New version of the manual explaining briefly collisional processes and

the examples.

README.md updated to include basic installation instructions.

Small changes to input files (just formatting)

runs/1D_Cathode/inputCart.json

@@ -30,11 +30,11 @@
   ],
   "boundaryEM": [
     {"name": "Cathode",  "type": "dirichlet", "potential":  -10.0, "physicalSurface": 1},
-    {"name": "Infinit",  "type": "dirichlet", "potential":    0.0, "physicalSurface": 2}
+    {"name": "Infinite", "type": "dirichlet", "potential":    0.0, "physicalSurface": 2}
   ],
   "inject": [
     {"name": "Cathode Electron", "species": "Electron", "flow":  9.0e-5, "units": "A", "v": 27500.0, "T": [2500.0, 2500.0, 2500.0],
-                             "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"],     "n": [ 1, 0, 0], "physicalSurface": 1}
+                                 "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"],     "n": [ 1, 0, 0], "physicalSurface": 1}
   ],
   "case": {
     "tau":  [1.0e-11],

runs/1D_Cathode/inputRad.json

@@ -22,7 +22,7 @@
   ],
   "boundary": [ 
     {"name": "Cathode",  "physicalSurface": 1, "bTypes": [
-                                                 {"type": "absorption"}
+                                                  {"type": "absorption"}
                                                 ]},
     {"name": "Infinite", "physicalSurface": 2, "bTypes": [
                                                   {"type": "transparent"}

runs/ALPHIE_Grid/mesh.geo

@@ -0,0 +1,114 @@
+Lz  = 0.0100;
+Lr  = 0.0006;
+zg1 = 0.0025;
+tg1 = 0.0004;
+rg1 = 0.0005;
+dg  = 0.0025;
+zg2 = zg1+tg1+dg;
+tg2 = tg1;
+rg2 = rg1;
+
+Lcell = 0.0001;
+
+Point(1)  = {      0,     0,     0, 1};
+Point(2)  = {    zg1,     0,     0, 1};
+Point(3)  = {zg1+tg1,     0,     0, 1};
+Point(4)  = {    zg2,     0,     0, 1};
+Point(5)  = {zg2+tg2,     0,     0, 1};
+Point(6)  = {     Lz,     0,     0, 1};
+Point(7)  = {     Lz,   rg2,     0, 1};
+Point(8)  = {     Lz,    Lr,     0, 1};
+Point(9)  = {zg2+tg2,    Lr,     0, 1};
+Point(10) = {zg2+tg2,   rg2,     0, 1};
+Point(11) = {    zg2,   rg2,     0, 1};
+Point(12) = {    zg2,    Lr,     0, 1};
+Point(13) = {zg1+tg1,    Lr,     0, 1};
+Point(14) = {zg1+tg1,   rg1,     0, 1};
+Point(15) = {    zg1,   rg1,     0, 1};
+Point(16) = {    zg1,    Lr,     0, 1};
+Point(17) = {      0,    Lr,     0, 1};
+Point(18) = {      0,   rg1,     0, 1};
+
+Line(1)  = {1,  2};
+Line(2)  = {2,  3};
+Line(3)  = {3,  4};
+Line(4)  = {4,  5};
+Line(5)  = {5,  6};
+Line(6)  = {6,  7};
+Line(7)  = {7,  8};
+Line(8)  = {8,  9};
+Line(9)  = {9,  10};
+Line(10) = {10, 11};
+Line(11) = {11, 12};
+Line(12) = {12, 13};
+Line(13) = {13, 14};
+Line(14) = {14, 15};
+Line(15) = {15, 16};
+Line(16) = {16, 17};
+Line(17) = {17, 18};
+Line(18) = {18, 1};
+Line(19) = {2,  15};
+Line(20) = {3,  14};
+Line(21) = {4,  11};
+Line(22) = {5,  10};
+Line(23) = {10, 7};
+Line(24) = {14, 11};
+Line(25) = {18, 15};
+
+Line Loop(1) = {1, 19, -25, 18};
+Plane Surface(1) = {1};
+Line Loop(2) = {2, 20,  14,-19};
+Plane Surface(2) = {2};
+Line Loop(3) = {3, 21, -24,-20};
+Plane Surface(3) = {3};
+Line Loop(4) = {4, 22,  10,-21};
+Plane Surface(4) = {4};
+Line Loop(5) = {5,  6, -23,-22};
+Plane Surface(5) = {5};
+Line Loop(6) = {23, 7,   8,  9};
+Plane Surface(6) = {6};
+Line Loop(7) = {24, 11, 12, 13};
+Plane Surface(7) = {7};
+Line Loop(8) = {25, 15, 16, 17};
+Plane Surface(8) = {8};
+
+Physical Line(1) = {18, 17};
+Physical Line(2) = {6, 7};
+Physical Line(3) = {16, 12, 8};
+Physical Line(4) = {15, 14, 13};
+Physical Line(5) = {11, 10, 9};
+Physical Line(6) = {1, 2, 3, 4, 5};
+
+Physical Surface(1) = {1};
+Physical Surface(2) = {2};
+Physical Surface(3) = {3};
+Physical Surface(4) = {4};
+Physical Surface(5) = {5};
+Physical Surface(6) = {6};
+Physical Surface(7) = {7};
+Physical Surface(8) = {8};
+
+Transfinite Line {1, 25, 16} = zg1/Lcell + 1 Using Progression 1;
+Transfinite Line {2, 14, 4, 10} = tg1/Lcell + 1 Using Progression 1;
+Transfinite Line {3, 24, 12} = dg/Lcell + 1 Using Progression 1;
+Transfinite Line {5, 23, 8}  = (Lz-tg2-zg2)/Lcell + 1 Using Progression 1;
+Transfinite Line {18, 19, 20, 21, 22, 6} = rg1/Lcell + 1 Using Progression 1;
+Transfinite Line {17, 15, 13, 11, 9, 7}  = (Lr-rg1)/Lcell + 1 Using Progression 1;
+
+
+#Transfinite Surface{1};
+#Recombine Surface {1};
+#Transfinite Surface{2};
+#Recombine Surface {2};
+#Transfinite Surface{3};
+#Recombine Surface {3};
+#Transfinite Surface{4};
+#Recombine Surface {4};
+#Transfinite Surface{5};
+#Recombine Surface {5};
+#Transfinite Surface{6};
+#Recombine Surface {6};
+#Transfinite Surface{7};
+#Recombine Surface {7};
+#Transfinite Surface{8};
+#Recombine Surface {8};