Merge branch 'dev-unstable-pointers' into f/AD-shear

CMakeLists.txt

@@ -67,7 +67,10 @@ endif()
 option(BUILD_TESTING "Build the testing tree." OFF)
 if(BUILD_TESTING)
   option(CODECOVERAGE "Enable infrastructure for measuring code coverage." OFF)
-  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -DUNIT_TEST")
+  option(BUILD_UNIT_TESTING "Enable unit testing" ON)
+  if(BUILD_UNIT_TESTING)
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -DUNIT_TEST")
+  endif()
 endif()
 
 # Setup Fortran Compiler options based on architecture/compiler
@@ -184,6 +187,7 @@ set(OPENFAST_MODULES
   nwtc-library
   version
   inflowwind
+  extloads
   aerodyn
   aerodyn14
   servodyn
@@ -277,8 +281,10 @@ if(BUILD_TESTING)
   add_subdirectory(reg_tests)
 
   # unit tests
-  if(NOT (${CMAKE_Fortran_COMPILER_ID} STREQUAL "Flang"))
-    add_subdirectory(unit_tests)
+  if(BUILD_UNIT_TESTING)
+    if(NOT (${CMAKE_Fortran_COMPILER_ID} STREQUAL "Flang"))
+      add_subdirectory(unit_tests)
+    endif()
   endif()
 endif()
 

cmake/FindNetCDF.cmake

@@ -0,0 +1,124 @@
+#
+# This file was copied from the VTK repository: 
+# https://github.com/Kitware/VTK/blob/master/CMake/FindNetCDF.cmake
+# VTK is distributed under the OSI-approved BSD 3-clause License.
+#
+#
+# - Find NetCDF
+# Find the native NetCDF includes and library
+#
+#  NETCDF_INCLUDE_DIR  - user modifiable choice of where netcdf headers are
+#  NETCDF_LIBRARY      - user modifiable choice of where netcdf libraries are
+#
+# 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
+#
+# Or equivalently by calling FindNetCDF with a COMPONENTS argument containing one or
+# more of "CXX;F77;F90".
+#
+# When interfaces are requested the user has access to interface specific hints:
+#
+#  NETCDF_${LANG}_INCLUDE_DIR - where to search for interface header files
+#  NETCDF_${LANG}_LIBRARY     - where to search for interface libraries
+#
+# This module returns these variables for the rest of the project to use.
+#
+#  NETCDF_FOUND          - True if NetCDF found including required interfaces (see below)
+#  NETCDF_LIBRARIES      - All netcdf related libraries.
+#  NETCDF_INCLUDE_DIRS   - All directories to include.
+#  NETCDF_HAS_INTERFACES - Whether requested interfaces were found or not.
+#  NETCDF_${LANG}_INCLUDE_DIRS/NETCDF_${LANG}_LIBRARIES - C/C++/F70/F90 only interface
+#
+# Normal usage would be:
+#  set (NETCDF_F90 "YES")
+#  find_package (NetCDF REQUIRED)
+#  target_link_libraries (uses_everthing ${NETCDF_LIBRARIES})
+#  target_link_libraries (only_uses_f90 ${NETCDF_F90_LIBRARIES})
+
+#search starting from user editable cache var
+if (NETCDF_INCLUDE_DIR AND NETCDF_LIBRARY)
+  # Already in cache, be silent
+  set (NETCDF_FIND_QUIETLY TRUE)
+endif ()
+
+set(USE_DEFAULT_PATHS "NO_DEFAULT_PATH")
+if(NETCDF_USE_DEFAULT_PATHS)
+  set(USE_DEFAULT_PATHS "")
+endif()
+
+find_path (NETCDF_INCLUDE_DIR netcdf.h
+  HINTS "${NETCDF_DIR}/include")
+mark_as_advanced (NETCDF_INCLUDE_DIR)
+set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
+
+find_library (NETCDF_LIBRARY NAMES netcdf
+  HINTS "${NETCDF_DIR}/lib")
+mark_as_advanced (NETCDF_LIBRARY)
+
+set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
+
+#start finding requested language components
+set (NetCDF_libs "")
+set (NetCDF_includes "${NETCDF_INCLUDE_DIR}")
+
+get_filename_component (NetCDF_lib_dirs "${NETCDF_LIBRARY}" PATH)
+set (NETCDF_HAS_INTERFACES "YES") # will be set to NO if we're missing any interfaces
+
+macro (NetCDF_check_interface lang header libs)
+  if (NETCDF_${lang})
+    #search starting from user modifiable cache var
+    find_path (NETCDF_${lang}_INCLUDE_DIR NAMES ${header}
+      HINTS "${NETCDF_INCLUDE_DIR}"
+      HINTS "${NETCDF_${lang}_ROOT}/include"
+      ${USE_DEFAULT_PATHS})
+
+    find_library (NETCDF_${lang}_LIBRARY NAMES ${libs}
+      HINTS "${NetCDF_lib_dirs}"
+      HINTS "${NETCDF_${lang}_ROOT}/lib"
+      ${USE_DEFAULT_PATHS})
+
+    mark_as_advanced (NETCDF_${lang}_INCLUDE_DIR NETCDF_${lang}_LIBRARY)
+
+    #export to internal varS that rest of project can use directly
+    set (NETCDF_${lang}_LIBRARIES ${NETCDF_${lang}_LIBRARY})
+    set (NETCDF_${lang}_INCLUDE_DIRS ${NETCDF_${lang}_INCLUDE_DIR})
+
+    if (NETCDF_${lang}_INCLUDE_DIR AND NETCDF_${lang}_LIBRARY)
+      list (APPEND NetCDF_libs ${NETCDF_${lang}_LIBRARY})
+      list (APPEND NetCDF_includes ${NETCDF_${lang}_INCLUDE_DIR})
+    else ()
+      set (NETCDF_HAS_INTERFACES "NO")
+      message (STATUS "Failed to find NetCDF interface for ${lang}")
+    endif ()
+  endif ()
+endmacro ()
+
+list (FIND NetCDF_FIND_COMPONENTS "CXX" _nextcomp)
+if (_nextcomp GREATER -1)
+  set (NETCDF_CXX 1)
+endif ()
+list (FIND NetCDF_FIND_COMPONENTS "F77" _nextcomp)
+if (_nextcomp GREATER -1)
+  set (NETCDF_F77 1)
+endif ()
+list (FIND NetCDF_FIND_COMPONENTS "F90" _nextcomp)
+if (_nextcomp GREATER -1)
+  set (NETCDF_F90 1)
+endif ()
+NetCDF_check_interface (CXX netcdfcpp.h netcdf_c++)
+NetCDF_check_interface (F77 netcdf.inc  netcdff)
+NetCDF_check_interface (F90 netcdf.mod  netcdff)
+
+#export accumulated results to internal varS that rest of project can depend on
+list (APPEND NetCDF_libs "${NETCDF_C_LIBRARIES}")
+set (NETCDF_LIBRARIES ${NetCDF_libs})
+set (NETCDF_INCLUDE_DIRS ${NetCDF_includes})
+
+# 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_INCLUDE_DIRS NETCDF_HAS_INTERFACES)

cmake/OpenfastFortranOptions.cmake

@@ -109,9 +109,9 @@ endmacro(check_f2008_features)
 #
 macro(set_fast_gfortran)
   if(NOT WIN32)
-    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fpic ")
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fpic")
-    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fpic")
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fPIC ")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
   endif(NOT WIN32)
 
   # Fix free-form compilation for OpenFAST

docs/changelogs/v3.5.2.md

@@ -0,0 +1,70 @@
+**Feature or improvement description**
+Pull request to merge `rc-3.5.2` into `main` and create a tagged release for v3.5.2.
+
+See the milestone and project pages for additional information
+
+    https://github.com/OpenFAST/openfast/milestone/12
+
+Test results, if applicable
+See GitHub Actions
+
+### Release checklist:
+- [ ] Update the documentation version in docs/conf.py
+- [ ] Update the versions in docs/source/user/api_change.rst
+- [ ] Verify readthedocs builds correctly
+- [ ] Create a tag in OpenFAST
+- [ ] Create a merge commit in r-test and add a corresponding tag
+- [ ] Compile executables for Windows builds
+    - [ ] FAST_SFunc.mexw64
+    - [ ] OpenFAST-Simulink_x64.dll
+    - [ ] openfast_x64.exe
+    - [ ] DISCON.dll (x64)
+    - [ ] AeroDyn_Driver
+    - [ ] AeroDyn_Inflow_C_Binding
+    - [ ] BeamDyn_Driver
+    - [ ] HydroDyn_Driver
+    - [ ] HydroDyn_C_Binding (x64)
+    - [ ] InflowWind_Driver
+    - [ ] IfW_C_Binding (x64)
+    - [ ] MoorDyn_Driver
+    - [ ] FAST.Farm (x64)
+
+# Changelog
+
+## General
+
+### Build systems
+
+#1948 Pass Python_EXECUTABLE to pfunit, add error check on Python version
+
+
+## Module changes
+
+### AeroDyn
+
+#1913 ADI: memory leak in ADI_UpdateStates
+
+### AWAE
+
+#1963 FAST.Farm, Mod_AmbWind=3: add error if HR grid not centered on turbine in Y dimension
+
+### HydroDyn
+
+#1872 Fix segfault in HD when no outputs specified
+
+
+
+## Regression tests
+
+#1886  Update floating MHK case input files
+
+
+
+## Input file changes
+
+No input files change with this release, as this only includes minor bugfixes.
+
+Full list of changes: https://openfast.readthedocs.io/en/main/source/user/api_change.html
+
+Full input file sets: https://github.com/OpenFAST/r-test/tree/v3.5.2 (example input files from the regression testing)
+

docs/conf.py

@@ -66,6 +66,7 @@ def runDoxygen(sourcfile, doxyfileIn, doxyfileOut):
     'sphinxcontrib.doxylink',
     'sphinxcontrib.bibtex',
     'sphinxcontrib.mermaid',
+#    'breathe',
 ]
 bibtex_bibfiles = [
     'source/user/aerodyn-aeroacoustics/references.bib',
@@ -76,7 +77,8 @@ def runDoxygen(sourcfile, doxyfileIn, doxyfileOut):
     'source/user/fast.farm/bibliography.bib',
     'source/user/hydrodyn/references.bib',
     'source/user/servodyn-stc/StC_Refs.bib',
-    'source/user/subdyn/references_SD.bib'
+    'source/user/subdyn/references_SD.bib',
+    'source/dev/cppapi/bibliography.bib'
 ]
 
 autodoc_default_flags = [
@@ -89,6 +91,11 @@ def runDoxygen(sourcfile, doxyfileIn, doxyfileOut):
 
 mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
 
+## Breathe Configuration -- for cpp interface
+#breathe_projects = {"cppapi": "source/dev/cppapi"}
+#breathe_default_project = "cppapi"
+
+
 # FIXME: Naively assuming build directory one level up locally, and two up on readthedocs
 if useDoxygen:
     if readTheDocs:
@@ -130,7 +137,7 @@ def runDoxygen(sourcfile, doxyfileIn, doxyfileOut):
 # The short X.Y version.
 version = u'3.5'
 # The full version, including alpha/beta/rc tags.
-release = u'v3.5.1'
+release = u'v3.5.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -51,8 +51,9 @@ package:
 
    source/this_doc.rst
    source/install/index.rst
-   source/testing/index.rst
+   source/working.rst
    source/user/index.rst
+   source/testing/index.rst
    source/dev/index.rst
    source/license.rst
    source/help.rst

docs/source/dev/cppapi/README.txt

@@ -0,0 +1,8 @@
+2023.12.15 ADP
+
+We don't currently run doxygen on RTD due to some configuration issues.  So the doxygen content for the cpp was manually run and stored (really not ideal and should be fixed).
+
+doxygenclass and doygenstruct are commented out in the following places.  When doxygen is working, turn these back on.
+api.rst:8:    .. doxygenclass:: fast::OpenFAST
+index.rst:18: .. doxygenclass:: fast::fastInputs
+index.rst:27: .. doxygenstruct:: fast::turbineDataType

docs/source/dev/cppapi/api.rst

@@ -0,0 +1,15 @@
+C++ API Documentation
+=====================
+
+OpenFAST
+--------
+
+
+FIXME: **doxygenclass** is needed to render the class structure
+
+..
+ .. doxygenclass:: fast::OpenFAST
+   :members:
+   :protected-members:
+   :undoc-members:
+