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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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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-56.801 79.676 m f
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- c 62.609 73.625 62.734 74.355 62.734 75.082 c 62.734 75.813 62.609 76.547
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- 60.922 71.379 60.484 70.629 c h
-60.484 70.629 m f
-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}
@@ -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.
@@ -585,12 +589,20 @@ 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.
+          \item \textbf{potential}: Real.
-                                     Fixed potential for Dirichlet boundary condition.
+                                    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}
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -611,7 +623,7 @@ make
                                 \begin{itemize}
                                   \item \textbf{A}: Ampere.
                                   \item \textbf{Am2}: Ampere per square meter.
-                                                      This value will be multiplied by the surface of injection.
+                                                      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}
@@ -717,7 +729,7 @@ 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.

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
@@ -32,10 +32,13 @@ PROGRAM fpakc
   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()
@@ -49,19 +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
 
@@ -79,7 +84,7 @@ PROGRAM fpakc
     !$OMP END SINGLE
 
     IF (doMCCollisions) THEN
-      CALL meshForMCC%doCollisions(t)
+      CALL meshForMCC%doCollisions()
 
     END IF
 
@@ -124,12 +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

@@ -47,24 +47,41 @@ MODULE moduleRandom
 
     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)
+    FUNCTION randomHalfMaxwellian() RESULT(rnd)
-      USE moduleConstParam, ONLY: PI
       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)

src/modules/init/moduleInput.f90

@@ -259,13 +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
+            WRITE(iString, '(i2)') i
-            CALL config%get(object // '.B(' // istring // ')', B(i), found)
+            CALL config%get(object // '.B(' // iString // ')', B(i), found)
             IF (.NOT. found) THEN
               CALL criticalError('Constant magnetic field not provided in direction ' // iString, 'readSolver')
 
@@ -799,7 +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
@@ -815,8 +819,8 @@ MODULE moduleInput
       CALL config%info('boundary', found, n_children = nBoundary)
       ALLOCATE(boundary(1:nBoundary))
       DO i = 1, nBoundary
-        WRITE(istring, '(i2)') i
+        WRITE(iString, '(i2)') i
-        object = 'boundary(' // TRIM(istring) // ')'
+        object = 'boundary(' // TRIM(iString) // ')'
 
         boundary(i)%n = i
         CALL config%get(object // '.name',            boundary(i)%name,            found)
@@ -825,71 +829,77 @@ 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
-          WRITE(sString,'(i2)') s
+          associate(bound => boundary(i)%bTypes(s)%obj)
-          object = 'boundary(' // TRIM(iString) // ').bTypes(' // TRIM(sString) // ')'
+            WRITE(sString,'(i2)') s
-          CALL config%get(object // '.type', bType, found)
+            object = 'boundary(' // TRIM(iString) // ').bTypes(' // TRIM(sString) // ')'
-          SELECT CASE(bType)
+            CALL config%get(object // '.type', bType, found)
-          CASE('reflection')
+            SELECT CASE(bType)
-            ALLOCATE(boundaryReflection:: boundary(i)%bTypes(s)%obj)
+            CASE('reflection')
+              ALLOCATE(boundaryReflection:: bound)
 
-          CASE('absorption')
+            CASE('absorption')
-            ALLOCATE(boundaryAbsorption:: boundary(i)%bTypes(s)%obj)
+              ALLOCATE(boundaryAbsorption:: bound)
 
-          CASE('transparent')
+            CASE('transparent')
-            ALLOCATE(boundaryTransparent:: boundary(i)%bTypes(s)%obj)
+              ALLOCATE(boundaryTransparent:: bound)
 
-          CASE('ionization')
+            CASE('axis')
-            !Neutral parameters
+              ALLOCATE(boundaryAxis:: bound)
-            CALL config%get(object // '.neutral.ion', speciesName, found)
-            IF (.NOT. found) CALL criticalError("missing parameter 'ion' for neutrals in ionization", 'readBoundary')
-            speciesID = speciesName2Index(speciesName)
-            CALL config%get(object // '.neutral.mass', m0, found)
-            IF (.NOT. found) THEN
-              m0 = species(s)%obj%m*m_ref
-            END IF
-            CALL config%get(object // '.neutral.density', n0, found)
-            IF (.NOT. found) CALL criticalError("missing parameter 'density' for neutrals in ionization", 'readBoundary')
-            CALL config%get(object // '.neutral.velocity', v0, found)
-            IF (.NOT. found) CALL criticalError("missing parameter 'velocity' for neutrals in ionization", 'readBoundary')
-            CALL config%get(object // '.neutral.temperature', T0, found)
-            IF (.NOT. found) CALL criticalError("missing parameter 'temperature' for neutrals in ionization", 'readBoundary')
 
