Refactor: change R_index in class AtomPair to type ModuleBase::vector3<int>

[DylanWRh]

Reminder

• Have you explained the changes of codes in core modules of ESolver, HSolver, ElecState, Hamilt, Operator or Psi? (ignore if not applicable)

What's changed?

This pull request addresses the type inconsistency of the R_index variable across different modules. Previously, the R_index variable in the AtomPair class was of type std::vector<int>, while in some other modules it was of type ModuleBase::Vector3<int>. This inconsistency could potentially lead to confusion and errors. So I modify the code under AtomPair and also other modules which use its R_index for code consistency and maintenance.

• Type of AtomPair::R_index is changed from std::vector<int> to std::vector<ModuleBase::Vector3<int>>.
• Type of HContainer::tmp_R_index is changed from std::vector<int> to std::vector<ModuleBase::Vector3<int>>.
• Return value of function AtomPair::get_R_index is changed from int* to ModuleBase::Vector3<int>.
• Indexing of R_index is changed from R_index[i*3], R_index[i*3+1], R_index[i*3+2] to R_index[i].x, R_index[i].y, R_index[i].z. The functions of size and memory calculation is also modified. (i.e. remove some *3 and /3 operations).
• Other modules that calls the function HContainer::tmp_R_index is changed to fit the new return type. For example, line 87 and 88 in module_io/td_current_io.cpp is changed from

  const int* r_index = tmp_ap.get_R_index(ir);
  hamilt::BaseMatrix<double>* tmp_matrix = tmp_ap.find_matrix(r_index[0], r_index[1], r_index[2]);

  to

  const ModuleBase::Vector3<int> r_index = tmp_ap.get_R_index(ir);
  hamilt::BaseMatrix<double>* tmp_matrix = tmp_ap.find_matrix(r_index.x, r_index.y, r_index.z);

Important Notes

• When fail to find R_index, the original AtomPair::get_R_index will return nullptr while the modified version will return ModuleBase::Vector3<int>(-1, -1, -1))
• TESTING code in test_hcontainer.cpp and test_hcontainer_complex.cpp is changed to fit the new return type.
• Though the checks are passed, I still cannot guarantee that the related code is thoroughly and properly modified. So it really need careful reviewing before merging into the main branch.