diff --git a/cpp_sources/ChemSyn.cpp b/cpp_sources/ChemSyn.cpp
index be78c2f..63b8b2f 100755
--- a/cpp_sources/ChemSyn.cpp
+++ b/cpp_sources/ChemSyn.cpp
@@ -7,12 +7,10 @@
 
 #include "ChemSyn.h"
 
-ChemSyn::ChemSyn(const double dt_input, const int step_tot_input, const char delim_input, const char indicator_input){
+ChemSyn::ChemSyn(const double dt_input, const int step_tot_input){
 	
 	dt = dt_input;
 	step_tot = step_tot_input;
-	delim = delim_input;
-	indicator = indicator_input;
 	
 	// Default parameters
 	V_ex = 0.0;     // Excitatory reversal, 0.0
@@ -508,6 +506,7 @@ void ChemSyn::sample_data(const int step_current){
 
 
 void ChemSyn::set_para(string para_str){
+	const char delim = ',';
 	if (!para_str.empty()){
 		istringstream para(para_str);
 		string para_name, para_value_str; 
@@ -532,9 +531,10 @@ void ChemSyn::set_para(string para_str){
 
 
 string ChemSyn::dump_para(){
+	const char delim = ',';
+	
 	stringstream dump;
 
-
 	dump << "pop_ind_pre" << delim << pop_ind_pre << delim << endl;
 	dump << "pop_ind_post" << delim << pop_ind_post << delim << endl;
 	dump << "syn_type" << delim << syn_type << delim << endl;
@@ -589,44 +589,6 @@ void ChemSyn::start_cov_record(const int time_start, const int time_end){
 }
 
 
-void ChemSyn::output_results(ofstream& output_file){
-	// SYND001 # synapse parameters
-	// count number of variables
-	stringstream dump_count;
-	string para_str = dump_para();
-	dump_count << para_str;
-	string str_temp;
-	int var_number = 0;
-	while(getline(dump_count,str_temp)){++var_number;} // count number of variables
-	output_file << indicator << " SYND001" << endl;
-	output_file << var_number << delim << endl;
-	output_file << para_str;
-	
-	
-	// SYND002 # sampled synapse data
-	if (!sample.neurons.empty()){
-		output_file << indicator << " SYND002" << endl;
-		output_file << pop_ind_pre << delim << pop_ind_post << delim << syn_type << delim << sample.neurons.size() << delim << endl;
-		write2file(output_file, sample.data); // 2D matrix
-	}
-
-	
-	// SYND003 # currents mean and std
-	if (stats.record){
-		output_file << indicator << " SYND003" << endl;
-		output_file << pop_ind_pre << delim << pop_ind_post << delim << syn_type << delim << endl;
-		write2file(output_file, stats.I_mean);
-		write2file(output_file, stats.I_std);
-	}
-	
-	// tmp data
-	if (tmp_data.size() != 0){
-		output_file << indicator << " SYND004" << endl;
-		output_file << pop_ind_pre << delim << pop_ind_post << delim << syn_type << delim << tmp_data.size() << delim << endl;
-		write2file(output_file, tmp_data);	
-	}
-}
-
 void ChemSyn::add_JH_Learning(vector<NeuroPop*> &NeuronPopArray,int isteps, double iscaleE, double iscaleI,double lrate_E, double lrateall_E,double lrate_I, double lrateall_I,int intau, double innoise,int type_pre,int type_post){
 	
 	jh_learn_syn.on=true; //indicates this learning is to be used
@@ -960,9 +922,6 @@ void ChemSyn::record_stats(int step_current){
 	}
 }
 
-
-#ifdef HDF5
-
 void ChemSyn::import_restart(H5File& file, int syn_ind){
 
 	string str;
@@ -1297,4 +1256,3 @@ void ChemSyn::output_results(H5File& file, int syn_ind){
 	}
 }
 
-#endif
diff --git a/cpp_sources/ChemSyn.h b/cpp_sources/ChemSyn.h
index 0c49bb4..f34984b 100755
--- a/cpp_sources/ChemSyn.h
+++ b/cpp_sources/ChemSyn.h
@@ -15,7 +15,7 @@ class ChemSyn
 {
 public:
 	ChemSyn(); /// default constructor
-	ChemSyn(const double dt, const int step_tot, const char delim, const char indicator); /// parameterised constructor
+	ChemSyn(const double dt, const int step_tot); /// parameterised constructor
 
 	void init(const int syn_type, const int pop_ind_pre, const int pop_ind_post, const int N_pre, const int N_post, const vector<int> &C_i, const vector<int> &C_j, const vector<double> &K_ij, const vector<double> &D_ij); /// initialise chemical synapses by reading already prepared connections
 
@@ -51,18 +51,15 @@ class ChemSyn
 	void old_pre_spikes_K_JH_Learn(vector<NeuroPop*> &NeuronPopArray);
 	void record_V_post_JH_Learn(vector<NeuroPop*> &NeuronPopArray);
 
-#ifdef HDF5
 	void import_restart(H5File& file, int syn_ind);
 	void export_restart(Group& Group, int syn_ind);
 	void output_results(H5File& file_HDF5, int syn_ind);
-#endif
+
 	const int & get_syn_type(); /// get synapse type
 	const int & get_pop_ind_pre(); /// get index of pre-synaptic population
 	const int & get_pop_ind_post(); /// get index of post-synaptic population
 private:
 
-	char delim; /// delimiter for input and output files, usually comma
-	char indicator; /// indicator for protocols, usually a single greater than operator
 	void init(); /// parameter-dependent initialisation
 	
 	string dump_para(); // dump all the parameter values used
diff --git a/cpp_sources/MyIO.cpp b/cpp_sources/MyIO.cpp
index ee44ebc..a7c6912 100644
--- a/cpp_sources/MyIO.cpp
+++ b/cpp_sources/MyIO.cpp
@@ -56,10 +56,6 @@ void write2file(ofstream& output_file, const vector<double>& v){
 }
 
 
-
-
-#ifdef HDF5
-
 /*--------------------------------------- HDF5 --------------------------------------------*/
 void write_scalar_HDF5(Group & group, unsigned int s, const string & v_name){
 	vector<unsigned int> v_tmp;
@@ -485,4 +481,3 @@ template int read_scalar_HDF5<int>(const H5File & file, const string & name);
 template unsigned int read_scalar_HDF5<unsigned int>(const H5File & file, const string & name);
 
 
-#endif
\ No newline at end of file
diff --git a/cpp_sources/MyIO.h b/cpp_sources/MyIO.h
index 07e9099..4b70096 100644
--- a/cpp_sources/MyIO.h
+++ b/cpp_sources/MyIO.h
@@ -5,49 +5,47 @@
 #include <iostream> // cout/cin, ofstream: Stream class to write on files, ifstream : Stream class to read from files, istringstream is for input, ostringstream for output
 #include <fstream> // fstream : Stream class to both read and write from / to files
 
-#ifdef HDF5
-	#include <H5Cpp.h>
-	#include <hdf5_hl.h>
-	#ifndef H5_NO_NAMESPACE
-	    using namespace H5;
-	#endif
+#include <H5Cpp.h>
+#include <hdf5_hl.h>
+#ifndef H5_NO_NAMESPACE
+    using namespace H5;
 #endif
+
 using namespace std;
 
 const char delim = ',';  /// Bad practice: this is hard-coded here!
 
-#ifdef HDF5
-	void write_vector_HDF5(Group & group, const vector<bool> & v, const string & v_name);
-	void write_vector_HDF5(Group & group, const vector<unsigned int> & v, const string & v_name);
-	void write_vector_HDF5(Group & group, const vector<int> & v, const string & v_name);
-	void write_vector_HDF5(Group & group, const vector<double> & v, const string & v_name);
-	void append_vector_to_matrix_HDF5(DataSet & dataset_tmp, const vector<double> & v, const int colNum);
-	void append_vector_to_matrix_HDF5(DataSet & dataset_tmp, const vector<int> & v, const int colNum);
-	void write_matrix_HDF5(Group & group, const vector< vector<double> > & m, const string & m_name);
-	void write_matrix_HDF5(Group & group, const vector< vector<int> > & m, const string & m_name);
-	void write_matrix_HDF5(Group & group, const vector< vector<bool> > & m, const string & m_name);
+void write_vector_HDF5(Group & group, const vector<bool> & v, const string & v_name);
+void write_vector_HDF5(Group & group, const vector<unsigned int> & v, const string & v_name);
+void write_vector_HDF5(Group & group, const vector<int> & v, const string & v_name);
+void write_vector_HDF5(Group & group, const vector<double> & v, const string & v_name);
+void append_vector_to_matrix_HDF5(DataSet & dataset_tmp, const vector<double> & v, const int colNum);
+void append_vector_to_matrix_HDF5(DataSet & dataset_tmp, const vector<int> & v, const int colNum);
+void write_matrix_HDF5(Group & group, const vector< vector<double> > & m, const string & m_name);
+void write_matrix_HDF5(Group & group, const vector< vector<int> > & m, const string & m_name);
+void write_matrix_HDF5(Group & group, const vector< vector<bool> > & m, const string & m_name);
 	
-	void write_string_HDF5(Group & group, const string & s, const string & s_name);
-	void write_scalar_HDF5(Group & group, unsigned int s, const string & v_name);
-	void write_scalar_HDF5(Group & group, int s, const string & v_name);
-	void write_scalar_HDF5(Group & group, double s, const string & v_name);
+void write_string_HDF5(Group & group, const string & s, const string & s_name);
+void write_scalar_HDF5(Group & group, unsigned int s, const string & v_name);
+void write_scalar_HDF5(Group & group, int s, const string & v_name);
+void write_scalar_HDF5(Group & group, double s, const string & v_name);
 	
-	void read_string_HDF5(const H5File & file, const string &  s_name,  string & s);
-	void read_matrix_HDF5(const H5File & file, const string & name, vector< vector<int> > & m_tmp);
-	void read_matrix_HDF5(const H5File & file, const string & name, vector< vector<bool> > & m_tmp);
-	void read_matrix_HDF5(const H5File & file, const string & name, vector< vector<double> > & m_tmp);
-	void read_vector_HDF5(const H5File & file, const string & name, vector<unsigned int> & v_tmp);
-	void read_vector_HDF5(const H5File & file, const string & name, vector<int> & v_tmp);
-	void read_vector_HDF5(const H5File & file, const string & name, vector<bool> & v_tmp);
-	void read_vector_HDF5(const H5File & file, const string & name, vector<double> & v_tmp);
-	bool dataset_exist_HDF5(const H5File & file, const string & name);
-	bool group_exist_HDF5(const H5File & file, const string & name);
-	bool group_exist_HDF5(const string & filename, const string & name);
-	template < typename Type > Type read_scalar_HDF5(const H5File & file, const string & name);
-#endif
-	void write2file(ofstream& output_file, const vector< vector<int> >& v); /// write integer matrix to output file
-	void write2file(ofstream& output_file, const vector< vector<double> >& v); /// write double matrix to output file
-	void write2file(ofstream& output_file, const vector<int>& v); /// write integer vector to output file
-	void write2file(ofstream& output_file, const vector<double>& v); /// write double vector to output file
+void read_string_HDF5(const H5File & file, const string &  s_name,  string & s);
+void read_matrix_HDF5(const H5File & file, const string & name, vector< vector<int> > & m_tmp);
+void read_matrix_HDF5(const H5File & file, const string & name, vector< vector<bool> > & m_tmp);
+void read_matrix_HDF5(const H5File & file, const string & name, vector< vector<double> > & m_tmp);
+void read_vector_HDF5(const H5File & file, const string & name, vector<unsigned int> & v_tmp);
+void read_vector_HDF5(const H5File & file, const string & name, vector<int> & v_tmp);
+void read_vector_HDF5(const H5File & file, const string & name, vector<bool> & v_tmp);
+void read_vector_HDF5(const H5File & file, const string & name, vector<double> & v_tmp);
+bool dataset_exist_HDF5(const H5File & file, const string & name);
+bool group_exist_HDF5(const H5File & file, const string & name);
+bool group_exist_HDF5(const string & filename, const string & name);
+template < typename Type > Type read_scalar_HDF5(const H5File & file, const string & name);
+
+void write2file(ofstream& output_file, const vector< vector<int> >& v); /// write integer matrix to output file
+void write2file(ofstream& output_file, const vector< vector<double> >& v); /// write double matrix to output file
+void write2file(ofstream& output_file, const vector<int>& v); /// write integer vector to output file
+void write2file(ofstream& output_file, const vector<double>& v); /// write double vector to output file
 
 #endif
\ No newline at end of file
diff --git a/cpp_sources/NeuroNet.cpp b/cpp_sources/NeuroNet.cpp
index da2804a..2280ecc 100755
--- a/cpp_sources/NeuroNet.cpp
+++ b/cpp_sources/NeuroNet.cpp
@@ -10,13 +10,11 @@
 
 using namespace std;
 
-NeuroNet::NeuroNet(vector<int> N_array_input, double dt_input, int step_tot_input, char delim_input, char indicator_input){
+NeuroNet::NeuroNet(vector<int> N_array_input, double dt_input, int step_tot_input){
 
 	N_array = N_array_input;
 	dt = dt_input;
 	step_tot = step_tot_input;
-	delim = delim_input;
-	indicator = indicator_input;
 	Num_pop = N_array.size();
 	runaway_killed = false;
 	step_killed = -1;
@@ -88,35 +86,11 @@ void NeuroNet::update(int step_current){
 
 }
 
-
-
-void NeuroNet::output_results(ofstream& output_file){
-
-	// write data
-	// cout << "Outputting results into text file..." << endl;
-	
-	// KILL002 # step at which runaway activity is killed
-	output_file << indicator << " KILL002" << endl;
-	output_file << step_killed << delim << endl;
-
-	// dump population data
-	for (int i = 0; i < Num_pop; i++){
-		NeuroPopArray[i]->output_results(output_file);
-	}
-
-	// dump synapse data
-	for (unsigned int i = 0; i < ChemSynArray.size(); i++){
-		ChemSynArray[i]->output_results(output_file);
-	}
-	
-}
-
-#ifdef HDF5
 void NeuroNet::import_restart(H5File & file,string out_filename){
 
 	Num_pop=read_scalar_HDF5<int>(file,string("/Net/Num_pop"));
 	for (unsigned int ind = 0; ind < N_array.size(); ++ind){
-		NeuroPopArray.push_back(new NeuroPop(ind, N_array[ind], dt, step_tot, delim, indicator));
+		NeuroPopArray.push_back(new NeuroPop(ind, N_array[ind], dt, step_tot));
 		cout << "\t Initialising neuron pop " << ind+1 << "..." << endl;
 
 		NeuroPopArray[ind]->import_restart(file,ind,out_filename);
@@ -126,7 +100,7 @@ void NeuroNet::import_restart(H5File & file,string out_filename){
 	int n_syns=read_scalar_HDF5<int>(file,syn_str+"n_syns");
 	for (int ind = 0; ind < n_syns; ++ind){
 
-		ChemSynArray.push_back(new ChemSyn(dt, step_tot, delim, indicator));
+		ChemSynArray.push_back(new ChemSyn(dt, step_tot));
 		// network.ChemSynArray.back()->init(type, i_pre, j_post, N_array[i_pre], N_array[j_post], I, J, K, D);
 
 		ChemSynArray[ind]->import_restart(file,ind);
@@ -178,6 +152,3 @@ void NeuroNet::output_results(H5File & file_HDF5){
 	}
 	
 }
-
-#endif
-
diff --git a/cpp_sources/NeuroNet.h b/cpp_sources/NeuroNet.h
index fd21f1b..419805c 100755
--- a/cpp_sources/NeuroNet.h
+++ b/cpp_sources/NeuroNet.h
@@ -10,7 +10,7 @@ using namespace std;
 class NeuroNet{
 public:
 	NeuroNet();
-	NeuroNet(vector<int> N_array, double dt, int step_tot, char delim, char indicator); // parameterised constructor for heterogeneous coupling
+	NeuroNet(vector<int> N_array, double dt, int step_tot); // parameterised constructor for heterogeneous coupling
 
 	vector<int> N_array; // number of neurons in each pupolation
 	double dt; // (ms)
@@ -24,18 +24,10 @@ class NeuroNet{
 	int step_killed; // initialised as -1
 	
 	void update(int step_current); // update the network to current time step, use "virtual" if want override by derived class
-
 	
-	char delim;
-	char indicator;
-	void output_results(ofstream& output_file);
-
-
-#ifdef HDF5
 	void import_restart(H5File & file, string out_filename);
 	void export_restart(H5File& file_HDF5, int restart_no);
 	void output_results(H5File& file_HDF5);
-#endif
 	
 
 
diff --git a/cpp_sources/NeuroPop.cpp b/cpp_sources/NeuroPop.cpp
index 1a95198..4b533c0 100755
--- a/cpp_sources/NeuroPop.cpp
+++ b/cpp_sources/NeuroPop.cpp
@@ -9,14 +9,12 @@
 #include "NeuroPop.h"
 #include <functional> // for bind(), plus
 
