Update ABACUS output formats, accept it after 3.10 version (#6076)

* update some timers

* update timer

* update output formats

* update print_cell

* add ofs in print_tau

* update print_tau

* update output formats

* update md outputs

* beging modifying the autotests

* update integrate tests

* update some timers

* fix total force and total stress

* update integrate tests

* update print_band

* fix print_band

* update md print out information

* update print_stress

* update print_stress in dp, but still has problems in lj

* fix dp_test.cpp

* update esolver_lj

* set mulliken charge accuracy from 4 to 3

* update print force and print stress

Author: mohanchen

source/driver.cpp

@@ -23,24 +23,27 @@ Driver::~Driver()
 
 void Driver::init()
 {
-    ModuleBase::TITLE("Driver", "init");
+    // 1) Let's start by printing a title.
+    ModuleBase::TITLE("Driver", "ABACUS_begins");
 
+    // 2) Print the current time, since it may run a long time.
     time_t time_start = std::time(nullptr);
     ModuleBase::timer::start();
 
-    // (1) read the input parameters.
-    // INPUT should be initalized here and then pass to atomic world, mohan
-    // 2024-05-12 INPUT should not be GlobalC, mohan 2024-05-12
-    Driver::reading();
-
-    // (2) welcome to the atomic world!
+    // 3) Welcome to the atomic world! Let's do some fancy stuff here.
     this->atomic_world();
 
-    // (3) output information
+    // 4) All timers recorders are printed.
+    ModuleBase::timer::finish(GlobalV::ofs_running);
+
+    // 5) All memory recorders are printed.
+    ModuleBase::Memory::print_all(GlobalV::ofs_running);
+
+    // 6) Print the final time, hopefully it will not cost too long. 
     time_t time_finish = std::time(nullptr);
     ModuleIO::print_time(time_start, time_finish);
 
-    // (4) close all of the running logs
+    // 7) Clean up: close all of the running logs
     ModuleBase::Global_File::close_all_log(GlobalV::MY_RANK, PARAM.inp.out_alllog,PARAM.inp.calculation);
 
 }
@@ -169,16 +172,13 @@ void Driver::reading()
 void Driver::atomic_world()
 {
     ModuleBase::TITLE("Driver", "atomic_world");
-    //--------------------------------------------------
-    // choose basis sets:
-    // pw: plane wave basis set
-    // lcao_in_pw: LCAO expaned by plane wave basis set
-    // lcao: linear combination of atomic orbitals
-    //--------------------------------------------------
+    ModuleBase::timer::tick("Driver", "atomic_world");
+
+    // reading information 
+    this->reading();
 
     // where the actual stuff is done
     this->driver_run();
 
-    ModuleBase::timer::finish(GlobalV::ofs_running);
-    ModuleBase::Memory::print_all(GlobalV::ofs_running);
+    ModuleBase::timer::tick("Driver", "atomic_world");
 }

source/driver_run.cpp

@@ -25,12 +25,13 @@
  */
 void Driver::driver_run()
 {
-    ModuleBase::TITLE("Driver", "driver_line");
+    ModuleBase::TITLE("Driver", "driver_run");
 
     //! 1: setup cell and atom information
     // this warning should not be here, mohan 2024-05-22
 #ifndef __LCAO
     if (PARAM.inp.basis_type == "lcao_in_pw" || PARAM.inp.basis_type == "lcao") {
+        ModuleBase::timer::tick("Driver","driver_run");
         ModuleBase::WARNING_QUIT("driver",
                                  "to use LCAO basis, compile with __LCAO");
     }
@@ -92,5 +93,6 @@ void Driver::driver_run()
 
     //! 6: output the json file
     Json::create_Json(&ucell, PARAM);
+
     return;
 }

source/module_base/memory.cpp

@@ -385,8 +385,9 @@ void Memory::print_all(std::ofstream &ofs)
 	Parallel_Reduce::reduce_all(Memory::total_gpu);
 #endif
 #endif
-	ofs <<"\n NAME-------------------------|MEMORY(MB)--------" << std::endl;
-	ofs <<std::setw(30)<< "total" << std::setw(15) <<std::setprecision(4)<< Memory::total << std::endl;
+	ofs <<"\n NAME-------------------------|MEMORY(MB)------------------" << std::endl;
+    ofs << std::right;
+	ofs << std::setw(30)<< "total" << std::setw(15) <<std::setprecision(4)<< Memory::total << std::endl;
 
     assert(n_memory>0);
 
@@ -440,7 +441,7 @@ void Memory::print_all(std::ofstream &ofs)
 		return;
 	}
 
-	ofs <<"\n NAME-------------------------|GPU MEMORY(MB)----" << std::endl;
+	ofs <<"\n NAME-------------------------|GPU MEMORY(MB)--------------" << std::endl;
 	ofs <<std::setw(30)<< "total" << std::setw(15) <<std::setprecision(4)<< Memory::total_gpu << std::endl;
 
     assert(n_memory>0);

source/module_cell/module_neighbor/sltk_atom_arrange.cpp

@@ -74,8 +74,9 @@ void atom_arrange::search(const bool pbc_flag,
         ModuleBase::WARNING_QUIT("atom_arrange::search", " search_radius_bohr < 0,forbidden");
     }
 
-    ModuleBase::GlobalFunc::OUT(ofs_in, "searching radius is (Bohr))", search_radius_bohr);
-    ModuleBase::GlobalFunc::OUT(ofs_in, "searching radius unit is (Bohr))", ucell.lat0);
+    ofs_in << " SEARCH ADJACENT ATOMS" << std::endl;
+    ModuleBase::GlobalFunc::OUT(ofs_in, "searching radius is (Bohr)", search_radius_bohr);
+    ModuleBase::GlobalFunc::OUT(ofs_in, "searching radius unit is (Bohr)", ucell.lat0);
 
     assert(ucell.nat > 0);
 

source/module_cell/module_neighbor/sltk_grid.cpp

@@ -195,9 +195,10 @@ void Grid::setMemberVariables(std::ofstream& ofs_in, //  output data to ofs
             }
         }
     }
-    ModuleBase::GlobalFunc::OUT(ofs_in, "Find the coordinate range of the input atom(unit:lat0).");
-    ModuleBase::GlobalFunc::OUT(ofs_in, "min_tau", x_min, y_min, z_min);
-    ModuleBase::GlobalFunc::OUT(ofs_in, "max_tau", x_max, y_max, z_max);
+
+    ofs_in << " RANGE OF ATOMIC COORDINATES (unit: lat0)" << std::endl;
+    ModuleBase::GlobalFunc::OUT(ofs_in, "smallest coordinates of atoms", x_min, y_min, z_min);
+    ModuleBase::GlobalFunc::OUT(ofs_in, "largest  coordinates of atoms", x_max, y_max, z_max);
 
     this->box_edge_length = sradius + 0.1; // To avoid edge cases, the size of the box is slightly increased.
 
@@ -220,7 +221,7 @@ void Grid::setMemberVariables(std::ofstream& ofs_in, //  output data to ofs
     this->box_nx = glayerX + glayerX_minus;
     this->box_ny = glayerY + glayerY_minus;
     this->box_nz = glayerZ + glayerZ_minus;
-    ModuleBase::GlobalFunc::OUT(ofs_in, "BoxNumber", box_nx, box_ny, box_nz);
+    ModuleBase::GlobalFunc::OUT(ofs_in, "number of needed cells", box_nx, box_ny, box_nz);
 
     atoms_in_box.resize(this->box_nx);
     for (int i = 0; i < this->box_nx; i++)

source/module_cell/print_cell.cpp

@@ -11,7 +11,8 @@ namespace unitcell
     void print_tau(Atom* atoms,
                    const std::string& Coordinate,
                    const int ntype,
-                   const double lat0)
+                   const double lat0,
+                   std::ofstream &ofs)
     {
         ModuleBase::TITLE("UnitCell", "print_tau");
         // assert (direct || Coordinate == "Cartesian" || Coordinate == "Cartesian_angstrom"); // this line causes abort in unittest ReadAtomPositionsCACXY.
@@ -22,7 +23,7 @@ namespace unitcell
         assert(std::regex_search(Coordinate, pattern));
         bool direct = (Coordinate == "Direct");
         std::string table;
-        table += direct? "DIRECT COORDINATES\n": FmtCore::format("CARTESIAN COORDINATES ( UNIT = %20.12f Bohr ).\n", lat0);
+        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");
         for(int it = 0; it < ntype; it++)
         {
@@ -43,7 +44,7 @@ namespace unitcell
             }
         }
         table += "\n";
-        GlobalV::ofs_running << table << std::endl;
+        ofs << table << std::endl;
         return;
     }
 

source/module_cell/print_cell.h

@@ -8,7 +8,8 @@ namespace unitcell
     void print_tau(Atom* atoms,
                    const std::string& Coordinate,
                    const int ntype,
-                   const double lat0);
+                   const double lat0,
+                   std::ofstream &ofs);
 
       /**
      * @brief UnitCell class is too heavy, this function would be moved
@@ -40,4 +41,4 @@ namespace unitcell
                          const int& iproc = 0);
 }
 
