Search found 97 matches

by neuromau
Fri Sep 19, 2014 4:57 pm
Forum: Anatomically detailed models
Topic: Computing impedance after running define_shape
Replies: 2
Views: 6713

Computing impedance after running define_shape

I want to run the compute function of the impedance mechanism after running define_shape(). However, it leads to the following error: Fatal Complex arithmetic error. Attempted division by zero. If I use the compute function prior to running define_shape(), it works just fine. I'm not sure why it doe...
by neuromau
Tue Jun 24, 2014 4:37 pm
Forum: Other questions
Topic: When using a model with a custom init procedure...
Replies: 0
Views: 1617

When using a model with a custom init procedure...

When using a model with a custom init procedure, check to make sure the initialization was done correctly. This means, compare the functions called by the custom init procedure with those called in the regular init procedure as shown in Chapter 8.3 of The NEURON Book, to make sure no necessary funct...
by neuromau
Wed Jun 18, 2014 1:32 am
Forum: The GUI
Topic: Programmatically remove shape plot label
Replies: 6
Views: 8408

Re: Programmatically remove shape plot label

Thanks, I was able to move the cell far enough away that the label doesn't appear anymore. I will remember the .cpp edit option in case I decide to compile NEURON later.
by neuromau
Tue Jun 17, 2014 9:04 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: TITLE block in NMODL file
Replies: 2
Views: 1292

Re: TITLE block in NMODL file

Okay, thanks! In that case I may just use a system call to grep for now to avoid recompiling.
by neuromau
Tue Jun 17, 2014 8:48 pm
Forum: The GUI
Topic: Programmatically remove shape plot label
Replies: 6
Views: 8408

Re: Programmatically remove shape plot label

On those occasions when I need something aesthetic Okay, hmm. My problem now is that I have many dozens of those occasions so I will have to stick with something programmatic. The variable I am plotting is not actually "v", but one that is 10-18 characters long and tends to obscure a good portion o...
by neuromau
Tue Jun 17, 2014 7:47 pm
Forum: The GUI
Topic: Programmatically remove shape plot label
Replies: 6
Views: 8408

Re: Programmatically remove shape plot label

If I create a Shape instead, I won't be able to use the .variable("v") method though, correct? I still want the PlotShape functionality, I just don't want the label text to appear directly on top of the plotted cell. Should I try changing the 3d coordinates of the cell or experimenting with g.view()...
by neuromau
Tue Jun 17, 2014 6:11 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: TITLE block in NMODL file
Replies: 2
Views: 1292

TITLE block in NMODL file

Is it possible to programmatically access (read-only) the TITLE block (or COMMENTS block) of a compiled NMODL file via hoc?
by neuromau
Tue Jun 17, 2014 5:58 pm
Forum: The GUI
Topic: Programmatically remove shape plot label
Replies: 6
Views: 8408

Programmatically remove shape plot label

Hello, I made a plot using hoc: create soma objref g g = new PlotShape(0) g.variable("v") g.view(-199.999, -147.615, 399.998, 295.23, 49, 151, 467.1, 344.8) g.exec_menu("Shape Plot") How can I then remove the "v" label from the plot itself using hoc? I understand how to add labels, but I am not sure...
by neuromau
Wed Jun 04, 2014 5:22 pm
Forum: Other questions
Topic: Resolved: calculating/recording LFP, actually was a psolve q
Replies: 1
Views: 2554

Resolved: calculating/recording LFP, actually was a psolve q

Note: the problem I had here turned out to be relying on advance() while trying to use pc.solve(), which does not call advance(). But I'm posting my whole thought & debugging process anyway in case this is helpful for others: I'm just starting to wrap my head around LFPs, the extracellular mechanism...
by neuromau
Tue May 20, 2014 6:57 pm
Forum: MSWin
Topic: Running mknrndll from a Cygwin terminal in Windows 7
Replies: 1
Views: 6122

Running mknrndll from a Cygwin terminal in Windows 7

Hello, on Windows 8 I can run mknrndll from my Cygwin window (as opposed to rxvt or mintty bash) if I first enter: export N=/cygdrive/c/nrn73 My student who is running Windows 7 cannot run mknrndll from Cygwin. She always gets this error: make: *** No targets specified and no makefile found. Stop. S...
by neuromau
Mon Apr 07, 2014 3:39 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: functions in NMODL
Replies: 3
Views: 1415

Re: functions in NMODL

Great, thanks Michael! For some reason my mknrndll output did not report anything like warning: implicit declaration of function 'get_x_pos1' is invalid in C99 [-Wimplicit-function-declaration] . I made the update and now both functions are returning the same number in NMODL. Just for others' refere...
by neuromau
Sat Apr 05, 2014 11:41 am
Forum: Adding new mechanisms and functions to NEURON
Topic: functions in NMODL
Replies: 3
Views: 1415

functions in NMODL

Hello, I want to make a function in NMODL that I can call from NMODL and hoc. I tried something, but it gives me an odd result when I call it from NMODL. I suspect I'm mixing up ints and doubles somehow, but I'm not sure what to do. First I made an NMODL function that is callable from hoc: NEURON { ...
by neuromau
Thu Mar 06, 2014 1:42 pm
Forum: UNIX/Linux
Topic: NEURON on Stampede
Replies: 2
Views: 11891

Re: NEURON on Stampede

Occasionally you may want to make changes to the NEURON source code. If this becomes necessary for your static build installation on Stampede, you can make changes by following these steps from Michael: 1. Make the desired changes to the file(s) within your neuron/nrn/src directory. 2. Change direct...
by neuromau
Thu Mar 06, 2014 1:25 pm
Forum: UNIX/Linux
Topic: NEURON on Stampede
Replies: 2
Views: 11891

Re: NEURON on Stampede

Testing the installation and running job scripts are covered in the reply to this post. To test the installation of NEURON, we can create the following test program. 1. Move to the WORK file system: cdw 2. Create a directory called test: mkdir test 3. Move to the test directory: cd test 4. In the t...
by neuromau
Sun Mar 02, 2014 7:44 pm
Forum: MSWin
Topic: cannot export postscript
Replies: 8
Views: 8960

Re: cannot export postscript

I've been able to reproduce this error if I run a hoc file from the command line, but not if I run that same hoc file from within the GUI. I'm in Windows 8 with cygwin, NEURON 7.3. I have a hoc (printCell.hoc) file that contains: objref ss ss = new Shape(cell.all) ss.printfile("mycellview.ps") This ...