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Refactor: change R_index in class AtomPair to type ModuleBase::vector3<int> #4243

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merged 17 commits into from
Jun 13, 2024
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Refactor: change R_index in class AtomPair to type ModuleBase::vector3<int> #4243

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e2d5237
Refactor `R_index` in `AtomPair`
DylanWRh May 27, 2024
3f33970
fix a semicolon
DylanWRh May 27, 2024
45cae55
small fix
DylanWRh May 27, 2024
de7670a
Merge branch 'develop' into develop
DylanWRh May 27, 2024
e155bfa
Merge branch 'develop' into develop
DylanWRh May 28, 2024
e17dfa7
Merge branch 'develop' into develop
mohanchen Jun 1, 2024
a15d5ea
Merge branch 'deepmodeling:develop' into develop
DylanWRh Jun 3, 2024
36d490c
Merge branch 'develop' into develop
DylanWRh Jun 3, 2024
31e92ce
Merge branch 'deepmodeling:develop' into develop
DylanWRh Jun 4, 2024
614e454
remove useless line
DylanWRh Jun 4, 2024
57bd414
Merge branch 'develop' of https://github.com/DylanWRh/abacus-develop …
DylanWRh Jun 4, 2024
170f58e
Merge branch 'develop' into develop
DylanWRh Jun 4, 2024
f9eaaa4
Refactor `find_R` and `find_matrix`
DylanWRh Jun 4, 2024
713541b
Merge branch 'develop' of https://github.com/DylanWRh/abacus-develop …
DylanWRh Jun 4, 2024
c5d5a5e
Refactor `AtomPair` constructor
DylanWRh Jun 5, 2024
311874c
Refactor `get_R_index` to return reference
DylanWRh Jun 5, 2024
1c5da6f
rollback
DylanWRh Jun 5, 2024
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6 changes: 4 additions & 2 deletions source/module_base/vector3.h
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Expand Up @@ -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
Expand Down
26 changes: 13 additions & 13 deletions source/module_elecstate/module_dm/density_matrix.cpp
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Expand Up @@ -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);
}
}
Expand Down Expand Up @@ -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);
}
}
Expand Down Expand Up @@ -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)
{
Expand Down Expand Up @@ -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);
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hamilt::BaseMatrix<double>* tmp_matrix = tmp_ap.find_matrix(r_index);
#ifdef __DEBUG
if (tmp_matrix == nullptr)
{
Expand Down Expand Up @@ -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)
{
Expand Down Expand Up @@ -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)
Expand Down
8 changes: 4 additions & 4 deletions source/module_esolver/io_npz.cpp
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Expand Up @@ -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");
}
Expand All @@ -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");
}
Expand Down
4 changes: 2 additions & 2 deletions source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/ekinetic_new.cpp
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Expand Up @@ -83,7 +83,7 @@ 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);
}
}
Expand Down Expand Up @@ -121,7 +121,7 @@ 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());
Expand Down
7 changes: 3 additions & 4 deletions source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/overlap_new.cpp
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Expand Up @@ -65,7 +65,7 @@ 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);
}
}
Expand All @@ -91,9 +91,8 @@ 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);
}
Expand Down
8 changes: 4 additions & 4 deletions source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/td_ekinetic_lcao.cpp
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Expand Up @@ -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());
Expand Down Expand Up @@ -310,11 +310,11 @@ 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);
}
}
Expand Down
4 changes: 2 additions & 2 deletions source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/td_nonlocal_lcao.cpp
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Expand Up @@ -112,11 +112,11 @@ 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);
}
}
Expand Down
2 changes: 1 addition & 1 deletion source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/veff_lcao.cpp
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Expand Up @@ -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);
}
}
Expand Down
12 changes: 6 additions & 6 deletions source/module_hamilt_lcao/hamilt_lcaodft/spar_hsr.cpp
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Expand Up @@ -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];
Expand Down Expand Up @@ -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];
Expand Down Expand Up @@ -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];
Expand Down
4 changes: 2 additions & 2 deletions source/module_hamilt_lcao/module_gint/gint.cpp
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Expand Up @@ -725,10 +725,10 @@ 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)
Expand Down
8 changes: 4 additions & 4 deletions source/module_hamilt_lcao/module_gint/gint_k_pvpr.cpp
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Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
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