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 -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  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.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gromacs Runs On Most of All Computer Systems
  34  */
  35
  36 #ifndef _grompp_h
  37 #define _grompp_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include <stdio.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   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   bool          excl_set;       /* Have exclusions been generated?      */
  95   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 #include "gpp_atomtype.h"
 109
 110 extern void choose_ff(char *ff,int maxlen);
 111 /* Strange place for this function... */
 112
 113 extern bool is_int(double x);
 114 /* Returns TRUE when x is integer */
 115
 116 extern void print_top_comment(FILE *out,const char *filename,const char *title,bool bITP);
 117
 118 extern void print_top_header(FILE *out,const char *filename,const char *title,bool bITP,
 119                              const char *ff,real mHmult);
 120
 121 extern void print_top_mols(FILE *out, const char *title, const char *water,
 122                            int nincl, char **incls,
 123                            int nmol, t_mols *mols);
 124
 125 extern void write_top(FILE *out, char *pr,char *molname,
 126                       t_atoms *at,int bts[],t_params plist[],t_excls excls[],
 127                       gpp_atomtype_t atype,int *cgnr, int nrexcl);
 128 /* NOTE: nrexcl is not the size of *excl! */
 129
 130 typedef enum {
 131   d_defaults,
 132   d_atomtypes,
 133   d_bondtypes,
 134   d_constrainttypes,
 135   d_pairtypes,
 136   d_angletypes,
 137   d_dihedraltypes,
 138   d_nonbond_params,
 139   d_implicit_genborn_params,
 140   d_implicit_surface_params,
 141   d_cmaptypes,
 142   d_moleculetype,
 143   d_atoms,
 144   d_vsites2,
 145   d_vsites3,
 146   d_vsites4,
 147   d_vsitesn,
 148   d_bonds,
 149   d_exclusions,
 150   d_pairs,
 151   d_pairs_nb,
 152   d_angles,
 153   d_dihedrals,
 154   d_constraints,
 155   d_settles,
 156   d_polarization,
 157   d_water_polarization,
 158   d_thole_polarization,
 159   d_system,
 160   d_molecules,
 161   d_position_restraints,
 162   d_angle_restraints,
 163   d_angle_restraints_z,
 164   d_distance_restraints,
 165   d_orientation_restraints,
 166   d_dihedral_restraints,
 167   d_cmap,
 168   d_maxdir,
 169   d_invalid,
 170   d_none
 171 } directive;
 172
 173 static const char *ds[d_maxdir+1] = {
 174   "defaults",
 175   "atomtypes",
 176   "bondtypes",
 177   "constrainttypes",
 178   "pairtypes",
 179   "angletypes",
 180   "dihedraltypes",
 181   "nonbond_params",
 182   "implicit_genborn_params",
 183   "implicit_surface_params",
 184   "cmaptypes",
 185   /* All the directives above can not appear after moleculetype */
 186   "moleculetype",
 187   "atoms",
 188   "virtual_sites2",
 189   "virtual_sites3",
 190   "virtual_sites4",
 191   "virtual_sitesn",
 192   "bonds",
 193   "exclusions",
 194   "pairs",
 195   "pairs_nb",
 196   "angles",
 197   "dihedrals",
 198   "constraints",
 199   "settles",
 200   "polarization",
 201   "water_polarization",
 202   "thole_polarization",
 203   "system",
 204   "molecules",
 205   "position_restraints",
 206   "angle_restraints",
 207   "angle_restraints_z",
 208   "distance_restraints",
 209   "orientation_restraints",
 210   "dihedral_restraints",
 211   "cmap",
 212   "invalid"
 213   };
 214
 215 #ifdef __cplusplus
 216 }
 217 #endif
 218
 219 #endif  /* _grompp_h */
 220
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