I'm dying with hay fever but I have to commit

I'm feeling awful but I have work in my desktop that I need to commit so
I can work with my laptop while I'm at the IEPC 2022 in Boston.

src/modules/moduleInput.f90

@@ -132,6 +132,15 @@ MODULE moduleInput
       CALL config%get(object // '.temperature', T_ref, found)
       IF (.NOT. found) CALL criticalError('Reference temperature not found','readReference')
 
+      !Derived parameters
+      L_ref     = DSQRT(kb*T_ref*eps_0/n_ref)/qe !reference length
+      v_ref     = DSQRT(kb*T_ref/m_ref)          !reference velocity
+      ti_ref    = L_ref/v_ref                    !reference time
+      Vol_ref   = L_ref**3                       !reference volume
+      EF_ref    = qe*n_ref*L_ref/eps_0           !reference electric field
+      Volt_ref  = EF_ref*L_ref                   !reference voltage
+      B_ref     = m_ref / (ti_ref * qe)          !reference magnetic field
+
       !If a reference cross section is given, it is used
       CALL config%get(object // '.sigmaVrel', sigmavRel_ref, found)
 
@@ -147,15 +156,6 @@ MODULE moduleInput
         END IF
 
       END IF
-      
-      !Derived parameters
-      L_ref     = DSQRT(kb*T_ref*eps_0/n_ref)/qe !reference length
-      v_ref     = DSQRT(kb*T_ref/m_ref)          !reference velocity
-      ti_ref    = L_ref/v_ref                    !reference time
-      Vol_ref   = L_ref**3                       !reference volume
-      EF_ref    = qe*n_ref*L_ref/eps_0           !reference electric field
-      Volt_ref  = EF_ref*L_ref                   !reference voltage
-      B_ref     = m_ref / (ti_ref * qe)          !reference magnetic field
 
     END SUBROUTINE readReference
 
@@ -417,15 +417,6 @@ MODULE moduleInput
               END IF
               partNew%n_in   = .TRUE.
               partNew%weight = species(sp)%obj%weight
-              !If charged species, add qm to particle
-              SELECT TYPE(sp => species(sp)%obj)
-              TYPE IS (speciesCharged)
-                partNew%qm = sp%qm
-
-              CLASS DEFAULT
-                partNew%qm = 0.D0
-
-              END SELECT
 
               !Assign particle to temporal list of particles
               CALL partInitial%add(partNew)
@@ -642,11 +633,13 @@ MODULE moduleInput
       CHARACTER(:), ALLOCATABLE:: crossSecFilePath
       CHARACTER(:), ALLOCATABLE:: cType
       LOGICAL:: found
-      INTEGER:: nInteractions, nCollisions
+      INTEGER:: nPairs, nCollisions
       INTEGER:: i, k, ij
       INTEGER:: pt_i, pt_j
       REAL(8):: energyThreshold, energyBinding
       CHARACTER(:), ALLOCATABLE:: electron
+      INTEGER:: e
+      CLASS(meshVol), POINTER:: vol
 
       !Firstly, checks if the object 'interactions' exists
       CALL config%info('interactions', found)
@@ -681,8 +674,8 @@ MODULE moduleInput
           !Inits lock for list of particles
           CALL OMP_INIT_LOCK(lockCollisions)
 
-          CALL config%info('interactions.collisions', found, n_children = nInteractions)
-          DO i = 1, nInteractions
+          CALL config%info('interactions.collisions', found, n_children = nPairs)
+          DO i = 1, nPairs
             WRITE(iString, '(I2)') i
             object = 'interactions.collisions(' // TRIM(iString) // ')'
             CALL config%get(object // '.species_i', species_i, found)
@@ -691,6 +684,7 @@ MODULE moduleInput
             pt_j = speciesName2Index(species_j)
             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, pt_i, pt_j)
 
@@ -732,7 +726,7 @@ MODULE moduleInput
                                           crossSecFilePath, energyBinding, electron)
 
               CASE DEFAULT
-                CALL criticalError('Collision type' // cType // 'not defined yet', 'readInteractions')
+                CALL criticalError('Collision type' // cType // 'not defined', 'readInteractions')
 
               END SELECT
 
@@ -740,6 +734,26 @@ MODULE moduleInput
 
           END DO
 
+          !Init the required arrays in each volume to account for MCC.
+          DO e = 1, meshForMCC%numVols
+            vol => meshForMCC%vols(e)%obj
+
+            !Allocate Maximum cross section per collision pair and assign the initial collision rate
+            ALLOCATE(vol%sigmaVrelMax(1:nCollPairs))
+            vol%sigmaVrelMax = sigmaVrel_ref/(L_ref**2 * v_ref)
+
+            IF (collOutput) THEN
+              ALLOCATE(vol%tallyColl(1:nCollPairs))
+              DO k = 1, nCollPairs
+                ALLOCATE(vol%tallyColl(k)%tally(1:interactionmatrix(k)%amount))
+                vol%tallyColl(k)%tally = 0
+
+              END DO
+
+            END IF
+
+          END DO
+
         END IF
 
       END IF