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lammps/lib/colvars/colvarmodule.h

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#ifndef COLVARMODULE_H
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2013-04-17"
#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 for the given bias -
/// currently works for harmonic (force constant and/or centers)
void change_configuration (std::string const &bias_name, std::string const &conf);
/// Calculate change in energy from using alt. config. for the given bias -
/// currently works for harmonic (force constant and/or centers)
real energy_difference (std::string const &bias_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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