Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[Bruno Chareyre]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

Bruno Chareyre posted a new comment:
My point was to NOT use ignoredBody, as the warning suggests. Use mask
instead.

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Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[liucheng83]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

liucheng83 confirmed that the question is solved:
Thanks Robert Caulk, that solved my question.

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Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[liucheng83]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

Status: Answered => Solved

liucheng83 confirmed that the question is solved:
Dear Robert,

I must say sorry for not being aware of the problem that how to raise a
new question.  I will try to grasp the meaning from the documentation as
you suggested.  Thank you for your advice.


Dear Bruno,

I will try it to see whether ignoredBody method does work because
somethings went wrong. Thank you.

Cheng Liu

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Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[Chareyre]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

Status: Open => Answered

Chareyre proposed the following answer:
>ignoredBody(=-1)
>DEPRECATED, USE MASK - Id of a sphere to exclude from the triangulation.)

Excellent. I implemented the feature then I forgot.
So, there is this alternative to the blocking cell method: assign mask=1 to
flow engine, mask=1 to half of the particles on the good side, mask=2 for
the other half.
The fluid problem will simply not see the spheres which do not have the
right mask, as if they were not actually in the simulation. They are not
meshed, so there will be no cells to block.
Besides, the discussion becomes confusing...
Bruno

On 19 May 2017 at 02:03, liucheng83 
wrote:

> Question #632800 on Yade changed:
> https://answers.launchpad.net/yade/+question/632800
>
> Status: Answered => Open
>
> liucheng83 is still having a problem:
> Hello Robert and Bruno,
>
> Thanks for your reply.
> I will chose to use solver 3 and I will try to test the blocking cells.
>
> But before that, some results come out that I cannot understand,
>
> Q5:
> print flow.ignoredBody###it get -1 as the result
> How can I set a body to be ignoredBody, because it can be exclude from the
> triangulation from the documentation
> ---
> ignoredBody(=-1)
> DEPRECATED, USE MASK - Id of a sphere to exclude from the triangulation.)
> -
> Q6: I try to get information about flow cells just after "print the Qin"
> ---
> print "Qin=",Qin," Qout=",Qout," permeability=",permeability
>
> #print  information
> print "total num of nCells,flow.nCells()=", flow.nCells()
>  ### It get 0 as a result, why?
> print "total ids of bodies affected by this Engine,flow.ids=", flow.ids
>   ### It get [] as a result, why?
> print flow.ignoredBody  #get -1
> print flow.getVertices(0)
> -
>
> Q7: when I unload the top wall when FlowEngine is dead by using
> 
> ##unload
> triax.goal2=0; O.run(2000,1)
> ---
> and after FlowEngine is activated, set
> 
> flow.bndCondIsPressure=[0,0,1,1,0,0]
> flow.bndCondValue=[0,0,0,1,0,0]
> --
>
> I test the Qin and Qout, sometimes it comes out with a different value
> like, Qin=0 and Qout=-1.19524638635e-06
> Anything wrong with the input and output not equal?
>
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Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[liucheng83]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

liucheng83 gave more information on the question:
Q10:

Sorry, I execute O.load('１.yade.bz2') after print Qin, so it comes out the 
result after I print flow.nCells(

Result:  0
---
But, how can recover the state to the state when I execute 
O.save('１.yade.bz2'), every time I O.load('１.yade.bz2'),
it seems everything is lost.

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Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[liucheng83]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

liucheng83 gave more information on the question:
Q9:

And when I  execute O.step() after print Qin and Qout
The result comes out like this:
--
GS : j=0 p_moy=-nan dp_moy=-nan
GS iterations : 0
totalForce = 0 0 0
-
What is the meaning?

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Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[liucheng83]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

liucheng83 gave more information on the question:
Q8:
I want to use mask for spheres bodies to not affected by the flowEngine, Is it 
possible to do that？ How can I do it?
--
mask(=0)
If mask defined, only bodies with corresponding groupMask will be affected by 
this engine. If 0, all bodies will be affected.


In the , I add mask here

##Soil Packing creating
sp=pack.SpherePack()
sp.makeCloud(mn,mx,-1,0.,num_spheres,False, 0.95,seed=1) #"seed" make the 
"random" generation always the same
sp.toSimulation(material='spheres', mask=1)
---
But the TriaxialStressController seems not woking anymore, because the 
TriaxialStressController Engine cannot set mask, right?

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Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[liucheng83]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

Status: Answered => Open

liucheng83 is still having a problem:
Hello Robert and Bruno,

Thanks for your reply. 
I will chose to use solver 3 and I will try to test the blocking cells.

But before that, some results come out that I cannot understand,

Q5: 
print flow.ignoredBody###it get -1 as the result
How can I set a body to be ignoredBody, because it can be exclude from the 
triangulation from the documentation
---
ignoredBody(=-1)
DEPRECATED, USE MASK - Id of a sphere to exclude from the triangulation.)
-
Q6: I try to get information about flow cells just after "print the Qin"
---
print "Qin=",Qin," Qout=",Qout," permeability=",permeability

#print  information
print "total num of nCells,flow.nCells()=", flow.nCells() ### 
It get 0 as a result, why?
print "total ids of bodies affected by this Engine,flow.ids=", flow.ids 
 ### It get [] as a result, why?
print flow.ignoredBody  #get -1
print flow.getVertices(0)
-
 
Q7: when I unload the top wall when FlowEngine is dead by using

##unload
triax.goal2=0; O.run(2000,1)
--- 
and after FlowEngine is activated, set 

flow.bndCondIsPressure=[0,0,1,1,0,0]
flow.bndCondValue=[0,0,0,1,0,0]
--

I test the Qin and Qout, sometimes it comes out with a different value like, 
Qin=0 and Qout=-1.19524638635e-06
Anything wrong with the input and output not equal?

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Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[Bruno Chareyre]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

Bruno Chareyre proposed the following answer:
> 0=Gauss Seidel 1=Taucs 2=Pardiso 3=Eigen

This was some time ago. Although the code is there technically it will
not work with Taucs/Pardiso unless yade is linked vs. these libs (by
default cmake will not). So I confirm that 3 is the only good option. So
1 or 2 would just return "Flow engine not compiled with taucs, nothing
computed if useSolver=1".

Anyway, Q3: 
Taucs, Pardiso, or Eigen are (were) all used for exactly the same solver: 
Cholesky factorization implemented for sparse linear systems. It turned out 
that eigen/cholmod was the (slightly) most efficient in terms of CPU time, 
hence no need to consider the other ones since they are mathematicaly 
equivalent.

Q4. Robert's answer is excellent. You can do that.

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Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[Robert Caulk]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

Status: Open => Answered

Robert Caulk proposed the following answer:
Hello,

>Do you have the information about the solver used for Flowengine

 The solvers basically use different libraries/methods to solve the same
system of equations. The key to the numbers: 0=Gauss Seidel 1=Taucs
2=Pardiso 3=Eigen. The interfaces to these libraries are coded in [1] if
you are interested in diving into the rabbit hole. My recommendation is
to stick with 3, it is quite robust in my experience (not to mention it
is free, while pardiso requires a license if I am not mistaken).

>Q4:

Hmm, basically you want half of your cube to not participate in fluid
flow? You still want the top and bottom halves to interact mechanically,
correct?

You might want to try experimenting with blocking cells [2]. For
example, you'd set up the entire cube with flow, and then sweep through
the bottom half of the cells with blockCell. I've never used it though,
so I am unsure how that will work out. Good luck.

Cheers,

Robert

[1]https://github.com/yade/trunk/blob/master/lib/triangulation/FlowBoundingSphereLinSolv.ipp
[2]https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.FlowEngine.blockCell

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Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[liucheng83]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

Status: Answered => Open

liucheng83 is still having a problem:
Hello Robert,

Thanks for your reply. It's great.

