prepare_unitcell.h

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#ifndef PREPARE_UNITCELL_H
#define PREPARE_UNITCELL_H
#include<map>
#include<string>
 
class UcellTestPrepare
{
public:
    UcellTestPrepare()=default;
    UcellTestPrepare(std::string latname_in,
        int lmaxmax_in,
        bool init_vel_in,
        bool selective_dynamics_in,
        bool relax_new_in,
        std::string fixed_axes_in,
        double lat0_in,
        std::valarray<double> latvec_in,
        std::vector<std::string> elements_in,
        std::vector<std::string> pp_files_in,
        std::vector<std::string> pp_types_in,
        std::vector<std::string> orb_files_in,
        std::valarray<int> natom_in,
        std::vector<double> atomic_mass_in,
        std::string coor_type_in,
        std::valarray<double> coordinates_in);
    UcellTestPrepare(std::string latname_in,
        int lmaxmax_in,
        bool init_vel_in,
        bool selective_dynamics_in,
        bool relax_new_in,
        std::string fixed_axes_in,
        double lat0_in,
        std::valarray<double> latvec_in,
        std::vector<std::string> elements_in,
        std::vector<std::string> pp_files_in,
        std::vector<std::string> pp_types_in,
        std::vector<std::string> orb_files_in,
        std::valarray<int> natom_in,
        std::vector<double> atomic_mass_in,
        std::string coor_type_in,
        std::valarray<double> coordinates_in,
        std::valarray<double> mbl_in,
        std::valarray<double> velocity_in);
    UcellTestPrepare(const UcellTestPrepare &utp);
 
    std::string latname;
    int lmaxmax;
    bool init_vel;
    bool selective_dynamics;
    bool relax_new;
    std::string fixed_axes;
    double lat0;
    std::valarray<double> latvec;
    std::vector<std::string> elements;
    std::vector<std::string> pp_files;
    std::vector<std::string> pp_types;
    std::vector<std::string> orb_files;
    std::valarray<int> natom;
    std::vector<double> atomic_mass;
    std::string coor_type;
    std::valarray<double> coordinates;
    std::valarray<double> mbl;
    std::valarray<double> velocity;
    // ntype
    int ntype;
    int atomic_index;
 
    std::unique_ptr<UnitCell> SetUcellInfo()
    {
        //basic info
        this->ntype = this->elements.size();
        std::unique_ptr<UnitCell> ucell(new UnitCell);
        ucell->setup(this->latname,
                this->ntype,
                this->lmaxmax,
                this->init_vel,
                this->fixed_axes);
        
        delete[] ucell->magnet.start_mag; //mag set here
        ucell->atom_label.resize(ucell->ntype);
        ucell->atom_mass.resize(ucell->ntype);
        ucell->pseudo_fn.resize(ucell->ntype);
        ucell->pseudo_type.resize(ucell->ntype);
        ucell->orbital_fn.resize(ucell->ntype);
        ucell->magnet.start_mag = new double[ucell->ntype]; //mag set here
        ucell->magnet.ux_[0] = 0.0; // ux_ set here
        ucell->magnet.ux_[1] = 0.0;
        ucell->magnet.ux_[2] = 0.0;
        for(int it=0;it<ucell->ntype;++it)
        {
            ucell->atom_label[it] = this->elements[it];
            ucell->atom_mass[it] = this->atomic_mass[it];
            ucell->pseudo_fn[it] = this->pp_files[it];
            ucell->pseudo_type[it] = this->pp_types[it];
            ucell->orbital_fn[it] = this->orb_files[it];
            ucell->magnet.start_mag[it] = 0.0; //mag set here
        }
        //lattice info
        ucell->lat0 = this->lat0;
        ucell->lat0_angstrom = ucell->lat0 * 0.529177;
        ucell->tpiba = ModuleBase::TWO_PI/ucell->lat0;
        ucell->tpiba2 = ucell->tpiba * ucell->tpiba;
        ucell->latvec.e11 = this->latvec[0];
        ucell->latvec.e12 = this->latvec[1];
        ucell->latvec.e13 = this->latvec[2];
        ucell->latvec.e21 = this->latvec[3];
        ucell->latvec.e22 = this->latvec[4];
        ucell->latvec.e23 = this->latvec[5];
        ucell->latvec.e31 = this->latvec[6];
        ucell->latvec.e32 = this->latvec[7];
        ucell->latvec.e33 = this->latvec[8];
        ucell->a1.x = ucell->latvec.e11;
        ucell->a1.y = ucell->latvec.e12;
        ucell->a1.z = ucell->latvec.e13;
        ucell->a2.x = ucell->latvec.e21;
        ucell->a2.y = ucell->latvec.e22;
        ucell->a2.z = ucell->latvec.e23;
        ucell->a3.x = ucell->latvec.e31;
        ucell->a3.y = ucell->latvec.e32;
        ucell->a3.z = ucell->latvec.e33;
        ucell->GT = ucell->latvec.Inverse();
        ucell->G = ucell->GT.Transpose();
        ucell->GGT = ucell->G*ucell->GT;
        ucell->invGGT = ucell->GGT.Inverse();
        ucell->omega = std::abs(ucell->latvec.Det())*(ucell->lat0)*(ucell->lat0)*(ucell->lat0);
        //atomic info
        ucell->Coordinate = this->coor_type;
        ucell->atoms = new Atom[ucell->ntype];
        ucell->set_atom_flag = true;
        this->atomic_index = 0;
        for(int it=0;it<ucell->ntype;++it)
        {
            ucell->atoms[it].label = this->elements[it];
            ucell->atoms[it].nw = 0;
            ucell->atoms[it].nwl = 2;
            ucell->atoms[it].l_nchi.resize(ucell->atoms[it].nwl+1);
            for(int L=0; L<ucell->atoms[it].nwl+1; L++)
            {
                ucell->atoms[it].l_nchi[L] = 1;
                ucell->atoms[it].nw += (2*L + 1) * ucell->atoms[it].l_nchi[L];
            }
            ucell->atoms[it].na = this->natom[it];
            //coordinates and related physical quantities
            ucell->atoms[it].tau.resize(ucell->atoms[it].na);
            ucell->atoms[it].dis.resize(ucell->atoms[it].na);
            ucell->atoms[it].taud.resize(ucell->atoms[it].na);
            ucell->atoms[it].vel.resize(ucell->atoms[it].na);
            ucell->atoms[it].mag.resize(ucell->atoms[it].na);
            ucell->atoms[it].angle1.resize(ucell->atoms[it].na);
            ucell->atoms[it].angle2.resize(ucell->atoms[it].na);
            ucell->atoms[it].m_loc_.resize(ucell->atoms[it].na);
            ucell->atoms[it].mbl.resize(ucell->atoms[it].na);
            ucell->atoms[it].lambda.resize(ucell->atoms[it].na);
            ucell->atoms[it].constrain.resize(ucell->atoms[it].na);
            ucell->atoms[it].mass = ucell->atom_mass[it]; // mass set here
            for(int ia=0; ia<ucell->atoms[it].na; ++ia)
            {
                if (ucell->Coordinate == "Direct")
                {
                    ucell->atoms[it].taud[ia].x = this->coordinates[this->atomic_index*3+0];
                    ucell->atoms[it].taud[ia].y = this->coordinates[this->atomic_index*3+1];
                    ucell->atoms[it].taud[ia].z = this->coordinates[this->atomic_index*3+2];
                    ucell->atoms[it].tau[ia] = ucell->atoms[it].taud[ia]*ucell->latvec;
                }
                else if (ucell->Coordinate == "Cartesian")
                {
                    ucell->atoms[it].tau[ia].x = this->coordinates[this->atomic_index*3+0];
                    ucell->atoms[it].tau[ia].y = this->coordinates[this->atomic_index*3+1];
                    ucell->atoms[it].tau[ia].z = this->coordinates[this->atomic_index*3+2];
                    ModuleBase::Mathzone::Cartesian_to_Direct(
                        ucell->atoms[it].tau[ia].x, ucell->atoms[it].tau[ia].y, ucell->atoms[it].tau[ia].z,
                        ucell->latvec.e11, ucell->latvec.e12, ucell->latvec.e13,
                        ucell->latvec.e21, ucell->latvec.e22, ucell->latvec.e23,
                        ucell->latvec.e31, ucell->latvec.e32, ucell->latvec.e33,
                        ucell->atoms[it].taud[ia].x, ucell->atoms[it].taud[ia].y, ucell->atoms[it].taud[ia].z);
                }
                ucell->atoms[it].dis[ia].set(0, 0, 0);
                if(this->init_vel)
                {
                    ucell->atoms[it].vel[ia].x = this->velocity[this->atomic_index*3+0];
                    ucell->atoms[it].vel[ia].y = this->velocity[this->atomic_index*3+1];
                    ucell->atoms[it].vel[ia].z = this->velocity[this->atomic_index*3+2];
                }
                else
                {
                    ucell->atoms[it].vel[ia].set(0,0,0);
                }
                ucell->atoms[it].m_loc_[ia].set(0,0,0);
                ucell->atoms[it].angle1[ia] = 0;
                ucell->atoms[it].angle2[ia] = 0;
                if(this->selective_dynamics)
                {
                    ucell->atoms[it].mbl[ia].x = this->mbl[this->atomic_index*3+0];
                    ucell->atoms[it].mbl[ia].y = this->mbl[this->atomic_index*3+1];
                    ucell->atoms[it].mbl[ia].z = this->mbl[this->atomic_index*3+2];
                }
                else
                {
                    ucell->atoms[it].mbl[ia] = {1,1,1};
                }
                ++(this->atomic_index);
            }
        }
        ucell->nat = this->natom.sum();
        return ucell;
    }
};
 
