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These scripts document the code used to analyze the Death Valley Regional Flow System (DVRFS) microbial community for a manuscript titled "Subsurface Planktonic Microbial Communities Reflect Regional-Scale Groundwater Hydraulic Connectivity".
The Chicxulub impact crater in northwestern Yucatan, Mexico is the primary candidate for the proposed impact that caused mass extinctions at the end of the Cretaceous Period. The crater is buried by up to a kilometer of Tertiary sediment and the most prominent surface expression is a ring of sink holes, known locally as cenotes, mapped with Landsat imagery. This 165 +/- 5 km diameter Cenote Ring demarcates a boundary between unfractured limestones inside the ring, and fractured limestones outside. The boundary forms a barrier to lateral ground water migration, resulting in increased flows, dissolution, and collapse thus forming the cenotes. The subsurface geology indicates that the fracturing that created the Cenote Ring is related to slumping in the rim of the buried crater, differential thicknesses in the rocks overlying the crater, or solution collapse within porous impact deposits. The Cenote Ring provides the most accurate position of the Chicxulub crater's center, and the associated faults, fractures, and stratigraphy indicate that the crater may be approximately 240 km in diameter.
The Chicxulub impact crater in northwestern Yucatan, Mexico is the primary candidate for the proposed impact that caused mass extinctions at the end of the Cretaceous Period. The crater is buried by up to a kilometer of Tertiary sediment and the most prominent surface expression is a ring of sink holes, known locally as cenotes, mapped with Landsat imagery. This 165 +/- 5 km diameter Cenote Ring demarcates a boundary between unfractured limestones inside the ring, and fractured limestones outside. The boundary forms a barrier to lateral ground water migration, resulting in increased flows, dissolution, and collapse thus forming the cenotes. The subsurface geology indicates that the fracturing that created the Cenote Ring is related to slumping in the rim of the buried crater, differential thicknesses in the rocks overlying the crater, or solution collapse within porous impact deposits. The Cenote Ring provides the most accurate position of the Chicxulub crater's center, and the associated faults, fractures, and stratigraphy indicate that the crater may be approx. 240 km in diameter.
Project Overview: NASA’s 12th Discovery Program mission that will place a single geophysical lander on Mars to study its deep interior using seismic (tidal, marsquake, and impact), rotational, and thermal measurements -First mission to unveil the composition, structure and thermal state of martian crust, mantle and core; Rebuild of the Phoenix flight system, upgraded with Juno/GRAIL avionics -Phoenix cruise stage: 3-axis stabilized, 3.2 square meter UTJ (Ultra Triple-Junction) solar array, X-band telecom -Phoenix aeroshell (heat shield, backshell, parachute) -Phoenix lander: radar, pulsed thrusters, legs, payload deck, 5.1 square meter UTJ solar arrays, two redundant Li-ion batteries, UHF (Ultra High Frequency)/X-band telecom -Dual string: Internally or functionally-redundant equipment; Science Payload -SEIS (Seismic Experiment for Interior Structure) / CNES (Centre National d’Etudes Spatiales); Three-axis seismometry, to measure seismic waves traveling through the interior -HP3 (Heat Flow and Physical Properties Probe) / DLR (German Aerospace Center) -Subsurface heat probe, to measure the heat flux from the interior - RISE (Rotation and Interior Structure Experiment) / JPL (Jet Propulsion Laboratory) -Radiometric geodesy, to determine precession & nutation of the planet’s rotation axis. 2016 Disclaimer: The InSight launch in 2016 was suspended due to critical issues with the Seismic Experiment for Interior Structure (SEIS) instrument that could not be fixed prior to the planned launch period. This presentation and its corresponding paper represent the state of the design for the 2016 mission. No attempt has been made to reflect the latest developments. [2018 Note: InSight (Mars Lander) was later launched and arrived on Mars on Nov. 26, 2018.]
Fractured systems in the subsurface play a role in many natural and engineered applications such as geologic carbon sequestration, hydraulic fracturing and underground nuclear test detection. Structural information (fracture size, orientation, etc.) plays a key role in governing the dominant physics for these systems but can only be known statistically. Traditional modeling approaches either ignore or idealize structural information at these larger scales because we lack a computational framework that utilizes it in its entirety. The work presented here integrates computational physics, machine learning and graph theory to make a paradigm shift from computationally intensive high-fidelity models to coarse-scale graphs without loss of critical structural information. We exploit the underlying discrete structure of fracture networks in systems considering flow through fractures and fracture propagation. We demonstrate that compact graph representations require significantly fewer degrees of freedom (dof) to capture micro-fracture information and further accelerate these models with Machine Learning.
