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)

README.md

@@ -13,8 +13,36 @@ The codefpakc makes use of finite elements to generate meshes in complex geometr
 
 # User Manual
 
-You will find the user manual in the *doc* folder.
+You will find the user manual in the *doc/user-manual/* folder. It contains information about the installation of fpkac, how to run the software, the example cases distributed with the code and how the code operates.
 
 # Installation
 
-To install the software ...
+Once you have been added to the fpakc gitlab repository, and have added an ssh key to your account, you will be able to clone the repository using:
+```
+git clone git@gitlab.com:<YourGitLabUsername>/fpakc.git
+```
+in which you have to substitute `<YourGitLabUsername>` for your gitlab username.
+
+Go into the new downloaded directory with
+```
+cd fpakc
+```
+Clone the json-fortran repository with:
+```
+git clone https://github.com/jacobwilliams/json-fortran.git
+```
+This will create the  `json-fortran-8.2.0` directory. Go into this new folder and create a new `build-gfortran` directory, enter it and execute:
+```
+cmake ../
+```
+Once it finish, just compile the json-fortran library with
+```
+make
+```
+This creates the `include` and `lib` folders that contain the required files for fpakc compilation.
+
+Go back to the fpakc root folder and execute
+```
+make
+```
+to compile the code. If everything is correct, an executable named `fpakc` will be generated.

doc/user-manual/fpakc_UserManual.tex

@@ -175,15 +175,25 @@
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{Elastic collision}
+        In this type of collision, particles exchange energy due to hard-sphere model.
+        Total energy is conserved.
+        Resulting velocity directions are chosen from Maxwellian distribution functions.
+        This interaction is useful for short-range collisions as neutral-neutral and charged-neutral elastic collisions.
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{Charge Exchange}
+        When an ion interacts with a neutral particle, an electron is exchanged between the two particles with no exchange of energy.
+        This is called a resonant charge-exchange.
         
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-      \subsection{Ionization}
+      \subsection{Electron Impact Ionization}
+        When the relative energy between a neutral and an electron is above the ionization threshold, there is a probability that the neutral particle will become ionized.
+        This ionization emits and additional electron
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{Recombination}
+        When an electron and an ion interact, there is a possibility for them to be recombined into a neutral particle.
+        The photon emitted by this process is not modeled yet.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Scattering}
@@ -269,9 +279,10 @@ make
     \section{Running the code}
       To run a case, simply execute:
       \begin{lstlisting}
-./fpakc path-to-input-file.json
+./fpakc path/to/input-file.json
       \end{lstlisting}
-  	  in a command line.
+  	  in a command line from the root \acrshort{fpakc} folder.
+      Substitute \lstinline|path/to/input-file.json| with the path to the input file of the case you want to run.
       The examples in the run directory are presented in Chapter \ref{ch:exampleRuns}.
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -578,12 +589,20 @@ make
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   \chapter{Example runs\label{ch:exampleRuns}}
     \section{1D Cathode}
+      Emission from a 1D cathond in both, cartesian and radial coordinates.
+      Both cases insert the same amount of electrons from the minimum coordinate and have the same boundary conditions for particles and the electrostatic field.
+      This case is useful to ilustrate hoy \acrshort{fpakc} can deal with different geometries by just modifiying some parameters in the input file.
+      The same mesh file (\lstinline|mesh.msh|) is used for both cases.
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{ALPHIE Grid system}
+      Two-dimensional axialsymmetry case to study the counterflow of electrons and Argon ions going trhough the ALPHIE grid system.
+      A \lstinline|mesh.geo| file is provided to easily modify the parameters of the grid system and generate a new mesh with \Gls{gmsh}.
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Flow around cylinder}
+      Simple case of neutral Argon flow around a cylinder in a 2D axialsymmetry geometry.
+      Elastic collisions between argon particles are included as default.
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   \printglossaries

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};