void CState::fillBoxes()
{
cout << "CState::fillBoxes()" << endl;
vec3 atomPosition;
ivec3 boxIndex;
CAtom* atomptr;
for (int i = 0; i < nAtoms; i++)
{
atomptr = atoms[i];
atomPosition = atomptr->getPosition();
for (int j = 0; j < 3; j++)
{
boxIndex(j) = int(floor(atomPosition(j)/boxDimensions(j)));
}
boxes[calculate_box_number(boxIndex, NBoxes)]->addAtom(atomptr);
}
cout << "Exiting CState::fillBoxes()" << endl << endl;
}
void TubeGenerator::generateCarbonTube(int n1, int n2, int k, float transition, float bondLength, std::vector<Molecule::Atom>& atoms, std::vector<Molecule::Link>& links)
{
if (n1 < n2)
std::swap(n1, n2);
atoms.clear();
links.clear();
gameplay::Vector2 a1(1.7320508f, 0.0f);
gameplay::Vector2 a2(-0.8660254f, 1.5f);
gameplay::Vector2 R = (a1 * static_cast<float>(n1) + a2 * static_cast<float>(n2))* bondLength;
gameplay::Vector2 L(-R.y, R.x);
L.normalize();
L.scale(k * bondLength);
int ymin = -1;
int ymax = static_cast<int>(ceilf(std::max(L.y, R.y) / bondLength)) + 1;
int xmin = static_cast<int>(floorf(L.x / bondLength / a1.x)) - 1;
int xmax = static_cast<int>(ceilf(R.x / bondLength / a1.x - a2.x * ymax)) + 1;
std::map<std::tuple<int, int, int>, int> clippedAtoms;
float Rlen = R.length();
float Llen = L.length();
float eps = 0.0001f;
for (int y = ymin; y <= ymax; y++)
for (int x = xmin; x <= xmax; x++)
{
// process hexagon atoms
gameplay::Vector2 hexagonCenter(x * bondLength * a1.x + a2.x * y * bondLength, y * bondLength * a2.y);
// process only two hexagon's atoms
// these are unique to hexagon
// the rest will be processed by other hexagons
// each atom then can be uniquely defined by hexagon coordinates (x, y) and one index (0-1)
for (int i = 0; i < 2; i++)
{
float phi = MATH_PI / 6.0f + MATH_PI / 3.0f * i;
gameplay::Vector2 atomPosition(cosf(phi), sinf(phi));
atomPosition = hexagonCenter + atomPosition * bondLength;
// clip atoms by square defined by R and L vectors
float u = gameplay::Vector2::dot(atomPosition, R) / Rlen;
float v = gameplay::Vector2::dot(atomPosition, L) / Llen;
if (u >= -eps && v >= -eps && u < Rlen - eps && v < Llen - eps)
{
clippedAtoms.insert(std::make_pair(std::make_tuple(x, y, i), static_cast<int>(atoms.size())));
atoms.push_back({ 1, 0.0f, gameplay::Vector3(u, v, 0.0f) });
//atoms.push_back({ 1, 0.0f, gameplay::Vector3(atomPosition.x, atomPosition.y, 0.0f) });
}
}
}
std::vector<std::tuple<int, int, int>> unboundAtoms;
// check links
for (auto it = clippedAtoms.begin(), end_it = clippedAtoms.end(); it != end_it; it++)
{
int x = std::get<0>((*it).first);
int y = std::get<1>((*it).first);
if (std::get<2>((*it).first) == 0)
{
auto next = clippedAtoms.find(std::make_tuple(x, y, 1));
if (next != clippedAtoms.end())
links.push_back({ (*it).second, (*next).second, 1 });
else
unboundAtoms.push_back((*it).first);
next = clippedAtoms.find(std::make_tuple(x, y - 1, 1));
if (next != clippedAtoms.end())
links.push_back({ (*it).second, (*next).second, 1 });
else
unboundAtoms.push_back((*it).first);
next = clippedAtoms.find(std::make_tuple(x + 1, y, 1));
if (next != clippedAtoms.end())
links.push_back({ (*it).second, (*next).second, 1 });
else
unboundAtoms.push_back((*it).first);
}
}
// bend graphene
if (transition > 0.0f)
{
for (auto it = atoms.begin(), end_it = atoms.end(); it != end_it; it++)
{
float radius = R.length() / MATH_PIX2 / transition;
float phi = (*it).pos.x / radius;
(*it).pos.x = radius * sinf(phi);
(*it).pos.z = radius * cosf(phi);
}
}
// add new links
//for (auto it = unboundAtoms.begin(), end_it = unboundAtoms.end(); it != end_it; it++)
//{
// auto first = clippedAtoms.find(std::make_tuple(x, y, 0));
// if (first != clippedAtoms.end())
// {
// auto next = clippedAtoms.find(std::make_tuple(x, y, 1));
// if (next == clippedAtoms.end())
// {
// for (int x1 = xmax; x1 > x; x1--)
// {
// auto last = clippedAtoms.find(std::make_tuple(x1, y, 1));
// if (last != clippedAtoms.end())
// {
// links.push_back({ (*first).second, (*last).second, 1 });
// break;
// }
// }
// }
// next = clippedAtoms.find(std::make_tuple(x, y - 1, 1));
// if (next == clippedAtoms.end())
// {
// for (int x1 = xmin; x1 < x; x1++ )
// {
// auto last = clippedAtoms.find(std::make_tuple(x1, y - 1, 1));
// if (last != clippedAtoms.end())
// {
// links.push_back({ (*first).second, (*last).second, 1 });
// break;
// }
// }
// }
// next = clippedAtoms.find(std::make_tuple(x + 1, y, 1));
// if (next == clippedAtoms.end())
// {
// for (int x1 = xmin; x1 < x; x1++)
// {
// auto last = clippedAtoms.find(std::make_tuple(x1, y, 1));
// if (last != clippedAtoms.end())
// {
// links.push_back({ (*first).second, (*last).second, 1 });
// break;
// }
// }
// }
// }
//}
}