Merge branch 'feature/collisionPairs' into feature/electromagnetic

Merging branches and fixing a number of important issues:

- Initial particles were not being assigned to the list of particles.

- List of particles was being erased every iteration, even if species
  was not pushed.

These caused issues with the calculation of collisions when a species
was frozen.

Now, things should work properly. All particles are properly added to
the volume list and the list is erased ONLY if the species has been
updated.

I hope that collisions are now properly accounted for per species pair.

src/modules/moduleCollisions.f90

@@ -67,6 +67,8 @@ MODULE moduleCollisions
 
   !Type for interaction matrix
   TYPE:: interactionsBinary
+    CLASS(speciesGeneric), POINTER:: sp_i
+    CLASS(speciesGeneric), POINTER:: sp_j
     INTEGER:: amount
     REAL(8):: rMass !Reduced mass
     TYPE(collisionCont), ALLOCATABLE:: collisions(:)
@@ -142,16 +144,24 @@ MODULE moduleCollisions
     END FUNCTION interactionIndex
 
     !Inits the binary interaction
-    SUBROUTINE initInteractionBinary(self, amount, mass_i, mass_j)
+    SUBROUTINE initInteractionBinary(self, amount,  i, j)
       USE moduleMath
+      USE moduleSpecies
       IMPLICIT NONE
 
       CLASS(interactionsBinary), INTENT(inout):: self
       INTEGER, INTENT(in):: amount
-      REAL(8), INTENT(in):: mass_i, mass_j
+      INTEGER, INTENT(in):: i, j
+      REAL(8):: mass_i, mass_j
+
+      self%sp_i => species(i)%obj
+      self%sp_j => species(j)%obj
 
       self%amount = amount
 
+      mass_i = species(i)%obj%m
+      mass_j = species(j)%obj%m
+
       self%rMass = reducedMass(mass_i, mass_j)
 
       ALLOCATE(self%collisions(1:self%amount))
@@ -165,14 +175,14 @@ MODULE moduleCollisions
       REAL(8), INTENT(in):: vRel, eRel
       REAL(8), INTENT(out):: sigmaVrelTotal
       REAL(8), INTENT(out), ALLOCATABLE:: sigmaVrel(:)
-      INTEGER:: k
+      INTEGER:: c
 
       sigmaVrelTotal = 0.D0
 
       ALLOCATE(sigmaVrel(1:self%amount))
 
-      DO k = 1, self%amount
-        sigmaVrel(k) = self%collisions(k)%obj%crossSec%get(eRel)*vRel
+      DO c = 1, self%amount
+        sigmaVrel(c) = self%collisions(c)%obj%crossSec%get(eRel)*vRel
 
       END DO
       sigmaVrelTotal = SUM(sigmaVrel)
@@ -222,8 +232,13 @@ MODULE moduleCollisions
       vp  = vRel*randomDirectionVHS()
 
       !Assign velocities to particles
+      PRINT *, part_i%v
       part_i%v = vCM + m_j*vp / (m_i + m_j)
+      PRINT *, part_i%v
+      PRINT *, part_j%v
       part_j%v = vCM - m_i*vp / (m_i + m_j)
+      PRINT *, part_j%v
+      PRINT *
 
     END SUBROUTINE collideBinaryElastic