lammps/lib/colvars/colvarbias_opes.h

#ifndef COLVARBIAS_OPES_H
#define COLVARBIAS_OPES_H

// This code is mainly adapted from the PLUMED opes module, which uses the
// LGPLv3 license as shown below:
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Copyright (c) 2020-2021 of Michele Invernizzi.

   This file is part of the OPES plumed module.

   The OPES plumed module is free software: you can redistribute it and/or modify
   it under the terms of the GNU Lesser General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.

   The OPES plumed module is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU Lesser General Public License for more details.

   You should have received a copy of the GNU Lesser General Public License
   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */

#include "colvarbias.h"

#include <vector>
#include <memory>

// OPES_METAD implementation: swiped from OPESmetad.cpp of PLUMED
class colvarbias_opes: public colvarbias {
public:
  /// The Gaussian kernel data structure
  struct kernel {
    cvm::real m_height;
    std::vector<cvm::real> m_center;
    std::vector<cvm::real> m_sigma;
    kernel() {}
    kernel(cvm::real h, const std::vector<cvm::real>& c,
           const std::vector<cvm::real>& s):
      m_height(h), m_center(c), m_sigma(s) {}
  };
  /// Communication between different replicas
  enum Communication {
    /// One replica (default)
    single_replica,
    /// Hills added concurrently by several replicas
    multiple_replicas
  };
  /// Constructor
  colvarbias_opes(char const *key);
  /// Initializer
  int init(std::string const &conf) override;
  /// Per-timestep update
  int update() override;
  /// Save the state to a text file for restarting
  std::ostream &write_state_data(std::ostream &os) override;
  /// Read the state from a text file for restarting
  std::istream &read_state_data(std::istream &is) override;
  /// Save the state to a binary file for restarting
  cvm::memory_stream &write_state_data(cvm::memory_stream &os) override;
  /// Read the state from a binary file for restarting
  cvm::memory_stream &read_state_data(cvm::memory_stream &is) override;
  /// Write to files at restart steps
  int write_output_files() override;
private:
  int update_opes();
  int calculate_opes();
  void save_state();
  cvm::real getProbAndDerivatives(const std::vector<cvm::real>& cv, std::vector<cvm::real>& der_prob) const;
  cvm::real evaluateKernel(const kernel& G, const std::vector<cvm::real>& x) const;
  cvm::real evaluateKernel(const kernel& G, const std::vector<cvm::real>& x, std::vector<cvm::real>& accumulated_derivative, std::vector<cvm::real>& dist) const;
  void addKernel(const double height, const std::vector<cvm::real>& center, const std::vector<cvm::real>& sigma, const double logweight);
  void addKernel(const double height, const std::vector<cvm::real>& center, const std::vector<cvm::real>& sigma);
  size_t getMergeableKernel(const std::vector<cvm::real>& giver_center, const size_t giver_k) const;
  void mergeKernels(kernel& k1, const kernel& k2) const;
  void updateNlist(const std::vector<cvm::real>& center);
  struct traj_line {
    double rct;
    double zed;
    double neff;
    double work;
    size_t nker;
    size_t nlker;
    size_t nlsteps;
  };
  void writeTrajBuffer();
  void showInfo() const;
  template <typename OST> OST &write_state_data_template_(OST &os) const;
  template <typename IST> IST &read_state_data_template_(IST &os);
  std::string const traj_file_name(const std::string& suffix) const;
  int collectSampleToPMFGrid();
  int computePMF();
  int writePMF(const std::unique_ptr<colvar_grid_scalar>& pmf_grid, const std::string &filename, bool keep_open);
private:
  cvm::real m_kbt;
  cvm::real m_barrier;
  cvm::real m_biasfactor;
  cvm::real m_bias_prefactor;
  cvm::real m_temperature;
  cvm::step_number m_pace;
  cvm::step_number m_adaptive_sigma_stride;
  cvm::step_number m_adaptive_counter;
  unsigned long long m_counter;
  cvm::real m_compression_threshold;
  cvm::real m_compression_threshold2;
  bool m_adaptive_sigma;
  bool m_fixed_sigma;
  bool m_no_zed;
  // bool m_restart;
  bool m_nlist;
  bool m_recursive_merge;
  std::vector<cvm::real> m_nlist_param;
  std::vector<cvm::real> m_sigma0;
  std::vector<cvm::real> m_sigma_min;
  cvm::real m_epsilon;
  cvm::real m_sum_weights;
  cvm::real m_sum_weights2;
  cvm::real m_cutoff;
  cvm::real m_cutoff2;
  cvm::real m_zed;
  cvm::real m_old_kdenorm;
  cvm::real m_kdenorm;
  cvm::real m_val_at_cutoff;
  cvm::real m_rct;
  cvm::real m_neff;
  std::vector<kernel> m_kernels;
  std::vector<kernel> m_delta_kernels;
  std::vector<cvm::real> m_av_cv;
  std::vector<cvm::real> m_av_M2;
  std::ostringstream m_kernels_output;
  std::vector<cvm::real> m_nlist_center;
  std::vector<size_t> m_nlist_index;
  std::vector<cvm::real> m_nlist_dev2;
  size_t m_nlist_steps;
  bool m_nlist_update;
  bool m_nlist_pace_reset;
  size_t m_nker;
  bool m_calc_work;
  cvm::real m_work;
  /// Communication between different replicas
  Communication comm;
  /// \brief Identifier for this replica
  std::string            replica_id;
  size_t m_num_walkers;
  size_t shared_freq;
  size_t m_num_threads;
  size_t m_nlker;
  // size_t m_state_stride;
  // std::unordered_map<std::string, std::string> m_kernel_output_components;
  std::string m_kernels_output_headers;
  cvm::step_number m_traj_output_frequency;
  traj_line m_traj_line;
  std::ostringstream m_traj_oss;
  bool m_is_first_step;
  std::vector<cvm::real> m_cv;
  // For saving states
  decltype(m_zed) m_saved_zed;
  decltype(m_sum_weights) m_saved_sum_weights;
  decltype(m_sum_weights2) m_saved_sum_weights2;
  decltype(m_kernels) m_saved_kernels;
  // PMF grid from reweighting
  bool m_pmf_grid_on;
  std::vector<colvar*> m_pmf_cvs;
  std::string grid_conf;
  std::shared_ptr<colvar_grid_scalar> m_reweight_grid;
  std::unique_ptr<colvar_grid_scalar> m_pmf_grid;
  cvm::step_number m_pmf_hist_freq;
  bool m_pmf_shared; // shared PMF among replicas
  std::unique_ptr<colvar_grid_scalar> m_global_reweight_grid;
  std::unique_ptr<colvar_grid_scalar> m_global_pmf_grid;
  bool m_explore;
  bool m_inf_biasfactor;
};

#endif // COLVARBIAS_OPES_H