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Pore-scale modeling of carbonates

Ayaz Mehmani, Rahul Verma, Maša Prodanović

PII: S0264-8172(19)30593-8
DOI: https://doi.org/10.1016/j.marpetgeo.2019.104141
Reference: JMPG 104141

To appear in: Marine and Petroleum Geology

Received Date: 27 July 2019

Revised Date: 7 November 2019
Accepted Date: 14 November 2019

Please cite this article as: Mehmani, A., Verma, R., Prodanović, Maš., Pore-scale modeling
of carbonates, Marine and Petroleum Geology (2019), doi: https://doi.org/10.1016/
j.marpetgeo.2019.104141.

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2 Pore-Scale Modeling of Carbonates
3
4 Ayaz Mehmani, Rahul Verma, and Maša Prodanović
5 Hildebrand Department of Petroleum and Geosystems Engineering, The University of Texas at Austin
6
7 Abstract
8 Carbonate rocks display complex pore textures with heterogeneities that extend over several
9 length scales. Identifying and capturing the significant pore space properties in a computationally
10 tractable model is therefore nontrivial. Pore-scale models bridge predictions of transport
11 properties from sub-pore to core scale and attempts have been made to render such methods cost-
12 effective. This chapter reviews several methods for fabricating pore-scale models of carbonate
13 rocks and discusses approaches to simulating their fluid flow and solute transport properties. The
14 advantages and limitations of each method in reducing the reservoir development uncertainties
15 are explained. We argue that pore-scale models can play an important role in predicting the
16 petrophysical properties of carbonate rocks. Even more importantly, they provide sensitivity
17 analyses of pore-scale features on macroscopic transport observations and offer explanations for
18 anomalous flow behaviors.
19

20 1.Introduction
21 The length scales involved in modeling subsurface formations span from micrometers/sub-
22 micrometers (size of a pore) to meters/kilometers (e.g. formation thickness or distance between
23 wells). Although it is desirable to conduct transport simulations solely on the field scale,
24 typically sparse formation evaluation data sets (such as log and core data) may not be sufficient
25 to statistically extrapolate necessary transport properties to the entire reservoir domain. In
26 general, a posteriori prediction of the fluid behavior in subsurface porous media is problematic
27 given the wide range of values in core-scale macroscopic measurements and their spatial
28 heterogeneity in a given reservoir. Although constraining the data based on lithology or rock
29 typing schemes improves predictions, obtaining such classes is challenging when it comes to
30 heterogeneous formations such as carbonates.
31
32 In addition to rock typing, determining the transport properties based on direct formation
33 evaluation can become complicated in carbonates as commonly used formulas needed to
34 interpret log/core measurements may result in high errors. For instance, researchers have pointed
35 out that utilizing the Carman-Kozeny model for predicting absolute permeability from porosity
36 measurements in carbonates requires fitting the model to core data in order to incorporate a
37 quantification of the “rock fabric” as an independent parameter. For accurate predictions, the
38 model needs to be continuously adjusted as data become available (Jennings and Lucia, 2001) –
39 which is not necessarily practical.
40
41 The uncertainties in predicting carbonate transport properties a priori are due to the fact that
42 traditional relationships such as Archie’s equation relating resistivity to saturation, Brooks-Corey
43 for relative permeability and Carman-Kozeny for absolute permeability (Peters, 2012) were
44 originally derived for rocks with well sorted grains and narrowly distributed pores such as
45 unconsolidated sandstones. Such relationships are erroneous for carbonates because of pore size

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46 distribution ranges that span orders of magnitude and high heterogeneity in pore connectivity. It
47 becomes therefore imperative to delve into the pore scale to gain a fundamental understanding of
48 flow through porous media for finding closure relationships.
49
50 Pore-scale modeling is rooted in first principles. If the pore structure is correctly represented and
51 the initial conditions, such as initial contact angle values, and details of a physical phenomenon,
52 such as evolution of wettability during two-phase flow, are understood, then any emergent
53 macroscopic fluid behavior, such as relative permeability, can be captured accurately. Pore-scale
54 models however require to be “upscaled” to reservoir grid domains which can become a
55 nontrivial problem. In addition, uncertainties of the relevant input information for a pore-scale
56 model, such as in situ contact angle values, inevitably creates tuning parameters that will require
57 adjustments to match macroscopic experimental measurements.
58
59 Pore-scale modeling allows direct identification of quantitative parameters related to pore
60 structure and fluid properties to link the rock transport properties with geological information in
61 order to establish reliable rock classes. Once corroborated, pore-scale models can offer data
62 points away from wells where empirical relationships are unavailable. Conducting experimental
63 measurements is difficult in tight media. Heavily cemented but microporous limestones certainly
64 fall into this category for which obtaining experimental measurements become scarce due to time
65 and financial limitations. A cost-effective pore-scale model can optimize the number of
66 experimental measurements needed for linking petrophysical rock types to depositional
67 classifications (Chandra et al., 2015; Skalinski and Kenter, 2015; van der Land et al., 2013).
68
69 A robust pore-scale model in general provides an understanding of the relationship between
70 various petrophysical properties and therefore is valuable in long term reservoir development.
71 An a priori knowledge obtained via pore-scale modeling of the fluid phase distributions can play
72 a significant role in establishing the performance of water flooding, surfactant flooding, the
73 efficacy of injecting wettability altering chemicals, and water flooding during improved oil
74 recovery (Lerdahl et al., 2000), in addition to providing clarity in the potential of environmental
75 operations such as predicting the fate of pollutants during hazardous waste storage and
76 remediation and carbon storage and sequestration.
77
78 Figure 1 shows an example of utilizing pore-scale modeling in formation evaluation. During well
79 log acquisition, core plugs from a flow unit can be extracted to construct a pore-scale model. The
80 pore-scale model can subsequently be used to establish the relationships between several
81 macroscopic petrophysical properties. Such relationships can then be deployed on other flow
82 units for which laboratory measurements are either expensive or not feasible.
83
84 This chapter reviews methods and challenges in reconstructing pore-scale models and elaborates
85 on the various approaches used in simulating the fluid/solute behavior. Figure 2 illustrates the
86 topics covered in this chapter and their contributions to the creation of a pore-scale model. We
87 start by covering three major pore-space generation methods. Subsequently a discussion on pore-
88 network modeling and direct numerical simulation of fluid and solute through the reconstructed
89 pore space is provided. Algorithms for integrating pores from multiples length scales is then
90 discussed next. We note here that direct numerical simulation can be used to benchmark
91 reduced-ordered pore-network models as well and a synthesis of these two methods is given in

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 92 Section 3 (Discussion). We focus on challenges in developing pore-scale models for carbonate
93 rocks as much as possible. Each section is written such that the reader can obtain the most
94 relevant concepts and literature independently from other sections. When a relevant review
95 article is referenced, we provide a succinct summary of already reviewed concepts (to the extent
96 that the reader has gather the most pertinent information) and discuss supplemental topics not
97 synthesized in the literature. We have attempted to review a wide range of methods for geometry
98 preparation in various pore scale modeling methods, as well as highlight the transport modeling
99 methods themselves. That is a hard-balancing act, and we apologize to any researchers in
100 advance for not referencing their papers.
101
102 Since pore-scale models hinge upon capturing key characteristics of the pore geometry, we
103 specifically discuss pore geometry generation methods that follow the geological history of the
104 rock, utilize three-dimensional image acquisition methods, or extrapolate two-dimensional
105 information to three dimensions via statistical algorithms. Integration of pores from multiple
106 length scales can be a key element in correctly capturing macroscopic behavior of carbonates and
107 therefore must be addressed in each generation method. We subsequently discuss pore-network
108 modeling and direct numerical simulation as two complementary approaches for upscaling sub-
109 pore scale transport dynamics to a representative elementary volume or REV (or a volume
110 approaching it). The REV is a minimum volume for which continuum assumption of a particular
111 rock property is valid and was first introduced by Bear (1972) and (Hill) 1963. As is discussed
112 later, pore-network models are computationally more effective than direct numerical simulation
113 methods; but both are viable for making a priori predictions of a transport property if they
114 capture the correct pore geometry, fluid/fluid (for example interfacial tension) and fluid/rock
115 conditions (for example wettability). The ultimate choice of the method to be used depends on
116 the available information for constraining the input parameters as well as computational budget
117 associated with the physical process to be modeled: the methods should be viewed as
118 complementary rather than competing. In addition, direct numerical simulations can determine
119 input variables for pore-network models and therefore assist in further upscaling macroscopic
120 calculations (Raeini et al., 2014a).
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137 Figure 1: Schematic of the application of pore-scale modeling. The green line depicts a well log (such as porosity)
138 identifying the flow unit (a lithologically preferable zone for production). At a particular flow unit, core plugs are
139 extracted and images of them acquired to quantify the pore structure. The information is fed to a pore-scale model in
140 order to determine the relationship between several macroscopic properties. These relationships are used subsequently in

141 other flow units. Pc: capillary pressure; Sw: water saturation; φ: porosity; K: permeability; XCT: X-ray computed
142 tomography; SEM: scanning electron microscopy.

143
144 Figure 2: Topics covered in this chapter and their contribution to the creation of a pore-scale model. Since pore-network
145 modeling is a reduced-ordered method, direct numerical simulations can not only be used for predicting the rock
146 sample’s transport properties, but also inform pore-network modeling algorithms. In carbonates, similar to other
147 unconventional systems, experimental data is not always available for benchmarking purposes. Since direct numerical
148 simulations sacrifice pore space geometry and fluid flow behaviors to a lesser extent than pore-network models, they can
149 serve a purpose in reducing the latter’s uncertainty.

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151 2.Methods
152 2.1. Pore geometry creation
153 Capturing the pore geometry is essential to fabricating a reliable pore-scale model. Three
154 approaches that pursue this purpose gather their information from images (image-based method),
155 replicate the geologic processes of the rock (process-based method) or are based on statistical
156 description of the porous medium (stochastic).
157
158 2.1.1. Imaging as a source of information for rock models
159 Imaging techniques have the potential for providing detailed descriptions of the pore space that
160 can be utilized for numerical simulation schemes. X-ray computed tomography (X-ray CT) is a
161 well-established and rapid approach to acquiring three-dimensional visualizations of the pore
162 structure. The method distinguishes phases based on density and atomic number variations that
163 attenuate the X-rays differently. X-ray CT is non-destructive, meaning that unlike other imaging
164 techniques such as petrographic light microscopy and scanning electron microscopy, the rock
165 sample is not cut or polished. The resolution of X-ray CT ranges from 100 nm to 1 millimeter
166 (Bultreys et al., 2016) and has an inverse relationship with the domain size.
167
168 Once a three-dimensional visualization is obtained and processed such that its quality is
169 acceptable, the image is “segmented” into phases of interest, normally the pore space and the
170 solid phase. Any pore-scale numerical analysis of the image is thus conducted based on the
171 segmented image. Image processing, although conceptually simple, can be challenging in
172 geomaterials due to the presence of artefacts such as beam hardening (Van de Casteel et al.,
173 2002) or when the sample is not held in a stable position properly. Given the many sources of
174 uncertainty in processing a micro-CT image, completely automatic processing workflows are not
175 yet established, leaving many image filtering and segmentation attempts dependent on the
176 operator’s judgement (Iassonov et al., 2009). The current subjective nature of image analysis
177 highlights the importance of core data measurements to validate a processed image prior to using
178 it to predict unavailable transport properties. Such validations may become especially important
179 in carbonates given the higher sensitivity of near-resolution pores of becoming dismissed during
180 image filtering and segmentation. Carbonates present an additional challenge for capturing their
181 pore-space in a single micro-CT image given their multiscale pore structure. Pore scales can
182 range from sub-resolution nanometer sized pores to interparticle pores and up to larger scale
183 vugs and microfractures. This range in scale can make the capture of carbonate pore spaces in a
184 single image unfeasible (Victor, 2017). To circumvent this limitation, a top-to-bottom approach
185 can be adopted where following a coarse-scale three-dimensional CT image, high resolution
186 micro-CT images from targeted regions are acquired (Arns et al., 2005). A combination of other
187 imaging methods to gather the higher resolutions information can be implemented as well. The
188 transport properties determined from the high-resolution pore structures are subsequently scaled
189 up to establish the transport property of the larger domain (we provide a discussion on this topic
190 in Section 2.3). For a complete review on image processing refer to Heilbronner and Barrett
191 (2013), Serra (1982), and Wildenschild and Sheppard (2013). Figure 3 shows an example of (a) a
192 micro-CT image, (b) pore-solid surface visualization after segmentation and (c) a pore-network
193 representation of the pore space (to be discussed later in the chapter). In this paper, we refer to a
194 pore space generation that is completely based on a three-dimensional image as an “image-based
195 pore-scale model”. As we discuss other pore space generation methods, overlaps between the

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196 three methods exist and our classification serves as a point of reference rather than a rigid
197 framework.
198

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200 (a) (b) (c)
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202 Figure 3: (a) Example of micro-CT images of a Ketton limestone sample at a resolution of 2.65
m (b) pore-solid surface
203 extracted after segmentation and (c) a pore-network representation of the pore space (Blunt et al., 2013).

204
205 Light microscopy and scanning electron microscopy are two-dimensional image acquisition
206 techniques that provide micrometer and nanometer scale information respectively (see Figure 4a-
207 b for an example of each). For light microscopy, the pore space of a rock sample is filled with
208 blue epoxy and a 30-micrometer-thick thin-section is cut. Polarized light is emitted through the
209 sample to determine the grain mineralogy, visible porosity and paragenesis (the chronology of
210 geological events occurring during rock formation). For scanning electron microscopy, electrons
211 are bombarded on a polished carbon coated rock surface. The surface scattered electrons (called
212 secondary electrons) and those that are backscattered due to elasticity, which carry information
213 from a higher depth, are analyzed to infer the surface topography of the solid phase. Using
214 similar bombardment, mineral atoms can be excited which release X-rays when they return to
215 their stable state. This is referred to as Energy Dispersive Spectroscopy (EDS) which gives
216 information of the mineral composition of the rock. The disadvantage of utilizing light and
217 scanning electron microscopy is the fact that they are two-dimensional. Numerical methods for
218 extrapolating such information to three-dimensions are non-trivial and will be discussed further
219 in Section 2.1.3 as part of stochastic methods. Confocal laser scanning microscopy (CLSM),
220 with a prior application in biology, has been leveraged to quantify the pore texture of rocks
221 (Fredrich, 1999; Fredrich et al., 1995). In this method, a laser beam is focused on the domain of
222 interest and its reflection is detected and analyzed. This method produces sub-micron lateral
223 resolution with lower vertical resolution depending on material type and magnification (with the
224 higher magnification having larger vertical resolutions). Given the limitations in vertical
225 resolution, two-dimensional CLSM images can benefit from extrapolation techniques discussed
226 in Section 2.1.3 as well. Recent work by Jobe et al. (2018) has shown CLSM’s application in
227 acquiring two-dimensional images of micropores in carbonate samples (Figure 4c) and utilizing
228 them to capture their pore topology with stochastic extrapolation methods (Wu et al., 2006).
229

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231 (a) (b)
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255 Figure 4: Examples of (a) a plane polarized light microscopy image of ooids in a carbonate rock sample – the horizontal
256 axis is 2.0mm (Scholle and Ulmer-Scholle, 2003), (b) an Indiana limestone secondary electron image (Freire-Gormaly et
257 al., 2015) and (c) confocal laser microscopy images of intraparticle microporosity of Arab D carbonate rock samples (Jobe
258 et al., 2018).

