Merge branch 'develop' into feature/baseline

Fixes ufs-community#574.

sorc/chgres_cube.fd/docs/user_guide.md

@@ -11,8 +11,8 @@ Common Data Form (NetCDF) data.
 This document is part of the <a href="../index.html">UFS_UTILS
 documentation</a>.
 
-The chgres_cube program is part of the [NCEPLIBS
-UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.
+The chgres_cube program is part of the
+[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.
 
 ## Where to find GFS GRIB2, NEMSIO and NetCDF data
 

sorc/emcsfc_ice_blend.fd/docs/user_guide.md

@@ -10,9 +10,5 @@ analysis used to update the GFS once per day.
 This document is part of the <a href="../index.html">UFS_UTILS
 documentation</a>.
 
-The emcsfc_ice_blend program is part of the [NCEPLIBS
-UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.
-
-
-
-
+The emcsfc_ice_blend program is part of the
+[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.

sorc/emcsfc_snow2mdl.fd/docs/user_guide.md

@@ -10,7 +10,5 @@ analysis used to update the GFS snow field once per day.
 This document is part of the <a href="../index.html">UFS_UTILS
 documentation</a>.
 
-The emcsfc_snow2mdl program is part of the [NCEPLIBS
-UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.
-
-
+The emcsfc_snow2mdl program is part of the
+[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.

sorc/fvcom_tools.fd/CMakeLists.txt

@@ -7,9 +7,10 @@ set(fortran_src
    kinds.f90
    module_ncio.f90
    module_nwp_base.f90
-   module_nwp.f90
-   process_FVCOM.f90)
+   module_nwp.f90)
+#   process_FVCOM.f90)
 
+set(exe_src process_FVCOM.f90)
 
 if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel)$")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -r8")
@@ -18,15 +19,27 @@ elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU|Clang|AppleClang)$")
 endif()
 
 set(exe_name fvcom_to_FV3)
-add_executable(${exe_name} ${fortran_src})
+
+add_library(fvcom_tools_lib STATIC ${fortran_src})
+add_executable(${exe_name} ${exe_src})
+
+set(mod_dir "${CMAKE_CURRENT_BINARY_DIR}/mod")
+set_target_properties(fvcom_tools_lib PROPERTIES Fortran_MODULE_DIRECTORY ${mod_dir})
+target_include_directories(fvcom_tools_lib INTERFACE ${mod_dir})
+
 target_link_libraries(
-  ${exe_name}
+#  ${exe_name}
+  fvcom_tools_lib
+  PUBLIC
   MPI::MPI_Fortran
   NetCDF::NetCDF_Fortran)
 
+target_link_libraries(${exe_name} PRIVATE fvcom_tools_lib)
+
 install(TARGETS ${exe_name} RUNTIME DESTINATION ${exec_dir})
 
 # If doxygen documentation we enabled, build it.
 if(ENABLE_DOCS)
   add_subdirectory(docs)  
 endif()
+

sorc/fvcom_tools.fd/docs/user_guide.md

@@ -1,18 +1,56 @@
-
 # fvcom_tools
 
 # Introduction
 
-The process_FVCOM.f90 program replaces lake surface and lake ice
-temperature along with aerial ice concentration generated from the
-Great Lakes Operational Forecast System (GLOFS) in an FV3 surface
-restart file. See [fvcom documentation](@ref fvcom_readme).
+This code replaces lake surface and lake ice temperature along
+with aerial ice concentration generated from Great Lakes 
+Operational Forecast System (GLOFS), an FVCOM-based model, into 
+sfc_data.nc.
 
 This document is part of the <a href="../index.html">UFS_UTILS
 documentation</a>.
 
