How to access the area and vol of RBCs in a multiblock domain

[mojtabaAmiraslanpour]

Hi,

I am following the code provided for the onecellShear case to have access to cells volumes and area but I keep getting zero values. If I do this with one processor it works. But as soon as I use more than one, I would get zero.

So this:

      CellInformationFunctionals::calculateCellVolume(&hemocell);
      CellInformationFunctionals::calculateCellArea(&hemocell);
      CellInformationFunctionals::calculateCellPosition(&hemocell);
      CellInformationFunctionals::calculateCellStretch(&hemocell);
      CellInformationFunctionals::calculateCellBoundingBox(&hemocell);
      CellInformationFunctionals::calculateCellDiameters(&hemocell);

      T volume = (CellInformationFunctionals::info_per_cell[0].volume)/pow(1e-6/param::dx,3);
      T surface = (CellInformationFunctionals::info_per_cell[0].area)/pow(1e-6/param::dx,2);
      hemo::Array<T,3> position = CellInformationFunctionals::info_per_cell[0].position/(1e-6/param::dx);
      hemo::Array<T,6> bbox = CellInformationFunctionals::info_per_cell[0].bbox/(1e-6/param::dx);
      T largest_diam = (CellInformationFunctionals::info_per_cell[0].stretch)/(1e-6/param::dx);
      T rel_D2 = (largest_diam/D0)*(largest_diam/D0);
      T def_idx = (rel_D2 - 1.0) / (rel_D2 + 1.0) * 100.0;

      hlog << "\t Cell center at: {" <<position[0]<<","<<position[1]<<","<<position[2] << "} µm" << endl;  
      hlog << "\t Diameters: {" << bbox[1]-bbox[0] <<", " << bbox[3]-bbox[2] <<", " << bbox[5]-bbox[4] <<"}  µm" << endl;
      hlog << "\t Surface: " << surface << " µm^2" << " (" << surface / surface_eq * 100.0 << "%)" << "  Volume: " << volume << " µm^3" << " (" << volume / volume_eq * 100.0 << "%)"<< endl;
      hlog << "\t Largest diameter: " << largest_diam << " µm." << endl;
      hlog << "\t Deformation index: " << def_idx << " [%]" << endl;

Only works when I am running with 1 block:

    <mABx> 1 </mABx>
    <mABy> 1 </mABy>
    <mABz> 1 </mABz>

Any suggestions?

[mojtabaAmiraslanpour]

Even iterating over all blocks didn't work:

`void CellInformationFunctionals::CellVolume::processGenericBlocks(Box3D domain, std::vector<AtomicBlock3D*> blocks) {
hlog << "Starting processGenericBlocks with " << blocks.size() << " blocks." << std::endl;

for (AtomicBlock3D* block : blocks) {
    HemoCellParticleField* pf = dynamic_cast<HemoCellParticleField*>(block);

    if (!pf) {
        hlog << "Dynamic cast to HemoCellParticleField failed." << std::endl;
        continue;
    }

    // Log the location of the block
    Dot3D location = block->getLocation();
    hlog << "Processing block at location: (" << location.x << ", " << location.y << ", " << location.z << ")" << std::endl;

    for (const auto& pair : pf->get_lpc()) {
        T volume = 0.;
        const int& cid = pair.first;
        const std::vector<int>& cell = pf->get_particles_per_cell().at(cid);
        const pluint ctype = pf->particles[cell[0]].sv.celltype;
        
        // Calculate volume using the vertices of triangles
        for (hemo::Array<plint, 3> triangle : (*hemocell->cellfields)[ctype]->mechanics->cellConstants.triangle_list) {
            const hemo::Array<T, 3>& v0 = pf->particles[cell[triangle[0]]].sv.position;
            const hemo::Array<T, 3>& v1 = pf->particles[cell[triangle[1]]].sv.position;
            const hemo::Array<T, 3>& v2 = pf->particles[cell[triangle[2]]].sv.position;

            // Volume calculation
            const T v210 = v2[0] * v1[1] * v0[2];
            const T v120 = v1[0] * v2[1] * v0[2];
            const T v201 = v2[0] * v0[1] * v1[2];
            const T v021 = v0[0] * v2[1] * v1[2];
            const T v102 = v1[0] * v0[1] * v2[2];
            const T v012 = v0[0] * v1[1] * v2[2];
            volume += (1.0 / 6.0) * (-v210 + v120 + v201 - v021 - v102 + v012);
        }
        info_per_cell[cid].volume = volume;
    }

    hlog << "\t ============================================ " << std::endl;
}

hlog << "Finished processing all blocks." << std::endl;

}`

Apparently there is only one block passed to the function.

[gzavo]

Hi @mojtabaAmiraslanpour,

While I'm traveling atm and can't give a full answer, some quick info from the top of my head:
The functions in oneCellShear, such as calculateCellVolume were only implemented for single cell and single core execution.
Please look into the I/O functions that save the CSV files, since those can output per cell statistics, including volume.