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dyzheng merged 1 commit into from
Aug 30, 2021
Merged

module cell:replace all GlobalC::ORB by passing variable; replace Glo… #337

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30 changes: 22 additions & 8 deletions source/module_cell/read_atoms.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,11 @@
#endif
#include <cstring> // Peize Lin fix bug about strcmp 2016-08-02

#ifdef __LCAO
void UnitCell_pseudo::read_atom_species(std::ifstream &ifa, std::ofstream &ofs_running, LCAO_Orbitals &orb )
#else
void UnitCell_pseudo::read_atom_species(std::ifstream &ifa, std::ofstream &ofs_running)
#endif
{
ModuleBase::TITLE("UnitCell_pseudo","read_atom_species");

Expand Down Expand Up @@ -53,7 +57,7 @@ void UnitCell_pseudo::read_atom_species(std::ifstream &ifa, std::ofstream &ofs_r
{
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "NUMERICAL_ORBITAL") )
{
GlobalC::ORB.read_in_flag = true;
orb.read_in_flag = true;
for(int i=0; i<ntype; i++)
{
std::string ofile;
Expand All @@ -73,13 +77,13 @@ void UnitCell_pseudo::read_atom_species(std::ifstream &ifa, std::ofstream &ofs_r
//-----------------------------------
//ModuleBase::GlobalFunc::READ_VALUE(ifa, nfile);

GlobalC::ORB.orbital_file.push_back(ofile);
orb.orbital_file.push_back(ofile);

//-----------------------------------
// Turn off the read in NONLOCAL file
// function since 2013-08-02 by mohan
//-----------------------------------
//GlobalC::ORB.nonlocal_file.push_back(nfile);
//orb.nonlocal_file.push_back(nfile);

// GlobalV::ofs_running << " For atom type " << i + 1 << std::endl;
// GlobalV::ofs_running << " Read in numerical orbitals from file " << ofile << std::endl;
Expand All @@ -89,11 +93,12 @@ void UnitCell_pseudo::read_atom_species(std::ifstream &ifa, std::ofstream &ofs_r
}
// caoyu add 2021-03-16
if (ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "NUMERICAL_DESCRIPTOR")) {
ifa >> GlobalC::ORB.descriptor_file;
ifa >> orb.descriptor_file;
}
}

// Peize Lin add 2016-09-23
#ifndef __CELL
if( Exx_Global::Hybrid_Type::HF == GlobalC::exx_lcao.info.hybrid_type ||
Exx_Global::Hybrid_Type::PBE0 == GlobalC::exx_lcao.info.hybrid_type ||
Exx_Global::Hybrid_Type::HSE == GlobalC::exx_lcao.info.hybrid_type )
Expand All @@ -108,6 +113,7 @@ void UnitCell_pseudo::read_atom_species(std::ifstream &ifa, std::ofstream &ofs_r
}
}
}
#endif
#endif
//==========================
// read in lattice constant
Expand Down Expand Up @@ -338,7 +344,11 @@ void UnitCell_pseudo::read_atom_species(std::ifstream &ifa, std::ofstream &ofs_r
// Read atomic positions
// return 1: no problem.
// return 0: some problems.
#ifdef __LCAO
bool UnitCell_pseudo::read_atom_positions(std::ifstream &ifpos, std::ofstream &ofs_running, std::ofstream &ofs_warning, LCAO_Orbitals &orb)
#else
bool UnitCell_pseudo::read_atom_positions(std::ifstream &ifpos, std::ofstream &ofs_running, std::ofstream &ofs_warning)
#endif
{
ModuleBase::TITLE("UnitCell_pseudo","read_atom_positions");

Expand Down Expand Up @@ -452,13 +462,13 @@ bool UnitCell_pseudo::read_atom_positions(std::ifstream &ifpos, std::ofstream &o
#ifdef __LCAO
if (GlobalV::BASIS_TYPE == "lcao" || GlobalV::BASIS_TYPE == "lcao_in_pw")
{
std::ifstream ifs(GlobalC::ORB.orbital_file[it].c_str(), ios::in); // pengfei 2014-10-13
std::ifstream ifs(orb.orbital_file[it].c_str(), ios::in); // pengfei 2014-10-13

