Search found 1456 matches

by hines
Fri Dec 15, 2017 10:41 am
Forum: Other questions
Topic: na_ion mechanism not inserted in section axon
Replies: 14
Views: 2445

Re: na_ion mechanism not inserted in section axon

This means that it is not possible to have access to the icl produced by the point process in mA/cm2 in the nmodl code No. Only icl mus be nA. My change to i was just one of several ways to establish units consistency. It wold be ok to declare icl (mA/cm2) but then your original i=ica/(area*0,01) w...
by hines
Fri Dec 15, 2017 9:38 am
Forum: Other questions
Topic: na_ion mechanism not inserted in section axon
Replies: 14
Views: 2445

Re: na_ion mechanism not inserted in section axon

when I used modlunit on the fragment you sent (copied to temp.mod) I get $ modlunit temp.mod model 1.1.1.1 1994/10/12 17:22:51 Checking units of temp.mod Need declaration in UNITS block of the form: (mV) (units) Cannot recognize the units: mV at line 1 in file temp.mod NEURON<<ERROR>> { adding a uni...
by hines
Fri Dec 15, 2017 7:14 am
Forum: OS X
Topic: Install on Mac High Sierra
Replies: 4
Views: 3369

Re: Install on Mac High Sierra

The problem with NRN_PYLIB is fixed with a new version of nrnpyenv.sh. The difference between new and old is https://github.com/nrnhines/nrn/commit/c693a84702c2941f010a2c3fe02abbd678c72b4d You can get the new file from https://github.com/nrnhines/nrn/blob/master/bin/nrnpyenv.sh and use it to replace...
by hines
Wed Dec 13, 2017 1:46 pm
Forum: Other questions
Topic: na_ion mechanism not inserted in section axon
Replies: 14
Views: 2445

Re: na_ion mechanism not inserted in section axon

The conversion of a density current sec.icl(x) which has the units mA/cm2 to absolute current (nA) through the segment containing position x is
in the hoc interpreter
sec {
absolute_icl = icl(x)*area(x)*0.01
}

and in the python interpreter
absolute_icl = sec(x).icl*sec(x).area()*0.01
by hines
Wed Dec 06, 2017 1:00 am
Forum: Adding new mechanisms and functions to NEURON
Topic: "My mechanisms don't load!"
Replies: 18
Views: 17002

Re: "My mechanisms don't load!"

No. Only drag folder to mknrndll if you change a mod file
by hines
Mon Dec 04, 2017 7:19 am
Forum: Other questions
Topic: Suppress "First Instance Of"
Replies: 5
Views: 2691

Re: Suppress "First Instance Of"

put
first_instance_message:off
in the .nrn.defaults file in your $HOME directory
Note: there was a bug in handling this and a fix is pushed to the GitHub repository
by hines
Fri Dec 01, 2017 6:27 am
Forum: Getting started
Topic: Dynamic clamp?
Replies: 9
Views: 7794

Re: Dynamic clamp?

I believe the variable name is SEClamp[0].rs if it is the first instance. All range varialbles are playable if they are PARAMETER. It becomes ambiguous if they are ASSIGNED or STATE as those are usually changed in the mod file and it is implementation dependent if the "play" takes place before or af...
by hines
Thu Nov 30, 2017 4:00 pm
Forum: Getting started
Topic: Dynamic clamp?
Replies: 9
Views: 7794

Re: Dynamic clamp?

Set SEClamp.dur1 = 1e9 and then play a Vector into SEClamp.amp1 Without looking too closely, using your GCLamp is very similar. Please note, though the abuse of syntax used there as well as in the line above. SECla mp cannot be used as an instance without its instance index. eg. SEClamp[0], or via a...
by hines
Fri Nov 17, 2017 7:52 am
Forum: UNIX/Linux
Topic: "Point process not located in a section" error with v7.5 but not v7.4
Replies: 26
Views: 18421

Re: "Point process not located in a section" error with v7.5 but not v7.4

I reverted my build to download the 9fc719735a2d0a9446f59065534d5326a6bd179d commit directly I was wondering about that possibility when I made the tag but could not quickly find the answer. Since the hash can be used there does not seem to be any real need for the tag and it can be deleted. Let me...
by hines
Wed Nov 15, 2017 9:14 pm
Forum: UNIX/Linux
Topic: "Point process not located in a section" error with v7.5 but not v7.4
Replies: 26
Views: 18421

Re: "Point process not located in a section" error with v7.5 but not v7.4

I unchecked the 'prerelease' item so it is now a release. Does that fix the problem? I admit to knowing nothing about why things work the way
they do in this domain. Is there a simple explanation of why a prerelease would cause an error but a release does not in your situation?
by hines
Tue Nov 14, 2017 11:58 am
Forum: Other questions
Topic: Values for Gas and Faraday constants
Replies: 4
Views: 10265

Re: Values for Gas and Faraday constants

The configuration variable --disable-LegacyFR (the default is --enable-LegacyFR) uses the new NIST values for / Nov, 2017 updated faraday, R, e, planck, hbar, mole, k according to / https://physics.nist.gov/cuu/Constants/index.html So no one will see any difference without the explicit configure req...
by hines
Tue Nov 14, 2017 9:44 am
Forum: UNIX/Linux
Topic: "Point process not located in a section" error with v7.5 but not v7.4
Replies: 26
Views: 18421

Re: "Point process not located in a section" error with v7.5 but not v7.4

Ok. The 1665alpha tag for f6c657c master contains the desired 9fc7197 changeset
by hines
Mon Nov 13, 2017 11:30 am
Forum: Other questions
Topic: Values for Gas and Faraday constants
Replies: 4
Views: 10265

Re: Values for Gas and Faraday constants

Thanks. I've made the relevant changes in src/oc/init.c, src/nrnoc/eion.c and share/lib/nrnunits.lib . I have not pushed to github yet as I'm still thinking about the consequence of changing double precision consistency with respect to legacy models. I looked in the current linux units database and ...
by hines
Thu Nov 09, 2017 3:32 pm
Forum: UNIX/Linux
Topic: "Point process not located in a section" error with v7.5 but not v7.4
Replies: 26
Views: 18421

Re: "Point process not located in a section" error with v7.5 but not v7.4

https://neuron.yale.edu/ftp/neuron/versions/alpha/
contains a mac and windows installer that has that change (anything after Nov 6, 2017)
by hines
Wed Nov 08, 2017 10:48 am
Forum: OS X
Topic: OSX: NEURON runs in Terminal, gui runs in XQuartz
Replies: 1
Views: 6594

Re: OSX: NEURON runs in Terminal, gui runs in XQuartz

You can start an xterm and launch from there.