src/gromacs/gmxpreprocess/topshake.cpp

   1 /*
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   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2018,2019, 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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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "topshake.h"
  41
  42 #include <cctype>
  43 #include <cmath>
  44
  45 #include "gromacs/gmxpreprocess/grompp_impl.h"
  46 #include "gromacs/gmxpreprocess/notset.h"
  47 #include "gromacs/gmxpreprocess/readir.h"
  48 #include "gromacs/gmxpreprocess/topdirs.h"
  49 #include "gromacs/gmxpreprocess/toppush.h"
  50 #include "gromacs/gmxpreprocess/toputil.h"
  51 #include "gromacs/math/units.h"
  52 #include "gromacs/topology/ifunc.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 static void copy_bond (InteractionTypeParameters *pr, int to, int from)
  57 /* copies an entry in a bond list to another position.
  58  * does no allocing or freeing of memory
  59  */
  60 {
  61     /*memcpy((char*) &(pr->param[to]),(char*) &(pr->param[from]),
  62        (size_t)sizeof(pr->param[from]));*/
  63     int i;
  64
  65     if (to != from)
  66     {
  67         range_check(to, 0, pr->nr);
  68         range_check(from, 0, pr->nr);
  69         for (i = 0; (i < MAXATOMLIST); i++)
  70         {
  71             pr->param[to].a[i] = pr->param[from].a[i];
  72         }
  73         for (i = 0; (i < MAXFORCEPARAM); i++)
  74         {
  75             pr->param[to].c[i] = pr->param[from].c[i];
  76         }
  77         for (i = 0; (i < MAXSLEN); i++)
  78         {
  79             pr->param[to].s[i] = pr->param[from].s[i];
  80         }
  81     }
  82 }
  83
  84 static int count_hydrogens (char ***atomname, int nra, const int a[])
  85 {
  86     int  nh;
  87
  88     if (!atomname)
  89     {
  90         gmx_fatal(FARGS, "Cannot call count_hydrogens with no atomname (%s %d)",
  91                   __FILE__, __LINE__);
  92     }
  93
  94     nh = 0;
  95     for (int i = 0; (i < nra); i++)
  96     {
  97         if (toupper(**(atomname[a[i]])) == 'H')
  98         {
  99             nh++;
 100         }
 101     }
 102
 103     return nh;
 104 }
 105
 106 void make_shake(gmx::ArrayRef<InteractionTypeParameters> plist, t_atoms *atoms, int nshake)
 107 {
 108     char                  ***info = atoms->atomname;
 109     real                     b_ij, b_jk;
 110     int                      i, j;
 111
 112     if (nshake != eshNONE)
 113     {
 114         switch (nshake)
 115         {
 116             case eshHBONDS:
 117                 printf("turning H bonds into constraints...\n");
 118                 break;
 119             case eshALLBONDS:
 120                 printf("turning all bonds into constraints...\n");
 121                 break;
 122             case eshHANGLES:
 123                 printf("turning all bonds and H angles into constraints...\n");
 124                 break;
 125             case eshALLANGLES:
 126                 printf("turning all bonds and angles into constraints...\n");
 127                 break;
 128             default:
 129                 gmx_fatal(FARGS, "Invalid option for make_shake (%d)", nshake);
 130         }
 131
 132         if ((nshake == eshHANGLES) || (nshake == eshALLANGLES))
 133         {
 134             /* Add all the angles with hydrogens to the shake list
 135              * and remove them from the bond list
 136              */
 137             for (int ftype = 0; (ftype < F_NRE); ftype++)
 138             {
 139                 if (interaction_function[ftype].flags & IF_BTYPE)
 140                 {
 141                     InteractionTypeParameters *bonds = &(plist[ftype]);
 142
 143                     for (int ftype_a = 0; (bonds->nr > 0 && ftype_a < F_NRE); ftype_a++)
 144                     {
 145                         if (interaction_function[ftype_a].flags & IF_ATYPE)
 146                         {
 147                             InteractionTypeParameters *pr = &(plist[ftype_a]);
 148
 149                             for (int i = 0; (i < pr->nr); )
 150                             {
 151                                 t_param *ang = &(pr->param[i]);
 152 #ifdef DEBUG
 153                                 printf("Angle: %d-%d-%d\n", ang->ai(), ang->aj(), ang->ak());
 154 #endif
 155                                 int numhydrogens = count_hydrogens(info, 3, ang->a);
 156                                 if ((nshake == eshALLANGLES) ||
 157                                     (numhydrogens > 1) ||
 158                                     (numhydrogens == 1 && toupper(**(info[ang->a[1]])) == 'O'))
 159                                 {
 160                                     /* Can only add hydrogen angle shake, if the two bonds
 161                                      * are constrained.
 162                                      * append this angle to the shake list
 163                                      */
 164                                     t_param p;
 165                                     p.ai() = ang->ai();
 166                                     p.aj() = ang->ak();
 167
 168                                     /* Calculate length of constraint */
 169                                     bool bFound = false;
 170                                     b_ij   = b_jk = 0.0;
 171                                     for (int j = 0; !bFound && (j < bonds->nr); j++)
 172                                     {
 173                                         t_param *bond = &(bonds->param[j]);
 174                                         if (((bond->ai() == ang->ai()) &&
 175                                              (bond->aj() == ang->aj())) ||
 176                                             ((bond->ai() == ang->aj()) &&
 177                                              (bond->aj() == ang->ai())))
 178                                         {
 179                                             b_ij = bond->c0();
 180                                         }
 181                                         if (((bond->ai() == ang->ak()) &&
 182                                              (bond->aj() == ang->aj())) ||
 183                                             ((bond->ai() == ang->aj()) &&
 184                                              (bond->aj() == ang->ak())))
 185                                         {
 186                                             b_jk = bond->c0();
 187                                         }
 188                                         bFound = (b_ij != 0.0) && (b_jk != 0.0);
 189                                     }
 190                                     if (bFound)
 191                                     {
 192                                         /* apply law of cosines */
 193                                         p.c0() = std::sqrt( b_ij*b_ij + b_jk*b_jk -
 194                                                             2.0*b_ij*b_jk*cos(DEG2RAD*ang->c0()) );
 195                                         p.c1() = p.c0();
 196 #ifdef DEBUG
 197                                         printf("p: %d, q: %d, dist: %12.5e\n", p.ai(), p.aj(), p.c0());
 198 #endif
 199                                         add_param_to_list (&(plist[F_CONSTR]), &p);
 200                                         /* move the last bond to this position */
 201                                         copy_bond (pr, i, pr->nr-1);
 202                                         /* should free memory here!! */
 203                                         pr->nr--;
 204                                     }
 205                                 }
 206                                 else
 207                                 {
 208                                     i++;
 209                                 }
 210                             }
 211                         } /* if IF_ATYPE */
 212                     }     /* for ftype_A */
 213                 }         /* if IF_BTYPE */
 214             }             /* for ftype */
 215         }                 /* if shake angles */
 216
 217         /* Add all the bonds with hydrogens to the shake list
 218          * and remove them from the bond list
 219          */
 220         for (int ftype = 0; (ftype < F_NRE); ftype++)
 221         {
 222             if (interaction_function[ftype].flags & IF_BTYPE)
 223             {
 224                 InteractionTypeParameters *pr = &(plist[ftype]);
 225                 j  = 0;
 226                 for (i = 0; i < pr->nr; i++)
 227                 {
 228                     if ( (nshake != eshHBONDS) ||
 229                          (count_hydrogens (info, 2, pr->param[i].a) > 0) )
 230                     {
 231                         /* append this bond to the shake list */
 232                         t_param p;
 233                         p.ai() = pr->param[i].ai();
 234                         p.aj() = pr->param[i].aj();
 235                         p.c0() = pr->param[i].c0();
 236                         p.c1() = pr->param[i].c2();
 237                         add_param_to_list (&(plist[F_CONSTR]), &p);
 238                     }
 239                     else
 240                     {
 241                         copy_bond(pr, j++, i);
 242                     }
 243                 }
 244                 pr->nr = j;
 245             }
 246         }
 247     }
 248 }