// mohan add return 2021-04-26
if (!ifs)
{
std::cout << " Element index " << it+1 << std::endl;
std::cout << " orbital file: " << GlobalC::ORB.orbital_file[it] << std::endl;
std::cout << " orbital file: " << orb.orbital_file[it] << std::endl;
ModuleBase::WARNING("read_atom_positions","ABACUS Cannot find the ORBITAL file (basis sets)");
return 0; // means something wrong
}
Expand Down Expand Up @@ -820,7 +830,11 @@ bool UnitCell_pseudo::check_tau(void)const
return 1;
}

#ifdef __LCAO
void UnitCell_pseudo::print_stru_file(const std::string &fn, const LCAO_Orbitals &orb, const int &type)const
#else
void UnitCell_pseudo::print_stru_file(const std::string &fn, const int &type)const
#endif
{
ModuleBase::TITLE("UnitCell_pseudo","print_stru_file");

Expand All @@ -847,9 +861,9 @@ void UnitCell_pseudo::print_stru_file(const std::string &fn, const int &type)con
// Turn off the read in NONLOCAL file
// function since 2013-08-02 by mohan
//-----------------------------------
// ofs << GlobalC::ORB.orbital_file[it] << " " << GlobalC::ORB.nonlocal_file[it] << " #local_orbital; non-local projector" << std::endl;
// ofs << orb.orbital_file[it] << " " << orb.nonlocal_file[it] << " #local_orbital; non-local projector" << std::endl;
//modified by zhengdy 2015-07-24
ofs << GlobalC::ORB.orbital_file[it] << std::endl;
ofs << orb.orbital_file[it] << std::endl;
}
}
#endif
Expand Down
126 changes: 74 additions & 52 deletions source/module_cell/unitcell_pseudo.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,9 @@ UnitCell_pseudo::~UnitCell_pseudo()
//Calculate various lattice related quantities for given latvec
//==============================================================
void UnitCell_pseudo::setup_cell(
#ifdef __LCAO
LCAO_Orbitals &orb,
#endif
const std::string &s_pseudopot_dir,
output &outp,
const std::string &fn,
Expand Down Expand Up @@ -62,32 +65,40 @@ void UnitCell_pseudo::setup_cell(
if(ok)
{

GlobalV::ofs_running << "\n\n\n\n";
GlobalV::ofs_running << " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" << std::endl;
GlobalV::ofs_running << " | |" << std::endl;
GlobalV::ofs_running << " | Reading atom information in unitcell: |" << std::endl;
GlobalV::ofs_running << " | From the input file and the structure file we know the number of |" << std::endl;
GlobalV::ofs_running << " | different elments in this unitcell, then we list the detail |" << std::endl;
GlobalV::ofs_running << " | information for each element, especially the zeta and polar atomic |" << std::endl;
GlobalV::ofs_running << " | orbital number for each element. The total atom number is counted. |" << std::endl;
GlobalV::ofs_running << " | We calculate the nearest atom distance for each atom and show the |" << std::endl;
GlobalV::ofs_running << " | Cartesian and Direct coordinates for each atom. We list the file |" << std::endl;
GlobalV::ofs_running << " | address for atomic orbitals. The volume and the lattice vectors |" << std::endl;
GlobalV::ofs_running << " | in real and reciprocal space is also shown. |" << std::endl;
GlobalV::ofs_running << " | |" << std::endl;
GlobalV::ofs_running << " <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<" << std::endl;
GlobalV::ofs_running << "\n\n\n\n";

GlobalV::ofs_running << " READING UNITCELL INFORMATION" << std::endl;
log << "\n\n\n\n";
log << " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" << std::endl;
log << " | |" << std::endl;
log << " | Reading atom information in unitcell: |" << std::endl;
log << " | From the input file and the structure file we know the number of |" << std::endl;
log << " | different elments in this unitcell, then we list the detail |" << std::endl;
log << " | information for each element, especially the zeta and polar atomic |" << std::endl;
log << " | orbital number for each element. The total atom number is counted. |" << std::endl;
log << " | We calculate the nearest atom distance for each atom and show the |" << std::endl;
log << " | Cartesian and Direct coordinates for each atom. We list the file |" << std::endl;
log << " | address for atomic orbitals. The volume and the lattice vectors |" << std::endl;
log << " | in real and reciprocal space is also shown. |" << std::endl;
log << " | |" << std::endl;
log << " <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<" << std::endl;
log << "\n\n\n\n";

log << " READING UNITCELL INFORMATION" << std::endl;
//========================
// call read_atom_species
//========================
this->read_atom_species(ifa, GlobalV::ofs_running);
#ifdef __LCAO
this->read_atom_species(ifa, log, orb);
#else
this->read_atom_species(ifa, log);
#endif

//==========================
// call read_atom_positions
//==========================
ok2 = this->read_atom_positions(ifa, GlobalV::ofs_running, GlobalV::ofs_warning);
#ifdef __LCAO
ok2 = this->read_atom_positions(ifa, log, GlobalV::ofs_warning, orb);
#else
ok2 = this->read_atom_positions(ifa, log, GlobalV::ofs_warning);
#endif

if(ok2)
{
Expand Down Expand Up @@ -121,7 +132,7 @@ void UnitCell_pseudo::setup_cell(

// mohan add 2010-09-29
#ifdef __LCAO
GlobalC::ORB.bcast_files(ntype, GlobalV::MY_RANK);
orb.bcast_files(ntype, GlobalV::MY_RANK);
#endif
#endif

Expand All @@ -138,9 +149,9 @@ void UnitCell_pseudo::setup_cell(
}
else
{
GlobalV::ofs_running << std::endl;
ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running,"Volume (Bohr^3)", this->omega);
ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running,"Volume (A^3)", this->omega * pow(ModuleBase::BOHR_TO_A, 3));
log << std::endl;
ModuleBase::GlobalFunc::OUT(log,"Volume (Bohr^3)", this->omega);
ModuleBase::GlobalFunc::OUT(log,"Volume (A^3)", this->omega * pow(ModuleBase::BOHR_TO_A, 3));
}

//==========================================================
Expand All @@ -158,31 +169,31 @@ void UnitCell_pseudo::setup_cell(
this->GGT0 = G * GT;
this->invGGT0 = GGT.Inverse();

GlobalV::ofs_running << std::endl;
outp.printM3(GlobalV::ofs_running,"Lattice vectors: (Cartesian coordinate: in unit of a_0)",latvec);
outp.printM3(GlobalV::ofs_running,"Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0)",G);
// OUT(GlobalV::ofs_running,"lattice center x",latcenter.x);
// OUT(GlobalV::ofs_running,"lattice center y",latcenter.y);
// OUT(GlobalV::ofs_running,"lattice center z",latcenter.z);
log << std::endl;
outp.printM3(log,"Lattice vectors: (Cartesian coordinate: in unit of a_0)",latvec);
outp.printM3(log,"Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0)",G);
// OUT(log,"lattice center x",latcenter.x);
// OUT(log,"lattice center y",latcenter.y);
// OUT(log,"lattice center z",latcenter.z);

// read in non-local pseudopotential and ouput the projectors.

