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52 #include <unordered_set>
53 #include <sys/types.h>
55 #include "gromacs/fileio/gmxfio.h"
56 #include "gromacs/fileio/warninp.h"
57 #include "gromacs/gmxpreprocess/gmxcpp.h"
58 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
59 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
60 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
61 #include "gromacs/gmxpreprocess/grompp_impl.h"
62 #include "gromacs/gmxpreprocess/readir.h"
63 #include "gromacs/gmxpreprocess/topdirs.h"
64 #include "gromacs/gmxpreprocess/toppush.h"
65 #include "gromacs/gmxpreprocess/topshake.h"
66 #include "gromacs/gmxpreprocess/toputil.h"
67 #include "gromacs/gmxpreprocess/vsite_parm.h"
68 #include "gromacs/math/units.h"
69 #include "gromacs/math/utilities.h"
70 #include "gromacs/mdtypes/inputrec.h"
71 #include "gromacs/mdtypes/md_enums.h"
72 #include "gromacs/pbcutil/pbc.h"
73 #include "gromacs/topology/block.h"
74 #include "gromacs/topology/exclusionblocks.h"
75 #include "gromacs/topology/ifunc.h"
76 #include "gromacs/topology/symtab.h"
77 #include "gromacs/topology/topology.h"
78 #include "gromacs/utility/cstringutil.h"
79 #include "gromacs/utility/fatalerror.h"
80 #include "gromacs/utility/futil.h"
81 #include "gromacs/utility/gmxassert.h"
82 #include "gromacs/utility/pleasecite.h"
83 #include "gromacs/utility/smalloc.h"
85 #define OPENDIR '[' /* starting sign for directive */
86 #define CLOSEDIR ']' /* ending sign for directive */
88 static void gen_pairs(t_params *nbs, t_params *pairs, real fudge, int comb)
90 int i, j, ntp, nrfp, nrfpA, nrfpB, nnn;
93 nnn = static_cast<int>(std::sqrt(static_cast<double>(ntp)));
94 GMX_ASSERT(nnn * nnn == ntp, "Number of pairs of generated non-bonded parameters should be a perfect square");
96 nrfpA = interaction_function[F_LJ14].nrfpA;
97 nrfpB = interaction_function[F_LJ14].nrfpB;
100 if ((nrfp != nrfpA) || (nrfpA != nrfpB))
102 gmx_incons("Number of force parameters in gen_pairs wrong");
105 fprintf(stderr, "Generating 1-4 interactions: fudge = %g\n", fudge);
106 snew(pairs->param, pairs->nr);
107 for (i = 0; (i < ntp); i++)
110 pairs->param[i].a[0] = i / nnn;
111 pairs->param[i].a[1] = i % nnn;
112 /* Copy normal and FEP parameters and multiply by fudge factor */
116 for (j = 0; (j < nrfp); j++)
118 /* If we are using sigma/epsilon values, only the epsilon values
119 * should be scaled, but not sigma.
120 * The sigma values have even indices 0,2, etc.
122 if ((comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS) && (j%2 == 0))
131 pairs->param[i].c[j] = scaling*nbs->param[i].c[j];
132 /* NOTE: this should be clear to the compiler, but some gcc 5.2 versions
133 * issue false positive warnings for the pairs->param.c[] indexing below.
135 assert(2*nrfp <= MAXFORCEPARAM);
136 pairs->param[i].c[nrfp+j] = scaling*nbs->param[i].c[j];
141 double check_mol(const gmx_mtop_t *mtop, warninp *wi)
148 /* Check mass and charge */
151 for (const gmx_molblock_t &molb : mtop->molblock)
153 const t_atoms *atoms = &mtop->moltype[molb.type].atoms;
154 for (i = 0; (i < atoms->nr); i++)
156 q += molb.nmol*atoms->atom[i].q;
157 m = atoms->atom[i].m;
158 mB = atoms->atom[i].mB;
159 pt = atoms->atom[i].ptype;
160 /* If the particle is an atom or a nucleus it must have a mass,
161 * else, if it is a shell, a vsite or a bondshell it can have mass zero
163 if (((m <= 0.0) || (mB <= 0.0)) && ((pt == eptAtom) || (pt == eptNucleus)))
165 ri = atoms->atom[i].resind;
166 sprintf(buf, "atom %s (Res %s-%d) has mass %g (state A) / %g (state B)\n",
167 *(atoms->atomname[i]),
168 *(atoms->resinfo[ri].name),
169 atoms->resinfo[ri].nr,
171 warning_error(wi, buf);
174 if (((m != 0) || (mB != 0)) && (pt == eptVSite))
176 ri = atoms->atom[i].resind;
177 sprintf(buf, "virtual site %s (Res %s-%d) has non-zero mass %g (state A) / %g (state B)\n"
178 " Check your topology.\n",
179 *(atoms->atomname[i]),
180 *(atoms->resinfo[ri].name),
181 atoms->resinfo[ri].nr,
183 warning_error(wi, buf);
184 /* The following statements make LINCS break! */
185 /* atoms->atom[i].m=0; */
192 /*! \brief Returns the rounded charge of a molecule, when close to integer, otherwise returns the original charge.
