Read the std. dev. instead of the variance

src/soca/LinearVariableChange/BkgErr/soca_bkgerr_mod.F90

@@ -61,25 +61,32 @@ subroutine soca_bkgerr_setup(self, f_conf, bkg, geom)
   integer :: i
   type(datetime) :: vdate
   character(len=800) :: fname = 'soca_bkgerrsoca.nc'
+  logical :: stddev, save_bkgerr
 
   self%geom => geom
 
   ! Allocate memory for bkgerror
   call self%std_bkgerr%copy(bkg)
   !call create_copy(self%std_bkgerr, bkg)
 
-  ! Read variance
+  ! Read variance (default) or standard deviation
   ! Precomputed from an ensemble of (K^-1 dx)
+  stddev = .false.
+  if (f_conf%has("standard deviation")) then
+     call f_conf%get_or_die("standard deviation", stddev)
+  end if
   call self%std_bkgerr%read(f_conf, vdate)
 
   ! Convert to standard deviation
-  do i=1,size(self%std_bkgerr%fields)
-    field => self%std_bkgerr%fields(i)
-    select case(field%name)
-    case ("tocn", "socn", "ssh")
-      field%val = sqrt(field%val)
-    end select
-  end do
+  if (.not.stddev) then
+    do i=1,size(self%std_bkgerr%fields)
+      field => self%std_bkgerr%fields(i)
+      select case(field%name)
+      case ("tocn", "socn", "ssh")
+        field%val = sqrt(field%val)
+      end select
+    end do
+  end if
 
   ! Get bounds from configuration
   call self%bounds%read(f_conf)
@@ -116,7 +123,10 @@ subroutine soca_bkgerr_setup(self, f_conf, bkg, geom)
   call self%bounds%apply(self%std_bkgerr)
 
   ! Save filtered background error
-  call self%std_bkgerr%write_file(fname)
+  if (f_conf%has("save bkgerr")) then
+     call f_conf%get_or_die("save bkgerr", save_bkgerr)
+     if (save_bkgerr) call self%std_bkgerr%write_file(fname)
+  end if
 
 end subroutine soca_bkgerr_setup
 

test/CMakeLists.txt

@@ -74,6 +74,7 @@ set( soca_test_input
   testinput/varchange_bkgerrfilt.yml
   testinput/varchange_bkgerrgodas.yml
   testinput/varchange_bkgerrsoca.yml
+  testinput/varchange_bkgerrsoca_stddev.yml
   testinput/varchange_horizfilt.yml
   testinput/varchange_vertconv.yml
 )
@@ -396,6 +397,10 @@ soca_add_test( NAME varchange_bkgerrsoca
                SRC  TestVariableChange.cc
                TEST_DEPENDS test_soca_gridgen )
 
+soca_add_test( NAME varchange_bkgerrsoca_stddev
+               SRC  TestVariableChange.cc
+               TEST_DEPENDS test_soca_gridgen )
+
 soca_add_test( NAME varchange_bkgerrgodas
                SRC  TestVariableChange.cc
                TEST_DEPENDS test_soca_gridgen )

test/testinput/varchange_bkgerrsoca_stddev.yml

@@ -0,0 +1,42 @@
+geometry:
+  geom_grid_file: data_generated/gridgen/soca_gridspec.72x35x25.nc
+  mom6_input_nml: data_static/72x35x25/input.nml
+  fields metadata: data_static/fields_metadata.yml
+
+background:
+  read_from_file: 1
+  date: &date 2018-04-15T00:00:00Z
+  basename: data_static/72x35x25/restarts/
+  ocn_filename: MOM.res.nc
+  ice_filename: cice.res.nc
+  state variables: &soca_vars [cicen, hicen, socn, tocn, ssh, hocn]
+
+linear variable change tests:
+- tolerance inverse: 1e-12
+  test inverse: 0
+  linear variable change:
+    input variables: *soca_vars
+    output variables: *soca_vars
+    linear variable changes:
+    - linear variable change name: BkgErrSOCA
+      tolerance inverse: 1e-12
+      test inverse: 1
+      read_from_file: 3
+      basename: data_static/72x35x25/
+      ocn_filename: ocn.bkgerror.nc
+      ice_filename: ice.bkgerror.nc
+      date: *date
+      standard deviation: true
+      save bkgerr: true
+      t_min: 0.0
+      t_max: 2.5
+      s_min: 0.0
+      s_max: 0.2
+      ssh_min: 0.0 # std ssh=0 => ssh balance applied as
+      ssh_max: 0.0 #              strong constraint
+      cicen_min: 0.1
+      cicen_max: 0.5
+      hicen_min: 10.0
+      hicen_max: 100.0
+      #fixed_std_sst: 0.005 # OK to create pretty increments
+      #fixed_std_sss: 0.001 # but that option should not exist!