From 5d82ea2ddcb59a816fa32111b064c46cefe43bce Mon Sep 17 00:00:00 2001
From: JGonzalez <jorge.gonzalez@upm.es>
Date: Fri, 6 Mar 2026 09:30:33 +0100
Subject: [PATCH] Code cleanup

---
 src/modules/init/moduleInput.f90              | 56 +++++++++----------
 src/modules/mesh/0D/moduleMesh0D.f90          | 18 +++---
 src/modules/mesh/1DCart/moduleMesh1DCart.f90  |  2 +-
 src/modules/mesh/1DRad/moduleMesh1DRad.f90    |  2 +-
 .../mesh/inout/0D/moduleMeshInput0D.f90       |  2 +-
 .../mesh/inout/text/moduleMeshInputText.f90   |  1 +
 .../mesh/inout/text/moduleMeshOutputText.f90  |  1 -
 .../mesh/moduleMesh@boundaryParticle.f90      |  2 +-
 src/modules/mesh/moduleMeshCommon.f90         |  8 +--
 src/modules/moduleCollisions.f90              |  2 +-
 src/modules/moduleInject.f90                  | 16 +++---
 src/modules/moduleProbe.f90                   |  1 -
 .../solver/electromagnetic/moduleEM.f90       |  1 -
 src/modules/solver/pusher/modulePusher.f90    |  4 +-
 14 files changed, 56 insertions(+), 60 deletions(-)

diff --git a/src/modules/init/moduleInput.f90 b/src/modules/init/moduleInput.f90
index 077e9d6..9494517 100644
--- a/src/modules/init/moduleInput.f90
+++ b/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'
 
diff --git a/src/modules/mesh/0D/moduleMesh0D.f90 b/src/modules/mesh/0D/moduleMesh0D.f90
index 133ae8e..21bfde8 100644
--- a/src/modules/mesh/0D/moduleMesh0D.f90
+++ b/src/modules/mesh/0D/moduleMesh0D.f90
@@ -43,7 +43,7 @@ MODULE moduleMesh0D
 
       CLASS(meshNode0D), INTENT(out):: self
       INTEGER, INTENT(in):: n
-      REAL(8), INTENT(in):: r(1:3) !Unused variable
+      REAL(8), INTENT(in):: r(1:3) ! NOTE: Required by interface but unused
 
       self%n = n
 
@@ -117,7 +117,7 @@ MODULE moduleMesh0D
     PURE FUNCTION fPsi0D(Xi, nNodes) RESULT(fPsi)
       IMPLICIT NONE
 
-      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8), INTENT(in):: Xi(1:3) ! NOTE: Required by interface but unused
       INTEGER, INTENT(in):: nNodes
       REAL(8):: fPsi(1:nNodes)
 
@@ -128,7 +128,7 @@ MODULE moduleMesh0D
     PURE FUNCTION dPsi0D(Xi, nNodes) RESULT(dPsi)
       IMPLICIT NONE
 
-      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8), INTENT(in):: Xi(1:3) ! NOTE: Required by interface but unused
       INTEGER, INTENT(in):: nNodes
       REAL(8):: dPsi(1:3,1:nNodes)
 
@@ -142,7 +142,7 @@ MODULE moduleMesh0D
       CLASS(meshCell0D), INTENT(in):: self
       INTEGER, INTENT(in):: nNodes
       REAL(8), INTENT(in):: dPsi(1:3,1:nNodes)
-      REAL(8):: pDer(1:3, 1:3)
+      REAL(8):: pDer(1:3, 1:3) ! NOTE: Required by interface but unused
 
       pDer = 0.D0
 
@@ -205,7 +205,7 @@ MODULE moduleMesh0D
       IMPLICIT NONE
 
       CLASS(meshCell0D), INTENT(in):: self
-      REAL(8), INTENT(in):: r(1:3)
+      REAL(8), INTENT(in):: r(1:3) ! NOTE: Required by interface but unused
       REAL(8):: xN(1:3)
 
       xN = 0.D0
@@ -215,7 +215,7 @@ MODULE moduleMesh0D
     PURE FUNCTION inside0D(Xi) RESULT(ins)
       IMPLICIT NONE
 
-      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8), INTENT(in):: Xi(1:3) ! NOTE: Required by interface but unused
       LOGICAL:: ins
 
       ins = .TRUE.
@@ -226,7 +226,7 @@ MODULE moduleMesh0D
       IMPLICIT NONE
 
       CLASS(meshCell0D), INTENT(in):: self
-      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8), INTENT(in):: Xi(1:3) ! NOTE: Required by interface but unused
       CLASS(meshElement), POINTER, INTENT(out):: neighbourElement
 
       neighbourElement => NULL()
@@ -237,7 +237,7 @@ MODULE moduleMesh0D
     PURE FUNCTION detJ0D(pDer) RESULT(dJ)
       IMPLICIT NONE
 
-      REAL(8), INTENT(in):: pDer(1:3, 1:3)
+      REAL(8), INTENT(in):: pDer(1:3, 1:3) ! NOTE: Required by interface but unused
       REAL(8):: dJ
 
       dJ = 0.D0
@@ -247,7 +247,7 @@ MODULE moduleMesh0D
     PURE FUNCTION invJ0D(pDer) RESULT(invJ)
       IMPLICIT NONE
 
-      REAL(8), INTENT(in):: pDer(1:3, 1:3)
+      REAL(8), INTENT(in):: pDer(1:3, 1:3) ! NOTE: Required by interface but unused
       REAL(8):: invJ(1:3,1:3)
 
       invJ = 0.D0
diff --git a/src/modules/mesh/1DCart/moduleMesh1DCart.f90 b/src/modules/mesh/1DCart/moduleMesh1DCart.f90
index 25a3fd7..117b77d 100644
--- a/src/modules/mesh/1DCart/moduleMesh1DCart.f90
+++ b/src/modules/mesh/1DCart/moduleMesh1DCart.f90
@@ -156,7 +156,7 @@ MODULE moduleMesh1DCart
       IMPLICIT NONE
 
       CLASS(meshEdge1DCart), INTENT(in):: self
-      REAL(8), DIMENSION(1:3), INTENT(in):: r0
+      REAL(8), DIMENSION(1:3), INTENT(in):: r0 ! NOTE: Required by interface but unused
       REAL(8), DIMENSION(1:3):: r
 
       r = (/ self%x, 0.D0, 0.D0 /)
diff --git a/src/modules/mesh/1DRad/moduleMesh1DRad.f90 b/src/modules/mesh/1DRad/moduleMesh1DRad.f90
index ca09561..3f6df2b 100644
--- a/src/modules/mesh/1DRad/moduleMesh1DRad.f90
+++ b/src/modules/mesh/1DRad/moduleMesh1DRad.f90
@@ -156,7 +156,7 @@ MODULE moduleMesh1DRad
       IMPLICIT NONE
 
       CLASS(meshEdge1DRad), INTENT(in):: self
-      REAL(8), DIMENSION(1:3), INTENT(in):: r0
+      REAL(8), DIMENSION(1:3), INTENT(in):: r0 ! NOTE: Required by interface but unused
       REAL(8), DIMENSION(1:3):: r
 
       r = (/ self%r, 0.D0, 0.D0 /)
diff --git a/src/modules/mesh/inout/0D/moduleMeshInput0D.f90 b/src/modules/mesh/inout/0D/moduleMeshInput0D.f90
index d968ba3..798d2b2 100644
--- a/src/modules/mesh/inout/0D/moduleMeshInput0D.f90
+++ b/src/modules/mesh/inout/0D/moduleMeshInput0D.f90
@@ -34,7 +34,7 @@ MODULE moduleMeshInput0D
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(inout):: self
-      CHARACTER(:), ALLOCATABLE, INTENT(in):: filename !Dummy file, not used
+      CHARACTER(:), ALLOCATABLE, INTENT(in):: filename ! NOTE: Required by interface but unused
       REAL(8):: r(1:3)
 
