Working on init for new physical surfaces

src/modules/init/moduleInput.f90

@@ -49,6 +49,9 @@ MODULE moduleInput
       CALL checkStatus(config, "readBoundaryEM")
 
       ! Read Physical Surfaces
+      call verboseError('Reading Physical Surfaces...')
+      call readPhysicalSurfaces(config)
+      call checkStatus(config, 'readPhysicalSurfaces')
 
       !Read Geometry
       CALL verboseError('Reading Geometry...')
@@ -895,6 +898,8 @@ MODULE moduleInput
         write(ps, '(I2)') ps
         object = 'physicalSurfaces(' // TRIM(bString) // ')'
 
+        allocate(physicalSurfaces(ps)%nodes(0))
+        allocate(physicalSurfaces(ps)%edges(0))
         call config%get(object // '.index', physicalSurfaces(ps)%index, found) 
         if (.not. found) then
           call criticalError('Physical surface index not found', 'readPhysicalSurfaces')

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

@@ -104,7 +104,7 @@ MODULE moduleMesh3DCart
 
     !EDGE FUNCTIONS
     !Init surface element
-    SUBROUTINE initEdge3DCartTria(self, n, p, btPart, btEM)
+    SUBROUTINE initEdge3DCartTria(self, n, p, ps)
       USE moduleSpecies, only: nSpecies
       USE moduleErrors
       USE moduleMath
@@ -114,8 +114,8 @@ MODULE moduleMesh3DCart
       CLASS(meshEdge3DCartTria), INTENT(out):: self
       INTEGER, INTENT(in):: n
       INTEGER, INTENT(in):: p(:)
-      INTEGER, INTENT(in):: btPart(1:nSpecies)
-      integer, intent(in):: btEM
+      INTEGER, INTENT(in):: ps
+      integer:: ps_index
       REAL(8), DIMENSION(1:3):: r1, r2, r3
       REAL(8), DIMENSION(1:3):: vec1, vec2
       INTEGER:: s
@@ -144,16 +144,8 @@ MODULE moduleMesh3DCart
 
       self%surface = 1.D0/L_ref**2 !TODO: FIX THIS WHEN MOVING TO 3D
 
-      !Boundary particle linking
-      allocate(self%boundariesParticle(1:nSpecies))
-      !Assign functions to particle boundary
-      do s = 1, nSpecies
-        self%boundariesParticle(s)%obj => boundariesParticle(btPart(s))%obj
+      ps_index = physicalSurface_to_index(ps)
       
-      end do
-
-      ! Add nodes to EM boundary
-      call boundariesEMLinking(btEM)%model%addNodes(self%getNodes(self%nNodes))
 
     END SUBROUTINE initEdge3DCartTria
 

src/modules/mesh/inout/vtu/moduleMeshInputVTU.f90

@@ -364,12 +364,8 @@ MODULE moduleMeshInputVTU
 
           END SELECT
 
-          !Associate boundary condition procedure.
-          btPart = physicalSurface_to_id(boundariesParticleLinking, entitiesID(n))
-          btEM   = physicalSurface_to_id(boundariesEMLinking,       entitiesID(n))
-
           !Init edge
-          CALL self%edges(e)%obj%init(n, p, boundariesParticleLinking(btPart)%speciesIndex, btEM)
+          CALL self%edges(e)%obj%init(n, p, entitiesID(n))
 
           DEALLOCATE(p)
 

src/modules/mesh/moduleMesh.f90

@@ -937,9 +937,27 @@ MODULE moduleMesh
     class(meshEdgePointer), allocatable:: edges(:)
     class(boundaryParticlePointer), allocatable:: particles(:)
     class(boundaryEMGeneric), pointer:: EM => null()
+    contains
+      procedure, pass:: addNode
+      procedure, pass:: addEdge
 
   end type
 
+  interface
+    module subroutine addNode(self, node)
+      class(physicalSurface), intent(inout):: self
+      integer, intent(in):: node
+
+    end subroutine addNode
+
+    module subroutine addEdge(self, edge)
+      class(physicalSurface), intent(inout):: self
+      integer, intent(in):: edge
+
+    end subroutine addEdge
+
+  end interface
+
   integer:: nPhysicalSurfaces
   type(physicalSurface), allocatable:: physicalSurfaces(:)
 

src/modules/mesh/moduleMesh@boundaryEM.f90

@@ -24,42 +24,6 @@ submodule(moduleMesh) boundaryEM
     
     end function boundaryEMName_to_Index
 
-    subroutine addNodes(self, nodes)
-      implicit none
-
-      class(boundaryEMGeneric), intent(inout):: self
-      integer, intent(in)::                     nodes(:)
-      integer:: n, nn, nNodes
-      logical:: inArray
-      type(meshNodePointer):: nodeToAdd
-
-
-      nNodes = size(nodes)
-      ! Collect all nodes that are not already in the boundary
-      DO n = 1, nNodes
-        nodeToAdd%obj => mesh%nodes(nodes(n))%obj
-        inArray = .false.
-        ! I cannot use the procedure 'any' for this
-        do nn = 1 , size(self%nodes)
-          IF (self%nodes(nn) == nodeToAdd) THEN
-            ! Node already in array
-            inArray = .true.
-            exit
-
-          end if
-
-        end do
-
-        if (.not. inArray) then
-          ! If not, add element to array of nodes
-          self%nodes = [self%nodes, nodeToAdd]
-
-        end if
-
-      end do
-
-    end subroutine addNodes
-
     module subroutine initBoundaryEM(self, config, object, b)
       use json_module
       use moduleErrors

src/modules/mesh/moduleMesh@surfaces.f90

@@ -19,4 +19,68 @@ submodule(moduleMesh) surfaces
 
     end function physicalSurface_to_index
 
+    subroutine addNode(self, node)
+      implicit none
+
+      class(physicalSurface), intent(inout):: self
+      integer, intent(in):: node
+      integer:: n, nn
+      logical:: inArray
+
+
+      associate(nodeToAdd => mesh%nodes(node)%obj)
+        inArray = .false.
+        ! I cannot use the procedure 'any' for this
+        do nn = 1 , size(self%nodes)
+          IF (self%nodes(nn)%obj == nodeToAdd) THEN
+            ! Node already in array
+            inArray = .true.
+            exit
+
+          end if
+
+        end do
+
+        if (.not. inArray) then
+          ! If not, add element to array of nodes
+          self%nodes = [self%nodes, nodeToAdd]
+
+        end if
+
+      end associate
+
+    end subroutine addNode
+
+    subroutine addEdge(self, edge)
+      implicit none
+
+      class(physicalSurface), intent(inout):: self
+      integer, intent(in):: edge
+      integer:: n, nn
+      logical:: inArray
+
+
+      associate(edgeToAdd => mesh%edges(edge)%obj)
+        inArray = .false.
+        ! I cannot use the procedure 'any' for this
+        do nn = 1 , size(self%edges)
+          IF (self%edges(nn) == edgeToAdd) THEN
+            ! Node already in array
+            inArray = .true.
+            exit
+
+          end if
+
+        end do
+
+        if (.not. inArray) then
+          ! If not, add element to array of nodes
+          self%edges = [self%edges, edgeToAdd]
+
+        end if
+
+      end associate
+
+    end subroutine addEdge
+
 end submodule surfaces