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/*
* $Id$
*
* This source code is part of
*
* G R O M A C S
*
* GROningen MAchine for Chemical Simulations
*
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team,
* check out http://www.gromacs.org for more information.
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
*
* For more info, check our website at http://www.gromacs.org
*
* And Hey:
* Gromacs Runs On Most of All Computer Systems
*/
#ifndef _grompp_h
#define _grompp_h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdio.h>
#include "typedefs.h"
#include "macros.h"
#define MAXSLEN 32
typedef struct {
bool bSet; /* Has this combination been set */
real c[4]; /* The non-bonded parameters */
} t_nbparam;
/* The t_nbparam struct is used to temporary store the explicit
* non-bonded parameter combinations, which will be copied to t_params.
*/
typedef struct {
atom_id a[MAXATOMLIST]; /* The atom list (eg. bonds: particle */
/* i = a[0] (AI), j = a[1] (AJ)) */
real c[MAXFORCEPARAM]; /* Force parameters (eg. b0 = c[0]) */
char s[MAXSLEN]; /* A string (instead of parameters), *
* read from the .rtp file in pdb2gmx */
} t_param;
typedef struct {
int nr; /* The number of bonds in this record */
t_param *param; /* Array of parameters (dim: nr) */
} t_params;
typedef struct {
int nr; /* The number of exclusions */
atom_id *e; /* The excluded atoms */
} t_excls;
typedef struct {
char **name;
int nrexcl; /* Number of exclusions per atom */
bool excl_set; /* Have exclusions been generated? */
bool bProcessed; /* Has the mol been processed */
t_atoms atoms; /* Atoms */
t_block cgs; /* Charge groups */
t_block mols; /* Molecules */
t_blocka excls; /* Exclusions */
t_params plist[F_NRE]; /* Parameters in old style */
} t_molinfo;
typedef struct {
char *name;
int nr;
} t_mols;
extern void print_top_comment(FILE *out,char *filename,char *title,bool bITP);
extern void print_top_header(FILE *out,char *filename,char *title,bool bITP,
char *ff,real mHmult);
extern void print_top_mols(FILE *out, char *title, char *water,
int nincl, char **incls,
int nmol, t_mols *mols);
typedef enum {
d_defaults,
d_atomtypes,
d_bondtypes,
d_constrainttypes,
d_pairtypes,
d_angletypes,
d_dihedraltypes,
d_nonbond_params,
d_moleculetype,
d_atoms,
d_vsites2,
d_vsites3,
d_vsites4,
d_vsitesn,
d_bonds,
d_exclusions,
d_pairs,
d_pairs_nb,
d_angles,
d_dihedrals,
d_constraints,
d_settles,
d_polarization,
d_water_polarization,
d_thole_polarization,
d_system,
d_molecules,
d_position_restraints,
d_angle_restraints,
d_angle_restraints_z,
d_distance_restraints,
d_orientation_restraints,
d_dihedral_restraints,
d_maxdir,
d_invalid,
d_none
} directive;
static char *ds[d_maxdir+1] = {
"defaults",
"atomtypes",
"bondtypes",
"constrainttypes",
"pairtypes",
"angletypes",
"dihedraltypes",
"nonbond_params",
/* All the directives above can not appear after moleculetype */
"moleculetype",
"atoms",
"virtual_sites2",
"virtual_sites3",
"virtual_sites4",
"virtual_sitesn",
"bonds",
"exclusions",
"pairs",
"pairs_nb",
"angles",
"dihedrals",
"constraints",
"settles",
"polarization",
"water_polarization",
"thole_polarization",
"system",
"molecules",
"position_restraints",
"angle_restraints",
"angle_restraints_z",
"distance_restraints",
"orientation_restraints",
"dihedral_restraints",
"invalid"
};
#endif /* _grompp_h */
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