include/types/genborn.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  10  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  11  * Copyright (c) 2001-2008, The GROMACS development team,
  12  * check out http://www.gromacs.org for more information.
  13
  14  * This program is free software; you can redistribute it and/or
  15  * modify it under the terms of the GNU General Public License
  16  * as published by the Free Software Foundation; either version 2
  17  * of the License, or (at your option) any later version.
  18  *
  19  * If you want to redistribute modifications, please consider that
  20  * scientific software is very special. Version control is crucial -
  21  * bugs must be traceable. We will be happy to consider code for
  22  * inclusion in the official distribution, but derived work must not
  23  * be called official GROMACS. Details are found in the README & COPYING
  24  * files - if they are missing, get the official version at www.gromacs.org.
  25  *
  26  * To help us fund GROMACS development, we humbly ask that you cite
  27  * the papers on the package - you can find them in the top README file.
  28  *
  29  * For more info, check our website at http://www.gromacs.org
  30  *
  31  * And Hey:
  32  * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  33  */
  34
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39
  40 typedef struct
  41 {
  42         int nbonds;
  43         int bond[10];
  44         real length[10];
  45 } genborn_bonds_t;
  46
  47 typedef struct gbtmpnbls *gbtmpnbls_t;
  48
  49 /* Struct to hold all the information for GB */
  50 typedef struct
  51 {
  52         int nr;                   /* number of atoms, length of arrays below */
  53         int n12;                  /* number of 1-2 (bond) interactions       */
  54         int n13;                  /* number of 1-3 (angle) terms             */
  55         int n14;                  /* number of 1-4 (torsion) terms           */
  56         int nlocal;               /* Length of local arrays (with DD)        */
  57
  58         /* Arrays below that end with _globalindex are used for setting up initial values of
  59          * all gb parameters and values. They all have length natoms, which for DD is the
  60          * global atom number.
  61          * Values are then taken from these arrays to local copies, that have names without
  62          * _globalindex, in the routine make_local_gb(), which is called once for single
  63          * node runs, and for DD at every call to dd_partition_system
  64          */
  65
  66         real  *gpol;              /* Atomic polarisation energies */
  67         real  *gpol_globalindex;  /*  */
  68         real  *gpol_still_work;   /* Work array for Still model */
  69         real  *gpol_hct_work;     /* Work array for HCT/OBC models */
  70         real  *bRad;              /* Atomic Born radii */
  71         real  *vsolv;             /* Atomic solvation volumes */
  72         real  *vsolv_globalindex; /*  */
  73         real  *gb_radius;          /* Radius info, copied from atomtypes */
  74         real  *gb_radius_globalindex;
  75
  76         int  *use;                 /* Array that till if this atom does GB */
  77         int  *use_globalindex;     /* Global array for parallelization */
  78
  79         real es;                  /* Solvation energy and derivatives */
  80         real *asurf;              /* Atomic surface area */
  81         rvec *dasurf;             /* Surface area derivatives */
  82         real as;                  /* Total surface area */
  83
  84         real *drobc;              /* Parameters for OBC chain rule calculation */
  85         real *param;              /* Precomputed factor rai*atype->S_hct for HCT/OBC */
  86         real *param_globalindex;  /*  */
  87
  88         real *log_table;          /* Table for logarithm lookup */
  89
  90         real obc_alpha;           /* OBC parameters */
  91         real obc_beta;            /* OBC parameters */
  92         real obc_gamma;           /* OBC parameters */
  93         real gb_doffset;          /* Dielectric offset for Still/HCT/OBC */
  94         real gb_epsilon_solvent;  /*   */
  95
  96         real *work;               /* Used for parallel summation and in the chain rule, length natoms         */
  97         real *buf;                /* Used for parallel summation and in the chain rule, length natoms         */
  98         real *dd_work;            /* Used for domain decomposition parallel runs, length natoms              */
  99         int  *count;              /* Used for setting up the special gb nblist, length natoms                 */
 100         gbtmpnbls_t nblist_work;  /* Used for setting up the special gb nblist, dim natoms*nblist_work_nalloc */
 101         int  nblist_work_nalloc;  /* Length of second dimension of nblist_work                                */
 102 }
 103 gmx_genborn_t;