Testing only - do not merge #9
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* Modify the computation at defined points. * The second part of changes from debug mode. * The third part of changes from debug_mode. * The fourth part of changes from debug_mode. * The fifth part of changes from debug_mode. * Update per comments from code reviewer. * Remove legacy sigma level temperature from PRSLEV dataset. * Fix MCONV computation on undefined grids. * Fixes for global and regional inline post in debug mode. * Update VERSION to 10.0.9. * Remove duplicated line.
* add and update parm files for SSMIS-F17 channels for HAFS satellite products * source code changes for add SSMIS-F17 channels for HAFS satelllite products * add ssmis-f17 varibles to params_grib2_tbl_new and params_grib2_tbl_new.text, remove the params_grib2_tbl_new_ssmisf17 * add change logs in RQSTFLD.f and CALRAD_WCLOUD_newcrtm.f Co-authored-by: Lin.L.Zhu@noaa.gov <Lin.L.Zhu@m72a1.ncep.noaa.gov>
…ayer in high latitudes (NOAA-EMC#371) from Huiya.
…MC#358) * Update params_grib2_tbl_new * Update post_avblflds.xml * This commit includes changes to the computation of the effective layer top and bottom. * This commit includes changes to the computation of the effective layer top and bottom. * Update ALLOCATE_ALL.f i loop indices corrected. * Update MISCLN.f * Update MISCLN.f Removed EL_SCHEME flag and the EL_SCHEME 2 as it was intended as a method of validating the output of EL_SCHEME effective layer top and bottom calculations. The HWT/SFE confirmed that the EL_SCHEME 1 computations were viable making EL_SCHEME 2 superfluous. The debugprint flag was also set to false as it currently not needed in the execution of the MISCLN subprogram, however, it may be switch on at any point it becomes necessary to trace a problem. * Update UPP_PHYSICS.f Removed the definition of CALCAPE1D which was invoked in MISCLN.f as the CAPE/CIN computational routine used in EL_SCHEME 2. It is now a defunct option. * Update MISCLN.f * Update MISCLN.f * Added conditional block that only invokes the effective layer top and bottom correction for RTMA. * Addressed remaining bug linked to the use of the FV3R first guess. * minor code changes made to ALLOCATE_ALL.f, MISCNL.f and UPP_PHYSICS.f to address segmentation fault occurring during the rtma regression tests * Clean up before merging.
* add some extra surface fields to the model output * correct the name of the variable * fix typo * correct the index in the surface.f * fix the time stamp * put most extra fields to the flux instead of the master file * update control file * clean the code
* switched to local copy of FindNetCDF.cmake * fixed path to FindNetCDF
* updated Doxyfile, turned on warnings * turn off WARN_AS_ERROR in Doxyfile
* Remove old Himawari lines used by grib1 * add Himawari-8 parameters to Grib2 table * update params_grib2_tbl_new and params_grib2_tbl_new.text with himawari-8 channels Co-authored-by: Tracy <tracy.hertneky@noaa.gov>
* Add fixes for 1000 mb HGT corrupted at RRFS 3KM parallel run. * Remove debugging line. * Remove debugging line. * Remove debugging line. * Update VERSION with 10.0.10
* Starting UPP version numbers with 10.0.0 for develop branch * Add codeowners file to develop
…documentation (NOAA-EMC#400) Co-authored-by: Tracy <tracy.hertneky@noaa.gov>
* fixed doxygen for function * more doxygen fixes * fixing doxygen in AVIATION.f * fixing doxygen in AVIATION.f * fixing doxygen in AVIATION.f * Changed to F77 doxygen comment marker * changed doxygen comment marker back
* Created formal fortran namelist for itag. * This is a legacy script. No updates are needed. * Further code refinement from Wen. * Added a change log. * Replace replace "fullmodelname" with "modelname, submodelname" in "model_inputs". * bug fix * Replace FULLMODELNAME to MODELNAME. * Further clean up for FULLMODELNAME. * Further code refinement from Wen. * Rename control file variable name. * Removed fileNameFlat in gfs itag. * Further code refinement from Wen.
