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54 #include "mtop_util.h"
55 #include "chargegroup.h"
57 static real box_margin;
59 static real max_dist(rvec *x, real *r, int start, int end)
65 for (i = start; i < end; i++)
67 for (j = i+1; j < end; j++)
69 maxd = max(maxd, sqrt(distance2(x[i], x[j]))+0.5*(r[i]+r[j]));
76 static gmx_bool outside_box_minus_margin2(rvec x, matrix box)
78 return ( (x[XX] < 2*box_margin) || (x[XX] > box[XX][XX]-2*box_margin) ||
79 (x[YY] < 2*box_margin) || (x[YY] > box[YY][YY]-2*box_margin) ||
80 (x[ZZ] < 2*box_margin) || (x[ZZ] > box[ZZ][ZZ]-2*box_margin) );
83 static gmx_bool outside_box_plus_margin(rvec x, matrix box)
85 return ( (x[XX] < -box_margin) || (x[XX] > box[XX][XX]+box_margin) ||
86 (x[YY] < -box_margin) || (x[YY] > box[YY][YY]+box_margin) ||
87 (x[ZZ] < -box_margin) || (x[ZZ] > box[ZZ][ZZ]+box_margin) );
90 static int mark_res(int at, gmx_bool *mark, int natoms, t_atom *atom, int *nmark)
94 resind = atom[at].resind;
95 while ( (at > 0) && (resind == atom[at-1].resind) )
99 while ( (at < natoms) && (resind == atom[at].resind) )
112 static real find_max_real(int n, real radius[])
121 for (i = 1; (i < n); i++)
123 rmax = max(rmax, radius[i]);
129 static void combine_atoms(t_atoms *ap, t_atoms *as,
130 rvec xp[], rvec *vp, rvec xs[], rvec *vs,
131 t_atoms **a_comb, rvec **x_comb, rvec **v_comb)
134 rvec *xc, *vc = NULL;
135 int i, j, natot, res0;
137 /* Total number of atoms */
138 natot = ap->nr+as->nr;
141 init_t_atoms(ac, natot, FALSE);
149 /* Fill the new structures */
150 for (i = j = 0; (i < ap->nr); i++, j++)
152 copy_rvec(xp[i], xc[j]);
155 copy_rvec(vp[i], vc[j]);
157 memcpy(&(ac->atom[j]), &(ap->atom[i]), sizeof(ap->atom[i]));
158 ac->atom[j].type = 0;
161 for (i = 0; (i < as->nr); i++, j++)
163 copy_rvec(xs[i], xc[j]);
166 copy_rvec(vs[i], vc[j]);
168 memcpy(&(ac->atom[j]), &(as->atom[i]), sizeof(as->atom[i]));
169 ac->atom[j].type = 0;
170 ac->atom[j].resind += res0;
173 ac->nres = ac->atom[j-1].resind+1;
174 /* Fill all elements to prevent uninitialized memory */
175 for (i = 0; i < ac->nr; i++)
181 ac->atom[i].type = 0;
182 ac->atom[i].typeB = 0;
183 ac->atom[i].ptype = eptAtom;
192 static t_forcerec *fr = NULL;
194 static void do_nsgrid(FILE *fp, gmx_bool bVerbose,
195 matrix box, rvec x[], t_atoms *atoms, real rlong,
196 const output_env_t oenv)
215 /* Charge group index */
216 snew(cg_index, natoms);
217 for (i = 0; (i < natoms); i++)
222 /* Topology needs charge groups and exclusions */
225 mtop->natoms = natoms;
226 /* Make one moltype that contains the whol system */
228 snew(mtop->moltype, mtop->nmoltype);
229 molt = &mtop->moltype[0];
230 molt->name = mtop->name;
231 molt->atoms = *atoms;
232 stupid_fill_block(&molt->cgs, mtop->natoms, FALSE);
233 stupid_fill_blocka(&molt->excls, natoms);
234 /* Make one molblock for the whole system */
236 snew(mtop->molblock, mtop->nmolblock);
237 mtop->molblock[0].type = 0;
238 mtop->molblock[0].nmol = 1;
239 mtop->molblock[0].natoms_mol = natoms;
240 /* Initialize a single energy group */
