abacus-develop/source/source_cell/read_pp_vwr.cpp at develop · pplab/abacus-develop · GitHub

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#include "read_pp.h"

//----------------------------------------------------------

// This code is used to read in vwr pseudopotential format,

// Now we only use LDA, so if PBE or other functionals are used,

// one needs to change the following code. The vwr format

// needs we to generate NL projectors by ourself.

// One way to check this is correct

// is to use opium to generate .ncpp pseudopotential first,

// which contains the same informaiton in vwr, then we had

// both UPF format from upftools in Quantum Espresso and

// we can write a short code to transform ncpp to vwr.

// Then compare the two results.

// mohan 2013-05-25

//-----------------------------------------------------------

int Pseudopot_upf::read_pseudo_vwr(std::ifstream &ifs, Atom_pseudo& pp)

{

GlobalV::ofs_running << " -------------------------------------------------" << std::endl;

std::cout << " READ IN VWR TYPE PSEUDOPOTENTIALS." << std::endl;

GlobalV::ofs_running << " Read in vwr type pseudopotentials " << std::endl;

// --------------------------------------

// (1) read in data

// --------------------------------------

pp.xc_func="PZ";

pp.pp_type="NC";

pp.tvanp = false;

// (1) read in mesh

std::string value;

size_t length=0;

ifs >> value; length = value.find(","); value.erase(length,1);

pp.mesh = std::atoi( value.c_str() );

//the mesh should be odd, which is forced in Simpson integration

this->mesh_changed = false;

if(pp.mesh%2==0)

{

pp.mesh=pp.mesh-1;

this->mesh_changed = true;

GlobalV::ofs_running << " Mesh number - 1, we need odd number, \n this may affect some polar atomic orbitals." << std::endl;

}

GlobalV::ofs_running << std::setw(15) << "MESH" << std::setw(15) << pp.mesh << std::endl;

// (2) read in nlcc: nonlinear core correction

ifs >> value; length = value.find(","); value.erase(length,1);

pp.nlcc = std::atoi( value.c_str() );

GlobalV::ofs_running << std::setw(15) << "NLCC" << std::setw(15) << pp.nlcc << std::endl;

// (3) iatom : index for atom

ifs >> value; length = value.find(","); value.erase(length,1);

pp.psd = value;

GlobalV::ofs_running << std::setw(15) << "ATOM" << std::setw(15) << pp.psd << std::endl;

// (4) valence electron number

ifs >> value; length = value.find(","); value.erase(length,1);

pp.zv = std::stod( value );

GlobalV::ofs_running << std::setw(15) << "Z(VALENCE)" << std::setw(15) << pp.zv << std::endl;

// (5) spd_loc, which local pseudopotential should I choose

ifs >> value; length = value.find(","); value.erase(length,1);

spd_loc = std::atoi( value.c_str() );

GlobalV::ofs_running << std::setw(15) << "LOC(spd)" << std::setw(15) << spd_loc << std::endl;

// (6) read in the occupations

std::vector<double> tmp_oc(3, 0.0);

ifs >> value; length = value.find(","); value.erase(length,1);

tmp_oc[0]= std::atoi( value.c_str() );

ifs >> value; length = value.find(","); value.erase(length,1);

tmp_oc[1]= std::atoi( value.c_str() );

ifs >> value; length = value.find(","); value.erase(length,1);

tmp_oc[2]= std::atoi( value.c_str() );

GlobalV::ofs_running << std::setw(15) << "OCCUPATION" << std::setw(15) << tmp_oc[0]

<< std::setw(15) << tmp_oc[1] << std::setw(15) << tmp_oc[2] << std::endl;

// (7) spin orbital

ifs >> pp.has_so;

// label to count the projector or atomic wave functions

getline(ifs,value);

int iref_s, iref_p, iref_d;

ifs >> iref_s >> iref_p >> iref_d;

GlobalV::ofs_running << std::setw(15) << "Vnl_USED" << std::setw(15) << iref_s

<< std::setw(15) << iref_p << std::setw(15) << iref_d << std::endl;

if(spd_loc==1) { iref_s=0;

} else if(spd_loc==2) { iref_p=0;

} else if(spd_loc==3) { iref_d=0;

}

ifs >> iTB_s >> iTB_p >> iTB_d;

GlobalV::ofs_running << std::setw(15) << "Orb_USED" << std::setw(15) << iTB_s

<< std::setw(15) << iTB_p << std::setw(15) << iTB_d << std::endl;

// calculate the number of wave functions

pp.nchi = 0;

if(iTB_s) { ++pp.nchi;

