Rename module_io to source_io

Author: Critsium-xy

docs/CONTRIBUTING.md

@@ -79,7 +79,7 @@ For those who are interested in the source code, the following figure shows the
 |   `-- hamilt_stodft           The module for defining the Hamiltonian in STODFT calculations.
 |-- source_hsolver              The module for solving the Hamiltonian with different diagonalization methods, including CG, Davidson in PW
 |   |                           calculations, and scalapack and genelpa in LCAO calculations.
-|-- module_io                   The module for reading of INPUT files and output properties including band structure, density of states, charge density, etc.
+|-- source_io                   The module for reading of INPUT files and output properties including band structure, density of states, charge density, etc.
 |-- source_md                   The module for performing molecular dynamics.
 |-- source_psi                  The module for defining the wave function and its operations.
 |-- source_relax                The module for performing structural optimization.

docs/advanced/json/json_add.md

@@ -145,7 +145,7 @@ AbacusJson::add_json({"Json","key6","key7",3}, "cp2k", false);
 
 The current code structure of JSON functionality in Abacus is roughly as follows:
 
-- source/module_io
+- source/source_io
   - para_json.cpp: Contains JSON generation and output interfaces directly called by the device in Abacus.
   - json_output/: Contains the functionality encapsulation class `abacusjson.cpp` of RapidJSON in Abacus and code classes for parameter generation in various JSON modules.
     - test: Code testing files in `json_output`.
@@ -160,7 +160,7 @@ In Abacus JSON addition, the following principles need to be followed:
 
 3. Use classes as function parameters as much as possible instead of using global classes for obtained parameters. (For example, in `gen_general_info`, `Input`)
 
-4. After adding parameters, supplement test code in `module_io/json_output/test`.
+4. After adding parameters, supplement test code in `source_io/json_output/test`.
 
 For the current JSON file, there are two JSON modules: `init` and `general_info`,  `output_info`.
 Taking `general_info` as an example, the code to be added is as follows:

source/CMakeLists.txt

@@ -12,7 +12,7 @@ add_subdirectory(source_md)
 add_subdirectory(source_basis/module_pw)
 add_subdirectory(source_esolver)
 add_subdirectory(source_lcao/module_gint)
-add_subdirectory(module_io)
+add_subdirectory(source_io)
 add_subdirectory(source_relax)
 add_subdirectory(module_ri)
 add_subdirectory(module_parameter)

source/Makefile.Objects

@@ -63,8 +63,8 @@ VPATH=./src_global:\
 ./source_lcao/module_gint:\
 ./source_relax:\
 ./source_hamilt/module_vdw:\
-./module_io:\
-./module_io/json_output:\
+./source_io:\
+./source_io/json_output:\
 ./src_ri:\
 ./module_ri:\
 ./module_parameter:\

source/module_lr/esolver_lrtd_lcao.cpp

@@ -8,9 +8,9 @@
 #include "module_lr/lr_spectrum.h"
 #include <memory>
 #include "source_lcao/hamilt_lcaodft/hamilt_lcao.h"
-#include "module_io/read_wfc_nao.h"
-#include "module_io/cube_io.h"
-#include "module_io/print_info.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"

source/module_lr/potentials/xc_kernel.cpp

@@ -6,7 +6,7 @@
 #include "module_lr/utils/lr_util_xc.hpp"
 #include <set>
 #include <chrono>
-#include "module_io/cube_io.h"
+#include "source_io/cube_io.h"
 #ifdef USE_LIBXC
 #include <xc.h>
 #include "source_hamilt/module_xc/xc_functional_libxc.h"

source/module_lr/utils/test/CMakeLists.txt

@@ -3,7 +3,7 @@ AddTest(
   TARGET lr_util_phys_test
   LIBS parameter base ${math_libs} device container planewave #for FFT
   SOURCES lr_util_physics_test.cpp  ../lr_util.cpp
-  ../../../module_io/orb_io.cpp
+  ../../../source_io/orb_io.cpp
 )
 
 AddTest(

source/module_ri/Exx_LRI_interface.hpp

@@ -10,8 +10,8 @@
 #include "source_base/parallel_common.h"
 #include "source_base/formatter.h"
 
-#include "module_io/csr_reader.h"
-#include "module_io/write_HS_sparse.h"
+#include "source_io/csr_reader.h"
+#include "source_io/write_HS_sparse.h"
 #include "source_estate/elecstate_lcao.h"
 
 #include <sys/time.h>

source/module_ri/module_exx_symmetry/test/CMakeLists.txt

@@ -6,5 +6,5 @@ AddTest(
   LIBS base ${math_libs} device symmetry neighbor parameter
   SOURCES symmetry_rotation_test.cpp ../symmetry_rotation.cpp ../irreducible_sector.cpp ../irreducible_sector_bvk.cpp
   ../../../source_basis/module_ao/parallel_orbitals.cpp
-  ../../../module_io/output.cpp
+  ../../../source_io/output.cpp
 )

source/source_base/module_device/device.h

@@ -38,13 +38,13 @@ std::string get_device_info(std::string device_flag);
 
 /**
  * @brief Get the device kpar object
- * for module_io GlobalV::KPAR
+ * for source_io GlobalV::KPAR
  */
 int get_device_kpar(const int& kpar, const int& bndpar);
 
 /**
  * @brief Get the device flag object
- * for module_io PARAM.inp.device
+ * for source_io PARAM.inp.device
  */
 std::string get_device_flag(const std::string& device,
                             const std::string& basis_type);