Code quality improvements (#7001)

* fix some small places in source_base

* refactor(cell_index): replace std::out_of_range with WARNING_QUIT

Replace standard exception handling with project-specific error handling
in cell_index.cpp to comply with ABACUS code style guidelines.

Changes:
- Replace 3 instances of 'throw std::out_of_range' with ModuleBase::WARNING_QUIT
  in functions: iw2l(), iw2z(), iw2m()
- Remove unnecessary #include <stdexcept>
- Fix incorrect error message strings in iw2z() and iw2m() (was 'iw2l')

This change follows the cpp-code-style skill rule that requires using
ModuleBase::WARNING/WARNING_QUIT instead of standard exceptions for
error handling in the ABACUS project.

* refactor(cell_index): add const qualifier to member functions

Add const qualifier to all getter and helper member functions in
CellIndex class to improve const-correctness according to cpp-code-style
skill guidelines.

Changes in cell_index.h:
- Add const to all public getter functions: get_nat(), get_ntype(),
  get_nw(), get_iwt(), get_maxL(), get_nchi(), get_atom_label()
- Add const to write_orb_info() and change parameter to const reference
- Add const to private helper functions: iat2it(), iat2ia(), iw2l(),
  iw2z(), iw2m()

Changes in cell_index.cpp:
- Update all function definitions to match header declarations
- Change write_orb_info parameter from std::string to const std::string&

This follows the ABACUS code style rule that getter functions and
functions that do not modify member state should be marked const.

* fix(density_matrix): 使用WARNING_QUIT替代throw语句

- 在density_matrix.cpp中添加了tool_quit.h头文件
- 将第616行的throw std::string替换为ModuleBase::WARNING_QUIT
- 统一了项目的错误处理方式，符合ABACUS代码规范

修改文件：
- source/source_estate/module_dm/density_matrix.cpp

影响范围：错误处理流程

* fix(symmetry_rotation): 修复C++14泛型lambda语法，改为C++11兼容写法

- 将泛型lambda [](auto x) 改为 [](double x)
- 符合ABACUS项目只支持C++11标准的要求
- Matrix3的元素类型为double，无需泛型

修改文件：
- source/source_lcao/module_ri/module_exx_symmetry/symmetry_rotation_output.cpp

* refactor(restart): replace std::runtime_error with WARNING_QUIT

Replace standard exception handling with project-specific error handling
in restart.cpp to comply with cpp-code-style skill guidelines.

Changes:
- Replace 4 instances of 'throw std::runtime_error' with ModuleBase::WARNING_QUIT
  in functions: write_file2() and read_file2()
- Remove unnecessary #include <stdexcept>
- Add #include "source_base/tool_quit.h"

This follows the ABACUS code style rule that requires using
ModuleBase::WARNING/WARNING_QUIT instead of standard exceptions.

* refactor(write_libxc_r): replace std::exception with WARNING_QUIT

Replace standard exception handling with project-specific error handling
in write_libxc_r.cpp to comply with cpp-code-style skill guidelines.

Changes:
- Replace 9 instances of throw with ModuleBase::WARNING_QUIT
  - throw std::domain_error -> WARNING_QUIT
  - throw std::invalid_argument -> WARNING_QUIT
- Remove #include <stdexcept>
- Add #include "source_base/tool_quit.h"

This follows the ABACUS code style rule that requires using
ModuleBase::WARNING/WARNING_QUIT instead of standard exceptions.

* style: unify code indentation to 4-space in source_md files

- Replace tabs with 4 spaces in md_func.cpp (lines 198-209)
- Replace tabs with 4 spaces in md_base.cpp (line 65)
- Replace tabs with 4 spaces in run_md.cpp (lines 59-61)

* refactor(source_io): replace std::exception with WARNING_QUIT

Replace standard exception handling with project-specific error handling
in source_io directory to comply with cpp-code-style skill guidelines.

Changes:
- Replace all instances of throw with ModuleBase::WARNING_QUIT
  - throw std::runtime_error -> WARNING_QUIT
  - throw std::logic_error -> WARNING_QUIT
  - throw std::invalid_argument -> WARNING_QUIT
  - throw std::domain_error -> WARNING_QUIT
- Remove unnecessary #include <stdexcept>
- Add #include "source_base/tool_quit.h" where needed

Files modified:
- module_restart/restart.cpp (4 instances)
- module_chgpot/write_libxc_r.cpp (9 instances)
- module_wannier/to_wannier90_lcao.h (1 instance)
- module_wannier/to_wannier90_lcao_in_pw.h (1 instance)
- module_wannier/to_wannier90_pw.h (1 instance)
- module_wannier/to_wannier90.cpp (1 instance)
- module_unk/berryphase.h (1 instance)
- module_parameter/read_input_tool.h (1 instance)
- module_parameter/input_conv.cpp (1 instance)

This follows the ABACUS code style rule that requires using
ModuleBase::WARNING/WARNING_QUIT instead of standard exceptions.

