forked from lijiext/lammps
598 lines
18 KiB
C++
598 lines
18 KiB
C++
// -*- c++ -*-
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// This file is part of the Collective Variables module (Colvars).
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// The original version of Colvars and its updates are located at:
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// https://github.com/colvars/colvars
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// Please update all Colvars source files before making any changes.
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// If you wish to distribute your changes, please submit them to the
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// Colvars repository at GitHub.
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#ifndef COLVARPROXY_H
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#define COLVARPROXY_H
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#include <fstream>
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#include <list>
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#include "colvarmodule.h"
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#include "colvarvalue.h"
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/// \file colvarproxy.h
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/// \brief Colvars proxy classes
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///
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/// This file declares the class for the object responsible for interfacing
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/// Colvars with other codes (MD engines, VMD, Python). The \link colvarproxy
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/// \endlink class is a derivative of multiple classes, each devoted to a
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/// specific task (e.g. \link colvarproxy_atoms \endlink to access data for
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/// individual atoms).
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///
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/// To interface to a new MD engine, the simplest solution is to derive a new
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/// class from \link colvarproxy \endlink. Currently implemented are: \link
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/// colvarproxy_lammps, \endlink, \link colvarproxy_namd, \endlink, \link
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/// colvarproxy_vmd, \endlink.
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// forward declarations
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class colvarscript;
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/// Methods for accessing the simulation system (PBCs, integrator, etc)
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class colvarproxy_system {
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public:
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/// Constructor
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colvarproxy_system();
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/// Destructor
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virtual ~colvarproxy_system();
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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 Target temperature of the simulation (K units)
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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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/// \brief Pseudo-random number with Gaussian distribution
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virtual cvm::real rand_gaussian(void) = 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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/// \brief Get the PBC-aware distance vector between two positions
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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 PBC-aware square distance between two positions;
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/// may need to be reimplemented independently from position_distance() for optimization purposes
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virtual cvm::real position_dist2(cvm::atom_pos const &pos1,
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cvm::atom_pos const &pos2);
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/// Tell the proxy whether total forces are needed (may not always be available)
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virtual void request_total_force(bool yesno);
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/// Are total forces being used?
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virtual bool total_forces_enabled() const;
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/// Are total forces from the current step available?
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virtual bool total_forces_same_step() const;
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};
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/// \brief Container of atomic data for processing by Colvars
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class colvarproxy_atoms {
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public:
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/// Constructor
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colvarproxy_atoms();
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/// Destructor
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virtual ~colvarproxy_atoms();
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/// Prepare this atom for collective variables calculation, selecting it by
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/// numeric index (1-based)
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virtual int init_atom(int atom_number) = 0;
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/// Check that this atom number is valid, but do not initialize the
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/// corresponding atom yet
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virtual int check_atom_id(int atom_number) = 0;
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/// Select this atom for collective variables calculation, using name and
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/// residue number. Not all programs support this: leave this function as
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/// is in those cases.
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virtual int init_atom(cvm::residue_id const &residue,
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std::string const &atom_name,
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std::string const &segment_id);
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/// Check that this atom is valid, but do not initialize it yet
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virtual int check_atom_id(cvm::residue_id const &residue,
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std::string const &atom_name,
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std::string const &segment_id);
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/// \brief Used by the atom class destructor: rather than deleting the array slot
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/// (costly) set the corresponding atoms_ncopies to zero
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virtual void clear_atom(int index);
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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 int load_atoms(char const *filename,
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cvm::atom_group &atoms,
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std::string const &pdb_field,
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double const pdb_field_value = 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 int 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);
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/// Clear atomic data
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int reset();
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/// Get the numeric ID of the given atom (for the program)
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inline int get_atom_id(int index) const
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{
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return atoms_ids[index];
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}
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/// Get the mass of the given atom
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inline cvm::real get_atom_mass(int index) const
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{
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return atoms_masses[index];
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}
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/// Get the charge of the given atom
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inline cvm::real get_atom_charge(int index) const
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{
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return atoms_charges[index];
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}
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/// Read the current position of the given atom
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inline cvm::rvector get_atom_position(int index) const
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{
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return atoms_positions[index];
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}
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/// Read the current total force of the given atom
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inline cvm::rvector get_atom_total_force(int index) const
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{
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return atoms_total_forces[index];
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}
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/// Request that this force is applied to the given atom
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inline void apply_atom_force(int index, cvm::rvector const &new_force)
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{
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atoms_new_colvar_forces[index] += new_force;
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}
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/// Read the current velocity of the given atom
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inline cvm::rvector get_atom_velocity(int index)
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{
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cvm::error("Error: reading the current velocity of an atom "
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"is not yet implemented.\n",
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COLVARS_NOT_IMPLEMENTED);
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return cvm::rvector(0.0);
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}
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inline std::vector<int> *modify_atom_ids()
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{
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return &atoms_ids;
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}
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inline std::vector<cvm::real> *modify_atom_masses()
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{
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return &atoms_masses;
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}
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inline std::vector<cvm::real> *modify_atom_charges()
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{
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return &atoms_charges;
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}
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inline std::vector<cvm::rvector> *modify_atom_positions()
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{
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return &atoms_positions;
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}
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inline std::vector<cvm::rvector> *modify_atom_total_forces()
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{
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return &atoms_total_forces;
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}
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inline std::vector<cvm::rvector> *modify_atom_new_colvar_forces()
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{
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return &atoms_new_colvar_forces;
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}
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protected:
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/// \brief Array of 0-based integers used to uniquely associate atoms
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/// within the host program
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std::vector<int> atoms_ids;
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/// \brief Keep track of how many times each atom is used by a separate colvar object
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std::vector<size_t> atoms_ncopies;
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/// \brief Masses of the atoms (allow redefinition during a run, as done e.g. in LAMMPS)
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std::vector<cvm::real> atoms_masses;
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/// \brief Charges of the atoms (allow redefinition during a run, as done e.g. in LAMMPS)
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std::vector<cvm::real> atoms_charges;
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/// \brief Current three-dimensional positions of the atoms
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std::vector<cvm::rvector> atoms_positions;
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/// \brief Most recent total forces on each atom
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std::vector<cvm::rvector> atoms_total_forces;
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/// \brief Forces applied from colvars, to be communicated to the MD integrator
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std::vector<cvm::rvector> atoms_new_colvar_forces;
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/// Used by all init_atom() functions: create a slot for an atom not
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/// requested yet; returns the index in the arrays
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int add_atom_slot(int atom_id);
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};
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/// \brief Container of atom group data (allow collection of aggregated atomic
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/// data)
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class colvarproxy_atom_groups {
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public:
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/// Contructor
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colvarproxy_atom_groups();
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/// Destructor
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virtual ~colvarproxy_atom_groups();
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/// Clear atom group data
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int reset();
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/// \brief Whether this proxy implementation has capability for scalable groups
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virtual int scalable_group_coms();
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/// Prepare this group for collective variables calculation, selecting atoms by internal ids (0-based)
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virtual int init_atom_group(std::vector<int> const &atoms_ids);
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/// \brief Used by the atom_group class destructor
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virtual void clear_atom_group(int index);
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/// Get the numeric ID of the given atom group (for the MD program)
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inline int get_atom_group_id(int index) const
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{
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return atom_groups_ids[index];
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}
