CITATION.cff

@@ -1,50 +0,0 @@
-# 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)"}}
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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
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+c 57.918 76.02 57.691 75.941 57.41 75.941 c 57.211 75.941 56.996 75.98 56.77
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+ c 57.707 78.75 57.309 79.156 56.801 79.676 c h
+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
+ 62.359 77.285 c 62.117 78.027 61.754 78.773 61.266 79.535 c 60.484 79.535
+ l 60.922 78.793 61.242 78.059 61.453 77.316 c 61.672 76.578 61.781 75.832
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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}
@@ -460,10 +460,6 @@ 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.
@@ -589,20 +585,12 @@ make
                                Type of boundary.
                                 Accepted values are:
                                \begin{itemize}
-                                 \item \textbf{dirichlet}: Constant value of electric potential on the surface.
+                                 \item \textbf{dirichlet}: Elastic reflection of particles.
-                                 \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}
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -623,7 +611,7 @@ make
                                 \begin{itemize}
                                   \item \textbf{A}: Ampere.
                                   \item \textbf{Am2}: Ampere per square meter.
-                                                      This value will be multiplied by the area of injection.
+                                                      This value will be multiplied by the surface of injection.
                                   \item \textbf{sccm}: Standard cubic centimetre.
                                   \item \textbf{part/s}: Particles (real) per second.
                                 \end{itemize}
@@ -729,7 +717,7 @@ 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 in \textbf{output.path}.
+                                                         File must be located at \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
@@ -32,13 +32,10 @@ PROGRAM fpakc
   CALL initOutput(inputFile)
 
   !Do '0' iteration
-  timeStep = tInitial
+  t = tInitial
 
   !$OMP PARALLEL DEFAULT(SHARED)
   !$OMP SINGLE
-  ! Initial reset of probes
-  CALL resetProbes()
-
   CALL verboseError("Initial scatter of particles...")
   !$OMP END SINGLE
   CALL doScatter()
@@ -52,21 +49,19 @@ PROGRAM fpakc
   tStep = omp_get_wtime() - tStep
 
   !Output initial state
-  CALL doOutput()
+  CALL doOutput(t)
   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()
+    CALL solver%updatePushSpecies(t)
 
     !Checks if probes need to be calculated this iteration
-    CALL resetProbes()
+    CALL resetProbes(t)
     tPush = omp_get_wtime()
     !$OMP END SINGLE
 
@@ -84,7 +79,7 @@ PROGRAM fpakc
     !$OMP END SINGLE
 
     IF (doMCCollisions) THEN
-      CALL meshForMCC%doCollisions()
+      CALL meshForMCC%doCollisions(t)
 
     END IF
 
@@ -129,12 +124,12 @@ PROGRAM fpakc
     !$OMP SINGLE
     tEMField = omp_get_wtime() - tEMField
 
-    CALL doAverage()
+    CALL doAverage(t)
 
     tStep = omp_get_wtime() - tStep
 
     !Output data
-    CALL doOutput()
+    CALL doOutput(t)
     !$OMP END SINGLE
 
   END DO

src/makefile

@@ -9,7 +9,6 @@ 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

@@ -2,13 +2,8 @@
 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

@@ -47,41 +47,24 @@ 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 randomHalfMaxwellian() RESULT(rnd)
+    FUNCTION randomMaxwellian() RESULT(rnd)
+      USE moduleConstParam, ONLY: PI
       IMPLICIT NONE
 
       REAL(8):: rnd
-      REAL(8):: x
+      REAL(8):: x, y
 
       rnd = 0.D0
       x = 0.D0
       DO WHILE (x == 0.D0)
         CALL RANDOM_NUMBER(x)
       END DO
+      CALL RANDOM_NUMBER(y)
 
-      rnd = DSQRT(-DLOG(x))
+      rnd = DSQRT(-2.D0*DLOG(x))*DCOS(2.D0*PI*y)
 
-    END FUNCTION randomHalfMaxwellian
+    END FUNCTION randomMaxwellian
 
     !Returns a random number weighted with the cumWeight array
     FUNCTION randomWeighted(cumWeight, sumWeight) RESULT(rnd)

src/modules/init/moduleInput.f90

@@ -259,17 +259,13 @@ 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')
 
@@ -803,7 +799,7 @@ 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
@@ -819,8 +815,8 @@ 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)
@@ -829,77 +825,71 @@ MODULE moduleInput
         IF (nTypes /= nSpecies) CALL criticalError('Not enough boundary types defined in ' // object, 'readBoundary')
         ALLOCATE(boundary(i)%bTypes(1:nSpecies))
         DO s = 1, nSpecies
-          associate(bound => boundary(i)%bTypes(s)%obj)
+          WRITE(sString,'(i2)') s
-            WRITE(sString,'(i2)') s
+          object = 'boundary(' // TRIM(iString) // ').bTypes(' // TRIM(sString) // ')'
-            object = 'boundary(' // TRIM(iString) // ').bTypes(' // TRIM(sString) // ')'
+          CALL config%get(object // '.type', bType, found)
-            CALL config%get(object // '.type', bType, found)
+          SELECT CASE(bType)
-            SELECT CASE(bType)
+          CASE('reflection')
-            CASE('reflection')
+            ALLOCATE(boundaryReflection:: boundary(i)%bTypes(s)%obj)
-              ALLOCATE(boundaryReflection:: bound)
 
-            CASE('absorption')
+          CASE('absorption')
-              ALLOCATE(boundaryAbsorption:: bound)
+            ALLOCATE(boundaryAbsorption:: boundary(i)%bTypes(s)%obj)
 
-            CASE('transparent')
+          CASE('transparent')
-              ALLOCATE(boundaryTransparent:: bound)
+            ALLOCATE(boundaryTransparent:: boundary(i)%bTypes(s)%obj)
 
-            CASE('axis')
+          CASE('ionization')
-              ALLOCATE(boundaryAxis:: bound)
+            !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')
 
-            CASE('wallTemperature')
+            CALL config%get(object // '.effectiveTime', effTime, found)
-              CALL config%get(object // '.temperature', Tw, found)
+            IF (.NOT. found) CALL criticalError("missing parameter 'effectiveTime' for ionization", 'readBoundary')
-              IF (.NOT. found) CALL criticalError("temperature not found for wallTemperature boundary type", 'readBoundary')
-              CALL config%get(object // '.specificHeat', cw, found)
-              IF (.NOT. found) CALL criticalError("specificHeat not found for wallTemperature boundary type", 'readBoundary')
 
-              CALL initWallTemperature(bound, Tw, cw)
+            CALL config%get(object // '.energyThreshold', eThreshold, found)
+            IF (.NOT. found) CALL criticalError("missing parameter 'eThreshold' in ionization", 'readBoundary')
 
