const gmx_mtop_t *mtop,
const t_idef *idef)
{
- int mb, a_start, a_end;
- const gmx_molblock_t *molb;
- const gmx_reverse_top_t *rt;
-
- rt = cr->dd->reverse_top;
+ const gmx_reverse_top_t *rt = cr->dd->reverse_top;
/* Print the atoms in the missing interactions per molblock */
- a_end = 0;
- for (mb = 0; mb < mtop->nmolblock; mb++)
+ int a_end = 0;
+ for (const gmx_molblock_t &molb : mtop->molblock)
{
- molb = &mtop->molblock[mb];
- a_start = a_end;
- a_end = a_start + molb->nmol*molb->natoms_mol;
+ int a_start = a_end;
+ a_end = a_start + molb.nmol*molb.natoms_mol;
print_missing_interactions_mb(fplog, cr, rt,
- *(mtop->moltype[molb->type].name),
- &rt->ril_mt[molb->type],
- a_start, a_end, molb->natoms_mol,
- molb->nmol,
+ *(mtop->moltype[molb.type].name),
+ &rt->ril_mt[molb.type],
+ a_start, a_end, molb.natoms_mol,
+ molb.nmol,
idef);
}
}
gmx_bool bConstr, gmx_bool bSettle,
gmx_bool bBCheck, int *nint)
{
- int mt, i, mb;
gmx_reverse_top_t *rt;
int *nint_mt;
- gmx_moltype_t *molt;
int thread;
snew(rt, 1);
rt->bBCheck = bBCheck;
rt->bInterCGInteractions = mtop->bIntermolecularInteractions;
- snew(nint_mt, mtop->nmoltype);
- snew(rt->ril_mt, mtop->nmoltype);
+ snew(nint_mt, mtop->moltype.size());
+ snew(rt->ril_mt, mtop->moltype.size());
rt->ril_mt_tot_size = 0;
- for (mt = 0; mt < mtop->nmoltype; mt++)
+ for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
{
- molt = &mtop->moltype[mt];
- if (molt->cgs.nr > 1)
+ const gmx_moltype_t &molt = mtop->moltype[mt];
+ if (molt.cgs.nr > 1)
{
rt->bInterCGInteractions = TRUE;
}
/* Make the atom to interaction list for this molecule type */
nint_mt[mt] =
- make_reverse_ilist(molt->ilist, &molt->atoms,
+ make_reverse_ilist(molt.ilist, &molt.atoms,
vsite_pbc_molt ? vsite_pbc_molt[mt] : nullptr,
rt->bConstr, rt->bSettle, rt->bBCheck, FALSE,
&rt->ril_mt[mt]);
- rt->ril_mt_tot_size += rt->ril_mt[mt].index[molt->atoms.nr];
+ rt->ril_mt_tot_size += rt->ril_mt[mt].index[molt.atoms.nr];
}
if (debug)
{
}
*nint = 0;
- for (mb = 0; mb < mtop->nmolblock; mb++)
+ for (const gmx_molblock_t &molblock : mtop->molblock)
{
- *nint += mtop->molblock[mb].nmol*nint_mt[mtop->molblock[mb].type];
+ *nint += molblock.nmol*nint_mt[molblock.type];
}
sfree(nint_mt);
}
/* Make a molblock index for fast searching */
- snew(rt->mbi, mtop->nmolblock);
- rt->nmolblock = mtop->nmolblock;
- i = 0;
- for (mb = 0; mb < mtop->nmolblock; mb++)
+ snew(rt->mbi, mtop->molblock.size());
+ rt->nmolblock = mtop->molblock.size();
+ int i = 0;
+ for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
{
rt->mbi[mb].a_start = i;
i += mtop->molblock[mb].nmol*mtop->molblock[mb].natoms_mol;
rt->bExclRequired = (ir->cutoff_scheme == ecutsGROUP &&
inputrecExclForces(ir));
- int nexcl, mb;
-
- nexcl = 0;
+ int nexcl = 0;
dd->n_intercg_excl = 0;
rt->n_excl_at_max = 0;
- for (mb = 0; mb < mtop->nmolblock; mb++)
+ for (const gmx_molblock_t &molb : mtop->molblock)
{
- gmx_molblock_t *molb;
- gmx_moltype_t *molt;
- int n_excl_mol, n_excl_icg, n_excl_at_max;
