virtual bool step(HMMparticle::sequence_vector_iterator_type current_path_ref, boost::random::mt19937& random_generator, bool CollapsedVersion)
{
bool accepted = false;
// define random number generators
boost::uniform_int<arma::uword> unidist(0, std::numeric_limits<arma::uword>::max());
boost::random::variate_generator<boost::random::mt19937&, boost::uniform_int<arma::uword> > unirandoms(random_generator, unidist);
boost::random::variate_generator<boost::random::mt19937&, boost::uniform_real<> > central_vargen(random_generator, boost::uniform_real<>(0.0, 1.0));
boost::uniform_int<arma::uword> jumpdist(1, parameter);
boost::random::variate_generator<boost::random::mt19937&, boost::uniform_int<arma::uword> > jumplength(random_generator, jumpdist);
arma::urowvec current_genotype = arma::zeros<arma::urowvec>(associatedParticle->get_emission_matrix().n_cols);
arma::urowvec new_sequence = arma::zeros<arma::urowvec>(associatedParticle->MAXDEPTH);
bool clockwise = central_vargen() < 0.5;
base_pseudo_generator_type new_generator(unirandoms());
bool old_path_found = false;
arma::uword aimed_jump = jumplength();
//~ std::cout << "\nAlt: "; std::cout.flush();
//~ for (arma::uword i=0; i < current_path_ref->get<2>().n_elem; ++i ) std::cout << current_path_ref->get<2>()[i] << " ";
//~ std::cout << "\nNeu: "; std::cout.flush();
IDRefSequenceCountTuple proposal = *current_path_ref;
bool success = recursive_tree_search( proposal, 0, new_sequence, false, current_genotype, 1, clockwise, old_path_found, new_generator, aimed_jump);
if (success)
{
double likelihood_difference;
if (!CollapsedVersion)
{
double likelihood_star = associatedParticle->single_path_likelihood(proposal.get<3>());
double likelihood_old = associatedParticle->single_path_likelihood(current_path_ref->get<3>());
likelihood_difference = likelihood_star - likelihood_old;
}
else {
likelihood_difference = associatedParticle->collapsed_likelihood_difference(current_path_ref->get<3>(), proposal.get<3>());
}
if (log(central_vargen()) < likelihood_difference)
{
accepted = true;
if (CollapsedVersion) associatedParticle->update_countmatrix(current_path_ref->get<3>(), proposal.get<3>());
(*current_path_ref) = proposal;
}
}
else
throw(std::runtime_error("Some weird error occured!"));
return accepted;
//~ for (arma::uword i=0; i < current_path_ref->get<2>().n_elem; ++i ) std::cout << current_path_ref->get<2>()[i] << " ";
//~ std::cout << " !\n"; std::cout.flush();
}
void create_ic(Particle *p, int npart){
int npoints = 1000;
double *kk, *pofk;
// Read in and store P(k,z=0)
kk = new double[npoints];
pofk = new double[npoints];
ifstream fp("pofk.txt");
for(int i = 0;i < npoints; i++){
fp >> kk[i];
fp >> pofk[i];
}
DSpline pofk_spline = DSpline(kk, pofk, npoints, "P(k) spline");
// Integrate growth-factor
// ... not implemented
// Generate random numbers
random_device rd;
int seed = rd();
mt19937 rg(seed);
uniform_real_distribution<double> unidist(0, 1);
int nrandom = npart * 3 * 2;
double *randoms = new double[nrandom];
for(int i = 0; i < nrandom; i++){
randoms[i] = unidist(rg);
}
// Make realisation in Fourier space
// ... not implemented
// FFT back to get displacement field
// ... not implemented
// Assign particles and move them
// ... not implemented
delete[] randoms;
}
int main(int argc, char** argv)
{
double T(1);
double L(1.44e-6);
unsigned N(100);
double R(2.5e-9);
double D(1e-12);
if (argc == 6) {
T = std::stod(argv[1]);
L = std::stod(argv[2]);
N = std::stoi(argv[3]);
R = std::stod(argv[4]);
D = std::stod(argv[5]);
}
const double dt(2*R*R/3/D);
const unsigned nSim(T/dt);
std::random_device rd;
std::mt19937 gen(rd());
std::uniform_real_distribution<> unidist(0, L);
std::normal_distribution<> normdist(0, pow(2*D*dt,0.5));
std::vector<Coordinate> mols;
for (unsigned i(0); i < N; ++i) {
Coordinate mol(unidist(gen), unidist(gen), unidist(gen));
mols.push_back(mol);
}
auto start = std::chrono::high_resolution_clock::now();
for (unsigned n(0); n < nSim; ++n) {
for (unsigned j(0); j < N; ++j) {
mols[j].x = mod(mols[j].x+normdist(gen), L);
mols[j].y = mod(mols[j].y+normdist(gen), L);
mols[j].z = mod(mols[j].z+normdist(gen), L);
}
}
auto finish = std::chrono::high_resolution_clock::now();
std::chrono::duration<double> elapsed = finish - start;
std::cout << "elapsed:" << elapsed.count() << " s" << std::endl;
}
