Remove SOCA internal variable names (#1082)

* adjust print size automatically

* ssh

* tocn

* mld

* socn

* more vars

* make a bunch of tests work

* more tests updated

* all tests pass

* revert depth_below_sea_surface

* get rid of unused metadata fields

* fix everything else I forgot

* forgot a "<"

src/soca/Fields/Fields.cc

@@ -137,6 +137,12 @@ double Fields::norm() const {
 void Fields::print(std::ostream & os) const {
   os << std::endl << "  Valid time: " << validTime();
 
+  // find the longest field name, for use in formatting of the print
+  size_t maxNameLen = 0;
+  for (const auto & field : fieldSet_) {
+    maxNameLen = std::max(maxNameLen, field.name().size());
+  }
+
   // for each field
   for (const auto & field : fieldSet_) {
     size_t count = 0;
@@ -175,7 +181,7 @@ void Fields::print(std::ostream & os) const {
     if (count > 0) sum /= count;
 
     // done with this field, print information
-    os << std::endl << std::right << std::setw(7) << field.name()
+    os << std::endl << std::right << std::setw(maxNameLen) << field.name()
         << "   min="  <<  std::fixed << std::setw(12) <<
                           std::right << min
         << "   max="  <<  std::fixed << std::setw(12) <<

src/soca/Fields/FieldsMetadata.cc

@@ -33,21 +33,18 @@ FieldsMetadata::FieldsMetadata(const std::string & filename) {
     // read in portion of the values (not all are read in on the C++ side, until
     // needed)
     f->name = config.getString("name");
-    f->getvalName = config.getString("getval name", f->name);
-    f->getvalNameSurface = config.getString("getval name surface", "");
+    f->nameSurface = config.getString("name surface", "");
 
     // check for duplicates
     if (fieldMetadata_.count(f->name) > 0 ||
-        fieldMetadata_.count(f->getvalName) > 0 ||
-        fieldMetadata_.count(f->getvalNameSurface) > 0) {
+        fieldMetadata_.count(f->nameSurface) > 0) {
       util::abor1_cpp("Duplicate field metadata: " + f->name);
     }
 
     // insert into the maps, multiple copies are inserted for valid name
     fieldMetadata_[f->name] = f;
-    fieldMetadata_[f->getvalName] = f;
-    if (f->getvalNameSurface != "") {
-      fieldMetadata_[f->getvalNameSurface] = f;
+    if (f->nameSurface != "") {
+      fieldMetadata_[f->nameSurface] = f;
     }
   }
 }

src/soca/Fields/FieldsMetadata.h

@@ -21,10 +21,9 @@ namespace soca {
 /// variable name used by UFO, and the variable name used by UFO for the surface
 /// (if this is a 3D field).
 struct FieldMetadata {
-  std::string name;  ///< The internal (within soca) variable name.
-  std::string getvalName;  ///< The variable name used by UFO.
-  std::string getvalNameSurface;  ///< The variable name used by UFO for the surface
-                                  ///  (if this is a 3D field).
+  std::string name;  ///< The soca and JEDI name.
+  std::string nameSurface;  ///< The variable name used by UFO for the surface
+                            ///  (if this is a 3D field).
 };
 
 // --------------------------------------------------------------------------------------

src/soca/Fields/soca_fields_metadata_mod.F90

@@ -19,12 +19,11 @@ module soca_fields_metadata_mod
 !!
 !! Instances of these types are to be held by soca_fields_metadata
 type, public :: soca_field_metadata
-  character(len=:),  allocatable :: name     !< internal name used only by soca code
+  character(len=:),  allocatable :: name     !< name used by soca and JEDI
+  character(len=:),  allocatable :: name_surface  !< name used by UFO for the surface (if this is a 3D field)
   character(len=1)               :: grid     !< "h", "u" or "v"
   logical                        :: masked   !< should use land mask when interpolating
   character(len=:),  allocatable :: levels   !< "1", or "full_ocn"
-  character(len=:),  allocatable :: getval_name !< variable name used by UFO
-  character(len=:),  allocatable :: getval_name_surface  ! name used by UFO for the surface (if this is a 3D field)
   character(len=:),  allocatable :: io_file  !< the restart file domain (ocn, sfc, ice). Or if "CONSTANT" use the value in "constant_value"
   character(len=:),  allocatable :: io_name  !< the name use in the restart IO
   character(len=:),  allocatable :: property  !< physical property of the field, "none" or "positive_definite"
@@ -88,6 +87,9 @@ subroutine soca_fields_metadata_create(self, filename)
 
