csg_stat_imc.h

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/*
 * 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_CSG_STAT_IMC_H
#define VOTCA_CSG_CSG_STAT_IMC_H
 
// 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 {
class Imc {
 public:
  void Initialize(void);
 
  void LoadOptions(const std::string &file);
 
  void BeginEvaluate(Topology *top, Topology *top_atom);
 
  void EndEvaluate();
 
  void BlockLength(votca::Index length) { block_length_ = length; }
  void DoImc(bool do_imc) { do_imc_ = do_imc; }
  void IncludeIntra(bool include_intra) { include_intra_ = include_intra; }
  void Extension(std::string ext) { extension_ = ext; }
 
 protected:
  tools::Average<double> avg_vol_;
 
  using group_matrix = Eigen::MatrixXd;
  using pair_matrix = Eigen::Block<group_matrix>;
 
  struct interaction_t {
    votca::Index index_;
    tools::Property *p_;
    tools::HistogramNew average_;
    tools::HistogramNew average_force_;
    double min_, max_, step_;
    double norm_;
    double cut_;
    bool is_bonded_;
    bool threebody_;
    bool force_;
  };
 
  // a pair of interactions which are correlated
  struct pair_t {
    interaction_t *i1_;
    interaction_t *i2_;
    votca::Index offset_i_, offset_j_;
    pair_matrix corr_;
    pair_t(interaction_t *i1, interaction_t *i2, votca::Index offset_i,
           votca::Index offset_j, const pair_matrix &corr);
  };
 
  struct group_t {
    std::vector<interaction_t *> interactions_;
    group_matrix corr_;
    std::vector<pair_t> pairs_;
  };
 
  tools::Property options_;
  // length of the block to write out and averages are clear after every write
  votca::Index block_length_ = 0;
  // calculate the inverse monte carlos parameters (cross correlations)
  bool do_imc_ = false;
  // include the intramolecular neighbors
  bool include_intra_ = false;
 
  // file extension for the distributions
  std::string extension_;
 
  // number of frames we processed
  votca::Index nframes_;
  votca::Index nblock_;
 
  std::vector<tools::Property *> bonded_;
  std::vector<tools::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(tools::Property *p, bool is_bonded);
 
  group_t *getGroup(const std::string &name);
 
  void InitializeGroups();
 
  void WriteDist(const std::string &suffix = "");
  void WriteIMCData(const std::string &suffix = "");
  void WriteIMCBlock(const std::string &suffix);
 
  void CalcDeltaS(interaction_t *interaction,
                  Eigen::VectorBlock<Eigen::VectorXd> &dS);
 
  void ClearAverages();
 
  class Worker : public CsgApplication::Worker {
   public:
    std::vector<tools::HistogramNew> current_hists_;
    std::vector<tools::HistogramNew> current_hists_force_;
    Imc *imc_;
    double cur_vol_;
 
    void EvalConfiguration(Topology *top, Topology *top_atom) override;
    void DoNonbonded(Topology *top);
    void DoBonded(Topology *top);
  };
  void DoCorrelations(Imc::Worker *worker);
 
  bool processed_some_frames_ = false;
 
 public:
  std::unique_ptr<CsgApplication::Worker> ForkWorker();
  void MergeWorker(CsgApplication::Worker *worker_);
};
 
inline Imc::pair_t::pair_t(Imc::interaction_t *i1, Imc::interaction_t *i2,
                           votca::Index offset_i, votca::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_CSG_STAT_IMC_H