Code cleanup

src/modules/init/moduleInput.f90

@@ -509,6 +509,7 @@ MODULE moduleInput
       USE moduleRefParam
       USE moduleList
       USE json_module
+      use moduleMesh, only: qSpecies
       IMPLICIT NONE
 
       TYPE(json_file), INTENT(inout):: config
@@ -517,7 +518,7 @@ MODULE moduleInput
       CHARACTER(:), ALLOCATABLE:: speciesType
       REAL(8):: mass, charge
       LOGICAL:: found
-      INTEGER:: i
+      INTEGER:: s
       CHARACTER(:), ALLOCATABLE:: linkName
       INTEGER:: linkID
 
@@ -529,8 +530,8 @@ MODULE moduleInput
       ALLOCATE(species(1:nSpecies))
 
       !Reads information of individual species
-      DO i = 1, nSpecies
-        WRITE(iString, '(I2)') i
+      DO s = 1, nSpecies
+        WRITE(iString, '(I2)') s
         object = 'species(' // TRIM(iString) // ')'
         CALL config%get(object // '.type', speciesType, found)
         CALL config%get(object // '.mass', mass,        found)
@@ -539,12 +540,12 @@ MODULE moduleInput
         !Allocate species depending on type and assign specific parameters
         SELECT CASE(speciesType)
         CASE ("neutral")
-          ALLOCATE(species(i)%obj, source=speciesNeutral())
+          ALLOCATE(species(s)%obj, source=speciesNeutral())
 
         CASE ("charged")
           CALL config%get(object // '.charge', charge,      found)
           IF (.NOT. found) CALL criticalError("Required parameter charge not found for species " // object, 'readSpecies')
-          ALLOCATE(species(i)%obj, source=speciesCharged(q  = charge, &
+          ALLOCATE(species(s)%obj, source=speciesCharged(q  = charge, &
                                                          qm = charge/mass))
 
         CASE DEFAULT
@@ -552,18 +553,32 @@ MODULE moduleInput
 
         END SELECT
         !Assign shared parameters for all species
-        CALL config%get(object // '.name',   species(i)%obj%name,   found)
-        CALL config%get(object // '.weight', species(i)%obj%weight, found)
-        species(i)%obj%n = i
-        species(i)%obj%m = mass
+        CALL config%get(object // '.name',   species(s)%obj%name,   found)
+        CALL config%get(object // '.weight', species(s)%obj%weight, found)
+        species(s)%obj%n = s
+        species(s)%obj%m = mass
+
+      END DO
+
+      ! Allocate the vector with the species charges for calculating the EM field
+      ALLOCATE(qSpecies(1:nSpecies))
+      DO s = 1, nSpecies
+        SELECT TYPE(sp => species(s)%obj)
+        TYPE IS (speciesCharged)
+          qSpecies(s) = sp%q
+
+        CLASS DEFAULT
+          qSpecies(s) = 0.D0
+
+        END SELECT
 
       END DO
 
       !Read relations between species
-      DO i = 1, nSpecies
-        WRITE(iString, '(I2)') i
+      DO s = 1, nSpecies
+        WRITE(iString, '(I2)') s
         object = 'species(' // TRIM(iString) // ')'
-        SELECT TYPE(sp => species(i)%obj)
+        SELECT TYPE(sp => species(s)%obj)
         TYPE IS (speciesNeutral)
           !Get species linked ion
           CALL config%get(object // '.ion', linkName, found)
@@ -921,7 +936,7 @@ MODULE moduleInput
       TYPE(json_file), INTENT(inout):: config
       CHARACTER(:), ALLOCATABLE:: object
       LOGICAL:: found
-      INTEGER:: b, s
+      INTEGER:: b
       CHARACTER(2):: bString
       character(:), allocatable:: bType
 
@@ -976,20 +991,6 @@ MODULE moduleInput
 
       end do
 
-      ! TODO: Move this to the init of species
-      ALLOCATE(qSpecies(1:nSpecies))
-      DO s = 1, nSpecies
-        SELECT TYPE(sp => species(s)%obj)
-        TYPE IS (speciesCharged)
-          qSpecies(s) = sp%q
-
-        CLASS DEFAULT
-          qSpecies(s) = 0.D0
-
-        END SELECT
-
-      END DO
-
     END SUBROUTINE readBoundaryEM
 
     subroutine readPhysicalSurfaces(config)
@@ -1081,7 +1082,6 @@ MODULE moduleInput
       integer:: b, ps, s
       integer:: e
       integer:: nVolColl
-      integer:: boundaryIndex
 
       object = 'geometry'