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From: Anna Rácz-M. <li...@gm...> - 2012-03-23 15:03:52
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Dear Anyone, who can help me, I installed Oscill8 recently. I tried to run the tutorial, but I had several problems, here I try to write them in detail. 1. I try to run, but it writes, that is "Unable to create workspace, access is denied". Which is very strange for me, as I am the administrator of the computer. 2. I gave another directory so that the program can put the data there. Then I receive the following message: "connecting to o8core on localhost:28472..." and the program is not responding. And then several minutes later, I receive the message that it was unable to create new workspace, as it was time over. I would like to run bifurcation diagrams in the future, so I would need this program to be running. I would be very grateful if someone could help me! Thank you in advance Anna Racz-Monus |
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From: Emery C. <ec...@vt...> - 2005-09-13 17:42:59
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Herbert and Vijay,<br>
<br>
The limit cycle continuation IS the right way to get min/max for the
amplitude of the oscillations; this is exactly the same feature that
XPPAUT has by using AUTO, except it's easier in Oscill8 (may take
longer to run for default parameters, but more accurate output). The
sample period/min/max feature does that same thing, it just doesn't use
continuation methods.<br>
<br>
This LC feature is easy to use, I believe. Here's what you do:<br>
<br>
1) alt-click on a HB (or choose "run"-->"limit cycle continuation"
and set label and parameter properly).<br>
2) choose limit cycle continuation<br>
3) choose parameters (exactly as you would in XPPAUT), ensuring that
ds/dsmin/dsmax etc are appropriate for your system.<br>
4) run and wait for output<br>
5) choose which state variables you want to plot the MIN/MAX of,
deselecting all others<br>
6) drag and drop this run (the limit cycle run) onto the one-parameter
bifurcation diagram you started with!<br>
<br>
DONE!<br>
<br>
Vijay, if you're having trouble using the interface, please let me know
and I'll be happy to rethink how things are done.<br>
<br>
Emery<br>
<br>
<br>
<br>
Herbert Sauro wrote:
<blockquote
cite="mid...@de..."
type="cite">
<meta http-equiv="Content-Type" content="text/html; ">
<meta content="MSHTML 6.00.2900.2722" name="GENERATOR">
<div align="left" dir="ltr"><span class="877112716-13092005"><font
color="#0000ff" face="Arial" size="2">Emery, I think what Vijay wanted
was a step by step list of instructions on how to generate the min/max
for the amplitude of the oscillations. We are hoping to introduce
oscill8 at the tutorial we will give at ICSB but at the moment we're
not sure how to use this feature. In fact Vijay has for the time being
decided to learn XPP in order to generate the min/max curves. It is
important that we try to convince him to go back to oscill8. I am not
familiar with xpp very much (only used it a few times) but if it turns
out that it is easier to use xpp over oscill8 then I think there is a
lot of work to do on the oscill8's interfacee. </font></span></div>
<div align="left" dir="ltr"><span class="877112716-13092005"></span><span
class="877112716-13092005"></span> </div>
<div align="left" dir="ltr"><span class="877112716-13092005"><font
color="#0000ff" face="Arial" size="2">Perhaps you would send me a step
by step list of instructions on how to generate a min/max plot (eg for
the oscil.xml file I sent) .</font></span></div>
<div><span class="877112716-13092005"></span> </div>
<div><span class="877112716-13092005"><font color="#0000ff"
face="Arial" size="2">Herbert</font></span></div>
<div align="left" dir="ltr"><br>
</div>
<div class="OutlookMessageHeader" align="left" dir="ltr" lang="en-us">
<hr tabindex="-1"><font face="Tahoma" size="2"><b>From:</b> Emery
Conrad [<a class="moz-txt-link-freetext" href="mailto:ec...@vt...">mailto:ec...@vt...</a>] <br>
<b>Sent:</b> Monday, September 12, 2005 8:38 AM<br>
<b>To:</b> Vijay Chickarmane<br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:osc...@li...">osc...@li...</a>; Herbert Sauro<br>
<b>Subject:</b> Re: Issues with Oscill8<br>
</font><br>
</div>
Vijay,<br>
<br>
Now that limit cycle continuation works, that would be your preferred
method to get period/min/max done (although it may take longer). You
first must have a good 1 parameter bifurcation diagram; then continue
from a HB using limit cycle continuation. The output is the same as
that from sample period/min/max, but is more intelligent (see attached
png). BEWARE that limit cycle continuation can take a VERY long time if
you leave the settings ds, dsmin and dsmax as they are, but you will
have nice results. If you set ds, dsmin too large, you will get
spurious results (they should be obviously bad...).<br>
<br>
BUT, if you want a quick sampling, this can be very quick IF YOU SET
THE PARAMETERS CORRECTLY. This requires that you study the wave forms
and changes in period for some small perturbations BEFORE RUNNING THE
SAMPLING! If you want to use the sample period/min/max, you need to
ensure that dp is small enough so that you get several samples within
the region of oscillation (i.e., look at the 1p bd first), but make
sure that x_match_tol and period_match_tol is large enough (I changed
period_max = 10000, x_match_tol = 60, period_match_tol = 10 to get the
second attached graph). Sometimes you will get inaccuracies or
anomalies, but you can cut these out of the data set...<br>
<br>
It all takes work, but you just must be patient and analyze the system
locally to get the basic behavior, and then set your parameters.<br>
<br>
FYI, limit cycle continuation works MUCH BETTER, but is slower; once
you have a basic picture with the "sample period/min/max" run a
lengthy, accurate limit cycle continuation to get nicer graphs.<br>
<br>
[BTW, I added you and Herbert to the oscill8-help list; this is where
all the hints and help will go to from now on]<br>
<br>
Emery<br>
<br>
<br>
<br>
Vijay Chickarmane wrote:
<blockquote
cite="mid...@de..."
type="cite">
<blockquote style="margin-right: 0px;" dir="ltr"><span
class="104151705-10092005"><font face="Tahoma" size="2">Hi Emory,</font></span>
<blockquote style="margin-right: 0px;" dir="ltr">
<div><span class="104151705-10092005"><font face="Tahoma"
size="2">I am having trouble with the min-max of oscillations for a
couple of models, so I would be</font></span></div>
<div><span class="104151705-10092005"><font face="Tahoma"
size="2">grateful for your help. I tried to get the max-min for the
foll</font></span></div>
<div><span class="104151705-10092005"><font face="Tahoma"
size="2">two models, but was unable to. Could you try and generate the
plots, </font></span><span class="104151705-10092005"><font
face="Tahoma" size="2">and send them as well</font></span></div>
<div><span class="104151705-10092005"><font face="Tahoma"
size="2">as the parameter settings you used to generate them.</font></span></div>
<div><span class="104151705-10092005"></span> </div>
<div><span class="104151705-10092005"></span><span
class="104151705-10092005"><font face="Tahoma" size="2">model 1:
mapkfinal.xml ------ bifurcation parameter J5_k (currently set at
0.0001)</font></span></div>
<div><span class="104151705-10092005"></span> </div>
<div><span class="104151705-10092005"><font face="Tahoma"
size="2">model 2: mapknew.xml ------- bifurcation parameter kI
(currently set at 100)</font></span></div>
<div><span class="104151705-10092005"></span> </div>
<div><span class="104151705-10092005"><font face="Tahoma"
size="2">Thanks in advance,</font></span></div>
<div><span class="104151705-10092005"><font face="Tahoma"
size="2">best,</font></span></div>
<div><span class="104151705-10092005"><font face="Tahoma"
size="2">vijay</font></span></div>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
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|
From: Emery C. <ec...@vt...> - 2005-09-12 15:37:59
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Vijay,<br>
<br>
Now that limit cycle continuation works, that would be your preferred
method to get period/min/max done (although it may take longer). You
first must have a good 1 parameter bifurcation diagram; then continue
from a HB using limit cycle continuation. The output is the same as
that from sample period/min/max, but is more intelligent (see attached
png). BEWARE that limit cycle continuation can take a VERY long time if
you leave the settings ds, dsmin and dsmax as they are, but you will
have nice results. If you set ds, dsmin too large, you will get
spurious results (they should be obviously bad...).<br>
<br>
BUT, if you want a quick sampling, this can be very quick IF YOU SET
THE PARAMETERS CORRECTLY. This requires that you study the wave forms
and changes in period for some small perturbations BEFORE RUNNING THE
SAMPLING! If you want to use the sample period/min/max, you need to
ensure that dp is small enough so that you get several samples within
the region of oscillation (i.e., look at the 1p bd first), but make
sure that x_match_tol and period_match_tol is large enough (I changed
period_max = 10000, x_match_tol = 60, period_match_tol = 10 to get the
second attached graph). Sometimes you will get inaccuracies or
anomalies, but you can cut these out of the data set...<br>
<br>
It all takes work, but you just must be patient and analyze the system
locally to get the basic behavior, and then set your parameters.<br>
<br>
FYI, limit cycle continuation works MUCH BETTER, but is slower; once
you have a basic picture with the "sample period/min/max" run a
lengthy, accurate limit cycle continuation to get nicer graphs.<br>
<br>
[BTW, I added you and Herbert to the oscill8-help list; this is where
all the hints and help will go to from now on]<br>
<br>
Emery<br>
<br>
<br>
<br>
Vijay Chickarmane wrote:
<blockquote
cite="mid...@de..."
type="cite">
<blockquote style="margin-right: 0px;" dir="ltr">
<span class="104151705-10092005"><font face="Tahoma" size="2">Hi
Emory,</font></span>
<blockquote style="margin-right: 0px;" dir="ltr">
<div><span class="104151705-10092005"><font face="Tahoma" size="2">I am
having trouble with the min-max of oscillations for a couple of models,
so I would be</font></span></div>
<div><span class="104151705-10092005"><font face="Tahoma" size="2">grateful
for your help. I tried to get the max-min for the foll</font></span></div>
<div><span class="104151705-10092005"><font face="Tahoma" size="2">two
models, but was unable to. Could you try and generate the plots, </font></span><span
class="104151705-10092005"><font face="Tahoma" size="2">and send them
as well</font></span></div>
<div><span class="104151705-10092005"><font face="Tahoma" size="2">as
the parameter settings you used to generate them.</font></span></div>
<div><span class="104151705-10092005"></span> </div>
<div><span class="104151705-10092005"></span><span
class="104151705-10092005"><font face="Tahoma" size="2">model 1:
mapkfinal.xml ------ bifurcation parameter J5_k (currently set at
0.0001)</font></span></div>
<div><span class="104151705-10092005"></span> </div>
<div><span class="104151705-10092005"><font face="Tahoma" size="2">model
2: mapknew.xml ------- bifurcation parameter kI (currently set at
100)</font></span></div>
<div><span class="104151705-10092005"></span> </div>
<div><span class="104151705-10092005"><font face="Tahoma" size="2">Thanks
in advance,</font></span></div>
<div><span class="104151705-10092005"><font face="Tahoma" size="2">best,</font></span></div>
<div><span class="104151705-10092005"><font face="Tahoma" size="2">vijay</font></span></div>
</blockquote>
</blockquote>
</blockquote>
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