Merge pull request #43 from stan-donarise/master

coincided atoms handling
tilde-lab · Jul 29, 2024 · 4dfe534 · 4dfe534
2 parents b4c9bb2 + aef5daf
commit 4dfe534
Show file tree

Hide file tree

Showing 5 changed files with 112 additions and 72 deletions.
diff --git a/matinfio/cif/cif.ts b/matinfio/cif/cif.ts
@@ -148,7 +148,7 @@ namespace $ {
 							atom.overlays.label = atom.label
 							if( !atom.symbol ) atom.symbol = atom.label.replace( /[0-9]/g, '' )
 						}
-						if( !( $optimade_cifplayer_matinfio_chemical_elements.JmolColors as any )[ atom.symbol ]
+						if( ! $optimade_cifplayer_matinfio_chemical_elements.JmolColors[ atom.symbol ]
 							&& atom.symbol
 							&& atom.symbol.length > 1
 						) {

diff --git a/matinfio/matinfio.web.ts b/matinfio/matinfio.web.ts
@@ -1,6 +1,9 @@
 namespace $ {
 
-	export const $optimade_cifplayer_matinfio_chemical_elements = {
+	export const $optimade_cifplayer_matinfio_chemical_elements: {
+		JmolColors: Record< string, string >,
+		AseRadii: Record< string, number >,
+	} = {
 		JmolColors: { "D": "#FFFFC0", "H": "#FFFFFF", "He": "#D9FFFF", "Li": "#CC80FF", "Be": "#C2FF00", "B": "#FFB5B5", "C": "#909090", "N": "#3050F8", "O": "#FF0D0D", "F": "#90E050", "Ne": "#B3E3F5", "Na": "#AB5CF2", "Mg": "#8AFF00", "Al": "#BFA6A6", "Si": "#F0C8A0", "P": "#FF8000", "S": "#FFFF30", "Cl": "#1FF01F", "Ar": "#80D1E3", "K": "#8F40D4", "Ca": "#3DFF00", "Sc": "#E6E6E6", "Ti": "#BFC2C7", "V": "#A6A6AB", "Cr": "#8A99C7", "Mn": "#9C7AC7", "Fe": "#E06633", "Co": "#F090A0", "Ni": "#50D050", "Cu": "#C88033", "Zn": "#7D80B0", "Ga": "#C28F8F", "Ge": "#668F8F", "As": "#BD80E3", "Se": "#FFA100", "Br": "#A62929", "Kr": "#5CB8D1", "Rb": "#702EB0", "Sr": "#00FF00", "Y": "#94FFFF", "Zr": "#94E0E0", "Nb": "#73C2C9", "Mo": "#54B5B5", "Tc": "#3B9E9E", "Ru": "#248F8F", "Rh": "#0A7D8C", "Pd": "#006985", "Ag": "#C0C0C0", "Cd": "#FFD98F", "In": "#A67573", "Sn": "#668080", "Sb": "#9E63B5", "Te": "#D47A00", "I": "#940094", "Xe": "#429EB0", "Cs": "#57178F", "Ba": "#00C900", "La": "#70D4FF", "Ce": "#FFFFC7", "Pr": "#D9FFC7", "Nd": "#C7FFC7", "Pm": "#A3FFC7", "Sm": "#8FFFC7", "Eu": "#61FFC7", "Gd": "#45FFC7", "Tb": "#30FFC7", "Dy": "#1FFFC7", "Ho": "#00FF9C", "Er": "#00E675", "Tm": "#00D452", "Yb": "#00BF38", "Lu": "#00AB24", "Hf": "#4DC2FF", "Ta": "#4DA6FF", "W": "#2194D6", "Re": "#267DAB", "Os": "#266696", "Ir": "#175487", "Pt": "#D0D0E0", "Au": "#FFD123", "Hg": "#B8B8D0", "Tl": "#A6544D", "Pb": "#575961", "Bi": "#9E4FB5", "Po": "#AB5C00", "At": "#754F45", "Rn": "#428296", "Fr": "#420066", "Ra": "#007D00", "Ac": "#70ABFA", "Th": "#00BAFF", "Pa": "#00A1FF", "U": "#008FFF", "Np": "#0080FF", "Pu": "#006BFF", "Am": "#545CF2", "Cm": "#785CE3", "Bk": "#8A4FE3", "Cf": "#A136D4", "Es": "#B31FD4", "Fm": "#B31FBA", "Md": "#B30DA6", "No": "#BD0D87", "Lr": "#C70066", "Rf": "#CC0059", "Db": "#D1004F", "Sg": "#D90045", "Bh": "#E00038", "Hs": "#E6002E", "Mt": "#EB0026" },
 
 		// NB starting from Bk the radii data are incorrect
@@ -30,7 +33,7 @@ namespace $ {
 			x: number,
 			y: number,
 			z: number,
-		},
+		} | null,
 		x: number,
 		y: number,
 		z: number,
@@ -60,19 +63,7 @@ namespace $ {
 			symlabel?: string,
 		},
 		overlayed: Record< string, string >,
-		atoms: {
-			fract: {
-				x: number,
-				y: number,
-				z: number,
-			} | null,
-			x: number,
-			y: number,
-			z: number,
-			c: string, //color
-			r: number, //radius
-			overlays: Record< string, string | number >,
-		}[],
+		atoms: $optimade_cifplayer_matinfio_internal_obj_atom[]
 		sg_name: string,
 		ng_name: number,
 		info: string,
@@ -82,6 +73,8 @@ namespace $ {
 
 	export class $optimade_cifplayer_matinfio extends $mol_object2 {
 
+		static pos_overlap_limit = 0.1
+
 		static log = this.$.$optimade_cifplayer_matinfio_log
 
 		/** Guessing what to do */

diff --git a/matinfio/player/player.web.ts b/matinfio/player/player.web.ts
@@ -37,63 +37,98 @@ namespace $ {
 			mpds_data: crystal.mpds_data,
 			mpds_demo: crystal.mpds_demo
 		}
-		const pos2els: any = {}
-		const hashes: any = {}
 
+		const groups: { fpos: number[] | null, cpos: number[], atoms: $optimade_cifplayer_matinfio_internal_obj_atom[] }[] = []
+
+		// make atoms unique, i.e. remove collisions;
 		for( let i = 0; i < crystal.atoms.length; i++ ) {
-			const pos = [ crystal.atoms[ i ].x, crystal.atoms[ i ].y, crystal.atoms[ i ].z ]
-			const hash = pos.map( function( item ) { return item.toFixed( 2 ) } ).join( ',' )
-			// make atoms unique, i.e. remove collisions;
-			// makes special sense for partial occupancies
-			if( hashes.hasOwnProperty( hash ) ) {
-				var update = ""
-				for( let oprop in render.atoms[ hashes[ hash ] ].overlays ) {
+			const atom = crystal.atoms[ i ]
+
+			const pos = [ atom.x, atom.y, atom.z ]
+
+			// CIF has fractional positions
+			// OPTIMADE has cartesian positions
+			// POSCAR may have either of two
+			const fpos: number[] | null = crystal.cartesian
+				? cell_matrix ? math.divide( pos, cell_matrix ).map( fract_cord_norm ) : null
+				: pos.map( fract_cord_norm )
+
+			const cpos: number[] = fpos ? math.multiply( fpos, cell_matrix ) : pos
+
+			if( groups.some( group => {
+				if( is_overlap( cpos, group.cpos, $optimade_cifplayer_matinfio.pos_overlap_limit ) ) {
+
+					const AseRadii = $optimade_cifplayer_matinfio_chemical_elements.AseRadii[ atom.symbol ]
+					const pos = group.atoms.findIndex( atom2 => {
+						return AseRadii > $optimade_cifplayer_matinfio_chemical_elements.AseRadii[ atom2.symbol ]
+					} )
+
+					if( pos == -1 ) group.atoms.push( atom )
+					else group.atoms.splice( pos, 0, atom )
+
+					return true
+
+				}
+			} ) ) {
+				continue
+			}
+
+			groups.push( { fpos, cpos, atoms: [ atom ] } )
+		}
+
+		for( let i = 0; i < groups.length; i++ ) {
+
+			const { fpos, cpos, atoms } = groups[i]
+
+			const overlays: Record< string, string | number > = {
+				"S": atoms[0].symbol,
+				"N": i + 1,
+			}
+			for( let oprop in atoms[0].overlays ) {
+				overlays[ oprop ] = atoms[0].overlays[ oprop ]
+			}
+
+			atoms.slice(1).forEach( atom => {
+				for( let oprop in overlays ) {
+
 					if( oprop == 'S' ) {
-						if( pos2els[ hash ].indexOf( crystal.atoms[ i ].symbol ) == -1 ) {
-							update = " " + crystal.atoms[ i ].symbol
-							pos2els[ hash ].push( crystal.atoms[ i ].symbol )
+						if( atoms.every( a => a.symbol != atom.symbol ) ) {
+							overlays[ oprop ] += ' ' + atom.symbol
 						}
+
+					} else if( oprop == 'N' ) {
+						overlays[ oprop ] += ', ' + ( i + 1 )
+
+					} else if( oprop == '_atom_site_occupancy' ) {
+						overlays[ oprop ] += '+' + atom.overlays[ oprop ]
+
+					} else {
+						overlays[ oprop ] += ' ' + atom.overlays[ oprop ]
 					}
-					else if( oprop == 'N' )
-						update = ", " + ( i + 1 )
-					else if( oprop == '_atom_site_occupancy' )
-						update = "+" + crystal.atoms[ i ].overlays[ oprop ]
-					else
-						update = " " + crystal.atoms[ i ].overlays[ oprop ]
-
-					render.atoms[ hashes[ hash ] ].overlays[ oprop ] += update
-				}
-			} else {
-				const color = ($optimade_cifplayer_matinfio_chemical_elements.JmolColors as any)[ crystal.atoms[ i ].symbol ] || '#FFFF00'
-				const radius = ($optimade_cifplayer_matinfio_chemical_elements.AseRadii as any)[ crystal.atoms[ i ].symbol ] || 0.66
-
-				const overlays: Record< string, string | number > = {
-					"S": crystal.atoms[ i ].symbol,
-					"N": i + 1,
-				}
-				for( let oprop in crystal.atoms[ i ].overlays ) {
-					overlays[ oprop ] = crystal.atoms[ i ].overlays[ oprop ]
+
 				}
+			} )
 
