ModuleIO Namespace Reference

This class has two functions: restart psi from the previous calculation, and write psi to the disk. More...

Classes
class	AngularMomentumCalculator
class	Cal_ldos
class	Cal_MLKEDF_Descriptors
	A class to calculate the descriptors for ML KEDF. Sun, Liang, and Mohan Chen. Physical Review B 109.11 (2024): 115135. Sun, Liang, and Mohan Chen. Electronic Structure 6.4 (2024): 045006. More...
class	CifParser
class	csrFileReader
	Class to read CSR file. More...
class	FileReader
	A base class of file reader. More...
class	Input_Item
class	Output_DMK
class	Output_Mulliken
	the output interface to write the Mulliken population charges More...
class	Output_Sk
class	ReadInput
class	SparseMatrix
	Sparse matrix class designed mainly for csr format input and output. More...
class	Write_MLKEDF_Descriptors

Typedefs
using	TC = std::array< int, 3 >
using	TAC = std::pair< int, TC >
template<typename T >
using	Real = typename GetTypeReal< T >::type

Functions
void	prepare_dos (std::ofstream &ofs_running, const elecstate::efermi &energy_fermi, const ModuleBase::matrix &ekb, const int nks, const int nbands, const double &dos_edelta_ev, const double &dos_scale, double &emax, double &emin)
bool	cal_dos (const int &is, const std::string &fn, const double &de_ev, const double &emax_ev, const double &emin_ev, const double &bcoeff, const int &nks, const int &nkstot, const std::vector< double > &wk, const std::vector< int > &isk, const int &nbands, const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg)
void	cal_ldos_pw (const elecstate::ElecStatePW< std::complex< double > > *pelec, const psi::Psi< std::complex< double > > &psi, const Parallel_Grid &pgrid, const UnitCell &ucell)
void	stm_mode_pw (const elecstate::ElecStatePW< std::complex< double > > *pelec, const psi::Psi< std::complex< double > > &psi, const Parallel_Grid &pgrid, const UnitCell &ucell)
void	ldos_mode_pw (const elecstate::ElecStatePW< std::complex< double > > *pelec, const psi::Psi< std::complex< double > > &psi, const Parallel_Grid &pgrid, const UnitCell &ucell)
void	get_grid_points (const std::vector< double > &start, const std::vector< double > &end, const int &npoints, const int &nx, const int &ny, const int &nz, std::vector< std::vector< int > > &points, std::vector< std::vector< double > > &shifts)
void	trilinear_interpolate (const std::vector< std::vector< int > > &points, const std::vector< std::vector< double > > &shifts, const Parallel_Grid &pgrid, const std::vector< double > &data, std::vector< double > &results)
void	cal_pdos (const psi::Psi< double > *psi, hamilt::Hamilt< double > *p_ham, const Parallel_Orbitals &pv, const UnitCell &ucell, const K_Vectors &kv, const int nspin0, const int nbands, const ModuleBase::matrix &ekb, const double &emax, const double &emin, const double &dos_edelta_ev, const double &bcoeff)
void	print_tdos_gamma (const ModuleBase::matrix *pdos, const int nlocal, const int npoints, const double &emin, const double &dos_edelta_ev)
void	print_pdos_gamma (const UnitCell &ucell, const ModuleBase::matrix *pdos, const int nlocal, const int npoints, const double &emin, const double &dos_edelta_ev)
void	cal_pdos (const psi::Psi< std::complex< double > > *psi, hamilt::Hamilt< std::complex< double > > *p_ham, const Parallel_Orbitals &pv, const UnitCell &ucell, const K_Vectors &kv, const int nspin0, const int nbands, const ModuleBase::matrix &ekb, const double &emax, const double &emin, const double &dos_edelta_ev, const double &bcoeff)
void	print_tdos_multik (const ModuleBase::matrix *pdos, const int nlocal, const int npoints, const double &emin, const double &dos_edelta_ev)
void	print_pdos_multik (const UnitCell &ucell, const ModuleBase::matrix *pdos, const int nlocal, const int npoints, const double &emin, const double &dos_edelta_ev)
std::complex< double >	cal_LzijR (const std::unique_ptr< TwoCenterIntegrator > &calculator, const int it, const int ia, const int il, const int iz, const int mi, const int jt, const int ja, const int jl, const int jz, const int mj, const ModuleBase::Vector3< double > &vR)
	calculate the <phi_i|Lz|phi_j> matrix elements, in which the Lz are the angular momentum operators, |phi_i> and |phi_j> are the numerical atomic orbitals (NAOs).
std::complex< double >	cal_LyijR (const std::unique_ptr< TwoCenterIntegrator > &calculator, const int it, const int ia, const int il, const int iz, const int im, const int jt, const int ja, const int jl, const int jz, const int jm, const ModuleBase::Vector3< double > &vR)
	calculate the <phi_i|Ly|phi_j> matrix elements, in which the Lz are the angular momentum operators, |phi_i> and |phi_j> are the numerical atomic orbitals (NAOs).
std::complex< double >	cal_LxijR (const std::unique_ptr< TwoCenterIntegrator > &calculator, const int it, const int ia, const int il, const int iz, const int im, const int jt, const int ja, const int jl, const int jz, const int jm, const ModuleBase::Vector3< double > &vR)
	calculate the <phi_i|Lx|phi_j> matrix elements, in which the Lz are the angular momentum operators, |phi_i> and |phi_j> are the numerical atomic orbitals (NAOs).
template<typename TK , typename TR >
void	ctrl_output_fp (UnitCell &ucell, elecstate::ElecStateLCAO< TK > *pelec, const int istep)
template<typename TK , typename TR >
void	ctrl_output_lcao (UnitCell &ucell, K_Vectors &kv, elecstate::ElecStateLCAO< TK > *pelec, Parallel_Orbitals &pv, Grid_Driver &gd, psi::Psi< TK > *psi, hamilt::HamiltLCAO< TK, TR > *p_hamilt, TwoCenterBundle &two_center_bundle, Gint_k &gk, LCAO_Orbitals &orb, const ModulePW::PW_Basis_K *pw_wfc, const ModulePW::PW_Basis *pw_rho, Grid_Technique &gt, const ModulePW::PW_Basis_Big *pw_big, const Structure_Factor &sf, rdmft::RDMFT< TK, TR > &rdmft_solver, LCAO_Deepks< TK > &ld, const int istep)
bool	read_vdata_palgrid (const Parallel_Grid &pgrid, const int my_rank, std::ofstream &ofs_running, const std::string &fn, double *const data, const int nat)
	read volumetric data from .cube file into the parallel distributed grid.
void	write_vdata_palgrid (const Parallel_Grid &pgrid, const double *const data, const int is, const int nspin, const int iter, const std::string &fn, const double ef, const UnitCell *const ucell, const int precision=11, const int out_fermi=1, const bool reduce_all_pool=false)
	write volumetric data on the parallized grid into a .cube file
bool	read_cube (const std::string &file, std::vector< std::string > &comment, int &natom, std::vector< double > &origin, int &nx, int &ny, int &nz, std::vector< double > &dx, std::vector< double > &dy, std::vector< double > &dz, std::vector< int > &atom_type, std::vector< double > &atom_charge, std::vector< std::vector< double > > &atom_pos, std::vector< double > &data)
	read the full data from a cube file
void	write_cube (const std::string &file, const std::vector< std::string > &comment, const int &natom, const std::vector< double > &origin, const int &nx, const int &ny, const int &nz, const std::vector< double > &dx, const std::vector< double > &dy, const std::vector< double > &dz, const std::vector< int > &atom_type, const std::vector< double > &atom_charge, const std::vector< std::vector< double > > &atom_pos, const std::vector< double > &data, const int precision, const int ndata_line=6)
	write a cube file
void	trilinear_interpolate (const double *const data_in, const int &nx_read, const int &ny_read, const int &nz_read, const int &nx, const int &ny, const int &nz, double *data_out)
	The trilinear interpolation method.
void	write_dipole (const UnitCell &ucell, const double *rho_save, const ModulePW::PW_Basis *rhopw, const int &is, const int &istep, const std::string &fn, const int &precision=11)
double	prepare (const UnitCell &cell, int &dir)
std::string	filename_output (const std::string &directory, const std::string &property, const std::string &basis, const int ik_local, const std::vector< int > &ik2iktot, const int nspin, const int nkstot, const int out_type, const bool out_app_flag, const bool gamma_only, const int istep)
template<typename Device >
void	get_pchg_pw (const std::vector< int > &out_pchg, const int nbands, const int nspin, const int nxyz, const int chr_ngmc, UnitCell *ucell, const psi::Psi< std::complex< double >, Device > *kspw_psi, const ModulePW::PW_Basis *pw_rhod, const ModulePW::PW_Basis_K *pw_wfc, const Device *ctx, const Parallel_Grid &pgrid, const std::string &global_out_dir, const bool if_separate_k, const K_Vectors &kv, const int kpar, const int my_pool, const Charge *chr)
template<typename Device >
void	get_wf_pw (const std::vector< int > &out_wfc_norm, const std::vector< int > &out_wfc_re_im, const int nbands, const int nspin, const int nxyz, UnitCell *ucell, const psi::Psi< std::complex< double >, Device > *kspw_psi, const ModulePW::PW_Basis_K *pw_wfc, const Device *ctx, const Parallel_Grid &pgrid, const std::string &global_out_dir, const K_Vectors &kv, const int kpar, const int my_pool)
std::string	dmk_gen_fname (const bool gamma_only, const int ispin, const int ik)
	Generates the filename for the DMK file based on the given parameters.
void	dmk_write_ucell (std::ofstream &ofs, const UnitCell *ucell)
	Writes the unit cell information to a DMK file.
void	dmk_read_ucell (std::ifstream &ifs)
	Reads the unit cell information lines in a DMK file.
void	dmk_readData (std::ifstream &ifs, double &data)
	Read one double from a file.
void	dmk_readData (std::ifstream &ifs, std::complex< double > &data)
	Read one complex double from a file.
template<typename T >
bool	read_dmk (const int nspin, const int nk, const Parallel_2D &pv, const std::string &dmk_dir, std::vector< std::vector< T > > &dmk, std::ofstream &ofs_running)
	Reads the DMK data from a file.
template<typename T >
void	write_dmk (const std::vector< std::vector< T > > &dmk, const int precision, const std::vector< double > &efs, const UnitCell *ucell, const Parallel_2D &pv)
	Writes the DMK data to a file.
void	read_mat_npz (const Parallel_Orbitals *paraV, const UnitCell &ucell, std::string &zipname, hamilt::HContainer< double > &hR)
void	output_mat_npz (const UnitCell &ucell, std::string &zipname, const hamilt::HContainer< double > &hR)
void	nscf_band (const int &is, const std::string &eig_file, const int &nband, const double &fermie, const int &precision, const ModuleBase::matrix &ekb, const K_Vectors &kv)
	calculate the band structure
void	nscf_fermi_surface (const std::string &out_band_dir, const int &nband, const double &ef, const K_Vectors &kv, const UnitCell &ucell, const ModuleBase::matrix &ekb)
void	read_abacus_orb (std::ifstream &ifs, std::string &elem, double &ecut, int &nr, double &dr, std::vector< int > &nzeta, std::vector< std::vector< double > > &radials, const int rank=0)
	static version of read_abacus_orb. A delete-new operation may cause the memory leak, it is better to use std::vector to replace the raw pointer.
void	write_abacus_orb (std::ofstream &ofs, const std::string &elem, const double &ecut, const int nr, const double dr, const std::vector< int > &nzeta, const std::vector< std::vector< double > > &radials, const int rank=0)
void	output_convergence_after_scf (const bool &convergence, double &energy, std::ofstream &ofs_running=GlobalV::ofs_running)
	output if is convergence and energy after scf
void	output_after_relax (bool conv_ion, bool conv_esolver, std::ofstream &ofs_running=GlobalV::ofs_running)
	output after relaxation
void	output_efermi (const bool &convergence, double &efermi, std::ofstream &ofs_running=GlobalV::ofs_running)
	output the fermi energy
void	output_vacuum_level (const UnitCell *ucell, const double *const *rho, const double *v_elecstat, const int &nx, const int &ny, const int &nz, const int &nxyz, const int &nrxx, const int &nplane, const int &startz_current, std::ofstream &ofs_running=GlobalV::ofs_running)
	calculate and output the vacuum level We first determine the vacuum direction, then get the vacuum position based on the minimum of charge density, finally output the vacuum level, i.e., the electrostatic potential at the vacuum position.
void	print_force (std::ofstream &ofs, const UnitCell &cell, const std::string &name, const ModuleBase::matrix &force, bool ry=true)
	output atomic forces
void	print_stress (const std::string &name, const ModuleBase::matrix &scs, const bool screen, const bool ry, std::ofstream &ofs)
	output stress components
void	write_head (std::ofstream &ofs_running, const int &istep, const int &iter, const std::string &basisname)
	write head for scf iteration
void	write_head_td (std::ofstream &ofs_running, const int &istep, const int &estep, const int &iter, const std::string &basisname)
	write head for scf iteration
template<>
void	output_mat_sparse (const bool &out_mat_hsR, const bool &out_mat_dh, const bool &out_mat_ds, const bool &out_mat_t, const bool &out_mat_r, const int &istep, const ModuleBase::matrix &v_eff, const Parallel_Orbitals &pv, Gint_k &gint_k, const TwoCenterBundle &two_center_bundle, const LCAO_Orbitals &orb, UnitCell &ucell, const Grid_Driver &grid, const K_Vectors &kv, hamilt::Hamilt< double > *p_ham)
template<>
void	output_mat_sparse (const bool &out_mat_hsR, const bool &out_mat_dh, const bool &out_mat_ds, const bool &out_mat_t, const bool &out_mat_r, const int &istep, const ModuleBase::matrix &v_eff, const Parallel_Orbitals &pv, Gint_k &gint_k, const TwoCenterBundle &two_center_bundle, const LCAO_Orbitals &orb, UnitCell &ucell, const Grid_Driver &grid, const K_Vectors &kv, hamilt::Hamilt< std::complex< double > > *p_ham)
template<typename T >
void	output_mat_sparse (const bool &out_mat_hsR, const bool &out_mat_dh, const bool &out_mat_ds, const bool &out_mat_t, const bool &out_mat_r, const int &istep, const ModuleBase::matrix &v_eff, const Parallel_Orbitals &pv, Gint_k &gint_k, const TwoCenterBundle &two_center_bundle, const LCAO_Orbitals &orb, UnitCell &ucell, const Grid_Driver &grid, const K_Vectors &kv, hamilt::Hamilt< T > *p_ham)
	the output interface to write the sparse matrix of H, S, T, and r
template<typename TK >
void	cal_mag (Parallel_Orbitals *pv, hamilt::Hamilt< TK > *p_ham, K_Vectors &kv, elecstate::ElecState *pelec, const TwoCenterBundle &two_center_bundle, const LCAO_Orbitals &orb, UnitCell &ucell, const Grid_Driver &gd, const int istep, const bool print)
void	parse_args (int argc, char **argv)
	This function reture the version information when using command "abacus --version", "abacus -v" or "abacus -V". Otherwise, it does nothing.
void	setup_parameters (UnitCell &ucell, K_Vectors &kv)
void	print_time (time_t &time_start, time_t &time_finish)
void	print_rhofft (ModulePW::PW_Basis *pw_rhod, ModulePW::PW_Basis *pw_rho, ModulePW::PW_Basis_Big *pw_big, std::ofstream &ofs)
	Print charge density using FFT.
void	print_wfcfft (const Input_para &inp, ModulePW::PW_Basis_K &pw_wfc, std::ofstream &ofs)
void	print_screen (const int &stress_step, const int &force_step, const int &istep)
int	read_exit_file (const int &my_rank, const std::string &filename, std::ofstream &ofs_running)
	read file to determine whether to stop the current execution
std::string	longstring (const std::vector< std::string > &words)
bool	assume_as_boolean (const std::string &val)
std::string	to_dir (const std::string &str)
void	read_information (std::ifstream &ifs, std::vector< std::string > &output, const std::string &delimiters)
std::string	nofound_str (std::vector< std::string > init_chgs, const std::string &str)
void	read_wf2rho_pw (const ModulePW::PW_Basis_K *pw_wfc, ModuleSymmetry::Symmetry &symm, Charge &chg, const std::string &readin_dir, const int kpar, const int my_pool, const int my_rank, const int nproc_in_pool, const int rank_in_pool, const int nbands, const int nspin, const int npol, const int nkstot, const std::vector< int > &ik2iktot, const std::vector< int > &isk, std::ofstream &ofs_running)
	read wave functions and occupation numbers to charge density
void	read_wfc_nao_one_data (std::ifstream &ifs, double &data)
	Reads a single data value from an input file stream.
void	read_wfc_nao_one_data (std::ifstream &ifs, std::complex< double > &data)
	Reads a single complex data value from an input file stream.
template<typename T >
bool	read_wfc_nao (const std::string &global_readin_dir, const Parallel_Orbitals &ParaV, psi::Psi< T > &psid, elecstate::ElecState *const pelec, const std::vector< int > &ik2iktot, const int nkstot, const int nspin, const int skip_band=0, const int nstep=-1)
	Reads the wavefunction coefficients from an input file.
void	read_wfc_pw (const std::string &filedir, const ModulePW::PW_Basis_K *pw_wfc, const int rank_in_pool, const int nproc_in_pool, const int nbands, const int npol, const int &ik, const int &ikstot, const int &nkstot, ModuleBase::ComplexMatrix &wfc)
	read wave functions from binary file
template<typename Tdata >
void	read_Hexxs_csr (const std::string &file_name, const UnitCell &ucell, const int nspin, const int nbasis, std::vector< std::map< int, std::map< TAC, RI::Tensor< Tdata > > > > &Hexxs)
	read Hexxs in CSR format
template<typename Tdata >
void	read_Hexxs_cereal (const std::string &file_name, std::vector< std::map< int, std::map< TAC, RI::Tensor< Tdata > > > > &Hexxs)
	read Hexxs in cereal format
template<typename Tdata >
void	write_Hexxs_csr (const std::string &file_name, const UnitCell &ucell, const std::map< int, std::map< TAC, RI::Tensor< Tdata > > > &Hexxs)
	write Hexxs in CSR format
template<typename Tdata >
std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, Tdata > > >	calculate_RI_Tensor_sparse (const double &sparse_threshold, const std::vector< std::map< int, std::map< TAC, RI::Tensor< Tdata > > > > &Hexxs, const UnitCell &ucell)
template<typename Tdata >
std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, Tdata > > >	calculate_RI_Tensor_sparse (const double &sparse_threshold, const std::map< int, std::map< TAC, RI::Tensor< Tdata > > > &Hexxs, const UnitCell &ucell)
template<typename Tdata >
void	write_Hexxs_csr (const std::string &file_name, const UnitCell &ucell, const std::vector< std::map< int, std::map< TAC, RI::Tensor< Tdata > > > > &Hexxs)
bool	read_rhog (const std::string &filename, const ModulePW::PW_Basis *pw_rhod, std::complex< double > **rhog)
bool	write_rhog (const std::string &fchg, const bool gamma_only, const ModulePW::PW_Basis *pw_rho, const int nspin, const ModuleBase::Matrix3 &GT, std::complex< double > **rhog, const int ipool, const int irank, const int nrank)
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)
std::vector< double >	read_k (std::string filename, int ik)
std::string	dmr_gen_fname (const int out_type, const int ispin, const bool append, const int istep)
void	write_dmr_csr (std::string &fname, hamilt::HContainer< double > *dm_serial, const int istep)
void	write_dmr (const std::vector< hamilt::HContainer< double > * > dmr, const Parallel_2D &paraV, const bool append, const int *iat2iwt, const int nat, const int istep)
template<typename T >
void	write_dos_lcao (const psi::Psi< T > *psi, hamilt::Hamilt< T > *p_ham, const Parallel_Orbitals &pv, const UnitCell &ucell, const K_Vectors &kv, const int nbands, const elecstate::efermi &energy_fermi, const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg, const double &dos_edelta_ev, const double &dos_scale, const double &bcoeff, const bool out_app_flag, const int istep, std::ofstream &ofs_running)
	calculate density of states(DOS), partial density of states(PDOS), and mulliken charge for LCAO base
template void	write_dos_lcao (const psi::Psi< double > *psi, hamilt::Hamilt< double > *p_ham, const Parallel_Orbitals &pv, const UnitCell &ucell, const K_Vectors &kv, const int nbands, const elecstate::efermi &energy_fermi, const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg, const double &dos_edelta_ev, const double &dos_scale, const double &bcoeff, const bool out_app_flag, const int istep, std::ofstream &ofs_running)
template void	write_dos_lcao (const psi::Psi< std::complex< double > > *psi, hamilt::Hamilt< std::complex< double > > *p_ham, const Parallel_Orbitals &pv, const UnitCell &ucell, const K_Vectors &kv, const int nbands, const elecstate::efermi &energy_fermi, const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg, const double &dos_edelta_ev, const double &dos_scale, const double &bcoeff, const bool out_app_flag, const int istep, std::ofstream &ofs_running)
void	write_dos_pw (const UnitCell &ucell, const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg, const K_Vectors &kv, const int nbands, const elecstate::efermi &energy_fermi, const double &dos_edelta_ev, const double &dos_scale, const double &bcoeff, std::ofstream &ofs_running)
	calculate density of states(DOS) for PW base
template<typename TK , typename TR >
void	write_eband_terms (const int nspin, const int nbasis, const int drank, const Parallel_Orbitals *pv, const psi::Psi< TK > &psi, const UnitCell &ucell, Structure_Factor &sf, surchem &solvent, const ModulePW::PW_Basis &rho_basis, const ModulePW::PW_Basis &rhod_basis, const ModuleBase::matrix &vloc, const Charge &chg, Gint_Gamma &gint_gamma, Gint_k &gint_k, const K_Vectors &kv, const ModuleBase::matrix &wg, Grid_Driver &gd, const std::vector< double > &orb_cutoff, const TwoCenterBundle &two_center_bundle)
void	write_eig_iter (const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg, const K_Vectors &kv)
void	write_eig_file (const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg, const K_Vectors &kv)
void	write_elecstat_pot (const int &bz, const int &nbz, const std::string &fn, const int &istep, ModulePW::PW_Basis *rho_basis, const Charge *const chr, const UnitCell *ucell_, const double *v_effective_fixed, const surchem &solvent)
	write electric static potential to file
void	write_elf (const int &bz, const int &nbz, const std::string &out_dir, const int &istep, const int &nspin, const double *const *rho, const double *const *tau, ModulePW::PW_Basis *rho_basis, const Parallel_Grid &pgrid, const UnitCell *ucell_, const int &precision)
template<typename T >
void	write_hsk (const std::string &global_out_dir, const int nspin, const int nks, const int nkstot, const std::vector< int > &ik2iktot, const std::vector< int > &isk, hamilt::Hamilt< T > *p_hamilt, const Parallel_Orbitals &pv, const bool gamma_only, const bool out_app_flag, const int istep, std::ofstream &ofs_running)
template<typename T >
void	save_mat (const int istep, const T *mat, const int dim, const bool bit, const int precision, const bool tri, const bool app, const std::string &file_name, const Parallel_2D &pv, const int drank, const bool reduce=true)
	save a square matrix, such as H(k) and S(k)
void	output_HSR (const UnitCell &ucell, const int &istep, const ModuleBase::matrix &v_eff, const Parallel_Orbitals &pv, LCAO_HS_Arrays &HS_Arrays, const Grid_Driver &grid, const K_Vectors &kv, hamilt::Hamilt< std::complex< double > > *p_ham, const std::string &SR_filename="srs1_nao.csr", const std::string &HR_filename_up="hrs1_nao.csr", const std::string HR_filename_down="hrs2_nao.csr", const bool &binary=false, const double &sparse_threshold=1e-10)
void	output_dHR (const int &istep, const ModuleBase::matrix &v_eff, Gint_k &gint_k, const UnitCell &ucell, const Parallel_Orbitals &pv, LCAO_HS_Arrays &HS_Arrays, const Grid_Driver &grid, const TwoCenterBundle &two_center_bundle, const LCAO_Orbitals &orb, const K_Vectors &kv, const bool &binary=false, const double &sparse_threshold=1e-10)
void	output_dSR (const int &istep, const UnitCell &ucell, const Parallel_Orbitals &pv, LCAO_HS_Arrays &HS_Arrays, const Grid_Driver &grid, const TwoCenterBundle &two_center_bundle, const LCAO_Orbitals &orb, const K_Vectors &kv, const bool &binary=false, const double &sparse_thr=1e-10)
void	output_TR (const int istep, const UnitCell &ucell, const Parallel_Orbitals &pv, LCAO_HS_Arrays &HS_Arrays, const Grid_Driver &grid, const TwoCenterBundle &two_center_bundle, const LCAO_Orbitals &orb, const std::string &TR_filename="trs1_nao.csr", const bool &binary=false, const double &sparse_threshold=1e-10)
void	output_SR (Parallel_Orbitals &pv, const Grid_Driver &grid, hamilt::Hamilt< std::complex< double > > *p_ham, const std::string &SR_filename="srs1_nao.csr", const bool &binary=false, const double &sparse_threshold=1e-10)
void	save_HSR_sparse (const int &istep, const Parallel_Orbitals &pv, LCAO_HS_Arrays &HS_Arrays, const double &sparse_thr, const bool &binary, const std::string &SR_filename, const std::string &HR_filename_up, const std::string &HR_filename_down)
void	save_dH_sparse (const int &istep, const Parallel_Orbitals &pv, LCAO_HS_Arrays &HS_Arrays, const double &sparse_thr, const bool &binary, const std::string &fileflag="h")
template<typename Tdata >
void	save_sparse (const std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, Tdata > > > &smat, const std::set< Abfs::Vector3_Order< int > > &all_R_coor, const double &sparse_thr, const bool &binary, const std::string &filename, const Parallel_Orbitals &pv, const std::string &label, const int &istep=-1, const bool &reduce=true)
void	write_orb_info (const UnitCell *ucell)
void	print_PAOs (const UnitCell &ucell)
	print chi (PAO) in pseudopotential file
template<typename TK >
void	write_proj_band_lcao (const psi::Psi< TK > *psi, const Parallel_Orbitals &pv, const elecstate::ElecState *pelec, const K_Vectors &kv, const UnitCell &ucell, hamilt::Hamilt< TK > *p_ham)
void	set_para2d_MO (const Parallel_Orbitals &pv, const int nbands, Parallel_2D &p2d)
template<typename T >
std::vector< T >	cVc (T *V, T *c, const int nbasis, const int nbands, const Parallel_Orbitals &pv, const Parallel_2D &p2d)
double	get_real (const std::complex< double > &c)
double	get_real (const double &d)
template<typename T >
double	all_band_energy (const int ik, const std::vector< T > &mat_mo, const Parallel_2D &p2d, const ModuleBase::matrix &wg)
template<typename T >
std::vector< double >	orbital_energy (const int ik, const int nbands, const std::vector< T > &mat_mo, const Parallel_2D &p2d)
template<typename T >
void	set_gint_pointer (Gint_Gamma &gint_gamma, Gint_k &gint_k, typename TGint< T >::type *&gint)
template<>
void	set_gint_pointer< double > (Gint_Gamma &gint_gamma, Gint_k &gint_k, typename TGint< double >::type *&gint)
template<>
void	set_gint_pointer< std::complex< double > > (Gint_Gamma &gint_gamma, Gint_k &gint_k, typename TGint< std::complex< double > >::type *&gint)
void	write_orb_energy (const K_Vectors &kv, const int nspin0, const int nbands, const std::vector< std::vector< double > > &e_orb, const std::string &term, const std::string &label, const bool app=false)
template<typename TK , typename TR >
void	write_Vxc (const int nspin, const int nbasis, const int drank, const Parallel_Orbitals *pv, const psi::Psi< TK > &psi, const UnitCell &ucell, Structure_Factor &sf, surchem &solvent, const ModulePW::PW_Basis &rho_basis, const ModulePW::PW_Basis &rhod_basis, const ModuleBase::matrix &vloc, const Charge &chg, Gint_Gamma &gint_gamma, Gint_k &gint_k, const K_Vectors &kv, const std::vector< double > &orb_cutoff, const ModuleBase::matrix &wg, Grid_Driver &gd)
	write the Vxc matrix in KS orbital representation, usefull for GW calculation including terms: local/semi-local XC, EXX, DFTU
template<typename FPTYPE >
FPTYPE	get_real (const std::complex< FPTYPE > &c)
template<typename FPTYPE >
FPTYPE	get_real (const FPTYPE &d)
template<typename T >
std::vector< T >	cVc (T *const V, T *const c, int nbasis, int nbands)
template<typename FPTYPE >
std::vector< std::complex< FPTYPE > >	psi_Hpsi (std::complex< FPTYPE > *const psi, std::complex< FPTYPE > *const hpsi, const int nbasis, const int nbands)
template<typename FPTYPE >
std::vector< FPTYPE >	orbital_energy (const int ik, const int nbands, const std::vector< std::complex< FPTYPE > > &mat_mo)
template<typename FPTYPE >
FPTYPE	all_band_energy (const int ik, const int nbands, const std::vector< std::complex< FPTYPE > > &mat_mo, const ModuleBase::matrix &wg)
template<typename FPTYPE >
FPTYPE	all_band_energy (const int ik, const std::vector< FPTYPE > &orbital_energy, const ModuleBase::matrix &wg)
template<typename FPTYPE >
void	write_Vxc (int nspin, int naos, int drank, const psi::Psi< std::complex< FPTYPE > > &psi_pw, const UnitCell &ucell, Structure_Factor &sf, surchem &solvent, const ModulePW::PW_Basis_K &wfc_basis, const ModulePW::PW_Basis &rho_basis, const ModulePW::PW_Basis &rhod_basis, const ModuleBase::matrix &vloc, const Charge &chg, const K_Vectors &kv, const ModuleBase::matrix &wg)
	write the Vxc matrix in KS orbital representation, usefull for GW calculation including terms: local/semi-local XC and EXX
template<>
void	set_gint_pointer< double > (Gint_Gamma &gint_gamma, Gint_k &gint_k, typename TGint< double >::type *&gint)
template<>
void	set_gint_pointer< std::complex< double > > (Gint_Gamma &gint_gamma, Gint_k &gint_k, typename TGint< std::complex< double > >::type *&gint)
template<typename TR >
std::set< Abfs::Vector3_Order< int > >	get_R_range (const hamilt::HContainer< TR > &hR)
template<typename TR >
std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, TR > > >	cal_HR_sparse (const hamilt::HContainer< TR > &hR, const int current_spin, const double sparse_thr)
template<>
std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, double > > >	cal_HR_sparse (const hamilt::HContainer< double > &hR, const int current_spin, const double sparse_thr)
template<>
std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, std::complex< double > > > >	cal_HR_sparse (const hamilt::HContainer< std::complex< double > > &hR, const int current_spin, const double sparse_thr)
template<typename TK , typename TR >
void	write_Vxc_R (const int nspin, const Parallel_Orbitals *pv, const UnitCell &ucell, Structure_Factor &sf, surchem &solvent, const ModulePW::PW_Basis &rho_basis, const ModulePW::PW_Basis &rhod_basis, const ModuleBase::matrix &vloc, const Charge &chg, Gint_Gamma &gint_gamma, Gint_k &gint_k, const K_Vectors &kv, const std::vector< double > &orb_cutoff, Grid_Driver &gd, const double sparse_thr=1e-10)
	write the Vxc matrix in KS orbital representation, usefull for GW calculation including terms: local/semi-local XC, EXX, DFTU
void	wfc_nao_write2file (const std::string &name, const double *ctot, const int nlocal, const int ik, const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg, const bool &writeBinary, const bool &append_flag)
void	wfc_nao_write2file_complex (const std::string &name, const std::complex< double > *ctot, const int nlocal, const int &ik, const ModuleBase::Vector3< double > &kvec_c, const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg, const bool &writeBinary, const bool &append_flag)
template<typename T >
void	write_wfc_nao (const int out_type, const bool out_app_flag, const psi::Psi< T > &psi, const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg, const std::vector< ModuleBase::Vector3< double > > &kvec_c, const std::vector< int > &ik2iktot, const int nkstot, const Parallel_Orbitals &pv, const int nspin, const int istep)
template void	write_wfc_nao< double > (const int out_type, const bool out_app_flag, const psi::Psi< double > &psi, const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg, const std::vector< ModuleBase::Vector3< double > > &kvec_c, const std::vector< int > &ik2iktot, const int nkstot, const Parallel_Orbitals &pv, const int nspin, const int istep)
template void	write_wfc_nao< std::complex< double > > (const int out_type, const bool out_app_flag, const psi::Psi< std::complex< double > > &psi, const ModuleBase::matrix &ekb, const ModuleBase::matrix &wg, const std::vector< ModuleBase::Vector3< double > > &kvec_c, const std::vector< int > &ik2iktot, const int nkstot, const Parallel_Orbitals &pv, const int nspin, const int istep)
void	write_wfc_pw (const int kpar, const int my_pool, const int my_rank, const int nbands, const int nspin, const int npol, const int rank_in_pool, const int nproc_in_pool, const int out_wfc_pw, const double &ecutwfc, const std::string &global_out_dir, const psi::Psi< std::complex< double > > &psi, const K_Vectors &kv, const ModulePW::PW_Basis_K *wfcpw, std::ofstream &ofs_running)

