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Merge pull request #538 from xylar/add-smooth-topo-tool
Add ocean topography smoothing tool
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‎conda_package/recipe/build.sh

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

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

‎ocean/smooth_topo/README

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

‎ocean/smooth_topo/cmake/FindNetCDF.cmake

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

‎ocean/smooth_topo/cmake/LICENSE

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

‎ocean/smooth_topo/cmake/README

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These files are from https://github.com/jedbrown/cmake-modules

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