Reproducing grudzien2020

[cgrudz]

Re #70 I'm not sure that my new commits made it into my old pull request -- if this is redundant we can kill this request. In any case, I have an updated example for you to take a look at.

[patnr]

I have made the document generation automatic. So please remove all html files listed under "Conflicting files" right below. Also, there is a conflict in dapper/mods/integration.py since I just made some changes there. In order to resolve, pull from upstream, fix conflicts, and push to origin (which will automatically update this PR).

[cgrudz]

I have made the document generation automatic. So please remove all html files listed under "Conflicting files" right below. Also, there is a conflict in dapper/mods/integration.py since I just made some changes there. In order to resolve, pull from upstream, fix conflicts, and push to origin (which will automatically update this PR).

Nice, will do. I have plans to finish off some of this merger today, along with hopefully having time after meetings to build some exercises and further examples. Take a look at the example if you got a chance -- the simulation is looking good, confirming the results of the GMD work.

[patnr]

Noice!

[cgrudz]

Yeah, I think it should be fun to play with some of these time series, especially tuning the amount of stochasticity. It begins to look more and more like a Brownian motion with enough noise, or more like the standard Lorenz 96 in the small noise, there should be some nice exercises to look at in an Jupyter notebook.

[patnr]

I think the model should be named Lorenz96s which lines up logically with the other models

Also, please de-capitalize Grudzien2020. Nobody else gets capitalization :laughing:

[cgrudz]

Hahaha, yeah, I have to wait until I have my own toy model until I get capitalization....

[cgrudz]

Hey, I thought I merged the changes you wanted from integrate, but now I get this commit error dapper/mods/integration.py 94: 18 F821 undefined name 'functools' [

[patnr]

Hey, I thought I merged the changes you wanted from integrate, but now I get this commit error dapper/mods/integration.py 94: 18 F821 undefined name 'functools' [

I's functools somewhere in the file? Line 94?

[cgrudz]

Sorry my bad, incorrectly was merging changes. Let's see how the new pushes look.

[patnr]

The tests are crashing coz it still says L96s in grudzien2020

I'm offline rest of the evening! Will check in tomorrow

[patnr]

Sorry, I am on holiday and am not active. How's this looking? AFAICT there's still some suggested changes and comments have not been addressed.

[cgrudz]

No worries, getting back to finishing some of this off tomorrow, just juggling this with finishing off some other loose ends.

On 7/25/21 4:31 AM, Patrick N. Raanes wrote:

Sorry, I am on holiday and am not active. How's this looking? AFAICT there's still some suggested changes and comments have not been addressed.

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[patnr]

Apart from the suggested changes in rk4 everything looks great now.

[patnr]

I just upgraded the documentation for setup quite a bit. Please have a look.

Also added to bib.py, unfortunately causing conflict. Please pull, resolve, push.

I also think you should mainly build on basic_2, not basic_3. Because although basic_3 illustrates the use of setup it also contains other complications. So start with basic_2. Use a simple for-loop to generate several xps, not the methods shown in basic_3. Sorry I don't have time right now to look in more detail.

[cgrudz]

Don't worry, I'm probably not going to touch this again this week -- most of the template for the replication based on basic_3 is already done though, I just need to make some plotting scripts.

On 7/28/21 5:07 AM, Patrick N. Raanes wrote:

I just upgraded the documentation for |setup| https://nansencenter.github.io/DAPPER/dapper/xp_launch.html#dapper.xp_launch.run_experiment quite a bit. Please have a look.

Also added to |bib.py|, unfortunately causing conflict. Please pull, resolve, push.

I also think you should mainly build on |basic_2|, not |basic_3|. Because although |basic_3| illustrates the use of |setup| it also contains other complications. So start with |basic_2|. Use a simple for-loop to generate several |xp|s, not the methods shown in |basic_3|. Sorry I don't have time right now to look in more detail.

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[patnr]

Yeah, it just seems to me like there might be some confusion still, and it is much easier to consult on this when the script follows the template of basic_2, without the complications of basic_3. Maybe just stash the plotting stuff for later?

[cgrudz]

No worries, I had meetings cancelled and had extra time today, got this debugged and fully reproducing results from the manuscript now.  The README is updated accordingly, along with some additional references that I think are useful... including my own Julia code base hehehe.  I'll work on plotting probably next week.

On 7/28/21 10:39 AM, Patrick N. Raanes wrote:

Yeah, it just seems to me like there might be some confusion still, and it is much easier to consult on this when the script follows the template of |basic_2|, without the complications of |basic_3|. Maybe just stash the plotting stuff for later?

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[cgrudz]

Will probably spend some time on plotting scripts later this week, minor changes have addressed items above. If you have any extra docs or comments to push to the plotting example based on basic 3, let me know, otherwise I'll just try tinkering with this more.

[cgrudz]

In fact, I'm getting bogged down a bit on the plotting code, I'm thinking to remove the draft that I have currently, push the change and go for a merger of branches for now. Does that sound good? I'll get back to this again shortly but I'll need a bit of lead time as I'm prepping for the semester.