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Refactor: hs file output #7367

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5fdd954
feat(io): extend out_mat_hs2 to support all 4 CSR sparse output formats
goodchong May 20, 2026
5cb0124
fix(io): include sparse_matrix.h in write_HS_R.cpp
goodchong May 20, 2026
7b44e92
fix(io): fix null pointer dereference in save_sparse binary mode
goodchong May 20, 2026
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79 changes: 52 additions & 27 deletions source/source_io/module_hs/cal_r_overlap_R.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -595,7 +595,7 @@ void cal_r_overlap_R::get_psi_r_beta(const UnitCell& ucell,
}


void cal_r_overlap_R::out_rR(const UnitCell& ucell, const Grid_Driver& gd, const int& istep)
void cal_r_overlap_R::out_rR(const UnitCell& ucell, const Grid_Driver& gd, const int& istep, const bool& reduce)
{
ModuleBase::TITLE("cal_r_overlap_R", "out_rR");
ModuleBase::timer::start("cal_r_overlap_R", "out_rR");
Expand Down Expand Up @@ -631,10 +631,14 @@ void cal_r_overlap_R::out_rR(const UnitCell& ucell, const Grid_Driver& gd, const

std::stringstream tem1;
tem1 << PARAM.globalv.global_out_dir << "tmp-rr.csr";
if (!reduce && GlobalV::NPROC > 1)
{
tem1 << "." << GlobalV::DRANK;
}
std::ofstream ofs_tem1;
std::ifstream ifs_tem1;

if (GlobalV::DRANK == 0)
if (!reduce || GlobalV::DRANK == 0)
{
if (binary)
{
Expand Down Expand Up @@ -754,26 +758,32 @@ void cal_r_overlap_R::out_rR(const UnitCell& ucell, const Grid_Driver& gd, const
}
}

Parallel_Reduce::reduce_all(rR_nonzero_num, 3);
if (reduce)
{
Parallel_Reduce::reduce_all(rR_nonzero_num, 3);
}

if (rR_nonzero_num[0] || rR_nonzero_num[1] || rR_nonzero_num[2])
{
output_R_number++;

if (binary)
{
ofs_tem1.write(reinterpret_cast<char*>(&dRx), sizeof(int));
ofs_tem1.write(reinterpret_cast<char*>(&dRy), sizeof(int));
ofs_tem1.write(reinterpret_cast<char*>(&dRz), sizeof(int));
}
else
if (!reduce || GlobalV::DRANK == 0)
{
ofs_tem1 << dRx << " " << dRy << " " << dRz << std::endl;
if (binary)
{
ofs_tem1.write(reinterpret_cast<char*>(&dRx), sizeof(int));
ofs_tem1.write(reinterpret_cast<char*>(&dRy), sizeof(int));
ofs_tem1.write(reinterpret_cast<char*>(&dRz), sizeof(int));
}
else
{
ofs_tem1 << dRx << " " << dRy << " " << dRz << std::endl;
}
}

for (int direction = 0; direction < 3; ++direction)
{
if (GlobalV::DRANK == 0)
if (!reduce || GlobalV::DRANK == 0)
{
if (binary)
{
Expand All @@ -791,7 +801,8 @@ void cal_r_overlap_R::out_rR(const UnitCell& ucell, const Grid_Driver& gd, const
psi_r_psi_sparse[direction],
sparse_threshold,
binary,
*(this->ParaV));
*(this->ParaV),
reduce);
}
else
{
Expand All @@ -801,7 +812,7 @@ void cal_r_overlap_R::out_rR(const UnitCell& ucell, const Grid_Driver& gd, const
}
}

if (GlobalV::DRANK == 0)
if (!reduce || GlobalV::DRANK == 0)
{
std::ofstream out_r;
std::stringstream ssr;
Expand All @@ -814,6 +825,10 @@ void cal_r_overlap_R::out_rR(const UnitCell& ucell, const Grid_Driver& gd, const
{
ssr << PARAM.globalv.global_out_dir << "rr.csr";
}
if (!reduce && GlobalV::NPROC > 1)
{
ssr << "." << GlobalV::DRANK;
}

if (binary) // .dat
{
Expand Down Expand Up @@ -864,7 +879,7 @@ void cal_r_overlap_R::out_rR(const UnitCell& ucell, const Grid_Driver& gd, const
return;
}

void cal_r_overlap_R::out_rR_other(const UnitCell& ucell, const int& istep, const std::set<Abfs::Vector3_Order<int>>& output_R_coor)
void cal_r_overlap_R::out_rR_other(const UnitCell& ucell, const int& istep, const std::set<Abfs::Vector3_Order<int>>& output_R_coor, const bool& reduce)
{
ModuleBase::TITLE("cal_r_overlap_R", "out_rR_other");
ModuleBase::timer::start("cal_r_overlap_R", "out_rR_other");
Expand All @@ -887,8 +902,12 @@ void cal_r_overlap_R::out_rR_other(const UnitCell& ucell, const int& istep, cons
{
ssr << PARAM.globalv.global_out_dir << "rr.csr";
}
if (!reduce && GlobalV::NPROC > 1)
{
ssr << "." << GlobalV::DRANK;
}

if (GlobalV::DRANK == 0)
if (!reduce || GlobalV::DRANK == 0)
{
if (binary)
{
Expand Down Expand Up @@ -1030,22 +1049,28 @@ void cal_r_overlap_R::out_rR_other(const UnitCell& ucell, const int& istep, cons
}
}

Parallel_Reduce::reduce_all(rR_nonzero_num, 3);

if (binary) // .dat
if (reduce)
{
out_r.write(reinterpret_cast<char*>(&dRx), sizeof(int));
out_r.write(reinterpret_cast<char*>(&dRy), sizeof(int));
out_r.write(reinterpret_cast<char*>(&dRz), sizeof(int));
Parallel_Reduce::reduce_all(rR_nonzero_num, 3);
}
else // .txt

if (!reduce || GlobalV::DRANK == 0)
{
out_r << dRx << " " << dRy << " " << dRz << std::endl;
if (binary) // .dat
{
out_r.write(reinterpret_cast<char*>(&dRx), sizeof(int));
out_r.write(reinterpret_cast<char*>(&dRy), sizeof(int));
out_r.write(reinterpret_cast<char*>(&dRz), sizeof(int));
}
else // .txt
{
out_r << dRx << " " << dRy << " " << dRz << std::endl;
}
}

for (int direction = 0; direction < 3; ++direction)
{
if (GlobalV::DRANK == 0)
if (!reduce || GlobalV::DRANK == 0)
{
if (binary)
{
Expand All @@ -1059,7 +1084,7 @@ void cal_r_overlap_R::out_rR_other(const UnitCell& ucell, const int& istep, cons

if (rR_nonzero_num[direction])
{
ModuleIO::output_single_R(out_r, psi_r_psi_sparse[direction], sparse_threshold, binary, *(this->ParaV));
ModuleIO::output_single_R(out_r, psi_r_psi_sparse[direction], sparse_threshold, binary, *(this->ParaV), reduce);
}
else
{
Expand All @@ -1068,7 +1093,7 @@ void cal_r_overlap_R::out_rR_other(const UnitCell& ucell, const int& istep, cons
}
}

if (GlobalV::DRANK == 0)
if (!reduce || GlobalV::DRANK == 0)
{
out_r.close();
}
Expand Down
4 changes: 2 additions & 2 deletions source/source_io/module_hs/cal_r_overlap_R.h
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56,8 +56,8 @@ class cal_r_overlap_R
const ModuleBase::Vector3<double>& R2,
const int& T2
);
void out_rR(const UnitCell& ucell, const Grid_Driver& gd, const int& istep);
void out_rR_other(const UnitCell& ucell, const int& istep, const std::set<Abfs::Vector3_Order<int>>& output_R_coor);
void out_rR(const UnitCell& ucell, const Grid_Driver& gd, const int& istep, const bool& reduce = true);
void out_rR_other(const UnitCell& ucell, const int& istep, const std::set<Abfs::Vector3_Order<int>>& output_R_coor, const bool& reduce = true);

private:
void initialize_orb_table(const UnitCell& ucell, const LCAO_Orbitals& orb);
Expand Down
26 changes: 22 additions & 4 deletions source/source_io/module_hs/output_mat_sparse.cpp
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

#include "cal_r_overlap_R.h"
#include "source_io/module_hs/write_HS_R.h"
#include "source_io/module_parameter/parameter.h"

namespace ModuleIO
{
Expand All @@ -23,10 +24,13 @@ void output_mat_sparse(const bool& out_mat_dh,
{
LCAO_HS_Arrays HS_Arrays; // store sparse arrays

const int out_mat_hsR = PARAM.inp.out_mat_hs2[0];
const bool reduce = (out_mat_hsR != 3 && out_mat_hsR != 4);
const bool binary = (out_mat_hsR == 2 || out_mat_hsR == 4);
//! generate a file containing the kinetic energy matrix
if (out_mat_t)
{
output_TR(istep, ucell, pv, HS_Arrays, grid, two_center_bundle, orb);
output_TR(istep, ucell, pv, HS_Arrays, grid, two_center_bundle, orb, "trs1_nao.csr", binary, 1e-10, reduce);
}

//! generate a file containing the derivatives of the Hamiltonian matrix (in Ry/Bohr)
Expand All @@ -40,7 +44,10 @@ void output_mat_sparse(const bool& out_mat_dh,
grid,
two_center_bundle,
orb,
kv);
kv,
binary,
1e-10,
reduce);
}
//! generate a file containing the derivatives of the overlap matrix (in Ry/Bohr)
if (out_mat_ds)
Expand All @@ -52,15 +59,26 @@ void output_mat_sparse(const bool& out_mat_dh,
grid,
two_center_bundle,
orb,
kv);
kv,
binary,
1e-10,
reduce);
}

// add by jingan for out r_R matrix 2019.8.14
if (out_mat_r)
{
cal_r_overlap_R r_matrix;
r_matrix.init(ucell, pv, orb);
r_matrix.out_rR(ucell, grid, istep);
r_matrix.binary = binary;
if (out_mat_hsR != 0)
{
r_matrix.out_rR_other(ucell, istep, HS_Arrays.output_R_coor, reduce);
}
else
{
r_matrix.out_rR(ucell, grid, istep, reduce);
}
}

return;
Expand Down
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