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Created: Tue, Jun 18, 10:27

colvarproxy_lammps.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_LAMMPS_H
	#define COLVARPROXY_LAMMPS_H

	#include "colvarmodule.h"
	#include "colvarproxy.h"
	#include "colvarvalue.h"

	#include "lammps.h"
	#include "domain.h"
	#include "force.h"
	#include "update.h"

	#include <string>
	#include <vector>
	#include <iostream>

	#if defined(_OPENMP)
	#include <omp.h>
	#endif

	#ifndef COLVARPROXY_VERSION
	#define COLVARPROXY_VERSION "2016-12-27"
	#endif

	/* struct for packed data communication of coordinates and forces. */
	struct commdata {
	int tag,type;
	double x,y,z,m,q;
	};

	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 total_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;

	std::vector<int> atoms_types;

	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*);
	int 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 total_forces_enabled() const { return total_force_requested; };
	bool want_exit() const { return do_exit; };

	// 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_total_force(bool yesno) { total_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 backup_file(char const *filename);

	cvm::real rand_gaussian(void) { return _random->gaussian(); };

	int init_atom(int atom_number);
	int check_atom_id(int atom_number);

	inline std::vector<int> *modify_atom_types() { return &atoms_types; }

	// implementation of optional methods from base class
	public:

	#if defined(_OPENMP)
	// SMP support
	int smp_enabled();
	int smp_colvars_loop();
	int smp_biases_loop();
	int smp_thread_id();
	int smp_num_threads();
	protected:
	omp_lock_t smp_lock_state;
	public:
	int smp_lock();
	int smp_trylock();
	int smp_unlock();
	#endif

	// 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

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