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- - - - -Journal of Open Source Software -JOSS - -2475-9066 - -Open Journals - - - -0 -N/A - -tRIBS v5.2: A multi-resolution, parallel platform for -tributary hydrology in forest applications - - - -https://orcid.org/0000-0003-2204-4621 - -Raming -L. W. - - - -* - - -https://orcid.org/0000-0002-2659-9459 - -Vivoni -E. R. - - - - - -https://orcid.org/0000-0003-4516-1206 - -Mascaro -G. - - - - - - -Cederstrom -C. J. - - - - - -Ko -A. - - - - -https://orcid.org/0000-0003-3424-9202 - -Schreiner-McGraw -A. P - - - - -https://orcid.org/0000-0002-0893-4268 - -Lizarraga-Celaya -C. - - - - - -School of Sustainable Engineering and the Built -Environment, Arizona State University, Tempe, AZ, USA, -85287. - - - - -Center for Hydrologic Innovations, Arizona State -University, Tempe, AZ, USA, 85287. - - - - -* E-mail: - - -19 -3 -2024 - -¿VOL? -¿ISSUE? -¿PAGE? - -Authors of papers retain copyright and release the -work under a Creative Commons Attribution 4.0 International License (CC -BY 4.0) -2022 -The article authors - -Authors of papers retain copyright and release the work under -a Creative Commons Attribution 4.0 International License (CC BY -4.0) - - - -C++ -hydrology -distributed hydrological models -numerical modeling - - - - - - Summary -

Distributed hydrologic models provide earth scientists and - engineers with tools to test and explore hypotheses related to the - movement and storage of water within a landscape - (Fatichi - et al., 2016; - Grayson - et al., 2002; - Keller - et al., 2023). The Triangulated Irregular Network (TIN)-based - Real-Time Integrated Basin Simulator denoted as tRIBS - (Ivanov - et al., 2004a, - 2004b), - is an example of such a process-based distributed model and has been - used to address a wide range of problems from hillslope scale - processes in ecohydrology (e.g.,  - Mahmood - & Vivoni, 2011) to flood management of large watersheds - (e.g.,  - Cázares-Rodríguez - et al., 2017). Yet, in spite of the extensive use and - application of tRIBS to current topics in hydrology, engineering, and - the earth sciences, the code has been essentially maintained as a - proprietary software. Here, we document the release of tRIBS v5.2, an - updated open source code base and its application for forested - watersheds that serve as tributaries to larger river systems. This - release includes improvements in hydrologic processes with new - functionality for simulating channel transmission losses - (Schreiner-McGraw - & Vivoni, 2018) and reservoir routing - (Cázares-Rodríguez - et al., 2017). Additionally, it features updated documentation, - improved infrastructure for sustainable code development and - employment, and improved computational efficiency. These additions - provide a robust and sustainable code base, enhancing access and - applications of the model.

- - - Statement of Needs - - Model Description -

tRIBS is written in C++ and uses an object oriented design - founded on a hydrologically conditioned TIN mesh (see  - Tucker - et al., 2001 and; - Vivoni - et al., 2004). Building on the work of Garrote & Bras - (1995), - tRIBS is a continuous hydrologic model simulating the coupled - dynamics between the vadose and saturated zones - (Vivoni - et al., 2007). Accounting for these key hydrologic processes - while using computationally efficient methods - ([fig:Fig_1]), - tRIBS actively tracks both the evolution of wetting fronts and - moisture losses, allowing for continuous simulation throughout wet - and dry periods - (Ivanov - et al., 2004a). With the addition of a single-layer snowpack - module - (Rinehart - et al., 2008), tRIBS can also be applied in cold and - mountainous forest environments - ([fig:Fig_2]).

-

Furthermore, the unstructured TIN mesh in tRIBS provides a - multiresolution approach to distributed hydrologic modeling - ([fig:Fig_1] and - [fig:Fig_3]). As - a consequence, tRIBS allows for detailed control in resolving - hydrologic dynamics across multiple scales - (Vivoni - et al., 2004), maximizing model fidelity to physical - processes, while minimizing computational expenses. This - multi-scaling behavior when paired with parallelization - (Vivoni - et al., 2011) allows for hyper-resolution modeling - (Wood - et al., 2011) of hydrologic dynamics at unprecedented scales, - from simulations rendered at a point - (Vivoni - et al., 2010) to 21,000 km2 watersheds simulated - for a period of 10 years at a nominal cell resolution of ~88 m - (Ko et - al., 2019).

- -

Conceptual overview of tRIBS end-to-end workflow - highlighting key processes. Asterisks indicate new features or - processes available in tRIBS v5.2. Soil and vegetation parameters - may be provided in a raster with continuous values or in a - classification - table.

- - - - - Updates and Modifications -

Building on core tRIBS functionality, as described by Ivanov et - al. - (2004a), - Rinehart et al. - (2008), - and Vivoni et al. - (2011), - tRIBS v5.2 provides two new process additions: (1) reservoir routing - using the level-pool method - (Cázares-Rodríguez - et al., 2017), and (2) channel transmission losses - (Schreiner-McGraw - & Vivoni, 2018). In addition, the code base has been - restructured with mechanisms for improved maintainability, - robustness, performance, and integration. This includes updates for - code compatibility with newer compilers (Clang and GCC), the - introduction of a CMake build system providing flexibility for - compiling serial and parallel versions, and modernization of the - model version control system and documentation. Additionally, we - refactored the snow module - (Rinehart - et al., 2008), resulting in a reduction of redundant code and - enhanced code organization. Memory leaks associated with parallel - operations were fixed, allowing for increased scalability. Finally, - we included Docker images for both tRIBS v5.2 and the auxiliary - program MeshBuilder. The Docker image for MeshBuilder facilitates an - end-to-end workflow that utilizes METIS - (Karypis - & Kumar, 1998), enabling rapid and easy partitioning of a - watershed domain for parallel simulations - (Vivoni - et al., 2011).

-

These and other features of tRIBS v5.2 can be explored using two - newly updated benchmark scenarios. This first benchmark is a - point-scale simulation of the Happy Jack SNOTEL site in northern - Arizona, USA - ([fig:Fig_2]). - The second is a basin-scale simulation of the Big Spring watershed - located in the headwaters of Sycamore Creek in northern Arizona - ([fig:Fig_3]). - Both benchmarks are hosted on Zenodo, see - [fig:Fig_2] and - [fig:Fig_3] for - more details.

- -

A point-scale (i.e. a single Voronoi cell) tRIBS - simulation of snow water equivalent (SWE) at the Happy Jack SNOTEL - site in northern Arizona, USA. Top panel shows the time series of - observed (black) and simulated SWE (blue). Bottom panel compares - the observed and simulated peak SWE from 2002 to 2017. Dashed - black line is a one-to-one relation. The color bar indicates the - time difference in the occurrence of the peak SWE for each water - year. Zenodo repository for this simulation with additional - details can be found at: - https://zenodo.org/records/10909507.

- - - - - Conclusion -

Embracing the FAIR principles (Findability, Accessibility, - Interoperability, and Reusability; - Wilkinson - et al., 2016) and recognizing the importance of free and open - source software in hydrology - (Kabo-bah - et al., 2012), here we document the release of tRIBS v5.2. - This version represents years of cumulative efforts with major code - improvements related to maintainability, robustness, performance, - and integration as well as new process based functionality. The - benchmarks provided exemplify tRIBS v5.2 applications in forested - tributary watersheds of larger river systems. We anticipate that - tRIBS v5.2 will be a valuable asset in addressing a wide range of - problems for the broader hydrology community.

- -

An example of a basin-scale tRIBS simulation showing a - spatial map of mean hourly evapotranspiration rates averaged over - the course of a 4-year simulation period. Big Spring basin is a - tributary to Sycamore Creek in northern Arizona, USA. Zenodo - repository for this simulation with additional details can be - found at: - https://zenodo.org/records/10909729. -

- - - - - - Acknowledgements -

We thank the tRIBS developers at the Massachusetts Institute of - Technology, New Mexico Institute of Mining and Technology, Los Alamos - National Laboratory, and Arizona State University, including Valeriy - Y. Ivanov, Scott M. Rybarczyk, Greg E. Tucker, Sue Mniszewski, Pat - Fasel, and Alex J. Rinehart. We also thank Rafael L. Bras, Dara - Entekhabi, and Everett P. Springer, for guidance on model development. - Lastly, we are grateful for the support of Elvy Barton and Bruce - Hallin for encouraging further development and application of tRIBS to - new and pressing problems. Over the years, tRIBS model development has - been funded by: Army Research Office, National Science Foundation, - National Oceanic and Atmospheric Administration, National Aeronautics - and Space Administration, Los Alamos National Laboratory, Salt River - Project, and Arizona State University. The most current contribution - documented here was facilitated by the Arizona Water Innovation - Initiative.

