Refinement GPU: the X-ray target and the restraints in one submission with one wait

RefinementEngine::EvaluateWithRestraints evaluates both targets at the model's atoms. On the GPU the X-ray
chain is queued first, the restraints' coordinates are written into a pinned buffer while the device works
on it, the restraint kernels follow on the same stream, and the host waits once; the sums and gradients
come back through pinned buffers. Same kernels on the same inputs, same bits. The CPU engine keeps calling
the two in turn.

9yl4: evaluation 5.1 -> 4.7 ms, refinement 14.2 -> 13.4 s; 5reo 4.0 -> 3.9 s (RTX 5080, -N 8).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 51434b98b62a9e6322ffe811bf272a45ff6ce003)
(cherry picked from commit 0bcfa3f8041cec4bb4bc376b8559f30c36d3ac80)

image_analysis/structure_refinement/RefinementXray.cpp

@@ -313,6 +313,15 @@ RFactors ComputeRFactors(const RefinementReflections &refl, const std::vector<st
     return r;
 }
 
+std::vector<std::array<double, 4>> ModelXyzB(const gemmi::Model &model) {
+    std::vector<std::array<double, 4>> out;
+    for (const gemmi::Chain &ch : model.chains)
+        for (const gemmi::Residue &r : ch.residues)
+            for (const gemmi::Atom &a : r.atoms)
+                out.push_back({a.pos.x, a.pos.y, a.pos.z, a.b_iso});
+    return out;
+}
+
 namespace {
 std::mutex stage_mutex;
 std::map<std::string, std::pair<double, int>> stage_times;