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Data2Dynamics / d2d

a modeling environment tailored to parameter estimation in dynamical systems
https://github.com/Data2Dynamics/d2d
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Running d2d for ODEs #132

Closed ChristophStelzer closed 6 years ago

ChristophStelzer commented 6 years ago

I downloaded the latest version of d2d and ran it with MATLAB_R2018b. There seems to be a problem when using ODEs instead of REACTIONS. All example projects (containing ODEs) crash with this error:

Data 2 Dynamics Software
(arFramework3, def-version 3, c-version code_180926b)
Website: http://www.data2dynamics.org
Contact: Andreas Raue - andreas.raue@fdm.uni-freiburg.de
Copyright 2016 D2D Development Team. All rights reserved.

Clearing old D2D mex files from memory  [OK]
loading model #1, from file Models/TwoStepSynthesisWithGlu.def...
Index exceeds the number of array elements (0).

Error in arCheckForNegFluxes (line 5)
        reversible = ar.model(m).reversible(jf);

Error in arLoadModel (line 1082)
    arCheckForNegFluxes(m, fid);

Error in Setup_IndiBac (line 5)
arLoadModel('TwoStepSynthesisWithGlu');

I ran it with multiple models and also with a model of myself (which used to work with a previous release of d2d/MATLAB_R2015a) and all of them show the same error.

Any idea/help? Christoph

JoepVanlier commented 6 years ago

Thanks for the bug report. I just committed a fix for this here 470634347ffea15e3d634976d7f35871c14b5ae7

You have two options, either update to the version I just committed. Or setting ar.config.checkForNegFluxes to 0. Either should get you back up and running.

Best, Joep.