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Python script for modifying fsurdat files (after they have been generated with the tool-chain) #1448
Commits on Jul 21, 2021
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Commits on Aug 13, 2021
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Moved fsurdat_modifier.py to /python/ctsm and created wrapper script
...following yesterday's ctsm python organization meeting with Bill, Erik, and Negin.
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Commits on Sep 17, 2021
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Continued reorganization of scripts in this PR
...according to mtgs with Bill, Erik, and Negin. Here I moved the ModifyFsurdat class out of fsurdat_modifier.py into its own file and placed both those files in a new directory: /python/ctsm/modify_fsurdat
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Commits on Sep 19, 2021
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Commits on Sep 20, 2021
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Commits on Sep 21, 2021
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Also replacing default fsurdat_in and fsurdat_out to work with this test: SMS_D_Ld1.f10_f10_mg37.I1850Clm50Sp.cheyenne_intel.clm-collapse_pfts_78_to_16_decStart_f10 although ultimately we plan to remove these defaults.
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Commits on Oct 4, 2021
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Commits on Oct 5, 2021
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Updated the order in which the modify functions are called
This allows potentially overriding variables that may get set by the first function, which identifies a user-defined idealized land swath. I also completed the list of fsurdat variables that I believe need updating in that first function (def land_swath). I still need to address various TODOs.
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Commits on Oct 8, 2021
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Merge tag 'ctsm5.1.dev058' into cssi_1
Change ceta from 450 to 358 for CTSM5.1 See Leo VanKamenhout's work on this in ESCOMP#250. Note, this is used in the PPE work. See van Kampenhout et al. (2017). Turn Medlyn on for PHS off for clm51 and clm50. Make max CO2 partial pressure consistent in Photosynthesis. Change surface datasets to only use 78PFT versions Fix GSSUN and GSSHA history variables so now not just writing missing values. Changes FATES to run with use_nitrif_dentrif=T by default. Change dynlakes test to methane/use_nitrif_=T.
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Adding user options to enter lai, sai, hgt_top, hgt_bot
Reordered function calls again to what makes sense to me right now
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Correction to get fsurdat_out to work correctly in CTSM test
Testing with SMS_D_Ld1.f10_f10_mg37.I1850Clm50Sp.cheyenne_intel.clm-collapse_pfts_78_to_16_decStart_f10
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Commits on Oct 11, 2021
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Updating function that sets variables in user-specified rectangle
For explanation see github post after this commit
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Commits on Oct 14, 2021
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Use True/False rectangle instead of lon/lat ranges to define rectangle
Work in progress. Nevertheless, the code runs and the CTSM test SMS_D_Ld1.f10_f10_mg37.I1850Clm50Sp.cheyenne_intel.clm-collapse_pfts_78_to_16_decStart_f10 passes.
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Commits on Oct 15, 2021
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Use configparser instead of argparse
A few other small modifications. Python code runs and this test SMS_D_Ld1.f10_f10_mg37.I1850Clm50Sp.cheyenne_intel.clm-collapse_pfts_78_to_16_decStart_f10 passes.
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Commits on Oct 16, 2021
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Introduce user-defined idealized option
If True, then most fsurdat variables get modified, some with user-selected values and some with default settings. If False, then only user-selected variables change; other fsurdat variables remain unchanged.
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Commits on Oct 27, 2021
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Commits on Oct 28, 2021
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Remove obsolete get_config_value from lilac_make_runtime_inputs.py
...because I placed it in utils.py in an earlier commit.
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Commits on Oct 29, 2021
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Changed self.file to self._file and stopped initializing 4D vars to 0
Still setting the 4D vars (lai, sai, and hgts) to 0 when dom_nat_pft = 0 (bare ground).
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Use getboolean inst. of get_config_value for booleans
Also now reading .cfg file's section name(s) on the fly.
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Trying getfloat inst. of get_config_value for the lat/lon arguments
As far as I can tell, this simplifies without loss of functionality.
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Commits on Oct 30, 2021
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Add return to def _get_not_rectangle; remove more lead. underscores
Code didn't work correctly without the return statmt. Removed leading underscores from _file and _not_rectangle bc I use them outside of the class, ie they are not private.
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Merge tag 'ctsm5.1.dev061' into cssi_1
Changes needed to get aux history output with cmeps These changes are needed to create auxiliary land history files when the new cmeps configuration variable is set to true. histaux_l2x1yrg = .true. The changes needed in CTSM enable lnd2glc fields to be sent to the mediator even if glc is not present - based on querying the histaux_l2x1yrg setting. This includes a related change to set most lnd -> mediator fields to spval over ocean, instead of sending zero values over ocean.
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Commits on Oct 31, 2021
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Commits on Nov 1, 2021
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Commits on Nov 2, 2021
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Early draft of test_sys_fsurdat_modifier.py
Currently gives errors: - No such file or directory: 'rm ../tools/modify_fsurdat/test_modify.nc' - No such file or directory: 'rm ../tools/modify_fsurdat/test_modify_minimal.nc'
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Commits on Nov 10, 2021
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Early updates to test_sys_fsurdat_modifier.py
Does not do much, yet, but runs successfully
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Commits on Nov 11, 2021
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Drafts of sys test minimal and sys test all that work
sys test all not entirely done
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Commits on Nov 17, 2021
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Reduce repetition when calling set_lai_sai_hgts
Also add @staticmethod before def _get_not_rectangle. These changes were pending before Bill's latest code review.
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Replace _UNSET with None in lilac_make_runtime_inputs.py
Remove _PLACEHOLDER in same. Add relevant comment in get_config_value's docstring in utils.py.
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Commits on Nov 18, 2021
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Commits on Nov 19, 2021
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Commits on Nov 20, 2021
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Commits on Nov 23, 2021
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Towards getting FSURDATMODIFYCTSM test working
Worked on this commit with Bill
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Commits on Nov 24, 2021
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Commits on Nov 29, 2021
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Replace prepare_cfg_file w _create_config_file in test_sys_fsurdat_mo...
Followed the approach used in cime_config/SystemTests/fsurdatmodifyctsm.py that creates cfg files starting from the pre-existing modify_template.cfg rather than requiring separate pre-existing .cfg files for every test
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Change setvar functions to expect unstructured rather than gridded data
In the process I updated function zero_nonveg to operate on the rectangle (as all the other functions) rather than on the whole domain. Doing so makes this function redundant if idealized = True, so I removed it from the system test test_allInfo at this time.
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Commits on Nov 30, 2021
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Run fsurdat_modifier via an appropriate python version on cheyenne
Thanks to Brian Vanderwende in CISL for guidance on this. This is still a bit of a kludge, and is hard-coded for cheyenne, but at least it seems to work for now.
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Commits on Dec 1, 2021
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Merge pull request #3 from billsacks/cssi_1
Run fsurdat_modifier via an appropriate python version on cheyenne
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Merge remote-tracking branch 'slevisconsulting/cssi_1' into cssi_1
Gets Bill's mods to cime_config/SystemTests/fsurdatmodifyctsm.py as recommended by Brian Vanderwende
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Correction to bypass recent error documented by Bill
Not all fsurdat files contain the variable F0, so I removed this variable from the list of variables modified by fsurdat_modify
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Commits on Dec 3, 2021
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Commits on Dec 4, 2021
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Merge pull request #4 from billsacks/nc_via_lfs
Store netCDF files via Git LFS
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Commits on Dec 6, 2021
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Add unit tests for _handle_config_value
...plus corrected a couple of typos
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Commits on Dec 7, 2021
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Commits on Dec 8, 2021
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Commits on Dec 9, 2021
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Add FSURDATMODIFYCTSM test to aux_clm tests
FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.cheyenne_intel
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Renamed file and corresponding class to TestModifyFsurdat
...instead of TestFsurdatModifier
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Move _handle_config_value tests to test_unit_utils.py
...from test_unit_modify_fsurdat.py and add to them is_list = False test. Also break up lonRange0To360 tests to a test per case.
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In array comparisons, replace self.assertTrue logic w np.array_equal
...or np.any(np.not_equal(arr1, arr2))
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Commits on Dec 10, 2021
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Merge remote-tracking branch 'escomp/master' into cssi_1
Resolved conflicts: cime_config/testdefs/testlist_clm.xml doc/ChangeLog doc/ChangeSum
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For test_sys_fsurdat_modifier: use a python call rather than subprocess
I don't think it makes a huge difference either way, but I see some advantages to calling inline: - It makes the tests run faster - I think we'll be able to get more useful error messages and easier debugging in some situations - It allows us to suppress output, so that the unit test output remains clean and easy to read through This is consistent with how we do it for test_sys_lilac_build_ctsm; I think it's good to maintain consistency in this respect.
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Commits on Dec 11, 2021
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Was missusing np.array_equal and np.not_equal as assertions. Also I was checking for not_equal (at least I thought I was) in a few places when I should have been checking for equal. I think I got them right now.
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Commits on Dec 13, 2021
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Add an __init__.py file in modify_fsurdat
This is needed for pylint to run on the files in this directory
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Commits on Dec 14, 2021
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Add a new clm_pymods test suite that is a subset of aux_clm
This test suite will include tests that are potentially impacted by changes in the python directory, and so should be run whenever making a tag that changes the python code, even if no Fortran code is changed.
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