-				// CIF has fractional positions
-				// OPTIMADE has cartesian positions
-				// POSCAR may have either of two
-				const cpos = crystal.cartesian ? pos : math.multiply( pos, cell_matrix )
-				const fpos = !crystal.cartesian ? pos : cell_matrix ? math.divide( pos, cell_matrix ) : null
-				const fract = fpos ? { 'x': fpos[ 0 ], 'y': fpos[ 1 ], 'z': fpos[ 2 ] } : null
-
-				render.atoms.push( { 
-					'fract': fract,
-					'x': cpos[ 0 ],
-					'y': cpos[ 1 ],
-					'z': cpos[ 2 ],
-					'c': color,
-					'r': radius,
-					'overlays': overlays
-				} )
-				hashes[ hash ] = render.atoms.length - 1
-				pos2els[ hash ] = [ crystal.atoms[ i ].symbol ]
+			const color = $optimade_cifplayer_matinfio_chemical_elements.JmolColors[ atoms[0].symbol ] || '#FFFF00'
+			const radius = $optimade_cifplayer_matinfio_chemical_elements.AseRadii[ atoms[0].symbol ] || 0.66
+			const atom_result = { 
+				fract: fpos ? {
+					x: fpos[ 0 ],
+					y: fpos[ 1 ],
+					z: fpos[ 2 ],
+				} : null,
+				x: cpos[ 0 ],
+				y: cpos[ 1 ],
+				z: cpos[ 2 ],
+				c: color,
+				r: radius,
+				overlays,
+				symbol: atoms[0].symbol,
+				label: atoms[0].label,
 			}
+
+			render.atoms.push( atom_result )
+
 		}
 
 		for( let oprop in crystal.atoms.at(-1)!.overlays ) {
@@ -102,5 +137,18 @@ namespace $ {
 
 		return render
 	}
+
+
+	function fract_cord_norm( cord: number ){
+		const res = cord % 1
+		return res > 0 ? res : res + 1
+	}
+
+	function is_overlap( pos1: number[], pos2: number[], threshold: number ) {
+		for( let i = 0; i < 3; i++ ) {
+			if ( pos1[i] < pos2[i] - threshold || pos1[i] > pos2[i] + threshold ) return false
+		}
+		return true
+	}
 
 }
diff --git a/matinfio/spacegroup/spacegroup.web.ts b/matinfio/spacegroup/spacegroup.web.ts
@@ -42,9 +42,9 @@ namespace $ {
 			const spans = symmetry.split( ',' )
 
 			const fract = {
-				x: fract_cord_norm( calc_symmetry_span( spans[ 0 ], atom.fract ) ),
-				y: fract_cord_norm( calc_symmetry_span( spans[ 1 ], atom.fract ) ),
-				z: fract_cord_norm( calc_symmetry_span( spans[ 2 ], atom.fract ) ),
+				x: fract_cord_norm( calc_symmetry_span( spans[ 0 ], atom.fract! ) ),
+				y: fract_cord_norm( calc_symmetry_span( spans[ 1 ], atom.fract! ) ),
+				z: fract_cord_norm( calc_symmetry_span( spans[ 2 ], atom.fract! ) ),
 			}
 
 			const [ x, y, z ] = math.multiply( [ fract.x, fract.y, fract.z ], cell )
@@ -96,9 +96,8 @@ namespace $ {
 	}
 
 	function fract_cord_norm( cord: number ){
-		let res = cord % 1
-		if( res < 0 ) res = res + 1
-		return res
+		const res = cord % 1
+		return res > 0 ? res : res + 1
 	}
 
 }
diff --git a/player/player.view.web.ts b/player/player.view.web.ts
@@ -261,7 +261,7 @@ namespace $.$$ {
 					for (const name of next_symmetries) {
 
 						const atoms = this.symmetry_atoms( name )!
-						if( is_overlap( data, atoms, 0.01 ) ) {
+						if( is_overlap( data, atoms, $optimade_cifplayer_matinfio.pos_overlap_limit ) ) {
 							return
 						}
 					}