New input file sections in the user manual

doc/user-manual/fpakc_UserManual.tex

@@ -502,39 +502,40 @@ make
         \end{itemize}
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-      \subsection{boundary}
+      \subsection{boundaries}
-        The array object \textbf{boundary} determines the interaction between surfaces and particles.
+        The object \textbf{boundaries} has two main arrays that define the particle boundaries and the ones that must be applied to the electromagnetic field.
-        These boundaries need to be linked to a specific edge in the mesh.
+        \begin{itemize}
-        The accepted variables are:
+        \item \textbf{particles}. Array of objects.
+          Different models for interaction between particles and edges.
           \begin{itemize}
             \item \textbf{name}: Character.
               Name of the boundary.
-          \item \textbf{physicalSurface}: Integer.
+            \item \textbf{type}: Character.
-                                          Identification of the surface in the mesh file.
+              Model for the interaction between particles and the edge.
-          \item \textbf{bType}: Array of objects of dimension 'number of species'.
+              Available options are:
-                                Per each species defined in the case, a boundary \textbf{type} needs to be provided.
-                                Accepted values for \textbf{type} are:
               \begin{itemize}
                 \item \textbf{reflection}: Elastic reflection of particles.
                 \item \textbf{absorption}: Particle is eliminated from the domain.
                   The particle is first moved into the edge and its properties are scattered among the edge nodes.
                 \item \textbf{transparent}: Particle abandon the numerical domain.                  
+                \item \textbf{axis}: Identifies the symmetry axis for 2D cylindrical simulations.
+                  If , for some reason, a particle interacts with this axis, it is reflected.
                 \item \textbf{wallTemperature}: Reflective wall with constant temperature that exchange heat with particles.
                 Required parameters are:
-                                                                  \begin{itemize}
+                
-                                                                    \item \textbf{temperature}: Real.
+                \textbf{temperature}: Real.
                   Units of $\unit{K}$.
                   Temperature wall.
-                                                                    \item \textbf{specificHeat}: Real.
+                  
+                \textbf{specificHeat}: Real.
                    Units of $\unit{J kg^{-1} K^{-1}}$.
                    Specific heat capacity of the material.
-                                                                  \end{itemize}
+                   
                 \item \textbf{ionization}: Per each particle crossing the surface with this type of boundary, a number of ionization events are calculated.
                   A pair of ion-electron is generated for each ionization event, taking as a reference a neutral background.
-                                                             The secondary electron is taken as the same type as the incident particle.
                   The available input is:
-                                                             \begin{itemize}
+                  
-                                                               \item \textbf{neutral}: Object.
+                  \textbf{neutral}: Object.
                     Information about the neutral background.
                     Required parameters are:
                     \begin{itemize}
@@ -558,28 +559,27 @@ make
                         Units in $\unit{K}$.
                         Temperature of neutral background.
                         Required parameter.                        
-                                                                                                              
                     \end{itemize}
-                                                               \item \textbf{effectiveTime}: Real.
+                    
+                  \textbf{effectiveTime}: Real.
                     Units in $\unit{s}$.
                     As the particle is no longer simulated once it crossed the boundary, this time represents the effective time in which the particle produces ionization processes in the neutral background.
                     Required parameter.
-                                                               \item \textbf{energyThreashold}: Real.
+                    
+                  \textbf{energyThreashold}: Real.
                     Units in $\unit{eV}$.
                     Ionization energy threshold for the simulated process.
                     Required parameter.
-                                                               \item \textbf{crossSection}: Character.
+                    
+                  \textbf{electronSecondary}. Character.
+                    Name of the species for the secondary electrons produced.
+                    I none is provided, the input species is used.
+                    
+                  \textbf{crossSection}: Character.
                     Complete path to the cross-section data for the ionization process.
-                                                                                             
-                                                             \end{itemize}
-                                  \item \textbf{axis}: Identifies the symmetry axis for 2D cylindrical simulations.
-                                                       If , for some reason, a particle interacts with this axis, it is reflected.
             \end{itemize}
           \end{itemize}
-      
+        \item \textbf{EM}. Array of objects.determines the boundary conditions for the electromagnetic field.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-      \subsection{boundaryEM}
-        The array object \textbf{boundaryEM} determines the boundary conditions for the electromagnetic field.
           As with the \textbf{boundary} definition, these must be linked to an edge identified in the mesh file.
           The variables for each array element are:
           \begin{itemize}
@@ -590,21 +590,44 @@ make
               Accepted values are:
               \begin{itemize}
                 \item \textbf{dirichlet}: Constant value of electric potential on the surface.
-                                 \item \textbf{dirichletTime}: Constant value of the electric potential with a time variable profile.
+                  Required values are:
-                                                               The value of \textbf{boundaryEM.potential} will be multiplied for the corresponding value in the file \textbf{boundaryEM.temporalProfile}.
+                
-                                \end{itemize}
+                  \textbf{potential}: Real.
-          \item \textbf{potential}: Real.
                   Fixed potential for Dirichlet boundary condition.
-          \item \textbf{physicalSurface}: Integer.
+                  
-                                          Identification of the edge in the mesh file.
+                \item \textbf{dirichletTime}: Constant value of the electric potential with a time variable profile.
-          \item \textbf{temporalProfile}: Character.
+                  Required values are:
+                                   
+                  \textbf{potential}: Real.
+                  Potential for Dirichlet boundary condition.
+                   
+                  \textbf{temporalProfile}: Character.
                     Filename of the 2 column file containing the time variable profile.
                     File must be located in \textbf{output.path}.
                     The first column is the time in $\unit{s}$.
-                                          The second column is the factor that will multiply the value of the boundary.
+                    The second column is the factor that will multiply the value set in \textbf{potential}.
                      
               \end{itemize}
           
+          \end{itemize}
+          
+        \end{itemize}
+      
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+      \subsection{physicalSurfaces}
+        Array of objects that links the named surfaces of the mesh to the models in \textbf{boundaries.particles} and \textbf{boundaries.EM}.
+        Each element of the array has the following items:
+        \begin{itemize}
+          \item \textbf{index}. Integer.
+            Index of the edge surface as defined in the mesh file.
+          \item \textbf{particles}. Array of characters.
+            Size equal to the number of species.
+            Each element of the array is the name of the \textbf{boundaries.particles} that the species will experience when interacting with the edge in this physical surface.
+          \item \textbf{EM}. Character.
+            Name of the model in \textbf{boundaries.EM}.
+            If none is provided, the default reflection boundary condition is applied.
+        \end{itemize}
+
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       \subsection{inject}
         The array \textbf{inject} specifies the injection of particles from different surfaces.