src/gromacs/mdlib/vcm.h

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  37 #ifndef GMX_MDLIB_VCM_H
  38 #define GMX_MDLIB_VCM_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/mdtypes/mdatom.h"
  44 #include "gromacs/utility/basedefinitions.h"
  45 #include "gromacs/utility/real.h"
  46
  47 struct gmx_groups_t;
  48 struct t_inputrec;
  49
  50 typedef struct {
  51     rvec      p;        /* Linear momentum                     */
  52     rvec      x;        /* Center of mass                      */
  53     rvec      j;        /* Angular momentum                    */
  54     tensor    i;        /* Moment of inertia                   */
  55     real      mass;     /* Mass                                */
  56 } t_vcm_thread;
  57
  58 typedef struct {
  59     int           nr;          /* Number of groups                    */
  60     int           size;        /* Size of group arrays                */
  61     int           stride;      /* Stride for thread data              */
  62     int           mode;        /* One of the enums above              */
  63     gmx_bool      ndim;        /* The number of dimensions for corr.  */
  64     real          timeStep;    /* The time step for COMM removal      */
  65     real         *group_ndf;   /* Number of degrees of freedom        */
  66     rvec         *group_p;     /* Linear momentum per group           */
  67     rvec         *group_v;     /* Linear velocity per group           */
  68     rvec         *group_x;     /* Center of mass per group            */
  69     rvec         *group_j;     /* Angular momentum per group          */
  70     rvec         *group_w;     /* Angular velocity (omega)            */
  71     tensor       *group_i;     /* Moment of inertia per group         */
  72     real         *group_mass;  /* Mass per group                      */
  73     char        **group_name;  /* These two are copies to pointers in */
  74     t_vcm_thread *thread_vcm;  /* Temporary data per thread and group */
  75 } t_vcm;
  76
  77 t_vcm *init_vcm(FILE *fp, gmx_groups_t *groups, const t_inputrec *ir);
  78
  79 /* Do a per group center of mass things */
  80 void calc_vcm_grp(int start, int homenr, t_mdatoms *md,
  81                   rvec x[], rvec v[], t_vcm *vcm);
  82
  83 /* Set the COM velocity to zero and potentially correct the COM position.
  84  *
  85  * With linear modes nullptr can be passed for x.
  86  */
  87 void do_stopcm_grp(int homenr,
  88                    const unsigned short *group_id,
  89                    rvec x[], rvec v[], const t_vcm &vcm);
  90
  91 void check_cm_grp(FILE *fp, t_vcm *vcm, t_inputrec *ir, real Temp_Max);
  92
  93 #endif