colvarmodule.h
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Created: Wed, Nov 6, 15:04

colvarmodule.h
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	#ifndef COLVARMODULE_H
	#define COLVARMODULE_H

	#ifndef COLVARS_VERSION
	#define COLVARS_VERSION "2012-06-20"
	#endif

	#ifndef COLVARS_DEBUG
	#define COLVARS_DEBUG false
	#endif

	/// \file colvarmodule.h
	/// \brief Collective variables main module
	///
	/// This file declares the main class for defining and manipulating
	/// collective variables: there should be only one instance of this
	/// class, because several variables are made static (i.e. they are
	/// shared between all object instances) to be accessed from other
	/// objects.


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


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


	/// \brief Collective variables module (main class)
	///
	/// Class to control the collective variables calculation. An object
	/// (usually one) of this class is spawned from the MD program,
	/// containing all i/o routines and general interface.
	///
	/// At initialization, the colvarmodule object creates a proxy object
	/// to provide a transparent interface between the MD program and the
	/// child objects
	class colvarmodule {

	private:

	/// Impossible to initialize the main object without arguments
	colvarmodule();

	public:

	friend class colvarproxy;

	/// Defining an abstract real number allows to switch precision
	typedef double real;
	/// Residue identifier
	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;

	/// \brief Atom position (different type name from rvector, to make
	/// possible future PBC-transparent implementations)
	typedef rvector atom_pos;

	/// \brief 3x3 matrix of real numbers
	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;

	/// Current step number
	static size_t it;
	/// Starting step number for this run
	static size_t it_restart;

	/// Return the current step number from the beginning of this run
	static inline size_t step_relative()
	{
	return it - it_restart;
	}

	/// Return the current step number from the beginning of the whole
	/// calculation
	static inline size_t step_absolute()
	{
	return it;
	}

	/// If true, get it_restart from the state file; if set to false,
	/// the MD program is providing it
	bool it_restart_from_state_file;

	/// \brief Finite difference step size (if there is no dynamics, or
	/// if gradients need to be tested independently from the size of
	/// dt)
	static real debug_gradients_step_size;

	/// Prefix for all output files for this run
	static std::string output_prefix;

	/// Prefix for files from a previous run (including restart/output)
	static std::string input_prefix;

	/// input restart file name (determined from input_prefix)
	static std::string restart_in_name;


	/// Array of collective variables
	static std::vector<colvar *> colvars;

	/* TODO: implement named CVCs
	/// Array of named (reusable) collective variable components
	static std::vector<cvc *> cvcs;
	/// Named cvcs register themselves at initialization time
	inline void register_cvc (cvc *p) {
	cvcs.push_back(p);
	}
	*/

	/// Array of collective variable biases
	static std::vector<colvarbias *> biases;
	/// \brief Number of ABF biases initialized (in normal conditions
	/// should be 1)
	static size_t n_abf_biases;
	/// \brief Number of metadynamics biases initialized (in normal
	/// conditions should be 1)
	static size_t n_meta_biases;
	/// \brief Number of harmonic biases initialized (no limit on the
	/// number)
	static size_t n_harm_biases;
	/// \brief Number of histograms initialized (no limit on the
	/// number)
	static size_t n_histo_biases;

	/// \brief Whether debug output should be enabled (compile-time option)
	static inline bool debug()
	{
	return COLVARS_DEBUG;
	}


	/// \brief Constructor \param config_name Configuration file name
	/// \param restart_name (optional) Restart file name
	colvarmodule (char const *config_name,
	colvarproxy *proxy_in);
	/// Destructor
	~colvarmodule();

	/// Initialize collective variables
	void init_colvars (std::string const &conf);

	/// Initialize collective variable biases
	void init_biases (std::string const &conf);

	/// Load new configuration - force constant and/or centers only
	void change_configuration(std::string const &name, std::string const &conf);

	/// Calculate change in energy from using alternate configuration
	real energy_difference(std::string const &name, std::string const &conf);

	/// Calculate collective variables and biases
	void calc();
	/// Read the input restart file
	std::istream & read_restart (std::istream &is);
	/// Write the output restart file
	std::ostream & write_restart (std::ostream &os);
	/// Write all output files (called by the proxy)
	void write_output_files();
	/// \brief Call colvarproxy::backup_file()
	static void backup_file (char const *filename);

	/// Perform analysis
	void analyze();
	/// \brief Read a collective variable trajectory (post-processing
	/// only, not called at runtime)
	bool read_traj (char const *traj_filename,
	size_t traj_read_begin,
	size_t traj_read_end);

	/// Get the pointer of a colvar from its name (returns NULL if not found)
	static colvar * colvar_p (std::string const &name);

	/// Quick conversion of an object to a string
	template<typename T> static std::string to_str (T const &x,
	size_t const &width = 0,
	size_t const &prec = 0);
	/// Quick conversion of a vector of objects to a string
	template<typename T> static std::string to_str (std::vector<T> const &x,
	size_t const &width = 0,
	size_t const &prec = 0);

	/// Reduce the number of characters in a string
	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)) );
	}

	/// Number of characters to represent a time step
	static size_t const it_width;
	/// Number of digits to represent a collective variables value(s)
	static size_t const cv_prec;
	/// Number of characters to represent a collective variables value(s)
	static size_t const cv_width;
	/// Number of digits to represent the collective variables energy
	static size_t const en_prec;
	/// Number of characters to represent the collective variables energy
	static size_t const en_width;
	/// Line separator in the log output
	static std::string const line_marker;


	// proxy functions

	/// \brief Value of the unit for atomic coordinates with respect to
	/// angstroms (used by some variables for hard-coded default values)
	static real unit_angstrom();

	/// \brief Boltmann constant
	static real boltzmann();

	/// \brief Temperature of the simulation (K)
	static real temperature();

	/// \brief Time step of MD integrator (fs)
	static real dt();

	/// Request calculation of system force from MD engine
	static void request_system_force();

	/// Print a message to the main log
	static void log (std::string const &message);

	/// Print a message to the main log and exit with error code
	static void fatal_error (std::string const &message);

	/// Print a message to the main log and exit normally
	static void exit (std::string const &message);


	/// \brief Get the distance between two atomic positions with pbcs handled
	/// correctly
	static rvector position_distance (atom_pos const &pos1,
	atom_pos const &pos2);


	/// \brief Get the square distance between two positions (with
	/// periodic boundary conditions handled transparently)
	///
	/// Note: in the case of periodic boundary conditions, this provides
	/// an analytical square distance (while taking the square of
	/// position_distance() would produce leads to a cusp)
	static real position_dist2 (atom_pos const &pos1,
	atom_pos const &pos2);

	/// \brief Get the closest periodic image to a reference position
	/// \param pos The position to look for the closest periodic image
	/// \param ref_pos (optional) The reference position
	static void select_closest_image (atom_pos &pos,
	atom_pos const &ref_pos);

	/// \brief Perform select_closest_image() on a set of atomic positions
	///
	/// After that, distance vectors can then be calculated directly,
	/// without using position_distance()
	static void select_closest_images (std::vector<atom_pos> &pos,
	atom_pos const &ref_pos);


	/// \brief Create atoms from a file \param filename name of the file
	/// (usually a PDB) \param atoms array of the atoms to be allocated
	/// \param pdb_field (optiona) if "filename" is a PDB file, use this
	/// field to determine which are the atoms to be set
	static void load_atoms (char const *filename,
	std::vector<atom> &atoms,
	std::string const &pdb_field,
	double const pdb_field_value = 0.0);

	/// \brief Load the coordinates for a group of atoms from a file
	/// (usually a PDB); the number of atoms in "filename" must match
	/// the number of elements in "pos"
	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);


	/// Frequency for collective variables trajectory output
	static size_t cv_traj_freq;

	/// \brief True if only analysis is performed and not a run
	static bool b_analysis;

	/// Frequency for saving output restarts
	static size_t restart_out_freq;
	/// Output restart file name
	std::string restart_out_name;

	/// Pseudo-random number with Gaussian distribution
	static real rand_gaussian (void);
	protected:

	/// Configuration file
	std::ifstream config_s;

	/// Configuration file parser object
	colvarparse *parse;

	/// Name of the trajectory file
	std::string cv_traj_name;

	/// Collective variables output trajectory file
	std::ofstream cv_traj_os;

	/// Appending to the existing trajectory file?
	bool cv_traj_append;

	/// Output restart file
	std::ofstream restart_out_os;

	/// \brief Pointer to the proxy object, used to retrieve atomic data
	/// from the hosting program; it is static in order to be accessible
	/// from static functions in the colvarmodule class
	static colvarproxy *proxy;

	/// \brief Counter for the current depth in the object hierarchy (useg e.g. in outpu
	static size_t depth;

	public:

	/// Increase the depth (number of indentations in the output)
	static void increase_depth();

	/// Decrease the depth (number of indentations in the output)
	static void decrease_depth();
	};


	/// Shorthand for the frequently used type prefix
	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


	// Emacs
	// Local Variables:
	// mode: C++
	// End:

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