CMIP6 Refine Diag Script #163

jkrasting · 2017-09-20T00:12:17Z

I opened a PR so that we can discuss this development via GitHub. I'll update this branch as needed and we can close out the PR once we are all happy.

Work in progress ...

Dev/master

- basin average overturning - basin average heat transports

- z_i now used instead of z_l - MOC at the bottom-most interface is 0. by definition - topo masking appears to be correct

adcroft · 2017-09-20T17:11:26Z

Status of the masking for this PR?

jkrasting · 2017-09-20T18:36:10Z

You mean the topography masking?

adcroft · 2017-09-20T19:14:59Z

Yes - I mean is this the final version where the topography masking works as we discussed?

…

-- Dr Alistair Adcroft (Alistair.Adcroft@noaa.gov) Princeton University Tel: (609) 987-5073 NOAA/GFDL, 201 Forrestal Road, Princeton, NJ 08540

On Wed, Sep 20, 2017 at 2:36 PM, John Krasting ***@***.***> wrote: You mean the topography masking? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#163 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFlo8zXwRV0cMAhJ4OLGoBdEOK9gO9UNks5skVsbgaJpZM4PdLSq> .

jkrasting · 2017-09-21T13:14:39Z

It looks reasonable to me. Can we keep this PR open for discussion until we have all of the offline diagnostic scripts complete? The GitHub code review feature is helpful. Still on the docket are the heat transports and the passage flows ('mfo').

- Introduced "--refineDiagDir" command line option for saving output history file - Added refineDiag script for overturning diagnostics saved on rho vertical coordines (work-in-progress). - Added refineDiag script for heat transport diagnostics (work-in-progress) - Updated main MOM6_refineDiag.csh driver script

A requested variable 'wmo' the upwards mass transport is a requested CMIP6 diagnostic which as of yet is not available from the prognostic model in z* space. Transport across a vertical interface in hybrid coordinates can be slightly different than what users may canonically think of as a upward (towards the surface) direction which is orthogonal to strictly meridional/zonal directions. To be consistent with this colloquial understanding of vertical direction, wmo is calculated from the convergence of umo and vmo which have been remapped to a z* coordinate.

Include wmo as part of refine diags

Merge from dev/gfdl

- Also temporarily commented out daily variance of zos for testing purposes.

The diag table outputs diagnostic along some straits on a daily basis. The CMIP/OMIP requested 'mfo' diagnostic is a timeseries of monthly averaged, summed mass transport across the strait. The included script does this averaging and sums. The script can be extended if additional sections are added.

Add 'mfo' (mass transport through straits' to refine_diag

- Southern latititude boudaries different between the Indian and Pacific basins. This shows up as a discontinuity in the Y-ward ocean heat transport when summing the two basins. - Data masked below 34 S and comment added to the 'hfbasin' diagnostic

- infile and gridspec arguments appear to be unused. - temporarily commented out mfo diagnostic ; failing after merge

- Script now either created the ocean_month_refined.nc file if it does not exist, or it appends variables to the file if does exist. - For CMIP6 runs, recommended that this script be called last in the refineDiag call order for best compatibility

ashao · 2017-10-04T17:19:09Z

@jkrasting - That's correct. All that it needs are the netcdf variable handles to umo and vmo.

- T_ady_2d and T_adx_2d now in ocean_month output stream (needed for CMIP6) - Added umo to ocean_month output stream

- Added 'runpath' to filenames in strait_transport_timeseries.py - Added additional strlen2 dimension - Added netCDF attributes for mfo and wmo diagnostics - Cast mfo as np.array before posting (netCDF4 Python did not like 0-D mask attributes)

- removed print statements used in debugging - added '-s' option to MOM6_refineDiag.csh - collpased back to single strlen dimension in refineDiag_ocean_month_z.py

adcroft · 2017-10-05T15:52:19Z

I gather we might still have issues for the scripts? Let me know when we're ready to pull this PR in.

This PR has changes to the diag_table that look like the ones in #179 (which might need to be corrected for umo). Fix #179 so that we can pull it in and then we can remove the diag_table changes from this PR.

jkrasting · 2017-10-05T15:56:32Z

Yes, @ashao is working on the wmo diagnostic and I am cleaning up the cell methods attributes. Other than that, we are almost ready to go. The plumbing is all connected and tested in the workflow. How about I just retract #179 and I give you an all-encompassing PR later today?

- Now in both the monthly and annual streams

adcroft · 2017-10-05T16:38:16Z

The diag_table in this PR looks right so, yes, go ahead and close #179.

The scripts look good but where do we stand with the wo results?

For an east-west section:
vmo, cell_methods:"z:sum y:point x:sum"
thetao, cell_methods:"z:mean y:point x:mean"
vo, cell_methods:"z:mean y:point x:mean"

cell_measures are a bit more complicated because volcello is a volume which doesn't apply to a section. LIkewise for areacello, so I'd leave them out.

jkrasting · 2017-10-05T17:07:33Z

Our sections are N-S, however. For msftyyz, I have: 'z_i:sum yq:sum time:mean' Does that make sense? Confidence low on this ...

