Merge branch 'develop' into ccache-cuda

Author: dzzz2001

.github/workflows/test.yml

@@ -48,9 +48,16 @@ jobs:
         run: |
           cmake --build build -j8
           cmake --install build
-      - name: Test
+      - name: Unit Test
         env:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
-          cmake --build build --target test ARGS="-V --timeout 1700"
+          cmake --build build --target test ARGS="-V --timeout 1700 -E integrated_test"
+      - name: Integrated Test
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R integrated_test"
+

CMakeLists.txt

@@ -798,4 +798,4 @@ install(PROGRAMS ${ABACUS_BIN_PATH}
 
 if(ENABLE_COVERAGE)
   coverage_evaluate()
-endif()
+endif()

docs/advanced/input_files/input-main.md

@@ -1645,10 +1645,13 @@ These variables are used to control the output of properties.
 ### out_dm
 
 - **Type**: Boolean
-- **Availability**: Numerical atomic orbital basis (gamma-only algorithm)
+- **Availability**: Numerical atomic orbital basis
 - **Description**: Whether to output the density matrix of localized orbitals into files in the folder `OUT.${suffix}`. The files are named as:
-  - nspin = 1: SPIN1_DM;
-  - nspin = 2: SPIN1_DM, and SPIN2_DM.
+  - For gamma only case:
+    - nspin = 1: SPIN1_DM;
+    - nspin = 2: SPIN1_DM, and SPIN2_DM.
+  - For multi-k points case:
+    - SPIN\*_K\*_DM, where \* stands for index of spin and kpoints;
 - **Default**: False
 
 ### out_dm1

source/module_basis/module_ao/ORB_gaunt_table.cpp

@@ -162,16 +162,6 @@ int ORB_gaunt_table::get_lm_index(
 }
 
 
-/**********************//**
-  * Rasch and Yu's Method
-  ***********************/
-///total pointers
-//int ORB_gaunt_table::P_EL(const int& L)
-//{
-//	return (L+1) * (L+2) * (L+3) * (L+4) / 24;
-//}
-
-
 ///effective pointers
 int ORB_gaunt_table::EP_EL(const int& L)
 {
@@ -201,13 +191,7 @@ void ORB_gaunt_table::init_Gaunt_CH(const int& Lmax)
 	ModuleBase::TITLE("ORB_gaunt_table","init_Gaunt_CH");
 	ModuleBase::timer::tick("ORB_gaunt_table","init_Gaunt_CH");
 
-//	assert(Lmax <= 6);			// Peize Lin delete 2016-08-26. why?
-
 	int L = 2*Lmax + 1;
-	
-	//int Np = this->P_EL(L);
-//	assert(Np <= 5000);			// Peize Lin delete 2016-08-26. why?
-
 	int Eff_Np = this->EP_EL(L);
 
 	ModuleBase::Memory::record("ORB::Gaunt_CH", sizeof(double) * Eff_Np * 30);
@@ -228,9 +212,6 @@ void ORB_gaunt_table::init_Gaunt_CH(const int& Lmax)
 					if((l_sum % 2 == 0) && (l2 + l3 >= l1))
 					{
 						int uplmt_m2 = l1 - m3 > l2 ? l2 : l1 - m3;
-						//int dim = l2 + uplmt_m2 + 1;
-						
-//						assert(dim <= 30);			// Peize Lin delete 2016-08-26. why?
 
 						int ic2 = 0;
 						for(int m2 = -l2; m2 <= uplmt_m2; m2++)
@@ -239,9 +220,6 @@ void ORB_gaunt_table::init_Gaunt_CH(const int& Lmax)
 							int m1 = -m2 - m3;
 							assert(std::abs(m1) <= l1);
 
-							// Peize Lin delete assert 2016-08-26
-//							assert(ic1 < 5000);
-//							assert(ic2 < 30);
 							Gaunt_CH[ic1][ic2] = Calc_Gaunt_CH(l1, m1, l2, m2, l3, m3);
 							ic2++;
 						}
@@ -269,7 +247,6 @@ double ORB_gaunt_table::Calc_Gaunt_CH
 	const int& m3
 )
 {
-//	ModuleBase::TITLE("ORB_gaunt_table","Calc_Gaunt_CH");
 	ModuleBase::timer::tick("ORB_gaunt_table","Calc_Gaunt_CH");
 
 	double fac = sqrt((2*l1+1) * (2*l2+1) * (2*l3+1) / ModuleBase::FOUR_PI);
@@ -281,7 +258,8 @@ double ORB_gaunt_table::Calc_Gaunt_CH
 
 	double aux1 = sqrt(Fact(l1+m1) * Fact(l1-m1) * Fact(l2+m2) * Fact(l2-m2) * Fact(l3+m3) * Fact(l3-m3));
 
