From 3f9edb2fad7a145f1ca1f3803e1800201a186aed Mon Sep 17 00:00:00 2001
From: jordanschnell <jordan.schnell@noaa.gov>
Date: Tue, 19 Mar 2024 16:12:16 +0000
Subject: [PATCH 01/16] Add capability to ingest RAP/HRRR smoke for IC/BC

---
 parm/varmap_tables/GSDphys_var_map.txt |  3 +-
 sorc/chgres_cube.fd/atm_input_data.F90 | 50 ++++++++++++++++++++++----
 2 files changed, 45 insertions(+), 8 deletions(-)

diff --git a/parm/varmap_tables/GSDphys_var_map.txt b/parm/varmap_tables/GSDphys_var_map.txt
index 28a5b0ca7..0d7215fea 100644
--- a/parm/varmap_tables/GSDphys_var_map.txt
+++ b/parm/varmap_tables/GSDphys_var_map.txt
@@ -24,4 +24,5 @@ cnwat               cnwat     set_to_fill   0.0       S
 icetk               icetk     set_to_fill   265.0     S
 weasd               weasd     set_to_fill   0.0       S
 snod                snod      set_to_fill   0.0       S
-tprcp               tprcp     set_to_fill   0.0       S       	
+tprcp               tprcp     set_to_fill   0.0       S
+massden             smoke     set_to_fill   1E-12     T	
diff --git a/sorc/chgres_cube.fd/atm_input_data.F90 b/sorc/chgres_cube.fd/atm_input_data.F90
index fd7d254c1..1b1d76eb4 100644
--- a/sorc/chgres_cube.fd/atm_input_data.F90
+++ b/sorc/chgres_cube.fd/atm_input_data.F90
@@ -1978,7 +1978,7 @@ subroutine read_input_atm_grib2_file(localpet)
 
  integer, intent(in)                   :: localpet
  
- integer, parameter                    :: ntrac_max=14
+ integer, parameter                    :: ntrac_max=15
  integer, parameter                    :: max_levs=1000
 
  character(len=300)                    :: the_file
@@ -2015,7 +2015,8 @@ subroutine read_input_atm_grib2_file(localpet)
  real(esmf_kind_r8), allocatable       :: rlevs(:)
  real(esmf_kind_r4), allocatable       :: dummy2d(:,:)
  real(esmf_kind_r8), allocatable       :: dummy3d(:,:,:), dummy2d_8(:,:),&
-                                          u_tmp_3d(:,:,:), v_tmp_3d(:,:,:)
+                                          u_tmp_3d(:,:,:), v_tmp_3d(:,:,:),&
+                                          dummy3d_pres(:,:,:)
  real(esmf_kind_r8), pointer           :: presptr(:,:,:), psptr(:,:),tptr(:,:,:), &
                                           qptr(:,:,:), wptr(:,:,:),  &
                                           uptr(:,:,:), vptr(:,:,:)
@@ -2030,18 +2031,19 @@ subroutine read_input_atm_grib2_file(localpet)
  
  tracers(:) = "NULL"
  
- trac_names_oct10 = (/1,  1,  14,  1,  1,  1,  1, 6,  6,   1,  6,  13,  13, 2 /)
- trac_names_oct11 = (/0, 22, 192, 23, 24, 25, 32, 1, 29, 100, 28, 193, 192, 2 /)
+ trac_names_oct10 = (/1,  1,  14,  1,  1,  1,  1, 6,  6,   1,  6,  13,  13, 2, 20 /)
+ trac_names_oct11 = (/0, 22, 192, 23, 24, 25, 32, 1, 29, 100, 28, 193, 192, 2,  0 /)
+
 
  trac_names_vmap = (/"sphum   ", "liq_wat ", "o3mr    ", "ice_wat ", &
                      "rainwat ", "snowwat ", "graupel ", "cld_amt ", "ice_nc  ", &
                      "rain_nc ", "water_nc", "liq_aero", "ice_aero", &
-                     "sgs_tke "/)
+                     "sgs_tke ", "massden"/)
 
  tracers_default = (/"sphum   ", "liq_wat ", "o3mr    ", "ice_wat ", &
                      "rainwat ", "snowwat ", "graupel ", "cld_amt ", "ice_nc  ", &
                      "rain_nc ", "water_nc", "liq_aero", "ice_aero", &
-                     "sgs_tke "/)
+                     "sgs_tke ", "smoke   "/)
 
  the_file = trim(data_dir_input_grid) // "/" // trim(grib2_file_input_grid)
 
@@ -2393,11 +2395,19 @@ subroutine read_input_atm_grib2_file(localpet)
    allocate(dummy2d(i_input,j_input))
    allocate(dummy2d_8(i_input,j_input))
    allocate(dummy3d(i_input,j_input,lev_input))
+   if (trim(external_model) .eq. 'RAP' .or. &  ! for smoke conversion
+       trim(external_model) .eq. 'HRRR' ) then
+      allocate(dummy3d_pres(i_input,j_input,lev_input))
+    endif
    allocate(dum2d_1(i_input,j_input))
  else
    allocate(dummy2d(0,0))
    allocate(dummy2d_8(0,0))
    allocate(dummy3d(0,0,0))
+   if (trim(external_model) .eq. 'RAP' .or. &  ! for smoke conversion
+       trim(external_model) .eq. 'HRRR' ) then
+      allocate(dummy3d_pres(0,0,0))
+   endif
    allocate(dum2d_1(0,0))
  endif
 
@@ -2457,12 +2467,26 @@ subroutine read_input_atm_grib2_file(localpet)
    call get_var_cond(vname,this_miss_var_method=method, this_miss_var_value=value, &
                        this_field_var_name=tmpstr,loc=varnum)
 
-   if (n==1 .and. .not. hasspfh) then 
+   if (n==1 .and. .not. hasspfh .or. &
+     ( (trim(external_model) .eq. 'RAP' .or. &  ! for smoke conversion
+       trim(external_model) .eq. 'HRRR' ) .and. &
+       (tracers_input_vmap(n) == trac_names_vmap(15)))) then 
      print*,"- CALL FieldGather TEMPERATURE." 
      call ESMF_FieldGather(temp_input_grid,dummy3d,rootPet=0, tile=1, rc=rc)
      if(ESMF_logFoundError(rcToCheck=rc,msg=ESMF_LOGERR_PASSTHRU,line=__LINE__,file=__FILE__)) &
      call error_handler("IN FieldGet", rc) 
    endif
+
+   if ( (trim(external_model) .eq. 'RAP' .or. &  ! for smoke conversion
+       trim(external_model) .eq. 'HRRR' ) .and. &
+       tracers_input_vmap(n) == trac_names_vmap(15)) then
+     print*,"- CALL FieldGather 3D Pressure."
+     call ESMF_FieldGather(pres_input_grid,dummy3d_pres,rootPet=0, tile=1, rc=rc)
+     if(ESMF_logFoundError(rcToCheck=rc,msg=ESMF_LOGERR_PASSTHRU,line=__LINE__,file=__FILE__)) &
+     call error_handler("IN FieldGet", rc)
+   else
+     continue ! massden/smoke only in RAP/HRRR
+   endif
    
    if (localpet == 0) then
 
@@ -2557,6 +2581,18 @@ subroutine read_input_atm_grib2_file(localpet)
         end if
       endif
 