       !Allocates one node
diff --git a/src/modules/mesh/inout/text/moduleMeshInputText.f90 b/src/modules/mesh/inout/text/moduleMeshInputText.f90
index 9946bba..c5fe9ef 100644
--- a/src/modules/mesh/inout/text/moduleMeshInputText.f90
+++ b/src/modules/mesh/inout/text/moduleMeshInputText.f90
@@ -197,6 +197,7 @@ module moduleMeshInputText
       fileID = 10
 
       open(fileID, file=trim(filename))
+      nNodes = 0
 
       do 
         read(fileID, *, iostat=reason) line
diff --git a/src/modules/mesh/inout/text/moduleMeshOutputText.f90 b/src/modules/mesh/inout/text/moduleMeshOutputText.f90
index d69ddda..e243c80 100644
--- a/src/modules/mesh/inout/text/moduleMeshOutputText.f90
+++ b/src/modules/mesh/inout/text/moduleMeshOutputText.f90
@@ -27,7 +27,6 @@ module moduleMeshOutputText
     subroutine writeCollOutput(self, fileID)
       use moduleMesh
       use moduleCollisions
-      use moduleRefParam, only: L_ref
       implicit none
 
       class(meshGeneric), intent(in):: self
diff --git a/src/modules/mesh/moduleMesh@boundaryParticle.f90 b/src/modules/mesh/moduleMesh@boundaryParticle.f90
index 9e79835..de4edee 100644
--- a/src/modules/mesh/moduleMesh@boundaryParticle.f90
+++ b/src/modules/mesh/moduleMesh@boundaryParticle.f90
@@ -99,7 +99,6 @@ submodule(moduleMesh) boundaryParticle
       implicit none
 
       class(boundaryParticleGeneric), allocatable, intent(inout):: boundary
-      integer:: e, et
 
       allocate(boundaryQuasiNeutrality:: boundary)
 
@@ -336,6 +335,7 @@ submodule(moduleMesh) boundaryParticle
       real(8):: EF_dir
       real(8):: alpha
 
+      alpha = 0.85d0
 
       if (associated(edge%e1)) then
         cell => edge%e1
diff --git a/src/modules/mesh/moduleMeshCommon.f90 b/src/modules/mesh/moduleMeshCommon.f90
index ee5f13b..e4413aa 100644
--- a/src/modules/mesh/moduleMeshCommon.f90
+++ b/src/modules/mesh/moduleMeshCommon.f90
@@ -28,7 +28,7 @@ module moduleMeshCommon
     pure function fPsiPoint(Xi, nNodes) RESULT(fPsi)
       implicit none
 
-      real(8), intent(in):: Xi(1:3)
+      real(8), intent(in):: Xi(1:3) ! NOTE: Required by interface but unused
       integer, intent(in):: nNodes
       real(8):: fPsi(1:nNodes)
 
@@ -104,7 +104,7 @@ module moduleMeshCommon
     pure function dPsiSegm(Xi, nNodes) result(dPsi)
       implicit none
 
-      real(8), intent(in):: Xi(1:3)
+      real(8), intent(in):: Xi(1:3) ! NOTE: Required by interface but unused
       integer, intent(in):: nNodes
       real(8):: dPsi(1:3,1:nNodes)
 
@@ -142,7 +142,7 @@ module moduleMeshCommon
     pure function dPsiTria(Xi, nNodes) result(dPsi)
       implicit none
 
-      real(8), intent(in):: Xi(1:3)
+      real(8), intent(in):: Xi(1:3) ! NOTE: Required by interface but unused
       integer, intent(in):: nNodes
       real(8):: dPsi(1:3,1:nNodes)
 
@@ -157,7 +157,7 @@ module moduleMeshCommon
     pure function dPsiTetra(Xi, nNodes) result(dPsi)
       implicit none
 
-      real(8), intent(in):: Xi(1:3)
+      real(8), intent(in):: Xi(1:3) ! NOTE: Required by interface but unused
       integer, intent(in):: nNodes
       real(8):: dPsi(1:3, 1:nNodes)
 
diff --git a/src/modules/moduleCollisions.f90 b/src/modules/moduleCollisions.f90
index 36eca2e..dfe2338 100644
--- a/src/modules/moduleCollisions.f90
+++ b/src/modules/moduleCollisions.f90
@@ -553,7 +553,7 @@ MODULE moduleCollisions
       IMPLICIT NONE
 
       CLASS(collisionBinaryChargeExchange), INTENT(in):: self
-      REAL(8), INTENT(in):: vRel
+      REAL(8), INTENT(in):: vRel ! NOTE: Required by itnerface but unused
       TYPE(particle), INTENT(inout), TARGET:: part_i, part_j
 
       SELECT TYPE(sp => part_i%species)
diff --git a/src/modules/moduleInject.f90 b/src/modules/moduleInject.f90
index 44c0f80..324d83b 100644
--- a/src/modules/moduleInject.f90
+++ b/src/modules/moduleInject.f90
@@ -48,9 +48,7 @@ MODULE moduleInject
       REAL(8):: tauInject
       REAL(8), INTENT(in):: flow
       CHARACTER(:), ALLOCATABLE, INTENT(in):: units
-      INTEGER:: e, et
-      INTEGER:: phSurface(1:mesh%numEdges)
-      INTEGER:: nVolColl
+      INTEGER:: e
       REAL(8):: fluxPerStep = 0.D0
 
       self%id          =  i
@@ -70,8 +68,8 @@ MODULE moduleInject
 
       !Calculates total area
       self%surface = 0.D0
-      DO et = 1, self%nEdges
-        self%surface = self%surface + self%edges(et)%obj%surface
+      DO e = 1, self%nEdges
+        self%surface = self%surface + self%edges(e)%obj%surface
 
       END DO
 
@@ -121,8 +119,8 @@ MODULE moduleInject
       IF (particlesPerEdge > 0) THEN
         ! Particles per edge defined by the user
         self%particlesPerEdge = particlesPerEdge
-        DO et = 1, self%nEdges
-          self%weightPerEdge(et) = fluxPerStep * self%edges(et)%obj%surface / real(particlesPerEdge)
+        DO e = 1, self%nEdges
+          self%weightPerEdge(e) = fluxPerStep * self%edges(e)%obj%surface / real(particlesPerEdge)
 
         END DO
 
@@ -131,8 +129,8 @@ MODULE moduleInject
       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*self%edges(et)%obj%surface / self%species%weight))
+        DO e = 1, self%nEdges
+          self%particlesPerEdge(e) = max(1,FLOOR(fluxPerStep*self%edges(e)%obj%surface / self%species%weight))
         END DO
 
         self%nParticles = SUM(self%particlesPerEdge)
diff --git a/src/modules/moduleProbe.f90 b/src/modules/moduleProbe.f90
index 754d56a..1e1339e 100644
--- a/src/modules/moduleProbe.f90
+++ b/src/modules/moduleProbe.f90
@@ -253,7 +253,6 @@ MODULE moduleProbe
     END SUBROUTINE doProbes
 
     SUBROUTINE outputProbes()
-      USE moduleCaseParam, ONLY: timeStep
       IMPLICIT NONE
 
       INTEGER:: i
diff --git a/src/modules/solver/electromagnetic/moduleEM.f90 b/src/modules/solver/electromagnetic/moduleEM.f90
index b8d9b55..4b115aa 100644
--- a/src/modules/solver/electromagnetic/moduleEM.f90
+++ b/src/modules/solver/electromagnetic/moduleEM.f90
@@ -121,7 +121,6 @@ MODULE moduleEM
       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))
 
diff --git a/src/modules/solver/pusher/modulePusher.f90 b/src/modules/solver/pusher/modulePusher.f90
index f75c733..a7dac57 100644
--- a/src/modules/solver/pusher/modulePusher.f90
+++ b/src/modules/solver/pusher/modulePusher.f90
@@ -231,8 +231,8 @@ MODULE modulePusher
       USE moduleSpecies
       IMPLICIT NONE
 
-      TYPE(particle), INTENT(inout):: part
-      REAL(8), INTENT(in):: tauIn
+      TYPE(particle), INTENT(inout):: part ! NOTE: Required by interface but unused
+      REAL(8), INTENT(in):: tauIn ! NOTE: Required by interface but unused
 
     END SUBROUTINE push0D