Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / legacyheaders / update.h

diff --git a/src/gromacs/legacyheaders/update.h b/src/gromacs/legacyheaders/update.h
index 8591327ccc4a1d0eb860deb58685fb59f4f98aa8..ce3e00d722eae19631d8c222c2613149385cdec5 100644 (file)
--- a/src/gromacs/legacyheaders/update.h
+++ b/src/gromacs/legacyheaders/update.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -38,18 +38,17 @@
 #ifndef _update_h
 #define _update_h
 
-#include "typedefs.h"
-#include "mshift.h"
-#include "tgroup.h"
-#include "network.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;
 
@@ -72,7 +71,6 @@ void update_tcouple(gmx_int64_t       step,
                     t_inputrec       *inputrec,
                     t_state          *state,
                     gmx_ekindata_t   *ekind,
-                    gmx_update_t      upd,
                     t_extmass        *MassQ,
                     t_mdatoms        *md
                     );
@@ -94,6 +92,7 @@ void update_coords(FILE             *fplog,
                    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,
@@ -107,7 +106,7 @@ void update_coords(FILE             *fplog,
 
 /* Return TRUE if OK, FALSE in case of Shake Error */
 
-extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_int64_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_int64_t       step,
@@ -117,7 +116,7 @@ void update_constraints(FILE             *fplog,
                         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,
@@ -175,7 +174,8 @@ restore_ekinstate_from_state(t_commrec *cr,
 
 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);
@@ -196,9 +196,9 @@ real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
 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[]);