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Merge 4.3.3 #55

Merged
merged 160 commits into from
Mar 1, 2022
Merged

Merge 4.3.3 #55

merged 160 commits into from
Mar 1, 2022

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letmaik
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@letmaik letmaik commented Jan 15, 2022

Some minor CMake changes were needed updating from 4.2.2. See last commit in this PR. macOS is excluded for this release as it is segfaulting for unknown reasons.

This also adds ndown and tc (fixes #53).

smileMchen and others added 30 commits March 10, 2020 10:02
…l#1144)

TYPE: bug fix

KEYWORDS: remove conflict marker "<<<<<" and ">>>>"

SOURCE: Jan Mandel (CU Denver)

DESCRIPTION OF CHANGES: 
In the surface driver, we have:
```
<<<<<<< HEAD
     END IF
  END IF
=======
      ENDIF
  ENDIF
>>>>>>> origin/master
```

LIST OF MODIFIED FILES: 
M       phys/module_surface_driver.F

TESTS CONDUCTED:  
1. Jenkins auto testing  is PASS
TYPE: new feature

KEYWORDS: WRFDA, AHI, Cloud detection

SOURCE: Deqin Li (Liaoning Meteorological Bureau of CMA/NCAR), Dongmei Xu (NUIST/NCAR),  Jonathan Guerrette (NCAR).

DESCRIPTION OF CHANGES:
A cloud detection method is added for AHI radiance data assimilation based on an infrared-only cloud mask (CM) algorithm.

LIST OF MODIFIED FILES: 
	A:   var/da/da_physics/da_trop_wmo.inc
	A:   var/da/da_radiance/mod_clddet_geoir.f90
	M:   Registry/registry.var
	M:   var/build/da.make
	M:   var/build/depend.txt
	M:   var/da/da_define_structures/da_define_structures.f90
	M:   var/da/da_physics/da_physics.f90
	M:   var/da/da_radiance/da_allocate_rad_iv.inc
	M:   var/da/da_radiance/da_crtm.f90
	M:   var/da/da_radiance/da_deallocate_radiance.inc
	M:   var/da/da_radiance/da_get_innov_vector_crtm.inc
	M:   var/da/da_radiance/da_initialize_rad_iv.inc
        M:   var/da/da_radiance/da_qc_ahi.inc
	M:   var/da/da_radiance/da_radiance.f90
	M:   var/da/da_radiance/da_radiance1.f90
	M:   var/da/da_radiance/da_read_obs_netcdf4ahi_jaxa.inc
	M:   var/da/da_radiance/da_setup_radiance_structures.inc

TESTS CONDUCTED: 
WRFDA regression tests ran successfully with gnu/ifort+mpt on Cheyenne.

RELEASE NOTE: New capability for an IR-only cloud detection scheme for AHI radiance data assimilation.
Wu et al., 2020, Improving forecasts of a record-breaking rainstorm in Guangzhou by assimilating every 10-min AHI radiances with WRF 4DVAR. Atmospheric Research, 239, 104912.

Zhuge, X., Zou, X., 2016. Test of a modified infrared-only ABI cloud mask algorithm for
AHI radiance observations. J. Appl. Meteorol. Climatol. 55 (11), 2529–2546.
TYPE: new feature

KEYWORDS: superobbing, cloud detection, cloud fraction, AHI 

SOURCE: Yali Wu (NCAR/MMM), Jonathan Guerrette (NCAR/MMM).

DESCRIPTION OF CHANGES: This PR adds a new function of superobbing AHI radiances and retrieving cloud fraction based on AHI cloud detection results. The default namelist parameter `ahi_superob_halfwidth` is set to zero, which means no superobbing will be applied.  

ISSUE: no issue

LIST OF MODIFIED FILES: 
M       Registry/registry.var
M       var/da/da_define_structures/da_define_structures.f90
M       var/da/da_monitor/da_rad_diags.f90
M       var/da/da_radiance/da_allocate_rad_iv.inc
M       var/da/da_radiance/da_deallocate_radiance.inc
M       var/da/da_radiance/da_initialize_rad_iv.inc
M       var/da/da_radiance/da_qc_ahi.inc
M       var/da/da_radiance/da_radiance.f90
M       var/da/da_radiance/da_radiance1.f90
M       var/da/da_radiance/da_read_obs_netcdf4ahi_jaxa.inc
M       var/da/da_radiance/da_write_iv_rad_ascii.inc
M       var/da/da_radiance/da_write_oa_rad_ascii.inc

TESTS CONDUCTED:
This capability has been tested in generating one-month AHI obs files for MPAS-JEDI DA purpose. WRFDA regression tests passed.
TYPE: enhancement

KEYWORDS: WRFDA, gen_be_v3, cv_options=5

SOURCE: Jamie Bresch (NCAR)

DESCRIPTION OF CHANGES:
A collection of fixes and enhancements for gen_be_v3
1. add multi-variate statistics capability for stream function, velocity potential, temperature and surface pressure
2. bug fix for be_method=ENS with multiple valid dates
3. add time_lag_ens option for calculating statistics from time lagged ensembles
4. add a sample makefile that uses WRFDA-compiled lapack-lib.

LIST OF MODIFIED FILES:
M var/gen_be_v3/README.gen_be_v3
D var/gen_be_v3/compile_casper
D var/gen_be_v3/compile_cheyenne
M var/gen_be_v3/gen_be_v3.F90
A var/gen_be_v3/makefile
A var/gen_be_v3/util/combine_be_cv5.f90
A var/gen_be_v3/util/makefile

TESTS CONDUCTED:
1. The updated code has been used by Taiwan's Central Weather Bureau and NCAR's Antarctic Mesoscale Prediction System.
2. Jenkins tests all passed.

RELEASE NOTE: WRFDA gen_be_v3 is updated for cv_options=5 and ensemble applications. Please see var/gen_be_v3/README.gen_be_v3.
TYPE: New Feature

KEYWORDS: WRF-CTSM coupling, Community Terrestrial Systems Model (CTSM), Community Land Model (CLM), 
coupled land-atmosphere models

SOURCE: Negin Sobhani <sup>1</sup> , Dave Lawrence <sup>1</sup> , Bill Sacks <sup>1</sup>, 
Sam Levis <sup>2</sup>, Mariana Vertenstein <sup>1</sup>, Dave Gill <sup>1</sup>, Mike Barlage  <sup>1,3</sup>, 
and Fei Chen <sup>1</sup> 

<sup>1</sup> National Center for Atmospheric Research (NCAR)
<sup>2</sup> SLevis Consulting 
<sup>3</sup> National Centers for Environmental Prediction (NCEP)

DESCRIPTION OF CHANGES:
This PR includes the capability to couple WRF with Community Terrestrial Systems Model (CTSM) via LILAC 
(Lightweight Infrastructure for Land-Atmosphere Coupling). CTSM can be used with WRF as one of WRF's land 
surface model schemes by setting `sf_surface_physics` in the WRF namelist.input file:

```
&physics
sf_surface_physics = 6, 6, 6,
/
```

For instructions on how to run WRF with CTSM please check [instructions on using CTSM with WRF.](https://escomp.github.io/ctsm-docs/versions/master/html/lilac/specific-atm-models/index.html)

LIST OF MODIFIED FILES: 
M       Registry/Registry.EM_COMMON
M       arch/Config.pl
M       arch/configure.defaults
M       arch/postamble
M       arch/preamble
A        doc/README.CTSM
M       dyn_em/module_first_rk_step_part1.F
M       dyn_em/module_initialize_real.F
M       dyn_em/solve_em.F
M       main/depend.common
M       phys/Makefile
M       phys/module_physics_init.F
A       phys/module_sf_ctsm.F
M       phys/module_surface_driver.F
M       share/input_wrf.F
M       share/module_check_a_mundo.F
M       wrftladj/solve_em_ad.F 

TESTS CONDUCTED:
1. The jenkins tests are all passing.
2. Initial assessment of the performance of WRF-CTSM5(NWP) compared to WRF-Noah and WRF-NoahMP has been 
completed over the CONUS domain.  Overall, we are finding that WRF-CTSM5(NWP) is performing reasonably well, in 
some cases even showing improved performance improvement. For example, the following plot shows the bias for 
maximum daily temperature from NOAH, NOAH-MP, and CTSM for June 2013 over METAR observation sites:

![CTSM_PR_2013-04_Tmin_Tmax](https://user-images.githubusercontent.com/17344536/90686072-05acc780-e228-11ea-91fa-4d239e548d1b.png)

RELEASE NOTE: 
The capability to couple CTSM with WRF is added and activated by setting namelist option `sf_surface_physics` to 6.
This is the initial beta release of WRF-CTSM coupling capability. For instructions on how to run WRF with CTSM please
check [instructions on using CTSM with WRF.](https://escomp.github.io/ctsm-docs/versions/master/html/lilac/specific-atm-models/index.html)
This large PR adds the new capability for multi-resolution incremental 4DVar.

TYPE: new feature

KEYWORDS: MRI-4DVar, Inverse transform, square root of B, 3-stage

SOURCE: Zhiquan (Jake) Liu, Junmei Ban, Jamie Bresch, Yali Wu, Xin Zhang, Jianyu Liu (NCAR/MMM)

DESCRIPTION OF CHANGES:
Existing 4DVar algorithm is run at the same model resolution for inner loop minimization of different outer loops (default namelist setting with multi_inc=0). This adds MRI-4DVar capability that can run 4DVar at lower resolution for inner loop minimization with a 3-stage procedure (observer, minimizer, regridder) as described by Liu et al. (2020) and can substantially speed up 4DVar. Three major changes include:

3-stage procedure controlled by a script and offline programs under ~var/mri4dvar;
Set multi_inc=1 for the "observer" step and multi_inc=2 for the "minimizer" step. The "regridder' step is done using the offline programs.

Inverse transform of square root B introduced under ~var/da/da_vtox_transforms;
New namelist parameter use_inverse_squarerootb needs to be set .true. when multi_inc=2 and works together with cv_options=5, 6, or 7 and cloud_cv_options=2 or 3.

New namelist parameter use_interpolate_cvt=.false. (default), which is supposed to work together with the obsolete cv_options=3, which is not recommended to use for non-expert users.

Additional file I/O for control variable and radar/radiance OMB files from the observer step. This I/O part will need some further code clean-up and improvement in the future.
LIST OF MODIFIED FILES: 48 files
M Registry/registry.var
M var/build/depend.txt
M var/da/da_main/da_solve.inc
M var/da/da_main/da_wrfvar_top.f90
M var/da/da_minimisation/da_get_innov_vector.inc
M var/da/da_minimisation/da_minimisation.f90
M var/da/da_obs_io/da_obs_io.f90
M var/da/da_obs_io/da_read_iv_for_multi_inc.inc
M var/da/da_obs_io/da_read_obs_radar.inc
M var/da/da_obs_io/da_scan_obs_radar.inc
M var/da/da_obs_io/da_search_obs.inc
M var/da/da_obs_io/da_write_iv_for_multi_inc.inc
M var/da/da_radiance/da_radiance1.f90
A var/da/da_radiance/da_read_iv_rad_for_multi_inc.inc
A var/da/da_radiance/da_write_iv_rad_for_multi_inc.inc
M var/da/da_recursive_filter/da_recursive_filter.f90
A var/da/da_recursive_filter/da_recursive_filter_1d_inv.inc
M var/da/da_recursive_filter/da_transform_through_rf.inc
A var/da/da_recursive_filter/da_transform_through_rf_inv.inc
M var/da/da_setup_structures/da_setup_structures.f90
A var/da/da_setup_structures/da_write_vp.inc
M var/da/da_tools/da_llxy.inc
M var/da/da_vtox_transforms/da_transform_vptox.inc
A var/da/da_vtox_transforms/da_transform_vptox_inv.inc
A var/da/da_vtox_transforms/da_transform_vtovv_inv.inc
A var/da/da_vtox_transforms/da_transform_vtox_inv.inc
M var/da/da_vtox_transforms/da_transform_vvtovp.inc
M var/da/da_vtox_transforms/da_transform_vvtovp_adj.inc
A var/da/da_vtox_transforms/da_transform_vvtovp_inv.inc
M var/da/da_vtox_transforms/da_vertical_transform.inc
M var/da/da_vtox_transforms/da_vtox_transforms.f90
A var/mri4dvar/Makefile
A var/mri4dvar/README.MRI-4DVar
A var/mri4dvar/da_bdy.f90
A var/mri4dvar/da_bilin.f90
A var/mri4dvar/da_thin.f90
A var/mri4dvar/da_vp_bilin.f90
A var/mri4dvar/da_vp_split.f90
A var/mri4dvar/nc_increment.ncl
A var/mri4dvar/nc_vpglobal.ncl
A var/mri4dvar/nc_vphires.ncl
A var/mri4dvar/nc_vpinput.ncl
A var/mri4dvar/nc_vplocal.ncl
A var/mri4dvar/rsl_lite.h
A var/mri4dvar/run_mri3d4dvar.csh_lsf
A var/mri4dvar/run_mri3d4dvar.csh_pbs
A var/mri4dvar/task_for_point.c
A var/mri4dvar/wraper_mri3d4dvar.csh

TESTS CONDUCTED: WRFDA regression test passed. Cycling MRI-4DVar tests were performed over an Arctic domain.

