PreProcessing module

class PreProcessing.PreProcessing(args)

Bases: object

Class to handle all preprocessing for the MD simulation Idea is that this class stores all information in the two objects settings and atoms which are supposed to input for the MD class

checkDistances()

Checks that interatomic distances are reasonable. No atomic overlap

checkLattice()

Check that the lattice is valid.

createSimulationList()

Function that creates a simulation list wherer each element dictates a specific run and settings for that run.

Returns:

A list of String describing simulation and SimulationSettings objects

Return type:

simulation_list (list)

getIntegrator(ensemble)

getPotential()

readAtomicStructure(input_structure)

Reads atomic structure from a file, and extend cell according to supercell setting

readSettings(input_settings)

Reads settings from json file, checks all expected settings present. Overwrite settings file if a terminal flag is set.

sanityCheckAtomicStructure()

Sanity check for the input atomic structure. Such as valid lattice angles, constants and atomic positions

sanityCheckSettings()

Sanity check for the settings.json file. Makes sure that we only use EMT for valid metals. Also checks that relevant values is given.