refactor(cell): replace raw pointer members with std::vector in Symmetry

source/source_cell/module_symmetry/symm_analysis.cpp

@@ -36,20 +36,14 @@ void Symmetry::analy_sys(const Lattice& lat, const Statistics& st, Atom* atoms,
 
     assert(ntype>0);
 
-    this->na = new int[ntype];
-    this->istart = new int[ntype];  // start number of atom.
-    this->index = new int [nat + 2];   // index of atoms
-
-    ModuleBase::GlobalFunc::ZEROS(na, ntype);
-    ModuleBase::GlobalFunc::ZEROS(istart, ntype);
-    ModuleBase::GlobalFunc::ZEROS(index, nat+2);
+    this->na.assign(ntype, 0);
+    this->istart.assign(ntype, 0);  // start number of atom.
+    this->index.assign(nat + 2, 0);   // index of atoms
 
     // atom positions
     // used in checksym.
-    newpos = new double[3*nat]; // positions of atoms before rotation
-    rotpos = new double[3*nat]; // positions of atoms after rotation
-    ModuleBase::GlobalFunc::ZEROS(newpos, 3*nat);
-    ModuleBase::GlobalFunc::ZEROS(rotpos, 3*nat);
+    newpos.assign(3 * nat, 0.0); // positions of atoms before rotation
+    rotpos.assign(3 * nat, 0.0); // positions of atoms after rotation
 
     this->a1 = lat.a1;
     this->a2 = lat.a2;
@@ -91,7 +85,7 @@ void Symmetry::analy_sys(const Lattice& lat, const Statistics& st, Atom* atoms,
             // s: the input lattice vectors, input
             // find the real_brav type accordiing to lattice vectors.
             this->lattice_type(this->a1, this->a2, this->a3, this->s1, this->s2, this->s3,
-                    this->cel_const, this->pre_const, this->real_brav, ilattname, atoms, true, this->newpos, symmetry_prec);
+                    this->cel_const, this->pre_const, this->real_brav, ilattname, atoms, true, this->newpos.data(), symmetry_prec);
 
             ofs_running << " For optimal symmetric configuration:" << std::endl;
             ModuleBase::GlobalFunc::OUT(ofs_running, "BRAVAIS TYPE", real_brav);
@@ -104,7 +98,7 @@ void Symmetry::analy_sys(const Lattice& lat, const Statistics& st, Atom* atoms,
             optlat.e31 = a3.x; optlat.e32 = a3.y; optlat.e33 = a3.z;
 
             // count the number of primitive cells in the supercell
-            this->pricell(this->newpos, atoms);
+            this->pricell(this->newpos.data(), atoms);
 
             test_brav = true; // output the real ibrav and point group
 
@@ -129,9 +123,9 @@ void Symmetry::analy_sys(const Lattice& lat, const Statistics& st, Atom* atoms,
                 // get the real symmetry operations according to the input structure
                 // nrot_out: the number of pure point group rotations
                 // nrotk_out: the number of all space group operations
-                this->getgroup(nrot_out, nrotk_out, ofs_running, this->nop, this->symop, 
-                        this->gmatrix, this->gtrans, this->newpos, this->rotpos, this->index, 
-                        this->ntype, this->itmin_type, this->itmin_start, this->istart, this->na);
+                this->getgroup(nrot_out, nrotk_out, ofs_running, this->nop, this->symop,
+                        this->gmatrix, this->gtrans, this->newpos.data(), this->rotpos.data(), this->index.data(),
+                        this->ntype, this->itmin_type, this->itmin_start, this->istart.data(), this->na.data());
             }
         };
 
@@ -309,11 +303,6 @@ void Symmetry::analy_sys(const Lattice& lat, const Statistics& st, Atom* atoms,
         }
     }
 
-    delete[] newpos;
-    delete[] na;
-    delete[] rotpos;
-    delete[] index;
-    delete[] istart;
     ModuleBase::timer::end("Symmetry","analy_sys");
     return;
 }

source/source_cell/module_symmetry/symm_magnetic.cpp

@@ -70,10 +70,10 @@ void Symmetry::analyze_magnetic_group(const Atom* atoms, const Statistics& st, i
     }
 
     // 3. analyze the effective structure
-    this->getgroup(nrot_out, nrotk_out, GlobalV::ofs_running, 
-            this->nop, this->symop, this->gmatrix, 
-            this->gtrans, mag_pos.data(), this->rotpos, 
-            this->index, mag_type_atoms.size(), mag_itmin_type, 
+    this->getgroup(nrot_out, nrotk_out, GlobalV::ofs_running,
+            this->nop, this->symop, this->gmatrix,
+            this->gtrans, mag_pos.data(), this->rotpos.data(),
+            this->index.data(), mag_type_atoms.size(), mag_itmin_type,
             mag_itmin_start, mag_istart.data(), mag_na.data());
 
 }

source/source_cell/module_symmetry/symm_pricell.cpp

@@ -20,7 +20,7 @@ void Symmetry::pricell(double* pos, const Atom* atoms)
         }
 
         //order original atomic positions for current species
-        this->atom_ordering_new(pos + istart[it] * 3, na[it], index + istart[it]);
+        this->atom_ordering_new(pos + istart[it] * 3, na[it], index.data() + istart[it]);
         //copy pos to rotpos
         for (int j = istart[it]; j < istart[it] + na[it]; ++j)
         {
@@ -63,7 +63,7 @@ void Symmetry::pricell(double* pos, const Atom* atoms)
                 this->check_boundary( rotpos[ia*3+2] );
             }
             //order translated atomic positions for current species
-            this->atom_ordering_new(rotpos + istart[it] * 3, na[it], index + istart[it]);
+            this->atom_ordering_new(rotpos.data() + istart[it] * 3, na[it], index.data() + istart[it]);
         }
 
         no_diff = true;
@@ -130,7 +130,7 @@ void Symmetry::pricell(double* pos, const Atom* atoms)
         ptrans_array[i*3+1]=ptrans[i].y;
         ptrans_array[i*3+2]=ptrans[i].z;
     }
-    this->atom_ordering_new(ptrans_array, ntrans, index);
+    this->atom_ordering_new(ptrans_array, ntrans, index.data());
     // std::cout<<"final ptrans:"<<std::endl;
     for(int i=0;i<ntrans;++i)
     {

source/source_cell/module_symmetry/symmetry.cpp

@@ -19,9 +19,9 @@ void Symmetry::set_atom_map(const Atom* atoms)
         this->isym_rotiat_[i].resize(this->nat, -1);
     }
 
-    double* pos = this->newpos;
-    double* rotpos = this->rotpos;
-    ModuleBase::GlobalFunc::ZEROS(pos, this->nat * 3);
+    std::fill(this->newpos.begin(), this->newpos.end(), 0.0);
+    double* pos = this->newpos.data();
+    double* rotpos = this->rotpos.data();
     int iat = 0;
     for (int it = 0; it < this->ntype; it++)
     {

source/source_cell/module_symmetry/symmetry.h

@@ -12,6 +12,8 @@
 #include "source_base/constants.h"
 #include "symm_basic.h"
 
+#include <vector>
+
 namespace ModuleSymmetry
 {
 
@@ -57,20 +59,20 @@ class Symmetry : public Symmetry_Basic
 
     int ntype=0;      ///< the number of atomic species
     int nat  =0;       ///< the number of all atoms
-    int *na  =nullptr;///< number of atoms for each species
-    int *istart=nullptr; ///< start number of atom
+    std::vector<int> na;     ///< number of atoms for each species
+    std::vector<int> istart; ///< start number of atom
     int itmin_type=0; ///< the type has smallest number of atoms
     int itmin_start=0;
 
     /// @brief direct coordinates of atoms
-    double *newpos=nullptr;
+    std::vector<double> newpos;
     /// @brief positions of atoms after rotation
-    double *rotpos=nullptr;
+    std::vector<double> rotpos;
 
 
     std::vector<ModuleBase::Vector3<double>> ptrans; ///< the translation vectors of the primitive cell in the input structure
     int ncell=1;    ///< the number of primitive cells within one supercell
-    int *index=nullptr;
+    std::vector<int> index;
 
     double cel_const[6]={0.0};
     double pcel_const[6]={0.0};    ///< cel_const of primitive cell