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.
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  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  *
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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   char *include;
  60   char *define;
  61   gmx_bool bGenVel;
  62   gmx_bool bGenPairs;
  63   real tempi;
  64   int  seed;
  65   gmx_bool bOrire;
  66   gmx_bool bMorse;
  67   char *wall_atomtype[2];
  68   gmx_bool pull_start;
  69   char *couple_moltype;
  70   int  couple_lam0;
  71   int  couple_lam1;
  72   gmx_bool bCoupleIntra;
  73 } t_gromppopts;
  74
  75
  76 extern void init_ir(t_inputrec *ir, t_gromppopts *opts);
  77 /* Initiate stuff */
  78
  79 extern void check_ir(const char *mdparin,t_inputrec *ir, t_gromppopts *opts,
  80                      warninp_t wi);
  81 /* Validate inputrec data.
  82  * Fatal errors will be added to nerror.
  83  */
  84 extern int search_string(char *s,int ng,char *gn[]);
  85 /* Returns the index of string s in the index groups */
  86
  87 extern void double_check(t_inputrec *ir,matrix box,gmx_bool bConstr,
  88                          warninp_t wi);
  89 /* Do more checks */
  90
  91 extern void triple_check(const char *mdparin,t_inputrec *ir,gmx_mtop_t *sys,
  92                          warninp_t wi);
  93 /* Do even more checks */
  94
  95 extern void check_chargegroup_radii(const gmx_mtop_t *mtop,const t_inputrec *ir,
  96                                     rvec *x,
  97                                     warninp_t wi);
  98 /* Even more checks, charge group radii vs. cut-off's only. */
  99
 100 extern void get_ir(const char *mdparin,const char *mdparout,
 101                    t_inputrec *ir,t_gromppopts *opts,
 102                    warninp_t wi);
 103 /* Read the input file, and retrieve data for inputrec.
 104  * More data are read, but the are only evaluated when the next
 105  * function is called. Also prints the input file back to mdparout.
 106  */
 107
 108 extern void do_index(const char* mdparin,
 109                      const char *ndx,
 110                      gmx_mtop_t *mtop,
 111                      gmx_bool bVerbose,
 112                      t_inputrec *ir,
 113                      rvec *v,
 114                      warninp_t wi);
 115 /* Read the index file and assign grp numbers to atoms.
 116  * If v is not NULL, the velocities will be scaled to the correct number
 117  * of degrees of freedom.
 118  */
 119
 120 /* Routines In readpull.c */
 121
 122 extern char **read_pullparams(int *ninp_p,t_inpfile **inp,
 123                               t_pull *pull,gmx_bool *bStart,
 124                               warninp_t wi);
 125 /* Reads the pull parameters, returns a list of the pull group names */
 126
 127 extern void make_pull_groups(t_pull *pull,char **pgnames,
 128                              t_blocka *grps,char **gnames);
 129 /* Process the pull parameters after reading the index groups */
 130
 131 extern void set_pull_init(t_inputrec *ir,gmx_mtop_t *mtop,rvec *x,matrix box,
 132                           const output_env_t oenv, gmx_bool bStart);
 133 /* Prints the initial pull group distances in x.
 134  * If bStart adds the distance to the initial reference location.
 135  */
 136
 137 extern int str_nelem(const char *str,int maxptr,char *ptr[]);
 138 /* helper function from readir.c to convert strings */
 139
 140 extern void read_adressparams(int *ninp_p,t_inpfile **inp_p,t_adress *adress, warninp_t wi);
 141 /* Reads in AdResS related parameters */
 142
 143 extern void do_adress_index(t_adress *adress, gmx_groups_t *groups,char **gnames,t_grpopts *opts,warninp_t wi);
 144 /* Generate adress groups */
 145
 146 extern char **read_rotparams(int *ninp_p,t_inpfile **inp,t_rot *rot,warninp_t wi);
 147 /* Reads enforced rotation parameters, returns a list of the rot group names */
 148
 149 extern void make_rotation_groups(t_rot *rot,char **rotgnames,
 150                  t_blocka *grps,char **gnames);
 151 /* Process the rotation parameters after reading the index groups */
 152
 153 extern void set_reference_positions(t_rot *rot, gmx_mtop_t *mtop, rvec *x, matrix box,
 154         const char *fn, gmx_bool bSet, warninp_t wi);
 155
 156 #endif  /* _readir_h */