void Mcmc::run(size_t kIterations) {
/* Let user know what we are doing */
if ( generation == 0 )
std::cout << "Running MCMC simulation for " << kIterations << " iterations" << std::endl;
else
std::cout << "Appending " << kIterations << " iterations to previous MCMC simulation of " << generation << " iterations" << std::endl;
if ( scheduleType == "single" )
{
std::cout << "The simulator uses " << moves.size() << " different moves, with a" << std::endl;
std::cout << "single move picked randomly per iteration" << std::endl;
}
else if ( scheduleType == "random" )
{
std::cout << "The simulator uses " << moves.size() << " different moves in a random" << std::endl;
std::cout << "move schedule with " << schedule->getNumberMovesPerIteration() << " moves per iteration" << std::endl;
}
else if ( scheduleType == "sequential" )
{
std::cout << "The simulator uses " << moves.size() << " different moves in a sequential" << std::endl;
std::cout << "move schedule with " << schedule->getNumberMovesPerIteration() << " moves per iteration" << std::endl;
}
// Initialize objects used in run
initializeChain();
initializeMonitors();
if ( generation == 0 )
{
// Monitor
startMonitors();
monitor(0);
}
// reset the counters for the move schedules
for (RbIterator<Move> it = moves.begin(); it != moves.end(); ++it)
{
it->resetCounters();
}
// Run the chain
for (int k=1; k<=kIterations; k++)
{
nextCycle(true);
// Monitor
monitor(generation);
}
}
/**
* Reset the sampler.
* We reset the counters of all moves.
*/
void HillClimber::reset( void )
{
double movesPerIteration = 0.0;
for (RbIterator<Move> it = moves.begin(); it != moves.end(); ++it)
{
it->resetCounters();
movesPerIteration += it->getUpdateWeight();
}
}