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Merge branch 'feature/collisionPairs' into feature/electromagnetic

Browse source 
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.
This commit is contained in:
Jorge Gonzalez 2022-04-23 20:48:34 +02:00
commit cbb5fe0bf2
12 changed files with 179 additions and 81 deletions
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4
src/modules/mesh/0D/moduleMesh0D.f90
View file

@ -63,6 +63,7 @@ MODULE moduleMesh0D
!Inits dummy 0D volume
SUBROUTINE initVol0D(self, n, p, nodes)
USE moduleRefParam
USE moduleSpecies
IMPLICIT NONE
CLASS(meshVol0D), INTENT(out):: self
@ -80,6 +81,9 @@ MODULE moduleMesh0D
CALL OMP_INIT_LOCK(self%lock)
ALLOCATE(self%listPart_in(1:nSpecies))
ALLOCATE(self%totalWeight(1:nSpecies))
END SUBROUTINE initVol0D
PURE FUNCTION getNodes0D(self) RESULT(n)

3
src/modules/mesh/1DCart/moduleMesh1DCart.f90
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@ -220,6 +220,9 @@ MODULE moduleMesh1DCart
CALL OMP_INIT_LOCK(self%lock)
ALLOCATE(self%listPart_in(1:nSpecies))
ALLOCATE(self%totalWeight(1:nSpecies))
END SUBROUTINE initVol1DCartSegm
!Calculates a random position in 1D volume

3
src/modules/mesh/1DRad/moduleMesh1DRad.f90
View file

@ -222,6 +222,9 @@ MODULE moduleMesh1DRad
CALL OMP_INIT_LOCK(self%lock)
ALLOCATE(self%listPart_in(1:nSpecies))
ALLOCATE(self%totalWeight(1:nSpecies))
END SUBROUTINE initVol1DRadSegm
!Calculates a random position in 1D volume

6
src/modules/mesh/2DCart/moduleMesh2DCart.f90
View file

@ -311,6 +311,9 @@ MODULE moduleMesh2DCart
CALL OMP_INIT_LOCK(self%lock)
ALLOCATE(self%listPart_in(1:nSpecies))
ALLOCATE(self%totalWeight(1:nSpecies))
END SUBROUTINE initVolQuad2DCart
!Computes element area
@ -638,6 +641,9 @@ MODULE moduleMesh2DCart
CALL OMP_INIT_LOCK(self%lock)
ALLOCATE(self%listPart_in(1:nSpecies))
ALLOCATE(self%totalWeight(1:nSpecies))
END SUBROUTINE initVolTria2DCart
!Random position in quadrilateral volume

6
src/modules/mesh/2DCyl/moduleMesh2DCyl.f90
View file

@ -299,6 +299,9 @@ MODULE moduleMesh2DCyl
CALL OMP_INIT_LOCK(self%lock)
ALLOCATE(self%listPart_in(1:nSpecies))
ALLOCATE(self%totalWeight(1:nSpecies))
END SUBROUTINE initVolQuad2DCyl
!Computes element area
@ -659,6 +662,9 @@ MODULE moduleMesh2DCyl
CALL OMP_INIT_LOCK(self%lock)
ALLOCATE(self%listPart_in(1:nSpecies))
ALLOCATE(self%totalWeight(1:nSpecies))
END SUBROUTINE initVolTria2DCyl
!Random position in quadrilateral volume

3
src/modules/mesh/3DCart/moduleMesh3DCart.f90
View file

@ -285,6 +285,9 @@ MODULE moduleMesh3DCart
CALL OMP_INIT_LOCK(self%lock)
ALLOCATE(self%listPart_in(1:nSpecies))
ALLOCATE(self%totalWeight(1:nSpecies))
END SUBROUTINE initVolTetra3DCart
!Random position in volume tetrahedron

162
src/modules/mesh/moduleMesh.f90
View file

@ -152,13 +152,13 @@ MODULE moduleMesh
!Volume
REAL(8):: volume = 0.D0
!List of particles inside the volume
TYPE(listNode):: listPart_in
TYPE(listNode), ALLOCATABLE:: listPart_in(:)
!Lock indicator for listPart_in
INTEGER(KIND=OMP_LOCK_KIND):: lock
!Number of collisions per volume
INTEGER:: nColl = 0
!Total weight of particles inside cell
REAL(8):: totalWeight = 0.D0
REAL(8), ALLOCATABLE:: totalWeight(:)
CONTAINS
PROCEDURE(initVol_interface), DEFERRED, PASS:: init
PROCEDURE(getNodesVol_interface), DEFERRED, PASS:: getNodes
@ -516,6 +516,7 @@ MODULE moduleMesh
CLASS(meshVol), OPTIONAL, INTENT(in):: oldCell
REAL(8):: xi(1:3)
CLASS(meshElement), POINTER:: nextElement
INTEGER:: sp
xi = self%phy2log(part%r)
!Checks if particle is inside 'self' cell
@ -525,8 +526,9 @@ MODULE moduleMesh
part%n_in = .TRUE.
!Assign particle to listPart_in
CALL OMP_SET_LOCK(self%lock)
CALL self%listPart_in%add(part)
self%totalWeight = self%totalWeight + part%weight
sp = part%species%n
CALL self%listPart_in(sp)%add(part)
self%totalWeight(sp) = self%totalWeight(sp) + part%weight
CALL OMP_UNSET_LOCK(self%lock)
ELSE
@ -586,6 +588,7 @@ MODULE moduleMesh
CLASS(meshVol), POINTER:: vol
REAL(8), DIMENSION(1:3):: xii
CLASS(meshElement), POINTER:: nextElement
INTEGER:: sp
found = .FALSE.
@ -595,8 +598,9 @@ MODULE moduleMesh
IF (vol%inside(xii)) THEN
part%volColl = vol%n
CALL OMP_SET_LOCK(vol%lock)
CALL vol%listPart_in%add(part)
vol%totalWeight = vol%totalWeight + part%weight
sp = part%species%n
CALL vol%listPart_in(sp)%add(part)
vol%totalWeight(sp) = vol%totalWeight(sp) + part%weight
CALL OMP_UNSET_LOCK(vol%lock)
found = .TRUE.
@ -660,13 +664,12 @@ MODULE moduleMesh
INTEGER, INTENT(in):: t
INTEGER:: e
CLASS(meshVol), POINTER:: vol
INTEGER:: nPart !Number of particles inside the cell
INTEGER:: k, nPairs, i, j
INTEGER:: nPart_i, nPart_j, nPart!Number of particles inside the cell
REAL(8):: pMax !Maximum probability of collision
TYPE(pointerArray), ALLOCATABLE:: partTemp(:)
INTEGER:: i, j !random particle indexes
TYPE(pointerArray), ALLOCATABLE:: partTemp_i(:), partTemp_j(:)
TYPE(particle), POINTER:: part_i, part_j
INTEGER:: n !collision
INTEGER:: ij, k
INTEGER:: n, c
REAL(8):: vRel, eRel
REAL(8):: sigmaVrelTotal
REAL(8), ALLOCATABLE:: sigmaVrel(:), probabilityColl(:)
@ -681,80 +684,111 @@ MODULE moduleMesh
realCollisions = 0
vol => self%vols(e)%obj
nPart = vol%listPart_in%amount
!Resets the number of collisions
vol%nColl = 0
!TODO: Simplify this, to many sublevels
!Iterate over the number of pairs
nPairs = SIZE(interactionMatrix) !TODO: This does not change, make a variable in a module
DO k = 1, nPairs
IF (interactionMatrix(k)%amount > 0) THEN
!Select the species for the collision pair
i = interactionMatrix(k)%sp_i%n
j = interactionMatrix(k)%sp_j%n
!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*tauColl/vol%volume
!Number of particles per species in the collision pair
nPart_i = vol%listPart_in(i)%amount
nPart_j = vol%listPart_in(j)%amount
!Number of collisions in the cell
vol%nColl = NINT(REAL(nPart)*pMax*0.5D0)
IF (nPart_i > 0 .AND. nPart_j > 0) THEN
!Total number of particles for the collision pair
nPart = nPart_i + nPart_j
IF (vol%nColl > 0) THEN
!Converts the list of particles to an array for easy access
partTemp = vol%listPart_in%convert2Array()
!Resets the number of collisions in the cell
vol%nColl = 0
END IF
!Probability of collision for pair i-j
pMax = (vol%totalWeight(i) + vol%totalWeight(j))*vol%sigmaVrelMax*tauColl/vol%volume