-NeuroPop::NeuroPop(const int pop_ind_input, const int N_input, const double dt_input, const int step_tot_input, const char delim_input, const char indicator_input)
+NeuroPop::NeuroPop(const int pop_ind_input, const int N_input, const double dt_input, const int step_tot_input)
 {
 	pop_ind = pop_ind_input;
 	N = N_input;
 	dt = dt_input;
 	step_tot = step_tot_input; // this parameter is designed to be self-adapting (step_killed), so should be any other stuff that relies on it!!
-	delim = delim_input;
-	indicator = indicator_input;
 
 	// Using consistant units: msec+mV+nF+miuS+nA
 	// Initialise default parameters
@@ -200,6 +198,7 @@ void NeuroPop::start_LFP_record(const vector <vector<double> >& LFP_neurons_inpu
 }
 
 void NeuroPop::set_para(string para_str) {
+	const char delim = ',';
 	if (!para_str.empty()) {
 		istringstream para(para_str);
 		string para_name, para_value_str;
@@ -427,10 +426,7 @@ void NeuroPop::update_V(const int step_current) {
 
 	// Data sampling, which must be done here!
 	// sample_data(step_current);  // this is deprecated due to poor memory performance
-#ifdef HDF5
 	output_sampled_data_real_time_HDF5(step_current);
-#endif
-	output_sampled_data_real_time(step_current);
 
 	// update menbrane potentials
 	double Vdot;
@@ -460,58 +456,6 @@ void NeuroPop::update_V(const int step_current) {
 }
 
 
-void NeuroPop::add_sampling_real_time(const vector<int>& sample_neurons_input, const vector<bool>& sample_type_input, const vector<bool>& sample_time_points_input, string sample_file_name_input) {
-	sample.file_type = 1;
-	sample.neurons = sample_neurons_input;
-	sample.type = sample_type_input;
-	sample.time_points = sample_time_points_input;
-
-	sample.file_name = sample_file_name_input.append(to_string(pop_ind)).append(".ygout_samp");
-	sample.file.open(sample.file_name);
-
-	sample.N_steps = 0;
-	for (int tt = 0; tt < step_tot; ++tt) {
-		if (sample.time_points[tt]) {sample.N_steps += 1;}
-	}
-	sample.N_neurons = sample.neurons.size();
-}
-
-
-
-
-void NeuroPop::output_sampled_data_real_time(const int step_current) {
-	if (!sample.neurons.empty() && step_current == 0 && sample.file_type == 1) {
-
-		sample.file << indicator << " POPD006" << endl;
-		sample.file << pop_ind << delim << sample.N_neurons << delim << sample.N_steps << delim << endl;
-		vector< string > data_types = { "V", "I_leak", "I_AMPA", "I_GABA", "I_NMDA", "I_GJ", "I_ext", "I_K" };
-		for (unsigned int tt = 0; tt < data_types.size(); ++tt) {
-			if (sample.type[tt]) {sample.file << data_types[tt] << delim; }
-		}
-		sample.file << endl;
-	}
-
-	if (!sample.neurons.empty() && sample.file_type == 1) {
-		if (sample.time_points[step_current]) { // push_back is amazing
-			for (int i = 0; i < sample.N_neurons; ++i) { // performance issue when sampling many neurons?
-				int ind_temp = sample.neurons[i];
-				if (sample.type[0]) {sample.file << V[ind_temp] << delim;}
-				if (sample.type[1]) {sample.file << I_leak[ind_temp] << delim;}
-				if (sample.type[2]) {sample.file << I_AMPA[ind_temp] << delim;}
-				if (sample.type[3]) {sample.file << I_GABA[ind_temp] << delim;}
-				if (sample.type[4]) {sample.file << I_NMDA[ind_temp] << delim;}
-				if (sample.type[5]) {sample.file << I_GJ[ind_temp] << delim;}
-				if (sample.type[6]) {sample.file << I_ext[ind_temp] << delim;}
-				if (sample.type[7]) {sample.file << I_K[ind_temp] << delim;}
-				sample.file << endl;
-			}
-		}
-	}
-
-}
-
-
-
 void NeuroPop::add_sampling(const vector<int>& sample_neurons_input, const vector<bool>& sample_type_input, const vector<bool>& sample_time_points_input) {
 	sample.neurons = sample_neurons_input;
 	sample.type = sample_type_input;
@@ -642,82 +586,6 @@ void NeuroPop::reset_Q() {
 }
 
 
-void NeuroPop::output_results(ofstream& output_file) {
-
-	// POPD001 # spike history of neuron population
-	output_file << indicator << " POPD001" << endl;
-	output_file << pop_ind << delim << endl;
-	write2file(output_file, spike_hist_tot);
-	write2file(output_file, num_spikes_pop);
-	write2file(output_file, num_ref_pop);
-
-	// POPD002 # neuron parameters in the population
-	stringstream dump_count;
-	string para_str = dump_para();
-	dump_count << para_str;
-	string str_temp;
-	int var_number = 0;
-	while (getline(dump_count, str_temp)) {++var_number;} // count number of variables
-	output_file << indicator << " POPD002" << endl;
-	output_file << pop_ind << delim << var_number << delim << endl;
-	output_file << para_str;
-
-	// POPD003 # membrane potential mean and std
-	if (stats.record) {
-		output_file << indicator << " POPD003" << endl;
-		output_file << pop_ind << delim << endl;
-		write2file(output_file, stats.V_mean);
-		write2file(output_file, stats.V_std);
-		write2file(output_file, stats.I_input_mean);
-		write2file(output_file, stats.I_input_std);
-	}
-
-	// POPD007 # local field potential
-	if (LFP.record) {
-		output_file << indicator << " POPD007" << endl;
-		output_file << pop_ind << delim << LFP.data.size() << delim << endl;
-		write2file(output_file, LFP.data);
-	}
-
-	// POPD005 # E-I ratio for each neuron
-	if (stats.record) {
-		output_file << indicator << " POPD005" << endl;
-		output_file << pop_ind << delim << endl;
-		write2file(output_file, stats.IE_ratio);
-	}
-
-	// SAMF001 # sampled data file name
-	if (!sample.file_name.empty()) {
-		output_file << indicator << " SAMF001" << endl;
-		output_file << sample.file_name << endl;
-	}
-
-
-	/* // This following output protocol is deprecated due to poor memeory performance
-	// POPD004 # sampled neuron data
-	if (!sample_neurons.empty()){
-		output_file << indicator << " POPD004" << endl;
-		output_file << pop_ind << delim << sample.neurons.size() << delim << endl;
-
-		vector< string > data_types = { "V", "I_leak", "I_AMPA", "I_GABA", "I_NMDA", "I_GJ", "I_ext", "I_K" };
-		for (unsigned int tt = 0; tt < data_types.size(); ++tt){
-			if (sample.type[tt] == true){output_file << data_types[tt] << delim;}
-		}
-		output_file << endl;
-
-
-		for (unsigned int c = 0; c < sample.type.size(); ++c){
-			if (!sample.data[c].empty()){
-				NeuroPop::write2file(output_file, sample.data[c]); // 2D matrix
-			}
-		}
-	}
-	*/
-
-}
-
-
-
 void NeuroPop::record_LFP() {
 	if (LFP.record) {
 		for (unsigned int ind = 0; ind < LFP.neurons.size(); ++ind) {
@@ -857,10 +725,6 @@ void Welford_online(const vector<double>& new_data, vector<double>& M, const int
 }
 
 
-
-
-#ifdef HDF5
-
 void NeuroPop::load_file_current_input(string fname) {
 	cout << "\t\tLoading currents from file... " << fname;
 	H5File file(  fname, H5F_ACC_RDONLY );
@@ -1373,5 +1237,3 @@ void NeuroPop::output_sampled_data_real_time_HDF5(const int step_current) {
 }
 
 
-#endif
-
diff --git a/cpp_sources/NeuroPop.h b/cpp_sources/NeuroPop.h
index b982e8f..236c1d4 100755
--- a/cpp_sources/NeuroPop.h
+++ b/cpp_sources/NeuroPop.h
@@ -30,16 +30,12 @@ using namespace std;
 class NeuroPop {
 public:
 	NeuroPop(); /// default constructor
-	NeuroPop(const int pop_ind, const int N_input, const double dt_input, const int step_tot, const char delim, const char indicator); /// parameterised constructor
+	NeuroPop(const int pop_ind, const int N_input, const double dt_input, const int step_tot); /// parameterised constructor
 
 	void init(); // initialise neurons, called by constructor after parameter assignment
 	void set_para(string para); /// set parameters if not using default ones
 	void set_seed(int seed); /// manually set RNG seed
 
-	void output_results(ofstream& output_file);
-
-
-
 	void recv_I(vector<double>& I_add, const int pop_ind_pre, const int syn_type);
 	const vector< int >& get_spikes_current();
 	const vector< double >& get_V();
@@ -64,9 +60,6 @@ class NeuroPop {
 	void set_gaussian_I_ext(const vector<double>& mean, const vector<double>& std);
 	void set_gaussian_g_ext(const vector<double>& mean, const vector<double>& std);
 
-	void add_sampling(const vector<int>& sample_neurons, const vector<bool>& sample_type, const vector<bool>& sample_time_points);
-	void add_sampling_real_time(const vector<int>& sample_neurons_input, const vector<bool>& sample_type_input, const vector<bool>& sample_time_points_input, string samp_file_name);
-
 	void load_file_spike_input(string fname);
 	void load_file_current_input(string fname);
 	void get_current_from_file();
@@ -84,12 +77,11 @@ class NeuroPop {
 	// However it is tolerable in development.
 	// Once the JH learning algorithm is published, consider fix it.
 
-#ifdef HDF5
 	void import_restart(H5File & file, int pop_ind, string out_filename);
 	void export_restart(Group & group);
 	void output_results(H5File& file_HDF5);
 	void add_sampling_real_time_HDF5(const vector<int>& sample_neurons_input, const vector<bool>& sample_type_input, const vector<bool>& sample_time_points_input, string samp_file_name);
-#endif
+	void add_sampling(const vector<int>& sample_neurons_input, const vector<bool>& sample_type_input, const vector<bool>& sample_time_points_input);
 	void init_runaway_killer(const double min_ms, const double Hz, const double Hz_ms); /// kill the simulation when runaway activity of the network is detected:
 	// mean number of refractory neurons over previous steps "runaway_steps" in any population exceeding "mean_num_ref"
 
@@ -100,14 +92,8 @@ class NeuroPop {
 private:
 	void generate_I_ext(const int step_current);
 	void record_stats(const int step_current);
-	void output_sampled_data_real_time(const int step_current);
-
-#ifdef HDF5
 	void output_sampled_data_real_time_HDF5(const int step_current);
-#endif
 	string dump_para(); /// dump all the parameter values used
-	char delim;
-	char indicator;
 	void sample_data(const int step_current);
 	void runaway_check(const int step_current);
 	void record_LFP();
@@ -231,14 +217,10 @@ class NeuroPop {
 		int file_type; /// 0 for no sample, 1 for text-based, 2 for hdf5-based
 		string
 		file_name; /// the file name for sampled time series
-		ofstream
-		file; /// the output file stream for sampled time series
-#ifdef HDF5
 		H5File *
 		file_HDF5;
 		DataSet
 		V_dataset, I_leak_dataset, I_AMPA_dataset, I_GABA_dataset, I_NMDA_dataset, I_GJ_dataset, I_ext_dataset, I_K_dataset;
-#endif
 		int
 		ctr = 0; /// counter that counts how many steps have been sampled
 		vector<int>
diff --git a/cpp_sources/SimuInterface.cpp b/cpp_sources/SimuInterface.cpp
index 9c1e658..c21424c 100755
--- a/cpp_sources/SimuInterface.cpp
+++ b/cpp_sources/SimuInterface.cpp
@@ -8,677 +8,9 @@ using namespace std;
 SimuInterface::SimuInterface(){
 	// define default output data file format
 	output_suffix = ".ygout"; // filename extension
-	delim = ',';
-	indicator = '>';
-	commentor = '#';
 	
