Documentation change and testing examples

Documentation adapted to the new way to define geometry and pushers.

Examples are currently being tested and small modifications are being
done to include a reference output.

runs/0D_Argon/README.txt

@@ -0,0 +1,11 @@
+Example of 0D geometry.
+
+Mostly used to test collision processes.
+
+This example includes Ar and Ar+ with self-collisions for Ar and elastic collisions for AR-Ar+.
+
+Different starting temperatures for each species that end up in equilibrium.
+
+The gnuplpot script 'plot_Temperature.gp' generates a plot of the species temperatures.
+
+The result is provided in the output folder to compare if modifications to the code are made.

runs/0D_Argon/input.json

@@ -21,8 +21,8 @@
     {"name": "Argon",  "type": "neutral", "mass": 6.633e-26,                "weight": 1.0e0}
   ],
   "solver": {
-    "tau":  [1.0e-6, 1.0e-6],
-    "finalTime": 1.0e-3,
+    "tau":  [1.0e-3, 1.0e-3],
+    "finalTime": 1.0e0,
     "initial": [
       {"species": "Argon+", "file": "Argon+_Initial.dat"},
       {"species": "Argon",  "file": "Argon_Initial.dat"}

runs/0D_Argon/plot_Temperature.gp

@@ -43,6 +43,8 @@ set output "comp_temp.eps"
 filename1 = "OUTPUT_Argon.dat"
 filename2 = "OUTPUT_Argon+.dat"
 
+folder = 'output/'
+
 set lmargin at screen lmar 
 set rmargin at screen rmar
 
@@ -58,7 +60,6 @@ set ylabel "Temperature (K)" offset 1.4,0.0
 set key width 0.5 height 0.1 spacing 1.3 samplen 0.2 box opaque font ",16"
 set key at graph 0.95, graph 0.9 right top
 
-plot filename1 u ($1):($7)                                          t "Ar"     ls 1 with lines, \
-     filename2 u ($1):($7)                                          t "Ar^{+}" ls 2 with lines, \
-     '< paste OUTPUT_Argon.dat OUTPUT_Argon+.dat' u ($1):($7 + $14) t "Sum"    ls 3 with lines
+plot folder.filename1 u ($1):($7)                                          t "Ar"     ls 1 with lines, \
+     folder.filename2 u ($1):($7)                                          t "Ar^{+}" ls 2 with lines