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dtc/hwrf-physics: HWRF Ferrier-Aligo MP scheme updates #435

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merged 1 commit into from
Apr 16, 2020
Merged

dtc/hwrf-physics: HWRF Ferrier-Aligo MP scheme updates #435

merged 1 commit into from
Apr 16, 2020

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climbfuji
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@climbfuji climbfuji commented Apr 14, 2020 •
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This PR contains:

Associated PRs:

#435
NCAR/fv3atm#43
NCAR/ufs-weather-model#41

For regression testing information, see NCAR/ufs-weather-model#41.

@mzhangw @climbfuji
Merge mzhangw:HAFS_fer_hires into NCAR:dtc/hwrf-physics
6a8c80e 
Squashed commit of the following:

commit 406f740
Author: Man.Zhang <[email protected]>
Date:   Mon Apr 13 20:24:59 2020 -0600

    FA uses progcld5

commit 682fab9
Merge: 25b3f66 d979604
Author: Man.Zhang <[email protected]>
Date:   Mon Mar 16 10:42:12 2020 -0600

    Merge branch 'dtc/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit 25b3f66
Author: Man.Zhang <[email protected]>
Date:   Mon Mar 16 10:37:42 2020 -0600

    modify stateout update of FA scheme

commit 05c5331
Author: Man Zhang <[email protected]>
Date:   Tue Feb 11 16:45:48 2020 -0700

    sci doc updates

commit 982a11d
Author: Man Zhang <[email protected]>
Date:   Fri Feb 7 16:47:00 2020 -0700

    FA sci doc updates

commit 27c1fcb
Merge: 8d87e55 73f9f09
Author: Man.Zhang <[email protected]>
Date:   Fri Feb 7 14:26:54 2020 -0700

    Merge branch 'dtc/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit 8d87e55
Author: Man.Zhang <[email protected]>
Date:   Fri Feb 7 14:24:47 2020 -0700

    FA scientific documentation

commit 67ad5a5
Author: Man.Zhang <[email protected]>
Date:   Wed Dec 11 13:13:48 2019 -0700

    consolidate with Chunxis version

commit 76b5475
Merge: 7c6a472 02812f6
Author: Man.Zhang <[email protected]>
Date:   Wed Dec 11 11:49:22 2019 -0700

    Merge branch 'dtc/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit 7c6a472
Author: Man.Zhang <[email protected]>
Date:   Thu Dec 5 16:28:50 2019 -0700

    output mass weighted RF in GFS_suite_stateout_update_run, it will used in FA

commit 41086af
Merge: 92d9edf f895fc0
Author: Man.Zhang <[email protected]>
Date:   Thu Dec 5 12:08:30 2019 -0700

    Merge branch 'dtc/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit 92d9edf
Author: Man.Zhang <[email protected]>
Date:   Mon Nov 25 14:16:16 2019 -0700

    chunxi fix : f_rimef = qg in FA code

commit f9e3ee0
Author: Man.Zhang <[email protected]>
Date:   Mon Nov 25 11:39:54 2019 -0700

     From Eric: convert wet mixing ratios of cloud species to mixing ratio
    before the scheme, and convert back after scheme.

     From Chunxi, modify: 1. FA interface with GFS RRTMG using progcld2;
    2.air pressure improvement; 3. add f_qrimef mixing in PBL

commit f497d40
Merge: bd4a30c 73b8c0d
Author: Man.Zhang <[email protected]>
Date:   Mon Nov 25 09:44:14 2019 -0700

    Merge branch 'dtc/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit bd4a30c
Author: Man.Zhang <[email protected]>
Date:   Fri Nov 22 14:30:16 2019 -0700

    monir format fix

commit 4c2abd1
Merge: db7fc8d a7c38a6
Author: Man.Zhang <[email protected]>
Date:   Thu Nov 21 19:29:50 2019 -0700

    Merge branch 'dtc/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit db7fc8d
Author: Man.Zhang <[email protected]>
Date:   Thu Nov 21 19:29:04 2019 -0700

    minor change

commit ab52b26
Author: Man.Zhang <[email protected]>
Date:   Thu Nov 21 18:48:53 2019 -0700

    delete update_moist module

commit db9e3a7
Author: Man.Zhang <[email protected]>
Date:   Mon Nov 18 14:40:10 2019 -0700

    cleanup FA codes

commit 482a43b
Merge: 380229c 74851c1
Author: Man.Zhang <[email protected]>
Date:   Mon Nov 18 14:31:07 2019 -0700

    Merge branch 'dtc/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit 380229c
Author: Man.Zhang <[email protected]>
Date:   Thu Nov 14 13:46:13 2019 -0700

     1. do some code cleanup
     2. correct tracer diffusions definition before/after PBL in
    GFS_PBL_generic

commit a312444
Author: Man.Zhang <[email protected]>
Date:   Mon Nov 11 10:52:21 2019 -0700

     Chunxi's email 11/07/2019: the srflag is based on sr. so we need to
     make sure 'cal_pre' is always set to false in namelist file.

commit f2c9271
Merge: 6777489 333980d
Author: Man.Zhang <[email protected]>
Date:   Thu Nov 7 11:03:56 2019 -0700

    Merge branch 'dtc/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit 6777489
Author: Man.Zhang <[email protected]>
Date:   Thu Nov 7 10:56:33 2019 -0700

    add Chunxi GFS_MP_generic change related to FA scheme

commit 327b07f
Author: Man.Zhang <[email protected]>
Date:   Wed Oct 23 19:56:11 2019 -0600

    minor fix

commit bfedaab
Author: Man.Zhang <[email protected]>
Date:   Wed Oct 23 09:44:46 2019 -0600

    add meta files for FA scheme and HAFS_update_moist

commit a5b5fa9
Merge: 1ff46c7 cfafb29
Author: Man.Zhang <[email protected]>
Date:   Fri Oct 18 09:56:40 2019 -0600

    Merge branch 'gmtb/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit 1ff46c7
Author: Man.Zhang <[email protected]>
Date:   Tue Oct 8 20:42:58 2019 -0600

    add update_moist() module to F-A suite

commit 258fceb
Merge: 53fba5b ecb641e
Author: Man.Zhang <[email protected]>
Date:   Mon Oct 7 15:36:47 2019 -0600

    Merge branch 'gmtb/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit 53fba5b
Author: Man.Zhang <[email protected]>
Date:   Mon Oct 7 14:55:21 2019 -0600

    1. recalculate some FAmp tables which depend on physics time step in F-A scheme
    2. change ncw value to HWRF application

commit 1656aac
Author: Man.Zhang <[email protected]>
Date:   Mon Sep 30 12:02:24 2019 -0600

    revert MP_generic to original version to obtain B4B for control/csawmg/satmedmf

commit dfccc5b
Author: Man.Zhang <[email protected]>
Date:   Sun Sep 29 11:06:55 2019 -0600

    fix bugs in GFS_PBL_generic

commit fc744d3
Merge: 1a024b7 dc74b57
Author: Man.Zhang <[email protected]>
Date:   Mon Sep 23 14:17:29 2019 -0600

    Merge branch 'gmtb/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit 1a024b7
Author: Man.Zhang <[email protected]>
Date:   Fri Sep 20 22:01:07 2019 -0600

    fix ccpp_control crashed problem

commit 957ff82
Author: Man.Zhang <[email protected]>
Date:   Thu Sep 19 10:14:59 2019 -0600

    turn on/off spec_adv option is working in CCPP F-A scheme.

commit 370d49f
Author: Man.Zhang <[email protected]>
Date:   Tue Sep 17 16:55:24 2019 -0600

    use progcld5 for F-A in GFS_rrtmg_pre

commit bbbf155
Author: Man.Zhang <[email protected]>
Date:   Thu Sep 12 09:19:17 2019 -0600

    F-A scheme modification related to meta data file update

commit 2b8d9e4
Merge: 08662ae 9fc5ac1
Author: Man.Zhang <[email protected]>
Date:   Wed Sep 11 16:15:30 2019 -0600

    Merge branch 'HAFS_fer_hires' of https://github.com/mzhangw/ccpp-physics into HAFS_fer_hires

commit 08662ae
Author: Man.Zhang <[email protected]>
Date:   Wed Sep 11 16:14:47 2019 -0600

    add vars to meta table

commit 9fc5ac1
Author: Man Zhang <[email protected]>
Date:   Wed Sep 11 16:12:00 2019 -0600

    initialize Doxygen documentation in F-A scheme

commit d749a68
Merge: dff5b0f 20dd8d2
Author: Man.Zhang <[email protected]>
Date:   Tue Sep 10 15:19:15 2019 -0600

    Merge branch 'gmtb/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit dff5b0f
Merge: bed9c0e 727417c
Author: Man.Zhang <[email protected]>
Date:   Wed Sep 4 14:30:28 2019 -0600

    Merge branch 'chunxi_physics' of https://github.com/ChunxiZhang-NOAA/ccpp-physics into HAFS_fer_hires

commit bed9c0e
Merge: 1f8a26a 44137a3
Author: Man.Zhang <[email protected]>
Date:   Wed Sep 4 14:26:51 2019 -0600

    Merge branch 'HAFS_fer_hires' of https://github.com/mzhangw/ccpp-physics into HAFS_fer_hires

commit 1f8a26a
Author: Man.Zhang <[email protected]>
Date:   Wed Sep 4 14:24:27 2019 -0600

    bug fixed in augument list of FER_HIRES

commit 44137a3
Merge: 1808226 6abba22
Author: Man.Zhang <[email protected]>
Date:   Tue Sep 3 10:33:04 2019 -0600

    Merge branch 'gmtb/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit 1808226
Author: Man.Zhang <[email protected]>
Date:   Sat Aug 31 17:51:49 2019 -0600

    tracer treatment fix

commit 727417c
Author: Chunxi.Zhang-NOAA <[email protected]>
Date:   Fri Aug 30 22:13:06 2019 +0000

