# 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" : ['spine18', 'spine19', 'spine20', 'spine60', 'spine61', 
                            'spine62', 'spine94', 'spine95', 'spine96'],
    
    "spine18" : ['ampa_s1', 'nmda_s1', 'ampa_s4', 'nmda_s4'],
    "spine19" : ['ampa_s1', 'nmda_s1', 'ampa_s4', 'nmda_s4'],
    "spine20" : ['ampa_s2', 'nmda_s2', 'ampa_s4', 'nmda_s4'],
    
    "spine60" : ['ampa_s3', 'nmda_s3'],
    "spine61" : ['ampa_s3', 'nmda_s3'],
    "spine62" : ['ampa_s3', 'nmda_s3'],
    
    "spine94" : ['ampa_s2', 'nmda_s2'],
    "spine95" : ['ampa_s2', 'nmda_s2'],
    "spine96" : ['ampa_s2', 'nmda_s2'],
    
    "ampa_s1" : 
        {"t_stim" : 2, # t_stim [s]  
         "numbers" : 400, # number
         "delay" : 0.1, # delay [s]
         "type" : "ampa" # , type
         },
    "nmda_s1" :
        {"t_stim" : 2, # t_stim [s]  
         "numbers" : 400, # number
         "delay" : 0.1, # delay [s]
         "type" : "nmda" # , type
         },
    "ampa_s2" :
        {"t_stim" : 6, # t_stim [s]  
         "numbers" : 20, # number
         "delay" : 0.1, # delay [s]
         "type" : "ampa" # , type
         },

    "nmda_s2" :
        {"t_stim" : 6, # t_stim [s]  
         "numbers" : 20, # number
         "delay" : 0.1, # delay [s]
         "type" : "nmda" # , type
         },
         
    "ampa_s3" : 
        {"t_stim" : 10, # t_stim [s]  
         "numbers" : 400, # number
         "delay" : 0.1, # delay [s]
         "type" : "ampa" # , type
         },
    "nmda_s3" :
        {"t_stim" : 10, # t_stim [s]  
         "numbers" : 400, # number
         "delay" : 0.1, # delay [s]
         "type" : "nmda" # , type
         },
         
    "ampa_s4" : 
        {"t_stim" : 15, # t_stim [s]  
         "numbers" : 40, # number
         "delay" : 0.1, # delay [s]
         "type" : "ampa" # , type
         },
    "nmda_s4" :
        {"t_stim" : 15, # t_stim [s]  
         "numbers" : 40, # number
         "delay" : 0.1, # 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" : ['MSP_Cell[0].soma', 'MSP_Cell[0].dend3_1[1]', 
    #'MSP_Cell[0].dend3_1[0]', 'MSP_Cell[0].dend3', 'spine1_head','spine2_head', 
    #'spine_1_psd', 'spine1_neck', 'spine2_psd', 'spine2_neck', 'spine531_head',
    #'spine531_psd', 'spine531_neck', 'spine532_head', 'spine532_psd', 'spine532_neck'],
    "section_to_plot" : ['MSP_Cell[0].soma', 'MSP_Cell[0].dend3_1[1]', 
    'MSP_Cell[0].dend3_1[0]', 'MSP_Cell[0].dend3', 'spine1_head','spine2_head', 
    'spine_1_psd', 'spine1_neck', 'spine2_psd', 'spine2_neck'],
    "ca_leak_vmax" : 4e-3,
    "ca_pump_vmax" : 4e-3    
}