static int gmx_mtop_maxresnr(const gmx_mtop_t *mtop, int maxres_renum)
{
- int maxresnr, mt, r;
- const t_atoms *atoms;
+ int maxresnr = 0;
- maxresnr = 0;
-
- for (mt = 0; mt < mtop->nmoltype; mt++)
+ for (const gmx_moltype_t &moltype : mtop->moltype)
{
- atoms = &mtop->moltype[mt].atoms;
- if (atoms->nres > maxres_renum)
+ const t_atoms &atoms = moltype.atoms;
+ if (atoms.nres > maxres_renum)
{
- for (r = 0; r < atoms->nres; r++)
+ for (int r = 0; r < atoms.nres; r++)
{
- if (atoms->resinfo[r].nr > maxresnr)
+ if (atoms.resinfo[r].nr > maxresnr)
{
- maxresnr = atoms->resinfo[r].nr;
+ maxresnr = atoms.resinfo[r].nr;
}
}
}
int residueIndex = 0;
int residueNumberStart = mtop->maxresnr + 1;
int moleculeIndexStart = 0;
- for (int mb = 0; mb < mtop->nmolblock; mb++)
+ for (gmx_molblock_t &molb : mtop->molblock)
{
- gmx_molblock_t *molb = &mtop->molblock[mb];
- int numResPerMol = mtop->moltype[molb->type].atoms.nres;
- molb->globalAtomStart = atomIndex;
- molb->globalResidueStart = residueIndex;
- atomIndex += molb->nmol*molb->natoms_mol;
- residueIndex += molb->nmol*numResPerMol;
- molb->globalAtomEnd = atomIndex;
- molb->residueNumberStart = residueNumberStart;
+ const int numResPerMol = mtop->moltype[molb.type].atoms.nres;
+ molb.globalAtomStart = atomIndex;
+ molb.globalResidueStart = residueIndex;
+ atomIndex += molb.nmol*molb.natoms_mol;
+ residueIndex += molb.nmol*numResPerMol;
+ molb.globalAtomEnd = atomIndex;
+ molb.residueNumberStart = residueNumberStart;
if (numResPerMol <= mtop->maxres_renum)
{
- residueNumberStart += molb->nmol*numResPerMol;
+ residueNumberStart += molb.nmol*numResPerMol;
}
- molb->moleculeIndexStart = moleculeIndexStart;
- moleculeIndexStart += molb->nmol;
+ molb.moleculeIndexStart = moleculeIndexStart;
+ moleculeIndexStart += molb.nmol;
}
}
{
char *env;
- if (mtop->nmolblock == 1 && mtop->molblock[0].nmol == 1)
+ if (mtop->molblock.size() == 1 && mtop->molblock[0].nmol == 1)
{
/* We have a single molecule only, no renumbering needed.
