Merge branch 'develop' into remove-comment-lenlim

Author: kirk0830

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

@@ -39,18 +39,18 @@ 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;
 |   |                           (4) Utility functions: timer, random number generator, etc.
 |   |                           (5) Global parameters: input parameters, element names, mathematical and physical constants.
 |   |-- module_container        The container module for storing data and performing operations on them and on different architectures.
-|-- module_basis                Basis means the basis set to expand the wave function.
+|-- source_basis                Basis means the basis set to expand the wave function.
 |   |-- module_ao               Atomic orbital basis set to be refactored.
 |   |-- module_nao              New numerical atomic orbital basis set for two-center integrals in LCAO calculations
 |   `-- module_pw               Data structures and relevant methods for planewave involved calculations
-|-- module_cell                 The module for defining the unit cell and its operations, and reading pseudopotentials.
+|-- source_cell                 The module for defining the unit cell and its operations, and reading pseudopotentials.
 |   |-- 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.
@@ -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:
@@ -257,7 +257,7 @@ To add a unit test:
     ./cell_unitcell_test
     ```
 
-    under the directory of `build/source/module_cell/test` to run the test `cell_unitcell_test`.
+    under the directory of `build/source/source_cell/test` to run the test `cell_unitcell_test`.
     However, it is more convenient to run unit tests with `ctest` command under the `build` directory. You can check all unit tests by
 
     ```bash

docs/advanced/input_files/input-main.md

@@ -12,8 +12,8 @@ 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(NAO_PATH "${ABACUS_SOURCE_DIR}/module_basis/module_nao")
+set(BASE_PATH "${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(ENABLE_LCAO ON)
@@ -69,20 +69,20 @@ 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 ${PARAMETER_BINARY_DIR})
 # add orb
 set(ORB_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/orb")
-add_subdirectory(${ABACUS_SOURCE_DIR}/module_basis/module_ao ${ORB_BINARY_DIR})
+add_subdirectory(${ABACUS_SOURCE_DIR}/source_basis/module_ao ${ORB_BINARY_DIR})
 # set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
 # set RPATH

python/pyabacus/CMakeLists.txt

@@ -72,8 +72,8 @@ 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(NAO_PATH "${ABACUS_SOURCE_DIR}/module_basis/module_nao")
+set(BASE_PATH "${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(ENABLE_LCAO ON)
@@ -131,7 +131,7 @@ endif()
 include_directories(
     ${BASE_PATH} 
     ${ABACUS_SOURCE_DIR}
-    ${ABACUS_SOURCE_DIR}/module_base/module_container
+    ${ABACUS_SOURCE_DIR}/source_base/module_container
     )
 ```
 - This section adds the necessary include directories for the project.
@@ -141,13 +141,13 @@ include_directories(
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 # Add base
 set(BASE_BINARY_DIR "${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 ${PARAMETER_BINARY_DIR})
 # Add orb
 set(ORB_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/orb")
-add_subdirectory(${ABACUS_SOURCE_DIR}/module_basis/module_ao ${ORB_BINARY_DIR})
+add_subdirectory(${ABACUS_SOURCE_DIR}/source_basis/module_ao ${ORB_BINARY_DIR})
 ```
 - This section sets the position-independent code flag and adds subdirectories for the base, parameter, and orb modules. It specifies the build directories for these modules.
 

python/pyabacus/CONTRIBUTING.md

@@ -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/examples/indexmap.py

@@ -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/ModuleBase/py_base_math.cpp

@@ -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/CMakeLists.txt

@@ -2,9 +2,9 @@
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
-#include "module_base/vector3.h"
-#include "module_basis/module_nao/radial_collection.h"
-#include "module_basis/module_nao/two_center_integrator.h"
+#include "source_base/vector3.h"
+#include "source_basis/module_nao/radial_collection.h"
+#include "source_basis/module_nao/two_center_integrator.h"
 
 namespace py = pybind11;
 using namespace pybind11::literals;

python/pyabacus/src/ModuleNAO/py_m_nao.cpp

@@ -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;