deepmodeling · mohanchen · Jun 21, 2025 · Jun 20, 2025 · Jun 20, 2025 · Jun 20, 2025
diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
@@ -46,11 +46,11 @@ For those who are interested in the source code, the following figure shows the
 |   |                           (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.
@@ -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

diff --git a/python/pyabacus/CMakeLists.txt b/python/pyabacus/CMakeLists.txt
@@ -13,7 +13,7 @@ find_package(pybind11 CONFIG REQUIRED)
 # set source path
 set(ABACUS_SOURCE_DIR "${PROJECT_SOURCE_DIR}/../../source")
 set(BASE_PATH "${ABACUS_SOURCE_DIR}/source_base")
-set(NAO_PATH "${ABACUS_SOURCE_DIR}/module_basis/module_nao")
+set(NAO_PATH "${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)
@@ -82,7 +82,7 @@ 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

diff --git a/python/pyabacus/CONTRIBUTING.md b/python/pyabacus/CONTRIBUTING.md
@@ -73,7 +73,7 @@ find_package(pybind11 CONFIG REQUIRED)
 # Set source path
 set(ABACUS_SOURCE_DIR "${PROJECT_SOURCE_DIR}/../../source")
 set(BASE_PATH "${ABACUS_SOURCE_DIR}/source_base")
-set(NAO_PATH "${ABACUS_SOURCE_DIR}/module_basis/module_nao")
+set(NAO_PATH "${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)
@@ -147,7 +147,7 @@ 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.
 

diff --git a/python/pyabacus/src/ModuleNAO/py_m_nao.cpp b/python/pyabacus/src/ModuleNAO/py_m_nao.cpp
@@ -3,8 +3,8 @@
 #include <pybind11/stl.h>
 
 #include "source_base/vector3.h"
-#include "module_basis/module_nao/radial_collection.h"
-#include "module_basis/module_nao/two_center_integrator.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;

diff --git a/python/pyabacus/src/py_numerical_radial.cpp b/python/pyabacus/src/py_numerical_radial.cpp
@@ -1,7 +1,7 @@
 #include <pybind11/numpy.h>
 #include <pybind11/pybind11.h>
 
-#include "module_basis/module_nao/numerical_radial.h"
+#include "source_basis/module_nao/numerical_radial.h"
 
 namespace py = pybind11;
 using namespace pybind11::literals;

diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
@@ -1,15 +1,15 @@
 add_subdirectory(source_base)
-add_subdirectory(module_cell)
+add_subdirectory(source_cell)
 add_subdirectory(module_psi)
 add_subdirectory(module_elecstate)
 add_subdirectory(module_hamilt_general)
 add_subdirectory(module_hamilt_pw)
 add_subdirectory(module_hamilt_lcao)
 add_subdirectory(source_hsolver)
-add_subdirectory(module_basis/module_ao)
-add_subdirectory(module_basis/module_nao)
+add_subdirectory(source_basis/module_ao)
+add_subdirectory(source_basis/module_nao)
 add_subdirectory(module_md)
-add_subdirectory(module_basis/module_pw)
+add_subdirectory(source_basis/module_pw)
 add_subdirectory(source_esolver)
 add_subdirectory(module_hamilt_lcao/module_gint)
 add_subdirectory(module_io)
@@ -34,7 +34,7 @@ list(APPEND device_srcs
   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
-  module_basis/module_pw/kernels/pw_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
@@ -64,7 +64,7 @@ if(USE_CUDA)
     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
-    module_basis/module_pw/kernels/cuda/pw_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
@@ -91,7 +91,7 @@ if(USE_ROCM)
     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
-    module_basis/module_pw/kernels/rocm/pw_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

diff --git a/source/Makefile.Objects b/source/Makefile.Objects
@@ -13,11 +13,11 @@ HEADERS = source_main/*.h
 
 VPATH=./src_global:\
 ./source_main:\
-./module_basis/module_ao:\
-./module_basis/module_nao:\
-./module_cell/module_neighbor:\
-./module_cell/module_symmetry:\
-./module_cell:\
+./source_basis/module_ao:\
+./source_basis/module_nao:\
+./source_cell/module_neighbor:\
+./source_cell/module_symmetry:\
+./source_cell:\
 ./source_base:\
 ./source_base/kernels:\
 ./source_base/module_container/base/core:\
@@ -27,8 +27,8 @@ VPATH=./src_global:\
 ./source_base/module_device:\
 ./source_base/module_mixing:\
 ./module_md:\
-./module_basis/module_pw:\
-./module_basis/module_pw/module_fft:\
+./source_basis/module_pw:\
+./source_basis/module_pw/module_fft:\
 ./source_esolver:\
 ./source_hsolver:\
 ./source_hsolver/kernels:\

diff --git a/source/module_elecstate/cal_nelec_nband.h b/source/module_elecstate/cal_nelec_nband.h
@@ -1,7 +1,7 @@
 #ifndef CAL_NELEC_NBAND_H
 #define CAL_NELEC_NBAND_H
 
-#include "module_cell/atom_spec.h"
+#include "source_cell/atom_spec.h"
 
 namespace elecstate {
 

diff --git a/source/module_elecstate/cal_ux.h b/source/module_elecstate/cal_ux.h
@@ -1,7 +1,7 @@
 #ifndef CAL_UX_H
 #define CAL_UX_H
 
-#include "module_cell/unitcell.h"
+#include "source_cell/unitcell.h"
 
 namespace elecstate {
 

diff --git a/source/module_elecstate/elecstate.h b/source/module_elecstate/elecstate.h
@@ -2,7 +2,7 @@
 #define ELECSTATE_H
 
 #include "fp_energy.h"
-#include "module_cell/klist.h"
+#include "source_cell/klist.h"
 #include "module_elecstate/module_charge/charge.h"
 #include "module_parameter/parameter.h"
 #include "module_psi/psi.h"

diff --git a/source/module_elecstate/elecstate_pw.h b/source/module_elecstate/elecstate_pw.h
@@ -4,7 +4,7 @@
 #include <source_base/macros.h>
 
 #include "elecstate.h"
-#include "module_basis/module_pw/pw_basis_k.h"
+#include "source_basis/module_pw/pw_basis_k.h"
 #include "module_elecstate/kernels/elecstate_op.h"
 #include "module_hamilt_pw/hamilt_pwdft/kernels/meta_op.h"
 #include "source_base/kernels/math_kernel_op.h"

diff --git a/source/module_elecstate/module_charge/charge.cpp b/source/module_elecstate/module_charge/charge.cpp
@@ -26,7 +26,7 @@
 #include "source_base/parallel_reduce.h"
 #include "source_base/timer.h"
 #include "source_base/tool_threading.h"
-#include "module_cell/unitcell.h"
+#include "source_cell/unitcell.h"
 #include "module_elecstate/magnetism.h"
 #include "module_hamilt_general/module_xc/xc_functional.h"
 #include "module_parameter/parameter.h"

diff --git a/source/module_elecstate/module_charge/charge.h b/source/module_elecstate/module_charge/charge.h
@@ -5,8 +5,8 @@
 #include "source_base/global_function.h"
 #include "source_base/global_variable.h"
 #include "source_base/parallel_global.h"
-#include "module_basis/module_pw/pw_basis.h"
-#include "module_cell/module_symmetry/symmetry.h"
+#include "source_basis/module_pw/pw_basis.h"
+#include "source_cell/module_symmetry/symmetry.h"
 #include "module_elecstate/fp_energy.h"
 #include "module_hamilt_pw/hamilt_pwdft/parallel_grid.h"
 

diff --git a/source/module_elecstate/module_charge/charge_extra.h b/source/module_elecstate/module_charge/charge_extra.h
@@ -2,7 +2,7 @@
 #define CHARGE_EXTRA_H
 
 #include "charge.h"
-#include "module_cell/unitcell.h"
+#include "source_cell/unitcell.h"
 #include "module_hamilt_pw/hamilt_pwdft/structure_factor.h"
 #ifdef __MPI
 #include "module_hamilt_pw/hamilt_pwdft/parallel_grid.h"

diff --git a/source/module_elecstate/module_charge/symmetry_rho.h b/source/module_elecstate/module_charge/symmetry_rho.h
@@ -1,7 +1,7 @@
 #ifndef SYMMETRY_RHO_H
 #define SYMMETRY_RHO_H
-#include "module_basis/module_pw/pw_basis.h"
-#include "module_cell/module_symmetry/symmetry.h"
+#include "source_basis/module_pw/pw_basis.h"
+#include "source_cell/module_symmetry/symmetry.h"
 #include "module_elecstate/module_charge/charge.h"
 #include "module_hamilt_pw/hamilt_pwdft/parallel_grid.h"
 

diff --git a/source/module_elecstate/module_dm/cal_edm_tddft.h b/source/module_elecstate/module_dm/cal_edm_tddft.h
@@ -1,8 +1,8 @@
 #ifndef CAL_EDM_TDDFT_H
 #define CAL_EDM_TDDFT_H
 
-#include "module_basis/module_ao/parallel_orbitals.h"
-#include "module_cell/klist.h"
+#include "source_basis/module_ao/parallel_orbitals.h"
+#include "source_cell/klist.h"
 #include "module_elecstate/elecstate_lcao.h"
 #include "module_hamilt_general/hamilt.h"
 

diff --git a/source/module_elecstate/module_dm/density_matrix.cpp b/source/module_elecstate/module_dm/density_matrix.cpp
@@ -5,7 +5,7 @@
 #include "source_base/memory.h"
 #include "source_base/timer.h"
 #include "source_base/tool_title.h"
-#include "module_cell/klist.h"
+#include "source_cell/klist.h"
 
 namespace elecstate
 {

diff --git a/source/module_elecstate/module_dm/density_matrix.h b/source/module_elecstate/module_dm/density_matrix.h
@@ -3,7 +3,7 @@
 
 #include <string>
 
-#include "module_cell/module_neighbor/sltk_grid_driver.h"
+#include "source_cell/module_neighbor/sltk_grid_driver.h"
 #include "module_hamilt_lcao/hamilt_lcaodft/record_adj.h"
 #include "module_hamilt_lcao/module_hcontainer/hcontainer.h"
 

diff --git a/source/module_elecstate/module_dm/density_matrix_io.cpp b/source/module_elecstate/module_dm/density_matrix_io.cpp
@@ -5,7 +5,7 @@
 #include "source_base/memory.h"
 #include "source_base/timer.h"
 #include "source_base/tool_title.h"
-#include "module_cell/klist.h"
+#include "source_cell/klist.h"
 
 namespace elecstate
 {

diff --git a/source/module_elecstate/module_dm/test/CMakeLists.txt b/source/module_elecstate/module_dm/test/CMakeLists.txt
@@ -15,7 +15,7 @@ AddTest(
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/base_matrix.cpp
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/hcontainer.cpp
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/atom_pair.cpp
-  ${ABACUS_SOURCE_DIR}/module_basis/module_ao/parallel_orbitals.cpp
+  ${ABACUS_SOURCE_DIR}/source_basis/module_ao/parallel_orbitals.cpp
   ${ABACUS_SOURCE_DIR}/module_io/output.cpp
 )
 
@@ -26,7 +26,7 @@ AddTest(
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/base_matrix.cpp
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/hcontainer.cpp
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/atom_pair.cpp
-  ${ABACUS_SOURCE_DIR}/module_basis/module_ao/parallel_orbitals.cpp
+  ${ABACUS_SOURCE_DIR}/source_basis/module_ao/parallel_orbitals.cpp
 )
 
 AddTest(
@@ -36,7 +36,7 @@ AddTest(
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/base_matrix.cpp
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/hcontainer.cpp
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/atom_pair.cpp
-  ${ABACUS_SOURCE_DIR}/module_basis/module_ao/parallel_orbitals.cpp
+  ${ABACUS_SOURCE_DIR}/source_basis/module_ao/parallel_orbitals.cpp
 )
 
 AddTest(
@@ -46,5 +46,5 @@ AddTest(
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/base_matrix.cpp
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/hcontainer.cpp
   ${ABACUS_SOURCE_DIR}/module_hamilt_lcao/module_hcontainer/atom_pair.cpp
-  ${ABACUS_SOURCE_DIR}/module_basis/module_ao/parallel_orbitals.cpp
+  ${ABACUS_SOURCE_DIR}/source_basis/module_ao/parallel_orbitals.cpp
 )
diff --git a/source/module_elecstate/module_dm/test/test_cal_dm_R.cpp b/source/module_elecstate/module_dm/test/test_cal_dm_R.cpp
@@ -4,7 +4,7 @@
 #include "gtest/gtest.h"
 #include "module_elecstate/module_dm/density_matrix.h"
 #include "module_hamilt_lcao/module_hcontainer/hcontainer.h"
-#include "module_cell/klist.h"
+#include "source_cell/klist.h"
 
 /************************************************
  *  unit test of DensityMatrix constructor

diff --git a/source/module_elecstate/module_dm/test/test_cal_dmk_psi.cpp b/source/module_elecstate/module_dm/test/test_cal_dmk_psi.cpp
@@ -4,7 +4,7 @@
 #include "gtest/gtest.h"
 #include "module_elecstate/module_dm/density_matrix.h"
 #include "module_hamilt_lcao/module_hcontainer/hcontainer.h"
-#include "module_cell/klist.h"
+#include "source_cell/klist.h"
 
 /************************************************
  *  unit test of DensityMatrix constructor

diff --git a/source/module_elecstate/module_dm/test/test_dm_R_init.cpp b/source/module_elecstate/module_dm/test/test_dm_R_init.cpp
@@ -5,7 +5,7 @@
 #define private public
 #include "module_elecstate/module_dm/density_matrix.h"
 #include "module_hamilt_lcao/module_hcontainer/hcontainer.h"
-#include "module_cell/klist.h"
+#include "source_cell/klist.h"
 #undef private
 /************************************************
  *  unit test of DensityMatrix constructor

diff --git a/source/module_elecstate/module_dm/test/test_dm_constructor.cpp b/source/module_elecstate/module_dm/test/test_dm_constructor.cpp
@@ -4,7 +4,7 @@
 #include "gtest/gtest.h"
 #include "module_elecstate/module_dm/density_matrix.h"
 #include "module_hamilt_lcao/module_hcontainer/hcontainer.h"
-#include "module_cell/klist.h"
+#include "source_cell/klist.h"
 /************************************************
  *  unit test of DensityMatrix constructor
  ***********************************************/

diff --git a/source/module_elecstate/module_dm/test/test_dm_io.cpp b/source/module_elecstate/module_dm/test/test_dm_io.cpp
@@ -2,7 +2,7 @@
 
 #include "gmock/gmock.h"
 #include "gtest/gtest.h"
-#include "module_cell/unitcell.h"
+#include "source_cell/unitcell.h"
 #include "module_elecstate/module_dm/density_matrix.h"
 #include "prepare_unitcell.h"
 
@@ -32,8 +32,8 @@ Magnetism::~Magnetism()
     delete[] this->start_mag;
 }
 
-#include "module_cell/klist.h"
-#include "module_cell/module_neighbor/sltk_grid_driver.h"
+#include "source_cell/klist.h"
+#include "source_cell/module_neighbor/sltk_grid_driver.h"
 // mock find_atom() function
 void Grid_Driver::Find_atom(const UnitCell& ucell,
                             const ModuleBase::Vector3<double>& tau,

diff --git a/source/module_elecstate/module_dm/test/tmp_mocks.cpp b/source/module_elecstate/module_dm/test/tmp_mocks.cpp
@@ -1,6 +1,6 @@
 
 
-#include "module_cell/unitcell.h"
+#include "source_cell/unitcell.h"
 
 // constructor of Atom
 Atom::Atom()
@@ -72,7 +72,7 @@ void UnitCell::set_iat2iwt(const int& npol_in)
     return;
 }
 
-#include "module_cell/module_neighbor/sltk_grid_driver.h"
+#include "source_cell/module_neighbor/sltk_grid_driver.h"
 // mock find_atom() function
 void Grid_Driver::Find_atom(const UnitCell& ucell,
                             const ModuleBase::Vector3<double>& tau,

diff --git a/source/module_elecstate/module_pot/H_Hartree_pw.h b/source/module_elecstate/module_pot/H_Hartree_pw.h
@@ -4,8 +4,8 @@
 #include "source_base/global_function.h"
 #include "source_base/global_variable.h"
 #include "source_base/matrix.h"
-#include "module_cell/unitcell.h"
-#include "module_basis/module_pw/pw_basis.h"
+#include "source_cell/unitcell.h"
+#include "source_basis/module_pw/pw_basis.h"
 
 namespace elecstate
 {

diff --git a/source/module_elecstate/module_pot/efield.h b/source/module_elecstate/module_pot/efield.h
@@ -1,8 +1,8 @@
 #ifndef EFIELD_H
 #define EFIELD_H
 
-#include "module_basis/module_pw/pw_basis.h"
-#include "module_cell/unitcell.h"
+#include "source_basis/module_pw/pw_basis.h"
+#include "source_cell/unitcell.h"
 #include "module_hamilt_general/module_surchem/surchem.h"
 #include "module_parameter/parameter.h"