Replace species by kind

demo/demo.js

@@ -1,10 +1,10 @@
-import { WEAS, Atoms, Species, parseXYZ, parseCIF, parseCube } from "../src/index.js"; // Adjust the path as necessary
+import { WEAS, Atoms, Kind, parseXYZ, parseCIF, parseCube } from "../src/index.js"; // Adjust the path as necessary
 import * as THREE from "three";
 
 window.THREE = THREE;
 window.WEAS = WEAS;
 window.Atoms = Atoms;
-window.Species = Species;
+window.Kind = Kind;
 
 async function fetchFile(filename) {
   const response = await fetch(`datas/${filename}`);
@@ -68,8 +68,8 @@ async function updateAtoms(filename, fileContent = null) {
       const atomsList = parseXYZ(structureData);
       // atomsList[0].newAttribute("moment", [1, 1, 1, 1, 1, -1, -1, -1, -1, -1], "atom");
       // atomsList[0].newAttribute("charge", [-1, 0.5, 1, 0.5, 0.3, 0.2, 2, 1, 0, -0.5], "atom");
-      // atomsList[0].newAttribute("color", { C: "##eb4034", H: "#b434eb", O: "#34eb77", S: "#FFFF00" }, "species");
-      // atomsList[0].newAttribute("radii", { C: 1.5, H: 1.0, O: 1.5, S: 1.5 }, "species");
+      // atomsList[0].newAttribute("color", { C: "##eb4034", H: "#b434eb", O: "#34eb77", S: "#FFFF00" }, "kind");
+      // atomsList[0].newAttribute("radii", { C: 1.5, H: 1.0, O: 1.5, S: 1.5 }, "kind");
       editor.avr.atoms = atomsList;
       // editor.avr.bondManager.settings[1].color1 = "blue";
       // editor.avr.VFManager.addSetting({ origins: "positions", vectors: "movement", color: "#ff0000", radius: 0.1 });
@@ -232,12 +232,12 @@ async function updateAtoms(filename, fileContent = null) {
       editor.anyMesh.fromSettings(data);
       editor.anyMesh.drawMesh();
       break;
-    case "species":
+    case "kinds":
       editor.clear();
       filename = "c2h6so.xyz";
       structureData = fileContent || (await fetchFile(filename));
       atoms = parseXYZ(structureData);
-      atoms[0].addSpecies("C1", "C");
+      atoms[0].addKind("C1", "C");
       atoms[0].symbols[3] = "C1";
       editor.avr.atoms = atoms;
       // editor.avr.bondManager.settings[1].color1 = "blue";

demo/index.html

@@ -34,7 +34,7 @@ <h1>WEAS (Web Environment For Atomistic Structures)</h1>
       <option value="mesh_primitives_settings.json">Primitives instance</option>
       <option value="any_mesh_settings.json">Any Mesh</option>
       <option value="phonon">Phonon</option>
-      <option value="species">Species</option>
+      <option value="kinds">Kinds</option>
     </select>
 
     <!-- Add Upload Button Here -->

docs/source/atoms/atoms.rst

@@ -1,6 +1,6 @@
 Atoms
 =========
-The Atoms object represents a collection of atoms. It is used to store the positions, species, and other properties of the atoms. The sytax is very similar to ASE `Atoms <https://wiki.fysik.dtu.dk/ase/ase/atoms.html#module-ase.atoms>`_ object. However, there are also some key differences regarding the species and attributes.
+The Atoms object represents a collection of atoms. It is used to store the positions, symbols, and other properties of the atoms. The sytax is very similar to ASE `Atoms <https://wiki.fysik.dtu.dk/ase/ase/atoms.html#module-ase.atoms>`_ object. However, there are also some key differences regarding the kinds and attributes.
 
 
 Example:
@@ -16,42 +16,42 @@ Example:
 
 In this example, an Atoms object is created to represent a water molecule within a cubic unit cell with periodic boundaries. The object includes definitions for the symbols, positions of the atoms.
 
-Species
+Kind
 -------
-Why do we use species instead of elements? Because of we want to store different properties for the same element:
+Why do we use kinds instead of elements? Because of we want to store different properties for the same element:
 
 - such as: colors, bonds, etc.
 - In DFT calculation, different potentials, basis sets, charge, magnetic moment, etc.
 
-A species has:
+A kind has:
 
-- symbol: the name of the species, e.g. 'O', 'H1', 'Fe_up', etc.
+- symbol: the name of the kind, e.g. 'O', 'H1', 'Fe_up', etc.
 - element: the element symbol, e.g. 'O', 'H', 'Fe', etc.
 - number: the atomic number of the element, e.g. 8, 1, 26, etc.
 
-One can define the species explicitly using the `species` attribute.
+One can define the kinds explicitly using the `kinds` attribute.
 
 .. code-block:: javascript
 
     const myAtoms = new Atoms({
         symbols: ['O', 'H1', 'H2'], // symbols of the atoms
-        species: {'H1': 'H', 'H2': 'H'}, // Defining the species
+        kinds: {'H1': 'H', 'H2': 'H'}, // Defining the kinds
     });
 
 Attributes and domain
 ----------------------
 One can store additional data in the Atoms object using the `attributes`. The `attributes` has two domains:
 
-- `atoms`: store data that is specific to each atom, such as the charge or force.
-- `species`: store data that is specific to each species, such as the mass, color, or radius.
+- `atom`: store data that is specific to each atom, such as the charge or force.
+- `kind`: store data that is specific to each kind, such as the mass, color, or radius.
 
 
 .. code-block:: javascript
 
-    attributes: {'atoms': {'charge': [0, 0, 0],
+    attributes: {'atom': {'charge': [0, 0, 0],
                             'force': [[0, 0, 0], [0, 0, 0], [0, 0, 0]],
                             },
-                'species': {'mass': {'O': 15.999, 'H': 1.008},
+                'kind': {'mass': {'O': 15.999, 'H': 1.008},
                             "color", {C: "red", H: "#b434eb", O: "#34eb77", S: "#FFFF00" },
                             "radius", {C: 0.77, H: 0.37, O: 0.66, S: 1.04},
                             },
@@ -63,13 +63,12 @@ Methods
 The Atoms object has a number of methods that can be used to manipulate the data. These include methods to:
 
 
-Atomic and Species Manipulation
+Atomic and Kind Manipulation
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-- addSpecies(symbol, element = null)
+- addKind(symbol, element = null)
 - addAtom(atom)
-- removeAtom(index)
-- replaceAtoms(indices, newSpeciesSymbol)
+- replaceAtoms(indices, newKindSymbol)
 
 Cell and Boundary Conditions
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -100,7 +99,7 @@ Information and Export
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 - getAtomsCount()
-- getSpeciesCount()
+- getKindsCount()
 - getCellLengthsAndAngles()
 - calculateFractionalCoordinates()
 - toDict()

docs/source/atoms/color.rst

@@ -21,9 +21,9 @@ Supported style are:
 
 
 -----------------------------
-Custom color for each species
+Custom color for each kind
 -----------------------------
-Use can set custom color for each species. The color can be in the form of hex code or color name.
+Use can set custom color for each kind. The color can be in the form of hex code or color name.
 
 
 .. code-block:: javascript
@@ -35,7 +35,7 @@ Use can set custom color for each species. The color can be in the form of hex c
     weas.avr.drawModels()
 
 
-.. image:: ../_static/images/example_color_by_species.png
+.. image:: ../_static/images/example_color_by_kind.png
    :width: 6cm
 
 

docs/source/quickstart.rst

@@ -77,7 +77,7 @@ Here is the result of the above code:
 Features
 --------
 
-- **Structure Manipulation**: Enables manipulation of the structure, such as adding, removing, translating, rotating atoms and modifying species, and cell parameters.
+- **Structure Manipulation**: Enables manipulation of the structure, such as adding, removing, translating, rotating atoms and modifying kind, and cell parameters.
 
 - **Customizable Appearance**: Allows customization of atom and bond appearances, including colors, sizes, and visibility, polyhedra, and unit cell.
 

src/atoms/AtomsViewer.js

@@ -369,7 +369,7 @@ class AtomsViewer {
       // Remove labels
       this.ALManager.settings = [];
     } else if (newValue === "Symbol") {
-      this.ALManager.settings = [{ origins: "positions", texts: "species" }];
+      this.ALManager.settings = [{ origins: "positions", texts: "symbols" }];
     } else if (newValue === "Index") {
       this.ALManager.settings = [{ origins: "positions", texts: "index" }];
     }
@@ -572,7 +572,7 @@ 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.addSpecies(element);
+    this.atoms.addKind(element);
     this.atoms.addAtom(atom);
     // this.logger.debug("atoms: ", this.atoms);
 
@@ -598,7 +598,7 @@ class AtomsViewer {
     }
     const copied_atoms = this.atoms.getAtomsByIndices(indices);
     this.logger.debug("copied_atoms: ", copied_atoms);
-    this.atoms.addToSelf(copied_atoms);
+    this.atoms.add(copied_atoms);
     this.logger.debug("atoms: ", this.atoms);
 
     // also copy the properties, e.g. modelStyles, that are associated with the copied atoms