Detailed Description

This class has two functions: restart psi from the previous calculation, and write psi to the disk.

calculate the <phi_i|Lx/Ly/Lz|phi_j> matrix elements, in which the Lx/Ly/Lz are the angular momentum operators, |phi_i> and |phi_j> are the numerical atomic orbitals (NAOs).

Formulation

Calculate the <phi_i|Lx/Ly/Lz|phi_j> with ladder operator L+ and L-.

The relation between Lx, Ly and L+, L- are:

                             Lx = (L+ + L-) / 2
                             Ly = (L+ - L-) / 2i

With L+, the spherical harmonic function Ylm (denoted as |l, m> in the following) can be raised:

                     L+|l, m> = sqrt((l-m)(l+m+1))|l, m+1>

Likely, with L-, the spherical harmonic function Ylm can be lowered:

                     L-|l, m> = sqrt((l+m)(l-m+1))|l, m-1>

Therefore the Lx matrix element can be calculated as:

           <l, m|Lx|l, m'> =   sqrt((l-m)(l+m+1)) * delta(m, m'+1) / 2
                             + sqrt((l+m)(l-m+1)) * delta(m, m'-1) / 2

The Ly matrix element can be calculated as:

           <l, m|Ly|l, m'> =   sqrt((l-m)(l+m+1)) * delta(m, m'+1) / 2i
                             - sqrt((l+m)(l-m+1)) * delta(m, m'-1) / 2i

The Lz matrix element can be calculated as:

                     <l, m|Lz|l, m'> = m * delta(m, m')

However, things will change when there are more than one centers.

Technical Details

0. The calculation of matrix elements involves the two-center-integral calculation, this is supported by ABACUS built-in class TwoCenterIntegrator. see: source/source_basis/module_nao/two_center_integrator.h.