259 Focused ion beam scanning electron microscopy (FIBSEM) is a technique with nanometer scale
260 resolution for capturing the pore texture of sub-resolution micro-CT pores in three dimensions
261 (Bera et al., 2012; Wirth, 2009). Figure 5 shows an example FIBSEM image stack of a chalk
262 sample. In FIBSEM the sample is sliced with ion beams and an SEM image is taken for each
263 stack. Although valuable information can be gained with this imaging modality, namely the 3D
264 interconnectivity of pores, the financial and time cost of acquiring a FIBSEM image stack
265 renders them intractable for routine use. Given the destructive nature of FIBSEM acquisition

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266 during beam slicing, uncertainties associated with pore space connectivity can be exasperated as
267 well. Finally, in addition to challenges in image registration, the rendered domain is very small
268 such that a quantitative assessment of flow properties become questionable (Kelly et al., 2016).
269 FIBSEM therefore is an ideal technique for diagnostic purposes and as a supplemental tool along
270 with other image acquisition methods for carbonates (Sok et al., 2010). When micro-CT imaging
271 becomes insufficient to reveal the sub-resolution pore space, FIBSEM can provide information
272 on the presence of critical pore connectivity within sub-resolution pores as well as at the
273 interface of sub-resolution and resolved pores. Furthermore, given the complex carbonate
274 diagenesis that result in amorphous pore shapes, FIBSEM can provide a clearer picture of pore
275 morphology. FIBSEM uncertainties associated with ion beam slicing, electron charging and
276 resolution limitations (Dewers et al., 2012) can be mitigated by calibration with macroscopic
277 measurements such as nitrogen-sorption hysteresis (Mehmani and Prodanovic, 2014a;Xu and
278 Prodanovic, 2018). However, much work is needed to establish robust workflows for such
279 calibration purposes.
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281

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283 (a) (b)
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285 Figure 5: (a) A two-dimensional FIB image of a chalk sample and (b) its corresponding three-dimensional reconstruction.
286 From Tomutsa et al. (2007).

287 Data storage and management are challenges in image-based characterization of porous media.
288 For instance, X-ray microtomography images typically have 20003 voxels (the storage necessary
289 is 8GB or 16GB depending on whether 1-byte or 2-byte integers are used to store attenuation
290 coefficients for each voxel) and can triple in size if stitching along axial direction or if helical
291 scanning is conducted. Furthermore, recent multi-beam scanning electron microscopes (e.g.
292 Zeiss MultiSEM) use up to 91 parallel beams and can collect areal images with approximately 5-
293 nm resolution at a scale of several square millimeters. While the resulting tiled images are
294 getting close to covering representative areas (Keller et al., 2014; Kemen et al., 2015) for
295 heterogeneous media, with a size of more than 200GB their display and analysis is challenging.
296 Due to the resultant “big data”, a repository for retaining, retrieval, sharing, and organization of

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297 acquired images and their analyses can be valuable for enhancing research for
298 modeling/prediction of porous material properties.
299
300 One of the new research data management tools, Digital Rocks Portal (Prodanovic et al. 2015)
301 allows managing, preserving, visualization and basic image analysis of available images of
302 porous materials and experiments performed on them. It can accommodate storage of any
303 accompanying measurements (porosity, capillary pressure, permeability, electrical, NMR and
304 elastic properties, etc.) required for both validations on modeling approaches and the upscaling
305 and building of larger (hydro)geological models. As of the end of 2018, Digital Rocks Portal
306 currently published 58 samples, and is expected to have a representative population of samples
307 for every lithology. Carbonate examples range from petrophysical characterization of
308 pore/vug/fracture space, to wettability (contact angle) measurements and precipitation
309 experiments
310 (Alhammadi et al., 2018; Baek and Tae-Hyuk Kwon, 2018; Bultreys et al., 2017a, 2017b, 2018;
311 Heidari and Posenato Garcia, 2016; Khan et al., 2018; Khan and Pope, 2018; Muljadi, 2015;
312 Prodanovic et al., 2016; Scanziani et al., 2018; Singh and Blunt, 2018; Victor and Prodanovic,
313 2017). While other general data storage options exist (e.g. Mendeley Data for any data1, and
314 Energy Data Exchange2 for energy/subsurface focus), they lack tools for viewing 3D datasets
315 within browser and specialized analysis or ability to produce digital object identifiers for
316 referencing in publications.
317
318 2.1.2. Process-based rock models
319
320 Process-based methods are based on replicating the chemical and mechanical rock formation
321 processes on grain scale. Following this approach, the pore-scale model can link formation
322 properties with any burial stage process throughout the diagenesis. This pore space generation
323 method is important not only for understanding the first principles of the rock transport
324 properties, but also as a practical tool in extrapolating information from one portion of the
325 reservoir to the next (that is extrapolating transport information from one burial stage to another).
326 Process-based implementations on image-based methods (a hybrid process-image-based method)
327 is considerably difficult since image acquisition during an experiment that is scaled to laboratory
328 conditions and capturing the mechanical and chemical processes throughout the formation stages
329 is not trivial. Most often it is essentially the “end result” that is imaged and characterized. The
330 starting point of process-based methods is typically an unconsolidated grain pack. At each burial
331 stage, pertinent diagenetic processes are included. Such processes can be grain rearrangement
332 and ductile deformation due to compaction, cementation of various minerals as well as grain
333 dissolution. Process-based approach, though powerful in its motivation, compromises complexity
334 by simplifying the grains to ideal shapes such as spheres or ellipsoids. This approach is in
335 particular challenging in carbonates given their complex diagenesis rendering it difficult to
336 formulate each diagenetic step to be quantitatively.
337

1 https://data.mendeley.com/
2 https://edx.netl.doe.gov/

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338 In a pioneering work on process-based methods, Bryant et al. (1993b) modeled compaction and
339 cementation on a disordered monodisperse grain pack. In this technique, the grain deposit is
340 replicated based on experimental measurements of ball-bearings packed in a rubber bladder
341 (Finney, 1970a). Compaction is modeled by overlapping the grains and for cementation, the radii
342 are increased without moving the grain centers. The researchers subsequently used a pore-
343 network model to simulate permeability and drainage capillary pressure and relative permeability
344 curves (Bryant and Blunt, 1992; Bryant et al., 1993a). Bakke and Øren (1997) and Øren et al.
345 (1998) developed low-energy and high-energy sedimentation modeling schemes for the initial
346 grain pack and subsequently added cementation and compaction to represent the formation of the
347 rock. Thin-section analysis of a Bentheimer sandstone sample was used to inform the model in a
348 case study. In addition, Torskaya et al. (2014) have included pore-filling and throat-filling
349 cementations into a disordered packing and studied its effects on absolute permeability and
350 drainage fluid properties. Hosa and Wood (2017) utilized a single-scale process-based method to
351 investigate the impacts of early calcite cementation on porosity-permeability relationships in
352 carbonate rocks. They differentiated grains into monocrystalline (capable of syntaxial
353 cementation) and polycrystalline (with a characteristic isopachous cementation) and simulated
354 single-phase incompressible flow directly on the pore space with a lattice Boltzmann algorithm.
355 Although their method captured the log-log relationship between permeability and porosity
356 observed in experiments, they overestimated permeability potentially due to the very high
357 permeability value of the initial synthetic grain pack.
358
359 Establishing the initial grain pack is not trivial. One of the recent, popular grain packing
360 algorithms is cooperative sphere rearrangement (Thane, 2006). In this method, a set of initial
361 points in a three-dimensional domain is randomly selected. Spheres of a predetermined size
362 distribution are grown with their centers at randomly selected points. Each sphere grows at a rate
363 proportional to its ultimate size. When overlaps occur, the sphere centers are moved apart. If the
364 removal of overlap is not possible, a different sphere size is selected. Another approach to
365 establish the starting point is based on a discrete element method (DEM) in which the translation,
366 rotation as well as interaction of grains are numerically modeled (Cundall and Strack, 1979;
367 Holtzman et al., 2008; Jin et al., 2003).
368
369 Torskaya et al. (2014) studied the impact of grain shapes on permeability, formation factor and
370 drainage capillary pressure. They concluded that permeability can have a difference of up to 1.6
371 times for a sandstone sample if grain shapes are ignored. Formation factor and drainage capillary
372 pressure however remain within a 20% difference in their study. Garcia et al. (2009) developed a
373 method to study the impact of irregular grain shape on single phase flow properties. Each
374 irregular grain was a cluster of several spherical ones that made the implementation of DEM in
375 simulating its sedimentation feasible. DEM has also been coupled with drainage capillary
376 movements (Prodanović et al., 2009) to investigate the impact of invasion forces to grain
377 displacement. In other work, Mirabolghasemi et al. (2015) coupled DEM with computational
378 dynamic modeling for single phase flow to predict the amount of particle entrapment in porous
379 media. Modeling ductility has been introduced by Mousavi and Bryant (2012) and Thane (2006)
380 to a well-arranged grain pack. In this method, a ductile grain is assumed to have a hard center.
381 The ductile shell is penetrated by an adjacent rigid grain and the ductile materials are conserved
382 by increasing the radius of the ductile grain. For carbonate rocks, several classifications for pore-
383 scale process-based modeling has been introduced based on thin-section observations (Mousavi

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384 et al., 2012). Figure 6 shows three of such diagenetic processes namely, cementation, fracturing
385 and grain dissolution that originated from sedimentary packings. Because certain types of
386 diagenesis, such as dissolution and micro-fracture generation, impose integration of pores from
387 multiple scales, the development of such models is not straightforward.
388

389
390 (a) (b) (c)
391 Figure 6: Examples of modeling approaches for cementation (a) inclusion of fractures (b) and grain dissolution (c)
392 (Mousavi et al., 2012)

393 Recent advances in process-based methods have focused on modeling the integration of pores
394 over multiple length scales for both carbonates and tight porous media. van der Land et al.
395 (2013) used conceptual thin-section models of several carbonate rock types and predicted the
396 impacts of cementation and dissolution on the permeability, drainage capillary pressure and
397 relative permeability curves. Pore-network models were extracted after translating the two-
398 dimensional conceptualizations into three dimensions using stereographical methods as
399 discussed in Section 2.1.3. A secondary smaller scale pore network was then connected with the
400 pre-dissolution pore network model following a stochastic method developed by Jiang et al.
401 (2013b). Mehmani and Prodanović (2014b) introduced novel deterministic methods to explicitly
402 integrate intraparticle microporosity with interparticle macroporosity following geological
403 causes. In their method to include microporosity, a network model is scaled down and planted to
404 targeted grains and interparticle pores based on information gathered from light or scanning
405 electron microscopy. The micro-network is then stitched to its adjacent (interparticle)
406 macropores. Figure 7 shows a schematic of the method. Mehmani et al. (2015) developed
407 algorithms to explicitly include vugs and microcracks adjacent to interparticle pores. Vugs are
408 included as larger pores centered on a randomly chosen interparticle pore and subsequently
409 connected to the vug’s surrounding pores (Figure 8a). A microcrack is included by two parallel
410 planes with a particular orientation that is imposed on a single-scale network model. All pores
411 falling within the planes are removed and microcrack pores are added to the empty space instead
412 (Figure 8b). Mehmani and Prodanović (2014b) present several simulations of drainage and
413 imbibition for networks that include microporosity. Figures 9 presents the primary quasi-static
414 capillary pressure drainage simulations for vuggy carbonates with different porosities (φ) and a
415 vug to pore scale difference of 5, and carbonates with a single microcrack with varying angles θ
416 of the crack axis with respect to the flow direction. The initial grain pack of each network has a
417 uniform radius of unit 1 and the side length of the cube is 20 units. The considerably lower

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418 percolation threshold of the vuggy pore-network model at a porosity of 0.62 is due to the
419 significant volume of a well-connected network of vugs. As was shown by Pak et al. (2016),
420 such percolation thresholds can be used as calibration points to fine-tune multiscale pore
421 networks by matching mercury injection data. Systematic comparisons of two-phase flow
422 behaviors of multiscale pore-network models with experimental data is however currently
423 pending.
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446 Figure 7: Two-dimensional schematic (top) of explicitly including (a) grain-filling and (b) pore-filling microporosity. Red
447 lines indicate throats that connect two different scales (that have been referred to as micro and macro network). Three-
448 dimensional visualizations of the pore-network models are at the bottom (Mehmani and Prodanović, 2014b).

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486 Figure 8: (a) 2D schematic on top shows how a vug is incorporated into the pore throat network: the grains as well as
487 original pores are removed from the location where a disk-shaped (sphere-shaped) vug is placed. 3D model on bottom
488 shows the original network, as well as the model after placement of a number of vugs. (b) 2D schematic and a 3d
489 example model of including a fracture (plane) into an
490 interparticle pore-network model (Mehmani et al., 2015).

491
492 (a) (b)
493 Figure 9: Primary drainage capillary pressure curves of (a) a vuggy carbonate rock (with a scale difference of 5) and (b) a
494 carbonate rock with a single microcrack (with a scale difference of 5) at three axis angles with respect to the pressure
495 gradient direction. Drainage is simulated on pore-network models described in Figure 8.

496
497 2.1.3. Stochastic methods for geometry creation
498

13
499 Stochastic methods rely on several critical source information to generate the pore space. This
500 method is in contrast with image-based methods which capture the entire pore space from a
501 three-dimensional image, and process-based methods, which attempt to generate the pore space
502 by following the diagenesis. It is important to note that the three pore-space generation
503 techniques can have overlaps, for instance, two-dimensional images with process-based
504 adjustments (van der Land et al., 2013) can be a source for stochastic methods. Given the
505 aforementioned uncertainties in capturing the carbonate pore texture via images and difficulties
506 in replicating the geological processes for a process-based approach, statistical descriptions have
507 the potential to constrain pore-scale models if accurate quantitative descriptions of the pore space
508 are provided. Stochastic approaches can in addition expand the limited domain size of an image
509 by extrapolating the mathematical descriptions to larger domains. Furthermore, three-
510 dimensional images of a porous medium may not be available, may not provide important
511 information on mineralogy where microscopy is crucial or may cover too small of a volume to
512 infer representative information on porosity (or any other property). In such cases, extrapolating
513 two-dimensional information to three-dimensions can be possible via stochastic methods. One
514 stochastic method is multiple-point statistics which utilizes two-dimensional images as “training
515 images” to construct the pore-space pattern in three-dimensions (Caers, 2001; Okabe and Blunt,
516 2004; Tahmasebi and Sahimi, 2013). In the context of predicting the transport properties of
517 porous media, it has shown to perform better than two other stochastic reconstruction methods:
518 object-based methods, which relies on the geometrical descriptions of the “objects” comprising
519 the porous medium such as grains, and pixel-based methods, that typically aim to minimize the
520 lower order statistical properties of a sample (Tahmasebi et al., 2016).
521
522 Conceptually, stochastic creation can apply to both pore space images and pore networks. For
523 pore networks, however, Sok et al. (2002) showed that a sole reliance on a finite number of
524 statistical descriptors extracted from images, and attempting to replicate them by modifying a
525 regular network without including the topological properties of the pore space, can result in high
526 errors in flow predictions. Multiple point statistics for imaged pore space reconstruction, on the
527 other hand, honors the pore space patterns and spatial relationships of the pore space by
528 matching a multipoint statistical property such as the cross-correlation function of a “training
529 image”. Figures 10 and 11 give examples of utilizing multiple point statistics in reconstructing
530 the pore space of carbonate rock samples. The method’s accuracy, however, relies on the
531 representativeness of the two-dimensional training image. A two-dimensional training image, as
532 was discussed in Section 2.1.1, might not capture the multiscale pores of a carbonate sample that
533 exist in close proximity due to the selected field-of-view (which has an inverse relationship with
534 voxel resolution). Further, image acquisition artifacts, as a result of milling in SEM for example,
535 propagate to the three-dimensional reconstruction. Finally, the reconstruction extrapolates the
536 cross-section information (pore space shape, etc.) into the orthogonal direction, whether that is
537 correct or not.
538
539 Although predictions of single phase permeability using multiple-point statistics reconstructions
540 are encouraging when compared to experimental data (Okabe and Blunt, 2004), further work is
541 required to investigate the reliability of multiple point statistics, or other stochastic methods (van
542 der Land et al., 2013; Wu et al., 2006), for multi-phase flow behaviors. This necessity for
543 additional work is because multiphase transport properties in general are more sensitive to pore
544 structural properties. Recent work on stochastic methods have involved machine learning

14
545 techniques. Mosser et al. (2017) for example utilized a generative adversarial neural network
546 (GAN) method to reconstruct three-dimensional pore space representations using training micro-
547 CT images in a computationally effective way. The method is capable of capturing pore space
548 heterogeneity in all three dimensions and can store the trained hyper-parameters and reuse them
549 for multiple realizations. The researchers applied GAN to recreate Keystone limestone and the
550 statistical descriptions of pore morphology and single-phase permeability between the original
551 and reconstruction were in close agreement. Experimental verification of such methods is
552 currently pending.
553

554
555
556 Figure 10: Example multipoint statistics method for extrapolating two-dimensional images of a carbonate sample to
557 three-dimensions and predicting the permeability-porosity relationship (Karimpouli and Tahmasebi, 2016).

558
559
560
561
562
563
564
565
566
567
568
569
570 (a) (b)
571 Figure 11: (a) A binarized image of a back scattered electron image of a carbonate rock sample (512x512 with 0.345
572 m/pixel) and (b) a three-dimensional reconstruction of it using a multi-point statistical reconstruction method (Okabe
573 and Blunt, 2005). Predicted permeabilities for carbonates have shown to overestimate by a factor of 3 when compared
574 with experimental data but were considered acceptable given the model and experimental domain size differences (Okabe
575 and Blunt, 2004).

576 2.2. Simulation methods

577 2.2.1. Pore-network generation schemes
578 Modeling the transport properties of a porous medium depends on its pore structure. It is
579 therefore imperative in a predictive model to capture the pore space of a rock as accurately as
580 possible. Once the pore-space is fully resolved, so-called “direct numerical” methods can be

15
581 implemented to conduct multiphase flow simulations (see Section 2.2.4). A major challenge in
582 direct numerical methods is the computational cost that comes with the detailed description of
583 the pore space. Pore-network modeling was first introduced by Fatt, (1956a, 1956b, 1956c) to
584 introduce interconnectivity and three-dimensional spatial organization; which was in contrast to
585 a previous representation of pore space as bundle of tubes. Although pore-network modeling is
586 conceptually represented as three-dimensional diagrams composed of balls (for pores) and sticks
587 (for throat), details for their generation vary. Fluid interaction rules in pore-network modeling
588 are based on analytical derivations of meniscus instability based on experimental fluid dynamic
589 observations which were first attempted by Lenormand and Zarcone (1984). Although in its early
590 conception pore-network modeling was considered a computationally cost-effective method for
591 fluid flow predictions in porous media, with the advancements in computational power, modern
592 pore-network models have become essentially upscaling schemes that incorporate sub-pore scale
593 physics derived from either direct numerical simulations or experiments (Aghaei and Piri, 2015;
594 Zolfaghari and Piri, 2017a, 2017b). Pore-network models and direct numerical simulation should
595 therefore not be considered as rivals.
596
597 In a pore-network model, throats are defined by Bear (1991) as fluid pathway cross-sections with
598 minimal hydraulic radius (defined as the ratio of area to perimeter of the cross-section). Pores are
599 then spaces enclosed by grains and throats. Although the concept of a pore-network
600 representation is simple, dividing any given pore space into pores separated by throats in a
601 unique way is non-trivial. Figure 12 demonstrates how an image-based pore-network
602 construction algorithm can add uncertainties in numbers of pores. However, as hinted in the
603 caption of Figure 12, regardless of the local choice made in identifying a local throat (and/or
604 whether it separates two pores), the flow simulation should ultimately make that local choice
605 irrelevant.
606

607 (a) (b) (c)

608
609 Figure 12: In each of these conceptual cases (figure reprinted from (Prodanović et al., 2006)), pore
610 partitioning algorithms will likely place a throat labeled “a-b” given the local minimum of hydraulic radii.
611 From the point of drainage, however, case (a) acts like a single pore, and the fact that it was identified as two
612 pores does not make a difference in averaged flow properties. Case (b) can be considered having two pores or
613 only one and case (c) is a two-pore system.
614
615 We next describe several generations of pore partitioning algorithms for image-based porous
616 media. We start with medial-axis algorithms. Maximal balls and watershed algorithms are
617 described next. The latter two use intuitive ideas to partition pores and are less computationally
618 demanding. Thus, they are currently most commonly used in the digital rock petrophysics
619 community.
620

16
621 Early pore-throat network extraction methods utilize medial axis as a search tool (Liang et al.,
622 2000; Lindquist and Venkatarangan, 1999). After image filtering and segmentation, the medial
623 axis (Lee et al., 1994), that is, the pore space skeleton that runs approximately in its middle, is
624 extracted. Throats are identified on a medial axis path that has a continuous sequence of
625 grains/particles and minimal area/perimeter (Lindquist et al., 2005; Shin et al., 2005) along that
626 path is recognized as the throat perimeter. Pores are subsequently determined following a
627 labeling algorithm after throat barriers are identified in digital space (Jiang et al., 2007;
628 Prodanović et al., 2006) – see Figure 13 for a schematic from (Mehmani et al., 2011), and Figure
629 14 and Figure 15 for the example 3D throat and pore. The algorithms in this group work well for
630 consolidated materials where continuous path of grain voxels bounding a throat barrier (see
631 Figure 14a) can be identified in desired location. Despite the throat channel visualization shown
632 in Figure 14, its limits are somewhat arbitrary. The algorithm finds each throat surface and
633 barrier (barrier refers to a collection of voxels intersected by a throat surface) but there are no
634 clear criteria based on an image that can identify the beginning and end of a corresponding throat
635 channel. This is the case for most algorithms. Either pore-throat-network visualization or pore-
636 network models, however, often require definition of a straight throat channel and those are often
637 taken as straight lines between pore centroids (though in reality, those paths are not straight).
638 Some level of arbitrariness thus exists in establishing image-based pore-throat networks. In an
639 extension of medial-axis pore partitioning algorithms, Jiang et al. (2017) have extracted pore-
640 network models from fractured rocks and demonstrated good agreement with analytical
641 equations and direct numerical simulations for single phase flow and experimental values for
642 drainage residual saturations. For unconsolidated/granular packs (in general, more porous
643 materials) watershed and/or Delaunay tessellation perform better.
644

645
646 Figure 13: Image-based pore-throat network extraction. After segmenting the raw image into grain and pore spaces, the
647 medial axis of the pore space is extracted using a thinning algorithm (Lee et al., 1994). The medial axis is then used to
648 identify throat barriers and partition pores.

649
650 (a) (b) (c)
651 Figure 14: (a) Medial axis path voxels extracted from a 3D Berea sandstone image in red with a throat
652 perimeter voxels identified in brown. Grain and pore voxels are not shown. Voxels in blue are throat barrier
653 voxels used in subsequent pore labeling. (b) Corresponding triangulated throat surface is shown in white. (c)

17
654 Dark red shows the pore-grain surface corresponding to the channel where the throat (surface shown in
655 white) is identified.
656

657
658 Figure 15: An example pore from a sandstone image with throats barriers, medial axis paths in the search
659 are identified in red. Note that there are two branching points of the medial axis identified within this pore:
660 the branching points of medial axis and pore centers are not in one-to-one correspondence.
661
662 In maximal balls algorithm (Silin et al., 2003), Euclidian distance labels are interpreted as a
663 radius of a maximal ball that can be inscribed inside of the pore space at that point. After that,
664 the balls are processed to identify intersections. For two balls that intersect, the smaller one is
665 identified as a “slave” of the larger (“master”). At the end of the algorithm, master balls represent
666 pore centers. If two master balls have two intersecting slave balls, that location (and radius)
667 identifies a throat. If throat location and radius are ample information for characterization and/or
668 modeling, these algorithms work well. The actual throat barrier such as the ones exemplified in
669 Figure 15 (or those by watershed algorithm in Appendix) are more difficult to obtain.
670
671 Watershed partitioning locates throat surfaces and is relatively easy to implement. This makes it
672 one of the most popular algorithms: we describe it next and we exemplify it in Appendix. In the
673 watershed pore partitioning algorithm, the binarized image is processed to produce the Euclidean
674 distance field (i.e. for each voxel of the phase of interest is labeled by the distance to the closest
675 voxel of the other phase). The Euclidean distance is thought of as the topographic height function
676 and inverted so that local maxima become local minima. The algorithm partitions the phase of
677 interest into “watershed basins”: water dropped inside a region will end up at the same low point.
678 This type of algorithm is widely implemented in software (e.g. ImageJ, MATLAB, Avizo) and is
679 used in a number of partitioning applications, e.g. for separating individual grains in a sand or
680 sandstone image (Thompson et al., 2006) and pore-throat networks (Sheppard et al., 2006). Since
681 watersheds are very intuitive and widely implemented, we provide an example in the Appendix.
682 All watershed algorithms suffer from noise, however, in the sense that every local minimum
683 (maximum in the original image) will produce a corresponding region. Thus, one has to filter the
684 number of starting local minima in some way in order to produce meaningful partitioning or find
685 a criterion for region merging afterwards (see 3D example in the Appendix for example). If one
686 was to compare to medial-axis based search algorithm result in Figure 14, the local minima
687 corresponding to the medial axis branching points would have to be merged or else the algorithm

18
688 would result in labeling two pores instead of one. Such discrepancies in pore indexing should not
689 affect the average flow properties.
690
691 For granular materials or weakly consolidated sandstones with relatively narrow distribution of
692 grain sizes, a simple pore-network generation method based on the early work of Finney (1970a)
693 can be used. This method, which is very suitable for process-based modeling, assigns the pores
694 and throats to the interiors and faces of tetrahedra identified in tessellation of grain centers.
695 Figure 16 shows a schematic of extracting a pore-throat networks from a grain pack. Some
696 merging of the pores (identified by corresponding overlap of inscribed spheres) is typically
697 necessary (Al-Raoush et al., 2003). The above pore-network generation algorithms are general
698 and any adjustment to the pore-network that is required to establish a model more suitable for a
699 carbonate sample (such as integration of sub-resolution micropores or inclusion of rugosity for
700 film flow) should be implemented on the extracted pore-network.

701
702 (a) (b) (c)
703 Figure 16: Delaunay tessellation schematic for identifying a pore-throat network in granular media. (a)
704 Delaunay tessellation input is a packing of grains (spheres in this work). (b) Tetrahedral cell representing a
705 pore defined by four neighboring spheres. The pore space within each tetrahedron represents pore, and the
706 tetrahedral sides are the tightest cross-sections (throats) on the path between two neighboring pore centers.
707 (c) The final result is a network of pores (shown as spheres, colored/shaded by size) and throats (identified as
708 cylindrical connections). Figure modified after Mehmani and Prodanović (2014b).

