Refactor: remove dead cross module includes (deepmodeling#7574)

* refactor(cell): remove unused cross-module includes in read_atoms.cpp

Drop two dead includes that create needless reverse dependencies from
source_cell onto higher layers:
  - source_estate/read_orb.h  (elecstate::read_orb_file not used here;
    the real user is read_atoms_helper.cpp)
  - source_basis/module_ao/ORB_read.h  (ORB / LCAO_Orbitals not used here)

Verified by compiling the `cell` target with ENABLE_LCAO=ON so the
former `#ifdef __LCAO` block was actually exercised.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* refactor: remove dead cross-module includes on reverse-dependency edges

Static scan + per-target compile verification identified 9 unused
includes that create reverse/lateral dependency edges between modules.
Removing them weakens the coupling without any behavior change:

  io   -> md    input_conv.cpp        (md_func.h)
  estate -> lcao  elecstate_energy_terms.cpp, elecstate_print.cpp
                                       (module_deepks/LCAO_deepks.h)
  lcao -> pw    rdmft_tools.cpp (structure_factor.h),
                wavefunc_in_pw.cpp (soc.h)
  lcao -> io    FORCE_gamma.cpp, FORCE_k.cpp (module_hs/write_HS.h)
  pw   -> io    forces_cc.cpp, forces_scc.cpp (module_output/output_log.h)

Verified by building io_basic, elecstate, rdmft, hamilt_lcao and
module_pwdft (ENABLE_LCAO=ON) after removal; all link targets compile.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* refactor(esolver): remove 29 dead io includes (esolver -> io hygiene)

Remove unused source_io includes across the esolver drivers. These are
on the allowed esolver->io direction, so this is include hygiene rather
than decoupling, but it trims 29 needless includes.

Verified three ways:
  1. `make esolver` (ENABLE_LCAO=ON) recompiles all 21 TUs, 0 errors.
  2. Feature-guarded headers checked explicitly since __RAPIDJSON,
     __EXX/__LIBRI and __MLALGO are OFF in this build: the json
     (init_info.h/output_info.h) and restart_exx_csr.h symbols are
     unused in their consumers (Json::add_output_scf_mag in
     esolver_ks.cpp comes from output_info.h, which is kept).
  3. Whole-file precise-symbol sweep (incl. all #ifdef blocks) finds
     no specific symbol of any removed header in its consumer.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* refactor: remove 2 more dead cross-module includes

Two dead includes missed by the first reverse-edge pass:

  estate -> lcao   elecstate_energy_terms.cpp
                   (module_deltaspin/spin_constrain.h; SpinConstrain
                   is not referenced anywhere in the file)
  esolver -> io    esolver_double_xc.cpp
                   (module_hs/write_HS.h; only a comment mentions
                   ModuleIO::write_hsk(), no actual call)

Verified: no header symbol appears anywhere in the consumer (guards
included), and `make elecstate` / `make esolver` build cleanly.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: Critsium-xy

source/source_cell/read_atoms.cpp

@@ -8,16 +8,11 @@
 #include "source_io/module_parameter/parameter.h"
 #include "print_cell.h"
 #include "read_stru.h"
-#include "source_estate/read_orb.h"
 #include "source_base/timer.h"
 #include "source_base/constants.h"
 #include "source_base/formatter.h"
 #include "source_base/mathzone.h"
 
-#ifdef __LCAO
-#include "source_basis/module_ao/ORB_read.h" // to use 'ORB' -- mohan 2021-01-30
-#endif
-
 bool unitcell::read_atom_positions(UnitCell& ucell,
                          std::ifstream &ifpos,
                          std::ofstream &ofs_running,

source/source_esolver/esolver.cpp

@@ -19,7 +19,6 @@
 #include "esolver_lj.h"
 #include "esolver_of.h"
 #include "esolver_of_tddft.h"
-#include "source_io/module_parameter/md_parameter.h"
 
 #include <stdexcept>
 

source/source_esolver/esolver_dm2rho.cpp

@@ -9,7 +9,6 @@
 #include "source_lcao/module_operator_lcao/operator_lcao.h"
 #include "source_io/module_output/cube_io.h"
 #include "source_io/module_ml/io_npz.h"
-#include "source_io/module_output/print_info.h"
 #include "source_lcao/rho_tau_lcao.h" // mohan add 2025-10-24
 
 namespace ModuleESolver

source/source_esolver/esolver_double_xc.cpp

@@ -15,7 +15,6 @@
 #include "source_lcao/hamilt_lcao.h"
 #include "source_hsolver/hsolver_lcao.h"
 #include "source_io/module_parameter/parameter.h"
-#include "source_io/module_hs/write_HS.h" // use ModuleIO::write_hsk()
 #include "source_lcao/setup_deepks.h" // use deepks, mohan add 2025-10-10
 
 namespace ModuleESolver

source/source_esolver/esolver_fp.cpp

@@ -6,9 +6,6 @@
 #include "source_hamilt/module_ewald/H_Ewald_pw.h"
 #include "source_hamilt/module_vdw/vdw.h"
 #include "source_io/module_output/cif_io.h"
-#include "source_io/module_output/cube_io.h" // use write_vdata_palgrid
-#include "source_io/module_json/init_info.h"
-#include "source_io/module_json/output_info.h"
 #include "source_io/module_output/output_log.h"
 #include "source_io/module_output/print_info.h"
 #include "source_io/module_chgpot/rhog_io.h"

source/source_esolver/esolver_ks.cpp

@@ -2,7 +2,6 @@
 #include "source_base/timer_wrapper.h"
 
 // for jason output information
-#include "source_io/module_json/init_info.h"
 #include "source_io/module_json/output_info.h"
 
 #include "source_estate/update_pot.h" // mohan add 20251016
@@ -14,7 +13,6 @@
 #include "source_hamilt/module_xc/xc_functional.h"
 #include "source_io/module_output/output_log.h" // use write_head
 #include "source_estate/elecstate_print.h" // print_etot
-#include "source_io/module_output/print_info.h" // print_parameters
 #include "source_lcao/module_dftu/dftu.h" // mohan add 2025-11-07
 
 namespace ModuleESolver

source/source_esolver/esolver_ks_lcao_tddft.cpp

@@ -4,8 +4,6 @@
 //----------------IO-----------------
 #include "source_base/global_variable.h"
 #include "source_io/module_ctrl/ctrl_output_td.h"
-#include "source_io/module_current/td_current_io.h"
-#include "source_io/module_dipole/dipole_io.h"
 #include "source_io/module_output/output_log.h"
 #include "source_io/module_wf/read_wfc_nao.h"
 //------LCAO HSolver ElecState-------

source/source_esolver/esolver_ks_lcaopw.cpp

@@ -2,15 +2,13 @@
 
 #include "source_pw/module_pwdft/elecond.h"
 #include "source_io/module_parameter/input_conv.h"
-#include "source_io/module_output/output_log.h"
 
 #include <iostream>
 
 //--------------temporary----------------------------
 #include "source_estate/module_charge/symmetry_rho.h"
 #include "source_estate/occupy.h"
 #include "source_hamilt/module_ewald/H_Ewald_pw.h"
-#include "source_io/module_output/print_info.h"
 //-----force-------------------
 #include "source_pw/module_pwdft/forces.h"
 //-----stress------------------
@@ -23,11 +21,6 @@
 #include "source_hsolver/hsolver_lcaopw.h"
 #include "source_hsolver/kernels/hegvd_op.h"
 #include "source_base/kernels/math_kernel_op.h"
-#include "source_io/module_unk/berryphase.h"
-#include "source_io/module_bessel/numerical_basis.h"
-#include "source_io/module_bessel/numerical_descriptor.h"
-#include "source_io/module_wannier/to_wannier90_pw.h"
-#include "source_io/module_chgpot/write_elecstat_pot.h"
 #include "source_io/module_parameter/parameter.h"
 #include "source_hamilt/module_xc/xc_functional.h"
 

source/source_esolver/esolver_of.cpp

@@ -1,14 +1,10 @@
 #include "esolver_of.h"
 
 #include "source_io/module_parameter/parameter.h"
-#include "source_io/module_output/cube_io.h"
-#include "source_io/module_output/output_log.h"
-#include "source_io/module_chgpot/write_elecstat_pot.h"
 //-----------temporary-------------------------
 #include "source_base/global_function.h"
 #include "source_estate/module_charge/symmetry_rho.h"
 #include "source_hamilt/module_ewald/H_Ewald_pw.h"
-#include "source_io/module_output/print_info.h"
 #include "source_estate/cal_ux.h"
 #include "source_pw/module_pwdft/forces.h"
 #include "source_pw/module_ofdft/of_stress_pw.h"

source/source_esolver/esolver_of_tddft.cpp

@@ -1,14 +1,10 @@
 #include "esolver_of_tddft.h"
 
 #include "source_io/module_parameter/parameter.h"
-#include "source_io/module_output/cube_io.h"
-#include "source_io/module_output/output_log.h"
-#include "source_io/module_chgpot/write_elecstat_pot.h"
 //-----------temporary-------------------------
 #include "source_base/global_function.h"
 #include "source_estate/module_charge/symmetry_rho.h"
 #include "source_hamilt/module_ewald/H_Ewald_pw.h"
-#include "source_io/module_output/print_info.h"
 #include "source_estate/cal_ux.h"
 //-----force-------------------
 #include "source_pw/module_pwdft/forces.h"