Merge pull request #13 from Exabyte-io/epic/SOF-6265

Epic/sof 6265
Exabyte-io · Nov 11, 2022 · a9bf80e · a9bf80e
2 parents c1615d9 + f478de0
commit a9bf80e
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Showing 6 changed files with 248 additions and 246 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -36,7 +36,7 @@
         "@babel/preset-react": "7.16.7",
         "@babel/register": "^7.16.0",
         "@babel/runtime-corejs3": "7.16.8",
-        "@exabyte-io/application-flavors.js": "2022.7.24-0",
+        "@exabyte-io/application-flavors.js": "2022.11.10-0",
         "@exabyte-io/periodic-table.js": "2022.6.8-0",
         "lodash": "^4.17.21",
         "mixwith": "^0.1.1",
@@ -45,7 +45,7 @@
         "underscore.string": "^3.3.4"
     },
     "devDependencies": {
-        "@exabyte-io/code.js": "2022.9.2-0",
+        "@exabyte-io/code.js": "2022.11.11-0",
         "@exabyte-io/made.js": "2022.6.15-0",
         "chai": "^4.3.4",
         "eslint": "7.32.0",

diff --git a/src/context/providers/espresso/providers.js b/src/context/providers/espresso/providers.js
@@ -10,29 +10,62 @@ import { Made } from "@exabyte-io/made.js";
 import { PERIODIC_TABLE } from "@exabyte-io/periodic-table.js";
 import lodash from "lodash";
 import { mix } from "mixwith";
-import _ from "underscore";
 import s from "underscore.string";
 
 import { ExecutableContextProvider } from "../../providers";
 
 export class QEPWXContextProvider extends mix(ExecutableContextProvider).with(
     MaterialContextMixin,
+    MaterialsContextMixin,
     MethodDataContextMixin,
     WorkflowContextMixin,
     JobContextMixin,
 ) {
     static Material = Made.Material;
 
-    get atomSymbols() {
-        return this.material.Basis.uniqueElements;
+    static atomSymbols(material) {
+        return material.Basis.uniqueElements;
+    }
+
+    /** Returns the input text block for atomic positions WITH constraints.
+     */
+    static atomicPositionsWithConstraints(material) {
+        return material.Basis.atomicPositionsWithConstraints.join("\n");
+    }
+
+    /** Returns the input text block for atomic positions
+     *  Note: does NOT include constraints
+     */
+    static atomicPositions(material) {
+        return material.Basis.atomicPositions.join("\n");
+    }
+
+    static NAT(material) {
+        return material.Basis.atomicPositions.length;
+    }
+
+    static NTYP(material) {
+        return material.Basis.uniqueElements.length;
     }
 
-    get atomicPositionsWithoutConstraints() {
-        return this.material.Basis.atomicPositions;
+    buildQEPWXContext(material) {
+        const IBRAV = 0; // use CELL_PARAMETERS to define Bravais lattice
+
+        return {
+            IBRAV,
+            RESTART_MODE: this.RESTART_MODE,
+            ATOMIC_SPECIES: this.ATOMIC_SPECIES(material),
+            NAT: QEPWXContextProvider.NAT(material),
+            NTYP: QEPWXContextProvider.NTYP(material),
+            ATOMIC_POSITIONS: QEPWXContextProvider.atomicPositionsWithConstraints(material),
+            ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS: QEPWXContextProvider.atomicPositions(material),
+            CELL_PARAMETERS: QEPWXContextProvider.CELL_PARAMETERS(material),
+        };
     }
 
-    get atomicPositions() {
-        return this.material.Basis.atomicPositionsWithConstraints;
+    getDataPerMaterial() {
+        if (!this.materials || this.materials.length <= 1) return {};
+        return { perMaterial: this.materials.map((material) => this.buildQEPWXContext(material)) };
     }
 
     /*
@@ -44,17 +77,9 @@ export class QEPWXContextProvider extends mix(ExecutableContextProvider).with(
         // 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,
+            ...this.buildQEPWXContext(this.material),
+            ...this.getDataPerMaterial(),
         };
     }
 
@@ -66,16 +91,25 @@ export class QEPWXContextProvider extends mix(ExecutableContextProvider).with(
         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");
+    /** Builds ATOMIC SPECIES block of pw.x input in the format
+     *  X   Mass_X   PseudoPot_X
+     *  where X            is the atom label
+     *        Mass_X       is the mass of element X [amu]
+     *        PseudoPot_X  is the pseudopotential filename associated with element X
+     *
+     *  Note: assumes this.methodData is defined
+     */
+    ATOMIC_SPECIES(material) {
+        return QEPWXContextProvider.atomSymbols(material)
+            .map((symbol) => {
+                const pseudo = this.getPseudoBySymbol(symbol);
+                return QEPWXContextProvider.symbolToAtomicSpecie(symbol, pseudo);
+            })
+            .join("\n");
     }
 
-    get CELL_PARAMETERS() {
-        return this.material.Lattice.vectorArrays
+    static CELL_PARAMETERS(material) {
+        return material.Lattice.vectorArrays
             .map((x) => {
                 return x
                     .map((y) => {
@@ -114,7 +148,10 @@ export class QENEBContextProvider extends mix(ExecutableContextProvider).with(
         });
 
         return {
-            ..._.omit(PWXContexts[0], ["ATOMIC_POSITIONS", "ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS"]),
+            ...lodash.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(

diff --git a/src/context/providers/vasp/providers.js b/src/context/providers/vasp/providers.js
@@ -13,12 +13,27 @@ import { ExecutableContextProvider } from "../../providers";
 
 export class VASPContextProvider extends mix(ExecutableContextProvider).with(
     MaterialContextMixin,
+    MaterialsContextMixin,
     MethodDataContextMixin,
     WorkflowContextMixin,
     JobContextMixin,
 ) {
     static Material = Made.Material;
 
+    // eslint-disable-next-line class-methods-use-this
+    buildVASPContext(material) {
+        return {
+            // TODO: figure out whether we need two separate POSCARS, maybe one is enough
+            POSCAR: material.getAsPOSCAR(true, true),
+            POSCAR_WITH_CONSTRAINTS: material.getAsPOSCAR(true),
+        };
+    }
+
+    getDataPerMaterial() {
+        if (!this.materials || this.materials.length <= 1) return {};
+        return { perMaterial: this.materials.map((material) => this.buildVASPContext(material)) };
+    }
+
     /*
      * @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).
@@ -29,9 +44,8 @@ export class VASPContextProvider extends mix(ExecutableContextProvider).with(
         // ECUTRHO;
 
         return {
-            // TODO: figure out whether we need two separate POSCARS, maybe one is enough
-            POSCAR: this.material.getAsPOSCAR(true, true),
-            POSCAR_WITH_CONSTRAINTS: this.material.getAsPOSCAR(true),
+            ...this.buildVASPContext(this.material),
+            ...this.getDataPerMaterial(),
         };
     }
 }

diff --git a/src/executable.js b/src/executable.js
@@ -1,14 +1,11 @@
-import { mix } from "mixwith";
 import { NamedDefaultableInMemoryEntity, RuntimeItemsMixin } from "@exabyte-io/code.js/dist/entity";
+import { mix } from "mixwith";
+
 import { Flavor } from "./flavor";
 
 export class Executable extends mix(NamedDefaultableInMemoryEntity).with(RuntimeItemsMixin) {
     static Flavor = Flavor;
 
-    constructor(config) {
-        super(config);
-    }
-
     toJSON(exclude) {
         return super.toJSON(["flavors"].concat(exclude));
     }
@@ -18,18 +15,18 @@ export class Executable extends mix(NamedDefaultableInMemoryEntity).with(Runtime
     }
 
     get flavors() {
-        return Object.keys(this.flavorsTree).map(key => {
-            return this.constructor.Flavor.create(
-                Object.assign({}, this.flavorsTree[key], {name: key, executable: this})
-            );
+        return Object.keys(this.flavorsTree).map((key) => {
+            return this.constructor.Flavor.create({
+                ...this.flavorsTree[key],
+                name: key,
+                executable: this,
+            });
         });
     }
 
     get flavorsFromTree() {
-        return Object.keys(this.flavorsTree).map(key => {
-            return new this.constructor.Flavor(
-                Object.assign({}, this.flavorsTree[key], {name: key})
-            );
+        return Object.keys(this.flavorsTree).map((key) => {
+            return new this.constructor.Flavor({ ...this.flavorsTree[key], name: key });
         });
     }
 
@@ -44,5 +41,4 @@ export class Executable extends mix(NamedDefaultableInMemoryEntity).with(Runtime
     getFlavorByConfig(config) {
         return config ? this.getFlavorByName(config.name) : this.defaultFlavor;
     }
-
 }