struct AtomTypeData
{
//! Explicit constructor.
- AtomTypeData(const t_atom &a,
- char **name,
- const InteractionOfType &nb,
- const int bondAtomType,
- const int atomNumber) :
- atom_(a), name_(name), nb_(nb),
+ AtomTypeData(const t_atom& a, char** name, const InteractionOfType& nb, const int bondAtomType, const int atomNumber) :
+ atom_(a),
+ name_(name),
+ nb_(nb),
bondAtomType_(bondAtomType),
atomNumber_(atomNumber)
{
}
//! Actual atom data.
- t_atom atom_;
+ t_atom atom_;
//! Atom name.
- char **name_;
+ char** name_;
//! Nonbonded data.
- InteractionOfType nb_;
+ InteractionOfType nb_;
//! Bonded atomtype for the type.
- int bondAtomType_;
+ int bondAtomType_;
//! Atom number for the atom type.
- int atomNumber_;
+ int atomNumber_;
};
class PreprocessingAtomTypes::Impl
{
- public:
- //! The number for currently loaded entries.
- size_t size() const { return types.size(); }
- //! The actual atom type data.
-
std::vector<AtomTypeData> types;
+public:
+ //! The number for currently loaded entries.
+ size_t size() const { return types.size(); }
+ //! The actual atom type data.
+ std::vector<AtomTypeData> types;
};
bool PreprocessingAtomTypes::isSet(int nt) const
return ((nt >= 0) && (nt < gmx::ssize(*this)));
}
-int PreprocessingAtomTypes::atomTypeFromName(const std::string &str) const
+int PreprocessingAtomTypes::atomTypeFromName(const std::string& str) const
{
/* Atom types are always case sensitive */
auto found = std::find_if(impl_->types.begin(), impl_->types.end(),
- [&str](const auto &type)
- { return str == *type.name_; });
+ [&str](const auto& type) { return str == *type.name_; });
if (found == impl_->types.end())
{
return NOTSET;
return impl_->size();
}
-const char *PreprocessingAtomTypes::atomNameFromAtomType(int nt) const
+const char* PreprocessingAtomTypes::atomNameFromAtomType(int nt) const
{
return isSet(nt) ? *(impl_->types[nt].name_) : nullptr;
}
return forceParam[param];
}
-PreprocessingAtomTypes::PreprocessingAtomTypes()
- : impl_(new Impl)
-{}
+PreprocessingAtomTypes::PreprocessingAtomTypes() : impl_(new Impl) {}
-PreprocessingAtomTypes::PreprocessingAtomTypes(PreprocessingAtomTypes &&old) noexcept
- : impl_(std::move(old.impl_))
-{}
+PreprocessingAtomTypes::PreprocessingAtomTypes(PreprocessingAtomTypes&& old) noexcept :
+ impl_(std::move(old.impl_))
+{
+}
-PreprocessingAtomTypes &PreprocessingAtomTypes::operator=(PreprocessingAtomTypes &&old) noexcept
+PreprocessingAtomTypes& PreprocessingAtomTypes::operator=(PreprocessingAtomTypes&& old) noexcept
{
impl_ = std::move(old.impl_);
return *this;
}
-PreprocessingAtomTypes::~PreprocessingAtomTypes()
-{}
+PreprocessingAtomTypes::~PreprocessingAtomTypes() {}
-int PreprocessingAtomTypes::addType(t_symtab *tab,
- const t_atom &a,
- const std::string &name,
- const InteractionOfType &nb,
+int PreprocessingAtomTypes::addType(t_symtab* tab,
+ const t_atom& a,
+ const std::string& name,
+ const InteractionOfType& nb,
int bondAtomType,
int atomNumber)
{
int position = atomTypeFromName(name);
if (position == NOTSET)
{
- impl_->types.emplace_back(a,
- put_symtab(tab, name.c_str()),
- nb,
- bondAtomType,
- atomNumber);
+ impl_->types.emplace_back(a, put_symtab(tab, name.c_str()), nb, bondAtomType, atomNumber);
return atomTypeFromName(name);
}
else
}
int PreprocessingAtomTypes::setType(int nt,
- t_symtab *tab,
- const t_atom &a,
- const std::string &name,
- const InteractionOfType &nb,
+ t_symtab* tab,
+ const t_atom& a,
+ const std::string& name,
+ const InteractionOfType& nb,
int bondAtomType,
int atomNumber)
{
return nt;
}
-void PreprocessingAtomTypes::printTypes(FILE * out)
+void PreprocessingAtomTypes::printTypes(FILE* out)
{
- fprintf (out, "[ %s ]\n", dir2str(Directive::d_atomtypes));
- fprintf (out, "; %6s %8s %8s %8s %12s %12s\n",
- "type", "mass", "charge", "particle", "c6", "c12");
- for (auto &entry : impl_->types)
+ fprintf(out, "[ %s ]\n", dir2str(Directive::d_atomtypes));
+ fprintf(out, "; %6s %8s %8s %8s %12s %12s\n", "type", "mass", "charge", "particle", "c6",
+ "c12");
+ for (auto& entry : impl_->types)
{
- fprintf(out, "%8s %8.3f %8.3f %8s %12e %12e\n",
- *(entry.name_), entry.atom_.m, entry.atom_.q, "A",
- entry.nb_.c0(), entry.nb_.c1());
+ fprintf(out, "%8s %8.3f %8.3f %8s %12e %12e\n", *(entry.name_), entry.atom_.m,
+ entry.atom_.q, "A", entry.nb_.c0(), entry.nb_.c1());
}
- fprintf (out, "\n");
+ fprintf(out, "\n");
}
-static int search_atomtypes(const PreprocessingAtomTypes *ga,
- int *n,
+static int search_atomtypes(const PreprocessingAtomTypes* ga,
+ int* n,
gmx::ArrayRef<int> typelist,
int thistype,
gmx::ArrayRef<const InteractionOfType> interactionTypes,
for (int j = 0; j < ntype && bFound; j++)
{
/* Check nonbonded parameters */
- gmx::ArrayRef<const real> forceParam1 = interactionTypes[ntype*typelist[i]+j].forceParam();
- gmx::ArrayRef<const real> forceParam2 = interactionTypes[ntype*thistype+j].forceParam();
+ gmx::ArrayRef<const real> forceParam1 =
+ interactionTypes[ntype * typelist[i] + j].forceParam();
+ gmx::ArrayRef<const real> forceParam2 = interactionTypes[ntype * thistype + j].forceParam();
for (int k = 0; (k < nrfp) && bFound; k++)
{
bFound = forceParam1[k] == forceParam2[k];
}
/* Check atomnumber */
- int tli = typelist[i];
- bFound = bFound &&
- (ga->atomNumberFromAtomType(tli) == ga->atomNumberFromAtomType(thistype));
+ int tli = typelist[i];
+ bFound = bFound && (ga->atomNumberFromAtomType(tli) == ga->atomNumberFromAtomType(thistype));
}
if (bFound)
{
return i;
}
-void PreprocessingAtomTypes::renumberTypes(gmx::ArrayRef<InteractionsOfType> plist,
- gmx_mtop_t *mtop,
- int *wall_atomtype,
- bool bVerbose)
+void PreprocessingAtomTypes::renumberTypes(gmx::ArrayRef<InteractionsOfType> plist,
+ gmx_mtop_t* mtop,
+ int* wall_atomtype,
+ bool bVerbose)
{
- int nat, ftype, ntype;
+ int nat, ftype, ntype;
ntype = size();
std::vector<int> typelist(ntype);
* can determine if two types should be merged.
*/
nat = 0;
- for (const gmx_moltype_t &moltype : mtop->moltype)
+ for (const gmx_moltype_t& moltype : mtop->moltype)
{
- const t_atoms *atoms = &moltype.atoms;
+ const t_atoms* atoms = &moltype.atoms;
for (int i = 0; (i < atoms->nr); i++)
{
- atoms->atom[i].type =
- search_atomtypes(this, &nat, typelist, atoms->atom[i].type,
- plist[ftype].interactionTypes, ftype);
- atoms->atom[i].typeB =
- search_atomtypes(this, &nat, typelist, atoms->atom[i].typeB,
- plist[ftype].interactionTypes, ftype);
+ atoms->atom[i].type = search_atomtypes(this, &nat, typelist, atoms->atom[i].type,
+ plist[ftype].interactionTypes, ftype);
+ atoms->atom[i].typeB = search_atomtypes(this, &nat, typelist, atoms->atom[i].typeB,
+ plist[ftype].interactionTypes, ftype);
}
}
for (int j = 0; (j < nat); j++)
{
int mj = typelist[j];
- const InteractionOfType &interactionType = plist[ftype].interactionTypes[ntype*mi+mj];
- nbsnew.emplace_back(interactionType.atoms(), interactionType.forceParam(), interactionType.interactionTypeName());
+ const InteractionOfType& interactionType = plist[ftype].interactionTypes[ntype * mi + mj];
+ nbsnew.emplace_back(interactionType.atoms(), interactionType.forceParam(),
+ interactionType.interactionTypeName());
}
new_types.push_back(impl_->types[mi]);
}
plist[ftype].interactionTypes = nbsnew;
}
-void PreprocessingAtomTypes::copyTot_atomtypes(t_atomtypes *atomtypes) const
+void PreprocessingAtomTypes::copyTot_atomtypes(t_atomtypes* atomtypes) const
{
/* Copy the atomtype data to the topology atomtype list */
- int ntype = size();
+ int ntype = size();
atomtypes->nr = ntype;
snew(atomtypes->atomnumber, ntype);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff