bool Cube::setLimits(const Molecule &mol, double spacing_, double padding)
{
Index numAtoms = mol.atomCount();
Vector3 min_, max_;
if (numAtoms) {
Vector3 curPos = min_ = max_ = mol.atomPositions3d()[0];
for (Index i = 1; i < numAtoms; ++i) {
curPos = mol.atomPositions3d()[i];
if (curPos.x() < min_.x())
min_.x() = curPos.x();
if (curPos.x() > max_.x())
max_.x() = curPos.x();
if (curPos.y() < min_.y())
min_.y() = curPos.y();
if (curPos.y() > max_.y())
max_.y() = curPos.y();
if (curPos.z() < min_.z())
min_.z() = curPos.z();
if (curPos.z() > max_.z())
max_.z() = curPos.z();
}
}
else {
min_ = max_ = Vector3::Zero();
}
// Now to take care of the padding term
min_ += Vector3(-padding,-padding,-padding);
max_ += Vector3( padding, padding, padding);
return setLimits(min_, max_, spacing_);
}
TEST_F(MoleculeSerializationTest, roundTrip)
{
MoleculeSerializer serializer(&this->ethane);
size_t size = serializer.size();
uint8 *data = new uint8[size];
bool success = serializer.serialize(data, size);
EXPECT_TRUE(success);
Molecule after;
MoleculeDeserializer deserializer(&after);
success = deserializer.deserialize(data, size);
EXPECT_TRUE(success);
delete[] data;
EXPECT_EQ(this->ethane.atomicNumbers(), after.atomicNumbers());
std::vector<Avogadro::Vector2> expected2d = this->ethane.atomPositions2d();
std::vector<Avogadro::Vector2> actual2d = after.atomPositions2d();
EXPECT_EQ(expected2d.size(), actual2d.size());
for (size_t i = 0; i < expected2d.size(); i++)
EXPECT_TRUE(this->equal(expected2d[i], actual2d[i]));
std::vector<Avogadro::Vector3> expected3d = this->ethane.atomPositions3d();
std::vector<Avogadro::Vector3> actual3d = after.atomPositions3d();
EXPECT_EQ(expected3d.size(), actual3d.size());
for (size_t i = 0; i < expected3d.size(); i++)
EXPECT_TRUE(this->equal(expected3d[i], actual3d[i]));
const std::vector<std::pair<size_t, size_t> > expectedBondPairs
= this->ethane.bondPairs();
const std::vector<std::pair<size_t, size_t> > actualBondPairs
= after.bondPairs();
EXPECT_EQ(expectedBondPairs.size(), actualBondPairs.size());
for (size_t i = 0; i < expectedBondPairs.size(); i++) {
EXPECT_EQ(expectedBondPairs[i].first, actualBondPairs[i].first);
EXPECT_EQ(expectedBondPairs[i].second, actualBondPairs[i].second);
}
const std::vector<unsigned char> expectedBondOrder
= this->ethane.bondOrders();
const std::vector<unsigned char> actualBondOrder = after.bondOrders();
for (size_t i = 0; i < expectedBondOrder.size(); i++)
EXPECT_EQ(expectedBondOrder[i], actualBondOrder[i]);
}
TEST(UnitCellTest, fractionalCoordinates)
{
Molecule mol = createCrystal(static_cast<Real>(3.0),
static_cast<Real>(4.0),
static_cast<Real>(5.0),
static_cast<Real>(90.0),
static_cast<Real>(120.0),
static_cast<Real>(77.0));
mol.addAtom(1).setPosition3d(Vector3(static_cast<Real>(0),
static_cast<Real>(0),
static_cast<Real>(0)));
mol.addAtom(1).setPosition3d(Vector3(static_cast<Real>(0.7),
static_cast<Real>(2.23733),
static_cast<Real>(2.14574)));
mol.addAtom(1).setPosition3d(Vector3(static_cast<Real>(2.07490),
static_cast<Real>(2.09303),
static_cast<Real>(1.07287)));
mol.addAtom(1).setPosition3d(Vector3(static_cast<Real>(3),
static_cast<Real>(0),
static_cast<Real>(0)));
mol.addAtom(1).setPosition3d(Vector3(static_cast<Real>(0.89980),
static_cast<Real>(3.89748),
static_cast<Real>(0)));
mol.addAtom(1).setPosition3d(Vector3(static_cast<Real>(-2.5),
static_cast<Real>(0.57717),
static_cast<Real>(4.29149)));
Array<Vector3> ccoords_ref = mol.atomPositions3d();
Array<Vector3> fcoords;
EXPECT_TRUE(CrystalTools::fractionalCoordinates(mol, fcoords));
EXPECT_EQ(mol.atomCount(), fcoords.size());
EXPECT_TRUE(std::fabs(fcoords[0][0] - static_cast<Real>(0)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[0][1] - static_cast<Real>(0)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[0][2] - static_cast<Real>(0)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[1][0] - static_cast<Real>(0.5)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[1][1] - static_cast<Real>(0.5)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[1][2] - static_cast<Real>(0.5)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[2][0] - static_cast<Real>(0.75)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[2][1] - static_cast<Real>(0.5)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[2][2] - static_cast<Real>(0.25)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[3][0] - static_cast<Real>(1)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[3][1] - static_cast<Real>(0)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[3][2] - static_cast<Real>(0)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[4][0] - static_cast<Real>(0)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[4][1] - static_cast<Real>(1)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[4][2] - static_cast<Real>(0)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[5][0] - static_cast<Real>(0)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[5][1] - static_cast<Real>(0)) < 1e-4);
EXPECT_TRUE(std::fabs(fcoords[5][2] - static_cast<Real>(1)) < 1e-4);
mol.atomPositions3d().clear();
EXPECT_TRUE(CrystalTools::setFractionalCoordinates(mol, fcoords));
Array<Vector3> ccoords = mol.atomPositions3d();
for (int i = 0; i < 6; ++i) {
for (int j = 0; j < 3; ++j) {
EXPECT_FLOAT_EQ(static_cast<float>(ccoords_ref[i][j]),
static_cast<float>(ccoords[i][j]))
<< " (i=" << i << "j=" << j << ")";
}
}
}
