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Award Abstract # 1739145
SI2-SSE: Infrastructure Enabling Broad Adoption of New Methods That Yield Orders-of-Magnitude Speedup of Molecular Simulation Averaging

NSF Org: OAC
Office of Advanced Cyberinfrastructure (OAC)
Recipient: THE RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK
Initial Amendment Date: August 29, 2017
Latest Amendment Date: June 27, 2018
Award Number: 1739145
Award Instrument: Standard Grant
Program Manager: Seung-Jong Park
OAC
 Office of Advanced Cyberinfrastructure (OAC)
CSE
 Directorate for Computer and Information Science and Engineering
Start Date: October 1, 2017
End Date: September 30, 2021 (Estimated)
Total Intended Award Amount: $499,734.00
Total Awarded Amount to Date: $508,234.00
Funds Obligated to Date: FY 2017 = $499,734.00
FY 2018 = $8,500.00
History of Investigator:
  • David Kofke (Principal Investigator)
    kofke@buffalo.edu
  • Andrew Schultz (Co-Principal Investigator)
Recipient Sponsored Research Office: SUNY at Buffalo
520 LEE ENTRANCE STE 211
AMHERST
NY  US  14228-2577
(716)645-2634
Sponsor Congressional District: 26
Primary Place of Performance: SUNY at Buffalo
303 Furnas Hall
Buffalo
NY  US  14260-4200
Primary Place of Performance
Congressional District:
26
Unique Entity Identifier (UEI): LMCJKRFW5R81
Parent UEI: GMZUKXFDJMA9
NSF Program(s): DMR SHORT TERM SUPPORT,
Software Institutes
Primary Program Source: 01001718DB NSF RESEARCH & RELATED ACTIVIT
01001819DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 054Z, 7433, 8004, 8005, 9216, 9251
Program Element Code(s): 171200, 800400
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.070

ABSTRACT

There is, today, a strong expectation that future materials will be studied in huge numbers first on the computer, and the best candidates for synthesis in the laboratory will be identified computationally. In this way engineers can efficiently formulate new materials that are lighter, stronger, or otherwise more functionally effective. Such advances are needed across all fields of technology, from energy to medicine to transportation to manufacturing. Recent advances from the molecular modeling community toward quantifying atomic interactions are rapidly eliminating a key obstacle to realization of this vision. Yet, an important obstacle remains: the thermal properties of materials -- those that are important at all but the lowest temperatures -- are needed to predict crystal structures and properties at conditions of practical interest. These properties are too expensive to compute for many materials at once, as needed for a computation-based screening effort. The project team has developed an algorithm that significantly accelerates these calculations without any loss of accuracy, and therefore goes a long way toward removing this obstacle. The aim of this project is to make this breakthrough available to researchers who are using molecular simulation to understand and develop new materials. To this end, this project will refine and extend these methods, and then add computer code to widely-used molecular simulation packages so that they can perform calculations using these new techniques. The team is additionally making efforts to promote awareness and ensure ease-of-use of the methods and their implementation.

"Mapped averaging" is a recently published scheme for the reformulation of ensemble averages. The framework uses approximate results from statistical mechanical theory to derive new ensemble averages (mapped averages) that represent exactly the error in the theory. Well-conceived mapped averages can be computed by molecular simulation with remarkable precision and efficiency; in favorable cases the computational savings are many orders of magnitude. For crystalline systems, a harmonic approximation provides a suitable starting point, allowing simulation to compute precisely the anharmonic contribution to the properties. The result is a technique for computing crystalline properties with unprecedented, transformative efficiency. The aim of this project is to implement these methods on well-established and widely used software packages for simulation of crystalline systems, and to develop mapped averages for new applications of interest to the users of these systems. The theoretical basis for this project appeared in the literature very recently (2015), so the proposed work is completely novel. The techniques are not trivial to understand and are tedious implement, hence adoption by the larger community will require this targeted infrastructure development to make them more accessible to casual users. The full development team includes the computational scientists and software engineers who coded, maintain and distribute the packages where these elements will be introduced. This group assists the project investigators to interface with the simulation packages while ensuring that the new codes are written to the highest standards. The full development team works together also to ensure that the software elements are thoroughly validated for correctness and usability. In addition to the implementation, the project also aims to expand the scope of the mapped-averaging method to encompass properties and substances to which it was not previously applied. This project enables mapped averaging methods to be employed on several widely-used molecular simulation packages: viz, LAMMPS, HOOMD, Cassandra, and VASP, which altogether have a base encompassing thousands of users. Software elements implemented in this project are in many cases completely transparent to the users of these packages, and can be employed by them with no added complication, to speed up their calculations by orders of magnitude. Thus the efforts made in this project will produce an enabling technology, giving scientists and engineers new capabilities to formulate materials for practical applications. Development tools and scripts are constructed in this project, which will facilitate the extension of mapped-averaging methods by other developers to even more molecular simulation packages, material properties, and molecular model systems. Software developed for this project is distributed open-source. Knowledge developed in this project is consolidated to form course materials made available on the web, and used as part of a large component of a graduate molecular simulation course taught by the PI. Training of 1 PhD student and numerous MS and undergraduates occurs across the project period. A strong dissemination effort involving papers, documentation, presentations, and workshops ensure that these methods and tools are understood and adopted by the community. Finally, instructional, graphically-oriented molecular simulation modules are developed and made available on the web to convey concepts related to harmonic and anharmonic components of crystalline behavior, with unique capabilities made possible by the mapped averaging framework.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Moustafa, Sabry G. and Purohit, Apoorva and Schultz, Andrew J. and Kofke, David A. "pyHMA: A VASP post-processor for precise measurement of crystalline anharmonic properties using harmonically mapped averaging" Computer Physics Communications , v.258 , 2021 https://doi.org/10.1016/j.cpc.2020.107554 Citation Details
Moustafa, Sabry G. and Schultz, Andrew J. and Kofke, David A. "Effects of thermostatting in molecular dynamics on anharmonic properties of crystals: Application to fcc Al at high pressure and temperature" The Journal of Chemical Physics , v.149 , 2018 10.1063/1.5043614 Citation Details
Purohit, Apoorva and Schultz, Andrew J. and Kofke, David A. "Force-sampling methods for density distributions as instances of mapped averaging" Molecular Physics , 2019 10.1080/00268976.2019.1572243 Citation Details
Purohit, Apoorva and Schultz, Andrew J. and Kofke, David A. "Implementation of harmonically mapped averaging in LAMMPS, and effect of potential truncation on anharmonic properties" The Journal of Chemical Physics , v.152 , 2020 https://doi.org/10.1063/1.5129942 Citation Details
Purohit, Apoorva and Schultz, Andrew J. and Moustafa, Sabry G. and Errington, Jeffrey R. and Kofke, David A. "Free energy and concentration of crystalline vacancies by molecular simulation" Molecular Physics , v.116 , 2018 10.1080/00268976.2018.1481542 Citation Details
Schultz, Andrew J and Kofke, David A "Alternatives to conventional ensemble averages for thermodynamic properties" Current Opinion in Chemical Engineering , v.23 , 2019 10.1016/j.coche.2019.02.002 Citation Details
Schultz, Andrew J. and Kofke, David A. "Comprehensive high-precision high-accuracy equation of state and coexistence properties for classical Lennard-Jones crystals and low-temperature fluid phases" The Journal of Chemical Physics , v.149 , 2018 10.1063/1.5053714 Citation Details
Schultz, Andrew J. and Moustafa, Sabry G. and Kofke, David A. "No system-size anomalies in entropy of bcc iron at Earth?s inner-core conditions" Scientific Reports , v.8 , 2018 10.1038/s41598-018-25419-3 Citation Details

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

Physical properties are the crux of all technologies. The way materials respond to their environment must be known quantitatively to be able to design new engineered systems, or to control and understand natural processes. Over a century of effort has been put toward developing more accurate and more reliable ways to do this for a broader range of substances. The state-of-the-art methods start from knowledge or estimates of intermolecular forces, and apply lengthy calculations to determine the physical properties that emerge from this multitude of interactions. These "computer experiments" now drive many of our advances in understanding physical systems, and progress can be accelerated by improving the way that these calculations are performed.  The aim of this project has been to contribute to these improvements, and to make these advances available to the user base that needs them.

Physical properties are formally expressed as an average over relevant configurations of the modeled molecules.  The goal of the computer experiments is to compute these averages while sampling the molecular configurations on a computer. More sampling leads to better, more precise averages, but also adds disproportionately to the computation time --- a 10-fold reduction in uncertainty requires a 100-fold increase in computational effort. Hence, it is valuable to find other ways to reduce this uncertainty. Such reductions would allow the application of better molecular models, yielding truer, more precise estimates of properties.

"Mapped averaging" is a technique that allows the averages needed to evaluate properties to be expressed in an alternative way. Rather than computing the property directly, it takes a known but approximate starting point, and computes the average needed to correct the approximation, yielding an accurate and more precise value for the property. The actual reduction of uncertainty depends on many details, but it can range from 2-fold to over 100-fold, corresponding to a reduction in calculation time of 4-fold, to many 1000s times less.

The focus of this project has been on applications to crystalline systems, where we have a good "known but approximate starting point" for many properties of interest.  Previously, we developed formulas for some of these, and during the project period we developed additional formulas for others (for example, elastic constants, which describe how a solid deforms when under stress).  The formulas can be tedious to code on a computer, so another major aim of the project has been to implement them so they could be applied by some general-purpose molecular simulation computer codes that are widely used in the simulation community (specifically: LAMMPS at Sandia National Laboratory; VASP at the University of Vienna; HOOMD at the University of Michigan; and Cassandra, at Notre Dame University; as well as our own code, Etomica, developed at the University at Buffalo).  These implementations were completed for each of these code bases, for at least some of the properties of interest where we have developed mapped-averaging formulas.  An example of the performance improvement is shown in the accompanying figure.


Last Modified: 01/16/2022
Modified by: David A Kofke

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