upf2.hpp

Go to the documentation of this file.

#ifndef PSEUDO_UPF2_HPP
#define PSEUDO_UPF2_HPP
 
/*
  Copyright (C) 2018 Xavier Andrade
 
  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU Lesser General Public License as published by
  the Free Software Foundation; either version 3 of the License, or
  (at your option) any later version.
 
  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU Lesser General Public License for more details.
 
  You should have received a copy of the GNU Lesser General Public License
  along with this program; if not, write to the Free Software
  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
*/
 
#include <cassert>
#include <cmath>
#include <fstream>
#include <iostream>
#include <sstream>
#include <vector>
 
#include "anygrid.hpp"
#include "base.hpp"
#include <rapidxml.hpp>
 
#include "element.hpp"
 
namespace pseudopotential {
 
class upf2 : public pseudopotential::upf {
 
public:
  upf2(const std::string &filename, bool uniform_grid = false)
      : pseudopotential::upf(uniform_grid), file_(filename.c_str()),
        buffer_((std::istreambuf_iterator<char>(file_)),
                std::istreambuf_iterator<char>()) {
 
    filename_ = filename;
 
    buffer_.push_back('\0');
    doc_.parse<0>(&buffer_[0]);
 
    root_node_ = doc_.first_node("UPF");
 
    if (!root_node_)
      throw status::FORMAT_NOT_SUPPORTED;
 
    if (root_node_->first_attribute("version")->value()[0] != '2')
      throw status::FORMAT_NOT_SUPPORTED;
 
    std::string pseudo_type = root_node_->first_node("PP_HEADER")
                                  ->first_attribute("pseudo_type")
                                  ->value();
 
    if (pseudo_type == "NC" || pseudo_type == "SL") {
      type_ = pseudopotential::type::KLEINMAN_BYLANDER;
    } else if (pseudo_type == "USPP") {
      throw status::UNSUPPORTED_TYPE_ULTRASOFT;
    } else if (pseudo_type == "PAW") {
      throw status::UNSUPPORTED_TYPE_PAW;
    } else {
      throw status::UNSUPPORTED_TYPE;
    }
 
    assert(root_node_);
 
    // Read the grid
    {
      rapidxml::xml_base<> *xmin =
          root_node_->first_node("PP_MESH")->first_attribute("xmin");
 
      start_point_ = 0;
      if (xmin && fabs(value<double>(xmin)) > 1.0e-10)
        start_point_ = 1;
 
      rapidxml::xml_node<> *node =
          root_node_->first_node("PP_MESH")->first_node("PP_R");
 
      assert(node);
 
      rapidxml::xml_attribute<> *size_attr = node->first_attribute("size");
 
      // some files seems to have this information elsewhere
      if (size_attr == NULL)
        size_attr = root_node_->first_node("PP_MESH")->first_attribute("mesh");
 
      if (size_attr == NULL)
        throw status::FORMAT_NOT_SUPPORTED;
 
      int size = value<int>(size_attr);
 
      grid_.resize(size + start_point_);
      std::istringstream stst(node->value());
      grid_[0] = 0.0;
      for (int ii = 0; ii < size; ii++)
        stst >> grid_[start_point_ + ii];
 
      assert(fabs(grid_[0]) <= 1e-10);
    }
 
    {
      rapidxml::xml_node<> *node =
          root_node_->first_node("PP_MESH")->first_node("PP_RAB");
 
      assert(node);
 
      int size = get_size(node);
 
      grid_weights_.resize(size + start_point_);
      std::istringstream stst(node->value());
      grid_weights_[0] = 0.5 * (grid_[1] - grid_[0]);
      for (int ii = 0; ii < size; ii++)
        stst >> grid_weights_[start_point_ + ii];
 
      mesh_size_ = 0;
      for (double rr = 0.0; rr <= grid_[grid_.size() - 1]; rr += mesh_spacing())
        mesh_size_++;
    }
 
    // calculate lmax (we can't trust the one given by the file :-/)
 
    std::vector<bool> has_l(MAX_L, false);
 
    lmax_ = 0;
    nchannels_ = 0;
 
    proj_l_.resize(nprojectors());
    proj_c_.resize(nprojectors());
 
    // projector info
    for (int iproj = 0; iproj < nprojectors(); iproj++) {
      std::ostringstream tag;
      tag << "PP_BETA." << iproj + 1;
      rapidxml::xml_node<> *node =
          root_node_->first_node("PP_NONLOCAL")->first_node(tag.str().c_str());
 
      assert(node);
 
      int read_l = value<int>(node->first_attribute("angular_momentum"));
 
      lmax_ = std::max(lmax_, read_l);
      proj_l_[iproj] = read_l;
      has_l[read_l] = true;
 
      // now calculate the channel index, by counting previous projectors with
      // the same l
      proj_c_[iproj] = 0;
      for (int jproj = 0; jproj < iproj; jproj++)
        if (read_l == proj_l_[jproj])
          proj_c_[iproj]++;
 
      nchannels_ = std::max(nchannels_, proj_c_[iproj] + 1);
    }
 
    assert(lmax_ >= 0);
 
    llocal_ = -1;
    for (int l = 0; l <= lmax_; l++)
      if (!has_l[l])
        llocal_ = l;
 
    // Read dij once
    {
 
      rapidxml::xml_node<> *node =
          root_node_->first_node("PP_NONLOCAL")->first_node("PP_DIJ");
 
      assert(node);
 
      dij_.resize((lmax_ + 1) * nchannels_ * nchannels_);
 
      for (unsigned kk = 0; kk < dij_.size(); kk++)
        dij_[kk] = 0.0;
 
      std::istringstream stst(node->value());
      for (int ii = 0; ii < nprojectors(); ii++) {
        for (int jj = 0; jj < nprojectors(); jj++) {
          double val;
          stst >> val;
 
          if (proj_l_[ii] != proj_l_[jj]) {
            assert(fabs(val) < 1.0e-10);
            continue;
          }
 
          val *= 0.5; // convert from Rydberg to Hartree
          d_ij(proj_l_[ii], proj_c_[ii], proj_c_[jj]) = val;
        }
      }
    }
  }
 
  pseudopotential::format format() const {
    return pseudopotential::format::UPF2;
  }
 
  int size() const { return buffer_.size(); };
 
  std::string description() const {
    return root_node_->first_node("PP_INFO")->value();
  }
 
  std::string symbol() const {
    return element::trim(root_node_->first_node("PP_HEADER")
                             ->first_attribute("element")
                             ->value());
  }
 
  int atomic_number() const {
    element el(symbol());
    return el.atomic_number();
  }
 
  double mass() const {
    element el(symbol());
    return el.mass();
  }
 
  double valence_charge() const {
    return value<double>(
        root_node_->first_node("PP_HEADER")->first_attribute("z_valence"));
  }
 
  pseudopotential::exchange exchange() const {
    std::string functional = root_node_->first_node("PP_HEADER")
                                 ->first_attribute("functional")
                                 ->value();
    if (functional == "PBE")
      return pseudopotential::exchange::PBE;
    if (functional == "PBESOL")
      return pseudopotential::exchange::PBE_SOL;
    if (functional == "SLA  PW   NOGX NOGC")
      return pseudopotential::exchange::LDA;
    if (functional == "BLYP")
      return pseudopotential::exchange::B88;
    return pseudopotential::exchange::UNKNOWN;
  }
 
  pseudopotential::correlation correlation() const {
    std::string functional = root_node_->first_node("PP_HEADER")
                                 ->first_attribute("functional")
                                 ->value();
    if (functional == "PBE")
      return pseudopotential::correlation::PBE;
    if (functional == "PBESOL")
      return pseudopotential::correlation::PBE_SOL;
    if (functional == "SLA  PW   NOGX NOGC")
      return pseudopotential::correlation::LDA_PW;
    if (functional == "BLYP")
      return pseudopotential::correlation::LYP;
    return pseudopotential::correlation::UNKNOWN;
  }
 
