Examples¶

In this section, we provide the necessary inputs to run several of the examples in section 4.2 of the RASPA manual.

Tip

Pre-tabulated force fields and molecule definition files can be found in the share directory.

Example 1: Monte Carlo of Methane in a Box¶

from ase import Atoms
from raspa_ase import Raspa

atoms = Atoms()  #  (1)!
boxes = [  #  (2)!
    {
        "BoxLengths": [30, 30, 30],
        "ExternalTemperature": 300,
        "Movies": True,  # (3)!
        "WriteMoviesEvery": 100,
    }
]
components = [  # (4)!
    {
        "MoleculeName": "methane",
        "MoleculeDefinition": "ExampleDefinitions",
        "TranslationProbability": 1.0,
        "CreateNumberOfMolecules": 100,
    }
]
parameters = {  # (5)!
    "SimulationType": "MonteCarlo",
    "NumberOfCycles": 10000,
    "NumberOfInitializationCycles": 1000,
    "PrintEvery": 1000,
    "Forcefield": "ExampleMoleculeForceField",
}
calc = Raspa(boxes=boxes, components=components, parameters=parameters)

atoms.calc = calc
atoms.get_potential_energy()
print(calc.results)

Use an empty Atoms object to create a system without a framework.
You do not need to specify the box number. It will be determined automatically based on the order in which the components are listed. We define the box parameters as a dictionary to be provided to the boxes keyword argument.
True and False will be automatically translated to "Yes" and "No", respectively.
You do not need to specify the component number. It will be determined automatically based on the order in which the components are listed. We define the component parameters as a dictionary to be provided to the components keyword argument.
The remaining force field parameters (i.e. all those beyond the box, component, and framework parameters) are to be specified as a dictionary to be provided to the parameters keyword argument.

Example 2: Monte Carlo of CO2 in a Box and N2 in Another Box¶

from ase import Atoms
from raspa_ase import Raspa

atoms = Atoms()
boxes = [
    {
        "BoxLengths": [25, 25, 25],
        "ExternalTemperature": 300.0,
        "Movies": True,
        "WriteMoviesEvery": 10,
    },
    {
        "BoxLengths": [30, 30, 30],
        "BoxAngles": [90, 120, 120],
        "ExternalTemperature": 500,
        "Movies": True,
        "WriteMoviesEvery": 10,
    },
]
components = [
    {
        "MoleculeName": "N2",
        "MoleculeDefinition": "ExampleDefinitions",
        "TranslationProbability": 1.0,
        "RotationProbability": 1.0,
        "ReinsertionProbability": 1.0,
        "CreateNumberOfMolecules": [50, 25],
    },
    {
        "MoleculeName": "CO2",
        "MoleculeDefinition": "ExampleDefinitions",
        "TranslationProbability": 1.0,
        "RotationProbability": 1.0,
        "ReinsertionProbability": 1.0,
        "CreateNumberOfMolecules": [25, 50],
    },
]
parameters = {
    "SimulationType": "MonteCarlo",
    "NumberOfCycles": 10000,
    "NumberOfInitializationCycles": 1000,
    "PrintEvery": 100,
    "Forcefield": "ExampleMoleculeForceField",
}
calc = Raspa(boxes=boxes, components=components, parameters=parameters)

atoms.calc = calc
atoms.get_potential_energy()
print(calc.results)

Example 7: Adsorption isotherm of methane in MFI¶

from ase.io import read
from raspa_ase import Raspa

atoms = read("MFI_SI.cif")  # (1)!
atoms.info = {  # (2)!
    "UnitCells": [2, 2, 2],
    "HeliumVoidFraction": 0.29,
    "ExternalTemperature": 300.0,
    "ExternalPressure": [1e4, 1e5],
}
components = [
    {
        "MoleculeName": "methane",
        "MoleculeDefinition": "ExampleDefinitions",
        "TranslationProbability": 0.5,
        "ReinsertionProbability": 0.5,
        "SwapProbability": 1.0,
        "CreateNumberOfMolecules": 0,
    }
]
parameters = {
    "SimulationType": "MonteCarlo",
    "NumberOfCycles": 25000,
    "NumberOfInitializationCycles": 2000,
    "PrintEvery": 1000,
    "Forcefield": "ExampleZeolitesForceField",
    "RemoveAtomNumberCodeFromLabel": True,
    "ComputeNumberOfMoleculesHistogram": True,
    "WriteNumberOfMoleculesHistogramEvery": 5000,
    "NumberOfMoleculesHistogramSize": 1100,
    "NumberOfMoleculesRange": 80,
    "ComputeEnergyHistogram": True,
    "WriteEnergyHistogramEvery": 5000,
    "EnergyHistogramSize": 400,
    "EnergyHistogramLowerLimit": -110000,
    "EnergyHistogramUpperLimit": -20000,
}
calc = Raspa(components=components, parameters=parameters)

atoms.calc = calc
atoms.get_potential_energy()
print(calc.results)

This file is provided in raspa_ase/docs/files/MFI_SI.cif for the sake of this tutorial. The Atoms object represents the framework to be studied and will be written out to the current working directory to be used by RASPA.
The framework parameters are to be specified as info attributes of the Atoms object. You do not need to include the framework number or framework name. These will be included automatically.