-	int kmin, kmax;
+	int kmin = 0;
+    int kmax = 0;
 
 	kmin = (l2-l3-m1) > (l1-l3+m2) ? (l2-l3-m1) : (l1-l3+m2);
 	kmin = kmin > 0 ? kmin : 0;
@@ -324,16 +302,14 @@ double ORB_gaunt_table::Get_Gaunt_CH
 
 	if( (m1 + m2 + m3) != 0) return 0.0;
 
-	int L1, M1, L2, M2, L3, M3;
-	
-	L1 = l1;
-	M1 = m1;
-	L2 = l2;
-	M2 = m2;
+    int L1 = l1;
+	int M1 = m1;
+	int L2 = l2;
+    int M2 = m2;
 	Swap(L1, M1, L2, M2);
 
-	L3 = l3;
-	M3 = m3;
+	int L3 = l3;
+	int M3 = m3;
 	Swap(L1, M1, L3, M3);
 
 	Swap(L2, M2, L3, M3);
@@ -345,19 +321,17 @@ double ORB_gaunt_table::Get_Gaunt_CH
 		M3 = -M3;
 	}
 
-	/*	
-	if(l1 == 2 && m1 == -1 && l2 == 2 && m2 == 2 && l3 == 2 && m3 == -1)
-	{
-		std::cout << L1 << " " << L2 << " " << L3 << std::endl;
-		std::cout << M1 << " " << M2 << " " << M3 <<std::endl;
-	}
-	*/
-	
 	int ic1 = index_func(L1, L2, L3, M3);
 	int ic2 = M2 + L2;
 
-	try{ return Gaunt_CH.at(ic1).at(ic2); }			// Peize Lin add 2016-08-26
-	catch( std::out_of_range ){ return 0; }
+	try
+	{ 
+		return Gaunt_CH.at(ic1).at(ic2); 
+	} // Peize Lin add 2016-08-26
+	catch( std::out_of_range )
+	{ 
+		return 0; 
+	}
 }
 
 
@@ -374,8 +348,6 @@ double ORB_gaunt_table::Get_Gaunt_SH
 	const int& mm3
 )
 {
-//	ModuleBase::TITLE("ORB_gaunt_table","Get_Gaunt_SH");
-	ModuleBase::timer::tick("ORB_gaunt_table","Get_Gaunt_SH");
 
 	//Tranform M index
 	int m1 = Index_M(mm1);
@@ -442,7 +414,6 @@ double ORB_gaunt_table::Get_Gaunt_SH
 		else return 0.0;
 	}
 
-	ModuleBase::timer::tick("ORB_gaunt_table","Get_Gaunt_SH");
 }
 
 

source/module_cell/print_cell.cpp

@@ -18,33 +18,61 @@ namespace unitcell
         // assert (direct || Coordinate == "Cartesian" || Coordinate == "Cartesian_angstrom"); // this line causes abort in unittest ReadAtomPositionsCACXY.
         // previously there are two if-statements, the first is `if(Coordinate == "Direct")` and the second is `if(Coordinate == "Cartesian" || Coordiante == "Cartesian_angstrom")`
         // however the Coordinate can also be value among Cartesian_angstrom_center_xy, Cartesian_angstrom_center_xz, Cartesian_angstrom_center_yz and Cartesian_angstrom_center_xyz
+
         // if Coordinate has value one of them, this print_tau will not print anything.
         std::regex pattern("Direct|Cartesian(_angstrom)?(_center_(xy|xz|yz|xyz))?");
         assert(std::regex_search(Coordinate, pattern));
         bool direct = (Coordinate == "Direct");
+
+        //----------------------
+        // print atom positions
+        //----------------------
         std::string table;
-        table += direct? "DIRECT COORDINATES\n": FmtCore::format(" CARTESIAN COORDINATES ( UNIT = %15.8f Bohr ).\n", lat0);
-        table += FmtCore::format("%8s%10s%10s%10s%8s%8s%8s%8s\n", "atom", "x", "y", "z", "mag", "vx", "vy", "vz");
+        table += direct? " DIRECT COORDINATES\n": FmtCore::format(" CARTESIAN COORDINATES ( UNIT = %15.8f Bohr ).\n", lat0);
+        table += FmtCore::format("%5s%19s%19s%19s%8s\n", "atom", "x", "y", "z", "mag");
         for(int it = 0; it < ntype; it++)
         {
             for (int ia = 0; ia < atoms[it].na; ia++)
             {
                 const double& x = direct? atoms[it].taud[ia].x: atoms[it].tau[ia].x;
                 const double& y = direct? atoms[it].taud[ia].y: atoms[it].tau[ia].y;
                 const double& z = direct? atoms[it].taud[ia].z: atoms[it].tau[ia].z;
-                table += FmtCore::format("%8s%10.3f%10.3f%10.3f%8.3f%8.3f%8.3f%8.3f\n", 
+                table += FmtCore::format("%5s%19.12f%19.12f%19.12f%8.4f\n", 
                                         atoms[it].label, 
                                         x, 
                                         y, 
                                         z, 
-                                        atoms[it].mag[ia], 
-                                        atoms[it].vel[ia].x, 
-                                        atoms[it].vel[ia].y, 
-                                        atoms[it].vel[ia].z);
+                                        atoms[it].mag[ia]); 
             }
         }
         table += "\n";
-        ofs << table << std::endl;
+        ofs << table; 
+
+
+        // print velocities
+        ofs << " ATOMIC VELOCITIES" << std::endl;
+        ofs << std::setprecision(12);
+        ofs << std::setw(5) << "atom" 
+            << std::setw(19) << "vx" 
+            << std::setw(19) << "vy" 
+            << std::setw(19) << "vz"
+            << std::endl;
+ 
+		for(int it = 0; it < ntype; it++)
+		{
+			for (int ia = 0; ia < atoms[it].na; ia++)
+			{
+                ofs << std::setw(5) << atoms[it].label;
+                ofs << " " << std::setw(18) << atoms[it].vel[ia].x;
+                ofs << " " << std::setw(18) << atoms[it].vel[ia].y;
+                ofs << " " << std::setw(18) << atoms[it].vel[ia].z;
+                ofs << std::endl;
+			}
+		}
+        ofs << std::endl;
+        ofs << std::setprecision(6); // return to 6, as original
+
+
         return;
     }
 

source/module_cell/test/unitcell_test.cpp

@@ -1022,11 +1022,10 @@ TEST_F(UcellTest, PrintTauDirect)
     ifs.open("print_tau_direct");
     std::string str((std::istreambuf_iterator<char>(ifs)), std::istreambuf_iterator<char>());
     EXPECT_THAT(str, testing::HasSubstr("DIRECT COORDINATES"));
-    EXPECT_THAT(str, testing::HasSubstr("       C     0.100     0.100     0.100   0.000   0.100   0.100   0.100"));
-    EXPECT_THAT(str, testing::HasSubstr("       H     0.150     0.150     0.150   0.000   0.100   0.100   0.100"));
+    EXPECT_THAT(str, testing::HasSubstr("    C     0.100000000000     0.100000000000     0.100000000000  0.0000"));
+    EXPECT_THAT(str, testing::HasSubstr("    H     0.150000000000     0.150000000000     0.150000000000  0.0000")); 
     ifs.close();
 
-    // remove the file
     remove("print_tau_direct");
 }
 
@@ -1047,8 +1046,8 @@ TEST_F(UcellTest, PrintTauCartesian)
     ifs.open("print_tau_Cartesian");
     std::string str((std::istreambuf_iterator<char>(ifs)), std::istreambuf_iterator<char>());
     EXPECT_THAT(str, testing::HasSubstr("CARTESIAN COORDINATES"));
-    EXPECT_THAT(str, testing::HasSubstr("       C     1.000     1.000     1.000   0.000   0.000   0.000   0.000"));
-    EXPECT_THAT(str, testing::HasSubstr("       H     1.500     1.500     1.500   0.000   0.000   0.000   0.000"));
+    EXPECT_THAT(str, testing::HasSubstr("    C     1.000000000000     1.000000000000     1.000000000000  0.0000"));
+    EXPECT_THAT(str, testing::HasSubstr("    H     1.500000000000     1.500000000000     1.500000000000  0.0000"));
     ifs.close();
 
