src/gromacs/mdlib/force.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) 2013,2014,2015,2016,2017, 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_FORCE_H
  38 #define GMX_MDLIB_FORCE_H
  39
  40 #include "gromacs/domdec/dlbtiming.h"
  41 #include "gromacs/mdlib/force_flags.h"
  42 #include "gromacs/mdlib/vsite.h"
  43 #include "gromacs/mdtypes/fcdata.h"
  44 #include "gromacs/mdtypes/forcerec.h"
  45 #include "gromacs/timing/wallcycle.h"
  46 #include "gromacs/utility/arrayref.h"
  47
  48 struct gmx_edsam;
  49 struct gmx_gpu_info_t;
  50 struct gmx_groups_t;
  51 struct gmx_vsite_t;
  52 class history_t;
  53 struct nonbonded_verlet_t;
  54 struct t_blocka;
  55 struct t_commrec;
  56 struct t_fcdata;
  57 struct t_graph;
  58 struct t_grpopts;
  59 struct t_inputrec;
  60 struct t_lambda;
  61 struct t_mdatoms;
  62 struct t_nrnb;
  63 struct t_pbc;
  64
  65 namespace gmx
  66 {
  67 class MDLogger;
  68 }
  69
  70 void calc_vir(int nxf, rvec x[], rvec f[], tensor vir,
  71               gmx_bool bScrewPBC, matrix box);
  72 /* Calculate virial for nxf atoms, and add it to vir */
  73
  74 void f_calc_vir(int i0, int i1, rvec x[], rvec f[], tensor vir,
  75                 t_graph *g, rvec shift_vec[]);
  76 /* Calculate virial taking periodicity into account */
  77
  78 real RF_excl_correction(const t_forcerec *fr, t_graph *g,
  79                         const t_mdatoms *mdatoms, const t_blocka *excl,
  80                         rvec x[], rvec f[], rvec *fshift, const t_pbc *pbc,
  81                         real lambda, real *dvdlambda);
  82 /* Calculate the reaction-field energy correction for this node:
  83  * epsfac q_i q_j (k_rf r_ij^2 - c_rf)
  84  * and force correction for all excluded pairs, including self pairs.
  85  */
  86
  87 void calc_rffac(FILE *fplog, int eel, real eps_r, real eps_rf,
  88                 real Rc, real Temp,
  89                 real zsq, matrix box,
  90                 real *kappa, real *krf, real *crf);
  91 /* Determine the reaction-field constants */
  92
  93 void init_generalized_rf(FILE *fplog,
  94                          const gmx_mtop_t *mtop, const t_inputrec *ir,
  95                          t_forcerec *fr);
  96 /* Initialize the generalized reaction field parameters */
  97
  98
  99 /* In wall.c */
 100 void make_wall_tables(FILE *fplog,
 101                       const t_inputrec *ir, const char *tabfn,
 102                       const gmx_groups_t *groups,
 103                       t_forcerec *fr);
 104
 105 real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
 106               rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb);
 107
 108 gmx_bool can_use_allvsall(const t_inputrec *ir,
 109                           gmx_bool bPrintNote, t_commrec *cr, FILE *fp);
 110 /* Returns if we can use all-vs-all loops.
 111  * If bPrintNote==TRUE, prints a note, if necessary, to stderr
 112  * and fp (if !=NULL) on the master node.
 113  */
 114
 115 gmx_bool nbnxn_simd_supported(const gmx::MDLogger &mdlog,
 116                               const t_inputrec    *ir);
 117 /* Return if CPU SIMD support exists for the given inputrec
 118  * If the return value is FALSE and fplog/cr != NULL, prints a fallback
 119  * message to fplog/stderr.
 120  */
 121
 122 gmx_bool uses_simple_tables(int                 cutoff_scheme,
 123                             nonbonded_verlet_t *nbv,
 124                             int                 group);
 125 /* Returns whether simple tables (i.e. not for use with GPUs) are used
 126  * with the type of kernel indicated.
 127  */
 128
 129 void init_enerdata(int ngener, int n_lambda, gmx_enerdata_t *enerd);
 130 /* Intializes the energy storage struct */
 131
 132 void destroy_enerdata(gmx_enerdata_t *enerd);
 133 /* Free all memory associated with enerd */
 134
 135 void reset_foreign_enerdata(gmx_enerdata_t *enerd);
 136 /* Resets only the foreign energy data */
 137
 138 void reset_enerdata(gmx_enerdata_t *enerd);
 139 /* Resets the energy data */
 140
 141 void sum_epot(gmx_grppairener_t *grpp, real *epot);
 142 /* Locally sum the non-bonded potential energy terms */
 143
 144 void sum_dhdl(gmx_enerdata_t *enerd, gmx::ConstArrayRef<real> lambda, t_lambda *fepvals);
 145 /* Sum the free energy contributions */
 146
 147 /* Compute the average C6 and C12 params for LJ corrections */
 148 void set_avcsixtwelve(FILE *fplog, t_forcerec *fr,
 149                       const gmx_mtop_t *mtop);
 150
 151 void do_force(FILE *log, t_commrec *cr,
 152               t_inputrec *inputrec,
 153               gmx_int64_t step, struct t_nrnb *nrnb, gmx_wallcycle_t wcycle,
 154               gmx_localtop_t *top,
 155               gmx_groups_t *groups,
 156               matrix box, PaddedRVecVector *coordinates, history_t *hist,
 157               PaddedRVecVector *force,
 158               tensor vir_force,
 159               t_mdatoms *mdatoms,
 160               gmx_enerdata_t *enerd, t_fcdata *fcd,
 161               gmx::ArrayRef<real> lambda, t_graph *graph,
 162               t_forcerec *fr,
 163               gmx_vsite_t *vsite, rvec mu_tot,
 164               double t, struct gmx_edsam *ed,
 165               gmx_bool bBornRadii,
 166               int flags,
 167               DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
 168               DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion);
 169
 170 /* Communicate coordinates (if parallel).
 171  * Do neighbor searching (if necessary).
 172  * Calculate forces.
 173  * Communicate forces (if parallel).
 174  * Spread forces for vsites (if present).
 175  *
 176  * f is always required.
 177  */
 178
 179 void ns(FILE              *fplog,
 180         t_forcerec        *fr,
 181         matrix             box,
 182         gmx_groups_t      *groups,
 183         gmx_localtop_t    *top,
 184         t_mdatoms         *md,
 185         t_commrec         *cr,
 186         t_nrnb            *nrnb,
 187         gmx_bool           bFillGrid);
 188 /* Call the neighborsearcher */
 189
 190 void do_force_lowlevel(t_forcerec   *fr,
 191                        t_inputrec   *ir,
 192                        t_idef       *idef,
 193                        t_commrec    *cr,
 194                        t_nrnb       *nrnb,
 195                        gmx_wallcycle_t wcycle,
 196                        t_mdatoms    *md,
 197                        rvec         x[],
 198                        history_t    *hist,
 199                        rvec         f_shortrange[],
 200                        gmx_enerdata_t *enerd,
 201                        t_fcdata     *fcd,
 202                        gmx_localtop_t *top,
 203                        gmx_genborn_t *born,
 204                        gmx_bool         bBornRadii,
 205                        matrix       box,
 206                        t_lambda     *fepvals,
 207                        real         *lambda,
 208                        t_graph      *graph,
 209                        t_blocka     *excl,
 210                        rvec         mu_tot[2],
 211                        int          flags,
 212                        float        *cycles_pme);
 213 /* Call all the force routines */
 214
 215 void free_gpu_resources(const t_forcerec            *fr,
 216                         const t_commrec             *cr,
 217                         const gmx_gpu_info_t        *gpu_info,
 218                         const gmx_gpu_opt_t         *gpu_opt);
 219
 220 #endif