RELEASE NOTE: New capability for Multi-Resolution Incremental 4DVar (MRI-4DVar).
Liu, Z., J. Ban, J.-S, Hong, and Y.-H. Kuo, 2020: Multi-resolution incremental 4D-Var for WRF: Implementation and application at convective scale, Q. J. R. Meteorol. Soc., 146, 3661-3674.
TYPE: new feature

KEYWORDS: Chemical DA, Surface Observations, 3DVar, GENBE_2.0

SOURCE: Wei Sun (NCAR/MMM, CAS), Jake Liu (NCAR/MMM), Dan Chen (IUM, Beijing)

DESCRIPTION OF CHANGES:
1. This PR adds the new capability for assimilating the surface chemical/aerosol observations (pm2.5, pm10, O3, NO2, SO2, CO) using 3DVar. 

2. Several new namelist parameters are defined in registry.var_chem under wrfvarchem. The setting of chemicda_opt only works for MOSAIC scheme. The inflation factors of chemical background errors work for both aerosol schemes, but they are only tested under the MOSAIC scheme.
 
&wrfvarchem
chem_cv_options= 10/20: control variables are 4 gas + 15/32 GOCART/MOSAIC (4bin) aerosol variables

chemicda_opt=1/2/3/4/5 # assimilate pm2.5/pm10/pm2.5+pm10/co+o3+so2+no2/6-species
 
var_scaling12=36xmax_outer_iterations, # inflation factors of chemical background errors.

len_scaling12=36xmax_outer_iterations, # inflation factors of chemical background errors.

use_chemic_surfobs = .true., # read in ob_chemsfc.ascii
 /

3. To compile 3DVar with chemical DA capability, set the environment variable "WRF_CHEM" as 1, then ./configure wrfda; compile all_wrfvar as usual. The executable remains da_wrfvar.exe.

4. The chemical background error file be.dat needs to be generated using GENBE_2.0 on https://github.com/wrf-model/GENBE_2.0.

LIST OF MODIFIED FILES:
A       Registry/Registry.wrfchemvar
M       Registry/registry.var_chem
M       compile
M       external/RSL_LITE/gen_comms.c
M       frame/module_domain.F
M       frame/module_driver_constants.F
M       share/mediation_integrate.F
M       share/output_wrf.F
M       tools/gen_allocs.c
M       var/build/da.make
M       var/build/depend.txt
A       var/da/da_chem_sfc/da_ao_stats_chem_sfc.inc
A       var/da/da_chem_sfc/da_calculate_grady_chem_sfc.inc
A       var/da/da_chem_sfc/da_check_max_iv_chem_sfc.inc
A       var/da/da_chem_sfc/da_chem_sfc.f90
A       var/da/da_chem_sfc/da_get_innov_vector_chem_sfc.inc
A       var/da/da_chem_sfc/da_jo_and_grady_chem_sfc.inc
A       var/da/da_chem_sfc/da_jo_chem_sfc.inc
A       var/da/da_chem_sfc/da_oi_stats_chem_sfc.inc
A       var/da/da_chem_sfc/da_print_stats_chem_sfc.inc
A       var/da/da_chem_sfc/da_residual_chem_sfc.inc
A       var/da/da_chem_sfc/da_transform_xtoy_chem_sfc.inc
A       var/da/da_chem_sfc/da_transform_xtoy_chem_sfc_adj.inc
M       var/da/da_control/da_control.f90
A       var/da/da_define_structures/da_allocate_observations_chem_sfc.inc
A       var/da/da_define_structures/da_allocate_y_chem_sfc.inc
M       var/da/da_define_structures/da_deallocate_background_errors.inc
A       var/da/da_define_structures/da_deallocate_y_chem_sfc.inc
M       var/da/da_define_structures/da_define_structures.f90
A       var/da/da_define_structures/da_zero_xchem_type.inc
M       var/da/da_main/da_solve.inc
M       var/da/da_main/da_solve_init.inc
M       var/da/da_main/da_update_firstguess.inc
M       var/da/da_main/da_wrfvar_init2.inc
M       var/da/da_main/da_wrfvar_top.f90
M       var/da/da_minimisation/da_amat_mul.inc
M       var/da/da_minimisation/da_calculate_gradj.inc
M       var/da/da_minimisation/da_calculate_grady.inc
M       var/da/da_minimisation/da_calculate_j.inc
M       var/da/da_minimisation/da_calculate_residual.inc
M       var/da/da_minimisation/da_dot_cv.inc
M       var/da/da_minimisation/da_get_innov_vector.inc
M       var/da/da_minimisation/da_get_var_diagnostics.inc
M       var/da/da_minimisation/da_jo_and_grady.inc
M       var/da/da_minimisation/da_minimisation.f90
M       var/da/da_minimisation/da_minimise_cg.inc
M       var/da/da_minimisation/da_minimise_lz.inc
M       var/da/da_minimisation/da_sensitivity.inc
M       var/da/da_minimisation/da_transform_vtoy.inc
M       var/da/da_minimisation/da_transform_vtoy_adj.inc
M       var/da/da_minimisation/da_write_diagnostics.inc
A       var/da/da_obs/da_fill_obs_structures_chem_sfc.inc
M       var/da/da_obs/da_obs.f90
M       var/da/da_obs/da_transform_xtoy.inc
M       var/da/da_obs/da_transform_xtoy_adj.inc
A       var/da/da_obs_io/da_final_write_obs_chem_sfc.inc
A       var/da/da_obs_io/da_final_write_obs_gas_sfc.inc
M       var/da/da_obs_io/da_obs_io.f90
A       var/da/da_obs_io/da_read_obs_chem_sfc.inc
M       var/da/da_obs_io/da_read_omb_tmp.inc
A       var/da/da_obs_io/da_scan_obs_chem_sfc.inc
A       var/da/da_obs_io/da_write_obs_chem_sfc.inc
M       var/da/da_par_util/da_cv_to_vv.inc
M       var/da/da_par_util/da_par_util.f90
M       var/da/da_par_util/da_vv_to_cv.inc
M       var/da/da_setup_structures/da_rescale_background_errors.inc
M       var/da/da_setup_structures/da_scale_background_errors.inc
M       var/da/da_setup_structures/da_setup_background_errors.inc
M       var/da/da_setup_structures/da_setup_be_regional.inc
M       var/da/da_setup_structures/da_setup_cv.inc
M       var/da/da_setup_structures/da_setup_firstguess.inc
M       var/da/da_setup_structures/da_setup_firstguess_wrf.inc
M       var/da/da_setup_structures/da_setup_obs_structures.inc
A       var/da/da_setup_structures/da_setup_obs_structures_chem_sfc.inc
M       var/da/da_setup_structures/da_setup_structures.f90
M       var/da/da_statistics/da_analysis_stats.inc
M       var/da/da_statistics/da_statistics.f90
M       var/da/da_test/da_check.inc
A       var/da/da_test/da_check_cvtovv_adjoint_chem.inc
M       var/da/da_test/da_check_gradient.inc
A       var/da/da_test/da_check_vchemtox_adjoint.inc
A       var/da/da_test/da_check_vtox_adjoint_chem.inc
M       var/da/da_test/da_test.f90
M       var/da/da_transfer_model/da_transfer_model.f90
A       var/da/da_transfer_model/da_transfer_wrftoxb_chem.inc
M       var/da/da_transfer_model/da_transfer_xatoanalysis.inc
M       var/da/da_transfer_model/da_transfer_xatowrf.inc
A       var/da/da_vtox_transforms/da_transform_vchemtox.inc
A       var/da/da_vtox_transforms/da_transform_vchemtox_adj.inc
M       var/da/da_vtox_transforms/da_transform_vtovv.inc
M       var/da/da_vtox_transforms/da_transform_vtovv_adj.inc
M       var/da/da_vtox_transforms/da_transform_vtox.inc
M       var/da/da_vtox_transforms/da_transform_vtox_adj.inc
M       var/da/da_vtox_transforms/da_vtox_transforms.f90

TESTS CONDUCTED: 
1. WRFDA regression tests passed.
2. New chemical DA is tested with 6 types of surface obs and 4-bin MOSAIC aerosol scheme.

RELEASE NOTE: Add new capability for assimilating surface pm2.5, pm10, O3, CO, NO2, SO2 using 3DVar.
Sun, W., Liu, Z., Chen, D., Zhao, P., and Chen, M., 2020: Development and application of the WRFDA-Chem three-dimensional variational (3DVAR) system: aiming to improve air quality forecasting and diagnose model deficiencies, Atmos. Chem. Phys., 20, 9311-9329.
…odel#1368)

**TYPE:** bug fix

**KEYWORDS:** `chem_opt = 202`, `n2o5_hetchem = 1`

**SOURCE:** Luke Conibear (University of Leeds)

**DESCRIPTION OF CHANGES:**
_Problem:_
N2O5 heterogeneous chemistry without the Cl- pathway (`n2o5_hetchem = 1`) already works with default MOSAIC aerosol schemes (e.g. `chem_opt = 201/202/601/611`). However, `chem_opt = 202` was not included in the `config_flags%n2o5_hetchem == 1` conditional within `chemics_init.F`.

_Solution:_
Added `chem_opt = 202` to the `config_flags%n2o5_hetchem == 1` conditional within `chemics_init.F`.

**ISSUE:** None

**LIST OF MODIFIED FILES:**
```bash
M       chem/chemics_init.F
```
KEYWORDS: RAINPROD, EVAPPROD, wetscav

SOURCE: Stacy Walters (NCAR)

Originally submitted as PR wrf-model#682, but was resubmitted due to conflicts

DESCRIPTION OF CHANGES:

Package the state variables RAINPROD and EVAPPROD into the 4D variable
wetscav_frcing. This allows for a memory footprint reduction when chemistry
is enabled but wet scavenging is disabled.

Add logic to control setting rainprod and evapprod variables only when
the chem group namelist variable wetscav_onoff is set to 1; wetscav_onoff
defaults to 0. This logical "gate" has been added to the following files:

phys/module_mp_morr_two_moment.F
phys/module_mp_morr_two_moment_aero.F
phys/module_mp_nssl_2mom.F
phys/module_mp_thompson.F
phys/module_mp_wsm6.F

This change affects the following microphysics schemes:

MORR_TWO_MOMENT, MORR_TM_AERO
NSSL_2MOM, NSSL_2MOMG, NSSL_2MOMCCN
THOMPSON, THOMPSON_AERO
WSM6SCHEME

LIST OF MODIFIED FILES:

M Registry/registry.chem
M share/module_trajectory.F
M chem/chem_driver.F
M phys/module_microphysics_driver.F
M phys/module_mp_morr_two_moment.F
M phys/module_mp_morr_two_moment_aero.F
M phys/module_mp_nssl_2mom.F
M phys/module_mp_thompson.F
M phys/module_mp_wsm6.F
M dyn_em/em_solve.F

TESTS CONDUCTED:

Stacy Walters compared results from one hour simulations of the modified
and original code. There was bit for bit agreement for the RAINPROD and
EVAPRPOD variables as well as BFB agreement for key washout chemical species
such as H2O2 and HNO3. The comparison was done for the following microphyscis
schemes:

MORR_TWO_MOMENT, NSSL_2MOM, THOMPSON, WSM6SCHEME
KEYWORDS: pH, cloud water, aerosols, mozart_mosaic_4bin_aq

SOURCE: Mary Barth (ACOM/MMM NCAR) and Stacy Walters (formerly NCAR)

DESCRIPTION OF CHANGES:

Originally submitted as PR wrf-model#999, but was resubmitted due to inconsistencies

Alter Registry/registry.chem to include diagnostic pH variables ph_cw, ph_aer01, ph_aer02,
ph_aer03, and ph_aer04.
Modify files, listed below, to calculate and set pH diagnostic variables
MOZART is a gas-phase chemistry mechanism (set of reactions) in WRF-Chem

Diagnostics are activated with namelist,chem option mozart_ph_diag=1

MOSAIC is one of the aerosol models in WRF-Chem that represents the size distribution
of the aerosols with 4 size bins (hence "4bin")

The pH is calculated for each of the 4 aerosol size bins. That is why there are 4 variables: pH_aer1,
aer2, aer3, aer4.

pH is a diagnostic variable and is calculated as part of the aerosol model. However what we added
was the ability to write out the field to the history file. It is by default turned off as an output field,
but can be "turned on" using the iofields.txt file.

There is also cloud water pH (pH_CW) which is calculated as part of the cloud chemistry routine.
Same thing as aerosol pH, by default it is not an output field, but can be included in history files
via iofields.txt.

For pretty pictures and a description of what we learned, feel free to look at the report for the
ACOM lab: https://nar.ucar.edu/2019/acom/predicting-acidity-aerosols-and-cloud-water.

LIST OF MODIFIED FILES:
Registry/registry.chem
chem/chem_driver.F
chem/cloudchem_driver.F
chem/module_mosaic_cloudchem.F
chem/aerosol_driver.F
chem/module_mosaic_driver.F
chem/module_mosaic_therm.F
chem/module_chem_cup.F
TYPE: feature removed

KEYWORDS: UM trajectory, NCAR ACOM trajectory

SOURCE: Internal

DESCRIPTION OF CHANGES:
The UM trajectory option has been replaced by NCAR ACOM trajectory option. Therefore, the initialization for UM
trajectory (in the real program) is no longer needed.

LIST OF MODIFIED FILES:
M dyn_em/module_initialize_real.F

TESTS CONDUCTED:
(1) A single test case has been conducted to demonstrate that the UM trajectory no longer works. NCAR ACOM trajectory option gives expected results.
(2) Jenkins test is done successfully.

RELEASE NOTE: Not necessary
wrf-model#1391)

TYPE: new feature

KEYWORDS: pressure, height level diagnostics, vertical interpolation

SOURCE: Jared A. Lee (NCAR/RAL)

DESCRIPTION OF CHANGES:
Problem:
To compare WRF simulations against observations from above-ground barometers (e.g., mounted on a wind turbine 
nacelle), it is useful to add air pressure to the list of available height-level diagnostics within WRF.

