Merge branch 'main' into wrf-wrf-chem

Latest from main, note keep wrf-wrf-chem version of wrf/model_mod.f90 note need to add #661 #649
NCAR · May 29, 2024 · 0bd4d47 · 0bd4d47
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -34,5 +34,5 @@ If your code changes are available on GitHub, please provide the repository.
 
 ### Build information
 Please describe:  
- 1. The machine you are running on (e.g. windows laptop, NCAR supercomputer Cheyenne).   
+ 1. The machine you are running on (e.g. windows laptop, NSF NCAR supercomputer Derecho).   
  2. The compiler you are using (e.g. gnu, intel).  
diff --git a/.github/workflows/action_on_pull_request.yml b/.github/workflows/action_on_pull_request.yml
@@ -16,7 +16,7 @@ jobs:
       options: "--cap-add=SYS_PTRACE"
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set checked out repo as a safe git directory
         run: git config --global --add safe.directory /__w/${{ github.event.repository.name }}/${{ github.event.repository.name }}
       - name: Build and run lorenz_96 with mpi
@@ -35,7 +35,7 @@ jobs:
       options: '--cap-add=SYS_PTRACE'
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set checked out repo as a safe git directory
         run: git config --global --add safe.directory /__w/${{ github.event.repository.name }}/${{ github.event.repository.name }}
       - name: Build and run lorenz_63 with no mpi
@@ -53,7 +53,7 @@ jobs:
       options: '--cap-add=SYS_PTRACE'
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set checked out repo as a safe git directory
         run: git config --global --add safe.directory /__w/${{ github.event.repository.name }}/${{ github.event.repository.name }}
       - name: Build and run lorenz_96 with mpif08

diff --git a/.gitignore b/.gitignore
@@ -90,6 +90,8 @@ gitm_to_netcdf
 netcdf_to_gitm_blocks
 streamflow_obs_diag
 cam_dart_obs_preprocessor
+aether_to_dart
+dart_to_aether
 
 # Observation converter exectutables
 convert_aviso
@@ -158,6 +160,10 @@ ssec_satwnd
 gts_to_dart
 littler_tf_dart
 rad_3dvar_to_dart
+L1_AMSUA_to_netcdf
+convert_airs_L2
+convert_amsu_L1
+convert_L2b
 
 # Test programs built by developer_tests
 rttov_test

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -22,6 +22,93 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**May 16 2024 :: WRF v4. Tag v11.5.0**
+
+- WRF-DART and WRF-DART Tutorial updated to WRFv4. Note, not backwards compatible with WRFv3.9. 
+- local particle filter default value for pf_enkf_hybrid=.false. *contributed by Jon Poterjoy*
+
+**April 23 2024 :: Bug-fix: WRF hybrid vertical coordinate. Tag v11.4.1**
+
+- DART now detects whether WRF is using Hybrid Vertical Coordinate (HVC) introduced in WRFv3.9 or terrain following (TF) system.
+  This fix is also compatible with pre WRFv3.9 versions which did not include explicit attribute information for vertical coordinate system.
+- Improved obs_impact_tool documentation.
+
+**March 27 2024 :: WRF-Hydro Developments; AIRS converter documentation update; Add citation.cff file. Tag v11.4.0**
+
+- WRF-Hydro:
+
+  - Added a new perfect model obs experimental capability to HydroDART
+  - Modified the Streamflow obs converter to allow for better diagnostics: allows DART to
+    compute obs space diagnostics on all gauges from the Routelink
+  - Enhanced performance in the model_mod and noah_hydro_mod when running a full CONUS domain
+  - Improved HydroDART Diagnostics with new capabilities (saves the hydrographs in a high-resolution
+    pdf, handles hybrid DA components, separate plots for the hybrid statistics, allows the openloop
+    to have different ens size and gauges than the DA runs)
+
+- AIRS and AMSU-A observation converters:
+
+  - Updated the documentation to use up-to-date build suggestions for the HDFEOS library
+  - Updated the AIRS converter code to be able to use version 7 of the AIRS data formats
+  - Removed unused and non-functional code: AIRS/BUILD_HDF-EOS.sh, AIRS/L1_AMSUA_to_netcdf.f90,
+    AIRS/shell_scripts/Build_HDF_to_netCDF.sh, AIRS/shell_scripts/Convert_HDF_to_netCDF.csh
+  - Removed the unnecessary entries from obs_def_rttov_nml in the input.nml
+
+- Added a citation.cff file to help users correctly cite DART software - creates a link to cite
+  the repository on the landing page sidebar on GitHub.
+
+**March 13 2024 :: Update WRF-DART scripts and bug template to Derecho; remove no-op routines in ensemble manager. Tag v11.3.1**
+
+- Updated the csh scripting templates used to run WRF-DART and WRF-DART tutorial from Cheyenne to Derecho
+- Updated bug report template to use Derecho instead of Cheyenne
+- Removed the following no-op routines from ensemble manager: prepare_to_write_to_vars, prepare_to_write_to_copies,
+  prepare_to_read_from_vars, prepare_to_read_from_copies, prepare_to_update_vars, prepare_to_update_copies
+
+**March 12 2024 :: MITgcm/N-BLING with Compressed Staggered Grids. Tag v11.3.0**
+
+- The DART-MITgcm code now supports compressed grids, especially suited for areas like 
+  the Red Sea where land occupies more than 90% of the domain.  
+  Built upon work *contributed by Jiachen Liu*.
+- Allows writing the BGC fields into MITgcm's pickup files.
+- Allows different compression for the regular and staggered grids.
+
+**March 12 2024 :: Aether lat-lon. Tag v11.2.0**
+
+- Aether lat-lon interface added to DART.
+
+**March 11 2024 :: SEIR model for infectious diseases. Tag v11.1.0**
+
+- Added SEIR model which simulates the spread of infectious diseases, for example COVID-19.
+
+**February 13 2024 :: Fortran Standards. Tag v11.0.3**
+
+- Replace f2kcli with Fortran intrinsics for command line arguments.
+- AIRS and quikscat mkmf.templates with appropriate HDF, HDFEOS, RTTOV library flags.
+- Simplified noah_hydro_mod.f90 number of non-zero element counts.
+- WRF pert_sounding_module random iseed now integer.
+
+**February 1 2024 :: RTTOV13 cloud bug-fix. Tag v11.0.2**
+
+- Initialize RTTOV13 profile cloud arrays to zero for profiles.
+- Updated docs with RTTOV13 namelist info.
+- New obs_def_rttov13_mod.f90 namelist option wfetch_value.
+- Updated mkmf.templates for RTTOV on Derecho: HDF5 library flags.
+
+GitHub actions changes:
+
+  - checkout action updated to v4.
+
+**January 17 2024 :: CLM bug-fixes. Tag v11.0.1**
+
+- CLM5-DART SourceMods path variable correction
+
+- dart_to_clm:
+
+  - Resolved compiler error by changing the arrays for number of snow layers (snlsno and clm_SNLSNO) to integer types 
+
+  - Forcing h2oliq_po to be slightly larger than zero to be consistent with h2oice_po and dzsno_po
+
+  - Adding checks to ensure that the values for h2oliq_po, h2oice_po, dzsno_po, and snowdp_po are never negative 
+
 **January 11 2024 :: QCEFF. Tag v11.0.0**
 
 Nonlinear and Non-Gaussian Data Assimilation Capabilities in DART

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,9 @@
+cff-version: 1.2.0
+message: "To cite DART, please use the following metadata. Update the DART version and year as appropriate."
+title: "The Data Assimilation Research Testbed"
+version: "X.Y.Z"
+date-released: "2024-03-13"
+doi: "10.5065/D6WQ0202"
+authors:
+  - name: "UCAR/NSF NCAR/CISL/DAReS"
+    city: "Boulder, Colorado"
diff --git a/README.md b/README.md
@@ -28,7 +28,7 @@ git clone https://github.com/NCAR/DART.git
 
 To cite DART, please use the following text:
 
-> The Data Assimilation Research Testbed (Version X.Y.Z) [Software]. (2021). Boulder, Colorado: UCAR/NCAR/CISL/DAReS.
+> The Data Assimilation Research Testbed (Version X.Y.Z) [Software]. (2021). Boulder, Colorado: UCAR/NSF NCAR/CISL/DAReS.
 > http://doi.org/10.5065/D6WQ0202
 
 and update the DART version and year as appropriate.

diff --git a/assimilation_code/modules/assimilation/assim_tools_mod.pf.f90 b/assimilation_code/modules/assimilation/assim_tools_mod.pf.f90
@@ -62,7 +62,7 @@ module assim_tools_mod
 
 use ensemble_manager_mod, only : ensemble_type, get_my_num_vars, get_my_vars,             &
                                  compute_copy_mean_var, get_var_owner_index,              &
-                                 prepare_to_update_copies, map_pe_to_task
+                                 map_pe_to_task
 
 use mpi_utilities_mod,    only : my_task_id, broadcast_send, broadcast_recv,              &
                                  sum_across_tasks, task_count, start_mpi_timer,           &
@@ -165,7 +165,7 @@ module assim_tools_mod
 real(r8) :: pf_alpha                        = 0.30_r8
 integer  :: pf_kddm                         = 0
 logical  :: sampling_weighted_prior         = .true.
-logical  :: pf_enkf_hybrid                  = .true.
+logical  :: pf_enkf_hybrid                  = .false.
 real(r8) :: min_residual                    = 0.5_r8
 integer  :: pf_maxiter                      = 3
 real(r8) :: pf_kf_rtps_coeff                = 0.0_r8
@@ -496,10 +496,6 @@ subroutine filter_assim(ens_handle, obs_ens_handle, obs_seq, keys,           &
          my_state_loc(         ens_handle%my_num_vars))
 ! end alloc
 
