include/grompp.h

   1 /*
   2  * $Id$
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.1
  11  * Copyright (c) 1991-2001, University of Groningen, The Netherlands
  12  * This program is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU General Public License
  14  * as published by the Free Software Foundation; either version 2
  15  * of the License, or (at your option) any later version.
  16  *
  17  * If you want to redistribute modifications, please consider that
  18  * scientific software is very special. Version control is crucial -
  19  * bugs must be traceable. We will be happy to consider code for
  20  * inclusion in the official distribution, but derived work must not
  21  * be called official GROMACS. Details are found in the README & COPYING
  22  * files - if they are missing, get the official version at www.gromacs.org.
  23  *
  24  * To help us fund GROMACS development, we humbly ask that you cite
  25  * the papers on the package - you can find them in the top README file.
  26  *
  27  * For more info, check our website at http://www.gromacs.org
  28  *
  29  * And Hey:
  30  * Getting the Right Output Means no Artefacts in Calculating Stuff
  31  */
  32
  33 #ifndef _grompp_h
  34 #define _grompp_h
  35
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <stdio.h>
  41 #include "typedefs.h"
  42 #include "macros.h"
  43
  44 #define MAXSLEN 32
  45
  46 typedef struct {
  47   bool bSet;                    /* Has this combination been set        */
  48   real c[3];                    /* The non-bonded parameters            */
  49 } t_nbparam;
  50 /* The t_nbparam struct is used to temporary store the explicit
  51  * non-bonded parameter combinations, which will be copied to t_params.
  52  */
  53
  54 typedef struct {
  55   atom_id a[MAXATOMLIST];       /* The atom list (eg. bonds: particle   */
  56                                 /* i = a[0] (AI), j = a[1] (AJ))        */
  57   real    c[MAXFORCEPARAM];     /* Force parameters (eg. b0 = c[0])     */
  58   char    s[MAXSLEN];           /* A string (instead of parameters),    *
  59                                  * read from the .rtp file in pdb2gmx   */
  60 } t_param;
  61
  62 typedef struct {
  63   int           nr;             /* The number of bonds in this record   */
  64   t_param       *param;         /* Array of parameters (dim: nr)        */
  65 } t_params;
  66
  67 typedef struct {
  68   int           nr;             /* The number of exclusions             */
  69   atom_id       *e;             /* The excluded atoms                   */
  70 } t_excls;
  71
  72 typedef struct {
  73   char          **name;
  74   int           nrexcl;         /* Number of exclusions per atom        */
  75   bool          excl_set;       /* Have exclusions been generated?      */
  76   bool          bProcessed;     /* Has the mol been processed           */
  77   t_atoms       atoms;          /* Atoms                                */
  78   t_block       cgs;            /* Charge groups                        */
  79   t_block       mols;           /* Molecules                            */
  80   t_params      plist[F_NRE];   /* Parameters in old style              */
  81
  82 } t_molinfo;
  83
  84 typedef struct {
  85   int           nr;             /* The number of atomtypes              */
  86   t_atom        *atom;          /* Array of atoms                       */
  87   char          ***atomname;    /* Names of the atomtypes               */
  88   t_param       *nb;            /* Nonbonded force default params       */
  89   int           *bondatomtype;  /* The bond_atomtype for each atomtype  */
  90   real          *radius;        /* Radius for GBSA stuff                */
  91   real          *vol;           /* Effective volume for GBSA            */
  92   real          *surftens;      /* Surface tension with water, for GBSA */
  93 } t_atomtype;
  94
  95 typedef struct {
  96   int           nr;             /* Number of bond_atomtypes             */
  97   char          ***atomname;    /* Names of the bond_atomtypes          */
  98 } t_bond_atomtype;
  99
 100
 101 typedef enum {
 102   d_defaults,
 103   d_atomtypes,
 104   d_bondtypes,
 105   d_constrainttypes,
 106   d_pairtypes,
 107   d_angletypes,
 108   d_dihedraltypes,
 109   d_nonbond_params,
 110   d_blocktype,
 111   d_moleculetype,
 112   d_atoms,
 113   d_dum2,
 114   d_dum3,
 115   d_dum4,
 116   d_bonds,
 117   d_exclusions,
 118   d_pairs,
 119   d_angles,
 120   d_dihedrals,
 121   d_constraints,
 122   d_settles,
 123   d_system,
 124   d_molecules,
 125   d_position_restraints,
 126   d_angle_restraints,
 127   d_angle_restraints_z,
 128   d_distance_restraints,
 129   d_orientation_restraints,
 130   d_dihedral_restraints,
 131   d_maxdir,
 132   d_invalid,
 133   d_none
 134 } directive;
 135
 136 static char *ds[d_maxdir+1] = {
 137   "defaults",
 138   "atomtypes",
 139   "bondtypes",
 140   "constrainttypes",
 141   "pairtypes",
 142   "angletypes",
 143   "dihedraltypes",
 144   "nonbond_params",
 145   "blocktype",
 146   /* All the directives above can not appear after moleculetype */
 147   "moleculetype",
 148   "atoms",
 149   "dummies2",
 150   "dummies3",
 151   "dummies4",
 152   "bonds",
 153   "exclusions",
 154   "pairs",
 155   "angles",
 156   "dihedrals",
 157   "constraints",
 158   "settles",
 159   "system",
 160   "molecules",
 161   "position_restraints",
 162   "angle_restraints",
 163   "angle_restraints_z",
 164   "distance_restraints",
 165   "orientation_restraints",
 166   "dihedral_restraints",
 167   "invalid"
 168   };
 169
 170 extern void convert_harmonics(int nrmols,t_molinfo mols[],t_atomtype *atype);
 171
 172 #endif  /* _grompp_h */
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