GaussianFCHKParser.cpp

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//////////////////////////////////////////////////////////////////////////////////////
// This file is distributed under the University of Illinois/NCSA Open Source License.
// See LICENSE file in top directory for details.
//
// Copyright (c) 2016 Jeongnim Kim and QMCPACK developers.
//
// File developed by: Jordan E. Vincent, University of Illinois at Urbana-Champaign
//                    Jeongnim Kim, jeongnim.kim@gmail.com, University of Illinois at Urbana-Champaign
//                    Miguel Morales, moralessilva2@llnl.gov, Lawrence Livermore National Laboratory
//                    Jeremy McMinnis, jmcminis@gmail.com, University of Illinois at Urbana-Champaign
//                    Mark A. Berrill, berrillma@ornl.gov, Oak Ridge National Laboratory
//
// File created by: Jordan E. Vincent, University of Illinois at Urbana-Champaign
//////////////////////////////////////////////////////////////////////////////////////


#include "GaussianFCHKParser.h"
#include <fstream>
#include <iterator>
#include <algorithm>
#include <set>
#include <map>


GaussianFCHKParser::GaussianFCHKParser()
{
  basisName  = "Gaussian-G2";
  Normalized = "no";
  FixValence = true;
}

GaussianFCHKParser::GaussianFCHKParser(int argc, char** argv) : QMCGaussianParserBase(argc, argv)
{
  basisName  = "Gaussian-G2";
  Normalized = "no";
  FixValence = true;
}

void GaussianFCHKParser::parse(const std::string& fname)
{
  std::ifstream fin(fname.c_str());
  getwords(currentWords, fin); //1
  Title = currentWords[0];
  getwords(currentWords, fin); //2  SP RHF Gen
  //if(currentWords[1]=="ROHF" || currentWords[1]=="UHF") {
  if (currentWords[1] == "UHF")
  {
    // mmorales: this should be determined by the existence of "Beta MO", since
    // there are many ways to get unrestricted runs without UHF (e.g. UMP2,UCCD,etc)
    SpinRestricted = false;
    //std::cout << " Spin Unrestricted Calculation (UHF). " << std::endl;
  }
  else
  {
    SpinRestricted = true;
    //std::cout << " Spin Restricted Calculation (RHF). " << std::endl;
  }
  getwords(currentWords, fin); //3  Number of atoms
  NumberOfAtoms = atoi(currentWords.back().c_str());
  // TDB: THIS FIX SHOULD BE COMPATIBLE WITH MY OLD FCHK FILES
  //getwords(currentWords,fin); //4 Charge
  bool notfound = true;
  while (notfound)
  {
    std::string aline;
    getwords(currentWords, fin);
    for (int i = 0; i < currentWords.size(); i++)
    {
      if ("Charge" == currentWords[i])
      {
        notfound = false;
      }
    }
  }
  getwords(currentWords, fin); //5 Multiplicity
  SpinMultiplicity = atoi(currentWords.back().c_str());
  getwords(currentWords, fin); //6 Number of electrons
  NumberOfEls = atoi(currentWords.back().c_str());
  getwords(currentWords, fin); //7 Number of alpha electrons
  int nup = atoi(currentWords.back().c_str());
  getwords(currentWords, fin); //8 Number of beta electrons
  int ndown = atoi(currentWords.back().c_str());
  //NumberOfAlpha=nup-ndown;
  NumberOfAlpha = nup;
  NumberOfBeta  = ndown;
  getwords(currentWords, fin); //9 Number of basis functions
  SizeOfBasisSet = atoi(currentWords.back().c_str());
  getwords(currentWords, fin); //10 Number of independent functions
  int NumOfIndOrb = atoi(currentWords.back().c_str());
  std::cout << "Number of independent orbitals: " << NumOfIndOrb << std::endl;
  numMO = NumOfIndOrb;
  // TDB: THIS ADDITION SHOULD BE COMPATIBLE WITH MY OLD FCHK FILES
  std::streampos pivottdb = fin.tellg();
  int ng                  = 0;
  notfound                = true;
  while (notfound)
  {
    std::string aline;
    getwords(currentWords, fin);
    for (int i = 0; i < currentWords.size(); i++)
    {
      if ("contracted" == currentWords[i])
