Search found 11 matches

by ngreiner
Thu Apr 25, 2019 6:03 pm
Forum: Other questions
Topic: Event delivery (CVode.event) not impacting simulation time
Replies: 4
Views: 2128

Re: Event delivery (CVode.event) not impacting simulation time

Dear Ted, Thank you for your reply and sorry for the delay of mine. I ran a test using played vector with interpolation to drive my extracellular batteries instead of abrupt changes delivered using the event delivery system. It successfully got rid of the IDA initialization failures. However, I naiv...
by ngreiner
Thu Apr 25, 2019 8:15 am
Forum: NEURON + Python
Topic: Delete a section does not work
Replies: 14
Views: 8280

Re: Delete a section does not work

Hello, I have also fell into a trap where HOC sections were not deleted as I wanted to. I had two python objects which referenced each other (thus forming a reference cycle), and one of which held a list of references to HOC sections. When dereferencing the python objects (either using 'del obj' or ...
by ngreiner
Fri Oct 12, 2018 9:28 am
Forum: Other questions
Topic: Event delivery (CVode.event) not impacting simulation time
Replies: 4
Views: 2128

Re: Event delivery (CVode.event) not impacting simulation time

Hi again, After reading this post: https://www.neuron.yale.edu/phpBB/viewtopic.php?t=3034 , I found the means to force the integrator to stop at the times of the specified events by inserting a cvode.re_init() call in the py_callable called by my events. def switch_on_eext(): print 'switching on' pr...
by ngreiner
Thu Oct 11, 2018 12:01 pm
Forum: Other questions
Topic: Event delivery (CVode.event) not impacting simulation time
Replies: 4
Views: 2128

Event delivery (CVode.event) not impacting simulation time

Dear all, I am encountering an issue with the use of custom event deliveries using the CVode.event method. My problem, reproducible with the MWE below, is that the delivery of events does not impact the progress of the simulation time. Specifically, when I use the variable time step method with maxs...
by ngreiner
Thu Oct 11, 2018 11:13 am
Forum: Other questions
Topic: Conflict between CVode.maxstep, NetCon instances, and extracellular
Replies: 1
Views: 1232

Conflict between CVode.maxstep, NetCon instances, and extracellular

Dear all, I have encountered a conflict between the use of the variable time step method and instances of NetCon objects when using the extracellular mechanism . I found a workaround while writing this post but I decided to share my finding anyway. The problem, materialised by the MWE below, is that...
by ngreiner
Tue Aug 28, 2018 4:00 am
Forum: Anatomically detailed models
Topic: area() function -- stylized method -- 3d-method
Replies: 4
Views: 1693

Re: area() function -- stylized method -- 3d-method

Thank you for your replies. I was puzzled by the value returned by sec(0.5).area() in the case of the 3d-method, but that was because my formula for calculating the side area of a frustum was incorrect. After using the appropriate formula (given at http://mathworld.wolfram.com/ConicalFrustum.html ),...
by ngreiner
Mon Aug 27, 2018 5:58 pm
Forum: Anatomically detailed models
Topic: area() function -- stylized method -- 3d-method
Replies: 4
Views: 1693

area() function -- stylized method -- 3d-method

Hello, I am encountering a behaviour of the area() function which I don't understand, materialised by the code-example below. The mentioned behaviour is that when I define the geometry of a section using the 3d-method, the formula `sec(0.5).area()` and `sec.L * sec.diam * h.PI` yield different resul...
by ngreiner
Fri Jun 29, 2018 2:13 pm
Forum: Other questions
Topic: Using event delivery system with fixed time step method.
Replies: 7
Views: 2671

Re: Using event delivery system with fixed time step method.

I see. Thank you for the quick reply.

Would you be kind enough to also explain to me why using h.cvode.solve(h.tstop) leads to h.t=10000000 (despite the fact that h.tstop==5.0) when cvode.active()==0 ?
by ngreiner
Fri Jun 29, 2018 5:56 am
Forum: Other questions
Topic: Using event delivery system with fixed time step method.
Replies: 7
Views: 2671

Using event delivery system with fixed time step method.

Dear Ted, I am encountering an issue when using the event delivery system while cvode_active() == 0. Basically, the following code from neuron import h h.load_file('stdrun.hoc') sec = h.Section() sec.insert('hh') def hi(): print 'hi' h.dt = 0.025 h.tstop = 5.0 h.finitialize() h.cvode.event(2.5, hi) ...
by ngreiner
Fri Jun 09, 2017 7:35 am
Forum: NEURON + Python
Topic: uninsert python
Replies: 6
Views: 11102

Re: uninsert python

Thank you for your prompt reply.
Nathan
by ngreiner
Thu Jun 08, 2017 3:22 pm
Forum: NEURON + Python
Topic: uninsert python
Replies: 6
Views: 11102

Re: uninsert python

Dear Ted, I am encountering the following issues when trying to uninsert the extracellular mechanism from a section using python: >>> fiber.internodes[1].hoc_internal_name() '__nrnsec_0x7ff9e6804bc0' >>> h('__nrnsec_0x7ff9e6804bc0 uninsert extracellular') NEURON: Can't uninsert mechanism extracellul...