683 Software Engineering in and for the Molecular Sciences


Description:
This session showcases projects where coding developments have advanced the science of molecular simulation. Submissions are encouraged for projects that automate/accelerate first principles calculations (including through machine learning), new trajectory analysis tools, advanced sampling techniques, image processing, plugins to established packages, and work improving the software and compiler stacks that determine runtime performance. Presenters are encouraged to explain the enabling components of the work, their best coding practices, and quantify performance improvements over existing techniques, as well as encourage open and reproducible science. This session is focused on the HOW of the discovery.

Sponsor:
Computational Molecular Science and Engineering Forum


Chair:
Eric Jankowski
Assistant Professor
Boise State University
Micron School of Materials Science and Engineering
Boise, ID
80207
Email: ericjankowski@boisestate.edu

Co-chairs:
Heather J. Kulik
Assistant Professor
Massachusetts Institute of Technology
Chemical Engineering
Cambridge, MA
02139
Email: hjkulik@mit.edu

Heather Mayes
Assistant Professor
University of Michigan
Ann Arbor
Email: hbmayes@umich.edu


Papers:
Chemlg - a Smart and Massively Parallel Code to Accelerate the Molecular Library Generation
Mohammad Atif Faiz Afzal, University at Buffalo, SUNY; Johannes Hachmann, University at Buffalo
GOMC: GPU Optimized Monte Carlo for the Simulation of Phase Equilibria and Physical Properties of Complex Fluids.
Mohammad Barhaghi, Wayne State University; Younes Nejahi, Wayne State University; Jason R. Mick, Wayne State University; Brock Jackman, Wayne State University; Kamel I. Rushaidat, Wayne State University; Yuanzhe Li, Wayne State University; Loren Schwiebert, Wayne State University; Jeffrey J. Potoff, Wayne State University
Lancelot - an Open-Source Codebase for Simplified Computational Chemistry
Henry C. Herbol, Cornell University; James Stevenson, Cornell University; Yaset Acevedo, Cornell University; Andrew Ruttinger, Cornell University; Paulette Clancy, Cornell University
Saffire: Enabling Large Scale Simulations of Rare Events
Sapna Sarupria, Clemson University; Ryan DeFever, Clemson University; Walter Hanger, Clemson University; Linh Ngo, Clemson University; Amy Apon, Clemson University
Quantifying Nanostructure within Molecular Simulations Using Geometry-Based Criteria
Michael L. Greenfield, University of Rhode Island; Faramarz Joodaki, University of Rhode Island
Runtime Code Generation for User-Configurable Metropolis Monte Carlo Energy Evaluation in HOOMD-Blue
Joshua A. Anderson, University of Michigan; William Zygmunt, University of Michigan; Luis Y. Rivera-Rivera, University of Michigan; Jens Glaser, University of Michigan; Sharon C. Glotzer, University of Michigan
Implementation of Harmonically Mapped Averaging Methods in Popular Molecular Simulation Codebases
Apoorva Purohit, University at Buffalo, SUNY; Sabry G. Moustafa, University at Buffalo, The State University of New York; Arpit Bansal, University at Buffalo, NY; Andrew J. Schultz, University at Buffalo, The State University of New York; David A. Kofke, University at Buffalo, The State University of New York
Abstract Submissions Closed