rdf_calculator.h

Go to the documentation of this file.

/*
 * Copyright 2009-2021 The VOTCA Development Team (http://www.votca.org)
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
 
#ifndef VOTCA_CSG_RDF_CALCULATOR_H
#define VOTCA_CSG_RDF_CALCULATOR_H
 
// Standard includes
#include <cmath>
#include <memory>
 
// Third party includes
#include <boost/numeric/ublas/io.hpp>
#include <boost/numeric/ublas/matrix.hpp>
#include <boost/numeric/ublas/matrix_proxy.hpp>
#include <boost/numeric/ublas/symmetric.hpp>
#include <boost/numeric/ublas/vector.hpp>
#include <boost/numeric/ublas/vector_proxy.hpp>
 
// VOTCA includes
#include <votca/tools/average.h>
#include <votca/tools/histogramnew.h>
#include <votca/tools/property.h>
 
// Local VOTCA includes
#include <votca/csg/csgapplication.h>
 
namespace votca {
namespace csg {
using namespace votca::tools;
 
class RDFCalculator {
 public:
  RDFCalculator();
  ~RDFCalculator();
 
  void Initialize(void);
 
  void LoadOptions(const std::string &file);
 
  void BeginEvaluate(Topology *top, Topology *top_atom);
 
  void EndEvaluate();
 
  void WriteEvery(Index write_every) { write_every_ = write_every; }
  void DoBlocks(bool do_blocks) { do_blocks_ = do_blocks; }
  void DoVolumeCorrection(bool do_vol_corr) { do_vol_corr_ = do_vol_corr; }
  void SetSubvolRadius(double r) { subvol_rad_ = r; }
  double AnalyticVolumeCorrection(double t) {
 
    std::cout << "DBG " << t << " "
              << 1.0 / 24.0 *
                     (16.0 * t * t - 12.0 * t * t * t + t * t * t * t * t)
              << std::endl;
    return 1.0 / 24.0 * (16.0 * t * t - 12.0 * t * t * t + t * t * t * t * t);
  }
 
 protected:
  Average<double> avg_vol_;
 
  using group_matrix = Eigen::MatrixXd;
  using pair_matrix = Eigen::Block<group_matrix>;
 
  struct interaction_t {
    Index index_;
    Property *p_;
    HistogramNew average_;
    double min_, max_, step_;
    double norm_;
    bool is_bonded_;
    Average<double> avg_beadlist_1_count_;
    Average<double> avg_beadlist_2_count_;
  };
 
  // a pair of interactions which are correlated
  struct pair_t {
    interaction_t *i1_;
    interaction_t *i2_;
    Index offset_i_, offset_j_;
    pair_matrix corr_;
    pair_t(interaction_t *i1, interaction_t *i2, Index offset_i, Index offset_j,
           const pair_matrix &corr);
  };
 
  struct group_t {
    std::list<interaction_t *> interactions_;
    group_matrix corr_;
    std::vector<pair_t> pairs_;
  };
 
  Property options_;
  // we want to write out every so many frames
  Index write_every_;
  // we want do do block averaging -> clear averagings every write out
  bool do_blocks_;
 
  // number of frames we processed
  Index nframes_;
  Index nblock_;
  double subvol_rad_;
  Eigen::Vector3d boxc_;  // center of box
  bool do_vol_corr_;
 
  std::vector<Property *> bonded_;
  std::vector<Property *> nonbonded_;
 
  std::map<std::string, std::unique_ptr<interaction_t>> interactions_;
  std::map<std::string, std::unique_ptr<group_t>> groups_;
 
  interaction_t *AddInteraction(Property *p);
 
  group_t *getGroup(const std::string &name);
 
  void WriteDist(const std::string &suffix = "");
 
  void ClearAverages();
 
  class Worker : public CsgApplication::Worker {
   public:
    std::vector<HistogramNew> current_hists_;
    RDFCalculator *rdfcalculator_;
    double cur_vol_;
    double cur_beadlist_1_count_;  // need to normalize to avg density for
                                   // subvol
    double cur_beadlist_2_count_;
 
    void EvalConfiguration(Topology *top, Topology *top_atom) override;
    void DoNonbonded(Topology *top);
    void DoBonded(Topology *top);
  };
  void DoCorrelations(RDFCalculator::Worker *worker);
 
  bool processed_some_frames_;
 
 public:
  std::unique_ptr<CsgApplication::Worker> ForkWorker();
  void MergeWorker(CsgApplication::Worker *worker_);
};
 
inline RDFCalculator::pair_t::pair_t(RDFCalculator::interaction_t *i1,
                                     RDFCalculator::interaction_t *i2,
                                     Index offset_i, Index offset_j,
                                     const pair_matrix &corr)
    : i1_(i1), i2_(i2), offset_i_(offset_i), offset_j_(offset_j), corr_(corr) {}
 
}  // namespace csg
}  // namespace votca
 
#endif  // VOTCA_CSG_RDF_CALCULATOR_H