* revert(vector3): 撤销operator==的eps精度比较修改

- 恢复Vector3的operator==为直接比较
- 移除之前添加的eps精度比较逻辑

修改文件：
- source/source_base/vector3.h

* Revert "refactor(source_io): replace std::exception with WARNING_QUIT"

This reverts commit 39811c4.

* Revert "refactor(write_libxc_r): replace std::exception with WARNING_QUIT"

This reverts commit f0558c5.

* Revert "refactor(restart): replace std::runtime_error with WARNING_QUIT"

This reverts commit 5682e00.

---------

Co-authored-by: abacus_fixer <mohanchen@pku.eud.cn>

Author: mohanchen

source/source_base/matrix.cpp

@@ -323,35 +323,6 @@ double matrix::trace_on(void) const
     return tr;
 }
 
-//this function is wrong, and there is no file use this function.
-// void matrix::get_extreme_eigen_values(double &ev_lower, double &ev_upper)const
-// {
-//     double *a = new double[nr];
-//     double *b = new double[nr];
-//     for (int i = 0; i < nr; ++i)
-//     {
-//         double sum = 0.0;
-//         for(int j = 0; j < nc; ++j)
-//         {
-//             sum += fabs(c[i * nc + j]);
-//         }
-//         sum -= fabs(c[i * nc + i]);
-//         a[i] = c[i * nc + i] - sum;
-//         b[i] = c[i * nc + i] + sum;
-//     }
-
-//     ev_lower = a[0];
-//     ev_upper = b[0];
-
-//     for (int i = 1; i < nr; ++i)
-//     {
-//         if (a[i] < ev_lower) ev_lower = a[i];
-//         if (b[i] > ev_upper) ev_upper = b[i];
-//     }
-//     delete[] a;
-//     delete[] b;
-// }
-
 // Peize Lin add 2017-05-27
 void matrix::reshape( const int nr_new, const int nc_new, const bool flag_zero )
 {

source/source_base/matrix.h

@@ -10,7 +10,7 @@
 #include <ostream>
 #include<cassert>
 
-#include<fstream>// test
+#include <fstream> // test
 
 namespace ModuleBase
 {
@@ -80,7 +80,7 @@ class matrix
 
 	std::ostream & print( std::ostream & os, const double threshold=0.0 ) const;		// Peize Lin add 2021.09.08
 
-	using type=double;					// Peiae Lin add 2022.08.08 for template
+	using type=double;					// Peize Lin add 2022.08.08 for template
 };
 
 

source/source_cell/cell_index.cpp

@@ -2,7 +2,6 @@
 
 #include "source_base/name_angular.h"
 #include "source_base/tool_quit.h"
-#include <stdexcept>
 
 CellIndex::CellIndex(const std::vector<std::string>& atomLabels_in,
                      const std::vector<int>& atomCounts_in,
@@ -18,12 +17,12 @@ CellIndex::CellIndex(const std::vector<std::string>& atomLabels_in,
     this->cal_orbitalCounts();
 }
 
-int CellIndex::get_ntype()
+int CellIndex::get_ntype() const
 {
     return this->atomCounts.size();
 }
 
-int CellIndex::get_nat()
+int CellIndex::get_nat() const
 {
     int nat = 0;
     for (int it = 0; it < this->atomCounts.size(); ++it)
@@ -33,12 +32,12 @@ int CellIndex::get_nat()
     return nat;
 }
 
-int CellIndex::get_nat(int it)
+int CellIndex::get_nat(int it) const
 {
     return this->atomCounts[it];
 }
 
-int CellIndex::get_nw()
+int CellIndex::get_nw() const
 {
     int nw = 0;
     for (int it = 0; it < this->orbitalCounts.size(); ++it)
@@ -48,13 +47,13 @@ int CellIndex::get_nw()
     return nw;
 }
 
-int CellIndex::get_nw(int iat)
+int CellIndex::get_nw(int iat) const
 {
     int it = this->iat2it(iat);
     return this->orbitalCounts[it];
 }
 
-int CellIndex::get_iwt(int iat, int orbital_index)
+int CellIndex::get_iwt(int iat, int orbital_index) const
 {
     if (iat < 0 || iat >= this->get_nat())
     {
@@ -83,14 +82,14 @@ int CellIndex::get_iwt(int iat, int orbital_index)
     return iwt;
 }
 
