Articles | Volume 14, issue 12
https://doi.org/10.5194/gmd-14-7391-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-14-7391-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Model description paper
| 
01 Dec 2021
Model description paper |
| 01 Dec 2021
| 01 Dec 2021
POET (v0.1): speedup of many-core parallel reactive transport simulations with fast DHT lookups
GFZ German Research Centre for Geosciences, Fluid Systems Modelling, Telegrafenberg, 14473 Potsdam, Germany
Michael Kühn
GFZ German Research Centre for Geosciences, Fluid Systems Modelling, Telegrafenberg, 14473 Potsdam, Germany
University of Potsdam, Institute of Geosciences, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
Alexander Lindemann
University of Potsdam, Institute of Computer Science, Operating Systems and Distributed Systems, An der Bahn 2, 14476 Potsdam, Germany
Max Lübke
GFZ German Research Centre for Geosciences, Fluid Systems Modelling, Telegrafenberg, 14473 Potsdam, Germany
University of Potsdam, Institute of Computer Science, Operating Systems and Distributed Systems, An der Bahn 2, 14476 Potsdam, Germany
Bettina Schnor
University of Potsdam, Institute of Computer Science, Operating Systems and Distributed Systems, An der Bahn 2, 14476 Potsdam, Germany
Related authors
Marco De Lucia
Adv. Geosci., 65, 45–54, https://doi.org/10.5194/adgeo-65-45-2024, https://doi.org/10.5194/adgeo-65-45-2024, 2024
Short summary
Short summary
This paper presents a surrogate modelling approach applied to a geochemical system of uranium sorption on clay, relevant for the safety assessment of nuclear waste repositories. The surrogate uses knowledge about the underlying process to recursively partition the dataset into regions of reduced dimensionality. It achieves high accuracy with a competitive prediction throughput, and is a promising method to speedup computationally demanding coupled reactive transport models.
Morgan Tranter, Maria Wetzel, Marco De Lucia, and Michael Kühn
Adv. Geosci., 56, 57–65, https://doi.org/10.5194/adgeo-56-57-2021, https://doi.org/10.5194/adgeo-56-57-2021, 2021
Short summary
Short summary
Barite formation is an important factor for many use cases of the geological subsurface because it may change the rock.
In this modelling study, the replacement reaction of celestite to barite is investigated.
The steps that were identified to play a role are celestite dissolution followed by two-step precipitation of barite: spontaneous formation of small crystals and their subsequent growth.
Explicitly including the processes improve the usability of the models for quantified prediction.
Marco De Lucia and Michael Kühn
Adv. Geosci., 56, 33–43, https://doi.org/10.5194/adgeo-56-33-2021, https://doi.org/10.5194/adgeo-56-33-2021, 2021
Short summary
Short summary
RedModRphree is an R extension package to leverage the PHREEQC engine for geochemical models, providing convenience functions to efficiently setup computations and program algorithms involving geochemical models. Version 0.3.6 ships with a novel implementation of Pourbaix (potential/pH) diagram computation which considers the full speciation of the solution at each diagram point.
Marco De Lucia and Michael Kühn
Geosci. Model Dev., 14, 4713–4730, https://doi.org/10.5194/gmd-14-4713-2021, https://doi.org/10.5194/gmd-14-4713-2021, 2021
Short summary
Short summary
DecTree evaluates a hierarchical coupling method for reactive transport simulations in which pre-trained surrogate models are used to speed up the geochemical subprocess, and equation-based
full-physicssimulations are called only if the surrogate predictions are implausible. Furthermore, we devise and evaluate a decision tree surrogate approach designed to inject domain knowledge of the surrogate by defining engineered features based on law of mass action or stoichiometric reaction equations.
Michael Kühn
Adv. Geosci., 67, 5–14, https://doi.org/10.5194/adgeo-67-5-2025, https://doi.org/10.5194/adgeo-67-5-2025, 2025
Short summary
Short summary
The prevailing view in the scientific community is that large amounts of carbon dioxide (CO2) from the atmosphere and highly radioactive waste must be disposed of safely. In that regard, studies on natural processes that extend over thousands of years help to assess the long-term behaviour of deep geological repositories. From a purely scientific point of view, CO2 storage and final disposal of highly radioactive waste are feasible.
Michael Kühn, Sonja Martens, Johannes Miocic, Viktor J. Bruckman, and Giorgia Stasi
Adv. Geosci., 67, 1–4, https://doi.org/10.5194/adgeo-67-1-2025, https://doi.org/10.5194/adgeo-67-1-2025, 2025
Short summary
Short summary
The division on Energy, Resources, and the Environment (ERE) of the European Geosciences Union (EGU) follows an interdisciplinary approach. This volume of Advances in Geosciences presents papers covering key themes from recent developments, beside others, in geothermal systems, critical raw materials, carbon cycle dynamics and renewable energy integration, emphasizing the role of interdisciplinary research in overcoming technical, economic, and societal challenges.
Michael Kühn, Giorgia Stasi, Viktor J. Bruckman, Sonja Martens, and Johannes Miocic
Adv. Geosci., 65, 113–115, https://doi.org/10.5194/adgeo-65-113-2024, https://doi.org/10.5194/adgeo-65-113-2024, 2024
Marco De Lucia
Adv. Geosci., 65, 45–54, https://doi.org/10.5194/adgeo-65-45-2024, https://doi.org/10.5194/adgeo-65-45-2024, 2024
Short summary
Short summary
This paper presents a surrogate modelling approach applied to a geochemical system of uranium sorption on clay, relevant for the safety assessment of nuclear waste repositories. The surrogate uses knowledge about the underlying process to recursively partition the dataset into regions of reduced dimensionality. It achieves high accuracy with a competitive prediction throughput, and is a promising method to speedup computationally demanding coupled reactive transport models.
Michael Kühn, Vaughan Stagpoole, Graham Paul D. Viskovic, and Thomas Kempka
Adv. Geosci., 65, 1–7, https://doi.org/10.5194/adgeo-65-1-2024, https://doi.org/10.5194/adgeo-65-1-2024, 2024
Short summary
Short summary
Waiwera is a small coastal village located on New Zealand's North Island above a geothermal reservoir. The origin of the warm water is not well understood. An inferred fault zone at the base of the reservoir is thought to channelise the uprising thermal water. The observed characteristic cold and hot water distribution in the system was simulated and the temperature profiles show an improved agreement in the near field around the centre of the reservoir.
Michael Kühn, Viktor J. Bruckman, Sonja Martens, Johannes Miocic, and Giorgia Stasi
Adv. Geosci., 62, 67–69, https://doi.org/10.5194/adgeo-62-67-2024, https://doi.org/10.5194/adgeo-62-67-2024, 2024
Theresa Hennig and Michael Kühn
Adv. Geosci., 62, 21–30, https://doi.org/10.5194/adgeo-62-21-2023, https://doi.org/10.5194/adgeo-62-21-2023, 2023
Short summary
Short summary
Uranium migration for a close to real case situation is quantified with reactive transport simulations using input data from the deep geothermal borehole Schlattingen, which is near the targeted area in Switzerland, and including the effect of the multi-barrier system on the source term. The hydrogeological system must always be considered in safety assessments since adjacent aquifers have a major impact on the pore water geochemistry, and hence sorption processes.
Theresa Hennig and Michael Kühn
Saf. Nucl. Waste Disposal, 2, 147–147, https://doi.org/10.5194/sand-2-147-2023, https://doi.org/10.5194/sand-2-147-2023, 2023
Short summary
Short summary
Migration of uranium in the potential host rock Opalinus Clay is used as an example to demonstrate the extent to which simulated migration lengths can vary for a million years, depending on the model concept and on the underlying data and parameters. To reduce the uncertainty in this context, the calcite carbonate ion and the hydrogeological system at a potential disposal site need to be known, whereas the quantity of clay minerals plays a subordinate role, as long as it is enough.
Michael Kühn, Dirk Bosbach, Horst Geckeis, Vinzenz Brendler, and Olaf Kolditz
Saf. Nucl. Waste Disposal, 2, 195–195, https://doi.org/10.5194/sand-2-195-2023, https://doi.org/10.5194/sand-2-195-2023, 2023
Short summary
Short summary
The Repository Site Selection Act explicitly emphasises that targeting the disposal of high-level radioactive waste is a so-called learning process. We are of the opinion that the procedure and the available data should be combined with geoscientific knowledge to support the identification of siting regions. We propose this workshop and invite all experts who have dealt with the search for a repository site from a geoscientific perspective.
Viktor J. Bruckman, Gregor Giebel, Christopher Juhlin, Sonja Martens, and Michael Kühn
Adv. Geosci., 58, 87–91, https://doi.org/10.5194/adgeo-58-87-2022, https://doi.org/10.5194/adgeo-58-87-2022, 2022
Elena Chabab, Michael Kühn, and Thomas Kempka
Adv. Geosci., 58, 47–54, https://doi.org/10.5194/adgeo-58-47-2022, https://doi.org/10.5194/adgeo-58-47-2022, 2022
Short summary
Short summary
The present study, uses density-driven flow and transport models to evaluate mechanisms of saline water intrusion from deep aquifers into the freshwater column used for drinking water supply under different boundary conditions and for a specific site in the German Federal State of Brandenburg. Results show that mainly decreasing groundwater recharge leads to increased and earlier salinisation which highlights the need for waterworks to initiate effective countermeasures quickly and in time.
Michael Kühn, Melissa Präg, Ivy Becker, Christoph Hilgers, Andreas Grafe, and Thomas Kempka
Adv. Geosci., 58, 31–39, https://doi.org/10.5194/adgeo-58-31-2022, https://doi.org/10.5194/adgeo-58-31-2022, 2022
Short summary
Short summary
The geothermal hot water reservoir below the small town of Waiwera in New Zealand has been known to the indigenous Maori for many centuries. Overproduction by European immigrants led to a water level decrease and consequently artesian flow from the wells and the seeps on the beach ceased. The Te Kaunihera o Tāmaki Makaurau Auckland Council established the Waiwera Thermal Groundwater Allocation and Management Plan to allow the geothermal system to recover.
Thomas Kempka, Svenja Steding, and Michael Kühn
Adv. Geosci., 58, 19–29, https://doi.org/10.5194/adgeo-58-19-2022, https://doi.org/10.5194/adgeo-58-19-2022, 2022
Short summary
Short summary
The TRANSPORT Simulation Environment (TRANSPORTSE) was coupled with the geochemical reaction module PHREEQC, providing multiple new features that make it applicable to complex reactive transport problems in various geoscientific fields. Two computationally demanding and complex geochemical benchmarks were used in the present study to successfully verify the code implementation.
Theresa Hennig and Michael Kühn
Adv. Geosci., 58, 11–18, https://doi.org/10.5194/adgeo-58-11-2022, https://doi.org/10.5194/adgeo-58-11-2022, 2022
Short summary
Short summary
Safety assessments must demonstrate that radionuclides in potential disposal sites are retained within the containment providing rock zone using reactive transport simulations. Here, this is quantified for the example of uranium in the hydrogeological system of the Opalinus Clay at Mont Terri. Our work clearly shows how sensitive migration lengths resulting from simulations are to the model conceptualisation and selection of underlying data.
Maria Wetzel, Thomas Kempka, and Michael Kühn
Adv. Geosci., 58, 1–10, https://doi.org/10.5194/adgeo-58-1-2022, https://doi.org/10.5194/adgeo-58-1-2022, 2022
Short summary
Short summary
Porosity-permeability relations are simulated for a precipitation-dissolution cycle in a virtual sandstone. A hysteresis in permeability is observed depending on the geochemical process and dominating reaction regime, whereby permeability varies by more than two orders of magnitude. Controlling parameters for this hysteresis phenomenon are the closure and re-opening of micro-scale flow channels, derived from changes in pore throat diameter and connectivity of the pore network.
Michael Kühn and Leonard Grabow
Adv. Geosci., 56, 107–116, https://doi.org/10.5194/adgeo-56-107-2021, https://doi.org/10.5194/adgeo-56-107-2021, 2021
Short summary
Short summary
The geothermal reservoir at Waiwera has been subject to active exploitation for a long time. However, the continuous production of geothermal water, to supply hotels and spas, had a negative impact on the reservoir. The aim of this work was to link the influence of the abstraction rates to the measured water level data to derive reservoir properties. For the analysis, a modified deconvolution algorithm was implemented and shown to be applicable and in accordance to results of a pumping test.
Dirk Bosbach, Horst Geckeis, Frank Heberling, Olaf Kolditz, Michael Kühn, Katharina Müller, Thorsten Stumpf, and the iCROSS team
Saf. Nucl. Waste Disposal, 1, 85–87, https://doi.org/10.5194/sand-1-85-2021, https://doi.org/10.5194/sand-1-85-2021, 2021
Short summary
Short summary
The present contribution provides an overview on the collaborative project iCROSS and reports selected results. The impact of considering complex coupled processes in repository subsystems for the assessment of the integrity of a given (generic) repository arrangement will be discussed. The interdisciplinary team combines experimental work in the lab, in the underground rock laboratory and environmental simulations in order to achieve process understanding across variable scales.
Theresa Hennig and Michael Kühn
Adv. Geosci., 56, 97–105, https://doi.org/10.5194/adgeo-56-97-2021, https://doi.org/10.5194/adgeo-56-97-2021, 2021
Short summary
Short summary
Uranium migration in the Swiss Opalinus Clay is used as an example to quantify the influence of varying values of a stability constant in the underlying thermodynamic database within the law of mass action on the migration lengths. The difference of the stability constant of 1.33 log units lead to changed migration lengths of 5 m to 7 m. With a maximum diffusion distance of 22 m the influence of an uncertain stability constant is negligible for the host rock scale.
Morgan Tranter, Maria Wetzel, Marco De Lucia, and Michael Kühn
Adv. Geosci., 56, 57–65, https://doi.org/10.5194/adgeo-56-57-2021, https://doi.org/10.5194/adgeo-56-57-2021, 2021
Short summary
Short summary
Barite formation is an important factor for many use cases of the geological subsurface because it may change the rock.
In this modelling study, the replacement reaction of celestite to barite is investigated.
The steps that were identified to play a role are celestite dissolution followed by two-step precipitation of barite: spontaneous formation of small crystals and their subsequent growth.
Explicitly including the processes improve the usability of the models for quantified prediction.
Marco De Lucia and Michael Kühn
Adv. Geosci., 56, 33–43, https://doi.org/10.5194/adgeo-56-33-2021, https://doi.org/10.5194/adgeo-56-33-2021, 2021
Short summary
Short summary
RedModRphree is an R extension package to leverage the PHREEQC engine for geochemical models, providing convenience functions to efficiently setup computations and program algorithms involving geochemical models. Version 0.3.6 ships with a novel implementation of Pourbaix (potential/pH) diagram computation which considers the full speciation of the solution at each diagram point.
Viktor J. Bruckman, Gregor Giebel, Christopher Juhlin, Sonja Martens, Antonio P. Rinaldi, and Michael Kühn
Adv. Geosci., 56, 13–18, https://doi.org/10.5194/adgeo-56-13-2021, https://doi.org/10.5194/adgeo-56-13-2021, 2021
Marco De Lucia and Michael Kühn
Geosci. Model Dev., 14, 4713–4730, https://doi.org/10.5194/gmd-14-4713-2021, https://doi.org/10.5194/gmd-14-4713-2021, 2021
Short summary
Short summary
DecTree evaluates a hierarchical coupling method for reactive transport simulations in which pre-trained surrogate models are used to speed up the geochemical subprocess, and equation-based
full-physicssimulations are called only if the surrogate predictions are implausible. Furthermore, we devise and evaluate a decision tree surrogate approach designed to inject domain knowledge of the surrogate by defining engineered features based on law of mass action or stoichiometric reaction equations.
Melissa Präg, Ivy Becker, Christoph Hilgers, Thomas R. Walter, and Michael Kühn
Adv. Geosci., 54, 165–171, https://doi.org/10.5194/adgeo-54-165-2020, https://doi.org/10.5194/adgeo-54-165-2020, 2020
Short summary
Short summary
Utilization of geothermal reservoirs as alternative energy source is becoming increasingly important worldwide. Here, we studied the surface expression of a warm water reservoir in Waiwera, New Zealand, that has been known for many centuries but remained little explored. Using thermal infrared cameras we were able to show renewed activity of the hot springs on the beachfront and identified faults and fractures as important fluid pathways, as well as individual fluid conducting lithologies.
Michael Kühn, Natalie C. Nakaten, and Thomas Kempka
Adv. Geosci., 54, 173–178, https://doi.org/10.5194/adgeo-54-173-2020, https://doi.org/10.5194/adgeo-54-173-2020, 2020
Short summary
Short summary
Energy supply in Germany is subject to a profound change. The present paper addresses the German potential of storing excess energy from renewable power sources in the geological subsurface. Wind and solar electricity can be transformed into hydrogen, and with carbon dioxide subsequently into methane. The current potential for combined subsurface storage of methane and carbon dioxide allows to store far more than required to date and is estimated to provide the entire coverage in 2050.
Maria Wetzel, Thomas Kempka, and Michael Kühn
Adv. Geosci., 54, 33–39, https://doi.org/10.5194/adgeo-54-33-2020, https://doi.org/10.5194/adgeo-54-33-2020, 2020
Cited articles
Afanasyev, A.: Hydrodynamic Modelling of Petroleum Reservoirs using Simulator MUFITS, Enrgy. Proced., 76, 427–435,
https://doi.org/10.1016/j.egypro.2015.07.861, 2015. a
Afanasyev, A. A.: Application of the Reservoir Simulator MUFITS for 3D Modelling of CO2 Storage in Geological Formations, Enrgy. Proced., 40, 365–374, https://doi.org/10.1016/j.egypro.2013.08.042, 2013. a
Appelo, C. A. J., Parkhurst, D. L., and Post, V. E. A.: Equations for
calculating hydrogeochemical reactions of minerals and gases such as CO2 at high pressures and temperatures, Geochim. Cosmochim. Ac., 125, 49–67, https://doi.org/10.1016/j.gca.2013.10.003, 2013. a
Beisman, J. J., Maxwell, R. M., Navarre-Sitchler, A. K., Steefel, C. I., and
Molins, S.: ParCrunchFlow: an efficient, parallel reactive transport
simulation tool for physically and chemically heterogeneous saturated
subsurface environments, Comput. Geosci., 19, 403–422,
https://doi.org/10.1007/s10596-015-9475-x, 2015. a
Christgau, S. and Schnor, B.: Design of MPI Passive Target Synchronization for a Non-Cache-Coherent Many-Core Processor, in: Parallel-Algorithmen,
-Rechnerstrukturen und -Systemsoftware: 27. PARS Workshop, 4–5 April 2017, Hagen, Germany, vol. 34 of Mitteilungen, Gesellschaft für Informatik e.V., 2017. a, b, c
Damiani, L. H., Kosakowski, G., Glaus, M. A., and Churakov, S. V.: A framework for reactive transport modeling using FEniCS–Reaktoro: governing equations and benchmarking results, Comput. Geosci., 24, 1071–1085,
https://doi.org/10.1007/s10596-019-09919-3, 2020. a, b
De Lucia, M. and Kühn, M.: Coupling R and PHREEQC: Efficient
Programming of Geochemical Models, Enrgy. Proced., 40, 464–471,
https://doi.org/10.1016/j.egypro.2013.08.053, 2013. a, b
De Lucia, M. and Kühn, M.: Geochemical and reactive transport modelling in R with the RedModRphree package, Adv. Geosci., 56, 33–43, https://doi.org/10.5194/adgeo-56-33-2021, 2021b. a, b
De Lucia, M., Kempka, T., Afanasyev, A., Melnik, O., and Kühn, M.: Coupling
of Geochemical and Multiphase Flow Processes for Validation of the
MUFITS Reservoir Simulator Against TOUGH, Enrgy. Proced., 97,
502–508, https://doi.org/10.1016/j.egypro.2016.10.060, 2016. a
Eddelbuettel, D., Francois, R., and Bachmeier, L.: RInside: Easy embedding of R inside C++ (and C), available at: http://dirk.eddelbuettel.com/code/rinside.html,
last access: 25 January 2021. a
Engesgaard, P. and Kipp, K. L.: A geochemical transport model for
redox-controlled movement of mineral fronts in groundwater flow systems: A
case of nitrate removal by oxidation of pyrite, Water Resour. Res., 28,
2829–2843, https://doi.org/10.1029/92WR01264, 1992. a
Foster, I.: Designing and Building Parallel Programs: Concepts and Tools for
Parallel Software Engineering, Addison-Wesley Longman Publishing Co., Inc., Reading, USA, 1995. a
Gerstenberger, R., Besta, M., and Hoefler, T.: Enabling highly-scalable remote memory access programming with MPI-3 One Sided, Sci. Programming-Neth., 22, 75–91, https://doi.org/10.3233/SPR-140383, 2014. a
Guérillot, D. and Bruyelle, J.: Geochemical equilibrium determination using an artificial neural network in compositional reservoir flow simulation,
Comput. Geosci., 24, 697–707, https://doi.org/10.1007/s10596-019-09861-4,
2020. a
He, W., Beyer, C., Fleckenstein, J. H., Jang, E., Kolditz, O., Naumov, D., and Kalbacher, T.: A parallelization scheme to simulate reactive transport in the subsurface environment with OGS#IPhreeqc 5.5.7-3.1.2, Geosci. Model Dev., 8, 3333–3348, https://doi.org/10.5194/gmd-8-3333-2015, 2015. a, b, c
Howard, J., Dighe, S., Hoskote, Y. V., Vangal, S. R., Finan, D., Ruhl,
G., Jenkins, D., Wilson, H., Borkar, N., Schrom, G., Pailet, F., Jain, S., Jacob, T., Yada, S., Marella, S., Salihundam, P., Erraguntla, V., Konow, M., Riepen, M., Droege, G., Lindemann, J., Gries, M., Apel, T., Henriss, K., Lund-Larsen, T., Steibl, S., Borkar, S. B., De, V., Wijngaart, R. F., and Mattson, T. G.: A 48-Core IA-32 message-passing processor with DVFS in 45 nm CMOS, in: 2010 IEEE International Solid-State Circuits Conference – (ISSCC), 7–11 February 2010, San Francisco, USA, 108–109, https://doi.org/10.1109/ISSCC.2010.5434077, 2010. a
Huang, Y., Shao, H., Wieland, E., Kolditz, O., and Kosakowski, G.: A new
approach to coupled two-phase reactive transport simulation for long-term
degradation of concrete, Constr. Build. Mater., 190, 805–829,
https://doi.org/10.1016/j.conbuildmat.2018.09.114, 2018. a
Jatnieks, J., De Lucia, M., Dransch, D., and Sips, M.: Data-driven
Surrogate Model Approach for Improving the Performance of
Reactive Transport Simulations, Enrgy. Proced., 97, 447–453,
https://doi.org/10.1016/j.egypro.2016.10.047, 2016. a, b
Karp, A. H. and Flatt, H. P.: Measuring parallel processor performance,
Commun. ACM, 33, 539–543, https://doi.org/10.1145/78607.78614, 1990. a
Kempka, T.: Verification of a Python-based TRANsport Simulation Environment for density-driven fluid flow and coupled transport of heat and chemical species, Adv. Geosci., 54, 67–77, https://doi.org/10.5194/adgeo-54-67-2020, 2020. a
Kempka, T., Klein, E., De Lucia, M., Tillner, E., and Kühn, M.: Assessment
of Long-term CO2 Trapping Mechanisms at the Ketzin Pilot Site (Germany) by Coupled Numerical Modelling, Enrgy. Proced., 37, 5419–5426, https://doi.org/10.1016/j.egypro.2013.06.460, 2013. a
Kempka, T., De Lucia, M., and Kühn, M.: Geomechanical integrity verification
and mineral trapping quantification for the Ketzin CO2 storage pilot site
by coupled numerical simulations, Enrgy. Proced., 63, 3330–3338,
https://doi.org/10.1016/j.egypro.2014.11.361, 2014. a
Klein, E., De Lucia, M., Kempka, T., and Kühn, M.: Evaluation of long-term
mineral trapping at the Ketzin pilot site for CO2 storage: An
integrative approach using geochemical modelling and reservoir simulation,
Int. J. Greenh. Gas Con., 19, 720–730,
https://doi.org/10.1016/j.ijggc.2013.05.014, 2013. a
Kyas, S., Volpatto, D., Saar, M. O., and Leal, A. M. M.: Accelerated reactive
transport simulations in heterogeneous porous media using Reaktoro and
Firedrake, arXiv [preprint], arXiv:2009.01194, 29 October 2020. a, b, c
Laloy, E. and Jacques, D.: Emulation of CPU-demanding reactive transport
models: a comparison of Gaussian processes, polynomial chaos expansion, and
deep neural networks, Comput. Geosci., 23, 1193–1215,
https://doi.org/10.1007/s10596-019-09875-y, 2019. a, b, c
Leal, A. M. M., Kulik, D. A., and Saar, M. O.: Ultra-Fast Reactive Transport
Simulations When Chemical Reactions Meet Machine Learning: Chemical
Equilibrium, arXiv [preprint], arXiv:1708.04825, 16 August 2017. a
Li, T., Zhou, X., Wang, K., Zhao, D., Sadooghi, I., Zhang, Z., and Raicu, I.: A Convergence of Key-value Storage Systems from Clouds to Supercomputers,
Concurr. Comp.-Pract. E., 28, 44–69, https://doi.org/10.1002/cpe.3614, 2016. a
Lu, H., Ermakova, D., Wainwright, H. M., Zheng, L., and Tartakovsky, D. M.:
Data-informed Emulators for Multi-Physics Simulations, arXiv [preprint], arXiv:2012.15488,
31 December 2020. a, b
Martens, S., Liebscher, A., Möller, F., Henninges, J., Kempka, T., Lüth, S.,
Norden, B., Prevedel, B., Szizybalski, A., Zimmer, M., Kühn, M., and Group,
K.: CO2 Storage at the Ketzin Pilot Site, Germany: Fourth
Year of Injection, Monitoring, Modelling and Verification, Enrgy.
Proced., 37, 6434–6443, https://doi.org/10.1016/j.egypro.2013.06.573, 2013. a
Maymounkov, P. and Mazières, D.: Kademlia: A Peer-to-Peer Information
System Based on the XOR Metric, in: Peer-to-Peer Systems, First
International Workshop, IPTPS 2002, 7–8 March 2002, Cambridge, MA, USA,
Revised Papers, 53–65, https://doi.org/10.1007/3-540-45748-8_5, 2002. a
Maynard, C. M.: Comparing UPC and One-sided MPI: A Distributed Hash Table for GAP, in: Fifth Conference on Partitioned Global Address Space Programming Models (PGAS 2011), 15–18 October 2017, Galveston Island, Texas, USA, available at: http://pgas11.rice.edu/papers/Maynard-Distributed-Hash-Table-PGAS11.pdf (last access: 29 November 2021), 2011. a
Memcached: High-Performance, Distributed Memory Object Caching System, available at: http://memcached.org/, last access: 29 November 2021. a
Monnerat, L. R. and Amorim, C. L.: An effective single-hop distributed hash
table with high lookup performance and low traffic overhead, Concurr. Comp.-Pract. E., 27, 1767–1788, https://doi.org/10.1002/cpe.3342, 2015. a
Moortgat, J., Li, M., Amooie, M. A., and Zhu, D.: A higher-order finite element reactive transport model for unstructured and fractured grids, Sci. Rep., 10, 15572, https://doi.org/10.1038/s41598-020-72354-3, 2020. a
Palandri, J. L. and Kharaka, Y. K.: A compilation of rate parameters of
water-mineral interaction kinetics for application to geochemical modeling,
Tech. rep., USGS Menlo Park, California, USA, available at: https://pubs.usgs.gov/of/2004/1068/ (last access: 29 November 2021),
2004. a
Parkhurst, D. L. and Wissmeier, L.: PhreeqcRM: A reaction module for transport simulators based on the geochemical model PHREEQC, Adv. Water
Resour., 83, 176–189, https://doi.org/10.1016/j.advwatres.2015.06.001, 2015. a
Permann, C. J., Gaston, D. R., Andrš, D., Carlsen, R. W., Kong, F., Lindsay, A. D., Miller, J. M., Peterson, J. W., Slaughter, A. E., Stogner, R. H., and Martineau, R. C.: MOOSE: Enabling massively parallel multiphysics simulation,
SoftwareX, 11, 100430, https://doi.org/10.1016/j.softx.2020.100430, 2020. a, b
Prasianakis, N. I., Haller, R., Mahrous, M., Poonoosamy, J., Pfingsten, W., and Churakov, S. V.: Neural network based process coupling and parameter
upscaling in reactive transport simulations, Geochim. Cosmochim. Ac., 291, 126–143, https://doi.org/10.1016/j.gca.2020.07.019, 2020. a, b
Redis: https://redis.io/, last access: 29 November 2021. a
Schnor, B., Lübke, M., Lindemann, A., De Lucia, M., and Kühn, M.: POET version 1.0 (1.0), Zenodo [code], https://doi.org/10.5281/zenodo.4757913, 2021. a
Shao, H., Dmytrieva, S. V., Kolditz, O., Kulik, D. A., Pfingsten, W., and
Kosakowski, G.: Modeling reactive transport in non-ideal aqueous–solid
solution system, Appl. Geochem., 24, 1287–1300,
https://doi.org/10.1016/j.apgeochem.2009.04.001, 2009. a
Soulaine, C., Pavuluri, S., Claret, F., and Tournassat, C.: porousMedia4Foam: Multi-scale open-source platform for hydro-geochemical simulations with OpenFOAM, Environ. Model. Softw., 145, 105199, https://doi.org/10.1016/j.envsoft.2021.105199, 2021. a
Steefel, C. I., Appelo, C. A. J., Arora, B., Jacques, D., Kalbacher, T.,
Kolditz, O., Lagneau, V., Lichtner, P. C., Mayer, K. U., Meeussen, J. C. L.,
Molins, S., Moulton, D., Shao, H., Šimůnek, J., Spycher, N., Yabusaki,
S. B., and Yeh, G. T.: Reactive transport codes for subsurface environmental
simulation, Comput. Geosci., 19, 445–478,
https://doi.org/10.1007/s10596-014-9443-x, 2015. a, b, c
Stockmann, M., Schikora, J., Becker, D.-A., Flügge, J., Noseck, U., and
Brendler, V.: Smart Kd-values, their uncertainties and sensitivities –
Applying a new approach for realistic distribution coefficients in
geochemical modeling of complex systems, Chemosphere, 187, 277–285,
https://doi.org/10.1016/j.chemosphere.2017.08.115, 2017. a
Stoica, I., Morris, R. T., Liben-Nowell, D., Karger, D. R., Kaashoek, M. F.,
Dabek, F., and Balakrishnan, H.: Chord: a scalable peer-to-peer lookup
protocol for internet applications, IEEE/ACM Trans. Netw., 11, 17–32,
https://doi.org/10.1109/TNET.2002.808407, 2003. a
Tsukamoto, D. and Nakashima, T.: Implementation and Evaluation of Distributed
Hash Table Using MPI, in: Proceedings of the Fifth International Conference
on Broadband and Wireless Computing, Communication and Applications, BWCCA
2010, 4–6 November 2010, Fukuoka Institute of Technology, Fukuoka, Japan (In
conjunction with the 3PGCIC-2010 International Conference), 684–688,
https://doi.org/10.1109/BWCCA.2010.155, 2010. a, b
Short summary
POET is a parallel reactive transport simulator which implements a mechanism to store and reuse previous results of geochemical simulations through distributed hash tables. POET parallelizes chemistry using a master/worker design with noncontiguous grid partitions to maximize its efficiency and load balance on shared-memory machines and compute clusters.
POET is a parallel reactive transport simulator which implements a mechanism to store and reuse...
