Merge pull request 'issue/edgesVolume' (#59) from issue/edgesVolume into development

Reviewed-on: https://plasmalab.aero.upm.es/git/git/JGonzalez/fpakc/pulls/59

CITATION.cff

@@ -0,0 +1,50 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: Finite element Particle Kinetic Code
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Jorge
+    family-names: Gonzalez
+    email: jorge.gonzalez@upm.es
+    affiliation: Universidad Politécnica de Madrid
+    orcid: 'https://orcid.org/0000-0001-7905-5001'
+repository-code: 'https://gitlab.com/JorgeGonz/fpakc'
+abstract: >-
+  Welcome to fpakc (Finite element PArticle Kinetic Code), a
+  modern object oriented Fortran open-source code for
+  particle simulations of plasma and gases. This code works
+  by simulating charged and neutral particles, following
+  their trajectories, collisions and boundary conditions
+  imposed by the user.
+
+  One of our aims is to make a code easy to maintain as well
+  as easy to use by a variety of reserchers and students.
+
+  This code is currenlty in very early steps of development.
+
+  The code aims to be easy to maintain and easy to use,
+  allowing its application from complex problems to easy
+  examples that can be used, for example, as teaching
+  exercises.
+
+  Parallelization techniques such as OpenMP, MPI will be
+  used to distribute the cpu load. We aim to make fpakc GPU
+  compatible in the future.
+
+  The codefpakc makes use of finite elements to generate
+  meshes in complex geometries. Particle properties are
+  deposited in the nodes and cells of the mesh. The
+  electromagnetic field, with the boundary conditions
+  imposed by the user, is solved also in this mesh.
+keywords:
+  - particle-in-cell
+  - plasma
+  - finite elements
+license: GPL-3.0
+version: beta
+date-released: '2025-10-01'

data/collisions/IO_e-Kr.dat

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+# D108525 "refs": {"B56": {"note": "CLM-R294 (1989)"}}
+# Relative energy (eV) cross section (m^2)
+1.40E+01 0
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+1.72E+04 1.009E-21
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data/collisions/IO_e-Xe.dat

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+# EL cross sections extracted from PROGRAM MAGBOLTZ, VERSION 7.1 JUNE 2004 www.lxcat.net/Biagi-v7.1
+# Relative energy (eV) cross section (m^2)
+1.21E+01 0
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+1.91E+01 2.1E-20
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+2.00E+04 1.602E-21

doc/user-manual/.gitignore

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-Q Q
-showpage
-%%Trailer
-end
-%%EOF

doc/user-manual/fpakc_UserManual.tex

@@ -1,5 +1,5 @@
 \documentclass[10pt,a4paper,twoside]{book}
-\usepackage[latin1]{inputenc}
+%\usepackage[latin1]{inputenc}
 \usepackage{amsmath}
 \usepackage{amsfonts}
 \usepackage{amssymb}
@@ -72,7 +72,7 @@
       The \Gls{fpakc} is a simulation tool that models species in plasma (ions, electrons and neutrals) following the trajectories of macro-particles as they move and interact between them and the boundaries of the domain.
       Particles properties are scattered into a finite element mesh in 1, 2 or three dimensions, with the possibility to choose different geometries.
       The official repository can be found at: \url{https://gitlab.com/JorgeGonz/fpakc.git}.
-      The code is currently in very early steps of development and further improvements are expected very soon.
+      The code is currently in the very early steps of development and further refinements are expected very soon.
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Main Guidelines}
@@ -86,11 +86,11 @@
         \item \acrshort{fpakc} is coded in a \textit{understandable} way.
               This means that the code is required to be written in a clear way that is easy to understand and maintain.
               Variables and procedure names need to be self-understanding.
-              This ease the process of fixing bugs and improving the codes by a large team of developers.
+              This eases the process of fixing bugs and improving the codes by a large team of developers.
               For more information, please refer to the \acrshort{fpakc} Coding Style document.
-        \item \acrshort{fpakc} requires to be ease to use.
+        \item \acrshort{fpakc} requires being ease to use.
               Input files are required to be in a \textit{human} format, meaning that the different options can be easily understood without constant reference to the user guide.
-              \acrshort{fpakc} is aimed to be used in a wide range of applications and by a variety of scientist: from very established ones to newcomers to the field and also students.
+              \acrshort{fpakc} is aimed to be used in a wide range of applications and by various scientists: from well-established ones to newcomers to the field and also students.
       \end{enumerate}
     
       These are foundation stones of \acrshort{fpakc} and its development and should always be followed, at least for the releases in the official repository.
@@ -105,16 +105,16 @@
     \section{The Particle Method}
       \Gls{fpakc} uses macro-particles to simulate the dynamics of different plasma species (mainly ions, electrons and neutrals).
       These macro-particles could represent a large amount of real particles.
-      For now own, macro-particles will be referred as just particles by abusing of language.
+      For now own, macro-particles will be referred as just particles by abuse of language.
       During the initiation phase, the input and mesh file(s) are reading.
       If an initial distribution for a species is specified in the input file, particles to match that distribution are loaded into the cells.
       
       The general steps performed in each iteration are:
       \begin{enumerate}
         \item Firstly, new particles are introduced into the domain as specified in the input file.
-        \item Particles are then pushed accounting for possible acceleration by external forces.
-              During this process, if a particle changes cell it is found using the connectivity between elements.
-              If a particle encounters a boundary instead a new cell, the interaction between the boundary and the wall is computed.
+        \item Particles are then pushed, accounting for possible acceleration by external forces.
+              During this process, if a particle changes cell, it is found using the connectivity between elements.
+              If a particle encounters a boundary instead a new cell, the interaction between the boundary and the wall are computed.
               A particle may abandon the computational domain and is no longer accounted for.
         \item Next, collisions for the particles inside each cell are carried out.
               This may include different collision processes for each particle.
@@ -124,10 +124,10 @@
         \item Finally, particle properties are scattered among the mesh nodes.
               These properties are density, momentum and the stress tensor.
         \item If requested, the electromagnetic field is computed.
-        \item If the number of iteration requires writing output files, it is done after all steps for the particles is completed.
+        \item If the number of iteration requires writing output files, it is done after all steps for the particles are completed.
       \end{enumerate}
     
-      \Gls{fpakc} has the capability to configure all the behavior of the simulation via the input file.
+      \Gls{fpakc} has the capability to configure all the behaviour of the simulation via the input file.
       Parameters as injection, the kind of pusher used for each species, boundary conditions or collisions are user-input parameters and will be described in Chap.~\ref{ch:input_file}.
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -168,8 +168,8 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Find new cell}      
       Once the position and velocity of the particle are updated, the new cell that contains the particle is searched.
-      This is done by a neighbor search, starting from the previous cell containing the particle.
-      In the process of finding the new cell, it is possible that a particle encounters a boundary.
+      This is done by a neighbour search, starting from the previous cell containing the particle.
+      In the process of finding the new cell, a particle might encounter a boundary.
       When the particle interacts with the boundary, the particle may continue its life in the simulation or might be eliminated from it.
       Once that the new cell is found or that the particle life has been terminated, the pushing is complete.
       If a secondary mesh is used for the Monte-Carlo Collision method, the new cell in that mesh in which the particle reside is also found by the same method, although no interaction with the boundaries is accounted for this step.
@@ -178,7 +178,7 @@
     \section{Variable Weighting Scheme\label{sec:weightingScheme}}
       One of the issues in particle simulations, specially for axial-symmetrical cases, is that due to the disparate volume of cells, specially close to the axis, the statistics in some cells is usually poor.
       To try to fix that, the possibility to include a Variable Weighting Scheme in the simulations is available in \Gls{fpakc}.
-      These schemes detect when a particle change cells and split it if necessary to improve statistics.
+      These schemes detect when a particle changes cells and split it if necessary to improve statistics.
       The use of a Variable Weighting Scheme is defined by the user in the input file.
       
       Beware that this can increase the number of particles in the simulation and increase computational time.
@@ -189,16 +189,16 @@
       \Gls{fpakc} distinguish between two types of interactions: \acrfull{mcc} and \acrfull{cs}.
       \acrshort{mcc} refers to the process in which two particles interact in short range.
       These processes include, but are not limited to: elastic collisions, ionization/recombination, charge-exchange, excitation/de-excitation\ldots
-      A secondary mesh, with cell sizes in the range of the mean-free path, can be used for this type of collisions.
+      A secondary mesh, with cell sizes in the range of the mean-free path, can be used for this type of collision.
       \acrshort{cs} refers to the large range interaction that a charged species suffer do to the charge of other particles.
       The interactions between the different species is defined by the user.
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{\acrlong{mcc}}
-        For each cell the maximum number of collisions between particle is computed.
+        For each cell, the maximum number of collisions between particle is computed.
         For each collision, a random pair of particles is chosen.
         A loop over all possible collisions for the pair of particles chosen is performed.
-        If a random number is above the probability of collision for that specific type, the collision take place.
+        If a random number is above the probability of collision for that specific type, the collision takes place.
         If not, the next type for the particle pair is checked.
               
         Below are described the type of collision process implemented in \acrshort{fpakc}:
@@ -219,7 +219,7 @@
 
           \item 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 modelled yet.
+                The photons emitted by this process are not modelled yet.
         \end{itemize}
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -238,7 +238,7 @@
       Once that the pushing is complete, the array of particles that remain inside the domain is copied to a new array.
       The new array containing only the particles inside the domain will be the one used in the next steps.
       In this section, particles are assigned to the list of particles inside each individual cell.
-      Unfortunately, this is done right now without parallelisation and is very CPU consuming.
+      Unfortunately, this is done right now without parallelization and is very CPU consuming.
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Probing}\label{sec:probing}
@@ -250,21 +250,21 @@
       The user can decide the grid width and the number of points in each direction.
       The distribution function will be calculated and wrote with a time step decided by the user.
       
-      If a particle velocity resides outside of the velocity grid (in any direction), it wont be added to the tally of the distribution function.
-      Due to the limitation of only taking into account particles in the cell, and not neighbour particles, two probes for the same species at different positions but in the same cell will output the same results.
-      A more advance method taking into account distance between the particles and the probe position as well as particles in neighbour cells could be implemented to improve the statistics of the distribution function.
+      If a particle velocity resides outside the velocity grid (in any direction), it will not be added to the tally of the distribution function.
+      Due to the limitation of only considering particles in the cell, and not neighbour particles, two probes for the same species at different positions but in the same cell will output the same results.
+      A more advance method considering distance between the particles and the probe position as well as particles in neighbour cells could be implemented to improve the statistics of the distribution function.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Scattering}
       The properties of each particle are deposited in the nodes from the containing cell.
-      This process depend on the cell type, but in general, each node receive a proportional part of the particle properties as a function of the particle position inside the cell.
-      Figure \ref{fig:scatteringQuad} shows how a particle at a generic position $p(x_1, x_2)$ inside the cell is scattered to the four nodes.
+      This process depends on the cell type, but in general, each node receives a proportional part of the particle properties as a function of the particle position inside the cell.
+      The figure \ref{fig:scatteringQuad} shows how a particle at a generic position $p(x_1, x_2)$ inside the cell is scattered to the four nodes.
       \begin{wrapfigure}{l}{0.4\textwidth}
         \centering
         \includegraphics{figures/scatteringQuad}
         \caption{\label{fig:scatteringQuad}Example of how a particle is weighted in a quadrilateral cell.}
       \end{wrapfigure}
-      Each node receives a proportional part of the area formed by dividing the cell in for rectangles using as an additional vertex the particle position.
+      Each node receives a proportional part of the area formed by dividing the cell in for rectangles, using as an additional vertex the particle position.
       These properties are dimensionless, but they are converted to the correct units once the output is printed.
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -273,11 +273,11 @@
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Average scheme}
-      Particle-in-cell codes has an intrinsic statistical noise associated with them.
+      Particle-in-cell codes have an intrinsic statistical noise associated with them.
       Although this can be reduced by increasing the number of particles, this also increases the CPU requirements of the case.
       
       It is quite common that most cases reach a quasi-steady state after a number of iterations and time-average results can be obtained after to improve analysis, plotting and restarting the case using these time-average results as new species backgrounds.
-      Although this is possible to do once the simulation is finished with post-processing tools, this is limited to the amount of iterations printed.
+      Although this is possible to do once the simulation is finished with post-processing tools, this is limited to the number of iterations printed.
       
       \Gls{fpakc} implements a simple average scheme that, after a start time provided by the user, scores a mean and standard deviation of all the main species properties, and the electromagnetic field.
       This scheme is based on the Welford's online algorithm~\cite{welford1962note}.
@@ -286,7 +286,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  
   \chapter{Installation}
     \section{Required Packages}
-      In order to properly compile \gls{fpakc}, the following packages are required.
+      To properly compile \gls{fpakc}, the following packages are required.
       \subsection{Gfortran}
         The \Gls{opensource} free compiler \Gls{gfortran}\cite{gfortranURL} from GCC is the basic way to compile \acrshort{fpakc}.
         It is distributed with all GNU/Linux distributions.
@@ -369,7 +369,7 @@ make
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Case file}
       The required format for the case file is \Gls{json}.
-      \Gls{json} is a case-sensitive format, so input must be written with the correct capitalisation.
+      \Gls{json} is a case-sensitive format, so input must be written with the correct capitalization.
       The basic structure and options available for the case file are explained below.
       The order of the objects and variables is irrelevant, but the structure needs to be maintained.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -380,9 +380,9 @@ make
           \item \textbf{path}: Character.
                                Path for the output files. This path is also used to locate the mesh input file.
           \item \textbf{folder}: Character.
-                                 Base name of the folder in wich output files are placed.
+                                 Base name of the folder in which output files are placed.
                                  The date and time is appended to this name.
-                                 If none is provided, only the date and time is writted as the folder name.
+                                 If none is provided, only the date and time is written as the folder name.
           \item \textbf{triggerOutput}: Integer.
                                         Determines the number of iterations between writing output files for macroscopic quantities.
           \item \textbf{cpuTime}: Logical. 
@@ -460,6 +460,10 @@ make
                                    \begin{itemize}
                                      \item \textbf{gmsh2}: \Gls{gmsh} file format in version 2.0. This has to be in ASCII format.
                                      \item \textbf{vtu}: \Gls{vtu} file format. This has to be in ASCII format.
+                                     \item \textbf{text}: Plain text file format only intended for 1D cases.
+                                                          This has to be in ASCII format and comma separated.
+                                                          The first column represents the position and the second column the physical ID of the node.
+                                                          Values have to be $1$ (left boundary), $2$ (right boundary), or $0$ (no boundary.)
                                    \end{itemize}
           \item \textbf{meshFile}: Character.
                                    Mesh filename.
@@ -515,7 +519,7 @@ make
                                   \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{wallTemperature}: Reflective wall with cosntant temperature that exchange heat with particles.
+                                  \item \textbf{wallTemperature}: Reflective wall with constant temperature that exchange heat with particles.
                                                                   Required parameters are:
                                                                   \begin{itemize}
                                                                     \item \textbf{temperature}: Real.
@@ -526,8 +530,8 @@ make
                                                                                                  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.
-                                                             Secondary electron is taken as same type as incident particle.
+                                                             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.
@@ -540,7 +544,7 @@ make
                                                                                          \item \textbf{mass}: Real.
                                                                                                               Units in $\unit{kg}$.
                                                                                                               Mass of neutral species.
-                                                                                                              If missing, the mass of the ion is ussed
+                                                                                                              If missing, the mass of the ion is used
                                                                                          \item \textbf{density}: Real.
                                                                                                                  Units in $\unit{m^{-3}}$.
                                                                                                                  Density of neutral background.
@@ -558,18 +562,18 @@ make
                                                                                        \end{itemize}
                                                                \item \textbf{effectiveTime}: Real.
                                                                                              Units in $\unit{s}$.
-                                                                                             As the particle is no longer simulated once it crossed the boundary, this time represent the effective time in which the particle produces ionization processes in the neutral background.
+                                                                                             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.
                                                                                                 Units in $\unit{eV}$.
                                                                                                 Ionization energy threshold for the simulated process.
                                                                                                 Required parameter.
                                                                \item \textbf{crossSection}: Character.
-                                                                                            Complete path to the cross section data for the ionization process.
+                                                                                            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 interact with this axis, it is reflected.
+                                                       If , for some reason, a particle interacts with this axis, it is reflected.
                                 \end{itemize}
         \end{itemize}
       
@@ -585,18 +589,26 @@ make
                                Type of boundary.
                                 Accepted values are:
                                \begin{itemize}
-                                 \item \textbf{dirichlet}: Elastic reflection of particles.
+                                 \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.
+                                                               The value of \textbf{boundaryEM.potential} will be multiplied for the corresponding value in the file \textbf{boundaryEM.temporalProfile}.
                                 \end{itemize}
           \item \textbf{potential}: Real.
                                     Fixed potential for Dirichlet boundary condition.
           \item \textbf{physicalSurface}: Integer.
                                           Identification of the edge in the mesh file.
+          \item \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.
+        
         \end{itemize}
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{inject}
         The array \textbf{inject} specifies the injection of particles from different surfaces.
-        The injection of particles need to be associated to a physicalSurface in the mesh file.
+        The injection of particles needs to be associated to a physicalSurface in the mesh file.
         Multiple injections can be associated to the same surface.
         \begin{itemize}
           \item \textbf{name}: Character.
@@ -610,7 +622,9 @@ make
                                 Available values are:
                                 \begin{itemize}
                                   \item \textbf{A}: Ampere.
-                                  \item \textbf{sccm}: Standard cubic centimeter.
+                                  \item \textbf{Am2}: Ampere per square meter.
+                                                      This value will be multiplied by the area of injection.
+                                  \item \textbf{sccm}: Standard cubic centimetre.
                                   \item \textbf{part/s}: Particles (real) per second.
                                 \end{itemize}
           \item \textbf{v}: Real.
@@ -627,7 +641,7 @@ make
                                   \begin{itemize}
                                     \item \textbf{Maxwellian}: Maxwellian distribution of temperature \textbf{T} and mean \textbf{v} times the value of \textbf{n} in the specified direction.
                                     \item \textbf{Half-Maxwellian}: Half-Maxwellian distribution of temperature \textbf{T} and mean \textbf{v} times the value of \textbf{n} in the specified direction.
-                                                                    Only takes into account the positive part of the half-Maxwellian.
+                                                                    Only considers the positive part of the half-Maxwellian.
                                     \item \textbf{Delta}: Dirac's delta distribution function. All particles are injected with velocity \textbf{v} times the value of \textbf{n} in the specified direction.
                                   \end{itemize}
           \item \textbf{T}: Real.
@@ -636,6 +650,11 @@ make
                             Temperature in each direction.
           \item \textbf{physicalSurface}: Integer.
                                           Identification of the edge in the mesh file.
+          \item \textbf{particlesPerEdge}: Integer.
+                                           Optional.
+                                           Number of particles to be injected by each edge in the numerical domain.
+                                           The weight of the particles for each edge will modified by the surface of the edge to ensure the right flux is injected.
+                                           If no value is provided, the number of particles to inject per edge will be calculated with the species weight and the surface of the edge respect to the total one.
         \end{itemize}        
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{reference}
@@ -651,7 +670,7 @@ make
           \item \textbf{radius}: Real.
                                  Reference atomic radius in $\unit{m}$.
           \item \textbf{crossSection}: Real.
-                                       Reference cross section in $\unit{m^2}$.
+                                       Reference cross-section in $\unit{m^2}$.
                                        If this value is present, radius is ignored.
         \end{itemize}
       
@@ -677,8 +696,8 @@ make
                                  Indicates the type of pusher used for each species:
                                  \begin{itemize}
                                    \item \textbf{Neutral}: Pushes a particle without any external force.
-                                   \item \textbf{Electrostatic}: Pushes a particle including the effect of the electrostatic field.
-                                   \item \textbf{Electromagnetic}: Pushes particles accounting for the electromagnetic field.
+                                   \item \textbf{Electrostatic}: Pushes a particle, including the effect of the electrostatic field.
+                                   \item \textbf{Electromagnetic}: Pushes a particle, accounting for the electromagnetic field.
                                  \end{itemize}
           \item \textbf{WeightingScheme}: Character.
                                           Indicates the variable weighting scheme to be used in the simulation.
@@ -710,7 +729,11 @@ make
                                                          Output file from previous run used as an initial state for the species.
                                                          The file format must be the same as in \textbf{geometry.meshType}
                                                          Initial particles are assumed to have a Maxwellian distribution.
-                                                            File must be located at \textbf{output.path}.
+                                                         File must be located in \textbf{output.path}.
+                                    \item \textbf{particlesPerCell}: Integer.
+                                                                     Optional.
+                                                                     Initial number of particles per cell.
+                                                                     If not, the number of particles per cell will be assigned based on the species weight and the cell volume.
                                   \end{itemize}
         \end{itemize}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -726,11 +749,11 @@ make
         \end{itemize}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{interactions}\label{ssec:input_interactions}
-        This object determine the different interactions among species.
+        This object determines the different interactions among species.
         Acceptable values are:
         \begin{itemize}
           \item \textbf{folderCollisions}: Character.
-                                           Indicates the path to in which the cross section tables are allocated.
+                                           Indicates the path to in which the cross-section tables are allocated.
           \item \textbf{meshCollisions}: Character.
                                          Determines a specific mesh for \acrshort{mcc} processes.
                                          The file needs to be located in the folder \textbf{output.folder}.
@@ -757,13 +780,18 @@ make
                                                                                      Accepted values are \textbf{elastic}, \textbf{chargeExchange}, \textbf{ionization} and \textbf{recombination}.
                                                                                      Please refer to Sec.~\ref{ssec:collisions} for a description of the different collision types.
                                                                 \item \textbf{crossSection}: Character.
-                                                                                             File in \textbf{interactions.folderCollisions} that contains the cross section data as a 1D table of relative energy (in $\unit{eV}$) and cross section (in $\unit{m^-2}$).
+                                                                                             File in \textbf{interactions.folderCollisions} that contains the cross-section data as a 1D table of relative energy (in $\unit{eV}$) and cross-section (in $\unit{m^-2}$).
                                                                 \item \textbf{energyThreshold}: Real.
                                                                                                 Energy threshold of the collisional process in $\unit{eV}$.
                                                                                                 Only valid for \textbf{ionization} and \textbf{recombination} processes.
                                                                 \item \textbf{electron}: Character.
                                                                                          Name of species designed as electrons.
                                                                                          Only valid for \textbf{ionization} and \textbf{recombination} processes.
+                                                                \item \textbf{electronSecondary}: Character.
+                                                                                                  Optional.
+                                                                                                  Name of species designed as secondary electrons.
+                                                                                                  If none provided, \textbf{electron} is used.
+                                                                                                  Only valid for \textbf{ionization}.
                                                               \end{itemize}
                                      \end{itemize}
           \item \textbf{Coulomb}: Array of objects.
@@ -773,7 +801,7 @@ make
                                   \begin{itemize}
                                     \item \textbf{species\_i}, \textbf{species\_j}: Character.
                                                                                     Define the two species involved in the collision processes.
-                                                                                    Order is indiferent.
+                                                                                    Order is indifferent.
                                   
                                   \end{itemize}
         \end{itemize}
@@ -799,9 +827,9 @@ make
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{1D Emissive Cathode (1D\_Cathode)}
-      Emission from a 1D cathode 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 modifying some parameters in the input file.
+      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.
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

src/fpakc.f90

@@ -11,12 +11,12 @@ PROGRAM fpakc
   USE OMP_LIB
   IMPLICIT NONE
 
-  ! t = time step
-  INTEGER:: t
   ! arg1 = Input argument 1 (input file)
   CHARACTER(200):: arg1
   ! inputFile = path+name of input file
   CHARACTER(:), ALLOCATABLE:: inputFile
+  ! generic integer for time step
+  INTEGER:: t
 
   tStep = omp_get_wtime()
   !Gets the input file
@@ -27,11 +27,18 @@ PROGRAM fpakc
 
   !Reads the json configuration file
   CALL readConfig(inputFile)
+
+  !Create output folder and initial files
+  CALL initOutput(inputFile)
+
   !Do '0' iteration
-  t = tInitial
+  timeStep = tInitial
 
   !$OMP PARALLEL DEFAULT(SHARED)
   !$OMP SINGLE
+  ! Initial reset of probes
+  CALL resetProbes()
+
   CALL verboseError("Initial scatter of particles...")
   !$OMP END SINGLE
   CALL doScatter()
@@ -45,19 +52,21 @@ PROGRAM fpakc
   tStep = omp_get_wtime() - tStep
 
   !Output initial state
-  CALL doOutput(t)
+  CALL doOutput()
   CALL verboseError('Starting main loop...')
   !$OMP PARALLEL DEFAULT(SHARED) 
   DO t = tInitial + 1, tFinal
-    !Insert new particles and push them
     !$OMP SINGLE
     tStep = omp_get_wtime()
 
+    ! Update global time step index
+    timeStep = t
+
     !Checks if a species needs to me moved in this iteration
-    CALL solver%updatePushSpecies(t)
+    CALL solver%updatePushSpecies()
 
     !Checks if probes need to be calculated this iteration
-    CALL resetProbes(t)
+    CALL resetProbes()
     tPush = omp_get_wtime()
     !$OMP END SINGLE
 
@@ -75,7 +84,7 @@ PROGRAM fpakc
     !$OMP END SINGLE
 
     IF (doMCCollisions) THEN
-      CALL meshForMCC%doCollisions(t)
+      CALL meshForMCC%doCollisions()
 
     END IF
 
@@ -120,12 +129,12 @@ PROGRAM fpakc
     !$OMP SINGLE
     tEMField = omp_get_wtime() - tEMField
 
-    CALL doAverage(t)
+    CALL doAverage()
 
     tStep = omp_get_wtime() - tStep
 
     !Output data
-    CALL doOutput(t)
+    CALL doOutput()
     !$OMP END SINGLE
 
   END DO

src/makefile

@@ -9,6 +9,7 @@ OBJECTS = $(OBJDIR)/moduleMesh.o $(OBJDIR)/moduleMeshBoundary.o $(OBJDIR)/module
 			  	$(OBJDIR)/moduleMeshInputVTU.o $(OBJDIR)/moduleMeshOutputVTU.o \
 			  	$(OBJDIR)/moduleMeshInputGmsh2.o $(OBJDIR)/moduleMeshOutputGmsh2.o \
 			  	$(OBJDIR)/moduleMeshInput0D.o $(OBJDIR)/moduleMeshOutput0D.o \
+				$(OBJDIR)/moduleMeshInputText.o $(OBJDIR)/moduleMeshOutputText.o \
 			  	$(OBJDIR)/moduleMesh3DCart.o \
 			  	$(OBJDIR)/moduleMesh2DCyl.o  \
 			  	$(OBJDIR)/moduleMesh2DCart.o \

src/modules/common/moduleCaseParam.f90

@@ -2,8 +2,13 @@
 MODULE moduleCaseParam
   !Final and initial iterations
   INTEGER:: tFinal, tInitial = 0
+  ! Global index of current iteration
+  INTEGER:: timeStep
+  ! Time step for all species
   REAL(8), ALLOCATABLE:: tau(:)
+  ! Minimum time step
   REAL(8):: tauMin
+  ! Time step for Monte-Carlo Collisions
   REAL(8):: tauColl
 
 END MODULE moduleCaseParam

src/modules/common/moduleRandom.f90

@@ -40,31 +40,48 @@ MODULE moduleRandom
       INTEGER:: rnd
       REAL(8):: rnd01
 
-      rnd = 0.D0
+      rnd = 0
       CALL RANDOM_NUMBER(rnd01)
 
-      rnd = INT(REAL(b - a) * rnd01) + 1
+      rnd = a + FLOOR((b+1-a)*rnd01)
 
     END FUNCTION randomIntAB
 
+    !Returns a random number in a Maxwellian distribution of mean 0 and width 1 with the Box-Muller Method
+    function randomMaxwellian() result(rnd)
+      USE moduleConstParam, only: pi
+      implicit none
+
+      real(8):: rnd
+      real(8):: v1, v2, Rsquare
+
+      v1 = 0.d0
+      do while (v1 <= 0.d0)
+        v1 = random()
+
+      end do
+      v2 = random()
+
+      rnd = sqrt(-2.d0*log(v1))*cos(2*pi*v2)
+
+    end function randomMaxwellian
+
     !Returns a random number in a Maxwellian distribution of mean 0 and width 1
-    FUNCTION randomMaxwellian() RESULT(rnd)
-      USE moduleConstParam, ONLY: PI
+    FUNCTION randomHalfMaxwellian() RESULT(rnd)
       IMPLICIT NONE
 
       REAL(8):: rnd
-      REAL(8):: x, y
+      REAL(8):: x
 
       rnd = 0.D0
       x = 0.D0
       DO WHILE (x == 0.D0)
         CALL RANDOM_NUMBER(x)
       END DO
-      CALL RANDOM_NUMBER(y)
 
-      rnd = DSQRT(-2.D0*DLOG(x))*DCOS(2.D0*PI*y)
+      rnd = DSQRT(-DLOG(x))
 
-    END FUNCTION randomMaxwellian
+    END FUNCTION randomHalfMaxwellian
 
     !Returns a random number weighted with the cumWeight array
     FUNCTION randomWeighted(cumWeight, sumWeight) RESULT(rnd)
@@ -73,10 +90,21 @@ MODULE moduleRandom
       REAL(8), INTENT(in):: cumWeight(1:)
       REAL(8), INTENT(in):: sumWeight
       REAL(8):: rnd0b
-      INTEGER:: rnd
+      INTEGER:: rnd, i
 
-      rnd0b = random(0.D0, sumWeight)
-      rnd = MINLOC(DABS(rnd0b - cumWeight), 1)
+      rnd0b = random()
+      i = 1
+      DO 
+        IF (rnd0b <= cumWeight(i)/sumWeight) THEN
+          rnd = i
+          EXIT
+
+        ELSE
+          i = i +1
+
+        END IF
+      END DO
+      ! rnd = MINLOC(DABS(rnd0b - cumWeight), 1)
 
     END FUNCTION randomWeighted
 

src/modules/common/moduleTable.f90

@@ -93,7 +93,7 @@ MODULE moduleTable
         f = self%fMax
 
       ELSE
-        i = MINLOC(x - self%x, 1)
+        i = MINLOC(ABS(x - self%x), 1)
         deltaX = x - self%x(i)
         IF (deltaX < 0 ) THEN 
           i = i - 1

src/modules/init/moduleInput.f90

@@ -84,20 +84,6 @@ MODULE moduleInput
       CALL readParallel(config)
       CALL checkStatus(config, "readParallel")
 
-      !If everything is correct, creates the output folder
-      CALL EXECUTE_COMMAND_LINE('mkdir ' // path // folder )
-      !Copies input file to output folder
-      CALL EXECUTE_COMMAND_LINE('cp ' // inputFile // ' ' // path // folder)
-      !Copies particle mesh
-      IF (mesh%dimen > 0) THEN
-        CALL EXECUTE_COMMAND_LINE('cp ' // pathMeshParticle // ' ' // path // folder)
-        IF (doubleMesh) THEN
-          CALL EXECUTE_COMMAND_LINE('cp ' // pathMeshColl // ' ' // path // folder)
-
-        END IF
-
-      END IF
-
     END SUBROUTINE readConfig
     
     !Checks the status of the JSON case file and, if failed, exits the execution.
@@ -273,13 +259,17 @@ MODULE moduleInput
           !Read BC
           CALL readEMBoundary(config)
 
+        CASE("ElectrostaticBoltzmann")
+          !Read BC
+          CALL readEMBoundary(config)
+
         CASE("ConstantB")
           !Read BC
           CALL readEMBoundary(config)
           !Read constant magnetic field
           DO i = 1, 3
-            WRITE(istring, '(i2)') i
-            CALL config%get(object // '.B(' // istring // ')', B(i), found)
+            WRITE(iString, '(i2)') i
+            CALL config%get(object // '.B(' // iString // ')', B(i), found)
             IF (.NOT. found) THEN
               CALL criticalError('Constant magnetic field not provided in direction ' // iString, 'readSolver')
 
@@ -322,7 +312,7 @@ MODULE moduleInput
       LOGICAL:: found
       CHARACTER(:), ALLOCATABLE:: object
       INTEGER:: nInitial
-      INTEGER:: i, j, p, e
+      INTEGER:: i, p, e
       CHARACTER(LEN=2):: iString
       CHARACTER(:), ALLOCATABLE:: spName
       INTEGER:: sp
@@ -338,7 +328,8 @@ MODULE moduleInput
       REAL(8):: densityCen
       !Mean velocity and temperature at particle position
       REAL(8):: velocityXi(1:3), temperatureXi
-      INTEGER:: nNewPart = 0.D0
+      INTEGER:: nNewPart = 0
+      REAL(8):: weight = 0.D0
       CLASS(meshCell), POINTER:: cell
       TYPE(particle), POINTER:: partNew
       REAL(8):: vTh
@@ -357,6 +348,9 @@ MODULE moduleInput
           !Reads node values at the nodes
           filename = path // spFile
           CALL mesh%readInitial(filename, density, velocity, temperature)
+          !Check if initial number of particles is given
+          CALL config%get(object // '.particlesPerCell', nNewPart, found)
+
           !For each volume in the node, create corresponding particles
           DO e = 1, mesh%numCells
             !Scale variables
@@ -369,7 +363,11 @@ MODULE moduleInput
             densityCen = mesh%cells(e)%obj%gatherF((/ 0.D0, 0.D0, 0.D0 /), nNodes, sourceScalar)
 
             !Calculate number of particles
-            nNewPart = INT(densityCen * (mesh%cells(e)%obj%volume*Vol_ref) / species(sp)%obj%weight)
+            IF (.NOT. found) THEN
+              nNewPart = FLOOR(densityCen * (mesh%cells(e)%obj%volume*Vol_ref) / species(sp)%obj%weight)
+
+            END IF
+            weight = densityCen * (mesh%cells(e)%obj%volume*Vol_ref) / REAL(nNewPart)
 
             !Allocate new particles
             DO p = 1, nNewPart
@@ -406,7 +404,7 @@ MODULE moduleInput
 
               partNew%n_in   = .TRUE.
 
-              partNew%weight = species(sp)%obj%weight
+              partNew%weight = weight
 
               !Assign particle to temporal list of particles
               CALL partInitial%add(partNew)
@@ -634,7 +632,7 @@ MODULE moduleInput
       INTEGER:: i, k, ij
       INTEGER:: pt_i, pt_j
       REAL(8):: energyThreshold, energyBinding
-      CHARACTER(:), ALLOCATABLE:: electron
+      CHARACTER(:), ALLOCATABLE:: electron, electronSecondary
       INTEGER:: e
       CLASS(meshCell), POINTER:: cell
 
@@ -711,9 +709,17 @@ MODULE moduleInput
                 IF (.NOT. found) CALL criticalError('energyThreshold not found for collision' // object, 'readInteractions')
                 CALL config%get(object // '.electron', electron, found)
                 IF (.NOT. found) CALL criticalError('electron not found for collision' // object, 'readInteractions')
+                CALL config%get(object // '.electronSecondary', electronSecondary, found)
+                IF (found) THEN
+                  CALL initBinaryIonization(interactionMatrix(ij)%collisions(k)%obj, &
+                                            crossSecFilePath, energyThreshold, electron, electronSecondary)
+
+                ELSE
                   CALL initBinaryIonization(interactionMatrix(ij)%collisions(k)%obj, &
                                             crossSecFilePath, energyThreshold, electron)
 
+                END IF
+
               CASE ('recombination')
                 !Electorn impact ionization
                 CALL config%get(object // '.energyBinding', energyBinding, found)
@@ -797,7 +803,7 @@ MODULE moduleInput
 
       TYPE(json_file), INTENT(inout):: config
       INTEGER:: i, s
-      CHARACTER(2):: istring, sString
+      CHARACTER(2):: iString, sString
       CHARACTER(:), ALLOCATABLE:: object, bType
       REAL(8):: Tw, cw !Wall temperature and specific heat
       !Neutral Properties
@@ -805,16 +811,16 @@ MODULE moduleInput
       REAL(8), DIMENSION(:), ALLOCATABLE:: v0
       REAL(8):: effTime
       REAL(8):: eThreshold !Energy threshold
-      INTEGER:: speciesID
-      CHARACTER(:), ALLOCATABLE:: speciesName, crossSection
+      INTEGER:: speciesID, electronSecondaryID
+      CHARACTER(:), ALLOCATABLE:: speciesName, crossSection, electronSecondary
       LOGICAL:: found
       INTEGER:: nTypes
 
       CALL config%info('boundary', found, n_children = nBoundary)
       ALLOCATE(boundary(1:nBoundary))
       DO i = 1, nBoundary
-        WRITE(istring, '(i2)') i
-        object = 'boundary(' // TRIM(istring) // ')'
+        WRITE(iString, '(i2)') i
+        object = 'boundary(' // TRIM(iString) // ')'
 
         boundary(i)%n = i
         CALL config%get(object // '.name',            boundary(i)%name,            found)
@@ -823,18 +829,30 @@ MODULE moduleInput
         IF (nTypes /= nSpecies) CALL criticalError('Not enough boundary types defined in ' // object, 'readBoundary')
         ALLOCATE(boundary(i)%bTypes(1:nSpecies))
         DO s = 1, nSpecies
+          associate(bound => boundary(i)%bTypes(s)%obj)
             WRITE(sString,'(i2)') s
             object = 'boundary(' // TRIM(iString) // ').bTypes(' // TRIM(sString) // ')'
             CALL config%get(object // '.type', bType, found)
             SELECT CASE(bType)
             CASE('reflection')
-            ALLOCATE(boundaryReflection:: boundary(i)%bTypes(s)%obj)
+              ALLOCATE(boundaryReflection:: bound)
 
             CASE('absorption')
-            ALLOCATE(boundaryAbsorption:: boundary(i)%bTypes(s)%obj)
+              ALLOCATE(boundaryAbsorption:: bound)
 
             CASE('transparent')
-            ALLOCATE(boundaryTransparent:: boundary(i)%bTypes(s)%obj)
+              ALLOCATE(boundaryTransparent:: bound)
+
+            CASE('axis')
+              ALLOCATE(boundaryAxis:: bound)
+
+            CASE('wallTemperature')
+              CALL config%get(object // '.temperature', Tw, found)
+              IF (.NOT. found) CALL criticalError("temperature not found for wallTemperature boundary type", 'readBoundary')
+              CALL config%get(object // '.specificHeat', cw, found)
+              IF (.NOT. found) CALL criticalError("specificHeat not found for wallTemperature boundary type", 'readBoundary')
+
+              CALL initWallTemperature(bound, Tw, cw)
 
             CASE('ionization')
               !Neutral parameters
@@ -861,25 +879,28 @@ MODULE moduleInput
               CALL config%get(object // '.crossSection', crossSection, found)
               IF (.NOT. found) CALL criticalError("missing parameter 'crossSection' for neutrals in ionization", 'readBoundary')
 
-            CALL initIonization(boundary(i)%bTypes(s)%obj, species(s)%obj%m, m0, n0, v0, T0, &
+              CALL config%get(object // '.electronSecondary', electronSecondary, found)
+              electronSecondaryID = speciesName2Index(electronSecondary)
+              IF (found) THEN
+                CALL initIonization(bound, species(s)%obj%m, m0, n0, v0, T0, &
+                                                               speciesID, effTime, crossSection, eThreshold,electronSecondaryID)
+
+              ELSE
+                CALL initIonization(bound, species(s)%obj%m, m0, n0, v0, T0, &
                                                                speciesID, effTime, crossSection, eThreshold)
 
-          CASE('wallTemperature')
-            CALL config%get(object // '.temperature', Tw, found)
-            IF (.NOT. found) CALL criticalError("temperature not found for wallTemperature boundary type", 'readBoundary')
-            CALL config%get(object // '.specificHeat', cw, found)
-            IF (.NOT. found) CALL criticalError("specificHeat not found for wallTemperature boundary type", 'readBoundary')
+              END IF
 
-            CALL initWallTemperature(boundary(i)%bTypes(s)%obj, Tw, cw)
-
-          CASE('axis')
-            ALLOCATE(boundaryAxis:: boundary(i)%bTypes(s)%obj)
+            case('outflowAdaptive')
+              allocate(boundaryOutflowAdaptive:: bound)
 
             CASE DEFAULT
               CALL criticalError('Boundary type ' // bType // ' undefined', 'readBoundary')
 
             END SELECT
 
+          end associate
+
         END DO
 
       END DO
@@ -895,6 +916,7 @@ MODULE moduleInput
       USE moduleMeshInputGmsh2, ONLY: initGmsh2
       USE moduleMeshInputVTU,   ONLY: initVTU
       USE moduleMeshInput0D,    ONLY: init0D
+      USE moduleMeshInputText,  ONLY: initText
       USE moduleMesh3DCart
       USE moduleMesh2DCyl
       USE moduleMesh2DCart
@@ -912,7 +934,6 @@ MODULE moduleInput
       LOGICAL:: found
       CHARACTER(:), ALLOCATABLE:: meshFormat, meshFile
       REAL(8):: volume
-      CHARACTER(:), ALLOCATABLE:: meshFileVTU !Temporary to test VTU OUTPUT
 
       object = 'geometry'
 
@@ -954,9 +975,9 @@ MODULE moduleInput
         !Read the 0D mesh
         CALL mesh%readMesh(pathMeshParticle)
 
-        !Get the volumne
+        !Get the volume
         CALL config%get(object // '.volume', volume, found)
-        !Rescale the volumne
+        !Rescale the volume
         IF (found) THEN
           mesh%cells(1)%obj%volume = mesh%cells(1)%obj%volume*volume / Vol_ref
           mesh%nodes(1)%obj%v     = mesh%cells(1)%obj%volume
@@ -1044,6 +1065,20 @@ MODULE moduleInput
 
           END IF
 
+        case ("text")
+          !Check if the geometry is right.
+          if (mesh%dimen /= 1) then
+            call criticalError("Text mesh is only allowed for 1D geometries", 'readGeometry')
+          
+          end if
+
+          !Read the mesh
+          call initText(mesh)
+          if (doubleMesh) then
+            call initText(meshColl)
+
+          end if
+
         CASE DEFAULT
           CALL criticalError('Mesh format ' // meshFormat // ' not defined.', 'readGeometry')
 
@@ -1090,13 +1125,13 @@ MODULE moduleInput
       TYPE(json_file), INTENT(inout):: config
       CHARACTER(:), ALLOCATABLE:: object
       LOGICAL:: found
-      CHARACTER(2):: istring
+      CHARACTER(2):: iString
       INTEGER:: i
       CHARACTER(:), ALLOCATABLE:: speciesName
       REAL(8), ALLOCATABLE, DIMENSION(:):: r
       REAL(8), ALLOCATABLE, DIMENSION(:):: v1, v2, v3
       INTEGER, ALLOCATABLE, DIMENSION(:):: points
-      REAL(8):: timeStep
+      REAL(8):: everyTimeStep
 
       CALL config%info('output.probes', found, n_children = nProbes)
 
@@ -1104,7 +1139,7 @@ MODULE moduleInput
 
       DO i = 1, nProbes
         WRITE(iString, '(I2)') i
-        object = 'output.probes(' // trim(istring) // ')'
+        object = 'output.probes(' // trim(iString) // ')'
 
         CALL config%get(object // '.species', speciesName, found)
         CALL config%get(object // '.position', r, found)
@@ -1112,16 +1147,14 @@ MODULE moduleInput
         CALL config%get(object // '.velocity_2', v2, found)
         CALL config%get(object // '.velocity_3', v3, found)
         CALL config%get(object // '.points', points, found)
-        CALL config%get(object // '.timeStep', timeStep, found)
+        CALL config%get(object // '.timeStep', everyTimeStep, found)
 
         IF (ANY(points < 2)) CALL criticalError("Number of points in probe " // iString // " incorrect", 'readProbes')
 
-        CALL probe(i)%init(i, speciesName, r, v1, v2, v3, points, timeStep)
+        CALL probe(i)%init(i, speciesName, r, v1, v2, v3, points, everyTimeStep)
 
       END DO
 
-      CALL resetProbes(tInitial)
-
     END SUBROUTINE readProbes
 
     SUBROUTINE readEMBoundary(config)
@@ -1129,7 +1162,6 @@ MODULE moduleInput
       USE moduleOutput
       USE moduleErrors
       USE moduleEM
-      USE moduleRefParam
       USE moduleSpecies
       USE json_module
       IMPLICIT NONE
@@ -1137,34 +1169,72 @@ MODULE moduleInput
       TYPE(json_file), INTENT(inout):: config
       CHARACTER(:), ALLOCATABLE:: object
       LOGICAL:: found
-      CHARACTER(2):: istring
-      INTEGER:: i, e, s
+      CHARACTER(:), ALLOCATABLE:: typeEM
+      REAL(8):: potential
+      INTEGER:: physicalSurface
+      CHARACTER(:), ALLOCATABLE:: temporalProfile, temporalProfilePath
+      INTEGER:: b, s, n, ni
+      CHARACTER(2):: bString
       INTEGER:: info
       EXTERNAL:: dgetrf
 
       CALL config%info('boundaryEM', found, n_children = nBoundaryEM)
       
-      IF (found) ALLOCATE(boundEM(1:nBoundaryEM))
+      IF (found) THEN
+        ALLOCATE(boundaryEM(1:nBoundaryEM))
 
-      DO i = 1, nBoundaryEM
-        WRITE(istring, '(I2)') i
-        object = 'boundaryEM(' // trim(istring) // ')'
+      END IF
       
-        CALL config%get(object // '.type', boundEM(i)%typeEM, found)
+      DO b = 1, nBoundaryEM
+        WRITE(bString, '(I2)') b
+        object = 'boundaryEM(' // TRIM(bString) // ')'
 
-        SELECT CASE(boundEM(i)%typeEM)
+        CALL config%get(object // '.type', typeEM, found)
+
+        SELECT CASE(typeEM)
         CASE ("dirichlet")
-          CALL config%get(object // '.potential', boundEM(i)%potential, found)
-          IF (.NOT. found) &
+          CALL config%get(object // '.potential', potential, found)
+          IF (.NOT. found) THEN
             CALL criticalError('Required parameter "potential" for Dirichlet boundary condition not found', 'readEMBoundary')
-          boundEM(i)%potential = boundEM(i)%potential/Volt_ref
 
-          CALL config%get(object // '.physicalSurface', boundEM(i)%physicalSurface, found)
-          IF (.NOT. found) &
-            CALL criticalError('Required parameter "physicalSurface" for Dirichlet boundary condition not found', 'readEMBoundary')
+          END IF
+
+          CALL config%get(object // '.physicalSurface', physicalSurface, found)
+          IF (.NOT. found) THEN
+            CALL criticalError('Required parameter "physicalSurface" for Dirichlet boundary condition not found', &
+                               'readEMBoundary')
+
+          END IF
+
+          CALL initDirichlet(boundaryEM(b)%obj, physicalSurface, potential)
+
+        CASE ("dirichletTime")
+          CALL config%get(object // '.potential', potential, found)
+          IF (.NOT. found) THEN
+            CALL criticalError('Required parameter "potential" for Dirichlet Time boundary condition not found', &
+                               'readEMBoundary')
+
+          END IF
+
+          CALL config%get(object // '.temporalProfile', temporalProfile, found)
+          IF (.NOT. found) THEN
+            CALL criticalError('Required parameter "temporalProfile" for Dirichlet Time boundary condition not found', &
+                               'readEMBoundary')
+
+          END IF
+          temporalProfilePath = path // temporalProfile
+
+          CALL config%get(object // '.physicalSurface', physicalSurface, found)
+          IF (.NOT. found) THEN
+            CALL criticalError('Required parameter "physicalSurface" for Dirichlet Time boundary condition not found', &
+                               'readEMBoundary')
+
+          END IF
+
+          CALL initDirichletTime(boundaryEM(b)%obj, physicalSurface, potential, temporalProfilePath)
 
         CASE DEFAULT
-          CALL criticalError('Boundary type ' // boundEM(i)%typeEM // ' not yet supported', 'readEMBoundary')
+          CALL criticalError('Boundary type ' // typeEM // ' not yet supported', 'readEMBoundary')
 
         END SELECT
 
@@ -1183,18 +1253,28 @@ MODULE moduleInput
 
       END DO
 
-      IF (ALLOCATED(boundEM)) THEN
-        DO e = 1, mesh%numEdges
-          IF (ANY(mesh%edges(e)%obj%physicalSurface == boundEM(:)%physicalSurface)) THEN
-            DO i = 1, nBoundaryEM
-              IF (mesh%edges(e)%obj%physicalSurface == boundEM(i)%physicalSurface) THEN
-                CALL boundEM(i)%apply(mesh%edges(e)%obj)
+      ! Modify K matrix due to boundary conditions
+      DO b = 1, nBoundaryEM
+        SELECT TYPE(boundary => boundaryEM(b)%obj)
+        TYPE IS(boundaryEMDirichlet)
+          DO n = 1, boundary%nNodes
+            ni = boundary%nodes(n)%obj%n
+            mesh%K(ni, :)  = 0.D0
+            mesh%K(ni, ni) = 1.D0
 
-              END IF
           END DO
-          END IF
+
+        TYPE IS(boundaryEMDirichletTime)
+          DO n = 1, boundary%nNodes
+            ni = boundary%nodes(n)%obj%n
+            mesh%K(ni, :)  = 0.D0
+            mesh%K(ni, ni) = 1.D0
+
+          END DO
+
+        END SELECT
+
       END DO
-      END IF
 
       !Compute the PLU factorization of K once boundary conditions have been read
       CALL dgetrf(mesh%numNodes, mesh%numNodes, mesh%K, mesh%numNodes, mesh%IPIV, info)
@@ -1215,24 +1295,25 @@ MODULE moduleInput
 
       TYPE(json_file), INTENT(inout):: config
       INTEGER:: i
-      CHARACTER(2):: istring
+      CHARACTER(2):: iString
       CHARACTER(:), ALLOCATABLE:: object
       LOGICAL:: found
       CHARACTER(:), ALLOCATABLE:: speciesName
       CHARACTER(:), ALLOCATABLE:: name
       REAL(8):: v
-      REAL(8), ALLOCATABLE:: T(:), normal(:)
+      REAL(8), ALLOCATABLE:: temperature(:), normal(:)
       REAL(8):: flow
       CHARACTER(:), ALLOCATABLE:: units
       INTEGER:: physicalSurface
+      INTEGER:: particlesPerEdge
       INTEGER:: sp
 
       CALL config%info('inject', found, n_children = nInject)
       ALLOCATE(inject(1:nInject))
       nPartInj = 0
       DO i = 1, nInject
-        WRITE(istring, '(i2)') i
-        object = 'inject(' // trim(istring) // ')'
+        WRITE(iString, '(i2)') i
+        object = 'inject(' // trim(iString) // ')'
 
         !Find species
         CALL config%get(object // '.species', speciesName, found)
@@ -1240,7 +1321,7 @@ MODULE moduleInput
 
         CALL config%get(object // '.name',            name,            found)
         CALL config%get(object // '.v',               v,               found)
-        CALL config%get(object // '.T',               T,               found)
+        CALL config%get(object // '.T',               temperature,     found)
         CALL config%get(object // '.n',               normal,          found)
         IF (.NOT. found) THEN
           ALLOCATE(normal(1:3))
@@ -1249,8 +1330,10 @@ MODULE moduleInput
         CALL config%get(object // '.flow',            flow,            found)
         CALL config%get(object // '.units',           units,           found)
         CALL config%get(object // '.physicalSurface', physicalSurface, found)
+        particlesPerEdge = 0
+        CALL config%get(object // '.particlesPerEdge', particlesPerEdge, found)
 
-        CALL inject(i)%init(i, v, normal, T, flow, units, sp, physicalSurface)
+        CALL inject(i)%init(i, v, normal, temperature, flow, units, sp, physicalSurface, particlesPerEdge)
 
         CALL readVelDistr(config, inject(i), object)
         
@@ -1269,6 +1352,7 @@ MODULE moduleInput
       USE moduleCaseParam, ONLY: tauMin
       USE moduleMesh, ONLY: mesh
       USE moduleSpecies, ONLY: nSpecies
+      USE moduleRefParam, ONLY: ti_ref
       IMPLICIT NONE
 
       TYPE(json_file), INTENT(inout):: config
@@ -1282,7 +1366,10 @@ MODULE moduleInput
         CALL config%get('average.startTime', tStart, found)
 
         IF (found) THEN
-          tAverageStart = INT(tStart / tauMin)
+          tAverageStart = INT(tStart / ti_ref / tauMin)
+
+        ELSE
+          tAverageStart = 0
           
         END IF
 
@@ -1310,28 +1397,28 @@ MODULE moduleInput
       TYPE(injectGeneric), INTENT(inout):: inj
       CHARACTER(:), ALLOCATABLE, INTENT(in):: object
       INTEGER:: i
-      CHARACTER(2):: istring
+      CHARACTER(2):: iString
       CHARACTER(:), ALLOCATABLE:: fvType
       LOGICAL:: found
-      REAL(8):: v, T, m
+      REAL(8):: v, temperature, m
 
       !Reads species mass
       m = inj%species%m
       !Reads distribution functions for velocity
       DO i = 1, 3
-        WRITE(istring, '(i2)') i
-        CALL config%get(object // '.velDist('// TRIM(istring) //')', fvType, found)
-        IF (.NOT. found) CALL criticalError("No velocity distribution in direction " // istring // &
+        WRITE(iString, '(i2)') i
+        CALL config%get(object // '.velDist('// TRIM(iString) //')', fvType, found)
+        IF (.NOT. found) CALL criticalError("No velocity distribution in direction " // iString // &
                                             " found for " // object, 'readVelDistr')
 
         SELECT CASE(fvType)
         CASE ("Maxwellian")
-          T = inj%T(i)
-          CALL initVelDistMaxwellian(inj%v(i)%obj, t, m)
+          temperature = inj%temperature(i)
+          CALL initVelDistMaxwellian(inj%v(i)%obj, temperature, m)
 
         CASE ("Half-Maxwellian")
-          T = inj%T(i)
-          CALL initVelDistHalfMaxwellian(inj%v(i)%obj, t, m)
+          temperature = inj%temperature(i)
+          CALL initVelDistHalfMaxwellian(inj%v(i)%obj, temperature, m)
 
         CASE ("Delta")
           v = inj%vMod*inj%n(i)
@@ -1372,5 +1459,37 @@ MODULE moduleInput
 
     END SUBROUTINE readParallel
 
+    SUBROUTINE initOutput(inputFile)
+      USE moduleRefParam
+      USE moduleMesh,   ONLY: mesh, doubleMesh, pathMeshParticle, pathMeshColl
+      USE moduleOutput, ONLY: path, folder
+      IMPLICIT NONE
+
+      CHARACTER(:), ALLOCATABLE, INTENT(in):: inputFile
+      INTEGER:: fileReference = 30
+      !If everything is correct, creates the output folder
+      CALL EXECUTE_COMMAND_LINE('mkdir ' // path // folder )
+      !Copies input file to output folder
+      CALL EXECUTE_COMMAND_LINE('cp ' // inputFile // ' ' // path // folder)
+      !Copies particle mesh
+      IF (mesh%dimen > 0) THEN
+        CALL EXECUTE_COMMAND_LINE('cp ' // pathMeshParticle // ' ' // path // folder)
+        IF (doubleMesh) THEN
+          CALL EXECUTE_COMMAND_LINE('cp ' // pathMeshColl // ' ' // path // folder)
+
+        END IF
+
+      END IF
+
+      ! Write commit of fpakc
+      CALL SYSTEM('git rev-parse HEAD > ' // path // folder // '/' // 'fpakc_commit.txt')
+
+      ! Write file with reference values
+      OPEN (fileReference, file=path // folder // '/' // 'reference.txt')
+      WRITE(fileReference, "(7(1X,A20))")      'L_ref', 'v_ref', 'ti_ref', 'Vol_ref', 'EF_ref', 'Volt_ref', 'B_ref'
+      WRITE(fileReference, "(7(1X,ES20.6E3))")  L_ref,   v_ref,   ti_ref,   Vol_ref,   EF_ref,   Volt_ref,   B_ref
+      CLOSE(fileReference)
+
+    END SUBROUTINE initOutput
 
 END MODULE moduleInput

src/modules/mesh/1DCart/moduleMesh1DCart.f90

@@ -122,6 +122,8 @@ MODULE moduleMesh1DCart
 
       self%x = r1(1)
 
+      self%surface = 1.D0
+
       self%normal = (/ 1.D0, 0.D0, 0.D0 /)
 
       !Boundary index

src/modules/mesh/1DRad/moduleMesh1DRad.f90

@@ -122,6 +122,8 @@ MODULE moduleMesh1DRad
 
       self%r = r1(1)
 
+      self%surface = 1.D0
+
       self%normal = (/ 1.D0, 0.D0, 0.D0 /)
 
       !Boundary index

src/modules/mesh/2DCart/moduleMesh2DCart.f90

@@ -163,7 +163,7 @@ MODULE moduleMesh2DCart
       r2 = self%n2%getCoordinates()
       self%x  = (/r1(1), r2(1)/)
       self%y  = (/r1(2), r2(2)/)
-      self%weight = 1.D0
+      self%surface = SQRT((self%x(2) - self%x(1))**2 + (self%y(2) - self%y(1))**2)
       !Normal vector
       self%normal = (/ -(self%y(2)-self%y(1)), &
                          self%x(2)-self%x(1) , &
@@ -318,6 +318,8 @@ MODULE moduleMesh2DCart
       INTEGER, INTENT(in):: nNodes
       REAL(8):: fPsi(1:nNodes)
 
+      fPsi = 0.D0
+
       fPsi = (/ (1.D0 - Xi(1)) * (1.D0 - Xi(2)), &
                 (1.D0 + Xi(1)) * (1.D0 - Xi(2)), &
                 (1.D0 + Xi(1)) * (1.D0 + Xi(2)), &
@@ -492,34 +494,36 @@ MODULE moduleMesh2DCart
 
     END FUNCTION insideQuad
 
-    !Transform physical coordinates to element coordinates
+    !Transform physical coordinates to element coordinates with a Taylor series
     PURE FUNCTION phy2logQuad(self,r) RESULT(Xi) 
       IMPLICIT NONE
 
       CLASS(meshCell2DCartQuad), INTENT(in):: self
       REAL(8), INTENT(in):: r(1:3)
       REAL(8):: Xi(1:3)
-      REAL(8):: XiO(1:3), detJ, invJ(1:3,1:3), f(1:3)
+      REAL(8):: Xi0(1:3), detJ, pDerInv(1:2,1:2), deltaR(1:2), x0(1:2)
       REAL(8):: dPsi(1:3,1:4), fPsi(1:4)
       REAL(8):: pDer(1:3, 1:3)
       REAL(8):: conv
 
       !Iterative newton method to transform coordinates
       conv  = 1.D0
-      XiO  = 0.D0
+      Xi0   = 0.D0
+      Xi(3) = 0.D0
 
       DO WHILE(conv > 1.D-4)
-        dPsi = self%dPsi(XiO, 4)
+        fPsi           = self%fPsi(Xi0, 4)
+        x0(1)          = dot_product(fPsi, self%x)
+        x0(2)          = dot_product(fPsi, self%y)
+        deltaR         = r(1:2) - x0
+        dPsi           = self%dPsi(Xi0, 4)
         pDer           = self%partialDer(4, dPsi)
         detJ           = self%detJac(pDer)
-        invJ = self%invJac(pDer)
-        fPsi = self%fPsi(XiO, 4)
-        f = (/ DOT_PRODUCT(fPsi,self%x), &
-               DOT_PRODUCT(fPsi,self%y), &
-               0.D0 /) - r
-        Xi = XiO - MATMUL(invJ, f)/detJ
-        conv = MAXVAL(DABS(Xi-XiO),1)
-        XiO = Xi
+        pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
+        pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+        Xi(1:2)        = Xi0(1:2) + MATMUL(pDerInv, deltaR)/detJ
+        conv           = MAXVAL(DABS(Xi(1:2)-Xi0(1:2)),1)
+        Xi0(1:2)       = Xi(1:2)
 
       END DO
 
@@ -569,6 +573,7 @@ MODULE moduleMesh2DCart
       pDer = self%partialDer(4, dPsi)
       detJ = self%detJac(pDer)
       fPsi = self%fPsi(Xi, 4)
+
       !Compute total volume of the cell
       self%volume  = detJ*4.D0
       !Compute volume per node
@@ -675,8 +680,8 @@ MODULE moduleMesh2DCart
 
       dPsi = 0.D0
 
-      dPsi(1,:) = (/ -1.D0, 1.D0, 0.D0 /)
-      dPsi(2,:) = (/ -1.D0, 0.D0, 1.D0 /)
+      dPsi(1,1:3) = (/ -1.D0, 1.D0, 0.D0 /)
+      dPsi(2,1:3) = (/ -1.D0, 0.D0, 1.D0 /)
 
     END FUNCTION dPsiTria
 
@@ -762,6 +767,7 @@ MODULE moduleMesh2DCart
         pDer   = self%partialDer(3, dPsi)
         detJ   = self%detJac(pDer)
         invJ   = self%invJac(pDer)
+
         localK = localK + MATMUL(TRANSPOSE(MATMUL(invJ,dPsi)),MATMUL(invJ,dPsi))*wTria(l)/detJ
 
       END DO
@@ -820,19 +826,19 @@ MODULE moduleMesh2DCart
       CLASS(meshCell2DCartTria), INTENT(in):: self
       REAL(8), INTENT(in):: r(1:3)
       REAL(8):: Xi(1:3)
-      REAL(8):: deltaR(1:3)
-      REAL(8):: dPsi(1:3, 1:3)
+      REAL(8):: detJ, pDerInv(1:2,1:2), deltaR(1:2)
+      REAL(8):: dPsi(1:3,1:4)
       REAL(8):: pDer(1:3, 1:3)
-      REAL(8):: invJ(1:3,  1:3), detJ
 
       !Direct method to convert coordinates
-      Xi     = 0.D0
-      deltaR = (/ r(1) - self%x(1), r(2) - self%y(1), 0.D0 /)
+      Xi(3)          = 0.D0
+      deltaR         = (/ r(1) - self%x(1), r(2) - self%y(1) /)
       dPsi           = self%dPsi(Xi, 3)
       pDer           = self%partialDer(3, dPsi)
-      invJ   = self%invJac(pDer)
       detJ           = self%detJac(pDer)
-      Xi     = MATMUL(invJ,deltaR)/detJ
+      pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
+      pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+      Xi(1:2)        = MATMUL(pDerInv,deltaR)/detJ
 
     END FUNCTION phy2logTria
 
@@ -907,8 +913,8 @@ MODULE moduleMesh2DCart
 
       invJ = 0.D0
 
-      invJ(1, 1:2) = (/  pDer(2,2), -pDer(1,2) /)
-      invJ(2, 1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+      invJ(1, 1:2) = (/  pDer(2,2), -pDer(2,1) /)
+      invJ(2, 1:2) = (/ -pDer(1,2),  pDer(1,1) /)
       invJ(3, 3)   = 1.D0
 
     END FUNCTION invJ2DCart

src/modules/mesh/2DCyl/moduleMesh2DCyl.f90

@@ -144,6 +144,7 @@ MODULE moduleMesh2DCyl
       USE moduleSpecies
       USE moduleBoundary
       USE moduleErrors
+      USE moduleConstParam, ONLY: PI
       IMPLICIT NONE
 
       CLASS(meshEdge2DCyl), INTENT(out):: self
@@ -163,7 +164,15 @@ MODULE moduleMesh2DCyl
       r2 = self%n2%getCoordinates()
       self%z  = (/r1(1), r2(1)/)
       self%r  = (/r1(2), r2(2)/)
-      self%weight = r2(2)**2 - r1(2)**2
+      !Edge surface
+      IF (self%z(2) /= self%z(1)) THEN
+        self%surface = ABS(self%r(2) + self%r(1))*ABS(self%z(2) - self%z(1))
+
+      ELSE
+        self%surface = ABS(self%r(2)**2 - self%r(1)**2)
+
+      END IF
+      self%surface = self%surface * PI
       !Normal vector
       self%normal = (/ -(self%r(2)-self%r(1)), &
                          self%z(2)-self%z(1) , &
@@ -223,21 +232,13 @@ MODULE moduleMesh2DCyl
       CLASS(meshEdge2DCyl), INTENT(in):: self
       REAL(8):: rnd
       REAL(8):: r(1:3)
-      REAL(8):: dr, dz
+      REAL(8):: p1(1:2), p2(1:2)
 
       rnd = random()
-      dr  = self%r(2) - self%r(1)
-      dz  = self%z(2) - self%z(1)
-      IF (dr /= 0.D0) THEN
-        r(2) = dr * DSQRT(rnd) + self%r(1)
-        r(1) = dz * (r(2) - self%r(1))/dr + self%z(1)
-
-      ELSE
-        r(2) = self%r(1)
-        r(1) = dz * rnd + self%z(1)
-
-      END IF
 
+      p1 = (/self%z(1), self%r(1) /)
+      p2 = (/self%z(2), self%r(2) /)
+      r(1:2) = (1.D0 - rnd)*p1 + rnd*p2
       r(3)   =  0.D0
 
     END FUNCTION randPosEdge
@@ -246,7 +247,6 @@ MODULE moduleMesh2DCyl
     !QUAD FUNCTIONS
     !Init element
     SUBROUTINE initCellQuad2DCyl(self, n, p, nodes)
-      USE moduleRefParam
       IMPLICIT NONE
 
       CLASS(meshCell2DCylQuad), INTENT(out):: self
@@ -326,6 +326,8 @@ MODULE moduleMesh2DCyl
       INTEGER, INTENT(in):: nNodes
       REAL(8):: fPsi(1:nNodes)
 
+      fPsi = 0.D0
+
       fPsi = (/ (1.D0 - Xi(1)) * (1.D0 - Xi(2)), &
                 (1.D0 + Xi(1)) * (1.D0 - Xi(2)), &
                 (1.D0 + Xi(1)) * (1.D0 + Xi(2)), &
@@ -496,7 +498,7 @@ MODULE moduleMesh2DCyl
 
     END FUNCTION elemFQuad
 
-    !Checks if Xi is inside the element
+    !Check if Xi is inside the element
     PURE FUNCTION insideQuad(Xi) RESULT(ins)
       IMPLICIT NONE
 
@@ -508,34 +510,36 @@ MODULE moduleMesh2DCyl
 
     END FUNCTION insideQuad
 
-    !Transform physical coordinates to element coordinates
+    !Transform physical coordinates to element coordinates with a Taylor series
     PURE FUNCTION phy2logQuad(self,r) RESULT(Xi) 
       IMPLICIT NONE
 
       CLASS(meshCell2DCylQuad), INTENT(in):: self
       REAL(8), INTENT(in):: r(1:3)
       REAL(8):: Xi(1:3)
-      REAL(8):: XiO(1:3), detJ, invJ(1:3,1:3), f(1:3)
+      REAL(8):: Xi0(1:3), detJ, pDerInv(1:2,1:2), deltaR(1:2), x0(1:2)
       REAL(8):: dPsi(1:3,1:4), fPsi(1:4)
       REAL(8):: pDer(1:3, 1:3)
       REAL(8):: conv
 
       !Iterative newton method to transform coordinates
       conv  = 1.D0
-      XiO  = 0.D0
+      Xi0   = 0.D0
+      Xi(3) = 0.D0
 
       DO WHILE(conv > 1.D-4)
-        dPsi = self%dPsi(XiO, 4)
+        fPsi           = self%fPsi(Xi0, 4)
+        x0(1)          = dot_product(fPsi, self%z)
+        x0(2)          = dot_product(fPsi, self%r)
+        deltaR         = r(1:2) - x0
+        dPsi           = self%dPsi(Xi0, 4)
         pDer           = self%partialDer(4, dPsi)
         detJ           = self%detJac(pDer)
-        invJ = self%invJac(pDer)
-        fPsi = self%fPsi(XiO, 4)
-        f = (/ DOT_PRODUCT(fPsi,self%z), &
-               DOT_PRODUCT(fPsi,self%r), &
-               0.D0 /) - r
-        Xi = XiO - MATMUL(invJ, f)/detJ
-        conv = MAXVAL(DABS(Xi-XiO),1)
-        XiO = Xi
+        pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
+        pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+        Xi(1:2)        = Xi0(1:2) + MATMUL(pDerInv, deltaR)/detJ
+        conv           = MAXVAL(DABS(Xi(1:2)-Xi0(1:2)),1)
+        Xi0(1:2)       = Xi(1:2)
 
       END DO
 
@@ -553,7 +557,7 @@ MODULE moduleMesh2DCyl
 
       XiArray = (/ -Xi(2), Xi(1), Xi(2), -Xi(1) /)
       nextInt = MAXLOC(XiArray,1)
-      !Selects the higher value of directions and searches in that direction
+      !Select the higher value of directions and searches in that direction
       NULLIFY(neighbourElement)
       SELECT CASE (nextInt)
       CASE (1)
@@ -581,6 +585,7 @@ MODULE moduleMesh2DCyl
       REAL(8):: dPsi(1:3, 1:4), pDer(1:3, 1:3)
 
       self%volume  = 0.D0
+
       !2D 1 point Gauss Quad Integral
       Xi = 0.D0
       dPsi = self%dPsi(Xi, 4)
@@ -589,18 +594,18 @@ MODULE moduleMesh2DCyl
       fPsi = self%fPsi(Xi, 4)
       r = DOT_PRODUCT(fPsi,self%r)
       !Computes total volume of the cell
-      self%volume  = r*detJ*PI8 !4*2*pi
-      !Computes volume per node
-      Xi = (/-5.D-1, -5.D-1, 0.D0/)
+      self%volume  = r*detJ*PI8 !2*pi * 4 (weight of 1 point 2D-Gaussian integral)
+      !Computes volume per node. Change the radius point to calculate the area to improve accuracy near the axis.
+      Xi = (/-5.D-1, -0.25D0, 0.D0/)
       r = self%gatherF(Xi, 4, self%r)
       self%n1%v = self%n1%v + fPsi(1)*r*detJ*PI8
-      Xi = (/ 5.D-1, -5.D-1, 0.D0/)
+      Xi = (/ 5.D-1, -0.25D0, 0.D0/)
       r = self%gatherF(Xi, 4, self%r)
       self%n2%v = self%n2%v + fPsi(2)*r*detJ*PI8
-      Xi = (/ 5.D-1,  5.D-1, 0.D0/)
+      Xi = (/ 5.D-1,  0.75D0, 0.D0/)
       r = self%gatherF(Xi, 4, self%r)
       self%n3%v = self%n3%v + fPsi(3)*r*detJ*PI8
-      Xi = (/-5.D-1,  5.D-1, 0.D0/)
+      Xi = (/-5.D-1,  0.75D0, 0.D0/)
       r = self%gatherF(Xi, 4, self%r)
       self%n4%v = self%n4%v + fPsi(4)*r*detJ*PI8
 
@@ -702,8 +707,8 @@ MODULE moduleMesh2DCyl
 
       dPsi = 0.D0
 
-      dPsi(1,:) = (/ -1.D0, 1.D0, 0.D0 /)
-      dPsi(2,:) = (/ -1.D0, 0.D0, 1.D0 /)
+      dPsi(1,1:3) = (/ -1.D0, 1.D0, 0.D0 /)
+      dPsi(2,1:3) = (/ -1.D0, 0.D0, 1.D0 /)
 
     END FUNCTION dPsiTria
 
@@ -855,19 +860,19 @@ MODULE moduleMesh2DCyl
       CLASS(meshCell2DCylTria), INTENT(in):: self
       REAL(8), INTENT(in):: r(1:3)
       REAL(8):: Xi(1:3)
-      REAL(8):: deltaR(1:3)
-      REAL(8):: dPsi(1:3, 1:3)
+      REAL(8):: detJ, pDerInv(1:2,1:2), deltaR(1:2)
+      REAL(8):: dPsi(1:3,1:4)
       REAL(8):: pDer(1:3, 1:3)
-      REAL(8):: invJ(1:3,  1:3), detJ
 
       !Direct method to convert coordinates
-      Xi     = 0.D0
-      deltaR = (/ r(1) - self%z(1), r(2) - self%r(1), 0.D0 /)
+      Xi(3)          = 0.D0
+      deltaR         = (/ r(1) - self%z(1), r(2) - self%r(1) /)
       dPsi           = self%dPsi(Xi, 3)
       pDer           = self%partialDer(3, dPsi)
-      invJ   = self%invJac(pDer)
       detJ           = self%detJac(pDer)
-      Xi     = MATMUL(invJ,deltaR)/detJ
+      pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
+      pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+      Xi(1:2)        = MATMUL(pDerInv,deltaR)/detJ
 
     END FUNCTION phy2logTria
 
@@ -945,8 +950,8 @@ MODULE moduleMesh2DCyl
 
       invJ = 0.D0
 
-      invJ(1, 1:2) = (/  pDer(2,2), -pDer(1,2) /)
-      invJ(2, 1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+      invJ(1, 1:2) = (/  pDer(2,2), -pDer(2,1) /)
+      invJ(2, 1:2) = (/ -pDer(1,2),  pDer(1,1) /)
       invJ(3, 3)   = 1.D0
 
     END FUNCTION invJ2DCyl

src/modules/mesh/3DCart/moduleMesh3DCart.f90

@@ -109,6 +109,7 @@ MODULE moduleMesh3DCart
       USE moduleBoundary
       USE moduleErrors
       USE moduleMath
+      USE moduleRefParam, ONLY: L_ref
       IMPLICIT NONE
 
       CLASS(meshEdge3DCartTria), INTENT(out):: self
@@ -142,6 +143,8 @@ MODULE moduleMesh3DCart
       self%normal = crossProduct(vec1, vec2)
       self%normal = normalize(self%normal)
 
+      self%surface = 1.D0/L_ref**2 !TODO: FIX THIS WHEN MOVING TO 3D
+
       !Boundary index
       self%boundary => boundary(bt)
       ALLOCATE(self%fBoundary(1:nSpecies))

src/modules/mesh/inout/0D/moduleMeshOutput0D.f90

@@ -1,22 +1,22 @@
 MODULE moduleMeshOutput0D
 
   CONTAINS
-    SUBROUTINE printOutput0D(self, t)
+    SUBROUTINE printOutput0D(self)
       USE moduleMesh
       USE moduleRefParam
       USE moduleSpecies
       USE moduleOutput
+      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
-      INTEGER, INTENT(in):: t
       INTEGER:: i
       TYPE(outputFormat):: output
       CHARACTER(:), ALLOCATABLE:: fileName
 
       DO i = 1, nSpecies
         fileName='OUTPUT_' // species(i)%obj%name // '.dat'
-        IF (t == 0) THEN
+        IF (timeStep == 0) THEN
           OPEN(20, file = path // folder // '/' // fileName, action = 'write')
           WRITE(20, "(A1, 14X, A5, A20, 40X, A20, 2(A20))") "#","t (s)","density (m^-3)", "velocity (m/s)", &
                                                                         "pressure (Pa)", "temperature (K)"
@@ -27,14 +27,17 @@ MODULE moduleMeshOutput0D
         
         OPEN(20, file = path // folder // '/' // fileName, position = 'append', action = 'write')
         CALL calculateOutput(self%nodes(1)%obj%output(i), output, self%nodes(1)%obj%v, species(i)%obj)
-        WRITE(20, "(7(ES20.6E3))") REAL(t)*tauMin*ti_ref, output%density, output%velocity, output%pressure, output%temperature
+        WRITE(20, "(7(ES20.6E3))") REAL(timeStep)*tauMin*ti_ref, output%density,    &
+                                                                 output%velocity,   &
+                                                                 output%pressure,   &
+                                                                 output%temperature
         CLOSE(20)
 
       END DO
 
     END SUBROUTINE printOutput0D
 
-    SUBROUTINE printColl0D(self, t)
+    SUBROUTINE printColl0D(self)
       USE moduleMesh
       USE moduleRefParam
       USE moduleCaseParam
@@ -43,12 +46,11 @@ MODULE moduleMeshOutput0D
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(in):: self
-      INTEGER, INTENT(in):: t
       CHARACTER(:), ALLOCATABLE:: fileName
       INTEGER:: k
 
       fileName='OUTPUT_Collisions.dat'
-      IF (t == tInitial) THEN
+      IF (timeStep == tInitial) THEN
         OPEN(20, file = path // folder // '/' // fileName, action = 'write')
         WRITE(20, "(A1, 14X, A5, A20)") "#","t (s)","collisions"
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
@@ -57,12 +59,12 @@ MODULE moduleMeshOutput0D
       END IF
       
       OPEN(20, file = path // folder // '/' // fileName, position = 'append', action = 'write')
-      WRITE(20, "(ES20.6E3, 10I20)") REAL(t)*tauMin*ti_ref, (self%cells(1)%obj%tallyColl(k)%tally, k=1,nCollPairs)
+      WRITE(20, "(ES20.6E3, 10I20)") REAL(timeStep)*tauMin*ti_ref, (self%cells(1)%obj%tallyColl(k)%tally, k=1,nCollPairs)
       CLOSE(20)
 
     END SUBROUTINE printColl0D
 
-    SUBROUTINE printEM0D(self, t)
+    SUBROUTINE printEM0D(self)
       USE moduleMesh
       USE moduleRefParam
       USE moduleCaseParam
@@ -70,7 +72,6 @@ MODULE moduleMeshOutput0D
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
-      INTEGER, INTENT(in):: t
 
     END SUBROUTINE printEM0D
 

src/modules/mesh/inout/gmsh2/moduleMeshInputGmsh2.f90

@@ -108,6 +108,7 @@ MODULE moduleMeshInputGmsh2
       READ(10, *) totalNumElem
 
       !Count edges and volume elements
+      numEdges = 0
       SELECT TYPE(self)
       TYPE IS(meshParticles)
         self%numEdges = 0
@@ -328,7 +329,7 @@ MODULE moduleMeshInputGmsh2
 
       DO i = 1, numNodes
         !Reads the density
-        READ(10, *), e, density(i)
+        READ(10, *) e, density(i)
 
       END DO
 
@@ -339,7 +340,7 @@ MODULE moduleMeshInputGmsh2
 
       DO i = 1, numNodes
         !Reads the velocity
-        READ(10, *), e, velocity(i, 1:3)
+        READ(10, *) e, velocity(i, 1:3)
 
       END DO
 

src/modules/mesh/inout/gmsh2/moduleMeshOutputGmsh2.f90

@@ -80,50 +80,50 @@ MODULE moduleMeshOutputGmsh2
     END SUBROUTINE writeGmsh2FooterElementData
 
     !Prints the scattered properties of particles into the nodes
-    SUBROUTINE printOutputGmsh2(self, t)
+    SUBROUTINE printOutputGmsh2(self)
       USE moduleMesh
       USE moduleRefParam
       USE moduleSpecies
       USE moduleOutput
       USE moduleMeshInoutCommon
+      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
-      INTEGER, INTENT(in):: t
       INTEGER:: n, i
       TYPE(outputFormat):: output(1:self%numNodes)
       REAL(8):: time
       CHARACTER(:), ALLOCATABLE:: fileName
 
-      time = DBLE(t)*tauMin*ti_ref
+      time = DBLE(timeStep)*tauMin*ti_ref
 
       DO i = 1, nSpecies
-        fileName = formatFileName(prefix, species(i)%obj%name, 'msh', t)
+        fileName = formatFileName(prefix, species(i)%obj%name, 'msh', timeStep)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (60, file = path // folder // '/' //  fileName)
 
         CALL writeGmsh2HeaderMesh(60)
 
-        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' density (m^-3)', t, time, 1, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' density (m^-3)', timeStep, time, 1, self%numNodes)
         DO n=1, self%numNodes
           CALL calculateOutput(self%nodes(n)%obj%output(i), output(n), self%nodes(n)%obj%v, species(i)%obj)
           WRITE(60, "(I6,ES20.6E3)") n, output(n)%density
         END DO
         CALL writeGmsh2FooterNodeData(60)
 
-        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' velocity (m s^-1)', t, time, 3, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' velocity (m s^-1)', timeStep, time, 3, self%numNodes)
         DO n=1, self%numNodes
           WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%velocity
         END DO
         CALL writeGmsh2FooterNodeData(60)
 
-        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' Pressure (Pa)', t, time, 1, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' Pressure (Pa)', timeStep, time, 1, self%numNodes)
         DO n=1, self%numNodes
           WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%pressure
         END DO
         CALL writeGmsh2FooterNodeData(60)
 
-        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' Temperature (K)', t, time, 1, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' Temperature (K)', timeStep, time, 1, self%numNodes)
         DO n=1, self%numNodes
           WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%temperature
         END DO
@@ -135,7 +135,7 @@ MODULE moduleMeshOutputGmsh2
     END SUBROUTINE printOutputGmsh2
 
     !Prints the number of collisions into the volumes
-    SUBROUTINE printCollGmsh2(self, t)
+    SUBROUTINE printCollGmsh2(self)
       USE moduleMesh
       USE moduleRefParam
       USE moduleCaseParam
@@ -145,7 +145,6 @@ MODULE moduleMeshOutputGmsh2
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(in):: self
-      INTEGER, INTENT(in):: t
       INTEGER:: numEdges
       INTEGER:: k, c
       INTEGER:: n
@@ -167,9 +166,9 @@ MODULE moduleMeshOutputGmsh2
       END SELECT
 
       IF (collOutput) THEN
-        time = DBLE(t)*tauMin*ti_ref
+        time = DBLE(timeStep)*tauMin*ti_ref
 
-        fileName = formatFileName(prefix, 'Collisions', 'msh', t)
+        fileName = formatFileName(prefix, 'Collisions', 'msh', timeStep)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (60, file = path // folder // '/' //  fileName)
 
@@ -179,7 +178,7 @@ MODULE moduleMeshOutputGmsh2
           DO c = 1, interactionMatrix(k)%amount
             WRITE(cString, "(I2)") c
             title = '"Pair ' // interactionMatrix(k)%sp_i%name // '-' // interactionMatrix(k)%sp_j%name // ' collision ' // cString
-            CALL writeGmsh2HeaderElementData(60, title, t, time, 1, self%numCells)
+            CALL writeGmsh2HeaderElementData(60, title, timeStep, time, 1, self%numCells)
             DO n=1, self%numCells
               WRITE(60, "(I6,I10)") n + numEdges, self%cells(n)%obj%tallyColl(k)%tally(c)
             END DO
@@ -196,7 +195,7 @@ MODULE moduleMeshOutputGmsh2
     END SUBROUTINE printCollGmsh2
 
     !Prints the electrostatic EM properties into the nodes and volumes
-    SUBROUTINE printEMGmsh2(self, t)
+    SUBROUTINE printEMGmsh2(self)
       USE moduleMesh
       USE moduleRefParam
       USE moduleCaseParam
@@ -205,7 +204,6 @@ MODULE moduleMeshOutputGmsh2
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
-      INTEGER, INTENT(in):: t
       INTEGER:: n, e
       REAL(8):: time
       CHARACTER(:), ALLOCATABLE:: fileName
@@ -214,27 +212,27 @@ MODULE moduleMeshOutputGmsh2
       Xi = (/ 0.D0, 0.D0, 0.D0 /)
 
       IF (emOutput) THEN
-        time = DBLE(t)*tauMin*ti_ref
+        time = DBLE(timeStep)*tauMin*ti_ref
 
-        fileName = formatFileName(prefix, 'EMField', 'msh', t)
+        fileName = formatFileName(prefix, 'EMField', 'msh', timeStep)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (20, file = path // folder // '/' //  fileName)
 
         CALL writeGmsh2HeaderMesh(20)
 
-        CALL writeGmsh2HeaderNodeData(20, 'Potential (V)', t, time, 1, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(20, 'Potential (V)', timeStep, time, 1, self%numNodes)
         DO n=1, self%numNodes
           WRITE(20, *) n, self%nodes(n)%obj%emData%phi*Volt_ref
         END DO
         CALL writeGmsh2FooterNodeData(20)
         
-        CALL writeGmsh2HeaderElementData(20, 'Electric Field (V m^-1)', t, time, 3, self%numCells)
+        CALL writeGmsh2HeaderElementData(20, 'Electric Field (V m^-1)', timeStep, time, 3, self%numCells)
         DO e=1, self%numCells
           WRITE(20, *) e+self%numEdges, self%cells(e)%obj%gatherElectricField(Xi)*EF_ref
         END DO
         CALL writeGmsh2FooterElementData(20)
 
-        CALL writeGmsh2HeaderNodeData(20, 'Magnetic Field (T)', t, time, 3, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(20, 'Magnetic Field (T)', timeStep, time, 3, self%numNodes)
         DO n=1, self%numNodes
           WRITE(20, *) n, self%nodes(n)%obj%emData%B * B_ref
         END DO

src/modules/mesh/inout/makefile

@@ -1,4 +1,4 @@
-all: vtu.o gmsh2.o 0D.o
+all: vtu.o gmsh2.o 0D.o text.o
 
 vtu.o: moduleMeshInoutCommon.o
 	$(MAKE) -C vtu all
@@ -9,5 +9,8 @@ gmsh2.o:
 0D.o:
 	$(MAKE) -C 0D all
 
+text.o:
+	$(MAKE) -C text all
+
 %.o: %.f90
 	$(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@

src/modules/mesh/inout/moduleMeshInoutCommon.f90

@@ -3,17 +3,17 @@ MODULE moduleMeshInoutCommon
   CHARACTER(LEN=4):: prefix = 'Step'
 
   CONTAINS
-    PURE FUNCTION formatFileName(prefix, suffix, extension, t) RESULT(fileName)
+    PURE FUNCTION formatFileName(prefix, suffix, extension, timeStep) RESULT(fileName)
       USE moduleOutput
       IMPLICIT NONE
 
       CHARACTER(*), INTENT(in):: prefix, suffix, extension
-      INTEGER, INTENT(in), OPTIONAL:: t
+      INTEGER, INTENT(in), OPTIONAL:: timeStep
       CHARACTER (LEN=iterationDigits):: tString
       CHARACTER(:), ALLOCATABLE:: fileName
 
-      IF (PRESENT(t)) THEN
-        WRITE(tString, iterationFormat) t
+      IF (PRESENT(timeStep)) THEN
+        WRITE(tString, iterationFormat) timeStep
         fileName = prefix //  '_' // tString // '_' // suffix // '.' // extension
 
       ELSE

src/modules/mesh/inout/text/makefile

@@ -0,0 +1,7 @@
+all: moduleMeshInputText.o moduleMeshOutputText.o
+
+moduleMeshInputText.o: moduleMeshOutputText.o moduleMeshInputText.f90
+	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
+
+%.o: %.f90
+	$(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@

src/modules/mesh/inout/text/moduleMeshInputText.f90

@@ -0,0 +1,232 @@
+module moduleMeshInputText
+  !The mesh is stored as a column-wise text file.
+  !Aimed for simple geometries in 1D
+
+  contains
+    !Inits the text mesh
+    subroutine initText(self)
+      use moduleMesh
+      use moduleMeshOutputText
+      implicit none
+
+      class(meshGeneric), intent(inout), target:: self 
+
+      if (associated(meshForMCC,self)) then
+        self%printColl => printCollText
+
+      end if
+
+      select type(self)
+      type is (meshParticles)
+        self%printOutput  => printOutputText
+        self%printEM      => printEMText
+        self%printAverage => printAverageText
+
+        self%readInitial  => readInitialText
+
+      end select
+
+      self%readMesh => readText
+
+    end subroutine initText
+
+    !Reads the text mesh
+    subroutine readText(self, filename)
+      use moduleMesh
+      use moduleMesh1DCart
+      use moduleMesh1DRad
+      use moduleErrors
+      implicit none
+
+      class(meshGeneric), intent(inout):: self
+      character(:), allocatable, intent(in):: filename !Dummy file, not used
+      integer:: fileID, reason
+      character(len=256):: line
+      integer:: nNodes
+      real(8):: r(1:3) !dummy 3D coordinate
+      integer:: physicalID
+      integer:: n, c
+      integer, allocatable:: p(:)
+      integer:: bt
+
+      fileID = 10
+
+      open(fileID, file=trim(filename))
+
+      !Skip header
+      read(fileID, *)
+
+      !Get number of nodes
+      nNodes = 0
+      do
+        read(fileID, *, iostat=reason) line
+
+        if (reason > 0) then
+          call criticalError('Error reading mesh file', 'readText')
+
+        else if (reason < 0) then
+          exit
+
+        else if (len(line) > 0) then
+          nNodes = nNodes + 1
+
+        end if
+
+      end do
+
+      if (nNodes == 0) then
+        call criticalError('No nodes read in mesh file', 'readText')
+
+      end if
+
+      self%numNodes = nNodes
+      allocate(self%nodes(1:self%numNodes))
+
+      SELECT TYPE(self)
+      TYPE IS(meshParticles)
+        ALLOCATE(self%K(1:self%numNodes, 1:self%numNodes))
+        ALLOCATE(self%IPIV(1:self%numNodes, 1:self%numNodes))
+        self%K = 0.D0
+        self%IPIV = 0
+
+      END SELECT
+
+      self%numCells = nNodes - 1
+      allocate(self%cells(1:self%numCells))
+
+      select type(self)
+      type is (meshParticles)
+        self%numEdges = 2
+
+        allocate(self%edges(1:self%numEdges))
+
+      end select
+
+      !Read the mesh now
+      rewind(fileID)
+      
+      !Skip header
+      read(fileID, *)
+
+      !Allocate nodes and edges
+      do n = 1, self%numNodes
+        r = 0.D0
+
+        read(fileID, *) r(1), physicalID
+
+        select case(self%geometry)
+        case("Cart")
+          allocate(meshNode1DCart:: self%nodes(n)%obj)
+
+        case("Rad")
+          allocate(meshNode1DRad:: self%nodes(n)%obj)
+
+        end select
+
+        !Init nodes
+        call self%nodes(n)%obj%init(n, r)
+
+        !Allocate edges if required)
+        select type(self)
+        type is (meshParticles)
+          if ((physicalID == 1) .or. (physicalID == 2)) then
+            select case(self%geometry)
+            case("Cart")
+              allocate(meshEdge1DCart:: self%edges(physicalID)%obj)
+
+            case("Rad")
+              allocate(meshEdge1DRad:: self%edges(physicalID)%obj)
+            
+            end select
+
+            allocate(p(1))
+            p(1) = n
+            bt = getBoundaryId(physicalID)
+            call self%edges(physicalID)%obj%init(physicalID, p, physicalID, physicalID)
+            deallocate(p)
+
+          end if
+
+        end select
+
+      end do
+
+      !Allocate cells
+      n = 1
+      allocate(p(1:2))
+      do c = 1, self%numCells
+        p(1) = n
+        n = n + 1
+        p(2) = n
+        
+        select case(self%geometry)
+        case("Cart")
+          allocate(meshCell1DCartSegm:: self%cells(c)%obj)
+
+        case("Rad")
+          allocate(meshCell1DRadSegm:: self%cells(c)%obj)
+
+        end select
+
+        call self%cells(c)%obj%init(c, p, self%nodes)
+
+
+      end do
+      deallocate(p)
+
+      close(fileID)
+
+      !Call mesh connectivity
+      CALL self%connectMesh
+
+    end subroutine readText
+
+    subroutine readInitialText(filename, density, velocity, temperature)
+      use moduleErrors
+      implicit none
+
+      character(:), allocatable, intent(in):: filename
+      real(8), allocatable, intent(out), dimension(:):: density
+      real(8), allocatable, intent(out), dimension(:,:):: velocity
+      real(8), allocatable, intent(out), dimension(:):: temperature
+      integer:: fileID, reason
+      character(len=256):: line
+      integer:: nNodes
+      integer:: n
+
+      fileID = 10
+
+      open(fileID, file=trim(filename))
+
+      do 
+        read(fileID, *, iostat=reason) line
+      
+        if (reason > 0) then
+          call criticalError('Error reading mesh file', 'readText')
+
+        else if (reason < 0) then
+          exit
+
+        else if (len(line) > 0) then
+          nNodes = nNodes + 1
+
+        end if
+
+      end do
+
+      allocate(density(1:nNodes))
+      allocate(velocity(1:nNodes, 1:3))
+      allocate(temperature(1:nNodes))
+
+      rewind(fileID)
+
+      do n = 1, nNodes
+        read(fileID, *) density(n), velocity(n, 1:3), temperature(n)
+
+      end do
+
+      close(fileID)
+
+    end subroutine readInitialText
+
+end module moduleMeshInputText

src/modules/mesh/inout/text/moduleMeshOutputText.f90

@@ -0,0 +1,265 @@
+module moduleMeshOutputText
+  contains
+
+    subroutine writeSpeciesOutput(self, fileID, speciesIndex)
+      use moduleMesh
+      use moduleOutput
+      use moduleRefParam, only: L_ref
+      implicit none
+
+      class(meshParticles), INTENT(in):: self
+      integer, intent(in):: fileID
+      integer, intent(in):: speciesIndex
+      real(8):: r(1:3)
+      type(outputFormat):: output
+      integer:: n
+
+      do n = 1, self%numNodes
+        r = self%nodes(n)%obj%getCoordinates()
+        call calculateOutput(self%nodes(n)%obj%output(speciesIndex), output, self%nodes(n)%obj%v, species(speciesIndex)%obj)
+
+        write(fileID, '(5(ES0.6E3,","),ES0.6E3)') r(1)*L_ref, output%density, output%velocity, output%temperature
+
+      end do
+
+    end subroutine writeSpeciesOutput
+
+    subroutine writeCollOutput(self, fileID)
+      use moduleMesh
+      use moduleCollisions
+      use moduleRefParam, only: L_ref
+      implicit none
+
+      class(meshGeneric), intent(in):: self
+      integer, intent(in):: fileID
+      integer:: n, k, c
+      
+      do n = 1, self%numCells
+        write(fileID, '(I0)', advance='no') n
+
+        do k = 1, nCollPairs
+          do c = 1, interactionMatrix(k)%amount
+            write(fileID, '(",",I0)', advance='no') self%cells(n)%obj%tallyColl(k)%tally(c)
+
+          end do
+
+        end do
+        write(fileID, *)
+
+      end do
+
+    end subroutine writeCollOutput
+
+    subroutine writeEMOutput(self, fileID)
+      use moduleMesh
+      use moduleRefParam, only: L_ref, Volt_ref, B_ref, EF_ref
+      implicit none
+
+      class(meshParticles), intent(in):: self
+      integer, intent(in):: fileID
+      integer:: n, c
+      real(8):: r(1:3), Xi(1:3)
+
+      do n = 1, self%numNodes
+        r = self%nodes(n)%obj%getCoordinates()
+        if (n == self%numNodes) then
+          Xi = (/ 1.D0, 0.D0, 0.D0 /)
+          c = self%numNodes - 1
+
+        else
+          Xi = (/ 0.D0, 0.D0, 0.D0 /)
+          c = n
+
+        end if
+
+        associate(output => self%nodes(n)%obj%emData)
+          write(fileID, '(7(ES0.6E3,","),ES0.6E3)') r(1)*L_ref, &
+                                                    output%phi*Volt_ref, &
+                                                    self%cells(c)%obj%gatherElectricField(Xi)*EF_ref, &
+                                                    output%B*B_ref
+
+        end associate
+
+      end do
+
+    end subroutine writeEMOutput
+
+    subroutine writeAverage(self, fileIDMean, &
+                                  fileIDDeviation, &
+                                  speciesIndex)
+
+      use moduleMesh
+      use moduleOutput
+      use moduleAverage
+      use moduleRefParam, only: L_ref
+      implicit none
+
+      class(meshParticles), intent(in):: self
+      integer, intent(in):: fileIDMean, fileIDDeviation
+      INTEGER, intent(in):: speciesIndex
+      real(8):: r(1:3)
+      type(outputFormat):: outputMean
+      type(outputFormat):: outputDeviation
+      integer:: n
+
+      do n = 1, self%numNodes
+        r = self%nodes(n)%obj%getCoordinates()
+
+        call calculateOutput(averageScheme(n)%mean%output(speciesIndex),      outputMean,      &
+                             self%nodes(n)%obj%v, species(speciesIndex)%obj)
+
+        write(fileIDMean, '(5(ES0.6E3,","),ES0.6E3)') r(1)*L_ref, outputMean%density, outputMean%velocity, outputMean%temperature
+
+        call calculateOutput(averageScheme(n)%deviation%output(speciesIndex), outputDeviation, &
+                             self%nodes(n)%obj%v, species(speciesIndex)%obj)
+
+        write(fileIDDeviation, '(5(ES0.6E3,","),ES0.6E3)') r(1)*L_ref, outputDeviation%density, outputDeviation%velocity, outputDeviation%temperature
+
+      end do
+
+    end subroutine writeAverage
+
+    subroutine printOutputText(self)
+      use moduleMesh
+      use moduleSpecies
+      use moduleMeshInoutCommon
+      use moduleCaseParam, ONLY: timeStep
+      implicit none
+      
+      class(meshParticles), intent(in):: self
+
+      INTEGER:: s, fileID
+      character(:), allocatable:: fileName
+
+      fileID = 60
+
+      do s = 1, nSpecies
+        fileName = formatFileName(prefix, species(s)%obj%name, 'csv', timeStep)
+        write(*, "(6X,A15,A)") "Creating file: ", fileName
+        open (fileID, file = path // folder // '/' //  fileName)
+
+        write(fileID, '(5(A,","),A)') 'Position (m)', &
+                                      'Density (m^-3)', &
+                                      'Velocity (m s^-1):0', 'Velocity (m s^-1):1', 'Velocity (m s^-1):2', &
+                                      'Temperature (K)'
+
+        call writeSpeciesOutput(self, fileID, s)
+
+        close(fileID)
+
+      end do
+
+    end subroutine printOutputText
+
+    subroutine printCollText(self)
+      use moduleMesh
+      use moduleOutput
+      use moduleMeshInoutCommon
+      use moduleCaseParam, only: timeStep
+      implicit none
+      
+      class(meshGeneric), intent(in):: self
+      integer:: fileID
+      character(:), allocatable:: fileName
+      integer:: k, c
+      character (len=2):: cString
+
+      fileID = 62
+
+      if (collOutput) then
+        fileName = formatFileName(prefix, 'Collisions', 'csv', timeStep)
+        write(*, "(6X,A15,A)") "Creating file: ", fileName
+        open (fileID, file = path // folder // '/' //  fileName)
+
+        write(fileID, '(A)', advance='no') "Cell"
+        do k = 1, nCollPairs
+          do c = 1, interactionMatrix(k)%amount
+            write(cString, "(I2)") c
+            write(fileID, '(",",A)', advance='no') 'Pair ' // interactionMatrix(k)%sp_i%name // '-' // interactionMatrix(k)%sp_j%name // ' collision ' // cString
+
+          end do
+        end do
+
+        write(fileID, *)
+
+        call writeCollOutput(self, fileID)
+
+        close(fileID)
+
+      end if
+
+    end subroutine printCollText
+
+    subroutine printEMText(self)
+      use moduleMesh
+      use moduleMeshInoutCommon
+      use moduleCaseParam, only: timeStep
+      implicit none
+      
+      class(meshParticles), intent(in):: self
+      integer:: fileID
+      character(:), allocatable:: fileName
+
+      fileID = 64
+
+      if (emOutput) then
+        fileName = formatFileName(prefix, 'EMField', 'csv', timeStep)
+        write(*, "(6X,A15,A)") "Creating file: ", fileName
+        open (fileID, file = path // folder // '/' //  fileName)
+
+        write(fileID, '(8(A,","),A)') 'Position (m)', &
+                                      'Potential (V)', &
+                                      'Electric Field (V m^-1):0', 'Electric Field (V m^-1):1', 'Electric Field (V m^-1):2', &
+                                      'Magnetic Field (T):0',      'Magnetic Field (T):1',      'Magnetic Field (T):2'
+
+        call writeEMOutput(self, fileID)
+
+        close(fileID)
+
+      end if
+
+    end subroutine printEMText
+
+    subroutine printAverageText(self)
+      use moduleMesh
+      use moduleSpecies
+      use moduleMeshInoutCommon
+      implicit none
+      
+      class(meshParticles), intent(in):: self
+      integer:: s
+      integer:: fileIDMean, fileIDDeviation
+      character(:), allocatable:: fileNameMean, fileNameDeviation
+
+      fileIDMean = 66
+      fileIDDeviation = 67
+
+      do s = 1, nSpecies
+        fileNameMean = formatFileName('Average_mean', species(s)%obj%name, 'csv', timeStep)
+        write(*, "(6X,A15,A)") "Creating file: ", fileNameMean
+        open (fileIDMean, file = path // folder // '/' //  fileNameMean)
+
+        write(fileIDMean, '(5(A,","),A)') 'Position (m)', &
+                                          'Density, mean (m^-3)', &
+                                          'Velocity, mean (m s^-1):0', 'Velocity (m s^-1):1', 'Velocity (m s^-1):2', &
+                                          'Temperature, mean (K)'
+
+        fileNameDeviation = formatFileName('Average_deviation', species(s)%obj%name, 'csv', timeStep)
+        write(*, "(6X,A15,A)") "Creating file: ", fileNameDeviation
+        open (fileIDDeviation, file = path // folder // '/' //  fileNameDeviation)
+
+        write(fileIDDeviation, '(5(A,","),A)') 'Position (m)', &
+                                               'Density, deviation (m^-3)', &
+                                               'Velocity, deviation (m s^-1):0', 'Velocity (m s^-1):1', 'Velocity (m s^-1):2', &
+                                               'Temperature, deviation (K)'
+
+        call writeAverage(self, fileIDMean, fileIDDeviation, s)
+
+        close(fileIDMean)
+        close(fileIDDeviation)
+
+      end do
+
+    end subroutine printAverageText
+
+end module moduleMeshOutputText

src/modules/mesh/inout/vtu/moduleMeshInputVTU.f90

@@ -167,7 +167,7 @@ MODULE moduleMeshInputVTU
       CLASS(meshGeneric), INTENT(inout):: self
       CHARACTER(:), ALLOCATABLE, INTENT(in):: filename
       REAL(8):: r(1:3) !3 generic coordinates
-      INTEGER:: fileID, error, found
+      INTEGER:: fileID
       CHARACTER(LEN=256):: line
       INTEGER:: numNodes, numElements, numEdges
       INTEGER, ALLOCATABLE, DIMENSION(:):: entitiesID, offsets, connectivity, types
@@ -275,6 +275,7 @@ MODULE moduleMeshInputVTU
       END DO
 
       !Count the number of edges
+      numEdges = 0
       SELECT CASE(self%dimen)
       CASE(3)
         !Edges are triangles, type 5 in VTK
@@ -547,6 +548,8 @@ MODULE moduleMeshInputVTU
       CALL readDataBlock(fileID, numNodes, temperature)
       REWIND(fileID)
 
+      close(fileID)
+
     END SUBROUTINE readInitialVTU
 
 END MODULE moduleMeshInputVTU

src/modules/mesh/inout/vtu/moduleMeshOutputVTU.f90

@@ -11,7 +11,7 @@ MODULE moduleMeshOutputVTU
 
       WRITE(fileID,"(A)") '<?xml version="1.0"?>'
       WRITE(fileID,"(2X, A)") '<VTKFile type="UnstructuredGrid">'
-      WRITE(fileID,"(4X, A,ES20.6E3,A)") '<UnstructuredGrid>'
+      WRITE(fileID,"(4X, A)") '<UnstructuredGrid>'
       WRITE(fileID,"(6X, A, I10, A, I10, A)") '<Piece NumberOfPoints="', nNodes, '" NumberOfCells="', nCells, '">'
 
