Refactor the test directories of 02_NAO_Gamma and 03_NAO_multik, and several related output formats (#6973)

* Refactor: Encapsulate timer functionality in timer_wrapper.h

* Refactor timer code and clean_esolver function

1. Remove #ifdef __MPI from timer code, encapsulate in timer_wrapper.h
2. Move ESolver clean logic to after_all_runners method
3. Replace clean_esolver calls with direct delete p_esolver
4. Remove #ifdef __MPI from delete p_esolver
5. Add Cblacs_exit(1) in after_all_runners for LCAO calculations

* add module_energy directory

* updates

* Rename json_output to module_json and move para_json files, update include paths

* Update CMakeLists.txt: change json_output to module_json

* Fix CMakeLists.txt: update source_io file paths to module_output directory

* Fix csr_reader.h include paths: update to module_output directory

* fix bugs related to libxc

* fix

* fix

* fix several CMakeLists

* update CMake and other test files

* update cmakelists

* fix bugs

* Fix: Correct para_json.cpp path in test CMakeLists.txt

* fix cmake

* fix

* fix

* fix

* fix

* fix

* json!

* small updates of mulliken file format

* update mulliken charge output nspin=1

* Fix: Create symbolic link 'abacus' for test compatibility

* update mulliken output

* update mulliken spin 2

* update mulliken 4

* mulliken for spin 1

* update mulliken and refs

* update mulliken test to match new output format

* update pchg

* update mulliken test

* update directories in 02_NAO_Gamma

* change the directories in 02_NAO_Gamma to make it more clear

* exclude a test

* Update INPUT files: replace tabs with spaces and align columns

* update write_dmk.cpp

* update out_dmr_dmk example in 03

* fix write_dmk_test.cpp

* fix bug

* update write_dmk.cpp

* update write_dmk

* update

* update dmr output format, and change all the output of sparsematrix format

* update dmrs1_nap.csr.ref

* fix reader of dmr matrix

* fix bug, now it works!

* update format

* add spin information in dmr

* update example in 03: scf_in_dmr_GaAs

* add reference data

* update example in 03: scf_in_dmr_Si

* add example: scf_in_dmr_Si_spin2_hasbug

* update example 03: scf_out_dmr_dmk_pot

* change pot from int to vector!

* fix bug about out_pot

* update potential, now it works with 2 parameters

* fix bug, out_chg 2 now supports precision control of chginit.cube file!

* fix tests

* fix example

* fix example reference data

* update tab of write_HS.hpp

* replace tab with blank in write_HS_R.cpp

* fix elf test

* delete 40_NO_ELF test

* update nscf_out_pot test

* update pot in nscf_out_pot

* update md_out_syns test

* update meta-gga output charge density and kinetic energy density

* update test chg tau in metagga

* update examples

* fix tests!

* update 03 CASES_CPU.txt

* fix 03 scf_in_dmr_GaAs test

* update 02 CASES_CPU.txt

* fix 054 test in 01

* fix another test scf_out_elf in 01

* fix ldos test

* fix test in scf_out_chg_tau

* fix two tests in OFDFT

* update deepks examples

* fix the unittest of csr_reader.cpp

* fix sparse_matrix.cpp unit tests

* fix read_input_item_test.cpp

* fix dmk

* comment out read_dmk

* fix rho_io test

* fix bug

* update unitcell, about changing none to user_defined_lattice

* fix scf_in_dmr_GaAs

* temporaly remove csr reader test in Hcontainer, will add back later

---------

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

Author: mohanchen

source/Makefile.Objects

@@ -590,6 +590,7 @@ OBJS_IO=module_parameter/input_conv.o\
     orb_io.o\
     cal_pLpR.o\
     filename.o\
+    ucell_io.o\
 
 OBJS_IO_LCAO=cal_r_overlap_R.o\
       write_orb_info.o\

source/source_cell/read_atom_species.cpp

@@ -162,7 +162,7 @@ bool read_lattice_constant(std::ifstream& ifa,
     // Read in latticies vector
     //===========================
 
-    if(latName=="none")
+    if(latName=="user_defined_lattice")
     {
         // check the existence of keyword "LATTICE_PARAMETERS"
         if (ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa,

source/source_cell/test/unitcell_test.cpp

@@ -172,7 +172,7 @@ using UcellDeathTest = UcellTest;
 TEST_F(UcellTest, Constructor)
 {
     EXPECT_EQ(ucell->Coordinate, "Direct");
-    EXPECT_EQ(ucell->latName, "none");
+    EXPECT_EQ(ucell->latName, "user_defined_lattice");
     EXPECT_DOUBLE_EQ(ucell->lat0, 0.0);
     EXPECT_DOUBLE_EQ(ucell->lat0_angstrom, 0.0);
     EXPECT_EQ(ucell->ntype, 0);
@@ -547,7 +547,7 @@ TEST_F(UcellTest, RemakeCell)
 
 TEST_F(UcellDeathTest, RemakeCellWarnings)
 {
-    std::vector<std::string> latname_in = {"none", "trigonal", "bacm", "triclinic", "arbitrary"};
+    std::vector<std::string> latname_in = {"user_defined_lattice", "trigonal", "bacm", "triclinic", "arbitrary"};
     for (int i = 0; i < latname_in.size(); ++i)
     {
         ucell->latvec.e11 = 10.0;
@@ -563,7 +563,7 @@ TEST_F(UcellDeathTest, RemakeCellWarnings)
         testing::internal::CaptureStdout();
         EXPECT_EXIT(unitcell::remake_cell(ucell->lat), ::testing::ExitedWithCode(1), "");
         std::string output = testing::internal::GetCapturedStdout();
-        if (latname_in[i] == "none")
+        if (latname_in[i] == "user_defined_lattice")
         {
             EXPECT_THAT(output, testing::HasSubstr("to use fixed_ibrav, latname must be provided"));
         }

source/source_cell/unitcell_data.h

@@ -7,7 +7,7 @@
 struct Lattice
 {
     std::string Coordinate = "Direct"; // "Direct" or "Cartesian" or "Cartesian_angstrom"
-    std::string latName = "none";      // Lattice name
+    std::string latName = "user_defined_lattice";  // Lattice name
     double lat0 = 0.0;                 // Lattice constant(bohr)(a.u.)
     double lat0_angstrom = 0.0;        // Lattice constant(angstrom)
     double tpiba = 0.0;                // 2*pi / lat0;
@@ -64,4 +64,4 @@ struct Statistics
     }
 };
 
-#endif
+#endif