Merge pull request #538 from xylar/add-smooth-topo-tool

Add ocean topography smoothing tool

conda_package/recipe/build.sh

@@ -8,6 +8,17 @@ cp -r ocean landice visualization mesh_tools conda_package
 cd conda_package
 ${PYTHON} -m pip install . --no-deps -vv
 
+# build and install ocean topography smoothing tool
+cd ${SRC_DIR}/conda_package/ocean/smooth_topo
+mkdir build
+cd build
+cmake \
+  -D CMAKE_INSTALL_PREFIX=${PREFIX} \
+  -D CMAKE_BUILD_TYPE=Release \
+  ..
+cmake --build .
+cmake --install .
+
 # build and install sea ice partitioning tool
 cd ${SRC_DIR}/conda_package/mesh_tools/seaice_grid_tools
 mkdir build
@@ -40,4 +51,3 @@ cmake \
   ..
 cmake --build .
 cmake --install .
-

ocean/smooth_topo/CMakeLists.txt

@@ -0,0 +1,21 @@
+cmake_minimum_required (VERSION 3.0.2)
+enable_language(Fortran)
+project (ocean_smooth_topo)
+
+list (APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
+
+set (NETCDF_F90 "YES")
+find_package (NetCDF REQUIRED)
+
+message (STATUS "NETCDF_INCLUDES=${NETCDF_INCLUDES}")
+message (STATUS "NETCDF_LIBRARIES=${NETCDF_LIBRARIES}")
+
+include_directories(${NETCDF_INCLUDES})
+
+add_executable (ocean_smooth_topo_skip_land_ice smooth_topo_skip_land_ice.F90)
+target_link_libraries (ocean_smooth_topo_skip_land_ice ${NETCDF_LIBRARIES})
+
+add_executable (ocean_smooth_topo_before_init smooth_topo_before_init.F90)
+target_link_libraries (ocean_smooth_topo_before_init ${NETCDF_LIBRARIES})
+
+install (TARGETS ocean_smooth_topo_skip_land_ice ocean_smooth_topo_before_init DESTINATION bin)

ocean/smooth_topo/README

@@ -0,0 +1,30 @@
+Authors: Adrian Turner, Mat Maltrud
+
+Tools for smoothing bathymetry in an MPAS-Ocean with a Gaussian filter with a
+characteristic length scale (stdDeviation) and cut-off distance
+(distanceLimit). Smoothing is applied over a given number of iterations
+(numSmoothingPasses). The tools do not currently work on meshes without
+ice-shelf cavities.
+
+The smooth_topo_skip_land_ice tool can be applied to topography after an
+initial condition has been created.  The smoothing is only applied if the
+original maxLevelCell is deeper than a given threshold (minLevelForSmoothing)
+and ice-shelf cavities are ignored.
+
+The smooth_topo_before_init tool is used to smooth topography data on the MPAS
+mesh before an initial condition has been created.
+
+An example namelist file (smooth_depth_in) is:
+
+&smooth
+    filename_depth_in  = "mpaso.IcoswISC30E3r2.20230901.nc"
+    filename_depth_out = "smooth.IcoswISC30E3r2.r200e100.1pass.min5.skipLandIce.231115.nc"
+    filename_mpas_mesh   = "mpaso.IcoswISC30E3r2.20230901.nc"
+    distanceLimit    = 200.
+    stdDeviation     = 100.
+    numSmoothingPasses = 1
+    minLevelForSmoothing = 5
+/
+
+The minLevelForSmoothing namelist option only applies to
+smooth_topo_skip_land_ice.

ocean/smooth_topo/cmake/FindNetCDF.cmake

@@ -0,0 +1,71 @@
+# - Find NetCDF
+# Find the native NetCDF includes and library
+#
+#  NETCDF_INCLUDES    - where to find netcdf.h, etc
+#  NETCDF_LIBRARIES   - Link these libraries when using NetCDF
+#  NETCDF_FOUND       - True if NetCDF found including required interfaces (see below)
+#
+# Your package can require certain interfaces to be FOUND by setting these
+#
+#  NETCDF_CXX         - require the C++ interface and link the C++ library
+#  NETCDF_F77         - require the F77 interface and link the fortran library
+#  NETCDF_F90         - require the F90 interface and link the fortran library
+#
+# The following are not for general use and are included in
+# NETCDF_LIBRARIES if the corresponding option above is set.
+#
+#  NETCDF_LIBRARIES_C    - Just the C interface
+#  NETCDF_LIBRARIES_CXX  - C++ interface, if available
+#  NETCDF_LIBRARIES_F77  - Fortran 77 interface, if available
+#  NETCDF_LIBRARIES_F90  - Fortran 90 interface, if available
+#
+# Normal usage would be:
+#  set (NETCDF_F90 "YES")
+#  find_package (NetCDF REQUIRED)
+#  target_link_libraries (uses_f90_interface ${NETCDF_LIBRARIES})
+#  target_link_libraries (only_uses_c_interface ${NETCDF_LIBRARIES_C})
+
+if (NETCDF_INCLUDES AND NETCDF_LIBRARIES)
+  # Already in cache, be silent
+  set (NETCDF_FIND_QUIETLY TRUE)
+endif (NETCDF_INCLUDES AND NETCDF_LIBRARIES)
+
+find_path (NETCDF_INCLUDES netcdf.h
+  HINTS NETCDF_DIR ENV NETCDF_DIR)
+
+find_library (NETCDF_LIBRARIES_C       NAMES netcdf)
+mark_as_advanced(NETCDF_LIBRARIES_C)
+
+set (NetCDF_has_interfaces "YES") # will be set to NO if we're missing any interfaces
+set (NetCDF_libs "${NETCDF_LIBRARIES_C}")
+
+get_filename_component (NetCDF_lib_dirs "${NETCDF_LIBRARIES_C}" PATH)
+
+macro (NetCDF_check_interface lang header libs)
+  if (NETCDF_${lang})
+    find_path (NETCDF_INCLUDES_${lang} NAMES ${header}
+      HINTS "${NETCDF_INCLUDES}" NO_DEFAULT_PATH)
+    find_library (NETCDF_LIBRARIES_${lang} NAMES ${libs}
+      HINTS "${NetCDF_lib_dirs}" NO_DEFAULT_PATH)
+    mark_as_advanced (NETCDF_INCLUDES_${lang} NETCDF_LIBRARIES_${lang})
+    if (NETCDF_INCLUDES_${lang} AND NETCDF_LIBRARIES_${lang})
+      list (INSERT NetCDF_libs 0 ${NETCDF_LIBRARIES_${lang}}) # prepend so that -lnetcdf is last
+    else (NETCDF_INCLUDES_${lang} AND NETCDF_LIBRARIES_${lang})
+      set (NetCDF_has_interfaces "NO")
+      message (STATUS "Failed to find NetCDF interface for ${lang}")
+    endif (NETCDF_INCLUDES_${lang} AND NETCDF_LIBRARIES_${lang})
+  endif (NETCDF_${lang})
+endmacro (NetCDF_check_interface)
+
+NetCDF_check_interface (CXX netcdfcpp.h netcdf_c++)
+NetCDF_check_interface (F77 netcdf.inc  netcdff)
+NetCDF_check_interface (F90 netcdf.mod  netcdff)
+
+set (NETCDF_LIBRARIES "${NetCDF_libs}" CACHE STRING "All NetCDF libraries required for interface level")
+
+# handle the QUIETLY and REQUIRED arguments and set NETCDF_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (NetCDF DEFAULT_MSG NETCDF_LIBRARIES NETCDF_INCLUDES NetCDF_has_interfaces)
+
+mark_as_advanced (NETCDF_LIBRARIES NETCDF_INCLUDES)

ocean/smooth_topo/cmake/LICENSE

@@ -0,0 +1,23 @@
+Copyright $(git shortlog -s)
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ocean/smooth_topo/cmake/README

@@ -0,0 +1 @@
+These files are from https://github.com/jedbrown/cmake-modules