Adds free surface gradient forcing for idealized 1D turbulence by pwolfram · Pull Request #615 · MPAS-Dev/MPAS-Model

pwolfram · 2020-06-29T23:51:43Z

Adds free surface gradient forcing for

config_zonal_ssh_grad (x-component for planar)
config_meridional_ssh_grad (y-component for planar)

Case is applied in periodic flow in
ocean/periodic_planar/2.5km/default_gotm case, which can be
used to validate vertical momentum balances with constant forcing
due to double periodicity, which is useful to indicate potential
instabilities with constant forcing due to unstructured mesh.

Note, for full case comparison against literature (e.g., section 5.1 of https://www.sciencedirect.com/science/article/pii/S1463500319302082), needs to have Generaliized
Ocean Turbulence Model to be incorporated.

SedimentFluxIndex - I SedimentFluxIndex -I add the following files - Registry_sediment_flux_index.xml - mpas_con_sediment_flux_index.F sedimentFluxIndex - I update add four variables - sedimentFluxIndexVAX : Vertically-Averaged sFI in X-direction - sedimentFluxIndexVAY : Vertically-Averaged sFI in Y-direction - sedimentFluxIndexBX: Bottom sFI in X-direction - sedimentFluxIndexBY: Bottom sFI in Y-direction Adds sediment flux calculation calculate sediment fall velocity by Goldstein and Coco 2013 calculate ratio "a" of sediment flux Q and U3 by Grawe et al 2014 calculate vertically-averaged and close bottom sediment flux (kg/m/s) test the AM on the case ziso/2.5km/default Add Soulsby and Damgaard bedload transport formulae Goldstein and Coco's fall velocity equation seems to overestimate Ws, might be repaced by VanRijn [1989] or Zhu & Cheng [1993] in next commit

Add three bedload transport formulae and four sediment fall velocity formulae Bedload transport formulae - Soulbsy-Damgaard [2005] - Meyer-Peter-Meuller [1948] - Engelund-Hansen [1967] Sediment fall velocity formulae - Goldstein-Coco2013 - VanRijn1993 - Soulsby1997 - Cheng1997 Add Manning equation to calculate Chezy roughnes coefficient in Engelund-Hansen bedload formula. The Manning equaiton reads: Chezy = 1/Manning*(bottomDepth)^(1/6) Chezy value is manually restricted between [20 ,100] Add suspended sediment concentration (SSC) algorithms SSC is solved by bottom reference concentration and Rouse profile Bottom reference concentration is computed by one of the following formulae - Lee et al., 2004 - Goldstein et al., 2014 - Zyserman-Fredsoe 1997 Rouse profle assumes the eddy diffusivity to vary parabolically with height Fixed bugs in calculations of SSC and theta in sediment_transport.F Fixed two bugs in mpas_ocn_sediment_transport.F - Corrected SSC Rouse profile equation The old equation from Page 138 of Soulsby's book "Dynamics of Marine Snads" (1997) is wrong. The right equation(s) can be found in (1) van Rijn 1984: Sediment Transport, Phase II: Suspended Load Transport. J. Hydraul. Eng. (2) Wang 2012: Measuring and Modeling Suspended Sediment Concentration Profile in the Surf Zone. Marine Sedimentology - Corrected z-coordinate calculation The global variable zMid is zero at surface and negative downward. The water depth from bottom z was mistakely set to -zMid. Now the calculation is z=ssh+bottomDepth+zMid Fixed a bug in mpas_ocn_sediment_transport.F zMid is the distance from the mean surface layer, with positve upward. So for each vertical layer center, the distance above the sea bottom is bottomDepth+zMid, which was wrongly set as ssh+bottomDepth+zMid in the last commit. Replaced Rouse profile equation by van Rijn's equations; modified xml files to output ssh, mesh and velocity in sediment transport output file. Mannually set a maximum value for Rouse number to avoid "Float-point exception" error; fixed a bug in the implementation of 'Zyserman-Fredsoe1994' equation.

…coastal This PR adds sediment transport analysis member (Phase I) to the model, with the following variables computed: - sediment settling velocity - sediment erosion flux - sediment bedload transport flux - suspended sediment concentration in water column

Adds examples of JIGSAW workflow for coastal cases. Adds HI refined case West coast mesh from SF to LA

This currently only affects coastal test cases.

This should let us set $CARTOPY_DIR in a compass activation script on LANL IC

Fixes analysis script based on new xarray api

…ean/coastal Near as I can tell, this script is not used and the test case works without it. closes MPAS-Dev#431

Adds spatially-variable Cd and Mannings n drag capabilities. Adds comparison of different use for Cd: ocean/drying_slope/zstar_variableCd/1km Adds variable Manning's n drying slope: ocean/drying_slope/zstar_variableManningn/1km

Adds spatially variable drag coefficient capability based on Cd and n.

Fix cartopy issues with tricontourf

Refractors the zstar test case to allow for above-land wetting/drying.

…above_land Refractors the zstar test case to allow for above-land wetting/drying in a new test case. * Adds drying slope wetting and drying above land

Switch COMPASS from basemap to cartopy

- Add missing +1 offset to cell IDs used in the points.nc file generated in the init step of the hurricane Sandy cases.

…oastal Fix bug in pointwiseStats locations for Sandy cases Simple 0 vs 1 offset error

- Includes the hurricane_wind_pressure code from Donatella Pasqualini that interpolates a parametric wind field onto the MPAS-O mesh - New test case (ocean/hurricane/USDEQU120at30cr10rr2/synthetic_sandy) includes a tidal spin-up period before the storm winds begin. This is needed because the storm winds only cover a 3 day period prior to landfall (not enough time to spin-up tides accurately) - Also, adds the ability to delay the ramp for the atmospheric forcing. In this case this is used to delay the wind/pressure forcing ramp until after the tidal spin-up.

pwolfram · 2020-06-29T23:53:37Z

Code generates the following profile (which is non-physical without an appropriate vertical turbulence model to produce the log-law in the vertical):

Case follows section 5.1 of https://www.sciencedirect.com/science/article/pii/S1463500319302082

pwolfram · 2020-06-29T23:54:37Z

@nairita87, this is a good case that can be used to test your implmentation of z_0 at #606

pwolfram · 2020-06-30T00:00:05Z

@qingli411, can you please try out to see if this provides a log-law in the vertical and parabolic eddy viscosity using GOTM? This should work with just using a standard C_d=1e-3, but to match the paper @nairita87 's z_0 bottom drag implementation will be needed.

qingli411

@pwolfram With the pressure gradient term fixed I was able to run GOTM in this test. I computed the bottom friction velocity using a constant drag coefficient c_d=1e-3 and assuming a constant bottom roughness length z_0=1.5e-3 m, both needed by GOTM. However, it stopped after running for about 9 hours. The run using CVMix with a constant viscosity also stopped after 8 hours and the run with both CVMix and GOTM off stopped after 7 hours. Below is the velocity profiles in the three cases at hour 7. Note that for the 'none' case it shows the velocity profile right before it breaks. I'm not sure what is happening at the bottom... Also in all cases the bottom shear is very big -- I think perhaps we need the bottom drag @nairita87 is working on to fix this?

qingli411 · 2020-07-02T14:59:07Z

src/core_ocean/shared/mpas_ocn_vel_pressure_grad.F

+            pressureGrad = config_zonal_ssh_grad * cos(angleEdge(iEdge)) + config_meridional_ssh_grad * sin(angleEdge(iEdge))
+
+            do k=1,maxLevelEdgeTop(iEdge)
+               tend(k,iEdge) = tend(k,iEdge) - edgeMask(k,iEdge) * density0Inv * pressureGrad


I think this line should be

tend(k,iEdge) = tend(k,iEdge) - gravity * edgeMask(k,iEdge) * pressureGrad

as pressureGrad seems to be the SSH gradient

qingli411 · 2020-07-02T14:59:43Z

src/core_ocean/shared/mpas_ocn_vel_pressure_grad.F

+            cell1 = cellsOnEdge(1,iEdge)
+            cell2 = cellsOnEdge(2,iEdge)


cell1 and cell2 are not used

qingli411 · 2020-07-02T15:03:07Z

testing_and_setup/compass/ocean/periodic_planar/2.5km/default_gotm/config_init.xml

+	<namelist name="namelist.ocean" mode="init">
+		<option name="config_init_configuration">'periodic_planar'</option>
+		<option name="config_vert_levels">-1</option>
+		<option name="config_periodic_planar_vert_levels">25</option>


Should be 250 to match the test in section 5.1 of Kärnä, 2020

nairita87 · 2020-07-02T16:15:20Z

@pwolfram With the pressure gradient term fixed I was able to run GOTM in this test. I computed the bottom friction velocity using a constant drag coefficient c_d=1e-3 and assuming a constant bottom roughness length z_0=1.5e-3 m, both needed by GOTM. However, it stopped after running for about 9 hours. The run using CVMix with a constant viscosity also stopped after 8 hours and the run with both CVMix and GOTM off stopped after 7 hours. Below is the velocity profiles in the three cases at hour 7. Note that for the 'none' case it shows the velocity profile right before it breaks. I'm not sure what is happening at the bottom... Also in all cases the bottom shear is very big -- I think perhaps we need the bottom drag @nairita87 is working on to fix this?

Hi @qingli411 I am looking through the changes now. Will update soon. Can you tell me what is the 'none' case? CVMix and GOTM are switched off? So bottom friction is off?

qingli411 · 2020-07-02T16:25:56Z

@nairita87 Yes, both CVMix and GOTM are switched off in the 'none' case (I should have used a better name...). It is basically zero viscosity. In all three cases I didn't change the configuration of the bottom drag. It should all be using config_use_implicit_bottom_drag = .true. and config_implicit_bottom_drag_coeff = 1.0e-3. The bottom friction velocity I computed is separate and is only used in GOTM to compute the viscosity.

nairita87 · 2020-07-02T16:34:29Z

Okay @qingli411 . I have added a bottom friction case with a variable config_use_implicit_bottom_roughness = .true. Do you have access to that?
I will get back with some updates in a bit

qingli411 · 2020-07-02T16:44:17Z

@nairita87 Is that in your PR #606? I think I have the access but haven't looked at the code... I will need to merge your changes into my branch.

nairita87 · 2020-07-02T16:48:52Z

@qingli411 yes. Okay let me have a look at this

pwolfram · 2020-07-02T19:50:31Z

@qingli411 and @nairita87, please feel free to take the PR from here and make any edits you'd like. This case really needs combined with GOTM and z_0 in order to do the full validation and thank you both for digging in.

I'll leave it to you both as this is my last full week working on this work. Will be around to help with high-level questions if needed, however.

qingli411 · 2020-07-09T17:19:01Z

@pwolfram Here are some updates. Please correct me if I'm wrong @nairita87 .

@nairita87 sets up a run with the new bottom drag in Add NCOM bottom drag formulation #606 with GOTM. The results look much more reasonable than before. See the figure below. Note that this figure plots the velocity profile at one of the center cells (realized that this test case is periodic in x but not in y) whereas the figure I posted earlier was the velocity profile at one of the boundary cells.
With the new bottom drag we can stably run the test case for 12 hours. We will try a longer run to see how fast it can approach equilibrium.

A few things to do next:

I don't think GOTM knows the updated bottom drag coefficient and roughness length in the present setup. I will work with @nairita87 to make these changes to the GOTM module and have everything consistent.
Then we can do a more careful comparison with the case in Kärnä, 2020

sbrus89 · 2020-08-18T21:13:36Z

@qingli411, I cherry-picked 853756ef7 onto the current ocean/coastal here: https://github.com/sbrus89/MPAS-Model/tree/coastal/const_pressure_turb_channel. I can push it @pwolfram's fork to clean up the conflicts. You can see the differences here: sbrus89#4

qingli411 · 2020-08-18T21:38:59Z

Thanks, @sbrus89! I will rebase my changes in my GOTM branch to the current ocean/coastal branch and create a PR from there

sbrus89 · 2020-08-18T21:52:28Z

@qingli411, that sounds great. It may be easier to cherry-pick the specific commits that add the feature rather than do a full rebase since the current ocean/coastal has diverged so much from where you likely started. But either way works.

qingli411 · 2020-08-19T20:42:57Z

Hi @sbrus89, I find the history of the ocean/coastal branch very confusing... I started cherry-picking my changes to include GOTM on top of the ocean/coastal branch this morning. But now the commit history is completely changed... I notice that you did a force-push on ocean/coastal. I wonder what was the change?

sbrus89 · 2020-08-19T20:54:50Z

@qingli411, it is very confusing. We are trying to sync up ocean/coastal and ocean/develop to do the #485 merge. I've had to rebase ocean/coastal several times as ocean/develop has been updated with performance PRs over the last couple weeks. I rebased it again this morning and should have let you know. Sorry for the confusion!

qingli411 · 2020-08-19T21:07:11Z

@sbrus89 OK I see. Thanks! So should I use this version of ocean/coastal or should I wait a little bit?

sbrus89 · 2020-08-19T21:10:53Z

@qingli411, Maybe just hold off until #485 gets merged. I think this should be happening within the next day or two. That way we avoid any wasted effort.

qingli411 · 2020-08-19T21:16:10Z

@sbrus89 Sounds good!

mark-petersen · 2021-03-03T23:32:49Z

@qingli411, this was originally a PR into ocean/coastal, so the history is a bit messed up here. But I think the only relevant commit is 853756e. Looking at that one, I think it is all already included in #704. At least, it definitely includes the same 'constant_forced' version of the pressure gradient. I think the test case additions are in #704 as well, in the directory

testing_and_setup/compass/ocean/periodic_planar/2.5km/default_gotm

Please take a look. If you agree, I will close this PR.

qingli411 · 2021-03-04T02:36:52Z

@mark-petersen Yes, I think this test case is already included in #704 and I agree that we can close this PR.

caozd999 and others added 30 commits December 3, 2019 10:22

compass file cleanup

a0e7ee1

Small formatting clean-up

2c9f465

West coast mesh from SF to LA

657ee2e

Adds HI refined case

b40fe33

Merge MPAS-Dev#424 'coastal/CAcoastMesh' into ocean/coastal

e4f2608

Adds examples of JIGSAW workflow for coastal cases. Adds HI refined case West coast mesh from SF to LA

Fixes analysis script based on new xarray api

546e5a2

Remove link to missing jigsaw Matlab script

dd27d1e

Switch COMPASS from basemap to cartopy

3bb1c0c

This currently only affects coastal test cases.

Set cartopy "pre_existing_data_dir" from $CARTOPY_DIR

899ce0c

This should let us set $CARTOPY_DIR in a compass activation script on LANL IC

Merge MPAS-Dev#428 from pwolfram/coastal/fix_drying_slope

4f0acdc

Fixes analysis script based on new xarray api

Merge PR MPAS-Dev#432 'xylar/ocean/remove_broken_jigsaw_link' into oc…

f6d92a0

…ean/coastal Near as I can tell, this script is not used and the test case works without it. closes MPAS-Dev#431

Adds spatially variable drag coefficient

99d14c7

Adds spatially-variable Cd and Mannings n drag capabilities. Adds comparison of different use for Cd: ocean/drying_slope/zstar_variableCd/1km Adds variable Manning's n drying slope: ocean/drying_slope/zstar_variableManningn/1km

Merge MPAS-Dev#389 'coastal/variable_bottom_drag' into ocean/coastal

fc1700f

Adds spatially variable drag coefficient capability based on Cd and n.

Fix cartopy issues with tricontourf

c7b961f

Merge pull request #1 from sbrus89/basemap_to_cartopy

695ae39

Fix cartopy issues with tricontourf

Adds drying slope wetting and drying above land

8a904e1

Refractors the zstar test case to allow for above-land wetting/drying.

Merge pull request MPAS-Dev#456 from pwolfram/coastal/wetting_drying_…

db21064

…above_land Refractors the zstar test case to allow for above-land wetting/drying in a new test case. * Adds drying slope wetting and drying above land

Merge MPAS-Dev#441 from xylar/ocean/compass/basemap_to_cartopy

58502f1

Switch COMPASS from basemap to cartopy

Fix bug in pointwiseStats locations for Sandy cases

1a9094a

- Add missing +1 offset to cell IDs used in the points.nc file generated in the init step of the hurricane Sandy cases.

Merge MPAS-Dev#483 from sbrus89/hurricane_pointstats_fix into ocean/c…

8cfc422

…oastal Fix bug in pointwiseStats locations for Sandy cases Simple 0 vs 1 offset error

Merge branch 'ocean/develop' into ocean/coastal

9ff39dc

Add separate tendency term for tidal potential forcing

bc4ed8f

Merge tidal potential modules

7de1150

Rename init routine

74649a9

Make 'ssh_gradient' the default pressure gradient type

e7ad894

Add to hurricane_wind_pressure README

f659e42

pwolfram requested a review from vanroekel June 29, 2020 23:51

pwolfram assigned vanroekel Jun 29, 2020

pwolfram added the coastal label Jun 29, 2020

qingli411 suggested changes Jul 2, 2020

View reviewed changes

sbrus89 force-pushed the ocean/coastal branch from 1d6da01 to b88a37f Compare August 3, 2020 20:45

sbrus89 force-pushed the ocean/coastal branch from 5f1875b to f53d3f0 Compare August 14, 2020 22:02

sbrus89 force-pushed the ocean/coastal branch from 025c036 to acea49c Compare August 19, 2020 18:00

qingli411 mentioned this pull request Sep 24, 2020

GOTM in MPAS-Ocean #704

Merged

mark-petersen added the Ocean label Mar 2, 2021

mark-petersen closed this Mar 9, 2021

Conversation

pwolfram commented Jun 29, 2020

Uh oh!

pwolfram commented Jun 29, 2020

Uh oh!

pwolfram commented Jun 29, 2020

Uh oh!

pwolfram commented Jun 30, 2020

Uh oh!

qingli411 left a comment

Choose a reason for hiding this comment

Uh oh!

qingli411 Jul 2, 2020

Choose a reason for hiding this comment

Uh oh!

qingli411 Jul 2, 2020

Choose a reason for hiding this comment

Uh oh!

qingli411 Jul 2, 2020

Choose a reason for hiding this comment

Uh oh!

nairita87 commented Jul 2, 2020

Uh oh!

qingli411 commented Jul 2, 2020

Uh oh!

nairita87 commented Jul 2, 2020

Uh oh!

qingli411 commented Jul 2, 2020

Uh oh!

nairita87 commented Jul 2, 2020

Uh oh!

pwolfram commented Jul 2, 2020

Uh oh!

qingli411 commented Jul 9, 2020

Uh oh!

sbrus89 commented Aug 18, 2020

Uh oh!

qingli411 commented Aug 18, 2020

Uh oh!

sbrus89 commented Aug 18, 2020

Uh oh!

qingli411 commented Aug 19, 2020

Uh oh!

sbrus89 commented Aug 19, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

qingli411 commented Aug 19, 2020

Uh oh!

sbrus89 commented Aug 19, 2020

Uh oh!

qingli411 commented Aug 19, 2020

Uh oh!

mark-petersen commented Mar 3, 2021

Uh oh!

qingli411 commented Mar 4, 2021

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

8 participants

sbrus89 commented Aug 19, 2020 •

edited

Loading