Merge pull request #2 from abacusmodeling/master

Merge recent changes on master

ABACUS.develop/examples/H2O-deepks-lcao/INPUT

@@ -27,3 +27,4 @@ mixing_beta             0.4
 out_band                0
 out_descriptor          1 
 lmax_descriptor			2
+newdm		1

ABACUS.develop/examples/H2O-deepks-lcao/STRU

@@ -6,6 +6,10 @@ NUMERICAL_ORBITAL
 H_gga_8au_60Ry_2s1p.orb
 O_gga_7au_60Ry_2s2p1d.orb
 
+NUMERICAL_DESCRIPTOR
+jle.orb
+
+
 LATTICE_CONSTANT
 10
 

ABACUS.develop/source/Makefile.Objects

@@ -81,6 +81,7 @@ memory.o\
 print_info.o\
 mathzone.o\
 mathzone_add1.o\
+math_integral.o\
 integral.o \
 poission.o \
 polint.o \
@@ -153,6 +154,7 @@ LCAO_matrix.o\
 LCAO_nnr.o \
 LCAO_diago.o\
 LCAO_evolve.o\
+LCAO_descriptor.o\
 ylm.o\
 FORCE_STRESS.o\
 FORCE_gamma.o\
@@ -262,7 +264,6 @@ variable_cell.o\
 dftu.o\
 dftu_yukawa.o\
 dftu_relax.o\
-lscc.o\
 
 OBJS_COMMON=atom_spec.o \
 unitcell.o \

ABACUS.develop/source/README

@@ -1,29 +1,5 @@
+
 Currently we are working on optimizing the code structure of ABACUS,
 implementing new functions, and adding more autotests.
 
 -- mohan 2021-02-11
-
-URGENT:
-
-Ask Xiaohui Liu: all functions named with 'after_vc' should be reconstructed.
-The 'FINAL_SCF' global varialble should be removed. 
-(condition: need to reconstruct these codes within a given time)
-
-Ask Xiaohui Liu and Daye Zheng: We need test examples.
-
-Ask Fuxiang He: we need to remove all TDDFT-related global variables
-in global_variable.h, we need TDDFT examples.
-(condition: need to reconstruct these codes within a given time)
-
-Ask Daye Zheng: MD, force, stress modules need reconstruction
-
-NEED TO DO:
-
-Ask Xiaohui: we need to remove DQ and NQX in global_variable.h, 
-but the NQX is computed in ./src_pw/pseudopot_cell_vnl.cpp
-
-Ask Peize: exx_lip.h and related Exx codes
-
-QUESTION:
-
-* in pw_basis.cpp, why ggwfc2=ggwfc if gamma_only is used?

ABACUS.develop/source/input.cpp

@@ -115,6 +115,7 @@ void Input::Default(void)
     atom_file = "";//xiaohui modify 2015-02-01
     kpoint_file = "";//xiaohui modify 2015-02-01
     pseudo_dir = "";
+	read_file_dir = "auto";
     pseudo_type = "auto"; // mohan add 2013-05-20 (xiaohui add 2013-06-23)
 	wannier_card = "";
     latname = "test";
@@ -359,7 +360,7 @@ void Input::Default(void)
 	kernel_type="rpa";
 	eels_method=0;
 	absorption_method=0;
-	system="bulk";
+	system_type="bulk";
 	eta=0.05;
 	domega=0.01;
 	nomega=300;
@@ -456,7 +457,7 @@ void Input::Default(void)
 
 	cell_factor = 1.2; //LiuXh add 20180619
 
-	newDM=1; // Shen Yu add 2019/5/9
+	new_dm=1; // Shen Yu add 2019/5/9
 	mulliken=0;// qi feng add 2019/9/10
 
 //----------------------------------------------------------			//Peize Lin add 2020-04-04
@@ -949,6 +950,10 @@ bool Input::Read(const string &fn)
         {
             read_value(ifs, restart_mode);
         }
+		else if (strcmp("read_file_dir", word) == 0)
+		{
+			read_value(ifs, read_file_dir);
+		}
         else if (strcmp("start_wfc", word) == 0)
         {
             read_value(ifs, start_wfc);
@@ -1404,7 +1409,7 @@ bool Input::Read(const string &fn)
 	    }
 	    else if (strcmp("system", word) == 0)
 	    {
-	        read_value(ifs, system);
+	        read_value(ifs, system_type);
 	    }
 	    else if (strcmp("eta", word) == 0)
 	    {
@@ -1657,7 +1662,7 @@ bool Input::Read(const string &fn)
 		}
 		else if (strcmp("newdm", word) == 0)
 		{
-			read_value(ifs, newDM);
+			read_value(ifs, new_dm);
 		}
 //----------------------------------------------------------------------------------
 //         Xin Qu added on 2020-10-29 for DFT+U
@@ -2040,6 +2045,7 @@ void Input::Bcast()
     Parallel_Common::bcast_double( mixing_gg0 ); //mohan add 2014-09-27
 
     Parallel_Common::bcast_string( restart_mode );
+	Parallel_Common::bcast_string( read_file_dir);
     Parallel_Common::bcast_string( start_wfc );
 	Parallel_Common::bcast_int( mem_saver );
 	Parallel_Common::bcast_int( printe );
@@ -2161,7 +2167,7 @@ void Input::Bcast()
 	Parallel_Common::bcast_string( kernel_type );
 	Parallel_Common::bcast_int( eels_method );
 	Parallel_Common::bcast_int( absorption_method );
-    Parallel_Common::bcast_string( system );
+    Parallel_Common::bcast_string( system_type );
     Parallel_Common::bcast_double( eta );
     Parallel_Common::bcast_double( domega );
     Parallel_Common::bcast_int( nomega );
@@ -2259,7 +2265,7 @@ void Input::Bcast()
 
 		//Parallel_Common::bcast_int( epsilon0_choice );
     Parallel_Common::bcast_double( cell_factor); //LiuXh add 20180619
-    Parallel_Common::bcast_int( newDM ); // Shen Yu add 2019/5/9
+    Parallel_Common::bcast_int( new_dm ); // Shen Yu add 2019/5/9
     Parallel_Common::bcast_bool( restart_save ); // Peize Lin add 2020.04.04
     Parallel_Common::bcast_bool( restart_load ); // Peize Lin add 2020.04.04
 
@@ -2646,7 +2652,8 @@ void Input::Check(void)
 			else if (ks_solver == "hpseps")
 			{
 #ifdef __MPI
-				ofs_warning << "It's a good choice to use hpseps!" << endl;
+				ofs_warning << "It's not a good choice to use hpseps!" << endl;
+				if(gamma_only) WARNING_QUIT("Input","hpseps can not be used for gamma_only.");
 #else
 				WARNING_QUIT("Input","hpseps can not be used for series version.");
 #endif
@@ -2814,7 +2821,7 @@ void Input::Check(void)
 	// pengfei 2016-12-14
 	if(spectral_type!="None")
 	{
-		if( system!="bulk" && system!="surface")
+		if( system_type!="bulk" && system_type!="surface")
 		{
 			WARNING_QUIT("Input","system must be bulk or surface");
 		}
@@ -2936,6 +2943,20 @@ void Input::Check(void)
 			}
 		}
 	}
+
+	const string ss = "test -d " + read_file_dir;
+	if(read_file_dir=="auto")
+	{
+		global_readin_dir = global_out_dir;
+	}
+	else if( system( ss.c_str() ))
+	{
+		WARNING_QUIT("Input","please set right files directory for reading in.");
+	}
+	else
+	{
+		global_readin_dir = read_file_dir + '/';
+	}
 
     return;
 }

ABACUS.develop/source/input.h

@@ -29,6 +29,7 @@ class Input
     string suffix;			// suffix of out put dir
     string atom_file;		// file contains atomic positions -- xiaohui modify 2015-02-01
     string pseudo_dir;      // directory of pseudopotential
+	string read_file_dir;   // directory of files for reading
     string pseudo_type;     // the type of pseudopotential, mohan add 2013-05-20, ABACUS supports
 			    			// UPF format (default) and vwr format. (xiaohui add 2013-06-23)
     string kpoint_file;		// file contains k-points -- xiaohui modify 2015-02-01
@@ -296,7 +297,7 @@ class Input
 	int      absorption_method;      // 0: vasp's method  1: pwscf's method
 	//int		 epsilon_choice;         // 0: hilbert_transform method; 1: standard method
 	string   kernel_type;           // the kernel type: rpa, tdlda ...
-	string system;                 // bulk or surface
+	string system_type;                 // bulk or surface
 	double  eta;                   // unit(Ry)
 	double  domega;                // unit(Ry)
 	int     nomega;
@@ -398,7 +399,7 @@ class Input
 //  2: use new DM algorithm and only show key debug information
 //  3: use new DM algorithm and show all detail debug information
 //==========================================================
-    int newDM;
+    int new_dm;
 
 //==========================================================
 //    DFT+U       Xin Qu added on 2020-10-29

ABACUS.develop/source/input_conv.cpp

@@ -274,7 +274,7 @@ void Input_Conv::Convert(void)
 		}
 		//chi0_hilbert.epsilon = INPUT.epsilon;
 		chi0_hilbert.kernel_type = INPUT.kernel_type;
-		chi0_hilbert.system = INPUT.system;
+		chi0_hilbert.system = INPUT.system_type;
 		chi0_hilbert.eta = INPUT.eta;
 		chi0_hilbert.domega = INPUT.domega;
 		chi0_hilbert.nomega = INPUT.nomega;
@@ -314,7 +314,7 @@ void Input_Conv::Convert(void)
 	{
 		//chi0_standard.epsilon = INPUT.epsilon;
 		chi0_standard.epsilon = true;
-		chi0_standard.system = INPUT.system;
+		chi0_standard.system = INPUT.system_type;
 		chi0_standard.eta = INPUT.eta;
 		chi0_standard.domega = INPUT.domega;
 		chi0_standard.nomega = INPUT.nomega;
@@ -397,6 +397,8 @@ void Input_Conv::Convert(void)
 #endif
 	}
 	else{
+		delete[] soc.m_loc;
+		soc.m_loc = new Vector3<double> [INPUT.ntype];
 		LSPINORB = false;
 		NONCOLIN = false;
 		DOMAG = false;
@@ -578,7 +580,7 @@ void Input_Conv::Convert(void)
 
     ppcell.cell_factor = INPUT.cell_factor; //LiuXh add 20180619
 
-    NEW_DM=INPUT.newDM;  // Shen Yu add 2019/5/9
+//    NEW_DM=INPUT.new_dm;  // Shen Yu add 2019/5/9
 
 //----------------------------------------------------------
 // main parameters / electrons / spin ( 2/16 )
@@ -625,10 +627,11 @@ void Input_Conv::Convert(void)
 //----------------------------------------------------------
 // About LCAO
 //----------------------------------------------------------
-	ORB.ecutwfc = INPUT.lcao_ecut;
-	ORB.dk = INPUT.lcao_dk;
-	ORB.dR = INPUT.lcao_dr;
-	ORB.Rmax = INPUT.lcao_rmax; 
+// mohan add 2021-04-16
+//	ORB.ecutwfc = INPUT.lcao_ecut;
+//	ORB.dk = INPUT.lcao_dk;
+//	ORB.dR = INPUT.lcao_dr;
+//	ORB.Rmax = INPUT.lcao_rmax; 
 
 	// mohan add 2021-02-16
 	berryphase::berry_phase_flag = INPUT.berry_phase;

ABACUS.develop/source/run_lcao.cpp

@@ -45,7 +45,15 @@ void Run_lcao::lcao_line(void)
 
     // * reading the localized orbitals/projectors 
 	// * construct the interpolation tables.
-	hm.orb_con.set_orb_tables();
+	hm.orb_con.set_orb_tables(
+		UOT, 
+		ORB,
+		INPUT.lcao_ecut,
+		INPUT.lcao_dk,
+		INPUT.lcao_dr,
+		INPUT.lcao_rmax, 
+		ucell.lat0, 
+		Exx_Abfs::Lmax);
 
 	// * allocate H and S matrices according to computational resources
 	// * set the 'trace' between local H/S and global H/S

