update: remove keys from CChecks

package.json

@@ -27,7 +27,7 @@
         "node": ">=0.12"
     },
     "devDependencies": {
-        "@exabyte-io/code.js": "https://github.com/Exabyte-io/code.js#2c6290b74be5f4001ec72950f2c67d0880ebbe57",
+        "@exabyte-io/code.js": "https://github.com/Exabyte-io/code.js#3eb3e812265cb75bac2c06a007cb76e684c1d0f9",
         "@exabyte-io/eslint-config": "^2022.11.17-0",
         "chai": "^4.3.4",
         "chai-almost": "^1.0.1",

src/basis/basis.js

@@ -446,17 +446,17 @@ export class Basis {
      */
     getOverlappingAtoms() {
         // to simplify calculations, convert to cartesian coordinates
-        const _basis = this;
-        _basis.toCartesian();
-        const { coordinates, elements } = _basis;
+        this.toCartesian();
+        const { coordinates, elements } = this;
         const overlaps = [];
 
         coordinates.forEach((entry1) => {
             coordinates.forEach((entry2) => {
-                if (entry1.id === entry2.id) return; // Don't compare an atom with itself
+                if (entry1.id === entry2.id) return;
                 const el1 = elements.find((el) => el.id === entry1.id).value;
                 const el2 = elements.find((el) => el.id === entry2.id).value;
-                const overlapCoefficient = 0.75; // temporary value for overlap approximation, where atoms most certainly can't be located
+                // temporary value for overlap approximation, where atoms most certainly can't be located
+                const overlapCoefficient = 0.75;
                 const tolerance =
                     overlapCoefficient *
                     (getElementAtomicRadius(el1) + getElementAtomicRadius(el2)); // in angstroms
@@ -473,6 +473,8 @@ export class Basis {
             });
         });
 
+        this.toCrystal();
+
         return overlaps;
     }
 

src/material.js

@@ -322,41 +322,38 @@ export class Material extends HasConsistencyChecksHasMetadataNamedDefaultableInM
 
     /**
      * @summary a series of checks for the material and returns an array of results in ConsistencyChecks format.
-     * @returns {{keys: *[], messages: *[]}} - Array of checks results
+     * @returns {*[]}} - Array of checks results
      */
     getConsistencyChecks() {
         const basisChecks = this.getBasisConsistencyChecks();
 
         // any other Material checks can be added here
 
         return {
-            keys: Array.from(basisChecks.keys),
-            messages: basisChecks.messages,
+            checks: basisChecks,
         };
     }
 
     /**
      * @summary a series of checks for the material's basis and returns an array of results in ConsistencyChecks format.
-     * @returns {{keys: Set<any>, messages: *[]}}
+     * @returns {*[]} - Array of checks results
      */
     getBasisConsistencyChecks() {
-        const keys = new Set();
-        const messages = [];
+        const checks = [];
 
         const basis = this.Basis;
         const overlappingAtomsGroups = basis.getOverlappingAtoms();
 
         overlappingAtomsGroups.forEach(({ id1, id2, element1, element2 }) => {
             const key = `basis.coordinates.${id1}`;
-            keys.add(key);
-            messages.push({
+            checks.push({
                 key,
-                checkName: "atomsOverlap",
+                name: "atomsOverlap",
                 severity: "warning",
                 message: `Atom ${element1} is too close to ${element2} at position ${id2 + 1}`,
             });
         });
 
-        return { keys, messages };
+        return checks;
     }
 }