deepmodeling · mohanchen · Jun 27, 2026 · Jun 25, 2026 · Jun 25, 2026 · Jun 25, 2026
diff --git a/source/source_base/CMakeLists.txt b/source/source_base/CMakeLists.txt
@@ -40,6 +40,7 @@ add_library(
     mymath.cpp
     opt_CG.cpp
     opt_DCsrch.cpp
+    output.cpp
     para_gemm.cpp
     realarray.cpp
     sph_bessel_recursive-d1.cpp

diff --git a/source/source_io/module_output/output.cpp → source/source_base/output.cpp b/source/source_io/module_output/output.cpp → source/source_base/output.cpp
diff --git a/source/source_io/module_output/output.h → source/source_base/output.h b/source/source_io/module_output/output.h → source/source_base/output.h
@@ -5,10 +5,10 @@
 #ifndef OUTPUT_H
 #define OUTPUT_H
 
-#include "../../source_base/realarray.h"
-#include "../../source_base/matrix3.h"
-#include "../../source_base/complexmatrix.h"
-#include "../../source_base/matrix.h"
+#include "realarray.h"
+#include "matrix3.h"
+#include "complexmatrix.h"
+#include "matrix.h"
 class output
 {
 public:

diff --git a/source/source_cell/CMakeLists.txt b/source/source_cell/CMakeLists.txt
@@ -23,6 +23,7 @@ add_library(
     cell_index.cpp
     check_atomic_stru.cpp
     update_cell.cpp
+    magnetism.cpp
     bcast_cell.cpp
     read_stru.cpp
     print_cell.cpp

diff --git a/source/source_cell/atom_spec.cpp b/source/source_cell/atom_spec.cpp
@@ -1,6 +1,6 @@
 #include "atom_spec.h"
 #include "source_io/module_parameter/parameter.h"
-#include "source_io/module_output/output.h"
+#include "source_base/output.h"
 #include <cstdlib>
 
 Atom::Atom()

diff --git a/source/source_estate/magnetism.cpp → source/source_cell/magnetism.cpp b/source/source_estate/magnetism.cpp → source/source_cell/magnetism.cpp
diff --git a/source/source_estate/magnetism.h → source/source_cell/magnetism.h b/source/source_estate/magnetism.h → source/source_cell/magnetism.h
diff --git a/source/source_cell/module_neighbor/test/CMakeLists.txt b/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/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/module_output/output.cpp
+
 )
diff --git a/source/source_cell/module_symmetry/symm_analysis.cpp b/source/source_cell/module_symmetry/symm_analysis.cpp
@@ -1,6 +1,6 @@
 #include "symmetry.h"
 #include "source_io/module_parameter/parameter.h"
-#include "source_io/module_output/output.h"
+#include "source_base/output.h"
 
 using namespace ModuleSymmetry;
 

diff --git a/source/source_cell/module_symmetry/test/symmetry_test_analysis.cpp b/source/source_cell/module_symmetry/test/symmetry_test_analysis.cpp
@@ -1,5 +1,5 @@
 #include "symmetry_test_cases.h"
-#include "source_io/module_output/output.h"
+#include "source_base/output.h"
 #include "mpi.h"
 /************************************************
  *  unit test of class Symmetry
@@ -20,7 +20,6 @@
  * is different from its point group.
  ***********************************************/
 // mock the useless functions
-void output::printM3(std::ofstream &ofs, const std::string &description, const ModuleBase::Matrix3 &m){}
 pseudo::pseudo()
 {
 }

diff --git a/source/source_cell/module_symmetry/test/symmetry_test_symtrz.cpp b/source/source_cell/module_symmetry/test/symmetry_test_symtrz.cpp
@@ -1,5 +1,5 @@
 #include "symmetry_test_cases.h"
-#include "source_io/module_output/output.h"
+#include "source_base/output.h"
 #include "mpi.h"
 
 /************************************************
@@ -9,7 +9,6 @@
  *
 ***********************************************/
 // mock the useless functions
-void output::printM3(std::ofstream& ofs, const std::string& description, const ModuleBase::Matrix3& m) {}
 pseudo::pseudo() {}
 pseudo::~pseudo() {}
 Atom::Atom() {}

diff --git a/source/source_cell/pseudo.cpp b/source/source_cell/pseudo.cpp
@@ -1,6 +1,6 @@
 #include "pseudo.h"
 #include "source_base/tool_title.h"
-#include "source_io/module_output/output.h"
+#include "source_base/output.h"
 #include <cstdint>
 
 pseudo::pseudo()

diff --git a/source/source_cell/read_atom_species.cpp b/source/source_cell/read_atom_species.cpp
@@ -1,10 +1,9 @@
 #include "read_stru.h"
 
+#include <sstream>
+
 #include "source_io/module_parameter/parameter.h"
 #include "source_base/tool_title.h"
-#ifdef __EXX
-#include "source_lcao/module_ri/serialization_cereal.h"
-#endif
 #include "source_hamilt/module_xc/exx_info.h" // use GlobalC::exx_info
 
 namespace unitcell

diff --git a/source/source_cell/sep.cpp b/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/module_output/output.h"
+#include "source_base/output.h"
 
 #include <fstream>
 #include <sstream>

diff --git a/source/source_cell/test/CMakeLists.txt b/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/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/module_output/output.cpp
+  	../read_pp_blps.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/module_output/output.cpp
+  	../read_pp_vwr.cpp ../read_pp_blps.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/module_output/output.cpp
+  	../read_pp_upf100.cpp ../read_pp_vwr.cpp ../read_pp_blps.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/module_output/output.cpp ../k_vector_utils.cpp
+  SOURCES klist_test.cpp ../klist.cpp ../parallel_kpoints.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/module_output/output.cpp ../k_vector_utils.cpp
+  SOURCES klist_test_para.cpp ../klist.cpp ../parallel_kpoints.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/module_output/output.cpp ../../source_estate/cal_ux.cpp
+  SOURCES unitcell_test.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/module_output/output.cpp
+  SOURCES unitcell_test_readpp.cpp
 )
 
 AddTest(
   TARGET MODULE_CELL_unitcell_test_para
   LIBS parameter  ${math_libs} base device cell_info
-  SOURCES unitcell_test_para.cpp ../../source_io/module_output/output.cpp
+  SOURCES unitcell_test_para.cpp
 )
 
 AddTest(
   TARGET MODULE_CELL_unitcell_test_setupcell
   LIBS parameter  ${math_libs} base device cell_info
-  SOURCES unitcell_test_setupcell.cpp ../../source_io/module_output/output.cpp
+  SOURCES unitcell_test_setupcell.cpp
 )
 
 add_test(NAME MODULE_CELL_unitcell_test_parallel

diff --git a/source/source_cell/test/klist_test.cpp b/source/source_cell/test/klist_test.cpp
@@ -11,7 +11,7 @@
 #include "source_cell/pseudo.h"
 #include "source_cell/setup_nonlocal.h"
 #include "source_cell/unitcell.h"
-#include "source_estate/magnetism.h"
+#include "source_cell/magnetism.h"
 #include "source_pw/module_pwdft/vl_pw.h"
 #include "source_pw/module_pwdft/vnl_pw.h"
 #include "source_pw/module_pwdft/parallel_grid.h"

diff --git a/source/source_cell/test/klist_test_para.cpp b/source/source_cell/test/klist_test_para.cpp
@@ -19,7 +19,7 @@
 #include "source_cell/pseudo.h"
 #include "source_cell/setup_nonlocal.h"
 #include "source_cell/unitcell.h"
-#include "source_estate/magnetism.h"
+#include "source_cell/magnetism.h"
 #include "source_pw/module_pwdft/vl_pw.h"
 #include "source_pw/module_pwdft/vnl_pw.h"
 #include "source_pw/module_pwdft/parallel_grid.h"

diff --git a/source/source_cell/test/read_atoms_helper_test.cpp b/source/source_cell/test/read_atoms_helper_test.cpp
@@ -3,7 +3,7 @@
 #include "../read_atoms_helper.h"
 #include "source_base/vector3.h"
 #include "source_base/matrix3.h"
-#include "source_io/module_output/output.h"
+#include "source_base/output.h"
 #include <sstream>
 #include <fstream>
 
@@ -15,15 +15,6 @@ namespace elecstate {
     }
 }
 
-// Mock output class methods
-void output::printM3(std::ofstream& ofs, const std::string& description, const ModuleBase::Matrix3& m) {
-    // Mock implementation
-}
-
-void output::printrm(std::ofstream& ofs, const std::string& description, const ModuleBase::matrix& m, const double& limit) {
-    // Mock implementation
-}
-
 // Mock InfoNonlocal class
 InfoNonlocal::InfoNonlocal() {}
 InfoNonlocal::~InfoNonlocal() {}

diff --git a/source/source_cell/test_pw/CMakeLists.txt b/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/module_output/output.cpp
+	../read_pp_vwr.cpp ../read_pp_blps.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

diff --git a/source/source_cell/unitcell.cpp b/source/source_cell/unitcell.cpp
@@ -7,7 +7,7 @@
 #include "unitcell.h"
 #include "bcast_cell.h"
 #include "source_base/tool_quit.h"
-#include "source_io/module_output/output.h"
+#include "source_base/output.h"
 #include "source_io/module_parameter/parameter.h"
 #include "source_cell/read_stru.h"
 #include "source_base/atom_in.h"

diff --git a/source/source_cell/unitcell.h b/source/source_cell/unitcell.h
@@ -3,7 +3,7 @@
 
 #include "source_base/global_function.h"
 #include "source_cell/sep_cell.h"
-#include "source_estate/magnetism.h"
+#include "source_cell/magnetism.h"
 #include "module_symmetry/symmetry.h"
 #include "source_cell/module_neighlist/atom_provider.h"
 

diff --git a/source/source_cell/update_cell.cpp b/source/source_cell/update_cell.cpp
@@ -1,7 +1,7 @@
 #include "update_cell.h"
 #include "bcast_cell.h"
 #include "source_base/global_function.h"
-#include "source_io/module_output/output.h"
+#include "source_base/output.h"
 
 namespace unitcell
 {

diff --git a/source/source_estate/CMakeLists.txt b/source/source_estate/CMakeLists.txt
@@ -37,7 +37,6 @@ list(APPEND objects
     module_charge/symmetry_rho.cpp
     module_charge/symmetry_rhog.cpp
     fp_energy.cpp
-    magnetism.cpp
     occupy.cpp
     cal_ux.cpp
     read_orb.cpp

diff --git a/source/source_estate/module_charge/charge.cpp b/source/source_estate/module_charge/charge.cpp
@@ -27,7 +27,7 @@
 #include "source_base/timer.h"
 #include "source_base/tool_threading.h"
 #include "source_cell/unitcell.h"
-#include "source_estate/magnetism.h"
+#include "source_cell/magnetism.h"
 #include "source_hamilt/module_xc/xc_functional.h"
 #include "source_io/module_parameter/parameter.h"
 

diff --git a/source/source_estate/module_charge/charge_init.cpp b/source/source_estate/module_charge/charge_init.cpp
@@ -11,7 +11,7 @@
 #include "source_base/parallel_reduce.h"
 #include "source_base/timer.h"
 #include "source_base/tool_threading.h"
-#include "source_estate/magnetism.h"
+#include "source_cell/magnetism.h"
 #include "source_pw/module_pwdft/parallel_grid.h"
 #include "source_io/module_output/cube_io.h"
 #include "source_io/module_chgpot/rhog_io.h"

diff --git a/source/source_estate/module_dm/test/CMakeLists.txt b/source/source_estate/module_dm/test/CMakeLists.txt
@@ -16,7 +16,7 @@ AddTest(
   ${ABACUS_SOURCE_DIR}/source_lcao/module_hcontainer/hcontainer.cpp
   ${ABACUS_SOURCE_DIR}/source_lcao/module_hcontainer/atom_pair.cpp
   ${ABACUS_SOURCE_DIR}/source_basis/module_ao/parallel_orbitals.cpp
-  ${ABACUS_SOURCE_DIR}/source_io/module_output/output.cpp
+
 )
 
 AddTest(

diff --git a/source/source_estate/test/CMakeLists.txt b/source/source_estate/test/CMakeLists.txt
@@ -26,7 +26,7 @@ AddTest(
 AddTest(
   TARGET MODULE_ESTATE_elecstate_magnetism
   LIBS parameter  ${math_libs} base device
-  SOURCES elecstate_magnetism_test.cpp ../magnetism.cpp
+  SOURCES elecstate_magnetism_test.cpp ../../source_cell/magnetism.cpp
 )
 
 AddTest(
@@ -86,7 +86,7 @@ AddTest(
   TARGET MODULE_ESTATE_charge_test
   LIBS parameter  ${math_libs} planewave_serial base device cell_info 
   SOURCES charge_test.cpp ../module_charge/charge.cpp
-    ../../source_io/module_output/output.cpp
+
 )
 
 AddTest(
@@ -95,14 +95,14 @@ AddTest(
   SOURCES charge_mixing_test.cpp  
   ../module_charge/charge_mixing.cpp ../module_charge/charge_mixing_dmr.cpp ../module_charge/charge_mixing_residual.cpp
   ../module_charge/charge_mixing_preconditioner.cpp ../module_charge/charge_mixing_rho.cpp
-  ../module_charge/charge_mixing_uspp.cpp ../../source_io/module_output/output.cpp
+  ../module_charge/charge_mixing_uspp.cpp
 )
 
 AddTest(
   TARGET MODULE_ESTATE_charge_extra
   LIBS parameter ${math_libs} base device cell_info
   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_base/module_fft/fft_bundle.cpp ../../source_base/module_fft/fft_cpu.cpp
 )
 
 AddTest(

diff --git a/source/source_estate/test/elecstate_magnetism_test.cpp b/source/source_estate/test/elecstate_magnetism_test.cpp
@@ -25,7 +25,7 @@
 */
 
 #define private public
-#include "source_estate/magnetism.h"
+#include "source_cell/magnetism.h"
 #undef private
 Charge::Charge()
 {

diff --git a/source/source_io/CMakeLists.txt b/source/source_io/CMakeLists.txt
@@ -19,7 +19,6 @@ list(APPEND objects
     module_bessel/numerical_basis.cpp
     module_bessel/numerical_basis_jyjy.cpp
     module_bessel/numerical_descriptor.cpp
-    module_output/output.cpp
     module_output/print_info.cpp
     module_output/read_cube.cpp
     module_chgpot/rhog_io.cpp

diff --git a/source/source_io/module_json/test/CMakeLists.txt b/source/source_io/module_json/test/CMakeLists.txt
@@ -7,5 +7,5 @@ AddTest(
   TARGET MODULE_IO_JSON_OUTPUT_TEST
   LIBS parameter ${math_libs} base device cell_info 
   SOURCES para_json_test.cpp ../general_info.cpp ../init_info.cpp ../readin_info.cpp 
-  ../para_json.cpp ../abacusjson.cpp ../../module_output/output.cpp 
+  ../para_json.cpp ../abacusjson.cpp 
 )