include/update.h

   1 /*
   2  * $Id$
   3  *
   4  *       This source code is part of
   5  *
   6  *        G   R   O   M   A   C   S
   7  *
   8  * GROningen MAchine for Chemical Simulations
   9  *
  10  *               VERSION 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * Green Red Orange Magenta Azure Cyan Skyblue
  28  */
  29
  30 #ifndef _update_h
  31 #define _update_h
  32
  33 static char *SRCID_update_h = "$Id$";
  34
  35 #ifdef HAVE_IDENT
  36 #ident  "@(#) update.h 1.33 24 Jun 1996"
  37 #endif /* HAVE_IDENT */
  38
  39 #include "typedefs.h"
  40 #include "mshift.h"
  41 #include "tgroup.h"
  42 #include "network.h"
  43 #include "force.h"
  44 #include "pull.h"
  45
  46 extern void update(int          natoms, /* number of atoms in simulation */
  47                    int           start,
  48                    int          homenr, /* number of home particles     */
  49                    int          step,
  50                    real         lambda, /* FEP scaling parameter */
  51                    real         *dvdlambda, /* FEP stuff */
  52                    t_inputrec   *ir,    /* input record with constants  */
  53                    t_mdatoms    *md,
  54                    rvec         x[],    /* coordinates of home particles */
  55                    t_graph      *graph,
  56                    rvec         shift_vec[],
  57                    rvec         force[],/* forces on home particles     */
  58                    rvec         delta_f[],
  59                    rvec         vold[], /* Old velocities                  */
  60                    rvec         v[],    /* velocities of home particles */
  61                    rvec         vt[],   /* velocity at time t           */
  62                    tensor       pressure,/* instantaneous pressure tensor */
  63                    tensor       box,    /* instantaneous box lengths    */
  64                    t_topology   *top,
  65                    t_groups     *grps,
  66                    tensor       vir_part,
  67                    t_commrec    *cr,
  68                    t_nrnb       *nrnb,
  69                    bool         bTYZ,
  70                    bool         bDoUpdate,
  71                    t_edsamyn    *edyn,
  72                    t_pull       *pulldata);
  73
  74 extern void calc_ke_part(bool bFirstStep,int start,int homenr,
  75                          rvec vold[],rvec v[],rvec vt[],
  76                          t_grpopts *opts,t_mdatoms *md,
  77                          t_groups *grps,t_nrnb *nrnb,
  78                          real lambda,real *dvdlambda);
  79 /*
  80  * Compute the partial kinetic energy for home particles;
  81  * will be accumulated in the calling routine.
  82  * The tensor is
  83  *
  84  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
  85  *
  86  *     use v[i] = v[i] - u[i] when calculating temperature
  87  *
  88  * u must be accumulated already.
  89  *
  90  * Now also computes the contribution of the kinetic energy to the
  91  * free energy
  92  *
  93  */
  94
  95 /* Routines from coupling.c to do with Temperature, Pressure and coupling
  96  * algorithms.
  97  */
  98 extern real run_aver(real old,real cur,int step,int nmem);
  99
 100 extern void tcoupl(bool bTC,t_grpopts *opts,t_groups *grps,
 101                    real dt,real SAfactor,int step,int nmem);
 102 /* Compute temperature scaling factors */
 103
 104 extern real calc_temp(real ekin,int nrdf);
 105 /* Calculate the temperature */
 106
 107 extern void calc_pres(int eBox,matrix box,
 108                       tensor ekin,tensor vir,tensor pres,real Elr);
 109 /* Calculate the pressure. Unit of pressure is bar, If Elr != 0
 110  * a long range correction based on Ewald/PPPM is made (see c-code)
 111  */
 112
 113 extern void do_pcoupl(t_inputrec *ir,int step,tensor pres,
 114                       matrix box,int start,int nr_atoms,
 115                       rvec x[],unsigned short cFREEZE[],
 116                       t_nrnb *nrnb,ivec nFreeze[]);
 117
 118 #endif  /* _update_h */
 119