Merge branch 'develop' into ccp_param_INPUT_2

Author: PeizeLin

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;
@@ -77,7 +77,7 @@ For those who are interested in the source code, the following figure shows the
 |   |-- hamilt_pwdft            The module for defining the Hamiltonian in PW-DFT calculations.
 |   |   |-- operator_pw         The module for defining the operators in PW-DFT calculations.
 |   `-- hamilt_stodft           The module for defining the Hamiltonian in STODFT calculations.
-|-- module_hsolver              The module for solving the Hamiltonian with different diagonalization methods, including CG, Davidson in PW
+|-- source_hsolver              The module for solving the Hamiltonian with different diagonalization methods, including CG, Davidson in PW
 |   |                           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.
@@ -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:

docs/advanced/acceleration/cuda.md

@@ -12,7 +12,7 @@ In ABACUS, we provide the option to use GPU devices to accelerate performance. T
 
 - **Parallel strategy**: K point parallel.
 
-Unlike PW basis, only the grid integration module (module_gint) and the diagonalization of the Hamiltonian matrix (module_hsolver) have been implemented with GPU acceleration under LCAO basis.
+Unlike PW basis, only the grid integration module (module_gint) and the diagonalization of the Hamiltonian matrix (source_hsolver) have been implemented with GPU acceleration under LCAO basis.
 
 ## Required hardware/software
 

docs/advanced/input_files/input-main.md

@@ -118,7 +118,7 @@
     - [cal\_force](#cal_force)
     - [force\_thr](#force_thr)
     - [force\_thr\_ev](#force_thr_ev)
-    - [force\_thr\_ev2](#force_thr_ev2)
+    - [force\_zero\_out](#force_zero_out)
     - [relax\_bfgs\_w1](#relax_bfgs_w1)
     - [relax\_bfgs\_w2](#relax_bfgs_w2)
     - [relax\_bfgs\_rmax](#relax_bfgs_rmax)
@@ -134,6 +134,7 @@
   - [Output Variables](#variables-related-to-output-information)
     - [out\_freq\_elec](#out_freq_elec)
     - [out\_chg](#out_chg)
+    - [out\_xc\_r](#out_xc_r)
     - [out\_pot](#out_pot)
     - [out\_dm](#out_dmk)
     - [out\_dm1](#out_dmr)
@@ -1508,10 +1509,10 @@ These variables are used to control the geometry relaxation.
 - **Default**: 0.0257112
 - **Unit**: eV/Angstrom (0.03889 Ry/Bohr)
 
-### force_thr_ev2
+### force_zero_out
 
 - **Type**: Real
-- **Description**: The calculated force will be set to 0 when it is smaller than the parameter `force_thr_ev2`.
+- **Description**: The force whose value is smaller than `force_zero_out` will be treated as zero.
 - **Default**: 0.0
 - **Unit**: eV/Angstrom
 
@@ -1654,6 +1655,25 @@ These variables are used to control the output of properties.
 - **Default**: 0 3
 - **Note**: In the 3.10-LTS version, the file names are SPIN1_CHG.cube and SPIN1_CHG_INI.cube, etc. 
 
+### out_xc_r
+
+- **Type**: Integer \[Integer\](optional)
+- **Description**: 
+  The first integer controls whether to output the exchange-correlation (in Bohr^-3) on real space grids using Libxc to folder `OUT.${suffix}`:
+  - 0: rho, amag, sigma, exc
+  - 1: vrho, vsigma
+  - 2: v2rho2, v2rhosigma, v2sigma2
+  - 3: v3rho3, v3rho2sigma, v3rhosigma2, v3sigma3
+  - 4: v4rho4, v4rho3sigma, v4rho2sigma2, v4rhosigma3, v4sigma4
+  The meaning of the files is presented in [Libxc](https://libxc.gitlab.io/manual/libxc-5.1.x/)
+
+  The second integer controls the precision of the charge density output, if not given, will use `3` as default.
+
+  ---
+  The circle order of the charge density on real space grids is: x is the outer loop, then y and finally z (z is moving fastest).
+
+- **Default**: -1 3
+
 ### out_pot
 
 - **Type**: Integer

python/pyabacus/CMakeLists.txt

@@ -12,9 +12,9 @@ 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 "${ABACUS_SOURCE_DIR}/module_hsolver")
+set(HSOLVER_PATH "${ABACUS_SOURCE_DIR}/source_hsolver")
 set(PSI_PATH "${ABACUS_SOURCE_DIR}/module_psi")
 set(ENABLE_LCAO ON)
 list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/../../cmake")
@@ -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

@@ -72,9 +72,9 @@ 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 "${ABACUS_SOURCE_DIR}/module_hsolver")
+set(HSOLVER_PATH "${ABACUS_SOURCE_DIR}/source_hsolver")
 set(PSI_PATH "${ABACUS_SOURCE_DIR}/module_psi")
 set(ENABLE_LCAO ON)
 list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/../../cmake")
@@ -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/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"