Modeling Supercritical CO<sub>2</sub> Flow and Mineralization in Reactive Host Rocks with PFLOTRAN v7.0

Nole, Michael; Muller, Katherine; Hammond, Glenn; He, Xiaoliang; Lichtner, Peter

doi:10.5194/egusphere-2025-1343

Preprints

https://doi.org/10.5194/egusphere-2025-1343

Preprints

03 Jun 2025

| 03 Jun 2025

Modeling Supercritical CO₂ Flow and Mineralization in Reactive Host Rocks with PFLOTRAN v7.0

Michael Nole, Katherine Muller, Glenn Hammond, Xiaoliang He, and Peter Lichtner

Abstract. Understanding the flow and reactivity of CO₂ injected into geologic reservoirs is important for many subsurface applications including secure geologic carbon storage (GCS), critical mineral extraction, enhanced geothermal systems (EGS), and enhanced oil recovery (EOR). Traditionally, subsurface CO₂ injection for GCS applications has focused on geologic formations with favorable subsurface configurations for CO₂ migration and trapping through non-reactive mechanisms such as structural, solubility, and petrophysical trapping to isolate CO₂ in the subsurface. Recently, CO₂-reactive rocks such as mafic and ultramafic basalts have been investigated for their potential to react with injected CO₂ in situ to simultaneously dissolve host rock minerals and mineralize CO₂ as carbonates. Engineering rapid CO₂ mineralization in the subsurface is attractive because of the increased density of stored CO₂, the additional safety factors associated with solidification, and the potential to extract valuable critical minerals. However, the limited availability of tools that are capable of modeling the associated coupled multiphase flow and reactive transport processes, especially at scale, makes it difficult to predict the long term behavior of a commercial-scale CO₂ injection into a reactive host rock. Here we present recent developments in the parallel flow and reactive transport simulator PFLOTRAN to model coupled CO₂-brine flow and reactive transport for a wide range of injection and production applications involving reactive CO₂-brine systems. These developments are based on the well established and trusted CO₂ flow capabilities in the STOMP-CO2 simulator. New capabilities added to PFLOTRAN include new CO₂-brine equations of state with optional thermal coupling, several new constitutive relationships like capillary pressure smoothing and scanning path hysteresis, a fully implicit well model, and native linkage with PFLOTRAN’s well-established reactive transport libraries. A series of numerical benchmarks between PFLOTRAN and STOMP-CO2 verify the newly developed CO₂-brine flow capabilities, and demonstrations of coupled CO₂-brine flow modeling and reactive transport show how CO₂ mineralization can be engineered in reactive host rocks. Finally, an example use case involving copper leaching by CO₂ and critical mineral extraction is presented to showcase the strengths of this new implementation. Several limitations still remain, including limited availability of field data to parameterize models. Future work should constrain the evolution of mineral surface area during mineralization and the temperature/pH dependence of geochemical reactions for specific systems of interest.

Received: 21 Mar 2025 – Discussion started: 03 Jun 2025

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Michael Nole, Katherine Muller, Glenn Hammond, Xiaoliang He, and Peter Lichtner

Status: final response (author comments only)

CC1: 'Comment on egusphere-2025-1343', Giacomo Medici, 19 Jun 2025

General comments
Very good research on flow and transport of fluids in geological media. Please, see the specific comments to improve your manuscript.

Specific comments
Line 24. I would enlarge the views to the flow and reactive transport of contaminants in geological media in your introduction.
Line 41. Here, the parallel with flow and transport of contaminants given the fact that you also mention the Darcy and the Fick laws (later in the methodology). Please, insert the parallel with groundwater flow with caprocks vs. aquitard/aquitude, and PFLOTRAN vs. PHREEQC/MT3DMS. See literature below on this parallel where CO2 storage is discussed:
- Medici, G., Munn, J.D., Parker, B.L. 2024. Delineating aquitard characteristics within a Silurian dolostone aquifer using high-density hydraulic head and fracture datasets. Hydrogeology Journal 32, 1663-1691.
- Steel L., Mackay E., Maroto-Valter M.M. 2018. Experimental investigation of CO2-brine-calcite interactions under reservoir conditions. Fuel Processing Technology 169, 122-131.
Line 50. Specify the 3 to 4 objectives of your research by using numbers (e.g., i, ii, and iii).
Line 97. “Advective fluxes”, I would also mention laminar flow either here or in the introduction.
Line 755. Very interesting paragraph. There is a small contrast with part of the title “host rock”. Please, provide explanation for this issue.

Figures and tables
Figure 1. Do you need an approximate spatial scale?
Figure 2. Do you need a spatial scale?
Figure 7. By contrast, I can see cells with a spatial scale in this figure.
Figure 8. Important output. You can move PFLOTRAN and STOMP on the right to gain space, and make the figure larger.
Figure 10. Same here. You can move PFLOTRAN and STOMP on the right to gain space, and make the figure larger.
Figure 11. Do you need a scale bar for your reservoir?

Citation: https://doi.org/10.5194/egusphere-2025-1343-CC1
RC1:
'Comment on egusphere-2025-1343', Anonymous Referee #1, 24 Jul 2025
The manuscript provides a comprehensive description of a simulator framework and reviews the primary references relevant to its development. The current format resembles a user manual rather than a scientific paper. A revision may be needed to align the manuscript more closely with the structure and style of a journal article. Other recommendations:

Review the manuscript for repeated information, especially when describing benchmark problems, equations, or simulation steps. Consolidate where possible. For instance, similar descriptions of PFLOTRAN and STOMP-CO2 verification could be summarized once, with differences highlighted as needed.

Preface each benchmark case with a concise statement of its objectives and its relevance to the study.

After each benchmark, briefly summarize the findings and their implications before moving on to the next section.

The authors should consider using SPE Comparative Study No. 11 to validate STOMP-CO2 outcomes against other group solutions. Although this case excludes geochemical reactions, it would be helpful to test additional capabilities such as mutual solubility, diffusion, and mechanical dispersion.

In the conclusion, reinforce the main outcomes, their significance, and future directions in a tightly structured paragraph sequence.

Minors:
Shorten and simplify complex sentences. Several sentences in the manuscript are long and contain multiple clauses, which can make them challenging to follow. Consider breaking these into shorter, more direct sentences.

Example:

Original: “Understanding the flow and reactivity of CO2 injected into geologic reservoirs is important for many subsurface applications including secure geologic carbon storage (GCS), critical mineral extraction, enhanced geothermal systems (EGS), and enhanced oil recovery (EOR).”
Improved: “Understanding the flow and reactivity of CO2 injected into geologic reservoirs is crucial for many subsurface applications. These include secure geologic carbon storage (GCS), critical mineral extraction, enhanced geothermal systems (EGS), and enhanced oil recovery (EOR).”

Add transition sentences at the beginning and end of sections to guide readers.

Example:
End of a section: “Several limitations still remain, including limited availability of field data to parameterize models.”
Transition to next section: “In the following section, we discuss recent advancements in simulation capabilities that address some of these challenges.”
Citation: https://doi.org/10.5194/egusphere-2025-1343-RC1
RC2:
'Comment on egusphere-2025-1343', Anonymous Referee #2, 03 Oct 2025
General comments:
This manuscript provides detailed development and demonstration of a newly developed simulator capability for reactive CO2 flow in PFLOTRAN, a well-established existing software for thermal multiphase flow and reactive transport in subsurface porous media.
Significance: This additional capability is highly relevant for the CO2 storage industry and demonstrates intriguing potential application for studying critical mineral extraction without mining. The newly developed well model has broad potential utility across subsurface fluid production applications and is a long-awaited improvement to the software.
Quality and reproducibility: This manuscript represents an impressive amount of high-quality work by the authors. The numerical approach is founded on accepted first-principles and is carefully validated in the benchmark problems and additional test cases in the appendices. The authors provide link to the software repository and input decks for all benchmarks and test cases to ensure reproducibility of the results. The authors have updated the PFLOTRAN online user’s manual to include the SCO2 mode capability options discussed in the manuscript.
Presentation: I agree with RC1 that the manuscript has sections that read more like a user manual than a journal publication. I feel that this is to some extent inevitable, as the purpose of the paper is to introduce and validate the new simulation capability, however I also have some suggestions below that the authors may find useful.
Specific comments
Section 2:
Line 93: how are transitions between gas and liquid CO2-phase properties handed? Particularly in thermal simulations it is possible that CO2 will cross this phase boundary in situ.

Section 2.3.1 Does the formulation for the liquid-phase density account for the increase in density when CO2 is dissolved in brine?

Section 2.4.1 line 198 do the capillary pressure extensions depend on salinity to reflect the changes in IFT with salt concentrations? If not, does this create a discrepancy between the capillary pressure extensions and the capillary pressure curves when there are two mobile phases, which do depend on IFT?

Section 2.5 well model
Does the new well model allow for leakage from one completion interval to another in the same well, like T2-well and the PFLOTRAN WIPP-model wells?

Line 227 “top hole mass flow rate” this is usually referred to as the surface (mass) flowrate

Can the wells be controlled by volume constraint or exclusively using pressure constraints (either surface or downhole?)

Are the pressures enforced at each well-cell in the well trajectory, or is the determination to switch to pressure constraint based on an average pressure?

Section 3:
I feel like much of the material in Section 3 could be moved to either an appendix or to the online documentation. This is essential information for fellow PFLOTRAN users but adds significantly to the manuscript length. Moving it out of the main manuscript would also make the paper feel less like a user’s manual.

The code snippets would be easier to cross-reference if they were made into figures or tables.

Section 4
Line 765 is the gas-phase boundary condition at the bottom boundary a Dirichlet or Neumann boundary?

Table 7: add the depth to the top of the shale layers to the table for this benchmark problem for completeness.

Figure 6 and 7 it would be much easier for readers to compare the STOMP/PFLOTRAN simulation results if the same color bar was used for both simulators

Line 853 how does mineralization impact porosity and/or two-phase flow properties in PFLOTRAN? Is it different than STOMP?
Citation: https://doi.org/10.5194/egusphere-2025-1343-RC2
AC1:
'Comment on egusphere-2025-1343', Michael Nole, 30 Oct 2025
The authors would like to thank Giacomo Medici and two anonymous reviewers for their constructive feedback. These comments have greatly improved the clarity of the manuscript. We have responded to each reviewer comment here.

CC1.
Line 24. I would enlarge the views to the flow and reactive transport of contaminants in geological media in your introduction.
Thank you. We have added a reference for CO₂ as a contaminant, and broadened the description of the PFLOTRAN software.

Line 41. Here, the parallel with flow and transport of contaminants given the fact that you also mention the Darcy and the Fick laws (later in the methodology). Please, insert the parallel with groundwater flow with caprocks vs. aquitard/aquitude, and PFLOTRAN vs. PHREEQC/MT3DMS. See literature below on this parallel where CO2 storage is discussed:
- Medici, G., Munn, J.D., Parker, B.L. 2024. Delineating aquitard characteristics within a Silurian dolostone aquifer using high-density hydraulic head and fracture datasets. Hydrogeology Journal 32, 1663-1691.
- Steel L., Mackay E., Maroto-Valter M.M. 2018. Experimental investigation of CO2-brine-calcite interactions under reservoir conditions. Fuel Processing Technology 169, 122-131.
Thank you. Darcy flow and Fickian diffusion were tested as part of the benchmarks between PFLOTRAN and STOMP-CO2.

Line 50. Specify the 3 to 4 objectives of your research by using numbers (e.g., i, ii, and iii).
We have clearly stated the objectives now, thank you.

Line 97. “Advective fluxes”, I would also mention laminar flow either here or in the introduction.
Thank you. This has been added for clarity.

Line 755. Very interesting paragraph. There is a small contrast with part of the title “host rock”. Please, provide explanation for this issue.
This is a 1D vertical simulation meant to test buoyant 1D flow. The “fault” designation is merely to highlight the role of high permeability pathways for potential CO₂

Figures and tables
Figure 1. Do you need an approximate spatial scale?
Spatial scales are decided by the modeler. This is a generic schematic of a well model in a discrete system.

Figure 2. Do you need a spatial scale?
Same as above. Spatial scales are decided by the modeler. This is a generic schematic of a well model in a discrete system.

Figure 7. By contrast, I can see cells with a spatial scale in this figure.
This is a specific benchmark simulation with defined constraints, so spatial scales are necessary.

Figure 8. Important output. You can move PFLOTRAN and STOMP on the right to gain space, and make the figure larger.
Thank you. This figure has been updated based off of reviewer responses.

Figure 10. Same here. You can move PFLOTRAN and STOMP on the right to gain space, and make the figure larger.
Thank you. This figure has been updated based off of reviewer responses.

Figure 11. Do you need a scale bar for your reservoir?
Thank you for the suggestion. Scale bars have been added.

RC1.
Review the manuscript for repeated information, especially when describing benchmark problems, equations, or simulation steps. Consolidate where possible. For instance, similar descriptions of PFLOTRAN and STOMP-CO2 verification could be summarized once, with differences highlighted as needed.

Thank you. RC2 suggested moving the verification test section into an Appendix. We have moved this section and believe this focuses the bulk of the manuscript with less repetition.

Preface each benchmark case with a concise statement of its objectives and its relevance to the study.

We agree, the motivation got buried in the text and was not completely clear. We have added motivating statements at the beginning of each benchmark description.

After each benchmark, briefly summarize the findings and their implications before moving on to the next section.

Summarizing conclusions have been added to each benchmark

The authors should consider using SPE Comparative Study No. 11 to validate STOMP-CO2 outcomes against other group solutions. Although this case excludes geochemical reactions, it would be helpful to test additional capabilities such as mutual solubility, diffusion, and mechanical dispersion.

Thank you. Both PFLOTRAN and STOMP-CO2 were involved in the SPE CSP 11 benchmark.

In the conclusion, reinforce the main outcomes, their significance, and future directions in a tightly structured paragraph sequence.

Thank you. An additional paragraph has been added that emphasizes the significance of the work and future directions.

Minors:
Shorten and simplify complex sentences. Several sentences in the manuscript are long and contain multiple clauses, which can make them challenging to follow. Consider breaking these into shorter, more direct sentences.

Thank you. We have cleaned up the wording throughout the manuscript.

Add transition sentences at the beginning and end of sections to guide readers.

Transition sentences have been added.

RC2.
Section 2:

Line 93: how are transitions between gas and liquid CO2-phase properties handed? Particularly in thermal simulations it is possible that CO2 will cross this phase boundary in situ.

This is a good point. Within a given grid cell, the CO₂-rich phase is treated as a single phase whose properties are defined by the Span-Wagner EOS. So if it is transitioning between liquid and gas, this interface is not explicitly modeled and the CO₂-rich phase is modeled with bulk averaged properties. We have updated the language here to be clearer about this limitation.

Section 2.3.1 Does the formulation for the liquid-phase density account for the increase in density when CO2 is dissolved in brine?

Yes.

Section 2.4.1 line 198 do the capillary pressure extensions depend on salinity to reflect the changes in IFT with salt concentrations? If not, does this create a discrepancy between the capillary pressure extensions and the capillary pressure curves when there are two mobile phases, which do depend on IFT?

Yes, CO₂-water IFT scaling as a function of salinity is optional using the UPDATE_SURFACE_TENSION keyword. This capability has not been benchmarked and therefore was not included in the test problems in the manuscript. If the user were to invoke IFT scaling, they would need to ensure that capillary pressure measurements were consistent with reference conditions.

Section 2.5 well model

Does the new well model allow for leakage from one completion interval to another in the same well, like T2-well and the PFLOTRAN WIPP-model wells?

No, this is a hydrostatic well model and can only simulate either injection or production, not combinations. We have added a clarification to this effect.

Line 227 “top hole mass flow rate” this is usually referred to as the surface (mass) flowrate

Thank you. We have changed this wording

Can the wells be controlled by volume constraint or exclusively using pressure constraints (either surface or downhole?)

Wells are mass rate controlled, with the option to impose minimum or maximum pressures. If wells hit a max/min pressure, they become pressure controlled. There is currently no option to only constrain by surface or downhole pressure, but this could presumably be achieved by setting an unrealistically high rate constraint in addition to a maximum and/or minimum pressure.

Are the pressures enforced at each well-cell in the well trajectory, or is the determination to switch to pressure constraint based on an average pressure?

Fracture pressure and minimum pressure are both imposed on the well bottom hole pressure, the primary variable in the well model. This has been clarified in the manuscript.

Section 3:

I feel like much of the material in Section 3 could be moved to either an appendix or to the online documentation. This is essential information for fellow PFLOTRAN users but adds significantly to the manuscript length. Moving it out of the main manuscript would also make the paper feel less like a user’s manual.

Thank you. This section has been moved to the Appendix for users to reference.

The code snippets would be easier to cross-reference if they were made into figures or tables.

Thank you for the suggestion. Input deck snippets have been made into individual tables for easy cross reference

Section 4

Line 765 is the gas-phase boundary condition at the bottom boundary a Dirichlet or Neumann boundary?

A Dirichlet BC is imposed. This has been clarified.

Table 7: add the depth to the top of the shale layers to the table for this benchmark problem for completeness.

Thank you. These have been added to the table.

Figure 6 and 7 it would be much easier for readers to compare the STOMP/PFLOTRAN simulation results if the same color bar was used for both simulators

Thank you for the suggestion. The color bars have been updated

Line 853 how does mineralization impact porosity and/or two-phase flow properties in PFLOTRAN? Is it different than STOMP?

PFLOTRAN can calculate porosity as a function of mineral volume fractions to account for CO2 mineralization. However, this capability is not employed in this example to be consistent with STOMP’s implementation of the benchmarks.
Citation: https://doi.org/10.5194/egusphere-2025-1343-AC1

Michael Nole, Katherine Muller, Glenn Hammond, Xiaoliang He, and Peter Lichtner

Data sets

Modeling Supercritical CO2 Flow and Mineralization in Reactive Host Rocks with PFLOTRAN v7.0: Data Michael Nole, Glenn Hammond, Katherine Muller, Xiaoliang He https://zenodo.org/records/14969297

Model code and software

PFLOTRAN v7.0 Glenn Hammond et al. https://www.pflotran.org

Michael Nole, Katherine Muller, Glenn Hammond, Xiaoliang He, and Peter Lichtner

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Short summary

Subsurface injection of carbon dioxide (CO₂) can be used for a variety of purposes including geologic carbon storage and enhanced oil recovery. Recently, CO₂ injection into reactive host rocks has been explored as a way to transform CO₂ into dense solid minerals. We present a simulation framework for modeling flow of CO₂ due to injection and subsequent reactions that take place to mineralize CO₂.


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