Solution:
Following the definition and development of variables like t_zl, s_zl, and ght_zl, I added a definition for p_zl in the Registry 
file, set an initial value for output, and then added the new variable to the diagnostic call tree. In the height-level 
diagnostic routine, I set the new variable p_zl to be equal to the already computed (but local) height-interpolated 
pressure. The interpolation to compute the pressure was being done linearly in height with respect to pressure, whereas 
the interpolation should actually have been linear in height with respect to ln(pressure). The computed pressure variable 
is used in the relative humidity height-level diagnostic (rh_zl), so this modification creates small changes for the 
diagnosed relative humidity. At height levels in the lowest 1 km AGL, this change results in negligible differences in 
pressure (<0.1 Pa), and also negligible differences in relative humidity (<0.0001%). Higher up in the troposphere, these 
differences may be more noticeable.

LIST OF MODIFIED FILES:
M       Registry/registry.diags
M       dyn_em/start_em.F
M       phys/module_diag_zld.F
M       phys/module_diagnostics_driver.F

TESTS CONDUCTED: 
1. I verified that WRF compiles (opt15: intel/dmpar) on Cheyenne and runs with these modifications. I ran a simulation for 
3 h. The new pressure variable was output successfully to stream 22 at 6 height levels (78, 100, 200, 300, 400, and 
500 m AGL), with expected/sensible values.
2. For the change in how pressure is interpolated vertically for height-level diagnostics, I compared a 3-h simulation 
before/after this modification, using the same 6 heights. I found differences to be negligible for both pressure and 
relative humidity.
3. Jenkins test status is all pass.

RELEASE NOTE: Air pressure was added as a new height-level diagnostic, which is useful for a model validation against barometers mounted above ground (e.g., on a wind turbine nacelle). Also, the vertical interpolation of pressure to height surfaces was switched to linear in ln(p). The resultant pressure and relative humidity changes are negligible in the lowest 1 km AGL.
…l#1395)

TYPE: enhancement

KEYWORDS: clean script, HLC.TBL, wind-turbine-1.tbl

SOURCE: internal

DESCRIPTION OF CHANGES:
Problem:
When executing 'clean -a', two files are not removed: HLC.TBL, and wind-turbine-1.tbl

Solution:
Add these two files to the list of files to be removed in the clean script

LIST OF MODIFIED FILES:
M clean

TESTS CONDUCTED:
It does remove the two files.
Jenkins tests are passing.

RELEASE NOTE: The files HLC.TBL, and wind-turbine-1.tbl are now removed from the test/* directories when doing 'clean -a'.
…model#1306)

TYPE: no impact

KEYWORDS: namelist, update, dates, e_we, e_sn, domain size

SOURCE: internal

DESCRIPTION OF CHANGES:
Problem:
The default namelist.input file for real cases had several settings that go against best practices and recommendations.

e_we and e_sn default values were 74x61, 112x97. We tell users to never use a domain smaller than 100x100, and we continue to have many users running small domains, and then seeking help.
default case and dates were very old (2000).
default grid space was very coarse, which isn't used as often with finer resolution input data available.
default num_metgrid_levels was set to 32, which is the number of levels in older GFS data
default cudt was set to 5, and we recommend 0
Solution:

Updated the case to the 2019 Hurricane Dorian case (Sept 2019). This included the case dates, run_hours (36) and domain specifications.
Updated dx/dy to 15 km - which meant updating time_step and radt
Added a comment after time_step to 1) show that comments are allowed in the namelist, when using a "!" and 2) to not set that value larger than 6xDX (a very common user problem we see)
Updated domain size to larger, more realistic dimensions, which meant updating e_vert and i/j_parent_start
Updated num_metgrid_levels to 34, which is the number of levels in the current GFS data
Updated cudt to 0
Also added a new file (namelist.input.default) that has descriptions for all the default parameters, including when NOT to add additional columns (a common user issue is when they try to add columns to non max_dom parameters).
*Note: WPS PR#160 was also created to modify corresponding values in namelist.wps
LIST OF MODIFIED FILES:
M test/em_real/namelist.input
A test/em_real/namelist.input.default

TESTS CONDUCTED:

I ran a test for the new case to make sure it all looked good - used GFS 0.25 degree data.
Are the Jenkins tests all passing?
TYPE: enhancement

KEYWORDS: hydro, wrf-hydro

SOURCE: WRF-Hydro Team

DESCRIPTION OF CHANGES:

- Compatibility with GNU Fortran (gfortran) v10.x
- Correctly supports 1D domains (n x 1 grids)
- Correctly supports ISLAKE in NoahMP
- Updated NUOPC cap for LIS coupling
- Updated default channel parameters in gridded configuration
- Updated comments in namelist templates
- Added missing crop and soil NoahMP options
- Removed deprecated / unnecessary namelist options for reach-based lakes
- Performance improvements for channel network initialization
- Output file metadata revisions
- Changed medium-range RTOUT output frequency
- National Water Model template files removed to their own repository

