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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...

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...

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.

Okay, thanks! In that case I may just use a system call to grep for now to avoid recompiling.

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...

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 wit...

Is it possible to programmatically access (read-only) the TITLE block (or COMMENTS block) of a compiled NMODL file via hoc?

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...

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 mecha...

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...

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...

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 { ...

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...

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...

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&qu...