myroms · hga007 · Jul 15, 2024 · Aug 11, 2024 · Aug 11, 2024 · Aug 11, 2024
diff --git a/IRENE/Coupled_RBL4DVAR/Readme.md b/IRENE/Coupled_RBL4DVAR/Readme.md
@@ -155,7 +155,7 @@ They are activated in the build scripts.
     links files created by the build script and needed to run **WRF**:
   ```
     alias ltl '/bin/ls -ltHF | grep -v ^l'
-  ```      
+  ```
 ### How to Compile ROMS:
 
 - **ROMS** is the driver of the coupling system. In this application, the **WRF** Surface
@@ -168,7 +168,7 @@ They are activated in the build scripts.
     The option **bulk_flux = 1** in the **ROMS** build script IS NOT RECOMMENDED FOR THIS
     APPLICATION because the **bulk_flux.F** module is not tunned for Hurricane regimes,
     and will get the wrong solution
-   
+
     To compile **ROMS** coupling (nonlinear kernel) and data assimilation kernels, use:
    ```
     build_split.csh -nl -j 10                     creates executable romsM_nl
@@ -187,7 +187,7 @@ They are activated in the build scripts.
     submit.sh > & log &
    ```
     You can modify **submit.sh** for your appropriate computer environment.
-  
+
     The **submit.sh** script creates the sub-directory **2011.08.27** and includes all
     the required input scripts to run the **coupled/RBL4D-Var** system. The input
     scripts are generated from the templates.  The **submit.sh** script is quite

diff --git a/IRENE/Coupled_RBL4DVAR/coupling_esmf_atm_sbl.tmp b/IRENE/Coupled_RBL4DVAR/coupling_esmf_atm_sbl.tmp
@@ -687,7 +687,7 @@ nDataExport(seaice) == 0                ! number of fields to export
 !                    flag to ESMF_FieldRegridStore.
 !
 !------------------------------------------------------------------------------
-! Melding weighting coefficients. 
+! Melding weighting coefficients.
 !------------------------------------------------------------------------------
 !
 ! Melding coefficients used to combine fields from DATA and ESM components.

diff --git a/IRENE/Coupled_RBL4DVAR/coupling_esmf_atm_sbl_wmc.tmp b/IRENE/Coupled_RBL4DVAR/coupling_esmf_atm_sbl_wmc.tmp
@@ -691,7 +691,7 @@ nDataExport(seaice) == 0                ! number of fields to export
 !                    flag to ESMF_FieldRegridStore.
 !
 !------------------------------------------------------------------------------
-! Melding weighting coefficients. 
+! Melding weighting coefficients.
 !------------------------------------------------------------------------------
 !
 ! Melding coefficients used to combine fields from DATA and ESM components.

diff --git a/IRENE/Coupled_RBL4DVAR/coupling_esmf_bulk_flux.tmp b/IRENE/Coupled_RBL4DVAR/coupling_esmf_bulk_flux.tmp
@@ -680,7 +680,7 @@ nDataExport(seaice) == 0                ! number of fields to export
 !                    flag to ESMF_FieldRegridStore.
 !
 !------------------------------------------------------------------------------
-! Melding weighting coefficients. 
+! Melding weighting coefficients.
 !------------------------------------------------------------------------------
 !
 ! Melding coefficients used to combine fields from DATA and ESM components.

diff --git a/IRENE/Coupled_RBL4DVAR/irene.h b/IRENE/Coupled_RBL4DVAR/irene.h
@@ -32,7 +32,7 @@
 #define CHARNOK
 
 #define ATM_PRESS
- 
+
 
 /* Basic numerics options */
 

diff --git a/IRENE/Coupled_RBL4DVAR/namelist.input.tmp b/IRENE/Coupled_RBL4DVAR/namelist.input.tmp
@@ -22,8 +22,8 @@
  input_from_file                     = .true., .false., .false.,
  force_use_old_data                  = .false.,
  input_inname                        = "MyInpName"
- bdy_inname                          = "MyBryName" 
- history_outname                     = "MyHisName" 
+ bdy_inname                          = "MyBryName"
+ history_outname                     = "MyHisName"
  history_interval                    = 60,   60,   60,       ! minutes
  frames_per_outfile                  = 1000, 1000, 1000,
  restart                             = .false.,

diff --git a/IRENE/Coupled_RBL4DVAR/roms_da_irene.tmp b/IRENE/Coupled_RBL4DVAR/roms_da_irene.tmp
@@ -1139,7 +1139,7 @@ PIO_I2C_Preq = 65                 ! Maximum pending I2C requests
 
 ! Input tidal forcing file name.
 
-     TIDENAME == ../../Data/ROMS/irene_roms_tides.nc 
+     TIDENAME == ../../Data/ROMS/irene_roms_tides.nc
 
 ! Input forcing NetCDF file name(s).
 !

diff --git a/IRENE/Coupled_RBL4DVAR/roms_nl_irene.tmp b/IRENE/Coupled_RBL4DVAR/roms_nl_irene.tmp
@@ -1139,7 +1139,7 @@ PIO_I2C_Preq = 65                 ! Maximum pending I2C requests
 
 ! Input tidal forcing file name.
 
-     TIDENAME == ../../Data/ROMS/irene_roms_tides.nc 
+     TIDENAME == ../../Data/ROMS/irene_roms_tides.nc
 
 ! Input forcing NetCDF file name(s).
 !

diff --git a/IRENE/Coupled_RBL4DVAR/s4dvar.in b/IRENE/Coupled_RBL4DVAR/s4dvar.in
@@ -165,6 +165,11 @@ balance(isVvel) =  F                      ! 3D momentum (u, v)
 
        tl_Tdiff ==  50.0d0  50.0d0        ! NT tracers
 
+! Duration of the Incremental Analysis Update (days) [1:Ngrids].
+! NOTE: This option is only available for RBL4DVAR and when using RPCG.
+
+        timeIAU == 0.0d0
+
 ! Switches (T/F) to create and write error covariance normalization
 ! factors for model, initial conditions, boundary conditions, and
 ! surface forcing. If TRUE, these factors are computed and written
@@ -326,25 +331,25 @@ HdecayF(isTsur) == 100.0d+3  100.0d+3             ! 1:NT surface tracers flux
 ! error has the similar field profile shape, but the difference with its
 ! ture error value is due to a vertical displacement.
 !
-! If COMPUTE_MLD is activated, the mixed-layer depth is computes using the
+! If COMPUTE_MLD is activated, the mixed-layer depth is computed using the
 ! criterion from kara et al. (2000). Otherwise, it will be set to uniform
 ! value provided below.
 
 Sigma_max(isFsur) == 0.025d0           ! free surface  maximum STD value
 
 Sigma_max(isUvel) == 0.06d0            ! U-velocity maximum STD value
  Sigma_ml(isUvel) == 0.05d0            ! U-velocity minimum STD at mixed layer
- Sigma_do(isUvel) == 0.02d0            ! U-velocity minimum STD in deep ocean 
+ Sigma_do(isUvel) == 0.02d0            ! U-velocity minimum STD in deep ocean
  Sigma_dz(isUvel) == 500.0d0           ! U-velocity vertical displacement
 
 Sigma_max(isVvel) == 0.06d0            ! V-velocity maximum STD
  Sigma_ml(isVvel) == 0.05d0            ! V-velocity minimum STD at mixed layer
- Sigma_do(isVvel) == 0.02d0            ! V-velocity minimum STD in deep ocean 
+ Sigma_do(isVvel) == 0.02d0            ! V-velocity minimum STD in deep ocean
  Sigma_dz(isVvel) == 500.0d0           ! V-velocity vertical displacement
 
 Sigma_max(isTvar) == 0.33d0   0.056d0  ! 1:NT tracers maximum STD
  Sigma_ml(isTvar) == 0.05d0   0.05d0   ! 1:NT tracers minimum STD at mixed layer
- Sigma_do(isTvar) == 0.02d0   0.0028d0 ! 1:NT tracers minimum STD in deep ocean 
+ Sigma_do(isTvar) == 0.02d0   0.0028d0 ! 1:NT tracers minimum STD in deep ocean
  Sigma_dz(isTvar) == 40.0d0   40.0d0   ! 1:NT tracer vertical displacement
 
       mld_uniform == -75.0d0           ! Uniform mixed layer depth value
@@ -711,6 +716,25 @@ Sigma_max(isTvar) == 0.33d0   0.056d0  ! 1:NT tracers maximum STD
 !                 (m2/s).  NT values are expected.
 !
 !------------------------------------------------------------------------------
+! Incremental Analysis Update (IAU)
+!------------------------------------------------------------------------------
+!
+!  timeIAU        Duration of the Incremental Analysis Update (days),
+!                 [1:Ngrids]. It controls the time interval over which
+!                 the IAU is applied.
+!
+!                 This option is only available for RBL4DVAR and when using
+!                 RPCG minimizer.
+!
+!                 In SPLIT_RBL4DVAR, you can the analysis phase multiple
+!                 times experimenting with different values of timeIAU
+!                 to see which works best, without having to rerun the
+!                 inner-loops again (increment phase). You can only do
+!                 this if SPLIT_RBL4DVAR is first run with a non-zero
+!                 value of timeIAU, otherwise the initial condition will
+!                 get overwritten in the initial NetCDF file.
+!
+!------------------------------------------------------------------------------
 ! Background/model correlation parameters.
 !------------------------------------------------------------------------------
 !
@@ -896,7 +920,7 @@ Sigma_max(isTvar) == 0.33d0   0.056d0  ! 1:NT tracers maximum STD
 !
 ! Sigma_ml(:)       Minimum STD at mixed layer
 !
-! Sigma_do(:)       Minimum STD in deep ocean 
+! Sigma_do(:)       Minimum STD in deep ocean
 !
 ! Sigma_dz(:)       Vertical profile displacement
 !

diff --git a/IRENE/Coupled_RBL4DVAR/submit.sh b/IRENE/Coupled_RBL4DVAR/submit.sh
@@ -450,7 +450,7 @@ while [ "$(bc <<< "$SDAY <= $L_DN")" == "1" ]; do
   done
 
   end=()                                      # WRF end simulation time
-  i=0                                         # integer vector 
+  i=0                                         # integer vector
   for element in ${StopTime// / }; do         # (YYYY MM DD hh mm ss)
     end[$i]=${element}
     ((i=$i+1))

diff --git a/IRENE/Coupling/data_wrf_roms/Readme.md b/IRENE/Coupling/data_wrf_roms/Readme.md
@@ -5,7 +5,7 @@
 This directory includes various files to run the **DATA-WRF-ROMS**
 coupling system for Hurricane Irene using the **ESMF/NUOPC** library. It
 uses our Coupled Forecast Framework (**CFF**) configuration for the
-US East Coast **`CFF-EC7`** (**ROMS** 7km grid), and the simulation is 
+US East Coast **`CFF-EC7`** (**ROMS** 7km grid), and the simulation is
 only run for 42 hours as Hurricane Irene approached the Outer Banks
 of North Carolina on August 27, 2011.
 
@@ -26,7 +26,7 @@ diagnostics.
 
 All the components interact with the same coupling time step.
 The connector from **ROMS** to **WRF** is explicit, whereas the connector
-from **WRF** to **ROMS** is semi-implicit. 
+from **WRF** to **ROMS** is semi-implicit.
 
 It uses **ROMS**'s native, **NUOPC**-based coupling system. For more information,
 visit **WikiROMS**:
@@ -143,7 +143,7 @@ They are activated in the build scripts.
     links files created by the build script and needed to run **WRF**:
   ```
     alias ltl '/bin/ls -ltHF | grep -v ^l'
-  ```      
+  ```
 ### How to Compile ROMS:
 
 - **ROMS** is the driver of the coupling system. In this application, the **WRF** Surface
@@ -156,7 +156,7 @@ They are activated in the build scripts.
     The option **bulk_flux = 1** in the **ROMS** build script IS NOT RECOMMENDED FOR THIS
     APPLICATION because the **bulk_flux.F** module is not tunned for Hurricane regimes,
     and will get the wrong solution
-   
+
     To compile **ROMS**, use:
    ```
     build_roms.csh -j 10
@@ -167,7 +167,7 @@ They are activated in the build scripts.
     submit.sh > & log &
    ```
   You can modify **submit.sh** for your appropriate computer environment.
-   
+
 ### The output Files:
 
 - Standard Output Files:
@@ -180,7 +180,7 @@ They are activated in the build scripts.
   ```
 
 - **ROMS** NetCDF Files:
- 
+
    ```
     irene_avg.nc                                  6-hour averages
     irene_his.nc                                  hourly history

diff --git a/IRENE/Coupling/data_wrf_roms/cbuild_roms.csh b/IRENE/Coupling/data_wrf_roms/cbuild_roms.csh
@@ -378,10 +378,10 @@ if ( $dprint == 0 ) then
     echo ""
     cd src
     git checkout $branch_name
-  
+
     # If we are using the COMPILERS from the ROMS source code
     # overide the value set above
-  
+
     if ( ${COMPILERS} =~ ${MY_ROMS_SRC}* ) then
       setenv COMPILERS ${MY_PROJECT_DIR}/src/Compilers
     endif

diff --git a/IRENE/Coupling/data_wrf_roms/cbuild_roms.sh b/IRENE/Coupling/data_wrf_roms/cbuild_roms.sh
@@ -367,7 +367,7 @@ if [ $dprint -eq 0 ]; then
 
     # If we are using the COMPILERS from the ROMS source code
     # overide the value set above
-  
+
     if [[ ${COMPILERS} == ${MY_ROMS_SRC}* ]]; then
       export COMPILERS=${MY_PROJECT_DIR}/src/Compilers
     fi

diff --git a/IRENE/Coupling/data_wrf_roms/irene.h b/IRENE/Coupling/data_wrf_roms/irene.h
@@ -32,7 +32,7 @@
 #define CHARNOK
 
 #define ATM_PRESS
- 
+
 
 /* Basic numerics options */
 

diff --git a/IRENE/Coupling/data_wrf_roms/roms_irene.in b/IRENE/Coupling/data_wrf_roms/roms_irene.in
@@ -1140,7 +1140,7 @@ PIO_I2C_Preq = 65                 ! Maximum pending I2C requests
 
 ! Input tidal forcing file name.
 
-     TIDENAME == ../../Data/ROMS/irene_roms_tides.nc 
+     TIDENAME == ../../Data/ROMS/irene_roms_tides.nc
 
 ! Input forcing NetCDF file name(s).
 !

diff --git a/IRENE/Coupling/data_wrf_roms/submit.sh b/IRENE/Coupling/data_wrf_roms/submit.sh
@@ -56,7 +56,7 @@ fi
 ##---------------------------------------------------------------------
 
 if [ ${BATCH} -eq 1 ]; then
-   ${SRUN} ${ROMS_EXE} ${ESMFinp} > log.wrf 2>&1 
+   ${SRUN} ${ROMS_EXE} ${ESMFinp} > log.wrf 2>&1
 else
    ${MPIrun} ${nPETs} ${ROMS_EXE} ${ESMFinp} > log.wrf 2>&1
 fi

diff --git a/IRENE/Coupling/data_wrf_roms_wmc/Readme.md b/IRENE/Coupling/data_wrf_roms_wmc/Readme.md
@@ -7,12 +7,12 @@ coupling system for Hurricane Irene using the **ESMF/NUOPC** library. It
 uses our Coupled Forecast Framework (**CFF**) configuration for the
 US East Coast **`CFF-EC7`** (**ROMS** 7km grid), and the simulation is only
 run for 42 hours as Hurricane Irene approached the Outer Banks
-of North Carolina on August 27, 2011. 
+of North Carolina on August 27, 2011.
 
 This test is a variant of the one available in [data_wrf_roms](../data_wrf_roms)
 since **ROMS** and **DATA** export surface ocean currents to compute the
 effective surface wind forcing by subtracting surface ocean currents from
-**WRF** surface wind. 
+**WRF** surface wind.
 
 <img width="940" alt="image" src="https://github.com/myroms/roms_test/assets/23062912/43010527-1cb7-4ba0-aec4-a888f46369c4">
 
@@ -30,7 +30,7 @@ activating the **RAMS**-averaged diagnostics.
 
 All the components interact with the same coupling time step.
 The connector from **ROMS** to **WRF** is explicit, whereas the connector
-from **WRF** to **ROMS** is semi-implicit. 
+from **WRF** to **ROMS** is semi-implicit.
 
 It uses **ROMS**'s native, **NUOPC**-based coupling system. For more information,
 visit **WikiROMS**:
@@ -41,7 +41,7 @@ https://www.myroms.org/wiki/Model_Coupling_ESMF
 
 As shown by Renault _et al._ (2016), the feedback from surface ocean currents to
 the atmosphere is an eddy-killing effect stabilizing the Gulf Stream separation
-at Cape Hatteras in **WRF-ROMS** fully coupled applications. The result is 
+at Cape Hatteras in **WRF-ROMS** fully coupled applications. The result is
 around 0.3 N/m2 weaker surface wind stress in the core of the Gulf Stream. Since
 **ROMS** doesn't cover all the ocean points in the **WRF** grid, a **DATA**
 component is used to supply those values from the 3-hour **HyCOM** dataset.
@@ -120,7 +120,7 @@ They are activated in the build scripts.
   coupling_esmf_wrf.yaml        Coupling fields exchange YAML metadata
   irene.h                       ROMS header file
   namelist.input                WRF standard input script
-  plot_debug.m                  Matlab plotting  driver for debugging (for DebugLevel=3) 
+  plot_debug.m                  Matlab plotting  driver for debugging (for DebugLevel=3)
   plot_esmf.m                   Matlab plotting script for field maps (for DebugLevel=3)
   rbl4dvar.in                   ROMS observation input script
   roms_irene.in                 ROMS standard input script
@@ -129,7 +129,7 @@ They are activated in the build scripts.
   ```
 
 - To download **WRF** latest forked repository, you may use:
-- 
+-
   ```
     git clone  https://github.com/myroms/WRF
   ```
@@ -183,7 +183,7 @@ They are activated in the build scripts.
     links files created by the build script and needed to run **WRF**:
   ```
     alias ltl '/bin/ls -ltHF | grep -v ^l'
-  ```      
+  ```
 ### How to Compile ROMS:
 
 - **ROMS** is the driver of the coupling system. In this application, the **WRF** Surface
@@ -196,7 +196,7 @@ They are activated in the build scripts.
     The option **bulk_flux = 1** in the **ROMS** build script IS NOT RECOMMENDED FOR THIS
     APPLICATION because the **bulk_flux.F** module is not tunned for Hurricane regimes,
     and will get the wrong solution
-   
+
     To compile **ROMS**, use:
    ```
     build_roms.csh -j 10
@@ -207,7 +207,7 @@ They are activated in the build scripts.
     submit.sh > & log &
    ```
   You can modify **submit.sh** for your appropriate computer environment.
-   
+
 ### Debugging:
 
 The **ROMS** native coupling framework allows writing the selected exchange fields in
@@ -265,7 +265,7 @@ exporting surface ocean currents. An example of the figures generated and shown
   ```
 
 - **ROMS** NetCDF Files:
- 
+
    ```
     irene_avg.nc                                  6-hour averages
     irene_his.nc                                  hourly history

diff --git a/IRENE/Coupling/data_wrf_roms_wmc/cbuild_roms.csh b/IRENE/Coupling/data_wrf_roms_wmc/cbuild_roms.csh
@@ -380,10 +380,10 @@ if ( $dprint == 0 ) then
     echo ""
     cd src
     git checkout $branch_name
-  
+
     # If we are using the COMPILERS from the ROMS source code
     # overide the value set above
-  
+
     if ( ${COMPILERS} =~ ${MY_ROMS_SRC}* ) then
       setenv COMPILERS ${MY_PROJECT_DIR}/src/Compilers
     endif

diff --git a/IRENE/Coupling/data_wrf_roms_wmc/cbuild_roms.sh b/IRENE/Coupling/data_wrf_roms_wmc/cbuild_roms.sh
@@ -369,7 +369,7 @@ if [ $dprint -eq 0 ]; then
 
     # If we are using the COMPILERS from the ROMS source code
     # overide the value set above
-  
+
     if [[ ${COMPILERS} == ${MY_ROMS_SRC}* ]]; then
       export COMPILERS=${MY_PROJECT_DIR}/src/Compilers
     fi

diff --git a/IRENE/Coupling/data_wrf_roms_wmc/irene.h b/IRENE/Coupling/data_wrf_roms_wmc/irene.h
@@ -32,7 +32,7 @@
 #define CHARNOK
 
 #define ATM_PRESS
- 
+
 
 /* Basic numerics options */