     END SUBROUTINE writeHeader
@@ -209,23 +209,22 @@ MODULE moduleMeshOutputVTU
       WRITE(fileID,"(8X,A)") '<CellData>'
       !Electric field
       WRITE(fileID,"(10X,A, A, A)") '<DataArray type="Float64" Name="Electric Field (V m^-1)" NumberOfComponents="3">'
-      WRITE(fileID, "(6(ES20.6E3))") (self%cells(n)%obj%gatherElectricField(Xi)*EF_ref, n = 1, self%numCells)
+      WRITE(fileID,"(6(ES20.6E3))") (self%cells(n)%obj%gatherElectricField(Xi)*EF_ref, n = 1, self%numCells)
       WRITE(fileID,"(10X,A)") '</DataArray>'
       WRITE(fileID,"(8X,A)") '</CellData>'
 
     END SUBROUTINE writeEM
 
-    SUBROUTINE writeCollection(fileID, t, fileNameStep, fileNameCollection)
+    SUBROUTINE writeCollection(fileID, fileNameStep, fileNameCollection)
       USE moduleCaseParam
       USE moduleOutput
       USE moduleRefParam
       IMPLICIT NONE
 
       INTEGER:: fileID
-      INTEGER, INTENT(in):: t
       CHARACTER(*):: fileNameStep, fileNameCollection
 
-      IF (t == tInitial) THEN
+      IF (timeStep == tInitial) THEN
         !Create collection file
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileNameCollection
         OPEN (fileID + 1, file = path // folder  // '/' // fileNameCollection)
@@ -237,10 +236,11 @@ MODULE moduleMeshOutputVTU
 
       !Write iteration file in collection
       OPEN (fileID + 1, file = path // folder  // '/' // fileNameCollection, ACCESS='APPEND')
-      WRITE(fileID + 1, "(4X, A, ES20.6E3, A, A, A)") '<DataSet timestep="', DBLE(t)*tauMin*ti_ref,'" file="', fileNameStep,'"/>'
+      WRITE(fileID + 1, "(4X, A, ES20.6E3, A, A, A)") &
+            '<DataSet timestep="', DBLE(timeStep)*tauMin*ti_ref,'" file="', fileNameStep,'"/>'
 
       !Close collection file
-      IF (t == tFinal) THEN
+      IF (timeStep == tFinal) THEN
         WRITE (fileID + 1, "(2X, A)") '</Collection>'
         WRITE (fileID + 1, "(A)") '</VTKFile>'
 
@@ -307,22 +307,21 @@ MODULE moduleMeshOutputVTU
 
     END SUBROUTINE writeAverage
 
-    SUBROUTINE printOutputVTU(self,t)
+    SUBROUTINE printOutputVTU(self)
       USE moduleMesh
       USE moduleSpecies
       USE moduleMeshInoutCommon
+      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
-      INTEGER, INTENT(in):: t
-      INTEGER:: n, i, fileID
+      INTEGER:: i, fileID
       CHARACTER(:), ALLOCATABLE:: fileName, fileNameCollection
-      TYPE(outputFormat):: output(1:self%numNodes)
 
       fileID = 60
 
       DO i = 1, nSpecies
-        fileName = formatFileName(prefix, species(i)%obj%name, 'vtu', t)
+        fileName = formatFileName(prefix, species(i)%obj%name, 'vtu', timeStep)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (fileID, file = path // folder // '/' //  fileName)
 
@@ -338,29 +337,27 @@ MODULE moduleMeshOutputVTU
 
         !Write collection file for time plotting
         fileNameCollection = formatFileName('Collection', species(i)%obj%name, 'pvd')
-        CALL writeCollection(fileID, t, fileName, filenameCollection)
+        CALL writeCollection(fileID, fileName, filenameCollection)
 
       END DO
 
     END SUBROUTINE printOutputVTU
 
-    SUBROUTINE printCollVTU(self,t)
+    SUBROUTINE printCollVTU(self)
       USE moduleMesh
       USE moduleOutput
       USE moduleMeshInoutCommon
+      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(in):: self
-      INTEGER, INTENT(in):: t
-      INTEGER:: n, i, fileID
+      INTEGER:: fileID
       CHARACTER(:), ALLOCATABLE:: fileName, fileNameCollection
-      CHARACTER (LEN=iterationDigits):: tstring
-      TYPE(outputFormat):: output(1:self%numNodes)
 
       fileID = 62
 
       IF (collOutput) THEN
-        fileName = formatFileName(prefix, 'Collisions', 'vtu', t)
+        fileName = formatFileName(prefix, 'Collisions', 'vtu', timeStep)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (fileID, file = path // folder // '/' //  fileName)
 
@@ -376,26 +373,26 @@ MODULE moduleMeshOutputVTU
 
         !Write collection file for time plotting
         fileNameCollection = formatFileName('Collection', 'Collisions', 'pvd')
-        CALL writeCollection(fileID, t, fileName, filenameCollection)
+        CALL writeCollection(fileID, fileName, filenameCollection)
 
       END IF
 
     END SUBROUTINE printCollVTU
 
-    SUBROUTINE printEMVTU(self, t)
+    SUBROUTINE printEMVTU(self)
       USE moduleMesh
       USE moduleMeshInoutCommon
+      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
-      INTEGER, INTENT(in):: t
       INTEGER:: fileID
       CHARACTER(:), ALLOCATABLE:: fileName, fileNameCollection
 
       fileID = 64
 
       IF (emOutput) THEN
-        fileName = formatFileName(prefix, 'EMField', 'vtu', t)
+        fileName = formatFileName(prefix, 'EMField', 'vtu', timeStep)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (fileID, file = path // folder // '/' //  fileName)
 
@@ -411,7 +408,7 @@ MODULE moduleMeshOutputVTU
 
         !Write collection file for time plotting
         fileNameCollection = formatFileName('Collection', 'EMField', 'pvd')
-        CALL writeCollection(fileID, t, fileName, filenameCollection)
+        CALL writeCollection(fileID, fileName, filenameCollection)
 
       END IF
 
@@ -424,9 +421,8 @@ MODULE moduleMeshOutputVTU
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
-      INTEGER:: n, i, fileIDMean, fileIDDeviation
+      INTEGER:: i, fileIDMean, fileIDDeviation
       CHARACTER(:), ALLOCATABLE:: fileNameMean, fileNameDeviation
-      TYPE(outputFormat):: output(1:self%numNodes)
 
       fileIDMean = 66
       fileIDDeviation = 67

src/modules/mesh/moduleMesh.f90

@@ -59,6 +59,13 @@ MODULE moduleMesh
 
   END TYPE meshNodeCont
 
+  ! Array of pointers to nodes.
+  TYPE:: meshNodePointer
+    CLASS(meshNode), POINTER:: obj
+    CONTAINS
+
+  END TYPE meshNodePointer
+
   !Type for array of boundary functions (one per species)
   TYPE, PUBLIC:: fBoundaryGeneric
     PROCEDURE(boundary_interface), POINTER, NOPASS:: apply => NULL()
@@ -76,8 +83,8 @@ MODULE moduleMesh
     CLASS(meshCell), POINTER:: eColl => NULL()
     !Normal vector
     REAL(8):: normal(1:3)
-    !Weight for random injection of particles
-    REAL(8):: weight = 1.D0
+    ! Surface of edge
+    REAL(8):: surface = 0.D0
     !Pointer to boundary type
     TYPE(boundaryCont), POINTER:: boundary
     !Array of functions for boundary conditions
@@ -372,10 +379,9 @@ MODULE moduleMesh
     END SUBROUTINE connectMesh_interface
 
     !Prints number of collisions in each cell
-    SUBROUTINE printColl_interface(self, t)
+    SUBROUTINE printColl_interface(self)
       IMPORT meshGeneric
       CLASS(meshGeneric), INTENT(in):: self
-      INTEGER, INTENT(in):: t
 
     END SUBROUTINE printColl_interface
 
@@ -403,18 +409,16 @@ MODULE moduleMesh
 
   ABSTRACT INTERFACE
     !Prints Species data
-    SUBROUTINE printOutput_interface(self, t)
+    SUBROUTINE printOutput_interface(self)
       IMPORT meshParticles
       CLASS(meshParticles), INTENT(in):: self
-      INTEGER, INTENT(in):: t
 
     END SUBROUTINE printOutput_interface
 
     !Prints EM info
-    SUBROUTINE printEM_interface(self, t)
+    SUBROUTINE printEM_interface(self)
       IMPORT meshParticles
       CLASS(meshParticles), INTENT(in):: self
-      INTEGER, INTENT(in):: t
 
     END SUBROUTINE printEM_interface
 
@@ -495,18 +499,17 @@ MODULE moduleMesh
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(inout):: self
-      INTEGER:: e
-      INTEGER:: nNodes
+      INTEGER:: c
       INTEGER, ALLOCATABLE:: n(:)
       REAL(8), ALLOCATABLE:: localK(:,:)
       INTEGER:: i, j
 
-      DO e = 1, self%numCells
-        nNodes = self%cells(e)%obj%nNodes
+      DO c = 1, self%numCells
+        associate(nNodes => self%cells(c)%obj%nNodes)
           ALLOCATE(n(1:nNodes))
           ALLOCATE(localK(1:nNodes, 1:nNodes))
-        n      = self%cells(e)%obj%getNodes(nNodes)
-        localK = self%cells(e)%obj%elemK(nNodes)
+          n      = self%cells(c)%obj%getNodes(nNodes)
+          localK = self%cells(c)%obj%elemK(nNodes)
 
           DO i = 1, nNodes
             DO j = 1, nNodes
@@ -518,6 +521,8 @@ MODULE moduleMesh
 
           DEALLOCATE(n, localK)
 
+        end associate
+
       END DO
 
     END SUBROUTINE constructGlobalK
@@ -613,6 +618,7 @@ MODULE moduleMesh
       INTEGER:: sp
       INTEGER:: i
       CLASS(meshNode), POINTER:: node
+      REAL(8):: pFraction !Particle fraction
 
       cellNodes = self%getNodes(nNodes)
       fPsi = self%fPsi(part%Xi, nNodes)
@@ -623,10 +629,11 @@ MODULE moduleMesh
 
       DO i = 1, nNodes
         node => mesh%nodes(cellNodes(i))%obj
+        pFraction = fPsi(i)*part%weight
         CALL OMP_SET_LOCK(node%lock)
-        node%output(sp)%den          = node%output(sp)%den          + part%weight*fPsi(i)
-        node%output(sp)%mom(:)       = node%output(sp)%mom(:)       + part%weight*fPsi(i)*part%v(:)
-        node%output(sp)%tensorS(:,:) = node%output(sp)%tensorS(:,:) + part%weight*fPsi(i)*tensorS
+        node%output(sp)%den          = node%output(sp)%den          + pFraction
+        node%output(sp)%mom(:)       = node%output(sp)%mom(:)       + pFraction*part%v(:)
+        node%output(sp)%tensorS(:,:) = node%output(sp)%tensorS(:,:) + pFraction*tensorS
         CALL OMP_UNSET_LOCK(node%lock)
 
       END DO
@@ -787,7 +794,7 @@ MODULE moduleMesh
     END FUNCTION findCellBrute
 
     !Computes collisions in element
-    SUBROUTINE doCollisions(self, t)
+    SUBROUTINE doCollisions(self)
       USE moduleCollisions
       USE moduleSpecies
       USE moduleList
@@ -795,10 +802,10 @@ MODULE moduleMesh
       USE moduleRandom
       USE moduleOutput
       USE moduleMath
+      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(inout), TARGET:: self
-      INTEGER, INTENT(in):: t
       INTEGER:: e
       CLASS(meshCell), POINTER:: cell
       INTEGER:: k, i, j
@@ -814,7 +821,7 @@ MODULE moduleMesh
       REAL(8):: rnd_real !Random number for collision
       INTEGER:: rnd_int  !Random number for collision
 
-      IF (MOD(t, everyColl) == 0) THEN
+      IF (MOD(timeStep, everyColl) == 0) THEN
         !Collisions need to be performed in this iteration
         !$OMP DO SCHEDULE(DYNAMIC) PRIVATE(part_i, part_j, partTemp_i, partTemp_j)
         DO e=1, self%numCells
@@ -911,7 +918,9 @@ MODULE moduleMesh
                     !Loop over collisions
                     DO c = 1, interactionMatrix(k)%amount
                       IF (rnd_real <= probabilityColl(c)) THEN
+                        !$OMP CRITICAL
                         CALL interactionMatrix(k)%collisions(c)%obj%collide(part_i, part_j, vRel)
+                        !$OMP END CRITICAL
 
                         !If collisions are gonna be output, count the collision
                         IF (collOutput) THEN
@@ -1021,6 +1030,9 @@ MODULE moduleMesh
           ALLOCATE(deltaV_ij(1:cell%listPart_in(i)%amount, 1:3))
           ALLOCATE(p_ij(1:cell%listPart_in(i)%amount, 1:3))
           ALLOCATE(mass_ij(1:cell%listPart_in(i)%amount))
+          deltaV_ij = 0.D0
+          p_ij      = 0.D0
+          mass_ij   = 0.D0
           !Loop over particles of species_i
           partTemp => cell%listPart_in(i)%head
           p = 1
@@ -1105,6 +1117,9 @@ MODULE moduleMesh
             ALLOCATE(deltaV_ji(1:cell%listPart_in(j)%amount, 1:3))
             ALLOCATE(p_ji(1:cell%listPart_in(j)%amount, 1:3))
             ALLOCATE(mass_ji(1:cell%listPart_in(j)%amount))
+            deltaV_ji = 0.D0
+            p_ji      = 0.D0
+            mass_ji   = 0.D0
             !Loop over particles of species_j
             partTemp => cell%listPart_in(j)%head
             p = 1

src/modules/mesh/moduleMeshBoundary.f90

@@ -77,6 +77,20 @@ MODULE moduleMeshBoundary
 
     END SUBROUTINE transparent
 
+    !Symmetry axis. Reflects particles.
+    !Although this function should never be called, it is set as a reflective boundary
+    !to properly deal with possible particles reaching a corner and selecting this boundary.
+    SUBROUTINE symmetryAxis(edge, part)
+      USE moduleSpecies
+      IMPLICIT NONE
+
+      CLASS(meshEdge), INTENT(inout):: edge
+      CLASS(particle), INTENT(inout):: part
+
+      CALL reflection(edge, part)
+
+    END SUBROUTINE symmetryAxis
+
     !Wall with temperature
     SUBROUTINE wallTemperature(edge, part)
       USE moduleSpecies
@@ -147,7 +161,13 @@ MODULE moduleMeshBoundary
             ALLOCATE(newElectron)
             ALLOCATE(newIon)
 
+            IF (ASSOCIATED(bound%electronSecondary)) THEN
+              newElectron%species => bound%electronSecondary
+
+            ELSE
               newElectron%species => part%species
+
+            END IF
             newIon%species      => bound%species
 
             newElectron%v = v0 + (1.D0 + bound%deltaV*v0/NORM2(v0))
@@ -198,19 +218,27 @@ MODULE moduleMeshBoundary
 
     END SUBROUTINE ionization
 
-    !Symmetry axis. Reflects particles.
-    !Although this function should never be called, it is set as a reflective boundary
-    !to properly deal with possible particles reaching a corner and selecting this boundary.
-    SUBROUTINE symmetryAxis(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
+    subroutine outflowAdaptive(edge, part)
+      use moduleRandom
+      implicit none
 
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
+      class(meshEdge), intent(inout):: edge
+      class(particle), intent(inout):: part
 
-      CALL reflection(edge, part)
+      select type(bound => edge%boundary%bTypes(part%species%n)%obj)
+      type is(boundaryOutflowAdaptive)
 
-    END SUBROUTINE symmetryAxis
+        if (random() < 0.844d0) then
+          call reflection(edge, part)
+
+        else
+          call transparent(edge, part)
+
+        end if
+
+      end select
+
+    end subroutine outflowAdaptive
 
     !Points the boundary function to specific type
     SUBROUTINE pointBoundaryFunction(edge, s)
@@ -230,14 +258,17 @@ MODULE moduleMeshBoundary
       TYPE IS(boundaryTransparent)
         edge%fBoundary(s)%apply => transparent
 
+      TYPE IS(boundaryAxis)
+        edge%fBoundary(s)%apply => symmetryAxis
+
       TYPE IS(boundaryWallTemperature)
         edge%fBoundary(s)%apply => wallTemperature
 
       TYPE IS(boundaryIonization)
         edge%fBoundary(s)%apply => ionization
 
-      TYPE IS(boundaryAxis)
-        edge%fBoundary(s)%apply => symmetryAxis
+      type is(boundaryOutflowAdaptive)
+        edge%fBoundary(s)%apply => outflowAdaptive
 
       CLASS DEFAULT
         CALL criticalError("Boundary type not defined in this geometry", 'pointBoundaryFunction')

src/modules/moduleBoundary.f90

@@ -26,6 +26,12 @@ MODULE moduleBoundary
 
   END TYPE boundaryTransparent
 
+  !Symmetry axis
+  TYPE, PUBLIC, EXTENDS(boundaryGeneric):: boundaryAxis
+    CONTAINS
+
+  END TYPE boundaryAxis
+
   !Wall Temperature boundary
   TYPE, PUBLIC, EXTENDS(boundaryGeneric):: boundaryWallTemperature
     !Thermal velocity of the wall: square root(Wall temperature X specific heat)
@@ -38,6 +44,7 @@ MODULE moduleBoundary
   TYPE, PUBLIC, EXTENDS(boundaryGeneric):: boundaryIonization
     REAL(8):: m0, n0, v0(1:3), vTh !Properties of background neutrals.
     CLASS(speciesGeneric), POINTER:: species !Ion species
+    CLASS(speciesCharged), POINTER:: electronSecondary !Pointer to species considerer as secondary electron
     TYPE(table1D):: crossSection
     REAL(8):: effectiveTime
     REAL(8):: eThreshold
@@ -46,11 +53,13 @@ MODULE moduleBoundary
 
   END TYPE boundaryIonization
 
-  !Symmetry axis
-  TYPE, PUBLIC, EXTENDS(boundaryGeneric):: boundaryAxis
-    CONTAINS
+  !Boundary for quasi-neutral outflow adjusting reflection coefficient
+  type, public, extends(boundaryGeneric):: boundaryOutflowAdaptive
+    real(8):: outflowCurrent
+    real(8):: reflectionFraction
+    contains
 
-  END TYPE boundaryAxis
+  end type boundaryOutflowAdaptive
 
   !Wrapper for boundary types (one per species)
   TYPE:: bTypesCont
@@ -103,17 +112,19 @@ MODULE moduleBoundary
 
     END SUBROUTINE initWallTemperature
 
-    SUBROUTINE initIonization(boundary, me, m0, n0, v0, T0, speciesID, effTime, crossSection, eThreshold)
+    SUBROUTINE initIonization(boundary, me, m0, n0, v0, T0, ion, effTime, crossSection, eThreshold, electronSecondary)
       USE moduleRefParam
       USE moduleSpecies
       USE moduleCaseParam
       USE moduleConstParam
+      USE moduleErrors
       IMPLICIT NONE
 
       CLASS(boundaryGeneric), ALLOCATABLE, INTENT(out):: boundary
       REAL(8), INTENT(in):: me !Electron mass
       REAL(8), INTENT(in):: m0, n0, v0(1:3), T0 !Neutral properties
-      INTEGER:: speciesID
+      INTEGER, INTENT(in):: ion
+      INTEGER, OPTIONAL, INTENT(in):: electronSecondary
       REAL(8):: effTime
       CHARACTER(:), ALLOCATABLE, INTENT(in):: crossSection
       REAL(8), INTENT(in):: eThreshold
@@ -126,7 +137,22 @@ MODULE moduleBoundary
         boundary%n0 = n0 * Vol_ref
         boundary%v0 = v0 / v_ref
         boundary%vTh = DSQRT(kb*T0/m0)/v_ref
-        boundary%species => species(speciesID)%obj
+        boundary%species => species(ion)%obj
+        IF (PRESENT(electronSecondary)) THEN
+          SELECT TYPE(sp => species(electronSecondary)%obj)
+          TYPE IS(speciesCharged)
+            boundary%electronSecondary => sp
+
+          CLASS DEFAULT
+            CALL criticalError("Species " // sp%name // " chosen for " // &
+                               "secondary electron is not a charged species", 'initIonization')
+
+          END SELECT
+
+        ELSE
+          boundary%electronSecondary => NULL()
+
+        END IF
         boundary%effectiveTime = effTime / ti_ref
         CALL boundary%crossSection%init(crossSection)
         CALL boundary%crossSection%convert(eV2J/(m_ref*v_ref**2), 1.D0/L_ref**2)

src/modules/moduleCollisions.f90

@@ -44,6 +44,7 @@ MODULE moduleCollisions
     REAL(8):: eThreshold !Minimum energy (non-dimensional units) required for ionization
     REAL(8):: deltaV !Change in velocity due to exchange of eThreshold
     CLASS(speciesCharged), POINTER:: electron          !Pointer to species considerer as electrons
+    CLASS(speciesCharged), POINTER:: electronSecondary !Pointer to species considerer as secondary electron
     CONTAINS
       PROCEDURE, PASS:: collide => collideBinaryIonization
 
