Now the Collections in vut format can be read during execution!

doc/user-manual/fpakc_UserManual.tex

@@ -398,6 +398,9 @@ make
                                   Trigger between writings is the same as in \textbf{triggerOutput}.
           \item \textbf{EMField}: Logical.
                                   Determines if the electromagnetic field is printed.
+          \item \textbf{bounraiesParticle}: Logical.
+                                            Determines if the properties of the boundaries are written.
+                                            \textit{Warning}: Not all particle models produce this output, only those whose properties change during the simulation.
           \item \textbf{probes}: Array of objects.
                                  Defines the probes employed for obtaining the distribution function at specific positions.
                                  See Sec.~\ref{sec:probing} for more information.

runs/0D_Argon/input.json

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

runs/0D_Argon/output/reference.csv

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

src/makefile

@@ -6,7 +6,6 @@ OBJECTS = $(OBJDIR)/moduleMesh.o $(OBJDIR)/moduleMeshCommon.o $(OBJDIR)/moduleCo
 			  	$(OBJDIR)/moduleCollisions.o $(OBJDIR)/moduleTable.o $(OBJDIR)/moduleParallel.o \
 			  	$(OBJDIR)/moduleEM.o $(OBJDIR)/moduleRandom.o $(OBJDIR)/moduleMath.o \
 					$(OBJDIR)/moduleProbe.o $(OBJDIR)/moduleAverage.o $(OBJDIR)/moduleCoulomb.o \
-					$(OBJDIR)/moduleMeshInoutCommon.o \
 			  	$(OBJDIR)/moduleMeshInputVTU.o $(OBJDIR)/moduleMeshOutputVTU.o \
 			  	$(OBJDIR)/moduleMeshInputGmsh2.o $(OBJDIR)/moduleMeshOutputGmsh2.o \
 			  	$(OBJDIR)/moduleMeshInput0D.o $(OBJDIR)/moduleMeshOutput0D.o \

src/modules/init/moduleInput.f90

@@ -492,6 +492,7 @@ MODULE moduleInput
       CALL config%get(object // '.cpuTime', timeOutput, found)
       CALL config%get(object // '.numColl', collOutput, found)
       CALL config%get(object // '.EMField', emOutput, found)
+      call config%get(object // '.boundariesParticle', boundaryParticleOutput, found)
 
       CALL config%get(object // '.triggerCPUTime', triggerCPUTime, found)
       IF (.NOT. found) THEN
@@ -1569,35 +1570,29 @@ MODULE moduleInput
     END SUBROUTINE readParallel
 
     SUBROUTINE initOutput(inputFile)
-      USE moduleRefParam
       USE moduleMesh,   ONLY: mesh, doubleMesh, pathMeshParticle, pathMeshColl
-      USE moduleOutput, ONLY: path, folder
+      USE moduleOutput, ONLY: createOutputFolder, writeReference, copyFileToOutput, writeCommit
       IMPLICIT NONE
 
       CHARACTER(:), ALLOCATABLE, INTENT(in):: inputFile
-      INTEGER:: fileReference = 30
       !If everything is correct, creates the output folder
-      CALL EXECUTE_COMMAND_LINE('mkdir ' // path // folder )
+      call createOutputFolder()
       !Copies input file to output folder
-      CALL EXECUTE_COMMAND_LINE('cp ' // inputFile // ' ' // path // folder)
+      call copyFileToOutput(inputFile)
       !Copies particle mesh
       IF (mesh%dimen > 0) THEN
-        CALL EXECUTE_COMMAND_LINE('cp ' // pathMeshParticle // ' ' // path // folder)
+        call copyFileToOutput(pathMeshParticle)
         IF (doubleMesh) THEN
-          CALL EXECUTE_COMMAND_LINE('cp ' // pathMeshColl // ' ' // path // folder)
+          call copyFileToOutput(pathMeshColl)
 
         END IF
 
       END IF
 
       ! Write commit of fpakc
-      CALL SYSTEM('git rev-parse HEAD > ' // path // folder // '/' // 'fpakc_commit.txt')
+      call writeCommit()
 
-      ! Write file with reference values
-      OPEN (fileReference, file=path // folder // '/' // 'reference.txt')
-      WRITE(fileReference, "(7(1X,A20))")      'L_ref', 'v_ref', 'ti_ref', 'Vol_ref', 'EF_ref', 'Volt_ref', 'B_ref'
-      WRITE(fileReference, "(7(1X,ES20.6E3))")  L_ref,   v_ref,   ti_ref,   Vol_ref,   EF_ref,   Volt_ref,   B_ref
-      CLOSE(fileReference)
+      call writeReference()
 
     END SUBROUTINE initOutput
 

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

@@ -15,19 +15,21 @@ MODULE moduleMeshOutput0D
       CHARACTER(:), ALLOCATABLE:: fileName
 
       DO i = 1, nSpecies
-        fileName='OUTPUT_' // species(i)%obj%name // '.dat'
+        fileName = formatFileName('Output', species(i)%obj%name, 'csv')
         IF (timeStep == 0) THEN
-          OPEN(20, file = path // folder // '/' // fileName, action = 'write')
-          WRITE(20, "(A1, 14X, A5, A20, 40X, A20, 2(A20))") "#","t (s)","density (m^-3)", "velocity (m/s)", &
-                                                                        "pressure (Pa)", "temperature (K)"
-          WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
+          OPEN(20, file = generateFilePath(fileName), action = 'write')
+          WRITE(20, "(*("//fmtColStr//"))")'"t (s)"','"density (m^-3)"',                                               &
+                                                     '"velocity (m/s):0"', '"velocity (m/s):1"', '"velocity (m/s):2"', &
+                                                     '"pressure (Pa)"',                                                &
+                                                     '"temperature (K)"'
+          call informFileCreation(fileName)
           CLOSE(20)
 
         END IF
         
-        OPEN(20, file = path // folder // '/' // fileName, position = 'append', action = 'write')
+        OPEN(20, file = generateFilePath(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, "(*("//fmtColReal//"))") REAL(timeStep)*tauMin*ti_ref, output%density,    &
                                                                          output%velocity,   &
                                                                          output%pressure,   &
                                                                          output%temperature
@@ -49,17 +51,22 @@ MODULE moduleMeshOutput0D
       CHARACTER(:), ALLOCATABLE:: fileName
       INTEGER:: k
 
-      fileName='OUTPUT_Collisions.dat'
+      fileName = formatFileName('Output', 'Collisions', 'csv')
       IF (timeStep == tInitial) THEN
-        OPEN(20, file = path // folder // '/' // fileName, action = 'write')
-        WRITE(20, "(A1, 14X, A5, A20)") "#","t (s)","collisions"
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
+        OPEN(20, file = generateFilePath(fileName), action = 'write')
+        call informFileCreation(fileName)
+        WRITE(20, "(A,A)", advance='no') "t (s)", ','
+        do k = 1, nCollPairs-1
+          write(20, '(A,A,I3,A,A)', advance='no') '"',"pair", k, '"', ','
+
+        end do
+        write(20, "(A,A,I3,A)", advance='no') '"',"pair",k, '"'
         CLOSE(20)
 
       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)
+      OPEN(20, file = generateFilePath(fileName), position = 'append', action = 'write')
+      WRITE(20, "("//fmtColReal//", *("//fmtColInt//"))") REAL(timeStep)*tauMin*ti_ref, (self%cells(1)%obj%tallyColl(k)%tally, k=1,nCollPairs)
       CLOSE(20)
 
     END SUBROUTINE printColl0D

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

@@ -16,6 +16,7 @@ MODULE moduleMeshOutputGmsh2
     !Node data subroutines
     !Header
     SUBROUTINE writeGmsh2HeaderNodeData(fileID, title, iteration, time, dimensions, nNodes)
+      use moduleOutput
       IMPLICIT NONE
 
       INTEGER, INTENT(in):: fileID
@@ -25,14 +26,14 @@ MODULE moduleMeshOutputGmsh2
 
 
       WRITE(fileID, "(A)") '$NodeData'
-      WRITE(fileID, "(I10)") 1
+      WRITE(fileID, "("//fmtInt//")") 1
       WRITE(fileID, "(A1, A, A1)") '"' , title , '"'
-      WRITE(fileID, "(I10)") 1
-      WRITE(fileID, "(ES20.6E3)") time
-      WRITE(fileID, "(I10)") 3
-      WRITE(fileID, "(I10)") iteration
-      WRITE(fileID, "(I10)") dimensions
-      WRITE(fileID, "(I10)") nNodes
+      WRITE(fileID, "("//fmtInt//")") 1
+      WRITE(fileID, "("//fmtReal//")") time
+      WRITE(fileID, "("//fmtInt//")") 3
+      WRITE(fileID, "("//fmtInt//")") iteration
+      WRITE(fileID, "("//fmtInt//")") dimensions
+      WRITE(fileID, "("//fmtInt//")") nNodes
 
     END SUBROUTINE writeGmsh2HeaderNodeData
 
@@ -49,6 +50,7 @@ MODULE moduleMeshOutputGmsh2
     !Element data subroutines
     !Header
     SUBROUTINE writeGmsh2HeaderElementData(fileID, title, iteration, time, dimensions, nVols)
+      use moduleOutput
       IMPLICIT NONE
 
       INTEGER, INTENT(in):: fileID
@@ -58,14 +60,14 @@ MODULE moduleMeshOutputGmsh2
 
 
       WRITE(fileID, "(A)") '$ElementData'
-      WRITE(fileID, "(I10)") 1
+      WRITE(fileID, "("//fmtInt//")") 1
       WRITE(fileID, "(A1, A, A1)") '"' , title , '"'
-      WRITE(fileID, "(I10)") 1
-      WRITE(fileID, "(ES20.6E3)") time
-      WRITE(fileID, "(I10)") 3
-      WRITE(fileID, "(I10)") iteration
-      WRITE(fileID, "(I10)") dimensions
-      WRITE(fileID, "(I10)") nVols
+      WRITE(fileID, "("//fmtInt//")") 1
+      WRITE(fileID, "("//fmtReal//")") time
+      WRITE(fileID, "("//fmtInt//")") 3
+      WRITE(fileID, "("//fmtInt//")") iteration
+      WRITE(fileID, "("//fmtInt//")") dimensions
+      WRITE(fileID, "("//fmtInt//")") nVols
 
     END SUBROUTINE writeGmsh2HeaderElementData
 
@@ -85,7 +87,6 @@ MODULE moduleMeshOutputGmsh2
       USE moduleRefParam
       USE moduleSpecies
       USE moduleOutput
-      USE moduleMeshInoutCommon
       USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
@@ -99,33 +100,33 @@ MODULE moduleMeshOutputGmsh2
 
       DO i = 1, nSpecies
         fileName = formatFileName(prefix, species(i)%obj%name, 'msh', timeStep)
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
-        OPEN (60, file = path // folder // '/' //  fileName)
+        call informFileCreation(fileName)
+        OPEN (60, file = generateFilePath(fileName))
 
         CALL writeGmsh2HeaderMesh(60)
 
         CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' density (m^-3)', timeStep, time, 1, self%numNodes)
         DO n=1, self%numNodes
           CALL calculateOutput(self%nodes(n)%obj%output(i), output(n), self%nodes(n)%obj%v, species(i)%obj)
-          WRITE(60, "(I6,ES20.6E3)") n, output(n)%density
+          WRITE(60, "(I6,"//fmtReal//")") 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)
         DO n=1, self%numNodes
-          WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%velocity
+          WRITE(60, "(I6,3("//fmtReal//"))") n, output(n)%velocity
         END DO
         CALL writeGmsh2FooterNodeData(60)
 
         CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' Pressure (Pa)', timeStep, time, 1, self%numNodes)
         DO n=1, self%numNodes
-          WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%pressure
+          WRITE(60, "(I6,3("//fmtReal//"))") n, output(n)%pressure
         END DO
         CALL writeGmsh2FooterNodeData(60)
 
         CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' Temperature (K)', timeStep, time, 1, self%numNodes)
         DO n=1, self%numNodes
-          WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%temperature
+          WRITE(60, "(I6,3("//fmtReal//"))") n, output(n)%temperature
         END DO
         CALL writeGmsh2FooterNodeData(60)
         CLOSE (60)
@@ -141,7 +142,6 @@ MODULE moduleMeshOutputGmsh2
       USE moduleCaseParam
       USE moduleCollisions
       USE moduleOutput
-      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(in):: self
@@ -169,8 +169,8 @@ MODULE moduleMeshOutputGmsh2
         time = DBLE(timeStep)*tauMin*ti_ref
 
         fileName = formatFileName(prefix, 'Collisions', 'msh', timeStep)
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
-        OPEN (60, file = path // folder // '/' //  fileName)
+        call informFileCreation(fileName)
+        OPEN (60, file = generateFilePath(fileName))
 
         CALL writeGmsh2HeaderMesh(60)
 
@@ -180,7 +180,7 @@ MODULE moduleMeshOutputGmsh2
             title = '"Pair ' // interactionMatrix(k)%sp_i%name // '-' // interactionMatrix(k)%sp_j%name // ' collision ' // cString
             CALL writeGmsh2HeaderElementData(60, title, timeStep, time, 1, self%numCells)
             DO n=1, self%numCells
-              WRITE(60, "(I6,I10)") n + numEdges, self%cells(n)%obj%tallyColl(k)%tally(c)
+              WRITE(60, "(I6,"//fmtInt//")") n + numEdges, self%cells(n)%obj%tallyColl(k)%tally(c)
             END DO
             CALL writeGmsh2FooterElementData(60)
 
@@ -200,7 +200,6 @@ MODULE moduleMeshOutputGmsh2
       USE moduleRefParam
       USE moduleCaseParam
       USE moduleOutput
-      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
@@ -215,8 +214,8 @@ MODULE moduleMeshOutputGmsh2
         time = DBLE(timeStep)*tauMin*ti_ref
 
         fileName = formatFileName(prefix, 'EMField', 'msh', timeStep)
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
-        OPEN (20, file = path // folder // '/' //  fileName)
+        call informFileCreation(fileName)
+        OPEN (20, file = generateFilePath(fileName))
 
         CALL writeGmsh2HeaderMesh(20)
 
@@ -251,7 +250,6 @@ MODULE moduleMeshOutputGmsh2
       USE moduleSpecies
       USE moduleOutput
       USE moduleAverage
-      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
@@ -262,12 +260,12 @@ MODULE moduleMeshOutputGmsh2
 
       DO i = 1, nSpecies
         fileName = formatFileName('Average_mean', species(i)%obj%name, 'msh')
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
-        OPEN (fileMean, file = path // folder // '/' //  fileName)
+        call informFileCreation(fileName)
+        OPEN (fileMean, file = generateFilePath(fileName))
 
         fileName = formatFileName('Average_deviation', species(i)%obj%name, 'msh')
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
-        OPEN (filedeviation, file = path // folder // '/' //  fileName)
+        call informFileCreation(fileName)
+        OPEN (filedeviation, file = generateFilePath(fileName))
 
         CALL writeGmsh2HeaderMesh(fileMean)
         CALL writeGmsh2HeaderMesh(fileDeviation)
@@ -276,9 +274,9 @@ MODULE moduleMeshOutputGmsh2
         CALL writeGmsh2HeaderNodeData(fileDeviation, species(i)%obj%name // ' density, sd (m^-3)', 0, 0.D0, 1, self%numNodes)
         DO n=1, self%numNodes
           CALL calculateOutput(averageScheme(n)%mean%output(i),      outputMean(n),      self%nodes(n)%obj%v, species(i)%obj)
-          WRITE(fileMean,      "(I6,ES20.6E3)") n, outputMean(n)%density
+          WRITE(fileMean,      "(I6,"//fmtReal//")") n, outputMean(n)%density
           CALL calculateOutput(averageScheme(n)%deviation%output(i), outputDeviation(n), self%nodes(n)%obj%v, species(i)%obj)
-          WRITE(fileDeviation, "(I6,ES20.6E3)") n, outputDeviation(n)%density
+          WRITE(fileDeviation, "(I6,"//fmtReal//")") n, outputDeviation(n)%density
         END DO
         CALL writeGmsh2FooterNodeData(fileMean)
         CALL writeGmsh2FooterNodeData(fileDeviation)
@@ -286,8 +284,8 @@ MODULE moduleMeshOutputGmsh2
         CALL writeGmsh2HeaderNodeData(fileMean,      species(i)%obj%name // ' velocity, mean (m s^-1)', 0, 0.D0, 3, self%numNodes)
         CALL writeGmsh2HeaderNodeData(fileDeviation, species(i)%obj%name // ' velocity, sd (m s^-1)', 0, 0.D0, 3, self%numNodes)
         DO n=1, self%numNodes
-          WRITE(fileMean,      "(I6,3(ES20.6E3))") n, outputMean(n)%velocity
-          WRITE(fileDeviation, "(I6,3(ES20.6E3))") n, outputDeviation(n)%velocity
+          WRITE(fileMean,      "(I6,3("//fmtReal//"))") n, outputMean(n)%velocity
+          WRITE(fileDeviation, "(I6,3("//fmtReal//"))") n, outputDeviation(n)%velocity
         END DO
         CALL writeGmsh2FooterNodeData(fileMean)
         CALL writeGmsh2FooterNodeData(fileDeviation)
@@ -295,8 +293,8 @@ MODULE moduleMeshOutputGmsh2
         CALL writeGmsh2HeaderNodeData(fileMean,      species(i)%obj%name // ' Pressure, mean (Pa)', 0, 0.D0, 1, self%numNodes)
         CALL writeGmsh2HeaderNodeData(fileDeviation, species(i)%obj%name // ' Pressure, sd (Pa)', 0, 0.D0, 1, self%numNodes)
         DO n=1, self%numNodes
-          WRITE(fileMean,      "(I6,3(ES20.6E3))") n, outputMean(n)%pressure
-          WRITE(fileDeviation, "(I6,3(ES20.6E3))") n, outputDeviation(n)%pressure
+          WRITE(fileMean,      "(I6,3("//fmtReal//"))") n, outputMean(n)%pressure
+          WRITE(fileDeviation, "(I6,3("//fmtReal//"))") n, outputDeviation(n)%pressure
         END DO
         CALL writeGmsh2FooterNodeData(fileMean)
         CALL writeGmsh2FooterNodeData(fileDeviation)
@@ -304,8 +302,8 @@ MODULE moduleMeshOutputGmsh2
         CALL writeGmsh2HeaderNodeData(fileMean,      species(i)%obj%name // ' Temperature, mean (K)', 0, 0.D0, 1, self%numNodes)
         CALL writeGmsh2HeaderNodeData(fileDeviation, species(i)%obj%name // ' Temperature, sd (K)', 0, 0.D0, 1, self%numNodes)
         DO n=1, self%numNodes
-          WRITE(fileMean,      "(I6,3(ES20.6E3))") n, outputMean(n)%temperature
-          WRITE(fileDeviation, "(I6,3(ES20.6E3))") n, outputDeviation(n)%temperature
+          WRITE(fileMean,      "(I6,3("//fmtReal//"))") n, outputMean(n)%temperature
+          WRITE(fileDeviation, "(I6,3("//fmtReal//"))") n, outputDeviation(n)%temperature
         END DO
         CALL writeGmsh2FooterNodeData(fileMean)
         CALL writeGmsh2FooterNodeData(fileDeviation)

src/modules/mesh/inout/makefile

@@ -1,6 +1,6 @@
 all: vtu.o gmsh2.o 0D.o text.o
 
-vtu.o: moduleMeshInoutCommon.o
+vtu.o: 
 	$(MAKE) -C vtu all
 
 gmsh2.o:

src/modules/mesh/inout/moduleMeshInoutCommon.f90

@@ -1,27 +0,0 @@
-MODULE moduleMeshInoutCommon
-
-  CHARACTER(LEN=4):: prefix = 'Step'
-
-  CONTAINS
-    PURE FUNCTION formatFileName(prefix, suffix, extension, timeStep) RESULT(fileName)
-      USE moduleOutput
-      IMPLICIT NONE
-
-      CHARACTER(*), INTENT(in):: prefix, suffix, extension
-      INTEGER, INTENT(in), OPTIONAL:: timeStep
-      CHARACTER (LEN=iterationDigits):: tString
-      CHARACTER(:), ALLOCATABLE:: fileName
-
-      IF (PRESENT(timeStep)) THEN
-        WRITE(tString, iterationFormat) timeStep
-        fileName = prefix //  '_' // tString // '_' // suffix // '.' // extension
-
-      ELSE
-        fileName = prefix //  '_' // suffix // '.' // extension
-
-      END IF
-
-    END FUNCTION formatFileName
-
-
-END MODULE moduleMeshInoutCommon

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

@@ -121,7 +121,6 @@ module moduleMeshOutputText
     subroutine printOutputText(self)
       use moduleMesh
       use moduleSpecies
-      use moduleMeshInoutCommon
       use moduleCaseParam, ONLY: timeStep
       implicit none
       
@@ -134,8 +133,8 @@ module moduleMeshOutputText
 
       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)
+        call informFileCreation(fileName)
+        open (fileID, file = generateFilePath(fileName))
 
         write(fileID, '(5(A,","),A)') '"Position (m)"', &
                                       '"Density (m^-3)"', &
@@ -153,7 +152,6 @@ module moduleMeshOutputText
     subroutine printCollText(self)
       use moduleMesh
       use moduleOutput
-      use moduleMeshInoutCommon
       use moduleCaseParam, only: timeStep
       implicit none
       
@@ -167,8 +165,8 @@ module moduleMeshOutputText
 
       if (collOutput) then
         fileName = formatFileName(prefix, 'Collisions', 'csv', timeStep)
-        write(*, "(6X,A15,A)") "Creating file: ", fileName
-        open (fileID, file = path // folder // '/' //  fileName)
+        call informFileCreation(fileName)
+        open (fileID, file = generateFilePath(fileName))
 
         write(fileID, '(A)', advance='no') "Cell"
         do k = 1, nCollPairs
@@ -191,7 +189,6 @@ module moduleMeshOutputText
 
     subroutine printEMText(self)
       use moduleMesh
-      use moduleMeshInoutCommon
       use moduleCaseParam, only: timeStep
       implicit none
       
@@ -203,8 +200,8 @@ module moduleMeshOutputText
 
       if (emOutput) then
         fileName = formatFileName(prefix, 'EMField', 'csv', timeStep)
-        write(*, "(6X,A15,A)") "Creating file: ", fileName
-        open (fileID, file = path // folder // '/' //  fileName)
+        call informFileCreation(fileName)
+        open (fileID, file = generateFilePath(fileName))
 
         write(fileID, '(8(A,","),A)') '"Position (m)"', &
                                       '"Potential (V)"', &
@@ -222,7 +219,6 @@ module moduleMeshOutputText
     subroutine printAverageText(self)
       use moduleMesh
       use moduleSpecies
-      use moduleMeshInoutCommon
       implicit none
       
       class(meshParticles), intent(in):: self
@@ -235,8 +231,8 @@ module moduleMeshOutputText
 
       do s = 1, nSpecies
         fileNameMean = formatFileName('Average_mean', species(s)%obj%name, 'csv')
-        write(*, "(6X,A15,A)") "Creating file: ", fileNameMean
-        open (fileIDMean, file = path // folder // '/' //  fileNameMean)
+        call informFileCreation(fileNameMean)
+        open (fileIDMean, file = generateFilePath(fileNameMean))
 
         write(fileIDMean, '(5(A,","),A)') '"Position (m)"', &
                                           '"Density, mean (m^-3)"', &
@@ -244,8 +240,8 @@ module moduleMeshOutputText
                                           '"Temperature, mean (K)"'
 
         fileNameDeviation = formatFileName('Average_deviation', species(s)%obj%name, 'csv')
-        write(*, "(6X,A15,A)") "Creating file: ", fileNameDeviation
-        open (fileIDDeviation, file = path // folder // '/' //  fileNameDeviation)
+        call informFileCreation(fileNameDeviation)
+        open (fileIDDeviation, file = generateFilePath(fileNameDeviation))
 
         write(fileIDDeviation, '(5(A,","),A)') '"Position (m)"', &
                                                '"Density, deviation (m^-3)"', &

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

@@ -12,7 +12,7 @@ MODULE moduleMeshOutputVTU
       WRITE(fileID,"(A)") '<?xml version="1.0"?>'
       WRITE(fileID,"(2X, A)") '<VTKFile type="UnstructuredGrid">'
       WRITE(fileID,"(4X, A)") '<UnstructuredGrid>'
-      WRITE(fileID,"(6X, A, I10, A, I10, A)") '<Piece NumberOfPoints="', nNodes, '" NumberOfCells="', nCells, '">'
+      WRITE(fileID,"(6X, A, "//fmtInt//", A, "//fmtInt//", A)") '<Piece NumberOfPoints="', nNodes, '" NumberOfCells="', nCells, '">'
 
     END SUBROUTINE writeHeader
 
@@ -87,14 +87,14 @@ MODULE moduleMeshOutputVTU
       !Write nodes coordinates
       WRITE(fileID, "(8X, A)") '<Points>'
       WRITE(fileID, "(10X,A)") '<DataArray type="Float32" NumberOfComponents="3" format="ascii">'
-      WRITE(fileID, "(6(ES20.6E3))") (self%nodes(e)%obj%getCoordinates()*L_ref, e = 1, self%numNodes)
+      WRITE(fileID, "(6("//fmtReal//"))") (self%nodes(e)%obj%getCoordinates()*L_ref, e = 1, self%numNodes)
       WRITE(fileID, "(10X, A)") '</DataArray>'
       WRITE(fileID, "(8X, A)") '</Points>'
 
       WRITE(fileID, "(8X, A)") '<Cells>'
       !Write nodes connectivity of each cell
       WRITE(fileID, "(10X,A)") '<DataArray type="Int32" Name="connectivity"  format="ascii">'
-      WRITE(fileID, "(6(I10))") (self%cells(e)%obj%getNodes(self%cells(e)%obj%nNodes) - 1, e = 1, self%numCells) !Array starts on 0
+      WRITE(fileID, "(6("//fmtInt//"))") (self%cells(e)%obj%getNodes(self%cells(e)%obj%nNodes) - 1, e = 1, self%numCells) !Array starts on 0
       WRITE(fileID, "(10X, A)") '</DataArray>'
       !Write offset of each cell
       offset(1) = self%cells(1)%obj%nNodes
@@ -103,7 +103,7 @@ MODULE moduleMeshOutputVTU
         offset(e) = offset(e - 1) + self%cells(e)%obj%nNodes
 
       END DO
-      WRITE(fileID, "(6(I10))") offset
+      WRITE(fileID, "(6("//fmtInt//"))") offset
       WRITE(fileID, "(10X, A)") '</DataArray>'
       !Write type of each cell
       WRITE(fileID, "(10X,A)") '<DataArray type="Int32" Name="types"  format="ascii">'
@@ -111,7 +111,7 @@ MODULE moduleMeshOutputVTU
         types(e) = getCellType(self%cells(e)%obj)
 
       END DO
-      WRITE(fileID, "(6(I10))") types
+      WRITE(fileID, "(6("//fmtInt//"))") types
       WRITE(fileID, "(10X, A)") '</DataArray>'
       WRITE(fileID, "(8X, A)") '</Cells>'
 
@@ -137,19 +137,19 @@ MODULE moduleMeshOutputVTU
       WRITE(fileID,"(8X,A)") '<PointData>'
       !Write density
       WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Density (m^-3)" NumberOfComponents="1">'
-      WRITE(fileID,"(6(ES20.6E3))") (output(n)%density, n  = 1, self%numNodes)
+      WRITE(fileID,"(6("//fmtReal//"))") (output(n)%density, n  = 1, self%numNodes)
       WRITE(fileID,"(10X,A)") '</DataArray>'
       !Write velocity
       WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Velocity (m s^-1)" NumberOfComponents="3">'
-      WRITE(fileID,"(6(ES20.6E3))") (output(n)%velocity, n  = 1, self%numNodes)
+      WRITE(fileID,"(6("//fmtReal//"))") (output(n)%velocity, n  = 1, self%numNodes)
       WRITE(fileID,"(10X,A)") '</DataArray>'
       !Write pressure
       WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Pressure (Pa)" NumberOfComponents="1">'
-      WRITE(fileID,"(6(ES20.6E3))") (output(n)%pressure, n  = 1, self%numNodes)
+      WRITE(fileID,"(6("//fmtReal//"))") (output(n)%pressure, n  = 1, self%numNodes)
       WRITE(fileID,"(10X,A)") '</DataArray>'
       !Write temperature
       WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Temperature (K)" NumberOfComponents="1">'
-      WRITE(fileID,"(6(ES20.6E3))") (output(n)%temperature, n  = 1, self%numNodes)
+      WRITE(fileID,"(6("//fmtReal//"))") (output(n)%temperature, n  = 1, self%numNodes)
       WRITE(fileID,"(10X,A)") '</DataArray>'
       !End node data
       WRITE(fileID,"(8X,A)") '</PointData>'
@@ -173,7 +173,7 @@ MODULE moduleMeshOutputVTU
           WRITE(cString, "(I2)") c
           title = 'Pair ' // interactionMatrix(k)%sp_i%name // '-' // interactionMatrix(k)%sp_j%name // ' collision ' // cString
           WRITE(fileID,"(10X,A, A, A)") '<DataArray type="Float64" Name="',title, '" NumberOfComponents="1">'
-          WRITE(fileID, "(6(I10))") (self%cells(n)%obj%tallyColl(k)%tally(c), n = 1, self%numCells)
+          WRITE(fileID, "(6("//fmtInt//"))") (self%cells(n)%obj%tallyColl(k)%tally(c), n = 1, self%numCells)
           WRITE(fileID, "(10X, A)") '</DataArray>'
 
         END DO
@@ -196,11 +196,11 @@ MODULE moduleMeshOutputVTU
       WRITE(fileID,"(8X,A)") '<PointData>'
       !Electric potential
       WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Potential (V)" NumberOfComponents="1">'
-      WRITE(fileID,"(6(ES20.6E3))") (self%nodes(n)%obj%emData%phi*Volt_ref, n  = 1, self%numNodes)
+      WRITE(fileID,"(6("//fmtReal//"))") (self%nodes(n)%obj%emData%phi*Volt_ref, n  = 1, self%numNodes)
       WRITE(fileID,"(10X,A)") '</DataArray>'
       !Magnetic Field
       WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Magnetic Field (T)" NumberOfComponents="3">'
-      WRITE(fileID,"(6(ES20.6E3))") (self%nodes(n)%obj%emData%B*B_ref, n  = 1, self%numNodes)
+      WRITE(fileID,"(6("//fmtReal//"))") (self%nodes(n)%obj%emData%B*B_ref, n  = 1, self%numNodes)
       WRITE(fileID,"(10X,A)") '</DataArray>'
       WRITE(fileID,"(8X,A)") '</PointData>'
 
@@ -209,7 +209,7 @@ MODULE moduleMeshOutputVTU
       WRITE(fileID,"(8X,A)") '<CellData>'
       !Electric field
       WRITE(fileID,"(10X,A, A, A)") '<DataArray type="Float64" Name="Electric Field (V m^-1)" NumberOfComponents="3">'
-      WRITE(fileID,"(6(ES20.6E3))") (self%cells(n)%obj%gatherElectricField(Xi)*EF_ref, n = 1, self%numCells)
+      WRITE(fileID,"(6("//fmtReal//"))") (self%cells(n)%obj%gatherElectricField(Xi)*EF_ref, n = 1, self%numCells)
       WRITE(fileID,"(10X,A)") '</DataArray>'
       WRITE(fileID,"(8X,A)") '</CellData>'
 
@@ -221,30 +221,31 @@ MODULE moduleMeshOutputVTU
       USE moduleRefParam
       IMPLICIT NONE
 
-      INTEGER:: fileID
-      CHARACTER(*):: fileNameStep, fileNameCollection
+      INTEGER, intent(in):: fileID
+      CHARACTER(*), intent(in):: fileNameStep, fileNameCollection
 
       IF (timeStep == tInitial) THEN
         !Create collection file
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileNameCollection
-        OPEN (fileID + 1, file = path // folder  // '/' // fileNameCollection)
+        call informFileCreation(fileNameCollection)
+        OPEN (fileID + 1, file = generateFilePath(fileNameCollection))
         WRITE (fileID + 1, "(A)") '<VTKFile type="Collection">'
         WRITE (fileID + 1, "(2X, A)") '<Collection>'
-        CLOSE(fileID + 1)
+
+      else
+        OPEN (fileID + 1, file = generateFilePath(fileNameCollection), ACCESS='APPEND')
+        ! Append removing the last two lines that close the <tags>
+        backspace(fileID + 1)
+        backspace(fileID + 1)
 
       END IF
 
       !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, "//fmtReal//", A, A, A)") &
             '<DataSet timestep="', DBLE(timeStep)*tauMin*ti_ref,'" file="', fileNameStep,'"/>'
 
-      !Close collection file
-      IF (timeStep == tFinal) THEN
       WRITE (fileID + 1, "(2X, A)") '</Collection>'
       WRITE (fileID + 1, "(A)") '</VTKFile>'
 
-      END IF
       CLOSE(fileID + 1)
 
     END SUBROUTINE writeCollection
@@ -276,29 +277,29 @@ MODULE moduleMeshOutputVTU
       !Write density
       WRITE(fileIDMean,     "(10X,A)") '<DataArray type="Float64" Name="Density, mean (m^-3)"      NumberOfComponents="1">'
       WRITE(fileIDDeviation,"(10X,A)") '<DataArray type="Float64" Name="Density, deviation (m^-3)" NumberOfComponents="1">'
-      WRITE(fileIDMean,     "(6(ES20.6E3))") (outputMean(n)%density,      n  = 1, self%numNodes)
-      WRITE(fileIDDeviation,"(6(ES20.6E3))") (outputDeviation(n)%density, n  = 1, self%numNodes)
+      WRITE(fileIDMean,     "(6("//fmtReal//"))") (outputMean(n)%density,      n  = 1, self%numNodes)
+      WRITE(fileIDDeviation,"(6("//fmtReal//"))") (outputDeviation(n)%density, n  = 1, self%numNodes)
       WRITE(fileIDMean,"(10X,A)")      '</DataArray>'
       WRITE(fileIDDeviation,"(10X,A)") '</DataArray>'
       !Write velocity
       WRITE(fileIDMean,     "(10X,A)") '<DataArray type="Float64" Name="Velocity, mean (m s^-1)"      NumberOfComponents="3">'
       WRITE(fileIDDeviation,"(10X,A)") '<DataArray type="Float64" Name="Velocity, deviation (m s^-1)" NumberOfComponents="3">'
-      WRITE(fileIDMean,     "(6(ES20.6E3))") (outputMean(n)%velocity,      n  = 1, self%numNodes)
-      WRITE(fileIDDeviation,"(6(ES20.6E3))") (outputDeviation(n)%velocity, n  = 1, self%numNodes)
+      WRITE(fileIDMean,     "(6("//fmtReal//"))") (outputMean(n)%velocity,      n  = 1, self%numNodes)
+      WRITE(fileIDDeviation,"(6("//fmtReal//"))") (outputDeviation(n)%velocity, n  = 1, self%numNodes)
       WRITE(fileIDMean,     "(10X,A)") '</DataArray>'
       WRITE(fileIDDeviation,"(10X,A)") '</DataArray>'
       !Write pressure
       WRITE(fileIDMean,     "(10X,A)") '<DataArray type="Float64" Name="Pressure, mean (Pa)"      NumberOfComponents="1">'
       WRITE(fileIDDeviation,"(10X,A)") '<DataArray type="Float64" Name="Pressure, deviation (Pa)" NumberOfComponents="1">'
-      WRITE(fileIDMean,     "(6(ES20.6E3))") (outputMean(n)%pressure,      n  = 1, self%numNodes)
-      WRITE(fileIDDeviation,"(6(ES20.6E3))") (outputDeviation(n)%pressure, n  = 1, self%numNodes)
+      WRITE(fileIDMean,     "(6("//fmtReal//"))") (outputMean(n)%pressure,      n  = 1, self%numNodes)
+      WRITE(fileIDDeviation,"(6("//fmtReal//"))") (outputDeviation(n)%pressure, n  = 1, self%numNodes)
       WRITE(fileIDMean,     "(10X,A)") '</DataArray>'
       WRITE(fileIDDeviation,"(10X,A)") '</DataArray>'
       !Write temperature
       WRITE(fileIDMean,     "(10X,A)") '<DataArray type="Float64" Name="Temperature, mean (K)"      NumberOfComponents="1">'
       WRITE(fileIDDeviation,"(10X,A)") '<DataArray type="Float64" Name="Temperature, deviation (K)" NumberOfComponents="1">'
-      WRITE(fileIDMean,     "(6(ES20.6E3))") (outputMean(n)%temperature,      n  = 1, self%numNodes)
-      WRITE(fileIDDeviation,"(6(ES20.6E3))") (outputDeviation(n)%temperature, n  = 1, self%numNodes)
+      WRITE(fileIDMean,     "(6("//fmtReal//"))") (outputMean(n)%temperature,      n  = 1, self%numNodes)
+      WRITE(fileIDDeviation,"(6("//fmtReal//"))") (outputDeviation(n)%temperature, n  = 1, self%numNodes)
       WRITE(fileIDMean,     "(10X,A)") '</DataArray>'
       WRITE(fileIDDeviation,"(10X,A)") '</DataArray>'
       !End node data
@@ -310,7 +311,6 @@ MODULE moduleMeshOutputVTU
     SUBROUTINE printOutputVTU(self)
       USE moduleMesh
       USE moduleSpecies
-      USE moduleMeshInoutCommon
       USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
@@ -322,8 +322,8 @@ MODULE moduleMeshOutputVTU
 
       DO i = 1, nSpecies
         fileName = formatFileName(prefix, species(i)%obj%name, 'vtu', timeStep)
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
-        OPEN (fileID, file = path // folder // '/' //  fileName)
+        call informFileCreation(fileName)
+        OPEN (fileID, file = generateFilePath(fileName))
 
         CALL writeHeader(self%numNodes, self%numCells, fileID)
 
@@ -346,7 +346,6 @@ MODULE moduleMeshOutputVTU
     SUBROUTINE printCollVTU(self)
       USE moduleMesh
       USE moduleOutput
-      USE moduleMeshInoutCommon
       USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
@@ -358,8 +357,8 @@ MODULE moduleMeshOutputVTU
 
       IF (collOutput) THEN
         fileName = formatFileName(prefix, 'Collisions', 'vtu', timeStep)
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
-        OPEN (fileID, file = path // folder // '/' //  fileName)
+        call informFileCreation(fileName)
+        OPEN (fileID, file = generateFilePath(fileName))
 
         CALL writeHeader(self%numNodes, self%numCells, fileID)
 
@@ -381,7 +380,6 @@ MODULE moduleMeshOutputVTU
 
     SUBROUTINE printEMVTU(self)
       USE moduleMesh
-      USE moduleMeshInoutCommon
       USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
@@ -393,8 +391,8 @@ MODULE moduleMeshOutputVTU
 
       IF (emOutput) THEN
         fileName = formatFileName(prefix, 'EMField', 'vtu', timeStep)
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
-        OPEN (fileID, file = path // folder // '/' //  fileName)
+        call informFileCreation(fileName)
+        OPEN (fileID, file = generateFilePath(fileName))
 
         CALL writeHeader(self%numNodes, self%numCells, fileID)
 
@@ -416,8 +414,8 @@ MODULE moduleMeshOutputVTU
 
     SUBROUTINE printAverageVTU(self)
       USE moduleMesh
+      use moduleOutput
       USE moduleSpecies
-      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
@@ -429,12 +427,12 @@ MODULE moduleMeshOutputVTU
 
       DO i = 1, nSpecies
         fileNameMean = formatFileName('Average_mean', species(i)%obj%name, 'vtu')
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileNameMean
-        OPEN (fileIDMean, file = path // folder // '/' //  fileNameMean)
+        call informFileCreation(fileNameMean)
+        OPEN (fileIDMean, file = generateFilePath(fileNameMean))
 
         fileNameDeviation = formatFileName('Average_deviation', species(i)%obj%name, 'vtu')
-        WRITE(*, "(6X,A15,A)") "Creating file: ", fileNameDeviation
-        OPEN (fileIDDeviation, file = path // folder // '/' //  fileNameDeviation)
+        call informFileCreation(fileNameDeviation)
+        OPEN (fileIDDeviation, file = generateFilePath(fileNameDeviation))
 
         CALL writeHeader(self%numNodes, self%numCells, fileIDMean)
         CALL writeHeader(self%numNodes, self%numCells, fileIDDeviation)

src/modules/mesh/moduleMesh.f90

@@ -4,7 +4,6 @@ MODULE moduleMesh
   USE moduleOutput
   USE moduleCollisions
   use moduleSpecies, only: nSpecies
-  IMPLICIT NONE
 
   ! MESH ELEMENTS
   !Generic mesh element
@@ -710,10 +709,11 @@ MODULE moduleMesh
     end subroutine updateParticle_interface
 
     ! Update the values of the particle boundary model
-    subroutine printParticle_interface(self)
+    subroutine printParticle_interface(self, fileID)
       import boundaryParticleGeneric
 
-      class(boundaryParticleGeneric), intent(inout):: self
+      class(boundaryParticleGeneric), intent(in):: self
+      integer, intent(in):: fileID
 
     end subroutine printParticle_interface
 
@@ -887,12 +887,16 @@ MODULE moduleMesh
   !Array for boundaries
   type(boundaryParticleCont), allocatable, target:: boundariesParticle(:)
 
-  ! Update the particle boundary models
   interface 
+    ! Update the particle boundary models
     module subroutine boundariesParticle_update()
 
     end subroutine boundariesParticle_update
 
+    ! Write data about particle boundaries
+    module subroutine boundariesParticle_write()
+
+    end subroutine boundariesParticle_write
   end interface
 
   ! BOUNDARY ELECTROMAGNETIC DEFINITIONS

src/modules/mesh/moduleMesh@boundaryParticle.f90

@@ -404,16 +404,21 @@ submodule(moduleMesh) boundaryParticle
 
     end subroutine quasiNeutrality_update
 
-    subroutine quasiNeutrality_print(self)
+    subroutine quasiNeutrality_print(self, fileID)
       implicit none
 
-      class(boundaryParticleGeneric), intent(inout):: self
-
-      print *, 'test'
+      class(boundaryParticleGeneric), intent(in):: self
+      integer, intent(in):: fileID
+      integer:: e
 
+      write(fileID, '(A)') self%name
       select type(self)
       type is(boundaryQuasiNeutrality)
-        print*, self%alpha
+        write(fileID, '(A,",",A)') '"Edge id"', '"alpha"'
+        do e = 1, size(self%edges)
+          write(fileID, '(I0,",",ES0.6E3)') self%edges(e)%obj%n, self%alpha(self%edges(e)%obj%n)
+
+        end do
 
       end select
 
@@ -472,4 +477,31 @@ submodule(moduleMesh) boundaryParticle
 
     end subroutine boundariesParticle_update
 
+    module subroutine boundariesParticle_write()
+      use moduleCaseparam, only: timeStep
+      use moduleOutput, only:fileID_boundaryParticle, formatFileName, informFileCreation
+      implicit none
+
+      integer:: b
+      character(:), allocatable:: fileName
+
+      if (boundaryParticleOutput) then
+        fileName = formatFileName(prefix, 'boundariesParticle', 'csv', timeStep)
+        call informFileCreation(fileName)
+        open(fileID_boundaryParticle, file = path // folder // '/' //  fileName)
+
+        do b = 1, nBoundariesParticle
+          if (associated(boundariesParticle(b)%obj%print)) then
+            call boundariesParticle(b)%obj%print(fileID_boundaryParticle)
+
+          end if
+
+        end do
+
+        close(fileID_boundaryParticle)
+
+      end if
+        
+    end subroutine boundariesParticle_write
+
 end submodule boundaryParticle

src/modules/moduleProbe.f90

@@ -208,7 +208,7 @@ MODULE moduleProbe
       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)
+      OPEN (10, file = generateFilePath(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"
@@ -216,7 +216,7 @@ MODULE moduleProbe
       DO i = 1, self%nv(1)
         DO j = 1, self%nv(2)
           DO k = 1, self%nv(3)
-            WRITE(10, "(4(ES20.6E3))") self%vi(i)*v_ref, &
+            WRITE(10, "(4("//fmtReal//"))") self%vi(i)*v_ref, &
                                             self%vj(j)*v_ref, &
                                             self%vk(k)*v_ref, &
                                             self%f(i, j, k)

src/modules/output/moduleOutput.f90

@@ -1,6 +1,40 @@
 !Contains information about output
 MODULE moduleOutput
-  IMPLICIT NONE
+  ! Path and folder for the output
+  CHARACTER(:), ALLOCATABLE:: path
+  CHARACTER(:), ALLOCATABLE:: folder
+  ! Number of digits for step files
+  INTEGER:: iterationDigits
+  CHARACTER(:), ALLOCATABLE:: iterationFormat
+  ! Triggers and counters for output
+  INTEGER:: triggerOutput,  counterOutput  = 0
+  INTEGER:: triggerCPUTime, counterCPUTime = 0
+  ! logicals to activate file output
+  LOGICAL:: timeOutput = .FALSE.
+  LOGICAL:: collOutput = .FALSE.
+  LOGICAL:: emOutput   = .FALSE.
+  logical:: boundaryParticleOutput = .false.
+
+  ! Prefix for iteration files
+  character(len=*), parameter:: prefix = 'Step'
+
+  ! Column separator
+  character(len=*), parameter:: colSep = '","'
+
+  ! General format for file outputs
+  character(len=*), parameter:: fmtColReal = 'ES0.6E3,:,'//colSep ! Column with real
+  character(len=*), parameter:: fmtColInt  = 'I0,:,'//colSep      ! Column with integer
+  character(len=*), parameter:: fmtColStr  = 'A,:,'//colSep       ! Column with text
+  character(len=*), parameter:: fmtReal    = 'ES14.6E3'           ! Fixed size real
+  character(len=*), parameter:: fmtInt     = 'I14'                ! Fixed size real
+
+  ! File IDs for different input/output
+  integer, parameter:: fileID_mesh = 10             ! Base id for mesh files
+  integer, parameter:: fileID_output = 20           ! Base id for species/collisions/EM output
+  integer, parameter:: fileID_boundaryParticle = 30 ! Particle boundaries
+  integer, parameter:: fileID_boundaryEM = 31       ! EM boundaries
+  integer, parameter:: fileID_reference = 40        ! Reference values
+  integer, parameter:: fileID_time =50              ! Computation time
 
   !Output for each node 
   TYPE, PUBLIC:: outputNode
@@ -33,17 +67,68 @@ MODULE moduleOutput
 
   END TYPE
 
-  CHARACTER(:), ALLOCATABLE:: path
-  CHARACTER(:), ALLOCATABLE:: folder
-  INTEGER:: iterationDigits
-  CHARACTER(:), ALLOCATABLE:: iterationFormat
-  INTEGER:: triggerOutput,  counterOutput  = 0
-  INTEGER:: triggerCPUTime, counterCPUTime = 0
-  LOGICAL:: timeOutput = .FALSE.
-  LOGICAL:: collOutput = .FALSE.
-  LOGICAL:: emOutput   = .FALSE.
-
   CONTAINS
+    PURE FUNCTION formatFileName(pref, suff, extension, timeStep) RESULT(fileName)
+      IMPLICIT NONE
+
+      CHARACTER(*), INTENT(in):: pref, suff, extension
+      INTEGER, INTENT(in), OPTIONAL:: timeStep
+      CHARACTER (LEN=iterationDigits):: tString
+      CHARACTER(:), ALLOCATABLE:: fileName
+
+      IF (PRESENT(timeStep)) THEN
+        WRITE(tString, iterationFormat) timeStep
+        fileName = pref //  '_' // tString // '_' // suff // '.' // extension
+
+      ELSE
+        fileName = pref //  '_' // suff // '.' // extension
+
+      END IF
+
+    END FUNCTION formatFileName
+
+    subroutine createOutputFolder()
+      implicit none
+
+      call execute_command_line('mkdir ' // path // folder )
+
+    end subroutine createOutputFolder
+
+    subroutine copyFileToOutput(fileName)
+      implicit none
+
+      character(*), intent(in):: fileName
+
+      call execute_command_line('cp ' // fileName // ' ' // path // folder)
+
+    end subroutine copyFileToOutput
+
+    subroutine writeCommit()
+      implicit none
+
+      call system('git rev-parse HEAD > ' // path // folder // '/' // 'fpakc_commit.txt')
+
+    end subroutine writeCommit
+
+    pure function generateFilePath(filename) result(completePath)
+      implicit none
+
+      character(*), intent(in):: fileName
+      character(:), allocatable:: completePath
+
+      completePath = path // folder // '/' // fileName
+
+    end function generateFilePath
+
+    subroutine informFileCreation(filename)
+      implicit none
+
+      character(*), intent(in):: fileName
+
+      write(*, "(6X,A15,A)") "Creating file: ", fileName
+
+    end subroutine informFileCreation
+
     PURE SUBROUTINE outputNode_equal_outputNode(self, from)
       IMPLICIT NONE
 
@@ -159,7 +244,7 @@ MODULE moduleOutput
 
     END SUBROUTINE calculateOutput
 
-    SUBROUTINE printTime(first)
+    SUBROUTINE writeTime(first)
       USE moduleSpecies
       USE moduleCompTime
       USE moduleCaseParam, ONLY: timeStep
@@ -168,31 +253,43 @@ MODULE moduleOutput
       LOGICAL, INTENT(in), OPTIONAL:: first
       CHARACTER(:), ALLOCATABLE:: fileName
 
-      fileName = 'cpuTime.dat'
+      fileName = 'cpuTime.csv'
 
       IF (timeOutput) THEN
         IF (PRESENT(first)) THEN
           IF (first) THEN
-            OPEN(20, file = path // folder // '/' // fileName, action = 'write')
-            WRITE(20, "(A1, 8X, A1, 9X, A1, 7(A20))") "#","t","n","total (s)","push (s)","reset (s)",        &
+            OPEN(fileID_time, file = generateFilePath(fileName), action = 'write')
+            WRITE(fileID_time, "(*("//fmtColStr//"))") "t","n","total (s)","push (s)","reset (s)",        &
                                                                "collision (s)","coulomb (s)", &
                                                                "weighting (s)","EMField (s)"
-            WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
-            CLOSE(20)
+            call informFileCreation(fileName)
+            CLOSE(fileID_time)
 
           END IF
 
         END IF
 
-        OPEN(20, file = path // folder // '/' // fileName, position = 'append', action = 'write')
+        OPEN(fileID_time, file = generateFilePath(fileName), position = 'append', action = 'write')
 
-        WRITE (20, "(I10, I10, 7(ES20.6E3))") timeStep, nPartOld, tStep, tPush, tReset, tColl, tCoul, tWeight, tEMField
+        WRITE (fileID_time, "(*("//fmtColInt//"),*("//fmtColReal//"))") timeStep, nPartOld, tStep, tPush, tReset, tColl, tCoul, tWeight, tEMField
 
-        CLOSE(20)
+        CLOSE(fileID_time)
 
       END IF
 
-    END SUBROUTINE printTime
+    END SUBROUTINE writeTime
+
+    ! Write file with reference values
+    subroutine writeReference()
+      use moduleRefParam
+      implicit none
+
+      open (fileID_reference, file=generateFilePath('reference.csv'))
+      write(fileID_reference, "(*("//fmtColStr//"))") '"L_ref"','"v_ref"','"ti_ref"','"Vol_ref"','"EF_ref"','"Volt_ref"','"B_ref"'
+      write(fileID_reference, "(*("//fmtColReal//"))")  L_ref,    v_ref,    ti_ref,    Vol_ref,    EF_ref,    Volt_ref,    B_ref
+      close(fileID_reference)
+
+    end subroutine writeReference
 
 END MODULE moduleOutput
 

src/modules/solver/moduleSolver.f90

@@ -523,8 +523,6 @@ MODULE moduleSolver
       USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
-      integer:: b ! TEMPORARY
-
       CALL outputProbes()
 
       counterOutput = counterOutput + 1
@@ -537,6 +535,10 @@ MODULE moduleSolver
         CALL mesh%printOutput()
         IF (ASSOCIATED(meshForMCC)) CALL meshForMCC%printColl()
         CALL mesh%printEM()
+
+        ! Output of boundaries
+        call boundariesParticle_write()
+
         WRITE(*, "(5X,A21,I10,A1,I10)") "t/tFinal: ", timeStep, "/", tFinal
         WRITE(*, "(5X,A21,I10)")        "Particles: ", nPartOld
         IF (timeStep == 0) THEN
@@ -553,17 +555,6 @@ MODULE moduleSolver
         END IF
         WRITE(*,*)
 
-        ! TEMPORARY
-        ! Output of boundaries. TODO: Move this to mesh module
-        do b = 1, nBoundariesParticle
-          if (associated(boundariesParticle(b)%obj%print)) then
-            print *, b
-            call boundariesParticle(b)%obj%print()
-
-          end if
-
-        end do
-
       END IF
 
       counterCPUTime = counterCPUTime + 1
@@ -573,7 +564,7 @@ MODULE moduleSolver
         !Reset CPU Time counter
         counterCPUTime = 0
 
-        CALL printTime(timeStep == 0)
+        CALL writeTime(timeStep == 0)
 
       END IF