Adjusted initial condition, dimensions of output, and output file header

Now it is uses the text mesh format.
All output files are now included as they are simple csv files easy to
understand.

doc/user-manual/fpakc_UserManual.tex

@@ -48,8 +48,9 @@
 \newglossaryentry{openblas}{name={OpenBLAS},description={Open-source implementation of BLAS and LAPACK APIs}}
 \newglossaryentry{git}{name={Git},description={Git is a distributed version-control system for tracking changes in a set of files}}
 \newglossaryentry{gitlab}{name={GitLab},description={GitLab is a web-based lifecycle tool that provides a \Gls{git}-repository manager}}
-\newglossaryentry{gmsh}{name={Gmsh},description={A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities.}}
+\newglossaryentry{gmsh}{name={Gmsh},description={A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities}}
-\newglossaryentry{gnuplot}{name={Gnuplot},description={A portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.}}
+\newglossaryentry{gnuplot}{name={Gnuplot},description={A portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms}}
+\newglossaryentry{paraview}{name={ParaView},description={Tool for post-processing and visualizing data from various formats like vtu}}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \bibliography{bibliography}
@@ -397,6 +398,12 @@ make
                                   Trigger between writings is the same as in \textbf{triggerOutput}.
           \item \textbf{EMField}: Logical.
                                   Determines if the electromagnetic field is printed.
+          \item \textbf{bounraiesParticle}: Logical.
+                                            Determines if the properties of the boundaries are written.
+                                            \textit{Warning}: Not all particle models produce this output, only those whose properties change during the simulation.
+          \item \textbf{injects}: Logical.
+                                  Determines if the properties of the injection of particles are written.
+                                  \textit{Warning}: Not all injection types produce this output, only those whose properties change during the simulation.
           \item \textbf{probes}: Array of objects.
                                  Defines the probes employed for obtaining the distribution function at specific positions.
                                  See Sec.~\ref{sec:probing} for more information.
@@ -502,39 +509,40 @@ 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 +566,40 @@ 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{quasiNeutrality}: Maintains equal density between the species defined by the \textbf{incident} parameter and the others in the case by modifying the reflection coefficient and reflecting incident particles of the species.
-                                  \item \textbf{axis}: Identifies the symmetry axis for 2D cylindrical simulations.
+              The required input is:
-                                                       If , for some reason, a particle interacts with this axis, it is reflected.
-                                \end{itemize}
-        \end{itemize}
                 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+                \textbf{incident}: Character.
-      \subsection{boundaryEM}
+                  Name of the incident species that will be reflected.
-        The array object \textbf{boundaryEM} determines the boundary conditions for the electromagnetic field.
+                    
+              \item \textbf{outflowAdaptive}: Changes the velocity of the reflected particles in the species defined by the \textbf{incident} parameter to maintain the mean velocity equal to the average mean velocity of the others in the case.
+              The required input is:
+                
+                \textbf{incident}: Character.
+                  Name of the incident species that will be reflected.
+                  
+            \end{itemize}
+          \end{itemize}
+        \item \textbf{EM}. Array of objects.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}
@@ -590,19 +610,51 @@ 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}.
                     
+                 \item \textbf{floating}: The potential is adjusted over time to maintain a zero current on the surface, \textit{i. e.}, the surface is \textit{floating}.                                   
+                   \textbf{potential}: Real.
+                     Initial potential of the surface.
+                     The initial charge value for the simulation will be calculated by the potential times the capacitance.
+                   
+                   \textbf{capacitance}: Real.
+                     Capacitance of the surface in Farads.
+                     If none is provided, a default value of $1$ nF is used.
+                     
+              \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}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -648,6 +700,14 @@ make
                             Units of $\unit{K}$
                             Array dimension $3$.
                             Temperature in each direction.
+          \item \textbf{type}: Character.
+                               Type of injection.
+                               Available values are:
+                               \begin{itemize}
+                               \item \textbf{constant}: The flow does not change.
+                                 This is the default value if none is provided.
+                               \item \textbf{quasiNeutral}: The weight of the injected species' particles is changed over time to keep a zero electric field at the boundary.
+                               \end{itemize}
           \item \textbf{physicalSurface}: Integer.
                                           Identification of the edge in the mesh file.
           \item \textbf{particlesPerEdge}: Integer.
@@ -823,14 +883,14 @@ make
   \chapter{Example runs}\label{ch:exampleRuns}
     This chapter presents a description of the different example files distributed with \acrshort{fpakc}.
     All examples in the repository have a \lstinline|README.txt| file and a reference output.
-    Plotting of the output is done with \Gls{gnuplot} or \Gls{gmsh}.
+    Plotting of the output is done with \Gls{gnuplot} or \Gls{paraview}.
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{1D Emissive Cathode (1D\_Cathode)}
       Emission from a 1D cathode in both, Cartesian and radial coordinates.
       Both cases insert the same number of electrons from the minimum coordinate and have the same boundary conditions for particles and the electrostatic field.
       This case is useful to illustrate how \acrshort{fpakc} can deal with different geometries by just modifying some parameters in the input file.
-      The same mesh file (\lstinline|mesh.msh|) is used for both cases.
+      The same mesh file (\lstinline|mesh.csv|) is used for both cases.
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{0D \ce{Ar}-\ce{Ar+} Elastic Collision (0D\_Argon)}

runs/0D_Argon/input.json

@@ -4,7 +4,7 @@
     "path": "./runs/0D_Argon/",
     "triggerOutput": 1,
     "numColl": true,
-	"folder": "test"
+	"folder": "output"
   },
   "reference": {
     "density": 1.0e16,

runs/0D_Argon/output/reference.csv

@@ -0,0 +1,2 @@
+"L_ref","v_ref","ti_ref","Vol_ref","EF_ref","Volt_ref","B_ref"
+7.433780E-005,1.554141E+003,4.783208E-008,4.107987E-013,1.345150E+004,9.999550E-001,8.655264E+000

runs/1D_Cathode/README.txt

@@ -6,3 +6,5 @@ The electric potential at the left is fixed at 0.
 Depending on the geometry (which affects the symmetry) different distributions of the electron density and electric potential are achieved.
 
 The last iteration obtained for these cases is in the output folder.
+
+The case uses the simple 1D text mesh format so it is easier to plot by novel users.

runs/1D_Cathode/inputCart.json

@@ -1,4 +1,3 @@
-
 {
   "output": {
     "path": "./runs/1D_Cathode/",
@@ -16,22 +15,24 @@
   "geometry": {
     "dimension": 1,
     "type":     "Cart",
-    "meshType": "gmsh2",
+    "meshType": "text",
-    "meshFile": "mesh.msh"
+    "meshFile": "mesh.csv"
   },
   "species": [
     {"name": "Electron", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e1}
   ],
-  "boundary": [ 
+  "boundaries": { 
-    {"name": "Cathode",  "physicalSurface": 1, "bTypes": [
+    "particles": [
-                                                  {"type": "absorption"}
+      {"name": "Infinite", "type": "transparent"},
-                                                ]},
+      {"name": "Cathode",  "type": "absorption"}
-    {"name": "Infinite", "physicalSurface": 2, "bTypes": [
-                                                  {"type": "transparent"}
-                                                ]}
     ],
-  "boundaryEM": [
+    "EM": [
-    {"name": "Cathode",  "type": "dirichlet", "potential": 0.0, "physicalSurface": 1}
+      {"name": "Cathode", "type": "dirichlet", "potential": 0.0}
+    ]
+  },
+  "physicalSurfaces": [
+    {"index": 1, "particles":["Cathode"], "EM": "Cathode"},
+    {"index": 2, "particles":["Infinite"]}
   ],
   "inject": [
     {"name": "Plasma Cat e",     "species": "Electron", "flow":  2.64e-5, "units": "A", "v": 180000.0,   "T": [ 2300.0,  2300.0,  2300.0],

runs/1D_Cathode/inputRad.json

@@ -1,4 +1,3 @@
-
 {
   "output": {
     "path": "./runs/1D_Cathode/",
@@ -16,22 +15,24 @@
   "geometry": {
     "dimension": 1,
     "type":     "Rad",
-    "meshType": "gmsh2",
+    "meshType": "text",
-    "meshFile": "mesh.msh"
+    "meshFile": "mesh.csv"
   },
   "species": [
     {"name": "Electron", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e1}
   ],
-  "boundary": [ 
+  "boundaries": { 
-    {"name": "Cathode",  "physicalSurface": 1, "bTypes": [
+    "particles": [
-                                                  {"type": "absorption"}
+      {"name": "Infinite", "type": "transparent"},
-                                                ]},
+      {"name": "Cathode",  "type": "absorption"}
-    {"name": "Infinite", "physicalSurface": 2, "bTypes": [
-                                                  {"type": "transparent"}
-                                                ]}
     ],
-  "boundaryEM": [
+    "EM": [
-    {"name": "Cathode",  "type": "dirichlet", "potential": 0.0, "physicalSurface": 1}
+      {"name": "Cathode", "type": "dirichlet", "potential": 0.0}
+    ]
+  },
+  "physicalSurfaces": [
+    {"index": 1, "particles":["Cathode"], "EM": "Cathode"},
+    {"index": 2, "particles":["Infinite"]}
   ],
   "inject": [
     {"name": "Plasma Cat e",     "species": "Electron", "flow":  2.64e-5, "units": "A", "v": 180000.0,   "T": [ 2300.0,  2300.0,  2300.0],

runs/1D_Cathode/mesh.csv

@@ -0,0 +1,52 @@
+Position(m),Physical ID
+0.0,1
+4e-05,0
+8e-05,0
+0.00012000000000000002,0
+0.00016,0
+0.0002,0
+0.00024000000000000003,0
+0.00028000000000000003,0
+0.00032,0
+0.00036,0
+0.0004,0
+0.00044,0
+0.00048000000000000007,0
+0.0005200000000000001,0
+0.0005600000000000001,0
+0.0006000000000000001,0
+0.00064,0
+0.00068,0
+0.00072,0
+0.00076,0
+0.0008,0
+0.00084,0
+0.00088,0
+0.00092,0
+0.0009600000000000001,0
+0.001,0
+0.0010400000000000001,0
+0.00108,0
+0.0011200000000000001,0
+0.00116,0
+0.0012000000000000001,0
+0.00124,0
+0.00128,0
+0.0013200000000000002,0
+0.00136,0
+0.0014000000000000002,0
+0.00144,0
+0.0014800000000000002,0
+0.00152,0
+0.0015600000000000002,0
+0.0016,0
+0.0016400000000000002,0
+0.00168,0
+0.0017200000000000002,0
+0.00176,0
+0.0018000000000000002,0
+0.00184,0
+0.0018800000000000002,0
+0.0019200000000000003,0
+0.0019600000000000004,0
+0.002,2

runs/1D_Cathode/mesh.geo

@@ -1,16 +0,0 @@
-Lcell = 4e-5;
-
-x0 = 0.001;
-xf = x0 + 50.0*Lcell;
-
-Point(1) = {x0, 0, 0, 1};
-Point(2) = {xf, 0, 0, 1};
-
-Line(1) = {1, 2};
-
-Physical Point(1) = {1};
-Physical Point(2) = {2};
-
-Physical Line(1) = {1};
-
-Transfinite Line {1} = (xf-x0)/Lcell + 1 Using Progression 1;

runs/1D_Cathode/mesh.msh

@@ -1,112 +0,0 @@
-$MeshFormat
-2.2 0 8
-$EndMeshFormat
-$Nodes
-51
-1 0.001 0 0
-2 0.003 0 0
-3 0.001039999999999907 0 0
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-10 0.001319999999999065 0 0
-11 0.001359999999998992 0 0
-12 0.001399999999998941 0 0
-13 0.00143999999999889 0 0
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-15 0.001519999999998928 0 0
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-20 0.001719999999998316 0 0
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-22 0.00179999999999778 0 0
-23 0.001839999999997513 0 0
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-45 0.002719999999998838 0 0
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-50 0.002919999999999668 0 0
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-$EndNodes
-$Elements
-52
-1 15 2 1 1 1
-2 15 2 2 2 2
-3 1 2 1 1 1 3
-4 1 2 1 1 3 4
-5 1 2 1 1 4 5
-6 1 2 1 1 5 6
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-8 1 2 1 1 7 8
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-49 1 2 1 1 48 49
-50 1 2 1 1 49 50
-51 1 2 1 1 50 51
-52 1 2 1 1 51 2
-$EndElements

runs/1D_Cathode/mesh.py

@@ -0,0 +1,18 @@
+import numpy as np
+import csv
+
+x0 = 0.0
+Dx = 4.0e-5
+xF = x0 + 50.0*Dx
+
+x = np.arange(x0,xF + Dx,Dx)
+p = np.zeros_like(x)
+p[ 0] = 1
+p[-1] = 2
+p = np.int32(p)
+
+with open('mesh.csv', 'w') as csvfile:
+    csvwriter = csv.writer(csvfile)
+    csvwriter.writerow(['Position(m)','Physical ID'])
+    for x_i, p_i in zip(x, p):
+        csvwriter.writerow([x_i,p_i])

runs/1D_Cathode/output/Cartesian/OUTPUT_1000_EMField.msh

@@ -1,185 +0,0 @@
-$MeshFormat
-2.2 0 8
-$EndMeshFormat
-$NodeData
-1
-"Potential (V)"
-           1
-   1.0000000000000000E-008
-           3
-        1000
-           1
-          51
-           1  -7.2180834934653183E-012
-           2  -1.6164415181357834     
-           3 -0.36980461527280883     
-           4 -0.57492573345192088     
-           5 -0.71403100967357258     
-           6 -0.82100545766928923     
-           7 -0.90752842743341133     
-           8 -0.97972921034487059     
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-          50  -1.6160774066120194     
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-$EndNodeData
-$ElementData
-1
-"Electric Field (V m^-1)"
-           1
-   1.0000000000000000E-008
-           3
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runs/1D_Cathode/output/Cartesian/Step_0000_Electron.csv

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runs/1D_Cathode/output/Cartesian/Step_0100_EMField.csv

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runs/1D_Cathode/output/Cartesian/Step_0100_Electron.csv

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runs/1D_Cathode/output/Cartesian/Step_0200_Electron.csv

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runs/1D_Cathode/output/Cartesian/Step_0300_Electron.csv

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runs/1D_Cathode/output/Cartesian/Step_0400_EMField.csv

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runs/1D_Cathode/output/Cartesian/Step_0400_Electron.csv

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runs/1D_Cathode/output/Cartesian/Step_0500_EMField.csv

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runs/1D_Cathode/output/Cartesian/Step_0600_EMField.csv

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runs/1D_Cathode/output/Cartesian/Step_0600_Electron.csv

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runs/1D_Cathode/output/Cartesian/Step_0900_EMField.csv

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runs/1D_Cathode/output/Cartesian/Step_1000_EMField.csv

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runs/1D_Cathode/output/Cartesian/Step_1000_Electron.csv

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runs/1D_Cathode/output/Cartesian/fpakc_commit.txt

@@ -0,0 +1 @@
+aad8675214c5d0687b31525ee99e2a4da16bd66c

runs/1D_Cathode/output/Cartesian/inputCart.json

@@ -0,0 +1,52 @@
+{
+  "output": {
+    "path": "./runs/1D_Cathode/",
+    "triggerOutput": 100,
+    "cpuTime": false,
+    "numColl": false,
+    "EMField": true,
+	"folder": "Cartesian_Emision"
+  },
+  "reference": {
+    "density": 1.0e16,
+    "mass": 9.109e-31,
+    "temperature": 11604.0
+  },
+  "geometry": {
+    "dimension": 1,
+    "type":     "Cart",
+    "meshType": "text",
+    "meshFile": "mesh.csv"
+  },
+  "species": [
+    {"name": "Electron", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e1}
+  ],
+  "boundaries": { 
+    "particles": [
+      {"name": "Infinite", "type": "transparent"},
+      {"name": "Cathode",  "type": "absorption"}
+    ],
+    "EM": [
+      {"name": "Cathode", "type": "dirichlet", "potential": 0.0}
+    ]
+  },
+  "physicalSurfaces": [
+    {"index": 1, "particles":["Cathode"], "EM": "Cathode"},
+    {"index": 2, "particles":["Infinite"]}
+  ],
+  "inject": [
+    {"name": "Plasma Cat e",     "species": "Electron", "flow":  2.64e-5, "units": "A", "v": 180000.0,   "T": [ 2300.0,  2300.0,  2300.0],
+                                 "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"],     "n": [ 1, 0, 0], "physicalSurface": 1}
+  ],
+  "solver": {
+    "tau":  [1.0e-11],
+    "finalTime": 1.0e-8,
+    "pusher": ["Electrostatic"],
+    "EMSolver": "Electrostatic"
+  },
+  "parallel": {
+    "OpenMP":{
+      "nThreads": 24
+    }
+  }
+}

runs/1D_Cathode/output/Cartesian/mesh.csv

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runs/1D_Cathode/output/Cartesian/reference.txt

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runs/1D_Cathode/output/Radial/Step_0000_Electron.csv

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runs/1D_Cathode/output/Radial/Step_0100_EMField.csv

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runs/1D_Cathode/output/Radial/Step_0100_Electron.csv

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runs/1D_Cathode/output/Radial/Step_0200_EMField.csv

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runs/1D_Cathode/output/Radial/Step_0200_Electron.csv

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runs/1D_Cathode/output/Radial/Step_0300_EMField.csv

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runs/1D_Cathode/output/Radial/Step_0300_Electron.csv

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runs/1D_Cathode/output/Radial/Step_0400_EMField.csv

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runs/1D_Cathode/output/Radial/Step_0400_Electron.csv

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runs/1D_Cathode/output/Radial/Step_0500_EMField.csv

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runs/1D_Cathode/output/Radial/Step_0500_Electron.csv

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runs/1D_Cathode/output/Radial/Step_0600_EMField.csv

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runs/1D_Cathode/output/Radial/Step_0600_Electron.csv

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runs/1D_Cathode/output/Radial/Step_0700_Electron.csv

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runs/1D_Cathode/output/Radial/Step_0800_Electron.csv

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runs/1D_Cathode/output/Radial/Step_0900_EMField.csv

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runs/1D_Cathode/output/Radial/Step_0900_Electron.csv

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runs/1D_Cathode/output/Radial/Step_1000_EMField.csv

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runs/1D_Cathode/output/Radial/Step_1000_Electron.csv

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+1.320000E-003,3.326867E+014,7.657469E+005,2.719951E-018,8.882043E+003,1.170748E+004
+1.360000E-003,3.055893E+014,7.970009E+005,3.863130E-016,-9.690819E+003,1.230068E+004
+1.400000E-003,3.227631E+014,7.986735E+005,-2.151469E-015,-2.494191E+003,1.166256E+004
+1.440000E-003,3.476931E+014,7.978323E+005,-9.198550E-016,2.777560E+003,1.127932E+004
+1.480000E-003,3.196409E+014,8.029631E+005,1.320223E-015,-5.330939E+003,1.029915E+004
+1.520000E-003,2.642317E+014,8.367782E+005,-1.845304E-015,-4.416563E+002,1.113199E+004
+1.560000E-003,2.678612E+014,8.271731E+005,1.238576E-015,2.380002E+003,1.077492E+004
+1.600000E-003,3.152970E+014,8.076487E+005,2.687690E-015,-2.734815E+003,9.664299E+003
+1.640000E-003,3.059683E+014,8.064795E+005,5.573429E-016,9.746938E+003,9.877775E+003
+1.680000E-003,2.507051E+014,8.619481E+005,-1.474062E-016,2.706734E+003,1.078358E+004
+1.720000E-003,2.306909E+014,8.214948E+005,3.370102E-016,7.920330E+003,1.111977E+004
+1.760000E-003,2.384336E+014,8.336226E+005,1.406120E-015,2.366996E+003,1.048286E+004
+1.800000E-003,2.576236E+014,7.991929E+005,9.394993E-016,-1.060375E+004,9.762269E+003
+1.840000E-003,2.401037E+014,8.423997E+005,1.606733E-015,-4.937150E+003,9.396222E+003
+1.880000E-003,2.254228E+014,8.600299E+005,7.039336E-016,9.942406E+003,9.500592E+003
+1.920000E-003,2.216428E+014,8.377193E+005,-1.062326E-015,2.887613E+003,9.405017E+003
+1.960000E-003,1.999006E+014,8.483726E+005,1.324557E-016,-3.679752E+003,8.699932E+003
+2.000000E-003,1.845568E+014,9.066756E+005,-1.793918E-015,6.439464E+003,9.004040E+003

runs/1D_Cathode/output/Radial/fpakc_commit.txt

@@ -0,0 +1 @@
+aad8675214c5d0687b31525ee99e2a4da16bd66c

runs/1D_Cathode/output/Radial/inputRad.json

@@ -0,0 +1,52 @@
+{
+  "output": {
+    "path": "./runs/1D_Cathode/",
+    "triggerOutput": 100,
+    "cpuTime": false,
+    "numColl": false,
+    "EMField": true,
+	"folder": "Radial_Emission"
+  },
+  "reference": {
+    "density": 1.0e16,
+    "mass": 9.109e-31,
+    "temperature": 11604.0
+  },
+  "geometry": {
+    "dimension": 1,
+    "type":     "Rad",
+    "meshType": "text",
+    "meshFile": "mesh.csv"
+  },
+  "species": [
+    {"name": "Electron", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e1}
+  ],
+  "boundaries": { 
+    "particles": [
+      {"name": "Infinite", "type": "transparent"},
+      {"name": "Cathode",  "type": "absorption"}
+    ],
+    "EM": [
+      {"name": "Cathode", "type": "dirichlet", "potential": 0.0}
+    ]
+  },
+  "physicalSurfaces": [
+    {"index": 1, "particles":["Cathode"], "EM": "Cathode"},
+    {"index": 2, "particles":["Infinite"]}
+  ],
+  "inject": [
+    {"name": "Plasma Cat e",     "species": "Electron", "flow":  2.64e-5, "units": "A", "v": 180000.0,   "T": [ 2300.0,  2300.0,  2300.0],
+                                 "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"],     "n": [ 1, 0, 0], "physicalSurface": 1}
+  ],
+  "solver": {
+    "tau":  [1.0e-11],
+    "finalTime": 1.0e-8,
+    "pusher": ["Electrostatic"],
+    "EMSolver": "Electrostatic"
+  },
+  "parallel": {
+    "OpenMP":{
+      "nThreads": 24
+    }
+  }
+}

runs/1D_Cathode/output/Radial/mesh.csv

@@ -0,0 +1,52 @@
+Position(m),Physical ID
+0.0,1
+4e-05,0
+8e-05,0
+0.00012000000000000002,0
+0.00016,0
+0.0002,0
+0.00024000000000000003,0
+0.00028000000000000003,0
+0.00032,0
+0.00036,0
+0.0004,0
+0.00044,0
+0.00048000000000000007,0
+0.0005200000000000001,0
+0.0005600000000000001,0
+0.0006000000000000001,0
+0.00064,0
+0.00068,0
+0.00072,0
+0.00076,0
+0.0008,0
+0.00084,0
+0.00088,0
+0.00092,0
+0.0009600000000000001,0
+0.001,0
+0.0010400000000000001,0
+0.00108,0
+0.0011200000000000001,0
+0.00116,0
+0.0012000000000000001,0
+0.00124,0
+0.00128,0
+0.0013200000000000002,0
+0.00136,0
+0.0014000000000000002,0
+0.00144,0
+0.0014800000000000002,0
+0.00152,0
+0.0015600000000000002,0
+0.0016,0
+0.0016400000000000002,0
+0.00168,0
+0.0017200000000000002,0
+0.00176,0
+0.0018000000000000002,0
+0.00184,0
+0.0018800000000000002,0
+0.0019200000000000003,0
+0.0019600000000000004,0
+0.002,2

runs/1D_Cathode/output/Radial/reference.txt

@@ -0,0 +1,2 @@
+                L_ref                v_ref               ti_ref              Vol_ref               EF_ref             Volt_ref                B_ref
+        7.433780E-005        4.193823E+005        1.772555E-010        4.107987E-013        1.345150E+004        9.999550E-001        3.207456E-002

runs/ALPHIE_Grid/README.txt

@@ -5,3 +5,4 @@ The file mesh.geo can be easily modified to generate new grids to test different
 Two cases are provided:
   Clasical case in which ions and electrons are input from the ionization chamber.
   Ionization case in which ion-electron pairs are generated due to the influx of electrons using the Ionization boundary condition.
+    To have the electrons produced by this boundary as a different species add "electronSecondary": "eSec" at the definition of the boundary model.

runs/ALPHIE_Grid/inputBaseCase.json

@@ -10,66 +10,58 @@
   "geometry": {
     "dimension": 2,
     "type":     "Cyl",
-    "meshType": "gmsh2",
+    "meshType": "vtu",
-    "meshFile": "mesh.msh"
+    "meshFile": "mesh.vtu"
   },
   "species": [
-    {"name": "Argon+",   "type": "charged", "mass": 6.633e-26, "charge": 1.0, "weight": 1.0e1},
+    {"name": "Ar+",  "type": "charged", "mass": 6.633e-26, "charge": 1.0, "weight": 1.0e1},
-    {"name": "Electron", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e2}
+    {"name": "e",    "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e1},
+    {"name": "eSec", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e1}
   ],
-  "boundary": [ 
+  "boundaries": {
-    {"name": "Ionization Chanber", "physicalSurface": 1, "bTypes": [
+    "particles": [
-                                                           {"type": "transparent"},
+      {"name": "Transparent", "type": "transparent"},
-                                                           {"type": "transparent"}
+      {"name": "Reflection",  "type": "reflection"},
-                                                          ]},
+      {"name": "Absorption",  "type": "absorption"},
-    {"name": "Vacuum Chamber",     "physicalSurface": 2, "bTypes": [
+      {"name": "Axis",        "type": "axis"}
-                                                           {"type": "transparent"},
-                                                           {"type": "transparent"}
-                                                          ]},
-    {"name": "Exterior",           "physicalSurface": 3, "bTypes": [
-                                                           {"type": "reflection"},
-                                                           {"type": "reflection"}
-                                                          ]},
-    {"name": "Grid Extraction",    "physicalSurface": 4, "bTypes": [
-                                                           {"type": "absorption"},
-                                                           {"type": "absorption"}
-                                                          ]},
-    {"name": "Grid Acceleration",  "physicalSurface": 5, "bTypes": [
-                                                           {"type": "absorption"},
-                                                           {"type": "absorption"}
-                                                          ]},
-    {"name": "Axis",               "physicalSurface": 6, "bTypes": [
-                                                           {"type": "axis"},
-                                                           {"type": "axis"}
-                                                          ]}
     ],
-  "boundaryEM": [
+    "EM": [
-    {"name": "Extraction Grid",    "type": "dirichlet", "potential": -150.0, "physicalSurface": 4},
+      {"name": "Extraction Grid",    "type": "dirichlet", "potential": -150.0},
-    {"name": "Acceleration Grid",  "type": "dirichlet", "potential": -600.0, "physicalSurface": 5},
+      {"name": "Cover Grid",         "type": "dirichlet", "potential": -600.0},
-    {"name": "Ionization Chamber", "type": "dirichlet", "potential":    0.0, "physicalSurface": 1},
+      {"name": "Ionization Chamber", "type": "dirichlet", "potential":    0.0}
-    {"name": "Infinite",           "type": "dirichlet", "potential": -600.0, "physicalSurface": 2}
+    ]
+  },
+  "physicalSurfaces": [
+    {"index": 1, "particles": ["Transparent", "Transparent", "Transparent"], "EM": "Ionization Chamber"},
+    {"index": 2, "particles": ["Transparent", "Transparent", "Transparent"]},
+    {"index": 3, "particles": ["Reflection",  "Reflection",  "Reflection"]},
+    {"index": 4, "particles": ["Absorption",  "Absorption",  "Absorption"], "EM": "Extraction Grid"},
+    {"index": 5, "particles": ["Absorption",  "Absorption",  "Absorption"], "EM": "Cover Grid"},
+    {"index": 6, "particles": ["Axis",        "Axis",        "Axis"]}
   ],
   "inject": [
-    {"name": "Ionization Argon+",   "species": "Argon+",   "flow":  1.0e-5, "units": "A", "v":   2500.0, "T": [ 500.0,  500.0,  500.0],
+    {"name": "Cathode",             "species": "e",    "flow":  1.0e-4, "units": "A", "v":   0.0, "T": [11604.5, 11604.5, 11604.5],
-                                    "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [ 1, 0, 0], "physicalSurface": 1},
+                                    "velDist": ["Half-Maxwellian", "Maxwellian", "Maxwellian"], "n": [-1, 0, 0], "physicalSurface": 2, "particlesPerEdge": 20},
-    {"name": "Ionization Electron", "species": "Electron", "flow":  1.0e-5, "units": "A", "v":  87000.0, "T": [30000.0, 30000.0, 30000.0],
+    {"name": "Ionization Argon+",   "species": "Ar+",  "flow":  1.0e-5, "units": "A", "v": 300.0, "T": [ 500.0,  500.0,  500.0],
-                                    "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [ 1, 0, 0], "physicalSurface": 1},
+                                    "velDist": ["Maxwellian",      "Maxwellian", "Maxwellian"], "n": [ 1, 0, 0], "physicalSurface": 1, "particlesPerEdge":  5},
-    {"name": "Cathode Electron",    "species": "Electron", "flow":  1.0e-4, "units": "A", "v":  87000.0, "T": [30000.0, 30000.0, 30000.0],
+    {"name": "Ionization Electron", "species": "eSec", "flow":  4.2e-5, "units": "A", "v":   0.0, "T": [11604.5, 11604.5, 11604.5],
-                                    "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [-1, 0, 0], "physicalSurface": 2}
+                                    "velDist": ["Half-Maxwellian", "Maxwellian", "Maxwellian"], "n": [ 1, 0, 0], "physicalSurface": 1, "particlesPerEdge": 20}
   ],
   "reference": {
-    "density": 1.0e16,
+    "density": 1.0e14,
     "mass": 9.109e-31,
-    "temperature": 2500.0,
+    "temperature": 11604.5,
     "radius": 1.88e-10
   },
   "solver": {
-    "tau":  [1.0e-9, 1.0e-11],
+    "tau":  [1.0e-9, 5.0e-12, 5.0e-12],
-    "finalTime": 1.0e-6,
+    "finalTime": 1.5e-6,
-    "pusher": ["Electrostatic", "Electrostatic"],
+    "pusher": ["Electrostatic", "Electrostatic", "Electrostatic"],
-    "WeightingScheme": "Volume",
     "EMSolver": "Electrostatic"
   },
+  "average":{
+    "startTime": 1.0e-6
+  },
   "parallel": {
     "OpenMP":{
       "nThreads": 24

runs/ALPHIE_Grid/inputIonization_0.10mA.json

@@ -5,68 +5,62 @@
     "cpuTime": false,
     "numColl": false,
     "EMField": true,
+    "boundariesParticle": true,
     "folder": "ionization_0.10mA"
   },
   "geometry": {
     "dimension": 2,
     "type":     "Cyl",
-    "meshType": "gmsh2",
+    "meshType": "vtu",
-    "meshFile": "mesh.msh"
+    "meshFile": "mesh.vtu"
   },
   "species": [
-    {"name": "Argon+",   "type": "charged", "mass": 6.633e-26, "charge": 1.0, "weight": 1.0e1},
+    {"name": "Ar+",  "type": "charged", "mass": 6.633e-26, "charge": 1.0, "weight": 1.0e1},
-    {"name": "Electron", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e2}
+    {"name": "e",    "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e1},
+    {"name": "eSec", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e1}
   ],
-  "boundary": [ 
+  "boundaries": {
-    {"name": "Ionization Chanber", "physicalSurface": 1, "bTypes": [
+    "particles": [
-                                                           {"type": "transparent"},
+      {"name": "Transparent", "type": "transparent"},
-                                                           {"type": "ionization", "neutral": {"ion": "Argon+", "mass": 6.633e-26, "density": 5.0e16, "velocity": [2500, 0, 0], "temperature": 300},
+      {"name": "Reflection",  "type": "reflection"},
+      {"name": "Absorption",  "type": "absorption"},
+      {"name": "Axis",        "type": "axis"},
+      {"name": "Ionization",  "type": "ionization", "neutral": {"ion": "Ar+", "mass": 6.633e-26, "density": 5.0e16, "velocity": [2500, 0, 0], "temperature": 300},
                                                                                "effectiveTime": 5.0e-6,"energyThreshold": 15.76, "crossSection": "./data/collisions/IO_e-Ar.dat"}
-                                                          ]},
-    {"name": "Vacuum Chamber",     "physicalSurface": 2, "bTypes": [
-                                                           {"type": "transparent"},
-                                                           {"type": "transparent"}
-                                                          ]},
-    {"name": "Exterior",           "physicalSurface": 3, "bTypes": [
-                                                           {"type": "reflection"},
-                                                           {"type": "reflection"}
-                                                          ]},
-    {"name": "Grid Extraction",    "physicalSurface": 4, "bTypes": [
-                                                           {"type": "absorption"},
-                                                           {"type": "absorption"}
-                                                          ]},
-    {"name": "Grid Acceleration",  "physicalSurface": 5, "bTypes": [
-                                                           {"type": "absorption"},
-                                                           {"type": "absorption"}
-                                                          ]},
-    {"name": "Axis",               "physicalSurface": 6, "bTypes": [
-                                                           {"type": "axis"},
-                                                           {"type": "axis"}
-                                                          ]}
     ],
-  "boundaryEM": [
+    "EM": [
-    {"name": "Extraction Grid",    "type": "dirichlet", "potential": -150.0, "physicalSurface": 4},
+      {"name": "Extraction Grid",    "type": "dirichlet", "potential": -150.0},
-    {"name": "Acceleration Grid",  "type": "dirichlet", "potential": -600.0, "physicalSurface": 5},
+      {"name": "Cover Grid",         "type": "dirichlet", "potential": -600.0},
-    {"name": "Ionization Chamber", "type": "dirichlet", "potential":    0.0, "physicalSurface": 1},
+      {"name": "Ionization Chamber", "type": "dirichlet", "potential":    0.0}
-    {"name": "Infinite",           "type": "dirichlet", "potential": -600.0, "physicalSurface": 2}
+    ]
+  },
+  "physicalSurfaces": [
+    {"index": 1, "particles": ["Transparent", "Ionization",  "Ionization"], "EM": "Ionization Chamber"},
+    {"index": 2, "particles": ["Transparent", "Transparent", "Transparent"]},
+    {"index": 3, "particles": ["Reflection",  "Reflection",  "Reflection"]},
+    {"index": 4, "particles": ["Absorption",  "Absorption",  "Absorption"], "EM": "Extraction Grid"},
+    {"index": 5, "particles": ["Absorption",  "Absorption",  "Absorption"], "EM": "Cover Grid"},
+    {"index": 6, "particles": ["Axis",        "Axis",        "Axis"]}
   ],
   "inject": [
-    {"name": "Cathode Electron",    "species": "Electron", "flow":  1.0e-4, "units": "A", "v":  87000.0, "T": [30000.0, 30000.0, 30000.0],
+    {"name": "Cathode",             "species": "e",    "flow":  1.0e-4, "units": "A", "v":   0.0, "T": [11604.5, 11604.5, 11604.5],
-                                    "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [-1, 0, 0], "physicalSurface": 2}
+                                    "velDist": ["Half-Maxwellian", "Maxwellian", "Maxwellian"], "n": [-1, 0, 0], "physicalSurface": 2, "particlesPerEdge": 20}
   ],
   "reference": {
-    "density": 1.0e16,
+    "density": 1.0e14,
     "mass": 9.109e-31,
-    "temperature": 2500.0,
+    "temperature": 11604.5,
     "radius": 1.88e-10
   },
   "solver": {
-    "tau":  [1.0e-9, 1.0e-11],
+    "tau":  [1.0e-9, 5.0e-12, 5.0e-12],
-    "finalTime": 1.0e-6,
+    "finalTime": 1.5e-6,
-    "pusher": ["Electrostatic", "Electrostatic"],
+    "pusher": ["Electrostatic", "Electrostatic", "Electrostatic"],
-    "WeightingScheme": "Volume",
     "EMSolver": "Electrostatic"
   },
+  "average":{
+    "startTime": 1.0e-6
+  },
   "parallel": {
     "OpenMP":{
       "nThreads": 24

runs/Argon_Expansion/CX_case.json

@@ -1,7 +1,7 @@
 {
   "output": {
     "path": "./runs/Argon_Expansion/",
-	"triggerOutput": 10,
+	"triggerOutput": 100,
 	"cpuTime": false,
 	"numColl": true,
 	"folder": "CX_case"
@@ -9,32 +9,29 @@
   "geometry": {
     "dimension": 2,
     "type":     "Cyl",
-    "meshType": "gmsh2",
+    "meshType": "vtu",
-    "meshFile": "mesh.msh"
+    "meshFile": "mesh.vtu"
   },
   "species": [
     {"name": "Argon",  "type": "neutral", "mass": 6.633e-26, "weight": 1.0e8,                "ion": "Argon+"},
     {"name": "Argon+", "type": "charged", "mass": 6.633e-26, "weight": 1.0e8, "charge": 1.0, "neutral": "Argon"}
   ],
-  "boundary": [ 
+  "boundaries": { 
-    {"name": "Injection", "physicalSurface": 1, "bTypes": [
+    "particles": [
-                                                  {"type": "transparent"},
+      {"name": "Transparent", "type": "transparent"},
-                                                  {"type": "transparent"}
+      {"name": "Axis",        "type": "axis"}
-                                                 ]},
+    ]
-    {"name": "Exterior",  "physicalSurface": 2, "bTypes": [
+  },
-                                                  {"type": "transparent"},
+  "physicalSurfaces": [
-                                                  {"type": "transparent"}
+    {"index": 1, "particles":["Axis",        "Axis"]},
-                                                 ]},
+    {"index": 2, "particles":["Transparent", "Transparent"]},
-    {"name": "Axis",      "physicalSurface": 3, "bTypes": [
+    {"index": 3, "particles":["Transparent", "Transparent"]}
-                                                  {"type": "axis"},
-                                                  {"type": "axis"}
-                                                 ]}
   ],
   "inject": [
     {"name": "Exhausts Ar", "species": "Argon", "flow": 0.7, "units": "sccm",     "v": 300.0, "T": [300.0, 300.0, 300.0],
-                            "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1},
+                            "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 3},
     {"name": "Exhausts Ar+", "species": "Argon+", "flow": 0.3, "units": "sccm",     "v": 40000.0, "T": [300.0, 300.0, 300.0],
-                             "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1}
+                             "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 3}
   ],
   "reference": {
     "density": 1.0e19,
@@ -43,13 +40,14 @@
     "radius": 1.88e-10
   },
   "solver": {
-    "tau":  [1.0e-6, 1.0e-6],
+    "tau":  [1.0e-7, 1.0e-7],
-    "finalTime": 4.0e-3,
+    "finalTime": 1.0e-3,
     "pusher": ["Neutral", "Neutral"],
     "WeightingScheme": "Volume"
   },
   "interactions": {
     "folderCollisions": "./data/collisions/",
+    "timeStep": 1.0e-5,
     "collisions": [
       {"species_i": "Argon", "species_j": "Argon", 
        "cTypes": [

runs/Argon_Expansion/README.txt

@@ -0,0 +1,3 @@
+Case to study the expansion of Ar plasma. Three input files: Without collisions, with elastic collisions, and with charge exchange collisions.
+
+It can be seen that for the charge-exchange case, neutrals of high velocity appear as these are previous ions of high velocity (40 km s^-1).

runs/Argon_Expansion/elastic_case.json

@@ -1,40 +1,37 @@
 {
   "output": {
     "path": "./runs/Argon_Expansion/",
-	"triggerOutput": 10,
+	"triggerOutput": 100,
 	"cpuTime": false,
-	"numColl": false,
+	"numColl": true,
 	"folder": "Elastic_case"
   },
   "geometry": {
     "dimension": 2,
     "type":     "Cyl",
-    "meshType": "gmsh2",
+    "meshType": "vtu",
-    "meshFile": "mesh.msh"
+    "meshFile": "mesh.vtu"
   },
   "species": [
     {"name": "Argon",  "type": "neutral", "mass": 6.633e-26, "weight": 1.0e8,                "ion": "Argon+"},
     {"name": "Argon+", "type": "charged", "mass": 6.633e-26, "weight": 1.0e8, "charge": 1.0, "neutral": "Argon"}
   ],
-  "boundary": [ 
+  "boundaries": { 
-    {"name": "Injection", "physicalSurface": 1, "bTypes": [
+    "particles": [
-                                                  {"type": "transparent"},
+      {"name": "Transparent", "type": "transparent"},
-                                                  {"type": "transparent"}
+      {"name": "Axis",        "type": "axis"}
-                                                 ]},
+    ]
-    {"name": "Exterior",  "physicalSurface": 2, "bTypes": [
+  },
-                                                  {"type": "transparent"},
+  "physicalSurfaces": [
-                                                  {"type": "transparent"}
+    {"index": 1, "particles":["Axis",        "Axis"]},
-                                                 ]},
+    {"index": 2, "particles":["Transparent", "Transparent"]},
-    {"name": "Axis",      "physicalSurface": 3, "bTypes": [
+    {"index": 3, "particles":["Transparent", "Transparent"]}
-                                                  {"type": "axis"},
-                                                  {"type": "axis"}
-                                                 ]}
   ],
   "inject": [
     {"name": "Exhausts Ar", "species": "Argon", "flow": 0.7, "units": "sccm",     "v": 300.0, "T": [300.0, 300.0, 300.0],
-                            "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1},
+                            "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 3},
     {"name": "Exhausts Ar+", "species": "Argon+", "flow": 0.3, "units": "sccm",     "v": 40000.0, "T": [300.0, 300.0, 300.0],
-                             "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1}
+                             "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 3}
   ],
   "reference": {
     "density": 1.0e19,
@@ -43,13 +40,14 @@
     "radius": 1.88e-10
   },
   "solver": {
-    "tau":  [1.0e-6, 1.0e-6],
+    "tau":  [1.0e-7, 1.0e-7],
-    "finalTime": 4.0e-3,
+    "finalTime": 1.0e-3,
     "pusher": ["Neutral", "Neutral"],
     "WeightingScheme": "Volume"
   },
   "interactions": {
     "folderCollisions": "./data/collisions/",
+    "timeStep": 1.0e-5,
     "collisions": [
       {"species_i": "Argon", "species_j": "Argon", 
        "cTypes": [
@@ -63,7 +61,7 @@
   },
   "parallel": {
     "OpenMP":{
-      "nThreads": 8
+      "nThreads": 24
     }
   }
 }

runs/Argon_Expansion/mesh.vtu

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runs/Argon_Expansion/nocoll_case.json

@@ -1,7 +1,7 @@
 {
   "output": {
     "path": "./runs/Argon_Expansion/",
-	"triggerOutput": 10,
+	"triggerOutput": 100,
 	"cpuTime": false,
 	"numColl": false,
 	"folder": "Nocoll_case"
@@ -9,32 +9,29 @@
   "geometry": {
     "dimension": 2,
     "type":     "Cyl",
-    "meshType": "gmsh2",
+    "meshType": "vtu",
-    "meshFile": "mesh.msh"
+    "meshFile": "mesh.vtu"
   },
   "species": [
     {"name": "Argon",  "type": "neutral", "mass": 6.633e-26, "weight": 1.0e8,                "ion": "Argon+"},
     {"name": "Argon+", "type": "charged", "mass": 6.633e-26, "weight": 1.0e8, "charge": 1.0, "neutral": "Argon"}
   ],
-  "boundary": [ 
+  "boundaries": { 
-    {"name": "Injection", "physicalSurface": 1, "bTypes": [
+    "particles": [
-                                                  {"type": "transparent"},
+      {"name": "Transparent", "type": "transparent"},
-                                                  {"type": "transparent"}
+      {"name": "Axis",        "type": "axis"}
-                                                 ]},
+    ]
-    {"name": "Exterior",  "physicalSurface": 2, "bTypes": [
+  },
-                                                  {"type": "transparent"},
+  "physicalSurfaces": [
-                                                  {"type": "transparent"}
+    {"index": 1, "particles":["Axis",        "Axis"]},
-                                                 ]},
+    {"index": 2, "particles":["Transparent", "Transparent"]},
-    {"name": "Axis",      "physicalSurface": 3, "bTypes": [
+    {"index": 3, "particles":["Transparent", "Transparent"]}
-                                                  {"type": "axis"},
-                                                  {"type": "axis"}
-                                                 ]}
   ],
   "inject": [
     {"name": "Exhausts Ar", "species": "Argon", "flow": 0.7, "units": "sccm",     "v": 300.0, "T": [300.0, 300.0, 300.0],
-                            "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1},
+                            "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 3},
     {"name": "Exhausts Ar+", "species": "Argon+", "flow": 0.3, "units": "sccm",     "v": 40000.0, "T": [300.0, 300.0, 300.0],
-                             "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1}
+                             "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 3}
   ],
   "reference": {
     "density": 1.0e19,
@@ -43,8 +40,8 @@
     "radius": 1.88e-10
   },
   "solver": {
-    "tau":  [1.0e-6, 1.0e-6],
+    "tau":  [1.0e-7, 1.0e-7],
-    "finalTime": 4.0e-3,
+    "finalTime": 1.0e-3,
     "pusher": ["Neutral", "Neutral"],
     "WeightingScheme": "Volume"
   },

runs/cylFlow/input.json

@@ -8,28 +8,25 @@
   "geometry": {
     "dimension": 2,
     "type":     "Cyl",
-    "meshType": "gmsh2",
+    "meshType": "vtu",
-    "meshFile": "meshSingle.msh"
+    "meshFile": "meshSingle.vtu"
   },
   "species": [
     {"name": "Argon",  "type": "neutral", "mass": 6.633e-26, "weight": 5.0e8}
   ],
-  "boundary": [ 
+  "boundaries": { 
-    {"name": "Injection",      "physicalSurface": 1, "bTypes": [
+    "particles": [
-                                                       {"type": "transparent"}
+      {"name": "Transparent", "type": "transparent"},
-                                                      ]},
+      {"name": "Reflection",  "type": "reflection"},
-    {"name": "Chamber Walls",  "physicalSurface": 2, "bTypes": [
+      {"name": "Axis",        "type": "axis"}
-                                                       {"type": "reflection"}
+    ],
-                                                      ]},
+  },
-    {"name": "Exterior",       "physicalSurface": 3, "bTypes": [
+  "physicalSurfaces": [
-                                                       {"type": "transparent"}
+    {"index": 1, "particles":["Transparent"]},
-                                                      ]},
+    {"index": 2, "particles":["Reflection"]},
-    {"name": "Cylinder Walls", "physicalSurface": 4, "bTypes": [
+    {"index": 3, "particles":["Transparent"]},
-                                                       {"type": "reflection"}
+    {"index": 4, "particles":["Reflection"]},
-                                                      ]},
+    {"index": 5, "particles":["Axis"]},
-    {"name": "Axis",           "physicalSurface": 5, "bTypes": [
-                                                       {"type": "axis"}
-                                                      ]}
   ],
   "inject": [
     {"name": "Nozzle", "species": "Argon", "flow": 10.0, "units": "sccm",     "v": 300.0, "T": [300.0, 300.0, 300.0],

runs/cylFlow/inputDualMesh.json

@@ -8,29 +8,26 @@
   "geometry": {
     "dimension": 2,
     "type":     "Cyl",
-    "meshType": "gmsh2",
+    "meshType": "vtu",
-    "meshFile": "mesh.msh",
+    "meshFile": "mesh.vtu",
-    "meshCollisions": "meshColl.msh"
+    "meshCollisions": "meshColl.vtu"
   },
   "species": [
     {"name": "Argon",  "type": "neutral", "mass": 6.633e-26, "weight": 5.0e8}
   ],
-  "boundary": [ 
+  "boundaries": { 
-    {"name": "Injection",      "physicalSurface": 1, "bTypes": [
+    "particles": [
-                                                       {"type": "transparent"}
+      {"name": "Transparent", "type": "transparent"},
-                                                      ]},
+      {"name": "Reflection",  "type": "reflection"},
-    {"name": "Chamber Walls",  "physicalSurface": 2, "bTypes": [
+      {"name": "Axis",        "type": "axis"}
-                                                       {"type": "reflection"}
+    ],
-                                                      ]},
+  },
-    {"name": "Exterior",       "physicalSurface": 3, "bTypes": [
+  "physicalSurfaces": [
-                                                       {"type": "transparent"}
+    {"index": 1, "particles":["Transparent"]},
-                                                      ]},
+    {"index": 2, "particles":["Reflection"]},
-    {"name": "Cylinder Walls", "physicalSurface": 4, "bTypes": [
+    {"index": 3, "particles":["Transparent"]},
-                                                       {"type": "reflection"}
+    {"index": 4, "particles":["Reflection"]},
-                                                      ]},
+    {"index": 5, "particles":["Axis"]},
-    {"name": "Axis",           "physicalSurface": 5, "bTypes": [
-                                                       {"type": "axis"}
-                                                      ]}
   ],
   "inject": [
     {"name": "Nozzle", "species": "Argon", "flow": 10.0, "units": "sccm",     "v": 300.0, "T": [300.0, 300.0, 300.0],

runs/cylFlow/output/dual/Collection_Argon.pvd

@@ -0,0 +1,105 @@
+<VTKFile type="Collection">
+  <Collection>
+    <DataSet timestep="       0.000000E+000" file="Step_0000_Argon.vtu"/>
+    <DataSet timestep="       5.000000E-006" file="Step_0010_Argon.vtu"/>
+    <DataSet timestep="       1.000000E-005" file="Step_0020_Argon.vtu"/>
+    <DataSet timestep="       1.500000E-005" file="Step_0030_Argon.vtu"/>
+    <DataSet timestep="       2.000000E-005" file="Step_0040_Argon.vtu"/>
+    <DataSet timestep="       2.500000E-005" file="Step_0050_Argon.vtu"/>
+    <DataSet timestep="       3.000000E-005" file="Step_0060_Argon.vtu"/>
+    <DataSet timestep="       3.500000E-005" file="Step_0070_Argon.vtu"/>
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runs/cylFlow/output/dual/Collection_Collisions.pvd

@@ -0,0 +1,105 @@
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