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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 SimulationGroups *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->groupNumbers[SimulationAtomGroupType::Freeze][i];
270 if (groups->groups[SimulationAtomGroupType::Freeze][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(SimulationGroups *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 gmx::EnumerationArray < SimulationAtomGroupType, std::vector < unsigned char>> new_egrp;
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 (auto group : keysOf(groups->groupNumbers))
709 if (!groups->groupNumbers[group].empty())
711 groups->groupNumbers[group].resize(state->natoms);
712 new_egrp[group].resize(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 (auto group : keysOf(groups->groupNumbers))
735 if (!groups->groupNumbers[group].empty())
737 new_egrp[group][i-rm] = groups->groupNumbers[group][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 (auto group : keysOf(groups->groupNumbers))
775 if (!groups->groupNumbers[group].empty())
777 groups->groupNumbers[group] = new_egrp[group];
781 /* remove empty molblocks */
783 for (size_t i = 0; i < mtop->molblock.size(); i++)
785 if (mtop->molblock[i].nmol == 0)
791 mtop->molblock[i-RMmolblock] = mtop->molblock[i];
794 mtop->molblock.resize(mtop->molblock.size() - RMmolblock);
797 /* remove al bonded interactions from mtop for the molecule to be embedded */
798 static int rm_bonded(t_block *ins_at, gmx_mtop_t *mtop)
801 int type, natom, nmol, at, atom1 = 0, rm_at = 0;
803 /*this routine lives dangerously by assuming that all molecules of a given type are in order in the structure*/
804 /*this routine does not live as dangerously as it seems. There is namely a check in init_membed to make *
805 * sure that g_membed exits with a warning when there are molecules of the same type not in the *
806 * ins_at index group. MGWolf 050710 */
809 snew(bRM, mtop->moltype.size());
810 for (size_t i = 0; i < mtop->moltype.size(); i++)
815 for (size_t i = 0; i < mtop->molblock.size(); i++)
817 /*loop over molecule blocks*/
818 type = mtop->molblock[i].type;
819 natom = mtop->moltype[type].atoms.nr;
820 nmol = mtop->molblock[i].nmol;
822 for (j = 0; j < natom*nmol && bRM[type]; j++)
824 /*loop over atoms in the block*/
825 at = j+atom1; /*atom index = block index + offset*/
828 for (m = 0; (m < ins_at->nr) && (!bINS); m++)
830 /*loop over atoms in insertion index group to determine if we're inserting one*/
831 if (at == ins_at->index[m])
838 atom1 += natom*nmol; /*update offset*/
841 rm_at += natom*nmol; /*increment bonded removal counter by # atoms in block*/
845 for (size_t i = 0; i < mtop->moltype.size(); i++)
849 for (j = 0; j < F_LJ; j++)
851 mtop->moltype[i].ilist[j].iatoms.clear();
854 for (j = F_POSRES; j <= F_VSITEN; j++)
856 mtop->moltype[i].ilist[j].iatoms.clear();
865 /* Write a topology where the number of molecules is correct for the system after embedding */
866 static void top_update(const char *topfile, rm_t *rm_p, gmx_mtop_t *mtop)
870 char buf[STRLEN], buf2[STRLEN], *temp;
871 int i, *nmol_rm, nmol, line;
872 char temporary_filename[STRLEN];
874 fpin = gmx_ffopen(topfile, "r");
875 strncpy(temporary_filename, "temp.topXXXXXX", STRLEN);
876 gmx_tmpnam(temporary_filename);
877 fpout = gmx_ffopen(temporary_filename, "w");
879 snew(nmol_rm, mtop->moltype.size());
880 for (i = 0; i < rm_p->nr; i++)
882 nmol_rm[rm_p->block[i]]++;
886 while (fgets(buf, STRLEN, fpin))
892 if ((temp = strchr(buf2, '\n')) != nullptr)
900 if ((temp = strchr(buf2, '\n')) != nullptr)
905 if (buf2[strlen(buf2)-1] == ']')
907 buf2[strlen(buf2)-1] = '\0';