* This case also covers an mtop converted from pdb/gro/... input,
void gmx_mtop_count_atomtypes(const gmx_mtop_t *mtop, int state, int typecount[])
{
- int i, mb, nmol, tpi;
- t_atoms *atoms;
-
- for (i = 0; i < mtop->ffparams.atnr; ++i)
+ for (int i = 0; i < mtop->ffparams.atnr; ++i)
{
typecount[i] = 0;
}
- for (mb = 0; mb < mtop->nmolblock; ++mb)
+ for (const gmx_molblock_t &molb : mtop->molblock)
{
- nmol = mtop->molblock[mb].nmol;
- atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
- for (i = 0; i < atoms->nr; ++i)
+ const t_atoms &atoms = mtop->moltype[molb.type].atoms;
+ for (int i = 0; i < atoms.nr; ++i)
{
+ int tpi;
if (state == 0)
{
- tpi = atoms->atom[i].type;
+ tpi = atoms.atom[i].type;
}
else
{
- tpi = atoms->atom[i].typeB;
+ tpi = atoms.atom[i].typeB;
}
- typecount[tpi] += nmol;
+ typecount[tpi] += molb.nmol;
}
}
}
int ncg_mtop(const gmx_mtop_t *mtop)
{
- int ncg;
- int mb;
-
- ncg = 0;
- for (mb = 0; mb < mtop->nmolblock; mb++)
+ int ncg = 0;
+ for (const gmx_molblock_t &molb : mtop->molblock)
{
- ncg +=
- mtop->molblock[mb].nmol*
- mtop->moltype[mtop->molblock[mb].type].cgs.nr;
+ ncg += molb.nmol*mtop->moltype[molb.type].cgs.nr;
}
return ncg;
int gmx_mtop_num_molecules(const gmx_mtop_t &mtop)
{
int numMolecules = 0;
- for (int mb = 0; mb < mtop.nmolblock; mb++)
+ for (const gmx_molblock_t &molb : mtop.molblock)
{
- numMolecules += mtop.molblock[mb].nmol;
+ numMolecules += molb.nmol;
}
return numMolecules;
}
int gmx_mtop_nres(const gmx_mtop_t *mtop)
{
int nres = 0;
- for (int mb = 0; mb < mtop->nmolblock; ++mb)
+ for (const gmx_molblock_t &molb : mtop->molblock)
{
- nres +=
- mtop->molblock[mb].nmol*
- mtop->moltype[mtop->molblock[mb].type].atoms.nres;
+ nres += molb.nmol*mtop->moltype[molb.type].atoms.nres;
}
return nres;
}
void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop)
{
- int mt;
- t_block *cgs;
- int i;
-
- for (mt = 0; mt < mtop->nmoltype; mt++)
+ for (gmx_moltype_t &molt : mtop->moltype)
{
- cgs = &mtop->moltype[mt].cgs;
- if (cgs->nr < mtop->moltype[mt].atoms.nr)
+ t_block &cgs = molt.cgs;
+ if (cgs.nr < molt.atoms.nr)
{
- cgs->nr = mtop->moltype[mt].atoms.nr;
- srenew(cgs->index, cgs->nr+1);
- for (i = 0; i < cgs->nr+1; i++)
+ cgs.nr = molt.atoms.nr;
+ srenew(cgs.index, cgs.nr + 1);
+ for (int i = 0; i < cgs.nr + 1; i++)
{
- cgs->index[i] = i;
+ cgs.index[i] = i;
}
}
}
typedef struct gmx_mtop_atomloop_all
{
const gmx_mtop_t *mtop;
- int mblock;
- t_atoms *atoms;
+ size_t mblock;
+ const t_atoms *atoms;
int mol;
int maxresnr;
int at_local;
if (aloop->mol >= aloop->mtop->molblock[aloop->mblock].nmol)
{
aloop->mblock++;
- if (aloop->mblock >= aloop->mtop->nmolblock)
+ if (aloop->mblock >= aloop->mtop->molblock.size())
{
gmx_mtop_atomloop_all_destroy(aloop);
return FALSE;
*resname = *(aloop->atoms->resinfo[resind_mol].name);
}
-void gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
- gmx_moltype_t **moltype, int *at_mol)
+void gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
+ const gmx_moltype_t **moltype,
+ int *at_mol)
{
*moltype = &aloop->mtop->moltype[aloop->mtop->molblock[aloop->mblock].type];
*at_mol = aloop->at_local;
typedef struct gmx_mtop_atomloop_block
{
const gmx_mtop_t *mtop;
- int mblock;
- t_atoms *atoms;
+ size_t mblock;
+ const t_atoms *atoms;
int at_local;
} t_gmx_mtop_atomloop_block;
if (aloop->at_local >= aloop->atoms->nr)
{
aloop->mblock++;
- if (aloop->mblock >= aloop->mtop->nmolblock)
+ if (aloop->mblock >= aloop->mtop->molblock.size())
{
gmx_mtop_atomloop_block_destroy(aloop);
return FALSE;
}
gmx_bool gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
- t_ilist **ilist_mol, int *nmol)
+ const t_ilist **ilist_mol, int *nmol)
{
if (iloop == nullptr)
{
}
iloop->mblock++;
- if (iloop->mblock >= iloop->mtop->nmolblock)
+ if (iloop->mblock >= static_cast<int>(iloop->mtop->molblock.size()))
{
- if (iloop->mblock == iloop->mtop->nmolblock &&
+ if (iloop->mblock == static_cast<int>(iloop->mtop->molblock.size()) &&
iloop->mtop->bIntermolecularInteractions)
{
*ilist_mol = iloop->mtop->intermolecular_ilist;
typedef struct gmx_mtop_ilistloop_all
{
const gmx_mtop_t *mtop;
- int mblock;
+ size_t mblock;
int mol;
int a_offset;
} t_gmx_mtop_ilist_all;
}
gmx_bool gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
- t_ilist **ilist_mol, int *atnr_offset)
+ const t_ilist **ilist_mol, int *atnr_offset)
{
if (iloop == nullptr)
* iloop->mblock == iloop->mtop->nmolblock, thus we should separately
* check for this value in this conditional.
*/
- if (iloop->mblock == iloop->mtop->nmolblock ||
+ if (iloop->mblock == iloop->mtop->molblock.size() ||
iloop->mol >= iloop->mtop->molblock[iloop->mblock].nmol)
{
iloop->mblock++;
iloop->mol = 0;
- if (iloop->mblock >= iloop->mtop->nmolblock)
+ if (iloop->mblock >= iloop->mtop->molblock.size())
{
- if (iloop->mblock == iloop->mtop->nmolblock &&
+ if (iloop->mblock == iloop->mtop->molblock.size() &&
iloop->mtop->bIntermolecularInteractions)
{
*ilist_mol = iloop->mtop->intermolecular_ilist;
int gmx_mtop_ftype_count(const gmx_mtop_t *mtop, int ftype)
{
gmx_mtop_ilistloop_t iloop;
- t_ilist *il;
+ const t_ilist *il;
int n, nmol;
n = 0;
t_block gmx_mtop_global_cgs(const gmx_mtop_t *mtop)
{
- t_block cgs_gl, *cgs_mol;
- int mb, mol, cg;
- gmx_molblock_t *molb;
-
+ t_block cgs_gl;
/* In most cases this is too much, but we realloc at the end */
snew(cgs_gl.index, mtop->natoms+1);
cgs_gl.nr = 0;
cgs_gl.index[0] = 0;
- for (mb = 0; mb < mtop->nmolblock; mb++)
+ for (const gmx_molblock_t &molb : mtop->molblock)
{
- molb = &mtop->molblock[mb];
- cgs_mol = &mtop->moltype[molb->type].cgs;
- for (mol = 0; mol < molb->nmol; mol++)
+ const t_block &cgs_mol = mtop->moltype[molb.type].cgs;
+ for (int mol = 0; mol < molb.nmol; mol++)
{
- for (cg = 0; cg < cgs_mol->nr; cg++)
+ for (int cg = 0; cg < cgs_mol.nr; cg++)
{
- cgs_gl.index[cgs_gl.nr+1] =
+ cgs_gl.index[cgs_gl.nr + 1] =
cgs_gl.index[cgs_gl.nr] +
- cgs_mol->index[cg+1] - cgs_mol->index[cg];
+ cgs_mol.index[cg + 1] - cgs_mol.index[cg];
cgs_gl.nr++;
}
}
return cgs_gl;
}
-static void atomcat(t_atoms *dest, t_atoms *src, int copies,
+static void atomcat(t_atoms *dest, const t_atoms *src, int copies,
int maxres_renum, int *maxresnr)
{
int i, j, l, size;
t_atoms gmx_mtop_global_atoms(const gmx_mtop_t *mtop)
{
t_atoms atoms;
- int maxresnr, mb;
- gmx_molblock_t *molb;
init_t_atoms(&atoms, 0, FALSE);
- maxresnr = mtop->maxresnr;
- for (mb = 0; mb < mtop->nmolblock; mb++)
+ int maxresnr = mtop->maxresnr;
+ for (const gmx_molblock_t &molb : mtop->molblock)
{
- molb = &mtop->molblock[mb];
- atomcat(&atoms, &mtop->moltype[molb->type].atoms, molb->nmol,
+ atomcat(&atoms, &mtop->moltype[molb.type].atoms, molb.nmol,
mtop->maxres_renum, &maxresnr);
}
* The cat routines below are old code from src/kernel/topcat.c
*/
-static void blockcat(t_block *dest, t_block *src, int copies)
+static void blockcat(t_block *dest, const t_block *src, int copies)
{
int i, j, l, nra, size;
{
dest->index[l++] = nra + src->index[i];
}
- nra += src->index[src->nr];
+ if (src->nr > 0)
+ {
+ nra += src->index[src->nr];
+ }
}
dest->nr += copies*src->nr;
dest->index[dest->nr] = nra;
}
-static void blockacat(t_blocka *dest, t_blocka *src, int copies,
+static void blockacat(t_blocka *dest, const t_blocka *src, int copies,
int dnum, int snum)
{
int i, j, l, size;
dest->index[dest->nr] = dest->nra;
}
-static void ilistcat(int ftype, t_ilist *dest, t_ilist *src, int copies,
+static void ilistcat(int ftype, t_ilist *dest, const t_ilist *src, int copies,
int dnum, int snum)
{
int nral, c, i, a;
}
}
-static void set_posres_params(t_idef *idef, gmx_molblock_t *molb,
+static void set_posres_params(t_idef *idef, const gmx_molblock_t *molb,
int i0, int a_offset)
{
t_ilist *il;
}
}
-static void set_fbposres_params(t_idef *idef, gmx_molblock_t *molb,
+static void set_fbposres_params(t_idef *idef, const gmx_molblock_t *molb,
int i0, int a_offset)
{
t_ilist *il;
bool bMergeConstr,
gmx_localtop_t *top)
{
- int mb, srcnr, destnr, ftype, natoms, mol, nposre_old, nfbposre_old;
- gmx_molblock_t *molb;
- gmx_moltype_t *molt;
+ int srcnr, destnr, ftype, natoms, nposre_old, nfbposre_old;
const gmx_ffparams_t *ffp;
t_idef *idef;
real *qA, *qB;
}
natoms = 0;
- for (mb = 0; mb < mtop->nmolblock; mb++)
+ for (const gmx_molblock_t &molb : mtop->molblock)
{
- molb = &mtop->molblock[mb];
- molt = &mtop->moltype[molb->type];
+ const gmx_moltype_t &molt = mtop->moltype[molb.type];
- srcnr = molt->atoms.nr;
+ srcnr = molt.atoms.nr;
destnr = natoms;
- blockcat(&top->cgs, &molt->cgs, molb->nmol);
+ blockcat(&top->cgs, &molt.cgs, molb.nmol);
- blockacat(&top->excls, &molt->excls, molb->nmol, destnr, srcnr);
+ blockacat(&top->excls, &molt.excls, molb.nmol, destnr, srcnr);
nposre_old = idef->il[F_POSRES].nr;
nfbposre_old = idef->il[F_FBPOSRES].nr;
for (ftype = 0; ftype < F_NRE; ftype++)
{
if (bMergeConstr &&
- ftype == F_CONSTR && molt->ilist[F_CONSTRNC].nr > 0)
+ ftype == F_CONSTR && molt.ilist[F_CONSTRNC].nr > 0)
{
/* Merge all constrains into one ilist.
* This simplifies the constraint code.
