Tsunami-wave-heights-from-fault-slip-distribution-with-linear-combinations.md

 Description of the procedure to get tsunami wave heights from a set of possible slip distributions provided for a pre-defined fault structure using tsunami linear combinations.
 
-## Create tsunami initial conditions
-Slip distributions for a given fault structure are grouped in a specific folder tree. For example
-`
+### 1\. Preparation of the procedure
+
+First of all, create a working directory `my_dir` where to run the procedure. Then create the following folders:
+
+```
+mkdir logs                             # where to store logs of job script
+mkdir ps_initial_conditions            # where to store tsunami initial conditions
+mkdir slip                             # where to put scenarios slip distributions
+```
+
+Slip distributions for a given fault structure are grouped in a specific folder tree. For example:
+
+```
 slip/
  |--- HellenicArc
      |--- 9_0260
@@ -17,8 +27,42 @@ slip/
          |--- Str_PropYes
      ...
      ...
-`
      
-### Create a list with the path of the slip distribution files for each fault structure. 
-For example: 
-`find $PWD -type f -path "*Hellenic*.vtk" -print > list_slip_hellenic_arc.txt`
+```
+
+Create a list with the path of the slip distribution files for each fault structure. A way to do it, for example, can be the following:
\ No newline at end of file
+
+```
+find $PWD -type f -path "*Hellenic*.vtk" -print > list_slip_hellenic_arc.txt
+```
+
+Then, copy the script to create tsunami initial conditions:
+
+```
+cp /work/tonini/works/heterogeneous_slip/run_ps_init_cond.sh ./ 
+chmod u+x run_ps_init_cond.sh
+```
+
+At the end, the structure of your `my_dir` folder should be the following:
+
+```
+logs/
+ps_initial_conditions/
+slip/
+run_ps_init_cond.sh
+list_files_hellenic_arc.txt
+```
+
+### 2\. Create tsunami initial conditions
+
+Tsunami initial conditions for this fault structure are created by running:
+
+```
+./run_ps_init_cond.sh < list_slip_hellenic_arc.txt
+```
+
+This bash script\* create and launch (and then also remove) a job script on the cluster for each slip distribution scenario in the list. Tsunami initial conditions will be saved as `netcdf` files and stored in the `ps_initial_conditions/` folder, converting the folder path structure of the slip distribution into the name of the tsunami initial condition file (for example: `HeA/hellenic_Hazard_slip_HeA_025_variable_mu_6_5000_Strasser_Slip4cells_02635_000.nc`).
+
+_\* At the moment, the script `run_ps_init_cond` is set for the auriga cluster only, because of mercalli cluster has different library versions._ 
+
+### 2\. Run linear combinations
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