* Add doxygen comments to BNDLYR.f * fix bullets * change to proper case, fix param order * add documentation note Co-authored-by: Tracy <tracy.hertneky@noaa.gov>
* Move package config to top-level CMakeLists.txt * Update version to 10.0.11
* remove grib1 control files from parm/ * Cleanup grib1 RQSTFLD.F, remove READCNTRL.f, INITPOST_NEMS.f, INITPOST_GFS_NEMS.f, INITPOST_GFS_SIGIO.f from CMakeLists.txt, remove unused variables from a number of INITPOST* routines that were initialized in RQSTFLD.F * Revert back to use nemsio_module in WRFPOST.f * Add INITPOST_NEMS.f back, since nmmb is still tested * remove INITPOST_GFS_NEMS.f and INITPOST_GFS_SIGIO.f from source directory * Add back GETNEMSANDSCATTER * Add INITPOST_GFS_NEMS back * remove use rqstfld_mod * WRFPOST mods * WRFPOST mods * remove sigio from module files * Remove READCNTRL.F from sorc dir since it is no longer used * Remove sigio lines from WRFPOST * rename RQSTFLD.F to RQSTFLD.f * Add change logs * Update to RQSTFLD.f in CMakeLists * Add sigio module back Co-authored-by: Tracy <tracy.hertneky@noaa.gov>
* update modules for jet * update modules for jet (#2) * feature/HAFS: Switch back to use netcdf/3.6.3 on Jet. Can consider switching to netcdf/4.x.x for all platforms later on. * support/HAFS: Update for regular lat-lon grids to FV3 output change on coordinate (Cherry-picked from Jili.Dong's commit). * update for jet; update for new write component coordinates * add post lib for jet * update for Lambert/rotated latlon to output earth relative wind * fix ref at -10C * Add the configuration for Orion. * Update modulefiles/post/v8.0.0-jet to use modules under the lfs4 disk. * Update modulefiles/post/v8.0.0-jet. * Symbolic link from modulefiles/post/v8.0.0-cray-intel to modulefiles/post/v8.0.0-wcoss_cray. * Update compile_upp.sh so that it can be called/run from the workflow level build driver script. More specifically, the following line is changed from source detect_machine.sh into source ./detect_machine.sh * Add HAFS nosat post control files (@LinZhu-NOAA). Co-authored-by: Jili Dong <Jili.Dong@noaa.gov> Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com> Co-authored-by: Wen Meng <wmeng@Orion-login-2.HPC.MsState.Edu>
* Add foundation temperature per request from coupling group * add founfation T to inline post control file * add founfation T to inline post control file flux file part instead * Change sea ice threshold for identifying sea ice from .1 to 0 * made updates to only use new ice fraction threshold to identify sea ice grid point for GFS and RRFS so that legacy models land masks won't be affected by this change. Co-authored-by: wx20hc <Hui-Ya.Chuang@m71a1.ncep.noaa.gov> Co-authored-by: wx20hc <Hui-Ya.Chuang@m71a2.ncep.noaa.gov> Co-authored-by: wx20hc <Hui-Ya.Chuang@m71a3.ncep.noaa.gov>
* Turn on GSD cloud ceiling calculation for RRFS dev. * Updates to UPP for RRFS applications (#3) * Updates to UPP for RRFS applications: 1) Adding a RRFS-specific .xml control file and a corresponding .txt flat file. Note that script changes (pending) are needed to leverage the new flat file. However, this code will work in current real-time configurations. 2) Adding GSL experimental ceiling diagnostics, GSL visibility diagnostic, and GSL sea-level pressure reduction (MAPS). Also adding TKE and aerosol number concentrations. 3) Code clean-up for ceiling-related diagnostics; added comments, etc. 4) Removing several non-needed variables, originally inherited from FV3-SAR community configuration. * Updating UPP control files to specify GRIB2 generating center as "noaa_fsl_boulder" and the generating process as "hrrr". The "hrrr" specification is temporary, and will eventually be switched to "rrfs" once required changes to the "NCEPLIBS-g2tmpl" library are available. (#4) * Fix some out-of-bounds reads that caused the RRFS UPP to crash. (#5) * Adding README file (#7) * Adding README file to describe process of making a "flat" file. * Updates to README to improve explanation of input/output files. * Code to read in Flash Flood Guidance (FFG) and Average Recurrence Interval (ARI) precipitation datasets for comparison with model QPF within UPP. * Fixed a syntax error in SURFCE.f * Getting rid of GRIB1 output option to be consistent with rest of code. * Changing field numbers to avoid conflict with existing RRFS-dev1 fields. * Putting exceedance grids in flat files for testing in RRFS UPP. * Corrected the 1h and run total precip names for calculating exceedances in SURFCE.f * Bug fix in SURFCE.f if statements. * Removing changes to RQSTFLD.F since GRIB1 is no longer used in UPP. * Merging NOAA-GSL development on top of NOAA-EMC UPP for testing. * Correcting minor typos in SURFCE.f to allow testing. * Update code based on testing with RRFS cases. * Update part of the code based on current EMC develop branch for comparing the test results with the merged version.(#9) * Fixed several bugs in the code. * Modifications to SURFCE.f to check for existence of FFG files. * Bug fixes for FFG file existence check, and changes to handle rotated lat-lon grid interpolation for FFG * Bug fixes for FFG existence checks in SURFCE.f * Another bug fix for SURFCE.f * Updating XML and flat txt files to include a 65th vertical level to be consistent with updated FV3LAM model with higher model top. (NOAA-EMC#13) * Code cleanup for QPF - FFG comparison. Comparison put into subroutine. * Cleanup of SURFCE.f; moving the FFG comparisons into a subroutine. * Final cleanup of exceedance code for QPF vs FFG. * Removing some commented out variable declarations. * Additional cleanup recommended by Ming: we really only need two exceedance variables; one for 1h FFG and one for run total FFG exceedances. * Further cleanup of FFG code, simplifying to two fields (1h acc and run total acc) * Adding ARI comparison fields for 2y, 5y, 10y, and 100y ARIs. * Changes to output 9 soil levels from FV3LAM if we are running 9 level RUC LSM. * Adding flat txt file for UPP. * Commenting out the use of the ARI exceedances for now. We can switch them on later. * Bug fix in INITPOST_NETCDF.f : need to use both ncid2d and ncid3d in this subroutine! * Adding NOAA-GSL code changes on top of latest NOAA-EMC UPP. * Couple of bug fixes in NOAA-EMC code. Bugs were leading to PRMSL and -10C REFD being all zeroes. * Cleaning up code to get rid of unnecessary differences from EMC. * Putting all new GSL variables into EMC's unified post_avblflds.xml. Note that EMC's unified post_avblflds.xml does not validate using the avblflds Schema. * Updating postconfig-NT.txt file for GSL RRFS based on merged post_avblflds.xml file. * Adding RRFS control files to makefile. * Changing back scale for WEASD_ON_SURFACE to previous default, thanks to suggestion from Wen Meng. * Reverting name of cldfra based on feedback from Eric Aligo. * Reverting changes in fv3lam_post_avblflds.xml since GSL new variables are now included in post_avblflds.xml * Changing experimental ceiling level type from "ceiling" to "cloud_ceilng" * Updating 3drtma_postcntrl.xml with revised name for GSD_EXP_CEILING. This also affects postxconfig-NT-3drtma.txt. postxconfig-NT-fv3lam_rrfs.txt also changed due to changes in post_avblflds.xml * Introducing if statement for call of NGMSLP, to avoid calling unless it is needed. Co-authored-by: Ming.Hu <Ming.Hu@noaa.gov> Co-authored-by: Christina Holt <56881914+christinaholtNOAA@users.noreply.github.com> Co-authored-by: Christina Holt <Christina.Holt@noaa.gov> Co-authored-by: Jaymes Kenyon <jaymes.kenyon@noaa.gov> Co-authored-by: Samuel Trahan (NOAA contractor) <39415369+SamuelTrahanNOAA@users.noreply.github.com>
Doxygen for CALDWP.f
* Doxygen for CALDRG.f * Delete CALDWP.f * Revert "Delete CALDWP.f" This reverts commit 575cd93.
