…OAA-EMC#740)

* Updating GRIB2 labeling for MSTAV, and adding SOILL on 9 RUC levels.

* Entering change log for INITPOST_NETCDF.f

* Changing shortname of MSTAV to specify RUC LSM (defined at 0 m below ground)

…om anywhere. correct bug when prefix is specified, the executable is not in the correct place. (NOAA-EMC#746)

* silence warnings on SMOOTH.f

* update GFIP3.f

* fix more warnings for CALHEL2 & CALHEL3

* silence warnings on CALPW.f

* silence warnings for CALPBL.f

* silence warnings for CALPBLREGIME.f

* silence warnings for CALMICT.f

* silence warnings on WRFPOST.f

* silence warnings on FDLVL.f

* silence warnings on SELECT_CHANNELS.f

* correct CALPBLREGIME.f

* fix errors for PMICRPH.f and GRIDSPEC.f

* partial updates to variables in several files

* CTLBLK updates

* define GRIDSPEC.f vars

* document PMICRPH.f

* update CALRAD_WCLOUD_newcrtm.f

* edits for COLLECT_LOC.f and GRIDSPEC.f

* update INITPOST_NEMS.f

* minor edits/additions

* Update INITPOST_GFS_NEMS_MPIIO.f

* update CTLBLK.f

* update variables for CLDRAD.f, INITPOST_NETCDF.f, MDL2P.f, PROCESS.f, xml_perl_data.f

* fix typo in CTLBLK.f

* fix typo in CTLBLK.f

* remove some deprecated Doxyfile.in settings

* upgrade Doxyfile.in w -u option

* fix Doxyfile.in

* fix Doxyfile.in

* revert Doxyfile to equivalent of commit 94a989e

* rm deprecated info in Doxyfile.in

* remove _____ for undefined vars

* add var defs to PMICRPH.f

* correct a4wide to a4 in Doxyfile.in

* rm blank spaces in xml_perl_data.f

* rm blank spaces in xml_perl_data.f

NOAA-EMC#750)

* Add bug fix of tke initialization from Huiya

* Clean up legacy fv3lam control files

* Clean up legacy control files

* Clean up legacy file params_grib2_tbl_new_dtc

…#758)

* (1) Updates to read-in the number concentrations of cloud ice, cloud water, and rain
(2) Slight reorganization of the "use vrbls3d" code section to re-group several microphysics-related variables

* Enabling RRFS output of cloud-ice number concentration (NCCICE), cloud-water number concentration (NCONCD), and rain number concentration (SPNCR) on native coordinate surfaces.

* Updates to static control files:
(1) In post_avblflds.xml, changing "NCIP" to "NCCICE" (ID 752)	and "NCRAIN" to "SPNCR" (ID 754).  This is consistent with the ID numbers used in post_avblflds_raphrrr.xml.
(2) Removing the "table_info" specification for "SPNCR" in fv3lam_rrfs.xml.
(3) Re-generated flat flie.

* In INITPOST_NETCDF.f, changing the "ncid2d" argument to "ncid3d" withinin several calls to "read_netcdf_3d_para".

* Reverting the read-in of "ext550" to its previous form.

* Update gefs control files based on EP4 settings.

* remove ICIP and ICSEV from gefs control files

* Delete gefs ana control files and update gefs control txt files.

* Delete machines not in operation

* Add modulefiles/hercules.lua.

---------

Co-authored-by: Wen Meng <[email protected]>

* Add GEFS WAFS control file

* 1. Change gtg_algo() interface in MDLFLD.f
2. Add CIT(:,:,:) array for In-Cloud Turbulence, ALLOCATE_ALL.f VRBLS3D_mod.f DEALLOCATE.f
3. Modify CMakeLists.txt for updated/new GTG source code files.
4. Add stub code for the new GTG source files in general UPP
5. Modify interpolation in MISCLN.f for RRFS GTG
6. Modify jobs/J_NCEPPOST to run WAFS downstream only
   Add scripts/exwafs_atmos_nceppost.sh
   Add ush/wafs_nceppost.sh

* 1. Add updates to the log/history of the related Fortran source code
2. Add gtg_on to POSTGPVARS in scripts/exwafs_atmos_nceppost.sh,
   and add gtg_on to namelist 'nampgb' in WRFPOST.f

* update gtg code revision

* Remove one duplicate line of comment

* Fix bug of GTG interpolations in MDL2P.f
Remove WAFS fields on ICAO standard atmospheric levels from post_avblflds.xml
And remove MDL2STD_P.f which does interpolation on ICAO standard atmospheric levels

* Fix a bug by initializing "gtg_interpolation = .false." in MDL2P.f

* Remove comments and a variable related to MDL2STD_P
Piggyback changes of parm/makefile for cleaning out GEFS anal control file generation

* Remove GTG related parm files. Instead, scripts will copy the parm file from
sorc/ncep_post.fd/post_gtg.fd

---------

Co-authored-by: yali mao <[email protected]>
Co-authored-by: yali mao <[email protected]>
Co-authored-by: yali mao <[email protected]>
Co-authored-by: yali mao <[email protected]>
Co-authored-by: yali mao <[email protected]>
Co-authored-by: yali mao <[email protected]>
Co-authored-by: yali mao <[email protected]>
Co-authored-by: yali mao <[email protected]>

Move changed results indicator to after rap_pe_test check otherwise may have false positive. Show run directory path for checking changed results.