LIST OF MODIFIED FILES: 
M	hydro/CPL/WRF_cpl/module_wrf_HYDRO.F
M	hydro/CPL/WRF_cpl/module_wrf_HYDRO_downscale.F
M	hydro/Data_Rec/module_RT_data.F
M	hydro/Data_Rec/module_namelist.F
M	hydro/Data_Rec/namelist.inc
M	hydro/Data_Rec/rt_include.inc
A      hydro/Debug_Utilities/Makefile
M	hydro/HYDRO_drv/module_HYDRO_drv.F
A      hydro/IO/Makefile
M	hydro/MPP/CPL_WRF.F
M	hydro/MPP/Makefile
A	hydro/MPP/hashtable.F
M	hydro/MPP/module_mpp_ReachLS.F
M	hydro/MPP/mpp_land.F
A      hydro/OrchestratorLayer/Makefile
M	hydro/Routing/Makefile
M	hydro/Routing/Noah_distr_routing.F
A	hydro/Routing/Noah_distr_routing_overland.F
A	hydro/Routing/Noah_distr_routing_subsurface.F
M	hydro/Routing/Overland/module_overland.F
M	hydro/Routing/Overland/module_overland_control.F
M	hydro/Routing/Overland/module_overland_routing_properties.F
A	hydro/Routing/Overland/overland.md
A	hydro/Routing/Reservoirs/.gitignore
A	hydro/Routing/Reservoirs/Level_Pool/Makefile
A	hydro/Routing/Reservoirs/Level_Pool/module_levelpool.F
A	hydro/Routing/Reservoirs/Level_Pool/module_levelpool_properties.F
A	hydro/Routing/Reservoirs/Level_Pool/module_levelpool_state.F
A	hydro/Routing/Reservoirs/Level_Pool/module_levelpool_tests.F
A	hydro/Routing/Reservoirs/Makefile
A	hydro/Routing/Reservoirs/Persistence_Level_Pool_Hybrid/Makefile
A	hydro/Routing/Reservoirs/Persistence_Level_Pool_Hybrid/module_persistence_levelpool_hybrid.F
A	hydro/Routing/Reservoirs/Persistence_Level_Pool_Hybrid/module_persistence_levelpool_hybrid_properties.F
A	hydro/Routing/Reservoirs/Persistence_Level_Pool_Hybrid/module_persistence_levelpool_hybrid_state.F
A	hydro/Routing/Reservoirs/Persistence_Level_Pool_Hybrid/module_persistence_levelpool_hybrid_tests.F
A	hydro/Routing/Reservoirs/Persistence_Level_Pool_Hybrid_Module_README.md
A	hydro/Routing/Reservoirs/RFC_Forecasts/Makefile
A	hydro/Routing/Reservoirs/RFC_Forecasts/module_rfc_forecasts.F
A	hydro/Routing/Reservoirs/RFC_Forecasts/module_rfc_forecasts_properties.F
A	hydro/Routing/Reservoirs/RFC_Forecasts/module_rfc_forecasts_state.F
A	hydro/Routing/Reservoirs/RFC_Forecasts/module_rfc_forecasts_tests.F
A	hydro/Routing/Reservoirs/RFC_Forecasts_Module_README.md
A	hydro/Routing/Reservoirs/module_reservoir.F
A	hydro/Routing/Reservoirs/module_reservoir_read_rfc_time_series_data.F
A	hydro/Routing/Reservoirs/module_reservoir_read_timeslice_data.F
A	hydro/Routing/Reservoirs/module_reservoir_utilities.F
A	hydro/Routing/Reservoirs/reservoir_tests.F
A	hydro/Routing/Subsurface/Makefile
A	hydro/Routing/Subsurface/module_subsurface.F
A	hydro/Routing/Subsurface/module_subsurface_grid_transform.F
A	hydro/Routing/Subsurface/module_subsurface_input.F
A	hydro/Routing/Subsurface/module_subsurface_output.F
A	hydro/Routing/Subsurface/module_subsurface_properties.F
A	hydro/Routing/Subsurface/module_subsurface_state.F
A	hydro/Routing/Subsurface/module_subsurface_static_data.F
A	hydro/Routing/Subsurface/subsurface_tests.F
M	hydro/Routing/module_GW_baseflow.F
M	hydro/Routing/module_HYDRO_io.F
M	hydro/Routing/module_HYDRO_utils.F
M	hydro/Routing/module_NWM_io.F
M	hydro/Routing/module_NWM_io_dict.F
M	hydro/Routing/module_RT.F
M	hydro/Routing/module_UDMAP.F
M	hydro/Routing/module_channel_routing.F
M	hydro/Routing/module_date_utilities_rt.F
M	hydro/Routing/module_gw_gw2d.F
M	hydro/Routing/module_lsm_forcing.F
M	hydro/Routing/module_reservoir_routing.F
M	hydro/arc/Makefile.mpp
M	hydro/arc/macros.gordon
M	hydro/arc/macros.gordon.debug
M	hydro/arc/macros.mpp.IBM.xlf90_r
M	hydro/arc/macros.mpp.gfort
M	hydro/arc/macros.mpp.ifort
M	hydro/arc/macros.mpp.ifort.luna
A	hydro/arc/macros.mpp.ifort.omp
A	hydro/arc/macros.mpp.ifort.summit_has
M	hydro/arc/macros.mpp.ifort.theia
A	hydro/arc/macros.mpp.intel.cray_xc
M	hydro/arc/macros.mpp.linux
M	hydro/arc/macros.mpp.mpiifort
M	hydro/arc/macros.seq.gfort
M	hydro/arc/macros.seq.linux
M	hydro/arc/macros.theia.debug
M	hydro/configure
M	hydro/nudging/module_date_utils_nudging.F
M	hydro/nudging/module_nudging_io.F
M	hydro/nudging/module_stream_nudging.F
M	hydro/template/HYDRO/CHANPARM.TBL
M	hydro/template/HYDRO/hydro.namelist
M	hydro/template/Noah/namelist.hrldas
M	hydro/template/NoahMP/namelist.hrldas
M	hydro/template/setEnvar.sh
M	hydro/utils/Makefile
A	hydro/utils/module_hydro_stop.F
M	hydro/utils/module_version.F

TESTS CONDUCTED: 
1. Code passes internal WRF-Hydro regression testing and output has been validated by team scientists
2. Jenkins test results all pass

RELEASE NOTE: WRF-Hydro has been updated to version v5.2.0
TYPE: enhancement

KEYWORDS: graupel, hail, microphysics, Y-intercept

SOURCE: Greg Thompson (JCSDA)

DESCRIPTION OF CHANGES:
Problem:
Since the prior version of the Thompson MP scheme, where a new relationship was created for Y-intercept parameter of one-moment graupel, the maximum radar reflectivity and max hail size were reduced lower than intended/desired.

Solution:
Minor changes to the diagnosis of the Y-intercept parameter, resulting in a slightly increased highest radar reflectivity and maximum hail size. It is not a very significant increase but fits better with the Paul Field et al. (2019) paper that analyzed T-28 aircraft hail data.

LIST OF MODIFIED FILES:
M phys/module_mp_thompson.F
M phys/module_diag_nwp.F

TESTS CONDUCTED:

- Numerous simulations run with HRRR-CONUS-like grid.
- jenkins status is pass

RELEASE NOTE: Relatively small tunings for Thompson MP one-moment graupel Y-intercept parameter diagnosis, creating a better fit to Paul Field et al (2019) analysis of T-28 aircraft hail data.
TYPE: no impact, clean up

KEYWORDS: un-used 3D array, rho_phy

SOURCE: reported by Xin-Liang Zhong of Univ of Maryland, internal

DESCRIPTION OF CHANGES:
Problem:
There is an un-used 3D array rho_phy.

Solution:
Remove it from the code.

LIST OF MODIFIED FILES:
M Registry/Registry.EM_COMMON
M Registry/registry.wrfplus
M dyn_em/module_after_all_rk_steps.F
M dyn_em/solve_em.F
M phys/module_diag_afwa.F
M phys/module_diagnostics_driver.F
M wrftladj/solve_em_ad.F
M wrftladj/solve_em_tl.F

TESTS CONDUCTED:
- No impact.
- Jenkins tests are all pass.

RELEASE NOTE: Removed an un-used 3D array from the ARW Registry and solver (rho_phy).
TYPE: bug fix

KEYWORDS: Deng shcu, limit updraft, cloud

SOURCE: Timothy W. Juliano and Pedro A. Jimenez (NCAR/RAL), Jimy Dudhia (NCAR/MMM)

DESCRIPTION OF CHANGES:
Problem:
The issue is in loop60 of the code. There are two exit statements within that loop. If either of these conditional statements are satisfied, then the loop exits and there is no bug. The problem arises if there is a clean exit of loop60. In this loop, variable NK (the index of the loop) goes from just below cloud base (KLCL-1) to #layers-1 (KLM). If there is a clean exit of the loop, then NK = #layers. This causes variable LTOP1 to have a value of #layers and therefore LTOP also equals #layers. When this happens, in line 2250 of the official WRF release [TMA = QQG(NK+1)*EMS(NK+1)], QQG goes out of bounds since QQG is defined from 1 to #layers and NK in this loop goes from 1 to LTOP which is #layers. Thus, it tries to access index NK+1 which is #layers+1.

Solution:
The solution is to limit the value of LTOP1 at the exit of loop60 to #layers-1 (KLM).

LIST OF MODIFIED FILES:
M phys/module_shcu_deng.F

TESTS CONDUCTED:
- We have run a 3km CONUS simulation with and without the bug fix. Without the bug fix, the simulation crashes as reported above. With the bug fix, the simulation integrates through without an issue.
- Jenkins tests all PASS.

RELEASE NOTE: A fix is introduced to the Deng shallow cumulus parameterization scheme. When the updraft top reached the domain top, the model would crash due to accessing out of bounds memory. The modification is to limit the vertical index of the updraft top.
… stepping (wrf-model#1398)

Fix for instances of dt = 0 when using adaptive time stepping

TYPE: bug fix

KEYWORDS: adaptive time stepping, time step

SOURCE: internal, reported from two sources

DESCRIPTION OF CHANGES:
Problem:
When using adaptive time stepping, and when option step_to_output_time is used, time step can be zero and cause the model to stop. The problem occurs in part because the function real_time becomes less accurate when feeding a large value of time interval, i.e. time since the simulation start time.

Solution:
This PR fixes the issue by changing the time interval calculation from relative to simulation start time to model start time, i.e. restart time.

ISSUE: For use when this PR closes an issue.
Fixes wrf-model#1369

LIST OF MODIFIED FILES:
M dyn_em/adapt_timestep_em.F

TESTS CONDUCTED:

- Test shows the fix prevents dt=0 from occurring in a case previously failed.
- Passed all Jenkins tests.

RELEASE NOTE: Fix for instances of dt = 0 when using adaptive time stepping together and when step_to_output_time is set to true.
… value in FARMS (wrf-model#1394)

TYPE: bug fix

KEYWORDS: FARMS, radiation, cloud optical thickness

SOURCE: Timothy W. Juliano and Pedro A. Jimenez (NCAR/RAL)

DESCRIPTION OF CHANGES:
Problem:
In the ICEMODEL subroutine, there is an issue with the calculation of Ptau (lines 602-608 in the official WRF version). If De <= 26.0 and solarangle (cosine of solar zenith angle) is really small, then Ptau (ice cloud optical thickness) can be negative. In my case, Ptau goes negative and causes the model to crash since PPDHI is later calculated using log10(Ptau). It looks like the original code accounted for a small value of Ptau but only when De > 26.0.

Solution:
I fixed the issue simply by moving the check on Ptau to be located after the conditional statements.

LIST OF MODIFIED FILES:
M phys/module_ra_farms.F

TESTS CONDUCTED:
- We have run a 3km CONUS simulation with and without the bug fix. Without the bug fix, the simulation crashes as reported above. With the bug fix, the simulation integrates through without an issue.
- Jenkins tests are passing.

RELEASE NOTE: A fix is introduced to the FARMS parameterization. When the cosine of solar zenith angle is small, the ice cloud optical thickness can be negative, and the model can crash due to log10 of a negative number. The modification is to limit the value of cloud optical thickness.
TYPE: enhancement

KEYWORDS: commit hash, source files verification, provenance, user support, development, version control

SOURCE: Jan Mandel (University of Colorado Denver) and internal

DESCRIPTION OF CHANGES: 

User support is more difficult without knowing if the user may have changed any files in the distribution. For 
developers, it is not possible to check if the binary executable is the same version as the source files, leading to 
unnecessary rebuilds. 

This PR includes a line in the WRF print output next to the WRF release version with the git commit hash. If any files 
are not part of a commit (local files changed), this modification prints a short diff statistic. Finally, if the files are not 
under git version control, the print out indicates that the git commit identification is not available. 

The command 
```
strings wrf.exe | grep -w 'git commit'
``` 
outputs the version of the source code from which the binary was constructed. This same identification line is also 
printed in the output of `./compile` step.

The new functionality is implemented by generating a new file, `inc/commit_decl`, during the `./compile` stage, and using 
this new file similarly as the `inc/version_decl` file. This new file is deleted by `./clean`.

Examples:

In WRF output: 
```
WRF V4.2 MODEL
git commit a599473
```

To identify the binary executable without running it:
```
strings wrf.exe | grep "git commit"
git commit a599473
```

In ./compile output, with some file changed: 
```
V4.2
git commit ccc58d7 1 file changed, 1 insertion(+)
```
Content of the generated ```commit_decl``` file: 
```
    CHARACTER (LEN=*), PARAMETER :: commit_version = 'git commit e5d6fe0'
```

Content of the generated ```commit_decl``` file, with source files not from github, or no git on the system:
```
    CHARACTER (LEN=*), PARAMETER :: commit_version = 'No git found or not a git repository, git commit version not available.'
```

LIST OF MODIFIED FILES:
Scripts:   
modified:   clean
modified:   compile

Files that are associated with the top-level executables:
modified:   chem/chemics_init.F
modified:   chem/convert_emiss.F
modified:   main/ideal_em.F
modified:   main/ideal_nmm.F
modified:   main/module_wrf_top.F
modified:   main/ndown_em.F
modified:   main/real_em.F
modified:   main/real_nmm.F
modified:   main/tc_em.F

Files that are associated with the git:
modified:   inc/.gitignore 

Files removing unnecessary `#include`:
modified:   share/input_wrf.F 

TESTS CONDUCTED: 
1. Built and run with Intel and GNU compilers, with and without git available, in a cloned repository, and in a directory 
not under git control.
2. Jenkins regression test passed.

RELEASE NOTE: The git commit information is part of the WRF modeling system standard output, one of the strings within the executables, and also in the output of the ./compile command.
…e gases (wrf-model#1354)

TYPE: new feature

KEYWORDS: GF-Cumulus Scheme, Convective transport of trace gases, Wet scavenging, subgrid scale

SOURCE: Yunyao Li (University of Maryland)

DESCRIPTION OF CHANGES:
I add the trace gases and aerosol subgrid-scale convective transport (Grell and Freitas, 2014; Li et al., 2018), subgrid-scale wet scavenging (including the improvements of ice retention factors and the conversion ratio of cloud water to rainwater, Li et al., 2019), and aqueous chemistry to the GF cumulus parameterization.
I also put some chem codes to share/ directory. So some of the chemistry process can be called in the physics part, and the model doesn't need to be compiled twice to get everything work.

