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colvarproxy.h

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// -*- 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 "colvarvalue.h"
#include "colvarproxy_io.h"
#include "colvarproxy_system.h"
#include "colvarproxy_tcl.h"
#include "colvarproxy_volmaps.h"



// forward declarations
class colvarscript;


class colvarproxy_atoms {

public:

  colvarproxy_atoms();

  virtual ~colvarproxy_atoms();

  virtual int init_atom(int atom_number);

  virtual int check_atom_id(int atom_number);

  virtual int init_atom(cvm::residue_id const &residue,
                        std::string const     &atom_name,
                        std::string const     &segment_id);

  virtual int check_atom_id(cvm::residue_id const &residue,
                            std::string const     &atom_name,
                            std::string const     &segment_id);

  virtual void clear_atom(int index);

  virtual int load_atoms(char const *filename,
                         cvm::atom_group &atoms,
                         std::string const &pdb_field,
                         double pdb_field_value = 0.0);

  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);

  int reset();

  inline int get_atom_id(int index) const
  {
    return atoms_ids[index];
  }

  inline cvm::real get_atom_mass(int index) const
  {
    return atoms_masses[index];
  }

  inline void increase_refcount(int index)
  {
    atoms_refcount[index] += 1;
  }

  inline cvm::real get_atom_charge(int index) const
  {
    return atoms_charges[index];
  }

  inline cvm::rvector get_atom_position(int index) const
  {
    return atoms_positions[index];
  }

  inline cvm::rvector get_atom_total_force(int index) const
  {
    return atoms_total_forces[index];
  }

  inline void apply_atom_force(int index, cvm::rvector const &new_force)
  {
    atoms_new_colvar_forces[index] += new_force;
  }

  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;
  }

  size_t get_num_active_atoms() const;

  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;
  }

  void compute_rms_atoms_applied_force();

  void compute_max_atoms_applied_force();

  inline cvm::real rms_atoms_applied_force() const
  {
    return atoms_rms_applied_force_;
  }

  inline cvm::real max_atoms_applied_force() const
  {
    return atoms_max_applied_force_;
  }

  inline int max_atoms_applied_force_id() const
  {
    return atoms_max_applied_force_id_;
  }

  inline bool updated_masses() const
  {
    return updated_masses_;
  }

  inline bool updated_charges() const
  {
    return updated_charges_;
  }

protected:

  std::vector<int>          atoms_ids;
  std::vector<size_t>       atoms_refcount;
  std::vector<cvm::real>    atoms_masses;
  std::vector<cvm::real>    atoms_charges;
  std::vector<cvm::rvector> atoms_positions;
  std::vector<cvm::rvector> atoms_total_forces;
  std::vector<cvm::rvector> atoms_new_colvar_forces;

  cvm::real atoms_rms_applied_force_;

  cvm::real atoms_max_applied_force_;

  int atoms_max_applied_force_id_;

  bool updated_masses_, updated_charges_;

  int add_atom_slot(int atom_id);

};


class colvarproxy_atom_groups {

public:

  colvarproxy_atom_groups();

  virtual ~colvarproxy_atom_groups();

  int reset();

  virtual int scalable_group_coms();

  virtual int init_atom_group(std::vector<int> const &atoms_ids);

  virtual void clear_atom_group(int index);

  inline int get_atom_group_id(int index) const
  {
    return atom_groups_ids[index];
  }

  inline cvm::real get_atom_group_mass(int index) const
  {
    return atom_groups_masses[index];
  }

  inline cvm::real get_atom_group_charge(int index) const
  {
    return atom_groups_charges[index];
  }

  inline cvm::rvector get_atom_group_com(int index) const
  {
    return atom_groups_coms[index];
  }

  inline cvm::rvector get_atom_group_total_force(int index) const
  {
    return atom_groups_total_forces[index];
  }

  inline void apply_atom_group_force(int index, cvm::rvector const &new_force)
  {
    atom_groups_new_colvar_forces[index] += new_force;
  }

  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;
  }

  size_t get_num_active_atom_groups() const;

  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;
  }

  void compute_rms_atom_groups_applied_force();

  void compute_max_atom_groups_applied_force();

  inline cvm::real rms_atom_groups_applied_force() const
  {
    return atom_groups_rms_applied_force_;
  }

  inline cvm::real max_atom_groups_applied_force() const
  {
    return atom_groups_max_applied_force_;
  }

protected:

  std::vector<int>          atom_groups_ids;
  std::vector<size_t>       atom_groups_refcount;
  std::vector<cvm::real>    atom_groups_masses;
  std::vector<cvm::real>    atom_groups_charges;
  std::vector<cvm::rvector> atom_groups_coms;
  std::vector<cvm::rvector> atom_groups_total_forces;
  std::vector<cvm::rvector> atom_groups_new_colvar_forces;

  cvm::real atom_groups_rms_applied_force_;

  cvm::real atom_groups_max_applied_force_;

  int add_atom_group_slot(int atom_group_id);
};


#if defined(_OPENMP)
#include <omp.h>
#else
struct omp_lock_t;
#endif

class colvarproxy_smp {

public:

  colvarproxy_smp();

  virtual ~colvarproxy_smp();

  bool b_smp_active;

  virtual int smp_enabled();

  virtual int smp_colvars_loop();

  virtual int smp_biases_loop();

  virtual int smp_biases_script_loop();

  virtual int smp_thread_id();

  virtual int smp_num_threads();

  virtual int smp_lock();

  virtual int smp_trylock();

  virtual int smp_unlock();

protected:

  omp_lock_t *omp_lock_state;
};


class colvarproxy_replicas {

public:

  colvarproxy_replicas();

  virtual ~colvarproxy_replicas();

  virtual int replica_enabled();

  virtual int replica_index();

  virtual int num_replicas();

  virtual void replica_comm_barrier();

  virtual int replica_comm_recv(char* msg_data, int buf_len, int src_rep);

  virtual int replica_comm_send(char* msg_data, int msg_len, int dest_rep);

};


class colvarproxy_script {

public:

  colvarproxy_script();

  virtual ~colvarproxy_script();

  colvarscript *script;

  bool have_scripts;

  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);
};



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:

  colvarmodule *colvars;

  colvarproxy();

  virtual ~colvarproxy();

  virtual bool io_available() /* override */;

  virtual int request_deletion();

  inline bool delete_requested()
  {
    return b_delete_requested;
  }

  virtual int reset();

  virtual int parse_module_config();

  virtual int setup();

  inline bool engine_ready() const
  {
    return engine_ready_;
  }

  void add_config(std::string const &cmd, std::string const &conf);

  virtual int update_input();

  virtual int update_output();

  int end_of_step();

  virtual void log(std::string const &message);

  virtual void error(std::string const &message);

  void add_error_msg(std::string const &message);

  std::string const & get_error_msgs();

  void clear_error_msgs();

  inline bool simulation_running() const
  {
    return b_simulation_running;
  }

  inline bool simulation_continuing() const
  {
    return b_simulation_continuing;
  }

  int post_run();

  void print_input_atomic_data();

  void print_output_atomic_data();

  int get_version_from_string(char const *version_string);

  int version_number() const
  {
    return version_int;
  }

protected:

  bool engine_ready_;

  std::string error_output;

  bool b_simulation_running;

  bool b_simulation_continuing;

  bool b_delete_requested;

  int version_int;

  size_t features_hash;

private:

  void *config_queue_;

};


#endif

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