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
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
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  36  */
  37 /* This file is completely threadsafe - keep it that way! */
  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <ctype.h>
  43 #include <math.h>
  44
  45 #include "sysstuff.h"
  46 #include "physics.h"
  47 #include "macros.h"
  48 #include "readir.h"
  49 #include "typedefs.h"
  50 #include "topshake.h"
  51 #include "toppush.h"
  52 #include "toputil.h"
  53 #include "topdirs.h"
  54 #include "gromacs/utility/smalloc.h"
  55 #include "gmx_fatal.h"
  56
  57 static void copy_bond (t_params *pr, int to, int from)
  58 /* copies an entry in a bond list to another position.
  59  * does no allocing or freeing of memory
  60  */
  61 {
  62     /*memcpy((char*) &(pr->param[to]),(char*) &(pr->param[from]),
  63        (size_t)sizeof(pr->param[from]));*/
  64     int i;
  65
  66     if (to != from)
  67     {
  68         range_check(to, 0, pr->nr);
  69         range_check(from, 0, pr->nr);
  70         for (i = 0; (i < MAXATOMLIST); i++)
  71         {
  72             pr->param[to].a[i] = pr->param[from].a[i];
  73         }
  74         for (i = 0; (i < MAXFORCEPARAM); i++)
  75         {
  76             pr->param[to].c[i] = pr->param[from].c[i];
  77         }
  78         for (i = 0; (i < MAXSLEN); i++)
  79         {
  80             pr->param[to].s[i] = pr->param[from].s[i];
  81         }
  82     }
  83 }
  84
  85 static int count_hydrogens (char ***atomname, int nra, atom_id a[])
  86 {
  87     int  i, nh;
  88
  89     if (!atomname)
  90     {
  91         gmx_fatal(FARGS, "Cannot call count_hydrogens with no atomname (%s %d)",
  92                   __FILE__, __LINE__);
  93     }
  94
  95     nh = 0;
  96     for (i = 0; (i < nra); i++)
  97     {
  98         if (toupper(**(atomname[a[i]])) == 'H')
  99         {
 100             nh++;
 101         }
 102     }
 103
 104     return nh;
 105 }
 106
 107 void make_shake (t_params plist[], t_atoms *atoms, int nshake)
 108 {
 109     char          ***info = atoms->atomname;
 110     t_params        *pr;
 111     t_params        *bonds;
 112     t_param          p, *bond, *ang;
 113     real             b_ij, b_jk;
 114     int              nb, b, i, j, ftype, ftype_a;
 115     gmx_bool         bFound;
 116
 117     if (nshake != eshNONE)
 118     {
 119         switch (nshake)
 120         {
 121             case eshHBONDS:
 122                 printf("turning H bonds into constraints...\n");
 123                 break;
 124             case eshALLBONDS:
 125                 printf("turning all bonds into constraints...\n");
 126                 break;
 127             case eshHANGLES:
 128                 printf("turning all bonds and H angles into constraints...\n");
 129                 break;
 130             case eshALLANGLES:
 131                 printf("turning all bonds and angles into constraints...\n");
 132                 break;
 133             default:
 134                 gmx_fatal(FARGS, "Invalid option for make_shake (%d)", nshake);
 135         }
 136
 137         if ((nshake == eshHANGLES) || (nshake == eshALLANGLES))
 138         {
 139             /* Add all the angles with hydrogens to the shake list
 140              * and remove them from the bond list
 141              */
 142             for (ftype = 0; (ftype < F_NRE); ftype++)
 143             {
 144                 if (interaction_function[ftype].flags & IF_BTYPE)
 145                 {
 146                     bonds = &(plist[ftype]);
 147
 148                     for (ftype_a = 0; (bonds->nr > 0 && ftype_a < F_NRE); ftype_a++)
 149                     {
 150                         if (interaction_function[ftype_a].flags & IF_ATYPE)
 151                         {
 152                             pr = &(plist[ftype_a]);
 153
 154                             for (i = 0; (i < pr->nr); )
 155                             {
 156                                 int numhydrogens;
 157
 158                                 ang = &(pr->param[i]);
 159 #ifdef DEBUG
 160                                 printf("Angle: %d-%d-%d\n", ang->AI, ang->AJ, ang->AK);
 161 #endif
 162                                 numhydrogens = count_hydrogens(info, 3, ang->a);
 163                                 if ((nshake == eshALLANGLES) ||
 164                                     (numhydrogens > 1) ||
 165                                     (numhydrogens == 1 && toupper(**(info[ang->a[1]])) == 'O'))
 166                                 {
 167                                     /* Can only add hydrogen angle shake, if the two bonds
 168                                      * are constrained.
 169                                      * append this angle to the shake list
 170                                      */
 171                                     p.AI = ang->AI;
 172                                     p.AJ = ang->AK;
 173
 174                                     /* Calculate length of constraint */
 175                                     bFound = FALSE;
 176                                     b_ij   = b_jk = 0.0;
 177                                     for (j = 0; !bFound && (j < bonds->nr); j++)
 178                                     {
 179                                         bond = &(bonds->param[j]);
 180                                         if (((bond->AI == ang->AI) &&
 181                                              (bond->AJ == ang->AJ)) ||
 182                                             ((bond->AI == ang->AJ) &&
 183                                              (bond->AJ == ang->AI)))
 184                                         {
 185                                             b_ij = bond->C0;
 186                                         }
 187                                         if (((bond->AI == ang->AK) &&
 188                                              (bond->AJ == ang->AJ)) ||
 189                                             ((bond->AI == ang->AJ) &&
 190                                              (bond->AJ == ang->AK)))
 191                                         {
 192                                             b_jk = bond->C0;
 193                                         }
 194                                         bFound = (b_ij != 0.0) && (b_jk != 0.0);
 195                                     }
 196                                     if (bFound)
 197                                     {
 198                                         /* apply law of cosines */
 199                                         p.C0 = sqrt( b_ij*b_ij + b_jk*b_jk -
 200                                                      2.0*b_ij*b_jk*cos(DEG2RAD*ang->C0) );
 201                                         p.C1 = p.C0;
 202 #ifdef DEBUG
 203                                         printf("p: %d, q: %d, dist: %12.5e\n", p.AI, p.AJ, p.C0);
 204 #endif
 205                                         add_param_to_list (&(plist[F_CONSTR]), &p);
 206                                         /* move the last bond to this position */
 207                                         copy_bond (pr, i, pr->nr-1);
 208                                         /* should free memory here!! */
 209                                         pr->nr--;
 210                                     }
 211                                 }
 212                                 else
 213                                 {
 214                                     i++;
 215                                 }
 216                             }
 217                         } /* if IF_ATYPE */
 218                     }     /* for ftype_A */
 219                 }         /* if IF_BTYPE */
 220             }             /* for ftype */
 221         }                 /* if shake angles */
 222
 223         /* Add all the bonds with hydrogens to the shake list
 224          * and remove them from the bond list
 225          */
 226         for (ftype = 0; (ftype < F_NRE); ftype++)
 227         {
 228             if (interaction_function[ftype].flags & IF_BTYPE)
 229             {
 230                 pr = &(plist[ftype]);
 231                 j  = 0;
 232                 for (i = 0; i < pr->nr; i++)
 233                 {
 234                     if ( (nshake != eshHBONDS) ||
 235                          (count_hydrogens (info, 2, pr->param[i].a) > 0) )
 236                     {
 237                         /* append this bond to the shake list */
 238                         p.AI = pr->param[i].AI;
 239                         p.AJ = pr->param[i].AJ;
 240                         p.C0 = pr->param[i].C0;
 241                         p.C1 = pr->param[i].C2;
 242                         add_param_to_list (&(plist[F_CONSTR]), &p);
 243                     }
 244                     else
 245                     {
 246                         copy_bond(pr, j++, i);
 247                     }
 248                 }
 249                 pr->nr = j;
 250             }
 251         }
 252     }
 253 }