Refactor/merge openmp

[lijianing-sudo]

PR: OpenMP Parallel Optimization for ABACUS MD Module and ML Potential Interfaces (NEP/DPMD/LJ)

Reminder

• Have you linked an issue with this pull request?
• Have you added adequate unit tests and/or case tests for your pull request?
• Have you noticed possible changes of behavior below or in the linked issue?
• Have you explained the changes of codes in core modules of ESolver, HSolver, ElecState, Hamilt, Operator or Psi? (ignore if not applicable)

Linked Issue

Fix #...

Unit Tests and/or Case Tests for my changes

• A unit test is added for each new feature or bug fix.

Existing Unit Tests Pass:

• MODULE_MD_LJ_pot (6 tests)
• MODULE_MD_func (7 tests)
• MODULE_MD_fire
• MODULE_MD_verlet
• MODULE_MD_nhc
• MODULE_MD_msst
• MODULE_MD_lgv

Test Infrastructure:

• Introduced shared MD test fixtures (source/source_md/test/md_test_fixture.h) to eliminate duplicated SetUp/TearDown across 6 test files.

Microbenchmark Verification:

• Independent C++ microbenchmarks were written for each optimized kernel (see Test/openmp_nep_basic_benchmark.cpp and companion scripts).
• 2 million atoms, repeated 5 times, tested at 1/2/4/8/16 threads on Intel Xeon Platinum 8163.
• All per-atom write loops produce bitwise-identical results (max_abs_diff = 0).
• Reduction loops show floating-point differences at the 1e-10 to 1e-8 level due to summation order changes — expected and acceptable for MD trajectories.

What's changed?

This PR integrates OpenMP parallelization from three feature branches (refactor/md-factory, refactor/parallel-optimize, refactor/md-openmp-remainder) into the ABACUS MD module and ML potential interfaces. 22 parallel loops or worksharing regions are added across 12 source files (+3934/−342 lines total).

1. MD Base Loops (source/source_md/)

Function	File	Strategy
MD_base::update_pos()	md_base.cpp	#pragma omp parallel for schedule(static)
MD_base::update_vel()	md_base.cpp	#pragma omp parallel for schedule(static)
kinetic_energy()	md_func.cpp	reduction(+:ke)
force_virial() force copy	md_func.cpp	Parallel per-atom copy
temp_vector()	md_func.cpp	9 scalar reductions instead of shared-matrix accumulation
rescale_vel()	md_func.cpp	schedule(static)

All loops use if (natom >= 256) to skip parallel overhead for small systems.

2. NEP Interface (source/source_esolver/esolver_nep.cpp/.h)

• Added atom_type_index / atom_local_index index caches for flat iat-based parallel loops.
• Parallelized: coordinate buffer fill, per-atom energy reduction, force copy-back with unit conversion, and 9-component per-atom virial reduction.
• NEP virial: reorganized from 9 separate full-array scans into a single per-atom scan with 9 scalar reductions — algorithmic + parallel gains combined (14.24× speedup at 8 threads).
• nep.compute() external library call remains serial.

3. DPMD Interface (source/source_esolver/esolver_dp.cpp/.h)

• Added iat → (it, ia) index caches.
• Parallelized: coordinate buffer fill and model force copy-back with unit conversion.
• Introduced persistent member buffers (dp_cell, dp_coord, dp_model_force, dp_model_virial) to avoid repeated allocations.
• dp.compute() external library call and 3×3 virial copy-back remain serial.

4. Thermostat and Barostat (source/source_md/)

Class	Method	File
Verlet	thermalize() velocity rescaling	verlet.cpp
MSST	rescale() shock-direction velocity scaling	msst.cpp
MSST	vel_sum() velocity norm reduction	msst.cpp
MSST	propagate_vel() per-atom velocity propagation	msst.cpp
NoseHoover	particle_thermo() final velocity scaling	nhchain.cpp
NoseHoover	vel_baro() barostat velocity update	nhchain.cpp

Thermostat chain recurrence integration and cell dilation remain serial.

5. FIRE Algorithm (source/source_md/fire.cpp)

FIRE::check_fire() parallelized in three phases:

1. Three-scalar reduction for P, sumforce, normvel
2. Parallel velocity-force mixing
3. Parallel velocity zeroing (in P <= 0 branch)

Scalar state updates (alpha, negative_count, dt) remain serial.