      {
        ng       = atoi(currentWords.back().c_str());
        notfound = false;
      }
    }
  }
  // TDB: THIS FIX SHOULD BE COMPATIBLE WITH MY OLD FCHK FILES
  // getwords(currentWords,fin); //Number of contracted shells
  // getwords(currentWords,fin); //Number of contracted shells
  // getwords(currentWords,fin); //Number of contracted shells
  // int nx=atoi(currentWords.back().c_str()); //Number of exponents
  int nx   = 0;
  notfound = true;
  while (notfound)
  {
    std::string aline;
    getwords(currentWords, fin);
    for (int i = 0; i < currentWords.size(); i++)
    {
      if ("primitive" == currentWords[i])
      {
        nx       = atoi(currentWords.back().c_str()); //Number of exponents
        notfound = false;
      }
    }
  }
  //allocate everything here
  IonSystem.create({NumberOfAtoms});
  GroupName.resize(NumberOfAtoms);
  gBound.resize(NumberOfAtoms + 1);
  gShell.resize(ng);
  gNumber.resize(ng);
  gExp.resize(nx);
  gC0.resize(nx);
  gC1.resize(nx);
  // TDB: THIS ADDITION SHOULD BE COMPATIBLE WITH MY OLD FCHK FILES
  fin.seekg(pivottdb); //rewind it
  getGeometry(fin);
  std::cout << "Number of gaussians " << ng << std::endl;
  std::cout << "Number of primitives " << nx << std::endl;
  std::cout << "Number of atoms " << NumberOfAtoms << std::endl;
  search(fin, "Shell types");
  getGaussianCenters(fin);
  std::cout << " Shell types reading: OK" << std::endl;
  // mmorales: SizeOfBasisSet > numMO always, so leave it like this
  EigVal_alpha.resize(SizeOfBasisSet);
  EigVal_beta.resize(SizeOfBasisSet);
  // mmorales HACK HACK HACK, look for a way to rewind w/o closing/opening a file
  SpinRestricted = !(lookFor(fin, "Beta MO"));
  fin.close();
  fin.open(fname.c_str());
  search(fin, "Alpha Orbital"); //search "Alpha Orbital Energies"
                                // only read NumOfIndOrb
  getValues(fin, EigVal_alpha.begin(), EigVal_alpha.begin() + numMO);
  std::cout << " Orbital energies reading: OK" << std::endl;
  if (SpinRestricted)
  {
    EigVec.resize(2 * numMO * SizeOfBasisSet);
    EigVal_beta = EigVal_alpha;
    std::vector<value_type> etemp;
    search(fin, "Alpha MO");
    getValues(fin, EigVec.begin(), EigVec.begin() + SizeOfBasisSet * numMO);
    copy(EigVec.begin(), EigVec.begin() + SizeOfBasisSet * numMO, EigVec.begin() + SizeOfBasisSet * numMO);
    std::cout << " Orbital coefficients reading: OK" << std::endl;
  }
  else
  {
    EigVec.resize(2 * numMO * SizeOfBasisSet);
    std::vector<value_type> etemp;
    search(fin, "Beta Orbital");
    getValues(fin, EigVal_beta.begin(), EigVal_beta.begin() + numMO);
    std::cout << " Read Beta Orbital energies: OK" << std::endl;
    search(fin, "Alpha MO");
    getValues(fin, EigVec.begin(), EigVec.begin() + SizeOfBasisSet * numMO);
    search(fin, "Beta MO");
    getValues(fin, EigVec.begin() + numMO * SizeOfBasisSet, EigVec.begin() + 2 * numMO * SizeOfBasisSet);
    std::cout << " Alpha and Beta Orbital coefficients reading: OK" << std::endl;
  }
  if (multideterminant)
  {
    std::ifstream ofile(outputFile.c_str());
    if (ofile.fail())
    {
      std::cerr << "Failed to open output file from gaussian. \n";
      exit(401);
    }
    int statesType          = 0;
    std::streampos beginpos = ofile.tellg();
    bool found              = lookFor(ofile, "SLATER DETERMINANT BASIS");
    if (!found)
    {
      ofile.close();
      ofile.open(outputFile.c_str());
      ofile.seekg(beginpos);
      found = lookFor(ofile, "Slater Determinants");
      if (found)
      {
        statesType = 1;
        ofile.close();
        ofile.open(outputFile.c_str());
        ofile.seekg(beginpos);
        search(ofile, "Total number of active electrons");
        getwords(currentWords, ofile);
