Merge remote-tracking branch 'upstream/develop' into develop

Author: jieli-matrix

docs/advanced/elec_properties/band.md

@@ -1,41 +1,40 @@
 # Extracting Band Structure
 
-ABACUS can calculate the energy band structure, and the examples can be found in [examples/band](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/band).
-Similar to the [DOS case](https://abacus-rtd.readthedocs.io/en/latest/advanced/elec_properties/dos.html), we first, do a ground-state energy calculation ***with one additional keyword "[out_chg](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-chg)" in the INPUT file***:
+In ABACUS, in order to obtain the eigenvalues of Hamiltonian, or generally called band structure, examples can be found in [examples/band](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/band).
+Similar to the [DOS case](https://abacus-rtd.readthedocs.io/en/latest/advanced/elec_properties/dos.html), one first needs to perform a ground-state energy calculation ***with one additional keyword "[out_chg](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-chg)" in the INPUT file***:
 
 ```
-out_chg             1
+out_chg 1
 ```
 
-This will produce the converged charge density, which is contained in the file SPIN1_CHG.cube.
-Then, use the same `STRU` file, pseudopotential file and atomic orbital file (and the local density matrix file onsite.dm if DFT+U is used) to do a non-self-consistent calculation. In this example, the potential is constructed from the ground-state charge density from the proceeding calculation. Now the INPUT file is like:
+With this input parameter, the converged charge density will be output in the files such as `chgs1.cube`, `chgs2.cube`, etc.
+Then, one can use the same `STRU` file, pseudopotential files and atomic orbital files (and the local density matrix file onsite.dm if DFT+U is used) to do a non-self-consistent (NSCF) calculation. In this example, the potential is constructed from the ground-state charge density from the proceeding calculation. Now the INPUT file is like:
 
 ```
 INPUT_PARAMETERS
 #Parameters (General)
-ntype 1
-nbands 8
-calculation nscf
-basis_type lcao
-read_file_dir   ./
+nbands        8
+calculation   nscf
+basis_type    lcao
+read_file_dir ./
 
 #Parameters (Accuracy)
-ecutwfc 60
-scf_nmax 50
-scf_thr 1.0e-9
-pw_diag_thr 1.0e-7
+ecutwfc       60
+scf_nmax      50
+scf_thr       1.0e-9
+pw_diag_thr   1.0e-7
 
 #Parameters (File)
-init_chg file
-out_band 1
+init_chg      file
+out_band      1
 out_proj_band 1
 
 #Parameters (Smearing)
 smearing_method gaussian
-smearing_sigma 0.02
+smearing_sigma  0.02
 ```
 
-Here the the relevant k-point file KPT looks like,
+Here is a relevant k-point file KPT (in LINE mode):
 
 ```
 K_POINTS # keyword for start
@@ -49,16 +48,16 @@ Line # line-mode
 0.0 0.0 0.0 1 # G
 ```
 
-This means we are using:
+This means we are using the following k-points:
 
-- 6 number of k points, here means 6 k points:
+- 6 k points, here means 6 k points:
   (0.5, 0.0, 0.5) (0.0, 0.0, 0.0) (0.5, 0.5, 0.5) (0.5, 0.25, 0.75) (0.375, 0.375, 0.75) (0.0, 0.0,
   0.0)
 - 20/1 number of k points along the segment line, which is constructed by two adjacent k
   points.
 
-Run the program, and you will see a file named BANDS_1.dat in the output directory. Plot it
-to get energy band structure.
+Next, run ABACUS and you will see a file named `eigs1.txt` in the output directory. 
+Plot it and you will obtain the energy band structure!
 
 If "out_proj_band" set 1, it will also produce the projected band structure in a file called PBAND_1 in xml format.
 
@@ -77,8 +76,8 @@ The rest of the files arranged in sections, each section with a header such as b
 
 ```
 <orbital
- index="                                       1"
- atom_index="                                       1"
+ index="                                   1"
+ atom_index="                              1"
  species="Si"
  l="                                       0"
  m="                                       0"

docs/advanced/input_files/input-main.md

@@ -24,20 +24,10 @@ For a complete list of input parameters, please consult this [instruction](../ad
 
 This file contains the information of all generated k-points, as well as the list of k-points actually used for calculations after considering symmetry.
 
-## *istate.info*
+## *eig.txt*
 
-This file includes the energy levels computed for all k-points. From left to right, the columns represent: energy level index, eigenenergy, and occupancy number.
-
-Below is an example `istate.info`:
-
-```
-BAND               Energy(ev)               Occupation                Kpoint = 1                        (0 0 0)
-      1                 -5.33892                  0.03125
-      2                  6.68535                0.0312006
-      3                  6.68535                0.0312006
-      4                  6.68535                0.0312006
-      5                  9.41058                        0
-```
+This file includes the energy levels and occupations computed for all k-points. 
+Note: In 3.10-LTS version, the file is named 'istate.info'
 
 ## *STRU.cif*
 

docs/quick_start/output.md

@@ -178,12 +178,6 @@ void K_Vectors::renew(const int& kpoint_number)
     isk.resize(kpoint_number);
     ngk.resize(kpoint_number);
 
-    /*ModuleBase::Memory::record("KV::kvec_c",sizeof(double) * kpoint_number*3);
-    ModuleBase::Memory::record("KV::kvec_d",sizeof(double) * kpoint_number*3);
-    ModuleBase::Memory::record("KV::wk",sizeof(double) * kpoint_number*3);
-    ModuleBase::Memory::record("KV::isk",sizeof(int) * kpoint_number*3);
-    ModuleBase::Memory::record("KV::ngk",sizeof(int) * kpoint_number*3);*/
-
     return;
 }
 

source/module_cell/klist.cpp

@@ -48,17 +48,12 @@ void Parallel_Kpoints::get_whichpool(const int& nkstot)
 {
     this->whichpool.resize(nkstot, 0);
 
-    // std::cout << " calculate : whichpool" << std::endl;
-    // std::cout << " nkstot is " << nkstot << std::endl;
-
-
     for (int i = 0; i < this->kpar; i++)
     {
         for (int ik = 0; ik < this->nks_pool[i]; ik++)
         {
             const int k_now = ik + startk_pool[i];
             this->whichpool[k_now] = i;
-            // ofs_running << "\n whichpool[" << k_now <<"] = " << whichpool[k_now];
         }
     }
 
@@ -72,19 +67,13 @@ void Parallel_Kpoints::get_nks_pool(const int& nkstot)
     const int nks_ave = nkstot / this->kpar;
     const int remain = nkstot % this->kpar;
 
-    // ofs_running << "\n nkstot = " << nkstot;
-    // ofs_running << "\n this->kpar = " << this->kpar;
-    // ofs_running << "\n nks_ave = " << nks_ave;
-
     for (int i = 0; i < this->kpar; i++)
-
     {
         this->nks_pool[i] = nks_ave;
         if (i < remain)
         {
             nks_pool[i]++;
         }
-        // ofs_running << "\n nks_pool[i] = " << nks_pool[i];
     }
     return;
 }
@@ -93,14 +82,10 @@ void Parallel_Kpoints::get_startk_pool(const int& nkstot)
 {
     startk_pool.resize(this->kpar, 0);
 
-    // const int remain = nkstot%this->kpar;
-
     startk_pool[0] = 0;
     for (int i = 1; i < this->kpar; i++)
-
     {
         startk_pool[i] = startk_pool[i - 1] + nks_pool[i - 1];
-        // ofs_running << "\n startk_pool[i] = " << startk_pool[i];
     }
     return;
 }
@@ -120,7 +105,6 @@ void Parallel_Kpoints::set_startpro_pool()
         {
             startpro_pool[i]++;
         }
-        // ofs_running << "\n startpro_pool[i] = " << startpro_pool[i];
     }
     return;
 }
@@ -138,8 +122,6 @@ void Parallel_Kpoints::gatherkvec(const std::vector<ModuleBase::Vector3<double>>
         {
             vec_global[i + startk_pool[this->my_pool]] = vec_local[i];
         }
-        // vec_global[i + startk_pool[MY_POOL]] = vec_local[i] / double(NPROC_IN_POOL);
-
     }
 
     MPI_Allreduce(MPI_IN_PLACE, &vec_global[0], 3 * this->nkstot_np, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
@@ -152,7 +134,6 @@ void Parallel_Kpoints::pool_collection(double& value, const double* wk, const in
 #ifdef __MPI
 
     const int ik_now = ik - this->startk_pool[this->my_pool];
-    // ofs_running << "\n\n ik=" << ik << " ik_now=" << ik_now;
 
     const int pool = this->whichpool[ik];
 
@@ -167,8 +148,6 @@ void Parallel_Kpoints::pool_collection(double& value, const double* wk, const in
             }
             else
             {
-
-                // ofs_running << " receive data.";
                 MPI_Status ierror;
                 MPI_Recv(&value, 1, MPI_DOUBLE, this->startpro_pool[pool], ik, MPI_COMM_WORLD, &ierror);
 
@@ -178,18 +157,12 @@ void Parallel_Kpoints::pool_collection(double& value, const double* wk, const in
         {
             if (this->my_pool == pool)
             {
-
-                // ofs_running << " send data.";
-
                 MPI_Send(&wk[ik_now], 1, MPI_DOUBLE, 0, ik, MPI_COMM_WORLD);
             }
         }
     }
     else
     {
-
-        // ofs_running << "\n do nothing.";
-
     }
 
     MPI_Barrier(MPI_COMM_WORLD);
@@ -238,13 +211,10 @@ void Parallel_Kpoints::pool_collection_aux(T* value, const V& w, const int& dim,
     T* p = &w.ptr[begin];
     // temprary restrict kpar=1 for NSPIN=2 case for generating_orbitals
     int pool = 0;
-    if (this->nspin != 2) {
-        pool = this->whichpool[ik];
-}
-
-
-    // ofs_running << "\n ik=" << ik;
-
+	if (this->nspin != 2) 
+	{
+		pool = this->whichpool[ik];
+	}
 
     if (this->rank_in_pool == 0)
     {
@@ -261,7 +231,6 @@ void Parallel_Kpoints::pool_collection_aux(T* value, const V& w, const int& dim,
             }
             else
             {
-                // ofs_running << " receive data.";
                 MPI_Status ierror;
                 MPI_Recv(value, dim, MPI_DOUBLE, this->startpro_pool[pool], ik * 2 + 0, MPI_COMM_WORLD, &ierror);
             }
@@ -270,14 +239,12 @@ void Parallel_Kpoints::pool_collection_aux(T* value, const V& w, const int& dim,
         {
             if (this->my_pool == pool)
             {
-                // ofs_running << " send data.";
                 MPI_Send(p, dim, MPI_DOUBLE, 0, ik * 2 + 0, MPI_COMM_WORLD);
             }
         }
     }
     else
     {
-        // ofs_running << "\n do nothing.";
     }
     MPI_Barrier(MPI_COMM_WORLD);
 
@@ -292,4 +259,4 @@ void Parallel_Kpoints::pool_collection_aux(T* value, const V& w, const int& dim,
     }
     // data transfer ends.
 #endif
-}
+}

source/module_cell/parallel_kpoints.cpp

@@ -148,98 +148,6 @@ void print_scf_iterinfo(const std::string& ks_solver,
     }
     std::cout << buf;
 }
-/// @brief print and check for band energy and occupations
-/// @param ofs
-void print_eigenvalue(const ModuleBase::matrix& ekb,
-                      const ModuleBase::matrix& wg,
-                      const K_Vectors* klist,
-                      std::ofstream& ofs)
-{
-     bool wrong = false;
-    const int nks = klist->get_nks();
-    const int nkstot = klist->get_nkstot();
-    for (int ik = 0; ik < nks; ++ik)
-    {
-        for (int ib = 0; ib < ekb.nc; ++ib)
-        {
-            if (std::abs(ekb(ik, ib)) > 1.0e10)
-            {
-                GlobalV::ofs_warning << " ik=" << ik + 1 << " ib=" << ib + 1 << " " << ekb(ik, ib) << " Ry" << std::endl;
-                wrong = true;
-            }
-        }
-    }
-#ifdef __MPI
-    MPI_Allreduce(MPI_IN_PLACE, &wrong, 1, MPI_C_BOOL, MPI_LOR, MPI_COMM_WORLD);
-#endif
-    if (wrong)
-    {
-        ModuleBase::WARNING_QUIT("print_eigenvalue", "Eigenvalues are too large!");
-    }
-
-    std::string filename = PARAM.globalv.global_out_dir + PARAM.globalv.log_file;
-    std::vector<int> ngk_tot = klist->ngk;
-
-#ifdef __MPI
-    MPI_Allreduce(MPI_IN_PLACE, ngk_tot.data(), nks, MPI_INT, MPI_SUM, POOL_WORLD);
-#endif
-
-    ModuleBase::TITLE("ESolver_KS_PW", "print_eigenvalue");
-
-    ofs << "\n STATE ENERGY(eV) AND OCCUPATIONS ";
-    const int nk_fac = PARAM.inp.nspin == 2 ? 2 : 1;
-    const int nks_np = nks / nk_fac;
-    const int nkstot_np = nkstot / nk_fac;
-    ofs << "   NSPIN == " << PARAM.inp.nspin << std::endl;
-    for (int is = 0; is < nk_fac; ++is)
-    {
-        if (is == 0 && nk_fac == 2)
-        {
-            ofs << "SPIN UP : " << std::endl;
-        }
-        else if (is == 1 && nk_fac == 2)
-        {
-            ofs << "SPIN DOWN : " << std::endl;
-        }
-
-        for (int ip = 0; ip < GlobalV::KPAR; ++ip)
-        {
-#ifdef __MPI
-            MPI_Barrier(MPI_COMM_WORLD);
-#endif
-            bool ip_flag = PARAM.inp.out_alllog || (GlobalV::RANK_IN_POOL == 0 && GlobalV::MY_BNDGROUP == 0);
-            if (GlobalV::MY_POOL == ip && ip_flag)
-            {
-                const int start_ik = nks_np * is;
-                const int end_ik = nks_np * (is + 1);
-                for (int ik = start_ik; ik < end_ik; ++ik)
-                {
-                    std::ofstream ofs_eig(filename.c_str(), std::ios::app);
-                    ofs_eig << std::setprecision(5);
-                    ofs_eig << std::setiosflags(std::ios::showpoint);
-                    ofs_eig << " " << klist->ik2iktot[ik] + 1 - is * nkstot_np << "/" << nkstot_np
-                            << " kpoint (Cartesian) = " << klist->kvec_c[ik].x << " " << klist->kvec_c[ik].y
-                            << " " << klist->kvec_c[ik].z << " (" << ngk_tot[ik] << " pws)" << std::endl;
-
-                    ofs_eig << std::setprecision(6);
-                    ofs_eig << std::setiosflags(std::ios::showpoint);
-                    for (int ib = 0; ib < ekb.nc; ib++)
-                    {
-                        ofs_eig << std::setw(8) << ib + 1 << std::setw(15) << ekb(ik, ib) * ModuleBase::Ry_to_eV
-                                << std::setw(15) << wg(ik, ib) << std::endl;
-                    }
-                    ofs_eig << std::endl;
-                    ofs_eig.close();
-                }
-            }
-        }
-#ifdef __MPI
-            MPI_Barrier(MPI_COMM_WORLD);
-#endif
-        ofs.seekp(0, std::ios::end);
-    }
-    return;
-}
 
 /// @brief function for printing eigenvalues : ekb
 /// @param ik: index of kpoints

source/module_elecstate/elecstate_print.cpp

@@ -16,11 +16,6 @@ namespace elecstate
     void print_format(const std::string& name, 
                     const double& value);
 
-    void print_eigenvalue(const ModuleBase::matrix& ekb,
-                      const ModuleBase::matrix& wg,
-                      const K_Vectors* klist,
-                      std::ofstream& ofs);
-    
     void print_etot(const Magnetism& magnet,
                     const ElecState& elec,
                     const bool converged,