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colvarmodule.h

Go to the documentation of this file.

// -*- 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 COLVARMODULE_H
#define COLVARMODULE_H

#include <cmath>

#include "colvars_version.h"

#ifndef COLVARS_DEBUG
#define COLVARS_DEBUG false
#endif










#define COLVARS_OK 0
#define COLVARS_ERROR   1
#define COLVARS_NOT_IMPLEMENTED (1<<1)
#define COLVARS_INPUT_ERROR     (1<<2) // out of bounds or inconsistent input
#define COLVARS_BUG_ERROR       (1<<3) // Inconsistent state indicating bug
#define COLVARS_FILE_ERROR      (1<<4)
#define COLVARS_MEMORY_ERROR    (1<<5)
#define COLVARS_NO_SUCH_FRAME   (1<<6) // Cannot load the requested frame

#include <sstream>
#include <string>
#include <vector>
#include <list>
#include <iosfwd>

class colvarparse;
class colvar;
class colvarbias;
class colvarproxy;
class colvarscript;
class colvarvalue;


class colvarmodule {

private:

  colvarmodule();

  int version_int;

public:

  std::string version() const
  {
    return std::string(COLVARS_VERSION);
  }

  int version_number() const
  {
    return version_int;
  }

  friend class colvarproxy;
  // TODO colvarscript should be unaware of colvarmodule's internals
  friend class colvarscript;

  typedef long long step_number;

  typedef  double    real;


  // Math functions

  static inline real integer_power(real const &x, int const n)
  {
    // Original code: math_special.h in LAMMPS
    double yy, ww;
    if (x == 0.0) return 0.0;
    int nn = (n > 0) ? n : -n;
    ww = x;
    for (yy = 1.0; nn != 0; nn >>= 1, ww *=ww) {
      if (nn & 1) yy *= ww;
    }
    return (n > 0) ? yy : 1.0/yy;
  }

  static inline real pow(real const &x, real const &y)
  {
    return ::pow(static_cast<double>(x), static_cast<double>(y));
  }

  static inline real floor(real const &x)
  {
    return ::floor(static_cast<double>(x));
  }

  static inline real fabs(real const &x)
  {
    return ::fabs(static_cast<double>(x));
  }

  static inline real sqrt(real const &x)
  {
    return ::sqrt(static_cast<double>(x));
  }

  static inline real sin(real const &x)
  {
    return ::sin(static_cast<double>(x));
  }

  static inline real cos(real const &x)
  {
    return ::cos(static_cast<double>(x));
  }

  static inline real asin(real const &x)
  {
    return ::asin(static_cast<double>(x));
  }

  static inline real acos(real const &x)
  {
    return ::acos(static_cast<double>(x));
  }

  static inline real atan2(real const &x, real const &y)
  {
    return ::atan2(static_cast<double>(x), static_cast<double>(y));
  }

  static inline real exp(real const &x)
  {
    return ::exp(static_cast<double>(x));
  }

  static inline real logn(real const &x)
  {
    return ::log(static_cast<double>(x));
  }

  // Forward declarations
  class rvector;
  template <class T> class vector1d;
  template <class T> class matrix2d;
  class quaternion;
  class rotation;
  class usage;

  typedef int residue_id;

  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;

private:

  static int errorCode;

public:

  static void set_error_bits(int code);

  static bool get_error_bit(int code);

  static inline int get_error()
  {
    return errorCode;
  }

  static void clear_error();

  static step_number it;
  static step_number it_restart;

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

  static inline step_number step_absolute()
  {
    return it;
  }

  static real debug_gradients_step_size;

private:

  std::string cvm_output_prefix;

public:
  static inline std::string &output_prefix()
  {
    colvarmodule *cv = colvarmodule::main();
    return cv->cvm_output_prefix;
  }

private:

  std::vector<colvar *> colvars;

  std::vector<colvar *> colvars_active;

  std::vector<colvar *> colvars_smp;
  std::vector<int> colvars_smp_items;

  std::vector<atom_group *> named_atom_groups;
public:
  void register_named_atom_group(atom_group *ag);

  void unregister_named_atom_group(atom_group *ag);

  std::vector<colvar *> *variables();

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

  std::vector<colvar *> *variables_active();

  std::vector<colvar *> *variables_active_smp();

  std::vector<int> *variables_active_smp_items();

  std::vector<colvarbias *> biases;

  real total_bias_energy;

private:

  void *num_biases_types_used_;

  std::vector<colvarbias *> biases_active_;

public:

  std::vector<colvarbias *> *biases_active();

  static inline bool debug()
  {
    return COLVARS_DEBUG;
  }

  size_t size() const;

  colvarmodule(colvarproxy *proxy);

  ~colvarmodule();

  int reset();

  int read_config_file(char const *config_file_name);

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

  int parse_config(std::string &conf);

  std::string const & get_config() const;

  // Parse functions (setup internal data based on a string)

  static std::istream & getline(std::istream &is, std::string &line);

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

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

  int run_tcl_script(std::string const &filename);

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

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

  void config_changed();

private:

  std::string config_string;

  std::string extra_conf;

  template <class bias_type>
  int parse_biases_type(std::string const &conf, char const *keyword);

  bool check_new_bias(std::string &conf, char const *key);

  std::string source_Tcl_script;

public:

  size_t num_variables() const;

  size_t num_variables_feature(int feature_id) const;

  size_t num_biases() const;

  size_t num_biases_feature(int feature_id) const;

  size_t num_biases_type(std::string const &type) const;

  std::vector<std::string> const time_dependent_biases() const;

private:
  int catch_input_errors(int result);

public:

  // "Setup" functions (change internal data based on related data
  // from the proxy that may change during program execution)
  // No additional parsing is done within these functions

  int update_engine_parameters();

  int setup_input();

  int setup_output();

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

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

  int print_total_forces_errning(bool warn_total_forces);

  std::ostream & write_restart(std::ostream &os);

  static std::string state_file_prefix(char const *filename);

  int open_traj_file(std::string const &file_name);
  int close_traj_file();
  std::ostream & write_traj(std::ostream &os);
  std::ostream & write_traj_label(std::ostream &os);

  int write_traj_files();
  int write_restart_file(std::string const &out_name);
  int write_output_files();
  static int backup_file(char const *filename);

  int write_restart_string(std::string &output);

  static colvarbias * bias_by_name(std::string const &name);

  static colvar * colvar_by_name(std::string const &name);

  static atom_group * atom_group_by_name(std::string const &name);

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

  std::string read_colvar(std::string const &name);

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

  int calc();

  int calc_colvars();

  int calc_biases();

  int update_colvar_forces();

  int analyze();

  int end_of_step();

  int read_traj(char const *traj_filename,
                long        traj_read_begin,
                long        traj_read_end);

  static std::string to_str(char const *s);

  static std::string to_str(std::string const &s);

  static std::string to_str(bool x);

  static std::string to_str(int const &x,
                            size_t width = 0, size_t prec = 0);

  static std::string to_str(size_t const &x,
                            size_t width = 0, size_t prec = 0);

  static std::string to_str(long int const &x,
                            size_t width = 0, size_t prec = 0);

  static std::string to_str(step_number const &x,
                            size_t width = 0, size_t prec = 0);

  static std::string to_str(real const &x,
                            size_t width = 0, size_t prec = 0);

  static std::string to_str(rvector const &x,
                            size_t width = 0, size_t prec = 0);

  static std::string to_str(quaternion const &x,
                            size_t width = 0, size_t prec = 0);

  static std::string to_str(colvarvalue const &x,
                            size_t width = 0, size_t prec = 0);

  static std::string to_str(vector1d<real> const &x,
                            size_t width = 0, size_t prec = 0);

  static std::string to_str(matrix2d<real> const &x,
                            size_t width = 0, size_t prec = 0);


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

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

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

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

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

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

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

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


  static std::string wrap_string(std::string const &s,
                                 size_t 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 const char * const line_marker;


  // proxy functions

  static real dt();

  static void request_total_force();

  int cite_feature(std::string const &feature);

  std::string feature_report(int flag = 0);

  static void log(std::string const &message, int min_log_level = 10);

  static int error(std::string const &message, int code = COLVARS_ERROR);

private:

  static int log_level_;

public:

  static inline int log_level()
  {
    return log_level_;
  }

  static inline int log_init_messages()
  {
    return 1;
  }

  static inline int log_user_params()
  {
    return 2;
  }

  static inline int log_default_params()
  {
    return 3;
  }

  static inline int log_output_files()
  {
    return 4;
  }

  static inline int log_input_files()
  {
    return 5;
  }

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

  std::vector<std::string> index_file_names;

  std::vector<std::string> index_group_names;

  std::vector<std::vector<int> *> index_groups;

  int read_index_file(char const *filename);

  int reset_index_groups();

  static int load_atoms(char const *filename,
                        atom_group &atoms,
                        std::string const &pdb_field,
                        double pdb_field_value = 0.0);

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

  int load_coords_xyz(char const *filename,
                      std::vector<rvector> *pos,
                      atom_group *atoms);

  static size_t cv_traj_freq;

  static size_t restart_out_freq;
  std::string   restart_out_name;

  static real rand_gaussian(void);

protected:

  colvarparse *parse;

  std::string cv_traj_name;

  bool cv_traj_write_labels;

  std::string restart_version_str;

  int restart_version_int;

  size_t depth_s;

  std::vector<size_t> depth_v;

  int xyz_reader_use_count;

  usage *usage_;

public:

  inline std::string restart_version() const
  {
    return restart_version_str;
  }

  inline int restart_version_number() const
  {
    return restart_version_int;
  }

  static size_t & depth();

  static void increase_depth();

  static void decrease_depth();

  static inline bool scripted_forces()
  {
    return use_scripted_forces;
  }

  static bool use_scripted_forces;

  static bool scripting_after_biases;

  int calc_scripted_forces();

  static colvarproxy *proxy;

  static colvarmodule *main();

};


typedef colvarmodule cvm;



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


#endif

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