diff --git a/.eslintrc.cjs b/.eslintrc.cjs index 4dcb439..333a011 100644 --- a/.eslintrc.cjs +++ b/.eslintrc.cjs @@ -2,19 +2,19 @@ module.exports = { root: true, env: { browser: true, es2020: true }, extends: [ - 'eslint:recommended', - 'plugin:react/recommended', - 'plugin:react/jsx-runtime', - 'plugin:react-hooks/recommended', + "eslint:recommended", + "plugin:react/recommended", + "plugin:react/jsx-runtime", + "plugin:react-hooks/recommended", ], - ignorePatterns: ['dist', '.eslintrc.cjs'], - parserOptions: { ecmaVersion: 'latest', sourceType: 'module' }, - settings: { react: { version: '18.2' } }, - plugins: ['react-refresh'], + ignorePatterns: ["dist", ".eslintrc.cjs"], + parserOptions: { ecmaVersion: "latest", sourceType: "module" }, + settings: { react: { version: "18.2" } }, + plugins: ["react-refresh"], rules: { - 'react-refresh/only-export-components': [ - 'warn', + "react-refresh/only-export-components": [ + "warn", { allowConstantExport: true }, ], }, -} +}; diff --git a/.github/workflows/deploy-gh-pages.yml b/.github/workflows/deploy-gh-pages.yml new file mode 100644 index 0000000..be8a35a --- /dev/null +++ b/.github/workflows/deploy-gh-pages.yml @@ -0,0 +1,49 @@ +name: Deploy to GitHub Pages + +on: + push: + branches: + - main + - develop + +permissions: + contents: write + +jobs: + build-and-deploy: + concurrency: ci-${{ github.ref }} + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v4 + + - name: Set up Node.js + uses: actions/setup-node@v4 + with: + node-version: "20" + + - name: Install dependencies + run: npm install + + - name: Set branch subpath variable (for vite) + # This is the URL subpath where a branch is deployed. + # '/' for main branch, otherwise . + run: | + if [ "${{ github.ref_name }}" == "main" ]; then + echo "BRANCH_SUBPATH=/" >> $GITHUB_ENV + else + echo "BRANCH_SUBPATH=/${{ github.ref_name }}/" >> $GITHUB_ENV + fi + + - name: Build project + run: npm run build + + - name: Deploy to GitHub Pages + uses: JamesIves/github-pages-deploy-action@v4 + with: + folder: ./dist + # Deploy main branch to root, other branches to their subfolders + target-folder: ${{ env.BRANCH_SUBPATH }} + # when deploying main to root, keep folders where other branches are deployed + clean-exclude: "develop" diff --git a/.github/workflows/prettier.yml b/.github/workflows/prettier.yml new file mode 100644 index 0000000..e2e0f27 --- /dev/null +++ b/.github/workflows/prettier.yml @@ -0,0 +1,30 @@ +name: Prettier + +on: + push: + branches: + - main + - develop + pull_request: + branches: + - main + - develop + +jobs: + prettier: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Setup Node.js + uses: actions/setup-node@v4 + with: + node-version: "20" + + - name: Install dependencies + run: npm install + + - name: Run Prettier + run: npx prettier --check . diff --git a/README.md b/README.md index 12b450c..59dbbc9 100644 --- a/README.md +++ b/README.md @@ -11,8 +11,23 @@ For local development: > npm run dev ``` -To publish the local version to GitHub pages: +To build an optimized package, use ``` -> npm run deploy +> npm run build ``` + +Preview locally with + +``` +> npm run preview +``` + +## Branches and deployment + +The following branches are automatically deployed via Github actions in the following manner: + +- `main` + - deployed to https://materialscloud-org.github.io/discover-mc2d-react/ +- `develop` + - deployed to https://materialscloud-org.github.io/discover-mc2d-react/develop diff --git a/index.html b/index.html index 12e6fea..e94dbf5 100644 --- a/index.html +++ b/index.html @@ -5,7 +5,26 @@ + Materials Cloud 2D crystals database + + + +
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"https://registry.npmjs.org/to-regex-range/-/to-regex-range-5.0.1.tgz", @@ -20178,6 +23042,26 @@ "node": ">=0.6" } }, + "node_modules/topojson-client": { + "version": "3.1.0", + "resolved": "https://registry.npmjs.org/topojson-client/-/topojson-client-3.1.0.tgz", + "integrity": "sha512-605uxS6bcYxGXw9qi62XyrV6Q3xwbndjachmNxu8HWTtVPxZfEJN9fd/SZS1Q54Sn2y0TMyMxFj/cJINqGHrKw==", + "license": "ISC", + "dependencies": { + "commander": "2" + }, + "bin": { + "topo2geo": "bin/topo2geo", + "topomerge": "bin/topomerge", + "topoquantize": "bin/topoquantize" + } + }, + "node_modules/topojson-client/node_modules/commander": { + "version": "2.20.3", + "resolved": "https://registry.npmjs.org/commander/-/commander-2.20.3.tgz", + "integrity": "sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ==", + "license": "MIT" + }, "node_modules/tough-cookie": { "version": "4.1.3", "resolved": "https://registry.npmjs.org/tough-cookie/-/tough-cookie-4.1.3.tgz", @@ -20287,6 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"https://registry.npmjs.org/update-diff/-/update-diff-1.1.0.tgz", + "integrity": "sha512-rCiBPiHxZwT4+sBhEbChzpO5hYHjm91kScWgdHf4Qeafs6Ba7MBl+d9GlGv72bcTZQO0sLmtQS1pHSWoCLtN/A==", + "license": "MIT" + }, "node_modules/upng-js": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/upng-js/-/upng-js-2.1.0.tgz", "integrity": "sha512-d3xzZzpMP64YkjP5pr8gNyvBt7dLk/uGI67EctzDuVp4lCZyVMo0aJO6l/VDlgbInJYDY6cnClLoBp29eKWI6g==", + "license": "MIT", "dependencies": { "pako": "^1.0.5" } @@ -20575,7 +23489,8 @@ "node_modules/upng-js/node_modules/pako": { "version": "1.0.11", "resolved": "https://registry.npmjs.org/pako/-/pako-1.0.11.tgz", - "integrity": "sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw==" + "integrity": "sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw==", + "license": "(MIT AND Zlib)" }, "node_modules/uri-js": { "version": "4.4.1", @@ -20715,6 +23630,17 @@ } } }, + "node_modules/vt-pbf": { + "version": "3.1.3", + "resolved": "https://registry.npmjs.org/vt-pbf/-/vt-pbf-3.1.3.tgz", + "integrity": "sha512-2LzDFzt0mZKZ9IpVF2r69G9bXaP2Q2sArJCmcCgvfTdCCZzSyz4aCLoQyUilu37Ll56tCblIZrXFIjNUpGIlmA==", + "license": "MIT", + "dependencies": { + "@mapbox/point-geometry": "0.1.0", + "@mapbox/vector-tile": "^1.3.1", + "pbf": "^3.2.1" + } + }, "node_modules/w3c-hr-time": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/w3c-hr-time/-/w3c-hr-time-1.0.2.tgz", @@ -20771,11 +23697,36 @@ "minimalistic-assert": "^1.0.0" } }, + "node_modules/weak-map": { + "version": "1.0.8", + "resolved": "https://registry.npmjs.org/weak-map/-/weak-map-1.0.8.tgz", + "integrity": "sha512-lNR9aAefbGPpHO7AEnY0hCFjz1eTkWCXYvkTRrTHs9qv8zJp+SkVYpzfLIFXQQiG3tVvbNFQgVg2bQS8YGgxyw==", + "license": "Apache-2.0" + }, + "node_modules/weas": { + "version": "0.1.26", + "resolved": "https://registry.npmjs.org/weas/-/weas-0.1.26.tgz", + "integrity": "sha512-chTisQepdW7cyQoV/jCBhNcBhPUz53r0a2iZvS2PbqJk6DObkDtfieFfemrxHdSSshHeywHdWzKvUyzXUmSdzg==", + "license": "MIT", + "dependencies": { + "dat.gui": "^0.7.9", + "three": "^0.169.0" + } + }, "node_modules/web-vitals": { "version": "2.1.4", "resolved": "https://registry.npmjs.org/web-vitals/-/web-vitals-2.1.4.tgz", "integrity": "sha512-sVWcwhU5mX6crfI5Vd2dC4qchyTqxV8URinzt25XqVh+bHEPGH4C3NPrNionCP7Obx59wrYEbNlw4Z8sjALzZg==" }, + "node_modules/webgl-context": { + "version": "2.2.0", + "resolved": "https://registry.npmjs.org/webgl-context/-/webgl-context-2.2.0.tgz", + "integrity": "sha512-q/fGIivtqTT7PEoF07axFIlHNk/XCPaYpq64btnepopSWvKNFkoORlQYgqDigBIuGA1ExnFd/GnSUnBNEPQY7Q==", + "license": "MIT", + "dependencies": { + "get-canvas-context": "^1.0.1" + } + }, "node_modules/webidl-conversions": { "version": "6.1.0", "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-6.1.0.tgz", @@ -21703,6 +24654,15 @@ "workbox-core": "6.6.0" } }, + "node_modules/world-calendars": { + "version": "1.0.3", + "resolved": "https://registry.npmjs.org/world-calendars/-/world-calendars-1.0.3.tgz", + "integrity": "sha512-sAjLZkBnsbHkHWVhrsCU5Sa/EVuf9QqgvrN8zyJ2L/F9FR9Oc6CvVK0674+PGAtmmmYQMH98tCUSO4QLQv3/TQ==", + "license": "MIT", + "dependencies": { + "object-assign": "^4.1.0" + } + }, "node_modules/wrap-ansi": { "version": "7.0.0", "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz", @@ -21842,6 +24802,15 @@ "resolved": "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz", "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==" }, + "node_modules/xtend": { + "version": "4.0.2", + "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", + "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==", + "license": "MIT", + "engines": { + "node": ">=0.4" + } + }, "node_modules/y18n": { "version": "5.0.8", "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", diff --git a/package.json b/package.json index 14b4018..9a96716 100644 --- a/package.json +++ b/package.json @@ -1,29 +1,30 @@ { "name": "discover-mc2d-react", - "private": true, "version": "0.0.0", + "private": true, "type": "module", "scripts": { "dev": "vite", "build": "vite build", "lint": "eslint . --ext js,jsx --report-unused-disable-directives --max-warnings 0", - "preview": "vite preview", - "predeploy": "vite build", - "deploy": "gh-pages -d dist" + "preview": "vite preview" }, "dependencies": { "bootstrap": "^5.3.2", "chart.js": "^4.4.1", "chartjs-plugin-annotation": "^3.0.1", "chartjs-plugin-zoom": "^2.0.1", - "mc-react-bands": "^0.3.7", + "mathjs": "^13.2.0", + "mc-react-bands": "^0.5.4", "mc-react-header": "^0.3.1", - "mc-react-library": "^0.3.0", - "mc-react-ptable-materials-grid": "^0.6.1", - "mc-react-structure-visualizer": "^0.6.1", + "mc-react-library": "^0.4.0", + "mc-react-phonon-visualizer": "^0.2.0", + "mc-react-ptable-materials-grid": "^0.8.3", + "mc-react-structure-visualizer": "^0.7.3", "react": "^18.2.0", "react-bootstrap": "^2.10.0", "react-dom": "^18.2.0", + "react-icons": "^5.3.0", "react-router-dom": "^6.21.3", "react-router-hash-link": "^2.4.3" }, diff --git a/src/App.css b/src/App.css index 633fd1c..77bf66e 100644 --- a/src/App.css +++ b/src/App.css @@ -1,12 +1,15 @@ -/* #root { - max-width: 1280px; - margin: 0 auto; - padding: 2rem; - text-align: center; -} */ - .App { display: flex; flex-direction: column; align-items: center; } + +.bs-overrides a { + color: #3366cc; + text-decoration: none; +} + +.bs-overrides a:hover { + color: #1a0dab; + text-decoration: underline; +} diff --git a/src/App.jsx b/src/App.jsx index 50cb922..f0dc466 100644 --- a/src/App.jsx +++ b/src/App.jsx @@ -17,7 +17,7 @@ function App() { } /> - } /> + } /> ); diff --git a/src/DetailPage/BandsSection/index.jsx b/src/DetailPage/BandsSection/index.jsx deleted file mode 100644 index 3409ea4..0000000 --- a/src/DetailPage/BandsSection/index.jsx +++ /dev/null @@ -1,76 +0,0 @@ -import React, { useState, useEffect } from "react"; - -import BandsVisualizer from "mc-react-bands"; - -import { ExploreButton } from "mc-react-library"; - -import { EXPLORE_URL } from "../../common/config"; -import { REST_API_AIIDA } from "../../common/config.js"; - -/** - * Fetches AiiDA bands data in json format. - * - * @param {string} uuid The uuid of the AiiDA node - * @returns the json response - */ -async function fetchAiidaBandsJson(uuid) { - // append '&download=false' to have json file as a string - const responseAiiDA = await fetch( - `${REST_API_AIIDA}/nodes/${uuid}/download?download_format=json`, - ); - const jsonAiiDA = await responseAiiDA.json(); - return jsonAiiDA; -} - -function shiftBands(bandsData, shift) { - bandsData.paths.forEach((path) => { - path.values.forEach((subpath) => { - subpath.forEach((val, idx, arr) => { - arr[idx] += shift; - }); - }); - }); -} - -function BandsSection(props) { - const [bandsData, setBandsData] = useState(null); - console.log(props); - - let bands_uuid = props.compoundInfo.bands_2D; - let bands_y_max = props.compoundInfo.bands_2D_y_max_lim; - let bands_y_min = props.compoundInfo.bands_2D_y_min_lim; - let bands_y_origin = props.compoundInfo.bands_2D_y_origin; - - useEffect(() => { - // Set state to null to show "loading" screen - setBandsData(null); - - fetchAiidaBandsJson(bands_uuid).then((loadedData) => { - shiftBands(loadedData, -bands_y_origin); - setBandsData(loadedData); - }); - }, []); - - let loading = bandsData == null; - - return ( -
- Electronic band structure{" "} - - {loading ? ( - loading - ) : ( - - )} -
- ); -} - -export default BandsSection; diff --git a/src/DetailPage/ElectronicSection/index.jsx b/src/DetailPage/ElectronicSection/index.jsx new file mode 100644 index 0000000..c3716b8 --- /dev/null +++ b/src/DetailPage/ElectronicSection/index.jsx @@ -0,0 +1,156 @@ +import React, { useState, useEffect } from "react"; + +import { McloudSpinner } from "mc-react-library"; + +import { MCInfoBox } from "../components/MCInfoBox"; + +import { Container, Row, Col } from "react-bootstrap"; + +import BandsVisualizer from "mc-react-bands"; + +import { ExploreButton } from "mc-react-library"; + +import { loadAiidaBands } from "../../common/restApiUtils"; + +import { AIIDA_REST_API_URL, EXPLORE_URL } from "../../common/restApiUtils"; + +import * as math from "mathjs"; + +import { formatAiidaProp } from "../utils"; + +function shiftBands(bandsData, shift) { + bandsData.paths.forEach((path) => { + path.values.forEach((subpath) => { + subpath.forEach((val, idx, arr) => { + arr[idx] += shift; + }); + }); + }); +} + +function ElectronicInfoBox({ electronicData, metadata }) { + let magStateStr = electronicData.magnetic_state; + if (magStateStr == null) { + magStateStr = "non-magnetic; untested"; + } + + return ( + +
+ General info +
    +
  • Band gap: {formatAiidaProp(electronicData.band_gap, "eV")}
    • +
  • Magnetic state: {magStateStr}
    • +
  • + Total magnetization:{" "} + {formatAiidaProp(electronicData.total_magnetization, "µB/cell", 2)} +
    • +
  • + Absolute magnetization:{" "} + {formatAiidaProp( + electronicData.absolute_magnetization, + "µB/cell", + 2, + )} +
    • +
+
+ + ); +} + +const ElectronicSection = (props) => { + const [bandsData, setBandsData] = useState(null); + const [loadingBands, setLoadingBands] = useState(true); + + let electronicData = props.loadedData.details.electronic; + console.log("electronicData", electronicData); + + // check if we can display bands + let bandsAvailable = true; + if ( + electronicData.bands_uuid == null || + electronicData.fermi_energy.value == null || + electronicData.band_gap.value == null + ) { + bandsAvailable = false; + } + + let bandShift = 0.0; + if (bandsAvailable) { + // Shifting the bands such that Fermi energy is 0: + // It looks like the fermi energy currently gives us the top of the conduction band + // instead of the middle of the band gap. Therefore, shift additionally by half the gap. + // Note: for spin-polarized calculations, there are 2 Fermi energies. Taking the maximum + // here seems to work best to align 0 to the middle of the gap (although not stricly correct). + bandShift = -math.max(electronicData.fermi_energy.value); + bandShift -= electronicData.band_gap.value / 2; + } + + useEffect(() => { + setBandsData(null); + if (bandsAvailable) { + loadAiidaBands(electronicData.bands_uuid).then((bands) => { + shiftBands(bands, bandShift); + setBandsData(bands); + setLoadingBands(false); + }); + } else { + setLoadingBands(false); + } + }, []); + + let bandsJsx = ""; + if (!bandsAvailable) { + bandsJsx = ( + Electronic bands are not available for this material. + ); + } else if (loadingBands) { + bandsJsx = ( +
+ +
+ ); + } else { + bandsJsx = ( + <> +
+ Electronic band structure{" "} + +
+ + + ); + } + + return ( +
+
Electronic properties
+ + + {bandsJsx} + +
+ +
+ + + +
