Evan Pretti

Repositories containing software related to my academic research are listed below. See also my personal page for other miscellaneous software tools.

MultiOpenMM

MultiOpenMM is a package that enables setting up and running parallel molecular dynamics simulations, including but not limited to replica exchange simulations, using the OpenMM molecular simulation package. MultiOpenMM supports running independent simulations of multiple, possibly topologically distinct, molecular systems, within a single OpenMM context. This can improve efficiency of, e.g., replica exchange simulations involving relatively small systems that still require large numbers of replicas to sample, or simulations of many systems having similar but distinct molecular topologies using identical force fields: through MultiOpenMM, independent replicas or distinct systems can be simultaneously simulated on single GPUs.

🚧 🚧 This library is a work in progress; some features may be incomplete, incompletely documented, or incompletely tested. 🚧 🚧

Code: available on GitHub (documentation is available within the repository).

PyPhase

PyPhase is a Python package for setting up and running crystal free energy calculations via the LAMMPS molecular dynamics package. PyPhase supports fully periodic, semi-infinite slab, and finite "crystallite" geometries in two and three dimensions. It also allows for parameters of the Frenkel-Ladd/Einstein molecule approach (extended to semi- and non-periodic systems) to be automatically tuned for accurate calculation of the free energies of any crystal lattice.

Code: available on Bitbucket.
Cite: E. Pretti and J. Mittal. "Extension of the Einstein molecule method for solid free energy calculation to non-periodic and semi-periodic systems." J. Chem. Phys., 2019, 151, 054105.
Documentation: available in HTML and PDF formats.

paccs

paccs is a Python package for colloidal crystal structure analysis, enumeration, optimization, prediction, and visualization. For two-dimensional colloidal crystal systems, it uses a wallpaper group-based algorithm to enumerate candidate structures. Cython implementations of performance-critical routines, and symmetric multiprocessing-based parallelization, permit high-throughput evaluation of many structures for the construction of phase diagrams of multicomponent colloidal systems.

Code: available on Github.
Cite: E. Pretti, N. A. Mahynski, V. K. Shen, and J. Mittal. "Symmetry-based crystal structure enumeration in two dimensions." J. Phys. Chem. A, 2020, 124, 3276-3285.
Documentation: available in HTML and PDF formats.