Edited ODR

conf/config_ODR.yml

@@ -1,122 +1,154 @@
-A_CORR:
-- 0.0025
-- 0.0025
-A_DIST:
-- 0.0
-- 0.0
-A_STIM:
-- 0.2
-- 0.0
-BUMP_SWITCH:
-- 0
-- 0
-CHECK_BISTABILITY: 0
-CORR_FF:
-- 0.25
-- 0.25
-DATA_PATH: /home/leon/models/lif_cpp/data/simul/odr_Ie_2.80_phi_180_ini_32
-DT: 0.1
-DURATION: 6000.0
-FRAC:
-- 0.8
-- 0.2
-GAIN: 1.0
-IF_FF_CORR: 0
-IF_FF_NOISE: 1
-IF_LOAD_MAT: 1
-IF_NMDA: 1
+##########################################
+# Simulation parameters
+##########################################
 IF_SAVE_DATA: 1
+# to load connectivity matrix from MAT_PATH
+IF_LOAD_MAT: 1
+# to save connectivity matrix from MAT_PATH
 IF_SAVE_MAT: 0
-IF_STP: 1
-Iext:
-- 0.0028
-- 0.00175
-Jab:
-- 7.5
-- -1.35
-- 1.25
-- -2.0
-K: 4000.0
-KAPPA:
-- 0.5
-- 0.45
-- 0.5
-- 0.5
-KAPPA_DIST:
-- 0.0
-- 0.0
-KAPPA_STIM:
-- 0.5
-- 0.0
-LR_LOAD: 0
-LR_MEAN:
-- 0.0
-- 0.0
-- 0.0
-LR_RANK: 3
-LR_RHO:
-- 0.0
-- 1.0
-- 0.0
-LR_SEED: 1
-LR_STD:
-- 1.0
-- 1.0
-- 1.0
-MAT_PATH: /home/leon/models/lif_cpp/data/matrix
-N: 40000
-N_POP: 2
-PHI_DIST:
-- 90.0
-- 0.0
-PHI_STIM:
-- 180.0
-- 0.0
-PROBA:
-- cos
-- cos
-- cos
-- cos
-R_NMDA:
-- 0.5
-- 0.5
-STD_DIST:
-- 0.0
-- 0.0
-STD_FF:
-- 2.5e-05
-- 2.5e-05
-STD_STIM:
-- 0.0
-- 0.0
-TAU_FAC:
-- 550
-- 850
-TAU_MEM:
-- 20.0
-- 10.0
-TAU_NMDA:
-- 80.0
-- 40.0
-TAU_REC:
-- 250
-- 200
-TAU_SYN:
-- 4.0
-- 2.0
-T_DIST:
-- 13500.0
-- 14500.0
+
+# saving the last T_SAVE ms
 T_SAVE: 500.0
+
+# path for the output files of the simulation
+DATA_PATH: /home/leon/models/lif_cpp/data/simul
+# path to load/save the connectivity matrix
+MAT_PATH: /home/leon/models/lif_cpp/data/matrix
+
+# output different prompts for debugging purpose
+verbose: 1
+
+# Time step in ms
+DT: 0.1
+# total simulation time in ms
+DURATION: 20000.0
+# time to start showing simulation result ms
 T_STEADY: 5000.0
-T_STIM:
-- 1000.0
-- 1500.0
+# Saving to files every T_WINDOW in ms
 T_WINDOW: 250.0
-USE:
-- 0.03
-- 0.03
-V_LEAK: 0.0
-V_REST: -70.0
+
+##########################################
+# Network parameters
+##########################################
+# Total number of neurons
+N: 40000
+# Number of populations
+N_POP: 2
+# Average number of presynaptic inputs
+K: 4000.0
+# K: 4000.0
+# Fraction of neurons in each population
+FRAC: [0.8, 0.2]
+
+##########################################
+# Parameters for the stimulus presentation
+##########################################
+# stimulus has a cosine shape
+# time for stimulus onset/offset in ms 
