Dear Mojtaba, your videos have been very helpful through my research. However, right now I am stuck with a problem; My mesh has more than one degradable volume and BIODEG receives only one label. I thought of uniting these volumes in order to have two regions, namely the medium and the biodegradable part but unfortunately, I ended up being here asking for your help. I would appreciate your guidance on this matter as I cannot move forward at this point.
very happy to know that the videos have been useful for you. thank you so much for pointing out to something I had never noticed before. yes, BioDeg doesn't support two regions by default. 2 options come to my mind for this problem at this moment: 1) you may consider modifying the BioDeg code in order to accept 2 regions (which can be a bit cumbersome), 2) grouping the biodegradable volumes in SALOME. I think you have already tried the second option, but I guess you have exported the mesh to GMF format (.mesh), which neglects the created groups unfortunately. in my biodegradation research, I was using a powerful tool called FEconv (github.com/victorsndvg/FEconv) for this purpose, by exporting the mesh in SALOME first to UNV format and then using FEconv to convert it to .mesh format. in this way, the created groups are preserved. you can do that by running a command like "feconv mesh_1.unv mesh_1.mesh". the tool can be easily compiled on Linux, but let me know if you failed and I will create a video or blog post on it (I should actually start to record some videos on BioDeg). if you use Windows, send me an email so that I can send you a compiled Windows binary I had compiled for a friend of mine.
@@TuxRiders I truley appreciate your thorough response, dear Mojtaba. I have not had the chance to go and try your suggested method. However, I encountered another fatal problem. The Mg thicknesses I work with are extremely small (i.e. in um and nm scales). Before I start simulating my thin Mg stick with several volumes, I was wondering if BioDeg could work with such tiny mesh elements. And, sadly, i ended up receiving PETC error. Caught signal number 8 FPE: Floating Point exception, ptobably divide by zero. I am baffled onve more. Could you please, open a window of light on this matter?
@@azarhadi9186 you're welcome :) BioDeg doesn't care that much about the dimensions, but I would say things in the scales you mentioned degrade quite fast, and it can cause a problem in your simulations. also, capturing this level of details requires a big mesh, which can cause problems for you if you don't run the simulations in an HPC environment. the error you are facing seems to be a problem with the mesh labels, like cases in which BioDeg cannot detect any element belonging to the degradable solid. you may need to double check your mesh to make sure it has correct labels.
Are you able to assist me in setting up an openFOAM case looking at a fluid flowing from a pipe? I want to visualise the heavier fluid draining from the outlet back to an S-Bend where the end of the pipe is within a less dense fluid. I am able to provide both a STEP file of a freecad geometry file and a more detailed explanation if you are interested and able to help me set it up. I have watched a number of your tutorials, but I am just struggling to get things bedded down in one of my own examples.
I think your problem is a sort of mixing problem, no? You have two fluids with different properties, and you want to simulate how they interact. I would say that the geometry is not the biggest challenge in your case, but rather, you need to find a good solver that can tackle this type of model. Unfortunately, I've never worked with mixing problems so I cannot be of a great help here.
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Very useful. Your channel is one of the best computational mathematics channel in the net.
Glad you think so :)
please, make some video defining and applying different regions using FEniCS
sure, I will.
Dear Mojtaba, your videos have been very helpful through my research. However, right now I am stuck with a problem; My mesh has more than one degradable volume and BIODEG receives only one label. I thought of uniting these volumes in order to have two regions, namely the medium and the biodegradable part but unfortunately, I ended up being here asking for your help. I would appreciate your guidance on this matter as I cannot move forward at this point.
very happy to know that the videos have been useful for you. thank you so much for pointing out to something I had never noticed before. yes, BioDeg doesn't support two regions by default. 2 options come to my mind for this problem at this moment: 1) you may consider modifying the BioDeg code in order to accept 2 regions (which can be a bit cumbersome), 2) grouping the biodegradable volumes in SALOME. I think you have already tried the second option, but I guess you have exported the mesh to GMF format (.mesh), which neglects the created groups unfortunately. in my biodegradation research, I was using a powerful tool called FEconv (github.com/victorsndvg/FEconv) for this purpose, by exporting the mesh in SALOME first to UNV format and then using FEconv to convert it to .mesh format. in this way, the created groups are preserved. you can do that by running a command like "feconv mesh_1.unv mesh_1.mesh". the tool can be easily compiled on Linux, but let me know if you failed and I will create a video or blog post on it (I should actually start to record some videos on BioDeg). if you use Windows, send me an email so that I can send you a compiled Windows binary I had compiled for a friend of mine.
@@TuxRiders I truley appreciate your thorough response, dear Mojtaba. I have not had the chance to go and try your suggested method. However, I encountered another fatal problem. The Mg thicknesses I work with are extremely small (i.e. in um and nm scales). Before I start simulating my thin Mg stick with several volumes, I was wondering if BioDeg could work with such tiny mesh elements.
And, sadly, i ended up receiving PETC error.
Caught signal number 8 FPE: Floating Point exception, ptobably divide by zero.
I am baffled onve more. Could you please, open a window of light on this matter?
@@azarhadi9186 you're welcome :)
BioDeg doesn't care that much about the dimensions, but I would say things in the scales you mentioned degrade quite fast, and it can cause a problem in your simulations. also, capturing this level of details requires a big mesh, which can cause problems for you if you don't run the simulations in an HPC environment.
the error you are facing seems to be a problem with the mesh labels, like cases in which BioDeg cannot detect any element belonging to the degradable solid. you may need to double check your mesh to make sure it has correct labels.
Are you able to assist me in setting up an openFOAM case looking at a fluid flowing from a pipe? I want to visualise the heavier fluid draining from the outlet back to an S-Bend where the end of the pipe is within a less dense fluid.
I am able to provide both a STEP file of a freecad geometry file and a more detailed explanation if you are interested and able to help me set it up.
I have watched a number of your tutorials, but I am just struggling to get things bedded down in one of my own examples.
I think your problem is a sort of mixing problem, no? You have two fluids with different properties, and you want to simulate how they interact. I would say that the geometry is not the biggest challenge in your case, but rather, you need to find a good solver that can tackle this type of model. Unfortunately, I've never worked with mixing problems so I cannot be of a great help here.