Read the Docs build information Build id: 340221 Project: mdolab-adflow Version: latest Commit: f5fd4b7be35bd719c2d0d2443ba5c36ae747b6bf Date: 2020-06-04T17:37:27.948150Z State: finished Success: True [rtd-command-info] start-time: 2020-06-04T17:37:30.082870Z, end-time: 2020-06-04T17:37:32.068449Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/mdolab/adflow.git . Cloning into '.'... [rtd-command-info] start-time: 2020-06-04T17:37:32.385510Z, end-time: 2020-06-04T17:37:32.688179Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at f5fd4b7 updated wrt openmdao api change for petscksp (#51) [rtd-command-info] start-time: 2020-06-04T17:37:32.840439Z, end-time: 2020-06-04T17:37:33.038161Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-06-04T17:37:34.590975Z, end-time: 2020-06-04T17:37:38.512097Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-06-04T17:37:38.647771Z, end-time: 2020-06-04T17:37:39.463488Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (20.1.1) [rtd-command-info] start-time: 2020-06-04T17:37:39.628316Z, end-time: 2020-06-04T17:37:49.033663Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.2-py2.py3-none-any.whl (39 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.4.5.1-py2.py3-none-any.whl (157 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=b17f5ce1e7c0962bceaf6a23934409c8a795b1f6f0802fb5825f67cd1030bf39 Stored in directory: /tmp/pip-ephem-wheel-cache-ej877sia/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491058 sha256=a9d689da76f9e618030db2b88421acd318501d49f98d9d72bbb567366565bd84 Stored in directory: /tmp/pip-ephem-wheel-cache-ej877sia/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, MarkupSafe, Jinja2, chardet, idna, certifi, urllib3, requests, sphinxcontrib-websupport, pyparsing, packaging, snowballstemmer, pytz, babel, imagesize, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 47.1.1 Uninstalling setuptools-47.1.1: Successfully uninstalled setuptools-47.1.1 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.4.5.1 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.23.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.2 urllib3-1.25.9 [rtd-command-info] start-time: 2020-06-04T17:37:49.174698Z, end-time: 2020-06-04T17:37:50.185726Z, duration: 1, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r doc/requirements.txt Collecting numpydoc Downloading numpydoc-1.0.0-py3-none-any.whl (47 kB) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from numpydoc->-r doc/requirements.txt (line 1)) (2.11.2) Requirement already satisfied: sphinx>=1.6.5 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from numpydoc->-r doc/requirements.txt (line 1)) (1.8.5) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->numpydoc->-r doc/requirements.txt (line 1)) (1.1.1) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) 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/home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (41.0.1) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2.3.1) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2.0.0) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2.8.0) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (0.14) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (1.2.0) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2.9) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (1.25.9) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (3.0.4) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2020.4.5.1) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from packaging->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2.4.7) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.6.5->numpydoc->-r doc/requirements.txt (line 1)) (2020.1) Installing collected packages: numpydoc Successfully installed numpydoc-1.0.0 [rtd-command-info] start-time: 2020-06-04T17:37:51.124804Z, end-time: 2020-06-04T17:37:51.326064Z, duration: 0, exit-code: 0 cat doc/conf.py # Configuration file for the Sphinx documentation builder. # # This file only contains a selection of the most common options. For a full # list see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. import os import sys sys.path.insert(0, os.path.abspath("../")) # -- Project information ----------------------------------------------------- project = 'ADflow' copyright = '2020, MDO Lab' # -- General configuration --------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = ['sphinx.ext.viewcode', 'sphinx.ext.imgmath', 'sphinx.ext.autodoc', 'numpydoc'] # mock import for autodoc autodoc_mock_imports = ['numpy', 'mpi4py', 'petsc4py', 'baseclasses'] # The master toctree document. master_doc = 'index' # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # # html_theme = 'alabaster' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'css_files': [ '_static/theme_overrides.css', # override wide tables in RTD theme ], } ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ("pdf", "//mdolab-adflow.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//mdolab-adflow.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//mdolab-adflow.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'mdolab-adflow', 'name': u'adflow', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://mdolab-adflow.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/doc/', 'api_host': 'https://readthedocs.com', 'github_user': 'mdolab', 'proxied_api_host': '/_', 'github_repo': 'adflow', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'f5fd4b7b', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' [rtd-command-info] start-time: 2020-06-04T17:37:51.445444Z, end-time: 2020-06-04T17:37:56.800189Z, duration: 5, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 11 source files that are out of date updating environment: 11 added, 0 changed, 0 removed reading sources... [ 9%] adjoint reading sources... [ 18%] autodiff reading sources... [ 27%] devguide reading sources... [ 36%] index reading sources... [ 45%] install reading sources... [ 54%] introduction reading sources... [ 63%] options reading sources... [ 72%] performance reading sources... [ 81%] pyADflow reading sources... [ 90%] solvers reading sources... 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document 'python.pyADflow.ADFLOW.writeVolumeSolutionFile' generating indices... genindex highlighting module code... 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The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2020-06-04T17:38:05.152285Z, end-time: 2020-06-04T17:38:05.359269Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2020-06-04T17:38:05.469534Z, end-time: 2020-06-04T17:38:07.646527Z, duration: 2, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=mdolab-adflow -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. [5] [6] Chapter 3. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8] [9] [10] Chapter 4. Underfull \hbox (badness 5787) in paragraph at lines 544--547 \T1/ptm/m/n/10 di-tion in-for-ma-tion con- Underfull \hbox (badness 10000) in paragraph at lines 566--568 []|\T1/ptm/m/n/10 Flag to use spec-i-fied Underfull \hbox (badness 5231) in paragraph at lines 633--636 \T1/ptm/m/n/10 pre-ci-sion can ad-versely Underfull \hbox (badness 10000) in paragraph at lines 643--649 \T1/ptm/m/n/10 ^^Pvol-umeVari-ables^^Q may Underfull \hbox (badness 10000) in paragraph at lines 643--649 \T1/ptm/m/n/10 `isoSurface':{`Vx':- Underfull \hbox (badness 10000) in paragraph at lines 656--661 []|\T1/ptm/m/n/10 Only ap-pli-ca-ble for Underfull \hbox (badness 10000) in paragraph at lines 656--661 \T1/ptm/m/n/10 RANS/laminar com-pu- Underfull \hbox (badness 5667) in paragraph at lines 656--661 \T1/ptm/m/n/10 ve-loc-i-ties as the value Underfull \hbox (badness 10000) in paragraph at lines 656--661 \T1/ptm/m/n/10 the ve-loc-i-ties on the Underfull \hbox (badness 10000) in paragraph at lines 668--669 []|\T1/ptm/m/n/10 Set the dis-cretiza-tion Underfull \hbox (badness 10000) in paragraph at lines 668--669 \T1/ptm/m/n/10 gen-er-ally rec-om-mended Underfull \hbox (badness 6608) in paragraph at lines 668--669 \T1/ptm/m/n/10 speed, at the cost of Underfull \hbox (badness 10000) in paragraph at lines 668--669 \T1/ptm/m/n/10 nu-mer-i-cal ac-cu-racy. Underfull \hbox (badness 10000) in paragraph at lines 688--690 []|\T1/ptm/m/n/10 Set the dis-cretiza-tion Underfull \hbox (badness 6412) in paragraph at lines 688--690 \T1/ptm/m/n/10 method for the coarse Underfull \hbox (badness 10000) in paragraph at lines 688--690 \T1/ptm/m/n/10 be the same as the Underfull \hbox (badness 10000) in paragraph at lines 707--712 []|\T1/ptm/m/n/10 Type of \T1/ptm/m/it/10 solver \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 707--712 \T1/ptm/m/n/10 smoother to use with Underfull \hbox (badness 10000) in paragraph at lines 707--712 \T1/ptm/m/n/10 ized diagonal-dominant Underfull \hbox (badness 10000) in paragraph at lines 707--712 \T1/ptm/m/n/10 alternating-direction im- Underfull \hbox (badness 6658) in paragraph at lines 728--733 \T1/ptm/m/n/10 ex-ten-sively tested from Underfull \hbox (badness 7631) in paragraph at lines 728--733 \T1/ptm/m/n/10 been ex-ten-sively tested Underfull \hbox (badness 10000) in paragraph at lines 740--743 \T1/ptm/m/n/10 sim-u-la-tions have been Underfull \hbox (badness 10000) in paragraph at lines 756--757 []\T1/ptm/m/it/10 sae \T1/ptm/m/n/10 - Sparart Underfull \hbox (badness 10000) in paragraph at lines 756--757 \T1/ptm/m/n/10 Allmaras-Edward Underfull \hbox (badness 10000) in paragraph at lines 793--795 []|\T1/ptm/m/n/10 This pa-ram-e-ter af-fects Underfull \hbox (badness 7291) in paragraph at lines 793--795 \T1/ptm/m/n/10 how the to-tal resid-ual Underfull \hbox (badness 10000) in paragraph at lines 793--795 \T1/ptm/m/n/10 what tur-bu-lence model Underfull \hbox (badness 10000) in paragraph at lines 797--798 \T1/ptm/m/it/10 scalar \T1/ptm/m/n/10 - De-fault: Underfull \hbox (badness 10000) in paragraph at lines 800--801 []\T1/ptm/m/it/10 sae \T1/ptm/m/n/10 - Sparart Underfull \hbox (badness 10000) in paragraph at lines 800--801 \T1/ptm/m/n/10 Allmaras-Edward Underfull \hbox (badness 10000) in paragraph at lines 800--801 \T1/ptm/m/n/10 model - NOT Underfull \hbox (badness 10000) in paragraph at lines 803--804 []\T1/ptm/m/it/10 k omega wilcox Underfull \hbox (badness 10000) in paragraph at lines 803--804 \T1/ptm/m/n/10 - NOT IM-PLE- Underfull \hbox (badness 10000) in paragraph at lines 806--807 \T1/ptm/m/n/10 - NOT IM-PLE- Underfull \hbox (badness 10000) in paragraph at lines 826--831 \T1/ptm/m/n/10 This is gen-er-ally not Underfull \hbox (badness 10000) in paragraph at lines 826--831 \T1/ptm/m/n/10 give (po-ten-tially very) Underfull \hbox (badness 10000) in paragraph at lines 826--831 \T1/ptm/m/n/10 poor drag es-ti-mates. Overfull \hbox (13.11995pt too wide) in paragraph at lines 832--833 []|\T1/ptm/m/it/10 useApproximateWallDistance| Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 dis-tance cal-cu-la-tion. Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 ex-act wall dis-tances Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 are com-puted dur-ing Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 ini-tial-iza-tion and the Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 para-met-ric lo-ca-tion of Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 the ge-om-e-try de-forms Underfull \hbox (badness 5288) in paragraph at lines 853--859 \T1/ptm/m/n/10 ary con-di-tions are im- Underfull \hbox (badness 10000) in paragraph at lines 853--859 \T1/ptm/m/n/10 ple-mented for in-vis-cid Underfull \hbox (badness 6808) in paragraph at lines 853--859 \T1/ptm/m/it/10 ex-trap-o-la-tion\T1/ptm/m/n/10 , \T1/ptm/m/it/10 quadratic Underfull \hbox (badness 10000) in paragraph at lines 853--859 \T1/ptm/m/it/10 pres-sure ex-trap-o-la-tion Underfull \hbox (badness 5105) in paragraph at lines 866--870 \T1/ptm/m/n/10 de-fault value need not Overfull \hbox (6.90999pt too wide) in paragraph at lines 871--872 []|\T1/ptm/m/it/10 dissipationScalingExponent| Underfull \hbox (badness 10000) in paragraph at lines 968--972 \T1/ptm/m/n/10 mean-ing-ful for RANS Underfull \hbox (badness 10000) in paragraph at lines 968--972 \T1/ptm/m/n/10 sim-u-la-tions. Cer-tain Underfull \hbox (badness 10000) in paragraph at lines 968--972 \T1/ptm/m/n/10 ben-e-fit from a slight Underfull \hbox (badness 10000) in paragraph at lines 979--985 []|\T1/ptm/m/n/10 The Underfull \hbox (badness 10000) in paragraph at lines 979--985 \T1/ptm/m/n/10 the Runge-Kutta sim- Underfull \hbox (badness 10000) in paragraph at lines 979--985 \T1/ptm/m/n/10 main pa-ram-e-ter that Underfull \hbox (badness 10000) in paragraph at lines 979--985 \T1/ptm/m/n/10 de-ter-mines the over-all Underfull \hbox (badness 10000) in paragraph at lines 979--985 \T1/ptm/m/n/10 some ex-per-i-men-ta-tion [11] [12] [13] [14] Underfull \hbox (badness 7649) in paragraph at lines 1048--1052 \T1/ptm/m/n/10 could be run with-iout Underfull \hbox (badness 7238) in paragraph at lines 1063--1064 []\T1/ptm/m/it/10 bdf \T1/ptm/m/n/10 - 2nd or-der Underfull \hbox (badness 10000) in paragraph at lines 1063--1064 \T1/ptm/m/n/10 back-wards dif-fer- Underfull \hbox (badness 10000) in paragraph at lines 1072--1073 []\T1/ptm/m/it/10 md \T1/ptm/m/n/10 - Mul-ti-dis- Underfull \hbox (badness 10000) in paragraph at lines 1072--1073 \T1/ptm/m/n/10 ci-plinary (md) Underfull \hbox (badness 10000) in paragraph at lines 1072--1073 \T1/ptm/m/n/10 / Ar-bi-trary La- Underfull \hbox (badness 10000) in paragraph at lines 1072--1073 \T1/ptm/m/n/10 grangian Eu-le-rian Underfull \hbox (badness 5832) in paragraph at lines 1111--1114 []|\T1/ptm/m/n/10 The num-ber of ^^Pspec- Underfull \hbox (badness 7667) in paragraph at lines 1139--1141 []|\T1/ptm/m/n/10 Use a spec-i-fied Mach Underfull \hbox (badness 10000) in paragraph at lines 1139--1141 \T1/ptm/m/n/10 Time spec-tral anal-y-sis. Underfull \hbox (badness 10000) in paragraph at lines 1148--1150 \T1/ptm/m/n/10 Time spec-tral anal-y-sis. Underfull \hbox (badness 6995) in paragraph at lines 1157--1159 \T1/ptm/m/n/10 (pitch) mo-tion for the Underfull \hbox (badness 10000) in paragraph at lines 1166--1168 \T1/ptm/m/n/10 (yaw) mo-tion for the Underfull \hbox (badness 10000) in paragraph at lines 1166--1168 \T1/ptm/m/n/10 Time spec-tral anal-y-sis. Underfull \hbox (badness 10000) in paragraph at lines 1193--1195 []|\T1/ptm/m/n/10 Flag to com-pute time Underfull \hbox (badness 6268) in paragraph at lines 1202--1209 \T1/ptm/m/n/10 1 to 2 or-ders mag-ni- Underfull \hbox (badness 5431) in paragraph at lines 1227--1231 []|\T1/ptm/m/n/10 The con-ver-gence fac-tor Underfull \hbox (badness 10000) in paragraph at lines 1227--1231 \T1/ptm/m/n/10 grids dur-ing multi-grid Underfull \hbox (badness 6078) in paragraph at lines 1238--1242 \T1/ptm/m/n/10 ual can be above the [15] [16] [17] [18] [19] [20] [21] Underfull \hbox (badness 10000) in paragraph at lines 1272--1277 []|\T1/ptm/m/n/10 Type of PETSc KSP Underfull \hbox (badness 6364) in paragraph at lines 1272--1277 \T1/ptm/m/n/10 ^^U Transpose-Free quasi Underfull \hbox (badness 10000) in paragraph at lines 1284--1289 []|\T1/ptm/m/n/10 The rel-a-tive tol-er-ance Underfull \hbox (badness 10000) in paragraph at lines 1284--1289 \T1/ptm/m/n/10 New-ton so-lu-tion tech- Underfull \hbox (badness 5862) in paragraph at lines 1284--1289 \T1/ptm/m/n/10 dif-fi-cult tran-sients have Underfull \hbox (badness 6268) in paragraph at lines 1296--1299 []|\T1/ptm/m/n/10 The size of the GM- Underfull \hbox (badness 5652) in paragraph at lines 1306--1310 \T1/ptm/m/n/10 so-lu-tion; there-after the [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 1528--1530 []|\T1/ptm/m/n/10 List of the vari-ables Underfull \hbox (badness 10000) in paragraph at lines 1528--1530 \T1/ptm/m/n/10 whose con-ver-gence Underfull \hbox (badness 10000) in paragraph at lines 1528--1530 \T1/ptm/m/n/10 should be mon-i-tored. Underfull \hbox (badness 10000) in paragraph at lines 1532--1533 []\T1/ptm/m/it/10 resrho \T1/ptm/m/n/10 (den-sity Underfull \hbox (badness 10000) in paragraph at lines 1535--1536 []\T1/ptm/m/it/10 resmom \T1/ptm/m/n/10 (mo-men- Underfull \hbox (badness 10000) in paragraph at lines 1553--1554 []\T1/ptm/m/it/10 cd \T1/ptm/m/n/10 (drag co-ef-fi- Underfull \hbox (badness 10000) in paragraph at lines 1562--1563 []\T1/ptm/m/it/10 cfx \T1/ptm/m/n/10 (force co- Underfull \hbox (badness 10000) in paragraph at lines 1562--1563 \T1/ptm/m/n/10 ef-fi-cient in x- Underfull \hbox (badness 10000) in paragraph at lines 1565--1566 []\T1/ptm/m/it/10 cfy \T1/ptm/m/n/10 (force co- Underfull \hbox (badness 10000) in paragraph at lines 1565--1566 \T1/ptm/m/n/10 ef-fi-cient in y- Underfull \hbox (badness 10000) in paragraph at lines 1568--1569 []\T1/ptm/m/it/10 cfz \T1/ptm/m/n/10 (force co- Underfull \hbox (badness 10000) in paragraph at lines 1568--1569 \T1/ptm/m/n/10 ef-fi-cient in z- Underfull \hbox (badness 10000) in paragraph at lines 1571--1572 []\T1/ptm/m/it/10 cmx \T1/ptm/m/n/10 (mo-ment Underfull \hbox (badness 10000) in paragraph at lines 1571--1572 \T1/ptm/m/n/10 co-ef-fi-cient in Underfull \hbox (badness 10000) in paragraph at lines 1574--1575 []\T1/ptm/m/it/10 cmy \T1/ptm/m/n/10 (mo-ment Underfull \hbox (badness 10000) in paragraph at lines 1574--1575 \T1/ptm/m/n/10 co-ef-fi-cient in Underfull \hbox (badness 10000) in paragraph at lines 1577--1578 []\T1/ptm/m/it/10 cmz \T1/ptm/m/n/10 (mo-ment Underfull \hbox (badness 10000) in paragraph at lines 1577--1578 \T1/ptm/m/n/10 co-ef-fi-cient in Underfull \hbox (badness 10000) in paragraph at lines 1580--1581 []\T1/ptm/m/it/10 hdiff \T1/ptm/m/n/10 (max-i-mum Underfull \hbox (badness 10000) in paragraph at lines 1580--1581 \T1/ptm/m/n/10 rel-a-tive dif-fer-ence Underfull \hbox (badness 10000) in paragraph at lines 1580--1581 \T1/ptm/m/n/10 be-tween H and Underfull \hbox (badness 10000) in paragraph at lines 1583--1584 []\T1/ptm/m/it/10 mach \T1/ptm/m/n/10 (max-i-mum Underfull \hbox (badness 10000) in paragraph at lines 1589--1590 []\T1/ptm/m/it/10 eddyv \T1/ptm/m/n/10 (max-i-mum Underfull \hbox (badness 10000) in paragraph at lines 1598--1599 []|\T1/ptm/m/n/10 [`cp','vx', `vy', `vz', Underfull \hbox (badness 7012) in paragraph at lines 1630--1631 []\T1/ptm/m/it/10 cf \T1/ptm/m/n/10 (mag-ni-tude of Underfull \hbox (badness 10000) in paragraph at lines 1662--1664 []|\T1/ptm/m/n/10 The vari-ables which Underfull \hbox (badness 10000) in paragraph at lines 1662--1664 \T1/ptm/m/n/10 restart, writ-ten to the Underfull \hbox (badness 10000) in paragraph at lines 1662--1664 \T1/ptm/m/n/10 CGNS vol-ume so-lu- Underfull \hbox (badness 10000) in paragraph at lines 1699--1700 []\T1/ptm/m/it/10 macht \T1/ptm/m/n/10 (tur-bu-lent Underfull \hbox (badness 10000) in paragraph at lines 1714--1715 []\T1/ptm/m/it/10 resrho \T1/ptm/m/n/10 (den-sity Underfull \hbox (badness 10000) in paragraph at lines 1717--1718 []\T1/ptm/m/it/10 resmom \T1/ptm/m/n/10 (mo-men- Overfull \hbox (0.85033pt too wide) in paragraph at lines 1767--1768 []|\T1/ptm/m/it/10 adjointL2ConvergenceAbs| [24] [25] [26] [27] Overfull \hbox (16.57002pt too wide) in paragraph at lines 1867--1868 []|\T1/ptm/m/it/10 dissipationLumpingParameter| Underfull \hbox (badness 6412) in paragraph at lines 1902--1904 []|\T1/ptm/m/n/10 The type of pre-con-di- Overfull \hbox (13.39014pt too wide) in paragraph at lines 1968--1969 []|\T1/ptm/m/it/10 applyAdjointPCSubspaceSize| [28] [29] [30] [31] [32] [33] [34] [35] [36] Chapter 5. LaTeX Warning: Hyper reference `pyADflow:python.pyADflow.ADFLOW.addActuatorRegi on' on page 37 undefined on input line 2090. LaTeX Warning: Hyper reference `pyADflow:python.pyADflow.ADFLOW.addFunction' on page 37 undefined on input line 2095. Underfull \hbox (badness 10000) in paragraph at lines 2095--2096 []|\T1/pcr/m/sl/10 addFunction\T1/ptm/m/n/10 (self, func-Name, group-Name[, LaTeX Warning: Hyper reference `pyADflow:python.pyADflow.ADFLOW.addFunctions' o n page 37 undefined on input line 2100. LaTeX Warning: Hyper reference `pyADflow:python.pyADflow.ADFLOW.addIntegrationS urface' on page 37 undefined on input line 2105. LaTeX Warning: Hyper reference `pyADflow:python.pyADflow.ADFLOW.addLiftDistribu tion' on page 37 undefined on input line 2110. LaTeX Warning: Hyper reference `pyADflow:python.pyADflow.ADFLOW.addSlices' on p age 37 undefined on input line 2115. LaTeX Warning: Hyper reference `pyADflow:python.pyADflow.ADFLOW.addUserFunction ' on page 37 undefined on input line 2120. 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[67] [68] Underfull \hbox (badness 10000) in paragraph at lines 4760--4761 \T1/ptm/m/n/10 The main Python meth-ods for deriva-tive seed ma-nip-u-la-tion i n AD-flow are Underfull \hbox (badness 5431) in paragraph at lines 4760--4761 \T1/pcr/m/n/10 computeJacobianVectorProductFwd \T1/ptm/m/n/10 and \T1/pcr/m/n/1 0 computeJacobianVectorProductBwd\T1/ptm/m/n/10 , both lo-cated Underfull \hbox (badness 10000) in paragraph at lines 4780--4781 []\T1/ptm/m/n/10 The re-verse mas-ter (\T1/pcr/m/n/10 master_b\T1/ptm/m/n/10 ) rou-tine is wrapped by a thin wrap-per which is the [69] [70] No file mdolab-adflow.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. [71] (./mdolab-adflow.aux) Package rerunfilecheck Warning: File `mdolab-adflow.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on mdolab-adflow.pdf (75 pages, 334503 bytes). Transcript written on mdolab-adflow.log. Latexmk: Index file 'mdolab-adflow.idx' was written Latexmk: Missing input file: 'mdolab-adflow.ind' from line 'No file mdolab-adflow.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'mdolab-adflow.pdf' Rule 'makeindex mdolab-adflow.idx': File changes, etc: Non-existent destination files: 'mdolab-adflow.ind' ------------ Run number 1 of rule 'makeindex mdolab-adflow.idx' ------------ ------------ Running 'makeindex -s python.ist -o "mdolab-adflow.ind" "mdolab-adflow.idx"' ------------ Latexmk: applying rule 'makeindex mdolab-adflow.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file mdolab-adflow.idx....done (71 entries accepted, 0 rejected). Sorting entries....done (393 comparisons). Generating output file mdolab-adflow.ind....done (116 lines written, 0 warnings). Output written in mdolab-adflow.ind. Transcript written in mdolab-adflow.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'mdolab-adflow.aux' 'mdolab-adflow.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="mdolab-adflow" "ADflow.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ADflow.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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Underfull \hbox (badness 10000) in paragraph at lines 1148--1150 \T1/ptm/m/n/10 Time spec-tral anal-y-sis. Underfull \hbox (badness 6995) in paragraph at lines 1157--1159 \T1/ptm/m/n/10 (pitch) mo-tion for the Underfull \hbox (badness 10000) in paragraph at lines 1166--1168 \T1/ptm/m/n/10 (yaw) mo-tion for the Underfull \hbox (badness 10000) in paragraph at lines 1166--1168 \T1/ptm/m/n/10 Time spec-tral anal-y-sis. Underfull \hbox (badness 10000) in paragraph at lines 1193--1195 []|\T1/ptm/m/n/10 Flag to com-pute time Underfull \hbox (badness 6268) in paragraph at lines 1202--1209 \T1/ptm/m/n/10 1 to 2 or-ders mag-ni- Underfull \hbox (badness 5431) in paragraph at lines 1227--1231 []|\T1/ptm/m/n/10 The con-ver-gence fac-tor Underfull \hbox (badness 10000) in paragraph at lines 1227--1231 \T1/ptm/m/n/10 grids dur-ing multi-grid Underfull \hbox (badness 6078) in paragraph at lines 1238--1242 \T1/ptm/m/n/10 ual can be above the [15] [16] [17] [18] [19] [20] [21] Underfull \hbox (badness 10000) in paragraph at lines 1272--1277 []|\T1/ptm/m/n/10 Type of PETSc KSP Underfull \hbox (badness 6364) in paragraph at lines 1272--1277 \T1/ptm/m/n/10 ^^U Transpose-Free quasi Underfull \hbox (badness 10000) in paragraph at lines 1284--1289 []|\T1/ptm/m/n/10 The rel-a-tive tol-er-ance Underfull \hbox (badness 10000) in paragraph at lines 1284--1289 \T1/ptm/m/n/10 New-ton so-lu-tion tech- Underfull \hbox (badness 5862) in paragraph at lines 1284--1289 \T1/ptm/m/n/10 dif-fi-cult tran-sients have Underfull \hbox (badness 6268) in paragraph at lines 1296--1299 []|\T1/ptm/m/n/10 The size of the GM- Underfull \hbox (badness 5652) in paragraph at lines 1306--1310 \T1/ptm/m/n/10 so-lu-tion; there-after the [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 1528--1530 []|\T1/ptm/m/n/10 List of the vari-ables Underfull \hbox (badness 10000) in paragraph at lines 1528--1530 \T1/ptm/m/n/10 whose con-ver-gence Underfull \hbox (badness 10000) in paragraph at lines 1528--1530 \T1/ptm/m/n/10 should be mon-i-tored. Underfull \hbox (badness 10000) in paragraph at lines 1532--1533 []\T1/ptm/m/it/10 resrho \T1/ptm/m/n/10 (den-sity Underfull \hbox (badness 10000) in paragraph at lines 1535--1536 []\T1/ptm/m/it/10 resmom \T1/ptm/m/n/10 (mo-men- Underfull \hbox (badness 10000) in paragraph at lines 1553--1554 []\T1/ptm/m/it/10 cd \T1/ptm/m/n/10 (drag co-ef-fi- Underfull \hbox (badness 10000) in paragraph at lines 1562--1563 []\T1/ptm/m/it/10 cfx \T1/ptm/m/n/10 (force co- Underfull \hbox (badness 10000) in paragraph at lines 1562--1563 \T1/ptm/m/n/10 ef-fi-cient in x- Underfull \hbox (badness 10000) in paragraph at lines 1565--1566 []\T1/ptm/m/it/10 cfy \T1/ptm/m/n/10 (force co- Underfull \hbox (badness 10000) in paragraph at lines 1565--1566 \T1/ptm/m/n/10 ef-fi-cient in y- Underfull \hbox (badness 10000) in paragraph at lines 1568--1569 []\T1/ptm/m/it/10 cfz \T1/ptm/m/n/10 (force co- Underfull \hbox (badness 10000) in paragraph at lines 1568--1569 \T1/ptm/m/n/10 ef-fi-cient in z- Underfull \hbox (badness 10000) in paragraph at lines 1571--1572 []\T1/ptm/m/it/10 cmx \T1/ptm/m/n/10 (mo-ment Underfull \hbox (badness 10000) in paragraph at lines 1571--1572 \T1/ptm/m/n/10 co-ef-fi-cient in Underfull \hbox (badness 10000) in paragraph at lines 1574--1575 []\T1/ptm/m/it/10 cmy \T1/ptm/m/n/10 (mo-ment Underfull \hbox (badness 10000) in paragraph at lines 1574--1575 \T1/ptm/m/n/10 co-ef-fi-cient in Underfull \hbox (badness 10000) in paragraph at lines 1577--1578 []\T1/ptm/m/it/10 cmz \T1/ptm/m/n/10 (mo-ment Underfull \hbox (badness 10000) in paragraph at lines 1577--1578 \T1/ptm/m/n/10 co-ef-fi-cient in Underfull \hbox (badness 10000) in paragraph at lines 1580--1581 []\T1/ptm/m/it/10 hdiff \T1/ptm/m/n/10 (max-i-mum Underfull \hbox (badness 10000) in paragraph at lines 1580--1581 \T1/ptm/m/n/10 rel-a-tive dif-fer-ence Underfull \hbox (badness 10000) in paragraph at lines 1580--1581 \T1/ptm/m/n/10 be-tween H and Underfull \hbox (badness 10000) in paragraph at lines 1583--1584 []\T1/ptm/m/it/10 mach \T1/ptm/m/n/10 (max-i-mum Underfull \hbox (badness 10000) in paragraph at lines 1589--1590 []\T1/ptm/m/it/10 eddyv \T1/ptm/m/n/10 (max-i-mum Underfull \hbox (badness 10000) in paragraph at lines 1598--1599 []|\T1/ptm/m/n/10 [`cp','vx', `vy', `vz', Underfull \hbox (badness 7012) in paragraph at lines 1630--1631 []\T1/ptm/m/it/10 cf \T1/ptm/m/n/10 (mag-ni-tude of Underfull \hbox (badness 10000) in paragraph at lines 1662--1664 []|\T1/ptm/m/n/10 The vari-ables which Underfull \hbox (badness 10000) in paragraph at lines 1662--1664 \T1/ptm/m/n/10 restart, writ-ten to the Underfull \hbox (badness 10000) in paragraph at lines 1662--1664 \T1/ptm/m/n/10 CGNS vol-ume so-lu- Underfull \hbox (badness 10000) in paragraph at lines 1699--1700 []\T1/ptm/m/it/10 macht \T1/ptm/m/n/10 (tur-bu-lent Underfull \hbox (badness 10000) in paragraph at lines 1714--1715 []\T1/ptm/m/it/10 resrho \T1/ptm/m/n/10 (den-sity Underfull \hbox (badness 10000) in paragraph at lines 1717--1718 []\T1/ptm/m/it/10 resmom \T1/ptm/m/n/10 (mo-men- Overfull \hbox (0.85033pt too wide) in paragraph at lines 1767--1768 []|\T1/ptm/m/it/10 adjointL2ConvergenceAbs| [24] [25] [26] [27] Overfull \hbox (16.57002pt too wide) in paragraph at lines 1867--1868 []|\T1/ptm/m/it/10 dissipationLumpingParameter| Underfull \hbox (badness 6412) in paragraph at lines 1902--1904 []|\T1/ptm/m/n/10 The type of pre-con-di- Overfull \hbox (13.39014pt too wide) in paragraph at lines 1968--1969 []|\T1/ptm/m/it/10 applyAdjointPCSubspaceSize| [28] [29] [30] [31] [32] [33] [34] [35] [36] Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 2095--2096 []|[][]\T1/pcr/m/sl/10 addFunction[][]\T1/ptm/m/n/10 (self, func-Name, group-Na me[, Overfull \hbox (2.64201pt too wide) in paragraph at lines 2255--2256 []|[][]\T1/pcr/m/sl/10 getUniqueSpatialPerturbationNorm[][]\T1/ptm/m/n/10 (self , Underfull \hbox (badness 10000) in paragraph at lines 2270--2271 []|[][]\T1/pcr/m/sl/10 mapVector[][]\T1/ptm/m/n/10 (self, vec1, group-Name1, gr oup- Underfull \hbox (badness 10000) in paragraph at lines 2275--2276 []|[][]\T1/pcr/m/sl/10 propagateUncertainty[][]\T1/ptm/m/n/10 (self, aero-Prob- lem[, [37] Underfull \hbox (badness 10000) in paragraph at lines 2330--2331 []|[][]\T1/pcr/m/sl/10 setRotationRate[][]\T1/ptm/m/n/10 (self, rot-Cen-ter, ro -tRate[, Underfull \hbox (badness 10000) in paragraph at lines 2340--2341 []|[][]\T1/pcr/m/sl/10 setSurfaceCoordinates[][]\T1/ptm/m/n/10 (self, co-or-di- nates[, [38] Underfull \hbox (badness 10000) in paragraph at lines 2400--2401 []|[][]\T1/pcr/m/sl/10 writeLiftDistributionFile[][]\T1/ptm/m/n/10 (self, file- Underfull \hbox (badness 10000) in paragraph at lines 2415--2416 []|[][]\T1/pcr/m/sl/10 writeSolution[][]\T1/ptm/m/n/10 (self[, out-put-Dir, bas e-Name, Underfull \hbox (badness 10000) in paragraph at lines 2420--2421 []|[][]\T1/pcr/m/sl/10 writeSurfaceSensitivity[][]\T1/ptm/m/n/10 (self, file-Na me, Underfull \hbox (badness 10000) in paragraph at lines 2430--2431 []|[][]\T1/pcr/m/sl/10 writeSurfaceSolutionFileTecplot[][]\T1/ptm/m/n/10 (self, [39] Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 2728--2728 []\T1/ptm/m/it/10 self\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res-Bar=None\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 funcs-Bar=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fBar=None\T 1/ptm/m/n/10 , Underfull \hbox (badness 6157) in paragraph at lines 2728--2728 \T1/ptm/m/it/10 wDeriv=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xVDeriv=None\T1/ptm /m/n/10 , \T1/ptm/m/it/10 xS-Deriv=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xD- [42] Underfull \hbox (badness 10000) in paragraph at lines 2782--2782 []\T1/ptm/m/it/10 self\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xD-v-Dot=None\T1/ptm/m/n /10 , \T1/ptm/m/it/10 xS-Dot=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xV-Dot=None\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2782--2782 \T1/ptm/m/it/10 wDot=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 resid-u-alDeriv=False \T1/ptm/m/n/10 , \T1/ptm/m/it/10 funcDeriv=False\T1/ptm/m/n/10 , [43] [44] [45] [46] [47] [48] [49] Underfull \hbox (badness 10000) in paragraph at lines 3727--3736 []\T1/ptm/m/n/10 [dict] Dic-tio-nary of func-tion DV pairs to solve: {`func':{` dv':str, [50] [51] Underfull \hbox (badness 7168) in paragraph at lines 3908--3910 []\T1/ptm/m/n/10 only used from an ex-ter-nal [52] Chapter 6. [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] Chapter 7. [65] [66] Chapter 8. [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 4760--4761 \T1/ptm/m/n/10 The main Python meth-ods for deriva-tive seed ma-nip-u-la-tion i n AD-flow are Underfull \hbox (badness 5431) in paragraph at lines 4760--4761 \T1/pcr/m/n/10 computeJacobianVectorProductFwd \T1/ptm/m/n/10 and \T1/pcr/m/n/1 0 computeJacobianVectorProductBwd\T1/ptm/m/n/10 , both lo-cated Underfull \hbox (badness 10000) in paragraph at lines 4780--4781 []\T1/ptm/m/n/10 The re-verse mas-ter (\T1/pcr/m/n/10 master_b\T1/ptm/m/n/10 ) rou-tine is wrapped by a thin wrap-per which is the [69] [70] (./mdolab-adflow.ind [71] [72] Underfull \hbox (badness 10000) in paragraph at lines 8--9 []\T1/pcr/m/n/10 addActuatorRegion() Underfull \hbox (badness 10000) in paragraph at lines 9--10 []\T1/pcr/m/n/10 addFunction() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 10--11 []\T1/pcr/m/n/10 addFunctions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow .ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 11--12 []\T1/pcr/m/n/10 addIntegrationSurface() Underfull \hbox (badness 10000) in paragraph at lines 12--13 []\T1/pcr/m/n/10 addLiftDistribution() Underfull \hbox (badness 10000) in paragraph at lines 14--15 []\T1/pcr/m/n/10 addUserFunction() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADf low.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 16--17 []\T1/pcr/m/n/10 advanceTimeStepCounter() Underfull \hbox (badness 10000) in paragraph at lines 20--21 []\T1/pcr/m/n/10 checkPartitioning() Underfull \hbox (badness 10000) in paragraph at lines 21--23 []\T1/pcr/m/n/10 computeJacobianVectorProductBwd() Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/pcr/m/n/10 computeJacobianVectorProductFwd() Underfull \hbox (badness 10000) in paragraph at lines 25--27 []\T1/pcr/m/n/10 computeStabilityParameters() Underfull \hbox (badness 10000) in paragraph at lines 27--28 []\T1/pcr/m/n/10 createSlaveAeroProblem() Underfull \hbox (badness 10000) in paragraph at lines 31--32 []\T1/pcr/m/n/10 evalFunctions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflo w.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 32--33 []\T1/pcr/m/n/10 evalFunctionsSens() Underfull \hbox (badness 10000) in paragraph at lines 37--38 []\T1/pcr/m/n/10 getAdjointResNorms() Underfull \hbox (badness 10000) in paragraph at lines 38--39 []\T1/pcr/m/n/10 getAdjointStateSize() Underfull \hbox (badness 10000) in paragraph at lines 40--41 []\T1/pcr/m/n/10 getHeatFluxes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflo w.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 41--42 []\T1/pcr/m/n/10 getPointSetName() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADf low.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 42--43 []\T1/pcr/m/n/10 getResidual() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 43--44 []\T1/pcr/m/n/10 getResNorms() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 44--45 []\T1/pcr/m/n/10 getSolution() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 45--46 []\T1/pcr/m/n/10 getSolverMeshIndices() Underfull \hbox (badness 10000) in paragraph at lines 46--47 []\T1/pcr/m/n/10 getSpatialPerturbation() Underfull \hbox (badness 10000) in paragraph at lines 47--48 []\T1/pcr/m/n/10 getSpatialSize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADfl ow.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 48--49 []\T1/pcr/m/n/10 getStatePerturbation() Underfull \hbox (badness 10000) in paragraph at lines 50--51 []\T1/pcr/m/n/10 getStateSize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow .ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 51--52 []\T1/pcr/m/n/10 getSurfaceConnectivity() Underfull \hbox (badness 10000) in paragraph at lines 52--53 []\T1/pcr/m/n/10 getSurfacePerturbation() Underfull \hbox (badness 10000) in paragraph at lines 54--56 []\T1/pcr/m/n/10 getUniqueSpatialPerturbationNorm() Underfull \hbox (badness 10000) in paragraph at lines 56--57 []\T1/pcr/m/n/10 globalAdjointPreCon() Underfull \hbox (badness 10000) in paragraph at lines 57--58 []\T1/pcr/m/n/10 globalNKPreCon() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADfl ow.ADFLOW [73] Underfull \hbox (badness 10000) in paragraph at lines 65--66 []\T1/pcr/m/n/10 propagateUncertainty() Underfull \hbox (badness 10000) in paragraph at lines 69--70 []\T1/pcr/m/n/10 releaseAdjointMemory() Underfull \hbox (badness 10000) in paragraph at lines 70--71 []\T1/pcr/m/n/10 resetAdjoint() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow .ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 75--76 []\T1/pcr/m/n/10 saveAdjointMatrix() Underfull \hbox (badness 10000) in paragraph at lines 77--78 []\T1/pcr/m/n/10 setAeroProblem() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADfl ow.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 81--82 []\T1/pcr/m/n/10 setResNorms() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 82--83 []\T1/pcr/m/n/10 setRotationRate() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADf low.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 84--85 []\T1/pcr/m/n/10 setSurfaceCoordinates() Underfull \hbox (badness 10000) in paragraph at lines 85--86 []\T1/pcr/m/n/10 setTargetCp() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 86--87 []\T1/pcr/m/n/10 setWallTemperature() Underfull \hbox (badness 10000) in paragraph at lines 87--88 []\T1/pcr/m/n/10 solveAdjointForRHS() Underfull \hbox (badness 10000) in paragraph at lines 89--90 []\T1/pcr/m/n/10 solveDirectForRHS() Underfull \hbox (badness 10000) in paragraph at lines 92--93 []\T1/pcr/m/n/10 solveTimeStep() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflo w.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 93--94 []\T1/pcr/m/n/10 solveTrimCL() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 97--98 []\T1/pcr/m/n/10 updateGeometryInfo() Underfull \hbox (badness 10000) in paragraph at lines 101--102 []\T1/pcr/m/n/10 writeForceFile() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADfl ow.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 102--104 []\T1/pcr/m/n/10 writeLiftDistributionFile() Underfull \hbox (badness 10000) in paragraph at lines 104--105 []\T1/pcr/m/n/10 writeMeshFile() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflo w.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 105--106 []\T1/pcr/m/n/10 writeSlicesFile() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADf low.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 106--107 []\T1/pcr/m/n/10 writeSolution() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflo w.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 107--109 []\T1/pcr/m/n/10 writeSurfaceSensitivity() Underfull \hbox (badness 10000) in paragraph at lines 109--111 []\T1/pcr/m/n/10 writeSurfaceSolutionFile() Underfull \hbox (badness 10000) in paragraph at lines 111--113 []\T1/pcr/m/n/10 writeSurfaceSolutionFileTecplot() Underfull \hbox (badness 10000) in paragraph at lines 113--115 []\T1/pcr/m/n/10 writeVolumeSolutionFile() [74]) (./mdolab-adflow.aux) Package rerunfilecheck Warning: File `mdolab-adflow.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on mdolab-adflow.pdf (78 pages, 346399 bytes). Transcript written on mdolab-adflow.log. Latexmk: Index file 'mdolab-adflow.idx' was written Latexmk: References changed. Latexmk: Log file says output to 'mdolab-adflow.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'mdolab-adflow.aux' 'mdolab-adflow.out' 'mdolab-adflow.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="mdolab-adflow" "ADflow.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] Chapter 2. [5] [6] Chapter 3. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8] [9] [10] Chapter 4. Underfull \hbox (badness 5787) in paragraph at lines 544--547 \T1/ptm/m/n/10 di-tion in-for-ma-tion con- Underfull \hbox (badness 10000) in paragraph at lines 566--568 []|\T1/ptm/m/n/10 Flag to use spec-i-fied Underfull \hbox (badness 5231) in paragraph at lines 633--636 \T1/ptm/m/n/10 pre-ci-sion can ad-versely Underfull \hbox (badness 10000) in paragraph at lines 643--649 \T1/ptm/m/n/10 ^^Pvol-umeVari-ables^^Q may Underfull \hbox (badness 10000) in paragraph at lines 643--649 \T1/ptm/m/n/10 `isoSurface':{`Vx':- Underfull \hbox (badness 10000) in paragraph at lines 656--661 []|\T1/ptm/m/n/10 Only ap-pli-ca-ble for Underfull \hbox (badness 10000) in paragraph at lines 656--661 \T1/ptm/m/n/10 RANS/laminar com-pu- Underfull \hbox (badness 5667) in paragraph at lines 656--661 \T1/ptm/m/n/10 ve-loc-i-ties as the value Underfull \hbox (badness 10000) in paragraph at lines 656--661 \T1/ptm/m/n/10 the ve-loc-i-ties on the Underfull \hbox (badness 10000) in paragraph at lines 668--669 []|\T1/ptm/m/n/10 Set the dis-cretiza-tion Underfull \hbox (badness 10000) in paragraph at lines 668--669 \T1/ptm/m/n/10 gen-er-ally rec-om-mended Underfull \hbox (badness 6608) in paragraph at lines 668--669 \T1/ptm/m/n/10 speed, at the cost of Underfull \hbox (badness 10000) in paragraph at lines 668--669 \T1/ptm/m/n/10 nu-mer-i-cal ac-cu-racy. Underfull \hbox (badness 10000) in paragraph at lines 688--690 []|\T1/ptm/m/n/10 Set the dis-cretiza-tion Underfull \hbox (badness 6412) in paragraph at lines 688--690 \T1/ptm/m/n/10 method for the coarse Underfull \hbox (badness 10000) in paragraph at lines 688--690 \T1/ptm/m/n/10 be the same as the Underfull \hbox (badness 10000) in paragraph at lines 707--712 []|\T1/ptm/m/n/10 Type of \T1/ptm/m/it/10 solver \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 707--712 \T1/ptm/m/n/10 smoother to use with Underfull \hbox (badness 10000) in paragraph at lines 707--712 \T1/ptm/m/n/10 ized diagonal-dominant Underfull \hbox (badness 10000) in paragraph at lines 707--712 \T1/ptm/m/n/10 alternating-direction im- Underfull \hbox (badness 6658) in paragraph at lines 728--733 \T1/ptm/m/n/10 ex-ten-sively tested from Underfull \hbox (badness 7631) in paragraph at lines 728--733 \T1/ptm/m/n/10 been ex-ten-sively tested Underfull \hbox (badness 10000) in paragraph at lines 740--743 \T1/ptm/m/n/10 sim-u-la-tions have been Underfull \hbox (badness 10000) in paragraph at lines 756--757 []\T1/ptm/m/it/10 sae \T1/ptm/m/n/10 - Sparart Underfull \hbox (badness 10000) in paragraph at lines 756--757 \T1/ptm/m/n/10 Allmaras-Edward Underfull \hbox (badness 10000) in paragraph at lines 793--795 []|\T1/ptm/m/n/10 This pa-ram-e-ter af-fects Underfull \hbox (badness 7291) in paragraph at lines 793--795 \T1/ptm/m/n/10 how the to-tal resid-ual Underfull \hbox (badness 10000) in paragraph at lines 793--795 \T1/ptm/m/n/10 what tur-bu-lence model Underfull \hbox (badness 10000) in paragraph at lines 797--798 \T1/ptm/m/it/10 scalar \T1/ptm/m/n/10 - De-fault: Underfull \hbox (badness 10000) in paragraph at lines 800--801 []\T1/ptm/m/it/10 sae \T1/ptm/m/n/10 - Sparart Underfull \hbox (badness 10000) in paragraph at lines 800--801 \T1/ptm/m/n/10 Allmaras-Edward Underfull \hbox (badness 10000) in paragraph at lines 800--801 \T1/ptm/m/n/10 model - NOT Underfull \hbox (badness 10000) in paragraph at lines 803--804 []\T1/ptm/m/it/10 k omega wilcox Underfull \hbox (badness 10000) in paragraph at lines 803--804 \T1/ptm/m/n/10 - NOT IM-PLE- Underfull \hbox (badness 10000) in paragraph at lines 806--807 \T1/ptm/m/n/10 - NOT IM-PLE- Underfull \hbox (badness 10000) in paragraph at lines 826--831 \T1/ptm/m/n/10 This is gen-er-ally not Underfull \hbox (badness 10000) in paragraph at lines 826--831 \T1/ptm/m/n/10 give (po-ten-tially very) Underfull \hbox (badness 10000) in paragraph at lines 826--831 \T1/ptm/m/n/10 poor drag es-ti-mates. Overfull \hbox (13.11995pt too wide) in paragraph at lines 832--833 []|\T1/ptm/m/it/10 useApproximateWallDistance| Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 dis-tance cal-cu-la-tion. Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 ex-act wall dis-tances Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 are com-puted dur-ing Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 ini-tial-iza-tion and the Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 para-met-ric lo-ca-tion of Underfull \hbox (badness 10000) in paragraph at lines 838--846 \T1/ptm/m/n/10 the ge-om-e-try de-forms Underfull \hbox (badness 5288) in paragraph at lines 853--859 \T1/ptm/m/n/10 ary con-di-tions are im- Underfull \hbox (badness 10000) in paragraph at lines 853--859 \T1/ptm/m/n/10 ple-mented for in-vis-cid Underfull \hbox (badness 6808) in paragraph at lines 853--859 \T1/ptm/m/it/10 ex-trap-o-la-tion\T1/ptm/m/n/10 , \T1/ptm/m/it/10 quadratic Underfull \hbox (badness 10000) in paragraph at lines 853--859 \T1/ptm/m/it/10 pres-sure ex-trap-o-la-tion Underfull \hbox (badness 5105) in paragraph at lines 866--870 \T1/ptm/m/n/10 de-fault value need not Overfull \hbox (6.90999pt too wide) in paragraph at lines 871--872 []|\T1/ptm/m/it/10 dissipationScalingExponent| Underfull \hbox (badness 10000) in paragraph at lines 968--972 \T1/ptm/m/n/10 mean-ing-ful for RANS Underfull \hbox (badness 10000) in paragraph at lines 968--972 \T1/ptm/m/n/10 sim-u-la-tions. Cer-tain Underfull \hbox (badness 10000) in paragraph at lines 968--972 \T1/ptm/m/n/10 ben-e-fit from a slight Underfull \hbox (badness 10000) in paragraph at lines 979--985 []|\T1/ptm/m/n/10 The Underfull \hbox (badness 10000) in paragraph at lines 979--985 \T1/ptm/m/n/10 the Runge-Kutta sim- Underfull \hbox (badness 10000) in paragraph at lines 979--985 \T1/ptm/m/n/10 main pa-ram-e-ter that Underfull \hbox (badness 10000) in paragraph at lines 979--985 \T1/ptm/m/n/10 de-ter-mines the over-all Underfull \hbox (badness 10000) in paragraph at lines 979--985 \T1/ptm/m/n/10 some ex-per-i-men-ta-tion [11] [12] [13] [14] Underfull \hbox (badness 7649) in paragraph at lines 1048--1052 \T1/ptm/m/n/10 could be run with-iout Underfull \hbox (badness 7238) in paragraph at lines 1063--1064 []\T1/ptm/m/it/10 bdf \T1/ptm/m/n/10 - 2nd or-der Underfull \hbox (badness 10000) in paragraph at lines 1063--1064 \T1/ptm/m/n/10 back-wards dif-fer- Underfull \hbox (badness 10000) in paragraph at lines 1072--1073 []\T1/ptm/m/it/10 md \T1/ptm/m/n/10 - Mul-ti-dis- Underfull \hbox (badness 10000) in paragraph at lines 1072--1073 \T1/ptm/m/n/10 ci-plinary (md) Underfull \hbox (badness 10000) in paragraph at lines 1072--1073 \T1/ptm/m/n/10 / Ar-bi-trary La- Underfull \hbox (badness 10000) in paragraph at lines 1072--1073 \T1/ptm/m/n/10 grangian Eu-le-rian Underfull \hbox (badness 5832) in paragraph at lines 1111--1114 []|\T1/ptm/m/n/10 The num-ber of ^^Pspec- Underfull \hbox (badness 7667) in paragraph at lines 1139--1141 []|\T1/ptm/m/n/10 Use a spec-i-fied Mach Underfull \hbox (badness 10000) in paragraph at lines 1139--1141 \T1/ptm/m/n/10 Time spec-tral anal-y-sis. Underfull \hbox (badness 10000) in paragraph at lines 1148--1150 \T1/ptm/m/n/10 Time spec-tral anal-y-sis. Underfull \hbox (badness 6995) in paragraph at lines 1157--1159 \T1/ptm/m/n/10 (pitch) mo-tion for the Underfull \hbox (badness 10000) in paragraph at lines 1166--1168 \T1/ptm/m/n/10 (yaw) mo-tion for the Underfull \hbox (badness 10000) in paragraph at lines 1166--1168 \T1/ptm/m/n/10 Time spec-tral anal-y-sis. Underfull \hbox (badness 10000) in paragraph at lines 1193--1195 []|\T1/ptm/m/n/10 Flag to com-pute time Underfull \hbox (badness 6268) in paragraph at lines 1202--1209 \T1/ptm/m/n/10 1 to 2 or-ders mag-ni- Underfull \hbox (badness 5431) in paragraph at lines 1227--1231 []|\T1/ptm/m/n/10 The con-ver-gence fac-tor Underfull \hbox (badness 10000) in paragraph at lines 1227--1231 \T1/ptm/m/n/10 grids dur-ing multi-grid Underfull \hbox (badness 6078) in paragraph at lines 1238--1242 \T1/ptm/m/n/10 ual can be above the [15] [16] [17] [18] [19] [20] [21] Underfull \hbox (badness 10000) in paragraph at lines 1272--1277 []|\T1/ptm/m/n/10 Type of PETSc KSP Underfull \hbox (badness 6364) in paragraph at lines 1272--1277 \T1/ptm/m/n/10 ^^U Transpose-Free quasi Underfull \hbox (badness 10000) in paragraph at lines 1284--1289 []|\T1/ptm/m/n/10 The rel-a-tive tol-er-ance Underfull \hbox (badness 10000) in paragraph at lines 1284--1289 \T1/ptm/m/n/10 New-ton so-lu-tion tech- Underfull \hbox (badness 5862) in paragraph at lines 1284--1289 \T1/ptm/m/n/10 dif-fi-cult tran-sients have Underfull \hbox (badness 6268) in paragraph at lines 1296--1299 []|\T1/ptm/m/n/10 The size of the GM- Underfull \hbox (badness 5652) in paragraph at lines 1306--1310 \T1/ptm/m/n/10 so-lu-tion; there-after the [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 1528--1530 []|\T1/ptm/m/n/10 List of the vari-ables Underfull \hbox (badness 10000) in paragraph at lines 1528--1530 \T1/ptm/m/n/10 whose con-ver-gence Underfull \hbox (badness 10000) in paragraph at lines 1528--1530 \T1/ptm/m/n/10 should be mon-i-tored. 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Underfull \hbox (badness 10000) in paragraph at lines 2095--2096 []|[][]\T1/pcr/m/sl/10 addFunction[][]\T1/ptm/m/n/10 (self, func-Name, group-Na me[, Overfull \hbox (2.64201pt too wide) in paragraph at lines 2255--2256 []|[][]\T1/pcr/m/sl/10 getUniqueSpatialPerturbationNorm[][]\T1/ptm/m/n/10 (self , Underfull \hbox (badness 10000) in paragraph at lines 2270--2271 []|[][]\T1/pcr/m/sl/10 mapVector[][]\T1/ptm/m/n/10 (self, vec1, group-Name1, gr oup- Underfull \hbox (badness 10000) in paragraph at lines 2275--2276 []|[][]\T1/pcr/m/sl/10 propagateUncertainty[][]\T1/ptm/m/n/10 (self, aero-Prob- lem[, [37] Underfull \hbox (badness 10000) in paragraph at lines 2330--2331 []|[][]\T1/pcr/m/sl/10 setRotationRate[][]\T1/ptm/m/n/10 (self, rot-Cen-ter, ro -tRate[, Underfull \hbox (badness 10000) in paragraph at lines 2340--2341 []|[][]\T1/pcr/m/sl/10 setSurfaceCoordinates[][]\T1/ptm/m/n/10 (self, co-or-di- nates[, [38] Underfull \hbox (badness 10000) in paragraph at lines 2400--2401 []|[][]\T1/pcr/m/sl/10 writeLiftDistributionFile[][]\T1/ptm/m/n/10 (self, file- Underfull \hbox (badness 10000) in paragraph at lines 2415--2416 []|[][]\T1/pcr/m/sl/10 writeSolution[][]\T1/ptm/m/n/10 (self[, out-put-Dir, bas e-Name, Underfull \hbox (badness 10000) in paragraph at lines 2420--2421 []|[][]\T1/pcr/m/sl/10 writeSurfaceSensitivity[][]\T1/ptm/m/n/10 (self, file-Na me, Underfull \hbox (badness 10000) in paragraph at lines 2430--2431 []|[][]\T1/pcr/m/sl/10 writeSurfaceSolutionFileTecplot[][]\T1/ptm/m/n/10 (self, [39] Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| Overfull \hbox (6.0pt too wide) in paragraph at lines 2469--2469 []| [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 2728--2728 []\T1/ptm/m/it/10 self\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res-Bar=None\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 funcs-Bar=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fBar=None\T 1/ptm/m/n/10 , Underfull \hbox (badness 6157) in paragraph at lines 2728--2728 \T1/ptm/m/it/10 wDeriv=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xVDeriv=None\T1/ptm /m/n/10 , \T1/ptm/m/it/10 xS-Deriv=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xD- [42] Underfull \hbox (badness 10000) in paragraph at lines 2782--2782 []\T1/ptm/m/it/10 self\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xD-v-Dot=None\T1/ptm/m/n /10 , \T1/ptm/m/it/10 xS-Dot=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xV-Dot=None\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2782--2782 \T1/ptm/m/it/10 wDot=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 resid-u-alDeriv=False \T1/ptm/m/n/10 , \T1/ptm/m/it/10 funcDeriv=False\T1/ptm/m/n/10 , [43] [44] [45] [46] [47] [48] [49] Underfull \hbox (badness 10000) in paragraph at lines 3727--3736 []\T1/ptm/m/n/10 [dict] Dic-tio-nary of func-tion DV pairs to solve: {`func':{` dv':str, [50] [51] Underfull \hbox (badness 7168) in paragraph at lines 3908--3910 []\T1/ptm/m/n/10 only used from an ex-ter-nal [52] Chapter 6. [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] Chapter 7. [65] [66] Chapter 8. [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 4760--4761 \T1/ptm/m/n/10 The main Python meth-ods for deriva-tive seed ma-nip-u-la-tion i n AD-flow are Underfull \hbox (badness 5431) in paragraph at lines 4760--4761 \T1/pcr/m/n/10 computeJacobianVectorProductFwd \T1/ptm/m/n/10 and \T1/pcr/m/n/1 0 computeJacobianVectorProductBwd\T1/ptm/m/n/10 , both lo-cated Underfull \hbox (badness 10000) in paragraph at lines 4780--4781 []\T1/ptm/m/n/10 The re-verse mas-ter (\T1/pcr/m/n/10 master_b\T1/ptm/m/n/10 ) rou-tine is wrapped by a thin wrap-per which is the [69] [70] (./mdolab-adflow.ind [71] [72] Underfull \hbox (badness 10000) in paragraph at lines 8--9 []\T1/pcr/m/n/10 addActuatorRegion() Underfull \hbox (badness 10000) in paragraph at lines 9--10 []\T1/pcr/m/n/10 addFunction() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 10--11 []\T1/pcr/m/n/10 addFunctions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow .ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 11--12 []\T1/pcr/m/n/10 addIntegrationSurface() Underfull \hbox (badness 10000) in paragraph at lines 12--13 []\T1/pcr/m/n/10 addLiftDistribution() Underfull \hbox (badness 10000) in paragraph at lines 14--15 []\T1/pcr/m/n/10 addUserFunction() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADf low.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 16--17 []\T1/pcr/m/n/10 advanceTimeStepCounter() Underfull \hbox (badness 10000) in paragraph at lines 20--21 []\T1/pcr/m/n/10 checkPartitioning() Underfull \hbox (badness 10000) in paragraph at lines 21--23 []\T1/pcr/m/n/10 computeJacobianVectorProductBwd() Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/pcr/m/n/10 computeJacobianVectorProductFwd() Underfull \hbox (badness 10000) in paragraph at lines 25--27 []\T1/pcr/m/n/10 computeStabilityParameters() Underfull \hbox (badness 10000) in paragraph at lines 27--28 []\T1/pcr/m/n/10 createSlaveAeroProblem() Underfull \hbox (badness 10000) in paragraph at lines 31--32 []\T1/pcr/m/n/10 evalFunctions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflo w.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 32--33 []\T1/pcr/m/n/10 evalFunctionsSens() Underfull \hbox (badness 10000) in paragraph at lines 37--38 []\T1/pcr/m/n/10 getAdjointResNorms() Underfull \hbox (badness 10000) in paragraph at lines 38--39 []\T1/pcr/m/n/10 getAdjointStateSize() Underfull \hbox (badness 10000) in paragraph at lines 40--41 []\T1/pcr/m/n/10 getHeatFluxes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflo w.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 41--42 []\T1/pcr/m/n/10 getPointSetName() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADf low.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 42--43 []\T1/pcr/m/n/10 getResidual() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 43--44 []\T1/pcr/m/n/10 getResNorms() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 44--45 []\T1/pcr/m/n/10 getSolution() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 45--46 []\T1/pcr/m/n/10 getSolverMeshIndices() Underfull \hbox (badness 10000) in paragraph at lines 46--47 []\T1/pcr/m/n/10 getSpatialPerturbation() Underfull \hbox (badness 10000) in paragraph at lines 47--48 []\T1/pcr/m/n/10 getSpatialSize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADfl ow.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 48--49 []\T1/pcr/m/n/10 getStatePerturbation() Underfull \hbox (badness 10000) in paragraph at lines 50--51 []\T1/pcr/m/n/10 getStateSize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow .ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 51--52 []\T1/pcr/m/n/10 getSurfaceConnectivity() Underfull \hbox (badness 10000) in paragraph at lines 52--53 []\T1/pcr/m/n/10 getSurfacePerturbation() Underfull \hbox (badness 10000) in paragraph at lines 54--56 []\T1/pcr/m/n/10 getUniqueSpatialPerturbationNorm() Underfull \hbox (badness 10000) in paragraph at lines 56--57 []\T1/pcr/m/n/10 globalAdjointPreCon() Underfull \hbox (badness 10000) in paragraph at lines 57--58 []\T1/pcr/m/n/10 globalNKPreCon() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADfl ow.ADFLOW [73] Underfull \hbox (badness 10000) in paragraph at lines 65--66 []\T1/pcr/m/n/10 propagateUncertainty() Underfull \hbox (badness 10000) in paragraph at lines 69--70 []\T1/pcr/m/n/10 releaseAdjointMemory() Underfull \hbox (badness 10000) in paragraph at lines 70--71 []\T1/pcr/m/n/10 resetAdjoint() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow .ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 75--76 []\T1/pcr/m/n/10 saveAdjointMatrix() Underfull \hbox (badness 10000) in paragraph at lines 77--78 []\T1/pcr/m/n/10 setAeroProblem() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADfl ow.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 81--82 []\T1/pcr/m/n/10 setResNorms() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 82--83 []\T1/pcr/m/n/10 setRotationRate() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADf low.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 84--85 []\T1/pcr/m/n/10 setSurfaceCoordinates() Underfull \hbox (badness 10000) in paragraph at lines 85--86 []\T1/pcr/m/n/10 setTargetCp() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 86--87 []\T1/pcr/m/n/10 setWallTemperature() Underfull \hbox (badness 10000) in paragraph at lines 87--88 []\T1/pcr/m/n/10 solveAdjointForRHS() Underfull \hbox (badness 10000) in paragraph at lines 89--90 []\T1/pcr/m/n/10 solveDirectForRHS() Underfull \hbox (badness 10000) in paragraph at lines 92--93 []\T1/pcr/m/n/10 solveTimeStep() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflo w.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 93--94 []\T1/pcr/m/n/10 solveTrimCL() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflow. ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 97--98 []\T1/pcr/m/n/10 updateGeometryInfo() Underfull \hbox (badness 10000) in paragraph at lines 101--102 []\T1/pcr/m/n/10 writeForceFile() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADfl ow.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 102--104 []\T1/pcr/m/n/10 writeLiftDistributionFile() Underfull \hbox (badness 10000) in paragraph at lines 104--105 []\T1/pcr/m/n/10 writeMeshFile() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflo w.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 105--106 []\T1/pcr/m/n/10 writeSlicesFile() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADf low.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 106--107 []\T1/pcr/m/n/10 writeSolution() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 python.pyADflo w.ADFLOW Underfull \hbox (badness 10000) in paragraph at lines 107--109 []\T1/pcr/m/n/10 writeSurfaceSensitivity() Underfull \hbox (badness 10000) in paragraph at lines 109--111 []\T1/pcr/m/n/10 writeSurfaceSolutionFile() Underfull \hbox (badness 10000) in paragraph at lines 111--113 []\T1/pcr/m/n/10 writeSurfaceSolutionFileTecplot() Underfull \hbox (badness 10000) in paragraph at lines 113--115 []\T1/pcr/m/n/10 writeVolumeSolutionFile() [74]) (./mdolab-adflow.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on mdolab-adflow.pdf (78 pages, 346165 bytes). Transcript written on mdolab-adflow.log. Latexmk: Index file 'mdolab-adflow.idx' was written Latexmk: Log file says output to 'mdolab-adflow.pdf' Latexmk: All targets (mdolab-adflow.pdf) are up-to-date [rtd-command-info] start-time: 2020-06-04T17:38:07.778650Z, end-time: 2020-06-04T17:38:07.979963Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/checkouts/latest/doc/_build/latex/mdolab-adflow.pdf /home/docs/checkouts/readthedocs.org/user_builds/mdolab-adflow/artifacts/latest/sphinx_pdf/mdolab-adflow.pdf [rtd-command-info] start-time: 2020-06-04T17:38:08.108717Z, end-time: 2020-06-04T17:38:12.200034Z, duration: 4, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [epub]: targets for 11 source files that are out of date updating environment: 11 added, 0 changed, 0 removed reading sources... 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