Adding a time step for collisions

A new option has been added in which MCC are computed with its own time
step.

If no time is provided, then the minimum time step of the simulation is
employed.

doc/user-manual/fpakc_UserManual.tex

@@ -29,8 +29,7 @@
 \makeglossaries
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
+\newacronym{fpakc}{fpakc}{Finite element PArticle Code}
-\newacronym{fpakc}{fpakc}{Finite Element PArticle Code}
 \newacronym{mpi}{MPI}{Message Passing Interface}
 \newacronym{gpu}{GPU}{Graphics Processing Unit}
 \newacronym{cpu}{CPU}{Central Processing Unit}
@@ -308,7 +307,6 @@ make
       \end{lstlisting}
       to compile the code.
       If everything is correct, an executable named \textit{fpakc} will be generated.
-  
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Running the code}
       To run a case, simply execute:
@@ -659,6 +657,10 @@ make
                                          The file needs to be located in the folder \textbf{output.folder}.
                                          If this value is not present, the mesh defined in \textbf{geometry.meshFile} is used for \acrshort{mcc}.
                                          The format of this mesh needs to be the same as the one defined in \textbf{geometry.meshType}.
+          \item \textbf{timeStep}: Real.
+                                   Units of $\unit{s}$.
+                                   Time step to calculate MCC.
+                                   If no time is provided, the minimum time step is used.
           \item \textbf{collisions}: Object.
                                      Array.
                                      Contains the different short range interactions (\acrshort{mcc}).

src/fpakc.f90

@@ -70,7 +70,7 @@ PROGRAM fpakc
     tColl = omp_get_wtime()
     !$OMP END SINGLE
 
-    IF (ASSOCIATED(meshForMCC)) CALL meshForMCC%doCollisions()
+    IF (ASSOCIATED(meshForMCC)) CALL meshForMCC%doCollisions(t)
 
     !$OMP SINGLE
     tColl = omp_get_wtime() - tColl

src/modules/mesh/inout/0D/moduleMeshOutput0D.f90

@@ -42,7 +42,7 @@ MODULE moduleMeshOutput0D
       USE moduleOutput
       IMPLICIT NONE
 
-      CLASS(meshGeneric), INTENT(in):: self
+      CLASS(meshGeneric), INTENT(inout):: self
       INTEGER, INTENT(in):: t
       CHARACTER(:), ALLOCATABLE:: fileName
 
@@ -56,7 +56,7 @@ MODULE moduleMeshOutput0D
       END IF
       
       OPEN(20, file = path // folder // '/' // fileName, position = 'append', action = 'write')
-      WRITE(20, "(ES20.6E3, I20)") REAL(t)*tauMin*ti_ref, mesh%vols(1)%obj%nColl
+      WRITE(20, "(ES20.6E3, I20)") REAL(t)*tauMin*ti_ref, self%vols(1)%obj%nColl
       CLOSE(20)
 
     END SUBROUTINE printColl0D

src/modules/mesh/inout/gmsh2/moduleMeshOutputGmsh2.f90

@@ -95,7 +95,7 @@ MODULE moduleMeshOutputGmsh2
       USE moduleOutput
       IMPLICIT NONE
 
-      CLASS(meshGeneric), INTENT(in):: self
+      CLASS(meshGeneric), INTENT(inout):: self
       INTEGER, INTENT(in):: t
       INTEGER:: numEdges
       INTEGER:: n

src/modules/mesh/moduleMesh.f90

@@ -310,7 +310,7 @@ MODULE moduleMesh
     SUBROUTINE printColl_interface(self, t)
       IMPORT meshGeneric
 
-      CLASS(meshGeneric), INTENT(in):: self
+      CLASS(meshGeneric), INTENT(inout):: self
       INTEGER, INTENT(in):: t
 
     END SUBROUTINE printColl_interface
@@ -637,7 +637,7 @@ MODULE moduleMesh
     END FUNCTION findCellBrute
 
     !Computes collisions in element
-    SUBROUTINE doCollisions(self)
+    SUBROUTINE doCollisions(self, t)
       USE moduleCollisions
       USE moduleSpecies
       USE moduleList
@@ -646,6 +646,7 @@ MODULE moduleMesh
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(inout), TARGET:: self
+      INTEGER, INTENT(in):: t
       INTEGER:: e
       CLASS(meshVol), POINTER:: vol
       INTEGER:: nPart !Number of particles inside the cell
@@ -657,14 +658,20 @@ MODULE moduleMesh
       REAL(8):: sigmaVrelMaxNew
       TYPE(pointerArray), ALLOCATABLE:: partTemp(:)
 
+      IF (MOD(t, everyColl) == 0) THEN
+        !Collisions need to be performed in this iteration
         !$OMP DO SCHEDULE(DYNAMIC)
         DO e=1, self%numVols
           vol => self%vols(e)%obj
           nPart = vol%listPart_in%amount
+
+          !Resets the number of collisions
+          vol%nColl = 0
+
           !Calculates number of collisions if there is more than one particle in the cell
           IF (nPart > 1) THEN
             !Probability of collision
-          pMax = vol%totalWeight*vol%sigmaVrelMax*tauMin/vol%volume
+            pMax = vol%totalWeight*vol%sigmaVrelMax*tauColl/vol%volume
 
             !Number of collisions in the cell
             vol%nColl = NINT(REAL(nPart)*pMax*0.5D0)
@@ -701,6 +708,8 @@ MODULE moduleMesh
         END DO
         !$OMP END DO
 
+      END IF
+
     END SUBROUTINE doCollisions
 
     SUBROUTINE doCoulomb(self)

src/modules/moduleCaseParam.f90

@@ -4,6 +4,7 @@ MODULE moduleCaseParam
   INTEGER:: tFinal, tInitial = 0
   REAL(8), ALLOCATABLE:: tau(:)
   REAL(8):: tauMin
+  REAL(8):: tauColl
 
 END MODULE moduleCaseParam
 

src/modules/moduleCollisions.f90

@@ -2,6 +2,9 @@ MODULE moduleCollisions
   USE moduleSpecies
   USE moduleTable
 
+  !Integer for when collisions are computed
+  INTEGER:: everyColl
+
   !Abstract type for collision between two particles
   TYPE, ABSTRACT:: collisionBinary
     REAL(8):: rMass !Reduced mass

src/modules/moduleInput.f90

@@ -40,6 +40,11 @@ MODULE moduleInput
       CALL readSpecies(config)
       CALL checkStatus(config, "readSpecies")
 
+      !Reads case parameters
+      CALL verboseError('Reading Case parameters...')
+      CALL readCase(config)
+      CALL checkStatus(config, "readCase")
+
       !Read interactions between species
       CALL verboseError('Reading interaction between species...')
       CALL readInteractions(config)
@@ -55,10 +60,10 @@ MODULE moduleInput
       CALL readGeometry(config)
       CALL checkStatus(config, "readGeometry")
 
-      !Reads case parameters
+      !Read initial state for species
-      CALL verboseError('Reading Case parameters...')
+      CALL verboseError('Reading Initial state...')
-      CALL readCase(config)
+      CALL readInitial(config)
-      CALL checkStatus(config, "readCase")
+      CALL checkStatus(config, "readInitial")
 
       !Read injection of particles
       CALL verboseError('Reading injection of particles from boundaries...')
@@ -233,11 +238,6 @@ MODULE moduleInput
       WRITE(tString, '(I1)') iterationDigits
       iterationFormat = "(I" // tString // "." // tString // ")"
 
-      !Read initial state for species
-      CALL verboseError('Reading Initial state...')
-      CALL readInitial(config)
-      CALL checkStatus(config, "readInitial")
-
     END SUBROUTINE readCase
 
     !Reads the initial information for the species
@@ -558,6 +558,8 @@ MODULE moduleInput
       USE moduleCollisions
       USE moduleErrors
       USE moduleMesh
+      USE moduleCaseParam
+      USE moduleRefParam
       USE OMP_LIB
       USE json_module
       IMPLICIT NONE
@@ -595,6 +597,24 @@ MODULE moduleInput
 
           END IF
 
+          !Reads collision time step
+          CALL config%info('interactions.timeStep', found)
+          IF (found) THEN
+            CALL config%get('interactions.timeStep', tauColl, found)
+            tauColl  = tauColl / ti_ref
+
+          ELSE
+            tauColl = tauMin
+
+          END IF
+
+          IF (tauColl < tauMin) THEN
+            CALL criticalError('Collisional time step below minimum time step.', 'readInteractions')
+
+          END IF
+
+          everyColl = NINT(tauColl / tauMin)
+
           !Inits the MCC matrix
           CALL initInteractionMatrix(interactionMatrix)