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