709
710 2.2.2. Pore-network modeling of single-phase flow and solute transport
711 Mechanisms contributing to the transport of a passive tracer are advection and molecular
712 diffusion. Their relative dominance is quantified by the dimensionless Péclet number vL/D),
713 where v is fluid velocity, L is a characteristic length scale and D is the bulk fluid diffusivity.
714 When majority of solute particles have had the opportunity to experience the entire range of
715 interstitial fluid velocity, in other words, solutes have traveled beyond the correlation length of
716 the porous medium, the traversing plume take the form of Gaussian distribution. In this scenario
717 diffusion follows Fick’s law in that mass diffusion rate becomes linearly proportional to the
718 concentration gradient. In addition, diffusion length scales with the square root of time and the
719 average solute velocity equals to Darcy velocity. This solute transport behavior is referred to as
720 “Fickian”. Due to the complex and heterogeneous pore structure of carbonates, solute transport
721 oftentimes takes a “non-Fickian” form and its prediction has been the focus of pore-scale
722 modeling efforts (Bijeljic et al., 2004, 2011).
723

19
724 The direct modeling of mass transport requires the solution of the Navier-Stokes equation
725 coupled with a set of species’ mass balance equations. The numerical framework can either be
726 grid-based (Eulerian) or based on tracking Brownian particles within the pore space
727 (Lagrangian). Given the computationally intensive nature of direct methods, pore-network
728 models are often used for modeling single-phase and solute transport, although direct numerical
729 simulation of single-phase flow has recently become more tractable. Prior to modeling transport,
730 the flow field is computed. In Eulerian pore-network models, species balance is imposed at each
731 pore. It is also often assumed that pore concentrations are uniform, which can potentially lead to
732 errors in high Péclet numbers. This is referred to as the Mixed Cell Method (MCM) (Acharya et
733 al., 2007; Bryntesson, 2002; Kim et al., 2011; Li et al., 2006; Mehmani et al., 2012; Nogues et
734 al., 2013). Mehmani et al. (2014) improved MCM by accounting for imperfect mixing within
735 pores using a streamline splitting based method. Significant improvements in macroscopic
736 transverse dispersion were reported in 2D ordered micromodels. The improvements however
737 were minor for 3D disordered sphere packs. Mehmani and Balhoff (2015a) addressed another
738 shortcoming of MCM by incorporating shear-induced dispersion caused by non-uniform velocity
739 profiles within pore throats. The result was an improvement in macroscopic longitudinal
740 dispersion in disordered media at high Péclet numbers. Lagrangian methods, which are more
741 accurate but computationally expensive for continuous injection problems, require the tracking
742 of particles via discrete (Bijeljic et al., 2004; Bruderer and Bernabé, 2001; Jha et al., 2011) or
743 continuous temporal transition probabilities (Rhodes et al., 2009; Sahimi et al., 1986; Sorbie and
744 Clifford, 1991). However, they have shown to reliably predict the non-Fickian behavior of
745 carbonate rocks when implemented directly on pore-scale images (DNS method) (Bijeljic et al.,
746 2013). Mehmani and Tchelepi (2017) showed that a pore-network framework for solute
747 transport at moderate to high Péclet numbers is accurate only if (1) network extraction is
748 informed by the interstitial flow rate (2) a Lagrangian framework is used for particle tracking and
749 (3) an accurate mapping of particles between pores is implemented. The accuracy of using pore-
750 networks for carbonates has not been established yet. For a detailed review of pore-network
751 modeling of solute transport in porous media we refer the reader to Mehmani and Balhoff
752 (2015b).
753 2.2.3. Quasi-static versus dynamic pore-network modeling of multiple phases
754 In a pore-network model, pores hold the volume and contribute to the critical curvature for
755 percolation during imbibition whereas throats represent conductivity and critical curvature
756 during drainage. Drainage and imbibition at low capillary numbers are modeled with an
757 invasion-percolation algorithm. In this method, a given capillary pressure is imposed on the
758 network domain at the inlet and the invading phase occupies the pores based on the critical
759 curvature of pores/throats and certain trapping criteria (Bryant and Blunt, 1992; Mason and
760 Mellor, 1995). The hydraulic conductivity (also referred to as effective permeability) for each
761 phase is then calculated by writing systems of equations based on imposing mass conservation at
762 each pore.
763
764 Table 1 shows a number of representative publications on pore network modeling over the past
765 several decades. The rows of the table are organized chronologically, starting with Fatt‘s seminal
766 work (Fatt, 1956a, 1956b, 1956c) which first introduced 2D pore networks as a way to study
767 porous media flow properties. The columns have been organized as follows:
768
769 • Contributing author(s) and year of publication.

20
770 • A short summary of the work, including key innovations and/or findings.
771 • Type of grids used, including nature of pore types: This also includes size of the grid
772 used to represent REV. If applicable, this also includes the resolution and size of the
773 physical sample image from which the pore network was derived, or which the pore
774 network was targeting. If no physical image was used, then the sides of the grid are
775 dimensionless. If multiple similar samples with different grid sizes were used, the largest
776 grid size is reported. The size is very interesting for future use in designing a pore-scale
777 study, as it shows increasing computational power does not necessarily mean using larger
778 sample sizes.
779 • The type of physics incorporated: Since pore networks can use either quasi-static or
780 dynamic methods to model fluid flow, this is an important feature. As one goes down the
781 rows of the table, towards more modern pore networks, the physics becomes increasingly
782 sophisticated, incorporating both two- and three-phase flow, wettability and trapping.
783
Table 1: Pore-network modeling literature: key representative journal publications over
the years
Author(s), Key innovation/summary Grid type(s)/size Physics
year incorporated

Fatt [1956] Introduced pore-network modeling. 2D Regular lattice, of Quasi-static, 2

Examined, qualitatively, effects of square and hexagonal phase
different properties of a 2D network shapes
on Pc-Sw, kr-Sw curves
Dodd, Kiel Generated Pc-Sw curves for drainage, 2D, square, hexagonal Quasi-static, 2
[1959] incorporating trapping and mixed-wet networks, targeting phase, including
conditions sandstone rocks wettability
Chatzis, Examined both 2D and 3D networks 2D and 3D regular Quasi-static, 2
Dullien for percolation properties, and lattices, targeting phase
[1977] drainage Pc-Sw curves, against sandstone rocks.
experimental data from sandstones
Payatakes Developed stochastic model for oil 2D regular lattice, Quasi-static, 2
et al. [1980] ganglion dynamics (mobilization, interconnected unit cells, phase
breakup and stranding) in granular each cell a constricted
media. tube. Targeted granular
media - glass beads,
sand.
Lin, Slattery Predicted hysteresis in kr-Sw, Pc- 3D regular lattice, Quasi-static, 2
[1982] Sw curves, though the method did not targeting packings of phase
work well for consolidated media glass beads, sand
Mohanty In I, tracer flows for a wide range of 3D cubic network, Quasi-static, 2
[1982] fractional flows were done. In II, a 12x12x20, 12x12x40, phase
network model was developed to 16x16x20, targeting
describe the physics. Predicted sandstones
consolidated media well for the first
time.
Koplik, Simulated waterflooding at different 2D network, 10x10 Dynamic, 2
Lasseter Ca, incorporating dynamic viscous phase
[1985] effects, and capillary forces, through

21
 an approximate numerical procedure
in the pore network.
Chen, Studied viscous fingering during 2D Square network, Dynamic, 2
Wilkinson dynamic flow, ignoring surface 100x100 phase
[1985] tension term, in micromodel
experiments and square lattice
networks. Confirmed DLA-like
patterns
Lenormand Modeled effects of Ca and viscosity 2D square lattice, Dynamic, 2
et al. [1988] ratio on flow patterns for drainage in a 100x100 phase
2D network. Percolation theory, DLA
and anti-DLA were used for
explaining results
Jerauld, Two-phase kr-Sw and Pc-Sw curves, 3D network of spheres Quasi-static, 2
Salter [1990] including hysteresis. Compared connected by tubes, both phase
predictions with experiments, but not cubic and Voronoi, size
quantitatively (used assumed 203, targeting sandstones
properties for the network) and bead packs
Blunt, King Demonstrate effects of both viscous Delaunay triangulation Quasi-static, 2
[1991] and capillary forces on a 2D and 3D of points in circular phase
networks region - 80,000 for 2D,
Voronoi networks with
50,000 points in 3D
Blunt et al. Predicted kr-Sw curves with pore 3D cubic, cylindrical Dynamic, 2
[1992] networks, examine results against bonds/spherical bodies, phase
different types of percolation 32x32x64
Bryant, Blunt Used realistic geometries to derive 3D unstructured grid, Quasi-static, 2
[1992] pore networks. Predicted absolute from a mono-size sphere phase
permeability without adjustable pack (Finney packing of
parameters. 3367 spheres)
Bryant et al. Physically representative network 3D unstructured grid, Single phase
[1993] models of transport in porous media from Delaunay
tessellation of central
2000 spheres from
Finney pack
McDougall, Study Pc-Sw and kr-Sw curves, 3D cubic, 203 Quasi-static, 2
Sorbie [1995] recovery efficiency, for waterflooding phase, with
in systems of varying wettability. Also wettability
relate macroscopic wettability indices
with pore-scale physics
Lowry, Examine various geometrical factors 3D cubic, cylindrical Quasi-static, 2
Miller [1995] affecting non-wetting phase residual bonds/spherical bodies, phase
after imbibition in a strongly water- 8000 pore bodies
wet system
Dixit et al. Use pore-network models to explain 3D cubic, equal-length Quasi-static, 2
[1996] higher oil recovery for intermediate- cylindrical pores phase, with
wet systems, propose "regimes" for wettability
wettability classification
Bakke, Oren Proposed technique for generating 3D 3D network, with Quasi-static, 2
[1997] pore networks based on geological angular pores, derived phase

22
 processes for sandstone creation, and from Bentheimer
information from thin sections, sandstones, 1703, 10µm
applying it to predict macroscale flow resolution
properties for water-wet systems
Fenwick, Modeled three-phase flow using pore 3D cubic lattice, cubic Quasi-static, 3-
Blunt [1998] networks, incorporating micromodel pores, 30x15x15 phase
observations and theory of three-phase
flow
Oren et al. Extended Bryant & Blunt (1992) 3D unstructured, angular Quasi-static, 2
[1998] [Bryant, Blunt, 1992] to unequal size pores, derived from phase, with
spheres. Used reconstruction different sandstones, wettability
algorithm from thin sections to 3003, 10 µm resolution
generate pore space, and then derived
networks. Also modeled wettability
effects
Mogensen, Dynamic network model to study 3D cubic lattice, cubic Dynamic, 2
Stenby residual oil saturation, with effects of pores, 153 phase, including
[1998] Ca, M, contact angle, aspect ratio wettability
Dixit et al. Hysteresis in kr-Sw curves, between 3D cubic lattice, Quasi-static, 2
[1998b] primary drainage, secondary cylindrical bonds, 153 phase, water-wet
imbibition and secondary drainage for systems
strongly water-wet and weakly water-
wet systems kr-Sw curves
Dixit et al. Hysteresis in kr-Sw curves in mixed- 3D cubic lattice, Quasi-static, 2
[1998a] wet systems cylindrical bonds, 153 phase, including
wettability
Dixit et al. Derive relationships between Amott- 3D cubic lattice, Quasi-static, 2
[2000] Harvey and USBM wettability indices cylindrical bonds, 253 phase, including
wettability
Lerdahl et al. Developed a stochastic reconstruction 3D, unstructured lattice, Quasi-static, 3
[2000] of Berea, and predicted Oak's [Oak, angular pores, phase
1990] data. This pore network was Reconstructed 3003, 10
then used in several subsequent µm resolution, targeting
publications. sandstones
Oren, Bakke Develop a method to reconstruct 3D, unstructured lattice, Single-phase
[2002] sandstones, using petrographical with angular pores,
information from thin sections related reconstructed 3003,
to sedimentation, compaction and resolution 7.5 µm
diagenesis
Oren, Bakke Extend earlier work to present a 3D, unstructured lattice, Quasi-static, 2
[2003] unified workflow for computing both with angular pores, phase, including
single and multi-phase transport reconstructed 1283, wettability
properties from reconstructed resolution 10 µm,
sandstones targeting sandstones
Singh, Developed a rule-based dynamic pore- 3D cubic lattice, square Dynamic, 2
Mohanty network model, studied effect of pores/throats, 30x8x8 phase
[2003] viscous and capillary forces.
Generated qualitative capillary
desaturation curves.
Valvatne, Predicted kr-Sw and Pc-Sw curves on 3D unstructured lattice, Quasi-static, 2

23
Blunt [2004] mixed-wet sand packs and Berea angular pores, phase, including
from Bakke, Oren [1997] wettability
Piri, Blunt Developed thermodynamic Individual angular pores Quasi-static, 3
[2004] relationships for three-phase phase, including
displacements in a single, constant wettability
cross-section angular pore
Piri, Blunt Expanded on earlier work in single 3D unstructured lattice, Quasi-static, 3
[2005a] pore to develop three-phase flow in angular pores, 3003, phase, including
pore networks, using thermodynamics resolution 10 µm, from wettability
to determine stability Berea sandstone
Løvoll et al. Drainage of more viscous wetting 2D, square network, Dynamic, 2
[2005] fluid by less viscous non-wetting 80x160 nodes phase
fluid- experiment, numerics and
percolation theory
Nguyen et al. Developed a dynamic pore-network 3D unstructured, 3003, Dynamic, 2
[2006] model for imbibition incorporating from Lerdahl et al. phase
film flow, film swelling and snap-off. [2000]],Valvatne, Blunt
Quantified effects of flow rate in [2004]
inhibiting snap-off
Spiteri et al. Use pore-network simulations to study 3D unstructured from Quasi-static, 2
[2008] new trapping and relative permeability [Valvatne, Blunt, phase
hysteresis models 2004],Lerdahl et al.,
2000]
Joekar-Niasar Study two types of pore-network 3D cubic lattice, 403 Quasi-static, 2
et al. [2008] models: only tubes, and spheres and phase
tubes - with and without trapping,
respectively. Also relate interfacial
area to capillary pressure, rel perm
Raeesi, Piri Used mixed-wet pore-network models 3D unstructured grid Quasi-static, 2
[2009] to study Pc-Sw-area relationships from [Piri, Blunt, 2005a], phase, including
Berea (3003, resolution wettability
10µm) and Saudi
reservoir sandstone
(2503, resolution 10µm)
Idowu, Blunt Study dynamic effects during 3D unstructured grid, Dynamic, 2
[2010] waterflooding, incorporating effects of 3003 from [Valvatne, phase, with
capillary number, viscosity ratio and Blunt, 2004] wettability
contact angles
Gharbi, Blunt Study effects of wettability in several 3D unstructured, from Quasi-static, 2
[2012] different carbonate samples carbonate CT images of phase, with
size 3203-3503, with wettability
angular pores, resolution
7.7-9 µm
Mehmani Presented a new multi-scale model for 3D unstructured, Single-phase,
et al. [2013] flows in shales, combining nano-meter multiscale with slip-flow
size pores with micro-meter size and Knudsen
pores, and studied effect of pore diffusion
connectivity and fraction of
microporosity on permeability
Ryazanov Figure out structure of residual oil 3D unstructured lattice, Quasi-static, 2

24
 et al. [2014] after water flooding as a function of Berea 3003, 10 µm phase, with
wettability. resolution, from [Oren, wettability
Bakke, 2003]
Bultreys et al. Developed a dual pore-network model 3D unstructured, Quasi-static, 2
[2015] to model microporosity multiscale, spherical phase
pores, with cylindrical
links, Estallaides
limestone, 10003,
resolution 3.1 µm
Ruspini et al. Improved pore-network models so 3D unstructured, from Quasi-static, 2
[2017] they predict trapping curves [Oren et al., 1998], 4503- phase, with
accurately, based on a new pore-body 12003, resolution 1.5-10 wettability
filling approach µm
784
785
786 The table reveals a number of interesting trends in pore network modeling. Many early works
787 were focused on building 2D networks with the pores arranged on a regular square lattice (Dodd
788 and Kiel, 1959; Fatt, 1956a). These regular grids continued in 3D (Chatzis and Dullien, 1977).
789 These networks modeled pore size distribution by adjusting the pore sizes at each lattice node
790 and could also change connectivity by adjusting the number of bonds from one lattice site to the
791 next. In most cases, these networks were not directly representative of any physical sample
792 (except micromodels (Chen and Wilkinson, 1985)). In addition, a number of researchers only
793 studied drainage capillary pressure curves, using invasion-percolation algorithms (Chatzis and
794 Dullien, 1977; Dodd and Kiel, 1959; Fatt, 1956a). With only drainage, no hysteresis was present
795 in their models, but they could model wettability effects by assigning different contact angles in
796 individual pores.
797
798 Payatakes and co-workers (Payatakes et al., 1973, 1980), formulated a population balance model
799 for the evolution of oil ganglia during water flooding. They studied granular media, where the
800 simplistic pore networks they used were more representative of the real sample. Shortly
801 afterwards, in a series of papers by different researchers (Dias and Wilkinson, 1986; Wilkinson,
802 1986; Wilkinson and Willemsen, 1983), advances in percolation theory led to a much better
803 understanding of displacement patterns formed during both drainage and imbibition, including
804 viscous effects. These papers had far-reaching impacts on how to upscale pore-scale model
805 relationships. Bryant et al. (1993a, 1993b) introduced sophisticated methods of modeling
806 compaction and cementation in granular media. They derived unstructured grids from the
807 resulting pore networks, and computed relative permeabilities from them, with very satisfactory
808 matches to experimental data in strongly water-wet sandpacks and sandstones. This work was
809 later extended by Bakke and Øren (1997) and Øren et al. (1998), who pioneered a process-based
810 method of reconstructing the pore space in consolidated media like sandstones, incorporating
811 information from high resolution thin sections of rocks. They also modeled effects of
812 heterogeneous wettability. This work was later extended to three phases by other researchers
813 (Piri and Blunt, 2004, 2005; Valvatne and Blunt, 2004). Recent papers have focused on modeling
814 trapping and the structure of residual phases by improving the pore-filling models used for
815 modeling imbibition processes - areas where earlier pore networks have struggled (Ruspini et al.,
816 2017; Ryazanov et al., 2010, 2014). Multi-scale pore networks are also a fairly recent
817 development (Bultreys et al., 2015b; Jiang et al., 2013b; Mehmani et al., 2011; Mehmani and

25
818 Prodanović, 2014b; Prodanović et al., 2015) but are vital for modeling systems with significant
819 microporosity like carbonates. As examples of these multiscale networks, Figure 17 shows the
820 drainage relative permeability curves for carbonates with vugs and microcracks as was described
821 in Section 2.1.2. Multiscale networks are a significant advancement over earlier works which
822 focused on more homogeneous porous media like sandstones and sandpacks. Carbonates have a
823 bimodal pore size distribution, as well as a much more complicated wettability state, and are
824 hence much harder to model.
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841 (a) (b)
842 Figure 17: Primary drainage relative permeability curves for (a) a vuggy carbonate rock (with a scale difference of 5) and
843 (b) a carbonate rock with a single microcrack (with a scale difference of 5 (at three axis angles with respect to the
844 direction of the pressure gradient). Drainage is simulated on pore-network models described in Figure 8, and the
845 corresponding capillary pressure curve is shown in Figure 9b.

846
847 The shortcoming of quasi-static modeling is its assumption that the movements of phases do not
848 affect each other. This is not the case in high capillary numbers when the phase distributions
849 become functions of viscosity ratios and flow rates as well as the interfacial tension. We note
850 that recent experiments using fast synchrotron x-ray imaging (Andrew et al., 2015; Berg et al.,
851 2013; Singh et al., 2017) have observed rapid movements and phase rearrangements at low
852 capillary numbers, which challenge the traditional assumption of quasi-static flow. In particular,
853 Pak et al. (2015) and Reynolds et al. (2017) have shown some completely new pore-scale
854 displacement mechanisms in carbonates that cannot be modeled with traditional pore-network
855 approaches.
856
857 Two computational schemes that are used in dynamic pore-network modeling are the single-
858 pressure (Aker et al., 1998; van der Marck et al., 1997) and two-pressure (Thompson, 2002)
859 schemes. In the single-pressure scheme, regardless of the simultaneous occupancy of a pore by
860 both phases, a single pressure is assigned to each pore as an unknown. The assumption therefore
861 is that the local capillary pressure within a pore is negligible. In addition, corner flow cannot be
862 implemented using the single-pressure scheme and therefore it is only applicable for lowly
863 angular and smooth granular media. In the two-phase pressure scheme, the local capillary
864 pressure within a pore is not ignored and therefore each phase’s pressure becomes an unknown

26
865 in the systems of equations. The problem that arises using this scheme in low capillary numbers
866 is a numerical instability called “capillary pinning” (Koplik and Lasseter, 1985) at which the
867 saturation of a pore is non-convergent. Joekar-Niasar et al. (2010) proposed a semi-implicit
868 saturation update at each time step by which the numerical instabilities improved. For a further
869 discussion on dynamic pore-network modeling the reader is referred to Joekar Niasar (2010) and
870 the references therein. From discretization standpoint, these pore-network models resemble
871 reservoir simulators (for instance, they update saturation), but operate on a smaller length scales
872 and are thus incorporating capillary forces directly (as opposed to through averaged functional
873 relationships).
874
875 Unlike voxel-based discretization in direct numerical simulation methods (Section 2.2.4),
876 discretization done via pore-network models is not scalable. In other words, voxel-based
877 discretization can offer an optimum space interval at which the solution will be satisfyingly
878 accurate and yet computationally feasible. In pore-network modeling, besides choosing the
879 domain size that does not fall below the representative elementary volume (REV), the concept of
880 an optimum discretization does not exist. Hybrid methods when coupling from different length
881 scales are an exception and this is discussed in Section 2.3. Open source pore-network modeling
882 code is available - please see (Gostick et al., 2016).
883
884 2.2.4. Principles of direct numerical simulation
885
886 Modeling the multiphase fluid behavior directly in the pore space domain is an attempt to
887 achieve accuracy that pore-network models may sacrifice for computational speed (Raeini et al.,
888 2014a). In addition, direct numerical methods provide sub-pore scale fluid dynamic insights that
889 can be utilized for improving pore-network models, which could potentially become a very
890 useful tool in upscaling simulation results – particularly for multi-scale systems like carbonates.
891 Direct numerical methods are implemented once the pore space has been either segmented from
892 an image (Iassonov Pavel et al., 2009) or digitally reconstructed through a process-based or
893 stochastic-based method.
894
895 The most popular methods for direct modeling are lattice Boltzmann methods and finite volume
896 methods based on discretization of Navier-Stokes equations (and addition of interfacial tension
897 when modeling immiscible flow). Lattice Boltzmann methods evolved from lattice gas automata
898 (LGA) techniques. They are pseudo-molecular methods, which track the distribution functions of
899 an ensemble of fluid particles. They work at a scale in between molecular dynamics, and the
900 continuum scale. Macroscopic variables such as velocity, pressure and density, which are part of
901 traditional computational fluid dynamics (CFD) methods, are recovered by moment integration
902 of the particle distribution functions. The particle distributions at each lattice point evolve by
903 interacting only with its immediate neighbors. Since each lattice point interacts only with its
904 neighbors, the problem is highly parallelizable, and well suited for modern multi-thread/core
905 processors. In addition, boundary conditions can be easily handled using the bounce-back
906 condition. This enables representing complex geometries easily using an underlying orthogonal
907 grid, without using complex meshing algorithms. It has hence become a very popular choice in
908 the porous media community which deals with very complex 3D pore spaces, which can have
909 features on many different scales.
910

27
911 LB methods follow a two-step procedure. First, there is an advection step, where the values
912 of the distribution function are propagated to their neighboring lattice points along defined
913 velocity vectors. Second, there is a collision step, where the particles at each lattice point are
914 redistributed according to a collision operator. The simplest collision operator is given by the
915 Bhatnagar-Gross Krook (BGK) relationship, which performs very well for a wide variety of
916 situations. Without going into mathematical details, the BGK operator is based on a single
917 relaxation time parameter, which results in viscosity-dependent permeability. A more complex
918 operator is the Multiple Relaxation Time (MRT), which is more computationally expensive, but
919 performs better at computing permeabilities in porous media images (Pan et al., 2006).
920
921 For multiphase flow, many different lattice Boltzmann models exist - the color gradient
922 model (Gunstensen et al., 1991), the Shan-Chen model (Shan and Chen, 1993), the free energy
923 model (Swift et al., 1996) and others. It is not clear if any one model is always superior to the
924 other (Liu et al., 2016a) and it is up to the user to decide which one to use for their application.
925 However, as reported by Liu et al. (2016b) some models, such as the color gradient model and
926 the stabilized diffuse-interface model, are better at handling high viscosity ratios at low capillary
927 numbers which is relevant in porous media flows, though this comes at a higher computational
928 cost and more complex equations. Similarly, the larger the porous domain is the longer the
929 computational time becomes. The issue of domain size is pertinent in carbonates as simulating
930 the injection of one pore-volume when large volumes of vugs are present can become
931 computationally difficult. It is currently not clear when these costs would be justified for a given
932 case.
933
934 Hazlett (1995) was one of the earliest works in direct modeling of flow in porous media
935 images. He simulated multiphase flow using a sphere-algorithm, and calculated relative
936 permeabilities using the multiphase color-gradient lattice Boltzmann method. Subsequently,
937 Martys and Chen (1996) performed multiphase flow simulations using the Shan-Chen lattice
938 Boltzmann method. These two early pioneering papers had limited predictive power, due to the
939 limited resolution and computational resources at the time. van Kats and Egberts (1999)
940 performed the first three-phase porous media simulations, but only in 2D. As computational
941 power improved, other researchers focused efforts on studying hysteresis in capillary pressure
942 curves, relating it to interfacial area (McClure et al., 2004; Pan et al., 2004; Porter et al., 2009;
943 Schaap et al., 2007). Liu et al. (2016) performed a detailed benchmark study on what viscosity
944 ratios can be simulated with each model in static and dynamic cases. Open source parallelized
945 codes for lattice Boltzmann method are available, e.g. Palabos3 and Taxila-LBM (Coon et al.,
946 2014).
947
948 The other popular class of direct simulation methods are based on discretization of Navier-
949 Stokes equations. These techniques have been for even longer than the lattice Boltzmann
950 method, and have very well-developed mathematical foundations. Difficulties with these
951 methods arise when more than one phase becomes involved. This is due to challenges in tracking
952 the two-phase fluid interface and the contact line with the solid phase. The volume-of-fluid
953 (VOF) method (Hirt and Nichols, 1981) is a continuum-based method that solves the Navier-
954 Stokes equation for each phase using saturation-averaged values for density and viscosity. The

3 http://www.palabos.org

28
955 interfacial tension is treated as a body force in this method (Brackbill et al., 1992). The drawback
956 of VOF is the emergence of spurious currents when capillary forces get high (Dupont and
957 Legendre, 2010). The problem of spurious currents at low capillary numbers is particularly
958 relevant for multiphase flows in porous media. Algorithms on correctly tracking the immiscible
959 interface has been the focus of eliminating spurious current (Popinet and Zaleski, 1999; Renardy
960 and Renardy, 2002;Abu-Al_Saud et a;., 2018), for instance Raeini et al. (2014a) and Shams et al.
961 (2018) showed that the non-physical instabilities can be improved by using a sharp surface force
962 model. For an open-source platform that incorporates single-phase and multiphase immiscible
963 flow using finite-volume methods refer to www.openfoam.org.
964
965 Level set methods are often proposed as an alternative to VOF for tracking moving interfaces
966 (Sussman, 2005; Sussman et al., 1994, 1999). These methods have their own problems, such as
967 mass loss (Enright et al., 2002) and high computational costs. Several authors have proposed
968 methods to address the mass loss issues in level set methods, such as the particle-level set
969 method (Enright et al., 2002), and non-graded adaptive grids (Min and Gibou, 2007). Other
970 researchers have combined the level set and VOF techniques to give hybrid methods which can
971 take advantage of the features of both methods, for example the Coupled Level Set VOF method
972 (CLSVOF) (Sussman and Puckett, 2000). In a benchmark study of these methods, Gerlach et al.
973 (2006) concluded that the CLSVOF method was the best one of these techniques. Thömmes et
974 al. (2009) attempted to couple level set methods with lattice Boltzmann to improve
975 characteristics of the flow behavior for large viscosity ratios. However, they only applied the
976 method to very simple cases, and the method has not been widely used since.
977
978 An alternative method for predicting the multiphase fluid distribution at a given capillary
979 pressure is the quasi-static level-set method (Prodanović and Bryant, 2006). In this method, the
980 immiscible interface is defined by a level set function that progresses with a velocity that is
981 directly linked to the balance between pressure and surface tension. Open source code is
982 available in (Prodanovic, 2010). Although the level-set method has a high accuracy in
983 describing the fluid morphology, it cannot be used for modeling viscosity-dominated regimes.
984 Later on, Jettestuen et al., (2013) and Verma et al. (2018) added the ability to incorporate
985 arbitrary contact angles to this simulation method. Figure 18 shows an example of each of the
986 discussed direct numerical methods (Harting et al., 2005; Prodanovic and Bryant, 2009; Raeini et
987 al., 2014a).
988
989

990
991 (a)
992
993
994
995

29
 996
997
998
999
1000
1001
1002
1003 (b-1) (b-2) (b-3)
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016 (c)
1017 Figure 18: Examples of (a) utilizing volume-of-fluid method to simulate drainage (throat length is 37.5
m)
1018 (Raeini et al., 2014a) (b) level-set method for a naturally fractured carbonate rock, (b-1) is a tomogram of size
1019 700x1x700, (b-2) is a media surface of size 200 x 230 x 190 and (b-3) is the non-wetting fluid distribution at a
1020 particular curvature during drainage (red is the fluid/fluid and gray is the fluid/solid interface) all with a
1021 voxel size of 3.1 m (Prodanovic and Bryant, 2009) and (c) drainage simulation for a Bentheimer sample
1022 (512 x 512 x 521 with a voxel size of 4.9
m) using Lattice-Boltzmann method (Harting et al., 2005).

1023 Table 2 summarizes publications over the past two decades for direct modeling. Like the pore-
1024 network modeling table, it is arranged chronologically. It includes papers based on lattice
1025 Boltzmann and Navier-Stokes discretization. It also incorporates other less popular techniques
1026 like the level set method and smoothed particle hydrodynamics (SPH). The columns are
1027 organized similarly to Table 1. However, the grids are always related to some physical sample,
1028 unlike pore-network models for which the concept of grid does not apply.
1029
1030
Table 2: Direct pore-scale modeling literature: key representative journal publications over
the years
Author(s), Key Sample type(s)/size Physics incorporated
year innovation/summary

Hazlett First work to directly Berea sandstone, 2563, Inscribed spheres for
[1995] try simulations on resolution 10 µm displacement, including
actual rock images. wettability, lattice Boltzmann
Predicts fluid for permeability
distributions based on
inscribed spheres in
image. Lattice

30
 Boltzmann was used
to get permeabilities
from equilibrium
distributions
Martys, First work to model Fontainebleau sandstone, 7.5 2-phase lattice Boltzmann,
Chen [1996] two-phase flow µm, resolution, 643 samples Shan-Chen model
directly using lattice-
Boltzmann
Hazlett et al. CMT image of 1283 reservoir sandstone, 10 2 phase lattice Boltzmann
[1998] sandstone used for µm resolution color gradient model,
drainage in strongly including wettability
water-wet and mixed-
wet cases
Kats, First lattice Boltzmann 210x350 2D lattice with square 3 phase lattice Boltzmann
Egberts work to model 3 phase elements color gradient model
[1999] flow in porous media
Manwart Computed 3003, 4 Fontainebleau Single phase lattice
et al. [2002] permeability for sandstone samples, resolution Boltzmann BGK model, finite
Fontainebleau 7.4 µm, one real, and three difference solver for Stokes
samples, generating generated equation
matches with
experiment. Shows
first order nature of
bounce-back BCs
Pan et al. LB simulations on 1283, 150 dimensionless 2 phase lattice Boltzmann
[2004] ideal sphere packing, spheres Shan-Chen model
to give Pc-Sw curves,
including hysteresis,
and subsequent
comparison with
experiments
Kang et al. Simulations of 2D channel, 400x66 2 phase lattice Boltzmann
[2004] fingering during Shan-Chen model
immiscible fluid
displacements in a
channel, studying
effects of capillary
number, viscosity ratio
and wettability
Huang et al. Studied multiphase 2D fractures, 60x400, Volume of fluid (VOF)
[2005] flow in unsaturated resolution 0.05 mm method Navier-Stokes solver
fractures, including
effects of viscosity,
contact angle, and
gravity
Harting et al. Performed lattice Benthemer sandstone, 5123, 4.9 2 phase lattice Boltzmann
[2005] Boltzmann µm resolution Shan-Chen model
simulations in porous
media samples as part
of a larger review on

31
 simulations for other
cases
Kang et al. Simulation of reactive 2D channel, 80x80 Lattice Boltzmann equations
[2006] flow at the pore scale, coupled with chemical
considering effects of reactions
advection, diffusion,
mineralogy, and
reaction between
species
Pan et al. Investigation of BGK 323 BCC sphere array; and Singe phase BGK and MRT
[2006] and MRT lattice 643 random sphere packing, lattice Boltzmann models
Boltzmann models to with 23 spheres
compute permeability,
as well as effect of
using different
boundary conditions.
Prodanović, Introduced a quasi- Mono-sized sphere packs, 383 2 phase quasi-static level set,
Bryant static level set method, with zero contact angle
[2006] studying multiphase
displacements in
idealized sphere
packs, with zero
contact angle
Tartakovsky, Simulated immiscible 2D 32x16 geometries Smoothed particle
Meakin and miscible flows in hydrodynamics, 2 phase, both
[2006] idealized 2D immiscible and miscible
geometries
Schaap et al. Study of water-air and Glass bead packs, 2-phase lattice Boltzmann
[2007] water-soltrol 405x405x100, resolution 17 Shan-Chen model
displacement µm
experiments in glass
bead packings,
relating interfacial
areas to capillary
pressure
characteristics
Hatiboglu, Studied spontaneous 2D micromodel, 4002, 0.125 2 phase lattice Boltzmann
Babadagli imbibition using mm resolution Shan-Chen model
[2008] micromodel
experiments and LB
Sukop et al. Compared LB vs 2563, 20 µm resolution, quartz 2 phase lattice Boltzmann
[2008] experimental fluid grain packing. (1283 really) Shan-Chen model
distributions, slice by
slice
Thömmes Combined LB with 2D Couette flow, bubble, Hele- 2 phase, lattice Boltzmann
et al. [2009] level set methods. Shaw cell, 1282 BGK model coupled with
Simulated flows with level sets
large viscosity ratios
and density
differences, for simple

32
 2D and 3D cases.
Porter et al. Matched interfacial Glass bead pack, 2 phase lattice Boltzmann
[2009] area measurement by 205x205x150, resolution 34 Shan-Chen model
CMT in glass beads µm
with LB simulations,
and related it to
hysteresis in Pc-
Sw curves
Boek, Performed simulations 1283 sample of Bentheimer 2 phase lattice Boltzmann
Venturoli for a 2D sample of sandstone, resolution 4.9 µm Shan-Chen model
[2010] Berea and 3D
Bentheimer sample
Ramstad Simulations in CMT Bentheimer sandstone, 2563, 2 phase, modified lattice
et al. [2010] and reconstructed resolution 6.67 µm (CMT), 5 Boltzmann color-gradient
sandstone images. µm (reconstructed) model Latva-Kokko, Rothman
Reproduce Pc- [2005]
Sw drainage curves
well, but underpredict
rel perms
Ramstad Relative permeability Bentheimer, 2563, resolution 2 phase, modified lattice
et al. [2012] from Bentheimer and 6.67 µm, Berea 2563, Boltzmann color-gradient
Berea sandstone using resolution 5.345 µm model Latva-Kokko, Rothman
LB [2005]
Jettestuen Proposed extension of 3D sphere packs, 66x66x62, 2 phase quasi-static level set,
et al. [2013] model by Prodanovic Castlegate sandstone, with non-zero contact angle
and 60x60x70, resolution 5.6 µm
Bryant Prodanović,
Bryant [2006] to
incorporate wettability
effects
Li et al. Extended the Berea, resolution 2.89 µm, 2 and 3 phase, Rothman-
[2013] Rothman-Keller 3003 for 2-phase simulation, Keller MRT LB model
multiphase LB model 643 for 3-phase
with MRT, and
simulated drainage-
imbibition
experiments Berea
samples. Also tried
preliminary 3 phase
simulations
Ferrari, Simulated immiscible 2D 1760x2280, resolution 50 Navier-Stokes VOF solver
Lunati displacements in 2D, µm, 10028 particles
[2013] and studied the
relation between
macroscopic capillary
pressure and pore-
scale properties
Raeini et al. Used their own Berea sandstone Navier-Stokes VOF solver
[2014] modified VOF (400x256x256), resolution 4.58
formulation Raeini µm; Sandpack (282x174x174),

33
 et al. [2012] to relate resolution 8.2 µm
pore scale forces with
Darcy-scale properties
including rel perms,
proposing an
upscaling algorithm
Liu et al. Used a new color-fluid 2D micromodel, 2816x2689, 2 phase lattice Boltzmann
[2014] model to simulate resolution 1.5 µm color-fluid model
flows in 2D
geometries of
heterogeneous
permeabilities
Landry et al. Used LB to get rel Glass bead pack, 1003, 2 phase lattice Boltzmann
[2014] perms for strongly resolution 26 µm Shan-Chen model
water-wet (glass
beads) and weakly oil-
wet (polyethylene
beads) cases,
comparing results with
bead pack CMT
experiments
Raeini et al. Studied trapping Berea sandstone Navier-Stokes VOF solver
[2015] trends in water-wet (330x210x210), resolution
consolidated and 5.549 µm; Sandpack
unconsolidated media, (230x142x142), resolution
matching against 10µm
experimental data
Liu et al. Extensive review of 2D samples, cylinder grids 2 phase Shan-Chen, color
[2016] popular LB multiphase (512x1280), reproduced from gradient, free energy, mean-
models, and points out other works field theory, stabilized diffuse-
limitations of each, in interface
the context of porous
media flows
McClure Revisit hysteresis in Randomly packed 1964 2-phase lattice Boltzmann
et al. [2016] Pc-Sw curves, conclude spheres, 9003 modified color-gradient model
that inclusion of [McClure et al., 2014]
interfacial area and
Euler characteristic
makes relationship
non-hysteretic
1031
1032
1033 Over the years, as more computational power and better imaging techniques have become
1034 available, the resolution used has grown better, increasing the REV size as well as match with
1035 the experiments. For instance, Ramstad et al. (2012) generated relative permeability curves for a
1036 reservoir sandstone but matching with experimentally measured values (on a larger core)
1037 improved predictions dramatically by using end-point saturations from experimental data. This is
1038 the same procedure used by pore-network modelers, though one has more parameters to play
1039 with in pore networks. Other methods like the quasi-static level set method (Prodanović and
1040 Bryant, 2006) and smoothed particle hydrodynamics (Tartakovsky et al., 2007; Tartakovsky and

34
1041 Meakin, 2006) have been limited by computational resources, but the VOF technique has been
1042 applied to study relative permeability (Raeini et al., 2014b) and trapping (Raeini et al., 2015).
1043 Trapping is in general typically modeled better using VOF or a direct method, though a carefully
1044 matched pore network model recently (Ruspini et al., 2017) showed promising results using a
1045 new pore-body filling model in the same pore network. For additional discussion on pore-scale
1046 modeling refer to Golparvar et al. (2018). In the context of carbonates, their two main challenges
1047 are their multiscale nature (discussed in Section 2.3) and their generally heterogeneous-wet
1048 condition. Current research efforts are focused on incorporating such heterogeneous-wet
1049 conditions to an accurate model. Zhao et al (2016) have shown the importance of film flow in
1050 determining macro-scale behavior under uniform wettability conditions. In a follow-up work,
1051 Zhao et al. (18) have compared 14 different pore-scale modeling methodologies for capturing the
1052 behavior seen in the micromodels. We note here that the micromodel experiments of Zhao et al.
1053 (2016) are not very representative of usual flow conditions in porous media - in particular the
1054 capillary number is extremely low, which means entirely different macro-scale behavior from
1055 typical subsurface flow conditions. However, this study still shows that current simulation
1056 methods are not quite up to the task of simulating all the complexities in a porous medium.
1057 Moreover, in carbonates, film flow, heterogeneous wettability, as well as highly non-uniform
1058 pore size distributions result in even more challenging systems which have not yet been validated
1059 comprehensively. Frank et al. (2018a-b) have recently applied a finite element formulation with
1060 the discontinuous Galerkin method which shows some promise in resolving some numerical
1061 issues which surround simulation of moving interfaces.
1062
1063 2.3. Combining multi-scale pore-geometries in pore-scale models
1064
1065 Given the continuous and wide distribution of pore sizes over multiple length scales in carbonate
1066 rocks, a proper integration of multiscale pores is essential for predicting their transport
1067 properties. Biswal et al. (2007) proposed a stochastic continuum reconstruction scheme for
1068 microporous carbonates, based on implementing a spatial correlation for various grains that is
1069 established from training images. The model was used to predict absolute permeability,
1070 formation factor and elastic moduli for carbonate samples. In their method, each voxel is
1071 segmented into pores, matrices or undecided. Undecided voxels are alternately assigned as pores
1072 or matrices. The method was implemented for a microporous oolithic dolostone. The predicted
1073 transport properties however were highly dependent on the chosen resolution which highlights
1074 the potential advantage of reduced-order computational methods such as pore-network modeling
1075 if they are supplied with correct a priori transport rules. Bauer et al. (2012) presented a dual
1076 pore-network model for carbonates where a three-dimensional micro-CT image is segmented
1077 into solid, macropores and microporous regions. The microporous regions however are not
1078 resolved but represented as continuous regions. The explicit integration of pores from two scales
1079 into a single-entity pore-network model has been developed via an image-based method in which
1080 a micropore network is stochastically created and indiscriminately (Jiang et al., 2013b), or with a
1081 spatial correlation (Jiang et al., 2013a), superimposed to a macropore network. In order to
1082 capture micropore generating diagenesis, Mehmani and Prodanović (2014b) have proposed a
1083 process-based approach to integrating micropores with macropores which was discussed
1084 previously in Section 2.1.2. The method can additionally be implemented to three-dimensional
1085 images where grains are segmented and subsequently filled with micropores (referred to as
1086 “grain-based” approach). For images where, due to considerable diagenesis, grain segmentation

35
1087 is not feasible, a “tile-based” approach has been developed. In this method, the domain is tiled
1088 and micropores are implanted on the appropriate areas (Prodanović et al., 2015) (see Figure 19
1089 for schematics of the methods). As one may intuit, the details captured by explicitly
1090 incorporating micropores into the pore-network model results in high numbers of unknowns and
1091 can significantly reduce the computational feasibility of solving the systems of equations. In an
1092 effort to amend the computational limitations of coupling micropores with macropores, Bultreys
1093 et al. (2015a) have represented the upscaled properties of microporous regions with microthroats.
1094 Determining the properties of the microporous clusters and microthroats a priori is challenging
1095 given the necessity for high resolution images for pore structure characterization. Tuning the
1096 micropore properties by matching predicted transported properties with macroscopic
1097 experimental measurement is not always possible either given the scarcity of experimental data
1098 points in highly microporous and tight carbonates. Verifying the fidelity of multiscale pore
1099 structure reconstruction is nontrivial and will likely require advanced real-time image
1100 acquisitions tools such as fast- synchrotron tomography to clarify the transport communication
1101 between the micropores and macropores.
1102

1103
1104
1105 (a) (b)
1106
1107 Figure 19: Schematic of modeling algorithms for (a) “grain-based” and (b) “tile-based” image-based two-scale pore-
1108 network creation (Prodanović et al., 2015). Impermeable grains and microporous regions are colored black and gray
1109 respectively. Throats linking pores from the same scale are colored red whereas throats connecting pores from two scales
1110 are blue.

1111 Direct numerical simulations have recently been implemented in imaged multiscale pore systems
1112 to predict their single-phase and two-phase properties. Soulaine et al. (2016) employed the
1113 Darcy-Brinkman (Whitaker, 1986) equation in a computationally parallel setting to demonstrate
1114 the high impact of even small percentage of sub-resolution pores on absolute permeability in a
1115 sandstone sample. The Darcy-Brinkman formulation renders the solution of the velocity field at
1116 the interface between sub-resolution and resolved pores tractable and provides a direct
1117 adjustment of the equations based on the microporous region’s permeability. A similar
1118 formulation for two-phase immiscible flow with nanoscale effects corrections including slip flow
1119 and Knudsen diffusion was extended by Soulaine, et al. (2019) to predict the transport properties
1120 of shale formations. Such nanoscale corrections can become relevant for carbonates as well
1121 (Yoon and Dewers, 2013). However, the practicality of the Darcy-Brinkman formulation

36
1122 imposes an abrupt change from the Darcy velocity in the sub-resolution porous systems to the
1123 interstitial velocity in the resolved pores. Beavers and Joseph (1967) for instance demonstrated a
1124 slip velocity region in the boundary between the pore space and the sub-resolution regions.
1125 Additional research is required to determine the importance of this additional interface condition
1126 to flow properties, including in case of immiscible flow, and their sensitivity to any associated
1127 parameters in carbonates. Another promising hybrid method for carbonates that have pores at
1128 inseparable scales is the mortar domain decomposition method (Y. Mehmani, 2014). In this
1129 method, a pore-scale subdomain can be coupled with a continuum subdomain by defining
1130 interface function space (the mortar space). For each subdomain an appropriate transport
1131 algorithm can be solved iteratively until the flux at the interface coincides with the two adjacent
1132 subdomains. Much work however on adopting mortar domain decomposition for predicting
1133 immiscible flow in carbonates is needed. Lattice Boltzmann methods have also been extended to
1134 predict fluid transport in multiscale settings. This approach is generally referred to as Gray
1135 Lattice Boltzmann (GLB) as the sub-resolved porous areas would have geometric properties in-
1136 between resolvable pores and the solid phase. The “grey” areas are considered to have a grain
1137 density in proportion to their porosities and X-ray attenuation intensities. In earlier models (Gao
1138 and Sharma, 1994), the impacts of sub-resolution pores on fluid propagation are incorporated in
1139 the collision step as described in Section 2.2.4. Subsequent worked have focused on increasing
1140 the accuracy and computational performance of GLB by modifying the collision step [Walsh et
1141 al., 2009]. Recently, multiscale algorithms for accelerating fluid dynamics simulations on
1142 digitized porous media have been proposed by (Mehmani and Tchelepi 2018, Mehmani and
1143 Tchelepi 2019, Guo et al. 2019). The Pore-Level Multiscale Method (PLMM) has been shown to
1144 produce highly accurate approximations to single-phase incompressible, immiscible two-phase,
1145 and compressible gas flow in single (e.g., sandstone) and dual porosity (e.g., shale) media. No
1146 simplification of the underlying geometry or governing equations are made. Broadly speaking,
1147 PLMM consists of four steps: (1) decomposition of the image into physical pores, (2)
1148 computation of local basis functions on each pore, (3) solution of a global interface problem, and
1149 (4) reconstruction of the final solution. Step (1) utilizes watershed segmentation, similar to PNM,
1150 and the subdomains created correspond to physical pores in the image. However, the
1151 decomposition cost is much lower than typical network extraction, which involves multiple
1152 additional steps. Step (2) can be thought of as a parametrization of upscaled flow parameters for
1153 each pore, which is loosely analogous to computing hydraulic conductivities for throats in certain
1154 PNM variants (ref: Masha's paper). Step (3) involves solving a coarse system, which is
1155 comparable in size to typical (non-)linear systems encountered in PNM. Step (4) is optional and
1156 is only executed if a sub-pore scale solution is desired. If only macroscopic parameters are of
1157 interest (e.g., permeability), step (4) may be omitted. The errors in PLMM can be further
1158 estimated a priori and controlled (not possible in PNM) through a rapidly convergent iterative
1159 strategy in (Mehmani and Tchelpi 2018). The DNS solver used in step (2) can be chosen from a
1160 number of available approaches (FVM, FEM, SPH, LBM). All computations in PLMM are
1161 massively scalable in parallel environments due to independence of calculations.
1162
1163
1164 3. Discussion
1165
1166 Conventional functional relationships, such as Archie’s law for resistivity (Archie, 1942), the
1167 Carman–Kozeny permeability estimate (Carman, 1937; Kozeny, 1927) and the Brooks–Corey

37
1168 parameterization of relative permeability (Brooks and Corey, 1964), were developed for rocks
1169 whose pores are mostly intergranular, single length scale and well connected. Since carbonates
1170 exhibit pore space heterogeneity such as high variations in pore size, shape, topology and
1171 wettability, traditional transport relationships are rarely satisfactory. Reliable pore-scale models
1172 have the potential to provide the petrophysical properties of all rocks at the REV scale (Figure
1173 1), and for carbonates such workflows are especially valuable given their complex flow behavior
1174 and scarcity of data during formation evaluation.
1175
1176 An accurate pore-scale model depends on the correct capturing of the pore space. While pore
1177 scale modeling (specifically, pore-network modeling) has been in existence since the first use of
1178 bundle-of-tubes models by Purcell (1949) and the first interconnected pore-scale models by Fatt
1179 (1956a, 1956b, 1956c), in this paper we have focused on reviewing methods that have a degree
1180 of physical representativeness in terms of pore space geometry and interconnectedness. We
1181 reviewed three philosophies for reconstructing the pore-space. The process-based method hinges
1182 on an appropriate description of the original granular packing followed by modeling diagenesis
1183 of the sample. The algorithm’s basis on sphere packing with a desired grain size distribution and
1184 tessellating of the sphere centers results in computational expedience. Multiple realizations of a
1185 diagenetically altered granular medium can therefore be generated to cover a range of pore-scale
1186 parameters. Advances in imaging technology and a continuous increase in computational power
1187 have catalyzed the explosion in pore-scale modeling since the late 1990s. Technologies such as
1188 computed tomography, X-Ray microtomography and (focused ion beam) scanning electron
1189 microscopy, provide a window into geologic materials that can be analyzed with a digital rock
1190 physics framework for characterization and creation of pore-scale models. The image-based and
1191 stochastic-based methods depend on acquiring a quality image using resolutions that can capture
1192 relevant pore space features. Once the pore space is rendered, either a pore-network method or a
1193 direct numerical simulation technique is chosen to achieve the desired macroscopic property.
1194
1195 The choice of the pore-scale model depends on several criteria including microstructure image
1196 availability, importance of sensitivity analysis, type of the transport process one wishes to study
1197 and complexity/availability of the software. If one wants to analyze a specific sample and it can
1198 be appropriately imaged so that pores are well-resolved, then direct numerical simulation is the
1199 clear choice. It could be that pores are of complex shape so that their representation with a pore-
1200 throat network is not well-defined. Further, if single phase permeability is desired, off-the-shelf
1201 parallelized direct simulators exist that make its calculation relatively straightforward.
1202 Nonetheless, direct-numerical methods can become unfeasible in “large” porous domain. A
1203 domain size for interparticle pores that is manageable with direct numerical methods can be
1204 considered “small” when vugs with sizes orders of of magnitude larger are present. In this case
1205 even though all pores are technically resolvable in the three-dimensional image, a pore-network
1206 model, despite uncertainties with defining the pores and throats during its extraction, is
1207 preferable. If an appropriate image is unavailable or sensitivity analyses for geometry in addition
1208 to transport parameters is needed, then process-based models are a preferred option. In creating a
1209 process-based model for carbonate samples, one faces the challenge of quantitatively describing
1210 the paragenesis given the uncertainty of particular diagenetic processes such as dissolution.
1211 Further, if geometry details such as surface roughness are important to the transport process, then
1212 direct numerical simulation is suggested as well. On the other hand, due to geometry
1213 simplification and use of analytical formulas, pore-network models offer “infinite resolution”,

38
1214 i.e. there is no numerical discretization involved in pore and throat cross-sectional geometries.
1215 Therefore, if film flow for instance is of interest, pore-network models are a good choice. One
1216 must bear in mind however, that the original complex geometry details of the pore space (such as
1217 surface roughness) have been discarded so that the term “infinite resolution” should be taken
1218 with caution. It might be that the ability to study phenomena on one’s laptop (as opposed to
1219 having access to a supercomputer) is important or that many images (and in large domain sizes)
1220 are needed for investigating relevant rock/fluid parameters. Analytical geometry descriptions
1221 allow for less computational effort and more complex physical processes and boundary
1222 conditions (e.g. three-phase flow, mixed wettability, combination of diffusion and convection in
1223 nano-scale flows) are explored with relative ease. Accordingly, to date, pore-network studies are
1224 more developed than direct simulation methods. Finally, the complexity of a particular pore-
1225 network generation method is proportional to its number of adjustable parameters, and since such
1226 parameters (for example detailed mineralogy of pore/grain surfaces) may not be available,
1227 uncertainties increase. Multiple adjustable parameters, of course, create situations where there is
1228 no unique optimal solution when matching a core-scale experiment. Having multiple plausible
1229 network model representations then creates uncertainty in modeling a different experiment. The
1230 predictive capability of pore-network models has been discussed in depth by Sorbie and Skauge
1231 (2012). They argued that pore-network modeling cannot be predictive of the multiphase flow
1232 properties of mixed-wet systems. This is due to the increased number of adjustment parameters
1233 that is needed in order to capture the pore-scale displacements accurately. In such cases, one
1234 might prefer to rely on empirical models and tune them with core measurements that are
1235 typically fewer than the number of adjustable parameters for a predictive pore-network model.
1236 Pore-network models are still valuable for mixed-wet systems in that they allow transport
1237 properties to be extrapolated for varying flow conditions after calibrating them with core
1238 measurements. Furthermore, they provide description of interstitial fluid flow behavior which
1239 can be insightful for any type of environmental remediation or enhanced oil recovery.
1240
1241 Capturing the heterogeneity of carbonate rocks is difficult using a single imaging modality. High
1242 resolution 2D SEM maps remain a helpful source of information for parameters such as
1243 minerology and pore size. In addition, they can be expanded into 3D with stochastic-based
1244 methods. The spatial distance of the extrapolation however can be limited due to anisotropy.
1245 Even though image-based direct simulation methods are limited by domain size and resolution,
1246 they can be useful in providing input parameters for pore-network models that can subsequently
1247 be expanded to larger domains. Hybrid DNS and PNM workflows however require further
1248 research to establish their benefits.
1249
1250 Wettability is an important parameter in determining the capillary pressure and relative
1251 permeability behaviors of porous media that we did not cover in detail in this paper but find that
1252 it is an essential research area for obtaining reliable pore-scale models for carbonates. In pore-
1253 scale modeling, it is typical to assume a uniform and unchanging value throughout the pore
1254 space. Recent visualizations of in situ contact angle subsequent to core-flooding (AlRatrout et
1255 al., 2017; Andrew et al., 2014) have shown that carbonate rocks demonstrate a wide contact
1256 angle distribution. This is partially due to the varying mineral makeup of the rock. In addition,
1257 given the commonly considerable chemical diagenesis of carbonates, surface textural
1258 heterogeneity such as surface roughness, can create a non-uniform mixed-wet system. An
1259 important property of carbonates that is difficult to capture in models, is its potential to change

39
1260 its wettability during two-phase flow. This dynamic wettability behavior was proposed (Kovscek
1261 et al., 1993) by linking the breakup of monolayer wetting films during primary drainage. The
1262 authors showed that once the imposed capillary pressure exceeds the summation of pore entry
1263 capillary pressure threshold and the wetting surface’s disjoining pressure, oil is able to contact
1264 the grain surface previously protected by wetting films. Recent efforts to incorporate the
1265 dynamic alteration of wettability during two-phase has been conducted (Kallel et al., 2016) but
1266 much work remains. Questions that remain are: (a) Can wettability alteration rules based on pore
1267 morphology for pore-network modeling be developed? (b) What insights can direct numerical
1268 simulation provide in regard to oil/water emulsion lens stability and contact line pinning? (c) Can
1269 core-flood experiments shed light into wettability alteration in real-time or should functionalized
1270 microfluidics experiments be leveraged? Microfluidics or lab-on-a-chip experiments are two-
1271 dimensional replicas of porous media. For a review of lab-on-a-chip devices see Anbari et al.
1272 (2018), Karadimitriou and Hassanizadeh (2012), and Mehmani et al. (2019).
1273
1274 Upscaling is an essential component in utilizing pore-scale modeling prediction of flow transport
1275 properties that we did not cover. Porous media with distinct hierarchies in scale, such as
1276 unconsolidated sandstones, allow upscaling to be conducted by establishing average values for
1277 transport properties. Volume average and homogenization techniques (Hornung, 1997; Whitaker,
1278 1999), fall into this category. In highly heterogeneous media, such as carbonates, where
1279 distinction between scale hierarchies is not possible, nonlocal hybrid multiscale methods are
1280 utilized. In hybrid multiscale methods, the parameter of interest is calculated in microscale
1281 directly and extrapolated to larger scales based on macroscale information. (Scheibe et al., 2015)
1282 provides a review of various hybrid methods and a flowchart referred to as MAP (multiscale
1283 analysis platform) that guides the researcher to a suitable upscaling approach following a series
1284 of questions. Given the high heterogeneity of carbonates, assessment of MAP for various
1285 carbonate rock types can shed light on the most useful upscaling scheme.
1286
1287
1288 4. Acknowledgement
1289 We acknowledge support from National Science Foundation CAREER grant 1255622. We are
1290 grateful to Prof. Martin Blunt, Prof. Sebastian Geiger, and Dr. Yashar Mehmani for constructive
1291 comments throughout the manuscript.
1292
1293