1. The interface of it is RadialCollection, which is a collection of radial functions. see: source/source_basis/module_nao/radial_collection.h
2. The radial functions are stored in AtomicRadials class, see: source/source_basis/module_nao/atomic_radials.h
3. The construction of AtomicRadials involves the filename of orbital, it is stored in the UnitCell instance
4. The calculation will run over all supercells in which the two-center-integral is not zero. This is done by the class SltkGridDriver, which is a driver for searching the neighboring cells.

I/O free function of rho(G) in binary format Author: YuLiu98, Kirk0830

The designed foramt of the binary file is kept similar to the one in QuantumESPRESSO Modules/io_base.f90, function write_rhog (non-HDF5):

/3/ /gammaonly/ /ngm_g/ /nspin/ /3/ ! bool, int, int. ngm_g is the global, total number of G-vectors /9/ /b11/ /b12/ /b13/ /b21/ /b22/ /b23/ /b31/ /b32/ /b33/ /9/ ! 9 real numbers, the three lattice vectors /ngm_g*3/ /miller(1,1)/ /miller(1,2)/ /miller(1,3)/ /miller(2,1)/ /miller(2,2)/ /miller(2,3)/ ... /miller(ngm_g,1)/ /miller(ngm_g,2)/ /miller(ngm_g,3)/ /ngm_g*3/ ! ngm_g*3 integers, the G-vectors in Miller indices /ngm_g/ /rhog(1)/ /rhog(2)/ /rhog(3)/ ... /ngm_g/ ! ngm_g complex numbers, the rho(G) values !/ngm_g/ ! ngm_g complex numbers, the rho(G) values for the second spin component !/rhog(1)/ /rhog(2)/ /rhog(3)/ ... !/ngm_g/ ! ngm_g complex numbers, the rho(G) values for the second spin component

There are some aspects needed to ensure:

1. the correspondence between ABACUS PW and QuantumESPRESSO ABACUS PW QuantumESPRESSO bij UnitCell::GT b1, b2, b3 miller index ibox[*] mill rho Charge::rhog rho
2. the unit of each quantity ABACUS PW QuantumESPRESSO bij a.u. miller index rho
   

Typedef Documentation

Real

template<typename T >

using ModuleIO::Real = typedef typename GetTypeReal<T>::type

TAC

typedef std::pair< int, std::array< int, 3 > > ModuleIO::TAC

TC

using ModuleIO::TC = typedef std::array<int, 3>

Function Documentation

all_band_energy() [1/3]

template<typename FPTYPE >

FPTYPE ModuleIO::all_band_energy	(	const int	ik,
		const int	nbands,
		const std::vector< std::complex< FPTYPE > > &	mat_mo,
		const ModuleBase::matrix &	wg
	)

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all_band_energy() [2/3]

template<typename FPTYPE >

FPTYPE ModuleIO::all_band_energy	(	const int	ik,
		const std::vector< FPTYPE > &	orbital_energy,
		const ModuleBase::matrix &	wg
	)

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all_band_energy() [3/3]

template<typename T >

double ModuleIO::all_band_energy	(	const int	ik,
		const std::vector< T > &	mat_mo,
		const Parallel_2D &	p2d,
		const ModuleBase::matrix &	wg
	)

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assume_as_boolean()

bool ModuleIO::assume_as_boolean

(

const std::string &

val

)

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cal_dos()

bool ModuleIO::cal_dos	(	const int &	is,
		const std::string &	fn,
		const double &	de_ev,
		const double &	emax_ev,
		const double &	emin_ev,
		const double &	bcoeff,
		const int &	nks,
		const int &	nkstot,
		const std::vector< double > &	wk,
		const std::vector< int > &	isk,
		const int &	nbands,
		const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg
	)

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cal_HR_sparse() [1/3]

template<>

std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, double > > > ModuleIO::cal_HR_sparse	(	const hamilt::HContainer< double > &	hR,
		const int	current_spin,
		const double	sparse_thr
	)

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cal_HR_sparse() [2/3]

template<>

std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, std::complex< double > > > > ModuleIO::cal_HR_sparse	(	const hamilt::HContainer< std::complex< double > > &	hR,
		const int	current_spin,
		const double	sparse_thr
	)

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cal_HR_sparse() [3/3]

template<typename TR >

std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, TR > > > ModuleIO::cal_HR_sparse	(	const hamilt::HContainer< TR > &	hR,
		const int	current_spin,
		const double	sparse_thr
	)

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cal_ldos_pw()

void ModuleIO::cal_ldos_pw	(	const elecstate::ElecStatePW< std::complex< double > > *	pelec,
		const psi::Psi< std::complex< double > > &	psi,
		const Parallel_Grid &	pgrid,
		const UnitCell &	ucell
	)

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cal_LxijR()

std::complex< double > ModuleIO::cal_LxijR	(	const std::unique_ptr< TwoCenterIntegrator > &	calculator,
		const int	it,
		const int	ia,
		const int	il,
		const int	iz,
		const int	im,
		const int	jt,
		const int	ja,
		const int	jl,
		const int	jz,
		const int	jm,
		const ModuleBase::Vector3< double > &	vR
	)

calculate the <phi_i|Lx|phi_j> matrix elements, in which the Lz are the angular momentum operators, |phi_i> and |phi_j> are the numerical atomic orbitals (NAOs).

Parameters

calculator	the std::unique_ptr<TwoCenterIntegrator> instance
it	atomtype index of the first atom
ia	atomic index of the first atom within the atomtype
il	angular momentum index of the first atom
iz	zeta function index of the first atom
mi	magnetic quantum number of the first atom
jt	atomtype index of the second atom
ja	atomic index of the second atom within the atomtype
jl	angular momentum index of the second atom
jz	zeta function index of the second atom
mj	magnetic quantum number of the second atom
vR	the vector from the first atom to the second atom

Returns

std::complex<double>

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cal_LyijR()

std::complex< double > ModuleIO::cal_LyijR	(	const std::unique_ptr< TwoCenterIntegrator > &	calculator,
		const int	it,
		const int	ia,
		const int	il,
		const int	iz,
		const int	im,
		const int	jt,
		const int	ja,
		const int	jl,
		const int	jz,
		const int	jm,
		const ModuleBase::Vector3< double > &	vR
	)

calculate the <phi_i|Ly|phi_j> matrix elements, in which the Lz are the angular momentum operators, |phi_i> and |phi_j> are the numerical atomic orbitals (NAOs).

Parameters

calculator	the std::unique_ptr<TwoCenterIntegrator> instance
it	atomtype index of the first atom
ia	atomic index of the first atom within the atomtype
il	angular momentum index of the first atom
iz	zeta function index of the first atom
mi	magnetic quantum number of the first atom
jt	atomtype index of the second atom
ja	atomic index of the second atom within the atomtype
jl	angular momentum index of the second atom
jz	zeta function index of the second atom
mj	magnetic quantum number of the second atom
vR	the vector from the first atom to the second atom

Returns

std::complex<double>

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cal_LzijR()

std::complex< double > ModuleIO::cal_LzijR	(	const std::unique_ptr< TwoCenterIntegrator > &	calculator,
		const int	it,
		const int	ia,
		const int	il,
		const int	iz,
		const int	mi,
		const int	jt,
		const int	ja,
		const int	jl,
		const int	jz,
		const int	mj,
		const ModuleBase::Vector3< double > &	vR
	)

calculate the <phi_i|Lz|phi_j> matrix elements, in which the Lz are the angular momentum operators, |phi_i> and |phi_j> are the numerical atomic orbitals (NAOs).

Parameters

calculator	the std::unique_ptr<TwoCenterIntegrator> instance
it	atomtype index of the first atom
ia	atomic index of the first atom within the atomtype
il	angular momentum index of the first atom
iz	zeta function index of the first atom
mi	magnetic quantum number of the first atom
jt	atomtype index of the second atom
ja	atomic index of the second atom within the atomtype
jl	angular momentum index of the second atom
jz	zeta function index of the second atom
mj	magnetic quantum number of the second atom
vR	the vector from the first atom to the second atom

Returns

std::complex<double>

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cal_mag()

template<typename TK >

void ModuleIO::cal_mag	(	Parallel_Orbitals *	pv,
		hamilt::Hamilt< TK > *	p_ham,
		K_Vectors &	kv,
		elecstate::ElecState *	pelec,
		const TwoCenterBundle &	two_center_bundle,
		const LCAO_Orbitals &	orb,
		UnitCell &	ucell,
		const Grid_Driver &	gd,
		const int	istep,
		const bool	print
	)

used in updating mag info in STRU file

write the Orbital file

write mulliken.txt

write atomic mag info in running log file

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cal_pdos() [1/2]

void ModuleIO::cal_pdos	(	const psi::Psi< double > *	psi,
		hamilt::Hamilt< double > *	p_ham,
		const Parallel_Orbitals &	pv,
		const UnitCell &	ucell,
		const K_Vectors &	kv,
		const int	nspin0,
		const int	nbands,
		const ModuleBase::matrix &	ekb,
		const double &	emax,
		const double &	emin,
		const double &	dos_edelta_ev,
		const double &	bcoeff
	)

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cal_pdos() [2/2]

void ModuleIO::cal_pdos	(	const psi::Psi< std::complex< double > > *	psi,
		hamilt::Hamilt< std::complex< double > > *	p_ham,
		const Parallel_Orbitals &	pv,
		const UnitCell &	ucell,
		const K_Vectors &	kv,
		const int	nspin0,
		const int	nbands,
		const ModuleBase::matrix &	ekb,
		const double &	emax,
		const double &	emin,
		const double &	dos_edelta_ev,
		const double &	bcoeff
	)

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calculate_RI_Tensor_sparse() [1/2]

template<typename Tdata >

std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, Tdata > > > ModuleIO::calculate_RI_Tensor_sparse	(	const double &	sparse_threshold,
		const std::map< int, std::map< TAC, RI::Tensor< Tdata > > > &	Hexxs,
		const UnitCell &	ucell
	)

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calculate_RI_Tensor_sparse() [2/2]

template<typename Tdata >

std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, Tdata > > > ModuleIO::calculate_RI_Tensor_sparse	(	const double &	sparse_threshold,
		const std::vector< std::map< int, std::map< TAC, RI::Tensor< Tdata > > > > &	Hexxs,
		const UnitCell &	ucell
	)

calculate CSR sparse matrix from the global matrix stored with RI::Tensor the return type is same as SR_sparse, HR_sparse, etc.

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ctrl_output_fp()

template<typename TK , typename TR >

void ModuleIO::ctrl_output_fp	(	UnitCell &	ucell,
		elecstate::ElecStateLCAO< TK > *	pelec,
		const int	istep
	)

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ctrl_output_lcao()

template<typename TK , typename TR >

void ModuleIO::ctrl_output_lcao	(	UnitCell &	ucell,
		K_Vectors &	kv,
		elecstate::ElecStateLCAO< TK > *	pelec,
		Parallel_Orbitals &	pv,
		Grid_Driver &	gd,
		psi::Psi< TK > *	psi,
		hamilt::HamiltLCAO< TK, TR > *	p_hamilt,
		TwoCenterBundle &	two_center_bundle,
		Gint_k &	gk,
		LCAO_Orbitals &	orb,
		const ModulePW::PW_Basis_K *	pw_wfc,
		const ModulePW::PW_Basis *	pw_rho,
		Grid_Technique &	gt,
		const ModulePW::PW_Basis_Big *	pw_big,
		const Structure_Factor &	sf,
		rdmft::RDMFT< TK, TR > &	rdmft_solver,
		LCAO_Deepks< TK > &	ld,
		const int	istep
	)

1) Output density matrix DM(R)

2) Output density matrix DM(k)

5) Output DeePKS information

6) Output <phi_i|O|phi_j> matrices, where O can be chosen as H, S, dH, dS, T, r. The format is CSR format.

