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)
leonarski_f
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