auryn::IFGroup Class Reference

Implements the standard integrate and file model used in Auryn. More...

#include <IFGroup.h>

Inheritance diagram for auryn::IFGroup:

Collaboration diagram for auryn::IFGroup:

Public Member Functions
	IFGroup (NeuronID size, NodeDistributionMode distmode=AUTO)
	Default constructor. More...
virtual	~IFGroup ()
void	set_tau_mem (AurynFloat taum)
	Sets the membrane time constant. More...
AurynFloat	get_tau_mem ()
	Returns the membrane time constant. More...
void	set_tau_ampa (AurynFloat tau)
	Sets the exponential decay time constant of the AMPA conductance (default=5ms). More...
AurynFloat	get_tau_ampa ()
	Returns the exponential decay time constant of the AMPA conductance. More...
void	set_tau_gaba (AurynFloat tau)
	Sets the exponential decay time constant of the GABA conductance (default=10ms). More...
AurynFloat	get_tau_gaba ()
	Returns the exponential decay time constant of the GABA conductance. More...
void	set_tau_nmda (AurynFloat tau)
	Sets the exponential decay time constant of the NMDA conductance (default=100ms). More...
void	set_tau_thr (AurynFloat tau)
	Sets the exponential decay time constant of the threshold (default=5). More...
AurynFloat	get_tau_nmda ()
void	set_ampa_nmda_ratio (AurynFloat ratio)
	Set ratio between ampa/nmda contribution to excitatory conductance. More...
void	set_nmda_ampa_current_ampl_ratio (AurynFloat ratio)
	Sets nmda-ampa amplitude ratio. More...
void	clear ()
virtual void	evolve ()
Public Member Functions inherited from auryn::NeuronGroup
	NeuronGroup (NeuronID n, NodeDistributionMode mode=AUTO)
	Default constructor. More...
	NeuronGroup (NeuronID n, double loadmultiplier, NeuronID total)
	Old default constructor. More...
virtual	~NeuronGroup ()
void	set_state (std::string name, AurynState val)
	Conveniently sets all values in a state vector identified by name in this group. More...
void	set_state (std::string name, NeuronID i, AurynState val)
	Conveniently sets a single value of element i in a state vector identified by name in this group. More...
virtual AurynStateVector *	get_default_exc_target ()
	Returns default exc target input. More...
virtual AurynStateVector *	get_default_inh_target ()
	Returns default inh target input. More...
void	random_mem (AurynState mean=-60e-3, AurynState sigma=5e-3)
virtual void	init_state ()
void	safe_tadd (NeuronID id, AurynWeight amount, TransmitterType t=GLUT)
void	tadd (NeuronID id, AurynWeight amount, TransmitterType t=GLUT)
void	tadd (AurynStateVector *state, NeuronID id, AurynWeight amount)
Public Member Functions inherited from auryn::SpikingGroup
void	add_state_vector (std::string key, AurynStateVector *state_vector)
	Adds a state vector passed as an argument to the dictinary. More...
void	remove_state_vector (std::string key)
	Removes a state vector passed as an argument to the dictinary. More...
AurynStateVector *	find_state_vector (std::string key)
	Returns existing state vector by name or NULL if it does not exist. More...
AurynStateVector *	get_state_vector (std::string key)
	Creates a new or returns an existing state vector by name. More...
AurynStateVector *	get_existing_state_vector (std::string key)
	Returns an existing state with the supplied name. More...
AurynStateVector *	create_state_vector (std::string key)
	Creates a new state vector and throws an exception if a vector with the same name exists. More...
AurynState *	get_state_variable (std::string key)
	Creates a new group-wide state variable or returns an existing group-wide variable by name then returns a pointer to it. More...
void	randomize_state_vector_gauss (std::string state_vector_name, AurynState mean, AurynState sigma, int seed=12239)
	Randomizes the content of a state vector with Gaussian random numbers. Seeding is MPI save. More...
	SpikingGroup (NeuronID size, NodeDistributionMode mode=AUTO)
	Default constructor. More...
virtual	~SpikingGroup ()
	Default destructor. More...
virtual void	evolve_traces ()
	Evolves traces. More...
void	set_name (std::string s)
	Set connection name. More...
std::string	get_name ()
	Retrieves the groups name. More...
std::string	get_file_name ()
	Extracts the class name of the connection from the file name. More...
std::string	get_log_name ()
	Returns a string which is the combination of file and connection name for logging. More...
void	inc_num_spike_attributes (int x)
	Instructs SpikingGroup to increase the number of spike attributes by x. More...
int	get_num_spike_attributes ()
void	conditional_evolve ()
	Conditional evolve functino which is called by System. More...
unsigned int	get_locked_rank ()
	Returns locked rank for SpikingGroups which are not distributed across all ranks. More...
unsigned int	get_locked_range ()
	Returns locked range of ranks for SpikingGroups which are not distributed across all ranks. More...
SpikeContainer *	get_spikes ()
	Returns pointer to a spike container that contains spikes which arrive in this timestep from all neurons in this group. More...
SpikeContainer *	get_spikes_immediate ()
	Returns pointer to SpikeContainer of spikes generated during the last evolve() step. More...
AttributeContainer *	get_attributes ()
	Returns pointer to Attributecontainer for usage in propagating Connection objects. Same as get_spikes_immediate(), however might be overwritten to contain Spikes that have been delayed. More...
AttributeContainer *	get_attributes_immediate ()
	Returns pointer to Attributecontainer of spikes generated during the last evolve() step. More...
NeuronID	get_size ()
	Returns the size of the group. More...
NeuronID	get_pre_size ()
	Returns the size of the group. More...
NeuronID	calculate_rank_size (int rank=-1)
	Determines rank size and stores it in local variable. More...
NeuronID	get_rank_size ()
	Returns the size on this rank. More...
NeuronID	get_post_size ()
	Returns the size on this rank. More...
void	set_clock_ptr (AurynTime *clock)
bool	evolve_locally ()
	Returns true if the calling instance has units which are integrated on the current rank. More...
NeuronID	get_uid ()
	Get the unique ID of the class. More...
Trace *	get_pre_trace (AurynFloat x)
	Returns a pre trace with time constant x. More...
void	add_pre_trace (Trace *tr)
	Adds trace to pretrace stack of a connection. More...
Trace *	get_post_trace (AurynFloat x)
	Returns a post trace with time constant x. More...
void	add_post_trace (Trace *tr)
	Adds trace to posttrace stack of a connection. More...
void	push_spike (NeuronID spike)
	Pushes a local NeuronID as spike into the axonal SpikeDelay buffer. More...
void	push_attribute (AurynFloat attrib)
	Pushes a spike attribute into the axonal SpikeDelay buffer. More...
void	clear_spikes ()
	Clears all spikes stored in the delays which is useful to reset a network during runtime. More...
Trace *	get_post_state_trace (std::string state_name="mem", AurynFloat tau=10e-3, AurynFloat b=0.0)
	Returns a post trace of a neuronal state variable e.g. the membrane potential with time constant tau. More...
Trace *	get_post_state_trace (AurynStateVector *state, AurynFloat tau=10e-3, AurynFloat b=0.0)
	Returns a post trace of a neuronal state variable specified by pointer. More...
void	set_delay (int d)
	Sets axonal delay for this SpikingGroup. More...
virtual bool	write_to_file (const char *filename)
	Writes current states of SpikingGroup to human-readible textfile if implemented in derived class. More...
virtual bool	load_from_file (const char *filename)
	Reads current states of SpikingGroup to human-readible textfile if implemented in derived class. More...
NeuronID	ranksize ()
	Returns size (num of neurons) on the current rank. More...
NeuronID	global2rank (NeuronID i)
	Converts global NeuronID within the SpikingGroup to the local NeuronID on this rank. More...
NeuronID	rank2global (NeuronID i)
	Converts local NeuronID from the local rank to a global NeuronID. More...
bool	localrank (NeuronID i)
	Checks if the global NeuronID i is integrated on this MPI rank. More...
NeuronID	get_vector_size ()
	Rank size but rounded up to multiples of 4 (or potentially some other and larger number in future versions) for SSE compatibility. More...

Public Attributes
AurynFloat	u_reset
	Reset voltage. More...
AurynFloat	u_rest
	Resting potential. More...
AurynFloat	u_inh_rev
	Inhibitory reversal potential. More...
Public Attributes inherited from auryn::NeuronGroup
AurynStateVector *	mem
AurynStateVector *	g_ampa
AurynStateVector *	g_gaba
AurynStateVector *	g_nmda
AurynStateVector *	thr
Public Attributes inherited from auryn::SpikingGroup
SpikeDelay *	delay
bool	active
	Toggles group active. More...
std::map< std::string, AurynStateVector * >	state_vectors
std::map< std::string, AurynState >	state_variables

Additional Inherited Members
Protected Member Functions inherited from auryn::NeuronGroup
void	init ()
void	free ()
Protected Member Functions inherited from auryn::SpikingGroup
virtual void	load_input_line (NeuronID i, const char *buf)
virtual std::string	get_output_line (NeuronID i)
virtual void	virtual_serialize (boost::archive::binary_oarchive &ar, const unsigned int version)
	Implementatinon of serialize function for writing. More...
virtual void	virtual_serialize (boost::archive::binary_iarchive &ar, const unsigned int version)
	Implementatinon of serialize function for reading. More...
void	free ()
	Frees potentially allocated memory. More...
Protected Attributes inherited from auryn::NeuronGroup
AurynStateVector *	default_exc_target_state
AurynStateVector *	default_inh_target_state
Protected Attributes inherited from auryn::SpikingGroup
std::vector< Trace * >	pretraces
	Pretraces. More...
std::vector< Trace * >	posttraces
	Posttraces. More...
std::vector< Trace * >	post_state_traces
	Post state traces. More...
std::vector< AurynFloat >	post_state_traces_spike_biases
std::vector< AurynStateVector * >	post_state_traces_states
std::string	group_name
	Identifying name for object. More...
NeuronID	size
	Stores the size of the group. More...
NeuronID	rank_size
	Stores the size of the group on this rank. More...
SpikeContainer *	spikes
	SpikeContainers to store spikes produced during one step of evolve. More...
AttributeContainer *	attribs
Static Protected Attributes inherited from auryn::SpikingGroup
static AurynTime *	clock_ptr = NULL

Detailed Description

Implements the standard integrate and file model used in Auryn.

This is the implementation of a standard leaky integrate and fire model with relative refractoriness and conductance based synapses. The model has two time constants for excitatory conductances (AMPA,NMDA). AMPA conductances are modelled as exponential decays. NMDA is implemented to have a double exponental timecourse, by low-pass filtering over the AMPA equation. The amplitude between the individual contributions can be ajusted via set_ampa_nmda_ratio. The voltage dependence of NMDA is ignored in this model.

Constructor & Destructor Documentation

IFGroup()

IFGroup::IFGroup	(	NeuronID	size,
		NodeDistributionMode	distmode = AUTO
	)

Default constructor.

Parameters

size	the size of the group.
distmode	Node distribution mode

                                                               : NeuronGroup(size, distmode)
{
        sys->register_spiking_group(this);
        if ( evolve_locally() ) init();
}

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~IFGroup()

IFGroup::~IFGroup ( )

virtual

{
        if ( evolve_locally() ) free();
}

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Member Function Documentation

clear()

void IFGroup::clear ( )

virtual

Implements auryn::NeuronGroup.

{
        clear_spikes();
        mem->set_all(u_rest);
        thr->set_zero();
        g_ampa->set_zero();
        g_gaba->set_zero();
        g_nmda->set_zero();
}

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evolve()

void IFGroup::evolve ( )

virtual

Internally used evolve function. Called by System.

Implements auryn::SpikingGroup.

{
        integrate_linear_nmda_synapses();
        integrate_membrane();
        check_thresholds();
}

get_tau_ampa()

AurynFloat IFGroup::get_tau_ampa

(

)

Returns the exponential decay time constant of the AMPA conductance.

{
        return tau_ampa;
}

get_tau_gaba()

AurynFloat IFGroup::get_tau_gaba

(

)

Returns the exponential decay time constant of the GABA conductance.

{
        return tau_gaba;
}

get_tau_mem()

AurynFloat IFGroup::get_tau_mem

(

)

Returns the membrane time constant.

{
        return tau_mem;
}

get_tau_nmda()

AurynFloat IFGroup::get_tau_nmda

(

)

Returns the exponential decay time constant of the NMDA conductance. The rise is governed by tau_ampa if tau_ampa << tau_nmda.

{
        return tau_nmda;
}

set_ampa_nmda_ratio()

void IFGroup::set_ampa_nmda_ratio

(

AurynFloat

ratio

)

Set ratio between ampa/nmda contribution to excitatory conductance.

This sets the ratio between the integrals between the conductance kernels.

{
        A_ampa = ratio/(ratio+1.0);
        A_nmda = 1./(ratio+1.0);
}

set_nmda_ampa_current_ampl_ratio()

void IFGroup::set_nmda_ampa_current_ampl_ratio

(

AurynFloat

ratio

)

Sets nmda-ampa amplitude ratio.

This sets the ratio between the amplitudes of nmda to ampa.

{
        const double tau_r = tau_ampa;
        const double tau_d = tau_nmda;

        // compute amplitude of NMDA conductance
        const double tmax = tau_r*std::log((tau_r+tau_d)/tau_r); // argmax
        const double ampl = (1.0-std::exp(-tmax/tau_r))*std::exp(-tmax/tau_d)*tau_r/(tau_d-tau_r); 

        // set relative amplitudes
        A_ampa = 1.0;
        A_nmda = ratio/ampl;

        // normalize sum to one
        const double sum = A_ampa+A_nmda;
        A_ampa /= sum;
        A_nmda /= sum;

        // write constants to logfile
        logger->parameter("A_ampa", A_ampa);
        logger->parameter("A_nmda", A_nmda);
}

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set_tau_ampa()

void IFGroup::set_tau_ampa

(

AurynFloat

tau

)

Sets the exponential decay time constant of the AMPA conductance (default=5ms).

{
        tau_ampa = taum;
        calculate_scale_constants();
}

set_tau_gaba()

void IFGroup::set_tau_gaba

(

AurynFloat

tau

)

Sets the exponential decay time constant of the GABA conductance (default=10ms).

{
        tau_gaba = taum;
        calculate_scale_constants();
}

set_tau_mem()

void IFGroup::set_tau_mem

(

AurynFloat

taum

)

Sets the membrane time constant.

{
        tau_mem = taum;
        calculate_scale_constants();
}

set_tau_nmda()

void IFGroup::set_tau_nmda

(

AurynFloat

tau

)

Sets the exponential decay time constant of the NMDA conductance (default=100ms).

The rise is governed by tau_ampa if tau_ampa << tau_nmda.

{
        if ( tau < tau_ampa ) { 
                logger->warning("tau_nmda has to be larger than tau_ampa in IFGroup");
                return;
        }
        tau_nmda = tau;
        calculate_scale_constants();
}

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set_tau_thr()

void IFGroup::set_tau_thr

(

AurynFloat

tau

)

Sets the exponential decay time constant of the threshold (default=5).

Reflects absolute and relative refractory period.

{
        tau_thr = tau;
        calculate_scale_constants();
}

Member Data Documentation

u_inh_rev

AurynFloat auryn::IFGroup::u_inh_rev

Inhibitory reversal potential.

u_reset

AurynFloat auryn::IFGroup::u_reset

Reset voltage.

u_rest

AurynFloat auryn::IFGroup::u_rest

Resting potential.

---

The documentation for this class was generated from the following files:

• /home/zenke/auryn/src/auryn/IFGroup.h
• /home/zenke/auryn/src/auryn/IFGroup.cpp