Investigations of coupled multiphysics processes in rivers and hyporheic zones have extensively used numerical models. Most existing models use a sequential, one-way coupling between the surface and subsurface domains. Such one-way coupling potentially introduces error. To overcome this, a fully coupled model, hyporheicFoam, was developed using the open-source computational platform OpenFOAM. It captures the coupled flow and multicomponent reactive transport processes within both surface and subsurface domains and across their interface. The coupling between two domains is implemented by mapping conservative flux boundary conditions at the interface through an iterative algorithm. Reactive transport is enabled by specifying a reaction network. To start, we have implemented reaction kinetics following the double Monod-type model with inhibition. The model capability is illustrated through modeling of both conservative and reactive hyporheic flow and transport through dune bedforms. With the novel coupled model, it is now possible to quantify reactions wherein the reactants and products are constantly exchanging between domains and have feedbacks. hyporheicFoam can simulate large, three-dimensional cases owing to the computational flexibility and power offered by the code structure and parallel design of OpenFOAM.
Due to the low thermal conductivity of CO2 ice and clathrate vs. water ice, we find that liquid water reservoirs would not be confined to the deep subsurface as predicted by the controversial White Mars model, even assuming low global heat flow. Additional information is contained in the original extended abstract.
Accurately modeling and constructing a geologically realistic subsurface model remains an outstanding problem as the morphology controls the flow behaviors. Particularly, one of the pattern-based methods, namely cross-correlation based simulation, has been proved to be an effective way to reconstruct a realistic model, at both small and large scales. However, conditioning to point data in the large-scale problems is still a crucial issue in these algorithms, since there is always a trade-off between the quality of the realizations and the degree of point data reproduction. Specifically, it is not practical to build a training image (TI) which includes all the possibilities and variabilities. Therefore, finding a pattern that can represent the point data and, at the same time, preserving the connectivities is difficult. This leads to producing highly-connected realizations with a significant mismatch or poor models with a reasonable degree of point data reproduction. To accurately reproduce the densely distributed hard data, pixel-based methods can also produce some unrealistic artifacts around the hard data. In this paper, to overcome this challenge, however, we use pattern-based methods as they often produce more disconnected geobodies when dealing with dense hard data, and proposed a hybrid algorithm using the pattern-based methods and convolutional neural network (CNN). The trained CNN model is utilized to improve the quality of conditioning to point data for the original realizations generated by the pattern-based algorithm. As such, the mismatch locations are identified, and the same regions are used in the training of CNN to mimic the procedure through which a missing region can be filled. To evaluate the performance of the proposed hybrid algorithm, it is tested on cases with different dimensions and different numbers of facies. Then, the newly improved realizations are compared with the initial realizations generated by the pattern-based algorithm. The comparison is also conducted by the flow simulation test. And it indicates that the proposed hybrid algorithm can better reproduce the point data, while the connectivities are better preserved.
The results of monitoring of carbon dioxide (CO 2 ) injection at the Illinois Basin—Decatur Project (IBDP) and the companion Illinois Industrial Carbon Capture and Sequestration Sources (IL-ICCS) project—have shown that reservoir response to fluid pressure changes can vary significantly at different injection locations within the same reservoir. Predrill reservoir characterization is important to identify potentially seismogenic faults. However, interpretations of newly reprocessed 3D seismic reflection data illustrate the challenges related to their identification in a region dominated by faulting with small vertical offsets. Faults interpreted in the 3D seismic volume range from ~300 to 1200 m wide and are in the same size range as faults that could have been the source of historical events up to Mw 2.7 in central Illinois. The array of monitoring sensors that was installed for the IBDP continues to collect data, as injection operates in IL-ICCS, the second injection well. CO 2 injection rates for the IL-ICCS well are on average 1.7 times the rates injected in the IBDP well, but a significantly reduced rate of induced seismicity is observed. This article presents results of passive seismic monitoring for the duration of the project to date, integrating active and passive seismic data to develop a new interpretation of the subsurface structure at the Decatur site that explicitly identifies pathways for fluid flow into the basement leading to induced seismicity, and provides a geological explanation for the sharp reduction of induced seismicity during injection at higher rates into the second well. The use of seismic moment to estimate the length of seismogenic slip planes in the local subsurface suggests that faults large enough to produce felt seismicity are unlikely to be present at or near the Decatur site.
We report simulation of multiphase flow in porous media is crucial for the effective management of subsurface energy and environment-related activities. The numerical simulators used for modeling such processes rely on spatial and temporal discretization of the governing mass and energy balance partial-differential equations (PDEs) into algebraic systems via finite-difference/volume/element methods. These simulators usually require dedicated software development and maintenance, and suffer low efficiency from a runtime and memory standpoint for problems with multi-scale heterogeneity, coupled-physics processes or fluids with complex phase behavior. Therefore, developing cost-effective, data-driven models can become a practical choice, and in this work, we choose deep learning approaches as they can handle high dimensional data and accurately predict state variables with strong nonlinearity. In this paper, we describe a gradient-based deep neural network (GDNN) constrained by the physics related to multiphase flow in porous media. We tackle the nonlinearity of flow in porous media induced by rock heterogeneity, fluid properties, and fluid-rock interactions by decomposing the nonlinear PDEs into a dictionary of elementary differential operators. We use a combination of operators to handle rock spatial heterogeneity and fluid flow by advection. Since the augmented differential operators are inherently related to the physics of fluid flow, we treat them as first principles prior knowledge to regularize the GDNN training. We use the example of pressure management at geologic CO 2 storage sites, where CO 2 is injected in saline aquifers and brine is produced, and apply GDNN to construct a predictive model that is trained with physics-based simulation data and emulates the physics process. We demonstrate that GDNN can effectively predict the nonlinear patterns of subsurface responses, including the temporal and spatial evolution of the pressure and saturation plumes. We also successfully extend the GDNN to convolutional neural network (CNN), namely gradient-based CNN (GCNN), and validate its capability to improve the prediction accuracy. GDNN has great potential to tackle challenging problems that are governed by highly nonlinear physics and enable the development of data-driven models with higher fidelity.
Predicting the evolution of fractured media is challenging due to coupled thermal, hydrological, chemical and mechanical processes that occur over a broad range of spatial scales, from the microscopic pore scale to field scale. We present a software framework and scientific workflow that couples the pore scale flow and reactive transport simulator Chombo-Crunch with the field scale geomechanics solver in GEOS to simulate fracture evolution in subsurface fluid-rock systems. This new multiphysics coupling capability comprises several novel features. An HDF5 data schema for coupling fracture positions between the two codes is employed and leverages the coarse resolution of the GEOS mechanics solver which limits the size of data coupled, and is, thus, not taxed by data resulting from the high resolution pore scale Chombo-Crunch solver. The coupling framework requires tracking of both before and after coarse nodal positions in GEOS as well as the resolved embedded boundary in Chombo-Crunch. We accomplished this by developing an approach to geometry generation that tracks the fracture interface between the two different methodologies. The GEOS quadrilateral mesh is converted to triangles which are organized into bins and an accessible tree structure; the nodes are then mapped to the Chombo representation using a continuous signed distance function that determines locations inside, on and outside of the fracture boundary. The GEOS positions are retained in memory on the Chombo-Crunch side of the coupling. The time stepping cadence for coupled multiphysics processes of flow, transport, reactions and mechanics is stable and demonstrates temporal reach to experimental time scales. The approach is validated by demonstration of 9 days of simulated time of a core flood experiment with fracture aperture evolution due to invasion of carbonated brine in wellbore-cement and sandstone. We also demonstrate usage of exascale computing resources by simulating a high resolution version of the validation problem on OLCF Frontier.
This study addresses coupled multiphase fluid flow and geomechanics effects on potential fault activation associated with subsurface CO 2 injection around intersecting faults. An enhanced fault-representation model is used to capture geomechanical responses of two intersecting faults with finite length during CO 2 injection. The faults are embedded in a strike-slip stress regime of a caprock-reservoir-basement system with the faults represented by zero-thickness interfaces with adjacent finite-thickness damage zones. A sensitivity analysis is conducted to study the effect of fault permeability, slip-weakening behavior, well location relative to the orientation of faults, and well placement (the number and location of injection wells). Five metrics (pressure, CO 2 plume, shear state on the fault, as well as shear displacement and stress path at selected fault monitoring points) are selected to assess CO 2 migration and reactivation of intersecting faults. The results show that induced ruptures are favored by low permeability faults due to high pressure buildup and by slip-weakening behavior resulting from fault strength reduction. The location of one injection well relative to fault orientation determines the magnitude of changes in effective normal stress and shear stress, affecting the location of induced ruptures. Well placement (two injection wells used in the paper) dominates pressure diffusion around the intersection and tips of faults. This redistributes changes in effective normal stress caused by each injection well, influencing the spatial distribution of ruptures along faults. A larger injection volume induces far-field ruptures that are controlled by stress transfer within the injection layer. The findings presented here can provide valuable insights into engineering operations for a long-term, safe, and reliable geologic CO 2 storage.
Here, in this paper, we introduce an effective United Filter method for jointly estimating the solution state and physical parameters in flow and transport problems within fractured porous media. Fluid flow and transport in fractured porous media are critical in subsurface hydrology, geophysics, and reservoir geomechanics. Reduced fracture models, which represent fractures as lower-dimensional interfaces, enable efficient multi-scale simulations. However, reduced fracture models also face accuracy challenges due to modeling errors and uncertainties in physical parameters such as permeability and fracture geometry. To address these challenges, we propose a United Filter method, which integrates the Ensemble Score Filter (EnSF) for state estimation with the Direct Filter for parameter estimation. EnSF, based on a score-based diffusion model framework, produces ensemble representations of the state distribution without deep learning. Meanwhile, the Direct Filter, a recursive Bayesian inference method, estimates parameters directly from state observations. The United Filter combines these methods iteratively: EnSF estimates are used to refine parameter values, which are then fed back to improve state estimation. Numerical experiments demonstrate that the United Filter method surpasses the state-of-the-art Augmented Ensemble Kalman Filter, delivering more accurate state and parameter estimation for reduced fracture models. This framework also provides a robust and efficient solution for PDE-constrained inverse problems with uncertainties and sparse observations.
Understanding the flow and reactivity of CO 2 injected into geological reservoirs is important for many subsurface applications including secure geologic carbon storage (GCS), critical mineral extraction, enhanced geothermal systems (EGS), and enhanced oil recovery (EOR). Traditionally, subsurface CO 2 injection for GCS applications has focused on geologic formations with favorable subsurface configurations for CO 2 migration and trapping through non-reactive mechanisms such as structural, solubility, and petrophysical trapping. Recently, CO 2 -reactive rocks such as mafic and ultramafic basalts have been investigated for their potential to react with injected CO 2 in situ to simultaneously dissolve host rock minerals and mineralize CO 2 as carbonates. Engineering rapid CO 2 mineralization in the subsurface is attractive because of the increased density of stored CO 2 , the additional safety factors associated with solidification, and the potential to extract valuable critical minerals. Here we present recent developments in the parallel flow and reactive transport simulator PFLOTRAN to model coupled CO 2 -brine flow and reactive transport for a wide range of injection and production applications involving reactive CO 2 -brine systems. These developments are based on the well established and trusted CO 2 flow capabilities in the STOMP-CO 2 simulator. New capabilities added to PFLOTRAN include new CO 2 -brine equations of state with optional thermal coupling, several new constitutive relationships like capillary pressure smoothing and scanning path hysteresis, a fully implicit well model, and native linkage with PFLOTRAN's well-established reactive transport libraries. A series of benchmarks between PFLOTRAN and STOMP-CO 2 verify the newly developed CO 2 -brine flow capabilities. Demonstrations of coupled CO 2 -brine flow modeling and reactive transport show how CO 2 mineralization can be engineered in reactive host rocks. Finally, an example use case involving copper leaching by CO 2 and critical mineral extraction is presented to showcase the strengths of this new implementation. Several limitations still remain, including limited availability of field data to parameterize models. Future work should constrain the evolution of mineral surface area during mineralization and the temperature and/or pH dependence of geochemical reactions for specific systems of interest.
In the Cydonia region of southern Acidalium Planitia are small, low-relief, apparently volcanic domelike structures, whose size, morphology, and general occurrence suggest they are martian analogs of terrestrial pseudocraters, a type of phreatic eruption. Average base diameters are about 800 m, which is somewhat larger than typical Icelandic examples. All the domes have summit pits; elongate domes generally have elongate summit pits or, in extreme cases, double pits. The greatest concentration of these domes is in a region of subdued fractured plains which may be old volcanic flows. Pseudocraters on the earth are produced when lava flows over water-logged ground. On Mars surface or subsurface ice was the likley medium that produced the steam eruptions resulting in cratered domelike structures on the lava surfaces.
