// -*- c++ -*- // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/Colvars/colvars // Please update all Colvars source files before making any changes. // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. #ifndef COLVARPROXY_H #define COLVARPROXY_H #include "colvarmodule.h" #include "colvartypes.h" #include "colvarproxy_io.h" #include "colvarproxy_system.h" #include "colvarproxy_tcl.h" #include "colvarproxy_volmaps.h" /// \file colvarproxy.h /// \brief Colvars proxy classes /// /// This file declares the class for the object responsible for interfacing /// Colvars with other codes (MD engines, VMD, Python). The \link colvarproxy /// \endlink class is a derivative of multiple classes, each devoted to a /// specific task (e.g. \link colvarproxy_atoms \endlink to access data for /// individual atoms). /// /// To interface to a new MD engine, the simplest solution is to derive a new /// class from \link colvarproxy \endlink. Currently implemented are: \link /// colvarproxy_lammps, \endlink, \link colvarproxy_namd, \endlink, \link /// colvarproxy_vmd \endlink. // forward declarations class colvarscript; /// \brief Container of atomic data for processing by Colvars class colvarproxy_atoms { public: /// Constructor colvarproxy_atoms(); /// Destructor virtual ~colvarproxy_atoms(); /// Prepare this atom for collective variables calculation, selecting it by /// numeric index (1-based) virtual int init_atom(int atom_number); /// Check that this atom number is valid, but do not initialize the /// corresponding atom yet virtual int check_atom_id(int atom_number); /// Check whether it is possible to select atoms by residue number name virtual int check_atom_name_selections_available(); /// Select this atom for collective variables calculation, using name and /// residue number. Not all programs support this: leave this function as /// is in those cases. virtual int init_atom(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id); /// Check that this atom is valid, but do not initialize it yet virtual int check_atom_id(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id); /// \brief Used by the atom class destructor: rather than deleting the array slot /// (costly) set the corresponding atoms_refcount to zero virtual void clear_atom(int index); /// Clear atomic data int reset(); /// Get the numeric ID of the given atom /// \param index Internal index in the Colvars arrays inline int get_atom_id(int index) const { return atoms_ids[index]; } /// Get the mass of the given atom /// \param index Internal index in the Colvars arrays inline cvm::real get_atom_mass(int index) const { return atoms_masses[index]; } /// Increase the reference count of the given atom /// \param index Internal index in the Colvars arrays inline void increase_refcount(int index) { atoms_refcount[index] += 1; } /// Get the charge of the given atom /// \param index Internal index in the Colvars arrays inline cvm::real get_atom_charge(int index) const { return atoms_charges[index]; } /// Read the current position of the given atom /// \param index Internal index in the Colvars arrays inline cvm::rvector get_atom_position(int index) const { return atoms_positions[index]; } /// Read the current total force of the given atom /// \param index Internal index in the Colvars arrays inline cvm::rvector get_atom_total_force(int index) const { return atoms_total_forces[index]; } /// Request that this force is applied to the given atom /// \param index Internal index in the Colvars arrays /// \param new_force Force to add inline void apply_atom_force(int index, cvm::rvector const &new_force) { atoms_new_colvar_forces[index] += new_force; } /// Read the current velocity of the given atom inline cvm::rvector get_atom_velocity(int /* index */) { cvm::error("Error: reading the current velocity of an atom " "is not yet implemented.\n", COLVARS_NOT_IMPLEMENTED); return cvm::rvector(0.0); } inline std::vector const *get_atom_ids() const { return &atoms_ids; } /// Return number of atoms with positive reference count size_t get_num_active_atoms() const; inline std::vector const *get_atom_masses() const { return &atoms_masses; } inline std::vector *modify_atom_masses() { // assume that we are requesting masses to change them updated_masses_ = true; return &atoms_masses; } inline std::vector const *get_atom_charges() { return &atoms_charges; } inline std::vector *modify_atom_charges() { // assume that we are requesting charges to change them updated_charges_ = true; return &atoms_charges; } inline std::vector const *get_atom_positions() const { return &atoms_positions; } inline std::vector *modify_atom_positions() { return &atoms_positions; } inline std::vector const *get_atom_total_forces() const { return &atoms_total_forces; } inline std::vector *modify_atom_total_forces() { return &atoms_total_forces; } inline std::vector const *get_atom_applied_forces() const { return &atoms_new_colvar_forces; } inline std::vector *modify_atom_applied_forces() { return &atoms_new_colvar_forces; } /// Compute the root-mean-square of the applied forces void compute_rms_atoms_applied_force(); /// Compute the maximum norm among all applied forces void compute_max_atoms_applied_force(); /// Get the root-mean-square of the applied forces inline cvm::real rms_atoms_applied_force() const { return atoms_rms_applied_force_; } /// Get the maximum norm among all applied forces inline cvm::real max_atoms_applied_force() const { return atoms_max_applied_force_; } /// Get the atom ID with the largest applied force inline int max_atoms_applied_force_id() const { return atoms_max_applied_force_id_; } /// Whether the atom list has been modified internally inline bool modified_atom_list() const { return modified_atom_list_; } /// Reset the modified atom list flag inline void reset_modified_atom_list() { modified_atom_list_ = false; } /// Record whether masses have been updated inline bool updated_masses() const { return updated_masses_; } /// Record whether masses have been updated inline bool updated_charges() const { return updated_charges_; } protected: /// \brief Array of 0-based integers used to uniquely associate atoms /// within the host program std::vector atoms_ids; /// \brief Keep track of how many times each atom is used by a separate colvar object std::vector atoms_refcount; /// \brief Masses of the atoms (allow redefinition during a run, as done e.g. in LAMMPS) std::vector atoms_masses; /// \brief Charges of the atoms (allow redefinition during a run, as done e.g. in LAMMPS) std::vector atoms_charges; /// \brief Current three-dimensional positions of the atoms std::vector atoms_positions; /// \brief Most recent total forces on each atom std::vector atoms_total_forces; /// \brief Forces applied from colvars, to be communicated to the MD integrator std::vector atoms_new_colvar_forces; /// Root-mean-square of the applied forces cvm::real atoms_rms_applied_force_; /// Maximum norm among all applied forces cvm::real atoms_max_applied_force_; /// ID of the atom with the maximum norm among all applied forces int atoms_max_applied_force_id_; /// Whether the atom list has been modified internally bool modified_atom_list_; /// Whether the masses and charges have been updated from the host code bool updated_masses_, updated_charges_; /// Used by all init_atom() functions: create a slot for an atom not /// requested yet; returns the index in the arrays int add_atom_slot(int atom_id); }; /// \brief Container of atom group data (allow collection of aggregated atomic /// data) class colvarproxy_atom_groups { public: /// Constructor colvarproxy_atom_groups(); /// Destructor virtual ~colvarproxy_atom_groups(); /// Clear atom group data int reset(); /// \brief Whether this proxy implementation has capability for scalable groups virtual int scalable_group_coms(); /// Prepare this group for collective variables calculation, selecting atoms by internal ids (0-based) virtual int init_atom_group(std::vector const &atoms_ids); /// \brief Used by the atom_group class destructor virtual void clear_atom_group(int index); /// Get the numeric ID of the given atom group (for the MD program) inline int get_atom_group_id(int index) const { return atom_groups_ids[index]; } /// Get the mass of the given atom group inline cvm::real get_atom_group_mass(int index) const { return atom_groups_masses[index]; } /// Get the charge of the given atom group inline cvm::real get_atom_group_charge(int index) const { return atom_groups_charges[index]; } /// Read the current position of the center of mass given atom group inline cvm::rvector get_atom_group_com(int index) const { return atom_groups_coms[index]; } /// Read the current total force of the given atom group inline cvm::rvector get_atom_group_total_force(int index) const { return atom_groups_total_forces[index]; } /// Request that this force is applied to the given atom group inline void apply_atom_group_force(int index, cvm::rvector const &new_force) { atom_groups_new_colvar_forces[index] += new_force; } /// Read the current velocity of the given atom group inline cvm::rvector get_atom_group_velocity(int /* index */) { cvm::error("Error: reading the current velocity of an atom group is not yet implemented.