# Parameters file for simulation.
# Should be used with spineIntegration.py
{
    "dtNeuron" : 0.025,  # integration dt [ms]
    "delta_calcium_sampling" : 1, # In millisecond [ms]. How often the calcium has 
        # to be synchronized within ecell and Neuron . 
    "t_equilibrium_neuron" : 100, # in milliseconds
    "t_equilibrium_ecell" : 300, # in seconds
    "tStop" : 20000, # [ms] Time to stop (NEURON time is the reference) the simulation  
    "t_buffer" : 10, #ms For how long the syncronization should be carried
    "neuron_time_recording_interval" : 0.1, # Recording at every ms
    "weight_sampling" : 50, # Total ms when the weight of the synapses will be updated
    "big_spine" : True,
    "bio_on" : True, 
    "spines_dist" : "all", #spines_dist = 'all' or spines_dist=zero or onebranch to populate one only#Number of spines
    "stimulated_spines" : ["spine558", "spine561", 
                           "spine557", "spine559", "spine560", "spine562"], #not stim
    "spine558" : ['ampa_s1', 'nmda_s1', 'ampa_s2', 'nmda_s2'],
    "spine561" : ['ampa_s1', 'nmda_s1', 'ampa_s2', 'nmda_s2'],
    "spine557" : ['ampa_non_stim'],
    "spine559" : ['ampa_non_stim'],
    "spine560" : ['ampa_non_stim'],
    "spine562" : ['ampa_non_stim'],
    
    "ampa_non_stim" : {}, # Empty dictionary to have the bio on, but not stim deployed.
    "ampa_s1" : 
        {"t_stim" : 2, # t_stim [s]  
         "numbers" : 50, # number
         "delay" : 0.05, # delay [s]
         "type" : "ampa" # , type
         },
    "nmda_s1" :
        {"t_stim" : 2, # t_stim [s]  
         "numbers" : 50, # number
         "delay" : 0.05, # delay [s]
         "type" : "nmda" # , type
         },
         
    "ampa_s2" : 
        {"t_stim" : 15, # t_stim [s]  
         "numbers" : 50, # number
         "delay" : 0.05, # delay [s]
         "type" : "ampa" # , type
         },
    "nmda_s2" :
        {"t_stim" : 15, # t_stim [s]  
         "numbers" : 50, # number
         "delay" : 0.05, # delay [s]
         "type" : "nmda" # , type
         },
         
    "kir_gkbar" : 0.00016, # S/cm2
    "biochemical_filename" : "biochemical_circuits/biomd183_loop.eml",
    'nthreads' : 2,
    'sec_to_rec' : ['all'],
    "var_to_plot" : ['v','cai','cali','ica'],
    "section_to_plot" : ['spine1_head','spine2_head'],
    "ca_leak_vmax" : 4e-3,
    "ca_pump_vmax" : 4e-3    
}