}

if(iTB_p) { ++pp.nchi;

}

if(iTB_d) { ++pp.nchi;

}

GlobalV::ofs_running << std::setw(15) << "NWFC" << std::setw(15) << pp.nchi << std::endl;

// allocate occupation number array for wave functions

pp.oc = std::vector<double>(pp.nchi, 0.0);

pp.els = std::vector<std::string>(pp.nchi, "");

// set the value of occupations

pp.lchi = std::vector<int>(pp.nchi, 0);

int iwfc=0;

if(iTB_s){pp.oc[iwfc]=tmp_oc[0];pp.lchi[iwfc]=0;pp.els[iwfc]="S";++iwfc;}

if(iTB_p){pp.oc[iwfc]=tmp_oc[1];pp.lchi[iwfc]=1;pp.els[iwfc]="P";++iwfc;}

if(iTB_d){pp.oc[iwfc]=tmp_oc[2];pp.lchi[iwfc]=2;pp.els[iwfc]="D";++iwfc;}

getline(ifs,value);

// global variables that will be used

// in other classes.

pp.r = std::vector<double>(pp.mesh, 0.0);

pp.rab = std::vector<double>(pp.mesh, 0.0);

pp.vloc_at = std::vector<double>(pp.mesh, 0.0);

pp.rho_at = std::vector<double>(pp.mesh, 0.0);

pp.rho_atc = std::vector<double>(pp.mesh, 0.0);

// local variables in this function

std::vector<double> vs = std::vector<double>(pp.mesh, 0.0); // local pseudopotential for s, unit is Hartree

std::vector<double> vp = std::vector<double>(pp.mesh, 0.0); // local pseudopotential for p

std::vector<double> vd = std::vector<double>(pp.mesh, 0.0); // local pseudopotential for d

std::vector<double> ws = std::vector<double>(pp.mesh, 0.0); // wave function for s

std::vector<double> wp = std::vector<double>(pp.mesh, 0.0); // wave function for p

std::vector<double> wd = std::vector<double>(pp.mesh, 0.0); // wave function for d

std::string line;

if(spd_loc>0 && pp.nlcc==0)

{

for(int ir=0; ir<pp.mesh; ++ir)

{

// it's an interesting question whether

// ws[ir] has 1/sqrt(4pi)

ifs >> pp.r[ir] >> vs[ir] >> vp[ir] >> vd[ir]

>> ws[ir] >> wp[ir] >> wd[ir];

getline(ifs, line);

}

else if(spd_loc==0 && pp.nlcc==0)

{

for(int ir=0; ir<pp.mesh; ++ir)

{

ifs >> pp.r[ir] >> vs[ir] >> vp[ir] >> vd[ir]

>> ws[ir] >> wp[ir] >> wd[ir] >> pp.vloc_at[ir];

getline(ifs, line);

}

else if(spd_loc>0 && pp.nlcc==1)

{

for(int ir=0; ir<pp.mesh; ++ir)

{

ifs >> pp.r[ir] >> vs[ir] >> vp[ir] >> vd[ir]

>> ws[ir] >> wp[ir] >> wd[ir] >> pp.rho_atc[ir];

getline(ifs, line);

}

else if(spd_loc==0 && pp.nlcc==1)

{

for(int ir=0; ir<pp.mesh; ++ir)

{

ifs >> pp.r[ir] >> vs[ir] >> vp[ir] >> vd[ir]

>> ws[ir] >> wp[ir] >> wd[ir] >> pp.vloc_at[ir] >> pp.rho_atc[ir];

getline(ifs, line);

}

// Hartree to Rydberg

for(int ir=0; ir<pp.mesh; ++ir)

{

vs[ir] *= 2.0;

vp[ir] *= 2.0;

vd[ir] *= 2.0;

pp.vloc_at[ir] *= 2.0;

}

// --------------------------------------

// (2) check unit

// --------------------------------------

// calculate rab;

// rab may not be accurate enough

pp.rab[0] = pp.r[0];

for(int ir=1; ir<pp.mesh-1; ++ir)

{

pp.rab[ir]=(pp.r[ir+1]-pp.r[ir-1])/2.0;

}

// check unit of vs, vp, vd

double units = 0.0;

double unitp = 0.0;

double unitd = 0.0;

for(int ir=1; ir<pp.mesh-1; ++ir)

{

double dr = (pp.r[ir+1]-pp.r[ir-1])/2.0;

units += ws[ir] * ws[ir] * pp.r[ir] * pp.r[ir] * dr;

unitp += wp[ir] * wp[ir] * pp.r[ir] * pp.r[ir] * dr;

unitd += wd[ir] * wd[ir] * pp.r[ir] * pp.r[ir] * dr;

}

GlobalV::ofs_running << std::setw(15) << "WFC_UNIT" << std::setw(15) << units

<< std::setw(15) << unitp << std::setw(15) << unitd << std::endl;

// because only the rank=0 procesor read the pseudopotential

// information, in order to make all the processors to stop

// the job, we need to return the error information first.