+ int n_excl_mol, n_excl_icg, n_excl_at_max;
- molb = &mtop->molblock[mb];
- molt = &mtop->moltype[molb->type];
- count_excls(&molt->cgs, &molt->excls,
+ const gmx_moltype_t &molt = mtop->moltype[molb.type];
+ count_excls(&molt.cgs, &molt.excls,
&n_excl_mol, &n_excl_icg, &n_excl_at_max);
- nexcl += molb->nmol*n_excl_mol;
- dd->n_intercg_excl += molb->nmol*n_excl_icg;
+ nexcl += molb.nmol*n_excl_mol;
+ dd->n_intercg_excl += molb.nmol*n_excl_icg;
rt->n_excl_at_max = std::max(rt->n_excl_at_max, n_excl_at_max);
}
if (rt->bExclRequired)
*/
static int make_bondeds_zone(gmx_domdec_t *dd,
const gmx_domdec_zones_t *zones,
- const gmx_molblock_t *molb,
+ const std::vector<gmx_molblock_t> &molb,
gmx_bool bRCheckMB, ivec rcheck, gmx_bool bRCheck2B,
real rc2,
int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
* are supported.
*/
static int make_exclusions_zone_cg(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
- const gmx_moltype_t *moltype,
+ const std::vector<gmx_moltype_t> &moltype,
gmx_bool bRCheck, real rc2,
int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
const int *cginfo,
/*! \brief Set the exclusion data for i-zone \p iz */
static void make_exclusions_zone(gmx_domdec_t *dd,
gmx_domdec_zones_t *zones,
- const gmx_moltype_t *moltype,
+ const std::vector<gmx_moltype_t> &moltype,
const int *cginfo,
t_blocka *lexcls,
int iz,
}
}
-/*! \brief Allocate and return an array of the charge group index for all atoms */
-static int *make_at2cg(t_block *cgs)
+/*! \brief Return a vector of the charge group index for all atoms */
+static std::vector<int> make_at2cg(const t_block &cgs)
{
- int *at2cg, cg, a;
-
- snew(at2cg, cgs->index[cgs->nr]);
- for (cg = 0; cg < cgs->nr; cg++)
+ std::vector<int> at2cg(cgs.index[cgs.nr]);
+ for (int cg = 0; cg < cgs.nr; cg++)
{
- for (a = cgs->index[cg]; a < cgs->index[cg+1]; a++)
+ for (int a = cgs.index[cg]; a < cgs.index[cg + 1]; a++)
{
at2cg[a] = cg;
}
cginfo_mb_t *cginfo_mb)
{
gmx_bool bExclRequired;
- int mb, cg_offset, cg, cg_gl, a, aj, i, j, ftype, nral, nlink_mol, mol, ncgi;
- gmx_molblock_t *molb;
- gmx_moltype_t *molt;
- t_block *cgs;
- t_blocka *excls;
- int *a2c;
reverse_ilist_t ril, ril_intermol;
t_blocka *link;
cginfo_mb_t *cgi_mb;
link->a = nullptr;
link->index[0] = 0;
- cg_offset = 0;
- ncgi = 0;
- for (mb = 0; mb < mtop->nmolblock; mb++)
+ int cg_offset = 0;
+ int ncgi = 0;
+ for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
{
- molb = &mtop->molblock[mb];
- if (molb->nmol == 0)
+ const gmx_molblock_t &molb = mtop->molblock[mb];
+ if (molb.nmol == 0)
{
continue;
}
- molt = &mtop->moltype[molb->type];
- cgs = &molt->cgs;
- excls = &molt->excls;
- a2c = make_at2cg(cgs);
+ const gmx_moltype_t &molt = mtop->moltype[molb.type];
+ const t_block &cgs = molt.cgs;
+ const t_blocka &excls = molt.excls;
+ std::vector<int> a2c = make_at2cg(cgs);
/* Make a reverse ilist in which the interactions are linked
* to all atoms, not only the first atom as in gmx_reverse_top.
* The constraints are discarded here.
*/
- make_reverse_ilist(molt->ilist, &molt->atoms,
+ make_reverse_ilist(molt.ilist, &molt.atoms,
nullptr, FALSE, FALSE, FALSE, TRUE, &ril);
cgi_mb = &cginfo_mb[mb];
- for (mol = 0; mol < (mtop->bIntermolecularInteractions ? molb->nmol : 1); mol++)
+ int mol;
+ for (mol = 0; mol < (mtop->bIntermolecularInteractions ? molb.nmol : 1); mol++)
{
- for (cg = 0; cg < cgs->nr; cg++)
+ for (int cg = 0; cg < cgs.nr; cg++)
{
- cg_gl = cg_offset + cg;
+ int cg_gl = cg_offset + cg;
link->index[cg_gl+1] = link->index[cg_gl];
- for (a = cgs->index[cg]; a < cgs->index[cg+1]; a++)
+ for (int a = cgs.index[cg]; a < cgs.index[cg + 1]; a++)
{
- i = ril.index[a];
+ int i = ril.index[a];
while (i < ril.index[a+1])
{
- ftype = ril.il[i++];
- nral = NRAL(ftype);
+ int ftype = ril.il[i++];
+ int nral = NRAL(ftype);
/* Skip the ifunc index */
i++;
- for (j = 0; j < nral; j++)
+ for (int j = 0; j < nral; j++)
{
- aj = ril.il[i+j];
+ int aj = ril.il[i + j];
if (a2c[aj] != cg)
{
check_link(link, cg_gl, cg_offset+a2c[aj]);
if (bExclRequired)
{
/* Exclusions always go both ways */
- for (j = excls->index[a]; j < excls->index[a+1]; j++)
+ for (int j = excls.index[a]; j < excls.index[a + 1]; j++)
{
- aj = excls->a[j];
+ int aj = excls.a[j];
if (a2c[aj] != cg)
{
check_link(link, cg_gl, cg_offset+a2c[aj]);
if (mtop->bIntermolecularInteractions)
{
- i = ril_intermol.index[a];
+ int i = ril_intermol.index[a];
while (i < ril_intermol.index[a+1])
{
- ftype = ril_intermol.il[i++];
- nral = NRAL(ftype);
+ int ftype = ril_intermol.il[i++];
+ int nral = NRAL(ftype);
/* Skip the ifunc index */
i++;
- for (j = 0; j < nral; j++)
+ for (int j = 0; j < nral; j++)
{
/* Here we assume we have no charge groups;
* this has been checked above.
*/
- aj = ril_intermol.il[i+j];
+ int aj = ril_intermol.il[i + j];
check_link(link, cg_gl, aj);
}
i += nral_rt(ftype);
}
}
- cg_offset += cgs->nr;
+ cg_offset += cgs.nr;
}
- nlink_mol = link->index[cg_offset] - link->index[cg_offset-cgs->nr];
+ int nlink_mol = link->index[cg_offset] - link->index[cg_offset - cgs.nr];
destroy_reverse_ilist(&ril);
- sfree(a2c);
if (debug)
{
- fprintf(debug, "molecule type '%s' %d cgs has %d cg links through bonded interac.\n", *molt->name, cgs->nr, nlink_mol);
+ fprintf(debug, "molecule type '%s' %d cgs has %d cg links through bonded interac.\n", *molt.name, cgs.nr, nlink_mol);
}
- if (molb->nmol > mol)
+ if (molb.nmol > mol)
{
/* Copy the data for the rest of the molecules in this block */
- link->nalloc_a += (molb->nmol - mol)*nlink_mol;
+ link->nalloc_a += (molb.nmol - mol)*nlink_mol;
srenew(link->a, link->nalloc_a);
- for (; mol < molb->nmol; mol++)
+ for (; mol < molb.nmol; mol++)
{
- for (cg = 0; cg < cgs->nr; cg++)
+ for (int cg = 0; cg < cgs.nr; cg++)
{
- cg_gl = cg_offset + cg;
