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/moduleInput.f90

@@ -333,6 +333,7 @@ MODULE moduleInput
       !Mean velocity and temperature at particle position
       REAL(8):: velocityXi(1:3), temperatureXi
       INTEGER:: nNewPart = 0.D0
+      CLASS(meshVol), POINTER:: vol
       TYPE(particle), POINTER:: partNew
       REAL(8):: vTh
       TYPE(lNode), POINTER:: partCurr, partNext
@@ -356,7 +357,6 @@ MODULE moduleInput
             !Density at centroid of cell
             nodes = mesh%vols(e)%obj%getNodes()
             nNodes = SIZE(nodes)
-            !TODO: Procedure to obtain centroid from element (also for printing Electric Field)
             fPsi = mesh%vols(e)%obj%fPsi((/0.D0, 0.D0, 0.D0/))
             ALLOCATE(source(1:nNodes))
             DO j = 1, nNodes
@@ -430,6 +430,13 @@ MODULE moduleInput
               !Assign particle to temporal list of particles
               CALL partInitial%add(partNew)
 
+              !Assign particle to list in volume
+              vol => meshforMCC%vols(partNew%volColl)%obj
+              CALL OMP_SET_LOCK(vol%lock)
+              CALL vol%listPart_in(sp)%add(partNew)
+              vol%totalWeight(sp) = vol%totalWeight(sp) + partNew%weight
+              CALL OMP_UNSET_LOCK(vol%lock)
+
             END DO
 
             DEALLOCATE(source)
@@ -685,7 +692,7 @@ MODULE moduleInput
             CALL config%info(object // '.cTypes', found, n_children = nCollisions)
             ij = interactionIndex(pt_i,pt_j)
             !Allocates the required number of collisions per each pair of species ij
-            CALL interactionMatrix(ij)%init(nCollisions, species(pt_i)%obj%m, species(pt_j)%obj%m)
+            CALL interactionMatrix(ij)%init(nCollisions, pt_i, pt_j)
 
             DO k = 1, nCollisions
               WRITE (kString, '(I2)') k