Diffusion causes numerical instability
ChrisCurrin opened this issue · 4 comments
With diffusion changing the value of e.g. cli for compartments, an error is encountered in Compartment step function:
`RuntimeWarning: invalid value encountered in log
dcl = _time.dt * self.Ar * (gcl * (self.V + R * np.log(self.clo / self.cli)) - self.jkcc2)`
Please advise on diffusion calculation and updating of values
Sounds like you need some backwards Euler!
Sent from a smartphone
On 26 Aug 2016 18:54, "Christopher" notifications@github.com wrote:
With diffusion changing the value of e.g. cli for compartments, an error
is encountered:
RuntimeWarning: invalid value encountered in log
dcl = _time.dt * self.Ar * (gcl * (self.V + R * np.log(self.clo /
self.cli)) - self.jkcc2)Please advise on diffusion calculation and updating of values
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#1,
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Or Ranga - Katta!
On Fri, 26 Aug 2016, 20:52 pyjamashark notifications@github.com wrote:
Sounds like you need some backwards Euler!
Sent from a smartphone
On 26 Aug 2016 18:54, "Christopher" notifications@github.com wrote:
With diffusion changing the value of e.g. cli for compartments, an error
is encountered:
RuntimeWarning: invalid value encountered in log
dcl = _time.dt * self.Ar * (gcl * (self.V + R * np.log(self.clo /
self.cli)) - self.jkcc2)Please advise on diffusion calculation and updating of values
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<#1
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#1 (comment),
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Latest changes appear to have diffusion working to a reasonable
extent. Values may need to be tweaked to be realistic, but it works in
principle.
I shall push changes tonight when I have Internet
On 26/08/2016, Christopher chris.crisur@gmail.com wrote:
Or Ranga - Katta!
On Fri, 26 Aug 2016, 20:52 pyjamashark notifications@github.com wrote:
Sounds like you need some backwards Euler!
Sent from a smartphone
On 26 Aug 2016 18:54, "Christopher" notifications@github.com wrote:
With diffusion changing the value of eg cli for compartments, an error
is encountered:
RuntimeWarning: invalid value encountered in log
dcl = _time.dt * self.Ar * (gcl * (self.V + R * np.log(self.clo /
self.cli)) - self.jkcc2)Please advise on diffusion calculation and updating of values
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#1,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AIFhTbV5JXJwZHucE2x23kWLT64N0VYKks5qjxmFgaJpZM4JuQ3w
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Chris
I'm going to close this issue for now. The exact values/implementation may need tweaking, but works in principle