-#endif
+#endif

source/module_cell/read_atoms.cpp

@@ -514,7 +514,9 @@ bool read_atom_positions(UnitCell& ucell,
                         ucell.atoms[it].m_loc_[ia].x = 1.0;
                         ucell.atoms[it].m_loc_[ia].y = 1.0;
                         ucell.atoms[it].m_loc_[ia].z = 1.0;
-                        ucell.atoms[it].mag[ia] = sqrt(pow(ucell.atoms[it].m_loc_[ia].x,2)+pow(ucell.atoms[it].m_loc_[ia].y,2)+pow(ucell.atoms[it].m_loc_[ia].z,2));
+						ucell.atoms[it].mag[ia] = sqrt(pow(ucell.atoms[it].m_loc_[ia].x,2)
+								+pow(ucell.atoms[it].m_loc_[ia].y,2)
+								+pow(ucell.atoms[it].m_loc_[ia].z,2));
                         ModuleBase::GlobalFunc::OUT(ofs_running,"Autoset magnetism for this atom", 1.0, 1.0, 1.0);
                     }
                 }
@@ -535,13 +537,14 @@ bool read_atom_positions(UnitCell& ucell,
         // End Autoset magnetization
     }   // end scan_begin
 
-//check if any atom can move in MD
+    //check if any atom can move in MD
     if(!ucell.if_atoms_can_move() && PARAM.inp.calculation=="md" && PARAM.inp.esolver_type!="tddft")
     {
         ModuleBase::WARNING("read_atoms", "no atom can move in MD!");
         return false;
     } 
 
+    
     ofs_running << std::endl;
     ModuleBase::GlobalFunc::OUT(ofs_running,"TOTAL ATOM NUMBER",ucell.nat);
 
@@ -556,7 +559,7 @@ bool read_atom_positions(UnitCell& ucell,
 
     if (unitcell::check_tau(ucell.atoms, ucell.ntype, ucell.lat0))
     {
-        unitcell::print_tau(ucell.atoms,ucell.Coordinate,ucell.ntype,ucell.lat0);
+        unitcell::print_tau(ucell.atoms,ucell.Coordinate,ucell.ntype,ucell.lat0,ofs_running);
         return true;
     }
     return false;

source/module_cell/test/unitcell_test.cpp

@@ -1010,17 +1010,23 @@ TEST_F(UcellTest, PrintTauDirect)
     UcellTestPrepare utp = UcellTestLib["C1H2-Index"];
     PARAM.input.relax_new = utp.relax_new;
     ucell = utp.SetUcellInfo();
-    GlobalV::ofs_running.open("print_tau_direct");
     EXPECT_EQ(ucell->Coordinate, "Direct");
-    unitcell::print_tau(ucell->atoms,ucell->Coordinate,ucell->ntype,ucell->lat0);
-    GlobalV::ofs_running.close();
+
+    // open a file
+    std::ofstream ofs("print_tau_direct");
+    unitcell::print_tau(ucell->atoms,ucell->Coordinate,ucell->ntype,ucell->lat0,ofs);
+    ofs.close();
+ 
+    // readin the data
     std::ifstream ifs;
     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"));
     ifs.close();
+
+    // remove the file
     remove("print_tau_direct");
 }
 
@@ -1029,17 +1035,23 @@ TEST_F(UcellTest, PrintTauCartesian)
     UcellTestPrepare utp = UcellTestLib["C1H2-Cartesian"];
     PARAM.input.relax_new = utp.relax_new;
     ucell = utp.SetUcellInfo();
-    GlobalV::ofs_running.open("print_tau_Cartesian");
     EXPECT_EQ(ucell->Coordinate, "Cartesian");
-    unitcell::print_tau(ucell->atoms,ucell->Coordinate,ucell->ntype,ucell->lat0);
-    GlobalV::ofs_running.close();
+
+    // open a file
+    std::ofstream ofs("print_tau_Cartesian");
+    unitcell::print_tau(ucell->atoms,ucell->Coordinate,ucell->ntype,ucell->lat0,ofs);
+    ofs.close();
+
+    // readin the data
     std::ifstream ifs;
     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"));
     ifs.close();
+
+    // remove the file
     remove("print_tau_Cartesian");
 }
 

