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Calcium diffusion and shells
Posted: Thu Nov 14, 2019 7:41 am
by ziemek
Hi there,
Is there any easy way to implement in NEURON a Calcium diffusion with shells similar in concept to the figure 6.8 from the Principles of Computational Modelling in Neuroscience, Sterrat et al. :
https://drive.google.com/file/d/13YeDmG ... PVVdB/view (image)
I would be very glad for your help :)
Re: Calcium diffusion and shells
Posted: Thu Nov 14, 2019 8:20 am
by ted
See chapter 9 of the NEURON Book. If you don't have the book, get this preprint
https://www.neuron.yale.edu/ftp/ted/boo ... xedref.pdf
If you installed NEURON from source code, see
nrn/share/examples/nrniv/nmodl/cadif.mod
which may be slightly different from the example in the book. If you didn't install from source code, suggest you get the source code files anyway and check out the examples in that directory.
Re: Calcium diffusion and shells
Posted: Tue Nov 19, 2019 7:27 am
by ziemek
Thanks for help. Unfortunatelly there is an error while I make
Code: Select all
"/usr/local/nrn/share/nrn/libtool" --tag=CC --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath "/usr/local/nrn/x86_64/lib" cadif.lo mod_func.lo -L"/usr/local/nrn/x86_64/lib" -lnrnoc -loc -lmemacs -lscopmath -lsparse13 -lreadline -lncurses -ltinfo -L"/usr/local/nrn/x86_64/lib" -lnrniv -livoc -lneuron_gnu -lmeschach -lsundials -lm -ldl
libtool: link: gcc -shared -fPIC -DPIC .libs/cadif.o .libs/mod_func.o -Wl,-rpath -Wl,/usr/local/nrn/x86_64/lib -Wl,-rpath -Wl,/usr/local/nrn/x86_64/lib -L/usr/local/nrn/x86_64/lib /usr/local/nrn/x86_64/lib/libnrnoc.so /usr/local/nrn/x86_64/lib/liboc.so -lX11 /usr/local/nrn/x86_64/lib/libmemacs.so /usr/local/nrn/x86_64/lib/libscopmath.so /usr/local/nrn/x86_64/lib/libsparse13.so -lreadline -lncurses -ltinfo /usr/local/nrn/x86_64/lib/libnrniv.so /usr/local/nrn/x86_64/lib/libivoc.so /usr/local/nrn/x86_64/lib/libneuron_gnu.so /usr/local/nrn/x86_64/lib/libmeschach.so /usr/local/nrn/x86_64/lib/libsundials.so -lm -ldl -g -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0
/usr/bin/ld: cannot find -lreadline
collect2: error: ld returned 1 exit status
I have
NEURON ver. 7.7.2 and the cadif.mod file come from today's master branch of NEURON from GitHub.
But it does work well with ver 7.5 and older (7.6 though still doesn't work).
Do you have any clue how to fix it?
Re: Calcium diffusion and shells
Posted: Tue Nov 19, 2019 9:43 am
by ted
Check to see if the readline library exists on your computer. If it doesn't, download and install it, then uninstall and reinstall NEURON.
How? Depends on your Linux distribution. For distributions that use rpm for package management,
rpm -q readline
and
rpm -ivh readline
are your friends.
Debian-related distributions use dpkg and apt--read the relevant documentation.
Re: Calcium diffusion and shells
Posted: Wed Nov 20, 2019 9:51 am
by ziemek
Thanks, indeed readline did the trick.
If anyone has the same problem in the future - this answer may help:
https://askubuntu.com/questions/194523/ ... u-readline
Re: Calcium diffusion and shells
Posted: Wed Nov 20, 2019 10:36 am
by ted
Thanks, that will be a useful tip for others who may read this thread.