GlobalV::ofs_running << "\n\n\n\n";
GlobalV::ofs_running << " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" << std::endl;
GlobalV::ofs_running << " | |" << std::endl;
GlobalV::ofs_running << " | Reading pseudopotentials files: |" << std::endl;
GlobalV::ofs_running << " | The pseudopotential file is in UPF format. The 'NC' indicates that |" << std::endl;
GlobalV::ofs_running << " | the type of pseudopotential is 'norm conserving'. Functional of |" << std::endl;
GlobalV::ofs_running << " | exchange and correlation is decided by 4 given parameters in UPF |" << std::endl;
GlobalV::ofs_running << " | file. We also read in the 'core correction' if there exists. |" << std::endl;
GlobalV::ofs_running << " | Also we can read the valence electrons number and the maximal |" << std::endl;
GlobalV::ofs_running << " | angular momentum used in this pseudopotential. We also read in the |" << std::endl;
GlobalV::ofs_running << " | trail wave function, trail atomic density and local-pseudopotential|" << std::endl;
GlobalV::ofs_running << " | on logrithmic grid. The non-local pseudopotential projector is also|" << std::endl;
GlobalV::ofs_running << " | read in if there is any. |" << std::endl;
GlobalV::ofs_running << " | |" << std::endl;
GlobalV::ofs_running << " <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<" << std::endl;
GlobalV::ofs_running << "\n\n\n\n";
log << "\n\n\n\n";
log << " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" << std::endl;
log << " | |" << std::endl;
log << " | Reading pseudopotentials files: |" << std::endl;
log << " | The pseudopotential file is in UPF format. The 'NC' indicates that |" << std::endl;
log << " | the type of pseudopotential is 'norm conserving'. Functional of |" << std::endl;
log << " | exchange and correlation is decided by 4 given parameters in UPF |" << std::endl;
log << " | file. We also read in the 'core correction' if there exists. |" << std::endl;
log << " | Also we can read the valence electrons number and the maximal |" << std::endl;
log << " | angular momentum used in this pseudopotential. We also read in the |" << std::endl;
log << " | trail wave function, trail atomic density and local-pseudopotential|" << std::endl;
log << " | on logrithmic grid. The non-local pseudopotential projector is also|" << std::endl;
log << " | read in if there is any. |" << std::endl;
log << " | |" << std::endl;
log << " <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<" << std::endl;
log << "\n\n\n\n";


this->read_cell_pseudopots(s_pseudopot_dir);
Expand Down Expand Up @@ -306,6 +317,9 @@ void UnitCell_pseudo::setup_cell(
}

void UnitCell_pseudo::setup_cell_classic(
#ifdef __LCAO
LCAO_Orbitals &orb,
#endif
const std::string &fn,
std::ofstream &ofs_running,
std::ofstream &ofs_warning)
Expand Down Expand Up @@ -352,11 +366,19 @@ void UnitCell_pseudo::setup_cell_classic(
//========================
// call read_atom_species
//========================
#ifdef __LCAO
this->read_atom_species(ifa, ofs_running, orb);
#else
this->read_atom_species(ifa, ofs_running);
#endif
//==========================
// call read_atom_positions
//==========================
#ifdef __LCAO
ok2 = this->read_atom_positions(ifa, ofs_running, ofs_warning, orb);
#else
ok2 = this->read_atom_positions(ifa, ofs_running, ofs_warning);
#endif
if(ok2)
{
for(int i=0;i<this->ntype;i++)
Expand Down Expand Up @@ -658,9 +680,9 @@ void UnitCell_pseudo::setup_cell_after_vc(
}
else
{
GlobalV::ofs_running << std::endl;
ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running, "Volume (Bohr^3)", this->omega);
ModuleBase::GlobalFunc::OUT(GlobalV::ofs_running, "Volume (A^3))", this->omega * pow(ModuleBase::BOHR_TO_A, 3));
log << std::endl;
ModuleBase::GlobalFunc::OUT(log, "Volume (Bohr^3)", this->omega);
ModuleBase::GlobalFunc::OUT(log, "Volume (A^3))", this->omega * pow(ModuleBase::BOHR_TO_A, 3));
}

//==========================================================
Expand Down Expand Up @@ -698,9 +720,9 @@ Parallel_Common::bcast_double( atom->taud[ia].z );
}
#endif

GlobalV::ofs_running << std::endl;
outp.printM3(GlobalV::ofs_running,"Lattice vectors: (Cartesian coordinate: in unit of a_0)",latvec);
outp.printM3(GlobalV::ofs_running,"Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0)",G);
log << std::endl;
outp.printM3(log,"Lattice vectors: (Cartesian coordinate: in unit of a_0)",latvec);
outp.printM3(log,"Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0)",G);

return;
}
Expand Down Expand Up @@ -728,4 +750,4 @@ bool UnitCell_pseudo::if_cell_can_change()const
return 1;
}
return 0;
}
}
16 changes: 16 additions & 0 deletions source/module_cell/unitcell_pseudo.h
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
#include "../src_pw/tools.h"
#include "../src_io/output.h"
#include "unitcell.h"
#include "../module_orbital/ORB_read.h"

class UnitCell_pseudo : public UnitCell
{
Expand Down Expand Up @@ -32,19 +33,34 @@ class UnitCell_pseudo : public UnitCell
UnitCell_pseudo();
~UnitCell_pseudo();
void setup_cell(
#ifdef __LCAO
LCAO_Orbitals &orb,
#endif
const std::string &s_pseudopot_dir,
output &outp,
const std::string &fn,
std::ofstream &log);
void setup_cell_classic(
#ifdef __LCAO
LCAO_Orbitals &orb,
#endif
const std::string &fn,
std::ofstream &ofs_running,
std::ofstream &ofs_warning); // liuyu 2021-07-13, RX changed ofs_running and ofs_warning from globalV to inputs. 2021-07-24
#ifdef __LCAO
void read_atom_species(std::ifstream &ifa, std::ofstream &ofs_running, LCAO_Orbitals &orb);
bool read_atom_positions(std::ifstream &ifpos, std::ofstream &ofs_running, std::ofstream &ofs_warning, LCAO_Orbitals &orb); // read in atomic positions
#else
void read_atom_species(std::ifstream &ifa, std::ofstream &ofs_running); // read in the atom information for each type of atom
bool read_atom_positions(std::ifstream &ifpos, std::ofstream &ofs_running, std::ofstream &ofs_warning); // read in atomic positions
#endif
int find_type(const std::string &label);
void print_tau(void)const;
#ifdef __LCAO
void print_stru_file(const std::string &fn, const LCAO_Orbitals &orb, const int &type=1)const; // mohan add 2011-03-22
#else
void print_stru_file(const std::string &fn, const int &type=1)const; // mohan add 2011-03-22
#endif
void check_dtau(void);
void setup_cell_after_vc(const std::string &s_pseudopot_dir, output &outp, const std::string &fn, std::ofstream &log); //LiuXh add 20180515

Expand Down
4 changes: 4 additions & 0 deletions source/module_md/MD_func.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -285,7 +285,11 @@ void MD_func::printpos(const std::string& file, const int& iter, const int& reco
ss << GlobalV::global_out_dir << "STRU_MD";

//zhengdy modify 2015-05-06, outputfile "STRU_Restart"
#ifdef __LCAO
unit_in.print_stru_file(ss.str(),GlobalC::ORB,2);
#else
unit_in.print_stru_file(ss.str(),2);
#endif

return;
}
Expand Down
6 changes: 5 additions & 1 deletion source/module_md/run_md_classic.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,11 @@ void Run_MD_CLASSIC::classic_md_line(void)
ModuleBase::timer::tick("Run_MD_CLASSIC", "classic_md_line");

// Setup the unitcell.
#ifdef __LCAO
ucell_c.setup_cell_classic(GlobalC::ORB, GlobalV::global_atom_card, GlobalV::ofs_running, GlobalV::ofs_warning);
#else
ucell_c.setup_cell_classic(GlobalV::global_atom_card, GlobalV::ofs_running, GlobalV::ofs_warning);
#endif
ModuleBase::GlobalFunc::DONE(GlobalV::ofs_running, "SETUP UNITCELL");

this->md_allocate_ions();
Expand Down Expand Up @@ -192,4 +196,4 @@ void Run_MD_CLASSIC::update_pos_classic(void)
}
this->ucell_c.save_cartesian_position(this->pos_now);
return;
}
}
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