- - - - - - - - MahmoodTaufique H. - VivoniE. R. - - A climate-induced threshold in hydrologic response in a semiarid ponderosa pine hillslope - Water Resources Research - 2011 - 20230214 - 47 - 9 - 1944-7973 - https://onlinelibrary.wiley.com/doi/abs/10.1029/2011WR010384 - 10.1029/2011WR010384 - - - - - - RinehartA. J. - VivoniE. R. - BrooksP. D. - - Effects of vegetation, albedo, and solar radiation sheltering on the distribution of snow in the Valles Caldera, New Mexico - Ecohydrology - 2008 - 20230214 - 1 - 3 - 1936-0592 - https://onlinelibrary.wiley.com/doi/abs/10.1002/eco.26 - 10.1002/eco.26 - 253 - 270 - - - - - - IvanovV. Y. - VivoniE. R. - BrasR. L. - EntekhabiD. - - Preserving high-resolution surface and rainfall data in operational-scale basin hydrology: A fully-distributed physically-based approach - Journal of Hydrology - 200410 - 20230214 - 298 - 1 - 0022-1694 - https://www.sciencedirect.com/science/article/pii/S0022169404002409 - 10.1016/j.jhydrol.2004.03.041 - 80 - 111 - - - - - - GarroteL. - BrasR. L. - - A distributed model for real-time flood forecasting using digital elevation models - Journal of Hydrology - 199505 - 20230213 - 167 - 1 - 0022-1694 - https://www.sciencedirect.com/science/article/pii/002216949402592Y - 10.1016/0022-1694(94)02592-Y - 279 - 306 - - - - - - TuckerG. - LancasterS. T. - GaspariniN. M. - BrasR. L. - RybarczykS. M. - - An object-oriented framework for distributed hydrologic and geomorphic modeling using triangulated irregular networks - Computers & Geosciences - 200110 - 20230213 - 27 - 8 - 0098-3004 - https://www.sciencedirect.com/science/article/pii/S0098300400001345 - 10.1016/S0098-3004(00)00134-5 - 959 - 973 - - - - - - IvanovV. Y. - VivoniE. R. - BrasR. L. - EntekhabiD. - - Catchment hydrologic response with a fully distributed triangulated irregular network model - Water Resources Research - 2004 - 20221216 - 40 - 11 - 1944-7973 - https://onlinelibrary.wiley.com/doi/abs/10.1029/2004WR003218 - 10.1029/2004WR003218 - - - - - - FatichiS. - VivoniE. R. - OgdenFred L. - IvanovV. Y. - MirusB. - GochisD. - DownerC. W. - CamporeseM. - DavisonJ. H. - EbelB. - JonesN. - KimJ. - MascaroG. - NiswongerR. - RestrepoP. - RigonR. - ShenC. - SulisM. - TarbotonD. - - An overview of current applications, challenges, and future trends in distributed process-based models in hydrology - Journal of Hydrology - 201606 - 20220221 - 537 - 0022-1694 - https://www.sciencedirect.com/science/article/pii/S0022169416301317 - 10.1016/j.jhydrol.2016.03.026 - 45 - 60 - - - - - - KoA. - MascaroG. - VivoniE. R. - - Strategies to Improve and Evaluate Physics-Based Hyperresolution Hydrologic Simulations at Regional Basin Scales - Water Resources Research - 2019 - 20230426 - 55 - 2 - 1944-7973 - https://onlinelibrary.wiley.com/doi/abs/10.1029/2018WR023521 - 10.1029/2018WR023521 - 1129 - 1152 - - - - - - Cázares-RodríguezJ. E. - VivoniE. R. - MascaroG. - - Comparison of Two Watershed Models for Addressing Stakeholder Flood Mitigation Strategies: Case Study of Hurricane Alex in Monterrey, México - Journal of Hydrologic Engineering - 201709 - 20230503 - 22 - 9 - 1943-5584 - https://ascelibrary.org/doi/10.1061/%28ASCE%29HE.1943-5584.0001560 - 10.1061/(ASCE)HE.1943-5584.0001560 - 05017018 - - - - - - - GraysonR. B. - BlöschlG. - WesternA. W. - McMahonT. A. - - Advances in the use of observed spatial patterns of catchment hydrological response - Advances in Water Resources - 200208 - 20230524 - 25 - 8 - 0309-1708 - https://www.sciencedirect.com/science/article/pii/S030917080200060X - 10.1016/S0309-1708(02)00060-X - 1313 - 1334 - - - - - - Schreiner-McGrawA. P. - VivoniE. R. - - On the Sensitivity of Hillslope Runoff and Channel Transmission Losses in Arid Piedmont Slopes - Water Resources Research - 2018 - 20230714 - 54 - 7 - 1944-7973 - https://onlinelibrary.wiley.com/doi/abs/10.1029/2018WR022842 - 10.1029/2018WR022842 - 4498 - 4518 - - - - - - Kabo-bahA. - YueboX. - OdoiJ. - - The Future of Free and Open Source Software (FOSS) for