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/// Get the mass of the given atom group
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inline cvm::real get_atom_group_mass(int index) const
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{
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return atom_groups_masses[index];
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}
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/// Get the charge of the given atom group
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inline cvm::real get_atom_group_charge(int index) const
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{
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return atom_groups_charges[index];
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}
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/// Read the current position of the center of mass given atom group
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inline cvm::rvector get_atom_group_com(int index) const
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{
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return atom_groups_coms[index];
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}
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/// Read the current total force of the given atom group
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inline cvm::rvector get_atom_group_total_force(int index) const
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{
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return atom_groups_total_forces[index];
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}
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/// Request that this force is applied to the given atom group
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inline void apply_atom_group_force(int index, cvm::rvector const &new_force)
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{
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atom_groups_new_colvar_forces[index] += new_force;
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}
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/// Read the current velocity of the given atom group
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inline cvm::rvector get_atom_group_velocity(int index)
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{
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cvm::error("Error: reading the current velocity of an atom group is not yet implemented.\n",
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COLVARS_NOT_IMPLEMENTED);
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return cvm::rvector(0.0);
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}
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protected:
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/// \brief Array of 0-based integers used to uniquely associate atom groups
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/// within the host program
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std::vector<int> atom_groups_ids;
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/// \brief Keep track of how many times each group is used by a separate cvc
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std::vector<size_t> atom_groups_ncopies;
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/// \brief Total masses of the atom groups
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std::vector<cvm::real> atom_groups_masses;
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/// \brief Total charges of the atom groups (allow redefinition during a run, as done e.g. in LAMMPS)
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std::vector<cvm::real> atom_groups_charges;
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/// \brief Current centers of mass of the atom groups
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std::vector<cvm::rvector> atom_groups_coms;
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/// \brief Most recently updated total forces on the com of each group
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std::vector<cvm::rvector> atom_groups_total_forces;
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/// \brief Forces applied from colvars, to be communicated to the MD integrator
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std::vector<cvm::rvector> atom_groups_new_colvar_forces;
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/// Used by all init_atom_group() functions: create a slot for an atom group not requested yet
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int add_atom_group_slot(int atom_group_id);
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};
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/// \brief Methods for SMP parallelization
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class colvarproxy_smp {
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public:
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/// Constructor
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colvarproxy_smp();
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/// Destructor
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virtual ~colvarproxy_smp();
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/// Whether threaded parallelization should be used (TODO: make this a
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/// cvm::deps feature)
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bool b_smp_active;
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/// Whether threaded parallelization is available (TODO: make this a cvm::deps feature)
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virtual int smp_enabled();
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/// Distribute calculation of colvars (and their components) across threads
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virtual int smp_colvars_loop();
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/// Distribute calculation of biases across threads
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virtual int smp_biases_loop();
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/// Distribute calculation of biases across threads 2nd through last, with all scripted biased on 1st thread
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virtual int smp_biases_script_loop();
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/// Index of this thread
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virtual int smp_thread_id();
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/// Number of threads sharing this address space
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virtual int smp_num_threads();
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/// Lock the proxy's shared data for access by a thread, if threads are implemented; if not implemented, does nothing
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virtual int smp_lock();
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/// Attempt to lock the proxy's shared data
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virtual int smp_trylock();
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/// Release the lock
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virtual int smp_unlock();
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protected:
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/// Lock state for OpenMP
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void *omp_lock_state;
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};
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/// \brief Methods for multiple-replica communication
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class colvarproxy_replicas {
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public:
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/// Constructor
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colvarproxy_replicas();
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/// Destructor
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virtual ~colvarproxy_replicas();
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/// \brief Indicate if multi-replica support is available and active
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virtual bool replica_enabled();
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/// \brief Index of this replica
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virtual int replica_index();
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/// \brief Total number of replica
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virtual int replica_num();
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/// \brief Synchronize replica
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virtual void replica_comm_barrier();
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/// \brief Receive data from other replica
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virtual int replica_comm_recv(char* msg_data, int buf_len, int src_rep);
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/// \brief Send data to other replica
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virtual int replica_comm_send(char* msg_data, int msg_len, int dest_rep);
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};
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/// Method for scripting language interface (Tcl or Python)
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class colvarproxy_script {
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public:
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/// Constructor
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colvarproxy_script();
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/// Destructor
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virtual ~colvarproxy_script();
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/// Convert a script object (Tcl or Python call argument) to a C string
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virtual char *script_obj_to_str(unsigned char *obj);
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/// Pointer to the scripting interface object
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/// (does not need to be allocated in a new interface)
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colvarscript *script;
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/// is a user force script defined?
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bool force_script_defined;
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/// Do we have a scripting interface?
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bool have_scripts;
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/// Run a user-defined colvar forces script
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virtual int run_force_callback();
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virtual int run_colvar_callback(
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std::string const &name,
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std::vector<const colvarvalue *> const &cvcs,
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colvarvalue &value);
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virtual int run_colvar_gradient_callback(
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std::string const &name,
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std::vector<const colvarvalue *> const &cvcs,
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std::vector<cvm::matrix2d<cvm::real> > &gradient);
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};
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/// Methods for data input/output
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class colvarproxy_io {
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public:
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/// Constructor
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colvarproxy_io();
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/// Destructor
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virtual ~colvarproxy_io();
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/// \brief Save the current frame number in the argument given
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// Returns error code
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virtual int get_frame(long int &);
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/// \brief Set the current frame number (as well as colvarmodule::it)
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// Returns error code
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virtual int set_frame(long int);
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/// \brief Returns a reference to the given output channel;
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/// if this is not open already, then open it
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virtual std::ostream *output_stream(std::string const &output_name,
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std::ios_base::openmode mode =
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std::ios_base::out);
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/// \brief Flushes the given output channel
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virtual int flush_output_stream(std::ostream *os);
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/// \brief Closes the given output channel
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virtual int close_output_stream(std::string const &output_name);
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/// \brief Rename the given file, before overwriting it
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virtual int backup_file(char const *filename);
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/// \brief Rename the given file, before overwriting it
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inline int backup_file(std::string const &filename)
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{
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return backup_file(filename.c_str());
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}
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/// \brief Prefix of the input state file
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inline std::string & input_prefix()
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{
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return input_prefix_str;
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}
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/// \brief Prefix to be used for output restart files
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inline std::string & restart_output_prefix()
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{
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return restart_output_prefix_str;
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}
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/// \brief Prefix to be used for output files (final system
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/// configuration)
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inline std::string & output_prefix()
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{
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return output_prefix_str;
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}
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protected:
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/// \brief Prefix to be used for input files (restarts, not
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/// configuration)
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std::string input_prefix_str, output_prefix_str, restart_output_prefix_str;
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/// \brief Currently opened output files: by default, these are ofstream objects.
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/// Allows redefinition to implement different output mechanisms
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std::list<std::ostream *> output_files;
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/// \brief Identifiers for output_stream objects: by default, these are the names of the files
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std::list<std::string> output_stream_names;
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};
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/// \brief Interface between the collective variables module and
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/// the simulation or analysis program (NAMD, VMD, LAMMPS...).
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/// This is the base class: each interfaced program is supported by a derived class.
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/// Only pure virtual functions ("= 0") must be reimplemented to ensure baseline functionality.
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class colvarproxy
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: public colvarproxy_system,
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public colvarproxy_atoms,
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public colvarproxy_atom_groups,
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public colvarproxy_smp,
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public colvarproxy_replicas,
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public colvarproxy_script,
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public colvarproxy_io
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{
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public:
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/// Pointer to the main object
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colvarmodule *colvars;
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/// Constructor
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colvarproxy();
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/// Destructor
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virtual ~colvarproxy();
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/// \brief Reset proxy state, e.g. requested atoms
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virtual int reset();
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/// (Re)initialize required member data after construction
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virtual int setup();
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/// \brief Update data required by the colvars module (e.g. cache atom positions)
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///
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/// TODO Break up colvarproxy_namd and colvarproxy_lammps function into these
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virtual int update_input();
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/// \brief Update data based from the results of a module update (e.g. send forces)
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virtual int update_output();
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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 let the rest of the program handle the error
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virtual void error(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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/// \brief Restarts will be written each time this number of steps has passed
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virtual size_t restart_frequency();
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/// Whether a simulation is running (warn against irrecovarable errors)
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inline bool simulation_running() const
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{
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return b_simulation_running;
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}
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protected:
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/// Whether a simulation is running (warn against irrecovarable errors)
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bool b_simulation_running;
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};
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#endif
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