LAKE-model.md

@@ -2,7 +2,7 @@ The LAKE model webpage: https://mathmod.org/lake/
 
 LAKE is an extended one-dimensional model of thermodynamic, hydrodynamic and biogeochemical processes in the water basin and the bottom sediments (Stepanenko and Lykosov 2005, Stepanenko et al. 2011). The model simulates vertical heat transfer taking into account the penetration of short-wave radiation in water layers (Heiskanen et al., 2015), ice, snow and bottom sediments. The model allows for the evolution of ice layer at the bottom after complete lake freezing in winter. The equations of the model are formulated in terms of quantities averaged over the horizontal section a water body, which leads to an explicit account of the exchange of momentum, heat, dissolved species and suspended matter between water and the inclined bottom. In the water column, $`k-\epsilon`$ parametrization of turbulence is applied, along with other options like Henderson-Sellers diffusivity and convective adaptation of predicted vertical distributions. The equations of motion take into account the barotropic (Stepanenko et al., 2016) and baroclinic pressure gradient (Степаненко, 2018; Stepanenko et al., 2020). In ice and snow, a coupled transport of heat and liquid water is reproduced (Volodina et al. 2000; Stepanenko et al., 2019). In bottom sediments, water phase changes are simulated. The water salinity effects include contributions to density, freezing point, the ice growth rate (Stepanenko et al., 2019). The water budget is explicitly simulated to reproduce lake level variations, as well as associated vertical motions in the water column (Степаненко и др., 2020). The model also describes vertical diffusion of dissolved gases (CO$`_2`$, CH$`_4`$, O$`_2`$), as well as their bubble transfer, methane oxidation, photosynthesis and processes of oxygen consumption in water column and sediments. The other biogeochemical species include particulate organic matter (both living and dead), chorophyll-a, dissolved organic carbon, dissolved inorganic phosphorus. Parameterization of methane production in sediments is included (Stepanenko et al. 2011), and for the case of thermokarst lakes, an original formulation for the methane production near the lower boundary of "talik" is implemented. Model has been tested in respect to thermal and ice regime at a number lakes in contrasting climate conditions, specifically, within the LakeMIP project (Lake Model Intercomparison Project, Stepanenko et al., 2010; Stepanenko et al., 2013; Stepanenko et al., 2014; Thiery et al., 2014). The modeled carbon dioxide and methane emissions has been reported for a number of natural and artificial reservoirs (Iakunin et al., 2020; Guseva et al., 2020; Stepanenko et al., 2011; Stepanenko et al., 2016; Степаненко и др., 2020).
 
-The current **version** of the model is 3.0
+The current **version** of the model is 3.1
 
 The complete **model archive** with sample input data: 
 * [LAKE2.0.zip](/uploads/93a0c94120a307d0fdd9bcdb069e3125/LAKE2.0.zip)
@@ -14,6 +14,7 @@ The complete **model archive** with sample input data:
 * [LAKE2.6.zip](uploads/0d22404df6562bbd5187d00ea6daae60/LAKE2.6.zip) (commit 08aa0758 in repository; new driving parameters, related to background diffusivity in thermocline, methane production and oxidation in water column, are included in setup file)
 * [LAKE-LAKE3.0.zip](uploads/834e6d605925da87c858afad66eb0131/LAKE-LAKE3.0.zip) (commit 
 6548bc92 in repository; a number of bugs fixed, esp. related to salinity; filling missing input radiation fluxes by values computed by empirical formulae; model code improved)
+* [LAKE3.1.zip](uploads/0313f0267596d950c639c8dbd7b3aab7/LAKE3.1.zip) (commit 16cfe649 in repository; bug in LAKE3.0 related to methane fixed, cmake compilation added)
 
 When **publishing** results using LAKE2.0 please refer to: 
 
@@ -22,6 +23,7 @@ Stepanenko, V., Mammarella, I., Ojala, A., Miettinen, H., Lykosov, V., & Vesala,
 Any **questions** regarding LAKE model please address to Victor Stepanenko (stepanen(at)srcc.msu.ru) 
 
 **References**
+* Clark Jason A., Elchin E. Jafarov, Ken D. Tape, Benjamin M. Jones, and Victor Stepanenko (2022). Thermal modeling of three lakes within the continuous permafrost zone in alaska using the lake 2.0 model. Geoscientific Model Development, 15:7421–7448. http://dx.doi.org/10.5194/gmd-15-7421-2022
 * Iakunin, Maksim, Victor Stepanenko, Rui Salgado, Miguel Potes, Alexandra Penha, Maria Helena Novais, and Gonçalo Rodrigues (2020). Numerical study of the seasonal thermal and gas regimes of the largest artificial reservoir in western europe using the LAKE 2.0 model. *Geoscientific Model Development*, 13(8):3475–3488.  http://dx.doi.org/10.5194/gmd-13-3475-2020 
 * Heiskanen, J. J., Mammarella, I., Ojala, A., Stepanenko, V., Erkkilä, K.-M., Miettinen, H., … Nordbo, A. (2015). Effects of water clarity on lake stratification and lake-atmosphere heat exchange. *Journal of Geophysical Research*, 120(15). http://doi.org/10.1002/2014JD022938
 * Gladskikh, D. S., V. M. Stepanenko, and E. V. Mortikov (2021). The effect of the horizontal dimensions of inland water bodies on the thickness of the upper mixed layer.  *Water Resources*, 48(2):226–234. http://dx.doi.org/10.1134/S0097807821020068
@@ -33,9 +35,11 @@ Any **questions** regarding LAKE model please address to Victor Stepanenko (step
 * Stepanenko, V., Jöhnk, K. D., Machulskaya, E., Perroud, M., Subin, Z., Nordbo, A., … Mironov, D. (2014). Simulation of surface energy fluxes and stratification of a small boreal lake by a set of one-dimensional models. *Tellus, Series A: Dynamic Meteorology and Oceanography*, 66(1). http://doi.org/10.3402/tellusa.v66.21389
 * Stepanenko, V., Mammarella, I., Ojala, A., Miettinen, H., Lykosov, V., & Vesala, T. (2016). LAKE 2.0: a model for temperature, methane, carbon dioxide and oxygen dynamics in lakes. *Geoscientific Model Development*, 9(5), 1977–2006. http://doi.org/10.5194/gmd-9-1977-2016
 * Stepanenko, V. M., Repina, I. A., Ganbat, G., and Davaa, G. Numerical simulation of ice cover of saline lakes (2019). *Izvestiya - Atmospheric and Oceanic Physics*, 55(1):129–138. http://dx.doi.org/10.1134/S0001433819010092
-* V. M. Stepanenko, G. Valerio, and M. Pilotti (2020). Horizontal pressure gradient parameterization for one-dimensional lake models. *JOURNAL OF ADVANCES IN MODELING EARTH SYSTEMS*, 12(2):e2019MS001906, http://dx.doi.org/10.1029/2019ms001906.   
+* V. M. Stepanenko, G. Valerio, and M. Pilotti (2020). Horizontal pressure gradient parameterization for one-dimensional lake models. *JOURNAL OF ADVANCES IN MODELING EARTH SYSTEMS*, 12(2):e2019MS001906, http://dx.doi.org/10.1029/2019ms001906. 
+* V. M. Stepanenko, M. G. Grechushnikova, and I. A. Repina (2022). Numerical simulation of methane emission from an artificial reservoir. *Izvestiya - Atmospheric and Oceanic Physics*, 58(6):649–659. http://dx.doi.org/10.1134/S0001433822060159
 * Thiery, W., Stepanenko, V., Fang, X., Jöhnk, K., Li, Z., Martynov, A., … van Lipzig, N. (2014). LakeMIP Kivu: evaluating the representation of a large, deep tropical lake by a set of one-dimensional lake models. *Tellus, Series A: Dynamic Meteorology and Oceanography*, 66. http://doi.org/doi:10.3402/tellusa.v66.21390
 * Volodina, E., Bengtsson, L., & Lykosov, V. N. (2000). Parameterization of heat and moisture transfer in a snow cover for modelling of seasonal variations of land hydrological cycle. *Russian Meteorology and Hydrology*, (5), 5–14.
+* Wang Mengxiao, Lijuan Wen, Li Zhaoguo, Matti Leppäranta, Victor Stepanenko, Yixin Zhao, Ruijia Niu, Liuyiyi Yang, and Georgiy Kirillin (2022). Mechanisms and effects of under-ice warming water in ngoring lake of qinghai–tibet plateau. The Cryosphere, 16:3635–3648. http://dx.doi.org/10.5194/tc-16-3635-2022
 * Степаненко В.М. (2018) Параметризация сейш для одномерной модели водоёма. *Труды Московского физико-технического института*. том 10, № 1, с. 97-111.
 * В. М. Степаненко, М. Г. Гречушникова, И. А. Репина. Численное моделирование эмиссии метана из водохранилища (2020). *Фундаментальная и прикладная климатология*, 2:76–99. http://dx.doi.org/10.21513/2410-8758-2020-2-76-99