Update test

docs/source/atoms/color.rst

@@ -21,9 +21,9 @@ Supported style are:
 
 
 -----------------------------
-Custom color for each specie
+Custom color for each species
 -----------------------------
-Use can set custom color for each specie. The color can be in the form of hex code or color name.
+Use can set custom color for each species. The color can be in the form of hex code or color name.
 
 
 .. code-block:: javascript

src/atoms/AtomsViewer.js

@@ -572,7 +572,10 @@ class AtomsViewer {
   addAtom(element, position = { x: 0, y: 0, z: 0 }) {
     // Remove the selected atoms from the scene and data
     const atom = new Atom(element, [position.x, position.y, position.z]);
-    this.atoms.addSpecie(element);
+    // if element is not in the species, add it to the species
+    if (!this.atoms.species[element]) {
+      this.atoms.addSpecie(element);
+    }
     this.atoms.addAtom(atom);
     // this.logger.debug("atoms: ", this.atoms);
 

src/atoms/atoms.js

@@ -246,7 +246,6 @@ class Atoms {
         ...this.attributes["specie"][name],
       };
     }
-    return result;
   }
 
   multiply(mx, my, mz) {

tests/atoms.test.mjs

@@ -1,32 +1,30 @@
-import { Species, Atom, Atoms } from "../dist/weas.mjs";
+import { Specie, Atom, Atoms } from "../dist/weas.mjs";
 
-describe("Species class", () => {
-  it("creates a new Species instance correctly", () => {
-    const species = new Species("C1", "C");
-    expect(species.symbol).toBe("C1");
+describe("Specie class", () => {
+  it("creates a new Specie instance correctly", () => {
+    const species = new Specie("C");
     expect(species.element).toBe("C");
     expect(species.number).toBe(6);
   });
-  it("creates a new Species use only symbol", () => {
-    const species = new Species("C");
-    expect(species.symbol).toBe("C");
+  it("creates a new Specie use only symbol", () => {
+    const species = new Specie("C");
     expect(species.element).toBe("C");
     expect(species.number).toBe(6);
   });
   it("throws an error when adding an unknown species", () => {
     const value = "Unknown";
     expect(() => {
-      const species = new Species("Unknown"); // This species does not exist in the atoms instance
-    }).toThrowError(`Element '${value}' is wrong.`);
+      const species = new Specie("Unknown"); // This species does not exist in the atoms instance
+    }).toThrowError(`Element '${value}' is invalid.`);
   });
 });
 
 describe("Atom class", () => {
   it("creates a new Atom instance correctly", () => {
-    const species = "H"; // Assuming this refers to an existing species
+    const symbol = "H"; // Assuming this refers to an existing symbol
     const position = [1.0, 2.0, 3.0];
-    const atom = new Atom(species, position);
-    expect(atom.species).toBe(species);
+    const atom = new Atom(symbol, position);
+    expect(atom.symbol).toBe(symbol);
     expect(atom.position).toEqual(position);
   });
 });
@@ -53,7 +51,7 @@ describe("Atoms class", () => {
   it("adds a species correctly", () => {
     atoms.addSpecie("H");
     expect(atoms.species).toHaveProperty("H");
-    expect(atoms.species["H"]).toEqual(new Species("H"));
+    expect(atoms.species["H"]).toEqual(new Specie("H"));
   });
 
   // Add more tests for other methods like setCell, addAtom, removeAtom, etc.

tests/parserXYZ.test.mjs

@@ -1,4 +1,4 @@
-import { parseXYZ, Species } from "../dist/weas.mjs";
+import { parseXYZ, Specie } from "../dist/weas.mjs";
 
 describe("parseXYZ", () => {
   it("parses valid XYZ data correctly", () => {
@@ -15,8 +15,8 @@ H 0.000000 0.757160 0.482080
     expect(atoms).toBeDefined();
     expect(atoms.species).toHaveProperty("H");
     expect(atoms.species).toHaveProperty("O");
-    expect(atoms.species["H"]).toEqual(new Species("H"));
-    expect(atoms.species["O"]).toEqual(new Species("O"));
+    expect(atoms.species["H"]).toEqual(new Specie("H"));
+    expect(atoms.species["O"]).toEqual(new Specie("O"));
     expect(atoms.positions.length).toBe(3);
     expect(atoms.symbols).toEqual(["O", "H", "H"]);
     console.log(atoms.positions[0]);