Initial upload tutorial 3

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/
+|   |   |   |-- $MASTER_NAME.htc
+|   |   |-- DLCs/
+|   |   |-- htc/
+|   |   |   |-- dlc12_iec61400-1ed3/
+|   |   |   |   |-- dlc12_wsp04_wdir000_s2001.htc
+|   |   |   |   |-- dlc12_wsp04_wdir000_s2002.htc
+|   |   |   |   |-- ...
+|   |   |   |-- dlc13_iec61400-1ed3/
+|   |   |   |-- ...
+```
+
+The PBS job scripts are a series of text files that are used to tell the job 
+scheduler on the high-performance computing (HPC) cluster how to run each job.
+These files end with ".p", and are saved to a folder ```pbs_in/``` that is 
+created in the main set ID folder on Gorm.
+
+
+## 2. Tutorial
+
+There are two ways to call ```dlctemplate.py```.
+The first is to call the function directly.
+The second is to wrap it in a job scheduler to submit the job to the HPC cluster.
+The first option is fine if you have only a few htc files or if the job 
+scheduler is not working for some reason.
+
+### 2.1 Directly generate htc files
+
+The htc and PBS files can be directly generated by running the following 
+commands from the set ID directory:
+```
+export PATH=/home/python/miniconda3/bin:$PATH
+source activate wetb_py3
+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 wetb_py3``` 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```.
+
+
+## 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.
+