src/gromacs/gmxpreprocess/topshake.cpp

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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
  44 #include <cmath>
  45
  46 #include "gromacs/gmxpreprocess/readir.h"
  47 #include "gromacs/gmxpreprocess/topdirs.h"
  48 #include "gromacs/gmxpreprocess/toppush.h"
  49 #include "gromacs/gmxpreprocess/toputil.h"
  50 #include "gromacs/legacyheaders/typedefs.h"
  51 #include "gromacs/legacyheaders/types/ifunc.h"
  52 #include "gromacs/math/units.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 static void copy_bond (t_params *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, atom_id a[])
  85 {
  86     int  i, 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 (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 (t_params plist[], t_atoms *atoms, int nshake)
 107 {
 108     char          ***info = atoms->atomname;
 109     t_params        *pr;
 110     t_params        *bonds;
 111     t_param          p, *bond, *ang;
 112     real             b_ij, b_jk;
 113     int              i, j, ftype, ftype_a;
 114     gmx_bool         bFound;
 115
 116     if (nshake != eshNONE)
 117     {
 118         switch (nshake)
 119         {
 120             case eshHBONDS:
 121                 printf("turning H bonds into constraints...\n");
 122                 break;
 123             case eshALLBONDS:
 124                 printf("turning all bonds into constraints...\n");
 125                 break;
 126             case eshHANGLES:
 127                 printf("turning all bonds and H angles into constraints...\n");
 128                 break;
 129             case eshALLANGLES:
 130                 printf("turning all bonds and angles into constraints...\n");
 131                 break;
 132             default:
 133                 gmx_fatal(FARGS, "Invalid option for make_shake (%d)", nshake);
 134         }
 135
 136         if ((nshake == eshHANGLES) || (nshake == eshALLANGLES))
 137         {
 138             /* Add all the angles with hydrogens to the shake list
 139              * and remove them from the bond list
 140              */
 141             for (ftype = 0; (ftype < F_NRE); ftype++)
 142             {
 143                 if (interaction_function[ftype].flags & IF_BTYPE)
 144                 {
 145                     bonds = &(plist[ftype]);
 146
 147                     for (ftype_a = 0; (bonds->nr > 0 && ftype_a < F_NRE); ftype_a++)
 148                     {
 149                         if (interaction_function[ftype_a].flags & IF_ATYPE)
 150                         {
 151                             pr = &(plist[ftype_a]);
 152
 153                             for (i = 0; (i < pr->nr); )
 154                             {
 155                                 int numhydrogens;
 156
 157                                 ang = &(pr->param[i]);
 158 #ifdef DEBUG
 159                                 printf("Angle: %d-%d-%d\n", ang->ai(), ang->aj(), ang->ak());
 160 #endif
 161                                 numhydrogens = count_hydrogens(info, 3, ang->a);
 162                                 if ((nshake == eshALLANGLES) ||
 163                                     (numhydrogens > 1) ||
 164                                     (numhydrogens == 1 && toupper(**(info[ang->a[1]])) == 'O'))
 165                                 {
 166                                     /* Can only add hydrogen angle shake, if the two bonds
 167                                      * are constrained.
 168                                      * append this angle to the shake list
 169                                      */
 170                                     p.ai() = ang->ai();
 171                                     p.aj() = ang->ak();
 172
 173                                     /* Calculate length of constraint */
 174                                     bFound = FALSE;
 175                                     b_ij   = b_jk = 0.0;
 176                                     for (j = 0; !bFound && (j < bonds->nr); j++)
 177                                     {
 178                                         bond = &(bonds->param[j]);
 179                                         if (((bond->ai() == ang->ai()) &&
 180                                              (bond->aj() == ang->aj())) ||
 181                                             ((bond->ai() == ang->aj()) &&
 182                                              (bond->aj() == ang->ai())))
 183                                         {
 184                                             b_ij = bond->c0();
 185                                         }
 186                                         if (((bond->ai() == ang->ak()) &&
 187                                              (bond->aj() == ang->aj())) ||
 188                                             ((bond->ai() == ang->aj()) &&
 189                                              (bond->aj() == ang->ak())))
 190                                         {
 191                                             b_jk = bond->c0();
 192                                         }
 193                                         bFound = (b_ij != 0.0) && (b_jk != 0.0);
 194                                     }
 195                                     if (bFound)
 196                                     {
 197                                         /* apply law of cosines */
 198                                         p.c0() = std::sqrt( b_ij*b_ij + b_jk*b_jk -
 199                                                             2.0*b_ij*b_jk*cos(DEG2RAD*ang->c0()) );
 200                                         p.c1() = p.c0();
 201 #ifdef DEBUG
 202                                         printf("p: %d, q: %d, dist: %12.5e\n", p.ai(), p.aj(), p.c0());
 203 #endif
 204                                         add_param_to_list (&(plist[F_CONSTR]), &p);
 205                                         /* move the last bond to this position */
 206                                         copy_bond (pr, i, pr->nr-1);
 207                                         /* should free memory here!! */
 208                                         pr->nr--;
 209                                     }
 210                                 }
 211                                 else
 212                                 {
 213                                     i++;
 214                                 }
 215                             }
 216                         } /* if IF_ATYPE */
 217                     }     /* for ftype_A */
 218                 }         /* if IF_BTYPE */
 219             }             /* for ftype */
 220         }                 /* if shake angles */
 221
 222         /* Add all the bonds with hydrogens to the shake list
 223          * and remove them from the bond list
 224          */
 225         for (ftype = 0; (ftype < F_NRE); ftype++)
 226         {
 227             if (interaction_function[ftype].flags & IF_BTYPE)
 228             {
 229                 pr = &(plist[ftype]);
 230                 j  = 0;
 231                 for (i = 0; i < pr->nr; i++)
 232                 {
 233                     if ( (nshake != eshHBONDS) ||
 234                          (count_hydrogens (info, 2, pr->param[i].a) > 0) )
 235                     {
 236                         /* append this bond to the shake list */
 237                         p.ai() = pr->param[i].ai();
 238                         p.aj() = pr->param[i].aj();
 239                         p.c0() = pr->param[i].c0();
 240                         p.c1() = pr->param[i].c2();
 241                         add_param_to_list (&(plist[F_CONSTR]), &p);
 242                     }
 243                     else
 244                     {
 245                         copy_bond(pr, j++, i);
 246                     }
 247                 }
 248                 pr->nr = j;
 249             }
 250         }
 251     }
 252 }