- link->index[cg_gl+1] =
- link->index[cg_gl+1-cgs->nr] + nlink_mol;
- for (j = link->index[cg_gl]; j < link->index[cg_gl+1]; j++)
+ int cg_gl = cg_offset + cg;
+ link->index[cg_gl + 1] =
+ link->index[cg_gl + 1 - cgs.nr] + nlink_mol;
+ for (int j = link->index[cg_gl]; j < link->index[cg_gl+1]; j++)
{
- link->a[j] = link->a[j-nlink_mol] + cgs->nr;
+ link->a[j] = link->a[j - nlink_mol] + cgs.nr;
}
if (link->index[cg_gl+1] - link->index[cg_gl] > 0 &&
cg_gl - cgi_mb->cg_start < cgi_mb->cg_mod)
ncgi++;
}
}
- cg_offset += cgs->nr;
+ cg_offset += cgs.nr;
}
}
}
}
/*! \brief Set the distance, function type and atom indices for the longest distance between charge-groups of molecule type \p molt for two-body and multi-body bonded interactions */
-static void bonded_cg_distance_mol(gmx_moltype_t *molt, int *at2cg,
+static void bonded_cg_distance_mol(const gmx_moltype_t *molt,
+ const std::vector<int> &at2cg,
gmx_bool bBCheck, gmx_bool bExcl, rvec *cg_cm,
bonded_distance_t *bd_2b,
bonded_distance_t *bd_mb)
real *r_2b, real *r_mb)
{
gmx_bool bExclRequired;
- int mb, at_offset, *at2cg, mol;
+ int at_offset;
t_graph graph;
- gmx_molblock_t *molb;
- gmx_moltype_t *molt;
rvec *xs, *cg_cm;
bonded_distance_t bd_2b = { 0, -1, -1, -1 };
bonded_distance_t bd_mb = { 0, -1, -1, -1 };
*r_2b = 0;
*r_mb = 0;
at_offset = 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];
- if (molt->cgs.nr == 1 || molb->nmol == 0)
+ const gmx_moltype_t &molt = mtop->moltype[molb.type];
+ if (molt.cgs.nr == 1 || molb.nmol == 0)
{
- at_offset += molb->nmol*molt->atoms.nr;
+ at_offset += molb.nmol*molt.atoms.nr;
}
else
{
if (ir->ePBC != epbcNONE)
{
- mk_graph_ilist(nullptr, molt->ilist, 0, molt->atoms.nr, FALSE, FALSE,
+ mk_graph_ilist(nullptr, molt.ilist, 0, molt.atoms.nr, FALSE, FALSE,
&graph);
}
- at2cg = make_at2cg(&molt->cgs);
- snew(xs, molt->atoms.nr);
- snew(cg_cm, molt->cgs.nr);
- for (mol = 0; mol < molb->nmol; mol++)
+ std::vector<int> at2cg = make_at2cg(molt.cgs);
+ snew(xs, molt.atoms.nr);
+ snew(cg_cm, molt.cgs.nr);
+ for (int mol = 0; mol < molb.nmol; mol++)
{
- get_cgcm_mol(molt, &mtop->ffparams, ir->ePBC, &graph, box,
+ get_cgcm_mol(&molt, &mtop->ffparams, ir->ePBC, &graph, box,
x+at_offset, xs, cg_cm);
bonded_distance_t bd_mol_2b = { 0, -1, -1, -1 };
bonded_distance_t bd_mol_mb = { 0, -1, -1, -1 };
- bonded_cg_distance_mol(molt, at2cg, bBCheck, bExclRequired, cg_cm,
+ bonded_cg_distance_mol(&molt, at2cg, bBCheck, bExclRequired, cg_cm,
&bd_mol_2b, &bd_mol_mb);
/* Process the mol data adding the atom index offset */
at_offset + bd_mol_mb.a2,
&bd_mb);
- at_offset += molt->atoms.nr;
+ at_offset += molt.atoms.nr;
}
sfree(cg_cm);
sfree(xs);
- sfree(at2cg);
if (ir->ePBC != epbcNONE)
{
done_graph(&graph);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff