src/gromacs/topology/topsort.c

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