Add suspended sediment concentration tracer #858

caozd999 · 2021-04-28T15:36:37Z

This PR added suspended sediment as a tracer (without source/sink terms) in MPAS-O. The existing lock_exchange code was modified to support a new test case called sed_tracer in the compass (MPAS-Dev/compass#87). The new test case is to simulate 1) a pure diffusion process and 2) a advection-diffusion process (momentum generated by temperature), of suspended sediment and a debug tracer. The results of suspended sediment and the debug tracer will be compared to validate the implementation of suspended sediment as a new tracer in the model.

xylar · 2021-04-28T15:45:25Z

src/core_ocean/mode_init/Registry.xml

+</nml_record>
+<nml_record name="init_vertical_grid" mode="init">
+  <nml_option name="config_init_vertical_grid_type" type="character" default_value="z-star" units="unitless"
+        description="Which vertical grid to initialize with.  Without ice-shelf cavities (i.e. ssh=0 everywhere), 'z-star' and 'z-level' are the same."
+        possible_values="'z-star', 'z-level', or 'haney-number'"
+/>


Oops, I don't think these whitespace changes should have happened. Can you figure out which commit they're in, do and interactive rebase (git rebase --interactive MPAS-Dev/MPAS-Model/ocean/develop) and edit that commit to remove these changes (e.g. git checkout src/core_ocean/mode_init/Registry.xml)?

Ok, I will do that. Thanks!

xylar · 2021-04-28T15:51:18Z

src/core_ocean/mode_init/mpas_ocn_init_lock_exchange.F

-            ! Set debugging tracer
-            if ( associated(debugTracers) ) then
-               do k = 1, nVertLevels
-                  debugTracers(index_tracer1, k, iCell) = 1.0_RKIND
-               enddo
-            end if
-


I'm not an expert in debug tracers but my sense was that debugTracers(1, :, :) was purposefully set to all ones to be a check on conservation in the model. It might be better to modify debugTracer(2 :, :) to serve the purpose you have above.

Thanks, I will put back the debugTracer(index_tracer1, :, :) content and use index_tracer2 for my test case.

Sounds good. Make sure that actually works.

I updated the code and the test case (MPAS-Dev/compass#87) accordingly. I re-ran the case and plot the outputs with no issues.

cbegeman · 2021-04-28T15:59:12Z

src/core_ocean/driver/mpas_ocn_core_interface.F

@@ -126,6 +126,8 @@ function ocn_setup_packages(configPool, packagePool, iocontext) result(ierr)!{{{
      logical, pointer :: tidalForcingActive
      logical, pointer :: tidalPotentialForcingPKGActive
      logical, pointer :: vegetationDragPKGActive
+      logical, pointer :: sedimentTransportPKGActive
+      logical, pointer :: sedimentTracersPKGActive


@caozd999 Does this package still exist?

The two packages both exist. sedimentTransportPKGActive is for general sediment transport, under which we define the sediment transport related variables such as sediment characteristics; sedimentTracersPKGActive is specifically for process-based suspended sediment transport.

cbegeman · 2021-04-28T16:01:36Z

src/core_ocean/mode_forward/mpas_ocn_forward_mode.F

@@ -226,6 +227,8 @@ function ocn_forward_mode_init(domain, startTimeStamp) result(ierr)!{{{
      call ocn_tracer_nonlocalflux_init(err_tmp)
      ierr = ior(ierr,err_tmp)
      call ocn_tracer_ecosys_init(domain, err_tmp)
+      call ocn_tracer_sediment_init(domain, err_tmp)
+      ierr = ior(ierr,err_tmp)


Suggested change

ierr = ior(ierr,err_tmp)

This appears to be a duplicate line

I actually missed one ierr = ior(ierr,err_tmp) after call ocn_tracer_ecosys_init(domain, err_tmp), thank you for pointing it out.

cbegeman · 2021-04-28T16:03:29Z

src/core_ocean/mode_init/Registry_lock_exchange.xml

+			description="Concentration of debug tracer1 in one half of the domain."
+			possible_values="Any real number"
+		/>
+		<nml_option name="config_lock_exchange_high_tracer1" type="real" default_value="10.0" units=""


Does having a default value >0 alter the behavior of the original test case?

Ok. I see now that the debug tracers are not active by default. Are you planning to post a comparison between the debugTracer behavior and the sedimentTracers behavior, perhaps in the compass PR?

@cbegeman yes I've submitted a separate PR to compass MPAS-Dev/compass#87

cbegeman · 2021-04-28T16:18:37Z

src/core_ocean/shared/mpas_ocn_tracer_sediment_mod.F

+    !   treat negative values as zero and apply mask to locals
+    !---------------------------------------------------------------------------
+
+   sedConcen_loc(k,column)      = max(0.0_SEDIMENT_r8, SEDIMENT_input%SEDIMENT_tracers(k,column,sedConcen_ind))


This is a naive question but can you explain why getting rid of negative values happens here as opposed to elsewhere?

I just emulated the codes of DMS and MACROS tracers.

we really don't want to act on any sed tracers with negative concentration, but for conservation we don't want to clip the value of the actual prognostic field, so it's done using a temporary.

cbegeman · 2021-04-28T16:21:49Z

src/core_ocean/shared/mpas_ocn_tracer_sediment_mod.F

+ subroutine SEDIMENT_init(SEDIMENT_indices)
+
+! !DESCRIPTION:
+!  Initialize tracegas tracer module. This involves setting metadata, reading


Are you describing the sediment tracer module as tracegas or something else?

Thanks for pointing them out. The code was for sediment source-sink, I just built the code structure but left the code empty. I will clean the comments.

cbegeman · 2021-04-28T16:30:44Z

src/core_ocean/shared/mpas_ocn_tendency.F

+         if ( groupName == 'sedimentTracers' ) then
+            call ocn_tracer_sediment_compute(tracerGroup, &
+                                     nTracersGroup,forcingPool,  &
+                                     nCellsOwned, maxLevelCell, &


We recently put in some code that allows for inactive top cells, so minLevelCell is needed here and in the subroutine.

@cbegeman is the designated enforcer of the minLevelCell requirement.

Thanks. I will add minLevelCell. The whole routine currently works as a placeholder, and I will modify it accordingly as the development work goes on.

xylar · 2021-05-03T15:34:30Z

@caozd999, could you change the name of the PR to something like "Add sediment concentration tracer"?

xylar

This branch needs to be rebased onto ocean/develop to resolve 2 conflicts with the last merge. Other than that, it looks great to me.

I ran the nightly suite from the legacy compass branch on ocean/develop and a merge of this branch into ocean/develop. I ran with gnu on my Ubuntu laptop and intel on Anvil. Both passed.

I also successfully ran the compass test cases in MPAS-Dev/compass#87. I have made some suggestions on that branch, but they don't affect merging this branch.

Step 1. no source/sink terms

xylar · 2021-05-25T08:09:19Z

@caozd999, I'm pretty sure you're aware at this point that this PR will eventually need to move to E3SM. However, if it isn't ready yet to merge into E3SM (e.g. needs more testing or review, which seems likely to be the case), we should chat about whether it makes sense to keep it here for now or move to the new https://github.com/E3SM-Ocean-Discussion/E3SM space where we will have PRs open for discussion. @mark-petersen, what is your plan for PRs like this one?

maltrud · 2021-05-26T16:58:06Z

@caozd999 did you create a design document for this? i think it would help me understand the implementation.

caozd999 · 2021-05-26T17:28:57Z

@caozd999 did you create a design document for this? i think it would help me understand the implementation.

@maltrud Thanks Mat. I will try to create a design document for this.

caozd999 · 2021-05-26T17:34:08Z

@caozd999, I'm pretty sure you're aware at this point that this PR will eventually need to move to E3SM. However, if it isn't ready yet to merge into E3SM (e.g. needs more testing or review, which seems likely to be the case), we should chat about whether it makes sense to keep it here for now or move to the new https://github.com/E3SM-Ocean-Discussion/E3SM space where we will have PRs open for discussion. @mark-petersen, what is your plan for PRs like this one?

Thanks @xylar. Yes I noticed what you mentioned. In addition, I will need to prepare a design doc for it as @maltrud suggested. Therefore, I am open to any decision.

maltrud · 2021-05-26T17:38:21Z

@caozd999 thanks, Zhendong. it doesn't have to be really detailed. like @cbegeman i'm curious why there are 2 new modules that are very similar. can we combine them?

Also, i'm glad you used the BGC as a guide for this, but i think it would be fine to remove the "parms" module and just include them at the top of the sediment module. the "parms" is a legacy from CESM that we are going to remove with the new BGC implementation (MARBL).

caozd999 · 2021-05-26T18:01:54Z

@maltrud Yes you are right - we can combine them. I am now working on the sediment erosion, and I realize that I can actually put everything into one module. I will do that. Thanks!

xylar · 2021-05-26T18:59:30Z

@caozd999, these sound like significant enough changes that I would suggest closing this PR and opening a new one (perhaps referencing this one) in https://github.com/E3SM-Ocean-Discussion/E3SM. That way, it will be a lot easier to move over the E3SM-Project/E3SM when you're ready to get final approval and merge. Sorry this has been such a moving target. Bad timing.

mark-petersen · 2021-08-12T17:13:38Z

PR moved to E3SM-Ocean-Discussion/E3SM#4

caozd999 requested review from xylar, mark-petersen, philipwjones, cbegeman and maltrud April 28, 2021 15:37

xylar reviewed Apr 28, 2021

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xylar assigned mark-petersen Apr 28, 2021

xylar added feature Ocean labels Apr 28, 2021

cbegeman reviewed Apr 28, 2021

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xylar mentioned this pull request Apr 28, 2021

Added a case to validate the implementation of suspended sediment as a tracer MPAS-Dev/compass#87

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caozd999 force-pushed the ocean/sediment_transport_PR branch from 1889c14 to 6a666d9 Compare April 28, 2021 21:09

caozd999 changed the title ~~Ocean/sediment transport pr~~ Add suspended sediment concentration tracer May 3, 2021

xylar approved these changes May 4, 2021

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caozd999 force-pushed the ocean/sediment_transport_PR branch from 6a666d9 to 0e70bb6 Compare May 4, 2021 16:29

caozd999 added 3 commits May 4, 2021 10:35

Initialize the prognostic sediment transport model

e3ee73f

Add suspended sediment concentration as a tracer

4e18d5c

Step 1. no source/sink terms

Validate the sediment tracer implementation

c36a9c8

caozd999 force-pushed the ocean/sediment_transport_PR branch from 0e70bb6 to c36a9c8 Compare May 4, 2021 17:11

mark-petersen closed this Aug 12, 2021

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Add suspended sediment concentration tracer #858

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