-            CASE('ionization')
+            CALL config%get(object // '.crossSection', crossSection, found)
-              !Neutral parameters
+            IF (.NOT. found) CALL criticalError("missing parameter 'crossSection' for neutrals in ionization", 'readBoundary')
-              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)
+            CALL config%get(object // '.electronSecondary', electronSecondary, found)
-              IF (.NOT. found) CALL criticalError("missing parameter 'effectiveTime' for ionization", 'readBoundary')
+            electronSecondaryID = speciesName2Index(electronSecondary)
+            IF (found) THEN
+              CALL initIonization(boundary(i)%bTypes(s)%obj, species(s)%obj%m, m0, n0, v0, T0, &
+                                                             speciesID, effTime, crossSection, eThreshold,electronSecondaryID)
 
-              CALL config%get(object // '.energyThreshold', eThreshold, found)
+            ELSE
-              IF (.NOT. found) CALL criticalError("missing parameter 'eThreshold' in ionization", 'readBoundary')
+              CALL initIonization(boundary(i)%bTypes(s)%obj, species(s)%obj%m, m0, n0, v0, T0, &
+                                                             speciesID, effTime, crossSection, eThreshold)
 
-              CALL config%get(object // '.crossSection', crossSection, found)
+            END IF
-              IF (.NOT. found) CALL criticalError("missing parameter 'crossSection' for neutrals in ionization", 'readBoundary')
 
-              CALL config%get(object // '.electronSecondary', electronSecondary, found)
+          CASE('wallTemperature')
-              electronSecondaryID = speciesName2Index(electronSecondary)
+            CALL config%get(object // '.temperature', Tw, found)
-              IF (found) THEN
+            IF (.NOT. found) CALL criticalError("temperature not found for wallTemperature boundary type", 'readBoundary')
-                CALL initIonization(bound, species(s)%obj%m, m0, n0, v0, T0, &
+            CALL config%get(object // '.specificHeat', cw, found)
-                                                               speciesID, effTime, crossSection, eThreshold,electronSecondaryID)
+            IF (.NOT. found) CALL criticalError("specificHeat not found for wallTemperature boundary type", 'readBoundary')
 
-              ELSE
+            CALL initWallTemperature(boundary(i)%bTypes(s)%obj, Tw, cw)
-                CALL initIonization(bound, species(s)%obj%m, m0, n0, v0, T0, &
-                                                               speciesID, effTime, crossSection, eThreshold)
 
-              END IF
+          CASE('axis')
+            ALLOCATE(boundaryAxis:: boundary(i)%bTypes(s)%obj)
 
-            case('outflowAdaptive')
+          CASE DEFAULT
-              allocate(boundaryOutflowAdaptive:: bound)
+            CALL criticalError('Boundary type ' // bType // ' undefined', 'readBoundary')
 
-            CASE DEFAULT
+          END SELECT
-              CALL criticalError('Boundary type ' // bType // ' undefined', 'readBoundary')
-
-            END SELECT
-
-          end associate
 
         END DO
 
@@ -916,7 +906,6 @@ MODULE moduleInput
       USE moduleMeshInputGmsh2, ONLY: initGmsh2
       USE moduleMeshInputVTU,   ONLY: initVTU
       USE moduleMeshInput0D,    ONLY: init0D
-      USE moduleMeshInputText,  ONLY: initText
       USE moduleMesh3DCart
       USE moduleMesh2DCyl
       USE moduleMesh2DCart
@@ -975,9 +964,9 @@ MODULE moduleInput
         !Read the 0D mesh
         CALL mesh%readMesh(pathMeshParticle)
 
-        !Get the volume
+        !Get the volumne
         CALL config%get(object // '.volume', volume, found)
-        !Rescale the volume
+        !Rescale the volumne
         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
@@ -1065,20 +1054,6 @@ 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')
 
@@ -1125,13 +1100,13 @@ 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):: everyTimeStep
+      REAL(8):: timeStep
 
       CALL config%info('output.probes', found, n_children = nProbes)
 
@@ -1139,7 +1114,7 @@ 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)
@@ -1147,14 +1122,16 @@ 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', everyTimeStep, found)
+        CALL config%get(object // '.timeStep', timeStep, 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, everyTimeStep)
+        CALL probe(i)%init(i, speciesName, r, v1, v2, v3, points, timeStep)
 
       END DO
 
+      CALL resetProbes(tInitial)
+
     END SUBROUTINE readProbes
 
     SUBROUTINE readEMBoundary(config)
@@ -1162,6 +1139,7 @@ MODULE moduleInput
       USE moduleOutput
       USE moduleErrors
       USE moduleEM
+      USE moduleRefParam
       USE moduleSpecies
       USE json_module
       IMPLICIT NONE
@@ -1169,72 +1147,34 @@ MODULE moduleInput
       TYPE(json_file), INTENT(inout):: config
       CHARACTER(:), ALLOCATABLE:: object
       LOGICAL:: found
-      CHARACTER(:), ALLOCATABLE:: typeEM
+      CHARACTER(2):: istring
-      REAL(8):: potential
+      INTEGER:: i, e, s
-      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) THEN
+      IF (found) ALLOCATE(boundEM(1:nBoundaryEM))
-        ALLOCATE(boundaryEM(1:nBoundaryEM))
-
-      END IF
       
-      DO b = 1, nBoundaryEM
+      DO i = 1, nBoundaryEM
-        WRITE(bString, '(I2)') b
+        WRITE(istring, '(I2)') i
-        object = 'boundaryEM(' // TRIM(bString) // ')'
+        object = 'boundaryEM(' // trim(istring) // ')'
 
-        CALL config%get(object // '.type', typeEM, found)
+        CALL config%get(object // '.type', boundEM(i)%typeEM, found)
 
-        SELECT CASE(typeEM)
+        SELECT CASE(boundEM(i)%typeEM)
         CASE ("dirichlet")
-          CALL config%get(object // '.potential', potential, found)
+          CALL config%get(object // '.potential', boundEM(i)%potential, found)
-          IF (.NOT. found) THEN
+          IF (.NOT. found) &
             CALL criticalError('Required parameter "potential" for Dirichlet boundary condition not found', 'readEMBoundary')
+          boundEM(i)%potential = boundEM(i)%potential/Volt_ref
 
-          END IF
+          CALL config%get(object // '.physicalSurface', boundEM(i)%physicalSurface, found)
-
+          IF (.NOT. found) &
-          CALL config%get(object // '.physicalSurface', physicalSurface, found)
+            CALL criticalError('Required parameter "physicalSurface" for Dirichlet boundary condition not found', 'readEMBoundary')
-          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 ' // typeEM // ' not yet supported', 'readEMBoundary')
+          CALL criticalError('Boundary type ' // boundEM(i)%typeEM // ' not yet supported', 'readEMBoundary')
 
         END SELECT
 
@@ -1253,28 +1193,18 @@ MODULE moduleInput
 
       END DO
 
-      ! Modify K matrix due to boundary conditions
+      IF (ALLOCATED(boundEM)) THEN
-      DO b = 1, nBoundaryEM
+        DO e = 1, mesh%numEdges
-        SELECT TYPE(boundary => boundaryEM(b)%obj)
+          IF (ANY(mesh%edges(e)%obj%physicalSurface == boundEM(:)%physicalSurface)) THEN
-        TYPE IS(boundaryEMDirichlet)
+            DO i = 1, nBoundaryEM
-          DO n = 1, boundary%nNodes
+              IF (mesh%edges(e)%obj%physicalSurface == boundEM(i)%physicalSurface) THEN
-            ni = boundary%nodes(n)%obj%n
+                CALL boundEM(i)%apply(mesh%edges(e)%obj)
-            mesh%K(ni, :)  = 0.D0
-            mesh%K(ni, ni) = 1.D0
 
-          END DO
+              END IF
-
+            END DO
-        TYPE IS(boundaryEMDirichletTime)
+          END IF
-          DO n = 1, boundary%nNodes
+        END DO
-            ni = boundary%nodes(n)%obj%n
+      END IF
-            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)
@@ -1295,13 +1225,13 @@ 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:: temperature(:), normal(:)
+      REAL(8), ALLOCATABLE:: T(:), normal(:)
       REAL(8):: flow
       CHARACTER(:), ALLOCATABLE:: units
       INTEGER:: physicalSurface
@@ -1312,8 +1242,8 @@ 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)
@@ -1321,7 +1251,7 @@ MODULE moduleInput
 
         CALL config%get(object // '.name',            name,            found)
         CALL config%get(object // '.v',               v,               found)
-        CALL config%get(object // '.T',               temperature,     found)
+        CALL config%get(object // '.T',               T,               found)
         CALL config%get(object // '.n',               normal,          found)
         IF (.NOT. found) THEN
           ALLOCATE(normal(1:3))
@@ -1333,7 +1263,7 @@ MODULE moduleInput
         particlesPerEdge = 0
         CALL config%get(object // '.particlesPerEdge', particlesPerEdge, found)
 
-        CALL inject(i)%init(i, v, normal, temperature, flow, units, sp, physicalSurface, particlesPerEdge)
+        CALL inject(i)%init(i, v, normal, T, flow, units, sp, physicalSurface, particlesPerEdge)
 
         CALL readVelDistr(config, inject(i), object)
         
@@ -1352,7 +1282,6 @@ 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
@@ -1366,11 +1295,8 @@ MODULE moduleInput
         CALL config%get('average.startTime', tStart, found)
 
         IF (found) THEN
-          tAverageStart = INT(tStart / ti_ref / tauMin)
+          tAverageStart = INT(tStart / tauMin)
 
-        ELSE
-          tAverageStart = 0
-          
         END IF
 
         ALLOCATE(averageScheme(1:mesh%numNodes))
@@ -1397,28 +1323,28 @@ 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, temperature, m
+      REAL(8):: v, T, 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")
-          temperature = inj%temperature(i)
+          T = inj%T(i)
-          CALL initVelDistMaxwellian(inj%v(i)%obj, temperature, m)
+          CALL initVelDistMaxwellian(inj%v(i)%obj, t, m)
 
         CASE ("Half-Maxwellian")
-          temperature = inj%temperature(i)
+          T = inj%T(i)
-          CALL initVelDistHalfMaxwellian(inj%v(i)%obj, temperature, m)
+          CALL initVelDistHalfMaxwellian(inj%v(i)%obj, t, m)
 
         CASE ("Delta")
           v = inj%vMod*inj%n(i)

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

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

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

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

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

@@ -144,6 +144,7 @@ MODULE moduleMesh2DCart
       USE moduleSpecies
       USE moduleBoundary
       USE moduleErrors
+      USE moduleRefParam, ONLY: L_ref
       IMPLICIT NONE
 
       CLASS(meshEdge2DCart), INTENT(out):: self
@@ -163,7 +164,7 @@ 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)
+      self%surface = SQRT((self%x(2) - self%x(1))**2 + (self%y(2) - self%y(1))**2) / L_ref
       !Normal vector
       self%normal = (/ -(self%y(2)-self%y(1)), &
                          self%x(2)-self%x(1) , &
@@ -494,36 +495,34 @@ MODULE moduleMesh2DCart
 
     END FUNCTION insideQuad
 
-    !Transform physical coordinates to element coordinates with a Taylor series
+    !Transform physical coordinates to element coordinates
     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):: Xi0(1:3), detJ, pDerInv(1:2,1:2), deltaR(1:2), x0(1:2)
+      REAL(8):: XiO(1:3), detJ, invJ(1:3,1:3), f(1:3)
       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
-      Xi0   = 0.D0
+      XiO  = 0.D0
-      Xi(3) = 0.D0
 
+      f(3) = 0.D0
       DO WHILE(conv > 1.D-4)
-        fPsi           = self%fPsi(Xi0, 4)
+        dPsi = self%dPsi(XiO, 4)
-        x0(1)          = dot_product(fPsi, self%x)
+        pDer = self%partialDer(4, dPsi)
-        x0(2)          = dot_product(fPsi, self%y)
+        detJ = self%detJac(pDer)
-        deltaR         = r(1:2) - x0
+        invJ = self%invJac(pDer)
-        dPsi           = self%dPsi(Xi0, 4)
+        fPsi = self%fPsi(XiO, 4)
-        pDer           = self%partialDer(4, dPsi)
+        f(1:2) = (/ DOT_PRODUCT(fPsi,self%x), &
-        detJ           = self%detJac(pDer)
+                    DOT_PRODUCT(fPsi,self%y) /) - r(1:2)
-        pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
+        Xi = XiO - MATMUL(invJ, f)/detJ
-        pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+        conv = MAXVAL(DABS(Xi-XiO),1)
-        Xi(1:2)        = Xi0(1:2) + MATMUL(pDerInv, deltaR)/detJ
+        XiO = Xi
-        conv           = MAXVAL(DABS(Xi(1:2)-Xi0(1:2)),1)
-        Xi0(1:2)       = Xi(1:2)
 
       END DO
 
@@ -558,6 +557,7 @@ 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
+      self%volume  = detJ*4.D0/L_ref
       !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(1,1:3) = (/ -1.D0, 1.D0, 0.D0 /)
+      dPsi(1,:) = (/ -1.D0, 1.D0, 0.D0 /)
-      dPsi(2,1:3) = (/ -1.D0, 0.D0, 1.D0 /)
+      dPsi(2,:) = (/ -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):: detJ, pDerInv(1:2,1:2), deltaR(1:2)
+      REAL(8):: deltaR(1:3)
-      REAL(8):: dPsi(1:3,1:4)
+      REAL(8):: dPsi(1:3, 1:3)
       REAL(8):: pDer(1:3, 1:3)
+      REAL(8):: invJ(1:3,  1:3), detJ
 
       !Direct method to convert coordinates
-      Xi(3)          = 0.D0
+      Xi     = 0.D0
-      deltaR         = (/ r(1) - self%x(1), r(2) - self%y(1) /)
+      deltaR = (/ r(1) - self%x(1), r(2) - self%y(1), 0.D0 /)
-      dPsi           = self%dPsi(Xi, 3)
+      dPsi   = self%dPsi(Xi, 3)
-      pDer           = self%partialDer(3, dPsi)
+      pDer   = self%partialDer(3, dPsi)
-      detJ           = self%detJac(pDer)
+      invJ   = self%invJac(pDer)
-      pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
+      detJ   = self%detJac(pDer)
-      pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+      Xi     = MATMUL(invJ,deltaR)/detJ
-      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(2,1) /)
+      invJ(1, 1:2) = (/  pDer(2,2), -pDer(1,2) /)
-      invJ(2, 1:2) = (/ -pDer(1,2),  pDer(1,1) /)
+      invJ(2, 1:2) = (/ -pDer(2,1),  pDer(1,1) /)
       invJ(3, 3)   = 1.D0
 
     END FUNCTION invJ2DCart

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

@@ -510,36 +510,34 @@ MODULE moduleMesh2DCyl
 
     END FUNCTION insideQuad
 
-    !Transform physical coordinates to element coordinates with a Taylor series
+    !Transform physical coordinates to element coordinates
     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):: Xi0(1:3), detJ, pDerInv(1:2,1:2), deltaR(1:2), x0(1:2)
+      REAL(8):: XiO(1:3), detJ, invJ(1:3,1:3), f(1:3)
       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
-      Xi0   = 0.D0
+      XiO  = 0.D0
-      Xi(3) = 0.D0
 
+      f(3) = 0.D0
       DO WHILE(conv > 1.D-4)
-        fPsi           = self%fPsi(Xi0, 4)
+        dPsi = self%dPsi(XiO, 4)
-        x0(1)          = dot_product(fPsi, self%z)
+        pDer = self%partialDer(4, dPsi)
-        x0(2)          = dot_product(fPsi, self%r)
+        detJ = self%detJac(pDer)
-        deltaR         = r(1:2) - x0
+        invJ = self%invJac(pDer)
-        dPsi           = self%dPsi(Xi0, 4)
+        fPsi = self%fPsi(XiO, 4)
-        pDer           = self%partialDer(4, dPsi)
+        f(1:2) = (/ DOT_PRODUCT(fPsi,self%z), &
-        detJ           = self%detJac(pDer)
+                    DOT_PRODUCT(fPsi,self%r) /) - r(1:2)
-        pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
+        Xi = XiO - MATMUL(invJ, f)/detJ
-        pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+        conv = MAXVAL(DABS(Xi-XiO),1)
-        Xi(1:2)        = Xi0(1:2) + MATMUL(pDerInv, deltaR)/detJ
+        XiO = Xi
-        conv           = MAXVAL(DABS(Xi(1:2)-Xi0(1:2)),1)
-        Xi0(1:2)       = Xi(1:2)
 
       END DO
 
@@ -707,8 +705,8 @@ MODULE moduleMesh2DCyl
 
       dPsi = 0.D0
 
-      dPsi(1,1:3) = (/ -1.D0, 1.D0, 0.D0 /)
+      dPsi(1,:) = (/ -1.D0, 1.D0, 0.D0 /)
-      dPsi(2,1:3) = (/ -1.D0, 0.D0, 1.D0 /)
+      dPsi(2,:) = (/ -1.D0, 0.D0, 1.D0 /)
 
     END FUNCTION dPsiTria
 
@@ -860,19 +858,19 @@ MODULE moduleMesh2DCyl
       CLASS(meshCell2DCylTria), INTENT(in):: self
       REAL(8), INTENT(in):: r(1:3)
       REAL(8):: Xi(1:3)
-      REAL(8):: detJ, pDerInv(1:2,1:2), deltaR(1:2)
+      REAL(8):: deltaR(1:3)
-      REAL(8):: dPsi(1:3,1:4)
+      REAL(8):: dPsi(1:3, 1:3)
       REAL(8):: pDer(1:3, 1:3)
+      REAL(8):: invJ(1:3,  1:3), detJ
 
       !Direct method to convert coordinates
-      Xi(3)          = 0.D0
+      Xi     = 0.D0
-      deltaR         = (/ r(1) - self%z(1), r(2) - self%r(1) /)
+      deltaR = (/ r(1) - self%z(1), r(2) - self%r(1), 0.D0 /)
-      dPsi           = self%dPsi(Xi, 3)
+      dPsi   = self%dPsi(Xi, 3)
-      pDer           = self%partialDer(3, dPsi)
+      pDer   = self%partialDer(3, dPsi)
-      detJ           = self%detJac(pDer)
+      invJ   = self%invJac(pDer)
-      pDerInv(1,1:2) = (/  pDer(2,2), -pDer(1,2) /)
+      detJ   = self%detJac(pDer)
-      pDerInv(2,1:2) = (/ -pDer(2,1),  pDer(1,1) /)
+      Xi     = MATMUL(invJ,deltaR)/detJ
-      Xi(1:2)        = MATMUL(pDerInv,deltaR)/detJ
 
     END FUNCTION phy2logTria
 
@@ -950,8 +948,8 @@ MODULE moduleMesh2DCyl
 
       invJ = 0.D0
 
-      invJ(1, 1:2) = (/  pDer(2,2), -pDer(2,1) /)
+      invJ(1, 1:2) = (/  pDer(2,2), -pDer(1,2) /)
-      invJ(2, 1:2) = (/ -pDer(1,2),  pDer(1,1) /)
+      invJ(2, 1:2) = (/ -pDer(2,1),  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)
+    SUBROUTINE printOutput0D(self, t)
       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 (timeStep == 0) THEN
+        IF (t == 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)"
@@ -27,17 +27,14 @@ 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(timeStep)*tauMin*ti_ref, output%density,    &
+        WRITE(20, "(7(ES20.6E3))") REAL(t)*tauMin*ti_ref, output%density, output%velocity, output%pressure, output%temperature
-                                                                 output%velocity,   &
-                                                                 output%pressure,   &
-                                                                 output%temperature
         CLOSE(20)
 
       END DO
 
     END SUBROUTINE printOutput0D
 
-    SUBROUTINE printColl0D(self)
+    SUBROUTINE printColl0D(self, t)
       USE moduleMesh
       USE moduleRefParam
       USE moduleCaseParam
@@ -46,11 +43,12 @@ MODULE moduleMeshOutput0D
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(in):: self
+      INTEGER, INTENT(in):: t
       CHARACTER(:), ALLOCATABLE:: fileName
       INTEGER:: k
 
       fileName='OUTPUT_Collisions.dat'
-      IF (timeStep == tInitial) THEN
+      IF (t == 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
@@ -59,12 +57,12 @@ MODULE moduleMeshOutput0D
       END IF
       
       OPEN(20, file = path // folder // '/' // fileName, position = 'append', action = 'write')
-      WRITE(20, "(ES20.6E3, 10I20)") REAL(timeStep)*tauMin*ti_ref, (self%cells(1)%obj%tallyColl(k)%tally, k=1,nCollPairs)
+      WRITE(20, "(ES20.6E3, 10I20)") REAL(t)*tauMin*ti_ref, (self%cells(1)%obj%tallyColl(k)%tally, k=1,nCollPairs)
       CLOSE(20)
 
     END SUBROUTINE printColl0D
 
-    SUBROUTINE printEM0D(self)
+    SUBROUTINE printEM0D(self, t)
       USE moduleMesh
       USE moduleRefParam
       USE moduleCaseParam
@@ -72,6 +70,7 @@ 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)
+    SUBROUTINE printOutputGmsh2(self, t)
       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(timeStep)*tauMin*ti_ref
+      time = DBLE(t)*tauMin*ti_ref
 
       DO i = 1, nSpecies
-        fileName = formatFileName(prefix, species(i)%obj%name, 'msh', timeStep)
+        fileName = formatFileName(prefix, species(i)%obj%name, 'msh', t)
         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)', timeStep, time, 1, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' density (m^-3)', t, 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)', timeStep, time, 3, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' velocity (m s^-1)', t, 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)', timeStep, time, 1, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' Pressure (Pa)', t, 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)', timeStep, time, 1, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' Temperature (K)', t, 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)
+    SUBROUTINE printCollGmsh2(self, t)
       USE moduleMesh
       USE moduleRefParam
       USE moduleCaseParam
@@ -145,6 +145,7 @@ MODULE moduleMeshOutputGmsh2
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(in):: self
+      INTEGER, INTENT(in):: t
       INTEGER:: numEdges
       INTEGER:: k, c
       INTEGER:: n
@@ -166,9 +167,9 @@ MODULE moduleMeshOutputGmsh2
       END SELECT
 
       IF (collOutput) THEN
-        time = DBLE(timeStep)*tauMin*ti_ref
+        time = DBLE(t)*tauMin*ti_ref
 
-        fileName = formatFileName(prefix, 'Collisions', 'msh', timeStep)
+        fileName = formatFileName(prefix, 'Collisions', 'msh', t)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (60, file = path // folder // '/' //  fileName)
 
@@ -178,7 +179,7 @@ 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, timeStep, time, 1, self%numCells)
+            CALL writeGmsh2HeaderElementData(60, title, t, 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
@@ -195,7 +196,7 @@ MODULE moduleMeshOutputGmsh2
     END SUBROUTINE printCollGmsh2
 
     !Prints the electrostatic EM properties into the nodes and volumes
-    SUBROUTINE printEMGmsh2(self)
+    SUBROUTINE printEMGmsh2(self, t)
       USE moduleMesh
       USE moduleRefParam
       USE moduleCaseParam
@@ -204,6 +205,7 @@ MODULE moduleMeshOutputGmsh2
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
+      INTEGER, INTENT(in):: t
       INTEGER:: n, e
       REAL(8):: time
       CHARACTER(:), ALLOCATABLE:: fileName
@@ -212,27 +214,27 @@ MODULE moduleMeshOutputGmsh2
       Xi = (/ 0.D0, 0.D0, 0.D0 /)
 
       IF (emOutput) THEN
-        time = DBLE(timeStep)*tauMin*ti_ref
+        time = DBLE(t)*tauMin*ti_ref
 
-        fileName = formatFileName(prefix, 'EMField', 'msh', timeStep)
+        fileName = formatFileName(prefix, 'EMField', 'msh', t)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (20, file = path // folder // '/' //  fileName)
 
         CALL writeGmsh2HeaderMesh(20)
 
-        CALL writeGmsh2HeaderNodeData(20, 'Potential (V)', timeStep, time, 1, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(20, 'Potential (V)', t, 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)', timeStep, time, 3, self%numCells)
+        CALL writeGmsh2HeaderElementData(20, 'Electric Field (V m^-1)', t, 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)', timeStep, time, 3, self%numNodes)
+        CALL writeGmsh2HeaderNodeData(20, 'Magnetic Field (T)', t, 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 text.o
+all: vtu.o gmsh2.o 0D.o
 
 vtu.o: moduleMeshInoutCommon.o
 	$(MAKE) -C vtu all
@@ -9,8 +9,5 @@ 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, timeStep) RESULT(fileName)
+    PURE FUNCTION formatFileName(prefix, suffix, extension, t) RESULT(fileName)
       USE moduleOutput
       IMPLICIT NONE
 
       CHARACTER(*), INTENT(in):: prefix, suffix, extension
-      INTEGER, INTENT(in), OPTIONAL:: timeStep
+      INTEGER, INTENT(in), OPTIONAL:: t
       CHARACTER (LEN=iterationDigits):: tString
       CHARACTER(:), ALLOCATABLE:: fileName
 
-      IF (PRESENT(timeStep)) THEN
+      IF (PRESENT(t)) THEN
-        WRITE(tString, iterationFormat) timeStep
+        WRITE(tString, iterationFormat) t
         fileName = prefix //  '_' // tString // '_' // suffix // '.' // extension
 
       ELSE

src/modules/mesh/inout/text/makefile

@@ -1,7 +0,0 @@
-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

@@ -1,232 +0,0 @@
-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

@@ -1,265 +0,0 @@
-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
+      INTEGER:: fileID, error, found
       CHARACTER(LEN=256):: line
       INTEGER:: numNodes, numElements, numEdges
       INTEGER, ALLOCATABLE, DIMENSION(:):: entitiesID, offsets, connectivity, types
@@ -548,8 +548,6 @@ 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)") '<UnstructuredGrid>'
+      WRITE(fileID,"(4X, A,ES20.6E3,A)") '<UnstructuredGrid>'
       WRITE(fileID,"(6X, A, I10, A, I10, A)") '<Piece NumberOfPoints="', nNodes, '" NumberOfCells="', nCells, '">'
 
     END SUBROUTINE writeHeader
@@ -215,16 +215,17 @@ MODULE moduleMeshOutputVTU
 
     END SUBROUTINE writeEM
 
-    SUBROUTINE writeCollection(fileID, fileNameStep, fileNameCollection)
+    SUBROUTINE writeCollection(fileID, t, fileNameStep, fileNameCollection)
       USE moduleCaseParam
       USE moduleOutput
       USE moduleRefParam
       IMPLICIT NONE
 
       INTEGER:: fileID
+      INTEGER, INTENT(in):: t
       CHARACTER(*):: fileNameStep, fileNameCollection
 
-      IF (timeStep == tInitial) THEN
+      IF (t == tInitial) THEN
         !Create collection file
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileNameCollection
         OPEN (fileID + 1, file = path // folder  // '/' // fileNameCollection)
@@ -236,11 +237,10 @@ 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)") &
+      WRITE(fileID + 1, "(4X, A, ES20.6E3, A, A, A)") '<DataSet timestep="', DBLE(t)*tauMin*ti_ref,'" file="', fileNameStep,'"/>'
-            '<DataSet timestep="', DBLE(timeStep)*tauMin*ti_ref,'" file="', fileNameStep,'"/>'
 
       !Close collection file
-      IF (timeStep == tFinal) THEN
+      IF (t == 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)
+    SUBROUTINE printOutputVTU(self,t)
       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', timeStep)
+        fileName = formatFileName(prefix, species(i)%obj%name, 'vtu', t)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (fileID, file = path // folder // '/' //  fileName)
 
@@ -337,27 +337,28 @@ MODULE moduleMeshOutputVTU
 
         !Write collection file for time plotting
         fileNameCollection = formatFileName('Collection', species(i)%obj%name, 'pvd')
-        CALL writeCollection(fileID, fileName, filenameCollection)
+        CALL writeCollection(fileID, t, fileName, filenameCollection)
 
       END DO
 
     END SUBROUTINE printOutputVTU
 
-    SUBROUTINE printCollVTU(self)
+    SUBROUTINE printCollVTU(self,t)
       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', timeStep)
+        fileName = formatFileName(prefix, 'Collisions', 'vtu', t)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (fileID, file = path // folder // '/' //  fileName)
 
@@ -373,26 +374,26 @@ MODULE moduleMeshOutputVTU
 
         !Write collection file for time plotting
         fileNameCollection = formatFileName('Collection', 'Collisions', 'pvd')
-        CALL writeCollection(fileID, fileName, filenameCollection)
+        CALL writeCollection(fileID, t, fileName, filenameCollection)
 
       END IF
 
     END SUBROUTINE printCollVTU
 
-    SUBROUTINE printEMVTU(self)
+    SUBROUTINE printEMVTU(self, t)
       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', timeStep)
+        fileName = formatFileName(prefix, 'EMField', 'vtu', t)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (fileID, file = path // folder // '/' //  fileName)
 
@@ -408,7 +409,7 @@ MODULE moduleMeshOutputVTU
 
         !Write collection file for time plotting
         fileNameCollection = formatFileName('Collection', 'EMField', 'pvd')
-        CALL writeCollection(fileID, fileName, filenameCollection)
+        CALL writeCollection(fileID, t, fileName, filenameCollection)
 
       END IF
 

src/modules/mesh/moduleMesh.f90

@@ -59,13 +59,6 @@ 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()
@@ -344,10 +337,10 @@ 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
@@ -379,9 +372,10 @@ MODULE moduleMesh
     END SUBROUTINE connectMesh_interface
 
     !Prints number of collisions in each cell
-    SUBROUTINE printColl_interface(self)
+    SUBROUTINE printColl_interface(self, t)
       IMPORT meshGeneric
       CLASS(meshGeneric), INTENT(in):: self
+      INTEGER, INTENT(in):: t
 
     END SUBROUTINE printColl_interface
 
@@ -409,16 +403,18 @@ MODULE moduleMesh
 
   ABSTRACT INTERFACE
     !Prints Species data
-    SUBROUTINE printOutput_interface(self)
+    SUBROUTINE printOutput_interface(self, t)
       IMPORT meshParticles
       CLASS(meshParticles), INTENT(in):: self
+      INTEGER, INTENT(in):: t
 
     END SUBROUTINE printOutput_interface
 
     !Prints EM info
-    SUBROUTINE printEM_interface(self)
+    SUBROUTINE printEM_interface(self, t)
       IMPORT meshParticles
       CLASS(meshParticles), INTENT(in):: self
+      INTEGER, INTENT(in):: t
 
     END SUBROUTINE printEM_interface
 
@@ -499,29 +495,28 @@ MODULE moduleMesh
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(inout):: self
-      INTEGER:: c
+      INTEGER:: e
+      INTEGER:: nNodes
       INTEGER, ALLOCATABLE:: n(:)
       REAL(8), ALLOCATABLE:: localK(:,:)
       INTEGER:: i, j
 
-      DO c = 1, self%numCells
+      DO e = 1, self%numCells
-        associate(nNodes => self%cells(c)%obj%nNodes)
+        nNodes = self%cells(e)%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(c)%obj%getNodes(nNodes)
+        n      = self%cells(e)%obj%getNodes(nNodes)
-          localK = self%cells(c)%obj%elemK(nNodes)
+        localK = self%cells(e)%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
 
-          DEALLOCATE(n, localK)
+        END DO
 
-        end associate
+        DEALLOCATE(n, localK)
 
       END DO
 
@@ -794,7 +789,7 @@ MODULE moduleMesh
     END FUNCTION findCellBrute
 
     !Computes collisions in element
-    SUBROUTINE doCollisions(self)
+    SUBROUTINE doCollisions(self, t)
       USE moduleCollisions
       USE moduleSpecies
       USE moduleList
@@ -802,10 +797,10 @@ 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
@@ -821,7 +816,7 @@ MODULE moduleMesh
       REAL(8):: rnd_real !Random number for collision
       INTEGER:: rnd_int  !Random number for collision
 
-      IF (MOD(timeStep, everyColl) == 0) THEN
+      IF (MOD(t, 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

@@ -77,20 +77,6 @@ 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
@@ -218,27 +204,19 @@ MODULE moduleMeshBoundary
 
     END SUBROUTINE ionization
 
-    subroutine outflowAdaptive(edge, part)
+    !Symmetry axis. Reflects particles.
-      use moduleRandom
+    !Although this function should never be called, it is set as a reflective boundary
-      implicit none
+    !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(meshEdge), INTENT(inout):: edge
-      class(particle), intent(inout):: part
+      CLASS(particle), INTENT(inout):: part
 
-      select type(bound => edge%boundary%bTypes(part%species%n)%obj)
+      CALL reflection(edge, part)
-      type is(boundaryOutflowAdaptive)
 
-        if (random() < 0.844d0) then
+    END SUBROUTINE symmetryAxis
-          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)
@@ -258,17 +236,14 @@ 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(boundaryOutflowAdaptive)
+      TYPE IS(boundaryAxis)
-        edge%fBoundary(s)%apply => outflowAdaptive
+        edge%fBoundary(s)%apply => symmetryAxis
 
       CLASS DEFAULT
         CALL criticalError("Boundary type not defined in this geometry", 'pointBoundaryFunction')

src/modules/moduleBoundary.f90

@@ -26,12 +26,6 @@ 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)
@@ -53,13 +47,11 @@ MODULE moduleBoundary
 
   END TYPE boundaryIonization
 
-  !Boundary for quasi-neutral outflow adjusting reflection coefficient
+  !Symmetry axis
-  type, public, extends(boundaryGeneric):: boundaryOutflowAdaptive
+  TYPE, PUBLIC, EXTENDS(boundaryGeneric):: boundaryAxis
-    real(8):: outflowCurrent
+    CONTAINS
-    real(8):: reflectionFraction
-    contains
 
-  end type boundaryOutflowAdaptive
+  END TYPE boundaryAxis
 
   !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):: temperature(1:3) !Temperature
+    REAL(8):: T(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, temperature, flow, units, sp, physicalSurface, particlesPerEdge)
+    SUBROUTINE initInject(self, i, v, n, T, 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), temperature(1:3)
+      REAL(8), INTENT(in):: v, n(1:3), T(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%temperature =  temperature / T_ref
+      self%T       =  T / T_ref
       !Gets the edge elements from which particles are injected
       DO e = 1, mesh%numEdges
         phSurface(e) = mesh%edges(e)%obj%physicalSurface
@@ -159,26 +159,11 @@ MODULE moduleInject
 
       CASE ("A")
         !Current in Ampers
-        SELECT TYPE(sp => self%species)
+        fluxPerStep = flow/qe
-        CLASS IS(speciesCharged)
-          fluxPerStep = flow/(qe*abs(sp%q))
-
-        CLASS DEFAULT
-          call criticalError('Attempted to assign a flux in "A" to a species without charge.', 'initInject')
-
-        END SELECT
 
       CASE ("Am2")
         !Input current in Ampers per square meter
-        SELECT TYPE(sp => self%species)
+        fluxPerStep = flow*self%surface*L_ref**2/qe
-        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
@@ -199,22 +184,18 @@ 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) = max(1,FLOOR(fluxPerStep*mesh%edges(self%edges(et))%obj%surface / self%species%weight))
+          self%particlesPerEdge(et) = FLOOR(fluxPerStep*mesh%edges(self%edges(et))%obj%surface /self%species%weight)
+
         END DO
 
-        self%nParticles = SUM(self%particlesPerEdge)
-
-        !Rescale weight to match flux
-        self%weightPerEdge = fluxPerStep * self%surface / (real(self%nParticles))
-
       END IF
 
+      self%nParticles = SUM(self%particlesPerEdge)
+
       !Scale particles for different species steps
       IF (self%nParticles == 0) CALL criticalError("The number of particles for inject is 0.", 'initInject')
 
@@ -251,23 +232,23 @@ MODULE moduleInject
 
     END SUBROUTINE doInjects
 
-    SUBROUTINE initVelDistMaxwellian(velDist, temperature, m)
+    SUBROUTINE initVelDistMaxwellian(velDist, T, m)
       IMPLICIT NONE
 
       CLASS(velDistGeneric), ALLOCATABLE, INTENT(out):: velDist
-      REAL(8), INTENT(in):: temperature, m
+      REAL(8), INTENT(in):: T, m
 
-      velDist = velDistMaxwellian(vTh = DSQRT(2.d0*temperature/m))
+      velDist = velDistMaxwellian(vTh = DSQRT(T/m))
 
     END SUBROUTINE initVelDistMaxwellian
 
-    SUBROUTINE initVelDistHalfMaxwellian(velDist, temperature, m)
+    SUBROUTINE initVelDistHalfMaxwellian(velDist, T, m)
       IMPLICIT NONE
 
       CLASS(velDistGeneric), ALLOCATABLE, INTENT(out):: velDist
-      REAL(8), INTENT(in):: temperature, m
+      REAL(8), INTENT(in):: T, m
 
-      velDist = velDistHalfMaxwellian(vTh = DSQRT(2.d0*temperature/m))
+      velDist = velDistHalfMaxwellian(vTh = DSQRT(T/m))
 
     END SUBROUTINE initVelDistHalfMaxwellian
 
@@ -289,7 +270,7 @@ MODULE moduleInject
       REAL(8):: v
       v = 0.D0
 
-      v = self%vTh*randomMaxwellian()/sqrt(2.d0)
+      v = self%vTh*randomMaxwellian()
 
     END FUNCTION randomVelMaxwellian
 
@@ -302,7 +283,10 @@ MODULE moduleInject
       REAL(8):: v
       v = 0.D0
 
-      v = self%vTh*randomHalfMaxwellian()/sqrt(2.d0)
+      DO WHILE (v <= 0.D0)
+        v = self%vTh*randomMaxwellian()
+
+      END DO
 
     END FUNCTION randomVelHalfMaxwellian
 
@@ -377,22 +361,19 @@ MODULE moduleInject
           !Assign particle type
           partInj(n)%species => self%species
 
-          if (all(self%n == 0.D0)) then
+          direction = self%n
-            direction =  randomEdge%normal
-
-          else
-            direction = self%n
-
-          end if
 
           partInj(n)%v = 0.D0
 
-          do while(dot_product(partInj(n)%v, direction) <= 0.d0)
+          partInj(n)%v = self%vMod*direction +  (/ self%v(1)%obj%randomVel(), &
-            partInj(n)%v = self%vMod*direction +  (/ self%v(1)%obj%randomVel(), &
+                                                   self%v(2)%obj%randomVel(), &
-                                                     self%v(2)%obj%randomVel(), &
+                                                   self%v(3)%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, everyTimeStep)
+    SUBROUTINE init(self, id, speciesName, r, v1, v2, v3, points, timeStep)
       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):: everyTimeStep
+      REAL(8), INTENT(in):: timeStep
       INTEGER:: sp, i
       REAL(8):: dv(1:3)
 
@@ -91,11 +91,11 @@ MODULE moduleProbe
                       1:self%nv(3)))
 
       !Number of iterations between output
-      IF (everyTimeStep == 0.D0) THEN
+      IF (timeStep == 0.D0) THEN
         self%every = 1
 
       ELSE
-        self%every = NINT(everyTimeStep/ tauMin / ti_ref)
+        self%every = NINT(timeStep/ tauMin / ti_ref)
 
       END IF
       
@@ -189,13 +189,13 @@ MODULE moduleProbe
           
     END SUBROUTINE calculate
 
-    SUBROUTINE output(self)
+    SUBROUTINE output(self, t)
       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) timeStep
+      WRITE(tstring, iterationFormat) t
       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(timeStep)*tauMin*ti_ref, " s"
+      WRITE(10, "(A6, ES15.6E3, A2)")    "# t = ", REAL(t)*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()
+    SUBROUTINE outputProbes(t)
-      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()
+          CALL probe(i)%output(t)
 
         END IF
 
@@ -268,15 +268,15 @@ MODULE moduleProbe
 
     END SUBROUTINE outputProbes
 
-    SUBROUTINE resetProbes()
+    SUBROUTINE resetProbes(t)
-      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
+      INTEGER, INTENT(in):: t
       INTEGER:: i
 
       DO i = 1, nProbes
         probe(i)%f = 0.D0
-        probe(i)%update = timeStep == tFinal .OR. timeStep == tInitial .OR. MOD(timeStep, probe(i)%every) == 0
+        probe(i)%update = t == tFinal .OR. t == tInitial .OR. MOD(t, probe(i)%every) == 0
 
       END DO
 

src/modules/output/moduleOutput.f90

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

src/modules/solver/electromagnetic/moduleEM.f90

@@ -1,202 +1,56 @@
 !Module to solve the electromagnetic field
 MODULE moduleEM
-  USE moduleMesh
-  USE moduleTable
   IMPLICIT NONE
 
-  ! Generic type for electromagnetic boundary conditions
+  TYPE:: boundaryEM
-  TYPE, PUBLIC, ABSTRACT:: boundaryEMGeneric
+    CHARACTER(:), ALLOCATABLE:: typeEM
-    INTEGER:: nNodes
+    INTEGER:: physicalSurface
-    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
-      ! boundaryEMGeneric DEFERRED PROCEDURES
+      PROCEDURE, PASS:: apply
-      PROCEDURE, PASS:: apply => applyDirichlet
 
-  END TYPE boundaryEMDirichlet
+  END TYPE boundaryEM
-
-  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(boundaryEMCont), ALLOCATABLE:: boundaryEM(:)
+  TYPE(boundaryEM), ALLOCATABLE:: boundEM(:)
 
   !Information of charge and reference parameters for rho vector
   REAL(8), ALLOCATABLE:: qSpecies(:)
 
   CONTAINS
-    SUBROUTINE findNodes(self, physicalSurface)
+    !Apply boundary conditions to the K matrix for Poisson's equation
+    SUBROUTINE apply(self, edge)
       USE moduleMesh
       IMPLICIT NONE
 
-      CLASS(boundaryEMGeneric), INTENT(inout):: self
+      CLASS(boundaryEM), INTENT(in):: self
-      INTEGER, INTENT(in):: physicalSurface
+      CLASS(meshEdge):: edge
-      CLASS(meshEdge), POINTER:: edge
+      INTEGER:: nNodes
-      INTEGER, ALLOCATABLE:: nodes(:), nodesEdge(:)
+      INTEGER, ALLOCATABLE:: nodes(:)
-      INTEGER:: nNodes, nodesNew
+      INTEGER:: n
-      INTEGER:: e, n
 
-      !Temporal array to hold nodes
+      nNodes = 1
-      ALLOCATE(nodes(0))
+      nNodes = edge%nNodes
+      nodes  = edge%getNodes(nNodes)
 
-      ! Loop thorugh the edges and identify those that are part of the boundary
-      DO e = 1, mesh%numEdges
-        edge => mesh%edges(e)%obj
-        IF (edge%physicalSurface == physicalSurface) THEN
-          ! Edge is of the right boundary index
-          ! Get nodes in the edge
-          nNodes = edge%nNodes
-          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
-
-            ELSE
-              ! If not, add element to array of nodes
-              nodes = [nodes, nodesEdge(n)]
-
-            END IF
-
-          END DO
-
-        END IF
-
-      END DO
-
-      ! Point boundary to nodes
-      nNodes = SIZE(nodes)
-      ALLOCATE(self%nodes(nNodes))
-      self%nNodes = nNodes
       DO n = 1, nNodes
-        self%nodes(n)%obj => mesh%nodes(nodes(n))%obj
+        SELECT CASE(self%typeEM)
+        CASE ("dirichlet")
+          mesh%K(nodes(n), :)        = 0.D0
+          mesh%K(nodes(n), nodes(n)) = 1.D0
+        
+          mesh%nodes(nodes(n))%obj%emData%type = self%typeEM
+          mesh%nodes(nodes(n))%obj%emData%phi  = self%potential
+
+        END SELECT
 
       END DO
 
-    END SUBROUTINE findNodes
+    END SUBROUTINE
-
-    ! 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, n_e)
+    SUBROUTINE assembleSourceVector(vectorF)
       USE moduleMesh
       USE moduleRefParam
       IMPLICIT NONE
@@ -205,9 +59,8 @@ 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, b
+      INTEGER:: e, i, ni
       CLASS(meshNode), POINTER:: node
 
       !$OMP SINGLE
@@ -225,10 +78,6 @@ 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
 
@@ -249,12 +98,18 @@ MODULE moduleEM
       !$OMP END DO
 
       !Apply boundary conditions
-      !$OMP SINGLE
+      !$OMP DO
-      do b = 1, nBoundaryEM
+      DO i = 1, mesh%numNodes
-        call boundaryEM(b)%obj%apply(vectorF)
+        node => mesh%nodes(i)%obj
 
-      end do
+        SELECT CASE(node%emData%type)
-      !$OMP END SINGLE
+        CASE ("dirichlet")
+          vectorF(i) = node%emData%phi
+
+        END SELECT
+
+      END DO
+      !$OMP END DO
 
     END SUBROUTINE assembleSourceVector
 
@@ -302,86 +157,4 @@ 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

@@ -138,9 +138,6 @@ MODULE moduleSolver
       CASE('Electrostatic','ConstantB')
         self%solveEM => solveElecField
 
-      CASE('ElectrostaticBoltzmann')
-        self%solveEM => solveElecFieldBoltzmann
-
       END SELECT
 
     END SUBROUTINE initEM
@@ -494,46 +491,47 @@ MODULE moduleSolver
     END SUBROUTINE updateParticleCell
 
     !Update the information about if a species needs to be moved this iteration
-    SUBROUTINE updatePushSpecies(self)
+    SUBROUTINE updatePushSpecies(self, t)
       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(timeStep, self%pusher(s)%every) == 0
+        self%pusher(s)%pushSpecies = MOD(t, self%pusher(s)%every) == 0
 
       END DO
 
     END SUBROUTINE updatePushSpecies
 
     !Output the different data and information
-    SUBROUTINE doOutput()
+    SUBROUTINE doOutput(t)
       USE moduleMesh
       USE moduleOutput
       USE moduleSpecies
       USE moduleCompTime
       USE moduleProbe
-      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
-      CALL outputProbes()
+      INTEGER, INTENT(in):: t
+
+      CALL outputProbes(t)
 
       counterOutput = counterOutput + 1
       IF (counterOutput >= triggerOutput .OR. &
-          timeStep == tFinal .OR. timeStep == tInitial) THEN
+          t == tFinal .OR. t == tInitial) THEN
 
         !Resets output counter
         counterOutput=0
 
-        CALL mesh%printOutput()
+        CALL mesh%printOutput(t)
-        IF (ASSOCIATED(meshForMCC)) CALL meshForMCC%printColl()
+        IF (ASSOCIATED(meshForMCC)) CALL meshForMCC%printColl(t)
-        CALL mesh%printEM()
+        CALL mesh%printEM(t)
-        WRITE(*, "(5X,A21,I10,A1,I10)") "t/tFinal: ", timeStep, "/", tFinal
+        WRITE(*, "(5X,A21,I10,A1,I10)") "t/tFinal: ", t, "/", tFinal
         WRITE(*, "(5X,A21,I10)")        "Particles: ", nPartOld
-        IF (timeStep == 0) THEN
+        IF (t == 0) THEN
           WRITE(*, "(5X,A21,F8.1,A2)")   "     init time: ",    1.D3*tStep, "ms"
 
         ELSE
@@ -551,32 +549,34 @@ MODULE moduleSolver
 
       counterCPUTime = counterCPUTime + 1
       IF (counterCPUTime >= triggerCPUTime .OR. &
-          timeStep == tFinal .OR. timeStep == tInitial) THEN
+          t == tFinal .OR. t == tInitial) THEN
 
         !Reset CPU Time counter
         counterCPUTime = 0
 
-        CALL printTime(timeStep == 0)
+        CALL printTime(t, t == 0)
 
       END IF
 
       !Output average values
-      IF (useAverage .AND. timeStep == tFinal) THEN
+      IF (useAverage .AND. t == tFinal) THEN
         CALL mesh%printAverage()
 
       END IF
 
     END SUBROUTINE doOutput
 
-    SUBROUTINE doAverage()
+    SUBROUTINE doAverage(t)
       USE moduleAverage
       USE moduleMesh
       IMPLICIT NONE
 
+      INTEGER, INTENT(in):: t
       INTEGER:: tAverage, n
 
+
       IF (useAverage) THEN
-        tAverage = timeStep - tAverageStart
+        tAverage = t - tAverageStart
 
         IF (tAverage == 1) THEN
           !First iteration in which average scheme is used