Minor improvement in mesh structure to allow different imput formats.

Organization of meshes per geometry type.
This commit is contained in:
Jorge Gonzalez 2020-12-08 18:28:24 +01:00
commit 3b125d0952
14 changed files with 158 additions and 100 deletions

View file

@ -0,0 +1,606 @@
!moduleMesh: General module for Finite Element mesh
MODULE moduleMesh
USE moduleList
USE moduleOutput
IMPLICIT NONE
!Parent of Node element
TYPE, PUBLIC, ABSTRACT:: meshNode
!Node index
INTEGER:: n = 0
!Node volume
REAL(8):: v = 0.D0
!Output values
TYPE(outputNode), ALLOCATABLE:: output(:)
TYPE(emNode):: emData
CONTAINS
PROCEDURE(initNode_interface), DEFERRED, PASS:: init
PROCEDURE(getCoord_interface), DEFERRED, PASS:: getCoordinates
END TYPE meshNode
ABSTRACT INTERFACE
!Interface of init a node (3D generic coordinates)
SUBROUTINE initNode_interface(self, n, r)
IMPORT:: meshNode
CLASS(meshNode), INTENT(out):: self
INTEGER, INTENT(in):: n
REAL(8), INTENT(in):: r(1:3)
END SUBROUTINE initNode_interface
!Interface to get coordinates from node
PURE FUNCTION getCoord_interface(self) RESULT(r)
IMPORT:: meshNode
CLASS(meshNode), INTENT(in):: self
REAL(8):: r(1:3)
END FUNCTION getCoord_interface
END INTERFACE
!Containers for nodes in the mesh
TYPE:: meshNodeCont
CLASS(meshNode), ALLOCATABLE:: obj
END TYPE meshNodeCont
!Parent of Edge element
TYPE, PUBLIC, ABSTRACT:: meshEdge
!Element index
INTEGER:: n = 0
!Connectivity to vols
CLASS(meshVol), POINTER:: e1 => NULL(), e2 => NULL()
!Normal vector
REAL(8):: normal(1:3)
!Physical surface in mesh
INTEGER:: physicalSurface
!id for boundary condition
INTEGER:: bt = 0
CONTAINS
PROCEDURE(initEdge_interface), DEFERRED, PASS:: init
PROCEDURE(boundary_interface), DEFERRED, PASS:: fBoundary
PROCEDURE(getNodesEdge_interface), DEFERRED, PASS:: getNodes
PROCEDURE(randPos_interface), DEFERRED, PASS:: randPos
END TYPE meshEdge
ABSTRACT INTERFACE
SUBROUTINE initEdge_interface(self, n, p, bt, physicalSurface)
IMPORT:: meshEdge
CLASS(meshEdge), INTENT(out):: self
INTEGER, INTENT(in):: n
INTEGER, INTENT(in):: p(:)
INTEGER, INTENT(in):: bt
INTEGER, INTENT(in):: physicalSurface
END SUBROUTINE initEdge_interface
SUBROUTINE boundary_interface(self, part)
USE moduleSpecies
IMPORT:: meshEdge
CLASS (meshEdge), INTENT(inout):: self
CLASS (particle), INTENT(inout):: part
END SUBROUTINE
PURE FUNCTION getNodesEdge_interface(self) RESULT(n)
IMPORT:: meshEdge
CLASS(meshEdge), INTENT(in):: self
INTEGER, ALLOCATABLE:: n(:)
END FUNCTION
FUNCTION randPos_interface(self) RESULT(r)
IMPORT:: meshEdge
CLASS(meshEdge), INTENT(in):: self
REAL(8):: r(1:3)
END FUNCTION randPos_interface
END INTERFACE
!Containers for edges in the mesh
TYPE:: meshEdgeCont
CLASS(meshEdge), ALLOCATABLE:: obj
END TYPE meshEdgeCont
!Parent of Volume element
TYPE, PUBLIC, ABSTRACT:: meshVol
!Volume index
INTEGER:: n = 0
!Maximum collision rate
REAL(8):: sigmaVrelMax = 1.D-15
!Volume
REAL(8):: volume = 0.D0
!List of particles inside the volume
TYPE(listNode):: 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
CONTAINS
PROCEDURE(initVol_interface), DEFERRED, PASS:: init
PROCEDURE(scatter_interface), DEFERRED, PASS:: scatter
PROCEDURE(gatherEF_interface), DEFERRED, PASS:: gatherEF
PROCEDURE(getNodesVol_interface), DEFERRED, PASS:: getNodes
PROCEDURE(elemF_interface), DEFERRED, PASS:: elemF
PROCEDURE, PASS:: findCell
PROCEDURE(phy2log_interface), DEFERRED, PASS:: phy2log
PROCEDURE(inside_interface), DEFERRED, NOPASS:: inside
PROCEDURE(nextElement_interface), DEFERRED, PASS:: nextElement
PROCEDURE, PASS:: collision
PROCEDURE(resetOutput_interface), DEFERRED, PASS:: resetOutput
END TYPE meshVol
ABSTRACT INTERFACE
SUBROUTINE initVol_interface(self, n, p)
IMPORT:: meshVol
CLASS(meshVol), INTENT(out):: self
INTEGER, INTENT(in):: n
INTEGER, INTENT(in):: p(:)
END SUBROUTINE initVol_interface
SUBROUTINE scatter_interface(self, part)
USE moduleSpecies
IMPORT:: meshVol
CLASS(meshVol), INTENT(in):: self
CLASS(particle), INTENT(in):: part
END SUBROUTINE scatter_interface
PURE FUNCTION gatherEF_interface(self, xi) RESULT(EF)
IMPORT:: meshVol
CLASS(meshVol), INTENT(in):: self
REAL(8), INTENT(in):: xi(1:3)
REAL(8):: EF(1:3)
END FUNCTION gatherEF_interface
PURE FUNCTION getNodesVol_interface(self) RESULT(n)
IMPORT:: meshVol
CLASS(meshVol), INTENT(in):: self
INTEGER, ALLOCATABLE:: n(:)
END FUNCTION getNodesVol_interface
PURE FUNCTION elemF_interface(self, source) RESULT(localF)
IMPORT:: meshVol
CLASS(meshVol), INTENT(in):: self
REAL(8), INTENT(in):: source(1:)
REAL(8), ALLOCATABLE:: localF(:)
END FUNCTION elemF_interface
SUBROUTINE nextElement_interface(self, xi, nextElement)
IMPORT:: meshVol
CLASS(meshVol), INTENT(in):: self
REAL(8), INTENT(in):: xi(1:3)
CLASS(*), POINTER, INTENT(out):: nextElement
END SUBROUTINE nextElement_interface
PURE FUNCTION phy2log_interface(self,r) RESULT(xN)
IMPORT:: meshVol
CLASS(meshVol), INTENT(in):: self
REAL(8), INTENT(in):: r(1:3)
REAL(8):: xN(1:3)
END FUNCTION phy2log_interface
PURE FUNCTION inside_interface(xi) RESULT(ins)
IMPORT:: meshVol
REAL(8), INTENT(in):: xi(1:3)
LOGICAL:: ins
END FUNCTION inside_interface
SUBROUTINE collision_interface(self)
IMPORT:: meshVol
CLASS(meshVol), INTENT(inout):: self
END SUBROUTINE collision_interface
PURE SUBROUTINE resetOutput_interface(self)
IMPORT:: meshVol
