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FAQ: Data ocean slab mode (DOCN-SOM)

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dbailey
FAQ: Data ocean slab mode (DOCN-SOM)

I get numerous questions about the new SOM in the data ocean model of CESM. So, I thought it appropriate to add a sort of FAQ here.

1. Why does the SOM mode no longer run out of the box?

Earlier versions were set up with a test SOM forcing file (pop_frc.1x1d.090130.nc) This forcing file was not intended for science purposes and should not be used except in testing. Hence we made the decision to remove a default SOM forcing file from CESM1.1 and onward.

2. How do I set the SOM forcing file?

As long as the forcing file you wish to use is in the standard input directory, i.e. $DIN_LOC_ROOT/ocn/docn7/SOM, then as of CESM 1.1., one simply modifies DOCN_SOM_FILENAME in env_run.xml. The default value of this variable is UNSET. In older versions of the code, this had to be modified in the docn.buildnml.csh script or the docn.stream.txt file.

3. What if my SOM forcing file is in a different directory?

Here you will need to modify the docn.streams.txt file to manually point to the directory you wish. As of CESM 1.1, you can copy $CASEROOT/CaseDocs/docn.streams.txt to $CASEROOT/user_docn.streams.txt and edit it.

4. Do you have some scientifically valid SOM forcing files available?

Yes! These are in the input data repository at:

https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/ocn/docn7/SOM/

For the most part, they are documented as to the run they came from by doing an 'ncdump -h' on the file.

5. Can I create my own SOM forcing file?

Yes! The tools for this are available from the release code repository at:

https://svn-ccsm-release.cgd.ucar.edu/model_versions/cesm1_1_1/models/ocn/docn/tools/pop_som_frc/

We are striving to keep these up to date, but there may still be issues with them. There is a simple README file here with a description of the tools.

6. Can I run the old CAM3 SOM method with gensom?

The short answer is no. This mode is no longer supported in CESM. If you wish to use this technique to generate SOM forcing, we cannot help you.

7. Why can't I run the old CAM3 SOM?

We believe that it is scientifically better to use the new SOM method. We recommend reading the following paper that discusses the old SOM versus the new SOM at:

Bitz et al. 2012, J. Climate, http://journals.ametsoc.org/doi/abs/10.1175/JCLI-D-11-00290.1

Also, there is a white paper on the subject under the CESM DOCN user's guide at:

http://www.cesm.ucar.edu/models/cesm1.1/data8/doc/x362.html

8. What compsets is the DOCN-SOM used in?

The E compset with fully active atmosphere, land, and sea ice components uses the DOCN-SOM component as does the active ice only compset (D).

9. Why do I have to run fully active ice with the SOM?

This is more of a scientific question, but we have found that when computing the sea surface temperature (SST) prognostically as is done in the DOCN-SOM, it is better to use fully active ice with it. One could potentially turn on thermodynamic-only ice by turning off the sea ice dynamics (kdyn = 0), but we do not routinely run that way. Much work has been done over the years stressing the importance of the sea ice dynamics. We do not support prescribed ice mode with the DOCN-SOM. When specifying the sea ice fraction, one must also use specified SST (in an F compset).

10. These did not answer my question:

If you have issues with parts of this, or further questions, you can post something to this forum and we will attempt to address it as soon as possible.

hsiehweichun@...

Thank you for posting instruction of DOCN-SOM. That is very helpful.

I have a question about formulation of qflux calculation.
I found in the white paper qflux is Fnet minus SST tendency term.
However, in Bitz et al. 2012 paper, qflux is calculated as SST tendency term minus Fnet.
So there will be a sign difference from these two calculations. 
I wonder which one we should use when calculating qflux for DOCN-SOM runs?
THank you so much for the reply.

dbailey

I believe the model uses the convention in the white paper. The tool mentioned in the white paper uses the right convention for the model. A version is available through the release repository at:

https://svn-ccsm-release.cgd.ucar.edu/model_versions/cesm1_2_0/models/oc...

Dave

hsiehweichun@...

Hi Dave,

Thank you so much for the reply and info. Finally I got it.