More Questions to add:
Q3:
Do you have the information about the solver used for Flowengine because I can 
only get this information:

useSolver(=0)
Solver to use. 0:Gauss-Seidel, >0: Cholesky factorization (sparse CHOLMOD)
-
Any lists here about the solver that is great than zero?

Q4:
I want to create a  two region of the model, one has the fluid cell to 
calculate the flow seepage  ( region one) , just the same way as oedometer.py 
to create the walls, boxes using  aabbWalls, and get the target state using 
TriaxialStressController.
-
walls=aabbWalls([mn,mx],thickness=0,material='walls')
--- 
I want to add another box region ( region two) just below the  bottom wall 
which store the balls that do not need to participate in fluid calculation. Is 
it possible? The main difficult is how to define the flowEngine boundary 
conditions of  region one.

For simple for above description , I like to create two  conjoint box，the upper 
one ( region one) need fluid calculation and the lower one ( region two) do not 
need fluid calculation. The lower one may share the same wall from the upper 
one.  Is it possible? 
How can I set the flowEngine boundary conditions of  region one?

Many thanks,
Cheng

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Re: [Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[Robert Caulk]

Question #632800 on Yade changed:
https://answers.launchpad.net/yade/+question/632800

Status: Open => Answered

Robert Caulk proposed the following answer:
Hello Cheng,

>Which Viscosity is used in FlowEngine, dynamic viscosity or kinematic
viscosity?

FlowEngine computes flow between cells using Poiseuilles law [1], so it
is using the dynamic viscosity of the fluid.

>I know some parameter value is just for a test, but I am not sure
whether any parameters are using SI Unit.

YADE is (generally) unitless. You decide which units you want your
system to adhere to, and assuming you are consistent, your results will
remain in the system you have chosen. I did not author oedometer.py, but
most of these examples are just demonstrations of functionality, I
wouldn't take the numbers to mean anything special if I were you (but
maybe they do, without comments I guess you need to really inspect it to
find out what unit system it is in). Same goes for default values in
general, these are values that worked for someone's simulation but you
will need to change them to obtain accurate behavior in your specific
model.

>And how can I find the FlowEngine source codes.

YADE source code is hosted on Github. The FlowEngine itself is contained
in [2], but it relies on [3] and [4] for permeability calculations and
the solver.


[1]Chareyre, B., Cortis, A., Catalano, E., & Barthélemy, E. (2012). Pore-Scale 
Modeling of Viscous Flow and Induced Forces in Dense Sphere Packings. Transport 
in Porous Media, 94(2), 595–615. http://doi.org/10.1007/s11242-012-0057-2

[2]https://github.com/yade/trunk/blob/master/pkg/pfv/FlowEngine.ipp.in
[3]https://github.com/yade/trunk/blob/master/lib/triangulation/FlowBoundingSphere.ipp
[4]https://github.com/yade/trunk/blob/master/lib/triangulation/FlowBoundingSphereLinSolv.ipp

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[Yade-users] [Question #632800]: Viscosity of water in FlowEngine

[liucheng83]

New question #632800 on Yade:
https://answers.launchpad.net/yade/+question/632800

Hi, everyone.

Which Viscosity is used in FlowEngine, dynamic viscosity or kinematic 
viscosity? And is the default value is water in T=20 degree celsius using SI 
Unit.

viscosity(=1.0)  why 1.0 here in class yade.wrapper.FlowEngine((object)arg1)
 
viscosity of the fluid

https://yade-dem.org/doc/yade.wrapper.html?highlight=flowengine#yade.wrapper.FlowEngine
-
Why  the example script oedometer.py in FluidCouplingPFV Folder using 
flow.viscosity=10, any consideration about it?

I know some parameter value is just for a test, but I am not sure whether any 
parameters are using SI Unit.

And how can I find the FlowEngine source codes.

Many thanks,
Cheng

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