lammps/lib/colvars/colvarproxy.h

138 lines
4.7 KiB
C++

#ifndef COLVARPROXY_H
#define COLVARPROXY_H
#include "colvarmodule.h"
/// \brief Interface class between the collective variables module and
/// the simulation program
class colvarproxy {
public:
/// Pointer to the instance of colvarmodule
colvarmodule *colvars;
/// \brief Value of the unit for atomic coordinates with respect to
/// angstroms (used by some variables for hard-coded default values)
virtual cvm::real unit_angstrom() = 0;
/// \brief Boltzmann constant
virtual cvm::real boltzmann() = 0;
/// \brief Temperature of the simulation (K)
virtual cvm::real temperature() = 0;
/// \brief Time step of the simulation (fs)
virtual cvm::real dt() = 0;
/// Pass restraint energy value for current timestep to MD engine
virtual void add_energy (cvm::real energy) = 0;
/// Tell the proxy whether system forces are needed
virtual void request_system_force (bool yesno) = 0;
/// Print a message to the main log
virtual void log (std::string const &message) = 0;
/// Print a message to the main log and exit with error code
virtual void fatal_error (std::string const &message) = 0;
/// Print a message to the main log and exit normally
virtual void exit (std::string const &message) = 0;
/// \brief Prefix to be used for input files (restarts, not
/// configuration)
virtual std::string input_prefix() = 0;
/// \brief Prefix to be used for output restart files
virtual std::string restart_output_prefix() = 0;
/// \brief Prefix to be used for output files (final system
/// configuration)
virtual std::string output_prefix() = 0;
/// \brief Restarts will be fritten each time this number of steps has passed
virtual size_t restart_frequency() = 0;
// **************** PERIODIC BOUNDARY CONDITIONS ****************
/// \brief Get the simple distance vector between two positions
/// (with periodic boundary conditions handled transparently)
virtual cvm::rvector position_distance (cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2) = 0;
/// \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)
virtual cvm::real position_dist2 (cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2) = 0;
/// \brief Get the closest periodic image to a reference position
/// \param pos The position to look for the closest periodic image
/// \param ref_pos The reference position
virtual void select_closest_image (cvm::atom_pos &pos,
cvm::atom_pos const &ref_pos) = 0;
/// \brief Perform select_closest_image() on a set of atomic positions
///
/// After that, distance vectors can then be calculated directly,
/// without using position_distance()
void select_closest_images (std::vector<cvm::atom_pos> &pos,
cvm::atom_pos const &ref_pos);
/// \brief Read atom identifiers from a file \param filename name of
/// the file (usually a PDB) \param atoms array to which atoms read
/// from "filename" will be appended \param pdb_field (optiona) if
/// "filename" is a PDB file, use this field to determine which are
/// the atoms to be set
virtual void load_atoms (char const *filename,
std::vector<cvm::atom> &atoms,
std::string const pdb_field,
double const pdb_field_value = 0.0) = 0;
/// \brief Load the coordinates for a group of atoms from a file
/// (usually a PDB); if "pos" is already allocated, the number of its
/// elements must match the number of atoms in "filename"
virtual void load_coords (char const *filename,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const pdb_field,
double const pdb_field_value = 0.0) = 0;
/// \brief Rename the given file, under the convention provided by
/// the MD program
virtual void backup_file (char const *filename) = 0;
/// \brief Pseudo-random number with Gaussian distribution
virtual cvm::real rand_gaussian (void) = 0;
virtual inline ~colvarproxy() {}
};
inline void colvarproxy::select_closest_images (std::vector<cvm::atom_pos> &pos,
cvm::atom_pos const &ref_pos)
{
for (std::vector<cvm::atom_pos>::iterator pi = pos.begin();
pi != pos.end(); pi++) {
select_closest_image (*pi, ref_pos);
}
}
#endif
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