Quick Start and Examples#

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Packaged Example Overview#

The examples run from the installed Python namespace with python -m. The input files are bundled with the package.

Example

Demonstrates

Command

Output files

periodic example

Periodic sheet wrinkling under uniaxial compression

python -m pymembrane.examples.periodic --quick

initial_mesh.vtk, periodic_t*.vtk; --quick reduces snapshots and MD steps

buckling example

Caspar-Klug shell buckling with Monte Carlo vertex moves

python -m pymembrane.examples.buckling --quick

initial mesh.vtk, sphere_t*.vtk, final_mesh.vtk; --quick reduces snapshots and MC steps

minimizer example

Constant-volume vesicle minimization with FIRE

python -m pymembrane.examples.minimizer --quick

initial mesh.vtk, minimization_t*.vtk; --quick reduces snapshots and minimizer iterations

disclination example

Brownian relaxation of an open +1 disclination

python -m pymembrane.examples.disclination --quick

initial mesh.vtk, pentagon_t*.vtk; --quick reduces snapshots and BD steps

disclination_mc example

Monte Carlo relaxation of the same disclination

python -m pymembrane.examples.disclination_mc --quick

initial mesh.vtk, pentagon_t*.vtk, final_mesh.vtk; --quick reduces snapshots and MC steps

disclination_verlet example

Velocity-Verlet relaxation of the same disclination

python -m pymembrane.examples.disclination_verlet --quick

initial mesh.vtk, pentagon_t*.vtk; --quick reduces snapshots and MD steps

hybrid_mc_bd example

Alternating Brownian dynamics and Monte Carlo vertex moves

python -m pymembrane.examples.hybrid_mc_bd --quick

initial_mesh.vtk, hybrid_t*.vtk; --quick reduces cycles and MD/MC step counts

liquid_membrane example

Bending-dominated dynamic triangulation with edge flips and vertex moves

python -m pymembrane.examples.liquid_membrane --quick

initial.vtk, final.vtk, final.obj, summary.json; --quick reduces Monte Carlo steps

size_scaling example

Spherical size scaling with mesh generation, Monte Carlo vertex moves, and Brownian dynamics

python -m pymembrane.examples.size_scaling --quick

--json writes a timing summary; --keep-meshes preserves the generated .inp files

All of the examples above write legacy ASCII .vtk output through the default dumper. None requires plotting packages or the VTK Python bindings to run.

Reproducibility Checklist#

  • [ ] package imports

  • [ ] example runs from outside repository

  • [ ] input files are bundled

  • [ ] output files are written

  • [ ] no import-path changes needed

  • [ ] no plotting packages needed