Restrained refinement on the GPU: ML amplitude target, FFT gradient, dictionary restraints, R1 + R2 driver, blobs
RefineModel (Refinement.h) refines a placed model against the merge, reading and writing nothing: - placement stage (R1): every chain of 50+ atoms as a rigid body at once (L-BFGS on six parameters per chain, their gradient from the per-atom one through Ceres jets), then one B shift per residue; - restrained stage (R2): positions and isotropic B of every atom of a residue the embedded dictionary describes, the rest held fixed but kept in Fcalc and the mask; riding hydrogens added by gemmi's topology, moved with their parents, re-placed every macro-cycle. Macro-cycles refit the mask, the scale and bulk solvent (FitModelScale / ModelScaleGPUPool) and the likelihood's D and beta (ML on the free set in resolution bins), rebuild the repulsion pairs (symmetry mates included), then L-BFGS on positions and, where chosen, on B. - weights: a ladder of full refinements at multiples of the gradient-balanced X-ray weight, chosen by R-free within bond/angle bounds (ties to the tighter geometry), then the B refinement tried at its own weights and kept only where it beats B held by more than the tie. The target and its gradient (RefinementXray, RefinementGPU): the Rice/centric amplitude likelihood (RefinementMath.h, shared host/device code), the gradient by Agarwal's FFT method - the adjoint of the reciprocal-space symmetry composition into a half-l (CPU) or half-u (cuFFT) spectrum, one inverse real transform, then each atom's density derivatives (xyz and B) summed over its box. On the GPU everything per evaluation stays on the device: ModelDensityGPU's gather, r2c, a fused compose + likelihood kernel, a CSR gather for the adjoint (no atomics), c2r, one warp per atom for the gradient; the restraints are one kernel per restraint plus a per-atom gather of gradient slots; cub reductions. Deterministic. Restraints (RefinementRestraints): bonds, angles, torsions (with esd, no phi/psi, no alternative sugar puckers), chiral volumes, least-squares planes from gemmi's Topo; repulsions beyond 1-4 (vdW radii from the dictionary's energy library, 2.6 A for H-bond pairs, 1.9 A metal-N/O/S); B similarity of bonded and angle-related atoms. DensityBlobs (D1): gemmi's flood-fill blobs of mFo-DFc above 3 sigma peaking above 4 sigma, placed beside the model and labelled WATER / ION / LIGAND / MODEL_ERROR by distance, contacts, volume and the anomalous map. tools/rugnux_refine_test refines a model against a finished run's p.mtz (developer utility, not installed). Tests: likelihood derivative, the embedded library, restraint values on ideal residues and every restraint kind's gradient against finite differences (CPU, and the GPU against the CPU), the X-ray gradient against finite differences in P1, P212121, C2 and P6122 (CPU and GPU), and a synthetic refinement that recovers a shaken model. Credits in docs/ACKNOWLEDGEMENT.md and at the algorithms. Measured on the open arm's battery outputs against REFMAC 5.8, 10 cycles, same p.mtz, free set and start model (R-free): 5reo 0.2228 vs 0.2236, 8dyz 0.1733 vs 0.1651, 9chw 0.1995 vs 0.1969 (CPU engine). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 8efe6f2322b3bfdae580bb34f256e67730dfc3c2)
This commit is contained in:
leonarski_f committed
1 parent
e58453a693
commit
b4b68d368f
19 files changed
+4220
No files matched your search
@@ -0,0 +1,452 @@
|
||||
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
|
||||
// SPDX-License-Identifier: GPL-3.0-only
|
||||
|
||||
#include <catch2/catch_all.hpp>
|
||||
|
||||
#include <cmath>
|
||||
#include <map>
|
||||
#include <random>
|
||||
#include <vector>
|
||||
|
||||
#include <gemmi/symmetry.hpp>
|
||||
|
||||
#include "../common/CUDAWrapper.h"
|
||||
#include "../common/Logger.h"
|
||||
#include "../image_analysis/structure_refinement/MonomerLibrary.h"
|
||||
#include "../image_analysis/structure_refinement/Refinement.h"
|
||||
#include "../image_analysis/structure_refinement/RefinementMath.h"
|
||||
#include "../image_analysis/structure_refinement/RefinementRestraints.h"
|
||||
#include "../image_analysis/structure_refinement/RefinementXray.h"
|
||||
#ifdef JFJOCH_USE_CUDA
|
||||
#include "../image_analysis/structure_refinement/RefinementGPU.h"
|
||||
#endif
|
||||
|
||||
namespace {
|
||||
|
||||
// Copies of residue `code` at the embedded dictionary's ideal coordinates (hydrogens left out), each turned and
|
||||
// moved to a place of its own in the cell.
|
||||
gemmi::Structure residue_crystal(const std::vector<std::string> &codes, const gemmi::UnitCell &cell, const char *group,
|
||||
unsigned seed) {
|
||||
std::mt19937 rng(seed);
|
||||
std::uniform_real_distribution<double> frac(0.0, 1.0), angle(-3.1, 3.1);
|
||||
gemmi::Structure st;
|
||||
st.cell = cell;
|
||||
st.spacegroup_hm = group;
|
||||
st.setup_cell_images();
|
||||
gemmi::Model model(1);
|
||||
gemmi::Chain chain("A");
|
||||
int seq = 1;
|
||||
for (const std::string &code : codes) {
|
||||
const gemmi::ChemComp &cc = EmbeddedMonomerLibrary().monomers.at(code);
|
||||
gemmi::Residue res;
|
||||
res.name = code;
|
||||
res.seqid = gemmi::SeqId(seq++, ' ');
|
||||
res.het_flag = 'H';
|
||||
res.entity_type = gemmi::EntityType::NonPolymer;
|
||||
const gemmi::Position centre = cell.orthogonalize(gemmi::Fractional(frac(rng), frac(rng), frac(rng)));
|
||||
const double ax = angle(rng), ay = angle(rng), az = angle(rng);
|
||||
const gemmi::Mat33 rot = gemmi::Mat33(1, 0, 0, 0, std::cos(ax), -std::sin(ax), 0, std::sin(ax), std::cos(ax))
|
||||
.multiply(gemmi::Mat33(std::cos(ay), 0, std::sin(ay), 0, 1, 0, -std::sin(ay), 0, std::cos(ay)))
|
||||
.multiply(gemmi::Mat33(std::cos(az), -std::sin(az), 0, std::sin(az), std::cos(az), 0, 0, 0, 1));
|
||||
for (const gemmi::ChemComp::Atom &ca : cc.atoms) {
|
||||
if (ca.is_hydrogen())
|
||||
continue;
|
||||
gemmi::Atom a;
|
||||
a.name = ca.id;
|
||||
a.element = ca.el;
|
||||
a.pos = gemmi::Position(rot.multiply(ca.xyz)) + centre;
|
||||
a.b_iso = 20.0f;
|
||||
a.occ = 1.0f;
|
||||
res.atoms.push_back(a);
|
||||
}
|
||||
chain.residues.push_back(res);
|
||||
}
|
||||
model.chains.push_back(chain);
|
||||
st.models.push_back(model);
|
||||
return st;
|
||||
}
|
||||
|
||||
// Atoms of a few elements scattered over the cell.
