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42 #include "gromacs/commandline/filenm.h"
43 #include "gromacs/fileio/readinp.h"
44 #include "gromacs/fileio/warninp.h"
45 #include "gromacs/gmxlib/network.h"
46 #include "gromacs/math/vec.h"
47 #include "gromacs/mdtypes/commrec.h"
48 #include "gromacs/mdtypes/inputrec.h"
49 #include "gromacs/mdtypes/md_enums.h"
50 #include "gromacs/mdtypes/state.h"
51 #include "gromacs/pbcutil/pbc.h"
52 #include "gromacs/topology/index.h"
53 #include "gromacs/topology/mtop_lookup.h"
54 #include "gromacs/topology/mtop_util.h"
55 #include "gromacs/topology/topology.h"
56 #include "gromacs/utility/cstringutil.h"
57 #include "gromacs/utility/exceptions.h"
58 #include "gromacs/utility/fatalerror.h"
59 #include "gromacs/utility/filestream.h"
60 #include "gromacs/utility/futil.h"
61 #include "gromacs/utility/smalloc.h"
63 /* information about scaling center */
65 rvec xmin; /* smallest coordinates of all embedded molecules */
66 rvec xmax; /* largest coordinates of all embedded molecules */
67 rvec *geom_cent; /* scaling center of each independent molecule to embed */
68 int pieces; /* number of molecules to embed independently */
69 int *nidx; /* n atoms for every independent embedded molecule (index in subindex) */
70 int **subindex; /* atomids for independent molecule *
71 * atoms of piece i run from subindex[i][0] to subindex[i][nidx[i]] */
74 /* variables needed in do_md */
76 int it_xy; /* number of iterations (steps) used to grow something in the xy-plane */
77 int it_z; /* same, but for z */
78 real xy_step; /* stepsize used during resize in xy-plane */
79 real z_step; /* same, but in z */
80 rvec fac; /* initial scaling of the molecule to grow into the membrane */
81 rvec *r_ins; /* final coordinates of the molecule to grow */
82 pos_ins_t *pos_ins; /* scaling center for each piece to embed */
85 /* membrane related variables */
87 char *name; /* name of index group to embed molecule into (usually membrane) */
88 t_block mem_at; /* list all atoms in membrane */
89 int nmol; /* number of membrane molecules overlapping with the molecule to embed */
90 int *mol_id; /* list of molecules in membrane that overlap with the molecule to embed */
91 real lip_area; /* average area per lipid in membrane (only correct for homogeneous bilayers)*/
92 real zmin; /* minimum z coordinate of membrane */
93 real zmax; /* maximum z coordinate of membrane */
94 real zmed; /* median z coordinate of membrane */
97 /* Lists all molecules in the membrane that overlap with the molecule to be embedded. *
98 * These will then be removed from the system */
100 int nr; /* number of molecules to remove */
101 int *mol; /* list of molecule ids to remove */
102 int *block; /* id of the molblock that the molecule to remove is part of */
105 /* Get the global molecule id, and the corresponding molecule type and id of the *
106 * molblock from the global atom nr. */
107 static int get_mol_id(int at, gmx_mtop_t *mtop, int *type, int *block)
114 mtopGetMolblockIndex(mtop, at, block, &mol_id, &atnr_mol);
115 for (i = 0; i < *block; i++)
117 mol_id += mtop->molblock[i].nmol;
119 *type = mtop->molblock[*block].type;
124 /* Get the id of the molblock from a global molecule id */
125 static int get_molblock(int mol_id, const std::vector<gmx_molblock_t> &mblock)
129 for (size_t i = 0; i < mblock.size(); i++)
131 nmol += mblock[i].nmol;
138 gmx_fatal(FARGS, "mol_id %d larger than total number of molecules %d.\n", mol_id, nmol);
141 /* Get a list of all the molecule types that are present in a group of atoms. *
142 * Because all interaction within the group to embed are removed on the topology *
143 * level, if the same molecule type is found in another part of the system, these *
144 * would also be affected. Therefore we have to check if the embedded and rest group *
145 * share common molecule types. If so, membed will stop with an error. */
146 static int get_mtype_list(t_block *at, gmx_mtop_t *mtop, t_block *tlist)
149 int type = 0, block = 0;
153 snew(tlist->index, at->nr);
154 for (i = 0; i < at->nr; i++)
157 get_mol_id(at->index[i], mtop, &type, &block);
158 for (j = 0; j < nr; j++)
160 if (tlist->index[j] == type)
168 tlist->index[nr] = type;
172 srenew(tlist->index, nr);
176 /* Do the actual check of the molecule types between embedded and rest group */
177 static void check_types(t_block *ins_at, t_block *rest_at, gmx_mtop_t *mtop)
179 t_block *ins_mtype, *rest_mtype;
184 ins_mtype->nr = get_mtype_list(ins_at, mtop, ins_mtype );
185 rest_mtype->nr = get_mtype_list(rest_at, mtop, rest_mtype);
187 for (i = 0; i < ins_mtype->nr; i++)
189 for (j = 0; j < rest_mtype->nr; j++)
191 if (ins_mtype->index[i] == rest_mtype->index[j])
193 gmx_fatal(FARGS, "Moleculetype %s is found both in the group to insert and the rest of the system.\n"
194 "1. Your *.ndx and *.top do not match\n"
195 "2. You are inserting some molecules of type %s (for example xray-solvent), while\n"
196 "the same moleculetype is also used in the rest of the system (solvent box). Because\n"
197 "we need to exclude all interactions between the atoms in the group to\n"
198 "insert, the same moleculetype can not be used in both groups. Change the\n"
199 "moleculetype of the molecules %s in the inserted group. Do not forget to provide\n"
200 "an appropriate *.itp file", *(mtop->moltype[rest_mtype->index[j]].name),
201 *(mtop->moltype[rest_mtype->index[j]].name), *(mtop->moltype[rest_mtype->index[j]].name));
206 done_block(ins_mtype);
207 done_block(rest_mtype);
212 static void get_input(const char *membed_input, real *xy_fac, real *xy_max, real *z_fac, real *z_max,
213 int *it_xy, int *it_z, real *probe_rad, int *low_up_rm, int *maxwarn,
214 int *pieces, gmx_bool *bALLOW_ASYMMETRY)
217 std::vector <t_inpfile> inp;
219 wi = init_warning(TRUE, 0);
222 gmx::TextInputFile stream(membed_input);
223 inp = read_inpfile(&stream, membed_input, wi);
226 *it_xy = get_eint(&inp, "nxy", 1000, wi);
227 *it_z = get_eint(&inp, "nz", 0, wi);
228 *xy_fac = get_ereal(&inp, "xyinit", 0.5, wi);
229 *xy_max = get_ereal(&inp, "xyend", 1.0, wi);
230 *z_fac = get_ereal(&inp, "zinit", 1.0, wi);
231 *z_max = get_ereal(&inp, "zend", 1.0, wi);
232 *probe_rad = get_ereal(&inp, "rad", 0.22, wi);
233 *low_up_rm = get_eint(&inp, "ndiff", 0, wi);
234 *maxwarn = get_eint(&inp, "maxwarn", 0, wi);
235 *pieces = get_eint(&inp, "pieces", 1, wi);
236 const char *yesno_names[BOOL_NR+1] =
240 *bALLOW_ASYMMETRY = (get_eeenum(&inp, "asymmetry", yesno_names, wi) != 0);
242 check_warning_error(wi, FARGS);
244 gmx::TextOutputFile stream(membed_input);
245 write_inpfile(&stream, membed_input, &inp, FALSE, WriteMdpHeader::yes, wi);
248 done_warning(wi, FARGS);
251 /* Obtain the maximum and minimum coordinates of the group to be embedded */
252 static int init_ins_at(t_block *ins_at, t_block *rest_at, t_state *state, pos_ins_t *pos_ins,
253 gmx_groups_t *groups, int ins_grp_id, real xy_max)
256 real xmin, xmax, ymin, ymax, zmin, zmax;
257 const real min_memthick = 6.0; /* minimum thickness of the bilayer that will be used to *
258 * determine the overlap between molecule to embed and membrane */
259 const real fac_inp_size = 1.000001; /* scaling factor to obtain input_size + 0.000001 (comparing reals) */
260 snew(rest_at->index, state->natoms);
261 auto x = makeArrayRef(state->x);
263 xmin = xmax = x[ins_at->index[0]][XX];
264 ymin = ymax = x[ins_at->index[0]][YY];
265 zmin = zmax = x[ins_at->index[0]][ZZ];
267 for (i = 0; i < state->natoms; i++)
269 gid = groups->grpnr[egcFREEZE][i];
270 if (groups->grps[egcFREEZE].nm_ind[gid] == ins_grp_id)
272 xmin = std::min(xmin, x[i][XX]);
273 xmax = std::max(xmax, x[i][XX]);
274 ymin = std::min(ymin, x[i][YY]);
275 ymax = std::max(ymax, x[i][YY]);
276 zmin = std::min(zmin, x[i][ZZ]);
277 zmax = std::max(zmax, x[i][ZZ]);
281 rest_at->index[c] = i;
287 srenew(rest_at->index, c);
289 if (xy_max > fac_inp_size)
291 pos_ins->xmin[XX] = xmin-((xmax-xmin)*xy_max-(xmax-xmin))/2;
292 pos_ins->xmin[YY] = ymin-((ymax-ymin)*xy_max-(ymax-ymin))/2;
294 pos_ins->xmax[XX] = xmax+((xmax-xmin)*xy_max-(xmax-xmin))/2;
295 pos_ins->xmax[YY] = ymax+((ymax-ymin)*xy_max-(ymax-ymin))/2;
299 pos_ins->xmin[XX] = xmin;
300 pos_ins->xmin[YY] = ymin;
302 pos_ins->xmax[XX] = xmax;
303 pos_ins->xmax[YY] = ymax;
306 if ( (zmax-zmin) < min_memthick)
308 pos_ins->xmin[ZZ] = zmin+(zmax-zmin)/2.0-0.5*min_memthick;
309 pos_ins->xmax[ZZ] = zmin+(zmax-zmin)/2.0+0.5*min_memthick;
313 pos_ins->xmin[ZZ] = zmin;
314 pos_ins->xmax[ZZ] = zmax;
320 /* Estimate the area of the embedded molecule by projecting all coordinates on a grid in the *
321 * xy-plane and counting the number of occupied grid points */
322 static real est_prot_area(pos_ins_t *pos_ins, rvec *r, t_block *ins_at, mem_t *mem_p)
324 real x, y, dx = 0.15, dy = 0.15, area = 0.0;
325 real add, memmin, memmax;
328 /* min and max membrane coordinate are altered to reduce the influence of the *
330 memmin = mem_p->zmin+0.1*(mem_p->zmax-mem_p->zmin);
331 memmax = mem_p->zmax-0.1*(mem_p->zmax-mem_p->zmin);
333 //NOLINTNEXTLINE(clang-analyzer-security.FloatLoopCounter)
334 for (x = pos_ins->xmin[XX]; x < pos_ins->xmax[XX]; x += dx)
336 //NOLINTNEXTLINE(clang-analyzer-security.FloatLoopCounter)
337 for (y = pos_ins->xmin[YY]; y < pos_ins->xmax[YY]; y += dy)
343 at = ins_at->index[c];
344 if ( (r[at][XX] >= x) && (r[at][XX] < x+dx) &&
345 (r[at][YY] >= y) && (r[at][YY] < y+dy) &&
346 (r[at][ZZ] > memmin) && (r[at][ZZ] < memmax) )
352 while ( (c < ins_at->nr) && (add < 0.5) );
361 static int init_mem_at(mem_t *mem_p, gmx_mtop_t *mtop, rvec *r, matrix box, pos_ins_t *pos_ins)
363 int i, j, at, mol, nmol, nmolbox, count;
365 real z, zmin, zmax, mem_area;
368 int type = 0, block = 0;
371 mem_a = &(mem_p->mem_at);
372 snew(mol_id, mem_a->nr);
373 zmin = pos_ins->xmax[ZZ];
374 zmax = pos_ins->xmin[ZZ];
375 for (i = 0; i < mem_a->nr; i++)
377 at = mem_a->index[i];
378 if ( (r[at][XX] > pos_ins->xmin[XX]) && (r[at][XX] < pos_ins->xmax[XX]) &&
379 (r[at][YY] > pos_ins->xmin[YY]) && (r[at][YY] < pos_ins->xmax[YY]) &&
380 (r[at][ZZ] > pos_ins->xmin[ZZ]) && (r[at][ZZ] < pos_ins->xmax[ZZ]) )
382 mol = get_mol_id(at, mtop, &type, &block);
384 for (j = 0; j < nmol; j++)
386 if (mol == mol_id[j])
414 srenew(mol_id, nmol);
415 mem_p->mol_id = mol_id;
417 if ((zmax-zmin) > (box[ZZ][ZZ]-0.5))
419 gmx_fatal(FARGS, "Something is wrong with your membrane. Max and min z values are %f and %f.\n"
420 "Maybe your membrane is not centered in the box, but located at the box edge in the z-direction,\n"
421 "so that one membrane is distributed over two periodic box images. Another possibility is that\n"
422 "your water layer is not thick enough.\n", zmax, zmin);
426 mem_p->zmed = (zmax-zmin)/2+zmin;
428 /*number of membrane molecules in protein box*/
429 nmolbox = count/mtop->moltype[mtop->molblock[block].type].atoms.nr;
430 /*membrane area within the box defined by the min and max coordinates of the embedded molecule*/
431 mem_area = (pos_ins->xmax[XX]-pos_ins->xmin[XX])*(pos_ins->xmax[YY]-pos_ins->xmin[YY]);
432 /*rough estimate of area per lipid, assuming there is only one type of lipid in the membrane*/
433 mem_p->lip_area = 2.0*mem_area/static_cast<double>(nmolbox);
435 return mem_p->mem_at.nr;
438 static void init_resize(t_block *ins_at, rvec *r_ins, pos_ins_t *pos_ins, mem_t *mem_p, rvec *r,
439 gmx_bool bALLOW_ASYMMETRY)
441 int i, j, at, c, outsidesum, gctr = 0;
445 for (i = 0; i < pos_ins->pieces; i++)
447 idxsum += pos_ins->nidx[i];
450 if (idxsum != ins_at->nr)
452 gmx_fatal(FARGS, "Piecewise sum of inserted atoms not same as size of group selected to insert.");
455 snew(pos_ins->geom_cent, pos_ins->pieces);
456 for (i = 0; i < pos_ins->pieces; i++)
460 for (j = 0; j < DIM; j++)
462 pos_ins->geom_cent[i][j] = 0;
465 for (j = 0; j < pos_ins->nidx[i]; j++)
467 at = pos_ins->subindex[i][j];
468 copy_rvec(r[at], r_ins[gctr]);
469 if ( (r_ins[gctr][ZZ] < mem_p->zmax) && (r_ins[gctr][ZZ] > mem_p->zmin) )
471 rvec_inc(pos_ins->geom_cent[i], r_ins[gctr]);
483 svmul(1/static_cast<double>(c), pos_ins->geom_cent[i], pos_ins->geom_cent[i]);
486 if (!bALLOW_ASYMMETRY)
488 pos_ins->geom_cent[i][ZZ] = mem_p->zmed;
491 fprintf(stderr, "Embedding piece %d with center of geometry: %f %f %f\n",
492 i, pos_ins->geom_cent[i][XX], pos_ins->geom_cent[i][YY], pos_ins->geom_cent[i][ZZ]);
494 fprintf(stderr, "\n");
497 /* resize performed in the md loop */
498 static void resize(rvec *r_ins, rvec *r, pos_ins_t *pos_ins, const rvec fac)
500 int i, j, k, at, c = 0;
501 for (k = 0; k < pos_ins->pieces; k++)
503 for (i = 0; i < pos_ins->nidx[k]; i++)
505 at = pos_ins->subindex[k][i];
506 for (j = 0; j < DIM; j++)
508 r[at][j] = pos_ins->geom_cent[k][j]+fac[j]*(r_ins[c][j]-pos_ins->geom_cent[k][j]);
515 /* generate the list of membrane molecules that overlap with the molecule to be embedded. *
516 * The molecule to be embedded is already reduced in size. */
517 static int gen_rm_list(rm_t *rm_p, t_block *ins_at, t_block *rest_at, t_pbc *pbc, gmx_mtop_t *mtop,
518 rvec *r, mem_t *mem_p, pos_ins_t *pos_ins, real probe_rad,
519 int low_up_rm, gmx_bool bALLOW_ASYMMETRY)
521 int i, j, k, l, at, at2, mol_id;
522 int type = 0, block = 0;
523 int nrm, nupper, nlower;
524 real r_min_rad, z_lip, min_norm;
530 r_min_rad = probe_rad*probe_rad;
531 gmx::RangePartitioning molecules = gmx_mtop_molecules(*mtop);
532 snew(rm_p->block, molecules.numBlocks());
535 for (i = 0; i < ins_at->nr; i++)
537 at = ins_at->index[i];
538 for (j = 0; j < rest_at->nr; j++)
540 at2 = rest_at->index[j];
541 pbc_dx(pbc, r[at], r[at2], dr);
543 if (norm2(dr) < r_min_rad)
545 mol_id = get_mol_id(at2, mtop, &type, &block);
547 for (l = 0; l < nrm; l++)
549 if (rm_p->mol[l] == mol_id)
557 rm_p->mol[nrm] = mol_id;
558 rm_p->block[nrm] = block;
561 for (l = 0; l < mem_p->nmol; l++)
563 if (mol_id == mem_p->mol_id[l])
565 for (int k : molecules.block(mol_id))
569 z_lip /= molecules.block(mol_id).size();
570 if (z_lip < mem_p->zmed)
585 /*make sure equal number of lipids from upper and lower layer are removed */
586 if ( (nupper != nlower) && (!bALLOW_ASYMMETRY) )
588 snew(dist, mem_p->nmol);
589 snew(order, mem_p->nmol);
590 for (i = 0; i < mem_p->nmol; i++)
592 at = molecules.block(mem_p->mol_id[i]).begin();
593 pbc_dx(pbc, r[at], pos_ins->geom_cent[0], dr);
594 if (pos_ins->pieces > 1)
597 min_norm = norm2(dr);
598 for (k = 1; k < pos_ins->pieces; k++)
600 pbc_dx(pbc, r[at], pos_ins->geom_cent[k], dr_tmp);
601 if (norm2(dr_tmp) < min_norm)
603 min_norm = norm2(dr_tmp);
604 copy_rvec(dr_tmp, dr);
608 dist[i] = dr[XX]*dr[XX]+dr[YY]*dr[YY];
610 while (j >= 0 && dist[i] < dist[order[j]])
612 order[j+1] = order[j];
619 while (nupper != nlower)
621 mol_id = mem_p->mol_id[order[i]];
622 block = get_molblock(mol_id, mtop->molblock);
624 for (l = 0; l < nrm; l++)
626 if (rm_p->mol[l] == mol_id)
635 for (int k : molecules.block(mol_id))
639 z_lip /= molecules.block(mol_id).size();
640 if (nupper > nlower && z_lip < mem_p->zmed)
642 rm_p->mol[nrm] = mol_id;
643 rm_p->block[nrm] = block;
647 else if (nupper < nlower && z_lip > mem_p->zmed)
649 rm_p->mol[nrm] = mol_id;
650 rm_p->block[nrm] = block;
659 gmx_fatal(FARGS, "Trying to remove more lipid molecules than there are in the membrane");
667 srenew(rm_p->mol, nrm);
668 srenew(rm_p->block, nrm);
670 return nupper+nlower;
673 /*remove all lipids and waters overlapping and update all important structures (e.g. state and mtop)*/
674 static void rm_group(gmx_groups_t *groups, gmx_mtop_t *mtop, rm_t *rm_p, t_state *state,
675 t_block *ins_at, pos_ins_t *pos_ins)
677 int j, k, n, rm, mol_id, at, block;
680 unsigned char *new_egrp[egcNR];
684 /* Construct the molecule range information */
685 gmx::RangePartitioning molecules = gmx_mtop_molecules(*mtop);
687 snew(list, state->natoms);
689 for (int i = 0; i < rm_p->nr; i++)
691 mol_id = rm_p->mol[i];
692 at = molecules.block(mol_id).size();
693 block = rm_p->block[i];
694 mtop->molblock[block].nmol--;
695 for (j = 0; j < mtop->moltype[mtop->molblock[block].type].atoms.nr; j++)
703 state_change_natoms(state, state->natoms - n);
704 snew(x_tmp, state->natoms);
705 snew(v_tmp, state->natoms);
707 for (int i = 0; i < egcNR; i++)
709 if (groups->grpnr[i] != nullptr)
711 groups->ngrpnr[i] = state->natoms;
712 snew(new_egrp[i], state->natoms);
716 auto x = makeArrayRef(state->x);
717 auto v = makeArrayRef(state->v);
719 for (int i = 0; i < state->natoms+n; i++)
722 for (j = 0; j < n; j++)
733 for (j = 0; j < egcNR; j++)
735 if (groups->grpnr[j] != nullptr)
737 new_egrp[j][i-rm] = groups->grpnr[j][i];
740 copy_rvec(x[i], x_tmp[i-rm]);
741 copy_rvec(v[i], v_tmp[i-rm]);
742 for (j = 0; j < ins_at->nr; j++)
744 if (i == ins_at->index[j])
746 ins_at->index[j] = i-rm;
750 for (j = 0; j < pos_ins->pieces; j++)
752 for (k = 0; k < pos_ins->nidx[j]; k++)
754 if (i == pos_ins->subindex[j][k])
756 pos_ins->subindex[j][k] = i-rm;
762 for (int i = 0; i < state->natoms; i++)
764 copy_rvec(x_tmp[i], x[i]);
767 for (int i = 0; i < state->natoms; i++)
769 copy_rvec(v_tmp[i], v[i]);
773 for (int i = 0; i < egcNR; i++)
775 if (groups->grpnr[i] != nullptr)
777 sfree(groups->grpnr[i]);
778 groups->grpnr[i] = new_egrp[i];
782 /* remove empty molblocks */
784 for (size_t i = 0; i < mtop->molblock.size(); i++)
786 if (mtop->molblock[i].nmol == 0)
792 mtop->molblock[i-RMmolblock] = mtop->molblock[i];
795 mtop->molblock.resize(mtop->molblock.size() - RMmolblock);
798 /* remove al bonded interactions from mtop for the molecule to be embedded */
799 static int rm_bonded(t_block *ins_at, gmx_mtop_t *mtop)
802 int type, natom, nmol, at, atom1 = 0, rm_at = 0;
804 /*this routine lives dangerously by assuming that all molecules of a given type are in order in the structure*/
805 /*this routine does not live as dangerously as it seems. There is namely a check in init_membed to make *
806 * sure that g_membed exits with a warning when there are molecules of the same type not in the *
807 * ins_at index group. MGWolf 050710 */
810 snew(bRM, mtop->moltype.size());
811 for (size_t i = 0; i < mtop->moltype.size(); i++)
816 for (size_t i = 0; i < mtop->molblock.size(); i++)
818 /*loop over molecule blocks*/
819 type = mtop->molblock[i].type;
820 natom = mtop->moltype[type].atoms.nr;
821 nmol = mtop->molblock[i].nmol;
823 for (j = 0; j < natom*nmol && bRM[type]; j++)
825 /*loop over atoms in the block*/
826 at = j+atom1; /*atom index = block index + offset*/
829 for (m = 0; (m < ins_at->nr) && (!bINS); m++)
831 /*loop over atoms in insertion index group to determine if we're inserting one*/
832 if (at == ins_at->index[m])
839 atom1 += natom*nmol; /*update offset*/
842 rm_at += natom*nmol; /*increment bonded removal counter by # atoms in block*/
846 for (size_t i = 0; i < mtop->moltype.size(); i++)
850 for (j = 0; j < F_LJ; j++)
852 mtop->moltype[i].ilist[j].iatoms.clear();
855 for (j = F_POSRES; j <= F_VSITEN; j++)
857 mtop->moltype[i].ilist[j].iatoms.clear();
866 /* Write a topology where the number of molecules is correct for the system after embedding */
867 static void top_update(const char *topfile, rm_t *rm_p, gmx_mtop_t *mtop)
871 char buf[STRLEN], buf2[STRLEN], *temp;
872 int i, *nmol_rm, nmol, line;
873 char temporary_filename[STRLEN];
875 fpin = gmx_ffopen(topfile, "r");
876 strncpy(temporary_filename, "temp.topXXXXXX", STRLEN);
877 gmx_tmpnam(temporary_filename);
878 fpout = gmx_ffopen(temporary_filename, "w");
880 snew(nmol_rm, mtop->moltype.size());
881 for (i = 0; i < rm_p->nr; i++)
883 nmol_rm[rm_p->block[i]]++;
887 while (fgets(buf, STRLEN, fpin))
893 if ((temp = strchr(buf2, '\n')) != nullptr)
901 if ((temp = strchr(buf2, '\n')) != nullptr)
906 if (buf2[strlen(buf2)-1] == ']')
908 buf2[strlen(buf2)-1] = '\0';
911 if (gmx_strcasecmp(buf2, "molecules") == 0)
916 fprintf(fpout, "%s", buf);
918 else if (bMolecules == 1)
920 for (size_t i = 0; i < mtop->molblock.size(); i++)
922 nmol = mtop->molblock[i].nmol;
923 sprintf(buf, "%-15s %5d\n", *(mtop->moltype[mtop->molblock[i].type].name), nmol);
924 fprintf(fpout, "%s", buf);
928 else if (bMolecules == 2)
934 fprintf(fpout, "%s", buf);
939 fprintf(fpout, "%s", buf);
944 /* use gmx_ffopen to generate backup of topinout */
945 fpout = gmx_ffopen(topfile, "w");
947 rename(temporary_filename, topfile);
950 void rescale_membed(int step_rel, gmx_membed_t *membed, rvec *x)
952 /* Set new positions for the group to embed */
953 if (step_rel <= membed->it_xy)
955 membed->fac[0] += membed->xy_step;
956 membed->fac[1] += membed->xy_step;
958 else if (step_rel <= (membed->it_xy+membed->it_z))
960 membed->fac[2] += membed->z_step;
962 resize(membed->r_ins, x, membed->pos_ins, membed->fac);
965 /* We would like gn to be const as well, but C doesn't allow this */
966 /* TODO this is utility functionality (search for the index of a
967 string in a collection), so should be refactored and located more
968 centrally. Also, it nearly duplicates the same string in readir.c */
969 static int search_string(const char *s, int ng, char *gn[])
973 for (i = 0; (i < ng); i++)
975 if (gmx_strcasecmp(s, gn[i]) == 0)
982 "Group %s selected for embedding was not found in the index file.\n"
983 "Group names must match either [moleculetype] names or custom index group\n"
984 "names, in which case you must supply an index file to the '-n' option\n"
989 gmx_membed_t *init_membed(FILE *fplog, int nfile, const t_filenm fnm[], gmx_mtop_t *mtop,
990 t_inputrec *inputrec, t_state *state, t_commrec *cr, real *cpt)
993 int i, rm_bonded_at, fr_id, fr_i = 0, tmp_id, warn = 0;
994 int ng, j, max_lip_rm, ins_grp_id, ntype, lip_rm;
996 rvec *r_ins = nullptr;
997 t_block *ins_at, *rest_at;
1001 gmx_groups_t *groups;
1002 gmx_bool bExcl = FALSE;
1005 char **piecename = nullptr;
1006 gmx_membed_t *membed = nullptr;
1008 /* input variables */
1015 real probe_rad = 0.22;
1019 gmx_bool bALLOW_ASYMMETRY = FALSE;
1021 /* sanity check constants */ /* Issue a warning when: */
1022 const real min_probe_rad = 0.2199999; /* A probe radius for overlap between embedded molecule *
1023 * and rest smaller than this value is probably too small */
1024 const real min_xy_init = 0.0999999; /* the initial shrinking of the molecule to embed is smaller */
1025 const int min_it_xy = 1000; /* the number of steps to embed in xy-plane is smaller */
1026 const int min_it_z = 100; /* the number of steps to embed in z is smaller */
1027 const real prot_vs_box = 7.5; /* molecule to embed is large (more then prot_vs_box) with respect */
1028 const real box_vs_prot = 50; /* to the box size (less than box_vs_prot) */
1036 fprintf(fplog, "Note: it is expected that in future gmx mdrun -membed will not be the "
1037 "way to access this feature, perhaps changing to e.g. gmx membed.");
1038 /* get input data out membed file */
1041 get_input(opt2fn("-membed", nfile, fnm),
1042 &xy_fac, &xy_max, &z_fac, &z_max, &it_xy, &it_z, &probe_rad, &low_up_rm,
1043 &maxwarn, &pieces, &bALLOW_ASYMMETRY);
1045 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1047 if (!EI_DYNAMICS(inputrec->eI) )
1049 gmx_input("Change integrator to a dynamics integrator in mdp file (e.g. md or sd).");
1054 gmx_input("Sorry, parallel membed is not yet fully functional.");
