#include "gromacs/topology/topology.h"
#include "gromacs/topology/topsort.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
-void gmx_mtop_count_atomtypes(const gmx_mtop_t* mtop, int state, int typecount[])
+void gmx_mtop_count_atomtypes(const gmx_mtop_t& mtop, int state, int typecount[])
{
- for (int i = 0; i < mtop->ffparams.atnr; ++i)
+ for (int i = 0; i < mtop.ffparams.atnr; ++i)
{
typecount[i] = 0;
}
- for (const gmx_molblock_t& molb : mtop->molblock)
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- const t_atoms& atoms = mtop->moltype[molb.type].atoms;
+ 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;
- }
- else
- {
- tpi = atoms.atom[i].typeB;
- }
+ const int tpi = (state == 0) ? atoms.atom[i].type : atoms.atom[i].typeB;
typecount[tpi] += molb.nmol;
}
}
return numMolecules;
}
-int gmx_mtop_nres(const gmx_mtop_t* mtop)
+int gmx_mtop_nres(const gmx_mtop_t& mtop)
{
int nres = 0;
- for (const gmx_molblock_t& molb : mtop->molblock)
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- nres += molb.nmol * mtop->moltype[molb.type].atoms.nres;
+ nres += molb.nmol * mtop.moltype[molb.type].atoms.nres;
}
return nres;
}
return it_->localAtomNumber_;
}
-typedef struct gmx_mtop_atomloop_block
+struct gmx_mtop_atomloop_block
{
const gmx_mtop_t* mtop;
size_t mblock;
const t_atoms* atoms;
int at_local;
-} t_gmx_mtop_atomloop_block;
+};
-gmx_mtop_atomloop_block_t gmx_mtop_atomloop_block_init(const gmx_mtop_t* mtop)
+gmx_mtop_atomloop_block_t gmx_mtop_atomloop_block_init(const gmx_mtop_t& mtop)
{
- struct gmx_mtop_atomloop_block* aloop;
+ struct gmx_mtop_atomloop_block* aloop = nullptr;
snew(aloop, 1);
- aloop->mtop = mtop;
+ aloop->mtop = &mtop;
aloop->mblock = 0;
- aloop->atoms = &mtop->moltype[mtop->molblock[aloop->mblock].type].atoms;
+ aloop->atoms = &mtop.moltype[mtop.molblock[aloop->mblock].type].atoms;
aloop->at_local = -1;
return aloop;
return TRUE;
}
-typedef struct gmx_mtop_ilistloop
+IListIterator::IListIterator(const gmx_mtop_t& mtop, size_t molblock) :
+ mtop_(&mtop), mblock_(molblock)
{
- const gmx_mtop_t* mtop;
- int mblock;
-} t_gmx_mtop_ilist;
+}
-gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t* mtop)
+IListIterator& IListIterator::operator++()
{
- struct gmx_mtop_ilistloop* iloop;
-
- snew(iloop, 1);
-
- iloop->mtop = mtop;
- iloop->mblock = -1;
-
- return iloop;
+ mblock_++;
+ return *this;
}
-gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t& mtop)
+bool IListIterator::operator==(const IListIterator& o) const
{
- return gmx_mtop_ilistloop_init(&mtop);
+ return mtop_ == o.mtop_ && mblock_ == o.mblock_;
}
-static void gmx_mtop_ilistloop_destroy(gmx_mtop_ilistloop_t iloop)
+const InteractionLists& IListProxy::list() const
{
- sfree(iloop);
+ // one past the end means we want to take the
+ // intermolecular list instead.
+ if (it_->mblock_ == it_->mtop_->molblock.size())
+ {
+ return *it_->mtop_->intermolecular_ilist;
+ }
+ else
+ {
+ return it_->mtop_->moltype[it_->mtop_->molblock[it_->mblock_].type].ilist;
+ }
}
-const InteractionLists* gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop, int* nmol)
+int IListProxy::nmol() const
{
- if (iloop == nullptr)
+ // one past the end means we want to take the
+ // intermolecular list instead.
+ if (it_->mblock_ == it_->mtop_->molblock.size())
{
- gmx_incons("gmx_mtop_ilistloop_next called without calling gmx_mtop_ilistloop_init");
+ return 1;
}
-
- iloop->mblock++;
- if (iloop->mblock >= gmx::ssize(iloop->mtop->molblock))
+ else
{
- if (iloop->mblock == gmx::ssize(iloop->mtop->molblock) && iloop->mtop->bIntermolecularInteractions)
- {
- *nmol = 1;
- return iloop->mtop->intermolecular_ilist.get();
- }
-
- gmx_mtop_ilistloop_destroy(iloop);
- return nullptr;
+ return it_->mtop_->molblock[it_->mblock_].nmol;
}
-
- *nmol = iloop->mtop->molblock[iloop->mblock].nmol;
-
- return &iloop->mtop->moltype[iloop->mtop->molblock[iloop->mblock].type].ilist;
}
-typedef struct gmx_mtop_ilistloop_all
-{
- const gmx_mtop_t* mtop;
- size_t mblock;
- int mol;
- int a_offset;
-} t_gmx_mtop_ilist_all;
-int gmx_mtop_ftype_count(const gmx_mtop_t* mtop, int ftype)
+IListRange::IListRange(const gmx_mtop_t& mtop) : begin_(mtop), end_(mtop, mtop.molblock.size())
{
- gmx_mtop_ilistloop_t iloop;
- int n, nmol;
+ if (mtop.bIntermolecularInteractions)
+ {
+ end_ = IListIterator(mtop, mtop.molblock.size() + 1);
+ }
+}
- n = 0;
+int gmx_mtop_ftype_count(const gmx_mtop_t& mtop, int ftype)
+{
+ int n = 0;
- iloop = gmx_mtop_ilistloop_init(mtop);
- while (const InteractionLists* il = gmx_mtop_ilistloop_next(iloop, &nmol))
+ for (const IListProxy il : IListRange(mtop))
{
- n += nmol * (*il)[ftype].size() / (1 + NRAL(ftype));
+ n += il.nmol() * il.list()[ftype].size() / (1 + NRAL(ftype));
}
- if (mtop->bIntermolecularInteractions)
+ if (mtop.bIntermolecularInteractions)
{
- n += (*mtop->intermolecular_ilist)[ftype].size() / (1 + NRAL(ftype));
+ n += (*mtop.intermolecular_ilist)[ftype].size() / (1 + NRAL(ftype));
}
return n;
}
-int gmx_mtop_ftype_count(const gmx_mtop_t& mtop, int ftype)
-{
- return gmx_mtop_ftype_count(&mtop, ftype);
-}
-
int gmx_mtop_interaction_count(const gmx_mtop_t& mtop, const int unsigned if_flags)
{
int n = 0;
- gmx_mtop_ilistloop_t iloop = gmx_mtop_ilistloop_init(mtop);
- int nmol;
- while (const InteractionLists* il = gmx_mtop_ilistloop_next(iloop, &nmol))
+ for (const IListProxy il : IListRange(mtop))
{
for (int ftype = 0; ftype < F_NRE; ftype++)
{
if ((interaction_function[ftype].flags & if_flags) == if_flags)
{
- n += nmol * (*il)[ftype].size() / (1 + NRAL(ftype));
+ n += il.nmol() * il.list()[ftype].size() / (1 + NRAL(ftype));
}
}
}
return n;
}
-std::array<int, eptNR> gmx_mtop_particletype_count(const gmx_mtop_t& mtop)
+gmx::EnumerationArray<ParticleType, int> gmx_mtop_particletype_count(const gmx_mtop_t& mtop)
{
- std::array<int, eptNR> count = { { 0 } };
+ gmx::EnumerationArray<ParticleType, int> count = { { 0 } };
for (const auto& molblock : mtop.molblock)
{
static void atomcat(t_atoms* dest, const t_atoms* src, int copies, int maxres_renum, int* maxresnr)
{
- int i, j, l, size;
+ int i = 0, j = 0, l = 0, size = 0;
int srcnr = src->nr;
int destnr = dest->nr;
/* residue information */
for (l = dest->nres, j = 0; (j < copies); j++, l += src->nres)
{
- memcpy(reinterpret_cast<char*>(&(dest->resinfo[l])), reinterpret_cast<char*>(&(src->resinfo[0])),
+ memcpy(reinterpret_cast<char*>(&(dest->resinfo[l])),
+ reinterpret_cast<char*>(&(src->resinfo[0])),
static_cast<size_t>(src->nres * sizeof(src->resinfo[0])));
}
for (l = destnr, j = 0; (j < copies); j++, l += srcnr)
{
- memcpy(reinterpret_cast<char*>(&(dest->atom[l])), reinterpret_cast<char*>(&(src->atom[0])),
+ memcpy(reinterpret_cast<char*>(&(dest->atom[l])),
+ reinterpret_cast<char*>(&(src->atom[0])),
static_cast<size_t>(srcnr * sizeof(src->atom[0])));
memcpy(reinterpret_cast<char*>(&(dest->atomname[l])),
reinterpret_cast<char*>(&(src->atomname[0])),
dest->nr += copies * src->nr;
}
-t_atoms gmx_mtop_global_atoms(const gmx_mtop_t* mtop)
+t_atoms gmx_mtop_global_atoms(const gmx_mtop_t& mtop)
{
t_atoms atoms;
init_t_atoms(&atoms, 0, FALSE);
- int maxresnr = mtop->maxResNumberNotRenumbered();
- for (const gmx_molblock_t& molb : mtop->molblock)
+ int maxresnr = mtop.maxResNumberNotRenumbered();
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- atomcat(&atoms, &mtop->moltype[molb.type].atoms, molb.nmol,
- mtop->maxResiduesPerMoleculeToTriggerRenumber(), &maxresnr);
+ atomcat(&atoms,
+ &mtop.moltype[molb.type].atoms,
+ molb.nmol,
+ mtop.maxResiduesPerMoleculeToTriggerRenumber(),
+ &maxresnr);
}
return atoms;
static void ilistcat(int ftype, InteractionList* dest, const InteractionList& src, int copies, int dnum, int snum)
{
- int nral, c, i, a;
-
- nral = NRAL(ftype);
+ const int nral = NRAL(ftype);
size_t destIndex = dest->iatoms.size();
dest->iatoms.resize(dest->iatoms.size() + copies * src.size());
- for (c = 0; c < copies; c++)
+ for (int c = 0; c < copies; c++)
{
- for (i = 0; i < src.size();)
+ for (int i = 0; i < src.size();)
{
dest->iatoms[destIndex++] = src.iatoms[i++];
- for (a = 0; a < nral; a++)
+ for (int a = 0; a < nral; a++)
{
dest->iatoms[destIndex++] = dnum + src.iatoms[i++];
}
static void ilistcat(int ftype, t_ilist* dest, const InteractionList& src, int copies, int dnum, int snum)
{
- int nral, c, i, a;
-
- nral = NRAL(ftype);
+ const int nral = NRAL(ftype);
dest->nalloc = dest->nr + copies * src.size();
srenew(dest->iatoms, dest->nalloc);
- for (c = 0; c < copies; c++)
+ for (int c = 0; c < copies; c++)
{
- for (i = 0; i < src.size();)
+ for (int i = 0; i < src.size();)
{
dest->iatoms[dest->nr++] = src.iatoms[i++];
- for (a = 0; a < nral; a++)
+ for (int a = 0; a < nral; a++)
{
dest->iatoms[dest->nr++] = dnum + src.iatoms[i++];
}
template<typename IdefType>
static void set_posres_params(IdefType* idef, const gmx_molblock_t* molb, int i0, int a_offset)
{
- int i1, i, a_molb;
- t_iparams* ip;
-
auto* il = &idef->il[F_POSRES];
- i1 = il->size() / 2;
+ int i1 = il->size() / 2;
resizeIParams(&idef->iparams_posres, i1);
- for (i = i0; i < i1; i++)
+ for (int i = i0; i < i1; i++)
{
- ip = &idef->iparams_posres[i];
+ t_iparams* ip = &idef->iparams_posres[i];
/* Copy the force constants */
- *ip = getIparams(*idef, il->iatoms[i * 2]);
- a_molb = il->iatoms[i * 2 + 1] - a_offset;
+ *ip = getIparams(*idef, il->iatoms[i * 2]);
+ int a_molb = il->iatoms[i * 2 + 1] - a_offset;
if (molb->posres_xA.empty())
{
gmx_incons("Position restraint coordinates are missing");
template<typename IdefType>
static void set_fbposres_params(IdefType* idef, const gmx_molblock_t* molb, int i0, int a_offset)
{
- int i1, i, a_molb;
- t_iparams* ip;
-
auto* il = &idef->il[F_FBPOSRES];
- i1 = il->size() / 2;
+ int i1 = il->size() / 2;
resizeIParams(&idef->iparams_fbposres, i1);
- for (i = i0; i < i1; i++)
+ for (int i = i0; i < i1; i++)
{
- ip = &idef->iparams_fbposres[i];
+ t_iparams* ip = &idef->iparams_fbposres[i];
/* Copy the force constants */
- *ip = getIparams(*idef, il->iatoms[i * 2]);
- a_molb = il->iatoms[i * 2 + 1] - a_offset;
+ *ip = getIparams(*idef, il->iatoms[i * 2]);
+ int a_molb = il->iatoms[i * 2 + 1] - a_offset;
if (molb->posres_xA.empty())
{
gmx_incons("Position restraint coordinates are missing");
*/
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 (!(mergeConstr && ftype == F_CONSTRNC))
if (mtop.atomtypes.atomnumber)
{
snew(atomtypes->atomnumber, mtop.atomtypes.nr);
- std::copy(mtop.atomtypes.atomnumber, mtop.atomtypes.atomnumber + mtop.atomtypes.nr,
+ std::copy(mtop.atomtypes.atomnumber,
+ mtop.atomtypes.atomnumber + mtop.atomtypes.nr,
atomtypes->atomnumber);
}
else
copyIListsFromMtop(mtop, &top->idef, bMergeConstr);
top->name = mtop.name;
- top->atoms = gmx_mtop_global_atoms(&mtop);
+ top->atoms = gmx_mtop_global_atoms(mtop);
top->mols = gmx_mtop_molecules_t_block(mtop);
top->bIntermolecularInteractions = mtop.bIntermolecularInteractions;
top->symtab = mtop.symtab;
return top;
}
-std::vector<int> get_atom_index(const gmx_mtop_t* mtop)
+std::vector<int> get_atom_index(const gmx_mtop_t& mtop)
{
std::vector<int> atom_index;
- for (const AtomProxy atomP : AtomRange(*mtop))
+ for (const AtomProxy atomP : AtomRange(mtop))
{
const t_atom& local = atomP.atom();
int index = atomP.globalAtomNumber();
- if (local.ptype == eptAtom)
+ if (local.ptype == ParticleType::Atom)
{
atom_index.push_back(index);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff