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

@@ -58,63 +58,51 @@ 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 Anaconda, activate root environment
-
-* Download and install Anaconda (Python 3.5 version, 64 bit installer is
-recommended) from <https://www.continuum.io/downloads>
+### Installing Miniconda
 
-> Note: The Python 2.7 or Python 3.5 choice of Anaconda only affects the
-root environment. You can always create additional environments using other
-Python versions, see below.
+* Download and install Anaconda (Python 3.8 version, 64 bit installer is
+recommended) from <https://docs.conda.io/en/latest/miniconda.html>.
 
-* Update the root Anaconda environment (type in a terminal):
+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:
 
 ```
->> conda update --all
+(base) C:\Users\>
 ```
 
-* Activate the Anaconda root environment in a terminal as follows:
+and where `(base)` refers to your base Miniconda installation environment. 
+You can keep the base environment updated as follows (type in a terminal):
 
 ```
->> activate
-```
-
-and your terminal will do something like:
-```
-C:\Users\> activate
-(root) C:\Users\>
+>> conda update --all
 ```
-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:
+different versions on your system independently. 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
+>> conda create -n py39 python=3.9
 ```
 
-These environments can be activated as follows:
+Where `-n py39` refers any user defined name that describes what is the environment
+used for. These environments can then be activated as follows:
 
 ```
->> activate py27
->> activate py34
->> activate py35
+>> conda activate py39
 ```
 
-The Python distribution in use will now be located in e.g. \<path_to_anaconda\>/env/py35/
+The Python distribution in use will now be located in e.g. \<path_to_anaconda\>/env/py39/
 
-use ```deactivate``` to deactivate the environment.
+use ```conda deactivate``` to deactivate the environment.
 
 
 ## Install/build dependencies
@@ -122,12 +110,11 @@ use ```deactivate``` to deactivate the environment.
 - Compiler (```wetb``` contains cython extensions that require a compiler):
     - Linux: gcc (should be installed by default)
     - Windows:
-        - Python 2.7: [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: MS Visual Studio 2010
-        - Python 3.5: MS Visual Studio 2015 or [Visual C++ Build Tools](http://landinghub.visualstudio.com/visual-cpp-build-tools)
+        - 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 2010 alongside the Visual C++ Build Tools.
+        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/)
@@ -137,28 +124,25 @@ use ```deactivate``` to deactivate the environment.
 - [h5py](http://www.h5py.org/)
 - [matplotlib](http://matplotlib.org/)
 - [pytables](http://www.pytables.org/)
-- [pyscaffold](http://pyscaffold.readthedocs.org/en/)
 - [pytest](https://pypi.python.org/pypi/pytest)
 - [pytest-cov](https://pypi.python.org/pypi/pytest-cov/)
-- six, [future](http://python-future.org/index.html)
-- nose, sphinx, blosc, pbr, psutil, coverage, setuptools_scm
-- [parimeko](http://www.paramiko.org/)
+- 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).
-- [twine](https://pypi.python.org/pypi/twine): upload package to
-[PyPi](https://pypi.python.org/pypi)
 
 Install the necessary Python dependencies using the conda package manager:
 
 ```
->> conda install setuptools_scm future h5py pytables pytest pytest-cov nose sphinx blosc pbr paramiko
->> conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl psutil pandoc
->> conda install -c conda-forge pyscaffold pypandoc sshtunnel --no-deps
->> conda install --channel https://conda.anaconda.org/pbrod twine --no-deps
+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
@@ -195,6 +179,43 @@ 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.
@@ -219,6 +240,14 @@ 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```
@@ -240,4 +269,3 @@ In case of problems:
 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

@@ -61,11 +61,11 @@ 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.). 
+    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").  
-    
+    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.
 
@@ -86,7 +86,7 @@ structure similar to this:
 
 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 
+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.
@@ -94,7 +94,7 @@ From a terminal, change to your htc directory. Then run the following code:
 
 ```
 $ export PATH=/home/python/miniconda3/bin:$PATH
-$ source activate wetb_py3
+$ source activate py36-wetb
 $ python /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/GenerateDLCs.py --folder=DLCs
 $ source deactivate
 ```
@@ -102,10 +102,7 @@ $ source deactivate
 This will create a subfolders DLCs and fill that new subfolder with the created
 subordinate Excel files.
 
-##### 6. Move your DLCs.xlsx file from the htc folder to the ```_master``` folder.
-It will cause errors in later scripts if left in the htc folder.
-
-##### 7. Create your htc files and PBS job scripts .
+##### 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
@@ -117,7 +114,7 @@ $ qsub-wrap.py -f /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/
 Your htc files should now be placed in subfolders in the htc folder, and PBS
 job files should be in folder ```pbs_in```.
 
-##### 8. Launch the htc files to the cluster.
+##### 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.,
@@ -128,7 +125,7 @@ $ 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 
+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:
 
@@ -136,9 +133,9 @@ help function to print available launch options:
 $ launch.py --help
 ```
 
-##### 9. Post-process results.
+##### 8. Post-process results.
 
-The wetb function ```qsub-wrap.py``` can not only generate htc files but also 
+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):

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/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.md

-
-
 # Anaconda (Windows/Mac/Linux)
 
 ## Installation
@@ -7,9 +5,9 @@
 Install the necessary Python dependencies using the ```conda``` package manager:
 
 ```
->> conda install setuptools_scm future h5py pytables pytest pytest-cov nose sphinx blosc pbr paramiko
+>> 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 pyscaffold sshtunnel --no-deps
+>> conda install -c conda-forge sshtunnel --no-deps
 ```
 
 Now you can install ```wetb``` with ```pip``` (there is no ```conda``` package
@@ -32,34 +30,12 @@ expclicitally tell ```pip``` to only install ```wetb``` and nothing more:
 
 # Pip (Windows/Mac/Linux)
 
+Do not use this procedure in conda environments. See above.
+
+
 ## Installation and update
 
 ```
 >> pip install --upgrade wetb
 ```
 
-
-# Works with Python 2 and Python 3
-
-This module is tested for Python 2.7 and 3.4+ compatibility, and works on both
-Windows and Linux. Testing for Mac is on the way, but in theory it should work.
-Python 2 and 3 compatibility is achieved with a single code base with the help
-of the Python module [future](http://python-future.org/index.html).
-
-Switching to Python 3 is in general a very good idea especially since Python 3.5
-was released. Some even dare to say it
-[is like eating your vegetables](http://nothingbutsnark.svbtle.com/porting-to-python-3-is-like-eating-your-vegetables).
-So if you are still on Python 2, we would recommend you to give Python 3 a try!
-
-You can automatically convert your code from Python 2 to 3 using the
-[2to3](https://docs.python.org/2/library/2to3.html) utility which is included
-in Python 2.7 by default. You can also write code that is compatible with both
-2 and 3 at the same time (you can find additional resources in
-[issue 1](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues/1)).
-
-
-# Note
-
-This project has been set up using PyScaffold 2.5. For details and usage
-information on PyScaffold see http://pyscaffold.readthedocs.org/.
-

docs/installation.rst

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

docs/make.bat

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

docs/notebooks/hawc2/RunningSimulations.ipynb

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

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

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

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.
+

docs/tutorials/3-creating-htc-pbs-files.md

+# Tutorial 3: Creating htc and PBS 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](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.
+4. Submit all PBS job scripts to the cluster
+5. Post-process results
+6. Visualize results
+
+This tutorial presents how to accomplish Step 3.
+
+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: htc and PBS file creation
+
+The main function used in this tutorial is [dlctemplate.py](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/wetb/prepost/dlctemplate.py),
+which creates all htc and PBS job scripts for the cases specified in the
+subordinate Excel file folder.
+
+The htc files are the main input files for HAWC2 simulations.
+They are created by copying the master htc file in the ```_master/``` folder in
+your htc directory and replacing all of the tags with the values specified in
+the subordinate Excel files.
+All of htc files for a single case are saved in a case-specific folder in your
+htc folder.
+Thus, if you were running a standard DLB calculation for IEC 61400-1, your
+folder structure after generating your htc files might look like this:
+```
+|-- $TURB_NAME/
+|   |-- $SET_ID/
+|   |   |-- DLCs.xlsx
+|   |   |-- _master/
+|   |   |   |-- $MASTER_NAME.htc
+|   |   |-- DLCs/
+|   |   |-- htc/
+|   |   |   |-- dlc12_iec61400-1ed3/
+|   |   |   |   |-- dlc12_wsp04_wdir000_s2001.htc
+|   |   |   |   |-- dlc12_wsp04_wdir000_s2002.htc
+|   |   |   |   |-- ...
+|   |   |   |-- dlc13_iec61400-1ed3/
+|   |   |   |-- ...
+```
+
+The PBS job scripts are a series of text files that are used to tell the job
+scheduler on the high-performance computing (HPC) cluster how to run each job.
+These files end with ".p", and are saved to a folder ```pbs_in/``` that is
+created in the main set ID folder on Gorm.
+
+
+## 2. Tutorial
+
+There are two ways to call ```dlctemplate.py```.
+The first is to call the function directly.
+The second is to wrap it in a job scheduler to submit the job to the HPC cluster.
+The first option is fine if you have only a few htc files or if the job
+scheduler is not working for some reason.
+The second option is generally preferred.
+
+### 2.1 Directly generate htc files
+
+The htc and PBS files can be directly generated by running the following
+commands from the set ID directory:
+```
+export PATH=/home/python/miniconda3/bin:$PATH
+source activate py36-wetb
+python /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py --prep
+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 ```--prep``` option tells the script to run in preparation mode, in which
+case it creates the htc and pbs files.
+
+After running the commands in the above box on Gorm, you should have all of your
+PBS input files in ```pbs_in/``` and all of your htc files in ```htc```.
+
+### 2.2 Generate files using job scheduler
+
+From the set ID folder, run the following code:
+```
+qsub-wrap.py -f /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py --prep
+```
+
+
+## 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.
+

docs/tutorials/data/DLCs_onshore/DLC12_IEC61400-1Ed3.txt

+C	F	V	V	V	F
+[Case folder]	[Case id.]	[wdir]	[seed]	[wsp]	[TI]
+DLC12_IEC61400-1Ed3	"""DLC12_wsp[wsp]_wdir[wdir]_s[seed]"""	0	6	4	"([ref_ti]*(0,75*[wsp]+5,6))/[wsp]"
+		350		6	
+		10		8	
+				10	
+				12	
+				14	
+				16	
+				18	
+				20	
+				22	
+				24	
+				26	
+					
+					
+					
+					
+					
+					
+					
+					
+					
+					
+					
+