910 if (gmx_strcasecmp(buf2, "molecules") == 0)
915 fprintf(fpout, "%s", buf);
917 else if (bMolecules == 1)
919 for (size_t i = 0; i < mtop->molblock.size(); i++)
921 nmol = mtop->molblock[i].nmol;
922 sprintf(buf, "%-15s %5d\n", *(mtop->moltype[mtop->molblock[i].type].name), nmol);
923 fprintf(fpout, "%s", buf);
927 else if (bMolecules == 2)
933 fprintf(fpout, "%s", buf);
938 fprintf(fpout, "%s", buf);
943 /* use gmx_ffopen to generate backup of topinout */
944 fpout = gmx_ffopen(topfile, "w");
946 rename(temporary_filename, topfile);
949 void rescale_membed(int step_rel, gmx_membed_t *membed, rvec *x)
951 /* Set new positions for the group to embed */
952 if (step_rel <= membed->it_xy)
954 membed->fac[0] += membed->xy_step;
955 membed->fac[1] += membed->xy_step;
957 else if (step_rel <= (membed->it_xy+membed->it_z))
959 membed->fac[2] += membed->z_step;
961 resize(membed->r_ins, x, membed->pos_ins, membed->fac);
964 gmx_membed_t *init_membed(FILE *fplog, int nfile, const t_filenm fnm[], gmx_mtop_t *mtop,
965 t_inputrec *inputrec, t_state *state, t_commrec *cr, real *cpt)
968 int i, rm_bonded_at, fr_id, fr_i = 0, tmp_id, warn = 0;
969 int ng, j, max_lip_rm, ins_grp_id, ntype, lip_rm;
971 rvec *r_ins = nullptr;
972 t_block *ins_at, *rest_at;
976 SimulationGroups *groups;
977 gmx_bool bExcl = FALSE;
980 char **piecename = nullptr;
981 gmx_membed_t *membed = nullptr;
983 /* input variables */
990 real probe_rad = 0.22;
994 gmx_bool bALLOW_ASYMMETRY = FALSE;
996 /* sanity check constants */ /* Issue a warning when: */
997 const real min_probe_rad = 0.2199999; /* A probe radius for overlap between embedded molecule *
998 * and rest smaller than this value is probably too small */
999 const real min_xy_init = 0.0999999; /* the initial shrinking of the molecule to embed is smaller */
1000 const int min_it_xy = 1000; /* the number of steps to embed in xy-plane is smaller */
1001 const int min_it_z = 100; /* the number of steps to embed in z is smaller */
1002 const real prot_vs_box = 7.5; /* molecule to embed is large (more then prot_vs_box) with respect */
1003 const real box_vs_prot = 50; /* to the box size (less than box_vs_prot) */
1011 fprintf(fplog, "Note: it is expected that in future gmx mdrun -membed will not be the "
1012 "way to access this feature, perhaps changing to e.g. gmx membed.");
1013 /* get input data out membed file */
1016 get_input(opt2fn("-membed", nfile, fnm),
1017 &xy_fac, &xy_max, &z_fac, &z_max, &it_xy, &it_z, &probe_rad, &low_up_rm,
1018 &maxwarn, &pieces, &bALLOW_ASYMMETRY);
1020 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1022 if (!EI_DYNAMICS(inputrec->eI) )
1024 gmx_input("Change integrator to a dynamics integrator in mdp file (e.g. md or sd).");
1029 gmx_input("Sorry, parallel membed is not yet fully functional.");
1034 fprintf(stderr, "\nSetting -cpt to -1, because embedding cannot be restarted from cpt-files.\n");
1037 groups = &(mtop->groups);
1038 std::vector<std::string> gnames;
1039 for (const auto &groupName : groups->groupNames)
1041 gnames.emplace_back(*groupName);
1044 atoms = gmx_mtop_global_atoms(mtop);
1046 fprintf(stderr, "\nSelect a group to embed in the membrane:\n");
1047 get_index(&atoms, opt2fn_null("-mn", nfile, fnm), 1, &(ins_at->nr), &(ins_at->index), &ins);
1049 auto found = std::find_if(gnames.begin(), gnames.end(),
1050 [&ins](const auto &name)
1051 { return gmx::equalCaseInsensitive(ins, name); });
1053 if (found == gnames.end())
1056 "Group %s selected for embedding was not found in the index file.\n"
1057 "Group names must match either [moleculetype] names or custom index group\n"
1058 "names, in which case you must supply an index file to the '-n' option\n"
1063 ins_grp_id = std::distance(gnames.begin(), found);
1065 fprintf(stderr, "\nSelect a group to embed %s into (e.g. the membrane):\n", ins);
1066 get_index(&atoms, opt2fn_null("-mn", nfile, fnm), 1, &(mem_p->mem_at.nr), &(mem_p->mem_at.index), &(mem_p->name));
1068 pos_ins->pieces = pieces;
1069 snew(pos_ins->nidx, pieces);
1070 snew(pos_ins->subindex, pieces);
1071 snew(piecename, pieces);
1074 fprintf(stderr, "\nSelect pieces to embed:\n");
1075 get_index(&atoms, opt2fn_null("-mn", nfile, fnm), pieces, pos_ins->nidx, pos_ins->subindex, piecename);
1079 /*use whole embedded group*/
1080 snew(pos_ins->nidx, 1);
1081 snew(pos_ins->subindex, 1);
1082 pos_ins->nidx[0] = ins_at->nr;
1083 pos_ins->subindex[0] = ins_at->index;
1086 if (probe_rad < min_probe_rad)
1089 fprintf(stderr, "\nWarning %d:\nA probe radius (-rad) smaller than 0.2 nm can result "
1090 "in overlap between waters and the group to embed, which will result "
1091 "in Lincs errors etc.\n\n", warn);
1094 if (xy_fac < min_xy_init)
1097 fprintf(stderr, "\nWarning %d:\nThe initial size of %s is probably too small.\n\n", warn, ins);
1100 if (it_xy < min_it_xy)
1103 fprintf(stderr, "\nWarning %d;\nThe number of steps used to grow the xy-coordinates of %s (%d)"
1104 " is probably too small.\nIncrease -nxy or.\n\n", warn, ins, it_xy);
1107 if ( (it_z < min_it_z) && ( z_fac < 0.99999999 || z_fac > 1.0000001) )
1110 fprintf(stderr, "\nWarning %d;\nThe number of steps used to grow the z-coordinate of %s (%d)"
1111 " is probably too small.\nIncrease -nz or the maxwarn setting in the membed input file.\n\n", warn, ins, it_z);
1114 if (it_xy+it_z > inputrec->nsteps)
1117 fprintf(stderr, "\nWarning %d:\nThe number of growth steps (-nxy + -nz) is larger than the "
1118 "number of steps in the tpr.\n"
1119 "(increase maxwarn in the membed input file to override)\n\n", warn);
1123 if (inputrec->opts.ngfrz == 1)
1125 gmx_fatal(FARGS, "You did not specify \"%s\" as a freezegroup.", ins);
1128 for (i = 0; i < inputrec->opts.ngfrz; i++)
1130 tmp_id = mtop->groups.groups[SimulationAtomGroupType::Freeze][i];
1131 if (ins_grp_id == tmp_id)
1140 gmx_fatal(FARGS, "\"%s\" not as freezegroup defined in the mdp-file.", ins);
1143 for (i = 0; i < DIM; i++)
1145 if (inputrec->opts.nFreeze[fr_i][i] != 1)
1147 gmx_fatal(FARGS, "freeze dimensions for %s are not Y Y Y\n", ins);
1151 ng = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
1154 gmx_input("No energy groups defined. This is necessary for energy exclusion in the freeze group");
1157 for (i = 0; i < ng; i++)
1159 for (j = 0; j < ng; j++)
1161 if (inputrec->opts.egp_flags[ng*i+j] == EGP_EXCL)
1164 if ( (groups->groups[SimulationAtomGroupType::EnergyOutput][i] != ins_grp_id) ||
1165 (groups->groups[SimulationAtomGroupType::EnergyOutput][j] != ins_grp_id) )
1167 gmx_fatal(FARGS, "Energy exclusions \"%s\" and \"%s\" do not match the group "
1168 "to embed \"%s\"", *groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][i]],
1169 *groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]], ins);
1177 gmx_input("No energy exclusion groups defined. This is necessary for energy exclusion in "
1178 "the freeze group");
1181 /* Obtain the maximum and minimum coordinates of the group to be embedded */
1183 init_ins_at(ins_at, rest_at, state, pos_ins, groups, ins_grp_id, xy_max);
1184 /* Check that moleculetypes in insertion group are not part of the rest of the system */
1185 check_types(ins_at, rest_at, mtop);
1187 init_mem_at(mem_p, mtop, state->x.rvec_array(), state->box, pos_ins);
1189 prot_area = est_prot_area(pos_ins, state->x.rvec_array(), ins_at, mem_p);
