src/kernel/readir.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
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  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
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  34  */
  35
  36 #ifndef _readir_h
  37 #define _readir_h
  38
  39 #include "typedefs.h"
  40 #include "string2.h"
  41 #include "readinp.h"
  42 #include "grompp.h"
  43
  44 enum { eshNONE, eshHBONDS, eshALLBONDS, eshHANGLES, eshALLANGLES, eshNR };
  45
  46 static const char *constraints[eshNR+1]    = {
  47   "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
  48 };
  49
  50 enum { ecouplamVDWQ, ecouplamVDW, ecouplamQ, ecouplamNONE, ecouplamNR };
  51
  52 static const char *couple_lam[ecouplamNR+1]    = {
  53   "vdw-q", "vdw", "q", "none", NULL
  54 };
  55
  56 typedef struct {
  57   int warnings;
  58   int nshake;
  59   real fourierspacing;
  60   char *include;
  61   char *define;
  62   gmx_bool bGenVel;
  63   gmx_bool bGenPairs;
  64   real tempi;
  65   int  seed;
  66   gmx_bool bOrire;
  67   gmx_bool bDihre;
  68   gmx_bool bMorse;
  69   char *wall_atomtype[2];
  70   gmx_bool pull_start;
  71   char *couple_moltype;
  72   int  couple_lam0;
  73   int  couple_lam1;
  74   gmx_bool bCoupleIntra;
  75 } t_gromppopts;
  76
  77
  78 extern void init_ir(t_inputrec *ir, t_gromppopts *opts);
  79 /* Initiate stuff */
  80
  81 extern void check_ir(const char *mdparin,t_inputrec *ir, t_gromppopts *opts,
  82                      warninp_t wi);
  83 /* Validate inputrec data.
  84  * Fatal errors will be added to nerror.
  85  */
  86 extern int search_string(char *s,int ng,char *gn[]);
  87 /* Returns the index of string s in the index groups */
  88
  89 extern void double_check(t_inputrec *ir,matrix box,gmx_bool bConstr,
  90                          warninp_t wi);
  91 /* Do more checks */
  92
  93 extern void triple_check(const char *mdparin,t_inputrec *ir,gmx_mtop_t *sys,
  94                          warninp_t wi);
  95 /* Do even more checks */
  96
  97 extern void check_chargegroup_radii(const gmx_mtop_t *mtop,const t_inputrec *ir,
  98                                     rvec *x,
  99                                     warninp_t wi);
 100 /* Even more checks, charge group radii vs. cut-off's only. */
 101
 102 extern void get_ir(const char *mdparin,const char *mdparout,
 103                    t_inputrec *ir,t_gromppopts *opts,
 104                    warninp_t wi);
 105 /* Read the input file, and retrieve data for inputrec.
 106  * More data are read, but the are only evaluated when the next
 107  * function is called. Also prints the input file back to mdparout.
 108  */
 109
 110 extern void do_index(const char* mdparin,
 111                      const char *ndx,
 112                      gmx_mtop_t *mtop,
 113                      gmx_bool bVerbose,
 114                      t_inputrec *ir,
 115                      rvec *v,
 116                      warninp_t wi);
 117 /* Read the index file and assign grp numbers to atoms.
 118  * If v is not NULL, the velocities will be scaled to the correct number
 119  * of degrees of freedom.
 120  */
 121
 122 /* Routines In readpull.c */
 123
 124 extern char **read_pullparams(int *ninp_p,t_inpfile **inp,
 125                               t_pull *pull,gmx_bool *bStart,
 126                               warninp_t wi);
 127 /* Reads the pull parameters, returns a list of the pull group names */
 128
 129 extern void make_pull_groups(t_pull *pull,char **pgnames,
 130                              t_blocka *grps,char **gnames);
 131 /* Process the pull parameters after reading the index groups */
 132
 133 extern void set_pull_init(t_inputrec *ir,gmx_mtop_t *mtop,rvec *x,matrix box,
 134                           const output_env_t oenv, gmx_bool bStart);
 135 /* Prints the initial pull group distances in x.
 136  * If bStart adds the distance to the initial reference location.
 137  */
 138
 139 extern char **read_rotparams(int *ninp_p,t_inpfile **inp,t_rot *rot,warninp_t wi);
 140 /* Reads enforced rotation parameters, returns a list of the rot group names */
 141
 142 extern void make_rotation_groups(t_rot *rot,char **rotgnames,
 143                  t_blocka *grps,char **gnames);
 144 /* Process the rotation parameters after reading the index groups */
 145
 146 extern void set_reference_positions(t_rot *rot, gmx_mtop_t *mtop, rvec *x, matrix box,
 147         const char *fn, gmx_bool bSet, warninp_t wi);
 148
 149 #endif  /* _readir_h */