leonarski_fandClaude Opus 5
1b414909cb
The map-coefficient to real-space transform was still gemmi's bundled pocketfft while the map to structure-factor direction had moved to FFTW. MapFromFPhi does that inverse with FFTW - the same half-l XYZ layout, the same 1/V scale, NaN coefficients read as zero, the same conjugation convention - and the output maps are now built with it. Plans are FFTW_ESTIMATE, cached per grid size and direction, and made under the shared planner lock. No pocketfft code is instantiated in rugnux any more (75 symbols -> 0); gemmi's fourier.hpp is still included for its non-FFT helpers (get_size_for_hkl, get_f_phi_on_grid), so the vendored header and its notice stay. Tested element-wise against gemmi on odd and even grids, with arbitrary phases, negative indices and symmetry/Friedel expansion in three space groups, plus a round trip; both new tests fail if the conjugation is dropped. On the eight --model audit sets the merged MTZ is byte-identical, the map coefficients are identical, the CCP4 maps agree to 3e-7 relative (map CC 1.00000000) and every reported key is unchanged. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_013nW6FNRP1bBJJ8pfHiByAT
113 lines
4.6 KiB
C++
113 lines
4.6 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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#include "ModelFFT.h"
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#include <algorithm>
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#include <array>
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#include <cmath>
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#include <complex>
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#include <map>
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#include <mutex>
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#include <fftw3.h>
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#include "gemmi/fail.hpp"
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#include "../common/FFTWPlannerLock.h"
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namespace {
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// The r2c plan (or, inverse, the c2r plan) for an (nu, nv, nw) map stored u fastest, halving w - the
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// layout gemmi's own transforms read and write. FFTW's planner is not thread-safe, so plans are made
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// under the process-wide planner lock (which also guards this cache); executing one on new arrays
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// (fftwf_execute_dft_r2c / _c2r) is, which is how every caller uses it.
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fftwf_plan PlanFor(int nu, int nv, int nw, bool inverse) {
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static std::map<std::array<int, 4>, fftwf_plan> plans;
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std::lock_guard lock(FFTWPlannerMutex());
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const std::array<int, 4> key{nu, nv, nw, inverse};
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if (const auto it = plans.find(key); it != plans.end())
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return it->second;
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float *real = fftwf_alloc_real(static_cast<size_t>(nu) * nv * nw);
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fftwf_complex *cplx = fftwf_alloc_complex(static_cast<size_t>(nu) * nv * (nw / 2 + 1));
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// The last dimension is the one r2c halves; the strides put u fastest on both sides.
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fftwf_iodim dims[3] = {{nu, 1, 1}, {nv, nu, nu}, {nw, nu * nv, nu * nv}};
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fftwf_plan plan = nullptr;
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if (real != nullptr && cplx != nullptr)
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plan = inverse ? fftwf_plan_guru_dft_c2r(3, dims, 0, nullptr, cplx, real, FFTW_ESTIMATE)
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: fftwf_plan_guru_dft_r2c(3, dims, 0, nullptr, real, cplx, FFTW_ESTIMATE);
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fftwf_free(real);
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fftwf_free(cplx);
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if (plan == nullptr)
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gemmi::fail("ModelFFT: no FFTW plan for the grid");
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plans.emplace(key, plan);
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return plan;
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}
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} // namespace
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gemmi::FPhiGrid<float> MapToFPhi(const gemmi::Grid<float> &map) {
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if (map.axis_order == gemmi::AxisOrder::ZYX)
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gemmi::fail("MapToFPhi(): ZYX order is not supported");
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gemmi::FPhiGrid<float> hkl;
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hkl.unit_cell = map.unit_cell;
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hkl.spacegroup = map.spacegroup;
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hkl.axis_order = map.axis_order;
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hkl.half_l = true;
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hkl.set_size_without_checking(map.nu, map.nv, map.nw / 2 + 1);
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const float norm = static_cast<float>(map.unit_cell.volume / map.point_count());
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const fftwf_plan plan = PlanFor(map.nu, map.nv, map.nw, false);
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// Buffers from fftwf_malloc: a plan may only be executed on arrays aligned as the ones it was made
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// on were, which the vectors' own allocations do not promise.
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float *in = fftwf_alloc_real(map.data.size());
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fftwf_complex *out = fftwf_alloc_complex(hkl.data.size());
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if (in == nullptr || out == nullptr) {
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fftwf_free(in);
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fftwf_free(out);
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gemmi::fail("MapToFPhi(): cannot allocate the FFT buffers");
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}
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std::copy(map.data.begin(), map.data.end(), in);
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fftwf_execute_dft_r2c(plan, in, out);
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// Conjugated, as gemmi does: FFTW's forward transform carries exp(-2 pi i h.x), and a structure
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// factor is the sum over exp(+2 pi i h.x).
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for (size_t i = 0; i < hkl.data.size(); ++i)
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hkl.data[i] = std::complex<float>(out[i][0] * norm, -out[i][1] * norm);
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fftwf_free(in);
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fftwf_free(out);
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return hkl;
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}
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gemmi::Grid<float> MapFromFPhi(const gemmi::FPhiGrid<float> &hkl) {
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if (hkl.axis_order == gemmi::AxisOrder::ZYX || !hkl.half_l)
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gemmi::fail("MapFromFPhi(): only an XYZ half-l grid is supported");
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gemmi::Grid<float> map;
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map.spacegroup = hkl.spacegroup;
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map.unit_cell = hkl.unit_cell;
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map.set_size(hkl.nu, hkl.nv, 2 * (hkl.nw - 1));
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map.axis_order = hkl.axis_order;
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const float norm = static_cast<float>(1.0 / hkl.unit_cell.volume);
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const fftwf_plan plan = PlanFor(map.nu, map.nv, map.nw, true);
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fftwf_complex *in = fftwf_alloc_complex(hkl.data.size());
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float *out = fftwf_alloc_real(map.data.size());
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if (in == nullptr || out == nullptr) {
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fftwf_free(in);
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fftwf_free(out);
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gemmi::fail("MapFromFPhi(): cannot allocate the FFT buffers");
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}
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// Conjugated, as gemmi does: rho(x) = 1/V sum F exp(-2 pi i h.x), and FFTW's backward transform
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// carries exp(+2 pi i h.x). A missing coefficient (NaN) counts as zero, also as gemmi does.
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for (size_t i = 0; i < hkl.data.size(); ++i) {
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const std::complex<float> x = hkl.data[i];
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in[i][0] = std::isnan(x.imag()) ? 0.0f : x.real();
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in[i][1] = std::isnan(x.imag()) ? 0.0f : -x.imag();
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}
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fftwf_execute_dft_c2r(plan, in, out);
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for (size_t i = 0; i < map.data.size(); ++i)
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map.data[i] = out[i] * norm;
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fftwf_free(in);
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fftwf_free(out);
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return map;
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}
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