    GFS_MP_generic.F90: recalculate srflag
    GFS_PBL_generic.F90: define tracers for vertical diffusion
    GFS_rrtmg_pre.F90: change ncnd
    module_mp_fer_hires_pre.F90: revised the definition to tracers
    mp_fer_hires.F90: revised the definition to tracers

commit ec729e8
Author: Man.Zhang <[email protected]>
Date:   Thu Aug 29 21:43:36 2019 -0600

    make consistent standard name as Chunxis implementation

commit 3a26975
Merge: 1426c6e c7faeb7
Author: Man.Zhang <[email protected]>
Date:   Thu Aug 29 21:02:59 2019 -0600

    Merge branch 'chunxi_physics' of https://github.com/ChunxiZhang-NOAA/ccpp-physics into HAFS_fer_hires

commit 1426c6e
Author: Man.Zhang <[email protected]>
Date:   Thu Aug 29 20:32:12 2019 -0600

    fix omp message and pass F-A scheme

commit c7faeb7
Author: Chunxi.Zhang-NOAA <[email protected]>
Date:   Thu Aug 29 16:20:51 2019 +0000

    mp_fer_hires.F90: changed the definitions for f_ice, f_rain and f_rimef.
                      Deleted QS since it will not be used. we only need QI.
    module_mp_fer_hires_pre.F90: changes related to f_ice, f_rain and f_rimef
    module_mp_fer_hires_pre.F90: added

commit 4e0d9bd
Merge: 9aaa575 01823bc
Author: Man.Zhang <[email protected]>
Date:   Tue Aug 27 17:13:12 2019 -0600

    Merge branch 'gmtb/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit 9aaa575
Author: Man.Zhang <[email protected]>
Date:   Tue Aug 27 15:57:43 2019 -0600

    minor fix

commit 6b88864
Author: Eric Aligo <[email protected]>
Date:   Tue Aug 27 17:31:03 2019 +0000

    Fixed bug to allow both Qi and Qc to be updated from CU scheme.

commit 73f95a6
Author: Man.Zhang <[email protected]>
Date:   Mon Aug 26 22:05:00 2019 -0600

    fortran format fix

commit d5f8a62
Author: Man.Zhang <[email protected]>
Date:   Mon Aug 26 17:16:30 2019 -0600

    minor fix

commit fb011da
Author: Man.Zhang <[email protected]>
Date:   Mon Aug 26 17:05:04 2019 -0600

    Aligo-use the dx of the 1st i poit to set an integer value of dx to be used for determining RHgrd

commit 80fedc4
Author: Man.Zhang <[email protected]>
Date:   Mon Aug 26 13:41:24 2019 -0600

    further constants fix

commit 473ff9e
Author: Man.Zhang <[email protected]>
Date:   Mon Aug 26 10:45:49 2019 -0600

    dimension fixed

commit c29c3cd
Author: Man.Zhang <[email protected]>
Date:   Sun Aug 25 22:44:04 2019 -0600

    convert USE ESMF to ccpp mpi method; temporary constant treatment

commit 8b886b9
Author: Man.Zhang <[email protected]>
Date:   Wed Aug 21 11:06:19 2019 -0600

    delete HWRF F-A scheme

commit b78a1a2
Merge: dbabee7 ff2c6d8
Author: Man.Zhang <[email protected]>
Date:   Mon Aug 19 13:42:42 2019 -0600

    Merge branch 'gmtb/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit dbabee7
Author: Man.Zhang <[email protected]>
Date:   Mon Aug 19 13:41:36 2019 -0600

    update

commit 7c481b5
Author: Man.Zhang <[email protected]>
Date:   Thu Aug 15 08:34:33 2019 -0600

    initialize FER_HIRES scheme

commit bbac675
Merge: d06f755 fb29006
Author: Man.Zhang <[email protected]>
Date:   Mon Aug 5 10:33:29 2019 -0600

    Merge branch 'gmtb/develop' of https://github.com/NCAR/ccpp-physics into HAFS_fer_hires

commit d06f755
Author: Man.Zhang <[email protected]>
Date:   Thu Aug 1 11:29:43 2019 -0600

    minor fix

commit 970ae66
Author: Man.Zhang <[email protected]>
Date:   Wed Jul 31 13:41:12 2019 -0600

    change file name

commit d666a3e
Author: Man Zhang <[email protected]>
Date:   Wed Jul 31 12:25:36 2019 -0600

    pass prebuild

commit 63f07c4
Merge: d0d4035 6bb0897
Author: Man Zhang <[email protected]>
Date:   Wed Jul 31 10:10:31 2019 -0600

    Merge branch 'gmtb/develop' of https://github.com/NCAR/ccpp-physics into FA-HWRF-V4_0a

commit d0d4035
Author: Man Zhang <[email protected]>
Date:   Wed Jul 31 10:09:44 2019 -0600

    initialize FER_HIRES implementation

commit e77c0a1
Author: Man Zhang <[email protected]>
Date:   Fri Jul 19 14:55:03 2019 -0600

    add fer_hires wrapper module

commit 193435b
Author: Man.Zhang <[email protected]>
Date:   Mon Jul 1 16:31:01 2019 -0600

    initialize Ferrier-Aligo MP scheme implementation from HWRF V4.0
@climbfuji climbfuji force-pushed the HAFS_fer_hires_for_dtc_hwrf-physics branch from 4f4203b to 6a8c80e Compare April 14, 2020 02:41
@climbfuji climbfuji mentioned this pull request Apr 14, 2020
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climbfuji commented Apr 14, 2020
View reviewed changes
physics/radiation_clouds.f
@@ -868,22 +868,24 @@ end subroutine progcld1
!!\param mtop (IX,3), vertical indices for low, mid, hi cloud tops
!!\param mbot (IX,3), vertical indices for low, mid, hi cloud bases
!!\param de_lgth (IX), clouds decorrelation length (km)
!>\section gen_progcld2 progcld2 General Algorithm
!>\section gen_progcld2 progcld2 General Algorithm for the F-A MP scheme
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Since progcld2 is no longer used by the Ferrier-Aligo MP scheme, does it make sense to update it? Or should we revert the changes to progcld2? @mzhangw @grantfirl @ligiabernardet

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ligiabernardet commented Apr 14, 2020 via email

@climbfuji climbfuji mentioned this pull request Apr 14, 2020
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mzhangw commented Apr 14, 2020 via email

@climbfuji climbfuji mentioned this pull request Apr 14, 2020
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@climbfuji climbfuji marked this pull request as ready for review April 14, 2020 21:09
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@mzhangw, a few things about SciDoc. Can be fixed in a follow up clean-up PR:

  • The F-A is appearing on the left bar alongside the various suites. I don't think it should show up there as no other scheme appears at that level.
  • Add F-A to list of mp schemes at /doc/html/allscheme_page.html
  • The scheme should be referred to as F-A (not HWRF F-A). It is used in other models as well.
  • Figures are mentioned but do not show up at physics/docs/doc/html/_h_w_r_f_famp.html

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@mzhangw, a few things about SciDoc. Can be fixed in a follow up clean-up PR:

  • The F-A is appearing on the left bar alongside the various suites. I don't think it should show up there as no other scheme appears at that level.
  • Add F-A to list of mp schemes at /doc/html/allscheme_page.html
  • The scheme should be referred to as F-A (not HWRF F-A). It is used in other models as well.
  • Figures are mentioned but do not show up at physics/docs/doc/html/_h_w_r_f_famp.html

Thanks @ligiabernardet - can you and/or Man please take care of creating this follow-up PR? Since they will be documentation changes only, I can probably merge them together with the Noah LSM PR. Thanks!

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mzhangw commented Apr 15, 2020 •
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This PR includes Eric's input. FA Sci doc in doxygen can be refined in the future PR.

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ligiabernardet commented Apr 15, 2020 via email

@climbfuji climbfuji merged commit 08bcc39 into NCAR:dtc/hwrf-physics Apr 16, 2020
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mzhangw commented Apr 17, 2020 via email

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ligiabernardet commented Apr 17, 2020 via email

@climbfuji climbfuji deleted the HAFS_fer_hires_for_dtc_hwrf-physics branch June 27, 2022 03:04
hannahcbarnes added a commit to hannahcbarnes/ccpp-physics that referenced this pull request Aug 3, 2022
@climbfuji @DomHeinzeller
@pjpegion @ShanSunNOAA @tanyasmirnova @mark-a-potts @SMoorthi-emc @dustinswales @junwang-noaa @XiaqiongZhou-NOAA @ValeryYudin-NOAA @mdtoyNOAA @XiaSun-Atmos @SamuelTrahanNOAA @hannahcbarnes
Merge NOAA-GSL gsl/develop into develop, update CCPP SDFs (NCAR#435)
e7687f4 
* Update .gitmodules and submodule pointers for ccpp-framework and ccpp-physics for gsl/develop branch

* RUC ice for gsl/develop (replaces NCAR#54 and NCAR#56) (NCAR#60)

Implementation of RUC LSM ice model in CCPP

* Squash-merge climbfuji:rucice_gfsv16dzmin into gsl/develop

* Fix bug in gfsphysics/GFS_layer/GFS_typedefs.F90 from merge

* Remove lsm_ruc_sfc_sice from suite FV3_GSD_v0_unified_ugwp_suite and update submodule pointer for ccpp-physics

* Remove sfc_sice from ccpp/suites/suite_FV3_GSD_v0_unified_ugwp_suite.xml

* Update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

Co-authored-by: Dom Heinzeller <[email protected]>

* Update gsl/develop from develop 2020/12/08 (NCAR#61)

* Fix for updating stochastic physics on separate time-step. (NCAR#199)

This bug fix allows the random patterns in the stochastic physics persist the for a period of time (defined as SKEBINT,SPPTINT, etc.) before calculating new patterns.
The fix is to move the allocation of the saved variables into the init section of stochastic_physics_wrapper, and remove the deallocates in the run section.

* Bug fixes in (1) running with frac_grid=T and GFDL MP and (2) restarting with frac_grid=T (NCAR#204)

* -- Pointing to Moorthi's modifications in ccpp/physics, which fixed the crash when running GFDL MP with frac_grid=T;
-- Not setting fice to zero in order to leave lake ice untouched;
-- Restart in the coupled model with the default physics is reproducible, if bad water temperature is only filtered at initial time;
Co-authored-with: Shrinivas Moorthi <[email protected]>
Co-authored-with: Denise Worthen <[email protected]>

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

Co-authored-by: Phil Pegion <[email protected]>
Co-authored-by: shansun6 <[email protected]>

* Update submodule pointer for ccpp-physics - MYNN surface layer updates and bugfixes (NCAR#63)

* Land stochastic perturbations (wrapper PR for NCAR#65) (NCAR#68)

* Move initialization of stochastic physics after the physics
initialization in CCPP.
* Add albedo variables to land perturbations with lndp_type=2 option. Change to accommodate soil perturbations with RUC LSM.

* Max/min soil moisture variables are introduced via GFS_Control_type
variables instead of through the use of namelist_soilveg*. This is a
more flexible way for different LSMs.

* Added pores and resid variables for max/min soil moisture to GFS_typedefs.f90.

* Remove tracer_sanitizer from all suites and from CCPP prebuild config

* Add namelist option to apply land surface perturbations at every time step, clean up stochastic_physics/stochastic_physics_wrapper.F90

Co-authored-by: tanyasmirnova <[email protected]>

* Stochastic land perturbations: add roughness length over land to the perturbed variables (NCAR#70)

* Added roughness length over land to the perturbed variables.
* Bugfix in gfsphysics/GFS_layer/GFS_typedefs.F90: remove Diag%cldcov, in particular the reset call because the variable is not allocated

Co-authored-by: Dom Heinzeller <[email protected]>

* Update gsl/develop from develop 2021/02/22 (NCAR#73)

* Fix for updating stochastic physics on separate time-step. (NCAR#199)

This bug fix allows the random patterns in the stochastic physics persist the for a period of time (defined as SKEBINT,SPPTINT, etc.) before calculating new patterns.
The fix is to move the allocation of the saved variables into the init section of stochastic_physics_wrapper, and remove the deallocates in the run section.

* Bug fixes in (1) running with frac_grid=T and GFDL MP and (2) restarting with frac_grid=T (NCAR#204)

* -- Pointing to Moorthi's modifications in ccpp/physics, which fixed the crash when running GFDL MP with frac_grid=T;
-- Not setting fice to zero in order to leave lake ice untouched;
-- Restart in the coupled model with the default physics is reproducible, if bad water temperature is only filtered at initial time;
Co-authored-with: Shrinivas Moorthi <[email protected]>
Co-authored-with: Denise Worthen <[email protected]>

* jedi-ufs with ccpp-physics submodule update (contains NCAR#201) (NCAR#211)

* updated CMakeLists.txt
* Changes for JEDI linking/control
* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing
* Revert change to .gitmodules and update submodule pointer for ccpp-physics

Co-authored-by: Mark Potts <[email protected]>

* Final-final GFS v16 updates / restart reproducibility bugfixes (NCAR#212)

* updates the submodule pointer for ccpp-physics for the final-final (!) GFS v16 physics updates
* fixes a bug in io/FV3GFS_io.F90 to obtain restart reproducibility for uncoupled and coupled runs - contributed by @SMoorthi-emc

Co-authored-by: Shrinivas.Moorthi <[email protected]>

* RRTMGP coupling to Thompson MP in ccpp-physics (NCAR#208)

* Updated physics. Added infrastructure to FV3 to handle new GP capabilities. Thompson MP, LW scattering, Use of LW-jacobian to update surface tendencies.
* Some small changes to work with physics improvements to RRTMGP.
* RRTMGP working with Thompson MP.
* Updated .gitmodules.
* Updated physics. New interstitials.
* Synced with NCAR/master
* Updated ccpp-physics
* Updated physics submodule.
* Cleanup
* Update physics
* Updated physics submodule pointer.
* Updated physics submodule hash.

* Minor bug fixes to CCPP UGWP (update submodule pointer for ccpp-physics) (NCAR#216)

Update the submodule pointer for ccpp-physics for minor bugfixes in CCPP's Unified Gravity Wave Drag parameterization.

* Remove IPD (step 1) (NCAR#215)

Remove all IPD source files that are not needed to compile with CCPP. Update gfsphysics/CMakeLists.txt and gfsphysics/GFS_layer/GFS_driver.F90 so that the code compiles after removing IPD sources.

Also: update submodule pointer for GFDL_atmos_cubed_sphere to include PR NOAA-EMC/GFDL_atmos_cubed_sphere#48 ("Removed use of mpp_node for use with FMS 2020.04").

* Update submodule pointers for ccpp-framework (ccpp_prebuild bugfix) and ccpp-physics (RRTMGP GFDL-MP bugfix) (NCAR#218)

Update the submodule pointers for ccpp-framework and ccpp-physics for the changes described in
NCAR/ccpp-framework#343 and NCAR#536.

