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47 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
48 #include "gromacs/gmxpreprocess/grompp_impl.h"
49 #include "gromacs/gmxpreprocess/notset.h"
50 #include "gromacs/gmxpreprocess/topdirs.h"
51 #include "gromacs/topology/block.h"
52 #include "gromacs/topology/ifunc.h"
53 #include "gromacs/topology/symtab.h"
54 #include "gromacs/utility/fatalerror.h"
55 #include "gromacs/utility/gmxassert.h"
56 #include "gromacs/utility/smalloc.h"
60 void add_param_to_list(InteractionTypeParameters *list, const InteractionType &b)
62 list->interactionTypes.emplace_back(b);
65 /* PRINTING STRUCTURES */
67 static void print_bt(FILE *out, Directive d, PreprocessingAtomTypes *at,
68 int ftype, int fsubtype, gmx::ArrayRef<const InteractionTypeParameters> plist,
71 /* This dihp is a DIRTY patch because the dih-types do not use
72 * all four atoms to determine the type.
74 const int dihp[2][2] = { { 1, 2 }, { 0, 3 } };
76 bool bDih = false, bSwapParity;
78 const InteractionTypeParameters *bt = &(plist[ftype]);
106 case F_CROSS_BOND_ANGLES:
109 case F_CROSS_BOND_BONDS:
159 fprintf(out, "[ %s ]\n", dir2str(d));
163 fprintf (out, "%3s %4s", "ai", "aj");
164 for (int j = 2; (j < nral); j++)
166 fprintf (out, " %3c%c", 'a', 'i'+j);
171 for (int j = 0; (j < 2); j++)
173 fprintf (out, "%3c%c", 'a', 'i'+dihp[f][j]);
177 fprintf (out, " funct");
178 for (int j = 0; (j < nrfp); j++)
180 fprintf (out, " %12c%1d", 'c', j);
184 /* print bondtypes */
185 for (const auto &parm : bt->interactionTypes)
187 bSwapParity = (parm.c0() == NOTSET) && (parm.c1() == -1);
188 gmx::ArrayRef<const int> atoms = parm.atoms();
191 for (int j = 0; (j < nral); j++)
193 fprintf (out, "%5s ", at->atomNameFromAtomType(atoms[j]));
198 for (int j = 0; (j < 2); j++)
200 fprintf (out, "%5s ", at->atomNameFromAtomType(atoms[dihp[f][j]]));
203 fprintf (out, "%5d ", bSwapParity ? -f-1 : f+1);
205 if (!parm.interactionTypeName().empty())
207 fprintf(out, " %s", parm.interactionTypeName().c_str());
211 gmx::ArrayRef<const real> forceParam = parm.forceParam();
212 for (int j = 0; (j < nrfp) && (forceParam[j] != NOTSET); j++)
214 fprintf (out, "%13.6e ", forceParam[j]);
224 void print_blocka(FILE *out, const char *szName,
225 const char *szIndex, const char *szA,
230 fprintf (out, "; %s\n", szName);
231 fprintf (out, "; %4s %s\n", szIndex, szA);
232 for (i = 0; (i < block->nr); i++)
234 for (i = 0; (i < block->nr); i++)
236 fprintf (out, "%6d", i+1);
237 for (j = block->index[i]; (j < (block->index[i+1])); j++)
239 fprintf (out, "%5d", block->a[j]+1);
247 void print_excl(FILE *out, int natoms, t_excls excls[])
254 for (i = 0; i < natoms && !have_excl; i++)
256 have_excl = (excls[i].nr > 0);
261 fprintf (out, "[ %s ]\n", dir2str(Directive::d_exclusions));
262 fprintf (out, "; %4s %s\n", "i", "excluded from i");
263 for (i = 0; i < natoms; i++)
267 fprintf (out, "%6d ", i+1);
268 for (j = 0; j < excls[i].nr; j++)
270 fprintf (out, " %5d", excls[i].e[j]+1);
280 static double get_residue_charge(const t_atoms *atoms, int at)
285 ri = atoms->atom[at].resind;
287 while (at < atoms->nr && atoms->atom[at].resind == ri)
289 q += atoms->atom[at].q;
296 void print_atoms(FILE *out, PreprocessingAtomTypes *atype, t_atoms *at, int *cgnr,
302 const char *tpnmA, *tpnmB;
305 as = dir2str(Directive::d_atoms);
306 fprintf(out, "[ %s ]\n", as);
307 fprintf(out, "; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n",
308 "nr", "type", "resnr", "residue", "atom", "cgnr", "charge", "mass", "typeB", "chargeB", "massB");
314 /* if the information is present... */
315 for (i = 0; (i < at->nr); i++)
317 ri = at->atom[i].resind;
318 if ((i == 0 || ri != at->atom[i-1].resind) &&
319 at->resinfo[ri].rtp != nullptr)
321 qres = get_residue_charge(at, i);
322 fprintf(out, "; residue %3d %-3s rtp %-4s q ",
324 *at->resinfo[ri].name,
325 *at->resinfo[ri].rtp);
326 if (fabs(qres) < 0.001)
328 fprintf(out, " %s", "0.0");
332 fprintf(out, "%+3.1f", qres);
336 tpA = at->atom[i].type;
337 if ((tpnmA = atype->atomNameFromAtomType(tpA)) == nullptr)
339 gmx_fatal(FARGS, "tpA = %d, i= %d in print_atoms", tpA, i);
342 /* This is true by construction, but static analysers don't know */
343 GMX_ASSERT(!bRTPresname || at->resinfo[at->atom[i].resind].rtp, "-rtpres did not have residue name available");
344 fprintf(out, "%6d %10s %6d%c %5s %6s %6d %10g %10g",
349 *(at->resinfo[at->atom[i].resind].rtp) :
350 *(at->resinfo[at->atom[i].resind].name),
351 *(at->atomname[i]), cgnr[i],
352 at->atom[i].q, at->atom[i].m);
353 if (PERTURBED(at->atom[i]))
355 tpB = at->atom[i].typeB;
356 if ((tpnmB = atype->atomNameFromAtomType(tpB)) == nullptr)
358 gmx_fatal(FARGS, "tpB = %d, i= %d in print_atoms", tpB, i);
360 fprintf(out, " %6s %10g %10g",
361 tpnmB, at->atom[i].qB, at->atom[i].mB);
363 // Accumulate the total charge to help troubleshoot issues.
364 qtot += static_cast<double>(at->atom[i].q);
365 // Round it to zero if it is close to zero, because
366 // printing -9.34e-5 confuses users.
367 if (fabs(qtot) < 0.0001)
371 // Write the total charge for the last atom of the system
372 // and/or residue, because generally that's where it is
373 // expected to be an integer.
374 if (i == at->nr-1 || ri != at->atom[i+1].resind)
376 fprintf(out, " ; qtot %.4g\n", qtot);
388 void print_bondeds(FILE *out, int natoms, Directive d,
389 int ftype, int fsubtype, gmx::ArrayRef<const InteractionTypeParameters> plist)
394 PreprocessingAtomTypes atype;
397 for (int i = 0; (i < natoms); i++)
400 sprintf(buf, "%4d", (i+1));
401 atype.addType(&stab, *a, buf, InteractionType({}, {}), 0, 0);
403 print_bt(out, d, &atype, ftype, fsubtype, plist, TRUE);