pymesh

Pymesh is a flexible, Python-based packed-bed column meshing tool for chromatography simulations, built as a wrapper around GMSH. It's a cleaner rewrite of genmesh, with a modular architecture and simpler setup.

It supports meshing unconfined periodic packed beds in addition to standard confined packings.

Install

## install dependencies
pip install -r requirements.txt

## install editable source
pip install -e .

If gmsh is built from source, ensure that

• PYTHONPATH points to $GMSH_ROOT/lib (or wherever the gmsh.py file is)
• LD_LIBRARY_PATH points to $GMSH_ROOT/lib (or wherever the gmsh{.so,.a} files are)

export PYTHONPATH=$GMSH_ROOT/lib
export LD_LIBRARY_PATH=$GMSH_ROOT/lib

Usage

The script in bin/ should be available in $PATH after the install. It is currently called mesh. Given the appropriate input file in yaml format, run: mesh input.yaml

📄 Example YAML Input

Example config

packedbed:
  packing_file:
    filename: packing.xyzd
    dataformat: <d
  nbeads: 4
  scaling_factor: 1.0
  # auto_translate: True
  particles:
    scaling_factor: 0.9997
    # modification: bridge | cut 
    # relative_bridge_radius: ...
container:
  shape: cylinder
  size: [ 0.0, 0.0, -0.5, 0.0, 0.0, 4.0, 0.5 ]
  # size: [-2, -2, 0, 4, 4, 4]
  # periodicity: 
  # linked: True
  # stack_method: planecut
  # inlet_length: 0.0
  # outlet_length: 0.0
mesh:
  # size: 0.15
  size_method: field
  field:
    threshold:
      size_in: 0.06
      size_out: 0.14
      rad_min_factor: 0.4
      rad_max_factor: 0.6
  algorithm: 5
  algorithm3D: 10
  generate: 2
output:
  filename: mesh.vtk
gmsh:
  General.Verbosity: 5
  Geometry.OCCParallel: 1
  Mesh.MaxNumThreads1D: 8
  Mesh.MaxNumThreads2D: 8
  Mesh.MaxNumThreads3D: 8
  Mesh.ScalingFactor: 0.0001
general:
  fragment: True

Notes

• For shape: cyl, size: [x, y, z, dx, dy, dz, r]
• For shape: box, size: [x, y, z, dx, dy, dz]
• If mesh.field.threshold.size_in and mesh.field.threshold.size_out are not given, they default to mesh.size
• Set general.fragment to False to run a quick mesh and manual visual check for correct dimensions and intersecting volumes.
  • Best with mesh.generate set to 2
  • Be aware that this breaks physical groups, matching periodic surfaces etc