UcellTestPrepare::UcellTestPrepare(std::string latname_in,
        int lmaxmax_in,
        bool init_vel_in,
        bool selective_dynamics_in,
        bool relax_new_in,
        std::string fixed_axes_in,
        double lat0_in,
        std::valarray<double> latvec_in,
        std::vector<std::string> elements_in,
        std::vector<std::string> pp_files_in,
        std::vector<std::string> pp_types_in,
        std::vector<std::string> orb_files_in,
        std::valarray<int> natom_in,
        std::vector<double> atomic_mass_in,
        std::string coor_type_in,
        std::valarray<double> coordinates_in):
    latname(latname_in),
    lmaxmax(lmaxmax_in),
    init_vel(init_vel_in),
    selective_dynamics(selective_dynamics_in),
    relax_new(relax_new_in),
    fixed_axes(fixed_axes_in),
    lat0(lat0_in),
    latvec(latvec_in),
    elements(elements_in),
    pp_files(pp_files_in),
    pp_types(pp_types_in),
    orb_files(orb_files_in),
    natom(natom_in),
    atomic_mass(atomic_mass_in),
    coor_type(coor_type_in),
    coordinates(coordinates_in)
{
    mbl = std::valarray<double>(0.0, coordinates_in.size());
    velocity = std::valarray<double>(0.0, coordinates_in.size());
}
 
UcellTestPrepare::UcellTestPrepare(std::string latname_in,
        int lmaxmax_in,
        bool init_vel_in,
        bool selective_dynamics_in,
        bool relax_new_in,
        std::string fixed_axes_in,
        double lat0_in,
        std::valarray<double> latvec_in,
        std::vector<std::string> elements_in,
        std::vector<std::string> pp_files_in,
        std::vector<std::string> pp_types_in,
        std::vector<std::string> orb_files_in,
        std::valarray<int> natom_in,
        std::vector<double> atomic_mass_in,
        std::string coor_type_in,
        std::valarray<double> coordinates_in,
        std::valarray<double> mbl_in,
        std::valarray<double> velocity_in):
    latname(latname_in),
    lmaxmax(lmaxmax_in),
    init_vel(init_vel_in),
    selective_dynamics(selective_dynamics_in),
    relax_new(relax_new_in),
    fixed_axes(fixed_axes_in),
    lat0(lat0_in),
    latvec(latvec_in),
    elements(elements_in),
    pp_files(pp_files_in),
    pp_types(pp_types_in),
    orb_files(orb_files_in),
    natom(natom_in),
    atomic_mass(atomic_mass_in),
    coor_type(coor_type_in),
    coordinates(coordinates_in),
    mbl(mbl_in),
    velocity(velocity_in) // velocity assume the existence of mbl in print_stru_file()
{}
 
