Merge remote-tracking branch 'origin/main' into dmUpdate

CHANGELOG.md

@@ -6,6 +6,26 @@ and this project uses `yyyy.rr[.pp]`, where `yyyy` is the year a patch is releas
 `rr` is a sequential release number (starting from `01`), and an optional two-digit
 sequential patch number (starting from `01`).
 
+## [2023.04] - 2023-12-04
+### Known Issues
+- GCC 9 and below as well as GCC 11.1.0 are unsupported due to compilation issues. See prior releases for more details.
+- `NO_QUAD_PRECISION` macro is no longer set by FMS, the `ENABLE_QUAD_PRECISION` macro has replaced prior usage of `NO_QUAD_PRECISION`. `-DENABLE_QUAD_PRECISION` should be set if quad precision is to be used, otherwise FMS will not use quad precision reals where applicable.
+
+### Added
+- DATA_OVERRIDE: A new namelist flag `use_data_table_yaml` has been added to enable usage of the yaml format data_override tables. This allows an executable built with yaml support be able to accept either format.
+
+### Changed
+- RESERVED KEYWORD CHANGES: Various routines in FMS have been updated to not use fortran keywords for variable names. The names changed were: `data`, `unit`, and `value`. This may affect usage of external code if argument names are explicitly used. Only required arguement names were changed to mitigate any breaking changes.
+- TESTS: Changes the testing scripts to allow for the `MPI_LAUNCHER` environment variable override to work with any provided arguments.
+
+### Fixed
+- CMAKE: Fixed build issue with CMake where precision default flags were being overwritten when using GNU and MPICH.
+- AUTOTOOLS: Fixes issue affecting installs where the global libFMS.F90 module was not being installed correctly and adds post-install message.
+- DIAG_MANAGER: Fixes issue with incorrect start_time functionality (from the 2023.02.01 patch)
+
+### Tag Commit Hashes
+- 2023.04-beta1 be1856c45accfe2fb15953c5f51e0d58a8816882
+
 ## [2023.03] - 2023-10-27
 ### Known Issues
 - GCC 9 and below as well as GCC 11.1.0 are unsupported due to compilation issues. See prior releases for more details.

CMakeLists.txt

@@ -26,7 +26,7 @@ set(CMAKE_Fortran_FLAGS_DEBUG)
 
 # Define the CMake project
 project(FMS
-  VERSION 2023.03.0
+  VERSION 2023.04.0
   DESCRIPTION  "GFDL FMS Library"
   HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms"
   LANGUAGES C Fortran)

axis_utils/include/axis_utils2.inc

@@ -46,6 +46,9 @@
                                               !! indicating to reproduce the mpp_io bug where
                                               !! the null characters were not removed after reading a string attribute
   integer, parameter                                   :: lkind = FMS_AU_KIND_
+  integer :: edge_index(2) !< Index to use when reading the edges from the file
+                           !! (/1, 2/) if the axis data is monotonically increasing
+                           !! (/2, 1/) if the axis data is monotonically decreasing
 
   ndims = get_variable_num_dimensions(fileobj, name)
   allocate(dim_sizes(ndims))
@@ -108,8 +111,10 @@
 
       allocate(r2d(dim_sizes(1), dim_sizes(2)))
       call read_data(fileobj, buffer, r2d)
-      edge_data(1:dim_sizes(2)) = r2d(1,:)
-      edge_data(dim_sizes(2)+1) = r2d(2,dim_sizes(2))
+      edge_index = (/1, 2/)
+      if (r2d(1,1) .gt. r2d(1,2)) edge_index = (/2, 1 /)
+      edge_data(1:dim_sizes(2)) = r2d(edge_index(1),:)
+      edge_data(dim_sizes(2)+1) = r2d(edge_index(2),dim_sizes(2))
       deallocate(r2d)
     endif
     deallocate(dim_sizes)
@@ -265,7 +270,7 @@
   !!     inputs:
   !!
   !!     rval   = arbitrary data...same units as elements in "array"
-  !!     array  = array of data points  (must be monotonically increasing)
+  !!     array  = array of data points  (must be monotonically)
   !!     ia     = dimension of "array"
   !!
   !!     output:
@@ -293,48 +298,71 @@
   !!     z(k1) would be the nearest data point to 12.5 and z(k2) would
   !!     be the nearest data point to 0.0
   !! @return integer nearest_index
-
-
-
   function NEAREST_INDEX_(rval, array)
+    real(kind=FMS_AU_KIND_), intent(in)               :: rval !< arbitrary data...same units as elements in "array"
+    real(kind=FMS_AU_KIND_), intent(in), dimension(:) :: array !< array of data points  (must be monotonic)
 
