/*
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*
- * This source code is part of
- *
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* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
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*/
#ifndef _update_h
#define _update_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"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/timing/wallcycle.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_graph;
+
/* 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);
+gmx_update_t init_update(t_inputrec *ir);
/* Store the random state from sd in state */
void get_stochd_state(gmx_update_t sd, t_state *state);
* as a reference state for simulations with box deformation.
*/
void set_deform_reference_box(gmx_update_t upd,
- gmx_large_int_t step, matrix box);
+ gmx_int64_t step, matrix box);
-void update_tcouple(FILE *fplog,
- gmx_large_int_t step,
+void update_tcouple(gmx_int64_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
);
void update_pcouple(FILE *fplog,
- gmx_large_int_t step,
+ gmx_int64_t step,
t_inputrec *inputrec,
t_state *state,
matrix pcoupl_mu,
matrix M,
- gmx_wallcycle_t wcycle,
- gmx_update_t upd,
gmx_bool bInitStep);
void update_coords(FILE *fplog,
- gmx_large_int_t step,
+ gmx_int64_t step,
t_inputrec *inputrec, /* input record and box stuff */
t_mdatoms *md,
t_state *state,
rvec *f, /* forces on home particles */
gmx_bool bDoLR,
rvec *f_lr,
+ tensor *vir_lr_constr,
t_fcdata *fcd,
gmx_ekindata_t *ekind,
matrix M,
- gmx_wallcycle_t wcycle,
gmx_update_t upd,
gmx_bool bInitStep,
int bUpdatePart,
/* Return TRUE if OK, FALSE in case of Shake Error */
-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);
+extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_int64_t step, const t_commrec *cr, t_mdatoms *md, t_state *state, gmx_update_t upd, gmx_constr_t constr);
void update_constraints(FILE *fplog,
- gmx_large_int_t step,
+ gmx_int64_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,
+ struct 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 */
void update_box(FILE *fplog,
- gmx_large_int_t step,
+ gmx_int64_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);
+ gmx_update_t upd);
/* Return TRUE if OK, FALSE in case of Shake Error */
void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
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 andersen_tcoupl(t_inputrec *ir, gmx_int64_t step,
+ const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac);
void nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt,
double xi[], double vxi[], t_extmass *MassQ);
void destroy_bufstate(t_state *state);
-void trotter_update(t_inputrec *ir, gmx_large_int_t step, gmx_ekindata_t *ekind,
+void trotter_update(t_inputrec *ir, gmx_int64_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);
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);
+void vrescale_tcoupl(t_inputrec *ir, gmx_int64_t step,
+ gmx_ekindata_t *ekind, real dt,
+ double therm_integral[]);
/* Compute temperature scaling. For V-rescale it is done in update. */
real vrescale_energy(t_grpopts *opts, double therm_integral[]);
* The unit of pressure is bar.
*/
-void parrinellorahman_pcoupl(FILE *fplog, gmx_large_int_t step,
+void parrinellorahman_pcoupl(FILE *fplog, gmx_int64_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,
+void berendsen_pcoupl(FILE *fplog, gmx_int64_t step,
t_inputrec *ir, real dt, tensor pres, matrix box,
matrix mu);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff