molstar
Version:
A comprehensive macromolecular library.
151 lines (150 loc) • 6.34 kB
JavaScript
;
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.gpuComputeAlphaOrbitalsGridValues = gpuComputeAlphaOrbitalsGridValues;
exports.gpuComputeAlphaOrbitalsDensityGridValues = gpuComputeAlphaOrbitalsDensityGridValues;
const grid3d_1 = require("../../../mol-gl/compute/grid3d");
const schema_1 = require("../../../mol-gl/renderable/schema");
const mol_util_1 = require("../../../mol-util");
const array_1 = require("../../../mol-util/array");
const spherical_functions_1 = require("../spherical-functions");
const shader_frag_1 = require("./shader.frag");
const Schema = {
tCenters: (0, schema_1.TextureSpec)('image-float32', 'rgba', 'float', 'nearest'),
tInfo: (0, schema_1.TextureSpec)('image-float32', 'rgba', 'float', 'nearest'),
tCoeff: (0, schema_1.TextureSpec)('image-float32', 'rgb', 'float', 'nearest'),
tAlpha: (0, schema_1.TextureSpec)('image-float32', 'alpha', 'float', 'nearest'),
uNCenters: (0, schema_1.UniformSpec)('i'),
uNAlpha: (0, schema_1.UniformSpec)('i'),
uNCoeff: (0, schema_1.UniformSpec)('i'),
uMaxCoeffs: (0, schema_1.UniformSpec)('i'),
};
const Orbitals = (0, grid3d_1.createGrid3dComputeRenderable)({
schema: Schema,
loopBounds: ['uNCenters', 'uMaxCoeffs'],
mainCode: shader_frag_1.MAIN,
utilCode: shader_frag_1.UTILS,
returnCode: 'v',
values(params) {
return createTextureData(params.grid, params.orbital);
}
});
const Density = (0, grid3d_1.createGrid3dComputeRenderable)({
schema: {
...Schema,
uOccupancy: (0, schema_1.UniformSpec)('f'),
},
loopBounds: ['uNCenters', 'uMaxCoeffs'],
mainCode: shader_frag_1.MAIN,
utilCode: shader_frag_1.UTILS,
returnCode: 'current + uOccupancy * v * v',
values(params) {
return {
...createTextureData(params.grid, params.orbitals[0]),
uOccupancy: 0
};
},
cumulative: {
states(params) {
return params.orbitals.filter(o => o.occupancy !== 0);
},
update({ grid }, state, values) {
const alpha = getNormalizedAlpha(grid.params.basis, state.alpha, grid.params.sphericalOrder);
mol_util_1.ValueCell.updateIfChanged(values.uOccupancy, state.occupancy);
mol_util_1.ValueCell.update(values.tAlpha, { width: alpha.length, height: 1, array: alpha });
}
}
});
function gpuComputeAlphaOrbitalsGridValues(ctx, webgl, grid, orbital) {
return Orbitals(ctx, webgl, grid, { grid, orbital });
}
function gpuComputeAlphaOrbitalsDensityGridValues(ctx, webgl, grid, orbitals) {
return Density(ctx, webgl, grid, { grid, orbitals });
}
function getNormalizedAlpha(basis, alphaOrbitals, sphericalOrder) {
const alpha = new Float32Array(alphaOrbitals.length);
let aO = 0;
for (const atom of basis.atoms) {
for (const shell of atom.shells) {
for (const L of shell.angularMomentum) {
const a0 = (0, spherical_functions_1.normalizeBasicOrder)(L, alphaOrbitals.slice(aO, aO + 2 * L + 1), sphericalOrder);
for (let i = 0; i < a0.length; i++)
alpha[aO + i] = a0[i];
aO += 2 * L + 1;
}
}
}
return alpha;
}
function createTextureData(grid, orbital) {
const { basis, sphericalOrder, cutoffThreshold } = grid.params;
let centerCount = 0;
let baseCount = 0;
let coeffCount = 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.');
}
centerCount++;
baseCount += 2 * L + 1;
coeffCount += shell.exponents.length;
}
}
}
const centers = new Float32Array(4 * centerCount);
// L, alpha_offset, coeff_offset_start, coeff_offset_end
const info = new Float32Array(4 * centerCount);
const alpha = new Float32Array(baseCount);
const coeff = new Float32Array(3 * coeffCount);
let maxCoeffs = 0;
let cO = 0, aO = 0, coeffO = 0;
for (const atom of basis.atoms) {
for (const shell of atom.shells) {
let amIndex = 0;
for (const L of shell.angularMomentum) {
const a0 = (0, spherical_functions_1.normalizeBasicOrder)(L, orbital.alpha.slice(aO, aO + 2 * L + 1), sphericalOrder);
const cutoffRadius = cutoffThreshold > 0
? Math.sqrt(-Math.log(cutoffThreshold) / (0, array_1.arrayMin)(shell.exponents))
: 10000;
centers[4 * cO + 0] = atom.center[0];
centers[4 * cO + 1] = atom.center[1];
centers[4 * cO + 2] = atom.center[2];
centers[4 * cO + 3] = cutoffRadius * cutoffRadius;
info[4 * cO + 0] = L;
info[4 * cO + 1] = aO;
info[4 * cO + 2] = coeffO;
info[4 * cO + 3] = coeffO + shell.exponents.length;
for (let i = 0; i < a0.length; i++)
alpha[aO + i] = a0[i];
const c0 = shell.coefficients[amIndex++];
for (let i = 0; i < shell.exponents.length; i++) {
coeff[3 * (coeffO + i) + 0] = c0[i];
coeff[3 * (coeffO + i) + 1] = shell.exponents[i];
}
if (c0.length > maxCoeffs) {
maxCoeffs = c0.length;
}
cO++;
aO += 2 * L + 1;
coeffO += shell.exponents.length;
}
}
}
return {
uNCenters: centerCount,
uNAlpha: baseCount,
uNCoeff: coeffCount,
uMaxCoeffs: maxCoeffs,
tCenters: { width: centerCount, height: 1, array: centers },
tInfo: { width: centerCount, height: 1, array: info },
tCoeff: { width: coeffCount, height: 1, array: coeff },
tAlpha: { width: baseCount, height: 1, array: alpha },
};
}