@ccp-nc/crystvis-js 0.4.13 → 0.5.0

package/lib/assets/fonts/index.js

@@ -7,8 +7,10 @@ import {
 import * as Fonts from './bmpfonts.js';
 
 // Load the actual fonts
-const RubikMedium = new BitmapFont(Fonts.rubikMediumFont, Fonts.rubikMediumTexture);
+// For some reason if I load more than one font at a time, it breaks...
+// const RubikMedium = new BitmapFont(Fonts.rubikMediumFont, Fonts.rubikMediumTexture);
+const OpenSans = new BitmapFont(Fonts.openSansFont, Fonts.openSansTexture);
 
 export {
-    RubikMedium
+    OpenSans
 };

package/lib/formats/cell.js

@@ -8,7 +8,7 @@
 import _ from 'lodash';
 import {
     Atoms
-} from 'crystcif-parse';
+} from '@ccp-nc/crystcif-parse';
 
 function cellBlocks(lines, units={}) {
     const block_re = /%BLOCK\s+([A-Z_]+)/;
@@ -56,8 +56,14 @@ function load(contents, filename='cell') {
 
     // Admissible units
     const units = {
-        'LATTICE_CART': ['ang'],
-        'POSITIONS_ABS': ['ang']
+        'LATTICE_CART':  ['ang', 'bohr'],
+        'LATTICE_ABC':   ['ang', 'bohr'],
+        'POSITIONS_ABS': ['ang', 'bohr'],
+    };
+    // conversion factors
+    const unit_conv = {
+        'ang': 1.0,
+        'bohr': 0.5291772108 // CODATA 2002
     };
 
     // Find blocks
@@ -90,6 +96,17 @@ function load(contents, filename='cell') {
     let cell = ccart? blocks['LATTICE_CART'].lines : blocks['LATTICE_ABC'].lines;
     cell = cell.map((l) => (_.trim(l).split(/\s+/).map(parseFloat)));
 
+    // Scale cell by units
+    if (ccart) {
+        let u = blocks['LATTICE_CART']['units'] || 'ang';
+        cell = cell.map((l) => (l.map((x) => (x*unit_conv[u]))));
+    }
+    else if (cabc) {
+        let u = blocks['LATTICE_ABC']['units'] || 'ang';
+        // scale just the first row by units
+        cell[0] = cell[0].map((x) => (x*unit_conv[u]));
+    }
+
     let elems = [];
     let positions = [];
 
@@ -101,6 +118,12 @@ function load(contents, filename='cell') {
             throw Error('Incomplete line in positions block');
         elems.push(l[0]);
         positions.push(l.slice(1,4).map(parseFloat));
+        // scale by units if in absolute units
+        if (pabs) {
+            // if units is not defined, assume angstroms
+            let u = blocks['POSITIONS_ABS']['units'] || 'ang';
+            positions[positions.length-1] = positions[positions.length-1].map((x) => (x*unit_conv[u]));
+        }
     });
     
     var a = new Atoms(elems, positions, cell, {}, pfrac);

package/lib/formats/cif.js

@@ -6,7 +6,7 @@
  */
 
 import _ from 'lodash';
-import { Atoms } from 'crystcif-parse';
+import { Atoms } from '@ccp-nc/crystcif-parse';
 
 function load(contents, filename) {
 

package/lib/formats/magres.js

@@ -8,7 +8,7 @@
 import _ from 'lodash';
 import {
     Atoms
-} from 'crystcif-parse';
+} from '@ccp-nc/crystcif-parse';
 import {
     TensorData
 } from '../tensor.js';
@@ -50,6 +50,36 @@ function parseNoAtomLine(line, units) {
 function parseOneAtomLine(line, units, labels) {
     // Species label + index, then nine numbers
     let sp = line[0];
+    // CASTEP <22.1.1 has a bug where species with in in-species index >99 
+    // runs into the species label.
+    // To handle those cases, we need to check if the species label has
+    // an integer >99 at the end, and if so, remove it from the label
+    // and add it to the index.
+    
+    // use regex to find any integer at the end of the species label
+    let sp_re = /([a-zA-Z]+)([0-9]+)$/;
+    let sp_match = sp.match(sp_re);
+    if (sp_match) {
+        // if the integer is >99 and the line has 10 elements instead of 11, 
+        // remove it from the label and add it to the index
+        let rogue_int = parseInt(sp_match[2]);
+        if (rogue_int > 99 && line.length == 10) {
+            console.log(`
+            Badly formatted .magres file. 
+            A line has a species label with an integer >99 at the end, 
+            which suggests a writing-overflow (known bug in CASTEP). 
+            e.g. 'Fe100' instead of 'Fe 100'.
+            The integer has been removed from the label and added to the index.
+            `)
+            
+            sp = sp_match[1];
+            // insert the rogue integer into 
+            // the line array at the correct position
+            line.splice(1, 0, rogue_int);
+        }
+    }
+
+
     let sp_i = parseInt(line[1]);
     let i = _.findIndex(labels, function(x) {
         return (x[0] == sp) && (x[1] == sp_i);
@@ -221,6 +251,11 @@ function load(contents, filename='magres') {
         }
     }
 
+    // Reject if we don't have a cell
+    if (!cell) {
+        throw Error('No unit cell found in Magres file. We only support Magres files with a Lattice block.');
+    }
+    
     // Read in the atom positions and species
     let elems = [];
     let pos = [];
@@ -243,8 +278,7 @@ function load(contents, filename='magres') {
             elems.push(l[0]);
             mlabels.push([l[1], parseInt(l[2])]);
             labels.push(l[1]);
-
-            pos.push(_.map(l.splice(3), function(x) {
+            pos.push(_.map(l.slice(3,6), function(x) {
                 return parseFloat(x) * u;
             }));
         }

package/lib/formats/xyz.js

@@ -6,7 +6,7 @@
  */
 
 import _ from 'lodash';
-import { Atoms } from 'crystcif-parse';
+import { Atoms } from '@ccp-nc/crystcif-parse';
 
 function load(contents, filename='xyz') {
 
@@ -23,7 +23,7 @@ function load(contents, filename='xyz') {
     let info = lines[1];
     // Check if it's extended format
     let ext = false;
-    let rext = /([A-Za-z]+)=(([A-Za-z0-9.:]+)|"([\s0-9.]+)")/g;
+    let rext = /([A-Za-z]+)=(([A-Za-z0-9.:]+)|"([\s0-9.e-]+)")/g;
     let m = rext.exec(info);
     let matches = [];
     let cell = null;
@@ -108,6 +108,11 @@ function load(contents, filename='xyz') {
         }
     }
 
+    // check if we have a cell
+    if (cell === null) {
+        throw Error('No cell found in XYZ file. Please use the Extended XYZ format.');
+    }
+
     let a = new Atoms(elems, pos, cell, info);
     if (ext) {
         for (let i = 0; i < arrays.length; ++i) {

package/lib/model.js

@@ -13,7 +13,7 @@ import {
 
 import {
     Atoms as Atoms
-} from 'crystcif-parse';
+} from '@ccp-nc/crystcif-parse';
 
 import * as utils from './utils.js';
 import * as data from './data.js';
@@ -976,9 +976,27 @@ class Model {
                 return c;
             });
 
+            let has_cif_labels = false;
+
             // Crystallographic labels
             if ('labels' in this._atoms_base._arrays) {
-                this._labels = this._atoms_base._arrays['labels'];
+                // If any of the labels don't match the element,
+                // then we're assuming they're crystallographic (CIF-style) labels
+                if (this._atoms_base._arrays['labels'].some((l, i) => {
+                    return l !== this._elems[i];
+                })) {
+                    // then use them
+                    has_cif_labels = true;
+                    this._labels = this._atoms_base._arrays['labels'];
+                } else {
+                    // otherwise, build new ones and
+                    // throw a warning to user syaing we're doing this
+                    this._labels = [];
+                    for (let i = 0; i < this._elems.length; ++i) {
+                        this._labels.push(this._elems[i] + '_' + (this._species_indices[i]+1));
+                    }
+                    console.warn('No crystallographic labels found in CIF file. Building new ones.');
+                }
             }
             else {
                 // Build them
@@ -988,13 +1006,15 @@ class Model {
                 }
             }
 
+            this._has_cif_labels = has_cif_labels; // defaults to false
 
             if (this._periodic) {
                 // R matrix: indispensable for calculations of periodic distances
                 this._r_matrix = mjs.multiply(this._cell, mjs.transpose(this._cell));
                 var ediag = mjs.eigs(this._r_matrix);
-                // Sort by eigenvalue
-                ediag = _.zip(ediag.values, ediag.vectors);
+                // Sort by eigenvalue 
+                var evecs = ediag.eigenvectors.map(e => e.vector);
+                ediag = _.zip(ediag.values, evecs);
                 ediag = _.sortBy(ediag, function(x) {
                     return x[0];
                 });
@@ -1003,7 +1023,7 @@ class Model {
                 this._r_diag = {
                     values: ediag[0],
                     vectors: ediag[1],
-                }
+                };
 
                 this._supercell = supercell; // Default
                 this._supercell_grid = utils.supercellGrid(supercell);
@@ -1021,7 +1041,11 @@ class Model {
 
         initMolecules(atoms, parameters.supercell);
 
-        if (parameters.molecularCrystal) {
+        // if parameters.molecularCrystal, is null, we need to check if the atoms 
+        // contains organic molecules -- i.e. if there is at least one  C-H bond
+        if (parameters.molecularCrystal || (parameters.molecularCrystal === null &&
+            this._queryCHBond())) {
+            this._molecularCrystal = true;
             atoms = _.cloneDeep(atoms);
             var pos = this.positions;
             for (let i = 0; i < this.length; ++i) {
@@ -1248,7 +1272,7 @@ class Model {
             if (this.periodic) {
                 // Create axes and box
                 if (!this._cartesian_box) {
-                    this._cartesian_box = new r.Primitives.BoxMesh(this.cell);
+                    this._cartesian_box = new r.Primitives.BoxMesh(this.cell, {color:r.theme.cell_line_color});
                 }
                 if (!this._cartesian_axes) {
                     this._cartesian_axes = new r.Primitives.AxesMesh(this.cell, {
@@ -1341,7 +1365,7 @@ class Model {
                     color: parameters.color,
                     fixScale: true,
                     faceCamera: true,
-                    height: LABEL_HEIGHT,
+                    height: parameters.height || LABEL_HEIGHT,
                     shift: [LABEL_HEIGHT, 0, 0],
                     onOverlay: parameters.onOverlay
                 });
@@ -1492,6 +1516,40 @@ class Model {
         }
     }
 
+    /**
+     * Check if any C-H bonds are present
+     * @return {bool} Whether any C-H bonds are present
+     * @private
+     */
+    _queryCHBond() {
+        // make sure bondmat is present
+        if (!this._bondmat) {
+            this._computeBonds();
+        }
+
+        var symbols = this._atoms_base.get_chemical_symbols();
+        var bondmat = this._bondmat;
+        var n = symbols.length;
+        for (var i = 0; i < n; i++) {
+            var bonds = bondmat[i];
+            var a = symbols[i];
+            if (a == 'C') {
+                // loop over bonds and check if any are H
+                for (var j = 0; j < n; j++) {
+                    // if bonds[j] is not an empty array
+                    if (bonds[j].length) { 
+                        if (symbols[j] == 'H') {
+                            return true;
+                        }
+                    }
+                }
+            }
+        }
+        return false;
+    }
+    
+    
+
     /**
      * Compute the molecules within the model. For internal use
      * @private
@@ -1804,6 +1862,23 @@ class Model {
         return this._queryIndices(indices);
     }
 
+   /**
+     * @private
+     */
+    _queryLabels(labels) {
+        if (_.isString(labels)) {
+            labels = [labels]; // A single label
+        }
+        var indices = _.reduce(this._labels, function(inds, s, i) {
+            if (labels.indexOf(s) > -1) {
+                inds.push(i);
+            }
+            return inds;
+        }, []);
+
+        return this._queryIndices(indices);
+    }
+
     /**
      * @private
      */

package/lib/modelview.js

@@ -169,6 +169,34 @@ class ModelView {
         return new ModelView(this._model, indices);
     }
 
+    /** 
+     * Remove all atoms in mview from the current view
+     */
+    remove(mview) {
+        if (this._model != mview._model)
+            throw 'The two ModelViews do not refer to the same Model';
+        return new ModelView(this._model,
+            _.differenceWith(this._indices, mview._indices));
+    }
+
+    /** 
+     * Unique atoms in the current view (based on site labels)
+     */
+    uniqueSites() {
+        // all labels:
+        var labels = this._images.map(function(a) { return a.crystLabel; });
+        var allIndices = this._indices;
+
+        // unique labels:
+        var ulabels = _.uniq(labels);
+        // indices of unique labels:
+        var uindices = ulabels.map(function(l) { return allIndices[labels.indexOf(l)]; });
+        // sort the uindices:
+        uindices.sort(function(a, b) { return a - b; });
+        // return the unique atoms:
+        return new ModelView(this._model, uindices);
+    }
+        
     /**
      * Internal function used to turn a single value, array of values, or
      * function into an array of values
@@ -220,6 +248,13 @@ class ModelView {
         return this;
     }
 
+    /** 
+     * Get sorted set of unique elements in the ModelView
+     */
+    get elements() {
+        return _.uniq(this.map(a => a.element).sort());
+    }
+       
     /**
      * Add labels to the atom images in this ModelView
      * 

package/lib/primitives/cell.js

@@ -8,6 +8,9 @@ import _ from 'lodash';
 import * as THREE from 'three';
 import { Vector3 } from 'three';
 import { cellMatrix3 } from '../utils.js';
+import { TextSprite } from './sprites.js';
+
+const LABEL_HEIGHT  = 0.04; // Height of the label
 
 // Cell box
 class BoxMesh extends THREE.LineSegments {
@@ -67,19 +70,21 @@ class AxesMesh extends THREE.Group {
      * 
      * @param  {Array}  lattice     Lattice parameters for the unit cell
      * @param  {Object} parameters  Options:
-     *                                  linewidth
+     *                                  linewidth (NB: on most platforms linewidth will always be 1 regardless of the set value. This is a known issue with three.js)
      *                                  xColor
      *                                  yColor
      *                                  zColor
+     *                                  labels: array of strings for the labels. Defaults to null, which means no labels
      * 
      */
     constructor(lattice, parameters = {}) {
 
         var defaults = {
-            linewidth: 1.2,
+            linewidth: 1.2, // this often is effectively 1.0. See: https://threejs.org/docs/?q=lineba#api/en/materials/LineBasicMaterial.linewidth
             xColor: 0xff0000,
             yColor: 0x00ff00,
-            zColor: 0x0000ff
+            zColor: 0x0000ff,
+            labels: null
         };
 
         parameters = _.merge(defaults, parameters);
@@ -112,6 +117,23 @@ class AxesMesh extends THREE.Group {
             var arr = new THREE.ArrowHelper(dir, origin, l, colors[i]);
             arr.line.material.linewidth = parameters.linewidth;
             this.add(arr);
+
+            if (parameters.labels) {
+                // assert parameters.labels.length == 3
+                var label = parameters.labels[i];
+                var labelPos = dir.clone().multiplyScalar(l * 1.1);
+                var text = new TextSprite(label, {
+                    position: labelPos,
+                    color: colors[i],
+                    height: LABEL_HEIGHT,
+                    faceCamera: true,
+                    fixScale: true,
+                    shift: [0.0,0,0.0],
+                    });
+                this.add(text);
+            }
+
+
         }
     }
 

package/lib/primitives/ellipsoid.js

@@ -31,6 +31,7 @@ class EllipsoidMesh extends THREE.Mesh {
             color: 0xff0000,
             opacity: 0.5,
             opacityMode: EllipsoidMesh.DITHER,
+            showEllipsoid: true,
             showCircles: true,
             showAxes: true,
             scalingFactor: 1.0
@@ -86,21 +87,36 @@ class EllipsoidMesh extends THREE.Mesh {
         if (parameters.showAxes) {
 
             let matline = new THREE.LineBasicMaterial({
-                color: new THREE.Color(c),
+                color: new THREE.Color(0xff0000),
             });
 
             let geoline = new THREE.BufferGeometry().setFromPoints([new THREE.Vector3(-1, 0, 0),
                 new THREE.Vector3(1, 0, 0)
             ]);
+            
+            // change the color of the x axis
+            matline = new THREE.LineBasicMaterial({
+                color: new THREE.Color(0xff0000),
+            });
+            let xseg = new THREE.LineSegments(geoline, matline);
+            this.add(xseg);
 
-            let cseg = new THREE.Line(geoline, matline);
-            this.add(cseg);
-            cseg = new THREE.Line(geoline, matline);
-            cseg.rotateZ(Math.PI / 2.0);
-            this.add(cseg);
-            cseg = new THREE.Line(geoline, matline);
-            cseg.rotateY(Math.PI / 2.0);
-            this.add(cseg);
+            // change the color of the y axis
+            matline = new THREE.LineBasicMaterial({
+                color: new THREE.Color(0x00ff00),
+            });
+            let yseg = new THREE.LineSegments(geoline, matline);
+            yseg.rotateZ(Math.PI / 2.0);
+            this.add(yseg);
+
+            // change the color of the z axis
+            matline = new THREE.LineBasicMaterial({
+                color: new THREE.Color(0x0000ff),
+            });
+            // matline.color = new THREE.Color(0x0000ff);
+            let zseg = new THREE.LineSegments(geoline, matline);
+            zseg.rotateY(Math.PI / 2.0);
+            this.add(zseg);
         }
 
         let c0 = parameters.center;
@@ -115,6 +131,10 @@ class EllipsoidMesh extends THREE.Mesh {
         this.eigenvalues = parameters.eigenvalues;
         this.eigenvectors = parameters.eigenvectors;
 
+        // set material to be invisible if showEllipsoid is false
+        if (!parameters.showEllipsoid) {
+            material.visible = false;
+        }
         this.renderOrder = 0.5;
     }
 

package/lib/primitives/sprites.js

@@ -7,7 +7,7 @@
 import _ from 'lodash';
 import * as THREE from 'three';
 import {
-    RubikMedium
+    OpenSans
 } from '../assets/fonts/index.js';
 
 
@@ -85,7 +85,7 @@ class TextSprite extends THREE.Mesh {
 
         var defaults = {
             position: [0, 0, 0],
-            font: RubikMedium,
+            font: OpenSans,
             color: 0xffffff,
             opacity: 1.0,
             height: 1.0,