src/gromacs/topology/topsort.c

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  37 #include "gromacs/topology/topsort.h"
  38
  39 #include "config.h"
  40
  41 #include <stdio.h>
  42
  43 #include "gromacs/legacyheaders/types/ifunc.h"
  44
  45 #include "gromacs/topology/topology.h"
  46 #include "gromacs/utility/fatalerror.h"
  47 #include "gromacs/utility/smalloc.h"
  48
  49 static gmx_bool ip_pert(int ftype, const t_iparams *ip)
  50 {
  51     gmx_bool bPert;
  52     int      i;
  53
  54     if (NRFPB(ftype) == 0)
  55     {
  56         return FALSE;
  57     }
  58
  59     switch (ftype)
  60     {
  61         case F_BONDS:
  62         case F_G96BONDS:
  63         case F_HARMONIC:
  64         case F_ANGLES:
  65         case F_G96ANGLES:
  66         case F_IDIHS:
  67             bPert = (ip->harmonic.rA  != ip->harmonic.rB ||
  68                      ip->harmonic.krA != ip->harmonic.krB);
  69             break;
  70         case F_MORSE:
  71             bPert = (ip->morse.b0A  != ip->morse.b0B ||
  72                      ip->morse.cbA  != ip->morse.cbB ||
  73                      ip->morse.betaA  != ip->morse.betaB);
  74             break;
  75         case F_RESTRBONDS:
  76             bPert = (ip->restraint.lowA  != ip->restraint.lowB ||
  77                      ip->restraint.up1A  != ip->restraint.up1B ||
  78                      ip->restraint.up2A  != ip->restraint.up2B ||
  79                      ip->restraint.kA    != ip->restraint.kB);
  80             break;
  81         case F_UREY_BRADLEY:
  82             bPert = (ip->u_b.thetaA  != ip->u_b.thetaB  ||
  83                      ip->u_b.kthetaA != ip->u_b.kthetaB ||
  84                      ip->u_b.r13A    != ip->u_b.r13B    ||
  85                      ip->u_b.kUBA    != ip->u_b.kUBB);
  86             break;
  87         case F_PDIHS:
  88         case F_PIDIHS:
  89         case F_ANGRES:
  90         case F_ANGRESZ:
  91             bPert = (ip->pdihs.phiA != ip->pdihs.phiB ||
  92                      ip->pdihs.cpA  != ip->pdihs.cpB);
  93             break;
  94         case F_RBDIHS:
  95             bPert = FALSE;
  96             for (i = 0; i < NR_RBDIHS; i++)
  97             {
  98                 if (ip->rbdihs.rbcA[i] != ip->rbdihs.rbcB[i])
  99                 {
 100                     bPert = TRUE;
 101                 }
 102             }
 103             break;
 104         case F_TABBONDS:
 105         case F_TABBONDSNC:
 106         case F_TABANGLES:
 107         case F_TABDIHS:
 108             bPert = (ip->tab.kA != ip->tab.kB);
 109             break;
 110         case F_POSRES:
 111             bPert = FALSE;
 112             for (i = 0; i < DIM; i++)
 113             {
 114                 if (ip->posres.pos0A[i] != ip->posres.pos0B[i] ||
 115                     ip->posres.fcA[i]   != ip->posres.fcB[i])
 116                 {
 117                     bPert = TRUE;
 118                 }
 119             }
 120             break;
 121         case F_DIHRES:
 122             bPert = ((ip->dihres.phiA != ip->dihres.phiB) ||
 123                      (ip->dihres.dphiA != ip->dihres.dphiB) ||
 124                      (ip->dihres.kfacA != ip->dihres.kfacB));
 125             break;
 126         case F_LJ14:
 127             bPert = (ip->lj14.c6A  != ip->lj14.c6B ||
 128                      ip->lj14.c12A != ip->lj14.c12B);
 129             break;
 130         case F_CMAP:
 131             bPert = FALSE;
 132             break;
 133         case F_RESTRANGLES:
 134         case F_RESTRDIHS:
 135         case F_CBTDIHS:
 136             bPert = FALSE;
 137             gmx_fatal(FARGS, "Function type %s does not support currentely free energy calculations",
 138                       interaction_function[ftype].longname);
 139         default:
 140             bPert = FALSE;
 141             gmx_fatal(FARGS, "Function type %s not implemented in ip_pert",
 142                       interaction_function[ftype].longname);
 143     }
 144
 145     return bPert;
 146 }
 147
 148 static gmx_bool ip_q_pert(int ftype, const t_iatom *ia,
 149                           const t_iparams *ip, const real *qA, const real *qB)
 150 {
 151     /* 1-4 interactions do not have the charges stored in the iparams list,
 152      * so we need a separate check for those.
 153      */
 154     return (ip_pert(ftype, ip+ia[0]) ||
 155             (ftype == F_LJ14 && (qA[ia[1]] != qB[ia[1]] ||
 156                                  qA[ia[2]] != qB[ia[2]])));
 157 }
 158
 159 gmx_bool gmx_mtop_bondeds_free_energy(const gmx_mtop_t *mtop)
 160 {
 161     const gmx_ffparams_t *ffparams;
 162     int                   i, ftype;
 163     int                   mb;
 164     t_atom               *atom;
 165     t_ilist              *il;
 166     t_iatom              *ia;
 167     gmx_bool              bPert;
 168
 169     ffparams = &mtop->ffparams;
 170
 171     /* Loop over all the function types and compare the A/B parameters */
 172     bPert = FALSE;
 173     for (i = 0; i < ffparams->ntypes; i++)
 174     {
 175         ftype = ffparams->functype[i];
 176         if (interaction_function[ftype].flags & IF_BOND)
 177         {
 178             if (ip_pert(ftype, &ffparams->iparams[i]))
 179             {
 180                 bPert = TRUE;
 181             }
 182         }
 183     }
 184
 185     /* Check perturbed charges for 1-4 interactions */
 186     for (mb = 0; mb < mtop->nmolblock; mb++)
 187     {
 188         atom = mtop->moltype[mtop->molblock[mb].type].atoms.atom;
 189         il   = &mtop->moltype[mtop->molblock[mb].type].ilist[F_LJ14];
 190         ia   = il->iatoms;
 191         for (i = 0; i < il->nr; i += 3)
 192         {
 193             if (atom[ia[i+1]].q != atom[ia[i+1]].qB ||
 194                 atom[ia[i+2]].q != atom[ia[i+2]].qB)
 195             {
 196                 bPert = TRUE;
 197             }
 198         }
 199     }
 200
 201     return bPert;
 202 }
 203
 204 void gmx_sort_ilist_fe(t_idef *idef, const real *qA, const real *qB)
 205 {
 206     int        ftype, nral, i, ic, ib, a;
 207     t_iparams *iparams;
 208     t_ilist   *ilist;
 209     t_iatom   *iatoms;
 210     gmx_bool   bPert;
 211     t_iatom   *iabuf;
 212     int        iabuf_nalloc;
 213
 214     if (qB == NULL)
 215     {
 216         qB = qA;
 217     }
 218
 219     iabuf_nalloc = 0;
 220     iabuf        = NULL;
 221
 222     iparams = idef->iparams;
 223
 224     for (ftype = 0; ftype < F_NRE; ftype++)
 225     {
 226         if (interaction_function[ftype].flags & IF_BOND)
 227         {
 228             ilist  = &idef->il[ftype];
 229             iatoms = ilist->iatoms;
 230             nral   = NRAL(ftype);
 231             ic     = 0;
 232             ib     = 0;
 233             i      = 0;
 234             while (i < ilist->nr)
 235             {
 236                 /* Check if this interaction is perturbed */
 237                 if (ip_q_pert(ftype, iatoms+i, iparams, qA, qB))
 238                 {
 239                     /* Copy to the perturbed buffer */
 240                     if (ib + 1 + nral > iabuf_nalloc)
 241                     {
 242                         iabuf_nalloc = over_alloc_large(ib+1+nral);
 243                         srenew(iabuf, iabuf_nalloc);
 244                     }
 245                     for (a = 0; a < 1+nral; a++)
 246                     {
 247                         iabuf[ib++] = iatoms[i++];
 248                     }
 249                 }
 250                 else
 251                 {
 252                     /* Copy in place */
 253                     for (a = 0; a < 1+nral; a++)
 254                     {
 255                         iatoms[ic++] = iatoms[i++];
 256                     }
 257                 }
 258             }
 259             /* Now we now the number of non-perturbed interactions */
 260             ilist->nr_nonperturbed = ic;
 261
 262             /* Copy the buffer with perturbed interactions to the ilist */
 263             for (a = 0; a < ib; a++)
 264             {
 265                 iatoms[ic++] = iabuf[a];
 266             }
 267
 268             if (debug)
 269             {
 270                 fprintf(debug, "%s non-pert %d pert %d\n",
 271                         interaction_function[ftype].longname,
 272                         ilist->nr_nonperturbed,
 273                         ilist->nr-ilist->nr_nonperturbed);
 274             }
 275         }
 276     }
 277
 278     sfree(iabuf);
 279
 280     idef->ilsort = ilsortFE_SORTED;
 281 }