snow/sea ice shortwave radiative transfer harmonization by chengdang · Pull Request #63 · MPAS-Dev/MPAS-Model

chengdang · 2018-08-10T06:58:49Z

This merge adds an optional subroutine to the snow-covered sea ice shortwave radiative transfer calculations that allows the snow to be treated the same to the land snow model (SNICAR). The same subroutine also improves the shortwave calculation of near-IR band for snow-covered sea ice with new parameterizations.

Added get_domain to testing system.

…se into cice/develop

This PR updates config flags/parameters and output biogeochemistry fields.

…o cice/develop

New namelist parameter, config_aggregate_halo_exch, to control use of aggregated halo exchanges Most halo exchanges now have option to be aggregated Removed multiple block test from test suite

… into cice/develop

…velop

Add bgc coupling namelist option

…ions' into cice/develop

Cleanup of a few namelist descriptions.

…lues

Added option for mpi_barriers before halo exchanges and timers around them Added new namelist option config_load_balance_timers

…develop Modify COMPASS scripts to be PEP8 compliant The four main scripts that drive the COMPASS testing infrastructure were written with tabs, long lines and many other coding conventions that are discouraged in python. This merge ensures that the scripts are compliant with the PEP8 specification, as determined by the automatic code analysis within the spyder editor. The following mode line (for vim) has been added to the bottom of each file: # vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python All empty except: clauses have been replaced with explicit exception names. Empty except clauses are considered a bad practice in python because (among other issues) even syntax errors in the code itself will be trapped by the except (a potential debugging nightmare). With one exception, the scripts are expected to function identically before and after this merge. Only formatting changes for PEP8 compliance have been performed. The exception is that support for the --verbose flag has been added to the cleanup phase of the manage_regression_suite.py script for consistency with the setup phase. Copying of the environment in subprocess calls has been removed, as this is the default behavior. Auto-generated scripts have been made PEP8 compliant to the extent possible. (The main PEP8 violations are that lines are often too long because of long strings that can not easily be broken into substrings.)

This fixes analysis members that currently write warnings on every call.

Added halo barriers after coupling and after halo exchange Added option to turn off halo exchanges

chengdang · 2018-09-21T00:28:43Z

@akturner I removed the files you mentioned and snicar_optics_5bnd_snow_and_aerosols.nc, and updated namelist.seaice and streams.seaice under directory: testing_and_setup/seaice/configurations/standard_physics/

akturner · 2018-09-24T18:12:46Z

testing_and_setup/seaice/configurations/standard_physics/namelist.seaice

    config_calendar_type = 'gregorian_noleap'
    config_start_time = '2000-01-01_00:00:00'
    config_stop_time = 'none'
-    config_run_duration = '00-00-01_00:00:00'


Don't make unnecessary changes to pre-exisiting configurations.

Okay, this change was made for model simulation. Revised

akturner · 2018-09-24T18:13:06Z

testing_and_setup/seaice/configurations/standard_physics/namelist.seaice

    config_AM_timeSeriesStatsCustom_reset_intervals = '00-00-07_00:00:00'
    config_AM_timeSeriesStatsCustom_backward_output_offset = '00-00-01_00:00:00'
 /
+&snicar_variables


Put this in the "shortwave" namelist section

akturner · 2018-09-24T18:13:31Z

testing_and_setup/seaice/configurations/standard_physics/namelist.seaice

    config_AM_timeSeriesStatsCustom_backward_output_offset = '00-00-01_00:00:00'
 /
+&snicar_variables
+    config_turn_snicar_system_on = true


Rename this config_use_snicar

testing_and_setup/seaice/configurations/standard_physics/streams.seaice

akturner · 2018-09-24T18:15:03Z

src/core_seaice/Registry.xml

 			possible_values="true or false"
 		/>
 	</nml_record>
+


Remove unnecessarly added blank line

akturner · 2018-09-24T18:20:56Z

src/core_seaice/Registry.xml

 	</var_struct>

+	<!-- Snicar 5-band optical property varables -->
+	<var_struct name="snicar_variables" time_levs="1" packages="pkgSnicarSystem">


Rename pool "snicar" from "snicar_variables"

src/core_seaice/shared/mpas_seaice_column.F

akturner · 2018-09-24T18:22:18Z

src/core_seaice/shared/mpas_seaice_column.F

               pondLidMeltFluxFraction(:,iCell), &
               .false., &
-               lInitialization)
+               lInitialization,          &


Excess spaces - fix formatting

akturner · 2018-09-24T18:22:32Z

src/core_seaice/shared/mpas_seaice_column.F

       call MPAS_pool_get_subpool(block % structs, "initial", initial)
       call MPAS_pool_get_subpool(block % structs, "velocity_solver", velocity_solver)

+


Remove excess blank line

akturner · 2018-09-24T18:22:47Z

src/core_seaice/shared/mpas_seaice_column.F

    call MPAS_pool_get_config(domain % configs, "config_scales_absorption_phaeocystis", config_scales_absorption_phaeocystis)
    call MPAS_pool_get_config(domain % configs, "config_ratio_C_to_N_proteins", config_ratio_C_to_N_proteins)

+


Remove excess space

…ormat

chengdang · 2018-09-25T06:55:31Z

Adrian, thanks for checking the code. Modified files have been pushed. Please check if there are more changes need to be made.

src/core_seaice/column/ice_shortwave.F90

testing_and_setup/seaice/configurations/standard_physics/streams.seaice

rewrote modified streams.seaice based off streams.seaice on master branch

akturner

Please pay attention to code formatting and ensure you keep indenting and general style the same as before.

akturner · 2018-10-22T14:50:29Z

testing_and_setup/seaice/configurations/standard_physics/namelist.seaice

 &shortwave
    config_shortwave_type = 'dEdd'
    config_albedo_type = 'ccsm3'
+    config_use_snicar = true


Why is this set to true?

It is set to false now

akturner · 2018-10-22T14:55:08Z

src/core_seaice/shared/mpas_seaice_column.F

         albedoIRDiffuseCategory, &
-         snowFractionCategory
+         snowFractionCategory,&
+         iceAsymmtryParameterDirect,     &


Fix this formatting: extra spaces

akturner · 2018-10-22T14:55:18Z

src/core_seaice/shared/mpas_seaice_column.F

         brineFraction, &
         modalBCabsorptionParameter, &
-         bioTracerShortwave
+         bioTracerShortwave,  &


akturner · 2018-10-22T14:56:44Z

src/core_seaice/column/ice_shortwave.F90

+         ext_cff_mss_ice_dfs    ! snow mass extinction cross section (m2/kg)
+
+      real (kind=dbl_kind), dimension(:,:), intent(in) :: &
+        kaer_tab_5bd, & ! aerosol mass extinction cross section (m2/kg)


Be consistent with indenting

akturner · 2018-10-22T14:57:10Z

src/core_seaice/column/ice_shortwave.F90


+      logical (kind=log_kind), intent(in) :: &
+         use_snicar    ! if true, use 5-band snicar IOPs for
+                           ! shortwave radiative calculation of


Consistent formatting

fixed comment format

akturner · 2018-10-22T14:57:29Z

src/core_seaice/column/ice_shortwave.F90

+          ext_cff_mss_ice_dfs    ! snow mass extinction cross section (m2/kg)
+
+      real (kind=dbl_kind), dimension(:,:), intent(in) :: &
+         kaer_tab_5bd, & ! aerosol mass extinction cross section (m2/kg)


consistent indenting: keep original style

akturner · 2018-10-22T14:57:43Z

src/core_seaice/column/ice_shortwave.F90

               srftyp = 1
-               call compute_dEdd(nilyr,       nslyr,   klev,   klevp,   & 
+
+              if (use_snicar) then ! use 5-band snicar IOPs for snow


akturner · 2018-10-22T14:57:52Z

src/core_seaice/column/ice_shortwave.F90

+
+              if (use_snicar) then ! use 5-band snicar IOPs for snow
+
+                call compute_dEdd_5bd(nilyr, nslyr, klev, klevp,      &


akturner · 2018-10-22T14:57:59Z

src/core_seaice/column/ice_shortwave.F90

+                        fswsfc,    fswint,                                &
+                        fswthru,   Sswabs,                                &
+                        Iswabs,    fswpenl,                               &
+                        asm_prm_ice_drc, asm_prm_ice_dfs, &


akturner

Currently doesn't run the test case without failure

akturner · 2018-10-22T20:28:15Z

src/core_seaice/shared/mpas_seaice_column.F

       call MPAS_pool_get_array(biogeochemistry, "verticalGrid", verticalGrid)

+       ! snicar 5-band snow IOPs
+       call MPAS_pool_get_array(snicar_variables, "iceAsymmtryParameterDirect",iceAsymmtryParameterDirect)


akturner · 2018-10-22T20:28:40Z

src/core_seaice/shared/mpas_seaice_column.F

+       call MPAS_pool_get_array(snicar_variables, "aerosolSingleScatterAlbedo5band", aerosolSingleScatterAlbedo5band)
+       call MPAS_pool_get_array(snicar_variables,"aerosolAsymmetryParameter5band", aerosolAsymmetryParameter5band)
+       call MPAS_pool_get_array(snicar_variables, "modalMassExtinctionCrossSection5band", modalMassExtinctionCrossSection5band)
+       call MPAS_pool_get_array(snicar_variables,"modalSingleScatterAlbedo5band", modalSingleScatterAlbedo5band)


akturner · 2018-10-22T20:28:41Z

src/core_seaice/shared/mpas_seaice_column.F

+       call MPAS_pool_get_array(snicar_variables, "iceMassExtinctionCrossSectionDiffuse", iceMassExtinctionCrossSectionDiffuse)
+       call MPAS_pool_get_array(snicar_variables, "aerosolMassExtinctionCrossSection5band", aerosolMassExtinctionCrossSection5band)
+       call MPAS_pool_get_array(snicar_variables, "aerosolSingleScatterAlbedo5band", aerosolSingleScatterAlbedo5band)
+       call MPAS_pool_get_array(snicar_variables,"aerosolAsymmetryParameter5band", aerosolAsymmetryParameter5band)


akturner · 2018-10-22T20:28:42Z

src/core_seaice/shared/mpas_seaice_column.F


+       ! snicar 5-band snow IOPs
+       call MPAS_pool_get_array(snicar_variables, "iceAsymmtryParameterDirect",iceAsymmtryParameterDirect)
+       call MPAS_pool_get_array(snicar_variables, "iceAsymmtryParameterDiffuse",iceAsymmtryParameterDiffuse)


chengdang · 2018-10-24T04:24:46Z

@akturner Hi, Thanks for checking it. Could you please send me the error log of your test run?

There are few things to note and I noticed when testing the current code:

To run the modified code, you would need a new input file called

snicar_optics_5bnd_snow_and_aerosols.nc

which I will send to you via email shortly. This file contains the new input data for new features.

In the run package distributed online (https://zenodo.org/record/1219191#.W86xJhNKiRs), MPAS-seaice aerosol input files are given as name

standard_optics_mpas_seaice.nc
snicar_optics_5bnd_mam_c140303_mpas_seaice.nc

while in MPAS-seaice code .../core_seaice/Registry.xml, these files are still named as

standard_optics_mpas_cice.nc
snicar_optics_5bnd_mam_c140303_mpas_cice.nc

So one would need to rename these files under run directory or change the source code for MPAS-seaice to read inputs.

Test run with the streams.seaice generated from building MPAS-seaice leads to the following error log

 ----------------------------------------------------------------------
Beginning MPAS-seaice Error Log File for task       0 of       1
    Opened at 2018/10/22 22:09:37
----------------------------------------------------------------------

CRITICAL ERROR: MPAS-Ocean there are no fields in the time series stats output stream "timeSeriesStatsMonthlyOutput" that time series stats can be applied to.
Logging complete.  Closing file at 2018/10/22 22:09:37

So I tested the codes with the above modifications 1 and 2 using my modified streams.seaice file (which I will send via email too), and it runs fine for one month test.

akturner · 2018-11-06T14:24:56Z

testing_and_setup/seaice/configurations/standard_physics/streams.seaice

                  filename_interval="none"
                  input_interval="initial_only" />

+<immutable_stream name="StandardAerosolsInput"


Why have these been added here? This now creates errors for the basic tests that dont involve this functionality,

Interesting. I added this because these were added in the stream.cice file you shared with me last year, which was probably used for a more advanced version of MPAS-seaice? I have never done any tests with these since I don't have any aerosol input data, neither did I modify the codes related to these. The stream file I used also contain these (per email I sent on Oct 23rd), and I am able to run MPAS-seaice model without errors.

Would you like me to remove these for this model merge? If so, there will be no aerosol optical properties inputs for the solar radiative transfer calculation.

Yes, please remove these. Theyre not needed for the base physics simulation.

Sure. They are removed.

akturner · 2018-11-06T14:36:46Z

In answer to your questions above:

Thanks!
Thanks for letting me know - I will look at this.
I will fix this, but generally this file shouldn't be used
You might want to add a directory to configurations, called "snicar_shortwave" with a streams file and namelist that tests your functionality.

…streams file and namelist for snicar_shortwave test

chengdang · 2018-11-07T00:07:36Z

Thanks! A directory (snicar_shortwave) with streams file and namelist is added to configurations for testing snicar related features.

akturner · 2018-11-08T14:14:36Z

testing_and_setup/seaice/configurations/standard_physics/streams.seaice

                  filename_interval="none"
                  input_interval="initial_only" />

+<immutable_stream name="SnicarInput"


This isnt needed in this configuration. Please remove it.

akturner · 2018-11-08T14:17:42Z

Please add a README file to the snicar_shortwave configuration describing its unique features

…hysics add README for configuration snicar_shortwave

chengdang · 2018-11-08T19:56:22Z

README file is added to configuration snicar_shortwave

akturner · 2018-11-09T09:44:53Z

Few more modifications:

Add config_use_snicar = .false. to the appropriate place in the other namelists in the MPAS-Model/testing_and_setup/seaice/configurations/ directories
Change the streams file in MPAS-Model/testing_and_setup/seaice/configurations/snicar_shortwave so that "forcing/" appears in front of the aerosol files since this is where they will be pulled automatically during testing
Change the name of standard_optics_mpas_cice.nc in that streams file to standard_optics_mpas_seaice.nc since this is the name in the testing data set.

The snicar streams file should read:

<immutable_stream name="StandardAerosolsInput"
type="input"
filename_template="forcing/standard_optics_mpas_seaice.nc"
filename_interval="none"
input_interval="initial_only" />

<immutable_stream name="SnicarInput"
type="input"
filename_template="forcing/snicar_optics_5bnd_snow_and_aerosols.nc"
filename_interval="none"
input_interval="initial_only" />

… configurations

chengdang · 2018-11-09T19:54:24Z

Thanks Adrian. These are modified.

akturner · 2018-11-14T18:21:29Z

testing_and_setup/seaice/configurations/snicar_shortwave/streams.seaice

+
+<immutable_stream name="SnicarInput"
+                  type="input"
+                  filename_template="forcing/snicar_optics_4bnd_snow_and_aerosols.nc"


Should not this be snicar_optics_5bnd_snow_and_aerosols.nc? Currently with the files I've been provided with this configuration fails because of this misnaming. Please test additions to PR.

You're right. Thanks for catching this typo. It is fixed.

…PAS-Dev#63) function that will completely turn off transpiration at wilting point soil moisture instead of allowing a very small transpiration.

akturner and others added 30 commits October 27, 2017 14:43

Merge pull request #1444 from akturner/cice/get_domain

d050e46

Added get_domain to testing system.

Removed all references to colpkg constants except in mpas_cice_constants

e253444

Merge remote-tracking branch akturner/cice/remove_icepack_constants_u…

86a9f29

…se into cice/develop

Add units and descritptions to Registry for BGC. BFB

4ba48bd

This PR updates config flags/parameters and output biogeochemistry fields.

Merge remote-tracking branch 'njeffery/cice/njeffery_cleanRegBGC' int…

1861227

…o cice/develop

Added option for aggregated halo exchanges

3baf8ff

New namelist parameter, config_aggregate_halo_exch, to control use of aggregated halo exchanges Most halo exchanges now have option to be aggregated Removed multiple block test from test suite

Merge remote-tracking branch 'akturner/cice/aggregated_halo_exchange'…

93b9a87

… into cice/develop

Merge remote-tracking branch 'MPAS-Dev/develop' into MPAS-Dev/cice/de…

89551fc

…velop

Added namelist option for bgc ocean coupling

ddcc863

Merge pull request #1461 from akturner/cice/add_bgc_namelist

29cde6b

Add bgc coupling namelist option

Add descriptions to namelist options

dd67f3e

Merge remote-tracking branch 'akturner/cice/improve_registry_descript…

9b405f0

…ions' into cice/develop

Cleanup of a few namelist descriptions.

9bfb45b

Merge pull request #1465 from akturner/cice/cleanup_namelist

f07ba78

Cleanup of a few namelist descriptions.

Removed newlines from namelist and variables comments and possible va…

81fb043

…lues

Merge 'akturner/cice/namelist_build_warnings' into cice/develop

0c900c9

Added load balance timers

0174176

Added option for mpi_barriers before halo exchanges and timers around them Added new namelist option config_load_balance_timers

Merge 'akturner/cice/load_balance_timer' into cice/develop

6d23798

Merge 'MPAS-Dev/develop' into cice/develop

c9533a1

Fix pool am problems that produce warnings

3baab50

Merge branch 'ocean/fix_am_pool_typos' into ocean/develop

af92a0f

This fixes analysis members that currently write warnings on every call.

Merge 'develop' into ocean/develop (reusable halo exchanges)

c01e7b4

Merge 'MPAS-Dev/develop' into cice/develop

04d7107

Added ability to reuse halo exchange lists

bf2be0a

Merge 'akturner/cice/add_halo_reuse' into cice/develop

e8d66ee

Improved halo exchange diagnostics

d3b72bf

Added halo barriers after coupling and after halo exchange Added option to turn off halo exchanges

Small formatting change in Registry

dfea51f

Merge 'akturner/cice/halo_diagnostics' into cice/develop

6f45783

Increased granularity of halo barrier timers

e3c45cd

akturner requested changes Sep 24, 2018

View reviewed changes

rename snicar related variables, remove extra lines, fix other code f…

1908cb6

…ormat

akturner requested changes Oct 9, 2018

View reviewed changes

src/core_seaice/column/ice_shortwave.F90 Show resolved Hide resolved

testing_and_setup/seaice/configurations/standard_physics/streams.seaice Show resolved Hide resolved

fixed minor format issues in ice_shortwave.F90

d9c07e1

rewrote modified streams.seaice based off streams.seaice on master branch

akturner requested changes Oct 22, 2018

View reviewed changes

fix code format

46f1a37

akturner requested changes Oct 22, 2018

View reviewed changes

modify Registry.xml and etc for updated stream names

b33753b

akturner requested changes Nov 6, 2018

View reviewed changes

add directory "snicar_shortwave" to configurations that contains the …

0961aab

…streams file and namelist for snicar_shortwave test

remove aerosol optical input in stream file for standard physics

ad3a5d1

akturner requested changes Nov 8, 2018

View reviewed changes

remove extra modification for stream file of configuration standard_p…

9b0916e

…hysics add README for configuration snicar_shortwave

modify namelist and stream file for to include snicar for all sea ice…

2cf4658

… configurations

akturner requested changes Nov 14, 2018

View reviewed changes

fix typo in stream.seaice

187eae3

akturner merged commit 187eae3 into MPAS-Dev:seaice/develop Nov 14, 2018

chengdang mentioned this pull request Dec 7, 2018

add constant for E3SM coupled simulation (follow up on PR#63) #122

Merged

matthewhoffman added feature Sea ice labels Mar 17, 2021

		call MPAS_pool_get_subpool(block % structs, "initial", initial)
		call MPAS_pool_get_subpool(block % structs, "velocity_solver", velocity_solver)

		call MPAS_pool_get_config(domain % configs, "config_scales_absorption_phaeocystis", config_scales_absorption_phaeocystis)
		call MPAS_pool_get_config(domain % configs, "config_ratio_C_to_N_proteins", config_ratio_C_to_N_proteins)


		if (use_snicar) then ! use 5-band snicar IOPs for snow

		call compute_dEdd_5bd(nilyr, nslyr, klev, klevp, &

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chengdang commented Aug 10, 2018

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chengdang commented Sep 25, 2018

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chengdang Nov 6, 2018 •

edited

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