- Removed call to calc_variance.py from MOM6_refineDiag.csh - 'zos' and 'zos_squared' ('zossq') are now in the diag_table.

adcroft · 2017-10-05T17:35:10Z

tools/analysis/refineDiag_ocean_month.py

@@ -119,6 +119,7 @@ def main(args):
    hfbasin = np.ma.array(hfbasin,fill_value=nc_misval)
    hfbasin.long_name = 'Northward Ocean Heat Transport'
    hfbasin.units = 'W'
+    hfbasin.coordinates = 'region'


That looks right to me, based on http://clipc-services.ceda.ac.uk/dreq/u/dim:basin.html.

Can you post a "ncdump -h" of a final file?

And it also looks right based on http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html#geographic-regions .

jkrasting · 2017-10-05T17:48:23Z

Thanks. What about the cell_methods, though? I'm running the latest codes now. Will post the ncdump -h soon.

jkrasting · 2017-10-05T18:07:16Z

00010101.ocean_month_z_refined.nc.txt
00010101.ocean_month_refined.nc.txt
00010101.ocean_month_rho2_refined.nc.txt

adcroft · 2017-10-05T18:22:28Z

(I will not explain how I managed to expand those attachments on my phone).

I think the following need to be corrected:

wmo:cell_methods = "z_i:point xh:sum yh:sum time:mean" ;
Full path in global :filename ?

netcdf 00010101.ocean_month_z_refined {
dimensions:
	time = UNLIMITED ; // (12 currently)
	basin = 3 ;
	strait = 17 ;
	strlen = 31 ;
	xh = 1440 ;
	yh = 1080 ;
	yq = 1080 ;
	z_l = 35 ;
	z_i = 36 ;
	nv = 2 ;
variables:
	double time(time) ;
		time:long_name = "time" ;
		time:units = "days since 0001-01-01 00:00:00" ;
		time:cartesian_axis = "T" ;
		time:calendar_type = "NOLEAP" ;
		time:calendar = "NOLEAP" ;
		time:bounds = "time_bnds" ;
	double xh(xh) ;
		xh:long_name = "h point nominal longitude" ;
		xh:units = "degrees_east" ;
		xh:cartesian_axis = "X" ;
	double yh(yh) ;
		yh:long_name = "h point nominal latitude" ;
		yh:units = "degrees_north" ;
		yh:cartesian_axis = "Y" ;
	double yq(yq) ;
		yq:long_name = "q point nominal latitude" ;
		yq:units = "degrees_north" ;
		yq:cartesian_axis = "Y" ;
	char region(basin, strlen) ;
		region:standard_name = "region" ;
	char strait(strait, strlen) ;
		strait:standard_name = "region" ;
	double z_l(z_l) ;
		z_l:long_name = "Depth at cell center" ;
		z_l:units = "meters" ;
		z_l:cartesian_axis = "Z" ;
		z_l:positive = "down" ;
		z_l:edges = "z_i" ;
	double z_i(z_i) ;
		z_i:long_name = "Depth at interface" ;
		z_i:units = "meters" ;
		z_i:cartesian_axis = "Z" ;
		z_i:positive = "down" ;
	double nv(nv) ;
		nv:long_name = "vertex number" ;
		nv:units = "none" ;
		nv:cartesian_axis = "N" ;
	float msftyyz(time, basin, z_i, yq) ;
		msftyyz:_FillValue = 1.e+20f ;
		msftyyz:missing_value = 1.e+20f ;
		msftyyz:time_avg_info = "average_T1,average_T2,average_DT" ;
		msftyyz:long_name = "Ocean Y Overturning Mass Streamfunction" ;
		msftyyz:standard_name = "ocean_y_overturning_mass_streamfunction" ;
		msftyyz:cell_methods = "z_i:sum yq:sum time:mean" ;
		msftyyz:coordinates = "region" ;
		msftyyz:units = "kg s-1" ;
	float msftyzsmpa(time, basin, z_i, yq) ;
		msftyzsmpa:_FillValue = 1.e+20f ;
		msftyzsmpa:missing_value = 1.e+20f ;
		msftyzsmpa:time_avg_info = "average_T1,average_T2,average_DT" ;
		msftyzsmpa:long_name = "ocean Y overturning mass streamfunction due to parameterized submesoscale advection" ;
		msftyzsmpa:standard_name = "ocean_meridional_overturning_mass_streamfunction_due_to_parameterized_submesoscale_advection" ;
		msftyzsmpa:cell_methods = "z_i:sum yq:sum time:mean" ;
		msftyzsmpa:coordinates = "region" ;
		msftyzsmpa:units = "kg s-1" ;
	float msftyzmpa(time, basin, z_i, yq) ;
		msftyzmpa:_FillValue = 1.e+20f ;
		msftyzmpa:missing_value = 1.e+20f ;
		msftyzmpa:time_avg_info = "average_T1,average_T2,average_DT" ;
		msftyzmpa:long_name = "ocean Y overturning mass streamfunction due to parameterized mesoscale advection" ;
		msftyzmpa:standard_name = "ocean_y_overturning_mass_streamfunction_due_to_parameterized_mesoscale_advection" ;
		msftyzmpa:cell_methods = "z_i:sum yq:sum time:mean" ;
		msftyzmpa:coordinates = "region" ;
		msftyzmpa:units = "kg s-1" ;
	float wmo(time, z_i, yh, xh) ;
		wmo:_FillValue = 1.e+20f ;
		wmo:missing_value = 1.e+20f ;
		wmo:time_avg_info = "average_T1,average_T2,average_DT" ;
		wmo:long_name = "Upward mass transport from resolved and parameterized advective transport" ;
		wmo:standard_name = "upward_ocean_mass_transport" ;
		wmo:cell_methods = "z_i:sum xh:sum yh:sum time:mean" ;
		wmo:units = "kg s-1" ;
	float mfo(time, strait) ;
		mfo:_FillValue = 1.e+20f ;
		mfo:missing_value = 1.e+20f ;
		mfo:time_avg_info = "average_T1,average_T2,average_DT" ;
		mfo:long_name = "Sea Water Transport" ;
		mfo:standard_name = "sea_water_transport_across_line" ;
		mfo:cell_methods = "time:mean" ;
		mfo:coordinates = "strait" ;
		mfo:units = "kg s-1" ;
	double average_T1(time) ;
		average_T1:long_name = "Start time for average period" ;
		average_T1:units = "days since 0001-01-01 00:00:00" ;
		average_T1:missing_value = 1.e+20 ;
		average_T1:_FillValue = 1.e+20 ;
	double average_T2(time) ;
		average_T2:long_name = "End time for average period" ;
		average_T2:units = "days since 0001-01-01 00:00:00" ;
		average_T2:missing_value = 1.e+20 ;
		average_T2:_FillValue = 1.e+20 ;
	double average_DT(time) ;
		average_DT:long_name = "Length of average period" ;
		average_DT:units = "days" ;
		average_DT:missing_value = 1.e+20 ;
		average_DT:_FillValue = 1.e+20 ;
	double time_bnds(time, nv) ;
		time_bnds:long_name = "time axis boundaries" ;
		time_bnds:units = "days" ;
		time_bnds:missing_value = 1.e+20 ;
		time_bnds:_FillValue = 1.e+20 ;

// global attributes:
		:filename = "/vftmp/John.Krasting/pid29605/mdt/20171002-dev/CM4_c96L33_am4p0_2010_30d15_tlt_geo_kd15/gfdl.ncrc4-intel16-prod-openmp/CM4_c96L33_am4p0_2010_30d15_tlt_geo_kd15_00010101/history_refineDiag/00010101.nc/00010101.ocean_month_z_refined.nc" ;
		:title = "CM4_c96L33_am4p0_2010_30d15_tlt_geo_kd15" ;
		:associated_files = "areacello: 00010101.ocean_static.nc" ;
		:grid_type = "regular" ;
		:grid_tile = "N/A" ;
}

adcroft · 2017-10-05T18:26:34Z

netcdf 00010101.ocean_month_refined {
dimensions:
	time = UNLIMITED ; // (12 currently)
	basin = 3 ;
	strlen = 21 ;
	yq = 1080 ;
	xh = 1440 ;
	nv = 2 ;
variables:
	double time(time) ;
		time:long_name = "time" ;
		time:units = "days since 0001-01-01 00:00:00" ;
		time:cartesian_axis = "T" ;
		time:calendar_type = "NOLEAP" ;
		time:calendar = "NOLEAP" ;
		time:bounds = "time_bnds" ;
	double yq(yq) ;
		yq:long_name = "q point nominal latitude" ;
		yq:units = "degrees_north" ;
		yq:cartesian_axis = "Y" ;
	char region(basin, strlen) ;
		region:standard_name = "region" ;
	double xh(xh) ;
		xh:long_name = "h point nominal longitude" ;
		xh:units = "degrees_east" ;
		xh:cartesian_axis = "X" ;
	double nv(nv) ;
		nv:long_name = "vertex number" ;
		nv:units = "none" ;
		nv:cartesian_axis = "N" ;
	float hfy(time, yq, xh) ;
		hfy:_FillValue = 1.e+20f ;
		hfy:missing_value = 1.e+20f ;
		hfy:time_avg_info = "average_T1,average_T2,average_DT" ;
		hfy:long_name = "Ocean Heat Y Transport" ;
		hfy:standard_name = "ocean_heat_y_transport" ;
		hfy:cell_methods = "yq:point xh:mean time:mean" ;
		hfy:units = "W" ;
	float hfx(time, yq, xh) ;
		hfx:_FillValue = 1.e+20f ;
		hfx:missing_value = 1.e+20f ;
		hfx:time_avg_info = "average_T1,average_T2,average_DT" ;
		hfx:long_name = "Ocean Heat X Transport" ;
		hfx:standard_name = "ocean_heat_x_transport" ;
		hfx:cell_methods = "yh:mean xq:point time:mean" ;
		hfx:units = "W" ;
	float hfbasin(time, basin, yq) ;
		hfbasin:_FillValue = 1.e+20f ;
		hfbasin:missing_value = 1.e+20f ;
		hfbasin:comment = "Indo-Pacific heat transport begins at 34 S" ;
		hfbasin:time_avg_info = "average_T1,average_T2,average_DT" ;
		hfbasin:long_name = "Northward Ocean Heat Transport" ;
		hfbasin:standard_name = "northward_ocean_heat_transport" ;
		hfbasin:cell_methods = "yq:sum time:mean" ;
		hfbasin:coordinates = "region" ;
		hfbasin:units = "W" ;
	double average_T1(time) ;
		average_T1:long_name = "Start time for average period" ;
		average_T1:units = "days since 0001-01-01 00:00:00" ;
		average_T1:missing_value = 1.e+20 ;
		average_T1:_FillValue = 1.e+20 ;
	double average_T2(time) ;
		average_T2:long_name = "End time for average period" ;
		average_T2:units = "days since 0001-01-01 00:00:00" ;
		average_T2:missing_value = 1.e+20 ;
		average_T2:_FillValue = 1.e+20 ;
	double average_DT(time) ;
		average_DT:long_name = "Length of average period" ;
		average_DT:units = "days" ;
		average_DT:missing_value = 1.e+20 ;
		average_DT:_FillValue = 1.e+20 ;
	double time_bnds(time, nv) ;
		time_bnds:long_name = "time axis boundaries" ;
		time_bnds:units = "days" ;
		time_bnds:missing_value = 1.e+20 ;
		time_bnds:_FillValue = 1.e+20 ;

// global attributes:
		:filename = "/vftmp/John.Krasting/pid29605/mdt/20171002-dev/CM4_c96L33_am4p0_2010_30d15_tlt_geo_kd15/gfdl.ncrc4-intel16-prod-openmp/CM4_c96L33_am4p0_2010_30d15_tlt_geo_kd15_00010101/history_refineDiag/00010101.nc/00010101.ocean_month_refined.nc" ;
		:title = "CM4_c96L33_am4p0_2010_30d15_tlt_geo_kd15" ;
		:associated_files = "areacello: 00010101.ocean_static.nc" ;
		:grid_type = "regular" ;
		:grid_tile = "N/A" ;
}

adcroft · 2017-10-05T18:30:48Z

That last file (ocean_month_refined) needs the following corrections:

hfbasin:cell_methods = "yq:point time:mean" ;
global:associated_files is not needed since areacello is not referenced (in ocean_month_refined)

adcroft · 2017-10-05T18:32:46Z

Also, in ocean_month_z_refined:

wmo:cell_measures: "area:areacello"

The associated_files is then correct in ocean_month_z_refined, but still not needed in ocean_month_refined.

adcroft · 2017-10-05T18:44:07Z

Corrections for

rho2_l:standard_name = "sea_water_potential_density" (see http://clipc-services.ceda.ac.uk/dreq/u/dim:rho.html)
msftyrho:cell_methods = "rho2_i:point yq:point time:mean" ;
msftyrhompa:cell_methods = "rho2_i:point yq:point time:mean" ;
global:associated_files is not needed because areacello is not referenced.

netcdf 00010101.ocean_month_rho2_refined {
dimensions:
	time = UNLIMITED ; // (12 currently)
	basin = 3 ;
	strlen = 21 ;
	yq = 1080 ;
	rho2_l = 35 ;
	rho2_i = 36 ;
	nv = 2 ;
variables:
	double time(time) ;
		time:long_name = "time" ;
		time:units = "days since 0001-01-01 00:00:00" ;
		time:cartesian_axis = "T" ;
		time:calendar_type = "NOLEAP" ;
		time:calendar = "NOLEAP" ;
		time:bounds = "time_bnds" ;
	double yq(yq) ;
		yq:long_name = "q point nominal latitude" ;
		yq:units = "degrees_north" ;
		yq:cartesian_axis = "Y" ;
	char region(basin, strlen) ;
		region:standard_name = "region" ;
	double rho2_l(rho2_l) ;
		rho2_l:long_name = "Target Potential Density at cell center" ;
		rho2_l:units = "kg m-3" ;
		rho2_l:cartesian_axis = "Z" ;
		rho2_l:positive = "down" ;
		rho2_l:edges = "rho2_i" ;
	double rho2_i(rho2_i) ;
		rho2_i:long_name = "Target Potential Density at interface" ;
		rho2_i:units = "kg m-3" ;
		rho2_i:cartesian_axis = "Z" ;
		rho2_i:positive = "down" ;
	double nv(nv) ;
		nv:long_name = "vertex number" ;
		nv:units = "none" ;
		nv:cartesian_axis = "N" ;
	float msftyrho(time, basin, rho2_i, yq) ;
		msftyrho:_FillValue = 1.e+20f ;
		msftyrho:missing_value = 1.e+20f ;
		msftyrho:time_avg_info = "average_T1,average_T2,average_DT" ;
		msftyrho:long_name = "Ocean Y Overturning Mass Streamfunction" ;
		msftyrho:standard_name = "ocean_y_overturning_mass_streamfunction" ;
		msftyrho:cell_methods = "rho2_i:sum yq:sum time:mean" ;
		msftyrho:coordinates = "region" ;
		msftyrho:units = "kg s-1" ;
	float msftyrhompa(time, basin, rho2_i, yq) ;
		msftyrhompa:_FillValue = 1.e+20f ;
		msftyrhompa:missing_value = 1.e+20f ;
		msftyrhompa:time_avg_info = "average_T1,average_T2,average_DT" ;
		msftyrhompa:long_name = "ocean Y overturning mass streamfunction due to parameterized mesoscale advection" ;
		msftyrhompa:standard_name = "ocean_y_overturning_mass_streamfunction_due_to_parameterized_mesoscale_advection" ;
		msftyrhompa:cell_methods = "rho2_i:sum yq:sum time:mean" ;
		msftyrhompa:coordinates = "region" ;
		msftyrhompa:units = "kg s-1" ;
	double average_T1(time) ;
		average_T1:long_name = "Start time for average period" ;
		average_T1:units = "days since 0001-01-01 00:00:00" ;
		average_T1:missing_value = 1.e+20 ;
		average_T1:_FillValue = 1.e+20 ;
	double average_T2(time) ;
		average_T2:long_name = "End time for average period" ;
		average_T2:units = "days since 0001-01-01 00:00:00" ;
		average_T2:missing_value = 1.e+20 ;
		average_T2:_FillValue = 1.e+20 ;
	double average_DT(time) ;
		average_DT:long_name = "Length of average period" ;
		average_DT:units = "days" ;
		average_DT:missing_value = 1.e+20 ;
		average_DT:_FillValue = 1.e+20 ;
	double time_bnds(time, nv) ;
		time_bnds:long_name = "time axis boundaries" ;
		time_bnds:units = "days" ;
		time_bnds:missing_value = 1.e+20 ;
		time_bnds:_FillValue = 1.e+20 ;

// global attributes:
		:filename = "/vftmp/John.Krasting/pid29605/mdt/20171002-dev/CM4_c96L33_am4p0_2010_30d15_tlt_geo_kd15/gfdl.ncrc4-intel16-prod-openmp/CM4_c96L33_am4p0_2010_30d15_tlt_geo_kd15_00010101/history_refineDiag/00010101.nc/00010101.ocean_month_rho2_refined.nc" ;
		:title = "CM4_c96L33_am4p0_2010_30d15_tlt_geo_kd15" ;
		:associated_files = "areacello: 00010101.ocean_static.nc" ;
		:grid_type = "regular" ;
		:grid_tile = "N/A" ;
}

jkrasting · 2017-10-05T18:47:18Z

I'm inheriting this from the MOM6 output. It would be better to make that change in the MOM6 code (I assume where the coordinate for remapping is defined). @aadcroft, @ashao, could either of you make that change? rho2_l:standard_name = "sea_water_potential_density" (see http://clipc-services.ceda.ac.uk/dreq/u/dim:rho.html I'll handle everything else. Thanks for the QC!

jkrasting · 2017-10-05T18:50:29Z

If msftyrho:cell_methods = "rho2_i:point yq:point time:mean", Shouldn't msftyyz.cell_methods = 'z_i:point yq:point time:mean' ? Currently have: msftyyz.cell_methods = 'z_i:sum yq:sum time:mean' ?

…

----- Dr. John Krasting, Physical Scientist Biogeochemistry, Ecosystems, and Climate Group NOAA/Geophysical Fluid Dynamics Laboratory 201 Forrestal Road, Princeton, NJ 08540 P. (609) 452-5359 | F. (609) 987-5063

On Thu, Oct 5, 2017 at 2:47 PM, John Krasting - NOAA Federal < ***@***.***> wrote: I'm inheriting this from the MOM6 output. It would be better to make that change in the MOM6 code (I assume where the coordinate for remapping is defined). @aadcroft, @ashao, could either of you make that change? rho2_l:standard_name = "sea_water_potential_density" (see http://clipc-services.ceda.ac.uk/dreq/u/dim:rho.html I'll handle everything else. Thanks for the QC!

adcroft · 2017-10-05T18:50:57Z

Also for ocean_month_z_refined:

msftyyz:cell_methods = "z_i:point yq:point time:mean" ;
msftyzsmpa:cell_methods = "z_i:point yq:point time:mean" ;
msftyzmpa:cell_methods = "z_i:point yq:point time:mean" ;

I think it's right that a stream function is :point in both directions because you can only interpolate it. The 3d lateral transports are :sum in the tangential directions because they have to be summed when combining, not interpolated.

adcroft · 2017-10-05T18:51:45Z

Sorry @jkrasting , just saw your comment saying what I just did.

- corrected cell_methods - cleaned up global attributes

- PR to main from NCAR - Adds diagnostics - NOAA-GFDL/MOM6@0f664aa82 Merge pull request #1275 from gustavo-marques/main-candidate-ncar-2020-12-15 - NOAA-GFDL/MOM6@9d04f3849 Sets CS%limiter_remap=.false. in near_boundary_unit_tests - NOAA-GFDL/MOM6@5739a3413 Merge branch 'delete_fotgotten_code_LBD' into main-candidate-ncar-2020-12-15 - NOAA-GFDL/MOM6@51ed387ae Delete forgotten code - NOAA-GFDL/MOM6@42d79c204 Merge branch 'main' into main-candidate-ncar-2020-12-15 - NOAA-GFDL/MOM6@eddbd6c09 Merge pull request #164 from gustavo-marques/LBD_regrid_merged_10nov2020 - NOAA-GFDL/MOM6@cf97095bd Fix bug in linear decay and set F_layer = 0 below htot_max - NOAA-GFDL/MOM6@8215b70d0 Merge pull request #163 from NCAR/stdout - NOAA-GFDL/MOM6@0c1680555 Merge pull request #168 from kshedstrom/gnu_fix - NOAA-GFDL/MOM6@37cea3690 A few fixes to get it to compile with gfortran. - NOAA-GFDL/MOM6@acdfdda71 Fix unit tests and declare max_depth - NOAA-GFDL/MOM6@ad9862b40 Set maximum depth of the LBD grid - NOAA-GFDL/MOM6@5ac184667 Merge pull request #165 from NCAR/deferred_char_len - NOAA-GFDL/MOM6@7a5a0f768 real_array_string to deferred length - NOAA-GFDL/MOM6@95271cdfb change mesg character var to be deferred length to prevent record overflow - NOAA-GFDL/MOM6@d5c87fc5a change left_reals character var to be deferred length to prevent record overflow - NOAA-GFDL/MOM6@fa2b4249b Undo chages in tracer_example and MOM_tracer_flow_control - NOAA-GFDL/MOM6@aa27f1c8e Add LBD clock, clean up, and document module - NOAA-GFDL/MOM6@48616d86a Delete uncessary comments - NOAA-GFDL/MOM6@11cc3dc5c Undo changes related to check_grid_def - NOAA-GFDL/MOM6@f5abc66b7 Fix bug in linear decay - NOAA-GFDL/MOM6@f0d8a4ae1 Merge branch 'dev/ncar' into HEAD - NOAA-GFDL/MOM6@3f092914e replace iso_fortran_env::stdout with MOM_io::stdout - NOAA-GFDL/MOM6@1269874f2 change all 'write(*,..' to 'write(stdout,...' - NOAA-GFDL/MOM6@cc82d1154 use MOM_io::stdout in MCT cap instead of glb%stdout or FMS stdout - NOAA-GFDL/MOM6@30fac75c0 introduce public module ints stdout and stderr for standard output - NOAA-GFDL/MOM6@165b1b27a Merge pull request #160 from gustavo-marques/merge-main-candidate-2020-09-18 - NOAA-GFDL/MOM6@9fbc3e663 Merge pull request #6 from NOAA-GFDL/main-candidate-2020-09-18 - NOAA-GFDL/MOM6@300b6e9cf Option to apply limiter in native and LBD grids - NOAA-GFDL/MOM6@60559ecc1 Code cleaning - NOAA-GFDL/MOM6@9fb6f7527 Fix unit tests - NOAA-GFDL/MOM6@e484bc87a Add option to set maximum value in subrotine unique - NOAA-GFDL/MOM6@3df9dbcc7 Merge branch 'dev/ncar' into merge-regrid_LBD - NOAA-GFDL/MOM6@9e7b08973 Improve flux limiter - NOAA-GFDL/MOM6@a962325d8 Add option to apply flux limiter - NOAA-GFDL/MOM6@4235bb2fc Merge pull request #159 from gustavo-marques/add_u_v_squared_diags - NOAA-GFDL/MOM6@ddbd9c7ae Merge pull request #158 from gustavo-marques/dev-master-candidate-ncar-2020-08-11 - NOAA-GFDL/MOM6@f0face43f Adds missing args for KPP_get_BLD and energetic_PBL_get_MLD - NOAA-GFDL/MOM6@87ba533e4 Adds missing args for KPP_get_BLD and energetic_PBL_get_MLD - NOAA-GFDL/MOM6@2538c4d2a Improve the merging of interfaces - NOAA-GFDL/MOM6@f444affd3 Comment out write statements - NOAA-GFDL/MOM6@4ab4a7af7 Remove hard-coded BLD and uncomment code for adv and PGF - NOAA-GFDL/MOM6@365b298be Cleanup + add unit tests - NOAA-GFDL/MOM6@e537ef233 Add option to initialize passive tracer from z file - NOAA-GFDL/MOM6@40136b6d2 Passes GV to lateral_boundary_diffusion_init - NOAA-GFDL/MOM6@441c34ef4 Define vertical grid on-the-fly using h's and BLDs - NOAA-GFDL/MOM6@75c587e5f Major re-arragement to remap u- and v-fluxes - NOAA-GFDL/MOM6@593ebfc1d Delete fluxes_bulk_method - NOAA-GFDL/MOM6@e0db9abcb Fix typo when posting vsq - NOAA-GFDL/MOM6@1849bccd4 Adding option to output u^2, v^2 and u*v - NOAA-GFDL/MOM6@5c56268ea Adding options to specify dz to apply LBD @ top - NOAA-GFDL/MOM6@fa376e4da Merge branch 'LBD_idealized_experiments2' into regrid_LBD - NOAA-GFDL/MOM6@2a8096497 First attempt to use remapping in LBD - NOAA-GFDL/MOM6@d8ae09f80 Rename lateral_boundary_diffusion_CS to lbd_CS - NOAA-GFDL/MOM6@9957e55c6 Fix bug in loop-indices when using discontinuous ND and interior_only - NOAA-GFDL/MOM6@1fd53935d Fix bug in loop-indices when applying linear decay - NOAA-GFDL/MOM6@a49954a73 comment calls to BLD schemes - NOAA-GFDL/MOM6@7e390593c Merge branch 'dev/ncar' into LBD_idealized_experiments - NOAA-GFDL/MOM6@09ad69505 Add option to apply linear decay at the base of hbl - NOAA-GFDL/MOM6@7299d8653 Fix bug when applying ND only in the interior - NOAA-GFDL/MOM6@92581e2be Minor improvements in the bulk method - NOAA-GFDL/MOM6@9dc47208a Add option to apply linear decay at the base of hbl - NOAA-GFDL/MOM6@3b121cbcd Merge branch 'fix_LBD_tests' into LBD_idealized_experiments - NOAA-GFDL/MOM6@51a4d2e11 Apply a linear transition in LBD methods 1, 2 - NOAA-GFDL/MOM6@b5132d99d Modifications to run idealized two-column LBD - NOAA-GFDL/MOM6@a446d0fb2 Remove dependence on the boundary layer scheme

Introduce a controllable stdout unit in MOM_io

- Rolled forward src/MOM6 and src/SIS2 to head of main circa Jan/Feb 2022. SIS2 commits since last sync to main: - NOAA-GFDL/SIS2@236fa72 (HEAD -> main, origin/main) Fix the result of a bad automated merge - NOAA-GFDL/SIS2@87ff9e5 Merge pull request #164 from Hallberg-NOAA/fix_unit_descriptions - NOAA-GFDL/SIS2@f020bba Merge branch 'dev/gfdl' into fix_unit_descriptions - NOAA-GFDL/SIS2@94ac8bd Merge pull request #163 from Hallberg-NOAA/stock_0degC - NOAA-GFDL/SIS2@b926925 Merge pull request #165 from Hallberg-NOAA/sum_output_cleanup - NOAA-GFDL/SIS2@9d0329a (*)Correct SIS summed output, including salt units - NOAA-GFDL/SIS2@d18605e Fixed 15 more variable unit descriptions - NOAA-GFDL/SIS2@41c76d8 Corrected spelling errors in comments - NOAA-GFDL/SIS2@98e926e Corrected comments in SIS_tracer_advect.F90 - NOAA-GFDL/SIS2@dde02fb Fixed 28 variable unit descriptions - NOAA-GFDL/SIS2@b6a9dfd +(*)Report heat stocks relative to liquid at 0 degC - NOAA-GFDL/SIS2@4e2454b Merge branch 'ridging_CS' into dev/gfdl - NOAA-GFDL/SIS2@ed5f20a Merge branch 'ridging_CS' of https://github.com/ESMG/SIS2 into ridging_CS - NOAA-GFDL/SIS2@04ab05d +Rescale G%Rad_Earth and set it via dG%Rad_Earth_L - NOAA-GFDL/SIS2@0cb6a0a Use allocate with source to initialize arrays - NOAA-GFDL/SIS2@e55a3eb Add a ridging control structure. - NOAA-GFDL/SIS2@ae2b2e3 Attempting to add a control structure for ridging - NOAA-GFDL/SIS2@0dc7d86 Merge remote-tracking branch 'gfdl/dev/gfdl' into dev/esmg - NOAA-GFDL/SIS2@906d26c Merge pull request #159 from marshallward/eos_ptr_removal - NOAA-GFDL/SIS2@55032ff MOM EOS pointer API update - NOAA-GFDL/SIS2@1c02a8f Add ice mass by category to diag options. - NOAA-GFDL/SIS2@e3b5574 Merge pull request #156 from Hallberg-NOAA/fix_set_massless_tracer_arg - NOAA-GFDL/SIS2@297ff46 +Change opt. arg. to set_massless_SIS_tracers MOM6 commits since last sync to main: - NOAA-GFDL/MOM6@e5563478 Improved fix for detecting symmetric mode output in refineDiag_ocean_month.py Update symmetric mode test to handle 2D or 3D input data. Also, check that the data and mask are 2 or 3D and 2D, respectively. - NOAA-GFDL/MOM6@f5a84968 Fix for detecting symmetric mode output in refineDiag_ocean_month.py The data has shape of TIME,Y,X and the mask has shape of Y,X, so the symmetric mode check should compare the 2nd index for the data and the 1st index for the mask. If the mask Y value is one greater than the data Y value, then the output is symmetric. - NOAA-GFDL/MOM6@6d9a98ef Update for locating basin codes in MOM6_refineDiag.csh The script currently looks for the codes in basin_codes.nc which does not exist in FRE output normally. Many FRE XMLs add basin_codes.nc to the history output before output staging, so the basin codes appear alongside the other history files with the YYYYMMDD.basin_codes.nc name. This update to the refineDiag wrapper script uses the YYYYMMDD.basin_codes.nc file as the basin codes if it exists. - NOAA-GFDL/MOM6@ef61d50c MOM6: (*)Updated version of MOM6 after MOM6 PR #41 - NOAA-GFDL/MOM6@95221af5 MOM6: (*)Updated version of MOM6 and MOM_parameter_doc files - NOAA-GFDL/MOM6@5ac8a699 Merge pull request #348 from Hallberg-NOAA/update_SIS2_version - NOAA-GFDL/MOM6@0aa93483 Updated version of SIS2 and MOM_parameter_doc files - NOAA-GFDL/MOM6@0b6dd99e MOM6: Fixes an uninitialized logical in FMS_cap - NOAA-GFDL/MOM6@611d6e6b SIS2: +Rescale G%Rad_Earth and set it via dG%Rad_Earth_L - NOAA-GFDL/MOM6@b5d2fa34 SIS2: Use allocate with source to initialize arrays - NOAA-GFDL/MOM6@f9377ca3 MOM6: +Rescale tides and ramp-up times - NOAA-GFDL/MOM6@1611c5c0 MOM6: Adding temperature restore capability for SPEAR. (#36) - NOAA-GFDL/MOM6@85556792 MOM6: +Obsolete ETA_TOLERANCE_AUX - NOAA-GFDL/MOM6@f05469d5 MOM6: change conversion H_to_MKS to H_to_m for u/veffA - NOAA-GFDL/MOM6@11dd3dff Add omitted file to "Merge in recent minor updates" - NOAA-GFDL/MOM6@d14218c5 MOM6 & SIS2: Merge in recent minor updates - NOAA-GFDL/MOM6@31114023 MOM6: (*)Fix compile-time issues with MOM_sum_driver.F90 - NOAA-GFDL/MOM6@7e56f0e8 MOM6: +Argument cleanup in vertical diffusivity code - NOAA-GFDL/MOM6@5d0c027e MOM6: Update available_diags and MOM_parameter_doc files - NOAA-GFDL/MOM6@e2bebd2b MOM6: Refactored solo_driver/MOM_driver.F90 - NOAA-GFDL/MOM6@109e7898 MOM6: +(*)Fix bug when RES_SCALE_MEKE_VISC = True (#1512) - NOAA-GFDL/MOM6@2276c470 MOM6: +Add new parameter FATAL_INCONSISTENT_RESTART_TIME (#1511) - NOAA-GFDL/MOM6@271ab0b0 MOM6: +*Change defaults for 3 parameters to better values (#1509) - NOAA-GFDL/MOM6@a90da93d MOM6: Done with EPBL docs? - NOAA-GFDL/MOM6@8c6c667f MOM6: Particle API (#1504) - NOAA-GFDL/MOM6@c138c521 MOM6: +Add BAROTROPIC_TIDAL_SAL_BUG to fix a tide bug - NOAA-GFDL/MOM6@c3c46494 Merge pull request #344 from Hallberg-NOAA/set_default_params - NOAA-GFDL/MOM6@10f46fd8 Explicitly set 3 parameters to default values - NOAA-GFDL/MOM6@f5d708bc MOM6: Testing: Generalized dimension testing

jkrasting added 3 commits September 14, 2017 13:44

Merge pull request #3 from NOAA-GFDL/dev/master

0814494

Dev/master

Initial commit of CMIP6 offline diag script

47cb72e

- basin average overturning - basin average heat transports

MOC reported on interfaces, not levels

7173edb

- z_i now used instead of z_l - MOC at the bottom-most interface is 0. by definition - topo masking appears to be correct

jkrasting and others added 13 commits September 26, 2017 20:26

w had the wrong sign because divergence was calculated, not convergence

a38e983

Merge pull request #4 from ashao/add_wmo_to_refine_diag

b979772

Include wmo as part of refine diags

Merge pull request #5 from NOAA-GFDL/dev/gfdl

b6a25d3

Merge from dev/gfdl

refineDiag script uses basin_codes.nc file

769eb6b

- Also temporarily commented out daily variance of zos for testing purposes.

Added hfbasin diagnostic to refineDiag script

7f0ab79

Merge pull request #6 from ashao/add_mfo_diagnostic

2ab368b

Add 'mfo' (mass transport through straits' to refine_diag

Updated coordinates in rho2 refineDiag script

350462b

Modified interface to calc_w_from_convergence()

6ff7aac

- infile and gridspec arguments appear to be unused. - temporarily commented out mfo diagnostic ; failing after merge

Updated calc_variance.py

69f35ec

- Script now either created the ocean_month_refined.nc file if it does not exist, or it appends variables to the file if does exist. - For CMIP6 runs, recommended that this script be called last in the refineDiag call order for best compatibility

jkrasting added 7 commits October 4, 2017 13:53

Updated diag table for transport diags

c7c3375

- T_ady_2d and T_adx_2d now in ocean_month output stream (needed for CMIP6) - Added umo to ocean_month output stream

Merge remote branch 'origin/post_9_27_updates' into basin_refinediag

839b026

Added thkcello/volcello for rho2 output

f4c5c95

Various fixes for mfo (straits) diagnostic

ab64e2a

- Added 'runpath' to filenames in strait_transport_timeseries.py - Added additional strlen2 dimension - Added netCDF attributes for mfo and wmo diagnostics - Cast mfo as np.array before posting (netCDF4 Python did not like 0-D mask attributes)

Merge remote branch 'origin/post_9_27_updates' into basin_refinediag

e8bd7e2

Flexible mask tiling based on time dimension

29c2b13

Miscellaneous clean-ups from testing

8fad2c9

- removed print statements used in debugging - added '-s' option to MOM6_refineDiag.csh - collpased back to single strlen dimension in refineDiag_ocean_month_z.py

Updated umo in diag_table

b1c65de

- Now in both the monthly and annual streams

jkrasting added 3 commits October 5, 2017 13:10

Updated cell_methods attrs. for refined diags

9d4536a

Removed call to calc_varaince.py

1ebf336

- Removed call to calc_variance.py from MOM6_refineDiag.csh - 'zos' and 'zos_squared' ('zossq') are now in the diag_table.

Added 'coordinates' attribute to basin/strait vars.

9647743

adcroft reviewed Oct 5, 2017

View reviewed changes

Tidy-up odds and ends after QC

bcd2b90

- corrected cell_methods - cleaned up global attributes

adcroft merged commit f15b916 into NOAA-GFDL:dev/gfdl Oct 5, 2017

OlgaSergienko pushed a commit to OlgaSergienko/MOM6-examples that referenced this pull request Dec 29, 2020

Merge pull request NOAA-GFDL#163 from NCAR/stdout

8215b70

Introduce a controllable stdout unit in MOM_io

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CMIP6 Refine Diag Script #163

CMIP6 Refine Diag Script #163

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CMIP6 Refine Diag Script #163

CMIP6 Refine Diag Script #163

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