Reaction Not Proceeding

Extending NEURON to handle reaction-diffusion problems.

Moderators: hines, wwlytton, ramcdougal

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npatel
Posts: 3
Joined: Thu Jul 27, 2017 2:09 pm

Reaction Not Proceeding

Post by npatel » Mon Jul 31, 2017 11:13 am

Hello all,

I have recently started using NEURON and have been facing difficulties running basic reactions in that the concentrations of generated species never deviate from the initial concentrations. I am using NEURON v 7.4 and executing my models out of the Spyder interface downloaded through Anaconda. Simulations without reactions run fine and produce reasonable output. I have been largely trying to execute the basic hydration reaction from the tutorial posted. I have included the code I have been using as well as some commented alternative methods I have tried to execute the reactions.

Code: Select all

from neuron import h, rxd
from matplotlib import pyplot

#h.load_file('stdrun.hoc')
#h.CVode().active(1) <- if uncommented gives unreasonable time steps
#h.initnrn(0, 0.025)

dend = h.Section()
r = rxd.Region(h.allsec())
#r = rxd.Region(h.allsec(), nrn_region='i')

hydrogen = rxd.Species(r, initial=1)
oxygen = rxd.Species(r, initial=1)
water = rxd.Species(r, initial=0)

reaction = rxd.Reaction(2 * hydrogen + oxygen > water, 1)
#reaction = rxd.Reaction(2 * hydrogen + oxygen > water, 1, regions=r)

h.finitialize()
#h.finitialize(-65)
#h.CVode().re_init()

heading = '{t:>10s}  {h:>10s}  {o:>10s}  {h2o:>10s}'
data = '{t:10g}  {h:10g}  {o:10g}  {h2o:10g}'

def advance_a_bit():
    for i in xrange(5):
        h.fadvance()
        print data.format(t=h.t, h=hydrogen.nodes[0].concentration,
                          o=oxygen.nodes[0].concentration,
                          h2o=water.nodes[0].concentration)

print heading.format(t='t', h='hydrogen', o='oxygen', h2o='H2O')
print heading.format(t='-', h='--------', o='------', h2o='---')

advance_a_bit()

"""
Method 2: Printing Concentrations Adapted form 'Calcium Waves in RxD'
h.CVode().re_init()


time = []
concentration = []

def save():
    print 't=', h.t, 'conc=', water.nodes[0].concentration #dend.wateri
    
for t in xrange(0, 1000, 10):
    h.CVode().event(t, save)
    time.append(h.t)
    #concentration.append(dend.wateri)

h.continuerun(1000)
"""

"""
Method 3: Using recording variables

#Set up recording variables
v_vec = h.Vector()     #Membrane potential vector
t_vec = h.Vector()     #Time stamp vector
v_vec.record(water.nodes[0].concentration)
t_vec.record(h._ref_t)

#Run the simulation
h.tstop = 40.0
h.run()

#Plot the results
from matplotlib import pyplot
pyplot.figure(figsize=(8,4))
pyplot.plot(t_vec, v_vec)
pyplot.xlabel('Time (ms)')
pyplot.ylabel('mV')
pyplot.show()
"""
I appreciate the help greatly, thank you much!

ramcdougal
Posts: 135
Joined: Fri Nov 28, 2008 3:38 pm
Location: Yale School of Medicine

Re: Reaction Not Proceeding

Post by ramcdougal » Mon Jul 31, 2017 1:45 pm

What operating system?

I just tried it on my Windows machine through Spyder, and it worked for me.

Could you try installing the latest alpha version (http://www.neuron.yale.edu/ftp/neuron/versions/alpha/) and seeing if that solves the problem?

npatel
Posts: 3
Joined: Thu Jul 27, 2017 2:09 pm

Re: Reaction Not Proceeding

Post by npatel » Mon Jul 31, 2017 3:18 pm

I am using Windows 10, I will try installing the latest alpha version. Thanks!

npatel
Posts: 3
Joined: Thu Jul 27, 2017 2:09 pm

Re: Reaction Not Proceeding

Post by npatel » Tue Aug 01, 2017 8:42 am

I wanted to provide an update on the situation. I tried updating the latest alpha version and the reactions now execute as expected. Thank you much!

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