/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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);
+void get_stochd_state(gmx_update_t sd, t_state *state);
/* Set the random in sd from state */
-void set_stochd_state(gmx_update_t sd,t_state *state);
+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.
*/
void set_deform_reference_box(gmx_update_t upd,
- gmx_large_int_t step,matrix box);
-
-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
-);
-
-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);
-
-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);
+ gmx_int64_t step, matrix box);
+
+void update_tcouple(gmx_int64_t step,
+ t_inputrec *inputrec,
+ t_state *state,
+ gmx_ekindata_t *ekind,
+ t_extmass *MassQ,
+ t_mdatoms *md
+ );
+
+void update_pcouple(FILE *fplog,
+ gmx_int64_t step,
+ t_inputrec *inputrec,
+ t_state *state,
+ matrix pcoupl_mu,
+ matrix M,
+ gmx_bool bInitStep);
+
+void update_coords(FILE *fplog,
+ gmx_int64_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,
+ tensor *vir_lr_constr,
+ t_fcdata *fcd,
+ gmx_ekindata_t *ekind,
+ matrix M,
+ 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 */
-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);
-
-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);
+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_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,
+ struct t_graph *graph,
+ rvec force[], /* forces on home particles */
+ t_idef *idef,
+ tensor vir_part,
+ t_commrec *cr,
+ t_nrnb *nrnb,
+ gmx_wallcycle_t wcycle,
+ gmx_update_t upd,
+ gmx_constr_t constr,
+ 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,
- 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);
+void update_box(FILE *fplog,
+ gmx_int64_t step,
+ t_inputrec *inputrec, /* input record and box stuff */
+ t_mdatoms *md,
+ t_state *state,
+ rvec force[], /* forces on home particles */
+ matrix *scale_tot,
+ matrix pcoupl_mu,
+ t_nrnb *nrnb,
+ 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,
- gmx_ekindata_t *ekind,t_nrnb *nrnb,gmx_bool bEkinAveVel, gmx_bool bSaveOld);
+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.
void
-init_ekinstate(ekinstate_t *ekinstate,const t_inputrec *ir);
+init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir);
void
-update_ekinstate(ekinstate_t *ekinstate,gmx_ekindata_t *ekind);
+update_ekinstate(ekinstate_t *ekinstate, gmx_ekindata_t *ekind);
void
restore_ekinstate_from_state(t_commrec *cr,
- gmx_ekindata_t *ekind,ekinstate_t *ekinstate);
+ gmx_ekindata_t *ekind, ekinstate_t *ekinstate);
-void berendsen_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt);
+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 nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt,
+ double xi[], double vxi[], t_extmass *MassQ);
t_state *init_bufstate(const t_state *template_state);
void destroy_bufstate(t_state *state);
-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);
+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);
-int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
+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);
+ 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[]);
+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[]);
+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 */
-void update_annealing_target_temp(t_grpopts *opts,real t);
+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);
+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);
+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);
+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_int64_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 */
}
#endif
-#endif /* _update_h */
-
+#endif /* _update_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff