Reorganize the source_psi and source_io directories

source/Makefile.Objects

@@ -434,12 +434,12 @@ OBJS_ORBITAL=ORB_atomic.o\
 OBJS_PSI=psi.o\
 
 OBJS_PSI_INITIALIZER=psi_initializer.o\
-                     psi_initializer_random.o\
-                     psi_initializer_file.o\
-                     psi_initializer_atomic.o\
-                     psi_initializer_atomic_random.o\
-                     psi_initializer_nao.o\
-                     psi_initializer_nao_random.o\
+                     psi_init_random.o\
+                     psi_init_file.o\
+                     psi_init_atomic.o\
+                     psi_init_atomic_random.o\
+                     psi_init_nao.o\
+                     psi_init_nao_random.o\
 
 OBJS_PW=fft_bundle.o\
     fft_cpu.o\
@@ -513,21 +513,21 @@ OBJS_XC=xc_functional.o\
     xc_funct_hcth.o\
     exx_info.o\
 
-OBJS_IO=input_conv.o\
-    berryphase.o\
-    bessel_basis.o\
+OBJS_IO=module_parameter/input_conv.o\
+    module_unk/berryphase.o\
+    module_bessel/bessel_basis.o\
     cal_test.o\
-    write_dos_pw.o\
+    module_dos/write_dos_pw.o\
     nscf_fermi_surf.o\
     write_bands.o\
-    cal_dos.o\
-    cal_pdos_gamma.o\
-    cal_pdos_multik.o\
-    cal_ldos.o\
+    module_dos/cal_dos.o\
+    module_dos/cal_pdos_gamma.o\
+    module_dos/cal_pdos_multik.o\
+    module_dos/cal_ldos.o\
     cif_io.o\
-    numerical_descriptor.o\
-    numerical_basis.o\
-    numerical_basis_jyjy.o\
+    module_bessel/numerical_descriptor.o\
+    module_bessel/numerical_basis.o\
+    module_bessel/numerical_basis_jyjy.o\
     output.o\
     print_info.o\
     read_cube.o\
@@ -537,15 +537,15 @@ OBJS_IO=input_conv.o\
     read_wf2rho_pw.o\
     restart.o\
     binstream.o\
-    to_wannier90.o\
-    to_qo_kernel.o\
-    to_qo_mpi.o\
-    to_qo_structures.o\
-    to_wannier90_pw.o\
-    to_wannier90_lcao_in_pw.o\
-    to_wannier90_lcao.o\
+    module_wannier/to_wannier90.o\
+    module_qo/to_qo_kernel.o\
+    module_qo/to_qo_mpi.o\
+    module_qo/to_qo_structures.o\
+    module_wannier/to_wannier90_pw.o\
+    module_wannier/to_wannier90_lcao_in_pw.o\
+    module_wannier/to_wannier90_lcao.o\
     fR_overlap.o\
-    unk_overlap_pw.o\
+    module_unk/unk_overlap_pw.o\
     write_pao.o\
     write_wfc_pw.o\
     write_cube.o\
@@ -558,34 +558,34 @@ OBJS_IO=input_conv.o\
     write_libxc_r.o\
     output_log.o\
     output_mat_sparse.o\
-    ctrl_scf_lcao.o\
-    ctrl_runner_lcao.o\
-    ctrl_iter_lcao.o\
-    ctrl_output_fp.o\
-    ctrl_output_pw.o\
-    ctrl_output_td.o\
+    module_ctrl/ctrl_scf_lcao.o\
+    module_ctrl/ctrl_runner_lcao.o\
+    module_ctrl/ctrl_iter_lcao.o\
+    module_ctrl/ctrl_output_fp.o\
+    module_ctrl/ctrl_output_pw.o\
+    module_ctrl/ctrl_output_td.o\
     para_json.o\
     abacusjson.o\
     general_info.o\
     init_info.o\
     readin_info.o\
     output_info.o\
     parse_args.o\
-    read_input.o\
-    read_input_item_system.o\
-    read_input_item_elec_stru.o\
-    read_input_item_relax.o\
-    read_input_item_md.o\
-    read_input_item_ofdft.o\
-    read_input_item_sdft.o\
-    read_input_item_tddft.o\
-    read_input_item_deepks.o\
-    read_input_item_model.o\
-    read_input_item_postprocess.o\
-    read_input_item_exx_dftu.o\
-    read_input_item_other.o\
-    read_input_item_output.o\
-    read_set_globalv.o\
+    module_parameter/read_input.o\
+    module_parameter/read_input_item_system.o\
+    module_parameter/read_input_item_elec_stru.o\
+    module_parameter/read_input_item_relax.o\
+    module_parameter/read_input_item_md.o\
+    module_parameter/read_input_item_ofdft.o\
+    module_parameter/read_input_item_sdft.o\
+    module_parameter/read_input_item_tddft.o\
+    module_parameter/read_input_item_deepks.o\
+    module_parameter/read_input_item_model.o\
+    module_parameter/read_input_item_postprocess.o\
+    module_parameter/read_input_item_exx_dftu.o\
+    module_parameter/read_input_item_other.o\
+    module_parameter/read_input_item_output.o\
+    module_parameter/read_set_globalv.o\
     orb_io.o\
     cal_pLpR.o\
     filename.o\
@@ -597,19 +597,19 @@ OBJS_IO_LCAO=cal_r_overlap_R.o\
       write_eig_occ.o\
       get_pchg_lcao.o\
       get_wf_lcao.o\
-      write_dmk.o\
-      unk_overlap_lcao.o\
+      module_dm/write_dmk.o\
+      module_unk/unk_overlap_lcao.o\
       read_wfc_nao.o\
       write_wfc_nao.o\
-      write_HS_sparse.o\
+      module_hs/write_HS_sparse.o\
       single_R_io.o\
-      write_HS_R.o\
-      write_dmr.o\
+      module_hs/write_HS_R.o\
+      module_dm/write_dmr.o\
       sparse_matrix.o\
-      output_mulliken.o\
-      output_sk.o\
-      output_dmk.o\
-      io_npz.o\
+      module_mulliken/output_mulliken.o\
+      module_mulliken/output_sk.o\
+      module_mulliken/output_dmk.o\
+      module_ml/io_npz.o\
 
