ReplicaDynamicsJob.h

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/*
** This file is part of eOn.
**
** SPDX-License-Identifier: BSD-3-Clause
**
** Copyright (c) 2010--present, eOn Development Team
** All rights reserved.
**
** Repo:
** https://github.com/TheochemUI/eOn
*/
#pragma once
#include "EonLogger.h"
#include "Job.h"
#include "Matter.h"
 
#include <memory>
#include <string>
#include <vector>
 
namespace eonc {

class ReplicaDynamicsJob : public Job {
public:
  using Job::Job;
  ~ReplicaDynamicsJob() override = default;
  std::vector<std::string> run() override;
  std::shared_ptr<Matter> runFromMatter(std::shared_ptr<Matter> initial);
 
protected:
  // -- Shared matter objects --
  std::shared_ptr<Matter> current;
  std::shared_ptr<Matter> reactant;
  std::shared_ptr<Matter> saddle;
  std::shared_ptr<Matter> product;
  std::shared_ptr<Matter> finalState;    // state at transition detection
  std::shared_ptr<Matter> finalStateTmp; // candidate before confirmation
 
  // -- Flags --
  bool metaStateFlag{false};
  bool newStateFlag{false};
 
  // -- Force call counters --
  size_t minimizeFCalls{0};
  size_t mdFCalls{0};
  size_t dephaseFCalls{0};
  size_t refineFCalls{0};
 
  // -- Dynamics state --
  long transitionStep{0};
  double time{0.0};
  double minCorrectedTime{1.0e200};
  double transitionTime{0.0};
 
  std::vector<std::string> returnFiles;
  eonc::log::Scoped log;
 
  // -- Shared methods --

  bool checkState(Matter *current, Matter *reactant);

  long refine(const std::vector<std::shared_ptr<Matter>> &buff,
              Matter *reactant);

  void dephase();

  struct PrdClock {
    long state_check{1};
    long record{1};
    long buffer{1};
  };
  PrdClock prdClock() const;

  void saveData(int status);
 
  // -- Template method hooks --

  virtual void initExtra() {}

  virtual int dynamics() = 0;

  virtual void reportResults() {}
};
 
} // namespace eonc