1059 fprintf(stderr, "\nSetting -cpt to -1, because embedding cannot be restarted from cpt-files.\n");
1062 groups = &(mtop->groups);
1063 snew(gnames, groups->ngrpname);
1064 for (i = 0; i < groups->ngrpname; i++)
1066 gnames[i] = *(groups->grpname[i]);
1069 atoms = gmx_mtop_global_atoms(mtop);
1071 fprintf(stderr, "\nSelect a group to embed in the membrane:\n");
1072 get_index(&atoms, opt2fn_null("-mn", nfile, fnm), 1, &(ins_at->nr), &(ins_at->index), &ins);
1073 ins_grp_id = search_string(ins, groups->ngrpname, gnames);
1074 fprintf(stderr, "\nSelect a group to embed %s into (e.g. the membrane):\n", ins);
1075 get_index(&atoms, opt2fn_null("-mn", nfile, fnm), 1, &(mem_p->mem_at.nr), &(mem_p->mem_at.index), &(mem_p->name));
1077 pos_ins->pieces = pieces;
1078 snew(pos_ins->nidx, pieces);
1079 snew(pos_ins->subindex, pieces);
1080 snew(piecename, pieces);
1083 fprintf(stderr, "\nSelect pieces to embed:\n");
1084 get_index(&atoms, opt2fn_null("-mn", nfile, fnm), pieces, pos_ins->nidx, pos_ins->subindex, piecename);
1088 /*use whole embedded group*/
1089 snew(pos_ins->nidx, 1);
1090 snew(pos_ins->subindex, 1);
1091 pos_ins->nidx[0] = ins_at->nr;
1092 pos_ins->subindex[0] = ins_at->index;
1095 if (probe_rad < min_probe_rad)
1098 fprintf(stderr, "\nWarning %d:\nA probe radius (-rad) smaller than 0.2 nm can result "
1099 "in overlap between waters and the group to embed, which will result "
1100 "in Lincs errors etc.\n\n", warn);
1103 if (xy_fac < min_xy_init)
1106 fprintf(stderr, "\nWarning %d:\nThe initial size of %s is probably too small.\n\n", warn, ins);
1109 if (it_xy < min_it_xy)
1112 fprintf(stderr, "\nWarning %d;\nThe number of steps used to grow the xy-coordinates of %s (%d)"
1113 " is probably too small.\nIncrease -nxy or.\n\n", warn, ins, it_xy);
1116 if ( (it_z < min_it_z) && ( z_fac < 0.99999999 || z_fac > 1.0000001) )
1119 fprintf(stderr, "\nWarning %d;\nThe number of steps used to grow the z-coordinate of %s (%d)"
1120 " is probably too small.\nIncrease -nz or the maxwarn setting in the membed input file.\n\n", warn, ins, it_z);
1123 if (it_xy+it_z > inputrec->nsteps)
1126 fprintf(stderr, "\nWarning %d:\nThe number of growth steps (-nxy + -nz) is larger than the "
1127 "number of steps in the tpr.\n"
1128 "(increase maxwarn in the membed input file to override)\n\n", warn);
1132 if (inputrec->opts.ngfrz == 1)
1134 gmx_fatal(FARGS, "You did not specify \"%s\" as a freezegroup.", ins);
1137 for (i = 0; i < inputrec->opts.ngfrz; i++)
1139 tmp_id = mtop->groups.grps[egcFREEZE].nm_ind[i];
1140 if (ins_grp_id == tmp_id)
1149 gmx_fatal(FARGS, "\"%s\" not as freezegroup defined in the mdp-file.", ins);
1152 for (i = 0; i < DIM; i++)
1154 if (inputrec->opts.nFreeze[fr_i][i] != 1)
1156 gmx_fatal(FARGS, "freeze dimensions for %s are not Y Y Y\n", ins);
1160 ng = groups->grps[egcENER].nr;
1163 gmx_input("No energy groups defined. This is necessary for energy exclusion in the freeze group");
1166 for (i = 0; i < ng; i++)
1168 for (j = 0; j < ng; j++)
1170 if (inputrec->opts.egp_flags[ng*i+j] == EGP_EXCL)
1173 if ( (groups->grps[egcENER].nm_ind[i] != ins_grp_id) ||
1174 (groups->grps[egcENER].nm_ind[j] != ins_grp_id) )
1176 gmx_fatal(FARGS, "Energy exclusions \"%s\" and \"%s\" do not match the group "
1177 "to embed \"%s\"", *groups->grpname[groups->grps[egcENER].nm_ind[i]],
1178 *groups->grpname[groups->grps[egcENER].nm_ind[j]], ins);
1186 gmx_input("No energy exclusion groups defined. This is necessary for energy exclusion in "
1187 "the freeze group");
1190 /* Obtain the maximum and minimum coordinates of the group to be embedded */
1192 init_ins_at(ins_at, rest_at, state, pos_ins, groups, ins_grp_id, xy_max);
1193 /* Check that moleculetypes in insertion group are not part of the rest of the system */
1194 check_types(ins_at, rest_at, mtop);
1196 init_mem_at(mem_p, mtop, state->x.rvec_array(), state->box, pos_ins);
1198 prot_area = est_prot_area(pos_ins, state->x.rvec_array(), ins_at, mem_p);
1199 if ( (prot_area > prot_vs_box) && ( (state->box[XX][XX]*state->box[YY][YY]-state->box[XX][YY]*state->box[YY][XX]) < box_vs_prot) )
1202 fprintf(stderr, "\nWarning %d:\nThe xy-area is very small compared to the area of the protein.\n"
1203 "This might cause pressure problems during the growth phase. Just try with\n"
1204 "current setup and increase 'maxwarn' in your membed settings file, but lower the\n"
1205 "compressibility in the mdp-file or disable pressure coupling if problems occur.\n\n", warn);
1210 gmx_fatal(FARGS, "Too many warnings (override by setting maxwarn in the membed input file)\n");
1213 printf("The estimated area of the protein in the membrane is %.3f nm^2\n", prot_area);
1214 printf("\nThere are %d lipids in the membrane part that overlaps the protein.\n"
1215 "The area per lipid is %.4f nm^2.\n", mem_p->nmol, mem_p->lip_area);
1217 /* Maximum number of lipids to be removed*/
1218 max_lip_rm = static_cast<int>(2*prot_area/mem_p->lip_area);
1219 printf("Maximum number of lipids that will be removed is %d.\n", max_lip_rm);
1221 printf("\nWill resize the protein by a factor of %.3f in the xy plane and %.3f in the z direction.\n"
1222 "This resizing will be done with respect to the geometrical center of all protein atoms\n"
1223 "that span the membrane region, i.e. z between %.3f and %.3f\n\n",
1224 xy_fac, z_fac, mem_p->zmin, mem_p->zmax);
1226 /* resize the protein by xy and by z if necessary*/
1227 snew(r_ins, ins_at->nr);
1228 init_resize(ins_at, r_ins, pos_ins, mem_p, state->x.rvec_array(), bALLOW_ASYMMETRY);
1229 membed->fac[0] = membed->fac[1] = xy_fac;
1230 membed->fac[2] = z_fac;
1232 membed->xy_step = (xy_max-xy_fac)/static_cast<double>(it_xy);
1233 membed->z_step = (z_max-z_fac)/static_cast<double>(it_z-1);
1235 resize(r_ins, state->x.rvec_array(), pos_ins, membed->fac);
1237 /* remove overlapping lipids and water from the membrane box*/
1238 /*mark molecules to be removed*/
1240 set_pbc(pbc, inputrec->ePBC, state->box);
1243 lip_rm = gen_rm_list(rm_p, ins_at, rest_at, pbc, mtop, state->x.rvec_array(), mem_p, pos_ins,
1244 probe_rad, low_up_rm, bALLOW_ASYMMETRY);
1245 lip_rm -= low_up_rm;
1249 for (i = 0; i < rm_p->nr; i++)
1251 fprintf(fplog, "rm mol %d\n", rm_p->mol[i]);
1255 for (size_t i = 0; i < mtop->molblock.size(); i++)
1258 for (j = 0; j < rm_p->nr; j++)
1260 if (rm_p->block[j] == static_cast<int>(i))
1265 printf("Will remove %d %s molecules\n", ntype, *(mtop->moltype[mtop->molblock[i].type].name));
1268 if (lip_rm > max_lip_rm)
1271 fprintf(stderr, "\nWarning %d:\nTrying to remove a larger lipid area than the estimated "
1272 "protein area\nTry making the -xyinit resize factor smaller or increase "
1273 "maxwarn in the membed input file.\n\n", warn);
1276 /*remove all lipids and waters overlapping and update all important structures*/
1277 rm_group(groups, mtop, rm_p, state, ins_at, pos_ins);
1279 rm_bonded_at = rm_bonded(ins_at, mtop);
1280 if (rm_bonded_at != ins_at->nr)
1282 fprintf(stderr, "Warning: The number of atoms for which the bonded interactions are removed is %d, "
1283 "while %d atoms are embedded. Make sure that the atoms to be embedded are not in the same"
1284 "molecule type as atoms that are not to be embedded.\n", rm_bonded_at, ins_at->nr);
1289 gmx_fatal(FARGS, "Too many warnings.\nIf you are sure these warnings are harmless,\n"
1290 "you can increase the maxwarn setting in the membed input file.");
1293 // Re-establish the invariants of the derived values within
1295 gmx_mtop_finalize(mtop);
1297 if (ftp2bSet(efTOP, nfile, fnm))
1299 top_update(opt2fn("-mp", nfile, fnm), rm_p, mtop);
1309 membed->it_xy = it_xy;
1310 membed->it_z = it_z;
1311 membed->pos_ins = pos_ins;
1312 membed->r_ins = r_ins;
1318 void free_membed(gmx_membed_t *membed)