deepmodeling · mohanchen · Jul 5, 2025 · Jul 4, 2025 · Jul 4, 2025 · Jul 4, 2025
diff --git a/python/pyabacus/CMakeLists.txt b/python/pyabacus/CMakeLists.txt
@@ -79,7 +79,7 @@ set(BASE_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/base")
 add_subdirectory(${ABACUS_SOURCE_DIR}/source_base ${BASE_BINARY_DIR})
 # add parameter
 set(PARAMETER_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/parameter")
-add_subdirectory(${ABACUS_SOURCE_DIR}/module_parameter ${PARAMETER_BINARY_DIR})
+add_subdirectory(${ABACUS_SOURCE_DIR}/source_io/module_parameter ${PARAMETER_BINARY_DIR})
 # add orb
 set(ORB_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/orb")
 add_subdirectory(${ABACUS_SOURCE_DIR}/source_basis/module_ao ${ORB_BINARY_DIR})

diff --git a/python/pyabacus/CONTRIBUTING.md b/python/pyabacus/CONTRIBUTING.md
@@ -144,7 +144,7 @@ set(BASE_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/base")
 add_subdirectory(${ABACUS_SOURCE_DIR}/source_base ${BASE_BINARY_DIR})
 # Add parameter
 set(PARAMETER_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/parameter")
-add_subdirectory(${ABACUS_SOURCE_DIR}/module_parameter ${PARAMETER_BINARY_DIR})
+add_subdirectory(${ABACUS_SOURCE_DIR}/source_io/module_parameter ${PARAMETER_BINARY_DIR})
 # Add orb
 set(ORB_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/orb")
 add_subdirectory(${ABACUS_SOURCE_DIR}/source_basis/module_ao ${ORB_BINARY_DIR})

diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
@@ -15,7 +15,7 @@ add_subdirectory(source_lcao/module_gint)
 add_subdirectory(source_io)
 add_subdirectory(source_relax)
 add_subdirectory(source_lcao/module_ri)
-add_subdirectory(module_parameter)
+add_subdirectory(source_io/module_parameter)
 add_subdirectory(module_lr)
 
 # add by jghan

diff --git a/source/Makefile.Objects b/source/Makefile.Objects
@@ -54,12 +54,12 @@ VPATH=./src_global:\
 ./source_pw/module_pwdft/module_exx_helper:\
 ./source_pw/module_stodft/kernels:\
 ./source_lcao/module_hcontainer:\
-./source_lcao/hamilt_lcaodft:\
+./source_lcao:\
 ./source_lcao/module_rt:\
 ./source_lcao/module_deepks:\
 ./source_lcao/module_dftu:\
 ./source_lcao/module_deltaspin:\
-./source_lcao/hamilt_lcaodft/operator_lcao:\
+./source_lcao/module_operator_lcao:\
 ./source_lcao/module_gint:\
 ./source_lcao/module_gint/temp_gint:\
 ./source_relax:\
@@ -68,7 +68,7 @@ VPATH=./src_global:\
 ./source_io/json_output:\
 ./src_ri:\
 ./source_lcao/module_ri:\
-./module_parameter:\
+./source_io/module_parameter:\
 ./module_lr:\
 ./module_lr/ao_to_mo_transformer:\
 ./module_lr/dm_trans:\

diff --git a/source/module_lr/dm_trans/dmr_complex.cpp b/source/module_lr/dm_trans/dmr_complex.cpp
@@ -1,6 +1,6 @@
 #include "source_estate/module_dm/density_matrix.h"
 #include "source_base/timer.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "source_base/libm/libm.h"
 namespace elecstate
 {

diff --git a/source/module_lr/esolver_lrtd_lcao.cpp b/source/module_lr/esolver_lrtd_lcao.cpp
@@ -7,14 +7,14 @@
 #include "module_lr/hsolver_lrtd.hpp"
 #include "module_lr/lr_spectrum.h"
 #include <memory>
-#include "source_lcao/hamilt_lcaodft/hamilt_lcao.h"
+#include "source_lcao/hamilt_lcao.h"
 #include "source_io/read_wfc_nao.h"
 #include "source_io/cube_io.h"
 #include "source_io/print_info.h"
 #include "source_cell/module_neighbor/sltk_atom_arrange.h"
 #include "module_lr/utils/lr_util_print.h"
 #include "source_base/scalapack_connector.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "module_lr/ri_benchmark/ri_benchmark.h"
 #include "module_lr/operator_casida/operator_lr_diag.h" // for precondition
 

diff --git a/source/module_lr/esolver_lrtd_lcao.h b/source/module_lr/esolver_lrtd_lcao.h
@@ -1,6 +1,6 @@
 #pragma once
 #include "source_esolver/esolver_fp.h"
-#include "module_parameter/input_parameter.h"
+#include "source_io/module_parameter/input_parameter.h"
 #include "source_cell/unitcell.h"
 #include "source_hamilt/hamilt.h"
 #include "source_estate/elecstate.h"

diff --git a/source/module_lr/hsolver_lrtd.hpp b/source/module_lr/hsolver_lrtd.hpp
@@ -1,5 +1,5 @@
 #pragma once
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "source_hsolver/diago_david.h"
 #include "source_hsolver/diago_dav_subspace.h"
 #include "source_hsolver/diago_cg.h"

diff --git a/source/module_lr/lr_spectrum.cpp b/source/module_lr/lr_spectrum.cpp
@@ -1,6 +1,6 @@
 #include "lr_spectrum.h"
 #include "module_lr/utils/lr_util.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "module_lr/dm_trans/dm_trans.h"
 #include "source_base/parallel_reduce.h"
 #include "module_lr/utils/lr_util.h"

diff --git a/source/module_lr/lr_spectrum_velocity.cpp b/source/module_lr/lr_spectrum_velocity.cpp
@@ -2,7 +2,7 @@
 #include "module_lr/dm_trans/dm_trans.h"
 #include "module_lr/utils/lr_util_hcontainer.h"
 #include "math.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "source_lcao/module_hcontainer/hcontainer_funcs.h"
 namespace LR
 {

diff --git a/source/module_lr/operator_casida/operator_lr_hxc.cpp b/source/module_lr/operator_casida/operator_lr_hxc.cpp
@@ -1,12 +1,12 @@
 #include "operator_lr_hxc.h"
 #include <vector>
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "source_base/blas_connector.h"
 #include "source_base/timer.h"
 #include "module_lr/utils/lr_util.h"
 #include "module_lr/utils/lr_util_hcontainer.h"
 #include "module_lr/utils/lr_util_print.h"
-// #include "source_lcao/hamilt_lcaodft/DM_gamma_2d_to_grid.h"
+// #include "source_lcao/DM_gamma_2d_to_grid.h"
 #include "source_lcao/module_hcontainer/hcontainer_funcs.h"
 #include "module_lr/ao_to_mo_transformer/ao_to_mo.h"
 #include "source_pw/module_pwdft/global.h"

diff --git a/source/module_lr/potentials/pot_hxc_lrtd.cpp b/source/module_lr/potentials/pot_hxc_lrtd.cpp
@@ -1,5 +1,5 @@
 #include "pot_hxc_lrtd.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "source_estate/module_pot/H_Hartree_pw.h"
 #include "source_base/timer.h"
 #include "source_hamilt/module_xc/xc_functional.h"

diff --git a/source/module_lr/potentials/xc_kernel.cpp b/source/module_lr/potentials/xc_kernel.cpp
@@ -1,6 +1,6 @@
 #include "xc_kernel.h"
 #include "source_hamilt/module_xc/xc_functional.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "source_base/timer.h"
 #include "module_lr/utils/lr_util.h"
 #include "module_lr/utils/lr_util_xc.hpp"

diff --git a/source/module_lr/utils/gint_move.hpp b/source/module_lr/utils/gint_move.hpp
@@ -1,6 +1,6 @@
 #include "lr_util.h"
 #include "source_lcao/module_gint/gint_gamma.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "source_lcao/module_gint/gint_k.h"
 #include "source_lcao/module_gint/grid_technique.h"
 

diff --git a/source/source_base/global_file.cpp b/source/source_base/global_file.cpp
@@ -11,7 +11,7 @@
 #include <unistd.h>
 #include <sstream>
 #include "global_function.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "global_variable.h"
 #include "source_base/parallel_common.h"
 #include "source_base/parallel_reduce.h"

diff --git a/source/source_base/parallel_global.cpp b/source/source_base/parallel_global.cpp
@@ -14,7 +14,7 @@
 #include "source_base/global_function.h"
 #include "source_base/parallel_common.h"
 #include "source_base/parallel_reduce.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 // #include "source_base/tool_quit.h"
 #include "source_main/version.h"
 

diff --git a/source/source_base/test/global_file_test.cpp b/source/source_base/test/global_file_test.cpp
@@ -1,7 +1,7 @@
 #include "gtest/gtest.h"
 #include "gmock/gmock.h"
 #define private public
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #undef private
 #include "../global_file.h"
 #include "../global_variable.h"

diff --git a/source/source_base/test/global_function_test.cpp b/source/source_base/test/global_function_test.cpp
@@ -1,7 +1,7 @@
 #include "../global_function.h"
 #include "../global_variable.h"
 #define private public
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #undef private
 #include "../vector3.h"
 #include "../tool_quit.h"

diff --git a/source/source_base/test/tool_quit_test.cpp b/source/source_base/test/tool_quit_test.cpp
@@ -1,7 +1,7 @@
 #include "../tool_quit.h"
 #include "../global_variable.h"
 #define private public
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #undef private
 #include "gtest/gtest.h"
 #include "gmock/gmock.h"

diff --git a/source/source_base/tool_quit.cpp b/source/source_base/tool_quit.cpp
@@ -7,7 +7,7 @@
 
 #else
 #include "global_variable.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "global_file.h"
 #include "timer.h"
 #include "memory.h"

diff --git a/source/source_basis/module_ao/ORB_atomic.cpp b/source/source_basis/module_ao/ORB_atomic.cpp
@@ -1,6 +1,6 @@
 #include "ORB_atomic.h"
 
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 Numerical_Orbital_AtomRelation Numerical_Orbital::NOAR;
 
 Numerical_Orbital::Numerical_Orbital()

diff --git a/source/source_basis/module_ao/ORB_atomic_lm.cpp b/source/source_basis/module_ao/ORB_atomic_lm.cpp
@@ -1,6 +1,6 @@
 #include "ORB_atomic_lm.h"
 #include "source_base/sph_bessel_recursive.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "source_base/blas_connector.h"
 #include "source_base/timer.h"
 #include "source_base/math_integral.h"

diff --git a/source/source_basis/module_ao/ORB_nonlocal_lm.cpp b/source/source_basis/module_ao/ORB_nonlocal_lm.cpp
@@ -7,7 +7,7 @@
 #include "source_base/math_sphbes.h"
 #include "source_base/mathzone.h"      /// use Polynomial_Interpolation_xy, Spherical_Bessel
 #include "source_base/mathzone_add1.h" /// use SplineD2
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 
 #include <cassert>
 #include <cmath>

diff --git a/source/source_basis/module_ao/ORB_read.cpp b/source/source_basis/module_ao/ORB_read.cpp
@@ -4,7 +4,7 @@
 #include "source_base/parallel_common.h"
 #include "source_base/timer.h"
 #include "source_base/tool_check.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 
 #include <algorithm>
 #include <cassert>

diff --git a/source/source_basis/module_ao/test/CMakeLists.txt b/source/source_basis/module_ao/test/CMakeLists.txt
@@ -37,8 +37,8 @@ list(APPEND depend_files
   ../ORB_nonlocal_lm.cpp
   ../ORB_gaunt_table.cpp
   ../parallel_orbitals.cpp
-  ../../../source_lcao/hamilt_lcaodft/center2_orb-orb11.cpp
-  ../../../source_lcao/hamilt_lcaodft/center2_orb.cpp
+  ../../../source_lcao/center2_orb-orb11.cpp
+  ../../../source_lcao/center2_orb.cpp
   )
 
 install(DIRECTORY GaAs DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/../../../tests)

diff --git a/source/source_basis/module_ao/test/ORB_atomic_lm_test.cpp b/source/source_basis/module_ao/test/ORB_atomic_lm_test.cpp
@@ -1,7 +1,7 @@
 #include "gtest/gtest.h"
 #include "source_base/math_integral.h"
 #define private public
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #undef private
 #include <algorithm>
 #include <string>

diff --git a/source/source_basis/module_ao/test/ORB_nonlocal_lm_test.cpp b/source/source_basis/module_ao/test/ORB_nonlocal_lm_test.cpp
@@ -1,7 +1,7 @@
 #include "gtest/gtest.h"
 #include "source_base/global_function.h"
 #define private public
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #undef private
 #include "source_base/global_variable.h"
 #include "source_base/math_integral.h"

diff --git a/source/source_basis/module_ao/test/ORB_unittest.h b/source/source_basis/module_ao/test/ORB_unittest.h
@@ -3,7 +3,7 @@
 
 #include "source_base/global_function.h"
 #include "source_basis/module_ao/ORB_control.h"
-#include "source_lcao/hamilt_lcaodft/center2_orb-orb11.h"
+#include "source_lcao/center2_orb-orb11.h"
 
 #include "gtest/gtest.h"
 //#include "mock_center2.h"

diff --git a/source/source_basis/module_nao/beta_radials.cpp b/source/source_basis/module_nao/beta_radials.cpp
@@ -1,6 +1,6 @@
 #include "source_basis/module_nao/beta_radials.h"
 
