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Tracer advection #262

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wants to merge 55 commits into from
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Tracer advection #262

wants to merge 55 commits into from

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fairaque1999
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Description:

Added a new tracer advection model based on the Lorenz-96 using a Semi-Lagrangian scheme.

Fixes issue

Types of changes

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • Documentation update

Documentation changes needed?

  • My change requires a change to the documentation.
    • I have updated the documentation accordingly.

Tests

Please describe any tests you ran to verify your changes.

Checklist for merging

  • Updated changelog entry
  • Documentation updated
  • Version tag

Testing Datasets

  • Dataset needed for testing available upon request
  • Dataset download instructions included
  • No dataset needed

hkershaw-brown and others added 17 commits July 1, 2021 14:35
@hkershaw-brown
remove workflow
3fc21d0
@fairaque1999
new lorenz96 model
cf1f795
@hkershaw-brown
changed path_names to lorenz_96_lag
b55b0d0
@fairaque1999
Added the semi-lagrangian tracer lorenz96 model
ba2db08
@hkershaw-brown
compiles
466f4b2
@hkershaw-brown
model size is 120
607a8a7
@fairaque1999
Merge pull request NCAR#1 from NCAR/helen
81b52d3 
Changes for compiling
@fairaque1999
fixed a few bugs to remove shocky behavior and now the lorenz_96_lag …
87424de 
…model assimilations
@fairaque1999
more debugging
f35ad2a
@fairaque1999
indexing fixed in advec_1step, but bug still present
59deae9
@hkershaw-brown
script for running ddt on Cheyenne
3625840 
start the ARM forge client on your machine

Then submit the job with:
qsub submit.sh

You will get a message on your machine when the job  starts
@fairaque1999
more indexing change
e73f177
@fairaque1999
Merge branch 'main' of github.com:NCAR/DART-lorenz96-lag into main
6448edb
@fairaque1999
moved submit.sh
3d55711
@fairaque1999
rewrote indexing in advec_1step. Seems to have fixed the tracer problem
dcd9df4
@fairaque1999
rewrote indexing in advec_1step. Seems to have fixed the tracer problem
e8786a8
@fairaque1999
Lorenz_96_lag works and perturbs all variables. New source perturbati…
154d840 
…on added

Working model lorenz 96 lag with source perturbation

Squashed commits
@hkershaw-brown
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hkershaw-brown commented Aug 3, 2021 •
edited
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To do list:

  • revert any unnecessary changed/deleted/new files. For example everything in models/lorenz_96
    • models/lorenz_96
    • models/simple_advection
    • models/lorenz_96_tracer_advection/tests
  • change model name: directory, diagnostic scripts. I believe the name is "lorenz_96_tracer_advection".
  • write a model_mod.rst

hkershaw-brown
hkershaw-brown reviewed Aug 18, 2021
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models/lorenz_96_tracer_advection/readme.rst

For Lorenz 96 Tracer Advection, DART advances the model, gets the model state and metadata describing this state, finds state variables that are close to a given location, and does spatial interpolation for model state variables.

The Lorenz 96 Tracer Advection model has a ``work/workshop_setup.csh`` script that compiles and
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Is this true? Does workshop_setup.csh work for lorenz_96_tracer_advection?

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no

@hkershaw-brown
Makefile is created by mkmf
b3b8f7b 
should not be under version control
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hkershaw-brown commented Aug 18, 2021 •
edited
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Notes:

  • shell_scripts directory - do these scripts work? remove the shell scripts directory removed https://github.com/NCAR/DART/tree/tracer_advection_siparcs
  • mkmfs - remove svn info (Helen do this done.)
  • There are some giant obs_seq.in files - I don't think these need to be in the repo.
  • The input/output_file_list does not match where the input files are. I don't think it is worth having the list, since there is one input file, one output file. The input file and output file are set in the namelist at the moment.
  • The readme.rst has some lornez_96 info
  • remove jupyter notebook file.
  • check netcdf files, various files are lorenz_96. Probably should create required netcdf files in quickbuild from .cdl file
  • Check the model runs on multiple processors
 ./quickbuild.csh -mpi 
mpirun -n 2 ./filter
  • Check model size option (how does this work with template.nc)

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Hello,

I'm updating this branch with the latest changes from main.

If this affects anything you are running for AGU, you can get the branch before the update from main by checkout out this commit:
85cf01f

Or, there is a backup of the branch you can checkout without the new changes from main from here:
https://github.com/hkershaw-brown/DART/tree/tracer_advection

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hkershaw-brown commented Dec 8, 2021 •
edited
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note for reviewers,

There are some large files in this branch (as of Dec 7 2021). These should not end up on main.

remote: Resolving deltas: 100% (467/467), completed with 66 local objects.
remote: warning: See http://git.io/iEPt8g for more information.
remote: warning: File models/lorenz_96_lag/work/obs_seq.final is 55.24 MB; this is larger than GitHub's recommended maximum file size of 50.00 MB
remote: warning: File models/lorenz_96_lag/work/obs_seq.final is 55.24 MB; this is larger than GitHub's recommended maximum file size of 50.00 MB
remote: warning: File models/lorenz_96_tracer_advection/work/obs_seq_state_tracer.in is 57.98 MB; this is larger than GitHub's recommended maximum file size of 50.00 MB
remote: warning: File models/lorenz_96_lag/work/obs_seq.final is 55.24 MB; this is larger than GitHub's recommended maximum file size of 50.00 MB
remote: warning: GH001: Large files detected. You may want to try Git Large File Storage - https://git-lfs.github.com.
remote:

nancycollins
nancycollins reviewed Dec 8, 2021
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i haven't yet tried running any of these cases (i will soon) but i'm filing review comments for the code i have looked at.

models/lorenz_96_tracer_advection/matlab/RunAllTests.m Show resolved Hide resolved
models/lorenz_96_tracer_advection/work/mkmf_closest_member_tool Show resolved Hide resolved
models/lorenz_96_tracer_advection/work/mkmf_closest_member_tool Show resolved Hide resolved
models/lorenz_96_tracer_advection/work/mkmf_create_fixed_network_seq Show resolved Hide resolved
models/lorenz_96_tracer_advection/work/mkmf_create_fixed_network_seq Show resolved Hide resolved
models/lorenz_96_tracer_advection/shell_scripts/run_filter_async4.csh Show resolved Hide resolved
models/lorenz_96_tracer_advection/shell_scripts/run_filter.lynx.sh Show resolved Hide resolved
models/lorenz_96_tracer_advection/shell_scripts/advance_model.csh Show resolved Hide resolved
models/lorenz_96_tracer_advection/shell_scripts/README Show resolved Hide resolved
diagnostics/matlab/plot_ens_err_spread.m Show resolved Hide resolved
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Hello, I have moved Ishraque's work to the branch https://github.com/NCAR/DART/tree/tracer_advection_siparcs

I think I have addressed Nancy comments and only moved the stuff that is needed. (leaving Ishrques large file and files that were copied wholesale from lorenz_96). 3ce7a74
Added Jeff's interpolate bug fix.

Closing this pull request, and will shortly open a pull request with tracer_advection_siparcs

@hkershaw-brown hkershaw-brown mentioned this pull request Jan 6, 2022
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@fairaque1999 @hkershaw-brown @nancycollins