Marine and Petroleum Geology 114 (2020) 104141

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Marine and Petroleum Geology

journal homepage: www.elsevier.com/locate/marpetgeo

Review article

Pore-scale modeling of carbonates T

Ayaz Mehmani , Rahul Verma, Maša Prodanović
∗

Hildebrand Department of Petroleum and Geosystems Engineering, The University of Texas at Austin, Texas, USA

ARTICLE INFO ABSTRACT

Keywords: Carbonate rocks display complex pore textures with heterogeneities that extend over several length scales.
Pore-scale modeling Identifying and capturing their significant pore space properties in a computationally tractable model is
Carbonates therefore nontrivial. Pore-scale models bridge predictions of transport properties from sub-pore to core scale
Petrophysics while attempting to render such methods cost effective. This chapter reviews several methods for fabricating
Digital rock physics
pore-scale models of carbonate rocks and discusses approaches to simulating their fluid flow and solute transport
Pore-structure reconstruction
properties. The advantages and limitations of each method in reducing the reservoir development uncertainties
are explained. We argue that pore-scale models can play an important role in predicting the petrophysical
properties of carbonate rocks. Even more importantly, they provide sensitivity analyses of pore-scale features on
macroscopic transport observations and offer explanations for anomalous flow behaviors.

1. Introduction
The length scales involved in modeling subsurface formations span
from sub-micrometers/micrometers (size of a pore) to meters/kilo-
meters (e.g. formation thickness or distance between wells). Although it
is desirable to conduct transport simulations solely on the field scale,
typically sparse formation evaluation datasets (such as log and core
data) may not be sufficient to statistically extrapolate necessary trans-
port properties to the entire reservoir domain. In general, a posteriori
prediction of the fluid behavior in subsurface porous media is proble-
matic given the wide range of values in core-scale macroscopic mea-
surements and their spatial heterogeneity in a given reservoir. Although
constraining the data based on lithology or rock typing schemes im-
proves predictions, obtaining such classes is challenging when it comes
to heterogeneous formations such as carbonates.
In addition to rock typing, determining the transport properties
based on direct formation evaluation can become complicated in car-
bonates as commonly used formulas needed to interpret log/core
measurements may result in high errors. For instance, researchers have
pointed out that utilizing the Carman-Kozeny model for predicting
absolute permeability from porosity measurements in carbonates re-
quires fitting the model to core data in order to incorporate a quanti-
fication of the “rock fabric” as an independent parameter. For accurate
predictions, the model needs to be continuously adjusted as data be-
come available (Jennings and Lucia, 2001) – which are not necessarily
available.
The uncertainties in predicting carbonate transport properties a
priori are due to the fact that traditional relationships such as Archie's
equation relating resistivity to saturation, Brooks-Corey for relative
permeability and Carman-Kozeny for absolute permeability (Peters,
2012) were originally derived for rocks with well sorted grains and
narrowly distributed pores such as unconsolidated sandstones. Such
relationships are erroneous for carbonates because of ranges in pore
size distribution that span orders of magnitude and high heterogeneity
in pore connectivity. It becomes therefore imperative to delve into the
pore scale to gain a fundamental understanding of flow through porous
media for finding closure relationships.
Pore-scale modeling is rooted in first principles. If the pore structure
is correctly represented and the initial conditions, such as initial contact
angle values, and details of a physical phenomenon, such as evolution
of wettability during two-phase flow, are understood, then any emer-
gent macroscopic fluid behavior, such as relative permeability, can be
captured accurately. Pore-scale models however require to be “up-
scaled” to reservoir grid domains which can become a nontrivial pro-
blem. In addition, uncertainties of the relevant input information for a
pore-scale model, such as in situ contact angle values, inevitably create
tuning parameters that will require adjustments to match macroscopic
experimental measurements.
Pore-scale modeling allows direct identification and quantification
of parameters related to pore structure and fluid properties for linking
the rock transport properties with geological information and estab-
lishing reliable rock classes. Once corroborated, pore-scale models can
offer data points away from wells where empirical relationships are
unavailable. Conducting experimental measurements is difficult in tight

∗
Corresponding author.
E-mail address: mehmani.ayaz@utexas.edu (A. Mehmani).

https://doi.org/10.1016/j.marpetgeo.2019.104141
Received 27 July 2019; Received in revised form 7 November 2019; Accepted 14 November 2019
Available online 20 November 2019
0264-8172/ © 2019 Published by Elsevier Ltd.
A. Mehmani, et al.
media. Heavily cemented but microporous limestones certainly fall into
this category for which obtaining experimental measurements become
scarce due to time and financial limitations. A cost-effective pore-scale
model can optimize the number of experimental measurements needed
for linking petrophysical rock types to depositional classifications
(Chandra et al., 2015; Skalinski and Kenter, 2015; van der Land et al.,
2013).
A robust pore-scale model provides general understanding of re-
lationships between various petrophysical properties and is therefore
valuable for long term reservoir development. An a priori knowledge
obtained through pore-scale modeling of fluid phase distributions can
assist in establishing the performance of water flooding, surfactant
flooding, and the efficacy of wettability altering chemicals during im-
proved oil recovery (Lerdahl et al., 2000). In addition such a model can
clarify the potential of environmental operations by predicting the fate
of pollutants during hazardous waste storage, determining NAPL re-
covery, and capacity of formations for carbon storage.
Fig. 1 shows an example of utilizing pore-scale modeling in for-
mation evaluation. During well log acquisition, core plugs from a flow
unit can be extracted to construct a pore-scale model. The model can
subsequently be used to establish the relationships between several
macroscopic petrophysical properties. Such relationships can then be
deployed to other flow units for which laboratory measurements are
expensive and not feasible.
This paper reviews methods and challenges in constructing pore-
scale models representative of rocks and elaborates on the various ap-
proaches used in simulating their fluid/solute behavior. Fig. 2 illus-
trates the topics covered in this paper and their contributions to the
creation of a pore-scale model. We start by covering three major pore-
space generation methods. Subsequently a discussion on pore-network
modeling and direct numerical simulation of fluid and solute through
the reconstructed pore space is provided. Algorithms for integrating
pores from multiple length scales is discussed next. We note that direct
numerical simulations can be used to benchmark reduced-ordered pore-
network models as well and a synthesis of these two methods is given in
Section 3 (Discussion). We focus on challenges in developing pore-scale
models for carbonate rocks as much as possible. Each section is written
such that the reader can obtain the most relevant concepts and litera-
ture independently from other sections. When a relevant review article
is referenced, we provide a succinct summary of already reviewed
concepts (to the extent that the reader can gather the most pertinent
information) and discuss supplemental topics not synthesized in the
literature. We have attempted to review a wide range of methods for
2
Marine and Petroleum Geology 114 (2020) 104141
Fig. 1. Schematic of the application of pore-scale mod-
eling. The green line depicts a well log (such as porosity)
identifying the flow unit (a lithologically preferable zone
for production). At a particular flow unit, core plugs are
extracted and images of them acquired to quantify the
pore structure. The information is fed to a pore-scale
model in order to determine the relationship between
several macroscopic properties. These relationships are
used subsequently in other flow units. Pc: capillary
pressure; Sw: water saturation; ϕ: porosity; K: perme-
ability; XCT: X-ray computed tomography; SEM: scanning
electron microscopy. (For interpretation of the references
to color in this figure legend, the reader is referred to the
Web version of this article.)
geometry preparation in various pore scale modeling methods, as well
as highlight the transport modeling methods themselves. That is a hard-
balancing act, and we apologize to any researchers in advance for not
referencing their papers.
Since pore-scale models hinge upon capturing key characteristics of
the pore geometry, we specifically discuss pore geometry generation
methods that follow the geological history of the rock, utilize three-
dimensional image acquisition methods, or extrapolate two-dimen-
sional information to three dimensions via statistical algorithms.
Integration of pores from multiple length scales can be a key element in
correctly capturing macroscopic behavior of carbonates and therefore
must be addressed in each generation method. We subsequently discuss
pore-network modeling and direct numerical simulation as two com-
plementary approaches for upscaling sub-pore scale transport dynamics
to a representative elementary volume (REV) or a volume approaching
it. The REV is a minimum volume for which continuum assumption of a
particular rock property is valid and was first introduced by Bear
(1972) and Hill (1963). As is discussed later, pore-network models are
computationally more effective than direct numerical simulation
methods; but both are viable for making a priori predictions of a
transport property if they capture the correct pore geometry, fluid/fluid
(for example interfacial tension) and fluid/rock conditions (for example
wettability). The ultimate choice of the method to be used depends on
the available information for constraining the input parameters as well
as computational budget associated with the physical process to be
modeled: the methods should be viewed as complementary rather than
competing. In addition, direct numerical simulations can determine
input variables for pore-network models and therefore assist in further
upscaling macroscopic calculations (Raeini et al., 2014a).
2. Methods
2.1. Pore geometry creation
Capturing pore geometry is essential to fabricating a reliable pore-
scale model. Three approaches that pursue this purpose gather their
information from images (image-based method), replicate the geologic
processes of the rock (process-based method) or are based on statistical
description of the porous medium (stochastic).
2.1.1. Imaging as a source of information for rock models
Imaging techniques have the potential for providing detailed de-
scriptions of the pore space that can be utilized for numerical
A. Mehmani, et al.
simulation schemes. X-ray computed tomography (X-ray CT) is a well-
established and rapid approach to acquiring three-dimensional visua-
lizations of the pore structure. The method distinguishes phases based
on density and atomic number variations that attenuate the X-rays
differently. X-ray CT is non-destructive, meaning that unlike other
imaging techniques such as petrographic light microscopy and scanning
electron microscopy, the rock sample is not cut or polished. The re-
solution of X-ray CT ranges from 100 nm to 1 mm (Bultreys et al., 2016)
and has an inverse relationship with the domain size.
Once a three-dimensional visualization is obtained and processed
such that its quality is acceptable, the image is “segmented” into phases
of interest, normally the pore space and the solid phase. Any pore-scale
numerical analysis of the image is thus conducted based on the seg-
mented image. Image processing, although conceptually simple, can be
challenging in geomaterials due to the presence of artefacts such as
beam hardening (Van de Casteel et al., 2002) or when the sample is not
held in a stable position properly. Given the many sources of un-
certainty in processing a micro-CT image, completely automatic pro-
cessing workflows are not yet established, leaving many image filtering
and segmentation attempts dependent on the operator's judgement
(Iassonov et al., 2009). The current subjective nature of image analysis
highlights the importance of core data measurements to validate a
processed image prior to using it to predict unavailable transport
properties. Such validations may become especially important in car-
bonates given the higher sensitivity of near-resolution pores of be-
coming dismissed during image filtering and segmentation. Carbonates
present an additional challenge for capturing their pore-space in a
single micro-CT image given their multiscale pore structure. Pore scales
can range from sub-resolution nanometer sized pores to interparticle
pores and up to larger scale vugs and microfractures. This range in scale
can make the capture of carbonate pore spaces in a single image un-
feasible (Victor, 2017). To circumvent this limitation, a top-to-bottom
approach can be adopted where following a coarse-scale three-dimen-
sional CT image, high resolution micro-CT images from targeted regions
are acquired (Arns et al., 2005). A combination of other imaging
methods to gather the higher resolutions information can be im-
plemented as well. The transport properties determined from the high-
resolution pore structures are subsequently scaled up to establish the
transport property of the larger domain (we provide a discussion on this
topic in Section 2.3). For a complete review on image processing refer
to Heilbronner and Barrett (2013), Serra (1982), and Wildenschild and
Sheppard (2013). Fig. 3 shows an example of (a) a micro-CT image, (b)
pore-solid surface visualization after segmentation and (c) a pore-
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Marine and Petroleum Geology 114 (2020) 104141
Fig. 2. Topics covered in this paper and their contributions
to the creation of a pore-scale model. Since pore-network
modeling is a reduced-ordered method, direct numerical
simulations can not only be used for predicting the rock
sample's transport properties, but also inform pore-network
modeling algorithms. In carbonates, similar to other un-
conventional systems, experimental data is not always
available for benchmarking purposes. Since direct numer-
ical simulations sacrifice pore space geometry and fluid flow
behaviors to a lesser extent than pore-network models, they
can serve a valuable purpose in reducing the latter's un-
certainty.
network representation of the pore space (to be discussed later in the
chapter). In this paper, we refer to a pore space generation that is
completely based on a three-dimensional image as an “image-based
pore-scale model”. As we discuss other pore space generation methods,
overlaps between the three methods exist and our classification serves
as a point of reference rather than a rigid framework.
Light microscopy and scanning electron microscopy are two-di-
mensional image acquisition techniques that provide micrometer and
nanometer scale information respectively (see Fig. 4a–b for an example
of each). For light microscopy, the pore space of a rock sample is filled
with blue epoxy and a 30-μm-thick thin-section is cut. Polarized light is
emitted through the sample to determine the grain mineralogy, visible
porosity and paragenesis (the chronology of geological events occurring
during rock formation). For scanning electron microscopy, electrons are
bombarded on a polished carbon coated rock surface. The surface
scattered electrons (called secondary electrons) and those that are
backscattered due to elasticity, which carry information from a higher
depth, are analyzed to infer the surface topography of the solid phase.
Using similar bombardment, mineral atoms can be excited which re-
lease X-rays when they return to their stable state. This is referred to as
Energy Dispersive Spectroscopy (EDS) which gives information of the
mineral composition of the rock. The disadvantage of utilizing light and
scanning electron microscopy is the fact that they are two-dimensional.
Numerical methods for extrapolating such information to three-di-
mensions are non-trivial and will be discussed further in Section 2.1.3
as part of stochastic methods. Confocal laser scanning microscopy
(CLSM), with a prior application in biology, has been leveraged to
quantify the pore texture of rocks (Fredrich, 1999; Fredrich et al.,
1995). In this method, a laser beam is focused on the domain of interest
and its reflection is detected and analyzed. This method produces sub-
micron lateral resolution with lower vertical resolution depending on
material type and magnification (with the higher magnification having
larger vertical resolutions). Given the limitations in vertical resolution,
two-dimensional CLSM images can benefit from extrapolation techni-
ques discussed in Section 2.1.3 as well. Recent work by Jobe et al.
(2018) has shown CLSM's application in acquiring two-dimensional
images of micropores in carbonate samples (Fig. 4c) and utilizing them
to capture their pore topology with stochastic extrapolation methods
(Wu et al., 2006).
Focused ion beam scanning electron microscopy (FIBSEM) is a
technique with nanometer scale resolution for capturing the pore tex-
ture of sub-resolution micro-CT pores in three dimensions (Bera et al.,
2012; Wirth, 2009). Fig. 5 shows an example FIBSEM image stack of a
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

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

chalk sample. In FIBSEM the sample is sliced with ion beams and an
SEM image is taken for each stack. Although valuable information can
be gained with this imaging modality, namely the 3D interconnectivity
of pores, the financial and time cost of acquiring a FIBSEM image stack
renders them intractable for routine use. Given the destructive nature of
FIBSEM acquisition during beam slicing, uncertainties associated with
pore space connectivity can be exasperated as well. Finally, in addition
to challenges in image registration, the rendered domain is very small
such that a quantitative assessment of flow properties become ques-
tionable (Kelly et al., 2016). FIBSEM therefore is an ideal technique for
diagnostic purposes and as a supplemental tool along with other image
acquisition methods for carbonates (Sok et al., 2010). When micro-CT
imaging becomes insufficient to reveal the sub-resolution pore space,
FIBSEM can provide information on the presence of critical pore con-
nectivity within sub-resolution pores as well as at the interface of sub-
resolution and resolved pores. Furthermore, given the complex carbo-
nate diagenesis that result in amorphous pore shapes, FIBSEM can
provide a clearer picture of pore morphology. FIBSEM uncertainties
associated with ion beam slicing, electron charging and resolution
limitations (Dewers et al., 2012) can be mitigated by calibration with

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

4
A. Mehmani, et al.
Fig. 5. (a) A two-dimensional FIB image of a chalk sample and (b) its corresponding three-dimensional reconstruction. From Tomutsa et al. (2007).
macroscopic measurements such as nitrogen-sorption hysteresis
(Mehmani and Prodanović, 2014a; Xu and Prodanovic, 2018). How-
ever, much work is needed to establish robust workflows for such ca-
libration purposes.
Data storage and management are challenges in image-based char-
acterization of porous media. For instance, X-ray microtomography
images typically have 20001 voxels (the storage necessary is 8 GB or
16 GB depending on whether 1-byte or 2-byte integers are used to store
attenuation coefficients for each voxel) and can triple in size if stitching
along axial direction or if helical scanning is conducted. Furthermore,
recent multi-beam scanning electron microscopes (e.g. Zeiss MultiSEM)
use up to 91 parallel beams and can collect areal images with ap-
proximately 5-nm resolution at a scale of several square millimeters.
While the resulting tiled images are getting close to covering re-
presentative areas (Keller et al., 2014; Kemen et al., 2015) for hetero-
geneous media, with a size of more than 200 GB their display and
analysis is challenging. Due to the resultant “big data”, a repository for
retaining, retrieval, sharing, and organization of acquired images and
their analyses can be valuable for enhancing research for modeling/
prediction of porous material properties.
One of the new research data management tools, Digital Rocks
Portal (Prodanovic et al., 2015a) allows managing, preserving, visua-
lization and basic image analysis of available images of porous mate-
rials and experiments performed on them. It can accommodate storage
of any accompanying measurements (porosity, capillary pressure, per-
meability, electrical, NMR and elastic properties, etc.) required for both
validations on modeling approaches and the upscaling and building of
larger (hydro)geological models. As of the end of 2018, Digital Rocks
Portal currently published 58 samples, and is expected to have a re-
presentative population of samples for every lithology. Carbonate ex-
amples range from petrophysical characterization of pore/vug/fracture
space, to wettability (contact angle) measurements and precipitation
experiments (Alhammadi et al., 2018; Baek and Tae-Hyuk Kwon, 2018;
Bultreys et al., 2017a, Bultreys et al., 2017b; 2018; Heidari and
Posenato Garcia, 2016; Khan et al., 2018; Khan and Pope, 2018;
Muljadi, 2015; Prodanovic et al., 2016; Scanziani et al., 2018; Singh
and Blunt, 2018; Victor and Prodanovic, 2017). While other general
data storage options exist (e.g. Mendeley Data for any data,2 and En-
ergy Data Exchange3 for energy/subsurface focus), they lack tools for
viewing 3D datasets within browser and specialized analysis or ability
to produce digital object identifiers for referencing in publications.
1 and polycrystalline (with a characteristic isopachous cementation) and
http://www.palabos.org.
2
https://data.mendeley.com/.
3
https://edx.netl.doe.gov/.
5
Marine and Petroleum Geology 114 (2020) 104141
2.1.2. Process-based rock models
Process-based methods are based on replicating the chemical and
mechanical rock formation processes on grain scale. Following this
approach, the pore-scale model can link formation properties with any
burial stage process throughout the diagenesis. This pore space gen-
eration method is important not only for understanding the first prin-
ciples of the rock transport properties, but also as a practical tool in
extrapolating information from one portion of the reservoir to the next
(that is extrapolating transport information from one burial stage to
another). Process-based implementations on image-based methods (a
hybrid process-image-based method) is considerably difficult since
capturing the mechanical and chemical processes in images throughout
the formation stages is not trivial. Most often it is essentially the “end
result” that is imaged and characterized. The starting point of process-
based methods is typically an unconsolidated grain pack. At each burial
stage, pertinent diagenetic processes are included. Such processes can
be grain rearrangement and ductile deformation due to compaction,
cementation of various minerals as well as grain dissolution. Process-
based approach, though powerful in its motivation, compromises
complexity by simplifying the grains to ideal shapes such as spheres or
ellipsoids. This approach is in particular challenging in carbonates
given their complex diagenesis rendering it difficult to formulate each
diagenetic step to be quantitatively.
In a pioneering work on process-based methods, Bryant et al.
(1993b) modeled compaction and cementation on a disordered mono-
disperse grain pack. In this technique, the grain deposit is replicated
based on experimental measurements of ball-bearings packed in a
rubber bladder (Finney, 1970, 2016). Compaction is modeled by
overlapping the grains and for cementation, the radii are increased
without moving the grain centers. The researchers subsequently used a
pore-network model to simulate permeability and drainage capillary
pressure and relative permeability curves (Bryant and Blunt, 1992;
Bryant et al., 1993a). Bakke and Øren (1997) and Øren et al. (1998)
developed low-energy and high-energy sedimentation modeling
schemes for the initial grain pack and subsequently added cementation
and compaction to represent the formation of the rock. Thin-section
analysis of a Bentheimer sandstone sample was used to inform the
model in a case study. In addition, Torskaya et al. (2014) have included
pore-filling and throat-filling cementations into a disordered packing
and studied its effects on absolute permeability and drainage fluid
properties. Hosa and Wood (2017) utilized a single-scale process-based
method to investigate the impacts of early calcite cementation on
porosity-permeability relationships in carbonate rocks. They differ-
entiated grains into monocrystalline (capable of syntaxial cementation)
simulated single-phase incompressible flow directly on the pore space
with a lattice Boltzmann algorithm. Although their method captured
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

the log-log relationship between permeability and porosity observed in

experiments, they overestimated permeability potentially due to the
very high permeability value of the initial synthetic grain pack.
Establishing the initial grain pack is not trivial. One of the recent,
popular grain packing algorithms is cooperative sphere rearrangement
(Thane, 2006). In this method, a set of initial points in a three-dimen-
sional domain is randomly selected. Spheres of a predetermined size
distribution are grown with their centers at randomly selected points.
Each sphere grows at a rate proportional to its ultimate size. When
overlaps occur, the sphere centers are moved apart. If the removal of
overlap is not possible, a different sphere size is selected. Another ap-
proach to establish the starting point grain pack is based on a discrete
element method (DEM) in which the translation, rotation as well as
interaction of grains are numerically modeled (Cundall and Strack,
1979; Holtzman et al., 2008; Jin et al., 2003).
Torskaya et al. (2014) studied the impact of grain shapes on per-
meability, formation factor and drainage capillary pressure. They con-
cluded that permeability can have a difference of up to 1.6 times for a
sandstone sample if grain shapes are ignored. Formation factor and
drainage capillary pressure values remain within a 20% difference in
their study. Garcia et al. (2009) developed a method to study the impact Fig. 7. Two-dimensional schematic (top) of explicitly including (a) grain-filling
of irregular grain shape on single phase flow properties. Each irregular and (b) pore-filling microporosity. Red lines indicate throats that connect two
grain was a cluster of several spherical ones that made the im- different scales (that have been referred to as micro and macro network). Three-
dimensional visualizations of the pore-network models are at the bottom
plementation of DEM in simulating its sedimentation feasible. DEM has
(Mehmani and Prodanović, 2014b). (For interpretation of the references to
also been coupled with drainage capillary movements (Prodanović
color in this figure legend, the reader is referred to the Web version of this
et al., 2009) to investigate the impact of invasion forces to grain dis- article.)
placement. In other work, Mirabolghasemi et al. (2015) coupled DEM
with computational fluid dynamic modeling for single phase flow to
predict the amount of particle entrapment in porous media. Modeling methods as discussed in Section 2.1.3. A secondary smaller scale pore
ductility has been introduced by Mousavi and Bryant (2012) and Thane network was then connected with the pre-dissolution pore network
(2006) for a grain pack. In this method, a ductile grain is assumed to model following a stochastic method developed by Jiang et al. (2013b).
have a hard center. The ductile shell is penetrated by an adjacent rigid Mehmani and Prodanović (2014b) introduced novel deterministic
grain and the ductile materials are conserved by increasing the radius of methods to explicitly integrate intraparticle microporosity with inter-
the ductile grain. For carbonate rocks, several classifications for pore- particle macroporosity following geological causes. In their method to
scale process-based modeling has been introduced based on thin-section include microporosity, a network model is scaled down and planted to
observations (Mousavi et al., 2012). Fig. 6 shows three of such diage- targeted grains and interparticle pores based on information gathered
netic processes namely, cementation, fracturing and grain dissolution from light or scanning electron microscopy. The micro-network is then
that originated from sedimentary packings. Because certain types of stitched to its adjacent (interparticle) macropores. Fig. 7 shows a
diagenesis, such as dissolution and micro-fracture generation, impose schematic of the method. Mehmani et al. (2015) developed algorithms
integration of pores from multiple scales, the development of such to explicitly include vugs and microcracks adjacent to interparticle
models is not straightforward. pores. Vugs are included as larger pores centered on a randomly chosen
Recent advances in process-based methods have focused on mod- interparticle pore and subsequently connected to the vug's surrounding
eling the integration of pores over multiple length scales for both car- pores (Fig. 8a). A microcrack is included by two parallel planes with a
bonates and tight porous media. van der Land et al. (2013) used con- particular orientation that is imposed on a single-scale network model.
ceptual thin-section models of several carbonate rock types and All pores falling within the planes are removed and microcrack pores
predicted the impacts of cementation and dissolution on the perme- are added to the empty space instead (Fig. 8b). Mehmani and
ability, drainage capillary pressure and relative permeability curves. Prodanović (2014b) present several simulations of drainage and im-
Pore-network models were extracted after translating the two-dimen- bibition for networks that include microporosity. Fig. 9 presents the
sional conceptualizations into three dimensions using stereographical primary quasi-static capillary pressure drainage simulations for vuggy

Fig. 6. Examples of modeling approaches for (a) cementation (b) inclusion of fractures and (c) grain dissolution (Mousavi et al., 2012).