Best,
weichun


sean.m.davis@...

Hi,


We are trying to run E_1850_CN at f19_g16 with CESM 1.2.0, and would like to know which SOM forcing file to use. It looks like the file pop_frc.b.c40.B1850CN.f19_g16.100105.nc might be appropritate, but that file looks to be from an older version of CESM since it was generated back in 2010. Is it appropriate to use a SOM forcing file from a previous version of CESM?

 

Thanks

Sean

huning425@...

Hi Dave,

I had tried to run the CESM1.1.1 E_1850_CAM5_CN compset. I would like to check the SST variable, but I found no output in ".../ocn/hist/" directory. I changed the  "f_sst" in ice_in file to "mxxxx", and find SST variable in the output file in "../ice/hist".
Did this way make sense?

Thanks!

Happiness is when what you think, what you say, and what you do are in harmony.

dbailey

The SST comes out in the CICE history. Have a look in ice/hist. A good way to check the variables as well is to write out coupler history files. Have a look at the user's guide to see how to do this.

Dave

sbshewale@...

hiiii,

I want to run cam5 with slab ocean model using source codeCESM1.2

My commands are as follow

./create_newcase -case som_f19_g16 -res f19_g16 -compset E_2000_CN_GLC_CISM1 -mach chandra

./cesm_setup

these 2 commands run successfully

./som_f19_g16.build

I have attatched the content of above command (after execution).

Please go through it.

suggest me what should be my next step.

(I mean how should I approach  step by step to get the necessary files required to run the model in slab ocean mode)

Thanks in advance

 

Attachment: 
drosa@...

hi dbailey

thanks for this info.

I just tried one file at

https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/ocn/docn7/SOM/


and I see some bands. For example, see west of South America in the attachment.

They all seem to be created a few years ago. Is there anything from new simulations.

Having the SOM prep files for this would be great for me:

https://www.earthsystemgrid.org/dataset/cmip5.output2.NCAR.CCSM4.histori...

d

Attachment: 

Rosa, D. LBNL

dbailey

Hello,

We do have one new SOM forcing file that is not on the repo yet. It is from the Large Ensemble control run. However, I'm not sure the banding will be any better. This is largely a function of the surface fluxes and you are seeing the imprinting of the atmospheric grid on the ocean. I will try to make the other one available soon.

Dave

drosa@...

Hi Dave,

this sounds promising. I am looking forward to getting this data.

For the banding I might end up applying some smoothing just for the very sharp gradients.

Daniele

Rosa, D. LBNL

dbailey

I just checked in the file pop_frc.b.e11.B1850C5CN.f09_g16.005.082914.nc. Give that a try and let me know.

 

Dave

drosa@...

Hi Dave, thank you! I checked the file and it looks like there is less banding. I am going to start from it. Daniele.

Rosa, D. LBNL

drosa@...

Dave,

(I am back on this)

I am running f09_g16 and I am planning to use this file pop_frc.b.e11.B1850C5CN.f09_g16.005.082914.nc for the SOM.

What do I want in these fields?

<!-- SSTICE_STREAM,                          -->
<!-- SSTICE_YEAR_ALIGN,                      -->
<!-- SSTICE_YEAR_START,                      -->
<!-- SSTICE_YEAR_END,                        -->
<!-- SSTICE_GRID_FILENAME,                   -->
<!-- SSTICE_DATA_FILENAME                    -->

Daniele

Rosa, D. LBNL

dbailey

The SOM configuration (E compset) uses fully-active sea ice and prognostic SST, so these are not used.

Dave

drosa@...

Dave,

(I was making my own compset but I'll take a look at the E compsets)

Where does SOM get the initial ice amount even if it is prognostic?
It's not on pop_frc.b.e11.B1850C5CN.f09_g16.005.082914.nc.

Daniele

Rosa, D. LBNL

dbailey

In the CICE namelist there is a variable called ice_ic. This the file name from where the initial ice state variables are set. If ice_ic = 'default', this means it sets it to a uniform ice cover wherever it is "cold". If ice_ic = 'none' it is initialized with no ice at all.

Dave

kai.zhang@...

Hi dbailey,

I would like to run SOM with the E_2000_CN_GLC_CISM1 compset that is avaialble for CESM_1_2. However, it seems to me that the Q-flux data for the 1990 control run under the input directory (e.g. pop_frc.1x1d.090130.nc from b40.999 and pop_frc.gx1v3.051202.nc from b30.004) were generated using the CCSM4 model with a different compset (B_2000?). Since the new compset uses a different sea ice component (CISM) from the one used in CCSM4, I am wondering whether it is possible to use these files in our SOM simulation. Could you please let me know if you see a problem in using these data? Or do you have new Q-flux data for this particular compset (E_2000_CN_GLC_CISM1)? We prefer to use the Q-flux data that were generated from a present-day simulation.

Thank you!

- Kai

dbailey

I'm afraid we have not run a present day control run with the new code. All of the newer control runs are for 1850.

Dave

kai.zhang@...

Hi Dave,

Thanks for your reply!

- Kai

drosa@...

Dave,

just checking if your reply #19 from november is still valid.

What would the best SOM input file be for a 20th century simulation?

I see this one ocn/docn7/SOM/pop_frc.1x1d.090130.nc comes from b40.999 but I cannot find info about b40.999.

Daniele

Rosa, D. LBNL

dbailey

As I said earlier, we don't have any SOM forcing files derived from 2000 control runs. I would not use pop_frc.1x1d.090130.nc for science runs. This is only there for software engineering test purposes. I would find one that best matches your CAM resolution from the files that are there. Even though they are derived from 1850 control runs, these are better suited for any science questions you are asking.

Dave

liurj04@...

 

I am running CAM4 coupled with a slab ocean model (SOM). I simulated the experiment using EGCN compset with f19_g16 resolution.

my questions:

1) my SOM forcing file is  pop_frc.gx1v6.100105.nc  downloaded from the input data repository. Is this SOM forcing file scientifically right for my experiment ?


2) how many years I need to run to make the model equilibrated, and how could I make sure the model is equilibrated ?

Thank you !

liurj

dbailey

There some information about where this SOM forcing file came from if you do ncdump -h on it. Basically it came from years 481-500 of the CCSM4-CAM4 2deg 1850 control run. This is probably fine for your purposes. Generally we find that the SOM runs are equilibrated after 30 years. You can look at global average SST or hemispheric ice volume to see the leveling off in these quantities.

Dave

liurj04@...

Hi, Dave

Thanks for your answer.

I look at the output history files , but I can not find SST variable in the output files . As I know, SST is not default output history fields in CAM. Is this right ?  I get TS (surface temperature) variable in the output history files and I am wondering how TS is calculated over ocean, is TS equal to SST value over ocean ?

And I found the same question in : https://bb.cgd.ucar.edu/node/1001327

It says the atmosperic energy balance (FSNT-FLNT) in the model should be close to zero for equilibrium. 

I ran EGCN compset using CESM1.2.0 for about 40 years , but the global average atmosperic energy balance (FSNT-FLNT) can not be zero .

I ploted the timeseries of annual/global average atmosphere energy balance(FSNT-FLNT) and surface temperature(TS) and attatched the content. 

Could you take a look the plot and give me some suggestions ?

Thank you !

liurj

dbailey

You can add SST to the CICE model namelist with f_sst = 'mxxxx' and it will appear on the CICE history files. I'm not sure how to add it to CAM's history. However, the timeseries of TS is probably sufficient as well. TS is equal to SST over the ocean, and it is the surface temperature of the land or sea ice elsewhere. Something doesn't seem right with your energy balance here. Have you run the atmospheric diagnostics package?

 

Dave

liurj04@...

Hi, Dave

 I didn't run the atmospheric diagnostics package. Are there some other ways to find where is wrong in my simulation ? 

 When I run CAM4 with prescribed climatological SST (10 years simulation), I also have the same problem that atmosperic energy balance

  (FSNT-FLNT) is not close to zero ,which is  about -26 W/m2. 


liurj

dbailey

I don't understand how you could be getting such a large imbalance. I am bringing in the AMWG liaison on this.