\n", COLVARS_NOT_IMPLEMENTED); return cvm::rvector(0.0); } inline std::vector const *get_atom_group_ids() const { return &atom_groups_ids; } /// Return number of atom groups with positive reference count size_t get_num_active_atom_groups() const; inline std::vector *modify_atom_group_masses() { // TODO updated_masses return &atom_groups_masses; } inline std::vector *modify_atom_group_charges() { // TODO updated masses return &atom_groups_charges; } inline std::vector *modify_atom_group_positions() { return &atom_groups_coms; } inline std::vector *modify_atom_group_total_forces() { return &atom_groups_total_forces; } inline std::vector *modify_atom_group_applied_forces() { return &atom_groups_new_colvar_forces; } /// Compute the root-mean-square of the applied forces void compute_rms_atom_groups_applied_force(); /// Compute the maximum norm among all applied forces void compute_max_atom_groups_applied_force(); /// Get the root-mean-square of the applied forces inline cvm::real rms_atom_groups_applied_force() const { return atom_groups_rms_applied_force_; } /// Get the maximum norm among all applied forces inline cvm::real max_atom_groups_applied_force() const { return atom_groups_max_applied_force_; } protected: /// \brief Array of 0-based integers used to uniquely associate atom groups /// within the host program std::vector atom_groups_ids; /// \brief Keep track of how many times each group is used by a separate cvc std::vector atom_groups_refcount; /// \brief Total masses of the atom groups std::vector atom_groups_masses; /// \brief Total charges of the atom groups (allow redefinition during a run, as done e.g. in LAMMPS) std::vector atom_groups_charges; /// \brief Current centers of mass of the atom groups std::vector atom_groups_coms; /// \brief Most recently updated total forces on the com of each group std::vector atom_groups_total_forces; /// \brief Forces applied from colvars, to be communicated to the MD integrator std::vector atom_groups_new_colvar_forces; /// Root-mean-square of the applied group forces cvm::real atom_groups_rms_applied_force_; /// Maximum norm among all applied group forces cvm::real atom_groups_max_applied_force_; /// Used by all init_atom_group() functions: create a slot for an atom group not requested yet int add_atom_group_slot(int atom_group_id); }; #if defined(_OPENMP) #include #else struct omp_lock_t; #endif /// \brief Methods for SMP parallelization class colvarproxy_smp { public: /// Constructor colvarproxy_smp(); /// Destructor virtual ~colvarproxy_smp(); /// Whether threaded parallelization should be used (TODO: make this a /// cvm::deps feature) bool b_smp_active; /// Whether threaded parallelization is available (TODO: make this a cvm::deps feature) virtual int check_smp_enabled(); /// Distribute calculation of colvars (and their components) across threads virtual int smp_colvars_loop(); /// Distribute calculation of biases across threads virtual int smp_biases_loop(); /// Distribute calculation of biases across threads 2nd through last, with all scripted biased on 1st thread virtual int smp_biases_script_loop(); /// Index of this thread virtual int smp_thread_id(); /// Number of threads sharing this address space virtual int smp_num_threads(); /// Lock the proxy's shared data for access by a thread, if threads are implemented; if not implemented, does nothing virtual int smp_lock(); /// Attempt to lock the proxy's shared data virtual int smp_trylock(); /// Release the lock virtual int smp_unlock(); protected: /// Lock state for OpenMP omp_lock_t *omp_lock_state; }; /// \brief Methods for multiple-replica communication class colvarproxy_replicas { public: /// Constructor colvarproxy_replicas(); /// Destructor virtual ~colvarproxy_replicas(); /// \brief Indicate if multi-replica support is available and active virtual int replica_enabled(); /// \brief Index of this replica virtual int replica_index(); /// \brief Total number of replicas virtual int num_replicas(); /// \brief Synchronize replica with others 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); /// \brief Send data to other replica virtual int replica_comm_send(char* msg_data, int msg_len, int dest_rep); }; /// Methods for scripting language interface (Tcl or Python) class colvarproxy_script { public: /// Constructor colvarproxy_script(); /// Destructor virtual ~colvarproxy_script(); /// Pointer to the scripting interface object /// (does not need to be allocated in a new interface) colvarscript *script; /// Do we have a scripting interface? bool have_scripts; /// Run a user-defined colvar forces script virtual int run_force_callback(); virtual int run_colvar_callback( std::string const &name, std::vector const &cvcs, colvarvalue &value); virtual int run_colvar_gradient_callback( std::string const &name, std::vector const &cvcs, std::vector > &gradient); }; /// Interface between Colvars and MD engine (GROMACS, LAMMPS, NAMD, VMD...) /// /// This is the base class: each engine is supported by a derived class. class colvarproxy : public colvarproxy_system, public colvarproxy_atoms, public colvarproxy_atom_groups, public colvarproxy_volmaps, public colvarproxy_smp, public colvarproxy_replicas, public colvarproxy_script, public colvarproxy_tcl, public colvarproxy_io { public: /// Pointer to the main object colvarmodule *colvars; /// Constructor colvarproxy(); /// Destructor ~colvarproxy() override; inline std::string const &engine_name() const { return engine_name_; } bool io_available() override; /// Request deallocation of the module (currently only implemented by VMD) virtual int request_deletion(); /// Whether deallocation was requested inline bool delete_requested() const { return b_delete_requested; } /// \brief Reset proxy state, e.g. requested atoms virtual int reset(); /// (Re)initialize the module virtual int parse_module_config(); /// \brief Read a selection of atom IDs from a PDB coordinate file /// \param[in] filename name of the file /// \param[in,out] atoms array into which atoms will be read from "filename" /// \param[in] pdb_field if the file is a PDB and this string is non-empty, /// select atoms for which this field is non-zero /// \param[in] pdb_field_value if non-zero, select only atoms whose pdb_field equals this virtual int load_atoms_pdb(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, double pdb_field_value); /// \brief Load a set of coordinates from a PDB file /// \param[in] filename name of the file /// \param[in,out] pos array of coordinates to fill; if not empty, the number of its elements must match /// the number of entries in "filename" /// \param[in] sorted_ids array of sorted internal IDs, used to loop through the file only once /// \param[in] pdb_field if non-empty, only atoms for which this field is non-zero will be processed /// \param[in] pdb_field_value if non-zero, process only atoms whose pdb_field equals this virtual int load_coords_pdb(char const *filename, std::vector &pos, std::vector const &sorted_ids, std::string const &pdb_field, double pdb_field_value); /// (Re)initialize required member data (called after the module) virtual int setup(); /// Whether the engine allows to fully initialize Colvars immediately inline bool engine_ready() const { return engine_ready_; } /// Enqueue new configuration text, to be parsed as soon as possible void add_config(std::string const &cmd, std::string const &conf); /// Update data required by Colvars module (e.g. read atom positions) /// /// TODO Break up colvarproxy_namd and colvarproxy_lammps function into these virtual int update_input(); /// Update data based on the results of a Colvars call (e.g. send forces) virtual int update_output(); /// Carry out operations needed before next simulation step is run int end_of_step(); /// Print a message to the main log virtual void log(std::string const &message); /// Print a message to the main log and/or let the host code know about it virtual void error(std::string const &message); /// Record error message (used by VMD to collect them after a script call) void add_error_msg(std::string const &message); /// Retrieve accumulated error messages std::string const & get_error_msgs(); /// As the name says void clear_error_msgs(); /// Whether a simulation is running (warn against irrecovarable errors) inline bool simulation_running() const { return b_simulation_running; } /// Is the current step a repetition of a step just executed? /// This is set to true when the step 0 of a new "run" command is being /// executed, regardless of whether a state file has been loaded. inline bool simulation_continuing() const { return b_simulation_continuing; } /// Called at the end of a simulation segment (i.e. "run" command) int post_run(); /// Print a full list of all input atomic arrays for debug purposes void print_input_atomic_data(); /// Print a full list of all applied forces for debug purposes void print_output_atomic_data(); /// Convert a version string "YYYY-MM-DD" into an integer int get_version_from_string(char const *version_string); /// Get the version number (higher = more recent) int version_number() const { return version_int; } protected: /// Whether the engine allows to fully initialize Colvars immediately bool engine_ready_; /// Collected error messages std::string error_output; /// Whether a simulation is running (warn against irrecovarable errors) bool b_simulation_running; /// Is the current step a repetition of a step just executed? /// This is set to true when the step 0 of a new "run" command is being /// executed, regardless of whether a state file has been loaded. bool b_simulation_continuing; /// Whether the entire module should be deallocated by the host engine bool b_delete_requested; /// Integer representing the version string (allows comparisons) int version_int; /// Track which features have been acknowledged during the last run size_t features_hash; protected: /// Name of the simulation engine that the derived proxy object supports std::string engine_name_ = "standalone"; /// Queue of config strings or files to be fed to the module void *config_queue_; }; #endif