|
||||
gemmi::Structure random_crystal(const gemmi::UnitCell &cell, const char *group, int n, unsigned seed) {
|
||||
std::mt19937 rng(seed);
|
||||
std::uniform_real_distribution<double> frac(0.0, 1.0), b(10.0, 40.0);
|
||||
const gemmi::El elements[] = {gemmi::El::C, gemmi::El::N, gemmi::El::O, gemmi::El::S};
|
||||
gemmi::Structure st;
|
||||
st.cell = cell;
|
||||
st.spacegroup_hm = group;
|
||||
st.setup_cell_images();
|
||||
gemmi::Model model(1);
|
||||
gemmi::Chain chain("A");
|
||||
gemmi::Residue res;
|
||||
res.name = "UNK";
|
||||
res.seqid = gemmi::SeqId(1, ' ');
|
||||
for (int i = 0; i < n; i++) {
|
||||
gemmi::Atom a;
|
||||
a.name = "X";
|
||||
a.element = elements[i % 4];
|
||||
a.pos = cell.orthogonalize(gemmi::Fractional(frac(rng), frac(rng), frac(rng)));
|
||||
a.b_iso = static_cast<float>(b(rng));
|
||||
a.occ = 1.0f;
|
||||
res.atoms.push_back(a);
|
||||
}
|
||||
chain.residues.push_back(res);
|
||||
model.chains.push_back(chain);
|
||||
st.models.push_back(model);
|
||||
return st;
|
||||
}
|
||||
|
||||
// Every reflection of the group's ASU to d_min, amplitude 1, one in twenty free.
|
||||
std::vector<MergedReflection> asu_reflections(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min) {
|
||||
std::vector<MergedReflection> out;
|
||||
const gemmi::ReciprocalAsu asu(&sg);
|
||||
const gemmi::GroupOps gops = sg.operations();
|
||||
const gemmi::Miller lim = cell.get_hkl_limits(d_min);
|
||||
int i = 0;
|
||||
for (int h = -lim[0]; h <= lim[0]; h++)
|
||||
for (int k = -lim[1]; k <= lim[1]; k++)
|
||||
for (int l = -lim[2]; l <= lim[2]; l++) {
|
||||
const gemmi::Miller m{{h, k, l}};
|
||||
if ((h == 0 && k == 0 && l == 0) || !asu.is_in(m) || gops.is_systematically_absent(m))
|
||||
continue;
|
||||
const double d = cell.calculate_d(m);
|
||||
if (d < d_min)
|
||||
continue;
|
||||
MergedReflection r;
|
||||
r.h = h;
|
||||
r.k = k;
|
||||
r.l = l;
|
||||
r.d = static_cast<float>(d);
|
||||
r.F = 1.0f;
|
||||
r.sigmaF = 0.05f;
|
||||
r.rfree_flag = (i++ % 20) == 0;
|
||||
out.push_back(r);
|
||||
}
|
||||
return out;
|
||||
}
|
||||
|
||||
// The observations set to |F| of `truth`, and a row model with no scale, no solvent and the likelihood's
|
||||
// parameters estimated against `model`.
|
||||
void set_observations(RefinementEngine &engine, RefinementReflections &refl, const gemmi::Model &truth,
|
||||
const gemmi::Model &model) {
|
||||
std::vector<std::complex<float>> f;
|
||||
engine.Fcalc(truth, f);
|
||||
for (size_t m = 0; m < refl.Size(); m++)
|
||||
refl.fo[m] = std::abs(f[m]);
|
||||
engine.Fcalc(model, f);
|
||||
XrayRowModel rows;
|
||||
rows.k_total.assign(refl.Size(), 1.0f);
|
||||
rows.fmask.assign(refl.Size(), {0, 0});
|
||||
EstimateLikelihoodParameters(refl, f, rows);
|
||||
engine.SetRowModel(rows);
|
||||
}
|
||||
|
||||
gemmi::Model shaken(const gemmi::Model &model, double sigma, double b_sigma, unsigned seed) {
|
||||
std::mt19937 rng(seed);
|
||||
std::normal_distribution<double> d(0, sigma), db(0, b_sigma);
|
||||
gemmi::Model out = model;
|
||||
for (gemmi::Chain &ch : out.chains)
|
||||
for (gemmi::Residue &r : ch.residues)
|
||||
for (gemmi::Atom &a : r.atoms) {
|
||||
a.pos += gemmi::Position(d(rng), d(rng), d(rng));
|
||||
a.b_iso = static_cast<float>(std::max(5.0, a.b_iso + db(rng)));
|
||||
}
|
||||
return out;
|
||||
}
|
||||
|
||||
std::vector<gemmi::Atom *> atoms_of(gemmi::Model &model) {
|
||||
std::vector<gemmi::Atom *> out;
|
||||
for (gemmi::Chain &ch : model.chains)
|
||||
for (gemmi::Residue &r : ch.residues)
|
||||
for (gemmi::Atom &a : r.atoms)
|
||||
out.push_back(&a);
|
||||
return out;
|
||||
}
|
||||
|
||||
// The engine's gradient of a few atoms against central differences of its own target.
|
||||
void check_xray_gradient(RefinementEngine &engine, gemmi::Model model, double tolerance) {
|
||||
std::vector<std::array<double, 4>> grad;
|
||||
engine.Evaluate(model, &grad);
|
||||
std::vector<gemmi::Atom *> atoms = atoms_of(model);
|
||||
const double hx = 2e-3, hb = 2e-2;
|
||||
double max_g = 0;
|
||||
for (const auto &g : grad)
|
||||
for (int c = 0; c < 4; c++)
|
||||
max_g = std::max(max_g, std::fabs(g[c]));
|
||||
for (size_t i = 0; i < atoms.size(); i += atoms.size() / 7) {
|
||||
for (int c = 0; c < 4; c++) {
|
||||
const gemmi::Position p0 = atoms[i]->pos;
|
||||
const float b0 = atoms[i]->b_iso;
|
||||
const double h = c < 3 ? hx : hb;
|
||||
auto set = [&](double s) {
|
||||
atoms[i]->pos = p0;
|
||||
atoms[i]->b_iso = b0;
|
||||
if (c < 3)
|
||||
atoms[i]->pos.at(c) += s;
|
||||
else
|
||||
atoms[i]->b_iso = static_cast<float>(b0 + s);
|
||||
};
|
||||
set(h);
|
||||
const double fp = engine.Evaluate(model, nullptr);
|
||||
set(-h);
|
||||
const double fm = engine.Evaluate(model, nullptr);
|
||||
set(0);
|
||||
const double fd = (fp - fm) / (2 * h);
|
||||
CAPTURE(i, c, fd, grad[i][c], max_g);
|
||||
CHECK(std::fabs(fd - grad[i][c]) < tolerance * std::max(std::fabs(fd), 0.05 * max_g));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} // namespace
|
||||
|
||||
TEST_CASE("RefinementLikelihood_derivative", "[Refinement]") {
|
||||
for (bool centric : {false, true})
|
||||
for (double fc : {0.3, 2.0, 9.0}) {
|
||||
double dfc = 0, dummy = 0;
|
||||
const double f0 = refine_math::AmplitudeNegLogLikelihood<double>(4.0, fc, 0.8, 2.5, centric, dfc);
|
||||
const double h = 1e-5;
|
||||
const double fp = refine_math::AmplitudeNegLogLikelihood<double>(4.0, fc + h, 0.8, 2.5, centric, dummy);
|
||||
const double fm = refine_math::AmplitudeNegLogLikelihood<double>(4.0, fc - h, 0.8, 2.5, centric, dummy);
|
||||
CAPTURE(centric, fc, f0);
|
||||
CHECK(dfc == Catch::Approx((fp - fm) / (2 * h)).epsilon(1e-5));
|
||||
}
|
||||
// the Bessel approximation on both sides of its switch
|
||||
double l0, r0, l1, r1;
|
||||
refine_math::BesselI0I1(3.75 * (1 - 1e-12), l0, r0);
|
||||
refine_math::BesselI0I1(3.75 * (1 + 1e-12), l1, r1);
|
||||
CHECK(l0 == Catch::Approx(l1).epsilon(1e-5));
|
||||
CHECK(r0 == Catch::Approx(r1).epsilon(1e-5));
|
||||
}
|
||||
|
||||
TEST_CASE("RefinementMonomerLibrary_embedded", "[Refinement]") {
|
||||
const gemmi::MonLib &monlib = EmbeddedMonomerLibrary();
|
||||
for (const char *code : {"ALA", "PRO", "MSE", "DA", "U", "ATP", "GOL", "SO4", "HOH", "ZN"})
|
||||
CHECK(InEmbeddedMonomerLibrary(code));
|
||||
CHECK_FALSE(InEmbeddedMonomerLibrary("XYZ"));
|
||||
for (const char *link : {"TRANS", "CIS", "PTRANS", "p", "SS"})
|
||||
CHECK(monlib.links.count(link) == 1);
|
||||
CHECK(monlib.modifications.count("NH3") == 1);
|
||||
CHECK(monlib.ener_lib.atoms.count("CH1") == 1);
|
||||
}
|
||||
|
||||
TEST_CASE("RefinementRestraints_ideal_residues", "[Refinement]") {
|
||||
const gemmi::UnitCell cell(60, 65, 70, 90, 90, 90);
|
||||
gemmi::Structure st = residue_crystal({"PHE", "DA", "ATP", "HOH", "ZN"}, cell, "P 21 21 21", 3);
|
||||
const RefinementTopology topo = BuildRefinementTopology(st);
|
||||
CHECK(topo.restrained_residues == 5);
|
||||
CHECK(topo.fixed_residues == 0);
|
||||
CHECK(topo.bonds > 60);
|
||||
CHECK(topo.planes >= 3);
|
||||
CHECK(topo.chirals >= 4);
|
||||
std::vector<std::array<double, 4>> xyzb;
|
||||
for (gemmi::Atom *a : atoms_of(st.models[0]))
|
||||
xyzb.push_back({a->pos.x, a->pos.y, a->pos.z, a->b_iso});
|
||||
const GeometryStatistics g = MeasureGeometry(topo.geometry, {}, xyzb);
|
||||
CHECK(g.rmsd_bonds < 0.02);
|
||||
CHECK(g.rmsd_angles < 2.5);
|
||||
CHECK(g.rmsd_chirals < 0.2);
|
||||
}
|
||||
|
||||
TEST_CASE("RefinementRestraints_gradient", "[Refinement]") {
|
||||
const gemmi::UnitCell cell(14, 15, 16, 90, 90, 90);
|
||||
gemmi::Structure st = residue_crystal({"TYR", "DG"}, cell, "P 21 21 21", 5);
|
||||
st.models[0] = shaken(st.models[0], 0.15, 3.0, 2);
|
||||
const RefinementTopology topo = BuildRefinementTopology(st);
|
||||
// the geometry, the B similarity and the repulsions (symmetry mates included, at a contact distance that
|
||||
// makes every pair within reach count)
|
||||
RestraintSet set = topo.geometry;
|
||||
set.Append(topo.adp);
|
||||
RefinementTopology wide = topo;
|
||||
for (float &r : wide.vdw_radius)
|
||||
r = 2.5f;
|
||||
std::fill(wide.hbond.begin(), wide.hbond.end(), 0);
|
||||
const RestraintSet rep = BuildRepulsions(wide, st.models[0], cell, *st.find_spacegroup(), 0.0);
|
||||
REQUIRE(rep.records.size() > 10);
|
||||
bool image = false;
|
||||
for (const RestraintRecord &r : rep.records)
|
||||
image = image || r.rot[0] != 1.0f || r.tran[0] != 0.0f || r.tran[1] != 0.0f || r.tran[2] != 0.0f;
|
||||
CAPTURE(rep.records.size());
|
||||
CHECK(image);
|
||||
set.Append(rep);
|
||||
set.Finalize(atoms_of(st.models[0]).size());
|
||||
|
||||
std::vector<std::array<double, 4>> xyzb;
|
||||
for (gemmi::Atom *a : atoms_of(st.models[0]))
|
||||
xyzb.push_back({a->pos.x, a->pos.y, a->pos.z, a->b_iso});
|
||||
// each kind of restraint on its own, against central differences
|
||||
for (int kind = 0; kind <= static_cast<int>(RestraintKind::BSimilarity); kind++) {
|
||||
RestraintSet one;
|
||||
for (const RestraintRecord &r : set.records)
|
||||
if (r.kind == kind) {
|
||||
