include/grompp.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  * check out http://www.gromacs.org for more information.
   7  * Copyright (c) 2012,2013, by the GROMACS development team, led by
   8  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
   9  * others, as listed in the AUTHORS file in the top-level source
  10  * directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38
  39 #ifndef _grompp_h
  40 #define _grompp_h
  41
  42 #include <stdio.h>
  43 #include "visibility.h"
  44 #include "typedefs.h"
  45 #include "macros.h"
  46
  47 #ifdef __cplusplus
  48 extern "C" {
  49 #endif
  50
  51 #define MAXSLEN 32
  52
  53 typedef struct {
  54     gmx_bool bSet;              /* Has this combination been set        */
  55     real     c[4];              /* The non-bonded parameters            */
  56 } t_nbparam;
  57 /* The t_nbparam struct is used to temporary store the explicit
  58  * non-bonded parameter combinations, which will be copied to t_params.
  59  */
  60
  61 typedef struct {
  62     atom_id    a[MAXATOMLIST];   /* The atom list (eg. bonds: particle  */
  63     /* i = a[0] (AI), j = a[1] (AJ))    */
  64     real       c[MAXFORCEPARAM]; /* Force parameters (eg. b0 = c[0])    */
  65     char       s[MAXSLEN];       /* A string (instead of parameters),    *
  66                                   * read from the .rtp file in pdb2gmx   */
  67 } t_param;
  68
  69 typedef struct {
  70     int          nr;    /* The number of bonds in this record   */
  71     int          maxnr; /* The amount of elements in the array  */
  72     t_param     *param; /* Array of parameters (dim: nr)        */
  73
  74     /* CMAP tmp data, there are probably better places for this */
  75     int         grid_spacing; /* Cmap grid spacing */
  76     int         nc;           /* Number of cmap angles */
  77
  78     real       *cmap;         /* Temporary storage of the raw cmap grid data */
  79     int         ncmap;        /* Number of allocated elements in cmap grid*/
  80
  81     int        *cmap_types;   /* Store the five atomtypes followed by a number that identifies the type */
  82     int         nct;          /* Number of allocated elements in cmap_types */
  83
  84 } t_params;
  85
  86 typedef struct {
  87     int            nr;          /* The number of exclusions             */
  88     atom_id       *e;           /* The excluded atoms                   */
  89 } t_excls;
  90
  91 typedef struct {
  92     char            **name;
  93     int               nrexcl;       /* Number of exclusions per atom    */
  94     gmx_bool          excl_set;     /* Have exclusions been generated?  */
  95     gmx_bool          bProcessed;   /* Has the mol been processed           */
  96     t_atoms           atoms;        /* Atoms                                */
  97     t_block           cgs;          /* Charge groups                        */
  98     t_block           mols;         /* Molecules                            */
  99     t_blocka          excls;        /* Exclusions                           */
 100     t_params          plist[F_NRE]; /* Parameters in old style              */
 101 } t_molinfo;
 102
 103 typedef struct {
 104     char *name;
 105     int   nr;
 106 } t_mols;
 107
 108 GMX_LIBGMXPREPROCESS_EXPORT
 109 gmx_bool is_int(double x);
 110 /* Returns TRUE when x is integer */
 111
 112 typedef enum {
 113     d_defaults,
 114     d_atomtypes,
 115     d_bondtypes,
 116     d_constrainttypes,
 117     d_pairtypes,
 118     d_angletypes,
 119     d_dihedraltypes,
 120     d_nonbond_params,
 121     d_implicit_genborn_params,
 122     d_implicit_surface_params,
 123     d_cmaptypes,
 124     d_moleculetype,
 125     d_atoms,
 126     d_vsites2,
 127     d_vsites3,
 128     d_vsites4,
 129     d_vsitesn,
 130     d_bonds,
 131     d_exclusions,
 132     d_pairs,
 133     d_pairs_nb,
 134     d_angles,
 135     d_dihedrals,
 136     d_constraints,
 137     d_settles,
 138     d_polarization,
 139     d_water_polarization,
 140     d_thole_polarization,
 141     d_system,
 142     d_molecules,
 143     d_position_restraints,
 144     d_angle_restraints,
 145     d_angle_restraints_z,
 146     d_distance_restraints,
 147     d_orientation_restraints,
 148     d_dihedral_restraints,
 149     d_cmap,
 150     d_maxdir,
 151     d_invalid,
 152     d_none
 153 } directive;
 154
 155 static const char *ds[d_maxdir+1] = {
 156     "defaults",
 157     "atomtypes",
 158     "bondtypes",
 159     "constrainttypes",
 160     "pairtypes",
 161     "angletypes",
 162     "dihedraltypes",
 163     "nonbond_params",
 164     "implicit_genborn_params",
 165     "implicit_surface_params",
 166     "cmaptypes",
 167     /* All the directives above can not appear after moleculetype */
 168     "moleculetype",
 169     "atoms",
 170     "virtual_sites2",
 171     "virtual_sites3",
 172     "virtual_sites4",
 173     "virtual_sitesn",
 174     "bonds",
 175     "exclusions",
 176     "pairs",
 177     "pairs_nb",
 178     "angles",
 179     "dihedrals",
 180     "constraints",
 181     "settles",
 182     "polarization",
 183     "water_polarization",
 184     "thole_polarization",
 185     "system",
 186     "molecules",
 187     "position_restraints",
 188     "angle_restraints",
 189     "angle_restraints_z",
 190     "distance_restraints",
 191     "orientation_restraints",
 192     "dihedral_restraints",
 193     "cmap",
 194     "invalid"
 195 };
 196
 197 #ifdef __cplusplus
 198 }
 199 #endif
 200
 201 #endif  /* _grompp_h */