Cassandra

Cassandra is an open source Monte Carlo package developed in the Maginn group at the University of Notre Dame. It is released under the GNU General Public License.

You may download Cassandra V1.2 by going to cassandra.nd.edu.

New features in V1.2 include:

  • Damped shifted force method for computing long-range electrostatic energies
  • Fixed errors in gfortran-compiled Cassandra
    • attempting volume change moves with Ewald summation
    • generating ring fragment libraries
  • Added tail corrections for Mie potential
  • Standardized format of input and output files, including:
    • Each word of a section header begins with an initial capital, e.g. # Run_Name
    • Keywords and arguments are all lowercase, e.g. cubic, units steps, coul ewald

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Features

Cassandra is capable of simulating any number of molecules composed of rings, chains, or both. We have used it to simulate small organic molecules, oligimers, and ionic liquids. It handles a standard "Class I"-type force field having fixed bond lengths, harmonic bond angles and improper angles, a CHARMM or OPLS-style dihedral potential, a Lennard-Jones 12-6 potential and fixed partial charges. Cassandra can simulated the following ensembles: canonical (NVT), isothermal-isobaric (NPT), grand (muVT), osmotic (muPT), and Gibbs (NVT and NPT versions). Cassandra is parallelized with openMP, and therefore runs efficiently on multi-core machines.Cassandra uses OpenMP parallelization and comes with a number of scripts, utilities and examples to help with simulation setup. The code is currently in beta release stage. If you wish to obtain a copy for beta testing, please send an email to Prof. Edward Maginn (ed@nd.edu).

Some of the advanced sampling features have been described in a recent publication:

A general and efficient Monte Carlo method for sampling intramolecular degrees of freedom of branched and cyclic molecules, J. Shah and E. J. Maginn, J. Chem. Phys., 135, 134121 (2011)

Cassandra was modified and then used by Neeraj Rai to carry out the first VLE simulations of an ionic liquid. Read more about it in these publications:

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Neeraj Rai andEdward J. Maginn, “Critical Behaviour and Vapour-Liquid Coexistence of 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide Ionic Liquids Via Monte Carlo Simulations”,Faraday Discussions,2012,154, 53-69.

Neeraj Rai andEdward J. Maginn, “Vapor-Liquid Coexistence and Critical Behavior of Ionic Liquids via Molecular Simulations”,Journal of Physical Chemistry Letters,2011, 2, 1439-1443. [DOI:10.1021/jz200526z ACS Articles on Request]

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Availability

Cassandra is now available for download under the GPL license. To register and download the code, go to cassandra.nd.edu

Workshop, June 6-10, 2016

A special hands-on workshop on Monte Carlo basics and how to use Cassandra was held on the Notre Dame camus Jne 6-10. A complete set of materials will be available for download soon. Here is a photo of the participants, who in addition from US institutions came from South America, Europe and the Middle East to attend the workshop.

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Where did Cassandra come from?

Cassandra evolved out of an academic code developed by Ed Maginn while he was a graduate student in the early 1990s. The code has been extended and refined in the Maginn group at Notre Dame since 1995. In 2007 while on sabbatical at the Computer Science Research Institute at Sandia National Laboratories, Ed were inspired by the success of the MD code LAMMPS(developed at Sandia) to re-write this code to make it a general purpose Monte Carlo code. Prof. Jindal Shah took the lead role in the development of the code, and Cassandra was born. It is now maintained and extended at Notre Dame by a team of postdocs and graduate students, with significant contributions coming from Neraaj Rai, Eliseo Marin, Sandip Khan and Andrew Paluch.

Where did the name Cassandra come from?

In Greek mythology, Cassandra was the beautiful daughter of Kingand Queen Hecuba of Troy. As the story goes, Cassandra fell asleep inApollo’s temple and, this being Greek mythology, Apollo made advances toward her. She resisted, and so as punishment Apollo gave her the power of accurate prophecy, but also cursed her so that nobody believed her predictions. Cassandra was then left with the knowledge of future events, but she could not convince others that her predictions would come true. When a strange horse appeared in Troy, Cassandra warned her father that the Greeks would use the horse to take control of Troy. Of course, he didn't believe her, and the rest is history. After the fall of Troy, Cassandra was abducted byAgamemnonand taken to Mycenae on Crete, where she was eventually killed by Clytemnestra. Of course, she knew all this would happen. We think Cassandra also has great predictive powers, but we hope you will take its predictions more seriously than those ancient Trojans. We really wanted to use this name for our code, so we made up the proper acronym: Cassandra stands for Computational Atomistic Simulation Software At Notre Dame for Research Advances. How about that?

Funding

We gratefully acknowledge funding from the National Science Foundation for funding our project "SI2-SSE: Development of Cassandra, A General, Efficient and Parallel Monte Carlo Multiscale Modeling Software Platform for Materials Research". Support comes from theDivision of Advanced CyberInfrastructure (ACI). Award Abstract #1339785

The Cassandra Team





Cassandra image: Evelyn de Morgan [Public domain], via Wikimedia Common


Edward Maginn 2017ed@nd.edu