[Refactor] Rename module_relax, module_io, module_md, module_hamilt_lcao

docs/CONTRIBUTING.md

@@ -64,7 +64,7 @@ For those who are interested in the source code, the following figure shows the
 |   |-- module_surchem          The module for calculating the surface charge correction.
 |   |-- module_vdw              The module for calculating the van der Waals correction.
 |   |-- module_xc               The module for calculating the exchange-correlation energy and potential.
-|-- module_hamilt_lcao          The module for defining the Hamiltonian in LCAO calculations.
+|-- source_lcao          The module for defining the Hamiltonian in LCAO calculations.
 |   |-- hamilt_lcaodft          The module for defining the Hamiltonian in LCAO-DFT calculations.
 |   |   |-- operator_lcao       The module for defining the operators in LCAO-DFT calculations.
 |   |-- module_deepks           The module for defining the Hamiltonian in DeepKS calculations.
@@ -79,10 +79,10 @@ 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.
-|-- module_md                   The module for performing molecular dynamics.
+|-- 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.
-|-- module_relax                The module for performing structural optimization.
+|-- source_relax                The module for performing structural optimization.
 |   |-- relax_new               The module for performing structural optimization with new algorithm, optimized for cell and ion simultaneously.
 |   `-- relax_old               The module for performing structural optimization with old algorithm, optimized for cell and ion separately.
 |-- module_ri                   The module for performing RI calculations.
@@ -101,7 +101,7 @@ For comments that need to be shown in documents, these formats should be used --
 
 A helpful VS Code extension -- [Doxygen Documentation Generator](https://marketplace.visualstudio.com/items?itemName=cschlosser.doxdocgen), can help you formating comments.
 
-An practical example is class [LCAO_Deepks](https://github.com/deepmodeling/abacus-develop/blob/deepks/source/module_hamilt_lcao/module_deepks/LCAO_deepks.h), the effects can be seen on [readthedocs page](https://abacus-deepks.readthedocs.io/en/latest/DeePKS_API/classLCAO__Descriptor.html#exhale-class-classLCAO-Descriptor)
+An practical example is class [LCAO_Deepks](https://github.com/deepmodeling/abacus-develop/blob/deepks/source/source_lcao/module_deepks/LCAO_deepks.h), the effects can be seen on [readthedocs page](https://abacus-deepks.readthedocs.io/en/latest/DeePKS_API/classLCAO__Descriptor.html#exhale-class-classLCAO-Descriptor)
 
 - Tips
   - Only comments in .h file will be visible in generated  by Doxygen + Sphinx;

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

@@ -4,16 +4,16 @@ add_subdirectory(source_psi)
 add_subdirectory(source_estate)
 add_subdirectory(source_hamilt)
 add_subdirectory(source_pw)
-add_subdirectory(module_hamilt_lcao)
+add_subdirectory(source_lcao)
 add_subdirectory(source_hsolver)
 add_subdirectory(source_basis/module_ao)
 add_subdirectory(source_basis/module_nao)
-add_subdirectory(module_md)
+add_subdirectory(source_md)
 add_subdirectory(source_basis/module_pw)
 add_subdirectory(source_esolver)
-add_subdirectory(module_hamilt_lcao/module_gint)
-add_subdirectory(module_io)
-add_subdirectory(module_relax)
+add_subdirectory(source_lcao/module_gint)
+add_subdirectory(source_io)
+add_subdirectory(source_relax)
 add_subdirectory(module_ri)
 add_subdirectory(module_parameter)
 add_subdirectory(module_lr)

