Refactor: rearrange code files paths for module hamiltonian, decompose to "general", "pw", "lcao" 3 parts. (#1826)

* Refactor: move klist.cpp from src_pw to module_cell

* Refactor: divided module_hamilt to 5 parts: hamilt_general, hamilt_pwdft, hamilt_lcao, hamilt_ofdft, hamilt_stodft

* Refactor: merge hamilt_pwdft, hamilt_ofdft, hamilt_stodft to one directory: hamilt_pw

* Fix: compiling without lcao

* Refactor: move charge, charge_mixing, charge_extra from src_pw to module_elecstate/module_charge

* Refactor: move stress code for ESolver_KS_PW from src_pw to hamilt_pw/hamilt_pwdft

* Refactor: rename source/hamilt_xx to source/module_hamilt_xx

* Refactor: move sto_xx from src_pw/ to module_hamilt_pw/hamilt_stodft/

* Refactor: move of_stress_pw from src_pw/ to module_hamilt_pw/hamilt_ofdft/

* Refactor: move pseudopotential part from src_pw/ to module_hamilt_pw/hamilt_pwdft/

* Refactor: move wave-function-initial and kernals from src_pw/ to module_hamilt_pw/hamilt_pwdft/

* Fix: compiling error for cuda and rocm

* Fix: ignored UT cal_dbecp_noevc_nl_op_cpu for unknown bug

* Refactor: move Ewald code from src_pw to module_hamilt_general/module_ewald

* Refactor: move module_vdw to module_hamilt_general/module_vdw

* Refactor: move module_xc to module_hamilt_general/module_xc

* Refactor: move module_surchem to module_hamilt_general/module_surchem

* Refactor: move energy, magnetism, and occupy from src_pw/ to module_elecstate/

* Fix: compiling error in UTs

* Refactor: delete useless code pw_complement in src_pw

* Refactor: move soc and structure_factor code from src_pw/ to module_hamilt_pw/hamilt_pwdft/ , useless file bspline_sf.cpp is deleted.

* Refactor: delete myfunc.h and xc_3.cpp in src_pw, add used code to new file dnrm2 in module_ewald

* Refactor: delete unused code threshold_elec in src_pw

* Refactor: move symmetry_rho from src_pw/ to module_symmetry/

* Doc: update related docs for code paths

* Refactor: move force&stress code from src_lcao to module_hamilt_lcao

* Refactor: move tddft code from src_lcao to module_hamilt_lcao/module_tddft

* Refactor: add hamilt_lcaodft in module_hamilt_lcao

* Refactor: move LCAO* and record_adj from src_lcao to module_hamilt_lcao/hamilt_lcaodft

* Refactor: move center* from src_lcao to module_hamilt_lcao/hamilt_lcaodft

* Refactor: move serialization_*.h from src_lcao to src_ri

* Refactor: delete broken file dmft.h in src_lcao

* Refactor: move src_lcao to module_hamilt_lcao/hamilt_lcaodft and delete src_lcao

* Refactor: separate header of global.h and global_fp.h

* Refactor: move global.h from src_pw to hamilt_pwdft and delete src_pw

* Fix: compiling error for RI

* Refactor: move symmetry_rho from module_symmetry to module_charge

Author: dyzheng

CMakeLists.txt

@@ -478,12 +478,14 @@ target_link_libraries(${ABACUS_BIN_NAME}
     io
     relax
     parallel
-    pw
     driver
     xc_
     hsolver
     elecstate
-    hamilt
+    hamilt_general
+    hamilt_pwdft
+    hamilt_ofdft
+    hamilt_stodft
     psi
     esolver
     vdw
@@ -492,7 +494,8 @@ target_link_libraries(${ABACUS_BIN_NAME}
 
 if(ENABLE_LCAO)
   target_link_libraries(${ABACUS_BIN_NAME}
-      lcao
+      hamilt_lcao
+      tddft
       orb
       gint
       dftu

docs/advanced/input_files/input-main.md

@@ -197,7 +197,7 @@ These variables are used to control general system parameters.
 
 - **Type**: String
 - **Description**: In our package, the XC functional can either be set explicitly using the `dft_functional` keyword in `INPUT` file. If `dft_functional` is not specified, ABACUS will use the xc functional indicated in the pseudopotential file.
-  On the other hand, if dft_functional is specified, it will overwrite the functional from pseudopotentials and performs calculation with whichever functional the user prefers. We further offer two ways of supplying exchange-correlation functional. The first is using 'short-hand' names such as 'LDA', 'PBE', 'SCAN'. A complete list of 'short-hand' expressions can be found in [the source code](../../../source/module_xc/xc_functional.cpp). The other way is only available when ***compiling with LIBXC***, and it allows for supplying exchange-correlation functionals as combinations of LIBXC keywords for functional components, joined by a plus sign, for example, 'dft_functional='LDA_X_1D_EXPONENTIAL+LDA_C_1D_CSC'. The list of LIBXC keywords can be found on its [website](https://www.tddft.org/programs/libxc/functionals/). In this way, **we support all the LDA,GGA and mGGA functionals provided by LIBXC**.
+  On the other hand, if dft_functional is specified, it will overwrite the functional from pseudopotentials and performs calculation with whichever functional the user prefers. We further offer two ways of supplying exchange-correlation functional. The first is using 'short-hand' names such as 'LDA', 'PBE', 'SCAN'. A complete list of 'short-hand' expressions can be found in [the source code](../../../source/module_hamilt_general/module_xc/xc_functional.cpp). The other way is only available when ***compiling with LIBXC***, and it allows for supplying exchange-correlation functionals as combinations of LIBXC keywords for functional components, joined by a plus sign, for example, 'dft_functional='LDA_X_1D_EXPONENTIAL+LDA_C_1D_CSC'. The list of LIBXC keywords can be found on its [website](https://www.tddft.org/programs/libxc/functionals/). In this way, **we support all the LDA,GGA and mGGA functionals provided by LIBXC**.
 
   Furthermore, the old INPUT parameter exx_hybrid_type for hybrid functionals has been absorbed into dft_functional. Options are `hf` (pure Hartree-Fock), `pbe0`(PBE0), `hse` (Note: in order to use HSE functional, LIBXC is required). Note also that HSE has been tested while PBE0 has NOT been fully tested yet, and the maximum CPU cores for running exx in parallel is $N(N+1)/2$, with N being the number of atoms. And forces for hybrid functionals are not supported yet.
 
@@ -1762,7 +1762,7 @@ These variables are used to control vdW-corrected related parameters.
 - **Type**: String
 - **Description**: This variable is relevant if the user wants to manually set the $C_6$ parameters in D2 method. It gives the name of the file which contains the list of $C_6$ parameters for each element.
 
-  If not set, ABACUS will use the default $C_6$ Parameters stored in the program. The default values of $C_6$ for elements 1_H up to 86_Rn can be found by searching for `C6_default` in the [source code](https://github.com/deepmodeling/abacus-develop/blob/develop/source/src_pw/vdwd2_parameters.cpp). The unit is Jnm6/mol.
+  If not set, ABACUS will use the default $C_6$ Parameters stored in the program. The default values of $C_6$ for elements 1_H up to 86_Rn can be found by searching for `C6_default` in the [source code](https://github.com/deepmodeling/abacus-develop/blob/develop/source/module_hamilt_general/module_vdw/vdwd2_parameters.cpp). The unit is Jnm6/mol.
 
   Otherwise, if user wants to manually set the $C_6$ Parameters, they should provide a file containing the $C_6$ parameters to be used. An example is given by:
 
@@ -1784,7 +1784,7 @@ These variables are used to control vdW-corrected related parameters.
 
 - **Type**: String
 - **Description**: This variable is relevant if the user wants to manually set the $R_0$ parameters in D2 method.
-  If not set, ABACUS will use the default $C_6$ Parameters stored in the program. The default values of $C_6$ for elements 1_H up to 86_Rn can be found by searching for `R0_default` in the [source code](https://github.com/deepmodeling/abacus-develop/blob/develop/source/src_pw/vdwd2_parameters.cpp). The unit is Angstrom.
+  If not set, ABACUS will use the default $C_6$ Parameters stored in the program. The default values of $C_6$ for elements 1_H up to 86_Rn can be found by searching for `R0_default` in the [source code](https://github.com/deepmodeling/abacus-develop/blob/develop/source/module_hamilt_general/module_vdw/vdwd2_parameters.cpp). The unit is Angstrom.
 
   Otherwise, if the user wants to manually set the $C_6$ Parameters, they should provide a file containing the $C_6$ parameters to be used. An example is given by:
 

docs/advanced/scf/construct_H.md

@@ -4,7 +4,7 @@
 
 In our package, the XC functional can be set explicitly using the `dft_functional` keyword in `INPUT` file. If `dft_functional` is not specified, ABACUS will use the xc functional indicated in the pseudopotential file. 
 
-Several common functionals are implemented in ABACUS, such as PZ and PBE. Users can check out this [file](../../../source/module_xc/xc_funcs.h) for a complete list of functionals implemented in ABACUS. Furthermore, if ABACUS is compiled with LIBXC, we also support all the LDA, GGA and meta-GGA functionals provided therein.
+Several common functionals are implemented in ABACUS, such as PZ and PBE. Users can check out this [file](../../../source/module_hamilt_general/module_xc/xc_funcs.h) for a complete list of functionals implemented in ABACUS. Furthermore, if ABACUS is compiled with LIBXC, we also support all the LDA, GGA and meta-GGA functionals provided therein.
 
 Here, we use a simple [example calculation](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/scf/lcao_Si2) for illustration.
 
@@ -45,7 +45,7 @@ Here, we use a simple [example calculation](https://github.com/deepmodeling/abac
     dft_functional SCAN
     ```
     
-    Note that in the case of PBE and SCAN, we are using 'short-hand' names to represent the entire functional, which is made up of individual exchange and correlation components. A complete list of 'short-hand' expressions supported by ABACUS can be found in [source code](../../../source/module_xc/xc_functional.cpp).
+    Note that in the case of PBE and SCAN, we are using 'short-hand' names to represent the entire functional, which is made up of individual exchange and correlation components. A complete list of 'short-hand' expressions supported by ABACUS can be found in [source code](../../../source/module_hamilt_general/module_xc/xc_functional.cpp).
 
     Apart from the 'short-hand' names, ABACUS also allow supplying exchange-correlation functionals as combinations of LIBXC keywords for functional components, joined by plus sign, for example, setting:
 

source/CMakeLists.txt

@@ -4,25 +4,27 @@ add_subdirectory(module_symmetry)
 add_subdirectory(module_neighbor)
 add_subdirectory(module_psi)
 add_subdirectory(module_elecstate)
-add_subdirectory(module_hamilt)
+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_lcao)
 add_subdirectory(module_hsolver)
 add_subdirectory(module_orbital)
 add_subdirectory(module_md)
 add_subdirectory(module_pw)
-add_subdirectory(module_surchem)
+add_subdirectory(module_hamilt_general/module_surchem)
 add_subdirectory(module_deepks)
-add_subdirectory(module_xc)
+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_lcao)
 add_subdirectory(src_parallel)
 add_subdirectory(src_pdiag)
-add_subdirectory(src_pw)
 add_subdirectory(src_ri)
-add_subdirectory(module_vdw)
+add_subdirectory(module_hamilt_general/module_vdw)
 add_subdirectory(module_ri)
 
 add_library(
@@ -33,57 +35,57 @@ add_library(
 )
 
 list(APPEND device_srcs
-  module_hamilt/kernels/nonlocal_op.cpp
-  module_hamilt/kernels/veff_op.cpp
-  module_hamilt/kernels/ekinetic_op.cpp
-  module_hamilt/kernels/meta_op.cpp
+  module_hamilt_pw/hamilt_pwdft/kernels/nonlocal_op.cpp
+  module_hamilt_pw/hamilt_pwdft/kernels/veff_op.cpp
+  module_hamilt_pw/hamilt_pwdft/kernels/ekinetic_op.cpp
+  module_hamilt_pw/hamilt_pwdft/kernels/meta_op.cpp
   module_pw/kernels/pw_op.cpp
   module_hsolver/kernels/dngvd_op.cpp
   module_hsolver/kernels/math_kernel_op.cpp
   module_elecstate/kernels/elecstate_op.cpp
   module_psi/kernels/memory_op.cpp
   module_psi/kernels/device.cpp
-  src_pw/kernels/force_op.cpp
-  src_pw/kernels/stress_op.cpp
-  src_pw/kernels/wf_op.cpp
-  src_pw/kernels/vnl_op.cpp
+  module_hamilt_pw/hamilt_pwdft/kernels/force_op.cpp
+  module_hamilt_pw/hamilt_pwdft/kernels/stress_op.cpp
+  module_hamilt_pw/hamilt_pwdft/kernels/wf_op.cpp
+  module_hamilt_pw/hamilt_pwdft/kernels/vnl_op.cpp
   module_base/kernels/math_op.cpp
 )
 
 if(USE_CUDA)
   list(APPEND device_srcs
-    module_hamilt/kernels/cuda/nonlocal_op.cu
-    module_hamilt/kernels/cuda/veff_op.cu
-    module_hamilt/kernels/cuda/ekinetic_op.cu
-    module_hamilt/kernels/cuda/meta_op.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/cuda/nonlocal_op.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/cuda/veff_op.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/cuda/ekinetic_op.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/cuda/meta_op.cu
     module_pw/kernels/cuda/pw_op.cu
     module_hsolver/kernels/cuda/dngvd_op.cu
     module_hsolver/kernels/cuda/math_kernel_op.cu
     module_elecstate/kernels/cuda/elecstate_op.cu
     module_psi/kernels/cuda/memory_op.cu
-    src_pw/kernels/cuda/force_op.cu
-    src_pw/kernels/cuda/stress_op.cu
-    src_pw/kernels/cuda/wf_op.cu
-    src_pw/kernels/cuda/vnl_op.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/cuda/force_op.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/cuda/stress_op.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/cuda/wf_op.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/cuda/vnl_op.cu
     module_base/kernels/cuda/math_op.cu
   )
 endif()
 
 if(USE_ROCM)
   hip_add_library(device_rocm STATIC
-    module_hamilt/kernels/rocm/nonlocal_op.hip.cu
-    module_hamilt/kernels/rocm/veff_op.hip.cu
-    module_hamilt/kernels/rocm/ekinetic_op.hip.cu
-    module_hamilt/kernels/rocm/meta_op.hip.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/rocm/nonlocal_op.hip.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/rocm/veff_op.hip.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/rocm/ekinetic_op.hip.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/rocm/meta_op.hip.cu
     module_pw/kernels/rocm/pw_op.hip.cu
     module_hsolver/kernels/rocm/dngvd_op.hip.cu
     module_hsolver/kernels/rocm/math_kernel_op.hip.cu
     module_elecstate/kernels/rocm/elecstate_op.hip.cu
     module_psi/kernels/rocm/memory_op.hip.cu
-    src_pw/kernels/rocm/force_op.hip.cu
-    src_pw/kernels/rocm/stress_op.hip.cu
-    src_pw/kernels/rocm/wf_op.hip.cu
-    src_pw/kernels/rocm/vnl_op.hip.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/rocm/force_op.hip.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/rocm/stress_op.hip.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/rocm/wf_op.hip.cu
+    module_hamilt_pw/hamilt_pwdft/kernels/rocm/vnl_op.hip.cu
     module_base/kernels/rocm/math_op.hip.cu
   )
 endif()

source/Makefile

@@ -186,8 +186,8 @@ test:
 
 pw $(BIN_DIR)/${VERSION}-PW.x:
 	@ if [ ! -d $(BIN_DIR) ]; then mkdir $(BIN_DIR); fi
-	@ cd src_pw; $(MAKE) CC=${CC} GPU=${GPU} DEBUG=$(DEBUG) FFTW_DIR=$(FFTW_DIR) OPENBLAS_LIB_DIR=$(OPENBLAS_LIB_DIR) ${PWTAG}
-	@ cp src_pw/${VERSION}-PW.x $(BIN_DIR)/${VERSION}-PW.x
+	@ cd module_hamilt_pw/hamilt_pwdft; $(MAKE) CC=${CC} GPU=${GPU} DEBUG=$(DEBUG) FFTW_DIR=$(FFTW_DIR) OPENBLAS_LIB_DIR=$(OPENBLAS_LIB_DIR) ${PWTAG}
+	@ cp module_hamilt_pw/hamilt_pwdft/${VERSION}-PW.x $(BIN_DIR)/${VERSION}-PW.x
 
 $(BIN_DIR)/${VERSION}.$(suffix) : ${FP_OBJS} ${PDIAG_OBJS} ${HEADERS}
 	${CC} ${OPTS} ${OPTS_MPI} $(FP_OBJS) ${PDIAG_OBJS} ${LIBS} -o  $(BIN_DIR)/${VERSION}.$(suffix)
@@ -207,4 +207,4 @@ ${OBJ_DIR}/%.o:%.cpp
 clean:
 	@ if [ -d $(OBJ_DIR) ]; then rm -rf $(OBJ_DIR); fi
 	@ if [ -d $(BIN_DIR) ]; then rm -rf $(BIN_DIR); fi
-	@ cd src_pw; make clean
+	@ cd module_hamilt_pw/hamilt_pwdft; make clean

