Merge branch 'develop' into perf/neighlist-build-openmp

Author: Audrey-777

CMakeLists.txt

@@ -691,11 +691,7 @@ if(ENABLE_MLALGO OR DEFINED Torch_DIR)
     set_if_higher(CMAKE_CXX_STANDARD 14)
   endif()
   include_directories(${TORCH_INCLUDE_DIRS})
-  if(MKL_FOUND)
-    list(PREPEND math_libs ${TORCH_LIBRARIES})
-  else()
-    list(APPEND math_libs ${TORCH_LIBRARIES})
-  endif()
+  list(APPEND math_libs ${TORCH_LIBRARIES})
   add_compile_options(${TORCH_CXX_FLAGS})
 endif()
 

docs/advanced/input_files/input-main.md

@@ -1964,7 +1964,7 @@
 
 - **Type**: Boolean \[Integer\](optional)
 - **Availability**: *Numerical atomic orbital basis (not gamma-only algorithm)*
-- **Description**: Whether to print the matrix representation of the position matrix into files named rxrs1_nao.csr, ryrs1_nao.csr, rzrs1_nao.csr in the directory OUT.${suffix}. If calculation is set to get_s, the position matrix can be obtained without scf iterations. For more information, please refer to position_matrix.md.
+- **Description**: Whether to print the matrix representation of the position matrix into files named rxrs1_nao.csr, ryrs1_nao.csr, rzrs1_nao.csr in the directory OUT.${suffix}. The optional second parameter controls text output precision. If calculation is set to get_s, the position matrix can be obtained without scf iterations. For more information, please refer to position_matrix.md.
 
   > Note: In the 3.10-LTS version, the file name is data-rR-sparse.csr.
 - **Default**: False 8
@@ -1974,17 +1974,17 @@
 
 - **Type**: Boolean \[Integer\](optional)
 - **Availability**: *Numerical atomic orbital basis (not gamma-only algorithm)*
-- **Description**: Generate files containing the kinetic energy matrix. The format will be the same as the Hamiltonian matrix and overlap matrix as mentioned in out_mat_hs2. The name of the files will be trs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag.
+- **Description**: Generate files containing the kinetic energy matrix. The optional second parameter controls text output precision. The format will be the same as the Hamiltonian matrix and overlap matrix as mentioned in out_mat_hs2. The name of the files will be trs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag.
 
   > Note: In the 3.10-LTS version, the file name is data-TR-sparse_SPIN0.csr.
 - **Default**: False 8
 - **Unit**: Ry
 
 ### out_mat_dh
 
-- **Type**: Integer
+- **Type**: Boolean \[Integer\](optional)
 - **Availability**: *Numerical atomic orbital basis (not gamma-only algorithm)*
-- **Description**: Whether to print files containing the derivatives of the Hamiltonian matrix. The format will be the same as the Hamiltonian matrix and overlap matrix as mentioned in out_mat_hs2. The name of the files will be dhrxs1_nao.csr, dhrys1_nao.csr, dhrzs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag.
+- **Description**: Whether to print files containing the derivatives of the Hamiltonian matrix. The optional second parameter controls text output precision. The format will be the same as the Hamiltonian matrix and overlap matrix as mentioned in out_mat_hs2. The name of the files will be dhrxs1_nao.csr, dhrys1_nao.csr, dhrzs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag.
 
   > Note: In the 3.10-LTS version, the file name is data-dHRx-sparse_SPIN0.csr and so on.
 - **Default**: 0 8
@@ -1994,7 +1994,7 @@
 
 - **Type**: Boolean \[Integer\](optional)
 - **Availability**: *Numerical atomic orbital basis (not gamma-only algorithm)*
-- **Description**: Whether to print files containing the derivatives of the overlap matrix. The format will be the same as the overlap matrix as mentioned in out_mat_dh. The name of the files will be dsxrs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag. This feature can be used with calculation get_s.
+- **Description**: Whether to print files containing the derivatives of the overlap matrix. The optional second parameter controls text output precision. The format will be the same as the overlap matrix as mentioned in out_mat_dh. The name of the files will be dsxrs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag. This feature can be used with calculation get_s.
 
   > Note: In the 3.10-LTS version, the file name is data-dSRx-sparse_SPIN0.csr and so on.
 - **Default**: False 8

docs/parameters.yaml

@@ -3058,7 +3058,7 @@ parameters:
     category: Output information
     type: "Boolean \\[Integer\\](optional)"
     description: |
-      Whether to print the matrix representation of the position matrix into files named rxrs1_nao.csr, ryrs1_nao.csr, rzrs1_nao.csr in the directory OUT.${suffix}. If calculation is set to get_s, the position matrix can be obtained without scf iterations. For more information, please refer to position_matrix.md.
+      Whether to print the matrix representation of the position matrix into files named rxrs1_nao.csr, ryrs1_nao.csr, rzrs1_nao.csr in the directory OUT.${suffix}. The optional second parameter controls text output precision. If calculation is set to get_s, the position matrix can be obtained without scf iterations. For more information, please refer to position_matrix.md.
 
       [NOTE] In the 3.10-LTS version, the file name is data-rR-sparse.csr.
     default_value: False 8
@@ -3068,17 +3068,17 @@ parameters:
     category: Output information
     type: "Boolean \\[Integer\\](optional)"
     description: |
-      Generate files containing the kinetic energy matrix. The format will be the same as the Hamiltonian matrix and overlap matrix as mentioned in out_mat_hs2. The name of the files will be trs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag.
+      Generate files containing the kinetic energy matrix. The optional second parameter controls text output precision. The format will be the same as the Hamiltonian matrix and overlap matrix as mentioned in out_mat_hs2. The name of the files will be trs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag.
 
       [NOTE] In the 3.10-LTS version, the file name is data-TR-sparse_SPIN0.csr.
     default_value: False 8
     unit: Ry
     availability: Numerical atomic orbital basis (not gamma-only algorithm)
   - name: out_mat_dh
     category: Output information
-    type: Integer
+    type: "Boolean \\[Integer\\](optional)"
     description: |
-      Whether to print files containing the derivatives of the Hamiltonian matrix. The format will be the same as the Hamiltonian matrix and overlap matrix as mentioned in out_mat_hs2. The name of the files will be dhrxs1_nao.csr, dhrys1_nao.csr, dhrzs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag.
+      Whether to print files containing the derivatives of the Hamiltonian matrix. The optional second parameter controls text output precision. The format will be the same as the Hamiltonian matrix and overlap matrix as mentioned in out_mat_hs2. The name of the files will be dhrxs1_nao.csr, dhrys1_nao.csr, dhrzs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag.
 
       [NOTE] In the 3.10-LTS version, the file name is data-dHRx-sparse_SPIN0.csr and so on.
     default_value: 0 8
@@ -3088,7 +3088,7 @@ parameters:
     category: Output information
     type: "Boolean \\[Integer\\](optional)"
     description: |
-      Whether to print files containing the derivatives of the overlap matrix. The format will be the same as the overlap matrix as mentioned in out_mat_dh. The name of the files will be dsxrs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag. This feature can be used with calculation get_s.
+      Whether to print files containing the derivatives of the overlap matrix. The optional second parameter controls text output precision. The format will be the same as the overlap matrix as mentioned in out_mat_dh. The name of the files will be dsxrs1_nao.csr and so on. Also controled by out_freq_ion and out_app_flag. This feature can be used with calculation get_s.
 
       [NOTE] In the 3.10-LTS version, the file name is data-dSRx-sparse_SPIN0.csr and so on.
     default_value: False 8

source/source_base/CMakeLists.txt

@@ -40,6 +40,7 @@ add_library(
     mymath.cpp
     opt_CG.cpp
     opt_DCsrch.cpp
+    output.cpp
     para_gemm.cpp
     realarray.cpp
     sph_bessel_recursive-d1.cpp

source/source_io/module_output/output.cpp source/source_base/output.cppsource/source_io/module_output/output.cpp renamed to source/source_base/output.cpp

@@ -5,10 +5,10 @@
 #ifndef OUTPUT_H
 #define OUTPUT_H
 
-#include "../../source_base/realarray.h"
-#include "../../source_base/matrix3.h"
-#include "../../source_base/complexmatrix.h"
-#include "../../source_base/matrix.h"
+#include "realarray.h"
+#include "matrix3.h"
+#include "complexmatrix.h"
+#include "matrix.h"
 class output
 {
 public:

source/source_io/module_output/output.h source/source_base/output.hsource/source_io/module_output/output.h renamed to source/source_base/output.h

@@ -23,6 +23,7 @@ add_library(
     cell_index.cpp
     check_atomic_stru.cpp
     update_cell.cpp
+    magnetism.cpp
     bcast_cell.cpp
     read_stru.cpp
     print_cell.cpp

source/source_cell/CMakeLists.txt

@@ -1,6 +1,6 @@
 #include "atom_spec.h"
 #include "source_io/module_parameter/parameter.h"
-#include "source_io/module_output/output.h"
+#include "source_base/output.h"
 #include <cstdlib>
 
 Atom::Atom()