Split generate and thermalize

[Chrisgant]

The generate function of the HMC class is doing the job of two functions. For better readability it should be split up.

NSL/src/NSL/MarkovChain/HMC.tpp

Lines 57 to 142 in 3dd24fc

	template<Chain chain, NSL::Concept::isNumber Type>
	std::conditional_t<chain == Chain::AllStates, std::vector<NSL::MCMC::MarkovState<Type>>, NSL::MCMC::MarkovState<Type>>
	generate(const NSL::MCMC::MarkovState<Type> & state, NSL::size_t Nconf, NSL::size_t saveFrequency = 1, std::string baseNode = "markovChain"){
	// ensure that saveFrequency is at least 1.
	if (saveFrequency <= 0) {
	saveFrequency = 1;
	}
	std::size_t logFrequency = 1;
	if(Nconf >= 100){
	logFrequency = static_cast<NSL::size_t>( 0.01*Nconf );
	}
	if constexpr(chain == Chain::AllStates) {
	// prepare some memory to all states
	std::vector<NSL::MCMC::MarkovState<Type>> MC(Nconf);
	// Put the initial configuration in the 0th element
	// check if the file already contains configs and if we are allowed to overwrite them
	NSL::size_t nstart = 0;
	if (h5_.exist(baseNode)){
	auto [minConfigID, maxConfigID] = h5_.getMinMaxConfigs(baseNode);
	nstart = maxConfigID;
	}
	if (nstart > 0){
	// this reader looks for the most recent markov state and reads it into the state
	MC[nstart] = state;
	h5_.read(MC[nstart], baseNode);
	} else{
	MC[nstart] = state;
	NSL::Logger::info("HMC: Starting new Markov Chain");
	h5_.write(MC[nstart],fmt::format("{}/{}",baseNode,nstart));
	}
	double runningAcceptance = 0;
	// generate Nconf-1 configurations
	auto mc_time = NSL::Logger::start_profile("HMC");
	for(NSL::size_t n = nstart+1; n < Nconf; ++n){
	auto tmp = MC[n-1];
	// between each configuration generate saveFrequency which
	// are not used for measurements
	for(NSL::size_t m = 0; m < saveFrequency-1; ++m){
	tmp = this->generate_(tmp);
	}
	MC[n] = this->generate_(tmp);
	h5_.write(MC[n],fmt::format("{}/{}",baseNode,n));
	runningAcceptance += static_cast<double>(MC[n].accepted);
	// ToDo: have a proper hook being called here
	if (n % logFrequency == 0){
	NSL::Logger::info("HMC: {}/{}; Running Acceptence Rate: {:.6}%", n, Nconf, runningAcceptance*100./(n-nstart));
	NSL::Logger::elapsed_profile(mc_time);
	}
	}
	NSL::Logger::stop_profile(mc_time);
	// return the Markov Chain
	return MC;
	} else {
	// for Chain::LastState we only need a new state that becomes overwritten over and over again.
	NSL::MCMC::MarkovState<Type> newState = state;
	// generate Nconf-1 configurations
	// As none is returned we just multiply the number of configurations
	for(NSL::size_t n = 1; n < Nconf*saveFrequency; ++n){
	newState = this->generate_(newState);
	if (n % logFrequency == 0){
	NSL::Logger::info("HMC: {}/{}", n, Nconf);
	}
	}
	// return the Markov Chain
	return newState;
	}
	}