Search found 11 matches
- Thu Apr 25, 2019 6:03 pm
- Forum: Other questions
- Topic: Event delivery (CVode.event) not impacting simulation time
- Replies: 4
- Views: 4893
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...
- Thu Apr 25, 2019 8:15 am
- Forum: NEURON + Python
- Topic: Delete a section does not work
- Replies: 14
- Views: 20241
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 ...
- Fri Oct 12, 2018 9:28 am
- Forum: Other questions
- Topic: Event delivery (CVode.event) not impacting simulation time
- Replies: 4
- Views: 4893
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...
- Thu Oct 11, 2018 12:01 pm
- Forum: Other questions
- Topic: Event delivery (CVode.event) not impacting simulation time
- Replies: 4
- Views: 4893
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...
- Thu Oct 11, 2018 11:13 am
- Forum: Other questions
- Topic: Conflict between CVode.maxstep, NetCon instances, and extracellular
- Replies: 1
- Views: 2412
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...
- Tue Aug 28, 2018 4:00 am
- Forum: Anatomically detailed models
- Topic: area() function -- stylized method -- 3d-method
- Replies: 4
- Views: 11270
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 ),...
- Mon Aug 27, 2018 5:58 pm
- Forum: Anatomically detailed models
- Topic: area() function -- stylized method -- 3d-method
- Replies: 4
- Views: 11270
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...
- Fri Jun 29, 2018 2:13 pm
- Forum: Other questions
- Topic: Using event delivery system with fixed time step method.
- Replies: 7
- Views: 5788
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 ?
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 ?
- Fri Jun 29, 2018 5:56 am
- Forum: Other questions
- Topic: Using event delivery system with fixed time step method.
- Replies: 7
- Views: 5788
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) ...
- Fri Jun 09, 2017 7:35 am
- Forum: NEURON + Python
- Topic: uninsert python
- Replies: 6
- Views: 14086
Re: uninsert python
Thank you for your prompt reply.
Nathan
Nathan
- Thu Jun 08, 2017 3:22 pm
- Forum: NEURON + Python
- Topic: uninsert python
- Replies: 6
- Views: 14086
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...