194 * The results of this routine are only used for checking and for
195 * printing warning messages. Thus we can assume that charges of molecules
196 * should be integer. If the user wanted non-integer molecular charge,
197 * an undesired warning is printed and the user should use grompp -maxwarn 1.
199 * \param qMol The total, unrounded, charge of the molecule
200 * \param sumAbsQ The sum of absolute values of the charges, used for determining the tolerance for the rounding.
202 static double roundedMoleculeCharge(double qMol, double sumAbsQ)
204 /* We use a tolerance of 1e-6 for inaccuracies beyond the 6th decimal
205 * of the charges for ascii float truncation in the topology files.
206 * Although the summation here uses double precision, the charges
207 * are read and stored in single precision when real=float. This can
208 * lead to rounding errors of half the least significant bit.
209 * Note that, unfortunately, we can not assume addition of random
210 * rounding errors. It is not entirely unlikely that many charges
211 * have a near half-bit rounding error with the same sign.
213 double tolAbs = 1e-6;
214 double tol = std::max(tolAbs, 0.5*GMX_REAL_EPS*sumAbsQ);
215 double qRound = std::round(qMol);
216 if (std::abs(qMol - qRound) <= tol)
226 static void sum_q(const t_atoms *atoms, int numMols,
227 double *qTotA, double *qTotB)
234 for (int i = 0; i < atoms->nr; i++)
236 qmolA += atoms->atom[i].q;
237 qmolB += atoms->atom[i].qB;
238 sumAbsQA += std::abs(atoms->atom[i].q);
239 sumAbsQB += std::abs(atoms->atom[i].qB);
242 *qTotA += numMols*roundedMoleculeCharge(qmolA, sumAbsQA);
243 *qTotB += numMols*roundedMoleculeCharge(qmolB, sumAbsQB);
246 static void get_nbparm(char *nb_str, char *comb_str, int *nb, int *comb,
250 char warn_buf[STRLEN];
253 for (i = 1; (i < eNBF_NR); i++)
255 if (gmx_strcasecmp(nb_str, enbf_names[i]) == 0)
262 *nb = strtol(nb_str, nullptr, 10);
264 if ((*nb < 1) || (*nb >= eNBF_NR))
266 sprintf(warn_buf, "Invalid nonbond function selector '%s' using %s",
267 nb_str, enbf_names[1]);
268 warning_error(wi, warn_buf);
272 for (i = 1; (i < eCOMB_NR); i++)
274 if (gmx_strcasecmp(comb_str, ecomb_names[i]) == 0)
281 *comb = strtol(comb_str, nullptr, 10);
283 if ((*comb < 1) || (*comb >= eCOMB_NR))
285 sprintf(warn_buf, "Invalid combination rule selector '%s' using %s",
286 comb_str, ecomb_names[1]);
287 warning_error(wi, warn_buf);
292 static char ** cpp_opts(const char *define, const char *include,
297 const char *cppadds[2];
298 char **cppopts = nullptr;
299 const char *option[2] = { "-D", "-I" };
300 const char *nopt[2] = { "define", "include" };
304 char warn_buf[STRLEN];
307 cppadds[1] = include;
308 for (n = 0; (n < 2); n++)
315 while ((*ptr != '\0') && isspace(*ptr))
320 while ((*rptr != '\0') && !isspace(*rptr))
328 strncpy(buf, ptr, len);
329 if (strstr(ptr, option[n]) != ptr)
331 set_warning_line(wi, "mdp file", -1);
332 sprintf(warn_buf, "Malformed %s option %s", nopt[n], buf);
333 warning(wi, warn_buf);
337 srenew(cppopts, ++ncppopts);
338 cppopts[ncppopts-1] = gmx_strdup(buf);
346 srenew(cppopts, ++ncppopts);
347 cppopts[ncppopts-1] = nullptr;
353 static void make_atoms_sys(gmx::ArrayRef<const gmx_molblock_t> molblock,
354 gmx::ArrayRef<const MoleculeInformation> molinfo,
358 atoms->atom = nullptr;
360 for (const gmx_molblock_t &molb : molblock)
362 const t_atoms &mol_atoms = molinfo[molb.type].atoms;
364 srenew(atoms->atom, atoms->nr + molb.nmol*mol_atoms.nr);
366 for (int m = 0; m < molb.nmol; m++)
368 for (int a = 0; a < mol_atoms.nr; a++)
370 atoms->atom[atoms->nr++] = mol_atoms.atom[a];
377 static char **read_topol(const char *infile, const char *outfile,
378 const char *define, const char *include,
382 std::vector<MoleculeInformation> *molinfo,
383 std::unique_ptr<MoleculeInformation> *intermolecular_interactions,
385 int *combination_rule,
389 std::vector<gmx_molblock_t> *molblock,
390 bool *ffParametrizedWithHBondConstraints,
393 bool usingFullRangeElectrostatics,
398 char *pline = nullptr, **title = nullptr;
399 char line[STRLEN], errbuf[256], comb_str[256], nb_str[256];
401 char *dirstr, *dummy2;
402 int nrcopies, nmol, nscan, ncombs, ncopy;
403 double fLJ, fQQ, fPOW;
404 MoleculeInformation *mi0 = nullptr;
407 t_nbparam **nbparam, **pair;
408 real fudgeLJ = -1; /* Multiplication factor to generate 1-4 from LJ */
409 bool bReadDefaults, bReadMolType, bGenPairs, bWarn_copy_A_B;
410 double qt = 0, qBt = 0; /* total charge */
411 gpp_bond_atomtype *batype;
413 int dcatt = -1, nmol_couple;
414 /* File handling variables */
418 char *tmp_line = nullptr;
419 char warn_buf[STRLEN];
420 const char *floating_point_arithmetic_tip =
421 "Total charge should normally be an integer. See\n"
422 "http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n"
423 "for discussion on how close it should be to an integer.\n";
424 /* We need to open the output file before opening the input file,
425 * because cpp_open_file can change the current working directory.
429 out = gmx_fio_fopen(outfile, "w");
436 /* open input file */
437 auto cpp_opts_return = cpp_opts(define, include, wi);
438 status = cpp_open_file(infile, &handle, cpp_opts_return);
441 gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
444 /* some local variables */
445 DS_Init(&DS); /* directive stack */
446 nmol = 0; /* no molecules yet... */
447 d = Directive::d_invalid; /* first thing should be a directive */
448 nbparam = nullptr; /* The temporary non-bonded matrix */
449 pair = nullptr; /* The temporary pair interaction matrix */
450 std::vector < std::vector < gmx::ExclusionBlock>> exclusionBlocks;
453 *reppow = 12.0; /* Default value for repulsion power */
455 /* Init the number of CMAP torsion angles and grid spacing */
456 plist[F_CMAP].grid_spacing = 0;
457 plist[F_CMAP].nc = 0;
459 bWarn_copy_A_B = bFEP;
461 batype = init_bond_atomtype();
462 /* parse the actual file */
463 bReadDefaults = FALSE;
465 bReadMolType = FALSE;
470 status = cpp_read_line(&handle, STRLEN, line);
471 done = (status == eCPP_EOF);
474 if (status != eCPP_OK)
476 gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
480 fprintf(out, "%s\n", line);
483 set_warning_line(wi, cpp_cur_file(&handle), cpp_cur_linenr(&handle));
485 pline = gmx_strdup(line);
487 /* Strip trailing '\' from pline, if it exists */
489 if ((sl > 0) && (pline[sl-1] == CONTINUE))
494 /* build one long line from several fragments - necessary for CMAP */
495 while (continuing(line))
497 status = cpp_read_line(&handle, STRLEN, line);
498 set_warning_line(wi, cpp_cur_file(&handle), cpp_cur_linenr(&handle));
500 /* Since we depend on the '\' being present to continue to read, we copy line
501 * to a tmp string, strip the '\' from that string, and cat it to pline
503 tmp_line = gmx_strdup(line);
505 sl = strlen(tmp_line);
506 if ((sl > 0) && (tmp_line[sl-1] == CONTINUE))
508 tmp_line[sl-1] = ' ';
511 done = (status == eCPP_EOF);
514 if (status != eCPP_OK)
516 gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
520 fprintf(out, "%s\n", line);
524 srenew(pline, strlen(pline)+strlen(tmp_line)+1);
525 strcat(pline, tmp_line);
529 /* skip trailing and leading spaces and comment text */
530 strip_comment (pline);
533 /* if there is something left... */
534 if (static_cast<int>(strlen(pline)) > 0)
536 if (pline[0] == OPENDIR)
538 /* A directive on this line: copy the directive
539 * without the brackets into dirstr, then
540 * skip spaces and tabs on either side of directive
542 dirstr = gmx_strdup((pline+1));
543 if ((dummy2 = strchr (dirstr, CLOSEDIR)) != nullptr)
549 if ((newd = str2dir(dirstr)) == Directive::d_invalid)
551 sprintf(errbuf, "Invalid directive %s", dirstr);
552 warning_error(wi, errbuf);
556 /* Directive found */
557 if (DS_Check_Order (DS, newd))
564 /* we should print here which directives should have
565 been present, and which actually are */
566 gmx_fatal(FARGS, "%s\nInvalid order for directive %s",
567 cpp_error(&handle, eCPP_SYNTAX), dir2str(newd));
568 /* d = Directive::d_invalid; */
571 if (d == Directive::d_intermolecular_interactions)
573 if (*intermolecular_interactions == nullptr)
575 /* We (mis)use the moleculetype processing
576 * to process the intermolecular interactions
577 * by making a "molecule" of the size of the system.
579 *intermolecular_interactions = std::make_unique<MoleculeInformation>( );
580 mi0 = intermolecular_interactions->get();
582 make_atoms_sys(*molblock, *molinfo,
589 else if (d != Directive::d_invalid)
591 /* Not a directive, just a plain string
592 * use a gigantic switch to decode,
593 * if there is a valid directive!