40
1294 Appendix: Example pore-throat network construction
1295
1296 We provide two simple examples in ImageJ/Fiji software (http://fiji.sc/) that outline acquiring
1297 basic grain and pore space analysis from segmented porous material images (with one additional
1298 analysis done in MATLAB/Octave). ImageJ is a widely used and free image analysis software,
1299 and Fiji is one of its variants with a number of useful plugins. Since contribution to ImageJ is
1300 public, the number of plugins are growing and there are often multiple implementations of the
1301 same algorithm. MATLAB programming environment
1302 (https://www.mathworks.com/products/matlab.html) is used for one small part of the example,
1303 and Octave (https://www.gnu.org/software/octave/) is its free alternative. The objective of this
1304 appendix is a demonstration on the fundamentals on how a pore network is obtained from
1305 images. Algorithms were chosen based on their conceptual simplicity and availability. Some
1306 advanced algorithms remain part of the individual research groups’ software solutions and are
1307 not readily available.
1308
1309 Sphere packing example
1310
1311 We start with a digitized two-dimensional cross-section from a synthetically generated
1312 monodisperse sphere pack (Finney, 1970b). The center of each sphere and a discretization of the
1313 pack can be found in Digital Rocks Portal (Finney, 2016). Slice 6 from the discretized image
1314 stack is selected for this example. The data are binarized into values of 0 and 1 that represent the
1315 pore and solid space respectively. The pixel values are converted to 255 (white) for pore space
1316 and 0 (black) for solid space in order to comply with the ImageJ input requirements. The file
1317 (shown in Figure A1a) is also available in supplementary information. Commands used to
1318 produce images are provided in the next section.
1319
1320 Duplicate the image and run Distance Map (see Figure A1b). Distance Map for each pore space
1321 pixel (labeled 255 in the original image) calculates the distance to the closest solid pixel and
1322 displays it in the proportional shade of gray. Local maxima in distances are the starting point for
1323 the watershed algorithm (the starting points can be observed by executing Ultimate Points). The
1324 watershed algorithm starts growing regions from the local maxima. When the regions meet, the
1325 borders are established such as those shown in Figure A2a. The regions can be considered
1326 individual pores. Subsequent to separating them with borders (which can be considered throats),
1327 we can label them using Find Connected Components (see result in Figure A2b).
1328

41
1329
1330 (a) (b)
1331
1332 Figure A1: Slice of the original sphere pack (a) and the distance map corresponding to the pore space (b).
1333
1334

1335
1336 (a) (b)
1337
1338 Figure A2: Watershed algorithm result for pore space (the borders that are identified in the process) (a) and
1339 subsequent labeling of individual connected components in the pore space (individual pores) (b).
1340
1341 Find Connected Components gives the area of each region (expressed in number of pixels in
1342 each region). The results can be saved as a .csv file (and opened in a spreadsheet software for
1343 analysis as needed). The histogram of the areas can be produced with ImageJ as well (see Figure
1344 A3).

42
1345

1346
1347 Figure A3: Histogram of pore areas using Analyze->Distribution applied to the Results from Find Connected
1348 Components and the snapshots of the entered parameters.
1349
1350 We can use similar tools to identify the throat information. However, in order to identify throats,
1351 we need to manipulate the images first. This is done by subtracting segmented and watershed-
1352 separated images (we remind the reader that images are arrays of numbers). The watershed
1353 image labels individual pores with pixel value of 255 and solid disks as well as throats with pixel
1354 value of 0. The original image labels pores and throats with pixel value of 255 and solid disks
1355 with 0. By subtracting the two we obtain an image with label 255 where throats are, and 0
1356 everywhere else (see Figure A4a). We can run Find Connected Components on the subtracted
1357 image (Figure A4b), and obtain labeling and statistics on throats.
1358
1359 The procedures above have identified the objects that are required to create a pore-throat
1360 network. Capturing the pore-throat connectivity, however, requires post-processing and we
1361 provide an example script for this purpose in MATLAB/Octave. The pore coordination number
1362 statistics is shown in Figure A5.
1363
1364

43
1365
1366 (a) (b)
1367
1368 Figure A4: Throats identified by subtracting the original and watershed images (a). Throats labeled
1369 (colored) by Find Connected Components (b).
1370
1371 The aforementioned tools can be used to acquire grain statistics. The original image can be
1372 inverted so that the solid phase is white (labeled with pixel value of 255), and the watershed
1373 procedure can be repeated. Most of the grains in this image are well separated, but the few that
1374 overlap can be segmented with watersheds and finding the connected components. The result is
1375 shown in Figure A6.

1376
1377
1378 Figure A5. Pore coordination number histogram (result from MATLAB/Octave script shown below).
1379

44
1380
1381
1382 Figure A6. Labeled individual grains.
1383
1384 List of relevant commands in ImageJ
1385
1386 1. Plugins->Macro->Record (records trace of all commands in the ImageJ session)
1387 2. File->Open (for 2D images)
1388 3. File->Import (for 3D images)
1389 4. Image->Adjust->Brightness/Contrast (when data is in 0,1 format, contrast needs to be
1390 adjusted in order to see the different image phases).
1391 5. Edit->Invert (2D, 3D) to invert phases (black to white, and white to black).
1392 6. File->Binary->Watershed (2D only)
1393 7. File->Binary->Distance Map (2D only)
1394 8. File->Binary->Ultimate Points (2D only) will show the extreme points of the distance
1395 map from which the watershed algorithm has started._
1396 9. Process->Image Calculator
1397
1398 Trace of commands in ImageJ
1399
1400 The following are commands obtained by Plugins->Macro->Record in ImageJ. The commands
1401 can be copied into an ImageJ Macro and executed via Plugins->New->Macro (the file with the
1402 commands SpherePack_Slice6_analysis_macro.ijm is provided in supplementary material).
1403
1404 // Reading in input image (Figure A1a)
1405 open("SpherePack_Slice6_Inverted.tif");
1406
1407 // Creating distance map of the pore space (Figure A1b)
1408 run("Duplicate...", " ");
1409 run("Distance Map");
1410 saveAs("PNG", "SpherePack_Slice6_DistanceMap.png");
1411

45
1412 // Figures A2,A3: watershed and identifying pores
1413 selectWindow("SpherePack_Slice6_Inverted.tif");
1414 run("Watershed");
1415 saveAs("PNG", "SpherePack_Slice6_WatershedResult.png");
1416
1417 selectWindow("SpherePack_Slice6_WatershedResult.png");
1418 run("Find Connected Regions", "allow_diagonal display_one_image display_results
1419 regions_for_values_over=100 minimum_number_of_points=1 stop_after=-1");
1420 saveAs("PNG", "SpherePack_Slice6_LabeledPores.png");
1421 saveAs("Results", "Results.csv");
1422 run("Distribution...", "parameter=[Points In Region] or=20 and=0-2375");
1423
1424 // save raw data for analysis in MATLAB
1425 selectWindow("SpherePack_Slice6_LabeledPores.png");
1426 saveAs("Raw Data", "SpherePack_Slice6_LabeledPores_nx500ny500_16bit.raw");
1427
1428 //Throat analysis in Figure A4:
1429
1430 open("SpherePack_Slice6_Inverted.tif"); //open again, just in case
1431 imageCalculator("Subtract
1432 create","SpherePack_Slice6_Inverted.tif","SpherePack_Slice6_WatershedResult.png");
1433 selectWindow("Result of SpherePack_Slice6_Inverted.tif");
1434 saveAs("PNG", "SpherePack_Slice6_Throats.png");
1435
1436 run("Find Connected Regions", "allow_diagonal display_one_image display_results
1437 regions_for_values_over=100 minimum_number_of_points=1 stop_after=-1");
1438 saveAs("PNG", "SpherePack_Slice6_LabeledThroats.png");
1439
1440 // save raw data for analysis in MATLAB
1441 selectWindow("SpherePack_Slice6_LabeledThroats.png");
1442 saveAs("Raw Data", "SpherePack_Slice6_LabeledThroats_nx500ny500_16bit.raw");
1443
1444 // Grain analysis in Figure A5:
1445
1446 open("SpherePack_Slice6.tif");
1447 run("Watershed");
1448 saveAs("PNG", "SpherePack_Slice6_GrainsWatershed.png");
1449 run("Find Connected Regions", "allow_diagonal display_one_image display_results
1450 regions_for_values_over=100 minimum_number_of_points=1 stop_after=-1");
1451 saveAs("PNG", "SpherePack_Slice6_GrainsLabeled.png");
1452
1453 MATLAB/Octave commands to establish pore-throat network
1454
1455 %% This script reads in images with labeled pores and throats
1456 %% For each throat, we search the neighborhood for neighboring
1457 %% pores and record this information. At the same time
1458 %% we record how many throats does each pore have in its
1459 %% neighborhood (pore coordination number).
1460
1461 pore_labels = imread('SpherePack_Slice6_LabeledPores.png');

46
1462 throat_labels = imread('SpherePack_Slice6_LabeledThroats.png');
1463
1464 % number of throats
1465 num_throats = max(throat_labels(:));
1466 num_pores = max(pore_labels(:));
1467
1468 % initialize array that will store pores that neighbor
1469 % each throat
1470 throat_neighbors = zeros(num_throats,2);
1471 pore_coord_number = zeros(num_pores,1);
1472
1473 for t=1:num_throats
1474
1475 % this is logical array corresponding to throat t
1476 individual_throat = (throat_labels == t);
1477
1478 % dilate this individual throat to get its immediate
1479 % neighborhood, and then and then investigate which
1480 % pore labels are found in its neighborhood
1481 se = strel('sphere',2);
1482 dilated_throat = imdilate(individual_throat, se);
1483
1484 % find pore labels in the neighborhood of a throat above
1485 A = pore_labels(dilated_throat);
1486
1487 % 0 in pore label array is throat or solid - setdiff avoids it
1488 % only unique labels are left
1489 A = unique( setdiff(A,0));
1490
1491 if numel(A) < 2
1492 fprintf('\nThroat %d not enough pores',t);
1493 elseif numel(A) > 2
1494 fprintf('\nThroat %d too many pores',t);
1495 end
1496
1497 % record information
1498 if numel(A) > 1
1499 throat_neighbors(t,1) = A(1);
1500 pore_coord_number(A(1))=pore_coord_number(A(1))+1;
1501 end
1502
1503 if numel(A) > 1
1504 throat_neighbors(t,2) = A(2);
1505 pore_coord_number(A(2))=pore_coord_number(A(2))+2;
1506 end
1507 end
1508
1509 % Plot histogram of pore coordination numbers
1510 max_coord_number = max(pore_coord_number);
1511 hist(pore_coord_number,0:max_coord_number);
1512 colormap gray

47
1513 set(gca,'fontsize',16);
1514 xlabel('pore coordination number');
1515 ylabel('frequency');
1516 axis tight
1517 saveas(gcf,'SpherePack_Slice6_PoreCoordNumber','png');
1518
1519 Ketton carbonate example
1520
1521 We downloaded Ketton carbonate image sample (available online4). The downloaded image is
1522 segmented; the tomographic original is not available. We work with slice 800 from that image (it
1523 is available for download in supplementary material).
1524
1525 Grain and pore labeling results of a watershed operation is demonstrated in Figure A7. The
1526 microporosity within some of the grains can create seemingly multiple “broken” components.
1527 Similarly, small pieces of grain as well as grain surface roughness results in exceeding number of
1528 pores. This is a common problem with such algorithms and typically can be resolved by reducing
1529 the number of the initial seeds of the watershed operation. Tools for such analysis are available
1530 in an ImageJ plugin by (Ollion et al., 2013).
1531
1532 Furthermore, we observe that because the Ketton carbonate pore space does not percolate in a
1533 single 2D cross-section, thus its pore-network representation can be of little value. In contrast, a
1534 grain network model is connected.
1535
1536 ImageJ commands producing Figure A7
1537
1538 //Grain analysis
1539 open("Ketton_Substack_Slice800.tif");
1540 run("Watershed");
1541 saveAs("PNG", "Ketton_Substack_Slice800_GrainWatershed.png");
1542 run("Find Connected Regions", "allow_diagonal display_one_image display_results regions_for_values_over=100
1543 minimum_number_of_points=1 stop_after=-1");
1544 saveAs("PNG", "Ketton_Substack_Slice800_GrainLabeled.png");
1545 selectWindow("Ketton_Substack_Slice800_GrainWatershed.png");
1546
1547
1548 //Pore analysis
1549 open("Ketton_Substack_Slice800.tif");
1550 run("Invert");
1551 run("Watershed");
1552 run("Find Connected Regions", "allow_diagonal display_one_image display_results regions_for_values_over=100
1553 minimum_number_of_points=1 stop_after=-1");
1554 saveAs("PNG", "Ketton_Substack_Slice800_PoresLabeled.png");
1555

4http://www.imperial.ac.uk/earth-science/research/research-
groups/perm/research/pore-scale-modelling/micro-ct-images-and-networks/

48
1556
1557 (a) (b)
1558
1559

1560
1561 (c)
1562 Figure A7: Ketton carbonate slice (a), labeled grains (b) and labeled pores (c).
1563
1564
1565 3D analysis
1566
1567 The reader will notice that some of the commands are labeled ‘2D only’ in the list provided
1568 above. Three-dimensional image operations are memory and computational time intensive and
1569 have been developed separately. Three-dimensional implementations are available (with no cost)

49
1570 in ‘3D ImageJ Suite’ plugin (Ollion et al., 2013), with documentation available online5. We
1571 show an example watershed performed to identify different pores in Figure A8. ImageJ
1572 instructions for creating it (including how to reduce number of starting points for watershed
1573 function, and thus noise) are available in Supplementary material
1574 (Ketton_Substack_nxyz500_3D_watershed.ijm).
1575

1576
1577
1578 Figure A8. A slice through 3D watershed result on pore space. Throat barriers dividing pores are shown in
1579 blue, and the rest of the colors show different pores.
1580
1581

5 http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start

50
1582 References
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2470
2471

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Highlights:

1) Major classifications of pore structure generation for heterogeneous carbonate rocks are
reviewed.
2) Various imaging methodologies appropriate for carbonate are discussed.
3) Direct numerical simulation and reduced-ordered models for predicting carbonate rock transport
properties are covered.
Declaration of interests

☒ The authors declare that they have no known competing financial interests or personal relationships
that could have appeared to influence the work reported in this paper.

☐The authors declare the following financial interests/personal relationships which may be considered
as potential competing interests: