lammps/lib/colvars/colvarproxy.h

// -*- 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 <fstream>
#include <list>

#include "colvarmodule.h"
#include "colvartypes.h"
#include "colvarvalue.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;


/// Methods for accessing the simulation system (PBCs, integrator, etc)
class colvarproxy_system {

public:

  /// Constructor
  colvarproxy_system();

  /// Destructor
  virtual ~colvarproxy_system();

  /// \brief Name of the unit system used internally by Colvars (by default, that of the back-end).
  /// Supported depending on the back-end: real (A, kcal/mol), metal (A, eV), electron (Bohr, Hartree), gromacs (nm, kJ/mol)
  /// Note: calls to back-end PBC functions assume back-end length unit
  /// We use different unit from back-end in VMD bc using PBC functions from colvarproxy base class
  /// Colvars internal units are user specified, because the module exchanges info in unknown
  /// composite dimensions with user input, while it only exchanges quantities of known
  /// dimension with the back-end (length and forces)
  std::string units;

  /// \brief Request to set the units used internally by Colvars
  virtual int set_unit_system(std::string const &units, bool check_only);

  /// \brief Value of 1 Angstrom in the internal (front-end) Colvars unit for atomic coordinates
  /// * defaults to 0. in the base class; derived proxy classes must set it
  /// * in VMD proxy, can only be changed when no variables are defined
  /// as user-defined values in composite units must be compatible with that system
  cvm::real angstrom_value;

  /// \brief Value of 1 Angstrom in the backend's unit for atomic coordinates
  virtual cvm::real backend_angstrom_value();

  /// \brief Value of 1 kcal/mol in the internal Colvars unit for energy
  cvm::real kcal_mol_value;

  /// \brief Convert a length from Angstrom to internal
  inline cvm::real angstrom_to_internal(cvm::real l) const
  {
    return l * angstrom_value;
  }

  /// \brief Convert a length from internal to Angstrom
  inline cvm::real internal_to_angstrom(cvm::real l) const
  {
    return l / angstrom_value;
  }

  // /// \brief Convert a length from back-end unit to internal
  // inline cvm::real back_end_to_internal_unit(cvm::real l) {
  //   if (angstrom_value == 0.) {
  //     return l / backend_angstrom_value();
  //   }
  //   return l * angstrom_value / backend_angstrom_value();
  // }

  /// \brief Boltzmann constant in internal Colvars units
  virtual cvm::real boltzmann();

  /// \brief Target temperature of the simulation (K units)
  virtual cvm::real temperature();

  /// \brief Time step of the simulation (fs)
  virtual cvm::real dt();

  /// \brief Pseudo-random number with Gaussian distribution
  virtual cvm::real rand_gaussian(void);

  /// Pass restraint energy value for current timestep to MD engine
  virtual void add_energy(cvm::real energy);

  /// \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) const;

  /// Recompute PBC reciprocal lattice (assumes XYZ periodicity)
  void update_pbc_lattice();

  /// Set the lattice vectors to zero
  void reset_pbc_lattice();

  /// \brief Tell the proxy whether total forces are needed (they may not
  /// always be available)
  virtual void request_total_force(bool yesno);

  /// Are total forces being used?
  virtual bool total_forces_enabled() const;

  /// Are total forces from the current step available?
  virtual bool total_forces_same_step() const;

  /// Get the molecule ID when called in VMD; raise error otherwise
  /// \param molid Set this argument equal to the current VMD molid
  virtual int get_molid(int &molid);

  /// Get value of alchemical lambda parameter from back-end (if available)
  virtual int get_alch_lambda(cvm::real* lambda);

  /// Set value of alchemical lambda parameter to be sent to back-end at end of timestep
  void set_alch_lambda(cvm::real lambda);

  /// Send cached value of alchemical lambda parameter to back-end (if available)
  virtual int send_alch_lambda();

  /// Get energy derivative with respect to lambda (if available)
  virtual int get_dE_dlambda(cvm::real* dE_dlambda);

  /// Apply a scalar force on dE_dlambda (back-end distributes it onto atoms)
  virtual int apply_force_dE_dlambda(cvm::real* force);

  /// Get energy second derivative with respect to lambda (if available)
  virtual int get_d2E_dlambda2(cvm::real* d2E_dlambda2);

  /// Force to be applied onto alch. lambda, propagated from biasing forces on dE_dlambda
  cvm::real indirect_lambda_biasing_force;

  /// Get weight factor from accelMD
  virtual cvm::real get_accelMD_factor() const {
    cvm::error("Error: accessing the reweighting factor of accelerated MD  "
               "is not yet implemented in the MD engine.\n",
               COLVARS_NOT_IMPLEMENTED);
    return 1.0;
  }
  virtual bool accelMD_enabled() const {
    return false;
  }

protected:
  /// Next value of lambda to be sent to back-end
  cvm::real cached_alch_lambda;

  /// Whether lambda has been set and needs to be updated in backend
  bool cached_alch_lambda_changed;

  /// Whether the total forces have been requested
  bool total_force_requested;

  /// \brief Type of boundary conditions
  ///
  /// Orthogonal and triclinic cells are made available to objects.
  /// For any other conditions (mixed periodicity, triclinic cells in LAMMPS)
  /// minimum-image distances are computed by the host engine regardless.
  enum Boundaries_type {
    boundaries_non_periodic,
    boundaries_pbc_ortho,
    boundaries_pbc_triclinic,
    boundaries_unsupported
  };

  /// Type of boundary conditions
  Boundaries_type boundaries_type;

  /// Bravais lattice vectors
  cvm::rvector unit_cell_x, unit_cell_y, unit_cell_z;

  /// Reciprocal lattice vectors
  cvm::rvector reciprocal_cell_x, reciprocal_cell_y, reciprocal_cell_z;
};


/// \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);

  /// 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_ncopies to zero
  virtual void clear_atom(int index);

  /// \brief Select atom IDs from a file (usually PDB) \param filename name of
  /// the file \param atoms array to which atoms read from "filename" will be
  /// appended \param pdb_field (optional) if the file is a PDB and this
  /// string is non-empty, select atoms for which this field is non-zero
  /// \param pdb_field_value (optional) if non-zero, select only atoms whose
  /// pdb_field equals this
  virtual int load_atoms(char const *filename,
                         cvm::atom_group &atoms,
                         std::string const &pdb_field,
                         double pdb_field_value = 0.0);

  /// \brief Load a set of coordinates from a file (usually PDB); if "pos" is
  /// already allocated, the number of its elements must match the number of
  /// entries in "filename" \param filename name of the file \param pos array
  /// of coordinates \param sorted_ids array of sorted internal IDs, used to
  /// loop through the file only once \param pdb_field (optional) if the file
  /// is a PDB and this string is non-empty, select atoms for which this field
  /// is non-zero \param pdb_field_value (optional) if non-zero, select only
  /// atoms whose pdb_field equals this
  virtual int load_coords(char const *filename,
                          std::vector<cvm::atom_pos> &pos,
                          std::vector<int> const &sorted_ids,
                          std::string const &pdb_field,
                          double pdb_field_value = 0.0);

  /// Clear atomic data
  int reset();

  /// Get the numeric ID of the given atom (for the program)
  inline int get_atom_id(int index) const
  {
    return atoms_ids[index];
  }

  /// Get the mass of the given atom
  inline cvm::real get_atom_mass(int index) const
  {
    return atoms_masses[index];
  }

  /// Get the charge of the given atom
  inline cvm::real get_atom_charge(int index) const
  {
    return atoms_charges[index];
  }

  /// Read the current position of the given atom
  inline cvm::rvector get_atom_position(int index) const
  {
    return atoms_positions[index];
  }

  /// Read the current total force of the given atom
  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
  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<int> const *get_atom_ids() const
  {
    return &atoms_ids;
  }

  inline std::vector<cvm::real> const *get_atom_masses() const
  {
    return &atoms_masses;
  }

  inline std::vector<cvm::real> *modify_atom_masses()
  {
    // assume that we are requesting masses to change them
    updated_masses_ = true;
    return &atoms_masses;
  }

  inline std::vector<cvm::real> const *get_atom_charges()
  {
    return &atoms_charges;
  }

  inline std::vector<cvm::real> *modify_atom_charges()
  {
    // assume that we are requesting charges to change them
    updated_charges_ = true;
    return &atoms_charges;
  }

  inline std::vector<cvm::rvector> const *get_atom_positions() const
  {
    return &atoms_positions;
  }

  inline std::vector<cvm::rvector> *modify_atom_positions()
  {
    return &atoms_positions;
  }

  inline std::vector<cvm::rvector> const *get_atom_total_forces() const
  {
    return &atoms_total_forces;
  }

  inline std::vector<cvm::rvector> *modify_atom_total_forces()
  {
    return &atoms_total_forces;
  }

  inline std::vector<cvm::rvector> const *get_atom_applied_forces() const
  {
    return &atoms_new_colvar_forces;
  }

  inline std::vector<cvm::rvector> *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_;
  }

  /// 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<int>          atoms_ids;
  /// \brief Keep track of how many times each atom is used by a separate colvar object
  std::vector<size_t>       atoms_ncopies;
  /// \brief Masses of the atoms (allow redefinition during a run, as done e.g. in LAMMPS)
  std::vector<cvm::real>    atoms_masses;
  /// \brief Charges of the atoms (allow redefinition during a run, as done e.g. in LAMMPS)
  std::vector<cvm::real>    atoms_charges;
  /// \brief Current three-dimensional positions of the atoms
  std::vector<cvm::rvector> atoms_positions;
  /// \brief Most recent total forces on each atom
  std::vector<cvm::rvector> atoms_total_forces;
  /// \brief Forces applied from colvars, to be communicated to the MD integrator
  std::vector<cvm::rvector> 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 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<int> 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<int> const *get_atom_group_ids() const
  {
    return &atom_groups_ids;
  }

  inline std::vector<cvm::real> *modify_atom_group_masses()
  {
    // TODO updated_masses
    return &atom_groups_masses;
  }

  inline std::vector<cvm::real> *modify_atom_group_charges()
  {
    // TODO updated masses
    return &atom_groups_charges;
  }

  inline std::vector<cvm::rvector> *modify_atom_group_positions()
  {
    return &atom_groups_coms;
  }

  inline std::vector<cvm::rvector> *modify_atom_group_total_forces()
  {
    return &atom_groups_total_forces;
  }

  inline std::vector<cvm::rvector> *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<int>          atom_groups_ids;
  /// \brief Keep track of how many times each group is used by a separate cvc
  std::vector<size_t>       atom_groups_ncopies;
  /// \brief Total masses of the atom groups
  std::vector<cvm::real>    atom_groups_masses;
  /// \brief Total charges of the atom groups (allow redefinition during a run, as done e.g. in LAMMPS)
  std::vector<cvm::real>    atom_groups_charges;
  /// \brief Current centers of mass of the atom groups
  std::vector<cvm::rvector> atom_groups_coms;
  /// \brief Most recently updated total forces on the com of each group
  std::vector<cvm::rvector> atom_groups_total_forces;
  /// \brief Forces applied from colvars, to be communicated to the MD integrator
  std::vector<cvm::rvector> 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);
};


/// \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 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
  void *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 colvarvalue *> const &cvcs,
                colvarvalue &value);

  virtual int run_colvar_gradient_callback(
                std::string const &name,
                std::vector<const colvarvalue *> const &cvcs,
                std::vector<cvm::matrix2d<cvm::real> > &gradient);
};


/// Methods for data input/output
class colvarproxy_io {

public:

  /// Constructor
  colvarproxy_io();

  /// Destructor
  virtual ~colvarproxy_io();

