Command line interface

Trimem offers a command line application that is available after installation as mc_app. This application implements an interface to the following simulation logic:

It offers the possibility to run either a minimization of the Helfrich functional or a statistical exploration by means of Markov Chain Monte Carlo sampling. Checkpointing allows for a versatile recombination of these two steps. Please have a look at the Quick-Start tutorial for an applied introduction.

cli reference

The command line interface mc_app can be queried with the --help flag to provide a verbose help message:

$ mc_app --help
usage: mc_app [-h] {config,run} ...

Trimem: Monte Carlo Sampling of lipid membranes. This application can be used
to run simulations that are parametrized by an INI-style configuration file. A
default config file can be generated by the `config` subcommand. Simulations
are executed with the `run` subcommand. Please refer to the specific
subcommand's help messages.

optional arguments:
  -h, --help    show this help message and exit

subcommands:
  {config,run}
    config      write default config file.
    run         run simulation.

The behavior of the application is controlled by an input configuration file. A default version can be generated by the config subcommand:

$ mc_app config --help
usage: mc_app config [-h] [--strip] [--conf CONF]

Generate default configuration file for trimem.

optional arguments:
  -h, --help   show this help message and exit
  --strip      strip comments from config file output.
  --conf CONF  file name to write to. If skipped or left empty, the
               configuration is printed on screen.

A simulation parametrized by an input configuration file can then be run with the run subcommand:

usage: mc_app run [-h] --conf CONF [--restart [RESTART]]

Run a simulation parametrized by a configuration file.

optional arguments:
  -h, --help           show this help message and exit
  --conf CONF          configuration file name (see `mc_app config --help`).
  --restart [RESTART]  restart index. If RESTART is specified, a restart from
                       a checkpoint file with number RESTART is attempted. If
                       RESTART is omitted, a restart from the last checkpoint
                       is attempted.