Simulation Codes
Code Description Originator Website
HOOMD-blue (Hierarchical Object Oriented MD) First MD code specifically written for high performance on GPUs. It has evolved into a general-purpose MD and MC particle simulation toolkit optimized for execution on both GPUs and CPUs. Joshua Anderson and Glotzer group14,15 https://glotzerlab.engin.umich.edu/hoomd-blue/index.html
Cassandra MC code with focus on complex molecular systems (e.g., ionic liquids) Maginn group16 https://cassandra.nd.edu
RASPA MC/MD code for simulating adsorption and diffusion of molecules in flexible nanoporous materials Snurr, Dubbeldam, Calero and Vlugt groups17 https://www.iraspa.org/RASPA/
GOMC (GPU-optimized MC) GPU-accelerated general purpose MC Potoff group18 http://gomc.eng.wayne.edu
MCCCS-Towhee MCCCS-MN MC for complex chemical systems code with a focus on phase and adsorption equilibria Marcus Martin Siepmann group http://towhee.sourceforge.net
Etomica Java-based MC/MD for use in education, with modules to demonstrate molecular basis for many phenomena Kofke group19 http://www.etomica.org/app/modules/
Other Utilities Other Utilities Other Utilities Other Utilities
iRASPA GPU-accelerated visualization package Snurr, Dubbeldam, Calero and Vlugt groups17 https://www.iraspa.org/index.html
freud Library for analyzing MD/MC simulation trajectories for metrics such as the radial distribution function and various order parameters Glotzer group20 https://freud.readthedocs.io/en/stable/
signac/signac-flow Framework to manage and scale large simulation workflows, facilitating data reuse, sharing, and reproducibility. Glotzer group21 https://signac.io, https://docs.signac.io/en/latest/
MoSDeF (Molecular Simulation Design Framework) Python-based software package for building complex molecular systems, applying forcefields, and generating input files for various simulation engines Cummings and McCabe groups22–24 https://mosdef.org
COSMO-SAC (COnductor-like Screening Model-Segment Activity Coefficient) Package to predict activity coefficients from quantum chemistry calculations for use in phase equilibria calculations relevant to chemical engineering separations Sandler, Lin and Bell groups25,26 https://github.com/usnistgov/COSMOSAC
pysimm (python simulation interface for molecular modeling) Python package for facilitating building of amorphous polymer systems and application of force fields Colina group27 https://pysimm.org, https://github.com/polysimtools/pysimm
pyprism (python-based Polymer Reference Interaction Site Model (PRISM)) Python-based, open-source framework for conducting PRISM theory calculations, with a user-friendly scripting interface for setting up and numerically solving the PRISM equations Jayaraman group28,29 https://pyprism.readthedocs.io/en/latest/
Notable Open-Source Codes Emerging from other Chemical Engineering Communities Notable Open-Source Codes Emerging from other Chemical Engineering Communities Notable Open-Source Codes Emerging from other Chemical Engineering Communities Notable Open-Source Codes Emerging from other Chemical Engineering Communities
GNU OCTAVE C++-based open-source high-level language, primarily intended for numerical computations; compatible with MATLAB John W. Eaton https://www.gnu.org/software/octave/
DWSIM5 Mixed code open-source chemical process simulator, compatible with the CAPE-OPEN standards for interoperability (https://www.colan.org) Daniel Medeiros https://github.com/DanWBR/dwsim5