pflotran-community.bib

@article{Trinchero2017,
  author = {Trinchero, Paolo
and Puigdomenech, Ignasi
and Molinero, Jorge
and Ebrahimi, Hedieh
and Gyllingb, Björn
and Svensson, Urban
and Dirk Bosbach, Dirk
and Deissmann, Guido},
  title = {Continuum-based DFN-consistent numerical framework for the simulation of oxygen infiltration into fractured crystalline rocks},
  journal = {Journal of Contaminant Hydrology},
  year = {2017},
  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.},
  doi = {10.1016/j.jconhyd.2017.04.001},
  url = {http://dx.doi.org/10.1016/j.jconhyd.2017.04.001}
}
@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{zachara:16,
  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{tang:16,
  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 = {Painter, Scott/C-2586-2016
   Xu, Xiaofeng/B-2391-2008
   Kumar, Jitendra/G-8601-2013},
  orcid-numbers = {Painter, Scott/0000-0002-0901-6987
   Xu, Xiaofeng/0000-0002-6553-6514
   Kumar, Jitendra/0000-0002-0159-0546},
  unique-id = {ISI:000376934900001}
}
@article{kumar:16,
  author = {Kumar, J. and Collier, N. and Bisht, G. and Mills, R. T.  and Thornton, P. E. and Iversen, C. M. and Romanovsky, V.},
  title = {Modeling the spatiotemporal variability in subsurface thermal regimes across a low-relief polygonal tundra landscape},
  journal = {The Cryosphere},
  volume = {10},
  year = {2016},
  number = {5},
  pages = {2241--2274},
  url = {http://www.the-cryosphere.net/10/2241/2016/},
  doi = {10.5194/tc-10-2241-2016}
}
@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{gardner:15,
  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}
}
@article{hammond:14,
  author = {Hammond, Glenn E. and Lichtner, Peter C. and Mills, Richard T.},
  title = {Evaluating the performance of parallel subsurface simulators: An
illustrative example with PFLOTRAN},
  journal = {WATER RESOURCES RESEARCH},
  year = {2014},
  volume = {50},
  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}
}
@article{chen:13,
  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},
  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}
}
@article{navarre:13,
  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},
  researcherid-numbers = {Maxwell, Reed/D-7980-2013},
  orcid-numbers = {Maxwell, Reed/0000-0002-1364-4441},
  unique-id = {ISI:000316580500005}
}
@article{chen:12,
  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},
  unique-id = {ISI:000304777000001}
}
@article{lichtner:12,
  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}
}
@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{hammond:11,
  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}
}
@article{hammond:10,
  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},
  unique-id = {ISI:000290249800002}
}
@inproceedings{mill:09,
  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},
  issn = {1742-6588},
  unique-id = {ISI:000281436700063}
}
@inproceedings{hammond:08,
  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 - art. no. 012051},
  booktitle = {SCIDAC 2008: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING},
  series = {JOURNAL OF PHYSICS CONFERENCE SERIES},
  year = {2008},
  volume = {125},
  pages = {12051},
  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},
  issn = {1742-6588},
  unique-id = {ISI:000260370700052}
}
@inproceedings{mills:07,
  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},
  pages = {U387-U393},
  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},
  unique-id = {ISI:000250667200051}
}