597 case Directive::d_defaults:
600 gmx_fatal(FARGS, "%s\nFound a second defaults directive.\n",
601 cpp_error(&handle, eCPP_SYNTAX));
603 bReadDefaults = TRUE;
604 nscan = sscanf(pline, "%s%s%s%lf%lf%lf",
605 nb_str, comb_str, genpairs, &fLJ, &fQQ, &fPOW);
616 get_nbparm(nb_str, comb_str, &nb_funct, combination_rule, wi);
619 bGenPairs = (gmx_strncasecmp(genpairs, "Y", 1) == 0);
620 if (nb_funct != eNBF_LJ && bGenPairs)
622 gmx_fatal(FARGS, "Generating pair parameters is only supported with LJ non-bonded interactions");
638 nb_funct = ifunc_index(Directive::d_nonbond_params, nb_funct);
641 case Directive::d_atomtypes:
642 push_at(symtab, atype, batype, pline, nb_funct,
643 &nbparam, bGenPairs ? &pair : nullptr, wi);
646 case Directive::d_bondtypes:
647 push_bt(d, plist, 2, nullptr, batype, pline, wi);
649 case Directive::d_constrainttypes:
650 push_bt(d, plist, 2, nullptr, batype, pline, wi);
652 case Directive::d_pairtypes:
655 push_nbt(d, pair, atype, pline, F_LJ14, wi);
659 push_bt(d, plist, 2, atype, nullptr, pline, wi);
662 case Directive::d_angletypes:
663 push_bt(d, plist, 3, nullptr, batype, pline, wi);
665 case Directive::d_dihedraltypes:
666 /* Special routine that can read both 2 and 4 atom dihedral definitions. */
667 push_dihedraltype(d, plist, batype, pline, wi);
670 case Directive::d_nonbond_params:
671 push_nbt(d, nbparam, atype, pline, nb_funct, wi);
674 case Directive::d_implicit_genborn_params:
675 // Skip this line, so old topologies with
676 // GB parameters can be read.
679 case Directive::d_implicit_surface_params:
680 // Skip this line, so that any topologies
681 // with surface parameters can be read
682 // (even though these were never formally
686 case Directive::d_cmaptypes:
687 push_cmaptype(d, plist, 5, atype, batype, pline, wi);
690 case Directive::d_moleculetype:
695 if (opts->couple_moltype != nullptr &&
696 (opts->couple_lam0 == ecouplamNONE ||
697 opts->couple_lam0 == ecouplamQ ||
698 opts->couple_lam1 == ecouplamNONE ||
699 opts->couple_lam1 == ecouplamQ))
701 dcatt = add_atomtype_decoupled(symtab, atype,
702 &nbparam, bGenPairs ? &pair : nullptr);
704 ntype = get_atomtype_ntypes(atype);
705 ncombs = (ntype*(ntype+1))/2;
706 generate_nbparams(*combination_rule, nb_funct, &(plist[nb_funct]), atype, wi);
707 ncopy = copy_nbparams(nbparam, nb_funct, &(plist[nb_funct]),
709 fprintf(stderr, "Generated %d of the %d non-bonded parameter combinations\n", ncombs-ncopy, ncombs);
710 free_nbparam(nbparam, ntype);
713 gen_pairs(&(plist[nb_funct]), &(plist[F_LJ14]), fudgeLJ, *combination_rule);
714 ncopy = copy_nbparams(pair, nb_funct, &(plist[F_LJ14]),
716 fprintf(stderr, "Generated %d of the %d 1-4 parameter combinations\n", ncombs-ncopy, ncombs);
717 free_nbparam(pair, ntype);
719 /* Copy GBSA parameters to atomtype array? */
724 push_molt(symtab, molinfo, pline, wi);
725 nmol = molinfo->size();
726 exclusionBlocks.emplace_back();
727 mi0 = &molinfo->back();
728 mi0->atoms.haveMass = TRUE;
729 mi0->atoms.haveCharge = TRUE;
730 mi0->atoms.haveType = TRUE;
731 mi0->atoms.haveBState = TRUE;
732 mi0->atoms.havePdbInfo = FALSE;
735 case Directive::d_atoms:
736 push_atom(symtab, &(mi0->cgs), &(mi0->atoms), atype, pline, &lastcg, wi);
739 case Directive::d_pairs:
740 push_bond(d, plist, mi0->plist, &(mi0->atoms), atype, pline, FALSE,
741 bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
743 case Directive::d_pairs_nb:
744 push_bond(d, plist, mi0->plist, &(mi0->atoms), atype, pline, FALSE,
745 FALSE, 1.0, bZero, &bWarn_copy_A_B, wi);
748 case Directive::d_vsites2:
749 case Directive::d_vsites3:
750 case Directive::d_vsites4:
751 case Directive::d_bonds:
752 case Directive::d_angles:
753 case Directive::d_constraints:
754 case Directive::d_settles:
755 case Directive::d_position_restraints:
756 case Directive::d_angle_restraints:
757 case Directive::d_angle_restraints_z:
758 case Directive::d_distance_restraints:
759 case Directive::d_orientation_restraints:
760 case Directive::d_dihedral_restraints:
761 case Directive::d_dihedrals:
762 case Directive::d_polarization:
763 case Directive::d_water_polarization:
764 case Directive::d_thole_polarization:
765 push_bond(d, plist, mi0->plist, &(mi0->atoms), atype, pline, TRUE,
766 bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
768 case Directive::d_cmap:
769 push_cmap(d, plist, mi0->plist, &(mi0->atoms), atype, pline, wi);
772 case Directive::d_vsitesn:
773 push_vsitesn(d, mi0->plist, &(mi0->atoms), pline, wi);
775 case Directive::d_exclusions:
776 GMX_ASSERT(!exclusionBlocks.empty(), "exclusionBlocks must always be allocated so exclusions can be processed");
777 if (exclusionBlocks.back().empty())
779 GMX_RELEASE_ASSERT(mi0, "Need to have a valid MoleculeInformation object to work on");
780 exclusionBlocks.back().resize(mi0->atoms.nr);
782 push_excl(pline, exclusionBlocks.back(), wi);
784 case Directive::d_system:
786 title = put_symtab(symtab, pline);
788 case Directive::d_molecules:
793 push_mol(*molinfo, pline, &whichmol, &nrcopies, wi);
794 mi0 = &((*molinfo)[whichmol]);
795 molblock->resize(molblock->size() + 1);
796 molblock->back().type = whichmol;
797 molblock->back().nmol = nrcopies;
799 bCouple = (opts->couple_moltype != nullptr &&
800 (gmx_strcasecmp("system", opts->couple_moltype) == 0 ||
801 strcmp(*(mi0->name), opts->couple_moltype) == 0));
804 nmol_couple += nrcopies;
807 if (mi0->atoms.nr == 0)
809 gmx_fatal(FARGS, "Molecule type '%s' contains no atoms",
813 "Excluding %d bonded neighbours molecule type '%s'\n",
814 mi0->nrexcl, *mi0->name);
815 sum_q(&mi0->atoms, nrcopies, &qt, &qBt);
816 if (!mi0->bProcessed)
819 generate_excl(mi0->nrexcl,
824 gmx::mergeExclusions(&(mi0->excls), exclusionBlocks[whichmol]);
825 make_shake(mi0->plist, &mi0->atoms, opts->nshake);
831 convert_moltype_couple(mi0, dcatt, *fudgeQQ,
832 opts->couple_lam0, opts->couple_lam1,
834 nb_funct, &(plist[nb_funct]), wi);
836 stupid_fill_block(&mi0->mols, mi0->atoms.nr, TRUE);
837 mi0->bProcessed = TRUE;
842 fprintf (stderr, "case: %d\n", static_cast<int>(d));
843 gmx_incons("unknown directive");
853 // Check that all strings defined with -D were used when processing topology
854 std::string unusedDefineWarning = checkAndWarnForUnusedDefines(*handle);
855 if (!unusedDefineWarning.empty())
857 warning(wi, unusedDefineWarning);
860 sfree(cpp_opts_return);
867 /* List of GROMACS define names for force fields that have been
868 * parametrized using constraints involving hydrogens only.
870 * We should avoid hardcoded names, but this is hopefully only
871 * needed temparorily for discouraging use of constraints=all-bonds.
873 const std::array<std::string, 3> ffDefines = {
878 *ffParametrizedWithHBondConstraints = false;
879 for (const std::string &ffDefine : ffDefines)
881 if (cpp_find_define(&handle, ffDefine))
883 *ffParametrizedWithHBondConstraints = true;
889 if (opts->couple_moltype)
891 if (nmol_couple == 0)
893 gmx_fatal(FARGS, "Did not find any molecules of type '%s' for coupling",
894 opts->couple_moltype);
896 fprintf(stderr, "Coupling %d copies of molecule type '%s'\n",
897 nmol_couple, opts->couple_moltype);
900 /* this is not very clean, but fixes core dump on empty system name */
903 title = put_symtab(symtab, "");
908 sprintf(warn_buf, "System has non-zero total charge: %.6f\n%s\n", qt, floating_point_arithmetic_tip);
909 warning_note(wi, warn_buf);
911 if (fabs(qBt) > 1e-4 && !gmx_within_tol(qBt, qt, 1e-6))
913 sprintf(warn_buf, "State B has non-zero total charge: %.6f\n%s\n", qBt, floating_point_arithmetic_tip);
914 warning_note(wi, warn_buf);
916 if (usingFullRangeElectrostatics && (fabs(qt) > 1e-4 || fabs(qBt) > 1e-4))
918 warning(wi, "You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration.");
919 please_cite(stdout, "Hub2014a");
924 done_bond_atomtype(&batype);
926 if (*intermolecular_interactions != nullptr)
928 sfree(intermolecular_interactions->get()->atoms.atom);
936 char **do_top(bool bVerbose,
938 const char *topppfile,
943 int *combination_rule,
944 double *repulsion_power,
948 std::vector<MoleculeInformation> *molinfo,
949 std::unique_ptr<MoleculeInformation> *intermolecular_interactions,
950 const t_inputrec *ir,
951 std::vector<gmx_molblock_t> *molblock,
952 bool *ffParametrizedWithHBondConstraints,
955 /* Tmpfile might contain a long path */
970 printf("processing topology...\n");
972 title = read_topol(topfile, tmpfile, opts->define, opts->include,
974 nrmols, molinfo, intermolecular_interactions,
975 plist, combination_rule, repulsion_power,
976 opts, fudgeQQ, molblock,
977 ffParametrizedWithHBondConstraints,
978 ir->efep != efepNO, bZero,
979 EEL_FULL(ir->coulombtype), wi);
981 if ((*combination_rule != eCOMB_GEOMETRIC) &&
982 (ir->vdwtype == evdwUSER))
984 warning(wi, "Using sigma/epsilon based combination rules with"
985 " user supplied potential function may produce unwanted"
993 * Generate exclusion lists for QM/MM.
995 * This routine updates the exclusion lists for QM atoms in order to include all other QM
996 * atoms of this molecule. Moreover, this routine replaces bonds between QM atoms with
997 * CONNBOND and, when MiMiC is not used, removes bonded interactions between QM and link atoms.
998 * Finally, in case if MiMiC QM/MM is used - charges of QM atoms are set to 0
1000 * @param molt molecule type with QM atoms
1001 * @param grpnr group informatio
1002 * @param ir input record
1003 * @param qmmmMode QM/MM mode switch: original/MiMiC
1005 static void generate_qmexcl_moltype(gmx_moltype_t *molt, const unsigned char *grpnr,
1006 t_inputrec *ir, GmxQmmmMode qmmmMode)
1008 /* This routine expects molt->ilist to be of size F_NRE and ordered. */
1010 /* generates the exclusions between the individual QM atoms, as
1011 * these interactions should be handled by the QM subroutines and
1012 * not by the gromacs routines
1014 int qm_max = 0, qm_nr = 0, link_nr = 0, link_max = 0;
1015 int *qm_arr = nullptr, *link_arr = nullptr;
1016 bool *bQMMM, *blink;
1018 /* First we search and select the QM atoms in an qm_arr array that
1019 * we use to create the exclusions.
1021 * we take the possibility into account that a user has defined more
1022 * than one QM group:
1024 * for that we also need to do this an ugly work-about just in case
1025 * the QM group contains the entire system...
1028 /* we first search for all the QM atoms and put them in an array
1030 for (int j = 0; j < ir->opts.ngQM; j++)
1032 for (int i = 0; i < molt->atoms.nr; i++)
1034 if (qm_nr >= qm_max)
1037 srenew(qm_arr, qm_max);
1039 if ((grpnr ? grpnr[i] : 0) == j)
1041 qm_arr[qm_nr++] = i;
1042 molt->atoms.atom[i].q = 0.0;
1043 molt->atoms.atom[i].qB = 0.0;
1047 /* bQMMM[..] is an array containin TRUE/FALSE for atoms that are
1048 * QM/not QM. We first set all elements to false. Afterwards we use
1049 * the qm_arr to change the elements corresponding to the QM atoms
1052 snew(bQMMM, molt->atoms.nr);
1053 for (int i = 0; i < molt->atoms.nr; i++)
1057 for (int i = 0; i < qm_nr; i++)
1059 bQMMM[qm_arr[i]] = TRUE;
1062 /* We remove all bonded interactions (i.e. bonds,
1063 * angles, dihedrals, 1-4's), involving the QM atoms. The way they
1064 * are removed is as follows: if the interaction invloves 2 atoms,
1065 * it is removed if both atoms are QMatoms. If it involves 3 atoms,
1066 * it is removed if at least two of the atoms are QM atoms, if the
1067 * interaction involves 4 atoms, it is removed if there are at least
1068 * 2 QM atoms. Since this routine is called once before any forces
1069 * are computed, the top->idef.il[N].iatom[] array (see idef.h) can
1070 * be rewritten at this poitn without any problem. 25-9-2002 */
1072 /* first check whether we already have CONNBONDS.
1073 * Note that if we don't, we don't add a param entry and set ftype=0,
1074 * which is ok, since CONNBONDS does not use parameters.
1076 int ftype_connbond = 0;
1077 int ind_connbond = 0;
1078 if (molt->ilist[F_CONNBONDS].size() != 0)
1080 fprintf(stderr, "nr. of CONNBONDS present already: %d\n",
1081 molt->ilist[F_CONNBONDS].size()/3);
1082 ftype_connbond = molt->ilist[F_CONNBONDS].iatoms[0];
1083 ind_connbond = molt->ilist[F_CONNBONDS].size();
1085 /* now we delete all bonded interactions, except the ones describing
1086 * a chemical bond. These are converted to CONNBONDS
1088 for (int ftype = 0; ftype < F_NRE; ftype++)
1090 if (!(interaction_function[ftype].flags & IF_BOND) ||
1091 ftype == F_CONNBONDS)
1095 int nratoms = interaction_function[ftype].nratoms;
1097 while (j < molt->ilist[ftype].size())
1103 /* Remove an interaction between two atoms when both are
1104 * in the QM region. Note that we don't have to worry about
1105 * link atoms here, as they won't have 2-atom interactions.
1107 int a1 = molt->ilist[ftype].iatoms[1 + j + 0];
1108 int a2 = molt->ilist[ftype].iatoms[1 + j + 1];
1109 bexcl = (bQMMM[a1] && bQMMM[a2]);
1110 /* A chemical bond between two QM atoms will be copied to
1111 * the F_CONNBONDS list, for reasons mentioned above.
1113 if (bexcl && IS_CHEMBOND(ftype))
1115 InteractionList &ilist = molt->ilist[F_CONNBONDS];
1116 ilist.iatoms.resize(ind_connbond + 3);
1117 ilist.iatoms[ind_connbond++] = ftype_connbond;
1118 ilist.iatoms[ind_connbond++] = a1;
1119 ilist.iatoms[ind_connbond++] = a2;
1124 /* MM interactions have to be excluded if they are included
1125 * in the QM already. Because we use a link atom (H atom)
1126 * when the QM/MM boundary runs through a chemical bond, this
1127 * means that as long as one atom is MM, we still exclude,
1128 * as the interaction is included in the QM via:
1129 * QMatom1-QMatom2-QMatom-3-Linkatom.
1132 for (int jj = j + 1; jj < j + 1 + nratoms; jj++)
1134 if (bQMMM[molt->ilist[ftype].iatoms[jj]])
1140 /* MiMiC treats link atoms as quantum atoms - therefore
1141 * we do not need do additional exclusions here */
1142 if (qmmmMode == GmxQmmmMode::GMX_QMMM_MIMIC)
1144 bexcl = numQmAtoms == nratoms;
1148 bexcl = (numQmAtoms >= nratoms - 1);
1151 if (bexcl && ftype == F_SETTLE)
1153 gmx_fatal(FARGS, "Can not apply QM to molecules with SETTLE, replace the moleculetype using QM and SETTLE by one without SETTLE");
1158 /* since the interaction involves QM atoms, these should be
1159 * removed from the MM ilist
1161 InteractionList &ilist = molt->ilist[ftype];
1162 for (int k = j; k < ilist.size() - (nratoms + 1); k++)
1164 ilist.iatoms[k] = ilist.iatoms[k + (nratoms + 1)];
1166 ilist.iatoms.resize(ilist.size() - (nratoms + 1));
1170 j += nratoms+1; /* the +1 is for the functype */
1174 /* Now, we search for atoms bonded to a QM atom because we also want
1175 * to exclude their nonbonded interactions with the QM atoms. The
1176 * reason for this is that this interaction is accounted for in the
1177 * linkatoms interaction with the QMatoms and would be counted
1180 if (qmmmMode != GmxQmmmMode::GMX_QMMM_MIMIC)
1182 for (int i = 0; i < F_NRE; i++)
1187 while (j < molt->ilist[i].size())
1189 int a1 = molt->ilist[i].iatoms[j + 1];
1190 int a2 = molt->ilist[i].iatoms[j + 2];
1191 if ((bQMMM[a1] && !bQMMM[a2]) || (!bQMMM[a1] && bQMMM[a2]))
1193 if (link_nr >= link_max)
1196 srenew(link_arr, link_max);
1200 link_arr[link_nr++] = a2;
1204 link_arr[link_nr++] = a1;
1212 snew(blink, molt->atoms.nr);
1213 for (int i = 0; i < molt->atoms.nr; i++)
1218 if (qmmmMode != GmxQmmmMode::GMX_QMMM_MIMIC)
1220 for (int i = 0; i < link_nr; i++)
1222 blink[link_arr[i]] = TRUE;
1225 /* creating the exclusion block for the QM atoms. Each QM atom has
1226 * as excluded elements all the other QMatoms (and itself).
1229 qmexcl.nr = molt->atoms.nr;
1230 qmexcl.nra = qm_nr*(qm_nr+link_nr)+link_nr*qm_nr;
1231 snew(qmexcl.index, qmexcl.nr+1);
1232 snew(qmexcl.a, qmexcl.nra);
1234 for (int i = 0; i < qmexcl.nr; i++)
1236 qmexcl.index[i] = j;
1239 for (int k = 0; k < qm_nr; k++)
1241 qmexcl.a[k+j] = qm_arr[k];
1243 for (int k = 0; k < link_nr; k++)
1245 qmexcl.a[qm_nr+k+j] = link_arr[k];
1247 j += (qm_nr+link_nr);
1251 for (int k = 0; k < qm_nr; k++)
1253 qmexcl.a[k+j] = qm_arr[k];
1258 qmexcl.index[qmexcl.nr] = j;
1260 /* and merging with the exclusions already present in sys.
1263 std::vector<gmx::ExclusionBlock> qmexcl2(molt->atoms.nr);
1264 gmx::blockaToExclusionBlocks(&qmexcl, qmexcl2);
1265 gmx::mergeExclusions(&(molt->excls), qmexcl2);
1267 /* Finally, we also need to get rid of the pair interactions of the
1268 * classical atom bonded to the boundary QM atoms with the QMatoms,
1269 * as this interaction is already accounted for by the QM, so also
1270 * here we run the risk of double counting! We proceed in a similar
1271 * way as we did above for the other bonded interactions: */
1272 for (int i = F_LJ14; i < F_COUL14; i++)
1274 int nratoms = interaction_function[i].nratoms;
1276 while (j < molt->ilist[i].size())
1278 int a1 = molt->ilist[i].iatoms[j+1];
1279 int a2 = molt->ilist[i].iatoms[j+2];
1280 bool bexcl = ((bQMMM[a1] && bQMMM[a2]) ||
1281 (blink[a1] && bQMMM[a2]) ||
1282 (bQMMM[a1] && blink[a2]));
1285 /* since the interaction involves QM atoms, these should be
1286 * removed from the MM ilist
1288 InteractionList &ilist = molt->ilist[i];
1289 for (int k = j; k < ilist.size() - (nratoms + 1); k++)
1291 ilist.iatoms[k] = ilist.iatoms[k + (nratoms + 1)];
1293 ilist.iatoms.resize(ilist.size() - (nratoms + 1));
1297 j += nratoms+1; /* the +1 is for the functype */
1306 } /* generate_qmexcl */
1308 void generate_qmexcl(gmx_mtop_t *sys, t_inputrec *ir, warninp *wi, GmxQmmmMode qmmmMode)
1310 /* This routine expects molt->molt[m].ilist to be of size F_NRE and ordered.
1313 unsigned char *grpnr;
1314 int mol, nat_mol, nr_mol_with_qm_atoms = 0;
1315 gmx_molblock_t *molb;
1317 int index_offset = 0;
1320 grpnr = sys->groups.grpnr[egcQMMM];
1322 for (size_t mb = 0; mb < sys->molblock.size(); mb++)
1324 molb = &sys->molblock[mb];
1325 nat_mol = sys->moltype[molb->type].atoms.nr;
1326 for (mol = 0; mol < molb->nmol; mol++)
1329 for (int i = 0; i < nat_mol; i++)
1331 if ((grpnr ? grpnr[i] : 0) < (ir->opts.ngQM))
1340 nr_mol_with_qm_atoms++;
1343 /* We need to split this molblock */
1346 /* Split the molblock at this molecule */
1347 auto pos = sys->molblock.begin() + mb + 1;
1348 sys->molblock.insert(pos, sys->molblock[mb]);
1349 sys->molblock[mb ].nmol = mol;
1350 sys->molblock[mb+1].nmol -= mol;
1352 molb = &sys->molblock[mb];
1356 /* Split the molblock after this molecule */
1357 auto pos = sys->molblock.begin() + mb + 1;
1358 sys->molblock.insert(pos, sys->molblock[mb]);
1359 molb = &sys->molblock[mb];
1360 sys->molblock[mb ].nmol = 1;
1361 sys->molblock[mb+1].nmol -= 1;
1364 /* Create a copy of a moltype for a molecule
1365 * containing QM atoms and append it in the end of the list
1367 std::vector<gmx_moltype_t> temp(sys->moltype.size());
1368 for (size_t i = 0; i < sys->moltype.size(); ++i)
1370 copy_moltype(&sys->moltype[i], &temp[i]);
1372 sys->moltype.resize(sys->moltype.size() + 1);
1373 for (size_t i = 0; i < temp.size(); ++i)
1375 copy_moltype(&temp[i], &sys->moltype[i]);
1377 copy_moltype(&sys->moltype[molb->type], &sys->moltype.back());
1378 /* Copy the exclusions to a new array, since this is the only
1379 * thing that needs to be modified for QMMM.
1381 copy_blocka(&sys->moltype[molb->type].excls,
1382 &sys->moltype.back().excls);
1383 /* Set the molecule type for the QMMM molblock */
1384 molb->type = sys->moltype.size() - 1;
1386 generate_qmexcl_moltype(&sys->moltype[molb->type], grpnr, ir, qmmmMode);
1392 index_offset += nat_mol;
1395 if (qmmmMode == GmxQmmmMode::GMX_QMMM_ORIGINAL &&
1396 nr_mol_with_qm_atoms > 1)
1398 /* generate a warning is there are QM atoms in different
1399 * topologies. In this case it is not possible at this stage to
1400 * mutualy exclude the non-bonded interactions via the
1401 * exclusions (AFAIK). Instead, the user is advised to use the
1402 * energy group exclusions in the mdp file
1405 "\nThe QM subsystem is divided over multiple topologies. "
1406 "The mutual non-bonded interactions cannot be excluded. "
1407 "There are two ways to achieve this:\n\n"
1408 "1) merge the topologies, such that the atoms of the QM "
1409 "subsystem are all present in one single topology file. "
1410 "In this case this warning will dissappear\n\n"
1411 "2) exclude the non-bonded interactions explicitly via the "
1412 "energygrp-excl option in the mdp file. if this is the case "
1413 "this warning may be ignored"