Merge branch 'main' into 499

NCAR · Oct 5, 2023 · a8b7d3b · a8b7d3b
2 parents 91bb7c8 + 689317f
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -11,3 +11,7 @@ build:
 
 sphinx:
   configuration: conf.py
+
+python:
+  install:
+  - requirements: guide/requirements.txt
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -22,6 +22,20 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**October 5 2023 :: WRF-DART tutorial diagnostic section. Tag v10.8.5**
+
+- Improvements:
+
+  - Added a more complete diagnostics section to the WRF-DART Tutorial.
+  - Developer test for Mersenne twister random number generator.
+
+- Bug-fix: 
+
+  - 1D location subsetting fixed for obs_sequence_tool.  
+
+   *contributed by Henry Santer*
+
+
 **September 18 2023 :: Fluxnet observation converter and obs_def_rttov13_mod.f90 bug-fixes. Tag v10.8.4**
 
 Fluxnet obs converter:

diff --git a/assimilation_code/programs/obs_sequence_tool/obs_sequence_tool.f90 b/assimilation_code/programs/obs_sequence_tool/obs_sequence_tool.f90
@@ -221,13 +221,13 @@ program obs_sequence_tool
 ! the values if so.  Note that if any of the values are not missing_r8, all of
 ! them must have good (and consistent) values.  i don't have code in here yet
 ! to idiotproof this, but i should add it.
+
+restrict_by_location = .false.
 if ((minval(min_box).ne.missing_r8) .or. (maxval(min_box).ne.missing_r8) .or. &
     (minval(max_box).ne.missing_r8) .or. (maxval(max_box).ne.missing_r8)) then
    restrict_by_location = .true.
    min_loc = set_location(min_box)
    max_loc = set_location(max_box)
-else
-   restrict_by_location = .false.
 endif
 
 ! 3d sphere box check - locations module dependent, but an important one.
@@ -302,8 +302,6 @@ program obs_sequence_tool
    max_box(3) = 0.0_r8
    max_box(4) = -2.0_r8 !! FIXME: VERTISUNDEF, but not all loc mods have it
    max_loc = set_location(max_box)
-else
-   restrict_by_location = .false.
 endif
 
 !%! ! SPECIAL: cut off all GPS obs below the given height

diff --git a/conf.py b/conf.py
@@ -21,7 +21,7 @@
 author = 'Data Assimilation Research Section'
 
 # The full version, including alpha/beta/rc tags
-release = '10.8.4'
+release = '10.8.5'
 root_doc = 'index'
 
 # -- General configuration ---------------------------------------------------

diff --git a/guide/images/WRF_tutorial_evolution1.png b/guide/images/WRF_tutorial_evolution1.png
diff --git a/guide/images/WRF_tutorial_evolution2.png b/guide/images/WRF_tutorial_evolution2.png
diff --git a/guide/images/WRF_tutorial_linkobs1.png b/guide/images/WRF_tutorial_linkobs1.png
diff --git a/guide/images/WRF_tutorial_linkobs2.png b/guide/images/WRF_tutorial_linkobs2.png
diff --git a/guide/images/WRF_tutorial_ncview1.png b/guide/images/WRF_tutorial_ncview1.png
diff --git a/guide/images/WRF_tutorial_ncview2.png b/guide/images/WRF_tutorial_ncview2.png
diff --git a/guide/images/WRF_tutorial_oneline1.png b/guide/images/WRF_tutorial_oneline1.png
diff --git a/guide/images/WRF_tutorial_oneline2.png b/guide/images/WRF_tutorial_oneline2.png
diff --git a/guide/images/WRF_tutorial_profile1.png b/guide/images/WRF_tutorial_profile1.png
diff --git a/guide/images/WRF_tutorial_profile2.png b/guide/images/WRF_tutorial_profile2.png
diff --git a/guide/images/WRF_tutorial_radiosonde_obs.png b/guide/images/WRF_tutorial_radiosonde_obs.png
diff --git a/guide/images/WRF_tutorial_surface_obs.png b/guide/images/WRF_tutorial_surface_obs.png
diff --git a/guide/requirements.txt b/guide/requirements.txt
@@ -0,0 +1,2 @@
+Sphinx==6.2.1
+sphinx-rtd-theme==1.2.2
diff --git a/models/clm/readme.rst b/models/clm/readme.rst
@@ -495,7 +495,7 @@ Inflation has been shown to be quite useful in our experience of
 DA with CLM and DART. The model is strongly influenced by the
 atmospheric forcing and will cause the CLM ensemble to
 relax to a state consistent with the forcing when the assimilation
-stops. [5]_ Depending on the forecast length between assimilations, and 
+stops. Depending on the forecast length between assimilations, and 
 sometimes just to restore the variance lost during an assimilation, 
 inflation should be used.
 
@@ -744,49 +744,49 @@ References
 
 The 
 `CTSM Documentation <https://escomp.github.io/ctsm-docs/versions/master/html/index.html>`__
-is THE reference for CLM.
+is THE reference for CLM. Below are a list of CLM-DART scientific publications:
 
-.. [1] Zhang, Y.-F., T. J. Hoar, Z.-L. Yang, J. L. Anderson, A. M. Toure and M. Rodell, 2014:
+       Zhang, Y.-F., T. J. Hoar, Z.-L. Yang, J. L. Anderson, A. M. Toure and M. Rodell, 2014:
        Assimilation of MODIS snow cover through the Data Assimilation Research Testbed 
        and the Community Land Model version 4.
        *Journal of Geophysical Research: Atmospheres*, **142** 1489-1508, 
        `doi:10.1002/2013JD021329 <https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2013JD021329>`__
 
-.. [2] Lin, P., J. Wei, Z. -L. Yang, Y. Zhang, K. Zhang, 2016:
+       Lin, P., J. Wei, Z. -L. Yang, Y. Zhang, K. Zhang, 2016:
        Snow data assimilation‐constrained land initialization improves seasonal 
        temperature prediction.
        *Geophysical Research Letters* **43** (21), 11,423-11,432
        `doi:10.1002/2016GL070966 <https://doi.org/10.1002/2016GL070966>`__
 
-.. [3] Zhao, L., Z. -L. Yang and T. J. Hoar, 2016:
+       Zhao, L., Z. -L. Yang and T. J. Hoar, 2016:
        Global soil moisture estimation by assimilating AMSR-E brightness temperatures 
        in a coupled CLM4-RTM-DART system.
        *Journal of Hydrometeorology*, **17**, 2431-2454, 
        `doi:10.1175/JHM-D-15-0218.1 <https://doi.org/10.1175/JHM-D-15-0218.1>`__
 
-.. [4] Kwon, Y., Z. -L. Yang, T. J. Hoar and A. M. Toure, 2017:
+       Kwon, Y., Z. -L. Yang, T. J. Hoar and A. M. Toure, 2017:
        Improving the radiance assimilation performance in estimating snow water storage across 
        snow and land-cover types in North America.
        *Journal of Hydrometeorology*, **18**, 651-668, 
        `doi:10.1175/JHM-D-16-0102.1 <https://doi.org/10.1175/JHM-D-16-0102.1>`__
 
-.. [5]  Fox, A. M., Hoar, T. J., Anderson, J. L., Arellano, A. F., Smith, W. K., Litvak, M. E., et al., 2018:
+       Fox, A. M., Hoar, T. J., Anderson, J. L., Arellano, A. F., Smith, W. K., Litvak, M. E., et al., 2018:
        Evaluation of a data assimilation system for land surface models using CLM4.5.
        *Journal of Advances in Modeling Earth Systems*, **10**, 2471–2494, 
        `doi.org/10.1029/2018MS001362 <https://doi.org/10.1029/2018MS001362>`__
 
-.. [6] Ling, X. L., Fu, C. B., Yang, Z. L., & Guo, W. D., 2019:
+       Ling, X. L., Fu, C. B., Yang, Z. L., & Guo, W. D., 2019:
        Comparison of different sequential assimilation algorithms for satellite-derived leaf area 
        index using the Data Assimilation Research Testbed (version Lanai).
        *Geoscientific Model Development*, 12(7), 3119-3133. 
        `doi.org/10.5194/gmd-12-3119-2019 <https://doi.org/10.5194/gmd-12-3119-2019>`__
 
-.. [7] Bian, Q., Xu, Z., Zhao, L., Zhang, Y. F., Zheng, H., Shi, C., … & Yang, Z. L., 2019:
+       Bian, Q., Xu, Z., Zhao, L., Zhang, Y. F., Zheng, H., Shi, C., … & Yang, Z. L., 2019:
        Evaluation and intercomparison of multiple snow water equivalent products over the Tibetan Plateau.
        *Journal of Hydrometeorology*, 20(10), 2043-2055. 
        `doi.org/10.1175/JHM-D-19-0011.1 <https://doi.org/10.1175/JHM-D-19-0011.1>`__
 
-.. [8] Raczka, B., Hoar T.J., Duarte H.F., Fox A.M., Anderson J.L., Bowling D.R., & Lin J.C., 2021
+       Raczka, B., Hoar T.J., Duarte H.F., Fox A.M., Anderson J.L., Bowling D.R., & Lin J.C., 2021
        Improving CLM5.0 Biomass and Carbon Exchange across the Western US Using a Data Assimilation System.
        *Journal of Advances in Modeling Earth Systems*, `doi.org/10.1029/2020MS002421 <https://doi.org/10.1029/2020MS002421>`__