 OBJS_LCAO=evolve_elec.o\
       evolve_psi.o\
@@ -746,7 +746,7 @@ OBJS_SRCPW=H_Ewald_pw.o\
     symmetry_rhog.o\
     setup_psi_pw.o\
     setup_psi.o\
-    psi_init.o\
+    psi_prepare.o\
     elecond.o\
     sto_tool.o\
     sto_elecond.o\

source/source_cell/atom_pseudo.h

@@ -3,7 +3,7 @@
 
 #include "source_base/global_variable.h"
 #include "source_base/vector3.h"
-#include "source_io/output.h"
+#include "source_io/module_output/output.h"
 #include "source_base/complexarray.h"
 #include "source_base/complexmatrix.h"
 #include "pseudo.h"

source/source_cell/atom_spec.h

@@ -1,7 +1,7 @@
 #ifndef ATOM_H
 #define ATOM_H
 
-#include "../source_io/output.h"
+#include "../source_io/module_output/output.h"
 #include "atom_pseudo.h"
 class Atom
 {

source/source_cell/klist.cpp

@@ -7,7 +7,7 @@
 #include "source_base/parallel_global.h"
 #include "source_base/parallel_reduce.h"
 #include "source_cell/module_symmetry/symmetry.h"
-#include "source_io/berryphase.h"
+#include "source_io/module_unk/berryphase.h"
 #include "source_io/module_parameter/parameter.h"
 
 void K_Vectors::cal_ik_global()

source/source_cell/module_neighbor/test/CMakeLists.txt

@@ -13,13 +13,13 @@ AddTest(
   TARGET MODULE_CELL_NEIGHBOR_sltk_grid
   LIBS parameter ${math_libs} base device cell_info 
   SOURCES sltk_grid_test.cpp ../sltk_grid.cpp ../sltk_atom.cpp
-    ../../../source_io/output.cpp
+    ../../../source_io/module_output/output.cpp
 )
 
 AddTest(
   TARGET MODULE_CELL_NEIGHBOR_sltk_atom_arrange
   LIBS parameter ${math_libs} base device cell_info 
   SOURCES sltk_atom_arrange_test.cpp  ../sltk_atom_arrange.cpp ../sltk_grid_driver.cpp ../sltk_grid.cpp
   ../sltk_atom.cpp
-  ../../../source_io/output.cpp
+  ../../../source_io/module_output/output.cpp
 )

source/source_cell/module_symmetry/symmetry.h

@@ -6,7 +6,7 @@
 #include "source_base/timer.h"
 #include "source_base/mathzone.h"
 #include "source_base/constants.h"
-#include "source_io/output.h"
+#include "source_io/module_output/output.h"
 #include "symmetry_basic.h"
 
 namespace ModuleSymmetry

source/source_cell/pseudo.h

@@ -3,7 +3,7 @@
 
 #include <cstdint>
 #include "source_base/global_function.h"
-#include "source_io/output.h"
+#include "source_io/module_output/output.h"
 
 //-----------------------------------------
 // read in pseudopotentials

source/source_cell/sep.cpp

@@ -3,7 +3,7 @@
 #include "source_base/global_variable.h"
 #include "source_base/parallel_common.h"
 #include "source_base/tool_title.h"
-#include "source_io/output.h"
+#include "source_io/module_output/output.h"
 
 #include <fstream>
 #include <sstream>

source/source_cell/test/CMakeLists.txt

@@ -46,40 +46,40 @@ AddTest(
   TARGET MODULE_CELL_read_pp
   LIBS parameter  ${math_libs} base device
   SOURCES read_pp_test.cpp ../atom_pseudo.cpp ../pseudo.cpp ../read_pp.cpp ../read_pp_complete.cpp ../read_pp_upf201.cpp ../read_pp_upf100.cpp ../read_pp_vwr.cpp ../read_pp_blps.cpp
-  ../../source_io/output.cpp
+  ../../source_io/module_output/output.cpp
 )
 
 AddTest(
   TARGET MODULE_CELL_pseudo_nc
   LIBS parameter  ${math_libs} base device
   SOURCES pseudo_nc_test.cpp ../pseudo.cpp ../atom_pseudo.cpp ../read_pp.cpp ../read_pp_complete.cpp ../read_pp_upf201.cpp ../read_pp_upf100.cpp ../read_pp_vwr.cpp
-  	../read_pp_blps.cpp ../../source_io/output.cpp
+  	../read_pp_blps.cpp ../../source_io/module_output/output.cpp
 )
 
 AddTest(
   TARGET MODULE_CELL_atom_pseudo
   LIBS parameter  ${math_libs} base device
   SOURCES atom_pseudo_test.cpp ../atom_pseudo.cpp ../pseudo.cpp ../read_pp.cpp ../read_pp_complete.cpp ../read_pp_upf201.cpp ../read_pp_upf100.cpp
-  	../read_pp_vwr.cpp ../read_pp_blps.cpp ../../source_io/output.cpp
+  	../read_pp_vwr.cpp ../read_pp_blps.cpp ../../source_io/module_output/output.cpp
 )
 
 AddTest(
   TARGET MODULE_CELL_atom_spec
   LIBS parameter ${math_libs} base device
   SOURCES atom_spec_test.cpp ../atom_spec.cpp ../atom_pseudo.cpp ../pseudo.cpp ../read_pp.cpp ../read_pp_complete.cpp ../read_pp_upf201.cpp
-  	../read_pp_upf100.cpp ../read_pp_vwr.cpp ../read_pp_blps.cpp ../../source_io/output.cpp
+  	../read_pp_upf100.cpp ../read_pp_vwr.cpp ../read_pp_blps.cpp ../../source_io/module_output/output.cpp
 )
 
 AddTest(
   TARGET MODULE_CELL_klist_test
   LIBS parameter  ${math_libs} base device symmetry
-  SOURCES klist_test.cpp ../klist.cpp ../parallel_kpoints.cpp ../../source_io/output.cpp ../k_vector_utils.cpp
+  SOURCES klist_test.cpp ../klist.cpp ../parallel_kpoints.cpp ../../source_io/module_output/output.cpp ../k_vector_utils.cpp
 )
 
 AddTest(
   TARGET MODULE_CELL_klist_test_para1
   LIBS parameter  ${math_libs} base device symmetry
-  SOURCES klist_test_para.cpp ../klist.cpp ../parallel_kpoints.cpp ../../source_io/output.cpp ../k_vector_utils.cpp
+  SOURCES klist_test_para.cpp ../klist.cpp ../parallel_kpoints.cpp ../../source_io/module_output/output.cpp ../k_vector_utils.cpp
 )
 
 add_test(NAME MODULE_CELL_klist_test_para4
@@ -139,26 +139,26 @@ add_test(NAME MODULE_CELL_parallel_kpoints_test
 AddTest(
   TARGET MODULE_CELL_unitcell_test
   LIBS parameter  ${math_libs} base device cell_info  symmetry
-  SOURCES unitcell_test.cpp ../../source_io/output.cpp ../../source_estate/cal_ux.cpp
+  SOURCES unitcell_test.cpp ../../source_io/module_output/output.cpp ../../source_estate/cal_ux.cpp
 
