molstar
Version:
A comprehensive macromolecular library.
101 lines (100 loc) • 4.62 kB
JavaScript
"use strict";
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Inspired by https://github.com/dgasmith/gau2grid.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.sphericalCollocation = sphericalCollocation;
const linear_algebra_1 = require("../../mol-math/linear-algebra");
const array_1 = require("../../mol-util/array");
const spherical_functions_1 = require("./spherical-functions");
async function sphericalCollocation(grid, orbital, taskCtx) {
const { basis, sphericalOrder, cutoffThreshold } = grid.params;
let baseCount = 0;
for (const atom of basis.atoms) {
for (const shell of atom.shells) {
for (const L of shell.angularMomentum) {
if (L > 4) {
// TODO: will L > 4 be required? Would need to precompute more functions in that case.
throw new Error('Angular momentum L > 4 not supported.');
}
baseCount += 2 * L + 1;
}
}
}
const matrix = new Float32Array(grid.npoints);
let baseIndex = 0;
for (const atom of basis.atoms) {
for (const shell of atom.shells) {
let amIndex = 0;
for (const L of shell.angularMomentum) {
const alpha = (0, spherical_functions_1.normalizeBasicOrder)(L, orbital.alpha.slice(baseIndex, baseIndex + 2 * L + 1), sphericalOrder);
baseIndex += 2 * L + 1;
collocationBasis(matrix, grid, L, shell.coefficients[amIndex++], shell.exponents, atom.center, cutoffThreshold, alpha);
if (taskCtx.shouldUpdate) {
await taskCtx.update({
message: 'Computing...',
current: baseIndex,
max: baseCount,
isIndeterminate: false,
});
}
}
}
}
return matrix;
}
function collocationBasis(matrix, grid, L, coefficients, exponents, center, cutoffThreshold, alpha) {
const ncoeff = exponents.length;
const sphericalFunc = spherical_functions_1.SphericalFunctions[L];
const cx = center[0], cy = center[1], cz = center[2];
const ny = grid.dimensions[1], nz = grid.dimensions[2];
const gdx = grid.delta[0], gdy = grid.delta[1], gdz = grid.delta[2];
const sx = grid.box.min[0], sy = grid.box.min[1], sz = grid.box.min[2];
const cutoffRadius = cutoffThreshold > 0
? Math.sqrt(-Math.log(cutoffThreshold) / (0, array_1.arrayMin)(exponents))
: 10000;
const cutoffSquared = cutoffRadius * cutoffRadius;
const radiusBox = getRadiusBox(grid, center, cutoffRadius);
const iMin = radiusBox[0][0], jMin = radiusBox[0][1], kMin = radiusBox[0][2];
const iMax = radiusBox[1][0], jMax = radiusBox[1][1], kMax = radiusBox[1][2];
for (let i = iMin; i <= iMax; i++) {
const x = sx + gdx * i - cx;
const oX = i * ny * nz;
for (let j = jMin; j <= jMax; j++) {
const y = sy + gdy * j - cy;
const oY = oX + j * nz;
for (let k = kMin; k <= kMax; k++) {
const z = sz + gdz * k - cz;
const R2 = x * x + y * y + z * z;
if (R2 > cutoffSquared) {
continue;
}
let gaussianSum = 0;
for (let c = 0; c < ncoeff; c++) {
gaussianSum +=
coefficients[c] * Math.exp(-exponents[c] * R2);
}
const sphericalSum = L === 0 ? alpha[0] : sphericalFunc(alpha, x, y, z);
matrix[k + oY] += gaussianSum * sphericalSum;
}
}
}
}
function getRadiusBox(grid, center, radius) {
const r = linear_algebra_1.Vec3.create(radius, radius, radius);
const min = linear_algebra_1.Vec3.scaleAndAdd((0, linear_algebra_1.Vec3)(), center, r, -1);
const max = linear_algebra_1.Vec3.add((0, linear_algebra_1.Vec3)(), center, r);
linear_algebra_1.Vec3.sub(min, min, grid.box.min);
linear_algebra_1.Vec3.sub(max, max, grid.box.min);
linear_algebra_1.Vec3.div(min, min, grid.delta);
linear_algebra_1.Vec3.floor(min, min);
linear_algebra_1.Vec3.max(min, min, (0, linear_algebra_1.Vec3)());
linear_algebra_1.Vec3.div(max, max, grid.delta);
linear_algebra_1.Vec3.ceil(max, max);
linear_algebra_1.Vec3.min(max, max, linear_algebra_1.Vec3.subScalar((0, linear_algebra_1.Vec3)(), grid.dimensions, 1));
return [min, max];
}