1190 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) )
1193 fprintf(stderr, "\nWarning %d:\nThe xy-area is very small compared to the area of the protein.\n"
1194 "This might cause pressure problems during the growth phase. Just try with\n"
1195 "current setup and increase 'maxwarn' in your membed settings file, but lower the\n"
1196 "compressibility in the mdp-file or disable pressure coupling if problems occur.\n\n", warn);
1201 gmx_fatal(FARGS, "Too many warnings (override by setting maxwarn in the membed input file)\n");
1204 printf("The estimated area of the protein in the membrane is %.3f nm^2\n", prot_area);
1205 printf("\nThere are %d lipids in the membrane part that overlaps the protein.\n"
1206 "The area per lipid is %.4f nm^2.\n", mem_p->nmol, mem_p->lip_area);
1208 /* Maximum number of lipids to be removed*/
1209 max_lip_rm = static_cast<int>(2*prot_area/mem_p->lip_area);
1210 printf("Maximum number of lipids that will be removed is %d.\n", max_lip_rm);
1212 printf("\nWill resize the protein by a factor of %.3f in the xy plane and %.3f in the z direction.\n"
1213 "This resizing will be done with respect to the geometrical center of all protein atoms\n"
1214 "that span the membrane region, i.e. z between %.3f and %.3f\n\n",
1215 xy_fac, z_fac, mem_p->zmin, mem_p->zmax);
1217 /* resize the protein by xy and by z if necessary*/
1218 snew(r_ins, ins_at->nr);
1219 init_resize(ins_at, r_ins, pos_ins, mem_p, state->x.rvec_array(), bALLOW_ASYMMETRY);
1220 membed->fac[0] = membed->fac[1] = xy_fac;
1221 membed->fac[2] = z_fac;
1223 membed->xy_step = (xy_max-xy_fac)/static_cast<double>(it_xy);
1224 membed->z_step = (z_max-z_fac)/static_cast<double>(it_z-1);
1226 resize(r_ins, state->x.rvec_array(), pos_ins, membed->fac);
1228 /* remove overlapping lipids and water from the membrane box*/
1229 /*mark molecules to be removed*/
1231 set_pbc(pbc, inputrec->ePBC, state->box);
1234 lip_rm = gen_rm_list(rm_p, ins_at, rest_at, pbc, mtop, state->x.rvec_array(), mem_p, pos_ins,
1235 probe_rad, low_up_rm, bALLOW_ASYMMETRY);
1236 lip_rm -= low_up_rm;
1240 for (i = 0; i < rm_p->nr; i++)
1242 fprintf(fplog, "rm mol %d\n", rm_p->mol[i]);
1246 for (size_t i = 0; i < mtop->molblock.size(); i++)
1249 for (j = 0; j < rm_p->nr; j++)
1251 if (rm_p->block[j] == static_cast<int>(i))
1256 printf("Will remove %d %s molecules\n", ntype, *(mtop->moltype[mtop->molblock[i].type].name));
1259 if (lip_rm > max_lip_rm)
1262 fprintf(stderr, "\nWarning %d:\nTrying to remove a larger lipid area than the estimated "
1263 "protein area\nTry making the -xyinit resize factor smaller or increase "
1264 "maxwarn in the membed input file.\n\n", warn);
1267 /*remove all lipids and waters overlapping and update all important structures*/
1268 rm_group(groups, mtop, rm_p, state, ins_at, pos_ins);
1270 rm_bonded_at = rm_bonded(ins_at, mtop);
1271 if (rm_bonded_at != ins_at->nr)
1273 fprintf(stderr, "Warning: The number of atoms for which the bonded interactions are removed is %d, "
1274 "while %d atoms are embedded. Make sure that the atoms to be embedded are not in the same"
1275 "molecule type as atoms that are not to be embedded.\n", rm_bonded_at, ins_at->nr);
1280 gmx_fatal(FARGS, "Too many warnings.\nIf you are sure these warnings are harmless,\n"
1281 "you can increase the maxwarn setting in the membed input file.");
1284 // Re-establish the invariants of the derived values within
1286 gmx_mtop_finalize(mtop);
1288 if (ftp2bSet(efTOP, nfile, fnm))
1290 top_update(opt2fn("-mp", nfile, fnm), rm_p, mtop);
1300 membed->it_xy = it_xy;
1301 membed->it_z = it_z;
1302 membed->pos_ins = pos_ins;
1303 membed->r_ins = r_ins;
1309 void free_membed(gmx_membed_t *membed)