void CanonicalEnsembleTest::UpdateNumMoleculesSequential() {
// remove the ifndef when canonicalensemble can be tested in parallel
#ifndef ENABLE_MPI
delete _domainDecomposition;
// will be deleted by tearDown()
_domainDecomposition = new DomainDecompDummy();
// the halo is cleared for freshly initialized particle containers.
ParticleContainer* container = initializeFromFile(ParticleContainerFactory::AdaptiveSubCell, "1clj-regular-12x12x12.inp", 1.0);
vector<Component>& components(_domain->getComponents());
CanonicalEnsemble ensemble(container, &components);
ensemble.updateGlobalVariable(NUM_PARTICLES);
// has the ensemble counted the right number of particles?
ASSERT_EQUAL(1728ul, ensemble.N());
// has the ensemble updated the count of particles per component right?
ASSERT_EQUAL(1728ul, components[0].getNumMolecules());
Molecule molecule(1729, 0, 5.5, 5.5, 5.5, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., &components);
container->addParticle(molecule);
ensemble.updateGlobalVariable(NUM_PARTICLES);
// has the ensemble counted the right number of particles?
ASSERT_EQUAL(1729ul, ensemble.N());
// has the ensemble updated the count of particles per component right?
ASSERT_EQUAL(1729ul, components[0].getNumMolecules());
#endif
}
void CuboidInitializer::initialize(ParticleContainer& container) {
double x[] = {0,0,0};
double m = _config.getMaterialConfig().getM();
double epsilon = _config.getMaterialConfig().getEpsilon();
double sigma = _config.getMaterialConfig().getSigma();
LOG4CXX_DEBUG(logger, "SphereInitializer material: m=" << m << " epsilon=" << epsilon << " sigma=" << sigma);
const utils::Vector<double,3>& v = _config.getV();
const utils::Vector<int, 3>& n = _config.getN();
LOG4CXX_DEBUG(logger, "Initializing CUBE at " << _config.getX().toString());
for (int i = 0; i < n[0]; i++) {
for (int j = 0; j < n[1]; j++) {
for (int k = 0; k < n[2]; k++) {
x[0] = _config.getX()[0] + ((double)i) * _config.getH();
x[1] = _config.getX()[1] + ((double)j) * _config.getH();
x[2] = _config.getX()[2] + ((double)k) * _config.getH();
LOG4CXX_TRACE(logger, "creating (x,y,z): (" << x[i] << "," << x[j] << "," << x[k] << ")");
Particle p(x, v, m, epsilon, sigma, _type_id);
//MaxwellBoltzmannDistribution(p, 0.1, dim);
container.addParticle(p);
}
}
}
}
void SphereInitializer::initialize(ParticleContainer& container) {
utils::Vector<double,3> x(0.);
double m = _config.getMaterialConfig().getM();
double epsilon = _config.getMaterialConfig().getEpsilon();
double sigma = _config.getMaterialConfig().getSigma();
LOG4CXX_DEBUG(logger, "SphereInitializer material: m=" << m << " epsilon=" << epsilon << " sigma=" << sigma);
int n = _config.getN();
double h = _config.getH();
double radius = ((double)n) * h;
const utils::Vector<double, 3>& center = _config.getX();
utils::Vector<double,3> radius_vector = radius;
utils::Vector<double,3> lower_left_front = center - radius_vector;
int dim = Configuration::getInstance().getDimension();
LOG4CXX_DEBUG(logger, "SphereINitializer dimension: " << dim );
bool two_d = (dim == 2);
if (two_d) {
lower_left_front[2] = center[2];
}
const utils::Vector<double, 3>& v = _config.getV();
int innerCount = two_d ? 1 : (2*n);
LOG4CXX_DEBUG(logger, "Initializing SPHERE at " << _config.getX().toString() << " two_d==" << two_d);
for (int i = 0; i < n*2; i++) {
for (int j = 0; j < n*2; j++) {
for (int k = 0; k < innerCount; k++) {
x[0] = lower_left_front[0] + ((double)i) * h;
x[1] = lower_left_front[1] + ((double)j) * h;
x[2] = lower_left_front[2] + ((double)k) * h;
LOG4CXX_TRACE(logger, "point at " << x.toString() << "has distance " << (x - center).L2Norm() << " and radius is "<< radius);
if ((x - center).L2Norm() < radius) {
LOG4CXX_TRACE(logger, "creating (x,y,z): (" << x[0] << "," << x[1] << "," << x[2] << ")");
Particle p(x, v, m, epsilon, sigma, _type_id);
//MaxwellBoltzmannDistribution(p, 0.1, dim);
container.addParticle(p);
}
}
}
}
}