7) Output kinetic matrix

8) Output expectation of angular momentum operator

9) Output Mulliken charge

10) Output atomic magnetization by using 'spin_constraint'

11) Output Berry phase

12) Wannier90 interface in LCAO basis

18) Perform RDMFT calculations, added by jghan, 2024-10-17

initialize the gradients of Etotal with respect to occupation numbers and wfc, and set all elements to 0. dedocc = d E/d Occ_Num

dedwfc = d E/d wfc

Output quasi orbitals

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cVc() [1/2]

template<typename T >

std::vector< T > ModuleIO::cVc	(	T *const	V,
		T *const	c,
		int	nbasis,
		int	nbands
	)

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cVc() [2/2]

template<typename T >

std::vector< T > ModuleIO::cVc ( T *  V, T *  c, const int  nbasis, const int  nbands, const Parallel_Orbitals &  pv, const Parallel_2D &  p2d  )

inline

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dmk_gen_fname()

std::string ModuleIO::dmk_gen_fname	(	const bool	gamma_only,
		const int	ispin,
		const int	ik
	)

Generates the filename for the DMK file based on the given parameters.

Parameters

gamma_only	Whether the calculation is gamma_only.
ispin	The index of the spin component.
ik	The index of the k-point.

Returns

The generated filename.

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dmk_read_ucell()

void ModuleIO::dmk_read_ucell

(

std::ifstream &

ifs

)

Reads the unit cell information lines in a DMK file.

Parameters

ifs	The input file stream.

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dmk_readData() [1/2]

void ModuleIO::dmk_readData	(	std::ifstream &	ifs,
		double &	data
	)

Read one double from a file.

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dmk_readData() [2/2]

void ModuleIO::dmk_readData	(	std::ifstream &	ifs,
		std::complex< double > &	data
	)

Read one complex double from a file.

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dmk_write_ucell()

void ModuleIO::dmk_write_ucell	(	std::ofstream &	ofs,
		const UnitCell *	ucell
	)

Writes the unit cell information to a DMK file.

Parameters

ofs	The output file stream.
ucell	A pointer to the UnitCell object.

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dmr_gen_fname()

std::string ModuleIO::dmr_gen_fname	(	const int	out_type,
		const int	ispin,
		const bool	append = true,
		const int	istep = -1
	)

Generates a filename for the DMR output based on the given parameters.

Parameters

out_type	The output type. 1: csr, 2: npz.
ispin	The spin value, starting from 0.
append	A boolean indicating whether append the data to one file or create a new file.
istep	The ION step (default: -1), starting from 0.

Returns

The generated filename as a string.

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filename_output()

std::string ModuleIO::filename_output	(	const std::string &	directory,
		const std::string &	property,
		const std::string &	basis,
		const int	ik_local,
		const std::vector< int > &	ik2iktot,
		const int	nspin,
		const int	nkstot,
		const int	out_type,
		const bool	out_app_flag,
		const bool	gamma_only,
		const int	istep = -1
	)

Generates the filename for the output files

Parameters

directory	directory of the file
property	wave function (wf), charge density (chg) or matrix (mat)
basis	nao or pw
ik_local	index of the k-points within each pool, and starting from 0.
ik2iktot	map from ik to iktot
nspin	number of spin channels, 1,2 or 4
nkstot	number of total k-points
out_type	two types of output file format, 1 for .txt and 2 for .dat (binary)
out_app_flag	whether to append to existing file.
gamma_only	gamma_only algorithm or not.
istep	index of the ion step starting from 0. If < 0, the step number is not included in the file name.

Returns

The generated filename.

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get_grid_points()

void ModuleIO::get_grid_points	(	const std::vector< double > &	start,
		const std::vector< double > &	end,
		const int &	npoints,
		const int &	nx,
		const int &	ny,
		const int &	nz,
		std::vector< std::vector< int > > &	points,
		std::vector< std::vector< double > > &	shifts
	)

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get_pchg_pw()

template<typename Device >

void ModuleIO::get_pchg_pw	(	const std::vector< int > &	out_pchg,
		const int	nbands,
		const int	nspin,
		const int	nxyz,
		const int	chr_ngmc,
		UnitCell *	ucell,
		const psi::Psi< std::complex< double >, Device > *	kspw_psi,
		const ModulePW::PW_Basis *	pw_rhod,
		const ModulePW::PW_Basis_K *	pw_wfc,
		const Device *	ctx,
		const Parallel_Grid &	pgrid,
		const std::string &	global_out_dir,
		const bool	if_separate_k,
		const K_Vectors &	kv,
		const int	kpar,
		const int	my_pool,
		const Charge *	chr
	)

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get_R_range()

template<typename TR >

std::set< Abfs::Vector3_Order< int > > ModuleIO::get_R_range

(

const hamilt::HContainer< TR > &

hR

)

get_real() [1/4]

double ModuleIO::get_real ( const double &  d )

inline

get_real() [2/4]

template<typename FPTYPE >

FPTYPE ModuleIO::get_real ( const FPTYPE &  d )

inline

get_real() [3/4]

double ModuleIO::get_real ( const std::complex< double > &  c )

inline

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get_real() [4/4]

template<typename FPTYPE >

FPTYPE ModuleIO::get_real ( const std::complex< FPTYPE > &  c )

inline

get_wf_pw()

template<typename Device >

void ModuleIO::get_wf_pw	(	const std::vector< int > &	out_wfc_norm,
		const std::vector< int > &	out_wfc_re_im,
		const int	nbands,
		const int	nspin,
		const int	nxyz,
		UnitCell *	ucell,
		const psi::Psi< std::complex< double >, Device > *	kspw_psi,
		const ModulePW::PW_Basis_K *	pw_wfc,
		const Device *	ctx,
		const Parallel_Grid &	pgrid,
		const std::string &	global_out_dir,
		const K_Vectors &	kv,
		const int	kpar,
		const int	my_pool
	)

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ldos_mode_pw()

void ModuleIO::ldos_mode_pw	(	const elecstate::ElecStatePW< std::complex< double > > *	pelec,
		const psi::Psi< std::complex< double > > &	psi,
		const Parallel_Grid &	pgrid,
		const UnitCell &	ucell
	)

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longstring()

std::string ModuleIO::longstring

(

const std::vector< std::string > &

words

)

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nofound_str()

std::string ModuleIO::nofound_str	(	std::vector< std::string >	init_chgs,
		const std::string &	str
	)

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nscf_band()

void ModuleIO::nscf_band	(	const int &	is,
		const std::string &	eig_file,
		const int &	nband,
		const double &	fermie,
		const int &	precision,
		const ModuleBase::matrix &	ekb,
		const K_Vectors &	kv
	)

calculate the band structure

Parameters

is	spin index is = 0 or 1
out_band_dir	directory to save the band structure
nband	number of bands
fermie	fermi energy
precision	precision of the output
ekb	eigenvalues of k points and bands
kv	klist

first find if present kpoint in present pool

then get the local kpoint index, which starts definitly from 0

if present kpoint corresponds the spin of the present one

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nscf_fermi_surface()

void ModuleIO::nscf_fermi_surface	(	const std::string &	out_band_dir,
		const int &	nband,
		const double &	ef,
		const K_Vectors &	kv,
		const UnitCell &	ucell,
		const ModuleBase::matrix &	ekb
	)

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orbital_energy() [1/2]

template<typename FPTYPE >

std::vector< FPTYPE > ModuleIO::orbital_energy	(	const int	ik,
		const int	nbands,
		const std::vector< std::complex< FPTYPE > > &	mat_mo
	)

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orbital_energy() [2/2]

template<typename T >

std::vector< double > ModuleIO::orbital_energy	(	const int	ik,
		const int	nbands,
		const std::vector< T > &	mat_mo,
		const Parallel_2D &	p2d
	)

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output_after_relax()

void ModuleIO::output_after_relax	(	bool	conv_ion,
		bool	conv_esolver,
		std::ofstream &	ofs_running = GlobalV::ofs_running
	)

output after relaxation

Parameters

conv_ion	if is convergence for ions
conv_esolver	if is convergence for electrons
ofs_running	the output stream

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output_convergence_after_scf()

void ModuleIO::output_convergence_after_scf	(	const bool &	convergence,
		double &	energy,
		std::ofstream &	ofs_running = GlobalV::ofs_running
	)

output if is convergence and energy after scf

Parameters

convergence	if is convergence
energy	the total energy in Ry
ofs_running	the output stream

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output_dHR()

void ModuleIO::output_dHR	(	const int &	istep,
		const ModuleBase::matrix &	v_eff,
		Gint_k &	gint_k,
		const UnitCell &	ucell,
		const Parallel_Orbitals &	pv,
		LCAO_HS_Arrays &	HS_Arrays,
		const Grid_Driver &	grid,
		const TwoCenterBundle &	two_center_bundle,
		const LCAO_Orbitals &	orb,
		const K_Vectors &	kv,
		const bool &	binary = false,
		const double &	sparse_threshold = 1e-10
	)

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output_dSR()

void ModuleIO::output_dSR	(	const int &	istep,
		const UnitCell &	ucell,
		const Parallel_Orbitals &	pv,
		LCAO_HS_Arrays &	HS_Arrays,
		const Grid_Driver &	grid,
		const TwoCenterBundle &	two_center_bundle,
		const LCAO_Orbitals &	orb,
		const K_Vectors &	kv,
		const bool &	binary = false,
		const double &	sparse_thr = 1e-10
	)

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output_efermi()

void ModuleIO::output_efermi	(	const bool &	convergence,
		double &	efermi,
		std::ofstream &	ofs_running = GlobalV::ofs_running
	)

output the fermi energy

Parameters

convergence	if is convergence
efermi
ofs_running	the output stream

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output_HSR()

void ModuleIO::output_HSR	(	const UnitCell &	ucell,
		const int &	istep,
		const ModuleBase::matrix &	v_eff,
		const Parallel_Orbitals &	pv,
		LCAO_HS_Arrays &	HS_Arrays,
		const Grid_Driver &	grid,
		const K_Vectors &	kv,
		hamilt::Hamilt< std::complex< double > > *	p_ham,
		const std::string &	SR_filename = "srs1_nao.csr",
		const std::string &	HR_filename_up = "hrs1_nao.csr",
		const std::string	HR_filename_down = "hrs2_nao.csr",
		const bool &	binary = false,
		const double &	sparse_threshold = 1e-10
	)

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output_mat_npz()

void ModuleIO::output_mat_npz	(	const UnitCell &	ucell,
		std::string &	zipname,
		const hamilt::HContainer< double > &	hR
	)

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output_mat_sparse() [1/3]

template<>

void ModuleIO::output_mat_sparse	(	const bool &	out_mat_hsR,
		const bool &	out_mat_dh,
		const bool &	out_mat_ds,
		const bool &	out_mat_t,
		const bool &	out_mat_r,
		const int &	istep,
		const ModuleBase::matrix &	v_eff,
		const Parallel_Orbitals &	pv,
		Gint_k &	gint_k,
		const TwoCenterBundle &	two_center_bundle,
		const LCAO_Orbitals &	orb,
		UnitCell &	ucell,
		const Grid_Driver &	grid,
		const K_Vectors &	kv,
		hamilt::Hamilt< double > *	p_ham
	)

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output_mat_sparse() [2/3]

template<>

void ModuleIO::output_mat_sparse	(	const bool &	out_mat_hsR,
		const bool &	out_mat_dh,
		const bool &	out_mat_ds,
		const bool &	out_mat_t,
		const bool &	out_mat_r,
		const int &	istep,
		const ModuleBase::matrix &	v_eff,
		const Parallel_Orbitals &	pv,
		Gint_k &	gint_k,
		const TwoCenterBundle &	two_center_bundle,
		const LCAO_Orbitals &	orb,
		UnitCell &	ucell,
		const Grid_Driver &	grid,
		const K_Vectors &	kv,
		hamilt::Hamilt< std::complex< double > > *	p_ham
	)

generate a file containing the Hamiltonian and S(overlap) matrices

generate a file containing the kinetic energy matrix

generate a file containing the derivatives of the Hamiltonian matrix (in Ry/Bohr)

generate a file containing the derivatives of the overlap matrix (in Ry/Bohr)

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output_mat_sparse() [3/3]

template<typename T >

void ModuleIO::output_mat_sparse	(	const bool &	out_mat_hsR,
		const bool &	out_mat_dh,
		const bool &	out_mat_ds,
		const bool &	out_mat_t,
		const bool &	out_mat_r,
		const int &	istep,
		const ModuleBase::matrix &	v_eff,
		const Parallel_Orbitals &	pv,
		Gint_k &	gint_k,
		const TwoCenterBundle &	two_center_bundle,
		const LCAO_Orbitals &	orb,
		UnitCell &	ucell,
		const Grid_Driver &	grid,
		const K_Vectors &	kv,
		hamilt::Hamilt< T > *	p_ham
	)

the output interface to write the sparse matrix of H, S, T, and r

output_single_R()

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 = true
	)

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output_SR()

void ModuleIO::output_SR	(	Parallel_Orbitals &	pv,
		const Grid_Driver &	grid,
		hamilt::Hamilt< std::complex< double > > *	p_ham,
		const std::string &	SR_filename = "srs1_nao.csr",
		const bool &	binary = false,
		const double &	sparse_threshold = 1e-10
	)

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output_TR()

void ModuleIO::output_TR	(	const int	istep,
		const UnitCell &	ucell,
		const Parallel_Orbitals &	pv,
		LCAO_HS_Arrays &	HS_Arrays,
		const Grid_Driver &	grid,
		const TwoCenterBundle &	two_center_bundle,
		const LCAO_Orbitals &	orb,
		const std::string &	TR_filename = "trs1_nao.csr",
		const bool &	binary = false,
		const double &	sparse_threshold = 1e-10
	)

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output_vacuum_level()

void ModuleIO::output_vacuum_level	(	const UnitCell *	ucell,
		const double *const *	rho,
		const double *	v_elecstat,
		const int &	nx,
		const int &	ny,
		const int &	nz,
		const int &	nxyz,
		const int &	nrxx,
		const int &	nplane,
		const int &	startz_current,
		std::ofstream &	ofs_running = GlobalV::ofs_running
	)

calculate and output the vacuum level We first determine the vacuum direction, then get the vacuum position based on the minimum of charge density, finally output the vacuum level, i.e., the electrostatic potential at the vacuum position.

Parameters

ucell	the unitcell
rho	charge density
v_elecstat	electrostatic potential
ofs_running	the output stream

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parse_args()

void ModuleIO::parse_args	(	int	argc,
		char **	argv
	)

This function reture the version information when using command "abacus --version", "abacus -v" or "abacus -V". Otherwise, it does nothing.

Parameters

[in]	argc	(ARGument Count) is an integer variable that stores the number of command-line arguments passed by the user including the name of the program. So if we pass a value to a program, the value of argc would be 2 (one for argument and one for program name)
[in]	argv	(ARGument Vector) is an array of character pointers listing all the arguments. If argc is greater than zero, the array elements from argv[0] to argv[argc-1] will contain pointers to strings. argv[0] is the name of the program , After that till argv[argc-1] every element is command -line arguments.

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prepare()

double ModuleIO::prepare	(	const UnitCell &	cell,
		int &	dir
	)

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prepare_dos()

void ModuleIO::prepare_dos	(	std::ofstream &	ofs_running,
		const elecstate::efermi &	energy_fermi,
		const ModuleBase::matrix &	ekb,
		const int	nks,
		const int	nbands,
		const double &	dos_edelta_ev,
		const double &	dos_scale,
		double &	emax,
		double &	emin
	)

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print_force()

void ModuleIO::print_force	(	std::ofstream &	ofs,
		const UnitCell &	cell,
		const std::string &	name,
		const ModuleBase::matrix &	force,
		bool	ry = true
	)

output atomic forces

Parameters

ofs	the output stream
cell	the unitcell
name	force term name
force	atomic forces
ry	true if the unit of force is a.u.

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print_PAOs()

void ModuleIO::print_PAOs

(

const UnitCell &

ucell

)

print chi (PAO) in pseudopotential file

Parameters

ucell

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print_pdos_gamma()

void ModuleIO::print_pdos_gamma	(	const UnitCell &	ucell,
		const ModuleBase::matrix *	pdos,
		const int	nlocal,
		const int	npoints,
		const double &	emin,
		const double &	dos_edelta_ev
	)

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print_pdos_multik()

void ModuleIO::print_pdos_multik	(	const UnitCell &	ucell,
		const ModuleBase::matrix *	pdos,
		const int	nlocal,
		const int	npoints,
		const double &	emin,
		const double &	dos_edelta_ev
	)

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print_rhofft()

void ModuleIO::print_rhofft	(	ModulePW::PW_Basis *	pw_rhod,
		ModulePW::PW_Basis *	pw_rho,
		ModulePW::PW_Basis_Big *	pw_big,
		std::ofstream &	ofs
	)

Print charge density using FFT.

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print_screen()

void ModuleIO::print_screen	(	const int &	stress_step,
		const int &	force_step,
		const int &	istep
	)

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print_stress()

void ModuleIO::print_stress	(	const std::string &	name,
		const ModuleBase::matrix &	scs,
		const bool	screen,
		const bool	ry,
		std::ofstream &	ofs
	)

output stress components

Parameters

name	stress term name
f	stress components
ry	true if the unit of force is a.u.

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print_tdos_gamma()

void ModuleIO::print_tdos_gamma	(	const ModuleBase::matrix *	pdos,
		const int	nlocal,
		const int	npoints,
		const double &	emin,
		const double &	dos_edelta_ev
	)

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print_tdos_multik()

void ModuleIO::print_tdos_multik	(	const ModuleBase::matrix *	pdos,
		const int	nlocal,
		const int	npoints,
		const double &	emin,
		const double &	dos_edelta_ev
	)

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print_time()

void ModuleIO::print_time	(	time_t &	time_start,
		time_t &	time_finish
	)

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print_wfcfft()

void ModuleIO::print_wfcfft	(	const Input_para &	inp,
		ModulePW::PW_Basis_K &	pw_wfc,
		std::ofstream &	ofs
	)

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psi_Hpsi()

template<typename FPTYPE >

std::vector< std::complex< FPTYPE > > ModuleIO::psi_Hpsi	(	std::complex< FPTYPE > *const	psi,
		std::complex< FPTYPE > *const	hpsi,
		const int	nbasis,
		const int	nbands
	)

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read_abacus_orb()

void ModuleIO::read_abacus_orb	(	std::ifstream &	ifs,
		std::string &	elem,
		double &	ecut,
		int &	nr,
		double &	dr,
		std::vector< int > &	nzeta,
		std::vector< std::vector< double > > &	radials,
		const int	rank = 0
	)

static version of read_abacus_orb. A delete-new operation may cause the memory leak, it is better to use std::vector to replace the raw pointer.

Parameters

ifs	[in] ifstream from the orbital file, via std::ifstream ifs(forb);
elem	[out] element symbol
ecut	[out] planewave energy cutoff
nr	[out] number of radial grid points
dr	[out] radial grid spacing
nzeta	[out] number of zeta functions for each angular momentum
radials	[out] radial orbitals
rank	[in] MPI rank

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read_cube()

bool ModuleIO::read_cube	(	const std::string &	file,
		std::vector< std::string > &	comment,
		int &	natom,
		std::vector< double > &	origin,
		int &	nx,
		int &	ny,
		int &	nz,
		std::vector< double > &	dx,
		std::vector< double > &	dy,
		std::vector< double > &	dz,
		std::vector< int > &	atom_type,
		std::vector< double > &	atom_charge,
		std::vector< std::vector< double > > &	atom_pos,
		std::vector< double > &	data
	)

read the full data from a cube file

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read_dmk()

template<typename T >

bool ModuleIO::read_dmk	(	const int	nspin,
		const int	nk,
		const Parallel_2D &	pv,
		const std::string &	dmk_dir,
		std::vector< std::vector< T > > &	dmk,
		std::ofstream &	ofs_running
	)

Reads the DMK data from a file.

Template Parameters

T	The type of the DMK data.

Parameters

nspin	The number of spin components.
nk	The number of k-points.
pv	The Parallel_2D object. Will get the global size and local size from it, and seperate the data into different processors accordingly.
dmk_dir	The directory path of the DMK file.
dmk	A vector to store the DMK data. If use MPI parallel, the data will be seperated into different processors based on the Parallel_2D object.

Returns

True if the DMK data is successfully read, false otherwise.

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read_exit_file()

int ModuleIO::read_exit_file	(	const int &	my_rank,
		const std::string &	filename,
		std::ofstream &	ofs_running
	)

read file to determine whether to stop the current execution

Parameters

my_rank	the rank of the current process
filename	the name of the file to read
ofs_running	the output stream

Returns

0 if the file is not found or does not contain correct keywords, do not stop the current execution

1 if the file is found and contains "stop_ion", the current execution stops at the next ionic step

2 if the file is found and contains "stop_elec", the current execution stops at the next electronic step

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read_Hexxs_cereal()

template<typename Tdata >

void ModuleIO::read_Hexxs_cereal	(	const std::string &	file_name,
		std::vector< std::map< int, std::map< TAC, RI::Tensor< Tdata > > > > &	Hexxs
	)

read Hexxs in cereal format

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read_Hexxs_csr()

template<typename Tdata >

void ModuleIO::read_Hexxs_csr	(	const std::string &	file_name,
		const UnitCell &	ucell,
		const int	nspin,
		const int	nbasis,
		std::vector< std::map< int, std::map< TAC, RI::Tensor< Tdata > > > > &	Hexxs
	)

read Hexxs in CSR format

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read_information()

void ModuleIO::read_information	(	std::ifstream &	ifs,
		std::vector< std::string > &	output,
		const std::string &	delimiters
	)

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read_k()

std::vector< double > ModuleIO::read_k	(	std::string	filename,
		int	ik
	)

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read_mat_npz()

void ModuleIO::read_mat_npz	(	const Parallel_Orbitals *	paraV,
		const UnitCell &	ucell,
		std::string &	zipname,
		hamilt::HContainer< double > &	hR
	)

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read_rhog()

bool ModuleIO::read_rhog	(	const std::string &	filename,
		const ModulePW::PW_Basis *	pw_rhod,
		std::complex< double > **	rhog
	)

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read_vdata_palgrid()

bool ModuleIO::read_vdata_palgrid	(	const Parallel_Grid &	pgrid,
		const int	my_rank,
		std::ofstream &	ofs_running,
		const std::string &	fn,
		double *const	data,
		const int	nat
	)

read volumetric data from .cube file into the parallel distributed grid.

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read_wf2rho_pw()

void ModuleIO::read_wf2rho_pw	(	const ModulePW::PW_Basis_K *	pw_wfc,
		ModuleSymmetry::Symmetry &	symm,
		Charge &	chg,
		const std::string &	readin_dir,
		const int	kpar,
		const int	my_pool,
		const int	my_rank,
		const int	nproc_in_pool,
		const int	rank_in_pool,
		const int	nbands,
		const int	nspin,
		const int	npol,
		const int	nkstot,
		const std::vector< int > &	ik2iktot,
		const std::vector< int > &	isk,
		std::ofstream &	ofs_running
	)

read wave functions and occupation numbers to charge density

Parameters

pw_wfc	pw basis for wave functions
symm	symmetry
nkstot	total number of k points
isk	k index to spin index
chg	charge density

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read_wfc_nao()

template<typename T >

bool ModuleIO::read_wfc_nao	(	const std::string &	global_readin_dir,
		const Parallel_Orbitals &	ParaV,
		psi::Psi< T > &	psid,
		elecstate::ElecState *const	pelec,
		const std::vector< int > &	ik2iktot,
		const int	nkstot,
		const int	nspin,
		const int	skip_band = 0,
		const int	nstep = -1
	)

Reads the wavefunction coefficients from an input file.

Template Parameters

T	The type of the wavefunction coefficients.

Parameters

global_readin_dir	The global directory for reading input files.
ParaV	The parallel orbitals object.
psid	The Psi object to store the wavefunction coefficients.
pelec	Pointer to the ElecState object.
skip_band	From which band to start reading.

Returns

True if the wavefunction coefficients are successfully read, false otherwise.

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read_wfc_nao_one_data() [1/2]

void ModuleIO::read_wfc_nao_one_data	(	std::ifstream &	ifs,
		double &	data
	)

Reads a single data value from an input file stream.

Parameters

ifs	The input file stream to read from.
data	The variable to store the read data value.

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read_wfc_nao_one_data() [2/2]

void ModuleIO::read_wfc_nao_one_data	(	std::ifstream &	ifs,
		std::complex< double > &	data
	)

Reads a single complex data value from an input file stream.

Parameters

ifs	The input file stream to read from.
data	The variable to store the read complex data value.

read_wfc_pw()

void ModuleIO::read_wfc_pw	(	const std::string &	filedir,
		const ModulePW::PW_Basis_K *	pw_wfc,
		const int	rank_in_pool,
		const int	nproc_in_pool,
		const int	nbands,
		const int	npol,
		const int &	ik,
		const int &	ikstot,
		const int &	nkstot,
		ModuleBase::ComplexMatrix &	wfc
	)

read wave functions from binary file

Parameters

filename	filename containing wave functions
pw_wfc	wave function FFT grids
ik	k index
ikstot	total index of k points
nkstot	total number of k points
wfc	wave functions

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save_dH_sparse()

void ModuleIO::save_dH_sparse	(	const int &	istep,
		const Parallel_Orbitals &	pv,
		LCAO_HS_Arrays &	HS_Arrays,
		const double &	sparse_thr,
		const bool &	binary,
		const std::string &	fileflag = "h"
	)

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save_HSR_sparse()

void ModuleIO::save_HSR_sparse	(	const int &	istep,
		const Parallel_Orbitals &	pv,
		LCAO_HS_Arrays &	HS_Arrays,
		const double &	sparse_thr,
		const bool &	binary,
		const std::string &	SR_filename,
		const std::string &	HR_filename_up,
		const std::string &	HR_filename_down = ""
	)

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save_mat()

template<typename T >

void ModuleIO::save_mat	(	const int	istep,
		const T *	mat,
		const int	dim,
		const bool	bit,
		const int	precision,
		const bool	tri,
		const bool	app,
		const std::string &	file_name,
		const Parallel_2D &	pv,
		const int	drank,
		const bool	reduce = true
	)

save a square matrix, such as H(k) and S(k)

Parameters

[in]	istep	: the step of the calculation
[in]	mat	: the local matrix
[in]	bit	: true for binary, false for decimal
[in]	tri	: true for upper triangle, false for full matrix
[in]	app	: true for append, false for overwrite
[in]	file_name	: the name of the output file
[in]	pv	: the 2d-block parallelization information
[in]	drank	: the rank of the current process

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save_sparse()

template<typename Tdata >

void ModuleIO::save_sparse	(	const std::map< Abfs::Vector3_Order< int >, std::map< size_t, std::map< size_t, Tdata > > > &	smat,
		const std::set< Abfs::Vector3_Order< int > > &	all_R_coor,
		const double &	sparse_thr,
		const bool &	binary,
		const std::string &	filename,
		const Parallel_Orbitals &	pv,
		const std::string &	label,
		const int &	istep = -1,
		const bool &	reduce = true
	)

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set_gint_pointer()

template<typename T >

void ModuleIO::set_gint_pointer	(	Gint_Gamma &	gint_gamma,
		Gint_k &	gint_k,
		typename TGint< T >::type *&	gint
	)

set_gint_pointer< double >() [1/2]

template<>

void ModuleIO::set_gint_pointer< double >	(	Gint_Gamma &	gint_gamma,
		Gint_k &	gint_k,
		typename TGint< double >::type *&	gint
	)

set_gint_pointer< double >() [2/2]

template<>

void ModuleIO::set_gint_pointer< double >	(	Gint_Gamma &	gint_gamma,
		Gint_k &	gint_k,
		typename TGint< double >::type *&	gint
	)

set_gint_pointer< std::complex< double > >() [1/2]

template<>

void ModuleIO::set_gint_pointer< std::complex< double > >	(	Gint_Gamma &	gint_gamma,
		Gint_k &	gint_k,
		typename TGint< std::complex< double > >::type *&	gint
	)

set_gint_pointer< std::complex< double > >() [2/2]

template<>

void ModuleIO::set_gint_pointer< std::complex< double > >	(	Gint_Gamma &	gint_gamma,
		Gint_k &	gint_k,
		typename TGint< std::complex< double > >::type *&	gint
	)

set_para2d_MO()

void ModuleIO::set_para2d_MO ( const Parallel_Orbitals &  pv, const int  nbands, Parallel_2D &  p2d  )

inline

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setup_parameters()

void ModuleIO::setup_parameters	(	UnitCell &	ucell,
		K_Vectors &	kv
	)

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stm_mode_pw()

void ModuleIO::stm_mode_pw	(	const elecstate::ElecStatePW< std::complex< double > > *	pelec,
		const psi::Psi< std::complex< double > > &	psi,
		const Parallel_Grid &	pgrid,
		const UnitCell &	ucell
	)

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to_dir()

std::string ModuleIO::to_dir

(

const std::string &

str

)

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trilinear_interpolate() [1/2]

void ModuleIO::trilinear_interpolate	(	const double *const	data_in,
		const int &	nx_read,
		const int &	ny_read,
		const int &	nz_read,
		const int &	nx,
		const int &	ny,
		const int &	nz,
		double *	data_out
	)

The trilinear interpolation method.

Trilinear interpolation is a method for interpolating grid data in 3D space. It estimates the value at a given position by interpolating the data along the three adjacent points.

Specifically, for 3D grid data, trilinear interpolation requires determining the eight data points that are closest to the point where the estimation is required. These data points form a cube, with vertices at (x0,y0,z0), (x0+1,y0,z0), (x0,y0+1,z0), (x0+1,y0+1,z0), (x0,y0,z0+1), (x0+1,y0,z0+1), (x0,y0+1,z0+1) and (x0+1,y0+1,z0+1). Here, (x0,y0,z0) is the data point closest to the estimation point and has coordinate values less than those of the estimation point.

For the estimation location (x,y,z), its estimated value in the grid can be calculated using the following formula: f(x,y,z) = f000(1-dx)(1-dy)(1-dz) + f100dx(1-dy)(1-dz) + f010(1-dx)dy(1-dz) + f001(1-dx)(1-dy)dz + f101dx(1-dy)dz + f011(1-dx)dydz + f110dxdy(1-dz) + f111dxdydz where fijk represents the data value at vertex i,j,k of the cube, and dx = x - x0, dy = y - y0, dz = z - z0 represent the distance between the estimation point and the closest data point in each of the three directions, divided by the grid spacing. Here, it is assumed that the grid spacing is equal and can be omitted during computation.

Parameters

data_in	the input data of size nxyz_read
nx_read	nx read from file
ny_read	ny read from file
nz_read	nz read from file
nx	the dimension of grids along x
ny	the dimension of grids along y
nz	the dimension of grids along z
data_out	the interpolated results of size nxyz

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trilinear_interpolate() [2/2]

void ModuleIO::trilinear_interpolate	(	const std::vector< std::vector< int > > &	points,
		const std::vector< std::vector< double > > &	shifts,
		const Parallel_Grid &	pgrid,
		const std::vector< double > &	data,
		std::vector< double > &	results
	)

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wfc_nao_write2file()

void ModuleIO::wfc_nao_write2file	(	const std::string &	name,
		const double *	ctot,
		const int	nlocal,
		const int	ik,
		const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg,
		const bool &	writeBinary,
		const bool &	append_flag
	)

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wfc_nao_write2file_complex()

void ModuleIO::wfc_nao_write2file_complex	(	const std::string &	name,
		const std::complex< double > *	ctot,
		const int	nlocal,
		const int &	ik,
		const ModuleBase::Vector3< double > &	kvec_c,
		const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg,
		const bool &	writeBinary,
		const bool &	append_flag
	)

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write_abacus_orb()

void ModuleIO::write_abacus_orb	(	std::ofstream &	ofs,
		const std::string &	elem,
		const double &	ecut,
		const int	nr,
		const double	dr,
		const std::vector< int > &	nzeta,
		const std::vector< std::vector< double > > &	radials,
		const int	rank = 0
	)

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write_cube()

void ModuleIO::write_cube	(	const std::string &	file,
		const std::vector< std::string > &	comment,
		const int &	natom,
		const std::vector< double > &	origin,
		const int &	nx,
		const int &	ny,
		const int &	nz,
		const std::vector< double > &	dx,
		const std::vector< double > &	dy,
		const std::vector< double > &	dz,
		const std::vector< int > &	atom_type,
		const std::vector< double > &	atom_charge,
		const std::vector< std::vector< double > > &	atom_pos,
		const std::vector< double > &	data,
		const int	precision,
		const int	ndata_line = 6
	)

write a cube file

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write_dipole()

void ModuleIO::write_dipole	(	const UnitCell &	ucell,
		const double *	rho_save,
		const ModulePW::PW_Basis *	rhopw,
		const int &	is,
		const int &	istep,
		const std::string &	fn,
		const int &	precision = 11
	)

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write_dmk()

template<typename T >

void ModuleIO::write_dmk	(	const std::vector< std::vector< T > > &	dmk,
		const int	precision,
		const std::vector< double > &	efs,
		const UnitCell *	ucell,
		const Parallel_2D &	pv
	)

Writes the DMK data to a file.

Template Parameters

T	The type of the DMK data.

Parameters

dmk	A vector containing the DMK data. The first dimension is nspin*nk, and the second dimension is nlocal*nlocal. DMK is parallel in 2d-block type if using MPI.
precision	The precision of the output of DMK.
efs	A vector containing the Fermi energies, and should have the same size as the number of SPIN.
ucell	A pointer to the UnitCell object.
pv	The Parallel_2D object. The 2d-block parallel information of DMK.

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write_dmr()

void ModuleIO::write_dmr	(	const std::vector< hamilt::HContainer< double > * >	dmr,
		const Parallel_2D &	paraV,
		const bool	append,
		const int *	iat2iwt,
		const int	nat,
		const int	istep
	)

Writes DMR to a file.

Parameters

dmr	The 2D block parallel matrix representing the density matrix. The first dimension is the spin index.
paraV	The parallel 2D object.
out_type	The output file type. 1: csr, 2: npz.
sparse	Whether output the sparse DM.
ispin	The spin index, starting from 0.
append	Whether to append the data to an existing file or create a new file. The file name is related to this flag.
istep	The ION step, starting from 0.

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write_dmr_csr()

void ModuleIO::write_dmr_csr	(	std::string &	fname,
		hamilt::HContainer< double > *	dm_serial,
		const int	istep
	)

Writes HContainer to a csr file.

Parameters

fname	The name of the file to write the CSR representation to.
dm_serial	A pointer to the Hamiltonian container.
istep	The current step number.

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write_dos_lcao() [1/3]

template void ModuleIO::write_dos_lcao	(	const psi::Psi< double > *	psi,
		hamilt::Hamilt< double > *	p_ham,
		const Parallel_Orbitals &	pv,
		const UnitCell &	ucell,
		const K_Vectors &	kv,
		const int	nbands,
		const elecstate::efermi &	energy_fermi,
		const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg,
		const double &	dos_edelta_ev,
		const double &	dos_scale,
		const double &	bcoeff,
		const bool	out_app_flag,
		const int	istep,
		std::ofstream &	ofs_running
	)

write_dos_lcao() [2/3]

template void ModuleIO::write_dos_lcao	(	const psi::Psi< std::complex< double > > *	psi,
		hamilt::Hamilt< std::complex< double > > *	p_ham,
		const Parallel_Orbitals &	pv,
		const UnitCell &	ucell,
		const K_Vectors &	kv,
		const int	nbands,
		const elecstate::efermi &	energy_fermi,
		const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg,
		const double &	dos_edelta_ev,
		const double &	dos_scale,
		const double &	bcoeff,
		const bool	out_app_flag,
		const int	istep,
		std::ofstream &	ofs_running
	)

write_dos_lcao() [3/3]

template<typename T >

void ModuleIO::write_dos_lcao	(	const psi::Psi< T > *	psi,
		hamilt::Hamilt< T > *	p_ham,
		const Parallel_Orbitals &	pv,
		const UnitCell &	ucell,
		const K_Vectors &	kv,
		const int	nbands,
		const elecstate::efermi &	energy_fermi,
		const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg,
		const double &	dos_edelta_ev,
		const double &	dos_scale,
		const double &	bcoeff,
		const bool	out_app_flag,
		const int	istep,
		std::ofstream &	ofs_running
	)

calculate density of states(DOS), partial density of states(PDOS), and mulliken charge for LCAO base

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write_dos_pw()

void ModuleIO::write_dos_pw	(	const UnitCell &	ucell,
		const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg,
		const K_Vectors &	kv,
		const int	nbands,
		const elecstate::efermi &	energy_fermi,
		const double &	dos_edelta_ev,
		const double &	dos_scale,
		const double &	bcoeff,
		std::ofstream &	ofs_running
	)

calculate density of states(DOS) for PW base

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write_eband_terms()

template<typename TK , typename TR >

void ModuleIO::write_eband_terms	(	const int	nspin,
		const int	nbasis,
		const int	drank,
		const Parallel_Orbitals *	pv,
		const psi::Psi< TK > &	psi,
		const UnitCell &	ucell,
		Structure_Factor &	sf,
		surchem &	solvent,
		const ModulePW::PW_Basis &	rho_basis,
		const ModulePW::PW_Basis &	rhod_basis,
		const ModuleBase::matrix &	vloc,
		const Charge &	chg,
		Gint_Gamma &	gint_gamma,
		Gint_k &	gint_k,
		const K_Vectors &	kv,
		const ModuleBase::matrix &	wg,
		Grid_Driver &	gd,
		const std::vector< double > &	orb_cutoff,
		const TwoCenterBundle &	two_center_bundle
	)

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write_eig_file()

void ModuleIO::write_eig_file	(	const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg,
		const K_Vectors &	kv
	)

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write_eig_iter()

void ModuleIO::write_eig_iter	(	const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg,
		const K_Vectors &	kv
	)

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write_elecstat_pot()

void ModuleIO::write_elecstat_pot	(	const int &	bz,
		const int &	nbz,
		const std::string &	fn,
		const int &	istep,
		ModulePW::PW_Basis *	rho_basis,
		const Charge *const	chr,
		const UnitCell *	ucell_,
		const double *	v_effective_fixed,
		const surchem &	solvent
	)

write electric static potential to file

Parameters

bz
nbz
fn
istep
rho_basis
chr
ucell_
v_effective_fixed

Dipole correction

Add hartree potential and local pseudopot

Get the vacuum level of the system

Write down the electrostatic potential

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write_elf()

void ModuleIO::write_elf	(	const int &	bz,
		const int &	nbz,
		const std::string &	out_dir,
		const int &	istep,
		const int &	nspin,
		const double *const *	rho,
		const double *const *	tau,
		ModulePW::PW_Basis *	rho_basis,
		const Parallel_Grid &	pgrid,
		const UnitCell *	ucell_,
		const int &	precision
	)

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write_head()

void ModuleIO::write_head	(	std::ofstream &	ofs_running,
		const int &	istep,
		const int &	iter,
		const std::string &	basisname
	)

write head for scf iteration

Parameters

ofs_running	output stream
istep	the ion step
iter	the scf iteration step
basisname	basis set name

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write_head_td()

void ModuleIO::write_head_td	(	std::ofstream &	ofs_running,
		const int &	istep,
		const int &	estep,
		const int &	iter,
		const std::string &	basisname
	)

write head for scf iteration

Parameters

ofs_running	output stream
istep	the ion step
estep	the electron step
iter	the scf iteration step
basisname	basis set name

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write_Hexxs_csr() [1/2]

template<typename Tdata >

void ModuleIO::write_Hexxs_csr	(	const std::string &	file_name,
		const UnitCell &	ucell,
		const std::map< int, std::map< TAC, RI::Tensor< Tdata > > > &	Hexxs
	)

write Hexxs in CSR format

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write_Hexxs_csr() [2/2]

template<typename Tdata >

void ModuleIO::write_Hexxs_csr	(	const std::string &	file_name,
		const UnitCell &	ucell,
		const std::vector< std::map< int, std::map< TAC, RI::Tensor< Tdata > > > > &	Hexxs
	)

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write_hsk()

template<typename T >

void ModuleIO::write_hsk	(	const std::string &	global_out_dir,
		const int	nspin,
		const int	nks,
		const int	nkstot,
		const std::vector< int > &	ik2iktot,
		const std::vector< int > &	isk,
		hamilt::Hamilt< T > *	p_hamilt,
		const Parallel_Orbitals &	pv,
		const bool	gamma_only,
		const bool	out_app_flag,
		const int	istep,
		std::ofstream &	ofs_running
	)

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write_orb_energy()

void ModuleIO::write_orb_energy ( const K_Vectors &  kv, const int  nspin0, const int  nbands, const std::vector< std::vector< double > > &  e_orb, const std::string &  term, const std::string &  label, const bool  app = false  )

inline

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write_orb_info()

void ModuleIO::write_orb_info

(

const UnitCell *

ucell

)

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write_proj_band_lcao()

template<typename TK >

void ModuleIO::write_proj_band_lcao	(	const psi::Psi< TK > *	psi,
		const Parallel_Orbitals &	pv,
		const elecstate::ElecState *	pelec,
		const K_Vectors &	kv,
		const UnitCell &	ucell,
		hamilt::Hamilt< TK > *	p_ham
	)

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write_rhog()

bool ModuleIO::write_rhog	(	const std::string &	fchg,
		const bool	gamma_only,
		const ModulePW::PW_Basis *	pw_rho,
		const int	nspin,
		const ModuleBase::Matrix3 &	GT,
		std::complex< double > **	rhog,
		const int	ipool,
		const int	irank,
		const int	nrank
	)

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write_vdata_palgrid()

void ModuleIO::write_vdata_palgrid	(	const Parallel_Grid &	pgrid,
		const double *const	data,
		const int	is,
		const int	nspin,
		const int	iter,
		const std::string &	fn,
		const double	ef,
		const UnitCell *const	ucell,
		const int	precision = 11,
		const int	out_fermi = 1,
		const bool	reduce_all_pool = false
	)

write volumetric data on the parallized grid into a .cube file

output header for cube file

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write_Vxc() [1/2]

template<typename TK , typename TR >

void ModuleIO::write_Vxc	(	const int	nspin,
		const int	nbasis,
		const int	drank,
		const Parallel_Orbitals *	pv,
		const psi::Psi< TK > &	psi,
		const UnitCell &	ucell,
		Structure_Factor &	sf,
		surchem &	solvent,
		const ModulePW::PW_Basis &	rho_basis,
		const ModulePW::PW_Basis &	rhod_basis,
		const ModuleBase::matrix &	vloc,
		const Charge &	chg,
		Gint_Gamma &	gint_gamma,
		Gint_k &	gint_k,
		const K_Vectors &	kv,
		const std::vector< double > &	orb_cutoff,
		const ModuleBase::matrix &	wg,
		Grid_Driver &	gd
	)

write the Vxc matrix in KS orbital representation, usefull for GW calculation including terms: local/semi-local XC, EXX, DFTU

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write_Vxc() [2/2]

template<typename FPTYPE >

void ModuleIO::write_Vxc	(	int	nspin,
		int	naos,
		int	drank,
		const psi::Psi< std::complex< FPTYPE > > &	psi_pw,
		const UnitCell &	ucell,
		Structure_Factor &	sf,
		surchem &	solvent,
		const ModulePW::PW_Basis_K &	wfc_basis,
		const ModulePW::PW_Basis &	rho_basis,
		const ModulePW::PW_Basis &	rhod_basis,
		const ModuleBase::matrix &	vloc,
		const Charge &	chg,
		const K_Vectors &	kv,
		const ModuleBase::matrix &	wg
	)

write the Vxc matrix in KS orbital representation, usefull for GW calculation including terms: local/semi-local XC and EXX

wrap psi and act band-by-band (the same result as act all bands at once)

add-up and write

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write_Vxc_R()

template<typename TK , typename TR >

void ModuleIO::write_Vxc_R	(	const int	nspin,
		const Parallel_Orbitals *	pv,
		const UnitCell &	ucell,
		Structure_Factor &	sf,
		surchem &	solvent,
		const ModulePW::PW_Basis &	rho_basis,
		const ModulePW::PW_Basis &	rhod_basis,
		const ModuleBase::matrix &	vloc,
		const Charge &	chg,
		Gint_Gamma &	gint_gamma,
		Gint_k &	gint_k,
		const K_Vectors &	kv,
		const std::vector< double > &	orb_cutoff,
		Grid_Driver &	gd,
		const double	sparse_thr = 1e-10
	)

write the Vxc matrix in KS orbital representation, usefull for GW calculation including terms: local/semi-local XC, EXX, DFTU

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write_wfc_nao()

template<typename T >

void ModuleIO::write_wfc_nao	(	const int	out_type,
		const bool	out_app_flag,
		const psi::Psi< T > &	psi,
		const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg,
		const std::vector< ModuleBase::Vector3< double > > &	kvec_c,
		const std::vector< int > &	ik2iktot,
		const int	nkstot,
		const Parallel_Orbitals &	pv,
		const int	nspin,
		const int	istep = -1
	)

Writes the wavefunction coefficients for the LCAO method to a file. Will loop all k-points by psi.get_nk(). The nbands are determined by ekb.nc. The nlocal is determined by psi.get_nbasis() if not compiled with MPI, otherwise it is determined by pv->desc[2].

Parameters

out_type	The output file type. 1 for text, 2 for binary.
psi	The Psi object containing the wavefunction coefficients.
ekb	The matrix of Kohn-Sham eigenvalues.
wg	The matrix of Kohn-Sham eigenvectors.
kvec_c	The vector of k-points in Cartesian coordinates.
pv	The Parallel_Orbitals object containing additional information.
istep	The current step number. if < 0, the step number is not included in the file name.

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write_wfc_nao< double >()

template void ModuleIO::write_wfc_nao< double >	(	const int	out_type,
		const bool	out_app_flag,
		const psi::Psi< double > &	psi,
		const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg,
		const std::vector< ModuleBase::Vector3< double > > &	kvec_c,
		const std::vector< int > &	ik2iktot,
		const int	nkstot,
		const Parallel_Orbitals &	pv,
		const int	nspin,
		const int	istep
	)

write_wfc_nao< std::complex< double > >()

template void ModuleIO::write_wfc_nao< std::complex< double > >	(	const int	out_type,
		const bool	out_app_flag,
		const psi::Psi< std::complex< double > > &	psi,
		const ModuleBase::matrix &	ekb,
		const ModuleBase::matrix &	wg,
		const std::vector< ModuleBase::Vector3< double > > &	kvec_c,
		const std::vector< int > &	ik2iktot,
		const int	nkstot,
		const Parallel_Orbitals &	pv,
		const int	nspin,
		const int	istep
	)

write_wfc_pw()

void ModuleIO::write_wfc_pw	(	const int	kpar,
		const int	my_pool,
		const int	my_rank,
		const int	nbands,
		const int	nspin,
		const int	npol,
		const int	rank_in_pool,
		const int	nproc_in_pool,
		const int	out_wfc_pw,
		const double &	ecutwfc,
		const std::string &	global_out_dir,
		const psi::Psi< std::complex< double > > &	psi,
		const K_Vectors &	kv,
		const ModulePW::PW_Basis_K *	wfcpw,
		std::ofstream &	ofs_running
	)

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