+      ! Convert smoke from mass density (RAP/HRRR = kg/m^3) to mixing ratio (ug/kg)
+      if ( (trim(external_model) .eq. 'RAP' .or. & 
+       trim(external_model) .eq. 'HRRR' ) .and. &
+        tracers_input_vmap(n) == trac_names_vmap(15)) then
+         do i = 1, i_input
+            do j = 1, j_input
+               dummy2d(i,j) = dummy2d(i,j) * 1.0d9 * &
+                              (287.05 * dummy3d(i,j,vlev) / dummy3d_pres(i,j,vlev))
+            enddo
+         enddo
+      endif
+
        dummy3d(:,:,vlev) = real(dummy2d,esmf_kind_r8)
 
      enddo !vlev

From a513d2983b5fc668d80c4fbb2a0a484402441d9f Mon Sep 17 00:00:00 2001
From: jordanschnell <jordan.schnell@noaa.gov>
Date: Tue, 19 Mar 2024 16:38:07 +0000
Subject: [PATCH 02/16] deallocate dummy3d_pres if allocated

---
 sorc/chgres_cube.fd/atm_input_data.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sorc/chgres_cube.fd/atm_input_data.F90 b/sorc/chgres_cube.fd/atm_input_data.F90
index 1b1d76eb4..4a13d0ab3 100644
--- a/sorc/chgres_cube.fd/atm_input_data.F90
+++ b/sorc/chgres_cube.fd/atm_input_data.F90
@@ -2557,7 +2557,7 @@ subroutine read_input_atm_grib2_file(localpet)
                   ". SET MISSING VARIABLE CONDITION TO 'INTRP' TO AVOID THIS ERROR.", 1)
             endif 
           ! If entire array is empty and method is set to intrp, switch method to fill
-          if (trim(method) .eq. 'intrp' .and. all_empty) method='set_to_fill' 
+ i         if (trim(method) .eq. 'intrp' .and. all_empty) method='set_to_fill' 
 
           call handle_grib_error(vname, slevs(vlev),method,value,varnum,read_from_input,iret,var=dummy2d)
           if (iret==1) then ! missing_var_method == skip or no entry
@@ -2642,6 +2642,7 @@ subroutine read_input_atm_grib2_file(localpet)
  enddo
  
  deallocate(dummy3d_col_in, dummy3d_col_out)
+ if allocated(dummy3d_pres) deallocate(dummy3d_pres)
  
  call read_winds(u_tmp_3d,v_tmp_3d,localpet,octet_23,rlevs,lugb,pdt_num)
 

From f3a0cdca85f06a57025b50df47dc9864f89b4eed Mon Sep 17 00:00:00 2001
From: jordanschnell <jordan.schnell@noaa.gov>
Date: Tue, 19 Mar 2024 17:41:07 +0000
Subject: [PATCH 03/16] Fix typos

---
 sorc/chgres_cube.fd/atm_input_data.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sorc/chgres_cube.fd/atm_input_data.F90 b/sorc/chgres_cube.fd/atm_input_data.F90
index 4a13d0ab3..15eb06cf8 100644
--- a/sorc/chgres_cube.fd/atm_input_data.F90
+++ b/sorc/chgres_cube.fd/atm_input_data.F90
@@ -2557,7 +2557,7 @@ subroutine read_input_atm_grib2_file(localpet)
                   ". SET MISSING VARIABLE CONDITION TO 'INTRP' TO AVOID THIS ERROR.", 1)
             endif 
           ! If entire array is empty and method is set to intrp, switch method to fill
- i         if (trim(method) .eq. 'intrp' .and. all_empty) method='set_to_fill' 
+          if (trim(method) .eq. 'intrp' .and. all_empty) method='set_to_fill' 
 
           call handle_grib_error(vname, slevs(vlev),method,value,varnum,read_from_input,iret,var=dummy2d)
           if (iret==1) then ! missing_var_method == skip or no entry
@@ -2642,7 +2642,7 @@ subroutine read_input_atm_grib2_file(localpet)
  enddo
  
  deallocate(dummy3d_col_in, dummy3d_col_out)
- if allocated(dummy3d_pres) deallocate(dummy3d_pres)
+ if (allocated(dummy3d_pres)) deallocate(dummy3d_pres)
  
  call read_winds(u_tmp_3d,v_tmp_3d,localpet,octet_23,rlevs,lugb,pdt_num)
 

From 047e3f134ff07cf8cc6cfdb1618ef51005c9fedc Mon Sep 17 00:00:00 2001
From: jordanschnell <jordan.schnell@noaa.gov>
Date: Tue, 19 Mar 2024 22:28:04 +0000
Subject: [PATCH 04/16] Explicit read of pressure during smoke portion of loop

---
 sorc/chgres_cube.fd/atm_input_data.F90 | 53 ++++++++++++++++++++------
 1 file changed, 42 insertions(+), 11 deletions(-)

diff --git a/sorc/chgres_cube.fd/atm_input_data.F90 b/sorc/chgres_cube.fd/atm_input_data.F90
index 15eb06cf8..ef974e907 100644
--- a/sorc/chgres_cube.fd/atm_input_data.F90
+++ b/sorc/chgres_cube.fd/atm_input_data.F90
@@ -2470,7 +2470,7 @@ subroutine read_input_atm_grib2_file(localpet)
    if (n==1 .and. .not. hasspfh .or. &
      ( (trim(external_model) .eq. 'RAP' .or. &  ! for smoke conversion
        trim(external_model) .eq. 'HRRR' ) .and. &
-       (tracers_input_vmap(n) == trac_names_vmap(15)))) then 
+       tracers_input_vmap(n) == trac_names_vmap(15) )) then 
      print*,"- CALL FieldGather TEMPERATURE." 
      call ESMF_FieldGather(temp_input_grid,dummy3d,rootPet=0, tile=1, rc=rc)
      if(ESMF_logFoundError(rcToCheck=rc,msg=ESMF_LOGERR_PASSTHRU,line=__LINE__,file=__FILE__)) &
@@ -2480,13 +2480,46 @@ subroutine read_input_atm_grib2_file(localpet)
    if ( (trim(external_model) .eq. 'RAP' .or. &  ! for smoke conversion
        trim(external_model) .eq. 'HRRR' ) .and. &
        tracers_input_vmap(n) == trac_names_vmap(15)) then
-     print*,"- CALL FieldGather 3D Pressure."
-     call ESMF_FieldGather(pres_input_grid,dummy3d_pres,rootPet=0, tile=1, rc=rc)
-     if(ESMF_logFoundError(rcToCheck=rc,msg=ESMF_LOGERR_PASSTHRU,line=__LINE__,file=__FILE__)) &
-     call error_handler("IN FieldGet", rc)
-   else
-     continue ! massden/smoke only in RAP/HRRR
+    if (localpet == 0) then
+
+    print*,"- READ PRESSURE FOR SMOKE CONVERSION."
+
+    jdisc   = 0     ! search for discipline - meteorological products
+    j = 0           ! search at beginning of file.
+    jpdt    = -9999  ! array of values in product definition template, set towildcard
+    jids    = -9999  ! array of values in identification section, set towildcard
+    jgdt    = -9999  ! array of values in grid definition template, set towildcard
+    jgdtn   = -1     ! search for any grid definition number.
+    jpdtn   =  pdt_num ! Search for the product definition template number.
+    jpdt(1) = 3      ! Sect4/oct 10 - parameter category - mass
+    jpdt(2) = 0      ! Sect4/oct 11 - parameter number - pressure
+    jpdt(10) = octet_23 ! Sect4/oct 23 - type of level.
+    unpack=.true.
+
+    do vlev = 1, lev_input
+
+      jpdt(12) = nint(rlevs(vlev))
+      call getgb2(lugb, lugi, j, jdisc, jids, jpdtn, jpdt, jgdtn, jgdt, &
+             unpack, k, gfld, iret)
+      if (iret /= 0) then
+        call error_handler("READING IN PRESSURE AT LEVEL"//trim(slevs(vlev)),iret)
+      endif
+
+      dum2d_1 = reshape(gfld%fld, (/i_input,j_input/) )
+
+      dummy3d_pres(:,:,vlev) = dum2d_1
+
+    enddo
+
+    endif  ! localpet == 0
+   endif   ! read pressure for smoke conversion
+
+   if (tracers_input_vmap(n) == trac_names_vmap(15) .and. &
+       (trim(external_model) .ne. 'RAP' .and. &  ! for smoke conversion
+       trim(external_model) .ne. 'HRRR' ) ) then
+       cycle ! Do not process smoke for non RAP/HRRR
    endif
+
    
    if (localpet == 0) then
 
@@ -2582,9 +2615,7 @@ subroutine read_input_atm_grib2_file(localpet)
       endif
 
       ! Convert smoke from mass density (RAP/HRRR = kg/m^3) to mixing ratio (ug/kg)
-      if ( (trim(external_model) .eq. 'RAP' .or. & 
-       trim(external_model) .eq. 'HRRR' ) .and. &
-        tracers_input_vmap(n) == trac_names_vmap(15)) then
+      if ( tracers_input_vmap(n) == trac_names_vmap(15) ) then
          do i = 1, i_input
             do j = 1, j_input
                dummy2d(i,j) = dummy2d(i,j) * 1.0d9 * &
@@ -2642,7 +2673,6 @@ subroutine read_input_atm_grib2_file(localpet)
  enddo
  
  deallocate(dummy3d_col_in, dummy3d_col_out)
- if (allocated(dummy3d_pres)) deallocate(dummy3d_pres)
  
  call read_winds(u_tmp_3d,v_tmp_3d,localpet,octet_23,rlevs,lugb,pdt_num)
 
@@ -2906,6 +2936,7 @@ subroutine read_input_atm_grib2_file(localpet)
  endif
 
  deallocate(dummy3d, dum2d_1) 
+ if (allocated(dummy3d_pres)) deallocate(dummy3d_pres)
  
 !---------------------------------------------------------------------------
 ! Convert from 2-d to 3-d component winds.

From 9273b883163fa160b8be34b35fd9e82e80e76766 Mon Sep 17 00:00:00 2001
From: jordanschnell <jordan.schnell@noaa.gov>
Date: Wed, 20 Mar 2024 13:37:28 +0000
Subject: [PATCH 05/16] cleanup

---
 sorc/chgres_cube.fd/atm_input_data.F90 | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/sorc/chgres_cube.fd/atm_input_data.F90 b/sorc/chgres_cube.fd/atm_input_data.F90
index ef974e907..834e58571 100644
--- a/sorc/chgres_cube.fd/atm_input_data.F90
+++ b/sorc/chgres_cube.fd/atm_input_data.F90
@@ -2480,6 +2480,7 @@ subroutine read_input_atm_grib2_file(localpet)
    if ( (trim(external_model) .eq. 'RAP' .or. &  ! for smoke conversion
        trim(external_model) .eq. 'HRRR' ) .and. &
        tracers_input_vmap(n) == trac_names_vmap(15)) then
+
     if (localpet == 0) then
 
     print*,"- READ PRESSURE FOR SMOKE CONVERSION."
@@ -2512,6 +2513,7 @@ subroutine read_input_atm_grib2_file(localpet)
     enddo
 
     endif  ! localpet == 0
+
    endif   ! read pressure for smoke conversion
 
    if (tracers_input_vmap(n) == trac_names_vmap(15) .and. &

From 8704aa4d7ad7096becfc1f28c0cbb23e37103984 Mon Sep 17 00:00:00 2001
From: jordanschnell <jordan.schnell@noaa.gov>
Date: Wed, 20 Mar 2024 14:19:04 +0000
Subject: [PATCH 06/16] Fix character length in massden

---
 sorc/chgres_cube.fd/atm_input_data.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sorc/chgres_cube.fd/atm_input_data.F90 b/sorc/chgres_cube.fd/atm_input_data.F90
index 834e58571..b9ed4dcbf 100644
--- a/sorc/chgres_cube.fd/atm_input_data.F90
+++ b/sorc/chgres_cube.fd/atm_input_data.F90
@@ -2038,7 +2038,7 @@ subroutine read_input_atm_grib2_file(localpet)
  trac_names_vmap = (/"sphum   ", "liq_wat ", "o3mr    ", "ice_wat ", &
                      "rainwat ", "snowwat ", "graupel ", "cld_amt ", "ice_nc  ", &
                      "rain_nc ", "water_nc", "liq_aero", "ice_aero", &
-                     "sgs_tke ", "massden"/)
+                     "sgs_tke ", "massden "/)
 
  tracers_default = (/"sphum   ", "liq_wat ", "o3mr    ", "ice_wat ", &
                      "rainwat ", "snowwat ", "graupel ", "cld_amt ", "ice_nc  ", &

From fb62769b467797fce8a7f8866226cd5dc00ac4f1 Mon Sep 17 00:00:00 2001
From: jordanschnell <jordan.schnell@noaa.gov>
Date: Wed, 2 Oct 2024 19:53:55 +0000
Subject: [PATCH 07/16] Created seperate file that contains smoke variable and
 removed smoke from the original varmap

---
 parm/varmap_tables/GSDphys_smoke_var_map.txt | 28 ++++++++++++++++++++
 parm/varmap_tables/GSDphys_var_map.txt       |  1 -
 2 files changed, 28 insertions(+), 1 deletion(-)
 create mode 100644 parm/varmap_tables/GSDphys_smoke_var_map.txt

