- New docs/CPU_DATA_ANALYSIS_REFINEMENT.md (§15): the ML amplitude target and its FFT gradient, scale/robust fit/fine solvent mask, D and the variance (work/free), the embedded Monomer Library subset and topology, geometry/metal/KL-B restraints, the minimiser, the weight trials, refined maps, blobs, GPU/CPU, and a "Not yet" list; with its own References. Linked from TECHNICAL.md and CPU_DATA_ANALYSIS.md; §14 no longer says the structure is never refined. - RUGNUX_REPORT.md: a Refinement (REFINE_*) section - every REFINE_ and REFINE_SCORE_ key, the --mode refine input keys and the _blobs.json fields. - RUGNUX_MODEL_AND_REFERENCE.md: "What it does not do yet"; RUGNUX_ADVANCED.md: --model mentions the refinement, --no-refine as in the usage, a --mode refine options table; GPU_DATA_ANALYSIS.md: the refinement's CUDA engines and the missing Metal path. - ACKNOWLEDGEMENT.md: Brunger, Karplus & Petsko 1989 (gradient-balanced starting weight), Nocedal 1980 (two-loop recursion), Charbonnier et al. 1997 (pseudo-Huber), Jiang & Brunger 1994 (flat solvent mask), Kullback & Leibler 1951; all DOIs checked against Crossref. - In-source credit lines: the weight balancing (replacing a "Brunger (1992)-style" line that named the R-free paper), Nocedal 1980, Charbonnier 1997, Jiang & Brunger 1994, Emsley et al. 2010 at FindDensityBlobs, Read 1986 at the refined maps. Comments only. - docs/THIRD_PARTY_NOTICES.md regenerated from the root file with update_version.sh's own step (it lacked the CCP4 Monomer Library row). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 09375dba351bae0cc73e9a6f0f79455dc92b3a10)
158 lines
6.2 KiB
C++
158 lines
6.2 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <algorithm>
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#include <cmath>
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#include <deque>
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#include <functional>
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#include <vector>
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// Limited-memory BFGS whose memory outlives one call, so that a refinement's macro-cycles - each a few dozen
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// iterations on a target whose scale and likelihood parameters were refitted in between - go on from what the
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// earlier ones learnt of the curvature instead of starting each from a steepest-descent step. The initial inverse
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// Hessian is a diagonal the caller gives (SetDiagonal: an estimate of the Hessian's diagonal, so that a parameter
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// with ten times the curvature of another takes a tenth of its step), scaled each iteration by the latest pair
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// (Oren-Shanno in that metric). The line search backtracks from the full step to sufficient decrease.
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// Following Nocedal (1980) Math. Comp. 35, 773-782 and Liu & Nocedal (1989) Math. Program. 45, 503-528
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class RefinementMinimiser {
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public:
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// f(x, g): the target at x, and its gradient in g (sized as x); false where it cannot be evaluated there.
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using Target = std::function<bool(const std::vector<double> &x, double &f, std::vector<double> &g)>;
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explicit RefinementMinimiser(size_t memory = 20) : memory_(memory) {}
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// Forget the pairs (the target changed beyond what the memory still describes, e.g. another weight).
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void Reset() {
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s_.clear();
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y_.clear();
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sy_.clear();
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}
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// The estimated diagonal of the Hessian; every element > 0.
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void SetDiagonal(std::vector<double> h) { h_ = std::move(h); }
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struct Outcome {
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int iterations = 0;
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int evaluations = 0;
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double f_start = 0, f_end = 0;
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};
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// At most `iterations` iterations from x (x is where it ended); stops early where an iteration lowers f by
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// less than `f_tolerance` relative to |f|, or `stop` says so (checked before every iteration). `max_step`, in
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// the parameters' units, is the most any parameter moves in the first trial of a line search.
