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[cellml-dev] FW: [Fwd: Re: [SOSlib-discuss] Identifying algebraic parts of DAE system]
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- From: r.britten at auckland.ac.nz (Randall Britten)
- Subject: [cellml-dev] FW: [Fwd: Re: [SOSlib-discuss] Identifying algebraic parts of DAE system]
- Date: Fri, 12 Sep 2008 02:01:59 +1200
Forwarding this with Rainer's permission.
> -----Original Message-----
> From: Rainer Machne [mailto:raim at tbi.univie.ac.at]
> Sent: Thursday, 11 September 2008 2:59 a.m.
> To: r.britten at auckland.ac.nz
> Cc: James Lu; Stefan Mueller; Christoph Flamm
> Subject: [Fwd: Re: [SOSlib-discuss] Identifying algebraic parts of DAE
> system]
>
> Hi Randall,
>
> Thanks for the information, we will certainly have a look at this code!
>
> A general note, since you have been looking at the SOSlib documentation
> (which is quite out-of-date with respect to current CVS version, btw).
>
> SOSlib is build quite modular, and actually can be used as a general ODE
> Solver, independent of SBML (but not libSBML whose formula
> representation as an abstract syntax tree is used throughout SOSlib). We
> currently have e.g. functions that allow to set up an ODE model from the
> ODEs in infix text description.
>
> So without the SBML->ODE construction part, it is merely a wrapper
> around SUNDIALS solvers to be used for any ODE model. We think, that we
> make quite efficient use of Sundials, and in the CVS version (soon to be
> released) we have e.g. our own custom-made internal compiler for
> equations. We also interface Sundials forward and adjoint sensitivity
> tools, which are quite handy for parameter identification strategies.
>
> It would be straightforward and probably quite easy to hook it up
> with CellML. I guess the CellML API allows to generate ODEs from a
> CellML model? Via libSBML's MathML or string-based equation interfaces,
> it could in the best case be just a matter of a few
> hours to link SOSlib to CellML API, generate ODEs with the CellML tool,
> and then generate SOSlib's internal ODE structures. From this point, all
> capabilities of SOSlib would be open for use with CellML.
>
> Would there be any interest from your side? We would be happy to help,
> or even support a CellML interface officially. It could work both ways,
> interface SOSlib from CellML API to provide simulation results
> (including sensitivities etc.), or CellML API from SOSlib to generate
> ODEs from a CellML model.
>
> Rainer
>
>
> Randall Britten wrote:
> > A simple example is the DAE:
> http://svnviewer.bioeng.auckland.ac.nz/projects/physiome/browser/CellML_
> DOM_API/trunk/tests/test_xml/SimpleDAE_NonLinear.xml?rev=2344
> >
> > And the code generated for it:
> >
> http://svnviewer.bioeng.auckland.ac.nz/projects/physiome/browser/CellML_
> DOM_API/trunk/tests/test_expected/SimpleDAE_NonLinear.c?rev=2344
> >
> > Currently, we are trying an experimental approach where we use just an
> ODE solver, and solve the algebraic subsystems in a "decoupled" manner.
> >
> > This is illustrated in the generated code above
> (SimpleDAE_NonLinear.c):
> > Line 71 is the function used by the ODE solver to compute the rates.
> But it calls a separate algebraic non-linear solver (line 73) to solve
> the decoupled algebraic part. Note that this example only has one
> decoupled algebraic subsystem, but the code generation service looks for
> any number of these, it just so happens that this example has only one.
> >
> > I'll find another example if you like that illustrates having more
> than one subsystem.
> >
> > But it is late here now, so hopefully you don't mind waiting till
> Friday for that one.
> >
> > Note that we are still not convinced that this is a numerically
> reliable way to do this, and are considering using IDA.
> >
> > Regards,
> > Randall
> >
> >> -----Original Message-----
> >> From: James Lu [mailto:james.lu at oeaw.ac.at]
> >> Sent: Thursday, 4 September 2008 11:12 p.m.
> >> To: Randall Britten
> >> Cc: Rainer Machne
> >> Subject: Re: [SOSlib-discuss] Identifying algebraic parts of DAE
> system
> >>
> >> On Thursday 04 September 2008 06:45, you wrote:
> >>> Hi
> >>>
> >>>
> >>>
> >>> Andrew Miller has created code for decomposing a system of DAE's
> into
> >>> possibly many algebraic subsystems and one differential system,
> which
> >> can
> >>> then be solved in a decoupled manner.
> >> hi Randall:
> >>
> >> That sounds interesting. Might you have a small example illustrating
> >> what the
> >> code does?
> >>
> >> Best,
> >>
> >> James
> >
>
- [cellml-dev] FW: [Fwd: Re: [SOSlib-discuss] Identifying algebraic parts of DAE system], Randall Britten, 09/12/2008
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