the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 03 Nov 2025
Benchmarking the reactive transport code SCEPTER v1.0.2
Abstract. One-dimensional reactive transport codes are powerful tools for examining a range of geologic, biogeochemical, and agronomic phenomena. The reactive transport code SCEPTER (Soil Cycles of Elements simulator for Predicting TERrestrial regulation of greenhouse gases) has been recently developed for simulating a range of processes controlling soil biogeochemistry in managed lands, with a particular emphasis on soil pH management and enhanced weathering as a carbon sequestration strategy. While much of the basic framework implemented in SCEPTER is structurally and parametrically akin to existing reactive transport codes, its behavior has not been systematically benchmarked against other longstanding reactive transport models. Here, we quantitatively evaluate the performance of SCEPTER relative to a range of other reactive-transport models through a series of benchmarking experiments designed to assess the capacity of the code to simulate: (1) soil hydrology and fluid transport; (2) charge balance during cation exchange; and (3) mineral dissolution/precipitation, with (2) and (3) accompanied by diffusive/advective fluid transport and equilibria for aqueous speciation and gas dissolution into pore fluids. We show that the performance of SCEPTER is functionally identical to all other hydrological and reactive transport codes across the simulated benchmark conditions and discuss the emerging need for a reactive transport model benchmarking procedure that is fit for the purpose of predictive modeling of soil pH management in agricultural lands.
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Status: closed (peer review stopped)
- RC1: 'Comment on egusphere-2025-4035', Anonymous Referee #1, 06 Dec 2025
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RC2: 'Comment on egusphere-2025-4035', Anonymous Referee #2, 09 Dec 2025
The paper presents a systematic comparison of modeling results from the SCELTER model against other established reactive transport codes. Such benchmarking exercises are essential for evaluating the robustness of a new model and for assessing the impact of novel parameterizations or numerical schemes. Overall, this is a valuable effort. However, I have two major comments that I believe are important for strengthening the manuscript, in particular regarding the scope of the benchmarking and the analysis of the results comparison:
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The SCELTER model was developed in the context of agricultural management and enhanced weathering. However, the benchmarking exercises presented do not appear to emphasize these components. This raises the question: what exactly is being benchmarked? To address this, the manuscript should include a more detailed discussion of the differences in parameterizations among the models being compared. If two models solve the same governing equations, why do their results differ? Are these discrepancies primarily due to differences in numerical schemes, boundary conditions, or other assumptions? Providing this context will help readers understand the relevance and implications of the comparisons.
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When slight differences between models are mentioned (e.g., lines 241, 251, 260), the manuscript should go beyond noting these discrepancies and attempt to explain their origin. While the differences are small, the number of scenarios analyzed is limited; under different conditions, these discrepancies could become more pronounced. A deeper investigation into why these differences occur—whether due to numerical methods, parameter choices, or other factors—would allow readers to extrapolate to other scenarios and assess whether these differences may become a concern in other applications.
These points are crucial for justifying the significance of the work, as without such analysis, the paper risks appearing as a routine coding exercise rather than a rigorous analysis of the model.Â
Citation: https://doi.org/10.5194/egusphere-2025-4035-RC2 -
Status: closed (peer review stopped)
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RC1: 'Comment on egusphere-2025-4035', Anonymous Referee #1, 06 Dec 2025
This manuscript conducts a systematic benchmarking of the core reactive transport capabilities of SCEPTER v1.0.2 across three classical benchmark tasks—soil hydrology via the Richards equation, cation exchange and charge balance on the soil exchange complex, and multi-mineral dissolution–precipitation under an acid rock drainage scenario—and compares the model performance against established codes including Hydrus-1D, openRE, PHREEQC, OpenGeoSys, CrunchFlow, MIN3P, Flotran, and HP1. The results demonstrate that SCEPTER is able to reproduce consistent trends in key profiles, fluxes, and time-series variables, supporting the model’s reliability and reproducibility across the core reactive transport processes. Suggested revisions are as follows: 1. The manuscript would benefit from a clearer articulation of the incremental contribution relative to previous SCEPTER publications, especially regarding the level of verification achieved or the advancement of benchmarking toward enhanced weathering applications; 2. In addition to visual comparison, consider including quantitative agreement metrics (e.g., RMSE, relative deviation, or integrated flux differences) to strengthen the rigor of the consistency assessment; 3. The discussion on the lack of dedicated benchmarking frameworks for enhanced weathering simulation could be expanded with more actionable directions, such as benchmarking for solid-phase transport, reactive surface area evolution, inversion for agronomic measurements, or greenhouse gas flux modules; 4. Clarify the representativeness and limitations of the selected benchmark cases with respect to enhanced weathering scenarios, to help readers understand the boundary of applicability; 5. Figures and parameter descriptions could be further optimized, including clearer indication of overlain versus differential plots and consolidation of key parameter tables to improve reproducibility; overall, moderate revision is recommended before the manuscript can be considered for publication.