  void local_potential(std::vector<double> &potential) const {
    rapidxml::xml_node<> *node = root_node_->first_node("PP_LOCAL");
 
    assert(node);
 
    int size = get_size(node);
 
    potential.resize(size + start_point_);
    std::istringstream stst(node->value());
    for (int ii = 0; ii < size; ii++) {
      stst >> potential[ii + start_point_];
      potential[ii + start_point_] *= 0.5; // Convert from Rydberg to Hartree
    }
    if (start_point_ > 0)
      extrapolate_first_point(potential);
 
    interpolate(potential);
  }
 
  int nprojectors() const {
    return value<int>(
        root_node_->first_node("PP_HEADER")->first_attribute("number_of_proj"));
  }
 
  int nprojectors_per_l(int l) const {
  
    int nchannel = 0;
    for (int jproj = 0; jproj < nprojectors(); jproj++)
        if (proj_l_[jproj] == l)
          nchannel = std::max(proj_c_[jproj]+1, nchannel);
    return nchannel;
  }
 
  void projector(int l, int i, std::vector<double> &proj) const {
    rapidxml::xml_node<> *node = NULL;
 
    int iproj = 0;
    while ((l != proj_l_[iproj] || i != proj_c_[iproj]) && iproj < nprojectors()) {
      iproj++;
    }
    std::stringstream tag;
    tag << "PP_BETA." << iproj+1;
    node = root_node_->first_node("PP_NONLOCAL")->first_node(tag.str().c_str());
 
    assert(node);
 
    int size = get_size(node);
 
    proj.resize(size + start_point_);
    std::istringstream stst(node->value());
    for (int ii = 0; ii < size; ii++)
      stst >> proj[ii + start_point_];
 
    // the projectors come multiplied by r, so we have to divide and fix the
    // first point
    for (int ii = 1; ii < size + start_point_; ii++)
      proj[ii] /= grid_[ii];
    extrapolate_first_point(proj);
 
    interpolate(proj);
  }
 
  bool has_radial_function(int l) const { return false; }
 
  void radial_function(int l, std::vector<double> &function) const {
    function.clear();
  }
 
  void radial_potential(int l, std::vector<double> &function) const {
    function.clear();
  }
 
  bool has_nlcc() const { return root_node_->first_node("PP_NLCC"); }
 
  void nlcc_density(std::vector<double> &density) const {
    rapidxml::xml_node<> *node = root_node_->first_node("PP_NLCC");
    assert(node);
 
    int size = get_size(node);
 
    density.resize(size + start_point_);
 
    std::istringstream stst(node->value());
    for (int ii = 0; ii < size; ii++)
      stst >> density[start_point_ + ii];
    extrapolate_first_point(density);
    // this charge does not come multiplied by anything
 
    interpolate(density);
  }
 
  bool has_total_angular_momentum() const {
    return root_node_->first_node("PP_SPIN_ORB");
  }
 
  void beta(int iproj, int &l, std::vector<double> &proj) const {
    rapidxml::xml_node<> *node = NULL;
 
    std::stringstream tag;
    tag << "PP_BETA." << iproj + 1;
    node = root_node_->first_node("PP_NONLOCAL")->first_node(tag.str().c_str());
 
    assert(node);
 
    l = value<int>(node->first_attribute("angular_momentum"));
 
    int size = get_size(node);
 
    proj.resize(size + start_point_);
    std::istringstream stst(node->value());
    for (int ii = 0; ii < size; ii++)
      stst >> proj[ii + start_point_];
 
    // the projectors come multiplied by r, so we have to divide and fix the
    // first point
    for (int ii = 1; ii < size + start_point_; ii++)
      proj[ii] /= grid_[ii];
    extrapolate_first_point(proj);
 
    interpolate(proj);
  }
 
  void dnm_zero(int nbeta, std::vector<std::vector<double>> &dnm) const {
    dnm.resize(nbeta);
    for (int i = 0; i < nbeta; i++) {
      dnm[i].resize(nbeta);
      for (int j = 0; j < nbeta; j++) {
        dnm[i][j] = dij_[i * nbeta + j];
      }
    }
  }
 
  bool has_density() const { return root_node_->first_node("PP_RHOATOM"); }
 
  void density(std::vector<double> &val) const {
    rapidxml::xml_node<> *node = root_node_->first_node("PP_RHOATOM");
    assert(node);
 
    int size = get_size(node);
 
    val.resize(size + start_point_);
 
    std::istringstream stst(node->value());
    for (int ii = 0; ii < size; ii++)
      stst >> val[start_point_ + ii];
 