source/Makefile.Objects

@@ -26,7 +26,7 @@ VPATH=./src_global:\
 ./source_base/module_container/ATen/ops:\
 ./source_base/module_device:\
 ./source_base/module_mixing:\
-./module_md:\
+./source_md:\
 ./source_basis/module_pw:\
 ./source_basis/module_pw/module_fft:\
 ./source_esolver:\
@@ -53,18 +53,18 @@ VPATH=./src_global:\
 ./source_pw/hamilt_pwdft/kernels:\
 ./source_pw/hamilt_pwdft/module_exx_helper:\
 ./source_pw/hamilt_stodft/kernels:\
-./module_hamilt_lcao/module_hcontainer:\
-./module_hamilt_lcao/hamilt_lcaodft:\
-./module_hamilt_lcao/module_tddft:\
-./module_hamilt_lcao/module_deepks:\
-./module_hamilt_lcao/module_dftu:\
-./module_hamilt_lcao/module_deltaspin:\
-./module_hamilt_lcao/hamilt_lcaodft/operator_lcao:\
-./module_hamilt_lcao/module_gint:\
-./module_relax:\
+./source_lcao/module_hcontainer:\
+./source_lcao/hamilt_lcaodft:\
+./source_lcao/module_tddft:\
+./source_lcao/module_deepks:\
+./source_lcao/module_dftu:\
+./source_lcao/module_deltaspin:\
+./source_lcao/hamilt_lcaodft/operator_lcao:\
+./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

@@ -7,10 +7,10 @@
 #include "module_lr/hsolver_lrtd.hpp"
 #include "module_lr/lr_spectrum.h"
 #include <memory>
-#include "module_hamilt_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_lcao/hamilt_lcaodft/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"

source/module_lr/esolver_lrtd_lcao.h

@@ -11,9 +11,9 @@
 #include <memory>
 
 #include "source_esolver/esolver_ks_lcao.h" //for the move constructor
-#include "module_hamilt_lcao/module_gint/gint_gamma.h"
-#include "module_hamilt_lcao/module_gint/gint_k.h"
-#include "module_hamilt_lcao/module_gint/grid_technique.h"
+#include "source_lcao/module_gint/gint_gamma.h"
+#include "source_lcao/module_gint/gint_k.h"
+#include "source_lcao/module_gint/grid_technique.h"
 #include "source_estate/module_dm/density_matrix.h"
 #include "module_lr/potentials/pot_hxc_lrtd.h"
 #include "module_lr/hamilt_casida.h"

source/module_lr/lr_spectrum.h

@@ -5,7 +5,7 @@
 #include "source_estate/module_dm/density_matrix.h"
 #include "module_lr/utils/lr_util.h"
 #include "source_basis/module_nao/two_center_bundle.h"
-#include "module_hamilt_lcao/module_tddft/td_current.h"
+#include "source_lcao/module_tddft/td_current.h"
 namespace LR
 {
     template<typename T>

source/module_lr/lr_spectrum_velocity.cpp

@@ -3,7 +3,7 @@
 #include "module_lr/utils/lr_util_hcontainer.h"
 #include "math.h"
 #include "module_parameter/parameter.h"
-#include "module_hamilt_lcao/module_hcontainer/hcontainer_funcs.h"
+#include "source_lcao/module_hcontainer/hcontainer_funcs.h"
 namespace LR
 {
     /// get the velocity matrix v(R)

source/module_lr/operator_casida/operator_lr_hxc.cpp

@@ -6,8 +6,8 @@
 #include "module_lr/utils/lr_util.h"
 #include "module_lr/utils/lr_util_hcontainer.h"
 #include "module_lr/utils/lr_util_print.h"
-// #include "module_hamilt_lcao/hamilt_lcaodft/DM_gamma_2d_to_grid.h"
-#include "module_hamilt_lcao/module_hcontainer/hcontainer_funcs.h"
+// #include "source_lcao/hamilt_lcaodft/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/hamilt_pwdft/global.h"
 

source/module_lr/operator_casida/operator_lr_hxc.h

@@ -2,7 +2,7 @@
 #include "source_cell/klist.h"
 #include "source_hamilt/operator.h"
 #include "module_lr/utils/gint_template.h"
-#include "module_hamilt_lcao/module_gint/grid_technique.h"
+#include "source_lcao/module_gint/grid_technique.h"
 #include "source_estate/module_dm/density_matrix.h"
 #include "module_lr/potentials/pot_hxc_lrtd.h"
 #include "module_lr/utils/lr_util.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/gint_move.hpp

@@ -1,8 +1,8 @@
 #include "lr_util.h"
-#include "module_hamilt_lcao/module_gint/gint_gamma.h"
+#include "source_lcao/module_gint/gint_gamma.h"
 #include "module_parameter/parameter.h"
-#include "module_hamilt_lcao/module_gint/gint_k.h"
-#include "module_hamilt_lcao/module_gint/grid_technique.h"
+#include "source_lcao/module_gint/gint_k.h"
+#include "source_lcao/module_gint/grid_technique.h"
 