diff --git a/parm/varmap_tables/GSDphys_smoke_var_map.txt b/parm/varmap_tables/GSDphys_smoke_var_map.txt
new file mode 100644
index 000000000..0d7215fea
--- /dev/null
+++ b/parm/varmap_tables/GSDphys_smoke_var_map.txt
@@ -0,0 +1,28 @@
+dzdt                dzdt      set_to_fill   0         D
+delta_p             delp      skip          0         D
+sphum               sphum     intrp         1E-7      T
+liq_wat             liq_wat   intrp         0         T
+o3mr                o3mr      intrp         1E-7      T
+rainwat             rainwat   intrp         0         T
+ice_wat             ice_wat   intrp         0         T
+snowwat             snowwat   intrp         0         T
+graupel             graupel   intrp         0         T
+ice_nc              ice_nc    intrp         -1.0      T
+rain_nc             rain_nc   intrp         -1.0      T
+water_nc            water_nc  intrp         -1.0      T
+liq_aero            liq_aero  intrp         0         T
+ice_aero            ice_aero  intrp         0         T
+sgs_tke             sgs_tke   intrp         0         T
+vtype               vtype     skip          0         S
+sotype              stype     skip          0         S
+vfrac               vfrac     skip          0         S
+fricv               uustar    skip          0         S
+sfcr                zorl      set_to_fill   0.01      S
+soilw               smc       stop          0         S
+soilt               stc       stop          0         S
+cnwat               cnwat     set_to_fill   0.0       S
+icetk               icetk     set_to_fill   265.0     S
+weasd               weasd     set_to_fill   0.0       S
+snod                snod      set_to_fill   0.0       S
+tprcp               tprcp     set_to_fill   0.0       S
+massden             smoke     set_to_fill   1E-12     T	
diff --git a/parm/varmap_tables/GSDphys_var_map.txt b/parm/varmap_tables/GSDphys_var_map.txt
index 0d7215fea..05544006a 100644
--- a/parm/varmap_tables/GSDphys_var_map.txt
+++ b/parm/varmap_tables/GSDphys_var_map.txt
@@ -25,4 +25,3 @@ icetk               icetk     set_to_fill   265.0     S
 weasd               weasd     set_to_fill   0.0       S
 snod                snod      set_to_fill   0.0       S
 tprcp               tprcp     set_to_fill   0.0       S
-massden             smoke     set_to_fill   1E-12     T	

From 89db7a9785049bb22487bf8b77bb905bcf3a63c0 Mon Sep 17 00:00:00 2001
From: jordanschnell <jordan.schnell@noaa.gov>
Date: Wed, 16 Oct 2024 15:40:03 +0000
Subject: [PATCH 08/16] add regtests for smoke

---
 .../chgres_cube/13km.conus.rap-smoke.grib2.sh | 102 ++++++++++++++++++
 reg_tests/chgres_cube/driver.jet.sh           |  92 +++++++++++-----
 2 files changed, 166 insertions(+), 28 deletions(-)
 create mode 100755 reg_tests/chgres_cube/13km.conus.rap-smoke.grib2.sh

diff --git a/reg_tests/chgres_cube/13km.conus.rap-smoke.grib2.sh b/reg_tests/chgres_cube/13km.conus.rap-smoke.grib2.sh
new file mode 100755
index 000000000..e80e05794
--- /dev/null
+++ b/reg_tests/chgres_cube/13km.conus.rap-smoke.grib2.sh
@@ -0,0 +1,102 @@
+#!/bin/bash
+
+#-----------------------------------------------------------------------------
+# Invoke chgres to create 13-km CONUS coldstart files using RAP GRIB2 data
+# as input.  The coldstart files are then compared to baseline files
+# using the 'nccmp' utility.  This script is run by the machine specific 
+# driver script.
+#-----------------------------------------------------------------------------
+
+set -x
+
+export DATA=$OUTDIR/13km_conus_rap-smoke_grib2
+rm -fr $DATA
+
+export CRES=778
+export KMRES=13km
+export FIXfv3=${HOMEreg}/fix/RRFS_CONUS_${KMRES}
+
+export COMIN=${HOMEreg}/input_data/rap.grib2
+
+export GRIB2_FILE_INPUT=1921221000900
+export VCOORD_FILE=${HOMEufs}/fix/am/global_hyblev.l64.txt
+export VARMAP_FILE=${HOMEufs}/parm/varmap_tables/GSDphys_smoke_var_map.txt
+export INPUT_TYPE='grib2'
+export CONVERT_NST=".false."
+export OROG_FILES_TARGET_GRID="C778_oro_data.tile7.nc"
+export REGIONAL=1
+export HALO_BLEND=0
+export HALO_BNDY=4 
+export CDATE=2019080100
+export EXTERNAL_MODEL="RAP"
+export NSOILL_OUT=9
+export TRACERS_TARGET='"NULL"'
+export TRACERS_INPUT='"NULL"'
+export SOTYP_FROM_CLIMO=.false.
+export VGTYP_FROM_CLIMO=.false.
+export VGFRC_FROM_CLIMO=.true.
+export MINMAX_VGFRC_FROM_CLIMO=.true.
+export TG3_FROM_SOIL=.true.
+export LAI_FROM_CLIMO=.true.
+export GEOGRID_FILE_INPUT=${HOMEufs}/fix/am/geo_em.d01.nc_RAPX
+
+export OMP_NUM_THREADS_CH=${OMP_NUM_THREADS:-1}
+
+NCCMP=${NCCMP:-$(which nccmp)}
+
+#-----------------------------------------------------------------------------
+# Invoke chgres program.
+#-----------------------------------------------------------------------------
+
+echo "Starting at: " `date`
+
+${HOMEufs}/ush/chgres_cube.sh
+
+iret=$?
+if [ $iret -ne 0 ]; then
+  set +x
+  echo "<<< 13-km CONUS RAP-SMOKE W/ GSD PHYSICS AND SFC FROM FILE GRIB2 TEST FAILED. <<<"
+  exit $iret
+fi
+
+echo "Ending at: " `date`
+
+#-----------------------------------------------------------------------------
+# Compare output from chgres to baseline set of data.
+#
+# orion's nccmp utility does not work with the netcdf
+# required to run ufs_utils.  So swap it.
+#-----------------------------------------------------------------------------
+
+machine=${machine:-NULL}
+if [ $machine == 'orion' ]; then
+  module unload netcdfp/4.7.4.release
+  module load netcdf/4.7.2
+fi
+
+cd $DATA
+
+test_failed=0
+for files in *.nc
+do
+  if [ -f $files ]; then
+    echo CHECK $files
+    $NCCMP -dmfqS $files $HOMEreg/baseline_data/13km_conus_rap_grib2/$files
+    iret=$?
+    if [ $iret -ne 0 ]; then
+      test_failed=1
+    fi
+  fi
+done
+
+set +x
+if [ $test_failed -ne 0 ]; then
+  echo "<<< 13-km CONUS RAP-SMOKE W/ GSD PHYSICS AND SFC FROM FILE GRIB2 TEST FAILED. >>>"
+  if [ "$UPDATE_BASELINE" = "TRUE" ]; then
+    $HOMEufs/reg_tests/update_baseline.sh $HOMEreg "13km_conus_rap-smoke_grib2" $commit_num
+  fi
+else
+  echo "<<< 13-km CONUS RAP-SMOKE W/ GSD PHYSICS AND SFC FROM FILE GRIB2 TEST PASSED. >>>"
+fi
+
+exit 0
diff --git a/reg_tests/chgres_cube/driver.jet.sh b/reg_tests/chgres_cube/driver.jet.sh
index f3b5ec1b5..0d2b9c42d 100755
--- a/reg_tests/chgres_cube/driver.jet.sh
+++ b/reg_tests/chgres_cube/driver.jet.sh
@@ -7,15 +7,15 @@
 # Set WORK_DIR to a general working location outside the UFS_UTILS directory.
 # The exact working directory (OUTDIR) will be WORK_DIR/reg_tests/chgres-cube. 
 # Set the PROJECT_CODE and QUEUE as appropriate.  To see which projects you 
-# are authorized to use, type "account_params".
+#are authorized to use, type "account_params".
 #
 # Invoke the script with no arguments.  A series of daisy-
 # chained jobs will be submitted.  To check the queue, type:
 # "squeue -u USERNAME".
 #
-# The run output will be stored in OUTDIR.  Standard output from
-# each test will be placed in its own log file. Once the suite
-# has completed, a summary of results is placed in SUM_FILE.
+# The run output will be stored in OUTDIR.  Log output from the suite
+# will be in LOG_FILE.  Once the suite has completed, a summary is
+# placed in SUM_FILE.
 #
 # A test fails when its output does not match the baseline files as
 # determined by the "nccmp" utility.  The baseline files are stored in
@@ -33,7 +33,7 @@ module list
 export OUTDIR="${WORK_DIR:-/lfs5/HFIP/emcda/$LOGNAME/stmp}"
 export OUTDIR="${OUTDIR}/reg-tests/chgres-cube"
 
-PROJECT_CODE="${PROJECT_CODE:-hfv3gfs}"
+PROJECT_CODE="rtwbl" #"${PROJECT_CODE:-hfv3gfs}"
 QUEUE="${QUEUE:-batch}"
 
 export machine="jet"
@@ -85,104 +85,140 @@ TEST2=$(sbatch --parsable --partition=xjet --nodes=2 --ntasks-per-node=6 -t 0:10
       --exclusive -o $LOG_FILE -e $LOG_FILE ./c192.fv3.history.sh)
 
 #-----------------------------------------------------------------------------
-# Initialize C96 using FV3 gaussian netcdf files.
+# Initialize C96 using FV3 gaussian nemsio files.
 #-----------------------------------------------------------------------------
 
 LOG_FILE=consistency.log03
 export OMP_NUM_THREADS=1
-TEST3=$(sbatch --parsable --partition=xjet --nodes=2 --ntasks-per-node=6 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.netcdf \
+TEST3=$(sbatch --parsable --partition=xjet --nodes=2 --ntasks-per-node=6 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.nemsio \
+      --exclusive -o $LOG_FILE -e $LOG_FILE ./c96.fv3.nemsio.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize C96 using spectral GFS sigio/sfcio files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log04
+export OMP_NUM_THREADS=6   # should match cpus-per-task
+TEST4=$(sbatch --parsable --partition=xjet --nodes=4 --ntasks-per-node=3 --cpus-per-task=6 -t 0:25:00 \
+      --exclusive -A $PROJECT_CODE -q $QUEUE -J c96.gfs.sigio -o $LOG_FILE -e $LOG_FILE ./c96.gfs.sigio.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize C96 using spectral GFS gaussian nemsio files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log05
+export OMP_NUM_THREADS=1
+TEST5=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J c96.gfs.nemsio \
+      --exclusive -o $LOG_FILE -e $LOG_FILE ./c96.gfs.nemsio.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize C96 using FV3 gaussian netcdf files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log06
+export OMP_NUM_THREADS=1
+TEST6=$(sbatch --parsable --partition=xjet --nodes=2 --ntasks-per-node=6 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.netcdf \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./c96.fv3.netcdf.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize C192 using GFS GRIB2 data.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log04
+LOG_FILE=consistency.log07
 export OMP_NUM_THREADS=1
-TEST4=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.gfs.grib2 \
+TEST7=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.gfs.grib2 \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./c192.gfs.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 25-KM USING GFS GRIB2 files.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log05
+LOG_FILE=consistency.log08
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST5=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 25km.conus.gfs.grib2.conus \
+TEST8=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 25km.conus.gfs.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./25km.conus.gfs.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 3-KM USING HRRR GRIB2 file WITH GFS PHYSICS.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log06
+LOG_FILE=consistency.log09
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST6=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 3km.conus.hrrr.gfssdf.grib2.conus \
+TEST9=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 3km.conus.hrrr.gfssdf.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./3km.conus.hrrr.gfssdf.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 3-KM USING HRRR GRIB2 file WITH GSD PHYSICS AND SFC VARS FROM FILE.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log07
+LOG_FILE=consistency.log10
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST7=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=3 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 3km.conus.hrrr.newsfc.grib2.conus \
+TEST10=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=3 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 3km.conus.hrrr.newsfc.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./3km.conus.hrrr.newsfc.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 13-KM USING NAM GRIB2 file WITH GFS PHYSICS .
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log08
+LOG_FILE=consistency.log11
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST8=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.nam.grib2.conus \
+TEST11=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.nam.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./13km.conus.nam.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 13-KM USING RAP GRIB2 file WITH GSD PHYSICS .
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log09
+LOG_FILE=consistency.log12
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST9=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap.grib2.conus \
+TEST12=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./13km.conus.rap.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 13-KM NA USING NCEI GFS GRIB2 file WITH GFS PHYSICS .
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log10
+LOG_FILE=consistency.log13
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST10=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 13km.na.gfs.ncei.grib2.conus \
+TEST13=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 13km.na.gfs.ncei.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./13km.na.gfs.ncei.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize C96 WAM IC using FV3 gaussian netcdf files.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log11
+LOG_FILE=consistency.log14
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST11=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.netcdf2wam \
+TEST14=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.netcdf2wam \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./c96.fv3.netcdf2wam.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 25-KM USING GFS PGRIB2+BGRIB2 files.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log12
+LOG_FILE=consistency.log15
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST12=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 25km.conus.gfs.pbgrib2.conus \
+TEST15=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 25km.conus.gfs.pbgrib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./25km.conus.gfs.pbgrib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize C96 using GEFS GRIB2 data.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log13
+LOG_FILE=consistency.log16
 export OMP_NUM_THREADS=1
-TEST13=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c96.gefs.grib2 \
+TEST16=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c96.gefs.grib2 \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./c96.gefs.grib2.sh)
 
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING RAP-SMOKE GRIB2 file WITH GSD PHYSICS .
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log17
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST17=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap-smoke.grib2.conus \
+      --exclusive -o $LOG_FILE -e $LOG_FILE ./13km.conus.rap-smoke.grib2.sh)
+
 #-----------------------------------------------------------------------------
 # Create summary log.
 #-----------------------------------------------------------------------------
@@ -190,7 +226,7 @@ TEST13=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:0
 LOG_FILE=consistency.log
 sbatch --partition=xjet --nodes=1  -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE -d\
-       afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13 << EOF
+       afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14:$TEST15:$TEST16:$TEST17 << EOF
 #!/bin/bash
 grep -a '<<<' $LOG_FILE*  > $SUM_FILE
 EOF

From f63fbbe3603af4a24412fbb8ad2c5031320e79c6 Mon Sep 17 00:00:00 2001
From: jordanschnell <jordan.schnell@noaa.gov>
Date: Wed, 16 Oct 2024 15:47:45 +0000
Subject: [PATCH 09/16] update reg

---
 reg_tests/chgres_cube/driver.jet.sh | 87 ++++++++++-------------------
 1 file changed, 30 insertions(+), 57 deletions(-)

diff --git a/reg_tests/chgres_cube/driver.jet.sh b/reg_tests/chgres_cube/driver.jet.sh
index 0d2b9c42d..e240144ec 100755
--- a/reg_tests/chgres_cube/driver.jet.sh
+++ b/reg_tests/chgres_cube/driver.jet.sh
@@ -7,15 +7,15 @@
 # Set WORK_DIR to a general working location outside the UFS_UTILS directory.
 # The exact working directory (OUTDIR) will be WORK_DIR/reg_tests/chgres-cube. 
 # Set the PROJECT_CODE and QUEUE as appropriate.  To see which projects you 
-#are authorized to use, type "account_params".
+# are authorized to use, type "account_params".
 #
 # Invoke the script with no arguments.  A series of daisy-
 # chained jobs will be submitted.  To check the queue, type:
 # "squeue -u USERNAME".
 #
-# The run output will be stored in OUTDIR.  Log output from the suite
-# will be in LOG_FILE.  Once the suite has completed, a summary is
-# placed in SUM_FILE.
+# The run output will be stored in OUTDIR.  Standard output from
+# each test will be placed in its own log file. Once the suite
+# has completed, a summary of results is placed in SUM_FILE.
 #
 # A test fails when its output does not match the baseline files as
 # determined by the "nccmp" utility.  The baseline files are stored in
@@ -33,7 +33,7 @@ module list
 export OUTDIR="${WORK_DIR:-/lfs5/HFIP/emcda/$LOGNAME/stmp}"
 export OUTDIR="${OUTDIR}/reg-tests/chgres-cube"
 
-PROJECT_CODE="rtwbl" #"${PROJECT_CODE:-hfv3gfs}"
+PROJECT_CODE="${PROJECT_CODE:-hfv3gfs}"
 QUEUE="${QUEUE:-batch}"
 
 export machine="jet"
@@ -84,139 +84,112 @@ export OMP_NUM_THREADS=1
 TEST2=$(sbatch --parsable --partition=xjet --nodes=2 --ntasks-per-node=6 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J c192.fv3.history \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./c192.fv3.history.sh)
 
-#-----------------------------------------------------------------------------
-# Initialize C96 using FV3 gaussian nemsio files.
-#-----------------------------------------------------------------------------
-
-LOG_FILE=consistency.log03
-export OMP_NUM_THREADS=1
-TEST3=$(sbatch --parsable --partition=xjet --nodes=2 --ntasks-per-node=6 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.nemsio \
-      --exclusive -o $LOG_FILE -e $LOG_FILE ./c96.fv3.nemsio.sh)
-
-#-----------------------------------------------------------------------------
-# Initialize C96 using spectral GFS sigio/sfcio files.
-#-----------------------------------------------------------------------------
-
-LOG_FILE=consistency.log04
-export OMP_NUM_THREADS=6   # should match cpus-per-task
-TEST4=$(sbatch --parsable --partition=xjet --nodes=4 --ntasks-per-node=3 --cpus-per-task=6 -t 0:25:00 \
-      --exclusive -A $PROJECT_CODE -q $QUEUE -J c96.gfs.sigio -o $LOG_FILE -e $LOG_FILE ./c96.gfs.sigio.sh)
-
-#-----------------------------------------------------------------------------
-# Initialize C96 using spectral GFS gaussian nemsio files.
-#-----------------------------------------------------------------------------
-
-LOG_FILE=consistency.log05
-export OMP_NUM_THREADS=1
-TEST5=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J c96.gfs.nemsio \
-      --exclusive -o $LOG_FILE -e $LOG_FILE ./c96.gfs.nemsio.sh)
-
 #-----------------------------------------------------------------------------
 # Initialize C96 using FV3 gaussian netcdf files.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log06
+LOG_FILE=consistency.log03
 export OMP_NUM_THREADS=1
-TEST6=$(sbatch --parsable --partition=xjet --nodes=2 --ntasks-per-node=6 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.netcdf \
+TEST3=$(sbatch --parsable --partition=xjet --nodes=2 --ntasks-per-node=6 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.netcdf \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./c96.fv3.netcdf.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize C192 using GFS GRIB2 data.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log07
+LOG_FILE=consistency.log04
 export OMP_NUM_THREADS=1
-TEST7=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.gfs.grib2 \
+TEST4=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.gfs.grib2 \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./c192.gfs.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 25-KM USING GFS GRIB2 files.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log08
+LOG_FILE=consistency.log05
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST8=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 25km.conus.gfs.grib2.conus \
+TEST5=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 25km.conus.gfs.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./25km.conus.gfs.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 3-KM USING HRRR GRIB2 file WITH GFS PHYSICS.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log09
+LOG_FILE=consistency.log06
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST9=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 3km.conus.hrrr.gfssdf.grib2.conus \
+TEST6=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 3km.conus.hrrr.gfssdf.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./3km.conus.hrrr.gfssdf.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 3-KM USING HRRR GRIB2 file WITH GSD PHYSICS AND SFC VARS FROM FILE.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log10
+LOG_FILE=consistency.log07
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST10=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=3 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 3km.conus.hrrr.newsfc.grib2.conus \
+TEST7=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=3 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 3km.conus.hrrr.newsfc.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./3km.conus.hrrr.newsfc.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 13-KM USING NAM GRIB2 file WITH GFS PHYSICS .
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log11
+LOG_FILE=consistency.log08
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST11=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.nam.grib2.conus \
+TEST8=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.nam.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./13km.conus.nam.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 13-KM USING RAP GRIB2 file WITH GSD PHYSICS .
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log12
+LOG_FILE=consistency.log09
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST12=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap.grib2.conus \
+TEST9=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./13km.conus.rap.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 13-KM NA USING NCEI GFS GRIB2 file WITH GFS PHYSICS .
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log13
+LOG_FILE=consistency.log10
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST13=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 13km.na.gfs.ncei.grib2.conus \
+TEST10=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 13km.na.gfs.ncei.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./13km.na.gfs.ncei.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize C96 WAM IC using FV3 gaussian netcdf files.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log14
+LOG_FILE=consistency.log11
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST14=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.netcdf2wam \
+TEST11=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=2 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.netcdf2wam \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./c96.fv3.netcdf2wam.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 25-KM USING GFS PGRIB2+BGRIB2 files.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log15
+LOG_FILE=consistency.log12
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST15=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 25km.conus.gfs.pbgrib2.conus \
+TEST12=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 25km.conus.gfs.pbgrib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./25km.conus.gfs.pbgrib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize C96 using GEFS GRIB2 data.
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log16
+LOG_FILE=consistency.log13
 export OMP_NUM_THREADS=1
-TEST16=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c96.gefs.grib2 \
+TEST13=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c96.gefs.grib2 \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./c96.gefs.grib2.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 13-KM USING RAP-SMOKE GRIB2 file WITH GSD PHYSICS .
 #-----------------------------------------------------------------------------
 
-LOG_FILE=consistency.log17
+LOG_FILE=consistency.log14
 export OMP_NUM_THREADS=1   # should match cpus-per-task
-TEST17=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap-smoke.grib2.conus \
+TEST14=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap-smoke.grib2.conus \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./13km.conus.rap-smoke.grib2.sh)
 
 #-----------------------------------------------------------------------------
@@ -226,7 +199,7 @@ TEST17=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:0
 LOG_FILE=consistency.log
 sbatch --partition=xjet --nodes=1  -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE -d\
-       afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14:$TEST15:$TEST16:$TEST17 << EOF
+       afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14 << EOF
 #!/bin/bash
 grep -a '<<<' $LOG_FILE*  > $SUM_FILE
 EOF

From a4de98bad9031e13d87ded66c9893dd001cb7a24 Mon Sep 17 00:00:00 2001
From: "jordan.schnell" <jordan.schnell@noaa.gov>
Date: Mon, 21 Oct 2024 15:29:25 +0000
Subject: [PATCH 10/16] add hera regtest

---
 reg_tests/chgres_cube/13km.conus.rap-smoke.grib2.sh |  7 ++++---
 reg_tests/chgres_cube/driver.hera.sh                | 13 ++++++++++++-
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/reg_tests/chgres_cube/13km.conus.rap-smoke.grib2.sh b/reg_tests/chgres_cube/13km.conus.rap-smoke.grib2.sh
index e80e05794..74fc88df5 100755
--- a/reg_tests/chgres_cube/13km.conus.rap-smoke.grib2.sh
+++ b/reg_tests/chgres_cube/13km.conus.rap-smoke.grib2.sh
@@ -1,8 +1,9 @@
 #!/bin/bash
 
 #-----------------------------------------------------------------------------
-# Invoke chgres to create 13-km CONUS coldstart files using RAP GRIB2 data
-# as input.  The coldstart files are then compared to baseline files
+# Invoke chgres to create 13-km CONUS coldstart files using RAP-SMOKE GRIB2 data
+# as input. i.e., if one desires MASSDEN/SMOKE in the ICs/LBCS
+# The coldstart files are then compared to baseline files
 # using the 'nccmp' utility.  This script is run by the machine specific 
 # driver script.
 #-----------------------------------------------------------------------------
@@ -81,7 +82,7 @@ for files in *.nc
 do
   if [ -f $files ]; then
     echo CHECK $files
-    $NCCMP -dmfqS $files $HOMEreg/baseline_data/13km_conus_rap_grib2/$files
+    $NCCMP -dmfqS $files $HOMEreg/baseline_data/13km_conus_rap-smoke_grib2/$files
     iret=$?
     if [ $iret -ne 0 ]; then
       test_failed=1
diff --git a/reg_tests/chgres_cube/driver.hera.sh b/reg_tests/chgres_cube/driver.hera.sh
index cd817ad43..86bf372b4 100755
--- a/reg_tests/chgres_cube/driver.hera.sh
+++ b/reg_tests/chgres_cube/driver.hera.sh
@@ -187,6 +187,17 @@ export OMP_NUM_THREADS=1   # should match cpus-per-task
 TEST13=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c96.gefs.grib2 \
       -o $LOG_FILE -e $LOG_FILE ./c96.gefs.grib2.sh)
 
+
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING RAP-SMOKE GRIB2 file WITH GSD PHYSICS .
+#-----------------------------------------------------------------------------
+LOG_FILE=consistency.log14
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST14=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap-smoke.grib2.conus \
+      -o $LOG_FILE -e $LOG_FILE ./13km.conus.rap-smoke.grib2.sh)
+
+
+
 #-----------------------------------------------------------------------------
 # Create summary log.
 #-----------------------------------------------------------------------------
@@ -194,7 +205,7 @@ TEST13=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_
 LOG_FILE=consistency.log
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
       --open-mode=append -q $QUEUE -d\
-     afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13 << EOF
+     afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}??  > summary.log
 EOF

From 0a954d1dd41c9786df5bbe7a7e4ddfe5af611aa4 Mon Sep 17 00:00:00 2001
From: "jordan.schnell" <jordan.schnell@noaa.gov>
Date: Mon, 21 Oct 2024 19:24:25 +0000
Subject: [PATCH 11/16] Update drivers for hercules, wcoss2, and orion

---
 reg_tests/chgres_cube/driver.hercules.sh | 11 ++++++++++-
 reg_tests/chgres_cube/driver.orion.sh    | 11 ++++++++++-
 reg_tests/chgres_cube/driver.wcoss2.sh   | 11 ++++++++++-
 3 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/reg_tests/chgres_cube/driver.hercules.sh b/reg_tests/chgres_cube/driver.hercules.sh
index 2ef2800b3..05e80bfc5 100755
--- a/reg_tests/chgres_cube/driver.hercules.sh
+++ b/reg_tests/chgres_cube/driver.hercules.sh
@@ -188,13 +188,22 @@ export OMP_NUM_THREADS=1  # needs to match cpus-per-task
 TEST13=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 --mem=75G -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c96.gefs.grib2 \
       --open-mode=append -o $LOG_FILE13 -e $LOG_FILE13 ./c96.gefs.grib2.sh)
 
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING RAP-SMOKE GRIB2 file WITH GSD PHYSICS.
+#-----------------------------------------------------------------------------
+
+LOG_FILE14=${LOG_FILE}14
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST14=$(sbatch --parsable --ntasks-per-node=12 --nodes=1 --mem=75G -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap-smoke.grib2 \
+      --open-mode=append -o $LOG_FILE14 -e $LOG_FILE14 ./13km.conus.rap-smoke.grib2.sh)
+
 #-----------------------------------------------------------------------------
 # Create summary log.
 #-----------------------------------------------------------------------------
 
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE \
-       -d afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13 << EOF
+       -d afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}*  > $SUM_FILE
 EOF
diff --git a/reg_tests/chgres_cube/driver.orion.sh b/reg_tests/chgres_cube/driver.orion.sh
index ae1ebf8ce..2c57df30b 100755
--- a/reg_tests/chgres_cube/driver.orion.sh
+++ b/reg_tests/chgres_cube/driver.orion.sh
@@ -186,13 +186,22 @@ export OMP_NUM_THREADS=1  # needs to match cpus-per-task
 TEST13=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 --mem=75G -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c96.gefs.grib2 \
       --open-mode=append -o $LOG_FILE13 -e $LOG_FILE13 ./c96.gefs.grib2.sh)
 
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING RAP-SMOKE GRIB2 file WITH GSD PHYSICS.
+#-----------------------------------------------------------------------------
+
+LOG_FILE14=${LOG_FILE}14
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST14=$(sbatch --parsable --ntasks-per-node=12 --nodes=1 --mem=75G -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap-smoke.grib2 \
+      --open-mode=append -o $LOG_FILE14 -e $LOG_FILE14 ./13km.conus.rap-smoke.grib2.sh)
+
 #-----------------------------------------------------------------------------
 # Create summary log.
 #-----------------------------------------------------------------------------
 
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE \
-       -d afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13 << EOF
+       -d afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}*  > $SUM_FILE
 EOF
diff --git a/reg_tests/chgres_cube/driver.wcoss2.sh b/reg_tests/chgres_cube/driver.wcoss2.sh
index fd81b4ea9..e38af7278 100755
--- a/reg_tests/chgres_cube/driver.wcoss2.sh
+++ b/reg_tests/chgres_cube/driver.wcoss2.sh
@@ -184,6 +184,15 @@ export APRUN="mpiexec -n 6 -ppn 6 --cpu-bind core"
 TEST13=$(qsub -V -o $LOG_FILE -e $LOG_FILE -q $QUEUE -A $PROJECT_CODE -l walltime=00:05:00 \
         -N c96.gefs.grib2 -l select=1:ncpus=6:ompthreads=1:mem=15GB $PWD/c96.gefs.grib2.sh)
 
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING RAP-SMOKE GRIB2 file WITH GSD PHYSICS.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log14
+export APRUN="mpiexec -n 6 -ppn 6 --cpu-bind core"
+TEST14=$(qsub -V -o $LOG_FILE -e $LOG_FILE -q $QUEUE -A $PROJECT_CODE -l walltime=00:05:00 \
+        -N 13km.conus.rap-smoke.grib2.conus -l select=1:ncpus=6:ompthreads=1:mem=15GB $PWD/13km.conus.rap-smoke.grib2.sh)
+
 #-----------------------------------------------------------------------------
 # Create summary log.
 #-----------------------------------------------------------------------------
@@ -191,7 +200,7 @@ TEST13=$(qsub -V -o $LOG_FILE -e $LOG_FILE -q $QUEUE -A $PROJECT_CODE -l walltim
 LOG_FILE=consistency.log
 qsub -V -o ${LOG_FILE} -e ${LOG_FILE} -q $QUEUE -A $PROJECT_CODE -l walltime=00:01:00 \
         -N chgres_summary -l select=1:ncpus=1:mem=100MB \
-        -W depend=afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13 << EOF
+        -W depend=afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14 << EOF
 #!/bin/bash
 cd ${this_dir}
 grep -a '<<<' ${LOG_FILE}?? | grep -v echo > $SUM_FILE

From 6dadfcac21d751d05332585a7a3e7d11d8809b0f Mon Sep 17 00:00:00 2001
From: "jordan.schnell" <jordan.schnell@noaa.gov>
Date: Mon, 4 Nov 2024 19:05:58 +0000
Subject: [PATCH 12/16] doc test

---
 docs/source/chgres_cube.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/source/chgres_cube.rst b/docs/source/chgres_cube.rst
index 7d3c9f3c1..f32e3a241 100644
--- a/docs/source/chgres_cube.rst
+++ b/docs/source/chgres_cube.rst
@@ -417,6 +417,8 @@ Column 1: Name the code searches for in the table. Do not change.  Some definiti
       * hice - sea/lake ice thickness
       * weasd - snow liquid equivalent
       * snod - physical snow depth
+      ---Optional---
+      * massden - smoke mass mixing ratio (only available in RAP/HRRR-Smoke)
 
 Column 2: Name of the variable in the output “coldstart” files. Unimplemented.
 

From 5bd91ce7a7e82c9ef2ad68a24195a157a2daab17 Mon Sep 17 00:00:00 2001
From: "jordan.schnell" <jordan.schnell@noaa.gov>
Date: Mon, 4 Nov 2024 19:08:57 +0000
Subject: [PATCH 13/16] more

---
 docs/source/chgres_cube.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/chgres_cube.rst b/docs/source/chgres_cube.rst
index f32e3a241..8c9e08738 100644
--- a/docs/source/chgres_cube.rst
+++ b/docs/source/chgres_cube.rst
@@ -418,7 +418,7 @@ Column 1: Name the code searches for in the table. Do not change.  Some definiti
       * weasd - snow liquid equivalent
       * snod - physical snow depth
       ---Optional---
-      * massden - smoke mass mixing ratio (only available in RAP/HRRR-Smoke)
+      * massden - smoke mass mixing ratio (only available in RAP/HRRR-Smoke and use of the GSDphys_smoke_var_map.txt varmap)
 
 Column 2: Name of the variable in the output “coldstart” files. Unimplemented.
 

From 8283affefbff5f83f4ecbdc4a107e05ff6b0282c Mon Sep 17 00:00:00 2001
From: "jordan.schnell" <jordan.schnell@noaa.gov>
Date: Mon, 4 Nov 2024 20:01:58 +0000
Subject: [PATCH 14/16] format fix attempt

---
 docs/source/chgres_cube.rst | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/source/chgres_cube.rst b/docs/source/chgres_cube.rst
index 8c9e08738..8a0da06c5 100644
--- a/docs/source/chgres_cube.rst
+++ b/docs/source/chgres_cube.rst
@@ -417,7 +417,9 @@ Column 1: Name the code searches for in the table. Do not change.  Some definiti
       * hice - sea/lake ice thickness
       * weasd - snow liquid equivalent
       * snod - physical snow depth
-      ---Optional---
+
+      --Optional--
+
       * massden - smoke mass mixing ratio (only available in RAP/HRRR-Smoke and use of the GSDphys_smoke_var_map.txt varmap)
 
 Column 2: Name of the variable in the output “coldstart” files. Unimplemented.

From 5b273d00dbd51f0ed32d6f2c7c1c4cbddbef8d51 Mon Sep 17 00:00:00 2001
From: "jordan.schnell" <jordan.schnell@noaa.gov>
Date: Mon, 4 Nov 2024 20:04:08 +0000
Subject: [PATCH 15/16] minimum docs

---
 docs/source/chgres_cube.rst | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/docs/source/chgres_cube.rst b/docs/source/chgres_cube.rst
index 8a0da06c5..194275a57 100644
--- a/docs/source/chgres_cube.rst
+++ b/docs/source/chgres_cube.rst
@@ -417,10 +417,7 @@ Column 1: Name the code searches for in the table. Do not change.  Some definiti
       * hice - sea/lake ice thickness
       * weasd - snow liquid equivalent
       * snod - physical snow depth
-
-      --Optional--
-
-      * massden - smoke mass mixing ratio (only available in RAP/HRRR-Smoke and use of the GSDphys_smoke_var_map.txt varmap)
+      * massden - smoke mass mixing ratio
 
 Column 2: Name of the variable in the output “coldstart” files. Unimplemented.
 

From 828db08dc2f7d2299f2446b08ccbdb4096dd3c22 Mon Sep 17 00:00:00 2001
From: "jordan.schnell" <jordan.schnell@noaa.gov>
Date: Mon, 4 Nov 2024 20:34:03 +0000
Subject: [PATCH 16/16] remove note that only GFS physics suite is supported

---
 docs/source/chgres_cube.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/chgres_cube.rst b/docs/source/chgres_cube.rst
index 194275a57..5eeadebf9 100644
--- a/docs/source/chgres_cube.rst
+++ b/docs/source/chgres_cube.rst
@@ -389,7 +389,7 @@ Namelist variables with “input” in their name refer to data input to chgres_
 Variable Mapping (VARMAP) table
 -------------------------------
 
-The VARMAP table, set in the chgres_cube namelist (variable varmap_file), controls how chgres_cube handles variables that might be missing from the GRIB2 files. Since there are so many different versions of GRIB2 files, it's often uncertain what fields are available even if you know what source model the data is coming from.  Each file contains the following:  (Note, only the GFS physics suite is currently supported.)
+The VARMAP table, set in the chgres_cube namelist (variable varmap_file), controls how chgres_cube handles variables that might be missing from the GRIB2 files. Since there are so many different versions of GRIB2 files, it's often uncertain what fields are available even if you know what source model the data is coming from.  Each file contains the following columns:
 
 Column 1: Name the code searches for in the table. Do not change.  Some definitions: