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We perform a set of flow and reactive transport simulations within three-dimensional fracture networks to learn the factors controlling mineral reactions. CO$_2$ mineralization requires CO$_2$-laden water, dissolution of a mineral that then leads to precipitation of a CO$_2$-bearing mineral. Our discrete fracture networks (DFN) are partially filled with quartz that gradually dissolves until it reaches a quasi-steady state. At the end of the simulation, we measure the quartz remaining in each fracture within the domain. We observe that a small backbone of fracture exists, where the quartz is fully dissolved which leads to increased flow and transport. However, depending on the DFN topology and the rate of dissolution, we observe a large variability of these changes, which indicates an interplay between the fracture network structure and the impact of geochemical dissolution. In this work, we developed a machine learning framework to extract the important features that support mineralization in the form of dissolution. In addition, we use structural and topological features of the fracture network to predict the remaining quartz volume in quasi-steady state conditions. As a first step to characterizing carbon mineralization, we study dissolution with this framework. We studied a variety of reaction and fracture parameters and their impact on the dissolution of quartz in fracture networks. We found that the dissolution reaction rate constant of quartz and the distance to the flowing backbone in the fracture network are the two most important features that control the amount of quartz left in the system. For the first time, we use a combination of a finite-volume reservoir model and graph-based approach to study reactive transport in a complex fracture network to determine the key features that control dissolution., Comment: 23 pages, 5 figures, 2 tables

Large-scale discrete fracture network (DFN) simulators are standard fare for studies involving the sub-surface transport of particles since direct observation of real world underground fracture networks is generally infeasible. While these simulators have seen numerous successes over several engineering applications, estimations on quantities of interest (QoI) - such as breakthrough time of particles reaching the edge of the system - suffer from a two distinct types of uncertainty. A run of a DFN simulator requires several parameter values to be set that dictate the placement and size of fractures, the density of fractures, and the overall permeability of the system; uncertainty on the proper parameter choices will lead to some amount of uncertainty in the QoI, called epistemic uncertainty. Furthermore, since DFN simulators rely on stochastic processes to place fractures and govern flow, understanding how this randomness affects the QoI requires several runs of the simulator at distinct random seeds. The uncertainty in the QoI attributed to different realizations (i.e. different seeds) of the same random process leads to a second type of uncertainty, called aleatoric uncertainty. In this paper, we perform a Sensitivity Analysis, which directly attributes the uncertainty observed in the QoI to the epistemic uncertainty from each input parameter and to the aleatoric uncertainty. We make several design choices to handle an observed heteroskedasticity in DFN simulators, where the aleatoric uncertainty changes for different inputs, since the quality makes several standard statistical methods inadmissible. Beyond the specific takeaways on which input variables affect uncertainty the most for DFN simulators, a major contribution of this paper is the introduction of a statistically rigorous workflow for characterizing the uncertainty in DFN flow simulations that exhibit heteroskedasticity., Comment: 23 pages, 6 figures, journal article

In this paper, we introduce Pysimfrac, a open-source python library for generating 3-D synthetic fracture realizations, integrating with fluid simulators, and performing analysis. Pysimfrac allows the user to specify one of three fracture generation techniques (Box, Gaussian, or Spectral) and perform statistical analysis including the autocorrelation, moments, and probability density functions of the fracture surfaces and aperture. This analysis and accessibility of a python library allows the user to create realistic fracture realizations and vary properties of interest. In addition, Pysimfrac includes integration examples to two different pore-scale simulators and the discrete fracture network simulator, dfnWorks. The capabilities developed in this work provides opportunity for quick and smooth adoption and implementation by the wider scientific community for accurate characterization of fluid transport in geologic media. We present Pysimfrac along with integration examples and discuss the ability to extend Pysimfrac from a single complex fracture to complex fracture networks.

Modeling gas flow through fractures of subsurface rock is a particularly challenging problem because of the heterogeneous nature of the material. High-fidelity simulations using discrete fracture network (DFN) models are one methodology for predicting gas particle breakthrough times at the surface, but are computationally demanding. We propose a Bayesian machine learning method that serves as an efficient surrogate model, or emulator, for these three-dimensional DFN simulations. Our model trains on a small quantity of simulation data and, using a graph/path-based decomposition of the fracture network, rapidly predicts quantiles of the breakthrough time distribution. The approach, based on Gaussian Process Regression (GPR), outputs predictions that are within 20-30% of high-fidelity DFN simulation results. Unlike previously proposed methods, it also provides uncertainty quantification, outputting confidence intervals that are essential given the uncertainty inherent in subsurface modeling. Our trained model runs within a fraction of a second, which is considerably faster than other methods with comparable accuracy and multiple orders of magnitude faster than high-fidelity simulations.

We model flow and transport in three-dimensional fracture networks with varying degrees of fracture-to-fracture aperture/permeability heterogeneity and network density to show how changes in these properties can cause the emergence of anomalous flow and transport behavior. If fracture-to-fracture aperture heterogeneity is increased in sparse networks, velocity fluctuations can inhibit high flow rates and solute transport can be delayed, even in cases where hydraulic aperture is monotonically increased. As the density of the networks is increased, more connected pathways allow for particles to bypass these effects. We discover transition behavior where with relatively few connected pathways in a network from inflow to outflow boundaries, the first arrival times of particles are not heavily affected by fracture-to-fracture aperture heterogeneity, but the scaling behavior of the tails is strongly influenced due to the particles being forced to sample some of the heterogeneity in the velocity field caused by aperture differences. These results reinforce the importance of considering multi-scale effects in fractured systems and can inform flow and transport processes in both natural and engineered fracture systems, especially the latter where high aperture fractures are often stimulated and connect to existing fracture networks with smaller apertures.

We performed a set of numerical simulations to characterize the interplay of fracture network topology, upscaling, and mesh refinement on flow and transport properties in fractured porous media. We generated a set of generic three-dimensional discrete fracture networks at various densities, where the radii of the fractures were sampled from a truncated power-law distribution, and whose parameters were loosely based on field site characterizations. We also considered five network densities, which were defined using a dimensionless version of density based on percolation theory. Once the networks were generated, we upscaled them into a single continuum model using the upscaled discrete fracture matrix model presented by Sweeney et al. We considered steady, isothermal pressure-driven flow through each domain and then simulated conservative, decaying, and adsorbing tracers using a pulse injection into the domain. For each simulation, we calculated the effective permeability and solute breakthrough curves as quantities of interest to compare between network realizations. We found that selecting a mesh resolution such that the global topology of the upscaled mesh matches the fracture network is essential. If the upscaled mesh has a connected pathway of fracture (higher permeability) cells but the fracture network does not, then the estimates for effective permeability and solute breakthrough will be incorrect. False connections cannot be eliminated entirely, but they can be managed by choosing appropriate mesh resolution and refinement for a given network. Adopting octree meshing to obtain sufficient levels of refinement leads to fewer computational cells (up to a 90% reduction in overall cell count) when compared to using a uniform resolution grid and can result in a more accurate continuum representation of the true fracture network., Comment: 31 pages, 11 figures, 3 tables

We present a comprehensive workflow to simulate single-phase flow and transport in fractured porous media using the discrete fracture matrix approach. The workflow has three primary parts: (1) a method for conforming mesh generation of and around a three-dimensional fracture network, (2) the discretization of the governing equations using a second-order mimetic finite difference method, and (3) implementation of numerical methods for high-performance computing environments. A method to create a conforming Delaunay tetrahedralization of the volume surrounding the fracture network, where the triangular cells of the fracture mesh are faces in the volume mesh, that addresses pathological cases which commonly arise and degrade mesh quality is also provided. Our open-source subsurface simulator uses a hierarchy of process kernels (one kernel per physical process) that allows for both strong and weak coupling of the fracture and matrix domains. We provide verification tests based on analytic solutions for flow and transport, as well as numerical convergence. We also provide multiple expositions of the method in complex fracture networks. In the first example, we demonstrate that the method is robust by considering two scenarios where the fracture network acts as a barrier to flow, as the primary pathway, or offers the same resistance as the surrounding matrix. In the second test, flow and transport through a three-dimensional stochastically generated network containing 257 fractures is presented.

