Refactor: change R_index in class AtomPair to type `ModuleBase::v…

…ector3<int>` (#4243) * Refactor `R_index` in `AtomPair` * fix a semicolon * small fix * remove useless line * Refactor `find_R` and `find_matrix` * Refactor `AtomPair` constructor * Refactor `get_R_index` to return reference * rollback --------- Co-authored-by: Mohan Chen <[email protected]>
deepmodeling · Jun 13, 2024 · 156dac2 · 156dac2
1 parent c557163
commit 156dac2
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Showing 23 changed files with 290 additions and 140 deletions.
diff --git a/source/module_base/vector3.h b/source/module_base/vector3.h
@@ -33,8 +33,10 @@ template <class T> class Vector3
      * @param z1
      */
     Vector3(const T &x1 = 0, const T &y1 = 0, const T &z1 = 0) : x(x1), y(y1), z(z1){};
-    Vector3(const Vector3<T> &v) : x(v.x), y(v.y), z(v.z){}; // Peize Lin add 2018-07-16
-	explicit Vector3(const std::array<T,3> &v) :x(v[0]), y(v[1]), z(v[2]){}
+    Vector3(const Vector3<T> &v) : x(v.x), y(v.y), z(v.z){}; // Peize Lin add 2018-07-16   
+    explicit Vector3(const std::array<T,3> &v) :x(v[0]), y(v[1]), z(v[2]){}
+
+    Vector3(Vector3<T> &&v) noexcept : x(v.x), y(v.y), z(v.z) {}
 
     /**
      * @brief set a 3d vector

diff --git a/source/module_elecstate/module_dm/density_matrix.cpp b/source/module_elecstate/module_dm/density_matrix.cpp
@@ -121,7 +121,7 @@ void DensityMatrix<TK, TR>::init_DMR(Grid_Driver* GridD_in, const UnitCell* ucel
             }
             ModuleBase::Vector3<int>& R_index = adjs.box[ad];
             // std::cout << "R_index: " << R_index.x << " " << R_index.y << " " << R_index.z << std::endl;
-            hamilt::AtomPair<TR> tmp_ap(iat1, iat2, R_index.x, R_index.y, R_index.z, this->_paraV);
+            hamilt::AtomPair<TR> tmp_ap(iat1, iat2, R_index, this->_paraV);
             tmp_DMR->insert_pair(tmp_ap);
         }
     }
@@ -237,8 +237,8 @@ void DensityMatrix<TK, TR>::init_DMR(const hamilt::HContainer<TRShift>& DMR_in)
             const int iat2 = DMR_in.get_atom_pair(iap).get_atom_j();
             for(int ir = 0;ir<DMR_in.get_atom_pair(iap).get_R_size();ir++)
             {
-                const int* R_index = DMR_in.get_atom_pair(iap).get_R_index(ir);
-                hamilt::AtomPair<TR> tmp_ap(iat1, iat2, R_index[0], R_index[1], R_index[2], paraV_);
+                const ModuleBase::Vector3<int> R_index = DMR_in.get_atom_pair(iap).get_R_index(ir);
+                hamilt::AtomPair<TR> tmp_ap(iat1, iat2, R_index, paraV_);
                 tmp_DMR->insert_pair(tmp_ap);
             }
         }
@@ -417,8 +417,8 @@ void DensityMatrix<TK,TR>::cal_DMR_test()
             }
             for (int ir = 0; ir < tmp_ap.get_R_size(); ++ir)
             {
-                const int* r_index = tmp_ap.get_R_index(ir);
-                hamilt::BaseMatrix<TR>* tmp_matrix = tmp_ap.find_matrix(r_index[0], r_index[1], r_index[2]);
+                const ModuleBase::Vector3<int> r_index = tmp_ap.get_R_index(ir);
+                hamilt::BaseMatrix<TR>* tmp_matrix = tmp_ap.find_matrix(r_index);
 #ifdef __DEBUG
 				if (tmp_matrix == nullptr)
 				{
@@ -484,8 +484,8 @@ void DensityMatrix<std::complex<double>, double>::cal_DMR()
             }
             for (int ir = 0; ir < tmp_ap.get_R_size(); ++ir)
             {
-                const int* r_index = tmp_ap.get_R_index(ir);
-                hamilt::BaseMatrix<double>* tmp_matrix = tmp_ap.find_matrix(r_index[0], r_index[1], r_index[2]);
+                const ModuleBase::Vector3<int> r_index = tmp_ap.get_R_index(ir);
+                hamilt::BaseMatrix<double>* tmp_matrix = tmp_ap.find_matrix(r_index);
 #ifdef __DEBUG
                 if (tmp_matrix == nullptr)
                 {
@@ -644,12 +644,12 @@ void DensityMatrix<double, double>::cal_DMR()
                 throw std::string("Atom-pair not belong this process");
             }
             // R index
-            const int* r_index = tmp_ap.get_R_index(0);
+            const ModuleBase::Vector3<int> r_index = tmp_ap.get_R_index(0);
 #ifdef __DEBUG
             assert(tmp_ap.get_R_size() == 1);
-            assert(r_index[0] == 0 && r_index[1] == 0 && r_index[2] == 0);
+            assert(r_index.x == 0 && r_index.y == 0 && r_index.z == 0);
 #endif
-            hamilt::BaseMatrix<double>* tmp_matrix = tmp_ap.find_matrix(r_index[0], r_index[1], r_index[2]);
+            hamilt::BaseMatrix<double>* tmp_matrix = tmp_ap.find_matrix(r_index);
 #ifdef __DEBUG
             if (tmp_matrix == nullptr)
             {
@@ -695,9 +695,9 @@ void DensityMatrix<TK, TR>::sum_DMR_spin()
             hamilt::AtomPair<TR>& tmp_ap_down = tmp_DMR_down->get_atom_pair(i);
             for (int ir = 0; ir < tmp_ap_up.get_R_size(); ++ir)
             {
-                const int* r_index = tmp_ap_up.get_R_index(ir);
-                hamilt::BaseMatrix<double>* tmp_matrix_up = tmp_ap_up.find_matrix(r_index[0], r_index[1], r_index[2]);
-                hamilt::BaseMatrix<double>* tmp_matrix_down = tmp_ap_down.find_matrix(r_index[0], r_index[1], r_index[2]);
+                const ModuleBase::Vector3<int> r_index = tmp_ap_up.get_R_index(ir);
+                hamilt::BaseMatrix<double>* tmp_matrix_up = tmp_ap_up.find_matrix(r_index);
+                hamilt::BaseMatrix<double>* tmp_matrix_down = tmp_ap_down.find_matrix(r_index);
                 TR* ptr_up = tmp_matrix_up->get_pointer();
                 TR* ptr_down = tmp_matrix_down->get_pointer();
                 for (int i = 0; i < tmp_ap_up.get_size(); ++i)

diff --git a/source/module_esolver/io_npz.cpp b/source/module_esolver/io_npz.cpp
@@ -448,9 +448,9 @@ void ESolver_KS_LCAO<TK, TR>::output_mat_npz(std::string& zipname, const hamilt:
             for(int iR=0;iR<HR_serial[0].get_atom_pair(iap).get_R_size();++iR)
             {
                 auto& matrix = HR_serial[0].get_atom_pair(iap).get_HR_values(iR);
-                int* r_index = HR_serial[0].get_atom_pair(iap).get_R_index(iR);
+                const ModuleBase::Vector3<int> r_index = HR_serial[0].get_atom_pair(iap).get_R_index(iR);
                 filename = "mat_"+std::to_string(atom_i)+"_"+std::to_string(atom_j)+"_"
-                    +std::to_string(r_index[0])+"_"+std::to_string(r_index[1])+"_"+std::to_string(r_index[2]);
+                    +std::to_string(r_index.x)+"_"+std::to_string(r_index.y)+"_"+std::to_string(r_index.z);
                 std::vector<size_t> shape = {(size_t)row_size,(size_t)col_size};
                 cnpy::npz_save(zipname,filename,matrix.get_pointer(),shape,"a");
             }
@@ -472,10 +472,10 @@ void ESolver_KS_LCAO<TK, TR>::output_mat_npz(std::string& zipname, const hamilt:
         for(int iR=0;iR<hR.get_atom_pair(iap).get_R_size();++iR)
         {
             auto& matrix = hR.get_atom_pair(iap).get_HR_values(iR);
-            int* r_index = hR.get_atom_pair(iap).get_R_index(iR);
+            const ModuleBase::Vector3<int> r_index = hR.get_atom_pair(iap).get_R_index(iR);
 
             filename = "mat_"+std::to_string(atom_i)+"_"+std::to_string(atom_j)+"_"
-                +std::to_string(r_index[0])+"_"+std::to_string(r_index[1])+"_"+std::to_string(r_index[2]);
+                +std::to_string(r_index.x)+"_"+std::to_string(r_index.y)+"_"+std::to_string(r_index.z);
             std::vector<size_t> shape = {(size_t)row_size,(size_t)col_size};
             cnpy::npz_save(zipname,filename,matrix.get_pointer(),shape,"a");
         }

diff --git a/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/ekinetic_new.cpp b/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/ekinetic_new.cpp
@@ -84,7 +84,7 @@ void hamilt::EkineticNew<hamilt::OperatorLCAO<TK, TR>>::initialize_HR(Grid_Drive
             const int I2 = adjs.natom[ad];
             int iat2 = ucell->itia2iat(T2, I2);
             ModuleBase::Vector3<int>& R_index = adjs.box[ad];
-            hamilt::AtomPair<TR> tmp(iat1, iat2, R_index.x, R_index.y, R_index.z, paraV);
+            hamilt::AtomPair<TR> tmp(iat1, iat2, R_index, paraV);
             this->hR->insert_pair(tmp);
         }
     }
@@ -122,7 +122,7 @@ void hamilt::EkineticNew<hamilt::OperatorLCAO<TK, TR>>::calculate_HR()
             const ModuleBase::Vector3<int>& R_index2 = adjs.box[ad];
             ModuleBase::Vector3<double> dtau = this->ucell->cal_dtau(iat1, iat2, R_index2);
 
-            hamilt::BaseMatrix<TR>* tmp = this->HR_fixed->find_matrix(iat1, iat2, R_index2.x, R_index2.y, R_index2.z);
+            hamilt::BaseMatrix<TR>* tmp = this->HR_fixed->find_matrix(iat1, iat2, R_index2);
             if (tmp != nullptr)
             {
                 this->cal_HR_IJR(iat1, iat2, paraV, dtau, tmp->get_pointer());

diff --git a/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/overlap_new.cpp b/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/overlap_new.cpp
@@ -66,7 +66,7 @@ void hamilt::OverlapNew<hamilt::OperatorLCAO<TK, TR>>::initialize_SR(Grid_Driver
             {
                 continue;
             }
-            hamilt::AtomPair<TR> tmp(iat1, iat2, R_index.x, R_index.y, R_index.z, paraV);
+            hamilt::AtomPair<TR> tmp(iat1, iat2, R_index, paraV);
             SR->insert_pair(tmp);
         }
     }
@@ -92,9 +92,8 @@ void hamilt::OverlapNew<hamilt::OperatorLCAO<TK, TR>>::calculate_SR()
 
         for (int iR = 0; iR < tmp.get_R_size(); ++iR)
         {
-            const int* R_index = tmp.get_R_index(iR);
-            ModuleBase::Vector3<int> R_vector(R_index[0], R_index[1], R_index[2]);
-            auto dtau = ucell->cal_dtau(iat1, iat2, R_vector);
+            const ModuleBase::Vector3<int> R_index = tmp.get_R_index(iR);
+            auto dtau = ucell->cal_dtau(iat1, iat2, R_index);
             TR* data_pointer = tmp.get_pointer(iR);
             this->cal_SR_IJR(iat1, iat2, paraV, dtau, data_pointer);
         }

diff --git a/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/td_ekinetic_lcao.cpp b/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/td_ekinetic_lcao.cpp
@@ -92,8 +92,8 @@ void TDEkinetic<OperatorLCAO<TK, TR>>::calculate_HR()
             const ModuleBase::Vector3<int>& R_index2 = adjs.box[ad];
             ModuleBase::Vector3<double> dtau = this->ucell->cal_dtau(iat1, iat2, R_index2);
 
-            hamilt::BaseMatrix<std::complex<double>>* tmp = this->hR_tmp->find_matrix(iat1, iat2, R_index2.x, R_index2.y, R_index2.z);
-            hamilt::BaseMatrix<TR>* tmp1 = this->SR->find_matrix(iat1, iat2, R_index2.x, R_index2.y, R_index2.z);
+            hamilt::BaseMatrix<std::complex<double>>* tmp = this->hR_tmp->find_matrix(iat1, iat2, R_index2);
+            hamilt::BaseMatrix<TR>* tmp1 = this->SR->find_matrix(iat1, iat2, R_index2);
             if (tmp != nullptr)
             {
                 this->cal_HR_IJR(iat1, iat2, paraV, dtau, tmp->get_pointer(),tmp1->get_pointer());
@@ -309,11 +309,11 @@ void TDEkinetic<OperatorLCAO<TK, TR>>::initialize_HR_tmp(const Parallel_Orbitals
         hamilt::AtomPair<TR>& tmp = this->hR->get_atom_pair(i);
         for(int ir = 0;ir < tmp.get_R_size(); ++ir )
         {
-            const int* R_index = tmp.get_R_index(ir);
+            const ModuleBase::Vector3<int> R_index = tmp.get_R_index(ir);
             const int iat1 = tmp.get_atom_i();
             const int iat2 = tmp.get_atom_j(); 
 
-            hamilt::AtomPair<std::complex<double>> tmp1(iat1, iat2, R_index[0], R_index[1], R_index[2], paraV);
+            hamilt::AtomPair<std::complex<double>> tmp1(iat1, iat2, R_index, paraV);
             this->hR_tmp->insert_pair(tmp1);
         }
     }

diff --git a/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/td_nonlocal_lcao.cpp b/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/td_nonlocal_lcao.cpp
@@ -113,11 +113,11 @@ void hamilt::TDNonlocal<hamilt::OperatorLCAO<TK, TR>>::initialize_HR_tmp(const P
         hamilt::AtomPair<TR>& tmp = this->hR->get_atom_pair(i);
         for(int ir = 0;ir < tmp.get_R_size(); ++ir )
         {
-            const int* R_index = tmp.get_R_index(ir);
+            const ModuleBase::Vector3<int> R_index = tmp.get_R_index(ir);
             const int iat1 = tmp.get_atom_i();
             const int iat2 = tmp.get_atom_j(); 
 
-            hamilt::AtomPair<std::complex<double>> tmp1(iat1, iat2, R_index[0], R_index[1], R_index[2], paraV);
+            hamilt::AtomPair<std::complex<double>> tmp1(iat1, iat2, R_index, paraV);
             this->hR_tmp->insert_pair(tmp1);
         }
     }

diff --git a/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/veff_lcao.cpp b/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/veff_lcao.cpp
@@ -44,7 +44,7 @@ void Veff<OperatorLCAO<TK, TR>>::initialize_HR(const UnitCell* ucell_in,
             if (ucell_in->cal_dtau(iat1, iat2, R_index2).norm() * ucell_in->lat0
                 < orb.Phi[T1].getRcut() + orb.Phi[T2].getRcut())
             {
-                hamilt::AtomPair<TR> tmp(iat1, iat2, R_index2.x, R_index2.y, R_index2.z, paraV);
+                hamilt::AtomPair<TR> tmp(iat1, iat2, R_index2, paraV);
                 this->hR->insert_pair(tmp);
             }
         }

diff --git a/source/module_hamilt_lcao/hamilt_lcaodft/spar_hsr.cpp b/source/module_hamilt_lcao/hamilt_lcaodft/spar_hsr.cpp
@@ -150,8 +150,8 @@ void sparse_format::cal_HContainer_d(
         for(int iR=0;iR<hR.get_atom_pair(iap).get_R_size();++iR)
         {
             auto& matrix = hR.get_atom_pair(iap).get_HR_values(iR);
-            int* r_index = hR.get_atom_pair(iap).get_R_index(iR);
-            Abfs::Vector3_Order<int> dR(r_index[0], r_index[1], r_index[2]);
+            const ModuleBase::Vector3<int> r_index = hR.get_atom_pair(iap).get_R_index(iR);
+            Abfs::Vector3_Order<int> dR(r_index.x, r_index.y, r_index.z);
             for(int i=0;i<row_size;++i)
             {
                 int mu = row_indexes[start_i+i];
@@ -194,8 +194,8 @@ void sparse_format::cal_HContainer_cd(
         for(int iR=0;iR<hR.get_atom_pair(iap).get_R_size();++iR)
         {
             auto& matrix = hR.get_atom_pair(iap).get_HR_values(iR);
-            int* r_index = hR.get_atom_pair(iap).get_R_index(iR);
-            Abfs::Vector3_Order<int> dR(r_index[0], r_index[1], r_index[2]);
+            const ModuleBase::Vector3<int> r_index = hR.get_atom_pair(iap).get_R_index(iR);
+            Abfs::Vector3_Order<int> dR(r_index.x, r_index.y, r_index.z);
             for(int i=0;i<row_size;++i)
             {
                 int mu = row_indexes[start_i+i];
@@ -238,8 +238,8 @@ void sparse_format::cal_HContainer_td(
         for(int iR=0;iR<hR.get_atom_pair(iap).get_R_size();++iR)
         {
             auto& matrix = hR.get_atom_pair(iap).get_HR_values(iR);
-            int* r_index = hR.get_atom_pair(iap).get_R_index(iR);
-            Abfs::Vector3_Order<int> dR(r_index[0], r_index[1], r_index[2]);
+            const ModuleBase::Vector3<int> r_index = hR.get_atom_pair(iap).get_R_index(iR);
+            Abfs::Vector3_Order<int> dR(r_index.x, r_index.y, r_index.z);
             for(int i=0;i<row_size;++i)
             {
                 int mu = row_indexes[start_i+i];

diff --git a/source/module_hamilt_lcao/module_gint/gint.cpp b/source/module_hamilt_lcao/module_gint/gint.cpp
@@ -715,10 +715,10 @@ void Gint::transfer_DM2DtoGrid(std::vector<hamilt::HContainer<double>*> DM2D)
 			int iat2 = ap.get_atom_j();
 			for(int ir = 0;ir<ap.get_R_size();++ir)
 			{
-				int* r_index = ap.get_R_index(ir);
+				const ModuleBase::Vector3<int> r_index = ap.get_R_index(ir);
 				for (int is = 0; is < 4; is++)
 				{
-					tmp_pointer[is] = this->DMRGint[is]->find_matrix(iat1, iat2, r_index[0], r_index[1], r_index[2])->get_pointer();
+					tmp_pointer[is] = this->DMRGint[is]->find_matrix(iat1, iat2, r_index)->get_pointer();
 				}
 				double* data_full = ap.get_pointer(ir);
 				for(int irow=0;irow<ap.get_row_size();irow += 2)

diff --git a/source/module_hamilt_lcao/module_gint/gint_k_pvpr.cpp b/source/module_hamilt_lcao/module_gint/gint_k_pvpr.cpp
@@ -492,7 +492,7 @@ void Gint_k::transfer_pvpR(hamilt::HContainer<double> *hR,const UnitCell* ucell_
 
                             int ixxx = DM_start + this->gridt->find_R2st[iat][nad];
 
-                            hamilt::BaseMatrix<double>* tmp_matrix = this->hRGint->find_matrix(iat, iat2, dR.x, dR.y, dR.z);
+                            hamilt::BaseMatrix<double>* tmp_matrix = this->hRGint->find_matrix(iat, iat2, dR);
 #ifdef __DEBUG
                             assert(tmp_matrix != nullptr);
 #endif
@@ -508,7 +508,7 @@ void Gint_k::transfer_pvpR(hamilt::HContainer<double> *hR,const UnitCell* ucell_
                             // save the lower triangle.
                             if(iat < iat2)//skip iat == iat2
                             {
-                                hamilt::BaseMatrix<double>* conj_matrix = this->hRGint->find_matrix(iat2, iat, -dR.x, -dR.y, -dR.z);
+                                hamilt::BaseMatrix<double>* conj_matrix = this->hRGint->find_matrix(iat2, iat, -dR);
 #ifdef __DEBUG
                                 assert(conj_matrix != nullptr);
 #endif
@@ -617,7 +617,7 @@ void Gint_k::transfer_pvpR(hamilt::HContainer<std::complex<double>> *hR,const Un
 
                             int ixxx = DM_start + this->gridt->find_R2st[iat][nad];
 
-                            hamilt::BaseMatrix<std::complex<double>>* tmp_matrix = this->hRGintCd->find_matrix(iat, iat2, dR.x, dR.y, dR.z);
+                            hamilt::BaseMatrix<std::complex<double>>* tmp_matrix = this->hRGintCd->find_matrix(iat, iat2, dR);
 #ifdef __DEBUG
                             assert(tmp_matrix != nullptr);
 #endif
@@ -666,7 +666,7 @@ void Gint_k::transfer_pvpR(hamilt::HContainer<std::complex<double>> *hR,const Un
                             // save the lower triangle.
                             if(iat < iat2)
                             {
-                                hamilt::BaseMatrix<std::complex<double>>* conj_matrix = this->hRGintCd->find_matrix(iat2, iat, -dR.x, -dR.y, -dR.z);
+                                hamilt::BaseMatrix<std::complex<double>>* conj_matrix = this->hRGintCd->find_matrix(iat2, iat, -dR);
 #ifdef __DEBUG
                                 assert(conj_matrix != nullptr);
 #endif