src/gromacs/mdlib/genborn.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) 2001-2008, 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_GENBORN_H
  38 #define GMX_MDLIB_GENBORN_H
  39
  40 #include "gromacs/math/utilities.h"
  41 #include "gromacs/math/vectypes.h"
  42
  43 struct gmx_genborn_t;
  44 struct gmx_enerdata_t;
  45 struct gmx_localtop_t;
  46 struct gmx_mtop_t;
  47 struct t_commrec;
  48 struct t_forcerec;
  49 struct t_graph;
  50 struct t_idef;
  51 struct t_inputrec;
  52 struct t_mdatoms;
  53 struct t_nblist;
  54 struct t_nrnb;
  55 struct t_pbc;
  56
  57 typedef struct
  58 {
  59     int  nbonds;
  60     int  bond[10];
  61     real length[10];
  62 } genborn_bonds_t;
  63
  64 typedef struct gbtmpnbls *gbtmpnbls_t;
  65
  66 /* Struct to hold all the information for GB */
  67 typedef struct gmx_genborn_t
  68 {
  69     int nr;                   /* number of atoms, length of arrays below */
  70     int n12;                  /* number of 1-2 (bond) interactions       */
  71     int n13;                  /* number of 1-3 (angle) terms             */
  72     int n14;                  /* number of 1-4 (torsion) terms           */
  73     int nalloc;               /* Allocation of local arrays (with DD)    */
  74
  75
  76     /* Arrays below that end with _globalindex are used for setting up initial values of
  77      * all gb parameters and values. They all have length natoms, which for DD is the
  78      * global atom number.
  79      * Values are then taken from these arrays to local copies, that have names without
  80      * _globalindex, in the routine make_local_gb(), which is called once for single
  81      * node runs, and for DD at every call to dd_partition_system
  82      */
  83
  84     real       *gpol;              /* Atomic polarisation energies */
  85     real       *gpol_globalindex;  /*  */
  86     real       *gpol_still_work;   /* Work array for Still model */
  87     real       *gpol_hct_work;     /* Work array for HCT/OBC models */
  88     real       *bRad;              /* Atomic Born radii */
  89     real       *vsolv;             /* Atomic solvation volumes */
  90     real       *vsolv_globalindex; /*  */
  91     real       *gb_radius;         /* Radius info, copied from atomtypes */
  92     real       *gb_radius_globalindex;
  93
  94     int        *use;                /* Array that till if this atom does GB */
  95     int        *use_globalindex;    /* Global array for parallelization */
  96
  97     real        es;                 /* Solvation energy and derivatives */
  98     real       *asurf;              /* Atomic surface area */
  99     rvec       *dasurf;             /* Surface area derivatives */
 100     real        as;                 /* Total surface area */
 101
 102     real       *drobc;              /* Parameters for OBC chain rule calculation */
 103     real       *param;              /* Precomputed factor rai*atype->S_hct for HCT/OBC */
 104     real       *param_globalindex;  /*  */
 105
 106     real       *log_table;          /* Table for logarithm lookup */
 107
 108     real        obc_alpha;          /* OBC parameters */
 109     real        obc_beta;           /* OBC parameters */
 110     real        obc_gamma;          /* OBC parameters */
 111     real        gb_doffset;         /* Dielectric offset for Still/HCT/OBC */
 112     real        gb_epsilon_solvent; /*   */
 113     real        epsilon_r;          /* Used for inner dielectric */
 114
 115     real        sa_surface_tension; /* Surface tension for non-polar solvation */
 116
 117     real       *work;               /* Used for parallel summation and in the chain rule, length natoms         */
 118     real       *buf;                /* Used for parallel summation and in the chain rule, length natoms         */
 119     int        *count;              /* Used for setting up the special gb nblist, length natoms                 */
 120     gbtmpnbls_t nblist_work;        /* Used for setting up the special gb nblist, dim natoms*nblist_work_nalloc */
 121     int         nblist_work_nalloc; /* Length of second dimension of nblist_work                                */
 122 }
 123 gmx_genborn_t;
 124 /* Still parameters - make sure to edit in genborn_sse.c too if you change these! */
 125 #define STILL_P1  0.073*0.1              /* length        */
 126 #define STILL_P2  0.921*0.1*CAL2JOULE    /* energy*length */
 127 #define STILL_P3  6.211*0.1*CAL2JOULE    /* energy*length */
 128 #define STILL_P4  15.236*0.1*CAL2JOULE
 129 #define STILL_P5  1.254
 130
 131 #define STILL_P5INV (1.0/STILL_P5)
 132 #define STILL_PIP5  (M_PI*STILL_P5)
 133
 134
 135 /* Initialise GB stuff */
 136 int init_gb(struct gmx_genborn_t **p_born,
 137             struct t_forcerec *fr, const struct t_inputrec *ir,
 138             const gmx_mtop_t *mtop, int gb_algorithm);
 139
 140
 141 /* Born radii calculations, both with and without SSE acceleration */
 142 int calc_gb_rad(struct t_commrec *cr, struct t_forcerec *fr, struct t_inputrec *ir, gmx_localtop_t *top, rvec x[], t_nblist *nl, struct gmx_genborn_t *born, t_mdatoms *md, t_nrnb     *nrnb);
 143
 144
 145
 146 /* Bonded GB interactions */
 147 real gb_bonds_tab(rvec x[], rvec f[], rvec fshift[], real *charge, real *p_gbtabscale,
 148                   real *invsqrta, real *dvda, real *GBtab, t_idef *idef, real epsilon_r,
 149                   real gb_epsilon_solvent, real facel, const struct t_pbc *pbc,
 150                   const struct t_graph *graph);
 151
 152
 153
 154
 155 /* Functions for calculating adjustments due to ie chain rule terms */
 156 void
 157 calc_gb_forces(struct t_commrec *cr, t_mdatoms *md, struct gmx_genborn_t *born, gmx_localtop_t *top,
 158                rvec x[], rvec f[], struct t_forcerec *fr, t_idef *idef, int gb_algorithm, int sa_algorithm, t_nrnb *nrnb,
 159                const struct t_pbc *pbc, const struct t_graph *graph, struct gmx_enerdata_t *enerd);
 160
 161
 162 int
 163 make_gb_nblist(struct t_commrec *cr, int gb_algorithm,
 164                rvec x[], matrix box,
 165                struct t_forcerec *fr, t_idef *idef, struct t_graph *graph, struct gmx_genborn_t *born);
 166
 167 void
 168 make_local_gb(const struct t_commrec *cr, struct gmx_genborn_t *born, int gb_algorithm);
 169
 170 #endif