Feat: xyz file parsing - nAtoms & nLines to check formatting. Created…

src/parsers/parsers.js

@@ -1,11 +1,31 @@
 import cif from "./cif";
+// eslint-disable-next-line import/no-cycle
 import espresso from "./espresso";
 import poscar from "./poscar";
+// eslint-disable-next-line import/no-cycle
 import xyz from "./xyz";
 
+/**
+ * Function returns the number of atoms in a file using the proper parser function based on the file extension.
+ * @param {String} fileExtension
+ * @param {String} fileContent
+ * @returns {Number}
+ */
+export function getNumberOfAtomsInFileByExtension(fileExtension, fileContent) {
+    let numberOfAtoms = 0;
+    if (fileExtension === "poscar") {
+        numberOfAtoms = poscar.poscarFileAtomsCount(fileContent);
+    }
+    if (fileExtension === "xyz") {
+        numberOfAtoms = xyz.xyzFileAtomsCount(fileContent);
+    }
+    return numberOfAtoms;
+}
+
 export default {
     xyz,
     poscar,
     cif,
     espresso,
+    getNumberOfAtomsInFileByExtension,
 };

src/parsers/poscar.js

@@ -58,13 +58,13 @@ function toPoscar(materialOrConfig, omitConstraints = false) {
  * @param poscarFileContent
  * @returns {Number}
  */
-export function atomsCount(poscarFileContent) {
+export function poscarFileAtomsCount(poscarFileContent) {
     const atomsLine = poscarFileContent.split("\n")[6].split(" ");
     return atomsLine.map((x) => parseInt(x, 10)).reduce((a, b) => a + b);
 }
 
 export default {
     toPoscar,
     atomicConstraintsCharFromBool,
-    atomsCount,
+    poscarFileAtomsCount,
 };

src/parsers/xyz.js

@@ -1,11 +1,15 @@
+import Integer from "lodash/string";
 import _ from "underscore";
 import s from "underscore.string";
 
 import { Basis } from "../basis/basis";
 import { ConstrainedBasis } from "../basis/constrained_basis";
 import { Lattice } from "../lattice/lattice";
+// eslint-disable-next-line import/no-cycle
+import { defaultMaterialConfig } from "../material";
 import math from "../math";
 import { InvalidLineError } from "./errors";
+import poscar from "./poscar";
 import { CombinatorialBasis } from "./xyz_combinatorial_basis";
 
 // Regular expression for an XYZ line with atomic constraints, eg. Si    0.000000    0.500000    0.446678 1 1 1`
@@ -140,10 +144,37 @@ function fromMaterial(materialOrConfig, fractional = false) {
     return fromBasis(basis, "%11.6f");
 }
 
+/**
+ * Function splits the xyzFile string at new lines and then returns the first element of the array.
+ * The first line of the XYZ file should contain the number of atoms in the structure.
+ * @param {String} xyzFile
+ * @returns {Number}
+ */
+export function xyzFileAtomsCount(xyzFile) {
+    return Integer.parseInt(xyzFile.split(/\r?\n/)[0]);
+}
+
+/**
+ * Function converts an XYZ formatted structure as a POSCAR formatted structure
+ * @param {String} xyzContent
+ * @returns {String}
+ */
+export function xyzToPoscar(xyzContent) {
+    const xyzConfig = defaultMaterialConfig;
+    const xyzArray = xyzContent.split(/\r?\n/);
+    const xyzArrayBasisOnly = xyzArray.slice(2, -1);
+    const xyzBasis = xyzArrayBasisOnly.join("\n");
+    xyzConfig.basis = toBasisConfig(xyzBasis);
+    xyzConfig.basis.units = "cartesian";
+    return poscar.toPoscar(xyzConfig);
+}
+
 export default {
     validate,
     fromMaterial,
     toBasisConfig,
     fromBasis,
     CombinatorialBasis,
+    xyzFileAtomsCount,
+    xyzToPoscar,
 };

tests/enums.js

@@ -31,3 +31,6 @@ export const SiPWSCFInput = readFile(path.join(FIXTURES_DIR, "Si-pwscf.in"));
 export const Zr1H23Zr1H1 = readJSONFile(path.join(FIXTURES_DIR, "Zr1H23Zr1H1.json"));
 export const Zr1H23Zr1H1Poscar = readFile(path.join(FIXTURES_DIR, "Zr1H23Zr1H1.poscar"));
 export const H2O = readFile(path.join(FIXTURES_DIR, "H2O.poscar"));
+
+export const CH4 = readFile(path.join(FIXTURES_DIR, "CH4.xyz"));
+export const CH4POSCAR = readFile(path.join(FIXTURES_DIR, "CH4.poscar"));

tests/parsers/poscar.js

@@ -1,7 +1,7 @@
 import { expect } from "chai";
 
 import { Material } from "../../src/material";
-import { atomsCount } from "../../src/parsers/poscar";
+import { poscarFileAtomsCount } from "../../src/parsers/poscar";
 import { H2O, Na4Cl4, Na4Cl4Poscar, Zr1H23Zr1H1, Zr1H23Zr1H1Poscar } from "../enums";
 
 describe("Parsers.POSCAR", () => {
@@ -16,6 +16,6 @@ describe("Parsers.POSCAR", () => {
     });
 
     it("should return the number of atoms for a molecule in a poscar file", () => {
-        expect(atomsCount(H2O)).to.be.equal(3);
+        expect(poscarFileAtomsCount(H2O)).to.be.equal(3);
     });
 });

tests/parsers/xyz.js

@@ -1,5 +1,8 @@
+import { expect } from "chai";
+
 import parsers from "../../src/parsers/parsers";
-import { Si } from "../enums";
+import { xyzFileAtomsCount, xyzToPoscar } from "../../src/parsers/xyz";
+import { CH4, CH4POSCAR, Si } from "../enums";
 import { assertDeepAlmostEqual } from "../utils";
 
 describe("Parsers:XYZ", () => {
@@ -11,4 +14,10 @@ describe("Parsers:XYZ", () => {
             "units",
         ]);
     });
+    it("should return the number of atoms for a molecule in an xyz file", () => {
+        expect(xyzFileAtomsCount(CH4)).to.be.equal(5);
+    });
+    it("should return the xyz file content in poscar file format", () => {
+        assertDeepAlmostEqual(xyzToPoscar(CH4), CH4POSCAR);
+    });
 });