[rafaelgabler]

Hello everyone!

I'm a new openFoam user and I'm trying to produce a solver based on the scalarTransportFoam that solves the energy equation in a biological medium containing a region with a tumour surrounded by a healthy tissue area.

My idea was to use the setFields to define the region of the tumour using an identifier, ID, which is 0 in the healthy tissue region and 1 inside the tumour region.

This identifier was defined as a volscalarField in my createFields.H file in the solver.

I also created an additional file named Weqn.H, which computes the blood perfusion field W using different algebric expresions according to the region that the volume occupies inside the mesh.

When I run the blockMesh command followed by setFields, the initial ID field is ok. However, when the solver executes the simulation my ID field is replaced by a null field during the time evolution process.

I would like to keep the ID field on the 0 folder, created through the setFields during the whole temporal loop of the simulation.

Any ideas of how can I achieve this goal?

Thanks in advance!

Best Regards!

[rafaelgabler]

Another ideia would be to call in the assemblying of the matrices for the linear system responsible for solving the temperature only the values of this identifier on the 0 folder.

Here is the piece of code I'm using to mount my energy equation:

fvScalarMatrix TEqn
(
fvm::ddt(T)
+ fvm::div(phi, T)
- fvm::laplacian(DT, T)
==
fvOptions(T) + ID*mu0*pi*H0*H0*freq*qui_imag*corr/(rho*cp)
+ rhob*cb*W*(T-Tb)/(rho*cp)
);

I would like to call the ID field always from the zero folder.

Any ideia on how to do this?

I feel that this should be a really simple thing to do, but I'm new in this OpenFOAM Universe and have no idea of what would be the proper synthax to do this.

If anyone could help me I would be very happy!

[geth03]

i am not sure if i understand what you are trying to do.

however, you might want to create a cellZone in which your "ID" is set to a constant value. and your equation picks up that value accordingly.
so your "ID"-value would remain independent of time evolution.

if that is what you want you can give a feedback.

[rafaelgabler]

Thanks a lot for your repply, geth03.

I will take a look in the cellZone documentation.

I figured out that my problem was in another piece of the code.

The solution for my problem envolved the following steps:

1 - I created a volScalarField to storage the identifier ID in the createFields.H:

volScalarField ID
(
IOobject
(
"ID",
runTime.timeName(),
mesh,
IOobject::MUST_READ,
IOobject::AUTO_WRITE
),
mesh
);

2 - Then I configured the setFieldsdict to produce this initial field and called it in the assembly of my linear system for temperature using the .internalField() atributte, which was something I did not know how to call it at the beggining and took a really long time to figure out.

fvScalarMatrix TEqn
(
fvm::ddt(T)
+ fvm::div(phi, T)
- fvm::laplacian(DT, T)
- ID.internalField()*mu0*pi*H0*H0*freq*qui_imag*corr/(rho*cp)
==
fvOptions(T)
+ rhob*cb*W.internalField()*(T-Tb)/(rho*cp)
);

Now the simulations are running as expected.

Thank you very much for your reply. I would like to learn how to create a cellZone in this case and how to call it. This could be useful in other steps of my project.

Best Regards!

Originally Posted by geth03

i am not sure if i understand what you are trying to do.

however, you might want to create a cellZone in which your "ID" is set to a constant value. and your equation picks up that value accordingly.
so your "ID"-value would remain independent of time evolution.

if that is what you want you can give a feedback.

[geth03]

i wanted to suggest another solution, that is basically similar to what you did but instead of setFields i wanted to do it with cellZone. a cellZone is basically a declaration of a zone in your mesh which you can access in your code for further calculations.

but i am glad you found a workaround.

[rafaelgabler]

Just a correction. In this quoted piece of code, ID.internalField() and W.internalField() should be simply replaced by ID and W in the assemblying of the temperature linear system.

The code seems to work fine, except for very low values of the thermal diffusivity DT. When I decrease my DT value bellow a certain limit (which I would like to reach) the solver does not run.

I'm using a Gauss linear corrected scheme for the Laplacian on the fvSchemes.

Any ideas?

Originally Posted by rafaelgabler

Thanks a lot for your repply, geth03.

I will take a look in the cellZone documentation.

I figured out that my problem was in another piece of the code.

The solution for my problem envolved the following steps:

1 - I created a volScalarField to storage the identifier ID in the createFields.H:

volScalarField ID
(
IOobject
(
"ID",
runTime.timeName(),
mesh,
IOobject::MUST_READ,
IOobject::AUTO_WRITE
),
mesh
);

2 - Then I configured the setFieldsdict to produce this initial field and called it in the assembly of my linear system for temperature using the .internalField() atributte, which was something I did not know how to call it at the beggining and took a really long time to figure out.

fvScalarMatrix TEqn
(
fvm::ddt(T)
+ fvm::div(phi, T)
- fvm::laplacian(DT, T)
- ID.internalField()*mu0*pi*H0*H0*freq*qui_imag*corr/(rho*cp)
==
fvOptions(T)
+ rhob*cb*W.internalField()*(T-Tb)/(rho*cp)
);

Now the simulations are running as expected.

Thank you very much for your reply. I would like to learn how to create a cellZone in this case and how to call it. This could be useful in other steps of my project.

Best Regards!

[geth03]

If you add terms to your equation you should decide if you want to add to the matrix or to the source, if you make wrong decisions your system will be hard to converge or even don‘t run.

Your implementation right now will put everything to the source. It can be possible that for low DT your matrix is not diagonally dominant. To offset this, you might decrease your time step.