pflotran-community.bib
@article{gmd-16-961-2023,
author = {Jaysaval, Piyoosh and Hammond, Glenn E. and Johnson, Timothy C.},
title = {Massively parallel modeling and inversion of electrical resistivity tomography data using {PFLOTRAN}},
journal = {Geoscientific Model Development},
volume = {16},
year = {2023},
number = {3},
pages = {961--976},
url = {https://gmd.copernicus.org/articles/16/961/2023/},
doi = {https://doi.org/10.5194/gmd-16-961-2023}
}
@article{laforce2022,
author = {Tara LaForce and Mohamed Ebeida and Spencer Jordan and Terry Miller and Philip Stauffer and Heeho Park and Rosie Leone and Glenn Hammond},
journal = {Mathematical Geosciences},
year = 2022,
doi = {https://doi.org/10.1007/s11004-022-10025-x}
}
@article{PARK2022104285,
title = {Newton trust-region methods with primary variable switching for simulating high temperature multiphase porous media flow},
journal = {Advances in Water Resources},
volume = {168},
pages = {104285},
year = {2022},
issn = {0309-1708},
doi = {https://doi.org/10.1016/j.advwatres.2022.104285},
url = {https://www.sciencedirect.com/science/article/pii/S030917082200149X},
author = {Heeho D. Park and Matthew Paul and Glenn E. Hammond and Albert J. Valocchi},
keywords = {Nonisothermal, High temperature, Porous media, Multiphase flow, Miscible, Trust-region},
abstract = {Coupling multiphase flow with energy transport due to high temperature heat sources introduces significant new challenges since boiling and condensation processes can lead to dry-out conditions with subsequent re-wetting. The transition between two-phase and single-phase behavior can require changes to the primary dependent variables adding discontinuities as well as extending constitutive nonlinear relations to extreme physical conditions. Practical simulations of large-scale engineered domains lead to Jacobian systems with a very large number of unknowns that must be solved efficiently using iterative methods in parallel on high-performance computers. Performance assessment of potential nuclear repositories, carbon sequestration sites and geothermal reservoirs can require numerous Monte-Carlo simulations to explore uncertainty in material properties, boundary conditions, and failure scenarios. Due to the numerical challenges, standard NR iteration may not converge over the range of required simulations and require more sophisticated optimization method like trust-region. We use the open-source simulator PFLOTRAN for the important practical problem of the safety assessment of future nuclear waste repositories in the U.S. DOE geologic disposal safety assessment Framework. The simulator applies the PETSc parallel framework and a backward Euler, finite volume discretization. We demonstrate failure of the conventional NR method and the success of trust-region modifications to Newton’s method for a series of test problems of increasing complexity. Trust-region methods essentially modify the Newton step size and direction under some circumstances where the standard NR iteration can cause the solution to diverge or oscillate. We show how the Newton Trust-Region method can be adapted for Primary Variable Switching (PVS) when the multiphase state changes due to boiling or condensation. The simulations with high-temperature heat sources which led to extreme nonlinear processes with many state changes in the domain did not converge with NR, but they do complete successfully with the trust-region methods modified for PVS. This implementation effectively decreased weeks of simulation time needing manual adjustments to complete a simulation down to a day. Furthermore, we show the strong scalability of the methods on a single node and multiple nodes in an HPC cluster.}
}
@article{rousseau2022,
author = {Moise Rousseau and Thomas Pabst},
title = {Topology optimization of in-pit codisposal of waste rocks and tailings to reduce advective contaminant transport to the environment},
journal = {Structural and Multidisciplinary Optimization},
volume = 68,
issue = 168,
year = 2022,
doi = {https://doi.org/10.1007/s00158-022-03266-1}
}
@article{TRINCHERO2022105166,
title = {Simulating electrochemical migration and anion exclusion in porous and fractured media using {PFLOTRANNP}},
journal = {Computers & Geosciences},
volume = {166},
pages = {105166},
year = {2022},
issn = {0098-3004},
doi = {https://doi.org/10.1016/j.cageo.2022.105166},
url = {https://www.sciencedirect.com/science/article/pii/S0098300422001200},
author = {Paolo Trinchero and Albert Nardi and Orlando Silva and Paula Bruch},
keywords = {Electrochemical migration, Anion exclusion, Multicomponent transport, PFLOTRAN},
abstract = {Multicomponent transport of dissolved charged species often involves electrostatic interactions among the different ions. These interactions are the result of the different diffusion rates of the chemical species, which create a diffusion potential and thus an electromigration term in the transport equation that is additive to the Fickian diffusion term due to the concentration gradient. The explicit consideration of the electromigration term involves the use of the Nernst–Planck equation, which tightly couples the transport of the charged species through the electro-diffusive term. Here, we have implemented the Nernst–Planck equation in the open source computer code PFLOTRAN. The advantages of the customised code, denoted as PFLOTRANNP, in comparison with other recent similar developments, are that (i) the implementation is extended also to the multiple continuum module of PFLOTRAN, which makes the code suitable for the modelling of electromigration processes in fractured rock, (ii) PFLOTRANNP leverages the parallelisation capabilities of one of the latest stable PFLOTRAN versions and thus it is suited for large-size simulations in supercomputers and (iii) the developed code is made available through a public repository. PFLOTRANNP was successfully validated against a standard benchmark involving 1D transport of a multicomponent electrolyte solution and a verification case, involving a fracture–matrix system, was also presented. Finally, PFLOTRANNP was used to interpret field and experimental data at Olkiluoto (Finland), which show that an imbalance exists between chloride concentration in the matrix pore water and in the fracture filling groundwater. The results of the simulations show that this imbalance is indeed caused by anion exclusion processes, which are more significant in gneiss rock types than in pegmatitic granitic rock.}
}
@article{https://doi.org/10.1029/2021WR030735,
author = {Chen, Kewei and Chen, Xingyuan and Song, Xuehang and Briggs, Martin A. and Jiang, Peishi and Shuai, Pin and Hammond, Glenn and Zhan, Hongbin and Zachara, John M.},
title = {Using Ensemble Data Assimilation to Estimate Transient Hydrologic Exchange Flow Under Highly Dynamic Flow Conditions},
journal = {Water Resources Research},
volume = {58},
number = {5},
pages = {e2021WR030735},
keywords = {hydrologic exchange flow, data assimilation, hyporheic zone, heat tracer},
doi = {https://doi.org/10.1029/2021WR030735},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2021WR030735},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2021WR030735},
note = {e2021WR030735 2021WR030735},
abstract = {Abstract Quantifying dynamic hydrologic exchange flows (HEFs) within river corridors that experience high-frequency flow variations caused by dam regulations is important for understanding the biogeochemical processes at the river water and groundwater interfaces. Heat has been widely used as a tracer to infer steady-state flow velocities through analytical solutions of heat transport defined by the diurnal temperature signals. Under sub-daily dynamic flow conditions, however, such analytical solutions are not applicable due to the violation of their fundamental assumptions. In this study, we developed a data assimilation-based approach to estimate the sub-daily flux under highly dynamic flow conditions using multi-depth temperature observations at a 5-min resolution. If the hydraulic gradient is measured, Darcy's law was used to calculate the flux with permeability estimated from temperature responses below the riverbed. Otherwise, flux was estimated directly by assimilating multi-depth temperature data at 1- or 2-hr time intervals assuming one-dimensional flow and heat transport governing equation. By comparing estimated fluxes with model-generated synthetic truth, we demonstrated that both schemes have robust performance in estimating fluxes under highly dynamic flow conditions. This data assimilation-based flux estimation method was able to capture the vertical sub-daily fluxes using multi-depth high-resolution temperature data alone, even in the presence of multi-dimensional flow. This approach has been successfully applied to real field temperature data collected at the Hanford site, which experiences highly dynamic HEFs. Our study shows the promise of adopting distributed 1-D temperature monitoring to capture spatial and temporal exchange dynamics in river corridors at a watershed scale or beyond.},
year = {2022}
}
@article{Kuhlman2022,
author = {Kuhlman, Kristopher L. and Mills, Melissa M. and Heath, Jason E. and Paul, Matthew J. and Wilson, Jennifer E. and Bower, John Eric},
title = {Parameter estimation from spontaneous imbibition into volcanic tuff},
journal = {Vadose Zone Journal},
year = {2022},
doi = {https://doi.org/10.1002/vzj2.20188},
url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.1002/vzj2.20188},
abstract = {Abstract Two-phase fluid flow properties underlie quantitative prediction of water and gas movement, but constraining these properties typically requires multiple time-consuming laboratory methods. The estimation of two-phase flow properties (van Genuchten parameters, porosity, and intrinsic permeability) is illustrated in cores of vitric nonwelded volcanic tuff using Bayesian parameter estimation that fits numerical models to observations from spontaneous imbibition experiments. The uniqueness and correlation of the estimated parameters is explored using different modeling assumptions and subsets of the observed data. The resulting estimation process is sensitive to both moisture retention and relative permeability functions, thereby offering a comprehensive method for constraining both functions. The data collected during this relatively simple laboratory experiment, used in conjunction with a numerical model and a global optimizer, result in a viable approach for augmenting more traditional capillary pressure data obtained from hanging water column, membrane plate extractor, or mercury intrusion methods. This method may be useful when imbibition rather than drainage parameters are sought, when larger samples (e.g., including heterogeneity or fractures) need to be tested that cannot be accommodated in more traditional methods, or when in educational laboratory settings.}
}
@article{gmd-15-1659-2022,
author = {Hammond, G. E.},
title = {The {PFLOTRAN Reaction Sandbox}},
journal = {Geoscientific Model Development},
volume = {15},
year = {2022},
number = {4},
pages = {1659--1676},
url = {https://gmd.copernicus.org/articles/15/1659/2022/},
doi = {10.5194/gmd-15-1659-2022},
abstract = {As modern reactive transport simulators evolve to accommodate the demands of a user community, researchers need a platform for prototyping new biogeochemical processes, many of which are niche and specific to laboratory or field experiments. The PFLOTRAN Reaction Sandbox leverages modern, object-oriented Fortran in an attempt to provide such an environment within an existing reactive transport simulator. This work describes the PFLOTRAN Reaction Sandbox concept and implementation through several illustrative examples. Reaction Sandbox Biodegradation Hill customizes the existing microbially mediated biodegradation reaction formulation within PFLOTRAN to better match empirical data. Reaction Sandbox Simple provides an isolated environment for testing numerous preconfigured kinetic rate expressions and developing user intuition. Reaction Sandbox Example serves as a template for creating new sandboxes within PFLOTRAN.}
}
@article{PARK2021104029,
title = {Linear and nonlinear solvers for simulating multiphase flow within large-scale engineered subsurface systems},
journal = {Advances in Water Resources},
volume = {156},
pages = {104029},
year = {2021},
issn = {0309-1708},
doi = {https://doi.org/10.1016/j.advwatres.2021.104029},
url = {https://www.sciencedirect.com/science/article/pii/S0309170821001834},
author = {Heeho D. Park and Glenn E. Hammond and Albert J. Valocchi and Tara LaForce},
keywords = {Preconditioner, Nonlinear, Porous media, Multiphase flow, Trust-region, Subsurface system},
abstract = {Multiphase flow simulation is well-known to be computationally demanding, and modeling large-scale engineered subsurface systems entails significant additional numerical challenges. These challenges arise from: (a) the presence of small-scale discrete features like shafts, tunnels, waste packages, and barriers; (b) the need to accurately represent both the waste form processes at the small spatial scale of the repository and the large-scale transport processes throughout heterogeneous geological formations; (c) the strong contrast in material properties such as porosity and permeability, as well as the nonlinear constitutive relations for multiphase flow. Numerical solution entails discretization of the coupled system of nonlinear governing equations and solving a linear system of equations at each Newton–Raphson iteration. Practical problems require a very large number of unknowns that must be solved efficiently using iterative methods in parallel on high-performance computers. The unique challenges noted above can lead to an ill-conditioned Jacobian matrix and non-convergence with Newton’s method due to discontinuous nonlinearity in constitutive models. Moreover, practical applications can require numerous Monte-Carlo simulations to explore uncertainly in material properties, geological heterogeneity, failure scenarios, or other factors; governmental regulatory agencies can mandate these as part of Performance Assessments. Hence there is a need for flexible, robust, and computationally efficient methods for multiphase flow in large-scale engineered subsurface systems. We apply the open-source simulator PFLOTRAN to the practical problem of performance assessment of the US DOE Waste Isolation Pilot Plant (WIPP) site. The simulator employs a finite volume discretization and uses the PETSc parallel framework. We evaluate the performance of several preconditioners for the iterative solution of the linearized Jacobian system; these range from stabilized-biconjugate-gradient with block-Jacobi preconditioning (BCGS) to methods adopted from reservoir modeling, such as the constrained pressure residual (CPR) two-stage preconditioner and flexible generalized residual solver (FGMRES). We also implement within PETSc the general-purpose nonlinear solver, Newton trust-region dogleg Cauchy (NTRDC), which truncates the Newton update or modifies the update with a Cauchy solution that is within the quadratic model trust-region of the objective function. We demonstrate the effectiveness of each method for a series of test problems with increasing difficulty. We find that the NTRDC and FGMRES-CPR-ABF (FCA) preconditioners generally perform best for the test problem having the extreme nonlinear processes, achieving a 50x speed-up compared with BCGS. The most ill-conditioned and extreme nonlinear simulations do not converge with BCGS (as one may expect), but they do complete the simulation with NTRDC and FCA. We also investigate the strong scalability of each method and demonstrate the impact of node-packing upon parallel performance on modern processor architectures.}
}
@article{Srinivasan2021,
author = {Srinivasan, S. and O'Malley, D. and Mudunuru, M.K. and Sweeney, M.R. and Hyman, J.D. and Karra, S. and Frash, L. and Carey, J.W. and Gross, M.R. and Guthrie, G.D. and Carr, T.},
title = {A machine learning framework for rapid forecasting and history matching in unconventional reservoirs},
year = 2021,
journal = {Scientific Reports},
doi = {10.1038/s41598-021-01023-w},
url = {https://doi.org/10.1038/s41598-021-01023-w},
abstract = {We present a novel workflow for forecasting production in unconventional reservoirs using reduced-order models and machine-learning. Our physics-informed machine-learning workflow addresses the challenges to real-time reservoir management in unconventionals, namely the lack of data (i.e., the time-frame for which the wells have been producing), and the significant computational expense of high-fidelity modeling. We do this by applying the machine-learning paradigm of transfer learning, where we combine fast, but less accurate reduced-order models with slow, but accurate high-fidelity models. We use the Patzek model (Proc Natl Acad Sci 11:19731–19736, https://doi.org/10.1073/pnas.1313380110, 2013) as the reduced-order model to generate synthetic production data and supplement this data with synthetic production data obtained from high-fidelity discrete fracture network simulations of the site of interest. Our results demonstrate that training with low-fidelity models is not sufficient for accurate forecasting, but transfer learning is able to augment the knowledge and perform well once trained with the small set of results from the high-fidelity model. Such a physics-informed machine-learning (PIML) workflow, grounded in physics, is a viable candidate for real-time history matching and production forecasting in a fractured shale gas reservoir.}
}
@proceedings{Rousseau2021b,
title = {Blast damaged zone influence on water and solute exchange between backfilled open-pit and the environment.},
booktitle = {Proceedings of GeoVirtual 2020},
address = {Online conference},
year = {2021},
url = {https://geovirtual2020.ca/wp-content/files/212.pdf}
}
@article{Roussseau2021,
author = {Rousseau, Moise and Pabst, Thomas},
title = {Analytical solution and numerical simulation of steady flow around a circular heterogeneity with anisotropic and concentrically varying permeability},
journal = {Water Resources Research},
year = {2021},
pages = {e2021WR029978},
keywords = {Analytical solution, Numerical simulation, Validation, Error analysis, Anisotropic media},
doi = {https://doi.org/10.1029/2021WR029978},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2021WR029978},
abstract = {Abstract Accurately simulating flow to assess the environmental impact of backfilled mine open-pit with hazardous waste is challenging. Excavation and blasting during mining operations often result in the creation of new fractures with preferential orientation, which leads to a variable and anisotropic permeability field around the excavation. Numerical simulations are often used to study such problems, but experimental data are scarce and analytical solutions for this configuration are not available in the literature, which make the code validation difficult and uncertain. Therefore, the present study aimed to address the numerical code validation by developing a new closed form head solution of a steady flow with a radially anisotropic and continuously varying permeability distribution around a heterogeneity. Numerical flow simulations using the finite volume code PFLOTRAN were then compared to the analytically calculated heads and flowrates on three cases of increasing complexity. Results showed a good agreement between analytical and simulated flowrates and heads, with a maximum absolute error not exceeding 3.5\% on flowrates and 1.8\% on heads. Errors were actually mainly caused by boundary effects and by the non respect of the K-orthogonality condition in the computational mesh. This study opens the way for accurate evaluation of the blast damage zone influence on groundwater flow in and around open pits backfilled with hazardous wastes. This article is protected by copyright. All rights reserved.}
}
@article{JIANG2021105074,
title = {{DART-PFLOTRAN}: An ensemble-based data assimilation system for estimating subsurface flow and transport model parameters},
journal = {Environmental Modelling & Software},
volume = {142},
pages = {105074},
year = {2021},
issn = {1364-8152},
doi = {https://doi.org/10.1016/j.envsoft.2021.105074},
url = {https://www.sciencedirect.com/science/article/pii/S1364815221001171},
author = {Peishi Jiang and Xingyuan Chen and Kewei Chen and Jeffrey Anderson and Nancy Collins and Mohamad EL. Gharamti},
keywords = {Data assimilation, Ensemble smoother, DART, PFLOTRAN, Inverse modeling, Subsurface flow and transport},
abstract = {Ensemble-based Data Assimilation (EDA) has been effectively applied to estimate model parameters through inverse modeling in subsurface flow and transport problems. To facilitate the management of EDA workflow and lower the barriers for adopting EDA-based parameter estimation in subsurface science, we develop a software framework linking the Data Assimilation Research Testbed (DART) with a massively parallel subsurface FLOw and TRANsport code PFLOTRAN. DART-PFLOTRAN enables an iterative EDA workflow based on the Ensemble Smoother for Multiple Data Assimilation method (ES-MDA) to improve estimation accuracy for nonlinear forward problems. We verify the implementation of ES-MDA in DART-PFLOTRAN using two synthetic cases designed to estimate static permeability and dynamic exchange fluxes across the riverbed from continuous temperature measurements. Both cases yield accurate estimations of the parameters compared to their synthetic truth. With a code base in Python and Fortran, DART-PFLOTRAN paves the way for large-scale inverse modeling using the sequential ES-MDA.}
}
@article{https://doi.org/10.1029/2020WR028235,
author = {Thiros, Nicholas E. and Gardner, W. Payton and Kuhlman, Kristopher L.},
title = {Utilizing Environmental Tracers to Reduce Groundwater Flow and Transport Model Parameter Uncertainties},
journal = {Water Resources Research},
volume = {57},
number = {7},
keywords = {Environmental tracers, groundwater age, groundwater hydrology, groundwater transport, model calibration, uncertainty quantification},
doi = {https://doi.org/10.1029/2020WR028235},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020WR028235},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020WR028235},
abstract = {Abstract Non-uniqueness in groundwater model calibration is a primary source of uncertainty in groundwater flow and transport predictions. In this study, we investigate the ability of environmental tracer information to constrain groundwater model parameters. We utilize a pilot point calibration procedure conditioned to subsets of observed data including: liquid pressures, tritium (3H), chlorofluorocarbon-12 (CFC-12), and sulfur hexafluoride (SF6) concentrations; and groundwater apparent ages inferred from these environmental tracers, to quantify uncertainties in the heterogeneous permeability fields and infiltration rates of a steady-state 2-D synthetic aquifer and a transient 3-D model of a field site located near Riverton, Wyoming (USA). To identify the relative data worth of each observation data type, the post-calibration uncertainties of the optimal parameters for a given observation subset are compared to that from the full observation data set. Our results suggest that the calibration-constrained permeability field uncertainties are largest when liquid pressures are used as the sole calibration data set. We find significant reduction in permeability uncertainty and increased predictive accuracy when the environmental tracer concentrations, rather than apparent groundwater ages, are used as calibration targets in the synthetic model. Calibration of the Riverton field site model using environmental tracer concentrations directly produces infiltration rate estimates with the lowest uncertainties, however; permeability field uncertainties remain similar between the environmental tracer concentration and apparent groundwater age calibration scenarios. This work provides insight on the data worth of environmental tracer information to calibrate groundwater models and highlights potential benefits of directly assimilating environmental tracer concentrations into model parameter estimation procedures.},
year = {2021}
}
@article{https://doi.org/10.1029/2020JB021271,
author = {Alt-Epping, Peter and Diamond, Larryn W. and Wanner, Christoph and Hammond, Glenn E.},
title = {Effect of Glacial/Interglacial Recharge Conditions on Flow of Meteoric Water Through Deep Orogenic Faults: Insights Into the Geothermal System at Grimsel Pass, Switzerland},
journal = {Journal of Geophysical Research: Solid Earth},
volume = {126},
number = {7},
keywords = {orogenic faults, geothermal system, climate change, flow pattern, convection},
doi = {https://doi.org/10.1029/2020JB021271},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JB021271},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020JB021271},
abstract = {Abstract Many meteoric-recharged, fault-hosted geothermal systems in amagmatic orogenic belts have been active through the Pleistocene glacial/interglacial climate fluctuations. The effects of climate-induced recharge variations on fluid flow patterns and residence times of the thermal waters are complex and may influence how the geothermal and mineralization potential of the systems are evaluated. We report systematic thermal-hydraulic simulations designed to reveal the effects of recharge variations, using a model patterned on the orogenic geothermal system at Grimsel Pass in the Swiss Alps. Previous studies have shown that fault-bounded circulation of meteoric water is driven to depths of ~10 km by the high alpine topography. Simulations suggest that the current single-pass flow is typical of interglacial periods, during which (a) meteoric recharge into the fault is high (above tens of centimeters per year), (b) conditions are at or somewhat below the critical Rayleigh number, and (c) hydraulic connectivity along the fault plane is extensive (an extent of at least 10 km into increasingly higher terrain is required to explain the 10 km penetration depth). The subcritical condition constrains the bulk fault permeability to <1e-14 m2. In contrast, the limited recharge during the numerous Pleistocene glaciation events likely induced a layered flow system, with single-pass flow confined to shallow depths while non-Rayleigh convection occurred deeper in the fault. The same layering can be observed at low aspect ratios (length/depth) of the fault plane, when the available recharge area limits flux through the fault.},
year = {2021}
}
@article{WU2021104959,
title = {Coupling surface flow with high-performance subsurface reactive flow and transport code {PFLOTRAN}},
journal = {Environmental Modelling & Software},
volume = {137},
year = {2021},
issn = {1364-8152},
doi = {https://doi.org/10.1016/j.envsoft.2021.104959},
url = {https://www.sciencedirect.com/science/article/pii/S1364815221000025},
author = {Runjian Wu and Xingyuan Chen and Glenn Hammond and Gautam Bisht and Xuehang Song and Maoyi Huang and Guo-Yue Niu and Ty Ferre},
keywords = {Surface flow, Integrated hydrological modeling, Boundary condition switching, Parallel computing},
abstract = {Water exchange between the surface and subsurface is important for both water resource management and environmental protection. In this paper, we develop coupled surface and subsurface flow simulation capability in a parallel subsurface flow and reactive transport code PFLOTRAN. We sequentially couple the diffusion wave-based surface flow with the subsurface flow governed by the Richards equation in PFLOTRAN. These two flow domains are linked with a boundary condition switching method that ensures the continuity of pressure and flux at the surface-subsurface interface. We verify the coupled code against other existing hydrologic models and observation data using a number of numerical experiments. The coupled hydrological model exhibits good performance in strong parallel scaling tests. The new coupled surface and subsurface simulator significantly advance community simulation capability towards improving integrated hydrologic and biogeochemical understanding of complex systems such as watersheds and river corridors.}
}
@article{https://doi.org/10.1029/2020GC009574,
author = {Eymold, William K. and Frederick, Jennifer M. and Nole, Michael and Phrampus, Benjamin J. and Wood, Warren T.},
title = {Prediction of Gas Hydrate Formation at Blake Ridge Using Machine Learning and Probabilistic Reservoir Simulation},
journal = {Geochemistry, Geophysics, Geosystems},
volume = 22,
number = 4,
keywords = {acoustic velocity, free gas, gas hydrate, geospatial machine learning, seafloor mapping},
doi = {https://doi.org/10.1029/2020GC009574},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020GC009574},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020GC009574},
abstract = {Abstract Methane hydrates are solid structures containing methane inside of a water lattice that form under low temperature and relatively high pressure. Appropriate hydrate-forming conditions exist along continental shelves or are associated with permafrost. Hydrates have garnered scientific interest via their potential as a source of natural gas and their role in the global carbon cycle. While methane hydrates have been collected in multiple diverse geographic settings, their quantities and distribution in sediments remain poorly constrained due to sparse relevant data. Using statistical and machine learning approaches, we have developed a workflow to probabilistically predict methane hydrate occurrence from local microbial methane sourcing. This approach utilizes machine-learned global maps produced by the Global Predictive Seabed Model (GPSM) as inputs for the statistical sampling software, Dakota, and multiphase reservoir simulation software, PFLOTRAN. Dakota performs Latin hypercube sampling of the GPSM-predicted values and uncertainties to generate unique sets of input parameters for 1-D PFLOTRAN simulations of gas hydrate and free gas formation resulting from methanogenesis to steady state. We ran 100 1-D simulations spanning a kilometer in depth at 5,297 locations near Blake Ridge. Masses of hydrate and free gas formed at each location were determined by integrating the predicted saturation profiles. Elevated hydrate formation is predicted to occur at depths >500 meters below sea level at this location, and is strongly associated with high seafloor total organic carbon values. We produce representative maps of expected hydrate occurrence for the study area based on multiple realizations that can be validated against geophysical observations.},
year = 2021
}
@article{en13246552,
author = {Ahmmed, Bulbul and Mudunuru, Maruti Kumar and Karra, Satish and James, Scott C. and Viswanathan, Hari and Dunbar, John A.},
title = {{PFLOTRAN-SIP}: A {PFLOTRAN} Module for Simulating Spectral-Induced Polarization of Electrical Impedance Data},
journal = {Energies},
volume = {13},
year = {2020},
number = {24},
article-number = {6552},
url = {https://www.mdpi.com/1996-1073/13/24/6552},
issn = {1996-1073},
abstract = {Spectral induced polarization (SIP) is a non-intrusive geophysical method that collects chargeability information (the ability of a material to retain charge) in the time domain or its phase shift in the frequency domain. Although SIP is a temporal method, it cannot measure the dynamics of flow and solute/species transport in the subsurface over long times (i.e., 10–100 s of years). Data collected with the SIP technique need to be coupled with fluid flow and reactive-transport models in order to capture long-term dynamics. To address this challenge, PFLOTRAN-SIP was built to couple SIP data to fluid flow and solute transport processes. Specifically, this framework couples the subsurface flow and transport simulator PFLOTRAN and geoelectrical simulator E4D without sacrificing computational performance. PFLOTRAN solves the coupled flow and solute-transport process models in order to estimate solute concentrations, which were used in Archie’s model to compute bulk electrical conductivities at near-zero frequency. These bulk electrical conductivities were modified while using the Cole–Cole model to account for frequency dependence. Using the estimated frequency-dependent bulk conductivities, E4D simulated the real and complex electrical potential signals for selected frequencies for SIP. These frequency-dependent bulk conductivities contain information that is relevant to geochemical changes in the system. This study demonstrated that the PFLOTRAN-SIP framework is able to detect the presence of a tracer in the subsurface. SIP offers a significant benefit over ERT in the form of greater information content. It provided multiple datasets at different frequencies that better constrained the tracer distribution in the subsurface. Consequently, this framework allows for practitioners of environmental hydrogeophysics and biogeophysics to monitor the subsurface with improved resolution.},
doi = {10.3390/en13246552}
}
@article{Tutolo2020,
title = {Contributions of visible and invisible pores to reactive transport in dolomite},
author = {Tutolo, B.M. and Luhmann, A.J. and Kong, X.-Z. and Bagley, B. and Alba-Venero, D. and Mitchell, N. and Saar, M.O. and Seyfried Jr., W.E.},
journal = {Geochemical Perspectives Letters},
volume = 14,
year = 2020,
doi = {http://dx.doi.org/10.7185/geochemlet.2022},
url = {http://www.geochemicalperspectivesletters.org/article2022},
abstract = {Recent technical advances have demonstrated the importance of pore-scale geochemical processes for governing Earth’s evolution. However, the contribution of pores at different scales to overall geochemical reactions remains poorly understood. Here, we integrate multiscale characterisation and reactive transport modelling to study the contribution of pore-scale geochemical processes to the hydrogeochemical evolution of dolomite rock samples during CO2-driven dissolution experiments. Our results demonstrate that approximately half of the total pore volume is invisible at the scale of commonly used imaging techniques. Comparison of pre- and post-experimental analyses demonstrate that porosity-increasing, CO2-driven dissolution processes preferentially occur in pores 600 nm–5 μm in size, but pores <600 nm in size show no change during experimental alteration. This latter observation, combined with the anomalously high rates of trace element release during the experiments, suggests that nanoscale pores are accessible to through-flowing fluids. A three dimensional simulation performed directly on one of the samples shows that steady state pore-scale trace element reaction rates must be ∼10× faster than that of dolomite in order to match measured effluent concentrations, consistent with the large surface area-to-volume ratio and high reactivity of these pores. Together, these results yield a new conceptual model of pore-scale processes, and urge caution when interpreting the trace element concentrations of ancient carbonate rocks.}
}
@article{TRINCHERO2020103644,
title = {Upscaling of radionuclide transport and retention in crystalline rocks exhibiting micro-scale heterogeneity of the rock matrix},
journal = {Advances in Water Resources},
volume = {142},
year = {2020},
issn = {0309-1708},
doi = {https://doi.org/10.1016/j.advwatres.2020.103644},
url = {https://www.sciencedirect.com/science/article/pii/S030917082030172X},
author = {Paolo Trinchero and Vladimir Cvetkovic and Jan-Olof Selroos and Dirk Bosbach and Guido Deissmann},
keywords = {Mineralogical heterogeneity, Heterogeneous retention, Fractured media, Upscaling},
abstract = {In different in-situ diffusion experiments carried out in fractured crystalline rocks, sorbing radionuclides have shown a behaviour that strongly differs from what is predicted by homogeneous-based models. Their breakthrough curves are in fact often characterised by a fast first-arrival and these radionuclides can penetrate surprisingly long distances deep into the matrix. The heterogeneous structure of mineral distribution and porosity geometry had been offered as an explanation for these discrepancies. Here, we use reactive transport simulations to investigate the effect of the sparse distribution of sorption sites on the breakthrough curves of sorbing radionuclides. At small scale, the computed breakthrough curves significantly differ from those predicted using homogeneous models. For instance, the early part of these curves does not show any clear separation with the corresponding part of the curve of a non-sorbing tracer and a long transition zone is observed, with a very smooth slope of the tailing. Two different upscaling strategies, aimed at propagating the signal of heterogeneous retention over larger scales, are proposed and demonstrated against independent solutions computed at intermediate scales. The upscaling strategies are also used to show that at large scales (e.g. the scale of interest in a safety assessment study for a deep geological repository for nuclear waste) the signature of mineralogical heterogeneity is smoothed out and the heterogeneous breakthrough curve is well approximated by a homogeneous solution where the radionuclide distribution coefficient for the pure mineral phase is scaled by the mineral volume fraction. However, the spatial persistence of the heterogeneous signature is significant when the sorbing mineral is present in a low amount.}
}
@article{10.3389/frwa.2020.533796,
author = {Chen, Xingyuan and Zachara, John M. and Vermuel, Vince R. and Hammond, Glenn and Freshley, Mark and Fang, Yilin},
title = {Understanding Contaminant Migration Within a Dynamic River Corridor Through Field Experiments and Reactive Transport Modeling},
journal = {Frontiers in Water},
volume = {2},
pages = {44},
year = {2020},
url = {https://www.frontiersin.org/article/10.3389/frwa.2020.533796},
doi = {10.3389/frwa.2020.533796},
issn = {2624-9375},
abstract = {The behavior of a persistent uranium plume within an extended river corridor at the DOE Hanford site is dominantly controlled by river stage fluctuations in the adjacent Columbia River. The plume behavior is further complicated by substantial heterogeneity in physical and geochemical properties of the host aquifer sediments. Multi-scale field and laboratory experiments and reactive transport modeling were integrated to understand the complex plume behavior influenced by highly variable hydrologic and geochemical conditions in time and space. In this paper, we (1) describe multiple data sets from field-scale uranium adsorption and desorption experiments performed at our experimental well-field, (2) develop a reactive transport model that incorporates hydrologic and geochemical heterogeneities characterized from multi-scale and multi-type datasets and a surface complexation reaction network based on laboratory studies, and (3) compare the modeling and observation results to provide insights on how to refine the conceptual model and reduce prediction uncertainties. The experimental results revealed significant spatial variability in uranium adsorption/desorption behavior, while modeling demonstrated that ambient hydrologic and geochemical conditions and heterogeneities in sediment physical and chemical properties both contributed to complex plume behavior and its persistence. This research underscores the great challenges in adequately characterizing this type of site to model the reactive transport processes over scales of 10 m or more. Our analysis provides important insights into the characterization, understanding, modeling, and remediation of groundwater contaminant plumes influenced by dynamic surface water and groundwater interactions.}
}
@article{ISI:000576786100009,
author = {Tso, Chak-Hau Michael and Johnson, Tim C. and Song, Xuehang and Chen,
Xingyuan and Kuras, Oliver and Wilkinson, Paul and Uhlemann, Sebastian
and Chambers, Jonathan and Binley, Andrew},
title = {Integrated hydrogeophysical modelling and data assimilation for
geoelectrical leak detection},
journal = {JOURNAL OF CONTAMINANT HYDROLOGY},
year = 2020,
volume = {234},
month = oct,
doi = {10.1016/j.jconhyd.2020.103679},
issn = {0169-7722},
abstract = {Time-lapse electrical resistivity tomography (ERT) measurements provide
indirectobservations of hydrological processes in the Earths shallow
subsurface at high spatial and temporal resolution. ERT has been used in
the past decades to detect leaks and monitor the evolution of associated
contaminant plumes. Specifically, inverted resistivity images allow
visualization of the dynamic changes in the structure of the plume.
However, existing methods do not allow the direct estimation of leak
parameters (e.g. leak rate, location, etc.) and their uncertainties. We
propose an ensemble-based data assimilation framework that evaluates
proposed hydrological models against observed time-lapse ERT
measurements without directly inverting for the resistivities. Each
proposed hydrological model is run through the parallel coupled
hydro-geophysical simulation code PFLOTRAN-E4D to obtain simulated ERT
measurements. The ensemble of model proposals is then updated using an
iterative ensemble smoother. We demonstrate the proposed framework on
synthetic and field ERT data from controlled tracer injection
experiments. Our results show that the approach allows joint
identification of contaminant source location, initial release time, and
solute loading from the cross-borehole time-lapse ERT data, alongside
with an assessment of uncertainties in these estimates. We demonstrate a
reduction in site-wide uncertainty by comparing the prior and posterior
plume mass discharges at a selected image plane. This framework is
particularly attractive to sites that have previously undergone
extensive geological investigation (e.g., nuclear sites). It is well
suited to complement ERT imaging and we discuss practical issues in its
application to field problems.}
}
@article{ISI:000562027400002,
author = {Fang, Yilin and Chen, Xingyuan and Velez, Jesus Gomez and Zhang, Xuesong and Duan, Zhuoran and Hammond, Glenn E. and Goldman, Amy E. and Garayburu-Caruso, Vanessa A. and Graham, Emily B.},
title = {A multirate mass transfer model to represent the interaction of multicomponent biogeochemical processes between surface water and hyporheic zones (SWAT-MRMT-R 1.0)},
journal = {GEOSCIENTIFIC MODEL DEVELOPMENT},
year = 2020,
volume = {13},
number = {8},
pages = {3553-3569},
month = aug,
abstract = {Surface water quality along river corridors can be modulated by
hyporheic zones (HZs) that are ubiquitous and biogeochemically active.
Watershed management practices often ignore the potentially important
role of HZs as a natural reactor. To investigate the effect of
hydrological exchange and biogeochemical processes on the fate of
nutrients in surface water and HZs, a novel model, SWAT-MRMT-R, was
developed coupling the Soil and Water Assessment Tool (SWAT) watershed
model and the reaction module from a flow and reactive transport code
(PFLOTRAN). SWAT-MRMT-R simulates concurrent nonlinear multicomponent
biogeochemical reactions in both the channel water and its surrounding
HZs, connecting the channel water and HZs through hyporheic exchanges
using multirate mass transfer (MRMT) representation. Within the model,
HZs are conceptualized as transient storage zones with distinguished
exchange rates and residence times. The biogeochemical processes within
HZs are different from those in the channel water. Hyporheic exchanges
are modeled as multiple first-order mass transfers between the channel
water and HZs. As a numerical example, SWAT-MRMT-R is applied to the
Hanford Reach of the Columbia River, a large river in the United States,
focusing on nitrate dynamics in the channel water. Major nitrate
contaminants entering the Hanford Reach include those from the legacy
waste, irrigation return flows (irrigation water that is not consumed by
crops and runs off as point sources to the stream), and groundwater
seepage resulting from irrigated agriculture. A two-step reaction
sequence for denitrification and an aerobic respiration reaction is
assumed to represent the biogeochemical transformations taking place
within the HZs. The spatially variable hyporheic exchange rates and
residence times in this example are estimated with the basin-scale
Networks with EXchange and Subsurface Storage (NEXSS) model. Our
simulation results show that (1), given a residence time distribution,
how the exchange fluxes to HZs are approximated when using MRMT can
significantly change the amount of nitrate consumption in HZs through
denitrification and (2) source locations of nitrate have a different
impact on surface water quality due to the spatially variable hyporheic
exchanges.},
doi = {10.5194/gmd-13-3553-2020},
issn = {1991-959X}
}
@article{ISI:000531051200016,
author = {Romano, Valentina and Bigi, Sabina and Carnevale, Francesco and Hyman, Jeffrey De'Haven and Karra, Satish and Valocchi, Albert J. and Tartarello, Maria Chiara and Battaglia, Maurizio},
title = {Hydraulic characterization of a fault zone from fracture distribution},
journal = {JOURNAL OF STRUCTURAL GEOLOGY},
year = 2020,
volume = {135},
month = jun,
abstract = {A quantitative assessment of how faults control the migration of
geofluids is critical in many areas of geosciences. We integrated
geological fieldwork, quantitative analysis of the fractures
distribution and numerical modeling to build a geometrical
representation of a fault zone and to characterize its hydraulic
properties. Our target is a fault located in the Majella Mountain
(Italy). We collected 21 scan lines across the fault profile in order to
characterize its architecture. The numerical modeling of the fracture
network of the damage zones and their hydraulic parameters was performed
using both commercial (Move (R)) and open source software (dfnWorks and
PFLOTRAN). Move (R) was used to build a representative model of the
fault zone using fracture spacing as a proxy, and to model the hydraulic
parameters of the different fault domains. dfnWorks and PFLOTRAN were
employed to infer the hydraulic parameters of the damage zones of the
fault and then upscale these properties to an equivalent continuum
domain, suitable for fluid flow simulations through the whole fault
zone. Our findings show how even in a relatively small area it is
possible to describe changes in terms of hydraulic properties of a fault
zone and to build models capable to represent these variations.},
doi = {10.1016/j.jsg.2020.104036},
issn = {0191-8141}
}
@article{ISI:000560371700036,
author = {Wallace, Corey D. and Sawyer, Audrey H. and Soltanian, Mohamad Reza and Barnes, Rebecca T.},
title = {Nitrate Removal Within Heterogeneous Riparian Aquifers Under Tidal Influence},
journal = {GEOPHYSICAL RESEARCH LETTERS},
year = 2020,
volume = {47},
number = {10},
month = may,
abstract = {Tides in coastal rivers drive river-groundwater (hyporheic) exchange and
provide opportunities for nitrate removal that may improve coastal water
quality. Silt and sand layers in coastal floodplain sediments can alter
the flow and transformation of nitrate. Our goal was to understand how
sediment heterogeneity influences nitrogen dynamics near tidal rivers.
Numerical simulations show that oxic, variably saturated sand layers and
anoxic, organic-rich silt layers are sites of nitrification and
denitrification, respectively. The exchange of river water and nitrate
through heterogeneous sediments increases with sand fraction, as sand
lenses become longer and more connected. The amount of nitrate removed
from river water also increases but represents a smaller portion of
total nitrate exchange through the hyporheic zone, causing removal
efficiency to decline. Our results suggest that accurate
characterization of aquifer heterogeneity leads to an improved
understanding of sites of nutrient transformation within floodplain
sediments.
Plain Language Summary Excess nitrate can degrade coastal water quality,
but microbial reactions reduce its concentration within the bed and
banks of tidal rivers, where surface water and groundwater mix. Spatial
arrangements of different sediments (sand and mud) affect the mixing of
river water and groundwater and thus affect nitrate removal. Here, we
use computer models to simulate nitrate transformation along a tidal
river with different amounts of coarse and fine sediments. Coarse
sediments promote groundwater flow and nitrate production, while fine
sediments promote nitrate removal. The amount of nitrate removed from
river water is greater in aquifers with coarser sediments, but the
removal efficiency decreases. Removal also varies with the spatial
distribution of sand and mud in sediments but to a lesser degree.
Computer models of nitrate transport should consider the distribution of
different sediment types.},
doi = {10.1029/2019GL085699},
issn = {0094-8276}
}
@article{https://doi.org/10.1029/2019WR026850,
author = {Yabusaki, Steven B. and Myers-Pigg, Allison N. and Ward, Nicholas D. and Waichler, Scott R. and Sengupta, Aditi and Hou, Zhangshuan and Chen, Xingyuan and Fang, Yilin and Duan, Zhuoran and Serkowski, John A. and Indivero, Julia and Wiese Moore, Cora and Gunn, Cailene M.},
title = {Floodplain Inundation and Salinization From a Recently Restored First-Order Tidal Stream},
journal = {Water Resources Research},
volume = {56},
number = {7},
pages = {e2019WR026850},
doi = {https://doi.org/10.1029/2019WR026850},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019WR026850},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2019WR026850},
abstract = {Abstract The systematic response of coastal ecosystems to inundation and salinity exposure is fundamental to their ecology and biogeochemical function. Here we observe and model freshwater-seawater interactions in a first-order stream—floodplain system where tidal access was recently restored. Subsurface flow and transport modeling were used to quantify and better understand the interplay of processes, properties, and conditions that control water level and salinity in the floodplain to the tidal stream. Water levels in the stream were highly correlated with tidal forcing, which resulted in episodic inundation of the floodplain at quasi-monthly frequency. The tidal stream is the only source of salinity to the floodplain, yet shallow groundwater salinity was considerably higher than average stream salinity. The low-permeability clay floodplain soils limit lateral groundwater flow and transport, resulting in floodplain groundwater and salinity dynamics driven almost exclusively by infiltration during inundation events. As inundation occurs during high tide, estuarine waters reach the floodplain with minor attenuation in salinity from the stream's freshwater discharge. Infiltration and salinity exposure are topography controlled and regulated by ponding depth and duration, seasonal ground saturation, and depth to water table. The model suggests that floodplain salinity is currently in an early stage of transition from pre-restoration freshwater conditions and will not reach equilibrium for ~20 years. These findings have broad relevance for understanding how and over what time scales coastal ecosystems will respond to increasing seawater exposure from sea level rise, ocean-originating storms, and changes in natural and man-made barriers.},
year = 2020
}
@article{ISI:000538987800029,
author = {Wallace, Corey D. and Sawyer, Audrey H. and Barnes, Rebecca T. and
Soltanian, Mohamad Reza and Gabor, Rachel S. and Wilkins, Michael J. and
Moore, Myles T.},
title = {A Model Analysis of the Tidal Engine That Drives Nitrogen Cycling in
Coastal Riparian Aquifers},
journal = {WATER RESOURCES RESEARCH},
year = 2020,
volume = {56},
number = {4},
month = apr,
abstract = {In coastal rivers, tides facilitate surface water-groundwater exchange
and strongly coupled nitrification-denitrification near the fluctuating
water table. We used numerical fluid flow and reactive transport models
to explore hydrogeologic and biogeochemical controls on nitrogen
transport along an idealized tidal freshwater zone based on field
observations from White Clay Creek, Delaware, USA. The capacity of the
riparian aquifer to remove nitrate depends largely on nitrate transport
rates, which initially increase with increasing tidal range but then
decline as sediments become muddier and permeability decreases. Over the
entire model reach, local nitrification provides a similar amount of
nitrate as surface and groundwater contributions combined. More than
half (similar to 66\%) of nitrate removed via denitrification is
produced in situ, while the vast majority of remaining nitrate removed
comes from groundwater sources. In contrast, average nitrate removal
from surface water due to tidal pumping amounts to only similar to 1\%
of the average daily in-channel riverine nitrate load or 1.77 kg of
nitrate along the reach each day. As a result, tidal bank storage zones
may not be major sinks for nitrate in coastal rivers but can act as
effective sinks for groundwater nitrate. By extension, tidal bank
storage zones provide a critical ecosystem service, reducing
contributions of groundwater nitrate, which is often derived from septic
tanks and fertilizers, to coastal rivers.
Plain Language Summary Nitrate is one of the most common pollutants and
can degrade coastal water quality. In the beds and banks of coastal
rivers, tides increase the mixing of river and groundwater, which
creates opportunities for nitrate production by nitrification and
removal by denitrification. It is unknown which process prevails along
tidal rivers and how these processes vary in strength as sediments
become muddier and tides become larger near the coast. In this study, we
used computer models to estimate rates of nitrate production and removal
and where they are greatest along tidal rivers. We found that nitrate is
ultimately removed from the aquifer, but that the majority of nitrate
removed is from nitrification near the water table and groundwater
sources. Although aquifers along tidal rivers are only marginally
effective at removing nitrate from river water, their ability to remove
groundwater nitrate is vital for maintaining coastal water quality.},
doi = {10.1029/2019WR025662},
issn = {0043-1397}
}
@article{ISI:000535672800040,
author = {Zachara, John M. and Chen, Xingyuan and Song, Xuehang and Shuai, Pin and Murray, Chris and Resch, C. Tom},
title = {Kilometer-Scale Hydrologic Exchange Flows in a Gravel Bed River Corridor and Their Implications to Solute Migration},
journal = {WATER RESOURCES RESEARCH},
year = 2020,
volume = {56},
number = {2},
month = feb,
abstract = {A well-characterized field site along a major, gravel bed river corridor
was used to investigate the dynamic pathways and impacts of subsurface
hydrogeologic structure on kilometer-scale hydrologic exchange flows
between river water and groundwater. An aqueous uranium (U-aq) plume
exists within a hyporheic alluvial aquifer at the site that discharges
to the Columbia River. We performed temporally intensive monitoring of
specific conductance (SpC) and U-aq concentrations within the plume for
a 2-year period at varying distances from the river shoreline, both
within and outside a presumed subsurface pathway of lateral hydrologic
exchange. SpC and U-aq were utilized as in situ tracers of hydrologic
exchange and associated groundwater-surface water mixing. Seasonal river
stage variations by more than 2 m caused distinct events of river water
intrusion and retreat from the nearshore, hyporheic alluvial aquifer,
resulting in highly dynamic SpC and U-aq patterns in monitoring wells.
Simulations of hydrologic exchange and mixing were performed with
PFLOTRAN to understand the observed SpC and U-aq behaviors linked to
predominant flow directions and velocities in the river corridor as
influenced by river stage dynamics and variable aquitard topography. By
coupling robust monitoring with numerical flow and transport modeling,
we demonstrate complicated multidirectional flow behaviors at the
kilometer scale that strongly influenced plume dynamics. Therefore,
hyporheic aquifer must be frequently monitored under different flow
conditions if water quality is of concern. The resulting hydrologic
understanding enables improved interpretation of hydrogeochemical data
from this site and other large gravel bed river corridors in the United
States and elsewhere.},
doi = {10.1029/2019WR025258},
issn = {0043-1397}
}
@article{ISI:000500371200024,
author = {Yang, Chen and Zheng, Fei and Liu, Yuanyuan and Zhang, You-Kuan and Liu, Wei and Zhang, Qiang and Yang, Xiaofan},
title = {Modeling hydro-biogeochemical transformation of chromium in hyporheic
zone: Effects of spatial and temporal resolutions},
journal = {JOURNAL OF HYDROLOGY},
year = 2019,
volume = {579},
month = dec,
abstract = {Effects of spatial and temporal resolutions (SR and TR) on modeling
hydro-biogeochemical transformation of chromium (Cr) are important in
simulating reactive transport processes. The current study was conducted
in the hyporheic zone (HZ) at the Hanford Site of the U.S. Department of
Energy, which has been known for its highly heterogeneous sediments and
transient hydrodynamics. Distributions of hydraulic conductivity and
sediment-associated Fe concentration were averaged at a group of SRs,
while measured hourly water levels were further moving averaged at daily
and monthly TRs. Fe concentration is selected for assembling geochemical
heterogeneity due to its important role in redox transformation of Cr at
the site. Three Fe distributions, with Fe concentrated on small, medium,
and large sediment grains, respectively, were also considered. A series
of flow and reactive transport simulations configured with different
combinations of SRs, TRs, and Fe distributions were conducted. Simulated
results revealed that Cr(VI) discharged to river is underestimated if SR
decreases. For both the hydrodynamics and the discharge of Cr(VI) to
river, difference caused by SR can be amplified with the decrease of TR.
Biogeochemical transformation of Cr is more dependent on SR while
hydrodynamics is on TR. The stronger control of SR than TR on
biogeochemical transformation of Cr is resulted from more sensitive
increase of Fe(II) with decreasing SR than with decreasing TR. Effect of
SR is highly sensitive to variations of SR with Fe on medium-size grains
while is persistent to a much smaller SR with Fe on small-size grains.
Results from the current study are expected to benefit modelers on the
selections of the spatial-temporal resolutions for in-house modeling and
field sampling, which may also have implications for upscaling.},
doi = {10.1016/j.jhydrol.2019.124152},
issn = {0022-1694}
}
@article{IRAOLA201912,
title = {Assessing dual continuum method for multicomponent reactive transport},
journal = {Computers & Geosciences},
volume = {130},
pages = {11 - 19},
year = {2019},
issn = {0098-3004},
doi = {https://doi.org/10.1016/j.cageo.2019.05.007},
url = {http://www.sciencedirect.com/science/article/pii/S0098300418307982},
author = {A. Iraola and P. Trinchero and S. Karra and J. Molinero},
keywords = {Fractured media, Matrix diffusion, Dual continuum formulation, Reactive transport},
abstract = {The subsurface flow and reactive transport code PFLOTRAN can accommodate fractureâmatrix interaction for multicomponent reactive transport using a Dual Continuum formulation. In this work we present two examples to assess this approach. Through these examples, we also illustrate how this Dual Continuum model can be parameterised and what kind of grid spacing is needed to accurately capture reactive transport in the secondary continuum. The results of the calculations show that when geochemical reactions in the matrix (or the secondary continuum) are included, a very fine grid spacing close to the fractureâmatrix interface is required to properly capture geochemical gradients at the interface. We also show that one can reduce the computational cost by using a variable grid spacing, that limits the total number in the secondary continuum, and yet obtain accurate results. This feature makes the Dual Continuum approach suitable for large-scale reactive transport modelling in fractured crystalline rock.}
}
@article{ISI:000490973700048,
author = {Tso, Chak-Hau Michael and Kuras, Oliver and Binley, Andrew},
title = {On the Field Estimation of Moisture Content Using Electrical Geophysics:
The Impact of Petrophysical Model Uncertainty},
journal = {WATER RESOURCES RESEARCH},
year = 2019,
volume = {55},
number = {8},
pages = {7196-7211},
month = aug,
abstract = {The spatiotemporal distribution of pore water in the vadose zone can
have a critical control on many processes in the near-surface Earth,
such as the onset of landslides, crop yield, groundwater recharge, and
runoff generation. Electrical geophysics has been widely used to monitor
the moisture content (theta) distribution in the vadose zone at field
sites, and often resistivity (rho) or conductivity (sigma) is converted
to moisture contents through petrophysical relationships (e.g., Archie's
law). Though both the petrophysical relationships (i.e., choices of
appropriate model and parameterization) and the derived moisture content
are known to be subject to uncertainty, they are commonly treated as
exact and error-free. This study examines the impact of uncertain
petrophysical relationships on the moisture content estimates derived
from electrical geophysics. We show from a collection of data from
multiple core samples that significant variability in the theta (rho)
relationship can exist. Using rules of error propagation, we demonstrate
the combined effect of inversion and uncertain petrophysical
parameterization on moisture content estimates and derive their
uncertainty bounds. Through investigation of a water injection
experiment, we observe that the petrophysical uncertainty yields a large
range of estimated total moisture volume within the water plume. The
estimates of changes in water volume, however, generally agree within
(large) uncertainty bounds. Our results caution against solely relying
on electrical geophysics to estimate moisture content in the field. The
uncertainty propagation approach is transferrable to other field studies
of moisture content estimation.
Plain Language Summary Maps and images of electrical resistivity have
been widely applied to effectively monitor the wetting or drying of the
Earths' near-surface. But how well can they quantify such change? How
variable are the petrophysical model parameters that relate resistivity
and moisture content? Does uncertainty in such relationships impact our
confidence in moisture content estimates from resistivity imaging? Our
analysis of field samples collected at a U.K. field site reveals great
variability in petrophysical parameters. Using an uncertainty
propagation method, which combines the uncertainty contributions from
both petrophysical parameters and resistivity data errors, we find that
the variable petrophysical parameters can lead to high uncertainty in
moisture content estimates and they appear to be the dominating factor
in many cases. These effects on uncertainty are greater than previously
appreciated. The implication is that realistic uncertainty bounds are
needed whenever electrical geophysical methods are used to quantify the
amount of water present underground or its changes over time. The
findings highlight the importance of better characterization of
petrophysical parameters and the need to supplement the interpretation
of resistivity-based moisture content estimates with other data sources.},
doi = {10.1029/2019WR024964},
issn = {0043-1397}
}
@article{doi:10.1029/2018WR024193,
author = {Shuai, Pin and Chen, Xingyuan and Song, Xuehang and Hammond, Glenn E. and Zachara, John and Royer, Patrick and Ren, Huiying and Perkins, William A. and Richmond, Marshall C. and Huang, Maoyi},
title = {Dam Operations and Subsurface Hydrogeology Control Dynamics of Hydrologic Exchange Flows in a Regulated River Reach},
journal = {Water Resources Research},
volume = {55},
number = {4},
pages = {2593-2612},
keywords = {River corridor, Hydrologic exchange, Dam regulation, Surface water-groundwater interactions, Subsurface hydrogeology, Channel morphology},
doi = {10.1029/2018WR024193},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018WR024193},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2018WR024193},
abstract = {Abstract Hydrologic exchange flows (HEFs) across the river-aquifer interface have important implications for biogeochemical processes and contaminant plume migration in the river corridor, yet little is known about the hydrogeomorphic factors that control HEFs dynamics under dynamic flow conditions. Here, we developed a 3-D numerical model for a large regulated river corridor along the Columbia River to study how HEFs are controlled by the interplays between dam-regulated flow conditions and hydrogeomorphic features of such river corridor system. Our results revealed highly variable intra-annual spatiotemporal patterns in HEFs along the 75-km river reach, as well as strong interannual variability with larger exchange volumes in wet years than dry years. In general, the river was losing during late spring to early summer when the river stage was high, and river was gaining in fall and winter when river stage was low. The magnitude and timing of river stage fluctuations controlled the timing of high exchange rates. Both river channel geomorphology and the thickness of a highly permeable river bank geologic layer controlled the locations of exchange hot spots, while the latter played a dominant role. Dam-induced, subdaily to daily river stage fluctuations drove high-frequency variations in HEFs across the river-aquifer interfaces, resulting in greater overall exchange volumes as compared to the case without high-frequency flows. Our results demonstrated that upstream dam operations enhanced the exchange between river water and groundwater with strong potential influence on the associated biogeochemical processes and on the fate and transport of groundwater contaminant plumes in such river corridors.},
year = 2019
}
@article{Poonoosamy2018,
author = {Poonoosamy, J.
and Wanner, C.
and Alt Epping, P.
and {\'A}guila, J. F.
and Samper, J.
and Montenegro, L.
and Xie, M.
and Su, D.
and Mayer, K. U.
and M{\"a}der, U.
and Van Loon, L. R.
and Kosakowski, G.},
title = {Benchmarking of reactive transport codes for 2D simulations with mineral dissolution--precipitation reactions and feedback on transport parameters},
journal = {Computational Geosciences},
year = {2018},
month = nov,
day = {19},
abstract = {Porosity changes due to mineral dissolution--precipitation reactions in porous media and the resulting impact on transport parameters influence the evolution of natural geological environments or engineered underground barrier systems. In the absence of long-term experimental studies, reactive transport codes are used to evaluate the long-term evolution of engineered barrier systems and waste disposal in the deep underground. Examples for such problems are the long-term fate of CO2 in saline aquifers and mineral transformations that cause porosity changes at clay--concrete interfaces. For porosity clogging under a diffusive transport regime and for simple reaction networks, the accuracy of numerical codes can be verified against analytical solutions. For clogging problems with more complex chemical interactions and transport processes, numerical benchmarks are more suitable to assess model performance, the influence of thermodynamic data, and sensitivity to the reacting mineral phases. Such studies increase confidence in numerical model descriptions of more complex, engineered barrier systems. We propose a reactive transport benchmark, considering the advective--diffusive transport of solutes; the effect of liquid-phase density on liquid flow and advective transport; kinetically controlled dissolution--precipitation reactions causing porosity, permeability, and diffusivity changes; and the formation of a solid solution. We present and analyze the results of five participating reactive transport codes (i.e., CORE2D, MIN3P-THCm, OpenGeoSys-GEM, PFLOTRAN, and TOUGHREACT). In all cases, good agreement of the results was obtained.},
issn = {1573-1499},
doi = {10.1007/s10596-018-9793-x},
url = {https://doi.org/10.1007/s10596-018-9793-x}
}
@article{ISI:000447091100001,
author = {Bisht, Gautam and Riley, William J. and Hammond, Glenn E. and
Lorenzetti, David M.},
title = {Development and evaluation of a variably saturated flow model in the
global E3SM Land Model (ELM) version 1.0},
journal = {GEOSCIENTIFIC MODEL DEVELOPMENT},
year = 2018,
volume = {11},
number = {10},
pages = {4085-4102},
month = oct,
abstract = {Improving global-scale model representations of near-surface soil
moisture and groundwater hydrology is important for accurately
simulating terrestrial processes and predicting climate change effects
on water resources. Most existing land surface models, including the
default E3SM Land Model (ELMv0), which we modify here, routinely employ
different formulations for water transport in the vadose and phreatic
zones. Clark et al. (2015) identified a variably saturated Richards
equation flow model as an important capability for improving simulation
of coupled soil moisture and shallow groundwater dynamics. In this work,
we developed the Variably Saturated Flow Model (VSFM) in ELMv1 to unify
the treatment of soil hydrologic processes in the unsaturated and
saturated zones. VSFM was tested on three benchmark problems and results
were evaluated against observations and an existing benchmark model
(PFLOTRAN). The ELMv1-VSFM's subsurface drainage parameter, f(d), was
calibrated to match an observationally constrained and spatially
explicit global water table depth (WTD) product. Optimal spatially
explicit f(d) values were obtained for 79\% of global 1.9 degrees x 2.5
degrees grid cells, while the remaining 21\% of global grid cells had
predicted WTD deeper than the observationally constrained estimate.
Comparison with predictions using the default f(d) value demonstrated
that calibration significantly improved predictions, primarily by
allowing much deeper WTDs. Model evaluation using the International Land
Model Benchmarking package (ILAMB) showed that improvements in WTD
predictions did not degrade model skill for any other metrics. We
evaluated the computational performance of the VSFM model and found that
the model is about 30\% more expensive than the default ELMv0 with an
optimal processor layout. The modular software design of VSFM not only
provides flexibility to configure the model for a range of problem
setups but also allows for building the model independently of the ELM
code, thus enabling straightforward testing of the model's physics
against other models.},
doi = {10.5194/gmd-11-4085-2018},
issn = {1991-959X},
eissn = {1991-9603},
researcherid-numbers = {Bisht, Gautam/P-4043-2019
Bisht, Gautam/J-4822-2014},
orcid-numbers = {Bisht, Gautam/0000-0001-6641-7595
Bisht, Gautam/0000-0001-6641-7595},
unique-id = {ISI:000447091100001}
}
@article{ISI:000450726000072,
author = {Dwivedi, Dipankar and Steefel, Carl I. and Arora, Bhavna and Newcomer,
Michelle and Moulton, J. David and Dafflon, Baptiste and Faybishenko,
Boris and Fox, Patricia and Nico, Peter and Spycher, Nicolas and
Carroll, Rosemary and Williams, Kenneth H.},
title = {Geochemical Exports to River From the Intrameander Hyporheic Zone Under
Transient Hydrologic Conditions: East River Mountainous Watershed,
Colorado},
journal = {WATER RESOURCES RESEARCH},
year = 2018,
volume = {54},
number = {10},
pages = {8456-8477},
month = oct,
abstract = {To understand how redox processes influence carbon, nitrogen, and iron
cycling within the intrameander hyporheic zone, we developed a biotic
and abiotic reaction network and incorporated it into the reactive
transport simulator PFLOTRAN. Two-dimensional reactive flow and
transport simulations were performed (1) to evaluate how transient
hydrological conditions control the lateral redox zonation within an
intrameander region of the East River in Colorado and (2) to quantify
the impact of a single meander on subsurface exports of carbon and other
geochemical species to the river. The meander's overall contribution to
the river was quantified by integrating geochemical outfluxes along the
outside of the meander bend. The model was able to capture the
field-observed trends of dissolved oxygen, nitrate, iron, pH, and total
inorganic carbon along a 2-D transect. Consistent with field
observations, simulated dissolved oxygen and nitrate decreased along the
intrameander flow paths while iron (Fe2+) concentration increased. The
simulation results further demonstrated that the reductive potential of
the lateral redox zonation was controlled by groundwater velocities
resulting from river stage fluctuations, with low-water conditions
promoting reducing conditions. The sensitivity analysis results showed
that permeability had a more significant impact on biogeochemical
zonation compared to the reaction pathways under transient hydrologic
conditions. The simulation results further indicated that the meander
acted as a sink for organic and inorganic carbon as well as iron during
the extended baseflow and high-water conditions; however, these
geochemical species were released into the river during the falling limb
of the hydrograph.
Plain Language Summary Hyporheic zones perform important ecological
functions by linking terrestrial and aquatic systems within watersheds.
Hyporheic zones can act as a source or sink for various metals and
nutrients. Transient hydrologic conditions alter redox conditions within
an intrameander hyporheic zone thus affecting the behavior of
redox-sensitive species. Here we investigate how transient hydrological
conditions control the lateral redox zonation within an intrameander
region of the East River and examine the contribution of a single
meander on subsurface exports of carbon, iron, and other geochemical
species to the river. The simulation results show that exports of carbon
and iron are primarily hydrologically driven, yet depend upon
intermittent oxic and reductive conditions resulting from river stage
fluctuations. In addition, the net exports of different geochemical
species increase as the river stage decreases. This study demonstrates
the importance of including hydrologic transients, using a modern
reactive transport approach, to quantify exports within the intrameander
hyporheic zone at the riverine scale.},
doi = {10.1029/2018WR023377},
issn = {0043-1397}
}
@article{ISI:000442502100006,
author = {Huang, Kun and Liu, Yuanyuan and Yang, Chen and Duan, Yanhua and Yang,
Xiaofan and Liu, Chongxuan},
title = {Identification of Hydrobiogeochemical Processes Controlling Seasonal
Variations in Arsenic Concentrations Within a Riverbank Aquifer at
Jianghan Plain, China},
journal = {WATER RESOURCES RESEARCH},
year = 2018,
volume = {54},
number = {7},
pages = {4294-4308},
month = jul,
abstract = {The arsenic concentration in groundwater varies significantly with time
and space in groundwater-surface water exchange zones. Various processes
have been identified that control arsenic concentration distribution and
mobility in laboratory systems. However, it is still challenging to
identify important processes controlling arsenic concentration
distribution at the field scale due to the complex coupling of
hydrobiogeochemical processes. In this study, a reactive flow and
transport model was used to identify dominant processes controlling
arsenic distribution and seasonal variations in groundwater-surface
water exchange zones using Jianghan Plain, China, as an example. The
results revealed the importance of river water and groundwater
interactions on seasonal changes in arsenic concentration; however, the
affected region is limited to within 50-m distance to the river. The
modeling results, unexpectedly, revealed the predominant importance of
groundwater extraction to the seasonal variation in arsenic
concentration. The groundwater extraction changed the groundwater flow
pattern and induced vertical leakage of oxygen-containing surface water
into the aquifer, which triggered a series of biogeochemical reactions
that changed groundwater redox conditions and promoted arsenic sorption,
resulting in a rapid decrease in arsenic concentrations in groundwater.
After groundwater extraction ceased, aquifer recovered to anoxic
condition, promoting arsenic release from the sorbed phase, leading to a
rapid rebounding in groundwater arsenic concentrations. Overall, this
study provided a tool to identify coupled hydrobiogeochemical processes
on arsenic spatiotemporal distribution and migration in groundwater.},
doi = {10.1029/2017WR022170},
issn = {0043-1397}
}
@article{ISI:000429329800006,
author = {Newell, Dennis L. and Carey, J. William and Backhaus, Scott N. and
Lichtner, Peter},
title = {Experimental study of gravitational mixing of supercritical CO2},
journal = {INTERNATIONAL JOURNAL OF GREENHOUSE GAS CONTROL},
year = 2018,
volume = {71},
pages = {62-73},
month = apr,
abstract = {CO2 injection into saline aquifers for sequestration will initially
result in buoyant supercritical (sc) CO2 trapped beneath the caprock
seal. During this period, there is risk of CO2 migration out of the
reservoir along wellbore defects or fracture zones. Dissolution of the
scCO(2) plume into brine results in solubility trapping and reduces this
risk, but based on diffusion alone, this mechanism could take thousands
of years. Gravitational (density-induced) mixing of CO2-saturated brine
is shown to significantly accelerate this process in computational
studies, but few experimental efforts have confirmed the phenomenon.
Here, constant-pressure, 3-dimensional bench-scale experiments used the
mass of added water to quantify the mass transfer of scCO(2) into
water-saturated porous media at 40-90 degrees C and 20 MPa, with
Rayleigh numbers from 2093 to 16256. Experiments exhibit a period of
7-35X enhancement in mass transfer rates over diffusion, interpreted as
gravitational mixing. Convective CO2 flux ranges from 1.6 x 10(-2) to
4.8 x 10(-3) mol s(-1) m(-2) in the experiments. Results are used to
benchmark a computational model using PFLOTRAN. Experiments show an
early diffusive onset period that is shorter with rates much higher than
predicted by models and observed in analog experiments. Both experiments
and models show convective mixing periods and similar overall rates of
CO2 mass transfer.},
doi = {10.1016/j.ijggc.2018.02.013},
issn = {1750-5836},
eissn = {1878-0148},
unique-id = {ISI:000429329800006}
}
@article{ISI:000424726000034,
author = {Tutolo, Benjamin M. and Luhmann, Andrew J. and Tosca, Nicholas J. and
Seyfried, Jr., William E.},
title = {Serpentinization as a reactive transport process: The brucite
silicification reaction},
journal = {EARTH AND PLANETARY SCIENCE LETTERS},
year = 2018,
volume = {484},
pages = {385-395},
month = feb,
abstract = {Serpentinization plays a fundamental role in the biogeochemical and
tectonic evolution of the Earth and perhaps many other rocky planetary
bodies. Yet, geochemical models still fail to produce accurate
predictions of the various modes of serpentinization, which limits our
ability to predict a variety of related geological phenomena over many
spatial and temporal scales. Here, we use kinetic and reactive transport
experiments to parameterize the brucite silicification reaction and
provide fundamental constraints on SiO2 transport during
serpentinization. We show that, at temperatures characteristic of the
sub-seafloor at the serpentinite-hosted Lost City Hydrothermal Field
(150 degrees C), the assembly of Si tetrahedra onto MgOH2 (i.e.,
brucite) surfaces is a rate-limiting elementary reaction in the
production of serpentine and/or talc from olivine. Moreover, this
reaction is exponentially dependent on the activity of aqueous silica
(a(SiO2(aq))), such that it can be calculated according to the rate law:
Rate = 2.3 x 10(-4)a(SiO2(aq))(1.5) (mol/m(2)/s).
Calculations performed with this rate law demonstrate that both brucite
and Si are surprisingly persistent in serpentinizing environments,
leading to elevated Si concentrations in fluids that can be transported
over comparatively large distances without equilibrating with brucite.
Moreover, applying this rate law to an open-system reactive transport
experiment indicates that advection, preferential flow pathways, and
reactive surface area armoring can diminish the net rate of Si uptake
resulting from this reaction even further. Because brucite
silicification is a fundamentally rate-limiting elementary reaction for
the production of both serpentine and talc from forsterite, our new
constraints are applicable across the many environments where
serpentinization occurs. The unexpected but highly consequential
behavior of this simple reaction emphasizes the need for considering
serpentinization and many other hydrothermal processes in a reactive
transport framework whereby fluid, solute, and heat transport are
intimately coupled to kinetically-controlled reactions. (C) 2017
Elsevier B.V. All rights reserved.},
doi = {10.1016/j.epsl.2017.12.029},
issn = {0012-821X},
eissn = {1385-013X},
orcid-numbers = {Tosca, Nicholas/0000-0003-4415-4231
Tutolo, Benjamin/0000-0002-3047-8828},
unique-id = {ISI:000424726000034}
}
@article{ISI:000428474500040,
author = {Birdsell, Daniel T. and Karra, Satish and Rajaram, Harihar},
title = {On the Representation of the Porosity-Pressure Relationship in General
Subsurface Flow Codes},
journal = {WATER RESOURCES RESEARCH},
year = 2018,
volume = {54},
number = {2},
pages = {1382-1388},
month = feb,
abstract = {The governing equations for subsurface flow codes in a deformable porous
media are derived from the balance of fluid mass and Darcy's equation.
One class of these codes, which we call general subsurface flow codes
(GSFs), allow for more general constitutive relations for material
properties such as porosity, permeability and density. Examples of GSFs
include PFLOTRAN, FEHM, TOUGH2, STOMP, and some reservoir simulators
such as BOAST. Depending on the constitutive relations used in GSFs, an
inconsistency arises between the standard groundwater flow equation and
the governing equation of GSFs, and we clarify that the reason for this
inconsistency is because the Darcy's equation used in the GSFs should
account for the velocity of fluid with respect to solid. Due to lack of
awareness of this inconsistency, users of the GSFs tend to use a
porosity-pressure relationship that comes from the standard groundwater
flow equation and assumes that the relative velocity is already
accounted for. For the Theis problem, we show that using this
traditional relationship in the GSFs leads to significantly large
errors. We propose an alternate porosity-pressure relationship that is
consistent with the derivation of the governing equations in the GSFs
where the solid velocity is not tracked, and show that, with this
relationship, the results are more accurate for the Theis problem. The
purpose of this note is to make the users and developers of these GSFs
aware of this inconsistency and to advocate that the alternate porosity
model derived here should be incorporated in GSFs.},
doi = {10.1002/2017WR022001},
issn = {0043-1397},
eissn = {1944-7973},
orcid-numbers = {Birdsell, Daniel/0000-0002-1896-4938
RAJARAM, HARIHAR/0000-0003-2040-358X},
unique-id = {ISI:000428474500040}
}
@article{MUDUNURU2017192,
title = {Regression-based reduced-order models to predict transient thermal output for enhanced geothermal systems},
journal = {Geothermics},
volume = {70},
pages = {192-205},
year = {2017},
issn = {0375-6505},
doi = {https://doi.org/10.1016/j.geothermics.2017.06.013},
url = {https://www.sciencedirect.com/science/article/pii/S0375650517302249},
author = {M.K. Mudunuru and S. Karra and D.R. Harp and G.D. Guthrie and H.S. Viswanathan},
keywords = {Enhanced geothermal systems (EGS), Reduced-order models (ROMs), Thermal drawdown, Regression},
abstract = {Reduced-order modeling is a promising approach, as many phenomena can be described by a few parameters/mechanisms. An advantage and attractive aspect of a reduced-order model is that it is computational inexpensive to evaluate when compared to running a high-fidelity numerical simulation. A reduced-order model takes couple of seconds to run on a laptop while a high-fidelity simulation may take couple of hours to run on a high-performance computing cluster. The goal of this paper is to assess the utility of regression-based reduced-order models (ROMs) developed from high-fidelity numerical simulations for predicting transient thermal power output for an enhanced geothermal reservoir while explicitly accounting for uncertainties in the subsurface system and site-specific details. Numerical simulations are performed based on equally spaced values in the specified range of model parameters. Key sensitive parameters are then identified from these simulations, which are fracture zone permeability, well/skin factor, bottom hole pressure, and injection flow rate. We found the fracture zone permeability to be the most sensitive parameter. The fracture zone permeability along with time, are used to build regression-based ROMs for the thermal power output. The ROMs are trained and validated using detailed physics-based numerical simulations. Finally, predictions from the ROMs are then compared with field data. We propose three different ROMs with different levels of model parsimony, each describing key and essential features of the power production curves. The coefficients in the proposed regression-based ROMs are developed by minimizing a non-linear least-squares misfit function using the Levenberg–Marquardt algorithm. The misfit function is based on the difference between numerical simulation data and reduced-order model. ROM-1 is constructed based on polynomials up to fourth order. ROM-1 is able to accurately reproduce the power output of numerical simulations for low values of permeabilities and certain features of the field-scale data. ROM-2 is a model with more analytical functions consisting of polynomials up to order eight, exponential functions and smooth approximations of Heaviside functions, and accurately describes the field-data. At higher permeabilities, ROM-2 reproduces numerical results better than ROM-1, however, there is a considerable deviation from numerical results at low fracture zone permeabilities. ROM-3 consists of polynomials up to order ten, and is developed by taking the best aspects of ROM-1 and ROM-2. ROM-1 is relatively parsimonious than ROM-2 and ROM-3, while ROM-2 overfits the data. ROM-3 on the other hand, provides a middle ground for model parsimony. Based on R2-values for training, validation, and prediction data sets we found that ROM-3 is better model than ROM-2 and ROM-1. For predicting thermal drawdown in EGS applications, where high fracture zone permeabilities (typically greater than 10−15 m2) are desired, ROM-2 and ROM-3 outperform ROM-1. As per computational time, all the ROMs are 104 times faster when compared to running a high-fidelity numerical simulation. This makes the proposed regression-based ROMs attractive for real-time EGS applications because they are fast and provide reasonably good predictions for thermal power output.}
}
@article{https://doi.org/10.1002/sam.11356,
author = {Mudunuru, Maruti Kumar and Karra, Satish and Makedonska, Nataliia and Chen, Ting},
title = {Sequential geophysical and flow inversion to characterize fracture networks in subsurface systems},
journal = {Statistical Analysis and Data Mining: The ASA Data Science Journal},
volume = {10},
number = {5},
pages = {326-342},
keywords = {clustering analysis, elbow method, flow, fracture, geophysics, k-means clustering, Latin hypercube sampling, multiple datastreams, sequential inversion, subsurface modeling},
doi = {https://doi.org/10.1002/sam.11356},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/sam.11356},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/sam.11356},
abstract = {Subsurface applications, including geothermal, geological carbon sequestration, and oil and gas, typically involve maximizing either the extraction of energy or the storage of fluids. Fractures form the main pathways for flow in these systems, and locating these fractures is critical for predicting flow. However, fracture characterization is a highly uncertain process, and data from multiple sources, such as flow and geophysical are needed to reduce this uncertainty. We present a nonintrusive, sequential inversion framework for integrating data from geophysical and flow sources to constrain fracture networks in the subsurface. In this framework, we first estimate bounds on the statistics for the fracture orientations using microseismic data. These bounds are estimated through a combination of a focal mechanism (physics-based approach) and clustering analysis (statistical approach) of seismic data. Then, the fracture lengths are constrained using flow data. The efficacy of this inversion is demonstrated through a representative example.},
year = {2017}
}
@article{https://doi.org/10.1002/hyp.11214,
author = {Thomas, Matthew A. and Kuhlman, Kristopher L. and Ward, Anderson L.},
title = {Anthropogenic influences on groundwater in the vicinity of a long-lived radioactive waste repository},
journal = {Hydrological Processes},
volume = 31,
number = 14,
pages = {2637-2647},
keywords = {hydrogeology, land use, numerical modeling, transient phenomena, transuranic waste disposal},
doi = {https://doi.org/10.1002/hyp.11214},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hyp.11214},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/hyp.11214},
abstract = {Abstract The groundwater flow system in the Culebra Dolomite Member (Culebra) of the Permian Rustler Formation is a potential radionuclide release pathway from the Waste Isolation Pilot Plant (WIPP), the only deep geological repository for transuranic waste in the United States. In early conceptual models of the Culebra, groundwater levels were not expected to fluctuate markedly, except in response to long-term climatic changes, with response times on the order of hundreds to thousands of years. Recent groundwater pressures measured in monitoring wells record more than 25 m of drawdown. The fluctuations are attributed to pumping activities at a privately owned well that may be associated with the demand of the Permian Basin hydrocarbon industry for water. The unprecedented magnitude of drawdown provides an opportunity to quantitatively assess the influence of unplanned anthropogenic forcings near the WIPP. Spatially variable realizations of Culebra saturated hydraulic conductivity and specific storage were used to develop groundwater flow models to estimate a pumping rate for the private well and investigate its effect on advective transport. Simulated drawdown shows reasonable agreement with observations (average Model Efficiency coefficient = 0.7). Steepened hydraulic gradients associated with the pumping reduce estimates of conservative particle travel times across the domain by one half and shift the intersection of the average particle track with the compliance boundary by more than 2 km. The value of the transient simulations conducted for this study lies in their ability to (a) improve understanding of the Culebra groundwater flow system and (b) challenge the notion of time-invariant land use in the vicinity of the WIPP.},
year = 2017
}
@article{ISI:000418215100002,
author = {Iraola, Aitor and Trinchero, Paolo and Voutilainen, Mikko and Gylling,
Bjorn and Selroos, Jan-Olof and Molinero, Jorge and Svensson, Urban and
Bosbach, Dirk and Deissmann, Guido},
title = {Microtomography-based Inter-Granular Network for the simulation of
radionuclide diffusion and sorption in a granitic rock},
journal = {JOURNAL OF CONTAMINANT HYDROLOGY},
year = 2017,
volume = {207},
pages = {8-16},
month = dec,
abstract = {Field investigation studies, conducted in the context of safety analyses
of deep geological repositories for nuclear waste, have pointed out that
in fractured crystalline rocks sorbing radionuclides can diffuse
surprisingly long distances deep into the intact rock matrix; i.e. much
longer distances than those predicted by reactive transport models based
on a homogeneous description of the properties of the rock matrix. Here,
we focus on cesium diffusion and use detailed micro characterisation
data, based on micro computed tomography, along with a grain-scale
Inter-Granular Network model, to offer a plausible explanation for the
anomalously long cesium penetration profiles observed in these in-situ
experiments. The sparse distribution of chemically reactive grains (i.e.
grains belonging to sorbing mineral phases) is shown to have a strong
control on the diffusive patterns of sorbing radionuclides. The computed
penetration profiles of cesium agree well with an analytical model based
on two parallel diffusive pathways. This agreement, along with visual
inspection of the spatial distribution of cesium concentration,
indicates that for sorbing radionuclides the medium indeed behaves as a
composite system, with most of the mass being retained close to the
injection boundary and a non-negligible part diffusing faster along
preferential diffusive pathways.},
doi = {10.1016/j.jconhyd.2017.10.003},
issn = {0169-7722},
eissn = {1873-6009},
orcid-numbers = {Voutilainen, Mikko/0000-0002-5534-149X
Trinchero, Paolo/0000-0003-1351-2788
Deissmann, Guido/0000-0001-6039-9533},
unique-id = {ISI:000418215100002}
}
@article{TRINCHERO201760,
title = {Continuum-based DFN-consistent numerical framework for the simulation of oxygen infiltration into fractured crystalline rocks},
journal = {Journal of Contaminant Hydrology},
volume = {200},
pages = {60 - 69},
year = {2017},
issn = {0169-7722},
doi = {https://doi.org/10.1016/j.jconhyd.2017.04.001},
url = {http://www.sciencedirect.com/science/article/pii/S0169772216302509},
author = {Paolo Trinchero and Ignasi Puigdomenech and Jorge Molinero and Hedieh Ebrahimi and Björn Gylling and Urban Svensson and Dirk Bosbach and Guido Deissmann},
keywords = {High performance reactive transport modelling, Oxygen intrusion, DFN-derived parameters},
abstract = {We present an enhanced continuum-based approach for the modelling of groundwater flow coupled with reactive transport in crystalline fractured rocks. In the proposed formulation, flow, transport and geochemical parameters are represented onto a numerical grid using Discrete Fracture Network (DFN) derived parameters. The geochemical reactions are further constrained by field observations of mineral distribution. To illustrate how the approach can be used to include physical and geochemical complexities into reactive transport calculations, we have analysed the potential ingress of oxygenated glacial-meltwater in a heterogeneous fractured rock using the Forsmark site (Sweden) as an example. The results of high-performance reactive transport calculations show that, after a quick oxygen penetration, steady state conditions are attained where abiotic reactions (i.e. the dissolution of chlorite and the homogeneous oxidation of aqueous iron(II) ions) counterbalance advective oxygen fluxes. The results show that most of the chlorite becomes depleted in the highly conductive deformation zones where higher mineral surface areas are available for reactions.}
}
@article{ISI:000417851000001,
author = {Bisht, Gautam and Huang, Maoyi and Zhou, Tian and Chen, Xingyuan and
Dai, Heng and Hammond, Glenn E. and Riley, William J. and Downs, Janelle
L. and Liu, Ying and Zachara, John M.},
title = {Coupling a three-dimensional subsurface flow and transport model with a
land surface model to simulate stream-aquifer-land interactions (CP
v1.0)},
journal = {GEOSCIENTIFIC MODEL DEVELOPMENT},
year = 2017,
volume = {10},
number = {12},
pages = {4539-4562},
month = dec,
abstract = {A fully coupled three-dimensional surface and subsurface land model is
developed and applied to a site along the Columbia River to simulate
three-way interactions among river water, groundwater, and land surface
processes. The model features the coupling of the Community Land Model
version 4.5 (CLM4.5) and a massively parallel multiphysics reactive
transport model (PFLOTRAN). The coupled model, named CP v1.0, is applied
to a 400m x 400m study domain instrumented with groundwater monitoring
wells along the Columbia River shoreline. CP v1.0 simulations are
performed at three spatial resolutions (i.e., 2, 10, and 20 m) over a
5-year period to evaluate the impact of hydroclimatic conditions and
spatial resolution on simulated variables. Results show that the coupled
model is capable of simulating groundwater-river-water interactions
driven by river stage variability along managed river reaches, which are
of global significance as a result of over 30 000 dams constructed
worldwide during the past half-century. Our numerical experiments
suggest that the land-surface energy partitioning is strongly modulated
by groundwater-river-water interactions through expanding the
periodically inundated fraction of the riparian zone, and enhancing
moisture availability in the vadose zone via capillary rise in response
to the river stage change. Meanwhile, CLM4.5 fails to capture the key
hydrologic process (i.e., groundwater-river-water exchange) at the site,
and consequently simulates drastically different water and energy
budgets. Furthermore, spatial resolution is found to significantly
impact the accuracy of estimated the mass exchange rates at the
boundaries of the aquifer, and it becomes critical when surface and
subsurface become more tightly coupled with groundwater table within 6
to 7 meters below the surface. Inclusion of lateral subsurface flow
influenced both the surface energy budget and subsurface transport
processes as a result of river-water intrusion into the subsurface in
response to an elevated river stage that increased soil moisture for
evapotranspiration and suppressed available energy for sensible heat in
the warm season. The coupled model developed in this study can be used
for improving mechanistic understanding of ecosystem functioning and
biogeochemical cycling along river corridors under historical and future
hydroclimatic changes. The dataset presented in this study can also
serve as a good benchmarking case for testing other integrated models.},
doi = {10.5194/gmd-10-4539-2017},
issn = {1991-959X},
eissn = {1991-9603},
researcherid-numbers = {Huang, Maoyi/I-8599-2012
Bisht, Gautam/J-4822-2014
Bisht, Gautam/P-4043-2019
Zhou, Tian/J-4007-2019
Zhou, Tian/F-8659-2015
Riley, William/D-3345-2015},
orcid-numbers = {Huang, Maoyi/0000-0001-9154-9485
Bisht, Gautam/0000-0001-6641-7595
Bisht, Gautam/0000-0001-6641-7595
Zhou, Tian/0000-0003-1582-4005
Zhou, Tian/0000-0003-1582-4005
Riley, William/0000-0002-4615-2304},
unique-id = {ISI:000417851000001}
}
@article{Dwivedi2017,
author = {Dwivedi, Dipankar and
and Arora, Bhavna
and Steefel, Carl I.
