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 <vector>
  43
  44 #include "gromacs/math/vectypes.h"
  45 #include "gromacs/mdtypes/mdatom.h"
  46 #include "gromacs/utility/basedefinitions.h"
  47 #include "gromacs/utility/real.h"
  48
  49 struct gmx_groups_t;
  50 struct t_inputrec;
  51 struct t_mdatoms;
  52
  53 struct t_vcm_thread{
  54     rvec      p    = {0};   /* Linear momentum                     */
  55     rvec      x    = {0};   /* Center of mass                      */
  56     rvec      j    = {0};   /* Angular momentum                    */
  57     tensor    i    = {{0}}; /* Moment of inertia                   */
  58     real      mass = 0;     /* Mass                                */
  59 };
  60
  61 struct t_vcm
  62 {
  63     int                       nr;         /* Number of groups                    */
  64     int                       size;       /* Size of group arrays                */
  65     int                       stride;     /* Stride for thread data              */
  66     int                       mode;       /* One of the enums above              */
  67     int                       ndim;       /* The number of dimensions for corr.  */
  68     real                      timeStep;   /* The time step for COMM removal      */
  69     std::vector<real>         group_ndf;  /* Number of degrees of freedom        */
  70     std::vector<real>         group_mass; /* Mass per group                      */
  71     std::vector<gmx::RVec>    group_p;    /* Linear momentum per group           */
  72     std::vector<gmx::RVec>    group_v;    /* Linear velocity per group           */
  73     std::vector<gmx::RVec>    group_x;    /* Center of mass per group            */
  74     std::vector<gmx::RVec>    group_j;    /* Angular momentum per group          */
  75     std::vector<gmx::RVec>    group_w;    /* Angular velocity (omega)            */
  76     tensor                   *group_i;    /* Moment of inertia per group         */
  77     std::vector<char *>       group_name; /* These two are copies to pointers in */
  78     ivec                     *nFreeze;    /* Tells whether dimensions are frozen per freeze group */
  79     std::vector<t_vcm_thread> thread_vcm; /* Temporary data per thread and group */
  80
  81     t_vcm(const gmx_groups_t &groups, const t_inputrec &ir);
  82     ~t_vcm();
  83 };
  84
  85 /* print COM removal info to log */
  86 void reportComRemovalInfo(FILE * fp, const t_vcm &vcm);
  87
  88
  89 /* Do a per group center of mass things */
  90 void calc_vcm_grp(int start, int homenr, t_mdatoms *md,
  91                   rvec x[], rvec v[], t_vcm *vcm);
  92
  93 /* Set the COM velocity to zero and potentially correct the COM position.
  94  *
  95  * With linear modes nullptr can be passed for x.
  96  */
  97 void do_stopcm_grp(const t_mdatoms &mdatoms,
  98                    rvec x[], rvec v[], const t_vcm &vcm);
  99
 100 void check_cm_grp(FILE *fp, t_vcm *vcm, t_inputrec *ir, real Temp_Max);
 101
 102 #endif