Package gromacs :: Module run

Module run


:mod:`gromacs.run` -- Running simulations
=========================================

Helper functions and classes around :class:`gromacs.tools.Mdrun`.

.. autoclass:: MDrunner
   :members:
.. autoclass:: MDrunnerOpenMP
.. autoclass:: MDrunnerOpenMP64
.. autoclass:: MDrunnerMpich2Smpd

.. autofunction:: check_mdrun_success

Classes

[hide private]

MDrunner
A class to manage running :program:`mdrun` in various ways.

MDrunnerDoublePrecision
Manage running :program:`mdrun_d`.

MDrunnerOpenMP
Manage running :program:`mdrun` as an OpenMP_ multiprocessor job.

MDrunnerOpenMP64
Manage running :program:`mdrun` as an OpenMP_ multiprocessor job (64-bit executable).

MDrunnerMpich2Smpd
Manage running :program:`mdrun` as mpich2_ multiprocessor job with the SMPD mechanism.

Functions

[hide private]

check_mdrun_success(logfile)
Check if mdrun finished successfully. source code

Variables

[hide private]

logger = logging.getLogger('gromacs.run')

Function Details

[hide private]

check_mdrun_success(logfile)

source code

Check if mdrun finished successfully.

Analyses the output from mdrun in logfile. Right now we are simply looking for the line "Finished mdrun on node" in the last 1kb of the file. (The file must be seeakable.)

Parameters:

logfile (filename) - Logfile produced by mdrun.

Returns:

boolean (True if all ok, False otherwise)