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.
+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. This procedure has some limitations: at the moment it works for the three PS fault structures defined in TSUMAPS hazard model (Hellenic Arc, Calabrian Arc and Cyprus Arc).
 
 ### 1\. Preparation of the procedure
 
@@ -55,6 +55,30 @@ list_files_hellenic_arc.txt
 
 ### 2\. Create tsunami initial conditions
 
+In `run_ps_init_cond.sh` users have to set a few variables:
+
+```
+# position of Python code script
+EXE=/work/tonini/tsumaps/src/make_init_cond_ps.py
+
+# PS_MESH provides path to mesh and attributes
+# HeA: TSUMAPS Hellenic Arc 
+# CaA: TSUMAPS Calabrian Arc 
+# CyA: TSUMAPS Cyprus Arc 
+PS_MESH=HeA
+
+# Path to the folder where netcdf will be saved.
+OUTPUT=MY_DIR/ps_initial_conditions/$PS_MESH   # full absolute path
+
+# Plotting slip 0(False)/1(True)
+PLOT_SLIP=0
+
+# Plotting initial condition 0(False)/1(True)  
+PLOT_INIT=0
+```
+
+If non necessary, please do not edit the `EXE` variable, since it links the main Python script to calculate tsunami initial conditions. In `PS_MESH` the user set the selected TSUMAPS fault structure and in `OUTPUT` the full path to save the tsunami initial conditions. The other two variables `PLOT_SLIP` and `PLOT_INIT` can take as values only 0 (False) or 1 (True). They generate a plot for each scenarios, but they were introduced only for testing since for massive number of scenarios they slow down the script performances too much. Also, the plot functions have not been tested recently, so I suggest to let them set to 0 for productivity.
+
 Tsunami initial conditions for this fault structure are created by running:
 
 ```