@ccp-nc/crystvis-js 0.5.0 → 0.6.1

package/test/loader.js

@@ -26,7 +26,22 @@ describe('#loading', function() {
         expect(a.get_chemical_symbols()).to.deep.equal(['C', 'C', 'C', 'N', 'C', 'C',
             'H', 'H', 'H', 'H', 'H'
         ]);
+        
+        // Check that positions were loaded correctly
+        expect(a.length()).to.equal(11);
+        expect(a.get_positions()[0]).to.deep.almost.equal([-0.180226841, 0.360945118, -1.120304970]);
+        
+        // Check cell
+        expect(a.get_cell()).to.deep.almost.equal([
+            [10, 0, 0],
+            [0, 10, 0],
+            [0, 0, 10]
+        ]);
+        
+        // Check that info contains the label
+        expect(a.info.Label).to.equal('Pyridine molecule (source: Wikipedia)');
     });
+    
     it('should load properly an extended XYZ file', function() {
 
         var loader = new Loader();
@@ -40,22 +55,119 @@ describe('#loading', function() {
             [0, 0, 5.44]
         ]);
         expect(a.get_array('spin')).to.deep.equal([1, 0, 0, 0, 0, 0, 0, 0]);
+        expect(a.length()).to.equal(8);
+        expect(a.get_chemical_symbols()[0]).to.equal('Si');
     });
-    it('should load properly a CIF file', function() {
 
+    it('should load all frames from a multi-frame extended XYZ file and be robust to blank lines', function() {
         var loader = new Loader();
+        var xyz = fs.readFileSync(path.join(__dirname, 'data', 'ethanol_with_tensors.xyz'), "utf8");
 
-        var cif = fs.readFileSync(path.join(__dirname, 'data', 'org.cif'), "utf8");
-        var a = loader.load(cif)['1501936'];
+        // Frame 0 (first)
+        var a0 = loader.load(xyz, 'xyz', null, { index: 0 })['xyz'];
+        expect(a0.length()).to.equal(9);
+        expect(a0.get_chemical_symbols()[0]).to.equal('C');
+        expect(a0.get_positions()[0]).to.deep.almost.equal([0.05539939, -0.60057807, 0.62649405]);
+        
+        // Check that ms tensors were loaded as TensorData objects
+        expect(a0.get_array('ms')).to.have.lengthOf(9);
+        expect(a0.get_array('ms')[0]).to.have.property('data');
+        expect(a0.get_array('ms')[0].data).to.deep.almost.equal([
+            [125.81813960, -9.69204056, 1.47151834],
+            [-9.69204056, 152.57296730, -15.37444798],
+            [1.47151834, -15.37444798, 153.40518054]
+        ]);
 
+        // Frame 1 (second)
+        var a1 = loader.load(xyz, 'xyz', null, { index: 1 })['xyz'];
+        expect(a1.length()).to.equal(9);
+        expect(a1.get_positions()[0]).to.deep.almost.equal([-0.40320021, -0.45122528, 0.73024166]);
+        expect(a1.get_array('ms')[0].data).to.deep.almost.equal([
+            [132.90497460, 3.59552794, -12.43391876],
+            [3.59552794, 127.77706275, -12.28247854],
+            [-12.43391876, -12.28247854, 148.26339821]
+        ]);
 
