Update CMakefile, refactor some files in source_io

CMakeLists.txt

@@ -129,16 +129,63 @@ if(NOT ENABLE_MPI)
 endif()
 
 # Different exe files of ABACUS
-if(ENABLE_LCAO AND ENABLE_MPI)
-  set(ABACUS_BIN_NAME abacus)
-elseif(NOT ENABLE_LCAO AND ENABLE_MPI)
-  set(ABACUS_BIN_NAME abacus_pw)
-elseif(NOT ENABLE_LCAO AND NOT ENABLE_MPI)
-  set(ABACUS_BIN_NAME abacus_pw_serial)
-elseif(ENABLE_LCAO AND NOT ENABLE_MPI)
-  set(ABACUS_BIN_NAME abacus_serial)
+unset(ABACUS_BIN_NAME CACHE)
+
+# Case : LCAO or PW
+if(ENABLE_LCAO)
+  # Case: CUDA is enabled (suffix with 'g' for GPU)
+  if(USE_CUDA)
+    if(ENABLE_MPI)
+      if(NOT ENABLE_LIBRI AND NOT ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_2g)
+      elseif(ENABLE_LIBRI AND NOT ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_3g)
+      elseif(NOT ENABLE_LIBRI AND ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_4g)
+      elseif(ENABLE_LIBRI AND ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_5g)
+      endif()
+    endif()
+  # Case: CPU is enabled (suffix with 'p' for parallel) 
+  else()
+    if(ENABLE_MPI)
+      if(NOT ENABLE_LIBRI AND NOT ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_2p)
+      elseif(ENABLE_LIBRI AND NOT ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_3p)
+      elseif(NOT ENABLE_LIBRI AND ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_4p)
+      elseif(ENABLE_LIBRI AND ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_5p)
+      endif()
+    else()
+      if(NOT ENABLE_LIBRI AND NOT ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_2s)
+      elseif(ENABLE_LIBRI AND NOT ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_3s)
+      elseif(NOT ENABLE_LIBRI AND ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_4s)
+      elseif(ENABLE_LIBRI AND ENABLE_MLALGO)
+        set(ABACUS_BIN_NAME abacus_5s)
+      endif()
+    endif()
+  endif()
+# Case : PW only
+else()
+  if(USE_CUDA)
+    if(ENABLE_MPI)
+      set(ABACUS_BIN_NAME abacus_1g)
+    endif()
+  else()
+    if(ENABLE_MPI)
+      set(ABACUS_BIN_NAME abacus_1p)
+    else()
+      set(ABACUS_BIN_NAME abacus_1s)
+    endif()
+  endif()
 endif()
 
+
 # Use DSP hardware
 if (USE_DSP)
   set(USE_ELPA OFF)
@@ -488,12 +535,12 @@ elseif(NOT USE_SW)
   find_package(Lapack REQUIRED)
   include_directories(${FFTW3_INCLUDE_DIRS})
   list(APPEND math_libs FFTW3::FFTW3 LAPACK::LAPACK BLAS::BLAS)
-if(USE_DSP)
-  target_link_libraries(${ABACUS_BIN_NAME} ${SCALAPACK_LIBRARY_DIR})
-else()
-  find_package(ScaLAPACK REQUIRED)
-  list(APPEND math_libs ScaLAPACK::ScaLAPACK)
-endif()
+  if(USE_DSP)
+    target_link_libraries(${ABACUS_BIN_NAME} ${SCALAPACK_LIBRARY_DIR})
+  else()
+    find_package(ScaLAPACK REQUIRED)
+    list(APPEND math_libs ScaLAPACK::ScaLAPACK)
+  endif()
   if(USE_OPENMP)
     list(APPEND math_libs FFTW3::FFTW3_OMP)
   endif()
@@ -735,7 +782,7 @@ if(ENABLE_LCAO)
     target_link_libraries(${ABACUS_BIN_NAME} genelpa)
   endif()
   if(USE_CUDA)
-    target_link_libraries(diag_cusolver)
+    target_link_libraries(${ABACUS_BIN_NAME} diag_cusolver)
   endif()
 endif()
 if(ENABLE_RAPIDJSON)

source/source_basis/module_nao/test/CMakeLists.txt

@@ -16,7 +16,7 @@ AddTest(
     ../numerical_radial.cpp
     ../../module_ao/ORB_atomic_lm.cpp
     ../../module_ao/ORB_atomic.cpp
-    ../../../source_io/orb_io.cpp
+    ../../../source_io/module_output/orb_io.cpp
   LIBS parameter ${math_libs} device base 
 )
 
@@ -29,7 +29,7 @@ AddTest(
     ../numerical_radial.cpp
     ../../module_ao/ORB_atomic_lm.cpp
     ../../module_ao/ORB_atomic.cpp
-    ../../../source_io/orb_io.cpp
+    ../../../source_io/module_output/orb_io.cpp
   LIBS parameter ${math_libs} device base 
 )
 
@@ -42,7 +42,7 @@ AddTest(
     ../numerical_radial.cpp
     ../../module_ao/ORB_atomic_lm.cpp
     ../../module_ao/ORB_atomic.cpp
-    ../../../source_io/orb_io.cpp
+    ../../../source_io/module_output/orb_io.cpp
   LIBS parameter ${math_libs} device base 
 )
 
@@ -55,7 +55,7 @@ AddTest(
     ../numerical_radial.cpp
     ../../module_ao/ORB_atomic_lm.cpp
     ../../module_ao/ORB_atomic.cpp
-    ../../../source_io/orb_io.cpp
+    ../../../source_io/module_output/orb_io.cpp
   LIBS parameter ${math_libs} device base 
 )
 
@@ -68,7 +68,7 @@ AddTest(
     ../numerical_radial.cpp
     ../../module_ao/ORB_atomic_lm.cpp
     ../../module_ao/ORB_atomic.cpp
-    ../../../source_io/orb_io.cpp
+    ../../../source_io/module_output/orb_io.cpp
  LIBS parameter ${math_libs} device base 
 )
 
@@ -86,7 +86,7 @@ AddTest(
     ../sphbes_radials.cpp
     ../../module_ao/ORB_atomic_lm.cpp
     ../../module_ao/ORB_atomic.cpp
-    ../../../source_io/orb_io.cpp
+    ../../../source_io/module_output/orb_io.cpp
   LIBS parameter ${math_libs} device base 
 )
 
@@ -106,7 +106,7 @@ AddTest(
     ../two_center_bundle.cpp
     ../two_center_integrator.cpp
     ../real_gaunt_table.cpp
-    ../../../source_io/orb_io.cpp
+    ../../../source_io/module_output/orb_io.cpp
   LIBS parameter ${math_libs} device base container orb 
 )
 
@@ -135,7 +135,7 @@ AddTest(
     ../radial_set.cpp
     ../numerical_radial.cpp
     ../two_center_bundle.cpp
-    ../../../source_io/orb_io.cpp
+    ../../../source_io/module_output/orb_io.cpp
   LIBS parameter ${math_libs} device base container orb 
 )
 
@@ -155,7 +155,7 @@ AddTest(
     ../sphbes_radials.cpp
     ../radial_set.cpp
     ../numerical_radial.cpp
-    ../../../source_io/orb_io.cpp
+    ../../../source_io/module_output/orb_io.cpp
   LIBS parameter ${math_libs} device base container orb 
 )
 
@@ -175,7 +175,7 @@ AddTest(
     ../sphbes_radials.cpp
     ../radial_set.cpp
     ../numerical_radial.cpp
-    ../../../source_io/orb_io.cpp
+    ../../../source_io/module_output/orb_io.cpp
   LIBS parameter ${math_libs} device base container orb 
 )
 

source/source_esolver/esolver_dm2rho.cpp

@@ -7,8 +7,8 @@
 #include "source_lcao/LCAO_domain.h"
 #include "source_lcao/hamilt_lcao.h"
 #include "source_lcao/module_operator_lcao/operator_lcao.h"
-#include "source_io/cube_io.h"
-#include "../source_io/module_ml/io_npz.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
 

source/source_esolver/esolver_dp.cpp

@@ -22,7 +22,7 @@
 #include "source_base/parallel_common.h"
 #include "source_base/timer.h"
 #include "source_io/module_output/output_log.h"
-#include "source_io/cif_io.h"
+#include "source_io/module_output/cif_io.h"
 
 #include <iomanip>
 #include <sstream>

source/source_esolver/esolver_fp.cpp

@@ -5,10 +5,10 @@
 #include "source_estate/read_pseudo.h"
 #include "source_hamilt/module_ewald/H_Ewald_pw.h"
 #include "source_hamilt/module_vdw/vdw.h"
-#include "source_io/cif_io.h"
-#include "source_io/cube_io.h" // use write_vdata_palgrid
-#include "source_io/json_output/init_info.h"
-#include "source_io/json_output/output_info.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_gets.cpp

@@ -7,7 +7,7 @@
 #include "source_lcao/LCAO_domain.h"
 #include "source_lcao/hamilt_lcao.h"
 #include "source_lcao/module_operator_lcao/operator_lcao.h"
-#include "source_io/cal_r_overlap_R.h"
+#include "source_io/module_hs/cal_r_overlap_R.h"
 #include "source_io/module_output/print_info.h"
 #include "source_io/module_hs/write_HS_R.h"
 

source/source_esolver/esolver_ks.cpp

@@ -2,15 +2,15 @@
 #include "source_base/timer_wrapper.h"
 
 // for jason output information
-#include "source_io/json_output/init_info.h"
-#include "source_io/json_output/output_info.h"
+#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
 #include "source_estate/module_charge/chgmixing.h" // mohan add 20251018
 #include "source_pw/module_pwdft/setup_pwwfc.h" // mohan add 20251018
 #include "source_hsolver/hsolver.h"
-#include "source_io/write_eig_occ.h"
-#include "source_io/write_bands.h"
+#include "source_io/module_energy/write_eig_occ.h"
+#include "source_io/module_energy/write_bands.h"
 #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

source/source_esolver/esolver_ks_lcao_tddft.cpp

@@ -1,7 +1,7 @@
 #include "esolver_ks_lcao_tddft.h"
 
 //----------------IO-----------------
-#include "source_io/dipole_io.h"
+#include "source_io/module_dipole/dipole_io.h"
 #include "source_io/module_ctrl/ctrl_output_td.h"
 #include "source_io/module_current/td_current_io.h"
 #include "source_io/module_output/output_log.h"

source/source_esolver/esolver_lj.cpp

@@ -3,7 +3,7 @@
 #include "source_cell/module_neighbor/sltk_atom_arrange.h"
 #include "source_cell/module_neighbor/sltk_grid_driver.h"
 #include "source_io/module_output/output_log.h"
-#include "source_io/cif_io.h"
+#include "source_io/module_output/cif_io.h"
 
 
 namespace ModuleESolver

source/source_esolver/esolver_nep.cpp

@@ -20,7 +20,7 @@
 #include "source_base/parallel_common.h"
 #include "source_base/timer.h"
 #include "source_io/module_output/output_log.h"
-#include "source_io/cif_io.h"
+#include "source_io/module_output/cif_io.h"
 
 #include <numeric>
 #include <unordered_map>

source/source_esolver/esolver_of.cpp

@@ -1,7 +1,7 @@
 #include "esolver_of.h"
 
 #include "source_io/module_parameter/parameter.h"
-#include "source_io/cube_io.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-------------------------

source/source_esolver/esolver_of_tddft.cpp

@@ -1,7 +1,7 @@
 #include "esolver_of_tddft.h"
 
 #include "source_io/module_parameter/parameter.h"
-#include "source_io/cube_io.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-------------------------

source/source_esolver/lcao_others.cpp

@@ -26,7 +26,7 @@
 #endif
 
 // mohan add 2025-03-06
-#include "source_io/cal_test.h"
+#include "source_io/module_output/cal_test.h"
 
 namespace ModuleESolver
 {

source/source_esolver/pw_others.cpp

@@ -7,7 +7,7 @@
 #include "source_base/formatter.h"
 
 // mohan add 2025-03-06
-#include "source_io/cal_test.h"
+#include "source_io/module_output/cal_test.h"
 
 namespace ModuleESolver {
 

source/source_esolver/test/CMakeLists.txt

@@ -6,5 +6,5 @@ install(DIRECTORY support DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 AddTest(
   TARGET esolver_dp_test
   LIBS parameter ${math_libs} base device 
-  SOURCES esolver_dp_test.cpp ../esolver_dp.cpp ../../source_io/cif_io.cpp ../../source_io/module_output/output_log.cpp
+  SOURCES esolver_dp_test.cpp ../esolver_dp.cpp ../../source_io/module_output/cif_io.cpp ../../source_io/module_output/output_log.cpp
 )

source/source_estate/module_charge/charge_extra.cpp

@@ -4,7 +4,7 @@
 #include "source_base/global_variable.h"
 #include "source_base/timer.h"
 #include "source_base/tool_threading.h"
-#include "source_io/cube_io.h"
+#include "source_io/module_output/cube_io.h"
 
 Charge_Extra::Charge_Extra()
 {

source/source_estate/module_charge/charge_init.cpp

@@ -13,7 +13,7 @@
 #include "source_base/tool_threading.h"
 #include "source_estate/magnetism.h"
 #include "source_pw/module_pwdft/parallel_grid.h"
-#include "source_io/cube_io.h"
+#include "source_io/module_output/cube_io.h"
 #include "source_io/module_chgpot/rhog_io.h"
 #include "source_io/module_wf/read_wf2rho_pw.h"
 #include "source_io/module_restart/restart.h"

source/source_estate/test/CMakeLists.txt

@@ -97,7 +97,7 @@ AddTest(
 AddTest(
   TARGET charge_extra
   LIBS parameter  ${math_libs} base device cell_info 
-  SOURCES charge_extra_test.cpp ../module_charge/charge_extra.cpp ../../source_io/read_cube.cpp ../../source_io/write_cube.cpp
+  SOURCES charge_extra_test.cpp ../module_charge/charge_extra.cpp ../../source_io/module_output/read_cube.cpp ../../source_io/module_output/write_cube.cpp
   ../../source_io/module_output/output.cpp ../../source_base/module_fft/fft_bundle.cpp ../../source_base/module_fft/fft_cpu.cpp
 )
 

source/source_hsolver/CMakeLists.txt

@@ -37,14 +37,14 @@ if(ENABLE_LCAO)
   endif ()
 
   if(USE_CUDA)
-      list(APPEND objects
+      set(cuda_objects
           ./kernels/hegvd_op.cpp
           ./kernels/cuda/diag_cusolver.cu
           diago_cusolver.cpp
           diago_cusolver.h
       )
       if(ENABLE_CUSOLVERMP)
-        list(APPEND objects
+        list(APPEND cuda_objects
             ./kernels/cuda/diag_cusolvermp.cu
             diago_cusolvermp.cpp
             diago_cusolvermp.h
@@ -53,7 +53,7 @@ if(ENABLE_LCAO)
     add_library(
         diag_cusolver
         OBJECT
-        ${objects}
+        ${cuda_objects}
     )
     if(ENABLE_COVERAGE)
       add_coverage(diag_cusolver)