 // Here will be  the only place where GlobalCs are used (to be moved) in module_lr
 #include "source_pw/hamilt_pwdft/global.h"

source/module_lr/utils/gint_template.h

@@ -1,6 +1,6 @@
 #pragma once
-#include "module_hamilt_lcao/module_gint/gint_gamma.h"
-#include "module_hamilt_lcao/module_gint/gint_k.h"
+#include "source_lcao/module_gint/gint_gamma.h"
+#include "source_lcao/module_gint/gint_k.h"
 namespace LR
 {
     template <typename T> struct TGint;

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_rdmft/rdmft.h

@@ -13,14 +13,14 @@
 #include "source_base/parallel_2d.h"
 #include "source_basis/module_ao/parallel_orbitals.h"
 #include "source_cell/unitcell.h"
-#include "module_hamilt_lcao/module_gint/gint_gamma.h"
-#include "module_hamilt_lcao/module_gint/gint_k.h"
+#include "source_lcao/module_gint/gint_gamma.h"
+#include "source_lcao/module_gint/gint_k.h"
 #include "source_basis/module_ao/ORB_read.h"
 #include "source_basis/module_nao/two_center_bundle.h"
 
-#include "module_hamilt_lcao/hamilt_lcaodft/operator_lcao/operator_lcao.h"
-#include "module_hamilt_lcao/module_hcontainer/hcontainer.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/hs_matrix_k.hpp"
+#include "source_lcao/hamilt_lcaodft/operator_lcao/operator_lcao.h"
+#include "source_lcao/module_hcontainer/hcontainer.h"
+#include "source_lcao/hamilt_lcaodft/hs_matrix_k.hpp"
 
 #ifdef __EXX
 #include "module_ri/Exx_LRI.h"

source/module_rdmft/rdmft_pot.cpp

@@ -10,11 +10,11 @@
 
 #ifdef __EXX
 #include "module_ri/RI_2D_Comm.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/operator_lcao/op_exx_lcao.h"
+#include "source_lcao/hamilt_lcaodft/operator_lcao/op_exx_lcao.h"
 #endif
-#include "module_hamilt_lcao/hamilt_lcaodft/operator_lcao/ekinetic_new.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/operator_lcao/nonlocal_new.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/operator_lcao/veff_lcao.h"
+#include "source_lcao/hamilt_lcaodft/operator_lcao/ekinetic_new.h"
+#include "source_lcao/hamilt_lcaodft/operator_lcao/nonlocal_new.h"
+#include "source_lcao/hamilt_lcaodft/operator_lcao/veff_lcao.h"
 
 namespace rdmft
 {

source/module_rdmft/rdmft_tools.h

@@ -9,8 +9,8 @@
 #include "source_base/matrix.h"
 #include "source_cell/module_neighbor/sltk_grid_driver.h"
 #include "source_cell/unitcell.h"
-#include "module_hamilt_lcao/module_gint/gint_gamma.h"
-#include "module_hamilt_lcao/module_gint/gint_k.h"
+#include "source_lcao/module_gint/gint_gamma.h"
+#include "source_lcao/module_gint/gint_k.h"
 #include "source_estate/module_pot/potential_new.h"
 #include "source_base/blas_connector.h"
 #include "source_base/scalapack_connector.h"
@@ -21,9 +21,9 @@
 #include "source_estate/module_dm/cal_dm_psi.h"
 #include "source_estate/module_dm/density_matrix.h"
 
-#include "module_hamilt_lcao/module_hcontainer/hcontainer.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/hs_matrix_k.hpp"
-#include "module_hamilt_lcao/hamilt_lcaodft/operator_lcao/operator_lcao.h"
+#include "source_lcao/module_hcontainer/hcontainer.h"
+#include "source_lcao/hamilt_lcaodft/hs_matrix_k.hpp"
+#include "source_lcao/hamilt_lcaodft/operator_lcao/operator_lcao.h"
 
 
 #ifdef __EXX

source/module_ri/Exx_LRI_interface.hpp

@@ -5,13 +5,13 @@
 #include "Exx_LRI_interface.h"
 #include "module_ri/exx_abfs-jle.h"
 #include "module_ri/exx_opt_orb.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/hamilt_lcao.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/operator_lcao/op_exx_lcao.h"
+#include "source_lcao/hamilt_lcaodft/hamilt_lcao.h"
+#include "source_lcao/hamilt_lcaodft/operator_lcao/op_exx_lcao.h"
 #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/Matrix_Orbs11.h

@@ -11,7 +11,7 @@
 #include "source_base/vector3.h"
 #include "source_basis/module_ao/ORB_gaunt_table.h"
 #include "source_basis/module_ao/ORB_read.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/center2_orb-orb11.h"
+#include "source_lcao/hamilt_lcaodft/center2_orb-orb11.h"
 #include "source_cell/unitcell.h"
 #include <RI/global/Tensor.h>
 #include <map>

source/module_ri/Matrix_Orbs21.h

@@ -10,7 +10,7 @@
 #include "source_base/vector3.h"
 #include "source_basis/module_ao/ORB_gaunt_table.h"
 #include "source_basis/module_ao/ORB_read.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/center2_orb-orb21.h"
+#include "source_lcao/hamilt_lcaodft/center2_orb-orb21.h"
 #include "source_cell/unitcell.h"
 #include <RI/global/Tensor.h>
 #include <map>

source/module_ri/Matrix_Orbs22.h

@@ -10,7 +10,7 @@
 #include "source_base/vector3.h"
 #include "source_basis/module_ao/ORB_gaunt_table.h"
 #include "source_basis/module_ao/ORB_read.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/center2_orb-orb22.h"
+#include "source_lcao/hamilt_lcaodft/center2_orb-orb22.h"
 #include "source_cell/unitcell.h"
 
 #include <RI/global/Tensor.h>

source/module_ri/RI_2D_Comm.h

@@ -7,7 +7,7 @@
 #define RI_2D_COMM_H
 
 #include "source_basis/module_ao/parallel_orbitals.h"
-#include "module_hamilt_lcao/module_hcontainer/hcontainer.h"
+#include "source_lcao/module_hcontainer/hcontainer.h"
 #include "source_cell/klist.h"
 
 #include <RI/global/Tensor.h>

source/module_ri/RI_2D_Comm.hpp

@@ -11,7 +11,7 @@
 #include "source_pw/hamilt_pwdft/global.h"
 #include "source_base/tool_title.h"
 #include "source_base/timer.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/LCAO_domain.h"
+#include "source_lcao/hamilt_lcaodft/LCAO_domain.h"
 #include "module_parameter/parameter.h"
 #include <RI/global/Global_Func-2.h>
 

source/module_ri/exx_lip.hpp

@@ -13,7 +13,7 @@
 #include "source_base/vector3.h"
 #include "source_pw/hamilt_pwdft/global.h"
 #include "source_cell/klist.h"
-#include "module_hamilt_lcao/hamilt_lcaodft/wavefunc_in_pw.h"
+#include "source_lcao/hamilt_lcaodft/wavefunc_in_pw.h"
 #include "source_base/lapack_connector.h"
 #include "source_base/parallel_global.h"
 #include "module_parameter/parameter.h"

source/module_ri/module_exx_symmetry/symmetry_rotation.h

@@ -2,7 +2,7 @@
 #include "irreducible_sector.h"
 #include "source_basis/module_ao/parallel_orbitals.h"
 #include <RI/global/Tensor.h>
-#include "module_hamilt_lcao/module_hcontainer/hcontainer.h"
+#include "source_lcao/module_hcontainer/hcontainer.h"
 #include "source_cell/module_neighbor/sltk_grid_driver.h"
 
 namespace ModuleSymmetry

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);

source/source_base/test/global_file_test.cpp

@@ -107,7 +107,7 @@ TEST_F(GlobalFile,closelog)
 TEST_F(GlobalFile,closealllog)
 {
 		/* 
-		For module_io/input.cpp:line3578 close_log() is a void function,
+		For source_io/input.cpp:line3578 close_log() is a void function,
 		All its contents is calling close_all_log() in source_base/global_file.cpp
 		For Input::close_log() what is left to test are the validities of parameters
 		GlobalV::MY_RANK and this->out_alllog.