 }
 
-bool SimuInterface::import(string in_filename_input){
-	// read main input file
-	in_filename = in_filename_input;
-	inputfile.open(in_filename, ifstream::in);
-	if (inputfile){
-		cout << "------------------------------------------------------------" << endl;
-		cout << "Importing " << in_filename << "..." << endl;
-	}
-	else {
-		cout << "Error: cannot open file " << in_filename << endl;
-		return 0;
-	}
-	
-	// claim variables to be assigned
-	int Num_pop;
-	double dt;
-	int step_tot;
-	vector<int> N_array;
-	// temporary data storage
-	vector<string> pop_para; // parameters of neuron popluation
-	string syn_para; // parameters of synapses
-	vector< vector<double> > ext_spike_settings; // (int pop_ind, int type_ext, double K_ext, int Num_ext, double rate_ext)
-	vector< vector<double> > rate_ext_t; // vector<duoble> rate_ext(t)
-	vector< vector<bool> > ext_spike_neurons; //
-	
-	vector<int> ext_current_settings_pop_ind; // (int pop_ind)
-	vector< vector<double> > ext_current_settings; // (vector<double> mean, vector<double> std)
-	vector<int> ext_conductance_settings_pop_ind; // (int pop_ind)
-	vector< vector<double> > ext_conductance_settings; // (vector<double> mean, vector<double> std)
-	
-	vector<double> init_condition_settings_depre; // (double p_fire)
-	vector< vector<double> >  init_condition_settings; // (double r_V0, double p_fire)
-	
-	vector<int> neuron_sample_pop_ind; //
-	vector< vector<int> > neuron_sample_neurons; //
-	vector< vector<bool> > neuron_sample_type; //
-	vector< vector<bool> > neuron_sample_time_points; // the length of time vector
-	
-	vector< vector<int> > syn_sample_pop_ind; //
-	vector< vector<int> > syn_sample_neurons; //
-	vector< vector<bool> > syn_sample_time_points; // the length of time vector
-	
-	vector<int> neuron_stats_setting;
-	vector< vector<int> > syn_stats_setting;
-	vector< vector<int> > STD_setting;
-	vector< vector<int> > inh_STDP_setting;
-	vector<int> spike_freq_adpt_setting; //
-	
-	vector<int> LFP_record_pop_ind; //
-	vector< vector < vector<double> > > LFP_record_setting; //
-	
-	string syn_filename; // name of file that defines synaptic connection
-	vector< vector<double> > runaway_killer_setting; // [pop_ind, min_ms, runaway_Hz, Hz_ms]
-	
-	vector< vector<int> > step_perturb_setting; // [pop_ind step_perturb]
-
-	int synapse_model_choice = 0;
-	
-	// read data
-	string line_str, entry_str; // temporary container for the entire while loop
-	size_t found;
-	while (getline(inputfile, line_str)){
-		istringstream line_ss(line_str); // local variable: lifetime is only a signle loop (scope is within "{}")! reusing it by ".str()" may cause fatal error because the internal error flag remains the same. Everytime using "while(getline(...)){}" will change internal error flag!
-		if (line_str.empty()){continue;}
-		else if (line_str.front() == commentor){continue;}
-		else if (line_str.front() == indicator){// read data-info line
-
-			// read number of neurons in each population
-			found = line_str.find("INIT001");
-			if (found != string::npos){// if found match
-				cout << "\t Reading number of neurons in each population..." << endl;
-				read_next_line_as_vector(N_array);
-
-				// Infer number of populations
-				Num_pop = N_array.size();
-				pop_para.resize(Num_pop); // ??????
-				continue; // move to next line
-			}
-
-
-			// read time step length and total steps
-			found = line_str.find("INIT002");
-			if (found != string::npos){// if found match
-				cout << "\t Reading time step length and total steps..." << endl;
-				getline(inputfile, line_str);istringstream line_ss(line_str);// Read next line
-
-				dt = read_next_entry<double>(line_ss);
-				step_tot = read_next_entry<int>(line_ss);
-				continue; // move to next line
-			}
-
-
-
-			// Random initial distributions for membrane potentials (deprecated)
-			found = line_str.find("INIT003");
-			if (found != string::npos){// if found match
-				cout << "\t Reading random initial distributions for membrane potentials..." << endl;
-				read_next_line_as_vector(init_condition_settings_depre); // p_fire
-				continue; // move to next line
-			}
-			
-			// read external current setting
-			found = line_str.find("INIT004");
-			if (found != string::npos){// if found match
-				cout << "\t Reading external current settings..." << endl;
-				getline(inputfile, line_str);istringstream line_ss(line_str);// Read next line 
-				ext_current_settings_pop_ind.push_back(read_next_entry<int>(line_ss));
-				ext_current_settings.resize(ext_current_settings.size()+1);
-				read_next_line_as_vector(ext_current_settings.back()); // vector<double> mean
-				ext_current_settings.resize(ext_current_settings.size()+1);
-				read_next_line_as_vector(ext_current_settings.back()); // vector<double> std
-				continue; // move to next line
-			}
-
-
-
-			// read external spike setting
-			found = line_str.find("INIT005");
-			if (found != string::npos){// if found match
-				cout << "\t Reading external spike settings..." << endl;
-				// [pop_ind,type_ext,K_ext,Num_ext]
-				ext_spike_settings.resize(ext_spike_settings.size()+1);
-				read_next_line_as_vector(ext_spike_settings.back());
-				//	ext_spike_neurons
-				ext_spike_neurons.resize(ext_spike_neurons.size()+1);
-				read_next_line_as_vector(ext_spike_neurons.back());
-				// [rate_ext_t]
-				rate_ext_t.resize(rate_ext_t.size()+1);
-				read_next_line_as_vector(rate_ext_t.back());
-				continue; // move to next line
-			}
-
-			// read perturbation setting
-			found = line_str.find("INIT007");
-			if (found != string::npos){// if found match
-				cout << "\t Reading perturbation settings..." << endl;
-				// [pop_ind, step_perturb]
-				step_perturb_setting.resize(step_perturb_setting.size()+1);
-				read_next_line_as_vector(step_perturb_setting.back());
-				continue; // move to next line
-			}
-
-			found = line_str.find("INIT008");
-			if (found != string::npos){// if found match
-				cout << "\t Reading short term depression settings..." << endl;
-				// [pop_ind_pre, pop_ind_post, STD_on_step]
-				STD_setting.resize(STD_setting.size()+1);
-				read_next_line_as_vector(STD_setting.back());
-				continue; // move to next line
-			}
-			
-			found = line_str.find("INIT009");
-			if (found != string::npos){// if found match
-				cout << "\t Reading inhibitory STDP settings..." << endl;
-				// [pop_ind_pre, pop_ind_post, inh_STDP_on_step]
-				inh_STDP_setting.resize(inh_STDP_setting.size()+1);
-				read_next_line_as_vector(inh_STDP_setting.back());
-				continue; // move to next line
-			}
-			
-			found = line_str.find("INIT010");
-			if (found != string::npos){// if found match
-				cout << "\t Reading spike-frequency adaptation settings..." << endl;
-				// [pop_ind]
-				getline(inputfile, line_str);istringstream line_ss(line_str);// Read next line 
-				spike_freq_adpt_setting.push_back(read_next_entry<int>(line_ss));			
-				continue; // move to next line
-			}
-			
-			// Random initial distributions for membrane potentials and initial firing probabilities
-			found = line_str.find("INIT011");
-			if (found != string::npos){// if found match
-				cout << "\t Reading random initial distributions for membrane potentials and initial firing probabilities..." << endl;
-				init_condition_settings.resize(2);
-				read_next_line_as_vector(init_condition_settings[0]); // r_V0
-				read_next_line_as_vector(init_condition_settings[1]); // p_fire
-				continue; // move to next line
-			}
-			
-			// read external conductance setting
-			found = line_str.find("INIT012");
-			if (found != string::npos){// if found match
-				cout << "\t Reading external conductance settings..." << endl;
-				getline(inputfile, line_str);istringstream line_ss(line_str);// Read next line 
-				ext_conductance_settings_pop_ind.push_back(read_next_entry<int>(line_ss));
-				ext_conductance_settings.resize(ext_conductance_settings.size()+1);
-				read_next_line_as_vector(ext_conductance_settings.back()); // vector<double> mean
-				ext_conductance_settings.resize(ext_conductance_settings.size()+1);
-				read_next_line_as_vector(ext_conductance_settings.back()); // vector<double> std
-				continue; // move to next line
-			}
-			
-			// read synapse model choice
-			found = line_str.find("INIT013");
-			if (found != string::npos){// if found match
-				cout << "\t Reading synapse model choice..." << endl;
-				getline(inputfile, line_str);istringstream line_ss(line_str);// Read next line
-				synapse_model_choice = read_next_entry<int>(line_ss); 
-				continue; // move to next line
-			}
-			
-			// read neuron population parameter setting
-			found = line_str.find("PARA001");
-			if (found != string::npos){// if found match
-				cout << "\t Reading non-default neuron population parameters..." << endl;
-				getline(inputfile, line_str);istringstream line_ss(line_str);// Read next line
-				// pop_ind and number of parameters
-				int pop_ind = read_next_entry<int>(line_ss); 
-				int num_para = read_next_entry<int>(line_ss);
-				// store parameter settings
-				for (int c = 0; c < num_para; ++c){
-					getline(inputfile, line_str); // read next line
-					pop_para[pop_ind] += line_str; // append (+=)
-				}
-				continue; // move to next line
-			}
-
-			// read synapse parameter setting
-			found = line_str.find("PARA002");
-			if (found != string::npos){// if found match
-				cout << "\t Reading non-default synapse parameters..." << endl;
-				getline(inputfile, line_str);istringstream line_ss(line_str);// Read next line
-				// number of parameters
-				int num_para = read_next_entry<int>(line_ss);
-				// store parameter settings
-				for (int c = 0; c < num_para; ++c){
-					getline(inputfile, line_str); // read next line
-					syn_para += line_str; // append (+=)
-				}
-				continue; // move to next line
-			}
-
-
-
-			// read runaway killer setting
-			found = line_str.find("KILL001");
-			if (found != string::npos){
-				cout << "\t Reading runaway killer setting..." << endl;
-				// double pop_ind, min_ms, double Hz, double Hz_ms
-				runaway_killer_setting.resize(runaway_killer_setting.size()+1);
-				read_next_line_as_vector(runaway_killer_setting.back());
-				continue;
-			}
-
-
-
-			// read neuron data sampling setting
-			found = line_str.find("SAMP001");
-			if (found != string::npos){// if found match
-				cout << "\t Reading neuron data sampling settings..." << endl;
-				getline(inputfile, line_str);istringstream line_ss(line_str);// Read next line
-				// int pop_ind;
-				neuron_sample_pop_ind.push_back(read_next_entry<int>(line_ss));
-				// sample_type
-				neuron_sample_type.resize(neuron_sample_type.size()+1);
-				read_next_line_as_vector(neuron_sample_type.back());
-				// sample_neurons
-				neuron_sample_neurons.resize(neuron_sample_neurons.size()+1);
-				read_next_line_as_vector(neuron_sample_neurons.back());
-				// sample_t_ind
-				neuron_sample_time_points.resize(neuron_sample_time_points.size()+1);
-				read_next_line_as_vector(neuron_sample_time_points.back());
-				continue; // move to next line
-			}
-
-			// read synapase data sampling setting
-			found = line_str.find("SAMP002");
-			if (found != string::npos){// if found match
-				cout << "\t Reading synapse data sampling settings..." << endl;
-				// pop indices
-				syn_sample_pop_ind.resize(syn_sample_pop_ind.size()+1);
-				read_next_line_as_vector(syn_sample_pop_ind.back());
-				// sample_neurons
-				syn_sample_neurons.resize(syn_sample_neurons.size()+1);
-				read_next_line_as_vector(syn_sample_neurons.back());
-				// sample_t_ind
-				syn_sample_time_points.resize(syn_sample_time_points.size()+1);
-				read_next_line_as_vector(syn_sample_time_points.back());
-				continue; // move to next line
-			}
-			
-			// neuron_stats_record
-			found = line_str.find("SAMP003");
-			if (found != string::npos){// if found match
-				cout << "\t Reading neuron stats record settings..." << endl;
-				getline(inputfile, line_str);istringstream line_ss(line_str);// Read next line
-				// int pop_ind;
-				neuron_stats_setting.push_back(read_next_entry<int>(line_ss));
-				continue; // move to next line
-			}
-			
-			
-			// syn_stats_record
-			found = line_str.find("SAMP004");
-			if (found != string::npos){// if found match
-				cout << "\t Reading synaptic stats record settings..." << endl;
-				syn_stats_setting.resize(syn_stats_setting.size()+1);
-				read_next_line_as_vector(syn_stats_setting.back());
-				continue; // move to next line
-			}
-			
-			// LFP record
-			found = line_str.find("SAMP005");
-			if (found != string::npos){// if found match
-				cout << "\t Reading LFP record settings..." << endl;
-				getline(inputfile, line_str);istringstream line_ss(line_str);// Read next line
-				// int pop_ind, sample_number;
-				LFP_record_pop_ind.push_back(read_next_entry<int>(line_ss));
-				int n = read_next_entry<int>(line_ss);
-				LFP_record_setting.resize(LFP_record_setting.size()+1);
-				for (int ind = 0; ind < n; ++ind){
-					LFP_record_setting.back().resize(LFP_record_setting.back().size()+1);
-					read_next_line_as_vector(LFP_record_setting.back().back());
-				}
-				continue; // move to next line
-			}
-			
-
-			// read non-default synapse definition file name
-			found = line_str.find("SYNF001");
-			if (found != string::npos){
-				cout << "\t Reading non-default synapse definition file name..." << endl;
-				getline(inputfile, syn_filename); // Read next line
-				cout << "\t\t non-default synapse definition: " << syn_filename << endl;
-				continue;
-			}
-
-			else{
-				cout << "Unrecognized command sequence: " << line_str << endl;
-			}
-
-		} //read data-info line	
-
-	} // while
-	inputfile.close();
-	inputfile.clear();
-
-	// read synapse definition input file
-	if (syn_filename.empty()){ // default file name
-		syn_filename = in_filename;
-		syn_filename.append("_syn"); // .ygin_syn
-	}
-	inputfile.open(syn_filename, ifstream::in); // close, clear and then open: reusing is a bad practice?
-	if (inputfile){}
-	else {
-		cout << "Error: cannot open syn file " << syn_filename << endl;
-		return 0;
-	}
-	
-	// temporary data storage
-	vector< vector<int> > I_temp, J_temp; //for chemical synapses
-	vector< vector<double> > K_temp, D_temp; //for chemical synapses
-	vector< vector<int> > IJKD_chem_info; // {Type(0:AMPA/1:GABAa/2:NMDA),Pre_pop_ind(0/1/...),Post_pop_ind(0/1/...)}
-	
-	// read data
-	while (getline(inputfile, line_str)){
-		istringstream line_ss(line_str);
-		if (line_str.empty()){continue;}
-		else if (line_str.front() == commentor){continue;}
-		else if (line_str.front() == indicator){// read data-info line
-			
-			// read connection data: [I;J;K;D] (chemical)
-			found = line_str.find("INIT006");
-			if (found != string::npos){// if found match
-				cout << "\t Reading chemical connection..." << endl;
-				// [type, pre_pop_ind, post_pop_ind]
-				IJKD_chem_info.resize(IJKD_chem_info.size()+1);
-				read_next_line_as_vector(IJKD_chem_info.back());
-				// I_temp
-				I_temp.resize(I_temp.size()+1);
-				read_next_line_as_vector(I_temp.back());
-				// J_temp
-				J_temp.resize(J_temp.size()+1);
-				read_next_line_as_vector(J_temp.back());
-				// K_temp
-				K_temp.resize(K_temp.size()+1);
-				read_next_line_as_vector(K_temp.back());
-				// D_temp
-				D_temp.resize(D_temp.size()+1);		
-				read_next_line_as_vector(D_temp.back());
-
-				continue; // move to next line
-			}
-		}//read data-info line	
-
-		
-	} // while
-
-	inputfile.close();
-	inputfile.clear();
-
-	out_filename = gen_out_filename();
-
-
-	// build NeuroNet based on data imported
-	network = NeuroNet(N_array, dt, step_tot, delim, indicator);
-	cout << "\t Network created." << endl;
-	cout << "\t Initialising neuron populations...";
-	for (unsigned int ind = 0; ind < N_array.size(); ++ind){
-		network.NeuroPopArray.push_back(new NeuroPop(ind, N_array[ind], network.dt, network.step_tot, delim, indicator));
-		network.NeuroPopArray.back()->set_para(pop_para[ind]);
-		cout << ind+1 << "...";
-	}
-	cout << "done." << endl;
-
-	// chemical connections
-	if (I_temp.size() != 0){
-		cout << "\t Initialising chemical synapses... ";
-		for (unsigned int ind = 0; ind < I_temp.size(); ++ind){
-			int type = IJKD_chem_info[ind][0];
-			int i_pre = IJKD_chem_info[ind][1];
-			int j_post = IJKD_chem_info[ind][2];
-			network.ChemSynArray.push_back(new ChemSyn(network.dt, network.step_tot, delim, indicator));
-			network.ChemSynArray.back()->init(type, i_pre, j_post, network.N_array[i_pre], network.N_array[j_post], I_temp[ind], J_temp[ind], K_temp[ind], D_temp[ind]);
-			network.ChemSynArray.back()->set_para(syn_para);
-			if (synapse_model_choice != 0){
-				network.ChemSynArray.back()->set_synapse_model(synapse_model_choice);
-			}
-			cout << ind+1 << "...";
-		}
-		cout << "done." << endl;
-	}
-
-	// external spike setting (int pop_ind, int type_ext, double K_ext, int Num_ext, 
-	// vector<double> rate_ext_t, int ia, int ib)
-	if (ext_spike_settings.size() != 0){
-		cout << "\t External spike settings...";
-		for (unsigned int ind = 0; ind < ext_spike_settings.size(); ++ind){
-			int j_post = int(ext_spike_settings[ind][0]);
-			int type_ext = int(ext_spike_settings[ind][1]);
-			double K_ext = ext_spike_settings[ind][2];
-			int Num_ext = int(ext_spike_settings[ind][3]);
-			network.ChemSynArray.push_back(new ChemSyn(network.dt, network.step_tot, delim, indicator));
-			network.ChemSynArray.back()->init(type_ext, j_post, network.N_array[j_post], K_ext, Num_ext, rate_ext_t[ind], ext_spike_neurons[ind]);
-			network.ChemSynArray.back()->set_para(syn_para);
-			cout << ind+1 << "...";
-		}
-		cout << "done." << endl;
-	}
-
-	// external current setting
-	if (ext_current_settings_pop_ind.size() != 0){
-		cout << "\t External current settings...";
-		for (unsigned int ind = 0; ind < ext_current_settings_pop_ind.size(); ++ind){
-			int pop_ind = ext_current_settings_pop_ind[ind];
-			vector<double> mean = ext_current_settings[ ind*2 ];
-			vector<double> std = ext_current_settings[ ind*2+1 ];
-			network.NeuroPopArray[pop_ind]->set_gaussian_I_ext(mean, std);
-			cout << ind+1 << "...";
-		}
-		cout << "done." << endl;
-	}
-
-	// external conductance setting
-	if (ext_conductance_settings_pop_ind.size() != 0){
-		cout << "\t External conductance settings...";
-		for (unsigned int ind = 0; ind < ext_conductance_settings_pop_ind.size(); ++ind){
-			int pop_ind = ext_conductance_settings_pop_ind[ind];
-			vector<double> mean = ext_conductance_settings[ ind*2 ];
-			vector<double> std = ext_conductance_settings[ ind*2+1 ];
-			network.NeuroPopArray[pop_ind]->set_gaussian_g_ext(mean, std);
-			cout << ind+1 << "...";
-		}
-		cout << "done." << endl;
-	}
-	
-	// random initial condition settings (double p_fire)
-	if (init_condition_settings_depre.size() != 0){
-		cout << "\t Random initial condition settings...";
-		for (unsigned int pop_ind = 0; pop_ind < init_condition_settings_depre.size(); ++pop_ind){
-			double p_fire = init_condition_settings_depre[pop_ind];
-			network.NeuroPopArray[pop_ind]->random_V(p_fire);
-			cout << pop_ind+1 << "...";
-		}
-		cout << "done." << endl;
-	}
-	
-	// random initial condition settings (double r_V0, double p_fire)
-	if (init_condition_settings.size() != 0){
-		cout << "\t Random initial condition settings...";
-		for (unsigned int pop_ind = 0; pop_ind < init_condition_settings.size(); ++pop_ind){
-			double r_V0 = init_condition_settings[0][pop_ind];
-			double p_fire = init_condition_settings[1][pop_ind];
-			network.NeuroPopArray[pop_ind]->set_init_condition(r_V0, p_fire);
-			cout << pop_ind+1 << "...";
-		}
-		cout << "done." << endl;
-	}
-	
-	
-	// perturbation setting
-	if (step_perturb_setting.size() != 0){
-		cout << "\t Perturbation settings...";
-		for (unsigned int i = 0; i < step_perturb_setting.size(); ++i){
-			int pop_ind = step_perturb_setting[i][0];
-			int step_perturb = step_perturb_setting[i][1];
-			network.NeuroPopArray[pop_ind]->add_perturbation(step_perturb);
-			cout << pop_ind+1 << "...";
-		}
-		cout << "done." << endl;
-	}
-	
-	
-	
-	if (STD_setting.size() != 0){
-		cout << "\t Short-term depression settings...";
-		for (unsigned int i = 0; i < STD_setting.size(); ++i){
-			int pop_ind_pre = STD_setting[i][0];
-			int pop_ind_post = STD_setting[i][1];
-			int STD_on_step = STD_setting[i][2];
-
-			int syn_match = false;
-			for (unsigned int s = 0; s < network.ChemSynArray.size(); ++s){
-				if (network.ChemSynArray[s]->get_pop_ind_pre() == pop_ind_pre &&
-				network.ChemSynArray[s]->get_pop_ind_post() == pop_ind_post){ // find the right synapse object
-					network.ChemSynArray[s]->add_short_term_depression(STD_on_step);
-					cout << i+1 << "...";
-					syn_match = true;
-				}
-			}
-			if (!syn_match){
-				cout << "(no match found!)...";
-			}
-		}
-		cout << "done." << endl;
-	}
-	
-	if (inh_STDP_setting.size() != 0){
-		cout << "\t Inhibitory STDP settings...";
-		
-		for (unsigned int i = 0; i < inh_STDP_setting.size(); ++i){
-			int pop_ind_pre = inh_STDP_setting[i][0];
-			int pop_ind_post = inh_STDP_setting[i][1];
-			int inh_STDP_on_step = inh_STDP_setting[i][2];
-
-			int syn_match = false;
-			for (unsigned int s = 0; s < network.ChemSynArray.size(); ++s){
-				if (network.ChemSynArray[s]->get_pop_ind_pre() == pop_ind_pre &&
-				network.ChemSynArray[s]->get_pop_ind_post() == pop_ind_post){ // find the right synapse object
-					network.ChemSynArray[s]->add_inh_STDP(inh_STDP_on_step);
-					cout << i+1 << "...";
-					syn_match = true;
-				}
-			}
-			if (!syn_match){
-				cout << "(no match found!)...";
-			}
-		}
-		cout << "done." << endl;
-	}
-	
-	if (spike_freq_adpt_setting.size() != 0){
-		cout << "\t Spike-frequency adaptation settings...";
-		for (unsigned int i = 0; i < spike_freq_adpt_setting.size(); ++i){
-			int pop_ind = spike_freq_adpt_setting[i];
-			network.NeuroPopArray[pop_ind]->add_spike_freq_adpt();
-			cout << pop_ind+1 << "...";
-		}
-		cout << "done." << endl;
-	}
-	
-	// neuron data sampling settings
-	if (neuron_sample_pop_ind.size() != 0){
-		cout << "\t Neuron data sampling settings...";
-		for (unsigned int ind = 0; ind < neuron_sample_pop_ind.size(); ++ind){
-			int pop_ind = neuron_sample_pop_ind[ind];
-			network.NeuroPopArray[pop_ind]->add_sampling_real_time(neuron_sample_neurons[ind], neuron_sample_type[ind], neuron_sample_time_points[ind], out_filename);
-			cout << ind+1 << "...";
-		}
-		cout << "done." << endl;
-	}	
-	
-	// neuron V mean std record settings
-	if (neuron_stats_setting.size() != 0){
-		cout << "\t Neuron stats record settings...";
-		for (unsigned int ind = 0; ind < neuron_stats_setting.size(); ++ind){
-			int pop_ind = neuron_stats_setting[ind];
-			network.NeuroPopArray[pop_ind]->start_stats_record();
-			cout << ind+1 << "...";
-		}
-		cout << "done." << endl;
-	}	
-	
-	// LFP record settings
-	if (LFP_record_pop_ind.size() != 0){
-		cout << "\t LFP record settings...";
-		for (unsigned int ind = 0; ind < LFP_record_pop_ind.size(); ++ind){
-			int pop_ind = LFP_record_pop_ind[ind];
-			network.NeuroPopArray[pop_ind]->start_LFP_record(LFP_record_setting[ind]);
-			cout << ind+1 << "...";
-		}
-		cout << "done." << endl;
-	}	
-	
-	// syn data sampling settings
-	if (syn_sample_pop_ind.size() != 0){
-		cout << "\t Synapse data sampling settings...";
-		for (unsigned int ind = 0; ind < syn_sample_pop_ind.size(); ++ind){
-			
-			int pop_ind_pre = syn_sample_pop_ind[ind][0];
-			int pop_ind_post = syn_sample_pop_ind[ind][1];
-			int syn_type = syn_sample_pop_ind[ind][2];
-			
-			int syn_sample_match = false;
-			for (unsigned int s = 0; s < network.ChemSynArray.size(); ++s){
-				if (network.ChemSynArray[s]->get_pop_ind_pre() == pop_ind_pre &&
-					network.ChemSynArray[s]->get_pop_ind_post() == pop_ind_post &&
-				network.ChemSynArray[s]->get_syn_type() == syn_type){ // find the right synapse object
-					network.ChemSynArray[s]->add_sampling(syn_sample_neurons[ind], syn_sample_time_points[ind]);
-					cout << ind+1 << "...";
-					syn_sample_match = true;
-				}
-			}
-			if (!syn_sample_match){
-				cout << "(no match found!)...";
-			}
-		}
-		cout << "done." << endl;
-	}	
-
-
-
-	// syn I mean std record settings
-	if (syn_stats_setting.size() != 0){
-		cout << "\t Synapse stats record settings...";
-		for (unsigned int ind = 0; ind < syn_stats_setting.size(); ++ind){
-			
-			int pop_ind_pre = syn_stats_setting[ind][0];
-			int pop_ind_post = syn_stats_setting[ind][1];
-			int syn_type = syn_stats_setting[ind][2];
-			
-			int syn_I_match = false;
-			for (unsigned int s = 0; s < network.ChemSynArray.size(); ++s){
-				if (network.ChemSynArray[s]->get_pop_ind_pre() == pop_ind_pre &&
-					network.ChemSynArray[s]->get_pop_ind_post() == pop_ind_post &&
-				network.ChemSynArray[s]->get_syn_type() == syn_type){ // find the right synapse object
-					network.ChemSynArray[s]->start_stats_record();
-					cout << ind+1 << "...";
-					syn_I_match = true;
-				}
-			}
-			if (!syn_I_match){
-				cout << "(no match found!)...";
-			}
-		}
-		cout << "done." << endl;
-	}	
-	
-	// initialise runaway-killer
-	if (runaway_killer_setting.size() != 0){
-		cout << "\t Runaway killer licensing for pop...";
-		for (unsigned int ind = 0; ind < runaway_killer_setting.size(); ++ind){
-			int pop_ind = int(runaway_killer_setting[ind][0]);
-			network.NeuroPopArray[pop_ind]->init_runaway_killer(runaway_killer_setting[ind][1], runaway_killer_setting[ind][2], runaway_killer_setting[ind][3]);
-			cout << pop_ind+1 << "...";
-		}
-		cout << "done." << endl;
-		cout << "\t \t No women, no kids." << endl;
-	}
-
-
-	cout << "Importing done." << endl;
-	return 1;
-}
-
 void SimuInterface::simulate(){
 	clock_t begin = clock();
 	  
@@ -712,40 +44,10 @@ void SimuInterface::simulate(){
 	cout << "Simulation done." << endl;
 
 	// output results into HDF5 file
-#ifdef HDF5
-	if(in_filename.substr(in_filename.find_last_of(".") + 1) == "h5") 
-	{
-		export_restart_HDF5();
-		output_results_HDF5();
-	} 
-	else if (in_filename.substr(in_filename.find_last_of(".") + 1) == "ygin")
-	{
-		output_results();
-	}
-#else
-	// output results into text file
-	output_results();
-#endif
-	
-}
-
-void SimuInterface::output_results(){
-	// output results into text file
-	ofstream output_file;
-	cout << "Creating text output file...";
-	output_file.open(out_filename.append(output_suffix));
-	network.output_results(output_file);
-	// attach input file (.ygin) to the output file for data completeness
- 	ifstream in_file_attach( in_filename );
-    output_file << in_file_attach.rdbuf();
+	export_restart_HDF5();
+	output_results_HDF5();
 
-	cout << "done." << endl;
-	cout << "Data file name is: " << endl;
-	cout << "	" << out_filename << endl;
-	cout << "------------------------------------------------------------" << endl;
-	// Write data file name to stdout and use "grep ygout" to extract it!
 	
-		
 }
 
 string SimuInterface::gen_out_filename(){
@@ -764,37 +66,6 @@ string SimuInterface::gen_out_filename(){
 	return convert_temp.str(); // set 'Result' to the contents of the stream
 }
 
-
-template < typename Type > Type SimuInterface::read_next_entry(istringstream &line_ss){
-	string entry_str;
-	Type entry;
-	getline(line_ss, entry_str, delim);
-	if (entry_str.empty()){
-		cout << "ERROR: SimuInterface::read_next_entry: empty content!" << endl;
-	}
-	stringstream(entry_str) >> entry;
-	return entry;
-}
-
-template < typename Type, typename A > void SimuInterface::read_next_line_as_vector(vector<Type, A> &vec){
-	
-	string line_str, entry_str;
-	Type entry;
-	getline(inputfile, line_str); istringstream line_ss(line_str); // read next line
-	if (line_str.empty()){
-		cout << "ERROR: SimuInterface::read_next_line_as_vector: empty string!" << endl;
-	}
-	while (getline(line_ss, entry_str, delim)){
-		stringstream(entry_str) >> entry;
-		vec.push_back(entry);
-	}
-
-}
-
-
-
-
-#ifdef HDF5
 bool SimuInterface::import_restart_HDF5(string in_filename_input){
 
 	out_filename = gen_out_filename();
@@ -811,7 +82,7 @@ bool SimuInterface::import_restart_HDF5(string in_filename_input){
 	int step_tot=read_scalar_HDF5<int>(file,string("/Net/step_tot")); 
 	double dt=read_scalar_HDF5<double>(file,string("/Net/dt")); 
 
-	network = NeuroNet( N_array, dt, step_tot, delim, indicator);
+	network = NeuroNet( N_array, dt, step_tot);
 	cout << "\t Network created." << endl;
 	network.import_restart(file, out_filename);
 	return 1;
@@ -890,7 +161,6 @@ void SimuInterface::output_results_HDF5(){
 
 }
 
-
 bool SimuInterface::import_HDF5(string in_filename_input){
 	in_filename = in_filename_input;
 	
@@ -905,12 +175,12 @@ bool SimuInterface::import_HDF5(string in_filename_input){
 		read_vector_HDF5(file, string("/config/Net/INIT001/N"), N_array);
 		int step_tot = read_scalar_HDF5<int>(file, string("/config/Net/INIT002/step_tot"));
 		double dt = read_scalar_HDF5<double>(file, string("/config/Net/INIT002/dt"));
-		network = NeuroNet( N_array, dt, step_tot, delim, indicator);
+		network = NeuroNet( N_array, dt, step_tot);
 		cout << "\t Network created." << endl;
 		
 		
 		for (unsigned int ind = 0; ind < N_array.size(); ++ind){
-			network.NeuroPopArray.push_back(new NeuroPop(ind, N_array[ind], network.dt, network.step_tot, delim, indicator));
+			network.NeuroPopArray.push_back(new NeuroPop(ind, N_array[ind], network.dt, network.step_tot));
 			cout << "\t Initialising neuron pop " << ind+1 << "..." << endl;
 
 			string pop_n = "/config/pops/pop" + to_string(ind);
@@ -1111,7 +381,7 @@ bool SimuInterface::import_HDF5(string in_filename_input){
 				read_vector_HDF5(file, syn_n + string("/INIT006/J"), J);
 				read_vector_HDF5(file, syn_n + string("/INIT006/K"), K);
 				read_vector_HDF5(file, syn_n + string("/INIT006/D"), D);
-				network.ChemSynArray.push_back(new ChemSyn(network.dt, network.step_tot, delim, indicator));
+				network.ChemSynArray.push_back(new ChemSyn(network.dt, network.step_tot));
 				network.ChemSynArray.back()->init(type, i_pre, j_post, network.N_array[i_pre], network.N_array[j_post], I, J, K, D);
 				
 				// parameters
@@ -1222,7 +492,7 @@ bool SimuInterface::import_HDF5(string in_filename_input){
 				read_vector_HDF5(file, syn_n + string("/INIT005/neurons"), neurons);
 				vector<double> rate_ext_t;
 				read_vector_HDF5(file, syn_n + string("/INIT005/rate_ext_t"), rate_ext_t);
-				network.ChemSynArray.push_back(new ChemSyn(network.dt, network.step_tot, delim, indicator));
+				network.ChemSynArray.push_back(new ChemSyn(network.dt, network.step_tot));
 				network.ChemSynArray.back()->init(type_ext, j_post, network.N_array[j_post], K_ext, Num_ext, rate_ext_t, neurons);
 				// network.ChemSynArray.back()->set_para(syn_para);
 				
@@ -1264,6 +534,5 @@ bool SimuInterface::import_HDF5(string in_filename_input){
 // 	return convert_temp.str(); // set 'Result' to the contents of the stream
 // }
 
-#endif
 
 
diff --git a/cpp_sources/SimuInterface.h b/cpp_sources/SimuInterface.h
index cefa169..59067d7 100644
--- a/cpp_sources/SimuInterface.h
+++ b/cpp_sources/SimuInterface.h
@@ -13,16 +13,10 @@ class SimuInterface{
 	SimuInterface();
 	NeuroNet network; // use container?
 	
-	// Format
-	char delim; // delim used to delimit the entries in the same line in files, note that the last entry of each line also has a delim
-	char indicator; // indicator of data-info line, always the first char in a line, followed by infomation about following data, say, name of the data variable, population index, etc
-	char commentor; // indicator of comment lines
-	
 	// Import Network Setup Data
 	string in_filename; // path+name
 	ifstream inputfile; // current input file (.ygin or .ygin_syn)
-	
-	bool import(string in_filename);
+
 	void simulate();
 	
 	// output data
@@ -30,20 +24,14 @@ class SimuInterface{
 	string out_filename; // without suffix
 	string gen_out_filename(); // generate unique file name using time stamp
 
-	void output_results();
-	
-#ifdef HDF5
-	
+
 	bool import_restart_HDF5(string in_filename_input);
 	void export_restart_HDF5();
 	// string gen_restart_filename();
 	
 	void output_results_HDF5();
 	bool import_HDF5(string in_filename);
-#endif
-	// Helper functions
-	template < typename Type > Type read_next_entry(istringstream &line_ss);
-	template < typename T, typename A > void read_next_line_as_vector( vector<T,A> &vec );
+
 };
 
 #endif
diff --git a/cpp_sources/main.cpp b/cpp_sources/main.cpp
index 1abf893..fdfb6f0 100755
--- a/cpp_sources/main.cpp
+++ b/cpp_sources/main.cpp
@@ -8,7 +8,7 @@ int main(int argc, char* argv[]){// arguments should be input file path
 		cout << "Processing input file No." << i << " out of " << argc-1 << "..." << endl;
 		SimuInterface simulator;
 		bool success = false;
-#ifdef HDF5
+
 		string filename = string(argv[i]);
 		if(filename.substr(filename.find_last_of(".") + 1) == "h5") 
 		{
@@ -19,13 +19,10 @@ int main(int argc, char* argv[]){// arguments should be input file path
 				success = simulator.import_HDF5(argv[i]);
 			}
 		} 
-		else if (filename.substr(filename.find_last_of(".") + 1) == "ygin")
+		else
 		{
-			success = simulator.import(argv[i]);
+			cout << "Unrecogized input filename extension. " << endl;
 		}
-#else
-		success = simulator.import(argv[i]);
-#endif
 		
 		if (success){ // return true if import is successful
 			simulator.simulate();
diff --git a/makefile.in b/makefile.in
index e3ca06e..9bc7679 100755
--- a/makefile.in
+++ b/makefile.in
@@ -5,8 +5,6 @@ SRC_FILES = $(SRC_DIR)/*.cpp
 HEADER_FILES = $(SRC_DIR)/*.h
 OBJ = main.o NeuroPop.o NeuroNet.o ChemSyn.o SimuInterface.o MyIO.o
 
-
-HDF5FLAG = -DHDF5
 HDF5INCLUDE =  @HDF5_CPPFLAGS@ #-I/usr/local/include
 HDF5LIBS = @HDF5_LDFLAGS@ -lhdf5_cpp -lhdf5 -lhdf5_hl
 
@@ -14,7 +12,7 @@ HDF5LIBS = @HDF5_LDFLAGS@ -lhdf5_cpp -lhdf5 -lhdf5_hl
 ###########################################################################
 CXX = @CXX@ # must use version that MATLAB supp
 
-CXXFLAGS = -std=c++11 @CXXFLAGS@ $(HDF5FLAG)
+CXXFLAGS = -std=c++11 @CXXFLAGS@ 
 
 CXXINCLUDE = $(HDF5INCLUDE)