perf/Optimize neighbor-list construction with OpenMP

[Audrey-777]

Summary

This PR optimizes MD neighbor-list construction in BinManager::build_atom_neighbors().

For larger OpenMP runs, the neighbor-list build now uses a conservative count / allocate / fill flow:

• Count per-atom neighbor sizes in parallel.
• Allocate per-atom neighbor segments through the existing PageAllocator.
• Fill neighbor IDs in parallel while preserving the existing bin scan order.

Small systems, single-thread runs, and OpenMP-disabled builds keep the serial path.

Correctness

The implementation preserves:

• Per-atom neighbor order.
• Existing PageAllocator ownership.
• firstneigh_[i] == nullptr for zero-neighbor atoms.
• C++11 compatibility.
• OpenMP OFF behavior.

Performance

Environment: 8 physical cores / 16 logical CPUs, Intel Xeon Platinum 8163, np=1.

2048 atom LJ NVE, 200 steps

• Wall time: 10.30 s -> 9.35 s, about 1.10x.
• BinManager::build_atom_neighbors: 1.26 s -> 0.31 s, about 4.06x.

8192 atom LJ NVE, 100 steps

• Wall time: 24.36 s -> 18.87 s, about 1.29x.
• BinManager::build_atom_neighbors: 2.67 s -> 0.62 s, about 4.31x.

Repeat check

• 2048 wall time: 11.16 s -> 10.13 s, about 1.10x.
• 8192 wall time: 24.01 s -> 19.95 s, about 1.20x.

Final energy, potential, kinetic, temperature, and pressure matched across tested thread counts.

Tests

• git diff --check
• OpenMP ON focused build
• OpenMP ON focused ctest: 4/4 passed
• OpenMP OFF focused build
• OpenMP OFF focused ctest: 4/4 passed
• GitHub check on 6dba4951c: passed

[Copilot]

Pull request overview

This PR improves molecular-dynamics neighbor-list construction performance by introducing an OpenMP-enabled count/allocate/fill path in BinManager::build_atom_neighbors(), while keeping serial behavior for small/single-thread/OpenMP-OFF cases. It also adds lightweight timing instrumentation around key neighbor-search phases to make the runtime impact visible in profiling.

Changes:

• Add an OpenMP parallel neighbor-list build path using per-atom counting, serial allocation via PageAllocator, then parallel fill while preserving neighbor order.
• Factor out the bin-scan logic into a reusable BinManager::visit_neighbors() helper to avoid duplicating traversal code between serial and parallel paths.
• Add ModuleBase::timer start/end instrumentation in NeighborSearch and BinManager hot-path methods.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
source/source_cell/module_neighlist/neighbor_search.cpp	Adds timers around set_member_variables(), init(), and build_neighbors() to profile neighbor-search stages.
source/source_cell/module_neighlist/bin_manager.h	Declares visit_neighbors() helper to share bin traversal logic used by both serial and OpenMP neighbor building.
source/source_cell/module_neighlist/bin_manager.cpp	Implements the OpenMP count/allocate/fill neighbor build path, the shared visit_neighbors() traversal, and timers around binning/build steps.

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