}
}
-double check_mol(gmx_mtop_t *mtop, warninp_t wi)
+double check_mol(const gmx_mtop_t *mtop, warninp_t wi)
{
char buf[256];
- int i, mb, nmol, ri, pt;
+ int i, ri, pt;
double q;
real m, mB;
- t_atoms *atoms;
/* Check mass and charge */
q = 0.0;
- for (mb = 0; mb < mtop->nmolblock; mb++)
+ for (const gmx_molblock_t &molb : mtop->molblock)
{
- atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
- nmol = mtop->molblock[mb].nmol;
+ const t_atoms *atoms = &mtop->moltype[molb.type].atoms;
for (i = 0; (i < atoms->nr); i++)
{
- q += nmol*atoms->atom[i].q;
+ q += molb.nmol*atoms->atom[i].q;
m = atoms->atom[i].m;
mB = atoms->atom[i].mB;
pt = atoms->atom[i].ptype;
}
-static void make_atoms_sys(int nmolb, const gmx_molblock_t *molb,
- const t_molinfo *molinfo,
- t_atoms *atoms)
+static void make_atoms_sys(const std::vector<gmx_molblock_t> &molblock,
+ const t_molinfo *molinfo,
+ t_atoms *atoms)
{
- int mb, m, a;
- const t_atoms *mol_atoms;
-
atoms->nr = 0;
atoms->atom = nullptr;
- for (mb = 0; mb < nmolb; mb++)
+ for (const gmx_molblock_t &molb : molblock)
{
- assert(molb);
- mol_atoms = &molinfo[molb[mb].type].atoms;
+ const t_atoms &mol_atoms = molinfo[molb.type].atoms;
- srenew(atoms->atom, atoms->nr + molb[mb].nmol*mol_atoms->nr);
+ srenew(atoms->atom, atoms->nr + molb.nmol*mol_atoms.nr);
- for (m = 0; m < molb[mb].nmol; m++)
+ for (int m = 0; m < molb.nmol; m++)
{
- for (a = 0; a < mol_atoms->nr; a++)
+ for (int a = 0; a < mol_atoms.nr; a++)
{
- atoms->atom[atoms->nr++] = mol_atoms->atom[a];
+ atoms->atom[atoms->nr++] = mol_atoms.atom[a];
}
}
}
double *reppow,
t_gromppopts *opts,
real *fudgeQQ,
- int *nmolblock,
- gmx_molblock_t **molblock,
+ std::vector<gmx_molblock_t> *molblock,
gmx_bool bFEP,
gmx_bool bZero,
gmx_bool usingFullRangeElectrostatics,
char line[STRLEN], errbuf[256], comb_str[256], nb_str[256];
char genpairs[32];
char *dirstr, *dummy2;
- int nrcopies, nmol, nmolb = 0, nscan, ncombs, ncopy;
+ int nrcopies, nmol, nscan, ncombs, ncopy;
double fLJ, fQQ, fPOW;
- gmx_molblock_t *molb = nullptr;
t_molinfo *mi0 = nullptr;
DirStack *DS;
directive d, newd;
snew(*intermolecular_interactions, 1);
init_molinfo(*intermolecular_interactions);
mi0 = *intermolecular_interactions;
- make_atoms_sys(nmolb, molb, *molinfo,
+ make_atoms_sys(*molblock, *molinfo,
&mi0->atoms);
}
}
push_mol(nmol, *molinfo, pline, &whichmol, &nrcopies, wi);
mi0 = &((*molinfo)[whichmol]);
- srenew(molb, nmolb+1);
- molb[nmolb].type = whichmol;
- molb[nmolb].nmol = nrcopies;
- nmolb++;
+ molblock->resize(molblock->size() + 1);
+ molblock->back().type = whichmol;
+ molblock->back().nmol = nrcopies;
bCouple = (opts->couple_moltype != nullptr &&
(gmx_strcasecmp("system", opts->couple_moltype) == 0 ||
*nrmols = nmol;
- *nmolblock = nmolb;
- *molblock = molb;
-
return title;
}
-char **do_top(gmx_bool bVerbose,
- const char *topfile,
- const char *topppfile,
- t_gromppopts *opts,
- gmx_bool bZero,
- t_symtab *symtab,
- t_params plist[],
- int *combination_rule,
- double *repulsion_power,
- real *fudgeQQ,
- gpp_atomtype_t atype,
- int *nrmols,
- t_molinfo **molinfo,
- t_molinfo **intermolecular_interactions,
- const t_inputrec *ir,
- int *nmolblock,
- gmx_molblock_t **molblock,
- warninp_t wi)
+char **do_top(gmx_bool bVerbose,
+ const char *topfile,
+ const char *topppfile,
+ t_gromppopts *opts,
+ gmx_bool bZero,
+ t_symtab *symtab,
+ t_params plist[],
+ int *combination_rule,
+ double *repulsion_power,
+ real *fudgeQQ,
+ gpp_atomtype_t atype,
+ int *nrmols,
+ t_molinfo **molinfo,
+ t_molinfo **intermolecular_interactions,
+ const t_inputrec *ir,
+ std::vector<gmx_molblock_t> *molblock,
+ warninp_t wi)
{
/* Tmpfile might contain a long path */
const char *tmpfile;
symtab, atype,
nrmols, molinfo, intermolecular_interactions,
plist, combination_rule, repulsion_power,
- opts, fudgeQQ, nmolblock, molblock,
+ opts, fudgeQQ, molblock,
ir->efep != efepNO, bZero,
EEL_FULL(ir->coulombtype), wi);
*/
unsigned char *grpnr;
- int mb, mol, nat_mol, i, nr_mol_with_qm_atoms = 0;
+ int mol, nat_mol, nr_mol_with_qm_atoms = 0;
gmx_molblock_t *molb;
gmx_bool bQMMM;
grpnr = sys->groups.grpnr[egcQMMM];
- for (mb = 0; mb < sys->nmolblock; mb++)
+ for (size_t mb = 0; mb < sys->molblock.size(); mb++)
{
molb = &sys->molblock[mb];
nat_mol = sys->moltype[molb->type].atoms.nr;
for (mol = 0; mol < molb->nmol; mol++)
{
bQMMM = FALSE;
- for (i = 0; i < nat_mol; i++)
+ for (int i = 0; i < nat_mol; i++)
{
if ((grpnr ? grpnr[i] : 0) < ir->opts.ngQM)
{
if (mol > 0)
{
/* Split the molblock at this molecule */
- sys->nmolblock++;
- srenew(sys->molblock, sys->nmolblock);
- for (i = sys->nmolblock-2; i >= mb; i--)
- {
- sys->molblock[i+1] = sys->molblock[i];
- }
+ auto pos = sys->molblock.begin() + mb + 1;
+ sys->molblock.insert(pos, sys->molblock[mb]);
sys->molblock[mb ].nmol = mol;
sys->molblock[mb+1].nmol -= mol;
mb++;
if (molb->nmol > 1)
{
/* Split the molblock after this molecule */
- sys->nmolblock++;
- srenew(sys->molblock, sys->nmolblock);
+ auto pos = sys->molblock.begin() + mb + 1;
+ sys->molblock.insert(pos, sys->molblock[mb]);
molb = &sys->molblock[mb];
- for (i = sys->nmolblock-2; i >= mb; i--)
- {
- sys->molblock[i+1] = sys->molblock[i];
- }
sys->molblock[mb ].nmol = 1;
sys->molblock[mb+1].nmol -= 1;
}
/* Add a moltype for the QMMM molecule */
- sys->nmoltype++;
- srenew(sys->moltype, sys->nmoltype);
- /* Copy the moltype struct */
- sys->moltype[sys->nmoltype-1] = sys->moltype[molb->type];
+ sys->moltype.push_back(sys->moltype[molb->type]);
/* Copy the exclusions to a new array, since this is the only
* thing that needs to be modified for QMMM.
*/
copy_blocka(&sys->moltype[molb->type ].excls,
- &sys->moltype[sys->nmoltype-1].excls);
+ &sys->moltype.back().excls);
/* Set the molecule type for the QMMM molblock */
- molb->type = sys->nmoltype - 1;
+ molb->type = sys->moltype.size() - 1;
}
generate_qmexcl_moltype(&sys->moltype[molb->type], grpnr, ir, wi);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff