[Refactor] Rename module_base to source_base

CMakeLists.txt

@@ -167,7 +167,7 @@ set(ABACUS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/source)
 set(ABACUS_TEST_DIR ${CMAKE_CURRENT_SOURCE_DIR}/tests)
 set(ABACUS_BIN_PATH ${CMAKE_CURRENT_BINARY_DIR}/${ABACUS_BIN_NAME})
 include_directories(${ABACUS_SOURCE_DIR})
-include_directories(${ABACUS_SOURCE_DIR}/module_base/module_container)
+include_directories(${ABACUS_SOURCE_DIR}/source_base/module_container)
 
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)

docs/CONTRIBUTING.md

@@ -39,7 +39,7 @@ The source code of ABACUS is based on several modules. Under the ABACUS root dir
 For those who are interested in the source code, the following figure shows the structure of the source code.
 
 ```text
-|-- module_base                 A basic module including
+|-- source_base                 A basic module including
 |   |                           (1) Mathematical library interface functions: BLAS, LAPACK, Scalapack;
 |   |                           (2) Custom data classes: matrix, vector definitions and related functions;
 |   |                           (3) Parallelization functions: MPI, OpenMP;
@@ -183,7 +183,7 @@ pre-commit install
 
 ## Adding a unit test
 
-We use [GoogleTest](https://github.com/google/googletest) as our test framework. Write your test under the corresponding module folder at `abacus-develop/tests`, then append the test to `tests/CMakeLists.txt`. If there are currently no unit tests provided for the module, do as follows. `module_base` provides a simple demonstration.
+We use [GoogleTest](https://github.com/google/googletest) as our test framework. Write your test under the corresponding module folder at `abacus-develop/tests`, then append the test to `tests/CMakeLists.txt`. If there are currently no unit tests provided for the module, do as follows. `source_base` provides a simple demonstration.
 
 - Add a folder named `test` under the module.
 - Append the content below to `CMakeLists.txt` of the module:

python/pyabacus/CMakeLists.txt

@@ -12,7 +12,7 @@ find_package(pybind11 CONFIG REQUIRED)
 
 # set source path
 set(ABACUS_SOURCE_DIR "${PROJECT_SOURCE_DIR}/../../source")
-set(BASE_PATH "${ABACUS_SOURCE_DIR}/module_base")
+set(BASE_PATH "${ABACUS_SOURCE_DIR}/source_base")
 set(NAO_PATH "${ABACUS_SOURCE_DIR}/module_basis/module_nao")
 set(HSOLVER_PATH "${ABACUS_SOURCE_DIR}/source_hsolver")
 set(PSI_PATH "${ABACUS_SOURCE_DIR}/module_psi")
@@ -69,14 +69,14 @@ endif()
 include_directories(
     ${BASE_PATH} 
     ${ABACUS_SOURCE_DIR}
-    ${ABACUS_SOURCE_DIR}/module_base/module_container
+    ${ABACUS_SOURCE_DIR}/source_base/module_container
     )
 
 # add basic libraries
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 # add base
 set(BASE_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/base")
-add_subdirectory(${ABACUS_SOURCE_DIR}/module_base ${BASE_BINARY_DIR})
+add_subdirectory(${ABACUS_SOURCE_DIR}/source_base ${BASE_BINARY_DIR})
 # add parameter
 set(PARAMETER_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/parameter")
 add_subdirectory(${ABACUS_SOURCE_DIR}/module_parameter ${PARAMETER_BINARY_DIR})

python/pyabacus/CONTRIBUTING.md

@@ -72,7 +72,7 @@ find_package(pybind11 CONFIG REQUIRED)
 ```cmake
 # Set source path
 set(ABACUS_SOURCE_DIR "${PROJECT_SOURCE_DIR}/../../source")
-set(BASE_PATH "${ABACUS_SOURCE_DIR}/module_base")
+set(BASE_PATH "${ABACUS_SOURCE_DIR}/source_base")
 set(NAO_PATH "${ABACUS_SOURCE_DIR}/module_basis/module_nao")
 set(HSOLVER_PATH "${ABACUS_SOURCE_DIR}/source_hsolver")
 set(PSI_PATH "${ABACUS_SOURCE_DIR}/module_psi")
@@ -131,7 +131,7 @@ endif()
 include_directories(
     ${BASE_PATH} 
     ${ABACUS_SOURCE_DIR}
-    ${ABACUS_SOURCE_DIR}/module_base/module_container
+    ${ABACUS_SOURCE_DIR}/source_base/module_container
     )
 ```
 - This section adds the necessary include directories for the project.
@@ -141,7 +141,7 @@ include_directories(
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 # Add base
 set(BASE_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/base")
-add_subdirectory(${ABACUS_SOURCE_DIR}/module_base ${BASE_BINARY_DIR})
+add_subdirectory(${ABACUS_SOURCE_DIR}/source_base ${BASE_BINARY_DIR})
 # Add parameter
 set(PARAMETER_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/parameter")
 add_subdirectory(${ABACUS_SOURCE_DIR}/module_parameter ${PARAMETER_BINARY_DIR})

python/pyabacus/examples/indexmap.py

@@ -60,7 +60,7 @@ def _index_map(ntype, natom, lmax, nzeta=None):
 
                                   0, 1, -1, 2, -2, 3, -3, ..., l, -l
 
-                    (see module_base/ylm.cpp and module_base/math_ylmreal.cpp
+                    (see source_base/ylm.cpp and source_base/math_ylmreal.cpp
                     for details)
 
                     '''

python/pyabacus/src/ModuleBase/CMakeLists.txt

@@ -1,4 +1,4 @@
-list(APPEND pymodule_base
+list(APPEND pysource_base
     ${PROJECT_SOURCE_DIR}/src/ModuleBase/py_base_math.cpp
     ${BASE_PATH}/kernels/math_ylm_op.cpp
     ${BASE_PATH}/kernels/math_kernel_op.cpp
@@ -7,7 +7,7 @@ list(APPEND pymodule_base
     ${BASE_PATH}/module_device/device.cpp
     )
 
-pybind11_add_module(_base_pack MODULE ${pymodule_base})
+pybind11_add_module(_base_pack MODULE ${pysource_base})
 
 target_link_libraries(_base_pack
     PRIVATE

python/pyabacus/src/ModuleBase/py_base_math.cpp

@@ -1,9 +1,9 @@
 #include <pybind11/numpy.h>
 #include <pybind11/pybind11.h>
 
-#include "module_base/math_sphbes.h"
-#include "module_base/math_integral.h"
-#include "module_base/spherical_bessel_transformer.h"
+#include "source_base/math_sphbes.h"
+#include "source_base/math_integral.h"
+#include "source_base/spherical_bessel_transformer.h"
 
 namespace py = pybind11;
 using namespace pybind11::literals;

python/pyabacus/src/ModuleNAO/CMakeLists.txt

@@ -13,12 +13,12 @@ list(APPEND _naos
     ${NAO_PATH}/two_center_integrator.cpp
     ${NAO_PATH}/two_center_table.cpp
     # dependency
-    ${ABACUS_SOURCE_DIR}/module_base/kernels/math_ylm_op.cpp
-    ${ABACUS_SOURCE_DIR}/module_base/kernels/math_kernel_op.cpp
-    ${ABACUS_SOURCE_DIR}/module_base/kernels/math_kernel_op_vec.cpp
+    ${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}/module_base/module_device/memory_op.cpp
-    ${ABACUS_SOURCE_DIR}/module_base/module_device/device.cpp
+    ${ABACUS_SOURCE_DIR}/source_base/module_device/memory_op.cpp
+    ${ABACUS_SOURCE_DIR}/source_base/module_device/device.cpp
 )
 add_library(naopack SHARED 
     ${_naos}

python/pyabacus/src/ModuleNAO/py_m_nao.cpp

@@ -2,7 +2,7 @@
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
-#include "module_base/vector3.h"
+#include "source_base/vector3.h"
 #include "module_basis/module_nao/radial_collection.h"
 #include "module_basis/module_nao/two_center_integrator.h"
 

python/pyabacus/src/hsolver/py_diago_cg.hpp

@@ -15,7 +15,7 @@
 #include <ATen/core/tensor_types.h>
 
 #include "source_hsolver/diago_cg.h"
-#include "module_base/module_device/memory_op.h"
+#include "source_base/module_device/memory_op.h"
 
 namespace py = pybind11;
 

python/pyabacus/src/hsolver/py_hsolver.cpp

@@ -6,8 +6,8 @@
 #include <pybind11/numpy.h>
 
 #include "source_hsolver/diago_dav_subspace.h"
-#include "module_base/kernels/math_kernel_op.h"
-#include "module_base/module_device/types.h"
+#include "source_base/kernels/math_kernel_op.h"
+#include "source_base/module_device/types.h"
 
 #include "./py_diago_dav_subspace.hpp"
 #include "./py_diago_david.hpp"

source/CMakeLists.txt

@@ -1,4 +1,4 @@
-add_subdirectory(module_base)
+add_subdirectory(source_base)
 add_subdirectory(module_cell)
 add_subdirectory(module_psi)
 add_subdirectory(module_elecstate)
@@ -42,17 +42,17 @@ list(APPEND device_srcs
   # module_psi/kernels/psi_memory_op.cpp
   # module_psi/kernels/device.cpp
 
-  module_base/module_device/device.cpp
-  module_base/module_device/memory_op.cpp
-  module_base/kernels/math_kernel_op.cpp
-  module_base/kernels/math_kernel_op_vec.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
-  module_base/kernels/math_ylm_op.cpp
+  source_base/kernels/math_ylm_op.cpp
   module_hamilt_general/module_xc/kernels/xc_functional_op.cpp
 )
 
@@ -70,15 +70,15 @@ if(USE_CUDA)
     module_elecstate/kernels/cuda/elecstate_op.cu
 
     # module_psi/kernels/cuda/memory_op.cu
-    module_base/module_device/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
-    module_base/kernels/cuda/math_ylm_op.cu
-    module_base/kernels/cuda/math_kernel_op.cu
-    module_base/kernels/cuda/math_kernel_op_vec.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
   )
 endif()
@@ -97,22 +97,22 @@ if(USE_ROCM)
     module_elecstate/kernels/rocm/elecstate_op.hip.cu
 
     # module_psi/kernels/rocm/memory_op.hip.cu
-    module_base/module_device/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
-    module_base/kernels/rocm/math_kernel_op.hip.cu
-    module_base/kernels/rocm/math_kernel_op_vec.hip.cu
-    module_base/kernels/rocm/math_ylm_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
   )
 endif()
 
 if(USE_DSP)
   list(APPEND device_srcs
-  module_base/kernels/dsp/dsp_connector.cpp
+  source_base/kernels/dsp/dsp_connector.cpp
   )
 endif()
 

source/Makefile

@@ -4,7 +4,7 @@ include Makefile.vars
 # Compiler information 
 #==========================
 
-INCLUDES = -I. -Isource_main -Isource_main/commands -Icommands -I../ -Imodule_base/module_container
+INCLUDES = -I. -Isource_main -Isource_main/commands -Icommands -I../ -Isource_base/module_container
 
 LIBS = -lm -lpthread
 OPTS = -std=c++14 -pedantic -m64 ${INCLUDES}

source/Makefile.Objects

@@ -18,14 +18,14 @@ VPATH=./src_global:\
 ./module_cell/module_neighbor:\
 ./module_cell/module_symmetry:\
 ./module_cell:\
-./module_base:\
-./module_base/kernels:\
-./module_base/module_container/base/core:\
-./module_base/module_container/ATen/core:\
-./module_base/module_container/ATen/kernels:\
-./module_base/module_container/ATen/ops:\
-./module_base/module_device:\
-./module_base/module_mixing:\
+./source_base:\
+./source_base/kernels:\
+./source_base/module_container/base/core:\
+./source_base/module_container/ATen/core:\
+./source_base/module_container/ATen/kernels:\
+./source_base/module_container/ATen/ops:\
+./source_base/module_device:\
+./source_base/module_mixing:\
 ./module_md:\
 ./module_basis/module_pw:\
 ./module_basis/module_pw/module_fft:\

source/module_basis/module_ao/ORB_atomic.h

@@ -3,8 +3,8 @@
 
 #include <string>
 
-#include "module_base/intarray.h"
-#include "module_base/vector3.h"
+#include "source_base/intarray.h"
+#include "source_base/vector3.h"
 #include "ORB_atomic_lm.h"
 
 class Numerical_Orbital_AtomRelation

source/module_basis/module_ao/ORB_atomic_lm.cpp

@@ -1,11 +1,11 @@
 #include "ORB_atomic_lm.h"
-#include "module_base/sph_bessel_recursive.h"
+#include "source_base/sph_bessel_recursive.h"
 #include "module_parameter/parameter.h"
-#include "module_base/blas_connector.h"
-#include "module_base/timer.h"
-#include "module_base/math_integral.h"
-#include "module_base/math_sphbes.h"
-#include "module_base/constants.h"
+#include "source_base/blas_connector.h"
+#include "source_base/timer.h"
+#include "source_base/math_integral.h"
+#include "source_base/math_sphbes.h"
+#include "source_base/constants.h"
 
 #ifdef _OPENMP
 #include <omp.h>
@@ -216,7 +216,7 @@ void Numerical_Orbital_Lm::copy_parameter(
 	this->kcut = (nk-1) * this->dk;
 }
 
-#include "module_base/mathzone_add1.h"
+#include "source_base/mathzone_add1.h"
 void Numerical_Orbital_Lm::extra_uniform(const double &dr_uniform_in, const bool &force_flag)
 {
 	ModuleBase::timer::tick("NOrbital_Lm", "extra_uniform");

source/module_basis/module_ao/ORB_atomic_lm.h

@@ -8,8 +8,8 @@
 
 #include <vector>
 using std::vector;
-#include "module_base/global_function.h"
-#include "module_base/global_variable.h"
+#include "source_base/global_function.h"
+#include "source_base/global_variable.h"
 
 /**
  * CLASS Num_orbital_lm

source/module_basis/module_ao/ORB_gaunt_table.cpp

@@ -1,13 +1,13 @@
 #include <math.h>
 #include <cassert>
 #include "ORB_gaunt_table.h"
-#include "module_base/timer.h"
-#include "module_base/memory.h"
-#include "module_base/mathzone.h"
-#include "module_base/global_function.h"
-#include "module_base/vector3.h"
-#include "module_base/constants.h"
-#include "module_base/math_ylmreal.h"
+#include "source_base/timer.h"
+#include "source_base/memory.h"
+#include "source_base/mathzone.h"
+#include "source_base/global_function.h"
+#include "source_base/vector3.h"
+#include "source_base/constants.h"
+#include "source_base/math_ylmreal.h"
 
 ORB_gaunt_table::ORB_gaunt_table(){}
 ORB_gaunt_table::~ORB_gaunt_table(){}

source/module_basis/module_ao/ORB_gaunt_table.h

@@ -2,8 +2,8 @@
 #define ORB_GAUNT_TABLE_H
 
 #include <map>
-#include "module_base/realarray.h"
-#include "module_base/matrix.h"
+#include "source_base/realarray.h"
+#include "source_base/matrix.h"
 
 class ORB_gaunt_table
 {

source/module_basis/module_ao/ORB_nonlocal.cpp

@@ -1,5 +1,5 @@
 #include "ORB_nonlocal.h"
-#include "module_base/global_function.h"
+#include "source_base/global_function.h"
 
 Numerical_Nonlocal::Numerical_Nonlocal()
 {

source/module_basis/module_ao/ORB_nonlocal.h

@@ -1,8 +1,8 @@
 #ifndef NUMERICAL_NONLOCAL_H
 #define NUMERICAL_NONLOCAL_H
 
-#include "module_base/complexarray.h"
-#include "module_base/complexmatrix.h"
+#include "source_base/complexarray.h"
+#include "source_base/complexmatrix.h"
 #include "ORB_nonlocal_lm.h"
 /**
  * \class Numerical_Nonlocal

source/module_basis/module_ao/ORB_nonlocal_lm.cpp

@@ -1,12 +1,12 @@
 #include "ORB_nonlocal_lm.h"
 
-#include "module_base/constants.h"
-#include "module_base/global_function.h"
-#include "module_base/math_integral.h"
-#include "module_base/math_polyint.h"
-#include "module_base/math_sphbes.h"
-#include "module_base/mathzone.h"      /// use Polynomial_Interpolation_xy, Spherical_Bessel
-#include "module_base/mathzone_add1.h" /// use SplineD2
+#include "source_base/constants.h"
+#include "source_base/global_function.h"
+#include "source_base/math_integral.h"
+#include "source_base/math_polyint.h"
+#include "source_base/math_sphbes.h"
+#include "source_base/mathzone.h"      /// use Polynomial_Interpolation_xy, Spherical_Bessel
+#include "source_base/mathzone_add1.h" /// use SplineD2
 #include "module_parameter/parameter.h"
 
 #include <cassert>