src/gromacs/topology/topsort.cpp

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