Command-Line Arguments#

The packaged examples provide command-line options for controlling runtime, output location, and the amount of work done in each example. The arguments documented below are taken directly from the installed example parsers.

Periodic#

Command#

python -m pymembrane.examples.periodic --quick

Arguments#

Argument	Default	Description
`--quick`	`False`	Run a short version of the example for testing the installation.
`--snapshots`	`None`	Number of output snapshots. Runtime default: `3` with `--quick` or `100` otherwise.
`--run_steps`	`None`	Number of Brownian-dynamics steps between output snapshots. Runtime default: `10` with `--quick` or `5000` otherwise.
`--epsilon`	`0.01`	Fractional compression applied to the x box length after each snapshot.
`--output-dir`	`.`	Directory where output mesh files are written.

Recommended commands#

python -m pymembrane.examples.periodic --quick
python -m pymembrane.examples.periodic --snapshots 5 --run_steps 1000 --output-dir periodic_output

Expected output#

initial_mesh.vtk and periodic_t*.vtk are written to the chosen output directory.

Quick mode#

--quick reduces the run to a short quick check with fewer snapshots and fewer Brownian-dynamics steps.

Buckling#

Command#

python -m pymembrane.examples.buckling --quick

Arguments#

Argument	Default	Description
`--quick`	`False`	Run a short version of the example for testing the installation.
`--snapshots`	`None`	Number of output snapshots. Runtime default: `3` with `--quick` or `100` otherwise.
`--run_steps`	`None`	Number of Monte Carlo steps between output snapshots. Runtime default: `10` with `--quick` or `5000` otherwise.
`--output-dir`	`.`	Directory where output mesh files are written.

Recommended commands#

python -m pymembrane.examples.buckling --quick
python -m pymembrane.examples.buckling --snapshots 5 --run_steps 1000 --output-dir buckling_output

Expected output#

initial mesh.vtk, sphere_t*.vtk, and final_mesh.vtk are written to the chosen output directory.

Quick mode#

--quick reduces the run to a short quick check with fewer snapshots and fewer Monte Carlo steps.

Minimizer#

Command#

python -m pymembrane.examples.minimizer --quick

Arguments#

Argument	Default	Description
`--quick`	`False`	Run a short version of the example for testing the installation.
`--snapshots`	`None`	Number of output snapshots. Runtime default: `2` with `--quick` or `50` otherwise.
`--max_iter`	`None`	Maximum number of FIRE iterations used for each minimization call. Runtime default: `25` with `--quick` or `2000` otherwise.
`--output-dir`	`.`	Directory where output mesh files are written.

Recommended commands#

python -m pymembrane.examples.minimizer --quick
python -m pymembrane.examples.minimizer --snapshots 5 --max_iter 2000 --output-dir minimizer_output

Expected output#

initial mesh.vtk and minimization_t*.vtk are written to the chosen output directory.

Quick mode#

--quick reduces the run to a short quick check with fewer snapshots and fewer minimizer iterations.

Disclination#

Command#

python -m pymembrane.examples.disclination --quick

Arguments#

Argument	Default	Description
`--quick`	`False`	Run a short version of the example for testing the installation.
`--snapshots`	`None`	Number of output snapshots. Runtime default: `3` with `--quick` or `4` otherwise.
`--run_steps`	`None`	Number of Brownian-dynamics steps between output snapshots. Runtime default: `10` with `--quick` or `25` otherwise.
`--N`	`14`	Pentagon mesh size used to select the bundled input mesh.
`--output-dir`	`.`	Directory where output mesh files are written.

Recommended commands#

python -m pymembrane.examples.disclination --quick
python -m pymembrane.examples.disclination --N 18 --snapshots 4 --run_steps 25 --output-dir disclination_output

Expected output#

initial mesh.vtk and pentagon_t*.vtk are written to the chosen output directory.

Quick mode#

--quick reduces the run to a short quick check with fewer snapshots and fewer Brownian-dynamics steps.

Monte Carlo disclination#

Command#

python -m pymembrane.examples.disclination_mc --quick

Arguments#

Argument	Default	Description
`--quick`	`False`	Run a short version of the example for testing the installation.
`--snapshots`	`None`	Number of output snapshots. Runtime default: `3` with `--quick` or `4` otherwise.
`--run_steps`	`None`	Number of Monte Carlo steps between output snapshots. Runtime default: `10` with `--quick` or `25` otherwise.
`--N`	`14`	Pentagon mesh size used to select the bundled input mesh.
`--output-dir`	`.`	Directory where output mesh files are written.

Recommended commands#

python -m pymembrane.examples.disclination_mc --quick
python -m pymembrane.examples.disclination_mc --N 18 --snapshots 4 --run_steps 25 --output-dir disclination_mc_output

Expected output#

initial mesh.vtk, pentagon_t*.vtk, and final_mesh.vtk are written to the chosen output directory.

Quick mode#

--quick reduces the run to a short quick check with fewer snapshots and fewer Monte Carlo steps.

Velocity-Verlet disclination#

Command#

python -m pymembrane.examples.disclination_verlet --quick

Arguments#

Argument	Default	Description
`--quick`	`False`	Run a short version of the example for testing the installation.
`--snapshots`	`None`	Number of output snapshots. Runtime default: `3` with `--quick` or `4` otherwise.
`--run_steps`	`None`	Number of velocity-Verlet steps between output snapshots. Runtime default: `10` with `--quick` or `25` otherwise.
`--N`	`14`	Pentagon mesh size used to select the bundled input mesh.
`--output-dir`	`.`	Directory where output mesh files are written.

Recommended commands#

python -m pymembrane.examples.disclination_verlet --quick
python -m pymembrane.examples.disclination_verlet --N 18 --snapshots 4 --run_steps 25 --output-dir disclination_verlet_output

Expected output#

initial mesh.vtk and pentagon_t*.vtk are written to the chosen output directory.

Quick mode#

--quick reduces the run to a short quick check with fewer snapshots and fewer velocity-Verlet steps.

Hybrid MC + BD#

Command#

python -m pymembrane.examples.hybrid_mc_bd --quick

Arguments#

Argument	Default	Description
`--quick`	`False`	Run a short version of the example for testing the installation.
`--cycles`	`None`	Number of alternating Brownian-dynamics and Monte Carlo cycles. Runtime default: `3` with `--quick` or `8` otherwise.
`--md-steps`	`None`	Brownian-dynamics steps per hybrid cycle. Runtime default: `10` with `--quick` or `25` otherwise.
`--mc-steps`	`None`	Monte Carlo steps per temperature value in each hybrid cycle. Runtime default: `10` with `--quick` or `25` otherwise.
`--N`	`14`	Pentagon mesh size used to select the bundled input mesh.
`--output-dir`	`.`	Directory where output mesh files are written.

Recommended commands#

python -m pymembrane.examples.hybrid_mc_bd --quick
python -m pymembrane.examples.hybrid_mc_bd --cycles 5 --md-steps 25 --mc-steps 25 --output-dir hybrid_output

Expected output#

initial_mesh.vtk and hybrid_t*.vtk are written to the chosen output directory.

Quick mode#

--quick reduces the run to a short quick check with fewer cycles and fewer Brownian-dynamics and Monte Carlo steps.

Size Scaling#

Command#

python -m pymembrane.examples.size_scaling --quick

Arguments#

Argument	Default	Description
`--quick`	`False`	Run a short version suitable for checking the installation and the benchmark workflow.
`--subdivisions`	`None`	Icosphere subdivision levels used to generate the spherical meshes. Runtime default: `[0, 1, 2]` with `--quick` or `[0, 1, 2, 3]` otherwise. This option is mutually exclusive with `--vertices`.
`--vertices`	`None`	Target vertex counts. Each requested size is mapped to the nearest available icosphere subdivision level. This option is mutually exclusive with `--subdivisions`.
`--steps`	`None`	Number of evolution steps used for the Monte Carlo and Brownian workflows. Runtime default: `100` with `--quick` or `1000` otherwise.
`--repeat`	`None`	Number of timed repeats collected for each workflow. Runtime default: `3`.
`--warmup`	`None`	Number of untimed warmup runs collected before timing each workflow. Runtime default: `1`.
`--json`	`None`	Write the timing summary to a JSON file.
`--csv`	`None`	Write the timing summary to a CSV file.
`--dump-output`	`False`	Time a representative VTK output write in addition to the compute benchmarks.
`--keep-meshes`	`False`	Keep the generated temporary mesh files on disk.
`--output-dir`	`size_scaling_meshes`	Directory used when keeping generated mesh files.

Recommended commands#

python -m pymembrane.examples.size_scaling --quick
python -m pymembrane.examples.size_scaling --vertices 1000 5000 10000 50000 --steps 10000 --repeat 3 --json size_scaling.json

Expected output#

The example prints a table with energy_eval_only, mc_vertex_move, mc_edge_flip, and brownian_dynamics rows. If --dump-output is used, a dump_vtk row is added. If --json or --csv is supplied, the timings are written to the chosen file.

Quick mode#

--quick reduces the default subdivision list to 0 1 2 and runs a short version of the benchmark with 100 steps, --repeat 3, and --warmup 1. For more stable timings, increase --steps and keep --repeat 3 or larger.

Liquid Membrane Example#

Command#

python -m pymembrane.examples.liquid_membrane --quick

Arguments#

Argument	Default	Description
`--quick`	`False`	Run a short version of the example for testing the installation.
`--steps`	`None`	Number of Monte Carlo steps used in the main simulation run. Runtime default: `100` with `--quick` or `1000` otherwise.
`--subdivision`	`None`	Icosphere subdivision level used to build the initial spherical mesh. Runtime default: `1` with `--quick` or `2` otherwise.
`--temperature`	`1e-1`	Monte Carlo temperature used for the liquid-membrane workflow.
`--output-dir`	`.`	Directory where the VTK, OBJ, and summary files are written.
`--json`	`summary.json`	Path to the summary JSON file.
`--seed`	`202208`	Base random seed used for the Monte Carlo integrators.
`--keep-meshes`	`False`	Keep the generated temporary mesh input files on disk.

Recommended commands#

python -m pymembrane.examples.liquid_membrane --quick
python -m pymembrane.examples.liquid_membrane --steps 1000 --output-dir liquid_output

Expected output#

initial.vtk, final.vtk, final.obj and summary.json are written to the chosen output directory. If generated mesh inputs are retained, the mesh_inputs/*.inp files are also available.

Quick mode#

--quick reduces the run to a short quick check with fewer Monte Carlo steps, while keeping the same mesh generation, force model, and integrator names.