241 mtop->groups.grps[egcENER].nr = 1;
242 mtop->groups.ngrpnr[egcENER] = 0;
243 mtop->groups.grpnr[egcENER] = NULL;
245 ffp = &mtop->ffparams;
250 snew(ffp->functype, 1);
251 snew(ffp->iparams, 1);
252 ffp->iparams[0].lj.c6 = 1;
253 ffp->iparams[0].lj.c12 = 1;
255 /* inputrec structure */
257 ir->cutoff_scheme = ecutsGROUP;
258 ir->coulomb_modifier = eintmodNONE;
259 ir->vdw_modifier = eintmodNONE;
260 ir->coulombtype = eelCUT;
261 ir->vdwtype = evdwCUT;
263 ir->ns_type = ensGRID;
264 snew(ir->opts.egp_flags, 1);
266 top = gmx_mtop_generate_local_top(mtop, ir);
268 /* Some nasty shortcuts */
271 /* mdatoms structure */
274 md = init_mdatoms(fp, mtop, FALSE);
275 atoms2md(mtop, ir, 0, NULL, mtop->natoms, md);
278 /* forcerec structure */
285 /* cr->nthreads = 1; */
287 /* ir->rlist = ir->rcoulomb = ir->rvdw = rlong;
288 printf("Neighborsearching with a cut-off of %g\n",rlong);
289 init_forcerec(stdout,fr,ir,top,cr,md,box,FALSE,NULL,NULL,NULL,TRUE);*/
291 fr->hcg = top->cgs.nr;
294 /* Prepare for neighboursearching */
297 /* Init things dependent on parameters */
298 ir->rlistlong = ir->rlist = ir->rcoulomb = ir->rvdw = rlong;
299 /* create free energy data to avoid NULLs */
300 snew(ir->fepvals, 1);
301 printf("Neighborsearching with a cut-off of %g\n", rlong);
302 init_forcerec(stdout, oenv, fr, NULL, ir, mtop, cr, box,
303 NULL, NULL, NULL, NULL, NULL, TRUE, -1);
306 pr_forcerec(debug, fr);
309 /* Calculate new stuff dependent on coords and box */
310 for (m = 0; (m < DIM); m++)
312 box_size[m] = box[m][m];
314 calc_shifts(box, fr->shift_vec);
315 put_charge_groups_in_box(fp, 0, cgs->nr, fr->ePBC, box, cgs, x, fr->cg_cm);
317 /* Do the actual neighboursearching */
318 snew(lambda, efptNR);
320 init_neighbor_list(fp, fr, md->homenr);
321 search_neighbours(fp, fr, box, top,
322 &mtop->groups, cr, &nrnb, md, TRUE, FALSE);
326 dump_nblist(debug, cr, fr, 0);
331 fprintf(stderr, "Successfully made neighbourlist\n");
335 static gmx_bool bXor(gmx_bool b1, gmx_bool b2)
337 return (b1 && !b2) || (b2 && !b1);
340 void add_conf(t_atoms *atoms, rvec **x, rvec **v, real **r, gmx_bool bSrenew,
341 int ePBC, matrix box, gmx_bool bInsert,
342 t_atoms *atoms_solvt, rvec *x_solvt, rvec *v_solvt, real *r_solvt,
343 gmx_bool bVerbose, real rshell, int max_sol, const output_env_t oenv)
347 real max_vdw, *r_prot, *r_all, n2, r2, ib1, ib2;
348 int natoms_prot, natoms_solvt;
349 int i, j, jj, m, j0, j1, jjj, jnres, jnr, inr, iprot, is1, is2;
350 int prev, resnr, nresadd, d, k, ncells, maxincell;
351 int dx0, dx1, dy0, dy1, dz0, dz1;
352 int ntest, nremove, nkeep;
353 rvec dx, xi, xj, xpp, *x_all, *v_all;
354 gmx_bool *remove, *keep;
357 natoms_prot = atoms->nr;
358 natoms_solvt = atoms_solvt->nr;
359 if (natoms_solvt <= 0)
361 fprintf(stderr, "WARNING: Nothing to add\n");
365 if (ePBC == epbcSCREW)
367 gmx_fatal(FARGS, "Sorry, %s pbc is not yet supported", epbc_names[ePBC]);
372 fprintf(stderr, "Calculating Overlap...\n");
375 /* Set margin around box edges to largest solvent dimension.
376 * The maximum distance between atoms in a solvent molecule should
377 * be calculated. At the moment a fudge factor of 3 is used.
380 box_margin = 3*find_max_real(natoms_solvt, r_solvt);
381 max_vdw = max(3*find_max_real(natoms_prot, r_prot), box_margin);
382 fprintf(stderr, "box_margin = %g\n", box_margin);
384 snew(remove, natoms_solvt);
389 for (i = 0; i < atoms_solvt->nr; i++)
391 if (outside_box_plus_margin(x_solvt[i], box) )
393 i = mark_res(i, remove, atoms_solvt->nr, atoms_solvt->atom, &nremove);
396 fprintf(stderr, "Removed %d atoms that were outside the box\n", nremove);
399 /* Define grid stuff */
400 /* Largest VDW radius */
401 snew(r_all, natoms_prot+natoms_solvt);
402 for (i = j = 0; i < natoms_prot; i++, j++)
404 r_all[j] = r_prot[i];
406 for (i = 0; i < natoms_solvt; i++, j++)
408 r_all[j] = r_solvt[i];
412 combine_atoms(atoms, atoms_solvt, *x, v ? *v : NULL, x_solvt, v_solvt,
413 &atoms_all, &x_all, &v_all);
415 /* Do neighboursearching step */
416 do_nsgrid(stdout, bVerbose, box, x_all, atoms_all, max_vdw, oenv);
418 /* check solvent with solute */
419 nlist = &(fr->nblists[0].nlist_sr[eNL_VDW]);
420 fprintf(stderr, "nri = %d, nrj = %d\n", nlist->nri, nlist->nrj);
421 for (bSolSol = 0; (bSolSol <= (bInsert ? 0 : 1)); bSolSol++)
424 fprintf(stderr, "Checking %s-Solvent overlap:",
425 bSolSol ? "Solvent" : "Protein");
426 for (i = 0; (i < nlist->nri && nremove < natoms_solvt); i++)
428 inr = nlist->iinr[i];
429 j0 = nlist->jindex[i];
430 j1 = nlist->jindex[i+1];
431 rvec_add(x_all[inr], fr->shift_vec[nlist->shift[i]], xi);
433 for (j = j0; (j < j1 && nremove < natoms_solvt); j++)
435 jnr = nlist->jjnr[j];
436 copy_rvec(x_all[jnr], xj);
438 /* Check solvent-protein and solvent-solvent */
439 is1 = inr-natoms_prot;
440 is2 = jnr-natoms_prot;
442 /* Check if at least one of the atoms is a solvent that is not yet
443 * listed for removal, and if both are solvent, that they are not in the
447 bXor((is1 >= 0), (is2 >= 0)) && /* One atom is protein */
448 ((is1 < 0) || ((is1 >= 0) && !remove[is1])) &&
449 ((is2 < 0) || ((is2 >= 0) && !remove[is2]))) ||
452 (is1 >= 0) && (!remove[is1]) && /* is1 is solvent */
453 (is2 >= 0) && (!remove[is2]) && /* is2 is solvent */
454 (bInsert || /* when inserting also check inside the box */
455 (outside_box_minus_margin2(x_solvt[is1], box) && /* is1 on edge */
456 outside_box_minus_margin2(x_solvt[is2], box)) /* is2 on edge */
458 (atoms_solvt->atom[is1].resind != /* Not the same residue */
459 atoms_solvt->atom[is2].resind)))
463 rvec_sub(xi, xj, dx);
465 r2 = sqr(r_all[inr]+r_all[jnr]);
470 nremove = natoms_solvt;
471 for (k = 0; k < nremove; k++)
476 /* Need only remove one of the solvents... */
479 (void) mark_res(is2, remove, natoms_solvt, atoms_solvt->atom,
484 (void) mark_res(is1, remove, natoms_solvt, atoms_solvt->atom,
489 fprintf(stderr, "Neither atom is solvent%d %d\n", is1, is2);
497 fprintf(stderr, " tested %d pairs, removed %d atoms.\n", ntest, nremove);
502 for (i = 0; i < natoms_solvt; i++)
504 fprintf(debug, "remove[%5d] = %s\n", i, bool_names[remove[i]]);
508 /* Search again, now with another cut-off */
511 do_nsgrid(stdout, bVerbose, box, x_all, atoms_all, rshell, oenv);
512 nlist = &(fr->nblists[0].nlist_sr[eNL_VDW]);
513 fprintf(stderr, "nri = %d, nrj = %d\n", nlist->nri, nlist->nrj);
515 snew(keep, natoms_solvt);
516 for (i = 0; i < nlist->nri; i++)
518 inr = nlist->iinr[i];
519 j0 = nlist->jindex[i];
520 j1 = nlist->jindex[i+1];
522 for (j = j0; j < j1; j++)
524 jnr = nlist->jjnr[j];
526 /* Check solvent-protein and solvent-solvent */
527 is1 = inr-natoms_prot;
528 is2 = jnr-natoms_prot;
530 /* Check if at least one of the atoms is a solvent that is not yet
531 * listed for removal, and if both are solvent, that they are not in the
534 if (is1 >= 0 && is2 < 0)
536 mark_res(is1, keep, natoms_solvt, atoms_solvt->atom, &nkeep);
538 else if (is1 < 0 && is2 >= 0)
540 mark_res(is2, keep, natoms_solvt, atoms_solvt->atom, &nkeep);
544 fprintf(stderr, "Keeping %d solvent atoms after proximity check\n",
546 for (i = 0; i < natoms_solvt; i++)
548 remove[i] = remove[i] || !keep[i];
552 /* count how many atoms and residues will be added and make space */
556 jnres = atoms_solvt->nres;
562 for (i = 0; ((i < atoms_solvt->nr) &&
563 ((max_sol == 0) || (jnres < max_sol))); i++)
569 (atoms_solvt->atom[i].resind != atoms_solvt->atom[i-1].resind))
578 fprintf(debug, "Will add %d atoms in %d residues\n", j, jnres);
582 /* Flag the remaing solvent atoms to be removed */
583 jjj = atoms_solvt->atom[i-1].resind;
584 for (; (i < atoms_solvt->nr); i++)
586 if (atoms_solvt->atom[i].resind > jjj)
599 srenew(atoms->resinfo, atoms->nres+jnres);
600 srenew(atoms->atomname, atoms->nr+j);
601 srenew(atoms->atom, atoms->nr+j);
602 srenew(*x, atoms->nr+j);
605 srenew(*v, atoms->nr+j);
607 srenew(*r, atoms->nr+j);
610 /* add the selected atoms_solvt to atoms */
613 resnr = atoms->resinfo[atoms->atom[atoms->nr-1].resind].nr;
621 for (i = 0; i < atoms_solvt->nr; i++)
626 atoms_solvt->atom[i].resind != atoms_solvt->atom[prev].resind)
631 atoms->resinfo[atoms->nres-1] =
632 atoms_solvt->resinfo[atoms_solvt->atom[i].resind];
633 atoms->resinfo[atoms->nres-1].nr = resnr;
634 /* calculate shift of the solvent molecule using the first atom */
635 copy_rvec(x_solvt[i], dx);
636 put_atoms_in_box(ePBC, box, 1, &dx);
637 rvec_dec(dx, x_solvt[i]);
639 atoms->atom[atoms->nr] = atoms_solvt->atom[i];
640 atoms->atomname[atoms->nr] = atoms_solvt->atomname[i];
641 rvec_add(x_solvt[i], dx, (*x)[atoms->nr]);
644 copy_rvec(v_solvt[i], (*v)[atoms->nr]);
646 (*r)[atoms->nr] = r_solvt[i];
647 atoms->atom[atoms->nr].resind = atoms->nres-1;
654 srenew(atoms->resinfo, atoms->nres+nresadd);
659 fprintf(stderr, "Added %d molecules\n", nresadd);
663 done_atom(atoms_all);