Merge dev and 3.5.1; some bug fixes

CMakeLists.txt

@@ -108,10 +108,18 @@ include(${CMAKE_SOURCE_DIR}/cmake/set_rpath.cmake)
 
 if (OPENMP OR BUILD_FASTFARM OR BUILD_OPENFAST_CPP_API)
   FIND_PACKAGE(OpenMP REQUIRED)
-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-  set(CMAKE_FORTRAN_FLAGS "${CMAKE_FORTRAN_FLAGS} ${OpenMP_FORTRAN_FLAGS}")
-  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+  if (OpenMP_Fortran_FOUND)
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${OpenMP_Fortran_FLAGS}")
+    link_libraries("${OpenMP_Fortran_LIBRARIES}")
+  endif()
+  if (OpenMP_C_FOUND)
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+    link_libraries("${OpenMP_C_LIBRARIES}")
+  endif()
+  if (OpenMP_CXX_FOUND)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+    link_libraries("${OpenMP_CXX_LIBRARIES}")
+  endif()
 endif()
 
 #-------------------------------------------------------------------------------
@@ -130,11 +138,13 @@ if (USE_LOCAL_STATIC_LAPACK)
   include(ExternalProject)
   ExternalProject_Add(lapack
     URL http://www.netlib.org/lapack/lapack.tgz
-    CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_SOURCE_DIR}/install
+    CMAKE_ARGS 
+      -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_SOURCE_DIR}/install 
+      -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON
     PREFIX ${CMAKE_BINARY_DIR}/dependencies
     BUILD_BYPRODUCTS ${BLAS_LIB_PATH} ${LAPACK_LIB_PATH}
   )
-  set(LAPACK_LIBRARIES ${BLAS_LIB_PATH} ${LAPACK_LIB_PATH} CACHE STRING "LAPACK library" FORCE)
+  set(LAPACK_LIBRARIES ${LAPACK_LIB_PATH} ${BLAS_LIB_PATH} CACHE STRING "LAPACK library" FORCE)
   install(FILES ${LAPACK_LIBRARIES} DESTINATION ${CMAKE_SOURCE_DIR}/install/lib)
   message(STATUS "Using LAPACK libraries: ${LAPACK_LIBRARIES}")
 else()
@@ -192,7 +202,7 @@ set(OPENFAST_MODULES
   map
   turbsim
   supercontroller
-  openfoam
+  externalinflow
   openfast-library
 )
 

docs/OtherSupporting/TurbSim/Corrections.md

@@ -0,0 +1,5 @@
+# Corrections to TurbSim_v2.00.pdf DRAFT
+
+## p. 34: Input file for User-Defined Profiles
+The User-Defined profiles listed in the "Profiles" section contain horizontal angles, not wind direction, so it should say
+  `3. Horizontal wind angle (degrees, measured counter-clockwise from above)`

docs/changelogs/v3.5.0.md

@@ -98,6 +98,12 @@ See GitHub Actions
 
 #1493 Allow Non-Uniform Force Point Distribution on Blades   @mchurchf
 
+### SubDyn
+
+#1413 Implementing directional cosine matrices and section properties for rectangular members
+#1526 Remove static improvement method (SIM) from the SubDyn elastic output mesh (y3mesh)
+#1531 BugFix - diameter not set properly for rectangular beams
+
 
 ## API changes
 

docs/source/user/aerodyn/appendix.rst

@@ -51,27 +51,34 @@ The blade data input file contains the nodal discretization, geometry, twist, ch
 AeroDyn List of Output Channels
 -------------------------------
 
-This is a list of output parameters for the AeroDyn module.  The names are grouped by meaning, but can be ordered in the OUTPUTS section of the AeroDyn input file as you see fit.  :math:`B \alpha N \beta`, refers to output node :math:`\beta` of blade :math:`\alpha`, where :math:`\alpha` is a number in the range [1,3] and :math:`\beta` is a number in the range [1,9], corresponding to entry :math:`\beta` in the :math:`\textit{BlOutNd}` list.  :math:`\textit{TwN}\beta` refers to output node :math:`\beta` of the tower and is in the range [1,9], corresponding to entry :math:`\beta` in the :math:`\textit{TwOutNd}` list. A comprehensive, up-to-date list of all possible output parameters is given in the Excel file :download:`OutListParameters.xlsx <../../../OtherSupporting/OutListParameters.xlsx>`.
 
-The local tower coordinate system is shown in :numref:`ad_tower_geom` and the local blade coordinate system is shown in :numref:`ad_blade_local_cs` below.  Figure :numref:`ad_blade_local_cs` also shows the direction of the local angles and force components.
+AeroDyn has regular outputs (see :numref:`AD-Outputs`) and nodal outputs (see :numref:`AD-Nodal-Outputs`).
 
-.. _ad_blade_local_cs:
+The coordinate systems used for the outputs (labeled, i, h, p, l, a) are described in :numref:`ad_coordsys`.
 
-.. figure:: figs/aerodyn_blade_local_cs.png
-   :width: 80%
-   :align: center
-   :alt: aerodyn_blade_local_cs.png
 
-   AeroDyn Local Blade Coordinate System (Looking Toward the Tip, 
-   from the Root) – l: Lift, d: Drag, m: Pitching, x: Normal (to Plane), 
-   y: Tangential (to Plane), n: Normal (to Chord), 
-   and t: Tangential (to Chord)
+A comprehensive, up-to-date list of all possible output parameters is given in the Excel file :download:`OutListParameters.xlsx <../../../OtherSupporting/OutListParameters.xlsx>`, in the tab `AeroDyn` and `AeroDyn_Nodes` for the regular and nodal outputs, respectively.
+The names in the Excel file are grouped by meaning, but can be ordered in the OUTPUTS section of the AeroDyn input file as you see fit. 
 
-.. _ad-output-channel:
 
-.. figure:: figs/aerodyn_output_channel.pdf
-   :width: 500px
-   :align: center
-   :alt: aerodyn_output_channel.pdf
 
-   AeroDyn Output Channel List
+**Regular outputs** 
+Some examples of regular outputs are given below (see :download:`OutListParameters.xlsx <../../../OtherSupporting/OutListParameters.xlsx>` for an exhaustive list):
+
+
+   -  `RtAeroCp` : aerodynamic power coefficient. 
+
+
+   - :math:`B \alpha N \beta`, refers to output node :math:`\beta` of blade :math:`\alpha`, where :math:`\alpha` is a number in the range [1,3] and :math:`\beta` is a number in the range [1,9], corresponding to entry :math:`\beta` in the :math:`\textit{BlOutNd}` list.
+
+   - :math:`\textit{TwN}\beta` refers to output node :math:`\beta` of the tower and is in the range [1,9], corresponding to entry :math:`\beta` in the :math:`\textit{TwOutNd}` list. 
+
+
+**Nodal outputs** 
+
+An example of nodal outputs is described below (see :download:`OutListParameters.xlsx <../../../OtherSupporting/OutListParameters.xlsx>` for an exhaustive list).
+
+The x-component of the undisturbed flow velocity (`VUnd`) at all blade nodes in the inertial frame (:math:`i`) is requested by placing  :math:`VUndxi` in the AeroDyn nodal output list. 
+This will result in output channels of the form `AB`:math:`\alpha N\beta` `Vundxi`, for node :math:`\beta` of blade :math:`\alpha`, where :math:`\alpha` is a number in the range [1,3] and :math:`\beta` is a number in the range [1,999] corresponding to the index of the AeroDyn blade node.
+
+

docs/source/user/aerodyn/conf.py

@@ -21,23 +21,43 @@
 import subprocess
 import re
 
-
 from sphinx.highlighting import PygmentsBridge
 from pygments.formatters.latex import LatexFormatter
 
+#sys.path.append(os.path.abspath('_extensions/'))
+
+readTheDocs = os.environ.get('READTHEDOCS', None) == 'True'
+builddir = sys.argv[-1]
+sourcedir = sys.argv[-2]
+
+# Use this to turn Doxygen on or off
+useDoxygen = False
+
+# This function was adapted from https://gitlab.kitware.com/cmb/smtk
+# Only run when on readthedocs
+def runDoxygen(sourcfile, doxyfileIn, doxyfileOut):
+    dx = open(os.path.join(sourcedir, doxyfileIn), 'r')
+    cfg = dx.read()
+    srcdir = os.path.abspath(os.path.join(os.getcwd(), '..'))
+    bindir = srcdir
+    c2 = re.sub('@CMAKE_SOURCE_DIR@', srcdir, re.sub('@CMAKE_BINARY_DIR@', bindir, cfg))
+    doxname = os.path.join(sourcedir, doxyfileOut)
+    dox = open(doxname, 'w')
+    print(c2, file=dox)
+    dox.close()
+    print("Running Doxygen on {}".format(doxyfileOut))
+    doxproc = subprocess.call(('doxygen', doxname))
+
+if readTheDocs and useDoxygen:
+    runDoxygen(sourcedir, 'Doxyfile.in', 'Doxyfile')
+
 class CustomLatexFormatter(LatexFormatter):
     def __init__(self, **options):
         super(CustomLatexFormatter, self).__init__(**options)
         self.verboptions = r"formatcom=\footnotesize"
 
 PygmentsBridge.latex_formatter = CustomLatexFormatter
 
-#sys.path.append(os.path.abspath('_extensions/'))
-
-readTheDocs = os.environ.get('READTHEDOCS', None) == 'True'
-sourcedir = sys.argv[-2]
-builddir = sys.argv[-1]
-
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -56,13 +76,32 @@ def __init__(self, **options):
               'sphinxcontrib.bibtex',
              ]
 
-autodoc_default_flags = ['members','show-inheritance','undoc-members']
+autodoc_default_flags = [
+    'members',
+    'show-inheritance',
+    'undoc-members'
+]
 
 autoclass_content = 'both'
 
 mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
 
 # FIXME: Naively assuming build directory one level up locally, and two up on readthedocs
+if useDoxygen:
+    if readTheDocs:
+        doxylink = {
+            'openfast': (
+                os.path.join(builddir, '..', '..', 'openfast.tag'),
+                os.path.join('html')
+            )
+        }
+    else:
+        doxylink = {
+            'openfast': (
+                os.path.join(builddir, '..', 'openfast.tag'),
+                os.path.join('html')
+            )
+        }
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -79,7 +118,7 @@ def __init__(self, **options):
 # General information about the project.
 project = u'AeroDyn'
 filename = project.replace(' ','_')
-copyright = u'2017, National Renewable Energy Laboratory'
+copyright = u'2023, National Renewable Energy Laboratory'
 author = u'OpenFAST Team'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -96,7 +135,7 @@ def __init__(self, **options):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+# language = None  # Default is English and None is not a valid option
 
 #If true, figures, tables and code-blocks are automatically numbered if they 
 #have a caption. At same time, the numref role is enabled. For now, it works 
@@ -108,6 +147,13 @@ def __init__(self, **options):
 # This patterns also effect to html_static_path and html_extra_path
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
+# FIXME: Naively assuming build directory one level up locally, and two up on readthedocs
+if useDoxygen:
+    if readTheDocs:
+        html_extra_path = [os.path.join(builddir, '..', '..', 'doxygen')]
+    else:
+        html_extra_path = [os.path.join(builddir, '..', 'doxygen')]
+
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
@@ -147,12 +193,15 @@ def __init__(self, **options):
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
+
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
+
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
+
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -162,8 +211,13 @@ def __init__(self, **options):
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, '{}.tex'.format(filename), u'{} Documentation'.format(project),
-     u'National Renewable Energy Laboratory', 'manual'),
+    (
+        master_doc,
+        '{}.tex'.format(filename), 
+        u'{} Documentation'.format(project),
+        u'National Renewable Energy Laboratory',
+        'manual'
+    ),
 ]
 
 
@@ -172,8 +226,13 @@ def __init__(self, **options):
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, project, u'{} Documentation'.format(project),
-     [author], 1)
+    (
+        master_doc,
+        project, 
+        u'{} Documentation'.format(project),
+        [author],
+        1
+    )
 ]
 
 
@@ -183,19 +242,34 @@ def __init__(self, **options):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, filename, u'{} Documentation'.format(project),
-     author, project, 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+    	filename,
+    	u'{} Documentation'.format(project),
+        author,
+        project,
+        'One line description of project.',
+        'Miscellaneous'
+    ),
 ]
 
 def setup(app):
-    app.add_object_type("confval", "confval",
-                        objname="input file parameter",
-                        indextemplate="pair: %s; input file parameter")
-    app.add_object_type("cmakeval", "cmakeval",
-                        objname="CMake configuration value",
-                        indextemplate="pair: %s; CMake configuration")
-
+    try:
+        app.add_css_file('css/math_eq.css')
+    except:
+        pass
+    app.add_object_type(
+        "confval",
+        "confval",
+        objname="input file parameter",
+        indextemplate="pair: %s; input file parameter"
+    )
+    app.add_object_type(
+        "cmakeval",
+        "cmakeval",
+        objname="CMake configuration value",
+        indextemplate="pair: %s; CMake configuration"
+    )
 # --- Prolog that will be included at the top of every rst file
 # Here: defining the role :red: for html and latex
 rst_prolog = r"""
@@ -216,3 +290,4 @@ def setup(app):
 .. role:: red
 
 """
+