Change names of MD subroutines and files

[19hello]

Reminder

• I have read AGENTS.md and docs/developers_guide/agent_governance.md.
• I have linked an issue or explained why this PR does not need one.
• I have added adequate unit tests and/or case tests, or explained why not.
• I have listed the exact verification commands run and their results.
• I have described user-visible behavior changes, including INPUT parameter changes.
• I have explained core-module impact for ESolver, HSolver, ElecState, Hamilt, Operator, Psi, or other source/ changes.
• I have requested any needed governance exception below.

Linked Issue

No linked issue. This is an internal refactor follow-up to #7812 and #7896.

Unit Tests and/or Case Tests for my changes

• Commands run:

  bash -c 'source toolchain/install/setup && cmake -S . -B build_parallel_md1_current'
  
  bash -c 'source toolchain/install/setup && cmake --build build_parallel_md1_current --target driver esolver md MODULE_ESOLVER_esolver_dp_test
  MODULE_MD_run MODULE_MD_func MODULE_MD_fire MODULE_MD_lgv MODULE_MD_msst MODULE_MD_nhc MODULE_MD_verlet MODULE_CELL_NEIGHBOR_mdcell_reader
  MODULE_CELL_NEIGHBOR_mdcell_migrate_mpi -j4'
  
  OMP_NUM_THREADS=1 ctest --test-dir build_parallel_md1_current --output-on-failure -R 'MODULE_ESOLVER_esolver_dp_test|MODULE_MD_(run|func|fire|lgv|
  msst|nhc|verlet)$|MODULE_CELL_NEIGHBOR_(mdcell_reader|mdcell_migrate_mpi)'
  
  python3 tools/03_code_analysis/agent_governance_check.py --staged
  git diff --check
  

• Result summary:

  • CMake configuration passed.
  • Driver, ESolver, MD, and affected test targets built successfully.
  • 10/10 focused ESolver, MD, and MPI tests passed.
  • git diff --check passed.
  • Governance check reported warnings only; no blocking findings.

• Checks not run, with reason:

  • The full CTest suite was not run; this PR is an internal refactor and focused tests cover all renamed MDCell/BaseCell/STRU metadata paths.
  • GPU, DeePMD, and NEP runtime tests were not run because the local build is CPU-only and does not enable those optional backends.

What's changed?

• Move parallel-MD cell preparation from Driver into Run_MD::prepare_mdcell.

• Keep the original UnitCell initialization path in driver_run.cpp; both MD initialization paths now prepare one MDCell and use the same md_line.

• Keep MD restart STRU metadata in MDCell, so Driver does not own MD output state.

• Simplify MD-related names:

  • DistributedMDCellReader → MDCellReader
  • distributed_mdcell_reader.* → mdcell_reader.*
  • base_cell.* → basecell.*
  • md_cell.* → mdcell.*
  • BaseCell::Kind::{unit_cell, md_cell} → {unitcell, mdcell}
  • MdStruFileMetadata / MdStruFileSpecies → StruMeta / StruSpecies
  • md_stru_file_metadata.h → strumeta.h

• Remove unused includes from driver_run.cpp.

• Add focused coverage for preparing an MDCell from a UnitCell.

No user-visible behavior or INPUT parameter behavior changes are intended.

Governance Notes

• INPUT/docs changes:

  • No INPUT behavior changed; no user documentation update is required.

• Core module impact:

  • source_cell: renames BaseCell/MDCell implementation files and moves restart STRU metadata ownership into MDCell.
  • source_md: owns MDCell preparation and consumes metadata through MDCell.
  • source_esolver: updates internal BaseCell::Kind references only; solver behavior is unchanged.

• Exceptions requested:

  • None.
  • Governance header-include warnings are rename-only: the affected headers continue to require the same complete types as before, with no
    dependency growth.

[mohanchen]

LGTM