Citation: https://doi.org/10.5194/egusphere-2025-4035-RC1 -
RC2: 'Comment on egusphere-2025-4035', Anonymous Referee #2, 09 Dec 2025
The paper presents a systematic comparison of modeling results from the SCELTER model against other established reactive transport codes. Such benchmarking exercises are essential for evaluating the robustness of a new model and for assessing the impact of novel parameterizations or numerical schemes. Overall, this is a valuable effort. However, I have two major comments that I believe are important for strengthening the manuscript, in particular regarding the scope of the benchmarking and the analysis of the results comparison:
-
The SCELTER model was developed in the context of agricultural management and enhanced weathering. However, the benchmarking exercises presented do not appear to emphasize these components. This raises the question: what exactly is being benchmarked? To address this, the manuscript should include a more detailed discussion of the differences in parameterizations among the models being compared. If two models solve the same governing equations, why do their results differ? Are these discrepancies primarily due to differences in numerical schemes, boundary conditions, or other assumptions? Providing this context will help readers understand the relevance and implications of the comparisons.
-
When slight differences between models are mentioned (e.g., lines 241, 251, 260), the manuscript should go beyond noting these discrepancies and attempt to explain their origin. While the differences are small, the number of scenarios analyzed is limited; under different conditions, these discrepancies could become more pronounced. A deeper investigation into why these differences occur—whether due to numerical methods, parameter choices, or other factors—would allow readers to extrapolate to other scenarios and assess whether these differences may become a concern in other applications.
These points are crucial for justifying the significance of the work, as without such analysis, the paper risks appearing as a routine coding exercise rather than a rigorous analysis of the model.Â
Citation: https://doi.org/10.5194/egusphere-2025-4035-RC2 -
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This manuscript conducts a systematic benchmarking of the core reactive transport capabilities of SCEPTER v1.0.2 across three classical benchmark tasks—soil hydrology via the Richards equation, cation exchange and charge balance on the soil exchange complex, and multi-mineral dissolution–precipitation under an acid rock drainage scenario—and compares the model performance against established codes including Hydrus-1D, openRE, PHREEQC, OpenGeoSys, CrunchFlow, MIN3P, Flotran, and HP1. The results demonstrate that SCEPTER is able to reproduce consistent trends in key profiles, fluxes, and time-series variables, supporting the model’s reliability and reproducibility across the core reactive transport processes. Suggested revisions are as follows: 1. The manuscript would benefit from a clearer articulation of the incremental contribution relative to previous SCEPTER publications, especially regarding the level of verification achieved or the advancement of benchmarking toward enhanced weathering applications; 2. In addition to visual comparison, consider including quantitative agreement metrics (e.g., RMSE, relative deviation, or integrated flux differences) to strengthen the rigor of the consistency assessment; 3. The discussion on the lack of dedicated benchmarking frameworks for enhanced weathering simulation could be expanded with more actionable directions, such as benchmarking for solid-phase transport, reactive surface area evolution, inversion for agronomic measurements, or greenhouse gas flux modules; 4. Clarify the representativeness and limitations of the selected benchmark cases with respect to enhanced weathering scenarios, to help readers understand the boundary of applicability; 5. Figures and parameter descriptions could be further optimized, including clearer indication of overlain versus differential plots and consolidation of key parameter tables to improve reproducibility; overall, moderate revision is recommended before the manuscript can be considered for publication.