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "source_base/global_variable.h"
 #include "source_base/parallel_common.h"
 #include "source_base/tool_quit.h"

diff --git a/source/source_basis/module_nao/numerical_radial.cpp b/source/source_basis/module_nao/numerical_radial.cpp
@@ -11,7 +11,7 @@
 #include "source_base/global_variable.h"
 #include "source_base/math_integral.h"
 #include "source_base/spherical_bessel_transformer.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 
 using ModuleBase::PI;
 

diff --git a/source/source_basis/module_nao/two_center_bundle.cpp b/source/source_basis/module_nao/two_center_bundle.cpp
@@ -5,7 +5,7 @@
 #include "source_base/parallel_common.h"
 #include "source_base/ylm.h"
 #include "source_basis/module_nao/real_gaunt_table.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 
 #include <memory>
 

diff --git a/source/source_basis/module_pw/pw_basis_k.cpp b/source/source_basis/module_pw/pw_basis_k.cpp
@@ -3,7 +3,7 @@
 #include "source_base/constants.h"
 #include "source_base/memory.h"
 #include "source_base/timer.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 
 #include <utility>
 namespace ModulePW

diff --git a/source/source_basis/module_pw/pw_basis_sup.cpp b/source/source_basis/module_pw/pw_basis_sup.cpp
@@ -1,6 +1,6 @@
 #include "source_base/timer.h"
 #include "pw_basis.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 namespace ModulePW
 {
 

diff --git a/source/source_basis/module_pw/pw_distributeg.cpp b/source/source_basis/module_pw/pw_distributeg.cpp
@@ -2,7 +2,7 @@
 #include "source_base/tool_quit.h"
 #include "source_base/global_function.h"
 #include "source_base/timer.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 namespace ModulePW
 {
 /**

diff --git a/source/source_basis/module_pw/test/Makefile b/source/source_basis/module_pw/test/Makefile
@@ -106,7 +106,7 @@ VPATH=../../../source_main\
 ../../../source_base/module_device\
 ../../../source_base/module_container/ATen/core\
 ../../../source_base/module_container/ATen\
-../../../module_parameter\
+../../../source_io/module_parameter\
 ../module_fft\
 ../\
 

diff --git a/source/source_cell/atom_pseudo.cpp b/source/source_cell/atom_pseudo.cpp
@@ -1,7 +1,7 @@
 #include "atom_pseudo.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 Atom_pseudo::Atom_pseudo()
 {
 }

diff --git a/source/source_cell/atom_spec.cpp b/source/source_cell/atom_spec.cpp
@@ -1,5 +1,5 @@
 #include "atom_spec.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include <cstdlib>
 
 Atom::Atom()

diff --git a/source/source_cell/bcast_cell.cpp b/source/source_cell/bcast_cell.cpp
@@ -1,6 +1,6 @@
 #include "unitcell.h"   
 #include "source_base/parallel_common.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #ifdef __EXX
 #include "source_lcao/module_ri/serialization_cereal.h"
 #include "source_pw/module_pwdft/global.h"

diff --git a/source/source_cell/cal_atoms_info.h b/source/source_cell/cal_atoms_info.h
@@ -1,6 +1,6 @@
 #ifndef CAL_ATOMS_INFO_H
 #define CAL_ATOMS_INFO_H
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "source_estate/cal_nelec_nband.h"
 class CalAtomsInfo
 {

diff --git a/source/source_cell/k_vector_utils.cpp b/source/source_cell/k_vector_utils.cpp
@@ -10,7 +10,7 @@
 #include "source_base/formatter.h"
 #include "source_base/parallel_common.h"
 #include "source_base/parallel_reduce.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 
 namespace KVectorUtils
 {

diff --git a/source/source_cell/klist.cpp b/source/source_cell/klist.cpp
@@ -9,7 +9,7 @@
 #include "source_cell/module_symmetry/symmetry.h"
 #include "source_pw/module_pwdft/global.h"
 #include "source_io/berryphase.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 
 void K_Vectors::cal_ik_global()
 {

diff --git a/source/source_cell/module_neighbor/sltk_atom_arrange.cpp b/source/source_cell/module_neighbor/sltk_atom_arrange.cpp
@@ -1,7 +1,7 @@
 #include "sltk_atom_arrange.h"
 
 #include "source_base/timer.h"
-#include "module_parameter/parameter.h"
+#include "source_io/module_parameter/parameter.h"
 #include "sltk_grid.h"
 #include "sltk_grid_driver.h"