6. LJ Interface (source/source_esolver/esolver_lj.cpp/.h)

• Added global atom index cache.
• Restructured nested type-iteration loops into flat iat-based loop.
• schedule(dynamic, 32) to handle neighbor-count imbalance.
• Thread-local potential and virial arrays with atomic (energy) and critical (virial) reduction at thread exit — no per-neighbor locks.

7. Code Quality Refactors

• Extracted MD statistics helpers: calc_kinetic_state() / calc_stress_state() (md_func.h, md_statistics.h).
• MD runner factory function: new/delete → std::unique_ptr (run_md.cpp).
• Shared test fixture base classes to reduce duplication across 6 MD test files.

Performance Summary (Microbenchmark, 8 threads, 2M atoms, Xeon Platinum 8163)

Category	Kernel	Speedup	Efficiency
MD Base	update_pos	7.36×	92.0%
MD Base	update_vel	7.19×	89.9%
MD Base	kinetic_energy	6.98×	87.2%
MD Base	temp_vector	7.38×	92.2%
NEP	coord_fill	7.15×	89.4%
NEP	energy_sum	8.03×	100.4%
NEP	force_fill	6.99×	87.4%
NEP	virial_sum	14.24×	177.9%*
DPMD	coord_fill	5.50×	68.8%
DPMD	force_copy	7.19×	89.9%
Verlet	thermalize	7.80×	97.5%
MSST	rescale	7.28×	91.1%
MSST	propagate_vel	7.18×	89.7%
NHC	particle_thermo	7.21×	90.2%
FIRE	check_fire (mix)	7.64×	95.6%
LJ	runner core loop	6.96×	87.0%

*NEP virial 14.24× includes loop reorganization benefits beyond pure 8-thread scaling.

Known Limitations & Future Work

• End-to-end tests: NEP and DPMD optimizations lack end-to-end tests with real external model libraries (__NEP, deepmd).
• LJ parallel path: existing LJ unit tests use 4 atoms (< 256 threshold), covering only the serial path.
• MPI + OpenMP hybrid: microbenchmarks are single-process; oversubscription risks under mixed MPI/OpenMP have not been characterized.
• Thread threshold: nat >= 256 is an empirical uniform threshold; per-kernel tuning (64/128/256/512) is recommended.
• LJ scheduling: schedule(dynamic, 32) vs static and optimal chunk size have not been systematically benchmarked across different neighbor distributions.
• Microbenchmark results ≠ end-to-end wall-time: excluded overheads include MPI communication, neighbor-list construction, file I/O, and external model computation.

Any changes of core modules? (ignore if not applicable)

The MD ESolver interface layer (esolver_nep.cpp, esolver_dp.cpp, esolver_lj.cpp) is modified to add index caches and parallel worksharing constructs. No changes to the ESolver base class virtual function signatures. All external library calls (nep.compute(), dp.compute()) remain serial and their calling convention is unchanged.

[mohanchen]

this file is not needed

[mohanchen]

You may first remove unnecessary files, then add tests to show the effects of code refactoring.

[lijianing-sudo]

Done. Removed unnecessary files (Planners/, Results/, Test/, opt_logs/). The PR now contains only 26 source files across source/source_md/ and source/source_esolver/, plus unit tests in source/source_md/test/. Please let me know if additional performance tests are needed.

You may first remove unnecessary files, then add tests to show the effects of code refactoring.

[lijianing-sudo]

Updated the PR: - Removed unnecessary non-code files (Planners/, Results/, Test/, opt_logs/)

• Excluded LJ esolver (upstream refactored to UnitCellLite API, incompatible)
• Rebased onto latest deepmodeling/develop
• Fixed test CMakeLists.txt for the new module_neighlist dependencies

PR now focuses on 23 source files: core MD loops (md_base, md_func, fire, msst, nhchain, verlet, run_md) + NEP/DPMD 

esolver interfaces + unit tests. All #pragma omp directives follow the same strategy: schedule(static) with ▎ if(nat>=256), reduction clauses for energy/virial, atomic/critical for shared accumulators.

Please let me know if any further changes are needed.

[lijianing-sudo]

All 16 CI checks are now passing.