-! we are going to read/write the copies array
-call prepare_to_update_copies(ens_handle)
-call prepare_to_update_copies(obs_ens_handle)
-
 ! Initialize assim_tools_module if needed
 if (.not. module_initialized) call assim_tools_init()
 

diff --git a/assimilation_code/modules/assimilation/assim_tools_mod.rst b/assimilation_code/modules/assimilation/assim_tools_mod.rst
@@ -1,3 +1,5 @@
+.. _assim_tools:
+
 MODULE assim_tools_mod
 ======================
 
@@ -289,7 +291,7 @@ Description of each namelist entry
    *type:* character(len=256)
 
    If adjust_obs_impact is true, the name of the file with the observation types and quantities and state quantities
-   that should have have an additional factor applied to the correlations during assimilation.
+   that should have an additional factor applied to the correlations during assimilation.
 
 ``allow_any_impact_values``
    *type:* logical

diff --git a/assimilation_code/modules/assimilation/filter_mod.dopplerfold.f90 b/assimilation_code/modules/assimilation/filter_mod.dopplerfold.f90
@@ -46,11 +46,10 @@ module filter_mod
                                   compute_copy_mean, compute_copy_mean_sd,                    &
                                   compute_copy_mean_var, duplicate_ens, get_copy_owner_index, &
                                   get_ensemble_time, set_ensemble_time, broadcast_copy,       &
-                                  map_pe_to_task, prepare_to_update_copies,  &
-                                  copies_in_window, set_num_extra_copies, get_allow_transpose, &
-                                  all_copies_to_all_vars, allocate_single_copy, allocate_vars, &
-                                  get_single_copy, put_single_copy, deallocate_single_copy,   &
-                                  print_ens_handle
+                                  map_pe_to_task, copies_in_window, set_num_extra_copies,     &
+                                  get_allow_transpose, all_copies_to_all_vars,                &
+                                  allocate_single_copy, allocate_vars, get_single_copy,       &
+                                  put_single_copy, deallocate_single_copy, print_ens_handle
 
 use adaptive_inflate_mod,  only : do_ss_inflate, mean_from_restart, sd_from_restart,  &
                                   inflate_ens, adaptive_inflate_init,                 &
@@ -806,7 +805,6 @@ subroutine filter_main()
       call trace_message('Before prior inflation damping and prep')
 
       if (inf_damping(PRIOR_INF) /= 1.0_r8) then
-         call prepare_to_update_copies(state_ens_handle)
          state_ens_handle%copies(PRIOR_INF_COPY, :) = 1.0_r8 + &
             inf_damping(PRIOR_INF) * (state_ens_handle%copies(PRIOR_INF_COPY, :) - 1.0_r8)
       endif
@@ -907,7 +905,6 @@ subroutine filter_main()
       call trace_message('Before posterior inflation damping')
 
       if (inf_damping(POSTERIOR_INF) /= 1.0_r8) then
-         call prepare_to_update_copies(state_ens_handle)
          state_ens_handle%copies(POST_INF_COPY, :) = 1.0_r8 + &
             inf_damping(POSTERIOR_INF) * (state_ens_handle%copies(POST_INF_COPY, :) - 1.0_r8)
       endif
@@ -1549,9 +1546,6 @@ subroutine filter_ensemble_inflate(ens_handle, inflate_copy, inflate, ENS_MEAN_C
 
 integer :: j, group, grp_bot, grp_top, grp_size
 
-! Assumes that the ensemble is copy complete
-call prepare_to_update_copies(ens_handle)
-
 ! Inflate each group separately;  Divide ensemble into num_groups groups
 grp_size = ens_size / num_groups
 
@@ -2827,8 +2821,6 @@ subroutine update_observations_radar(obs_ens_handle, ens_size, seq, keys, prior_
 ! for quiet execution, set it to false.
 verbose = .true.
 
