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colvar.h

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// -*- c++ -*-

// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.

#ifndef COLVAR_H
#define COLVAR_H

#include <iostream>

#if (__cplusplus >= 201103L)
#include <map>
#include <functional>
#endif

#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvardeps.h"

#ifdef LEPTON
#include "Lepton.h" // for runtime custom expressions
#endif


class colvar : public colvarparse, public colvardeps {

public:

  std::string name;

  colvarvalue const & value() const;

  colvarvalue const & actual_value() const;

  colvarvalue const & run_ave() const;

  cvm::real const & force_constant() const;

  colvarvalue const & velocity() const;

  colvarvalue const & total_force() const;

  cvm::real width;

  static std::vector<feature *> cv_features;

  virtual const std::vector<feature *> &features() const
  {
    return cv_features;
  }
  virtual std::vector<feature *> &modify_features()
  {
    return cv_features;
  }
  static void delete_features() {
    for (size_t i=0; i < cv_features.size(); i++) {
      delete cv_features[i];
    }
    cv_features.clear();
  }

  void do_feature_side_effects(int id);

  std::vector<colvarbias *> biases;

protected:


  /*
    extended:
    H = H_{0} + \sum_{i} 1/2*\lambda*(S_i(x(t))-s_i(t))^2 \\
    + \sum_{i} 1/2*m_i*(ds_i(t)/dt)^2 \\
    + \sum_{t'<t} W * exp(-1/2*\sum_{i} (s_i(t')-s_i(t))^2/(\delta{}s_i)^2) \\
    + \sum_{w} (\sum_{i}c_{w,i}s_i(t) - D_w)^M/(\Sigma_w)^M

    normal:
    H = H_{0} + \sum_{t'<t} W * exp(-1/2*\sum_{i} (S_i(x(t'))-S_i(x(t)))^2/(\delta{}S_i)^2) \\
    + \sum_{w} (\sum_{i}c_{w,i}S_i(t) - D_w)^M/(\Sigma_w)^M

    output:
    H = H_{0}   (only output S(x), no forces)

    Here:
    S(x(t)) = x
    s(t)    = x_ext
    DS = Ds = delta
  */


  colvarvalue x;

  // TODO: implement functionality to treat these
  // /// Vector of individual values from CVCs
  // colvarvalue x_cvc;

  // /// Jacobian matrix of individual values from CVCs
  // colvarvalue dx_cvc;

  colvarvalue x_reported;

  colvarvalue v_fdiff;

  inline colvarvalue fdiff_velocity(colvarvalue const &xold,
                                     colvarvalue const &xnew)
  {
    // using the gradient of the square distance to calculate the
    // velocity (non-scalar variables automatically taken into
    // account)
    cvm::real dt = cvm::dt();
    return ( ( (dt > 0.0) ? (1.0/dt) : 1.0 ) *
             0.5 * dist2_lgrad(xnew, xold) );
  }

  colvarvalue v_reported;

  // Options for extended_lagrangian
  colvarvalue x_ext;
  colvarvalue prev_x_ext;
  colvarvalue v_ext;
  colvarvalue prev_v_ext;
  cvm::real ext_mass;
  cvm::real ext_force_k;
  cvm::real ext_gamma;
  cvm::real ext_sigma;

  colvarvalue fr;

  colvarvalue fj;

  colvarvalue ft_reported;

public:


  colvarvalue fb;

  colvarvalue fb_actual;

  colvarvalue f;

  colvarvalue f_old;

  colvarvalue ft;

  cvm::real period;

  cvm::real wrap_center;

  bool expand_boundaries;

  colvarvalue lower_boundary;

  colvarvalue upper_boundary;

  bool periodic_boundaries() const;

  bool periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) const;


  colvar();

  int init(std::string const &conf);

  int init_components(std::string const &conf);

  int init_custom_function(std::string const &conf);

  int init_grid_parameters(std::string const &conf);

  int init_extended_Lagrangian(std::string const &conf);

  int init_output_flags(std::string const &conf);

  virtual int init_dependencies();

private:
  template<typename def_class_name> int init_components_type(std::string const & conf,
                                                             char const *def_desc,
                                                             char const *def_config_key);
#if (__cplusplus >= 201103L)
  int init_components_type_from_global_map(const std::string& conf,
                                           const char* def_config_key);
#endif

public:

  void setup();

  ~colvar();


  int calc();

  int end_of_step();

  int calc_cvcs(int first = 0, size_t num_cvcs = 0);

  int check_cvc_range(int first_cvc, size_t num_cvcs);

  int calc_cvc_values(int first, size_t num_cvcs);
  int calc_cvc_gradients(int first, size_t num_cvcs);
  int calc_cvc_total_force(int first, size_t num_cvcs);
  int calc_cvc_Jacobians(int first, size_t num_cvcs);

  int collect_cvc_data();

  int collect_cvc_values();
  int collect_cvc_gradients();
  int collect_cvc_total_forces();
  int collect_cvc_Jacobians();
  int calc_colvar_properties();

  inline colvarvalue const applied_force() const
  {
    if (is_enabled(f_cv_extended_Lagrangian)) {
      return fr;
    }
    return f;
  }

  void reset_bias_force();

  void add_bias_force(colvarvalue const &force);

  void add_bias_force_actual_value(colvarvalue const &force);

  cvm::real update_forces_energy();

  void update_extended_Lagrangian();

  void communicate_forces();

  int set_cvc_flags(std::vector<bool> const &flags);

  int update_cvc_flags();

  int update_cvc_config(std::vector<std::string> const &confs);

  int cvc_param_exists(std::string const &param_name);

  cvm::real get_cvc_param(std::string const &param_name);

  void const *get_cvc_param_ptr(std::string const &param_name);

  colvarvalue const *get_cvc_param_grad(std::string const &param_name);

  int set_cvc_param(std::string const &param_name, void const *new_value);

protected:

  size_t n_active_cvcs;

  cvm::real active_cvc_square_norm;

  void update_active_cvc_square_norm();

  cvm::step_number prev_timestep;

public:

  inline size_t num_dimensions() const
  {
    return value().size();
  }

  inline size_t num_cvcs() const
  {
    return cvcs.size();
  }

  inline size_t num_active_cvcs() const
  {
    return n_active_cvcs;
  }

  cvm::real dist2(colvarvalue const &x1,
                  colvarvalue const &x2) const;

  colvarvalue dist2_lgrad(colvarvalue const &x1,
                          colvarvalue const &x2) const;

  colvarvalue dist2_rgrad(colvarvalue const &x1,
                          colvarvalue const &x2) const;

  void wrap(colvarvalue &x_unwrapped) const;

  int parse_analysis(std::string const &conf);

  int analyze();

  std::istream & read_traj(std::istream &is);

  std::ostream & write_traj(std::ostream &os);
  std::ostream & write_traj_label(std::ostream &os);

  std::istream & read_state(std::istream &is);
  std::ostream & write_state(std::ostream &os);

  int write_output_files();

protected:

  colvarvalue            x_old;

  colvarvalue            x_restart;

  bool                   after_restart;

  std::list< std::list<colvarvalue> > acf_x_history, acf_v_history;
  std::list< std::list<colvarvalue> >::iterator acf_x_history_p, acf_v_history_p;

  std::list< std::list<colvarvalue> > x_history;
  std::list< std::list<colvarvalue> >::iterator x_history_p;

  std::string            acf_colvar_name;
  size_t                 acf_length;
  size_t                 acf_offset;
  size_t                 acf_stride;
  size_t                 acf_nframes;
  bool                   acf_normalize;
  std::vector<cvm::real> acf;
  std::string            acf_outfile;

  enum acf_type_e {
    acf_notset,
    acf_vel,
    acf_coor,
    acf_p2coor
  };

  acf_type_e             acf_type;

  void calc_vel_acf(std::list<colvarvalue> &v_history,
                    colvarvalue const      &v);

  void calc_coor_acf(std::list<colvarvalue> &x_history,
                     colvarvalue const      &x);

  void calc_p2coor_acf(std::list<colvarvalue> &x_history,
                       colvarvalue const      &x);

  int calc_acf();
  int write_acf(std::ostream &os);

  size_t         runave_length;
  size_t         runave_stride;
  std::string    runave_outfile;
  colvarvalue    runave;
  cvm::real      runave_variance;

  int calc_runave();

  cvm::real kinetic_energy;
  cvm::real potential_energy;

public:

  // collective variable component base class
  class cvc;

  // list of available collective variable components

  // scalar colvar components
  class distance;
  class distance_z;
  class distance_xy;
  class polar_theta;
  class polar_phi;
  class distance_inv;
  class distance_pairs;
  class dipole_magnitude;
  class angle;
  class dipole_angle;
  class dihedral;
  class coordnum;
  class selfcoordnum;
  class groupcoordnum;
  class h_bond;
  class rmsd;
  class orientation_angle;
  class orientation_proj;
  class tilt;
  class spin_angle;
  class gyration;
  class inertia;
  class inertia_z;
  class eigenvector;
  class alpha_dihedrals;
  class alpha_angles;
  class dihedPC;
  class alch_lambda;
  class alch_Flambda;
  class componentDisabled;
  class CartesianBasedPath;
  class gspath;
  class gzpath;
  class linearCombination;
  class CVBasedPath;
  class gspathCV;
  class gzpathCV;
  class aspathCV;
  class azpathCV;
  class euler_phi;
  class euler_psi;
  class euler_theta;
  class neuralNetwork;
  class customColvar;

  // non-scalar components
  class distance_vec;
  class distance_dir;
  class cartesian;
  class orientation;

  // components that do not handle any atoms directly
  class map_total;

#if (__cplusplus >= 201103L)

  static const std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>>& get_global_cvc_map() {
      return global_cvc_map;
  }
#endif

  static bool compare_cvc(const colvar::cvc* const i, const colvar::cvc* const j);

protected:

  std::vector<cvc *> cvcs;

  std::vector<bool> cvc_flags;

  void build_atom_list(void);

  std::string scripted_function;

  std::vector<const colvarvalue *> sorted_cvc_values;

#ifdef LEPTON

  std::vector<Lepton::CompiledExpression *> value_evaluators;

  std::vector<Lepton::CompiledExpression *> gradient_evaluators;

  std::vector<double *> value_eval_var_refs;
  std::vector<double *> grad_eval_var_refs;

  double dev_null;
#endif

#if (__cplusplus >= 201103L)

  static std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> global_cvc_map;
#endif

  std::vector<int> volmap_ids_;

public:

  std::vector<int> atom_ids;

  std::vector<cvm::rvector> atomic_gradients;

  virtual std::vector<std::vector<int> > get_atom_lists();

  std::vector<int> const &get_volmap_ids();

};


inline cvm::real const & colvar::force_constant() const
{
  return ext_force_k;
}


inline colvarvalue const & colvar::value() const
{
  return x_reported;
}


inline colvarvalue const & colvar::actual_value() const
{
  return x;
}


inline colvarvalue const & colvar::run_ave() const
{
  return runave;
}


inline colvarvalue const & colvar::velocity() const
{
  return v_reported;
}


inline colvarvalue const & colvar::total_force() const
{
  return ft_reported;
}


inline void colvar::add_bias_force(colvarvalue const &force)
{
  check_enabled(f_cv_gradient,
                std::string("applying a force to the variable \""+name+"\""));
  if (cvm::debug()) {
    cvm::log("Adding biasing force "+cvm::to_str(force)+" to colvar \""+name+"\".\n");
  }
  fb += force;
}


inline void colvar::add_bias_force_actual_value(colvarvalue const &force)
{
  if (cvm::debug()) {
    cvm::log("Adding biasing force "+cvm::to_str(force)+" to colvar \""+name+"\".\n");
  }
  fb_actual += force;
}


inline void colvar::reset_bias_force() {
  fb.type(value());
  fb.reset();
  fb_actual.type(value());
  fb_actual.reset();
}

#endif

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