feat: migrate ade as is

Author: tjduigna

README.md

@@ -46,3 +46,25 @@ npm run transpile
 npm run test
 ```
 
+ADe
+===
+
+The`ADe` package sits just below the `WoDe` package in the Mat3ra workflow
+ecosystem, where `ADe` houses entity definitions for:
+
+- `Application` - uniquely determined by `name, [version], [build]`
+- `Executable` - defined for a given application and accessible from application by name
+- `Flavor` - defined for a given executable and accessible from executable by name
+- `Template` - a jinja template for an application input file
+
+The relevant data parameterizing these entities is housed in
+the [Application Flavors](https://github.com/Exabyte-io/exabyte-application-flavors)
+repository. This includes the supported applications, executables, flavors,
+and defined templates.
+
+Templates themselves are organized by application in a top-level `assets`
+directory in `application-flavors` and the API for loading and working with templates can be found in
+each application's `assets.js` module.
+At build time, all templates are loaded and compiled into a single monolithic
+JS file using `build_templates.js` so that it can be used in the client as well as in NodeJS.
+This is how templates are consumed from `applicaton-flavors` in `ADe`.

src/application.js

@@ -0,0 +1,114 @@
+import lodash from "lodash";
+import { getAppTree, getAppData, allApplications } from "@exabyte-io/application-flavors.js";
+import { NamedDefaultableInMemoryEntity } from "@exabyte-io/code.js/dist/entity";
+
+import { Executable } from "./executable";
+import { getApplicationConfig, getExecutableConfig } from "./tree";
+
+
+export class Application extends NamedDefaultableInMemoryEntity {
+    static Executable = Executable;
+
+    constructor(config) {
+        const staticConfig = getApplicationConfig(config);
+        super({...staticConfig, ...config});
+    }
+
+    // TODO: extract this from application-flavors "global" default config for espresso 5.4.0
+    static get defaultConfig() {
+        return {
+            name: 'espresso',
+            shortName: 'qe',
+            version: '5.4.0',
+            summary: 'Quantum Espresso',
+            build: 'Default',
+        }
+    }
+
+    static create(config) {
+        return this.createFromNameVersionBuild(config);
+    }
+
+    static createFromNameVersionBuild({name, version = null, build = "Default"}) {
+        return new Application({name, version, build});
+    }
+
+    getExecutables() {
+        return this.executables;
+    }
+
+    getBuilds() {
+        const data = getAppData(this.prop("name"));
+        const {versions} = data;
+        const builds = ["Default"];
+        versions.map((v) => v.build && builds.push(v.build));
+        return lodash.uniq(builds);
+    }
+
+    getVersions() {
+        const data = getAppData(this.prop("name"));
+        const {versions} = data;
+        const these = versions.map((v) => v.version);
+        return lodash.uniq(these);
+    }
+
+    static getUniqueAvailableNames() {
+        return allApplications;
+    }
+
+    getExecutableByName(name = null) {
+        return new this.constructor.Executable(
+            getExecutableConfig({
+                appName: this.prop("name"),
+                execName: name,
+            })
+        );
+    }
+
+    getExecutableByConfig(config) {
+        return config ? this.getExecutableByName(config.name) : this.defaultExecutable;
+    }
+
+    get defaultExecutable() {
+        return this.getExecutableByName();
+    }
+
+    // override upon inheritance
+    get allowedModelTypes() {
+        return []
+    }
+
+    get summary() {
+        return this.prop("summary");
+    }
+
+    get version() {
+        return this.prop("version");
+    }
+
+    get build() {
+        return this.prop("build");
+    }
+
+    get shortName() {
+        return this.prop("shortName", this.prop("name"));
+    }
+
+    get executables() {
+        const tree = getAppTree(this.prop("name"));
+        return Object.keys(tree).map(key => {
+            return new this.constructor.Executable(
+                Object.assign({}, tree[key], {name: key})
+            )
+        })
+    }
+
+    get hasAdvancedComputeOptions() {
+        return this.prop("hasAdvancedComputeOptions");
+    }
+
+    get isLicensed() {
+        return this.prop("isLicensed");
+    }
+
+}

src/context.js

@@ -0,0 +1,4 @@
+export { NWChemTotalEnergyContextProvider } from "./context/providers/nwchem/providers";
+export { QEPWXContextProvider, QENEBContextProvider } from "./context/providers/espresso/providers";
+export { VASPContextProvider, VASPNEBContextProvider } from "./context/providers/vasp/providers";
+export { ExecutableContextProvider } from "./context/providers"

src/context/providers.js

@@ -0,0 +1,10 @@
+import { ContextProvider } from "@exabyte-io/code.js/dist/context";
+
+export class ExecutableContextProvider extends ContextProvider {
+    constructor(config) {
+        super({
+            ...config,
+            domain: "executable"
+        });
+    }
+}

src/context/providers/espresso/providers.js

@@ -0,0 +1,112 @@
+import _ from "underscore";
+import lodash from "lodash";
+import { mix } from "mixwith";
+import s from "underscore.string";
+
+import { Made } from "@exabyte-io/made.js";
+import { PERIODIC_TABLE } from "@exabyte-io/periodic-table.js";
+
+import {
+    MaterialContextMixinBuilder,
+    MaterialsContextMixinBuilder,
+    MaterialsSetContextMixin,
+    MethodDataContextMixin,
+    WorkflowContextMixin,
+    JobContextMixin
+} from "@exabyte-io/code.js/dist/context";
+import { ExecutableContextProvider } from "../../providers";
+
+export class QEPWXContextProvider extends mix(ExecutableContextProvider).with(
+    MaterialContextMixinBuilder(Made.Material),
+    MethodDataContextMixin,
+    WorkflowContextMixin,
+    JobContextMixin,
+) {
+
+    get atomSymbols() {return this.material.Basis.uniqueElements}
+
+    get atomicPositionsWithoutConstraints() {return this.material.Basis.atomicPositions}
+
+    get atomicPositions() {return this.material.Basis.atomicPositionsWithConstraints};
+
+    /*
+     * @NOTE: Overriding getData makes this provider "stateless", ie. delivering data from scratch each time and not
+     *        considering the content of `this.data`, and `this.isEdited` field(s).
+     */
+    getData() {
+
+        // the below values are read from PlanewaveDataManager instead
+        // ECUTWFC = 40;
+        // ECUTRHO = 200;
+
+        const IBRAV = 0;
+
+        return {
+            IBRAV,
+            RESTART_MODE: this.RESTART_MODE,
+            NAT: this.atomicPositions.length,
+            NTYP: this.atomSymbols.length,
+            ATOMIC_POSITIONS: this.atomicPositions.join('\n'),
+            ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS: this.atomicPositionsWithoutConstraints.join('\n'),
+            CELL_PARAMETERS: this.CELL_PARAMETERS,
+            ATOMIC_SPECIES: this.ATOMIC_SPECIES,
+        }
+    }
+
+    get RESTART_MODE() {
+        return (this.job.parentJob || this.workflow.hasRelaxation) ? 'restart' : 'from_scratch';
+    }
+
+    getPseudoBySymbol(symbol) {
+        return (this.methodData.pseudo || []).find(p => p.element === symbol);
+    }
+
+    get ATOMIC_SPECIES() {
+        // atomic species with pseudopotentials
+        return _.map(this.atomSymbols, (symbol) => {
+            const pseudo = this.getPseudoBySymbol(symbol);
+            return QEPWXContextProvider.symbolToAtomicSpecie(symbol, pseudo);
+        }).join('\n');
+    }
+
+    get CELL_PARAMETERS() {
+        return this.material.Lattice.vectorArrays.map(x => {
+            return x.map(y => {
+                return s.sprintf('%14.9f', y).trim();
+            }).join(' ');
+        }).join('\n');
+
+    }
+
+    static symbolToAtomicSpecie(symbol, pseudo) {
+        const el = PERIODIC_TABLE[symbol];
+        const filename = pseudo ? lodash.get(pseudo, 'filename', s.strRightBack(pseudo.path, '/')) : '';
+        return el ? s.sprintf('%s %f %s', symbol, el.atomic_mass, filename) : undefined;
+    }
+}
+
+export class QENEBContextProvider extends mix(ExecutableContextProvider).with(
+    MaterialContextMixinBuilder(Made.Material),
+    MaterialsContextMixinBuilder(Made.Material),
+    MaterialsSetContextMixin,
+    MethodDataContextMixin,
+    WorkflowContextMixin,
+    JobContextMixin,
+) {
+
+    getData() {
+        const sortedMaterials = this.sortMaterialsByIndexInSet(this.materials);
+        const PWXContexts = sortedMaterials.map(material => {
+            const context = Object.assign({}, this.config.context, {material: material});
+            const config = Object.assign({}, this.config, {context});
+            return new QEPWXContextProvider(config).getData();
+        });
+
+        return {
+            ..._.omit(PWXContexts[0], ["ATOMIC_POSITIONS", "ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS"]),
+            FIRST_IMAGE: PWXContexts[0].ATOMIC_POSITIONS,
+            LAST_IMAGE: PWXContexts[PWXContexts.length - 1].ATOMIC_POSITIONS,
+            INTERMEDIATE_IMAGES: PWXContexts.slice(1, PWXContexts.length - 1).map(data => data.ATOMIC_POSITIONS),
+        }
+    }
+}

src/context/providers/nwchem/providers.js

@@ -0,0 +1,69 @@
+import _ from "underscore";
+import lodash from "lodash";
+import {mix} from "mixwith";
+import s from "underscore.string";
+import { Made } from "@exabyte-io/made.js";
+import { PERIODIC_TABLE } from "@exabyte-io/periodic-table.js";
+
+import {
+    MaterialContextMixinBuilder,
+    MethodDataContextMixin,
+    WorkflowContextMixin,
+    JobContextMixin
+} from "@exabyte-io/code.js/dist/context";
+import { ExecutableContextProvider } from "../../providers";
+
+export class NWChemTotalEnergyContextProvider extends mix(ExecutableContextProvider).with(
+    MaterialContextMixinBuilder(Made.Material),
+    MethodDataContextMixin,
+    WorkflowContextMixin,
+    JobContextMixin,
+) {
+
+    get atomSymbols() {return this.material.Basis.uniqueElements}
+
+    get atomicPositionsWithoutConstraints() {return this.material.Basis.atomicPositions}
+
+    get atomicPositions() {return this.material.Basis.atomicPositionsWithConstraints};
+
+    get cartesianAtomicPositions() {return this.material.toCartesian()};
+
+    /*
+     * @NOTE: Overriding getData makes this provider "stateless", ie. delivering data from scratch each time and not
+     *        considering the content of `this.data`, and `this.isEdited` field(s).
+     */
+    getData() {
+        /*
+        TODO: Create ability for user to define CHARGE, MULT, BASIS and FUNCTIONAL parameters.
+         */
+        const CHARGE = 0;
+        const MULT = 1;
+        const BASIS = '6-31G';
+        const FUNCTIONAL = 'B3LYP';
+
+        return {
+            CHARGE: CHARGE,
+            MULT: MULT,
+            BASIS: BASIS,
+            NAT: this.atomicPositions.length,
+            NTYP: this.atomSymbols.length,
+            ATOMIC_POSITIONS: this.atomicPositions.join('\n'),
+            ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS: this.atomicPositionsWithoutConstraints.join('\n'),
+            ATOMIC_SPECIES: this.ATOMIC_SPECIES,
+            FUNCTIONAL: FUNCTIONAL,
+            CARTESIAN: this.cartesianAtomicPositions,
+        }
+    }
+
+    get ATOMIC_SPECIES() {
+        return _.map(this.atomSymbols, (symbol) => {
+            return NWChemTotalEnergyContextProvider.symbolToAtomicSpecies(symbol);
+        }).join('\n');
+    }
+
+    static symbolToAtomicSpecies(symbol, pseudo) {
+        const el = PERIODIC_TABLE[symbol];
+        const filename = pseudo ? lodash.get(pseudo, 'filename', s.strRightBack(pseudo.path, '/')) : '';
+        return el ? s.sprintf('%s %f %s', symbol, el.atomic_mass, filename) : undefined;
+    }
+}