Search found 5492 matches

by ted
Sat May 25, 2019 12:58 pm
Forum: Other questions
Topic: how to deal with "subscript out of range error" in printing out coordinate.
Replies: 11
Views: 126

Re: how to deal with "subscript out of range error" in printing out coordinate.

I have been trying to figure out the cause of the various symptoms you have reported without actually working with the code. But that means I have been limited to making guesses and giving suggestions, and progress has been very slow. This new symptom you report tells me that I really need to be abl...
by ted
Thu May 23, 2019 10:54 am
Forum: NEURON + Python
Topic: Adex neuron in neuron python
Replies: 5
Views: 62

Re: Adex neuron in neuron python

The error message suggests there is a problem with your model. Contact whoever developed it.
by ted
Tue May 21, 2019 11:08 am
Forum: Other questions
Topic: how to deal with "subscript out of range error" in printing out coordinate.
Replies: 11
Views: 126

Re: how to deal with "subscript out of range error" in printing out coordinate.

I didn't copy all the result. The error was still happened.
Would you like to share the last, say, 10 lines or so of the output? I ask because those lines are likely to contain a useful clue to the problem you encountered.
by ted
Tue May 21, 2019 11:06 am
Forum: Other questions
Topic: Variable file name
Replies: 2
Views: 33

Re: Variable file name

In hoc, by default, a user-created variable name is the name of a floating point scalar variable. If you want to use a user-created name as a strdef or objref, then you must first declare it to be a strdef or objref at the "top level of the hoc interpreter." This basically means that the declaration...
by ted
Mon May 20, 2019 2:53 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Where to find squid.hoc associated with hh.mod
Replies: 8
Views: 1449

Re: Where to find squid.hoc associated with hh.mod

When writing mod files for custom ionic currents, is there ever a situation where I would not want to include "THREADSAFE" within the NEURON block? There are many. The only reason to use the THREADSAFE directive is in NMODL code that contains statements that assign values to one or more GLOBAL vari...
by ted
Fri May 17, 2019 11:23 pm
Forum: Other questions
Topic: Plotting M for IntFire4
Replies: 1
Views: 40

Re: Plotting M for IntFire4

Example (pertains to all IntFire classes): if1 = h.IntFire1() The Python name of the function itself will be if1.M, but you want the numerical value returned by the function, so you need if1.M(). Note that if1.M() will not return a reasonable value unless h.finitialize() was called previously. Indee...
by ted
Fri May 17, 2019 4:34 pm
Forum: Other questions
Topic: how to deal with "subscript out of range error" in printing out coordinate.
Replies: 11
Views: 126

Re: how to deal with "subscript out of range error" in printing out coordinate.

And This is the result after inserting secname()
Do you see any error messages in that? If you don't, does that mean the problem went away?
by ted
Tue May 14, 2019 11:08 am
Forum: Other questions
Topic: how to deal with "subscript out of range error" in printing out coordinate.
Replies: 11
Views: 126

Re: how to deal with "subscript out of range error" in printing out coordinate.

Interesting result, but an essential clue is missing. What to do for the next test? 1. Why so many "print ii" statements? Nothing inside the loop affects the value of ii, so you can get rid of all but the first "print ii" statement. And it would be a good idea to make that "print ii" statement be th...
by ted
Mon May 13, 2019 7:00 pm
Forum: Parallel NEURON
Topic: Bulletin-Style Grid-Like Simulations: Indexing Getting Mixed Up
Replies: 4
Views: 94

Re: Bulletin-Style Grid-Like Simulations: Indexing Getting Mixed Up

No need to apologize. These threads have enormous potential tutelary value. A great deal can be learned from someone else's mistakes (including the facts that there area many ways for "working" code to fail, and how easy it can be to set a trap for oneself).
by ted
Mon May 13, 2019 11:22 am
Forum: Parallel NEURON
Topic: Bulletin-Style Grid-Like Simulations: Indexing Getting Mixed Up
Replies: 4
Views: 94

Re: Bulletin-Style Grid-Like Simulations: Indexing Getting Mixed Up

Three suggestions. 1. Keep your code simple. Drop the conditional statement and its "what to do if nhost == 1" clause--it's completely unnecessary. Your parallelized program should produce the same results for any value of nhost > 0; the only difference will be total run time. 2. Make sure that each...
by ted
Sat May 11, 2019 9:59 am
Forum: Other questions
Topic: how to deal with "subscript out of range error" in printing out coordinate.
Replies: 11
Views: 126

Re: how to deal with "subscript out of range error" in printing out coordinate.

I had already used print statement and found out the location of the crash.
No, you didn't. You localized the problem to a for loop. There are several statements in that for loop. Which statement is triggering the error message?
by ted
Fri May 10, 2019 7:05 pm
Forum: Other questions
Topic: how to deal with "subscript out of range error" in printing out coordinate.
Replies: 11
Views: 126

Re: how to deal with "subscript out of range error" in printing out coordinate.

Insert a series of print statements that report unique messages. Clearly the last message that is printed before the crash is located before the source of the error.
by ted
Fri May 10, 2019 6:58 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Where to find squid.hoc associated with hh.mod
Replies: 8
Views: 1449

Re: Where to find squid.hoc associated with hh.mod

Okay, I believe I found it here:
Nope. FYI anybody can put anything on the web and call it anything they like, but that doesn't mean that it is the same as something else with the same name. This is a corollary of "On the Internet, nobody knows you're a dog."
by ted
Fri May 10, 2019 6:54 pm
Forum: Getting started
Topic: How to enter the parameters of a number of channels for a neuron?
Replies: 12
Views: 1057

Re: How to enter the parameters of a number of channels for a neuron?

can I create the cell model first using Cell Builder and save it as ses. File, and then load it, and use it when I create channels using the Channel Builder? If you want to use a user-specified density mechanism (whether it is an ion channel, a pump, or some other density mechanism) in a CellBuilde...
by ted
Wed May 08, 2019 4:10 pm
Forum: Getting started
Topic: How to enter the parameters of a number of channels for a neuron?
Replies: 12
Views: 1057

Re: How to enter the parameters of a number of channels for a neuron?

Save your configured ChannelBuilder to its own session file. Read this https://neuron.yale.edu/neuron/static/docs/saveses/saveses.html for more information about session files and how to save them. If you need to use your new channel in a model, use load_file() or xopen() to make NEURON read its ses...