include/grompp.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  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
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  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
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  30  * For more info, check our website at http://www.gromacs.org
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  34  */
  35
  36 #ifndef _grompp_h
  37 #define _grompp_h
  38
  39 #include <stdio.h>
  40 #include "visibility.h"
  41 #include "typedefs.h"
  42 #include "macros.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 #define MAXSLEN 32
  49
  50 typedef struct {
  51   gmx_bool bSet;                    /* Has this combination been set        */
  52   real c[4];                    /* The non-bonded parameters            */
  53 } t_nbparam;
  54 /* The t_nbparam struct is used to temporary store the explicit
  55  * non-bonded parameter combinations, which will be copied to t_params.
  56  */
  57
  58 typedef struct {
  59   atom_id    a[MAXATOMLIST];    /* The atom list (eg. bonds: particle   */
  60                                 /* i = a[0] (AI), j = a[1] (AJ))        */
  61   real       c[MAXFORCEPARAM];  /* Force parameters (eg. b0 = c[0])     */
  62   char       s[MAXSLEN];        /* A string (instead of parameters),    *
  63                                  * read from the .rtp file in pdb2gmx   */
  64 } t_param;
  65
  66 typedef struct {
  67         int                 nr;         /* The number of bonds in this record   */
  68         int         maxnr;          /* The amount of elements in the array  */
  69         t_param         *param;         /* Array of parameters (dim: nr)        */
  70
  71         /* CMAP tmp data, there are probably better places for this */
  72         int        grid_spacing; /* Cmap grid spacing */
  73         int        nc;           /* Number of cmap angles */
  74
  75         real       *cmap;  /* Temporary storage of the raw cmap grid data */
  76         int        ncmap;    /* Number of allocated elements in cmap grid*/
  77
  78         int        *cmap_types;  /* Store the five atomtypes followed by a number that identifies the type */
  79         int         nct;         /* Number of allocated elements in cmap_types */
  80
  81 } t_params;
  82
  83 typedef struct {
  84   int           nr;             /* The number of exclusions             */
  85   atom_id       *e;             /* The excluded atoms                   */
  86 } t_excls;
  87
  88 typedef struct {
  89   char          **name;
  90   int           nrexcl;         /* Number of exclusions per atom        */
  91   gmx_bool              excl_set;       /* Have exclusions been generated?      */
  92   gmx_bool          bProcessed;     /* Has the mol been processed           */
  93   t_atoms       atoms;          /* Atoms                                */
  94   t_block       cgs;            /* Charge groups                        */
  95   t_block       mols;           /* Molecules                            */
  96   t_blocka      excls;          /* Exclusions                           */
  97   t_params      plist[F_NRE];   /* Parameters in old style              */
  98 } t_molinfo;
  99
 100 typedef struct {
 101   char *name;
 102   int  nr;
 103 } t_mols;
 104
 105 GMX_LIBGMXPREPROCESS_EXPORT
 106 gmx_bool is_int(double x);
 107 /* Returns TRUE when x is integer */
 108
 109 typedef enum {
 110   d_defaults,
 111   d_atomtypes,
 112   d_bondtypes,
 113   d_constrainttypes,
 114   d_pairtypes,
 115   d_angletypes,
 116   d_dihedraltypes,
 117   d_nonbond_params,
 118   d_implicit_genborn_params,
 119   d_implicit_surface_params,
 120   d_cmaptypes,
 121   d_moleculetype,
 122   d_atoms,
 123   d_vsites2,
 124   d_vsites3,
 125   d_vsites4,
 126   d_vsitesn,
 127   d_bonds,
 128   d_exclusions,
 129   d_pairs,
 130   d_pairs_nb,
 131   d_angles,
 132   d_dihedrals,
 133   d_constraints,
 134   d_settles,
 135   d_polarization,
 136   d_water_polarization,
 137   d_thole_polarization,
 138   d_system,
 139   d_molecules,
 140   d_position_restraints,
 141   d_angle_restraints,
 142   d_angle_restraints_z,
 143   d_distance_restraints,
 144   d_orientation_restraints,
 145   d_dihedral_restraints,
 146   d_cmap,
 147   d_maxdir,
 148   d_invalid,
 149   d_none
 150 } directive;
 151
 152 static const char *ds[d_maxdir+1] = {
 153   "defaults",
 154   "atomtypes",
 155   "bondtypes",
 156   "constrainttypes",
 157   "pairtypes",
 158   "angletypes",
 159   "dihedraltypes",
 160   "nonbond_params",
 161   "implicit_genborn_params",
 162   "implicit_surface_params",
 163   "cmaptypes",
 164   /* All the directives above can not appear after moleculetype */
 165   "moleculetype",
 166   "atoms",
 167   "virtual_sites2",
 168   "virtual_sites3",
 169   "virtual_sites4",
 170   "virtual_sitesn",
 171   "bonds",
 172   "exclusions",
 173   "pairs",
 174   "pairs_nb",
 175   "angles",
 176   "dihedrals",
 177   "constraints",
 178   "settles",
 179   "polarization",
 180   "water_polarization",
 181   "thole_polarization",
 182   "system",
 183   "molecules",
 184   "position_restraints",
 185   "angle_restraints",
 186   "angle_restraints_z",
 187   "distance_restraints",
 188   "orientation_restraints",
 189   "dihedral_restraints",
 190   "cmap",
 191   "invalid"
 192   };
 193
 194 #ifdef __cplusplus
 195 }
 196 #endif
 197
 198 #endif  /* _grompp_h */
 199
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