This code takes adaptive meshes from finite-element simulations and transforms them into a regularly spaced grid for faster field value lookup as reuqired by Monte Carlo simulations tools such as Allpix Squared.
The input consists of two files, one containing the vertex coordinates of each input mesh node, the other providing the relevant field values associated to each of these vertices.
One output file containing the regular interpolated mesh is produced.
This code takes adaptive meshes from finite-element simulations and transforms them into a regularly spaced grid for faster
field value lookup as required by Monte Carlo simulations tools such as Allpix Squared. The input consists of two files, one
containing the vertex coordinates of each input mesh node, the other providing the relevant field values associated to each
of these vertices. One output file containing the regular mesh is produced. This tool can work in two different modes, the
closest-neighbor mode and interpolation mode:
A new regular mesh is created by scanning the model volume in regular X, Y and Z steps (not necessarily coinciding with original mesh nodes) and using a barycentric interpolation method to calculate the respective electric field vector on the new point. The interpolation uses the four closest, no-coplanar, neighbor vertex nodes such, that the respective tetrahedron encloses the query point. For the neighbors search, the software uses the Octree implementation \[[@octree]\].
### Simple Closest-Neighbor Search
In this mode, selected by setting the parameter `interpolate = false`, no interpolation of field values is performed, but for
every output mesh point, the values from the closest neighbor of the input mesh is taken. In most cases this approach should
produce reasonably precise results with a granularity similar to the respective adaptive mesh granularity in the respective
region. The tool uses the Octree `findNeighbor` algorithm \[[@octree]\] to find the closest neighbor to the query point.
### Barycentric Interpolation Method
In this mode, the regular mesh is created by scanning the model volume in regular X, Y and Z steps and using a barycentric
interpolation method to calculate the respective electric field vector on the new point. The interpolation uses the four
closest, no-coplanar, neighbor vertex nodes such, that the respective tetrahedron encloses the query point. For the neighbors
search, the tool uses the Octree `radiusNeighbors` neighbor search algorithm \[[@octree]\].
## File Formats
@@ -77,11 +91,12 @@ It should be noted that the Mesh Converter depends on the core utilities of the
*`region`: Region name or list of region names to be meshed, such as for example `bulk` or `"bulk","epi"` (No default value; required parameter).
*`observable`: Observable to be interpolated, such as for example `ElectricField` (No default value; required parameter).
*`observable_units`: Units in which the observable is stored in the input file (No default value; required parameter).
*`interpolate`: Boolean switch to select either the barycentric interpolation method or the closest-neighbor method. Defaults to `true`, i.e. using the interpolation method.
*`initial_radius`: Initial node neighbors search radius in micro meters. Defaults to the minimal cell dimension of the final interpolated mesh.
*`radius_step`: Radius step if no neighbor is found (defaults to `0.5um`).
*`max_radius`: Maximum search radius (default is `50um`).
*`allow_failure`: Allow the interpolation of a single mesh point to fail, i.e. when no neighbors could be found. If set to `true`, the respective mesh element will be set to zero and the interpolation will continue, if `false` the interpolation will be aborted. Defaults to `false`.
*`volume_cut`: Minimum volume for tetrahedron for non-coplanar vertices (defaults to minimum double value).
*`radius_step`: Radius step if no neighbor is found (defaults to `0.5um`). Only used for barycentric interpolation.
*`max_radius`: Maximum search radius (default is `50um`). Only used for barycentric interpolation.
*`allow_failure`: Allow the interpolation of a single mesh point to fail, i.e. when no neighbors could be found. If set to `true`, the respective mesh element will be set to zero and the interpolation will continue, if `false` the interpolation will be aborted. Defaults to `false`. Only used for barycentric interpolation.
*`volume_cut`: Minimum volume for tetrahedron for non-coplanar vertices (defaults to minimum double value). Only used for barycentric interpolation.
*`divisions`: Number of divisions of the new regular mesh for each dimension, 2D or 3D vector depending on the `dimension` setting. Defaults to 100 bins in each dimension.
*`xyz`: Array to replace the system coordinates of the mesh. A detailed description of how to use this parameter is given below.
*`workers`: Number of worker threads to be used for the interpolation. Defaults to the available number of cores on the machine (hardware concurrency).