// we need to choose a threshold for the deviation of the

// norm of pseudo atomic orbitals, I set 0.2

// mohan 2013-06-28

if( std::abs(units-1.0) > 0.2 && (iTB_s==1 || iref_s==1)) {return 3;}

if( std::abs(unitp-1.0) > 0.2 && (iTB_p==1 || iref_p==1)) {return 3;}

if( std::abs(unitd-1.0) > 0.2 && (iTB_d==1 || iref_d==1)) {return 3;}

// calculate the phi*r*sqrt(4pi)

pp.chi.create(pp.nchi,pp.mesh);

for(int ir=0; ir<pp.mesh; ++ir)

{

int iwfc=0;

if(iTB_s==1){pp.chi(iwfc,ir) = ws[ir]*pp.r[ir];++iwfc;}

if(iTB_p==1){pp.chi(iwfc,ir) = wp[ir]*pp.r[ir];++iwfc;}

if(iTB_d==1){pp.chi(iwfc,ir) = wd[ir]*pp.r[ir];++iwfc;}

}

// rho atom

for(int ir=0; ir<pp.mesh; ++ir)

{

for(int iwfc=0; iwfc<pp.nchi; ++iwfc)

{

pp.rho_at[ir] += pp.oc[iwfc]*pp.chi(iwfc,ir)*pp.chi(iwfc,ir);

}

// --------------------------------------

// (4) local pseudopotential

// --------------------------------------

if(spd_loc==0) { for(int ir=0; ir<pp.mesh; ++ir)

{

// do nothing

}

} else if(spd_loc==1) { for(int ir=0; ir<pp.mesh; ++ir) { pp.vloc_at[ir] = vs[ir];

}

} else if(spd_loc==2) { for(int ir=0; ir<pp.mesh; ++ir) { pp.vloc_at[ir] = vp[ir];

}

} else if(spd_loc==3) { for(int ir=0; ir<pp.mesh; ++ir) { pp.vloc_at[ir] = vd[ir];

}

} else if(spd_loc==12) { for(int ir=0; ir<pp.mesh; ++ir) { pp.vloc_at[ir] = (vs[ir]+vp[ir])/2.0;

}

} else if(spd_loc==13) { for(int ir=0; ir<pp.mesh; ++ir) { pp.vloc_at[ir] = (vs[ir]+vd[ir])/2.0;

}

} else if(spd_loc==23) { for(int ir=0; ir<pp.mesh; ++ir) { pp.vloc_at[ir] = (vp[ir]+vd[ir])/2.0;

}

// --------------------------------------

// (5) setup nonlocal pseudopotentials

// --------------------------------------

// for non-local pseudopotentials.

if(iref_d==1) { pp.lmax=2;

} else if(iref_p==1) { pp.lmax=1;

} else if(iref_s==1) { pp.lmax=0;

} else

{

std::cout << "\n !!! READ THIS FIRST !!!" << std::endl;

std::cout << " Could not decide which is the max angular momentum from .vwr pseudopotential file." << std::endl;

std::cout << " No reference states in .vwr pseudopotential file." << std::endl;

std::cout << " That's incorrect, please check the refenrece states in .vwr file.";

std::cout << "\n !!! READ THIS FIRST !!!" << std::endl;

return 3;

}

// no projectors now

pp.nbeta = 0;

if(iref_s==1) { ++pp.nbeta; // add one s projector

}

if(iref_p==1) { ++pp.nbeta; // add one p projector

}

if(iref_d==1) { ++pp.nbeta; // add one p projector

}

GlobalV::ofs_running << std::setw(15) << "NPROJ" << std::setw(15) << pp.nbeta << std::endl;

this->nd = pp.nbeta;

GlobalV::ofs_running << std::setw(15) << "N-Dij" << std::setw(15) << nd << std::endl;

