leonarski_fandClaude Opus 5
440e19343c
gemmi::transform_map_to_f_phi conjugates the forward FFT at the end (a structure factor is the sum over exp(+2 pi i h.x), a forward FFT the sum over exp(-2 pi i h.x)); MapToFPhi did not, so every model-path Fcalc and Fmask came out with its phase negated. Amplitudes, and so the R-factors and the scale, were unaffected; the phases of the maps and everything read off them (map coefficients, density at atom centres) were not. Caught by ModelValidation_MapToFPhiMatchesGemmi, which now passes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_013nW6FNRP1bBJJ8pfHiByAT
78 lines
3.0 KiB
C++
78 lines
3.0 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 <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 for an (nu, nv, nw) map stored u fastest, halving w - the layout gemmi's own transform
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// reads and writes. FFTW's planner is not thread-safe, so plans are made under the process-wide planner
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// lock (which also guards this cache); executing one on new arrays (fftwf_execute_dft_r2c) is, which is
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// how every caller uses it.
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fftwf_plan PlanFor(int nu, int nv, int nw) {
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static std::map<std::array<int, 3>, fftwf_plan> plans;
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std::lock_guard lock(FFTWPlannerMutex());
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const std::array<int, 3> key{nu, nv, nw};
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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 *in = fftwf_alloc_real(static_cast<size_t>(nu) * nv * nw);
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fftwf_complex *out = 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 = (in != nullptr && out != nullptr)
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? fftwf_plan_guru_dft_r2c(3, dims, 0, nullptr, in, out, FFTW_ESTIMATE)
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: nullptr;
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fftwf_free(in);
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fftwf_free(out);
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if (plan == nullptr)
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gemmi::fail("MapToFPhi(): 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);
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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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