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Minor improvement in mesh structure to allow different imput formats.

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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
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2
makefile
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@ -9,7 +9,7 @@ JSONDIR := $(TOPDIR)/json-fortran-8.2.0/build
JSONLIB := $(JSONDIR)/lib/libjsonfortran.a
JSONINC := $(JSONDIR)/include
INCDIR :=
INCDIR :=
INCDIR += $(JSONINC)
VAR := ""

46
src/modules/makefile
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@ -1,46 +1,26 @@
OBJS = moduleCaseParam.o moduleCompTime.o moduleList.o\
moduleMesh.o moduleMeshCyl.o moduleMeshCylBoundary.o\
moduleMeshCylRead.o moduleOutput.o moduleInput.o \
moduleSolver.o moduleCollisions.o moduleTable.o \
moduleParallel.o moduleEM.o moduleMesh1D.o \
moduleMesh1DBoundary.o moduleMesh1DRead.o
OBJS = moduleCaseParam.o moduleCompTime.o moduleList.o \
moduleOutput.o moduleInput.o moduleSolver.o \
moduleCollisions.o moduleTable.o moduleParallel.o \
moduleEM.o
all: $(OBJS)
all: $(OBJS) mesh.o
moduleCollisions.o: moduleTable.o moduleSpecies.o moduleRefParam.o moduleConstParam.o moduleMeshCyl.f95
mesh.o: moduleCollisions.o moduleBoundary.o
$(MAKE) -C mesh all
moduleCollisions.o: moduleTable.o moduleSpecies.o moduleRefParam.o moduleConstParam.o moduleCollisions.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleInput.o: moduleParallel.o moduleRefParam.o moduleCaseParam.o moduleSolver.o moduleInject.o moduleBoundary.o moduleMesh.o moduleMeshCylRead.o moduleMesh1DRead.o moduleErrors.o moduleSpecies.o moduleInput.f95
moduleInput.o: moduleParallel.o moduleRefParam.o moduleCaseParam.o moduleSolver.o moduleInject.o moduleBoundary.o moduleErrors.o moduleSpecies.o moduleInput.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleInject.o: moduleSpecies.o moduleSolver.o moduleMesh.o moduleMeshCyl.o moduleInject.f95
moduleInject.o: moduleSpecies.o moduleSolver.o moduleInject.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleList.o: moduleSpecies.o moduleErrors.o moduleList.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleMesh.o: moduleCollisions.o moduleOutput.o moduleList.o moduleSpecies.o moduleMesh.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleMeshCyl.o: moduleRefParam.o moduleCollisions.o moduleOutput.o moduleMesh.o moduleMeshCyl.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleMeshCylBoundary.o: moduleMeshCyl.o moduleMeshCylBoundary.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleMeshCylRead.o: moduleBoundary.o moduleMeshCyl.o moduleMeshCylBoundary.o moduleMeshCylRead.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleMesh1D.o: moduleRefParam.o moduleCollisions.o moduleOutput.o moduleMesh.o moduleMesh1D.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleMesh1DBoundary.o: moduleMesh1D.o moduleMesh1DBoundary.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleMesh1DRead.o: moduleBoundary.o moduleMesh1D.o moduleMesh1DBoundary.o moduleMesh1DRead.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleOutput.o: moduleSpecies.o moduleRefParam.o moduleOutput.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
@ -50,13 +30,13 @@ moduleRefParam.o: moduleConstParam.o moduleRefParam.f95
moduleSpecies.o: moduleErrors.o moduleCaseParam.o moduleSpecies.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleSolver.o: moduleList.o moduleEM.o moduleSpecies.o moduleRefParam.o moduleMesh.o moduleOutput.o moduleSolver.f95
moduleSolver.o: mesh.o moduleList.o moduleEM.o moduleSpecies.o moduleRefParam.o moduleOutput.o moduleSolver.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleTable.o: moduleErrors.o moduleTable.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleEM.o: moduleSpecies.o moduleMesh.o moduleEM.f95
moduleEM.o: mesh.o moduleSpecies.o moduleEM.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
%.o: %.f95

11
src/modules/mesh/1DCart/makefile Normal file
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@ -0,0 +1,11 @@
all: moduleMesh1D.o moduleMesh1DBoundary.o moduleMesh1DRead.o
moduleMesh1D.o: moduleMesh1D.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleMesh1DBoundary.o: moduleMesh1D.o moduleMesh1DBoundary.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleMesh1DRead.o: moduleMesh1D.o moduleMesh1DBoundary.o moduleMesh1DRead.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@

6
src/modules/moduleMesh1D.f95 → src/modules/mesh/1DCart/moduleMesh1D.f95
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@ -109,10 +109,10 @@ MODULE moduleMesh1D
END SUBROUTINE initNode1D
FUNCTION getCoord1D(self) RESULT(r)
PURE FUNCTION getCoord1D(self) RESULT(r)
IMPLICIT NONE
CLASS(meshNode1D):: self
CLASS(meshNode1D), INTENT(in):: self
REAL(8):: r(1:3)
r = (/ self%x, 0.D0, 0.D0 /)
@ -369,7 +369,7 @@ MODULE moduleMesh1D
END FUNCTION gatherEFSegm
!Get nodes from segment
!Get nodes from 1D volume
PURE FUNCTION getNodesSegm(self) RESULT(n)
IMPLICIT NONE

0
src/modules/moduleMesh1DBoundary.f95 → src/modules/mesh/1DCart/moduleMesh1DBoundary.f95
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29
src/modules/moduleMesh1DRead.f95 → src/modules/mesh/1DCart/moduleMesh1DRead.f95
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@ -3,9 +3,11 @@ MODULE moduleMesh1DRead
USE moduleMesh1D
USE moduleMesh1DBoundary
!TODO: make this abstract to allow different mesh formats
TYPE, EXTENDS(meshGeneric):: mesh1DGeneric
CONTAINS
PROCEDURE, PASS:: readMesh => readMesh1D
PROCEDURE, PASS:: init => init1DMesh
PROCEDURE, PASS:: readMesh => readMesh1D
END TYPE
@ -15,11 +17,34 @@ MODULE moduleMesh1DRead
END INTERFACE connected
CONTAINS
!Init 1D mesh
SUBROUTINE init1DMesh(self, meshFormat)
USE moduleMesh
USE moduleErrors
IMPLICIT NONE
CLASS(mesh1DGeneric), INTENT(out):: self
CHARACTER(:), ALLOCATABLE, INTENT(in):: meshFormat
SELECT CASE(meshFormat)
CASE ("gmsh")
self%printOutput => printOutputGmsh
self%printColl => printCollGmsh
self%printEM => printEMGmsh
CASE DEFAULT
CALL criticalError("Mesh type " // meshFormat // " not supported.", "init1D")
END SELECT
END SUBROUTINE init1DMesh
!Reads 1D mesh
SUBROUTINE readMesh1D(self, filename)
USE moduleBoundary
IMPLICIT NONE
CLASS(mesh1DGeneric), INTENT(out):: self
CLASS(mesh1DGeneric), INTENT(inout):: self
CHARACTER(:), ALLOCATABLE, INTENT(in):: filename
REAL(8):: x
INTEGER:: p(1:2)

11
src/modules/mesh/Cyl/makefile Normal file
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@ -0,0 +1,11 @@
all : moduleMeshCyl.o moduleMeshCylBoundary.o moduleMeshCylRead.o
moduleMeshCyl.o: moduleMeshCyl.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleMeshCylBoundary.o: moduleMeshCyl.o moduleMeshCylBoundary.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@
moduleMeshCylRead.o: moduleMeshCyl.o moduleMeshCylBoundary.o moduleMeshCylRead.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@

10
src/modules/moduleMeshCyl.f95 → src/modules/mesh/Cyl/moduleMeshCyl.f95
View file

@ -154,10 +154,10 @@ MODULE moduleMeshCyl
END SUBROUTINE initNodeCyl
FUNCTION getCoordCyl(self) RESULT(r)
PURE FUNCTION getCoordCyl(self) RESULT(r)
IMPLICIT NONE
CLASS(meshNodeCyl):: self
CLASS(meshNodeCyl), INTENT(in):: self
REAL(8):: r(1:3)
r = (/self%z, self%r, 0.D0/)
@ -367,7 +367,7 @@ MODULE moduleMeshCyl
REAL(8):: r, xi(1:3)
REAL(8):: fPsi(1:4), dPsi(1:2,1:4)
REAL(8):: ke(1:4,1:4)
REAL(8):: j(1:2,1:2), detJ
REAL(8):: invJ(1:2,1:2), detJ
INTEGER:: l, m
ke=0.D0
@ -381,9 +381,9 @@ MODULE moduleMeshCyl
dPsi(2,:) = self%dPsiXi2(xi(1))
fPsi = self%fPsi(xi)
detJ = self%detJac(xi,dPsi)
j = self%invJac(xi,dPsi)
invJ = self%invJac(xi,dPsi)
r = DOT_PRODUCT(fPsi,self%r)
ke = ke + MATMUL(TRANSPOSE(MATMUL(j,dPsi)),MATMUL(j,dPsi))*r*wQuad(l)*wQuad(m)/detJ
ke = ke + MATMUL(TRANSPOSE(MATMUL(invJ,dPsi)),MATMUL(invJ,dPsi))*r*wQuad(l)*wQuad(m)/detJ
END DO
END DO

0
src/modules/moduleMeshCylBoundary.f95 → src/modules/mesh/Cyl/moduleMeshCylBoundary.f95
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33
src/modules/moduleMeshCylRead.f95 → src/modules/mesh/Cyl/moduleMeshCylRead.f95
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@ -3,9 +3,11 @@ MODULE moduleMeshCylRead
USE moduleMeshCyl
USE moduleMeshCylBoundary
!TODO: make this abstract to allow different mesh formats
TYPE, EXTENDS(meshGeneric):: meshCylGeneric
CONTAINS
PROCEDURE, PASS:: readMesh => readMeshCyl
PROCEDURE, PASS:: init => initCylMesh
PROCEDURE, PASS:: readMesh => readMeshCylGmsh
END TYPE
@ -15,11 +17,34 @@ MODULE moduleMeshCylRead
END INTERFACE connected
CONTAINS
SUBROUTINE readMeshCyl(self, filename)
USE moduleBoundary
!Init mesh
SUBROUTINE initCylMesh(self, meshFormat)
USE moduleMesh
USE moduleErrors
IMPLICIT NONE
CLASS(meshCylGeneric), INTENT(out):: self
CHARACTER(:), ALLOCATABLE, INTENT(in):: meshFormat
SELECT CASE(meshFormat)
CASE ("gmsh")
self%printOutput => printOutputGmsh
self%printColl => printCollGmsh
self%printEM => printEMGmsh
CASE DEFAULT
CALL criticalError("Mesh type " // meshFormat // " not supported.", "initCylMesh")
END SELECT
END SUBROUTINE initCylMesh
!Read mesh from gmsh file
SUBROUTINE readMeshCylGmsh(self, filename)
USE moduleBoundary
IMPLICIT NONE
CLASS(meshCylGeneric), INTENT(inout):: self
CHARACTER(:), ALLOCATABLE, INTENT(in):: filename
REAL(8):: r, z
INTEGER:: p(1:4)
@ -140,7 +165,7 @@ MODULE moduleMeshCylRead
END DO
END SUBROUTINE
END SUBROUTINE readMeshCylGmsh
!Selects type of elements to build connection
SUBROUTINE connectedVolVol(elemA, elemB)

11
src/modules/mesh/makefile Normal file
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@ -0,0 +1,11 @@
all: moduleMesh.o Cyl.o 1DCart.o
Cyl.o:
$(MAKE) -C Cyl all
1DCart.o:
$(MAKE) -C 1DCart all
moduleMesh.o: moduleMesh.f95
$(FC) $(FCFLAGS) -c $(subst .o,.f95,$@) -o $(OBJDIR)/$@

48
src/modules/moduleMesh.f95 → src/modules/mesh/moduleMesh.f95
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@ -30,9 +30,9 @@ MODULE moduleMesh
END SUBROUTINE initNode_interface
!Interface to get coordinates from node
FUNCTION getCoord_interface(self) RESULT(r)
PURE FUNCTION getCoord_interface(self) RESULT(r)
IMPORT:: meshNode
CLASS(meshNode):: self
CLASS(meshNode), INTENT(in):: self
REAL(8):: r(1:3)
END FUNCTION getCoord_interface
@ -210,7 +210,7 @@ MODULE moduleMesh
END SUBROUTINE collision_interface
SUBROUTINE resetOutput_interface(self)
PURE SUBROUTINE resetOutput_interface(self)
IMPORT:: meshVol
CLASS(meshVol), INTENT(inout):: self
@ -237,25 +237,44 @@ MODULE moduleMesh
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(readMesh_interface), DEFERRED, PASS:: readMesh
PROCEDURE, PASS:: printOutput
PROCEDURE, PASS:: printColl
PROCEDURE, PASS:: printEM
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(out):: self
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
@ -273,6 +292,7 @@ MODULE moduleMesh
INTEGER, INTENT(in):: t
END SUBROUTINE printEM_interface
END INTERFACE
!Generic mesh
@ -397,7 +417,7 @@ MODULE moduleMesh
END SUBROUTINE collision
SUBROUTINE printOutput(self, t)
SUBROUTINE printOutputGmsh(self, t)
USE moduleRefParam
USE moduleSpecies
USE moduleOutput
@ -478,9 +498,9 @@ MODULE moduleMesh
END DO
END SUBROUTINE printOutput
END SUBROUTINE printOutputGmsh
SUBROUTINE printColl(self, t)
SUBROUTINE printCollGmsh(self, t)
USE moduleRefParam
USE moduleCaseParam
USE moduleOutput
@ -522,9 +542,9 @@ MODULE moduleMesh
END IF
END SUBROUTINE printColl
END SUBROUTINE printCollGmsh
SUBROUTINE printEM(self, t)
SUBROUTINE printEMGmsh(self, t)
USE moduleRefParam
USE moduleCaseParam
USE moduleOutput
@ -581,6 +601,6 @@ MODULE moduleMesh
END IF
END SUBROUTINE printEM
END SUBROUTINE printEMGmsh
END MODULE moduleMesh