     call conf_list(i)%get_or_die("name", self%metadata(i)%name)
 
+    if(.not. conf_list(i)%get("name surface", str)) str=""
+    self%metadata(i)%name_surface = str
+
     if(.not. conf_list(i)%get("grid", str)) str = 'h'
     self%metadata(i)%grid = str
 
@@ -97,12 +99,6 @@ subroutine soca_fields_metadata_create(self, filename)
     if(.not. conf_list(i)%get("levels", str)) str = "1"
     self%metadata(i)%levels = str
 
-    if(.not. conf_list(i)%get("getval name", str)) str=self%metadata(i)%name
-    self%metadata(i)%getval_name = str
-
-    if(.not. conf_list(i)%get("getval name surface", str)) str=""
-    self%metadata(i)%getval_name_surface = str
-
     if(.not. conf_list(i)%get("io name", str)) str = ""
     self%metadata(i)%io_name = str
 
@@ -140,14 +136,9 @@ subroutine soca_fields_metadata_create(self, filename)
   do i=1,size(self%metadata)
     do j=i+1,size(self%metadata)
       if ( self%metadata(i)%name == self%metadata(j)%name .or. &
-           self%metadata(i)%name == self%metadata(j)%getval_name .or. &
-           self%metadata(i)%name == self%metadata(j)%getval_name_surface .or. &
-           self%metadata(i)%getval_name == self%metadata(j)%name .or. &
-           self%metadata(i)%getval_name == self%metadata(j)%getval_name .or. &
-           self%metadata(i)%getval_name == self%metadata(j)%getval_name_surface .or. &
-           ( self%metadata(i)%getval_name_surface /=  "" .and. ( &
-             self%metadata(i)%getval_name_surface == self%metadata(j)%name .or. &
-             self%metadata(i)%getval_name_surface == self%metadata(j)%getval_name ))) then
+           self%metadata(i)%name == self%metadata(j)%name_surface .or. &
+           ( self%metadata(i)%name_surface /=  "" .and. &
+             self%metadata(i)%name_surface == self%metadata(j)%name)) then
         str=repeat(" ",1024)
         write(str, *) "Duplicate field metadata: ", i, self%metadata(i)%name, &
                                                     j, self%metadata(j)%name
@@ -186,8 +177,7 @@ function soca_fields_metadata_get(self, name) result(field)
   ! find the field by any of its internal or getval names
   do i=1,size(self%metadata)
     if( trim(self%metadata(i)%name) == trim(name) .or. &
-        trim(self%metadata(i)%getval_name) == trim(name) .or. &
-        trim(self%metadata(i)%getval_name_surface) == trim(name) ) then
+        trim(self%metadata(i)%name_surface) == trim(name) ) then
       field = self%metadata(i)
       return
     endif

src/soca/Fields/soca_fields_mod.F90

@@ -433,7 +433,7 @@ subroutine soca_fields_init_vars(self, vars)
     end select
 
     ! determine number of levels
-    if (self%fields(i)%name == self%fields(i)%metadata%getval_name_surface) then
+    if (self%fields(i)%name == self%fields(i)%metadata%name_surface) then
       ! if this field is a surface getval, override the number of levels with 1
       nz = 1
     else
@@ -727,7 +727,7 @@ subroutine soca_fields_read(self, f_conf, vdate)
 
   ! iread = 1 (state) or 3 (increment): Read restart file
   if ((iread==1).or.(iread==3)) then
-    if (self%has("hocn")) call self%get("hocn", hocn)
+    if (self%has("sea_water_cell_thickness")) call self%get("sea_water_cell_thickness", hocn)
     ! filename for ocean
     call f_conf%get_or_die("basename", str)
     basename = str
@@ -900,19 +900,19 @@ subroutine soca_fields_read(self, f_conf, vdate)
 
     ! Initialize mid-layer depth from layer thickness
     ! TODO, this shouldn't live here, it should be part of the variable change class only
-    if (self%has("layer_depth")) then
-      call self%get("layer_depth", layer_depth)
+    if (self%has("sea_water_depth")) then
+      call self%get("sea_water_depth", layer_depth)
         layer_depth%val = 0.5 * hocn%val
         do k = 2, hocn%nz
           layer_depth%val(:,:,k) = layer_depth%val(:,:,k) + sum(hocn%val(:,:,1:k-1), dim=3)
         end do
     end if
 
     ! Compute mixed layer depth TODO: Move somewhere else ...
-    if (self%has("mld") .and. self%has("layer_depth")) then
-      call self%get("tocn", field)
-      call self%get("socn", field2)
-      call self%get("mld", mld)
+    if (self%has("ocean_mixed_layer_thickness") .and. self%has("sea_water_depth")) then
+      call self%get("sea_water_potential_temperature", field)
+      call self%get("sea_water_salinity", field2)
+      call self%get("ocean_mixed_layer_thickness", mld)
       mld%val = 0.0
       do i = isc, iec
         do j = jsc, jec

src/soca/Geometry/soca_geom.interface.F90

@@ -120,7 +120,7 @@ subroutine soca_geo_get_num_levels_c(c_key_self, c_vars, c_levels_size, c_levels
     case ("1")
       c_levels(i) = 1
     case ("full_ocn")
-      if (field_name == field%getval_name_surface) then
+      if (field_name == field%name_surface) then
         c_levels(i) = 1
       else
         c_levels(i) = self%nzo

src/soca/Increment/soca_increment_mod.F90

@@ -80,7 +80,7 @@ subroutine soca_increment_random(self)
     field => self%fields(i)
     ! TODO remove this once increment / state are fully separated
     ! NOTE: can't randomize "hocn", testIncrementInterpAD fails
-    if (field%name == 'hocn') cycle
+    if (field%name == "sea_water_cell_thickness") cycle
     call normal_distribution(field%val,  0.0_kind_real, 1.0_kind_real, rseed)
   end do
 
@@ -149,23 +149,23 @@ subroutine soca_increment_dirac(self, f_conf)
     field => null()
     select case(ifdir(n))
     case (1)
-      call self%get("tocn", field)
+      call self%get("sea_water_potential_temperature", field)
     case (2)
-      call self%get("socn", field)
+      call self%get("sea_water_salinity", field)
     case (3)
-      call self%get("ssh", field)
+      call self%get("sea_surface_height_above_geoid", field)
     case (4)
-      call self%get("cicen", field)
+      call self%get("sea_ice_category_area_fraction", field)
     case (5)
-      call self%get("hicen", field)
+      call self%get("sea_ice_category_thickness", field)
     case (6)
-      call self%get("chl", field)
+      call self%get("mass_concentration_of_chlorophyll_in_sea_water", field)
     case (7)
-      call self%get("biop", field)
+      call self%get("molar_concentration_of_biomass_in_sea_water_in_p_units", field)
     case (8)
-      call self%get("uocn", field)
+      call self%get("eastward_sea_water_velocity", field)
     case (9)
-      call self%get("vocn", field)
+      call self%get("northward_sea_water_velocity", field)
     case default
       ! TODO print error that out of range
     end select

src/soca/LinearVariableChange/Balance/soca_balance_mod.F90

@@ -105,12 +105,12 @@ subroutine soca_balance_setup(self, f_conf, traj, geom)
   jsd=geom%jsd; jed=geom%jed
 
