Updated the lake physics of flake

[YihuaWu-NOAA]

Related PRs:

ufs-weather-model #163
fv3atm #139
ccpp-physics #462

Modify files in ufs-weather-model-flake/FV3/gfsphysics/GFS_layer/
GFS_typedefs.F90
GFS_typedefs.meta
Note: Added two variables: lakedepth and LKM (logical)

Modify file in ufs-weather-model-flake/FV3/io/
FV3GFS_io.F90
Note: read in lake depth, and reset lakefraction and lakedepth to 0 when LKM is not one

Modify files in ufs-weather-model-flake/FV3/ccpp/physics/physics/

Added threes:
flake_driv.F90
flake_driv.meta
flake.F90*

Modified:
GFS_time_vary_pre.fv3.F90
Note: Flake need julian day

3.3 Modified:
GFS_surface_composites.F90
GFS_surface_composites.meta
Note: add lake depth, and define the logical variable lake based on lakefraction and lakedepth
Then, the logical variable lake is passed to flake drive and sfc_ocean.
When lake is true, flake will be called; when lake is false, ocean model will be called

3.4 Modified
sfc_ocean.F
sfc_ocean.meta
Note: add lake, if not lake, calculation will be conducted.

Modify files in ufs-weather-model-flake/FV3/ccpp/suites/
suite_FV3_GFS_v16beta_flake.xml

  Modify files in ufs-weather-model-flake/FV3/ccpp/config/
ccpp_prebuild_config.py

    Add file in ufs-weather-model-flake/tests/tests
			fv3_ccpp_gfs_v16beta_flake

    Modify  file in ufs-weather-model-flake/tests/fv3_conf/
			ccpp_gfs_v16_flake_run.IN

  Modify  files in  ufs-weather-model-flake/parm/
ccpp_v16beta_c96.nml.IN 

Modify files in mylakedir/sorc/orog.fd
lakefrac.F90 to create lake fraction and depth and add them to oro_data_tilex.nc

Replace oro_data_tilex.nc files on hera: /scratch2/NCEPDEV/fv3-cam/Yihua.Wu/noscrub/trunk-20200611 which provide model inputs.
A new baseline was created on hera: /scratch2/NCEPDEV/fv3-cam/Yihua.Wu/noscrub/REGRESSION_TEST_INTEL

[DusanJovic-NOAA]

Why the default account changed from nems to fv3-cam?

[DusanJovic-NOAA]

remove entire tests/log_orion.intel directory

[DusanJovic-NOAA]

Move these to rt.conf and delete this file.

[DusanJovic-NOAA]

remove this file. it's a temporary file created during the regression testing

[DusanJovic-NOAA]

remove this file. it's a temporary file created during the regression testing

[YihuaWu-NOAA]

Hi, Dusan, So, I delete these files/directories by another pushing? Thanks! *Yihua----------------------------------------------------Yihua Wu, Ph D*I.M. Systems Group NOAA/NWS/NCEP/EMC 5830 University Research Court, Room: 2031 College Park, Maryland 20740, USA Phone: (301)-683-3691 Fax: (301)-683-3703

…

On Wed, Jul 8, 2020 at 3:07 PM Dusan Jovic ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In tests/fv3_conf/fv3_slurm.IN <#163 (comment)> : > @@ -0,0 +1,43 @@ +#!/bin/sh remove this file. it's a temporary file created during the regression testing — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#163 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANJBYQAFAE4D4QSEIBV3YNLR2S7NVANCNFSM4OU25YKQ> .

[DusanJovic-NOAA]

Hi, Dusan, So, I delete these files/directories by another pushing? Thanks! Yihua----------------------------------------------------Yihua Wu, Ph DI.M. Systems Group NOAA/NWS/NCEP/EMC 5830 University Research Court, Room: 2031 College Park, Maryland 20740, USA Phone: (301)-683-3691 Fax: (301)-683-3703
…
On Wed, Jul 8, 2020 at 3:07 PM Dusan Jovic @.***> wrote: @DusanJovic-NOAA commented on this pull request. ------------------------------ In tests/fv3_conf/fv3_slurm.IN <#163 (comment)> : > @@ -0,0 +1,43 @@ +#!/bin/sh remove this file. it's a temporary file created during the regression testing — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#163 (review)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANJBYQAFAE4D4QSEIBV3YNLR2S7NVANCNFSM4OU25YKQ .

Yes.

[YihuaWu-NOAA]

It is done. Thanks! *Yihua----------------------------------------------------Yihua Wu, Ph D*I.M. Systems Group NOAA/NWS/NCEP/EMC 5830 University Research Court, Room: 2031 College Park, Maryland 20740, USA Phone: (301)-683-3691 Fax: (301)-683-3703

…

On Wed, Jul 8, 2020 at 4:15 PM Dusan Jovic ***@***.***> wrote: Hi, Dusan, So, I delete these files/directories by another pushing? Thanks! *Yihua----------------------------------------------------Yihua Wu, Ph D*I.M. Systems Group NOAA/NWS/NCEP/EMC 5830 University Research Court, Room: 2031 College Park, Maryland 20740, USA Phone: (301)-683-3691 Fax: (301)-683-3703 … <#m_-2097742219920196394_> On Wed, Jul 8, 2020 at 3:07 PM Dusan Jovic *@*.***> wrote: ***@***.*** <https://github.com/DusanJovic-NOAA>* commented on this pull request. ------------------------------ In tests/fv3_conf/fv3_slurm.IN <#163 (comment) <#163 (comment)>> : > @@ -0,0 +1,43 @@ +#!/bin/sh remove this file. it's a temporary file created during the regression testing — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#163 (review) <#163 (review)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANJBYQAFAE4D4QSEIBV3YNLR2S7NVANCNFSM4OU25YKQ . Yes. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#163 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANJBYQBNCAT66K7LM55QPVTR2THWTANCNFSM4OU25YKQ> .

[DusanJovic-NOAA]

FV3 submodule should point to your develop branch, not master. All your changes in your fv3atm fork are in develop branch.

[YihuaWu-NOAA]

Hi, Dusan, Thank you very much! *Yihua----------------------------------------------------Yihua Wu, Ph D*I.M. Systems Group NOAA/NWS/NCEP/EMC 5830 University Research Court, Room: 2031 College Park, Maryland 20740, USA Phone: (301)-683-3691 Fax: (301)-683-3703

…

On Thu, Jul 9, 2020 at 9:12 AM Dusan Jovic ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In .gitmodules <#163 (comment)> : > @@ -1,7 +1,7 @@ [submodule "FV3"] path = FV3 - url = https://github.com/NOAA-EMC/fv3atm - branch = develop + url = https://github.com/YihuaWu-NOAA/fv3atm + branch = master FV3 submodule should point to your develop branch, not master. All your changes in your fv3atm fork are in develop branch. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#163 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANJBYQGTYINU2OSHBAE2ROTR2W62JANCNFSM4OU25YKQ> .

[junwang-noaa]

Please see the new PR #164.

[YihuaWu-NOAA]

Hi, Jun, Thanks. I think you can also close #139. *Yihua----------------------------------------------------Yihua Wu, Ph D*I.M. Systems Group NOAA/NWS/NCEP/EMC 5830 University Research Court, Room: 2031 College Park, Maryland 20740, USA Phone: (301)-683-3691 Fax: (301)-683-3703

…

On Tue, Jul 14, 2020 at 3:12 PM Jun Wang ***@***.***> wrote: Please see the new PR #164 <#164>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#163 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANJBYQBGNZCQOSQIU4QJTELR3SU2XANCNFSM4OU25YKQ> .