*/
- for (mol = 0; mol < molb->nmol; mol++)
+ for (int mol = 0; mol < molb.nmol; mol++)
{
- ilistcat(ftype, &idef->il[F_CONSTR], &molt->ilist[F_CONSTR],
- 1, destnr+mol*srcnr, srcnr);
- ilistcat(ftype, &idef->il[F_CONSTR], &molt->ilist[F_CONSTRNC],
- 1, destnr+mol*srcnr, srcnr);
+ ilistcat(ftype, &idef->il[F_CONSTR], &molt.ilist[F_CONSTR],
+ 1, destnr + mol*srcnr, srcnr);
+ ilistcat(ftype, &idef->il[F_CONSTR], &molt.ilist[F_CONSTRNC],
+ 1, destnr + mol*srcnr, srcnr);
}
}
else if (!(bMergeConstr && ftype == F_CONSTRNC))
{
- ilistcat(ftype, &idef->il[ftype], &molt->ilist[ftype],
- molb->nmol, destnr, srcnr);
+ ilistcat(ftype, &idef->il[ftype], &molt.ilist[ftype],
+ molb.nmol, destnr, srcnr);
}
}
if (idef->il[F_POSRES].nr > nposre_old)
{
/* Executing this line line stops gmxdump -sys working
* correctly. I'm not aware there's an elegant fix. */
- set_posres_params(idef, molb, nposre_old/2, natoms);
+ set_posres_params(idef, &molb, nposre_old/2, natoms);
}
if (idef->il[F_FBPOSRES].nr > nfbposre_old)
{
- set_fbposres_params(idef, molb, nfbposre_old/2, natoms);
+ set_fbposres_params(idef, &molb, nfbposre_old/2, natoms);
}
- natoms += molb->nmol*srcnr;
+ natoms += molb.nmol*srcnr;
}
if (mtop->bIntermolecularInteractions)
int globalAtomIndex = 0;
int globalMolIndex = 0;
index[globalMolIndex] = globalAtomIndex;
- for (int mb = 0; mb < mtop.nmolblock; mb++)
+ for (const gmx_molblock_t &molb : mtop.molblock)
{
- const gmx_molblock_t &molb = mtop.molblock[mb];
for (int mol = 0; mol < molb.nmol; mol++)
{
globalAtomIndex += molb.natoms_mol;
t_topology gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop, bool freeMTop)
{
- int mt, mb;
gmx_localtop_t ltop;
t_topology top;
if (freeMTop)
{
- // Free pointers that have not been copied to top.
- for (mt = 0; mt < mtop->nmoltype; mt++)
- {
- done_moltype(&mtop->moltype[mt]);
- }
- sfree(mtop->moltype);
-
- for (mb = 0; mb < mtop->nmolblock; mb++)
- {
- done_molblock(&mtop->molblock[mb]);
- }
- sfree(mtop->molblock);
-
- done_gmx_groups_t(&mtop->groups);
+ // Clear pointers and counts, such that the pointers copied to top
+ // keep pointing to valid data after destroying mtop.
+ mtop->symtab.symbuf = nullptr;
+ mtop->symtab.nr = 0;
}
return top;
mtop->name = name;
- mtop->nmoltype = 1;
- // This snew clears all entries, we should replace it by an initializer
- snew(mtop->moltype, mtop->nmoltype);
- mtop->moltype[0].atoms = *atoms;
- init_block(&mtop->moltype[0].cgs);
- init_blocka(&mtop->moltype[0].excls);
+ mtop->moltype.clear();
+ mtop->moltype.resize(1);
+ mtop->moltype.back().atoms = *atoms;
- mtop->nmolblock = 1;
- // This snew clears all entries, we should replace it by an initializer
- snew(mtop->molblock, mtop->nmolblock);
+ mtop->molblock.resize(1);
mtop->molblock[0].type = 0;
mtop->molblock[0].nmol = 1;
- mtop->molblock[0].natoms_mol = atoms->nr;
+ mtop->molblock[0].natoms_mol = mtop->moltype[mtop->molblock[0].type].atoms.nr;
mtop->bIntermolecularInteractions = FALSE;
- mtop->natoms = atoms->nr;
+ mtop->natoms = mtop->molblock[0].natoms_mol;
mtop->haveMoleculeIndices = false;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff