deepmodeling · Critsium-xy · Jun 18, 2025 · Jun 18, 2025
diff --git a/CMakeLists.txt b/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)

diff --git a/docs/CONTRIBUTING.md b/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:

diff --git a/python/pyabacus/CMakeLists.txt b/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})

diff --git a/python/pyabacus/CONTRIBUTING.md b/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})

diff --git a/python/pyabacus/examples/indexmap.py b/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)
 
                     '''

diff --git a/python/pyabacus/src/ModuleBase/py_base_math.cpp b/python/pyabacus/src/ModuleBase/py_base_math.cpp
diff --git a/python/pyabacus/src/ModuleNAO/CMakeLists.txt b/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}

diff --git a/python/pyabacus/src/ModuleNAO/py_m_nao.cpp b/python/pyabacus/src/ModuleNAO/py_m_nao.cpp
@@ -1,11 +1,11 @@
+#include "module_basis/module_nao/radial_collection.h"
+#include "module_basis/module_nao/two_center_integrator.h"
+#include "source_base/vector3.h"
+
 #include <pybind11/numpy.h>
 #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"
-
 namespace py = pybind11;
 using namespace pybind11::literals;
 template <typename... Args>

diff --git a/python/pyabacus/src/hsolver/py_diago_cg.hpp b/python/pyabacus/src/hsolver/py_diago_cg.hpp
@@ -1,31 +1,31 @@
 #ifndef PYTHON_PYABACUS_SRC_PY_DIAGO_CG_HPP
 #define PYTHON_PYABACUS_SRC_PY_DIAGO_CG_HPP
 
+#include "source_base/module_device/memory_op.h"
+#include "source_hsolver/diago_cg.h"
+
+#include <ATen/core/tensor.h>
+#include <ATen/core/tensor_map.h>
+#include <ATen/core/tensor_types.h>
 #include <complex>
 #include <functional>
-
-#include <pybind11/pybind11.h>
 #include <pybind11/complex.h>
 #include <pybind11/functional.h>
 #include <pybind11/numpy.h>
+#include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
-#include <ATen/core/tensor.h>
-#include <ATen/core/tensor_map.h>
-#include <ATen/core/tensor_types.h>
-
-#include "source_hsolver/diago_cg.h"
-#include "module_base/module_device/memory_op.h"
-
 namespace py = pybind11;
 
 namespace py_hsolver
 {
 
 class PyDiagoCG
 {
-public:
-    PyDiagoCG(int dim, int num_eigs) : dim{dim}, num_eigs{num_eigs} { }
+  public:
+    PyDiagoCG(int dim, int num_eigs) : dim{dim}, num_eigs{num_eigs}
+    {
+    }
     PyDiagoCG(const PyDiagoCG&) = delete;
     PyDiagoCG& operator=(const PyDiagoCG&) = delete;
     PyDiagoCG(PyDiagoCG&& other)
@@ -37,9 +37,9 @@ class PyDiagoCG
         other.eig = nullptr;
     }
 
-    ~PyDiagoCG() 
+    ~PyDiagoCG()
     {
-        if (psi != nullptr) 
+        if (psi != nullptr)
         {
             delete psi;
             psi = nullptr;
@@ -52,19 +52,20 @@ class PyDiagoCG
         }
     }
 
-    void init_eig() 
+    void init_eig()
     {
         eig = new ct::Tensor(ct::DataType::DT_DOUBLE, {num_eigs});
         eig->zero();
     }
 
-    py::array_t<double> get_eig() 
+    py::array_t<double> get_eig()
     {
         py::array_t<double> eig_out(eig->NumElements());
         py::buffer_info eig_buf = eig_out.request();
         double* eig_out_ptr = static_cast<double*>(eig_buf.ptr);
 
-        if (eig == nullptr) {
+        if (eig == nullptr)
+        {
             throw std::runtime_error("eig is not initialized");
         }
         double* eig_ptr = eig->data<double>();
@@ -78,12 +79,10 @@ class PyDiagoCG
         py::buffer_info psi_buf = psi_in.request();
         std::complex<double>* psi_ptr = static_cast<std::complex<double>*>(psi_buf.ptr);
 
-        psi = new ct::TensorMap(
-            psi_ptr,
-            ct::DataType::DT_COMPLEX_DOUBLE,
-            ct::DeviceType::CpuDevice,
-            ct::TensorShape({num_eigs, dim})
-        );
+        psi = new ct::TensorMap(psi_ptr,
+                                ct::DataType::DT_COMPLEX_DOUBLE,
+                                ct::DeviceType::CpuDevice,
+                                ct::TensorShape({num_eigs, dim}));
     }
 
     py::array_t<std::complex<double>> get_psi()
@@ -92,7 +91,8 @@ class PyDiagoCG
         py::buffer_info psi_buf = psi_out.request();
         std::complex<double>* psi_out_ptr = static_cast<std::complex<double>*>(psi_buf.ptr);
 
-        if (psi == nullptr) {
+        if (psi == nullptr)
+        {
             throw std::runtime_error("psi is not initialized");
         }
         std::complex<double>* psi_ptr = psi->data<std::complex<double>>();
@@ -106,12 +106,7 @@ class PyDiagoCG
         py::buffer_info prec_buf = prec_in.request();
         double* prec_ptr = static_cast<double*>(prec_buf.ptr);
 
-        prec = new ct::TensorMap(
-            prec_ptr,
-            ct::DataType::DT_DOUBLE,
-            ct::DeviceType::CpuDevice,
-            ct::TensorShape({dim})
-        );
+        prec = new ct::TensorMap(prec_ptr, ct::DataType::DT_DOUBLE, ct::DeviceType::CpuDevice, ct::TensorShape({dim}));
     }
 
     void diag(std::function<py::array_t<std::complex<double>>(py::array_t<std::complex<double>>)> mm_op,
@@ -120,23 +115,25 @@ class PyDiagoCG
               const std::vector<double>& diag_ethr,
               bool need_subspace,
               bool scf_type,
-              int nproc_in_pool = 1
-    ) {
+              int nproc_in_pool = 1)
+    {
         const std::string basis_type = "pw";
         const std::string calculation = scf_type ? "scf" : "nscf";
 
-        auto hpsi_func = [mm_op] (const ct::Tensor& psi_in, ct::Tensor& hpsi_out) {
+        auto hpsi_func = [mm_op](const ct::Tensor& psi_in, ct::Tensor& hpsi_out) {
             const auto ndim = psi_in.shape().ndim();
             REQUIRES_OK(ndim <= 2, "dims of psi_in should be less than or equal to 2");
-            const int nvec   = ndim == 1 ? 1 : psi_in.shape().dim_size(0);
+            const int nvec = ndim == 1 ? 1 : psi_in.shape().dim_size(0);
             const int ld_psi = ndim == 1 ? psi_in.NumElements() : psi_in.shape().dim_size(1);
 
             // Note: numpy's py::array_t is row-major, and
             //       our tensor-array is row-major
             py::array_t<std::complex<double>> psi({ld_psi, nvec});
             py::buffer_info psi_buf = psi.request();
             std::complex<double>* psi_ptr = static_cast<std::complex<double>*>(psi_buf.ptr);
-            std::copy(psi_in.data<std::complex<double>>(), psi_in.data<std::complex<double>>() + nvec * ld_psi, psi_ptr);
+            std::copy(psi_in.data<std::complex<double>>(),
+                      psi_in.data<std::complex<double>>() + nvec * ld_psi,
+                      psi_ptr);
 
             py::array_t<std::complex<double>> hpsi = mm_op(psi);
 
@@ -145,34 +142,30 @@ class PyDiagoCG
             std::copy(hpsi_ptr, hpsi_ptr + nvec * ld_psi, hpsi_out.data<std::complex<double>>());
         };
 
-        auto subspace_func = [] (const ct::Tensor& psi_in, ct::Tensor& psi_out) { /*do nothing*/ };
+        auto subspace_func = [](const ct::Tensor& psi_in, ct::Tensor& psi_out) { /*do nothing*/ };
 
-        auto spsi_func = [this] (const ct::Tensor& psi_in, ct::Tensor& spsi_out) {
+        auto spsi_func = [this](const ct::Tensor& psi_in, ct::Tensor& spsi_out) {
             const auto ndim = psi_in.shape().ndim();
             REQUIRES_OK(ndim <= 2, "dims of psi_in should be less than or equal to 2");
-            const int nrow   = ndim == 1 ? psi_in.NumElements() : psi_in.shape().dim_size(1);
+            const int nrow = ndim == 1 ? psi_in.NumElements() : psi_in.shape().dim_size(1);
             const int nbands = ndim == 1 ? 1 : psi_in.shape().dim_size(0);
-            syncmem_z2z_h2h_op()(
-                spsi_out.data<std::complex<double>>(), 
-                psi_in.data<std::complex<double>>(), 
-                static_cast<size_t>(nrow * nbands)
-            );
+            syncmem_z2z_h2h_op()(spsi_out.data<std::complex<double>>(),
+                                 psi_in.data<std::complex<double>>(),
+                                 static_cast<size_t>(nrow * nbands));
         };
 
-        cg = std::make_unique<hsolver::DiagoCG<std::complex<double>, base_device::DEVICE_CPU>>(
-            basis_type,
-            calculation,
-            need_subspace,
-            subspace_func,
-            tol,
-            diag_ndim,
-            nproc_in_pool
-        );
+        cg = std::make_unique<hsolver::DiagoCG<std::complex<double>, base_device::DEVICE_CPU>>(basis_type,
+                                                                                               calculation,
+                                                                                               need_subspace,
+                                                                                               subspace_func,
+                                                                                               tol,
+                                                                                               diag_ndim,
+                                                                                               nproc_in_pool);
 
         cg->diag(hpsi_func, spsi_func, *psi, *eig, diag_ethr, *prec);
     }
 
-private:
+  private:
     base_device::DEVICE_CPU* ctx = {};
 
     int dim;