-call prepare_to_update_copies(obs_ens_handle)
-
 do j = 1, obs_ens_handle%my_num_vars
    ! get the key number associated with each of my subset of obs
    ! then get the obs and extract info from it.

diff --git a/assimilation_code/modules/assimilation/filter_mod.f90 b/assimilation_code/modules/assimilation/filter_mod.f90
@@ -46,11 +46,10 @@ module filter_mod
                                   compute_copy_mean, compute_copy_mean_sd,                    &
                                   compute_copy_mean_var, duplicate_ens, get_copy_owner_index, &
                                   get_ensemble_time, set_ensemble_time, broadcast_copy,       &
-                                  map_pe_to_task, prepare_to_update_copies,  &
-                                  copies_in_window, set_num_extra_copies, get_allow_transpose, &
-                                  all_copies_to_all_vars, allocate_single_copy, allocate_vars, &
-                                  get_single_copy, put_single_copy, deallocate_single_copy,   &
-                                  print_ens_handle
+                                  map_pe_to_task, copies_in_window, set_num_extra_copies,     &
+                                  get_allow_transpose, all_copies_to_all_vars,                &
+                                  allocate_single_copy, allocate_vars, get_single_copy,       &
+                                  put_single_copy, deallocate_single_copy, print_ens_handle
 
 use adaptive_inflate_mod,  only : do_ss_inflate, mean_from_restart, sd_from_restart,  &
                                   inflate_ens, adaptive_inflate_init,                 &
@@ -809,7 +808,6 @@ subroutine filter_main()
       call trace_message('Before prior inflation damping and prep')
 
       if (inf_damping(PRIOR_INF) /= 1.0_r8) then
-         call prepare_to_update_copies(state_ens_handle)
          state_ens_handle%copies(PRIOR_INF_COPY, :) = 1.0_r8 + &
             inf_damping(PRIOR_INF) * (state_ens_handle%copies(PRIOR_INF_COPY, :) - 1.0_r8)
       endif
@@ -910,7 +908,6 @@ subroutine filter_main()
       call trace_message('Before posterior inflation damping')
 
       if (inf_damping(POSTERIOR_INF) /= 1.0_r8) then
-         call prepare_to_update_copies(state_ens_handle)
          state_ens_handle%copies(POST_INF_COPY, :) = 1.0_r8 + &
             inf_damping(POSTERIOR_INF) * (state_ens_handle%copies(POST_INF_COPY, :) - 1.0_r8)
       endif
@@ -1566,9 +1563,6 @@ subroutine filter_ensemble_inflate(ens_handle, inflate_copy, inflate, ENS_MEAN_C
 real(r8) :: lower_bound,   upper_bound
 integer  :: dist_type
 
-! Assumes that the ensemble is copy complete
-call prepare_to_update_copies(ens_handle)
-
 ! Inflate each group separately;  Divide ensemble into num_groups groups
 grp_size = ens_size / num_groups
 

diff --git a/assimilation_code/modules/assimilation/obs_model_mod.f90 b/assimilation_code/modules/assimilation/obs_model_mod.f90
@@ -20,8 +20,8 @@ module obs_model_mod
                                  operator(/=), operator(>), operator(-),              &
                                  operator(/), operator(+), operator(<), operator(==), &
                                  operator(<=), operator(>=)
-use ensemble_manager_mod, only : get_ensemble_time, ensemble_type, map_task_to_pe, &
-                                 prepare_to_update_vars
+use ensemble_manager_mod, only : get_ensemble_time, ensemble_type, map_task_to_pe
+
 use mpi_utilities_mod,    only : my_task_id, task_sync, block_task, &
                                  sum_across_tasks, shell_execute, my_task_id
 use io_filenames_mod,     only : file_info_type
@@ -348,8 +348,6 @@ subroutine advance_state(ens_handle, ens_size, target_time, async, adv_ens_comma
    ! Ok, this task does need to advance something. 
    need_advance = 1
 
-   call prepare_to_update_vars(ens_handle)
-
    ! Increment number of ensemble member copies I have.
    my_num_state_copies = my_num_state_copies + 1
 

diff --git a/assimilation_code/modules/observations/forward_operator_mod.f90 b/assimilation_code/modules/observations/forward_operator_mod.f90
@@ -30,8 +30,6 @@ module forward_operator_mod
 use obs_kind_mod,          only : assimilate_this_type_of_obs, evaluate_this_type_of_obs
 
 use ensemble_manager_mod,  only : ensemble_type, compute_copy_mean_var, &
-                                  prepare_to_read_from_vars,            &
-                                  prepare_to_write_to_vars,             &
                                   get_my_num_copies, copies_in_window,  &
                                   get_allow_transpose, all_vars_to_all_copies, &
                                   all_copies_to_all_vars, allocate_single_copy, &
@@ -127,11 +125,6 @@ subroutine get_obs_ens_distrib_state(ens_handle, obs_fwd_op_ens_handle, &
 istatus = 999123
 expected_obs = MISSING_R8
 
-! FIXME: these no longer do anything?
-! call prepare_to_write_to_vars(obs_fwd_op_ens_handle)
-! call prepare_to_write_to_vars(qc_ens_handle)
-! call prepare_to_read_from_vars(ens_handle)
-
 ! Set up access to the state
 call create_state_window(ens_handle, obs_fwd_op_ens_handle, qc_ens_handle)