Minor improvement in mesh structure to allow different imput formats.

Organization of meshes per geometry type.

src/modules/makefile

@@ -1,46 +1,26 @@
 
-OBJS = moduleCaseParam.o moduleCompTime.o moduleList.o\
+OBJS = moduleCaseParam.o moduleCompTime.o moduleList.o \
-		   moduleMesh.o moduleMeshCyl.o moduleMeshCylBoundary.o\
+		   moduleOutput.o moduleInput.o moduleSolver.o \
-		   moduleMeshCylRead.o moduleOutput.o moduleInput.o \
+			 moduleCollisions.o moduleTable.o moduleParallel.o \
-		   moduleSolver.o moduleCollisions.o moduleTable.o \
+			 moduleEM.o 
-		   moduleParallel.o moduleEM.o moduleMesh1D.o \
-			 moduleMesh1DBoundary.o moduleMesh1DRead.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

src/modules/mesh/1DCart/makefile

@@ -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 $(OBJDIR)/$@
+

src/modules/mesh/1DCart/moduleMesh1D.f95

@@ -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
 

src/modules/mesh/1DCart/moduleMesh1DRead.f95

@@ -3,8 +3,10 @@ MODULE moduleMesh1DRead
   USE moduleMesh1D
   USE moduleMesh1DBoundary
   
+  !TODO: make this abstract to allow different mesh formats
   TYPE, EXTENDS(meshGeneric):: mesh1DGeneric
     CONTAINS
+      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)

src/modules/mesh/Cyl/makefile

@@ -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 $(OBJDIR)/$@
+

src/modules/mesh/Cyl/moduleMeshCyl.f95

@@ -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

src/modules/mesh/Cyl/moduleMeshCylRead.f95

@@ -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)
+    !Init mesh
-      USE moduleBoundary
+    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)

src/modules/mesh/makefile

@@ -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 $(OBJDIR)/$@
+

src/modules/mesh/moduleMesh.f95

@@ -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(initMesh_interface),    DEFERRED, PASS:: init
       PROCEDURE(readMesh_interface),    DEFERRED, PASS:: readMesh
-      PROCEDURE,                                 PASS:: printOutput
-      PROCEDURE,                                 PASS:: printColl
-      PROCEDURE,                                 PASS:: printEM
 
   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

src/modules/moduleInput.f95

@@ -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)
+      CALL config%get('geometry.meshType', meshFormat, found)
-      SELECT CASE(meshType)
+      CALL mesh%init(meshFormat)
-      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
-
       !Reads the mesh
+      CALL config%get('geometry.meshFile', meshFile, found)
       fullpath = path // meshFile
       CALL mesh%readMesh(fullPath)
 

src/modules/moduleSolver.f95

@@ -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
 
@@ -372,8 +367,11 @@ MODULE moduleSolver
     SUBROUTINE doEMField()
       IMPLICIT NONE
 
+      IF (ASSOCIATED(solver%solveEM)) THEN
         CALL solver%solveEM()
 
+      END IF
+
     END SUBROUTINE doEMField
 
     !Solving the Poisson equation for electrostatic potential
@@ -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
@@ -525,8 +505,11 @@ MODULE moduleSolver
       CALL volOld%findCell(part)
       volNew => mesh%vols(part%vol)%obj
       !Call the NA shcme
+      IF (ASSOCIATED(self%nonAnalogue)) THEN
         CALL self%nonAnalogue(part, volOld, volNew)
 
+      END IF
+
     END SUBROUTINE updateParticleCell
 
     !Update the information about if a species needs to be moved this iteration