6
A. Mehmani, et al.
Fig. 8. (a) 2D schematic on top shows how a vug is incorporated into the pore
throat network: the grains as well as original pores are removed from the lo-
cation where a disk-shaped (sphere-shaped) vug is placed. 3D model on bottom
shows the original network, as well as the model after placement of a number of
vugs. (b) 2D schematic and a 3 d example model of including a fracture (plane)
into an interparticle pore-network model (Mehmani et al., 2015).
carbonates with different porosities (ϕ) and a vug to pore scale differ-
ence of 5, and carbonates with a single microcrack with varying angles
θ of the crack axis with respect to the flow direction. The initial grain
pack of each network has a uniform radius of unit 1 and the side length
of the cube is 20 units. The considerably lower percolation threshold of
the vuggy pore-network model at a porosity of 0.62 is due to the
Fig. 9. Primary drainage capillary pressure curves of (a) a vuggy carbonate rock (with a scale difference of 5) and (b) a carbonate rock with a single microcrack (with
a scale difference of 5) at three axis angles with respect to the pressure gradient direction. Drainage is simulated on pore-network models described in Fig. 8.
7
Marine and Petroleum Geology 114 (2020) 104141
significant volume of a well-connected network of vugs. As was shown
by Pak et al. (2016), such percolation thresholds can be used as cali-
bration points to fine-tune multiscale pore networks by matching
mercury injection data. Systematic comparisons of two-phase flow be-
haviors of multiscale pore-network models with experimental data is
however currently pending.
2.1.3. Stochastic methods for geometry creation
Stochastic methods rely on several critical source information to
generate the pore space. This method is in contrast to image-based
methods which capture the entire pore space from a three-dimensional
image, and process-based methods, which attempt to generate the pore
space by following the diagenesis. It is important to note that the three
pore-space generation techniques can have overlaps. For instance, two-
dimensional images with process-based adjustments (van der Land
et al., 2013) can be a source for stochastic methods. Given the afore-
mentioned uncertainties in capturing the carbonate pore texture via
images and difficulties in replicating the geological processes for a
process-based approach, statistical descriptions have the potential to
constrain pore-scale models if accurate quantitative descriptions of the
pore space are provided. Stochastic approaches can in addition expand
the limited domain size of an image by extrapolating the mathematical
descriptions to larger domains. Furthermore, three-dimensional images
of a porous medium may not be available, may not provide important
information on mineralogy where microscopy is crucial or may cover
too small of a volume to infer representative information on porosity
(or any other property). In such cases, extrapolating two-dimensional
information to three-dimensions can be possible via stochastic methods.
One stochastic method is multiple-point statistics which utilizes two-
dimensional images as “training images” to construct the pore-space
pattern in three-dimensions (Caers, 2001; Okabe and Blunt, 2004;
Tahmasebi and Sahimi, 2013). In the context of predicting the transport
properties of porous media, it has shown to perform better than two
other stochastic reconstruction methods: object-based methods, which
relies on the geometrical descriptions of the “objects” comprising the
porous medium such as grains, and pixel-based methods, that typically
aim to minimize the lower order statistical properties of a sample.
Conceptually, stochastic creation can apply to both pore space
images and pore networks. For pore networks, however, Sok et al.
(2002) showed that a sole reliance on a finite number of statistical
descriptors extracted from images, and attempting to replicate them by
modifying a regular network without including the topological prop-
erties of the pore space, can result in high errors in flow predictions.
Multiple point statistics for imaged pore space reconstruction, on the
other hand, honors the pore space patterns and spatial relationships of
the pore space by matching a multipoint statistical property such as the
cross-correlation function of a “training image”. Figs. 10 and 11 give
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

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

examples of utilizing multiple point statistics in reconstructing the pore
space of carbonate rock samples. The method's accuracy, however, re-
lies on the representativeness of the two-dimensional training image. A
two-dimensional training image, as was discussed in Section 2.1.1,
might not capture the multiscale pores of a carbonate sample that exist
in close proximity due to the selected field-of-view (which has an in-
verse relationship with voxel resolution). Further, image acquisition
artefacts, as a result of milling in SEM for example, propagate to the
three-dimensional reconstruction. Finally, the reconstruction extra-
polates the cross-section information (pore space shape, etc.) into the
orthogonal direction, whether that is correct or not.
Although predictions of single phase permeability using multiple-
point statistics reconstructions are encouraging when compared to ex-
perimental data (Okabe and Blunt, 2004), further work is required to
investigate the reliability of multiple point statistics, or other stochastic
methods (van der Land et al., 2013; Wu et al., 2006), for multi-phase
flow behaviors. This necessity for additional work is because multi-
phase transport properties in general are more sensitive to pore struc-
tural properties. Recent work on stochastic methods have involved
machine learning techniques. Mosser et al. (2017) for example utilized
a generative adversarial neural network (GAN) method to reconstruct
three-dimensional pore space representations using training micro-CT
images in a computationally effective way. The method is capable of
capturing pore space heterogeneity in all three dimensions and can
store the trained hyper-parameters and reuse them for multiple reali-
zations. The researchers applied GAN to recreate Keystone limestone
and the statistical descriptions of pore morphology and single-phase
permeability between the original and reconstruction were in close
agreement. Experimental verification of such methods is currently
pending.
2.2. Simulation methods
2.2.1. Pore-network generation schemes
Modeling the transport properties of a porous medium depends on
its pore structure. It is therefore imperative in a predictive model to
capture the pore space of a rock as accurately as possible. Once the
pore-space is fully resolved, so-called “direct numerical” methods can
be implemented to conduct multiphase flow simulations (see Section
2.2.4). A major challenge in direct numerical methods is the compu-
tational cost that comes with the detailed description of the pore space.
Pore-network modeling was first introduced by Fatt, 1956, Fatt, 1956,
Fatt (1956a, 1956b, 1956c) to introduce interconnectivity and three-
dimensional spatial organization; which was in contrast to a previous

Fig. 11. (a) A binarized image of a back scattered electron image of a carbonate rock sample (512 × 512 with 0.345 µ m/pixel) and (b) a three-dimensional
reconstruction of it using a multi-point statistical reconstruction method (Okabe and Blunt, 2005). Predicted permeabilities for carbonates have shown to over-
estimate by a factor of 3 when compared with experimental data but were considered acceptable given the model and experimental domain size differences (Okabe
and Blunt, 2004).

8
A. Mehmani, et al.
representation of pore space as bundle of tubes. Although pore-network
modeling is conceptually represented as three-dimensional diagrams
composed of balls (for pores) and sticks (for throat), details for their
generation vary. Fluid interaction rules in pore-network modeling are
based on analytical derivations of meniscus instability based on ex-
perimental fluid dynamic observations which were pioneered by
Lenormand and Zarcone (1984). Although in its early conception pore-
network modeling was considered a computationally cost-effective
method for fluid flow predictions in porous media, with the advance-
ments in computational power, modern pore-network models have
become essentially upscaling schemes that incorporate sub-pore scale
physics derived from either direct numerical simulations or experi-
ments (Aghaei and Piri, 2015; Zolfaghari and Piri, 2017a, Zolfaghari
and Piri, 2017b). Pore-network models and direct numerical simulation
should therefore not be considered as rivals.
In a pore-network model, throats are defined by Bear (1991) as fluid
pathway cross-sections with minimal hydraulic radius (the ratio of area
to perimeter of the cross-section). Pores are then spaces enclosed by
grains and throats. Although the concept of a pore-network re-
presentation is simple, dividing any given pore space into pores sepa-
rated by throats in a unique way is non-trivial. Fig. 12 demonstrates
how an image-based pore-network construction algorithm can add
uncertainties in numbers of pores. However, as mentioned in the cap-
tion of Fig. 12, regardless of the local choice made in identifying a local
throat (and/or whether it separates two pores), the flow simulation
should ultimately make that local choice irrelevant.
We next describe several generations of pore partitioning algorithms
for image-based porous media. We start with medial-axis algorithms.
Maximal balls and watershed algorithms are described next. The latter
two use intuitive ideas to partition pores and are less computationally
demanding. Thus, they are currently most commonly used in the digital
rock petrophysics community.
Early pore-throat network extraction methods utilize medial axis as
a search tool (Liang et al., 2000; Lindquist and Venkatarangan, 1999).
After image filtering and segmentation, the medial axis (Lee et al.,
1994), that is, the pore space skeleton that runs approximately in its
middle, is extracted. Throats are identified on a medial axis path that
has a continuous sequence of grains/particles and minimal area/peri-
meter (Lindquist et al., 2005; Shin et al., 2005) along that path is re-
cognized as the throat perimeter. Pores are subsequently determined
following a labeling algorithm after throat barriers are identified in
digital space (Prodanović et al., 2006) – see Fig. 13 for a schematic from
(Mehmani et al., 2011), and Fig. 14 and Fig. 15 for the example 3D
throat and pore. The algorithms in this group work well for con-
solidated materials where continuous path of grain voxels bounding a
throat barrier (see Fig. 14a) can be identified in a desired location.
Despite the throat channel visualization shown in Fig. 14, its limits are
somewhat arbitrary. The algorithm finds each throat surface and barrier
(barrier refers to a collection of voxels intersected by a throat surface)
but there are no clear criteria based on an image that can identify the
beginning and end of a corresponding throat channel. This uncertainty
is the case for most algorithms. Either pore-throat-network visualiza-
tion or pore-network models, however, require definition of a straight
9
Marine and Petroleum Geology 114 (2020) 104141
throat channel and those are often taken as straight lines between pore
centroids (though in reality, those paths are not straight). Some level of
arbitrariness thus exists in establishing image-based pore-throat net-
works. In an extension of medial-axis pore partitioning algorithms,
Jiang et al. (2017) have extracted pore-network models from fractured
rocks and demonstrated good agreement with analytical equations and
direct numerical simulations for single phase flow and experimental
values for drainage residual saturations. For unconsolidated/granular
packs (in general, more porous materials) watershed and/or Delaunay
tessellation perform better.
In maximal balls algorithm (Silin et al., 2003), Euclidian distance
labels are interpreted as a radius of a maximal ball that can be inscribed
inside of the pore space at that point. Subsequently, the balls are pro-
cessed to identify intersections. For two balls that intersect, the smaller
one is identified as a “slave” of the larger (“master”). At the end of the
algorithm, master balls represent pore centers. If two master balls have
two intersecting slave balls, that location (and radius) identifies a
throat. If throat location and radius are ample information for char-
acterization and/or modeling, these algorithms work well. The actual
throat barrier such as the ones exemplified in Fig. 15 (or those by
watershed algorithm in Appendix) are more difficult to obtain.
Watershed partitioning locates throat surfaces and is relatively easy
to implement. This makes it one of the most popular algorithms: we
describe it next and provide an example in Appendix. In the watershed
pore partitioning algorithm, the binarized image is processed to pro-
duce the Euclidean distance field (i.e. each voxel of the phase of interest
is labeled by the distance to the closest voxel of the other phase). The
Euclidean distance is thought of as the topographic height function and
inverted so that local maxima become local minima. The algorithm
partitions the phase of interest into “watershed basins”: water dropped
inside a region will end up at the same low point. This type of algorithm
is widely implemented in software (e.g. ImageJ, MATLAB, Avizo) and is
used in a number of partitioning applications, e.g. for separating in-
dividual grains in a sand or sandstone image (Thompson et al., 2006)
and pore-throat networks (Sheppard et al., 2006). Since watersheds are
very intuitive and widely implemented, we provide an example in the
Appendix. All watershed algorithms suffer from noise, however, in the
sense that every local minimum (maximum in the original image) will
produce a corresponding region. Thus, one has to filter the number of
starting local minima in some way in order to produce meaningful
partitioning or find a criterion for region merging afterwards (see 3D
example in the Appendix for example). If one was to compare to medial-
axis based search algorithm result in Fig. 14, the local minima corre-
sponding to the medial axis branching points would have to be merged
or else the algorithm would result in labeling two pores instead of one.
Such discrepancies in pore indexing should not affect the average flow
properties.
For granular materials or weakly consolidated sandstones with re-
latively narrow distribution of grain sizes, a simple pore-network gen-
eration method based on the early work of Finney (1970) can be used.
This method, which is very suitable for process-based modeling, assigns
the pores and throats to the interiors and faces of tetrahedra identified
in tessellation of grain centers.
Fig. 12. In each of these conceptual cases
(figure reprinted from (Prodanović et al.,
2006)), pore partitioning algorithms will
likely place a throat labeled “a-b” given the
local minimum of hydraulic radii. From the
point of drainage, however, case (a) acts
like a single pore, and the fact that it was
identified as two pores does not make a
difference in averaged flow properties. Case
(b) can be considered having two pores or
be only one pore and case (c) is a two-pore
system.
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

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

Fig. 16 shows a schematic of extracting a pore-throat network from

a grain pack. Some merging of the pores (identified by corresponding
overlap of inscribed spheres) is typically necessary (Al-Raoush et al.,
2003). The above pore-network generation algorithms are general and
any adjustment to the pore-network that is required to establish a
model more suitable for a carbonate sample (such as integration of sub-
resolution micropores or inclusion of rugosity for film flow) should be
implemented on the extracted pore-network.

2.2.2. Pore-network modeling of single-phase flow and solute transport

Mechanisms contributing to the transport of a passive tracer are
advection and molecular diffusion. Their relative dominance is quan-
tified by the dimensionless Péclet number (vL/D), where v is fluid ve-
locity, L is a characteristic length scale and D is the bulk fluid diffu-
sivity. When majority of solute particles have had the opportunity to
experience the entire range of interstitial fluid velocity, in other words,
solutes have traveled beyond the correlation length of the porous
medium, the traversing plume takes the form of a Gaussian distribution.
In this scenario, diffusion follows Fick's law in that mass diffusion rate
becomes linearly proportional to the concentration gradient. In addi-
tion, diffusion length scales with the square root of time and the
average solute velocity equals to Darcy velocity. This solute transport
behavior is referred to as “Fickian”. Due to the complex and hetero-
geneous pore structure of carbonates, solute transport oftentimes takes
a “non-Fickian” form and its prediction has been the focus of pore-scale
modeling efforts (Bijeljic et al., 2004, 2011).
The direct modeling of mass transport requires the solution of the
Navier-Stokes equation coupled with a set of species’ mass balance
equations. The numerical framework can either be grid-based
(Eulerian) or based on tracking Brownian particles within the pore
space (Lagrangian). Given the computationally intensive nature of di-
rect methods, pore-network models are often used for modeling single-
phase and solute transport, although direct numerical simulation of
single-phase flow has recently become more tractable. Prior to mod-
eling transport, the flow field is computed. In Eulerian pore-network
Fig. 15. An example pore from a sandstone image with throats barriers, medial
axis paths in the search are identified in red. Note that there are two branching
points of the medial axis identified within this pore: the branching points of
medial axis and pore centers are not in one-to-one correspondence. (For in-
terpretation of the references to color in this figure legend, the reader is referred
to the Web version of this article.)
models, species balance is imposed at each pore. It is also often assumed
that pore concentrations are uniform, which can potentially lead to
errors in high Péclet numbers. This is referred to as the Mixed Cell
Method (MCM) (Acharya et al., 2007; Bryntesson, 2002; Kim et al.,
2011; Li et al., 2006; Mehmani et al., 2012; Nogues et al., 2013). Y.
Mehmani et al., 2014, improved MCM by accounting for imperfect
mixing within pores using a streamline splitting based method. Sig-
nificant improvements in macroscopic transverse dispersion were re-
ported in 2D ordered micromodels. The improvements however were
minor for 3D disordered sphere packs. Mehmani and Balhoff, (2015a)
addressed another shortcoming of MCM by incorporating shear-induced
dispersion caused by non-uniform velocity profiles within pore throats.
The result was an improvement in macroscopic longitudinal dispersion
in disordered media at high Péclet numbers. Lagrangian methods,
which are more accurate but computationally expensive for continuous
injection problems, require the tracking of particles via discrete (Bijeljic

Fig. 14. (a) Medial axis path voxels extracted from a 3D Berea sandstone image in red with a throat perimeter voxels identified in brown. Grain and pore voxels are
not shown. Voxels in blue are throat barrier voxels used in subsequent pore labeling. (b) Corresponding triangulated throat surface is shown in white. (c) Dark red
shows the pore-grain surface corresponding to the channel where the throat (surface shown in white) is identified. (For interpretation of the references to color in this
figure legend, the reader is referred to the Web version of this article.)

10
A. Mehmani, et al.
et al., 2004; Bruderer and Bernabé, 2001; Jha et al., 2011) or con-
tinuous temporal transition probabilities (Rhodes et al., 2009; Sahimi
et al., 1986; Sorbie and Clifford, 1991). However, they have shown to
reliably predict the non-Fickian behavior of carbonate rocks when im-
plemented directly on pore-scale images (DNS method) (Bijeljic et al.,
2013). Mehmani and Tchelepi (2017) showed that a pore-network
framework for solute transport at moderate to high Péclet numbers is
accurate only if (1) network extraction is informed by the interstitial
flow rate (2) a Lagrangian framework is used for particle tracking and
(3) an accurate mapping of particles between pores is implemented.
The accuracy of using pore-networks for carbonates has not been es-
tablished yet. For a detailed review of pore-network modeling of solute
transport in porous media we refer the reader to Mehmani and Balhoff,
(2015b).
2.2.3. Quasi-static versus dynamic pore-network modeling of multiple
phases
In a pore-network model, pores hold the volume and contribute to
the critical curvature for percolation during imbibition whereas throats
represent conductivity and critical curvature during drainage. Drainage
and imbibition at low capillary numbers are modeled with an invasion-
percolation algorithm. In this method, a given capillary pressure is
imposed on the network domain at the inlet and the invading phase
occupies the pores based on the critical curvature of pores/throats and
certain trapping criteria (Bryant and Blunt, 1992; Mason and Mellor,
1995). The hydraulic conductivity (also referred to as effective per-
meability) for each phase is then calculated by writing systems of
equations based on imposing mass conservation at each pore.
Table 1 shows a number of representative publications on pore
network modeling over the past several decades. The rows of the table
are organized chronologically, starting with Fatt's seminal work (Fatt,
1956a, 1956b, 1956c) which first introduced 2D pore networks as a
way to study porous media flow properties. The columns have been
organized as follows:
• Contributing author(s) and year of publication.
• A short summary of the work, including key innovations and/or
findings.
• Type of grids used, including nature of pore types: This also includes
size of the grid used to represent REV. If applicable, this also in-
cludes the resolution and size of the physical sample image from
which the pore network was derived, or which the pore network was
targeting. If no physical image was used, then the sides of the grid
are dimensionless. If multiple similar samples with different grid
sizes were used, the largest grid size is reported. The size is very
interesting for future use in designing a pore-scale study, as it shows
increasing computational power does not necessarily mean using
larger sample sizes.
• The type of physics incorporated: Since pore networks can use either
11
Marine and Petroleum Geology 114 (2020) 104141
Fig. 16. Schematic of Delaunay tessellation
for identifying a pore-throat network in
granular media. (a) Delaunay tessellation
input is a packing of grains (spheres in this
work). (b) Tetrahedral cell representing a
pore defined by four neighboring spheres.
The pore space within each tetrahedron re-
presents pore, and the tetrahedral sides are
the tightest cross-sections (throats) on the
path between two neighboring pore centers.
(c) The final result is a network of pores
(shown as spheres, colored/shaded by size)
and throats (identified as cylindrical con-
nections). Figure modified after Mehmani
and Prodanović, 2014b.
quasi-static or dynamic methods to model fluid flow, this is an im-
portant feature. As one goes down the rows of the table, towards
more modern pore networks, the physics becomes increasingly so-
phisticated, incorporating both two- and three-phase flow, wett-
ability and trapping.
The table reveals a number of interesting trends in pore network
modeling. Many early works were focused on building 2D networks
with the pores arranged on a regular square lattice (Dodd and Kiel,
1959; Fatt, 1956a). These regular grids continued in 3D (Chatzis and
Dullien, 1977). These networks modeled pore size distribution by ad-
justing the pore sizes at each lattice node and could also change con-
nectivity by adjusting the number of bonds from one lattice site to the
next. In most cases, these networks were not directly representative of
any physical sample (except micromodels (Chen and Wilkinson, 1985)).
In addition, a number of researchers only studied drainage capillary
pressure curves, using invasion-percolation algorithms (Chatzis and
Dullien, 1977; Dodd and Kiel, 1959; Fatt, 1956a). With only drainage,
no hysteresis was present in their models, but they could model wett-
ability effects by assigning different contact angles in individual pores.
Payatakes and co-workers (Payatakes et al., 1973, 1980), for-
mulated a population balance model for the evolution of oil ganglia
during water flooding. They studied granular media, where the sim-
plistic pore networks they used were more representative of the real
sample. Shortly afterwards, in a series of papers by different researchers
(Dias and Wilkinson, 1986; Wilkinson, 1986; Wilkinson and Willemsen,
1983), advances in percolation theory led to a much better under-
standing of displacement patterns formed during both drainage and
imbibition, including viscous effects. These papers had far-reaching
impacts on how to upscale pore-scale model relationships. Bryant et al.
(1993a), Bryant et al. (1993b) introduced sophisticated methods of
modeling compaction and cementation in granular media. They derived
unstructured grids from the resulting pore networks, and computed
relative permeabilities from them, with very satisfactory matches to
experimental data in strongly water-wet sandpacks and sandstones.
This work was later extended by Bakke and Øren (1997) and Øren et al.
(1998), who pioneered a process-based method of reconstructing the
pore space in consolidated media like sandstones, incorporating in-
formation from high resolution thin sections of rocks. They also mod-
eled effects of heterogeneous wettability. This work was later extended
to three phases by other researchers (Piri and Blunt, 2004, 2005;
Valvatne and Blunt, 2004). Recent papers have focused on modeling
trapping and the structure of residual phases by improving the pore-
filling models used for modeling imbibition processes - areas where
earlier pore networks have struggled (Ruspini et al., 2017; Ryazanov
et al., 2010, 2014). Multi-scale pore networks are also a fairly recent
development (Bultreys et al., 2015; Jiang et al., 2013b; Mehmani et al.,
2011; Mehmani and Prodanović, 2014b; Prodanović et al., 2015b) but
are vital for modeling systems with significant microporosity like
A. Mehmani, et al.
Table 1
Pore-network modeling literature: key representative journal publications over the years.
Author(s), year
Fatt, (1956)
Dodd, Kiel (1959)
Chatzis, Dullien (1977)
Payatakes et al. (1980)
Lin, Slattery (1982)
Mohanty (1982)
Koplik, Lasseter (1985)
Chen, Wilkinson (1985)
Lenormand et al. (1988)
Jerauld, Salter (1990)
Blunt, King (1991)
Blunt et al., 1992
Bryant, Blunt (1992)
Bryant et al., 1993, Bryant
et al. (1993a, 1993b)
McDougall, Sorbie (1995)
Lowry, Miller (1995)
Dixit et al. (1996)
Bakke, Oren (1997)
Fenwick, Blunt (1998)
Oren et al. (1998)
Mogensen, Stenby (1998)
Dixit et al. (1998b)
Dixit et al. (1998a)
Dixit et al. (2000)
Lerdahl et al. (2000)
Oren and Bakke (2002)
Oren and Bakke (2003)
Marine and Petroleum Geology 114 (2020) 104141
Key innovation/summary Grid type(s)/size Physics incorporated
Introduced pore-network modeling. Examined, qualitatively, 2D Regular lattice of square and hexagonal shapes Quasi-static, 2 phase
effects of different properties of a 2D network on Pc-Sw, kr-
Sw curves
Generated Pc-Sw curves for drainage, incorporating trapping and 2D, square, hexagonal networks, targeting Quasi-static, 2 phase,
mixed-wet conditions sandstone rocks including wettability
Examined both 2D and 3D networks for percolation properties, 2D and 3D regular lattices, targeting sandstone Quasi-static, 2 phase
and drainage Pc-Sw curves, against experimental data from rocks.
sandstones
Developed stochastic model for oil ganglion dynamics 2D regular lattice, interconnected unit cells, each Quasi-static, 2 phase
(mobilization, breakup and stranding) in granular media cell a constricted tube. Targeted granular media -
glass beads, sand
Predicted hysteresis in kr-Sw, Pc-Sw curves, though the method 3D regular lattice, targeting packings of glass Quasi-static, 2 phase
did not work well for consolidated media beads, sand
In I, tracer flows for a wide range of fractional flows were done. 3D cubic network, 12 × 12 × 20, 12 × 12 × 40, Quasi-static, 2 phase
In II, a network model was developed to describe the physics. 16 × 16 × 20, targeting sandstones
Predicted consolidated media well for the first time.
Simulated waterflooding at different Ca, incorporating dynamic 2D network, 10 × 10 Dynamic, 2 phase
viscous effects, and capillary forces, through an approximate
numerical procedure in the pore network.
Studied viscous fingering during dynamic flow, ignoring surface 2D Square network, 100 × 100 Dynamic, 2 phase
tension term, in micromodel experiments and square lattice
networks. Confirmed DLA-like patterns
Modeled effects of Ca and viscosity ratio on flow patterns for 2D square lattice, 100 × 100 Dynamic, 2 phase
drainage in a 2D network. Percolation theory, DLA and anti-DLA
were used for explaining results
Two-phase kr-Sw and Pc-Sw curves, including hysteresis. 3D network of spheres connected by tubes, both Quasi-static, 2 phase
Compared predictions with experiments, but not quantitatively cubic and Voronoi, size 203, targeting sandstones
(used assumed properties for the network) and bead packs
Demonstrate effects of both viscous and capillary forces on a 2D Delaunay triangulation of points in circular region - Quasi-static, 2 phase
and 3D networks 80,000 for 2D, Voronoi networks with 50,000
points in 3D
Predicted kr-Sw curves with pore networks, examine results 3D cubic, cylindrical bonds/spherical bodies, Dynamic, 2 phase
against different types of percolation 32 × 32 × 64
Used realistic geometries to derive pore networks. Predicted 3D unstructured grid, from a mono-size sphere Quasi-static, 2 phase
absolute permeability without adjustable parameters. pack (Finney packing of 3367 spheres)
Physically representative network models of transport in porous 3D unstructured grid, from Delaunay tessellation of Single phase
media central 2000 spheres from Finney pack
Study Pc-Sw and kr-Sw curves, recovery efficiency, for 3D cubic, 203 Quasi-static, 2 phase, with
waterflooding in systems of varying wettability. Also relate wettability
macroscopic wettability indices with pore-scale physics
Examine various geometrical factors affecting non-wetting phase 3D cubic, cylindrical bonds/spherical bodies, 8000 Quasi-static, 2 phase
residual after imbibition in a strongly water-wet system pore bodies
Use pore-network models to explain higher oil recovery for 3D cubic, equal-length cylindrical pores Quasi-static, 2 phase, with
intermediate-wet systems, propose “regimes” for wettability wettability
classification
Proposed technique for generating 3D pore networks based on 3D network, with angular pores, derived from Quasi-static, 2 phase
geological processes for sandstone creation, and information Bentheimer sandstones, 1703, 10 μm resolution
from thin sections, applying it to predict macroscale flow
properties for water-wet systems
Modeled three-phase flow using pore networks, incorporating 3D cubic lattice, cubic pores, 30 × 15 × 15 Quasi-static, 3-phase
micromodel observations and theory of three-phase flow
Extended Bryant and Blunt (1992) to unequal size spheres. Used 3D unstructured, angular pores, derived from Quasi-static, 2 phase, with
reconstruction algorithm from thin sections to generate pore different sandstones, 3003, 10 μm resolution wettability
space, and then derived networks. Also modeled wettability
effects
Dynamic network model to study residual oil saturation, with 3D cubic lattice, cubic pores, 153 Dynamic, 2 phase,
effects of Ca, M, contact angle, aspect ratio including wettability
3
Hysteresis in kr-Sw curves, between primary drainage, secondary 3D cubic lattice, cylindrical bonds, 15 Quasi-static, 2 phase,
imbibition and secondary drainage for strongly water-wet and water-wet systems
weakly water-wet systems kr-Sw curves
Hysteresis in kr-Sw curves in mixed-wet systems 3D cubic lattice, cylindrical bonds, 153 Quasi-static, 2 phase,
including wettability
Derive relationships between Amott-Harvey and USBM 3D cubic lattice, cylindrical bonds, 253 Quasi-static, 2 phase,
wettability indices including wettability
Developed a stochastic reconstruction of Berea, and predicted 3D, unstructured lattice, angular pores, Quasi-static, 3 phase
Oak's [Oak, 1990] data. This pore network was then used in Reconstructed 3003, 10 μm resolution, targeting
several subsequent publications sandstones
Develop a method to reconstruct sandstones, using 3D, unstructured lattice, with angular pores, Single-phase
petrographical information from thin sections related to reconstructed 3003, resolution 7.5 μm
sedimentation, compaction and diagenesis
Extend earlier work to present a unified workflow for computing 3D, unstructured lattice, with angular pores, Quasi-static, 2 phase,
both single and multi-phase transport properties from reconstructed 1283, resolution 10 μm, targeting including wettability
reconstructed sandstones sandstones
(continued on next page)
12
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

Table 1 (continued)

Author(s), year Key innovation/summary Grid type(s)/size Physics incorporated

Singh, Mohanty (2003)
Valvatne andBlunt (2004)
Piri and Blunt (2004)
Piri and Blunt (2005)
Løvoll et al. (2005)
Nguyen et al. (2006)
Spiteri et al. (2008)
Joekar-Niasar et al. (2007)
Raeesi, Piri (2009)
Idowu and Blunt (2010)
Gharbi and Blunt (2012)
Mehmani et al. (2013)
Ryazanov et al. (2014)
Bultreys et al. (2015)
Ruspini et al. (2017)
Developed a rule-based dynamic pore-network model, studied 3D cubic lattice, square pores/throats, 30 × 8 × 8 Dynamic, 2 phase
effect of viscous and capillary forces. Generated qualitative
capillary desaturation curves.
Predicted kr-Sw and Pc-Sw curves on mixed-wet sand packs and 3D unstructured lattice, angular pores, from Bakke Quasi-static, 2 phase,
Berea and Oren (1997) including wettability
Developed thermodynamic relationships for three-phase Individual angular pores Quasi-static, 3 phase,
displacements in a single, constant cross-section angular pore including wettability
Expanded on earlier work in single pore to develop three-phase 3D unstructured lattice, angular pores, 3003, Quasi-static, 3 phase,
flow in pore networks, using thermodynamics to determine resolution 10 μm, from Berea sandstone including wettability
stability
Drainage of more viscous wetting fluid by less viscous non- 2D, square network, 80 × 160 nodes Dynamic, 2 phase
wetting fluid- experiment, numerics and percolation theory
3
Developed a dynamic pore-network model for imbibition 3D unstructured, 300 , from Lerdahl et al. (2000), Dynamic, 2 phase
incorporating film flow, film swelling and snap-off. Quantified Valvatne andBlunt (2004)
effects of flow rate in inhibiting snap-off
Use pore-network simulations to study new trapping and relative 3D unstructured from [Valvatne andBlunt 2004, Quasi-static, 2 phase
permeability hysteresis models Lerdahl et al., 2000]
Study two types of pore-network models: only tubes, and spheres 3D cubic lattice, 403 Quasi-static, 2 phase
and tubes - with and without trapping, respectively. Also relate
interfacial area to capillary pressure, rel perm
Used mixed-wet pore-network models to study Pc-Sw-area 3D unstructured grid from [Piri and Blunt 2005], Quasi-static, 2 phase,
relationships Berea (3003, resolution 10 μm) and Saudi reservoir including wettability
sandstone (2503, resolution 10 μm)
Study dynamic effects during waterflooding, incorporating 3D unstructured grid, 3003 from [Valvatne Dynamic, 2 phase, with
effects of capillary number, viscosity ratio and contact angles andBlunt 2004] wettability
Study effects of wettability in several different carbonate 3D unstructured, from carbonate CT images of size Quasi-static, 2 phase, with
samples 3203-3503, with angular pores, resolution 7.7–9 μm wettability
Presented a new multi-scale model for flows in shales, 3D unstructured, multiscale Single-phase, with slip-
combining nano-meter size pores with micro-meter size pores, flow and Knudsen
and studied effect of pore connectivity and fraction of diffusion
microporosity on permeability
Figure out structure of residual oil after water flooding as a 3D unstructured lattice, Berea 3003, 10 μm Quasi-static, 2 phase, with
function of wettability resolution, from [Oren and Bakke, 2003] wettability
Developed a dual pore-network model to model microporosity 3D unstructured, multiscale, spherical pores, with Quasi-static, 2 phase
cylindrical links, Estallaides limestone, 10003,
resolution 3.1 μm
Improved pore-network models so they predict trapping curves 3D unstructured, from [Øren et al., 1998], 4503- Quasi-static, 2 phase, with
accurately, based on a new pore-body filling approach 12003, resolution 1.5–10 μm wettability

Fig. 17. Primary drainage relative permeability

curves for (a) a vuggy carbonate rock (with a scale
difference of 5) and (b) a carbonate rock with a
single microcrack (with a scale difference of 5 (at
three axis angles with respect to the direction of the
pressure gradient). Drainage is simulated on pore-
network models described in Fig. 8, and the corre-
sponding capillary pressure curve is shown in Fig. 9.

carbonates. As examples of these multiscale networks, Fig. 17 shows the
drainage relative permeability curves for carbonates with vugs and
microcracks as was described in Section 2.1.2. Multiscale networks are
a significant advancement over earlier works which focused on more
homogeneous porous media like sandstones and sandpacks. Carbonates
have a bimodal pore size distribution, as well as a much more com-
plicated wettability state, and are hence much harder to model.
The shortcoming of quasi-static modeling is its assumption that the
movements of phases do not affect each other. This is not the case in
high capillary numbers when the phase distributions become functions
of viscosity ratios and flow rates as well as the interfacial tension. We
note that recent experiments using fast synchrotron x-ray imaging
(Andrew et al., 2015; Berg et al., 2013; Singh et al., 2017) have ob-
served rapid movements and phase rearrangements at low capillary
numbers, which challenge the traditional assumption of quasi-static
flow. In particular, Pak et al. (2015) and Reynolds et al. (2017) have
shown some completely new pore-scale displacement mechanisms in
carbonates that cannot be modeled with traditional pore-network ap-
proaches.
Two computational schemes that are used in dynamic pore-network
modeling are the single-pressure (Aker et al., 1998; van der Marck
et al., 1997) and two-pressure (Thompson, 2002) schemes. In the
single-pressure scheme, regardless of the simultaneous occupancy of a
pore by both phases, a single pressure is assigned to each pore as an

13
A. Mehmani, et al.
unknown. The assumption therefore is that the local capillary pressure
within a pore is negligible. In addition, corner flow cannot be im-
plemented using the single-pressure scheme and therefore it is only
applicable for lowly angular and smooth granular media. In the two-
phase pressure scheme, the local capillary pressure within a pore is not
ignored and therefore each phase's pressure becomes an unknown in the
systems of equations. The problem that arises using this scheme in low
capillary numbers is a numerical instability called “capillary pinning”
(Koplik and Lasseter, 1985) at which the saturation of a pore is non-
convergent. Joekar-Niasar et al. (2010) proposed a semi-implicit sa-
turation update at each time step by which the numerical instabilities
improved. For a further discussion on dynamic pore-network modeling
the reader is referred to Joekar Niasar (2010) and the references
therein. From discretization standpoint, these pore-network models
resemble reservoir simulators (for instance, they update saturation), but
operate on a smaller length scales and are thus incorporating capillary
forces directly (as opposed to through averaged functional relation-
ships).
Unlike voxel-based discretization in direct numerical simulation
methods (Section 2.2.4), discretization done via pore-network models is
not scalable. In other words, voxel-based discretization can offer an
optimum space interval at which the solution will be satisfyingly ac-
curate and yet computationally feasible. In pore-network modeling,
besides choosing the domain size that does not fall below the re-
presentative elementary volume (REV), the concept of an optimum
discretization does not exist. Hybrid methods when coupling from dif-
ferent length scales are an exception and this is discussed in Section 2.3.
Open source pore-network modeling code is available - please see
(Gostick et al., 2016).
2.2.4. Principles of direct numerical simulation
Modeling the multiphase fluid behavior directly in the pore space
domain is an attempt to achieve accuracy that pore-network models
may sacrifice for computational speed (Raeini et al., 2014a). In addi-
tion, direct numerical methods provide sub-pore scale fluid dynamic
insights that can be utilized for improving pore-network models, which
could potentially become a very useful tool in upscaling simulation
results – particularly for multi-scale systems like carbonates. Direct
numerical methods are implemented once the pore space has been ei-
ther segmented from an image (Iassonov et al., 2009) or digitally re-
constructed through a process-based or stochastic-based method.
The most popular methods for direct modeling are lattice Boltzmann
methods and finite volume methods based on discretization of Navier-
Stokes equations (and addition of interfacial tension when modeling
immiscible flow). Lattice Boltzmann methods evolved from lattice gas
automata (LGA) techniques. They are pseudo-molecular methods,
which track the distribution functions of an ensemble of fluid particles.
They work at a scale in between molecular dynamics, and the con-
tinuum scale. Macroscopic variables such as velocity, pressure and
density, which are part of traditional computational fluid dynamics
(CFD) methods, are recovered by moment integration of the particle
distribution functions. The particle distributions at each lattice point
evolve by interacting only with its immediate neighbors. Since each
lattice point interacts only with its neighbors, the problem is highly
parallelizable, and well suited for modern multi-thread/core pro-
cessors. In addition, boundary conditions can be easily handled using
the bounce-back condition. This enables representing complex geome-
tries easily using an underlying orthogonal grid, without using complex
meshing algorithms. It has hence become a very popular choice in the
porous media community which deals with very complex 3D pore
spaces, which can have features on many different scales.
LB methods follow a two-step procedure. First, there is an advection
step, where the values of the distribution function are propagated to
their neighboring lattice points along defined velocity vectors. Second,
there is a collision step, where the particles at each lattice point are
redistributed according to a collision operator. The simplest collision
14
Marine and Petroleum Geology 114 (2020) 104141
operator is given by the Bhatnagar Gross Krook (BGK) relationship,
which performs very well for a wide variety of situations. Without
going into mathematical details, the BGK operator is based on a single
relaxation time parameter, which results in viscosity-dependent per-
meability. A more complex operator is the Multiple Relaxation Time
(MRT), which is more computationally expensive, but performs better
at computing permeabilities in porous media images (Pan et al., 2006).
For multiphase flow, many different lattice Boltzmann models exist -
the color gradient model (Gunstensen et al., 1991), the Shan-Chen
model (Shan and Chen, 1993), the free energy model (Swift et al., 1996)
and others. It is not clear if any one model is always superior to the
other (Liu et al., 2016) and it is up to the user to decide which one to
use for their application. However, as reported by Liu et al. (2016) some
models, such as the color gradient model and the stabilized diffuse-
interface model, are better at handling high viscosity ratios at low ca-
pillary numbers which is relevant in porous media flows, though this
comes at a higher computational cost and more complex equations.
Similarly, the larger the porous domain is the longer the computational
time becomes. The issue of domain size is pertinent in carbonates as
simulating the injection of one pore-volume when large volumes of
vugs are present can become computationally difficult. It is currently
not clear when these costs would be justified for a given case.
Hazlett (1995) was one of the earliest works in direct modeling of
flow in porous media images. He simulated multiphase flow using a
sphere-algorithm, and calculated relative permeabilities using the
multiphase color-gradient lattice Boltzmann method. Subsequently,
Martys and Chen (1996) performed multiphase flow simulations using
the Shan-Chen lattice Boltzmann method. These two early pioneering
papers had limited predictive power, due to the limited resolution and
computational resources at the time. Kats and Egberts, (1999) per-
formed the first three-phase porous media simulations, but only in 2D.
As computational power improved, other researchers focused efforts on
studying hysteresis in capillary pressure curves, relating it to interfacial
area (McClure et al., 2004; Pan et al., 2004; Porter et al., 2009; Schaap
et al., 2007). Liu et al. (2016) performed a detailed benchmark study on
what viscosity ratios can be simulated with each model in static and
dynamic cases. Open source parallelized codes for lattice Boltzmann
method are available, e.g. Palabos3 and Taxila-LBM (Coon et al., 2014).
The other popular class of direct simulation methods are based on
discretization of Navier-Stokes equations. These techniques have ex-
isted longer than the lattice Boltzmann method, and have very well-
developed mathematical foundations. Difficulties with these methods
arise when more than one phase becomes involved. This is due to
challenges in tracking the two-phase fluid interface and its contact line
with the solid phase. The volume-of-fluid (VOF) method (Hirt and
Nichols, 1981) is a continuum-based method that solves the Navier-
Stokes equation for each phase using saturation-averaged values for
density and viscosity. The interfacial tension is treated as a body force
in this method (Brackbill et al., 1992). The drawback of VOF is the
emergence of spurious currents when capillary forces become high
(Dupont and Legendre, 2010). The problem of spurious currents at low
capillary numbers is particularly relevant for multiphase flows in
porous media. Algorithms on correctly tracking the immiscible inter-
face has been the focus of eliminating spurious current (Popinet and
Zaleski, 1999; Renardy and Renardy, 2002; Abu-Al-Saud et al., 2018),
for instance Raeini et al. (2014a) and Shams et al. (2018) showed that
the non-physical instabilities can be improved by using a sharp surface
force model. For an open-source platform that incorporates single-
phase and multiphase immiscible flow using finite-volume methods
refer to www.openfoam.org.
Level set methods are often proposed as an alternative to VOF for
tracking moving interfaces (Sussman, 2005; Sussman et al., 1994,
1999). These methods have their own problems, such as mass loss
(Enright et al., 2002) and high computational costs. Several authors
have proposed methods to address the mass loss issues in level set
methods, such as the particle-level set method (Enright et al., 2002),
A. Mehmani, et al.
and non-graded adaptive grids (Min and Gibou, 2007). Other re-
searchers have combined the level set and VOF techniques to give hy-
brid methods which can take advantage of the features of both
methods, for example the Coupled Level Set VOF method (CLSVOF)
(Sussman and Puckett, 2000). In a benchmark study of these methods,
Gerlach et al. (2006) concluded that the CLSVOF method was the best
one of these techniques. Thömmes et al. (2009) attempted to couple
level set methods with lattice Boltzmann to improve characteristics of
the flow behavior for large viscosity ratios. However, they only applied
the method to very simple cases, and the method has not been widely
used since.
An alternative method for predicting the multiphase fluid distribu-
tion at a given capillary pressure is the quasi-static level-set method
(Prodanović and Bryant, 2006). In this method, the immiscible interface
is defined by a level set function that progresses with a velocity that is
directly linked to the balance between pressure and surface tension.
Open source code is available (Prodanovic, 2010). Although the level-
set method has a high accuracy in describing the fluid morphology, it
cannot be used for modeling viscosity-dominated regimes. Later on,
Jettestuen et al. (2013) and Verma et al. (2018) added the ability to
incorporate arbitrary contact angles to this simulation method. Fig. 18
shows an example of each of the discussed direct numerical methods
(Harting et al., 2005; Prodanovic and Bryant, 2009; Raeini et al.,
2014a).
Table 2 summarizes publications over the past two decades for di-
rect modeling. Like the pore-network modeling table, it is arranged
chronologically. It includes papers based on lattice Boltzmann and
Navier-Stokes discretization. It also incorporates other less popular
techniques like the level set method and smoothed particle hydro-
dynamics (SPH). The columns are organized similarly to Table 1.
However, the grids are always related to some physical sample, unlike
pore-network models for which the concept of grid does not apply.
Over the years, as more computational power and better imaging
techniques have become available, the resolution used has grown
better, increasing the REV size as well as match with the experiments.
For instance, Ramstad et al. (2012) generated relative permeability
curves for a reservoir sandstone but matching with experimentally
measured values (on a larger core) improved predictions dramatically
by using end-point saturations from experimental data. This is the same
procedure used by pore-network modelers, though one has more
parameters to adjust with in pore networks. Other methods like the
quasi-static level set method (Prodanović and Bryant, 2006) and
smoothed particle hydrodynamics (Tartakovsky et al., 2007;
Tartakovsky and Meakin, 2006) have been limited by computational
resources, but the VOF technique has been applied to study relative
permeability (Raeini et al., 2014b) and trapping (Raeini et al., 2015).
Trapping is in general typically modeled better using VOF or a direct
method, though a carefully matched pore network model recently
(Ruspini et al., 2017) showed promising results using a new pore-body
filling model in the same pore network. For an additional general dis-
cussion on pore-scale modeling refer to Golparvar et al. (2018). In the
context of carbonates, their two main challenges are their multiscale
nature (discussed in Section 2.3) and their generally heterogeneous-wet
condition. Current research efforts are focused on incorporating such
heterogeneous-wet conditions to an accurate model. Zhao et al. (2016)
have shown the importance of film flow in determining macro-scale
behavior under uniform wettability conditions. In a follow-up work,
Zhao et al. (2019) have compared 14 different pore-scale modeling
methodologies for capturing the behavior seen in the micromodels. We
note here that the micromodel experiments of Zhao et al. (2016) are not
very representative of usual flow conditions in porous media - in par-
ticular the capillary number is extremely high, which means entirely
different macro-scale behavior from typical subsurface flow conditions.
However, this study still shows that current simulation methods are not
quite up to the task of simulating all the complexities in a porous
medium. Moreover, in carbonates, film flow, heterogeneous wettability,
15
Marine and Petroleum Geology 114 (2020) 104141
as well as highly non-uniform pore size distributions result in even
more challenging systems which have not yet been validated compre-
hensively. Frank et al. (2018a), Frank et al. (2018) have recently ap-
plied a finite element formulation with the discontinuous Galerkin
method which shows promise in resolving some numerical issues which
surround simulation of moving interfaces.
2.3. Combining multi-scale pore-geometries in pore-scale models
Given the continuous and wide distribution of pore sizes over
multiple length scales in carbonate rocks, a proper integration of mul-
tiscale pores is essential for predicting their transport properties. Biswal
et al. (2007) proposed a stochastic continuum reconstruction scheme
for microporous carbonates, based on implementing a spatial correla-
tion for various grains that is established from training images. The
model was used to predict absolute permeability, formation factor and
elastic moduli for carbonate samples. In their method, each voxel is
segmented into pores, matrices or undecided. Undecided voxels are
alternately assigned as pores or matrices. The method was implemented
for a microporous oolithic dolostone. The predicted transport properties
however were highly dependent on the chosen resolution which high-
lights the potential advantage of reduced-order computational methods
such as pore-network modeling if they are supplied with correct a priori
transport rules. Bauer et al. (2012) presented a dual pore-network
model for carbonates where a three-dimensional micro-CT image is
segmented into solid, macropores and microporous regions. The mi-
croporous regions however are not resolved but represented as con-
tinuous regions. The explicit integration of pores from two scales into a
single-entity pore-network model has been developed via an image-
based method in which a micropore network is stochastically created
and indiscriminately (Jiang et al., 2013b), or with a spatial correlation
(Jiang et al., 2013a), superimposed to a macropore network. In order to
capture micropore generating diagenesis, Mehmani and Prodanović,
(2014b) have proposed a process-based approach to integrating mi-
cropores with macropores which was discussed previously in Section
2.1.2. The method can additionally be implemented to three-dimen-
sional images where grains are segmented and subsequently filled with
micropores (referred to as “grain-based” approach). For images where,
due to considerable diagenesis, grain segmentation is not feasible, a
“tile-based” approach has been developed. In this method, the domain
is tiled and micropores are implanted on the appropriate areas
(Prodanović et al., 2015b) (see Fig. 19 for schematics of the methods).
As one may intuit, the details captured by explicitly incorporating mi-
cropores into the pore-network model results in high numbers of un-
knowns and can significantly reduce the computational feasibility of
solving the systems of equations. In an effort to amend the computa-
tional limitations of coupling micropores with macropores, Bultreys
et al. (2015) have represented the upscaled properties of microporous
regions with microthroats. Determining the properties of the micro-
porous clusters and microthroats a priori is challenging given the ne-
cessity for high resolution images for pore structure characterization.
Tuning the micropore properties by matching predicted transport
properties with macroscopic experimental measurement is not always
possible either given the scarcity of experimental data points in highly
microporous and tight carbonates. Verifying the fidelity of multiscale
pore structure reconstruction is nontrivial and will likely require ad-
vanced real-time image acquisitions tools such as fast-synchrotron to-
mography to clarify the transport communication between the micro-
pores and macropores.
Direct numerical simulations have recently been implemented in
imaged multiscale pore systems to predict their single-phase and two-
phase properties. Soulaine et al. (2016) employed the Darcy-Brinkman
equation in a computationally parallel setting to demonstrate the high
impact of even small percentage of sub-resolution pores on absolute
permeability in a sandstone sample. The Darcy-Brinkman formulation
renders the solution of the velocity field at the interface between sub-
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