ABACUS.develop/source/src_external/GRID_api/Makefile

@@ -0,0 +1,63 @@
+# This is the Makefile of ABACUS-ORB API
+
+include Makefile.system
+include Makefile.Objects
+
+VPATH=../../src_global\
+:../../src_lcao\
+:./\
+
+#==========================
+# Define HONG
+#==========================
+HONG= -DMETIS -DMKL_ILP64
+
+#==========================
+# OPTIMIZE OPTIONS
+#==========================
+OPTS_GDB = -g -W
+
+#==========================
+# OBJECTS NEEDED
+#==========================
+#FP_OBJS_0=$(OBJS_ORBITAL)\
+#$(OBJS_GLOBAL)\
+#main.o\
+
+FP_OBJS_0=main.o\
+$(OBJS_TRY)\
+$(OBJS_ORBITAL)\
+
+FP_OBJS=$(patsubst %.o, ${OBJ_DIR}/%.o, ${FP_OBJS_0})
+PDIAG_OBJS=$(patsubst %.o, ${OBJ_DIR}/%.o, ${OBJS_PDIAG})
+PDIAG_MR=$(patsubst %.o, ${OBJ_DIR}/%.o, ${PDIAG_MR_0})
+
+#==========================
+# MAKING OPTIONS
+#==========================
+fp_mpi : 
+	@ make init
+	@ make -j $(NP) serial2 
+
+init :
+	@ if [ ! -d $(OBJ_DIR) ]; then mkdir $(OBJ_DIR); fi
+	@ if [ ! -d $(OBJ_DIR)/README ]; then echo "This directory contains all of the .o files" > $(OBJ_DIR)/README; fi
+	@ if [ ! -d ../bin ]; then mkdir ../bin; fi
+
+serial : ${FP_OBJS} ${HEADERS} 
+	${CPLUSPLUS} ${OPTS} $(FP_OBJS) ${LIBS} -o ${VERSION}.x 
+
+serial2 : ${FP_OBJS} 
+	${CPLUSPLUS} ${OPTS} $(FP_OBJS) ${LIBS} -o ${VERSION}.x 
+
+#==========================
+# rules
+#==========================
+${OBJ_DIR}/%.o:%.cpp
+	${CPLUSPLUS_MPI} ${OPTS} ${OPTS_MPI} -c ${HONG} $< -o $@
+${OBJ_DIR}/%.o:%.f
+	${FORTRAN} -c ${HONG} $< -o $@	 
+
+.PHONY:clean
+clean:
+	@ if [ -d $(OBJ_DIR) ]; then rm -rf $(OBJ_DIR); fi

ABACUS.develop/source/src_external/GRID_api/Makefile.Objects

@@ -0,0 +1,26 @@
+#
+# This is a test makefile for Electronic-structure
+#
+# This particular makefile defines all the executables and objects
+# files needed, who they depend on, and the compilation defaults.#
+# The file makefile.local is included below.
+# That file defines the actual commands to use to run the C++
+# compiler, library options and directories, etc., all of which are
+# machine specific and depend on the local installation.  Hence the name.
+#
+
+VERSION= ABACUS-GRID
+HEADERS= *.h
+
+OBJS_TRY=math_integral.o\
+complexarray.o\
+complexmatrix.o\
+matrix.o\
+
+OBJS_GRID=grid_base.o\
+grid_base_beta.o\
+grid_bigcell.o\
+grid_meshball.o\
+grid_meshk.o\
+grid_technique.o\
+

ABACUS.develop/source/src_external/GRID_api/Makefile.system

@@ -0,0 +1,14 @@
+include Makefile.vars
+
+#==========================
+# LIBS and INCLUDES
+#==========================
+LIBS = -lifcore -lm -lpthread 
+
+INCLUDES = -I. -Icommands 
+
+#==========================
+# OPTIMIZE OPTIONS
+#==========================
+OPTS     = ${INCLUDES} -Ofast -std=c++11 -simd -march=native -m64 -Werror -Wall -pedantic -g
+#OPTS_MPI = -cxx=${CPLUSPLUS}