docs/bladed/bladed2hawc.rst

+********************************
+BLADED to HAWC2 model conversion
+********************************
+
+**BLADED** is a tool developed by DNV, and ``wetb`` contains a basic reader that
+can interpret a BLADED project file (.prj) and convert the data structures into
+an equivalent set of **HAWC2** input files (htc, st, ae, pc).
+
+
+================================
+API and workflow
+================================
+
+---------------------------------
+Read BLADED project file
+---------------------------------
+
+The input from a Bladed model is given in a project file (*prj*) and is formatted
+in the XML definition. Within this file the core BLADED inputs are given in the
+CDATA field and which according to the XML standards refer to Character Data,
+see also `here <https://www.w3resource.com/xml/CDATA-sections.php>`_ and `here
+<https://en.wikipedia.org/wiki/CDATA>`_ for a more detailed technical description.
+Within the CDATA field a custom BLADED type markup definition is used. The ``wetb``
+reader includes an interpreter for this custom BLADED markup and outputs this
+data structure to the user as a nested dictionary, and which allows easy access
+to all the different key/value pairs defined in the BLADED CDATA field. This
+nested dictionary structure is accessible via the variable
+``wetb.bladed.readprj.ReadBladedProject.bd``.
+
+Outside the CDATA field the XML data is parsed via the ``lxml`` Python package,
+and the entire XML object ``lxml.objectify.fromstring(str)`` is exposed to the user
+via the ``wetb.bladed.readprj.ReadBladedProject.xmlroot`` variable.
+
+
+In ``wetb` the
+project file can be read using the following::
+
+     from wetb.bladed.readprj import ReadBladedProject
+     prj = ReadBladedProject('my_bladed_project_file.prj')
+     # XML object tree (and lxml data object)
+     prj.xmlroot
+     # CDATA field as nested dictionary
+     prj.bd
+
+
+A convenience function ``wetb.bladed.readprj.ReadBladedProject.get_key`` is also
+available to extract a ``numpy`` array, for example as follows::
+
+     from wetb.bladed.readprj import ReadBladedProject
+     prj = ReadBladedProject('my_bladed_project_file.prj')
+     # the following keys contain a data array
+     data_arr = prj.get_key('BSTIFFMB', 'EIFLAP')
+     # which is the similar calling (but excludes data conversion to int/float)
+     prj.bd['BSTIFFMB']['EIFLAP']
+     # if a key contains a section with sub-keys, a dictionary is returned:
+     data_dict = prj.get_key('BSTIFFMB')
+     # and is similar to
+     prj.bd['BSTIFFMB']
+
+
+------------------------------------
+Convert BLADED project file to HAWC2
+------------------------------------
+
+The class ``wetb.bladed.prj2hawc.Convert2Hawc`` will convert a Bladed project
+file into a set of HAWC2 input files. This process assumes that a standard
+3 bladed upwind turbine configuration is used, and a generic HAWC2 `htc template
+file  <https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/-/blob/master/wetb/bladed/template.htc>`_
+serves as the starting point for the conversion process. Note that the converter
+class ``wetb.bladed.prj2hawc.Convert2Hawc`` inherits from
+``wetb.bladed.readprj.ReadBladedProject``, and hence will first read the Bladed
+project file::
+
+    import os
+    import urllib.request
+    import shutil
+    from wetb.bladed.prj2hawc import Convert2Hawc
+    # download the htc template file,
+    url = 'https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/-/'
+    url += 'raw/master/wetb/bladed/template.htc'
+    fname_tmpl = '/path/to/my/template.htc'
+    with urllib.request.urlopen(url) as response, open(fname_tmpl, 'wb') as fout:
+        shutil.copyfileobj(response, fout)
+    # file name of the Bladed project file
+    fprj = '/path/to/my/bladed.prj'
+    # initiate the project converter object, will first read the prj file (see above)
+    prj = Convert2Hawc(fprj)
+    # convert to the HAWC2 formats: htc, ae, pc and st files
+    fname_htc = fname_tmpl.replace('template.htc', 'bladed-to-hawc2.htc')
+    prj.convert(fname_htc)
+    # note that the ae, pc and st files will be saved in the same directory as
+    # fname_htc, with .htc replaced by .ae, .pc, .st etc.
+
+
+================================
+Theoretical background
+================================
+
+---------------------------------
+Coordinate systems
+---------------------------------
+
+The coordinate systems used in both codes are different. Note that in HAWC2
+coordinate systems of general bodies are defined by the users. However,
+the HAWC2 global and blade cross-section coordinate systems are predetermined,
+and they differ from Bladed in the following manner:
+
+* Global Bladed *X* axis is positive pointing downwind whereas in HAWC2 the
+  global *Y* direction is positive in the downwind direction.
+
+* The HAWC2 global *Z* direction is in the same direction as the gravity vector
+  (positive down), while it is the opposite in Bladed (positive up).
+
+* The Bladed cross-section coordinate system is rotated 90 degrees around *Z* wrt HAWC2.
+
+The figures below illustrate clearly the HAWC2 and Bladed coordinate systems.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Bladed coordinate systems
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. figure:: Bladed_turbine_coord.png
+   :width: 200
+   :alt: bladed_turbine_coord
+
+   Bladed coordinate system, rotor rotation and radius definition.
+
+.. figure:: Bladed_st_centers.png
+   :width: 400
+   :alt: bladed_st_coord
+
+   Bladed cross-section structural centers, half chord location and structural pitch definition.
+
+.. figure:: Bladed_airfoil.png
+   :width: 400
+   :alt: bladed_airfoil_coord
+
+   Bladed airfoil geometric positioning along the blade.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+HAWC2 coordinate systems
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. figure:: HAWC2_turbine_coord.png
+    :width: 200
+    :alt: hawc2_turbine_coord
+
+    HAWC2 global, tower, shaft, hub, blade-i and meteorological coordinate systems.
+
+.. figure:: HAWC2_st_centers.png
+    :width: 400
+    :alt: hawc2_st_ccord
+
+    HAWC2 cross-section structural centers, half chord location and structural pitch definition.
+
+.. figure:: HAWC2_c2_def_ccord.png
+    :width: 400
+    :alt: hawc2_airfoil_coord
+
+    HAWC2 airfoil positioning in blade body coordinates and aerodynamic pitch given as in the *htc* file *c2_def* section.
+
+
+---------------------------------
+Cross-sectional parameters
+---------------------------------
+
+Bladed uses isotropic material definitions for all bodies and for the HAWC2
+conversion the same isotropic assumption is used. Since the HAWC2 *st* file definition
+splits the Young's (*E*) and shear modulus (*G*) from the actual stiffness terms, and Bladed
+defines the actual stiffness values (meaning the product of *EI* etc), the
+corresponding HAWC2 *st* input simply assumes a value for *E* and *G*, and
+specifies the inertia such that the product (i.e. stiffness) is correct.
+
+Bladed defines a mass polar moment of inertia in combination with the ratio
+between the mass radii of gyration around the airfoil's center of mass, while
+in HAWC2 the radii of gyration in *X* and *Y* direction are given wrt the elastic
+center.
+
+
+---------------------------------
+References
+---------------------------------
+
+[1] `HAWC2 User Manual v12.8 <http://tools.windenergy.dtu.dk/HAWC2/manual/>`_
+
+[2] Bladed 4.6 Manual
+

docs/conf.py

+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- 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.join(os.path.abspath('.'), '..', '..'))
+
+from wetb import __version__
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'WETB'
+copyright = '2018, DTU Wind Energy'
+author = 'DTU Wind Energy'
+
+# The short X.Y version
+version = __version__
+# The full version, including alpha/beta/rc tags
+release = __version__
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+    'nbsphinx',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# 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
+
+# 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 = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- 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 = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+html_theme_options = {
+    # TOC options
+    #'navigation_depth': 2,  # only show 2 levels on left sidebar
+    'collapse_navigation': False,  # don't allow sidebar to collapse
+}
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'WETBdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # 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',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    #(master_doc, 'PyWake.tex', 'PyWake Documentation', 'DTU Wind Energy', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'wetb', 'WETB Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'WETB', 'WETB Documentation',
+     author, 'WETB', 'Wind Energy Toolbox.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------

docs/configure-wine.md

+Background Information Regarding Wine
+-------------------------------------
+
+> Note that the steps described here are executed automatically by the
+configuration script [```config-wine-hawc2.sh```]
+(https://gitlab.windenergy.dtu.dk/toolbox/pbsutils/blob/master/config-wine-hawc2.sh)
+in ```pbsutils```.
+
+
+Configure Wine for Gorm
+------------------------
+
+You will also need to configure wine and place the HAWC2 executables in a
+directory that wine knows about. First, activate the correct wine environment by
+typing in a shell in the Gorm's home directory (it can be activated with
+ssh (Linux, Mac) or putty (MS Windows)):
+
+```
+g-000 $ WINEARCH=win32 WINEPREFIX=~/.wine32 wine test.exe
+```
+
+Optionally, you can also make an alias (a short format for a longer, more complex
+command). In the ```.bashrc``` file in your home directory
+(```/home/$USER/.bash_profile```), add at the bottom of the file:
+
+```
+alias wine32='WINEARCH=win32 WINEPREFIX=~/.wine32 wine'
+```
+
+Add a folder called ```~/wine_exe/win32``` to your wine system's PATH so we can
+copy all the HAWC2 executables in here:
+
+```
+$EXE_DIR_WINE="z:/home/$USER/wine_exe/win32/"
+printf 'REGEDIT4\n[HKEY_CURRENT_USER\\Environment]\n"PATH"="'"$EXE_DIR_WINE"'"\n' >> ./tmp.reg
+WINEARCH=win32 WINEPREFIX=~/.wine32 wine regedit ./tmp.reg
+rm ./tmp.reg
+```
+
+And now copy all the HAWC2 executables, DLL's (including the license manager)
+to your wine directory. You can copy all the required executables, dll's and
+the license manager are located at ```/home/MET/hawc2exe```. The following
+command will update your local directory with any new executables that have
+been placed in ```/home/MET/hawc2exe/win32/```:
+
+```
+g-000 $ rsync -a /home/MET/hawc2exe/win32/* /home/$USER/wine_exe/win32/
+```
+
+Notice that the HAWC2 executable names are ```hawc2-latest.exe```,
+```hawc2-118.exe```, etc. By default the latest version will be used and the user
+does not need to specify this. However, when you need to compare different version
+you can easily do so by specifying which case should be run with which
+executable. The file ```hawc2-latest.exe``` will always be the latest HAWC2
+version at ```/home/MET/hawc2exe/```. When a new HAWC2 is released you can
+simply copy all the files from there again to update.
+
+
+Configure Wine for Jess
+------------------------
+
+Same principles apply to Jess, and  [```config-wine-hawc2.sh```]
+(https://gitlab.windenergy.dtu.dk/toolbox/pbsutils/blob/master/config-wine-hawc2.sh)
+can be used to initialize and configure your wine environment.
+
+Note that due to a bug in the specific version of wine that is installed on
+Jess, ```config-wine-hawc2.sh``` will apply the following command to fix this.
+It is important to note that this fix will have to be executed on each node at
+the beginning of each new session:
+
+```
+j-000 $ WINEARCH=win32 WINEPREFIX=~/.wine32 winefix
+```
+
+```winefix``` is automatically included in the ```pbs_in``` scripts genetrated
+by the toolbox.
+

docs/developer-guide.md

+# Developer guide
+
+Thank you for your interest in developing wetb. This guide details how to
+contribute to wetb in a way that is efficient for everyone.
+
+
+## Contents
+
+- [Fork](#fork-project)
+- [Requirements](#requirements)
+- [Install Python](#install-python)
+- [Install/build dependencies](#installbuild-dependencies)
+- [Get wetb](#get-wetb)
+- [Install wetb](#install-wetb)
+- [Contributions](#contributions)
+- [Upload contributions](#upload-contributions)
+- [Make and upload wheels](#make-and-upload-wheels)
+
+
+## Fork project
+
+We prefer that you make your contributions in your own fork of the project,
+[make your changes](#Contributions) and [make a merge request](#Upload contributions).
+
+The project can be forked to your own user account via the \<Fork\> button on
+the [frontpage](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox)
+
+
+## Requirements
+
+
+### Command line
+
+This guide will use the command line (aka command prompt) frequently.
+You can launch a Windows terminal as follows: press Start> and type
+"cmd" + \<Enter\>. A link to the command prompt should be visible now.
+
+In case you want an alternative, more capable windows terminal, you could consider
+using [ConEmu](https://conemu.github.io/) (this is optional).
+
+> ConEmu-Maximus5 is a Windows console emulator with tabs, which presents
+> multiple consoles and simple GUI applications as one customizable GUI window
+> with various features.
+
+
+### Git
+
+* Download and install Git version control system for Windows 64-bit
+[here](https://git-scm.com/download/win). Only select the Windows Portable
+option if you know what you are doing or if you do not have administrative
+rights on your computer.
+
+* Git comes with a simple GUI, but there are more and different options available
+if you are not happy with it, see [here](https://git-scm.com/downloads/guis).
+
+* On windows we highly recommend [tortoisegit](https://tortoisegit.org/). It
+is a gui integrated into the windows explorer.
+
+
+## Install Python
+
+For all platforms we recommend that you download and install the Anaconda -
+a professional grade, full blown scientific Python distribution.
+
+
+### Installing Miniconda
+
+* Download and install Anaconda (Python 3.8 version, 64 bit installer is
+recommended) from <https://docs.conda.io/en/latest/miniconda.html>.
+
+You should now be able to find a `Anaconda Powershell (Miniconda)` or
+`Anaconda Prompt (Miniconda)` application launcher. This will drop you in a 
+terminal alike application, saying something like this:
+
+```
+(base) C:\Users\>
+```
+
+and where `(base)` refers to your base Miniconda installation environment. 
+You can keep the base environment updated as follows (type in a terminal):
+
+```
+>> conda update --all
+```
+
+
+### Optionally, create other independent Anaconda environments
+
+By using environments you can manage different Python installations with
+different versions on your system independently. Creating environments is as easy as:
+
+```
+>> conda create -n py39 python=3.9
+```
+
+Where `-n py39` refers any user defined name that describes what is the environment
+used for. These environments can then be activated as follows:
+
+```
+>> conda activate py39
+```
+
+The Python distribution in use will now be located in e.g. \<path_to_anaconda\>/env/py39/
+
+use ```conda deactivate``` to deactivate the environment.
+
+
+## Install/build dependencies
+
+- Compiler (```wetb``` contains cython extensions that require a compiler):
+    - Linux: gcc (should be installed by default)
+    - Windows:
+        - Python 3.5+: MS Visual Studio 2022 or [Visual C++ 2022 Redistributable](https://visualstudio.microsoft.com/downloads/#microsoft-visual-c-redistributable-for-visual-studio-2022)
+        https://visualstudio.microsoft.com/visual-cpp-build-tools/
+        
+        - Only one MS Visual Studio version can be installed, but you can for
+        example install MS Visual Studio 2022 alongside different Visual C++ Build Tools.
+- [numpy](http://www.numpy.org/)
+- [cython](http://cython.org/)
+- [scipy](http://scipy.org/scipylib/)
+- [pandas](http://pandas.pydata.org/)
+- xlrd and xlwt from [python-excel](http://www.python-excel.org/)
+- [openpyxl](http://openpyxl.readthedocs.org/en/default/)
+- [h5py](http://www.h5py.org/)
+- [matplotlib](http://matplotlib.org/)
+- [pytables](http://www.pytables.org/)
+- [pytest](https://pypi.python.org/pypi/pytest)
+- [pytest-cov](https://pypi.python.org/pypi/pytest-cov/)
+- nose, sphinx, blosc, pbr, psutil, coverage, six
+- [paramiko](http://www.paramiko.org/)
+- [sshtunnel](https://github.com/pahaz/sshtunnel)
+- [pandoc](http://pandoc.org/) , [pypandoc](https://pypi.python.org/pypi/pypandoc):
+- [click](https://click.palletsprojects.com/en/7.x/)
+- [jinja2](https://jinja.palletsprojects.com/en/2.10.x/)
+convert markdown formatted readme file to rst for PyPi compatibility. See also
+issue #22. ```pandoc``` is available in Anaconda. When installing
+```pypandoc``` via pip, you have to install ```pandoc``` via your package
+manager (Linux/Mac).
+
+Install the necessary Python dependencies using the conda package manager:
+
+```
+conda install mock h5py pytables pytest pytest-cov nose sphinx blosc pbr paramiko
+conda install scipy pandas matplotlib cython coverage openpyxl psutil click jinja2
+conda install -c conda-forge sshtunnel --no-deps
+```
+
+Note that ```--no-deps``` avoids that newer packages from the channel
+```conda-forge``` will be used instead of those from the default ```anaconda```
+channel. Depending on which packages get overwritten, this might brake your
+Anaconda root environment. As such, using ```--no-deps``` should be
+used for safety (especially when operating from the root environment).
+
+
+## Get wetb
+
+Copy the https - link on the front page of your fork of wetb
+
+```
+>> git clone <https-link>
+```
+
+or via tortoise-git:
+
+- Right-click in your working folder
+- "Git Clone..."
+- \<Ok\>
+
+
+## Install wetb
+
+```
+>> cd WindEnergyToolbox
+>> pip install -e . --no-deps
+```
+
+Note that the ```--no-deps``` option here is used for the same reason as explained
+above for the ```conda-forge``` channel: it is to avoid that pip will replace
+newer packages compared to the ones as available in the ```Anaconda``` channel.
+
+
+## Update wetb
+
+```
+>> cd WindEnergyToolbox
+>> git pull
+>> pip install -e . --no-deps
+```
+
+
+## Run tests
+
+Note that the test should be executed from a clean repository and which is not
+used as a development installation with ```pip install -e .```. For example,
+create a clone of your local git repository in which your development takes
+place, but name the top level folder to something else:
+
+```
+>> git clone WindEnergyToolbox/ wetb_tests
+>> cd wetb_tests
+```
+
+In order to make sure your git repository is clean, this will remove all
+untracked files, and undo all untracked changes. WARNING: you will loose all
+untracked files and changes!!
+```
+>> git clean -df & git checkout .
+```
+
+Now we have clean repository that is not used as a development installation
+directory, and we simply track our own local development git repository.
+Use ```git pull``` to get the latest local commits.
+
+```
+>> python -m pytest --cov=wetb
+```
+
+
+## Contributions
+
+If you make a change in the toolbox, that others can benefit from please make a merge request.
+
+If you can, please submit a merge request with the fix or improvements including tests.
+
+The workflow to make a merge request is as follows:
+
+- Create a feature branch, branch away from master
+- Write tests and code
+- Push the commit(s) to your fork
+- Submit a merge request (MR) to the master branch of
+- Link any relevant issues in the merge request description and leave a comment on them with a link back to the MR
+- Your tests should run as fast as possible, and if it uses test files, these files should be as small as possible.
+- Please keep the change in a single MR as small as possible. Split the functionality if you can
+
+
+## Upload contributions
+
+To be written
+
+
+## Make and upload wheels to PyPi
+
+### Linux
+
+For Linux the wheels are now automatically build and pushed to pypi when creating a tag.
+
+### Windows
+
+For Windows the automated build and push to pypi has not yet been implemented and the developer has to follow the manual procedure outlined below:
+
+Workflow for creating and uploading wheels is as follows:
+
+- Make tag: ```git tag "vX.Y.Z"```, and push tag to remote: ```git push --tags```
+- In order to have a clean version number (which is determined automagically)
+make sure your git working directory is clean (no uncommitted changes etc).
+- ```pip install -e . --upgrade```
+- ```python setup.py bdist_wheel -d dist``` (wheel includes compiled extensions)
+- On Linux you will have to rename the binary wheel file
+(see [PEP 513](https://www.python.org/dev/peps/pep-0513/) for a background discussion):
+    - from: ```wetb-0.0.5-cp35-cp35m-linux_x86_64.whl```
+    - to: ```wetb-0.0.5-cp35-cp35m-manylinux1_x86_64.whl```
+- ```python setup.py sdist -d dist``` (for general source distribution installs)
+- ```twine upload dist/*```
+
+In case of problems:
+
+- Make sure the version tag is compliant with
+[PEP 440](https://www.python.org/dev/peps/pep-0440/), otherwise ```twine upload```
+will fail. This means commit hashes can not be part of the version number.
+Note that when your git working directory is not clean, the scheme for automatic
+versioning number will add ```dirty``` to the version number.

docs/fatigue.rst

+Fatigue tools
+===========================
+
+``wetb`` includes functions to help with the calculation of fatigue
+equivalent loads for turbines. The documentation is in a Jupyter
+notebook format. You can download the source notebook from the
+``wetb`` repository, under ``docs/source/fatigue_tools``.
+
+.. toctree::
+    :caption: Fatigue tools
+    :maxdepth: 2
+
+    notebooks/Fatigue
\ No newline at end of file

docs/generate-spreadsheet.md

+Auto-generation of DLB Spreadsheets
+===================================
+
+Introduction
+------------
+
+This manual explains how to automatically generate the set of spreadsheets that
+defines a DLB and is required as input to the pre-processor.
+
+This tool comes handy in the following scenarios:
+* a DLB for a new turbine needs to be generated;
+* a different wind turbine class needs to be evaluated;
+* a new parameter needs to be included in the htc file;
+* different parameters variations are required, e.g. different wind speed range or different number of turbulent seed.
+
+The generator of the cases uses an input spreadsheet where the cases are defined
+in a more compact way.
+The tool is based on the "tags" concept that is used for the generation of the htc files.
+
+Main spreadsheet
+----------------
+
+A main spreadsheet is used to defines all the DLC of the DLB. The file specifies the tags that are then required in the htc files.
+
+The file has:
+* a Main sheet where some wind turbines parameters are defined, the tags are initialized, and the definitions of turbulence and gusts are given.
+* a series of other sheets, each defining a DLC. In these sheets the tags that changes in that DLC are defined.
+
+The tags are divided into three possible different categories:
+* Constants (C). Constants are tags that do not change in a DLC, e.g. simulation time, output format, ...;
+* Variables (V). Variables are tags that define the number of cases in a DLC through their combinations, e.g. wind speed, number of turbulence seeds, wind direction, ..;
+* Functions (F). Functions are tags that depend on other tags through an expression, e.g. turbulence intensity, case name, ....
+
+In each sheet the type of tag is defined in the line above the tag by typing one of the letters C, V, or F.
+
+Functions (F) tags
+------------------
+
+* Numbers can be converted to strings (for example when a tag refers to a file name)
+by using double quotes ```"``` for Functions (F):
+    * ```"wdir_[wdir]deg_wsp_[wsp]ms"``` will result in the tags ``` [wdir]```
+    and ```[wsp]```  being replaced with formatted text.
+    * following formatting rules are used:
+        * ```[wsp]```, ```[gridgustdelay]``` : ```02i```
+        * ```[wdir]```, ```[G_phi0]``` : ```03i```
+        * ```[Hs]```, ```[Tp]``` : ```05.02f```
+        * all other tags: ```04i```
+    * Only numbers in tags with double quotes are formatted. In all other cases
+    there is no formatting taking place and hence no loss of precision occurs.
+    * In this context, when using quotes, always use double quotes like ```"```.
+    Do not use single quotes ```'``` or any other quote character.
+
+Variable (V) tags
+-----------------
+
+* ```[seed]``` and ```[wave_seed]``` are special variable tags. Instead of defining
+a range of seeds, the user indicates the number of seeds to be used.
+* ```[wsp]``` is a required variable tag
+* ```[seed]``` should be placed in a column BEFORE ```[wsp]```
+
+Generate the files
+------------------
+
+To generate the files defining the different DLC the following lines need to be executed:
+
+    export PATH=/home/python/miniconda3/bin:$PATH
+    source activate py36-wetb
+    python /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/GenerateDLCs.py --folder=DLCs
+
+the first two lines activate the virtual environment. The third calls the routine *GenerateDLCs.py * that generates the files.
+The routine should be called from the folder *htc* where also the master spreadsheet *DLCs.xlsx* need to be located.
+The generated files are placed in the folder *DLCs*.

docs/getting-started-with-dlbs.md

+# Getting started with generating DLBs for HAWC2
+
+Note that DLB stands for Design Load Basis. It refers to a set of cases that are
+used to evaluate the fitness of a certain design. An example of a DLB definition
+is the IEC 61400-1ed3.
+
+
+## Overview
+
+This document intends to provide an extremely brief overview of how to run a set
+of HAWC2 simulations using the Gorm cluster at DTU and the Mimer storage.
+This document is a work in progress, and is by no means exhaustive.
+
+
+## Resources
+
+The majority of this information can be found in the Wind Energy Toolbox
+documentation. In particular, [generate-spreadsheet](docs/generate-spreadsheet.md)
+discusses how to use a "master" Excel spreadsheet to generate the subordinate
+Excel spreadsheets that will later be used to create the necessary HTC files.
+[howto-make-dlcs](docs/howto-make-dlcs.md) discusses how to create htc files
+from the subordinate spreadsheets, submit those HTC files to the cluster,
+and post-process results.
+[houserules-mimerhawc2sim](docs/houserules-mimerhawc2sim.md) has some
+"house rules" on storing simulations on mimer.
+[using-statistics-df.md](docs/using-statistics-df) has some information
+on loading the post-processing statistics using Python.
+
+
+## Steps
+
+##### 1. Make sure that you can access the cluster/mimer.
+See the instructions on [this page](docs/howto-make-dlcs.md).
+
+##### 2. Create a Set ID folder for this project/simulation.
+You should find that, within a given turbine model, the folder structure is
+similar to the following:
+
+```
+|-- DTU10MW/
+|   |-- AA0001
+|   |   |-- ...
+|   |-- AA0002
+|   |   |-- ...
+|   |-- ...
+|   |-- AB0001
+|   |-- ...
+|-- AA_log_DTUMW.xlsx
+|-- AB_log_DTUMW.xlsx
+|-- ...
+```
+
+Here, each of these alphanumeric folders are "set IDs", and you should have a
+unique set ID for each set of simulations. Detailed house rules on how you
+should store data on mimer can be found in the
+[houserules-mimerhawc2sim](docs/houserules-mimerhawc2sim.md) document.
+
+There are two steps to creating your new set ID folder:
+1. Determine if you need to create a new turbine model folder. You should only
+do this when the turbulence box size changes (e.g., if the rotor size changes)
+or if you have a model that's never been simulated on mimer.
+2. Determine your set ID code. There are two scenarios:
+    * No one else in your project has run simulations on mimer. In this case,
+    create a new set ID alpha code (e.g., "AA", "AB", etc.).
+    * Simulations for this project/turbine configuration already exist. In this
+    case, use a pre-existing set ID alpha code and add one to the most recent
+    Set ID (e.g., if "AB0008" exists, your new folder should be "AB0009").
+
+##### 3. Add proper log files for your Set ID folder.
+See the [house rules](docs/houserules-mimerhawc2sim.md) regarding log files.
+
+##### 4. Add your model files.
+Within your new Set ID folder, add your HAWC2 model files. Keep a folder
+structure similar to this:
+
+```
+|-- control/
+|   |-- ...
+|-- data/
+|   |-- ...
+|-- htc/
+|   |-- _master/
+|   |   |-- TURB_master_AA0001.htc
+|   |-- DLCs.xlsx
+```
+
+Your master htc file, stored in ```htc/_master/```, can take any desired naming
+convention, but it must have ```_master_``` in the name or future scripts will
+abort. ```htc/DLCs.xlsx``` is your master Excel file that will create the
+subordinate Excel files in the coming steps.
+
+##### 5. Create your subordinate Excel files.
+From a terminal, change to your htc directory. Then run the following code:
+
+```
+$ export PATH=/home/python/miniconda3/bin:$PATH
+$ source activate py36-wetb
+$ python /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/GenerateDLCs.py --folder=DLCs
+$ source deactivate
+```
+
+This will create a subfolders DLCs and fill that new subfolder with the created
+subordinate Excel files.
+
+##### 6. Create your htc files and PBS job scripts .
+These files and scripts are generated from the subordinate Excel files from
+Step 5. To do this, in the terminal, change up a level to your Set ID folder
+(e.g., to folder "AB0001"). Then run this code
+
+```
+$ qsub-wrap.py -f /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py --prep
+```
+
+Your htc files should now be placed in subfolders in the htc folder, and PBS
+job files should be in folder ```pbs_in```.
+
+##### 7. Launch the htc files to the cluster.
+Use the ```launch.py``` function to launch the jobs on the cluster.
+For example, the following code will launch the jobs in folder ```pbs_in``` on
+100 nodes. You must be in the top-level Set ID folder for this to work (e.g.,
+in folder "AB0001").
+
+```
+$ launch.py -n 100 -p pbs_in/
+```
+
+There are many launch options available. You can read more about the options
+and querying the cluster configurations/status/etc. on
+[this page](docs/howto-make-dlcs.md), or you can use the ```launchy.py```
+help function to print available launch options:
+
+```
+$ launch.py --help
+```
+
+##### 8. Post-process results.
+
+The wetb function ```qsub-wrap.py``` can not only generate htc files but also
+post-process results. For example, here is code to check the log files
+and calculate the statistics, the AEP and the lifetime equivalent loads
+(must be executed from the top-level Set ID folder):
+
+```
+$ qsub-wrap.py -f /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py --years=25 --neq=1e7 --stats --check_logs --fatigue
+```
+
+More details regarding loading the post-processed with statistics dataframes
+can be found here: [using-statistics-df](docs/using-statistics-df.md).
+

docs/hawc2.rst

+HAWC2 tools
+===========================
+
+``wetb`` includes functions to help with the writing of HAWC2 input
+files, also know as htc files. The documentation is in a Jupyter
+notebook format. You can download the source notebooks from the
+``wetb`` repository, under ``docs/source/hawc2``.
+
+.. toctree::
+    :caption: HAWC2
+
+    notebooks/hawc2/InputFileWriting
+    notebooks/hawc2/RunningSimulations
+    notebooks/hawc2/RunningSimulationsJess

docs/houserules-mimerhawc2sim.md

+
+House Rules for ```mimer/hawc2sim``` and HAWC2 model folder structure
+=====================================================================
+
+
+Objectives
+----------
+
+* Re-use turbulence boxes (save disk space)
+* Find each others simulations, review, re-run
+* Find working examples of simulations, DLB's
+* Avoid running the same DLB, simulations more than once
+
+* Disk usage quota review: administrators will create an overview of disk usage
+as used per turbine and user.
+
+
+Basic structure
+---------------
+
+The HAWC2 simulations are located on the data capacitor [mimer]
+(http://mimer.risoe.dk/mimerwiki), on the following address:
+
+```
+# on Windows, use the following address when mapping a new network drive
+\\mimer\hawc2sim
+
+# on Linux you can use sshfs or mount -t cifs
+//mimer.risoe.dk/hawc2sim
+```
+
+The following structure is currently used for this ```hawc2sim``` directory:
+* turbine model (e.g. DTU10MW, NREL5MW, etc)
+    * set ID: 2 alphabetic characters followed by 4 numbers (e.g. AA0001)
+* letters are task/project oriented, numbers are case oriented
+
+For example:
+* DTU10MW
+    * AA0001
+    * AA0002
+    * AB0001
+    * log_AA.xlsx
+    * log_BB.xlsx
+    * log_overview.xlsx
+* NREL5MW
+    * AA0001
+    * AA0002
+    * BA0001
+    * log_AA.xlsx
+    * log_BB.xlsx
+    * log_overview.xlsx
+
+
+House rules
+-----------
+
+* New Turbine model folder when a new size of the turbulence box is required
+(i.e. when the rotor size is different)
+* One "set ID" refers to one analysis, and it might contain more than one DLB
+	* If you realize more cases have to be included, add them in the same
+	"set ID". Don't start new "set ID" numbers.
+	* Each "set ID" number consists of 2 alphabetic followed by 4
+	numerical characters.
+* Log file
+	* Indicate which DLB used for the given "set ID" in the log file
+	* Indicate the changes wrt to a previous "set ID"
+	* Write clear and concise log messages so others can understand what
+	analysis or which DLB is considered
+	* Indicate in the log if something works or not.
+	* Indicate if a certain "set ID" is used for a certain publication or report
+* Keep a log file of the different letters. For instance AA might refer to load
+simulations carried out within a certain project
+* When results are outdated or wrong, delete the log and result files, but keep
+the htc, data and pbs input files so the "set ID" could be re-run again in the
+future. This is especially important if the given "set ID" has been used in a
+publication, report or Master/PhD thesis.
+
+
+File permissions
+----------------
+
+* By default only the person who generated the simulations within a given
+"set ID" can delete or modify the input files, other users have only read access.
+If you want to give everyone read and write access, you do:
+
+```
+# replace demo/AA0001 with the relevant turbine/set id
+g-000 $ cd /mnt/mimer/hawc2sim/demo
+g-000 $ chmod 777 -R AA0001
+```
+
+
+HAWC2 folder structure
+----------------------
+
+The current DLB setup assumes the following HAWC2 model folder structure:
+
+```
+|-- control
+|   |-- ...
+|-- data
+|   |-- ...
+|-- htc
+|   |-- DLCs
+|   |   |-- dlc12_iec61400-1ed3.xlsx
+|   |   |-- dlc13_iec61400-1ed3.xlsx
+|   |   |-- ...
+|   |-- _master
+|   |   `-- dtu10mw_master_C0013.htc
+```
+
+The load case definitions should be placed in Excel spreadsheets with a
+```*.xlsx``` extension. The above example shows one possible scenario whereby
+all the load case definitions are placed in ```htc/DLCs``` (all folder names
+are case sensitive). Alternatively, one can also place the spreadsheets in
+separate sub folders, for example:
+
+```
+|-- control
+|   |-- ...
+|-- data
+|   |-- ...
+|-- htc
+|   |-- dlc12_iec61400-1ed3
+|   |   |-- dlc12_iec61400-1ed3.xlsx
+|   |-- dlc13_iec61400-1ed3
+|   |   |-- dlc13_iec61400-1ed3.xlsx
+```
+
+In order to use this auto-configuration mode, there can only be one master file
+in ```_master``` that contains ```_master_``` in its file name.
+
+For the NREL5MW and the DTU10MW HAWC2 models, you can find their respective
+master files and DLC definition spreadsheet files on ```mimer/hawc2sim```.
+

docs/index.rst

+
+
+
+Welcome to WETB
+===========================================
+
+*- The Wind Energy Toolbox of DTU*
+
+This toolbox provides Python tools intended for use in the wind
+community, and especially HAWC2 users. Please see the Installation
+tab on the left to install the code and get started.
+
+
+Source code repository (and issue tracker):
+    https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox
+
+License:
+    GPLv3_
+
+.. _GPLv3: https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/LICENSE.txt
+
+
+Contents:
+    .. toctree::
+
+        installation
+        fatigue
+        hawc2
+        bladed/bladed2hawc
+

docs/install-anaconda.md

+
+# Installation manual
+
+
+## Anaconda or Miniconda on Linux
+
+```
+conda update --all
+conda create -n py36-wetb python=3.6
+source activate py36-wetb
+conda install setuptools_scm mock h5py pytables pytest nose sphinx blosc psutil
+conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl paramiko
+conda install -c https://conda.anaconda.org/conda-forge pyscaffold pytest-cov
+```
+
+## Anaconda or Miniconda on Windows
+
+```
+conda update --all
+conda create -n py36-wetb python=3.6
+source activate py36-wetb
+conda install setuptools_scm mock h5py pytables pytest nose sphinx psutil
+conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl paramiko
+conda install -c https://conda.anaconda.org/conda-forge pyscaffold pytest-cov
+```
+

docs/install.md

+# Anaconda (Windows/Mac/Linux)
+
+## Installation
+
+Install the necessary Python dependencies using the ```conda``` package manager:
+
+```
+>> conda install setuptools_scm mock h5py pytables pytest pytest-cov nose sphinx blosc pbr paramiko
+>> conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl psutil
+>> conda install -c conda-forge sshtunnel --no-deps
+```
+
+Now you can install ```wetb``` with ```pip``` (there is no ```conda``` package
+available yet, see [issue 21](toolbox/WindEnergyToolbox#21)).
+Since we prefer that ```conda``` manages and installs all dependencies we
+expclicitally tell ```pip``` to only install ```wetb``` and nothing more:
+
+```
+>> pip install wetb --upgrade --no-deps
+```
+
+## Update conda and ```wetb```
+
+```
+>> conda update --all
+>> pip install wetb --upgrade --no-deps
+
+```
+
+
+# Pip (Windows/Mac/Linux)
+
+Do not use this procedure in conda environments. See above.
+
+
+## Installation and update
+
+```
+>> pip install --upgrade wetb
+```
+

docs/installation.rst

+.. _installation:
+
+Installation
+===========================
+
+
+Normal user
+--------------------------------
+
+* Quick install::
+
+    pip install wetb
+
+* Install a specific version on PyPI::
+
+   pip install wetb==0.0.21
+
+* Update an installation to the most recent version::
+
+    pip install --upgrade wetb
+	
+* Install with dependencies needed by prepost
+  
+    pip install wetb[prepost]
+	
+* Install with all dependencies 
+  
+    pip install wetb[all]
+
+**NOTE**. Dependency conflicts can arise if you do not install
+``wetb`` into a clean environment. In particular, your installation
+might break if ``wetb`` is installed using ``pip``, and then later
+packages are installed using ``conda``. (See more details at
+`this article <https://www.anaconda.com/blog/using-pip-in-a-conda-environment>`_.
+We therefore recommend that you install ``wetb`` in a clean
+environment.
+
+
+Advanced user
+--------------------------------
+
+Clone the repository and install a local editable copy::
+
+  git clone https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox.git
+  cd WindEnergyToolbox
+  pip install -e .[all]
+  
+  
+  
+  
+

docs/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/notebooks/hawc2/RunningSimulations.ipynb

+%% Cell type:markdown id: tags:
+
+# Running simulations
+
+%% Cell type:markdown id: tags:
+
+## Single simulation on local pc
+
+%% Cell type:code id: tags:
+
+``` python
+from wetb import hawc2
+from wetb.hawc2 import HTCFile
+from wetb.hawc2.tests.test_files import tfp
+```
+
+%% Cell type:code id: tags:
+
+``` python
+hawc2_path = "HAWC2MB.exe" # make sure HAWC2MB.exe is on your path or specify the full path to HAWC2
+```
+
+%% Cell type:markdown id: tags:
+
+Generate and save a HAWC2 input htc file for a short simulation
+
+%% Cell type:code id: tags:
+
+``` python
+htc = HTCFile(tfp + "simulation_setup/DTU10MWRef6.0/htc/DTU_10MW_RWT.htc")
+htc.simulation.time_stop = 1 # stop the simulation after 1 s
+htc.save(tfp + 'simulation_setup/DTU10MWRef6.0/htc/tmp.htc')
+```
+
+%% Cell type:markdown id: tags:
+
+Execute the simulation
+
+%% Cell type:code id: tags:
+
+``` python
+stdout, log = htc.simulate(hawc2_path)
+```
+
+%% Cell type:code id: tags:
+
+``` python
+print(stdout)
+```
+
+%% Output
+
+     ***********************************************************************
+     *  Build information for HAWC2MB.exe (GIT)
+     *  Intel, version         1900 ,     20190206
+     *  WINDOWS 32-bit
+     ***********************************************************************
+     *  GIT-TAG        = 12.8.0
+     *  BUILDER        = mmpe
+     *  COMPUTER_NAME  = VINDRI-D17205
+     *  BUILD_DATE     = 30-01-2020
+     ***********************************************************************
+     Logfile: ./log/dtu_10mw_rwt_ver4.log is open for log outputs
+     Basic DTU Wind Energy Controller (ver. 2.3 v0.1.dev69.17400ca) loaded ...
+     Gen. torque Servo (ver. 2.2 v0.1.dev15.eddfec3) loaded...
+     Mech brake (ver. 2.2 v0.1.dev14.9e614a3) loaded...
+     Pitch Servo (ver. 2.2 v0.1.dev15.eddfec3) loaded...
+     Using licence_manager.dll, version: unknown
+     License verified - OK
+     Opening main command file: htc\tmp.htc
+     Current directory is
+     c:\mmpe\programming\python\windenergytoolbox\wetb\hawc2\tests\test_files\simula
+     tion_setup\DTU10MWRef6.0
+     Continue on no convergence = true
+    
+
+%% Cell type:code id: tags:
+
+``` python
+print(log)
+```
+
+%% Output
+
+     ***********************************************************************
+     *  Build information for HAWC2MB.exe (GIT)
+     *  Intel, version         1900 ,     20190206
+     *  WINDOWS 32-bit
+     ***********************************************************************
+     *  GIT-TAG        = 12.8.0
+     *  BUILDER        = mmpe
+     *  COMPUTER_NAME  = VINDRI-D17205
+     *  BUILD_DATE     = 30-01-2020
+     ***********************************************************************
+    ________________________________________________________________________________________________________________________
+      Log file output
+                                                                Time : 14:55:07
+                                                                Date : 26:05.2020
+    ________________________________________________________________________________________________________________________
+     Newmark commands read with succes
+     Simulation commands read with succes
+     Reading data of main body : tower
+     Succes opening ./data/dtu_10mw_rwt_tower_st.dat
+     timoschenko input commands read with succes
+     topologi_c2def_inputs read with succes
+     Topologi main body tower commands read with succes
+     Reading data of main body : towertop
+     Succes opening ./data/dtu_10mw_rwt_towertop_st.dat
+     timoschenko input commands read with succes
+     topologi_c2def_inputs read with succes
+     Topologi main body towertop commands read with succes
+     Reading data of main body : shaft
+     Succes opening ./data/dtu_10mw_rwt_shaft_st.dat
+     timoschenko input commands read with succes
+     topologi_c2def_inputs read with succes
+     Topologi main body shaft commands read with succes
+     Reading data of main body : hub1
+     Succes opening ./data/dtu_10mw_rwt_hub_st.dat
+     timoschenko input commands read with succes
+     topologi_c2def_inputs read with succes
+     Topologi main body hub1 commands read with succes
+     Reading data of main body : hub2
+     Topologi main body hub2 commands read with succes
+     Reading data of main body : hub3
+     Topologi main body hub3 commands read with succes
+     Reading data of main body : blade1
+     Succes opening ./data/dtu_10mw_rwt_blade_st.dat
+     timoschenko input commands read with succes
+     topologi_c2def_inputs read with succes
+     Topologi main body blade1 commands read with succes
+     Reading data of main body : blade2
+     Topologi main body blade2 commands read with succes
+     Reading data of main body : blade3
+     Topologi main body blade3 commands read with succes
+     Base orientation input commands read with succes
+     relative orientation input commands read with succes
+     relative orientation input commands read with succes
+     relative orientation input commands read with succes
+     relative orientation input commands read with succes
+     relative orientation input commands read with succes
+     relative orientation input commands read with succes
+     relative orientation input commands read with succes
+     relative orientation input commands read with succes
+     Orientation input commands read with succes
+     Fix0 constraint input commands read with succes
+     Fix1 constraint input commands read with succes
+     Bearing1 constraint input commands read with succes
+     Fix1 constraint input commands read with succes
+     Fix1 constraint input commands read with succes
+     Fix1 constraint input commands read with succes
+     bearing2 constraint input commands read with succes
+     bearing2 constraint input commands read with succes
+     bearing2 constraint input commands read with succes
+     constraint input commands read with succes
+     Topologi commands read with succes
+     Tower shadow (potential2 flow) commands read with succes
+     Wind commands read with succes
+     aerodrag element commands read with succes
+     aerodrag element commands read with succes
+     Aerodrag commands read with succes
+     Aerodynamic commands read with succes
+     output commands read with succes
+     Output commands read
+     Dll type2 input commands read with succes
+     output commands read with succes
+     Output commands read
+     Actions commands read
+     Dll type2 input commands read with succes
+     output commands read with succes
+     Output commands read
+     Actions commands read
+     Dll type2 input commands read with succes
+     output commands read with succes
+     Output commands read
+     Actions commands read
+     Dll type2 input commands read with succes
+     output commands read with succes
+     Output commands read
+     Dll type2 input commands read with succes
+     DLL commands read with succes
+     output commands read with succes
+     Output commands read
+     output_at read with succes
+     Initialization of structure
+     Initializing of aero rotor...
+     Initialization of rotor aerodynamics
+     Succes opening ./data/dtu_10mw_rwt_ae.dat
+     Succes opening ./data/dtu_10mw_rwt_pc.dat
+     Initialization of rotor induction
+     Initialization of wind
+     Initialization of external type2 DLL
+     External DLL ./control/dtu_we_controller.dll is attempted to open
+     Using ./control/dtu_we_controller.dll, version: unknown
+     Succes opening external DLL ./control/dtu_we_controller.dll
+     DLL subroutine init init_regulation is called
+     In initialization call of ./control/dtu_we_controller.dll Output is
+      0.000000000000000E+000
+     *** INFO *** The DLL subroutine message could not be loaded - bypassed!
+     Initialization of external type2 DLL
+     External DLL ./control/generator_servo.dll is attempted to open
+     Using ./control/generator_servo.dll, version: unknown
+     Succes opening external DLL ./control/generator_servo.dll
+     DLL subroutine init init_generator_servo is called
+     In initialization call of ./control/generator_servo.dll Output is
+      0.000000000000000E+000
+     *** INFO *** The DLL subroutine message could not be loaded - bypassed!
+     Initialization of external type2 DLL
+     External DLL ./control/mech_brake.dll is attempted to open
+     Using ./control/mech_brake.dll, version: unknown
+     Succes opening external DLL ./control/mech_brake.dll
+     DLL subroutine init init_mech_brake is called
+     In initialization call of ./control/mech_brake.dll Output is
+      0.000000000000000E+000
+     *** INFO *** The DLL subroutine message could not be loaded - bypassed!
+     Initialization of external type2 DLL
+     External DLL ./control/servo_with_limits.dll is attempted to open
+     Using ./control/servo_with_limits.dll, version: unknown
+     Succes opening external DLL ./control/servo_with_limits.dll
+     DLL subroutine init init_servo_with_limits is called
+     In initialization call of ./control/servo_with_limits.dll Output is
+      0.000000000000000E+000
+     *** INFO *** The DLL subroutine message could not be loaded - bypassed!
+     Initialization of external type2 DLL
+     External DLL ./control/towclearsens.dll is attempted to open
+     Using ./control/towclearsens.dll, version: unknown
+     Succes opening external DLL ./control/towclearsens.dll
+     DLL subroutine init initialize is called
+     In initialization call of ./control/towclearsens.dll Output is
+       2.66000000000000
+     *** INFO *** The DLL subroutine message could not be loaded - bypassed!
+     Creating link between structure and aerodynamics
+     Creating link between structure and aerodrag
+     Initialization of Aerodrag
+     Starting simulation
+    Dynamic stall method:  2 used for entire rotor
+     Global time =   2.000000000000000E-002 Iter =            2
+     Global time =   4.000000000000000E-002 Iter =            2
+     Global time =   6.000000000000000E-002 Iter =            2
+     Global time =   8.000000000000000E-002 Iter =            2
+     Global time =   0.100000000000000      Iter =            2
+     Global time =   0.120000000000000      Iter =            2
+     Global time =   0.140000000000000      Iter =            2
+     Global time =   0.160000000000000      Iter =            2
+     Global time =   0.180000000000000      Iter =            2
+     Global time =   0.200000000000000      Iter =            2
+     Global time =   0.220000000000000      Iter =            2
+     Global time =   0.240000000000000      Iter =            2
+     Global time =   0.260000000000000      Iter =            2
+     Global time =   0.280000000000000      Iter =            3
+     Global time =   0.300000000000000      Iter =            3
+     Global time =   0.320000000000000      Iter =            3
+     Global time =   0.340000000000000      Iter =            3
+     Global time =   0.360000000000000      Iter =            3
+     Global time =   0.380000000000000      Iter =            3
+     Global time =   0.400000000000000      Iter =            3
+     Global time =   0.420000000000000      Iter =            3
+     Global time =   0.440000000000000      Iter =            3
+     Global time =   0.460000000000000      Iter =            3
+     Global time =   0.480000000000000      Iter =            3
+     Global time =   0.500000000000000      Iter =            3
+     Global time =   0.520000000000000      Iter =            3
+     Global time =   0.540000000000000      Iter =            2
+     Global time =   0.560000000000000      Iter =            3
+     Global time =   0.580000000000000      Iter =            3
+     Global time =   0.600000000000000      Iter =            3
+     Global time =   0.620000000000000      Iter =            3
+     Global time =   0.640000000000000      Iter =            3
+     Global time =   0.660000000000000      Iter =            3
+     Global time =   0.680000000000000      Iter =            3
+     Global time =   0.700000000000000      Iter =            3
+     Global time =   0.720000000000000      Iter =            3
+     Global time =   0.740000000000000      Iter =            2
+     Global time =   0.760000000000000      Iter =            3
+     Global time =   0.780000000000000      Iter =            3
+     Global time =   0.800000000000000      Iter =            2
+     Global time =   0.820000000000000      Iter =            2
+     Global time =   0.840000000000000      Iter =            3
+     Global time =   0.860000000000000      Iter =            2
+     Global time =   0.880000000000000      Iter =            2
+     Global time =   0.900000000000000      Iter =            3
+     Global time =   0.920000000000000      Iter =            3
+     Global time =   0.940000000000000      Iter =            2
+     Global time =   0.960000000000000      Iter =            2
+     Global time =   0.980000000000000      Iter =            2
+     Global time =    1.00000000000000      Iter =            3
+     Closing of external type2 DLL
+     Closing of external type2 DLL
+     Closing of external type2 DLL
+     Closing of external type2 DLL
+     Closing of external type2 DLL
+     Elapsed time :   0.9218750
+    
+
+%% Cell type:code id: tags:
+
+``` python
+```

docs/tutorials/1-creating-master-excel.md

+# Tutorial 1: Creating master Excel file
+
+The Wind Energy Toolbox has a workflow for automatically running design load 
+bases (DLBs) on Gorm.
+This workflow has the following steps:
+1. Create a master Excel sheet defining each case in the DLB
+2. [Create subordinate Excel sheets from each tab in the master Excel sheet](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/tutorials/2-creating-subordinate-excels.md)
+3. [Create htc files and PBS job scripts for each requisite simulation using 
+the subordinate Excel files and a master htc file.](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/tutorials/3-creating-htc-pbs-files.md)
+4. Submit all PBS job scripts to the cluster
+5. Post-process results
+6. Visualize results
+
+This tutorial presents how to accomplish Step 1.
+
+Note that it is possible to customize your simulations by skipping/modifying 
+steps.
+Such a procedure will be discussed in a later tutorial.
+
+If there are any problems with this tutorial, please [submit an issue](
+https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues).
+
+## 1. Background: Master Excel File
+
+The master Excel file is an Excel file that is used to create subordinate 
+Excel files for generation of htc files and PBS job scripts.
+
+### Master file structure
+
+The master Excel file has a main tab, called "Main", that defines default 
+values  and necessary functions that are called in the other tabs.
+Each other tab defines a new case, and one subordinate Excel file will be 
+generated for each case.
+There are three variable types in the master Excel file:
+- Constants: values that do not change within a case
+- Variables: values that do change within a case, but are numbers that do not 
+depend on any other values (e.g., wind speed in DLC 1.2)
+- Functions: values that depend on other values
+
+### Tag names
+
+The values that are defined in the master Excel file (and eventually the 
+subordinate Excel files) are used to replace "tags" in the master htc file.
+These tags are of the form ```[$TAG_NAME]```.
+Theoretically, a user can define any new tags they desire, there are no 
+require naming conventions.
+However, there are some tags that are currently hard-coded into the Toolbox 
+that can result in errors if the tag names are changed.
+Thus, **we do not recommend you change the tag names from those in the 
+tutorial**.
+If you need new values that do not exist in the tutorial's master htc file 
+and produced master file, then it should be fine to add them.
+
+There are a few tags that deserve special mention:
+- ```[Case folder]```: the htc files for each case will be saved in this case 
+folder. We do not recommend changing the tag name or naming convention here 
+if you are doing a standard DLB.
+- ```[Case id.]```: this defines the naming convention for each htc file. We 
+do not recommend changing the tag name or naming convention here if you are 
+doing a standard DLB.
+- ```[seed]```: this variable indicates the desired number of seeds for each 
+set of variables. Thus, for example, in DLC 1.2, 1.3, the ```[seed]``` value 
+should be set to at least 6.
+
+Lastly, it is extremely important that your tag names in your master Excel 
+file match the tag names in your master htc file.
+Thus, **be sure to verify that your tag names in your master Excel and master 
+htc files are consistent**.
+
+## 2. Tutorial
+
+The procedure for creating the master Excel sheet is simple: each desired DLB 
+is defined in a tab-delimited text file, and these are loaded into a single 
+Excel file.
+It is assumed that the user has a collection of text files in a folder for 
+all of the DLBs to be simulated.
+This tutorial uses the text files located in 
+```wetb/docs/tutorials/data/DLCs_onshore```, which contain a series of text 
+files for a full DLB of an onshore turbine.
+These text files correspond to the onshore DTU 10 MW master htc file that is 
+located in the same directoy.
+
+Generate the master Excel file in a few easy steps:
+1. Open a command window.
+2. If you are running the tutorial locally (i.e., not on Gorm), navigate to 
+the Wind Energy Toolbox tutorials directory.
+3. From a terminal/command window, run the code to generate the Excel file 
+from a folder of text files:
+    * Windows (from the wetb tutorials folder):  
+    ```python ..\..\wetb\prepost\write_master.py --folder data\DLCs_onshore --filename DLCs_onshore.xlsx```
+    * Mac/Linux (from the wetb tutorials folder):  
+    ```python ../../wetb/prepost/write_master.py --folder data/DLCs_onshore  --filename DLCs_onshore.xlsx```
+    * Gorm (from any folder that contains a subfolder with your text files. Note
+you must activate the wetb environment (see Step 5 [here](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/getting-started-with-dlbs.md)
+) before this command will work. This command also assumes the folder with your
+text files is called "DLCs_onshore" and is located in the working directory.):  
+    ```python  /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/write_master.py --folder ./DLCs_onshore --filename ./DLCs_onshore.xlsx```
+ 
+The master Excel file "DLCs_onshore.xlsx" should now be in the your current 
+directory.
+
+Note that we have used the parser options ```--folder``` and ```--filename``` 
+to specify the folder with the text files and the name of the resulting Excel 
+file.
+Other parser options are also available.
+(See doc string in ```write_master.py``` function.)
+
+## 3. Generation options
+
+See doc string in ```write_master.py``` function.
+
+## 4. Issues
+
+If there are any problems with this tutorial, please [submit an issue](
+https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues).
+We will try to fix it as soon as possible.
+