Fixed 0D case, reference. Put everything in the moduleOutput

runs/0D_Argon/output/input.json

@@ -0,0 +1,49 @@
+
+{
+  "output": {
+    "path": "./runs/0D_Argon/",
+    "triggerOutput": 1,
+    "numColl": true,
+	"folder": "test"
+  },
+  "reference": {
+    "density": 1.0e16,
+    "mass": 6.633e-26,
+    "temperature": 11604.0,
+    "radius": 1.88e-10
+  },
+  "geometry": {
+    "dimension": 0,
+    "volume": 1e-11
+  },
+  "species": [
+    {"name": "Argon+", "type": "charged", "mass": 6.633e-26, "charge": 1.0, "weight": 1.0e0},
+    {"name": "Argon",  "type": "neutral", "mass": 6.633e-26,                "weight": 1.0e0}
+  ],
+  "solver": {
+    "tau":  [1.0e-3, 1.0e-3],
+    "finalTime": 1.0e0,
+    "initial": [
+      {"species": "Argon+", "file": "Argon+_Initial.dat"},
+      {"species": "Argon",  "file": "Argon_Initial.dat"}
+    ]
+  },
+  "interactions": {
+    "folderCollisions": "./data/collisions/",
+    "collisions": [
+      {"species_i": "Argon", "species_j": "Argon", 
+       "cTypes": [
+         {"type": "elastic", "crossSection": "EL_Ar-Ar.dat"}
+       ]},
+      {"species_i": "Argon+", "species_j": "Argon", 
+       "cTypes": [
+         {"type": "elastic", "crossSection": "EL_Ar-Ar.dat"}
+       ]}
+    ]
+  },
+  "parallel": {
+    "OpenMP":{
+      "nThreads": 4
+    }
+  }
+}

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/modules/init/moduleInput.f90

@@ -1569,35 +1569,29 @@ 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

@@ -50,18 +50,24 @@ MODULE moduleMeshOutput0D
       CLASS(meshGeneric), INTENT(in):: self
       CHARACTER(:), ALLOCATABLE:: fileName
       INTEGER:: k
+      character(:), allocatable:: kString
 
-      fileName='OUTPUT_Collisions.dat'
+      fileName = formatFileName('Output', 'Collisions', 'csv')
       IF (timeStep == tInitial) THEN
         OPEN(20, file = generateFilePath(fileName), action = 'write')
-        WRITE(20, "(A1, 14X, A5, A20)") "#","t (s)","collisions"
         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 = generateFilePath(fileName), position = 'append', action = 'write')
-      WRITE(20, "("//fmtReal//", 10I20)") REAL(timeStep)*tauMin*ti_ref, (self%cells(1)%obj%tallyColl(k)%tally, k=1,nCollPairs)
+      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/moduleMesh@boundaryParticle.f90

@@ -485,6 +485,7 @@ submodule(moduleMesh) boundaryParticle
       integer:: b
       character(:), allocatable:: fileName
 
+      if (boundaryParticleOutput) then
         fileName = formatFileName(prefix, 'boundariesParticle', 'csv', timeStep)
         call informFileCreation(fileName)
         open(fileID_boundaryParticle, file = path // folder // '/' //  fileName)
@@ -499,6 +500,8 @@ submodule(moduleMesh) boundaryParticle
 
         close(fileID_boundaryParticle)
 
+      end if
+        
     end subroutine boundariesParticle_write
 
 end submodule boundaryParticle

src/modules/output/moduleOutput.f90

@@ -1,6 +1,39 @@
 !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
 
   !Output for each node 
   TYPE, PUBLIC:: outputNode
@@ -33,36 +66,68 @@ 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.
-
-  ! 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
-
   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
 
@@ -213,43 +278,17 @@ MODULE moduleOutput
 
     END SUBROUTINE printTime
 
-    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
-
-    pure function generateFilePath(filename) result(completePath)
+    ! Write file with reference values
+    subroutine writeReference()
+      use moduleRefParam
       implicit none
 
-      character(*), intent(in):: fileName
-      character(:), allocatable:: completePath
+      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)
 
-      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
+    end subroutine writeReference
 
 END MODULE moduleOutput