/// -*- c++ -*- #ifndef COLVARPROXY_H #define COLVARPROXY_H #include #include #include "colvarmodule.h" #include "colvarvalue.h" // return values for the frame() routine #define COLVARS_NO_SUCH_FRAME -1 // forward declarations class colvarscript; /// \brief Interface between the collective variables module and /// the simulation or analysis program. /// This is the base class: each program is supported by a derived class. /// Only pure virtual functions ("= 0") must be reimplemented in a new interface. class colvarproxy { public: /// Pointer to the main object colvarmodule *colvars; /// Default constructor inline colvarproxy() : script(NULL) {} /// Default destructor virtual inline ~colvarproxy() {} /// (Re)initialize member data after construction virtual void setup() {} // **************** SYSTEM-WIDE PHYSICAL QUANTITIES **************** /// \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; /// \brief Pseudo-random number with Gaussian distribution virtual cvm::real rand_gaussian(void) = 0; /// \brief Get the current frame number virtual int frame() { return COLVARS_NOT_IMPLEMENTED; } /// \brief Set the current frame number // return 0 on success, -1 on failure virtual int frame(int) { return COLVARS_NOT_IMPLEMENTED; } // Replica exchange commands: /// \brief Indicate if multi-replica support is available and active virtual bool replica_enabled() { return false; } /// \brief Index of this replica virtual int replica_index() { return 0; } /// \brief Total number of replica virtual int replica_num() { return 1; } /// \brief Synchronize replica virtual void replica_comm_barrier() {} /// \brief Receive data from other replica virtual int replica_comm_recv(char* msg_data, int buf_len, int src_rep) { return COLVARS_NOT_IMPLEMENTED; } /// \brief Send data to other replica virtual int replica_comm_send(char* msg_data, int msg_len, int dest_rep) { return COLVARS_NOT_IMPLEMENTED; } // **************** SIMULATION PARAMETERS **************** /// \brief Prefix to be used for input files (restarts, not /// configuration) std::string input_prefix_str, output_prefix_str, restart_output_prefix_str; inline std::string input_prefix() { return input_prefix_str; } /// \brief Prefix to be used for output restart files inline std::string restart_output_prefix() { return restart_output_prefix_str; } /// \brief Prefix to be used for output files (final system /// configuration) inline std::string output_prefix() { return output_prefix_str; } /// \brief Restarts will be written each time this number of steps has passed virtual size_t restart_frequency() = 0; // **************** ACCESS ATOMIC DATA **************** /// 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 (may not always be available) virtual void request_system_force(bool yesno) = 0; // **************** PERIODIC BOUNDARY CONDITIONS **************** /// \brief Get the PBC-aware distance vector between two positions virtual cvm::rvector position_distance(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) = 0; /// \brief Get the PBC-aware square distance between two positions; /// may be implemented independently from position_distance() for optimization purposes virtual cvm::real position_dist2(cvm::atom_pos const &pos1, cvm::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 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 &pos, cvm::atom_pos const &ref_pos); // **************** SCRIPTING INTERFACE **************** /// Pointer to the scripting interface object /// (does not need to be allocated in a new interface) colvarscript *script; /// is a user force script defined? bool force_script_defined; /// Do we have a scripting interface? bool have_scripts; /// Run a user-defined colvar forces script virtual int run_force_callback() { return COLVARS_NOT_IMPLEMENTED; } virtual int run_colvar_callback(std::string const &name, std::vector const &cvcs, colvarvalue &value) { return COLVARS_NOT_IMPLEMENTED; } virtual int run_colvar_gradient_callback(std::string const &name, std::vector const &cvcs, std::vector > &gradient) { return COLVARS_NOT_IMPLEMENTED; } // **************** INPUT/OUTPUT **************** /// Print a message to the main log virtual void log(std::string const &message) = 0; /// Print a message to the main log and let the rest of the program handle the error virtual void error(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 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 int load_atoms(char const *filename, std::vector &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 int load_coords(char const *filename, std::vector &pos, const std::vector &indices, std::string const &pdb_field, double const pdb_field_value = 0.0) = 0; protected: /// \brief Open output files: by default, these are ofstream objects. /// Allows redefinition to implement different output mechanisms std::list output_files; /// \brief Identifiers for output_stream objects: by default, these are the names of the files std::list output_stream_names; public: // TODO the following definitions may be moved to a .cpp file /// \brief Returns a reference to the given output channel; /// if this is not open already, then open it virtual std::ostream * output_stream(std::string const &output_name) { std::list::iterator osi = output_files.begin(); std::list::iterator osni = output_stream_names.begin(); for ( ; osi != output_files.end(); osi++, osni++) { if (*osni == output_name) { return *osi; } } output_stream_names.push_back(output_name); std::ofstream * os = new std::ofstream(output_name.c_str()); if (!os->is_open()) { cvm::error("Error: cannot write to file \""+output_name+"\".\n", FILE_ERROR); } output_files.push_back(os); return os; } /// \brief Closes the given output channel virtual int close_output_stream(std::string const &output_name) { std::list::iterator osi = output_files.begin(); std::list::iterator osni = output_stream_names.begin(); for ( ; osi != output_files.end(); osi++, osni++) { if (*osni == output_name) { ((std::ofstream *) (*osi))->close(); output_files.erase(osi); output_stream_names.erase(osni); return COLVARS_OK; } } return COLVARS_ERROR; } /// \brief Rename the given file, before overwriting it virtual int backup_file(char const *filename) { return COLVARS_NOT_IMPLEMENTED; } }; inline void colvarproxy::select_closest_images(std::vector &pos, cvm::atom_pos const &ref_pos) { for (std::vector::iterator pi = pos.begin(); pi != pos.end(); ++pi) { select_closest_image(*pi, ref_pos); } } inline cvm::real colvarproxy::position_dist2(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) { return (position_distance(pos1, pos2)).norm2(); } #endif