@@ -241,7 +242,7 @@ MODULE moduleCollisions
 
     !ELECTRON IMPACT IONIZATION
     !Inits electron impact ionization
-    SUBROUTINE initBinaryIonization(collision, crossSectionFilename, energyThreshold, electron)
+    SUBROUTINE initBinaryIonization(collision, crossSectionFilename, energyThreshold, electron, electronSecondary)
       USE moduleTable
       USE moduleRefParam
       USE moduleConstParam
@@ -253,7 +254,8 @@ MODULE moduleCollisions
       CHARACTER(:), ALLOCATABLE, INTENT(in):: crossSectionFilename
       REAL(8), INTENT(in):: energyThreshold
       CHARACTER(:), ALLOCATABLE, INTENT(in):: electron
-      INTEGER:: electronIndex
+      CHARACTER(:), ALLOCATABLE, OPTIONAL, INTENT(in):: electronSecondary
+      INTEGER:: electronIndex, electronSecondaryIndex
 
       ALLOCATE(collisionBinaryIonization:: collision)
 
@@ -276,12 +278,29 @@ MODULE moduleCollisions
         TYPE IS(speciesCharged)
           collision%electron => sp
 
+        CLASS DEFAULT
+          CALL criticalError("Species " // sp%name // " chosen for " // &
+                             "impacting electron is not a charged species", 'initBinaryIonization')
+
+        END SELECT
+
+        IF (PRESENT(electronSecondary)) THEN
+          electronSecondaryIndex = speciesName2Index(electronSecondary)
+          SELECT TYPE(sp => species(electronSecondaryIndex)%obj)
+          TYPE IS(speciesCharged)
+            collision%electronSecondary => sp
+
           CLASS DEFAULT
             CALL criticalError("Species " // sp%name // " chosen for " // &
                                "secondary electron is not a charged species", 'initBinaryIonization')
 
           END SELECT
 
+        ELSE
+          collision%electronSecondary => NULL()
+
+        END IF
+
         !momentum change per ionization process
         collision%deltaV = sqrt(collision%eThreshold / collision%electron%m)
 
@@ -336,6 +355,12 @@ MODULE moduleCollisions
         !Copy basic information from primary electron
         newElectron = electron
 
+        !If secondary electron species indicates, convert
+        IF (ASSOCIATED(self%electronSecondary)) THEN
+          newElectron%species => self%electronSecondary
+
+        END IF
+
         !Secondary electorn gains energy from ionization
         newElectron%v       =  vChange
 
@@ -362,7 +387,7 @@ MODULE moduleCollisions
           CALL sp%ionize(neutral)
 
         CLASS DEFAULT
-          ! CALL criticalError(sp%name // " is not a neutral", 'collideBinaryIonization')
+          CALL criticalError(sp%name // " is not a neutral", 'collideBinaryIonization')
           RETURN
 
         END SELECT

src/modules/moduleInject.f90

@@ -54,15 +54,16 @@ MODULE moduleInject
     INTEGER:: id
     CHARACTER(:), ALLOCATABLE:: name
     REAL(8):: vMod !Velocity (module)
-    REAL(8):: T(1:3) !Temperature
+    REAL(8):: temperature(1:3) !Temperature
     REAL(8):: n(1:3) !Direction of injection
     LOGICAL:: fixDirection !The injection of particles has a fix direction defined by n
     INTEGER:: nParticles !Number of particles to introduce each time step
     CLASS(speciesGeneric), POINTER:: species !Species of injection
     INTEGER:: nEdges
     INTEGER, ALLOCATABLE:: edges(:) !Array with edges
-    REAL(8), ALLOCATABLE:: cumWeight(:) !Array of cummulative probability
-    REAL(8):: sumWeight
+    INTEGER, ALLOCATABLE:: particlesPerEdge(:) ! Particles per edge
+    REAL(8), ALLOCATABLE:: weightPerEdge(:) ! Weight per edge
+    REAL(8):: surface ! Total surface of injection
     TYPE(velDistCont):: v(1:3) !Velocity distribution function in each direction
     CONTAINS
       PROCEDURE, PASS:: init         => initInject
@@ -75,7 +76,7 @@ MODULE moduleInject
 
   CONTAINS
     !Initialize an injection of particles
-    SUBROUTINE initInject(self, i, v, n, T, flow, units, sp, physicalSurface)
+    SUBROUTINE initInject(self, i, v, n, temperature, flow, units, sp, physicalSurface, particlesPerEdge)
       USE moduleMesh
       USE moduleRefParam
       USE moduleConstParam
@@ -86,49 +87,29 @@ MODULE moduleInject
 
       CLASS(injectGeneric), INTENT(inout):: self
       INTEGER, INTENT(in):: i
-      REAL(8), INTENT(in):: v, n(1:3), T(1:3)
-      INTEGER, INTENT(in):: sp, physicalSurface
+      REAL(8), INTENT(in):: v, n(1:3), temperature(1:3)
+      INTEGER, INTENT(in):: sp, physicalSurface, particlesPerEdge
       REAL(8):: tauInject
       REAL(8), INTENT(in):: flow
       CHARACTER(:), ALLOCATABLE, INTENT(in):: units
       INTEGER:: e, et
       INTEGER:: phSurface(1:mesh%numEdges)
       INTEGER:: nVolColl
+      REAL(8):: fluxPerStep = 0.D0
 
       self%id          =  i
       self%vMod        =  v / v_ref
       self%n           =  n / NORM2(n)
-      self%T          =  T / T_ref
-      self%species    => species(sp)%obj
-      tauInject = tau(self%species%n)
-      SELECT CASE(units)
-      CASE ("sccm")
-        !Standard cubic centimeter per minute
-        self%nParticles = INT(flow*sccm2atomPerS*tauInject*ti_ref/species(sp)%obj%weight)
-
-      CASE ("A")
-        !Input current in Ampers
-        self%nParticles = INT(flow*tauInject*ti_ref/(qe*species(sp)%obj%weight))
-
-      CASE ("part/s")
-        !Input current in Ampers
-        self%nParticles = INT(flow*tauInject*ti_ref/species(sp)%obj%weight)
-
-      CASE DEFAULT
-        CALL criticalError("No support for units: " // units, 'initInject')
-        
-      END SELECT
-      !Scale particles for different species steps
-      IF (self%nParticles == 0) CALL criticalError("The number of particles for inject is 0.", 'initInject')
-
+      self%temperature =  temperature / T_ref
       !Gets the edge elements from which particles are injected
       DO e = 1, mesh%numEdges
         phSurface(e) = mesh%edges(e)%obj%physicalSurface
 
       END DO
-
       self%nEdges = COUNT(phSurface == physicalSurface)
-      ALLOCATE(inject(i)%edges(1:self%nEdges))
+      ALLOCATE(self%edges(1:self%nEdges))
+      ALLOCATE(self%particlesPerEdge(1:self%nEdges))
+      ALLOCATE(self%weightPerEdge(1:self%nEdges))
       et = 0
       DO e=1, mesh%numEdges
         IF (mesh%edges(e)%obj%physicalSurface == physicalSurface) THEN
@@ -160,15 +141,82 @@ MODULE moduleInject
 
       END DO
 
-      !Calculates cumulative probability
-      ALLOCATE(self%cumWeight(1:self%nEdges))
-      et = 1
-      self%cumWeight(1) = mesh%edges(self%edges(et))%obj%weight
-      DO et = 2, self%nEdges
-        self%cumWeight(et) = mesh%edges(self%edges(et))%obj%weight + self%cumWeight(et-1)
+      !Calculates total area
+      self%surface = 0.D0
+      DO et = 1, self%nEdges
+        self%surface = self%surface + mesh%edges(self%edges(et))%obj%surface
 
       END DO
-      self%sumWeight = self%cumWeight(self%nEdges)
+
+      ! Information about species and flux
+      self%species => species(sp)%obj
+      tauInject    = tau(self%species%n)
+      ! Convert units
+      SELECT CASE(units)
+      CASE ("sccm")
+        !Standard cubic centimeter per minute
+        fluxPerStep = flow*sccm2atomPerS
+
+      CASE ("A")
+        !Current in Ampers
+        SELECT TYPE(sp => self%species)
+        CLASS IS(speciesCharged)
+          fluxPerStep = flow/(qe*abs(sp%q))
+
+        CLASS DEFAULT
+          call criticalError('Attempted to assign a flux in "A" to a species without charge.', 'initInject')
+
+        END SELECT
+
+      CASE ("Am2")
+        !Input current in Ampers per square meter
+        SELECT TYPE(sp => self%species)
+        CLASS IS(speciesCharged)
+          fluxPerStep = flow*self%surface*L_ref**2/(qe*abs(sp%q))
+
+        CLASS DEFAULT
+          call criticalError('Attempted to assign a flux in "Am2" to a species without charge.', 'initInject')
+
+        END SELECT
+
+
+      CASE ("part/s")
+        !Input current in Ampers
+        fluxPerStep = flow
+
+      CASE DEFAULT
+        CALL criticalError("No support for units: " // units, 'initInject')
+
+      END SELECT
+      fluxPerStep = fluxPerStep * tauInject * ti_ref / self%surface
+
+      !Assign particles per edge
+      IF (particlesPerEdge > 0) THEN
+        ! Particles per edge defined by the user
+        self%particlesPerEdge = particlesPerEdge
+        DO et = 1, self%nEdges
+          self%weightPerEdge(et) = fluxPerStep*mesh%edges(self%edges(et))%obj%surface / REAL(particlesPerEdge)
+
+        END DO
+
+        self%nParticles = SUM(self%particlesPerEdge)
+
+      ELSE
+        ! No particles assigned per edge, use the species weight
+        self%weightPerEdge = self%species%weight
+        DO et = 1, self%nEdges
+          self%particlesPerEdge(et) = max(1,FLOOR(fluxPerStep*mesh%edges(self%edges(et))%obj%surface / self%species%weight))
+        END DO
+
+        self%nParticles = SUM(self%particlesPerEdge)
+
+        !Rescale weight to match flux
+        self%weightPerEdge = fluxPerStep * self%surface / (real(self%nParticles))
+
+      END IF
+
+      !Scale particles for different species steps
+      IF (self%nParticles == 0) CALL criticalError("The number of particles for inject is 0.", 'initInject')
 
     END SUBROUTINE initInject
 
@@ -203,23 +251,23 @@ MODULE moduleInject
 
     END SUBROUTINE doInjects
 
-    SUBROUTINE initVelDistMaxwellian(velDist, T, m)
+    SUBROUTINE initVelDistMaxwellian(velDist, temperature, m)
       IMPLICIT NONE
 
       CLASS(velDistGeneric), ALLOCATABLE, INTENT(out):: velDist
-      REAL(8), INTENT(in):: T, m
+      REAL(8), INTENT(in):: temperature, m
 
-      velDist = velDistMaxwellian(vTh = DSQRT(T/m))
+      velDist = velDistMaxwellian(vTh = DSQRT(2.d0*temperature/m))
 
     END SUBROUTINE initVelDistMaxwellian
 
-    SUBROUTINE initVelDistHalfMaxwellian(velDist, T, m)
+    SUBROUTINE initVelDistHalfMaxwellian(velDist, temperature, m)
       IMPLICIT NONE
 
       CLASS(velDistGeneric), ALLOCATABLE, INTENT(out):: velDist
-      REAL(8), INTENT(in):: T, m
+      REAL(8), INTENT(in):: temperature, m
 
-      velDist = velDistHalfMaxwellian(vTh = DSQRT(T/m))
+      velDist = velDistHalfMaxwellian(vTh = DSQRT(2.d0*temperature/m))
 
     END SUBROUTINE initVelDistHalfMaxwellian
 
@@ -241,7 +289,7 @@ MODULE moduleInject
       REAL(8):: v
       v = 0.D0
 
-      v = self%vTh*randomMaxwellian()
+      v = self%vTh*randomMaxwellian()/sqrt(2.d0)
 
     END FUNCTION randomVelMaxwellian
 
@@ -254,10 +302,7 @@ MODULE moduleInject
       REAL(8):: v
       v = 0.D0
 
-      DO WHILE (v <= 0.D0)
-        v = self%vTh*randomMaxwellian()
-
-      END DO
+      v = self%vTh*randomHalfMaxwellian()/sqrt(2.d0)
 
     END FUNCTION randomVelHalfMaxwellian
 
@@ -282,9 +327,8 @@ MODULE moduleInject
       IMPLICIT NONE
 
       CLASS(injectGeneric), INTENT(in):: self
-      INTEGER:: randomX
-      INTEGER, SAVE:: nMin, nMax !Min and Max index in partInj array
-      INTEGER:: i
+      INTEGER, SAVE:: nMin
+      INTEGER:: i, e
       INTEGER:: n, sp
       CLASS(meshEdge), POINTER:: randomEdge
       REAL(8):: direction(1:3)
@@ -299,22 +343,23 @@ MODULE moduleInject
         END IF
 
       END DO
-
       nMin = nMin + 1
-      nMax = nMin + self%nParticles - 1
-      !Assign weight to particle.
-      partInj(nMin:nMax)%weight = self%species%weight
-      !Particle is considered to be outside the domain
-      partInj(nMin:nMax)%n_in = .FALSE.
       !$OMP END SINGLE
 
       !$OMP DO
-      DO n = nMin, nMax
-        randomX = randomWeighted(self%cumWeight, self%sumWeight)
-
-        randomEdge => mesh%edges(self%edges(randomX))%obj
+      DO e = 1, self%nEdges
+        ! Select edge for injection
+        randomEdge => mesh%edges(self%edges(e))%obj
+        ! Inject particles in edge
+        DO i = 1, self%particlesPerEdge(e)
+          ! Index in the global partInj array
+          n = nMin - 1 + SUM(self%particlesPerEdge(1:e-1)) + i
+          !Particle is considered to be outside the domain
+          partInj(n)%n_in = .FALSE.
           !Random position in edge
           partInj(n)%r = randomEdge%randPos()
+          !Assign weight to particle.
+          partInj(n)%weight = self%weightPerEdge(e)
           !Volume associated to the edge:
           IF (ASSOCIATED(randomEdge%e1)) THEN
             partInj(n)%cell = randomEdge%e1%n
@@ -332,19 +377,22 @@ MODULE moduleInject
           !Assign particle type
           partInj(n)%species => self%species
 
+          if (all(self%n == 0.D0)) then
+            direction =  randomEdge%normal
+
+          else
             direction = self%n
 
+          end if
+
           partInj(n)%v = 0.D0
 
+          do while(dot_product(partInj(n)%v, direction) <= 0.d0)
             partInj(n)%v = self%vMod*direction +  (/ self%v(1)%obj%randomVel(), &
                                                      self%v(2)%obj%randomVel(), &
                                                      self%v(3)%obj%randomVel() /)
+          end do
 
-        !If velocity is not in the right direction, invert it
-        IF (DOT_PRODUCT(direction, partInj(n)%v) < 0.D0) THEN
-          partInj(n)%v = - partInj(n)%v
-
-        END IF
 
           !Obtain natural coordinates of particle in cell
           partInj(n)%Xi = mesh%cells(partInj(n)%cell)%obj%phy2log(partInj(n)%r)
@@ -354,6 +402,8 @@ MODULE moduleInject
           CALL solver%updateParticleCell(partInj(n))
 
         END DO
+
+      END DO
       !$OMP END DO
 
     END SUBROUTINE addParticles

src/modules/moduleProbe.f90

@@ -27,7 +27,7 @@ MODULE moduleProbe
 
   CONTAINS
     !Functions for probeDistFunc type
-    SUBROUTINE init(self, id, speciesName, r, v1, v2, v3, points, timeStep)
+    SUBROUTINE init(self, id, speciesName, r, v1, v2, v3, points, everyTimeStep)
       USE moduleCaseParam
       USE moduleRefParam
       USE moduleSpecies
@@ -41,7 +41,7 @@ MODULE moduleProbe
       REAL(8), INTENT(in):: r(1:3)
       REAL(8), INTENT(in):: v1(1:2), v2(1:2), v3(1:2)
       INTEGER, INTENT(in):: points(1:3)
-      REAL(8), INTENT(in):: timeStep
+      REAL(8), INTENT(in):: everyTimeStep
       INTEGER:: sp, i
       REAL(8):: dv(1:3)
 
@@ -91,17 +91,17 @@ MODULE moduleProbe
                       1:self%nv(3)))
 
       !Number of iterations between output
-      IF (timeStep == 0.D0) THEN
+      IF (everyTimeStep == 0.D0) THEN
         self%every = 1
 
       ELSE
-        self%every = NINT(timeStep/ tauMin / ti_ref)
+        self%every = NINT(everyTimeStep/ tauMin / ti_ref)
 
       END IF
       
       !Maximum radius
       !TODO: Make this an input parameter
-      self%maxR = 1.D0
+      self%maxR = 1.D-2/L_ref
 
       !Init the probe lock
       CALL OMP_INIT_LOCK(self%lock)
@@ -148,7 +148,7 @@ MODULE moduleProbe
         deltaR = NORM2(self%r - part%r)
 
         !Only include particle if it is inside the maximum radius
-        IF (deltaR < self%maxR) THEN
+        ! IF (deltaR < self%maxR) THEN
           !find lower index for all dimensions
           CALL self%findLowerIndex(part%v, i, j, k, inside)
 
@@ -162,40 +162,40 @@ MODULE moduleProbe
             fk  = self%vk(k+1) - part%v(3)
             fk1 = part%v(3)    - self%vk(k)
 
-            ! weight = part%weight * DEXP(deltaR/self%maxR)
-            weight = part%weight
+            weight = part%weight * DEXP(-deltaR/self%maxR)
+            ! weight = part%weight
 
             !Lock the probe
             CALL OMP_SET_LOCK(self%lock)
             
             !Assign particle weight to distribution function
-            self%f(i  , j  , k  ) = fi  * fj  * fk  * weight
-            self%f(i+1, j  , k  ) = fi1 * fj  * fk  * weight
-            self%f(i  , j+1, k  ) = fi  * fj1 * fk  * weight
-            self%f(i+1, j+1, k  ) = fi1 * fj1 * fk  * weight
-            self%f(i  , j  , k+1) = fi  * fj  * fk1 * weight
-            self%f(i+1, j  , k+1) = fi1 * fj  * fk1 * weight
-            self%f(i  , j+1, k+1) = fi  * fj1 * fk1 * weight
-            self%f(i+1, j+1, k+1) = fi1 * fj1 * fk1 * weight
+            self%f(i  , j  , k  ) = self%f(i  , j  , k  ) + fi  * fj  * fk  * weight
+            self%f(i+1, j  , k  ) = self%f(i+1, j  , k  ) + fi1 * fj  * fk  * weight
+            self%f(i  , j+1, k  ) = self%f(i  , j+1, k  ) + fi  * fj1 * fk  * weight
+            self%f(i+1, j+1, k  ) = self%f(i+1, j+1, k  ) + fi1 * fj1 * fk  * weight
+            self%f(i  , j  , k+1) = self%f(i  , j  , k+1) + fi  * fj  * fk1 * weight
+            self%f(i+1, j  , k+1) = self%f(i+1, j  , k+1) + fi1 * fj  * fk1 * weight
+            self%f(i  , j+1, k+1) = self%f(i  , j+1, k+1) + fi  * fj1 * fk1 * weight
+            self%f(i+1, j+1, k+1) = self%f(i+1, j+1, k+1) + fi1 * fj1 * fk1 * weight
 
             !Unlock the probe
             CALL OMP_UNSET_LOCK(self%lock)
 
           END IF
 
-        END IF
+        ! END IF
 
       END IF
           
     END SUBROUTINE calculate
 
-    SUBROUTINE output(self, t)
+    SUBROUTINE output(self)
       USE moduleOutput
       USE moduleRefParam
+      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
       CLASS(probeDistFunc), INTENT(inout):: self
-      INTEGER, INTENT(in):: t
       CHARACTER (LEN=iterationDigits):: tstring
       CHARACTER (LEN=3):: pstring
       CHARACTER(:), ALLOCATABLE:: filename
@@ -204,14 +204,14 @@ MODULE moduleProbe
       !Divide by the velocity cube volume
       self%f = self%f * self%dvInv
 
-      WRITE(tstring, iterationFormat) t
+      WRITE(tstring, iterationFormat) timeStep
       WRITE(pstring, "(I3.3)") self%id
       fileName='Probe_' // tstring// '_f_' // pstring // '.dat'
       WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
       OPEN (10, file = path // folder // '/' //  fileName)
       WRITE(10, "(A1, 1X, A)")               "# ", self%species%name
       WRITE(10, "(A6, 3(ES15.6E3), A2)") "# r = ", self%r(:)*L_ref, " m"
-      WRITE(10, "(A6, ES15.6E3, A2)")    "# t = ", REAL(t)*tauMin*ti_ref, " s"
+      WRITE(10, "(A6, ES15.6E3, A2)")    "# t = ", REAL(timeStep)*tauMin*ti_ref, " s"
       WRITE(10, "(A1, A19, 3(A20))")     "#", "v1 (m s^-1)", "v2 (m s^-1)", "v3 (m s^-1)", "f"
       DO i = 1, self%nv(1)
         DO j = 1, self%nv(2)
@@ -252,15 +252,15 @@ MODULE moduleProbe
 
     END SUBROUTINE doProbes
 
-    SUBROUTINE outputProbes(t)
+    SUBROUTINE outputProbes()
+      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
-      INTEGER, INTENT(in):: t
       INTEGER:: i
 
       DO i = 1, nProbes
         IF (probe(i)%update) THEN
-          CALL probe(i)%output(t)
+          CALL probe(i)%output()
 
         END IF
 
@@ -268,15 +268,15 @@ MODULE moduleProbe
 
     END SUBROUTINE outputProbes
 
-    SUBROUTINE resetProbes(t)
+    SUBROUTINE resetProbes()
+      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
-      INTEGER, INTENT(in):: t
       INTEGER:: i
 
       DO i = 1, nProbes
         probe(i)%f = 0.D0
-        probe(i)%update = t == tFinal .OR. t == tInitial .OR. MOD(t, probe(i)%every) == 0
+        probe(i)%update = timeStep == tFinal .OR. timeStep == tInitial .OR. MOD(timeStep, probe(i)%every) == 0
 
       END DO
 

src/modules/output/moduleOutput.f90

@@ -22,7 +22,6 @@ MODULE moduleOutput
 
   !Type for EM data in node
   TYPE emNode
-    CHARACTER(:), ALLOCATABLE:: type
     REAL(8):: phi
     REAL(8):: B(1:3)
 
@@ -160,12 +159,12 @@ MODULE moduleOutput
 
     END SUBROUTINE calculateOutput
 
-    SUBROUTINE printTime(t, first)
+    SUBROUTINE printTime(first)
       USE moduleSpecies
       USE moduleCompTime
+      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
-      INTEGER, INTENT(in):: t
       LOGICAL, INTENT(in), OPTIONAL:: first
       CHARACTER(:), ALLOCATABLE:: fileName
 
@@ -187,7 +186,7 @@ MODULE moduleOutput
 
         OPEN(20, file = path // folder // '/' // fileName, position = 'append', action = 'write')
 
-        WRITE (20, "(I10, I10, 7(ES20.6E3))") t, nPartOld, tStep, tPush, tReset, tColl, tCoul, tWeight, tEMField
+        WRITE (20, "(I10, I10, 7(ES20.6E3))") timeStep, nPartOld, tStep, tPush, tReset, tColl, tCoul, tWeight, tEMField
 
         CLOSE(20)
 

src/modules/solver/electromagnetic/moduleEM.f90

@@ -1,55 +1,202 @@
 !Module to solve the electromagnetic field
 MODULE moduleEM
+  USE moduleMesh
+  USE moduleTable
   IMPLICIT NONE
 
-  TYPE:: boundaryEM
-    CHARACTER(:), ALLOCATABLE:: typeEM
-    INTEGER:: physicalSurface
+  ! Generic type for electromagnetic boundary conditions
+  TYPE, PUBLIC, ABSTRACT:: boundaryEMGeneric
+    INTEGER:: nNodes
+    TYPE(meshNodePointer), ALLOCATABLE:: nodes(:)
+
+    CONTAINS
+      PROCEDURE(applyEM_interface), DEFERRED, PASS:: apply
+
+  END TYPE boundaryEMGeneric
+
+  ABSTRACT INTERFACE
+    ! Apply boundary condition to the load vector for the Poission equation
+    SUBROUTINE applyEM_interface(self, vectorF)
+      IMPORT boundaryEMGeneric
+      CLASS(boundaryEMGeneric), INTENT(in):: self
+      REAL(8), INTENT(inout):: vectorF(:)
+
+    END SUBROUTINE applyEM_interface
+
+  END INTERFACE
+
+  TYPE, EXTENDS(boundaryEMGeneric):: boundaryEMDirichlet
     REAL(8):: potential
 
     CONTAINS
-      PROCEDURE, PASS:: apply
+      ! boundaryEMGeneric DEFERRED PROCEDURES
+      PROCEDURE, PASS:: apply => applyDirichlet
 
-  END TYPE boundaryEM
+  END TYPE boundaryEMDirichlet
+
+  TYPE, EXTENDS(boundaryEMGeneric):: boundaryEMDirichletTime
+    REAL(8):: potential
+    TYPE(table1D):: temporalProfile
+
+    CONTAINS
+      ! boundaryEMGeneric DEFERRED PROCEDURES
+      PROCEDURE, PASS:: apply => applyDirichletTime
+
+  END TYPE boundaryEMDirichletTime
+
+  ! Container for boundary conditions
+  TYPE:: boundaryEMCont
+    CLASS(boundaryEMGeneric), ALLOCATABLE:: obj
+
+  END TYPE boundaryEMCont
 
   INTEGER:: nBoundaryEM
-  TYPE(boundaryEM), ALLOCATABLE:: boundEM(:)
+  TYPE(boundaryEMCont), ALLOCATABLE:: boundaryEM(:)
 
   !Information of charge and reference parameters for rho vector
   REAL(8), ALLOCATABLE:: qSpecies(:)
 
   CONTAINS
-    !Apply boundary conditions to the K matrix for Poisson's equation
-    SUBROUTINE apply(self, edge)
+    SUBROUTINE findNodes(self, physicalSurface)
       USE moduleMesh
       IMPLICIT NONE
 
-      CLASS(boundaryEM), INTENT(in):: self
-      CLASS(meshEdge):: edge
-      INTEGER:: nNodes
-      INTEGER, ALLOCATABLE:: nodes(:)
-      INTEGER:: n
+      CLASS(boundaryEMGeneric), INTENT(inout):: self
+      INTEGER, INTENT(in):: physicalSurface
+      CLASS(meshEdge), POINTER:: edge
+      INTEGER, ALLOCATABLE:: nodes(:), nodesEdge(:)
+      INTEGER:: nNodes, nodesNew
+      INTEGER:: e, n
 
+      !Temporal array to hold nodes
+      ALLOCATE(nodes(0))
+
+      ! Loop thorugh the edges and identify those that are part of the boundary
+      DO e = 1, mesh%numEdges
+        edge => mesh%edges(e)%obj
+        IF (edge%physicalSurface == physicalSurface) THEN
+          ! Edge is of the right boundary index
+          ! Get nodes in the edge
           nNodes = edge%nNodes
-      nodes = edge%getNodes(nNodes)
-
+          nodesEdge = edge%getNodes(nNodes)
+          ! Collect all nodes that are not already in the temporal array
           DO n = 1, nNodes
-        SELECT CASE(self%typeEM)
-        CASE ("dirichlet")
-          mesh%K(nodes(n), :)        = 0.D0
-          mesh%K(nodes(n), nodes(n)) = 1.D0
+            IF (ANY(nodes == nodesEdge(n))) THEN
+              ! Node already in array, skip
+              CYCLE
 
-          mesh%nodes(nodes(n))%obj%emData%type = self%typeEM
-          mesh%nodes(nodes(n))%obj%emData%phi  = self%potential
+            ELSE
+              ! If not, add element to array of nodes
+              nodes = [nodes, nodesEdge(n)]
 
-        END SELECT
+            END IF
 
           END DO
 
-    END SUBROUTINE
+        END IF
+
+      END DO
+
+      ! Point boundary to nodes
+      nNodes = SIZE(nodes)
+      ALLOCATE(self%nodes(nNodes))
+      self%nNodes = nNodes
+      DO n = 1, nNodes
+        self%nodes(n)%obj => mesh%nodes(nodes(n))%obj
+
+      END DO
+
+    END SUBROUTINE findNodes
+
+    ! Initialize Dirichlet boundary condition
+    SUBROUTINE initDirichlet(self, physicalSurface, potential)
+      USE moduleRefParam, ONLY: Volt_ref
+      IMPLICIT NONE
+
+      CLASS(boundaryEMGeneric), ALLOCATABLE, INTENT(out):: self
+      INTEGER, INTENT(in):: physicalSurface
+      REAL(8), INTENT(in):: potential
+
+      ! Allocate boundary edge
+      ALLOCATE(boundaryEMDirichlet:: self)
+
+      SELECT TYPE(self)
+      TYPE IS(boundaryEMDirichlet)
+        self%potential = potential / Volt_ref
+
+        CALL findNodes(self, physicalSurface)
+
+      END SELECT
+
+    END SUBROUTINE initDirichlet
+
+    ! Initialize Dirichlet boundary condition
+    SUBROUTINE initDirichletTime(self, physicalSurface, potential, temporalProfile)
+      USE moduleRefParam, ONLY: Volt_ref, ti_ref
+      IMPLICIT NONE
+
+      CLASS(boundaryEMGeneric), ALLOCATABLE, INTENT(out):: self
+      INTEGER, INTENT(in):: physicalSurface
+      REAL(8), INTENT(in):: potential
+      CHARACTER(:), ALLOCATABLE, INTENT(in):: temporalProfile
+
+      ! Allocate boundary edge
+      ALLOCATE(boundaryEMDirichletTime:: self)
+
+      SELECT TYPE(self)
+      TYPE IS(boundaryEMDirichletTime)
+        self%potential = potential / Volt_ref
+
+        CALL findNodes(self, physicalSurface)
+
+        CALL self%temporalProfile%init(temporalProfile)
+
+        CALL self%temporalProfile%convert(1.D0/ti_ref, 1.D0)
+
+      END SELECT
+
+    END SUBROUTINE initDirichletTime
+
+    !Apply Dirichlet boundary condition to the poisson equation
+    SUBROUTINE applyDirichlet(self, vectorF)
+      USE moduleMesh
+      IMPLICIT NONE
+
+      CLASS(boundaryEMDirichlet), INTENT(in):: self
+      REAL(8), INTENT(inout):: vectorF(:)
+      INTEGER:: n, ni
+
+      DO n = 1, self%nNodes
+        self%nodes(n)%obj%emData%phi  = self%potential
+        vectorF(self%nodes(n)%obj%n)  = self%nodes(n)%obj%emData%phi
+
+      END DO
+
+    END SUBROUTINE applyDirichlet
+
+    !Apply Dirichlet boundary condition with time temporal profile
+    SUBROUTINE applyDirichletTime(self, vectorF)
+      USE moduleMesh
+      USE moduleCaseParam, ONLY: timeStep, tauMin
+      IMPLICIT NONE
+
+      CLASS(boundaryEMDirichletTime), INTENT(in):: self
+      REAL(8), INTENT(inout):: vectorF(:)
+      REAL(8):: timeFactor
+      INTEGER:: n, ni
+
+      timeFactor = self%temporalProfile%get(DBLE(timeStep)*tauMin)
+
+      DO n = 1, self%nNodes
+        self%nodes(n)%obj%emData%phi  = self%potential * timeFactor
+        vectorF(self%nodes(n)%obj%n)  = self%nodes(n)%obj%emData%phi
+
+      END DO
+
+    END SUBROUTINE applyDirichletTime
 
     !Assemble the source vector based on the charge density to solve Poisson's equation
-    SUBROUTINE assembleSourceVector(vectorF)
+    SUBROUTINE assembleSourceVector(vectorF, n_e)
       USE moduleMesh
       USE moduleRefParam
       IMPLICIT NONE
@@ -58,8 +205,9 @@ MODULE moduleEM
       REAL(8), ALLOCATABLE:: localF(:)
       INTEGER, ALLOCATABLE:: nodes(:)
       REAL(8), ALLOCATABLE:: rho(:)
+      REAL(8), INTENT(in), OPTIONAL:: n_e(1:mesh%numNodes)
       INTEGER:: nNodes
-      INTEGER:: e, i, ni
+      INTEGER:: e, i, ni, b
       CLASS(meshNode), POINTER:: node
 
       !$OMP SINGLE
@@ -77,6 +225,10 @@ MODULE moduleEM
           ni = nodes(i)
           node => mesh%nodes(ni)%obj
           rho(i) = DOT_PRODUCT(qSpecies(:), node%output(:)%den/(vol_ref*node%v*n_ref))
+          IF (PRESENT(n_e)) THEN
+            rho(i) = rho(i) - n_e(i)
+
+          END IF
 
         END DO
 
@@ -97,18 +249,12 @@ MODULE moduleEM
       !$OMP END DO
 
       !Apply boundary conditions
-      !$OMP DO
-      DO i = 1, mesh%numNodes
-        node => mesh%nodes(i)%obj
+      !$OMP SINGLE
+      do b = 1, nBoundaryEM
+        call boundaryEM(b)%obj%apply(vectorF)
 
-        SELECT CASE(node%emData%type)
-        CASE ("dirichlet")
-          vectorF(i) = node%emData%phi
-
-        END SELECT
-
-      END DO
-      !$OMP END DO
+      end do
+      !$OMP END SINGLE
 
     END SUBROUTINE assembleSourceVector
 
@@ -156,4 +302,86 @@ MODULE moduleEM
 
     END SUBROUTINE solveElecField
 
+    FUNCTION BoltzmannElectron(phi, n) RESULT(n_e)
+      USE moduleRefParam
+      USE moduleConstParam
+      IMPLICIT NONE
+
+      INTEGER, INTENT(in):: n
+      REAL(8), INTENT(in):: phi(1:n)
+      REAL(8):: n_e(1:n)
+      REAL(8):: n_e0 = 1.0D16, phi_0 = -500.0D0, T_e = 11604.0
+      INTEGER:: i
+
+      n_e = n_e0 / n_ref * exp(qe * (phi*Volt_ref - phi_0) / (kb * T_e))
+
+      RETURN
+
+    END FUNCTION BoltzmannElectron
+
+    SUBROUTINE solveElecFieldBoltzmann()
+      USE moduleMesh
+      USE moduleErrors
+      IMPLICIT NONE
+
+      INTEGER, SAVE:: INFO
+      INTEGER:: n
+      REAL(8), ALLOCATABLE, SAVE:: tempF(:)
+      REAL(8), ALLOCATABLE, SAVE:: n_e(:), phi_old(:), phi(:)
+      INTEGER:: k
+      EXTERNAL:: dgetrs
+
+      !$OMP SINGLE
+      ALLOCATE(tempF(1:mesh%numNodes))
+      ALLOCATE(n_e(1:mesh%numNodes))
+      ALLOCATE(phi_old(1:mesh%numNodes))
+      ALLOCATE(phi(1:mesh%numNodes))
+      !$OMP END SINGLE
+
+      !$OMP DO
+      DO n = 1, mesh%numNodes
+        phi_old(n) = mesh%nodes(n)%obj%emData%phi
+
+      END DO
+      !$OMP END DO
+
+      !$OMP SINGLE
+      DO k = 1, 100
+        n_e = BoltzmannElectron(phi_old, mesh%numNodes)
+        CALL assembleSourceVector(tempF, n_e)
+
+        CALL dgetrs('N', mesh%numNodes, 1, mesh%K, mesh%numNodes, &
+                                mesh%IPIV, tempF,  mesh%numNodes, info)
+        phi = tempF
+
+        PRINT *, MAXVAL(n_e), MINVAL(n_e)
+        PRINT *, MAXVAL(phi), MINVAL(phi)
+        PRINT*, k, "diff = ", MAXVAL(ABS(phi - phi_old))
+        phi_old = phi
+
+      END DO
+      !$OMP END SINGLE
+
+      IF (info == 0) THEN
+        !Suscessful resolution of Poission equation
+        !$OMP DO
+        DO n = 1, mesh%numNodes
+          mesh%nodes(n)%obj%emData%phi = phi_old(n)
+
+        END DO
+        !$OMP END DO
+
+      ELSE
+        !$OMP SINGLE
+        CALL criticalError('Poisson equation failed', 'solveElecFieldBoltzmann')
+        !$OMP END SINGLE
+
+      END IF
+
+      !$OMP SINGLE
+      DEALLOCATE(tempF, n_e, phi_old, phi)
+      !$OMP END SINGLE
+
+    END SUBROUTINE solveElecFieldBoltzmann
+
 END MODULE moduleEM

src/modules/solver/moduleSolver.f90

@@ -138,6 +138,9 @@ MODULE moduleSolver
       CASE('Electrostatic','ConstantB')
         self%solveEM => solveElecField
 
+      CASE('ElectrostaticBoltzmann')
+        self%solveEM => solveElecFieldBoltzmann
+
       END SELECT
 
     END SUBROUTINE initEM
@@ -491,52 +494,46 @@ MODULE moduleSolver
     END SUBROUTINE updateParticleCell
 
     !Update the information about if a species needs to be moved this iteration
-    SUBROUTINE updatePushSpecies(self, t)
+    SUBROUTINE updatePushSpecies(self)
       USE moduleSpecies
+      USE moduleCaseparam, ONLY: timeStep
       IMPLICIT NONE
 
       CLASS(solverGeneric), INTENT(inout):: self
-      INTEGER, INTENT(in):: t
       INTEGER:: s
 
       DO s=1, nSpecies
-        self%pusher(s)%pushSpecies = MOD(t, self%pusher(s)%every) == 0
+        self%pusher(s)%pushSpecies = MOD(timeStep, self%pusher(s)%every) == 0
 
       END DO
 
     END SUBROUTINE updatePushSpecies
 
     !Output the different data and information
-    SUBROUTINE doOutput(t)
+    SUBROUTINE doOutput()
       USE moduleMesh
       USE moduleOutput
       USE moduleSpecies
       USE moduleCompTime
       USE moduleProbe
+      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
-      INTEGER, INTENT(in):: t
-
-      IF (t == tInitial) THEN
-        CALL SYSTEM('git rev-parse HEAD > ' // path // folder // '/' // 'fpack_commit.txt')
-
-      END IF
-
-      CALL outputProbes(t)
+      CALL outputProbes()
 
       counterOutput = counterOutput + 1
       IF (counterOutput >= triggerOutput .OR. &
-          t == tFinal .OR. t == tInitial) THEN
+          timeStep == tFinal .OR. timeStep == tInitial) THEN
 
         !Resets output counter
         counterOutput=0
 
-        CALL mesh%printOutput(t)
-        IF (ASSOCIATED(meshForMCC)) CALL meshForMCC%printColl(t)
-        CALL mesh%printEM(t)
-        WRITE(*, "(5X,A21,I10,A1,I10)") "t/tFinal: ", t, "/", tFinal
+        CALL mesh%printOutput()
+        IF (ASSOCIATED(meshForMCC)) CALL meshForMCC%printColl()
+        CALL mesh%printEM()
+        WRITE(*, "(5X,A21,I10,A1,I10)") "t/tFinal: ", timeStep, "/", tFinal
         WRITE(*, "(5X,A21,I10)")        "Particles: ", nPartOld
-        IF (t == 0) THEN
+        IF (timeStep == 0) THEN
           WRITE(*, "(5X,A21,F8.1,A2)")   "     init time: ",    1.D3*tStep, "ms"
 
         ELSE
@@ -554,34 +551,32 @@ MODULE moduleSolver
 
       counterCPUTime = counterCPUTime + 1
       IF (counterCPUTime >= triggerCPUTime .OR. &
-          t == tFinal .OR. t == tInitial) THEN
+          timeStep == tFinal .OR. timeStep == tInitial) THEN
 
         !Reset CPU Time counter
         counterCPUTime = 0
 
-        CALL printTime(t, t == 0)
+        CALL printTime(timeStep == 0)
 
       END IF
 
       !Output average values
-      IF (useAverage .AND. t == tFinal) THEN
+      IF (useAverage .AND. timeStep == tFinal) THEN
         CALL mesh%printAverage()
 
       END IF
 
     END SUBROUTINE doOutput
 
-    SUBROUTINE doAverage(t)
+    SUBROUTINE doAverage()
       USE moduleAverage
       USE moduleMesh
       IMPLICIT NONE
 
-      INTEGER, INTENT(in):: t
       INTEGER:: tAverage, n
 
-
       IF (useAverage) THEN
-        tAverage = t - tAverageStart
+        tAverage = timeStep - tAverageStart
 
         IF (tAverage == 1) THEN
           !First iteration in which average scheme is used