src/gromacs/mdtypes/group.h

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  37 #ifndef GMX_MDTYPES_GROUP_H
  38 #define GMX_MDTYPES_GROUP_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #include "gromacs/utility/basedefinitions.h"
  42 #include "gromacs/utility/real.h"
  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 gmx_ekindata_t {
  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 for *_work members */
  75     tensor         **ekin_work;       /* Work arrays for tcstat per thread    */
  76     real           **dekindl_work;    /* Work location for dekindl per thread */
  77     int              ngacc;           /* The number of acceleration groups    */
  78     t_grp_acc       *grpstat;         /* Acceleration data                      */
  79     tensor           ekin;            /* overall kinetic energy               */
  80     tensor           ekinh;           /* overall 1/2 step kinetic energy      */
  81     real             dekindl;         /* dEkin/dlambda at half step           */
  82     real             dekindl_old;     /* dEkin/dlambda at old half step       */
  83     t_cos_acc        cosacc;          /* Cosine acceleration data             */
  84 } gmx_ekindata_t;
  85
  86 #define GID(igid, jgid, gnr) ((igid < jgid) ? (igid*gnr+jgid) : (jgid*gnr+igid))
  87
  88 #endif