From fc2a9fe00067813299c579e284c7fe4fe2b7414c Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Thu, 2 Nov 2023 15:42:45 +0200 Subject: [PATCH 01/18] chore: add TS --- .eslintrc.json | 3 +- package-lock.json | 79 +++++++++++++++++++++++++++++++++-------------- package.json | 7 ++++- tsconfig.json | 32 +++++++++++++++++++ 4 files changed, 96 insertions(+), 25 deletions(-) create mode 100644 tsconfig.json diff --git a/.eslintrc.json b/.eslintrc.json index 325638ac..ab00fe06 100644 --- a/.eslintrc.json +++ b/.eslintrc.json @@ -1,3 +1,4 @@ { - "extends": ["@exabyte-io/eslint-config"] + "extends": ["@exabyte-io/eslint-config"], + "ignorePatterns": ["lib/"] } diff --git a/package-lock.json b/package-lock.json index 873f6a6a..040cdfa4 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1635,7 +1635,7 @@ "underscore": { "version": "1.8.3", "resolved": "https://registry.npmjs.org/underscore/-/underscore-1.8.3.tgz", - "integrity": "sha1-Tz+1OxBuYJf8+ctBCfKl6b36UCI=" + "integrity": "sha512-5WsVTFcH1ut/kkhAaHf4PVgI8c7++GiVcpCGxPouI6ZVjsqPnSDf8h/8HtVqc0t4fzRXwnMK70EcZeAs3PIddg==" } } }, @@ -1729,12 +1729,35 @@ "integrity": "sha512-s88O1aVtXftvp5bCPB7WnmXc5IwOZZ7YPuwNPt+GtOOXpPvad1LfbmjYv+qII7zP6RU2QGnqve27dnLycEnyEQ==", "optional": true }, + "@types/chai": { + "version": "4.3.9", + "resolved": "https://registry.npmjs.org/@types/chai/-/chai-4.3.9.tgz", + "integrity": "sha512-69TtiDzu0bcmKQv3yg1Zx409/Kd7r0b5F1PfpYJfSHzLGtB53547V4u+9iqKYsTu/O2ai6KTb0TInNpvuQ3qmg==" + }, "@types/json5": { "version": "0.0.29", "resolved": "https://registry.npmjs.org/@types/json5/-/json5-0.0.29.tgz", "integrity": "sha1-7ihweulOEdK4J7y+UnC86n8+ce4=", "dev": true }, + "@types/mocha": { + "version": "10.0.3", + "resolved": "https://registry.npmjs.org/@types/mocha/-/mocha-10.0.3.tgz", + "integrity": "sha512-RsOPImTriV/OE4A9qKjMtk2MnXiuLLbcO3nCXK+kvq4nr0iMfFgpjaX3MPLb6f7+EL1FGSelYvuJMV6REH+ZPQ==" + }, + "@types/node": { + "version": "20.8.10", + "resolved": "https://registry.npmjs.org/@types/node/-/node-20.8.10.tgz", + "integrity": "sha512-TlgT8JntpcbmKUFzjhsyhGfP2fsiz1Mv56im6enJ905xG1DAYesxJaeSbGqQmAw8OWPdhyJGhGSQGKRNJ45u9w==", + "requires": { + "undici-types": "~5.26.4" + } + }, + "@types/underscore": { + "version": "1.11.12", + "resolved": "https://registry.npmjs.org/@types/underscore/-/underscore-1.11.12.tgz", + "integrity": "sha512-beX81q12OQo809WJ/UYCvUDvJR3YQ4wtehYYQ6eNw5VLyd+KUNBRV4FgzZCHBmACbdPulH9F9ifhxzFFU9TWvQ==" + }, "@ungap/promise-all-settled": { "version": "1.1.2", "resolved": "https://registry.npmjs.org/@ungap/promise-all-settled/-/promise-all-settled-1.1.2.tgz", @@ -1778,12 +1801,12 @@ "almost-equal": { "version": "0.0.0", "resolved": "https://registry.npmjs.org/almost-equal/-/almost-equal-0.0.0.tgz", - "integrity": "sha1-56Wms0V7Z8g+4ARPmo0HY3NV8C0=" + "integrity": "sha512-/wvWNupeAr7sp7J2ZXvQvd97uyxsokx4TXdV6YMhd/EDwctlgY3wUGZCgQx1sJQyxU+c8EWRCWsLGOumdiS9aw==" }, "an-array": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/an-array/-/an-array-1.0.0.tgz", - "integrity": "sha1-wSWlu4JXd4419LT2qpx9D6nkJmU=" + "integrity": "sha512-M175GYI7RmsYu24Ok383yZQa3eveDfNnmhTe3OQ3bm70bEovz2gWenH+ST/n32M8lrwLWk74hcPds5CDRPe2wg==" }, "ansi-colors": { "version": "4.1.1", @@ -1876,7 +1899,7 @@ "array-almost-equal": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/array-almost-equal/-/array-almost-equal-1.0.0.tgz", - "integrity": "sha1-Q8VP9DUELpy/pCEqxJraX8c1n8U=", + "integrity": "sha512-NiQJq0vH5nEebm7FMs52fli23nwCh+RBKZZtA5g5qUmqGAkb9n8/WOTW8zjDocLADXXM1CRanFfPTMdrI2yZwg==", "requires": { "almost-equal": "0.0.0", "an-array": "^1.0.0" @@ -2287,7 +2310,7 @@ "color-name": { "version": "1.1.3", "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.3.tgz", - "integrity": "sha1-p9BVi9icQveV3UIyj3QIMcpTvCU=" + "integrity": "sha512-72fSenhMw2HZMTVHeCA9KCmpEIbzWiQsjN+BHcBbS9vr1mtt+vJjPdksIBNUmKAW8TFUDPJK5SUU3QhE9NEXDw==" }, "colorette": { "version": "2.0.16", @@ -2309,7 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"sha512-vbRorB5FUQWvla16U8R/qgaFIya2qGzwDrNmCZuYKrbdSUMG6I1ZCGQRefkRVhuOkIGVne7BQ35DSfo1qvJqFg==" }, "eslint": { "version": "7.32.0", @@ -3207,7 +3230,7 @@ "fs.realpath": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/fs.realpath/-/fs.realpath-1.0.0.tgz", - "integrity": "sha1-FQStJSMVjKpA20onh8sBQRmU6k8=" + "integrity": "sha512-OO0pH2lK6a0hZnAdau5ItzHPI6pUlvI7jMVnxUQRtw4owF2wk8lOSabtGDCTP4Ggrg2MbGnWO9X8K1t4+fGMDw==" }, "fsevents": { "version": "2.3.2", @@ -3330,7 +3353,7 @@ "has-flag": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-3.0.0.tgz", - "integrity": "sha1-tdRU3CGZriJWmfNGfloH87lVuv0=" + "integrity": "sha512-sKJf1+ceQBr4SMkvQnBDNDtf4TXpVhVGateu0t918bl30FnbE2m4vNLX+VWe/dpjlb+HugGYzW7uQXH98HPEYw==" }, "has-symbols": { "version": "1.0.2", @@ -3419,7 +3442,7 @@ "inflight": { "version": "1.0.6", "resolved": "https://registry.npmjs.org/inflight/-/inflight-1.0.6.tgz", - "integrity": "sha1-Sb1jMdfQLQwJvJEKEHW6gWW1bfk=", + "integrity": "sha512-k92I/b08q4wvFscXCLvqfsHCrjrF7yiXsQuIVvVE7N82W3+aqpzuUdBbfhWcy/FZR3/4IgflMgKLOsvPDrGCJA==", "requires": { "once": "^1.3.0", "wrappy": "1" @@ -3494,7 +3517,7 @@ "is-extglob": { "version": "2.1.1", "resolved": "https://registry.npmjs.org/is-extglob/-/is-extglob-2.1.1.tgz", - "integrity": "sha1-qIwCU1eR8C7TfHahueqXc8gz+MI=" + "integrity": "sha512-SbKbANkN603Vi4jEZv49LeVJMn4yGwsbzZworEoyEiutsN3nJYdbO36zfhGJ6QEDpOZIFkDtnq5JRxmvl3jsoQ==" }, "is-fullwidth-code-point": { "version": "3.0.0", @@ -3614,7 +3637,7 @@ "isobject": { "version": "3.0.1", "resolved": "https://registry.npmjs.org/isobject/-/isobject-3.0.1.tgz", - "integrity": "sha1-TkMekrEalzFjaqH5yNHMvP2reN8=" + "integrity": "sha512-WhB9zCku7EGTj/HQQRz5aUQEUeoQZH2bWcltRErOpymJ4boYE6wL9Tbr23krRPSZ+C5zqNSrSw+Cc7sZZ4b7vg==" }, "istanbul-lib-coverage": { "version": "3.2.0", @@ -3767,7 +3790,7 @@ "javascript-natural-sort": { "version": "0.7.1", "resolved": "https://registry.npmjs.org/javascript-natural-sort/-/javascript-natural-sort-0.7.1.tgz", - "integrity": "sha1-+eIwPUUH9tdDVac2ZNFED7Wg71k=" + "integrity": "sha512-nO6jcEfZWQXDhOiBtG2KvKyEptz7RVbpGP4vTD2hLBdmNQSsCiicO2Ioinv6UI4y9ukqnBpy+XZ9H6uLNgJTlw==" }, "js-tokens": { "version": "4.0.0", @@ -3986,7 +4009,7 @@ "lodash.debounce": { "version": "4.0.8", "resolved": "https://registry.npmjs.org/lodash.debounce/-/lodash.debounce-4.0.8.tgz", - "integrity": "sha1-gteb/zCmfEAF/9XiUVMArZyk168=" + "integrity": "sha512-FT1yDzDYEoYWhnSGnpE/4Kj1fLZkDFyqRb7fNt6FdYOSxlUWAtp42Eh6Wb0rGIv/m9Bgo7x4GhQbm5Ys4SG5ow==" }, "lodash.flattendeep": { "version": "4.4.0", @@ -4186,7 +4209,7 @@ "mixwith": { "version": "0.1.1", "resolved": "https://registry.npmjs.org/mixwith/-/mixwith-0.1.1.tgz", - "integrity": "sha1-yJlZGMW2H7/amtN3qFfNR3UFQcA=" + "integrity": "sha512-DQsf/liljH/9e+94jR+xfK8vlKceeKdOM9H9UEXLwGuvEEpO6debNtJ9yt1ZKzPKPrwqGxzMdu0BR1fnQb6i4A==" }, "mocha": { "version": "9.1.3", @@ -4671,7 +4694,7 @@ "once": { "version": "1.4.0", "resolved": "https://registry.npmjs.org/once/-/once-1.4.0.tgz", - "integrity": "sha1-WDsap3WWHUsROsF9nFC6753Xa9E=", + "integrity": "sha512-lNaJgI+2Q5URQBkccEKHTQOPaXdUxnZZElQTZY0MFUAuaEqe1E+Nyvgdz/aIyNi6Z9MzO5dv1H8n58/GELp3+w==", "requires": { "wrappy": "1" } @@ -4753,12 +4776,12 @@ "path-exists": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-3.0.0.tgz", - "integrity": "sha1-zg6+ql94yxiSXqfYENe1mwEP1RU=" + "integrity": "sha512-bpC7GYwiDYQ4wYLe+FA8lhRjhQCMcQGuSgGGqDkg/QerRWw9CmGRT0iSOVRSZJ29NMLZgIzqaljJ63oaL4NIJQ==" }, "path-is-absolute": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/path-is-absolute/-/path-is-absolute-1.0.1.tgz", - "integrity": "sha1-F0uSaHNVNP+8es5r9TpanhtcX18=" + "integrity": "sha512-AVbw3UJ2e9bq64vSaS9Am0fje1Pa8pbGqTTsmXfaIiMpnr5DlDhfJOuLj9Sf95ZPVDAUerDfEk88MPmPe7UCQg==" }, "path-key": { "version": "3.1.1", @@ -5047,7 +5070,7 @@ "seed-random": { "version": "2.2.0", "resolved": "https://registry.npmjs.org/seed-random/-/seed-random-2.2.0.tgz", - "integrity": "sha1-KpsZ4lCoFwmSMaW5mk2vgLf77VQ=" + "integrity": "sha512-34EQV6AAHQGhoc0tn/96a9Fsi6v2xdqe/dMUwljGRaFOzR3EgRmECvD0O8vi8X+/uQ50LGHfkNu/Eue5TPKZkQ==" }, "semver": { "version": "5.7.1", @@ -5382,7 +5405,7 @@ "to-fast-properties": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/to-fast-properties/-/to-fast-properties-2.0.0.tgz", - "integrity": "sha1-3F5pjL0HkmW8c+A3doGk5Og/YW4=" + "integrity": "sha512-/OaKK0xYrs3DmxRYqL/yDc+FxFUVYhDlXMhRmv3z915w2HF1tnN1omB354j8VUGO/hbRzyD6Y3sA7v7GS/ceog==" }, "to-regex-range": { "version": "5.0.1", @@ -5456,6 +5479,11 @@ "is-typedarray": "^1.0.0" } }, + "typescript": { + "version": "4.9.5", + "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.9.5.tgz", + "integrity": "sha512-1FXk9E2Hm+QzZQ7z+McJiHL4NW1F2EzMu9Nq9i3zAaGqibafqYwCVU6WyWAuyQRRzOlxou8xZSyXLEN8oKj24g==" + }, "unbox-primitive": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/unbox-primitive/-/unbox-primitive-1.0.1.tgz", @@ -5482,6 +5510,11 @@ "util-deprecate": "^1.0.2" } }, + "undici-types": { + "version": "5.26.5", + "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-5.26.5.tgz", + "integrity": "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA==" + }, "unicode-canonical-property-names-ecmascript": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/unicode-canonical-property-names-ecmascript/-/unicode-canonical-property-names-ecmascript-2.0.0.tgz", @@ -5518,7 +5551,7 @@ "util-deprecate": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz", - "integrity": "sha1-RQ1Nyfpw3nMnYvvS1KKJgUGaDM8=" + "integrity": "sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw==" }, "uuid": { "version": "3.4.0", @@ -5612,7 +5645,7 @@ "wrappy": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", - "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=" + "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==" }, "write-file-atomic": { "version": "3.0.3", diff --git a/package.json b/package.json index bca9adff..e41265c7 100644 --- a/package.json +++ b/package.json @@ -4,8 +4,8 @@ "description": "Materials Design in Javascript", "scripts": { "prepublishOnly": "rm -rf lib; npm run transpile", + "transpile": "tsc", "postinstall": "npm run transpile", - "transpile": "mkdir -p lib && babel src --out-dir lib", "test": "nyc --reporter=text mocha --recursive --bail --require @babel/register/lib --require tests/setup.js tests", "lint": "eslint src tests && prettier --write src tests", "lint:fix": "eslint --fix --cache src tests && prettier --write src tests", @@ -55,11 +55,16 @@ "@babel/preset-env": "^7.16.4", "@babel/register": "^7.16.0", "@exabyte-io/periodic-table.js": "2022.5.5-2", + "@types/chai": "^4.3.5", + "@types/mocha": "^10.0.1", + "@types/node": "^20.4.2", + "@types/underscore": "^1.11.6", "array-almost-equal": "^1.0.0", "crypto-js": "^3.1.9-1", "lodash": "^4.17.4", "mathjs": "^3.9.0", "mixwith": "^0.1.1", + "typescript": "^4.5.5", "underscore": "^1.8.3", "underscore.string": "^3.3.4" }, diff --git a/tsconfig.json b/tsconfig.json new file mode 100644 index 00000000..994732c4 --- /dev/null +++ b/tsconfig.json @@ -0,0 +1,32 @@ +{ + "compilerOptions": { + "target": "ES2018", + "jsx": "react", + "lib": ["ES2019", "dom"], + "allowJs": true, + "module": "commonjs", + "moduleResolution": "Node", + "declaration": true, + "outDir": "./lib", + "noEmitOnError": false, + "isolatedModules": true, + "esModuleInterop": true, + "forceConsistentCasingInFileNames": true, + "strict": true, + "skipLibCheck": true, + "types": ["mocha", "node"], + "rootDir": "./src", + "baseUrl": "./" + }, + "include": [ + "./src" + ], + "exclude": [ + "node_modules", + "lib" + ], + "ts-node": { + "files": true, + "compilerOptions": {} + }, +} From d0db0d91485f3e3f8cca72408270133be79b97ab Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Fri, 3 Nov 2023 18:17:06 +0200 Subject: [PATCH 02/18] chore: TS --- .mocharc.json | 5 + package-lock.json | 15430 ++++++++++++++-- package.json | 13 +- .../{array_with_ids.js => array_with_ids.ts} | 31 +- .../{scalar_with_id.js => scalar_with_id.ts} | 19 +- src/basis/{basis.js => basis.ts} | 23 +- .../{primitive_cell.js => primitive_cell.ts} | 55 +- src/lattice/{lattice.js => lattice.ts} | 63 +- ...{lattice_bravais.js => lattice_bravais.ts} | 120 +- ...{lattice_vectors.js => lattice_vectors.ts} | 62 +- src/lattice/{types.js => types.ts} | 67 +- src/lattice/unit_cell.js | 31 - src/lattice/unit_cell.ts | 66 + src/{material.js => material.ts} | 49 +- src/parsers/{xyz.js => xyz.ts} | 46 +- 15 files changed, 13849 insertions(+), 2231 deletions(-) create mode 100644 .mocharc.json rename src/abstract/{array_with_ids.js => array_with_ids.ts} (70%) rename src/abstract/{scalar_with_id.js => scalar_with_id.ts} (67%) rename src/basis/{basis.js => basis.ts} (97%) rename src/cell/{primitive_cell.js => primitive_cell.ts} (71%) rename src/lattice/{lattice.js => lattice.ts} (80%) rename src/lattice/{lattice_bravais.js => lattice_bravais.ts} (56%) rename src/lattice/{lattice_vectors.js => lattice_vectors.ts} (67%) rename src/lattice/{types.js => types.ts} (75%) delete mode 100644 src/lattice/unit_cell.js create mode 100644 src/lattice/unit_cell.ts rename src/{material.js => material.ts} (88%) rename src/parsers/{xyz.js => xyz.ts} (78%) diff --git a/.mocharc.json b/.mocharc.json new file mode 100644 index 00000000..a4d1f263 --- /dev/null +++ b/.mocharc.json @@ -0,0 +1,5 @@ +{ + "extension": ["ts", "js"], + "spec": "tests/**/*.*", + "require": ["ts-node/register", "tests/setup.js"] + } diff --git a/package-lock.json b/package-lock.json index 040cdfa4..a8e1fc81 100644 --- a/package-lock.json +++ b/package-lock.json 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"https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", diff --git a/package.json b/package.json index e41265c7..76de1183 100644 --- a/package.json +++ b/package.json @@ -6,7 +6,7 @@ "prepublishOnly": "rm -rf lib; npm run transpile", "transpile": "tsc", "postinstall": "npm run transpile", - "test": "nyc --reporter=text mocha --recursive --bail --require @babel/register/lib --require tests/setup.js tests", + "test": "mocha", "lint": "eslint src tests && prettier --write src tests", "lint:fix": "eslint --fix --cache src tests && prettier --write src tests", "prettier": "prettier --check src tests", @@ -27,8 +27,8 @@ "node": ">=0.12" }, "devDependencies": { - "@exabyte-io/code.js": "2022.6.15-1", - "@exabyte-io/eslint-config": "^2022.11.17-0", + "@exabyte-io/code.js": "^2023.11.1-0", + "@exabyte-io/eslint-config": "^2023.8.29-1", "chai": "^4.3.4", "chai-almost": "^1.0.1", "eslint": "^7.32.0", @@ -48,17 +48,12 @@ "prettier": "^2.5.1" }, "dependencies": { - "@babel/cli": "^7.16.0", - "@babel/core": "^7.16.0", - "@babel/eslint-parser": "^7.16.3", - "@babel/plugin-proposal-class-properties": "^7.16.0", - "@babel/preset-env": "^7.16.4", - "@babel/register": "^7.16.0", "@exabyte-io/periodic-table.js": "2022.5.5-2", "@types/chai": "^4.3.5", "@types/mocha": "^10.0.1", "@types/node": "^20.4.2", "@types/underscore": "^1.11.6", + "@types/underscore.string": "^0.0.40", "array-almost-equal": "^1.0.0", "crypto-js": "^3.1.9-1", "lodash": "^4.17.4", diff --git a/src/abstract/array_with_ids.js b/src/abstract/array_with_ids.ts similarity index 70% rename from src/abstract/array_with_ids.js rename to src/abstract/array_with_ids.ts index d038722b..165e6252 100644 --- a/src/abstract/array_with_ids.js +++ b/src/abstract/array_with_ids.ts @@ -2,15 +2,26 @@ import _ from "underscore"; import { ScalarWithId } from "./scalar_with_id"; +interface ObjectWithId { + id: number; + value?: object; +} + +type Predicate = (o: object) => boolean; + +type MapFunction = (value: object, index: number, array: object[]) => object; + /** * Helper class representing an ArrayWithIds. Used to explicitly track values assigned to atoms, for example. */ export class ArrayWithIds { + array: object[]; + /** * Create a an array with ids. * @param {Array} array - Either regular array or ArrayWithIds (see @example above) */ - constructor(array = []) { + constructor(array: ObjectWithId[] = []) { if (!_.isArray(array)) throw new Error("ArrayWithIds.constructor: pass array on initialization"); // if passed an array with ids as config, only store the values in array @@ -28,15 +39,15 @@ export class ArrayWithIds { /** * Apply function fn to each element of the array and replace `array` with the result. - * @param {Function} fn - The function to be applied to each array element. + * @param fn - The function to be applied to each array element. */ - mapArrayInPlace(fn) { + mapArrayInPlace(fn: MapFunction) { if (!_.isFunction(fn)) throw new Error("ArrayWithIds.mapArray: must pass function as argument"); this.array = this.array.map((...args) => fn(...args)); } - getArrayElementByIndex(idx) { + getArrayElementByIndex(idx: number) { return this.array[idx]; } @@ -44,24 +55,24 @@ export class ArrayWithIds { * Get the index of the array element that passes the predicate. * @param {Function} predicate - The function to be applied to each array element. */ - getArrayIndexByPredicate(predicate) { + getArrayIndexByPredicate(predicate: Predicate) { return this.array.findIndex((el) => predicate(el)); } /** * Add an entity to array. - * @param {Any} el - The entity to be added to array. If Object with 'value' key, its value will be added. + * @param el - The entity to be added to array. If Object with 'value' key, its value will be added. */ - addElement(el) { + addElement(el: ObjectWithId) { if (el) this.array.push(el.value || el); } /** * Remove an entity to array. Either by passing the entity, or the corresponding index. - * @param {Any} el - The entity to be added to array. If Object with 'value' key, its value will be added. - * @param {Any} idx - The entity to be added to array. If Object with 'value' key, its value will be added. + * @param el - The entity to be added to array. If Object with 'value' key, its value will be added. + * @param idx - The entity to be added to array. If Object with 'value' key, its value will be added. */ - removeElement(el, idx) { + removeElement(el: ObjectWithId, idx: number) { let _idx; if (idx === undefined) { _idx = this.array.findIndex((elm) => elm === el); diff --git a/src/abstract/scalar_with_id.js b/src/abstract/scalar_with_id.ts similarity index 67% rename from src/abstract/scalar_with_id.js rename to src/abstract/scalar_with_id.ts index 2241bf3c..6d655a31 100644 --- a/src/abstract/scalar_with_id.js +++ b/src/abstract/scalar_with_id.ts @@ -1,15 +1,24 @@ import _ from "underscore"; +interface ObjectWithId { + id: number; + value?: object; +} + /** * Helper class representing a scalar with an associated id. */ -export class ScalarWithId { +export class ScalarWithId implements ObjectWithId { + id: number; + + value?: object | ObjectWithId; + /** * Create a an array with ids. - * @param {Any} valueOrObject - a ScalarWithID, or any other type. - * @param {Number} id - numerical id (Integer). + * @param valueOrObject - a ScalarWithID, or any other type. + * @param id - numerical id (Integer). */ - constructor(valueOrObject, id = 0) { + constructor(valueOrObject: object | ObjectWithId, id = 0) { let _id, _value; // if already passing a ScalarWithId => preserve original if (_.isObject(valueOrObject) && !_.isArray(valueOrObject)) { @@ -28,7 +37,7 @@ export class ScalarWithId { * Serialize class instance to JSON. * @example {"id" : 0, "value" : "Si" } */ - toJSON() { + toJSON(): object { return { id: this.id, value: this.value, diff --git a/src/basis/basis.js b/src/basis/basis.ts similarity index 97% rename from src/basis/basis.js rename to src/basis/basis.ts index 3a8116af..7c4a99f9 100644 --- a/src/basis/basis.js +++ b/src/basis/basis.ts @@ -1,4 +1,5 @@ import { getElectronegativity, getElementAtomicRadius } from "@exabyte-io/periodic-table.js"; +import { Vector } from "src/lattice/types"; import _ from "underscore"; import s from "underscore.string"; @@ -7,10 +8,26 @@ import { ATOMIC_COORD_UNITS, HASH_TOLERANCE } from "../constants"; import { Lattice, nonPeriodicLatticeScalingFactor } from "../lattice/lattice"; import math from "../math"; +interface BasisProps { + elements: string[]; + coordinates: [number, number, number][]; + units: string; + cell: Vector[]; + isEmpty: boolean; +} + /** * A class representing a crystal basis. */ export class Basis { + _elements: ArrayWithIds; + + _coordinates: ArrayWithIds; + + units: string; + + cell: Vector[]; + /** * Create a Basis class. * @param {Object} - Config object. @@ -26,7 +43,7 @@ export class Basis { units, cell = Basis.defaultCell, // by default, assume a cubic unary cell isEmpty = false, // whether to generate an empty Basis - }) { + }: BasisProps) { let _elements, _coordinates, _units; if (!units) { _units = Basis.unitsOptionsDefaultValue; @@ -126,11 +143,11 @@ export class Basis { return new this.constructor({ ...this.toJSON(), ...extraContext }); } - getElementByIndex(idx) { + getElementByIndex(idx: number) { return this._elements.getArrayElementByIndex(idx); } - getCoordinateByIndex(idx) { + getCoordinateByIndex(idx: number) { return this._coordinates.getArrayElementByIndex(idx); } diff --git a/src/cell/primitive_cell.js b/src/cell/primitive_cell.ts similarity index 71% rename from src/cell/primitive_cell.js rename to src/cell/primitive_cell.ts index 15ddec38..6736a7d6 100644 --- a/src/cell/primitive_cell.js +++ b/src/cell/primitive_cell.ts @@ -1,5 +1,6 @@ /* eslint no-unused-vars: 0 */ -import { LATTICE_TYPE } from "../lattice/types"; +import { RequiredBravaisConfig } from "../lattice/lattice_bravais"; +import { LatticeType, VectorsAsArray } from "../lattice/types"; import math from "../math"; /** @@ -7,7 +8,7 @@ import math from "../math"; * Following Setyawan, W., & Curtarolo, S. (2010). doi:10.1016/j.commatsci.2010.05.010 */ const PRIMITIVE_CELLS = { - [LATTICE_TYPE.CUB]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.CUB]: ({ a }: RequiredBravaisConfig): VectorsAsArray => { return [ [a, 0, 0], [0, a, 0], @@ -15,7 +16,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.FCC]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.FCC]: ({ a }: RequiredBravaisConfig): VectorsAsArray => { return [ [0.0, a / 2, a / 2], [a / 2, 0.0, a / 2], @@ -23,7 +24,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.BCC]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.BCC]: ({ a }: RequiredBravaisConfig): VectorsAsArray => { return [ [-a / 2, a / 2, a / 2], [a / 2, -a / 2, a / 2], @@ -31,7 +32,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.TET]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.TET]: ({ a, c }: RequiredBravaisConfig): VectorsAsArray => { return [ [a, 0, 0], [0, a, 0], @@ -39,7 +40,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.BCT]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.BCT]: ({ a, c }: RequiredBravaisConfig): VectorsAsArray => { return [ [-a / 2, a / 2, c / 2], [a / 2, -a / 2, c / 2], @@ -47,7 +48,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.ORC]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.ORC]: ({ a, b, c }: RequiredBravaisConfig): VectorsAsArray => { return [ [a, 0, 0], [0, b, 0], @@ -55,7 +56,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.ORCF]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.ORCF]: ({ a, b, c }: RequiredBravaisConfig): VectorsAsArray => { return [ [0, b / 2, c / 2], [a / 2, 0, c / 2], @@ -63,7 +64,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.ORCI]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.ORCI]: ({ a, b, c }: RequiredBravaisConfig): VectorsAsArray => { return [ [-a / 2, b / 2, c / 2], [a / 2, -b / 2, c / 2], @@ -71,7 +72,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.ORCC]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.ORCC]: ({ a, b, c }: RequiredBravaisConfig): VectorsAsArray => { return [ [a / 2, b / 2, 0], [-a / 2, b / 2, 0], @@ -79,7 +80,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.HEX]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.HEX]: ({ a, c }: RequiredBravaisConfig): VectorsAsArray => { return [ [a / 2, (-a * math.sqrt(3)) / 2, 0], [a / 2, (a * math.sqrt(3)) / 2, 0], @@ -87,7 +88,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.RHL]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.RHL]: ({ a, alpha }: RequiredBravaisConfig): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); const cosHalfAlpha = math.sqrt((1 / 2) * (1 + cosAlpha)); const sinHalfAlpha = math.sqrt((1 / 2) * (1 - cosAlpha)); @@ -102,7 +103,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.MCL]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.MCL]: ({ a, b, c, alpha }: RequiredBravaisConfig): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); return [ [a, 0, 0], @@ -111,7 +112,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LATTICE_TYPE.MCLC]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.MCLC]: ({ a, b, c, alpha }: RequiredBravaisConfig): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); return [ [a / 2, b / 2, 0], @@ -121,7 +122,7 @@ const PRIMITIVE_CELLS = { }, // Algorithm from http://pymatgen.org/_modules/pymatgen/core/lattice.html (from_params) - [LATTICE_TYPE.TRI]: ({ a, b, c, alpha, beta, gamma }) => { + [LatticeType.TRI]: ({ a, b, c, alpha, beta, gamma }: RequiredBravaisConfig): VectorsAsArray => { // convert angles to Radians // eslint-disable-next-line no-param-reassign [alpha, beta, gamma] = [alpha, beta, gamma].map( @@ -129,7 +130,7 @@ const PRIMITIVE_CELLS = { ); const [cosAlpha, cosBeta, cosGamma] = [alpha, beta, gamma].map((x) => math.cos(x)); - const [sinAlpha, sinBeta, sinGamma] = [alpha, beta, gamma].map((x) => math.sin(x)); + const [sinAlpha, sinBeta] = [alpha, beta, gamma].map((x) => math.sin(x)); const gammaStar = math.acos((cosAlpha * cosBeta - cosGamma) / (sinAlpha * sinBeta)); const cosGammaStar = math.cos(gammaStar); const sinGammaStar = math.sin(gammaStar); @@ -142,7 +143,14 @@ const PRIMITIVE_CELLS = { }, // alternative implementation - [`${LATTICE_TYPE.TRI}alt`]: ({ a, b, c, alpha, beta, gamma }) => { + [`${LatticeType.TRI}alt`]: ({ + a, + b, + c, + alpha, + beta, + gamma, + }: RequiredBravaisConfig): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); const cosBeta = math.cos((beta / 180) * math.PI); const cosGamma = math.cos((gamma / 180) * math.PI); @@ -167,12 +175,15 @@ const PRIMITIVE_CELLS = { /** * Returns lattice vectors for a primitive cell for a lattice. - * @param {Lattice} lattice - Lattice instance. - * @param {Boolean[]} skipRounding - whether to skip rounding the lattice vectors. - * @return {Array[]} Cell.vectorsAsArray + * @param lattice - Lattice instance. + * @param skipRounding - whether to skip rounding the lattice vectors. + * @return Cell.vectorsAsArray */ -export function primitiveCell(lattice, skipRounding = false) { - const [vectorA, vectorB, vectorC] = PRIMITIVE_CELLS[lattice.type || LATTICE_TYPE.TRI](lattice); +export function primitiveCell( + lattice: RequiredBravaisConfig, + skipRounding = false, +): VectorsAsArray { + const [vectorA, vectorB, vectorC] = PRIMITIVE_CELLS[lattice.type || LatticeType.TRI](lattice); // set precision and remove JS floating point artifacts if (!skipRounding) { [vectorA, vectorB, vectorC].map((vec) => diff --git a/src/lattice/lattice.js b/src/lattice/lattice.ts similarity index 80% rename from src/lattice/lattice.js rename to src/lattice/lattice.ts index 222449e8..d271e968 100644 --- a/src/lattice/lattice.js +++ b/src/lattice/lattice.ts @@ -5,10 +5,18 @@ import { Cell } from "../cell/cell"; import { primitiveCell } from "../cell/primitive_cell"; import { HASH_TOLERANCE } from "../constants"; import math from "../math"; -import { LatticeBravais } from "./lattice_bravais"; -import { LatticeVectors } from "./lattice_vectors"; +import { FromVectorsProps, LatticeBravais, RequiredBravaisConfig } from "./lattice_bravais"; +import { + BravaisConfigProps, + LatticeVectors, + RequiredLatticeVectorsConfig, +} from "./lattice_vectors"; import { LATTICE_TYPE, LATTICE_TYPE_CONFIGS, LATTICE_TYPE_EXTENDED } from "./types"; -import { UnitCell } from "./unit_cell"; +import { UnitCell, UnitCellProps } from "./unit_cell"; + +interface RequiredBravaisConfigWithVectors extends RequiredBravaisConfig { + vectors: RequiredLatticeVectorsConfig; +} /** * Scaling factor used to calculate the new lattice size for non-periodic systems. @@ -21,12 +29,14 @@ export const nonPeriodicLatticeScalingFactor = 2.0; * Follows Bravais convention for lattice types and contains lattice vectors within. * Units for lattice vector coordinates are "angstroms", and "degrees" for the corresponding angles. */ -export class Lattice extends LatticeBravais { +export class Lattice extends LatticeBravais implements RequiredBravaisConfigWithVectors { + vectors: LatticeVectors; + /** * Create a Lattice class from a config object. * @param {Object} config - Config object. See LatticeVectors.fromBravais. */ - constructor(config = {}) { + constructor(config: BravaisConfigProps = {}) { super(config); this.vectors = LatticeVectors.fromBravais(config); } @@ -35,7 +45,7 @@ export class Lattice extends LatticeBravais { * Create a Lattice class from a list of vectors. * @param {Object} config - Config object. See LatticeBravais.fromVectors. */ - static fromVectors(config) { + static fromVectors(config: FromVectorsProps) { return new Lattice(LatticeBravais.fromVectors(config).toJSON()); } @@ -75,8 +85,8 @@ export class Lattice extends LatticeBravais { } } */ - toJSON(skipRounding = false) { - const round = skipRounding ? () => {} : Lattice._roundValue; // round values by default + toJSON(skipRounding = false): RequiredBravaisConfigWithVectors { + const round = skipRounding ? (x: number) => x : Lattice._roundValue; // round values by default return { a: round(this.a), b: round(this.b), @@ -93,13 +103,12 @@ export class Lattice extends LatticeBravais { }; } - clone(extraContext) { - return new this.constructor({ ...this.toJSON(), ...extraContext }); + clone(extraContext: BravaisConfigProps) { + return new (this.constructor as typeof Lattice)({ ...this.toJSON(), ...extraContext }); } /** * Get lattice vectors as a nested array - * @return {Array[]} */ get vectorArrays() { return this.vectors.vectorArrays; @@ -111,9 +120,8 @@ export class Lattice extends LatticeBravais { /** * Get a short label for the type of the lattice, eg. "MCLC". - * @return {String} */ - get typeLabel() { + get typeLabel(): string { return lodash.get( LATTICE_TYPE_CONFIGS.find((c) => c.code === this.type), "label", @@ -123,9 +131,8 @@ export class Lattice extends LatticeBravais { /** * Get a short label for the extended type of the lattice, eg. "MCLC-5". - * @return {String} */ - get typeExtended() { + get typeExtended(): string { const { a, b, c, alpha, beta, gamma, type } = this; const cosAlpha = math.cos((alpha / 180) * math.PI); @@ -162,9 +169,8 @@ export class Lattice extends LatticeBravais { /** * Calculate the volume of the lattice cell. - * @return {Number} */ - get volume() { + get volume(): number { return math.abs(math.det(this.vectorArrays)); } @@ -172,7 +178,7 @@ export class Lattice extends LatticeBravais { * Returns a "default" primitive lattice by type, with lattice parameters scaled by the length of "a", * @param latticeConfig {Object} LatticeBravais config (see constructor) */ - static getDefaultPrimitiveLatticeConfigByType(latticeConfig) { + static getDefaultPrimitiveLatticeConfigByType(latticeConfig: RequiredBravaisConfig) { const f_ = Lattice._roundValue; // construct new primitive cell using lattice parameters and skip rounding the vectors const pCell = primitiveCell(latticeConfig, true); @@ -193,25 +199,22 @@ export class Lattice extends LatticeBravais { // TODO: remove get unitCell() { - const vectors = _.flatten(this.vectorArrays); - vectors.push(this.units.length); - return new UnitCell(...vectors); + const vectors = [..._.flatten(this.vectorArrays), this.units.length] as UnitCellProps; + return new UnitCell(vectors); } /** * Returns a string further used for the calculation of an unique hash. - * @param {Boolean} isScaled - Whether to scale the vectors by the length of the first vector initially. - * @return {string} + * @param isScaled - Whether to scale the vectors by the length of the first vector initially. */ - getHashString(isScaled = false) { + getHashString(isScaled = false): string { // lattice vectors must be measured in angstroms - const latticeInAngstroms = this; - const scaleK = isScaled ? latticeInAngstroms.a : 1; + const scaleK = isScaled ? this.a : 1; const scaledLattice = { - ...latticeInAngstroms, - a: latticeInAngstroms.a / scaleK, - b: latticeInAngstroms.b / scaleK, - c: latticeInAngstroms.c / scaleK, + ...this, + a: this.a / scaleK, + b: this.b / scaleK, + c: this.c / scaleK, }; // form lattice string return `${[ diff --git a/src/lattice/lattice_bravais.js b/src/lattice/lattice_bravais.ts similarity index 56% rename from src/lattice/lattice_bravais.js rename to src/lattice/lattice_bravais.ts index 37ebf80a..09dd92a1 100644 --- a/src/lattice/lattice_bravais.js +++ b/src/lattice/lattice_bravais.ts @@ -1,26 +1,62 @@ import constants from "../constants"; import math from "../math"; -import { LATTICE_TYPE_CONFIGS } from "./types"; +import { LATTICE_TYPE_CONFIGS, LatticeType, Vector, VectorsAsArray } from "./types"; + +export interface BravaisConfig { + a?: number; // lattice constant a. + b?: number; // lattice constant b. + c?: number; // lattice constant c. + alpha?: number; // lattice angle alpha. + beta?: number; // lattice angle beta. + gamma?: number; // lattice angle gamma. + units?: { + // units container + length: string; // units for length (eg. "angstrom", "crystal") + angle: string; // units for angles (eg. "degree", "radian") + }; + type?: LatticeType; +} + +export type RequiredBravaisConfig = Required; + +export interface FromVectorsProps { + a: Vector; // vector of the lattice. + b: Vector; // vector of the lattice. + c: Vector; // vector of the lattice. + alat?: number; // scaling factor for the vector coordinates, defaults to 1. + units?: string; // units for the coordinates (eg. angstrom, crystal). + type?: LatticeType; // type of the lattice to be created, defaults to TRI when not provided. + skipRounding?: boolean; // whether to skip rounding the resulting lattice values, defaults to `false`. +} /* * @summary: class that holds parameters of a Bravais Lattice: a, b, c, alpha, beta, gamma + corresponding units. * When stored as class variables units for lengths are always "angstrom"s, angle - "degree"s */ -export class LatticeBravais { +export class LatticeBravais implements RequiredBravaisConfig { + a: number; + + b: number; + + c: number; + + alpha: number; + + beta: number; + + gamma: number; + + units: { + length: string; + angle: string; + }; + + type: LatticeType; + /** * Create a Bravais lattice. - * @param {Object} config - Config object. - * @param {Number} config.a - lattice constant a. - * @param {Number} config.b - lattice constant b. - * @param {Number} config.c - lattice constant c. - * @param {Number} config.alpha - lattice angle alpha. - * @param {Number} config.beta - lattice angle beta. - * @param {Number} config.gamma - lattice angle gamma. - * @param {Object} config.units - units container. - * @param {String} config.units.length - units for length (eg. "angstrom", "crystal"). - * @param {String} config.units.angle - units for angles (eg. "degree", "radian"). */ - constructor(config) { + constructor(config: BravaisConfig) { const { a = 1, // default lattice is cubic with unity in edge sizes b = a, @@ -29,40 +65,32 @@ export class LatticeBravais { beta = alpha, gamma = alpha, // if we do not know what lattice type this is => set to TRI - type = "TRI", + type = LatticeType.TRI, units = { length: "angstrom", angle: "degree", }, } = config; + const k = constants.units.bohr === units.length ? constants.coefficients.BOHR_TO_ANGSTROM : 1; - Object.assign(this, { - a: a * k, - b: b * k, - c: c * k, - alpha, - beta, - gamma, - type, - units, - }); + + this.a = a * k; + this.b = b * k; + this.c = c * k; + this.alpha = alpha; + this.beta = beta; + this.gamma = gamma; + this.type = type; + this.units = units; } - static _roundValue(x) { + static _roundValue(x: number): number { return math.precise(math.roundToZero(x)); } /** * Create a Bravais lattice from vectors. - * @param {Object} - Config object. - * @param {Array} a - vector of the lattice. - * @param {Array} b - vector of the lattice. - * @param {Array} c - vector of the lattice. - * @param {Number} alat - scaling factor for the vector coordinates, defaults to 1. - * @param {String} units - units for the coordinates (eg. angstrom, crystal). - * @param {String} type - type of the lattice to be created, defaults to TRI when not provided. - * @param {Boolean} skipRounding - whether to skip rounding the resulting lattice values, defaults to `false`. */ static fromVectors({ a, @@ -70,11 +98,12 @@ export class LatticeBravais { c, alat = 1, units = "angstrom", - type = "TRI", + type = LatticeType.TRI, skipRounding = false, - }) { - const roundValue = skipRounding ? (x) => x : this._roundValue; - return new this.prototype.constructor({ + }: FromVectorsProps) { + const roundValue = skipRounding ? (x: number) => x : this._roundValue; + + return new (this.prototype.constructor as typeof LatticeBravais)({ a: roundValue(math.vlen(a) * alat), b: roundValue(math.vlen(b) * alat), c: roundValue(math.vlen(c) * alat), @@ -93,7 +122,7 @@ export class LatticeBravais { /** * See fromVectors above. */ - static fromVectorArrays(array, type, skipRounding = true) { + static fromVectorArrays(array: VectorsAsArray, type: LatticeType, skipRounding = true) { return this.fromVectors({ a: array[0], b: array[1], @@ -112,13 +141,16 @@ export class LatticeBravais { const object = {}; const editablesList = LATTICE_TYPE_CONFIGS.find( (entry) => entry.code === this.type, - ).editables; + )?.editables; // ["a", "gamma"] => {a: true, gamma: true} - editablesList.forEach((element) => { - Object.assign(object, { - [element]: true, + if (editablesList) { + editablesList.forEach((element) => { + Object.assign(object, { + [element]: true, + }); }); - }); + } + return object; } @@ -139,7 +171,7 @@ export class LatticeBravais { "type" : "FCC" } */ - toJSON() { + toJSON(): RequiredBravaisConfig { return { ...this, units: { diff --git a/src/lattice/lattice_vectors.js b/src/lattice/lattice_vectors.ts similarity index 67% rename from src/lattice/lattice_vectors.js rename to src/lattice/lattice_vectors.ts index 6ca86cfc..01f76d6d 100644 --- a/src/lattice/lattice_vectors.js +++ b/src/lattice/lattice_vectors.ts @@ -1,34 +1,53 @@ import { primitiveCell } from "../cell/primitive_cell"; import constants from "../constants"; import math from "../math"; +import { BravaisConfig } from "./lattice_bravais"; +import { LatticeType, Vector } from "./types"; + +interface LatticeVectorsConfig { + a: Vector; // vector of the lattice. + b: Vector; // vector of the lattice. + c: Vector; // vector of the lattice. + alat: number; // scaling factor for the vector coordinates, defaults to 1. + units?: string; // units container. +} + +export type RequiredLatticeVectorsConfig = Required; + +export interface BravaisConfigProps extends BravaisConfig { + isConventional?: boolean; +} /* * @summary: class that holds parameters of a Bravais Lattice: a, b, c, alpha, beta, gamma + corresponding units. * When stored as class variables units for lengths are always "angstrom"s, angle - "degree"s */ -export class LatticeVectors { +export class LatticeVectors implements LatticeVectorsConfig { + a: Vector; + + b: Vector; + + c: Vector; + + alat: number; + + units: string; + /** * Create a Bravais lattice. - * @param {Object} config - Config object. - * @param {Array} config.a - vector of the lattice. - * @param {Array} config.b - vector of the lattice. - * @param {Array} config.c - vector of the lattice. - * @param {Number} config.alat - scaling factor for the vector coordinates, defaults to 1. - * @param {String} config.units - units container. */ - constructor(config) { + constructor(config: LatticeVectorsConfig) { const { a, b, c, alat = 1, units = "angstrom" } = config; const k = constants.units.bohr === units ? constants.coefficients.BOHR_TO_ANGSTROM : 1; - Object.assign(this, { - a: a.map((x) => x * k), - b: b.map((x) => x * k), - c: c.map((x) => x * k), - alat, - units: "angstrom", - }); + + this.a = a.map((x) => x * k) as Vector; + this.b = b.map((x) => x * k) as Vector; + this.c = c.map((x) => x * k) as Vector; + this.alat = alat; + this.units = "angstrom"; } - static _roundValue(arr) { + static _roundValue(arr: number[]) { return arr.map((el) => math.precise(math.roundToZero(el))); } @@ -49,12 +68,12 @@ export class LatticeVectors { length: "angstrom", angle: "degree", }, - type, + type = LatticeType.TRI, isConventional = false, - }) { + }: BravaisConfigProps) { // use "direct" lattice constructor for primitive lattice // eslint-disable-next-line no-param-reassign - if (!isConventional) type = "TRI"; + if (!isConventional) type = LatticeType.TRI; // set precision and remove JS floating point artifacts const [vectorA, vectorB, vectorC] = primitiveCell({ @@ -68,12 +87,11 @@ export class LatticeVectors { type, }); - return new LatticeVectors.prototype.constructor({ + return new LatticeVectors({ a: vectorA, b: vectorB, c: vectorC, alat: 1, - unis: units.length, }); } @@ -104,7 +122,7 @@ export class LatticeVectors { "units" : "angstrom" } */ - toJSON() { + toJSON(): RequiredLatticeVectorsConfig { return { ...this, a: LatticeVectors._roundValue(this.a), diff --git a/src/lattice/types.js b/src/lattice/types.ts similarity index 75% rename from src/lattice/types.js rename to src/lattice/types.ts index bed192ee..078a6497 100644 --- a/src/lattice/types.js +++ b/src/lattice/types.ts @@ -15,6 +15,24 @@ export const DEFAULT_LATTICE_UNITS = { * Challenges and tools. Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010 * Lattice parameters a, b, c are stored for CONVENTIONAL lattice, however the default unit cell is calculated for */ + +export enum LatticeType { + CUB = "CUB", + FCC = "FCC", + BCC = "BCC", + TET = "TET", + BCT = "BCT", + ORC = "ORC", + ORCF = "ORCF", + ORCI = "ORCI", + ORCC = "ORCC", + HEX = "HEX", + RHL = "RHL", + MCL = "MCL", + MCLC = "MCLC", + TRI = "TRI", +} + export const LATTICE_TYPE = { CUB: "CUB", FCC: "FCC", @@ -59,10 +77,29 @@ export const LATTICE_TYPE_EXTENDED = { TRI_1b: "TRI_1b", }; -export const LATTICE_TYPE_CONFIGS = [ +export interface Vector extends Array { + 0: number; + 1: number; + 2: number; +} + +export interface VectorsAsArray extends Array { + 0: Vector; + 1: Vector; + 2: Vector; +} + +interface LatticeTypeConfig { + label: string; + code: LatticeType; + editables: string[]; + editablesConventional: string[]; +} + +export const LATTICE_TYPE_CONFIGS: LatticeTypeConfig[] = [ { label: "Simple Cubic", - code: LATTICE_TYPE.CUB, + code: LatticeType.CUB, // editables for primitive cell => WARNING: not tested editables: ["a"], // editables for conventional cell, taken from the publication above @@ -70,79 +107,79 @@ export const LATTICE_TYPE_CONFIGS = [ }, { label: "Face-centered Cubic", - code: LATTICE_TYPE.FCC, + code: LatticeType.FCC, editables: ["a"], editablesConventional: ["a"], }, { label: "Body-centered Cubic", - code: LATTICE_TYPE.BCC, + code: LatticeType.BCC, editables: ["a"], editablesConventional: ["a"], }, { label: "Tetragonal", - code: LATTICE_TYPE.TET, + code: LatticeType.TET, editables: ["a", "c"], editablesConventional: ["a", "c"], }, { label: "Body-centered Tetragonal", - code: LATTICE_TYPE.BCT, + code: LatticeType.BCT, editables: ["a"], editablesConventional: ["a", "c"], }, { label: "Orthorombic", - code: LATTICE_TYPE.ORC, + code: LatticeType.ORC, editables: ["a", "b", "c"], editablesConventional: ["a", "b", "c"], }, { label: "Orthorombic Face-centered", - code: LATTICE_TYPE.ORCF, + code: LatticeType.ORCF, editables: ["a", "b", "c"], editablesConventional: ["a", "b", "c"], }, { label: "Orthorombic Body-centered", - code: LATTICE_TYPE.ORCI, + code: LatticeType.ORCI, editables: ["a", "alpha", "gamma"], editablesConventional: ["a", "b", "c"], }, { label: "Orthorombic Base-centered", - code: LATTICE_TYPE.ORCC, + code: LatticeType.ORCC, editables: ["a", "c", "alpha"], editablesConventional: ["a", "b", "c"], }, { label: "Hexagonal", - code: LATTICE_TYPE.HEX, + code: LatticeType.HEX, editables: ["a", "c"], editablesConventional: ["a", "c"], }, { label: "Rhombohedral", - code: LATTICE_TYPE.RHL, + code: LatticeType.RHL, editables: ["a", "alpha"], editablesConventional: ["a", "alpha"], }, { label: "Monoclinic", - code: LATTICE_TYPE.MCL, + code: LatticeType.MCL, editables: ["a", "b", "c", "alpha"], editablesConventional: ["a", "b", "c", "alpha"], }, { label: "Monoclinic Base-centered", - code: LATTICE_TYPE.MCLC, + code: LatticeType.MCLC, editables: ["a", "c", "alpha", "gamma"], editablesConventional: ["a", "b", "c", "alpha"], }, { label: "Triclinic", - code: LATTICE_TYPE.TRI, + code: LatticeType.TRI, editables: ["a", "b", "c", "alpha", "beta", "gamma"], editablesConventional: ["a", "b", "c", "alpha", "beta", "gamma"], }, diff --git a/src/lattice/unit_cell.js b/src/lattice/unit_cell.js deleted file mode 100644 index a6528e49..00000000 --- a/src/lattice/unit_cell.js +++ /dev/null @@ -1,31 +0,0 @@ -// TODO: refactor and remove the need for UnitCell -export class UnitCell { - constructor(ax, ay, az, bx, by, bz, cx, cy, cz, units) { - this.ax = ax; - this.ay = ay; - this.az = az; - this.bx = bx; - this.by = by; - this.bz = bz; - this.cx = cx; - this.cy = cy; - this.cz = cz; - this.units = units; - } - - vectorA() { - return [this.ax, this.ay, this.az]; - } - - vectorB() { - return [this.bx, this.by, this.bz]; - } - - vectorC() { - return [this.cx, this.cy, this.cz]; - } - - axes() { - return [this.vectorA(), this.vectorB(), this.vectorC()]; - } -} diff --git a/src/lattice/unit_cell.ts b/src/lattice/unit_cell.ts new file mode 100644 index 00000000..cd8e4044 --- /dev/null +++ b/src/lattice/unit_cell.ts @@ -0,0 +1,66 @@ +import { Vector } from "./types"; + +export type UnitCellProps = [ + number, + number, + number, + number, + number, + number, + number, + number, + number, + string, +]; + +// TODO: refactor and remove the need for UnitCell +export class UnitCell { + ax: number; + + ay: number; + + az: number; + + bx: number; + + by: number; + + bz: number; + + cx: number; + + cy: number; + + cz: number; + + units: string; + + constructor([ax, ay, az, bx, by, bz, cx, cy, cz, units]: UnitCellProps) { + this.ax = ax; + this.ay = ay; + this.az = az; + this.bx = bx; + this.by = by; + this.bz = bz; + this.cx = cx; + this.cy = cy; + this.cz = cz; + this.units = units; + } + + vectorA(): Vector { + return [this.ax, this.ay, this.az]; + } + + vectorB(): Vector { + return [this.bx, this.by, this.bz]; + } + + vectorC(): Vector { + return [this.cx, this.cy, this.cz]; + } + + axes(): [Vector, Vector, Vector] { + return [this.vectorA(), this.vectorB(), this.vectorC()]; + } +} diff --git a/src/material.js b/src/material.ts similarity index 88% rename from src/material.js rename to src/material.ts index aa39ed4a..ebbf913d 100644 --- a/src/material.js +++ b/src/material.ts @@ -1,4 +1,5 @@ import { HasMetadataNamedDefaultableInMemoryEntity } from "@exabyte-io/code.js/dist/entity"; +import { AnyObject } from "@exabyte-io/code.js/dist/entity/in_memory"; import CryptoJS from "crypto-js"; import lodash from "lodash"; @@ -10,6 +11,7 @@ import { } from "./cell/conventional_cell"; import { ATOMIC_COORD_UNITS, units } from "./constants"; import { Lattice } from "./lattice/lattice"; +import { BravaisConfigProps } from "./lattice/lattice_vectors"; import { LATTICE_TYPE } from "./lattice/types"; import parsers from "./parsers/parsers"; import supercellTools from "./tools/supercell"; @@ -56,7 +58,7 @@ export const defaultMaterialConfig = { }; export class Material extends HasMetadataNamedDefaultableInMemoryEntity { - constructor(config) { + constructor(config: AnyObject) { super(config); this._json = lodash.cloneDeep(config || {}); } @@ -74,7 +76,7 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { }; } - get name() { + get name(): string { return super.name || this.formula; } @@ -96,14 +98,13 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { * False = periodic, True = non-periodic */ get isNonPeriodic() { - return this.prop("isNonPeriodic", false, true); + return this.prop("isNonPeriodic", false); } /** * @summary Sets the value of isNonPeriodic based on Boolean value passed as an argument. - * @param {Boolean} bool */ - set isNonPeriodic(bool) { + set isNonPeriodic(bool: boolean) { this.setProp("isNonPeriodic", bool); } @@ -112,7 +113,7 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { * @param {String} name * @returns {Object} */ - getDerivedPropertyByName(name) { + getDerivedPropertyByName(name: string) { return this.getDerivedProperties().find((x) => x.name === name); } @@ -136,12 +137,12 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { } /** - * @param textOrObject {String} Basis text or JSON object. - * @param format {String} Format (xyz, etc.) - * @param unitz {String} crystal/cartesian + * @param textOrObject Basis text or JSON object. + * @param format Format (xyz, etc.) + * @param unitz crystal/cartesian */ - setBasis(textOrObject, format, unitz) { - let basis; + setBasis(textOrObject: string | object, format: string, unitz: string) { + let basis: object | undefined; switch (format) { case "xyz": basis = parsers.xyz.toBasisConfig(textOrObject, unitz); @@ -161,7 +162,7 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { } get basis() { - return this.prop("basis", undefined, true); + return this.prop("basis", undefined); } // returns the instance of {ConstrainedBasis} class @@ -180,16 +181,15 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { return this.Basis.uniqueElements; } - get lattice() { - return this.prop("lattice", undefined, true); + get lattice(): BravaisConfigProps | undefined { + return this.prop("lattice", undefined); } - set lattice(config) { + set lattice(config: BravaisConfigProps | undefined) { this.setProp("lattice", config); } - // returns the instance of {Lattice} class - get Lattice() { + get Lattice(): Lattice { return new Lattice(this.lattice); } @@ -213,10 +213,10 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { * - asserts basis coordinates and lattice measurements are rounded to hash precision * - forms strings for lattice and basis * - creates MD5 hash from basisStr + latticeStr + salt - * @param salt {String} Salt for hashing, empty string by default. - * @param isScaled {Boolean} Whether to scale the lattice parameter 'a' to 1. + * @param salt Salt for hashing, empty string by default. + * @param isScaled Whether to scale the lattice parameter 'a' to 1. */ - calculateHash(salt = "", isScaled = false, bypassNonPeriodicCheck = false) { + calculateHash(salt = "", isScaled = false, bypassNonPeriodicCheck = false): string { let message; if (!this.isNonPeriodic || bypassNonPeriodicCheck) { message = @@ -227,18 +227,18 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { return CryptoJS.MD5(message).toString(); } - set hash(hash) { + set hash(hash: string) { this.setProp("hash", hash); } - get hash() { + get hash(): string { return this.prop("hash"); } /** * Calculates hash from basis and lattice as above + scales lattice properties to make lattice.a = 1 */ - get scaledHash() { + get scaledHash(): string { return this.calculateHash("", true); } @@ -263,9 +263,8 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { /** * Returns material's basis in XYZ format. - * @return {String} */ - getBasisAsXyz(fractional = false) { + getBasisAsXyz(fractional = false): string { return parsers.xyz.fromMaterial(this.toJSON(), fractional); } diff --git a/src/parsers/xyz.js b/src/parsers/xyz.ts similarity index 78% rename from src/parsers/xyz.js rename to src/parsers/xyz.ts index 07b8e1db..17532c09 100644 --- a/src/parsers/xyz.js +++ b/src/parsers/xyz.ts @@ -16,10 +16,8 @@ const XYZ_LINE_REGEX = /** * Validates XYZ file's line. Line should be in following format "Si 0.5 0.5 0.5". * Raises an error if line is in wrong format. - * @param xyzLine {String} - * @param index {Number} */ -function validateLine(xyzLine, index) { +function validateLine(xyzLine: string, index: number) { const words = xyzLine.split(" ").filter((x) => x.trim() !== ""); if (!xyzLine.match(XYZ_LINE_REGEX)) { @@ -36,51 +34,57 @@ function validateLine(xyzLine, index) { /** * Validates that passed string is well-formed XYZ file. - * @param xyzTxt {String} */ -export function validate(xyzTxt) { +export function validate(xyzTxt: string) { + // The @types/underscore.string package does not provide interfaces for function chaining at the moment. Disable TS here + // @ts-ignore s(xyzTxt) .trim() .lines() - .filter((x) => x.trim() !== "") + .filter((x: string) => x.trim() !== "") .forEach(validateLine); } +interface ParsedObject { + element: string; + coordinates: [number, number, number]; + constraints: [boolean, boolean, boolean]; +} + /** * Parses XYZ line and returns an object. - * @param {String} line - line of text - * @return {Object} + * @param line - line of text */ -function _parseXYZLineAsWords(line) { +function _parseXYZLineAsWords(line: string): ParsedObject { const words = s.words(line); + const constraint = (n: number) => parseInt(`${n}`, 10) !== 0; return { element: words[0], coordinates: [+words[1], +words[2], +words[3]], // Below maps zero values to false (atom is fixed) and non-zero values to true (atom is moving) - constraints: [+words[4], +words[5], +words[6]].map((e) => parseInt(e, 10) !== 0), + constraints: [constraint(+words[4]), constraint(+words[5]), constraint(+words[6])], }; } /** * Parse XYZ text for basis. - * @param txt {String} Text - * @param units {String} Coordinate units - * @param cell {Array} Basis Cell - * @return {Object} + * @param txt Text + * @param units Coordinate units + * @param cell Basis Cell */ -function toBasisConfig(txt, units = "angstrom", cell = Basis.defaultCell) { - const lines = s(txt).trim().lines(); +function toBasisConfig(txt: string, units = "angstrom", cell = Basis.defaultCell) { + // @ts-ignore + const lines: string[] = s(txt).trim().lines(); const listOfObjects = _.map(lines, _parseXYZLineAsWords); return { - // using concat below to avoid modifying listOfObjects in place with map - elements: [].concat(listOfObjects).map((elm, idx) => { + elements: listOfObjects.map((elm, idx) => { return { id: idx, value: elm.element, }; }), - coordinates: [].concat(listOfObjects).map((elm, idx) => { + coordinates: listOfObjects.map((elm, idx) => { return { id: idx, value: elm.coordinates, @@ -88,7 +92,7 @@ function toBasisConfig(txt, units = "angstrom", cell = Basis.defaultCell) { }), units, cell, - constraints: [].concat(listOfObjects).map((elm, idx) => { + constraints: listOfObjects.map((elm, idx) => { return { id: idx, value: elm.constraints, @@ -125,7 +129,7 @@ function fromBasis(basisClsInstance, printFormat = "%9.5f", skipRounding = false * Create XYZ from Material class instance (or its JSON config). * @param materialOrConfig {Material|Object} Material. * @param fractional {Boolean} Coordinate units as fractional. - * @return {ConstrainedBasis} Class Instance + * @return Class Instance */ function fromMaterial(materialOrConfig, fractional = false) { const lattice = new Lattice(materialOrConfig.lattice); From aaa4dab14a4b3ed9076ae333fb553ba2d5ef3f0f Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Tue, 7 Nov 2023 14:47:28 +0200 Subject: [PATCH 03/18] chore: TS for material --- package.json | 2 +- src/abstract/array_with_ids.ts | 56 +++-- src/abstract/scalar_with_id.ts | 40 ++-- src/basis/basis.ts | 213 ++++++++---------- ...strained_basis.js => constrained_basis.ts} | 40 ++-- src/cell/{cell.js => cell.ts} | 50 ++-- src/cell/conventional_cell.js | 96 -------- src/cell/conventional_cell.ts | 87 +++++++ src/cell/primitive_cell.ts | 1 + .../{constraints.js => constraints.ts} | 29 ++- src/lattice/lattice.ts | 8 +- src/lattice/lattice_bravais.ts | 3 + src/lattice/lattice_vectors.ts | 2 +- src/material.ts | 112 +++++---- src/parsers/{espresso.js => espresso.ts} | 6 +- src/parsers/{poscar.js => poscar.ts} | 54 ++--- src/parsers/xyz.ts | 50 ++-- src/tools/{supercell.js => supercell.ts} | 11 +- 18 files changed, 466 insertions(+), 394 deletions(-) rename src/basis/{constrained_basis.js => constrained_basis.ts} (65%) rename src/cell/{cell.js => cell.ts} (63%) delete mode 100644 src/cell/conventional_cell.js create mode 100644 src/cell/conventional_cell.ts rename src/constraints/{constraints.js => constraints.ts} (54%) rename src/parsers/{espresso.js => espresso.ts} (80%) rename src/parsers/{poscar.js => poscar.ts} (77%) rename src/tools/{supercell.js => supercell.ts} (85%) diff --git a/package.json b/package.json index 76de1183..9a21df1b 100644 --- a/package.json +++ b/package.json @@ -27,7 +27,7 @@ "node": ">=0.12" }, "devDependencies": { - "@exabyte-io/code.js": "^2023.11.1-0", + "@exabyte-io/code.js": "git+https://github.com/Exabyte-io/code.js.git#update/SOF-6922", "@exabyte-io/eslint-config": "^2023.8.29-1", "chai": "^4.3.4", "chai-almost": "^1.0.1", diff --git a/src/abstract/array_with_ids.ts b/src/abstract/array_with_ids.ts index 165e6252..b5865c16 100644 --- a/src/abstract/array_with_ids.ts +++ b/src/abstract/array_with_ids.ts @@ -1,50 +1,63 @@ import _ from "underscore"; -import { ScalarWithId } from "./scalar_with_id"; +import { + isObjectWithIdAndValue, + ObjectWithIdAndValue, + ScalarWithId, + ValueOrObject, +} from "./scalar_with_id"; -interface ObjectWithId { - id: number; - value?: object; -} +type Predicate = (o: T) => boolean; -type Predicate = (o: object) => boolean; +type MapFunction = (value: T, index: number, array: T[]) => T; -type MapFunction = (value: object, index: number, array: object[]) => object; +export function isArrayOfObjectsWithIdAndValue( + valueOrObjects: ValueOrObject[], +): valueOrObjects is ObjectWithIdAndValue[] { + return isObjectWithIdAndValue(valueOrObjects[0]); +} /** * Helper class representing an ArrayWithIds. Used to explicitly track values assigned to atoms, for example. */ -export class ArrayWithIds { - array: object[]; +export class ArrayWithIds { + array: T[]; /** * Create a an array with ids. * @param {Array} array - Either regular array or ArrayWithIds (see @example above) */ - constructor(array: ObjectWithId[] = []) { - if (!_.isArray(array)) + constructor(array: ObjectWithIdAndValue[] | T[] = []) { + if (!_.isArray(array)) { throw new Error("ArrayWithIds.constructor: pass array on initialization"); + } // if passed an array with ids as config, only store the values in array - this.array = array.sort((a, b) => a.id - b.id).map((element) => element.value || element); + if (isArrayOfObjectsWithIdAndValue(array)) { + this.array = array.sort((a, b) => a.id - b.id).map((element) => element.value); + } else { + this.array = array; + } } /** * Serialize class instance to JSON. * @example [{"id" : 0, "value" : "Si" }, {"id" : 1, "value" : "Si" }] */ - toJSON() { + toJSON(): ObjectWithIdAndValue[] { // from ["a", "b"] to [{id: 0, value: "a"}, {id: 1, value: "b"}] - return this.array.map((el, idx) => new ScalarWithId(el, idx).toJSON()); + return this.array.map((el, idx) => new ScalarWithId(el, idx).toJSON()); } /** * Apply function fn to each element of the array and replace `array` with the result. * @param fn - The function to be applied to each array element. */ - mapArrayInPlace(fn: MapFunction) { - if (!_.isFunction(fn)) + mapArrayInPlace(fn: MapFunction) { + if (!_.isFunction(fn)) { throw new Error("ArrayWithIds.mapArray: must pass function as argument"); - this.array = this.array.map((...args) => fn(...args)); + } + + this.array = this.array.map(fn); } getArrayElementByIndex(idx: number) { @@ -55,7 +68,7 @@ export class ArrayWithIds { * Get the index of the array element that passes the predicate. * @param {Function} predicate - The function to be applied to each array element. */ - getArrayIndexByPredicate(predicate: Predicate) { + getArrayIndexByPredicate(predicate: Predicate) { return this.array.findIndex((el) => predicate(el)); } @@ -63,8 +76,9 @@ export class ArrayWithIds { * Add an entity to array. * @param el - The entity to be added to array. If Object with 'value' key, its value will be added. */ - addElement(el: ObjectWithId) { - if (el) this.array.push(el.value || el); + addElement(el: ValueOrObject) { + const value = isObjectWithIdAndValue(el) ? el.value : el; + if (el) this.array.push(value); } /** @@ -72,7 +86,7 @@ export class ArrayWithIds { * @param el - The entity to be added to array. If Object with 'value' key, its value will be added. * @param idx - The entity to be added to array. If Object with 'value' key, its value will be added. */ - removeElement(el: ObjectWithId, idx: number) { + removeElement(el: ValueOrObject | null, idx?: number) { let _idx; if (idx === undefined) { _idx = this.array.findIndex((elm) => elm === el); diff --git a/src/abstract/scalar_with_id.ts b/src/abstract/scalar_with_id.ts index 6d655a31..3a4a5dfa 100644 --- a/src/abstract/scalar_with_id.ts +++ b/src/abstract/scalar_with_id.ts @@ -1,43 +1,55 @@ import _ from "underscore"; -interface ObjectWithId { +export interface ObjectWithIdAndValue { id: number; - value?: object; + value: T; +} + +export type ValueOrObject = ObjectWithIdAndValue | T; + +export type ValueOrObjectArray = ObjectWithIdAndValue[] | T[]; + +export function isObjectWithIdAndValue( + valueOrObject: ValueOrObject, +): valueOrObject is ObjectWithIdAndValue { + return Boolean( + _.isObject(valueOrObject) && + !_.isArray(valueOrObject) && + valueOrObject.id && + valueOrObject.value, + ); } /** * Helper class representing a scalar with an associated id. */ -export class ScalarWithId implements ObjectWithId { +export class ScalarWithId { id: number; - value?: object | ObjectWithId; + value: T; /** * Create a an array with ids. * @param valueOrObject - a ScalarWithID, or any other type. * @param id - numerical id (Integer). */ - constructor(valueOrObject: object | ObjectWithId, id = 0) { - let _id, _value; + constructor(valueOrObject: ValueOrObject, id = 0) { // if already passing a ScalarWithId => preserve original - if (_.isObject(valueOrObject) && !_.isArray(valueOrObject)) { + if (isObjectWithIdAndValue(valueOrObject)) { // NOTE - Arrays are Objects too - _id = valueOrObject.id; - _value = valueOrObject.value; + this.id = valueOrObject.id; + this.value = valueOrObject.value; } else { - _id = id; - _value = valueOrObject; + this.id = id; + this.value = valueOrObject; } - this.value = _value; - this.id = _id; } /** * Serialize class instance to JSON. * @example {"id" : 0, "value" : "Si" } */ - toJSON(): object { + toJSON(): ObjectWithIdAndValue { return { id: this.id, value: this.value, diff --git a/src/basis/basis.ts b/src/basis/basis.ts index 7c4a99f9..df2c1865 100644 --- a/src/basis/basis.ts +++ b/src/basis/basis.ts @@ -1,42 +1,59 @@ +// @ts-ignore import { getElectronegativity, getElementAtomicRadius } from "@exabyte-io/periodic-table.js"; -import { Vector } from "src/lattice/types"; import _ from "underscore"; import s from "underscore.string"; import { ArrayWithIds } from "../abstract/array_with_ids"; +import { ObjectWithIdAndValue, ValueOrObjectArray } from "../abstract/scalar_with_id"; import { ATOMIC_COORD_UNITS, HASH_TOLERANCE } from "../constants"; import { Lattice, nonPeriodicLatticeScalingFactor } from "../lattice/lattice"; +import { Vector } from "../lattice/types"; import math from "../math"; -interface BasisProps { - elements: string[]; - coordinates: [number, number, number][]; +export interface BasisProps { + elements: ValueOrObjectArray; // chemical elements for atoms in basis. + coordinates: ValueOrObjectArray; // coordinates for the atoms in basis. + units: string; // units for the coordinates (eg. angstrom, crystal). + cell: Vector[]; // crystal cell corresponding to the basis (eg. to convert to crystal coordinates). + isEmpty?: boolean; // crystal cell corresponding to the basis (eg. to convert to crystal coordinates). +} + +export interface Atom { + id?: number; // numeric id of the element (optional). + element: string; // Chemical element + coordinate: Coordinate; // 3-dimensional coordinate +} + +export interface Coordinate extends Array { + 0: number; + 1: number; + 2: number; +} + +export interface ElementCount { + count: number; + value: string; +} + +export interface BasisJSON { + elements: ObjectWithIdAndValue[]; + coordinates: ObjectWithIdAndValue[]; units: string; cell: Vector[]; - isEmpty: boolean; } /** * A class representing a crystal basis. */ export class Basis { - _elements: ArrayWithIds; + _elements: ArrayWithIds; - _coordinates: ArrayWithIds; + _coordinates: ArrayWithIds; units: string; cell: Vector[]; - /** - * Create a Basis class. - * @param {Object} - Config object. - * @param {Array|ArrayWithIds} elements - chemical elements for atoms in basis. - * @param {Array|ArrayWithIds} coordinates - coordinates for the atoms in basis. - * @param {String} units - units for the coordinates (eg. angstrom, crystal). - * @param {Cell} cell - crystal cell corresponding to the basis (eg. to convert to crystal coordinates). - * @param {Boolean} isEmpty - crystal cell corresponding to the basis (eg. to convert to crystal coordinates). - */ constructor({ elements = ["Si"], coordinates = [[0, 0, 0]], @@ -44,23 +61,17 @@ export class Basis { cell = Basis.defaultCell, // by default, assume a cubic unary cell isEmpty = false, // whether to generate an empty Basis }: BasisProps) { - let _elements, _coordinates, _units; + const _elements = isEmpty ? [] : elements; + const _coordinates = isEmpty ? [] : coordinates; + const _units = units || Basis.unitsOptionsDefaultValue; + if (!units) { - _units = Basis.unitsOptionsDefaultValue; console.warn("Basis.constructor: units are not provided => set to crystal"); - } else { - _units = units; - } - if (isEmpty) { - _elements = []; - _coordinates = []; - } else { - _elements = elements; - _coordinates = coordinates; } + // assert that elements and coordinates have ids if not already passed in config + store Array helper classes - this._elements = new ArrayWithIds(_elements); - this._coordinates = new ArrayWithIds(_coordinates); + this._elements = new ArrayWithIds(_elements); + this._coordinates = new ArrayWithIds(_coordinates); this.units = _units; this.cell = cell; } @@ -129,45 +140,57 @@ export class Basis { ] } */ - toJSON() { - return JSON.parse( - JSON.stringify(_.pick(this, ["elements", "coordinates", "units", "cell"])), - ); + toJSON(): BasisJSON { + const json: BasisJSON = { + elements: this.elements, + coordinates: this.coordinates, + units: this.units, + cell: this.cell, + }; + + return JSON.parse(JSON.stringify(json)); } /** * Create an identical copy of the class instance. - * @param {Object} extraContext - Extra context to be passed to the new class instance on creation. + * @param extraContext - Extra context to be passed to the new class instance on creation. */ - clone(extraContext) { - return new this.constructor({ ...this.toJSON(), ...extraContext }); + clone(extraContext?: Partial): Basis { + return new (this.constructor as typeof Basis)({ + ...this.toJSON(), + ...extraContext + }); } - getElementByIndex(idx: number) { + getElementByIndex(idx: number): string { return this._elements.getArrayElementByIndex(idx); } - getCoordinateByIndex(idx: number) { + getCoordinateByIndex(idx: number): Coordinate { return this._coordinates.getArrayElementByIndex(idx); } - get elementsArray() { + get elementsArray(): string[] { return this._elements.array; } - get elements() { + get elements(): ObjectWithIdAndValue[] { return this._elements.toJSON(); } /** * Set basis elements to passed array. - * @param {Array|ArrayWithIds} elementsArray - New elements array. + * @param elementsArray - New elements array. */ - set elements(elementsArray) { - this._elements = new ArrayWithIds(elementsArray); + set elements(elementsArray: string[] | ObjectWithIdAndValue[]) { + this._elements = new ArrayWithIds(elementsArray); + } + + getElementsAsObject(): ObjectWithIdAndValue[] { + return this._elements.toJSON(); } - get coordinates() { + get coordinates(): ObjectWithIdAndValue[] { return this._coordinates.toJSON(); } @@ -175,8 +198,8 @@ export class Basis { * Set basis elements to passed array. * @param {Array|ArrayWithIds} coordinatesNestedArray - New coordinates array. */ - set coordinates(coordinatesNestedArray) { - this._coordinates = new ArrayWithIds(coordinatesNestedArray); + set coordinates(coordinatesNestedArray: Coordinate[] | ObjectWithIdAndValue[]) { + this._coordinates = new ArrayWithIds(coordinatesNestedArray); } get coordinatesAsArray() { @@ -194,14 +217,14 @@ export class Basis { toCartesian() { const unitCell = this.cell; if (this.units === ATOMIC_COORD_UNITS.cartesian) return; - this._coordinates.mapArrayInPlace((point) => math.multiply(point, unitCell)); + this._coordinates.mapArrayInPlace((point) => math.multiply(point, unitCell) as unknown as Coordinate); this.units = ATOMIC_COORD_UNITS.cartesian; } toCrystal() { const unitCell = this.cell; if (this.units === ATOMIC_COORD_UNITS.crystal) return; - this._coordinates.mapArrayInPlace((point) => math.multiply(point, math.inv(unitCell))); + this._coordinates.mapArrayInPlace((point) => math.multiply(point, math.inv(unitCell)) as unknown as Coordinate); this.units = ATOMIC_COORD_UNITS.crystal; } @@ -210,11 +233,11 @@ export class Basis { */ toStandardRepresentation() { this.toCrystal(); - this._coordinates.mapArrayInPlace((point) => point.map((x) => math.mod(x))); + this._coordinates.mapArrayInPlace((point) => point.map((x) => math.mod(x)) as Coordinate); } /** A representation where all coordinates are within 0 and 1 in crystal units */ - get standardRepresentation() { + get standardRepresentation(): BasisJSON { const originalUnits = this.units; this.toStandardRepresentation(); @@ -228,58 +251,32 @@ export class Basis { /** * Add atom with a chemical element at coordinate. - * @param {Object} config - * @param {String} element - Chemical element. - * @param {Array} coordinate - 3-dimensional coordinate. */ - addAtom({ element = "Si", coordinate = [0.5, 0.5, 0.5] }) { + addAtom({ element = "Si", coordinate = [0.5, 0.5, 0.5] }: Atom) { this._elements.addElement(element); this._coordinates.addElement(coordinate); } /** * Remove atom with a chemical element at coordinate either by passing the (element AND coordinate) OR id. - * @param {Object} config - * @param {String} element - Chemical element. - * @param {Array} coordinate - 3-dimensional coordinate. - * @param {Number} id - numeric id of the element (optional). */ - removeAtom({ element, coordinate, id }) { + removeAtom({ element, coordinate, id }: Atom) { if (element && coordinate.length > 0) { this._elements.removeElement(element, id); this._coordinates.removeElement(coordinate, id); } } - /** - * Remove atom at a particular coordinate. - * @param {Object} config - * @param {Array} coordinate - 3-dimensional coordinate. - */ - removeAtomAtCoordinate({ coordinate }) { - if (coordinate.length > 0) { - const index = this._coordinates.getArrayIndexByPredicate((arrayCoordinate) => { - return math.roundToZero(math.vDist(arrayCoordinate, coordinate)) === 0; - }); - if (index > -1) { - this._elements.removeElement(null, index); - this._coordinates.removeElement(null, index); - } - } - } - /** * Unique names (symbols) of the chemical elements basis. E.g. `['Si', 'Li']` - * @return {Array} */ - get uniqueElements() { + get uniqueElements(): string[] { return _.unique(this._elements.array); } /** * Returns unique chemical elements with their count sorted by electronegativity. * `{ "Fe": 4.0, "O": 8.0, "Li": 2.0}`. - * @return {Object} */ get uniqueElementCountsSortedByElectronegativity() { return _.chain(this.elements) @@ -293,12 +290,11 @@ export class Basis { * Returns chemical elements with their count wrt their original order in the basis. * Note: entries for the same element separated by another element are considered separately. * [{"count":1, "value":"Zr"}, {"count":23, "value":"H"}, {"count":11, "value":"Zr"}, {"count":1, "value":"H"}] - * @return {Object} */ - get elementCounts() { - const elementCounts = []; - this.elements.forEach((element, index) => { - const previousElement = this.elements[index - 1]; + get elementCounts(): ElementCount[] { + const elementCounts: ElementCount[] = []; + this.getElementsAsObject().forEach((element, index) => { + const previousElement = this.getElementsAsObject()[index - 1]; if (previousElement && previousElement.value === element.value) { const previousElementCount = elementCounts[elementCounts.length - 1]; previousElementCount.count += 1; @@ -314,9 +310,8 @@ export class Basis { /** * Reduced formula in IUPAC format. E.g., Na2SO4 - * @return {String} */ - get formula() { + get formula(): string { const counts = this.uniqueElementCountsSortedByElectronegativity; const countsValues = _.values(counts); const gcd = countsValues.length > 1 ? math.gcd(...countsValues) : countsValues[0]; @@ -329,9 +324,8 @@ export class Basis { /** * Returns the unit cell formula as object `{ "Fe": 4.0, "O": 8.0, "Li": 2.0}` - * @return {Array} */ - get unitCellFormula() { + get unitCellFormula(): string { const counts = this.uniqueElementCountsSortedByElectronegativity; return _.pairs(counts) .map((x) => x[0] + (x[1] === 1 ? "" : x[1])) @@ -343,12 +337,10 @@ export class Basis { /** * Returns a nested array with elements and their corresponding coordinates * @example Output: [ ["Si", [0,0,0]], ["Si", [0.5,0.5,0.5]] ] - * @return {Array} */ - get elementsAndCoordinatesArray() { - const clsInstance = this; + get elementsAndCoordinatesArray(): [string, Coordinate][] { return this._elements.array.map((element, idx) => { - const coordinates = clsInstance.getCoordinateByIndex(idx); + const coordinates = this.getCoordinateByIndex(idx); return [element, coordinates]; }); } @@ -363,9 +355,8 @@ export class Basis { * result: "Si 0,1,0;Si 1,0,0" * ``` * This guarantees the independence from the order in the elements array. - * @return {String} */ - getAsSortedString() { + getAsSortedString(): string { // make a copy to prevent modifying class values const clsInstance = new Basis(this.toJSON()); clsInstance.toStandardRepresentation(); @@ -380,9 +371,8 @@ export class Basis { /** * Returns a string for hash calculation (in crystal units) - * @return {String} */ - get hashString() { + get hashString(): string { const originallyInCartesianUnits = this.isInCartesianUnits; this.toCrystal(); @@ -397,9 +387,8 @@ export class Basis { /** * Returns an array of strings with chemical elements and their atomic positions. * E.g., ``` ['Si 0 0 0', 'Li 0.5 0.5 0.5']``` - * @return {String[]} */ - get atomicPositions() { + get atomicPositions(): string[] { return this.elementsAndCoordinatesArray.map((entry) => { const element = entry[0]; const coordinate = entry[1]; @@ -410,7 +399,7 @@ export class Basis { /** * @summary Returns number of atoms in material */ - get nAtoms() { + get nAtoms(): number { return this._elements.array.length; } @@ -419,18 +408,16 @@ export class Basis { /** * @summary Returns true if bases are equal, otherwise - false. * @param anotherBasisClsInstance {Basis} Another Basis. - * @return {Boolean} */ - isEqualTo(anotherBasisClsInstance) { + isEqualTo(anotherBasisClsInstance: Basis): boolean { return this.hashString === anotherBasisClsInstance.hashString; } /** * @summary Returns true if basis cells are equal, otherwise - false. * @param anotherBasisClsInstance {Basis} Another Basis. - * @return {Boolean} */ - hasEquivalentCellTo(anotherBasisClsInstance) { + hasEquivalentCellTo(anotherBasisClsInstance: Basis): boolean { // this.cell {Array} - Cell Vectors 1, eg. [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]] // prettier-ignore return !this.cell @@ -444,9 +431,8 @@ export class Basis { * @summary function returns the minimum basis lattice size for a structure. * The lattice size is based on the atomic radius of an element if the basis contains a single atom. * The lattice size is based on the maximum pairwise distance across a structure if the basis contains > 2 atoms. - * @returns {Number} */ - getMinimumLatticeSize(latticeScalingFactor = nonPeriodicLatticeScalingFactor) { + getMinimumLatticeSize(latticeScalingFactor = nonPeriodicLatticeScalingFactor): number { let latticeSizeAdditiveContribution = 0; if (this._elements.array.length === 1) { const elementSymbol = this._elements.getArrayElementByIndex(0); @@ -471,12 +457,11 @@ export class Basis { * - - - ... ... * - - - ... ... pair n-1, n * - * @returns {Number} */ - get maxPairwiseDistance() { + get maxPairwiseDistance(): number { const originalUnits = this.units; this.toCartesian(); - let maxDistance = 0; + let maxDistance: number = 0; if (this._elements.array.length >= 2) { for (let i = 0; i < this._elements.array.length; i++) { for (let j = i + 1; j < this._elements.array.length; j++) { @@ -484,7 +469,9 @@ export class Basis { this._coordinates.getArrayElementByIndex(i), this._coordinates.getArrayElementByIndex(j), ); + // @ts-ignore if (distance > maxDistance) { + // @ts-ignore maxDistance = distance; } } @@ -511,13 +498,12 @@ export class Basis { * [z1, z2, ...zn]] * * Returns an array = [xCenter, yCenter, zCenter] - * @returns {Array} */ - get centerOfCoordinatesPoint() { + get centerOfCoordinatesPoint(): number[] { const transposedBasisCoordinates = math.transpose(this._coordinates.array); const centerOfCoordinatesVectors = []; for (let i = 0; i < 3; i++) { - const center = + const center = // @ts-ignore transposedBasisCoordinates[i].reduce((a, b) => a + b) / this._elements.array.length; centerOfCoordinatesVectors.push(math.precise(center, 4)); } @@ -526,10 +512,9 @@ export class Basis { /** * @summary Function translates coordinates by the vector passed as an argument. - * @param {Array} translationVector - */ - translateByVector(translationVector) { + translateByVector(translationVector: number[]) { + // @ts-ignore this._coordinates.mapArrayInPlace((x) => math.add(x, translationVector)); } } diff --git a/src/basis/constrained_basis.js b/src/basis/constrained_basis.ts similarity index 65% rename from src/basis/constrained_basis.js rename to src/basis/constrained_basis.ts index 0969edeb..33506919 100644 --- a/src/basis/constrained_basis.js +++ b/src/basis/constrained_basis.ts @@ -1,34 +1,48 @@ import s from "underscore.string"; import { ArrayWithIds } from "../abstract/array_with_ids"; -import { AtomicConstraints } from "../constraints/constraints"; -import { Basis } from "./basis"; +import { AtomicConstraints, Constraint, ConstraintValue } from "../constraints/constraints"; +import { Basis, BasisJSON, BasisProps, Coordinate } from "./basis"; +import { ObjectWithIdAndValue } from "src/abstract/scalar_with_id"; + +export interface ConstrainedBasisProps extends BasisProps { + constraints: Constraint[] +} + +export interface ConstrainedBasisJSON extends BasisJSON { + constraints: ObjectWithIdAndValue[] +} /** * @summary Extension of the Basis class able to deal with atomic constraints. * @extends Basis */ export class ConstrainedBasis extends Basis { + _constraints: ArrayWithIds /** * Create a an array with ids. * @param {Object} config * @param {ArrayWithIds|Array} config.constraints - atomic constraints. */ - constructor(config) { + constructor(config: ConstrainedBasisProps) { super(config); - this._constraints = new ArrayWithIds(config.constraints); // `constraints` is an Array with ids + this._constraints = new ArrayWithIds(config.constraints); // `constraints` is an Array with ids } get constraints() { - return this._constraints; + return this._constraints.array; } - set constraints(newConstraints) { + set constraints(newConstraints: ConstraintValue[]) { this._constraints = new ArrayWithIds(newConstraints); } + getConstraintAsArray() { + return this._constraints; + } + get AtomicConstraints() { - return AtomicConstraints.fromArray(this.constraints.array); + return AtomicConstraints.fromArray(this.constraints); } /** @@ -48,22 +62,21 @@ export class ConstrainedBasis extends Basis { ] } */ - toJSON() { + toJSON(): ConstrainedBasisJSON { return { ...super.toJSON(), - constraints: this.constraints.toJSON(), + constraints: this._constraints.toJSON(), }; } - getConstraintByIndex(idx) { + getConstraintByIndex(idx: number): ConstraintValue { return this._constraints.getArrayElementByIndex(idx) || []; } /** * Helper function returning a nested array with [element, coordinates, constraints] as elements - * @return {Array[]} */ - get elementsCoordinatesConstraintsArray() { + get elementsCoordinatesConstraintsArray(): [string, Coordinate, ConstraintValue][] { const clsInstance = this; return this._elements.array.map((element, idx) => { const coordinates = clsInstance.getCoordinateByIndex(idx); @@ -75,9 +88,8 @@ export class ConstrainedBasis extends Basis { /** * Returns an array with atomic positions (with constraints) per atom stored as strings. * E.g., ``` ['Si 0 0 0 0 1 0', 'Li 0.5 0.5 0.5 1 0 1']``` - * @return {String[]} */ - get atomicPositionsWithConstraints() { + get atomicPositionsWithConstraints(): string[] { return this.elementsCoordinatesConstraintsArray.map((entry) => { const element = entry[0]; const coordinate = entry[1]; diff --git a/src/cell/cell.js b/src/cell/cell.ts similarity index 63% rename from src/cell/cell.js rename to src/cell/cell.ts index 70e19fe0..f75869dc 100644 --- a/src/cell/cell.js +++ b/src/cell/cell.ts @@ -1,11 +1,16 @@ +import { Vector } from "src/lattice/types"; import constants from "../constants"; import math from "../math"; +import { Coordinate } from "src/basis/basis"; const MATRIX = math.matrix; const MULT = math.multiply; const INV = math.inv; +// @ts-ignore const MATRIX_MULT = (...args) => MULT(...args.map((x) => MATRIX(x))).toArray(); +type Point = Coordinate | math.Matrix | math.MathType; + /* * Cell represents a unit cell in geometrical form: 3x3 matrix where rows are cell vectors. * Example: [[1, 0, 0], [0, 1, 0], [0, 0, 1]]. @@ -13,34 +18,39 @@ const MATRIX_MULT = (...args) => MULT(...args.map((x) => MATRIX(x))).toArray(); export class Cell { tolerance = 1; + vector1: Vector; + + vector2: Vector; + + vector3: Vector; + /** * Create a cell. * @param nestedArray {Number[][]} is an array of cell vectors in cartesian Angstrom units. */ - constructor(nestedArray) { + constructor(nestedArray: [Vector, Vector, Vector]) { [this.vector1, this.vector2, this.vector3] = nestedArray; } /** * Get cell vectors as (a nested) array. - * @return {Array[]} * @example [[1, 0, 0], [0, 1, 0], [0, 0, 1]] */ - get vectorsAsArray() { + get vectorsAsArray(): [Vector, Vector, Vector] { return [ this.vector1, this.vector2, this.vector3, // assert that no near-zero artifacts are present (ie. 1.6 x 10^-16) before attempting inversion // @param tolerance {Number} Maximum tolerance to small numbers, used to avoid artifacts on matrix inversion - ].map((v) => v.map((c) => (math.abs(c) < constants.tolerance.lengthAngstrom ? 0 : c))); + ].map((v) => v.map((c) => (math.abs(c) < constants.tolerance.lengthAngstrom ? 0 : c))) as [Vector, Vector, Vector]; } - clone() { - return new this.constructor(this.vectorsAsArray); + clone(): Cell { + return new (this.constructor as typeof Cell)(this.vectorsAsArray); } - cloneAndScaleByMatrix(matrix) { + cloneAndScaleByMatrix(matrix: number[][]) { const newCell = this.clone(); newCell.scaleByMatrix(matrix); return newCell; @@ -48,38 +58,36 @@ export class Cell { /** * Convert a point (in crystal coordinates) to cartesian. - * @return {Array} */ - convertPointToCartesian(point) { + convertPointToCartesian(point: Point) { return MULT(point, this.vectorsAsArray); } /** * Convert a point (in cartesian coordinates) to crystal (fractional). - * @return {Array} */ - convertPointToFractional(point) { - return MULT(point, INV(this.vectorsAsArray)); + convertPointToFractional(point: Point): Coordinate { + return MULT(point, INV(this.vectorsAsArray)) as Coordinate; } /** * Check whether a point is inside the cell. - * @param {Array} point - the point to conduct the check for. - * @param {Number} tolerance - numerical tolerance. - * @return {Boolean} + * @param point - the point to conduct the check for. + * @param tolerance - numerical tolerance. */ - isPointInsideCell(point, tolerance = constants.tolerance.length) { + isPointInsideCell(point: Point, tolerance = constants.tolerance.length): boolean { return this.convertPointToFractional(point) - .map((c) => math.isBetweenZeroInclusiveAndOne(c, tolerance)) - .reduce((a, b) => a && b); + .map((c: number) => math.isBetweenZeroInclusiveAndOne(c, tolerance)) + // @ts-ignore + .reduce((a: boolean, b: boolean): boolean => a && b); } /** * Returns the index of the cell vector, most collinear with the testVector. * @param testVector - * @return {Number} */ - getMostCollinearVectorIndex(testVector) { + getMostCollinearVectorIndex(testVector: Vector): number { + // @ts-ignore const angles = this.vectorsAsArray.map((v) => math.angleUpTo90(v, testVector)); return angles.findIndex((el) => el === math.min(angles)); } @@ -87,7 +95,7 @@ export class Cell { /** * Scale this cell by right-multiplying it to a matrix (nested array) */ - scaleByMatrix(matrix) { + scaleByMatrix(matrix: number[][]) { [this.vector1, this.vector2, this.vector3] = MATRIX_MULT(matrix, this.vectorsAsArray); } } diff --git a/src/cell/conventional_cell.js b/src/cell/conventional_cell.js deleted file mode 100644 index aa0f5704..00000000 --- a/src/cell/conventional_cell.js +++ /dev/null @@ -1,96 +0,0 @@ -import { LATTICE_TYPE } from "../lattice/types"; -import math from "../math"; - -/** - * Routines for calculating conventional cell vectors from primitive cell Bravais parameters. - * Following Setyawan, W., & Curtarolo, S. (2010). doi:10.1016/j.commatsci.2010.05.010 - */ - -const unitMatrix = [ - [1, 0, 0], - [0, 1, 0], - [0, 0, 1], -]; - -// (Conventional cellVectors) = (Primitive cellVectors) * (PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIER matrix) -export const PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS = { - // PRIMITIVE => CONVENTIONAL - [LATTICE_TYPE.CUB]: unitMatrix, - [LATTICE_TYPE.FCC]: [ - [-1, 1, 1], - [1, -1, 1], - [1, 1, -1], - ], - [LATTICE_TYPE.BCC]: [ - [0, 1, 1], - [1, 0, 1], - [1, 1, 0], - ], - [LATTICE_TYPE.TET]: unitMatrix, - [LATTICE_TYPE.BCT]: [ - [0, 1, 1], - [1, 0, 1], - [1, 1, 0], - ], - [LATTICE_TYPE.ORC]: unitMatrix, - [LATTICE_TYPE.ORCF]: [ - [-1, 1, 1], - [1, -1, 1], - [1, 1, -1], - ], - [LATTICE_TYPE.ORCI]: [ - [0, 1, 1], - [1, 0, 1], - [1, 1, 0], - ], - [LATTICE_TYPE.ORCC]: [ - [1, -1, 0], - [1, 1, 0], - [0, 0, 1], - ], - [LATTICE_TYPE.HEX]: unitMatrix, - [LATTICE_TYPE.RHL]: unitMatrix, - [LATTICE_TYPE.MCL]: unitMatrix, - [LATTICE_TYPE.MCLC]: [ - [1, -1, 0], - [1, 1, 0], - [0, 0, 1], - ], - [LATTICE_TYPE.TRI]: unitMatrix, - [`${LATTICE_TYPE.TRI}alt`]: unitMatrix, -}; - -export const PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES = { - // PRIMITIVE => CONVENTIONAL - [LATTICE_TYPE.CUB]: LATTICE_TYPE.CUB, - [LATTICE_TYPE.FCC]: LATTICE_TYPE.CUB, - [LATTICE_TYPE.BCC]: LATTICE_TYPE.CUB, - [LATTICE_TYPE.TET]: LATTICE_TYPE.TET, - [LATTICE_TYPE.BCT]: LATTICE_TYPE.TET, - [LATTICE_TYPE.ORC]: LATTICE_TYPE.ORC, - [LATTICE_TYPE.ORCF]: LATTICE_TYPE.ORC, - [LATTICE_TYPE.ORCI]: LATTICE_TYPE.ORC, - [LATTICE_TYPE.ORCC]: LATTICE_TYPE.ORC, - [LATTICE_TYPE.HEX]: LATTICE_TYPE.HEX, - [LATTICE_TYPE.RHL]: LATTICE_TYPE.RHL, - [LATTICE_TYPE.MCL]: LATTICE_TYPE.MCL, - [LATTICE_TYPE.MCLC]: LATTICE_TYPE.MCL, - [LATTICE_TYPE.TRI]: LATTICE_TYPE.TRI, - // TODO: Legacy `TRI_alt` type, assert not used and remove - [`${LATTICE_TYPE.TRI}alt`]: LATTICE_TYPE.TRI, -}; - -export function isConventionalCellSameAsPrimitiveForLatticeType(latticeType) { - const multiplier = PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS[latticeType || LATTICE_TYPE.TRI]; - return multiplier === unitMatrix; -} - -/** - * Returns lattice vectors of a conventional cell for a primitive lattice. - * @param {Lattice} lattice - Lattice instance. - * @return {Array[]} Cell.vectorsAsArray - */ -export function getConventionalCellFromPrimitiveLattice(lattice) { - const multiplier = PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS[lattice.type || LATTICE_TYPE.TRI]; - return math.multiply(math.matrix(multiplier), math.matrix(lattice.vectorArrays)).toArray(); -} diff --git a/src/cell/conventional_cell.ts b/src/cell/conventional_cell.ts new file mode 100644 index 00000000..0c0aa044 --- /dev/null +++ b/src/cell/conventional_cell.ts @@ -0,0 +1,87 @@ +import { LATTICE_TYPE, LatticeType } from "../lattice/types"; +import math from "../math"; + +/** + * Routines for calculating conventional cell vectors from primitive cell Bravais parameters. + * Following Setyawan, W., & Curtarolo, S. (2010). doi:10.1016/j.commatsci.2010.05.010 + */ + +const unitMatrix = [ + [1, 0, 0], + [0, 1, 0], + [0, 0, 1], +]; + +// (Conventional cellVectors) = (Primitive cellVectors) * (PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIER matrix) +export const PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS = { + // PRIMITIVE => CONVENTIONAL + [LatticeType.CUB]: unitMatrix, + [LatticeType.FCC]: [ + [-1, 1, 1], + [1, -1, 1], + [1, 1, -1], + ], + [LatticeType.BCC]: [ + [0, 1, 1], + [1, 0, 1], + [1, 1, 0], + ], + [LatticeType.TET]: unitMatrix, + [LatticeType.BCT]: [ + [0, 1, 1], + [1, 0, 1], + [1, 1, 0], + ], + [LatticeType.ORC]: unitMatrix, + [LatticeType.ORCF]: [ + [-1, 1, 1], + [1, -1, 1], + [1, 1, -1], + ], + [LatticeType.ORCI]: [ + [0, 1, 1], + [1, 0, 1], + [1, 1, 0], + ], + [LatticeType.ORCC]: [ + [1, -1, 0], + [1, 1, 0], + [0, 0, 1], + ], + [LatticeType.HEX]: unitMatrix, + [LatticeType.RHL]: unitMatrix, + [LatticeType.MCL]: unitMatrix, + [LatticeType.MCLC]: [ + [1, -1, 0], + [1, 1, 0], + [0, 0, 1], + ], + [LatticeType.TRI]: unitMatrix, + [`${LatticeType.TRI}alt`]: unitMatrix, +}; + +export const PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES = { + // PRIMITIVE => CONVENTIONAL + [LatticeType.CUB]: LatticeType.CUB, + [LatticeType.FCC]: LatticeType.CUB, + [LatticeType.BCC]: LatticeType.CUB, + [LatticeType.TET]: LatticeType.TET, + [LatticeType.BCT]: LatticeType.TET, + [LatticeType.ORC]: LatticeType.ORC, + [LatticeType.ORCF]: LatticeType.ORC, + [LatticeType.ORCI]: LatticeType.ORC, + [LatticeType.ORCC]: LatticeType.ORC, + [LatticeType.HEX]: LatticeType.HEX, + [LatticeType.RHL]: LatticeType.RHL, + [LatticeType.MCL]: LatticeType.MCL, + [LatticeType.MCLC]: LatticeType.MCL, + [LatticeType.TRI]: LatticeType.TRI, + // TODO: Legacy `TRI_alt` type, assert not used and remove + [`${LatticeType.TRI}alt`]: LatticeType.TRI, +}; + +export function isConventionalCellSameAsPrimitiveForLatticeType(latticeType: LatticeType): boolean { + const multiplier = PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS[latticeType || LatticeType.TRI]; + return multiplier === unitMatrix; +} + diff --git a/src/cell/primitive_cell.ts b/src/cell/primitive_cell.ts index 6736a7d6..c8f1a577 100644 --- a/src/cell/primitive_cell.ts +++ b/src/cell/primitive_cell.ts @@ -126,6 +126,7 @@ const PRIMITIVE_CELLS = { // convert angles to Radians // eslint-disable-next-line no-param-reassign [alpha, beta, gamma] = [alpha, beta, gamma].map( + // @ts-ignore (x) => math.unit(x, "degree").to("rad").value, ); diff --git a/src/constraints/constraints.js b/src/constraints/constraints.ts similarity index 54% rename from src/constraints/constraints.js rename to src/constraints/constraints.ts index b9e0cd40..9db905e3 100644 --- a/src/constraints/constraints.js +++ b/src/constraints/constraints.ts @@ -1,7 +1,21 @@ +import { ObjectWithIdAndValue } from "../abstract/scalar_with_id"; import { ArrayWithIds } from "../abstract/array_with_ids"; +export interface ConstraintValue extends Array { + 0: boolean; + 1: boolean; + 2: boolean; +} + +export type Constraint = ObjectWithIdAndValue; + + export class AtomicConstraints { - static fromArray(array) { + name: string; + + values: ArrayWithIds; + + static fromArray(array: ConstraintValue[]) { return new AtomicConstraints({ values: array }); } @@ -10,9 +24,9 @@ export class AtomicConstraints { * @param {Object} config * @param {ArrayWithIds|Array} config.values */ - constructor(config = {}) { + constructor({ values }: {values?: ConstraintValue[]}) { this.name = "atomic_constraints"; - this.values = new ArrayWithIds(config.values || []); + this.values = new ArrayWithIds(values || []); } /** @@ -35,17 +49,16 @@ export class AtomicConstraints { }; } - getByIndex(idx) { + getByIndex(idx: number): ConstraintValue { return this.values.getArrayElementByIndex(idx) || []; } /** * Get constraints for an atom with index as string. - * @param {Number} idx - atom index. - * @param {Function} mapFn (OPTIONAL) - a function to be applied to each constraint. By default 0 or 1 is returned. - * @return {String[]} + * @param idx - atom index. + * @param mapFn (OPTIONAL) - a function to be applied to each constraint. By default 0 or 1 is returned. */ - getAsStringByIndex(idx, mapFn = (boolean) => (boolean ? 1 : 0)) { + getAsStringByIndex(idx: number, mapFn = (val: boolean): string => (val ? "1" : "0")): string { return this.getByIndex(idx).map(mapFn).join(" "); } } diff --git a/src/lattice/lattice.ts b/src/lattice/lattice.ts index d271e968..7e8d13db 100644 --- a/src/lattice/lattice.ts +++ b/src/lattice/lattice.ts @@ -14,10 +14,12 @@ import { import { LATTICE_TYPE, LATTICE_TYPE_CONFIGS, LATTICE_TYPE_EXTENDED } from "./types"; import { UnitCell, UnitCellProps } from "./unit_cell"; -interface RequiredBravaisConfigWithVectors extends RequiredBravaisConfig { +export interface RequiredBravaisConfigWithVectors extends RequiredBravaisConfig { vectors: RequiredLatticeVectorsConfig; } +export type LatticeJSON = RequiredBravaisConfigWithVectors; + /** * Scaling factor used to calculate the new lattice size for non-periodic systems. * The scaling factor ensures that a non-periodic structure will have have a lattice greater than the structures size. @@ -29,7 +31,7 @@ export const nonPeriodicLatticeScalingFactor = 2.0; * Follows Bravais convention for lattice types and contains lattice vectors within. * Units for lattice vector coordinates are "angstroms", and "degrees" for the corresponding angles. */ -export class Lattice extends LatticeBravais implements RequiredBravaisConfigWithVectors { +export class Lattice extends LatticeBravais implements LatticeJSON { vectors: LatticeVectors; /** @@ -85,7 +87,7 @@ export class Lattice extends LatticeBravais implements RequiredBravaisConfigWith } } */ - toJSON(skipRounding = false): RequiredBravaisConfigWithVectors { + toJSON(skipRounding = false): LatticeJSON { const round = skipRounding ? (x: number) => x : Lattice._roundValue; // round values by default return { a: round(this.a), diff --git a/src/lattice/lattice_bravais.ts b/src/lattice/lattice_bravais.ts index 09dd92a1..c9107caf 100644 --- a/src/lattice/lattice_bravais.ts +++ b/src/lattice/lattice_bravais.ts @@ -104,8 +104,11 @@ export class LatticeBravais implements RequiredBravaisConfig { const roundValue = skipRounding ? (x: number) => x : this._roundValue; return new (this.prototype.constructor as typeof LatticeBravais)({ + // @ts-ignore a: roundValue(math.vlen(a) * alat), + // @ts-ignore b: roundValue(math.vlen(b) * alat), + // @ts-ignore c: roundValue(math.vlen(c) * alat), alpha: roundValue(math.angle(b, c, "deg")), beta: roundValue(math.angle(a, c, "deg")), diff --git a/src/lattice/lattice_vectors.ts b/src/lattice/lattice_vectors.ts index 01f76d6d..97e29b80 100644 --- a/src/lattice/lattice_vectors.ts +++ b/src/lattice/lattice_vectors.ts @@ -95,7 +95,7 @@ export class LatticeVectors implements LatticeVectorsConfig { }); } - get vectorArrays() { + get vectorArrays(): [Vector, Vector, Vector] { return [this.a, this.b, this.c]; } diff --git a/src/material.ts b/src/material.ts index ebbf913d..50753d11 100644 --- a/src/material.ts +++ b/src/material.ts @@ -1,20 +1,26 @@ import { HasMetadataNamedDefaultableInMemoryEntity } from "@exabyte-io/code.js/dist/entity"; -import { AnyObject } from "@exabyte-io/code.js/dist/entity/in_memory"; import CryptoJS from "crypto-js"; -import lodash from "lodash"; -import { ConstrainedBasis } from "./basis/constrained_basis"; +import { + MaterialSchema, +} from "@exabyte-io/code.js/src/types" + + +import { ConstrainedBasis, ConstrainedBasisJSON } from "./basis/constrained_basis"; import { isConventionalCellSameAsPrimitiveForLatticeType, PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES, PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS, } from "./cell/conventional_cell"; import { ATOMIC_COORD_UNITS, units } from "./constants"; -import { Lattice } from "./lattice/lattice"; +import { Lattice, LatticeJSON } from "./lattice/lattice"; import { BravaisConfigProps } from "./lattice/lattice_vectors"; import { LATTICE_TYPE } from "./lattice/types"; import parsers from "./parsers/parsers"; import supercellTools from "./tools/supercell"; +import { BasisConfig } from "./parsers/xyz"; +import { Constraint } from "./constraints/constraints"; +import { AnyObject } from "@exabyte-io/code.js/dist/entity/in_memory"; export const defaultMaterialConfig = { name: "Silicon FCC", @@ -57,33 +63,46 @@ export const defaultMaterialConfig = { }, }; -export class Material extends HasMetadataNamedDefaultableInMemoryEntity { - constructor(config: AnyObject) { - super(config); - this._json = lodash.cloneDeep(config || {}); - } +interface Property { + name: string; + value: string; +} + +export interface MaterialJSON extends AnyObject { + lattice:LatticeJSON; + basis: ConstrainedBasisJSON; + name: string; + isNonPeriodic: boolean; +} + +interface MaterialSchemaJSON extends MaterialSchema, AnyObject { + +} + + +export abstract class Material extends HasMetadataNamedDefaultableInMemoryEntity { + abstract src: { + extension: string; + text: string; + }; - toJSON() { - return this.toJSONDefault(); + _json: MaterialSchemaJSON; + + constructor(config: MaterialSchemaJSON) { + super(config); + this._json = {...config}; + this.name = super.name || this.formula } - toJSONDefault() { + toJSON(): MaterialJSON { return { lattice: this.Lattice.toJSON(), basis: this.Basis.toJSON(), - name: this.name || this.formula, - isNonPeriodic: this.isNonPeriodic || false, + name: this.name, + isNonPeriodic: this.isNonPeriodic, }; } - get name(): string { - return super.name || this.formula; - } - - set name(name) { - super.name = name; - } - static get defaultConfig() { return defaultMaterialConfig; } @@ -97,7 +116,7 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { * Gets Bolean value for whether or not a material is non-periodic vs periodic. * False = periodic, True = non-periodic */ - get isNonPeriodic() { + get isNonPeriodic(): boolean { return this.prop("isNonPeriodic", false); } @@ -110,29 +129,26 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { /** * @summary Returns the specific derived property (as specified by name) for a material. - * @param {String} name - * @returns {Object} */ - getDerivedPropertyByName(name: string) { + getDerivedPropertyByName(name: string): Property| undefined { return this.getDerivedProperties().find((x) => x.name === name); } /** * @summary Returns the derived properties array for a material. - * @returns {Array} */ - getDerivedProperties() { + getDerivedProperties(): Property[] { return this.prop("derivedProperties", []); } /** * Gets material's formula */ - get formula() { + get formula(): string { return this.prop("formula") || this.Basis.formula; } - get unitCellFormula() { + get unitCellFormula(): string { return this.prop("unitCellFormula") || this.Basis.unitCellFormula; } @@ -141,28 +157,25 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { * @param format Format (xyz, etc.) * @param unitz crystal/cartesian */ - setBasis(textOrObject: string | object, format: string, unitz: string) { - let basis: object | undefined; + setBasis(textOrObject: string | BasisConfig, format?: string, unitz?: string) { + let basis: BasisConfig | undefined; switch (format) { case "xyz": - basis = parsers.xyz.toBasisConfig(textOrObject, unitz); + basis = parsers.xyz.toBasisConfig(textOrObject as string, unitz); break; default: - basis = textOrObject; + basis = textOrObject as BasisConfig; } this.setProp("basis", basis); this.updateFormula(); } - setBasisConstraints(constraints) { - this.setBasis({ - ...this.basis, - constraints, - }); + setBasisConstraints(constraints: Constraint[]) { + this.setBasis({ ...this.basis, constraints }); } - get basis() { - return this.prop("basis", undefined); + get basis(): BasisConfig { + return this.prop("basis", undefined); } // returns the instance of {ConstrainedBasis} class @@ -173,9 +186,8 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { }); } - /** High-level access to unique elements from material instead of basis. - * - * @return {String[]} + /** + * High-level access to unique elements from material instead of basis. */ get uniqueElements() { return this.Basis.uniqueElements; @@ -198,7 +210,7 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { * inchi cannot be found. * @returns {String} */ - getInchiStringForHash() { + getInchiStringForHash(): string { const inchi = this.getDerivedPropertyByName("inchi"); if (inchi) { return inchi.value; @@ -280,16 +292,15 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { * Si 0.000000000 0.000000000 -0.000000000 * Si 0.250000000 0.250000000 0.250000000 * ``` - * @return {String} */ - getAsQEFormat() { + getAsQEFormat(): string { return parsers.espresso.toEspressoFormat(this.toJSON()); } /** * Returns material in POSCAR format. Pass `true` to ignore original poscar source and re-serialize. */ - getAsPOSCAR(ignoreOriginal = false, omitConstraints = false) { + getAsPOSCAR(ignoreOriginal = false, omitConstraints = false): string { const { src } = this; // By default return original source if exists if (src && src.extension === "poscar" && !ignoreOriginal) { @@ -302,7 +313,7 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { * Returns a copy of the material with conventional cell constructed instead of primitive. */ getACopyWithConventionalCell() { - const material = this.clone(); + const material = this.clone(); // if conventional and primitive cells are the same => return a copy. if (isConventionalCellSameAsPrimitiveForLatticeType(this.Lattice.type)) return material; @@ -311,11 +322,12 @@ export class Material extends HasMetadataNamedDefaultableInMemoryEntity { PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS[this.Lattice.type]; const conventionalLatticeType = PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES[this.Lattice.type]; - const config = supercellTools.generateConfig(material, conventionalSupercellMatrix, 1); + const config = supercellTools.generateConfig(material, conventionalSupercellMatrix); config.lattice.type = conventionalLatticeType; config.name = `${material.name} - conventional cell`; + // @ts-ignore return new this.constructor(config); } } diff --git a/src/parsers/espresso.js b/src/parsers/espresso.ts similarity index 80% rename from src/parsers/espresso.js rename to src/parsers/espresso.ts index 445129bb..ef2016bf 100644 --- a/src/parsers/espresso.js +++ b/src/parsers/espresso.ts @@ -3,13 +3,13 @@ import s from "underscore.string"; import { Lattice } from "../lattice/lattice"; import xyz from "./xyz"; +import { MaterialJSON } from "../material"; /** * Construct textual representation of a materialOrConfig according to Quantum ESPRESSO pw.x input format. - * @param {Material|Object} materialOrConfig - material class instance or its config object - * @return {String} + * @param materialOrConfig - material class instance or its config object */ -function toEspressoFormat(materialOrConfig) { +function toEspressoFormat(materialOrConfig: MaterialJSON): string { const l = new Lattice(materialOrConfig.lattice); const vectors = l.vectorArrays; const vectorsAsString = _.map(vectors, (v) => { diff --git a/src/parsers/poscar.js b/src/parsers/poscar.ts similarity index 77% rename from src/parsers/poscar.js rename to src/parsers/poscar.ts index 772f8f0f..564ccd99 100644 --- a/src/parsers/poscar.js +++ b/src/parsers/poscar.ts @@ -4,26 +4,29 @@ import { ConstrainedBasis } from "../basis/constrained_basis"; import { ATOMIC_COORD_UNITS } from "../constants"; import { Lattice } from "../lattice/lattice"; import math from "../math"; +import { Vector } from "../lattice/types"; +import { Coordinate } from "src/basis/basis"; +import { ConstraintValue, Constraint } from "src/constraints/constraints"; +import { MaterialJSON } from "src/material"; -const _print = (x, printFormat = "%14.9f") => s.sprintf(printFormat, math.precise(x)); -const _latticeVectorsToString = (vectors) => +const _print = (x: number, printFormat = "%14.9f") => s.sprintf(printFormat, math.precise(x)); +const _latticeVectorsToString = (vectors: Vector[]) => vectors.map((v) => v.map((c) => _print(c)).join("\t")).join("\n"); -const atomicConstraintsCharFromBool = (bool) => (bool ? "T" : "F"); +const atomicConstraintsCharFromBool = (bool: boolean): string => (bool ? "T" : "F"); /** * Obtain a textual representation of a material in POSCAR format. - * @param {Material|Object} materialOrConfig - material class instance or config object. - * @param {Boolean} omitConstraints - whether to discard constraints passed with material. - * @return {string} + * @param materialOrConfig - material class instance or config object. + * @param omitConstraints - whether to discard constraints passed with material. */ -function toPoscar(materialOrConfig, omitConstraints = false) { +function toPoscar(materialOrConfig: MaterialJSON, omitConstraints = false): string { const lattice = new Lattice(materialOrConfig.lattice); const vectorsAsString = _latticeVectorsToString(lattice.vectorArrays); const basis = new ConstrainedBasis({ ...materialOrConfig.basis, cell: lattice.vectorArrays, }); - const BasisLines = []; + const BasisLines: string[] = []; let addSelectiveDynamics = false; basis._elements.array.forEach((item, idx) => { const coord = basis.getCoordinateByIndex(idx).map((x) => _print(x)); @@ -35,7 +38,7 @@ function toPoscar(materialOrConfig, omitConstraints = false) { }); const basisContent = BasisLines.join("\n"); const elementsLine = basis.elementCounts.map((e) => e.value).join(" "); - const countsLine = basis.elementCounts.map((e) => parseInt(e.count, 10)).join(" "); + const countsLine = basis.elementCounts.map((e) => parseInt(`${e.count}`, 10)).join(" "); const coordsType = materialOrConfig.basis.units === ATOMIC_COORD_UNITS.cartesian ? "cartesian" : "direct"; @@ -55,20 +58,18 @@ function toPoscar(materialOrConfig, omitConstraints = false) { /** * @summary calculates the number of atoms in a poscar file based on the summation of the numbers in line 7 of the file. * Poscar file formatting: https://www.vasp.at/wiki/index.php/POSCAR - * @param poscarFileContent - * @returns {Number} */ -export function atomsCount(poscarFileContent) { +export function atomsCount(poscarFileContent: string): number { const atomsLine = poscarFileContent.split("\n")[6].split(/\s+/); return atomsLine.map((x) => parseInt(x, 10)).reduce((a, b) => a + b); } /** * Parses POSCAR file into a Material config object. - * @param {string} fileContent - POSCAR file content. - * @return {Object} Material config. + * @param fileContent - POSCAR file content. + * @return Material config. */ -function fromPoscar(fileContent) { +function fromPoscar(fileContent: string): object { const lines = fileContent.split("\n"); const comment = lines[0]; @@ -91,18 +92,18 @@ function fromPoscar(fileContent) { startLine = 8; } - const elements = atomSymbols - .map((symbol, i) => Array(atomCounts[i]).fill(symbol)) + const elements: string[] = atomSymbols + .map((symbol: string, i: number): string[] => Array(atomCounts[i]).fill(symbol)) .reduce((a, b) => a.concat(b), []); // Atom coordinates and constraints - const coordinates = []; - const constraints = []; + const coordinates: Coordinate[] = []; + const constraints: Constraint[] = []; let atomIndex = 0; for (let i = 0; i < atomSymbols.length; i++) { for (let j = 0; j < atomCounts[i]; j++) { const lineComponents = lines[startLine + atomIndex].trim().split(/\s+/); - const coordinate = [ + const coordinate: Coordinate = [ parseFloat(lineComponents[0]), parseFloat(lineComponents[1]), parseFloat(lineComponents[2]), @@ -111,7 +112,7 @@ function fromPoscar(fileContent) { // Add constraints if selective dynamics is used if (selectiveDynamics) { - const constraint = [ + const constraint: ConstraintValue = [ lineComponents[3] === "T", lineComponents[4] === "T", lineComponents[5] === "T", @@ -123,9 +124,9 @@ function fromPoscar(fileContent) { } const lattice = Lattice.fromVectors({ - a: lines[2].trim().split(/\s+/).map(Number), - b: lines[3].trim().split(/\s+/).map(Number), - c: lines[4].trim().split(/\s+/).map(Number), + a: lines[2].trim().split(/\s+/).map(Number) as Vector, + b: lines[3].trim().split(/\s+/).map(Number) as Vector, + c: lines[4].trim().split(/\s+/).map(Number) as Vector, alat: latticeConstant, units: "angstrom", }); @@ -150,10 +151,9 @@ function fromPoscar(fileContent) { /** * @summary Checks if a string has a POSCAR format (first 8 lines are read) - * @param {string} text - string to check - * @returns {boolean} + * @param text - string to check */ -function isPoscar(text) { +function isPoscar(text: string): boolean { const lines = text.split("\n"); // Checking number of lines, minimum requirement for POSCAR diff --git a/src/parsers/xyz.ts b/src/parsers/xyz.ts index 17532c09..e6712a7e 100644 --- a/src/parsers/xyz.ts +++ b/src/parsers/xyz.ts @@ -7,6 +7,9 @@ import { Lattice } from "../lattice/lattice"; import math from "../math"; import { InvalidLineError } from "./errors"; import { CombinatorialBasis } from "./xyz_combinatorial_basis"; +import { MaterialJSON } from "src/material"; +import { Vector } from "src/lattice/types"; +import { Constraint } from "src/constraints/constraints"; // Regular expression for an XYZ line with atomic constraints, eg. Si 0.000000 0.500000 0.446678 1 1 1` // eslint-disable-next-line max-len @@ -45,9 +48,9 @@ export function validate(xyzTxt: string) { .forEach(validateLine); } -interface ParsedObject { +export interface ParsedObject { element: string; - coordinates: [number, number, number]; + coordinates: Vector; constraints: [boolean, boolean, boolean]; } @@ -66,13 +69,27 @@ function _parseXYZLineAsWords(line: string): ParsedObject { }; } +export interface BasisConfig { + elements: { + id: number; + value: string; + }[]; + coordinates: { + id: number; + value: Vector + }[]; + units: string; + cell: Vector[]; + constraints: Constraint[]; +} + /** * Parse XYZ text for basis. * @param txt Text * @param units Coordinate units * @param cell Basis Cell */ -function toBasisConfig(txt: string, units = "angstrom", cell = Basis.defaultCell) { +function toBasisConfig(txt: string, units = "angstrom", cell = Basis.defaultCell): BasisConfig { // @ts-ignore const lines: string[] = s(txt).trim().lines(); const listOfObjects = _.map(lines, _parseXYZLineAsWords); @@ -103,22 +120,21 @@ function toBasisConfig(txt: string, units = "angstrom", cell = Basis.defaultCell /** * Create XYZ from Basis class instance. - * @param basisClsInstance {ConstrainedBasis} Basis class instance. - * @param printFormat {String} Output format for coordinates. - * @param skipRounding {Boolean} Whether to round the numbers (ie. to avoid negative zeros). - * @return {String} Basis string in XYZ format + * @param basisClsInstance Basis class instance. + * @param printFormat Output format for coordinates. + * @param skipRounding Whether to round the numbers (ie. to avoid negative zeros). + * @return Basis string in XYZ format */ -function fromBasis(basisClsInstance, printFormat = "%9.5f", skipRounding = false) { - const clsInstance = basisClsInstance; - const XYZArray = []; - clsInstance._elements.array.forEach((item, idx) => { +function fromBasis(basisClsInstance: ConstrainedBasis, printFormat = "%9.5f", skipRounding = false) { + const XYZArray: string[] = []; + basisClsInstance._elements.array.forEach((item, idx) => { // assume that _elements and _coordinates are indexed equivalently const element = s.sprintf("%-3s", item); - const coordinates = clsInstance.getCoordinateByIndex(idx).map((x) => { + const coordinates = basisClsInstance.getCoordinateByIndex(idx).map((x) => { return s.sprintf(printFormat, skipRounding ? x : math.precise(math.roundToZero(x))); }); - const constraints = clsInstance.constraints - ? clsInstance.AtomicConstraints.getAsStringByIndex(idx) + const constraints = basisClsInstance.constraints + ? basisClsInstance.AtomicConstraints.getAsStringByIndex(idx) : ""; XYZArray.push([element, coordinates.join(" "), constraints].join(" ")); }); @@ -127,11 +143,11 @@ function fromBasis(basisClsInstance, printFormat = "%9.5f", skipRounding = false /** * Create XYZ from Material class instance (or its JSON config). - * @param materialOrConfig {Material|Object} Material. - * @param fractional {Boolean} Coordinate units as fractional. + * @param materialOrConfig Material. + * @param fractional Coordinate units as fractional. * @return Class Instance */ -function fromMaterial(materialOrConfig, fractional = false) { +function fromMaterial(materialOrConfig: MaterialJSON, fractional = false): string { const lattice = new Lattice(materialOrConfig.lattice); const basis = new ConstrainedBasis({ ...materialOrConfig.basis, diff --git a/src/tools/supercell.js b/src/tools/supercell.ts similarity index 85% rename from src/tools/supercell.js rename to src/tools/supercell.ts index 7aa262a2..05897199 100644 --- a/src/tools/supercell.js +++ b/src/tools/supercell.ts @@ -1,6 +1,9 @@ +import { Basis, Coordinate } from "src/basis/basis"; import { LatticeBravais } from "../lattice/lattice_bravais"; import math from "../math"; import cellTools from "./cell"; +import { Cell } from "src/cell/cell"; +import { Material } from "../material"; const ADD = math.add; @@ -11,7 +14,7 @@ const ADD = math.add; * @param supercell {Cell} * @return {Basis} */ -function generateNewBasisWithinSupercell(basis, cell, supercell, supercellMatrix) { +function generateNewBasisWithinSupercell(basis: Basis, cell: Cell, supercell: Cell, supercellMatrix: number[][]) { const oldBasis = basis.clone(); const newBasis = basis.clone({ isEmpty: true }); @@ -28,7 +31,7 @@ function generateNewBasisWithinSupercell(basis, cell, supercell, supercellMatrix if (supercell.isPointInsideCell(newPoint)) { newBasis.addAtom({ element: element.value, - coordinate: supercell.convertPointToFractional(newPoint), + coordinate: supercell.convertPointToFractional(newPoint) as Coordinate, }); } }); @@ -39,10 +42,10 @@ function generateNewBasisWithinSupercell(basis, cell, supercell, supercellMatrix /** * @summary Generates supercell config for the specified material. - * @param material {Object} + * @param material * @param supercellMatrix {Number[][]} */ -function generateConfig(material, supercellMatrix) { +function generateConfig(material: Material, supercellMatrix: number[][]) { const det = math.det(supercellMatrix); if (det === 0) { throw new Error("Scaling matrix is degenerate."); From f8ac03b1458694d0a034de6a3e44278b4554fa0b Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Tue, 7 Nov 2023 15:39:06 +0200 Subject: [PATCH 04/18] chore: fix TS errors in tests --- .mocharc.json | 2 +- src/lattice/reciprocal/symmetry_points.ts | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.mocharc.json b/.mocharc.json index a4d1f263..a12ed926 100644 --- a/.mocharc.json +++ b/.mocharc.json @@ -1,5 +1,5 @@ { "extension": ["ts", "js"], - "spec": "tests/**/*.*", + "spec": "tests/**/*.js", "require": ["ts-node/register", "tests/setup.js"] } diff --git a/src/lattice/reciprocal/symmetry_points.ts b/src/lattice/reciprocal/symmetry_points.ts index 016f4c10..d814ba6d 100644 --- a/src/lattice/reciprocal/symmetry_points.ts +++ b/src/lattice/reciprocal/symmetry_points.ts @@ -720,9 +720,10 @@ const POINTS = { } // MCLC-5 e = (1 / 4) * ((b * b) / (a * a) + (1 - (b * cosAlpha) / c) / (1 - cosAlpha * cosAlpha)); + // @ts-ignore m = n / 2 + (b * b) / (a * a) / 4 - (b * c * cosAlpha) / (2 * a * a); // eslint-disable-next-line max-len - const w = + const w = // @ts-ignore ((4 * v - 1 - (b * b * (1 - cosAlpha * cosAlpha)) / (a * a)) * c) / (2 * b * cosAlpha); n = 1 / 2 + (2 * e * c * cosAlpha) / b; d = ((e * c) / b) * cosAlpha + w / 2 - 1 / 4; From b4df887e64e34bbca5c0c219a4e689a258c8b6d0 Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Tue, 7 Nov 2023 15:48:30 +0200 Subject: [PATCH 05/18] fix: arrayWithId class --- src/abstract/array_with_ids.ts | 2 +- src/abstract/scalar_with_id.ts | 7 +------ 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/src/abstract/array_with_ids.ts b/src/abstract/array_with_ids.ts index b5865c16..eea1bac6 100644 --- a/src/abstract/array_with_ids.ts +++ b/src/abstract/array_with_ids.ts @@ -35,7 +35,7 @@ export class ArrayWithIds { if (isArrayOfObjectsWithIdAndValue(array)) { this.array = array.sort((a, b) => a.id - b.id).map((element) => element.value); } else { - this.array = array; + this.array = [...array]; } } diff --git a/src/abstract/scalar_with_id.ts b/src/abstract/scalar_with_id.ts index 3a4a5dfa..e23105b8 100644 --- a/src/abstract/scalar_with_id.ts +++ b/src/abstract/scalar_with_id.ts @@ -12,12 +12,7 @@ export type ValueOrObjectArray = ObjectWithIdAndValue[] | T[]; export function isObjectWithIdAndValue( valueOrObject: ValueOrObject, ): valueOrObject is ObjectWithIdAndValue { - return Boolean( - _.isObject(valueOrObject) && - !_.isArray(valueOrObject) && - valueOrObject.id && - valueOrObject.value, - ); + return Boolean(_.isObject(valueOrObject) && !_.isArray(valueOrObject) && valueOrObject.value); } /** From 1494d1205b427ddefc8bb7ff8c410654d1628038 Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Tue, 7 Nov 2023 15:56:58 +0200 Subject: [PATCH 06/18] fix: tests --- tests/parsers/xyz_combinatorial_basis.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/parsers/xyz_combinatorial_basis.js b/tests/parsers/xyz_combinatorial_basis.js index 00119642..7d52171e 100644 --- a/tests/parsers/xyz_combinatorial_basis.js +++ b/tests/parsers/xyz_combinatorial_basis.js @@ -7,7 +7,7 @@ import { AsGeBasis, FeLiSiBasis, Ge2Basis, OSiBasis, Si2Basis } from "../enums"; describe("Parsers:CombinatorialBasis", () => { it("toBasisConfig", () => { // eslint-disable-next-line new-cap - const basisConfig2 = new CombinatorialBasis.toBasisConfig([ + const basisConfig2 = CombinatorialBasis.toBasisConfig([ { element: "Si", coordinates: [0, 0, 0], From b42ef3710361cd22e6a07e2d4b1926c8b3477040 Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Tue, 7 Nov 2023 18:16:19 +0200 Subject: [PATCH 07/18] chore: declare material _json as MaterialSchemaJSON --- src/material.ts | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/material.ts b/src/material.ts index 5ca966cf..f56e6947 100644 --- a/src/material.ts +++ b/src/material.ts @@ -82,11 +82,10 @@ export abstract class Material extends HasConsistencyChecksHasMetadataNamedDefau text: string; }; - _json: MaterialSchemaJSON; + declare _json: MaterialSchemaJSON; constructor(config: MaterialSchemaJSON) { super(config); - this._json = { ...config }; this.name = super.name || this.formula; } From 146757bff834a61727dcf5880aa70ad96f91653d Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Wed, 8 Nov 2023 15:44:21 +0200 Subject: [PATCH 08/18] chore: fix package.json --- package-lock.json | 49 ++++++++++++++++++++++------------------------- package.json | 5 ++--- 2 files changed, 25 insertions(+), 29 deletions(-) diff --git a/package-lock.json b/package-lock.json index 853ef7f0..24578790 100644 --- a/package-lock.json +++ b/package-lock.json @@ -14,7 +14,6 @@ "version": "2.2.1", "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.1.tgz", "integrity": "sha512-lFMjJTrFL3j7L9yBxwYfCq2k6qqwHyzuUl/XBnif78PWTJYyL/dfowQHWE3sp6U6ZzqWiiIZnpTMO96zhkjwtg==", - "dev": true, "requires": { "@jridgewell/gen-mapping": "^0.3.0", "@jridgewell/trace-mapping": "^0.3.9" @@ -61,7 +60,6 @@ "version": "7.23.2", "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.23.2.tgz", "integrity": "sha512-n7s51eWdaWZ3vGT2tD4T7J6eJs3QoBXydv7vkUM06Bf1cbVD2Kc2UrkzhiQwobfV7NwOnQXYL7UBJ5VPU+RGoQ==", - "dev": true, "requires": { "@ampproject/remapping": "^2.2.0", "@babel/code-frame": "^7.22.13", @@ -1307,7 +1305,7 @@ }, "@exabyte-io/code.js": { "version": "git+https://github.com/Exabyte-io/code.js.git#71996b93305219b3138f72bde277c6fa478107d0", - "from": "git+https://github.com/Exabyte-io/code.js.git#update/SOF-6922", + "from": "git+https://github.com/Exabyte-io/code.js.git#update/SOF-7096", "dev": true, "requires": { "@babel/cli": "7.16.0", @@ -1753,9 +1751,9 @@ "integrity": "sha512-69TtiDzu0bcmKQv3yg1Zx409/Kd7r0b5F1PfpYJfSHzLGtB53547V4u+9iqKYsTu/O2ai6KTb0TInNpvuQ3qmg==" }, "@types/crypto-js": { - "version": "4.2.0", - "resolved": "https://registry.npmjs.org/@types/crypto-js/-/crypto-js-4.2.0.tgz", - "integrity": "sha512-LW9TlhpMeoQKOu6I6HvOp7eInNNnvd7B+ndAfZb826HUl7eHJJApofbHnlAxrIVS/uiCjkkHGNEaKHoGxB5IHw==", + "version": "4.2.1", + "resolved": "https://registry.npmjs.org/@types/crypto-js/-/crypto-js-4.2.1.tgz", + "integrity": "sha512-FSPGd9+OcSok3RsM0UZ/9fcvMOXJ1ENE/ZbLfOPlBWj7BgXtEAM8VYfTtT760GiLbQIMoVozwVuisjvsVwqYWw==", "dev": true }, "@types/glob": { @@ -1769,9 +1767,9 @@ } }, "@types/js-yaml": { - "version": "4.0.8", - "resolved": "https://registry.npmjs.org/@types/js-yaml/-/js-yaml-4.0.8.tgz", - "integrity": "sha512-m6jnPk1VhlYRiLFm3f8X9Uep761f+CK8mHyS65LutH2OhmBF0BeMEjHgg05usH8PLZMWWc/BUR9RPmkvpWnyRA==", + "version": "4.0.9", + "resolved": "https://registry.npmjs.org/@types/js-yaml/-/js-yaml-4.0.9.tgz", + "integrity": "sha512-k4MGaQl5TGo/iipqb2UDG2UwjXziSWkh0uysQelTlJpX1qGlpUZYm8PnO4DxG1qBomtJUdYJ6qR6xdIah10JLg==", "dev": true }, "@types/json-schema": { @@ -1787,9 +1785,9 @@ "dev": true }, "@types/lodash": { - "version": "4.14.200", - "resolved": "https://registry.npmjs.org/@types/lodash/-/lodash-4.14.200.tgz", - "integrity": "sha512-YI/M/4HRImtNf3pJgbF+W6FrXovqj+T+/HpENLTooK9PnkacBsDpeP3IpHab40CClUfhNmdM2WTNP2sa2dni5Q==", + "version": "4.14.201", + "resolved": "https://registry.npmjs.org/@types/lodash/-/lodash-4.14.201.tgz", + "integrity": "sha512-y9euML0cim1JrykNxADLfaG0FgD1g/yTHwUs/Jg9ZIU7WKj2/4IW9Lbb1WZbvck78W/lfGXFfe+u2EGfIJXdLQ==", "dev": true }, "@types/mathjs": { @@ -1835,15 +1833,15 @@ "dev": true }, "@types/prop-types": { - "version": "15.7.9", - "resolved": "https://registry.npmjs.org/@types/prop-types/-/prop-types-15.7.9.tgz", - "integrity": "sha512-n1yyPsugYNSmHgxDFjicaI2+gCNjsBck8UX9kuofAKlc0h1bL+20oSF72KeNaW2DUlesbEVCFgyV2dPGTiY42g==", + "version": "15.7.10", + "resolved": "https://registry.npmjs.org/@types/prop-types/-/prop-types-15.7.10.tgz", + "integrity": "sha512-mxSnDQxPqsZxmeShFH+uwQ4kO4gcJcGahjjMFeLbKE95IAZiiZyiEepGZjtXJ7hN/yfu0bu9xN2ajcU0JcxX6A==", "dev": true }, "@types/react": { - "version": "18.2.36", - "resolved": "https://registry.npmjs.org/@types/react/-/react-18.2.36.tgz", - "integrity": "sha512-o9XFsHYLLZ4+sb9CWUYwHqFVoG61SesydF353vFMMsQziiyRu8np4n2OYMUSDZ8XuImxDr9c5tR7gidlH29Vnw==", + "version": "18.2.37", + "resolved": "https://registry.npmjs.org/@types/react/-/react-18.2.37.tgz", + "integrity": "sha512-RGAYMi2bhRgEXT3f4B92WTohopH6bIXw05FuGlmJEnv/omEn190+QYEIYxIAuIBdKgboYYdVved2p1AxZVQnaw==", "dev": true, "requires": { "@types/prop-types": "*", @@ -1852,9 +1850,9 @@ } }, "@types/react-jsonschema-form": { - "version": "1.7.10", - "resolved": "https://registry.npmjs.org/@types/react-jsonschema-form/-/react-jsonschema-form-1.7.10.tgz", - "integrity": "sha512-WycAa8c+f78wYVvEgCoN7Pv6u8t8LN2rgZirv898OWFAXSK96QXH1v0FnJvHvhdTqG7ap/Mk/ODaSZK2Aa0XLw==", + "version": "1.7.11", + "resolved": "https://registry.npmjs.org/@types/react-jsonschema-form/-/react-jsonschema-form-1.7.11.tgz", + "integrity": "sha512-VB7XtmxpU9alrhdXC250vn+UDKFglHnaYvER5eQjcolCtyiQGsSIenbfDwQDDatCxaGC7n6PIM+dOUJ0TcU+5A==", "dev": true, "requires": { "@types/json-schema": "*", @@ -1862,9 +1860,9 @@ } }, "@types/scheduler": { - 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"@exabyte-io/code.js": "git+https://github.com/Exabyte-io/code.js.git#update/SOF-6922", + "@exabyte-io/code.js": "git+https://github.com/Exabyte-io/code.js.git#update/SOF-7096", "@exabyte-io/eslint-config": "^2023.8.29-1", "@typescript-eslint/eslint-plugin": "^5.56.0", "@typescript-eslint/parser": "^5.56.0", @@ -47,10 +47,10 @@ "husky": "^7.0.4", "lint-staged": "^12.1.2", "mocha": "^9.1.3", - "nyc": "^15.1.0", "prettier": "^2.5.1" }, "dependencies": { + "@babel/core": "^7.16.0", "@exabyte-io/periodic-table.js": "2022.5.28-0", "@types/chai": "^4.3.5", "@types/mocha": "^10.0.1", @@ -61,7 +61,6 @@ "crypto-js": "^3.1.9-1", "lodash": "^4.17.4", "mathjs": "^3.9.0", - "mixwith": "^0.1.1", "typescript": "^4.5.5", "underscore": "^1.8.3", "underscore.string": "^3.3.4" From 0af2bac2a67bb014806c54e9ffe01aecb0b0d962 Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Fri, 10 Nov 2023 15:00:16 +0200 Subject: [PATCH 09/18] chore: use ne clone from in_memory --- package-lock.json | 717 +--------------------------------------------- src/material.ts | 3 +- 2 files changed, 4 insertions(+), 716 deletions(-) diff --git a/package-lock.json b/package-lock.json index 24578790..8e5c8ab0 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1560,95 +1560,6 @@ "integrity": "sha512-ZnQMnLV4e7hDlUvw8H+U8ASL02SS2Gn6+9Ac3wGGLIe7+je2AeAOxPY+izIPJDfFDb7eDjev0Us8MO1iFRN8hA==", "dev": true }, - 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"locate-path": "^5.0.0", - "path-exists": "^4.0.0" - } - }, - "js-yaml": { - "version": "3.14.1", - "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.14.1.tgz", - "integrity": "sha512-okMH7OXXJ7YrN9Ok3/SXrnu4iX9yOk+25nqX4imS2npuvTYDmo/QEZoqwZkYaIDk3jVvBOTOIEgEhaLOynBS9g==", - "dev": true, - "requires": { - "argparse": "^1.0.7", - "esprima": "^4.0.0" - } - }, - "locate-path": { - "version": "5.0.0", - "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-5.0.0.tgz", - "integrity": "sha512-t7hw9pI+WvuwNJXwk5zVHpyhIqzg2qTlklJOf0mVxGSbe3Fp2VieZcduNYjaLDoy6p9uGpQEGWG87WpMKlNq8g==", - "dev": true, - "requires": { - "p-locate": "^4.1.0" - } - }, - "p-limit": { - "version": "2.3.0", - "resolved": "https://registry.npmjs.org/p-limit/-/p-limit-2.3.0.tgz", - "integrity": "sha512-//88mFWSJx8lxCzwdAABTJL2MyWB12+eIY7MDL2SqLmAkeKU9qxRvWuSyTjm3FUmpBEMuFfckAIqEaVGUDxb6w==", - "dev": true, - "requires": { - "p-try": "^2.0.0" - } - }, - "p-locate": { - "version": "4.1.0", - "resolved": "https://registry.npmjs.org/p-locate/-/p-locate-4.1.0.tgz", - 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const material = this.clone(); + const material: Material = this.clone(); // if conventional and primitive cells are the same => return a copy. if (isConventionalCellSameAsPrimitiveForLatticeType(this.Lattice.type)) return material; From f955a7fc54df82b43178959932f7c103621bf46e Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Fri, 10 Nov 2023 16:29:07 +0200 Subject: [PATCH 10/18] chore: use types from esse --- package-lock.json | 6539 --------------------- src/cell/conventional_cell.ts | 6 +- src/cell/primitive_cell.ts | 35 +- src/lattice/lattice.ts | 17 +- src/lattice/lattice_bravais.ts | 45 +- src/lattice/lattice_vectors.ts | 33 +- src/lattice/reciprocal/symmetry_points.ts | 19 +- src/lattice/types.ts | 10 +- 8 files changed, 72 insertions(+), 6632 deletions(-) delete mode 100644 package-lock.json diff --git a/package-lock.json b/package-lock.json deleted file mode 100644 index 8e5c8ab0..00000000 --- a/package-lock.json +++ /dev/null @@ -1,6539 +0,0 @@ -{ - "name": "@exabyte-io/made.js", - 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(2010). doi:10.1016/j.commatsci.2010.05.010 */ const PRIMITIVE_CELLS = { - [LatticeType.CUB]: ({ a }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.CUB]: ({ a }: LatticeImplicitSchema): VectorsAsArray => { return [ [a, 0, 0], [0, a, 0], @@ -16,7 +17,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.FCC]: ({ a }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.FCC]: ({ a }: LatticeImplicitSchema): VectorsAsArray => { return [ [0.0, a / 2, a / 2], [a / 2, 0.0, a / 2], @@ -24,7 +25,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.BCC]: ({ a }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.BCC]: ({ a }: LatticeImplicitSchema): VectorsAsArray => { return [ [-a / 2, a / 2, a / 2], [a / 2, -a / 2, a / 2], @@ -32,7 +33,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.TET]: ({ a, c }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.TET]: ({ a, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [a, 0, 0], [0, a, 0], @@ -40,7 +41,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.BCT]: ({ a, c }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.BCT]: ({ a, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [-a / 2, a / 2, c / 2], [a / 2, -a / 2, c / 2], @@ -48,7 +49,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.ORC]: ({ a, b, c }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.ORC]: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [a, 0, 0], [0, b, 0], @@ -56,7 +57,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.ORCF]: ({ a, b, c }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.ORCF]: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [0, b / 2, c / 2], [a / 2, 0, c / 2], @@ -64,7 +65,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.ORCI]: ({ a, b, c }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.ORCI]: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [-a / 2, b / 2, c / 2], [a / 2, -b / 2, c / 2], @@ -72,7 +73,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.ORCC]: ({ a, b, c }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.ORCC]: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [a / 2, b / 2, 0], [-a / 2, b / 2, 0], @@ -80,7 +81,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.HEX]: ({ a, c }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.HEX]: ({ a, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [a / 2, (-a * math.sqrt(3)) / 2, 0], [a / 2, (a * math.sqrt(3)) / 2, 0], @@ -88,7 +89,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.RHL]: ({ a, alpha }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.RHL]: ({ a, alpha }: LatticeImplicitSchema): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); const cosHalfAlpha = math.sqrt((1 / 2) * (1 + cosAlpha)); const sinHalfAlpha = math.sqrt((1 / 2) * (1 - cosAlpha)); @@ -103,7 +104,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.MCL]: ({ a, b, c, alpha }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.MCL]: ({ a, b, c, alpha }: LatticeImplicitSchema): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); return [ [a, 0, 0], @@ -112,7 +113,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.MCLC]: ({ a, b, c, alpha }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.MCLC]: ({ a, b, c, alpha }: LatticeImplicitSchema): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); return [ [a / 2, b / 2, 0], @@ -122,7 +123,7 @@ const PRIMITIVE_CELLS = { }, // Algorithm from http://pymatgen.org/_modules/pymatgen/core/lattice.html (from_params) - [LatticeType.TRI]: ({ a, b, c, alpha, beta, gamma }: RequiredBravaisConfig): VectorsAsArray => { + [LatticeType.TRI]: ({ a, b, c, alpha, beta, gamma }: LatticeImplicitSchema): VectorsAsArray => { // convert angles to Radians // eslint-disable-next-line no-param-reassign [alpha, beta, gamma] = [alpha, beta, gamma].map( @@ -151,7 +152,7 @@ const PRIMITIVE_CELLS = { alpha, beta, gamma, - }: RequiredBravaisConfig): VectorsAsArray => { + }: LatticeImplicitSchema): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); const cosBeta = math.cos((beta / 180) * math.PI); const cosGamma = math.cos((gamma / 180) * math.PI); @@ -181,7 +182,7 @@ const PRIMITIVE_CELLS = { * @return Cell.vectorsAsArray */ export function primitiveCell( - lattice: RequiredBravaisConfig, + lattice: LatticeImplicitSchema, skipRounding = false, ): VectorsAsArray { const [vectorA, vectorB, vectorC] = PRIMITIVE_CELLS[lattice.type || LatticeType.TRI](lattice); diff --git a/src/lattice/lattice.ts b/src/lattice/lattice.ts index 41f5690c..f0ab22e1 100644 --- a/src/lattice/lattice.ts +++ b/src/lattice/lattice.ts @@ -1,3 +1,4 @@ +import { LatticeImplicitSchema } from "@exabyte-io/code.js/src/types"; import lodash from "lodash"; import _ from "underscore"; @@ -5,17 +6,13 @@ import { Cell } from "../cell/cell"; import { primitiveCell } from "../cell/primitive_cell"; import { HASH_TOLERANCE } from "../constants"; import math from "../math"; -import { FromVectorsProps, LatticeBravais, RequiredBravaisConfig } from "./lattice_bravais"; -import { - BravaisConfigProps, - LatticeVectors, - RequiredLatticeVectorsConfig, -} from "./lattice_vectors"; +import { FromVectorsProps, LatticeBravais, RequiredLatticeImplicitSchema } from "./lattice_bravais"; +import { BravaisConfigProps, LatticeVectors, RequiredLatticeExplicitUnit } from "./lattice_vectors"; import { LATTICE_TYPE_CONFIGS, LatticeType, LatticeTypeExtended } from "./types"; import { UnitCell, UnitCellProps } from "./unit_cell"; -export interface RequiredBravaisConfigWithVectors extends RequiredBravaisConfig { - vectors: RequiredLatticeVectorsConfig; +export interface RequiredBravaisConfigWithVectors extends RequiredLatticeImplicitSchema { + vectors: RequiredLatticeExplicitUnit; } export type LatticeJSON = RequiredBravaisConfigWithVectors; @@ -38,7 +35,7 @@ export class Lattice extends LatticeBravais implements LatticeJSON { * Create a Lattice class from a config object. * @param {Object} config - Config object. See LatticeVectors.fromBravais. */ - constructor(config: BravaisConfigProps = {}) { + constructor(config: Partial = {}) { super(config); this.vectors = LatticeVectors.fromBravais(config); } @@ -180,7 +177,7 @@ export class Lattice extends LatticeBravais implements LatticeJSON { * Returns a "default" primitive lattice by type, with lattice parameters scaled by the length of "a", * @param latticeConfig {Object} LatticeBravais config (see constructor) */ - static getDefaultPrimitiveLatticeConfigByType(latticeConfig: RequiredBravaisConfig) { + static getDefaultPrimitiveLatticeConfigByType(latticeConfig: LatticeImplicitSchema) { const f_ = Lattice._roundValue; // construct new primitive cell using lattice parameters and skip rounding the vectors const pCell = primitiveCell(latticeConfig, true); diff --git a/src/lattice/lattice_bravais.ts b/src/lattice/lattice_bravais.ts index c9107caf..3f4a49e3 100644 --- a/src/lattice/lattice_bravais.ts +++ b/src/lattice/lattice_bravais.ts @@ -1,31 +1,19 @@ +import { LatticeImplicitSchema } from "@exabyte-io/code.js/src/types"; + import constants from "../constants"; import math from "../math"; -import { LATTICE_TYPE_CONFIGS, LatticeType, Vector, VectorsAsArray } from "./types"; - -export interface BravaisConfig { - a?: number; // lattice constant a. - b?: number; // lattice constant b. - c?: number; // lattice constant c. - alpha?: number; // lattice angle alpha. - beta?: number; // lattice angle beta. - gamma?: number; // lattice angle gamma. - units?: { - // units container - length: string; // units for length (eg. "angstrom", "crystal") - angle: string; // units for angles (eg. "degree", "radian") - }; - type?: LatticeType; -} +import { LATTICE_TYPE_CONFIGS, LatticeTypeSchema, Vector, VectorsAsArray } from "./types"; -export type RequiredBravaisConfig = Required; +export type RequiredLatticeImplicitSchema = Required; +export type Units = RequiredLatticeImplicitSchema["units"]; export interface FromVectorsProps { a: Vector; // vector of the lattice. b: Vector; // vector of the lattice. c: Vector; // vector of the lattice. alat?: number; // scaling factor for the vector coordinates, defaults to 1. - units?: string; // units for the coordinates (eg. angstrom, crystal). - type?: LatticeType; // type of the lattice to be created, defaults to TRI when not provided. + units?: Units["length"]; // units for the coordinates (eg. angstrom, crystal). + type?: LatticeTypeSchema; // type of the lattice to be created, defaults to TRI when not provided. skipRounding?: boolean; // whether to skip rounding the resulting lattice values, defaults to `false`. } @@ -33,7 +21,7 @@ export interface FromVectorsProps { * @summary: class that holds parameters of a Bravais Lattice: a, b, c, alpha, beta, gamma + corresponding units. * When stored as class variables units for lengths are always "angstrom"s, angle - "degree"s */ -export class LatticeBravais implements RequiredBravaisConfig { +export class LatticeBravais implements LatticeImplicitSchema { a: number; b: number; @@ -46,17 +34,14 @@ export class LatticeBravais implements RequiredBravaisConfig { gamma: number; - units: { - length: string; - angle: string; - }; + units: Units; - type: LatticeType; + type: LatticeImplicitSchema["type"]; /** * Create a Bravais lattice. */ - constructor(config: BravaisConfig) { + constructor(config: Partial) { const { a = 1, // default lattice is cubic with unity in edge sizes b = a, @@ -65,7 +50,7 @@ export class LatticeBravais implements RequiredBravaisConfig { beta = alpha, gamma = alpha, // if we do not know what lattice type this is => set to TRI - type = LatticeType.TRI, + type = "TRI", units = { length: "angstrom", angle: "degree", @@ -98,7 +83,7 @@ export class LatticeBravais implements RequiredBravaisConfig { c, alat = 1, units = "angstrom", - type = LatticeType.TRI, + type = "TRI", skipRounding = false, }: FromVectorsProps) { const roundValue = skipRounding ? (x: number) => x : this._roundValue; @@ -125,7 +110,7 @@ export class LatticeBravais implements RequiredBravaisConfig { /** * See fromVectors above. */ - static fromVectorArrays(array: VectorsAsArray, type: LatticeType, skipRounding = true) { + static fromVectorArrays(array: VectorsAsArray, type: LatticeTypeSchema, skipRounding = true) { return this.fromVectors({ a: array[0], b: array[1], @@ -174,7 +159,7 @@ export class LatticeBravais implements RequiredBravaisConfig { "type" : "FCC" } */ - toJSON(): RequiredBravaisConfig { + toJSON(): RequiredLatticeImplicitSchema { return { ...this, units: { diff --git a/src/lattice/lattice_vectors.ts b/src/lattice/lattice_vectors.ts index 97e29b80..2a1a5cc3 100644 --- a/src/lattice/lattice_vectors.ts +++ b/src/lattice/lattice_vectors.ts @@ -1,20 +1,13 @@ +import { LatticeExplicitUnit, LatticeImplicitSchema } from "@exabyte-io/code.js/src/types"; + import { primitiveCell } from "../cell/primitive_cell"; import constants from "../constants"; import math from "../math"; -import { BravaisConfig } from "./lattice_bravais"; import { LatticeType, Vector } from "./types"; -interface LatticeVectorsConfig { - a: Vector; // vector of the lattice. - b: Vector; // vector of the lattice. - c: Vector; // vector of the lattice. - alat: number; // scaling factor for the vector coordinates, defaults to 1. - units?: string; // units container. -} - -export type RequiredLatticeVectorsConfig = Required; +export type RequiredLatticeExplicitUnit = Required; -export interface BravaisConfigProps extends BravaisConfig { +export interface BravaisConfigProps extends Partial { isConventional?: boolean; } @@ -22,21 +15,21 @@ export interface BravaisConfigProps extends BravaisConfig { * @summary: class that holds parameters of a Bravais Lattice: a, b, c, alpha, beta, gamma + corresponding units. * When stored as class variables units for lengths are always "angstrom"s, angle - "degree"s */ -export class LatticeVectors implements LatticeVectorsConfig { - a: Vector; +export class LatticeVectors implements RequiredLatticeExplicitUnit { + a: RequiredLatticeExplicitUnit["a"]; - b: Vector; + b: RequiredLatticeExplicitUnit["b"]; - c: Vector; + c: RequiredLatticeExplicitUnit["c"]; - alat: number; + alat: RequiredLatticeExplicitUnit["alat"]; - units: string; + units: RequiredLatticeExplicitUnit["units"]; /** * Create a Bravais lattice. */ - constructor(config: LatticeVectorsConfig) { + constructor(config: LatticeExplicitUnit) { const { a, b, c, alat = 1, units = "angstrom" } = config; const k = constants.units.bohr === units ? constants.coefficients.BOHR_TO_ANGSTROM : 1; @@ -47,7 +40,7 @@ export class LatticeVectors implements LatticeVectorsConfig { this.units = "angstrom"; } - static _roundValue(arr: number[]) { + static _roundValue(arr: number[]): number[] { return arr.map((el) => math.precise(math.roundToZero(el))); } @@ -122,7 +115,7 @@ export class LatticeVectors implements LatticeVectorsConfig { "units" : "angstrom" } */ - toJSON(): RequiredLatticeVectorsConfig { + toJSON(): RequiredLatticeExplicitUnit { return { ...this, a: LatticeVectors._roundValue(this.a), diff --git a/src/lattice/reciprocal/symmetry_points.ts b/src/lattice/reciprocal/symmetry_points.ts index d814ba6d..ba31c26d 100644 --- a/src/lattice/reciprocal/symmetry_points.ts +++ b/src/lattice/reciprocal/symmetry_points.ts @@ -4,8 +4,9 @@ * This file contains information about the Brillouin zone symmetry points by lattice type. * [AFLOW](https://arxiv.org/abs/1004.2974) methodology is used for implementation. */ +import { LatticeImplicitSchema } from "@exabyte-io/code.js/src/types"; + import { Lattice } from "../lattice"; -import { RequiredBravaisConfig } from "../lattice_bravais"; import { LatticeType } from "../types"; const POINTS = { @@ -93,7 +94,7 @@ const POINTS = { ]; }, - [LatticeType.BCT]: ({ a, c }: RequiredBravaisConfig) => { + [LatticeType.BCT]: ({ a, c }: LatticeImplicitSchema) => { let n; if (c < a) { // BCT-1 @@ -197,7 +198,7 @@ const POINTS = { ]; }, - [LatticeType.ORCF]: ({ a, b, c }: RequiredBravaisConfig) => { + [LatticeType.ORCF]: ({ a, b, c }: LatticeImplicitSchema) => { let n; if (1 / (a * a) >= 1 / (b * b) + 1 / (c * c)) { // ORCF-1,3 @@ -286,7 +287,7 @@ const POINTS = { ]; }, - [LatticeType.ORCI]: ({ a, b, c }: RequiredBravaisConfig) => { + [LatticeType.ORCI]: ({ a, b, c }: LatticeImplicitSchema) => { const n = (1 + (a * a) / (c * c)) / 4; const e = (1 + (b * b) / (c * c)) / 4; const d = (b * b - a * a) / (4 * c * c); @@ -343,7 +344,7 @@ const POINTS = { ]; }, - [LatticeType.ORCC]: ({ a, b }: RequiredBravaisConfig) => { + [LatticeType.ORCC]: ({ a, b }: LatticeImplicitSchema) => { const e = (1 + (a * a) / (b * b)) / 4; return [ { @@ -410,7 +411,7 @@ const POINTS = { ]; }, - [LatticeType.RHL]: ({ alpha }: RequiredBravaisConfig) => { + [LatticeType.RHL]: ({ alpha }: LatticeImplicitSchema) => { let n, v; const cosAlpha = Math.cos((alpha / 180) * Math.PI); if (cosAlpha > 0) { @@ -499,7 +500,7 @@ const POINTS = { ]; }, - [LatticeType.MCL]: ({ b, c, alpha }: RequiredBravaisConfig) => { + [LatticeType.MCL]: ({ b, c, alpha }: LatticeImplicitSchema) => { const cosAlpha = Math.cos((alpha / 180) * Math.PI); const n = ((1 / 2) * (1 - (b * cosAlpha) / c)) / (1 - cosAlpha * cosAlpha); const v = 1 / 2 - (n * c * cosAlpha) / b; @@ -567,7 +568,7 @@ const POINTS = { ]; }, - [LatticeType.MCLC]: ({ a, b, c, alpha, gamma }: RequiredBravaisConfig) => { + [LatticeType.MCLC]: ({ a, b, c, alpha, gamma }: LatticeImplicitSchema) => { const cosAlpha = Math.cos((alpha / 180) * Math.PI); let e, n, p, f, m, d, v; if (gamma >= 90) { @@ -805,7 +806,7 @@ const POINTS = { ]; }, - [LatticeType.TRI]: ({ alpha, beta, gamma }: RequiredBravaisConfig) => { + [LatticeType.TRI]: ({ alpha, beta, gamma }: LatticeImplicitSchema) => { if (alpha > 90 && beta > 90 && gamma >= 90) { // TRI-1a,2a return [ diff --git a/src/lattice/types.ts b/src/lattice/types.ts index 2ada091b..d9174107 100644 --- a/src/lattice/types.ts +++ b/src/lattice/types.ts @@ -1,3 +1,5 @@ +import { ArrayOf3NumberElementsSchema, LatticeImplicitSchema } from "@exabyte-io/code.js/src/types"; + export const DEFAULT_LATTICE_UNITS = { // by default lattice vectors shall be measured in angstrom, angles - in degrees length: { @@ -33,6 +35,8 @@ export enum LatticeType { TRI = "TRI", } +export type LatticeTypeSchema = LatticeImplicitSchema["type"]; + export enum LatticeTypeExtended { BCC = "BCC", BCT_1 = "BCT-1", @@ -60,11 +64,7 @@ export enum LatticeTypeExtended { TRI_1b = "TRI_1b", } -export interface Vector extends Array { - 0: number; - 1: number; - 2: number; -} +export type Vector = ArrayOf3NumberElementsSchema; export interface VectorsAsArray extends Array { 0: Vector; From 694d4fe0bac5cfbdd0a85aea05de6403100666aa Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Fri, 10 Nov 2023 19:33:51 +0200 Subject: [PATCH 11/18] chore: use types from esse --- src/basis/basis.ts | 9 +++++---- src/basis/constrained_basis.ts | 5 +++-- src/basis/types.ts | 6 +----- src/cell/cell.ts | 6 +++--- src/lattice/lattice.ts | 17 ++++++----------- src/lattice/lattice_bravais.ts | 5 ++--- src/lattice/lattice_vectors.ts | 2 +- src/lattice/types.ts | 1 - src/parsers/espresso.ts | 3 ++- src/parsers/poscar.ts | 1 + src/parsers/xyz.ts | 4 +++- src/types.ts | 11 ++--------- 12 files changed, 29 insertions(+), 41 deletions(-) diff --git a/src/basis/basis.ts b/src/basis/basis.ts index f56c01e6..49f9f244 100644 --- a/src/basis/basis.ts +++ b/src/basis/basis.ts @@ -1,3 +1,4 @@ +// import { BasisSchema } from "@exabyte-io/code.js/src/types"; // @ts-ignore import { getElectronegativity, getElementAtomicRadius } from "@exabyte-io/periodic-table.js"; import _ from "underscore"; @@ -30,7 +31,7 @@ export interface ElementCount { value: string; } -export interface BasisJSON { +export interface BasisSchema { elements: ObjectWithIdAndValue[]; coordinates: ObjectWithIdAndValue[]; units: string; @@ -142,8 +143,8 @@ export class Basis { ] } */ - toJSON(): BasisJSON { - const json: BasisJSON = { + toJSON(): BasisSchema { + const json = { elements: this.elements, coordinates: this.coordinates, units: this.units, @@ -243,7 +244,7 @@ export class Basis { } /** A representation where all coordinates are within 0 and 1 in crystal units */ - get standardRepresentation(): BasisJSON { + get standardRepresentation(): BasisSchema { const originalUnits = this.units; this.toStandardRepresentation(); diff --git a/src/basis/constrained_basis.ts b/src/basis/constrained_basis.ts index 7bcc8243..6b7609a3 100644 --- a/src/basis/constrained_basis.ts +++ b/src/basis/constrained_basis.ts @@ -1,16 +1,17 @@ +// import { BasisSchema } from "@exabyte-io/code.js/src/types"; import s from "underscore.string"; import { ArrayWithIds } from "../abstract/array_with_ids"; import { ObjectWithIdAndValue } from "../abstract/scalar_with_id"; import { AtomicConstraints, Constraint, ConstraintValue } from "../constraints/constraints"; -import { Basis, BasisJSON, BasisProps } from "./basis"; +import { Basis, BasisProps, BasisSchema } from "./basis"; import { Coordinate } from "./types"; export interface ConstrainedBasisProps extends BasisProps { constraints: Constraint[]; } -export interface ConstrainedBasisJSON extends BasisJSON { +export interface ConstrainedBasisJSON extends BasisSchema { constraints: ObjectWithIdAndValue[]; } diff --git a/src/basis/types.ts b/src/basis/types.ts index 1f98194a..b3f7b083 100644 --- a/src/basis/types.ts +++ b/src/basis/types.ts @@ -1,5 +1 @@ -export interface Coordinate extends Array { - 0: number; - 1: number; - 2: number; -} +export type Coordinate = [number, number, number]; diff --git a/src/cell/cell.ts b/src/cell/cell.ts index 7a9886ca..031836c0 100644 --- a/src/cell/cell.ts +++ b/src/cell/cell.ts @@ -1,6 +1,6 @@ import { Coordinate } from "../basis/types"; import constants from "../constants"; -import { Vector } from "../lattice/types"; +import { Vector, VectorsAsArray } from "../lattice/types"; import math from "../math"; const MATRIX = math.matrix; @@ -28,7 +28,7 @@ export class Cell { * Create a cell. * @param nestedArray {Number[][]} is an array of cell vectors in cartesian Angstrom units. */ - constructor(nestedArray: [Vector, Vector, Vector]) { + constructor(nestedArray: VectorsAsArray) { [this.vector1, this.vector2, this.vector3] = nestedArray; } @@ -36,7 +36,7 @@ export class Cell { * Get cell vectors as (a nested) array. * @example [[1, 0, 0], [0, 1, 0], [0, 0, 1]] */ - get vectorsAsArray(): [Vector, Vector, Vector] { + get vectorsAsArray(): VectorsAsArray { return [ this.vector1, this.vector2, diff --git a/src/lattice/lattice.ts b/src/lattice/lattice.ts index f0ab22e1..61560852 100644 --- a/src/lattice/lattice.ts +++ b/src/lattice/lattice.ts @@ -1,4 +1,4 @@ -import { LatticeImplicitSchema } from "@exabyte-io/code.js/src/types"; +import { LatticeImplicitSchema, LatticeSchema } from "@exabyte-io/code.js/src/types"; import lodash from "lodash"; import _ from "underscore"; @@ -6,17 +6,11 @@ import { Cell } from "../cell/cell"; import { primitiveCell } from "../cell/primitive_cell"; import { HASH_TOLERANCE } from "../constants"; import math from "../math"; -import { FromVectorsProps, LatticeBravais, RequiredLatticeImplicitSchema } from "./lattice_bravais"; -import { BravaisConfigProps, LatticeVectors, RequiredLatticeExplicitUnit } from "./lattice_vectors"; +import { FromVectorsProps, LatticeBravais } from "./lattice_bravais"; +import { BravaisConfigProps, LatticeVectors } from "./lattice_vectors"; import { LATTICE_TYPE_CONFIGS, LatticeType, LatticeTypeExtended } from "./types"; import { UnitCell, UnitCellProps } from "./unit_cell"; -export interface RequiredBravaisConfigWithVectors extends RequiredLatticeImplicitSchema { - vectors: RequiredLatticeExplicitUnit; -} - -export type LatticeJSON = RequiredBravaisConfigWithVectors; - /** * Scaling factor used to calculate the new lattice size for non-periodic systems. * The scaling factor ensures that a non-periodic structure will have have a lattice greater than the structures size. @@ -28,7 +22,7 @@ export const nonPeriodicLatticeScalingFactor = 2.0; * Follows Bravais convention for lattice types and contains lattice vectors within. * Units for lattice vector coordinates are "angstroms", and "degrees" for the corresponding angles. */ -export class Lattice extends LatticeBravais implements LatticeJSON { +export class Lattice extends LatticeBravais implements LatticeSchema { vectors: LatticeVectors; /** @@ -84,8 +78,9 @@ export class Lattice extends LatticeBravais implements LatticeJSON { } } */ - toJSON(skipRounding = false): LatticeJSON { + toJSON(skipRounding = false): LatticeSchema { const round = skipRounding ? (x: number) => x : Lattice._roundValue; // round values by default + return { a: round(this.a), b: round(this.b), diff --git a/src/lattice/lattice_bravais.ts b/src/lattice/lattice_bravais.ts index 3f4a49e3..9fe2781d 100644 --- a/src/lattice/lattice_bravais.ts +++ b/src/lattice/lattice_bravais.ts @@ -4,8 +4,7 @@ import constants from "../constants"; import math from "../math"; import { LATTICE_TYPE_CONFIGS, LatticeTypeSchema, Vector, VectorsAsArray } from "./types"; -export type RequiredLatticeImplicitSchema = Required; -export type Units = RequiredLatticeImplicitSchema["units"]; +export type Units = Required["units"]; export interface FromVectorsProps { a: Vector; // vector of the lattice. @@ -159,7 +158,7 @@ export class LatticeBravais implements LatticeImplicitSchema { "type" : "FCC" } */ - toJSON(): RequiredLatticeImplicitSchema { + toJSON(): LatticeImplicitSchema { return { ...this, units: { diff --git a/src/lattice/lattice_vectors.ts b/src/lattice/lattice_vectors.ts index 2a1a5cc3..98eea64b 100644 --- a/src/lattice/lattice_vectors.ts +++ b/src/lattice/lattice_vectors.ts @@ -5,7 +5,7 @@ import constants from "../constants"; import math from "../math"; import { LatticeType, Vector } from "./types"; -export type RequiredLatticeExplicitUnit = Required; +type RequiredLatticeExplicitUnit = Required; export interface BravaisConfigProps extends Partial { isConventional?: boolean; diff --git a/src/lattice/types.ts b/src/lattice/types.ts index d9174107..c4659244 100644 --- a/src/lattice/types.ts +++ b/src/lattice/types.ts @@ -15,7 +15,6 @@ export const DEFAULT_LATTICE_UNITS = { * Convention used is derived from: * Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: * Challenges and tools. Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010 - * Lattice parameters a, b, c are stored for CONVENTIONAL lattice, however the default unit cell is calculated for */ export enum LatticeType { diff --git a/src/parsers/espresso.ts b/src/parsers/espresso.ts index bc111bb5..2b33af56 100644 --- a/src/parsers/espresso.ts +++ b/src/parsers/espresso.ts @@ -1,3 +1,4 @@ +import { MaterialSchema } from "@exabyte-io/code.js/src/types"; import _ from "underscore"; import s from "underscore.string"; @@ -9,7 +10,7 @@ import xyz from "./xyz"; * Construct textual representation of a materialOrConfig according to Quantum ESPRESSO pw.x input format. * @param materialOrConfig - material class instance or its config object */ -function toEspressoFormat(materialOrConfig: MaterialJSON): string { +function toEspressoFormat(materialOrConfig: MaterialSchema): string { const l = new Lattice(materialOrConfig.lattice); const vectors = l.vectorArrays; const vectorsAsString = _.map(vectors, (v) => { diff --git a/src/parsers/poscar.ts b/src/parsers/poscar.ts index d4a5266f..e061d133 100644 --- a/src/parsers/poscar.ts +++ b/src/parsers/poscar.ts @@ -22,6 +22,7 @@ const atomicConstraintsCharFromBool = (bool: boolean): string => (bool ? "T" : " function toPoscar(materialOrConfig: MaterialJSON, omitConstraints = false): string { const lattice = new Lattice(materialOrConfig.lattice); const vectorsAsString = _latticeVectorsToString(lattice.vectorArrays); + // @ts-ignore const basis = new ConstrainedBasis({ ...materialOrConfig.basis, cell: lattice.vectorArrays, diff --git a/src/parsers/xyz.ts b/src/parsers/xyz.ts index 5bf988b1..8e857b4d 100644 --- a/src/parsers/xyz.ts +++ b/src/parsers/xyz.ts @@ -1,3 +1,4 @@ +import { MaterialSchema } from "@exabyte-io/code.js/src/types"; import _ from "underscore"; import s from "underscore.string"; @@ -151,8 +152,9 @@ function fromBasis( * @param fractional Coordinate units as fractional. * @return Class Instance */ -function fromMaterial(materialOrConfig: MaterialJSON, fractional = false): string { +function fromMaterial(materialOrConfig: MaterialSchema, fractional = false): string { const lattice = new Lattice(materialOrConfig.lattice); + // @ts-ignore const basis = new ConstrainedBasis({ ...materialOrConfig.basis, cell: lattice.vectorArrays, diff --git a/src/types.ts b/src/types.ts index dd673d13..8de80ead 100644 --- a/src/types.ts +++ b/src/types.ts @@ -1,11 +1,4 @@ import { AnyObject } from "@exabyte-io/code.js/dist/entity/in_memory"; +import { MaterialSchema } from "@exabyte-io/code.js/src/types"; -import { ConstrainedBasisJSON } from "./basis/constrained_basis"; -import { LatticeJSON } from "./lattice/lattice"; - -export interface MaterialJSON extends AnyObject { - lattice: LatticeJSON; - basis: ConstrainedBasisJSON; - name: string; - isNonPeriodic: boolean; -} +export type MaterialJSON = MaterialSchema & AnyObject; From 57c8cc5b77fffdb7b7575a52496e6fc743f0309a Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Fri, 10 Nov 2023 19:39:36 +0200 Subject: [PATCH 12/18] chore: use latest exabyte eslint --- package-lock.json | 4855 +++++++++++++++++++++++++++++++++++++++++++++ package.json | 12 - 2 files changed, 4855 insertions(+), 12 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"resolved": "https://registry.npmjs.org/underscore/-/underscore-1.13.6.tgz", @@ -4741,6 +6218,32 @@ "isexe": "^2.0.0" } }, + "which-boxed-primitive": { + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/which-boxed-primitive/-/which-boxed-primitive-1.0.2.tgz", + "integrity": "sha512-bwZdv0AKLpplFY2KZRX6TvyuN7ojjr7lwkg6ml0roIy9YeuSr7JS372qlNW18UQYzgYK9ziGcerWqZOmEn9VNg==", + "dev": true, + "requires": { + "is-bigint": "^1.0.1", + "is-boolean-object": "^1.1.0", + "is-number-object": "^1.0.4", + "is-string": "^1.0.5", + "is-symbol": "^1.0.3" + } + }, + "which-typed-array": { + "version": "1.1.13", + "resolved": "https://registry.npmjs.org/which-typed-array/-/which-typed-array-1.1.13.tgz", + "integrity": "sha512-P5Nra0qjSncduVPEAr7xhoF5guty49ArDTwzJ/yNuPIbZppyRxFQsRCWrocxIY+CnMVG+qfbU2FmDKyvSGClow==", + "dev": true, + "requires": { + "available-typed-arrays": "^1.0.5", + "call-bind": "^1.0.4", + "for-each": "^0.3.3", + "gopd": "^1.0.1", + "has-tostringtag": "^1.0.0" + } + }, "workerpool": { "version": "6.2.0", "resolved": "https://registry.npmjs.org/workerpool/-/workerpool-6.2.0.tgz", diff --git a/package.json b/package.json index ed7b6935..3e44cb35 100644 --- a/package.json +++ b/package.json @@ -27,11 +27,31 @@ "node": ">=0.12" }, "devDependencies": { + "@babel/eslint-parser": "^7.16.3", + "@babel/plugin-proposal-class-properties": "^7.16.0", + "@babel/preset-env": "^7.16.4", + "@babel/preset-react": "^7.16.7", + "@babel/register": "^7.22.15", + "@babel/runtime-corejs3": "^7.16.8", "@exabyte-io/code.js": "git+https://github.com/Exabyte-io/code.js.git#update/SOF-7096", "@exabyte-io/eslint-config": "^2023.8.29-1", + "@typescript-eslint/eslint-plugin": "^5.9.1", + "@typescript-eslint/parser": "^5.9.1", "chai": "^4.3.4", "chai-almost": "^1.0.1", - "eslint": "7.32.0", + "eslint": "^7.32.0", + "eslint-config-airbnb": "^19.0.2", + "eslint-config-prettier": "^8.5.0", + "eslint-import-resolver-exports": "^1.0.0-beta.5", + "eslint-import-resolver-meteor": "^0.4.0", + "eslint-import-resolver-node": "^0.3.9", + "eslint-plugin-import": "^2.25.3", + "eslint-plugin-jsdoc": "^37.1.0", + "eslint-plugin-jsx-a11y": "^6.5.1", + "eslint-plugin-mui-path-imports": "0.0.15", + "eslint-plugin-prettier": "^4.2.1", + "eslint-plugin-react": "^7.30.0", + "eslint-plugin-simple-import-sort": "^7.0.0", "husky": "^7.0.4", "lint-staged": "^12.1.2", "mocha": "^9.1.3", diff --git a/src/parsers/espresso.ts b/src/parsers/espresso.ts index 2b33af56..946bf40c 100644 --- a/src/parsers/espresso.ts +++ b/src/parsers/espresso.ts @@ -3,7 +3,6 @@ import _ from "underscore"; import s from "underscore.string"; import { Lattice } from "../lattice/lattice"; -import { MaterialJSON } from "../types"; import xyz from "./xyz"; /** diff --git a/src/parsers/xyz.ts b/src/parsers/xyz.ts index 8e857b4d..fa281ec6 100644 --- a/src/parsers/xyz.ts +++ b/src/parsers/xyz.ts @@ -8,7 +8,6 @@ import { Constraint } from "../constraints/constraints"; import { Lattice } from "../lattice/lattice"; import { Vector } from "../lattice/types"; import math from "../math"; -import { MaterialJSON } from "../types"; import { InvalidLineError } from "./errors"; import { CombinatorialBasis } from "./xyz_combinatorial_basis"; From 7cd2b3cf5b8c983fd80cb6b11f245a1fc7dba21a Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Thu, 30 Nov 2023 16:12:49 +0200 Subject: [PATCH 14/18] chore: use more esse types --- src/cell/conventional_cell.ts | 68 ++++++++++++----------- src/cell/primitive_cell.ts | 43 ++++++-------- src/lattice/lattice.ts | 38 +++++++------ src/lattice/lattice_bravais.ts | 4 +- src/lattice/lattice_vectors.ts | 6 +- src/lattice/reciprocal/symmetry_points.ts | 29 +++++----- src/lattice/types.ts | 58 ++++++------------- src/material.ts | 27 ++++----- 8 files changed, 121 insertions(+), 152 deletions(-) diff --git a/src/cell/conventional_cell.ts b/src/cell/conventional_cell.ts index 36ebb1cb..e8ab9194 100644 --- a/src/cell/conventional_cell.ts +++ b/src/cell/conventional_cell.ts @@ -1,4 +1,4 @@ -import { LatticeType, LatticeTypeSchema } from "../lattice/types"; +import { LatticeTypeSchema } from "@exabyte-io/code.js/src/types"; /** * Routines for calculating conventional cell vectors from primitive cell Bravais parameters. @@ -14,74 +14,76 @@ const unitMatrix = [ // (Conventional cellVectors) = (Primitive cellVectors) * (PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIER matrix) export const PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS = { // PRIMITIVE => CONVENTIONAL - [LatticeType.CUB]: unitMatrix, - [LatticeType.FCC]: [ + CUB: unitMatrix, + FCC: [ [-1, 1, 1], [1, -1, 1], [1, 1, -1], ], - [LatticeType.BCC]: [ + BCC: [ [0, 1, 1], [1, 0, 1], [1, 1, 0], ], - [LatticeType.TET]: unitMatrix, - [LatticeType.BCT]: [ + TET: unitMatrix, + BCT: [ [0, 1, 1], [1, 0, 1], [1, 1, 0], ], - [LatticeType.ORC]: unitMatrix, - [LatticeType.ORCF]: [ + ORC: unitMatrix, + ORCF: [ [-1, 1, 1], [1, -1, 1], [1, 1, -1], ], - [LatticeType.ORCI]: [ + ORCI: [ [0, 1, 1], [1, 0, 1], [1, 1, 0], ], - [LatticeType.ORCC]: [ + ORCC: [ [1, -1, 0], [1, 1, 0], [0, 0, 1], ], - [LatticeType.HEX]: unitMatrix, - [LatticeType.RHL]: unitMatrix, - [LatticeType.MCL]: unitMatrix, - [LatticeType.MCLC]: [ + HEX: unitMatrix, + RHL: unitMatrix, + MCL: unitMatrix, + MCLC: [ [1, -1, 0], [1, 1, 0], [0, 0, 1], ], - [LatticeType.TRI]: unitMatrix, - [`${LatticeType.TRI}alt`]: unitMatrix, + TRI: unitMatrix, + TRIalt: unitMatrix, }; -export const PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES = { +export const PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES: { + [key in LatticeTypeSchema | "TRIalt"]: LatticeTypeSchema; +} = { // PRIMITIVE => CONVENTIONAL - [LatticeType.CUB]: LatticeType.CUB, - [LatticeType.FCC]: LatticeType.CUB, - [LatticeType.BCC]: LatticeType.CUB, - [LatticeType.TET]: LatticeType.TET, - [LatticeType.BCT]: LatticeType.TET, - [LatticeType.ORC]: LatticeType.ORC, - [LatticeType.ORCF]: LatticeType.ORC, - [LatticeType.ORCI]: LatticeType.ORC, - [LatticeType.ORCC]: LatticeType.ORC, - [LatticeType.HEX]: LatticeType.HEX, - [LatticeType.RHL]: LatticeType.RHL, - [LatticeType.MCL]: LatticeType.MCL, - [LatticeType.MCLC]: LatticeType.MCL, - [LatticeType.TRI]: LatticeType.TRI, + CUB: "CUB", + FCC: "CUB", + BCC: "CUB", + TET: "TET", + BCT: "TET", + ORC: "ORC", + ORCF: "ORC", + ORCI: "ORC", + ORCC: "ORC", + HEX: "HEX", + RHL: "RHL", + MCL: "MCL", + MCLC: "MCL", + TRI: "TRI", // TODO: Legacy `TRI_alt` type, assert not used and remove - [`${LatticeType.TRI}alt`]: LatticeType.TRI, + TRIalt: "TRI", }; export function isConventionalCellSameAsPrimitiveForLatticeType( latticeType: LatticeTypeSchema, ): boolean { - const multiplier = PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS[latticeType || LatticeType.TRI]; + const multiplier = PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS[latticeType || "TRI"]; return multiplier === unitMatrix; } diff --git a/src/cell/primitive_cell.ts b/src/cell/primitive_cell.ts index 2c68356b..77fa1315 100644 --- a/src/cell/primitive_cell.ts +++ b/src/cell/primitive_cell.ts @@ -1,7 +1,7 @@ /* eslint no-unused-vars: 0 */ import { LatticeImplicitSchema } from "@exabyte-io/code.js/src/types"; -import { LatticeType, VectorsAsArray } from "../lattice/types"; +import { VectorsAsArray } from "../lattice/types"; import math from "../math"; /** @@ -9,7 +9,7 @@ import math from "../math"; * Following Setyawan, W., & Curtarolo, S. (2010). doi:10.1016/j.commatsci.2010.05.010 */ const PRIMITIVE_CELLS = { - [LatticeType.CUB]: ({ a }: LatticeImplicitSchema): VectorsAsArray => { + CUB: ({ a }: LatticeImplicitSchema): VectorsAsArray => { return [ [a, 0, 0], [0, a, 0], @@ -17,7 +17,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.FCC]: ({ a }: LatticeImplicitSchema): VectorsAsArray => { + FCC: ({ a }: LatticeImplicitSchema): VectorsAsArray => { return [ [0.0, a / 2, a / 2], [a / 2, 0.0, a / 2], @@ -25,7 +25,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.BCC]: ({ a }: LatticeImplicitSchema): VectorsAsArray => { + BCC: ({ a }: LatticeImplicitSchema): VectorsAsArray => { return [ [-a / 2, a / 2, a / 2], [a / 2, -a / 2, a / 2], @@ -33,7 +33,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.TET]: ({ a, c }: LatticeImplicitSchema): VectorsAsArray => { + TET: ({ a, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [a, 0, 0], [0, a, 0], @@ -41,7 +41,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.BCT]: ({ a, c }: LatticeImplicitSchema): VectorsAsArray => { + BCT: ({ a, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [-a / 2, a / 2, c / 2], [a / 2, -a / 2, c / 2], @@ -49,7 +49,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.ORC]: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { + ORC: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [a, 0, 0], [0, b, 0], @@ -57,7 +57,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.ORCF]: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { + ORCF: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [0, b / 2, c / 2], [a / 2, 0, c / 2], @@ -65,7 +65,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.ORCI]: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { + ORCI: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [-a / 2, b / 2, c / 2], [a / 2, -b / 2, c / 2], @@ -73,7 +73,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.ORCC]: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { + ORCC: ({ a, b, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [a / 2, b / 2, 0], [-a / 2, b / 2, 0], @@ -81,7 +81,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.HEX]: ({ a, c }: LatticeImplicitSchema): VectorsAsArray => { + HEX: ({ a, c }: LatticeImplicitSchema): VectorsAsArray => { return [ [a / 2, (-a * math.sqrt(3)) / 2, 0], [a / 2, (a * math.sqrt(3)) / 2, 0], @@ -89,7 +89,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.RHL]: ({ a, alpha }: LatticeImplicitSchema): VectorsAsArray => { + RHL: ({ a, alpha }: LatticeImplicitSchema): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); const cosHalfAlpha = math.sqrt((1 / 2) * (1 + cosAlpha)); const sinHalfAlpha = math.sqrt((1 / 2) * (1 - cosAlpha)); @@ -104,7 +104,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.MCL]: ({ a, b, c, alpha }: LatticeImplicitSchema): VectorsAsArray => { + MCL: ({ a, b, c, alpha }: LatticeImplicitSchema): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); return [ [a, 0, 0], @@ -113,7 +113,7 @@ const PRIMITIVE_CELLS = { ]; }, - [LatticeType.MCLC]: ({ a, b, c, alpha }: LatticeImplicitSchema): VectorsAsArray => { + MCLC: ({ a, b, c, alpha }: LatticeImplicitSchema): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); return [ [a / 2, b / 2, 0], @@ -123,7 +123,7 @@ const PRIMITIVE_CELLS = { }, // Algorithm from http://pymatgen.org/_modules/pymatgen/core/lattice.html (from_params) - [LatticeType.TRI]: ({ a, b, c, alpha, beta, gamma }: LatticeImplicitSchema): VectorsAsArray => { + TRI: ({ a, b, c, alpha, beta, gamma }: LatticeImplicitSchema): VectorsAsArray => { // convert angles to Radians // eslint-disable-next-line no-param-reassign [alpha, beta, gamma] = [alpha, beta, gamma].map( @@ -132,7 +132,7 @@ const PRIMITIVE_CELLS = { ); const [cosAlpha, cosBeta, cosGamma] = [alpha, beta, gamma].map((x) => math.cos(x)); - const [sinAlpha, sinBeta] = [alpha, beta, gamma].map((x) => math.sin(x)); + const [sinAlpha, sinBeta] = [alpha, beta].map((x) => math.sin(x)); const gammaStar = math.acos((cosAlpha * cosBeta - cosGamma) / (sinAlpha * sinBeta)); const cosGammaStar = math.cos(gammaStar); const sinGammaStar = math.sin(gammaStar); @@ -145,14 +145,7 @@ const PRIMITIVE_CELLS = { }, // alternative implementation - [`${LatticeType.TRI}alt`]: ({ - a, - b, - c, - alpha, - beta, - gamma, - }: LatticeImplicitSchema): VectorsAsArray => { + TRIalt: ({ a, b, c, alpha, beta, gamma }: LatticeImplicitSchema): VectorsAsArray => { const cosAlpha = math.cos((alpha / 180) * math.PI); const cosBeta = math.cos((beta / 180) * math.PI); const cosGamma = math.cos((gamma / 180) * math.PI); @@ -185,7 +178,7 @@ export function primitiveCell( lattice: LatticeImplicitSchema, skipRounding = false, ): VectorsAsArray { - const [vectorA, vectorB, vectorC] = PRIMITIVE_CELLS[lattice.type || LatticeType.TRI](lattice); + const [vectorA, vectorB, vectorC] = PRIMITIVE_CELLS[lattice.type || "TRI"](lattice); // set precision and remove JS floating point artifacts if (!skipRounding) { [vectorA, vectorB, vectorC].map((vec) => diff --git a/src/lattice/lattice.ts b/src/lattice/lattice.ts index 61560852..ce3e264f 100644 --- a/src/lattice/lattice.ts +++ b/src/lattice/lattice.ts @@ -1,4 +1,8 @@ -import { LatticeImplicitSchema, LatticeSchema } from "@exabyte-io/code.js/src/types"; +import { + LatticeImplicitSchema, + LatticeSchema, + LatticeTypeExtendedSchema, +} from "@exabyte-io/code.js/src/types"; import lodash from "lodash"; import _ from "underscore"; @@ -8,7 +12,7 @@ import { HASH_TOLERANCE } from "../constants"; import math from "../math"; import { FromVectorsProps, LatticeBravais } from "./lattice_bravais"; import { BravaisConfigProps, LatticeVectors } from "./lattice_vectors"; -import { LATTICE_TYPE_CONFIGS, LatticeType, LatticeTypeExtended } from "./types"; +import { LATTICE_TYPE_CONFIGS } from "./types"; import { UnitCell, UnitCellProps } from "./unit_cell"; /** @@ -126,36 +130,36 @@ export class Lattice extends LatticeBravais implements LatticeSchema { /** * Get a short label for the extended type of the lattice, eg. "MCLC-5". */ - get typeExtended(): string { + get typeExtended(): LatticeTypeExtendedSchema { const { a, b, c, alpha, beta, gamma, type } = this; const cosAlpha = math.cos((alpha / 180) * math.PI); switch (type) { - case LatticeType.BCT: - return c < a ? LatticeTypeExtended.BCT_1 : LatticeTypeExtended.BCT_2; - case LatticeType.ORCF: + case "BCT": + return c < a ? "BCT-1" : "BCT-2"; + case "ORCF": if (1 / (a * a) >= 1 / (b * b) + 1 / (c * c)) { - return LatticeTypeExtended.ORCF_1; + return "ORCF-1"; } - return LatticeTypeExtended.ORCF_2; - case LatticeType.RHL: - return cosAlpha > 0 ? LatticeTypeExtended.RHL_1 : LatticeTypeExtended.RHL_2; - case LatticeType.MCLC: + return "ORCF-2"; + case "RHL": + return cosAlpha > 0 ? "RHL-1" : "RHL-2"; + case "MCLC": if (gamma >= 90) { // MCLC-1,2 - return LatticeTypeExtended.MCLC_1; + return "MCLC-1"; } if ((b / c) * cosAlpha + ((b * b) / (a * a)) * (1 - cosAlpha * cosAlpha) <= 1) { // MCLC-3,4 - return LatticeTypeExtended.MCLC_3; + return "MCLC-3"; } - return LatticeTypeExtended.MCLC_5; - case LatticeType.TRI: + return "MCLC-5"; + case "TRI": if (alpha > 90 && beta > 90 && gamma >= 90) { // TRI-1a,2a - return LatticeTypeExtended.TRI_1a; + return "TRI_1a"; } - return LatticeTypeExtended.TRI_1b; + return "TRI_1b"; default: return type; } diff --git a/src/lattice/lattice_bravais.ts b/src/lattice/lattice_bravais.ts index 9fe2781d..ae9b664f 100644 --- a/src/lattice/lattice_bravais.ts +++ b/src/lattice/lattice_bravais.ts @@ -1,8 +1,8 @@ -import { LatticeImplicitSchema } from "@exabyte-io/code.js/src/types"; +import { LatticeImplicitSchema, LatticeTypeSchema } from "@exabyte-io/code.js/src/types"; import constants from "../constants"; import math from "../math"; -import { LATTICE_TYPE_CONFIGS, LatticeTypeSchema, Vector, VectorsAsArray } from "./types"; +import { LATTICE_TYPE_CONFIGS, Vector, VectorsAsArray } from "./types"; export type Units = Required["units"]; diff --git a/src/lattice/lattice_vectors.ts b/src/lattice/lattice_vectors.ts index 98eea64b..8bbf2701 100644 --- a/src/lattice/lattice_vectors.ts +++ b/src/lattice/lattice_vectors.ts @@ -3,7 +3,7 @@ import { LatticeExplicitUnit, LatticeImplicitSchema } from "@exabyte-io/code.js/ import { primitiveCell } from "../cell/primitive_cell"; import constants from "../constants"; import math from "../math"; -import { LatticeType, Vector } from "./types"; +import { Vector } from "./types"; type RequiredLatticeExplicitUnit = Required; @@ -61,12 +61,12 @@ export class LatticeVectors implements RequiredLatticeExplicitUnit { length: "angstrom", angle: "degree", }, - type = LatticeType.TRI, + type = "TRI", isConventional = false, }: BravaisConfigProps) { // use "direct" lattice constructor for primitive lattice // eslint-disable-next-line no-param-reassign - if (!isConventional) type = LatticeType.TRI; + if (!isConventional) type = "TRI"; // set precision and remove JS floating point artifacts const [vectorA, vectorB, vectorC] = primitiveCell({ diff --git a/src/lattice/reciprocal/symmetry_points.ts b/src/lattice/reciprocal/symmetry_points.ts index ba31c26d..6cb00cea 100644 --- a/src/lattice/reciprocal/symmetry_points.ts +++ b/src/lattice/reciprocal/symmetry_points.ts @@ -7,10 +7,9 @@ import { LatticeImplicitSchema } from "@exabyte-io/code.js/src/types"; import { Lattice } from "../lattice"; -import { LatticeType } from "../types"; const POINTS = { - [LatticeType.CUB]: () => { + CUB: () => { return [ { point: "R", @@ -27,7 +26,7 @@ const POINTS = { ]; }, - [LatticeType.FCC]: () => { + FCC: () => { return [ { point: "K", @@ -52,7 +51,7 @@ const POINTS = { ]; }, - [LatticeType.BCC]: () => { + BCC: () => { return [ { point: "H", @@ -69,7 +68,7 @@ const POINTS = { ]; }, - [LatticeType.TET]: () => { + TET: () => { return [ { point: "A", @@ -94,7 +93,7 @@ const POINTS = { ]; }, - [LatticeType.BCT]: ({ a, c }: LatticeImplicitSchema) => { + BCT: ({ a, c }: LatticeImplicitSchema) => { let n; if (c < a) { // BCT-1 @@ -165,7 +164,7 @@ const POINTS = { ]; }, - [LatticeType.ORC]: () => { + ORC: () => { return [ { point: "R", @@ -198,7 +197,7 @@ const POINTS = { ]; }, - [LatticeType.ORCF]: ({ a, b, c }: LatticeImplicitSchema) => { + ORCF: ({ a, b, c }: LatticeImplicitSchema) => { let n; if (1 / (a * a) >= 1 / (b * b) + 1 / (c * c)) { // ORCF-1,3 @@ -287,7 +286,7 @@ const POINTS = { ]; }, - [LatticeType.ORCI]: ({ a, b, c }: LatticeImplicitSchema) => { + ORCI: ({ a, b, c }: LatticeImplicitSchema) => { const n = (1 + (a * a) / (c * c)) / 4; const e = (1 + (b * b) / (c * c)) / 4; const d = (b * b - a * a) / (4 * c * c); @@ -344,7 +343,7 @@ const POINTS = { ]; }, - [LatticeType.ORCC]: ({ a, b }: LatticeImplicitSchema) => { + ORCC: ({ a, b }: LatticeImplicitSchema) => { const e = (1 + (a * a) / (b * b)) / 4; return [ { @@ -386,7 +385,7 @@ const POINTS = { ]; }, - [LatticeType.HEX]: () => { + HEX: () => { return [ { point: "A", @@ -411,7 +410,7 @@ const POINTS = { ]; }, - [LatticeType.RHL]: ({ alpha }: LatticeImplicitSchema) => { + RHL: ({ alpha }: LatticeImplicitSchema) => { let n, v; const cosAlpha = Math.cos((alpha / 180) * Math.PI); if (cosAlpha > 0) { @@ -500,7 +499,7 @@ const POINTS = { ]; }, - [LatticeType.MCL]: ({ b, c, alpha }: LatticeImplicitSchema) => { + MCL: ({ b, c, alpha }: LatticeImplicitSchema) => { const cosAlpha = Math.cos((alpha / 180) * Math.PI); const n = ((1 / 2) * (1 - (b * cosAlpha) / c)) / (1 - cosAlpha * cosAlpha); const v = 1 / 2 - (n * c * cosAlpha) / b; @@ -568,7 +567,7 @@ const POINTS = { ]; }, - [LatticeType.MCLC]: ({ a, b, c, alpha, gamma }: LatticeImplicitSchema) => { + MCLC: ({ a, b, c, alpha, gamma }: LatticeImplicitSchema) => { const cosAlpha = Math.cos((alpha / 180) * Math.PI); let e, n, p, f, m, d, v; if (gamma >= 90) { @@ -806,7 +805,7 @@ const POINTS = { ]; }, - [LatticeType.TRI]: ({ alpha, beta, gamma }: LatticeImplicitSchema) => { + TRI: ({ alpha, beta, gamma }: LatticeImplicitSchema) => { if (alpha > 90 && beta > 90 && gamma >= 90) { // TRI-1a,2a return [ diff --git a/src/lattice/types.ts b/src/lattice/types.ts index c4659244..1c2c1b8b 100644 --- a/src/lattice/types.ts +++ b/src/lattice/types.ts @@ -1,4 +1,4 @@ -import { ArrayOf3NumberElementsSchema, LatticeImplicitSchema } from "@exabyte-io/code.js/src/types"; +import { ArrayOf3NumberElementsSchema, LatticeTypeSchema } from "@exabyte-io/code.js/src/types"; export const DEFAULT_LATTICE_UNITS = { // by default lattice vectors shall be measured in angstrom, angles - in degrees @@ -10,32 +10,6 @@ export const DEFAULT_LATTICE_UNITS = { }, }; -/** - * Shortlist of lattice types (according to [AFLOW](https://arxiv.org/abs/1004.2974)) - * Convention used is derived from: - * Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: - * Challenges and tools. Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010 - */ - -export enum LatticeType { - CUB = "CUB", - FCC = "FCC", - BCC = "BCC", - TET = "TET", - BCT = "BCT", - ORC = "ORC", - ORCF = "ORCF", - ORCI = "ORCI", - ORCC = "ORCC", - HEX = "HEX", - RHL = "RHL", - MCL = "MCL", - MCLC = "MCLC", - TRI = "TRI", -} - -export type LatticeTypeSchema = LatticeImplicitSchema["type"]; - export enum LatticeTypeExtended { BCC = "BCC", BCT_1 = "BCT-1", @@ -73,7 +47,7 @@ export interface VectorsAsArray extends Array { interface LatticeTypeConfig { label: string; - code: LatticeType; + code: LatticeTypeSchema; editables: string[]; editablesConventional: string[]; } @@ -81,7 +55,7 @@ interface LatticeTypeConfig { export const LATTICE_TYPE_CONFIGS: LatticeTypeConfig[] = [ { label: "Simple Cubic", - code: LatticeType.CUB, + code: "CUB", // editables for primitive cell => WARNING: not tested editables: ["a"], // editables for conventional cell, taken from the publication above @@ -89,79 +63,79 @@ export const LATTICE_TYPE_CONFIGS: LatticeTypeConfig[] = [ }, { label: "Face-centered Cubic", - code: LatticeType.FCC, + code: "FCC", editables: ["a"], editablesConventional: ["a"], }, { label: "Body-centered Cubic", - code: LatticeType.BCC, + code: "BCC", editables: ["a"], editablesConventional: ["a"], }, { label: "Tetragonal", - code: LatticeType.TET, + code: "TET", editables: ["a", "c"], editablesConventional: ["a", "c"], }, { label: "Body-centered Tetragonal", - code: LatticeType.BCT, + code: "BCT", editables: ["a"], editablesConventional: ["a", "c"], }, { label: "Orthorombic", - code: LatticeType.ORC, + code: "ORC", editables: ["a", "b", "c"], editablesConventional: ["a", "b", "c"], }, { label: "Orthorombic Face-centered", - code: LatticeType.ORCF, + code: "ORCF", editables: ["a", "b", "c"], editablesConventional: ["a", "b", "c"], }, { label: "Orthorombic Body-centered", - code: LatticeType.ORCI, + code: "ORCI", editables: ["a", "alpha", "gamma"], editablesConventional: ["a", "b", "c"], }, { label: "Orthorombic Base-centered", - code: LatticeType.ORCC, + code: "ORCC", editables: ["a", "c", "alpha"], editablesConventional: ["a", "b", "c"], }, { label: "Hexagonal", - code: LatticeType.HEX, + code: "HEX", editables: ["a", "c"], editablesConventional: ["a", "c"], }, { label: "Rhombohedral", - code: LatticeType.RHL, + code: "RHL", editables: ["a", "alpha"], editablesConventional: ["a", "alpha"], }, { label: "Monoclinic", - code: LatticeType.MCL, + code: "MCL", editables: ["a", "b", "c", "alpha"], editablesConventional: ["a", "b", "c", "alpha"], }, { label: "Monoclinic Base-centered", - code: LatticeType.MCLC, + code: "MCLC", editables: ["a", "c", "alpha", "gamma"], editablesConventional: ["a", "b", "c", "alpha"], }, { label: "Triclinic", - code: LatticeType.TRI, + code: "TRI", editables: ["a", "b", "c", "alpha", "beta", "gamma"], editablesConventional: ["a", "b", "c", "alpha", "beta", "gamma"], }, diff --git a/src/material.ts b/src/material.ts index f95060f1..46884fba 100644 --- a/src/material.ts +++ b/src/material.ts @@ -1,6 +1,10 @@ import { HasConsistencyChecksHasMetadataNamedDefaultableInMemoryEntity } from "@exabyte-io/code.js/dist/entity"; import { AnyObject } from "@exabyte-io/code.js/dist/entity/in_memory"; -import { MaterialSchema } from "@exabyte-io/code.js/src/types"; +import { + ConsistencyCheck, + DerivedPropertiesSchema, + MaterialSchema, +} from "@exabyte-io/code.js/dist/types"; import CryptoJS from "crypto-js"; import { ConstrainedBasis } from "./basis/constrained_basis"; @@ -13,7 +17,6 @@ import { ATOMIC_COORD_UNITS, units } from "./constants"; import { Constraint } from "./constraints/constraints"; import { Lattice } from "./lattice/lattice"; import { BravaisConfigProps } from "./lattice/lattice_vectors"; -import { LatticeType } from "./lattice/types"; import parsers from "./parsers/parsers"; import { BasisConfig } from "./parsers/xyz"; // TODO: fix dependency cycle below @@ -48,7 +51,7 @@ export const defaultMaterialConfig = { }, lattice: { // Primitive cell for Diamond FCC Silicon at ambient conditions - type: LatticeType.FCC, + type: "FCC", a: 3.867, b: 3.867, c: 3.867, @@ -69,13 +72,6 @@ interface Property { interface MaterialSchemaJSON extends MaterialSchema, AnyObject {} -interface CheckResult { - key: string; - name: string; - severity: string; - message: string; -} - export abstract class Material extends HasConsistencyChecksHasMetadataNamedDefaultableInMemoryEntity { abstract src: { extension: string; @@ -126,14 +122,15 @@ export abstract class Material extends HasConsistencyChecksHasMetadataNamedDefau /** * @summary Returns the specific derived property (as specified by name) for a material. */ - getDerivedPropertyByName(name: string): Property | undefined { + getDerivedPropertyByName(name: string): DerivedPropertiesSchema | undefined { + // @ts-ignore return this.getDerivedProperties().find((x) => x.name === name); } /** * @summary Returns the derived properties array for a material. */ - getDerivedProperties(): Property[] { + getDerivedProperties(): DerivedPropertiesSchema[] { return this.prop("derivedProperties", []); } @@ -331,7 +328,7 @@ export abstract class Material extends HasConsistencyChecksHasMetadataNamedDefau * @summary a series of checks for the material and returns an array of results in ConsistencyChecks format. * @returns Array of checks results */ - getConsistencyChecks(): CheckResult[] { + getConsistencyChecks(): ConsistencyCheck[] { const basisChecks = this.getBasisConsistencyChecks(); // any other Material checks can be added here @@ -343,8 +340,8 @@ export abstract class Material extends HasConsistencyChecksHasMetadataNamedDefau * @summary a series of checks for the material's basis and returns an array of results in ConsistencyChecks format. * @returns Array of checks results */ - getBasisConsistencyChecks(): CheckResult[] { - const checks: CheckResult[] = []; + getBasisConsistencyChecks(): ConsistencyCheck[] { + const checks: ConsistencyCheck[] = []; const limit = 1000; const basis = this.Basis; From 967657b382f14136e9d077eca5ecb7acade9f139 Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Thu, 30 Nov 2023 18:39:34 +0200 Subject: [PATCH 15/18] chore: ts ignore for derived property --- src/material.ts | 1 + 1 file changed, 1 insertion(+) diff --git a/src/material.ts b/src/material.ts index 46884fba..4d9c59e1 100644 --- a/src/material.ts +++ b/src/material.ts @@ -206,6 +206,7 @@ export abstract class Material extends HasConsistencyChecksHasMetadataNamedDefau getInchiStringForHash(): string { const inchi = this.getDerivedPropertyByName("inchi"); if (inchi) { + // @ts-ignore return inchi.value; } throw new Error("Hash cannot be created. Missing InChI string in derivedProperties"); From e1b1ae209e3d38a2a77b1ed17c6d93cd29e125a5 Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Thu, 30 Nov 2023 21:09:27 +0200 Subject: [PATCH 16/18] chore: fix lint errors --- src/material.ts | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/src/material.ts b/src/material.ts index 4d9c59e1..1e4127c7 100644 --- a/src/material.ts +++ b/src/material.ts @@ -3,6 +3,7 @@ import { AnyObject } from "@exabyte-io/code.js/dist/entity/in_memory"; import { ConsistencyCheck, DerivedPropertiesSchema, + InChIRepresentationSchema, MaterialSchema, } from "@exabyte-io/code.js/dist/types"; import CryptoJS from "crypto-js"; @@ -65,11 +66,6 @@ export const defaultMaterialConfig = { }, }; -interface Property { - name: string; - value: string; -} - interface MaterialSchemaJSON extends MaterialSchema, AnyObject {} export abstract class Material extends HasConsistencyChecksHasMetadataNamedDefaultableInMemoryEntity { @@ -122,15 +118,14 @@ export abstract class Material extends HasConsistencyChecksHasMetadataNamedDefau /** * @summary Returns the specific derived property (as specified by name) for a material. */ - getDerivedPropertyByName(name: string): DerivedPropertiesSchema | undefined { - // @ts-ignore + getDerivedPropertyByName(name: string) { return this.getDerivedProperties().find((x) => x.name === name); } /** * @summary Returns the derived properties array for a material. */ - getDerivedProperties(): DerivedPropertiesSchema[] { + getDerivedProperties(): DerivedPropertiesSchema { return this.prop("derivedProperties", []); } @@ -206,8 +201,7 @@ export abstract class Material extends HasConsistencyChecksHasMetadataNamedDefau getInchiStringForHash(): string { const inchi = this.getDerivedPropertyByName("inchi"); if (inchi) { - // @ts-ignore - return inchi.value; + return (inchi as InChIRepresentationSchema).value; } throw new Error("Hash cannot be created. Missing InChI string in derivedProperties"); } From 71bba2c09ac4eea454c260d87f50898674266f65 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Thu, 30 Nov 2023 17:11:23 -0800 Subject: [PATCH 17/18] chore: add TODO item --- src/parsers/xyz.ts | 1 + 1 file changed, 1 insertion(+) diff --git a/src/parsers/xyz.ts b/src/parsers/xyz.ts index fa281ec6..10810f22 100644 --- a/src/parsers/xyz.ts +++ b/src/parsers/xyz.ts @@ -69,6 +69,7 @@ function _parseXYZLineAsWords(line: string): ParsedObject { }; } +// TODO: reuse Basis Definition(s) from ESSE/Code.js instead export interface BasisConfig { elements: { id: number; From 0730e84b7bf0ead5c6ad2cc0fb1c98c79f730536 Mon Sep 17 00:00:00 2001 From: Kostiantyn Dvornik Date: Fri, 1 Dec 2023 14:32:03 +0200 Subject: [PATCH 18/18] chore: update code.js version --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 3e44cb35..e591f119 100644 --- a/package.json +++ b/package.json @@ -33,7 +33,7 @@ "@babel/preset-react": "^7.16.7", "@babel/register": "^7.22.15", "@babel/runtime-corejs3": "^7.16.8", - "@exabyte-io/code.js": "git+https://github.com/Exabyte-io/code.js.git#update/SOF-7096", + "@exabyte-io/code.js": "2023.12.1-0", "@exabyte-io/eslint-config": "^2023.8.29-1", "@typescript-eslint/eslint-plugin": "^5.9.1", "@typescript-eslint/parser": "^5.9.1",