        ci_nstates = atoi(currentWords[5].c_str());
        search(ofile, "Slater Determinants");
      }
      else
      {
        std::cerr << "Gaussian parser currently works for slater determinant basis only. Use SlaterDet in CAS() or "
                     "improve parser.\n";
        abort();
      }
    }
    beginpos = ofile.tellg();
    // mmorales: gaussian by default prints only 50 states
    // if you want more you need to use, iop(5/33=1), but this prints
    // a lot of things. So far, I don't know how to change this
    // without modifying the source code, l510.F or utilam.F
    found = lookFor(ofile, "Do an extra-iteration for final printing");
    std::map<int, int> coeff2confg;
    //   290 FORMAT(1X,7('(',I5,')',F10.7,1X)/(1X,7('(',I5,')',F10.7,1X)))
    if (found)
    {
      // this is tricky, because output depends on diagonalizer used (Davidson or Lanczos) for now hope this works
      std::streampos tmppos = ofile.tellg();
      // long output with iop(5/33=1)
      int coeffType = 0;
      if (lookFor(ofile, "EIGENVECTOR USED TO COMPUTE DENSITY MATRICES SET"))
      {
        coeffType = 1;
      }
      else
      {
        // short list (50 states) with either Dav or Lanc
        ofile.close();
        ofile.open(outputFile.c_str());
        ofile.seekg(tmppos); //rewind it
        if (!lookFor(ofile, "EIGENVALUE "))
        {
          ofile.close();
          ofile.open(outputFile.c_str());
          ofile.seekg(tmppos); //rewind it
          if (!lookFor(ofile, "Eigenvalue"))
          {
            std::cerr << "Failed to find CI voefficients.\n";
            abort();
          }
        }
      }
      std::streampos strpos = ofile.tellg();
      ofile.close();
      ofile.open(outputFile.c_str());
      ofile.seekg(beginpos); //rewind it
      std::string aline;
      int numCI;
      if (lookFor(ofile, "NO OF BASIS FUNCTIONS", aline))
      {
        parsewords(aline.c_str(), currentWords);
        numCI = atoi(currentWords[5].c_str());
      }
      else
      {
        ofile.close();
        ofile.open(outputFile.c_str());
        if (lookFor(ofile, "Number of configurations", aline))
        {
          parsewords(aline.c_str(), currentWords);
          numCI = atoi(currentWords[3].c_str());
        }
        else
        {
          std::cerr << "Problems finding total number of configurations. \n";
          abort();
        }
      }
      std::cout << "Total number of CI configurations in file (w/o truncation): " << numCI << std::endl;
      ofile.close();
      ofile.open(outputFile.c_str());
      ofile.seekg(strpos); //rewind it
      int cnt = 0;
      CIcoeff.clear();
      CIalpha.clear();
      CIbeta.clear();
      if (coeffType == 0)
      {
        // short list
        for (int i = 0; i < 7; i++)
        {
          int pos = 2;
          std::string aline;
          getline(ofile, aline, '\n');
          //cout<<"aline: " <<aline << std::endl;
          for (int i = 0; i < 7; i++)
          {
            //int q = atoi( (aline.substr(pos,pos+4)).c_str() );
            //coeff2confg[q] = cnt++;
            //CIcoeff.push_back( atof( (aline.substr(pos+6,pos+15)).c_str() ) );
            //pos+=18;
            int q          = atoi((aline.substr(pos, pos + 7)).c_str());
            coeff2confg[q] = cnt++;
            CIcoeff.push_back(atof((aline.substr(pos + 9, pos + 18)).c_str()));
            pos += 21;
            //cout<<"confg, coeff: " <<q <<"  " <<CIcoeff.back() << std::endl;
          }
        }
        {
          int pos = 2;
          std::string aline;
          getline(ofile, aline, '\n');
          //int q = atoi( (aline.substr(pos,pos+4)).c_str() );
          //coeff2confg[q] = cnt++;
          //CIcoeff.push_back( atof( (aline.substr(pos+6,pos+15)).c_str() ) );
