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Overview


**MoSDeF Cassandra** is a Python interface for the
`Cassandra <https://cassandra.nd.edu>`_ Monte Carlo software.
It offers complete integration with the `MoSDeF <https://mosdef.org>`_
tools and provides a user-friendly interface for Cassandra.

Warning

MoSDeF Cassandra is still in early development (0.x releases). The API may change unexpectedly.

Resources


* `Reference documentation <https://mosdef-cassandra.readthedocs.io>`_:
  Examples, tutorials, guides, and API documentation
* `Installation guide <https://mosdef-cassandra.readthedocs.io/en/latest/getting_started/install.html>`_:
  Instructions for installing MoSDeF Cassandra
* `GitHub repository <https://github.com/MaginnGroup/mosdef_cassandra>`_:
  View the source code, contribute, and raise issues
* `Cassandra <https://cassandra.nd.edu>`_:
  Home of the Cassandra Monte Carlo package
* `MoSDeF tools <https://mosdef.org>`_:
  A generic collection of tools for constructing systems and applying
  forcefield parameters for particle-based simulations

Citation

Please cite MoSDeF Cassandra, Cassandra, and the MoSDeF suite of tools if you use this tool in your research. Details here <https://mosdef-cassandra.readthedocs.io/en/latest/reference/citing.html>_.

Installation


Complete installation instructions are
`here <https://mosdef-cassandra.readthedocs.io/en/latest/getting_started/install.html>`_.
However, for most users we recommend the conda installation:

.. code-block:: bash

    conda create --name mc mosdef_cassandra -c conda-forge

Examples

MoSDeF Cassandra provides a Python interface to Cassandra. The workflow consists of first constructing a system and move set. These two objects are passed to the runner that performs the Monte Carlo simulation with Cassandra. We use classes from the MoSDeF tools to structure some of the simulation inputs. The example below demonstrates an NVT Monte Carlo simulation of OPLS-AA methane. No other input files are required. Everything required to run the Monte Carlo calculation is self-contained in the script below.

.. code-block:: python

import mbuild import foyer import unyt as u import mosdef_cassandra as mc

Create a methane molecule from a SMILES string

methane = mbuild.load("C", smiles=True)

Load the forcefield via foyer

ff = foyer.forcefields.load_OPLSAA()

Apply the forcefield parameters to methane with foyer

methane_ff = ff.apply(methane)

Define an empty simulation box

box = mbuild.Box([3.0, 3.0, 3.0])

Define the boxes, species in the system, molecules in the box

ensemble = 'nvt' box_list = [box] species_list = [methane_ff] molecules_to_add = [[100]]

Create the System

system = mc.System(box_list, species_list, mols_to_add=molecules_to_add)

Create the MoveSet

moveset = mc.MoveSet(ensemble, species_list)

Run a Monte Carlo simulation!

mc.run( system=system, moveset=moveset, run_type="equilibration", run_length=1000, temperature=300.0 * u.K )

Credits



Development of MoSDeF Cassandra was supported by the National Science Foundation
under grant NSF Grant Number 1835874. Any opinions, findings, and conclusions or
recommendations expressed in this material are those of the author(s) and do
not necessarily reflect the views of the National Science Foundation.

MaginnGroup / mosdef_cassandra

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