Refactor: delete src_external and src_pdiag, move module deepks and dftu into hamilt_lcao (#1843)

* Refactor: move module deepks dftu into module_hamilt_lcao

* Refactor: move src_external to src_ri/test_code

* Refactor: delete useless directory src_pdiag

---------

Co-authored-by: dyzheng <[email protected]>

Author: dyzheng

CMakeLists.txt

@@ -506,7 +506,7 @@ if(ENABLE_LCAO)
     )
   endif ()
   if(USE_CUSOLVER_LCAO)
-    target_link_libraries(pdiag)
+    target_link_libraries(diag_cusolver)
   endif()
 endif()
 

docs/CONTRIBUTING.md

@@ -48,7 +48,7 @@ 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_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/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)
 
 - Tips
   - Only comments in .h file will be visible in generated  by Doxygen + Sphinx;

source/CMakeLists.txt

@@ -3,26 +3,18 @@ add_subdirectory(module_cell)
 add_subdirectory(module_psi)
 add_subdirectory(module_elecstate)
 add_subdirectory(module_hamilt_general)
-add_subdirectory(module_hamilt_pw/hamilt_pwdft)
-add_subdirectory(module_hamilt_pw/hamilt_ofdft)
-add_subdirectory(module_hamilt_pw/hamilt_stodft)
+add_subdirectory(module_hamilt_pw)
 add_subdirectory(module_hamilt_lcao)
 add_subdirectory(module_hsolver)
 add_subdirectory(module_orbital)
 add_subdirectory(module_md)
 add_subdirectory(module_pw)
-add_subdirectory(module_hamilt_general/module_surchem)
-add_subdirectory(module_deepks)
-add_subdirectory(module_hamilt_general/module_xc)
 add_subdirectory(module_esolver)
 add_subdirectory(module_gint)
-add_subdirectory(module_dftu)
 add_subdirectory(module_io)
 add_subdirectory(module_relax)
 add_subdirectory(src_parallel)
-add_subdirectory(src_pdiag)
 add_subdirectory(src_ri)
-add_subdirectory(module_hamilt_general/module_vdw)
 add_subdirectory(module_ri)
 
 add_library(

source/Makefile.Objects

@@ -20,9 +20,6 @@ VPATH=./src_global:\
 ./module_base/kernels:\
 ./module_md:\
 ./module_pw:\
-./module_hamilt_general/module_surchem:\
-./module_deepks:\
-./module_hamilt_general/module_xc:\
 ./module_esolver:\
 ./module_hsolver:\
 ./module_hsolver/kernels:\
@@ -35,23 +32,25 @@ VPATH=./src_global:\
 ./module_psi/kernels:\
 ./module_hamilt_general:\
 ./module_hamilt_general/module_ewald:\
+./module_hamilt_general/module_surchem:\
+./module_hamilt_general/module_xc:\
 ./module_hamilt_pw/hamilt_pwdft:\
-./module_hamilt_lcao/hamilt_lcaodft:\
-./module_hamilt_lcao/module_tddft:\
 ./module_hamilt_pw/hamilt_ofdft:\
 ./module_hamilt_pw/hamilt_stodft:\
 ./module_hamilt_pw/hamilt_pwdft/operator_pw:\
-./module_hamilt_lcao/hamilt_lcaodft/operator_lcao:\
 ./module_hamilt_pw/hamilt_pwdft/kernels:\
+./module_hamilt_lcao/hamilt_lcaodft:\
+./module_hamilt_lcao/module_tddft:\
+./module_hamilt_lcao/module_deepks:\
+./module_hamilt_lcao/module_dftu:\
+./module_hamilt_lcao/hamilt_lcaodft/operator_lcao:\
 ./module_gint:\
-./module_dftu:\
 ./module_relax:\
 ./module_relax/relax_old:\
 ./module_relax/relax_new:\
 ./module_hamilt_general/module_vdw:\
 ./module_io:\
 ./src_parallel:\
-./src_pdiag:\
 ./src_ri:\
 ./module_ri:\
 ./\

source/module_elecstate/energy.cpp

@@ -12,7 +12,7 @@
 #endif
 #include <sys/time.h>
 #ifdef __LCAO
-#include "module_dftu/dftu.h"  //Quxin adds for DFT+U on 20201029
+#include "module_hamilt_lcao/module_dftu/dftu.h"  //Quxin adds for DFT+U on 20201029
 #endif
 //new
 #include "module_hamilt_general/module_ewald/H_Ewald_pw.h"
@@ -21,7 +21,7 @@
 #include "module_elecstate/potentials/gatefield.h"    // liuyu add 2022-09-13
 #include "module_hamilt_general/module_surchem/surchem.h"
 #ifdef __DEEPKS
-#include "module_deepks/LCAO_deepks.h"
+#include "module_hamilt_lcao/module_deepks/LCAO_deepks.h"
 #endif
 
 

source/module_elecstate/module_charge/charge_broyden.cpp

@@ -2,6 +2,7 @@
 #include "module_hamilt_pw/hamilt_pwdft/global.h"
 #include "module_base/global_variable.h"
 #include "module_base/inverse_matrix.h"
+#include "module_base/lapack_connector.h"
 #include "src_parallel/parallel_reduce.h"
 #include "module_base/memory.h"
 #include "module_base/timer.h"

source/module_elecstate/test/CMakeLists.txt

@@ -37,7 +37,6 @@ if(ENABLE_LCAO)
               ../../module_gint/gint_fvl.cpp ../../module_gint/gint_rho.cpp
               ../../module_gint/gint_vl.cpp
               ../../module_hamilt_pw/hamilt_pwdft/charge.cpp
-              ../../src_pdiag/pdiag_common.cpp
               ../../module_io/output.cpp ../../module_hamilt_pw/hamilt_pwdft/soc.cpp ../../module_io/read_rho.cpp
   )
   if(USE_CUDA)

source/module_elecstate/test/elecstate_lcao_test.cpp

@@ -1,6 +1,6 @@
 #include "module_elecstate/elecstate_lcao.h"
 #include "src_parallel/parallel_reduce.h"
-#include "src_pdiag/test/diago_elpa_utils.h"
+#include "module_hsolver/test/diago_elpa_utils.h"
 #include "gtest/gtest.h"
 #include "mpi.h"
 

source/module_esolver/Makefile.Objects

@@ -51,7 +51,6 @@ VPATH=./src_global:\
 ./module_hamilt_general/module_vdw:\
 ./module_io:\
 ./src_parallel:\
-./src_pdiag:\
 ./src_ri:\
 ./module_ri:\
 ./\

source/module_esolver/esolver_ks_lcao.cpp

@@ -7,7 +7,7 @@
 #include "module_io/print_info.h"
 #include "module_hamilt_pw/hamilt_pwdft/global.h"
 #include "module_hamilt_lcao/hamilt_lcaodft/global_fp.h"
-#include "module_dftu/dftu.h"
+#include "module_hamilt_lcao/module_dftu/dftu.h"
 #include "module_elecstate/occupy.h"
 #include "module_elecstate/module_charge/symmetry_rho.h"
 #ifdef __EXX
@@ -16,7 +16,7 @@
 #endif
 
 #ifdef __DEEPKS
-#include "module_deepks/LCAO_deepks.h"
+#include "module_hamilt_lcao/module_deepks/LCAO_deepks.h"
 #endif
 //-----force& stress-------------------
 #include "module_hamilt_lcao/hamilt_lcaodft/FORCE_STRESS.h"