  /// \brief Save the current frame number in the argument given
  // Returns error code
  virtual int get_frame(long int &);

  /// \brief Set the current frame number (as well as colvarmodule::it)
  // Returns error code
  virtual int set_frame(long int);

  /// \brief Rename the given file, before overwriting it
  virtual int backup_file(char const *filename);

  /// \brief Rename the given file, before overwriting it
  inline int backup_file(std::string const &filename)
  {
    return backup_file(filename.c_str());
  }

  /// Remove the given file (on Windows only, rename to filename.old)
  virtual int remove_file(char const *filename);

  /// Remove the given file (on Windows only, rename to filename.old)
  inline int remove_file(std::string const &filename)
  {
    return remove_file(filename.c_str());
  }

  /// Rename the given file
  virtual int rename_file(char const *filename, char const *newfilename);

  /// Rename the given file
  inline int rename_file(std::string const &filename,
                         std::string const &newfilename)
  {
    return rename_file(filename.c_str(), newfilename.c_str());
  }

  /// Prefix of the input state file to be read next
  inline std::string & input_prefix()
  {
    return input_prefix_str;
  }

  /// Default prefix to be used for all output files (final configuration)
  inline std::string & output_prefix()
  {
    return output_prefix_str;
  }

  /// Prefix of the restart (checkpoint) file to be written next
  inline std::string & restart_output_prefix()
  {
    return restart_output_prefix_str;
  }

  /// Default restart frequency (as set by the simulation engine)
  inline int default_restart_frequency() const
  {
    return restart_frequency_engine;
  }

  /// Buffer from which the input state information may be read
  inline char const * & input_buffer()
  {
    return input_buffer_;
  }

protected:

  /// Prefix of the input state file to be read next
  std::string input_prefix_str;

  /// Default prefix to be used for all output files (final configuration)
  std::string output_prefix_str;

  /// Prefix of the restart (checkpoint) file to be written next
  std::string restart_output_prefix_str;

  /// How often the simulation engine will write its own restart
  int restart_frequency_engine;

  /// \brief Currently opened output files: by default, these are ofstream objects.
  /// Allows redefinition to implement different output mechanisms
  std::list<std::ostream *> output_files;
  /// \brief Identifiers for output_stream objects: by default, these are the names of the files
  std::list<std::string>    output_stream_names;

  /// Buffer from which the input state information may be read
  char const *input_buffer_;
};



/// \brief Interface between the collective variables module and
/// the simulation or analysis program (NAMD, VMD, LAMMPS...).
/// This is the base class: each interfaced program 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
  virtual ~colvarproxy();

  /// Request deallocation of the module (currently only implemented by VMD)
  virtual int request_deletion();

  /// Whether deallocation was requested
  inline bool delete_requested()
  {
    return b_delete_requested;
  }

  /// \brief Reset proxy state, e.g. requested atoms
  virtual int reset();

  /// Close any open files to prevent data loss
  int close_files();

  /// (Re)initialize required member data after construction
  virtual int setup();

  /// \brief Update data required by the colvars module (e.g. cache atom positions)
  ///
  /// TODO Break up colvarproxy_namd and colvarproxy_lammps function into these
  virtual int update_input();

  /// \brief Update data based from the results of a module update (e.g. send forces)
  virtual int update_output();

  /// Carry out operations needed before next 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;
  }

  /// \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::ios_base::openmode mode =
                                      std::ios_base::out);

  /// Returns a reference to output_name if it exists, NULL otherwise
  virtual std::ostream *get_output_stream(std::string const &output_name);

  /// \brief Flushes the given output channel
  virtual int flush_output_stream(std::ostream *os);

  /// \brief Flushes all output channels
  virtual int flush_output_streams();

  /// \brief Closes the given output channel
  virtual int close_output_stream(std::string const &output_name);

protected:

  /// 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;

  /// Raise when the output stream functions are used on threads other than 0
  void smp_stream_error();

};


#endif