Award Abstract # 1550482
SI2-SSI: Collaborative Research: ENKI: Software Infrastructure that ENables Knowledge Integration for Modeling Coupled Geochemical and Geodynamical Processes

NSF Org: OAC
Office of Advanced Cyberinfrastructure (OAC)
Recipient: OFM RESEARCH
Initial Amendment Date: August 19, 2016
Latest Amendment Date: August 19, 2016
Award Number: 1550482
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: September 1, 2016
End Date: August 31, 2020 (Estimated)
Total Intended Award Amount: $734,907.00
Total Awarded Amount to Date: $734,907.00
Funds Obligated to Date: FY 2016 = $734,907.00
History of Investigator:
  • Mark Ghiorso (Principal Investigator)
    ghiorso@ofm-research.org
Recipient Sponsored Research Office: OFM Research
7336 24TH AVE NE
SEATTLE
WA  US  98115-5810
(425)880-4418
Sponsor Congressional District: 07
Primary Place of Performance: OFM Research
7336 24th Ave NE
Seattle
WA  US  98115-5810
Primary Place of Performance
Congressional District:
07
Unique Entity Identifier (UEI): LF8GACLM9GM1
Parent UEI:
NSF Program(s): Petrology and Geochemistry,
Software Institutes,
EarthCube
Primary Program Source: 01001617DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 7433, 8004
Program Element Code(s): 157300, 800400, 807400
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.070

ABSTRACT

Earth scientists seek to understand the mechanisms of planetary evolution from a process perspective in order to promote the progress of science. They model the chemistry of melting of the interiors of planets as a result of heat flow within the body. They calculate the flows of energy and mass from the interior to the surface. They model the interaction of fluids and rocks, which drives chemical weathering and the formation of ore deposits. They seek to understand the synthesis and stabilities of organic compounds and their economic and biological roles. They study the interactions of atmosphere, oceans, biosphere and land as a dynamically coupled evolving chemical system. To achieve this level of understanding of planetary evolution, Earth scientists use software tools that encode two fundamentally different types of models: (1) thermodynamic models of naturally occurring materials, and (2) models of transport that track physical flows of both fluids and solids. Much of the fundamental science of planetary evolution lies in understanding coupled thermodynamic and transport models. This grant funds development of a software infrastructure that supports this coupled modeling of the chemical evolution of planetary bodies. It is their aim to establish an essential and active community resource that will engage a large number of researchers, especially early career scientists, in the exercise of model building and customization.

This is a project to create ENKI, a collaborative model configuration and testing portal that will transform research and education in the fields of geochemistry, petrology and geophysics. ENKI will provide software tools in computational thermodynamics and fluid dynamics. It will support development and access to thermochemical models of Earth materials, and establish a standard infrastructure of web services and libraries that permit these models to be integrated into fluid dynamical transport codes. This infrastructure will allow scientific questions to be answered by quantitative simulations that are presently difficult to impossible because of the lack of interoperable software frameworks. ENKI, via the adoption of state-of-the-art model interfacing (OpenMI) and deployment environments (HubZero), will modernize how thermodynamic and fluid dynamic models are used by the Earth science community in five fundamental ways: (1) provenance tracking will enable automatic documentation of model development and execution workflows, (2) new tools will assist users in updating thermochemical models as new data become available, with the ability to merge these data and models into existing repositories and frameworks, (3) automated code generation will eliminate the need for users to manually code web services and library modules, (4) visualization tools and standard test suites will facilitate validation of model outcomes against observational data, (5) collaborative groups will be able to share and archive models and modeling workflows with associated provenance for publication. With these tools we seek to transform the large community of model users, who currently depend on a small group of dedicated and experienced researchers for model development and maintenance, into an empowered ensemble of model developers who take ownership of the process and bring their own expertise, intuition and perspective to shaping the software tools they use in daily research. ENKI development will be community driven. Participation of a dedicated and diverse group of early career professionals will guide us in user interface development - insuring portal capabilities are responsive to user needs, and in development of a rich set of documentation, tutorials and examples. All software associated with this project will be released as open source.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Evans O, Spiegelman M, Kelemen PB "A poroelastic model of serpentinization: exploring the interplay between rheology, surface energy, reaction and fluid flow" J. Geophys. Res. , 2018 10.1029/2017JB015214
Wilson, C.R., Spiegelman, M., van Keken, P.E. "TerraFERMA: The Transparent Finite Element Rapid Model Assembler for multiphysics problems in Earth sciences" Geochem. Geophys. Geosyst. , v.18 , 2017 , p.769 10.1002/2016GC006702

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.

This grant provided funding to construct the ENKI software framework for computational thermodynamics and fluid dynamics modeling in the Earth Sciences.  ENKI provides tools that support the development and access to thermochemical models of Earth materials. Users interact with these tools using a Python programming interface.  The resulting software ecosystem provides standardized access to software libraries that permit thermodynamic models to be integrated into fluid dynamical transport codes.  The ENKI framework defines a common Application Programming Interface (API) for thermodynamic model usage and standard protocols for model interoperability.  Previous to development of the ENKI framework, geochemical, petrological, and fluid dynamical models were not interoperable; they were difficult to use, required a specialist to maintain, and were not generally available on all computing platforms. A significant advance is that ENKI has transformed the focus in using these models from running an app with a single purpose to calling appropriate software resources from a framework. This capability enhances flexibility of use and liberates users from tailoring their research objectives to the output of a particular model.

In addition to making commonly used modeling tools available via a web browser from a centralized cloud-based service platform, ENKI streamlines the workflow for new model development and the process of updating existing models.  It contains model parameter calibration methods, automated code generation modules, and visualization tools that transform the focus of this workflow from logistics to concept. The traditional workflow for thermodynamic model development is error prone, is tedious, and requires considerable expertise in code development. It is difficult to replicate and time intensive; typical projects require months to years to complete. The ENKI workflow involves symbolic model specification using the SymPy Python package, with model structure documented in a Jupyter notebook. The software framework automatically performs symbolic differentiation to generate a full thermodynamic specification, transforms the symbolic results to code (C or C++), compiles and wraps this code in Cython, and delivers the resulting module back to the framework. Because the generated code has a standardized API, it is immediately available for integration into the framework to utilize existing calibration, phase equilibrium, and visualization tools. It may also be integrated as libraries for materials property evaluation in fluid dynamics simulations. The ENKI model development workflow requires less coding expertise, is less error prone, may be easily replicated, and requires far less development time.  ENKI software tools are designed to promote replicable and reproducible scientific analysis.

Further information about the ENKI project may be found at http://enki-portal.org/

 


Last Modified: 12/30/2020
Modified by: Mark S Ghiorso

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