    // the density comes multiplied by 4\pi r
    for (int ii = 1; ii < size + start_point_; ii++)
      val[ii] /= 4.0 * M_PI * grid_[ii] * grid_[ii];
    extrapolate_first_point(val);
 
    interpolate(val);
  }
 
  int nwavefunctions() const {
    return value<int>(
        root_node_->first_node("PP_HEADER")->first_attribute("number_of_wfc"));
  }
 
  void wavefunction(int index, int &n, int &l, double &occ,
                    std::vector<double> &proj) const {
    rapidxml::xml_node<> *node = NULL;
 
    std::stringstream tag;
    tag << "PP_CHI." << index + 1;
    node = root_node_->first_node("PP_PSWFC")->first_node(tag.str().c_str());
 
    assert(node);
 
    // not all files have "n", so we might have to parse the label
    if (node->first_attribute("n")) {
      n = value<int>(node->first_attribute("n"));
    } else {
      std::string label = node->first_attribute("label")->value();
      n = atoi(label.substr(0, 1).c_str());
    }
 
    l = value<int>(node->first_attribute("l"));
 
    occ = value<double>(node->first_attribute("occupation"));
 
    int size = get_size(node);
 
    proj.resize(size + start_point_);
    std::istringstream stst(node->value());
    for (int ii = 0; ii < size; ii++)
      stst >> proj[ii + start_point_];
 
    // the wavefunctions come multiplied by r, so we have to divide and fix the
    // first point
    for (int ii = 1; ii < size + start_point_; ii++)
      proj[ii] /= grid_[ii];
    extrapolate_first_point(proj);
 
    interpolate(proj);
  }
 
  // Retreive the value of 2*j for relativistic projectors
  int projector_2j(int l, int ic) const {
 
    if (l == 0)
      return 1;
 
    for (int iproj = 0; iproj < nprojectors(); iproj++) {
      std::stringstream tag;
      tag << "PP_RELBETA." << iproj + 1;
 
      rapidxml::xml_node<> *node =
          root_node_->first_node("PP_SPIN_ORB")->first_node(tag.str().c_str());
      assert(node);
 
      std::string labell = node->first_attribute("lll")->value();
      if(atoi(labell.c_str()) == l && proj_c_[iproj] == ic){
        std::string labelj = node->first_attribute("jjj")->value();
        double j = atof(labelj.c_str());
 
        return lrint(j * 2.0);
      }
    }
    
    return -1;
  }
 
 
  // Retreive the value of 2*j for relativitstic wavefunctions
  int wavefunction_2j(int ii) const {
 
    std::stringstream tag;
    tag << "PP_RELWFC." << ii;
 
    rapidxml::xml_node<> *node =
          root_node_->first_node("PP_SPIN_ORB")->first_node(tag.str().c_str());
    assert(node);
    
    std::string label = node->first_attribute("jchi")->value();
    double j = atof(label.c_str());
 
    return lrint(j * 2.0);
  }
 
 
private:
  int get_size(const rapidxml::xml_node<> *node) const {
    int size = grid_.size() - start_point_;
 
    rapidxml::xml_attribute<> *size_attr = node->first_attribute("size");
 
    if (size_attr != NULL)
      size = value<int>(size_attr);
 
    return size;
  }
 
  std::ifstream file_;
  std::vector<char> buffer_;
  rapidxml::xml_document<> doc_;
  rapidxml::xml_node<> *root_node_;
  std::vector<int> proj_l_;
  std::vector<int> proj_c_;
};
 
} // namespace pseudopotential
 
#endif