     integer                               :: NEAREST_INDEX_
     integer                               :: ia !< dimension of "array"
-    integer                               :: i, ii, iunit
-    real(kind=FMS_AU_KIND_)               :: rval !< arbitrary data...same units as elements in "array"
-    real(kind=FMS_AU_KIND_), dimension(:) :: array !< array of data points  (must be monotonically increasing)
-    logical                               :: keep_going
-
-    ia = size(array(:))
-
-    do i = 2, ia
-       if (array(i) < array(i-1)) then
-          iunit = stdout()
-          write (iunit,*) '=> Error: "nearest_index" array must be monotonically increasing' &
-                         & // 'when searching for nearest value to ', rval
-          write (iunit,*) '          array(i) < array(i-1) for i=',i
-          write (iunit,*) '          array(i) for i=1..ia follows:'
-          do ii = 1, ia
-             write (iunit,*) 'i=',ii, ' array(i)=', array(ii)
-          enddo
-          call mpp_error(FATAL,' "nearest_index" array must be monotonically increasing.')
-       endif
-    enddo
+    integer                               :: i !< For looping through "array"
+
+    ia = SIZE(array(:))
+
+    ! check if array is monotonous
+    DO i = 2, ia-1
+       IF( (array(i-1)<array(i).AND.array(i)>array(i+1)) .OR. (array(i-1)>array(i).AND.array(i)<array(i+1))) THEN
+          ! <ERROR STATUS="FATAL">array NOT monotonously ordered</ERROR>
+          CALL mpp_error(FATAL, 'axis_utils2::nearest_index array is NOT monotonously ordered')
+       END IF
+    END DO
+
+    if (array(1) < array(ia)) then
+    !< increasing array
+
+      !< Check if the rval is outside the range of the array
+      if (rval < array(1)) then
+         NEAREST_INDEX_ = 1
+         return
+      elseif (rval > array(ia)) then
+         NEAREST_INDEX_ = ia
+         return
+      endif
 
-    if (rval < array(1) .or. rval > array(ia)) then
-       if (rval < array(1))  NEAREST_INDEX_ = 1
-       if (rval > array(ia)) NEAREST_INDEX_ = ia
+      DO i = 1, ia-1
+         IF ( (array(i)<=rval).AND.(array(i+1)>= rval) ) THEN
+            IF( rval - array(i) <= array(i+1) - rval ) THEN
+               NEAREST_INDEX_ = i
+               return
+            ELSE
+               NEAREST_INDEX_ = i+1
+               return
+            ENDIF
+            EXIT
+         END IF
+      END DO
     else
-       i = 1
-       keep_going = .true.
-       do while (i <= ia .and. keep_going)
-          i = i+1
-          if (rval <= array(i)) then
-             NEAREST_INDEX_ = i
-             if (array(i)-rval > rval-array(i-1)) NEAREST_INDEX_ = i-1
-             keep_going = .false.
-          endif
-       enddo
+    !< Decreasing Array
+
+      !< Check if the rval is outside the range of the array
+      if (rval < array(ia)) then
+         NEAREST_INDEX_ = ia
+         return
+      elseif (rval > array(1)) then
+         NEAREST_INDEX_ = 1
+         return
+      endif
+
+      DO i = 1, ia-1
+         IF ( (array(i)>=rval).AND.(array(i+1)<= rval) ) THEN
+            IF ( array(i)-rval <= rval-array(i+1) ) THEN
+               NEAREST_INDEX_ = i
+               return
+            ELSE
+               NEAREST_INDEX_ = i+1
+               return
+            END IF
+         END IF
+      END DO
     endif
   end function NEAREST_INDEX_
 

configure.ac

@@ -25,7 +25,7 @@ AC_PREREQ([2.69])
 
 # Initialize with name, version, and support email address.
 AC_INIT([GFDL FMS Library],
-  [2023.03.00-dev],
+  [2023.04.00-dev],
   [[email protected]],
   [FMS],
   [https://www.github.com/NOAA-GFDL/FMS])

data_override/README.MD

@@ -24,6 +24,13 @@ If it is desired to interpolate the data to a region of the model grid. The foll
 - **lat_start:** The starting longitude in the same units as the grid data in the file
 - **lon_end:** The ending longitude in the same units as the grid data in the file
 
+If it is desired to use multiple(3) input netcdf files instead of 1. The following **optional** keys are available.
+- **is_multi_file:** Set to `True` is using the multi-file feature
+- **prev_file_name:** The name of the first file in the set
+- **next_file_name:** The name of the third file in the set
+
+Note that **file_name** must be the second file in the set. **prev_file_name** and/or **next_file_name** are required if **is_multi_file** is set to `True`
+
 #### 2. How to use it?
 In order to use the yaml data format, [libyaml](https://github.com/yaml/libyaml) needs to be installed and linked with FMS. Additionally, FMS must be compiled with -Duse_yaml macro. If using autotools, you can add `--with-yaml`, which will add the macro for you and check that libyaml is linked correctly.
 ```