aiida_lammps.workflows.base

Workchain to run a LAMMPS calculation with automated error handling and restarts.

Module Contents

Classes

LammpsBaseWorkChain

Base workchain for calculations using LAMMPS

class aiida_lammps.workflows.base.LammpsBaseWorkChain(*args, **kwargs)

Bases: aiida.engine.BaseRestartWorkChain

Base workchain for calculations using LAMMPS

_process_class

classmethod define(spec)

Define the process specification.

setup()

Call the setup of the BaseRestartWorkChain and create the inputs dictionary in self.ctx.inputs.

This self.ctx.inputs dictionary will be used by the BaseRestartWorkChain to submit the calculations in the internal loop.

The parameters and settings input Dict nodes are converted into a regular dictionary and the default namelists for the parameters are set to empty dictionaries if not specified.

report_error_handled(calculation, action)

Report an action taken for a calculation that has failed.

This should be called in a registered error handler if its condition is met and an action was taken. :param calculation: the failed calculation node :param action: a string message with the action taken

_check_restart_in_remote(calculation)

Check if the remote folder of a previous calculation contains a restartfile

Parameters:

calculation – node from the previous calculation

Returns:

latest restartfile found or None

set_restart_type(restart_type, calculation)

Set the parameters to run the restart calculation

Depending on the type of restart several variables of the input parameters will be changed to try to ensure that the calculation can resume from the last stored structure

Parameters:

• restart_type – type of the restart approach to be used

• calculation – node from the previous calculation

handle_unrecoverable_failure(calculation)

Handle calculations with unrecoverable errors.

Checks if the calculation ended with an exit status below 400 if so abort the work chain.

handle_out_of_walltime(calculation)

Handle calculations where the walltime was reached.

The handler will try to find a configuration to restart from with the following priority

1. Use a stored restart file in the repository from the previous calculation.

2. Use a restartfile found in the remote folder from the previous calculation.

3. Use the structure from the last step of the trajectory from the previous calculation.

4. Restart from scratch

handle_minimization_not_converged(calculation)

Handle calculations where the minimization did not converge

The handler will try to find a configuration to restart from with the following priority

1. Use a stored restart file in the repository from the previous calculation.

2. Use a restartfile found in the remote folder from the previous calculation.

3. Use the structure from the last step of the trajectory from the previous calculation.

This handler should never start from restart as at least the trajectory should always exist, if the calculation finished successfully.