-int CellIndex::get_maxL(int iat)
+int CellIndex::get_maxL(int iat) const
 {
     int it = this->iat2it(iat);
     return this->lnchiCounts[it].size() - 1;
 }
 
 /// @brief  get nchi
-int CellIndex::get_nchi(int iat, int L)
+int CellIndex::get_nchi(int iat, int L) const
 {
     int it = this->iat2it(iat);
     if (L < 0 || L >= this->lnchiCounts[it].size())
@@ -119,7 +118,7 @@ void CellIndex::check_atomCounts()
     }
 }
 
-std::string CellIndex::get_atom_label(int iat, bool order)
+std::string CellIndex::get_atom_label(int iat, bool order) const
 {
     int it = this->iat2it(iat);
     int ia = this->iat2ia(iat);
@@ -129,7 +128,7 @@ std::string CellIndex::get_atom_label(int iat, bool order)
     return atomType;
 }
 
-int CellIndex::iat2it(int iat)
+int CellIndex::iat2it(int iat) const
 {
     int running_iat = 0;
     int it = -1; // Tracks the index of the atom in atomLabels
@@ -151,7 +150,7 @@ int CellIndex::iat2it(int iat)
     return it;
 }
 
-int CellIndex::iat2ia(int iat)
+int CellIndex::iat2ia(int iat) const
 {
     int it = this->iat2it(iat);
     // sum of atoms of previous types
@@ -163,7 +162,7 @@ int CellIndex::iat2ia(int iat)
     return iat - running_iat;
 }
 
-int CellIndex::iw2l(int iat, int iw)
+int CellIndex::iw2l(int iat, int iw) const
 {
     int it = this->iat2it(iat);
     int maxL = this->lnchiCounts[it].size() - 1;
@@ -185,10 +184,10 @@ int CellIndex::iw2l(int iat, int iw)
     {
         ModuleBase::WARNING_QUIT("CellIndex::iw2l", "localized wave funciton index out of range [0, nw)");
     }
-    throw std::out_of_range(std::string(__FILE__)+" line "+std::to_string(__LINE__));
+    ModuleBase::WARNING_QUIT("CellIndex::iw2l", "unreachable code reached");
 }
 
-int CellIndex::iw2z(int iat, int iw)
+int CellIndex::iw2z(int iat, int iw) const
 {
     int it = this->iat2it(iat);
     int maxL = this->lnchiCounts[it].size() - 1;
@@ -208,12 +207,12 @@ int CellIndex::iw2z(int iat, int iw)
     }
     if (iw >= 0)
     {
-        ModuleBase::WARNING_QUIT("CellIndex::iw2l", "localized wave funciton index out of range [0, nw)");
+        ModuleBase::WARNING_QUIT("CellIndex::iw2z", "localized wave funciton index out of range [0, nw)");
     }
-    throw std::out_of_range(std::string(__FILE__)+" line "+std::to_string(__LINE__));
+    ModuleBase::WARNING_QUIT("CellIndex::iw2z", "unreachable code reached");
 }
 
-int CellIndex::iw2m(int iat, int iw)
+int CellIndex::iw2m(int iat, int iw) const
 {
     int it = this->iat2it(iat);
     int maxL = this->lnchiCounts[it].size() - 1;
@@ -233,9 +232,9 @@ int CellIndex::iw2m(int iat, int iw)
     }
     if (iw >= 0)
     {
-        ModuleBase::WARNING_QUIT("CellIndex::iw2l", "localized wave funciton index out of range [0, nw)");
+        ModuleBase::WARNING_QUIT("CellIndex::iw2m", "localized wave funciton index out of range [0, nw)");
     }
-    throw std::out_of_range(std::string(__FILE__)+" line "+std::to_string(__LINE__));
+    ModuleBase::WARNING_QUIT("CellIndex::iw2m", "unreachable code reached");
 }
 
 bool CellIndex::check_nspin(int nspin)
@@ -262,7 +261,7 @@ void CellIndex::cal_orbitalCounts()
     }
 }
 
-void CellIndex::write_orb_info(std::string out_dir)
+void CellIndex::write_orb_info(const std::string& out_dir) const
 {
     std::stringstream os;
     os << out_dir << "Orbital";