UcellTestPrepare::UcellTestPrepare(const UcellTestPrepare &utp):
    latname(utp.latname),
    lmaxmax(utp.lmaxmax),
    init_vel(utp.init_vel),
    selective_dynamics(utp.selective_dynamics),
    relax_new(utp.relax_new),
    fixed_axes(utp.fixed_axes),
    lat0(utp.lat0),
    latvec(utp.latvec),
    elements(utp.elements),
    pp_files(utp.pp_files),
    pp_types(utp.pp_types),
    orb_files(utp.orb_files),
    natom(utp.natom),
    atomic_mass(utp.atomic_mass),
    coor_type(utp.coor_type),
    coordinates(utp.coordinates),
    mbl(utp.mbl),
    velocity(utp.velocity) // velocity assume the existence of mbl in print_stru_file()
{}
 
std::map<std::string,UcellTestPrepare> UcellTestLib
{
    {"C1H2-Index", UcellTestPrepare(
                "bcc",      //latname
                2,      //lmaxmax
                true,       //init_vel
                true,       //selective_dyanmics
                true,       //relax_new
                "volume",   //fixed_axes
                1.8897261254578281, //lat0
                {10.0,0.0,0.0,  //latvec
                 0.0,10.0,0.0,
                 0.0,0.0,10.0},
                {"C","H"},  //elements
                {"C.upf","H.upf"},  //upf file
                {"upf201","upf201"},    //upf types
                {"C.orb","H.orb"},  //orb file
                {1,2},      //number of each elements
                {12.0,1.0}, //atomic mass
                "Direct",   //coordination type
                {0.1,0.1,0.1,   //atomic coordinates
                 0.15,0.15,0.15,
                 0.05,0.05,0.05},
                {1,1,1, //if atom can move: mbl
                 0,0,0,
                 0,0,1},
                {0.1,0.1,0.1,   //velocity: vel
                 0.1,0.1,0.1,
                 0.1,0.1,0.1})},
    {"C1H2-Cartesian", UcellTestPrepare(
                "bcc",      //latname
                2,      //lmaxmax
                true,       //init_vel
                true,       //selective_dyanmics
                true,       //relax_new
                "volume",   //fixed_axes
                1.8897261254578281, //lat0
                {10.0,0.0,0.0,  //latvec
                 0.0,10.0,0.0,
                 0.0,0.0,10.0},
                {"C","H"},  //elements
                {"C.upf","H.upf"},  //upf file
                {"upf201","upf201"},    //upf types
                {"C.orb","H.orb"},  //orb file
                {1,2},      //number of each elements
                {12.0,1.0}, //atomic mass
                "Cartesian",    //coordination type
                {1,1,1, //atomic coordinates
                 1.5,1.5,1.5,
                 0.5,0.5,0.5})},
    {"C1H2-CheckDTau", UcellTestPrepare(
                "bcc",      //latname
                2,      //lmaxmax
                false,      //init_vel
                false,      //selective_dyanmics
                true,       //relax_new
                "volume",   //fixed_axes
                1.8897261254578281, //lat0
                {0.1,0.1,0.1,   //latvec
                 0.15,0.15,0.15,
                 0.05,0.05,0.05},
                {"C","H"},  //elements
                {"C.upf","H.upf"},  //upf file
                {"upf201","upf201"},    //upf types
                {"C.orb","H.orb"},  //orb file
                {1,2},      //number of each elements
                {12.0,1.0}, //atomic mass
                "Direct",   //coordination type
                {1.6,2.5,3.8,   //atomic coordinates
                 -0.15,1.0,-0.15,
                 -3.05,-2.8,0.0})},
    {"C1H2-CheckTau", UcellTestPrepare(
                "bcc",      //latname
                2,      //lmaxmax
                false,      //init_vel
                false,      //selective_dyanmics
                true,       //relax_new
                "volume",   //fixed_axes
                1.8897261254578281, //lat0
                {0.1,0.1,0.1,   //latvec
                 0.15,0.15,0.15,
                 0.05,0.05,0.05},
                {"C","H"},  //elements
