Parameter and MultiCompartmentReaction Error

Extending NEURON to handle reaction-diffusion problems.

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amerg
Posts: 4
Joined: Wed Jul 31, 2019 5:14 pm

Parameter and MultiCompartmentReaction Error

Post by amerg » Thu Aug 01, 2019 3:42 pm

I've been reading through the documentation and tutorials and I'm a bit confused on the rxd.Parameter object. I've used it to set different values between nodes for the rate in a rxd.Rate object, so I'm familiar with that usage. However, when I tried to use Parameter by multiplying a Species to set the rate of an rxd.MultiCompartmentReaction using this code:

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g_ip3r = rxd.Parameter(self.cyt, initial=g_ip3r_val)
ip3r_flux = rxd.MultiCompartmentReaction(ca[er], ca[cyt],  g_ip3r*(o5_ip3r[cyt]), membrane=cyt_er_membrane)
where o5_ip3r is a Species, I get this error.

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File "/home/adam/neuron/nrn/lib/python/neuron/rxd/species.py", line 431, in nodes
    initializer._do_init()
  File "/home/adam/neuron/nrn/lib/python/neuron/rxd/initializer.py", line 52, in _do_init
    rxd._init()
  File "/home/adam/neuron/nrn/lib/python/neuron/rxd/rxd.py", line 1486, in _init
    _update_node_data()
  File "/home/adam/neuron/nrn/lib/python/neuron/rxd/rxd.py", line 662, in _update_node_data
    if r is not None: r._update_indices()
  File "/home/adam/neuron/nrn/lib/python/neuron/rxd/generalizedReaction.py", line 193, in _update_indices
    active_regions = src_regions + dest_regions
TypeError: unsupported operand type(s) for +: 'set' and 'set'
I do not get this error if g_ip3r is replaced by a non Parameter object such as a float, but I do get the error if Species is replaced by a float. Is this due to my mistake, a bug, or is this a built-in limitation of Parameter and MultiCompartmentReaction? Thanks.

adamjhn
Posts: 34
Joined: Tue Apr 18, 2017 10:05 am

Re: Parameter and MultiCompartmentReaction Error

Post by adamjhn » Thu Aug 15, 2019 5:25 pm

Thanks for letting us know about this bug, it will be fixed in the next release. As you have identified, one workaround is to use a float instead of a Parameter.
Alternatively, like the calcium wave example, you could define the Parameter on the membrane instead of the cytosol;

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g_ip3r = rxd.Parameter(cyt_er_membrane, initial=g_ip3r_val)

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