source/source_cell/cell_index.h

@@ -28,25 +28,25 @@ class CellIndex
 
   public:
     /// @brief the total number of atoms
-    int get_nat();
+    int get_nat() const;
     /// @brief the total number of atoms of a given type
-    int get_nat(int it);
+    int get_nat(int it) const;
     /// @brief get ntype
-    int get_ntype();
+    int get_ntype() const;
     /// @brief get nw
-    int get_nw();
+    int get_nw() const;
     /// @brief get nw of a given type
-    int get_nw(int iat);
+    int get_nw(int iat) const;
     /// @brief get iwt
-    int get_iwt(int iat, int orbital_index);
+    int get_iwt(int iat, int orbital_index) const;
     /// @brief get maximum L of a given atom
-    int get_maxL(int iat);
+    int get_maxL(int iat) const;
     /// @brief  get nchi of a given atom and a give L
-    int get_nchi(int iat, int L);
+    int get_nchi(int iat, int L) const;
     /// @brief get atom label of a given atom
-    std::string get_atom_label(int iat, bool order = false);
+    std::string get_atom_label(int iat, bool order = false) const;
     /// @brief write orbital info into file
-    void write_orb_info(std::string out_dir);
+    void write_orb_info(const std::string& out_dir) const;
 
   private:
     /// atomCounts is a vector used to store the number of atoms for each type
@@ -66,15 +66,15 @@ class CellIndex
     /// check if atomCounts is set ok
     void check_atomCounts();
     /// get type of atom from total order
-    int iat2it(int iat);
+    int iat2it(int iat) const;
     /// get index of atom in the same type
-    int iat2ia(int iat);
+    int iat2ia(int iat) const;
     /// get L from iw
-    int iw2l(int iat, int iw);
+    int iw2l(int iat, int iw) const;
     /// get Z from iw
-    int iw2z(int iat, int iw);
+    int iw2z(int iat, int iw) const;
     /// get m from iw
-    int iw2m(int iat, int iw);
+    int iw2m(int iat, int iw) const;
 };
 
 #endif // CELL_INDEX_H

source/source_estate/module_dm/density_matrix.cpp

@@ -5,6 +5,7 @@
 #include "source_base/memory.h"
 #include "source_base/timer.h"
 #include "source_base/tool_title.h"
+#include "source_base/tool_quit.h"
 #include "source_base/constants.h"
 #include "source_cell/klist.h"
 
@@ -612,7 +613,7 @@ void DensityMatrix<TK, TR>::switch_dmr(const int mode)
             }
             break;
         default:
-            throw std::string("Unknown mode in switch_dmr");
+            ModuleBase::WARNING_QUIT("density_matrix.cpp", "Unknown mode in switch_dmr");
         }
         ModuleBase::timer::tick("DensityMatrix", "switch_dmr");
     }

source/source_lcao/module_ri/module_exx_symmetry/symmetry_rotation_output.cpp

@@ -3,7 +3,7 @@ namespace ModuleSymmetry
 {
     std::string mat3_fmt(const ModuleBase::Matrix3& m)
     {
-        auto s = [](auto x) { return std::to_string(x); };
+        auto s = [](double x) { return std::to_string(x); };
         return s(m.e11) + " " + s(m.e12) + " " + s(m.e13) + "\n" +
                s(m.e21) + " " + s(m.e22) + " " + s(m.e23) + "\n" +
                s(m.e31) + " " + s(m.e32) + " " + s(m.e33);

source/source_md/md_base.cpp

@@ -62,7 +62,7 @@ void MD_base::setup(ModuleESolver::ESolver* p_esolver, const std::string& global
 
     // mohan add 2026-01-04
     const int stress_step = 0;
-	const int force_step = 0;
+    const int force_step = 0;
     const int istep_print = step_ + step_rst_ + 1;
 
 	ModuleIO::print_screen(stress_step, force_step, istep_print);

source/source_md/md_func.cpp

@@ -195,18 +195,18 @@ void init_vel(const UnitCell& unit_in,
     ModuleBase::Vector3<int> frozen;
     get_mass_mbl(unit_in, allmass, frozen, ionmbl);
     frozen_freedom = frozen.x + frozen.y + frozen.z;
-	if (frozen.x == 0)
-	{
-		++frozen_freedom;
-	}
-	if (frozen.y == 0)
-	{
-		++frozen_freedom;
-	}
-	if (frozen.z == 0)
-	{
-		++frozen_freedom;
-	}
+    if (frozen.x == 0)
+    {
+        ++frozen_freedom;
+    }
+    if (frozen.y == 0)
+    {
+        ++frozen_freedom;
+    }
+    if (frozen.z == 0)
+    {
+        ++frozen_freedom;
+    }
 
     if (unit_in.init_vel)
     {

source/source_md/run_md.cpp

@@ -56,8 +56,8 @@ void md_line(UnitCell& unit_in, ModuleESolver::ESolver* p_esolver, const Paramet
         }
         else
         {
-			// mohan add 2026-01-04
-			const int stress_step = 0;
+            // mohan add 2026-01-04
+            const int stress_step = 0;
             const int force_step = 0;
             const int istep_print = mdrun->step_ + mdrun->step_rst_ + 1;
             ModuleIO::print_screen(stress_step, force_step, istep_print);