-The fvcom_tools program is part of the [NCEPLIBS
-UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.
-
-
-
+The fvcom_tools program is part of the
+[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.
+
+## NOTE
+
+The variables in the input files must reside on 
+the same grid. This means data from FVCOM must be horizontally 
+interpolated to the FV3 grid. This routine will also force a 
+minimum ice concentration of 15%. If ice concentration is less 
+than 15% in FVCOM, it will be set to 0% to avoid FV3 from 
+changing values less than 15% to 15% and generating unrealistic 
+lake ice temperatures.
+
+## Library Dependencies:
+
+Installation depends on the netCDF library and cmake.
+
+## Running
+
+This routine will take four variables from the command line:
+1. Name of FV3 sfc data file (e.g. sfc_data.tile7.halo0.nc)
+   which is generated from chgres_cube.exe.
+2. Name of FVCOM data file in netcdf format (e.g. fvcom.nc)
+3. "warm" or "cold" start. "warm" start will read in 
+    sfc_data.nc files generated from a restart of UFS-SRW.
+    "cold" start will read in sfc_data.nc files generated 
+    from chgres_cube. 
+4. String of time slice to use in the fvcom.nc file. This string
+    should match exactly what is in the Times variable of the .nc file.
+To run the script, use the following example, modifying file
+names as needed:
+   ./fvcom_to_FV3 sfc_data.tile7.halo0.nc fvcom.nc cold \
+     2020-01-31T18:00:00.000000
+Output will be to the sfc data file and include lake surface 
+and lake ice temperature, and lake ice concentration from the 
+first time in the FVCOM file.
+
+This routine is *strongly* based upon Eric James' (ESRL/GSL) work
+to update HRRR/WRF Great Lakes' temperature data with FVCOM.
+It also relies heavily on Ming Hu's (ESRL/GSL) ncio module.
+
+## For more information, please contact:
+
+David Wright, University of Michigan and GLERL: dmwright@umich.edu

sorc/fvcom_tools.fd/module_ncio.f90

@@ -85,7 +85,10 @@ module module_ncio
      procedure :: replace_var_nc_char_3d !< Replace 3D character type variable. @return
      procedure :: handle_err !< Handle netCDF errors. @return
      procedure :: convert_theta2t_2dgrid !< Convert theta T (Kelvin) to T (deg C). @return
-     procedure :: add_new_var => add_new_var_3d      !< Add a new 3d variable to output file. @return
+     generic   :: add_new_var => add_new_var_2d, &
+          add_new_var_3d !< Add a new 2d or 3d variable to ouput file. @return
+     procedure :: add_new_var_2d !< Add a new 2d variable to output file. @return
+     procedure :: add_new_var_3d !< Add a new 3d variable to output file. @return
   end type ncio
 
 contains
@@ -1306,10 +1309,10 @@ subroutine get_var_nc_double_2d(this,varname,nd1,nd2,field)
           field(:,j)=temp(istart:iend)
        enddo
        !
-       if(this%debug_level>100) then
-          write(*,*) trim(thissubname),' show samples:'
-          write(*,*) 'max,min:',maxval(field(:,:)),minval(field(:,:))
-       endif
+!       if(this%debug_level>100) then
+!          write(*,*) trim(thissubname),' show samples:'
+!          write(*,*) 'max,min:',maxval(field(:,:)),minval(field(:,:))
+!       endif
     else
        write(*,*) trim(thissubname),' ERROR: dimension does not match.'
        write(*,*) nd1,this%ends(1),nd2,this%ends(2)
@@ -1362,12 +1365,12 @@ subroutine get_var_nc_double_3d(this,varname,nd1,nd2,nd3,field)
           enddo
        enddo
        !
-       if(this%debug_level>100) then
-          write(*,*) trim(thissubname),' show samples:'
-          do k=1,nd3
-             write(*,*) 'k,max,min:',k,maxval(field(:,:,k)),minval(field(:,:,k))
-          enddo
-       endif
+!       if(this%debug_level>100) then
+!          write(*,*) trim(thissubname),' show samples:'
+!          do k=1,nd3
+!             write(*,*) 'k,max,min:',k,maxval(field(:,:,k)),minval(field(:,:,k))
+!          enddo
+!       endif
     else
        write(*,*) trim(thissubname),' ERROR: dimension does not match.'
        write(*,*) nd1,this%ends(1),nd2,this%ends(2),nd3,this%ends(3)
@@ -1441,6 +1444,7 @@ subroutine get_var_nc_double(this,varname,ilength,field)
     if(status /= nf90_NoErr) call this%handle_err(status)
     do i=1,nDims
        dimname="       "
+       write(*,*) 'dimids(i) = ', dimids(i)
        status = nf90_inquire_dimension(ncid, dimids(i), dimname, len = ndim)
        if (status /= nf90_noerr) call this%handle_err(status)
        ends(i)=ndim
@@ -2271,10 +2275,10 @@ subroutine get_var_nc_char_2d(this,varname,nd1,nd2,field)
           field(:,j)=temp(istart:iend)
        enddo
        !
-       if(this%debug_level>100) then
-          write(*,*) trim(thissubname),' show samples:'
-          write(*,*) field(1,1)
-       endif
+!       if(this%debug_level>100) then
+!          write(*,*) trim(thissubname),' show samples:'
+!          write(*,*) field(1,1)
+!       endif
     else
        write(*,*) trim(thissubname),' ERROR: dimension does not match.'
        write(*,*) nd1,this%ends(1),nd2,this%ends(2)
@@ -2327,10 +2331,10 @@ subroutine get_var_nc_char_3d(this,varname,nd1,nd2,nd3,field)
           enddo
        enddo
        !
-       if(this%debug_level>100) then
-          write(*,*) trim(thissubname),' show samples:'
-          write(*,*) field(1,1,1)
-       endif
+!       if(this%debug_level>100) then
+!          write(*,*) trim(thissubname),' show samples:'
+!          write(*,*) field(1,1,1)
+!       endif
     else
        write(*,*) trim(thissubname),' ERROR: dimension does not match.'
        write(*,*) nd1,this%ends(1),nd2,this%ends(2),nd3,this%ends(3)
@@ -2542,4 +2546,47 @@ subroutine add_new_var_3d(this,varname,dname1,dname2,dname3,lname,units)
 
   end subroutine add_new_var_3d
 
+  !> Add a new variable to sfc_data.nc with dimensions (yaxis_1,
+  !! xaxis_1).
+  !!
+  !! @param this instance of an ncio class
+  !! @param[in] varname Name of variable to be created in netcdf file
+  !! @param[in] dname1 1st dimension name
+  !! @param[in] dname2 2nd dimension name
+  !! @param[in] lname long name output for netcdf variable
+  !! @param[in] units units to use in netcdf variable
+  !!
+  !! @author David.M.Wright org: UM/GLERL @date 2021-10-07
+  subroutine add_new_var_2d(this,varname,dname1,dname2,lname,units)
+    implicit none
+    !
+    class(ncio) :: this
+    character(len=*),intent(in) :: varname,dname1,dname2  &
+         ,lname,units
+    integer :: status, ncid, dim1id, dim2id, varid
+
+    status = nf90_redef(this%ncid) !Enter Define Mode
+    if (status /= nf90_noerr) call this%handle_err(status)
+
+    status = nf90_inq_dimid(this%ncid, dname1, dim1id)
+    if (status /= nf90_noerr) call this%handle_err(status)
+    status = nf90_inq_dimid(this%ncid, dname2, dim2id)
+    if (status /= nf90_noerr) call this%handle_err(status)
+
+    status = nf90_def_var(this%ncid, varname, nf90_double, &
+         (/ dim1id, dim2id /), varid)
+    if (status /= nf90_noerr) call this%handle_err(status)
+
+    status = nf90_put_att(this%ncid, varid, 'long_name', lname)
+    if (status /= nf90_noerr) call this%handle_err(status)
+    status = nf90_put_att(this%ncid, varid, 'units', units)
+    if (status /= nf90_noerr) call this%handle_err(status)
+
+    status = nf90_enddef(this%ncid) !Exit Define Mode and
+    ! return to Data Mode
+    if (status /= nf90_noerr) call this%handle_err(status)
+
+  end subroutine add_new_var_2d
+
+
 end module module_ncio