auryn::AdExGroup Class Reference

Conductance based Adaptive Exponential neuron model - Brette and Gerstner (2005). More...

#include <AdExGroup.h>

Inheritance diagram for auryn::AdExGroup:

Collaboration diagram for auryn::AdExGroup:

Public Member Functions
	AdExGroup (NeuronID size)
virtual	~AdExGroup ()
void	set_refractory_period (AurynDouble t)
void	set_delta_t (AurynFloat d)
	Set value of slope factor deltat (default 2mV) More...
void	set_g_leak (AurynFloat g)
	Sets the leak conductance (default 30nS) More...
void	set_c_mem (AurynFloat cm)
	Sets the membrane capacitance (default 281pF) More...
void	set_a (AurynFloat _a)
	Set value of a in units S ( default 4nS ) More...
void	set_b (AurynFloat _b)
	Set value of b in units of A ( default 0.0805nA ) More...
void	set_e_reset (AurynFloat ereset)
void	set_e_rest (AurynFloat erest)
void	set_e_thr (AurynFloat ethr)
void	set_tau_w (AurynFloat tauw)
void	set_tau_ampa (AurynFloat tau)
AurynFloat	get_tau_ampa ()
void	set_tau_gaba (AurynFloat tau)
AurynFloat	get_tau_gaba ()
void	clear ()
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...

Additional Inherited Members
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
Protected Member Functions inherited from auryn::NeuronGroup
void	init ()
void	free ()
Protected Member Functions inherited from auryn::SpikingGroup
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

Conductance based Adaptive Exponential neuron model - Brette and Gerstner (2005).

This implements a NeuronGroup of AdEx neurons with default parameters from Brette, R., and Gerstner, W. (2005). Adaptive Exponential Integrate-and-Fire Model as an Effective Description of Neuronal Activity. J Neurophysiol 94, 3637–3642.

Constructor & Destructor Documentation

AdExGroup()

AdExGroup::AdExGroup

(

NeuronID

size

)

The default constructor of this NeuronGroup

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

Here is the call graph for this function:

~AdExGroup()

AdExGroup::~AdExGroup ( )

virtual

{
    if ( !evolve_locally() ) return;

    auryn_vector_ushort_free (ref);
}

Here is the call graph for this function:

Member Function Documentation

clear()

void AdExGroup::clear ( )

virtual

Resets all neurons to defined and identical initial state.

Implements auryn::NeuronGroup.

{
    clear_spikes();

        mem->set_all(e_rest);
        g_ampa->set_zero();
        g_gaba->set_zero();
        w->set_zero();
        ref->set_zero();
}

Here is the call graph for this function:

evolve()

void AdExGroup::evolve ( )

virtual

The evolve method internally used by System.

Implements auryn::SpikingGroup.

{

        // Compute
        //     t_mem[i] += scale_mem * (
        //             e_rest-t_mem[i]
        //             + deltat * exp((t_mem[i]-e_thr)/deltat)
        //             - t_g_ampa[i] * (t_mem[i]-e_rev_ampa)
        //             - t_g_gaba[i] * (t_mem[i]-e_rev_gaba) 
        //             -t_w[i] ) ;
        // as vectorized code

        // Compute currents
        I_leak->diff(e_rest,mem);

        I_exc->diff(e_rev_ampa, mem);
        I_exc->mul(g_ampa);

        I_inh->diff(e_rev_gaba, mem);
        I_inh->mul(g_gaba);

        // compute spike generating current 
        temp->diff(mem,e_thr);
        temp->scale(1.0/deltat);
        temp->fast_exp();
        temp->scale(deltat);

        // sum up all the currents
        temp->add(I_leak);
        temp->add(I_exc);
        temp->add(I_inh);
        temp->sub(w); // adaptation current

        // Euler update membrane
        mem->saxpy(scale_mem, temp);
        mem->clip(e_rev_gaba, 20e-3); // needs to be larger than 0.0 

        // check thresholds
    for (NeuronID i = 0 ; i < get_rank_size() ; ++i ) {
        if (t_ref[i]==0) {
            if (t_mem[i]>0.0) {
                push_spike(i);
                t_mem[i] = e_reset;
                t_w[i] += b;
                t_ref[i] += refractory_time ;
            }
        } else {
            t_ref[i]-- ;
            t_mem[i] = e_rest ;
        }
    }

        // computes
        // dw = scale_w * (a * (t_mem[i]-e_rest) - t_w[i]);
        // in vector lingo
        temp->diff(mem,e_rest);
        temp->scale(a);
        temp->sub(w);
        // Euler upgrade adaptation variable
        w->saxpy(scale_w,temp);


    g_ampa->scale(scale_ampa);
    g_gaba->scale(scale_gaba);
}

Here is the call graph for this function:

get_tau_ampa()

AurynFloat AdExGroup::get_tau_ampa

(

)

Gets the exponential time constant for the AMPA channel

{
    return tau_ampa;
}

get_tau_gaba()

AurynFloat AdExGroup::get_tau_gaba

(

)

Gets the exponential time constant for the GABA channel

{
    return tau_gaba;
}

set_a()

void AdExGroup::set_a

(

AurynFloat

_a

)

Set value of a in units S ( default 4nS )

Internally this is value s converted to natural units of g_leak for numerical stability. Thus, make sure you set g_leak first!

{
    a = _a/g_leak;
}

set_b()

void AdExGroup::set_b

(

AurynFloat

_b

)

Set value of b in units of A ( default 0.0805nA )

Internally this is value s converted to natural units of g_leak for numerical stability. Thus, make sure you set g_leak first!

{
    b = _b/g_leak;
}

set_c_mem()

void AdExGroup::set_c_mem

(

AurynFloat

cm

)

Sets the membrane capacitance (default 281pF)

Because these units are used to derive internal numerical values, they need to be set first!

{
    c_mem = cm;
    tau_mem = c_mem/g_leak;
    calculate_scale_constants();
}

Here is the call graph for this function:

set_delta_t()

void AdExGroup::set_delta_t

(

AurynFloat

d

)

Set value of slope factor deltat (default 2mV)

{
    deltat = d/g_leak;
}

set_e_reset()

void AdExGroup::set_e_reset

(

AurynFloat

ereset

)

Set value of V_r (default -70.6mV)

{
    e_reset = ereset;
}

set_e_rest()

void AdExGroup::set_e_rest

(

AurynFloat

erest

)

Set value of E_l (default -70.6mV)

{
    e_rest = erest;
    for (NeuronID i = 0; i < get_rank_size(); i++)
        auryn_vector_float_set (mem, i, e_rest);
}

Here is the call graph for this function:

set_e_thr()

void AdExGroup::set_e_thr

(

AurynFloat

ethr

)

Set value of V_t (default -50.4mV)

{
    e_thr = ethr;
}

set_g_leak()

void AdExGroup::set_g_leak

(

AurynFloat

g

)

Sets the leak conductance (default 30nS)

Because these units are used to derive internal numerical values, they need to be set first!

{
    g_leak = g;
    tau_mem = c_mem/g_leak;
    calculate_scale_constants();
}

set_refractory_period()

void AdExGroup::set_refractory_period

(

AurynDouble

t

)

Setter for refractory time [s]

{
    refractory_time = (unsigned short) (t/auryn_timestep);
}

Here is the call graph for this function:

set_tau_ampa()

void AdExGroup::set_tau_ampa

(

AurynFloat

tau

)

Sets the exponential time constant for the AMPA channel (default 5ms)

{
    tau_ampa = taum;
    calculate_scale_constants();
}

set_tau_gaba()

void AdExGroup::set_tau_gaba

(

AurynFloat

tau

)

Sets the exponential time constant for the GABA channel (default 10ms)

{
    tau_gaba = taum;
    calculate_scale_constants();
}

set_tau_w()

void AdExGroup::set_tau_w

(

AurynFloat

tauw

)

Sets the w time constant (default 144ms)

{
    tau_w = tauw;
    calculate_scale_constants();
}

---

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

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