 )
 
 AddTest(
   TARGET MODULE_CELL_unitcell_test_readpp
   LIBS parameter  ${math_libs} base device cell_info
-  SOURCES unitcell_test_readpp.cpp ../../source_io/output.cpp
+  SOURCES unitcell_test_readpp.cpp ../../source_io/module_output/output.cpp
 )
 
 AddTest(
   TARGET MODULE_CELL_unitcell_test_para
   LIBS parameter  ${math_libs} base device cell_info
-  SOURCES unitcell_test_para.cpp ../../source_io/output.cpp
+  SOURCES unitcell_test_para.cpp ../../source_io/module_output/output.cpp
 )
 
 AddTest(
   TARGET MODULE_CELL_unitcell_test_setupcell
   LIBS parameter  ${math_libs} base device cell_info
-  SOURCES unitcell_test_setupcell.cpp ../../source_io/output.cpp
+  SOURCES unitcell_test_setupcell.cpp ../../source_io/module_output/output.cpp
 )
 
 add_test(NAME MODULE_CELL_unitcell_test_parallel

source/source_cell/test/klist_test.cpp

@@ -15,7 +15,7 @@
 #include "source_pw/module_pwdft/vl_pw.h"
 #include "source_pw/module_pwdft/vnl_pw.h"
 #include "source_pw/module_pwdft/parallel_grid.h"
-#include "source_io/berryphase.h"
+#include "source_io/module_unk/berryphase.h"
 #include "source_io/module_parameter/parameter.h"
 #undef private
 #include "source_base/mathzone.h"

source/source_cell/test/klist_test_para.cpp

@@ -22,7 +22,7 @@
 #include "source_pw/module_pwdft/vl_pw.h"
 #include "source_pw/module_pwdft/vnl_pw.h"
 #include "source_pw/module_pwdft/parallel_grid.h"
-#include "source_io/berryphase.h"
+#include "source_io/module_unk/berryphase.h"
 #undef private
 bool berryphase::berry_phase_flag = false;
 

source/source_cell/test_pw/CMakeLists.txt

@@ -13,7 +13,7 @@ AddTest(
   SOURCES unitcell_test_pw.cpp ../unitcell.cpp ../read_atoms.cpp ../read_atoms_helper.cpp ../atom_spec.cpp ../update_cell.cpp ../bcast_cell.cpp
 	../atom_pseudo.cpp ../pseudo.cpp ../read_pp.cpp ../read_pp_complete.cpp ../read_pp_upf201.cpp ../read_pp_upf100.cpp
   ../read_stru.cpp   ../read_atom_species.cpp
-	../read_pp_vwr.cpp ../read_pp_blps.cpp ../../source_io/output.cpp
+	../read_pp_vwr.cpp ../read_pp_blps.cpp ../../source_io/module_output/output.cpp
   ../../source_estate/read_pseudo.cpp ../../source_estate/cal_nelec_nband.cpp
   ../../source_estate/read_orb.cpp    ../print_cell.cpp
   ../../source_estate/cal_wfc.cpp  ../sep.cpp   ../sep_cell.cpp

source/source_cell/unitcell.h

@@ -5,7 +5,7 @@
 #include "source_base/global_variable.h"
 #include "source_cell/sep_cell.h"
 #include "source_estate/magnetism.h"
-#include "source_io/output.h"
+#include "source_io/module_output/output.h"
 #include "module_symmetry/symmetry.h"
 
 #ifdef __LCAO

source/source_esolver/esolver_dm2rho.cpp

@@ -8,8 +8,8 @@
 #include "source_lcao/hamilt_lcao.h"
 #include "source_lcao/module_operator_lcao/operator_lcao.h"
 #include "source_io/cube_io.h"
-#include "source_io/io_npz.h"
-#include "source_io/print_info.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

@@ -14,7 +14,7 @@
 #include "source_lcao/hamilt_lcao.h"
 #include "source_hsolver/hsolver_lcao.h"
 #include "source_io/module_parameter/parameter.h"
-#include "source_io/write_HS.h" // use ModuleIO::write_hsk()
+#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_dp.cpp

@@ -21,7 +21,7 @@
 
 #include "source_base/parallel_common.h"
 #include "source_base/timer.h"
-#include "source_io/output_log.h"
+#include "source_io/module_output/output_log.h"
 #include "source_io/cif_io.h"
 
 #include <iomanip>