bool SimpleWireEngine::renderOpaque(PainterDevice *pd)
{
glDisable(GL_LIGHTING);
Color *map = colorMap(); // possible custom color map
if (!map) map = pd->colorMap(); // fall back to global color map
foreach(Bond *b, bonds()) {
const Atom* atom1 = b->beginAtom();
const Vector3d & v1 = *atom1->pos();
const Atom* atom2 = b->endAtom();
const Vector3d & v2 = *atom2->pos();
map->set(atom1);
pd->painter()->setColor(map);
if (atom1->atomicNumber() != atom2->atomicNumber()) {
// compute the mid-point between the two atoms
Vector3d v3((v1 + v2) / 2.0);
pd->painter()->drawLine(v1, v3, 1.0);
map->set(atom2);
pd->painter()->setColor(map);
pd->painter()->drawLine(v3, v2, 1.0);
}
else {
// Just draw a line
pd->painter()->drawLine(v1, v2, 1.0);
}
}
glEnable(GL_LIGHTING);
return true;
}
int main(){
atoms();
velocities();
bonds();
angles();
dihedrals();
}
void H2OAngleBondAnalysis::Analysis () {
h2os.Reload();
h2os.FindWaterSurfaceLocation ();
for (Wat_it it = h2os.begin(); it != h2os.end(); it++) {
double distance = system_t::Position((*it)->ReferencePoint()) - h2os.SurfaceLocation();
// calculate and bin the water OH bond lengths
bonds (distance, (*it)->OH1().norm());
bonds (distance, (*it)->OH2().norm());
// calculate the angle of the water molecule and bin it
double angle = (*it)->Angle();
angles (distance, acos(angle)*180.0/M_PI);
}
return;
}
void StabilizeStepper::initialize_neighbor_list_managers() {
const std::size_t num_beads(_space->num_beads());
PairList bond_pair(num_beads);
std::list<std::pair<std::size_t, std::size_t> > bonds(_model->list_bonds());
for (auto itr(bonds.begin()); itr != bonds.end(); itr++) {
bond_pair.add_pair(*itr);
bond_pair.add_pair(std::make_pair((*itr).second, (*itr).first));
}
PairList excludes(num_beads);
for (std::size_t i(0); i < num_beads; ++i) {
for (auto itr(bond_pair.begin(i)); itr != bond_pair.end(i); ++itr) {
excludes.add_pair(std::make_pair(i, *itr));
for (auto jtr(bond_pair.begin(*itr)); jtr != bond_pair.end(*itr); ++jtr) {
excludes.add_pair(std::make_pair(i, *jtr));
}
}
}
Model::inter_potential_container inter_potentials(_model->list_inter_potentials());
for (auto itr(inter_potentials.begin()); itr != inter_potentials.end(); ++itr) {
const double r_c((*itr)->get_cutoff_radius());
NeighborListManager manager(num_beads, r_c, r_c*3,
std::numeric_limits<double>::infinity()); // TODO parameter fitting
(*itr)->set_neighbor_list(manager.get_neighbor_list());
for (std::size_t i(0); i < num_beads-1; ++i) {
std::string symbol0(_space->symbol(i));
for (std::size_t j(i+1); j < num_beads; j++) {
std::string symbol1(_space->symbol(j));
if ((*itr)->is_valid_pair(symbol0, symbol1)) {
bool is_exclude(false);
for (auto itr2(excludes.begin(i)); itr2 != excludes.end(i); ++itr2)
if (j == *itr2) {
is_exclude = true;
break;
}
if (!is_exclude)
manager.add_candidate(std::make_pair(i,j));
}
}
}
manager.update(*(_space.get()));
_neighbor_list_managers.push_back(manager);
}
}
List Factory::convert(Data::Geometry& geometry)
{
List list;
Atoms* atoms(new Atoms());
Bonds* bonds(new Bonds());
list.append(atoms);
list.append(bonds);
unsigned nAtoms(geometry.nAtoms());
OpenBabel::OBMol obMol;
obMol.BeginModify();
AtomMap atomMap;
for (unsigned i = 0; i < nAtoms; ++i) {
unsigned Z(geometry.atomicNumber(i));
qglviewer::Vec position(geometry.position(i));
Atom* atom(new Atom(geometry.atomicNumber(i)));
atom->setPosition(geometry.position(i));
atoms->appendLayer(atom);
OpenBabel::OBAtom* obAtom(obMol.NewAtom());
obAtom->SetAtomicNum(Z);
obAtom->SetVector(position.x, position.y, position.z);
atomMap.insert(obAtom, atom);
}
obMol.SetTotalCharge(geometry.charge());
obMol.SetTotalSpinMultiplicity(geometry.multiplicity());
obMol.EndModify();
obMol.ConnectTheDots();
obMol.PerceiveBondOrders();
for (OpenBabel::OBMolBondIter obBond(&obMol); obBond; ++obBond) {
Atom* begin(atomMap.value(obBond->GetBeginAtom()));
Atom* end(atomMap.value(obBond->GetEndAtom()));
Bond* bond(new Bond(begin, end));
bond->setOrder(obBond->GetBondOrder());
bonds->appendLayer(bond);
}
return list;
}
int main(){
char *dumpAtoms;
dumpAtoms = (char*) malloc(2000);
char *restartFile;
restartFile = (char*) malloc(2000);
char *newRestartFile;
newRestartFile = (char*) malloc(2000);
dumpAtoms = "atom.restart.moveLiquid";
restartFile = "restart.250000.data";
newRestartFile = "restart.250000.data.consecutive";
intro(restartFile, newRestartFile);
consecutiveAtoms(dumpAtoms, newRestartFile);
bonds(restartFile, newRestartFile);
angles(restartFile, newRestartFile);
dihedrals(restartFile, newRestartFile);
}
void prepareBondInsert(int bonus=100)
{
if (bonds().size() == bonds().capacity())
bonds().reserve(bonds().size() + bonus);
}
/// Returns the number of bonds in the residue.
size_t Residue::bondCount() const
{
return bonds().size();
}
