src/gromacs/gmxpreprocess/topshake.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
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  10  *
  11  * GROMACS is free software; you can redistribute it and/or
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  13  * as published by the Free Software Foundation; either version 2.1
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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "topshake.h"
  41
  42 #include <ctype.h>
  43 #include <math.h>
  44
  45 #include "gromacs/gmxpreprocess/readir.h"
  46 #include "gromacs/gmxpreprocess/topdirs.h"
  47 #include "gromacs/gmxpreprocess/toppush.h"
  48 #include "gromacs/gmxpreprocess/toputil.h"
  49 #include "gromacs/legacyheaders/typedefs.h"
  50 #include "gromacs/math/units.h"
  51 #include "gromacs/utility/fatalerror.h"
  52 #include "gromacs/utility/smalloc.h"
  53
  54 static void copy_bond (t_params *pr, int to, int from)
  55 /* copies an entry in a bond list to another position.
  56  * does no allocing or freeing of memory
  57  */
  58 {
  59     /*memcpy((char*) &(pr->param[to]),(char*) &(pr->param[from]),
  60        (size_t)sizeof(pr->param[from]));*/
  61     int i;
  62
  63     if (to != from)
  64     {
  65         range_check(to, 0, pr->nr);
  66         range_check(from, 0, pr->nr);
  67         for (i = 0; (i < MAXATOMLIST); i++)
  68         {
  69             pr->param[to].a[i] = pr->param[from].a[i];
  70         }
  71         for (i = 0; (i < MAXFORCEPARAM); i++)
  72         {
  73             pr->param[to].c[i] = pr->param[from].c[i];
  74         }
  75         for (i = 0; (i < MAXSLEN); i++)
  76         {
  77             pr->param[to].s[i] = pr->param[from].s[i];
  78         }
  79     }
  80 }
  81
  82 static int count_hydrogens (char ***atomname, int nra, atom_id a[])
  83 {
  84     int  i, nh;
  85
  86     if (!atomname)
  87     {
  88         gmx_fatal(FARGS, "Cannot call count_hydrogens with no atomname (%s %d)",
  89                   __FILE__, __LINE__);
  90     }
  91
  92     nh = 0;
  93     for (i = 0; (i < nra); i++)
  94     {
  95         if (toupper(**(atomname[a[i]])) == 'H')
  96         {
  97             nh++;
  98         }
  99     }
 100
 101     return nh;
 102 }
 103
 104 void make_shake (t_params plist[], t_atoms *atoms, int nshake)
 105 {
 106     char          ***info = atoms->atomname;
 107     t_params        *pr;
 108     t_params        *bonds;
 109     t_param          p, *bond, *ang;
 110     real             b_ij, b_jk;
 111     int              nb, b, i, j, ftype, ftype_a;
 112     gmx_bool         bFound;
 113
 114     if (nshake != eshNONE)
 115     {
 116         switch (nshake)
 117         {
 118             case eshHBONDS:
 119                 printf("turning H bonds into constraints...\n");
 120                 break;
 121             case eshALLBONDS:
 122                 printf("turning all bonds into constraints...\n");
 123                 break;
 124             case eshHANGLES:
 125                 printf("turning all bonds and H angles into constraints...\n");
 126                 break;
 127             case eshALLANGLES:
 128                 printf("turning all bonds and angles into constraints...\n");
 129                 break;
 130             default:
 131                 gmx_fatal(FARGS, "Invalid option for make_shake (%d)", nshake);
 132         }
 133
 134         if ((nshake == eshHANGLES) || (nshake == eshALLANGLES))
 135         {
 136             /* Add all the angles with hydrogens to the shake list
 137              * and remove them from the bond list
 138              */
 139             for (ftype = 0; (ftype < F_NRE); ftype++)
 140             {
 141                 if (interaction_function[ftype].flags & IF_BTYPE)
 142                 {
 143                     bonds = &(plist[ftype]);
 144
 145                     for (ftype_a = 0; (bonds->nr > 0 && ftype_a < F_NRE); ftype_a++)
 146                     {
 147                         if (interaction_function[ftype_a].flags & IF_ATYPE)
 148                         {
 149                             pr = &(plist[ftype_a]);
 150
 151                             for (i = 0; (i < pr->nr); )
 152                             {
 153                                 int numhydrogens;
 154
 155                                 ang = &(pr->param[i]);
 156 #ifdef DEBUG
 157                                 printf("Angle: %d-%d-%d\n", ang->AI, ang->AJ, ang->AK);
 158 #endif
 159                                 numhydrogens = count_hydrogens(info, 3, ang->a);
 160                                 if ((nshake == eshALLANGLES) ||
 161                                     (numhydrogens > 1) ||
 162                                     (numhydrogens == 1 && toupper(**(info[ang->a[1]])) == 'O'))
 163                                 {
 164                                     /* Can only add hydrogen angle shake, if the two bonds
 165                                      * are constrained.
 166                                      * append this angle to the shake list
 167                                      */
 168                                     p.AI = ang->AI;
 169                                     p.AJ = ang->AK;
 170
 171                                     /* Calculate length of constraint */
 172                                     bFound = FALSE;
 173                                     b_ij   = b_jk = 0.0;
 174                                     for (j = 0; !bFound && (j < bonds->nr); j++)
 175                                     {
 176                                         bond = &(bonds->param[j]);
 177                                         if (((bond->AI == ang->AI) &&
 178                                              (bond->AJ == ang->AJ)) ||
 179                                             ((bond->AI == ang->AJ) &&
 180                                              (bond->AJ == ang->AI)))
 181                                         {
 182                                             b_ij = bond->C0;
 183                                         }
 184                                         if (((bond->AI == ang->AK) &&
 185                                              (bond->AJ == ang->AJ)) ||
 186                                             ((bond->AI == ang->AJ) &&
 187                                              (bond->AJ == ang->AK)))
 188                                         {
 189                                             b_jk = bond->C0;
 190                                         }
 191                                         bFound = (b_ij != 0.0) && (b_jk != 0.0);
 192                                     }
 193                                     if (bFound)
 194                                     {
 195                                         /* apply law of cosines */
 196                                         p.C0 = sqrt( b_ij*b_ij + b_jk*b_jk -
 197                                                      2.0*b_ij*b_jk*cos(DEG2RAD*ang->C0) );
 198                                         p.C1 = p.C0;
 199 #ifdef DEBUG
 200                                         printf("p: %d, q: %d, dist: %12.5e\n", p.AI, p.AJ, p.C0);
 201 #endif
 202                                         add_param_to_list (&(plist[F_CONSTR]), &p);
 203                                         /* move the last bond to this position */
 204                                         copy_bond (pr, i, pr->nr-1);
 205                                         /* should free memory here!! */
 206                                         pr->nr--;
 207                                     }
 208                                 }
 209                                 else
 210                                 {
 211                                     i++;
 212                                 }
 213                             }
 214                         } /* if IF_ATYPE */
 215                     }     /* for ftype_A */
 216                 }         /* if IF_BTYPE */
 217             }             /* for ftype */
 218         }                 /* if shake angles */
 219
 220         /* Add all the bonds with hydrogens to the shake list
 221          * and remove them from the bond list
 222          */
 223         for (ftype = 0; (ftype < F_NRE); ftype++)
 224         {
 225             if (interaction_function[ftype].flags & IF_BTYPE)
 226             {
 227                 pr = &(plist[ftype]);
 228                 j  = 0;
 229                 for (i = 0; i < pr->nr; i++)
 230                 {
 231                     if ( (nshake != eshHBONDS) ||
 232                          (count_hydrogens (info, 2, pr->param[i].a) > 0) )
 233                     {
 234                         /* append this bond to the shake list */
 235                         p.AI = pr->param[i].AI;
 236                         p.AJ = pr->param[i].AJ;
 237                         p.C0 = pr->param[i].C0;
 238                         p.C1 = pr->param[i].C2;
 239                         add_param_to_list (&(plist[F_CONSTR]), &p);
 240                     }
 241                     else
 242                     {
 243                         copy_bond(pr, j++, i);
 244                     }
 245                 }
 246                 pr->nr = j;
 247             }
 248         }
 249     }
 250 }