DO n = 1, vol%nColl
!Select random different particles
i = 0
j = 0
DO WHILE (i == j)
i = random(1, nPart)
j = random(1, nPart)
END DO
part_i => partTemp(i)%part
part_j => partTemp(j)%part
!TODO: I think that from here forward it can be passed to a procedure in interactionMatrix
ij = interactionIndex(part_i%species%n, part_j%species%n)
!Number of collisions in the cell
vol%nColl = NINT(REAL(nPart)*pMax*0.5D0)
IF (interactionMatrix(ij)%amount > 0) THEN
!Obtain the cross sections for the different processes
vRel = NORM2(part_i%v-part_j%v)
eRel = interactionMatrix(ij)%rMass*vRel**2
CALL interactionMatrix(ij)%getSigmaVrel(vRel, eRel, sigmaVrelTotal, sigmaVrel)
!Update maximum sigma*v_rel
IF (sigmaVrelTotal > vol%sigmaVrelMax) THEN
vol%sigmaVrelMax = sigmaVrelTotal
!Converts the list of particles to an array for easy access
IF (vol%nColl > 0) THEN
partTemp_i = vol%listPart_in(i)%convert2Array()
partTemp_j = vol%listPart_in(j)%convert2Array()
END IF
ALLOCATE(probabilityColl(0:interactionMatrix(ij)%amount))
probabilityColl(0) = 0.0
probabilityColl(1:interactionMatrix(ij)%amount) = sigmaVrel/vol%sigmaVrelMax
DO n = 1, vol%nColl
!Select random particles
part_i => NULL()
part_j => NULL()
rnd = random(1, nPart_i)
part_i => partTemp_i(rnd)%part
rnd = random(1, nPart_j)
part_j => partTemp_j(rnd)%part
!If they are the same particle, skip
!TODO: Maybe try to improve this
IF (ASSOCIATED(part_i, part_j)) THEN
CYCLE
!Selects random number between 0 and 1
rnd = random()
END IF
!If the random number is below the total probability of collision, do collisions
IF (rnd < sigmaVrelTotal / vol%sigmaVrelMax) THEN
!If particles do not belong to the species, skip collision
!This can happen, for example, if particle has been previously ionized or removed
!TODO: Try to find a way to no lose these collisions. Check new 'k' and use that for the collision, maybe?
IF (part_i%species%n /= i .OR. &
part_j%species%n /= j) THEN
CYCLE
!Loop over collisions
DO k = 1, interactionMatrix(ij)%amount
IF (SUM(probabilityColl(0:k-1)) + rnd <= probabilityColl(k)) THEN
CALL interactionMatrix(ij)%collisions(k)%obj%collide(part_i, part_j, vRel)
realCollisions = realCollisions + 1
END IF
END IF
!Obtain the cross sections for the different processes
!TODO: From here it might be a procedure in interactionMatrix
vRel = NORM2(part_i%v-part_j%v)
eRel = interactionMatrix(k)%rMass*vRel**2
CALL interactionMatrix(k)%getSigmaVrel(vRel, eRel, sigmaVrelTotal, sigmaVrel)
END DO
!Update maximum sigma*v_rel
IF (sigmaVrelTotal > vol%sigmaVrelMax) THEN
vol%sigmaVrelMax = sigmaVrelTotal
END IF
END IF
ALLOCATE(probabilityColl(0:interactionMatrix(k)%amount))
probabilityColl(0) = 0.0
probabilityColl(1:interactionMatrix(k)%amount) = sigmaVrel/vol%sigmaVrelMax
!Selects random number between 0 and 1
rnd = random()
!If the random number is below the total probability of collision, collide particles
IF (rnd < sigmaVrelTotal / vol%sigmaVrelMax) THEN
!Loop over collisions
DO c = 1, interactionMatrix(k)%amount
IF (SUM(probabilityColl(0:c-1)) + rnd <= probabilityColl(c)) THEN
CALL interactionMatrix(k)%collisions(c)%obj%collide(part_i, part_j, vRel)
realCollisions = realCollisions + 1
!A collision has ocurred, exit the loop
EXIT
END IF
END DO
END IF
!Deallocate arrays for next collision
DEALLOCATE(sigmaVrel, probabilityColl)
!Deallocate arrays for next collision
DEALLOCATE(sigmaVrel, probabilityColl)
END DO
END IF
END DO
END IF
END IF
END DO
vol%nColl = realCollisions