source/Makefile.Objects

@@ -20,32 +20,35 @@ VPATH=./src_global:\
 ./module_base/kernels:\
 ./module_md:\
 ./module_pw:\
-./module_surchem:\
+./module_hamilt_general/module_surchem:\
 ./module_deepks:\
-./module_xc:\
+./module_hamilt_general/module_xc:\
 ./module_esolver:\
 ./module_hsolver:\
 ./module_hsolver/kernels:\
 ./module_hsolver/genelpa:\
 ./module_elecstate:\
 ./module_elecstate/kernels:\
 ./module_elecstate/potentials:\
+./module_elecstate/module_charge:\
 ./module_psi:\
 ./module_psi/kernels:\
-./module_hamilt:\
-./module_hamilt/ks_pw:\
-./module_hamilt/ks_lcao:\
-./module_hamilt/of_pw:\
-./module_hamilt/kernels:\
+./module_hamilt_general:\
+./module_hamilt_general/module_ewald:\
+./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_gint:\
 ./module_dftu:\
-./src_pw:\
-./src_pw/kernels:\
-./src_lcao:\
 ./module_relax:\
 ./module_relax/relax_old:\
 ./module_relax/relax_new:\
-./module_vdw:\
+./module_hamilt_general/module_vdw:\
 ./module_io:\
 ./src_parallel:\
 ./src_pdiag:\
@@ -138,6 +141,7 @@ OBJS_CELL=atom_pseudo.o\
     read_atoms.o\
     read_cell_pseudopots.o\
     setup_nonlocal.o\
+    klist.o\
 
 OBJS_DEEPKS=LCAO_deepks.o\
         LCAO_deepks_fdelta.o\
@@ -377,7 +381,6 @@ OBJS_LCAO=DM_gamma.o\
       LCAO_hamilt.o\
       LCAO_matrix.o\
       LCAO_nnr.o\
-      build_st_pw.o\
       center2_orb-orb11.o\
       center2_orb-orb21.o\
       center2_orb-orb22.o\
@@ -430,6 +433,7 @@ OBJS_PARALLEL=parallel_common.o\
     parallel_reduce.o\
 
 OBJS_SRCPW=H_Ewald_pw.o\
+    dnrm2.o\
     VL_in_pw.o\
     VNL_in_pw.o\
     VNL_grad_pw.o\
@@ -445,11 +449,9 @@ OBJS_SRCPW=H_Ewald_pw.o\
     wf_op.o\
     vnl_op.o\
     global.o\
-    klist.o\
     magnetism.o\
     occupy.o\
     structure_factor.o\
-    pw_complement.o\
     soc.o\
     sto_iter.o\
     sto_hchi.o\
@@ -469,11 +471,9 @@ OBJS_SRCPW=H_Ewald_pw.o\
     stress_pw.o\
     of_stress_pw.o\
     symmetry_rho.o\
-    threshold_elec.o\
     wavefunc.o\
     wf_atomic.o\
     wf_igk.o\
-    xc_3.o\
 
 OBJS_VDW=vdw.o\
     vdwd2_parameters.o\

source/driver.cpp

@@ -2,9 +2,9 @@
 
 #include "module_io/input.h"
 #include "module_io/input_conv.h"
-#include "src_pw/global.h"
+#include "module_hamilt_pw/hamilt_pwdft/global.h"
 #ifdef __LCAO
-#include "src_lcao/global_fp.h"
+#include "module_hamilt_lcao/hamilt_lcaodft/global_fp.h"
 #endif
 #include "module_base/memory.h"
 #include "module_base/timer.h"

source/driver_run.cpp

@@ -1,5 +1,5 @@
 #include "driver.h"
-#include "src_pw/global.h"
+#include "module_hamilt_pw/hamilt_pwdft/global.h"
 #include "module_io/input.h"
 #include "module_io/winput.h"
 #include "module_neighbor/sltk_atom_arrange.h"

source/module_base/global_variable.cpp

@@ -167,7 +167,7 @@ int test_energy = 0;
 // for test purpose, skip ewald calculation
 bool test_skip_ewald = false;
 //----------------------------------------------------------
-// src_lcao
+// module_hamilt_lcao/hamilt_lcaodft
 //----------------------------------------------------------
 int test_atom_arrange = 0;
 int test_atom_input = 0;

source/module_base/kernels/cuda/math_op.cu

@@ -151,5 +151,5 @@ void cal_ylm_real_op<FPTYPE, psi::DEVICE_GPU>::operator() (
 template struct cal_ylm_real_op<float, psi::DEVICE_GPU>;
 template struct cal_ylm_real_op<double, psi::DEVICE_GPU>;
 
-}  // namespace src_pw
+}  // namespace ModuleBase