SOF-7354: show labels with atomic symbols when present

.github/workflows/cicd.yml

@@ -14,19 +14,19 @@ jobs:
 
     steps:
       - name: Checkout this repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           lfs: true
 
       - name: Checkout actions repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           repository: Exabyte-io/actions
           token: ${{ secrets.BOT_GITHUB_TOKEN }}
           path: actions
 
       - name: Login to GitHub Container registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         env:
           GITHUB_USER: ${{ github.actor }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -60,12 +60,12 @@ jobs:
 
     steps:
       - name: Checkout this repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           lfs: true
 
       - name: Checkout actions repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           repository: Exabyte-io/actions
           token: ${{ secrets.BOT_GITHUB_TOKEN }}

docker-compose.yml

@@ -1,5 +1,3 @@
-version: "3.8"
-
 services:
   wave:
     image: wave-${BASE_OS}:${IMAGE_TAG}

dockerfiles/ubuntu/Dockerfile

@@ -1,4 +1,8 @@
 FROM ubuntu:latest
+# TODO: with latest (24.04) version of ubuntu there are following errors
+# MESA: error: ZINK: vkCreateInstance failed (VK_ERROR_INCOMPATIBLE_DRIVER)
+# glx: failed to create drisw screen
+# NOTE: however the snapshots on 24.04 are identical to the ones from 22.04
 
 # Install base dependencies
 RUN apt-get update && apt-get install -y -q --no-install-recommends \

package.json

@@ -73,8 +73,8 @@
         "@exabyte-io/eslint-config": "^2023.8.29-1",
         "@mat3ra/tsconfig": "^2024.3.21-5",
         "@mat3ra/code": "^2024.3.25-3",
-        "@mat3ra/esse": "^2024.3.25-6",
-        "@mat3ra/made": "^2024.3.26-0",
+        "@mat3ra/esse": "2024.4.19-1",
+        "@mat3ra/made": "2024.5.3-0",
         "@exabyte-io/cove.js": "2024.2.21-1",
         "@types/react": "^18.2.8",
         "@types/react-dom": "^18.2.4",

src/components/SquareIconButton.tsx

@@ -1,6 +1,6 @@
 import IconButton, { IconButtonProps } from "@mui/material/IconButton";
 import Tooltip, { TooltipProps } from "@mui/material/Tooltip";
-import React, { useState } from "react";
+import React from "react";
 import _ from "underscore";
 
 interface SquareIconButtonProps extends IconButtonProps {

src/mixins/atoms.js

@@ -1,6 +1,7 @@
 import * as THREE from "three";
 
 import { ATOM_GROUP_NAME } from "../enums";
+import { ApplyGlow } from "./utils";
 
 /*
  * Mixin containing the logic for dealing with atoms.
@@ -88,13 +89,27 @@ export const AtomsMixin = (superclass) =>
         createAtomsGroup(basis, atomRadiiScale) {
             const atomsGroup = new THREE.Group();
             atomsGroup.name = ATOM_GROUP_NAME;
+            const { atomicLabelsArray, elementsWithLabelsArray } = basis;
             basis.coordinates.forEach((atomicCoordinate, atomicIndex) => {
                 const element = basis.getElementByIndex(atomicIndex);
                 const sphereMesh = this.getSphereMeshObject({
                     ...this._getDefaultSettingsForElement(element, atomRadiiScale),
                     coordinate: atomicCoordinate.value,
                 });
                 sphereMesh.name = `${element}-${atomicIndex}`;
+                // store any additional data in userData
+                // https://threejs.org/docs/#api/en/core/Object3D.userData
+                sphereMesh.userData = {
+                    ...sphereMesh.userData,
+                    symbolWithLabel: elementsWithLabelsArray[atomicIndex],
+                };
+                const atomColor = this.getAtomColorByElement(element).toLowerCase();
+                const label = parseInt(atomicLabelsArray[atomicIndex], 10) || 0;
+                // set glow according to the label value as offset, currently
+                // only single digit numeric labels are allowed, in practice we
+                // expect only two different labels: 1 and 2 for up and down
+                // spin representations
+                ApplyGlow(sphereMesh, atomColor, label);
                 atomsGroup.add(sphereMesh);
             });
             return atomsGroup;

src/mixins/bonds.js

@@ -1,8 +1,8 @@
-import { Made } from "@mat3ra/made";
 import {
     filterBondsDataByElementsAndOrder,
     getElementsBondsData,
 } from "@exabyte-io/periodic-table.js";
+import { Made } from "@mat3ra/made";
 import createKDTree from "static-kdtree";
 import * as THREE from "three";
 

src/mixins/labels.js

@@ -111,7 +111,7 @@ export const LabelsMixin = (superclass) =>
 
                 group.children.forEach((atom) => {
                     if (atom instanceof THREE.Mesh) {
-                        const text = atom.name.split("-")[0];
+                        const text = atom.userData.symbolWithLabel;
                         const position = new THREE.Vector3().setFromMatrixPosition(
                             atom.matrixWorld,
                         );

src/mixins/utils.js

@@ -1,3 +1,5 @@
+import * as THREE from "three";
+
 export const UtilsMixin = (superclass) =>
     class extends superclass {
         // toggles a boolean variable and optionally sets all variables in the antagonists array to the opposite value
@@ -27,3 +29,39 @@ export const UtilsMixin = (superclass) =>
             return resultingObject;
         }
     };
+
+/**
+ * Applies glow to a THREE object.
+ * @param meshObjet {Object}: THREE mesh object.
+ * @param baseColor {String}: hex color string of the glow
+ * @param offset {Number}: can be a single digit number, 0 means no offset
+ */
+export const ApplyGlow = (meshObjet, baseColor, offset = 0) => {
+    const atomHSL = {};
+    new THREE.Color(baseColor).getHSL(atomHSL);
+    let hue, saturation;
+    if (offset !== 0) {
+        if (offset % 2 === 0) {
+            // even labels
+            hue = atomHSL.h + (offset * 0.1) / 2;
+            saturation = atomHSL.s + (offset * 0.1) / 2;
+        } else {
+            // odd labels
+            hue = atomHSL.h - ((offset + 1) * 0.1) / 2;
+            saturation = atomHSL.s + ((offset + 1) * 0.1) / 2;
+        }
+
+        // hue is cyclic
+        while (hue > 1) {
+            hue -= 1;
+        }
+
+        while (hue < 0) {
+            hue += 1;
+        }
+
+        saturation = Math.max(0, Math.min(1, saturation));
+        meshObjet.material.emissiveIntensity = 0.25;
+        meshObjet.material.emissive.setHSL(hue, saturation, atomHSL.l);
+    }
+};

tests/__tests__/mixins/labels.js

@@ -19,7 +19,7 @@ describe("Atom labels", () => {
         const basisAtomsNumber = wave.structure.basis.elements.length;
 
         atoms.forEach((atom) => {
-            const atomName = atom.name.split("-")[0];
+            const atomName = atom.userData.symbolWithLabel;
             const atomPosition = new THREE.Vector3().setFromMatrixPosition(atom.matrixWorld);
 
             const offsetVector = wave.getLabelOffsetVector(atomPosition, atomName);
@@ -32,7 +32,6 @@ describe("Atom labels", () => {
                     label.position.distanceTo(expectedLabelPosition) < 0.00001
                 );
             });
-
             expect(labelSprite).toBeTruthy();
         });
 
@@ -49,7 +48,7 @@ describe("Atom labels", () => {
 
         const basisAtomsNumber = wave.structure.basis.elements.length;
         const doAllAtomsHaveLabels = atoms.every((atom) => {
-            const atomName = atom.name.split("-")[0];
+            const atomName = atom.userData.symbolWithLabel;
             const labelName = `labels-for-${atomName}`;
             const labelPointsByAtomName = labels.find(
                 (labelPoints) => labelPoints.name === labelName,

tests/__tests__/mixins/repetition.js

@@ -17,7 +17,7 @@ describe("Screen tests for repeats", () => {
         const wave = getWaveInstance({ ...settings, repetitionsAlongLatticeVectorB: 3 });
         return takeSnapshotAndAssertEqualityAsync(wave.renderer.getContext(), "vectorB");
     });
-    test("Repeat along lattice vector С", () => {
+    test("Repeat along lattice vector C", () => {
         const wave = getWaveInstance({ ...settings, repetitionsAlongLatticeVectorC: 3 });
         return takeSnapshotAndAssertEqualityAsync(wave.renderer.getContext(), "vectorC");
     });

tests/__tests__/wave.js

@@ -1,4 +1,4 @@
-import { getWaveInstance } from "../enums";
+import { getFeOWaveInstance, getWaveInstance } from "../enums";
 import { takeSnapshotAndAssertEqualityAsync } from "../utils";
 
 test("wave", async () => {
@@ -19,3 +19,17 @@ test("atomRepetitions", async () => {
     wave.rebuildScene();
     return takeSnapshotAndAssertEqualityAsync(wave.renderer.getContext(), "atomRepetitions");
 });
+
+test("colorsOfAtomsWithLabels", async () => {
+    const wave = getFeOWaveInstance();
+    // zoom-out to get full view of the cell
+    wave.toggleOrbitControls();
+    wave.renderer.domElement.dispatchEvent(new WheelEvent("wheel", { deltaY: 1 }));
+    wave.renderer.domElement.dispatchEvent(new WheelEvent("wheel", { deltaY: 1 }));
+    wave.renderer.domElement.dispatchEvent(new WheelEvent("wheel", { deltaY: 1 }));
+    wave.renderer.domElement.dispatchEvent(new WheelEvent("wheel", { deltaY: 1 }));
+    return takeSnapshotAndAssertEqualityAsync(
+        wave.renderer.getContext(),
+        "colorsOfAtomsWithLabels",
+    );
+});

tests/enums.js

@@ -19,6 +19,10 @@ export const ELEMENT_PROPERTIES = {
 const materialJsonFilePath = path.resolve(__dirname, "fixtures/material.json");
 export const MATERIAL_CONFIG = JSON.parse(fs.readFileSync(materialJsonFilePath));
 
+// config for material with atomic labels
+const FeOJsonFilePath = path.resolve(__dirname, "fixtures/FeO.json");
+export const FeO_CONFIG = JSON.parse(fs.readFileSync(FeOJsonFilePath));
+
 export const WAVE_SETTINGS = {
     atomRadiiScale: 0.2,
     repetitions: 1,
@@ -32,3 +36,12 @@ export function getWaveInstance(settings, material = new Made.Material(MATERIAL_
         settings: settings || WAVE_SETTINGS,
     });
 }
+
+export function getFeOWaveInstance(settings, material = new Made.Material(FeO_CONFIG)) {
+    return new Wave({
+        DOMElement: createElement("div", ELEMENT_PROPERTIES),
+        structure: material,
+        cell: material.Lattice.unitCell,
+        settings: settings || WAVE_SETTINGS,
+    });
+}