| 261 |
261 |
t_topology top;
|
| 262 |
262 |
gmx_bool *bKeep;
|
| 263 |
263 |
atom_id *invindex;
|
|
264 |
gmx_mtop_atomlookup_t alook;
|
| 264 |
265 |
int i;
|
|
266 |
int molb=-1, molnr=-1, atnr=-1;
|
|
267 |
int molnri=-1, atnri=-1;
|
|
268 |
int molbc, molnrc, atnrc;
|
|
269 |
int *mbnmol, *mbnatmol;
|
| 265 |
270 |
|
| 266 |
271 |
top = gmx_mtop_t_to_t_topology(mtop);
|
|
272 |
alook = gmx_mtop_atomlookup_init(mtop);
|
| 267 |
273 |
bKeep = bKeepIt(gnx, top.atoms.nr, index);
|
| 268 |
274 |
invindex = invind(gnx, top.atoms.nr, index);
|
| 269 |
275 |
|
| ... | ... | |
| 283 |
289 |
}
|
| 284 |
290 |
|
| 285 |
291 |
top.atoms.nr = gnx;
|
| 286 |
|
|
| 287 |
|
mtop->nmoltype = 1;
|
| 288 |
|
snew(mtop->moltype, mtop->nmoltype);
|
| 289 |
|
mtop->moltype[0].name = mtop->name;
|
| 290 |
|
mtop->moltype[0].atoms = top.atoms;
|
| 291 |
|
for (i = 0; i < F_NRE; i++)
|
|
292 |
fprintf(stderr, "check: mtop->nmolblock = %d\n", mtop->nmolblock);
|
|
293 |
snew(mbnmol, mtop->nmolblock);
|
|
294 |
snew(mbnatmol, mtop->nmolblock);
|
|
295 |
for(i=0;i<gnx;i++)
|
|
296 |
{
|
|
297 |
molbc = molb;
|
|
298 |
molnrc = molnr;
|
|
299 |
atnrc = atnr;
|
|
300 |
gmx_mtop_atomnr_to_molblock_ind(alook, index[i], &molb, &molnr, &atnr);
|
|
301 |
if (molb > molbc)
|
|
302 |
{
|
|
303 |
// block changed
|
|
304 |
molnrc = -1;
|
|
305 |
molnri = -1;
|
|
306 |
if (molnr > molnrc)
|
|
307 |
{
|
|
308 |
// mol changed
|
|
309 |
atnrc = -1;
|
|
310 |
atnri = -1;
|
|
311 |
molnri++;
|
|
312 |
molnrc = molnr;
|
|
313 |
mbnmol[molb] = molnri + 1;
|
|
314 |
if (atnr > atnrc)
|
|
315 |
{
|
|
316 |
// number of atoms changed
|
|
317 |
atnri++;
|
|
318 |
atnrc = atnr;
|
|
319 |
mbnatmol[molb] = atnri + 1;
|
|
320 |
}
|
|
321 |
} else {
|
|
322 |
// same mol
|
|
323 |
if (atnr > atnrc)
|
|
324 |
{
|
|
325 |
atnri++;
|
|
326 |
atnrc = atnr;
|
|
327 |
mbnatmol[molb] = atnri + 1;
|
|
328 |
}
|
|
329 |
}
|
|
330 |
} else {
|
|
331 |
// same block
|
|
332 |
if (molnr > molnrc)
|
|
333 |
{
|
|
334 |
// mol changed
|
|
335 |
atnrc = -1;
|
|
336 |
atnri = -1;
|
|
337 |
molnri++;
|
|
338 |
molnrc = molnr;
|
|
339 |
mbnmol[molb] = molnri + 1;
|
|
340 |
if (atnr > atnrc)
|
|
341 |
{
|
|
342 |
// number of atoms changed
|
|
343 |
atnri++;
|
|
344 |
atnrc = atnr;
|
|
345 |
mbnatmol[molb] = atnri + 1;
|
|
346 |
}
|
|
347 |
} else {
|
|
348 |
// same mol
|
|
349 |
if (atnr > atnrc)
|
|
350 |
{
|
|
351 |
atnri++;
|
|
352 |
atnrc = atnr;
|
|
353 |
mbnatmol[molb] = atnri + 1;
|
|
354 |
}
|
|
355 |
}
|
|
356 |
}
|
|
357 |
}
|
|
358 |
// correct number of mols in molblocks in new top
|
|
359 |
for(i=0; i<mtop->nmolblock;i++)
|
| 292 |
360 |
{
|
| 293 |
|
mtop->moltype[0].ilist[i] = top.idef.il[i];
|
|
361 |
fprintf(stderr, "nmol in block %d is %d with %d atoms\n", i, mbnmol[i], mbnatmol[i]);
|
|
362 |
mtop->molblock[i].nmol = mbnmol[i];
|
|
363 |
mtop->molblock[i].natoms_mol = mbnatmol[i];
|
| 294 |
364 |
}
|
| 295 |
|
mtop->moltype[0].atoms = top.atoms;
|
| 296 |
|
mtop->moltype[0].cgs = top.cgs;
|
| 297 |
|
mtop->moltype[0].excls = top.excls;
|
| 298 |
|
|
| 299 |
|
mtop->nmolblock = 1;
|
| 300 |
|
snew(mtop->molblock, mtop->nmolblock);
|
| 301 |
|
mtop->molblock[0].type = 0;
|
| 302 |
|
mtop->molblock[0].nmol = 1;
|
| 303 |
|
mtop->molblock[0].natoms_mol = top.atoms.nr;
|
| 304 |
|
mtop->molblock[0].nposres_xA = 0;
|
| 305 |
|
mtop->molblock[0].nposres_xB = 0;
|
|
365 |
fprintf(stderr, "check2: mtop->nmolblock = %d\n", mtop->nmolblock);
|
|
366 |
mtop->mols.nr = top.mols.nr;
|
|
367 |
|
|
368 |
// mtop->nmoltype = 1;
|
|
369 |
// snew(mtop->moltype, mtop->nmoltype);
|
|
370 |
// mtop->moltype[0].name = mtop->name;
|
|
371 |
// mtop->moltype[0].atoms = top.atoms;
|
|
372 |
// for (i = 0; i < F_NRE; i++)
|
|
373 |
// {
|
|
374 |
// mtop->moltype[0].ilist[i] = top.idef.il[i];
|
|
375 |
// }
|
|
376 |
// mtop->moltype[0].atoms = top.atoms;
|
|
377 |
// mtop->moltype[0].cgs = top.cgs;
|
|
378 |
// mtop->moltype[0].excls = top.excls;
|
| 306 |
379 |
|
| 307 |
380 |
mtop->natoms = top.atoms.nr;
|
|
381 |
gmx_mtop_atomlookup_destroy(alook);
|
| 308 |
382 |
}
|
| 309 |
383 |
|
| 310 |
384 |
static void zeroq(atom_id index[], gmx_mtop_t *mtop)
|