UFS-SRW v3.0.0 SciDoc updates

physics/cu_gf_deep.F90

@@ -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

physics/docs/ccpp_doxyfile

@@ -115,7 +115,7 @@ WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 
 INPUT                  =  pdftxt/mainpage.txt              \
-                          pdftxt/all_shemes_list.txt     \
+                          pdftxt/all_schemes_list.txt     \
                           pdftxt/GFS_v16_suite.txt       \
                           pdftxt/GFS_v17_p8_suite.txt    \
                           pdftxt/RAP_suite.txt           \

physics/docs/ccppsrw_doxyfile

@@ -1,8 +1,8 @@
 # Doxyfile 1.9.3
 
 DOXYFILE_ENCODING      = UTF-8
-PROJECT_NAME           = "CCPP Scidoc for SRW v2.1.0"
-PROJECT_NUMBER         = "SRW v2.1.0"
+PROJECT_NAME           = "CCPP SciDoc for UFS-SRW v3.0.0"
+PROJECT_NUMBER         = "SRW v3.0.0"
 PROJECT_BRIEF          = "Common Community Physics Package Developed at DTC"
 PROJECT_LOGO           = img/dtc_logo.png
 OUTPUT_DIRECTORY       = doc
@@ -115,9 +115,10 @@ WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 
 INPUT                  =  pdftxt/SRW_mainpage.txt              \
-                          pdftxt/SRW_all_shemes_list.txt     \
+                          pdftxt/SRW_all_schemes_list.txt     \
                           pdftxt/GFS_v16_suite.txt       \
                           pdftxt/HRRR_suite.txt          \
+                          pdftxt/RAP_suite.txt      \
                           pdftxt/RRFS_v1beta_suite.txt   \
                           pdftxt/WoFS_v0_suite.txt   \
                           pdftxt/RRFS_SGSCLOUD.txt       \
@@ -144,6 +145,7 @@ INPUT                  =  pdftxt/SRW_mainpage.txt              \
                           pdftxt/RUCLSM.txt          \
                           pdftxt/THOMPSON.txt        \
                           pdftxt/suite_input.nml.txt    \
+                          pdftxt/CLM_LAKE.txt     \
                           pdftxt/GFS_SPP.txt     \
                         ../fv_sat_adj.F90    \
                         ../GFS_time_vary_pre.fv3.F90 \
@@ -206,6 +208,7 @@ INPUT                  =  pdftxt/SRW_mainpage.txt              \
                         ../sfc_nst_pre.f              \
                         ../sfc_nst_post.f             \
                         ../sfc_ocean.F                \
+                        ../clm_lake.f90              \
                         ../module_nst_model.f90       \
                         ../module_nst_parameters.f90  \
                         ../module_nst_water_prop.f90  \
@@ -283,7 +286,6 @@ INPUT                  =  pdftxt/SRW_mainpage.txt              \
                         ../mp_nssl.F90        \
                         ../module_mp_nssl_2mom.F90    \
                         ../funcphys.f90     \
-                        ../physparam.f      \
                         ../physcons.F90     \
                         ../radcons.f90      \
                         ../mersenne_twister.f \
@@ -302,7 +304,7 @@ EXCLUDE                =
 EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       =
 EXCLUDE_SYMBOLS        =
-EXAMPLE_PATH           = pdftxt/RE210 \
+EXAMPLE_PATH           = pdftxt/RE300 \
                          doc/html
 EXAMPLE_PATTERNS       = 
 EXAMPLE_RECURSIVE      = NO
@@ -540,7 +542,7 @@ DIRECTORY_GRAPH        = YES
 DIR_GRAPH_MAX_DEPTH    = 1
 DOT_IMAGE_FORMAT       = SVG
 INTERACTIVE_SVG        = NO
-DOT_PATH               = 
+DOT_PATH               =
 DOTFILE_DIRS           =
 MSCFILE_DIRS           =
 DIAFILE_DIRS           =

physics/docs/library.bib

@@ -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}}
+
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