#include <cstring> // Peize Lin fix bug about strcmp 2016-08-02

#include <cassert>

#include <regex>

#include <fstream>

#include "unitcell.h"

#include "read_atoms_helper.h"

#include "source_io/module_parameter/parameter.h"

#include "print_cell.h"

#include "read_stru.h"

#include "source_estate/read_orb.h"

#include "source_base/timer.h"

#include "source_base/constants.h"

#include "source_base/formatter.h"

#include "source_base/mathzone.h"

#ifdef __LCAO

#include "source_basis/module_ao/ORB_read.h" // to use 'ORB' -- mohan 2021-01-30

#endif

bool unitcell::read_atom_positions(UnitCell& ucell,

std::ifstream &ifpos,

std::ofstream &ofs_running,

std::ofstream &ofs_warning)

{

ModuleBase::TITLE("UnitCell","read_atom_positions");

std::string& Coordinate = ucell.Coordinate;

const int ntype = ucell.ntype;

const int nspin = PARAM.inp.nspin;

assert (nspin==1 || nspin==2 || nspin==4);

if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifpos, "ATOMIC_POSITIONS"))

{

ModuleBase::GlobalFunc::READ_VALUE(ifpos, Coordinate);

if (!unitcell::validate_coordinate_system(Coordinate, ofs_warning))

{

return false;

}

ucell.nat = 0;

//======================================

// calculate total number of ucell.atoms

// and adjust the order of atom species

//======================================

for (int it = 0;it < ntype; it++)

{

ofs_running << "\n READING ATOM TYPE " << it+1 << std::endl;

bool set_element_mag_zero = false;

if (!unitcell::read_atom_type_header(it, ucell, ifpos, ofs_running,

ofs_warning, set_element_mag_zero))

{

return false;

}

int na = ucell.atoms[it].na;

ucell.nat += na;

if (na > 0)

{

unitcell::allocate_atom_properties(ucell.atoms[it], na, ucell.atom_mass[it]);

for (int ia = 0;ia < na; ia++)

{

// modify the reading of frozen ions and velocities -- Yuanbo Li 2021/8/20

ModuleBase::Vector3<double> v;

ModuleBase::Vector3<int> mv;

ifpos >> v.x >> v.y >> v.z;

mv.x = true ;

mv.y = true ;

mv.z = true ;

ucell.atoms[it].vel[ia].set(0,0,0);

ucell.atoms[it].mag[ia]=ucell.magnet.start_mag[it];

//if this line is used, default startmag_type would be 2

ucell.atoms[it].angle1[ia]=0;

ucell.atoms[it].angle2[ia]=0;

ucell.atoms[it].m_loc_[ia].set(0,0,0);

ucell.atoms[it].lambda[ia].set(0,0,0);

ucell.atoms[it].constrain[ia].set(0,0,0);

bool input_vec_mag=false;

bool input_angle_mag=false;

// Parse optional properties

if (!unitcell::parse_atom_properties(ifpos, ucell.atoms[it], ia, mv,

input_vec_mag, input_angle_mag,

set_element_mag_zero))

{

return false;

}

// Process magnetization

unitcell::process_magnetization(ucell.atoms[it], it, ia, nspin,

input_vec_mag, input_angle_mag, ofs_running);

// Transform coordinates

unitcell::transform_atom_coordinates(ucell.atoms[it], ia, Coordinate,

v, ucell.latvec, ucell.lat0, ucell.latcenter);

// Set movement flags

unitcell::set_atom_movement_flags(ucell.atoms[it], ia, mv);

ucell.atoms[it].dis[ia].set(0, 0, 0);

}//endj

} // end na

// reset some useless parameters

if (set_element_mag_zero)

{

ucell.magnet.start_mag[it] = 0.0;

}

} // end for ntype

// Auto-set magnetization if needed

unitcell::autoset_magnetization(ucell, nspin, ofs_running);

} // end scan_begin

// Final validation and output

return unitcell::finalize_atom_positions(ucell, ofs_running, ofs_warning);

}//end read_atom_positions