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Outcome Minimise(const Target &target, std::vector<double> &x, int iterations, double f_tolerance, double max_step,
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const std::function<bool()> &stop = nullptr) {
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const size_t n = x.size();
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if (h_.size() != n)
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h_.assign(n, 1.0);
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Outcome out;
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double f = 0;
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std::vector<double> g(n), d(n), x_new(n), g_new(n);
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if (!target(x, f, g))
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return out;
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out.evaluations++;
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out.f_start = out.f_end = f;
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for (int it = 0; it < iterations; it++) {
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if (stop && stop())
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break;
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Direction(g, d);
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double gd = Dot(g, d);
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if (!(gd < 0)) { // not a descent direction: the memory no longer fits, start again from the diagonal
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Reset();
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Direction(g, d);
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gd = Dot(g, d);
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if (!(gd < 0))
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break;
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}
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double d_max = 0;
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for (double v : d)
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d_max = std::max(d_max, std::fabs(v));
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double alpha = d_max > max_step ? max_step / d_max : 1.0;
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double f_new = 0;
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bool accepted = false;
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for (int ls = 0; ls < 10; ls++) {
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for (size_t k = 0; k < n; k++)
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x_new[k] = x[k] + alpha * d[k];
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const bool ok = target(x_new, f_new, g_new);
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out.evaluations++;
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if (ok && f_new <= f + 1e-4 * alpha * gd) {
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accepted = true;
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break;
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}
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// the minimum of the quadratic through f, its slope and f_new, kept within [0.1, 0.5] of the step
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const double q = ok ? -gd * alpha * alpha / (2.0 * (f_new - f - gd * alpha)) : 0.1 * alpha;
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alpha = std::clamp(q, 0.1 * alpha, 0.5 * alpha);
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}
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if (!accepted)
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break;
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std::vector<double> s(n), y(n);
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for (size_t k = 0; k < n; k++) {
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s[k] = x_new[k] - x[k];
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y[k] = g_new[k] - g[k];
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}
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const double sy = Dot(s, y);
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if (sy > 1e-10 * std::sqrt(Dot(s, s) * Dot(y, y))) {
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s_.push_back(std::move(s));
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y_.push_back(std::move(y));
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sy_.push_back(sy);
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if (s_.size() > memory_) {
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s_.pop_front();
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y_.pop_front();
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sy_.pop_front();
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}
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}
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const double decrease = f - f_new;
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x.swap(x_new);
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g.swap(g_new);
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f = f_new;
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out.iterations++;
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out.f_end = f;
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if (decrease <= f_tolerance * std::max(std::fabs(f), 1.0))
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break;
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}
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return out;
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}
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private:
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static double Dot(const std::vector<double> &a, const std::vector<double> &b) {
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double s = 0;
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for (size_t k = 0; k < a.size(); k++)
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s += a[k] * b[k];
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return s;
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}
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// d = -H g by the two-loop recursion, H0 = gamma diag(1/h).
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void Direction(const std::vector<double> &g, std::vector<double> &d) const {
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const size_t n = g.size(), m = s_.size();
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std::vector<double> q = g, a(m), rho(m);
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for (size_t i = m; i-- > 0;) {
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rho[i] = 1.0 / sy_[i];
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a[i] = rho[i] * Dot(s_[i], q);
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for (size_t k = 0; k < n; k++)
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q[k] -= a[i] * y_[i][k];
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}
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double gamma = 1.0;
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if (m > 0) {
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double yhy = 0;
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for (size_t k = 0; k < n; k++)
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yhy += y_[m - 1][k] * y_[m - 1][k] / h_[k];
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gamma = sy_[m - 1] / yhy;
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}
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for (size_t k = 0; k < n; k++)
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q[k] *= gamma / h_[k];
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for (size_t i = 0; i < m; i++) {
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const double b = rho[i] * Dot(y_[i], q);
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for (size_t k = 0; k < n; k++)
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q[k] += s_[i][k] * (a[i] - b);
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}
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for (size_t k = 0; k < n; k++)
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d[k] = -q[k];
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}
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size_t memory_;
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std::deque<std::vector<double>> s_, y_;
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std::deque<double> sy_; // s.y of each pair, as taken when it was kept
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std::vector<double> h_;
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};
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