+ ); +}; + +export default ElectronicSection; diff --git a/src/DetailPage/OverviewSection/index.css b/src/DetailPage/OverviewSection/index.css index 6f80e2b..4aa42da 100644 --- a/src/DetailPage/OverviewSection/index.css +++ b/src/DetailPage/OverviewSection/index.css @@ -1,55 +1,14 @@ -.overview-section { - display: flex; - align-items: flex-end; - justify-content: space-evenly; - margin-bottom: 5px; +.structure-view-box { position: relative; -} - -.structure-view-section { - position: relative; - display: flex; - flex-direction: column; -} - -.subsection-title-container { - margin: 2px 0px 6px 0px; -} - -.general-info-section { - height: 450px; - width: 450px; - /* background: rgb(240, 240, 240); */ - text-align: left; - border: 1px solid #d6d6d6; + min-height: 350px; + width: 100%; + flex: 1; border-radius: 5px; - padding: 10px; - /* margin: 5px; */ -} - -ul.no-bullets { - list-style-type: none; - padding: 0; - margin: 0px 10px 3px; -} - -ul.no-bullets li { - margin: 3px 0px; -} - -.source-a { - color: #303f9f; - text-decoration: none; -} - -.source-a:hover { - filter: brightness(80%); - text-decoration: underline; } .download-button-container { position: absolute; - top: 40px; + top: 10px; right: 10px; z-index: 3; } diff --git a/src/DetailPage/OverviewSection/index.jsx b/src/DetailPage/OverviewSection/index.jsx index fefd75b..e45e1ae 100644 --- a/src/DetailPage/OverviewSection/index.jsx +++ b/src/DetailPage/OverviewSection/index.jsx @@ -4,14 +4,21 @@ import "./index.css"; import StructureVisualizer from "mc-react-structure-visualizer"; +import { Container, Row, Col } from "react-bootstrap"; + import { - formatSpaceGroupSymbol, - formatChemicalFormula, - StructDownloadButton, ExploreButton, + StructDownloadButton, + formatChemicalFormula, + formatSpaceGroupSymbol, + getSymmetryInfo, } from "mc-react-library"; -import { EXPLORE_URL } from "../../common/config"; +import { MCInfoBox } from "../components/MCInfoBox"; + +import { AIIDA_REST_API_URL, EXPLORE_URL } from "../../common/restApiUtils"; + +import { formatAiidaProp, formatSourceLink } from "../utils"; function floatFormatter(val, prec = 1) { if (val >= 1e5 || (val < 0.01 && val !== 0)) { @@ -20,119 +27,173 @@ function floatFormatter(val, prec = 1) { return val.toFixed(prec); } -function InfoBox(props) { - let info = props.compoundInfo; - - function format_aiida_prop(key, unit, prec = 3, factor = 1) { - if (!(key in info)) { - return N/A; - } - let val = info[key]["value"] || 0.0; - val *= factor; - return ( - - {val.toFixed(prec)} {unit}{" "} - - - ); - } +function formatPowerOf10(number, precision = 2) { + const [base, exponent] = number.toExponential(precision).split("e"); + return ( + + {base} × 10{exponent} + + ); +} +function GeneralInfoBox({ + details, + metadata, + symmetryInfo, + primaryParentInfo, +}) { + let parentSymmInfo = getSymmetryInfo(primaryParentInfo.space_group_number); return ( -
+
+ General info
    -
  • Formula: {formatChemicalFormula(info["formula"])}
    • -
  • Space group: {formatSpaceGroupSymbol(info["space_group"])}
    • -
  • Point group: {formatSpaceGroupSymbol(info["point_group"])}
    • -
  • Prototype: {formatChemicalFormula(info["prototype"])}
    • -
  • Abundance: {floatFormatter(info["abundance"])}
    • -
  • Band gap: {format_aiida_prop("band_gap", "eV")}
    • +
  • Formula: {formatChemicalFormula(details.general.formula)}
    • +
  • + Space group symbol:{" "} + {formatSpaceGroupSymbol(symmetryInfo.space_group_symbol)} +
    • +
  • Space group number: {details.general.space_group_number}
    • +
  • Prototype: {formatChemicalFormula(details.general.prototype)}
    • +
  • Abundance: {formatPowerOf10(details.general.abundance)}
-
- Magnetic properties + {/*
+ Primary 3D parent (details in section "3D parent crystals")
    -
  • Magnetic state: {info["magnetic_state_long"]}
    • +
  • Formula: {formatChemicalFormula(primaryParentInfo.formula)}
  • - Total magnetization:{" "} - {format_aiida_prop("total_magnetization", "µB/cell", 2)} + Source database:{" "} + {formatSourceLink( + primaryParentInfo.source_db, + primaryParentInfo.source_db_id, + )}
  • - Absolute magnetization:{" "} - {format_aiida_prop("absolute_magnetization", "µB/cell", 2)} + Bravais lattice: {parentSymmInfo.bravais_lattice} ( + {parentSymmInfo.bravais_lattice_pearson})
    • -
-
-
- Binding energies -
  • - DF2-C09:{" "} - {format_aiida_prop( - "binding_energy_per_substructure_per_unit_area_df2", - "meV/Ų", - 1, - 1000, - )} + Space group:{" "} + {formatSpaceGroupSymbol(parentSymmInfo.space_group_symbol)} ( + {primaryParentInfo.space_group_number})
  • - rVV10:{" "} - {format_aiida_prop( - "binding_energy_per_substructure_per_unit_area_rvv10", + DF2-C09 Binding energy:{" "} + {formatAiidaProp(primaryParentInfo.binding_energy_df2, "meV/Ų", 1)} +
    • +
  • + rVV10 Binding energy:{" "} + {formatAiidaProp( + primaryParentInfo.binding_energy_rvv10, "meV/Ų", 1, - 1000, )}
    • +
  • + ΔDF2:{" "} + {formatAiidaProp(primaryParentInfo.delta_df2, "%", 1, 100)} +
    • +
  • + ΔrVV10:{" "} + {formatAiidaProp(primaryParentInfo.delta_rvv10, "%", 1, 100)} +
-
+
*/}
- Delta in interlayer distance (vdW vs revPBE) + Exfoliation info (from primary parent{" "} + {formatSourceLink( + primaryParentInfo.source_db, + primaryParentInfo.source_db_id, + )} + )
  • - ΔDF2: {format_aiida_prop("delta_df2", "%", 1, 100)} + Binding energies:
    • +
      +
    • + DF2-C09:{" "} + {formatAiidaProp( + primaryParentInfo.binding_energy_df2, + "meV/Ų", + 1, + )} +
      • +
    • + rVV10:{" "} + {formatAiidaProp( + primaryParentInfo.binding_energy_rvv10, + "meV/Ų", + 1, + )} +
      • +
  • - ΔrVV10: {format_aiida_prop("delta_rvv10", "%", 1, 100)} + Delta in interlayer distance (vdW vs revPBE):
    • +
      +
    • + ΔDF2:{" "} + {formatAiidaProp(primaryParentInfo.delta_df2, "%", 1, 100)} +
      • +
    • + ΔrVV10:{" "} + {formatAiidaProp(primaryParentInfo.delta_rvv10, "%", 1, 100)} +
      • +
-
+ ); } -function OverviewSection(props) { +const StructureViewerBox = ({ uuid, structureInfo }) => { return ( -
-
-
-
- Structure{" "} - -
- +
+ Structure +
+
+ +
+ -
- -
-
-
-
- Info and properties -
-
- -
+ + ); +}; + +function OverviewSection({ params, loadedData }) { + return ( +
+
General overview
+ + + + + + +
+ +
+ + +
); } diff --git a/src/DetailPage/ParentsSection/index.jsx b/src/DetailPage/ParentsSection/index.jsx new file mode 100644 index 0000000..b9ae01e --- /dev/null +++ b/src/DetailPage/ParentsSection/index.jsx @@ -0,0 +1,210 @@ +import React, { useState, useEffect } from "react"; + +import { McloudSpinner } from "mc-react-library"; + +import { MCInfoBox } from "../components/MCInfoBox"; + +import { Container, Row, Col } from "react-bootstrap"; + +import StructureVisualizer from "mc-react-structure-visualizer"; + +import { + ExploreButton, + StructDownloadButton, + formatChemicalFormula, + formatSpaceGroupSymbol, +} from "mc-react-library"; + +import { + AIIDA_REST_API_URL, + EXPLORE_URL, + loadAiidaAttributes, + loadAiidaCif, +} from "../../common/restApiUtils"; + +import { getSymmetryInfo } from "mc-react-library"; + +import Form from "react-bootstrap/Form"; + +import { formatAiidaProp, formatSourceLink } from "../utils"; + +function ParentInfoBox({ parentInfo, symmetryInfo }) { + return ( + +
+ General info +
    +
  • Formula: {formatChemicalFormula(parentInfo.formula)}
    • +
  • + Source database:{" "} + {formatSourceLink(parentInfo.source_db, parentInfo.source_db_id)} +
    • +
  • + Bravais lattice: {symmetryInfo.bravais_lattice} ( + {symmetryInfo.bravais_lattice_pearson}) +
    • +
  • + Space group symbol:{" "} + {formatSpaceGroupSymbol(symmetryInfo.space_group_symbol)} +
    • +
  • Space group number: {parentInfo.space_group_number}
    • +
+
+
+ Binding energies +
    +
  • + DF2-C09 Binding energy:{" "} + {formatAiidaProp(parentInfo.binding_energy_df2, "meV/Ų", 1)} +
    • +
  • + rVV10 Binding energy:{" "} + {formatAiidaProp(parentInfo.binding_energy_rvv10, "meV/Ų", 1)} +
    • +
+
+
+ Delta in interlayer distance (vdW vs revPBE) +
    +
  • + ΔDF2:{" "} + {formatAiidaProp(parentInfo.delta_df2, "%", 1, 100)} +
    • +
  • + ΔrVV10:{" "} + {formatAiidaProp(parentInfo.delta_rvv10, "%", 1, 100)} +
    • +
+
+ + ); +} + +const StructureViewerBox = ({ uuid, structureInfo }) => { + return ( + <> +
+ Structure +
+
+ +
