gromacs-dev 4.6.5-1build1 / usr / include / gromacs / update.h

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#ifndef _update_h
#define _update_h
#include "visibility.h"
#include "typedefs.h"
#include "mshift.h"
#include "tgroup.h"
#include "network.h"
#include "force.h"
#include "pull.h"
#include "gmx_random.h"
#include "maths.h"

#ifdef __cplusplus
extern "C" {
#endif

/* Abstract type for stochastic dynamics */
typedef struct gmx_update *gmx_update_t;

/* Initialize the stochastic dynamics struct */
gmx_update_t init_update(FILE *fplog, t_inputrec *ir);

/* Store the random state from sd in state */
GMX_LIBMD_EXPORT
void get_stochd_state(gmx_update_t sd, t_state *state);

/* Set the random in sd from state */
GMX_LIBMD_EXPORT
void set_stochd_state(gmx_update_t sd, t_state *state);

/* Store the box at step step
 * as a reference state for simulations with box deformation.
 */
GMX_LIBMD_EXPORT
void set_deform_reference_box(gmx_update_t upd,
                              gmx_large_int_t step, matrix box);

GMX_LIBMD_EXPORT
void update_tcouple(FILE             *fplog,
                    gmx_large_int_t   step,
                    t_inputrec       *inputrec,
                    t_state          *state,
                    gmx_ekindata_t   *ekind,
                    gmx_wallcycle_t   wcycle,
                    gmx_update_t      upd,
                    t_extmass        *MassQ,
                    t_mdatoms        *md
                    );

GMX_LIBMD_EXPORT
void update_pcouple(FILE             *fplog,
                    gmx_large_int_t   step,
                    t_inputrec       *inputrec,
                    t_state          *state,
                    matrix            pcoupl_mu,
                    matrix            M,
                    gmx_wallcycle_t   wcycle,
                    gmx_update_t      upd,
                    gmx_bool          bInitStep);

GMX_LIBMD_EXPORT
void update_coords(FILE             *fplog,
                   gmx_large_int_t   step,
                   t_inputrec       *inputrec, /* input record and box stuff	*/
                   t_mdatoms        *md,
                   t_state          *state,
                   gmx_bool          bMolPBC,
                   rvec             *f, /* forces on home particles */
                   gmx_bool          bDoLR,
                   rvec             *f_lr,
                   t_fcdata         *fcd,
                   gmx_ekindata_t   *ekind,
                   matrix            M,
                   gmx_wallcycle_t   wcycle,
                   gmx_update_t      upd,
                   gmx_bool          bInitStep,
                   int               bUpdatePart,
                   t_commrec        *cr, /* these shouldn't be here -- need to think about it */
                   t_nrnb           *nrnb,
                   gmx_constr_t      constr,
                   t_idef           *idef);

/* Return TRUE if OK, FALSE in case of Shake Error */

GMX_LIBMD_EXPORT
extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_large_int_t step, t_mdatoms *md, t_state *state, gmx_update_t upd, t_idef *idef, gmx_constr_t constr);

GMX_LIBMD_EXPORT
void update_constraints(FILE             *fplog,
                        gmx_large_int_t   step,
                        real             *dvdlambda, /* FEP stuff */
                        t_inputrec       *inputrec,  /* input record and box stuff	*/
                        gmx_ekindata_t   *ekind,
                        t_mdatoms        *md,
                        t_state          *state,
                        gmx_bool          bMolPBC,
                        t_graph          *graph,
                        rvec              force[], /* forces on home particles */
                        t_idef           *idef,
                        tensor            vir_part,
                        tensor            vir,
                        t_commrec        *cr,
                        t_nrnb           *nrnb,
                        gmx_wallcycle_t   wcycle,
                        gmx_update_t      upd,
                        gmx_constr_t      constr,
                        gmx_bool          bInitStep,
                        gmx_bool          bFirstHalf,
                        gmx_bool          bCalcVir,
                        real              vetanew);

/* Return TRUE if OK, FALSE in case of Shake Error */

GMX_LIBMD_EXPORT
void update_box(FILE             *fplog,
                gmx_large_int_t   step,
                t_inputrec       *inputrec, /* input record and box stuff	*/
                t_mdatoms        *md,
                t_state          *state,
                t_graph          *graph,
                rvec              force[], /* forces on home particles */
                matrix           *scale_tot,
                matrix            pcoupl_mu,
                t_nrnb           *nrnb,
                gmx_wallcycle_t   wcycle,
                gmx_update_t      upd,
                gmx_bool          bInitStep,
                gmx_bool          bFirstHalf);
/* Return TRUE if OK, FALSE in case of Shake Error */

void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
                  gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel, gmx_bool bSaveOld);
/*
 * Compute the partial kinetic energy for home particles;
 * will be accumulated in the calling routine.
 * The tensor is
 *
 * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 *
 *     use v[i] = v[i] - u[i] when calculating temperature
 *
 * u must be accumulated already.
 *
 * Now also computes the contribution of the kinetic energy to the
 * free energy
 *
 */


void
init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir);

GMX_LIBMD_EXPORT
void
update_ekinstate(ekinstate_t *ekinstate, gmx_ekindata_t *ekind);

void
restore_ekinstate_from_state(t_commrec *cr,
                             gmx_ekindata_t *ekind, ekinstate_t *ekinstate);

void berendsen_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt);

void andersen_tcoupl(t_inputrec *ir, t_mdatoms *md, t_state *state, gmx_rng_t rng, real rate, t_idef *idef, int nblocks, int *sblock, gmx_bool *randatom, int *randatom_list, gmx_bool *randomize, real *boltzfac);

void nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt,
                       double xi[], double vxi[], t_extmass *MassQ);

GMX_LIBMD_EXPORT
t_state *init_bufstate(const t_state *template_state);

void destroy_bufstate(t_state *state);

GMX_LIBMD_EXPORT
void trotter_update(t_inputrec *ir, gmx_large_int_t step, gmx_ekindata_t *ekind,
                    gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
                    t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);

GMX_LIBMD_EXPORT
int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);

real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
/* computes all the pressure/tempertature control energy terms to get a conserved energy */

void NBaroT_trotter(t_grpopts *opts, real dt,
                    double xi[], double vxi[], real *veta, t_extmass *MassQ);

void vrescale_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt,
                     double therm_integral[],
                     gmx_rng_t rng);
/* Compute temperature scaling. For V-rescale it is done in update. */

real vrescale_energy(t_grpopts *opts, double therm_integral[]);
/* Returns the V-rescale contribution to the conserved energy */

void rescale_velocities(gmx_ekindata_t *ekind, t_mdatoms *mdatoms,
                        int start, int end, rvec v[]);
/* Rescale the velocities with the scaling factor in ekind */

GMX_LIBMD_EXPORT
void update_annealing_target_temp(t_grpopts *opts, real t);
/* Set reference temp for simulated annealing at time t*/

real calc_temp(real ekin, real nrdf);
/* Calculate the temperature */

real calc_pres(int ePBC, int nwall, matrix box, tensor ekin, tensor vir,
               tensor pres);
/* Calculate the pressure tensor, returns the scalar pressure.
 * The unit of pressure is bar.
 */

void parrinellorahman_pcoupl(FILE *fplog, gmx_large_int_t step,
                             t_inputrec *ir, real dt, tensor pres,
                             tensor box, tensor box_rel, tensor boxv,
                             tensor M, matrix mu,
                             gmx_bool bFirstStep);

void berendsen_pcoupl(FILE *fplog, gmx_large_int_t step,
                      t_inputrec *ir, real dt, tensor pres, matrix box,
                      matrix mu);


void berendsen_pscale(t_inputrec *ir, matrix mu,
                      matrix box, matrix box_rel,
                      int start, int nr_atoms,
                      rvec x[], unsigned short cFREEZE[],
                      t_nrnb *nrnb);

void correct_ekin(FILE *log, int start, int end, rvec v[],
                  rvec vcm, real mass[], real tmass, tensor ekin);
/* Correct ekin for vcm */


#ifdef __cplusplus
}
#endif

#endif  /* _update_h */