ConfigIONovelty.cc

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#include "casm/clex/ConfigIONovelty.hh"
 
#include "casm/casm_io/dataformatter/EigenDataStream.hh"
#include "casm/clex/ConfigIO.hh"
#include "casm/clex/Configuration.hh"
#include "casm/clex/PrimClex.hh"
#include "casm/database/ConfigDatabase.hh"
#include "casm/database/Selection.hh"
 
namespace CASM {
 
namespace ConfigIO {
bool Novelty::init(const Configuration &_tmplt) const {
  m_format.clear();
  m_format.push_back(Corr());
 
  // setup DataStream
  //    -- fills a matrix so that each row corresponds to a configuration
  //       and column corresponds to correlation value
  MatrixXdDataStream mat_wrapper(DataStream::skipfail);
 
  DB::Selection<Configuration> select(_tmplt.primclex().db<Configuration>(),
                                      m_selection);
  mat_wrapper << m_format(select.all().begin(), select.all().end());
 
  m_avg_corr = mat_wrapper.matrix().colwise().sum().transpose() /
               double(mat_wrapper.matrix().cols());
 
  Eigen::MatrixXd tcovar = mat_wrapper.matrix().transpose() *
                               mat_wrapper.matrix() /
                               double(mat_wrapper.matrix().cols()) -
                           m_avg_corr * m_avg_corr.transpose();
 
  m_gram_mat = (double(tcovar.rows()) * tcovar +
                1E-6 * Eigen::MatrixXd::Identity(tcovar.rows(), tcovar.cols()))
                   .inverse();
  return true;
}
 
//****************************************************************************************
bool Novelty::parse_args(const std::string &args) {
  if (m_selection.size()) return false;
  if (args.empty())
    m_selection = "MASTER";
  else
    m_selection = args;
  return true;
}
 
// ****************************************************************************************
 
std::string Novelty::short_header(const Configuration &_tmplt) const {
  return name() + "(" + (m_selection.empty() ? "MASTER" : m_selection) + ")";
}
 
// ****************************************************************************************
/*
    void Novelty::inject(const Configuration &_config, DataStream &_stream,
   Index) const { _stream << _evaluate(_config);
    }
 
    //
   ****************************************************************************************
 
    void Novelty::print(const Configuration &_config, std::ostream &_stream,
   Index) const { _stream.flags(std::ios::showpoint | std::ios::fixed |
   std::ios::right); _stream.precision(8);
 
      _stream << _evaluate(_config);
    }
 
    //
   ****************************************************************************************
 
    jsonParser &Novelty::to_json(const Configuration &_config, jsonParser
   &json)const { json = _evaluate(_config); return json;
    }
*/
 
//****************************************************************************************
 
double Novelty::evaluate(const Configuration &_config) const {
  VectorDataStream<double> tstr;
  tstr << m_format(_config);
  Eigen::Map<const Eigen::VectorXd> corr(tstr.vector().data(),
                                         tstr.vector().size());
  return sqrt(double((corr - m_avg_corr).transpose() * m_gram_mat *
                     (corr - m_avg_corr)));
}
}  // namespace ConfigIO
}  // namespace CASM