+ +
+
+ + ); +}; + +async function fetchParentStructure(uuid) { + let aiidaAttributes = await loadAiidaAttributes(uuid); + let structureCif = await loadAiidaCif(uuid); + return { aiidaAttributes: aiidaAttributes, cif: structureCif }; +} + +const ParentsSection = (props) => { + const [selectedParentIndex, setSelectedParentIndex] = useState(0); + const [parentStructureInfo, setParentStructureInfo] = useState(null); + // const [selectedParent, setSelectedParent] = useState(parentsList[0]); + + let parentsList = props.loadedData.details.parents_3d; + let selectedParentUuid = + parentsList[selectedParentIndex].initial_structure_uuid; + + let symmetryInfoList = []; + parentsList.forEach((parent) => { + symmetryInfoList.push(getSymmetryInfo(parent.space_group_number)); + }); + + console.log("parentsList", parentsList); + + useEffect(() => { + if (selectedParentUuid) { + fetchParentStructure(selectedParentUuid).then((loaded) => { + setParentStructureInfo(loaded); + }); + } else { + setParentStructureInfo(null); + } + }, [selectedParentIndex]); + + let loadingStructure = + selectedParentUuid != null && parentStructureInfo == null; + + let naMsg = "Parent structure not available."; + if ( + parentsList[selectedParentIndex].source_db == "ICSD" || + parentsList[selectedParentIndex].source_db == "MPDS" + ) { + naMsg = + "Parent structures originating from ICSD" + + " and MPDS cannot be displayed here for licensing reasons."; + } + + let structurePanel =
{naMsg}
; + + if (loadingStructure) { + structurePanel = ( +
+ +
+ ); + } + + if (parentStructureInfo != null) { + structurePanel = ( + + ); + } + + return ( +
+
3D parent crystals
+ + + + + Select parent crystal: + { + setSelectedParentIndex(v.target.value); + }} + > + {parentsList.map((e, i) => ( + + ))} + + +
+ +
+ + {structurePanel} + + +
+ ); +}; + +export default ParentsSection; diff --git a/src/DetailPage/SelectionSection/index.jsx b/src/DetailPage/SelectionSection/index.jsx deleted file mode 100644 index 0b64cbb..0000000 --- a/src/DetailPage/SelectionSection/index.jsx +++ /dev/null @@ -1,59 +0,0 @@ -import React from "react"; - -import Form from "react-bootstrap/Form"; - -import { useNavigate } from "react-router-dom"; - -function extractIntId(strId) { - return parseInt(strId.split(/-|\//)[1]); -} - -function SelectionSection(props) { - const navigate = useNavigate(); - - let formula = props.currentStructure.compound; - - let currentId = `${props.currentStructure.id}`; - - let formatedArr = []; - - props.sameFormulaStructures.ids.forEach((id, index) => { - let sg = props.sameFormulaStructures.spacegrps[index]; - formatedArr.push({ id: id, sg: sg }); - }); - // sort by the numerical value of mc3d-id - formatedArr.sort((a, b) => extractIntId(a.id) - extractIntId(b.id)); - - return ( -
- Related structures -
- - Structures with this chemical formula - { - navigate( - `${import.meta.env.BASE_URL}/#/details/${formula}/${v.target.value}`, - ); - // navigate(0); - }} - > - {formatedArr.map((e) => ( - - ))} - - -
- ); -} - -export default SelectionSection; diff --git a/src/DetailPage/VibrationalSection/index.jsx b/src/DetailPage/VibrationalSection/index.jsx new file mode 100644 index 0000000..c933e5f --- /dev/null +++ b/src/DetailPage/VibrationalSection/index.jsx @@ -0,0 +1,109 @@ +import React, { useState, useEffect } from "react"; + +import { McloudSpinner } from "mc-react-library"; + +import { MCInfoBox } from "../components/MCInfoBox"; + +import { Container, Row, Col } from "react-bootstrap"; + +import BandsVisualizer from "mc-react-bands"; + +import { ExploreButton } from "mc-react-library"; + +import { loadAiidaBands, loadPhononVis } from "../../common/restApiUtils"; + +import { AIIDA_REST_API_URL, EXPLORE_URL } from "../../common/restApiUtils"; + +import PhononVisualizer from "mc-react-phonon-visualizer"; + +const VibrationalSection = (props) => { + const [bandsData, setBandsData] = useState(null); + const [loadingBands, setLoadingBands] = useState(true); + const [phononVisData, setPhononVisData] = useState(null); + + let vibrationalData = props.loadedData.details.vibrational; + console.log(vibrationalData); + + let bandsUuid = vibrationalData.phonon_bands_uuid; + + useEffect(() => { + setBandsData(null); + if (bandsUuid) { + loadAiidaBands(bandsUuid).then((bands) => { + setBandsData(bands); + setLoadingBands(false); + }); + } else { + setLoadingBands(false); + } + + loadPhononVis(props.params.id).then((data) => { + setPhononVisData(data); + console.log("PHONON VIS", data); + }); + }, []); + + let bandsAvailable = bandsData != null; + let bandsJsx = ""; + if (bandsAvailable) { + bandsJsx = ( + + +
+ Phonon band structure{" "} + +
+ + + + + ); + } + + let phononVisAvailable = phononVisData != null; + let phononVisJsx = ""; + if (phononVisAvailable) { + // NOTE: The PhononVisualizer plotly clicking doesn't seem to work + // inside bootstrap ! Keep it outside. + phononVisJsx = ( +
+
+
+ Interactive phonon visualizer{" "} + +
+
+ +
+ ); + } + + return ( +
+
Vibrational properties
+ + {loadingBands ? ( +
+ +
+ ) : !bandsAvailable ? ( + Vibrational properties not available for this structure. + ) : ( + <>{bandsJsx} + )} + + {phononVisJsx} +
+ ); +}; + +export default VibrationalSection; diff --git a/src/DetailPage/components/CitationsList.css b/src/DetailPage/components/CitationsList.css new file mode 100644 index 0000000..c6a118b --- /dev/null +++ b/src/DetailPage/components/CitationsList.css @@ -0,0 +1,8 @@ +.citation-a { + color: black; + text-decoration: none; +} +.citation-a:hover { + /* filter: brightness(80%); */ + text-decoration: underline; +} diff --git a/src/DetailPage/components/CitationsList.jsx b/src/DetailPage/components/CitationsList.jsx new file mode 100644 index 0000000..7cfdd36 --- /dev/null +++ b/src/DetailPage/components/CitationsList.jsx @@ -0,0 +1,39 @@ +import { FaBook } from "react-icons/fa"; + +import "./CitationsList.css"; + +export const CitationText = ({ info }) => ( + +); + +const CITATION_MAPPING = { + Mounet18: { + authorsText: "Mounet et al.", + journalText: "Nat. Nanotech.", + doi: "10.1038/s41565-017-0035-5", + year: 2018, + }, + Campi23: { + authorsText: "Campi et al.", + journalText: "ACS Nano", + doi: "10.1021/acsnano.2c11510", + year: 2023, + }, +}; + +export const CitationsList = ({ citationLabels }) => ( +
+ {citationLabels.map((label) => ( + + ))} +
+); diff --git a/src/DetailPage/components/MCInfoBox.css b/src/DetailPage/components/MCInfoBox.css new file mode 100644 index 0000000..3945dde --- /dev/null +++ b/src/DetailPage/components/MCInfoBox.css @@ -0,0 +1,11 @@ +.mc-info-container { + overflow-y: scroll; + /* max-height: 450px; */ + min-width: 200px; + background: #f8f8f8; + display: flex; + flex-direction: column; + justify-content: space-around; + height: 100%; + padding: 10px 15px; +} diff --git a/src/DetailPage/components/MCInfoBox.jsx b/src/DetailPage/components/MCInfoBox.jsx new file mode 100644 index 0000000..ff18a94 --- /dev/null +++ b/src/DetailPage/components/MCInfoBox.jsx @@ -0,0 +1,11 @@ +import "./MCInfoBox.css"; + +export const MCInfoBox = ({ children, style = null }) => { + return ( +
+
+ {children} +
+
+ ); +}; diff --git a/src/DetailPage/components/MCTable.css b/src/DetailPage/components/MCTable.css new file mode 100644 index 0000000..57cb497 --- /dev/null +++ b/src/DetailPage/components/MCTable.css @@ -0,0 +1,4 @@ +.mc-data-table-container { + overflow-y: scroll; + max-height: 305px; +} diff --git a/src/DetailPage/components/MCTable.jsx b/src/DetailPage/components/MCTable.jsx new file mode 100644 index 0000000..460ea85 --- /dev/null +++ b/src/DetailPage/components/MCTable.jsx @@ -0,0 +1,47 @@ +import Table from "react-bootstrap/Table"; + +import "./MCTable.css"; + +function formatIfFloat(value, precision) { + if (typeof value === "number" && !isNaN(value)) { + return value.toFixed(precision); + } + return value; +} + +export const MCTable = ({ + headerRow, + contents, + floatPrecision = 4, + style = null, +}) => { + // headerRow - array of header labels + // contents - array for each row (needs to match header size) + return ( +
+ + + + {headerRow.map((h, i) => ( + + ))} + + + + {contents.map((row, i) => ( + + {row.map((cell, j) => ( + + ))} + + ))} + +
+ {h} +
{formatIfFloat(cell, floatPrecision)}
+
+ ); +}; diff --git a/src/DetailPage/index.css b/src/DetailPage/index.css index 5f9c396..d389ebd 100644 --- a/src/DetailPage/index.css +++ b/src/DetailPage/index.css @@ -1,25 +1,50 @@ -.detail-page { - text-align: center; +.detail-page-heading { + font-size: 30px; + margin: 20px 0px 10px; +} + +.section-heading { + font-size: 24px; + margin: 10px 0px; + padding: 20px 0px 10px; + border-bottom: 1px solid #c4c4c4; +} + +.section-container { + border-radius: 5px; +} + +.flex-column { display: flex; flex-direction: column; - align-items: center; - justify-content: space-evenly; + justify-content: space-between; +} + +.subsection-title { + font-weight: bold; + padding: 5px; } -.detail-page > * { - margin: 0 auto; +.subsection-shadow { + box-shadow: 0 2px 6px 2px rgb(0 0 0 / 0.15); } -.mc3d-title-header { - /* background-color: rgb(250, 1, 1); */ - border: 1px solid #d6d6d6; +ul.no-bullets { + list-style-type: none; + padding: 4px; + margin: 0px 5px 0px 10px; } -.detail-page-inner > * { - width: 950px; - background-color: rgb(250, 250, 250); - border: 1px solid #d6d6d6; - border-radius: 0px; - padding: 5px; - margin: 10px; +ul.no-bullets li { + margin: 3px 0px 3px; +} + +.source-a { + color: #303f9f; + text-decoration: none; +} + +.source-a:hover { + filter: brightness(80%); + text-decoration: underline; } diff --git a/src/DetailPage/index.jsx b/src/DetailPage/index.jsx index 7f1a7be..5c16cdc 100644 --- a/src/DetailPage/index.jsx +++ b/src/DetailPage/index.jsx @@ -6,76 +6,81 @@ import { useParams, useNavigate } from "react-router-dom"; import MaterialsCloudHeader from "mc-react-header"; +import { formatChemicalFormula } from "mc-react-library"; + +import { Container, Row, Col } from "react-bootstrap"; + +import { getSymmetryInfo } from "mc-react-library"; + +import { FaBook } from "react-icons/fa"; + +import { CitationsList } from "./components/CitationsList"; + import { - formatTitle, - fetchAiidaAttributes, - fetchAiidaCifText, -} from "../common/utils.jsx"; + loadMetadata, + loadDetails, + loadAiidaAttributes, + loadAiidaCif, +} from "../common/restApiUtils"; -import { REST_API_COMPOUNDS } from "../common/config"; +// import { REST_API_COMPOUNDS } from "../common/config"; import "./index.css"; import { McloudSpinner } from "mc-react-library"; import OverviewSection from "./OverviewSection"; -import SelectionSection from "./SelectionSection"; -import BandsSection from "./BandsSection"; - -async function fetchCompoundData(compound, id) { - // 1. fetch the compound data from MC Rest API: - const responseCompound = await fetch(`${REST_API_COMPOUNDS}/${compound}`); - const jsonCompound = await responseCompound.json(); - // this returns a list of compounds with the given formula - // We need to find the correct one with the specified id - const compoundsArr = jsonCompound.data[`${compound}`]; - const spacegroupsArr = compoundsArr.map((stru) => stru.space_group); - const idsArr = compoundsArr.map((stru) => `mc2d-${stru.mc2d_id}`); - - const selectedCompoundInfo = compoundsArr[idsArr.indexOf(id)]; - - // Fetch structuredata here once, as that might be used for multiple subsections - // Other AiiDA data (e.g. bands) will be fetched within each subsection - const structure_uuid = selectedCompoundInfo.structure_2D; - - let loadedData = { - compoundInfo: selectedCompoundInfo, - sameFormulaStructures: { spacegrps: spacegroupsArr, ids: idsArr }, - structureAttributes: await fetchAiidaAttributes(structure_uuid), - structureCifText: await fetchAiidaCifText(structure_uuid), +import ElectronicSection from "./ElectronicSection"; +import VibrationalSection from "./VibrationalSection"; +import ParentsSection from "./ParentsSection"; + +function formatTitle(formulaStr, id) { + return ( + + {formatChemicalFormula(formulaStr)} ({id}) + + ); +} + +async function fetchCompoundData(id) { + let metadata = await loadMetadata(id); + let details = await loadDetails(id); + + let symmetryInfo = getSymmetryInfo(details.general.space_group_number); + + let structureUuid = details.general.structure_relaxed_uuid; + + let aiidaAttributes = await loadAiidaAttributes(structureUuid); + let structureCif = await loadAiidaCif(structureUuid); + + return { + metadata: metadata, + details: details, + symmetryInfo: symmetryInfo, + structureInfo: { aiidaAttributes: aiidaAttributes, cif: structureCif }, }; - return loadedData; } function DetailPage() { - const [compoundInfo, setCompoundInfo] = useState(null); - const [sameFormulaStructures, setSameFormulaStructures] = useState(null); - const [structureAttributes, setStructureAttributes] = useState(null); - const [structureCifText, setStructureCifText] = useState(null); + const [loadedData, setLoadedData] = useState(null); // for routing const navigate = useNavigate(); - const params = useParams(); + const params = useParams(); // Route parameters useEffect(() => { - // Set state to null to show "loading" screen - // while new parameters are loaded - setCompoundInfo(null); - setSameFormulaStructures(null); - setStructureAttributes(null); - setStructureCifText(null); - - let compound = params["compound"]; - let id = params["id"]; - - fetchCompoundData(compound, id).then((loadedData) => { - setCompoundInfo(loadedData.compoundInfo); - setSameFormulaStructures(loadedData.sameFormulaStructures); - setStructureAttributes(loadedData.structureAttributes); - setStructureCifText(loadedData.structureCifText); + setLoadedData(null); + fetchCompoundData(params.id).then((loadedData) => { + console.log("Loaded general data", loadedData); + setLoadedData(loadedData); }); - }, [params.compound, params.id]); // <- call when route params change + }, [params.id]); // <- call when route params change + + let title = null; + let loading = loadedData == null; + if (!loading) { + title = formatTitle(loadedData.details.general.formula, params.id); + } - let loading = compoundInfo == null; return ( -
+ -
-

{formatTitle(params)}

- {loading ? ( -
- -
- ) : ( - <> - - - - - )} -
-
+ {loading ? ( +
+ +
+ ) : ( + <> +
{title}
+ + + + + + + )} + ); } diff --git a/src/DetailPage/utils.jsx b/src/DetailPage/utils.jsx new file mode 100644 index 0000000..46060f7 --- /dev/null +++ b/src/DetailPage/utils.jsx @@ -0,0 +1,52 @@ +import { + ExploreButton, + StructDownloadButton, + formatChemicalFormula, + formatSpaceGroupSymbol, +} from "mc-react-library"; + +import { EXPLORE_URL } from "../common/restApiUtils"; + +export function formatAiidaProp(property, unit = null, prec = 3, factor = 1) { + if (property == null) { + return N/A; + } + let val = property.value ?? 0.0; + val *= factor; + let valStr = val.toFixed(prec); + if (unit) { + valStr += ` ${unit}`; + } + return ( + + {valStr}{" "} + + + ); +} + +function sourceUrl(db, id) { + if (db == "MPDS") { + return `https://mpds.io/#entry/${id}`; + } + if (db == "COD") { + return `http://www.crystallography.net/cod/${id}.html`; + } + if (db == "ICSD") { + return `https://icsd.fiz-karlsruhe.de/linkicsd.xhtml?coll_code=${id}`; + } + return null; +} + +export function formatSourceLink(db, id) { + return ( + + {db} - {id} + + ); +} diff --git a/src/MainPage/DownloadButton.css b/src/MainPage/DownloadButton.css new file mode 100644 index 0000000..8641a78 --- /dev/null +++ b/src/MainPage/DownloadButton.css @@ -0,0 +1,29 @@ +.aggrid-style-button { + padding: 10px; + background-color: #f8f8f8; + color: #000000; + font-family: var(--ag-font-family); + font-size: 12px; + font-weight: bold; + border: 1px solid #babfc7; + border-radius: 3px; + cursor: pointer; + margin-bottom: 3px; + margin-top: 2px; +} + +.aggrid-style-button:hover { + background-color: #dbdbdb; +} + +.aggrid-style-button-disabled { + opacity: 0.4; + cursor: none; + pointer-events: none; +} + +.download-button-outer-container { + display: flex; + align-items: center; + gap: 10px; +} diff --git a/src/MainPage/DownloadButton.jsx b/src/MainPage/DownloadButton.jsx new file mode 100644 index 0000000..eac60b3 --- /dev/null +++ b/src/MainPage/DownloadButton.jsx @@ -0,0 +1,80 @@ +import { saveAs } from "file-saver"; + +import { HelpButton } from "mc-react-library"; +import { Popover } from "react-bootstrap"; + +import "./DownloadButton.css"; + +const getCurrentDateString = () => { + const now = new Date(); + const year = now.getFullYear(); + const month = String(now.getMonth() + 1).padStart(2, "0"); + const day = String(now.getDate()).padStart(2, "0"); + const hours = String(now.getHours()).padStart(2, "0"); + const minutes = String(now.getMinutes()).padStart(2, "0"); + const seconds = String(now.getSeconds()).padStart(2, "0"); + return `${year}-${month}-${day}-${hours}-${minutes}-${seconds}`; +}; + +const popover = ( + + + Download filtered entries + + +

+ This button allows to download all currently filtered entries shown in + the Materials Grid. The data is downloaded in JSON format, as an array. + The array contains a JSON object for each material entry, with key-value + pairs corresponding to the column properties. Additionally, each entry + includes a link to the corresponding detail page. +

+ + +); + +export const DownloadButton = ({ materialSelectorRef, disabled }) => { + /* + Note: the plan is to potentially also include direct download links (via the AiiDA rest api) + to each of the materials in the downloaded file, but currently the index page doesn't have + the structure UUIDs. Including them in the default index download is not great, as they would + increase the initial download size considerably, while not really needed for the table. + + Therefore, it probably might make sense to implement an additional endpoint, e.g. pbe-v1/uuids + that is only called when this download button is clicked. + */ + + const handleDownload = () => { + if (materialSelectorRef.current) { + const data = materialSelectorRef.current.getFilteredRows(); + // href currently just contains the url subpath to the details page + // replace it with a better name and full url + let modData = data.map((entry) => { + let modEntry = { + ...entry, + details_link: `${window.location.origin}${entry.href}`, + }; + delete modEntry.href; + return modEntry; + }); + const json = JSON.stringify(modData, null, 2); + const blob = new Blob([json], { type: "application/json" }); + const filename = `mc2d_filtered_entries_${getCurrentDateString()}.json`; + saveAs(blob, filename); + } + }; + + return ( +
+ + +
+ ); +}; diff --git a/src/MainPage/index.css b/src/MainPage/index.css index 46e205b..ac7d19f 100644 --- a/src/MainPage/index.css +++ b/src/MainPage/index.css @@ -1,22 +1,7 @@ -.main-page { - width: 950px; - /* background-color: rgb(243, 243, 243); */ - /* text-align: left; */ - /* display: flex; - flex-direction: column; - align-items: center; - justify-content: center; */ - margin: 0 auto; -} - .description { padding: 20px 40px; } -.main-tabs { - width: 950px; -} - /* overload boostrap tab style */ .nav-tabs .nav-link { border-top: 1px solid #ddd !important; diff --git a/src/MainPage/index.jsx b/src/MainPage/index.jsx index 4ac4888..741427d 100644 --- a/src/MainPage/index.jsx +++ b/src/MainPage/index.jsx @@ -1,4 +1,4 @@ -import React, { useEffect, useState } from "react"; +import React, { useEffect, useState, useRef } from "react"; import "./index.css"; @@ -8,14 +8,15 @@ import MaterialSelector from "mc-react-ptable-materials-grid"; import TitleAndLogo from "../common/TitleAndLogo"; -import Tab from "react-bootstrap/Tab"; -import Tabs from "react-bootstrap/Tabs"; +import { Container, Tab, Tabs, Form } from "react-bootstrap"; import { aboutText } from "./about"; import { restapiText } from "./restapiText"; import { loadIndexMc2d } from "./loadIndexMc2d"; +import { DownloadButton } from "./DownloadButton.jsx"; + function MainPage() { const [columns, setColumns] = useState([]); const [rows, setRows] = useState([]); @@ -27,6 +28,8 @@ function MainPage() { }); }, []); + const materialSelectorRef = useRef(null); + return ( -
-
- -
- Results from screening most known 3D crystal structures finding - those that can be computationally exfoliated producing 2D materials - candidates. -
- - -
+ + +
+ Materials Cloud 2D crystals database is a curated set of 2D materials + obtained by screening most known 3D crystal structures by a + computational exfoliation procedure. This database contains the + relaxed 2D materials and their various properties. +
+ + + {/*
Search for materials by filtering based on the periodic table and the columns of the table below: -
- - - - {aboutText} - - - {restapiText} - - -
-
+
*/} +
+ + + + + {aboutText} + + + {restapiText} + + + ); } diff --git a/src/MainPage/loadIndexMc2d.js b/src/MainPage/loadIndexMc2d.js index 7495f95..f22c42f 100644 --- a/src/MainPage/loadIndexMc2d.js +++ b/src/MainPage/loadIndexMc2d.js @@ -1,193 +1,220 @@ -import { REST_API_COMPOUNDS } from "../common/config"; - -/* The MaterialsSelector needs two inputs: - 1) column definitions - 2) async function that loads data - - The data needs to be an array of row objects, whereas each row needs contain - * entries for all the columns, with the key matching the 'field' string of the column. - * 'elem_array', which is used in the periodic table filtering. - */ - -/* Define the columns - some columns are special: id, formula (see the implementation) - * colType: "text", "integer", "float" - defines formatting & filters - * hide: true if the column is hidden initially - any additional input is passed to ag-grid column definitions (e.g. width) - */ -function columns(info) { - return [ - { - field: "id", - headerName: "ID", - colType: "id", - infoText: "The unique MC2D identifier of each structure.", - width: 100, - }, - { - field: "formula", - headerName: "Formula", - colType: "formula", - infoText: "The full formula in Hill notation.", - }, - { - field: "prototype", - headerName: "Prototype", - colType: "text", - infoText: "Prototype structure.", - width: 140, - }, - { - field: "point_group", - headerName: "Point group", - colType: "text", - infoText: "The point group symmetry of the material.", - width: 100, - }, - { - field: "band_gap", - headerName: "Band gap", - colType: "float", - infoText: "Band gap of the 2D material.", - unit: "eV", - width: 110, - }, - { - field: "abundance", - headerName: "Abundance", - colType: "float", - infoText: - "Abundance on the Earth of the rarest of the elements present in the compound (mass fraction).", - width: 120, - }, - { - field: "mag_state", - headerName: "Magnetic state", - colType: "text", - infoText: "Magnetic state", - width: 110, - }, - { - field: "df2_c09", - headerName: "E(bind) DF2-C09", - colType: "float", - infoText: - "Binding energy of the bulk 3D, per 2D layer and per unit area, obtained with the vdw-DF2-C09 functional.", - unit: "meV/Ų", - width: 115, - }, - { - field: "rvv10", - headerName: "E(bind) rVV10", - colType: "float", - infoText: - "Binding energy of the bulk 3D, per 2D layer and per unit area, obtained with the vdw-rVV10 functional.", - unit: "meV/Ų", - width: 115, +import { loadIndex, loadMetadata } from "../common/restApiUtils"; + +import { countNumberOfAtoms, countNumberOfElements } from "../common/utils"; + +import { getSymmetryInfo } from "mc-react-library"; + +// Order the columns and define which ones to show by default +// refer to the label/field of the column +// columns not listed, will be not shown by default and placed at the bottom +const COLUMN_ORDER_AND_SETTINGS = [ + { field: "id", hide: false, width: 120 }, + { field: "formula", hide: false }, + { field: "num_elements", hide: false }, + { field: "num_atoms", hide: true }, + { field: "prototype", hide: false }, + { field: "space_group_number", hide: false }, + { field: "space_group_int", hide: true }, + { field: "band_gap", hide: false }, + { field: "abundance", hide: false }, + { field: "magnetic_state", hide: true }, + { field: "total_magnetization", hide: true, minWidth: 130 }, + { field: "absolute_magnetization", hide: true, minWidth: 130 }, + { field: "binding_energy_df2", hide: false, minWidth: 140 }, + { field: "binding_energy_rvv10", hide: false }, + { field: "parent_formula", hide: false }, + { field: "parent_space_group_number", hide: true }, + { field: "parent_source_db", hide: false }, + { field: "parent_source_db_id", hide: false }, +]; + +const FRONTEND_COLUMNS = [ + { + columnDef: { + field: "num_elements", + headerName: "Number of elements", + colType: "integer", }, - { - field: "parent_formula", - headerName: "3D parent formula", - colType: "formula", - infoText: - "Chemical formula for the 3D parent (lowest energy parent, if multiple exist).", - hide: true, + calcFunc: (entry) => countNumberOfElements(entry["formula"]), + }, + { + columnDef: { + field: "num_atoms", + headerName: "Num. of atoms/cell", + colType: "integer", }, - { - field: "parent_spg", - headerName: "3D parent space group", + calcFunc: (entry) => countNumberOfAtoms(entry["formula"]), + }, + // { + // columnDef: { + // field: "bravais_lat", + // headerName: "Bravais lattice", + // colType: "text", + // infoText: "Bravais lattice in Pearson notation.", + // }, + // calcFunc: (entry) => getSymmetryInfo(entry["sg"]).bravais_lattice_pearson, + // }, + { + columnDef: { + field: "space_group_int", + headerName: "Space group international", colType: "spg_symbol", - infoText: - "Space group for the 3D parent (lowest energy parent, if multiple exist).", - hide: true, - width: 120, - }, - { - field: "parent_source_db", - headerName: "3D parent source DB", - colType: "text", - infoText: - "Source database for the 3D parent (lowest energy parent, if multiple exist).", - hide: true, - width: 120, + infoText: "International short symbol for the space group.", }, + calcFunc: (entry) => getSymmetryInfo(entry["sg"]).space_group_symbol, + }, +]; + +function formatColumns(metadata) { + /* + The column definitions of the MaterialsSelector need to follow the format of + + { + field: str, // Internal label for the column + headerName: str, // Column title displayed in header + unit: str, // unit displayed in header + colType: str, // type that determines formatting & filtering, see below + infoText: str, // info text in the header menu + hide: bool, // whether to hide the column by default + }, + + Possible colTypes: + * "id" - always on the left; and href to the detail page; + * "formula" - special formatting with subscripts + * "spg_symbol" - special formatting + * "text" + * "integer" + * "float" + * ... + */ + let columns = [ { - field: "parent_source_id", - headerName: "3D parent source ID", - colType: "text", - infoText: - "Source database ID for the 3D parent (lowest energy parent, if multiple exist).", - hide: true, - width: 120, + field: "id", + headerName: "ID", + colType: "id", + infoText: "The unique MC3D identifier of each structure.", }, ]; -} -function calcElementArray(formula) { - var formula_no_numbers = formula.replace(/[0-9]/g, ""); - var elements = formula_no_numbers.split(/(?=[A-Z])/); - return elements; -} + // convert the columns from metadata + metadata["index-columns"].forEach((col) => { + columns.push({ + field: col.label, + headerName: col.name, + unit: col.unit || null, + colType: col.type || "text", + infoText: col.description || null, + }); + }); + + // Add frontend columns + FRONTEND_COLUMNS.forEach((frontCol) => { + columns.push(frontCol.columnDef); + }); + + console.log(columns); -function countNumberOfAtoms(formula) { - // split on capital letters to get element+number strings - var elnum = formula.split(/(?=[A-Z])/); - var num = 0; - elnum.forEach((v) => { - let match = v.match(/\d+/); - let n = match == null ? 1 : parseInt(match[0]); - num += n; + // order and hide columns + let orderedColumns = []; + COLUMN_ORDER_AND_SETTINGS.forEach((set) => { + let colIndex = columns.findIndex((col) => col.field === set.field); + if (colIndex !== -1) { + let col = columns[colIndex]; + col.hide = set.hide; + ["width", "minWidth"].forEach((prop) => { + if (prop in set) { + col[prop] = set[prop]; + } + }); + orderedColumns.push(col); + // Remove the column from the array + columns.splice(colIndex, 1); + } }); - return num; + columns.forEach((col) => { + col.hide = true; + orderedColumns.push(col); + }); + + return orderedColumns; } -function formatRows(entries) { +function formatRows(indexData, metadata) { + /* + The row data for the MaterialsSelector needs to contain + * key-value for each column definition (key = "field" of the column); + * 'href' - this link is added to the id column; + + The raw index data from the API needs: + * href + * mapping the short data_label to label/field of columns + * calculating the frontend columns + */ let rows = []; + let labelMap = {}; + metadata["index-columns"].forEach((col) => { + labelMap[col.data_label] = col.label; + }); + // for testing a small subset: - // entries = { - // 1: entries["1"], - // 2: entries["2"], - // }; - - Object.keys(entries).forEach((i) => { - let comp = entries[i]; - let elemArr = calcElementArray(comp["formula"]); - let mc2d_id = `mc2d-${i}`; - - let row = { - id: mc2d_id, - formula: comp["formula"], - prototype: comp["prototype"], - point_group: comp["point_group"], - band_gap: comp["band_gap"], - abundance: comp["abundance"], - mag_state: comp["mag_state"], - df2_c09: comp["df2_c09"] !== null ? comp["df2_c09"] * 1000 : null, // convert to meV/Å^2 - rvv10: comp["rvv10"] !== null ? comp["rvv10"] * 1000 : null, // convert to meV/Å^2 - parent_formula: comp["parent"]["formula"], - parent_spg: comp["parent"]["spg"], - parent_source_db: comp["parent"]["source_db"], - parent_source_id: comp["parent"]["source_id"], - n_elem: elemArr.length, - elem_array: elemArr, - n_atoms: countNumberOfAtoms(comp["formula"]), - href: `${import.meta.env.BASE_URL}/#/details/${comp["formula"]}/${mc2d_id}`, + // indexData = indexData.slice(0, 10); + + indexData.forEach((entry) => { + // console.log(entry); + let href = `${import.meta.env.BASE_URL}#/details/${entry["id"]}`; + + let row = {}; + Object.entries(entry).map(([key, value]) => { + if (key in labelMap) { + row[labelMap[key]] = value; + } + }); + + let modifiedKeys = { + id: entry["id"], + href: href, }; + + FRONTEND_COLUMNS.forEach((frontCol) => { + modifiedKeys[frontCol.columnDef.field] = frontCol.calcFunc(entry); + }); + + row = { ...row, ...modifiedKeys }; + rows.push(row); }); return rows; } export async function loadIndexMc2d() { - const index_response = await fetch(REST_API_COMPOUNDS, { method: "get" }); - const index_json = await index_response.json(); - const index_compounds = index_json["data"]["compounds"]; - const index_observables = index_json["data"]["observables"]; + let start = performance.now(); + let indexData = await loadIndex(); + let end = performance.now(); + console.log(`loadIndex: ${end - start} ms`); + + start = performance.now(); + let metadata = await loadMetadata(); + end = performance.now(); + console.log(`loadMetadata: ${end - start} ms`); + + console.log(indexData); + // console.log(metadata); + + start = performance.now(); + let rows = formatRows(indexData, metadata); + end = performance.now(); + console.log(`formatRows: ${end - start} ms`); + + let columns = formatColumns(metadata); + + console.log("Rows", rows); + console.log("Rows keys", Object.keys(rows[0])); + console.log("Columns", columns); // return a Promise of the correctly formatted data return { - columns: columns(index_observables), - rows: formatRows(index_compounds), + columns: columns, + rows: rows, }; } diff --git a/src/MainPage/restapiText.jsx b/src/MainPage/restapiText.jsx index c97d9cf..37e4f8e 100644 --- a/src/MainPage/restapiText.jsx +++ b/src/MainPage/restapiText.jsx @@ -1,7 +1,10 @@ -import { REST_API_COMPOUNDS, REST_API_AIIDA } from "../common/config"; +import { MC_REST_API_URL, AIIDA_REST_API_URL } from "../common/restApiUtils"; import "./restapiText.css"; +const INDEX_URL = `${MC_REST_API_URL}/entries`; +const SINGLE_ENTRY_URL = `${MC_REST_API_URL}/entries/mc2d-1`; + export const restapiText = (

@@ -14,20 +17,20 @@ export const restapiText = (

diff --git a/src/common/TitleAndLogo.css b/src/common/TitleAndLogo.css index 0346fee..0f298b3 100644 --- a/src/common/TitleAndLogo.css +++ b/src/common/TitleAndLogo.css @@ -1,11 +1,12 @@ .title-and-logo { - width: 950px; + /* width: 950px; */ /* text-align: left; */ /* font-size: 24px; */ border-bottom: 1px solid grey; display: flex; align-items: center; justify-content: space-between; + overflow: hidden; } .title-and-doi { diff --git a/src/common/config.js b/src/common/config.js deleted file mode 100644 index c61e280..0000000 --- a/src/common/config.js +++ /dev/null @@ -1,13 +0,0 @@ -// ------------------------------------------------------------------------------------------------ -// REST API ENDPOINTS -// In principle, these URLs should be read from -// https://www.materialscloud.org/mcloud/api/v2/discover/mc2d/info -// or -// https://dev-www.materialscloud.org/mcloud/api/v2/discover/mc2d/info -// but both always point to the production API, so you can't switch between develop and production - -export const REST_API_COMPOUNDS = - "https://dev-www.materialscloud.org/mcloud/api/v2/discover/mc2d/compounds"; -export const REST_API_AIIDA = "https://aiida.materialscloud.org/mc2d/api/v4"; - -export const EXPLORE_URL = "https://www.materialscloud.org/explore/mc2d"; diff --git a/src/common/restApiUtils.js b/src/common/restApiUtils.js new file mode 100644 index 0000000..bda539c --- /dev/null +++ b/src/common/restApiUtils.js @@ -0,0 +1,95 @@ +// ------------------------------------------------------------------------------------------------ +// REST API UTILITIES +// Define all functions for api calls here. + +export const MC_REST_API_URL = + "https://dev-aiida.materialscloud.org/mc-rest-api/mc2d/pbe-v1"; +export const AIIDA_REST_API_URL = + "https://dev-aiida.materialscloud.org/mc2d-new/api/v4"; +export const EXPLORE_URL = "https://dev-www.materialscloud.org/explore/mc2d"; + +// delay function for testing loading animations: +const delay = (ms) => new Promise((resolve) => setTimeout(resolve, ms)); + +export async function loadIndex() { + // await delay(2000); + let endpoint = `${MC_REST_API_URL}/entries`; + try { + const response = await fetch(endpoint, { method: "get" }); + const json = await response.json(); + return json; + } catch (error) { + console.error("Error fetching index:", error); + } +} + +export async function loadMetadata() { + let endpoint = `${MC_REST_API_URL}/meta`; + try { + const response = await fetch(endpoint, { method: "get" }); + const json = await response.json(); + return json; + } catch (error) { + console.error("Error fetching metadata:", error); + } +} + +export async function loadDetails(id) { + let endpoint = `${MC_REST_API_URL}/entries/${id}`; + try { + const response = await fetch(endpoint, { method: "get" }); + const json = await response.json(); + return json; + } catch (error) { + console.error("Error fetching details:", error); + } +} + +export async function loadAiidaAttributes(uuid) { + let endpoint = `${AIIDA_REST_API_URL}/nodes/${uuid}/contents/attributes`; + try { + const response = await fetch(endpoint, { method: "get" }); + const json = await response.json(); + return json.data.attributes; + } catch (error) { + console.error("Error fetching AiiDA attributes:", error); + } +} + +export async function loadAiidaCif(uuid) { + let endpoint = `${AIIDA_REST_API_URL}/nodes/${uuid}/download?download_format=cif&download=false`; + try { + const response = await fetch(endpoint, { method: "get" }); + const json = await response.json(); + return json.data.download.data; + } catch (error) { + console.error("Error fetching AiiDA cif:", error); + } +} + +export async function loadAiidaBands(uuid) { + await delay(2000); + let endpoint = `${AIIDA_REST_API_URL}/nodes/${uuid}/download?download_format=json`; + try { + const response = await fetch(endpoint, { method: "get" }); + const json = await response.json(); + return json; + } catch (error) { + console.error("Error fetching AiiDA bands:", error); + } +} + +export async function loadPhononVis(id) { + let endpoint = `${MC_REST_API_URL}/phonon-vis/${id}`; + try { + const response = await fetch(endpoint, { method: "get" }); + if (!response.ok) { + return null; + } + const json = await response.json(); + return json; + } catch (error) { + console.error("Error fetching phonon-vis:", error); + return null; + } +} diff --git a/src/common/utils.jsx b/src/common/utils.jsx index b4fabed..7789bb5 100644 --- a/src/common/utils.jsx +++ b/src/common/utils.jsx @@ -1,39 +1,17 @@ -import { REST_API_AIIDA } from "./config"; - -import { formatChemicalFormula } from "mc-react-library"; - -export function formatTitle(params) { - return ( - - {formatChemicalFormula(params["compound"])} ({params["id"]}) - - ); -} - -/** - * Fetches all AiiDA attributes for the node. - * - * @param {string} uuid The uuid of the AiiDA node - * @returns The AiiDA attributes available through the restAPI - */ -export async function fetchAiidaAttributes(uuid) { - const responseAiiDA = await fetch( - `${REST_API_AIIDA}/nodes/${uuid}/contents/attributes`, - ); - const jsonAiiDA = await responseAiiDA.json(); - return jsonAiiDA.data.attributes; +export function countNumberOfAtoms(formula) { + // split on capital letters to get element+number strings + var elnum = formula.split(/(?=[A-Z])/); + var num = 0; + elnum.forEach((v) => { + let match = v.match(/\d+/); + let n = match == null ? 1 : parseInt(match[0]); + num += n; + }); + return num; } -/** - * For an AiiDA StructureData node, fetches the structure in CIF format - * - * @param {string} uuid The uuid of the AiiDA node - * @returns The structure in CIF format as a continuous string - */ -export async function fetchAiidaCifText(uuid) { - const responseAiiDACif = await fetch( - `${REST_API_AIIDA}/nodes/${uuid}/download?download_format=cif&download=false`, - ); - const jsonAiiDACif = await responseAiiDACif.json(); - return jsonAiiDACif.data.download.data; +export function countNumberOfElements(formula) { + // just count the number of capital letters + let matches = formula.match(/[A-Z]/g); + return matches ? matches.length : 0; } diff --git a/src/index.css b/src/index.css index f74bbe8..4c15f02 100644 --- a/src/index.css +++ b/src/index.css @@ -14,3 +14,23 @@ body { min-width: 320px; min-height: 100vh; } + +/* consistent browser-independent scrollbars to the whole site */ + +::-webkit-scrollbar { + width: 8px; + height: 8px; +} + +::-webkit-scrollbar-track { + background: #f1f1f1; +} + +::-webkit-scrollbar-thumb { + background: #b9b5b5; + border-radius: 5px; +} + +::-webkit-scrollbar-thumb:hover { + background: #919191; +} diff --git a/vite.config.js b/vite.config.js index 31ea115..aac5043 100644 --- a/vite.config.js +++ b/vite.config.js @@ -1,8 +1,13 @@ import { defineConfig } from "vite"; import react from "@vitejs/plugin-react"; -// https://vitejs.dev/config/ +// `base:` is the full subpath of the URL. +// Set it dynamically from an env variable, +// as different gh branches are deployed to different subpaths + export default defineConfig({ plugins: [react()], - base: "/discover-mc2d-react/", + base: process.env.BRANCH_SUBPATH + ? `/discover-mc2d-react/${process.env.BRANCH_SUBPATH}` + : "/", });