-            CALL config%get(object // '.effectiveTime', effTime, found)
+            CASE('wallTemperature')
-            IF (.NOT. found) CALL criticalError("missing parameter 'effectiveTime' for ionization", 'readBoundary')
+              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 config%get(object // '.energyThreshold', eThreshold, found)
+              CALL initWallTemperature(bound, Tw, cw)
-            IF (.NOT. found) CALL criticalError("missing parameter 'eThreshold' in ionization", 'readBoundary')
 
-            CALL config%get(object // '.crossSection', crossSection, found)
+            CASE('ionization')
-            IF (.NOT. found) CALL criticalError("missing parameter 'crossSection' for neutrals in ionization", 'readBoundary')
+              !Neutral parameters
+              CALL config%get(object // '.neutral.ion', speciesName, found)
+              IF (.NOT. found) CALL criticalError("missing parameter 'ion' for neutrals in ionization", 'readBoundary')
+              speciesID = speciesName2Index(speciesName)
+              CALL config%get(object // '.neutral.mass', m0, found)
+              IF (.NOT. found) THEN
+                m0 = species(s)%obj%m*m_ref
+              END IF
+              CALL config%get(object // '.neutral.density', n0, found)
+              IF (.NOT. found) CALL criticalError("missing parameter 'density' for neutrals in ionization", 'readBoundary')
+              CALL config%get(object // '.neutral.velocity', v0, found)
+              IF (.NOT. found) CALL criticalError("missing parameter 'velocity' for neutrals in ionization", 'readBoundary')
+              CALL config%get(object // '.neutral.temperature', T0, found)
+              IF (.NOT. found) CALL criticalError("missing parameter 'temperature' for neutrals in ionization", 'readBoundary')
 
-            CALL config%get(object // '.electronSecondary', electronSecondary, found)
+              CALL config%get(object // '.effectiveTime', effTime, found)
-            electronSecondaryID = speciesName2Index(electronSecondary)
+              IF (.NOT. found) CALL criticalError("missing parameter 'effectiveTime' for ionization", 'readBoundary')
-            IF (found) THEN
-              CALL initIonization(boundary(i)%bTypes(s)%obj, species(s)%obj%m, m0, n0, v0, T0, &
-                                                             speciesID, effTime, crossSection, eThreshold,electronSecondaryID)
 
-            ELSE
+              CALL config%get(object // '.energyThreshold', eThreshold, found)
-              CALL initIonization(boundary(i)%bTypes(s)%obj, species(s)%obj%m, m0, n0, v0, T0, &
+              IF (.NOT. found) CALL criticalError("missing parameter 'eThreshold' in ionization", 'readBoundary')
-                                                             speciesID, effTime, crossSection, eThreshold)
 
-            END IF
+              CALL config%get(object // '.crossSection', crossSection, found)
+              IF (.NOT. found) CALL criticalError("missing parameter 'crossSection' for neutrals in ionization", 'readBoundary')
 
-          CASE('wallTemperature')
+              CALL config%get(object // '.electronSecondary', electronSecondary, found)
-            CALL config%get(object // '.temperature', Tw, found)
+              electronSecondaryID = speciesName2Index(electronSecondary)
-            IF (.NOT. found) CALL criticalError("temperature not found for wallTemperature boundary type", 'readBoundary')
+              IF (found) THEN
-            CALL config%get(object // '.specificHeat', cw, found)
+                CALL initIonization(bound, species(s)%obj%m, m0, n0, v0, T0, &
-            IF (.NOT. found) CALL criticalError("specificHeat not found for wallTemperature boundary type", 'readBoundary')
+                                                               speciesID, effTime, crossSection, eThreshold,electronSecondaryID)
 
-            CALL initWallTemperature(boundary(i)%bTypes(s)%obj, Tw, cw)
+              ELSE
+                CALL initIonization(bound, species(s)%obj%m, m0, n0, v0, T0, &
+                                                               speciesID, effTime, crossSection, eThreshold)
 
-          CASE('axis')
+              END IF
-            ALLOCATE(boundaryAxis:: boundary(i)%bTypes(s)%obj)
 
-          CASE DEFAULT
+            case('outflowAdaptive')
-            CALL criticalError('Boundary type ' // bType // ' undefined', 'readBoundary')
+              allocate(boundaryOutflowAdaptive:: bound)
 
-          END SELECT
+            CASE DEFAULT
+              CALL criticalError('Boundary type ' // bType // ' undefined', 'readBoundary')
+
+            END SELECT
+
+          end associate
 
         END DO
 
@@ -906,6 +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
@@ -964,9 +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
@@ -1054,6 +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')
 
@@ -1100,13 +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)
 
@@ -1114,7 +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)
@@ -1122,16 +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)
@@ -1139,7 +1162,6 @@ MODULE moduleInput
       USE moduleOutput
       USE moduleErrors
       USE moduleEM
-      USE moduleRefParam
       USE moduleSpecies
       USE json_module
       IMPLICIT NONE
@@ -1147,34 +1169,72 @@ MODULE moduleInput
       TYPE(json_file), INTENT(inout):: config
       CHARACTER(:), ALLOCATABLE:: object
       LOGICAL:: found
-      CHARACTER(2):: istring
+      CHARACTER(:), ALLOCATABLE:: typeEM
-      INTEGER:: i, e, s
+      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))
+
+      END IF
       
-      DO i = 1, nBoundaryEM
+      DO b = 1, nBoundaryEM
-        WRITE(istring, '(I2)') i
+        WRITE(bString, '(I2)') b
-        object = 'boundaryEM(' // trim(istring) // ')'
+        object = 'boundaryEM(' // TRIM(bString) // ')'
 
-        CALL config%get(object // '.type', boundEM(i)%typeEM, found)
+        CALL config%get(object // '.type', typeEM, found)
 
-        SELECT CASE(boundEM(i)%typeEM)
+        SELECT CASE(typeEM)
         CASE ("dirichlet")
-          CALL config%get(object // '.potential', boundEM(i)%potential, found)
+          CALL config%get(object // '.potential', potential, found)
-          IF (.NOT. 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)
+          END IF
-          IF (.NOT. found) &
+
-            CALL criticalError('Required parameter "physicalSurface" for Dirichlet boundary condition not found', 'readEMBoundary')
+          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
 
@@ -1193,18 +1253,28 @@ MODULE moduleInput
 
       END DO
 
-      IF (ALLOCATED(boundEM)) THEN
+      ! Modify K matrix due to boundary conditions
-        DO e = 1, mesh%numEdges
+      DO b = 1, nBoundaryEM
-          IF (ANY(mesh%edges(e)%obj%physicalSurface == boundEM(:)%physicalSurface)) THEN
+        SELECT TYPE(boundary => boundaryEM(b)%obj)
-            DO i = 1, nBoundaryEM
+        TYPE IS(boundaryEMDirichlet)
-              IF (mesh%edges(e)%obj%physicalSurface == boundEM(i)%physicalSurface) THEN
+          DO n = 1, boundary%nNodes
-                CALL boundEM(i)%apply(mesh%edges(e)%obj)
+            ni = boundary%nodes(n)%obj%n
+            mesh%K(ni, :)  = 0.D0
+            mesh%K(ni, ni) = 1.D0
 
-              END IF
+          END DO
-            END DO
+
-          END IF
+        TYPE IS(boundaryEMDirichletTime)
-        END DO
+          DO n = 1, boundary%nNodes
-      END IF
+            ni = boundary%nodes(n)%obj%n
+            mesh%K(ni, :)  = 0.D0
+            mesh%K(ni, ni) = 1.D0
+
+          END DO
+
+        END SELECT
+
+      END DO
 
       !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)
@@ -1225,13 +1295,13 @@ 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
@@ -1242,8 +1312,8 @@ MODULE moduleInput
       ALLOCATE(inject(1:nInject))
       nPartInj = 0
       DO i = 1, nInject
-        WRITE(istring, '(i2)') i
+        WRITE(iString, '(i2)') i
-        object = 'inject(' // trim(istring) // ')'
+        object = 'inject(' // trim(iString) // ')'
 
         !Find species
         CALL config%get(object // '.species', speciesName, found)
@@ -1251,7 +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))
@@ -1263,7 +1333,7 @@ MODULE moduleInput
         particlesPerEdge = 0
         CALL config%get(object // '.particlesPerEdge', particlesPerEdge, found)
 
-        CALL inject(i)%init(i, v, normal, T, flow, units, sp, physicalSurface, particlesPerEdge)
+        CALL inject(i)%init(i, v, normal, temperature, flow, units, sp, physicalSurface, particlesPerEdge)
 
         CALL readVelDistr(config, inject(i), object)
         
@@ -1282,6 +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
@@ -1295,8 +1366,11 @@ 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
 
         ALLOCATE(averageScheme(1:mesh%numNodes))
@@ -1323,28 +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
+        WRITE(iString, '(i2)') i
-        CALL config%get(object // '.velDist('// TRIM(istring) //')', fvType, found)
+        CALL config%get(object // '.velDist('// TRIM(iString) //')', fvType, found)
-        IF (.NOT. found) CALL criticalError("No velocity distribution in direction " // istring // &
+        IF (.NOT. found) CALL criticalError("No velocity distribution in direction " // iString // &
                                             " found for " // object, 'readVelDistr')
 
         SELECT CASE(fvType)
         CASE ("Maxwellian")
-          T = inj%T(i)
+          temperature = inj%temperature(i)
-          CALL initVelDistMaxwellian(inj%v(i)%obj, t, m)
+          CALL initVelDistMaxwellian(inj%v(i)%obj, temperature, m)
 
         CASE ("Half-Maxwellian")
-          T = inj%T(i)
+          temperature = inj%temperature(i)
-          CALL initVelDistHalfMaxwellian(inj%v(i)%obj, t, m)
+          CALL initVelDistHalfMaxwellian(inj%v(i)%obj, temperature, m)
 
         CASE ("Delta")
           v = inj%vMod*inj%n(i)

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

@@ -104,7 +104,6 @@ MODULE moduleMesh1DCart
       USE moduleSpecies
       USE moduleBoundary
       USE moduleErrors
-      USE moduleRefParam, ONLY: L_ref
       IMPLICIT NONE
 
       CLASS(meshEdge1DCart), INTENT(out):: self
@@ -123,7 +122,7 @@ MODULE moduleMesh1DCart
 
       self%x = r1(1)
 
-      self%surface = 1.D0 / L_ref**2
+      self%surface = 1.D0
 
       self%normal = (/ 1.D0, 0.D0, 0.D0 /)
 

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

@@ -104,7 +104,6 @@ MODULE moduleMesh1DRad
       USE moduleSpecies
       USE moduleBoundary
       USE moduleErrors
-      USE moduleRefParam, ONLY: L_ref
       IMPLICIT NONE
 
       CLASS(meshEdge1DRad), INTENT(out):: self
@@ -123,7 +122,7 @@ MODULE moduleMesh1DRad
 
       self%r = r1(1)
 
-      self%surface = 1.D0 / L_ref**2
+      self%surface = 1.D0
 
       self%normal = (/ 1.D0, 0.D0, 0.D0 /)
 

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

@@ -144,7 +144,6 @@ MODULE moduleMesh2DCart
       USE moduleSpecies
       USE moduleBoundary
       USE moduleErrors
-      USE moduleRefParam, ONLY: L_ref
       IMPLICIT NONE
 
       CLASS(meshEdge2DCart), INTENT(out):: self
@@ -164,7 +163,7 @@ MODULE moduleMesh2DCart
       r2 = self%n2%getCoordinates()
       self%x  = (/r1(1), r2(1)/)
       self%y  = (/r1(2), r2(2)/)
-      self%surface = SQRT((self%x(2) - self%x(1))**2 + (self%y(2) - self%y(1))**2) / L_ref
+      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) , &
@@ -495,34 +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
+      conv  = 1.D0
-      XiO  = 0.D0
+      Xi0   = 0.D0
+      Xi(3) = 0.D0
 
-      f(3) = 0.D0
       DO WHILE(conv > 1.D-4)
-        dPsi = self%dPsi(XiO, 4)
+        fPsi           = self%fPsi(Xi0, 4)
-        pDer = self%partialDer(4, dPsi)
+        x0(1)          = dot_product(fPsi, self%x)
-        detJ = self%detJac(pDer)
+        x0(2)          = dot_product(fPsi, self%y)
-        invJ = self%invJac(pDer)
+        deltaR         = r(1:2) - x0
-        fPsi = self%fPsi(XiO, 4)
+        dPsi           = self%dPsi(Xi0, 4)
-        f(1:2) = (/ DOT_PRODUCT(fPsi,self%x), &
+        pDer           = self%partialDer(4, dPsi)
-                    DOT_PRODUCT(fPsi,self%y) /) - r(1:2)
+        detJ           = self%detJac(pDer)
-        Xi = XiO - MATMUL(invJ, f)/detJ
+        pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
-        conv = MAXVAL(DABS(Xi-XiO),1)
+        pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
-        XiO = Xi
+        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
 
@@ -557,7 +558,6 @@ MODULE moduleMesh2DCart
 
     !Compute element volume
     PURE SUBROUTINE volumeQuad(self)
-      USE moduleRefParam, ONLY: L_ref
       IMPLICIT NONE
 
       CLASS(meshCell2DCartQuad), INTENT(inout):: self
@@ -575,7 +575,7 @@ MODULE moduleMesh2DCart
       fPsi = self%fPsi(Xi, 4)
 
       !Compute total volume of the cell
-      self%volume  = detJ*4.D0/L_ref
+      self%volume  = detJ*4.D0
       !Compute volume per node
       self%n1%v = self%n1%v + fPsi(1)*self%volume
       self%n2%v = self%n2%v + fPsi(2)*self%volume
@@ -680,8 +680,8 @@ MODULE moduleMesh2DCart
 
       dPsi = 0.D0
 
-      dPsi(1,:) = (/ -1.D0, 1.D0, 0.D0 /)
+      dPsi(1,1:3) = (/ -1.D0, 1.D0, 0.D0 /)
-      dPsi(2,:) = (/ -1.D0, 0.D0, 1.D0 /)
+      dPsi(2,1:3) = (/ -1.D0, 0.D0, 1.D0 /)
 
     END FUNCTION dPsiTria
 
@@ -826,19 +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):: detJ, pDerInv(1:2,1:2), deltaR(1:2)
-      REAL(8):: dPsi(1:3, 1:3)
+      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
+      Xi(3)          = 0.D0
-      deltaR = (/ r(1) - self%x(1), r(2) - self%y(1), 0.D0 /)
+      deltaR         = (/ r(1) - self%x(1), r(2) - self%y(1) /)
-      dPsi   = self%dPsi(Xi, 3)
+      dPsi           = self%dPsi(Xi, 3)
-      pDer   = self%partialDer(3, dPsi)
+      pDer           = self%partialDer(3, dPsi)
-      invJ   = self%invJac(pDer)
+      detJ           = self%detJac(pDer)
-      detJ   = self%detJac(pDer)
+      pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
-      Xi     = MATMUL(invJ,deltaR)/detJ
+      pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+      Xi(1:2)        = MATMUL(pDerInv,deltaR)/detJ
 
     END FUNCTION phy2logTria
 
@@ -913,8 +913,8 @@ MODULE moduleMesh2DCart
 
       invJ = 0.D0
 
-      invJ(1, 1:2) = (/  pDer(2,2), -pDer(1,2) /)
+      invJ(1, 1:2) = (/  pDer(2,2), -pDer(2,1) /)
-      invJ(2, 1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+      invJ(2, 1:2) = (/ -pDer(1,2),  pDer(1,1) /)
       invJ(3, 3)   = 1.D0
 
     END FUNCTION invJ2DCart

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

@@ -510,34 +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
+      conv  = 1.D0
-      XiO  = 0.D0
+      Xi0   = 0.D0
+      Xi(3) = 0.D0
 
-      f(3) = 0.D0
       DO WHILE(conv > 1.D-4)
-        dPsi = self%dPsi(XiO, 4)
+        fPsi           = self%fPsi(Xi0, 4)
-        pDer = self%partialDer(4, dPsi)
+        x0(1)          = dot_product(fPsi, self%z)
-        detJ = self%detJac(pDer)
+        x0(2)          = dot_product(fPsi, self%r)
-        invJ = self%invJac(pDer)
+        deltaR         = r(1:2) - x0
-        fPsi = self%fPsi(XiO, 4)
+        dPsi           = self%dPsi(Xi0, 4)
-        f(1:2) = (/ DOT_PRODUCT(fPsi,self%z), &
+        pDer           = self%partialDer(4, dPsi)
-                    DOT_PRODUCT(fPsi,self%r) /) - r(1:2)
+        detJ           = self%detJac(pDer)
-        Xi = XiO - MATMUL(invJ, f)/detJ
+        pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
-        conv = MAXVAL(DABS(Xi-XiO),1)
+        pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
-        XiO = Xi
+        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
 
@@ -705,8 +707,8 @@ MODULE moduleMesh2DCyl
 
       dPsi = 0.D0
 
-      dPsi(1,:) = (/ -1.D0, 1.D0, 0.D0 /)
+      dPsi(1,1:3) = (/ -1.D0, 1.D0, 0.D0 /)
-      dPsi(2,:) = (/ -1.D0, 0.D0, 1.D0 /)
+      dPsi(2,1:3) = (/ -1.D0, 0.D0, 1.D0 /)
 
     END FUNCTION dPsiTria
 
@@ -858,19 +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):: detJ, pDerInv(1:2,1:2), deltaR(1:2)
-      REAL(8):: dPsi(1:3, 1:3)
+      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
+      Xi(3)          = 0.D0
-      deltaR = (/ r(1) - self%z(1), r(2) - self%r(1), 0.D0 /)
+      deltaR         = (/ r(1) - self%z(1), r(2) - self%r(1) /)
-      dPsi   = self%dPsi(Xi, 3)
+      dPsi           = self%dPsi(Xi, 3)
-      pDer   = self%partialDer(3, dPsi)
+      pDer           = self%partialDer(3, dPsi)
-      invJ   = self%invJac(pDer)
+      detJ           = self%detJac(pDer)
-      detJ   = self%detJac(pDer)
+      pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
-      Xi     = MATMUL(invJ,deltaR)/detJ
+      pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+      Xi(1:2)        = MATMUL(pDerInv,deltaR)/detJ
 
     END FUNCTION phy2logTria
 
@@ -948,8 +950,8 @@ MODULE moduleMesh2DCyl
 
       invJ = 0.D0
 
-      invJ(1, 1:2) = (/  pDer(2,2), -pDer(1,2) /)
+      invJ(1, 1:2) = (/  pDer(2,2), -pDer(2,1) /)
-      invJ(2, 1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+      invJ(2, 1:2) = (/ -pDer(1,2),  pDer(1,1) /)
       invJ(3, 3)   = 1.D0
 
     END FUNCTION invJ2DCyl

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/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
+      IF (PRESENT(timeStep)) THEN
-        WRITE(tString, iterationFormat) t
+        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
@@ -548,6 +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
@@ -215,17 +215,16 @@ MODULE moduleMeshOutputVTU
 
     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>'
 
@@ -307,21 +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:: i, fileID
       CHARACTER(:), ALLOCATABLE:: fileName, fileNameCollection
 
       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)
 
@@ -337,28 +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:: fileID
       CHARACTER(:), ALLOCATABLE:: fileName, fileNameCollection
-      CHARACTER (LEN=iterationDigits):: tstring
 
       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)
 
@@ -374,26 +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)
 
@@ -409,7 +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
 

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()
@@ -337,10 +344,10 @@ MODULE moduleMesh
     !Array of cell elements
     TYPE(meshCellCont),  ALLOCATABLE:: cells(:)
     !PROCEDURES SPECIFIC OF FILE TYPE
-    PROCEDURE(readMesh_interface),     POINTER, PASS::   readMesh     => NULL()
+    PROCEDURE(readMesh_interface),    POINTER, PASS::   readMesh     => NULL()
-    PROCEDURE(readInitial_interface),  POINTER, NOPASS:: readInitial  => NULL()
+    PROCEDURE(readInitial_interface), POINTER, NOPASS:: readInitial  => NULL()
-    PROCEDURE(connectMesh_interface),  POINTER, PASS::   connectMesh  => NULL()
+    PROCEDURE(connectMesh_interface), POINTER, PASS::   connectMesh  => NULL()
-    PROCEDURE(printColl_interface),    POINTER, PASS::   printColl    => NULL()
+    PROCEDURE(printColl_interface),   POINTER, PASS::   printColl    => NULL()
     CONTAINS
       !GENERIC PROCEDURES
       PROCEDURE, PASS:: doCollisions
@@ -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
 
@@ -495,28 +499,29 @@ MODULE moduleMesh
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(inout):: self
-      INTEGER:: e
+      INTEGER:: c
-      INTEGER:: nNodes
       INTEGER, ALLOCATABLE:: n(:)
       REAL(8), ALLOCATABLE:: localK(:,:)
       INTEGER:: i, j
 
-      DO e = 1, self%numCells
+      DO c = 1, self%numCells
-        nNodes = self%cells(e)%obj%nNodes
+        associate(nNodes => self%cells(c)%obj%nNodes)
-        ALLOCATE(n(1:nNodes))
+          ALLOCATE(n(1:nNodes))
-        ALLOCATE(localK(1:nNodes, 1:nNodes))
+          ALLOCATE(localK(1:nNodes, 1:nNodes))
-        n      = self%cells(e)%obj%getNodes(nNodes)
+          n      = self%cells(c)%obj%getNodes(nNodes)
-        localK = self%cells(e)%obj%elemK(nNodes)
+          localK = self%cells(c)%obj%elemK(nNodes)
 
-        DO i = 1, nNodes
+          DO i = 1, nNodes
-          DO j = 1, nNodes
+            DO j = 1, nNodes
-            self%K(n(i), n(j)) = self%K(n(i), n(j)) + localK(i, j)
+              self%K(n(i), n(j)) = self%K(n(i), n(j)) + localK(i, j)
+
+            END DO
 
           END DO
 
-        END DO
+          DEALLOCATE(n, localK)
 
-        DEALLOCATE(n, localK)
+        end associate
 
       END DO
 
@@ -789,7 +794,7 @@ MODULE moduleMesh
     END FUNCTION findCellBrute
 
     !Computes collisions in element
-    SUBROUTINE doCollisions(self, t)
+    SUBROUTINE doCollisions(self)
       USE moduleCollisions
       USE moduleSpecies
       USE moduleList
@@ -797,10 +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
@@ -816,7 +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

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
@@ -204,19 +218,27 @@ MODULE moduleMeshBoundary
 
     END SUBROUTINE ionization
 
-    !Symmetry axis. Reflects particles.
+    subroutine outflowAdaptive(edge, part)
-    !Although this function should never be called, it is set as a reflective boundary
+      use moduleRandom
-    !to properly deal with possible particles reaching a corner and selecting this boundary.
+      implicit none
-    SUBROUTINE symmetryAxis(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
 
-      CLASS(meshEdge), INTENT(inout):: edge
+      class(meshEdge), intent(inout):: edge
-      CLASS(particle), INTENT(inout):: part
+      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)
@@ -236,14 +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)
+      type is(boundaryOutflowAdaptive)
-        edge%fBoundary(s)%apply => symmetryAxis
+        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)
@@ -47,11 +53,13 @@ MODULE moduleBoundary
 
   END TYPE boundaryIonization
 
-  !Symmetry axis
+  !Boundary for quasi-neutral outflow adjusting reflection coefficient
-  TYPE, PUBLIC, EXTENDS(boundaryGeneric):: boundaryAxis
+  type, public, extends(boundaryGeneric):: boundaryOutflowAdaptive
-    CONTAINS
+    real(8):: outflowCurrent
+    real(8):: reflectionFraction
+    contains
 
-  END TYPE boundaryAxis
+  end type boundaryOutflowAdaptive
 
   !Wrapper for boundary types (one per species)
   TYPE:: bTypesCont

src/modules/moduleInject.f90

@@ -54,7 +54,7 @@ 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
@@ -76,7 +76,7 @@ MODULE moduleInject
 
   CONTAINS
     !Initialize an injection of particles
-    SUBROUTINE initInject(self, i, v, n, T, flow, units, sp, physicalSurface, particlesPerEdge)
+    SUBROUTINE initInject(self, i, v, n, temperature, flow, units, sp, physicalSurface, particlesPerEdge)
       USE moduleMesh
       USE moduleRefParam
       USE moduleConstParam
@@ -87,7 +87,7 @@ MODULE moduleInject
 
       CLASS(injectGeneric), INTENT(inout):: self
       INTEGER, INTENT(in):: i
-      REAL(8), INTENT(in):: v, n(1:3), T(1:3)
+      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
@@ -97,10 +97,10 @@ MODULE moduleInject
       INTEGER:: nVolColl
       REAL(8):: fluxPerStep = 0.D0
 
-      self%id      =  i
+      self%id          =  i
-      self%vMod    =  v / v_ref
+      self%vMod        =  v / v_ref
-      self%n       =  n / NORM2(n)
+      self%n           =  n / NORM2(n)
-      self%T       =  T / T_ref
+      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
@@ -159,11 +159,26 @@ MODULE moduleInject
 
       CASE ("A")
         !Current in Ampers
-        fluxPerStep = flow/qe
+        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
-        fluxPerStep = flow*self%surface*L_ref**2/qe
+        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
@@ -184,17 +199,21 @@ MODULE moduleInject
 
         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) = FLOOR(fluxPerStep*mesh%edges(self%edges(et))%obj%surface /self%species%weight)
+          self%particlesPerEdge(et) = max(1,FLOOR(fluxPerStep*mesh%edges(self%edges(et))%obj%surface / self%species%weight))
-
         END DO
 
-      END IF
+        self%nParticles = SUM(self%particlesPerEdge)
 
-      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')
@@ -232,23 +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
 
@@ -270,7 +289,7 @@ MODULE moduleInject
       REAL(8):: v
       v = 0.D0
 
-      v = self%vTh*randomMaxwellian()
+      v = self%vTh*randomMaxwellian()/sqrt(2.d0)
 
     END FUNCTION randomVelMaxwellian
 
@@ -283,10 +302,7 @@ MODULE moduleInject
       REAL(8):: v
       v = 0.D0
 
-      DO WHILE (v <= 0.D0)
+      v = self%vTh*randomHalfMaxwellian()/sqrt(2.d0)
-        v = self%vTh*randomMaxwellian()
-
-      END DO
 
     END FUNCTION randomVelHalfMaxwellian
 
@@ -361,19 +377,22 @@ MODULE moduleInject
           !Assign particle type
           partInj(n)%species => self%species
 
-          direction = self%n
+          if (all(self%n == 0.D0)) then
+            direction =  randomEdge%normal
+
+          else
+            direction = self%n
+
+          end if
 
           partInj(n)%v = 0.D0
 
-          partInj(n)%v = self%vMod*direction +  (/ self%v(1)%obj%randomVel(), &
+          do while(dot_product(partInj(n)%v, direction) <= 0.d0)
-                                                   self%v(2)%obj%randomVel(), &
+            partInj(n)%v = self%vMod*direction +  (/ self%v(1)%obj%randomVel(), &
-                                                   self%v(3)%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)

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)
 
@@ -91,11 +91,11 @@ 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
       
@@ -189,13 +189,13 @@ MODULE moduleProbe
           
     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

@@ -1,56 +1,202 @@
 !Module to solve the electromagnetic field
 MODULE moduleEM
+  USE moduleMesh
+  USE moduleTable
   IMPLICIT NONE
 
-  TYPE:: boundaryEM
+  ! Generic type for electromagnetic boundary conditions
-    CHARACTER(:), ALLOCATABLE:: typeEM
+  TYPE, PUBLIC, ABSTRACT:: boundaryEMGeneric
-    INTEGER:: physicalSurface
+    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 findNodes(self, physicalSurface)
-    SUBROUTINE apply(self, edge)
       USE moduleMesh
       IMPLICIT NONE
 
-      CLASS(boundaryEM), INTENT(in):: self
+      CLASS(boundaryEMGeneric), INTENT(inout):: self
-      CLASS(meshEdge):: edge
+      INTEGER, INTENT(in):: physicalSurface
-      INTEGER:: nNodes
+      CLASS(meshEdge), POINTER:: edge
-      INTEGER, ALLOCATABLE:: nodes(:)
+      INTEGER, ALLOCATABLE:: nodes(:), nodesEdge(:)
-      INTEGER:: n
+      INTEGER:: nNodes, nodesNew
+      INTEGER:: e, n
 
-      nNodes = 1
+      !Temporal array to hold nodes
-      nNodes = edge%nNodes
+      ALLOCATE(nodes(0))
-      nodes  = edge%getNodes(nNodes)
 
-      DO n = 1, nNodes
+      ! Loop thorugh the edges and identify those that are part of the boundary
-        SELECT CASE(self%typeEM)
+      DO e = 1, mesh%numEdges
-        CASE ("dirichlet")
+        edge => mesh%edges(e)%obj
-          mesh%K(nodes(n), :)        = 0.D0
+        IF (edge%physicalSurface == physicalSurface) THEN
-          mesh%K(nodes(n), nodes(n)) = 1.D0
+          ! Edge is of the right boundary index
-        
+          ! Get nodes in the edge
-          mesh%nodes(nodes(n))%obj%emData%type = self%typeEM
+          nNodes = edge%nNodes
-          mesh%nodes(nodes(n))%obj%emData%phi  = self%potential
+          nodesEdge = edge%getNodes(nNodes)
+          ! Collect all nodes that are not already in the temporal array
+          DO n = 1, nNodes
+            IF (ANY(nodes == nodesEdge(n))) THEN
+              ! Node already in array, skip
+              CYCLE
 
-        END SELECT
+            ELSE
+              ! If not, add element to array of nodes
+              nodes = [nodes, nodesEdge(n)]
+
+            END IF
+
+          END DO
+
+        END IF
 
       END DO
 
-    END SUBROUTINE
+      ! 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
@@ -59,8 +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
@@ -78,6 +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
 
@@ -98,18 +249,12 @@ MODULE moduleEM
       !$OMP END DO
 
       !Apply boundary conditions
-      !$OMP DO
+      !$OMP SINGLE
-      DO i = 1, mesh%numNodes
+      do b = 1, nBoundaryEM
-        node => mesh%nodes(i)%obj
+        call boundaryEM(b)%obj%apply(vectorF)
 
-        SELECT CASE(node%emData%type)
+      end do
-        CASE ("dirichlet")
+      !$OMP END SINGLE
-          vectorF(i) = node%emData%phi
-
-        END SELECT
-
-      END DO
-      !$OMP END DO
 
     END SUBROUTINE assembleSourceVector
 
@@ -157,4 +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
@@ -491,47 +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
+      CALL outputProbes()
-
-      CALL outputProbes(t)
 
       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)
+        CALL mesh%printOutput()
-        IF (ASSOCIATED(meshForMCC)) CALL meshForMCC%printColl(t)
+        IF (ASSOCIATED(meshForMCC)) CALL meshForMCC%printColl()
-        CALL mesh%printEM(t)
+        CALL mesh%printEM()
-        WRITE(*, "(5X,A21,I10,A1,I10)") "t/tFinal: ", t, "/", tFinal
+        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
@@ -549,34 +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