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

Author: ErjieWu

docs/advanced/input_files/input-main.md

@@ -153,6 +153,7 @@
     - [out\_mat\_t](#out_mat_t)
     - [out\_mat\_dh](#out_mat_dh)
     - [out\_mat\_xc](#out_mat_xc)
+    - [out\_mat\_xc2](#out_mat_xc2)
     - [out\_eband\_terms](#out_eband_terms)
     - [out\_hr\_npz/out\_dm\_npz](#out_hr_npzout_dm_npz)
     - [dm\_to\_rho](#dm_to_rho)
@@ -1799,6 +1800,13 @@ These variables are used to control the output of properties.
 The band (KS orbital) energy for each (k-point, spin, band) will be printed in the file `OUT.${suffix}/vxc_out.dat`. If EXX is calculated, the local and EXX part of band energy will also be printed in `OUT.${suffix}/vxc_local_out.dat`and `OUT.${suffix}/vxc_exx_out.dat`, respectively. All the `vxc*_out.dat` files contains 3 integers (nk, nspin, nband) followed by nk\*nspin\*nband lines of energy Hartree and eV.
 - **Default**: False
 
+### out_mat_xc2
+
+- **Type**: Boolean
+- **Availability**: Numerical atomic orbital (NAO) basis
+- **Description**: Whether to print the exchange-correlation matrices in **numerical orbital representation** (unit: Ry): $\braket{\phi_i|V_\text{xc}^\text{(semi-)local}+V_\text{exx}+V_\text{DFTU}|\phi_j}(\mathbf{R})$ in CSR format (the same format as [out_mat_hs2](../elec_properties/hs_matrix.md#out_mat_hs2)) in the directory `OUT.${suffix}`. (Note that currently DeePKS term is not included. ) The files are named `Vxc_R_spin$s`.
+- **Default**: False
+
 ### out_eband_terms
 
 - **Type**: Boolean

docs/quick_start/output.md

@@ -14,7 +14,7 @@ For a complete list of input parameters, please consult this [instruction](../ad
 
 `running_scf.log` contains information on nearly all function calls made during the execution of ABACUS.
 
-## *KPT*
+## *KPT.info*
 
 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.
 
@@ -39,4 +39,4 @@ ABACUS generates a `.cif` format structure file based on the input file `STRU`,
 
 ## *warning.log*
 
-The file contains all the warning messages generated during the ABACUS run.
+The file contains all the warning messages generated during the ABACUS run.

source/Makefile.Objects

@@ -267,6 +267,7 @@ OBJS_ESOLVER_LCAO=esolver_ks_lcao.o\
       lcao_after_scf.o\
       esolver_gets.o\
       lcao_others.o\
+      esolver_dm2rho.o\
 
 OBJS_GINT=gint.o\
       gint_gamma_env.o\
@@ -462,6 +463,14 @@ OBJS_SURCHEM=surchem.o\
 
 OBJS_SYMMETRY=symm_other.o\
     symmetry_basic.o\
+    symm_analysis.o\
+    symm_check.o\
+    symm_getgroup.o\
+    symm_hermite.o\
+    symm_lattice.o\
+    symm_magnetic.o\
+    symm_pricell.o\
+    symm_rho.o\
     symmetry.o\
 
 OBJS_XC=xc_functional.o\

source/driver_run.cpp

@@ -26,7 +26,6 @@
 void Driver::driver_run()
 {
     ModuleBase::TITLE("Driver", "driver_line");
-    ModuleBase::timer::tick("Driver", "driver_line");
 
     //! 1: setup cell and atom information
     // this warning should not be here, mohan 2024-05-22
@@ -93,6 +92,5 @@ void Driver::driver_run()
 
     //! 6: output the json file
     Json::create_Json(&ucell, PARAM);
-    ModuleBase::timer::tick("Driver", "driver_line");
     return;
 }

source/module_base/formatter.h

@@ -191,17 +191,22 @@ class FmtTable
      * 
      * @param titles titles, its size should be the same as the number of columns
      * @param nrows number of rows
-     * @param aligns Alignments instance, can be constructed with initializer_list<char> like {'r', 'c'}, for right and center alignment for values and titles
+     * @param fmts format strings for each column, its size should be the same as the number of columns
+     * @param indent indent for each column, default is 0
+     * @param aligns Alignments instance, for alignment of values and titles, e.g. {Align::LEFT, Align::RIGHT} for left alignment of values and right alignment of titles
      * @param frames Frames instance, can be constructed with initializer_list<char> like {'-', '-', '-', ' ', ' '}, for up, middle, down, left and right frames
      * @param delimiters Delimiters instance, can be constructed with initializer_list<char> like {'-', ' '}, for horizontal and vertical delimiters
      */
     FmtTable(const std::vector<std::string>& titles, 
-             const size_t& nrows, 
+             const size_t nrows, 
              const std::vector<std::string>& fmts,
+             const size_t indent = 0,
              const Alignments& aligns = {},
              const Frames& frames = {},
-             const Delimiters& delimiters = {}): titles_(titles), data_(nrows, titles.size()), fmts_(fmts), aligns_(aligns), frames_(frames), delimiters_(delimiters)
-    { assert(titles.size() == fmts.size()); };
+             const Delimiters& delimiters = {}): 
+             titles_(titles), data_(nrows, titles.size()), // data
+             fmts_(fmts), indent_(indent), aligns_(aligns), frames_(frames), delimiters_(delimiters) // styles
+    { assert(titles.size() == fmts.size()||titles.size() == 0); };
     ~FmtTable() {};
     /**
      * @brief import data from std::vector
@@ -269,22 +274,24 @@ class FmtTable
      */
     std::string concat_title(const std::vector<std::string>& titles) const
     {
-        std::string dst;
+        std::string dst = "";
         // first sum width of all titles
         size_t width = std::accumulate(titles.begin(), titles.end(), 0, [](const size_t& acc, const std::string& s) { return acc + s.size(); });
         // add width of delimiters
         width += titles.size() - 1;
         // add width of left and right frames
         width += 2;
-        dst += std::string(width, frames_.up_) + "\n" + std::string(1, frames_.l_);
+        dst += std::string(indent_, ' ') + std::string(width, frames_.up_) + "\n"; // first line: the upper frame
+        dst += std::string(indent_, ' ') + std::string(1, frames_.l_); // second line: the left frame + titles + right frame
         for(size_t i = 0; i < titles.size(); i++)
         {
             dst += titles[i];
             if (i != titles.size() - 1) {
                 dst += delimiters_.v_;
             }
         }
-        dst += std::string(1, frames_.r_) + "\n" + std::string(width, frames_.mid_) + "\n";
+        dst += std::string(1, frames_.r_) + "\n";
+        dst += std::string(indent_, ' ') + std::string(width, frames_.mid_) + "\n"; // third line: the middle frame
         return dst;
     }
     /**
@@ -303,10 +310,10 @@ class FmtTable
         width += row.size() - 1;
         // for the left and right frame
         width += 2;
-        if (pos == 't') {
-            dst += std::string(width, frames_.up_) + "\n";
+        if (pos == 't') { // 't' for top
+            dst += std::string(indent_, ' ') + std::string(width, frames_.up_) + "\n";
         }
-        dst += std::string(1, frames_.l_);
+        dst += std::string(indent_, ' ') + std::string(1, frames_.l_);
         for(size_t i = 0; i < row.size(); i++)
         {
             dst += row[i];
@@ -315,8 +322,8 @@ class FmtTable
             }
         }
         dst += std::string(1, frames_.r_) + "\n";
-        if (pos == 'b') {
-            dst += std::string(width, frames_.dw_) + "\n";
+        if (pos == 'b') { // 'b' for bottom
+            dst += std::string(indent_, ' ') + std::string(width, frames_.dw_) + "\n"; // the last line
         }
         return dst;
     }
@@ -397,6 +404,7 @@ class FmtTable
     std::vector<std::string> titles_;
     NDArray<std::string> data_; // data
     std::vector<std::string> fmts_; // format strings for each column
+    size_t indent_ = 0; // indent for each column
 };
 