Dave

hannay

If you ran CAM4 with prescribed SSTs, I would expect that FSNT-FLNT would be of teh order of 1 or 2 W/m2 at the most.

Here is an example of the AMWG diags with CAM4:

http://www.cesm.ucar.edu/experiments/cesm1.0/diagnostics/cam4_diag/f40.1...

It sounds like there is a problem with your setting or your calculation of FSNT-FLNT.  

 

If you run the AMWG diags, it would help to determine whether your problem is into the setting of teh experiemnt or in the post processing of the data.

Documentation about AMWG diags are in:
https://www2.cesm.ucar.edu/working-groups/amwg/amwg-diagnostics-package

liurj04@...

Hi, hannay

 Thanks a lot for your information. I will run the AMWG diags to find the problem.

liurj

liufukaiouc@...

Hi, hanny,

I'm running a E1850CN run (the SOM forcing file is pop_frc.b.e11.B1850CN.f09_g16.130418.nc), and the global averaged TS experience too much decrease for the first 40 years, I was wondering if you have encountered similar problems and how to solve it, thanks!

Fukai

1475922792@...

Hello, have you solved the problem? I have encountered the same problem like you. I  set the same compset and use the same SOM data as you did. How did you solve the problem at that time?

zhao

hanj@...

Hi dbailey,

could you email me the files of SOM forcing?

I have no account of that website.

Jing

Jing Han

dbailey

You need to apply for an account on the inputdata server. I cannot email the files to you.

Dave

hanj@...

Thanks very much.

I had got those files.

 

Best,

Jing

Jing Han

hanj@...

Hi Dbailey,

In ".../models/ocn/docn/tools/pop_som_frc", the file "pop_frc_interp.ncl", which is used to interpolate the data onto a standard 1x1d grid, is not available. I tried to use a NCL command "PopLatLon" to interpolate data by myself, but it did not work with the model. It caused a error as follows:

" (lnd_init_mct) :Atmospheric input is from a prognostic model

  urban net longwave radiation error: no convergence

  clm model is stopping"

When I change nothing except for using pop_frc.1x1d.090130.nc in folder ".../pop_som_frc" instead of the one I created, the model works.

I guess the problem may be associated with the SOM forcing file. Could you help me solve this problem? 

Could you update the file "pop_frc_interp.ncl", or provide a 1x1d SOM forcing file of B1850 simulation

I will appreciate that.

Look forward to your reply.


Cheers,

Jing

Jing Han

dbailey

In the CESM, we require the ocean and sea ice components to run on the same grid. We do not generally recommend interpolating data to a 1x1d grid and then interpolating back to the gx1 (Greenland Pole) grid. Hopefully one of the exisiting datasets in the inputdata directory will work for your gx1 data ocean. The majority of these came from long 1850 control runs with 1-degree atmosphere, ocean, sea ice, and land and represent a well-equilibrated climate. If you have a long fully-coupled control run with the CESM, you can use the tools in pop_som_frc to derive SOM forcing files from the POP ocean model history files. Otherwise you should use something that is reasonably close to the SOM configuration you are using. I don't know your resolution combination, but the file pop_frc.b.e11.B1850C5CN.f09_g16.005.150217.nc is probably the best choice. This comes from the CESM1.2 large ensemble 1850 control run.

Dave

hanj@...

Thanks for your reply.

The resolution of my B1850 simulation is T31_g37.

Now, I run a E1850CN simulation, using restart files from my B1850 simulation. The thing is about the SOM forcing files.

I failed to use the file pop_frc.b.c40.B1850CN.T31_g37.110128.nc but succeed with the file pop_frc.1x1d.090130.nc.

The error reported is that X coordinate is not regular and does not increase monotonically. Obviously, gx3v7 is a irregular grid.

That is why I try to interpolate data to a 1x1d.

So, do you think the file pop_frc.b.e11.B1850C5CN.f09_g16.005.150217.nc will be OK in this case? 

Appreciate your reply.

