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[cellml-discussion] how to units make a difference to simulation


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  • From: j.lawson at auckland.ac.nz (James Lawson)
  • Subject: [cellml-discussion] how to units make a difference to simulation
  • Date: Tue, 07 Aug 2007 13:50:32 +1200
Alan Garny wrote:
>> -----Original Message-----
>> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-
>> bounces at cellml.org] On Behalf Of James Lawson
>> Sent: 06 August 2007 00:40
>> To: For those interested in contributing to the development of CellML.
>> Subject: [cellml-discussion] how to units make a difference to
>> simulation
>>
>> Hi all,
>>
>> Recently Catherine said that she had a model that was running but not
>> producing the right output. Instead of producing a train of spikes, it
>> was just producing some kind of curve flattening off at an asymptote.
>> Then when she changed some units on a relevant variable from
>> dimensionless to the right units, she got the nice spiking output.
>>
>> As for myself, I've been looking at a model which has both a normal
>> version and a scaled/non-dimensionalized version. When I consulted him
>> about the output I was getting and which equations I should be using
>> from his paper, the model author suggested that I use the
>> non-dimensionalised set of equations, since the model describes a very
>> stiff problem, and as such, that is what the ND'd equations are there
>> for. Wheras before I was just getting curves that looked nothing like
>> I
>> want, I am now getting trains of spikes.
>>
>> I realise the first example might be slightly different from the first
>> (damn I am sick of people who don't know how to write English, the
>> Americans, that is, telling me I need a 'z' everywhere!) but...
>>
>> The point/question I want to raise here, is how does PCEnv / other
>> simulators treat units? Is it possible that some of the models in the
>> repository simply don't run or produce the right outputs because of
>> the
>> units? If so, this would be news to me! It would also be frustrating
>> given the number of times we have to guess or spend hours poring over
>> equations trying to work out the units of a variable.
>
> Hi James,
>
> As you know we (Catherine, you and I) spent a bit of time this morning
> trying to understand some models. One of the models that Catherine has been
> working on had problems with units. My understanding is that PCEnv didn't
> pick those problems up, while COR did. Correcting the problems, Catherine
> was able to get the model to "work" (I believe there might still be another
> problem, but not related to units this time).
>
> Anyway, the view we have now taken in Oxford is that models shouldn't have
> any problem related to units.

I absolutely agree that models should not have units problems. The
problem is that many of them do, and, speaking for myself, I do not have
the skills or the knowledge to know how to rearrange someone else's
model to fix the units. Especially with big models, it can just get too
complex. I'd like to see unit checking in PCEnv, but I wouldn't want a
model with bad units to not run - I'd just want error messages telling
me there is a problem.

This means that, dimensional equivalences,
> which are allowed in the CellML specification, are not "acceptable" to us.
> We should always have strict equivalences. E.g. A = B+C (with A and B in mV,
> while C in V) would be seen as being dimensionally equivalent and "OK" in
> regards to the CellML specification (and therefore COR, since it will only
> generate a warning). Yet, we would modify the equation so that it now reads:
> A = B+1000{millivolt_per_millivolt}*C. This may not be a great example, but
> I think you got the gist of it.
>
> The idea is, therefore, to have models that have no unit issues *at all*. I
> appreciate that this may seem a bit restrictive, but we have had so many
> issues with units over the years that we believe it will be worth it in the
> long term.

This would be great. I think it needs to start with the model authors
though, which is where standards such as MIRIAM come in.

>
> Alternatively, we could have the software doing units conversion for the
> user... but that's another issue... and I understand that some are against
> that idea.

Again, this is a feature that it would be useful to be able to turn on
and off. However I think in most cases the software will not be smart
enough to figure out what the units should be.

>
> Alan.
>
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