* Remove unnecessary SIMD instruction sets from ccpp/CMakeLists.txt (NCAR#220)

* Remove additional/unnecessary SIMD instruction sets from ccpp/CMakeLists.txt

* Implementation of CCPP timestep_init and timestep_final phases (NCAR#217)

- replace calls to CCPP step `time_vary` with `timestep_init` in `atmos_model.F90`, add call to CCPP step `timestep_final` 
- update `ccpp/driver/CCPP_driver.F90` with calls to CCPP `timestep_init` and `timestep_final`
- add `h2o_def.f` and `ozne_def.` to `ccpp_prebuild_config.py`
- update of `gfsphysics/GFS_layer/GFS_typedefs.F90`: cleanup work for o3 and h2o physics (required by the updates to the CCPP time vary physics)
- update metadata in `gfsphysics/GFS_layer/GFS_typedefs.meta` for the above changes, and clean up the index used for the surface wind enhancement due to convection in the `phy_f2d` array (use proper index, not just the last entry in the array)

* add radiation_clouds_thompson_dependency in ccpp physics  (NCAR#225)

* using radiation_clouds_thompson_dependency ccpp physics branch
* point to ccpp master branch

* Remove IPD steps 3 and 5 (NCAR#224)

* Implementation of CCPP timestep_init and timestep_final phases in fv3atm; cleanup work in GFS_typedefs for o3 and h2o physics as a result of the changes to the time vary physics in CCPP
* Use proper index variable for surface wind enhancement due to convection in phy_f2d array in GFS_typedefs.{F90,meta}, move code to clear diagnostic buckets using GFS DDT bound procedures from atmos_model.F90 to CCPP_driver.F90
* First step of cleanup process: remove CCPP preprocessor directives, remove parts of unused IPD code, update cmake build system, Delete IPD source code, Replace IPD DDTs with GFS DDTs, Bugfix in atmos_model.F90; add missing call to GFS_externaldiag_populate, Move contents of gfsphysics/{CCPP_layer,GFS_layer} to ccpp/{data,driver}, entirely deleted IPD typedefs, Rename module GFS_driver to GFS_init
* Fix indentation in ccpp/data/CMakeLists.txt and ccpp/driver/CMakeLists.txt
* Add logic to set DYN32 depending on 32BIT setting
* Pass preprocessor directive GFS_TYPES to dycore to enable use of GFS data types
* Compile GFS_diagnostics.F90 without optimization, this leads to out of memory errors on wcoss_dell_p3

* Add CCPP rrtmgp fix (NCAR#237)

* ccpp physics merged with top of master
* point back to ccpp master branch

* Update develop from NOAA-GSL: RUC ice, MYNN sfclay, stochastic land perturbations (NCAR#239)

* Update .gitmodules and submodule pointers for ccpp-framework and ccpp-physics for gsl/develop branch
* RUC ice for gsl/develop (replaces NCAR#54 and NCAR#56) (NCAR#60) Implementation of RUC LSM ice model in CCPP
* Fix bug in gfsphysics/GFS_layer/GFS_typedefs.F90 from merge
* Remove lsm_ruc_sfc_sice from suite FV3_GSD_v0_unified_ugwp_suite and update submodule pointer for ccpp-physics
* Remove sfc_sice from ccpp/suites/suite_FV3_GSD_v0_unified_ugwp_suite.xml
* Update gsl/develop from develop 2020/12/08 (NCAR#61)
* Fix for updating stochastic physics on separate time-step. (NCAR#199)
This bug fix allows the random patterns in the stochastic physics persist the for a period of time (defined as SKEBINT,SPPTINT, etc.) before calculating new patterns.
The fix is to move the allocation of the saved variables into the init section of stochastic_physics_wrapper, and remove the deallocates in the run section.
* Bug fixes in (1) running with frac_grid=T and GFDL MP and (2) restarting with frac_grid=T (NCAR#204)
* -- Pointing to Moorthi's modifications in ccpp/physics, which fixed the crash when running GFDL MP with frac_grid=T;
-- Not setting fice to zero in order to leave lake ice untouched;
-- Restart in the coupled model with the default physics is reproducible, if bad water temperature is only filtered at initial time;
Co-authored-with: Shrinivas Moorthi <[email protected]>
Co-authored-with: Denise Worthen <[email protected]>
* Revert change to .gitmodules and update submodule pointer for ccpp-physics
* Update submodule pointer for ccpp-physics - MYNN surface layer updates and bugfixes (NCAR#63)
* Land stochastic perturbations (wrapper PR for NCAR#65) (NCAR#68)
* Move initialization of stochastic physics after the physics
initialization in CCPP.
* Add albedo variables to land perturbations with lndp_type=2 option. Change to accommodate soil perturbations with RUC LSM.
* Max/min soil moisture variables are introduced via GFS_Control_type
variables instead of through the use of namelist_soilveg*. This is a
more flexible way for different LSMs.
* Added pores and resid variables for max/min soil moisture to GFS_typedefs.f90.
* Remove tracer_sanitizer from all suites and from CCPP prebuild config
* Add namelist option to apply land surface perturbations at every time step, clean up stochastic_physics/stochastic_physics_wrapper.F90
* Stochastic land perturbations: add roughness length over land to the perturbed variables (NCAR#70)
* Added roughness length over land to the perturbed variables.
* Bugfix in gfsphysics/GFS_layer/GFS_typedefs.F90: remove Diag%cldcov, in particular the reset call because the variable is not allocated
* Update .gitmodules and submodule pointer for GFDL_atmos_cubed_sphere for code review and testing
* Revert change to .gitmodules for ccpp-physics, update submodule pointer for ccpp-physics
* Revert change to .gitmodules and update submodule pointer for GFDL_atmos_cubed_sphere
Co-authored-by: DomHeinzeller <[email protected]>
Co-authored-by: Phil Pegion <[email protected]>
Co-authored-by: shansun6 <[email protected]>
Co-authored-by: tanyasmirnova <[email protected]>

* Dycore change to add an option to zero-gradient BC for height advection and change dz_min as a namelist input (NCAR#232)

* Point dycore to a personal branch
* Point to new version of dycore
* Update the dycore version
* Update the dycore version
* Point to NOAA-EMC dev/emc dycore branch

* Remove gnumake build remnants, change v16beta to v16 (NCAR#234)

* Remove gnumake files
* Replace v16beta with v16 for all CCPP suites
* Remove unused CCPP_INCLUDE_DIRS/CCPP_LIB_DIRS from ccpp/CMakeLists.txt

* Move LSM vegetation lookup tables into CCPP, clean up RUC snow cover on ice initialization  (remove IPD step 2) (NCAR#244)

* Move LSM vegetation lookup tables into CCPP, clean up RUC snow cover on ice initialization
* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* UGWP v0 v1 combined (NCAR#241)

* .gitmodules/gsl atmos-cubed cccp-fram cccp/physics
* update fv3atm from NOAA-EMC Jan 9
* new suite_FV3_GFS_v16b_ugwpv1.xml and modifications Jan 11/2021
* Added new logical flag do_ugwp_v0_nst_only which allows non-stationary drag from ugwp_v0 to be run with GSL drag suite
* Fix formatting in ccpp/data/GFS_typedefs.*
* Clean up allocation of arrays in ccpp/data/GFS_typedefs.F90, add active attribute (pass 1) to ccpp/data/GFS_typedefs.meta, strip trailing whitespaces from both
* Update and cleanup of metadata for UGWPv0, UGWPv1, drag suite
* Reorganize UGWP diagnostic variables in data/GFS_typedefs.{F90,meta}
* Bugfix for uninitialized data in ccpp/data/GFS_typedefs.F90
* Update submodule pointer for ccpp-physics
* Allocate 3d diagnostic arrays as dummy arrays if not used

Co-authored-by: valery.yudin <[email protected]>
Co-authored-by: Michael Toy <[email protected]>

* SDF for GFSv16 with Thompson (NCAR#238)

* SDF for GFSv16 with Thompson
* Delete suite_FV3_GFS_v16beta_thompson.xml
* update to new commit of Thompson MP in ccpp physics

Co-authored-by: Phil Pegion <[email protected]>
Co-authored-by: shansun6 <[email protected]>
Co-authored-by: Mark Potts <[email protected]>
Co-authored-by: Shrinivas.Moorthi <[email protected]>
Co-authored-by: dustinswales <[email protected]>
Co-authored-by: Jun Wang <[email protected]>
Co-authored-by: XiaqiongZhou-NOAA <[email protected]>
Co-authored-by: valery.yudin <[email protected]>
Co-authored-by: Michael Toy <[email protected]>
Co-authored-by: XiaSun-NOAA <[email protected]>

* Remove inconsistencies in computation of air density with Thompson MP (NCAR#74)

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* Update thompson mp 20210213 (NCAR#567) for gsl/develop (NCAR#75)

* Add logical convert_dry_rho for Thompson MP, hardcoded to false
* Initialize all variables to NaN in ccpp-physics in DEBUG mode
* Update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointer for ccpp-framework and ccpp-physics

* &gfs_physics_nml print_diff_pgr=.true. will print per-timestep pgr change stats

* point to sam's repository for atmos_cubed_sphere

* Add units and lat/lon to per-timestep pgr stats

* Rebase atmos_cubed_sphere to NOAA-GFDL dev/emc branch

* Print mean pgr change as hPa/hr and other pgr data as bars.

* Remove changes from atmos_cubed_sphere and simplify atmos_model.F90 changes.

* print mean abs change instead of mean change in pgr

* Update .gitmodules and submodule pointers for ccpp-framework and ccpp-physics for code review and testing

* Revert change to .gitmodules and update submodule pointers for ccpp-framework and ccpp-physics

* clarify one print

* More 3D diagnostic tendencies (NCAR#76)

Add diagnostic tendencies for all tracers. Move all d*3dt variables into a 4D sparse array stored as `dtend(i,k,dtidx(tracer,process))` to reduce memory usage.

* Fix incorrect units in dtend metadata (NCAR#82)

* Fix incorrect units in dtend metadata

* Make the tracer tendency units mandatory.

* Add SO2 tendency units (NCAR#86)

* Update .gitmodules and submodule pointers for ccpp-framework and ccpp-physics

* Update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointer for ccpp-framework and ccpp-physics

* dtend: add missing tendencies and fix bugs in convection tendencies (NCAR#92)

* Fix incorrect units in dtend metadata

* Point to corresponding ccpp/physics branch

* fixes to dtend support:

1. Store rtg (AKA clw AKA qtr) instead of gq0 in DCNV and SCNV
pre/post for schemes that use convective transport. Tracers handled
solely by convective transport (ones not in rtg) are reported as
convective transport tendencies. Tendencies for variables in rtg are
reported as dcnv and scnv tendencies.

2. Report TKE tendencies from gfs v16 PBL.

3. Add diagnostic tendencies to drag_suite

4. Only report rayleigh damping tendencies if rayleigh damping is enabled

5. List all possible diagnostic tendencies, even if they are not
enabled. In the output, label them "selected" or "disabled."

6. Add phys_tend to the fv3_rap suite.

* Merge gsl/develop into ccpp/physics

* Add phys_tend to suite_FV3_GSD_SAR and remove some debug prints

* Remove some debug prints and commented-out code.

* Correct error in dtend variable availability list print.

* Enable convtrans diagnostic tendencies for number concentrations and qrimef.

* Disable cnvtrans diagnostic tendencies for schemes that do their own diagnostic tendency reporting.

* Point to gsl repositories

* Update .gitmodules for code review and regression testing

* Formatting changes in ccpp/data/GFS_typedefs.F90

* Update submodule pointer for ccpp-physics

* Update submodule pointer for ccpp-physics

* Point update_gsl_develop_from_develop_20210531 to NOAA-GSL branches of ccpp/physics and ccpp/framework

* GF aerosols updates and tunings

* GF aerosol updates and tunings from physics

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Update submodule pointer for ccpp-physics

* Update submodule pointer for ccpp-physics

* Update submodule pointer for ccpp-physics

* Make aod_gf and cactiv_m work appriopriately for restarts
Minor code cleanup

* Add missing metadata for new GF arrays

* Bug fix in ccpp/driver/GFS_restart.F90 for GF

* Update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* Add missing active attribute for aod_gf in ccpp/data/GFS_typedefs.meta

* Update submodule pointer for ccpp-physics

* Update submodule pointer for ccpp-physocs

* Change name of sfc_name2(39) from 'weasd' to 'weasdl' in io/FV3GFS_io.F90

* Revert change to .gitmodules and update submodule pointers for ccpp-framework and ccpp-physics

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* Changed dimensions of variables tsnow_land and sncovr_ice from
horizontal_dimension to horizontal_loop_extent

* Added Flake to two suites: FV3_GSD_v0 and FV3_HRRR.

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* Update to ccpp/data/GFS_typedefs.meta following CCPP standard names update

* Update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointers for ccpp-physics and ccpp-framework

* Revert change to .gitmodules and update submodule pointers for ccpp-framework and ccpp-physics

* Turn on GF aerosol-awareness
Tune clwdet (cloud water detrainment)
Make evfact (evaporation factor) and radiation factor scale-aware

* Update .gitmodules and submodule pointers for ccpp-framework and ccpp-physics for code review and testing

* Switch back to NCAR ccpp-framework main, abandon NOAA-GSL fork

* Update submodule pointer for ccpp-physics

* Update submodule pointer for ccpp/physics

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* Update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* Update .gitmodules and submodule pointer for ccpp-physics for code review aand testing

* Update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Update submodule pointer for ccpp-physics

* Revert .gitmodules and update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Revert .gitmodules and update submodule pointer for ccpp-physics

* Update CCPP metadata and several suite defiition files for new GSL regression tests

* Bug fix for compiling with Intel on macOS, remove clutter from stdout in io/FV3GFS_io.F90

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Rename GSL suites to RAP suites, add new RAP suites

* rename suite FV3_GSD_v0 to FV3_RAP_noah_sfcdiff_cires_ugwp, delete suite FV3_SAR

* Update submodule pointer for ccpp-physics

* Address reviewer comments

* Update submodule pointer for ccpp-physics

* Revert .gitmodules and update submodule pointer for ccpp-physics

Co-authored-by: DomHeinzeller <[email protected]>
Co-authored-by: Phil Pegion <[email protected]>
Co-authored-by: shansun6 <[email protected]>
Co-authored-by: tanyasmirnova <[email protected]>
Co-authored-by: tanyasmirnova <[email protected]>
Co-authored-by: Mark Potts <[email protected]>
Co-authored-by: Shrinivas.Moorthi <[email protected]>
Co-authored-by: dustinswales <[email protected]>
Co-authored-by: Jun Wang <[email protected]>
Co-authored-by: XiaqiongZhou-NOAA <[email protected]>
Co-authored-by: valery.yudin <[email protected]>
Co-authored-by: Michael Toy <[email protected]>
Co-authored-by: XiaSun-NOAA <[email protected]>
Co-authored-by: samuel.trahan <[email protected]>
Co-authored-by: Samuel Trahan (NOAA contractor) <[email protected]>
Co-authored-by: hannah barnes <[email protected]>
Co-authored-by: Hannah C Barnes <[email protected]>
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Reviewers

@mzhangw mzhangw mzhangw approved these changes

@grantfirl grantfirl Awaiting requested review from grantfirl

@llpcarson llpcarson Awaiting requested review from llpcarson

@ligiabernardet ligiabernardet Awaiting requested review from ligiabernardet

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@climbfuji @ligiabernardet @mzhangw