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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"
48 static gmx_bool ip_pert(int ftype, const t_iparams *ip)
53 if (NRFPB(ftype) == 0)
66 bPert = (ip->harmonic.rA != ip->harmonic.rB ||
67 ip->harmonic.krA != ip->harmonic.krB);
70 bPert = (ip->morse.b0A != ip->morse.b0B ||
71 ip->morse.cbA != ip->morse.cbB ||
72 ip->morse.betaA != ip->morse.betaB);
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);
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);
90 bPert = (ip->pdihs.phiA != ip->pdihs.phiB ||
91 ip->pdihs.cpA != ip->pdihs.cpB);
95 for (i = 0; i < NR_RBDIHS; i++)
97 if (ip->rbdihs.rbcA[i] != ip->rbdihs.rbcB[i])
107 bPert = (ip->tab.kA != ip->tab.kB);
111 for (i = 0; i < DIM; i++)
113 if (ip->posres.pos0A[i] != ip->posres.pos0B[i] ||
114 ip->posres.fcA[i] != ip->posres.fcB[i])
121 bPert = ((ip->dihres.phiA != ip->dihres.phiB) ||
122 (ip->dihres.dphiA != ip->dihres.dphiB) ||
123 (ip->dihres.kfacA != ip->dihres.kfacB));
126 bPert = (ip->lj14.c6A != ip->lj14.c6B ||
127 ip->lj14.c12A != ip->lj14.c12B);
136 gmx_fatal(FARGS, "Function type %s does not support currentely free energy calculations",
137 interaction_function[ftype].longname);
140 gmx_fatal(FARGS, "Function type %s not implemented in ip_pert",
141 interaction_function[ftype].longname);
147 static gmx_bool ip_q_pert(int ftype, const t_iatom *ia,
148 const t_iparams *ip, const real *qA, const real *qB)
150 /* 1-4 interactions do not have the charges stored in the iparams list,
151 * so we need a separate check for those.
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]])));
158 gmx_bool gmx_mtop_bondeds_free_energy(const gmx_mtop_t *mtop)
160 const gmx_ffparams_t *ffparams;
168 ffparams = &mtop->ffparams;
170 /* Loop over all the function types and compare the A/B parameters */
172 for (i = 0; i < ffparams->ntypes; i++)
174 ftype = ffparams->functype[i];
175 if (interaction_function[ftype].flags & IF_BOND)
177 if (ip_pert(ftype, &ffparams->iparams[i]))
184 /* Check perturbed charges for 1-4 interactions */
185 for (mb = 0; mb < mtop->nmolblock; mb++)
187 atom = mtop->moltype[mtop->molblock[mb].type].atoms.atom;
188 il = &mtop->moltype[mtop->molblock[mb].type].ilist[F_LJ14];
190 for (i = 0; i < il->nr; i += 3)
192 if (atom[ia[i+1]].q != atom[ia[i+1]].qB ||
193 atom[ia[i+2]].q != atom[ia[i+2]].qB)
203 void gmx_sort_ilist_fe(t_idef *idef, const real *qA, const real *qB)
205 int ftype, nral, i, ic, ib, a;
221 iparams = idef->iparams;
223 for (ftype = 0; ftype < F_NRE; ftype++)
225 if (interaction_function[ftype].flags & IF_BOND)
227 ilist = &idef->il[ftype];
228 iatoms = ilist->iatoms;
233 while (i < ilist->nr)
235 /* Check if this interaction is perturbed */
236 if (ip_q_pert(ftype, iatoms+i, iparams, qA, qB))
238 /* Copy to the perturbed buffer */
239 if (ib + 1 + nral > iabuf_nalloc)
241 iabuf_nalloc = over_alloc_large(ib+1+nral);
242 srenew(iabuf, iabuf_nalloc);
244 for (a = 0; a < 1+nral; a++)
246 iabuf[ib++] = iatoms[i++];
252 for (a = 0; a < 1+nral; a++)
254 iatoms[ic++] = iatoms[i++];
258 /* Now we now the number of non-perturbed interactions */
259 ilist->nr_nonperturbed = ic;
261 /* Copy the buffer with perturbed interactions to the ilist */
262 for (a = 0; a < ib; a++)
264 iatoms[ic++] = iabuf[a];
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);
279 idef->ilsort = ilsortFE_SORTED;