aiida_gromacs package

Subpackages

Submodules

aiida_gromacs.helpers module

Helper functions for automatically setting up computer & code. Helper functions for setting up

  1. An AiiDA localhost computer

  2. A “gmx” code on localhost

Note: Point 2 is made possible by the fact that the diff executable is available in the PATH on almost any UNIX system.

aiida_gromacs.helpers.get_code(entry_point, computer)[source]

Get local code. Sets up code for given entry point on given computer.

Parameters:

  • entry_point – Entry point of calculation plugin

  • computer – (local) AiiDA computer

Returns:

The code node

Return type:

aiida.orm.nodes.data.code.installed.InstalledCode

aiida_gromacs.helpers.get_computer(name='localhost', workdir=None)[source]

Get AiiDA computer. Loads computer ‘name’ from the database, if exists. Sets up local computer ‘name’, if it isn’t found in the DB.

Parameters:

  • name – Name of computer to load or set up.

  • workdir – path to work directory Used only when creating a new computer.

Returns:

The computer node

Return type:

aiida.orm.computers.Computer

aiida_gromacs.helpers.get_path_to_executable(executable)[source]

Get path to local executable.

Parameters:

executable (str) – Name of executable in the $PATH variable

Returns:

path to executable

Return type:

str

aiida_gromacs.helpers.setup_generic_code(code)[source]

Try to set up any code for running a genericMD process

Parameters:

code – executable@computer of the code being run

Module contents

aiida_gromacs

A plugin for using GROMACS with AiiDA for molecular dymanics simulations.