src/gromacs/topology/topsort.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "topsort.h"
  40
  41 #include <cstdio>
  42
  43 #include "gromacs/topology/ifunc.h"
  44 #include "gromacs/topology/topology.h"
  45 #include "gromacs/utility/arrayref.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             gmx_fatal(FARGS, "Function type %s does not support currentely free energy calculations",
 137                       interaction_function[ftype].longname);
 138         default:
 139             gmx_fatal(FARGS, "Function type %s not implemented in ip_pert",
 140                       interaction_function[ftype].longname);
 141     }
 142
 143     return bPert;
 144 }
 145
 146 static gmx_bool ip_q_pert(int ftype, const t_iatom *ia,
 147                           const t_iparams *ip, const real *qA, const real *qB)
 148 {
 149     /* 1-4 interactions do not have the charges stored in the iparams list,
 150      * so we need a separate check for those.
 151      */
 152     return (ip_pert(ftype, ip+ia[0]) ||
 153             (ftype == F_LJ14 && (qA[ia[1]] != qB[ia[1]] ||
 154                                  qA[ia[2]] != qB[ia[2]])));
 155 }
 156
 157 gmx_bool gmx_mtop_bondeds_free_energy(const gmx_mtop_t *mtop)
 158 {
 159     const gmx_ffparams_t *ffparams = &mtop->ffparams;
 160
 161     /* Loop over all the function types and compare the A/B parameters */
 162     gmx_bool bPert = FALSE;
 163     for (int i = 0; i < ffparams->numTypes(); i++)
 164     {
 165         int ftype = ffparams->functype[i];
 166         if (interaction_function[ftype].flags & IF_BOND)
 167         {
 168             if (ip_pert(ftype, &ffparams->iparams[i]))
 169             {
 170                 bPert = TRUE;
 171             }
 172         }
 173     }
 174
 175     /* Check perturbed charges for 1-4 interactions */
 176     for (const gmx_molblock_t &molb : mtop->molblock)
 177     {
 178         const t_atom             *atom = mtop->moltype[molb.type].atoms.atom;
 179         const InteractionList    &il   = mtop->moltype[molb.type].ilist[F_LJ14];
 180         gmx::ArrayRef<const int>  ia   = il.iatoms;
 181         for (int i = 0; i < il.size(); i += 3)
 182         {
 183             if (atom[ia[i+1]].q != atom[ia[i+1]].qB ||
 184                 atom[ia[i+2]].q != atom[ia[i+2]].qB)
 185             {
 186                 bPert = TRUE;
 187             }
 188         }
 189     }
 190
 191     return bPert;
 192 }
 193
 194 void gmx_sort_ilist_fe(t_idef *idef, const real *qA, const real *qB)
 195 {
 196     int        ftype, nral, i, ic, ib, a;
 197     t_ilist   *ilist;
 198     t_iatom   *iatoms;
 199     t_iatom   *iabuf;
 200     int        iabuf_nalloc;
 201
 202     if (qB == nullptr)
 203     {
 204         qB = qA;
 205     }
 206
 207     iabuf_nalloc = 0;
 208     iabuf        = nullptr;
 209
 210     const t_iparams *iparams = idef->iparams;
 211
 212     for (ftype = 0; ftype < F_NRE; ftype++)
 213     {
 214         if (interaction_function[ftype].flags & IF_BOND)
 215         {
 216             ilist  = &idef->il[ftype];
 217             iatoms = ilist->iatoms;
 218             nral   = NRAL(ftype);
 219             ic     = 0;
 220             ib     = 0;
 221             i      = 0;
 222             while (i < ilist->nr)
 223             {
 224                 /* Check if this interaction is perturbed */
 225                 if (ip_q_pert(ftype, iatoms+i, iparams, qA, qB))
 226                 {
 227                     /* Copy to the perturbed buffer */
 228                     if (ib + 1 + nral > iabuf_nalloc)
 229                     {
 230                         iabuf_nalloc = over_alloc_large(ib+1+nral);
 231                         srenew(iabuf, iabuf_nalloc);
 232                     }
 233                     for (a = 0; a < 1+nral; a++)
 234                     {
 235                         iabuf[ib++] = iatoms[i++];
 236                     }
 237                 }
 238                 else
 239                 {
 240                     /* Copy in place */
 241                     for (a = 0; a < 1+nral; a++)
 242                     {
 243                         iatoms[ic++] = iatoms[i++];
 244                     }
 245                 }
 246             }
 247             /* Now we now the number of non-perturbed interactions */
 248             ilist->nr_nonperturbed = ic;
 249
 250             /* Copy the buffer with perturbed interactions to the ilist */
 251             for (a = 0; a < ib; a++)
 252             {
 253                 iatoms[ic++] = iabuf[a];
 254             }
 255
 256             if (debug)
 257             {
 258                 fprintf(debug, "%s non-pert %d pert %d\n",
 259                         interaction_function[ftype].longname,
 260                         ilist->nr_nonperturbed,
 261                         ilist->nr-ilist->nr_nonperturbed);
 262             }
 263         }
 264     }
 265
 266     sfree(iabuf);
 267
 268     idef->ilsort = ilsortFE_SORTED;
 269 }