 

Cheers,

Jing

Jing Han

dbailey

Ok. I believe I understand now. Are you setting up your E1850CN case as T31_g37? The error implies that DOCN is attempting to interpolate from the gx3v7 forcing dataset and it cannot do this. Make sure your namelist for the DOCN component is correct. It might think it needs to interpolate. Also, if your B1850CN case is long enough (100 years or more), you can derive your own SOM forcing from the POP history files of that instead of using that very old gx3v7 case that we have. We do not have a newer SOM forcing file. That is all that I can suggest.

Dave

hanj@...

Thanks, Dave.

Please forgive me bother you again and again.

I indeed want to create my own SOM forcing file. So, I try to make everything clear. 

I arrange my questions as follows:

  (1) What does the resolution of SOM forcing file indicate? Should the resolution of the SOM forcing be the same as the case's resolution? 

        I found it seemed not.  I failed to run a T31_g37 simulation with the file "pop_frc.b.c40.B1850CN.T31_g37.110128.nc" where the error was "X coordinate is not regular and does not increase monotonically". However, I can do that with the file "pop_frc.1x1d.090130.nc". Does that mean I must interpolate the T31_g37 forcing file to a 1x1d forcing file?

  (2) For conducting a T31_g37 E1850CN simulation, I used a T31_g37 SOM forcing file in place of a default 1x1d by revising the "docn.buildnml.csh" file like that:

           $DIN_LOC_ROOT = /glade/p/cesm/cseg/inputdata/

           set mod_dompath = $DIN_LOC_ROOT/ocn/docn7

           set mod_domfile = domain.ocn.gx3v7.090903.nc

           set dat_dompath = $DIN_LOC_ROOT/ocn/docn7/SOM

           set dat_domfile = pop_frc.b.c40.B1850CN.T31_g37.110128.nc

           set dat_datpath = $DIN_LOC_ROOT/ocn/docn7/SOM

           set dat_datfile = pop_frc.b.c40.B1850CN.T31_g37.110128.nc

       Are there any problems here? Are there any other files I should revise?

  (3) I indeed tried to create my own SOM forcing file, using a NCL command "PopLatLon" to interpolate data to 1x1d. But it did not work with the model. It caused a error as follows:

             (lnd_init_mct) :Atmospheric input is from a prognostic model

             urban net longwave radiation error: no convergence

             clm model is stopping. 

        I did not interpolate data to T31_g37 because I thought gx3v7 would cause the problem "X coordinate is not regular and does not increase monotonically". So, what are the key points when I create a SOM forcing file? 

 

Appreciate your help.

 

Cheers,

Jing

Jing Han

dbailey

The model resolution of T31_g37 is just a short form of T31 atmosphere (CAM) plus gx3v7 ocean and ice. Please see the overall CESM documentation.

http://www.cesm.ucar.edu/models/cesm1.2/

hanj@...

I had read CESM1.0 user guide and those files in /pop_som_frc folder before asking questions. I certainly know what T31_g37 is. 

I do not know why I cannot use a same resolution of SOM forcing file to perform simulations. 

Should SOM forcing files be interpolated to a regular grid for any resolution simulations?

These things cannot be found in a user guide.

 

Cheers,

Jing

Jing Han

dbailey

I just set up a sample test using the CESM1.2.2 code base as follows:

./create_newcase -compset E1850CN -mach yellowstone -res T31_g37 -case ~/cases/somtest

cd ~/cases/somtest

./cesm_setup

./xmlchange DOCN_SOM_FILENAME=pop_frc.gx3v7.110128.nc

./somtest.build

./somtest.submit

It runs 6 days with no trouble.

hanj@...

All right. It work for CESM1.2.2.

However, I'm using CESM1.0.5. I set up a test like that:

./create_newcase -compset E1850CN -mach yellowstone -res T31_g37 -case */som_try

cd */som_try

./configure -case

cd Buildconf

changing docn.buildnml.csh as:

           $DIN_LOC_ROOT = /glade/p/cesm/cseg/inputdata/

           set mod_dompath = $DIN_LOC_ROOT/ocn/docn7

           set mod_domfile = domain.ocn.gx3v7.090903.nc

           set dat_dompath = $DIN_LOC_ROOT/ocn/docn7/SOM

           set dat_domfile = pop_frc.gx3v7.110128.nc

           set dat_datpath = $DIN_LOC_ROOT/ocn/docn7/SOM

           set dat_datfile = pop_frc.gx3v7.110128.nc

./som_try.yellowstone.build

./som_try.yellowstone.submit

Unfortunately, the model gave the error "Xc should be regular and increase monotonically" in ocn.log.

 

Cheers,

Jing

 

 

Jing Han

dbailey

Ok. This is much clearer now. I would recommend moving to CESM1.2.2, however if you absolutely must use CESM1.0.5 then you need to use a different domain file:

set mod_dompath = $DIN_LOC_ROOT/ocn/docn7/SOM

set mod_domfile = pop_frc.gx3v7.110128.nc

i.e. use the SOM forcing file for your domain information. I had to dig bag several years, but the gx3v7 domain definition changed ever so slightly. So, the DOCN thought it had to remap from gx3v7 to gx3v7 which it shouldn't.

hanj@...

Great.

I prefer to the relative old version because I have a long-term B1850 simulation using CESM1.0.

I have tried this method. It works.

I really appreciate your help.

 

Best regards,

Jing

Jing Han

pdn@...

Hi Dave, I'm running an E case using CESM1.2.1 with CAM4 physics and f45_gx37 grid. I computed the Q-flux from a B control ran with the exact same setup (CAM4 physics, same grid). My problem is: the climatology of the slab control does not agree that of the coupled run, mainly over the high latitudes due to reduced sea ice extent. I would welcome any advise on how to diagnose the cause of the discrepancy between the two climates. I expected them to be the same. Thanks!

dbailey

Hi Pedro,

I have no experience with running the SOM at the f45_g37 resolution combination. I have run with the T31 CAM atmosphere, but not the f45. The T31 CAM atmosphere produces very extensive and unrealistic sea ice. How does it look with the f45 atmosphere? The SOM configuration does generally have less extensive ice and a warm bias in the SST of 0.1-0.3C. What are the default shortwave parameters in ice_in? I'm looking for R_snw, dT_mlt, and rsnw_mlt in particular. Are these the same for your fully coupled run as well as the SOM run? Was the fully-coupled run an 1850 control or a present-day control?

Dave

pdn@...

I didn't know about the excessive ice extent in the T31 CAM runs. My simulations are idealized, so I'm not overly concerned about the realism of the sea ice extent. Howver, I'm concerned about the different sea ice extent of the slab run relative to the coupled control. I get differences in ice coverage (ICEFRAC) of 20% and SSTs of 5 K in the slab relative the coupled case. The slab case has less sea ice and warmer high latitudes (I can send you a plot if you want to look at the spatial extent, the reductions are at the sea ice edge). I compared the ice_in namelists and they are the exact same, the paramenters you mention are:

r_snw =  -2.00

dt_mlt_in =  2.00

rsnw_melt_in =  2000.

The coupled run was a B1850 compset with CAM4 physics. For the slab run I started from an E1850C5 case and modified the physics to be CAM4. I did this by changing the following parameters in env_run.xml:

CAM_CONFIG_OPTS"   value="-phys cam4"

CLM_NAMELIST_OPTS"   value=""

Maybe I'm missing some other settings to go from CAM5 physics to CAM4... would that affect CICE?

To answer your last question, I computed the Q-flux from the last 100 years of a nearly equilibrated control.

dbailey

Oh wait, did you select the E compset (default E2000) or the E1850 compset? Check your CO2 value and I bet that is it. An SST difference of 5K could only be CO2 methinks.

Dave

pdn@...

I used the E_1850_CAM5 compset so the CO2 are correct. I actually used the same namelists for CAM,CLM, and RTM than my coupled run. Looks like the Q-flux is not doing the right thing under the ice. I computed the Q-flux using the pop_frc_mlt.ncl. The version of that script that I'm using computes the surface heat flux as SHF + QFLUX, however other variables are loaded, for instance MELTH_F. I don't fully understand what the difference between QFLUX and MELTH_F so I thought I double check with you.

 

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