#include <ostream>
#include <user_errors.h>

Include dependency graph for carlsim_datastructures.h:

This graph shows which files directly or indirectly include this file:

Classes
struct	ConnSTDPInfo_s
	A struct for retrieving STDP related information of a connection. More...

struct	ExpCurve
	A struct to assign exponential STDP curves. More...

struct	Grid3D
	A struct to arrange neurons on a 3D grid (a primitive cubic Bravais lattice with cubic side length 1) More...

struct	GroupNeuromodulatorInfo_s
	A struct for retrieving neuromodulator information of a group. More...

struct	PkaPlcModulation

struct	PulseCurve
	struct to assign a pulse I-STDP curve More...

struct	RadiusRF
	A struct to specify the receptive field (RF) radius in 3 dimensions. More...

struct	RangeDelay
	a range struct for synaptic delays More...

struct	RangeRmem
	Struct defines the minimum and maximum membrane resisatnces of the LIF neuron group. More...

struct	RangeWeight
	a range struct for synaptic weight magnitudes More...

struct	TimingBasedCurve
	A struct to assign a timing-based E-STDP curve. More...

Typedefs
typedef struct ConnSTDPInfo_s	ConnSTDPInfo
	A struct for retrieving STDP related information of a connection. More...

typedef struct GroupNeuromodulatorInfo_s	GroupNeuromodulatorInfo
	A struct for retrieving neuromodulator information of a group. More...

Enumerations
enum	CARLsimState { CONFIG_STATE, SETUP_STATE, RUN_STATE }
	CARLsim states. More...

enum	ComputingBackend { CPU_CORES, GPU_CORES }
	computing backend More...

enum	IcalcType { CUBA, COBA, NM4W_LN21, GPCR_NB14, DASEAC_CK09, ACNE_ANCK12, ACNE_K12, ACNE_K13, D1D2_AK12, ACDA_BK19, alpha1_ADK13, alpha2A_ADK13, D1_ADK13, D2_AK15, UNKNOWN_ICALC }
	input current calculation More...

enum	integrationMethod_t { FORWARD_EULER, RUNGE_KUTTA4, UNKNOWN_INTEGRATION }
	Integration methods. More...

enum	LoggerMode { USER, DEVELOPER, SHOWTIME, SILENT, CUSTOM, UNKNOWN_LOGGER }
	Logger modes. More...

enum	Neuromodulator { NM_DA, NM_5HT, NM_ACh, NM_NE, NM_UNKNOWN }
	GroupMonitor flag. More...

enum	SimMode { CPU_MODE, GPU_MODE, HYBRID_MODE }
	simulation mode More...

enum	SpikeMonMode { COUNT, AER }
	SpikeMonitor mode. More...

enum	STDPCurve { EXP_CURVE, PULSE_CURVE, TIMING_BASED_CURVE, UNKNOWN_CURVE }
	STDP curves. More...

enum	STDPType { STANDARD, DA_MOD, SE_MOD, AC_MOD, NE_MOD, AC_DA_MOD, AC_NE_MOD, SE_DA_MOD, NM4_MOD, PKA_PLC_MOD, UNKNOWN_STDP }
	STDP flavors. More...

enum	UpdateInterval { INTERVAL_10MS, INTERVAL_100MS, INTERVAL_1000MS }
	Update frequency for weights. More...

Variables
static const char *	carlsimState_string []

static const char *	ComputingBackend_string []
	LN20201016. More...

static const char *	IcalcType_string []

static const char *	integrationMethod_string []

static const char *	loggerMode_string []

static const char *	neuromodulator_string []

static const char *	simMode_string []

static const char *	spikeMonMode_string []

static const char *	stdpCurve_string []

static const char *	stdpType_desc []

static const char *	stdpType_string []

static const char *	updateInterval_string []

Typedef Documentation

◆ ConnSTDPInfo

typedef struct ConnSTDPInfo_s ConnSTDPInfo

The struct is used in test suite only. CARLsim API call provides a getter function CARLsim::getConnSTDPInfo() for retrieving STDP related information of a connection. A developer can write his/her test cases to test the STDP parameters

See also: CARLsim::getConnSTDPInfo()

◆ GroupNeuromodulatorInfo

typedef struct GroupNeuromodulatorInfo_s GroupNeuromodulatorInfo

The struct is used in test suite only. CARLsim API call provides a getter function CARLsim::getGroupNeuromodulatorInfo() for retrieving neuromodulator information of a group. A developer can write his/her test cases to test the neuromodulator parameters

See also: CARLsim::getGroupNeuromodulatorInfo()

Enumeration Type Documentation

◆ CARLsimState

enum CARLsimState

A CARLsim simulation goes through the following states: CONFIG_STATE configuration state, where the neural network is configured SETUP_STATE setup state, where the neural network is prepared for execution RUN_STATE run state, where the simulation is executed Certain methods can only be called in certain states. Check their documentation to see which method can be called in which state.

Certain methods perform state transitions. CARLsim::setupNetwork will change the state from CONFIG_STATE to SETUP_STATE. The first call to CARLsim::runNetwork will change the state from SETUP_STATE to RUN_STATE.

Enumerator
CONFIG_STATE	configuration state, where the neural network is configured
SETUP_STATE	setup state, where the neural network is prepared for execution and monitors are set
RUN_STATE	run state, where the model is stepped

Definition at line 384 of file carlsim_datastructures.h.

◆ ComputingBackend

enum ComputingBackend

CARLsim supports execution on standard x86 CPU Cores or off-the-shelf NVIDIA GPU (CUDA Cores)

Enumerator
CPU_CORES	x86/x64 Multi Core Processor (LN20201016)
GPU_CORES	NVIDIA Many CUDA Core Processor (LN20201016)

Definition at line 149 of file carlsim_datastructures.h.

◆ IcalcType

enum IcalcType

CARLsim6 extends the current calculation for the post synaptic neuron that was CUBA and COBA in the following ways: it now can be configured on neuron group level, for instance on group is CUBA and the other COBA. Also the conductance parameters can be configured individually on distinct groups to be more biorealistic. More than that, CARlsim6 respects now the distinct neuromodulator state in the target neuron group that affects the receptors and so the the effective input current used by the Izhikevich model.

Enumerator
CUBA	current
COBA	conductance
NM4W_LN21	4 NM weighted (and normalized,boosted,damped), Niedermeier (2021)
GPCR_NB14	G protein-coupled receptors for 2 modulators and conductance, Nadim, Bucher (2014)
DASEAC_CK09	dopamine,serotonin,acetylcholine modulated Cox, Krichmar (2009)
ACNE_ANCK12	acetylcholin, norepinephrine modulated Avery, Nitz, Chiba, Krichmar (2012)
ACNE_K12	acetylcholin, norepinephrine modulated Krichmar (2012)
ACNE_K13	acetylcholin, norepinephrine modulated Krichmar (2013)
D1D2_AK12	D1,D2 dopamine receptors Avery, Krichmar (2012)
ACDA_BK19	acetylcholin influence to dopamine, Belkaid, Krichmar (2019)
alpha1_ADK13	NE alpha1 receptor with DA antagonist, Avery, Dutt, Krichmar (2013)
alpha2A_ADK13	NE alpha2 receptor (connection), Avery, Dutt, Krichmar (2013)
D1_ADK13	DA D1 receptor (connection), Avery, Dutt, Krichmar (2013)
D2_AK15	DA D2 receptor (connection), Avery, Krichmar (2015)
UNKNOWN_ICALC	used to initialize by default constructor

Definition at line 256 of file carlsim_datastructures.h.

◆ integrationMethod_t

enum integrationMethod_t

CARLsim supports different integration methods. Currently available:

FORWARD_EULER: Forward-Euler (aka Euler method). Most basic explicit method for numerical integration of ODEs. Suggest time step of 0.5ms or lower for stability. RUNGE_KUTTA4: Fourth-order Runge-Kutta (aka classical Runge-Kutta, aka RK4). Suggest time step of 0.1ms or lower.

Enumerator
FORWARD_EULER
RUNGE_KUTTA4
UNKNOWN_INTEGRATION

Definition at line 134 of file carlsim_datastructures.h.

◆ LoggerMode

enum LoggerMode

The logger mode defines where to print all status, error, and debug messages. Several predefined modes exist (USER, DEVELOPER, SHOWTIME, SILENT). However, the user can also set each file pointer to a location of their choice (CUSTOM mode). The following logger modes exist: USER User mode, for experiment-oriented simulations. Errors and warnings go to stderr, status information goes to stdout. Debug information can only be found in the log file. DEVELOPER Developer mode, for developing and debugging code. Same as user, but additionally, all debug information is printed to stdout. SHOWTIME Showtime mode, will only output warnings and errors. SILENT Silent mode, no output is generated. CUSTOM Custom mode, the user can set the location of all the file pointers.

The following file pointers exist: fpOut_ where CARLSIM_INFO messages go fpErr_ where CARLSIM_ERROR and CARLSIM_WARN messages go fpDeb_ where CARLSIM_DEBUG messages go fpLog_ typically a log file, where all of the above messages go

The file pointers are automatically set to different locations, depending on the loggerMode:

*          |    USER    | DEVELOPER  |  SHOWTIME  |   SILENT   |  CUSTOM
* ---------|------------|------------|------------|------------|---------
* fpOut_   |   stdout   |   stdout   | /dev/null  | /dev/null  |    ?
* fpErr_   |   stderr   |   stderr   |   stderr   | /dev/null  |    ?
* fpDeb_   | /dev/null  |   stdout   | /dev/null  | /dev/null  |    ?
* fpLog_   | debug.log  | debug.log  | debug.log  | /dev/null  |    ?
*

Location of the debug log file can be set in any mode using CARLsim::setLogDebugFp. In mode CUSTOM, the other file pointers can be set using CARLsim::setLogsFp.

Enumerator
USER	User mode, for experiment-oriented simulations.
DEVELOPER	Developer mode, for developing and debugging code.
SHOWTIME	Showtime mode, will only output warnings and errors.
SILENT	Silent mode, no output is generated.
CUSTOM	Custom mode, the user can set the location of all the file pointers.
UNKNOWN_LOGGER

Definition at line 92 of file carlsim_datastructures.h.

◆ Neuromodulator

enum Neuromodulator

To monitor concentration of neuromodulator through GroupMonitor following flags can be used NM_DA Dopamine NM_5HT Serotonin NM_ACh Acetylcholine NM_NE Noradrenaline

Enumerator
NM_DA	dopamine
NM_5HT	serotonin
NM_ACh	acetylcholine
NM_NE
NM_UNKNOWN	unknown type TODO: synonym norepinephrine

Definition at line 339 of file carlsim_datastructures.h.

◆ SimMode

enum SimMode

CARLsim supports execution on standard x86 central processing units (CPUs) and off-the-shelf NVIDIA GPUs.

When creating a new CARLsim object, you can set your prefferred simulation mode: CPU_MODE: run on CPU core(s) GPU_MODE: try to run on GPU card(s), if any HYBRID_MODE: allow CARLsim to decide running on CPU Core(s), GPU card(s) or both

Enumerator
CPU_MODE	model is run on CPU core(s)
GPU_MODE	model is run on GPU card(s)
HYBRID_MODE	model is run on CPU Core(s), GPU card(s) or both

Definition at line 115 of file carlsim_datastructures.h.

◆ SpikeMonMode

enum SpikeMonMode

SpikeMonitors can be run in different modes: COUNT: Will collect only spike count information (such as number of spikes per neuron), not the explicit spike times. COUNT mode cannot retrieve exact spike times per neuron, and is thus not capable of computing spike train correlation etc. AER: Will collect spike information in AER format (will collect both neuron IDs and spike times).

Enumerator
COUNT	mode in which only spike count information is collected
AER	mode in which spike information is collected in AER format

Definition at line 321 of file carlsim_datastructures.h.

◆ STDPCurve

enum STDPCurve

CARLsim supports different STDP curves

Enumerator
EXP_CURVE	standard exponential curve
PULSE_CURVE	symmetric pulse curve
TIMING_BASED_CURVE	timing-based curve
UNKNOWN_CURVE	unknown curve type

Definition at line 298 of file carlsim_datastructures.h.

◆ STDPType

enum STDPType

CARLsim6 supports extents the two different flavors of STDP. STANDARD: The standard model of Bi & Poo (2001), nearest-neighbor. DA_MOD: Dopamine-modulated STDP, nearest-neighbor.

Enumerator
STANDARD	standard STDP of Bi & Poo (2001), nearest-neighbor
DA_MOD	dopamine-modulated STDP, nearest-neighbor
SE_MOD	serotonin-modulated STDP, nearest-neighbor
AC_MOD	acetylcholine-modulated STDP, nearest-neighbor
NE_MOD	norepinephrine-modulated STDP, nearest-neighbor
AC_DA_MOD	acetylcholine-influenced dopamine-modulated STDP, Belkaid & Krichmar (2019)
AC_NE_MOD	acetylcholine-norephinephrine encoded uncertainty, Avery & Krichmar (2017)
SE_DA_MOD	serotonin-dopamin cost/reward assessment, Asher, Craig, Zaldivar, Brewer, Krichmar (2013)
NM4_MOD	multivariate modulatated STDP, (experimental)
PKA_PLC_MOD	protein kinase/phospholiphase controlled LTP/LPD adopted from Nadim & Bucher (2014)
UNKNOWN_STDP

Definition at line 168 of file carlsim_datastructures.h.

◆ UpdateInterval

enum UpdateInterval

CARLsim supports different update frequency for weight update and weightChange update INTERVAL_10MS: the update interval will be 10 ms, which is 100Hz update frequency INTERVAL_100MS: the update interval will be 100 ms, which is 10Hz update frequency INTERVAL_1000MS: the update interval will be 1000 ms, which is 1Hz update frequency

Enumerator
INTERVAL_10MS	the update interval will be 10 ms, which is 100Hz update frequency
INTERVAL_100MS	the update interval will be 100 ms, which is 10Hz update frequency
INTERVAL_1000MS	the update interval will be 1000 ms, which is 1Hz update frequency

Definition at line 362 of file carlsim_datastructures.h.

Variable Documentation

◆ carlsimState_string

const char* carlsimState_string[]

static

Initial value:

= {
    "Configuration state", "Setup state", "Run state"
}

Definition at line 389 of file carlsim_datastructures.h.

◆ ComputingBackend_string

const char* ComputingBackend_string[]

static

Initial value:

= {
    "CPU (x86/x64 Multi Core Processor)", 
    "GPU (NVIDIA Many CUDA Core Processor)",
}

Definition at line 154 of file carlsim_datastructures.h.

◆ IcalcType_string

const char* IcalcType_string[]

static

Initial value:

= {
    "CUBA",
    "COBA",
    "NM4-mod.(LN21)",
    "GPCRs(NB14)"
    "DA/5HT/ACh-mod.(CK09)",
    "ACh/NE-mod.(ANCK12)",
    "ACh/NE-mod.(K12)",
    "ACh/NE-mod.(K13)",
    "D1,D2-rec.(AK12)",
    "ACh->DA(BK19)",
    "alpha1(ADK13)",
    "alpha2A(ADK13)",
    "D1(ADK13)",
    "D2(AK15)",
    "Unknown mode"
}

Definition at line 274 of file carlsim_datastructures.h.

◆ integrationMethod_string

const char* integrationMethod_string[]

static

Initial value:

= {
    "Forward-Euler", "4-th order Runge-Kutta", "Unknown integration method"
}

Definition at line 139 of file carlsim_datastructures.h.

◆ loggerMode_string

const char* loggerMode_string[]

static

Initial value:

= {
    "USER","DEVELOPER","SHOWTIME","SILENT","CUSTOM","Unknown mode"
}

Definition at line 100 of file carlsim_datastructures.h.

◆ neuromodulator_string

const char* neuromodulator_string[]

static

Initial value:

= {
    "Dopamine", 
    "Serotonin", 
    "Acetylcholine", 
    "Noradrenaline",    
    "Unknown neuromodulator"  
}

Definition at line 346 of file carlsim_datastructures.h.

◆ simMode_string

const char* simMode_string[]

static

Initial value:

= {
    "CPU mode","GPU mode","Hybrid mode"
}

Definition at line 120 of file carlsim_datastructures.h.

◆ spikeMonMode_string

const char* spikeMonMode_string[]

static

Initial value:

= {
    "SpikeCount Mode","SpikeTime Mode"
}

Definition at line 325 of file carlsim_datastructures.h.

◆ stdpCurve_string

const char* stdpCurve_string[]

static

Initial value:

= {
    "exponential curve",
    "pulse curve",
    "timing-based curve",
    "Unknow curve"
}

Definition at line 304 of file carlsim_datastructures.h.

◆ stdpType_desc

const char* stdpType_desc[]

static

Initial value:

= {
    "Standard STDP",
    "Dopamine-modulated STDP",
    "Serotonin-modulated STDP",
    "Acetylcholine-modulated STDP",
    "Norepinphrine-modulated STDP",
    "Acetylcholine-influenced-Dopamine-modulated STDP",
    "Acetylcholine-Norephinephrine encoded uncertainty STDP",
    "Serotonin-Dopamin encoded cost/reward STDP",
    "Multivariate-modulated STDP",
    "PKA/PLC-modulated STDP",
    
    
    
    
    
    
    
    
    
    "Unknown mode"
}

Definition at line 219 of file carlsim_datastructures.h.

◆ stdpType_string

const char* stdpType_string[]

static

Initial value:

= {
    "STANDARD",
    "DA_MOD",
    "SE_MOD",
    "AC_MOD",
    "NE_MOD",
    "AC_DA_MOD",
    "AC_NE_MOD",
    "SE_DA_MOD",
    "NM4_MOD",
    "PKA_PLC_MOD",
    
    
    
    
    
    
    
    
    
    "UNKNOWN_STDP"
}

Definition at line 194 of file carlsim_datastructures.h.

◆ updateInterval_string

const char* updateInterval_string[]

static

Initial value:

= {
    "10 ms interval", "100 ms interval", "1000 ms interval"
}

Definition at line 367 of file carlsim_datastructures.h.

Classes

Typedefs

Enumerations

Variables

Typedef Documentation

◆ ConnSTDPInfo

◆ GroupNeuromodulatorInfo

Enumeration Type Documentation

◆ CARLsimState

◆ ComputingBackend

◆ IcalcType

◆ integrationMethod_t

◆ LoggerMode

◆ Neuromodulator

◆ SimMode

◆ SpikeMonMode

◆ STDPCurve

◆ STDPType

◆ UpdateInterval

Variable Documentation

◆ carlsimState_string

◆ ComputingBackend_string

◆ IcalcType_string

◆ integrationMethod_string

◆ loggerMode_string

◆ neuromodulator_string

◆ simMode_string

◆ spikeMonMode_string

◆ stdpCurve_string

◆ stdpType_desc

◆ stdpType_string

◆ updateInterval_string