+T_STIM: [1000.0, 1500.0]
+# amplitude of the stimulus
+A_STIM: [0.2, 0.0]
+# std of the stimulus
+STD_STIM: [0.0, 0.0]
+# Phase of the 1st stimulus
+PHI_STIM: [180.0, 0.0]
+# Tuning of the stimulus
+KAPPA_STIM: [0.5, 0.0]
+
+T_DIST: [135000.0, 145000.0]
+# amplitude of the stimulus
+A_DIST: [0.0, 0.0]
+# std of the stimulus
+STD_DIST: [0.0, 0.0]
+# Phase of the 1st stimulus
+PHI_DIST: [90.0, 0.0]
+# Tuning of the stimulus
+KAPPA_DIST: [0.0, 0.0]
+
+CHECK_BISTABILITY: 0
+BUMP_SWITCH: [0, 0]
+##############
+# Network Dynamics
+##############
+# Threshold in mV
 V_THRESH: -50.0
-verbose: 1
+# Resting potential in mV
+V_REST: -70.0
+# Leak in mV
+V_LEAK: 0.0
+
+# Membrane time constants in ms
+TAU_MEM: [20.0, 10.0]
+# Synaptic time constants in ms
+TAU_SYN: [4.0, 2.0]
+
+# Adding NMDA currents
+IF_NMDA: 1
+# NMDA time constants in s
+TAU_NMDA: [80.0, 40.0]
+# NMDA strength ratio
+R_NMDA: [0.5, 0.5]
+
+# Network's gain
+GAIN: 1.0
+
+# Feedforward inputs strengths
+Iext: [.002, 0.00175]
+# Synaptic strengths 
+# Jab: [15.0, -1.35, 2.5, -2.0]
+Jab: [10.0, -1.25, 1.25, -1.7]
+# Jab: [14.0, -1.35, 2.1, -1.95]
+
+##############
+# CONNECTIVITY
+##############
+# PROBA can be 'cos', 'spec', 'gauss', 'None'
+# By default the matrix is a random sparse matrix Cij
+# 'cos' gives a sparse matrix with strong cosine structure,
+# Pij = (1 + KAPPA cos(theta_ij) / sqrt(Kb)), Cij = 1 with proba Pij
+# 'spec' gives a sparse matrix with weak cosine structure,
+# Pij = (1 + KAPPA cos(theta_ij) / sqrt(Kb)) , Cij = 1 with proba Pij
+PROBA: ['cos', 'cos', 'cos', 'cos']
+KAPPA: [1.0, 0.85, 1.0, 1.0]
+# KAPPA: [0.5, 0.425, 0.5, 0.5]
+
+# PROBA: ['lr', 'rand', 'rand', 'rand']
+# KAPPA: [3.0, 0.0, 0.0, 0.0]
+
+##############
+# STP
+##############
+# adds STP (as in Mato & Hansel, J Neurosci, 2012)
+IF_STP: 1
+USE: [0.03, 0.03]
+TAU_FAC: [550, 850]
+TAU_REC: [250, 200]
+
+##############
+# Feed Forward
+##############
+# adds gaussian noise to feedforward
+IF_FF_NOISE: 0
+# variance of the noise
+STD_FF: [0.00002, 0.00002]
+
+# adds cosine correlation to the feedforward
+IF_FF_CORR: 0
+# amplitude of the correlations
+A_CORR: [0.001, 0.001]
+# tuning of the correlations
+CORR_FF: [1.0, 1.0]
+
+######################
+# Low rank
+####################
+LR_SEED: 1
+LR_LOAD: 0
+
+LR_RANK: 3
+LR_MEAN: [0.0, 0.0, 0.0]
+LR_STD: [1.0, 1.0, 1.0]
+# ksi_1 ksi_2, ksi_1 h_s, ksi_2 h_s
+# LR_RHO: [0.05, 0.8, 0.2]
+# LR_RHO: [0.0, 0.8, -0.2]
+LR_RHO: [0.0, 1.0, 0.0]

conf/config_ODR.yml.bak

@@ -2,6 +2,11 @@
 # Simulation parameters
 ##########################################
 IF_SAVE_DATA: 1
+# to load connectivity matrix from MAT_PATH
+IF_LOAD_MAT: 1
+# to save connectivity matrix from MAT_PATH
+IF_SAVE_MAT: 0
+
 # saving the last T_SAVE ms
 T_SAVE: 500.0
 
@@ -16,7 +21,7 @@ verbose: 1
 # Time step in ms
 DT: 0.1
 # total simulation time in ms
-DURATION: 6000.0
+DURATION: 20000.0
 # time to start showing simulation result ms
 T_STEADY: 5000.0
 # Saving to files every T_WINDOW in ms
@@ -31,6 +36,7 @@ N: 40000
 N_POP: 2
 # Average number of presynaptic inputs
 K: 4000.0
+# K: 4000.0
 # Fraction of neurons in each population
 FRAC: [0.8, 0.2]
 
@@ -49,7 +55,7 @@ PHI_STIM: [180.0, 0.0]
 # Tuning of the stimulus
 KAPPA_STIM: [0.5, 0.0]
 
-T_DIST: [13500.0, 14500.0]
+T_DIST: [135000.0, 145000.0]
 # amplitude of the stimulus
 A_DIST: [0.0, 0.0]
 # std of the stimulus
@@ -87,51 +93,28 @@ R_NMDA: [0.5, 0.5]
 GAIN: 1.0
 
 # Feedforward inputs strengths
-Iext: [.0025, 0.00175]
+Iext: [.002, 0.00175]
 # Synaptic strengths 
 # Jab: [15.0, -1.35, 2.5, -2.0]
-Jab: [7.5, -1.35, 1.25, -2.0]
+Jab: [10.0, -1.25, 1.25, -1.7]
 # Jab: [14.0, -1.35, 2.1, -1.95]
 
-# # External inputs strengths
-# Iext: [.004, .001]
-# # Synaptic strengths 
-# Jab: [1.0, -1.5, 1.0, -1.0]
-
 ##############
 # CONNECTIVITY
 ##############
-# to load connectivity matrix from MAT_PATH
-IF_LOAD_MAT: 1
-# to save connectivity matrix from MAT_PATH
-IF_SAVE_MAT: 0
-
-# connectivity type
 # PROBA can be 'cos', 'spec', 'gauss', 'None'
 # By default the matrix is a random sparse matrix Cij
 # 'cos' gives a sparse matrix with strong cosine structure,
 # Pij = (1 + KAPPA cos(theta_ij) / sqrt(Kb)), Cij = 1 with proba Pij
 # 'spec' gives a sparse matrix with weak cosine structure,
 # Pij = (1 + KAPPA cos(theta_ij) / sqrt(Kb)) , Cij = 1 with proba Pij
-
 PROBA: ['cos', 'cos', 'cos', 'cos']
-KAPPA: [0.5, 0.45, 0.5, 0.5]
+KAPPA: [1.0, 0.85, 1.0, 1.0]
+# KAPPA: [0.5, 0.425, 0.5, 0.5]
 
 # PROBA: ['lr', 'rand', 'rand', 'rand']
 # KAPPA: [3.0, 0.0, 0.0, 0.0]
 
-# Low rank
-LR_SEED: 1
-LR_LOAD: 0
-
-LR_RANK: 3
-LR_MEAN: [0.0, 0.0, 0.0]
-LR_STD: [1.0, 1.0, 1.0]
-# ksi_1 ksi_2, ksi_1 h_s, ksi_2 h_s
-# LR_RHO: [0.05, 0.8, 0.2]
-# LR_RHO: [0.0, 0.8, -0.2]
-LR_RHO: [0.0, 1.0, 0.0]
-
 ##############
 # STP
 ##############
@@ -145,13 +128,27 @@ TAU_REC: [250, 200]
 # Feed Forward
 ##############
 # adds gaussian noise to feedforward
-IF_FF_NOISE: 1
+IF_FF_NOISE: 0
 # variance of the noise
-STD_FF: [0.000025, 0.000025]
+STD_FF: [0.00002, 0.00002]
 
 # adds cosine correlation to the feedforward
 IF_FF_CORR: 0
 # amplitude of the correlations
-A_CORR: [0.0025, 0.0025]
-# 
-CORR_FF: [0.25, 0.25]
+A_CORR: [0.001, 0.001]
+# tuning of the correlations
+CORR_FF: [1.0, 1.0]
+
+######################
+# Low rank
+####################
+LR_SEED: 1
+LR_LOAD: 0
+
+LR_RANK: 3
+LR_MEAN: [0.0, 0.0, 0.0]
+LR_STD: [1.0, 1.0, 1.0]
+# ksi_1 ksi_2, ksi_1 h_s, ksi_2 h_s
+# LR_RHO: [0.05, 0.8, 0.2]
+# LR_RHO: [0.0, 0.8, -0.2]
+LR_RHO: [0.0, 1.0, 0.0]