src/gromacs/mdlib/settle.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \libinternal \file
  36  * \brief Declares interface to SETTLE code.
  37  *
  38  * \author Berk Hess <hess@kth.se>
  39  * \author Mark Abraham <mark.j.abraham@gmail.com>
  40  * \ingroup module_mdlib
  41  * \inlibraryapi
  42  */
  43
  44 #ifndef GMX_MDLIB_SETTLE_H
  45 #define GMX_MDLIB_SETTLE_H
  46
  47 #include "gromacs/topology/idef.h"
  48
  49 struct gmx_cmap_t;
  50 struct gmx_mtop_t;
  51 struct t_inputrec;
  52 struct t_mdatoms;
  53 struct t_pbc;
  54
  55 namespace gmx
  56 {
  57
  58 enum class ConstraintVariable : int;
  59
  60 /* Abstract type for SETTLE that is defined only in the file that uses it */
  61 struct settledata;
  62
  63 /*! \brief Initializes and returns a structure with SETTLE parameters */
  64 settledata *settle_init(const gmx_mtop_t &mtop);
  65
  66 //! Cleans up.
  67 void settle_free(settledata *settled);
  68
  69 /*! \brief Set up the indices for the settle constraints */
  70 void settle_set_constraints(settledata       *settled,
  71                             const t_ilist    *il_settle,
  72                             const t_mdatoms  &mdatoms);
  73
  74 /*! \brief Constrain coordinates using SETTLE.
  75  * Can be called on any number of threads.
  76  */
  77 void csettle(settledata         *settled,          /* The SETTLE structure */
  78              int                 nthread,          /* The number of threads used */
  79              int                 thread,           /* Our thread index */
  80              const t_pbc        *pbc,              /* PBC data pointer, can be NULL */
  81              const real          x[],              /* Reference coordinates */
  82              real                xprime[],         /* New coords, to be settled */
  83              real                invdt,            /* 1/delta_t */
  84              real               *v,                /* Also constrain v if v!=NULL */
  85              bool                bCalcVirial,      /* Calculate the virial contribution */
  86              tensor              vir_r_m_dr,       /* sum r x m delta_r */
  87              bool               *bErrorHasOccurred /* True if a settle error occurred */
  88              );
  89
  90 /*! \brief Analytical algorithm to subtract the components of derivatives
  91  * of coordinates working on settle type constraint.
  92  */
  93 void settle_proj(settledata *settled, ConstraintVariable econq,
  94                  int nsettle, t_iatom iatoms[],
  95                  const t_pbc *pbc,   /* PBC data pointer, can be NULL  */
  96                  const rvec x[],
  97                  rvec *der, rvec *derp,
  98                  int CalcVirAtomEnd, tensor vir_r_m_dder);
  99
 100 } // namespace
 101
 102 #endif