                {"C.upf","H.upf"},  //upf file
                {"upf201","upf201"},    //upf types
                {"C.orb","H.orb"},  //orb file
                {1,2},      //number of each elements
                {12.0,1.0}, //atomic mass
                "Direct",   //coordination type
                {0.0,0.0,0.0,   //atomic coordinates
                 0.00001,0.00001,0.00001,
                 -3.05,-2.8,0.0})},
    {"C1H2-SD", UcellTestPrepare(
                "bcc",      //latname
                2,      //lmaxmax
                false,      //init_vel
                false,      //selective_dyanmics
                true,       //relax_new
                "volume",   //fixed_axes
                1.8897261254578281, //lat0
                {0.1,0.1,0.1,   //latvec
                 0.15,0.15,0.15,
                 0.05,0.05,0.05},
                {"C","H"},  //elements
                {"C.upf","H.upf"},  //upf file
                {"upf201","upf201"},    //upf types
                {"C.orb","H.orb"},  //orb file
                {1,2},      //number of each elements
                {12.0,1.0}, //atomic mass
                "Direct",   //coordination type
                {0.1,0.1,0.1,   //atomic coordinates
                 0.15,0.15,0.15,
                 0.05,0.05,0.05})},
    {"C1H2-PBA", UcellTestPrepare(
                "bcc",      //latname
                2,      //lmaxmax
                false,      //init_vel
                false,      //selective_dyanmics
                true,       //relax_new
                "volume",   //fixed_axes
                1.8897261254578281, //lat0
                {0.1,0.1,0.1,   //latvec
                 0.15,0.15,0.15,
                 0.05,0.05,0.05},
                {"C","H"},  //elements
                {"C.upf","H.upf"},  //upf file
                {"upf201","upf201"},    //upf types
                {"C.orb","H.orb"},  //orb file
                {1,2},      //number of each elements
                {12.0,1.0}, //atomic mass
                "Direct",   //coordination type
                {-0.1,-0.1,-0.1,    //atomic coordinates
                 1.2,1.2,1.2,
                 -3.05,-2.8,0.0})},
    {"C1H2-Read", UcellTestPrepare(
                "bcc",      //latname
                2,      //lmaxmax
                true,       //init_vel
                true,       //selective_dyanmics
                true,       //relax_new
                "volume",   //fixed_axes
                1.8897261254578281, //lat0
                {10.0,0.0,0.0,  //latvec
                 0.0,10.0,0.0,
                 0.0,0.0,10.0},
                {"C","H"},  //elements
                {"C.upf","H.upf"},  //upf file
                {"upf201","upf201"},    //upf types
                {"C.orb","H.orb"},  //orb file
                {1,2},      //number of each elements
                {12.0,1.0}, //atomic mass
                "Direct",   //coordination type
                {0.1,0.1,0.1,   //atomic coordinates
                 0.12,0.12,0.12,
                 0.08,0.08,0.08})},
    {"flz-Read", UcellTestPrepare(
                "bcc",      //latname
                2,      //lmaxmax
                false,      //init_vel
                false,      //selective_dyanmics
                false,      //relax_new
                "volume",   //fixed_axes
                1.8897261254578281, //lat0
                {10.0,0.0,0.0,  //latvec
                 0.0,10.0,0.0,
                 0.0,0.0,10.0},
                {"C","H"},  //elements
                {"C.upf","H.upf"},  //upf file
                {"upf201","upf201"},    //upf types
                {"C_gga_8au_100Ry_2s2p1d.orb","H_gga_8au_100Ry_2s1p.orb"},  //orb file
                {1,2},      //number of each elements
                {12.0,1.0}, //atomic mass
                "Direct",   //coordination type
                {0.1,0.1,0.1,   //atomic coordinates
                 0.12,0.12,0.12,
                 0.08,0.08,0.08}
        )
    }
};
#endif