* Add gtg code as submodule. * Remove manage_externals. * Sync with the changes from GFSV16. * Add change logs for POSTGRB2TBL default setting.
* add option to build with GTG code or stubs * make IP optional depending on GTG option. * GTG code depends on a file that only resides in the gtg repo * fix a big boo-boo * move sorc/post_gtg.fd to sorc/ncep_post.fd/post_gtg.fd and update build path to GTG * correct the name of the submodule. fix mixed indents * move map_routines.F90 into the GTG src list
* Add command line arguments in compile_upp.sh for options, e.g. building with gtg code, building with wrfio stub code, turning on cmake verbose. * Remove legacy GNU make capability.
* Remove read interfaces INITPOST_GFS_NEMS, INITPOST_GFS_NEMS_MPIIO and INITPOST_GFS_NMM. * Change linking order for w3nco and nemsio * Remove INITPOST_GFS_NETCDF * Remove INITPOST_GFS_NEMS.f, INITPOST_GFS_NETCDF.f, INITPOST_NEMS.f, INITPOST_NEMS_MPIIO.f from UPP code. * Fix build failture. * Clean up legacy makefile * Clean up another two makefiles * Add back INITPOST_GFS_NETCDF
…del (NOAA-EMC#579) * 1)Add nitrate look-up table based on NASA optics_NI.v2_5.nc. 2)Implement the nitrate AOD calculation for UFS-Aerosols model, which is also included into the total AOD. * Remove unused variables in CLDRAD.f * Add chemical products into global_1x1_paramlist_g2 file
* Miscellaneous GSL changes / bug fixes. * Including postxconfig file * Bug fix for if statement * Reverting change to max precip rate encoding. * Minor bug fix. * Adding change log entries for code modifications from GSL RRFS_dev * Fixing error with multiple variables using the same IGET value (922) in SURFCE. * Getting rid of unnecessary IF statement * Commenting out setting smstav to missing * Changing name of soil moisture availability to be consistent with latest RRFS * Adding check for model type before multiplying MSTAV by 100 * Adding definition for ITSRFC in GRIB2 bug fix sections.
* Adding smoke and dust output, smoke emissions, aerosol optical thickness, and hourly wildfire potential from RRFS. * Updating change logs for addition of smoke / dust in RRFS * Reverting cldfra_bl to cldfra. * Changing syntax on one line. * Adding model name check for computing AOD (used in visibility). * Moving reading of EBB and HWP to section for regional FV3 phy files. * Fixing accidental change in length of recname. * Making extsmoke and extdust into local variables within INITPOST_NETCDF.f * Adding deallocate statement for fv3dust, debug flag for print statements, and bug fix for reading in soil moisture availability. * Using 1E9 for multiplication in CALPW instead of 1000000000 * Bug fix from Wen Meng, and also updated RAP/HRRR/RTMA fix files with new GRIB2 template for smoke-related fields. * Adding checks for missing values in aod loop.
* 1)Add new control file for AQM; 2)Output hourly averaged PM2.5 and O3 concentration; 3)Remove instant PM2.5 and O3 concentraction. * 1)output hourly averaged PM2.5 and O3; 2)Remove instant PM2.5 calculation. * Remove unit conversion for hourly pm2.5 * Remove O3MR from AQM control files * 1)Add new variable entire atmosphere aod; 2)add entire atmosphere aod and HPBL in aqm control files; 3)remove fv3lam_cmaq control files. * Add some fixes for CI failture per Alex's suggestions. * Add gfortan 12 installed in ubuntu-latest * Add "sudo apt install cmake" * Add "sudo apt install cmake" in gcc.yml * Pick up the changes from Alex. * Add back "spack compiler find" * tweaking gcc.yml * 1) Add changes based on Kai's comments; 2) Pick up changes of CI from Alex. * 1)tweak aod ouput; 2)add latest changes of CI from Alex. * update change logs * update change log based on Huiya's comments
* github links * remove DTC
…OAA-EMC#604) * remove MAX_PRATE_ON_SURFACE, add ACM_ACPCP_ON_SURFACE for hafs_nosat * update wcoss2 g2tmpl version
* Bug fixes for RRFS snow accumulation variables. * Adding check to only divide var density snow by 1000 if we are dealing with RRFS. * Bug fix for missing endif * Updating RRFS control files to make MAXUVV and MAXDVV GRIB2 labeling consistent with calculation in FV3. * Correcting missed MAXUVV / MAXDVV fields in NATLEV files.
* read in six new winter weather diags, allocate, deallocate,and add new vrbs (3 of them), plus for continuous fields modify timestamp for FV3R and GFS and add fields to the GFS and fv3lam xml and flat files. * Rename winter wx diags * removed log file * remove six winter wx diags from f00 file * remove winter weather diags from gfs f00 xml and txt files * Add one line to both acfrain and acgraup sections to ensure the correct time stamp in grib2 file for accumulated fields. * Add change log to SURFCE.f and INITPOST_NETCDF.f
* remove hafs.xml and hafs.txt, add hafs_sat.xml and hafs_sat.txt, also add AVE_CPRAT, MAXUVV, MAXDVV, GUST, MXUPHL(0-3km,2-5km) and replace INST_PRATE to AVE_PRATE in hafs_nosat.xml and hafs_nosat.txt * add MAXUVV and MAXDVV in postxconfig-NT-hafs_nosat.txt
* 20220715 Jesse Meng initiate variable snow desity SDEN and calslr subroutine in UPP_PHYSICS * 20220902 Jesse Meng modify gfs and fv3lam txt files for SLR/snoden test * 20220919 Jesse Meng update progress in UPP_PHYSICS/CALSLR_ROEBBER * 20220928 Jesse Meng update progress in UPP_PHYSICS/CALSLR_ROEBBER * 20221003 Jesse Meng update progress on SLR * 20221007 Jesse Meng update progress on SLR * 20221028 Jesse Meng updates for SLR branch * 20221102 Jesse Meng merge with develop * 20221214 Jesse Meng merge slr branch with UPP/develop * 20221219 Jesse Meng add a new fix directory and save SLR/Roebber/Breadboard * 20221219 Jesse Meng add WPC climo_snoden files * 20221222 Jesse Meng add SDEN to configure files * 20221222 Jesse Meng add develop and SLR configures files * 20230103 Jesse Meng added SDEN to xml and txt files. * 20230103 Jesse Meng fixed parm/postcntrl_gfs_two.xml and parm/postxconfig-NT-GFS-TWO.txt. * 20230103 Jesse Meng deleted temperary slr testing related txt files. * 202230103 Jesse Meng revised documentation for subroutine UPP_PHYSICS/CALSLR_ROEBBER. * 20230106 Jesse Meng moved all the SLR Roebber Breadboard coefficients into UPP_PHYSICS module to reduce I/O time. * 20230109 Jesse Meng updated comment block of subroutine calslr. * 20230109 Jesse Meng output 1006 SDEN in NATLEV files only and remove it from PRSLEV files. * 20230109 Jesse Meng output 1006 SDEN in NATLEV files only and remove it from PRSLEV files. * 20230110 Jesse Meng updated SLR field in parm/ files. Co-authored-by: shrinivas.moorthi <shrinivas.moorthi@noaa.gov> Co-authored-by: jesse meng <jesse.meng@dlogin01.dogwood.wcoss2.ncep.noaa.gov> Co-authored-by: jesse meng <jesse.meng@dlogin04.dogwood.wcoss2.ncep.noaa.gov>
* Connect to IFI * Correct CAPE&CIN calculations * Changes to get IFI working. * Connect to latest version of libIFI, but in an ugly way. Also, this is sending the wrong CAPE, CIN, and APCP * Output libIFI-style diagnostic NetCDF files on full grid instead of per-rank. * Send the right CAPE, CIN, and APCP to libIFI * IFI connection: disable smoothing and precision drop. Add more diagnostic output. All results match standalone program. * IFI smoother works in MPI * Without IFI, output missing values for IFI fields. If IFI is requested and missing, build anyway. * delete old file RQSTFLD.F * bug fixes to get IFI to run * IFI works 2D * Missing value in ifi debug files & some logging * missing EXCH_c_float.f file * double-specified access specification * fix two syntax errors (missing <0) * Build with IFI by default, if it is present. * bug fixes for build and namelist reporting * disable ifi by default * Add c++ linker flags * Bug fixes to allow IFI fields to be generated when nothing else is requested * add ifi fields to fv3lam xml & txt files * remove cpp directives from a file that is not passed through cpp * -i flag to compile ifi * Missing IGET(ient)>0 check in IFI.F caused crashes * compile_upp.sh -i can compile with libIFI on hera * many bug fixes * update ifi module version on hera * remove unused variable * add a missing allocate() * remove unused code and switch from abort to mpi_abort * Point to ifi on acorn * remove halo regions from variables sent to libIFI * Change loops 1,IM -> ISTA,IEND in several places * revert some problematic changes * IFI fields * can build with ifi inside upp * simplify code a bit * update hera ifi module version for unit conversion bugfix * update internal ifi for unit conversion bugfix * revert to develop version of post_gtg.fd * bug fixes to get UPP to run IFI build internally, after latest few merges * updated libifi * correct error in postxconfig-NT-fv3lam_rrfs.txt * switch to 1007-1010 IGET numbers for IFI * IFI_APCP(i,jj) -> IFI_APCP(ii,jj) * missing variables from postxconfig-NT-fv3lam_rrfs.txt * 20220901 => 20230112 on jet * update ifi module version * remove duplicate code * bug fix in libifi test program (will not affect post) * comment-out wordy print statement * libIFI submodule: https & update=none * update changelogs * remove NCEP table from non-NCEP-table variable Co-authored-by: samuel trahan <samuel.trahan@alogin01.acorn.wcoss2.ncep.noaa.gov>
…ocates (NOAA-EMC#621) * inline post bug fix: deallocate ifi arrays before next iteration of post * Update sorc/ncep_post.fd/IFI.F
* GSL UPP developments up to January 2023 1. Increases precision of VIL_ON_ENTIRE_ATMOS from `<scale>4.0</scale>` to `<scale>7.0</scale>` 2. Adds an experimental diagnostic, developed for the HRRR to correct for the HRRR's low bias in cloud cover. For an FAA deliverable due Feb 2023. 3. Switches from cldfra to cldfra_bl when reading cloud fraction from INITPPOST_NETCDF * inline post bug fix: deallocate ifi arrays before next iteration of post * Update sorc/ncep_post.fd/IFI.F * automatically choose cldfra or cldfra_bl * update author info
* To make 'cmake' go through for GTG, 1. GTG source code file extensions are changed from f90 to F90 2. Add ip::ip_4 back to sorc/ncep_post.fd/CMakeLists.txt * Made a new tag of NCAR GTG to change file extension from f90 to F90, then updated Externals.cfg with this new tag * Update GTG tag to fix two issues: 1. Fix buzillar #1207 http://www2.spa.ncep.noaa.gov/bugzilla/show_bug.cgi?id=1207 2. EMC_post issue NOAA-EMC#272 * Pick up GTG new tag fixing the failure because of strong wind * Add debug mode option to tests/compile_upp.sh --------- Co-authored-by: wx20yam <Yali.Mao@v71a3.ncep.noaa.gov> Co-authored-by: yali mao <yali.mao@clogin02.cactus.wcoss2.ncep.noaa.gov>
* Correcting name of MAPS SLP variable in post_avblflds.xml, and removing from RRFS postxconfig file, and a slight change to exp2 ceiling diagnostic. * Small change to MDLFLD to make sure REFD at -10C still gets output after getting rid of MSLMA output. * Adding change logs. * Adding NCEP local use for MSLMA
…C#630) * Correct DEPTH param in CALHEL * add def for LPBL and ZPBL * reorder variables in header --------- Co-authored-by: gspetro <gillian.s.petro@gmail.com>
Co-authored-by: yali mao <yali.mao@dlogin02.dogwood.wcoss2.ncep.noaa.gov>
* Revised calculation of wind GUST for UFS applications * Revised calculation of wind GUST for UFS applications * Revised Calculation of Wind Gust for UFS Applications * Revised calculation of wind GUST for UFS applications * Revised calculation of wind GUST for UFS applications
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