Fig. 18. Examples of (a) utilizing volume-of-fluid method to simulate drainage (throat length is 37.5 µ m) (Raeini et al., 2014a) (b) level-set method for a naturally
fractured carbonate rock, (b-1) is a tomogram of size 700 × 1 × 700, (b-2) is a media surface of size 200 × 230 x 190 and (b-3) is the non-wetting fluid distribution
at a particular curvature during drainage (red is the fluid/fluid and gray is the fluid/solid interface) all with a voxel size of 3.1 µ m (Prodanovic and Bryant, 2009) and
(c) drainage simulation for a Bentheimer sample (512 × 512 x 521 with a voxel size of 4.9 µ m) using lattice Boltzmann method (Harting et al., 2005). (For
interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

resolution and resolved pores tractable and provides a direct adjust-
ment of the equations based on the microporous region's permeability.
A similar formulation for two-phase immiscible flow with nanoscale
effects corrections including slip flow and Knudsen diffusion was ex-
tended by Soulaine et al. (2019) to predict the transport properties of
shale formations. Such nanoscale corrections can become relevant for
carbonates as well (Yoon and Dewers, 2013). However, the practicality
of the Darcy-Brinkman formulation imposes an abrupt change from the
Darcy velocity in the sub-resolution porous systems to the interstitial
velocity in the resolved pores. Beavers and Joseph (1967) for instance
demonstrated a slip velocity region in the boundary between the pore
space and the sub-resolution regions. Additional research is required to
determine the importance of this additional interface condition to flow
properties, including in case of immiscible flow, and their sensitivity to
any associated parameters in carbonates. Another promising hybrid
method for carbonates that have pores at inseparable scales is the
mortar domain decomposition method (Y. Mehmani, 2014). In this
method, a pore-scale subdomain can be coupled with a continuum
subdomain by defining an interface function space (the mortar space).
For each subdomain an appropriate transport algorithm can be solved
iteratively until the flux at the interface coincides with the two adjacent
subdomains. Much work however on adopting mortar domain decom-
position for predicting immiscible flow in carbonates is needed. Lattice
Boltzmann methods have also been extended to predict fluid transport
in multiscale settings. This approach is generally referred to as Gray
Lattice Boltzmann (GLB) as the sub-resolved porous areas would have
geometric properties in-between resolvable pores and the solid phase.
The “gray” areas are considered to have a grain density in proportion to
their porosities and X-ray attenuation intensities. In earlier models (Gao
and Sharma, 1994), the impacts of sub-resolution pores on fluid

16
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

Table 2
Direct pore-scale modeling literature: key representative journal publications over the years.
Author(s), year Key innovation/summary Sample type(s)/size Physics incorporated

3
Hazlett (1995) First work to directly try simulations on actual rock images. Berea sandstone, 256 , resolution 10 μm Inscribed spheres for displacement,
Predicts fluid distributions based on inscribed spheres in including wettability, lattice
image. Lattice Boltzmann was used to get permeabilities from Boltzmann for permeability
equilibrium distributions
Martys, Chen (1996) First work to model two-phase flow directly using lattice- Fontainebleau sandstone, 7.5 μm, resolution, 2-phase lattice Boltzmann, Shan-Chen
Boltzmann 643 samples model
Hazlett et al. (1998) CMT image of sandstone used for drainage in strongly water- 1283 reservoir sandstone, 10 μm resolution 2 phase lattice Boltzmann color
wet and mixed-wet cases gradient model, including wettability
Kats and Egberts, First lattice Boltzmann work to model 3 phase flow in porous 210 × 350 2D lattice with square elements 3 phase lattice Boltzmann color
(1999) media gradient model
Manwart et al. (2002) Computed permeability for Fontainebleau samples, generating 3003, 4 Fontainebleau sandstone samples, Single phase lattice Boltzmann BGK
matches with experiment. Shows first order nature of bounce- resolution 7.4 μm, one real, and three model, finite difference solver for
back BCs generated Stokes equation
Pan et al. (2004) LB simulations on ideal sphere packing, to give Pc-Sw curves, 1283, 150 dimensionless spheres 2 phase lattice Boltzmann Shan-Chen
including hysteresis, and subsequent comparison with model
experiments
Kang et al. (2004) Simulations of fingering during immiscible fluid 2D channel, 400 × 66 2 phase lattice Boltzmann Shan-Chen
displacements in a channel, studying effects of capillary model
number, viscosity ratio and wettability
Huang et al. (2005) Studied multiphase flow in unsaturated fractures, including 2D fractures, 60 × 400, resolution 0.05 mm Volume of fluid (VOF) method Navier-
effects of viscosity, contact angle, and gravity Stokes solver
3
Harting et al. (2005) Performed lattice Boltzmann simulations in porous media Benthemer sandstone, 512 , 4.9 μm resolution 2 phase lattice Boltzmann Shan-Chen
samples as part of a larger review on simulations for other model
cases
Kang et al. (2006) Simulation of reactive flow at the pore scale, considering 2D channel, 80 × 80 Lattice Boltzmann equations coupled
effects of advection, diffusion, mineralogy, and reaction with chemical reactions
between species
Pan et al. (2006) Investigation of BGK and MRT lattice Boltzmann models to 323 BCC sphere array; and 643 random sphere Singe phase BGK and MRT lattice
compute permeability, as well as effect of using different packing, with 23 spheres Boltzmann models
boundary conditions.
Prodanović et al. Introduced a quasi-static level set method, studying Mono-sized sphere packs, 383 2 phase quasi-static level set, with zero
(2006) multiphase displacements in idealized sphere packs, with zero contact angle
contact angle
Tartakovsky, Meakin Simulated immiscible and miscible flows in idealized 2D 2D 32 × 16 geometries Smoothed particle hydrodynamics, 2
(2006) geometries phase, both immiscible and miscible
Schaap et al. (2007) Study of water-air and water-soltrol displacement experiments Glass bead packs, 405 × 405 × 100, 2-phase lattice Boltzmann Shan-Chen
in glass bead packings, relating interfacial areas to capillary resolution 17 μm model
pressure characteristics
Hatiboglu, Babadagli Studied spontaneous imbibition using micromodel 2D micromodel, 4002, 0.125 mm resolution 2 phase lattice Boltzmann Shan-Chen
(2008) experiments and LB model
Sukop et al. (2008) Compared LB vs experimental fluid distributions, slice by slice 2563, 20 μm resolution, quartz grain packing. 2 phase lattice Boltzmann Shan-Chen
(1283 really) model
Thömmes et al. Combined LB with level set methods. Simulated flows with 2D Couette flow, bubble, Hele-Shaw cell, 1282 2 phase, lattice Boltzmann BGK model
(2009) large viscosity ratios and density differences, for simple 2D coupled with level sets
and 3D cases.
Porter et al. (2009) Matched interfacial area measurement by CMT in glass beads Glass bead pack, 205 × 205 × 150, resolution 2 phase lattice Boltzmann Shan-Chen
with LB simulations, and related it to hysteresis in Pc- 34 μm model
Sw curves
Boek, Venturoli Performed simulations for a 2D sample of Berea and 3D 1283 sample of Bentheimer sandstone, 2 phase lattice Boltzmann Shan-Chen
(2010) Bentheimer sample resolution 4.9 μm model
Ramstad et al. (2010) Simulations in CMT and reconstructed sandstone images. Bentheimer sandstone, 2563, resolution 2 phase, modified lattice Boltzmann
Reproduce Pc-Sw drainage curves well, but underpredict rel 6.67 μm (CMT), 5 μm (reconstructed) color-gradient model Latva-Kokko,
perms Rothman [2005]
Ramstad et al. (2012) Relative permeability from Bentheimer and Berea sandstone Bentheimer, 2563, resolution 6.67 μm, Berea 2 phase, modified lattice Boltzmann
using LB 2563, resolution 5.345 μm color-gradient model Latva-Kokko and
Rothman (2005)
Jettestuen et al. Proposed extension of model by Prodanovic and 3D sphere packs, 66 × 66 × 62, Castlegate 2 phase quasi-static level set, with non-
(2013) Bryant Prodanović, Bryant [2006] to incorporate wettability sandstone, 60 × 60 × 70, resolution 5.6 μm zero contact angle
effects
Li et al. (2013) Extended the Rothman-Keller multiphase LB model with MRT, Berea, resolution 2.89 μm, 3003 for 2-phase 2 and 3 phase, Rothman-Keller MRT LB
and simulated drainage-imbibition experiments Berea simulation, 643 for 3-phase model
samples. Also tried preliminary 3 phase simulations
Ferrari, Lunati (2013) Simulated immiscible displacements in 2D, and studied the 2D 1760 × 2280, resolution 50 μm, 10028 Navier-Stokes VOF solver
relation between macroscopic capillary pressure and pore- particles
scale properties
Raeini et al. [2014] Used their own modified VOF formulation Raeini et al. Berea sandstone (400 × 256 × 256), Navier-Stokes VOF solver
[2012] to relate pore scale forces with Darcy-scale properties resolution 4.58 μm; Sandpack
including rel perms, proposing an upscaling algorithm (282 × 174 × 174), resolution 8.2 μm
Liu et al. (2014) Used a new color-fluid model to simulate flows in 2D 2D micromodel, 2816 × 2689, resolution 2 phase lattice Boltzmann color-fluid
geometries of heterogeneous permeabilities 1.5 μm model
Landry et al. (2014) Used LB to get rel perms for strongly water-wet (glass beads) Glass bead pack, 1003, resolution 26 μm 2 phase lattice Boltzmann Shan-Chen
and weakly oil-wet (polyethylene beads) cases, comparing model
results with bead pack CMT experiments
(continued on next page)

