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TOPIC: Tips to Calibrate/Validate my 3D model case - with some figures!!

Tips to Calibrate/Validate my 3D model case - with some figures!! 5 years 6 months ago #33591

  • Jose_filho
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Hello Everyone,

I am a PhD student and I am trying to validate my model simulations against some observational data I have. My study site is in Brazil, tropical zone with low freshwater input into two very polluted short estuaries and shelf sea.

I've been reading a lot and playing with the parameters in my cas file to reach a nice validation for the 3D model, however its still quite different of the observation in the 3D model. I mean, the 2D free surface calibration seems ok (or close to it), however the 3D is still very different.

Could anyone help me just showing me the main parameters I should change to reach a nicer validation? After I validate it, my intention is to couple it with with sysyphe and put some drogues on it to see the behavior. I am trying now to define variable bottom friction coefficient into the domain...I can send my files (cli,geometry etc..) in private, just give me your e-mail if you are interested to see it better.

I am attaching some figures and my CASE file to assist you on the assessment. Please, feel free to give me suggestions and tips to improve it.
I will be very grateful!

Thanks in advance and best regards for everyone.

José
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Tips to Calibrate/Validate my 3D model case - with some figures!! 5 years 6 months ago #33592

  • aleroy
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Hello,

If it's not too bad for you to increase your computational time, here is what I suggest (hoping it improves your results, but these are only my own suggestions):

Advection
- use the predictor-corrector distributive scheme with local implicitation for tidal flats, based on the PSI scheme, for the velocity and all tracers, including k and epsilon if you have them:
/ PSI scheme
SCHEME FOR ADVECTION OF VELOCITIES = 5
SCHEME FOR ADVECTION OF K-EPSILON = 5
SCHEME FOR ADVECTION OF TRACERS = 5
/ predictor-corrector with local implicitation implicite
SCHEME OPTION FOR ADVECTION OF VELOCITIES = 4
SCHEME OPTION FOR ADVECTION OF K-EPSILON = 4
SCHEME OPTION FOR ADVECTION OF TRACERS = 4
- without tidal flats, use the predictor-corrector without tidal flats treatment to gain some time
/ Predictor-corrector without tidal flats treatment
SCHEME OPTION FOR ADVECTION OF VELOCITIES = 2
SCHEME OPTION FOR ADVECTION OF K-EPSILON = 2
SCHEME OPTION FOR ADVECTION OF TRACERS = 2

Friction
- use the Nikuradse law, which is the only one that's really 3D compatible: the other options have been implemented to ensure an easy correspondance between 2D and 3D simulations, but their use is not recommended for fully 3D studies:
LAW OF BOTTOM FRICTION = 5
- use a friction coefficient that is representative of the physics of your case: with the Nikuradse law, the friction coefficient corresponds to the characteristic height of the roughness
FRICTION COEFFICIENT FOR THE BOTTOM = 3*d90
for a natural bed with sediment of characteristic size d90 and without riddles or dunes, its value should be taken from van Rijn, equal to 3*d90. In the presence of dunes, van Rijn proposes another formula.
- depending on the nature of the lateral walls, either use a Nikuradse law or no friction
LAW OF FRICTION ON LATERAL BOUNDARIES = 0 or 5
- as for the bed, use a physical value for
FRICTION COEFFICIENT FOR LATERAL SOLID BOUNDARIES
- remark: contrary to the friction coefficients used with the laws derived from the shallow water context (Manning, Strickler, Chézy, Haaland), the friction coefficient with the Nikuradse law does not "hide" physical effects like diffusion-dispersion, like it does with the shallow-water equations. Thus, it is less prone to being used as a calibration parameter in the studies.

Mass-lumping
- avoid using mass-lumping, unless you really have a strong constraint on computational time (this is the default behaviour of TELEMAC-3D) : it introduces artificial dispersion in the results

Semi-implicitation
- do not change the default value for
IMPLICITATION FOR DEPTH ( = 0.55)
and use
IMPLICITATION FOR VELOCITIES = 0.55 instead of the default value of 1. Warning: never use a value lower or equal to 0.5 for these coefficients, otherwise the scheme becomes unconditionnally unstable. Avoid using the value 1 too, we have observed a strange behaviour of the scheme in this case: it seems to introduce quite a lot of spurious diffusion, even though 0.99 does not... We should perform more testing and analysis to better understand this behaviour.
- the keyword IMPLICITATION FOR DIFFUSION can be left to its value by default, 1.

Linear solvers
- Use the solver 7, GMRES, for the matrices inversion, except diffusion (SOLVER FOR PPE, SOLVER FOR VERTICAL VELOCITY, SOLVER FOR PROPAGATION). For the diffusion, the conjugate gradients should be good enough (solver number 1).
- use an accuracy equal to 10^-8 or lower for all solvers (ACCURACY FOR PPE, ACCURACY FOR VERTICAL VELOCITY, ACCURACY FOR PROPAGATION, ACCURACY FOR DIFFUSION OF VELOCITIES, ACCURACY FOR DIFFUSION OF K-EPSILON, ACCURACY FOR DIFFUSION OF TRACERS, ACCURACY FOR DIFFUSION OF SEDIMENT)
- Be careful to always check in your listing that your solvers have actually converged, otherwise the simulation may complete but with wrong results. In case you don't reach the accuracy you asked for with these options, try increasing the value of OPTION OF SOLVER FOR [...] to 10. It sets the size of the Krylov subspace used in the GMRES solver. You can also try increasing the maximum number of iterations of the solvers, or try using the preconditionning number 34 to make the matrix inversions faster.

Fractional steps method
- the keyword DYNAMIC PRESSURE IN WAVE EQUATION can be left to its value by default, NO, but setting it to YES may slightly reduce the numerical diffusion (altough we need to test it further to really characterize the behaviour of these two choices).

Free surface
- if you observe free-surface instabilities (wiggles) in your results, you can try using a lower value for the
FREE SURFACE GRADIENT COMPATIBILITY
than the one by default, for example 0.9.

Liquid boundaries
- I would suggest trying not to use the Thompson boundary conditions, because they are actually only valid in the shallow water context. However, I admit that they may help stabilise the simulations involving liquid boundaries, so it's not always that easy not to use them. You should try without it I would suggest.

Tidal flats
- use TREATMENT OF NEGATIVE DEPTHS = 2
- use TREATMENT ON TIDAL FLATS FOR TRACERS = 1 to ensure conservation


Turbulence
- I would recommend trying ot use the k-epsilon model (3) on the vertical and the horizontal directions, or the Spallart-Almaras one (5), also in both directions, instead of the mixing length model which is not flexible, since it is a zero-equation model.


Other numerical options
- do not change the matrix storage, simply remove it from the steering file

I hope this helps.
Agnès
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Tips to Calibrate/Validate my 3D model case - with some figures!! 5 years 6 months ago #33593

  • Jose_filho
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Thank you so much, Agnès.
I will apply these changes you suggested and let you know what happened.
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Tips to Calibrate/Validate my 3D model case - with some figures!! 5 years 5 months ago #33609

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Good Morning, Agnès.

I have been trying to set your suggestions however seems that K-Epsilon and Spallart-Almaras turbulence models are too unstable and exceeds the maximum number of iterations even if I set it to 5000.

I tried a lot of different keyword combinations, different solvers, as well as accuracy and preconditioning, but the model always blows up.

The only way of functioning is when I set the horizontal model (K-epsilon) together with mixing length for the vertical and timestep of 10s. I've read that K-epsilon works well when you refine your mesh and also reduce the timestep, but for the vertical one is not working at all...

Anymore ideas for improve the calibration/validation?


Thanks in advance,

José
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Tips to Calibrate/Validate my 3D model case - with some figures!! 5 years 5 months ago #33610

  • aleroy
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Hi José,

Have you tried decreasing the time-step size when using k-epsilon or Spallart-Almaras?

Did your results improve with the changes I suggested, even using the mixing length model?

Cheers,
Agnès
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Tips to Calibrate/Validate my 3D model case - with some figures!! 5 years 5 months ago #33611

  • aleroy
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By the way, what is the size of your smallest element, what is your smallest water depth and how mayn layers have you used on the vertical?

Cheers,
Agnès
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Tips to Calibrate/Validate my 3D model case - with some figures!! 5 years 5 months ago #33612

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"Have you tried decreasing the time-step size when using k-epsilon or Spallart-Almaras?"
a: yes, I have decreased it to 10s, but it did not work well. So, I am using Mixing Length in vertical and K-epsilon as horizontal. It working, but exceeding max iterations for temperature.

"Did your results improve with the changes I suggested, even using the mixing length model?"
a: I do not know yet, because I have been trying to run as you suggested. I will try in this afternoon and let you know what happened.

"By the way, what is the size of your smallest element, what is your smallest water depth and how mayn layers have you used on the vertical?"
a: Minimum Element Area: 5.125000
Maximum Element Area: 7315091.500000
Mean Element Area: 40837.719570
Area Distribution:
10 Percentile: 47173
20 Percentile: 106
30 Percentile: 113
40 Percentile: 49
50 Percentile: 41
60 Percentile: 49
70 Percentile: 50
80 Percentile: 21
90 Percentile: 12
100 Percentile: 3

The smallest depth is -58 and maximum is 1.8. I do have tidal flats and the estuaries are surrounded by mangroves with great mud deposits.

I have used 11 layers.


Cheers,

José
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Tips to Calibrate/Validate my 3D model case - with some figures!! 5 years 5 months ago #33613

  • aleroy
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Ok, thanks for the information. Based on what you tell me your minimum triangle size is around 5m, and imagining velocities around 0.5m/s, with a CFL chosen to 0.8 your time step size should be around 5 seconds. Am I wrong about these numbers? Is it possible for you to try such a value with k-eps or Spallart-Almaras?

Cheers,
Agnès
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Tips to Calibrate/Validate my 3D model case - with some figures!! 5 years 5 months ago #33614

  • aleroy
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If you are using GMRES for the temperature diffusion, what you can try to improve convergence is set a value of 10, for example, for the number of Krylov subspace dimensions, instead of the default which is 3 (OPTION OF SOLVER FOR DIFFUSION OF TRACERS).

Best regards,
Agnès
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Tips to Calibrate/Validate my 3D model case - with some figures!! 5 years 5 months ago #33623

  • Jose_filho
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Salut Agnés,

"If you are using GMRES for the temperature diffusion, what you can try to improve convergence is set a value of 10, for example, for the number of Krylov subspace dimensions, instead of the default which is 3 (OPTION OF SOLVER FOR DIFFUSION OF TRACERS)."
A: yes, I am using 10 for Krylov subspace for temp diffusion together with GMRES.

"Ok, thanks for the information. Based on what you tell me your minimum triangle size is around 5m, and imagining velocities around 0.5m/s, with a CFL chosen to 0.8 your time step size should be around 5 seconds. Am I wrong about these numbers? Is it possible for you to try such a value with k-eps or Spallart-Almaras?"
a: Yes, you are right about the numbers. Maybe the velocity could be stronger. Nevertheless, I reduced the timestep to 5sec, 1sec, 0.5sec, and it keeps exceeding the MNI.

Do you want my files to try it by yourself when you have some free-time? I will appreciate that. I am working now in a 28 cores cluster, but, as soon as validate it, I will work on a more powerful cluster, so I it not a problem to reduce the timestep.

Cheers,

José
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