src/gromacs/mdlib/shake.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
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   4  * Copyright (c) 2018, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  35 /*! \libinternal \file
  36  * \brief Declares interface to SHAKE code.
  37  *
  38  * \author David van der Spoel <david.vanderspoel@icm.uu.se>
  39  * \author Berk Hess <hess@kth.se>
  40  * \author Mark Abraham <mark.j.abraham@gmail.com>
  41  * \ingroup module_mdlib
  42  * \inlibraryapi
  43  */
  44
  45 #ifndef GMX_MDLIB_SHAKE_H
  46 #define GMX_MDLIB_SHAKE_H
  47
  48 #include "gromacs/topology/block.h"
  49 #include "gromacs/topology/idef.h"
  50
  51 struct gmx_domdec_t;
  52 struct t_inputrec;
  53 struct t_mdatoms;
  54 struct t_nrnb;
  55
  56 namespace gmx
  57 {
  58
  59 enum class ConstraintVariable : int;
  60
  61 /* Abstract type for SHAKE that is defined only in the file that uses it */
  62 struct shakedata;
  63
  64 /*! \brief Initializes and return the SHAKE data structure */
  65 shakedata *shake_init();
  66
  67 //! Destroy SHAKE. Needed to solve memory leaks.
  68 void done_shake(shakedata *d);
  69
  70 //! Make SHAKE blocks when not using DD.
  71 void
  72 make_shake_sblock_serial(shakedata *shaked,
  73                          const t_idef *idef, const t_mdatoms &md);
  74
  75 //! Make SHAKE blocks when using DD.
  76 void
  77 make_shake_sblock_dd(shakedata *shaked,
  78                      const t_ilist *ilcon, const t_block *cgs,
  79                      const gmx_domdec_t *dd);
  80
  81 /*! \brief Shake all the atoms blockwise. It is assumed that all the constraints
  82  * in the idef->shakes field are sorted, to ascending block nr. The
  83  * sblock array points into the idef->shakes.iatoms field, with block 0
  84  * starting
  85  * at sblock[0] and running to ( < ) sblock[1], block n running from
  86  * sblock[n] to sblock[n+1]. Array sblock should be large enough.
  87  * Return TRUE when OK, FALSE when shake-error
  88  */
  89 bool
  90 constrain_shake(FILE              *log,          /* Log file                    */
  91                 shakedata         *shaked,       /* Total number of atoms       */
  92                 const real         invmass[],    /* Atomic masses               */
  93                 const t_idef      &idef,         /* The interaction def         */
  94                 const t_inputrec  &ir,           /* Input record                        */
  95                 const rvec         x_s[],        /* Coords before update                */
  96                 rvec               xprime[],     /* Output coords when constraining x */
  97                 rvec               vprime[],     /* Output coords when constraining v */
  98                 t_nrnb            *nrnb,         /* Performance measure          */
  99                 real               lambda,       /* FEP lambda                   */
 100                 real              *dvdlambda,    /* FEP force                    */
 101                 real               invdt,        /* 1/delta_t                    */
 102                 rvec              *v,            /* Also constrain v if v!=NULL  */
 103                 bool               bCalcVir,     /* Calculate r x m delta_r      */
 104                 tensor             vir_r_m_dr,   /* sum r x m delta_r            */
 105                 bool               bDumpOnError, /* Dump debugging stuff on error*/
 106                 ConstraintVariable econq);       /* which type of constraint is occurring */
 107
 108 /*! \brief Regular iterative shake */
 109 void cshake(const int iatom[], int ncon, int *nnit, int maxnit,
 110             const real dist2[], real xp[], const real rij[], const real m2[], real omega,
 111             const real invmass[], const real tt[], real lagr[], int *nerror);
 112
 113 }  // namespace gmx
 114
 115 #endif