2f:Tca2,generated_extxyz = ` 16 Lattice="7.71799898147583 0.0 4.448462009429932 2.5859015364511597 7.278167851195626 4.446800231933594 0.0 0.0 8.935214042663574" Properties=species:S:1:pos:R:3 pbc="T T T" Sm 2.27211063 4.49376721 4.47406865 Sm 6.13154030 4.51704516 6.70475409 Sm 6.18235925 4.55392444 11.04790090 Sm 1.00202145 0.84617953 2.25388999 Te 8.74255191 6.33933663 15.56574534 Te 3.59057189 2.70033144 11.11731100 Sb 7.45029358 2.69853351 8.87792791 Hg 4.88099803 6.33933706 8.87609669 Sm 2.35344277 4.54927397 8.83946138 Sb 8.74347457 6.34101939 11.09803178 Sb 3.59075985 2.70077046 6.64874573 Sm 4.82792963 0.84858502 4.45753022 Sm 4.90979958 0.90633735 8.82510718 Te 4.88290898 6.33882560 13.34388905 Te 7.45039897 2.70032949 13.34405640 Sm 1.05167871 0.88328764 6.60153927 10 Lattice="5.329399108886719 0.0 -1.8263120651245117 0.0008457228690450765 6.853819318091046 0.009369509294629097 0.0 0.0 8.748780250549316" Properties=species:S:1:pos:R:3 pbc="T T T" La 1.81973938 1.13766543 -0.58510008 La 0.93474415 4.56686321 5.57584073 La 5.08821578 6.23441884 0.29071017 Pr 2.99023792 2.82435121 2.86695378 La 5.08567063 2.89482858 0.28371019 Pr 4.14681572 4.57229407 6.26855999 Pr 2.99079930 6.30547875 2.86747591 Pr 3.92132140 1.13698586 5.60000618 Al 2.06148449 4.56215176 0.13575388 Al 0.68754649 1.13691018 4.84154127 11 Lattice="4.655209064483643 0.0 -0.8266423940658569 -0.13831591512285676 4.652140057822718 -0.8226146697998047 0.0 0.0 13.475762367248535" Properties=species:S:1:pos:R:3 pbc="T T T" Dy 3.13001169 2.49033973 4.82671660 La 0.29742177 1.96497577 2.39923083 Dy 0.87214123 0.16381871 5.66071698 Dy 1.60957491 0.91942783 9.77842793 Pb 4.35592067 1.34903989 11.69578243 Pb 2.64799938 4.38516329 2.10265384 Dy 3.86963808 3.24644819 8.95872726 O 1.59167182 3.29874160 9.64508571 La 2.05164674 3.76918068 12.22036692 Pb 3.56844367 0.54228345 7.30065404 O 0.75365973 2.43843286 4.96621252 9 Lattice="3.186168670654297 0.0 0.0038394720759242773 0.025182018369836044 7.25213971699987 -4.177804470062256 0.0 0.0 8.370259284973145" Properties=species:S:1:pos:R:3 pbc="T T T" Cd 0.76657573 2.19635445 4.41191603 Cd 0.78262687 6.75957720 3.94270451 Cd 0.77798940 4.88432173 -0.24593322 Cd 2.36707088 4.41672705 2.59310346 Ag 2.37729016 7.03122787 1.31282849 Cd 2.36014227 2.19307877 -1.25573900 Cd 2.37765979 7.22737418 -1.58876914 Ag 2.36769117 4.61423196 5.49490693 Hg 0.76660732 2.19470386 1.30712938 `30:T568d,crystalView = (extxyzContent) => { // --- User Adjustable Parameters --- // Adjust these values to customize the visualization: const [Nx, Ny, Nz] = [3, 3, 3]; // Number of unit cells to replicate along X, Y, Z axes const radius = 0.6; // Base atomic radius (affects all atoms uniformly) const canvasWidth = 800; // Width of each 3D viewer (in pixels) const canvasHeight = 600; // Height of each 3D viewer (in pixels) // ------------------------------------ // --- New ExtXYZ Parser --- function parseExtXYZ(extxyzContent) { const frames = []; const lines = extxyzContent.split('\n').map(line => line.trim()).filter(line => line.length > 0); let i = 0; while (i < lines.length) { const numAtoms = parseInt(lines[i++], 10); if (isNaN(numAtoms)) break; const commentLine = lines[i++]; const latticeMatch = commentLine.match(/Lattice="([^"]+)"/); const propertiesMatch = commentLine.includes("Properties=species:S:1:pos:R:3"); if (!latticeMatch || !propertiesMatch) { console.warn("Skipping frame due to missing Lattice or Properties info:", commentLine); i += numAtoms; continue; } const latticeVals = latticeMatch[1].split(/\s+/).map(parseFloat); if (latticeVals.length !== 9) { console.warn("Skipping frame: Lattice string malformed with", latticeVals.length, "values."); i += numAtoms; continue; } const v1_extxyz = new three.Vector3(latticeVals[0], latticeVals[1], latticeVals[2]); const v2_extxyz = new three.Vector3(latticeVals[3], latticeVals[4], latticeVals[5]); const v3_extxyz = new three.Vector3(latticeVals[6], latticeVals[7], latticeVals[8]); const a = v1_extxyz.length(); const b = v2_extxyz.length(); const c = v3_extxyz.length(); const cos_gamma = Math.max(-1, Math.min(1, v1_extxyz.dot(v2_extxyz) / (a * b))); const cos_beta = Math.max(-1, Math.min(1, v1_extxyz.dot(v3_extxyz) / (a * c))); const cos_alpha = Math.max(-1, Math.min(1, v2_extxyz.dot(v3_extxyz) / (b * c))); const alpha = Math.acos(cos_alpha); const beta = Math.acos(cos_beta); const gamma = Math.acos(cos_gamma); const currentAtoms = []; const currentSpecies = []; for (let j = 0; j < numAtoms; j++) { if (i >= lines.length) { console.warn("Incomplete frame, reached end of file prematurely."); break; } const atomLine = lines[i++].split(/\s+/).filter(Boolean); if (atomLine.length < 4) { console.warn("Skipping malformed atom line:", atomLine.join(' ')); continue; } const symbol = atomLine[0]; const x = parseFloat(atomLine[1]); const y = parseFloat(atomLine[2]); const z = parseFloat(atomLine[3]); currentAtoms.push([x, y, z]); currentSpecies.push(symbol); } frames.push({ cell: { a, b, c, alpha, beta, gamma }, latticeVectors: [v1_extxyz, v2_extxyz, v3_extxyz], basis: currentAtoms, species: currentSpecies }); } return frames; } const allCrystalsData = parseExtXYZ(extxyzContent); if (allCrystalsData.length === 0) { return html`

No valid crystal frames found in the EXTXYZ file.

`; } // --- Common Configuration --- const aspectRatio = canvasWidth / canvasHeight; const colorMap = { H: { color: 0xFFFFFF, Z: 1 }, // white He: { color: 0xDDA0DD, Z: 2 }, // plum (added) Li: { color: 0x8B008B, Z: 3 }, // dark magenta (added) Be: { color: 0x32CD32, Z: 4 }, // lime green (added) B: { color: 0xFFD700, Z: 5 }, // gold (added) C: { color: 0x222222, Z: 6 }, // dark gray N: { color: 0x0000FF, Z: 7 }, // blue O: { color: 0xFF0000, Z: 8 }, // red F: { color: 0x00FF00, Z: 9 }, // green Ne: { color: 0xFFA500, Z: 10 }, // orange (added) Na: { color: 0x0000FF, Z: 11 }, // sodium blue Mg: { color: 0x1E90FF, Z: 12 }, // dodger blue Al: { color: 0xA9A9A9, Z: 13 }, // dark gray Si: { color: 0xDAA520, Z: 14 }, // goldenrod P: { color: 0xFFA500, Z: 15 }, // orange S: { color: 0xFFFF00, Z: 16 }, // yellow Cl: { color: 0x00FF00, Z: 17 }, // lime green Ar: { color: 0xADD8E6, Z: 18 }, // light blue (added) K: { color: 0x8B00FF, Z: 19 }, // violet Ca: { color: 0x40E0D0, Z: 20 }, // turquoise Sc: { color: 0x4B0082, Z: 21 }, // indigo (added) Ti: { color: 0xB0C4DE, Z: 22 }, // light steel blue V: { color: 0x228B22, Z: 23 }, // forest green Cr: { color: 0x008080, Z: 24 }, // teal Mn: { color: 0x800080, Z: 25 }, // purple Fe: { color: 0xD2691E, Z: 26 }, // chocolate Co: { color: 0x4169E1, Z: 27 }, // royal blue Ni: { color: 0xA9A9A9, Z: 28 }, // dark gray Cu: { color: 0xB87333, Z: 29 }, // copper Zn: { color: 0x7FFFD4, Z: 30 }, // aquamarine Ga: { color: 0xC0C0C0, Z: 31 }, // silver Ge: { color: 0x696969, Z: 32 }, // dim gray As: { color: 0x556B2F, Z: 33 }, // dark olive green Se: { color: 0xFFA07A, Z: 34 }, // light salmon Br: { color: 0xA52A2A, Z: 35 }, // brown Kr: { color: 0xFFEFD5, Z: 36 }, // papaya whip (added) Rb: { color: 0x9932CC, Z: 37 }, // dark orchid Sr: { color: 0x00CED1, Z: 38 }, // dark turquoise Y: { color: 0x708090, Z: 39 }, // slate gray Zr: { color: 0x4682B4, Z: 40 }, // steel blue Nb: { color: 0x2F4F4F, Z: 41 }, // dark slate gray Mo: { color: 0x00FA9A, Z: 42 }, // medium spring green Tc: { color: 0x8B0000, Z: 43 }, // dark red (added) Ru: { color: 0x40E0D0, Z: 44 }, // turquoise (added) Rh: { color: 0x8A2BE2, Z: 45 }, // blue violet (added) Pd: { color: 0x708090, Z: 46 }, // slate gray (added) Ag: { color: 0xC0C0C0, Z: 47 }, // silver Cd: { color: 0xFFD700, Z: 48 }, // gold In: { color: 0x7CFC00, Z: 49 }, // lawn green Sn: { color: 0xD3D3D3, Z: 50 }, // light gray Sb: { color: 0x8B4513, Z: 51 }, // saddle brown Te: { color: 0x008B8B, Z: 52 }, // dark cyan I: { color: 0x9400D3, Z: 53 }, // dark violet Xe: { color: 0x87CEEB, Z: 54 }, // sky blue (added) Cs: { color: 0xFF4500, Z: 55 }, // orange red Ba: { color: 0x00FFEF, Z: 56 }, // cyan La: { color: 0xADD8E6, Z: 57 }, // light blue Ce: { color: 0x4682B4, Z: 58 }, // steel blue (added) Pr: { color: 0x7FFFD4, Z: 59 }, // aquamarine (added) Nd: { color: 0x00CED1, Z: 60 }, // dark turquoise (added) Pm: { color: 0x9932CC, Z: 61 }, // dark orchid (added) Sm: { color: 0x90EE90, Z: 62 }, // light green (added) Eu: { color: 0xDAA520, Z: 63 }, // goldenrod (added) Gd: { color: 0xFFA500, Z: 64 }, // orange (added) Tb: { color: 0x228B22, Z: 65 }, // forest green (added) Dy: { color: 0x66CDAA, Z: 66 }, // medium aquamarine (added) Ho: { color: 0x800080, Z: 67 }, // purple (added) Er: { color: 0xD2691E, Z: 68 }, // chocolate (added) Tm: { color: 0x4169E1, Z: 69 }, // royal blue (added) Yb: { color: 0xA9A9A9, Z: 70 }, // dark gray (added) Lu: { color: 0xB87333, Z: 71 }, // copper (added) Hf: { color: 0x4682B4, Z: 72 }, // steel blue Ta: { color: 0x00FFFF, Z: 73 }, // cyan W: { color: 0xDAA520, Z: 74 }, // goldenrod Re: { color: 0xFFDAB9, Z: 75 }, // peach puff Os: { color: 0x1E90FF, Z: 76 }, // dodger blue Ir: { color: 0xBA55D3, Z: 77 }, // medium orchid Pt: { color: 0xE5E4E2, Z: 78 }, // platinum Au: { color: 0xFFD700, Z: 79 }, // gold Hg: { color: 0xB0C4DE, Z: 80 }, // light steel blue Tl: { color: 0x696969, Z: 81 }, // dim gray (added) Pb: { color: 0x708090, Z: 82 }, // slate gray Bi: { color: 0x8B0000, Z: 83 }, // dark red Po: { color: 0x8B008B, Z: 84 }, // dark magenta At: { color: 0xA52A2A, Z: 85 }, // brown (added) Rn: { color: 0xFFDAB9, Z: 86 }, // peach puff (added) Fr: { color: 0xFF4500, Z: 87 }, // orange red (added) Ra: { color: 0x00FFEF, Z: 88 }, // cyan (added) Ac: { color: 0xADD8E6, Z: 89 } // light blue (added) }; // --- Material Definitions (Shared across all viewers) --- const createSpeciesMaterials = (baseColor, exteriorPlanes, interiorPlanes) => ({ outside: new three.MeshStandardMaterial({ color: baseColor, transparent: true, opacity: 0.2, side: three.DoubleSide, clippingPlanes: exteriorPlanes, clipIntersection: true, depthWrite: false }), inside: new three.MeshStandardMaterial({ color: baseColor, transparent: true, opacity: 0.6, side: three.DoubleSide, clippingPlanes: interiorPlanes, clipIntersection: false, depthWrite: true }) }); // --- Helper to Create Corners --- function createCorners(scaleVectors, signs) { const corners = []; signs.forEach(s1 => signs.forEach(s2 => signs.forEach(s3 => { corners.push( new three.Vector3() .addScaledVector(scaleVectors[0], s1) .addScaledVector(scaleVectors[1], s2) .addScaledVector(scaleVectors[2], s3) ); }))); return corners; } // --- Helper to create Text Sprites for Legend --- const createTextSprite = (message, color, fontSize = 36) => { const canvas = document.createElement('canvas'); const context = canvas.getContext('2d'); const font = `Bold ${fontSize}px system-ui, sans-serif`; context.font = font; const metrics = context.measureText(message); const textWidth = metrics.width; const textHeight = fontSize * 1.2; canvas.width = textWidth + 20; canvas.height = textHeight + 20; context.font = font; context.fillStyle = `#${color.getHexString()}`; context.textBaseline = 'top'; context.fillText(message, 10, 10); const texture = new three.CanvasTexture(canvas); texture.minFilter = three.LinearFilter; texture.needsUpdate = true; const spriteMaterial = new three.SpriteMaterial({ map: texture, transparent: true }); const sprite = new three.Sprite(spriteMaterial); sprite.scale.set(canvas.width / canvas.height * 0.8 * 1.5, 0.8 * 1.5, 1); return sprite; }; // --- Array to hold all viewer instances and their HTML containers --- const viewerInstances = []; let currentActiveViewerIndex = 0; // --- Create a viewer for each crystal frame --- allCrystalsData.forEach((crystalData, index) => { const { cell, latticeVectors, basis, species } = crystalData; const { a, b, c } = cell; // --- Scene Setup for EACH viewer --- const scene = new three.Scene(); const camera = new three.PerspectiveCamera(45, aspectRatio, 0.1, 1000); const renderer = new three.WebGLRenderer({ antialias: true, alpha: true }); renderer.setSize(canvasWidth, canvasHeight); renderer.setPixelRatio(devicePixelRatio); renderer.setClearColor(0xffffff, 1); renderer.localClippingEnabled = true; const viewerContainer = html``; viewerContainer.appendChild(renderer.domElement); const controls = new OrbitControls(camera, renderer.domElement); controls.enablePan = false; controls.enableZoom = true; controls.minPolarAngle = 0; controls.maxPolarAngle = Math.PI / 2; controls.enableDamping = true; controls.dampingFactor = 0.1; scene.add(new three.AmbientLight(0xffffff, 0.5)); // --- Directional Light Setup --- const dl = new three.DirectionalLight(0xffffff, 0.8); dl.position.set(-10, -30, -20); scene.add(dl); const fillLight = new three.DirectionalLight(0xffffff, 0.4); fillLight.position.set(10, 30, 20); scene.add(fillLight); // Groups unique to this viewer instance const atomsGroup = new three.Group(); const cellEdgesGroup = new three.Group(); const supercellEdgesGroup = new three.Group(); scene.add(atomsGroup, cellEdgesGroup, supercellEdgesGroup); // --- Lattice Setup --- const scaled = latticeVectors; const scaledLengths = scaled.map(v => v.length()); // --- Clipping Planes --- const planes = []; for (let i = 0; i < 3; i++) { const normal = scaled[(i + 1) % 3].clone().cross(scaled[(i + 2) % 3]).normalize(); const point1 = new three.Vector3(0,0,0); const point2 = scaled[i].clone(); planes.push(new three.Plane().setFromNormalAndCoplanarPoint(normal, point2)); planes.push(new three.Plane().setFromNormalAndCoplanarPoint(normal.clone().negate(), point1)); } const exteriorPlanes = planes; const interiorPlanes = planes.map(p => p.clone().negate()); // --- Materials (per species, based on current crystal's planes) --- const speciesMats = {}; species.forEach(sp => { if (!speciesMats[sp]) { const baseColor = new three.Color(colorMap[sp]?.color ?? 0x008080); speciesMats[sp] = createSpeciesMaterials(baseColor, exteriorPlanes, interiorPlanes); } }); // --- Atoms in Supercell --- for (let ix = 0; ix < Nx; ix++) { for (let iy = 0; iy < Ny; iy++) { for (let iz = 0; iz < Nz; iz++) { basis.forEach(([x, y, z], i) => { const atomOriginalCartesian = new three.Vector3(x,y,z); const pos = atomOriginalCartesian .clone() .add(scaled[0].clone().multiplyScalar(ix)) .add(scaled[1].clone().multiplyScalar(iy)) .add(scaled[2].clone().multiplyScalar(iz)); const sp = species[i]; const mats = speciesMats[sp]; const Z = colorMap[sp]?.Z || 20; const r = radius * (0.5 + 0.5 * (1 - Math.exp(-Z / 20))); const geo = new three.SphereGeometry(r, 32, 32); const outMesh = new three.Mesh(geo, mats.outside); outMesh.position.copy(pos); outMesh.renderOrder = 0; atomsGroup.add(outMesh); const inMesh = new three.Mesh(geo, mats.inside); inMesh.position.copy(pos); inMesh.renderOrder = 1; atomsGroup.add(inMesh); }); } } } // --- Unit cell edges --- const unitCellCorners = createCorners(scaled, [0, 1]); const edgeMat = new three.LineBasicMaterial({ color: 0x222222, depthTest: true }); unitCellCorners.forEach((c1, i) => unitCellCorners.slice(i + 1).forEach(c2 => { const d = c1.distanceTo(c2); if (Math.abs(d - scaledLengths[0]) < 1e-6 || Math.abs(d - scaledLengths[1]) < 1e-6 || Math.abs(d - scaledLengths[2]) < 1e-6) { const line = new three.Line(new three.BufferGeometry().setFromPoints([c1, c2]), edgeMat); line.renderOrder = 2; cellEdgesGroup.add(line); } }) ); // --- Supercell edges --- const supercellCenter = new three.Vector3().addScaledVector(scaled[0], Nx / 2).addScaledVector(scaled[1], Ny / 2).addScaledVector(scaled[2], Nz / 2); const superCornersCentered = createCorners( [scaled[0].clone().multiplyScalar(Nx / 2), scaled[1].clone().multiplyScalar(Ny / 2), scaled[2].clone().multiplyScalar(Nz / 2)], [-1, 1] ); const superCorners = superCornersCentered.map(c => c.add(supercellCenter)); const superMat = new three.LineBasicMaterial({ color: 0xcccccc, depthTest: false }); superCorners.forEach((c1, i) => superCorners.slice(i + 1).forEach(c2 => { const d = c1.distanceTo(c2); if (Math.abs(d - scaledLengths[0] * Nx) < 1e-6 || Math.abs(d - scaledLengths[1] * Ny) < 1e-6 || Math.abs(d - scaledLengths[2] * Nz) < 1e-6) { const superLine = new three.Line(new three.BufferGeometry().setFromPoints([c1, c2]), superMat); superLine.renderOrder = 1; supercellEdgesGroup.add(superLine); } }) ); // --- Camera Positioning for (-3, -1, 0) direction --- const unitCellCenter = new three.Vector3().addScaledVector(scaled[0], 0.5).addScaledVector(scaled[1], 0.5).addScaledVector(scaled[2], 0.5); controls.target.copy(unitCellCenter); // Still look at the center of the first unit cell const viewDirection = new three.Vector3(-3, -1, 0).normalize(); // Normalized view direction const unitCellMaxDim = Math.max(a, b, c); camera.position.copy(unitCellCenter).add(viewDirection.multiplyScalar(unitCellMaxDim * 1.5)); // Zoomed onto unit cell camera.lookAt(unitCellCenter); // --- HTML Legend (REINSTATED AND POSITIONED WITHIN VIEWER CONTAINER) --- const legendDiv = html`

Elements

`; const legendList = legendDiv.querySelector('ul'); // Sort by Atomic Number (Z) const uniqueSpeciesForLegend = [...new Set(species)].sort((spA, spB) => { const ZA = colorMap[spA]?.Z || Infinity; const ZB = colorMap[spB]?.Z || Infinity; return ZA - ZB; }); uniqueSpeciesForLegend.forEach(sp => { const colorData = colorMap[sp] ?? { color: 0x008080 }; const cssColor = '#' + new three.Color(colorData.color).getHexString(); const listItem = html`

${sp}

`; legendList.appendChild(listItem); }); viewerContainer.appendChild(legendDiv); // Add this HTML legend to the current viewer's container // Store this viewer instance's data viewerInstances.push({ container: viewerContainer, renderer: renderer, scene: scene, camera: camera, controls: controls, animationFrameId: null, animate: () => { // No try-catch in animate loop as we're reverting to a stable version controls.update(); renderer.render(scene, camera); viewerInstances[index].animationFrameId = requestAnimationFrame(viewerInstances[index].animate); } }); }); // End of forEach crystalData // --- UI for Tabs --- const tabsContainer = html`

`; const viewerContainersWrapper = html`

`; let activeViewer = null; let activeTabButton = null; const switchTab = (index) => { // Hide current viewer and deactivate its tab if (activeViewer) { activeViewer.container.style.display = 'none'; cancelAnimationFrame(activeViewer.animationFrameId); // Removed controls.stop() as it might not be needed or cause other issues if (activeTabButton) { activeTabButton.style.backgroundColor = '#f0f0f0'; activeTabButton.style.color = '#333'; activeTabButton.style.fontWeight = 'normal'; activeTabButton.style.borderBottom = '1px solid #ccc'; } } // Show new viewer and activate its tab activeViewer = viewerInstances[index]; activeViewer.container.style.display = 'block'; currentActiveViewerIndex = index; // Keep track of the active index if needed activeViewer.controls.update(); // Update controls for new view immediately activeViewer.animationFrameId = requestAnimationFrame(activeViewer.animate); // Start its animation loop // Update tab button styling activeTabButton = tabsContainer.children[index]; activeTabButton.style.backgroundColor = '#fff'; activeTabButton.style.color = '#000'; activeTabButton.style.fontWeight = 'bold'; activeTabButton.style.borderBottom = '1px solid #fff'; }; allCrystalsData.forEach((crystalData, idx) => { // Generate tab name: unique sorted species by Atomic Number (Z) const tabName = [...new Set(crystalData.species)].sort((spA, spB) => { const ZA = colorMap[spA]?.Z || Infinity; const ZB = colorMap[spB]?.Z || Infinity; return ZA - ZB; }).join('-'); const button = document.createElement('button'); // Create button imperatively button.textContent = tabName; // Set text content button.style.cssText = ` padding: 10px 15px; border: 1px solid #ccc; border-bottom: 1px solid #ccc; border-top-left-radius: 8px; border-top-right-radius: 8px; cursor: pointer; background: #f0f0f0; font-family: system-ui, sans-serif; margin-right: 2px; position: relative; bottom: -1px; outline: none; color: #333; font-weight: normal; `; // Imperatively add event listener button.addEventListener('click', () => switchTab(idx)); tabsContainer.appendChild(button); viewerContainersWrapper.appendChild(viewerInstances[idx].container); }); // --- Initial Display --- switchTab(0); // --- Cleanup on invalidation --- // This cleans up all renderers and controls when the script is re-run (e.g., in Observable) // or when the page is unloaded (in a browser). invalidation.then(() => { viewerInstances.forEach(viewer => { cancelAnimationFrame(viewer.animationFrameId); // Ensure all loops are stopped viewer.renderer.dispose(); viewer.controls.dispose(); }); }); // Return a wrapper that contains both the tabs and the 3D viewers return html`

${tabsContainer}${viewerContainersWrapper}

`; };31:Tad0,colorMap = ({ H: { color: 0xFFFFFF, Z: 1 }, // white C: { color: 0x222222, Z: 6 }, // dark gray N: { color: 0x0000FF, Z: 7 }, // blue O: { color: 0xFF0000, Z: 8 }, // red F: { color: 0x00FF00, Z: 9 }, // green Na: { color: 0x0000FF, Z: 11 }, // sodium blue Mg: { color: 0x1E90FF, Z: 12 }, // dodger blue Al: { color: 0xA9A9A9, Z: 13 }, // dark gray Si: { color: 0xDAA520, Z: 14 }, // goldenrod P: { color: 0xFFA500, Z: 15 }, // orange S: { color: 0xFFFF00, Z: 16 }, // yellow Cl: { color: 0x00FF00, Z: 17 }, // lime green K: { color: 0x8B00FF, Z: 19 }, // violet Ca: { color: 0x40E0D0, Z: 20 }, // turquoise Ti: { color: 0xB0C4DE, Z: 22 }, // light steel blue V: { color: 0x228B22, Z: 23 }, // forest green Cr: { color: 0x008080, Z: 24 }, // teal Mn: { color: 0x800080, Z: 25 }, // purple Fe: { color: 0xD2691E, Z: 26 }, // chocolate Co: { color: 0x4169E1, Z: 27 }, // royal blue Ni: { color: 0xA9A9A9, Z: 28 }, // dark gray Cu: { color: 0xB87333, Z: 29 }, // copper Zn: { color: 0x7FFFD4, Z: 30 }, // aquamarine Ga: { color: 0xC0C0C0, Z: 31 }, // silver Ge: { color: 0x696969, Z: 32 }, // dim gray As: { color: 0x556B2F, Z: 33 }, // dark olive green Se: { color: 0xFFA07A, Z: 34 }, // light salmon Br: { color: 0xA52A2A, Z: 35 }, // brown Rb: { color: 0x9932CC, Z: 37 }, // dark orchid Sr: { color: 0x00CED1, Z: 38 }, // dark turquoise Y: { color: 0x708090, Z: 39 }, // slate gray Zr: { color: 0x4682B4, Z: 40 }, // steel blue Nb: { color: 0x2F4F4F, Z: 41 }, // dark slate gray Mo: { color: 0x00FA9A, Z: 42 }, // medium spring green Ag: { color: 0xC0C0C0, Z: 47 }, // silver Cd: { color: 0xFFD700, Z: 48 }, // gold In: { color: 0x7CFC00, Z: 49 }, // lawn green Sn: { color: 0xD3D3D3, Z: 50 }, // light gray Sb: { color: 0x8B4513, Z: 51 }, // saddle brown Te: { color: 0x008B8B, Z: 52 }, // dark cyan I: { color: 0x9400D3, Z: 53 }, // dark violet Cs: { color: 0xFF4500, Z: 55 }, // orange red Ba: { color: 0x00FFEF, Z: 56 }, // cyan La: { color: 0xADD8E6, Z: 57 }, // light blue Hf: { color: 0x4682B4, Z: 72 }, // steel blue Ta: { color: 0x00FFFF, Z: 73 }, // cyan W: { color: 0xDAA520, Z: 74 }, // goldenrod Re: { color: 0xFFDAB9, Z: 75 }, // peach puff Os: { color: 0x1E90FF, Z: 76 }, // dodger blue Ir: { color: 0xBA55D3, Z: 77 }, // medium orchid Pt: { color: 0xE5E4E2, Z: 78 }, // platinum Au: { color: 0xFFD700, Z: 79 }, // gold Hg: { color: 0xB0C4DE, Z: 80 }, // light steel blue Pb: { color: 0x708090, Z: 82 }, // slate gray Bi: { color: 0x8B0000, Z: 83 }, // dark red Po: { color: 0x8B008B, Z: 84 } // dark magenta })32:[] 2d:{"title":"Crystal structure","cells":[{"id":0,"value":"# Crystal structure","pinned":false,"hidden":false,"mode":"md"},{"id":763,"value":"crystalView(generated_extxyz)","pinned":true,"hidden":false,"mode":"ojs"},{"id":31,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs"},{"id":87,"value":"$30","pinned":true,"hidden":false,"mode":"ojs"},{"id":394,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":730,"value":"## Imports","pinned":false,"hidden":false,"mode":"md"},{"id":20,"value":"three = require(\"three@0.150.1\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":45,"value":"OrbitControls = (await import(\n \"three@0.150.1/examples/jsm/controls/OrbitControls.js\"\n)).OrbitControls","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W32","stdlib":"1","titling":"auto"}