Search found 6048 matches

by ted
Fri Sep 30, 2022 4:13 am
Forum: NEURON + Python
Topic: Insert an ion channel written in a .mod file
Replies: 8
Views: 133

Re: Insert an ion channel written in a .mod file

That's because you put the NMODL files in a directory other than the one that contains your hoc and Python files. When NEURON starts, it automatically looks in the current directory for a library of compiled mechanisms; under MSWin, that library is called nrnmech.dll. If that file is in some directo...
by ted
Tue Sep 20, 2022 12:19 am
Forum: MSWin
Topic: bash:........bad interepter. no such file or directory
Replies: 12
Views: 121

Re: bash:........bad interepter. no such file or directory

NEURON and Anaconda generally work well together under Windows. But who knows what conflicts might arise when multiple Python distributions are installed. I am sure that there are people who use other Python distributions with NEURON under Windows, and maybe some of them have multiple distributions ...
by ted
Mon Sep 19, 2022 10:38 pm
Forum: MSWin
Topic: bash:........bad interepter. no such file or directory
Replies: 12
Views: 121

Re: bash:........bad interepter. no such file or directory

Python version:3.9 What distribution? That is, who created the installer? python.org? Anaconda? Microsoft? Some other source? If that sounds like a strange question, read this: https://www.infoworld.com/article/3267976/12-pythons-for-every-programming-need.html And also: what version of Windows are...
by ted
Mon Sep 19, 2022 2:21 pm
Forum: MSWin
Topic: bash:........bad interepter. no such file or directory
Replies: 12
Views: 121

Re: bash:........bad interepter. no such file or directory

Which version of NEURON are you using, and exactly what version and distribution Python are you using? And what bash are you using--the one that comes with NEURON, or something else? And are you first starting a bash shell, and then executing the command
nrngui
at the bash prompt?
by ted
Fri Sep 16, 2022 12:20 pm
Forum: NEURON + Python
Topic: Insert an ion channel written in a .mod file
Replies: 8
Views: 133

Re: Insert an ion channel written in a .mod file

Which Python are you using? If you're using Anaconda, just open an Anaconda terminal (they probably call it a "shell") and use the commad line to do everything--cd to the directory that contains your source code, run nrnivmodl to compile mod files, execute nrngui someprogram.hoc or python ...
by ted
Tue Sep 13, 2022 2:50 pm
Forum: NEURON + Python
Topic: Insert an ion channel written in a .mod file
Replies: 8
Views: 133

Re: Insert an ion channel written in a .mod file

Hints: First make sure that SHL1_pas is supposed to be the name of a density mechanism. How can you find out? An NMODL file's NEURON block will contain a statement that declares the name of the mechanism. For a density mechanism, the statement is of the form SUFFIX foo and for a point process the st...
by ted
Tue Sep 13, 2022 2:19 pm
Forum: NEURON + Python
Topic: Mining Code from Channel Builder
Replies: 11
Views: 4967

Re: Mining Code from Channel Builder

Reply to cassiehu: I see that your posts in this discussion thread are actually about the same problem that you are asking in a separate thread ("Insert an ion channel written in a .mod file"). Further discussion of your problem will continue in that thread. After you have had the opportun...
by ted
Mon Sep 12, 2022 12:25 pm
Forum: NEURON hacks
Topic: conditional statements in DERIVATIVE block of mod files
Replies: 3
Views: 87

Re: conditional statements in DERIVATIVE block of mod files

You can write whatever you like, but the important questions are: will it work, and will you be planting bugs that will bite you or others in the future? In this particular case, the answers are "no" and "absolutely", respectively. First, the first "if statement" will n...
by ted
Mon Sep 12, 2022 11:44 am
Forum: NEURON + Python
Topic: Insert an ion channel written in a .mod file
Replies: 8
Views: 133

Re: Insert an ion channel written in a .mod file

Time to read some documentation. Go to https://nrn.readthedocs.io/en/latest/guide/how_to_get_started.html#how-to-get-started-with-neuron and find the part about NMODL. Read the referenced articles (you'll find links to them at https://nrn.readthedocs.io/en/latest/publications.html , but the most com...
by ted
Mon Sep 12, 2022 11:34 am
Forum: NEURON + Python
Topic: Mining Code from Channel Builder
Replies: 11
Views: 4967

Re: Mining Code from Channel Builder

I think there may be some problems or bugs of my .mod document.
When you ran mknrndll (or was it nrnivmodl?), did any error messages appear?
by ted
Wed Aug 24, 2022 11:26 am
Forum: NEURON + Python
Topic: Accessing Pointers instantiated through Python
Replies: 6
Views: 262

Re: Accessing Pointers instantiated through Python

The best answer to your question depends on what you are trying to do. So what is it that you are trying to do by "programmatically accessing" pointers?
by ted
Thu Aug 11, 2022 9:58 pm
Forum: NEURON + Python
Topic: POINTER is not thread safe
Replies: 6
Views: 546

Re: POINTER is not thread safe

I was not able to open the links you shared in the previous thread Hmm, the Forum automatically (and incorrectly) "promoted" those to incorrect URLs. I have now revised that post. Alternatively, you could try modeldb.science/3815 and modeldb.science/3264 entered into your browser's URL fi...
by ted
Wed Aug 10, 2022 7:28 pm
Forum: NEURON + Python
Topic: POINTER is not thread safe
Replies: 6
Views: 546

Re: POINTER is not thread safe

The sample mod file provided has several fatal problems. non-Ascii character in line 42 This is trivially easy to fix; unfixed, it could cause a lot of trouble. Has it been resolved? Strong hint: stick with the ASCII character set until this particular limitation of NMODL code has been resolved. The...
by ted
Wed Aug 03, 2022 2:34 pm
Forum: NEURON + Python
Topic: mechanisms written in python?
Replies: 5
Views: 293

Re: mechanisms written in python?

AG synthesis? arachidonoylglycerol? The best way to do this depends on the details of your conceptual model for what's going on. Presumably you have already expressed your conceptual model in the form of a reaction scheme or mathematical equations. My question at this point is: what aspects of your ...