Tractor Implementation Call, 05.07.2021

j.schmoelder · July 5, 2021, 3:44pm

Here a short overview about today’s implementation call.

Intro

After some introduction by @j.schmoelder and @h.lanzrath, @s.leweke showed us some of the relevant places in CADET where we need to make modifications.

The general plan is to use the 2D-GRM as a template and strip is of all unnecessary functionality before adding the relevant fluxes.

Remark: next to actually implementing the fluxes in the residual, we also need to modify the sparsity pattern:

github.com

modsim/CADET/blob/8fe0d0203a94242a0c51032704ab3585b14a1caf/src/libcadet/model/parts/TractorConvectionDispersionOperator.cpp#L1122

    
      
          	// right cell face (lower + 1 + upper) and to the left cell face (shift the stencil by -1 because influx of cell i
          	// is outflux of cell i-1)
          	// We also have to make sure that there's at least one sub and super diagonal for the dispersion term
          	const unsigned int lowerNonZeros = std::max(_weno.lowerBandwidth() + 1u, 1u);
          	const unsigned int upperNonZeros = std::max(_weno.upperBandwidth(), 1u);
          	// Total number of non-zeros per row is WENO stencil (lowerNonZeros + 1u + upperNonZeros) + radial dispersion (2)
          	cadet::linalg::SparsityPattern pattern(_nComp * _nCol * _nRad, lowerNonZeros + 1u + upperNonZeros + 2u);
          
          
	// Handle convection, axial dispersion (WENO)
          	for (unsigned int i = 0; i < _nRad; ++i)
          		cadet::model::parts::convdisp::sparsityPattern(pattern.row(i * _nComp), _nComp, _nCol, _nComp * _nRad, static_cast<double>(_curVelocity[i]), _weno);
          
          
    //TODO: Tractor add sparsity pattern for non-adjacent transport
          
          
	// Handle radial dispersion
          	if (_nRad > 1)
          	{
          		for (unsigned int col = 0; col < _nCol; ++col)
          		{
          			const unsigned int idxColBlock = col * _nRad * _nComp;

Because it turned out that it was not so trivial to remove particles from the 2D-GRM, as it would require modifying indices, memory allocation, etc, we decided for now to just leave it as is. Instead, we will recommend (or force) setting the film diffusion to zero and disabling all binding models / particle types. This way, we can leave all the internal structure in place and only need to focus on adding the fluxes.

General Information

Publication: http://dx.doi.org/10.1016/j.jtbi.2013.09.023
PR: Include compartment model for Tractor by schmoelder · Pull Request #95 · modsim/CADET
Files: https://fz-juelich.sciebo.de/apps/files/?dir=/ModSim-Projektbox/Projects&fileid=979725932
2D-GRM Config Gist for CADET-Python: GRM2D · GitHub

@h.lanzrath : can you please also add the slides of your presentation to the project box? Let me know if you need access.

I suggest, we leave this forum discussion for more general topics and conceptual questions, as well as the notes of the calls. Implementation details should be discussed on Github.