@mat3ra/made 2026.5.28-0 → 2026.6.11-0

package/constants.json

@@ -0,0 +1,13 @@
+{
+  "molecule": {
+    "nonPeriodicMinimumLatticeSize": 3.0,
+    "diatomicLatticePaddingFactor": 3.0,
+    "molecularLatticePaddingFactor": 2.0
+  },
+  "precision": {
+    "coordinatesCrystal": 9,
+    "coordinatesCartesian": 6,
+    "latticeLengths": 6,
+    "latticeAngles": 4
+  }
+}

package/dist/js/basis/basis.d.ts

@@ -147,11 +147,12 @@ export declare class Basis extends InMemoryEntity implements BasisSchema {
      */
     hasEquivalentCellTo(anotherBasisClsInstance: Basis): boolean;
     /**
-     * @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.
+     * @summary Returns the minimum cubic lattice size for a non-periodic structure.
+     * Single-atom structures use the element atomic radius floored at defaultMinimumLatticeSize.
+     * Multi-atom structures scale the maximum pairwise distance by 3 when W=min/max pairwise distance
+     * is ~1 (diatomic), otherwise by 2.
      */
-    getMinimumLatticeSize(latticeScalingFactor?: number): number;
+    getMinimumLatticeSize(defaultMinimumLatticeSize?: number): number;
     /**
      * @summary function returns an array of overlapping atoms within specified tolerance.
      */
@@ -172,6 +173,8 @@ export declare class Basis extends InMemoryEntity implements BasisSchema {
      *
      */
     get maxPairwiseDistance(): number;
+    get minPairwiseDistance(): number;
+    getPairwiseDistanceExtremum(extremum: "max" | "min"): number;
     /**
      * @summary Function takes basis coordinates and transposes them so that the values for each dimension of the
      *  the basis are in their own nested array.

package/dist/js/basis/basis.js

@@ -366,19 +366,25 @@ class Basis extends entity_1.InMemoryEntity {
             .some((x) => !x);
     }
     /**
-     * @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.
+     * @summary Returns the minimum cubic lattice size for a non-periodic structure.
+     * Single-atom structures use the element atomic radius floored at defaultMinimumLatticeSize.
+     * Multi-atom structures scale the maximum pairwise distance by 3 when W=min/max pairwise distance
+     * is ~1 (diatomic), otherwise by 2.
      */
-    getMinimumLatticeSize(latticeScalingFactor = lattice_1.nonPeriodicLatticeScalingFactor) {
-        let latticeSizeAdditiveContribution = 0;
+    getMinimumLatticeSize(defaultMinimumLatticeSize = lattice_1.defaultNonPeriodicMinimumLatticeSize) {
         if (this._elements.values.length === 1) {
             const elementSymbol = this._elements.getElementValueByIndex(0);
-            latticeSizeAdditiveContribution = (0, periodic_table_js_1.getElementAtomicRadius)(elementSymbol);
+            const atomicRadius = (0, periodic_table_js_1.getElementAtomicRadius)(elementSymbol);
+            return Math.max(defaultMinimumLatticeSize, atomicRadius);
         }
-        const moleculeLatticeSize = this.maxPairwiseDistance * latticeScalingFactor;
-        const latticeSize = latticeSizeAdditiveContribution + moleculeLatticeSize;
-        return latticeSize;
+        const maxDistance = this.maxPairwiseDistance;
+        const minDistance = this.minPairwiseDistance;
+        const widthRatio = maxDistance > 0 ? minDistance / maxDistance : 1;
+        const latticeScalingFactor = math_1.math.almostEqual(widthRatio, 1)
+            ? lattice_1.diatomicLatticePaddingFactor
+            : lattice_1.molecularLatticePaddingFactor;
+        const moleculeLatticeSize = maxDistance * latticeScalingFactor;
+        return Math.max(defaultMinimumLatticeSize, moleculeLatticeSize);
     }
     /**
      * @summary function returns an array of overlapping atoms within specified tolerance.
@@ -428,22 +434,33 @@ class Basis extends entity_1.InMemoryEntity {
      *
      */
     get maxPairwiseDistance() {
+        return this.getPairwiseDistanceExtremum("max");
+    }
+    get minPairwiseDistance() {
+        return this.getPairwiseDistanceExtremum("min");
+    }
+    getPairwiseDistanceExtremum(extremum) {
         const originalUnits = this.units;
         this.toCartesian();
-        let maxDistance = 0;
+        let resultDistance = extremum === "max" ? 0 : Infinity;
         if (this._elements.values.length >= 2) {
             for (let i = 0; i < this._elements.values.length; i++) {
                 for (let j = i + 1; j < this._elements.values.length; j++) {
                     const distance = math_1.math.vDist(this._coordinates.getElementValueByIndex(i), this._coordinates.getElementValueByIndex(j));
-                    if (distance && distance > maxDistance) {
-                        maxDistance = distance;
+                    if (!distance)
+                        continue;
+                    if (extremum === "max" && distance > resultDistance) {
+                        resultDistance = distance;
+                    }
+                    if (extremum === "min" && distance < resultDistance) {
+                        resultDistance = distance;
                     }
                 }
             }
         }
         if (originalUnits !== constants_1.ATOMIC_COORD_UNITS.cartesian)
             this.toCrystal();
-        return maxDistance;
+        return extremum === "min" && resultDistance === Infinity ? 0 : resultDistance;
     }
     /**
      * @summary Function takes basis coordinates and transposes them so that the values for each dimension of the

package/dist/js/constants/molecule.d.ts

@@ -0,0 +1,16 @@
+/**
+ * Constants for molecule handling and precision.
+ * Source of truth: /constants.json at repository root
+ *
+ * These values are duplicated here for TypeScript compilation.
+ * When updating these, also update constants.json.
+ */
+export declare const defaultNonPeriodicMinimumLatticeSize = 3;
+export declare const diatomicLatticePaddingFactor = 3;
+export declare const molecularLatticePaddingFactor = 2;
+export declare const PRECISION_MAP: {
+    coordinatesCrystal: number;
+    coordinatesCartesian: number;
+    latticeLengths: number;
+    latticeAngles: number;
+};

package/dist/js/constants/molecule.js

@@ -0,0 +1,19 @@
+"use strict";
+/**
+ * Constants for molecule handling and precision.
+ * Source of truth: /constants.json at repository root
+ *
+ * These values are duplicated here for TypeScript compilation.
+ * When updating these, also update constants.json.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.PRECISION_MAP = exports.molecularLatticePaddingFactor = exports.diatomicLatticePaddingFactor = exports.defaultNonPeriodicMinimumLatticeSize = void 0;
+exports.defaultNonPeriodicMinimumLatticeSize = 3.0;
+exports.diatomicLatticePaddingFactor = 3.0;
+exports.molecularLatticePaddingFactor = 2.0;
+exports.PRECISION_MAP = {
+    coordinatesCrystal: 9,
+    coordinatesCartesian: 6,
+    latticeLengths: 6,
+    latticeAngles: 4,
+};

package/dist/js/lattice/lattice.d.ts

@@ -6,7 +6,7 @@ import { UnitCell } from "./unit_cell";
  * 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.
  */
-export declare const nonPeriodicLatticeScalingFactor = 2;
+export { defaultNonPeriodicMinimumLatticeSize, diatomicLatticePaddingFactor, molecularLatticePaddingFactor, } from "../constants/molecule";
 export declare class LatticeVectors extends Cell implements LatticeVectorsSchema {
 }
 export type { LatticeVectorsSchema };

package/dist/js/lattice/lattice.js

@@ -23,7 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Lattice = exports.LatticeVectors = exports.nonPeriodicLatticeScalingFactor = void 0;
+exports.Lattice = exports.LatticeVectors = exports.molecularLatticePaddingFactor = exports.diatomicLatticePaddingFactor = exports.defaultNonPeriodicMinimumLatticeSize = void 0;
 const constants_1 = require("@mat3ra/code/dist/js/constants");
 const entity_1 = require("@mat3ra/code/dist/js/entity");
 const math_1 = require("@mat3ra/code/dist/js/math");
@@ -36,7 +36,10 @@ const unit_cell_1 = require("./unit_cell");
  * 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.
  */
-exports.nonPeriodicLatticeScalingFactor = 2.0;
+var molecule_1 = require("../constants/molecule");
+Object.defineProperty(exports, "defaultNonPeriodicMinimumLatticeSize", { enumerable: true, get: function () { return molecule_1.defaultNonPeriodicMinimumLatticeSize; } });
+Object.defineProperty(exports, "diatomicLatticePaddingFactor", { enumerable: true, get: function () { return molecule_1.diatomicLatticePaddingFactor; } });
+Object.defineProperty(exports, "molecularLatticePaddingFactor", { enumerable: true, get: function () { return molecule_1.molecularLatticePaddingFactor; } });
 class LatticeVectors extends cell_1.Cell {
 }
 exports.LatticeVectors = LatticeVectors;

package/dist/js/made.d.ts

@@ -2,7 +2,7 @@ import { Basis } from "./basis/basis";
 import { Cell } from "./cell/cell";
 import { ATOMIC_COORD_UNITS, coefficients, tolerance, units } from "./constants";
 import { AtomicConstraints } from "./constraints/constraints";
-import { Lattice, nonPeriodicLatticeScalingFactor } from "./lattice/lattice";
+import { Lattice, defaultNonPeriodicMinimumLatticeSize, diatomicLatticePaddingFactor, molecularLatticePaddingFactor } from "./lattice/lattice";
 import { DEFAULT_LATTICE_UNITS, LATTICE_TYPE_CONFIGS } from "./lattice/lattice_types";
 import { ReciprocalLattice } from "./lattice/reciprocal/lattice_reciprocal";
 import { UnitCell } from "./lattice/unit_cell";
@@ -37,7 +37,9 @@ export declare const Made: {
     Lattice: typeof Lattice;
     Cell: typeof Cell;
     UnitCell: typeof UnitCell;
-    nonPeriodicLatticeScalingFactor: number;
+    defaultNonPeriodicMinimumLatticeSize: number;
+    diatomicLatticePaddingFactor: number;
+    molecularLatticePaddingFactor: number;
     ReciprocalLattice: typeof ReciprocalLattice;
     Basis: typeof Basis;
     AtomicConstraints: typeof AtomicConstraints;
@@ -54,7 +56,6 @@ export declare const Made: {
             toPoscar: (materialOrConfig: import("@mat3ra/esse/dist/js/types").MaterialSchema, omitConstraints?: boolean) => string;
             fromPoscar: (fileContent: string) => object;
             atomicConstraintsCharFromBool: (bool: boolean) => string;
-            atomsCount: typeof import("./parsers/poscar").atomsCount;
         };
         cif: {
             parseMeta: (txt: string) => import("./parsers/cif").Meta;
@@ -99,4 +100,4 @@ export declare const Made: {
         };
     };
 };
-export { coefficients, tolerance, units, ATOMIC_COORD_UNITS, Material, defaultMaterialConfig, Lattice, Cell, UnitCell, nonPeriodicLatticeScalingFactor, ReciprocalLattice, Basis, AtomicConstraints, parsers, tools, LATTICE_TYPE_CONFIGS, DEFAULT_LATTICE_UNITS, };
+export { coefficients, tolerance, units, ATOMIC_COORD_UNITS, Material, defaultMaterialConfig, Lattice, Cell, UnitCell, defaultNonPeriodicMinimumLatticeSize, diatomicLatticePaddingFactor, molecularLatticePaddingFactor, ReciprocalLattice, Basis, AtomicConstraints, parsers, tools, LATTICE_TYPE_CONFIGS, DEFAULT_LATTICE_UNITS, };

package/dist/js/made.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DEFAULT_LATTICE_UNITS = exports.LATTICE_TYPE_CONFIGS = exports.tools = exports.parsers = exports.AtomicConstraints = exports.Basis = exports.ReciprocalLattice = exports.nonPeriodicLatticeScalingFactor = exports.UnitCell = exports.Cell = exports.Lattice = exports.defaultMaterialConfig = exports.Material = exports.ATOMIC_COORD_UNITS = exports.units = exports.tolerance = exports.coefficients = exports.Made = void 0;
+exports.DEFAULT_LATTICE_UNITS = exports.LATTICE_TYPE_CONFIGS = exports.tools = exports.parsers = exports.AtomicConstraints = exports.Basis = exports.ReciprocalLattice = exports.molecularLatticePaddingFactor = exports.diatomicLatticePaddingFactor = exports.defaultNonPeriodicMinimumLatticeSize = exports.UnitCell = exports.Cell = exports.Lattice = exports.defaultMaterialConfig = exports.Material = exports.ATOMIC_COORD_UNITS = exports.units = exports.tolerance = exports.coefficients = exports.Made = void 0;
 const basis_1 = require("./basis/basis");
 Object.defineProperty(exports, "Basis", { enumerable: true, get: function () { return basis_1.Basis; } });
 const cell_1 = require("./cell/cell");
@@ -17,7 +17,9 @@ const constraints_1 = require("./constraints/constraints");
 Object.defineProperty(exports, "AtomicConstraints", { enumerable: true, get: function () { return constraints_1.AtomicConstraints; } });
 const lattice_1 = require("./lattice/lattice");
 Object.defineProperty(exports, "Lattice", { enumerable: true, get: function () { return lattice_1.Lattice; } });
-Object.defineProperty(exports, "nonPeriodicLatticeScalingFactor", { enumerable: true, get: function () { return lattice_1.nonPeriodicLatticeScalingFactor; } });
+Object.defineProperty(exports, "defaultNonPeriodicMinimumLatticeSize", { enumerable: true, get: function () { return lattice_1.defaultNonPeriodicMinimumLatticeSize; } });
+Object.defineProperty(exports, "diatomicLatticePaddingFactor", { enumerable: true, get: function () { return lattice_1.diatomicLatticePaddingFactor; } });
+Object.defineProperty(exports, "molecularLatticePaddingFactor", { enumerable: true, get: function () { return lattice_1.molecularLatticePaddingFactor; } });
 const lattice_types_1 = require("./lattice/lattice_types");
 Object.defineProperty(exports, "DEFAULT_LATTICE_UNITS", { enumerable: true, get: function () { return lattice_types_1.DEFAULT_LATTICE_UNITS; } });
 Object.defineProperty(exports, "LATTICE_TYPE_CONFIGS", { enumerable: true, get: function () { return lattice_types_1.LATTICE_TYPE_CONFIGS; } });
@@ -42,7 +44,9 @@ exports.Made = {
     Lattice: lattice_1.Lattice,
     Cell: cell_1.Cell,
     UnitCell: unit_cell_1.UnitCell,
-    nonPeriodicLatticeScalingFactor: lattice_1.nonPeriodicLatticeScalingFactor,
+    defaultNonPeriodicMinimumLatticeSize: lattice_1.defaultNonPeriodicMinimumLatticeSize,
+    diatomicLatticePaddingFactor: lattice_1.diatomicLatticePaddingFactor,
+    molecularLatticePaddingFactor: lattice_1.molecularLatticePaddingFactor,
     ReciprocalLattice: lattice_reciprocal_1.ReciprocalLattice,
     Basis: basis_1.Basis,
     AtomicConstraints: constraints_1.AtomicConstraints,

package/dist/js/parsers/parsers.d.ts

@@ -11,7 +11,6 @@ declare const _default: {
         toPoscar: (materialOrConfig: import("@mat3ra/esse/dist/js/types").MaterialSchema, omitConstraints?: boolean) => string;
         fromPoscar: (fileContent: string) => object;
         atomicConstraintsCharFromBool: (bool: boolean) => string;
-        atomsCount: typeof import("./poscar").atomsCount;
     };
     cif: {
         parseMeta: (txt: string) => import("./cif").Meta;

package/dist/js/parsers/poscar.d.ts

@@ -26,6 +26,5 @@ declare const _default: {
     toPoscar: typeof toPoscar;
     fromPoscar: typeof fromPoscar;
     atomicConstraintsCharFromBool: (bool: boolean) => string;
-    atomsCount: typeof atomsCount;
 };
 export default _default;

package/dist/js/parsers/poscar.js

@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.atomsCount = void 0;
 const math_1 = require("@mat3ra/code/dist/js/math");
+const utils_1 = require("@mat3ra/utils");
 const underscore_string_1 = __importDefault(require("underscore.string"));
 const constrained_basis_1 = require("../basis/constrained_basis");
 const cell_1 = require("../cell/cell");
@@ -58,7 +59,8 @@ function toPoscar(materialOrConfig, omitConstraints = false) {
  * Poscar file formatting: https://www.vasp.at/wiki/index.php/POSCAR
  */
 function atomsCount(poscarFileContent) {
-    const atomsLine = poscarFileContent.split("\n")[6].split(/\s+/);
+    const lines = utils_1.Utils.str.removeCommentsFromSourceCode(poscarFileContent).split("\n");
+    const atomsLine = lines[6].split(/\s+/);
     return atomsLine.map((x) => parseInt(x, 10)).reduce((a, b) => a + b);
 }
 exports.atomsCount = atomsCount;
@@ -68,7 +70,8 @@ exports.atomsCount = atomsCount;
  * @return Material config.
  */
 function fromPoscar(fileContent) {
-    const lines = fileContent.split("\n");
+    const cleanContent = utils_1.Utils.str.removeCommentsFromSourceCode(fileContent, "fortran");
+    const lines = cleanContent.split("\n");
     const comment = lines[0];
     // TODO: alat should be handled!!!!
     // const latticeConstant = parseFloat(lines[1].trim());
@@ -143,7 +146,7 @@ function fromPoscar(fileContent) {
  * @param text - string to check
  */
 function isPoscar(text) {
-    const lines = text.split("\n");
+    const lines = utils_1.Utils.str.removeCommentsFromSourceCode(text, "fortran").split("\n");
     // Checking number of lines, minimum requirement for POSCAR
     if (lines.length < 7) {
         return false;
@@ -178,5 +181,4 @@ exports.default = {
     toPoscar,
     fromPoscar,
     atomicConstraintsCharFromBool,
-    atomsCount,
 };

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/made",
-    "version": "2026.5.28-0",
+    "version": "2026.6.11-0",
     "description": "MAterials DEsign library",
     "scripts": {
         "lint": "eslint --cache src/js tests/js && prettier --write src/js tests/js",
@@ -37,7 +37,7 @@
         "@mat3ra/code": "2026.5.27-0",
         "@mat3ra/esse": "2026.5.27-0",
         "@mat3ra/tsconfig": "2024.6.3-0",
-        "@mat3ra/utils": "2025.4.14-0",
+        "@mat3ra/utils": "^2026.6.11-0",
         "@types/crypto-js": "^4.2.2",
         "@typescript-eslint/eslint-plugin": "^5.9.1",
         "@typescript-eslint/parser": "^5.9.1",
@@ -79,7 +79,8 @@
     },
     "peerDependencies": {
         "@mat3ra/code": "*",
-        "@mat3ra/esse": "*"
+        "@mat3ra/esse": "*",
+        "@mat3ra/utils": "*"
     },
     "lint-staged": {
         "*.js": "eslint --cache --fix",

package/src/js/basis/basis.ts

@@ -7,7 +7,11 @@ import { chain, toPairs, uniq, values } from "lodash";
 
 import { Cell } from "../cell/cell";
 import { ATOMIC_COORD_UNITS, HASH_TOLERANCE } from "../constants";
-import { nonPeriodicLatticeScalingFactor } from "../lattice/lattice";
+import {
+    defaultNonPeriodicMinimumLatticeSize,
+    diatomicLatticePaddingFactor,
+    molecularLatticePaddingFactor,
+} from "../lattice/lattice";
 import { AtomicCoordinateValue, Coordinates } from "./coordinates";
 import { AtomicElementValue, Elements } from "./elements";
 import { AtomicLabelValue, Labels } from "./labels";
@@ -476,19 +480,27 @@ export class Basis extends InMemoryEntity implements BasisSchema {
     }
 
     /**
-     * @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.
+     * @summary Returns the minimum cubic lattice size for a non-periodic structure.
+     * Single-atom structures use the element atomic radius floored at defaultMinimumLatticeSize.
+     * Multi-atom structures scale the maximum pairwise distance by 3 when W=min/max pairwise distance
+     * is ~1 (diatomic), otherwise by 2.
      */
-    getMinimumLatticeSize(latticeScalingFactor = nonPeriodicLatticeScalingFactor): number {
-        let latticeSizeAdditiveContribution = 0;
+    getMinimumLatticeSize(
+        defaultMinimumLatticeSize = defaultNonPeriodicMinimumLatticeSize,
+    ): number {
         if (this._elements.values.length === 1) {
             const elementSymbol = this._elements.getElementValueByIndex(0);
-            latticeSizeAdditiveContribution = getElementAtomicRadius(elementSymbol);
+            const atomicRadius = getElementAtomicRadius(elementSymbol);
+            return Math.max(defaultMinimumLatticeSize, atomicRadius);
         }
-        const moleculeLatticeSize = this.maxPairwiseDistance * latticeScalingFactor;
-        const latticeSize = latticeSizeAdditiveContribution + moleculeLatticeSize;
-        return latticeSize;
+        const maxDistance = this.maxPairwiseDistance;
+        const minDistance = this.minPairwiseDistance;
+        const widthRatio = maxDistance > 0 ? minDistance / maxDistance : 1;
+        const latticeScalingFactor = math.almostEqual(widthRatio, 1)
+            ? diatomicLatticePaddingFactor
+            : molecularLatticePaddingFactor;
+        const moleculeLatticeSize = maxDistance * latticeScalingFactor;
+        return Math.max(defaultMinimumLatticeSize, moleculeLatticeSize);
     }
 
     /**
@@ -545,9 +557,17 @@ export class Basis extends InMemoryEntity implements BasisSchema {
      *
      */
     get maxPairwiseDistance(): number {
+        return this.getPairwiseDistanceExtremum("max");
+    }
+
+    get minPairwiseDistance(): number {
+        return this.getPairwiseDistanceExtremum("min");
+    }
+
+    getPairwiseDistanceExtremum(extremum: "max" | "min"): number {
         const originalUnits = this.units;
         this.toCartesian();
-        let maxDistance = 0;
+        let resultDistance = extremum === "max" ? 0 : Infinity;
         if (this._elements.values.length >= 2) {
             for (let i = 0; i < this._elements.values.length; i++) {
                 for (let j = i + 1; j < this._elements.values.length; j++) {
@@ -555,14 +575,18 @@ export class Basis extends InMemoryEntity implements BasisSchema {
                         this._coordinates.getElementValueByIndex(i) as Coordinate3DSchema,
                         this._coordinates.getElementValueByIndex(j) as Coordinate3DSchema,
                     );
-                    if (distance && distance > maxDistance) {
-                        maxDistance = distance;
+                    if (!distance) continue;
+                    if (extremum === "max" && distance > resultDistance) {
+                        resultDistance = distance;
+                    }
+                    if (extremum === "min" && distance < resultDistance) {
+                        resultDistance = distance;
                     }
                 }
             }
         }
         if (originalUnits !== ATOMIC_COORD_UNITS.cartesian) this.toCrystal();
-        return maxDistance;
+        return extremum === "min" && resultDistance === Infinity ? 0 : resultDistance;
     }
 
     /**

package/src/js/constants/molecule.ts

@@ -0,0 +1,18 @@
+/**
+ * Constants for molecule handling and precision.
+ * Source of truth: /constants.json at repository root
+ * 
+ * These values are duplicated here for TypeScript compilation.
+ * When updating these, also update constants.json.
+ */
+
+export const defaultNonPeriodicMinimumLatticeSize = 3.0;
+export const diatomicLatticePaddingFactor = 3.0;
+export const molecularLatticePaddingFactor = 2.0;
+
+export const PRECISION_MAP = {
+    coordinatesCrystal: 9,
+    coordinatesCartesian: 6,
+    latticeLengths: 6,
+    latticeAngles: 4,
+};

package/src/js/lattice/lattice.ts

@@ -20,7 +20,11 @@ import { UnitCell, UnitCellProps } from "./unit_cell";
  * 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.
  */
-export const nonPeriodicLatticeScalingFactor = 2.0;
+export {
+    defaultNonPeriodicMinimumLatticeSize,
+    diatomicLatticePaddingFactor,
+    molecularLatticePaddingFactor,
+} from "../constants/molecule";
 
 export class LatticeVectors extends Cell implements LatticeVectorsSchema {}
 

package/src/js/made.ts

@@ -2,7 +2,12 @@ import { Basis } from "./basis/basis";
 import { Cell } from "./cell/cell";
 import { ATOMIC_COORD_UNITS, coefficients, tolerance, units } from "./constants";
 import { AtomicConstraints } from "./constraints/constraints";
-import { Lattice, nonPeriodicLatticeScalingFactor } from "./lattice/lattice";
+import {
+    Lattice,
+    defaultNonPeriodicMinimumLatticeSize,
+    diatomicLatticePaddingFactor,
+    molecularLatticePaddingFactor,
+} from "./lattice/lattice";
 import { DEFAULT_LATTICE_UNITS, LATTICE_TYPE_CONFIGS } from "./lattice/lattice_types";
 import { ReciprocalLattice } from "./lattice/reciprocal/lattice_reciprocal";
 import { UnitCell } from "./lattice/unit_cell";
@@ -21,7 +26,9 @@ export const Made = {
     Lattice,
     Cell,
     UnitCell,
-    nonPeriodicLatticeScalingFactor,
+    defaultNonPeriodicMinimumLatticeSize,
+    diatomicLatticePaddingFactor,
+    molecularLatticePaddingFactor,
     ReciprocalLattice,
     Basis,
     AtomicConstraints,
@@ -42,7 +49,9 @@ export {
     Lattice,
     Cell,
     UnitCell,
-    nonPeriodicLatticeScalingFactor,
+    defaultNonPeriodicMinimumLatticeSize,
+    diatomicLatticePaddingFactor,
+    molecularLatticePaddingFactor,
     ReciprocalLattice,
     Basis,
     AtomicConstraints,

package/src/js/parsers/poscar.ts

@@ -5,6 +5,7 @@ import {
     MaterialSchema,
     Vector3DSchema,
 } from "@mat3ra/esse/dist/js/types";
+import { Utils } from "@mat3ra/utils";
 import s from "underscore.string";
 
 import { ConstrainedBasis } from "../basis/constrained_basis";
@@ -67,7 +68,8 @@ function toPoscar(materialOrConfig: MaterialSchema, omitConstraints = false): st
  * Poscar file formatting: https://www.vasp.at/wiki/index.php/POSCAR
  */
 export function atomsCount(poscarFileContent: string): number {
-    const atomsLine = poscarFileContent.split("\n")[6].split(/\s+/);
+    const lines = Utils.str.removeCommentsFromSourceCode(poscarFileContent).split("\n");
+    const atomsLine = lines[6].split(/\s+/);
     return atomsLine.map((x) => parseInt(x, 10)).reduce((a, b) => a + b);
 }
 
@@ -77,7 +79,8 @@ export function atomsCount(poscarFileContent: string): number {
  * @return Material config.
  */
 function fromPoscar(fileContent: string): object {
-    const lines = fileContent.split("\n");
+    const cleanContent = Utils.str.removeCommentsFromSourceCode(fileContent, "fortran");
+    const lines = cleanContent.split("\n");
 
     const comment = lines[0];
     // TODO: alat should be handled!!!!
@@ -163,7 +166,7 @@ function fromPoscar(fileContent: string): object {
  * @param text - string to check
  */
 function isPoscar(text: string): boolean {
-    const lines = text.split("\n");
+    const lines = Utils.str.removeCommentsFromSourceCode(text, "fortran").split("\n");
 
     // Checking number of lines, minimum requirement for POSCAR
     if (lines.length < 7) {
@@ -205,5 +208,4 @@ export default {
     toPoscar,
     fromPoscar,
     atomicConstraintsCharFromBool,
-    atomsCount,
 };

package/src/py/mat3ra/made/constants.py

@@ -0,0 +1,11 @@
+import json
+import os
+
+_CONSTANTS_FILE = os.path.join(os.path.dirname(__file__), "../../../../constants.json")
+with open(_CONSTANTS_FILE) as f:
+    _CONSTANTS = json.load(f)
+
+DEFAULT_NON_PERIODIC_MIN_LATTICE_SIZE = _CONSTANTS["molecule"]["nonPeriodicMinimumLatticeSize"]
+DIATOMIC_LATTICE_PADDING_FACTOR = _CONSTANTS["molecule"]["diatomicLatticePaddingFactor"]
+MOLECULAR_LATTICE_PADDING_FACTOR = _CONSTANTS["molecule"]["molecularLatticePaddingFactor"]
+PRECISION_MAP = _CONSTANTS["precision"]

package/src/py/mat3ra/made/tools/convert/__init__.py

@@ -2,6 +2,7 @@ import inspect
 from functools import wraps
 from typing import Any, Callable, Dict, Union
 
+from mat3ra.utils import remove_comments_from_source_code
 from mat3ra.utils.mixins import RoundNumericValuesMixin
 
 from mat3ra.made.material import Material
@@ -151,6 +152,10 @@ def to_poscar(material_or_material_data: Union[Material, Dict[str, Any]]) -> str
     return poscar.get_str()
 
 
+def clean_qe_input(poscar):
+    return remove_comments_from_source_code(remove_comments_from_source_code(poscar, "fortran"), "python")
+
+
 def from_poscar(poscar: str) -> Dict[str, Any]:
     """
     Converts a POSCAR string to a material object in ESSE format.
@@ -161,10 +166,22 @@ def from_poscar(poscar: str) -> Dict[str, Any]:
     Returns:
         dict: A dictionary containing the material information in ESSE format.
     """
-    structure = PymatgenStructure.from_str(poscar, "poscar")
+    poscar_clean = clean_qe_input(poscar)
+    structure = PymatgenStructure.from_str(poscar_clean, "poscar")
     return from_pymatgen(structure)
 
 
+def from_poscar_molecule(poscar: str) -> Dict[str, Any]:
+    """
+    Converts a molecule POSCAR string to a non-periodic ESSE material.
+    """
+    poscar_clean = clean_qe_input(poscar)
+    structure = PymatgenStructure.from_str(poscar_clean, "poscar")
+    ase_atoms = PymatgenAseAtomsAdaptor.get_atoms(structure)
+    ase_atoms.set_pbc(False)
+    return from_ase(ase_atoms)
+
+
 def to_ase(material_or_material_data: Union[Material, Dict[str, Any]]) -> ASEAtoms:
     """
     Converts material object in ESSE format to an ASE Atoms object.

package/src/py/mat3ra/made/tools/convert/utils.py

@@ -2,12 +2,39 @@ import json
 from typing import Any, Dict, List, Union
 
 import numpy as np
+from mat3ra.made.constants import (
+    DEFAULT_NON_PERIODIC_MIN_LATTICE_SIZE,
+    DIATOMIC_LATTICE_PADDING_FACTOR,
+    MOLECULAR_LATTICE_PADDING_FACTOR,
+)
+from mat3ra.made.utils import get_center_of_coordinates, map_array_to_array_with_id_value
 from mat3ra.utils.object import NumpyNDArrayRoundEncoder
 from scipy.spatial.distance import pdist
 
-from mat3ra.made.utils import map_array_to_array_with_id_value, get_center_of_coordinates
-from .interface_parts_enum import INTERFACE_LABELS_MAP
 from ..third_party import ASEAtoms, PymatgenInterface, PymatgenStructure
+from .interface_parts_enum import INTERFACE_LABELS_MAP
+
+
+def _get_non_periodic_lattice_padding_factor(max_distance: float, min_distance: float) -> float:
+    if max_distance <= 0:
+        return MOLECULAR_LATTICE_PADDING_FACTOR
+    width_ratio = min_distance / max_distance
+    if np.isclose(width_ratio, 1.0):
+        return DIATOMIC_LATTICE_PADDING_FACTOR
+    return MOLECULAR_LATTICE_PADDING_FACTOR
+
+
+def _get_non_periodic_lattice_size(
+    shifted_positions: np.ndarray,
+    default_min_size: float = DEFAULT_NON_PERIODIC_MIN_LATTICE_SIZE,
+) -> float:
+    if len(shifted_positions) < 2:
+        return max(default_min_size, 10.0)
+    distances = pdist(shifted_positions)
+    max_distance = float(np.max(distances))
+    min_distance = float(np.min(distances))
+    padding_factor = _get_non_periodic_lattice_padding_factor(max_distance, min_distance)
+    return max(default_min_size, max_distance * padding_factor)
 
 
 def extract_labels_from_pymatgen_structure(structure: PymatgenStructure) -> List[int]:
@@ -42,21 +69,21 @@ def extract_tags_from_ase_atoms(atoms: ASEAtoms) -> List[Union[str, int]]:
 
 
 def calculate_padded_cell_simple_cubic(
-    coordinates: List[List[float]], padding_factor: float = 2.0
+    coordinates: List[List[float]],
+    default_min_size: float = DEFAULT_NON_PERIODIC_MIN_LATTICE_SIZE,
 ) -> List[List[float]]:
     """
     Calculate values for a padded cell for a molecule based on its coordinates.
     Args:
         coordinates (Array[Array[float]]): A list of atomic coordinates.
-        padding_factor (float): The factor by which to multiply the maximum distance for padding.
+        default_min_size (float): Minimum cubic lattice parameter in angstroms.
     Returns:
         Array[float]: A list containing the final cell latice vectors with padding applied.
     """
     positions = np.array(coordinates)
     center = get_center_of_coordinates(positions)
     shifted_positions = positions - center
-    max_distance = np.max(pdist(shifted_positions)) if len(positions) >= 2 else 10.0
-    padding_value = padding_factor * max_distance
+    padding_value = _get_non_periodic_lattice_size(shifted_positions, default_min_size)
 
     return [
         [padding_value, 0.0, 0.0],

package/tests/js/basis/basis.ts

@@ -217,7 +217,7 @@ describe("Basis", () => {
      */
     it("should return minimum lattice size for an atom", () => {
         const basis = new Basis(Na.basis);
-        const minimumLatticeSize = 1.8;
+        const minimumLatticeSize = 3;
         const latticeSize = basis.getMinimumLatticeSize();
         expect(latticeSize).to.be.equal(minimumLatticeSize);
     });

package/tests/js/parsers/poscar.ts

@@ -4,6 +4,18 @@ import { AtomicConstraints } from "../../../src/js/constraints/constraints";
 import { Material } from "../../../src/js/material";
 import parsers from "../../../src/js/parsers/parsers";
 import { atomsCount } from "../../../src/js/parsers/poscar";
+
+const O2_POSCAR_WITH_COMMENTS = `O2 molecule in a box
+1.0 ! universal scaling parameters
+12.0 0.0 0.0 ! lattice vector a(1)
+0.0 12.0 0.0 ! lattice vector a(2)
+0.0 0.0 12.0 ! lattice vector a(3)
+O
+2 ! number of atoms
+cart ! positions in cartesian coordinates
+0 0 0 O
+0 0 1.21 O
+`;
 import {
     atomicConstraints,
     H2OPoscar,
@@ -29,6 +41,21 @@ describe("Parsers.POSCAR", () => {
         expect(atomsCount(H2OPoscar)).to.be.equal(3);
     });
 
+    it("should detect POSCAR with VASP-style comments", () => {
+        expect(parsers.poscar.isPoscar(O2_POSCAR_WITH_COMMENTS)).to.be.equal(true);
+        expect(parsers.nativeFormatParsers.detectFormat(O2_POSCAR_WITH_COMMENTS)).to.be.equal(
+            "poscar",
+        );
+    });
+
+    it("should parse POSCAR with VASP-style comments", () => {
+        const materialConfig = parsers.poscar.fromPoscar(O2_POSCAR_WITH_COMMENTS);
+        expect(materialConfig).to.have.property("basis");
+        expect((materialConfig as { basis: { elements: object[] } }).basis.elements).to.have.length(
+            2,
+        );
+    });
+
     it("should return constraints as string with given map function", () => {
         const constraints = AtomicConstraints.fromObjects(atomicConstraints);
         expect(

package/tests/py/unit/test_tools_convert.py

@@ -1,19 +1,24 @@
 import numpy as np
 import pytest
 from ase import Atoms
+from ase.build import molecule
 from mat3ra.code.array_with_ids import ArrayWithIds
+from mat3ra.made.material import Material
+from mat3ra.made.tools.convert import from_ase, from_poscar, from_pymatgen, to_ase, to_poscar, to_pymatgen
+from mat3ra.made.tools.convert.utils import (
+    DEFAULT_NON_PERIODIC_MIN_LATTICE_SIZE,
+    calculate_padded_cell_simple_cubic,
+)
 from mat3ra.utils import assertion as assertion_utils
 from pymatgen.core.structure import Element, Lattice, Structure
 
-from mat3ra.made.material import Material
-from mat3ra.made.tools.convert import from_ase, from_poscar, from_pymatgen, to_ase, to_poscar, to_pymatgen
 from .fixtures.monolayer import GRAPHENE
 from .fixtures.thrid_party.ase_atoms import (
-    ASE_BULK_Si,
     ASE_MOLECULE_H2O,
+    BULK_SI_LABELS,
     BULK_SI_LATTICE_A,
     BULK_SI_LATTICE_ALPHA,
-    BULK_SI_LABELS,
+    ASE_BULK_Si,
 )
 
 PYMATGEN_LATTICE = Lattice.from_parameters(a=3.84, b=3.84, c=3.84, alpha=120, beta=90, gamma=60)
@@ -143,3 +148,30 @@ def test_from_ase(
     assert material_data["isNonPeriodic"] == expected_is_non_periodic
     if expected_lattice_type is not None:
         assert material_data["lattice"]["type"] == expected_lattice_type
+
+
+TOLERANCE = 1e-4
+
+H2_EXPECTED_LATTICE_A = DEFAULT_NON_PERIODIC_MIN_LATTICE_SIZE
+O2_EXPECTED_LATTICE_A = 3.7379
+H2O_EXPECTED_LATTICE_A = 3.0530
+C2H4_EXPECTED_LATTICE_A = 6.1754
+
+
+@pytest.mark.parametrize(
+    "molecule_name, expected_lattice_a",
+    [
+        ("H2", H2_EXPECTED_LATTICE_A),
+        ("O2", O2_EXPECTED_LATTICE_A),
+        ("H2O", H2O_EXPECTED_LATTICE_A),
+        ("C2H4", C2H4_EXPECTED_LATTICE_A),
+    ],
+)
+def test_calculate_padded_cell_simple_cubic(molecule_name, expected_lattice_a):
+    atoms = molecule(molecule_name)
+    cell_vectors = calculate_padded_cell_simple_cubic(atoms.get_positions().tolist())
+    lattice_a = cell_vectors[0][0]
+    assert np.isclose(lattice_a, expected_lattice_a, atol=TOLERANCE)
+    assert lattice_a >= DEFAULT_NON_PERIODIC_MIN_LATTICE_SIZE
+    assert np.isclose(cell_vectors[0][0], cell_vectors[1][1], atol=TOLERANCE)
+    assert np.isclose(cell_vectors[0][0], cell_vectors[2][2], atol=TOLERANCE)