include/types/group.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
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  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * GRoups of Organic Molecules in ACtion for Science
  34  */
  35
  36
  37 #include "simple.h"
  38
  39 #ifdef __cplusplus
  40 extern "C" {
  41 #endif
  42
  43
  44 typedef struct {
  45   real    Th;           /* Temperature at half step        */
  46   real    T;            /* Temperature at full step        */
  47   tensor  ekinh;        /* Kinetic energy at half step     */
  48   tensor  ekinh_old;    /* Kinetic energy at old half step */
  49   tensor  ekinf;        /* Kinetic energy at full step     */
  50   real    lambda;       /* Berendsen coupling lambda       */
  51   double  ekinscalef_nhc;/* Scaling factor for NHC- full step */
  52   double  ekinscaleh_nhc;/* Scaling factor for NHC- half step */
  53   double  vscale_nhc;   /* Scaling factor for NHC- velocity */
  54 } t_grp_tcstat;
  55
  56 typedef struct {
  57   int     nat;          /* Number of atoms in this group                */
  58   rvec    u;            /* Mean velocities of home particles            */
  59   rvec    uold;         /* Previous mean velocities of home particles   */
  60   double  mA;           /* Mass for topology A                          */
  61   double  mB;           /* Mass for topology B                          */
  62 } t_grp_acc;
  63
  64 typedef struct {
  65   real    cos_accel;    /* The acceleration for the cosine profile      */
  66   real    mvcos;        /* The cos momenta of home particles            */
  67   real    vcos;         /* The velocity of the cosine profile           */
  68 } t_cos_acc;
  69
  70 typedef struct {
  71   gmx_bool         bNEMD;
  72   int          ngtc;            /* The number of T-coupling groups      */
  73   t_grp_tcstat *tcstat;         /* T-coupling data                      */
  74   tensor       **ekin_work_alloc; /* Allocated locations of ekin_work   */
  75   tensor       **ekin_work;     /* Work arrays for tcstat per thread    */
  76   int          ngacc;           /* The number of acceleration groups    */
  77   t_grp_acc    *grpstat;        /* Acceleration data                    */
  78   tensor       ekin;            /* overall kinetic energy               */
  79   tensor       ekinh;           /* overall 1/2 step kinetic energy      */
  80   real         dekindl;         /* dEkin/dlambda at half step           */
  81   real         dekindl_old;     /* dEkin/dlambda at old half step       */
  82   t_cos_acc    cosacc;          /* Cosine acceleration data             */
  83 } gmx_ekindata_t;
  84
  85 #define GID(igid,jgid,gnr) ((igid < jgid) ? (igid*gnr+jgid) : (jgid*gnr+igid))
  86
  87 #ifdef __cplusplus
  88 }
  89 #endif
  90