   ! Get required fields
-  call traj%get("tocn", tocn)
-  call traj%get("socn", socn)
-  call traj%get("hocn", hocn)
-  call traj%get("mld", mld)
-  call traj%get("layer_depth", layer_depth)
-  if (traj%has("cicen"))  call traj%get("cicen", cicen)
+  call traj%get("sea_water_potential_temperature", tocn)
+  call traj%get("sea_water_salinity", socn)
+  call traj%get("sea_water_cell_thickness", hocn)
+  call traj%get("ocean_mixed_layer_thickness", mld)
+  call traj%get("sea_water_depth", layer_depth)
+  if (traj%has("sea_ice_category_area_fraction"))  call traj%get("sea_ice_category_area_fraction", cicen)
 
   ! allocate space
   nl = hocn%nz
@@ -179,7 +179,7 @@ subroutine soca_balance_setup(self, f_conf, traj, geom)
   deallocate(jac)
 
   ! Compute Kct
-  if (traj%has("cicen")) then
+  if (traj%has("sea_ice_category_area_fraction")) then
     ! Setup dc/dT
     allocate(kct(isd:ied,jsd:jed))
     kct = 0.0_kind_real
@@ -240,8 +240,8 @@ subroutine soca_balance_mult(self, dxa, dxm)
   !> K= [ Ketat Ketas I  0 ]
   !>    [ Kct     0   0  I ]
 
-  call dxa%get("tocn",tocn_a)
-  call dxa%get("socn",socn_a)
+  call dxa%get("sea_water_potential_temperature",tocn_a)
+  call dxa%get("sea_water_salinity",socn_a)
 
   do n=1, size(dxm%fields)
     fld_m => dxm%fields(n)
@@ -253,19 +253,19 @@ subroutine soca_balance_mult(self, dxa, dxm)
         case default
           fld_m%val(i,j,:) = fld_a%val(i,j,:)
 
-        case("socn") ! Salinity
+        case("sea_water_salinity") ! Salinity
           fld_m%val(i,j,:) = fld_a%val(i,j,:) + &
             & self%kst%jacobian(i,j,:) * tocn_a%val(i,j,:)
 
-        case ("ssh") ! SSH
+        case ("sea_surface_height_above_geoid") ! SSH
           fld_m%val(i,j,:) = fld_a%val(i,j,:)
           do k = 1, tocn_a%nz
             fld_m%val(i,j,:) = fld_m%val(i,j,:) + &
               & self%ksshts%kssht(i,j,k) * tocn_a%val(i,j,k) + &
               & self%ksshts%ksshs(i,j,k) * socn_a%val(i,j,k)
           end do
 
-        case ("cicen") ! Ice fraction
+        case ("sea_ice_category_area_fraction") ! Ice fraction
           do k = 1, fld_m%nz
             fld_m%val(i,j,k) = fld_a%val(i,j,k) + &
               & self%kct(i,j) * tocn_a%val(i,j,1)
@@ -293,9 +293,9 @@ subroutine soca_balance_multad(self, dxa, dxm)
 
   cicen_m => null()
 
-  call dxm%get("socn", socn_m)
-  call dxm%get("ssh",  ssh_m)
-  if (dxm%has("cicen")) call dxm%get("cicen",cicen_m)
+  call dxm%get("sea_water_salinity", socn_m)
+  call dxm%get("sea_surface_height_above_geoid",  ssh_m)
+  if (dxm%has("sea_ice_category_area_fraction")) call dxm%get("sea_ice_category_area_fraction",cicen_m)
 
   do n = 1, size(dxa%fields)
     fld_a => dxa%fields(n)
@@ -307,7 +307,7 @@ subroutine soca_balance_multad(self, dxa, dxm)
         case default
           fld_a%val(i,j,:) = fld_m%val(i,j,:)
 
-        case ("tocn") ! Temperature
+        case ("sea_water_potential_temperature") ! Temperature
           fld_a%val(i,j,:) = fld_m%val(i,j,:) + &
             & self%kst%jacobian(i,j,:) * socn_m%val(i,j,:) + &
             & self%ksshts%kssht(i,j,:) * ssh_m%val(i,j,1)
@@ -317,7 +317,7 @@ subroutine soca_balance_multad(self, dxa, dxm)
               & self%kct(i,j) * sum(cicen_m%val(i,j,:))
           end if
 
-        case ("socn") ! Salinity
+        case ("sea_water_salinity") ! Salinity
           fld_a%val(i,j,:) = fld_m%val(i,j,:) + &
             & self%ksshts%ksshs(i,j,:) * ssh_m%val(i,j, 1)
 
@@ -341,8 +341,8 @@ subroutine soca_balance_multinv(self, dxa, dxm)
   type(soca_field), pointer :: fld_m, fld_a
   type(soca_field), pointer :: tocn_m, socn_m
 
-  call dxm%get("tocn", tocn_m)
-  call dxm%get("socn", socn_m)
+  call dxm%get("sea_water_potential_temperature", tocn_m)
+  call dxm%get("sea_water_salinity", socn_m)
 
   do n = 1, size(dxa%fields)
     fld_a => dxa%fields(n)
@@ -354,11 +354,11 @@ subroutine soca_balance_multinv(self, dxa, dxm)
         case default
           fld_a%val(i,j,:) = fld_m%val(i,j,:)
 
-        case ('socn') ! Salinity
+        case ('sea_water_salinity') ! Salinity
           fld_a%val(i,j,:) = fld_m%val(i,j,:) - &
             & self%kst%jacobian(i,j,:) * tocn_m%val(i,j,:)
 
-        case ('ssh') ! SSH
+        case ('sea_surface_height_above_geoid') ! SSH
           fld_a%val(i,j, :) = fld_m%val(i,j, :)
           do k = 1, tocn_m%nz
             fld_a%val(i,j,:) = fld_a%val(i,j,:) + &
@@ -367,7 +367,7 @@ subroutine soca_balance_multinv(self, dxa, dxm)
               & self%ksshts%ksshs(i,j,k) * socn_m%val(i,j,k)
           end do
 
-        case ('cicen') ! Ice fraction
+        case ('sea_ice_category_area_fraction') ! Ice fraction
           fld_a%val(i,j,:) =  fld_m%val(i,j,:)
           do k = 1, fld_m%nz
             fld_a%val(i,j,k) = fld_a%val(i,j,k) - &
@@ -396,9 +396,9 @@ subroutine soca_balance_multinvad(self, dxa, dxm)
 
   cicen_a => null()
 
-  call dxa%get("socn", socn_a)
-  call dxa%get("ssh",  ssh_a)
-  if (dxa%has("cicen")) call dxa%get("cicen",cicen_a)
+  call dxa%get("sea_water_salinity", socn_a)
+  call dxa%get("sea_surface_height_above_geoid",  ssh_a)
+  if (dxa%has("sea_ice_category_area_fraction")) call dxa%get("sea_ice_category_area_fraction",cicen_a)
 
   do n = 1, size(dxm%fields)
     fld_m => dxm%fields(n)
@@ -410,7 +410,7 @@ subroutine soca_balance_multinvad(self, dxa, dxm)
         case default
           fld_m%val(i,j,:) = fld_a%val(i,j,:)
 
-        case ('tocn') ! Temperature
+        case ('sea_water_potential_temperature') ! Temperature
           fld_m%val(i,j,:) = fld_a%val(i,j,:) &
             & - self%kst%jacobian(i,j,:) * socn_a%val(i,j,:) &
             & + ( self%ksshts%ksshs(i,j,:) * self%kst%jacobian(i,j,:) &
@@ -421,7 +421,7 @@ subroutine soca_balance_multinvad(self, dxa, dxm)
               & - self%kct(i,j) * sum(cicen_a%val(i,j,:))
           end if
 
-        case ('socn') ! Salinity
+        case ('sea_water_salinity') ! Salinity
           fld_m%val(i,j,:) = fld_a%val(i,j,:) - &
             & self%ksshts%ksshs(i,j,:) * ssh_a%val(i,j,1)