Search found 163 matches

by ramcdougal
Sun Sep 13, 2009 12:55 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: mod file CVODE compatibility
Replies: 9
Views: 7333

Re: mod file CVODE compatibility

Thanks for clarifying about the K.

Can I safely include mod files without SOLVE statements without affecting the stability of the rest of the system?
by ramcdougal
Sat Sep 12, 2009 10:37 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: mod file CVODE compatibility
Replies: 9
Views: 7333

Re: mod file CVODE compatibility

I was looking at the same file earlier today. It seems like I can do without using any solve statements or state variables, as in: NEURON { SUFFIX nap USEION na READ ena WRITE ina RANGE gnabar,vhalf, K } UNITS { (mA) = (milliamp) (mV) = (millivolt) } PARAMETER { : parameters that can be entered when...
by ramcdougal
Wed Sep 09, 2009 9:06 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: cvode quirks
Replies: 1
Views: 1276

cvode quirks

I recently discovered from http://www.neuron.yale.edu/phpBB/viewtopic.php?f=16&t=489 that cvode should work with kinetic models (but does it work with LONGITUDINAL_DIFFUSION?) My first couple attempts ended in mysterious "bus error(s)," so I decided to start over from the beginning, and I discovered...
by ramcdougal
Fri Jun 12, 2009 5:06 am
Forum: NEURON + Python
Topic: output windows in python
Replies: 2
Views: 2088

Re: output windows in python

I have a partial solution to my own question. I can open a shape plot and resize, etc... it entirely* in python by # ready shape plot h.newshapeplot() shapeWindow=h.fast_flush_list.object(h.fast_flush_list.count()-1) shapeWindow.size(-380.24,488.164,-624.858,170.347) shapeWindow.variable('cai') shap...
by ramcdougal
Thu Jun 11, 2009 11:09 pm
Forum: NEURON + Python
Topic: output windows in python
Replies: 2
Views: 2088

output windows in python

I have recently decided to learn the Python interface for Neuron. I decided the best way to learn would be to convert some of my old scripts from hoc to python. I came so close to being successful on my own, but I haven't been able to figure out how to control shape plots without invoking the hoc in...
by ramcdougal
Tue Mar 31, 2009 11:13 am
Forum: NEURON + Python
Topic: Neuron GUI with python?
Replies: 7
Views: 4273

Re: Neuron GUI with python?

Works great. Thanks.
by ramcdougal
Mon Mar 30, 2009 11:33 pm
Forum: NEURON + Python
Topic: Neuron GUI with python?
Replies: 7
Views: 4273

Re: Neuron GUI with python?

Sorry to resurrect an old conversation, but... Did anyone ever figure out a good way to get the gui from python? If I start with "nrngui -python" and get a python interpretor that way, everything works wonderfully, but what I want to do is: $ python Python 2.5.2 (r252:60911, Oct 5 2008, 19:29:17) [G...
by ramcdougal
Mon Mar 30, 2009 2:31 pm
Forum: Parallel NEURON
Topic: multisplit checkbox preconditions
Replies: 4
Views: 2373

Re: multisplit checkbox preconditions

Hines tells me "Multisplit does not work with LONGITUDINAL_DIFFUSION."
by ramcdougal
Mon Mar 30, 2009 2:15 pm
Forum: Parallel NEURON
Topic: multisplit checkbox preconditions
Replies: 4
Views: 2373

Re: multisplit checkbox preconditions

mkthreadsafe reports no problems: $ /usr/local/nrn/x86_64/bin/mkthreadsafe diff.mod What assumptions are made by the code that executes when the multisplit checkbox is selected? Thanks. A side note: For those who installed NEURON on Ubuntu like I did (converted the rpm to deb via alien), there are t...
by ramcdougal
Sun Mar 29, 2009 3:10 pm
Forum: Parallel NEURON
Topic: multisplit checkbox preconditions
Replies: 4
Views: 2373

Re: multisplit checkbox preconditions

I can now give a simple example of how I'm getting a "segmentation violation." Suppose we have a simple mod file implementing diffusion: NEURON { SUFFIX diff } BREAKPOINT { SOLVE state METHOD sparse } STATE { z (1) } KINETIC state { COMPARTMENT 1 {z} LONGITUDINAL_DIFFUSION 1 {z} ~z << (0) } (No, I w...
by ramcdougal
Sun Mar 29, 2009 12:34 am
Forum: Parallel NEURON
Topic: multisplit checkbox preconditions
Replies: 4
Views: 2373

multisplit checkbox preconditions

I'm running Neuron 7.0 (281:80827e3cd201) and have been experimenting with multisplit. What preconditions are necessary before checking the "multisplit" box in the parallel computing toolbox so that the simple act of checking the box does not result in an error? For example, I experimented with the ...
by ramcdougal
Fri Nov 28, 2008 4:30 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: longitudinal_diffusion caching?
Replies: 2
Views: 1751

Re: longitudinal_diffusion caching?

Upon further reflection, I realize that I could use delete_section to remove the sections and start over from scratch, but I would prefer to preserve all the geometry, biophysics, etc...
by ramcdougal
Fri Nov 28, 2008 4:01 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: longitudinal_diffusion caching?
Replies: 2
Views: 1751

longitudinal_diffusion caching?

I was experimenting with longitudinal_diffusion and the results were not quite as I expected: I'd create a section of length 10, put some stuff on the left side, and then it would diffuse across a certain rate. If now I change the length of the section and rerun it, my substance diffuses across the ...