 #endif

source/module_base/test/formatter_test.cpp

@@ -217,6 +217,28 @@ TEST(FormatterTest, FmtTableDefaultArgs)
     EXPECT_EQ(result, ref);
 }
 
+TEST(FormatterTest, FmtTableHeadless)
+{
+    const std::vector<std::string> titles = {"", "", ""};
+    const std::vector<std::string> fmts = {"%s", "%d", "%f"};
+    FmtTable table(titles, 5, fmts);
+    const std::vector<std::string> col1 = {"row1", "row2", "row3", "row4", "row5"};
+    const std::vector<int> col2 = {1, 2, 3, 4, 5};
+    const std::vector<float> col3 = {1.1, 2.2, 3.3, 4.4, 5.5};
+    table << col1 << col2 << col3;
+    const std::string result = table.str();
+    std::cout << result << std::endl;
+    std::string ref = "";
+    ref += "-----------------\n";
+    ref += " row1 1 1.100000 \n";
+    ref += " row2 2 2.200000 \n";
+    ref += " row3 3 3.300000 \n";
+    ref += " row4 4 4.400000 \n";
+    ref += " row5 5 5.500000 \n";
+    ref += "-----------------\n";
+    EXPECT_EQ(result, ref);
+}
+
 TEST(FormatterTest, FmtTableCustomArgsAlign)
 {
     // shared data
@@ -226,7 +248,7 @@ TEST(FormatterTest, FmtTableCustomArgsAlign)
     std::vector<int> col2 = {1, 2, 3, 4, 5};
     std::vector<float> col3 = {1.1, 2.2, 3.3, 4.4, 5.5};
     // align: l and l
-    FmtTable table(titles, 5, fmts, {FmtTable::Align::LEFT, FmtTable::Align::LEFT});
+    FmtTable table(titles, 5, fmts, 0, {FmtTable::Align::LEFT, FmtTable::Align::LEFT});
     table << col1 << col2 << col3;
     std::string result = table.str();
     std::cout << result << std::endl;
@@ -243,7 +265,7 @@ TEST(FormatterTest, FmtTableCustomArgsAlign)
     EXPECT_EQ(result, ref);
 
     // align: r and r
-    FmtTable table2(titles, 5, fmts, {FmtTable::Align::RIGHT, FmtTable::Align::RIGHT});
+    FmtTable table2(titles, 5, fmts, 0, {FmtTable::Align::RIGHT, FmtTable::Align::RIGHT});
     table2 << col1 << col2 << col3;
     result = table2.str();
     std::cout << result << std::endl;
@@ -260,7 +282,7 @@ TEST(FormatterTest, FmtTableCustomArgsAlign)
     EXPECT_EQ(result, ref);
 
     // align: l and r
-    FmtTable table3(titles, 5, fmts, {FmtTable::Align::RIGHT, FmtTable::Align::LEFT});
+    FmtTable table3(titles, 5, fmts, 0, {FmtTable::Align::RIGHT, FmtTable::Align::LEFT});
     table3 << col1 << col2 << col3;
     result = table3.str();
     std::cout << result << std::endl;
@@ -277,7 +299,7 @@ TEST(FormatterTest, FmtTableCustomArgsAlign)
     EXPECT_EQ(result, ref);
 
     // align: r and l
-    FmtTable table4(titles, 5, fmts, {FmtTable::Align::LEFT, FmtTable::Align::RIGHT});
+    FmtTable table4(titles, 5, fmts, 0, {FmtTable::Align::LEFT, FmtTable::Align::RIGHT});
     table4 << col1 << col2 << col3;
     result = table4.str();
     std::cout << result << std::endl;
@@ -303,7 +325,12 @@ TEST(FormatterTest, FmtTableCustomArgsAlignFrame)
     std::vector<int> col2 = {1, 2, 3, 4, 5};
     std::vector<float> col3 = {1.1, 2.2, 3.3, 4.4, 5.5};
 
-    FmtTable table1(titles, 5, fmts, {FmtTable::Align::LEFT, FmtTable::Align::LEFT}, {'+', '?', '*', '.', '^'});
+    FmtTable table1(titles, 
+                    5, 
+                    fmts, 
+                    0, 
+                    {FmtTable::Align::LEFT, FmtTable::Align::LEFT}, 
+                    {'+', '?', '*', '.', '^'});
     table1 << col1 << col2 << col3;
     std::string result = table1.str();
     std::cout << result << std::endl;
@@ -328,7 +355,10 @@ TEST(FormatterTest, FmtTableCustomArgsAlignFrameDelim)
     std::vector<std::string> col1 = {"row1", "row2", "row3", "row4", "row5"};
     std::vector<int> col2 = {1, 2, 3, 4, 5};
     std::vector<float> col3 = {1.1, 2.2, 3.3, 4.4, 5.5};
-    FmtTable table1(titles, 5, fmts, 
+    FmtTable table1(titles, 
+                    5, 
+                    fmts, 
+                    0,
                     {FmtTable::Align::LEFT, FmtTable::Align::LEFT}, 
                     {'=', '/', '&', '#', '%'},
                     {'"', ']'});
@@ -348,6 +378,30 @@ TEST(FormatterTest, FmtTableCustomArgsAlignFrameDelim)
     EXPECT_EQ(result, ref);
 }
 
+TEST(FormatterTest, FmtTableCustomIndent)
+{
+    const std::vector<std::string> titles = {"title1", "t i t l e 2", "t-i-t-l-e-3"};
+    const std::vector<std::string> fmts = {"%s", "%d", "%f"};
+    FmtTable table(titles, 5, fmts, 4);
+    const std::vector<std::string> col1 = {"row1", "row2", "row3", "row4", "row5"};
+    const std::vector<int> col2 = {1, 2, 3, 4, 5};
+    const std::vector<float> col3 = {1.1, 2.2, 3.3, 4.4, 5.5};
+    table << col1 << col2 << col3;
+    const std::string result = table.str();
+    std::cout << result << std::endl;
+    std::string ref = "";
+    ref += "    --------------------------------\n";
+    ref += "     title1 t i t l e 2 t-i-t-l-e-3 \n";
+    ref += "    --------------------------------\n";
+    ref += "       row1           1    1.100000 \n";
+    ref += "       row2           2    2.200000 \n";
+    ref += "       row3           3    3.300000 \n";
+    ref += "       row4           4    4.400000 \n";
+    ref += "       row5           5    5.500000 \n";
+    ref += "    --------------------------------\n";
+    EXPECT_EQ(result, ref);
+}
+
 int main(int argc, char** argv) {
   ::testing::InitGoogleTest(&argc, argv);
   return RUN_ALL_TESTS();

source/module_base/timer.cpp

@@ -300,7 +300,11 @@ void timer::print_all(std::ofstream &ofs)
 
 	std::vector<std::string> titles = {"CLASS_NAME", "NAME", "TIME/s", "CALLS", "AVG/s", "PER/%"};
 	std::vector<std::string> formats = {"%-10s", "%-10s", "%6.2f", "%8d", "%6.2f", "%6.2f"};
-	FmtTable time_statistics(titles, pers.size(), formats, {FmtTable::Align::LEFT, FmtTable::Align::CENTER});
+	FmtTable time_statistics(/*titles=*/titles, 
+							 /*nrows=*/pers.size(), 
+							 /*formats=*/formats, 
+							 /*indent=*/0, 
+							 /*align=*/{/*value*/FmtTable::Align::LEFT, /*title*/FmtTable::Align::CENTER});
 	time_statistics << class_names << names << times << calls << avgs << pers;
 	const std::string table = "TIME STATISTICS\n" + time_statistics.str();
 	std::cout<<table<<std::endl;

source/module_basis/module_pw/pw_gatherscatter.h

@@ -14,7 +14,7 @@ namespace ModulePW
 template <typename T>
 void PW_Basis::gatherp_scatters(std::complex<T>* in, std::complex<T>* out) const
 {
-    ModuleBase::timer::tick(this->classname, "gatherp_scatters");
+    //ModuleBase::timer::tick(this->classname, "gatherp_scatters");
 
     if(this->poolnproc == 1) //In this case nst=nstot, nz = nplane, 
     {
@@ -32,7 +32,7 @@ void PW_Basis::gatherp_scatters(std::complex<T>* in, std::complex<T>* out) const
                 outp[iz] = inp[iz];
             }
         }
-        ModuleBase::timer::tick(this->classname, "gatherp_scatters");
+        //ModuleBase::timer::tick(this->classname, "gatherp_scatters");
         return;
     }
 #ifdef __MPI
@@ -55,10 +55,15 @@ void PW_Basis::gatherp_scatters(std::complex<T>* in, std::complex<T>* out) const
 
     //exchange data
     //(nplane,nstot) to (numz[ip],ns, poolnproc)
-    if(typeid(T) == typeid(double))
-	    MPI_Alltoallv(out, numr, startr, MPI_DOUBLE_COMPLEX, in, numg, startg, MPI_DOUBLE_COMPLEX, this->pool_world);
-    else if(typeid(T) == typeid(float))
-        MPI_Alltoallv(out, numr, startr, MPI_COMPLEX, in, numg, startg, MPI_COMPLEX, this->pool_world);
+	if(typeid(T) == typeid(double))
+	{
+		MPI_Alltoallv(out, numr, startr, MPI_DOUBLE_COMPLEX, in, numg, startg, MPI_DOUBLE_COMPLEX, this->pool_world);
+	}
+	else if(typeid(T) == typeid(float))
+	{
+		MPI_Alltoallv(out, numr, startr, MPI_COMPLEX, in, numg, startg, MPI_COMPLEX, this->pool_world);
+	}
+
     // change (nz,ns) to (numz[ip],ns, poolnproc)
 #ifdef _OPENMP
 #pragma omp parallel for collapse(2)
@@ -80,7 +85,7 @@ void PW_Basis::gatherp_scatters(std::complex<T>* in, std::complex<T>* out) const
 	}
 
 #endif
-    ModuleBase::timer::tick(this->classname, "gatherp_scatters");
+    //ModuleBase::timer::tick(this->classname, "gatherp_scatters");
     return;
 }
 
@@ -94,7 +99,7 @@ void PW_Basis::gatherp_scatters(std::complex<T>* in, std::complex<T>* out) const
 template <typename T>
 void PW_Basis::gathers_scatterp(std::complex<T>* in, std::complex<T>* out) const
 {
-    ModuleBase::timer::tick(this->classname, "gathers_scatterp");
+    //ModuleBase::timer::tick(this->classname, "gathers_scatterp");
 
     if(this->poolnproc == 1) //In this case nrxx=fftnx*fftny*nz, nst = nstot, 
     {
@@ -147,10 +152,15 @@ void PW_Basis::gathers_scatterp(std::complex<T>* in, std::complex<T>* out) const
 
 	//exchange data
     //(numz[ip],ns, poolnproc) to (nplane,nstot)
-    if(typeid(T) == typeid(double))
-	    MPI_Alltoallv(out, numg, startg, MPI_DOUBLE_COMPLEX, in, numr, startr, MPI_DOUBLE_COMPLEX, this->pool_world);
-    else if(typeid(T) == typeid(float))
-        MPI_Alltoallv(out, numg, startg, MPI_COMPLEX, in, numr, startr, MPI_COMPLEX, this->pool_world);
+	if(typeid(T) == typeid(double))
+	{
+		MPI_Alltoallv(out, numg, startg, MPI_DOUBLE_COMPLEX, in, numr, startr, MPI_DOUBLE_COMPLEX, this->pool_world);
+	}
+	else if(typeid(T) == typeid(float))
+	{
+		MPI_Alltoallv(out, numg, startg, MPI_COMPLEX, in, numr, startr, MPI_COMPLEX, this->pool_world);
+	}
+
 #ifdef _OPENMP
 #pragma omp parallel for schedule(static, 4096/sizeof(T))
 #endif
@@ -175,10 +185,10 @@ void PW_Basis::gathers_scatterp(std::complex<T>* in, std::complex<T>* out) const
 	}
 
 #endif
-    ModuleBase::timer::tick(this->classname, "gathers_scatterp");
+    //ModuleBase::timer::tick(this->classname, "gathers_scatterp");
     return;
 }
 
 
 
-}
+}