17
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

Table 2 (continued)

Author(s), year Key innovation/summary Sample type(s)/size Physics incorporated

Raeini et al. (2015) Studied trapping trends in water-wet consolidated and
unconsolidated media, matching against experimental data
Liu et al. (2016) Extensive review of popular LB multiphase models, and points
out limitations of each, in the context of porous media flows
McClure et al. (2016) Revisit hysteresis in Pc-Sw curves, conclude that inclusion of
interfacial area and Euler characteristic makes relationship
non-hysteretic
Berea sandstone (330 × 210 × 210),
resolution 5.549 μm; Sandpack
(230 × 142 × 142), resolution 10 μm
2D samples, cylinder grids (512 × 1280),
reproduced from other works
Randomly packed 1964 spheres, 9003
Navier-Stokes VOF solver
2 phase Shan-Chen, color gradient, free
energy, mean-field theory, stabilized
diffuse-interface
2-phase lattice Boltzmann modified
color-gradient model [McClure et al.,
2014]

propagation are incorporated in the collision step as described in Sec-
tion 2.2.4. Subsequent works have focused on increasing the accuracy
and computational performance of GLB by modifying the collision step
(Walsh et al., 2009). Recently, multiscale algorithms for accelerating
fluid dynamics simulations on digitized porous media have been pro-
posed (Mehmani and Tchelepi 2018, 2019; Guo et al., 2019). The Pore-
Level Multiscale Method (PLMM) has been shown to produce highly
accurate approximations to single-phase incompressible, immiscible
two-phase, and compressible gas flow in single (e.g., sandstone) and
dual porosity (e.g., shale) media. No simplification of the underlying
geometry or governing equations are made. Broadly speaking, PLMM
consists of four steps: (1) decomposition of the image into physical
pores, (2) computation of local basis functions on each pore, (3) solu-
tion of a global interface problem, and (4) reconstruction of the final
solution. Step (1) utilizes watershed segmentation, similar to PNM, and
the subdomains created correspond to physical pores in the image.
However, the decomposition cost is much lower than typical network
extraction, which involves multiple additional steps. Step (2) can be
thought of as a parametrization of upscaled flow parameters for each
pore, which is loosely analogous to computing hydraulic conductivities
for throats in certain PNM variants (Prodanović et al., 2015b). Step (3)
involves solving a coarse system, which is comparable in size to typical
(non-)linear systems encountered in PNM. Step (4) is optional and is
only executed if a sub-pore scale solution is desired. If only macroscopic
parameters are of interest (e.g., permeability), step (4) may be omitted.
The errors in PLMM can be further estimated a priori and controlled
(not possible in PNM) through a rapidly convergent iterative strategy in
(Mehmani and Tchelpi, 2018). The DNS solver used in step (2) can be
chosen from a number of available approaches (FVM, FEM, SPH, LBM).
All computations in PLMM are massively scalable in parallel environ-
ments due to independence of calculations.
3. Discussion
Conventional functional relationships, such as Archie's law for re-
sistivity (Archie, 1942), the Carman–Kozeny permeability estimate
(Carman, 1937; Kozeny, 1927) and the Brooks–Corey parameterization
of relative permeability (Brooks and Corey, 1964), were developed for
rocks whose pores are mostly intergranular, single length scale and well
connected. Since carbonates exhibit pore space heterogeneity such as
high variations in pore size, shape, topology and wettability, traditional
transport relationships are rarely satisfactory. Reliable pore-scale
models have the potential to provide the petrophysical properties of all
rocks at the REV scale (Fig. 1), and for carbonates such workflows are
especially valuable given their complex flow behavior and scarcity of
data during formation evaluation.
An accurate pore-scale model depends on the correct capturing of
the pore space. While pore scale modeling (specifically, pore-network
modeling) has been in existence since the first use of bundle-of-tubes
models by Purcell (1949) and the first interconnected pore-scale models
by Fatt (1956a, 1956b, 1956c), in this paper we have focused on re-
viewing methods that have a degree of physical representativeness in
terms of pore space geometry and interconnectedness. We reviewed
three philosophies for reconstructing the pore-space. The process-based
method hinges on an appropriate description of the original granular
packing followed by modeling diagenesis of the sample. The algorithm's
basis on sphere packing with a desired grain size distribution and tes-
sellating of the sphere centers results in computational expedience.
Multiple realizations of a diagenetically altered granular medium can
therefore be generated to cover a range of pore-scale parameters. Ad-
vances in imaging technology and a continuous increase in computa-
tional power have catalyzed the explosion in pore-scale modeling since
the late 1990s. Technologies such as computed tomography, X-Ray
microtomography and (focused ion beam) scanning electron micro-
scopy, provide a window into geologic materials that can be analyzed
with a digital rock physics framework for characterization and creation
of pore-scale models. The image-based and stochastic-based methods
depend on acquiring a quality image using resolutions that can capture
relevant pore space features. Once the pore space is rendered, either a
pore-network method or a direct numerical simulation technique is
chosen to achieve the desired macroscopic property.
The choice of the pore-scale model depends on several criteria

Fig. 19. Schematic of algorithms for (a) “grain-

based” and (b) “tile-based” image-based two-scale
pore-network creation (Prodanović et al., 2015b).
Impermeable grains and microporous regions are
colored black and gray respectively. Throats linking
pores from the same scale are colored red whereas
throats connecting pores from two scales are blue.
(For interpretation of the references to color in this
figure legend, the reader is referred to the Web ver-
sion of this article.)

18
A. Mehmani, et al.
including microstructure image availability, importance of sensitivity
analysis, type of the transport process one wishes to study and com-
plexity/availability of the software. If one wants to analyze a specific
sample and it can be appropriately imaged so that pores are well-re-
solved, then direct numerical simulation is the clear choice. It could be
that pores are of complex shape so that their representation with a pore-
throat network is not well-defined. Further, if single phase permeability
is desired, off-the-shelf parallelized direct simulators exist that make its
calculation relatively straightforward. Nonetheless, direct-numerical
methods can become unfeasible in “large” porous domain. A domain
size for interparticle pores that is manageable with direct numerical
methods can be considered “small” when vugs with sizes orders of
magnitude larger are present. In this case even though all pores are
technically resolvable in the three-dimensional image, a pore-network
model, despite uncertainties with defining the pores and throats during
its extraction, is preferable. If an appropriate image is unavailable or
sensitivity analyses for geometry in addition to transport parameters is
needed, then process-based models are a preferred option. In creating a
process-based model for carbonate samples, one faces the challenge of
quantitatively describing the paragenesis given the uncertainty of par-
ticular diagenetic processes such as dissolution. Further, if geometry
details such as surface roughness are important to the transport process,
then direct numerical simulation is suggested as well. On the other
hand, due to geometry simplification and use of analytical formulas,
pore-network models offer “infinite resolution”, i.e. there is no nu-
merical discretization involved in pore and throat cross-sectional geo-
metries. Therefore, if film flow for instance is of interest, pore-network
models are a good choice. One must bear in mind however, that the
original complex geometry details of the pore space (such as surface
roughness) have been discarded so that the term “infinite resolution”
should be taken with caution. It might be that the ability to study
phenomena on one's laptop (as opposed to having access to a super-
computer) is important or that many images (and in large domain sizes)
are needed for investigating relevant rock/fluid parameters. Analytical
geometry descriptions allow for less computational effort and more
complex physical processes and boundary conditions (e.g. three-phase
flow, mixed wettability, combination of diffusion and convection in
nano-scale flows) are explored with relative ease. Accordingly, to date,
pore-network studies are more developed than direct simulation
methods. Finally, the complexity of a particular pore-network genera-
tion method is proportional to its number of adjustable parameters, and
since such parameters (for example detailed mineralogy of pore/grain
surfaces) may not be available, uncertainties increase. Multiple ad-
justable parameters, of course, create situations where there is no un-
ique optimal solution when matching a core-scale experiment. Having
multiple plausible network model representations then creates un-
certainty in modeling a different experiment. The predictive capability
of pore-network models has been discussed in depth by Sorbie and
Skauge (2012). They argued that pore-network modeling cannot be
predictive of the multiphase flow properties of mixed-wet systems. This
is due to the increased number of adjustment parameters that is needed
in order to capture the pore-scale displacements accurately. In such
cases, one might prefer to rely on empirical models and tune them with
core measurements that are typically fewer than the number of ad-
justable parameters for a predictive pore-network model. Pore-network
models are still valuable for mixed-wet systems in that they allow
transport properties to be extrapolated for varying flow conditions after
calibrating them with core measurements. Furthermore, they provide
description of interstitial fluid flow behavior which can be insightful for
any type of environmental remediation or enhanced oil recovery.
Capturing the heterogeneity of carbonate rocks is difficult using a
single imaging modality. High resolution 2D SEM maps remain a
19
Marine and Petroleum Geology 114 (2020) 104141
helpful source of information for parameters such as minerology and
pore size. In addition, they can be expanded into 3D with stochastic-
based methods. The spatial distance of the extrapolation however can
be limited due to anisotropy. Even though image-based direct simula-
tion methods are limited by domain size and resolution, they can be
useful in providing input parameters for pore-network models that can
subsequently be expanded to larger domains. Hybrid DNS and PNM
workflows however require further research to establish their benefits.
Wettability is an important parameter in determining the capillary
pressure and relative permeability behaviors of porous media that we
did not cover in detail in this paper but find that it is an essential re-
search area for obtaining reliable pore-scale models for carbonates. In
pore-scale modeling, it is typical to assume a uniform and unchanging
value throughout the pore space. Recent visualizations of in situ contact
angle subsequent to core-flooding (AlRatrout et al., 2017; Andrew et al.,
2014) have shown that carbonate rocks demonstrate a wide contact
angle distribution. This is partially due to the varying mineral makeup
of the rock. In addition, given the commonly considerable chemical
diagenesis of carbonates, surface textural heterogeneity such as surface
roughness, can create a non-uniform mixed-wet system. An important
property of carbonates that is difficult to capture in models, is its po-
tential to change its wettability during two-phase flow. This dynamic
wettability behavior was proposed (Kovscek et al., 1993) by linking the
breakup of monolayer wetting films during primary drainage. The au-
thors showed that once the imposed capillary pressure exceeds the
summation of pore entry capillary pressure threshold and the wetting
surface's disjoining pressure, oil is able to contact the grain surface
previously protected by wetting films. Recent efforts to incorporate the
dynamic alteration of wettability during two-phase has been conducted
(Kallel et al., 2016) but much work remains. Questions that remain are:
(a) Can wettability alteration rules based on pore morphology for pore-
network modeling be developed? (b) What insights can direct numer-
ical simulation provide in regard to oil/water emulsion lens stability
and contact line pinning? (c) Can core-flood experiments shed light into
wettability alteration in real-time or should functionalized micro-
fluidics experiments be leveraged? Microfluidics or lab-on-a-chip ex-
periments are two-dimensional replicas of porous media. For a review
of lab-on-a-chip devices see Anbari et al. (2018), Karadimitriou and
Hassanizadeh (2012), and Mehmani et al. (2019).
Upscaling is an essential component in utilizing pore-scale modeling
prediction of flow transport properties that we did not cover. Porous
media with distinct hierarchies in scale, such as unconsolidated sand-
stones, allow upscaling to be conducted by establishing average values
for transport properties. Volume average and homogenization techni-
ques (Hornung, 1997; Whitaker, 1999), fall into this category. In highly
heterogeneous media, such as carbonates, where distinction between
scale hierarchies is not possible, nonlocal hybrid multiscale methods
are utilized. In hybrid multiscale methods, the parameter of interest is
calculated in microscale directly and extrapolated to larger scales based
on macroscale information. Scheibe et al., (2015) provides a review of
various hybrid methods and a flowchart referred to as MAP (multiscale
analysis platform) that guides the researcher to a suitable upscaling
approach following a series of questions. Given the high heterogeneity
of carbonates, assessment of MAP for various carbonate rock types can
shed light on the most useful upscaling scheme.
Acknowledgement
We acknowledge support from National Science Foundation
CAREER grant 1255622. We are grateful to Prof. Martin Blunt, Prof.
Sebastian Geiger, and Dr. Yashar Mehmani for constructive comments
throughout the manuscript.
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

Symbols

Pc Capillary pressure
Sw Water saturation
Φ Porosity
K Permeability
Kr Relative permeability
V Velocity
L Characteristic length scale
D Bulk fluid diffusivity
Ca Capillary number
M Mobility ratio
Acronyms

NAPL Nonaqueous phase liquid

XCT X-ray computed tomography
SEM Scanning electron microscopy
μCT X-ray microtomography
VOF Volume-of-fluid method
CLSVOF Coupled level set method
SPH Smoothed particle hydrodynamics
GLB Gray lattice Boltzmann
PLMM Pore-level multiscale method
PNM Pore-network model
MAP Multiscale analysis platform
DNS Direct numerical simulation
FVM Finite volume method
FEM Finite element method
BC Boundary condition
BGK Bhannagar Gross Krook
MRT Multiple relaxation time
EDS Energy dispersive spectroscopy
CLSM Confocal laser scanning microscopy
CFD Computational fluid dynamics
LBM Lattice Boltzmann method
DLA Diffusion-limited aggregation
BCC Body-centered cubic

Appendix. Example pore-throat network construction

We provide two simple examples in ImageJ/Fiji software (http://fiji.sc/) that outline acquiring basic grain and pore space analysis from seg-
mented porous material images (with one additional analysis done in MATLAB/Octave). ImageJ is a widely used and free image analysis software,
and Fiji is one of its variants with a number of useful plugins. Since contribution to ImageJ is public, the number of plugins are growing and there are
often multiple implementations of the same algorithm. MATLAB programming environment (https://www.mathworks.com/products/matlab.html)
is used for one small part of the example, and Octave (https://www.gnu.org/software/octave/) is its free alternative. The objective of this appendix
is a demonstration on the fundamentals on how a pore network is obtained from images. Algorithms were chosen based on their conceptual
simplicity and availability. Some advanced algorithms remain part of the individual research groups’ software solutions and are not readily available.

Sphere packing example

We start with a digitized two-dimensional cross-section from a synthetically generated monodisperse sphere pack (Finney, 1970). The center of
each sphere and a discretization of the pack can be found in Digital Rocks Portal (Finney, 2016). Slice 6 from the discretized image stack is selected
for this example. The data are binarized into values of 0 and 1 that represent the pore and solid space respectively. The pixel values are converted to
255 (white) for pore space and 0 (black) for solid space in order to comply with the ImageJ input requirements. The file (shown in Figure A1a) is also
available in supplementary information. Commands used to produce images are provided in the next section.
Duplicate the image and run Distance Map (see Figure A1b). Distance Map for each pore space pixel (labeled 255 in the original image) calculates
the distance to the closest solid pixel and displays it in the proportional shade of gray. Local maxima in distances are the starting point for the
watershed algorithm (the starting points can be observed by executing Ultimate Points). The watershed algorithm starts growing regions from the
local maxima. When the regions meet, the borders are established such as those shown in Figure A2a. The regions can be considered individual pores.
Subsequent to separating them with borders (which can be considered throats), we can label them using Find Connected Components (see result in
Figure A2b).

20
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

Fig. A1. Slice of the (a) original sphere pack and (b) the distance map corresponding to the pore space .

Fig. A2. Watershed algorithm result for (a) pore space (the borders that are identified in the process) and (b) subsequent labeling of individual connected com-
ponents in the pore space (individual pores).

Find Connected Components gives the area of each region (expressed in number of pixels in each region). The results can be saved as a.csv file (and
opened in a spreadsheet software for analysis as needed). The histogram of the areas can be produced with ImageJ as well (see Figure A3).

Fig. A3. Histogram of pore areas using Analyze- > Distribution applied to the Results from Find Connected Components and the snapshots of the entered parameters.

21
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

We can use similar tools to identify the throat information. However, in order to identify throats, we need to manipulate the images first. This is
done by subtracting segmented and watershed-separated images (we remind the reader that images are arrays of numbers). The watershed image
labels individual pores with pixel value of 255 and solid disks as well as throats with pixel value of 0. The original image labels pores and throats
with pixel value of 255 and solid disks with 0. By subtracting the two we obtain an image with label 255 where throats are, and 0 everywhere else
(see Figure A4a). We can run Find Connected Components on the subtracted image (Figure A4b), and obtain labeling and statistics on throats.
The procedures above have identified the objects that are required to create a pore-throat network. Capturing the pore-throat connectivity,
however, requires post-processing and we provide an example script for this purpose in MATLAB/Octave. The pore coordination number statistics is
shown in Figure A5.

Fig. A4. (a) Throats identified by subtracting the original and watershed images (a). (b)Throats labeled (colored) by Find Connected Components .

The aforementioned tools can be used to acquire grain statistics. The original image can be inverted so that the solid phase is white (labeled with
pixel value of 255), and the watershed procedure can be repeated. Most of the grains in this image are well separated, but the few that overlap can be
segmented with watersheds and finding the connected components. The result is shown in Figure A6.

Fig. A5. Pore coordination number histogram (result from MATLAB/Octave script shown below).

22
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

Fig. A6. Labeled individual grains.

List of relevant commands in ImageJ.

1. Plugins- > Macro- > Record (records trace of all commands in the ImageJ session)
2. File- > Open (for 2D images)
3. File- > Import (for 3D images)
4. Image- > Adjust- > Brightness/Contrast (when data is in 0,1 format, contrast needs to be adjusted in order to see the different image phases).
5. Edit- > Invert (2D, 3D) to invert phases (black to white, and white to black).
6. File- > Binary- > Watershed (2D only)
7. File- > Binary- > Distance Map (2D only)
8. File- > Binary- > Ultimate Points (2D only) will show the extreme points of the distance map from which the watershed algorithm has started.
9. Process- > Image Calculator

Trace of commands in ImageJ

The following are commands obtained by Plugins- > Macro- > Record in ImageJ. The commands can be copied into an ImageJ Macro and
executed via Plugins- > New- > Macro (the file with the commands SpherePack_Slice6_analysis_macro.ijm is provided in supplementary material).

//Reading in input image (Figure A1a)

open(“SpherePack_Slice6_Inverted.tif");

//Creating distance map of the pore space (Figure A1b)

run(“Duplicate … ", " ");
run(“Distance Map");
saveAs(“PNG”, “SpherePack_Slice6_DistanceMap.png");

//Figures A2,A3: watershed and identifying pores

selectWindow(“SpherePack_Slice6_Inverted.tif");
run(“Watershed");
saveAs(“PNG”, “SpherePack_Slice6_WatershedResult.png");

selectWindow(“SpherePack_Slice6_WatershedResult.png");
run(“Find Connected Regions”, “allow_diagonal display_one_image display_results regions_for_values_over = 100 minimum_number_of_points = 1 stop_after = −1″);
saveAs(“PNG”, “SpherePack_Slice6_LabeledPores.png");
saveAs(“Results”, “Results.csv");
run(“Distribution … ", “parameter = [Points In Region] or = 20 and = 0–2375″);

//save raw data for analysis in MATLAB

selectWindow(“SpherePack_Slice6_LabeledPores.png");
saveAs(“Raw Data”, “SpherePack_Slice6_LabeledPores_nx500ny500_16bit.raw");

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A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

//Throat analysis in Figure A4:

open(“SpherePack_Slice6_Inverted.tif”);//open again, just in case

imageCalculator(“Subtract create","SpherePack_Slice6_Inverted.tif","SpherePack_Slice6_WatershedResult.png");
selectWindow(“Result of SpherePack_Slice6_Inverted.tif");
saveAs(“PNG”, “SpherePack_Slice6_Throats.png");

run(“Find Connected Regions”, “allow_diagonal display_one_image display_results regions_for_values_over = 100 minimum_number_of_points = 1 stop_after = −1″);
saveAs(“PNG”, “SpherePack_Slice6_LabeledThroats.png");

//save raw data for analysis in MATLAB

selectWindow(“SpherePack_Slice6_LabeledThroats.png");
saveAs(“Raw Data”, “SpherePack_Slice6_LabeledThroats_nx500ny500_16bit.raw");

//Grain analysis in Figure A5:

open(“SpherePack_Slice6.tif");
run(“Watershed");
saveAs(“PNG”, “SpherePack_Slice6_GrainsWatershed.png");
run(“Find Connected Regions”, “allow_diagonal display_one_image display_results regions_for_values_over = 100 minimum_number_of_points = 1 stop_after = −1″);
saveAs(“PNG”, “SpherePack_Slice6_GrainsLabeled.png");

MATLAB/Octave commands to establish pore-throat network

%% This script reads in images with labeled pores and throats

%% For each throat, we search the neighborhood for neighboring
%% pores and record this information. At the same time
%% we record how many throats does each pore have in its
%% neighborhood (pore coordination number).

pore_labels = imread(‘SpherePack_Slice6_LabeledPores.png');
throat_labels = imread(‘SpherePack_Slice6_LabeledThroats.png');

% number of throats
num_throats = max(throat_labels());
num_pores = max(pore_labels());

% initialize array that will store pores that neighbor

% each throat
throat_neighbors = zeros(num_throats,2);
pore_coord_number = zeros(num_pores,1);

for t = 1:num_throats

% this is logical array corresponding to throat t

individual_throat = (throat_labels = = t);

% dilate this individual throat to get its immediate

% neighborhood, and then and then investigate which
% pore labels are found in its neighborhood
se = strel(‘sphere',2);
dilated_throat = imdilate(individual_throat, se);

% find pore labels in the neighborhood of a throat above

A = pore_labels(dilated_throat);

% 0 in pore label array is throat or solid - setdiff avoids it

% only unique labels are left
A = unique(setdiff(A,0));

if numel(A) < 2
fprintf(‘\nThroat %d not enough pores',t);
elseif numel(A) > 2
fprintf(‘\nThroat %d too many pores',t);
end

% record information
if numel(A) > 1
throat_neighbors(t,1) = A(1);
pore_coord_number(A(1)) = pore_coord_number(A(1))+1;
end

24
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

if numel(A) > 1
throat_neighbors(t,2) = A(2);
pore_coord_number(A(2)) = pore_coord_number(A(2))+2;
end
end

% Plot histogram of pore coordination numbers

max_coord_number = max(pore_coord_number);
hist(pore_coord_number,0:max_coord_number);
colormap gray
set(gca,'fontsize',16);
xlabel(‘pore coordination number');
ylabel(‘frequency');
axis tight
saveas(gcf,'SpherePack_Slice6_PoreCoordNumber','png');

Ketton carbonate example

We downloaded Ketton carbonate image sample (available online4). The downloaded image is segmented; the tomographic original is not
available. We work with slice 800 from that image (it is available for download in supplementary material).
Grain and pore labeling results of a watershed operation is demonstrated in Figure A7. The microporosity within some of the grains can create
seemingly multiple “broken” components. Similarly, small pieces of grain as well as grain surface roughness results in exceeding number of pores.
This is a common problem with such algorithms and typically can be resolved by reducing the number of the initial seeds of the watershed operation.
Tools for such analysis are available in an ImageJ plugin (Ollion et al., 2013).
Furthermore, we observe that because the Ketton carbonate pore space does not percolate in a single 2D cross-section, thus its pore-network
representation can be of little value. In contrast, a grain network model is connected.

ImageJ commands producing Figure A7

//Grain analysis
open(“Ketton_Substack_Slice800.tif");
run(“Watershed");
saveAs(“PNG”, “Ketton_Substack_Slice800_GrainWatershed.png");
run(“Find Connected Regions”, “allow_diagonal display_one_image display_results regions_for_values_over = 100 minimum_number_of_points = 1 stop_after = −1″);
saveAs(“PNG”, “Ketton_Substack_Slice800_GrainLabeled.png");
selectWindow(“Ketton_Substack_Slice800_GrainWatershed.png");

//Pore analysis
open(“Ketton_Substack_Slice800.tif");
run(“Invert");
run(“Watershed");
run(“Find
Connected Regions”, “allow_diagonal display_one_image display_results regions_for_values_over = 100 minimum_number_of_points = 1 stop_after = −1″);
saveAs(“PNG”, “Ketton_Substack_Slice800_PoresLabeled.png");

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

25
A. Mehmani, et al. Marine and Petroleum Geology 114 (2020) 104141

Fig. A7. (a) Ketton carbonate slice , (b) labeled grains and (c) labeled pores .

3D analysis

The reader will notice that some of the commands are labeled ‘2D only’ in the list provided above. Three-dimensional image operations are
memory and computational time intensive and have been developed separately. Three-dimensional implementations are available (with no cost) in
‘3D ImageJ Suite’ plugin (Ollion et al., 2013), with documentation available online.5 We show an example watershed performed to identify different
pores in Figure A8. ImageJ instructions for creating it (including how to reduce number of starting points for watershed function, and thus noise) are
available in Supplementary material m).

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

26
A. Mehmani, et al.
Fig. A8. A slice through 3D watershed result on pore space. Throat barriers dividing pores are shown in blue, and the rest of the colors show different pores.
Appendix A. Supplementary data
Supplementary data to this article can be found online at https://doi.org/10.1016/j.marpetgeo.2019.104141.
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