Move some files from source_io to source_base and source_cell (deepmodeling#7789)

* move binstream from source_io to module_out in source_base

* move filename to source_base

* move file_reader and sparse_matrix to source_base

* move csr_reader and cif_io

* move ucell_io

* move test files

* refactor parallel_grid.h and cpp

* update parallel_grid

* refactor parallel_grid

* update parallel grid

* move parallel grid to source_base

* fix small bugs

* increase the threshold from 0.005 to 0.006

* fix bug

* fix makefile

---------

Co-authored-by: abacus_fixer <mohanchen@pku.eud.cn>

Author: mohanchen

source/Makefile.Objects

@@ -28,6 +28,7 @@ VPATH=./src_global:\
 ./source_base/module_container/ATen/ops:\
 ./source_base/module_device:\
 ./source_base/module_mixing:\
+./source_base/module_out:\
 ./source_md:\
 ./source_basis/module_pw:\
 ./source_base/module_fft:\
@@ -181,6 +182,11 @@ OBJS_BASE=assoc_laguerre.o\
     device_helpers.o\
     output_device.o\
     parallel_2d.o\
+    binstream.o\
+    filename.o\
+    sparse_matrix.o\
+    read_exit_file.o\
+    orb_io.o\
 
 OBJS_CELL=atom_pseudo.o\
     atom_spec.o\
@@ -211,6 +217,8 @@ OBJS_CELL=atom_pseudo.o\
     read_pseudo.o\
     cal_wfc.o\
     cal_ux.o\
+    cif_io.o\
+    ucell_io.o\
 
 OBJS_DEEPKS=LCAO_deepks.o\
         deepks_basic.o\
@@ -548,19 +556,16 @@ OBJS_IO=module_parameter/input_conv.o\
     module_dos/cal_pdos_gamma.o\
     module_dos/cal_pdos_multik.o\
     module_dos/cal_ldos.o\
-    cif_io.o\
     module_bessel/numerical_descriptor.o\
     module_bessel/numerical_basis.o\
     module_bessel/numerical_basis_jyjy.o\
     output.o\
     print_info.o\
     read_cube.o\
     rhog_io.o\
-    read_exit_file.o\
     read_wfc_pw.o\
     read_wf2rho_pw.o\
     restart.o\
-    binstream.o\
     module_wannier/to_wannier90.o\
     module_qo/to_qo_kernel.o\
     module_qo/to_qo_mpi.o\
@@ -612,10 +617,7 @@ OBJS_IO=module_parameter/input_conv.o\
     module_parameter/read_input_item_other.o\
     module_parameter/read_input_item_output.o\
     module_parameter/read_set_globalv.o\
-    orb_io.o\
     cal_pLpR.o\
-    filename.o\
-    ucell_io.o\
 
 OBJS_IO_LCAO=cal_r_overlap_R.o\
       write_orb_info.o\
@@ -632,7 +634,6 @@ OBJS_IO_LCAO=cal_r_overlap_R.o\
       single_R_io.o\
       module_hs/write_HS_R.o\
       module_dm/write_dmr.o\
-      sparse_matrix.o\
       module_mulliken/output_mulliken.o\
       module_mulliken/output_sk.o\
       module_mulliken/output_dmk.o\

source/source_base/CMakeLists.txt

@@ -55,10 +55,18 @@ add_library(
     parallel_comm.cpp
     parallel_reduce.cpp
     parallel_device.cpp
+    parallel_grid.cpp
     spherical_bessel_transformer.cpp
     cubic_spline.cpp
     parallel_2d.cpp
     projgen.cpp
+    module_out/binstream.cpp
+    module_out/filename.cpp
+    module_out/sparse_matrix.cpp
+    module_out/file_reader.cpp
+    module_out/csr_reader.cpp
+    module_out/read_exit_file.cpp
+    module_out/orb_io.cpp
     module_mixing/mixing_data.cpp
     module_mixing/mixing.cpp
     module_mixing/plain_mixing.cpp

…ce/source_io/module_output/binstream.cpp …rce/source_base/module_out/binstream.cppsource/source_io/module_output/binstream.cpp renamed to source/source_base/module_out/binstream.cpp source/source_io/module_output/binstream.cpp renamed to source/source_base/module_out/binstream.cpp

@@ -1,6 +1,6 @@
 #include <stdio.h>
 #include <string>
-#include "binstream.h"
+#include "source_base/module_out/binstream.h"
 
 namespace
 {

…urce/source_io/module_output/binstream.h source/source_base/module_out/binstream.hsource/source_io/module_output/binstream.h renamed to source/source_base/module_out/binstream.h source/source_io/module_output/binstream.h renamed to source/source_base/module_out/binstream.h

@@ -1,5 +1,5 @@
 #include <set>
-#include "source_io/module_output/filename.h"
+#include "source_base/module_out/filename.h"
 #include "source_base/tool_quit.h"
 
 namespace ModuleIO
@@ -19,7 +19,7 @@ std::string filename_output(
 			const int istep,
             const int iter)
 {
-    // output filename = "{PARAM.globalv.global_out_dir}/property{s}{spin index}
+    // output filename = "{global_out_dir}/property{s}{spin index}
     // {k(optional)}{k-point index}{g(optional)}{geometry index1}{_basis(nao|pw)} 
     // + {".txt"/".dat"}"