Merge branch 'refactor' of https://github.com/ErjieWu/abacus-develop into refactor

Author: ErjieWu

CMakeLists.txt

@@ -114,11 +114,13 @@ You can install Git first and reinstall abacus.")
   endif()
 endif()
 
+# Serial version of ABACUS will not use ELPA
 if(NOT ENABLE_MPI)
   set(USE_ELPA OFF)
   set(ENABLE_DEEPKS OFF)
 endif()
 
+# Different exe files of ABACUS
 if(ENABLE_LCAO AND ENABLE_MPI)
   set(ABACUS_BIN_NAME abacus)
 elseif(NOT ENABLE_LCAO AND ENABLE_MPI)
@@ -129,6 +131,7 @@ elseif(ENABLE_LCAO AND NOT ENABLE_MPI)
   set(ABACUS_BIN_NAME abacus_serial)
 endif()
 
+# Use DSP hardware
 if (USE_DSP)
   set(USE_ELPA OFF)
   set(ENABLE_LCAO OFF)
@@ -212,7 +215,7 @@ if(CMAKE_CXX_COMPILER_ID MATCHES Intel)
   add_compile_options(-fp-model=strict)
   set(USE_ABACUS_LIBM OFF) # Force turn off USE_ABACUS_LIBM on Intel Compiler
   set(CMAKE_CXX_FLAGS
-      "${CMAKE_CXX_FLAGS} -Wno-write-strings -Wno-tautological-constant-compare"
+      "${CMAKE_CXX_FLAGS} -Wno-write-strings "
   )
 endif()
 

docs/advanced/input_files/input-main.md

@@ -1705,7 +1705,8 @@ These variables are used to control the output of properties.
 - **Description**: Whether to output the density of states (DOS). For more information, refer to the [dos.md](../elec_properties/dos.md).
   - 0: no output
   - 1: output the density of states (DOS)
-  - 2: (lcao-only) output the density of states (DOS) and the projected density of states (PDOS)
+  - 2: (LCAO) output the density of states (DOS) and the projected density of states (PDOS)
+  - 3: output the Fermi surface file (fermi.bxsf) in BXSF format that can be visualized by XCrySDen 
 - **Default**: 0
 
 ### out_ldos

source/Makefile.Objects

@@ -259,6 +259,7 @@ OBJS_ESOLVER=esolver.o\
     esolver_of_tool.o\
     esolver_of_interface.o\
     pw_others.o\
+    pw_setup.o\
 
 OBJS_ESOLVER_LCAO=esolver_ks_lcao.o\
       esolver_ks_lcao_tddft.o\
@@ -495,13 +496,13 @@ OBJS_IO=input_conv.o\
     bessel_basis.o\
     cal_test.o\
     write_dos_pw.o\
+    nscf_fermi_surf.o\
     nscf_band.o\
     cal_dos.o\
     cal_pdos_gamma.o\
     cal_pdos_multik.o\
     cal_ldos.o\
     cif_io.o\
-    dos_nao.o\
     numerical_descriptor.o\
     numerical_basis.o\
     numerical_basis_jyjy.o\
@@ -564,7 +565,6 @@ OBJS_IO_LCAO=cal_r_overlap_R.o\
       write_dos_lcao.o\
       write_proj_band_lcao.o\
       write_istate_info.o\
-      nscf_fermi_surf.o\
       get_pchg_lcao.o\
       get_wf_lcao.o\
       io_dmk.o\

source/module_base/parallel_comm.h

@@ -13,30 +13,33 @@ extern MPI_Comm DIAG_WORLD; // mohan add 2012-01-13
 
 class MPICommGroup
 {
-public:
-    MPICommGroup(MPI_Comm parent_comm);
-    ~MPICommGroup();
-    void divide_group_comm(const int& ngroup, const bool assert_even = true);
-public:
-  bool is_even = false; ///< whether the group is even
-
-  MPI_Comm parent_comm = MPI_COMM_NULL; ///< parent communicator
-  int gsize = 0;                        ///< size of parent communicator
-  int grank = 0;                        ///< rank of parent communicator
-
-  MPI_Comm group_comm = MPI_COMM_NULL; ///< group communicator
-  int ngroups = 0;                     ///< number of groups
-  int nprocs_in_group = 0;             ///<  number of processes in the group
-  int my_group = 0;                    ///< the group index
-  int rank_in_group = 0;               ///< the rank in the group
-
-  MPI_Comm inter_comm = MPI_COMM_NULL; ///< inter communicator
-  bool has_inter_comm = false;         ///< whether has inter communicator
-  int& nprocs_in_inter = ngroups;      ///< number of processes in the inter communicator
-  int& my_inter = rank_in_group;  ///< the rank in the inter communicator
-  int& rank_in_inter = my_group;  ///< the inter group index
+
+	public:
+
+		MPICommGroup(MPI_Comm parent_comm);
+		~MPICommGroup();
+
+		void divide_group_comm(const int& ngroup, const bool assert_even = true);
+
+		bool is_even = false; ///< whether the group is even
+
+		MPI_Comm parent_comm = MPI_COMM_NULL; ///< parent communicator
+		int gsize = 0;                        ///< size of parent communicator
+		int grank = 0;                        ///< rank of parent communicator
+
+		MPI_Comm group_comm = MPI_COMM_NULL; ///< group communicator
+		int ngroups = 0;                     ///< number of groups
+		int nprocs_in_group = 0;             ///<  number of processes in the group
+		int my_group = 0;                    ///< the group index
+		int rank_in_group = 0;               ///< the rank in the group
+
+		MPI_Comm inter_comm = MPI_COMM_NULL; ///< inter communicator
+		bool has_inter_comm = false;         ///< whether has inter communicator
+		int& nprocs_in_inter = ngroups;      ///< number of processes in the inter communicator
+		int& my_inter = rank_in_group;  ///< the rank in the inter communicator
+		int& rank_in_inter = my_group;  ///< the inter group index
 };
 
 #endif
 
-#endif // PARALLEL_COMM_H
+#endif // PARALLEL_COMM_H

source/module_cell/bcast_cell.cpp

@@ -85,7 +85,7 @@ namespace unitcell
     {
     #ifdef __MPI
         MPI_Barrier(MPI_COMM_WORLD);
-        Parallel_Common::bcast_double(magnet.start_magnetization, ntype);
+        Parallel_Common::bcast_double(magnet.start_mag, ntype);
         if (PARAM.inp.nspin == 4) 
         {
             Parallel_Common::bcast_double(magnet.ux_[0]);
@@ -118,4 +118,4 @@ namespace unitcell
         return;
     #endif
     }
-}
+}

source/module_cell/module_neighbor/sltk_atom_arrange.cpp

@@ -37,7 +37,7 @@ double atom_arrange::set_sr_NL(std::ofstream& ofs_in,
 
     if (output_level != "m") // xiaohui add 'output_level', 2015-09-16
     {
-        ofs_in << "\n\n\n\n";
+        ofs_in << "\n\n";
         ofs_in << " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" << std::endl;
         ofs_in << " |                                                                    |" << std::endl;
         ofs_in << " | Search adjacent atoms:                                             |" << std::endl;
@@ -47,7 +47,7 @@ double atom_arrange::set_sr_NL(std::ofstream& ofs_in,
         ofs_in << " | for each atom.                                                     |" << std::endl;
         ofs_in << " |                                                                    |" << std::endl;
         ofs_in << " <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<" << std::endl;
-        ofs_in << "\n\n\n\n";
+        ofs_in << "\n\n";
 
         ofs_in << "\n SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS" << std::endl;
         ofs_in << std::setprecision(3);

source/module_cell/module_neighbor/test/prepare_unitcell.h

@@ -77,13 +77,13 @@ class UcellTestPrepare
 				this->init_vel,
 				this->fixed_axes);
 
-		delete[] ucell->magnet.start_magnetization; //mag set here
+		delete[] ucell->magnet.start_mag; //mag set here
 		ucell->atom_label.resize(ucell->ntype);
 		ucell->atom_mass.resize(ucell->ntype);
 		ucell->pseudo_fn.resize(ucell->ntype);
 		ucell->pseudo_type.resize(ucell->ntype);
 		ucell->orbital_fn.resize(ucell->ntype);
-		ucell->magnet.start_magnetization = new double[ucell->ntype]; //mag set here
+		ucell->magnet.start_mag = new double[ucell->ntype]; //mag set here
 		ucell->magnet.ux_[0] = 0.0; // ux_ set here
 		ucell->magnet.ux_[1] = 0.0;
 		ucell->magnet.ux_[2] = 0.0;
@@ -94,7 +94,7 @@ class UcellTestPrepare
 			ucell->pseudo_fn[it] = this->pp_files[it];
 			ucell->pseudo_type[it] = this->pp_types[it];
 			ucell->orbital_fn[it] = this->orb_files[it];
-			ucell->magnet.start_magnetization[it] = 0.0; //mag set here
+			ucell->magnet.start_mag[it] = 0.0; //mag set here
 		}
 		//lattice info
 		ucell->lat0 = this->lat0;

source/module_cell/module_neighbor/test/sltk_atom_arrange_test.cpp

@@ -26,13 +26,13 @@ LCAO_Orbitals::~LCAO_Orbitals()
 #endif
 Magnetism::Magnetism()
 {
-    this->tot_magnetization = 0.0;
-    this->abs_magnetization = 0.0;
-    this->start_magnetization = nullptr;
+    this->tot_mag = 0.0;
+    this->abs_mag = 0.0;
+    this->start_mag = nullptr;
 }
 Magnetism::~Magnetism()
 {
-    delete[] this->start_magnetization;
+    delete[] this->start_mag;
 }
 
 /************************************************
@@ -152,4 +152,4 @@ TEST_F(SltkAtomArrangeTest, Filteradjs)
     is_adjs[0] = true;
     filter_adjs(is_adjs, adjs);
     EXPECT_EQ(adjs.adj_num, 0);
-}
+}

source/module_cell/module_neighbor/test/sltk_grid_test.cpp

@@ -23,13 +23,13 @@ LCAO_Orbitals::~LCAO_Orbitals()
 #endif
 Magnetism::Magnetism()
 {
-    this->tot_magnetization = 0.0;
-    this->abs_magnetization = 0.0;
-    this->start_magnetization = nullptr;
+    this->tot_mag = 0.0;
+    this->abs_mag = 0.0;
+    this->start_mag = nullptr;
 }
 Magnetism::~Magnetism()
 {
-    delete[] this->start_magnetization;
+    delete[] this->start_mag;
 }
 
 /************************************************

source/module_cell/print_cell.cpp

@@ -104,7 +104,7 @@ namespace unitcell
         for(int it = 0; it < ucell.ntype; it++)
         {
             str += "\n" + ucell.atoms[it].label + " #label\n";
-            str += FmtCore::format("%-8.4f #magnetism\n", ucell.magnet.start_magnetization[it]);
+            str += FmtCore::format("%-8.4f #magnetism\n", ucell.magnet.start_mag[it]);
             str += FmtCore::format("%d #number of atoms\n", atoms[it].na);
             for(int ia = 0; ia < atoms[it].na; ia++)
             {