We present the near-Maximal Algorithm for Poisson-disk Sampling (nMAPS) to generate point distributions for variable resolution Delaunay triangular and tetrahedral meshes in two and three-dimensions, respectively. nMAPS consists of two principal stages. In the first stage, an initial point distribution is produced using a cell-based rejection algorithm. In the second stage, holes in the sample are detected using an efficient background grid and filled in to obtain a near-maximal covering. Extensive testing shows that nMAPS generates a variable resolution mesh in linear run time with the number of accepted points. We demonstrate nMAPS capabilities by meshing three-dimensional discrete fracture networks (DFN) and the surrounding volume. The discretized boundaries of the fractures, which are represented as planar polygons, are used as the seed of 2D-nMAPS to produce a conforming Delaunay triangulation. The combined mesh of the DFN is used as the seed for 3D-nMAPS, which produces conforming Delaunay tetrahedra surrounding the network. Under a set of conditions that naturally arise in maximal Poisson-disk samples and are satisfied by nMAPS, the two-dimensional Delaunay triangulations are guaranteed to only have well-behaved triangular faces. While nMAPS does not provide triangulation quality bounds in more than two dimensions, we found that low-quality tetrahedra in 3D are infrequent, can be readily detected and removed, and a high quality balanced mesh is produced., Comment: arXiv admin note: substantial text overlap with arXiv:2105.10079

We propose a two-stage algorithm for generating Delaunay triangulations in 2D and Delaunay tetrahedra in 3D that employs near maximal Poisson-disk sampling. The method generates a variable resolution mesh in 2- and 3-dimensions in linear run time. The effectiveness of the algorithm is demonstrated by generating an unstructured 3D mesh on a discrete fracture network (DFN). Even though Poisson-disk sampling methods do not provide triangulation quality bounds in more than two-dimensions, we found that low quality tetrahedra are infrequent enough and could be successfully removed to obtain high quality balanced three-dimensional meshes with topologically acceptable tetrahedra.

We present a topology-based method for mesh-partitioning in three-dimensional discrete fracture network (DFN) simulations that take advantage of the intrinsic multi-level nature of a DFN. DFN models are used to simulate flow and transport through low-permeability fractured media in the subsurface by explicitly representing fractures as discrete entities. The governing equations for flow and transport are numerically integrated on computational meshes generated on the interconnected fracture networks. Modern high-fidelity DFN simulations require high-performance computing on multiple processors where performance and scalability depend partially on obtaining a high-quality partition of the mesh to balance work-loads and minimize communication across all processors. The discrete structure of a DFN naturally lends itself to various graph representations. We develop two applications of the multilevel graph partitioning algorithm to partition the mesh of a DFN. In the first, we project a partition of the graph based on the DFN topology onto the mesh of the DFN and in the second, this projection is used as the initial condition for further partitioning refinement of the mesh. We compare the performance of these methods with standard multi-level graph partitioning using graph-based metrics (cut, imbalance, partitioning time), computational-based metrics (FLOPS, iterations, solver time), and total run time. The DFN-based and the mesh-based partitioning methods are comparable in terms of the graph-based metrics, but the time required to obtain the partition is several orders of magnitude faster using the DFN-based partitions. In combination, these partitions are several orders of magnitude faster than the mesh-based partition. In turn, this hybrid method outperformed both of the other methods in terms of the total run time.

Structural and topological information play a key role in modeling flow and transport through fractured rock in the subsurface. Discrete fracture network (DFN) computational suites such as dfnWorks are designed to simulate flow and transport in such porous media. Flow and transport calculations reveal that a small backbone of fractures exists, where most flow and transport occurs. Restricting the flowing fracture network to this backbone provides a significant reduction in the network's effective size. However, the particle tracking simulations needed to determine the reduction are computationally intensive. Such methods may be impractical for large systems or for robust uncertainty quantification of fracture networks, where thousands of forward simulations are needed to bound system behavior. In this paper, we develop an alternative network reduction approach to characterizing transport in DFNs, by combining graph theoretical and machine learning methods. We consider a graph representation where nodes signify fractures and edges denote their intersections. Using random forest and support vector machines, we rapidly identify a subnetwork that captures the flow patterns of the full DFN, based primarily on node centrality features in the graph. Our supervised learning techniques train on particle-tracking backbone paths found by dfnWorks, but run in negligible time compared to those simulations. We find that our predictions can reduce the network to approximately 20% of its original size, while still generating breakthrough curves consistent with those of the original network., Comment: Computational Geosciences (2018)