeepAlmostEqual } = Utils.assertion;
 
+const generateSlabWithVacuum = (slabConfig, vacuumRatio) => {
+    const slabMaterial = new Material(slabConfig);
+    const { outOfPlaneAxisIndex } = slabConfig;
+
+    tools.material.scaleOneLatticeVector(
+        slabMaterial,
+        ["a", "b", "c"][outOfPlaneAxisIndex],
+        1 / (1 - vacuumRatio),
+    );
+
+    return slabMaterial;
+};
+
 describe("Tools:Surface", () => {
     it("should return slab (100)", () => {
         const material = new Material(Silicon);
@@ -23,15 +36,47 @@ describe("Tools:Surface", () => {
         const material = new Material(Silicon);
         const slabConfig = tools.surface.generateConfig(material, [1, 1, 1], 3, 1, 1);
         const vacuumRatio = 0.5;
-        const slabMaterial = new Material(slabConfig);
-        const { outOfPlaneAxisIndex } = slabConfig;
-        // Add 0.5 vacuum ratio, which is used in MD
-        tools.material.scaleOneLatticeVector(
-            slabMaterial,
-            ["a", "b", "c"][outOfPlaneAxisIndex],
-            1 / (1 - vacuumRatio),
-        );
+        const slabMaterial = generateSlabWithVacuum(slabConfig, vacuumRatio);
+        const expectedSlabMaterial = new Material(SiSlab111);
+        const expectedMaterialJSON = expectedSlabMaterial.toJSON();
+        const slabMaterialJSON = slabMaterial.toJSON();
+        assertDeepAlmostEqual(expectedMaterialJSON, slabMaterialJSON);
+    });
+
+    it("should return slab (111) with vacuum (gamma~=120) for gamma = 59.999", () => {
+        const adjustedSilicon = {
+            ...Silicon,
+            lattice: {
+                ...Silicon.lattice,
+                gamma: 59.999,
+            },
+        };
+        const material = new Material(adjustedSilicon);
+        const slabConfig = tools.surface.generateConfig(material, [1, 1, 1], 3, 1, 1);
+        const vacuumRatio = 0.5;
+        const slabMaterial = generateSlabWithVacuum(slabConfig, vacuumRatio);
+        // With original gamma being below 60, the surface generated differently, with a different gamma
+        const expectedSlabMaterial = new Material(SiSlab111Gamma120);
+        const expectedMaterialJSON = expectedSlabMaterial.toJSON();
+        const slabMaterialJSON = slabMaterial.toJSON();
+        assertDeepAlmostEqual(expectedMaterialJSON, slabMaterialJSON);
+    });
+
+    it("should return slab (111) with vacuum for gamma = 60.001", () => {
+        const adjustedSilicon = {
+            ...Silicon,
+            lattice: {
+                ...Silicon.lattice,
+                gamma: 60.001,
+            },
+        };
+        const material = new Material(adjustedSilicon);
+        const slabConfig = tools.surface.generateConfig(material, [1, 1, 1], 3, 1, 1);
+        const vacuumRatio = 0.5;
+        const slabMaterial = generateSlabWithVacuum(slabConfig, vacuumRatio);
         const expectedSlabMaterial = new Material(SiSlab111);
-        assertDeepAlmostEqual(expectedSlabMaterial.toJSON(), slabMaterial.toJSON());
+        const expectedMaterialJSON = expectedSlabMaterial.toJSON();
+        const slabMaterialJSON = slabMaterial.toJSON();
+        assertDeepAlmostEqual(expectedMaterialJSON, slabMaterialJSON);
     });
 });