25
src/modules/moduleCollisions.f90
View file

@ -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

11
src/modules/moduleInput.f90
View file

@ -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

1
src/modules/moduleList.f90
View file

@ -71,6 +71,7 @@ MODULE moduleList
DO n=1, self%amount
!Point element in array to element in list
partArray(n)%part => tempNode%part
!Go to next element
tempNode => tempNode%next

32
src/modules/moduleSolver.f90
View file

@ -457,6 +457,7 @@ MODULE moduleSolver
INTEGER, SAVE:: nPartNew
INTEGER, SAVE:: nInjIn, nOldIn, nWScheme, nCollisions, nSurfaces
TYPE(particle), ALLOCATABLE, SAVE:: partTemp(:)
INTEGER:: s
!$OMP SECTIONS
!$OMP SECTION
@ -540,18 +541,30 @@ MODULE moduleSolver
END DO
!$OMP SECTION
!Erase the list of particles inside the cell
DO e = 1, mesh%numVols
mesh%vols(e)%obj%totalWeight = 0.D0
CALL mesh%vols(e)%obj%listPart_in%erase()
!Erase the list of particles inside the cell if particles have been pushed
DO s = 1, nSpecies
DO e = 1, mesh%numVols
IF (solver%pusher(s)%pushSpecies) THEN
CALL mesh%vols(e)%obj%listPart_in(s)%erase()
mesh%vols(e)%obj%totalWeight(s) = 0.D0
END IF
END DO
END DO
!$OMP SECTION
!Erase the list of particles inside the cell in coll mesh
DO e = 1, meshColl%numVols
meshColl%vols(e)%obj%totalWeight = 0.D0
CALL meshColl%vols(e)%obj%listPart_in%erase()
DO s = 1, nSpecies
DO e = 1, meshColl%numVols
IF (solver%pusher(s)%pushSpecies) THEN
CALL meshColl%vols(e)%obj%listPart_in(s)%erase()
meshColl%vols(e)%obj%totalWeight(s) = 0.D0
END IF
END DO
END DO
@ -685,6 +698,7 @@ MODULE moduleSolver
REAL(8):: newWeight
TYPE(particle), POINTER:: newPart
INTEGER:: p
INTEGER:: sp
newWeight = part%weight / nSplit
@ -697,12 +711,14 @@ MODULE moduleSolver
ALLOCATE(newPart)
!Copy data from original particle
newPart = part
!Add particle to list of new particles from weighting scheme
CALL OMP_SET_LOCK(lockWScheme)
CALL partWScheme%add(newPart)
CALL OMP_UNSET_LOCK(lockWScheme)
!Add particle to cell list
CALL OMP_SET_lock(vol%lock)
CALL vol%listPart_in%add(newPart)
sp = part%species%n
CALL vol%listPart_in(sp)%add(newPart)
CALL OMP_UNSET_lock(vol%lock)
END DO

4
src/modules/moduleSpecies.f90
View file

@ -91,7 +91,7 @@ MODULE moduleSpecies
part%species => self%ion
ELSE
CALL criticalError('No ion defined for species' // self%name, 'ionizeNeutral')
CALL criticalError('No ion defined for species :' // self%name, 'ionizeNeutral')
END IF
@ -109,7 +109,7 @@ MODULE moduleSpecies
part%species => self%ion
ELSE
CALL criticalError('No ion defined for species' // self%name, 'ionizeCharged')
CALL criticalError('No ion defined for species :' // self%name, 'ionizeCharged')
END IF