[Refactor] Rename module_elecstate and module_psi and module_hamilt_pw (#6334)

* Rename module_elecstate to source_estate

* Rename module_psi to source_psi

* Rename module_hamilt_pw to source_pw

* Rename module_hamilt_general to source_hamilt

Author: Critsium-xy

.github/workflows/test.yml

@@ -91,12 +91,12 @@ jobs:
         run: |
           cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_MD"
       
-      - name: Module_Psi Unittests
+      - name: source_psi Unittests
         env:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
-          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_PSI"
+          cmake --build build --target test ARGS="-V --timeout 1700 -R source_psi"
       
       - name: Module_RI Unittests
         env:
@@ -180,4 +180,4 @@ jobs:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
-          cmake --build build --target test ARGS="-V --timeout 1700 -E 'integrate_test|01_PW|02_NAO_Gamma|03_NAO_multik|04_LJ_DP|05_rtTDDFT|06_SDFT|07_OFDFT|08_EXX|09_DeePKS|10_others|11_PW_GPU|12_NAO_Gamma_GPU|13_NAO_multik_GPU|15_rtTDDFT_GPU|16_SDFT_GPU|MODULE_BASE|MODULE_IO|MODULE_HSOLVER|MODULE_CELL|MODULE_MD|MODULE_PSI|MODULE_RI'"
+          cmake --build build --target test ARGS="-V --timeout 1700 -E 'integrate_test|01_PW|02_NAO_Gamma|03_NAO_multik|04_LJ_DP|05_rtTDDFT|06_SDFT|07_OFDFT|08_EXX|09_DeePKS|10_others|11_PW_GPU|12_NAO_Gamma_GPU|13_NAO_multik_GPU|15_rtTDDFT_GPU|16_SDFT_GPU|MODULE_BASE|MODULE_IO|MODULE_HSOLVER|MODULE_CELL|MODULE_MD|source_psi|MODULE_RI'"

docs/CONTRIBUTING.md

@@ -54,12 +54,12 @@ For those who are interested in the source code, the following figure shows the
 |   |-- module_neighbor         The module for finding the neighbors of each atom in the unit cell.
 |   |-- module_paw              The module for performing PAW calculations.
 |   |-- module_symmetry         The module for finding the symmetry operations of the unit cell.
-|-- module_elecstate            The module for defining the electronic state and its operations.
+|-- source_estate            The module for defining the electronic state and its operations.
 |   |-- module_charge           The module for calculating the charge density, charge mixing
 |   |-- potentials              The module for calculating the potentials, including Hartree, exchange-correlation, local pseudopotential, etc.
 |-- source_esolver              The module defining task-specific driver of corresponding workflow for evaluating energies, forces, etc., including lj, dp, ks, sdft, ofdft, etc.
 |   |                           TDDFT, Orbital-free DFT, etc.
-|-- module_hamilt_general       The module for defining general Hamiltonian that can be used both in PW and LCAO calculations.
+|-- source_hamilt       The module for defining general Hamiltonian that can be used both in PW and LCAO calculations.
 |   |-- module_ewald            The module for calculating the Ewald summation.
 |   |-- module_surchem          The module for calculating the surface charge correction.
 |   |-- module_vdw              The module for calculating the van der Waals correction.
@@ -72,7 +72,7 @@ For those who are interested in the source code, the following figure shows the
 |   |-- module_gint             The module for performing grid integral in LCAO calculations.
 |   |-- module_hcontainer       The module for storing the Hamiltonian matrix in LCAO calculations.
 |   `-- module_tddft            The module for defining the Hamiltonian in TDDFT calculations.
-|-- module_hamilt_pw            The module for defining the Hamiltonian in PW calculations.
+|-- source_pw            The module for defining the Hamiltonian in PW calculations.
 |   |-- hamilt_ofdft            The module for defining the Hamiltonian in OFDFT calculations.
 |   |-- hamilt_pwdft            The module for defining the Hamiltonian in PW-DFT calculations.
 |   |   |-- operator_pw         The module for defining the operators in PW-DFT calculations.
@@ -81,7 +81,7 @@ For those who are interested in the source code, the following figure shows the
 |   |                           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.
-|-- module_psi                  The module for defining the wave function and its operations.
+|-- source_psi                  The module for defining the wave function and its operations.
 |-- module_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.

docs/advanced/input_files/input-main.md

@@ -1048,7 +1048,7 @@ calculations.
 
 - **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_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://libxc.gitlab.io/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/source_hamilt/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://libxc.gitlab.io/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.
 
@@ -3474,7 +3474,7 @@ These variables are used to control vdW-corrected related parameters.
 
 - **Type**: String
 - **Availability**: `vdw_method` is set to `d2`
-- **Description**: Specifies the name of the file containing $C_6$ parameters for each element when using the D2 method. If not set, ABACUS uses the default $C_6$ parameters (Jnm6/mol) stored in the [program](https://github.com/deepmodeling/abacus-develop/blob/develop/source/module_hamilt_general/module_vdw/vdwd2_parameters.cpp). To manually set the $C_6$ parameters, provide a file containing the parameters. An example is given by:
+- **Description**: Specifies the name of the file containing $C_6$ parameters for each element when using the D2 method. If not set, ABACUS uses the default $C_6$ parameters (Jnm6/mol) stored in the [program](https://github.com/deepmodeling/abacus-develop/blob/develop/source/source_hamilt/module_vdw/vdwd2_parameters.cpp). To manually set the $C_6$ parameters, provide a file containing the parameters. An example is given by:
 
   ```text
   H  0.1
@@ -3497,7 +3497,7 @@ These variables are used to control vdW-corrected related parameters.
 
 - **Type**: String
 - **Availability**: `vdw_method` is set to `d2`
-- **Description**: Specifies the name of the file containing $R_0$ parameters for each element when using the D2 method. If not set, ABACUS uses the default $R_0$ parameters (Angstrom) stored in the [program](https://github.com/deepmodeling/abacus-develop/blob/develop/source/module_hamilt_general/module_vdw/vdwd2_parameters.cpp). To manually set the $R_0$ parameters, provide a file containing the parameters. An example is given by:
+- **Description**: Specifies the name of the file containing $R_0$ parameters for each element when using the D2 method. If not set, ABACUS uses the default $R_0$ parameters (Angstrom) stored in the [program](https://github.com/deepmodeling/abacus-develop/blob/develop/source/source_hamilt/module_vdw/vdwd2_parameters.cpp). To manually set the $R_0$ parameters, provide a file containing the parameters. An example is given by:
 
   ```text
   Li 1.0

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_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.
+Several common functionals are implemented in ABACUS, such as PZ and PBE. Users can check out this [file](../../../source/source_hamilt/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_hamilt_general/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/source_hamilt/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:
 

python/pyabacus/CMakeLists.txt

@@ -15,7 +15,7 @@ set(ABACUS_SOURCE_DIR "${PROJECT_SOURCE_DIR}/../../source")
 set(BASE_PATH "${ABACUS_SOURCE_DIR}/source_base")
 set(NAO_PATH "${ABACUS_SOURCE_DIR}/source_basis/module_nao")
 set(HSOLVER_PATH "${ABACUS_SOURCE_DIR}/source_hsolver")
-set(PSI_PATH "${ABACUS_SOURCE_DIR}/module_psi")
+set(PSI_PATH "${ABACUS_SOURCE_DIR}/source_psi")
 set(ENABLE_LCAO ON)
 list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/../../cmake")
 

python/pyabacus/CONTRIBUTING.md

@@ -75,7 +75,7 @@ set(ABACUS_SOURCE_DIR "${PROJECT_SOURCE_DIR}/../../source")
 set(BASE_PATH "${ABACUS_SOURCE_DIR}/source_base")
 set(NAO_PATH "${ABACUS_SOURCE_DIR}/source_basis/module_nao")
 set(HSOLVER_PATH "${ABACUS_SOURCE_DIR}/source_hsolver")
-set(PSI_PATH "${ABACUS_SOURCE_DIR}/module_psi")
+set(PSI_PATH "${ABACUS_SOURCE_DIR}/source_psi")
 set(ENABLE_LCAO ON)
 list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/../../cmake")
 ```

python/pyabacus/src/ModuleNAO/CMakeLists.txt

@@ -16,7 +16,7 @@ list(APPEND _naos
     ${ABACUS_SOURCE_DIR}/source_base/kernels/math_ylm_op.cpp
     ${ABACUS_SOURCE_DIR}/source_base/kernels/math_kernel_op.cpp
     ${ABACUS_SOURCE_DIR}/source_base/kernels/math_kernel_op_vec.cpp
-    # ${ABACUS_SOURCE_DIR}/module_psi/kernels/psi_memory_op.cpp
+    # ${ABACUS_SOURCE_DIR}/source_psi/kernels/psi_memory_op.cpp
     ${ABACUS_SOURCE_DIR}/source_base/module_device/memory_op.cpp
     ${ABACUS_SOURCE_DIR}/source_base/module_device/device.cpp
 )

source/CMakeLists.txt

@@ -1,9 +1,9 @@
 add_subdirectory(source_base)
 add_subdirectory(source_cell)
-add_subdirectory(module_psi)
-add_subdirectory(module_elecstate)
-add_subdirectory(module_hamilt_general)
-add_subdirectory(module_hamilt_pw)
+add_subdirectory(source_psi)
+add_subdirectory(source_estate)
+add_subdirectory(source_hamilt)
+add_subdirectory(source_pw)
 add_subdirectory(module_hamilt_lcao)
 add_subdirectory(source_hsolver)
 add_subdirectory(source_basis/module_ao)
@@ -29,84 +29,84 @@ add_library(
 )
 
 list(APPEND device_srcs
-  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_hamilt_pw/hamilt_stodft/kernels/hpsi_norm_op.cpp
+  source_pw/hamilt_pwdft/kernels/nonlocal_op.cpp
+  source_pw/hamilt_pwdft/kernels/veff_op.cpp
+  source_pw/hamilt_pwdft/kernels/ekinetic_op.cpp
+  source_pw/hamilt_pwdft/kernels/meta_op.cpp
+  source_pw/hamilt_stodft/kernels/hpsi_norm_op.cpp
   source_basis/module_pw/kernels/pw_op.cpp
   source_hsolver/kernels/dngvd_op.cpp
   source_hsolver/kernels/bpcg_kernel_op.cpp
-  module_elecstate/kernels/elecstate_op.cpp
+  source_estate/kernels/elecstate_op.cpp
 
-  # module_psi/kernels/psi_memory_op.cpp
-  # module_psi/kernels/device.cpp
+  # source_psi/kernels/psi_memory_op.cpp
+  # source_psi/kernels/device.cpp
 
   source_base/module_device/device.cpp
   source_base/module_device/memory_op.cpp
   source_base/kernels/math_kernel_op.cpp
   source_base/kernels/math_kernel_op_vec.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/onsite_op.cpp
-  module_hamilt_pw/hamilt_pwdft/kernels/wf_op.cpp
-  module_hamilt_pw/hamilt_pwdft/kernels/vnl_op.cpp
+  source_pw/hamilt_pwdft/kernels/force_op.cpp
+  source_pw/hamilt_pwdft/kernels/stress_op.cpp
+  source_pw/hamilt_pwdft/kernels/onsite_op.cpp
+  source_pw/hamilt_pwdft/kernels/wf_op.cpp
+  source_pw/hamilt_pwdft/kernels/vnl_op.cpp
   source_base/kernels/math_ylm_op.cpp
-  module_hamilt_general/module_xc/kernels/xc_functional_op.cpp
+  source_hamilt/module_xc/kernels/xc_functional_op.cpp
 )
 
 if(USE_CUDA)
   list(APPEND device_srcs
-    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_hamilt_pw/hamilt_stodft/kernels/cuda/hpsi_norm_op.cu
-    module_hamilt_pw/hamilt_pwdft/kernels/cuda/onsite_op.cu
+    source_pw/hamilt_pwdft/kernels/cuda/nonlocal_op.cu
+    source_pw/hamilt_pwdft/kernels/cuda/veff_op.cu
+    source_pw/hamilt_pwdft/kernels/cuda/ekinetic_op.cu
+    source_pw/hamilt_pwdft/kernels/cuda/meta_op.cu
+    source_pw/hamilt_stodft/kernels/cuda/hpsi_norm_op.cu
+    source_pw/hamilt_pwdft/kernels/cuda/onsite_op.cu
     source_basis/module_pw/kernels/cuda/pw_op.cu
     source_hsolver/kernels/cuda/dngvd_op.cu
     source_hsolver/kernels/cuda/bpcg_kernel_op.cu
-    module_elecstate/kernels/cuda/elecstate_op.cu
+    source_estate/kernels/cuda/elecstate_op.cu
 
-    # module_psi/kernels/cuda/memory_op.cu
+    # source_psi/kernels/cuda/memory_op.cu
     source_base/module_device/cuda/memory_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
+    source_pw/hamilt_pwdft/kernels/cuda/force_op.cu
+    source_pw/hamilt_pwdft/kernels/cuda/stress_op.cu
+    source_pw/hamilt_pwdft/kernels/cuda/wf_op.cu
+    source_pw/hamilt_pwdft/kernels/cuda/vnl_op.cu
     source_base/kernels/cuda/math_ylm_op.cu
     source_base/kernels/cuda/math_kernel_op.cu
     source_base/kernels/cuda/math_kernel_op_vec.cu
-    module_hamilt_general/module_xc/kernels/cuda/xc_functional_op.cu
+    source_hamilt/module_xc/kernels/cuda/xc_functional_op.cu
   )
 endif()
 
 if(USE_ROCM)
   hip_add_library(device_rocm STATIC
-    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_hamilt_pw/hamilt_pwdft/kernels/rocm/onsite_op.hip.cu
-    module_hamilt_pw/hamilt_stodft/kernels/rocm/hpsi_norm_op.hip.cu
+    source_pw/hamilt_pwdft/kernels/rocm/nonlocal_op.hip.cu
+    source_pw/hamilt_pwdft/kernels/rocm/veff_op.hip.cu
+    source_pw/hamilt_pwdft/kernels/rocm/ekinetic_op.hip.cu
+    source_pw/hamilt_pwdft/kernels/rocm/meta_op.hip.cu
+    source_pw/hamilt_pwdft/kernels/rocm/onsite_op.hip.cu
+    source_pw/hamilt_stodft/kernels/rocm/hpsi_norm_op.hip.cu
     source_basis/module_pw/kernels/rocm/pw_op.hip.cu
     source_hsolver/kernels/rocm/dngvd_op.hip.cu
     source_hsolver/kernels/rocm/bpcg_kernel_op.hip.cu
-    module_elecstate/kernels/rocm/elecstate_op.hip.cu
+    source_estate/kernels/rocm/elecstate_op.hip.cu
 
-    # module_psi/kernels/rocm/memory_op.hip.cu
+    # source_psi/kernels/rocm/memory_op.hip.cu
     source_base/module_device/rocm/memory_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
+    source_pw/hamilt_pwdft/kernels/rocm/force_op.hip.cu
+    source_pw/hamilt_pwdft/kernels/rocm/stress_op.hip.cu
+    source_pw/hamilt_pwdft/kernels/rocm/wf_op.hip.cu
+    source_pw/hamilt_pwdft/kernels/rocm/vnl_op.hip.cu
     source_base/kernels/rocm/math_kernel_op.hip.cu
     source_base/kernels/rocm/math_kernel_op_vec.hip.cu
     source_base/kernels/rocm/math_ylm_op.hip.cu
-    module_hamilt_general/module_xc/kernels/rocm/xc_functional_op.hip.cu
+    source_hamilt/module_xc/kernels/rocm/xc_functional_op.hip.cu
   )
 endif()
 

source/Makefile

@@ -222,8 +222,8 @@ test:
 
 pw $(BIN_DIR)/${VERSION}-PW.x:
 	@ if [ ! -d $(BIN_DIR) ]; then mkdir $(BIN_DIR); fi
-	@ cd module_hamilt_pw/hamilt_pwdft; $(MAKE) CXX=${CXX} 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
+	@ cd source_pw/hamilt_pwdft; $(MAKE) CXX=${CXX} GPU=${GPU} DEBUG=$(DEBUG) FFTW_DIR=$(FFTW_DIR) OPENBLAS_LIB_DIR=$(OPENBLAS_LIB_DIR) ${PWTAG}
+	@ cp source_pw/hamilt_pwdft/${VERSION}-PW.x $(BIN_DIR)/${VERSION}-PW.x
 
 $(BIN_DIR)/${VERSION}.$(suffix) : ${FP_OBJS} ${PDIAG_OBJS} ${HEADERS}
 	${CXX} ${OPTS} ${OPTS_MPI} $(FP_OBJS) ${PDIAG_OBJS} ${LIBS} -o  $(BIN_DIR)/${VERSION}.$(suffix)
@@ -239,4 +239,4 @@ ${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 module_hamilt_pw/hamilt_pwdft; make clean
+	@ cd source_pw/hamilt_pwdft; make clean