Code

MARBL Support#92

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gustavo-marques merged 153 commits intoESCOMP:mainESCOMP/MOM_interface:mainfrom mnlevy1981:MARBL_supportmnlevy1981/MOM_interface:MARBL_supportCopy head branch name to clipboardAug 5, 2024

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Commits

Commits on Sep 10, 2019

• Build MARBL

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• Merge branch 'master' into MARBL_support

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Commits on Sep 11, 2019

• Add a C1850MOMECO compset

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• Add G1850MOMECO compset

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• Add MARBL tracers to diagnostic output list

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• Update PE layouts for compsets with MARBL

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Commits on Sep 12, 2019

• Generate marbl_in in RUNDIR

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Commits on Oct 9, 2019

• Merge branch 'master' into MARBL_support

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Commits on Feb 13, 2020

• Merge branch 'master' into MARBL_support

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• Re-run yaml_to_json.py

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• Update Externals.cfg and Externals_MOM.cfg

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• Add transports to diag_table

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Commits on Mar 11, 2020

• Merge branch 'master' into MARBL_support

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Commits on May 1, 2020

• MARBL is no longer a submodule of MOM

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Commits on May 4, 2020

• Group calls needed to add MARBL

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• Update comment to refer to cime mods

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Commits on Jun 11, 2020

• Split BGC fields into separate monthly stream

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• Clean up additional stream definition

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Commits on Jun 12, 2020

• Merge branch 'master' into MARBL_support

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Commits on Jul 26, 2020

• Merge branch 'master' into MARBL_support

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• Update to latest MARBL

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Commits on Aug 28, 2020

• Update PE layouts and output list

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Commits on Sep 21, 2020

• Add hm_bgc stream to testing

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Commits on Sep 29, 2020

• Add DUST_FLUX and IRON_FLUX to output stream

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Commits on Oct 2, 2020

• Add NOx_FLUX and NHy_FLUX to hm_bgc

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Commits on Nov 12, 2020

• Add FESEDFLUX to diag table

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Commits on Jan 20, 2021

• Merge branch 'master' into MARBL_support

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Commits on Jan 22, 2021

• Multiple json files to generate diag_table

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• Previous commit assumed momconf/ existed

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Commits on Feb 4, 2021

• generate Buildconf/momconf/ecosys_diagnostics

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• Refactor buildnml

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Commits on Feb 5, 2021

• Updates to ecosys_diagnostics generation

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• Add STF_O2 and J_DIC to output lists

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Commits on Feb 9, 2021

• diag_table_MARBL.json from ecosys_diagnostics

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Commits on Feb 10, 2021

• Update some diag_manager namelist defaults

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Commits on Feb 11, 2021

• 3D tracers should be on z levels

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Commits on Feb 18, 2021

• Add env_build.xml flag for building MARBL

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• Improvements for testing

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Commits on Mar 2, 2021

• Add nuopc tests to test list

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Commits on Mar 18, 2021

• Add more MARBL output to default diag_table

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• New compsets

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• Add JRA compsets with MOM6%ECO

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Commits on Apr 1, 2021

• Some general clean-up

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Commits on Apr 2, 2021

• Add FLUX_CPL diagnostics to history output

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Commits on Apr 3, 2021

• Add RIV_FLUX output to history files

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Commits on Apr 16, 2021

• Merge tag 'mi_20210409' into HEAD

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Commits on Jul 8, 2021

• Update to latest MARBL release

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Commits on Jul 13, 2021

• Improved diagnostic handling

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Commits on Jul 25, 2021

• Set MIX_BOUNDARY_TRACER_ALE=True for MARBL

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Commits on Jul 26, 2021

• Updates from testing on izumi

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Commits on Aug 13, 2021

• Merge branch 'main' into MARBL_support

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Commits on Aug 25, 2021

• Update to latest MARBL tag

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Commits on Sep 2, 2021

• Easier to set vertical grid for BGC history files

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• Revert changes to MOM_ecosys_diagnostics.py

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Commits on Sep 10, 2021

• Update to latest MARBL tag

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Commits on Sep 15, 2021

• Make sure MARBL streams are archived / tested

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Commits on Sep 23, 2021

• Easier to switch between monthly and nstep output

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Commits on Sep 24, 2021

• Remove "none" as valid OCN_BGC_CONFIG option

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• Get use_MARBL from MOM_input_final

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Commits on Sep 27, 2021

• ECO -> MARBL in compset names

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Commits on Oct 6, 2021

• Update default PE layouts

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• Avoid duplicate PE match

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• _SURF and _zint_100m diagnostics are 2D

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Commits on Oct 7, 2021

• Pare down variables in 3D native output

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Commits on Apr 8, 2022

• Merge tag 'mi_220225' into MARBL_support

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Commits on Apr 15, 2022

• More PEs when running with MARBL

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Commits on Apr 25, 2022

• Three different updates rolled into one

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Commits on Sep 14, 2022

• Merge branch 'main' into MARBL_support

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Commits on Sep 20, 2022

• set CPL_I2O_PER_CAT to match use_MARBL

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Commits on Sep 21, 2022

• Add additional comment buildnml

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Commits on Oct 3, 2022

• Add ICE_NCAT and USE_ICE_CATEGORIES to MOM_input

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Commits on Oct 5, 2022

• add per-category fraction / sw diags

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Commits on Oct 13, 2022

• Clean up CPL_I2O_PER_CAT and add some defaults

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Commits on Jan 27, 2023

• Merge tag 'mi_230121' into MARBL_support

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Commits on Jan 28, 2023

• Update standalone to include KPP_MARBL

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Commits on Feb 1, 2023

• Improvements to standalone KPP_MARBL

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Commits on Feb 2, 2023

• Move KPP_MARBL INPUT to new directory

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• Add support for standalone cases on macOS

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Commits on Feb 3, 2023

• Update forcings to be uniform across grid cells

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Commits on Feb 24, 2023

• CHL_FROM_FILE=FALSE when MARBL is active

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Commits on Mar 7, 2023

• Make it easier to turn off ice categories

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Commits on Mar 23, 2023

• Updates for stand-alone examples

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Commits on Mar 29, 2023

• Two small updates

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Commits on Mar 31, 2023

• Added NDEP and SEAICE forcings from A compset

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• Switch T&S IC file to TS_IC_FILE_COLUMN.nc

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• Add support for submitting build script to PBS

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Commits on Apr 11, 2023

• Bugfix plus parameter reversion

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Commits on Apr 14, 2023

• Updated INPUT files

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Commits on Apr 19, 2023

• Update MOM_parameter_doc files

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Commits on Apr 20, 2023

• Improve default values for CO2 variables

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• Logic to add ALT_CO2 diagnostics when necessary

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Commits on Apr 21, 2023

• Some code clean-up following review

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Commits on Apr 25, 2023

• ParamGen computes DUST_RATIO_TO_FE_BIOAVAIL_FRAC

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Commits on May 2, 2023

• Updates to support 4p2z

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• Update MOM_parameter_doc.all

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• single_column/KPP_MARBL -> single_column_MARBL/BATS

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• single_column_MARBL, not single_column_KPP

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Commits on May 3, 2023

• Update forcing files and MOM_input for BATS

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• Updated BATS test, added EQPAC test

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• Removed some unnecessary files

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Commits on May 4, 2023

• Add inputs for HOT

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• Some directory restructuring and a bug fix

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Commits on May 5, 2023

• Moved marbl_in to INPUT/

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• Adding more data for single-column locations

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Commits on May 10, 2023

• Update forcing for each column

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• Remove tracer restoring from marbl_in

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Commits on May 11, 2023

• PFT_defaults = "4p2z" is supported now

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Commits on May 17, 2023

• Update SST_RESTORE in all forcing files

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• Add submit scripts for running single_column_MARBL

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• Update .gitignore

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Commits on Jun 1, 2023

• Add script to run all 7 tests simultaneously

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Commits on Jun 16, 2023

• Move MOM_input and diag_table to INPUT/

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Commits on Aug 9, 2023

• Generate marbl_in in mks, not cgs

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Commits on Aug 14, 2023

• Merge tag 'mi_230601' into MARBL_support

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Commits on Aug 15, 2023

• Update stream names to fit CESM convention

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Commits on Aug 17, 2023

• Add Fe forcing files to MOM_input

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Commits on Aug 25, 2023

• Add riverine input file to MOM_input

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Commits on Oct 20, 2023

• Small updates for t232 and single column

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Commits on Oct 23, 2023

• Update darwin build template

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Commits on Nov 15, 2023

• Use restoring for single_column_MARBL tests

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Commits on Nov 28, 2023

• Merge tag 'mi_231107' into MARBL_support

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• Update casper build template

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Commits on Dec 1, 2023

• MARBL_generate_diagnostics needs unit_system

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• Update build template for casper

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• Cleaned up casper / derecho builds

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Commits on Dec 15, 2023

• Update tx2_3v2 forcing files

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Commits on Dec 21, 2023

• Update to support ABIO tracers

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• Add MARBL pe layouts for derecho

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Commits on Dec 23, 2023

• Update to get volcello in correct cells

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• Update input_nml.yaml for MARBL support

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• Previous commit was missing a "value" key

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Commits on Dec 29, 2023

• Update a few functions to handle base_bio_on=False

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Commits on Feb 2, 2024

• Update river flux forcing file

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Commits on Mar 1, 2024

• Allow ABIO to be enabled from compset

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Commits on Mar 7, 2024

• Support for latest MARBL

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Commits on Mar 8, 2024

• Update MARBL_TRACER_OPT values

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Commits on Mar 14, 2024

• Update to latest MARBL tag

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• Merge tag 'mi_240311' into MARBL_support

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Commits on Mar 26, 2024

• Move CICE onto same node as CMEPS / CDEPS / etc

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Commits on Mar 27, 2024

• Remove '=====' from testlist

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Commits on May 2, 2024

• Moved MARBL input files to input data

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Commits on May 6, 2024

• Precision of MARBL fields matches rest of diags

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• OCN_DIAG_MODE = "none" => no MARBL fields

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Commits on May 16, 2024

• Update to marbl0.47.0

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• Merge tag 'mi_240510' into MARBL_support

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Commits on May 17, 2024

• Add ability to have Jint_100m in minimal output

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• Add thetao and so back to bgc stream

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Commits on Jun 5, 2024

• Fix input_data logic for river flux file

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Commits on Jul 17, 2024

• Lots of updates from code review

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• Ran black in cime_config/MARBL_scripts/

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Commits on Aug 2, 2024

• Merge tag 'mi_240730' into MARBL_support

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• Fix change in case in .gitmodules

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• Added G1850MARBL_JRA tests to prealpha and prebeta

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