source/module_elecstate/elecstate_print.cpp

@@ -250,13 +250,16 @@ void print_band(const ModuleBase::matrix& ekb,
                 const K_Vectors* klist,
                 const int& ik,
                 const int& printe,
-                const int& iter)
+                const int& iter,
+                std::ofstream &ofs)
 {
+    const double largest_eig = 1.0e10;
+
     // check the band energy.
     bool wrong = false;
     for (int ib = 0; ib < PARAM.globalv.nbands_l; ++ib)
     {
-        if (std::abs(ekb(ik, ib)) > 1.0e10)
+        if (std::abs(ekb(ik, ib)) > largest_eig)
         {
             GlobalV::ofs_warning << " ik=" << ik + 1 << " ib=" << ib + 1 << " " << ekb(ik, ib) << " Ry" << std::endl;
             wrong = true;
@@ -271,18 +274,18 @@ void print_band(const ModuleBase::matrix& ekb,
     {
         if (printe > 0 && ((iter + 1) % printe == 0))
         {
-            GlobalV::ofs_running << std::setprecision(6);
-            GlobalV::ofs_running << " Energy (eV) & Occupations  for spin=" << klist->isk[ik] + 1
-                                 << " K-point=" << ik + 1 << std::endl;
-            GlobalV::ofs_running << std::setiosflags(std::ios::showpoint);
+            ofs << std::setprecision(6);
+            ofs << " Energy (eV) & Occupations for spin=" << klist->isk[ik] + 1
+                                 << " k-point=" << ik + 1 << std::endl;
+            ofs << std::setiosflags(std::ios::showpoint);
             for (int ib = 0; ib < PARAM.globalv.nbands_l; ib++)
             {
-                GlobalV::ofs_running << " " << std::setw(6) << ib + 1 << std::setw(15)
+                ofs << " " << std::setw(6) << ib + 1 << std::setw(15)
                                      << ekb(ik, ib) * ModuleBase::Ry_to_eV;
                 // for the first electron iteration, we don't have the energy
                 // spectrum, so we can't get the occupations.
-                GlobalV::ofs_running << std::setw(15) << wg(ik, ib);
-                GlobalV::ofs_running << std::endl;
+                ofs << std::setw(15) << wg(ik, ib);
+                ofs << std::endl;
             }
         }
     }
@@ -317,7 +320,7 @@ void print_etot(const Magnetism& magnet,
 
     GlobalV::ofs_running << std::setprecision(12);
     GlobalV::ofs_running << std::setiosflags(std::ios::right);
-    GlobalV::ofs_running << "\n Density error is " << scf_thr << std::endl;
+    GlobalV::ofs_running << " Electron density error is " << scf_thr << std::endl;
 
     if (PARAM.inp.basis_type == "pw")
     {
@@ -327,6 +330,7 @@ void print_etot(const Magnetism& magnet,
     std::vector<std::string> titles;
     std::vector<double> energies_Ry;
     std::vector<double> energies_eV;
+
     if (printe > 0 && ((iter + 1) % printe == 0 || converged || iter == PARAM.inp.scf_nmax))
     {
         int n_order = std::max(0, Occupy::gaussian_type);
@@ -384,7 +388,7 @@ void print_etot(const Magnetism& magnet,
         }
 
 #ifdef __DEEPKS
-        if (PARAM.inp.deepks_scf) // caoyu add 2021-08-10
+        if (PARAM.inp.deepks_scf)
         {
             titles.push_back("E_DeePKS");
             energies_Ry.push_back(elec.f_en.edeepks_delta);
@@ -399,6 +403,7 @@ void print_etot(const Magnetism& magnet,
         energies_Ry.push_back(elec.f_en.etot_harris);
     }
 
+    // print out the Fermi energy if needed
     if (PARAM.globalv.two_fermi)
     {
         titles.push_back("E_Fermi_up");
@@ -411,6 +416,8 @@ void print_etot(const Magnetism& magnet,
         titles.push_back("E_Fermi");
         energies_Ry.push_back(elec.eferm.ef);
     }
+
+    // print out the band gap if needed
     if (PARAM.inp.out_bandgap)
     {
         if (!PARAM.globalv.two_fermi)
@@ -430,14 +437,21 @@ void print_etot(const Magnetism& magnet,
     std::transform(energies_Ry.begin(), energies_Ry.end(), energies_eV.begin(), [](double ener) {
         return ener * ModuleBase::Ry_to_eV;
     });
+
+    // for each SCF step, we print out energy
     FmtTable table(/*titles=*/{"Energy", "Rydberg", "eV"},
                    /*nrows=*/titles.size(),
                    /*formats=*/{"%-14s", "%20.10f", "%20.10f"}, 
                    /*indents=*/0,
                    /*align=*/{/*value*/FmtTable::Align::LEFT, /*title*/FmtTable::Align::CENTER});
+    // print out the titles
     table << titles << energies_Ry << energies_eV;
+
     GlobalV::ofs_running << table.str() << std::endl;
-    if (PARAM.inp.out_level == "ie" || PARAM.inp.out_level == "m") // xiaohui add 'm' option, 2015-09-16
+
+
+    
+    if (PARAM.inp.out_level == "ie" || PARAM.inp.out_level == "m")
     {
         std::vector<double> mag;
         switch (PARAM.inp.nspin)