RestraintRecord copy = r;
|
||||
if (kind == static_cast<int>(RestraintKind::Plane)) {
|
||||
copy.atom[0] = static_cast<int>(one.plane_atoms.size());
|
||||
for (int k = 0; k < r.atom[1]; k++)
|
||||
one.plane_atoms.push_back(set.plane_atoms[r.atom[0] + k]);
|
||||
}
|
||||
one.Add(copy, kind == static_cast<int>(RestraintKind::Plane) ? r.atom[1] : 4);
|
||||
}
|
||||
CAPTURE(kind, one.records.size());
|
||||
std::vector<std::array<double, 4>> grad(xyzb.size(), {0, 0, 0, 0});
|
||||
EvaluateRestraints(one, xyzb, &grad);
|
||||
const double h = 1e-6;
|
||||
for (size_t i = 0; i < xyzb.size(); i++)
|
||||
for (int c = 0; c < 4; c++) {
|
||||
auto x = xyzb;
|
||||
x[i][c] += h;
|
||||
const double fp = EvaluateRestraints(one, x, nullptr);
|
||||
x[i][c] -= 2 * h;
|
||||
const double fm = EvaluateRestraints(one, x, nullptr);
|
||||
CAPTURE(i, c);
|
||||
CHECK(grad[i][c] == Catch::Approx((fp - fm) / (2 * h)).epsilon(1e-4).margin(1e-3));
|
||||
}
|
||||
}
|
||||
|
||||
#ifdef JFJOCH_USE_CUDA
|
||||
if (get_gpu_count() > 0) {
|
||||
// the GPU's float evaluation of the same set
|
||||
std::vector<MergedReflection> merged = asu_reflections(cell, *st.find_spacegroup(), 3.0);
|
||||
RefinementReflections refl = PrepareRefinementReflections(merged, cell, *st.find_spacegroup(), 3.0);
|
||||
auto gpu = MakeRefinementEngineGPU(0, cell, *st.find_spacegroup(), 3.0, refl, st.models[0], 100.0, SIZE_MAX);
|
||||
REQUIRE(gpu);
|
||||
gpu->SetRestraints(0, set);
|
||||
std::vector<std::array<double, 4>> ggpu;
|
||||
const double egpu = gpu->EvaluateRestraints(0, xyzb, &ggpu);
|
||||
std::vector<std::array<double, 4>> gcpu(xyzb.size(), {0, 0, 0, 0});
|
||||
const double ecpu = EvaluateRestraints(set, xyzb, &gcpu);
|
||||
CHECK(egpu == Catch::Approx(ecpu).epsilon(1e-4));
|
||||
for (size_t i = 0; i < xyzb.size(); i++)
|
||||
for (int c = 0; c < 4; c++)
|
||||
CHECK(ggpu[i][c] == Catch::Approx(gcpu[i][c]).epsilon(2e-3).margin(2e-2));
|
||||
}
|
||||
#endif
|
||||
}
|
||||
|
||||
TEST_CASE("RefinementXray_gradient_CPU", "[Refinement]") {
|
||||
for (const char *group : {"P 1", "P 21 21 21", "C 1 2 1", "P 61 2 2"}) {
|
||||
CAPTURE(group);
|
||||
const gemmi::SpaceGroup &sg = *gemmi::find_spacegroup_by_name(group);
|
||||
const gemmi::UnitCell cell = sg.crystal_system() == gemmi::CrystalSystem::Hexagonal
|
||||
? gemmi::UnitCell(30, 30, 45, 90, 90, 120)
|
||||
: gemmi::UnitCell(28, 31, 34, 90, sg.number == 5 ? 104 : 90, 90);
|
||||
gemmi::Structure truth = random_crystal(cell, group, 240, 7);
|
||||
gemmi::Model model = shaken(truth.models[0], 0.3, 4.0, 8);
|
||||
RefinementReflections refl = PrepareRefinementReflections(asu_reflections(cell, sg, 2.2), cell, sg, 2.2);
|
||||
REQUIRE(refl.Size() > 500);
|
||||
auto cpu = MakeRefinementEngineCPU(cell, sg, 2.2, refl, 4);
|
||||
cpu->SetBlur(RefinementBlur(cell, sg, 2.2, 5.0));
|
||||
set_observations(*cpu, refl, truth.models[0], model);
|
||||
check_xray_gradient(*cpu, model, 0.03);
|
||||
}
|
||||
}
|
||||
|
||||
#ifdef JFJOCH_USE_CUDA
|
||||
TEST_CASE("RefinementXray_gradient_GPU", "[Refinement]") {
|
||||
if (get_gpu_count() == 0)
|
||||
return;
|
||||
for (const char *group : {"P 1", "P 21 21 21", "C 1 2 1", "P 61 2 2"}) {
|
||||
CAPTURE(group);
|
||||
const gemmi::SpaceGroup &sg = *gemmi::find_spacegroup_by_name(group);
|
||||
const gemmi::UnitCell cell = sg.crystal_system() == gemmi::CrystalSystem::Hexagonal
|
||||
? gemmi::UnitCell(30, 30, 45, 90, 90, 120)
|
||||
: gemmi::UnitCell(28, 31, 34, 90, sg.number == 5 ? 104 : 90, 90);
|
||||
gemmi::Structure truth = random_crystal(cell, group, 240, 7);
|
||||
gemmi::Model model = shaken(truth.models[0], 0.3, 4.0, 8);
|
||||
RefinementReflections refl = PrepareRefinementReflections(asu_reflections(cell, sg, 2.2), cell, sg, 2.2);
|
||||
auto cpu = MakeRefinementEngineCPU(cell, sg, 2.2, refl, 4);
|
||||
cpu->SetBlur(RefinementBlur(cell, sg, 2.2, 5.0));
|
||||
set_observations(*cpu, refl, truth.models[0], model);
|
||||
// the GPU engine sees the same observations: it is made after they are set
|
||||
auto gpu = MakeRefinementEngineGPU(0, cell, sg, 2.2, refl, model, 300.0, SIZE_MAX);
|
||||
REQUIRE(gpu);
|
||||
gpu->SetBlur(RefinementBlur(cell, sg, 2.2, 5.0));
|
||||
std::vector<std::complex<float>> f;
|
||||
cpu->Fcalc(model, f);
|
||||
XrayRowModel rows;
|
||||
rows.k_total.assign(refl.Size(), 1.0f);
|
||||
rows.fmask.assign(refl.Size(), {0, 0});
|
||||
EstimateLikelihoodParameters(refl, f, rows);
|
||||
cpu->SetRowModel(rows);
|
||||
gpu->SetRowModel(rows);
|
||||
|
||||
std::vector<std::complex<float>> fg;
|
||||
gpu->Fcalc(model, fg);
|
||||
double num = 0, den = 0;
|
||||
for (size_t m = 0; m < f.size(); m++) {
|
||||
num += std::abs(f[m] - fg[m]);
|
||||
den += std::abs(f[m]);
|
||||
}
|
||||
CHECK(num / den < 1e-3);
|
||||
|
||||
std::vector<std::array<double, 4>> gc, gg;
|
||||
const double tc = cpu->Evaluate(model, &gc);
|
||||
const double tg = gpu->Evaluate(model, &gg);
|
||||
CHECK(tg == Catch::Approx(tc).epsilon(1e-4));
|
||||
double max_g = 0;
|
||||
for (const auto &g : gc)
|
||||
for (int c = 0; c < 4; c++)
|
||||
max_g = std::max(max_g, std::fabs(g[c]));
|
||||
for (size_t i = 0; i < gc.size(); i++)
|
||||
for (int c = 0; c < 4; c++) {
|
||||
CAPTURE(i, c);
|
||||
CHECK(std::fabs(gg[i][c] - gc[i][c]) < 0.01 * max_g);
|
||||
}
|
||||
check_xray_gradient(*gpu, model, 0.05);
|
||||
}
|
||||
}
|
||||
#endif
|
||||
|
||||
TEST_CASE("Refinement_restrained_recovers_model", "[Refinement]") {
|
||||
const gemmi::UnitCell cell(36, 40, 44, 90, 90, 90);
|
||||
const gemmi::SpaceGroup &sg = *gemmi::find_spacegroup_by_name("P 21 21 21");
|
||||
gemmi::Structure truth = residue_crystal({"PHE", "TRP", "DA", "DG", "TYR", "HOH", "HOH", "HOH"}, cell,
|
||||
"P 21 21 21", 11);
|
||||
gemmi::Structure start = truth;
|
||||
start.models[0] = shaken(truth.models[0], 0.25, 5.0, 12);
|
||||
std::vector<MergedReflection> merged = asu_reflections(cell, sg, 1.8);
|
||||
{
|
||||
RefinementReflections refl = PrepareRefinementReflections(merged, cell, sg, 1.8 * 0.999);
|
||||
auto cpu = MakeRefinementEngineCPU(cell, sg, 1.8 * 0.999, refl, 4);
|
||||
cpu->SetBlur(RefinementBlur(cell, sg, 1.8, 5.0));
|
||||
std::vector<std::complex<float>> f;
|
||||
cpu->Fcalc(truth.models[0], f);
|
||||
std::map<gemmi::Miller, double> amplitude;
|
||||
for (size_t m = 0; m < refl.Size(); m++)
|
||||
amplitude[refl.hkl[m]] = std::abs(f[m]);
|
||||
std::mt19937 rng(3);
|
||||
std::normal_distribution<double> noise(0.0, 0.03);
|
||||
for (MergedReflection &r : merged) {
|
||||
const auto it = amplitude.find(gemmi::Miller{{r.h, r.k, r.l}});
|
||||
r.F = it == amplitude.end() ? NAN : static_cast<float>(it->second * (1 + noise(rng)));
|
||||
r.sigmaF = 0.03f * r.F + 0.01f;
|
||||
}
|
||||
}
|
||||
Logger logger("RefinementTest");
|
||||
for (bool gpu : {false, true}) {
|
||||
if (gpu && get_gpu_count() == 0)
|
||||
continue;
|
||||
CAPTURE(gpu);
|
||||
RefinementSettings settings;
|
||||
settings.gpu = gpu;
|
||||
settings.nthreads = 4;
|
||||
settings.macro_cycles = 3;
|
||||
settings.weight_ladder = {0.0625, 0.25};
|
||||
settings.adp_ladder = {4.0};
|
||||
settings.riding_hydrogens = false; // the data were made without them
|
||||
const RefinementResult r = RefineModel(start, merged, cell, sg, 1.0, logger, settings);
|
||||
REQUIRE(r.ok);
|
||||
CHECK(r.on_gpu == gpu);
|
||||
CHECK(r.restrained_residues == 8);
|
||||
CHECK(r.r_free < 0.6 * r.r_free_start);
|
||||
CHECK(r.geometry.rmsd_bonds < r.geometry_start.rmsd_bonds);
|
||||
double rms = 0;
|
||||
std::vector<gemmi::Atom *> refined = atoms_of(r.model->models[0]);
|
||||
std::erase_if(refined, [](const gemmi::Atom *a) { return a->is_hydrogen(); }); // the riding hydrogens
|
||||
const std::vector<gemmi::Atom *> ref = atoms_of(truth.models[0]);
|
||||
REQUIRE(refined.size() == ref.size());
|
||||
for (size_t i = 0; i < ref.size(); i++)
|
||||
rms += refined[i]->pos.dist_sq(ref[i]->pos);
|
||||
rms = std::sqrt(rms / ref.size());
|
||||
CHECK(rms < 0.15);
|
||||
}
|
||||
}
|
||||
Reference in new issue
Block a user