16
src/modules/moduleInput.f95
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@ -369,7 +369,7 @@ MODULE moduleInput
TYPE(json_file), INTENT(inout):: config
LOGICAL:: found
CHARACTER(:), ALLOCATABLE:: geometryType, meshType, meshFile
CHARACTER(:), ALLOCATABLE:: geometryType, meshFormat, meshFile
CHARACTER(:), ALLOCATABLE:: fullPath
!Selects the type of geometry.
@ -389,18 +389,10 @@ MODULE moduleInput
END SELECT
!Gets the type of mesh
CALL config%get('geometry.meshType', meshType, found)
SELECT CASE(meshType)
CASE ("gmsh")
!Gets the gmsh file
CALL config%get('geometry.meshFile', meshFile, found)
CASE DEFAULT
CALL criticalError("Mesh type " // meshType // " not supported.", "readGeometry")
END SELECT
CALL config%get('geometry.meshType', meshFormat, found)
CALL mesh%init(meshFormat)
!Reads the mesh
CALL config%get('geometry.meshFile', meshFile, found)
fullpath = path // meshFile
CALL mesh%readMesh(fullPath)

35
src/modules/moduleSolver.f95
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@ -95,9 +95,6 @@ MODULE moduleSolver
CASE('Electrostatic')
self%solveEM => solveElecField
CASE DEFAULT
self%solveEM => noEMField
END SELECT
END SUBROUTINE initEM
@ -114,9 +111,6 @@ MODULE moduleSolver
CASE ('Volume')
self%nonAnalogue => volumeNAScheme
CASE DEFAULT
self%nonAnalogue => noNAScheme
END SELECT
END SUBROUTINE initNA
@ -356,6 +350,7 @@ MODULE moduleSolver
SUBROUTINE doScatter
USE moduleSpecies
USE moduleMesh
IMPLICIT NONE
INTEGER:: n
@ -372,7 +367,10 @@ MODULE moduleSolver
SUBROUTINE doEMField()
IMPLICIT NONE
CALL solver%solveEM()
IF (ASSOCIATED(solver%solveEM)) THEN
CALL solver%solveEM()
END IF
END SUBROUTINE doEMField
@ -421,12 +419,6 @@ MODULE moduleSolver
END SUBROUTINE solveElecField
!Empty procedure that does no computation of EM field for neutral cases
SUBROUTINE noEMField()
IMPLICIT NONE
END SUBROUTINE noEMField
!Modify particle weight as a function of cell volume and splits particle
SUBROUTINE volumeNAScheme(part, volOld, volNew)
USE moduleSpecies
@ -500,18 +492,6 @@ MODULE moduleSolver
END SUBROUTINE splitParticle
!Empty procedure that does no computation of EM field for neutral cases
SUBROUTINE noNAScheme(part, volOld, volNew)
USE moduleSpecies
USE moduleMesh
IMPLICIT NONE
TYPE(particle), INTENT(inout):: part
CLASS(meshVol), POINTER, INTENT(in):: volOld
CLASS(meshVol), POINTER, INTENT(inout):: volNew
END SUBROUTINE noNAScheme
SUBROUTINE updateParticleCell(self, part)
USE moduleSpecies
USE moduleMesh
@ -525,7 +505,10 @@ MODULE moduleSolver
CALL volOld%findCell(part)
volNew => mesh%vols(part%vol)%obj
!Call the NA shcme
CALL self%nonAnalogue(part, volOld, volNew)
IF (ASSOCIATED(self%nonAnalogue)) THEN
CALL self%nonAnalogue(part, volOld, volNew)
END IF
END SUBROUTINE updateParticleCell