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--- examples:sim_epsp [2014/01/10 19:10] – created zenke
+++ examples:sim_epsp [2016/08/11 07:37] (current) – Removes full prog zenke
@@ Line 24: / Line 24: @@
 In the default configuration of the simulation the [[manual:ras]] file stays empty since the neuron does not emit any spikes. The [[manual:mem]] file contains the trace of the membrane potential over time. The other files (with extensions ''ampa'',''gaba'' and ''nmda'') contain traces of the neuron's conductance variables.
-===== Output example =====
+==== Output example ====
 This plot shows the membrane potential of the single neuron in the simulation.
-{{ :manual:epsp.png |}}
+{{ :examples:epsp.png?300 |}}
 This plot can be generated by running gnuplot and issueing the follwing commands in the same directory
@@ Line 39: / Line 39: @@
 ===== The importand bits =====
- --- todo //[[fzenke@gmx.net|Friedemann Zenke]] 2014/01/10 20:08//
-===== The full program =====
 <code c++>
-/*
+PoissonGroup * poisson = new PoissonGroup(N,1.);
-* Copyright 2014 Friedemann Zenke
+PoissonGroup * poisson2 = new PoissonGroup(N,1.);
-*
+IFGroup * neuron = new IFGroup(1);
-* This file is part of Auryn, a simulation package for plastic
+</code>
-* spiking neural networks.
+Sets up the two Poisson neurons (two groups containing a single Poisson cell each) and a single integrate-and-fire cell from the [[manual:IFGroup]] type.
-*
-* Auryn is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* Auryn is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with Auryn.  If not, see <http://www.gnu.org/licenses/>.
-*/
-#include <iostream>
+<code cpp>
-#include <iomanip>
+IdentityConnection * con = new IdentityConnection(poisson,neuron,w,GLUT);
-#include <stdlib.h>
+IdentityConnection * con2 = new IdentityConnection(poisson2,neuron,w,GABA);
-#include <string>
+</code>
+Creates two one-to-one connetions between the Poisson neurons and the integrate-and-fire cell.
-#include <boost/program_options.hpp>
+<code>
-#include <boost/mpi/environment.hpp>
+SpikeMonitor * smon = new SpikeMonitor( neuron, tmpstr.c_str() );
-#include <boost/mpi/communicator.hpp>
+</code>
-#include <boost/mpi.hpp>
+Sets up a [[manual:SpikeMonitor]] and tells it to record from  our ''neuron''. The output is written to a file that is specified by ''tmpstr''.
-#include "auryn_global.h"
+<code>
-#include "auryn_definitions.h"
+VoltageMonitor * vmon = new VoltageMonitor( neuron, 0, tmpstr.c_str() );
-#include "System.h"
+</code>
-#include "Logger.h"
+Creates a [[manual:VoltageMonitor]] that records the voltage to a different file which is again specified in ''tmpstr''. Note that an equivalent alternative syntax would be to recorde voltages would be directly using a [[manual:StateMonitor]]. The conductance monitors are set up in a similar way.
-#include "NeuronGroup.h"
-#include "IFGroup.h"
-#include "AIFGroup.h"
-#include "PoissonGroup.h"
-#include "SparseConnection.h"
-#include "IdentityConnection.h"
-#include "TripletConnection.h"
-#include "TripletDecayConnection.h"
-#include "WeightMonitor.h"
-#include "WeightMatrixMonitor.h"
-#include "PopulationRateMonitor.h"
-#include "SpikeMonitor.h"
-#include "VoltageMonitor.h"
-#include "AmpaMonitor.h"
-#include "GabaMonitor.h"
-#include "NmdaMonitor.h"
-#include "DelayedSpikeMonitor.h"
-#include "RateChecker.h"
-#include "FileInputGroup.h"
-#define N 1
-using namespace std;
+<code c++>
+logger->msg("Running ...",PROGRESS);
-namespace po = boost::program_options;
+sys->run(10);
-namespace mpi = boost::mpi;
-int main(int ac, char* av[])
-{
-	int errcode = 0;
-	char strbuf [255];
-	string outputfile = "out_epsp";
-	string tmpstr;
-	AurynWeight w = 1.0;
-	// BEGIN Global definitions
-	mpi::environment env(ac, av);
-	mpi::communicator world;
-	communicator = &world;
-	sprintf(strbuf, "out_epsp.%d.log", world.rank());
-	string logfile = strbuf;
-	logger = new Logger(logfile,world.rank(),PROGRESS,EVERYTHING);
-	sys = new System(&world);
-	// END Global definitions
-	PoissonGroup * poisson = new PoissonGroup(N,1.);
-	PoissonGroup * poisson2 = new PoissonGroup(N,1.);
-	IFGroup * neuron = new IFGroup(1);
-	IdentityConnection * con = new IdentityConnection(poisson,neuron,w,GLUT);
-	IdentityConnection * con2 = new IdentityConnection(poisson2,neuron,w,GABA);
-	tmpstr = outputfile;
-	tmpstr += ".ras";
-	SpikeMonitor * smon = new SpikeMonitor( neuron, tmpstr.c_str() );
-	tmpstr = outputfile;
-	tmpstr += ".mem";
-	VoltageMonitor * vmon = new VoltageMonitor( neuron, 0, tmpstr.c_str() );
-	tmpstr = outputfile;
-	tmpstr += ".ampa";
-	AmpaMonitor * amon = new AmpaMonitor( neuron, 0, tmpstr.c_str() );
-	tmpstr = outputfile;
-	tmpstr += ".gaba";
-	GabaMonitor * gmon = new GabaMonitor( neuron, 0, tmpstr.c_str() );
-	tmpstr = outputfile;
-	tmpstr += ".nmda";
-	NmdaMonitor * nmon = new NmdaMonitor( neuron, 0, tmpstr.c_str() );
-	logger->msg("Running ...",PROGRESS);
-	sys->run(10);
-	logger->msg("Freeing ...",PROGRESS,true);
-	delete sys;
-	if (errcode)
-		env.abort(errcode);
-	return errcode;
-}
 </code>
+This finally outputs a message ''Running...'' on the console and triggers the run for 10s. Note the call of the global variable sys of type [[manual:System]].