All actions related to path/fodler should be in moduleOutput now

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/input.json

@@ -1,49 +0,0 @@
-
-{
-  "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
-    }
-  }
-}

src/modules/init/moduleInput.f90

@@ -491,7 +491,8 @@ 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 // '.EMField', emOutput, found)
+      call config%get(object // '.boundaryParticle', boundaryParticleOutput, found)
 
       CALL config%get(object // '.triggerCPUTime', triggerCPUTime, found)
       IF (.NOT. found) THEN

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

@@ -134,7 +134,7 @@ module moduleMeshOutputText
       do s = 1, nSpecies
         fileName = formatFileName(prefix, species(s)%obj%name, 'csv', timeStep)
         call informFileCreation(fileName)
-        open (fileID, file = path // folder // '/' //  fileName)
+        open (fileID, file = generateFilePath(fileName))
 
         write(fileID, '(5(A,","),A)') '"Position (m)"', &
                                       '"Density (m^-3)"', &
@@ -166,7 +166,7 @@ module moduleMeshOutputText
       if (collOutput) then
         fileName = formatFileName(prefix, 'Collisions', 'csv', timeStep)
         call informFileCreation(fileName)
-        open (fileID, file = path // folder // '/' //  fileName)
+        open (fileID, file = generateFilePath(fileName))
 
         write(fileID, '(A)', advance='no') "Cell"
         do k = 1, nCollPairs
@@ -201,7 +201,7 @@ module moduleMeshOutputText
       if (emOutput) then
         fileName = formatFileName(prefix, 'EMField', 'csv', timeStep)
         call informFileCreation(fileName)
-        open (fileID, file = path // folder // '/' //  fileName)
+        open (fileID, file = generateFilePath(fileName))
 
         write(fileID, '(8(A,","),A)') '"Position (m)"', &
                                       '"Potential (V)"', &
@@ -232,7 +232,7 @@ module moduleMeshOutputText
       do s = 1, nSpecies
         fileNameMean = formatFileName('Average_mean', species(s)%obj%name, 'csv')
         call informFileCreation(fileNameMean)
-        open (fileIDMean, file = path // folder // '/' //  fileNameMean)
+        open (fileIDMean, file = generateFilePath(fileNameMean))
 
         write(fileIDMean, '(5(A,","),A)') '"Position (m)"', &
                                           '"Density, mean (m^-3)"', &
@@ -241,7 +241,7 @@ module moduleMeshOutputText
 
         fileNameDeviation = formatFileName('Average_deviation', species(s)%obj%name, 'csv')
         call informFileCreation(fileNameDeviation)
-        open (fileIDDeviation, file = path // folder // '/' //  fileNameDeviation)
+        open (fileIDDeviation, file = generateFilePath(fileNameDeviation))
 
         write(fileIDDeviation, '(5(A,","),A)') '"Position (m)"', &
                                                '"Density, deviation (m^-3)"', &

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"
@@ -216,10 +216,10 @@ 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%vj(j)*v_ref, &
-                                       self%vk(k)*v_ref, &
+                                            self%vk(k)*v_ref, &
-                                       self%f(i, j, k)
+                                            self%f(i, j, k)
 
           END DO
           WRITE(10, *)

src/modules/output/moduleOutput.f90

@@ -257,7 +257,7 @@ MODULE moduleOutput
       IF (timeOutput) THEN
         IF (PRESENT(first)) THEN
           IF (first) THEN
-            OPEN(20, file = path // folder // '/' // fileName, action = 'write')
+            OPEN(20, file = generateFilePath(fileName), action = 'write')
             WRITE(20, "(A1, 8X, A1, 9X, A1, 7(A20))") "#","t","n","total (s)","push (s)","reset (s)",        &
                                                                               "collision (s)","coulomb (s)", &
                                                                               "weighting (s)","EMField (s)"
@@ -268,7 +268,7 @@ MODULE moduleOutput
 
         END IF
 
-        OPEN(20, file = path // folder // '/' // fileName, position = 'append', action = 'write')
+        OPEN(20, file = generateFilePath(fileName), position = 'append', action = 'write')
 
         WRITE (20, "(I10, I10, 7(ES20.6E3))") timeStep, nPartOld, tStep, tPush, tReset, tColl, tCoul, tWeight, tEMField
 

src/modules/solver/moduleSolver.f90

@@ -536,7 +536,7 @@ MODULE moduleSolver
         IF (ASSOCIATED(meshForMCC)) CALL meshForMCC%printColl()
         CALL mesh%printEM()
 
-        ! Output of boundaries. TODO: Add an if
+        ! Output of boundaries
         call boundariesParticle_write()
 
         WRITE(*, "(5X,A21,I10,A1,I10)") "t/tFinal: ", timeStep, "/", tFinal