          int q          = atoi((aline.substr(pos, pos + 7)).c_str());
          coeff2confg[q] = cnt++;
          CIcoeff.push_back(atof((aline.substr(pos + 9, pos + 18)).c_str()));
          //cout<<"confg, coeff: " <<q <<"  " <<CIcoeff.back() << std::endl;
        }
      }
      else
      {
        // long list
        int nrows  = numCI / 5;
        int nextra = numCI - nrows * 5;
        int indx[5];
        ofile.close();
        ofile.open(outputFile.c_str());
        ofile.seekg(strpos); //rewind it
        for (int i = 0; i < nrows; i++)
        {
          getwords(currentWords, ofile);
          if (currentWords.size() != 5)
          {
            std::cerr << "Error reading CI configurations-line: " << i << "\n";
            abort();
          }
          for (int k = 0; k < 5; k++)
            indx[k] = atoi(currentWords[k].c_str());
          getwords(currentWords, ofile);
          if (currentWords.size() != 6)
          {
            std::cerr << "Error reading CI configurations-line: " << i << "\n";
            abort();
          }
          for (int k = 0; k < 5; k++)
          {
            // HACK HACK HACK - how is this done formally???
            for (int j = 0; j < currentWords[k + 1].size(); j++)
              if (currentWords[k + 1][j] == 'D')
                currentWords[k + 1][j] = 'E';
            double ci = atof(currentWords[k + 1].c_str());
            if (std::abs(ci) > ci_threshold)
            {
              coeff2confg[indx[k]] = cnt++;
              CIcoeff.push_back(ci);
              //cout<<"ind,cnt,c: " <<indx[k] <<"  " <<cnt-1 <<"  " <<CIcoeff.back() << std::endl;
            }
          }
        }
        if (nextra > 0)
        {
          getwords(currentWords, ofile);
          if (currentWords.size() != nextra)
          {
            std::cerr << "Error reading CI configurations last line \n";
            abort();
          }
          for (int k = 0; k < nextra; k++)
            indx[k] = atoi(currentWords[k].c_str());
          getwords(currentWords, ofile);
          if (currentWords.size() != nextra + 1)
          {
            std::cerr << "Error reading CI configurations last line \n";
            abort();
          }
          for (int k = 0; k < nextra; k++)
          {
            double ci = atof(currentWords[k + 1].c_str());
            if (std::abs(ci) > ci_threshold)
            {
              coeff2confg[indx[k]] = cnt++;
              CIcoeff.push_back(ci);
            }
          }
        }
      }
      std::cout << "Found " << CIcoeff.size() << " coeffficients after truncation. \n";
      if (statesType == 0)
      {
        ofile.close();
        ofile.open(outputFile.c_str());
        ofile.seekg(beginpos); //rewind it
                               // this might not work, look for better entry point later
        search(ofile, "Truncation Level=");
        //cout<<"found Truncation Level=" << std::endl;
        getwords(currentWords, ofile);
        while (!ofile.eof() &&
               (currentWords[0] != "no." || currentWords[1] != "active" || currentWords[2] != "orbitals"))
        {
          //        std::cout <<"1. " <<currentWords[0] << std::endl;
          getwords(currentWords, ofile);
        }
        ci_nstates = atoi(currentWords[4].c_str());
        getwords(currentWords, ofile);
        // can choose specific irreps if I want...
        while (currentWords[0] != "Configuration" || currentWords[2] != "Symmetry")
        {
          //        std::cout <<"2. " <<currentWords[0] << std::endl;
          getwords(currentWords, ofile);
        }
        CIbeta.resize(CIcoeff.size());
        CIalpha.resize(CIcoeff.size());
        bool done = false;
        // can choose specific irreps if I want...
        while (currentWords[0] == "Configuration" && currentWords[2] == "Symmetry")
        {
          int pos                         = atoi(currentWords[1].c_str());
          std::map<int, int>::iterator it = coeff2confg.find(pos);
          //cout<<"3. configuration: " <<currentWords[1].c_str() << std::endl;
          if (it != coeff2confg.end())
          {
            std::string alp(currentWords[4]);
            std::string beta(currentWords[4]);
            if (alp.size() != ci_nstates)
            {
              std::cerr << "Problem with ci string. \n";
              abort();
            }
            for (int i = 0; i < alp.size(); i++)
            {
              if (alp[i] == 'a')
                alp[i] = '1';
              if (alp[i] == 'b')
                alp[i] = '0';
              if (beta[i] == 'a')
                beta[i] = '0';
              if (beta[i] == 'b')
                beta[i] = '1';
            }
            if (done)
            {
              // check number of alpha/beta electrons
              int n1 = 0;
              for (int i = 0; i < alp.size(); i++)
                if (alp[i] == '1')
                  n1++;
              if (n1 != ci_nea)
              {
                std::cerr << "Problems with alpha ci string: " << std::endl
                          << alp << std::endl
                          << currentWords[3] << std::endl;
                abort();
              }
              n1 = 0;
              for (int i = 0; i < beta.size(); i++)
                if (beta[i] == '1')
                  n1++;
              if (n1 != ci_neb)
              {
                std::cerr << "Problems with beta ci string: " << std::endl
                          << beta << std::endl
                          << currentWords[3] << std::endl;
                abort();
              }
            }
            else
            {
              // count number of alpha/beta electrons
              ci_nea = 0;
              for (int i = 0; i < alp.size(); i++)
                if (alp[i] == '1')
                  ci_nea++;
              ci_neb = 0;
              for (int i = 0; i < beta.size(); i++)
                if (beta[i] == '1')
                  ci_neb++;
              ci_nca = nup - ci_nea;
              ci_ncb = ndown - ci_neb;
            }
            CIalpha[it->second] = alp;
            CIbeta[it->second]  = beta;
            //cout<<"alpha: " <<alp <<"  -   "  <<CIalpha[it->second] << std::endl;
          }
          getwords(currentWords, ofile);
        }
        //cout.flush();
      }
      else
      {
        // coefficient list obtained with iop(4/21=110)
        ofile.close();
        ofile.open(outputFile.c_str());
        ofile.seekg(beginpos); //rewind it
        bool first_alpha = true;
        bool first_beta  = true;
        std::string aline;
        getline(ofile, aline, '\n');
        CIbeta.resize(CIcoeff.size());
        CIalpha.resize(CIcoeff.size());
        for (int nst = 0; nst < numCI; nst++)
        {
          getwords(currentWords, ofile); // state number
          int pos                         = atoi(currentWords[0].c_str());
          std::map<int, int>::iterator it = coeff2confg.find(pos);
          if (it != coeff2confg.end())
          {
            getwords(currentWords, ofile); // state number
            if (first_alpha)
            {
              first_alpha = false;
              ci_nea      = currentWords.size();
              ci_nca      = nup - ci_nea;
              std::cout << "nca, nea, nstates: " << ci_nca << "  " << ci_nea << "  " << ci_nstates << std::endl;
            }
            else
            {
              if (currentWords.size() != ci_nea)
              {
                std::cerr << "Problems with alpha string: " << pos << std::endl;
                abort();
              }
            }
            std::string alp(ci_nstates, '0');
            for (int i = 0; i < currentWords.size(); i++)
            {
              //              std::cout <<"i, alpOcc: " <<i <<"  " <<atoi(currentWords[i].c_str())-1 << std::endl; std::cout.flush();
              alp[atoi(currentWords[i].c_str()) - 1] = '1';
            }
            getwords(currentWords, ofile); // state number
            if (first_beta)
            {
              first_beta = false;
              ci_neb     = currentWords.size();
              ci_ncb     = ndown - ci_neb;
              std::cout << "ncb, neb, nstates: " << ci_ncb << "  " << ci_neb << "  " << ci_nstates << std::endl;
            }
            else
            {
              if (currentWords.size() != ci_neb)
              {
                std::cerr << "Problems with beta string: " << pos << std::endl;
                abort();
              }
            }
            std::string beta(ci_nstates, '0');
            for (int i = 0; i < currentWords.size(); i++)
            {
              //              std::cout <<"i, alpOcc: " <<i <<"  " <<atoi(currentWords[i].c_str())-1 << std::endl; std::cout.flush();
              beta[atoi(currentWords[i].c_str()) - 1] = '1';
            }
            CIalpha[it->second] = alp;
            CIbeta[it->second]  = beta;
            //cout<<"alpha: " <<alp << std::endl <<"beta: " <<beta << std::endl;
            std::string aline1;
            getline(ofile, aline1, '\n');
          }
          else
          {
            getwords(currentWords, ofile);
            getwords(currentWords, ofile);
            std::string aline1;
            getline(ofile, aline1, '\n');
          }
        }
      }
      ofile.close();
    }
    else
    {
      std::cerr << "Could not find CI coefficients in gaussian output file. \n";
      abort();
    }
    std::cout << " size of CIalpha,CIbeta: " << CIalpha.size() << "  " << CIbeta.size() << std::endl;
  }
}

void GaussianFCHKParser::getGeometry(std::istream& is)
{
  //atomic numbers
  std::vector<int> atomic_number(NumberOfAtoms);
  std::vector<double> q(NumberOfAtoms);
  //read atomic numbers
  search(is, "Atomic numbers"); //search for Atomic numbers
  getValues(is, atomic_number.begin(), atomic_number.end());
  std::streampos pivot = is.tellg();
  //read effective nuclear charges
  search(is, "Nuclear"); //search for Nuclear
  getValues(is, q.begin(), q.end());
  is.seekg(pivot); //rewind it
  search(is, "coordinates");
  std::vector<double> pos(NumberOfAtoms * OHMMS_DIM);
  getValues(is, pos.begin(), pos.end());
  SpeciesSet& species(IonSystem.getSpeciesSet());
  for (int i = 0, ii = 0; i < NumberOfAtoms; i++)
  {
    IonSystem.R[i][0]                     = pos[ii++];
    IonSystem.R[i][1]                     = pos[ii++];
    IonSystem.R[i][2]                     = pos[ii++];
    GroupName[i]                          = IonName[atomic_number[i]];
    int speciesID                         = species.addSpecies(GroupName[i]);
    IonSystem.GroupID[i]                  = speciesID;
    species(AtomicNumberIndex, speciesID) = atomic_number[i];
    species(IonChargeIndex, speciesID)    = q[i];
  }
}

void GaussianFCHKParser::getGaussianCenters(std::istream& is)
{
  //map between Gaussian to Casino Shell notation
  std::map<int, int> gsMap;
  gsMap[0]  = 1;  //s
  gsMap[-1] = 2;  //sp
  gsMap[1]  = 3;  //p
  gsMap[-2] = 4;  //d
  gsMap[-3] = 5;  //f
  gsMap[-4] = 6;  //g
  gsMap[-5] = 7;  //l=5 h
  gsMap[-6] = 8;  //l=6 h1??
  gsMap[-7] = 9;  //l=7 h2??
  gsMap[-8] = 10; //l=8 h3??
  std::vector<int> n(gShell.size()), dn(NumberOfAtoms, 0);
  bool SPshell(false);
  getValues(is, n.begin(), n.end());
  for (int i = 0; i < n.size(); i++)
  {
    gShell[i] = gsMap[n[i]];
    if (n[i] == -1)
      SPshell = true;
  }
  search(is, "Number");
  getValues(is, gNumber.begin(), gNumber.end());
  search(is, "Shell");
  getValues(is, n.begin(), n.end());
  for (int i = 0; i < n.size(); i++)
    dn[n[i] - 1] += 1;
  gBound[0] = 0;
  for (int i = 0; i < NumberOfAtoms; i++)
  {
    gBound[i + 1] = gBound[i] + dn[i];
  }
  search(is, "Primitive");
  getValues(is, gExp.begin(), gExp.end());
  search(is, "Contraction");
  getValues(is, gC0.begin(), gC0.end());
  if (SPshell)
  {
    search(is, "P(S=P)");
    getValues(is, gC1.begin(), gC1.end());
  }
}