colvarmodule.h

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#ifndef COLVARMODULE_H
#define COLVARMODULE_H

#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2013-01-30"
#endif

#ifndef COLVARS_DEBUG
#define COLVARS_DEBUG false
#endif



#include <iostream>
#include <iomanip>
#include <string>
#include <sstream>
#include <fstream>
#include <cmath>
#include <vector>
#include <list>


class colvarparse;
class colvar;
class colvarbias;
class colvarproxy;


class colvarmodule {

private:

  colvarmodule();

public:

  friend class colvarproxy;
  
  typedef  double    real;
  typedef  int       residue_id;

  class rvector;
  template <class T,
            size_t const length> class vector1d;
  template <class T,
            size_t const outer_length,
            size_t const inner_length> class matrix2d;
  class quaternion;
  class rotation;

  typedef rvector atom_pos;

  class rmatrix;

  // allow these classes to access protected data
  class atom;
  class atom_group;
  friend class atom;
  friend class atom_group;
  typedef std::vector<atom>::iterator       atom_iter;
  typedef std::vector<atom>::const_iterator atom_const_iter;

  static size_t it;
  static size_t it_restart;

  static inline size_t step_relative()
  {
    return it - it_restart;
  }

  static inline size_t step_absolute()
  {
    return it;
  }

  bool it_restart_from_state_file;

  static real debug_gradients_step_size;

  static std::string output_prefix;

  static std::string input_prefix;

  static std::string restart_in_name;


  static std::vector<colvar *>     colvars;

  /* TODO: implement named CVCs
  static std::vector<cvc *>     cvcs;
  inline void register_cvc (cvc *p) {
    cvcs.push_back(p);
  }
  */

  static std::vector<colvarbias *> biases;
  static size_t n_abf_biases;
  static size_t n_meta_biases;
  static size_t n_harm_biases;
  static size_t n_histo_biases;
   
  static inline bool debug()
  {
    return COLVARS_DEBUG;
  }


  colvarmodule (char const *config_name, 
                colvarproxy *proxy_in);
  ~colvarmodule();

  void init_colvars (std::string const &conf);

  void init_biases (std::string const &conf);

  void change_configuration (std::string const &bias_name, std::string const &conf);

  real energy_difference (std::string const &bias_name, std::string const &conf);

  void calc();
  std::istream & read_restart (std::istream &is);
  std::ostream & write_restart (std::ostream &os);
  void write_output_files();
  static void backup_file (char const *filename);

  void analyze();
  bool read_traj (char const *traj_filename,
                  size_t      traj_read_begin,
                  size_t      traj_read_end);
 
  static colvar * colvar_p (std::string const &name);

  template<typename T> static std::string to_str (T const &x, 
                                                  size_t const &width = 0,
                                                  size_t const &prec = 0);
  template<typename T> static std::string to_str (std::vector<T> const &x, 
                                                  size_t const &width = 0,
                                                  size_t const &prec = 0);

  static inline std::string wrap_string (std::string const &s,
                                         size_t const &nchars)
  {
    if (!s.size())
      return std::string (nchars, ' ');
    else
      return ( (s.size() <= size_t (nchars)) ?
               (s+std::string (nchars-s.size(), ' ')) :
               (std::string (s, 0, nchars)) );
  }

  static size_t const it_width;
  static size_t const cv_prec;
  static size_t const cv_width;
  static size_t const en_prec;
  static size_t const en_width;
  static std::string const line_marker;


