Merge branch 'feature/collisionTimeStep' into 'development'

Adding a time step for collisions

See merge request JorgeGonz/fpakc!22

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}
@@ -308,14 +307,13 @@ 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:
       \begin{lstlisting}
 ./fpakc path/to/input-file.json
       \end{lstlisting}
-  	  in a command line from the root \acrshort{fpakc} folder.
+      in a command line from the root \acrshort{fpakc} folder.
       Substitute \lstinline|path/to/input-file.json| with the path to the input file of the case you want to run.
       The examples in the run directory are presented in Chapter \ref{ch:exampleRuns}.
 
@@ -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
@@ -657,49 +658,57 @@ MODULE moduleMesh
       REAL(8):: sigmaVrelMaxNew
       TYPE(pointerArray), ALLOCATABLE:: partTemp(:)
 
-      !$OMP DO SCHEDULE(DYNAMIC)
+      IF (MOD(t, everyColl) == 0) THEN
-      DO e=1, self%numVols
+        !Collisions need to be performed in this iteration
-        vol => self%vols(e)%obj
+        !$OMP DO SCHEDULE(DYNAMIC)
-        nPart = vol%listPart_in%amount
+        DO e=1, self%numVols
-        !Calculates number of collisions if there is more than one particle in the cell
+          vol => self%vols(e)%obj
-        IF (nPart > 1) THEN
+          nPart = vol%listPart_in%amount
-          !Probability of collision
-          pMax = vol%totalWeight*vol%sigmaVrelMax*tauMin/vol%volume
 
-          !Number of collisions in the cell
+          !Resets the number of collisions
-          vol%nColl = NINT(REAL(nPart)*pMax*0.5D0)
+          vol%nColl = 0
 
-          IF (vol%nColl > 0) THEN
+          !Calculates number of collisions if there is more than one particle in the cell
-            !Converts the list of particles to an array for easy access
+          IF (nPart > 1) THEN
-            partTemp = vol%listPart_in%convert2Array()
+            !Probability of collision
+            pMax = vol%totalWeight*vol%sigmaVrelMax*tauColl/vol%volume
 
-          END IF
+            !Number of collisions in the cell
+            vol%nColl = NINT(REAL(nPart)*pMax*0.5D0)
 
-          DO n = 1, vol%nColl
+            IF (vol%nColl > 0) THEN
-            !Select random numbers
+              !Converts the list of particles to an array for easy access
-            rnd = random(1, nPart)
+              partTemp = vol%listPart_in%convert2Array()
-            part_i => partTemp(rnd)%part
-            rnd = random(1, nPart)
-            part_j => partTemp(rnd)%part
-            ij = interactionIndex(part_i%species%n, part_j%species%n)
-            sigmaVrelMaxNew = 0.D0
-            DO k = 1, interactionMatrix(ij)%amount
-              CALL interactionMatrix(ij)%collisions(k)%obj%collide(vol%sigmaVrelMax, sigmaVrelMaxNew, part_i, part_j)
-
-            END DO
-
-            !Update maximum cross section*v_rel per each collision
-            IF (sigmaVrelMaxNew > vol%sigmaVrelMax) THEN
-              vol%sigmaVrelMax = sigmaVrelMaxNew
 
             END IF
 
-          END DO
+            DO n = 1, vol%nColl
+              !Select random numbers
+              rnd = random(1, nPart)
+              part_i => partTemp(rnd)%part
+              rnd = random(1, nPart)
+              part_j => partTemp(rnd)%part
+              ij = interactionIndex(part_i%species%n, part_j%species%n)
+              sigmaVrelMaxNew = 0.D0
+              DO k = 1, interactionMatrix(ij)%amount
+                CALL interactionMatrix(ij)%collisions(k)%obj%collide(vol%sigmaVrelMax, sigmaVrelMaxNew, part_i, part_j)
 
-        END IF
+              END DO
 
-      END DO
+              !Update maximum cross section*v_rel per each collision
-      !$OMP END DO
+              IF (sigmaVrelMaxNew > vol%sigmaVrelMax) THEN
+                vol%sigmaVrelMax = sigmaVrelMaxNew
+
+              END IF
+
+            END DO
+
+          END IF
+
+        END DO
+        !$OMP END DO
+
+      END IF
 
     END SUBROUTINE doCollisions
 

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)