ISSUE: N/A

LIST OF MODIFIED FILES:
M chem/Makefile
M chem/chem_driver.F
M chem/depend.chem
D chem/module_HLaw.F
D chem/module_ctrans_aqchem.F
M chem/module_input_chem_data.F
M phys/Makefile
M phys/module_cu_gf_deep.F
M phys/module_cu_gf_sh.F
M phys/module_cu_gf_wrfdrv.F
M phys/module_cumulus_driver.F
M share/Makefile

Note: chem/module_HLaw.F and chem/module_ctrans_aqchem.F are moved to share/
Two new files are added:
share/module_chem_share.F
phys/module_cu_gf_ctrans.F

TESTS CONDUCTED:
Li, Y., Pickering, K.E., Barth, M.C., Bela, M.M., Cummings, K.A., and Allen, D.J. (2019). Wet Scavenging in WRF-Chem Simulations of Parameterized Convection for a Severe Storm during the DC3 Field Campaign, J. Geophys. Res. Atmos. 124, 7413–7428. https://doi.org/10.1029/2019JD030484.

Li, Y., Pickering, K.E., Barth, M.C., Bela, M.M., Cummings, K.A., and Allen, D.J. (2018). Evaluation of Parameterized Convective Transport of Trace Gases in Simulation of Storms Observed During the DC3 Field Campaign. J. Geophys. Res. Atmos. 123, 11,238-11,261.
TYPE: new feature

KEYWORDS: cloud fraction, cloud initialization

SOURCE: Greg Thompson (JCSDA)

DESCRIPTION OF CHANGES:
Problem:
Cold start simulations without microphysics species take significant time to 'spin-up' the clouds causing the radiation
to be way off balance at the start of most model simulations. This greatly affects the first few hours up to 12 hours
or more.

Solution:
The setting of initial cloud fraction and associated cloud water/ice mixing ratio gives a big advantage to 'spin up'
the clouds by assuming that clouds can be created from conditions of very high relative humidity. The cloud fraction
scheme of icloud=3 is a viable solution to making initial clouds along with the setting of the water vapor mixing ratio
to the point of saturation at initialization in association with the inserted cloud fields.

LIST OF MODIFIED FILES:
M Registry/Registry.EM_COMMON
M dyn_em/module_initialize_real.F
M dyn_em/depend.dyn_em
M run/README.namelist

TESTS CONDUCTED:

Numerous simulations in case studies plus real-time simulations with 3km spacing (nearly HRRR-CONUS) in
support of FAA's ICICLE field project (2019Jan28-2019Mar08).
Simulations by P. Jimenez in testing WRF-Solar-V2
Jenkins is pass.
RELEASE NOTE: In combination with updates to the cloud fraction scheme (icloud=3), a new feature permits the usage of the cloud fraction scheme as part of real.exe, specifically designed to use with "cold start" simulations to reduce the spin-up problem of clouds and associated radiation.* add in possibility to initialize clouds in cold-start using icloud3 option

Co-authored-by: Dave Gill <[email protected]>
…es (wrf-model#1409)

Created README.physics_files to describe dependencies with linked files

TYPE: text only

KEYWORDS: README, README.physics_files, linked, link, physics, schemes

SOURCE: internal

DESCRIPTION OF CHANGES:
Problem:
There are several files that must reside in (or be linked to) the running directory for many physics schemes. These files
are in the run/ directory, but are linked to the test/em_real directory during compilation. There is no user documentation
of which files are mandatory for which schemes.

Solution:
Created a README.physics_files to list all schemes that require additional files, and what those files are. Set the Makefile
to link this README file to the test/em_real directory upon compilation. Also added this README.physics_files to the clean script.

LIST OF MODIFIED FILES:
M Makefile
M clean
A run/README.physics_files

TESTS CONDUCTED:

Text only. Verified it compiles and links the new README file to the test/em_real directory.
Jenkins tests passed.
RELEASE NOTE: A README.physics_files is now available in the run directory (and is linked to the test/em_real directory during the compile). This file lists all physics options that require additional files for running, and the files necessary for each scheme. These additional files are already in the run/ directory and are linked automatically to the test/em_real directory during compile.
TYPE: enhancement, new feature

KEYWORDS: Noah-MP dynamic irrigation scheme, Sprinkler, micro, and flood irrigation

SOURCE: Prasanth Valayamkunnath (NCAR)

DESCRIPTION OF CHANGES:
Problem: Current version of Noah-MP missing agriculture water management practices. 

Solution:
A new dynamic irrigation scheme is implemented to estimate irrigation water requirements and apply water in the 
irrigated croplands. This new scheme irrigates the croplands based on sprinkler, micro, or surface flooding methods.

The various options are selected from the namelist, and are described in the run/README.namelist file.

You may have part of the domain do one kind of irrigation (for example, flood) and another part of the domain use 
a different kind of irrigation (for example, sprinkler). This can be done with the geo_em option that provides a map. 
So far, the only map for different methods is the USA. There is a global map of irrigated fraction that can be used 
outside the US, but then the irrigation method has to be selected.

The irrigation option only operates on the cropland landuse category.

As expected, effects of irrigation show up longer term. It is usually run at least seasonally not just for a few days.

LIST OF MODIFIED FILES: 
M       Registry/Registry.EM_COMMON
M       Registry/Registry.NMM
M       Registry/registry.noahmp
M       dyn_em/module_first_rk_step_part1.F
M       dyn_em/start_em.F
M       dyn_nmm/module_PHYSICS_CALLS.F
M       dyn_nmm/start_domain_nmm.F
M       phys/module_physics_init.F
M       phys/module_sf_noahmpdrv.F
M       phys/module_sf_noahmplsm.F
M       phys/module_surface_driver.F
M       run/MPTABLE.TBL
M       run/README.namelist
M       share/output_wrf.F

TESTS CONDUCTED: 
1. Conducted compilation and official em_real simulation tests with successful results in Cheyenne (by Prasanth Valayamkunnath, NCAR)
2. Jenkins regression tests are OK.

RELEASE NOTE: A new dynamic irrigation scheme is implemented to estimate irrigation water requirements and apply water in the irrigated croplands. This new scheme irrigates the croplands based on sprinkler, micro, or surface flooding methods. The various options are selected from the namelist, and are described in the run/README.namelist file.
@letmaik letmaik force-pushed the letmaik/wrf-4.3.3 branch 23 times, most recently from f175dfb to bf1fc68 Compare January 19, 2022 22:29
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letmaik commented Jan 21, 2022

Plots look fine. macOS is excluded as it is segfaulting for unknown reasons.

make vs cmake

single ref

@letmaik letmaik marked this pull request as ready for review January 21, 2022 19:31
@dmey
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dmey commented Feb 23, 2022

This looks OK with me.

@letmaik letmaik merged commit 5d8114b into wrf-cmake Mar 1, 2022
@letmaik letmaik deleted the letmaik/wrf-4.3.3 branch March 1, 2022 08:17
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ndown.exe is missing