MolecularDynamicsMeltQuench

class MolecularDynamicsMeltQuench(amorphous_quality=None, max_retries=None, melt_quality=None, max_melt_retries=None, melt_temperature=None, melt_time=None, quench_temperature=None, quench_rate=None, time_step=None, random_seed=None)

Base class for melt/quench amorphization methods

Parameters:
  • amorphous_quality (float) – Expected quality for the amorphous material, 0 to 1. 1 being free of defects.
    Default: 0.75

  • max_retries (int) – Maximum number of tries to satisfy amorphous quality
    Default: 30

  • melt_quality (float) – Requested percentage of melted material
    Default: 0.35

  • max_melt_retries (float) – Maximum number of tries to melt the material with the requested quality
    Default: same as max_retries

  • melt_temperature (PhysicalQuantity of type temperature) – Suggested melt temperature
    Default: 5000*Kelvin

  • melt_time (PhysicalQuantity of type time) – The length of the melt MD simulation.
    Default: 40*picosecond

  • quench_temperature (PhysicalQuantity of type temperature) – The target temperature during the quenching MD simulation.
    Default: 300*Kelvin

  • quench_rate (PhysicalQuantity of type temperature per time) – The rate of temperature change during the quenching. This rate will be used to calculate the length of the quenching MD simulation.
    Default: 400*Kelvin/picosecond

  • time_step (PhysicalQuantity of time time) – Time step per iteration
    Default: 1*femtosecond

  • random_seed (int) – Random seed
    Default: 1234

amorphousQuality()
Returns:

requested amorphous quality

Return type:

float

maxMeltRetries()
Returns:

requested maximum number of melt tries

Return type:

int

maxRetries()
Returns:

requested number of maximum tries

Return type:

int

meltQuality()
Returns:

requested melt quality

Return type:

float

meltSteps()
Returns:

The calculated number of melt steps.

Return type:

int

meltTemperature()
Returns:

requested melt temperature

Return type:

PhysicalQuantity of type temperature

meltTime()
Returns:

requested melt time

Return type:

PhysicalQuantity of type time

quenchRate()
Returns:

requested quench rate

Return type:

PhysicalQuantity of type temperature per time

quenchTemperature()
Returns:

requested quench temperature

Return type:

PhysicalQuantity of type temperature

randomSeed()
Returns:

random seed

Return type:

int

timeStep()
Returns:

returns time step

Return type:

int

uniqueString()

Return a unique string representing the state of the object.

Example

This class is to be used as a method of amorphize:

method = MolecularDynamicsMeltQuench(amorphous_quality=0.75)
amorphous = amorphize(reference, method, 'amorphous-Si.hdf5', 'amorphous')