Error simulating tutorial 3a

[ddelpiano]

• load tutorial 3a
• create network
• back to edit
• edit the populations number of cells (info provided below).

Only the popParams number of cells have been edited

{E2: {'cellType': 'E', 'yRange': [50, 150], 'numCells': 125}, I2: {'cellType': 'I', 'yRange': [50, 150], 'numCells': 100}, E4: {'cellType': 'E', 'yRange': [150, 300], 'numCells': 20}, I4: {'cellType': 'I', 'yRange': [150, 300], 'numCells': 40}, E5: {'cellType': 'E', 'ynormRange': [0.6, 1.0], 'numCells': 66}, I5: {'cellType': 'I', 'ynormRange': [0.6, 1.0], 'numCells': 77}}

Error while instantiating the NetPyNE model
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
~/git/netpyne-ui/netpyne_ui/netpyne_geppetto.py in instantiateNetPyNEModelInGeppetto(self=<netpyne_ui.netpyne_geppetto.NetPyNEGeppetto object>, args={})
    193             with redirect_stdout(sys.__stdout__):
    194                 if not args.get("usePrevInst", False):
--> 195                     netpyne_model = self.instantiateNetPyNEModel()
        netpyne_model = undefined
        self.instantiateNetPyNEModel = <bound method NetPyNEGeppetto.instantiateNetPyNEModel of <netpyne_ui.netpyne_geppetto.NetPyNEGeppetto object at 0x7fa378da58d0>>
    196                     self.geppetto_model = self.model_interpreter.getGeppettoModel(netpyne_model)
    197 

~/git/netpyne-ui/netpyne_ui/netpyne_geppetto.py in instantiateNetPyNEModel(self=<netpyne_ui.netpyne_geppetto.NetPyNEGeppetto object>)
    665             #netcoded = jsonpickle.encode(self.netParams, unpicklable=False)
    666             #simcoded = jsonpickle.encode(self.simConfig, unpicklable=False)
--> 667             sim.create(self.netParams, self.simConfig)
        global sim.create = <function create at 0x7fa379ce49e0>
        self.netParams = <netpyne.specs.netParams.NetParams object at 0x7fa3149cb5d0>
        self.simConfig = <netpyne.specs.simConfig.SimConfig object at 0x7fa314193f90>
    668             sim.net.defineCellShapes()  # creates 3d pt for cells with stylized geometries
    669             sim.gatherData(gatherLFP=False)

~/git/netpyne-ui/src/netpyne/netpyne/sim/wrappers.py in create(netParams=<netpyne.specs.netParams.NetParams object>, simConfig=<netpyne.specs.simConfig.SimConfig object>, output=False, clearAll=False)
     55     conns = sim.net.connectCells()                # create connections between cells based on params
     56     stims = sim.net.addStims()                    # add external stimulation to cells (IClamps etc)
---> 57     rxd = sim.net.addRxD()                    # add reaction-diffusion (RxD)
        rxd = undefined
        sim.net.addRxD = <bound method addRxD of <netpyne.network.network.Network object at 0x7fa365a42dd0>>
     58     simData = sim.setupRecording()             # setup variables to record for each cell (spikes, V traces, etc)
     59 

~/git/netpyne-ui/src/netpyne/netpyne/network/netrxd.py in addRxD(self=<netpyne.network.network.Network object>, nthreads=None)
     80             self._addExtracellularRegion('extracellular', rxdParams['extracellular'])
     81         if 'species' in rxdParams:
---> 82             self._addSpecies(rxdParams['species'])
        self._addSpecies = <bound method _addSpecies of <netpyne.network.network.Network object at 0x7fa365a42dd0>>
        rxdParams = {constants: {ip3_init: 0.0, caDiff: 0.08, ip3Diff: 1.41, caci_init: 1e-05, caco_init: 2.0, gip3r: 1204000, gserca: 0.3913, gleak: 6.02, kserca: 0.1, kip3: 0.15, kact: 0.4, ip3rtau: 2000, fc: 0.8, fe: 0.2, margin: 20}, regions: {cyt: {'cells': 'all', 'secs': ['all'], 'nrn_region': 'i', 'geometry': {'class': 'FractionalVolume', 'args': {'volume_fraction': 0.8, 'surface_fraction': 1}}, 'dimension': None, 'dx': None}, er: {'cells': 'all', 'secs': ['all'], 'geometry': {'class': 'FractionalVolume', 'args': {'volume_fraction': 0.2}}, 'nrn_region': None, 'dimension': None, 'dx': None}, cyt_er_membrane: {'cells': 'all', 'secs': ['all'], 'geometry': {'class': 'ScalableBorder', 'args': {'scale': 1, 'on_cell_surface': False}}, 'nrn_region': None, 'dimension': None, 'dx': None}, ecs: {'extracellular': True, 'xlo': -20, 'ylo': -520, 'zlo': -20, 'xhi': 120, 'yhi': 20, 'zhi': 120, 'dx': 5, 'volume_fraction': 0.2, 'tortuosity': 1.6}}, species: {ca: {'regions': ['cyt', 'er', 'ecs'], 'd': 0.08, 'charge': 2, 'initial': 'caco_init if isinstance(node,rxd.node.NodeExtracellular) else (0.0017 - caci_init * fc) / fe if node.region == er else caci_init', 'ecs_boundary_conditions': None, 'atolscale': 1}, ip3: {'regions': ['cyt'], 'd': 1.41, 'initial': 0.0, 'charge': 0, 'ecs_boundary_conditions': None, 'atolscale': 1}}, states: {ip3r_gate_state: {'regions': ['cyt_er_membrane'], 'initial': 0.8}}, multicompartmentReactions: {serca: {'reactant': 'ca[cyt]', 'product': 'ca[er]', 'rate_f': 'gserca / ((kserca / (1000. * ca[cyt])) ** 2 + 1)', 'membrane': 'cyt_er_membrane', 'custom_dynamics': True, 'rate_b': None, 'regions': [None], 'membrane_flux': False}, leak: {'reactant': 'ca[er]', 'product': 'ca[cyt]', 'rate_f': 6.02, 'rate_b': 6.02, 'membrane': 'cyt_er_membrane', 'regions': [None], 'custom_dynamics': False, 'membrane_flux': False}, ip3r: {'reactant': 'ca[er]', 'product': 'ca[cyt]', 'rate_f': 'gip3r * (ip3[cyt] * 1000. * ca[cyt] / (ip3[cyt] + kip3) / (1000. * ca[cyt] + kact) * ip3r_gate_state[cyt_er_membrane]) ** 3', 'rate_b': 'gip3r * (ip3[cyt] * 1000. * ca[cyt] / (ip3[cyt] + kip3) / (1000. * ca[cyt] + kact) * ip3r_gate_state[cyt_er_membrane]) ** 3', 'membrane': 'cyt_er_membrane', 'regions': [None], 'custom_dynamics': False, 'membrane_flux': False}}, rates: {ip3rg: {'species': 'ip3r_gate_state[cyt_er_membrane]', 'rate': '(1. / (1 + 1000. * ca[cyt] / (0.3)) - ip3r_gate_state[cyt_er_membrane]) / ip3rtau', 'regions': [], 'membrane_flux': False}}}
     83         if 'states' in rxdParams:
     84             self._addStates(rxdParams['states'])

~/git/netpyne-ui/src/netpyne/netpyne/network/netrxd.py in _addSpecies(self=<netpyne.network.network.Network object>, params={ca: {'regions': ['cyt', 'er', 'ecs'], 'd': 0.08...'ecs_boundary_conditions': None, 'atolscale': 1}})
    283                                                             atolscale=param['atolscale'],
    284                                                             name=name,
--> 285                                                             ecs_boundary_conditions=param['ecs_boundary_conditions'])
        global ecs_boundary_conditions = undefined
        param = {'regions': ['cyt', 'er', 'ecs'], 'd': 0.08, 'charge': 2, 'initial': 'caco_init if isinstance(node,rxd.node.NodeExtracellular) else (0.0017 - caci_init * fc) / fe if node.region == er else caci_init', 'ecs_boundary_conditions': None, 'atolscale': 1}
    286         else: self.rxd['species'][label]['hObj'] = None
    287 

~/miniconda3/envs/netpyne/lib/python3.7/site-packages/neuron/rxd/species.py in __init__(self=Species(regions=[Region(..., nrn_region='i', geo...=2, initial=<function initial at 0x7fa315234e60>), regions=[Region(..., nrn_region='i', geometry=FractionalV...eighbor_areas_fraction=0.8), dx=0.25, name='cyt'), Region(..., nrn_region=None, geometry=Fractional...neighbor_areas_fraction=0.2), dx=0.25, name='er'), Extracellular(xlo=-20, ylo=-520, zlo=-20, xhi=12..., zhi=120.0, tortuosity=1.6, volume_fraction=0.2)], d=0.08, name='ca', charge=2, initial=<function initial>, atolscale=1, ecs_boundary_conditions=None, represents=None)
   1633             if initializer.is_initialized():
   1634                 self._do_init()
-> 1635                 rxd._update_node_data(True, True)
        rxd._update_node_data = <function _update_node_data at 0x7fa379ab8320>
   1636 
   1637     def _do_init(self):

~/miniconda3/envs/netpyne/lib/python3.7/site-packages/neuron/rxd/rxd.py in _update_node_data(force=True, newspecies=True)
    638                 # TODO: separate compiling reactions -- so the indices can be updated without recompiling
    639                 _include_flux(True)
--> 640                 _setup_units(force=True)
        global _setup_units = <function _setup_units at 0x7fa379ab8290>
        force = True
    641 
    642             # end#if

~/miniconda3/envs/netpyne/lib/python3.7/site-packages/neuron/rxd/rxd.py in _setup_units(force=True)
    597             clear_rates()
    598             _setup_memb_currents()
--> 599             _compile_reactions()
        global _compile_reactions = <function _compile_reactions at 0x7fa379ab8560>
    600             if _cvode_object.active():
    601                 _cvode_object.re_init()

~/miniconda3/envs/netpyne/lib/python3.7/site-packages/neuron/rxd/rxd.py in _compile_reactions()
   1141     c_region_list = []
   1142     for sets in matched_regions:
-> 1143         c_region_list.append(_c_region(sets))
        c_region_list.append = <built-in method append of list object at 0x7fa30ef23370>
        _c_region = <class 'neuron.rxd.region._c_region'>
        sets = set()
   1144 
   1145     for rptr in _all_reactions:

~/miniconda3/envs/netpyne/lib/python3.7/site-packages/neuron/rxd/region.py in __init__(self=<neuron.rxd.region._c_region object>, regions=set())
     55         global _c_region_lookup
     56         self._regions = [weakref.ref(r) for r in regions]
---> 57         self._overlap = self._regions[0]()._secs1d
        self._overlap = undefined
        self._regions._secs1d = undefined
     58         self.num_regions = len(self._regions)
     59         self.num_species = 0

IndexError: list index out of range

[ddelpiano]

from a further analysis it seems that the changes in the population number of cells are not impacting the outcome.
The problem seems to be the fact that the network is instantiated and then we try to instantiate this a second time.

[ddelpiano]

To check that the sim.clearAll() gets called when we try to re-instantiate.