  // proxy functions

  static real unit_angstrom();

  static real boltzmann();

  static real temperature();

  static real dt();
  
  static void request_system_force();
  
  static void log (std::string const &message);

  static void fatal_error (std::string const &message);

  static void exit (std::string const &message);


  static rvector position_distance (atom_pos const &pos1,
                                    atom_pos const &pos2);


  static real position_dist2 (atom_pos const &pos1,
                              atom_pos const &pos2);

  static void select_closest_image (atom_pos &pos,
                                    atom_pos const &ref_pos);

  static void select_closest_images (std::vector<atom_pos> &pos,
                                     atom_pos const &ref_pos);


  static void load_atoms (char const *filename,
                          std::vector<atom> &atoms,
                          std::string const &pdb_field,
                          double const pdb_field_value = 0.0);

  static void load_coords (char const *filename,
                           std::vector<atom_pos> &pos,
                           const std::vector<int> &indices,
                           std::string const &pdb_field,
                           double const pdb_field_value = 0.0);


  static size_t cv_traj_freq;

  static bool   b_analysis;

  static size_t restart_out_freq;
  std::string   restart_out_name;

  static real rand_gaussian (void);
protected:

  std::ifstream config_s;

  colvarparse *parse;

  std::string   cv_traj_name;

  std::ofstream cv_traj_os;

  bool          cv_traj_append;

  std::ofstream restart_out_os;

  static colvarproxy *proxy;

  static size_t depth;

public:

  static void increase_depth();

  static void decrease_depth();
};


typedef colvarmodule cvm;


#include "colvartypes.h"


std::ostream & operator << (std::ostream &os, cvm::rvector const &v);
std::istream & operator >> (std::istream &is, cvm::rvector &v);


template<typename T> std::string cvm::to_str (T const &x, 
                                              size_t const &width,
                                              size_t const &prec) {
  std::ostringstream os;
  if (width) os.width (width);
  if (prec) {
    os.setf (std::ios::scientific, std::ios::floatfield);
    os.precision (prec);
  }
  os << x;
  return os.str();
}

template<typename T> std::string cvm::to_str (std::vector<T> const &x, 
                                              size_t const &width,
                                              size_t const &prec) {
  if (!x.size()) return std::string ("");
  std::ostringstream os;
  if (prec) {
    os.setf (std::ios::scientific, std::ios::floatfield);
  }
  os << "{ ";
  if (width) os.width (width);
  if (prec) os.precision (prec);
  os << x[0];
  for (size_t i = 1; i < x.size(); i++) {
    os << ", ";
    if (width) os.width (width);
    if (prec) os.precision (prec);
    os << x[i];
  }
  os << " }";
  return os.str();
}


#include "colvarproxy.h"


inline cvm::real cvm::unit_angstrom()
{
  return proxy->unit_angstrom();
}

inline cvm::real cvm::boltzmann()
{
  return proxy->boltzmann();
}

inline cvm::real cvm::temperature()
{
  return proxy->temperature();
}

inline cvm::real cvm::dt()
{
  return proxy->dt();
}

inline void cvm::request_system_force()
{
  proxy->request_system_force (true);
}
  
inline void cvm::select_closest_image (atom_pos &pos,
                                       atom_pos const &ref_pos)
{
  proxy->select_closest_image (pos, ref_pos);
}

inline void cvm::select_closest_images (std::vector<atom_pos> &pos,
                                        atom_pos const &ref_pos)
{
  proxy->select_closest_images (pos, ref_pos);
}

inline cvm::rvector cvm::position_distance (atom_pos const &pos1,
                                            atom_pos const &pos2)
{
  return proxy->position_distance (pos1, pos2);
}

inline cvm::real cvm::position_dist2 (cvm::atom_pos const &pos1,
                                      cvm::atom_pos const &pos2)
{
  return proxy->position_dist2 (pos1, pos2);
}

inline void cvm::load_atoms (char const *file_name,
                             std::vector<cvm::atom> &atoms,
                             std::string const &pdb_field,
                             double const pdb_field_value)
{
  proxy->load_atoms (file_name, atoms, pdb_field, pdb_field_value);
}

inline void cvm::load_coords (char const *file_name,
                              std::vector<cvm::atom_pos> &pos,
                              const std::vector<int> &indices,
                              std::string const &pdb_field,
                              double const pdb_field_value)
{
  proxy->load_coords (file_name, pos, indices, pdb_field, pdb_field_value);
}

inline void cvm::backup_file (char const *filename)
{
  proxy->backup_file (filename);
}

inline cvm::real cvm::rand_gaussian (void)
{
  return proxy->rand_gaussian();
}

#endif


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