Merge branch 'develop' of https://github.com/deepmodeling/abacus-develop into docs

Author: YuLiu98

source/module_cell/module_symmetry/symmetry.cpp

@@ -423,7 +423,7 @@ int Symmetry::standard_lat(
 
     Symm_Other::right_hand_sense(a, b, c);
 	ModuleBase::GlobalFunc::ZEROS(cel_const, 6);
-	const double small = 1.0e-5;
+	const double small = PARAM.inp.symmetry_prec;
 
 	//---------------------------	
 	// 1. alpha == beta == gamma 

source/module_cell/module_symmetry/symmetry_basic.cpp

@@ -73,7 +73,7 @@ double Symmetry_Basic::check_diff(const double& x1, const double& x2)const
 	double diff = x1 - x2;
 	diff = fmod(diff + 100,1);
 	//for reasons of safety
-	if(fabs(diff - 1.0) < epsilon * 0.5)
+	if(fabs(diff - 1.0) < epsilon)
 	{
 		diff = 0;
 	}

source/module_esolver/esolver_gets.cpp

@@ -8,6 +8,7 @@
 #include "module_hamilt_lcao/hamilt_lcaodft/operator_lcao/operator_lcao.h"
 #include "module_io/print_info.h"
 #include "module_io/write_HS_R.h"
+#include "module_io/cal_r_overlap_R.h"
 
 namespace ModuleESolver
 {
@@ -128,6 +129,13 @@ void ESolver_GetS::runner(UnitCell& ucell, const int istep)
     std::cout << " The file is saved in " << fn << std::endl;
     ModuleIO::output_SR(pv, GlobalC::GridD, this->p_hamilt, fn);
 
+    if (PARAM.inp.out_mat_r)
+    {
+        cal_r_overlap_R r_matrix;
+        r_matrix.init(pv, orb_);
+        r_matrix.out_rR(istep);
+    }
+
     ModuleBase::timer::tick("ESolver_GetS", "runner");
 }