// calculate the angular momentum for each pp.betar

pp.lll = std::vector<int>(pp.nbeta, 0);

int icount=0;

if(iref_s==1) {pp.lll[icount]=0; ++icount;}// s projector

if(iref_p==1) {pp.lll[icount]=1; ++icount;}// p projector

if(iref_d==1) {pp.lll[icount]=2; ++icount;}// p projector

for(int i=0; i<pp.nbeta; ++i)

{

GlobalV::ofs_running << " lll[" << i << "]=" << pp.lll[i] << std::endl;

}

// this->kbeta(pp.nbeta): number of mesh points for projector i (must be .le.mesh )

this->kbeta = std::vector<int>(pp.nbeta, 0);

pp.kkbeta = 0;

for (int ib = 0; ib < pp.nbeta; ++ib)

{

this->kbeta[ib] = pp.mesh;

pp.kkbeta = (this->kbeta[ib] > pp.kkbeta) ? this->kbeta[ib] : pp.kkbeta;

}

// nonlocal projector

pp.betar.create(pp.nbeta,pp.mesh);

// coefficients

pp.dion.create(pp.nbeta,pp.nbeta);

// --------------------------------------

// (6) generate nonlocal pseudopotentials

// --------------------------------------

// tmp function to evaluate < pp.betar | delta_v | pp.betar>

std::vector<double> func = std::vector<double>(pp.mesh, 0.0);

// tmp value (vs, vp or vd)

std::vector<double> vl = std::vector<double>(pp.mesh, 0.0);

// tmp wave function (ws, wp or wd with r)

std::vector<double> wlr = std::vector<double>(pp.mesh, 0.0);

double rcut = 5.0/1.03;

GlobalV::ofs_running << std::setw(15) << "RCUT_NL" << std::setw(15) << rcut << std::endl;

for(int ib=0; ib<pp.nbeta; ++ib)

{

double coef = 0.0;

const int lnow = pp.lll[ib];

if(lnow==0) { for(int ir=0; ir<pp.mesh; ++ir){vl[ir]=vs[ir]; wlr[ir]=ws[ir]*pp.r[ir];}

} else if(lnow==1) { for(int ir=0; ir<pp.mesh; ++ir){vl[ir]=vp[ir]; wlr[ir]=wp[ir]*pp.r[ir];}

} else if(lnow==2) { for(int ir=0; ir<pp.mesh; ++ir){vl[ir]=vd[ir]; wlr[ir]=wd[ir]*pp.r[ir];}

}

// for non-local projectors

// note that < phi | dV | phi > integration must have 4pi,

// this 4pi is also needed in < phi | phi > = 1 integration.

// However, this phi has sqrt(sphi) already because I

// found < phi | phi > = 1 directly.

GlobalV::ofs_running << " Projector index = " << ib+1 << ", L = " << lnow << std::endl;

for(int ir=2; ir<pp.mesh-1; ++ir)

{

// p nl

pp.betar(ib,ir)=(vl[ir]-pp.vloc_at[ir])*wlr[ir];

if(pp.r[ir]<rcut)

{

coef=coef+(vl[ir]-pp.vloc_at[ir])*wlr[ir]*wlr[ir]*(pp.r[ir+1]-pp.r[ir-1])/2.0;

}

// In pw they did this:

// pp.dion(ib,ib)=1.0/coef;

if(coef<0.0) { pp.dion(ib,ib) = -1.0;

}

if(coef>=0.0) { pp.dion(ib,ib) = 1.0;

}

//!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

// suppose wave function have sqrt(4pi) already

//!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

coef=1.0/sqrt(std::abs(coef));

GlobalV::ofs_running << std::setw(25) << "1/sqrt(<phi|deltaV|phi>)" << std::setw(15) << coef << std::endl;

for(int ir=0; ir<pp.mesh; ++ir)

{

pp.betar(ib,ir) *= coef;

// --------- FOR TEST ---------

if(ib>2)

{

// pp.betar(ib,ir) *= 0.0; // for test, disable Non-local

}

// --------- FOR TEST ---------

}

// print out the projector.

GlobalV::ofs_running << " Nonlocal projector : " << std::endl;

for(int ir=0; ir<mesh; ++ir)

{

if(r[ir]<rcut)

{

GlobalV::ofs_running << " " << std::setw(15) << r[ir];

for(int ib=0; ib<pp.nbeta; ++ib)

{

GlobalV::ofs_running << std::setw(25) << pp.betar(ib,ir);

}

GlobalV::ofs_running << std::endl;

}

GlobalV::ofs_running << " -------------------------------------------------" << std::endl;

return 0;

}

abacus-develop/source/source_cell/read_pp_vwr.cpp at develop · pplab/abacus-develop · GitHub

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