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colvarproxy_lammps.h
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Mon, Oct 7, 19:57

colvarproxy_lammps.h
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#ifndef COLVARPROXY_LAMMPS_H
#define COLVARPROXY_LAMMPS_H
#include "colvarmodule.h"
#include "colvarproxy.h"
#include "lammps.h"
#include "domain.h"
#include "force.h"
#include "random_park.h"
#include "update.h"
#include <string>
#include <vector>
#include <iostream>
#ifndef COLVARPROXY_VERSION
#define COLVARPROXY_VERSION "2015-07-21"
#endif
/* struct for packed data communication of coordinates and forces. */
struct commdata {
int tag,type;
double x,y,z,m;
};
inline std::ostream & operator<< (std::ostream &out, const commdata &cd)
{
out << " (" << cd.tag << "/" << cd.type << ": "
<< cd.x << ", " << cd.y << ", " << cd.z << ") ";
return out;
}
/// \brief Communication between colvars and LAMMPS
/// (implementation of \link colvarproxy \endlink)
class colvarproxy_lammps : public colvarproxy {
// LAMMPS specific data objects and flags
protected:
// pointers to LAMMPS class instances
class LAMMPS_NS::LAMMPS *_lmp;
class LAMMPS_NS::RanPark *_random;
// state of LAMMPS properties
double t_target, my_timestep, my_boltzmann, my_angstrom;
double bias_energy;
int restart_every;
int previous_step;
bool first_timestep;
bool system_force_requested;
bool do_exit;
std::vector<int> colvars_atoms;
std::vector<size_t> colvars_atoms_ncopies;
std::vector<struct commdata> positions;
std::vector<struct commdata> total_forces;
std::vector<struct commdata> applied_forces;
std::vector<struct commdata> previous_applied_forces;
MPI_Comm inter_comm; // MPI comm with 1 root proc from each world
int inter_me, inter_num; // rank for the inter replica comm
public:
friend class cvm::atom;
colvarproxy_lammps (LAMMPS_NS::LAMMPS *lmp, const char *,
const char *, const int, const double, MPI_Comm);
virtual ~colvarproxy_lammps();
void init(const char*);
void setup();
// disable default and copy constructor
private:
colvarproxy_lammps() {};
colvarproxy_lammps(const colvarproxy_lammps &) {};
// methods for lammps to move data or trigger actions in the proxy
public:
void set_temperature(double t) { t_target = t; };
bool need_system_forces() const { return system_force_requested; };
bool want_exit() const { return do_exit; };
std::vector<int> * get_tags() { return &colvars_atoms; };
std::vector<struct commdata> * get_coords() { return &positions; };
std::vector<struct commdata> * get_forces() { return &applied_forces; };
std::vector<struct commdata> * get_oforce() { return &total_forces; };
// initialize atom structure
int init_lammps_atom(const int &, cvm::atom *);
// perform colvars computation. returns biasing energy
double compute();
// dump status to string
void serialize_status(std::string &);
// set status from string
bool deserialize_status(std::string &);
// implementation of pure methods from base class
public:
inline cvm::real unit_angstrom() { return my_angstrom; };
inline cvm::real boltzmann() { return my_boltzmann; };
inline cvm::real temperature() { return t_target; };
inline cvm::real dt() { return my_timestep; }; // return _lmp->update->dt * _lmp->force->femtosecond; };
inline size_t restart_frequency() { return restart_every; };
void add_energy(cvm::real energy) { bias_energy += energy; };
void request_system_force(bool yesno) { system_force_requested = yesno; };
void log(std::string const &message);
void error(std::string const &message);
void fatal_error(std::string const &message);
void exit(std::string const &message);
cvm::rvector position_distance(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2);
cvm::real position_dist2(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2);
void select_closest_image(cvm::atom_pos &pos,
cvm::atom_pos const &ref_pos);
int load_atoms(char const *filename,
std::vector<cvm::atom> &atoms,
std::string const &pdb_field,
double const pdb_field_value = 0.0);
int load_coords(char const *filename,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const &pdb_field,
double const pdb_field_value = 0.0);
int backup_file(char const *filename);
cvm::real rand_gaussian(void) { return _random->gaussian(); };
// implementation of optional methods from base class
public:
// Multi-replica support
// Indicate if multi-replica support is available and active
virtual bool replica_enabled() { return (inter_comm != MPI_COMM_NULL); }
// Index of this replica
virtual int replica_index() { return inter_me; }
// Total number of replica
virtual int replica_num() { return inter_num; }
// Synchronize replica
virtual void replica_comm_barrier();
// Receive data from other replica
virtual int replica_comm_recv(char* msg_data, int buf_len, int src_rep);
// Send data to other replica
virtual int replica_comm_send(char* msg_data, int msg_len, int dest_rep);
};
#endif
// Emacs
// Local Variables:
// mode: C++
// End:

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