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/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

@@ -14,10 +14,10 @@ This tool comes handy in the following scenarios:
 * 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 genetaion of the htc files.
+in a more compact way.
+The tool is based on the "tags" concept that is used for the generation of the htc files.
 
-Main spreatsheet
+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.
@@ -26,22 +26,47 @@ 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 devided into three possible different categories:
+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 turbilence seeds, wind direction, ..;
+* 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 wetb_py3
-    python /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/GenerateDLCs.py --folder=DLCs 
-    
+    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/howto-make-dlcs.md

@@ -4,15 +4,18 @@ Auto-generation of Design Load Cases
 
 <!---
 TODO, improvements:
-putty reference and instructions (fill in username in the address username@gorm
-how to mount gorm home on windows
 do as on Arch Linux wiki: top line is the file name where you need to add stuff
-point to the gorm/jess wiki's
 explain the difference in the paths seen from a windows computer and the cluster
+
+DONE:
+- putty reference and instructions (fill in username in the address
+  username@gorm) [rink]
+- how to mount gorm home on windows [rink]
+- point to the gorm/jess wiki's [rink]
 -->
 
 > WARNING: these notes contain configuration settings that are specif to the
-DTU Wind Energy cluster Gorm. Only follow this guide in another environment if
+DTU Wind Energy cluster Jess. Only follow this guide in another environment if
 you know what you are doing!
 
 
@@ -38,7 +41,7 @@ result and log files with lower case file names, regardless of the user input.
 Hence, in order to avoid possible ambiguities at all times, make sure that there
 are no upper case symbols defined in the value of the following tags (as defined
 in the Excel spreadsheets): ```[Case folder]```,  ```[Case id.]```, and
-```[Turb base name]```.
+```[turb_base_name]```.
 
 The system will always force the values of the tags to be lower case anyway, and
 when working on Windows, this might cause some confusing and unexpected behavior.
@@ -50,70 +53,130 @@ either let the system fill that in for you (by using the variable ```$USER```),
 or explicitly user your user name instead. This user name is the same as your
 DTU account name (or student account/number).
 
-This document refers to commands to be entered in the terminal on Gorm when the
-line starts with ```g-000 $```. The command that needs to be entered starts
+This document refers to commands to be entered in the terminal on Jess when the
+line starts with ```j-000 $```. The command that needs to be entered starts
 after the ```$```.
 
 
+Pdap
+----
+
+You can also use the Pdap for post-processing, which includes a MS Word report
+generator based on a full DLB, a GUI for easy plotting of HAWC2 result files,
+and a Python scripting interface:
+
+* [Pdap](http://www.hawc2.dk/Download/Post-processing-tools/Pdap)
+* [Pdap report/docs](http://orbit.dtu.dk/en/publications/post-processing-of-design-load-cases-using-pdap%28827c432b-cf7d-44eb-899b-93e9c0648ca5%29.html)
+
+
 Connecting to the cluster
 -------------------------
 
-You connect to the cluster via an SSH terminal. SSH is supported out of the box
-for Linux and Mac OSX terminals (such as bash), but requires a separate
-terminal client under Windows. Windows users are advised to use PuTTY and can
-be downloaded at:
-[http://www.chiark.greenend.org.uk/~sgtatham/putty/](http://www.chiark.greenend.org.uk/~sgtatham/putty/).
-Here's a random
-[tutorial](http://www.ghacks.net/2008/02/09/about-putty-and-tutorials-including-a-putty-tutorial/),
-you can use your favourite search engine if you need more or different instructions.
-More answers regarding PuTTY can also be found in the online
+We provide here an overview of how to connect to the cluster, but general,
+up-to-date information can be found in the [HPC documentation](https://docs.hpc.ait.dtu.dk).
+
+You connect to the cluster via an SSH terminal, and there are different SSH
+terminals based on your operating system (see the platform-specific
+instructions in the next subsections). The cluster can only be reached when
+on the DTU network (wired, or only from a DTU computer when using a wireless
+connection), when connected to the DTU VPN, or from one of the DTU
+[databars](http://www.databar.dtu.dk/).
+
+### Windows
+
+Windows users are advised to use PuTTY, which can
+be downloaded from
+[this link](http://www.chiark.greenend.org.uk/~sgtatham/putty/).
+
+Once you have installed PuTTY and placed the executable somewhere convenient
+(e.g., the Desktop), double click on the executable. In the window that opens
+up, enter/verify the following settings:
+* Session > Host Name: jess.dtu.dk
+* Session > Port: 22
+* Session > Connection type: SSH
+* Session > Saved Sessions: Jess
+* Connection > Data > Auto-login username: your DTU username
+* Connection > Data > When username is not specified: Use system username
+* Window > Colours > Select a colour to adjust > ANSI Blue: RGB = 85, 85, 255
+* Window > Colours > Select a colour to adjust > ANSI Bold Blue: RGB = 128, 128, 255
+
+Note that these last two options are optional. We've found that the default
+color for comments, ANSI Blue, is too dark to be seen on the black
+background. The last two options in the list set ANSI Blue and ANSI Blue Bold
+to be lighter and therefore easier to read when working in the terminal. Once
+you have entered these options, click "Save" on the "Session" tab and close
+the window.
+
+With PuTTY configured, you can connect to Jess by double-clicking the PuTTY
+executable; then, in the window that opens select "Jess" in "Saved Sessions",
+click the "Load" button, and finally click the "Open" button. A terminal
+window will open up. Type your DTU password in this new window when prompted
+(your text will not appear in the window) and then hit the Enter key. You
+should now be logged into Jess.
+
+To close the PuTTY window, you can either hit the red "X" in the upper-right
+corner of the window or type "exit" in the terminal and hit enter.
+
+More information on using PuTTY and how it works can be found in this
+[PuTTY tutorial](http://www.ghacks.net/2008/02/09/about-putty-and-tutorials-including-a-putty-tutorial/)
+or in the online
 [documentation](http://the.earth.li/~sgtatham/putty/latest/htmldoc/).
+You are also welcome to use Google and read the many online resources.
 
-The cluster that is setup for using the pre- and post-processing tools for HAWC2
-has the following address: ```gorm.risoe.dk```.
+### Unix
 
-On Linux/Mac connecting to the cluster is as simple as running the following
-command in the terminal:
+Unlike Windows, SSH is supported out of the box for Linux and Mac OSX
+terminals. To connect to the cluster, enter the following command into
+the terminal:
 
 ```
-ssh $USER@gorm.risoe.dk
+ssh $USER@jess.dtu.dk
 ```
 
-Use your DTU password when asked. This will give you terminal access to the
-cluster called Gorm.
-
-The cluster can only be reached when on the DTU network (wired, or only from a
-DTU computer when using a wireless connection), when connected to the DTU VPN,
-or from one of the DTU [databars](http://www.databar.dtu.dk/).
-
-More information about the cluster can be found on the
-[Gorm-wiki](http://gorm.risoe.dk/gormwiki)
+Enter your DTU password when prompted. This will give you terminal access
+to the Jess cluster.
 
 
 Mounting the cluster discs
 --------------------------
 
-You need to be connected to the DTU network in order for this to work. You can
-also connect to the DTU network over VPN. When doing the HAWC2 simulations, you
-will interact regularly with the cluster file system and discs.
+When doing the HAWC2 simulations, you will interact regularly with the cluster
+file system and discs. Thus, it can be very useful to have two discs mounted
+locally so you can easily access them: 1) your home directory on Jess and 2)
+the HAWC2 simulation folder on Mimer.
 
-### Windows
+You need to be connected to the DTU network (either directly or via VPN) for
+the following instructions to work.
 
-It is convenient to map these discs as network drives (in Windows terms).
-Map the following network drives (replace ```$USER``` with your user name):
 
-```
-\\mimer\hawc2sim
-\\gorm\$USER # this is your Gorm home directory
-```
-
-Alternatively, on Windows you can use [WinSCP](http://winscp.net) to interact
-with the cluster discs.
+### Windows
 
-Note that by default Windows Explorer will hide some of the files you will need edit.
-In order to show all files on your Gorm home drive, you need to un-hide system files:
-Explorer > Organize > Folder and search options > select tab "view" > select the
-option to show hidden files and folders.
+On Windows, we recommend mapping the two drives to local network drives, which
+means that you can navigate/copy/paste to/from them in Windows Explorer just as
+you would do with normal folders on your computer. You may also use [WinSCP](http://winscp.net)
+to interact with the cluster discs if you are more familiar with that option.
+
+Here we provide instructions for mapping network drives in Windows 7. If these
+instructions don't work for you, you can always find directions for your
+version of Windows by Googling "map network drive windows $WIN_VERSION", where
+$WIN_VERSION is your version number.
+
+In Windows 7, you can map a network drive in the following steps:
+1. Open a Windows Explorer window
+2. Right-click on "Computer" and select "Map network drive"
+3. Select any unused drive and type ```\\Jess.dtu.dk\$USER``` into the folder field,
+replacing "$USER" with your DTU username (e.g., DTU user "ABCD" has a Jess home
+drive of ```\\Jess.dtu.dk\abcd```)
+4. Check the "Reconnect at logon" box if you want to connect to this drive
+every time you log into your computer (recommended)
+5. Click the Finish button
+6. Repeat Steps 1 through 5, replacing the Jess home address in Step 3 with the
+HAWC2 simulation folder address: ```\\mimer.risoe.dk\hawc2sim```
+
+Note that by default Windows Explorer will hide some of the files you will need
+edit. In order to show all files on your Jess home drive, you need to un-hide
+system files: Explorer > Organize > Folder and search options > "View" tab >
+Hidden files and folders > "Show hidden files, folders, and drives".
 
 ### Unix
 
@@ -121,7 +184,7 @@ From Linux/Mac, you should be able to mount using either of the following
 addresses:
 ```
 //mimer.risoe.dk/hawc2sim
-//gorm.risoe.dk/$USER
+//jess.dtu.dk/$USER
 ```
 You can use either ```sshfs``` or ```mount -t cifs``` to mount the discs.
 
@@ -129,8 +192,8 @@ You can use either ```sshfs``` or ```mount -t cifs``` to mount the discs.
 Preparation
 -----------
 
-Add the cluster-tools script to your system's PATH of you Gorm environment,
-by editing the file ```.bash_profile``` file in your Gorm’s home directory
+Add the cluster-tools script to your system's PATH of you Jess environment,
+by editing the file ```.bash_profile``` file in your Jess’s home directory
 (```/home/$USER/.bash_profile```), and add the following lines (add at the end,
 or create a new file with this file name in case it doesn't exist):
 
@@ -146,12 +209,13 @@ are much appreciated!)
 > If you have been using an old version of this how-to, you might be pointing
 to an earlier version of these tools/utils and any references containing
 ```cluster-tools``` or ```prepost``` should be removed
-from your ```.bash_profile``` and/or ```.bashrc``` file on your gorm home drive.
+from your ```.bash_profile``` and/or ```.bashrc``` file on your Jess home drive.
 
 After modifying ```.bash_profile```, save and close it. Then, in the terminal,
 run the command (or logout and in again to be safe):
 ```
-g-000 $ source ~/.bash_profile
+j-000 $ source ~/.bash_profile
+j-000 $ source ~/.bashrc
 ```
 
 You will also need to configure wine and place the HAWC2 executables in your
@@ -159,7 +223,7 @@ local wine directory, which by default is assumed to be ```~/.wine32```, and
 ```pbsutils``` contains and automatic configuration script you can run:
 
 ```
-g-000 $ config-wine-hawc2.sh
+j-000 $ /home/MET/repositories/toolbox/pbsutils/config-wine-hawc2.sh
 ```
 
 If you need more information on what is going on, you can read a more detailed
@@ -179,12 +243,13 @@ Alternatively you can also include all the DLL's and executables in the root of
 your HAWC2 model folder. Executables and DLL's placed in the root folder take
 precedence over the ones placed in ```/home/$USER/wine_exe/win32```.
 
-Log out and in again from the cluster (close and restart PuTTY).
+> IMPORTANT: log out and in again from the cluster (close and restart PuTTY)
+> before trying to see if you can run HAWC2.
 
 At this stage you can run HAWC2 as follows:
 
 ```
-g-000 $ wine32 hawc2-latest htc/some-intput-file.htc
+j-000 $ wine32 hawc2-latest htc/some-intput-file.htc
 ```
 
 
@@ -195,7 +260,7 @@ When there is a new version of HAWC2, or when a new license manager is released,
 you can update your local wine directory as follows:
 
 ```
-g-000 $ cp /home/MET/hawc2exe/* /home/$USER/wine_exe/win32/
+j-000 $ rsync -au /home/MET/hawc2exe/win32 /home/$USER/wine_exe/win32 --progress
 ```
 
 The file ```hawc2-latest.exe``` will always be the latest HAWC2
@@ -235,23 +300,26 @@ from here (valid for the DTU10MW):
 /mnt/mimer/hawc2sim/DTU10MW/C0020/htc/DLCs
 ```
 
+Note that ```dlctemplate.py``` does not require any changes or modifications
+if you are only interested in running the standard DLB as explained here.
+
 For example, in order to generate all the HAWC2 htc input files and the
 corresponding ```*.p``` cluster launch files using this default DLB setup with:
 
 ```
-g-000 $ cd /mnt/mimer/hawc2sim/demo/A0001 # folder where the hawc2 model is located
-g-000 $ qsub-wrap.py -f /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py --prep
+j-000 $ cd /mnt/mimer/hawc2sim/demo/A0001 # folder where the hawc2 model is located
+j-000 $ qsub-wrap.py -f /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py --prep
 ```
 
 You could consider adding ```dlctemplate.py``` into the turbine folder or in
 the simulation set id folder for your convenience:
 
 ```
-g-000 $ cd /mnt/mimer/hawc2sim/demo/
+j-000 $ cd /mnt/mimer/hawc2sim/demo/
 # copy the dlctemplate to your turbine model folder and rename to myturbine.py
-g-000 $ cp /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py ./myturbine.py
-g-000 $ cd A0001
-g-000 $ qsub-wrap.py -f ../myturbine.py --prep
+j-000 $ cp /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py ./myturbine.py
+j-000 $ cd A0001
+j-000 $ qsub-wrap.py -f ../myturbine.py --prep
 ```
 
 
@@ -267,23 +335,23 @@ First activate the Anaconda Python environment by typing:
 
 ```bash
 # add the Anaconda Python environment paths to the system PATH
-g-000 $ export PATH=/home/python/miniconda3/bin:$PATH
+j-000 $ export PATH=/home/python/miniconda3/bin:$PATH
 # activate the custom python environment:
-g-000 $ source activate wetb_py3
+j-000 $ source activate py36-wetb
 ```
 For example, launch the auto-generation of DLCs input files:
 
 ```
 # folder where the HAWC2 model is located
-g-000 $ cd /mnt/mimer/hawc2sim/demo/AA0001
+j-000 $ cd /mnt/mimer/hawc2sim/demo/AA0001
 # assuming myturbine.py is copy of dlctemplate.py and is placed one level up
-g-000 $ python ../myturbine.py --prep
+j-000 $ python ../myturbine.py --prep
 ```
 
 Or start an interactive IPython shell:
 
 ```
-g-000 $ ipython
+j-000 $ ipython
 ```
 
 Users should be aware that running computational heavy loads on the login node
@@ -299,8 +367,9 @@ This approach gives you more flexibility and room for custimizations, but you
 will need to install a Python environment with all its dependencies locally.
 Additionally, you need access to the cluster discs from your local workstation.
 
-The installation procedure for wetb is outlined in the [installation manual]
-(https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/install-manual-detailed.md).
+The installation procedure for wetb is outlined in the
+[simple user](docs/install.md) or the
+[developer/contributor](docs/developer-guide.md) installation manual.
 
 
 Optional configuration
@@ -334,15 +403,30 @@ Required, and used for the PBS output and post-processing
 
 Optional
 * ```[turb_db_dir] = '../turb/'```
-* ```[wake_dir] = False```
-* ```[wake_db_dir] = False```
-* ```[wake_base_name] = 'turb_'```
+* ```[micro_dir] = False```
+* ```[micro_db_dir] = False```
+* ```[micro_base_name] = 'turb_'```
 * ```[meander_dir] = False```
-* ```[meand_db_dir] = False```
-* ```[meand_base_name] = 'turb_'```
+* ```[meander_db_dir] = False```
+* ```[meander_base_name] = 'turb_'```
 * ```[mooring_dir] = False```, all files and sub-folders copied to node
 * ```[hydro_dir] = False```, all files and sub-folders copied to node
 
+The mooring line dll has a fixed name init file that has to be in the root of
+the HAWC2 folder. When you have to use various init files (e.g. when the water
+depth is varying for different load cases) it would be convienent to be able
+to control which init file is used for which case (e.g. water depth).
+
+When running a load case for which the mooring lines will run in init mode:
+* ```[copyback_f1] = 'ESYSMooring_init.dat'```
+* ```[copyback_f1_rename] = 'mooringinits/ESYSMooring_init_vXYZ.dat'```
+
+When using an a priory cacluated init file for the mooring lines:
+* ```[copyto_f1] = 'mooringinits/ESYSMooring_init_vXYZ.dat'```
+* ```[copyto_generic_f1] = 'ESYSMooring_init.dat'```
+
+Replace ```vXYZ``` with an appropriate identifier for your case.
+
 A zip file will be created which contains all files in the model root directory,
 and all the contents (files and folders) of the following directories:
 ```[control_dir], [mooring_dir], [hydro_dir], 'externalforce/', [data_dir]```.
@@ -352,7 +436,7 @@ during simulation time in the ```[log_dir]```, ```[res_dir]```,
 ```[animation_dir]```, and ```[eigenfreq_dir]``` will be copied back.
 
 
-### Advanced configuration options
+### Advanced configuration options by modifying dlctemplate.py
 
 > Note that not all features are documented yet...
 
@@ -360,8 +444,8 @@ Special tags: copy special result files from the compute node back to the HAWC2
 working directory on the network drive, and optionally rename the file in case
 it would otherwise be overwritten by other cases in your DLB:
 * ```[copyback_files] = ['ESYSMooring_init.dat']```
-* ```[copyback_frename] = ['path/to/ESYSMooring_init_vXYZ.dat']```, optionally specify
-a different file path/name
+* ```[copyback_frename] = ['path/to/ESYSMooring_init_vXYZ.dat']```, optionally
+specify a different file path/name
 
 Copy files from the HAWC2 working directory with a special name to the compute
 node for which the a fixed file name is assumed
@@ -377,19 +461,80 @@ turbulence boxes using the 64-bit version of the stand alone Mann turbulence
 box generator. The appropriate input parameters are taken from the following
 tags:
 
-* ```[tu_model]```
-* ```[Turb base name]```
-* ```[MannAlfaEpsilon]```
-* ```[MannL]```
-* ```[MannGamma]```
-* ```[tu_seed]```
-* ```[turb_nr_u]``` : number of grid points in the u direction
-* ```[turb_nr_v]``` : number of grid points in the v direction
-* ```[turb_nr_w]``` : number of grid points in the w direction
-* ```[turb_dx]``` : grid spacing in meters in the u direction
-* ```[turb_dy]``` : grid spacing in meters in the v direction
-* ```[turb_dz]``` : grid spacing in meters in the w direction
-* ```[high_freq_comp]```
+* Atmospheric turbulence:
+    * ```[tu_model] = 1```
+    * ```[turb_base_name]```
+    * ```[MannAlfaEpsilon]```
+    * ```[MannL]```
+    * ```[MannGamma]```
+    * ```[seed]```
+    * ```[turb_nr_u]``` : number of grid points in the u direction
+    * ```[turb_nr_v]``` : number of grid points in the v direction
+    * ```[turb_nr_w]``` : number of grid points in the w direction
+    * ```[turb_dx]``` : grid spacing in meters in the u direction
+    * ```[turb_dy]``` : grid spacing in meters in the v direction
+    * ```[turb_dz]``` : grid spacing in meters in the w direction
+    * ```[high_freq_comp]```
+
+* Micro turbulence for DWM:
+    * ```[micro_base_name]```
+    * ```[MannAlfaEpsilon_micro]```
+    * ```[MannL_micro]```
+    * ```[MannGamma_micro]```
+    * ```[seed_micro]```
+    * ```[turb_nr_u_micro]``` : number of grid points in the u direction
+    * ```[turb_nr_v_micro]``` : number of grid points in the v direction
+    * ```[turb_nr_w_micro]``` : number of grid points in the w direction
+    * ```[turb_dx_micro]``` : grid spacing in meters in the u direction
+    * ```[turb_dy_micro]``` : grid spacing in meters in the v direction
+    * ```[turb_dz_micro]``` : grid spacing in meters in the w direction
+    * ```[high_freq_comp_micro]```
+
+* Meander turbulence for DWM
+    * ```[meander_base_name]```
+    * ```[MannAlfaEpsilon_meander]```
+    * ```[MannL_meander]```
+    * ```[MannGamma_meander]```
+    * ```[seed_meander]```
+    * ```[turb_nr_u_meander]``` : number of grid points in the u direction
+    * ```[turb_nr_v_meander]``` : number of grid points in the v direction
+    * ```[turb_nr_w_meander]``` : number of grid points in the w direction
+    * ```[turb_dx_meander]``` : grid spacing in meters in the u direction
+    * ```[turb_dy_meander]``` : grid spacing in meters in the v direction
+    * ```[turb_dz_meander]``` : grid spacing in meters in the w direction
+    * ```[high_freq_comp_meander]```
+
+
+### Tags required for hydro file generation
+
+* ```[hydro_dir]```
+* ```[hydro input name]```
+* ```[wave_type]``` : see HAWC2 manual for options
+* ```[wave_spectrum]``` : see HAWC2 manual for options
+* ```[wdepth]```
+* ```[Hs]``` : see HAWC2 manual for options
+* ```[Tp]``` : see HAWC2 manual for options
+* ```[wave_seed]``` : see HAWC2 manual for options
+* ```[wave_gamma]``` : see HAWC2 manual for options
+* ```[wave_coef]``` : see HAWC2 manual for options
+* ```[stretching]``` : see HAWC2 manual for options
+* ```[embed_sf]``` : see HAWC2 manual for options, and look for how it is implemented
+in [prepost.dlcsdefs.vartag_excel_stabcon(master)](wetb/prepost/dlcdefs.py).
+
+And the corresponding section the htc master file:
+
+```
+begin hydro;
+  begin water_properties;
+    rho 1027 ; kg/m^3
+    gravity 9.81 ; m/s^2
+    mwl 0.0;
+    mudlevel [wdepth];
+    wave_direction [wave_dir];
+    water_kinematics_dll ./wkin_dll.dll   ./[hydro_dir][hydro input name].inp;
+  end water_properties;
+end hydro;
+```
 
 
 Launching the jobs on the cluster
@@ -418,7 +563,7 @@ met:
 ```
 nr_cpus > cpu's used by user
 AND cpu's free on cluster > cpu_free
-AND jobs queued by user < cpu_user_queue)
+AND jobs queued by user < cpu_user_queue
 ```
 
 the program will sleep 5 seconds before trying to launch a new job again.
@@ -457,7 +602,7 @@ The ```launch.py``` script has various different options, and you can read about
 them by using the help function (the output is included for your convenience):
 
 ```bash
-g-000 $ launch.py --help
+j-000 $ launch.py --help
 Usage:
 
 launch.py -n nr_cpus
@@ -513,8 +658,8 @@ Then launch the actual jobs (each job is a ```*.p``` file in ```pbs_in```) using
 100 cpu's:
 
 ```bash
-g-000 $ cd /mnt/mimer/hawc2sim/demo/A0001
-g-000 $ launch.py -n 100 -p pbs_in/
+j-000 $ cd /mnt/mimer/hawc2sim/demo/A0001
+j-000 $ launch.py -n 100 -p pbs_in/
 ```
 
 If the launching process requires hours, and you have to close you SHH/PuTTY
@@ -527,8 +672,8 @@ simple and light job. ```launch.py``` will remove all the users crontab jobs
 at the end with ```crontab -r```.
 
 ```bash
-g-000 $ cd /mnt/mimer/hawc2sim/demo/A0001
-g-000 $ launch.py -n 100 -p pbs_in/ --crontab
+j-000 $ cd /mnt/mimer/hawc2sim/demo/A0001
+j-000 $ launch.py -n 100 -p pbs_in/ --crontab
 ```
 
 
@@ -546,25 +691,25 @@ length of the queue, etc
 
 Notice that the pbs output files in ```pbs_out``` are only created when the job
 has ended (or failed). When you want to inspect a running job, you can ssh from
-the Gorm login node to node that runs the job. First, find the job id by listing
+the Jess login node to node that runs the job. First, find the job id by listing
 all your current jobs (```qstat -u $USER```). The job id can be found in the
 first column, and you only need to consider the number, not the domain name
 attached to it. Now find the on which node it runs with (replace 123546 with the
 relevant job id):
 ```
-g-000 $ qstat -f 123456 | grep exec_host
+j-000 $ qstat -f 123456 | grep exec_host
 ```
 
-From here you login into the node as follows (replace g-078 with the relevant
+From here you login into the node as follows (replace j-078 with the relevant
 node):
 ```
-g-000 $ ssh g-078
+j-000 $ ssh j-078
 ```
 
 And browse to the scratch directory which lands you in the root directory of
 your running HAWC2 model (replace 123456 with the relevant job id):
 ```
-g-000 $ cd /scratch/$USER/123456.g-000.risoe.dk
+j-000 $ cd /scratch/$USER/123456.j-000.risoe.dk
 ```
 
 You can find what HAWC2 (or whatever other executable you are running) is
@@ -576,8 +721,6 @@ Or when watch what is happening at the end in real time
 ```
 # on Jess:
 tail -f /var/lib/torque/spool/JOBID.jess.dtu.dk.OU
-# on Gorm:
-tail -f /var/spool/pbs/spool/JOBID.g-000.risoe.dk.OU
 ```
 
 
@@ -592,7 +735,7 @@ found in the ```pbs_in``` folder) of the failed cases to a new folder (for
 example ```pbs_in_failed```). Now run ```launch.py``` again, but instead point
 to the folder that contains the ```*.p``` files of the failed cases, for example:
 ```
-g-000 $ launch.py -n 100 --node -p pbs_in_failed
+j-000 $ launch.py -n 100 --node -p pbs_in_failed
 ```
 
 2. Use the ```--cache``` option, and edit the PBS file list in the file
@@ -604,7 +747,7 @@ job will be launched.
 
 3. Each pbs file can be launched manually as follows:
 ```
-g-000 $ qsub path/to/pbs_file.p
+j-000 $ qsub path/to/pbs_file.p
 ```
 
 Alternatively, one can use the following options in ```launch.py```:
@@ -628,31 +771,54 @@ files, calculating the statistics, the AEP and the life time equivalent loads:
 
 ```
 # myturbine.py (copy of dlctemplate.py) is assumed to be located one folder up
-g-000 $ qsub-wrap.py -f ../myturbine.py --years=25 --neq=1e7 --stats --check_logs --fatigue
+j-000 $ qsub-wrap.py -f ../myturbine.py --years=25 --neq=1e7 --stats --check_logs --fatigue
 ```
 
 Other options for the original ```dlctemplate.py``` script:
 
 ```
-usage: dlctemplate.py [-h] [--prep] [--check_logs] [--stats] [--fatigue]
-                      [--csv] [--years YEARS] [--no_bins NO_BINS] [--neq NEQ]
-                      [--envelopeblade] [--envelopeturbine]
+(py36-wetb) [dave@jess]$ python dlctemplate.py --help
+usage: dlctemplate.py [-h] [--prep] [--check_logs]
+                      [--pbs_failed_path PBS_FAILED_PATH] [--stats]
+                      [--fatigue] [--AEP] [--csv] [--years YEARS]
+                      [--no_bins NO_BINS] [--neq NEQ] [--rotarea ROTAREA]
+                      [--save_new_sigs] [--dlcplot] [--envelopeblade]
+                      [--envelopeturbine] [--zipchunks] [--pbs_turb]
+                      [--walltime WALLTIME]
 
 pre- or post-processes DLC's
 
 optional arguments:
-  -h, --help         show this help message and exit
-  --prep             create htc, pbs, files (default=False)
-  --check_logs       check the log files (default=False)
-  --stats            calculate statistics and 1Hz equivalent loads (default=False)
-  --fatigue          calculate Leq for a full DLC (default=False)
-  --csv              Save data also as csv file (default=False)
-  --years YEARS      Total life time in years (default=20)
-  --no_bins NO_BINS  Number of bins for fatigue loads (default=46)
-  --neq NEQ          Equivalent cycles neq, default 1 Hz equivalent load
-                     (neq = simulation duration in seconds)
-  --envelopeblade    calculate the load envelope for sensors on the blades
-  --envelopeturbine  calculate the load envelope for sensors on the turbine
+  -h, --help            show this help message and exit
+  --prep                create htc, pbs, files
+  --check_logs          check the log files
+  --pbs_failed_path PBS_FAILED_PATH
+                        Copy pbs launch files of the failed cases to a new
+                        directory in order to prepare a re-run. Default value:
+                        pbs_in_failed.
+  --stats               calculate statistics and 1Hz equivalent loads
+  --fatigue             calculate Leq for a full DLC
+  --AEP                 calculate AEP, requires htc/DLCs/dlc_config.xlsx
+  --csv                 Save data also as csv file
+  --years YEARS         Total life time in years
+  --no_bins NO_BINS     Number of bins for fatigue loads
+  --neq NEQ             Equivalent cycles Neq used for Leq fatigue lifetime
+                        calculations.
+  --rotarea ROTAREA     Rotor area for C_T, C_P
+  --save_new_sigs       Save post-processed sigs
+  --dlcplot             Plot DLC load basis results
+  --envelopeblade       Compute envelopeblade
+  --envelopeturbine     Compute envelopeturbine
+  --zipchunks           Create PBS launch files forrunning in zip-chunk
+                        find+xargs mode.
+  --pbs_turb            Create PBS launch files to create the turbulence boxes
+                        in stand alone mode using the 64-bit Mann turbulence
+                        box generator. This can be usefull if your turbulence
+                        boxes are too big for running in HAWC2 32-bit mode.
+                        Only works on Jess.
+  --walltime WALLTIME   Queue walltime for each case/pbs file, format:
+                        HH:MM:SS Default: 04:00:00
+
 ```
 
 The load envelopes are computed for sensors specified in the

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

@@ -6,9 +6,9 @@
 
 ```
 conda update --all
-conda create -n wetb_py3 python=3.5
-source activate wetb_py3
-conda install setuptools_scm future h5py pytables pytest nose sphinx blosc psutil
+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
 ```
@@ -17,9 +17,9 @@ conda install -c https://conda.anaconda.org/conda-forge pyscaffold pytest-cov
 
 ```
 conda update --all
-conda create -n wetb_py3 python=3.4
-source activate wetb_py3
-conda install setuptools_scm future h5py pytables pytest nose sphinx psutil
+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-manual-detailed.md

-
-> !! This guide is not finished, and might contain innacuracies. Please report
-any mistakes/bugs by creating an
-[issue](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues).
-This is a WIP (Work In Progress) !!
-
-# Detailed Installation Manual
-
-Installing Python packages with compiled extensions can be a challenge especially
-on Windows systems. However, when using Miniconda things can be simplified to a
-great extent as this manual hopefully will show you.
-
-The this approach will require you to use the command line, but it is as easy
-as copy-pasting them from this page straight into your command prompt.
-
-Installation instructions follow in alphabetical orderby platorm.
-
-
-## Linux
-
-* Basic dependencies:
-
-> python (3.5 recommended) git gcc gcc-fortran (gfortran)
-
-* Use either your system package manager, pip + virtualenv, or Anaconda to
-install the following python dependencies:
-
-> numpy, cython, scipy, pandas, matplotlib, pyscaffold, future, nose, sphinx,
-> xlrd, (py)tables, h5py, pytest, pytest-cov, setuptools_scm, setuptools
-
-Note that often the pytables packages is called python-tables instead of
-python-pytables.
-
-
-## Dependencies on Mac
-
-People who now how to handle Python on the Mac side are kindly requested to
-complete this guide :-)
-
-
-## Dependencies on Windows
-
-A Python installation with compilers is required. If you already have this,
-or know how set up such an environment, you skip to
-[here](install-manual-detailed.md#and-finally-install-wetb).
-
-
-### Microsft Visual Studio 2010 Compiler
-
-```wetb``` contains extensions that need to be compiled.
-On Windows things are complicated because you need to use the same compiler as
-the one used for Python. This means that for compiling extensions on:
-* Python 2.7 you need [Microsoft Visual C++ Compiler for Python 2.7](http://aka.ms/vcpython27),
-or the [direct link](https://www.microsoft.com/en-gb/download/details.aspx?id=44266).
-* Python 3.4 you need MS Visual Studio 2010
-* Python 3.5 (and later) you need MS Visual Studio 2015
-* You can install Microsoft Visual C++ Compiler for Python 2.7 alongside
-MS Visual Studio 2010, but you can not install Visual Studio 2010 and 2015
-in parallel.
-
-You can find more background information and installation instructions
-[here](https://packaging.python.org/en/latest/extensions/#setting-up-a-build-environment-on-windows),
-[here](https://blogs.msdn.microsoft.com/pythonengineering/2016/04/11/unable-to-find-vcvarsall-bat/),
-[here](https://matthew-brett.github.io/pydagogue/python_msvc.html),
-or [here](http://stevedower.id.au/blog/building-for-python-3-5-part-two/).
-
-
-### 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).
-
-* If you would like to use a GUI for git, we recommend you to use
-[tortoisegit](https://tortoisegit.org/)
-
-
-## Recommended python distribution: Anaconda
-
-### Installing Anaconda, activate root environment
-
-* Anaconda is a professional grade, full blown scientific Python distribution.
-
-* Download and install Anaconda from
-[https://www.continuum.io/downloads](https://www.continuum.io/downloads).
-
-> Note: the choice of Anaconda for Python 2.7 or Python 3.5 only affects the
-root environment. You can always create additional environments using other
-Python versions, see below.
-
-* Update the root Anaconda environment (type in a terminal):
-
-```
-conda update --all
-```
-
-* Activate the Anaconda root environment in a terminal as follows:
-
-```
-activate
-```
-
-and your terminal will do something like:
-```
-C:\Users\> activate
-[Anaconda3] C:\Users\>
-```
-note that the name of the environment is now a prefix before the current path.
-
-use ```deactivate``` to deactivate the environment.
-
-
-### Optionally, create other independent Anaconda environments
-
-* By using environments you can manage different Python installations with
-different versions on your system. Creating environments is as easy as:
-
-```
-conda create -n py27 python=2.7
-conda create -n py34 python=3.4
-conda create -n py35 python=3.5
-```
-
-* These environments can be activated as follows:
-
-```
-activate py27
-activate py34
-activate py35
-```
-
-use ```deactivate``` to deactivate the environment.
-
-
-### Install dependencies with conda and pip
-
-* Install the necessary Python dependencies using the conda package manager:
-
-```
-conda install setuptools_scm future h5py pytables pytest nose sphinx
-conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl
-```
-
-* Not all packages are available in the conda repositories, but they can be
-easily installed with pip:
-
-```
-pip install pyscaffold pytest-cov --no-deps
-```
-
-
-## And Finally: install wetb
-
-```
-git clone https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox.git
-cd WindEnergyToolbox
-pip install -e . --no-deps
-```
-
-Note that ```pip install -e . --no-deps``` will install ```wetb``` in the source
-directory. This works best if you are also developing and regularly updating
-this package.
-
-You can run the tests cases from the source root directory:
-
-```
-python setup.py test
-```
-

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/install_windows.md

-# Install wetb on Windows
-
-For updating the toolbox jump to [Update wetb on Windows](#Update wetb on Windows)
-
-This guide describes a simple way to install the toolbox on Windows (1/9-2016)
-
-### Installing Anaconda
-
-* Anaconda is a professional grade, full blown scientific Python distribution.
-
-* Download and install Anaconda (Python 3.5 version, 64 bit installer) from <https://www.continuum.io/downloads>
-
-
-* Update the root Anaconda environment (type in a terminal):
-
-```
-conda update --all
-```
-
-### Create Anaconda environment
-
-* Create an environment :
-
-```
-conda create -n py35 python=3.5
-```
-
-* Activate the envirronment:
-
-```
-activate py35
-```
-
-The python distribution in use will now be located in \<path_to_anaconda\>/env/py35/
-
-
-### Install dependencies with conda and pip
-
-* Install the necessary Python dependencies using the conda package manager:
-
-```
-conda install setuptools_scm future h5py pytables pytest nose sphinx
-conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl psutil
-```
-
-* Not all packages are available in the conda repositories, but they can be
-easily installed with pip:
-
-```
-pip install pyscaffold pytest-cov --no-deps
-```
-
-
-## And Finally: install wetb
-
-```
-pip install wetb
-```
-
-# Update wetb on Windows
-
-* Activate the envirronment (type in a terminal):
-
-
-```
-activate py35
-```
-
-* Update the toolbox
-
-```
-pip install wetb --upgrade --no-deps
-```

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/InputFileWriting.ipynb

+%% Cell type:markdown id: tags:
+
+# Input file writing
+
+%% Cell type:markdown id: tags:
+
+## HTCFile
+
+### Quickstart
+
+The HTCFile class allows you to open, modify, save htc files and run HAWC2 simulations
+
+%% Cell type:code id: tags:
+
+``` python
+from wetb import hawc2
+from wetb.hawc2 import HTCFile
+from wetb.hawc2.tests.test_files import tfp
+htc = HTCFile(tfp + "htcfiles/DTU_10MW_RWT.htc")
+htc.wind.wsp=11
+print (htc)
+htc.save("tmp/tmp.htc")
+# htc.simulate('<path_to_hawc2>/hawc2mb.exe')
+```
+
+%% Output
+
+    ;DTU_10MW_RWT, version 9, 25-09-2017, mhha
+    ;
+      begin simulation;
+        time_stop	1000;
+        solvertype	1;	(newmark)
+        on_no_convergence	continue;
+        convergence_limits	1000 1 1e-07;
+        logfile	./log/DTU_10MW_RWT_ver09.log;
+        begin newmark;
+          deltat	0.01;
+        end newmark;
+      end simulation;
+    ;
+    ;----------------------------------------------------------------------------------------------------------------------------------------------------------------
+      begin new_htc_structure;
+    ;   beam_output_file_name  ./log/DTU_10MW_RWT_beam.dat;                    Optional - Calculated beam properties of the bodies are written to file
+    ;   body_output_file_name  ./log/DTU_10MW_RWT_body.dat;                    Optional - Body initial position and orientation are written to file
+    ;   body_eigenanalysis_file_name ./eig/DTU_10MW_RWT_body_eigen.dat;
+    ;   structure_eigenanalysis_file_name ./eig/DTU_10MW_RWT_strc_eigen.dat ;
+    ;-------------------------------------------------------------------------------------------------------------------------------
+    ;-------------------------------------------------------------------------------------------------------------------------------
+        begin main_body;	tower 115m
+          name	tower;
+          type	timoschenko;
+          nbodies	1;
+          node_distribution	c2_def;
+          damping_posdef	0 0 0 0.00412 0.00412 0.00045;	Mx My Mz Kx Ky Kz , M´s raises overall level, K´s raises high freguency level "tuned by Larh"
+          begin timoschenko_input;
+            filename	./data/DTU_10MW_RWT_Tower_st.dat;
+            set	1 1;
+          end timoschenko_input;
+          begin c2_def;	Definition of centerline (main_body coordinates)
+            nsec	11;
+            sec	1 0 0 0 0;	x,y,z,twist
+            sec	2 0 0 -11.5 0;
+            sec	3 0 0 -23 0;
+            sec	4 0 0 -34.5 0;
+            sec	5 0 0 -46 0;
+            sec	6 0 0 -57.5 0;
+            sec	7 0 0 -69 0;
+            sec	8 0 0 -80.5 0;
+            sec	9 0 0 -92 0;
+            sec	10 0 0 -103.5 0;
+            sec	11 0 0 -115.63 0;
+          end c2_def;
+        end main_body;
+    ;
+        begin main_body;
+          name	towertop;
+          type	timoschenko;
+          nbodies	1;
+          node_distribution	c2_def;
+          damping_posdef	0 0 0 0.007 0.007 0.007;	"changed by Larh"
+          concentrated_mass	2 0 2.687 0.30061 446040 4106000 410600 4106000;	Nacelle mass and inertia "corrected by Anyd 25/4/13"
+          begin timoschenko_input;
+            filename	./data/DTU_10MW_RWT_Towertop_st.dat;
+            set	1 2;
+          end timoschenko_input;
+          begin c2_def;	Definition of centerline (main_body coordinates)
+            nsec	2;
+            sec	1 0 0 0 0;	x,y,z,twist
+            sec	2 0 0 -2.75 0;
+          end c2_def;
+        end main_body;
+    ;
+        begin main_body;
+          name	shaft;
+          type	timoschenko;
+          nbodies	1;
+          node_distribution	c2_def;
+          damping_posdef	0 0 0 0.000465 0.000465 0.003983;	"tuned by Anyd 23/5/13 to 31.45 log decr. damping for free free with stiff rotor and tower"
+          concentrated_mass	1 0 0 0 0 0 0 3751000;	generator equivalent slow shaft "re_tuned by Anyd 20/2/13"
+          concentrated_mass	5 0 0 0 105520 0 0 325700;	hub mass and inertia;	"re_tuned by Anyd 20/2/13"
+          begin timoschenko_input;
+            filename	./data/DTU_10MW_RWT_Shaft_st.dat;
+            set	1 1;
+          end timoschenko_input;
+          begin c2_def;	Definition of centerline (main_body coordinates)
+            nsec	5;
+            sec	1 0 0 0 0;	Tower top x,y,z,twist
+            sec	2 0 0 1.5 0;
+            sec	3 0 0 3 0;
+            sec	4 0 0 4.4 0;	Main bearing
+            sec	5 0 0 7.1 0;	Rotor centre
+          end c2_def;
+        end main_body;
+    ;
+        begin main_body;
+          name	hub1;
+          type	timoschenko;
+          nbodies	1;
+          node_distribution	c2_def;
+          damping_posdef	0 0 0 3e-06 3e-06 2e-05;	"changed by Larh"
+          begin timoschenko_input;
+            filename	./data/DTU_10MW_RWT_Hub_st.dat;
+            set	1 2;
+          end timoschenko_input;
+          begin c2_def;	Definition of centerline (main_body coordinates)
+            nsec	2;
+            sec	1 0 0 0 0;	x,y,z,twist
+            sec	2 0 0 2.8 0;
+          end c2_def;
+        end main_body;
+    ;
+        begin main_body;
+          name	hub2;
+          copy_main_body	hub1;
+        end main_body;
+    ;
+        begin main_body;
+          name	hub3;
+          copy_main_body	hub1;
+        end main_body;
+    ;
+        begin main_body;
+          name	blade1;
+          type	timoschenko;
+          nbodies	10;
+          node_distribution	c2_def;
+          damping_posdef	0 0 0 0.00153 0.00255 0.00033;	" 3% damping tuned by tkim 23/03/13 unable to fit 3rd and higher mode"
+          begin timoschenko_input;
+            filename	./data/DTU_10MW_RWT_Blade_st.dat;
+            set	1 1;	set subset
+          end timoschenko_input;
+          begin c2_def;	Definition of centerline (main_body coordinates)
+            nsec	27;
+            sec	1 0 7.006e-05 4.44089e-16 -14.5;
+            sec	2 -2.06477e-05 -0.0122119 3 -14.5;
+            sec	3 -0.0072881 -0.0249251 6 -14.4851;
+            sec	4 -0.0189235 -0.0273351 7.00004 -14.461;
+            sec	5 -0.0541282 -0.0282163 8.70051 -14.3388;
+            sec	6 -0.126633 -0.021321 10.402 -14.0201;
+            sec	7 -0.225666 -0.0128378 12.2046 -13.3904;
+            sec	8 -0.288563 -0.00770659 13.2065 -12.9371;
+            sec	9 -0.399194 -0.00488317 15.01 -11.9445;
+            sec	10 -0.576634 -0.0180296 18.2151 -9.98243;
+            sec	11 -0.707136 -0.0501772 21.4178 -8.45147;
+            sec	12 -0.791081 -0.0941228 24.6189 -7.46417;
+            sec	13 -0.837195 -0.14888 27.8193 -6.72916;
+            sec	14 -0.853948 -0.214514 31.0194 -6.08842;
+            sec	15 -0.849367 -0.290618 34.2197 -5.49322;
+            sec	16 -0.79392 -0.462574 40.2204 -4.39222;
+            sec	17 -0.716284 -0.688437 46.6217 -3.09315;
+            sec	18 -0.634358 -0.960017 53.0232 -1.75629;
+            sec	19 -0.553179 -1.28424 59.4245 -0.50065;
+            sec	20 -0.475422 -1.66402 65.8255 0.601964;
+            sec	21 -0.40318 -2.10743 72.2261 1.5556;
+            sec	22 -0.330085 -2.6563 79.0266 2.51935;
+            sec	23 -0.31014 -2.78882 80.5267 2.7295;
+            sec	24 -0.286719 -2.92517 82.0271 2.93201;
+            sec	25 -0.255823 -3.06577 83.5274 3.11874;
+            sec	26 -0.207891 -3.20952 85.0277 3.28847;
+            sec	27 -0.089894 -3.33685 86.3655 3.42796;
+          end c2_def;
+        end main_body;
+    ;
+        begin main_body;
+          name	blade2;
+          copy_main_body	blade1;
+        end main_body;
+    ;
+        begin main_body;
+          name	blade3;
+          copy_main_body	blade1;
+        end main_body;
+    ;-------------------------------------------------------------------------------------------------------------------------------
+    ;
+        begin orientation;
+          begin base;
+            body	tower;
+            inipos	0 0 0;	initial position of node 1
+            body_eulerang	0 0 0;
+          end base;
+    ;
+          begin relative;
+            body1	tower last;
+            body2	towertop 1;
+            body2_eulerang	0 0 0;
+          end relative;
+    ;
+          begin relative;
+            body1	towertop last;
+            body2	shaft 1;
+            body2_eulerang	90 0 0;
+            body2_eulerang	5 0 0;	5 deg tilt angle
+            mbdy2_ini_rotvec_d1	0 0 -1 0.2;	mbdy2_ini_rotvec_d1 0.0 0.0 -1.0 [init_wr];
+          end relative;
+    ;
+          begin relative;
+            body1	shaft last;
+            body2	hub1 1;
+            body2_eulerang	-90 0 0;
+            body2_eulerang	0 180 0;
+            body2_eulerang	2.5 0 0;	2.5deg cone angle
+          end relative;
+    ;
+          begin relative;
+            body1	shaft last;
+            body2	hub2 1;
+            body2_eulerang	-90 0 0;
+            body2_eulerang	0 60 0;
+            body2_eulerang	2.5 0 0;	2.5deg cone angle
+          end relative;
+    ;
+          begin relative;
+            body1	shaft last;
+            body2	hub3 1;
+            body2_eulerang	-90 0 0;
+            body2_eulerang	0 -60 0;
+            body2_eulerang	2.5 0 0;	2.5deg cone angle
+          end relative;
+    ;
+          begin relative;
+            body1	hub1 last;
+            body2	blade1 1;
+            body2_eulerang	0 0 0;
+          end relative;
+    ;
+          begin relative;
+            body1	hub2 last;
+            body2	blade2 1;
+            body2_eulerang	0 0 0;
+          end relative;
+    ;
+          begin relative;
+            body1	hub3 last;
+            body2	blade3 1;
+            body2_eulerang	0 0 0;
+          end relative;
+    ;
+        end orientation;
+    ;-------------------------------------------------------------------------------------------------------------------------------
+        begin constraint;
+    ;
+          begin fix0;	fixed to ground in translation and rotation of node 1
+            body	tower;
+          end fix0;
+    ;
+          begin fix1;
+            body1	tower last;
+            body2	towertop 1;
+          end fix1;
+    ;
+          begin bearing1;	free bearing
+            name	shaft_rot;
+            body1	towertop last;
+            body2	shaft 1;
+            bearing_vector	2 0 0 -1;	x=coo (0=global.1=body1.2=body2) vector in body2 coordinates where the free rotation is present
+          end bearing1;
+    ;
+          begin fix1;
+            body1	shaft last;
+            body2	hub1 1;
+          end fix1;
+    ;
+          begin fix1;
+            body1	shaft last;
+            body2	hub2 1;
+          end fix1;
+    ;
+          begin fix1;
+            body1	shaft last;
+            body2	hub3 1;
+          end fix1;
+    ;
+          begin bearing2;
+            name	pitch1;
+            body1	hub1 last;
+            body2	blade1 1;
+            bearing_vector	2 0 0 -1;
+          end bearing2;
+    ;
+          begin bearing2;
+            name	pitch2;
+            body1	hub2 last;
+            body2	blade2 1;
+            bearing_vector	2 0 0 -1;
+          end bearing2;
+    ;
+          begin bearing2;
+            name	pitch3;
+            body1	hub3 last;
+            body2	blade3 1;
+            bearing_vector	2 0 0 -1;
+          end bearing2;
+        end constraint;
+    ;
+      end new_htc_structure;
+    ;----------------------------------------------------------------------------------------------------------------------------------------------------------------
+      begin wind;
+        density	1.225;
+        wsp	11;
+        tint	0;
+        horizontal_input	1;
+        windfield_rotations	0 0 0;	yaw, tilt, rotation
+        center_pos0	0 0 -119;	hub heigth
+        shear_format	1 0.2;
+        turb_format	0;	0=none, 1=mann,2=flex
+        tower_shadow_method	0;	0=none, 1=potential flow, 2=jet
+        scale_time_start	0;
+        wind_ramp_factor	0 40 0.6 1;
+    ; Steps ;
+        wind_ramp_abs	140 141 0 1;	wsp. after the step:  5.0
+        wind_ramp_abs	181 182 0 1;	wsp. after the step:  6.0
+        wind_ramp_abs	222 223 0 1;	wsp. after the step:  7.0
+        wind_ramp_abs	263 264 0 1;	wsp. after the step:  8.0
+        wind_ramp_abs	304 305 0 1;	wsp. after the step:  9.0
+        wind_ramp_abs	345 346 0 1;	wsp. after the step: 10.0
+        wind_ramp_abs	386 387 0 1;	wsp. after the step: 11.0
+        wind_ramp_abs	427 428 0 1;	wsp. after the step: 12.0
+        wind_ramp_abs	468 469 0 1;	wsp. after the step: 13.0
+        wind_ramp_abs	509 510 0 1;	wsp. after the step: 14.0
+        wind_ramp_abs	550 551 0 1;	wsp. after the step: 15.0
+        wind_ramp_abs	591 592 0 1;	wsp. after the step: 16.0
+        wind_ramp_abs	632 633 0 1;	wsp. after the step: 17.0
+        wind_ramp_abs	673 674 0 1;	wsp. after the step: 18.0
+        wind_ramp_abs	714 715 0 1;	wsp. after the step: 19.0
+        wind_ramp_abs	755 756 0 1;	wsp. after the step: 20.0
+        wind_ramp_abs	796 797 0 1;	wsp. after the step: 21.0
+        wind_ramp_abs	837 838 0 1;	wsp. after the step: 22.0
+        wind_ramp_abs	878 879 0 1;	wsp. after the step: 23.0
+        wind_ramp_abs	919 920 0 1;	wsp. after the step: 24.0
+        wind_ramp_abs	960 961 0 1;	wsp. after the step: 25.0
+    ;
+        begin tower_shadow_potential_2;
+          tower_mbdy_link	tower;
+          nsec	2;
+          radius	0 4.15;
+          radius	115.63 2.75;
+        end tower_shadow_potential_2;
+      end wind;
+    ;
+      begin aerodrag;
+        begin aerodrag_element;
+          mbdy_name	tower;
+          aerodrag_sections	uniform 10;
+          nsec	2;
+          sec	0 0.6 8.3;	tower bottom
+          sec	115.63 0.6 5.5;	tower top
+        end aerodrag_element;
+    ;
+        begin aerodrag_element;	Nacelle drag side
+          mbdy_name	shaft;
+          aerodrag_sections	uniform 2;
+          nsec	2;
+          sec	0 0.8 10;
+          sec	7.01 0.8 10;
+        end aerodrag_element;
+      end aerodrag;
+    ;
+      begin aero;
+        nblades	3;
+        hub_vec	shaft -3;	rotor rotation vector (normally shaft composant directed from pressure to sustion side)
+        link	1 mbdy_c2_def blade1;
+        link	2 mbdy_c2_def blade2;
+        link	3 mbdy_c2_def blade3;
+        ae_filename	./data/DTU_10MW_RWT_ae.dat;
+        pc_filename	./data/DTU_10MW_RWT_pc.dat;
+        induction_method	1;	0=none, 1=normal
+        aerocalc_method	1;	0=ingen aerodynamic, 1=med aerodynamic
+        aerosections	50;	def. 50
+        ae_sets	1 1 1;
+        tiploss_method	1;	0=none, 1=prandtl
+        dynstall_method	2;	0=none, 1=stig øye method,2=mhh method
+    ;
+      end aero;
+    ;-------------------------------------------------------------------------------------------------
+      begin dll;
+    ;
+        begin type2_dll;
+          name	dtu_we_controller;
+          filename	./control/dtu_we_controller.dll;
+          dll_subroutine_init	init_regulation_advanced;
+          dll_subroutine_update	update_regulation;
+          arraysizes_init	100 1;
+          arraysizes_update	100 100;
+          begin init;
+    ; Overall parameters
+            constant	1 10000;	Rated power [kW]
+            constant	2 0.628;	Minimum rotor (LSS) speed [rad/s]
+            constant	3 1.005;	Rated rotor (LSS) speed [rad/s]
+            constant	4 15600000;	Maximum allowable generator torque [Nm]
+            constant	5 100;	Minimum pitch angle, theta_min [deg],
+    ; if |theta_min|>90, then a table of <wsp,theta_min> is read ;
+    ; from a file named 'wptable.n', where n=int(theta_min)
+            constant	6 82;	Maximum pitch angle [deg]
+            constant	7 10;	Maximum pitch velocity operation [deg/s]
+            constant	8 0.4;	Frequency of generator speed filter [Hz]
+            constant	9 0.7;	Damping ratio of speed filter [-]
+            constant	10 1.8;	Frequency of free-free DT torsion mode [Hz], if zero no notch filter used
+    ; Partial load control parameters
+            constant	11 13013100;	Optimal Cp tracking K factor [Nm/(rad/s)^2], ;
+    ; Qg=K*Omega^2, K=eta*0.5*rho*A*Cp_opt*R^3/lambda_opt^3
+            constant	12 68345600;	Proportional gain of torque controller [Nm/(rad/s)]
+            constant	13 15336700;	Integral gain of torque controller [Nm/rad]
+            constant	14 0;	Differential gain of torque controller [Nm/(rad/s^2)]
+    ;     Full load control parameters
+            constant	15 1;	Generator control switch [1=constant power, 2=constant torque]
+            constant	16 1.06713;	Proportional gain of pitch controller [rad/(rad/s)]
+            constant	17 0.242445;	Integral gain of pitch controller [rad/rad]
+            constant	18 0;	Differential gain of pitch controller [rad/(rad/s^2)]
+            constant	19 4e-09;	Proportional power error gain [rad/W]
+            constant	20 4e-09;	Integral power error gain [rad/(Ws)]
+            constant	21 11.4;	Coefficient of linear term in aerodynamic gain scheduling, KK1 [deg]
+            constant	22 402.9;	Coefficient of quadratic term in aerodynamic gain scheduling, KK2 [deg^2] &
+    ; (if zero, KK1 = pitch angle at double gain)
+            constant	23 1.3;	Relative speed for double nonlinear gain [-]
+    ;     Cut-in simulation parameters
+            constant	24 -1;	Cut-in time [s], no cut-in is simulated if zero or negative
+            constant	25 1;	Time delay for soft start of torque [1/1P]
+    ;     Cut-out simulation parameters
+            constant	26 -1;	Shut-down time [s], no shut-down is simulated if zero or negative
+            constant	27 5;	Time of linear torque cut-out during a generator assisted stop [s]
+            constant	28 1;	Stop type [1=normal, 2=emergency]
+            constant	29 1;	Time delay for pitch stop after shut-down signal [s]
+            constant	30 3;	Maximum pitch velocity during initial period of stop [deg/s]
+            constant	31 3;	Time period of initial pitch stop phase [s] (maintains pitch speed specified in constant 30)
+            constant	32 4;	Maximum pitch velocity during final phase of stop [deg/s]
+    ;     Expert parameters (keep default values unless otherwise given)
+            constant	33 2;	Time for the maximum torque rate = Maximum allowable generator torque/(constant 33 + 0.01s) [s]
+            constant	34 2;	Upper angle above lowest minimum pitch angle for switch [deg], if equal then hard switch
+            constant	35 95;	Percentage of the rated speed when the torque limits are fully opened [%]
+            constant	36 2;	Time constant of 1st order filter on wind speed used for minimum pitch [1/1P]
+            constant	37 1;	Time constant of 1st order filter on pitch angle used for gain scheduling [1/1P]
+    ;     Drivetrain damper
+            constant	38 0;	Proportional gain of active DT damper [Nm/(rad/s)], requires frequency in input 10
+    ;	  Over speed
+            constant	39 25;	Overspeed percentage before initiating turbine controller alarm (shut-down) [%]
+    ;     Additional non-linear pitch control term (not used when all zero)
+            constant	40 0;	Rotor speed error scaling factor [rad/s]
+            constant	41 0;	Rotor acceleration error scaling factor [rad/s^2]
+            constant	42 0;	Pitch rate gain [rad/s]
+    ;     Storm control command
+            constant	43 28;	Wind speed 'Vstorm' above which derating of rotor speed is used [m/s]
+            constant	44 28;	Cut-out wind speed (only used for derating of rotor speed in storm) [m/s]
+    ;     Safety system parameters
+            constant	45 30;	Overspeed percentage before initiating safety system alarm (shut-down) [%]
+            constant	46 1.5;	Max low-pass filtered tower top acceleration level [m/s^2]
+    ;     Turbine parameter
+            constant	47 178;	Nominal rotor diameter [m]
+    ;     Parameters for rotor inertia reduction in variable speed region
+            constant	48 0;	Proportional gain on rotor acceleration in variable speed region [Nm/(rad/s^2)] (not used when zero)
+    ;     Parameters for alternative partial load controller with PI regulated TSR tracking
+            constant	49 7.8;	Optimal tip speed ratio [-] (only used when K=constant 11 = 0 otherwise  Qg=K*Omega^2 is used)
+    ;     Parameters for adding aerodynamic drivetrain damping on gain scheduling
+            constant	50 0;	Aerodynamic DT damping coefficient at the operational point of zero pitch angle [Nm/(rad/s)] (not used when zero)
+            constant	51 0;	Coefficient of linear term in aerodynamic DT damping scheduling, KK1 [deg]
+            constant	52 0;	Coefficient of quadratic term in aerodynamic DT damping scheduling, KK2 [deg^2]
+    ;     Torque exclusion zone
+            constant	53 0;	Exclusion zone: Lower speed limit [rad/s] (Default 0 used if zero)
+            constant	54 0;	Exclusion zone: Generator torque at lower limit [Nm] (Default 0 used if zero)
+            constant	55 0;	Exclusion zone: Upper speed limit [rad/s] (if =< 0 then exclusion zone functionality is inactive)
+            constant	56 0;	Exclusion zone: Generator torque at upper limit [Nm] (Default 0 used if zero)
+            constant	57 0;	Time constant of reference switching at exclusion zone [s] (Default 0 used if zero)
+    ;     DT torsion mode damper
+            constant	58 0;	Frequency of notch filter [Hz] (Default 10 x input 10 used if zero)
+            constant	59 0;	Damping of BP filter [-] (Default 0.02 used if zero)
+            constant	60 0;	Damping of notch filter [-] (Default 0.01 used if zero)
+            constant	61 0;	Phase lag of damper [s] =>  max 40*dt (Default 0 used if zero)
+    ;     Fore-aft Tower mode damper
+            constant	62 0;	Frequency of BP filter [Hz] (Default 10 used if zero)\\
+            constant	63 0;	Frequency of notch fiter [Hz] (Default 10 used if zero)\\
+            constant	64 0;	Damping of BP filter [-] (Default 0.02 used if zero)\\
+            constant	65 0;	Damping of notch filter [-] (Default 0.01 used if zero)\\
+            constant	66 0;	Gain of damper [-] (Default 0 used if zero)\\
+            constant	67 0;	Phase lag of damper [s] =>  max 40*dt (Default 0 used if zero)\\
+            constant	68 0;	Time constant of 1st order filter on PWR used for fore-aft Tower mode damper GS [Hz] (Default 10 used if zero)
+            constant	69 0;	Lower PWR limit used for fore-aft Tower mode damper GS [-] (Default 0 used if zero)
+            constant	70 0;	Upper PWR limit used for fore-aft Tower mode damper GS [-] (Default 0 used if zero)
+    ;     Side-to-side Tower mode filter
+            constant	71 0;	Frequency of Tower side-to-sede notch filter [Hz] (Default 100 used if zero)
+            constant	72 0;	Damping of notch filter [-] (Default 0.01 used if zero)
+            constant	73 0;	Max low-pass filtered tower top acceleration level before initiating safety system alarm (shut-down) [m/s^2] (Default 1.1 x input 46 used if zero)
+            constant	74 0;	Time constant of 1st order filter on tower top acceleration [1/1P] (Default 1 used if zero)
+    ;     Pitch deviation monitor parameters
+            constant	75 1005020;	Parameters for pitch deviation monitoring. The format is 1,nnn,mmm
+    ; where 'nnn' [s] is the period of the moving average and 'mmm' is threshold of the deviation [0.1 deg] (functionality is inactive if value $<$ 1,000,000)
+    ;     Gear ratio
+            constant	76 0;	Gear ratio used for the calculation of the LSS rotational speeds and the HSS generator torque reference [-] (Default 1 if zero)
+          end init;
+    ;
+          begin output;
+            general time;	[s]
+            constraint bearing1	shaft_rot 1 only 2;	Drivetrain speed [rad/s]
+            constraint bearing2	pitch1 1 only 1;	[rad]
+            constraint bearing2	pitch2 1 only 1;	[rad]
+            constraint bearing2	pitch3 1 only 1;	[rad]
+            wind free_wind	1 0 0 -119;	Global coordinates at hub height
+            dll inpvec	2 2;	Elec. power from generator servo .dll
+            dll inpvec	2 8;	Grid state flag from generator servo .dll
+            mbdy state	acc towertop 1 1 global only 1;	Tower top x-acceleration [m/s^2]
+            mbdy state	acc towertop 1 1 global only 2;	Tower top y-acceleration [m/s^2]
+          end output;
+        end type2_dll;
+    ;
+        begin type2_dll;
+          name	generator_servo;
+          filename	./control/generator_servo.dll;
+          dll_subroutine_init	init_generator_servo;
+          dll_subroutine_update	update_generator_servo;
+          arraysizes_init	100 1;
+          arraysizes_update	100 100;
+          begin init;
+            constant	1 20;	Frequency of 2nd order servo model of generator-converter system [Hz]
+            constant	2 0.9;	Damping ratio 2nd order servo model of generator-converter system [-]
+            constant	3 15600000;	Maximum allowable LSS torque (pull-out torque) [Nm]
+            constant	4 0.94;	Generator efficiency [-]
+            constant	5 1;	Gearratio [-]
+            constant	6 0;	Time for half value in softstart of torque [s]
+            constant	7 -1;	Time for grid loss [s] (never if lower than zero)
+          end init;
+    ;
+          begin output;
+            general time;	Time [s]
+            dll inpvec	1 1;	Electrical torque reference [Nm]
+            constraint bearing1	shaft_rot 1 only 2;	Generator LSS speed [rad/s]
+            mbdy momentvec	shaft 1 1 shaft only 3;	Shaft moment [kNm] (Qshaft)
+          end output;
+    ;
+          begin actions;
+            mbdy	moment_int shaft 1 -3 shaft towertop 2;	Generator LSS torque [Nm]
+          end actions;
+        end type2_dll;
+    ;
+        begin type2_dll;
+          name	mech_brake;
+          filename	./control/mech_brake.dll;
+          dll_subroutine_init	init_mech_brake;
+          dll_subroutine_update	update_mech_brake;
+          arraysizes_init	100 1;
+          arraysizes_update	100 100;
+          begin init;
+            constant	1 9360000;	Fully deployed maximum brake torque [Nm] (0.6*max torque)
+            constant	2 100;	Parameter alpha used in Q = tanh(omega*alpha), typically 1e2/Omega_nom
+            constant	3 0.5;	Delay time for before brake starts to deploy [s]
+            constant	4 0.6;	Time for brake to become fully deployed [s]
+          end init;
+    ;
+          begin output;
+            general time;	Time [s]
+            constraint bearing1	shaft_rot 1 only 2;	Generator LSS speed [rad/s]
+            dll inpvec	1 25;	Command to deploy mechanical disc brake [0,1]
+          end output;
+    ;
+          begin actions;
+            mbdy	moment_int shaft 1 -3 shaft towertop 2;	Brake LSS torque [Nm]
+          end actions;
+        end type2_dll;
+    ;
+        begin type2_dll;
+          name	servo_with_limits;
+          filename	./control/servo_with_limits.dll;
+          dll_subroutine_init	init_servo_with_limits;
+          dll_subroutine_update	update_servo_with_limits;
+          arraysizes_init	100 1;
+          arraysizes_update	100 100;
+          begin init;
+            constant	1 3;	Number of blades [-]
+            constant	2 1;	Frequency of 2nd order servo model of pitch system [Hz]
+            constant	3 0.7;	Damping ratio 2nd order servo model of pitch system [-]
+            constant	4 10;	Max. pitch speed [deg/s]
+            constant	5 15;	Max. pitch acceleration [deg/s^2]
+            constant	6 -5;	Min. pitch angle [deg]
+            constant	7 90;	Max. pitch angle [deg]
+            constant	8 -1;	Time for pitch runaway [s]
+            constant	9 -1;	Time for stuck blade 1 [s]
+            constant	10 0;	Angle of stuck blade 1 [deg] (if > 90 deg then blade is stuck at instantaneous angle)
+          end init;
+          begin output;
+            general time;	Time                         [s]
+            dll inpvec	1 2;	Pitch1 demand angle          [rad]
+            dll inpvec	1 3;	Pitch2 demand angle          [rad]
+            dll inpvec	1 4;	Pitch3 demand angle          [rad]
+            dll inpvec	1 26;	Flag for emergency pitch stop         [0=off/1=on]
+          end output;
+    ;
+          begin actions;
+            constraint	bearing2 angle pitch1;	Angle pitch1 bearing    [rad]
+            constraint	bearing2 angle pitch2;	Angle pitch2 bearing    [rad]
+            constraint	bearing2 angle pitch3;	Angle pitch3 bearing    [rad]
+          end actions;
+        end type2_dll;
+    ;
+    ;	--- DLL for tower-blade tip distance -- ;
+    ;-------------------------------------------
+        begin type2_dll;
+          name	towerclearance_mblade;
+          filename	./control/towerclearance_mblade.dll;
+          dll_subroutine_init	initialize;
+          dll_subroutine_update	update;
+          arraysizes_init	3 1;
+          arraysizes_update	15 6;
+          begin init;	Variables passed into initialization function
+            constant	1 4.15;	Tower radius at tower bottom [m]
+            constant	2 2.75;	Tower radius at tower top [m]
+            constant	3 3;	Number of points to check [-]
+          end init;
+          begin output;	Variables passed into update function
+            mbdy state	pos tower 1 0 global;	[1,2,3] global coordinates of tower base
+            mbdy state	pos tower 10 1 global;	[4,5,6] global coordinates of tower top
+            mbdy state	pos blade1 26 1 global;	[7,8,9] global coordinates of point 1 (blade 1 tip)
+            mbdy state	pos blade2 26 1 global;	[10,11,12] global coordinates of point 2 (blade 2 tip)
+            mbdy state	pos blade3 26 1 global;	[13,14,15] global coordinates of point 3 (blade 3 tip)
+          end output;
+        end type2_dll;
+    ;
+      end dll;
+    ;----------------------------------------------------------------------------------------------------------------------------------------------------------------
+    ;
+      begin output;
+        filename	./res/DTU_10MW_RWT_ver09;
+        data_format	hawc_binary;
+        buffer	1;
+    ;
+        general time;
+        constraint bearing1	shaft_rot 2;	angle and angle velocity
+        constraint bearing2	pitch1 5;	angle and angle velocity
+        constraint bearing2	pitch2 5;	angle and angle velocity
+        constraint bearing2	pitch3 5;	angle and angle velocity
+        aero omega;
+        aero torque;
+        aero power;
+        aero thrust;
+        wind free_wind	1 0 0 -119;	local wind at fixed position: coo (1=global,2=non-rotation rotor coo.), pos x, pos y, pos z
+    ; Moments:
+        mbdy momentvec	tower 1 1 tower # tower base;
+        mbdy momentvec	tower 10 2 tower # tower yaw bearing;
+        mbdy momentvec	shaft 4 1 shaft # main bearing;
+        mbdy momentvec	blade1 2 2 blade1 # blade 1 root;
+        mbdy momentvec	blade2 2 2 blade2 # blade 2 root;
+        mbdy momentvec	blade3 2 2 blade3 # blade 3 root;
+        mbdy momentvec	blade1 13 1 local # blade 1 50% local e coo;
+        mbdy momentvec	blade2 13 1 local # blade 2 50% local e coo;
+        mbdy momentvec	blade3 13 1 local # blade 3 50% local e coo;
+    ; Displacements and accellerations
+        mbdy state	pos tower 10 1 global only 1 # Tower top FA displ;
+        mbdy state	pos tower 10 1 global only 2 # Tower top SS displ;
+        mbdy state	acc tower 10 1 global only 1 # Tower top FA acc;
+        mbdy state	acc tower 10 1 global only 2 # Tower top SS acc;
+    ;
+        mbdy state	pos blade1 26 1 blade1 # blade 1 tip pos;
+        mbdy state	pos blade2 26 1 blade2 # blade 2 tip pos;
+        mbdy state	pos blade3 26 1 blade3 # blade 3 tip pos;
+        mbdy state	pos blade1 26 1 global # gl blade 1 tip pos;
+    ; - Monitor Aerodynamics - ;
+        aero windspeed	3 1 1 72.5;
+        aero alfa	1 72.5;
+        aero alfa	2 72.5;
+        aero alfa	3 72.5;
+        aero cl	1 72.5;
+        aero cl	2 72.5;
+        aero cl	3 72.5;
+        aero cd	1 72.5;
+        aero cd	2 72.5;
+        aero cd	3 72.5;
+    ; DLL outputs and into HAWC2
+        dll inpvec	1 1 # Generator torque reference [Nm];
+        dll inpvec	1 2 # Pitch angle reference of blade 1 [rad];
+        dll inpvec	1 3 # Pitch angle reference of blade 2 [rad];
+        dll inpvec	1 4 # Pitch angle reference of blade 3 [rad];
+        dll inpvec	1 5 # Power reference [W];
+        dll inpvec	1 6 # Filtered wind speed [m/s];
+        dll inpvec	1 7 # Filtered rotor speed [rad/s];
+        dll inpvec	1 8 # Filtered rotor speed error for torque [rad/s];
+        dll inpvec	1 9 # Bandpass filtered rotor speed [rad/s];
+        dll inpvec	1 10 # Proportional term of torque contr. [Nm];
+        dll inpvec	1 11 # Integral term of torque controller [Nm];
+        dll inpvec	1 12 # Minimum limit of torque [Nm];
+        dll inpvec	1 13 # Maximum limit of torque [Nm];
+        dll inpvec	1 14 # Torque limit switch based on pitch [-];
+        dll inpvec	1 15 # Filtered rotor speed error for pitch [rad/s];
+        dll inpvec	1 16 # Power error for pitch [W];
+        dll inpvec	1 17 # Proportional term of pitch controller [rad];
+        dll inpvec	1 18 # Integral term of pitch controller [rad];
+        dll inpvec	1 19 # Minimum limit of pitch [rad];
+        dll inpvec	1 20 # Maximum limit of pitch [rad];
+        dll inpvec	1 21 # Torque reference from DT dammper [Nm];
+        dll inpvec	1 22 # Status signal [-];
+        dll inpvec	1 23 # Total added pitch rate [rad/s];
+        dll inpvec	1 24 # Filtered Mean pitch for gain sch [rad];
+        dll inpvec	1 25 # Flag for mechnical brake [0=off/1=on];
+        dll inpvec	1 26 # Flag for emergency pitch stop [0=off/1=on];
+        dll inpvec	1 27 # LP filtered acceleration level [m/s^2];
+        dll inpvec	1 31 # Monitored average of reference pitch [rad];
+        dll inpvec	1 32 # Monitored ave. of actual pitch (blade 1) [rad];
+    ; Input from generator model
+        dll inpvec	2 1 # Mgen LSS [Nm];
+        dll inpvec	2 2 # Pelec [W];
+        dll inpvec	2 3 # Mframe [Nm];
+        dll inpvec	2 4 # Mgen HSS [Nm];
+        dll inpvec	2 8 # Grid flag [0=run/1=stop];
+    ; Input from mechanical brake
+        dll inpvec	3 1 # Brake torque [Nm];
+    ; Input from pitch servo
+        dll inpvec	4 1 # pitch 1 [rad];
+        dll inpvec	4 2 # pitch 2 [rad];
+        dll inpvec	4 3 # pitch 3 [rad];
+    ; Check tower clearence
+        dll inpvec	5 1 # Bltip tow min d [m];
+      end output;
+    ;
+    exit;
+
+%% Cell type:markdown id: tags:
+
+### Load htc files
+`HTCFile` takes the htc-filename and optionally the modelpath as input.
+
+The `modelpath` is the path from where HAWC2 should be run, i.e. the the origion for relative data file paths in the htc file. If not specified (default) the `modelpath` is autodetected if possible.
+
+%% Cell type:code id: tags:
+
+``` python
+htc = HTCFile(filename=tfp+"htcfiles/DTU_10MW_RWT.htc",
+              modelpath=None # modelpath autodetected
+             )
+print (htc.modelpath)
+```
+
+%% Output
+
+    C:/mmpe/programming/python/WindEnergyToolbox/wetb/hawc2/tests/test_files/
+
+%% Cell type:markdown id: tags:
+
+### Access htc contents
+
+Access elements(lines and sections) in the htc file via dot or string notation
+
+%% Cell type:code id: tags:
+
+``` python
+wsp = htc.wind.wsp # dot notation
+print (wsp)
+convergence_limits = htc['simulation.convergence_limits'] # string notation with dot
+print (convergence_limits)
+```
+
+%% Output
+
+    wsp	4;
+    
+    convergence_limits	1000 1 1e-07;
+    
+
+%% Cell type:markdown id: tags:
+
+you can also store a (sub)section in a varble and access subelements from that
+
+%% Cell type:code id: tags:
+
+``` python
+wind = htc.wind
+print (wind.wsp)
+```
+
+%% Output
+
+    wsp	4;
+    
+
+%% Cell type:markdown id: tags:
+
+Values of a line are obtained by
+
+%% Cell type:code id: tags:
+
+``` python
+print (wsp[0])
+print (htc.simulation.convergence_limits[:])
+```
+
+%% Output
+
+    4
+    [1000, 1, 1e-07]
+
+%% Cell type:markdown id: tags:
+
+In case there is more than one element with the same name, e.g. main_body sections in new_htc_structure:
+
+%% Cell type:code id: tags:
+
+``` python
+htc.new_htc_structure.keys()
+```
+
+%% Output
+
+    ['main_body',
+     'main_body__2',
+     'main_body__3',
+     'main_body__4',
+     'main_body__5',
+     'main_body__6',
+     'main_body__7',
+     'main_body__8',
+     'main_body__9',
+     'orientation',
+     'constraint']
+
+%% Cell type:markdown id: tags:
+
+Then the right element can be access by adding `__x` (where x is the section number).
+The first element can be accessed without `__x` or with `__1`
+
+%% Cell type:code id: tags:
+
+``` python
+htc.new_htc_structure.main_body__1 == htc.new_htc_structure.main_body
+```
+
+%% Output
+
+    True
+
+%% Cell type:markdown id: tags:
+
+Another way to access these elements are:
+
+%% Cell type:code id: tags:
+
+``` python
+htc.new_htc_structure.get_subsection_by_name('shaft')
+htc.new_htc_structure.main_body(name='shaft')
+```
+
+%% Output
+
+    <wetb.hawc2.htc_contents.HTCSection at 0x1ff94e5eb50>
+
+%% Cell type:markdown id: tags:
+
+#### HTC Section
+
+%% Cell type:code id: tags:
+
+``` python
+section = htc.new_htc_structure.main_body__3.c2_def
+print(section.section_name)
+print(section.keys())
+print(section.parent.section_name)
+print(section.parent.location())
+print()
+print(section)
+```
+
+%% Output
+
+    c2_def
+    ['nsec', 'sec', 'sec__2', 'sec__3', 'sec__4', 'sec__5']
+    main_body
+    DTU_10MW_RWT.htc/new_htc_structure/main_body__3
+    
+    begin c2_def;	Definition of centerline (main_body coordinates)
+      nsec	5;
+      sec	1 0 0 0 0;	Tower top x,y,z,twist
+      sec	2 0 0 1.5 0;
+      sec	3 0 0 3 0;
+      sec	4 0 0 4.4 0;	Main bearing
+      sec	5 0 0 7.1 0;	Rotor centre
+    end c2_def;
+    
+
+%% Cell type:markdown id: tags:
+
+#### HTC Line
+
+%% Cell type:code id: tags:
+
+``` python
+line = htc.new_htc_structure.main_body__3.c2_def.sec__4
+
+print(line.values) # print all values in line
+print(line.values[3]) # print value 4 (zero-indexed)
+print(line.comments) # print comments
+print()
+print(line) # print line
+```
+
+%% Output
+
+    [4, 0, 0, 4.4, 0]
+    4.4
+    Main bearing
+    
+    sec	4 0 0 4.4 0;	Main bearing
+    
+
+%% Cell type:markdown id: tags:
+
+#### Output sensor
+
+%% Cell type:code id: tags:
+
+``` python
+print (htc.output.sensors[3])
+print (htc.output.sensors[3].type)
+print (htc.output.sensors[3].sensor)
+print (htc.output.sensors[3].values)
+print (htc.output.sensors[3].comments)
+```
+
+%% Output
+
+    constraint bearing2	pitch2 5;	angle and angle velocity
+    
+    constraint
+    bearing2
+    ['pitch2', 5]
+    angle and angle velocity
+
+%% Cell type:markdown id: tags:
+
+### Add htc contents
+#### Add htc line
+
+%% Cell type:code id: tags:
+
+``` python
+htc.simulation.my_line = "value1", 2
+htc.simulation.my_line.comments = "MyComment"
+print (htc.simulation)
+```
+
+%% Output
+
+    begin simulation;
+      time_stop	1000;
+      solvertype	1;	(newmark)
+      on_no_convergence	continue;
+      convergence_limits	1000 1 1e-07;
+      logfile	./log/DTU_10MW_RWT_ver09.log;
+      begin newmark;
+        deltat	0.01;
+      end newmark;
+      my_line	value1 2;	MyComment
+    end simulation;
+    ;
+    ;----------------------------------------------------------------------------------------------------------------------------------------------------------------
+    
+
+%% Cell type:markdown id: tags:
+
+In case there is already one line with the same key, then you need to use the `add_line` function
+
+%% Cell type:code id: tags:
+
+``` python
+htc.simulation.add_line(name="my_line",
+                        values=["value1", 2],
+                        comments="MyComment for second my_line" #defaults to ""
+                       )
+print (htc.simulation)
+```
+
+%% Output
+
+    begin simulation;
+      time_stop	1000;
+      solvertype	1;	(newmark)
+      on_no_convergence	continue;
+      convergence_limits	1000 1 1e-07;
+      logfile	./log/DTU_10MW_RWT_ver09.log;
+      begin newmark;
+        deltat	0.01;
+      end newmark;
+      my_line	value1 2;	MyComment
+      my_line	value1 2;	MyComment for second my_line
+    end simulation;
+    ;
+    ;----------------------------------------------------------------------------------------------------------------------------------------------------------------
+    
+
+%% Cell type:markdown id: tags:
+
+#### Add htc section
+
+%% Cell type:code id: tags:
+
+``` python
+my_section = htc.simulation.add_section(section_name="my_section",
+                           members={"Line1":1, "line2":[21,22,23]},
+                           allow_duplicate=False,
+                           line3=[31,32])
+print (htc.simulation)
+```
+
+%% Output
+
+    begin simulation;
+      time_stop	1000;
+      solvertype	1;	(newmark)
+      on_no_convergence	continue;
+      convergence_limits	1000 1 1e-07;
+      logfile	./log/DTU_10MW_RWT_ver09.log;
+      begin newmark;
+        deltat	0.01;
+      end newmark;
+      my_line	value1 2;	MyComment
+      my_line	value1 2;	MyComment for second my_line
+      begin my_section;
+        line3	31 32;
+        Line1	1;
+        line2	21 22 23;
+      end my_section;
+    end simulation;
+    ;
+    ;----------------------------------------------------------------------------------------------------------------------------------------------------------------
+    
+
+%% Cell type:markdown id: tags:
+
+If `allow_duplicate` is `False` and a section with the same name already exists, then `add_section` has no effect
+
+%% Cell type:code id: tags:
+
+``` python
+my_section = htc.simulation.add_section(section_name="my_section",
+                                        allow_duplicate=False,
+                                        line4=4)
+print (htc.simulation)
+```
+
+%% Output
+
+    begin simulation;
+      time_stop	1000;
+      solvertype	1;	(newmark)
+      on_no_convergence	continue;
+      convergence_limits	1000 1 1e-07;
+      logfile	./log/DTU_10MW_RWT_ver09.log;
+      begin newmark;
+        deltat	0.01;
+      end newmark;
+      my_line	value1 2;	MyComment
+      my_line	value1 2;	MyComment for second my_line
+      begin my_section;
+        line3	31 32;
+        Line1	1;
+        line2	21 22 23;
+      end my_section;
+    end simulation;
+    ;
+    ;----------------------------------------------------------------------------------------------------------------------------------------------------------------
+    
+
+%% Cell type:markdown id: tags:
+
+#### Add output sensor
+
+%% Cell type:code id: tags:
+
+``` python
+htc.output.add_sensor('sensor_type', 'sensor_name', ['arg1', 2], comment = "MySensor", nr=3)
+print (htc.output)
+```
+
+%% Output
+
+    begin output;
+      filename	./res/DTU_10MW_RWT_ver09;
+      data_format	hawc_binary;
+      buffer	1;
+    ;
+      general time;
+      constraint bearing1	shaft_rot 2;	angle and angle velocity
+      constraint bearing2	pitch1 5;	angle and angle velocity
+      sensor_type sensor_name	arg1 2;	MySensor
+      constraint bearing2	pitch2 5;	angle and angle velocity
+      constraint bearing2	pitch3 5;	angle and angle velocity
+      aero omega;
+      aero torque;
+      aero power;
+      aero thrust;
+      wind free_wind	1 0 0 -119;	local wind at fixed position: coo (1=global,2=non-rotation rotor coo.), pos x, pos y, pos z
+    ; Moments:
+      mbdy momentvec	tower 1 1 tower # tower base;
+      mbdy momentvec	tower 10 2 tower # tower yaw bearing;
+      mbdy momentvec	shaft 4 1 shaft # main bearing;
+      mbdy momentvec	blade1 2 2 blade1 # blade 1 root;
+      mbdy momentvec	blade2 2 2 blade2 # blade 2 root;
+      mbdy momentvec	blade3 2 2 blade3 # blade 3 root;
+      mbdy momentvec	blade1 13 1 local # blade 1 50% local e coo;
+      mbdy momentvec	blade2 13 1 local # blade 2 50% local e coo;
+      mbdy momentvec	blade3 13 1 local # blade 3 50% local e coo;
+    ; Displacements and accellerations
+      mbdy state	pos tower 10 1 global only 1 # Tower top FA displ;
+      mbdy state	pos tower 10 1 global only 2 # Tower top SS displ;
+      mbdy state	acc tower 10 1 global only 1 # Tower top FA acc;
+      mbdy state	acc tower 10 1 global only 2 # Tower top SS acc;
+    ;
+      mbdy state	pos blade1 26 1 blade1 # blade 1 tip pos;
+      mbdy state	pos blade2 26 1 blade2 # blade 2 tip pos;
+      mbdy state	pos blade3 26 1 blade3 # blade 3 tip pos;
+      mbdy state	pos blade1 26 1 global # gl blade 1 tip pos;
+    ; - Monitor Aerodynamics - ;
+      aero windspeed	3 1 1 72.5;
+      aero alfa	1 72.5;
+      aero alfa	2 72.5;
+      aero alfa	3 72.5;
+      aero cl	1 72.5;
+      aero cl	2 72.5;
+      aero cl	3 72.5;
+      aero cd	1 72.5;
+      aero cd	2 72.5;
+      aero cd	3 72.5;
+    ; DLL outputs and into HAWC2
+      dll inpvec	1 1 # Generator torque reference [Nm];
+      dll inpvec	1 2 # Pitch angle reference of blade 1 [rad];
+      dll inpvec	1 3 # Pitch angle reference of blade 2 [rad];
+      dll inpvec	1 4 # Pitch angle reference of blade 3 [rad];
+      dll inpvec	1 5 # Power reference [W];
+      dll inpvec	1 6 # Filtered wind speed [m/s];
+      dll inpvec	1 7 # Filtered rotor speed [rad/s];
+      dll inpvec	1 8 # Filtered rotor speed error for torque [rad/s];
+      dll inpvec	1 9 # Bandpass filtered rotor speed [rad/s];
+      dll inpvec	1 10 # Proportional term of torque contr. [Nm];
+      dll inpvec	1 11 # Integral term of torque controller [Nm];
+      dll inpvec	1 12 # Minimum limit of torque [Nm];
+      dll inpvec	1 13 # Maximum limit of torque [Nm];
+      dll inpvec	1 14 # Torque limit switch based on pitch [-];
+      dll inpvec	1 15 # Filtered rotor speed error for pitch [rad/s];
+      dll inpvec	1 16 # Power error for pitch [W];
+      dll inpvec	1 17 # Proportional term of pitch controller [rad];
+      dll inpvec	1 18 # Integral term of pitch controller [rad];
+      dll inpvec	1 19 # Minimum limit of pitch [rad];
+      dll inpvec	1 20 # Maximum limit of pitch [rad];
+      dll inpvec	1 21 # Torque reference from DT dammper [Nm];
+      dll inpvec	1 22 # Status signal [-];
+      dll inpvec	1 23 # Total added pitch rate [rad/s];
+      dll inpvec	1 24 # Filtered Mean pitch for gain sch [rad];
+      dll inpvec	1 25 # Flag for mechnical brake [0=off/1=on];
+      dll inpvec	1 26 # Flag for emergency pitch stop [0=off/1=on];
+      dll inpvec	1 27 # LP filtered acceleration level [m/s^2];
+      dll inpvec	1 31 # Monitored average of reference pitch [rad];
+      dll inpvec	1 32 # Monitored ave. of actual pitch (blade 1) [rad];
+    ; Input from generator model
+      dll inpvec	2 1 # Mgen LSS [Nm];
+      dll inpvec	2 2 # Pelec [W];
+      dll inpvec	2 3 # Mframe [Nm];
+      dll inpvec	2 4 # Mgen HSS [Nm];
+      dll inpvec	2 8 # Grid flag [0=run/1=stop];
+    ; Input from mechanical brake
+      dll inpvec	3 1 # Brake torque [Nm];
+    ; Input from pitch servo
+      dll inpvec	4 1 # pitch 1 [rad];
+      dll inpvec	4 2 # pitch 2 [rad];
+      dll inpvec	4 3 # pitch 3 [rad];
+    ; Check tower clearence
+      dll inpvec	5 1 # Bltip tow min d [m];
+    end output;
+    ;
+    
+
+%% Cell type:markdown id: tags:
+
+### Modify htc contents
+
+%% Cell type:code id: tags:
+
+``` python
+htc.wind.wsp = 12 # set single value element
+print (htc.wind.wsp)
+
+c2def = htc.new_htc_structure.main_body__3.c2_def
+c2def.section_name = "c2_def_new"
+c2def.sec__4 = 1,2,3,4  # set element with four values
+c2def.sec__4[3] = 9
+print (c2def)
+```
+
+%% Output
+
+    wsp	12;
+    
+    begin c2_def_new;	Definition of centerline (main_body coordinates)
+      nsec	5;
+      sec	1 0 0 0 0;	Tower top x,y,z,twist
+      sec	2 0 0 1.5 0;
+      sec	3 0 0 3 0;
+      sec	1 2 3 9;	Main bearing
+      sec	5 0 0 7.1 0;	Rotor centre
+    end c2_def_new;
+    
+
+%% Cell type:markdown id: tags:
+
+Note, that you cannot change modify values of the current line, e.g.
+```python
+line = htc.new_htc_structure.main_body__3.c2_def.sec__4
+line = 1,2,3,4
+```
+as it will overwrite the variable `line` with the tuple (1,2,3,4) instead of updating the values
+
+%% Cell type:markdown id: tags:
+
+### Delete
+Sections and lines are deleted by calling their `delete` method
+
+%% Cell type:code id: tags:
+
+``` python
+htc.simulation.my_line.delete() # second my_line (my_line__2) remains
+htc.simulation.my_section.delete()
+print (htc.simulation)
+```
+
+%% Output
+
+    begin simulation;
+      time_stop	1000;
+      solvertype	1;	(newmark)
+      on_no_convergence	continue;
+      convergence_limits	1000 1 1e-07;
+      logfile	./log/DTU_10MW_RWT_ver09.log;
+      begin newmark;
+        deltat	0.01;
+      end newmark;
+      my_line	value1 2;	MyComment for second my_line
+    end simulation;
+    ;
+    ;----------------------------------------------------------------------------------------------------------------------------------------------------------------
+    
+
+%% Cell type:markdown id: tags:
+
+### HTC functions
+#### set_name()
+The `set_name` function sets the filename, as well as the
+
+- log filename
+- animation filename
+- visualization filename
+- output filename (only first output section)
+
+%% Cell type:code id: tags:
+
+``` python
+htc.set_name(name="new_name", subfolder='my_folder')
+print (htc.filename)
+print (htc.simulation.logfile)
+print (htc.output.filename)
+```
+
+%% Output
+
+    c:/mmpe/programming/python/windenergytoolbox/wetb/hawc2/tests/test_files/htc/my_folder/new_name.htc
+    logfile	./log/my_folder/new_name.log;
+    
+    filename	./res/my_folder/new_name;
+    
+
+%% Cell type:markdown id: tags:
+
+#### set_time()
+The `set_time(start=None, stop=None, step=None)` function sets the start, stop and step time if specified:
+
+%% Cell type:code id: tags:
+
+``` python
+htc.set_time(10,20,.1)
+print (htc.simulation.time_stop)
+print (htc.simulation.newmark.deltat)
+print (htc.wind.scale_time_start)
+print (htc.output.time)
+```
+
+%% Output
+
+    time_stop	20;
+    
+    deltat	0.1;
+    
+    scale_time_start	10;
+    
+    time	10 20;
+    
+
+%% Cell type:markdown id: tags:
+
+#### simulate()
+The `simulate(exe)` function saves the htc file, performs the simulation using the specified exe (HAWC2), raises an error if the simulation fails and returns the console output and log
+
+```python
+stdout, log = htc.simulate("<path_to_hawc2>\hawc2mb.exe")
+```
+
+%% Cell type:markdown id: tags:
+
+# Parameter study
+
+HTC files for parameter studies, can be generated by a loop that updates the desired values of the htc and saves the result:
+
+%% Cell type:code id: tags:
+
+``` python
+from wetb.hawc2 import HTCFile
+from wetb.hawc2.tests.test_files import tfp
+htc = HTCFile(tfp + "htcfiles/DTU_10MW_RWT.htc")
+
+for wsp in [4,6,8]:
+    htc.wind.wsp = wsp
+    htc.set_name("case_wsp%d"%wsp)
+    htc.save()
+```
+
+%% Cell type:markdown id: tags:
+
+## HAWC2InputWriter
+
+An easier way for more complicate studies is to use the HAWC2InputWriter which takes a case as input (see [Case list generation](#Case-list-generation))
+
+A case is dictionary of (key,value)-pairs. Keys can be:
+
+1. Htc address, e.g. wind.wsp
+2. Function name, e.g. `wsp` in which case `value` is passed to the `set_wsp` of `HAWC2InputWriter` (which you must implement)
+3. A tag that is replaced by `value`
+
+Note, all three types can be combined
+
+%% Cell type:markdown id: tags:
+
+First we create the htc file that we want the parameter study to be based on
+
+%% Cell type:code id: tags:
+
+``` python
+%%writefile "tmp/base.htc"
+
+begin simulation;
+    time_stop	600;
+    logfile log.txt
+end simulation;
+;
+begin wind;
+    wsp	10;
+end wind;
+exit;
+```
+
+%% Output
+
+    Writing tmp/base.htc
+
+%% Cell type:markdown id: tags:
+
+### htc address
+
+For (key-value) cases where the keys are htc addresses, we just need a `HAWC2InputWriter`
+
+%% Cell type:code id: tags:
+
+``` python
+from wetb.hawc2 import HTCFile
+from wetb.hawc2 import HAWC2InputWriter
+h2writer = HAWC2InputWriter(base_htc_file='tmp/base.htc')
+```
+
+%% Cell type:markdown id: tags:
+
+that allow us to make a case like this
+
+%% Cell type:code id: tags:
+
+``` python
+h2writer('tmp/my_case.htc', **{'wind.wsp':12, 'simulation.logfile': "my_case.log"})
+```
+
+%% Cell type:code id: tags:
+
+``` python
+print (HTCFile('tmp/my_case.htc'))
+```
+
+%% Output
+
+      begin simulation;
+        time_stop	600;
+        logfile	my_case.log;
+      end simulation;
+    ;
+      begin wind;
+        wsp	12;
+      end wind;
+    exit;
+
+%% Cell type:markdown id: tags:
+
+### Function name
+
+For (key-value) cases where the keys are function names, a subclass of `HAWC2InputWriter` with the required functions must be implemented:
+
+%% Cell type:code id: tags:
+
+``` python
+class MyInputWriter(HAWC2InputWriter):
+    def set_wsp(self, htc, wsp, **_):
+        htc.wind.wsp = wsp
+        bs = self.begin_step
+        for i, o in enumerate([0,50],1):
+            htc.wind.add_line("wind_ramp_abs", [bs+o, bs+o+1, 0, 1], "wsp. after the step:  %d.0"%(wsp+i))
+        # ...
+
+    def set_log(self, htc, log, **_):
+        if log:
+            htc.simulation.logfile = log
+        else:
+            htc.simulation.logfile.delete()
+```
+
+%% Cell type:markdown id: tags:
+
+This approach enables
+
+- Multiple values, e.g. wind speed, turbulence grid size, wind ramp etc., can be set by one (key,value)-pair
+- Lines or sections can be deleted
+- Use of constants (specified when creating the writer)
+- Modification of e.g. aerodynamic, profile or structural data files
+
+%% Cell type:code id: tags:
+
+``` python
+h2writer = MyInputWriter(base_htc_file='tmp/base.htc',
+                         begin_step=100, # constant need in the implemented functions (specify as many as you want)
+                        )
+h2writer('tmp/my_case.htc', wsp=12, log=None, sensor_y=[10,20])
+```
+
+%% Cell type:code id: tags:
+
+``` python
+print (HTCFile('tmp/my_case.htc'))
+```
+
+%% Output
+
+      begin simulation;
+        time_stop	600;
+      end simulation;
+    ;
+      begin wind;
+        wsp	12;
+        wind_ramp_abs	100 101 0 1;	wsp. after the step:  13.0
+        wind_ramp_abs	150 151 0 1;	wsp. after the step:  14.0
+      end wind;
+    exit;
+
+%% Cell type:markdown id: tags:
+
+### Tags
+
+The tag options offers template rendering via the [jinja](https://en.wikipedia.org/wiki/Jinja_(template_engine)) templating language. Jinja templates allows:
+
+- variable substitution,
+```
+wsp {{wsp}}
+```
+
+- conditionals
+```
+{% if logfilename %}
+    logfile  {{logfilename}}
+{% endif %}
+```
+
+- loops
+```
+{%- for y in sensor_y %}
+   wind free_wind 1 0.0 {{ y }} -119;
+{%- endfor %}
+```
+
+let us make a new template.htc
+
+%% Cell type:code id: tags:
+
+``` python
+%%writefile "tmp/template.htc"
+
+begin simulation;
+    time_stop	600;
+    {% if logfilename %}
+      logfile  {{logfilename}}
+    {% endif %}
+end simulation;
+;
+begin wind;
+    wsp	{{wsp}};
+    {%- for i in range(2) %}
+        wind_ramp_abs	{{begin_step+i*50}} {{begin_step+i*50+1}} 0 1;	wsp. after the step:  {{wsp+i+1}}
+    {%- endfor %}
+end wind;
+exit;
+```
+
+%% Output
+
+    Writing tmp/template.htc
+
+%% Cell type:code id: tags:
+
+``` python
+h2writer = HAWC2InputWriter(base_htc_file='tmp/template.htc')
+h2writer('tmp/my_case.htc', wsp=12, log=None, begin_step=100)
+```
+
+%% Cell type:code id: tags:
+
+``` python
+print (HTCFile('tmp/my_case.htc'))
+```
+
+%% Output
+
+      begin simulation;
+        time_stop	600;
+      end simulation;
+    ;
+      begin wind;
+        wsp	12;
+        wind_ramp_abs	100 101 0 1;	wsp. after the step:  13
+        wind_ramp_abs	150 151 0 1;	wsp. after the step:  14
+      end wind;
+    exit;
+
+%% Cell type:markdown id: tags:
+
+## Case list generation
+
+The `HAWC2InputWriter` can also handle a list of cases.
+
+These cases can be defined in a [Pandas DataFrame](https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html) or an excel sheet
+
+Note, case lists must contain a `Name` column
+
+%% Cell type:markdown id: tags:
+
+### Pandas Dataframe
+
+%% Cell type:code id: tags:
+
+``` python
+import pandas as pd
+df = pd.DataFrame({'Name':['case10', 'case12'], 'wsp':[10,12], 'log':['','log.txt']})
+df
+```
+
+%% Output
+
+         Name  wsp      log
+    0  case10   10
+    1  case12   12  log.txt
+
+%% Cell type:code id: tags:
+
+``` python
+h2writer = MyInputWriter(base_htc_file='tmp/base.htc',
+                         begin_step=100, # constant need in the implemented functions (specify as many as you want)
+                        )
+h2writer.from_pandas(df)
+h2writer.write_all(out_dir="tmp")
+```
+
+%% Output
+
+    Generating 2 htc files in directory: tmp
+
+%% Cell type:code id: tags:
+
+``` python
+print(HTCFile('tmp/case10.htc'))
+```
+
+%% Output
+
+      begin simulation;
+        time_stop	600;
+      end simulation;
+    ;
+      begin wind;
+        wsp	10;
+        wind_ramp_abs	100 101 0 1;	wsp. after the step:  11.0
+        wind_ramp_abs	150 151 0 1;	wsp. after the step:  12.0
+      end wind;
+    exit;
+
+%% Cell type:code id: tags:
+
+``` python
+print(HTCFile('tmp/case12.htc'))
+```
+
+%% Output
+
+      begin simulation;
+        time_stop	600;
+        logfile	log.txt;
+      end simulation;
+    ;
+      begin wind;
+        wsp	12;
+        wind_ramp_abs	100 101 0 1;	wsp. after the step:  13.0
+        wind_ramp_abs	150 151 0 1;	wsp. after the step:  14.0
+      end wind;
+    exit;
+
+%% Cell type:markdown id: tags:
+
+### Excel
+
+Saving previous dataframe as Excel spreadsheet
+
+%% Cell type:code id: tags:
+
+``` python
+df.to_excel('tmp/caselist.xlsx', index=False)
+```
+
+%% Cell type:markdown id: tags:
+
+which can be opened and modified in Excel
+
+%% Cell type:code id: tags:
+
+``` python
+# uncomment to open in excel
+# %system "tmp/caselist.xlsx"
+```
+
+%% Cell type:markdown id: tags:
+
+Loading case list from (modifyed) excel sheet and write htc files
+
+%% Cell type:code id: tags:
+
+``` python
+h2writer.from_excel('tmp/caselist.xlsx')
+h2writer.contents
+h2writer.write_all('tmp')
+```
+
+%% Output
+
+    Generating 2 htc files in directory: tmp
+
+%% Cell type:markdown id: tags:
+
+# Design Load Basis (DLB)
+
+The `DTU_IEC64100_1_Ref_DLB` can make a case list covering a subset of the full DLB as defined in IEC64100-1(2005).
+
+Note, some DLCs are missing.
+
+Some interpretation are made see [Hansen, M. H., Thomsen, K., Natarajan, A., & Barlas, A. (2015). Design Load Basis for onshore turbines - Revision 00. DTU Wind Energy. DTU Wind Energy E, No. 0074(EN)](https://backend.orbit.dtu.dk/ws/portalfiles/portal/106567720/Design_Load_Basis_for_onshore_turbines.pdf)
+
+%% Cell type:code id: tags:
+
+``` python
+from wetb.dlb.iec64100_1 import DTU_IEC64100_1_Ref_DLB, DLB, DLC
+dlb = DTU_IEC64100_1_Ref_DLB(iec_wt_class='1A', #IEC wind turbine class
+                             Vin=4, # cut-in wind speed
+                             Vout=25, # cut-out wind speed
+                             Vr=8, # rated wind speed
+                             D=180, # Rotor diameter
+                             z_hub=110 # hub height
+                            )
+```
+
+%% Cell type:markdown id: tags:
+
+## DLB definition
+You can work with a DLB on an definition level
+
+%% Cell type:code id: tags:
+
+``` python
+dlb.dlcs
+```
+
+%% Output
+
+              Name                                       Description  \
+    DLC12    DLC12                                 Normal production
+    DLC13    DLC13            Normal production with high turbulence
+    DLC14    DLC14  Normal production with gust and direction change
+    DLC15    DLC15         Normal production with extreme wind shear
+    DLC21    DLC21                         Loss of electical network
+    DLC22y  DLC22y                                Abnormal yaw error
+    
+                     WSP       Wdir    Turb  Seeds Shear  Gust       Fault  Time
+    DLC12     Vin:2:Vout   -10/0/10     NTM    6.0   NWP  None        None   600
+    DLC13     Vin:2:Vout   -10/0/10     ETM    6.0   NWP  None        None   600
+    DLC14   Vr/Vr+2/Vr-2          0  NoTurb    NaN   NWP   ECD        None   100
+    DLC15     Vin:2:Vout          0  NoTurb    NaN   EWS  None        None   100
+    DLC21     Vin:2:Vout   -10/0/10     NTM    4.0   NWP  None  GridLoss10   100
+    DLC22y    Vin:2:Vout  15:15:345     NTM    1.0   NWP  None        None   600
+
+%% Cell type:code id: tags:
+
+``` python
+dlb.variables
+```
+
+%% Output
+
+                          Name Value                      Description
+    Vin                    Vin     4                Cut-in wind speed
+    Vout                  Vout    25               Cut-out wind speed
+    Vr                      Vr     8                 Rated wind speed
+    D                        D   180                   Rotor diameter
+    z_hub                z_hub   110                       Hub height
+    Vstep                Vstep     2     Wind speed distribution step
+    iec_wt_class  iec_wt_class    1A  IEC wind turbine class, e.g. 1A
+
+%% Cell type:markdown id: tags:
+
+### Edit DLB definition
+
+`dlb.dlcs` is a Pandas DataFrame that you can edit in python
+
+%% Cell type:code id: tags:
+
+``` python
+dlb.dlcs.loc['DLC12','Seeds'] = 1
+dlb.dlcs
+```
+
+%% Output
+
+              Name                                       Description  \
+    DLC12    DLC12                                 Normal production
+    DLC13    DLC13            Normal production with high turbulence
+    DLC14    DLC14  Normal production with gust and direction change
+    DLC15    DLC15         Normal production with extreme wind shear
+    DLC21    DLC21                         Loss of electical network
+    DLC22y  DLC22y                                Abnormal yaw error
+    
+                     WSP       Wdir    Turb  Seeds Shear  Gust       Fault  Time
+    DLC12     Vin:2:Vout   -10/0/10     NTM    1.0   NWP  None        None   600
+    DLC13     Vin:2:Vout   -10/0/10     ETM    6.0   NWP  None        None   600
+    DLC14   Vr/Vr+2/Vr-2          0  NoTurb    NaN   NWP   ECD        None   100
+    DLC15     Vin:2:Vout          0  NoTurb    NaN   EWS  None        None   100
+    DLC21     Vin:2:Vout   -10/0/10     NTM    4.0   NWP  None  GridLoss10   100
+    DLC22y    Vin:2:Vout  15:15:345     NTM    1.0   NWP  None        None   600
+
+%% Cell type:markdown id: tags:
+
+`dlb.variables` is a Pandas DataFrame that you can edit in python
+
+%% Cell type:code id: tags:
+
+``` python
+dlb.variables.loc['Vin','Value'] = 8
+dlb.variables.loc['Vout', 'value']=10
+dlb.variables
+```
+
+%% Output
+
+                          Name Value                      Description  value
+    Vin                    Vin     8                Cut-in wind speed    NaN
+    Vout                  Vout    25               Cut-out wind speed   10.0
+    Vr                      Vr     8                 Rated wind speed    NaN
+    D                        D   180                   Rotor diameter    NaN
+    z_hub                z_hub   110                       Hub height    NaN
+    Vstep                Vstep     2     Wind speed distribution step    NaN
+    iec_wt_class  iec_wt_class    1A  IEC wind turbine class, e.g. 1A    NaN
+
+%% Cell type:markdown id: tags:
+
+### Edit DLB definition in Excel
+
+You can also save the DLB definition and variables as an Excel workbook
+
+%% Cell type:code id: tags:
+
+``` python
+dlb.to_excel('tmp/overview.xlsx')
+```
+
+%% Cell type:markdown id: tags:
+
+open, edit and save in Excel
+
+%% Cell type:code id: tags:
+
+``` python
+# uncomment to open file in excel
+# %system "tmp/overview.xlsx"
+```
+
+%% Cell type:markdown id: tags:
+
+and load the modified DLB
+
+%% Cell type:code id: tags:
+
+``` python
+dlb = DLB.from_excel('tmp/overview.xlsx')
+dlb.dlcs
+```
+
+%% Output
+
+              Name                                       Description  \
+    DLC12    DLC12                                 Normal production
+    DLC13    DLC13            Normal production with high turbulence
+    DLC14    DLC14  Normal production with gust and direction change
+    DLC15    DLC15         Normal production with extreme wind shear
+    DLC21    DLC21                         Loss of electical network
+    DLC22y  DLC22y                                Abnormal yaw error
+    
+                     WSP       Wdir    Turb  Seeds Shear Gust       Fault  Time
+    DLC12     Vin:2:Vout   -10/0/10     NTM    1.0   NWP  NaN         NaN   600
+    DLC13     Vin:2:Vout   -10/0/10     ETM    6.0   NWP  NaN         NaN   600
+    DLC14   Vr/Vr+2/Vr-2          0  NoTurb    NaN   NWP  ECD         NaN   100
+    DLC15     Vin:2:Vout          0  NoTurb    NaN   EWS  NaN         NaN   100
+    DLC21     Vin:2:Vout   -10/0/10     NTM    4.0   NWP  NaN  GridLoss10   100
+    DLC22y    Vin:2:Vout  15:15:345     NTM    1.0   NWP  NaN         NaN   600
+
+%% Cell type:markdown id: tags:
+
+## DLC cases
+
+%% Cell type:markdown id: tags:
+
+You can generate a Pandas DataFrame with all cases of all DLCs
+
+%% Cell type:code id: tags:
+
+``` python
+dlb.to_pandas()
+```
+
+%% Output
+
+            DLC                        Name  Folder  V_hub   wdir  \
+    0     DLC12   DLC12_wsp08_wdir350_s1001   DLC12    8.0  -10.0
+    1     DLC12   DLC12_wsp08_wdir000_s1001   DLC12    8.0    0.0
+    2     DLC12   DLC12_wsp08_wdir010_s1001   DLC12    8.0   10.0
+    3     DLC12   DLC12_wsp10_wdir350_s1101   DLC12   10.0  -10.0
+    4     DLC12   DLC12_wsp10_wdir000_s1101   DLC12   10.0    0.0
+    ..      ...                         ...     ...    ...    ...
+    225  DLC22y  DLC22y_wsp26_wdir285_s1901  DLC22y   26.0  285.0
+    226  DLC22y  DLC22y_wsp26_wdir300_s1901  DLC22y   26.0  300.0
+    227  DLC22y  DLC22y_wsp26_wdir315_s1901  DLC22y   26.0  315.0
+    228  DLC22y  DLC22y_wsp26_wdir330_s1901  DLC22y   26.0  330.0
+    229  DLC22y  DLC22y_wsp26_wdir345_s1901  DLC22y   26.0  345.0
+    
+         simulation_time        ti  seed  \
+    0                600  0.232000  1001
+    1                600  0.232000  1001
+    2                600  0.232000  1001
+    3                600  0.209600  1101
+    4                600  0.209600  1101
+    ..               ...       ...   ...
+    225              600  0.154462  1901
+    226              600  0.154462  1901
+    227              600  0.154462  1901
+    228              600  0.154462  1901
+    229              600  0.154462  1901
+    
+                                              shear Gust Fault
+    0    {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    1    {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    2    {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    3    {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    4    {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    ..                                          ...  ...   ...
+    225  {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    226  {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    227  {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    228  {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    229  {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    
+    [603 rows x 11 columns]
+
+%% Cell type:markdown id: tags:
+
+or the cases of a single DLC
+
+%% Cell type:code id: tags:
+
+``` python
+dlb['DLC14']
+```
+
+%% Output
+
+         DLC                 Name Folder  V_hub  wdir  simulation_time  seed  \
+    0  DLC14  DLC14_wsp06_wdir000  DLC14    6.0   0.0              100  None
+    1  DLC14  DLC14_wsp08_wdir000  DLC14    8.0   0.0              100  None
+    2  DLC14  DLC14_wsp10_wdir000  DLC14   10.0   0.0              100  None
+    
+                                            shear  \
+    0  {'type': 'NWP', 'profile': ('power', 0.2)}
+    1  {'type': 'NWP', 'profile': ('power', 0.2)}
+    2  {'type': 'NWP', 'profile': ('power', 0.2)}
+    
+                                                    Gust
+    0  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 120.0,...
+    1  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 90.0, ...
+    2  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 72.0, ...
+
+%% Cell type:markdown id: tags:
+
+### Edit DLC cases
+
+The dlc cases returned by `dlb.dlcs[<dlc>]` is a Pandas DataFrame that you can edit in python
+
+!!! Note, editing dlc cases will not influence the DLB
+
+%% Cell type:code id: tags:
+
+``` python
+dlc14_ed = dlb['DLC14']
+dlc14_ed.loc[0,'V_hub'] = 4
+dlc14_ed
+```
+
+%% Output
+
+         DLC                 Name Folder  V_hub  wdir  simulation_time  seed  \
+    0  DLC14  DLC14_wsp06_wdir000  DLC14    4.0   0.0              100  None
+    1  DLC14  DLC14_wsp08_wdir000  DLC14    8.0   0.0              100  None
+    2  DLC14  DLC14_wsp10_wdir000  DLC14   10.0   0.0              100  None
+    
+                                            shear  \
+    0  {'type': 'NWP', 'profile': ('power', 0.2)}
+    1  {'type': 'NWP', 'profile': ('power', 0.2)}
+    2  {'type': 'NWP', 'profile': ('power', 0.2)}
+    
+                                                    Gust
+    0  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 120.0,...
+    1  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 90.0, ...
+    2  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 72.0, ...
+
+%% Cell type:markdown id: tags:
+
+### Edit DLC cases in Excel
+
+You can also save the DLC case list as an Excel spreadsheet
+
+%% Cell type:code id: tags:
+
+``` python
+dlc14_ed.to_excel('tmp/dlc14_ed.xlsx')
+```
+
+%% Cell type:markdown id: tags:
+
+and open and edit the cases in Excel
+
+%% Cell type:code id: tags:
+
+``` python
+# uncomment to open file in excel
+# %system "tmp/dlc14_ed.xlsx"
+```
+
+%% Cell type:markdown id: tags:
+
+The modified cases can be loaded by the input writer, see below
+
+%% Cell type:markdown id: tags:
+
+### Write DLB/DLC cases as HAWC2 input files
+
+#### Load into HAWC2_IEC_DLC_Writer
+
+To write the HTC files correponding to the DLB cases, you need the `HAWC2_IEC_DLC_Writer` and a base htc file
+
+%% Cell type:code id: tags:
+
+``` python
+from wetb.hawc2.tests.test_files import tfp
+from wetb.dlb.hawc2_iec_dlc_writer import HAWC2_IEC_DLC_Writer
+
+path = tfp + '/simulation_setup/DTU10MWRef6.0/'
+writer = HAWC2_IEC_DLC_Writer(path + 'htc/DTU_10MW_RWT.htc', diameter=180)
+```
+
+%% Cell type:markdown id: tags:
+
+Load all cases into the writer
+
+%% Cell type:code id: tags:
+
+``` python
+writer.from_pandas(dlb)
+writer.contents
+```
+
+%% Output
+
+            DLC                        Name  Folder  V_hub   wdir  \
+    0     DLC12   DLC12_wsp08_wdir350_s1001   DLC12    8.0  -10.0
+    1     DLC12   DLC12_wsp08_wdir000_s1001   DLC12    8.0    0.0
+    2     DLC12   DLC12_wsp08_wdir010_s1001   DLC12    8.0   10.0
+    3     DLC12   DLC12_wsp10_wdir350_s1101   DLC12   10.0  -10.0
+    4     DLC12   DLC12_wsp10_wdir000_s1101   DLC12   10.0    0.0
+    ..      ...                         ...     ...    ...    ...
+    225  DLC22y  DLC22y_wsp26_wdir285_s1901  DLC22y   26.0  285.0
+    226  DLC22y  DLC22y_wsp26_wdir300_s1901  DLC22y   26.0  300.0
+    227  DLC22y  DLC22y_wsp26_wdir315_s1901  DLC22y   26.0  315.0
+    228  DLC22y  DLC22y_wsp26_wdir330_s1901  DLC22y   26.0  330.0
+    229  DLC22y  DLC22y_wsp26_wdir345_s1901  DLC22y   26.0  345.0
+    
+         simulation_time        ti  seed  \
+    0                600  0.232000  1001
+    1                600  0.232000  1001
+    2                600  0.232000  1001
+    3                600  0.209600  1101
+    4                600  0.209600  1101
+    ..               ...       ...   ...
+    225              600  0.154462  1901
+    226              600  0.154462  1901
+    227              600  0.154462  1901
+    228              600  0.154462  1901
+    229              600  0.154462  1901
+    
+                                              shear Gust Fault
+    0    {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    1    {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    2    {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    3    {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    4    {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    ..                                          ...  ...   ...
+    225  {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    226  {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    227  {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    228  {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    229  {'type': 'NWP', 'profile': ('power', 0.2)}  NaN   NaN
+    
+    [603 rows x 11 columns]
+
+%% Cell type:markdown id: tags:
+
+Load a single DLC
+
+%% Cell type:code id: tags:
+
+``` python
+writer.from_pandas(dlb['DLC14'])
+writer.contents
+```
+
+%% Output
+
+         DLC                 Name Folder  V_hub  wdir  simulation_time  seed  \
+    0  DLC14  DLC14_wsp06_wdir000  DLC14    6.0   0.0              100  None
+    1  DLC14  DLC14_wsp08_wdir000  DLC14    8.0   0.0              100  None
+    2  DLC14  DLC14_wsp10_wdir000  DLC14   10.0   0.0              100  None
+    
+                                            shear  \
+    0  {'type': 'NWP', 'profile': ('power', 0.2)}
+    1  {'type': 'NWP', 'profile': ('power', 0.2)}
+    2  {'type': 'NWP', 'profile': ('power', 0.2)}
+    
+                                                    Gust
+    0  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 120.0,...
+    1  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 90.0, ...
+    2  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 72.0, ...
+
+%% Cell type:markdown id: tags:
+
+Load the modified DLC
+
+%% Cell type:code id: tags:
+
+``` python
+writer.from_pandas(dlc14_ed)
+writer.contents
+```
+
+%% Output
+
+         DLC                 Name Folder  V_hub  wdir  simulation_time  seed  \
+    0  DLC14  DLC14_wsp06_wdir000  DLC14    4.0   0.0              100  None
+    1  DLC14  DLC14_wsp08_wdir000  DLC14    8.0   0.0              100  None
+    2  DLC14  DLC14_wsp10_wdir000  DLC14   10.0   0.0              100  None
+    
+                                            shear  \
+    0  {'type': 'NWP', 'profile': ('power', 0.2)}
+    1  {'type': 'NWP', 'profile': ('power', 0.2)}
+    2  {'type': 'NWP', 'profile': ('power', 0.2)}
+    
+                                                    Gust
+    0  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 120.0,...
+    1  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 90.0, ...
+    2  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 72.0, ...
+
+%% Cell type:markdown id: tags:
+
+Load the DLC from the (modified) excel file
+
+%% Cell type:code id: tags:
+
+``` python
+writer.from_excel('tmp/dlc14_ed.xlsx')
+writer.contents
+```
+
+%% Output
+
+         DLC                 Name Folder  V_hub  wdir  simulation_time seed  \
+    0  DLC14  DLC14_wsp06_wdir000  DLC14      4     0              100
+    1  DLC14  DLC14_wsp08_wdir000  DLC14      8     0              100
+    2  DLC14  DLC14_wsp10_wdir000  DLC14     10     0              100
+    
+                                            shear  \
+    0  {'type': 'NWP', 'profile': ('power', 0.2)}
+    1  {'type': 'NWP', 'profile': ('power', 0.2)}
+    2  {'type': 'NWP', 'profile': ('power', 0.2)}
+    
+                                                    Gust
+    0  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 120.0,...
+    1  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 90.0, ...
+    2  {'type': 'ECD', 'V_cg': 15, 'theta_cg': 72.0, ...
+
+%% Cell type:markdown id: tags:
+
+#### Write files
+
+%% Cell type:code id: tags:
+
+``` python
+writer.write_all(out_dir='tmp')
+```
+
+%% Output
+
+    Generating 3 htc files in directory: tmp
+
+%% Cell type:code id: tags:
+
+``` python
+%ls "tmp/DLC14"
+```
+
+%% Output
+
+     Volume in drive C is Windows
+     Volume Serial Number is 1AB2-743B
+    
+     Directory of c:\mmpe\programming\python\WindEnergyToolbox\notebooks\hawc2\tmp\DLC14
+    
+    29-04-2020  14:56    <DIR>          .
+    29-04-2020  14:56    <DIR>          ..
+    29-04-2020  14:56            28,439 DLC14_wsp06_wdir000.htc
+    29-04-2020  14:56            28,438 DLC14_wsp08_wdir000.htc
+    29-04-2020  14:56            28,439 DLC14_wsp10_wdir000.htc
+                   3 File(s)         85,316 bytes
+                   2 Dir(s)  56,159,342,592 bytes free

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/notebooks/hawc2/RunningSimulationsJess.ipynb

+%% Cell type:markdown id: tags:
+
+## Running simulations on Jess
+
+%% Cell type:code id: tags:
+
+``` python
+import os
+from wetb import hawc2
+from wetb.hawc2 import HTCFile
+from wetb.hawc2.tests.test_files import tfp
+```
+
+%% Cell type:markdown id: tags:
+
+Generate some HAWC2 input htc files
+
+%% Cell type:code id: tags:
+
+``` python
+htc_lst = []
+for wsp in [4,6]:
+    htc = HTCFile(tfp + "simulation_setup/DTU10MWRef6.0/htc/DTU_10MW_RWT.htc")
+    htc.simulation.time_stop = 1
+    htc.wind.wsp=wsp
+    htc.set_name("tmp%d"%wsp)
+    htc.save()
+    htc_lst.append(htc)
+    print (htc.filename)
+```
+
+%% Output
+
+    /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/htc/tmp4.htc
+    /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/htc/tmp6.htc
+
+%% Cell type:code id: tags:
+
+``` python
+pbs = htc.pbs_file("hawc2_path", "hawc2_cmd",
+               queue='workq', # workq, windq, xpresq
+               walltime=None, # defaults to expected (currently 600s) * 2
+               input_files=None, # If none, required files are autodetected from htc file
+               output_files=None, # If none, output files are autodetected from htc file
+               copy_turb=(True, True) # copy turbulence files (to, from) simulation
+              )
+```
+
+%% Cell type:markdown id: tags:
+
+### Generate PBS files
+
+A PBS file defines a job that can be submitted to the queuing system of PBS featured clusters, e.g. Jess.
+
+A PBS file has header that specifies:
+
+- output file for stdout and stderr
+- wall time (after which the job will be terminated)
+- nodes (numbers of nodes to request)
+- ppn (number of processors/CPUs to use at each node. Jess has 20 CPUs per node)
+- queue (e.g. `workq`, `windq`, `xpresq`)
+
+PBS files can be generated from a HAWC2 input htc file. The body (command section) of these files will:
+
+- Copy HAWC2 to a common folder on the the scratch drive (i.e. a hard drive local to the node) if it is not already there.
+- Create a run folder on the scratch drive for the current simulation
+- Copy HAWC2 to the run folder
+- Copy all required input files (turbulence files are optional) to a common folder on the scratch drive if they are not already there
+- Copy all required input files to the run folder
+- Launch the simulation
+- Copy all output files (turbulence files are optional) back from the model directory
+
+%% Cell type:markdown id: tags:
+
+HAWC2 can be copied from a local folder or from the shared group folder `/mnt/aiolos/groups/hawc2sim/HAWC2/<version>/<platform>`.
+HAWC2 can be a zip file, which will be unzipped at the scratch drive, and/or a set of files (exe, dll, ...)
+
+%% Cell type:code id: tags:
+
+``` python
+version = "v12.8.0.0"
+platform = "win32"
+hawc2_path="/mnt/aiolos/groups/hawc2sim/HAWC2/%s/%s/" % (version, platform)
+print(hawc2_path)
+```
+
+%% Output
+
+    /mnt/aiolos/groups/hawc2sim/HAWC2/v12.8.0.0/win32/
+
+%% Cell type:markdown id: tags:
+
+The command needed to run HAWC2 must be specified. It can be obtained via the `wine_cmd` function:
+
+%% Cell type:code id: tags:
+
+``` python
+from wetb.hawc2.hawc2_pbs_file import JESS_WINE32_HAWC2MB, wine_cmd
+hawc2_cmd = wine_cmd(platform='win32', hawc2='hawc2mb.exe', cluster='jess')
+print (hawc2_cmd)
+```
+
+%% Output
+
+    WINEARCH=win32 WINEPREFIX=~/.wine32 winefix
+    WINEARCH=win32 WINEPREFIX=~/.wine32 wine hawc2mb.exe
+
+%% Cell type:markdown id: tags:
+
+The PBS files are generated from the htc files
+
+%% Cell type:code id: tags:
+
+``` python
+pbs_lst = []
+for htc in htc_lst:
+    pbs = htc.pbs_file(hawc2_path, hawc2_cmd,
+                   queue='workq', # workq, windq, xpresq
+                   walltime=None, # defaults to expected (currently 600s) * 2
+                   input_files=None, # If none, required files are autodetected from htc file
+                   output_files=None, # If none, output files are autodetected from htc file
+                   copy_turb=(True, True) # copy turbulence files (to, from) simulation
+                  )
+    pbs.save()
+    pbs_lst.append(pbs)
+    print (os.path.join(pbs.workdir, pbs.filename))
+```
+
+%% Output
+
+    /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/pbs_in/tmp4.in
+    /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/pbs_in/tmp6.in
+
+%% Cell type:code id: tags:
+
+``` python
+from wetb.utils.cluster_tools.os_path import pjoin, relpath, abspath,\
+    cluster_path, repl
+print(abspath(pbs.exe_dir))
+print(pbs.modelpath)
+
+rel_exe_dir = relpath(pbs.exe_dir, pbs.modelpath)
+print (rel_exe_dir)
+```
+
+%% Output
+
+    /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0
+    /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0
+    .
+
+%% Cell type:markdown id: tags:
+
+You can see the contents of the last pbs file here
+
+%% Cell type:code id: tags:
+
+``` python
+print(pbs)
+```
+
+%% Output
+
+    ### Jobid
+    #PBS -N tmp6
+    ### Standard Output
+    #PBS -o /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/stdout/tmp6.out
+    ### merge stderr into stdout
+    #PBS -j oe
+    #PBS -W umask=0003
+    ### Maximum wallclock time format HOURS:MINUTES:SECONDS
+    #PBS -l walltime=00:20:00
+    #PBS -l nodes=1:ppn=1
+    ### Queue name
+    #PBS -q workq
+    cd "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0"
+    mkdir -p "stdout"
+    if [ -z "$PBS_JOBID" ]; then echo "Run using qsub"; exit ; fi
+    pwd
+    
+    
+    #===============================================================================
+    echo copy hawc2 to scratch
+    #===============================================================================
+    (flock -x 200
+    mkdir -p "/scratch/$USER/$PBS_JOBID/hawc2/"
+    unzip -u -o -q "/mnt/aiolos/groups/hawc2sim/HAWC2/v12.8.0.0/win32/"*.zip -d "/scratch/$USER/$PBS_JOBID/hawc2/"
+    find "/mnt/aiolos/groups/hawc2sim/HAWC2/v12.8.0.0/win32/"* ! -name *.zip -exec cp -u -t "/scratch/$USER/$PBS_JOBID/hawc2/" {} +
+    ) 200>"/scratch/$USER/$PBS_JOBID/lock_file_hawc2"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/."
+    cp "/scratch/$USER/$PBS_JOBID/hawc2/"* "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/."
+    
+    #===============================================================================
+    echo copy input
+    #===============================================================================
+    
+    cd "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0"
+    (flock -x 200
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data" && cp -u -r "data/DTU_10MW_RWT_Tower_st.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control" && cp -u -r "control/mech_brake.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data" && cp -u -r "data/DTU_10MW_RWT_Hub_st.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control" && cp -u -r "control/dtu_we_controller_64.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control" && cp -u -r "control/towclearsens.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data" && cp -u -r "data/DTU_10MW_RWT_Towertop_st.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control" && cp -u -r "control/servo_with_limits_64.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control" && cp -u -r "control/servo_with_limits.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control" && cp -u -r "control/wpdata.100" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control" && cp -u -r "control/mech_brake_64.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control" && cp -u -r "control/generator_servo.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control" && cp -u -r "control/dtu_we_controller.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control" && cp -u -r "control/generator_servo_64.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data" && cp -u -r "data/DTU_10MW_RWT_pc.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control" && cp -u -r "control/towclearsens_64.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data" && cp -u -r "data/DTU_10MW_RWT_ae.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/htc" && cp -u -r "htc/tmp6.htc" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/htc"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data" && cp -u -r "data/DTU_10MW_RWT_Shaft_st.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data" && cp -u -r "data/DTU_10MW_RWT_Blade_st.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/data"
+    ) 200>/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/lock_file_model
+    cd "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data" && cp -u -r "data/DTU_10MW_RWT_Tower_st.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control" && cp -u -r "control/mech_brake.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data" && cp -u -r "data/DTU_10MW_RWT_Hub_st.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control" && cp -u -r "control/dtu_we_controller_64.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control" && cp -u -r "control/towclearsens.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data" && cp -u -r "data/DTU_10MW_RWT_Towertop_st.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control" && cp -u -r "control/servo_with_limits_64.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control" && cp -u -r "control/servo_with_limits.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control" && cp -u -r "control/wpdata.100" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control" && cp -u -r "control/mech_brake_64.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control" && cp -u -r "control/generator_servo.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control" && cp -u -r "control/dtu_we_controller.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control" && cp -u -r "control/generator_servo_64.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data" && cp -u -r "data/DTU_10MW_RWT_pc.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control" && cp -u -r "control/towclearsens_64.dll" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/control"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data" && cp -u -r "data/DTU_10MW_RWT_ae.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/htc" && cp -u -r "htc/tmp6.htc" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/htc"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data" && cp -u -r "data/DTU_10MW_RWT_Shaft_st.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data"
+    mkdir -p "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data" && cp -u -r "data/DTU_10MW_RWT_Blade_st.dat" "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/data"
+    
+    
+    #===============================================================================
+    echo Run HAWC2
+    #===============================================================================
+    cd "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6/."
+    WINEARCH=win32 WINEPREFIX=~/.wine32 winefix
+    WINEARCH=win32 WINEPREFIX=~/.wine32 wine hawc2mb.exe htc/tmp6.htc
+    
+    #===============================================================================
+    echo Copy output
+    #===============================================================================
+    cd "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6"
+    mkdir -p "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/log" && cp -u -r "log/tmp6.log" "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/log"
+    mkdir -p "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/res" && cp -u -r "res/tmp6.sel" "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/res"
+    mkdir -p "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/res" && cp -u -r "res/tmp6.dat" "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/res"
+    mkdir -p "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/res" && cp -u -r "res/at.dat" "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/res"
+    
+    rm -r "/scratch/$USER/$PBS_JOBID/DTU10MWRef6.0/run_tmp6"
+    
+    echo Done
+    
+    exit
+    
+
+%% Cell type:markdown id: tags:
+
+### Run single simulation
+
+%% Cell type:markdown id: tags:
+
+You can run a simulation by executing the pbs file in an interactive seession. This way is very handy for debugging.
+
+```bash
+qsub -I -l nodes=1:ppn=1 -l walltime=01:00:00
+<...>/wetb/hawc2/tests/test_files/simulation_setup/pbs_in/tmp6.in
+```
+
+%% Cell type:markdown id: tags:
+
+or by summiting the pbs file to the queing system
+```
+qsub <...>/wetb/hawc2/tests/test_files/simulation_setup\pbs_in/tmp6.in
+```
+This done here:
+
+%% Cell type:code id: tags:
+
+``` python
+print(os.path.join(pbs.workdir,pbs.filename))
+!qsub {os.path.join(pbs.workdir,pbs.filename)}
+```
+
+%% Output
+
+    /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/pbs_in/tmp6.in
+    3221545.jess.dtu.dk
+
+%% Cell type:markdown id: tags:
+
+The job will now enter the cluster queue and be launched when free resoureces are available.
+You can check the status of the job:
+
+%% Cell type:code id: tags:
+
+``` python
+!qstat -n -u $USER
+```
+
+%% Cell type:markdown id: tags:
+
+Wait as long as the `qstat` command above prints information about the job
+
+When the job is finished we can check the output file
+
+%% Cell type:code id: tags:
+
+``` python
+!cat {pbs.stdout_filename}
+```
+
+%% Output
+
+    Start of prologue
+    /scratch/mmpe/3221545.jess.dtu.dk created
+    End of prologue
+    /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0
+    copy hawc2 to scratch
+    copy input
+    cp: cannot stat `control/dtu_we_controller_64.dll': No such file or directory
+    cp: cannot stat `control/servo_with_limits_64.dll': No such file or directory
+    cp: cannot stat `control/mech_brake_64.dll': No such file or directory
+    cp: cannot stat `control/generator_servo_64.dll': No such file or directory
+    cp: cannot stat `control/towclearsens_64.dll': No such file or directory
+    cp: cannot stat `control/dtu_we_controller_64.dll': No such file or directory
+    cp: cannot stat `control/servo_with_limits_64.dll': No such file or directory
+    cp: cannot stat `control/mech_brake_64.dll': No such file or directory
+    cp: cannot stat `control/generator_servo_64.dll': No such file or directory
+    cp: cannot stat `control/towclearsens_64.dll': No such file or directory
+    Run HAWC2
+     ***********************************************************************
+    
+     *  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
+    
+     ***********************************************************************
+    
+    fixme:console:GetNumberOfConsoleMouseButtons (0x684ec44): stub
+     Using licence_manager.dll, version: unknown
+    
+     License verified - OK
+    
+     Opening main command file: htc/tmp6.htc
+    
+     Current directory is Z:\scratch\mmpe\3221545.jess.dtu.dk\DTU10MWRef6.0\run_tmp6
+    
+     Continue on no convergence = true
+    
+     Logfile: ./log/tmp6.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...
+    
+    Copy output
+    Done
+    Start of epilogue on j-177
+    Resources Used: cput=00:00:04,mem=5744kb,vmem=3856592kb,walltime=00:00:07
+    End of epilogue on j-177
+
+%% Cell type:markdown id: tags:
+
+Highlights:
+- copy hawc2 to scratch
+- copy input
+    - It states that it cannot copy the 64-bit control dlls (control/*_64.dll) - which does not matter as we are using the 32-bit HAWC2
+- Run HAWC2
+- Copy output
+- Done
+
+%% Cell type:code id: tags:
+
+``` python
+!head -n 20 {os.path.join(htc.modelpath, htc.simulation.logfile[0])}
+```
+
+%% 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 : 12:19:17
+    
+                                                                Date : 29:05.2020
+    
+    ________________________________________________________________________________________________________________________
+    
+     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
+    
+
+%% Cell type:markdown id: tags:
+
+### Run multiple simulations
+
+%% Cell type:markdown id: tags:
+
+Multiple simulations can easily be executed using the `PBSMultiRunner`.
+
+The `PBSMultiRunner` generates a top-level `pbs_multirunner.all` pbs job capable of launching all the HTC-specific PBS files in a folder.
+
+The `PBSMultiRunner` needs some information:
+- queue (e.g. workq, windq, xpresq)
+- nodes (number of nodes)
+- ppn (processors per node). Be careful, ppn does not limit the job to this number of CPUs, i.e. you may occupy all resources of a full node even if you set ppn=10 - annoying other users of the node. Hence ppn should be 20 if you need to run more than a few simulations)
+- wall time in seconds (after which the job will be terminated, i.e. approximately total simulation time divided by number of)
+
+%% Cell type:code id: tags:
+
+``` python
+from wetb.utils.cluster_tools.pbsfile import PBSMultiRunner
+pbs_all = PBSMultiRunner(workdir=pbs.workdir,
+                     queue='workq', # alternatives workq, windq, xpresq
+                     walltime=10,   # expected total simulation time in seconds
+                     nodes=1,       # Number of nodes
+                     ppn=2,         # number of processors of each node (normally 20)
+                     pbsfiles=None  # If None, the multirunner searches for *.in files
+                     )
+pbs_all.save()
+print (os.path.join(pbs_all.workdir, pbs_all.filename))
+```
+
+%% Output
+
+    /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/pbs_multirunner.all
+
+%% Cell type:markdown id: tags:
+
+The pbs_multirunner.all will do the following:
+
+- Get list of nodes assigned for the current job
+- Make list of *.in pbs files.
+- Sort pbs files according to their wall time and distribute the files to the available nodes. Longest simulations are run first
+- Generate a file, `pbs.dict`, containing for each node a list of (pbs file, stdout filename, wall time):
+
+    `{'j-177': [('./pbs_in/tmp4.in', './stdout/tmp4.out', '00:20:00'), ('./pbs_in/tmp6.in', './stdout/tmp6.out', '00:20:00')]}`
+
+- On each node, launch the assigned pbs files in parallel via Python's multiprocessing module.
+
+You can see the content of the `pbs_multirunner.all` here:
+
+%% Cell type:code id: tags:
+
+``` python
+!cat {os.path.join(pbs_all.workdir, pbs_all.filename)}
+```
+
+%% Output
+
+    ### Jobid
+    #PBS -N pbs_multirunner
+    ### Standard Output
+    #PBS -o /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/stdout/pbs_multirunner.out
+    ### merge stderr into stdout
+    #PBS -j oe
+    #PBS -W umask=0003
+    ### Maximum wallclock time format HOURS:MINUTES:SECONDS
+    #PBS -l walltime=00:00:10
+    #PBS -l nodes=1:ppn=2
+    ### Queue name
+    #PBS -q workq
+    cd "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0"
+    mkdir -p "stdout"
+    if [ -z "$PBS_JOBID" ]; then echo "Run using qsub"; exit ; fi
+    pwd
+    echo "import os
+    import glob
+    import numpy as np
+    import re
+    
+    # find available nodes
+    with open(os.environ['PBS_NODEFILE']) as fid:
+        nodes = set([f.strip() for f in fid.readlines() if f.strip() != ''])
+    pbs_files = [os.path.join(root, f) for root, folders, f_lst in os.walk('.') for f in f_lst if f.endswith('.in')]
+    
+    # Make a list of [(pbs_in_filename, stdout_filename, walltime),...]
+    pat = re.compile(r'[\s\S]*#\s*PBS\s+-o\s+(.*)[\s\S]*(\d\d:\d\d:\d\d)[\s\S]*')
+    
+    def get_info(f):
+        try:
+            with open(f) as fid:
+                return (f,) + pat.match(fid.read()).groups()
+        except Exception:
+            return (f, f.replace('.in', '.out'), '00:30:00')
+    pbs_info_lst = map(get_info, pbs_files)
+    
+    # sort wrt walltime
+    pbs_info_lst = sorted(pbs_info_lst, key=lambda fow: tuple(map(int, fow[2].split(':'))))[::-1]
+    # make dict {node1: pbs_info_lst1, ...} and save
+    d = dict([(f, pbs_info_lst[i::len(nodes)]) for i, f in enumerate(nodes)])
+    with open('pbs.dict', 'w') as fid:
+        fid.write(str(d))
+    
+    " | python
+    
+    for node in `cat $PBS_NODEFILE | sort | uniq`
+    do
+    
+         ssh -T $node << EOF &
+    cd "/home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0"
+    python -c "import os
+    import multiprocessing
+    import platform
+    import time
+    with open('pbs.dict') as fid:
+        pbs_info_lst = eval(fid.read())[platform.node()]
+    arg_lst = ['echo starting %s && mkdir -p "%s" && env PBS_JOBID=$PBS_JOBID "%s" &> "%s" && echo finished %s' %
+               (f, os.path.dirname(o), f, o, f) for f, o, _ in pbs_info_lst]
+    print(arg_lst[0])
+    print('Starting %d jobs on %s' % (len(arg_lst), platform.node()))
+    pool = multiprocessing.Pool(int('$PBS_NUM_PPN'))
+    res = pool.map_async(os.system, arg_lst)
+    t = time.time()
+    for (f, _, _), r in zip(pbs_info_lst, res.get()):
+        print('%-50s\t%s' % (f, ('Errorcode %d' % r, 'Done')[r == 0]))
+    print('Done %d jobs on %s in %ds' % (len(arg_lst), platform.node(), time.time() - t))
+    
+    "
+    EOF
+    done
+    wait
+    
+    exit
+
+%% Cell type:markdown id: tags:
+
+You can launch the multirunner via
+```bash
+qsub <...>/wetb/hawc2/tests/test_files/simulation_setup\pbs_multirunner.all
+```
+It is done here:
+
+%% Cell type:code id: tags:
+
+``` python
+!qsub {os.path.join(pbs_all.workdir, pbs_all.filename)}
+```
+
+%% Output
+
+    3221548.jess.dtu.dk
+
+%% Cell type:markdown id: tags:
+
+The job will now enter the cluster queue and be launched when free resoureces are available. You can check the status of the job:
+
+%% Cell type:code id: tags:
+
+``` python
+!qstat -n -u $USER
+```
+
+%% Cell type:markdown id: tags:
+
+Wait as long as the qstat command above prints information about the job
+
+When the job is finished we can check the output file
+
+%% Cell type:code id: tags:
+
+``` python
+!cat {pbs_all.stdout_filename}
+```
+
+%% Output
+
+    Start of prologue
+    /scratch/mmpe/3221548.jess.dtu.dk created
+    End of prologue
+    /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0
+    Warning: Permanently added 'j-176,172.16.1.76' (RSA) to the list of known hosts.
+    
+    echo starting ./pbs_in/tmp4.in && mkdir -p /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/stdout && env PBS_JOBID=3221548.jess.dtu.dk ./pbs_in/tmp4.in &> /home/mmpe/gitlab/WindEnergyToolbox/wetb/hawc2/tests/test_files/simulation_setup/DTU10MWRef6.0/stdout/tmp4.out && echo finished ./pbs_in/tmp4.in
+    Starting 2 jobs on j-176
+    starting ./pbs_in/tmp4.in
+    starting ./pbs_in/tmp6.in
+    finished ./pbs_in/tmp6.in
+    finished ./pbs_in/tmp4.in
+    ./pbs_in/tmp4.in                                  	Done
+    ./pbs_in/tmp6.in                                  	Done
+    Done 2 jobs on j-176 in 4s
+    Start of epilogue on j-176
+    Resources Used: cput=00:00:00,mem=0kb,vmem=0kb,walltime=00:00:06
+    End of epilogue on j-176
+
+%% 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.
+

docs/tutorials/2-creating-subordinate-excels.md

+# Tutorial 2: Creating subordinate Excel files
+
+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](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/tutorials/1-creating-master-excel.md)
+2. Create subordinate Excel sheets from each tab in the master Excel sheet
+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 2.
+
+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: Subordinate Excel Files
+
+The subordinate Excel files are a series of basic Excel files that are
+generated from the master Excel file. (See our tutorial on generating the
+master Excel file [here]( https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/tut orials/1-creating-master-excel.md).)
+There is a different subordinate Excel file for every tab in the master Excel
+file, except for the "Main" tab, one for each case to simulate (e.g., design
+load case 1.2 from IEC-61400-1).
+Each subordinate Excel file has a single tab that lists the different tag
+values for the htc master file in the column, and each row corresponds to a
+different htc file to be generated.
+The generation of the htc files from the subordinate Excel files is discused
+in the next tutorial.
+
+
+## 2. Tutorial
+
+The generation of the subordinate Excel files is done using the
+[GenerateDLS.py](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/wetb/prepost/GenerateDLCs.py)
+function in the Wind Energy Toolbox.
+On Gorm, the command can be executed from the htc directory with the master
+Excel file as follows:
+```
+export PATH=/home/python/miniconda3/bin:$PATH
+source activate py36-wetb
+python /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/GenerateDLCs.py [--folder=$FOLDER_NAME] [--master=$MASTER_NAME]
+source deactivate
+```
+
+The ```export PATH``` command adds the miniconda bin directory to the path,
+which is necessary for the toolbox.
+The ```source activate py36-wetb``` and ```source deactivate``` are
+Gorm-specific commands to activate the Wind Energy Toolbox Python environment.
+The ```--folder``` and ```--master``` flags are optional flags to specify,
+respectively, the name of the folder to which the subordinate Excel files
+should be written to and the name of the master Excel file.
+The default values for these two options are './' (i.e., the current
+directory) and 'DLCs.xlsx', respectively.
+
+After running the commands in the above box on Gorm, you should see a folder in
+your htc directory with all of your subordinate Excel files.
+
+
+## 3. 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.
+