src/gromacs/mdlib/vsite.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #ifndef GMX_MDLIB_VSITE_H
  38 #define GMX_MDLIB_VSITE_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #include "gromacs/pbcutil/ishift.h"
  42 #include "gromacs/topology/idef.h"
  43 #include "gromacs/utility/basedefinitions.h"
  44 #include "gromacs/utility/real.h"
  45
  46 struct gmx_localtop_t;
  47 struct gmx_mtop_t;
  48 struct t_commrec;
  49 struct t_graph;
  50 struct t_ilist;
  51 struct t_mdatoms;
  52 struct t_nrnb;
  53
  54 typedef struct gmx_vsite_thread_t {
  55     t_ilist ilist[F_NRE];     /* vsite ilists for this thread            */
  56     rvec    fshift[SHIFTS];   /* fshift accumulation buffer              */
  57     matrix  dxdf;             /* virial dx*df accumulation buffer        */
  58 } gmx_vsite_thread_t;
  59
  60 typedef struct gmx_vsite_t {
  61     gmx_bool            bHaveChargeGroups;    /* Do we have charge groups?               */
  62     int                 n_intercg_vsite;      /* The number of inter charge group vsites */
  63     int                 nvsite_pbc_molt;      /* The array size of vsite_pbc_molt        */
  64     int              ***vsite_pbc_molt;       /* The pbc atoms for intercg vsites        */
  65     int               **vsite_pbc_loc;        /* The local pbc atoms                     */
  66     int                *vsite_pbc_loc_nalloc; /* Sizes of vsite_pbc_loc                  */
  67     int                 nthreads;             /* Number of threads used for vsites       */
  68     gmx_vsite_thread_t *tdata;                /* Thread local vsites and work structs    */
  69     int                *th_ind;               /* Work array                              */
  70     int                 th_ind_nalloc;        /* Size of th_ind                          */
  71 } gmx_vsite_t;
  72
  73 void construct_vsites(const gmx_vsite_t *vsite,
  74                       rvec x[],
  75                       real dt, rvec v[],
  76                       const t_iparams ip[], const t_ilist ilist[],
  77                       int ePBC, gmx_bool bMolPBC,
  78                       t_commrec *cr, matrix box);
  79 /* Create positions of vsite atoms based on surrounding atoms
  80  * for the local system.
  81  * If v is passed, the velocities of the vsites will be calculated
  82  * as the new positions minus the old positions divided by dt,
  83  * thus v should only be passed when the coordinates have been
  84  * updated with a full time step.
  85  * Note that velocitis of vsites are completely irrelevant
  86  * for the integration, they are only useful for analysis.
  87  */
  88
  89 void construct_vsites_mtop(gmx_vsite_t *vsite,
  90                            gmx_mtop_t *mtop, rvec x[]);
  91 /* Create positions of vsite atoms based on surrounding atoms
  92  * for the whole system.
  93  * This function assumes that all molecules are whole.
  94  */
  95
  96 void spread_vsite_f(gmx_vsite_t *vsite,
  97                     rvec x[], rvec f[], rvec *fshift,
  98                     gmx_bool VirCorr, matrix vir,
  99                     t_nrnb *nrnb, t_idef *idef,
 100                     int ePBC, gmx_bool bMolPBC, t_graph *g, matrix box,
 101                     t_commrec *cr);
 102 /* Spread the force operating on the vsite atoms on the surrounding atoms.
 103  * If fshift!=NULL also update the shift forces.
 104  * If VirCorr=TRUE add the virial correction for non-linear vsite constructs
 105  * to vir. This correction is required when the virial is not calculated
 106  * afterwards from the particle position and forces, but in a different way,
 107  * as for instance for the PME mesh contribution.
 108  */
 109
 110 gmx_vsite_t *init_vsite(const gmx_mtop_t *mtop, t_commrec *cr,
 111                         gmx_bool bSerial_NoPBC);
 112 /* Initialize the virtual site struct,
 113  * returns NULL when there are no virtual sites.
 114  * bSerial_NoPBC is to generate a simple vsite setup to be
 115  * used only serial (no MPI or thread parallelization) and without pbc;
 116  * this is useful for correction vsites of the initial configuration.
 117  */
 118
 119 void split_vsites_over_threads(const t_ilist   *ilist,
 120                                const t_iparams *ip,
 121                                const t_mdatoms *mdatoms,
 122                                gmx_bool         bLimitRange,
 123                                gmx_vsite_t     *vsite);
 124 /* Divide the vsite work-load over the threads.
 125  * Should be called at the end of the domain decomposition.
 126  */
 127
 128 void set_vsite_top(gmx_vsite_t *vsite, gmx_localtop_t *top, t_mdatoms *md,
 129                    t_commrec *cr);
 130 /* Set some vsite data for runs without domain decomposition.
 131  * Should be called once after init_vsite, before calling other routines.
 132  */
 133
 134 #endif