[MITgcm-support] {Disarmed} Re: Re: MITgcm-support Digest, Vol 247, Issue 1

Tue Jan 9 19:15:27 EST 2024

Hi Martin,

Thank you so much; that's clarified a lot of things for me. Can I ask a few follow-up questions? 3 small clarifying ones, and 1 further advice one (much appreciated).

(1) I misunderstood that data.cal's "startDate1" corresponded to nIter0=0, instead of just nIter0. Can I just check that that's correct? See the documentation that says: "Note that the first record read and used by the EXF package corresponds to the value ’startDate1’ set in data.cal." (https://mitgcm.readthedocs.io/en/latest/phys_pkgs/exf.html#compile-time-options)

(2) I also missed that MITgcm interpolated between records provided in T_air.bin! Would that maybe explain why I was getting an error "lib-4016 : UNRECOVERABLE library error.   A READ operation tried to read a nonexistent record (1002)." in a 1000yr long run? (However, my T_air.bin file in that case was 1001 records long, so I'm still not sure what the problem is.

(3) Also didn't know about "repeatPeriod" in &EXF_NML_01 of data.exf - thank you!! This will likely do exactly what I want to do. So if I set this to 31104000000.0 (1000yr in seconds) and set atempperiod = 31104000.0 (360 days in seconds) and have all other exf periods set as 0, does MITgcm know that that repeatPeriod parameter should only be applied to T_air.bin and won't throw an error? (And in this scenario, the T_air input file doesn't need an additional entry like you mentioned, correct?)

(4) Do you have any advice for running a simulation with time-varying T_air whose period is greater than 1000yr, given that I run simulations that last 1000 years, one after another, continuing on from pickup files. Say I want T_air with a periodicity of 10,000yr. And my simulation will be something like 20 or 40,000 years in total. I could make 10 separate T_air files to represent years 1-1000, 1001-2000, 2001-3000, and so on to 10,000 when the temp reaches its starting point again, and then just be very careful to just use the correct T_air file with each simulation. But there must be an easier way than this? (However your method of making use of the "repeatPeriod" parameter seems perfect for my experiments where T_air varies with periods of 500yr and 1000yr.)

Thank you so much again, can't say how appreciative I am.
M. Shankle

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Today's Topics:

   1. Re: Time-varying forcing and EXF package (Martin Losch)
   2. Re: MITgcm: Mixing in Vermix Experiment (Martin Losch)

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Message: 1
Date: Fri, 5 Jan 2024 10:05:41 +0100
From: Martin Losch <Martin.Losch at awi.de>
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] Time-varying forcing and EXF package
Message-ID: <53EEB5FE-584D-4936-B328-9391AB856B7D at awi.de>
Content-Type: text/plain; charset="utf-8"

Hi Madison,

startDate_1/2 ind data.cal specify the point in time to which nIter0=0 refers (interally this is called baseTime), so with your data.cal, your year has 360days (TheCalendar=?model?), where nIter0=0 refers to Jan01,39500,0:00 (assuming that startdate_2=000000). Alternatively you could set the startDate to 00010101 and for your pickup in year 39500 use an nIter0 that corresponds to this year, ie. 39500/deltaTclock

All constant-in-time forcing fields need to have a ?period? of 0. (e.g. ?uwindperiod=0.?). I am not sure if you need a startDate for those, but it wouldn?t hurt.
For your time varying forcing your setting says (again assuming atempstartdate2=000000), that the first record in the forcing file T_air.bin is on Jan01,39500,0:00, the second on Jan01,39501,0:00, etc, and the model interpolates bi-linearily between them. I don?t know about the details of your experiment, but you may want to shift this start time to the middle of the year (and then you?d need an additional record for year0-1 for the bilinear interpolation, but see below for an easy way out).

You can also set a repeat period, e.g. for your 1000 y file:

 repeatPeriod = 31104000000.0, ( 86400*360*1000 )

in &EXF_NML_01 to make the model start again with the first record, if it goes beyond 1000ys. So in the ?scenario? where your nIter0=39500/deltaTclock, you could use atempstartdate1=00010101 with repeatPeriod = 31104000000.0,

If your cycle is only 500y, then you could get away with a shorter forcing file and a repeatPeriod of 500y.

Hope that helps,

Martin

> On 30. Dec 2023, at 20:15, Madison Shankle <mgs23 at st-andrews.ac.uk> wrote:
>
> Dear all,
>
> Seeking help setting up time-varying forcing. I unfortunately can't submit jobs at the moment, so apologies for not doing more troubleshooting on my own, but at present it would be very helpful to just have my understanding of a few key parameters checked.
>
> Background: I have a time-varying T_air.bin forcing file (dimensions nTime, nY, nX = 1000, 140, 72) where the time dimension consists of annual air temp profiles (so the entire file represents a 1000yr-long record, that varies in time). All other forcing files are kept constant. T_air varies cyclically with a periodicity of 500yr, so two cycles are contained in T_air.bin. (I made the file 1000yrs long as I typically run my simulations for 1000yrs at a time, which takes about 24hr, and I can start the next simulation the next day.)
>
> Is my understanding of the following  parameters correct, and are there any other parameters to be changed that I have missed out?
>
> data.exf
> --> atempstartdate1 = 395000101
> --> atempperiod = 31104000
> Here "atempstartdate1" specifies that I have read in a T_air.bin file whose record starts on Jan 1, year 39500. (I am starting my simulations off of a previous study's output, which ran ~32000yr, from which it then took an additional ~7000yr to spin-up my simulations on ARCHER2 with some slight edits to the model configuration. So, with my model configuration properly spun up, I'm now ready to start the experimental (time-varying temp) simulation at year 39500).
>
> data.cal
> --> TheCalendar = 'model'
> --> startDate1 = 395000101
> Here "startDate1" tells the model which record to read first from T_air.bin. At this point, I can say that my 1000yr-long T_air record starts at 395000 (in data.exf) and this parameter tells the model to start reading from that first time step. So, I was planning on just updating these two parameters each time I start a new 1000yr-long run (e.g. to 40500, 41500, 42500, etc. each time I start a new run). However, I suppose I could also simply write a 40,000yr-long T_air file (40000,ny,nx) (as my goal is to run my simulation this long), in which case I could leave atempstartdate1 as 395000101, and only have to update data.cal's startDate1 parameter with each new model run.
>
>
> Is that all correct and am I missing anything else that would need to be changed to set up a time-varying run? Apologies again; I nearly got this working before the holidays but as I said can't submit jobs at the moment, so making some progress by getting feedback from this group while I sort that out would be very appreciated.
>
> Thanks and best wishes for the new year,
> M. Shankle
>
>
>
>
>
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Message: 2
Date: Fri, 5 Jan 2024 11:20:34 +0100
From: Martin Losch <Martin.Losch at awi.de>
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] MITgcm: Mixing in Vermix Experiment
Message-ID: <AA0AB524-7741-4E47-A198-139023A860C8 at awi.de>
Content-Type: text/plain; charset="utf-8"

Hi Martin,

currently ?RiLimit? is not a namelist of pkg/pp81. You can just add it in pp81_readparms.F

Similarly you could add a RiMax to the namelist defined in my82_readparms.F

In either case I do not know if modifying these parameters makes physical sense, as they are hard coded in the original implementations (I think it was SPEM a predecessor of ROMS) from which the MITgcm versions are derived.

Martin

> On 4. Dec 2023, at 18:17, Martin COUBARD <martin.coubard at imt-atlantique.net> wrote:
>
> Hello MITGCM Users,
>  I am implementing the vermix experiment available on Github (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMITgcm%2FMITgcm%2Ftree%2Fmaster%2Fverification%2Fvermix&data=05%7C02%7Cmgs23%40st-andrews.ac.uk%7C4cd314c936914946bbd808dc0e0fd17c%7Cf85626cb0da849d3aa5864ef678ef01a%7C0%7C0%7C638400709577522679%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C62000%7C%7C%7C&sdata=m3zNzYYdup3%2FKK4WUTIOa8Ys3O2FeUPWVM1C8QjFW0A%3D&reserved=0<https://github.com/MITgcm/MITgcm/tree/master/verification/vermix>) and https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmitgcm.readthedocs.io%2Fen%2Flatest%2Fexamples%2Fexamples.html&data=05%7C02%7Cmgs23%40st-andrews.ac.uk%7C4cd314c936914946bbd808dc0e0fd17c%7Cf85626cb0da849d3aa5864ef678ef01a%7C0%7C0%7C638400709577522679%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C62000%7C%7C%7C&sdata=37rk6oM6U7lgpOdllx7N5uPFj4pZT5WERJxxxNWNox4%3D&reserved=0<https://mitgcm.readthedocs.io/en/latest/examples/examples.html>.
> Everything is running smoothly with the KPP option, and we do see a mixed layer forming over timescales of a few days. Furthermore, a parameter may be tuned to increase/decrease mixing (Rincr, which may be find in data.kpp), which helps tune the model to our expectations.
>  <Capture d?e?cran 2023-12-04 a? 14.59.53.png>
>
> <Capture d?e?cran 2023-12-04 a? 15.13.24.png>
> <Capture d?e?cran 2023-12-04 a? 15.08.17.png>   However, we have a problem when using the PP81 and MY82 packages, when it comes to manipulating mixing. I changed RiMax in data.my82 and RiLimit in data.pp81, but apparently nothing happens when I adjust these values.
> Do you have any suggestions on how to effectively change these parameters and hence control the mixing in PP81 and MY82 packages?
>  <Capture d?e?cran 2023-12-04 a? 15.09.50.png>
>  If any of you can assist me with this, I would greatly appreciate it.
>
> Thank you very much.
>
> Martin Coubard
>
> --
>
> Coubard Martin
> FISE 2A
> 06 68 14 10 95 Technop?le Brest-Iroise
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