Hydrology and Water Resources Management - Hydrol Current Res - 2012 - 20240214 - 3 - 136 - 10.4172/2157-7587.1000136 - 2 - - - - - - - KarypisG. - KumarV. - - A Fast and High Quality Multilevel Scheme for Partitioning Irregular Graphs - SIAM Journal on Scientific Computing - 199801 - 20240308 - 20 - 1 - 1064-8275 - https://epubs.siam.org/doi/abs/10.1137/S1064827595287997 - 10.1137/S1064827595287997 - 359 - 392 - - - - - - KellerA. A. - GarnerK. - RaoN. - KnippingE. - ThomasJ. - - Hydrological models for climate-based assessments at the watershed scale: A critical review of existing hydrologic and water quality models - Science of The Total Environment - 202304 - 20240314 - 867 - 0048-9697 - https://www.sciencedirect.com/science/article/pii/S0048969722083139 - 10.1016/j.scitotenv.2022.161209 - 161209 - - - - - - - VivoniE. R. - MascaroG. - MniszewskiS. - FaselP. - SpringerE. P. - IvanovV. Y. - BrasR. L. - - Real-world hydrologic assessment of a fully-distributed hydrological model in a parallel computing environment - Journal of Hydrology - 201110 - 20230214 - 409 - 1 - 0022-1694 - https://www.sciencedirect.com/science/article/pii/S0022169411006093 - 10.1016/j.jhydrol.2011.08.053 - 483 - 496 - - - - - - VivoniE. R. - IvanovV. Y. - BrasR.l L. - EntekhabiD. - - Generation of Triangulated Irregular Networks Based on Hydrological Similarity - Journal of Hydrologic Engineering - 200407 - 20230427 - 9 - 4 - 1084-0699 - https://ascelibrary.org/doi/10.1061/%28ASCE%291084-0699%282004%299%3A4%28288%29 - 10.1061/(ASCE)1084-0699(2004)9:4(288) - 288 - 302 - - - - - - WoodEric F. - RoundyJoshua K. - TroyTara J. - BeekL. P. H. van - BierkensMarc F. P. - BlythEleanor - RooAd de - DöllPetra - EkMike - FamigliettiJames - GochisDavid - GiesenNick van de - HouserPaul - JafféPeter R. - KolletStefan - LehnerBernhard - LettenmaierDennis P. - Peters-LidardChrista - SivapalanMurugesu - SheffieldJustin - WadeAndrew - WhiteheadPaul - - Hyperresolution global land surface modeling: Meeting a grand challenge for monitoring Earth’s terrestrial water - Water Resources Research - 2011 - 20240214 - 47 - 5 - 1944-7973 - https://onlinelibrary.wiley.com/doi/abs/10.1029/2010WR010090 - 10.1029/2010WR010090 - - - - - - VivoniE. R. - RodríguezJ. C. - WattsC. J. - - On the spatiotemporal variability of soil moisture and evapotranspiration in a mountainous basin within the North American monsoon region - Water Resources Research - 2010 - 20240214 - 46 - 2 - 1944-7973 - https://onlinelibrary.wiley.com/doi/abs/10.1029/2009WR008240 - 10.1029/2009WR008240 - - - - - - WilkinsonMark D. - DumontierMichel - AalbersbergIJsbrand Jan - AppletonGabrielle - AxtonMyles - BaakArie - BlombergNiklas - BoitenJan-Willem - Silva SantosLuiz Bonino da - BournePhilip E. - BouwmanJildau - BrookesAnthony J. - ClarkTim - CrosasMercè - DilloIngrid - DumonOlivier - EdmundsScott - EveloChris T. - FinkersRichard - Gonzalez-BeltranAlejandra - GrayAlasdair J. G. - GrothPaul - GobleCarole - GretheJeffrey S. - HeringaJaap - HoenPeter A. C. ’t - HooftRob - KuhnTobias - KokRuben - KokJoost - LusherScott J. - MartoneMaryann E. - MonsAlbert - PackerAbel L. - PerssonBengt - Rocca-SerraPhilippe - RoosMarco - SchaikRene van - SansoneSusanna-Assunta - SchultesErik - SengstagThierry - SlaterTed - StrawnGeorge - SwertzMorris A. - ThompsonMark - LeiJohan van der - MulligenErik van - VelteropJan - WaagmeesterAndra - WittenburgPeter - WolstencroftKatherine - ZhaoJun - MonsBarend - - The FAIR Guiding Principles for scientific data management and stewardship - Scientific Data - 201603 - 20240214 - 3 - 1 - 2052-4463 - https://www.nature.com/articles/sdata201618 - 10.1038/sdata.2016.18 - 160018 - - - - - - - VivoniE. R. - EntekhabiD. - BrasR. L. - IvanovV. Y. - - Controls on runoff generation and scale-dependence in a distributed hydrologic model - Hydrology and Earth System Sciences - 200710 - 20230719 - 11 - 5 - 1027-5606 - https://hess.copernicus.org/articles/11/1683/2007/ - 10.5194/hess-11-1683-2007 - 1683 - 1701 - - - - -