In recent years the focus of helioseismology has shifted from the classical measurements of global properties using normal mode frequencies to possibly a more difficult problem of measuring the three-dimensional, time-dependent structure of the solar interior, now called local helioseismology. Problems to be studed include the subsurface structure of observed surface features such as sunspots, convective flow patterns, and the magnetic field of the 1 1-year sunspot cycle. A variety of techniques have been developed to attack these problems, including a 'local' normal mode method, a method of measuring travel times between &stant locations, and a method for holographically reconstructing the acoustic signal in the solar interior. Recent results from the field will be reviewed.
Identifying fluid flow maldistribution in planar geometries is a well–established problem in subsurface science/engineering. Of particular importance to the thermal performance of enhanced (or “engineered”) geothermal systems is identifying the existence of nonuniform (i.e., heterogeneous) permeability and subsequently predicting advective heat transfer. Here, machine learning via a genetic algorithm (GA) identifies the spatial distribution of an unknown permeability field in a two–dimensional Hele–Shaw geometry (i.e., parallel plates). The inverse problem is solved by minimizing the L2 norm between simulated residence time distribution (RTD) and measurements of an inert tracer breakthrough curve (BTC) (C–Dot nanoparticle). Principal component analysis (PCA) of spatially correlated permeability fields enabled reduction of the parameter space by more than a factor of 10 and restricted the inverse search to reservoir–scale permeability variations. Thermal experiments and tracer tests conducted at the mesoscale Altona Field Laboratory (AFL) demonstrate that the method accurately predicts the effects of extreme flow channeling on heat transfer in a single bedding–plane rock fracture. However, this is only true when the permeability distributions provide adequate matches to both tracer RTD and frictional pressure loss. Without good agreement to frictional pressure loss, it is still possible to match a simulated RTD to measurements, but subsequent predictions of heat transfer are grossly inaccurate. Here, the results of this study suggest that it is possible to anticipate the thermal effects of flow maldistribution, but only if both simulated RTDs and frictional pressure loss between fluid inlets and outlets are in good agreement with measurements.
The fate of water and water-soluble toxic wastes in the subsurface is of high importance for many scientific and practical applications. Although solute transport is proportional to water flow rates, theoretical and experimental studies show that heavy-tailed (power-law) solute transport distribution can cause chemical transport retardation, prolonging clean-up time-scales greatly. However, no consensus exists as to the physical basis of such transport laws. In percolation theory, the scaling behavior of such transport rarely relates to specific medium characteristics, but strongly to the dimensionality of the connectivity of the flow paths (for example, two- or three-dimensional, as in fractured-porous media or heterogeneous sediments), as well as to the saturation characteristics (i.e., wetting, drying, and entrapped air). In accordance with the proposed relevance of percolation models of solute transport to environmental clean-up, these predictions also prove relevant to transport-limited chemical weathering and soil formation, where the heavy-tailed distributions slow chemical weathering over time. The predictions of percolation theory have been tested in laboratory and field experiments on reactive solute transport, chemical weathering, and soil formation and found accurate. Recently, this theoretical framework has also been applied to the water partitioning at the Earth’s surface between evapotranspiration, ET, and run-off, Q, known as the water balance. A well-known phenomenological model by Budyko addressed the relationship between the ratio of the actual evapotranspiration (ET) and precipitation, ET/P, versus the aridity index, ET 0 /P, with P being the precipitation and ET 0 being the potential evapotranspiration. Existing work was able to predict the global fractions of P represented by Q and ET through an optimization of plant productivity, in which downward water fluxes affect soil depth, and upward fluxes plant growth. In the present work, based likewise on the concepts of percolation theory, we extend Budyko’s model, and address the partitioning of run-off Q into its surface and subsurface components, as well as the contribution of interception to ET. Using various published data sources on the magnitudes of interception and information regarding the partitioning of Q, we address the variability in ET resulting from these processes. The global success of this prediction demonstrated here provides additional support for the universal applicability of percolation theory for solute transport as well as guidance in predicting the component of subsurface run-off, important for predicting natural flow rates through contaminated aquifers.