-        chai.expect(a.get_cell()).to.deep.almost.equal([
-            [8.2302, 0.0, 0.0],
-            [1.7507207912272031, 8.096583378263006, 0.0],
-            [1.7848106706548383, 1.959874486240255, 12.914460443940394]
+        // Frame 2 (third)
+        var a2 = loader.load(xyz, 'xyz', null, { index: 2 })['xyz'];
+        expect(a2.length()).to.equal(9);
+        expect(a2.get_positions()[0]).to.deep.almost.equal([-0.69807410, -0.44723904, 0.24317208]);
+        expect(a2.get_array('ms')[0].data).to.deep.almost.equal([
+            [152.92455307, 16.26391385, -4.26821306],
+            [16.26391385, 125.77540629, -16.76320152],
+            [-4.26821306, -16.76320152, 130.73689699]
+        ]);
+        
+        // Check a different atom in frame 2
+        expect(a2.get_array('ms')[8].data).to.deep.almost.equal([
+            [15.18096611, -3.57189977, -7.34818913],
+            [-3.57189977, 25.05233266, -0.90280873],
+            [-7.34818913, -0.90280873, 24.27668518]
+        ]);
+
+        // Default (should be last frame)
+        var a_last = loader.load(xyz, 'xyz')['xyz'];
+        expect(a_last.get_array('ms')[0].data).to.deep.almost.equal([
+            [152.92455307, 16.26391385, -4.26821306],
+            [16.26391385, 125.77540629, -16.76320152],
+            [-4.26821306, -16.76320152, 130.73689699]
+        ]);
+
+        // Robustness: insert blank lines between frames and test again
+        // add blank line before each frame (match only counts at start of line)
+        var xyz_blank = xyz.replace(/^9\n/gm, '\n9\n');
+        var a_blank = loader.load(xyz_blank, 'xyz', null, { index: 1 })['xyz'];
+        expect(a_blank.get_array('ms')[0].data).to.deep.almost.equal([
+            [132.90497460, 3.59552794, -12.43391876],
+            [3.59552794, 127.77706275, -12.28247854],
+            [-12.43391876, -12.28247854, 148.26339821]
+        ]);
+    });
+    
+    it('should handle negative frame indices correctly', function() {
+        var loader = new Loader();
+        var xyz = fs.readFileSync(path.join(__dirname, 'data', 'ethanol_with_tensors.xyz'), "utf8");
+        
+        // -1 should be last frame (frame 2)
+        var a_neg1 = loader.load(xyz, 'xyz', null, { index: -1 })['xyz'];
+        expect(a_neg1.get_array('ms')[0].data[0][0]).to.almost.equal(152.92455307);
+        
+        // -2 should be second-to-last frame (frame 1)
+        var a_neg2 = loader.load(xyz, 'xyz', null, { index: -2 })['xyz'];
+        expect(a_neg2.get_array('ms')[0].data[0][0]).to.almost.equal(132.90497460);
+        
+        // -3 should be first frame (frame 0)
+        var a_neg3 = loader.load(xyz, 'xyz', null, { index: -3 })['xyz'];
+        expect(a_neg3.get_array('ms')[0].data[0][0]).to.almost.equal(125.81813960);
+    });
+    
+    it('should load properly a simple XYZ file with multiple atoms', function() {
+        var loader = new Loader();
+        var xyz = fs.readFileSync(path.join(__dirname, 'data', 'H2O.xyz'), "utf8");
+        var a = loader.load(xyz, 'xyz')['xyz'];
+        
+        expect(a.length()).to.equal(6);
+        expect(a.get_chemical_symbols()).to.deep.equal(['O', 'H', 'H', 'O', 'H', 'H']);
+        expect(a.get_positions()[0]).to.deep.almost.equal([0.0, 0.0, 0.11926200]);
+        expect(a.get_cell()).to.deep.almost.equal([
+            [10, 0, 0],
+            [0, 10, 0],
+            [0, 0, 10]
         ]);
     });
-    it ('should load a noisy .xyz file', function() {
+    
+    it('should load properly a file with periodic boundary conditions across cell', function() {
+        var loader = new Loader();
+        var xyz = fs.readFileSync(path.join(__dirname, 'data', 'H2_bound.xyz'), "utf8");
+        var a = loader.load(xyz, 'xyz')['xyz'];
+        
+        expect(a.length()).to.equal(2);
+        expect(a.get_chemical_symbols()).to.deep.equal(['H', 'H']);
+        expect(a.get_positions()[0]).to.deep.almost.equal([0.2, 0.2, 0.2]);
+        expect(a.get_positions()[1]).to.deep.almost.equal([9.8, 9.8, 9.8]);
+    });
+    
+    it('should load a noisy .xyz file', function() {
 
         var loader = new Loader();
 
