ufs-community · dustinswales · Aug 22, 2023 · Jun 8, 2023 · Jun 9, 2023 · Jun 15, 2023
@@ -28,6 +28,7 @@ module cu_gf_deep
      integer, parameter :: autoconv=1 !2
      integer, parameter :: aeroevap=1 !3
      real(kind=kind_phys), parameter :: scav_factor = 0.5
+
      real(kind=kind_phys), parameter :: dx_thresh = 6500.
 !> still 16 ensembles for clousres
      integer, parameter:: maxens3=16

diff --git a/physics/docs/ccppsrw3_doxyfile b/physics/docs/ccppsrw3_doxyfile
@@ -1,13 +1,176 @@
 %% This BibTeX bibliography file was created using BibDesk.
 %% https://bibdesk.sourceforge.io/
 
-%% Created for Man Zhang at 2022-10-13 16:15:17 -0600 
+%% Created for Man Zhang at 2023-06-28 14:13:48 -0600 
 
 
 %% Saved with string encoding Unicode (UTF-8) 
 
 
 
+@article{Chen_2022,
+	author = {Xiaomin Chen and George H. Bryan and Andrew Hazelton and Frank D. Marks and Pat Fitzpatrick},
+	date-added = {2023-06-28 14:13:19 -0600},
+	date-modified = {2023-06-28 14:13:19 -0600},
+	doi = {10.1175/waf-d-21-0168.1},
+	journal = {Weather and Forecasting},
+	month = {jun},
+	number = {6},
+	pages = {935--951},
+	publisher = {American Meteorological Society},
+	title = {Evaluation and Improvement of a {TKE}-Based Eddy-Diffusivity Mass-Flux ({EDMF}) Planetary Boundary Layer Scheme in Hurricane Conditions},
+	url = {https://doi.org/10.1175%2Fwaf-d-21-0168.1},
+	volume = {37},
+	year = 2022,
+	bdsk-url-1 = {https://doi.org/10.1175%2Fwaf-d-21-0168.1},
+	bdsk-url-2 = {https://doi.org/10.1175/waf-d-21-0168.1}}
+
+@article{Lin_2022,
+	author = {Jialin Lin and Taotao Qian and Peter Bechtold and Georg Grell and Guang J. Zhang and Ping Zhu and Saulo R. Freitas and Hannah Barnes and Jongil Han},
+	date-added = {2023-06-07 10:16:46 -0600},
+	date-modified = {2023-06-07 10:16:46 -0600},
+	doi = {10.1080/07055900.2022.2082915},
+	journal = {Atmosphere-Ocean},
+	month = {jul},
+	number = {3-4},
+	pages = {422--476},
+	publisher = {Informa {UK} Limited},
+	title = {Atmospheric Convection},
+	url = {https://doi.org/10.1080%2F07055900.2022.2082915},
+	volume = {60},
+	year = 2022,
+	bdsk-url-1 = {https://doi.org/10.1080%2F07055900.2022.2082915},
+	bdsk-url-2 = {https://doi.org/10.1080/07055900.2022.2082915}}
+
+@techreport{He_2023,
+	author = {He, Cenlin and Valayamkunnath, Prasanth and Barlage, Michael and Chen, Fei and Gochis, David and Cabell, Ryan and Schneider, Tim and Rasmussen, Roy and Niu, Guo-Yue and Yang, Zong-Liang and Niyogi, Dev and Ek, Michael},
+	date-added = {2023-06-06 12:37:33 -0600},
+	date-modified = {2023-06-06 12:39:16 -0600},
+	doi = {10.5065/EW8G-YR95},
+	publisher = {NCAR/UCAR},
+	title = {The Community Noah-MP Land Surface Modeling System Technical Description Version 5.0},
+	url = {https://opensky.ucar.edu/islandora/object/technotes:599},
+	year = {2023},
+	bdsk-url-1 = {https://opensky.ucar.edu/islandora/object/technotes:599},
+	bdsk-url-2 = {https://doi.org/10.5065/EW8G-YR95}}
+
+@article{Niu_2007,
+	author = {Guo-Yue Niu and Zong-Liang Yang},
+	date-added = {2023-06-05 14:03:26 -0600},
+	date-modified = {2023-06-05 14:03:26 -0600},
+	doi = {10.1029/2007jd008674},
+	journal = {Journal of Geophysical Research},
+	month = {nov},
+	number = {D21},
+	publisher = {American Geophysical Union ({AGU})},
+	title = {An observation-based formulation of snow cover fraction and its evaluation over large North American river basins},
+	url = {https://doi.org/10.1029%2F2007jd008674},
+	volume = {112},
+	year = 2007,
+	bdsk-url-1 = {https://doi.org/10.1029%2F2007jd008674},
+	bdsk-url-2 = {https://doi.org/10.1029/2007jd008674}}
+
+@techreport{Oleson2013,
+	author = {Oleson, Keith and Lawrence, David and Bonan, Gordon and Drewniak, Beth and Huang, Maoyi and Koven, Charles and Levis, Samuel and Li, Fang and Riley, William and Subin, Zachary and Swenson, Sean and Thornton, Peter and Bozbiyik, Anil and Fisher, Rosie and Heald, Colette and Kluzek, Erik and Lamarque, Jean-Francois and Lawrence, Peter and Leung, L and Lipscomb, William and Muszala, Stefan and Ricciuto, Daniel and Sacks, William and Sun, Ying and Tang, Jinyun and Yang, Zong-Liang},
+	date-added = {2023-06-05 09:28:16 -0600},
+	date-modified = {2023-06-05 09:30:30 -0600},
+	doi = {10.5065/D6RR1W7M},
+	keywords = {Land surface model, Climate model, Biogeochemistry, Biogeophysics},
+	language = {en},
+	publisher = {UCAR/NCAR},
+	title = {Technical description of version 4.5 of the Community Land Model (CLM)},
+	url = {http://opensky.ucar.edu/islandora/object/technotes:515},
+	year = {2013},
+	bdsk-url-1 = {http://opensky.ucar.edu/islandora/object/technotes:515},
+	bdsk-url-2 = {https://doi.org/10.5065/D6RR1W7M}}
+
+@article{Kourzeneva_2012,
+	author = {Ekaterina Kourzeneva and Hermann Asensio and Eric Martin and Stephanie Faroux},
+	date-added = {2023-05-30 11:29:07 -0600},
+	date-modified = {2023-05-30 11:29:07 -0600},
+	doi = {10.3402/tellusa.v64i0.15640},
+	journal = {Tellus A: Dynamic Meteorology and Oceanography},
+	month = {dec},
+	number = {1},
+	pages = {15640},
+	publisher = {Stockholm University Press},
+	title = {Global gridded dataset of lake coverage and lake depth for use in numerical weather prediction and climate modelling},
+	url = {https://doi.org/10.3402%2Ftellusa.v64i0.15640},
+	volume = {64},
+	year = 2012,
+	bdsk-url-1 = {https://doi.org/10.3402%2Ftellusa.v64i0.15640},
+	bdsk-url-2 = {https://doi.org/10.3402/tellusa.v64i0.15640}}
+
+@article{Gu2015,
+	abstract = {A one-dimensional (1-D) physically based lake model was coupled to the Weather Research and Forecasting (WRF) model version 3.2 developed by the National Center for Atmospheric Research to dynamically simulate physical processes of lakes and their effects on weather and climate at local and regional scales. Our study area is focused on the Great Lakes. This coupled model realistically reproduces the lake surface temperature (LST) at a buoy station in a shallow lake (Lake Erie) while generating strong LST biases ranging from −20 to 20 {\textdegree}C at a buoy station in a deep lake (Lake Superior). Through many sensitivity tests, we find that the biases in the deep lake LST simulations result from the drastic underestimation of heat transfer between the lower and upper parts of the lake through unrealistic eddy diffusion. Additional tests were made to calibrate the eddy diffusivity in WRF-Lake. It is found that when this parameter is multiplied by a factor ranging from 102 to 105 for various lake depths deeper than 15 m, the LST simulations for the deep lake buoy station show good agreement with observations, and the bias range reduces to {\textpm}4 {\textdegree}C. Essentially, the enlarged eddy diffusivity strengthens heat transfer within the lake columns in the deep lake, which is significantly underestimated in the lake model without calibration. Validation simulations with the calibrated eddy diffusivity were carried out for the whole of Lake Superior and Lake Erie. The LST simulations still have a substantial bias reduction when compared with those produced with the original eddy diffusivity, indicating that the calibrated parameter is representative. In addition, the improved 1-D lake model with WRF reasonably reproduces the remotely sensed LST geographic distribution.},
+	author = {Gu, Hongping and Jin, Jiming and Wu, Yihua and Ek, Michael B. and Subin, Zachary M.},
+	date-added = {2023-05-24 14:45:55 -0600},
+	date-modified = {2023-05-24 14:45:55 -0600},
+	day = {01},
+	doi = {10.1007/s10584-013-0978-y},
+	issn = {1573-1480},
+	journal = {Climatic Change},
+	month = {Apr},
+	number = {3},
+	pages = {471--483},
+	title = {Calibration and validation of lake surface temperature simulations with the coupled WRF-lake model},
+	url = {https://link.springer.com/content/pdf/10.1007/s10584-013-0978-y.pdf},
+	volume = {129},
+	year = {2015},
+	bdsk-url-1 = {https://link.springer.com/content/pdf/10.1007/s10584-013-0978-y.pdf},
+	bdsk-url-2 = {https://doi.org/10.1007/s10584-013-0978-y}}
+
+@article{Subin_2012,
+	author = {Zachary M. Subin and William J. Riley and Dmitrii Mironov},
+	date-added = {2023-05-24 14:35:27 -0600},
+	date-modified = {2023-05-24 14:35:27 -0600},
+	doi = {10.1029/2011ms000072},
+	journal = {Journal of Advances in Modeling Earth Systems},
+	month = {feb},
+	publisher = {American Geophysical Union ({AGU})},
+	title = {An improved lake model for climate simulations: Model structure, evaluation, and sensitivity analyses in {CESM}1},
+	url = {https://doi.org/10.1029%2F2011ms000072},
+	volume = {4},
+	year = 2012,
+	bdsk-url-1 = {https://doi.org/10.1029%2F2011ms000072},
+	bdsk-url-2 = {https://doi.org/10.1029/2011ms000072}}
+
+@article{Lawrence_2019,
+	author = {David M. Lawrence and Rosie A. Fisher and Charles D. Koven and Keith W. Oleson and Sean C. Swenson and Gordon Bonan and Nathan Collier and Bardan Ghimire and Leo van Kampenhout and Daniel Kennedy and Erik Kluzek and Peter J. Lawrence and Fang Li and Hongyi Li and Danica Lombardozzi and William J. Riley and William J. Sacks and Mingjie Shi and Mariana Vertenstein and William R. Wieder and Chonggang Xu and Ashehad A. Ali and Andrew M. Badger and Gautam Bisht and Michiel van den Broeke and Michael A. Brunke and Sean P. Burns and Jonathan Buzan and Martyn Clark and Anthony Craig and Kyla Dahlin and Beth Drewniak and Joshua B. Fisher and Mark Flanner and Andrew M. Fox and Pierre Gentine and Forrest Hoffman and Gretchen Keppel-Aleks and Ryan Knox and Sanjiv Kumar and Jan Lenaerts and L. Ruby Leung and William H. Lipscomb and Yaqiong Lu and Ashutosh Pandey and Jon D. Pelletier and Justin Perket and James T. Randerson and Daniel M. Ricciuto and Benjamin M. Sanderson and Andrew Slater and Zachary M. Subin and Jinyun Tang and R. Quinn Thomas and Maria Val Martin and Xubin Zeng},
+	date-added = {2023-05-24 14:34:12 -0600},
+	date-modified = {2023-05-24 14:34:12 -0600},
+	doi = {10.1029/2018ms001583},
+	journal = {Journal of Advances in Modeling Earth Systems},
+	month = {dec},
+	number = {12},
+	pages = {4245--4287},
+	publisher = {American Geophysical Union ({AGU})},
+	title = {The Community Land Model Version 5: Description of New Features, Benchmarking, and Impact of Forcing Uncertainty},
+	url = {https://doi.org/10.1029%2F2018ms001583},
+	volume = {11},
+	year = 2019,
+	bdsk-url-1 = {https://doi.org/10.1029%2F2018ms001583},
+	bdsk-url-2 = {https://doi.org/10.1029/2018ms001583}}
+
+@article{cite-key,
+	date-added = {2023-05-24 11:18:09 -0600},
+	date-modified = {2023-05-24 11:18:09 -0600}}
+
+@article{gmd-15-6659-2022,
+	author = {Benjamin, S. G. and Smirnova, T. G. and James, E. P. and Anderson, E. J. and Fujisaki-Manome, A. and Kelley, J. G. W. and Mann, G. E. and Gronewold, A. D. and Chu, P. and Kelley, S. G. T.},
+	date-added = {2023-05-24 10:51:47 -0600},
+	date-modified = {2023-05-24 10:51:47 -0600},
+	doi = {10.5194/gmd-15-6659-2022},
+	journal = {Geoscientific Model Development},
+	number = {17},
+	pages = {6659--6676},
+	title = {Inland lake temperature initialization via coupled cycling with atmospheric data assimilation},
+	url = {https://gmd.copernicus.org/articles/15/6659/2022/},
+	volume = {15},
+	year = {2022},
+	bdsk-url-1 = {https://gmd.copernicus.org/articles/15/6659/2022/},
+	bdsk-url-2 = {https://doi.org/10.5194/gmd-15-6659-2022}}
+
 @article{Chaboureau_2005,
 	author = {Jean-Pierre Chaboureau},
 	date-added = {2022-10-13 16:14:54 -0600},
@@ -3663,6 +3826,18 @@ @article{tsiringakis_et_al_2017
 	year = {2017},
 	bdsk-url-1 = {https://doi.org/10.1002/qj.3021}}
 
+@article{sturm_1997,
+	author = {Sturm, Matthew and Holmgren, Jon and K{\"o}nig, Max and Morris, Kim},
+	doi = {10.3189/S0022143000002781},
+	journal = {Journal of Glaciology},
+	number = {143},
+	pages = {26--41},
+	publisher = {Cambridge University Press},
+	title = {The thermal conductivity of seasonal snow},
+	volume = {43},
+	year = {1997},
+	bdsk-url-1 = {https://doi.org/10.3189/S0022143000002781}}
+
 @comment{BibDesk Static Groups{
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">

@@ -0,0 +1,59 @@
+/**
+\page CLM_LAKE_model CLM Lake Model 
+\section des_clmlake  Description
+
+The Community Land Model (CLM) lake model is a multi-level one-dimensional lake model that has been implemented within the operational 3-km HRRR and
+13-km RAP for small lakes (Benjamin et al. (2022) \cite gmd-15-6659-2022). It is the Community Land Model, version 4.5. 
+Subin et al. (2012) \cite Subin_2012 describe the  1-d CLM lake model as applied within the Community Earth System
+Model (CESM) as a component of the overall CESM CLM (Lawrence et al. (2019) \cite Lawrence_2019). Gu et al. (2015) \cite Gu2015 
+describe the introduction of the CLM lake model into the WRF model and inital experiments using its 1-d solution for both
+lakes Superior (average depth of 147 m) and Erie (average depth of 19 m).
+
+The atmospheric inputs into the model are temperature, water vapor, horizontal wind components from the lowest atmospheric level
+and short-wave and longwave radiative fluxes. The CLM lake model then provides latent heat and sensible heat fluxes back to the 
+atmosphere. It also computes 2-m temperature/moisture, skin temperature, lake temperature, ice fraction, ice thickness, snow water
+equivalent and snow depth. The CLM lake model divides the vertical lake profile into 10 layers driven by wind-driven eddies. The
+thickness of the top layer is fixed to 10-cm and the rest of the lake depth is divided evenly into the other 9 layers. Energy
+transfer (heat and kinetic energy) occurs between lake layers via eddy and molecular diffusion as a function of the vertical 
+temperature gradient. The CLM lake model also uses a 10-layer soil model beneath the lake, a multi-layer ice formation model and
+up to 5-layer snow-on-ice model. Multiple layers in lake model have the potential to better represent vertical mixing processes 
+in the lake.
+
+Testing of the CLM lake model within RAP/HRRR applications showed computational efficiency of the model with no change of even
+0.1% in run time. The lake/snow variables have to be continuously transfered within the CLM lake model from one forecast to another,
+constrained by the atmospheric data assimilation. The lake-cycling initialization in RAP/HRRR has been effective overall, owing to 
+accurate houly estimates of near-surface temperature, moisture and winds, and shortwave and longwave estimates provided to the 1-d CLM
+lake model every time step (Benjamin et al. (2022) \cite gmd-15-6659-2022). Cycling technique showed improvements over initializing
+lake temperatures from the SST analysis, problematic for small water bodies. The improvements are particularly eminent during transition 
+periods between cold and warm seasons, and in the regions with anomalies in weather conditions. The CLM lake model has the potential 
+to improve surface prediction in the vicinity of small lakes.
+
+The CLM lake model requires bathymetry for the lake points in the model domain. Grid points are assigned as lake points when the 
+fraction of lake coverage in the grid cell exceeds 50% and when this point is disconnected from oceans. The lake water mask is 
+therefore binary, set to either 1 or 0. This binary approach for models with higher horizontal resolution, for example, 3-km resolution in 
+in the UFS SRW App, is capable of capturing the effect of lakes on regional heat and moisture fluxes.
+
+Lake depths for the RRFS lake configuration (Fig.1) are assigned from a global dataset provided by Kourzeneva et al.(2012) \cite Kourzeneva_2012,
+this dataset is referred to as GLOBv3 bathymetry in the UFS_UTL.
+
+@image html https://user-images.githubusercontent.com/12705538/250180794-76af93a2-a7ba-4e9a-9478-5657198862b8.png "Figure 1: Lake depths for lakes in the 3-km RRFS domain." width=600
+
+To cold-start the CLM lake model in the UFS SRW App:
+- Use the CLM option in the input.nml
+\n  - lkm = 1
+\n  - iopt_lake = 2
+- Lake temperature is initialized from interpolation between SST at the surface and \f$-4^oC\f$ at 50-m depth
+\n  - A special case is for the Great Salt Lake, the temperature is limited with +/- 3 K from the bi-weekly climatology
+- Temperature for soil under the lake is initialized from bottom lake temperature at the top to the substrate soil temperature at the bottom of soil layer
+- Lake ice at the top level is initialized from the GFS ice concentration
+
+The differences of surface variables from the experimental RRFS 6-h forecast with/without CLM lake model are shown in Figure 2 for 2-m temperature and in Figure 3 for 2-m dewpoint.
+@image html https://user-images.githubusercontent.com/12705538/250180790-63159300-33f6-4b34-9e9c-b65885213c30.png "Figure 2: Differences of 2-m temperature between the RRFS coupled to the CLM model and the RRFS without CLM." width=600
+@image html https://user-images.githubusercontent.com/12705538/250180787-8fc9a820-5f80-4f06-b50a-88b2d20ebc53.png "Figure 3: Differences of 2-m dew point between the RRFS coupled to the CLM model and the RRFS without CLM." width=600
+
+
+
+\section intra_clmlake Intraphysics Communication
+- \ref arg_table_clm_lake_run
+
+*/