     // remove the file

source/module_cell/test/unitcell_test_readpp.cpp

@@ -173,11 +173,8 @@ TEST_F(UcellDeathTest, ReadCellPPWarning4) {
     testing::internal::CaptureStdout();
     EXPECT_NO_THROW(elecstate::read_cell_pseudopots(pp_dir, ofs, *ucell));
     output = testing::internal::GetCapturedStdout();
-    EXPECT_THAT(output, testing::HasSubstr("dft_functional readin is: LDA"));
-    EXPECT_THAT(output,
-                testing::HasSubstr("dft_functional in pseudopot file is: PBE"));
-    EXPECT_THAT(output,
-                testing::HasSubstr("Please make sure this is what you need"));
+    EXPECT_THAT(output, testing::HasSubstr("DFT FUNC. (PSEUDO)   : PBE"));
+    EXPECT_THAT(output, testing::HasSubstr("DFT FUNC. (SET TO)   : LDA"));
 }
 
 TEST_F(UcellDeathTest, ReadCellPPWarning5) {

source/module_elecstate/read_pseudo.cpp

@@ -332,17 +332,19 @@ void read_cell_pseudopots(const std::string& pp_dir, std::ofstream& log, UnitCel
                 transform(xc_func1.begin(), xc_func1.end(), xc_func1.begin(), (::toupper));
                 if (xc_func1 != ucell.atoms[i].ncpp.xc_func)
                 {
-                    std::cout << " dft_functional readin is: " << PARAM.inp.dft_functional << std::endl;
-                    std::cout << " dft_functional in pseudopot file is: " << ucell.atoms[i].ncpp.xc_func << std::endl;
-                    std::cout << " Please make sure this is what you need" << std::endl;
-                    GlobalV::ofs_warning << " dft_functional readin is: " << PARAM.inp.dft_functional << std::endl;
-                    GlobalV::ofs_warning << " dft_functional in pseudopot file is: " << ucell.atoms[i].ncpp.xc_func
-                                         << std::endl;
-                    GlobalV::ofs_warning << " Please make sure this is what you need" << std::endl;
+                    std::cout << " NAME OF ELEMENT      : " << ucell.atoms[i].label << std::endl;
+                    std::cout << " DFT FUNC. (PSEUDO)   : " << ucell.atoms[i].ncpp.xc_func << std::endl;
+                    std::cout << " DFT FUNC. (SET TO)   : " << xc_func1 << std::endl; 
+                    std::cout << " MAKE SURE THIS DFT FUNCTIONAL IS WHAT YOU NEED" << std::endl;
+
+
+                    GlobalV::ofs_warning << " NAME OF ELEMENT      : " << ucell.atoms[i].label << std::endl;
+                    GlobalV::ofs_warning << " DFT FUNC. (PSEUDO)   : " << ucell.atoms[i].ncpp.xc_func << std::endl;
+                    GlobalV::ofs_warning << " DFT FUNC. (SET TO)   : " << xc_func1 << std::endl; 
+                    GlobalV::ofs_warning << " MAKE SURE THIS DFT FUNCTIONAL IS WHAT YOU NEED" << std::endl;
 
                     ucell.atoms[i].ncpp.xc_func = xc_func1;
-                    log << " XC functional updated to : " << PARAM.inp.dft_functional << std::endl;
-                    ModuleBase::GlobalFunc::OUT(log, "exchange-correlation functional", ucell.atoms[i].ncpp.xc_func);
+                    ModuleBase::GlobalFunc::OUT(log, "DFT functional set to", xc_func1);
                 }
             }
         }

source/module_esolver/esolver.cpp

@@ -266,11 +266,12 @@ ESolver* init_esolver(const Input_para& inp, UnitCell& ucell)
         }
         p_esolver->before_all_runners(ucell, inp);
         p_esolver->runner(ucell, 0); // scf-only
+
         // force and stress is not needed currently,
         // they will be supported after the analytical gradient
         // of LR-TDDFT is implemented.
         // after_all_runners() is for output, it is not needed here.
-        std::cout << "Setting up the esolver for excited states..." << std::endl;
+        std::cout << " PREPARING FOR EXCITED STATES." << std::endl;
         // initialize the 2nd ESolver_LR at the temporary pointer
         ModuleESolver::ESolver* p_esolver_lr = nullptr;
         if (PARAM.globalv.gamma_only_local)

source/module_hamilt_general/module_surchem/surchem.cpp

@@ -55,4 +55,4 @@ void surchem::clear()
 surchem::~surchem()
 {
     this->clear();
-}
+}