@@ -67,6 +179,54 @@ describe('#loading', function() {
             [0, 5.475, 0],
             [0, 0, 5.475]
         ]);
+        
+        // Check that it loaded the right number of atoms
+        expect(a.length()).to.equal(8);
+        
+        // Check that initial_magmoms were loaded (all zeros)
+        expect(a.get_array('initial_magmoms')).to.deep.almost.equal([0, 0, 0, 0, 0, 0, 0, 0]);
+        
+        // Check that castep_labels were loaded (all "NULL")
+        expect(a.get_array('castep_labels')).to.deep.equal(['NULL', 'NULL', 'NULL', 'NULL', 'NULL', 'NULL', 'NULL', 'NULL']);
+    });
+    
+    it('should throw an error for files without a lattice', function() {
+        var loader = new Loader();
+        
+        // Create a plain XYZ file without Extended XYZ format
+        var plain_xyz = `3
+water molecule
+O 0.0 0.0 0.0
+H 1.0 0.0 0.0
+H 0.0 1.0 0.0`;
+        
+        expect(() => loader.load(plain_xyz, 'xyz')).to.throw('No unit cell');
+    });
+    
+    it('should throw an error for invalid frame indices', function() {
+        var loader = new Loader();
+        var xyz = fs.readFileSync(path.join(__dirname, 'data', 'ethanol_with_tensors.xyz'), "utf8");
+        
+        // Frame index too high
+        expect(() => loader.load(xyz, 'xyz', null, { index: 10 })).to.throw('Frame index out of range');
+        
+        // Frame index too low (negative)
+        expect(() => loader.load(xyz, 'xyz', null, { index: -10 })).to.throw('Frame index out of range');
+    });
+
+    it('should load properly a CIF file', function() {
+
+        var loader = new Loader();
+
+        var cif = fs.readFileSync(path.join(__dirname, 'data', 'org.cif'), "utf8");
+        var a = loader.load(cif)['1501936'];
+
+
+        chai.expect(a.get_cell()).to.deep.almost.equal([
+            [8.2302, 0.0, 0.0],
+            [1.7507207912272031, 8.096583378263006, 0.0],
+            [1.7848106706548383, 1.959874486240255, 12.914460443940394]
+        ]);
     });
 
     it('should load properly a Magres file', function() {

package/test/model.js

@@ -19,9 +19,6 @@ import {
     AtomImage,
     BondImage
 } from '../lib/model.js';
-import {
-    ModelView as ModelView
-} from '../lib/modelview.js';
 import {
     Loader as Loader
 } from '../lib/loader.js';
@@ -50,7 +47,8 @@ var loader = new Loader();
 try {
     loader.load(xyz, 'xyz');
 } catch (e) {
-    expect(e.message).to.be.equal('No unit cell found in xyz file');
+    // Accept either the short legacy message or the more descriptive one
+    expect(e.message).to.match(/No unit cell/);
 }
 
 // manually added in dummy cell:

package/.eslintrc.json

@@ -1,16 +0,0 @@
-{
-    "env": {
-        "browser": true,
-        "es2021": true
-    },
-    "extends": "eslint:recommended",
-    "parserOptions": {
-        "ecmaVersion": 12,
-        "sourceType": "module"
-    },
-    "rules": {
-        "no-unused-vars": ["error", {
-            "args": "none"
-        }]
-    }
-}

package/.github/workflows/test-mocha.yml

@@ -1,30 +0,0 @@
-# This workflow will do a clean install of node dependencies, build the source code and run tests across different versions of node
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-nodejs-with-github-actions
-
-name: Node.js CI
-
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-
-    strategy:
-      matrix:
-        node-version: [12.x, 14.x, 16.x, 18.x]
-        # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Use Node.js ${{ matrix.node-version }}
-      uses: actions/setup-node@v2
-      with:
-        node-version: ${{ matrix.node-version }}
-    - run: npm ci
-    - run: npm run build --if-present
-    - run: npm test