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/plot_Temperature.gp

@@ -0,0 +1,65 @@
+reset
+set macros
+term = 'postscript eps color enhanced'
+font = 'font "CMUSerif-Roman,20"'
+linew = 'lw 2.0'
+times='"{/Symbol \264}"'
+size_x=8.5
+size_y=5.2
+
+tmar=0.998
+bmar=0.145
+
+lmarLabel = 0.070
+
+lmar=lmarLabel+0.085
+rmar=0.97
+
+space_x=(rmar-lmar)
+
+xt_off_0=0.5
+yt_off_0=0.6
+
+set xtics nomirror offset 0.0,xt_off_0
+set mxtics 2
+
+set ytics nomirror offset yt_off_0,0.0
+set mytics 2
+
+set pointsize 1.5
+
+set style line 1  pt 4              lc rgb "#B50427" #Squares   red
+set style line 2  pt 6              lc rgb "#3B4CC1" #Circles   blue
+set style line 3  pt 1              lc rgb "#2CA02C" #Crosses   green
+set style line 4  pt 2              lc rgb "#FE7F0E" #Exes      orange
+set style line 5  pt 8              lc rgb "#D6696B" #Triangles light red
+set style line 10       lt 1 lw 2.0 lc rgb "black"   #Black solid line
+
+set terminal @term size size_x cm, size_y cm @linew @font
+
+set output "comp_temp.eps"
+
+#files
+filename1 = "OUTPUT_Argon.dat"
+filename2 = "OUTPUT_Argon+.dat"
+
+folder = 'output/'
+
+set lmargin at screen lmar 
+set rmargin at screen rmar
+
+set xrange [-0.01:1.01]
+set xtics 0.2
+set xlabel "Time (s)" offset 0.0,1.2
+
+set yrange [250:3550]
+set format y "%3.0f"
+set ytics 500
+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 folder.filename1 u ($1):($7)                                          t "Ar"     ls 1 with lines, \
+     folder.filename2 u ($1):($7)                                          t "Ar^{+}" ls 2 with lines
+