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Feature & Refactor: read and write Hexx(R) in CSR format #3727

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Merged
dyzheng merged 9 commits into from
Apr 2, 2024
Merged

Feature & Refactor: read and write Hexx(R) in CSR format #3727

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0534a7d
refactor sparse output
maki49 Mar 15, 2024
90e09ad
read HexxR in CSR
maki49 Mar 15, 2024
8b1c1ae
parallel support
maki49 Mar 15, 2024
969642e
remove test code
maki49 Mar 15, 2024
bf87dc1
comments
maki49 Mar 19, 2024
f5aa987
recover multiple process
maki49 Mar 23, 2024
99d047d
refactor singleR
maki49 Mar 23, 2024
9bede17
change func names
maki49 Mar 28, 2024
5f614a5
Merge branch 'develop' into HexxCSR
maki49 Apr 1, 2024
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6 changes: 3 additions & 3 deletions source/module_esolver/esolver_ks_lcao.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1024,14 +1024,14 @@ void ESolver_KS_LCAO<TK, TR>::after_scf(const int istep)
#ifdef __EXX
if (GlobalC::exx_info.info_global.cal_exx) // Peize Lin add if 2022.11.14
{
const std::string file_name_exx = GlobalV::global_out_dir + "HexxR_" + std::to_string(GlobalV::MY_RANK);
const std::string file_name_exx = GlobalV::global_out_dir + "HexxR" + std::to_string(GlobalV::MY_RANK);
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if (GlobalC::exx_info.info_ri.real_number)
{
this->exd->write_Hexxs(file_name_exx);
this->exd->write_Hexxs_csr(file_name_exx, GlobalC::ucell);
}
else
{
this->exc->write_Hexxs(file_name_exx);
this->exc->write_Hexxs_csr(file_name_exx, GlobalC::ucell);
}
}
#endif
Expand Down
6 changes: 3 additions & 3 deletions source/module_esolver/esolver_ks_lcao_elec.cpp
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Expand Up @@ -524,11 +524,11 @@ void ESolver_KS_LCAO<TK, TR>::nscf()
if (GlobalC::exx_info.info_global.cal_exx)
{
// GlobalC::exx_lcao.cal_exx_elec_nscf(this->LOWF.ParaV[0]);
const std::string file_name_exx = GlobalV::global_out_dir + "HexxR_" + std::to_string(GlobalV::MY_RANK);
const std::string file_name_exx = GlobalV::global_out_dir + "HexxR" + std::to_string(GlobalV::MY_RANK);
if (GlobalC::exx_info.info_ri.real_number)
this->exd->read_Hexxs(file_name_exx);
this->exd->read_Hexxs_csr(file_name_exx, GlobalC::ucell);
else
this->exc->read_Hexxs(file_name_exx);
this->exc->read_Hexxs_csr(file_name_exx, GlobalC::ucell);

hamilt::HamiltLCAO<TK, TR>* hamilt_lcao = dynamic_cast<hamilt::HamiltLCAO<TK, TR>*>(this->p_hamilt);
auto exx = new hamilt::OperatorEXX<hamilt::OperatorLCAO<TK, TR>>(&this->LM,
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2 changes: 1 addition & 1 deletion source/module_io/csr_reader.cpp
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Expand Up @@ -135,6 +135,6 @@ int csrFileReader<T>::getStep() const
// T of AtomPair can be double
template class csrFileReader<double>;
// ToDo: T of AtomPair can be std::complex<double>
// template class csrFileReader<std::complex<double>>;
template class csrFileReader<std::complex<double>>;

} // namespace ModuleIO
161 changes: 37 additions & 124 deletions source/module_io/single_R_io.cpp
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Expand Up @@ -3,132 +3,35 @@
#include "module_base/global_function.h"
#include "module_base/global_variable.h"

void ModuleIO::output_single_R(std::ofstream &ofs, const std::map<size_t, std::map<size_t, double>> &XR, const double &sparse_threshold, const bool &binary, const Parallel_Orbitals &pv)
inline void write_data(std::ofstream& ofs, const double& data)
{
double *line = nullptr;
std::vector<int> indptr;
indptr.reserve(GlobalV::NLOCAL + 1);
indptr.push_back(0);

std::stringstream tem1;
tem1 << GlobalV::global_out_dir << "temp_sparse_indices.dat";
std::ofstream ofs_tem1;
std::ifstream ifs_tem1;

if (GlobalV::DRANK == 0)
{
if (binary)
{
ofs_tem1.open(tem1.str().c_str(), std::ios::binary);
}
else
{
ofs_tem1.open(tem1.str().c_str());
}
}

line = new double[GlobalV::NLOCAL];
for(int row = 0; row < GlobalV::NLOCAL; ++row)
{
// line = new double[GlobalV::NLOCAL];
ModuleBase::GlobalFunc::ZEROS(line, GlobalV::NLOCAL);

if(pv.global2local_row(row) >= 0)
{
auto iter = XR.find(row);
if (iter != XR.end())
{
for (auto &value : iter->second)
{
line[value.first] = value.second;
}
}
}

Parallel_Reduce::reduce_all(line, GlobalV::NLOCAL);

if(GlobalV::DRANK == 0)
{
int nonzeros_count = 0;
for (int col = 0; col < GlobalV::NLOCAL; ++col)
{
if (std::abs(line[col]) > sparse_threshold)
{
if (binary)
{
ofs.write(reinterpret_cast<char *>(&line[col]), sizeof(double));
ofs_tem1.write(reinterpret_cast<char *>(&col), sizeof(int));
}
else
{
ofs << " " << std::fixed << std::scientific << std::setprecision(8) << line[col];
ofs_tem1 << " " << col;
}

nonzeros_count++;

}

}
nonzeros_count += indptr.back();
indptr.push_back(nonzeros_count);
}

// delete[] line;
// line = nullptr;

}

delete[] line;
line = nullptr;

if (GlobalV::DRANK == 0)
{
if (binary)
{
ofs_tem1.close();
ifs_tem1.open(tem1.str().c_str(), std::ios::binary);
ofs << ifs_tem1.rdbuf();
ifs_tem1.close();
for (auto &i : indptr)
{
ofs.write(reinterpret_cast<char *>(&i), sizeof(int));
}
}
else
{
ofs << std::endl;
ofs_tem1 << std::endl;
ofs_tem1.close();
ifs_tem1.open(tem1.str().c_str());
ofs << ifs_tem1.rdbuf();
ifs_tem1.close();
for (auto &i : indptr)
{
ofs << " " << i;
}
ofs << std::endl;
}

std::remove(tem1.str().c_str());

}

ofs << " " << std::fixed << std::scientific << std::setprecision(8) << data;
}
inline void write_data(std::ofstream& ofs, const std::complex<double>& data)
{
ofs << " (" << std::fixed << std::scientific << std::setprecision(8) << data.real() << ","
<< std::fixed << std::scientific << std::setprecision(8) << data.imag() << ")";
}

void ModuleIO::output_soc_single_R(std::ofstream &ofs, const std::map<size_t, std::map<size_t, std::complex<double>>> &XR, const double &sparse_threshold, const bool &binary, const Parallel_Orbitals &pv)
template<typename T>
void ModuleIO::output_single_R(std::ofstream& ofs,
const std::map<size_t, std::map<size_t, T>>& XR,
const double& sparse_threshold,
const bool& binary,
const Parallel_Orbitals& pv,
const bool& reduce)
{
std::complex<double> *line = nullptr;
T* line = nullptr;
std::vector<int> indptr;
indptr.reserve(GlobalV::NLOCAL + 1);
indptr.push_back(0);

std::stringstream tem1;
tem1 << GlobalV::global_out_dir << "temp_sparse_indices.dat";
tem1 << GlobalV::global_out_dir << std::to_string(GlobalV::DRANK) + "temp_sparse_indices.dat";
std::ofstream ofs_tem1;
std::ifstream ifs_tem1;

if (GlobalV::DRANK == 0)
if (!reduce || GlobalV::DRANK == 0)
{
if (binary)
{
Expand All @@ -140,13 +43,12 @@ void ModuleIO::output_soc_single_R(std::ofstream &ofs, const std::map<size_t, st
}
}

line = new std::complex<double>[GlobalV::NLOCAL];
line = new T[GlobalV::NLOCAL];
for(int row = 0; row < GlobalV::NLOCAL; ++row)
{
// line = new std::complex<double>[GlobalV::NLOCAL];
ModuleBase::GlobalFunc::ZEROS(line, GlobalV::NLOCAL);

if(pv.global2local_row(row) >= 0)
if (!reduce || pv.global2local_row(row) >= 0)
{
auto iter = XR.find(row);
if (iter != XR.end())
Expand All @@ -158,9 +60,9 @@ void ModuleIO::output_soc_single_R(std::ofstream &ofs, const std::map<size_t, st
}
}

Parallel_Reduce::reduce_all(line, GlobalV::NLOCAL);
if (reduce)Parallel_Reduce::reduce_all(line, GlobalV::NLOCAL);

if (GlobalV::DRANK == 0)
if (!reduce || GlobalV::DRANK == 0)
{
int nonzeros_count = 0;
for (int col = 0; col < GlobalV::NLOCAL; ++col)
Expand All @@ -169,13 +71,12 @@ void ModuleIO::output_soc_single_R(std::ofstream &ofs, const std::map<size_t, st
{
if (binary)
{
ofs.write(reinterpret_cast<char *>(&line[col]), sizeof(std::complex<double>));
ofs.write(reinterpret_cast<char*>(&line[col]), sizeof(T));
ofs_tem1.write(reinterpret_cast<char *>(&col), sizeof(int));
}
else
{
ofs << " (" << std::fixed << std::scientific << std::setprecision(8) << line[col].real() << ","
<< std::fixed << std::scientific << std::setprecision(8) << line[col].imag() << ")";
write_data(ofs, line[col]);
ofs_tem1 << " " << col;
}

Expand All @@ -196,7 +97,7 @@ void ModuleIO::output_soc_single_R(std::ofstream &ofs, const std::map<size_t, st
delete[] line;
line = nullptr;

if (GlobalV::DRANK == 0)
if (!reduce || GlobalV::DRANK == 0)
{
if (binary)
{
Expand Down Expand Up @@ -226,5 +127,17 @@ void ModuleIO::output_soc_single_R(std::ofstream &ofs, const std::map<size_t, st

std::remove(tem1.str().c_str());
}

}

template void ModuleIO::output_single_R<double>(std::ofstream& ofs,
const std::map<size_t, std::map<size_t, double>>& XR,
const double& sparse_threshold,
const bool& binary,
const Parallel_Orbitals& pv,
const bool& reduce);
template void ModuleIO::output_single_R<std::complex<double>>(std::ofstream& ofs,
const std::map<size_t, std::map<size_t, std::complex<double>>>& XR,
const double& sparse_threshold,
const bool& binary,
const Parallel_Orbitals& pv,
const bool& reduce);
9 changes: 7 additions & 2 deletions source/module_io/single_R_io.h
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Expand Up @@ -5,8 +5,13 @@

namespace ModuleIO
{
void output_single_R(std::ofstream &ofs, const std::map<size_t, std::map<size_t, double>> &XR, const double &sparse_threshold, const bool &binary, const Parallel_Orbitals &pv);
void output_soc_single_R(std::ofstream &ofs, const std::map<size_t, std::map<size_t, std::complex<double>>> &XR, const double &sparse_threshold, const bool &binary, const Parallel_Orbitals &pv);
template <typename T>
void output_single_R(std::ofstream& ofs,
const std::map<size_t, std::map<size_t, T>>& XR,
const double& sparse_threshold,
const bool& binary,
const Parallel_Orbitals& pv,
const bool& reduce = true);
}

#endif
2 changes: 1 addition & 1 deletion source/module_io/sparse_matrix.cpp
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Expand Up @@ -92,7 +92,7 @@ void SparseMatrix<T>::readCSR(const std::vector<T>& values,

// define the operator to index a matrix element
template <typename T>
T SparseMatrix<T>::operator()(int row, int col)
T SparseMatrix<T>::operator()(int row, int col) const
{
if (row < 0 || row >= _rows || col < 0 || col >= _cols)
{
Expand Down
2 changes: 1 addition & 1 deletion source/module_io/sparse_matrix.h
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Expand Up @@ -66,7 +66,7 @@ class SparseMatrix
}

// define the operator to index a matrix element
T operator()(int row, int col);
T operator()(int row, int col)const;

// set the threshold
void setSparseThreshold(double sparse_threshold)
Expand Down
4 changes: 2 additions & 2 deletions source/module_io/write_HS_R.cpp
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Expand Up @@ -120,7 +120,7 @@ void ModuleIO::output_S_R(
ModuleBase::timer::tick("ModuleIO","output_S_R");

UHM.cal_SR_sparse(sparse_threshold, p_ham);
ModuleIO::save_SR_sparse(*UHM.LM, sparse_threshold, binary, SR_filename);
ModuleIO::save_sparse(UHM.LM->SR_sparse, UHM.LM->all_R_coor, sparse_threshold, binary, SR_filename, *UHM.LM->ParaV, "S", 0);
UHM.destroy_all_HSR_sparse();

ModuleBase::timer::tick("ModuleIO","output_S_R");
Expand Down Expand Up @@ -149,7 +149,7 @@ void ModuleIO::output_T_R(
}

UHM.cal_TR_sparse(sparse_threshold);
ModuleIO::save_TR_sparse(istep, *UHM.LM, sparse_threshold, binary, sst.str().c_str());
ModuleIO::save_sparse(UHM.LM->TR_sparse, UHM.LM->all_R_coor, sparse_threshold, binary, sst.str().c_str(), *UHM.LM->ParaV, "T", istep);
UHM.destroy_TR_sparse();

ModuleBase::timer::tick("ModuleIO","output_T_R");
Expand Down
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