and Dafflon, Baptiste
and Versteeg, Roelof},
title = {Hot Spots and Hot Moments of Nitrogen in a Riparian Corridor},
journal = {Water Resources Research},
year = {2017},
abstract = {We use 3-D high-resolution reactive transport modeling to investigate whether the spatial distribution of organic-carbon-rich and chemically reduced sediments located in the riparian zone and temporal variability in groundwater flow direction impact the formation and distribution of nitrogen hotspots (regions that exhibit higher reaction rates when compared to other locations nearby) and hot moments (times that exhibit high reaction rates as compared to longer intervening time periods) within the Rifle floodplain in Colorado. Groundwater flows primarily toward the Colorado River from the floodplain butchanges direction at times of high river stage. The result is that oxic river water infiltrates the Rifle floodplain during these relatively short-term events. Simulation results indicate that episodic rainfall in the summer season leads to the formation of nitrogen hot moments associated with Colorado River rise and resulting river infiltration into the floodplain. The results further demonstrate that the naturally reduced zones (NRZs) present in sediments of the Rifle floodplain have a higher potential for nitrate removal, approximately 70\% greater than non-NRZs for typical hydrological conditions. During river water infiltration, nitrate reduction capacity remains the same within the NRZs, however, these conditions impact non-NRZs to a greater extent(approximately 95\% less nitrate removal). Model simulations indicate chemolithoautotrophs are primarily responsible for the removal of nitrate in the Rifle floodplain. These nitrogen hot spots and hot moments are sustained by microbial respiration and the chemolithoautotrophic oxidation of reduced minerals in theriparian zone.},
doi = {10.1002/2017WR022346},
url = {https://doi.org/10.1002/2017WR022346}
}
@article{ISI:000414887200039,
author = {Avasarala, Sumant and Lichtner, Peter C. and Ali, Abdul-Mehdi S. and
Gonzalez-Pinzon, Ricardo and Blake, Johanna M. and Cerrato, Jose M.},
title = {Reactive Transport of U and V from Abandoned Uranium Mine Wastes},
journal = {ENVIRONMENTAL SCIENCE \& TECHNOLOGY},
year = 2017,
volume = {51},
number = {21},
pages = {12385-12393},
month = nov,
abstract = {The reactive transport of uranium (U) and vanadium(V) from abandoned
mine wastes collected from the Blue Gap/Tachee Claim-28 mine site in
Arizona was investigated by integrating flow-through column experiments
with reactive transport modeling, and electron microscopy. The mine
wastes were sequentially reacted in flow-through columns at pH 7.9 (10
mM HCO3-) and pH 3.4 (10 mM CH3COOH) to evaluate the effect of
environmentally relevant conditions encountered at Blue Gap/Tachee on
the release of U and V. The reaction rate constants (k(m)) for the
dissolution of uranylvanadate (U-V) minerals predominant at Blue
Gap/Tachee were obtained from simulations with the reactive transport
software, PFLOTRAN. The estimated reaction rate constants were within 1
order of magnitude for pH 7.9 (k(m) = 4.8 x 10(-13) mol cm(-2) s(-1))
and pH 3.4 (k(m) = 3.2 x 10(-13) mol cm(-2) s(-1)). However, the
estimated equilibrium constants (K-eq) for U-V bearing minerals were
more than 6 orders of magnitude different for reaction at circumneutral
pH (K-eq = 10(-38.65)) compared to acidic pH (K-eq = 10(-44.81)). These
results coupled with electron microscopy data suggest that the release
of U and V is affected by water pH and the crystalline structure of U-V
bearing minerals. The findings from this investigation have important
implications for risk exposure assessment, remediation, and resource
recovery of U and V in locations where U-V-bearing minerals are
abundant.},
doi = {10.1021/acs.est.7b03823},
issn = {0013-936X},
eissn = {1520-5851},
researcherid-numbers = {Gonzalez-Pinzon, Ricardo/A-6877-2011
},
orcid-numbers = {Gonzalez-Pinzon, Ricardo/0000-0001-9387-6885
Cerrato, Jose/0000-0002-2473-6376},
unique-id = {ISI:000414887200039}
}
@article{https://doi.org/10.1002/2016WR019756,
author = {Dai, Heng and Chen, Xingyuan and Ye, Ming and Song, Xuehang and Zachara, John M.},
title = {A geostatistics-informed hierarchical sensitivity analysis method for complex groundwater flow and transport modeling},
journal = {Water Resources Research},
volume = 53,
number = 5,
pages = {4327-4343},
keywords = {sensitivity analysis, variance decomposition, parametric uncertainty, model uncertainty, groundwater transport modeling, geostatistics},
doi = {10.1002/2016WR019756},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016WR019756},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2016WR019756},
abstract = {Abstract Sensitivity analysis is an important tool for development and improvement of mathematical models, especially for complex systems with a high dimension of spatially correlated parameters. Variance-based global sensitivity analysis has gained popularity because it can quantify the relative contribution of uncertainty from different sources. However, its computational cost increases dramatically with the complexity of the considered model and the dimension of model parameters. In this study, we developed a new sensitivity analysis method that integrates the concept of variance-based method with a hierarchical uncertainty quantification framework. Different uncertain inputs are grouped and organized into a multilayer framework based on their characteristics and dependency relationships to reduce the dimensionality of the sensitivity analysis. A set of new sensitivity indices are defined for the grouped inputs using the variance decomposition method. Using this methodology, we identified the most important uncertainty source for a dynamic groundwater flow and solute transport model at the Department of Energy (DOE) Hanford site. The results indicate that boundary conditions and permeability field contribute the most uncertainty to the simulated head field and tracer plume, respectively. The relative contribution from each source varied spatially and temporally. By using a geostatistical approach to reduce the number of realizations needed for the sensitivity analysis, the computational cost of implementing the developed method was reduced to a practically manageable level. The developed sensitivity analysis method is generally applicable to a wide range of hydrologic and environmental problems that deal with high-dimensional spatially distributed input variables.},
year = 2017
}
@article{ISI:000412251900027,
author = {Zhang, Mingkan and Zhang, Ye and Lichtner, Peter},
title = {Evaluating model complexity in simulating supercritical CO2 dissolution,
leakage, footprint, and reservoir pressure for three-dimensional
hierarchical aquifer},
journal = {INTERNATIONAL JOURNAL OF GREENHOUSE GAS CONTROL},
year = 2017,
volume = {64},
pages = {284-299},
month = sep,
abstract = {A hierarchical fully heterogeneous aquifer model (FHM) provides a
reference for developing and testing 3 facies-based hydrostratigraphic
models (HSMs) each representing a CO2 storage aquifer with reduced
permeability (k) heterogeneity resolution: 8-unit, 3-unit, and 1-unit
homogeneous models. Under increasing aquifer Ink variances (0.1, 1.0,
4.5), flow upscaling was conducted to calculate equivalent
permeabilities for the HSMs. Within a Design of Experiment uncertainty
analysis framework varying geothermal gradient, salinity of formation
water, caprock permeability, and injection rate, CO2 injection coupled
to convective mixing was simulated by all models. In addition to the
injection phase, all simulations were carried out for 2000 years using
PFLOTRAN, a massively parallel, multiphase, multicomponent numerical
simulator that ran on the NCAR-Wyoming Supercomputing Center's
Yellowstone supercomputer. Simulation outcomes of the HSMs were compared
to those of the FHM within their full parameter space, and four
performance metrics were evaluated: dissolved CO2, CO2 leakage, plume
footprint, and pore pressure evolution in response to injection and
migration. Results suggest that aquifer variance, heterogeneity
resolution, and salinity can all affect the development of fingering and
convective mixing, and therefore the amount of dissolution storage. For
the modeling choices and assumptions made in this study, the 3-unit HSM
was found to be an all-around optimal model by capturing both the
sensitivity of the FHM and the performance metrics under different
reservoir storage or operational conditions. Implications for modeling
long-term CO2 storage in data-poor systems are discussed and future
research indicated.},
doi = {10.1016/j.ijggc.2017.07.022},
issn = {1750-5836},
eissn = {1878-0148},
unique-id = {ISI:000412251900027}
}
@article{ISI:000392690900008,
author = {Johnson, Timothy C. and Hammond, Glenn E. and Chen, Xingyuan},
title = {{PFLOTRAN-E4D}: A parallel open source {PFLOTRAN} module for simulating
time-lapse electrical resistivity data},
journal = {COMPUTERS \& GEOSCIENCES},
year = 2017,
volume = {99},
pages = {72-80},
month = feb,
abstract = {Time-lapse electrical resistivity tomography (ERT) is finding increased
application for remotely monitoring processes occurring in the near
subsurface in three-dimensions (i.e. 4D monitoring). However, there are
few codes capable of simulating the evolution of subsurface resistivity
and corresponding tomographic measurements arising from a particular
process, particularly in parallel and with an open source license.
Herein we describe and demonstrate an electrical resistivity tomography
module for the PFLOTRAN subsurface flow and reactive transport
simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in
parallel using a dedicated set of compute cores in a master-slave
configuration. At each time step, the master processes receives
subsurface states from PFLOTRAN, converts those states to bulk
electrical conductivity, and instructs the slave processes to simulate a
tomographic data set. The resulting multi-physics simulation capability
enables accurate feasibility studies for ERT imaging, the identification
of the ERT signatures that are unique to a given process, and
facilitates the joint inversion of ERT data with hydrogeological data
for subsurface characterization. PFLOTRAN-E4D is demonstrated herein
using a field study of stage-driven groundwater/river water interaction
ERT monitoring along the Columbia River, Washington, USA. Results
demonstrate the complex nature of subsurface electrical conductivity
changes, in both the saturated and unsaturated zones, arising from river
stage fluctuations and associated river water intrusion into the
aquifer. The results also demonstrate the sensitivity of surface based
ERT measurements to those changes over time. PFLOTRAN-E4D is available
with the PFLOTRAN development version with an open-source license at
https://bitbucket.org/pflotran/pflotrandev.},
doi = {10.1016/j.cageo.2016.09.006},
issn = {0098-3004},
eissn = {1873-7803},
unique-id = {ISI:000392690900008}
}
@inproceedings{ISI:000398020400102,
author = {Dwivedi, Dipankar and Steefel, Carl I. and Arora, Bhavna and Bisht,
Gautam},
editor = {Marques, JM and Chambel, A},
title = {Impact of intra-meander hyporheic flow on nitrogen cycling},
booktitle = {15TH WATER-ROCK INTERACTION INTERNATIONAL SYMPOSIUM, WRI-15},
series = {Procedia Earth and Planetary Science},
year = 2017,
volume = {17},
pages = {404-407},
note = {15th Water-Rock Interaction International Symposium (WRI), Evora,
PORTUGAL, OCT 16-21, 2016},
abstract = {Redox gradients within hyporheic zones significantly impact the
biogeochemical cycling of carbon and nitrogen. To investigate the effect
of these redox gradients on nitrogen transformation in the subsurface,
we integrated a genome-informed complex reaction network into PFLOTRAN,
which is an open source, massively parallel, three-dimensional, reactive
flow and transport code. This study was conducted in the lower East
River catchment in southwestern Colorado. The lower East River has
multiple river meanders extending over a distance of 11 km in rolling to
mountainous region of the East Taylor watershed. We carried out reactive
flow and transport simulations within two stream meanders to describe
the biogeochemical zonation that evolves due to upwelling of nutrient
rich groundwater and downwelling of oxygen rich stream. The specific
objectives were to examine (1) the effect of hyporheic flow on
biogeochemical zonation and (2) how meanders affect local nitrogen
fluxes and transformation. Simulation results demonstrate that hyporheic
flow paths within intra-meander regions lead to lateral redox zonation,
which significantly impact nitrogen export into the stream system. Also,
meander-driven hyporheic flow paths enhance denitrification rates
because of the extended hyporheic region. (C) 2017 The Authors.
Published by Elsevier B.V.},
doi = {10.1016/j.proeps.2016.12.102},
issn = {1878-5220},
researcherid-numbers = {Dwivedi, Dipankar/F-8725-2015
Bisht, Gautam/J-4822-2014
Bisht, Gautam/P-4043-2019
Arora, Bhavna/D-2293-2015},
orcid-numbers = {Dwivedi, Dipankar/0000-0003-1788-1900
Bisht, Gautam/0000-0001-6641-7595
Bisht, Gautam/0000-0001-6641-7595
Arora, Bhavna/0000-0001-7841-886X},
unique-id = {ISI:000398020400102}
}
@inproceedings{ISI:000398020400182,
author = {Wersin, Paul and Alt-Epping, Peter and Pekala, Marek and Pitkanen,
Petteri and Snellman, Margit},
editor = {Marques, JM and Chambel, A},
title = {Modelling sulfide fluxes and Cu canister corrosion rates in the
engineered barrier system of a spent fuel repository},
booktitle = {15TH WATER-ROCK INTERACTION INTERNATIONAL SYMPOSIUM, WRI-15},
series = {Procedia Earth and Planetary Science},
year = 2017,
volume = {17},
pages = {722-725},
note = {15th Water-Rock Interaction International Symposium (WRI), Evora,
PORTUGAL, OCT 16-21, 2016},
abstract = {Sulfide is a corrodant for the copper canister in the planned spent fuel
repository in Finland and Sweden. Sulfide fluxes and canister corrosion
rates in the clay barrier have been assessed by a reactive transport
model using the geochemical simulator PFLOTRAN. These rates are linked
to the dissolution of gypsum, present in the clay backfill, and the
fluxes of sulfate, organic carbon and Fe(II) into interface zones where
microbial activity occurs. The permeability of the rock adjacent to the
clay backfill exerts a strong control on the biogeochemical processes
and the resulting copper corrosion rates. (C) 2017 The Authors.
Published by Elsevier B.V.},
doi = {10.1016/j.proeps.2016.12.183},
issn = {1878-5220},
unique-id = {ISI:000398020400182}
}
@article{Trinchero2016,
author = {Trinchero, Paolo
and Molinero, Jorge
and Deissmann, Guido
and Svensson, Urban
and Gylling, Bj{\"o}rn
and Ebrahimi, Hedieh
and Hammond, Glenn
and Bosbach, Dirk
and Puigdomenech, Ignasi},
title = {Implications of Grain-Scale Mineralogical Heterogeneity for Radionuclide Transport in Fractured Media},
journal = {Transport in Porous Media},
year = {2016},
pages = {1--18},
abstract = {The geological disposal of nuclear waste is based on the multi-barrier concept, comprising various engineered and natural barriers, to confine the radioactive waste and isolate it from the biosphere. Some of the planned repositories for high-level nuclear waste will be hosted in fractured crystalline rock formations. The potential of these formations to act as natural transport barriers is related to two coupled processes: diffusion into the rock matrix and sorption onto the mineral surfaces available in the rock matrix. Different in situ and laboratory experiments have pointed out the ubiquitous heterogeneous nature of the rock matrix: mineral surfaces and pore space are distributed in complex microstructures and their distribution is far from being homogeneous (as typically assumed by Darcy-scale coarse reactive transport models). In this work, we use a synthetically generated fracture--matrix system to assess the implications of grain-scale physical and mineralogical heterogeneity on cesium transport and retention. The resulting grain-scale reactive transport model is solved using high-performance computing technologies, and the results are compared with those derived from two alternative models, denoted as upscaled models, where mineral abundance is averaged over the matrix volume. In the grain-scale model, the penetration of cesium into the matrix is faster and the penetration front is uneven and finger-shaped. The analysis of the cesium breakthrough curves computed at two different points in the fracture shows that the upscaled models provide later first-arrival time estimates compared to the grain-scale model. The breakthrough curves computed with the three models converge at late times. These results suggest that spatially averaged upscaled parameters of sorption site distribution can be used to predict the late-time behavior of breakthrough curves but could be inadequate to simulate the early behavior.},
issn = {1573-1634},
doi = {10.1007/s11242-016-0765-0},
url = {http://dx.doi.org/10.1007/s11242-016-0765-0}
}
@article{ISI:000386578200009,
author = {Islam, Akand and Sun, Alexander and Lu, Jiemin},
title = {Simulating in-zone chemistry changes from injection time to longer
periods of CO2 storage},
journal = {ENVIRONMENTAL EARTH SCIENCES},
year = 2016,
volume = {75},
number = {20},
month = oct,
abstract = {Geochemical reactions can play important role in the long-term
geological storage of CO2 in sites where the target formations have
reactive minerals. Although the use of batch models (experimental or
theoretical) is expedient, it leaves questions unanswered about how to
interpret or predict field-scale injection over long time periods. In
this study we present results of coupled multiphase, multicomponent
reactive transport simulation using geochemistry data derived from
Cranfield site, Mississippi, USA, a site that has long been used for
carbon sequestration R\&D activities. The simulation was performed using
PFLOTRAN, an open-source parallel reactive transport code. The
geochemical system consists of 22 primary or basis species, in situ CO2
and O-2 gaseous components, and 5 minerals. In this model, there are 37
secondary elements with brine molality being 1.81. The fluid chemical
compositions were measured from production fluids, and mineral
composition of the formation was obtained from XRD analysis of core
samples. Results show how brine chemistry changes in the reservoir and
shed insights into the need to monitor the mobility of cations such as
Mg, Ca, Al, Mn, Fe, Cu, Zn, Sr, Ba, and Cd. We delineate the reservoir
volume that is affected in order to provide simultaneous potential
mobile inventory of these metals in the storage formations and warn
possible risks through leakage into overlying zone. It is found that
during injection period considered in this study dissolved CO2 can
spread about 3.5 km(2) area around the injection well and, as a result,
pH drops to as low as 3.3-5.5 at the farthest location affected. Among
the metals considered, only concentrations of Ca and Al are increased by
1 and 2 orders, respectively. In longer periods, Al concentration can
increase by orders of magnitude of EPA's threshold limit. Compared to no
reactions, the CO2 plume's extent area is 50 \% less in 20 years;
however, more CO2 is trapped in solution.},
doi = {10.1007/s12665-016-6153-9},
article-number = {1346},
issn = {1866-6280},
eissn = {1866-6299},
researcherid-numbers = {Sun, Alexander/A-9959-2011
},
orcid-numbers = {Sun, Alexander/0000-0002-6365-8526
Islam, Akand/0000-0002-2565-0021},
unique-id = {ISI:000386578200009}
}
@article{ISI:000385413300001,
author = {Kumar, Jitendra and Collier, Nathan and Bisht, Gautam and Mills, Richard
T. and Thornton, Peter E. and Iversen, Colleen M. and Romanovsky,
Vladimir},
title = {Modeling the spatiotemporal variability in subsurface thermal regimes
across a low-relief polygonal tundra landscape},
journal = {CRYOSPHERE},
year = 2016,
volume = {10},
number = {5},
pages = {2241-2274},
month = sep,
abstract = {Vast carbon stocks stored in permafrost soils of Arctic tundra are under
risk of release to the atmosphere under warming climate scenarios.
Ice-wedge polygons in the low-gradient polygonal tundra create a complex
mosaic of microtopographic features. This microtopography plays a
critical role in regulating the fine-scale variability in thermal and
hydrological regimes in the polygonal tundra landscape underlain by
continuous permafrost. Modeling of thermal regimes of this sensitive
ecosystem is essential for understanding the landscape behavior under
the current as well as changing climate. We present here an end-to-end
effort for high-resolution numerical modeling of thermal hydrology at
real-world field sites, utilizing the best available data to
characterize and parameterize the models. We develop approaches to model
the thermal hydrology of polygonal tundra and apply them at four study
sites near Barrow, Alaska, spanning across low to transitional to
high-centered polygons, representing a broad polygonal tundra landscape.
A multi-phase subsurface thermal hydrology model (PFLOTRAN) was
developed and applied to study the thermal regimes at four sites. Using
a high-resolution lidar digital elevation model (DEM), microtopographic
features of the landscape were characterized and represented in the
high-resolution model mesh. The best available soil data from field
observations and literature were utilized to represent the complex
heterogeneous subsurface in the numerical model. Simulation results
demonstrate the ability of the developed modeling approach to capture -
without recourse to model calibration - several aspects of the complex
thermal regimes across the sites, and provide insights into the critical
role of polygonal tundra microtopography in regulating the thermal
dynamics of the carbon-rich permafrost soils. Areas of significant
disagreement between model results and observations highlight the
importance of field-based observations of soil thermal and hydraulic
properties for modeling-based studies of permafrost thermal dynamics,
and provide motivation and guidance for future observations that will
help address model and data gaps affecting our current understanding of
the system.},
doi = {10.5194/tc-10-2241-2016},
issn = {1994-0416},
eissn = {1994-0424},
researcherid-numbers = {Bisht, Gautam/J-4822-2014
Iversen, Colleen M/B-8983-2012
Kumar, Jitendra/Q-5214-2019
Bisht, Gautam/P-4043-2019
Thornton, Peter E/B-9145-2012
},
orcid-numbers = {Bisht, Gautam/0000-0001-6641-7595
Iversen, Colleen M/0000-0001-8293-3450
Kumar, Jitendra/0000-0002-0159-0546
Bisht, Gautam/0000-0001-6641-7595
Thornton, Peter E/0000-0002-4759-5158
Romanovsky, Vladimir/0000-0002-9515-2087},
unique-id = {ISI:000385413300001}
}
@article{ISI:000384333000040,
author = {Hokr, M. and Shao, H. and Gardner, W. P. and Balvin, A. and Kunz, H. and
Wang, Y. and Vencl, M.},
title = {Real-case benchmark for flow and tracer transport in the fractured rock},
journal = {ENVIRONMENTAL EARTH SCIENCES},
year = 2016,
volume = {75},
number = {18},
month = sep,
abstract = {The paper is intended to define a benchmark problem related to
groundwater flow and natural tracer transport using observations of
discharge and isotopic tracers in fractured, crystalline rock. Three
numerical simulators: Flow123d, OpenGeoSys, and PFLOTRAN are compared.
The data utilized in the project were collected in a water-supply tunnel
in granite of the Jizera Mountains, Bedrichov, Czech Republic. The
problem configuration combines subdomains of different dimensions, 3D
continuum for hard-rock blocks or matrix and 2D features for fractures
or fault zones, together with realistic boundary conditions for
tunnel-controlled drainage. Steady-state and transient flow and a pulse
injection tracer transport problem are solved. The results confirm
mostly consistent behavior of the codes. Both the codes Flow123d and
OpenGeoSys with 3D-2D coupling implemented differ by several percent in
most cases, which is appropriate to, e.g., effects of discrete unknown
placing in the mesh. Some of the PFLOTRAN results differ more, which can
be explained by effects of the dispersion tensor evaluation scheme and
of the numerical diffusion. The phenomenon can get stronger with
fracture/matrix coupling and with parameter magnitude contrasts.
Although the study was not aimed on inverse solution, the models were
fit to the measured data approximately, demonstrating the intended
real-case relevance of the benchmark.},
doi = {10.1007/s12665-016-6061-z},
article-number = {1273},
issn = {1866-6280},
eissn = {1866-6299},
unique-id = {ISI:000384333000040}
}
@article{ISI:000379329500015,
author = {Chen, Jie and McInnes, Lois C. and Zhang, Hong},
title = {Analysis and Practical Use of Flexible BiCGStab},
journal = {JOURNAL OF SCIENTIFIC COMPUTING},
year = 2016,
volume = {68},
number = {2},
pages = {803-825},
month = aug,
abstract = {A flexible version of the BiCGStab algorithm for solving a linear system
of equations is analyzed. We show that under variable preconditioning,
the perturbation to the outer residual norm is of the same order as that
to the application of the preconditioner. Hence, in order to maintain a
similar convergence behavior to BiCGStab while reducing the
preconditioning cost, the flexible version can be used with a moderate
tolerance in the preconditioning Krylov solves. We explored the use of
flexible BiCGStab in a large-scale reacting flow application, PFLOTRAN,
and showed that the use of a variable multigrid preconditioner
significantly accelerates the simulation time on extreme-scale computers
using - processor cores.},
doi = {10.1007/s10915-015-0159-4},
issn = {0885-7474},
eissn = {1573-7691},
unique-id = {ISI:000379329500015}
}
@article{ISI:000374706300002,
author = {Zachara, John M. and Chen, Xingyuan and Murray, Chris and Hammond, Glenn},
title = {River stage influences on uranium transport in a hydrologically dynamic
groundwater-surface water transition zone},
journal = {WATER RESOURCES RESEARCH},
year = 2016,
volume = {52},
number = {3},
pages = {1568-1590},
month = mar,
abstract = {A well-field within a uranium (U) plume in the groundwater-surface water
transition zone was monitored for a 3 year period for water table
elevation and dissolved solutes. The plume discharges to the Columbia
River, which displays a dramatic spring stage surge resulting from
snowmelt. Groundwater exhibits a low hydrologic gradient and chemical
differences with river water. River water intrudes the site in spring.
Specific aims were to assess the impacts of river intrusion on dissolved
uranium (U-aq), specific conductance (SpC), and other solutes, and to
discriminate between transport, geochemical, and source term
heterogeneity effects. Time series trends for U-aq and SpC were complex
and displayed large temporal and well-to-well variability as a result of
water table elevation fluctuations, river water intrusion, and changes
in groundwater flow directions. The wells were clustered into subsets
exhibiting common behaviors resulting from the intrusion dynamics of
river water and the location of source terms. Hot-spots in U-aq varied
in location with increasing water table elevation through the combined
effects of advection and source term location. Heuristic reactive
transport modeling with PFLOTRAN demonstrated that mobilized U-aq was
transported between wells and source terms in complex trajectories, and
was diluted as river water entered and exited the groundwater system.
While U-aq time-series concentration trends varied significantly from
year-to-year as a result of climate-caused differences in the spring
hydrograph, common and partly predictable response patterns were
observed that were driven by water table elevation, and the extent and
duration of river water intrusion.},
doi = {10.1002/2015WR018009},
issn = {0043-1397},
eissn = {1944-7973},
unique-id = {ISI:000374706300002}
}
@article{ISI:000372808400006,
author = {Liu, Yaning and Bisht, Gautam and Subin, Zachary M. and Riley, William
J. and Pau, George Shu Heng},
title = {A Hybrid Reduced-Order Model of Fine-Resolution Hydrologic Simulations
at a Polygonal Tundra Site},
journal = {VADOSE ZONE JOURNAL},
year = 2016,
volume = {15},
number = {2},
month = feb,
note = {1st Complex Soil Systems Conference, Lawrence Berkeley Natl Lab,
Berkeley, CA, SEP 03-05, 2014},
organization = {SSSA Bouyoucos Funds; Berkeley Lab; USDOE; MoBio Lab Inc},
abstract = {High-resolution predictions of land surface hydrological dynamics are
desirable for improved investigations of regional- and watershed-scale
processes. Direct deterministic simulations of fine-resolution land
surface variables present many challenges, including high computational
cost. We therefore propose the use of reduced-order modeling techniques
to facilitate emulation of fine-resolution simulations. We use an
emulator, Gaussian process regression, to approximate fine-resolution
four-dimensional soil moisture fields predicted using a
three-dimensional surface-subsurface hydrological simulator (PFLOTRAN).
A dimension-reduction technique known as ``proper orthogonal
decomposition{''} is further used to improve the efficiency of the
resulting reduced-order model (ROM). The ROM reduces simulation
computational demand to negligible levels compared to the underlying
fine-resolution model. In addition, the ROM that we constructed is
equipped with an uncertainty estimate, allowing modelers to construct a
ROM consistent with uncertainty in the measured data. The ROM is also
capable of constructing statistically equivalent analogs that can be
used in uncertainty and sensitivity analyses. We apply the technique to
four polygonal tundra sites near Barrow, Alaska that are part of the
Department of Energy's Next-Generation Ecosystem Experiments
(NGEE)-Arctic project. The ROM is trained for each site using simulated
soil moisture from 1998-2000 and validated using the simulated data for
2002 and 2006. The average relative RMSEs of the ROMs are under 1\%.},
doi = {10.2136/vzj2015.05.0068},
issn = {1539-1663},
researcherid-numbers = {Bisht, Gautam/J-4822-2014
Pau, George Shu Heng/F-2363-2015
Bisht, Gautam/P-4043-2019
Liu, Yaning/K-8547-2014
Riley, William/D-3345-2015},
orcid-numbers = {Bisht, Gautam/0000-0001-6641-7595
Pau, George Shu Heng/0000-0002-9198-6164
Bisht, Gautam/0000-0001-6641-7595
Liu, Yaning/0000-0002-3447-5843
Riley, William/0000-0002-4615-2304},
unique-id = {ISI:000372808400006}
}
@article{ISI:000376934900001,
author = {Tang, Guoping and Yuan, Fengming and Bisht, Gautam and Hammond, Glenn E.
and Lichtner, Peter C. and Kumar, Jitendra and Mills, Richard T. and Xu,
Xiaofeng and Andre, Ben and Hoffman, Forrest M. and Painter, Scott L.
and Thornton, Peter E.},
title = {Addressing numerical challenges in introducing a reactive transport code
into a land surface model: a biogeochemical modeling proof-of-concept
with {CLM-PFLOTRAN} 1.0},
journal = {GEOSCIENTIFIC MODEL DEVELOPMENT},
year = 2016,
volume = {9},
number = {3},
pages = {927-946},
abstract = {We explore coupling to a configurable subsurface reactive transport code
as a flexible and extensible approach to biogeochemistry in land surface
models. A reaction network with the Community Land Model carbon-nitrogen
(CLM-CN) decomposition, nitrification, denitrification, and plant uptake
is used as an example. We implement the reactions in the open-source
PFLOTRAN (massively parallel subsurface flow and reactive transport)
code and couple it with the CLM. To make the rate formulae designed for
use in explicit time stepping in CLMs compatible with the implicit time
stepping used in PFLOTRAN, the Monod substrate rate-limiting function
with a residual concentration is used to represent the limitation of
nitrogen availability on plant uptake and immobilization. We demonstrate
that CLM-PFLOTRAN predictions (without invoking PFLOTRAN transport) are
consistent with CLM4.5 for Arctic, temperate, and tropical sites.
Switching from explicit to implicit method increases rigor but
introduces numerical challenges. Care needs to be taken to use scaling,
clipping, or log transformation to avoid negative concentrations during
the Newton iterations. With a tight relative update tolerance (STOL) to
avoid false convergence, an accurate solution can be achieved with about
50\% more computing time than CLM in point mode site simulations using
either the scaling or clipping methods. The log transformation method
takes 60-100\% more computing time than CLM. The computing time
increases slightly for clipping and scaling; it increases substantially
for log transformation for half saturation decrease from 10(-3) to
10(-9) molm(-3), which normally results in decreasing nitrogen
concentrations. The frequent occurrence of very low concentrations (e.g.
below nanomolar) can increase the computing time for clipping or scaling
by about 20 \%, double for log transformation. Overall, the log
transformation method is accurate and robust, and the clipping and
scaling methods are efficient. When the reaction network is highly
nonlinear or the half saturation or residual concentration is very low,
the allowable time-step cuts may need to be increased for robustness for
the log transformation method, or STOL may need to be tightened for the
clipping and scaling methods to avoid false convergence.
As some biogeochemical processes (e.g., methane and nitrous oxide
reactions) involve very low half saturation and thresholds, this work
provides insights for addressing non-physical negativity issues and
facilitates the representation of a mechanistic biogeochemical
description in Earth system models to reduce climate prediction
uncertainty.},
doi = {10.5194/gmd-9-927-2016},
issn = {1991-959X},
eissn = {1991-9603},
researcherid-numbers = {Xu, Xiaofeng/B-2391-2008
Kumar, Jitendra/Q-5214-2019
Hoffman, Forrest M./B-8667-2012
Bisht, Gautam/J-4822-2014
Bisht, Gautam/P-4043-2019
Painter, Scott/C-2586-2016
Tian, Hanqin/A-6484-2012
Thornton, Peter E/B-9145-2012
},
orcid-numbers = {Xu, Xiaofeng/0000-0002-6553-6514
Kumar, Jitendra/0000-0002-0159-0546
Hoffman, Forrest M./0000-0001-5802-4134
Bisht, Gautam/0000-0001-6641-7595
Bisht, Gautam/0000-0001-6641-7595
Painter, Scott/0000-0002-0901-6987
Tian, Hanqin/0000-0002-1806-4091
Thornton, Peter E/0000-0002-4759-5158
Yuan, Fengming/0000-0003-0910-5231},
unique-id = {ISI:000376934900001}
}
@article{https://doi.org/10.1002/2014WR016829,
author = {Karra, Satish and Makedonska, Nataliia and Viswanathan, Hari S. and Painter, Scott L. and Hyman, Jeffrey D.},
title = {Effect of advective flow in fractures and matrix diffusion on natural gas production},
journal = {Water Resources Research},
volume = {51},
number = {10},
pages = {8646-8657},
keywords = {simulation, natural gas, fracture flow, diffusion},
doi = {https://doi.org/10.1002/2014WR016829},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2014WR016829},
abstract = {Although hydraulic fracturing has been used for natural gas production for the past couple of decades, there are significant uncertainties about the underlying mechanisms behind the production curves that are seen in the field. A discrete fracture network-based reservoir-scale work flow is used to identify the relative effect of flow of gas in fractures and matrix diffusion on the production curve. With realistic three-dimensional representations of fracture network geometry and aperture variability, simulated production decline curves qualitatively resemble observed production decline curves. The high initial peak of the production curve is controlled by advective fracture flow of free gas within the network and is sensitive to the fracture aperture variability. Matrix diffusion does not significantly affect the production decline curve in the first few years, but contributes to production after approximately 10 years. These results suggest that the initial flushing of gas-filled background fractures combined with highly heterogeneous flow paths to the production well are sufficient to explain observed initial production decline. These results also suggest that matrix diffusion may support reduced production over longer time frames.},
year = {2015}
}
@article{johnson:15,
author = {Johnson, Tim and Versteeg, Roelof and Thomle, Jon and Hammond, Glenn and Chen, Xingyuan and Zachara, John},
title = {Four-dimensional electrical conductivity monitoring of stage-driven river water intrusion: Accounting for water table effects using a transient mesh boundary and conditional inversion constraints},
journal = {WATER RESOURCES RESEARCH},
year = 2015,
volume = {51},
number = {8},
pages = {6177-6196},
month = aug,
abstract = {This paper describes and demonstrates two methods of providing a priori information to the surface-based time-lapse three-dimensional electrical resistivity tomography (ERT) problem for monitoring stage-driven or tide-driven surface water intrusion into aquifers. First, a mesh boundary is implemented that conforms to the known location of the water table through time, thereby enabling the inversion to place a sharp bulk conductivity contrast at that boundary without penalty. Second, a nonlinear inequality constraint is used to allow only positive or negative transient changes in EC to occur within the saturated zone, dependent on the relative contrast in fluid electrical conductivity between surface water and groundwater. A 3-D field experiment demonstrates that time-lapse imaging results using traditional smoothness constraints are unable to delineate river water intrusion. The water table and inequality constraints provide the inversion with the additional information necessary to resolve the spatial extent of river water intrusion through time.},
doi = {10.1002/2014WR016129},
issn = {0043-1397},
eissn = {1944-7973},
unique-id = {ISI:000363402800018}
}
@article{guthrie:15,
author = {Guthrie, George D. and Carey, J. William},
title = {A thermodynamic and kinetic model for paste-aggregate interactions and the alkali-silica reaction},
journal = {CEMENT AND CONCRETE RESEARCH},
year = 2015,
volume = {76},
pages = {107-120},
month = oct,
abstract = {A new conceptual model is developed for ASR formation based on geochemical principles tied to aqueous speciation, silica solubility, kinetically controlled mineral dissolution, and diffusion. ASR development is driven largely by pH and silica gradients that establish geochemical microenvironments between paste and aggregate, with gradients the strongest within the aggregate adjacent to the paste boundary (i.e., where ASR initially forms). Super-saturation of magadiite and okenite (crystalline ASR surrogates) occurs in the zone defined by gradients in pH, dissolved silica, Na+, and Ca2+. This model provides a thermodynamic rather than kinetic explanation of why quartz generally behaves differently from amorphous silica: quartz solubility does not produce sufficiently high concentrations of H4SiO4 to super-saturate magadiite, whereas amorphous silica does. The model also explains why pozzolans do not generate ASR: their fine-grained character precludes formation of chemical gradients. Finally, these gradients have interesting implications beyond the development of ASR, creating unique biogeochemical environments. (C) 2015 Elsevier Ltd. All rights reserved.},
doi = {10.1016/j.cemconres.2015.05.004},
issn = {0008-8846},
eissn = {1873-3948},
unique-id = {ISI:000359958300012}
}
@article{ISI:000362307700002,
author = {Hyman, Jeffrey D. and Karra, Satish and Makedonska, Nataliia and Gable,
Carl W. and Painter, Scott L. and Viswanathan, Hari S.},
title = {DFNWORKS: A discrete fracture network framework for modeling subsurface
flow and transport},
journal = {COMPUTERS \& GEOSCIENCES},
year = 2015,
volume = {84},
pages = {10-19},
month = nov,
abstract = {DFNWORKS is a parallelized computational suite to generate
three-dimensional discrete fracture networks (DFN) and simulate flow and
transport. Developed at Los Alamos National Laboratory over the past
five years, it has been used to study flow and transport in fractured
media at scales ranging from millimeters to kilometers. The networks are
created and meshed using DFNGEN, which combines FRAM (the feature
rejection algorithm for meshing) methodology to stochastically generate
three-dimensional DENs with the LAGRIT meshing toolbox to create a
high-quality computational mesh representation. The representation
produces a conforming Delaunay triangulation suitable for high
performance computing finite volume solvers in an intrinsically parallel
fashion. Flow through the network is simulated in DFNFLOW, which
utilizes the massively parallel subsurface flow and reactive transport
finite volume code PFLOTRAN. A Lagrangian approach to simulating
transport through the DFN is adopted within DFNTRANS to determine
pathlines and solute transport through the DFN. Example applications of
this suite in the areas of nuclear waste repository science, hydraulic
fracturing and CO2 sequestration are also included. (C) 2015 Elsevier
Ltd. All rights reserved.},
doi = {10.1016/j.cageo.2015.08.001},
issn = {0098-3004},
eissn = {1873-7803},
researcherid-numbers = {Painter, Scott/C-2586-2016
},
orcid-numbers = {Painter, Scott/0000-0002-0901-6987
Gable, Carl/0000-0001-7063-0815
Bui, Quan M./0000-0003-2648-0586
Makedonska, Nataliia/0000-0002-4183-5755
Karra, Satish/0000-0001-7847-6293
Hyman, Jeffrey/0000-0002-4224-2847},
unique-id = {ISI:000362307700002}
}
@article{ISI:000358627100026,
author = {Tutolo, Benjamin M. and Kong, Xiang-Zhao and Seyfried, Jr., William E.
and Saar, Martin O.},
title = {High performance reactive transport simulations examining the effects of
thermal, hydraulic, and chemical (THC) gradients on fluid injectivity at
carbonate CCUS reservoir scales},
journal = {INTERNATIONAL JOURNAL OF GREENHOUSE GAS CONTROL},
year = 2015,
volume = {39},
pages = {285-301},
month = aug,
abstract = {Carbonate minerals and CO2 are both considerably more soluble at low
temperatures than they are at elevated temperatures. This inverse
solubility has led a number of researchers to hypothesize that injecting
low-temperature (i.e., less than the background reservoir temperature)
CO2 into deep, saline reservoirs for CO2 Capture, Utilization, and
Storage (CCUS) will dissolve CO2 and carbonate minerals near the
injection well and subsequently exsolve and re-precipitate these phases
as the fluids flow into the geothermally warm portion of the reservoir.
In this study, we utilize high performance computing to examine the
coupled effects of cool CO2 injection and background hydraulic head
gradients on reservoir- scale mineral volume changes. We employ the
fully coupled reactive transport simulator PFLOTRAN with calculations
distributed over up to 800 processors to test 21 scenarios designed to
represent a range of reservoir depths, hydraulic head gradients, and CO2
injection rates and temperatures. In the default simulations, 50 degrees
C CO2 is injected at a rate of 50 kg/s into a 200 bar, 100 degrees C
calcite or dolomite reservoir. By comparing these simulations with
others run at varying conditions, we show that the effect of cool CO2
injection on reservoir-scale mineral volume changes tends to be
relatively minor. We conclude that the low heat capacity of CO2
effectively prevents low-temperature CO2 injection from decreasing the
temperature across large portions of the simulated carbonate reservoirs.
This small thermal perturbation, combined with the low relative
permeability-of brine within the supercritical CO2 plume, yields limited
dissolution and precipitation effects directly attributable to cool CO2
injection. Finally, we calculate that relatively high water-to-rock
ratios, which may occur over much longer CCUS reservoir lifetimes or in
materials with sufficiently high brine relative permeability within the
supercritical CO2 plume, would be required to substantially affect
injectivity through thermally-induced mineral dissolution and
precipitation. Importantly, this study shows the utility of reservoir
scale-reactive transport simulators for testing hypotheses and placing
laboratory-scale observations into a CCUS reservoir-scale context. (C)
2015 Elsevier Ltd. All rights reserved.},
doi = {10.1016/j.ijggc.2015.05.026},
issn = {1750-5836},
eissn = {1878-0148},
researcherid-numbers = {Saar, Martin/F-3542-2014
},
orcid-numbers = {Saar, Martin/0000-0002-4869-6452
Kong, Xiangzhao/0000-0001-6254-2428
Tutolo, Benjamin/0000-0002-3047-8828},
unique-id = {ISI:000358627100026}
}
@article{ISI:000356878900002,
author = {Steefel, C. I. and Appelo, C. A. J. and Arora, B. and Jacques, D. and
Kalbacher, T. and Kolditz, O. and Lagneau, V. and Lichtner, P. C. and
Mayer, K. U. and Meeussen, J. C. L. and Molins, S. and Moulton, D. and
Shao, H. and Simunek, J. and Spycher, N. and Yabusaki, S. B. and Yeh, G.
T.},
title = {Reactive transport codes for subsurface environmental simulation},
journal = {COMPUTATIONAL GEOSCIENCES},
year = 2015,
volume = {19},
number = {3, SI},
pages = {445-478},
month = jun,
abstract = {A general description of the mathematical and numerical formulations
used in modern numerical reactive transport codes relevant for
subsurface environmental simulations is presented. The formulations are
followed by short descriptions of commonly used and available subsurface
simulators that consider continuum representations of flow, transport,
and reactions in porous media. These formulations are applicable to most
of the subsurface environmental benchmark problems included in this
special issue. The list of codes described briefly here includes
PHREEQC, HPx, PHT3D, OpenGeoSys (OGS), HYTEC, ORCHESTRA, TOUGHREACT,
eSTOMP, HYDROGEOCHEM, CrunchFlow, MIN3P, and PFLOTRAN. The descriptions
include a high-level list of capabilities for each of the codes, along
with a selective list of applications that highlight their capabilities
and historical development.},
doi = {10.1007/s10596-014-9443-x},
issn = {1420-0597},
eissn = {1573-1499},
researcherid-numbers = {Steefel, Carl/B-7758-2010
Arora, Bhavna/D-2293-2015
Kalbacher, Thomas/C-9336-2017
Spycher, Nicolas F/E-6899-2010
Jacques, Diederik/C-5887-2009
Shao, Haibing/C-3466-2015
Molins, Sergi/A-9097-2012
},
orcid-numbers = {Arora, Bhavna/0000-0001-7841-886X
Kalbacher, Thomas/0000-0002-7866-5702
Shao, Haibing/0000-0002-9214-8349
Molins, Sergi/0000-0001-7675-3218
Kolditz, Olaf/0000-0002-8098-4905
Jacques, Diederik/0000-0001-9393-2963
Mayer, K. Ulrich/0000-0002-4168-781X},
unique-id = {ISI:000356878900002}
}
@article{ISI:000356878900013,
author = {Xie, Mingliang and Mayer, K. Ulrich and Claret, Francis and Alt-Epping,
Peter and Jacques, Diederik and Steefel, Carl and Chiaberge, Christophe
and Simunek, Jiri},
title = {Implementation and evaluation of permeability-porosity and
tortuosity-porosity relationships linked to mineral
dissolution-precipitation},
journal = {COMPUTATIONAL GEOSCIENCES},
year = 2015,
volume = {19},
number = {3, SI},
pages = {655-671},
month = jun,
abstract = {Changes of porosity, permeability, and tortuosity due to physical and
geochemical processes are of vital importance for a variety of
hydrogeological systems, including passive treatment facilities for
contaminated groundwater, engineered barrier systems (EBS), and host
rocks for high-level nuclear waste (HLW) repositories. Due to the
nonlinear nature and chemical complexity of the problem, in most cases,
it is impossible to verify reactive transport codes analytically, and
code intercomparisons are the most suitable method to assess code
capabilities and model performance. This paper summarizes model
intercomparisons for six hypothetical scenarios with generally
increasing geochemical or physical complexity using the reactive
transport codes CrunchFlow, HP1, MIN3P, PFlotran, and TOUGHREACT.
Benchmark problems include the enhancement of porosity and permeability
through mineral dissolution, as well as near complete clogging due to
localized mineral precipitation, leading to reduction of permeability
and tortuosity. Processes considered in the benchmark simulations are
advective-dispersive transport in saturated media, kinetically
controlled mineral dissolution-precipitation, and aqueous complexation.
Porosity changes are induced by mineral dissolution-precipitation
reactions, and the Carman-Kozeny relationship is used to describe
changes in permeability as a function of porosity. Archie's law is used
to update the tortuosity and the pore diffusion coefficient as a
function of porosity. Results demonstrate that, generally, good
agreement is reached amongst the computer models despite significant
differences in model formulations. Some differences are observed, in
particular for the more complex scenarios involving clogging; however,
these differences do not affect the interpretation of system behavior
and evolution.},
doi = {10.1007/s10596-014-9458-3},
issn = {1420-0597},
eissn = {1573-1499},
researcherid-numbers = {Steefel, Carl/B-7758-2010
Jacques, Diederik/C-5887-2009
Claret, Francis/A-1232-2010
},
orcid-numbers = {Jacques, Diederik/0000-0001-9393-2963
Claret, Francis/0000-0002-6203-7795
Mayer, K. Ulrich/0000-0002-4168-781X},
unique-id = {ISI:000356878900013}
}
@article{ISI:000352715600008,
author = {Gardner, William P. and Hammond, Glenn and Lichtner, Peter},
title = {High Performance Simulation of Environmental Tracers in Heterogeneous
Domains},
journal = {GROUNDWATER},
year = 2015,
volume = {53},
number = {1},
pages = {71-80},
month = apr,
abstract = {In this study, we use PFLOTRAN, a highly scalable, parallel, flow, and
reactive transport code to simulate the concentrations of H-3, He-3,
CFC-11, CFC-12, CFC-113, SF6, Ar-39, and the mean groundwater age in
heterogeneous fields on grids with an excess of 10 million nodes. We
utilize this computational platform to simulate the concentration of
multiple tracers in high-resolution, heterogeneous 2D and 3D domains,
and calculate tracer-derived ages. Tracer-derived ages show systematic
biases toward younger ages when the groundwater age distribution
contains water older than the maximum tracer age. The deviation of the
tracer-derived age distribution from the true groundwater age
distribution increases with increasing heterogeneity of the system.
However, the effect of heterogeneity is diminished as the mean travel
time gets closer to the tracer age limit. Age distributions in 3D
domains differ significantly from 2D domains. 3D simulations show
decreased mean age, and less variance in age distribution for identical
heterogeneity statistics. High-performance computing allows for
investigation of tracer and groundwater age systematics in
high-resolution domains, providing a platform for understanding and
utilizing environmental tracer and groundwater age information in
heterogeneous 3D systems.},
doi = {10.1111/gwat.12148},
issn = {0017-467X},
eissn = {1745-6584},
unique-id = {ISI:000352715600008}
}
@inproceedings{ISI:000408930200224,
author = {de Vries, L. M. and Molinero, J. and Ebrahimi, H. and Svensson, U. and
Lichtner, P. and Abarca, E.},
editor = {Caruge, D and Calvin, C and Diop, CM and Malvagi, F and Trama, JC},
title = {Regional Scale HPC Reactive Transport Simulation of Nuclear Spent Fuel
Repository in Forsmark, Sweden},
booktitle = {SNA + MC 2013 - JOINT INTERNATIONAL CONFERENCE ON SUPERCOMPUTING IN
NUCLEAR APPLICATIONS + MONTE CARLO},
year = 2014,
note = {Joint 8th International Conference on Supercomputing in Nuclear
Applications (SNA) / 4th Monte Carlo Meeting (MC), Paris, FRANCE, OCT
27-31, 2013},
organization = {CEA},
abstract = {The future nuclear spent fuel repository in the Forsmark area in Sweden,
constructed at a depth of 500 meters, is designed to be isolated from
people and nature for at least 100.000 years. As part of the safety
assessment of the repository, it is necessary to simulate the
interaction of the repository compounds with the surrounding groundwater
and rock. To evaluate the geochemical evolution in the region under
sealed repository conditions, a HPC framework, which couples a
groundwater flow simulator (DarcyTools) optimized for fractured rock
hydrology and a high performance reactive transport code (PFlotran) was
developed. The migration of a hyper-alkaline plume (high pH plume) over
10.000 years is simulated in a large scale 3D model (100 Million cells).
The results show the control of the rock fractures in the movement of
the reactive plume.},
doi = {10.1051/snamc/201405411},
article-number = {UNSP 05411},
unique-id = {ISI:000408930200224}
}
@inproceedings{ISI:000345414400039,
author = {Orsini, Paolo and Cantucci, Barbara and Quattrocchi, Fedora},
editor = {Rokke, NA and Svendsen, H},
title = {Large-scale numerical modelling of {CO2} injection and containment phases
for an Italian near-coast reservoir using {PFLOTRAN}},
booktitle = {7TH TRONDHEIM CONFERENCE ON CO2 CAPTURE, TRANSPORT AND STORAGE (2013)},
series = {Energy Procedia},
year = 2014,
volume = {51},
pages = {334-343},
note = {7th Trondheim Conference on CO2 Capture, Transport and Storage (TCCS),
Trondheim, NORWAY, JUN 05-06, 2013},
abstract = {A potential CO2 storage site located offshore the west coast of Italy,
has been modelled using PFLOTRAN assuming an injection rate of 1.5
Mtons/year for 20 years. The model predicts a CO2 footprint
characterised by a diameter of about 3.5 km and a maximum pressure build
up of 38 bars. The solubility trapping has been quantified, predicting a
dissolution in brine of 69\% and 79\% of the total amount of CO2
injected after 1000 and 2000 years respectively. The residual trapping
has also been found to play an important role, with 9\% and 6\% of the
injected CO2 being locked into the hosting matrix pores after 1000 and
2000 years respectively. Considering a worst-case scenario for leakages,
where zero critical capillarity pressure has been assumed, minor CO2
leakages through the caprock have been identified, caused by the
combined effects of the long-term structural trapping and the large and
lasting overpressure caused by the CO2 injection in an ideally closed
system. Finally, some preliminary work undertaken as part of an ongoing
effort to couple a geochemical model to the multi-phase flow simulations
reveals i) small changes in mineral volume fraction and porosity during
and after the injection (similar to 5\% after 1000 years), and ii) a not
negligible self-sealing effect due to precipitation of calcite in the
lower layer of the caprock. Further investigations and longer physical
time runs are needed to confirm this assumption, but also to gain more
confidence on the geochemical model built so far and to estimate the
mineral trapping potential for this site. (C) 2013 Elsevier Ltd. This is
an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/3.0/).},
doi = {10.1016/j.egypro.2014.07.040},
issn = {1876-6102},
orcid-numbers = {Cantucci, Barbara/0000-0001-7266-5106},
unique-id = {ISI:000345414400039}
}
@article{ISI:000344728900022,
author = {Karra, S. and Painter, S. L. and Lichtner, P. C.},
title = {Three-phase numerical model for subsurface hydrology in
permafrost-affected regions ({PFLOTRAN-ICE} v1.0)},
journal = {CRYOSPHERE},
year = 2014,
volume = {8},
number = {5},
pages = {1935-1950},
abstract = {Degradation of near-surface permafrost due to changes in the climate is
expected to impact the hydrological, ecological and biogeochemical
responses of the Arctic tundra. From a hydrological perspective, it is
important to understand the movement of the various phases of water
(gas, liquid and ice) during the freezing and thawing of near-surface
soils. We present a new non-isothermal, single-component (water),
three-phase formulation that treats air as an inactive component. This
single component model works well and produces similar results to a more
complete and computationally demanding two-component (air, water)
formulation, and is able to reproduce results of previously published
laboratory experiments. A proof-of-concept implementation in the
massively parallel subsurface flow and reactive transport code PFLOTRAN
is summarized, and parallel performance of that implementation is
demonstrated. When water vapor diffusion is considered, a large effect
on soil moisture dynamics is seen, which is due to dependence of thermal
conductivity on ice content. A large three-dimensional simulation (with
around 6 million degrees of freedom) of seasonal freezing and thawing is
also presented.},
doi = {10.5194/tc-8-1935-2014},
issn = {1994-0416},
eissn = {1994-0424},
researcherid-numbers = {Painter, Scott/C-2586-2016
},
orcid-numbers = {Painter, Scott/0000-0002-0901-6987
Karra, Satish/0000-0001-7847-6293},
unique-id = {ISI:000344728900022}
}
@article{ISI:000332914000002,
author = {McInnes, Lois Curfman and Smith, Barry and Zhang, Hong and Mills,
Richard Tran},
title = {Hierarchical Krylov and nested Krylov methods for extreme-scale
computing},
journal = {PARALLEL COMPUTING},
year = 2014,
volume = {40},
number = {1},
pages = {17-31},
month = jan,
abstract = {The solution of large, sparse linear systems is often a dominant phase
of computation for simulations based on partial differential equations,
which are ubiquitous in scientific and engineering applications. While
preconditioned Krylov methods are widely used and offer many advantages
for solving sparse linear systems that do not have highly convergent,
geometric multigrid solvers or specialized fast solvers, Krylov methods
encounter well-known scaling difficulties for over 10,000 processor
cores because each iteration requires at least one vector inner product,
which in turn requires a global synchronization that scales poorly
because of internode latency. To help overcome these difficulties, we
have developed hierarchical Krylov methods and nested Krylov methods in
the PETSc library that reduce the number of global inner products
required across the entire system (where they are expensive), though
freely allow vector inner products across smaller subsets of the entire
system (where they are inexpensive) or use inner iterations that do not
invoke vector inner products at all.
Nested Krylov methods are a generalization of inner-outer iterative
methods with two or more layers. Hierarchical Krylov methods are a
generalization of block Jacobi and overlapping additive Schwarz methods,
where each block itself is solved by Krylov methods on smaller blocks.
Conceptually, the hierarchy can continue recursively to an arbitrary
number of levels of smaller and smaller blocks. As a specific case, we
introduce the hierarchical FGMRES method, or h-FGMRES, and we
demonstrate the impact of two-level h-FGMRES with a variable
preconditioner on the PFLOTRAN subsurface flow application. We also
demonstrate the impact of nested FGMRES, BiCGStab and Chebyshev methods.
These hierarchical Krylov methods and nested Krylov methods
significantly reduced overall PFLOTRAN simulation time on the Cray XK6
when using 10,000 through 224,000 cores through the combined effects of
reduced global synchronization due to fewer global inner products and
stronger inner hierarchical or nested preconditioners. (C) 2013 Elsevier
B.V. All rights reserved.},
doi = {10.1016/j.parco.2013.10.001},
issn = {0167-8191},
eissn = {1872-7336},
unique-id = {ISI:000332914000002}
}
@article{ISI:000331798800015,
author = {Hammond, G. E. and Lichtner, P. C. and Mills, R. T.},
title = {Evaluating the performance of parallel subsurface simulators: An
illustrative example with {PFLOTRAN}},
journal = {WATER RESOURCES RESEARCH},
year = 2014,
volume = {50},
number = {1},
pages = {208-228},
month = jan,
abstract = {To better inform the subsurface scientist on the expected performance of
parallel simulators, this work investigates performance of the reactive
multiphase flow and multicomponent biogeochemical transport code
PFLOTRAN as it is applied to several realistic modeling scenarios run on
the Jaguar supercomputer. After a brief introduction to the code's
parallel layout and code design, PFLOTRAN's parallel performance
(measured through strong and weak scalability analyses) is evaluated in
the context of conceptual model layout, software and algorithmic design,
and known hardware limitations. PFLOTRAN scales well (with regard to
strong scaling) for three realistic problem scenarios: (1) in situ
leaching of copper from a mineral ore deposit within a 5-spot flow
regime, (2) transient flow and solute transport within a regional
doublet, and (3) a real-world problem involving uranium surface
complexation within a heterogeneous and extremely dynamic variably
saturated flow field. Weak scalability is discussed in detail for the
regional doublet problem, and several difficulties with its
interpretation are noted.},
doi = {10.1002/2012WR013483},
issn = {0043-1397},
eissn = {1944-7973},
unique-id = {ISI:000331798800015}
}
@article{ISI:000327432500066,
author = {Chen, Xingyuan and Hammond, Glenn E. and Murray, Chris J. and Rockhold,
Mark L. and Vermeul, Vince R. and Zachara, John M.},
title = {Application of ensemble-based data assimilation techniques for aquifer
characterization using tracer data at Hanford 300 area},
journal = {WATER RESOURCES RESEARCH},
year = 2013,
volume = {49},
number = {10},
pages = {7064-7076},
month = oct,
abstract = {Subsurface aquifer characterization often involves high parameter
dimensionality and requires tremendous computational resources if
employing a full Bayesian approach. Ensemble-based data assimilation
techniques, including filtering and smoothing, are computationally
efficient alternatives. Despite the increasing use of ensemble-based
methods in assimilating flow and transport related data for subsurface
aquifer characterization, most applications have been limited to
synthetic studies or two-dimensional problems. In this study, we applied
ensemble-based techniques adapted for parameter estimation, including
the p-space ensemble Kalman filter and ensemble smoother, for
assimilating field tracer experimental data obtained from the Integrated
Field Research Challenge (IFRC) site at the Hanford 300 Area. The
forward problem was simulated using the massively parallel
three-dimensional flow and transport code PFLOTRAN to effectively deal
with the highly transient flow boundary conditions at the site and to
meet the computational demands of ensemble-based methods. This study
demonstrates the effectiveness of ensemble-based methods for
characterizing a heterogeneous aquifer by assimilating experimental
tracer data, with refined prior information obtained from assimilating
other types of data available at the site. It is demonstrated that
high-performance computing enables the use of increasingly mechanistic
nonlinear forward simulations for a complex system within the data
assimilation framework with reasonable turnaround time.},
doi = {10.1002/2012WR013285},
issn = {0043-1397},
eissn = {1944-7973},
unique-id = {ISI:000327432500066}
}
@article{ISI:000316580500005,
author = {Navarre-Sitchler, Alexis K. and Maxwell, Reed M. and Siirila, Erica R.
and Hammond, Glenn E. and Lichtner, Peter C.},
title = {Elucidating geochemical response of shallow heterogeneous aquifers to
CO2 leakage using high-performance computing: Implications for
monitoring of CO2 sequestration},
journal = {ADVANCES IN WATER RESOURCES},
year = 2013,
volume = {53},
pages = {45-55},
month = mar,
abstract = {Predicting and quantifying impacts of potential carbon dioxide (CO2)
leakage into shallow aquifers that overlie geologic CO2 storage
formations is an important part of developing reliable carbon storage
techniques. Leakage of CO2 through fractures, faults or faulty wellbores
can reduce groundwater pH, inducing geochemical reactions that release
solutes into the groundwater and pose a risk of degrading groundwater
quality. In order to help quantify this risk, predictions of metal
concentrations are needed during geologic storage of CO2. Here, we
present regional-scale reactive transport simulations, at relatively
fine-scale, of CO2 leakage into shallow aquifers run on the PFLOTRAN
platform using high-performance computing. Multiple realizations of
heterogeneous permeability distributions were generated using standard
geostatistical methods. Increased statistical anisotropy of the
permeability field resulted in more lateral and vertical spreading of
the plume of impacted water, leading to increased Pb2+ (lead)
concentrations and lower pH at a well down gradient of the CO2 leak.
Pb2+ concentrations were higher in simulations where calcite was the
source of Pb2+ compared to galena. The low solubility of galena
effectively buffered the Pb2+ concentrations as galena reached
saturation under reducing conditions along the flow path. In all cases,
Pb2+ concentrations remained below the maximum contaminant level set by
the EPA. Results from this study, compared to natural variability
observed in aquifers, suggest that bicarbonate (HCO3) concentrations may
be a better geochemical indicator of a CO2 leak under the conditions
simulated here. (C) 2012 Elsevier Ltd. All rights reserved.},
doi = {10.1016/j.advwatres.2012.10.005},
issn = {0309-1708},
eissn = {1872-9657},
researcherid-numbers = {Siirila-Woodburn, Erica/B-6527-2015
Navarre-Sitchler, Alexis/J-3389-2014
Maxwell, Reed/D-7980-2013},
orcid-numbers = {Siirila-Woodburn, Erica/0000-0001-9406-124X
Maxwell, Reed/0000-0002-1364-4441},
unique-id = {ISI:000316580500005}
}
@inproceedings{ISI:000353685400047,
author = {Sreepathi, Sarat and Sripathi, Vamsi and Mills, Richard and Hammond,
Glenn and Mahinthakumar, G. Kumar},
book-group-author = {IEEE},
title = {SCORPIO: A Scalable Two-Phase Parallel I/O Library With Application To A
Large Scale Subsurface Simulator},
booktitle = {2013 20TH INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING (HIPC)},
series = {International Conference on High Performance Computing},
year = 2013,
pages = {443-451},
note = {20th International Conference on High Performance Computing (HiPC),
Bangalore, INDIA, DEC 18-21, 2013},
organization = {Shell India; IEEE Comp Soc Tech Comm Parallel Proc; ACM; CSIR; CCMB;
NGRI; IIT Delhi; IIT Madras; IIT Hyderabad; NARL; nVidia; Wipro; Intel;
Mellanox; Boston; Google; IBM; Netapp},
abstract = {Inefficient parallel I/O is known to be a major bottleneck among
scientific applications employed on supercomputers as the number of
processor cores grows into the thousands. Our prior experience indicated
that parallel I/O libraries such as HDF5 that rely on MPI-IO do not
scale well beyond 10K processor cores, especially on parallel file
systems (like Lustre) with single point of resource contention. Our
previous optimization efforts for a massively parallel multi-phase and
multi-component subsurface simulator (PFLOTRAN) led to a two-phase I/O
approach at the application level where a set of designated processes
participate in the I/O process by splitting the I/O operation into a
communication phase and a disk I/O phase. The designated I/O processes
are created by splitting the MPI global communicator into multiple
sub-communicators. The root process in each sub-communicator is
responsible for performing the I/O operations for the entire group and
then distributing the data to rest of the group. This approach resulted
in over 25X speedup in HDF I/O read performance and 3X speedup in write
performance for PFLOTRAN at over 100K processor cores on the ORNL Jaguar
supercomputer. This research describes the design and development of a
general purpose parallel I/O library called Scorpio that incorporates
our optimized two-phase I/O approach. The library provides a simplified
higher level abstraction to the user, sitting atop existing parallel I/O
libraries (such as HDF5) and implements optimized I/O access patterns
that can scale on larger number of processors. Performance results with
standard benchmark problems and PFLOTRAN indicate that our library is
able to maintain the same speedups as before with the added flexibility
of being applicable to a wider range of I/O intensive applications.},
issn = {1094-7256},
isbn = {978-1-4799-0729-8},
unique-id = {ISI:000353685400047}
}
@article{ISI:000304777000001,
author = {Chen, Xingyuan and Murakami, Haruko and Hahn, Melanie S. and Hammond,
Glenn E. and Rockhold, Mark L. and Zachara, John M. and Rubin, Yoram},
title = {Three-dimensional Bayesian geostatistical aquifer characterization at
the Hanford 300 Area using tracer test data},
journal = {WATER RESOURCES RESEARCH},
year = 2012,
volume = {48},
month = jun,
abstract = {Tracer tests performed under natural or forced gradient flow conditions
can provide useful information for characterizing subsurface properties,
through monitoring, modeling, and interpretation of the tracer plume
migration in an aquifer. Nonreactive tracer experiments were conducted
at the Hanford 300 Area, along with constant-rate injection tests and
electromagnetic borehole flowmeter tests. A Bayesian data assimilation
technique, the method of anchored distributions (MAD) (Rubin et al.,
2010), was applied to assimilate the experimental tracer test data with
the other types of data and to infer the three-dimensional heterogeneous
structure of the hydraulic conductivity in the saturated zone of the
Hanford formation. In this study, the Bayesian prior information on the
underlying random hydraulic conductivity field was obtained from
previous field characterization efforts using constant-rate injection
and borehole flowmeter test data. The posterior distribution of the
conductivity field was obtained by further conditioning the field on the
temporal moments of tracer breakthrough curves at various observation
wells. MAD was implemented with the massively parallel three-dimensional
flow and transport code PFLOTRAN to cope with the highly transient flow
boundary conditions at the site and to meet the computational demands of
MAD. A synthetic study proved that the proposed method could effectively
invert tracer test data to capture the essential spatial heterogeneity
of the three-dimensional hydraulic conductivity field. Application of
MAD to actual field tracer data at the Hanford 300 Area demonstrates
that inverting for spatial heterogeneity of hydraulic conductivity under
transient flow conditions is challenging and more work is needed.},
doi = {10.1029/2011WR010675},
article-number = {W06501},
issn = {0043-1397},
eissn = {1944-7973},
researcherid-numbers = {Wainwright, Haruko/A-5670-2015},
orcid-numbers = {Wainwright, Haruko/0000-0002-2140-6072},
unique-id = {ISI:000304777000001}
}
@incollection{hammond:12,
author = {Hammond, G. E. and Lichtner, P. C. and Lu, C. and Mills R.T.},
editor = {Fan Zhang and G.T. Yeh and Jack C. Parker},
booktitle = {Groundwater Reactive Transport Models},
title = {{PFLOTRAN}: Reactive flow and transport code for use on laptops to leadership-class supercomputers},
pages = {141-159},
publisher = {Bentham Science Publishers},
address = {Sharjah, UAE},
year = {2012},
doi = {10.2174/97816080530631120101}
}
@article{ISI:000306830700010,
author = {Lichtner, Peter C. and Hammond, Glenn E.},
title = {Using High Performance Computing to Understand Roles of Labile and
Nonlabile Uranium(VI) on Hanford 300 Area Plume Longevity},
journal = {VADOSE ZONE JOURNAL},
year = 2012,
volume = {11},
number = {2},
month = may,
abstract = {Evolution of a hexavalent uranium {[}U(VI)] plume at the Hanford 300
Area bordering the Columbia River was investigated to evaluate the roles
of labile and nonlabile forms of U(VI) on the longevity of the plume. A
high fidelity, three-dimensional, field-scale, reactive flow and
transport model was used to represent the system. Richards' equation
coupled to multicomponent reactitive transport equations were solved for
times up to 100 yr, taking into account rapid fluctuations in the
Columbia River stage resulting in pulse releases of U(VI) into the
river. The petascale computer code PFLOTRAN developed under a Department
of Energy Scientific Discovery through Advanced Computing (SciDAC-2)
project was used in the simulations and executed on Oak Ridge National
Laboratory's Jaguar XT5 Cray supercomputer. Labile U(VI) was represented
in the model through surface complexation reactions and its nonlabile
form through dissolution of metatorbernite used as a surrogate mineral.
Initial conditions were constructed corresponding to the U(VI) plume
already in place to avoid uncertainties associated with the lack of
historical data for the waste stream. The cumulative U(VI) flux into the
river was compared for cases of equilibrium and multirate sorption
models and for no sorption, and its sensitivity on the initial plume
configuration was investigated. The presence of nonlabile U(VI) was
found to be essential in explaining the longevity of the U(VI) plume and
the prolonged high U(VI) concentrations at the site exceeding the USEPA
maximum contaminant level for U(VI).},
doi = {10.2136/vzj2011.0097},
issn = {1539-1663},
unique-id = {ISI:000306830700010}
}
@article{ISI:000287889100009,
author = {Hammond, Glenn E. and Lichtner, Peter C. and Rockhold, Mark L.},
title = {Stochastic simulation of uranium migration at the Hanford 300 Area},
journal = {JOURNAL OF CONTAMINANT HYDROLOGY},
year = 2011,
volume = {120-21},
number = {SI},
pages = {115-128},
month = mar,
abstract = {This work focuses on the quantification of groundwater flow and
subsequent U(VI) transport uncertainty due to heterogeneity in the
sediment permeability at the Hanford 300 Area. U(VI) migration at the
site is simulated with multiple realizations of stochastically-generated
high resolution permeability fields and comparisons are made of
cumulative water and U(VI) flux to the Columbia River. The massively
parallel reactive flow and transport code PFLOTRAN is employed utilizing
40,960 processor cores on DOE's petascale Jaguar supercomputer to
simultaneously execute 10 transient, variably-saturated groundwater flow
and U(VI) transport simulations within 3D heterogeneous permeability
fields using the code's multi-realization simulation capability.
Simulation results demonstrate that the cumulative U(VI) flux to the
Columbia River is less responsive to fine scale heterogeneity in
permeability and more sensitive to the distribution of permeability
within the river hyporheic zone and mean permeability of larger-scale
geologic structures at the site. (C) 2010 Elsevier B.V. All rights
reserved.},
doi = {10.1016/j.jconhyd.2010.04.005},
issn = {0169-7722},
unique-id = {ISI:000287889100009}
}
@inproceedings{ISI:000306816800021,
author = {Geimer, Markus and Hermanns, Marc-Andre and Siebert, Christan and Wolf,
Felix and Wylie, Brian J. N.},
editor = {Cotronis, Y and Danalis, A and Nikolopoulos, DS and Dongarra, J},
title = {Scaling Performance Tool MPI Communicator Management},
booktitle = {RECENT ADVANCES IN THE MESSAGE PASSING INTERFACE},
series = {Lecture Notes in Computer Science},
year = 2011,
volume = {6960},
pages = {178+},
note = {18th European MPI Users Group Meeting (EuroMPI 2011), Santorini, GREECE,
SEP 18-21, 2011},
organization = {Microsoft; ParTec; Univ Tennessee, Innovat Comp Lab; Mellanox Technol;
Univ Athens},
abstract = {The Scalasca toolset has successfully demonstrated measurement and
analysis scalability on the largest computer systems, however,
applications have growing complexity and increasing demands on
performance tools. One such application is the PFLOTRAN code for
simulating multiphase subsurface flow and reactive transport. While
PFLOTRAN itself and Scalasca runtime summarization both scale well, MPI
communicator management becomes critical for trace collection with tens
of thousands of processes. Re-design and re-engineering of key
components of the Scalasca measurement system are presented which
encompass the representation of communicators, communicator definition
tracking and unification, and translation of ranks recorded in event
traces.},
issn = {0302-9743},
isbn = {978-3-642-24448-3},
researcherid-numbers = {Dongarra, Jack/E-3987-2014
},
orcid-numbers = {Hermanns, Marc-Andre/0000-0003-3895-7791},
unique-id = {ISI:000306816800021}
}
@inproceedings{ISI:000371301900061,
author = {Lee, Chee Wai and Malony, Allen D. and Morris, Alan},
editor = {Guarracino, MR and Vivien, F and Traff, JL and Cannataro, M and Danelutto, M and Hast, A and Perla, F and Knupfer, A and DiMartino, B and Alexander, M},
title = {TAUmon: Scalable Online Performance Data Analysis in TAU},
booktitle = {EURO-PAR 2010 PARALLEL PROCESSING WORKSHOPS},
series = {Lecture Notes in Computer Science},
year = 2011,
volume = {6586},
pages = {493-499},
note = {16th International Euro-Par Conference on Parallel Processing, Ischia,
ITALY, AUG 31-SEP 03, 2010},
organization = {Natl Res Council Italy, High Performance Comp \& Networking Inst},
abstract = {In this paper, we present an update on the scalable online support for
performance data analysis and monitoring in TAU. Extending on our prior
work with TAUoverSupermon and TAUoverMRNet, we show how online analysis
operations can also be supported directly and scalably using the
parallel infrastructure provided by an MPI application instrumented with
TAU. We also report on efforts to streamline and update TAUoverMRNet.
Together, these approaches form the basis for the investigation of
online analysis capabilities in a TAU monitoring framework TAUmon. We
discuss various analysis operations and capabilities enabled by online
monitoring and how operations like event unification enable merged
profiles to be produced with greatly reduced data volume prior to
application shutdown. Scaling results with PFLOTRAN on the Cray XT5 and
BG/P are presented along with a look at some initial performance
information generated from FLASH through our TAUmon prototype
frameworks.},
issn = {0302-9743},
isbn = {978-3-642-21878-1; 978-3-642-21877-4},
unique-id = {ISI:000371301900061}
}
@article{ISI:000290249800002,
author = {Hammond, Glenn E. and Lichtner, Peter C.},
title = {Field-scale model for the natural attenuation of uranium at the Hanford
300 Area using high-performance computing},
journal = {WATER RESOURCES RESEARCH},
year = 2010,
volume = {46},
month = sep,
abstract = {High-resolution, three-dimensional, reactive flow and transport
simulations are carried out to describe the migration of hexavalent
uranium {[}U(VI)] at the Hanford 300 Area bordering the Columbia River
and to better understand the persistence of the uranium plume at the
site. The computer code PFLOTRAN developed under a DOE SciDAC-2 project
is employed in the simulations that are executed on ORNL's Cray XT4/XT5
supercomputer Jaguar. The conceptual model used in the simulations is
based on the recognition of three distinct phases or time periods in the
evolution of the U(VI) plume. These correspond to (1) initial waste
emplacement; (2) initial presence of both labile and nonlabile U(VI)
with an evolved U(VI) plume extending from the source region to the
river boundary, representing present-day conditions; and (3) the
complete removal of all nonlabile U(VI) and labile U(VI) in the vadose
zone. This work focuses primarily on modeling Phase II using equilibrium
and multirate sorption models for labile U(VI) and a continuous source
release of nonlabile U(VI) in the South Process Pond through dissolution
of metatorbernite as a surrogate mineral. For this case, rapid
fluctuations in the Columbia River stage combined with the slow release
of nonlabile U(VI) from contaminated sediment are found to play a
predominant role in determining the migration behavior of U(VI) with
sorption only a second-order effect. Nevertheless, a multirate model was
essential in explaining breakthrough curves obtained from laboratory
column experiments using the same sediment and is demonstrated to be
important in Phase III. The calculations demonstrate that U(VI) is
discharged to the river at a highly fluctuating rate in a ratchet-like
behavior as the river stage rises and falls. The high-frequency
fluctuations must be resolved in the model to calculate the flux of
U(VI) at the river boundary. By time averaging the instantaneous flux to
average out noise superimposed on the river stage fluctuations, the
cumulative U(VI) flux to the river is found to increase approximately
linearly with time. The flow rate and U(VI) flux are highly sensitive to
the conductance boundary condition that describes the river-sediment
interface. By adjusting the conductance coefficient to give a better
match to the measured piezometric head, good agreement was obtained with
field studies for both the mean flux of water of 10(9) kg/yr and U(VI)
of 25 kg/yr at the river-aquifer boundary for a computational domain
encompassing the South Process Pond. Finally, it is demonstrated that,
through global mass conservation, the U(VI) leach rate from the source
region is related to the U(VI) flux at the river boundary.},
doi = {10.1029/2009WR008819},
article-number = {W09527},
issn = {0043-1397},
eissn = {1944-7973},
unique-id = {ISI:000290249800002}
}
@inproceedings{ISI:000281436700063,
author = {Mills, Richard Tran and Hammond, Glenn E. and Lichtner, Peter C. and
Sripathi, Vamsi and Mahinthakumar, G. (Kumar) and Smith, Barry F.},
editor = {Simon, H},
title = {Modeling Subsurface Reactive Flows Using Leadership-Class Computing},
booktitle = {SCIDAC 2009: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING},
series = {Journal of Physics Conference Series},
year = 2009,
volume = {180},
note = {5th Annual Conference of Scientific Discovery through Advanced Computing
(SciDAC 2009), San Diego, CA, JUN 14-18, 2009},
abstract = {We describe our experiences running PFLOTRAN-a code for simulation of
coupled hydro-thermal-chemical processes in variably saturated,
non-isothermal, porous media-on leadership-class supercomputers,
including initial experiences running on the petaflop incarnation of
Jaguar, the Cray XT5 at the National Center for Computational Sciences
at Oak Ridge National Laboratory. PFLOTRAN utilizes fully implicit
time-stepping and is built on top of the Portable, Extensible Toolkit
for Scientific Computation (PETSc). We discuss some of the hurdles to
``at scale{''} performance with PFLOTRAN and the progress we have made
in overcoming them on leadership-class computer architectures.},
doi = {10.1088/1742-6596/180/1/012062},
article-number = {UNSP 012062},
issn = {1742-6588},
eissn = {1742-6596},
unique-id = {ISI:000281436700063}
}
@inproceedings{ISI:000260370700052,
author = {Hammond, Glenn E. and Lichtner, Peter C. and Milis, Richard Tran and Lu,
Chuan},
editor = {Stevens, RL},
title = {Toward petascale computing in geosciences: application to the Hanford
300 Area},
booktitle = {SCIDAC 2008: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING},
series = {Journal of Physics Conference Series},
year = 2008,
volume = {125},
note = {4th Annual Scientific Discovery Through Advanced Computing Conference
(SciDAC 2008), Seattle, WA, JUL 13-17, 2008},
organization = {US DOE Off Sci; Cray; IBM; Intel; HP; SiCortex},
abstract = {Modeling uranium transport at the Hanford 300 Area presents new
challenges for high performance computing. A field-scale
three-dimensional domain with an hourly fluctuating Columbia river stage
coupled to flow in highly permeable sediments results in fast
groundwater flow rates requiring small time steps. In this work,
high-performance computing has been applied to simulate variably
saturated groundwater flow and tracer transport at the 300 Area using
PFLOTRAN. Simulation results are presented for discretizations up to
10.8 million degrees of freedom, while PFLOTRAN performance was assessed
on up to one billion degrees of freedom and 12,000 processor cores on
Jaguar, the Cray XT4 supercomputer at ORNL.},
doi = {10.1088/1742-6596/125/1/012051},
article-number = {012051},
issn = {1742-6588},
eissn = {1742-6596},
unique-id = {ISI:000260370700052}
}
@inproceedings{ISI:000250667200025,
author = {Hammond, Glenn and Lichtner, Peter and Lu, Chuan},
book-author = {Keyes, D},
title = {Subsurface multiphase flow and multicomponent reactive transport
modeling using high-performance computing},
booktitle = {SCIDAC 2007: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING},
series = {Journal of Physics Conference Series},
year = 2007,
volume = {78},
note = {3rd Annual Scientific Discovery through Advanced Computing Conference
(SciDAC 2007), Boston, MA, JUN 24-28, 2007},
organization = {US DOE Off Sci; Natl Nucl Security Adm; US NSF},
abstract = {Numerical modeling is a critical tool to the U.S. Department of Energy
for evaluating the environmental impact of remediation strategies for
subsurface legacy waste sites. Unfortunately, the physical and chemical
complexity of many sites overwhelms the capabilities of even most state
of the art groundwater models. Of particular concern is the
representation of highly-heterogeneous stratified rock/soil layers in
the subsurface and the biological and geochemical interactions of
chemical species within multiple fluid phases. There is clearly a need
for higher-resolution modeling (i.e. increased spatial and temporal
resolution) and increasingly mechanistic descriptions of subsurface
physicochemical processes (i.e. increased chemical degrees of freedom).
We present SciDAC-funded research being performed in furthering the
development of PFLOTRAN, a parallel multiphase flow and multicomponent
reactive transport model. Written in Fortran90, PFLOTRAN is founded upon
PETSc data structures and solvers. We are employing PFLOTRAN to simulate
uranium transport at the Hanford 300 Area, a contaminated site of major
concern to the Department of Energy, the State of Washington, and other
government agencies. By leveraging the billions of degrees of freedom
available through high-performance computation using tens of thousands
of processors, we can better characterize the release of uranium into
groundwater and its subsequent transport to the Columbia River, and
thereby better understand and evaluate the effectiveness of various
proposed remediation strategies.},
doi = {10.1088/1742-6596/78/1/012025},
issn = {1742-6588},
eissn = {1742-6596},
unique-id = {ISI:000250667200025}
}
@inproceedings{ISI:000250667200042,
author = {Lu, C. and Lichtner, P. C.},
book-author = {Keyes, D},
title = {High resolution numerical investigation on the effect of convective
instability on long term CO2 storage in saline aquifers},
booktitle = {SCIDAC 2007: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING},
series = {Journal of Physics Conference Series},
year = 2007,
volume = {78},
note = {3rd Annual Scientific Discovery through Advanced Computing Conference
(SciDAC 2007), Boston, MA, JUN 24-28, 2007},
organization = {US DOE Off Sci; Natl Nucl Security Adm; US NSF},
abstract = {CO2 sequestration (capture, separation, and long term storage) in
various geologic media including depleted oil reservoirs, saline
aquifers, and oceanic sediments is being considered as a possible
solution to reduce green house gas emissions. Dissolution of
supercritical CO2 in formation brines is considered an important storage
mechanism to prevent possible leakage. Accurate prediction of the plume
dissolution rate and migration is essential. Analytical analysis and
numerical experiments have demonstrated that convective instability
(Rayleigh instability) has a crucial effect on the dissolution behavior
and subsequent mineralization reactions. Global stability analysis
indicates that a certain grid resolution is needed to capture the
features of density-driven fingering phenomena. For 3-D field scale
simulations, high resolution leads to large numbers of grid nodes,
unfeasible for a single workstation. In this study, we investigate the
effects of convective instability on geologic sequestration Off, CO2 by
taking advantage of parallel computing using the code PFLOTRAN, a
massively parallel 3-D reservoir simulator for modeling subsurface
multiphase, multicomponent reactive flow ana transport based on
continuum scale mass and energy conservation equations. The onset,
development and long-term fate of a supercritical CO2 plume will be
resolved with high resolution numerical simulations to investigate the
rate of plume dissolution caused by fingering phenomena.},
doi = {10.1088/1742-6596/78/1/012042},
issn = {1742-6588},
unique-id = {ISI:000250667200042}
}
@inproceedings{ISI:000250667200051,
author = {Mills, Richard Tran and Lu, Chuan and Lichtner, Peter C. and Hammond,
Glenn E.},
book-author = {Keyes, D},
title = {Simulating subsurface flow and transport on ultrascale computers using
{PFLOTRAN}},
booktitle = {SCIDAC 2007: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING},
series = {Journal of Physics Conference Series},
year = 2007,
volume = {78},
note = {3rd Annual Scientific Discovery through Advanced Computing Conference
(SciDAC 2007), Boston, MA, JUN 24-28, 2007},
organization = {US DOE Off Sci; Natl Nucl Security Adm; US NSF},
abstract = {We describe PFLOTRAN, a recently developed code for modeling
multi-phase, multicomponent subsurface flow and reactive transport using
massively parallel computers. PFLOTRAN is built on top of PETSc, the
Portable, Extensible Toolkit for Scientific Computation. Leveraging
PETSc has allowed us to develop-with a relatively modest investment in
development effort-a code that exhibits excellent performance on the
largest-scale supercomputers. Very significant enhancements to the code
are planned during our SciDAC-2 project. Here we describe the current
state of the code, present an example of its use on Jaguar, the Cray
XT3/4 system at Oak Ridge National Laboratory consisting of H 706
dual-core Opteron processor nodes, and briefly outline our future plans
for the code.},
doi = {10.1088/1742-6596/78/1/012051},
issn = {1742-6588},
eissn = {1742-6596},
unique-id = {ISI:000250667200051}
}