CLASS(meshVol), INTENT(inout):: self
END SUBROUTINE resetOutput_interface
END INTERFACE
!Containers for volumes in the mesh
TYPE:: meshVolCont
CLASS(meshVol), ALLOCATABLE:: obj
END TYPE meshVolCont
!Abstract type of mesh
TYPE, PUBLIC, ABSTRACT:: meshGeneric
INTEGER:: numEdges, numNodes, numVols
!Array of nodes
TYPE(meshNodeCont), ALLOCATABLE:: nodes(:)
!Array of boundary elements
TYPE(meshEdgeCont), ALLOCATABLE:: edges(:)
!Array of volume elements
TYPE(meshVolCont), ALLOCATABLE:: vols(:)
!Global stiffness matrix
REAL(8), ALLOCATABLE, DIMENSION(:,:):: K
!Permutation matrix for P L U factorization
INTEGER, ALLOCATABLE, DIMENSION(:,:):: IPIV
PROCEDURE(printOutput_interface), POINTER, PASS:: printOutput => NULL()
PROCEDURE(printColl_interface), POINTER, PASS:: printColl => NULL()
PROCEDURE(printEM_interface), POINTER, PASS:: printEM => NULL()
CONTAINS
PROCEDURE(initMesh_interface), DEFERRED, PASS:: init
PROCEDURE(readMesh_interface), DEFERRED, PASS:: readMesh
END TYPE meshGeneric
ABSTRACT INTERFACE
!Inits the mesh
SUBROUTINE initMesh_interface(self, meshFormat)
IMPORT meshGeneric
CLASS(meshGeneric), INTENT(out):: self
CHARACTER(:), ALLOCATABLE, INTENT(in):: meshFormat
END SUBROUTINE initMesh_interface
!Reads the mesh from a file
SUBROUTINE readMesh_interface(self, filename)
IMPORT meshGeneric
CLASS(meshGeneric), INTENT(inout):: self
CHARACTER(:), ALLOCATABLE, INTENT(in):: filename
END SUBROUTINE readMesh_interface
!Prints Species data
SUBROUTINE printOutput_interface(self, t)
IMPORT meshGeneric
CLASS(meshGeneric), INTENT(in):: self
INTEGER, INTENT(in):: t
END SUBROUTINE printOutput_interface
!Prints number of collisions
SUBROUTINE printColl_interface(self, t)
IMPORT meshGeneric
CLASS(meshGeneric), INTENT(in):: self
INTEGER, INTENT(in):: t
END SUBROUTINE printColl_interface
!Prints EM info
SUBROUTINE printEM_interface(self, t)
IMPORT meshGeneric
CLASS(meshGeneric), INTENT(in):: self
INTEGER, INTENT(in):: t
END SUBROUTINE printEM_interface
END INTERFACE
!Generic mesh
CLASS(meshGeneric), ALLOCATABLE, TARGET:: mesh
CONTAINS
!Find next cell for particle
RECURSIVE SUBROUTINE findCell(self, part, oldCell)
USE moduleSpecies
USE OMP_LIB
IMPLICIT NONE
CLASS(meshVol), INTENT(inout):: self
CLASS(meshVol), OPTIONAL, INTENT(in):: oldCell
CLASS(particle), INTENT(inout), TARGET:: part
REAL(8):: xi(1:3)
CLASS(*), POINTER:: nextElement
xi = self%phy2log(part%r)
!Checks if particle is inside 'self' cell
IF (self%inside(xi)) THEN
part%vol = self%n
part%xi = xi
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
CALL OMP_UNSET_LOCK(self%lock)
ELSE
!If not, searches for a neighbour and repeats the process.
CALL self%nextElement(xi, nextElement)
!Defines the next step
SELECT TYPE(nextElement)
CLASS IS(meshVol)
!Particle moved to new cell, repeat find procedure
CALL nextElement%findCell(part, self)
CLASS IS (meshEdge)
!Particle encountered an edge, execute boundary
CALL nextElement%fBoundary(part)
!If particle is still inside the domain, call findCell
IF (part%n_in) THEN
IF(PRESENT(oldCell)) THEN
CALL self%findCell(part, oldCell)
ELSE
CALL self%findCell(part)
END IF
END IF
CLASS DEFAULT
WRITE(*,*) "ERROR, CHECK findCell"
END SELECT
END IF
END SUBROUTINE findCell
!Computes collisions in element
SUBROUTINE collision(self)
USE moduleCollisions
USE moduleSpecies
USE moduleList
use moduleRefParam
IMPLICIT NONE
CLASS(meshVol), INTENT(inout):: self
INTEGER:: nPart !Number of particles inside the cell
REAL(8):: pMax !Maximum probability of collision
INTEGER:: rnd !random index
TYPE(particle), POINTER:: part_i, part_j
INTEGER:: n !collision
INTEGER:: ij, k
REAL(8):: sigmaVrelMaxNew
TYPE(pointerArray), ALLOCATABLE:: partTemp(:)
self%nColl = 0
nPart = self%listPart_in%amount
IF (nPart > 1) THEN
pMax = self%totalWeight*self%sigmaVrelMax*tauMin/self%volume
self%nColl = INT(REAL(nPart)*pMax*0.5D0)
!Converts the list of particles to an array for easy access
IF (self%nColl > 0) THEN
partTemp = self%listPart_in%convert2Array()
END IF
DO n = 1, self%nColl
!Select random numbers
rnd = 1 + FLOOR(nPart*RAND())
part_i => partTemp(rnd)%part
rnd = 1 + FLOOR(nPart*RAND())
part_j => partTemp(rnd)%part
ij = interactionIndex(part_i%sp, part_j%sp)
sigmaVrelMaxNew = 0.D0
DO k = 1, interactionMatrix(ij)%amount
CALL interactionMatrix(ij)%collisions(k)%obj%collide(self%sigmaVrelMax, sigmaVrelMaxNew, part_i, part_j)
END DO
!Update maximum cross section*v_rel per each collision
IF (sigmaVrelMaxNew > self%sigmaVrelMax) THEN
self%sigmaVrelMax = sigmaVrelMaxNew
END IF
END DO
END IF
self%totalWeight = 0.D0
!Reset output in nodes
CALL self%resetOutput()
!Erase the list of particles inside the cell
CALL self%listPart_in%erase()
END SUBROUTINE collision
SUBROUTINE printOutputGmsh(self, t)
USE moduleRefParam
USE moduleSpecies
USE moduleOutput
IMPLICIT NONE
CLASS(meshGeneric), INTENT(in):: self
INTEGER, INTENT(in):: t
INTEGER:: n, i
TYPE(outputFormat):: output(1:self%numNodes)
REAL(8):: time
CHARACTER(:), ALLOCATABLE:: fileName
CHARACTER (LEN=6):: tstring !TODO: Review to allow any number of iterations
time = DBLE(t)*tauMin*ti_ref
DO i = 1, nSpecies
WRITE(tstring, '(I6.6)') t
fileName='OUTPUT_' // tstring// '_' // species(i)%obj%name // '.msh'
WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
OPEN (60, file = path // folder // '/' // fileName)
WRITE(60, "(A)") '$MeshFormat'
WRITE(60, "(A)") '2.2 0 8'
WRITE(60, "(A)") '$EndMeshFormat'
WRITE(60, "(A)") '$NodeData'
WRITE(60, "(A)") '1'
WRITE(60, "(A)") '"Density (m^-3)"'
WRITE(60, *) 1
WRITE(60, *) time
WRITE(60, *) 3
WRITE(60, *) t
WRITE(60, *) 1
WRITE(60, *) self%numNodes
DO n=1, self%numNodes
CALL calculateOutput(self%nodes(n)%obj%output(i), output(n), self%nodes(n)%obj%v, species(i)%obj)
WRITE(60, "(I6,ES20.6E3)") n, output(n)%density
END DO
WRITE(60, "(A)") '$EndNodeData'
WRITE(60, "(A)") '$NodeData'
WRITE(60, "(A)") '1'
WRITE(60, "(A)") '"Velocity (m/s)"'
WRITE(60, *) 1
WRITE(60, *) time
WRITE(60, *) 3
WRITE(60, *) t
WRITE(60, *) 3
WRITE(60, *) self%numNodes
DO n=1, self%numNodes
WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%velocity
END DO
WRITE(60, "(A)") '$EndNodeData'
WRITE(60, "(A)") '$NodeData'
WRITE(60, "(A)") '1'
WRITE(60, "(A)") '"Pressure (Pa)"'
WRITE(60, *) 1
WRITE(60, *) time
WRITE(60, *) 3
WRITE(60, *) t
WRITE(60, *) 1
WRITE(60, *) self%numNodes
DO n=1, self%numNodes
WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%pressure
END DO
WRITE(60, "(A)") '$EndNodeData'
WRITE(60, "(A)") '$NodeData'
WRITE(60, "(A)") '1'
WRITE(60, "(A)") '"Temperature (K)"'
WRITE(60, *) 1
WRITE(60, *) time
WRITE(60, *) 3
WRITE(60, *) t
WRITE(60, *) 1
WRITE(60, *) self%numNodes
DO n=1, self%numNodes
WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%temperature
END DO
WRITE(60, "(A)") '$EndNodeData'
CLOSE (60)
END DO
END SUBROUTINE printOutputGmsh
SUBROUTINE printCollGmsh(self, t)
USE moduleRefParam
USE moduleCaseParam
USE moduleOutput
IMPLICIT NONE
CLASS(meshGeneric), INTENT(in):: self
INTEGER, INTENT(in):: t
INTEGER:: n
REAL(8):: time
CHARACTER(:), ALLOCATABLE:: fileName
CHARACTER (LEN=6):: tstring !TODO: Review to allow any number of iterations
IF (collOutput) THEN
time = DBLE(t)*tauMin*ti_ref
WRITE(tstring, '(I6.6)') t
fileName='OUTPUT_' // tstring// '_Collisions.msh'
WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
OPEN (60, file = path // folder // '/' // fileName)
WRITE(60, "(A)") '$MeshFormat'
WRITE(60, "(A)") '2.2 0 8'
WRITE(60, "(A)") '$EndMeshFormat'
WRITE(60, "(A)") '$ElementData'
WRITE(60, "(A)") '1'
WRITE(60, "(A)") '"Collisions"'
WRITE(60, *) 1
WRITE(60, *) time
WRITE(60, *) 3
WRITE(60, *) t
WRITE(60, *) 1
WRITE(60, *) self%numVols
DO n=1, self%numVols
WRITE(60, "(I6,I10)") n + self%numEdges, self%vols(n)%obj%nColl
END DO
WRITE(60, "(A)") '$EndElementData'
CLOSE(60)
END IF
END SUBROUTINE printCollGmsh
SUBROUTINE printEMGmsh(self, t)
USE moduleRefParam
USE moduleCaseParam
USE moduleOutput
IMPLICIT NONE
CLASS(meshGeneric), INTENT(in):: self
INTEGER, INTENT(in):: t
INTEGER:: n, e
REAL(8):: time
CHARACTER(:), ALLOCATABLE:: fileName
CHARACTER (LEN=6):: tstring !TODO: Review to allow any number of iterations
REAL(8):: xi(1:3)
xi = (/ 0.D0, 0.D0, 0.D0 /)
IF (emOutput) THEN
time = DBLE(t)*tauMin*ti_ref
WRITE(tstring, '(I6.6)') t
fileName='OUTPUT_' // tstring// '_EMField.msh'
WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
OPEN (20, file = path // folder // '/' // fileName)
WRITE(20, "(A)") '$MeshFormat'
WRITE(20, "(A)") '2.2 0 8'
WRITE(20, "(A)") '$EndMeshFormat'
WRITE(20, "(A)") '$NodeData'
WRITE(20, "(A)") '1'
WRITE(20, "(A)") '"Potential (V)"'
WRITE(20, *) 1
WRITE(20, *) time
WRITE(20, *) 3
WRITE(20, *) t
WRITE(20, *) 1
WRITE(20, *) self%numNodes
DO n=1, self%numNodes
WRITE(20, *) n, self%nodes(n)%obj%emData%phi*Volt_ref
END DO
WRITE(20, "(A)") '$EndNodeData'
WRITE(20, "(A)") '$ElementData'
WRITE(20, "(A)") '1'
WRITE(20, "(A)") '"Electric Field (V/m)"'
WRITE(20, *) 1
WRITE(20, *) time
WRITE(20, *) 3
WRITE(20, *) t
WRITE(20, *) 3
WRITE(20, *) self%numVols
DO e=1, self%numVols
WRITE(20, *) e+self%numEdges, self%vols(e)%obj%gatherEF(xi)*EF_ref
END DO
WRITE(20, "(A)") '$EndElementData'
CLOSE(20)
END IF
END SUBROUTINE printEMGmsh
END MODULE moduleMesh