Creating of nodes and edges in .vtu format

Moving forward making vtu an independent format.

Now fpakc can generate nodes and edges from vtu input.
Next step is cells.

Some minor corrections in gmsh2 format to unify statements.
The reading of meshes needs a good overhaul.

Testing all geometries with vtu is gonna be fun...

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

@@ -124,7 +124,6 @@ MODULE moduleMeshInputVTU
       DO WHILE (iStart < nData)
         iStart = iStart + 1
         iEnd   = iStart - 1 + block
-        PRINT *, iStart, iEnd
         IF (iEnd > nData) THEN
           iEnd = nData
 
@@ -173,6 +172,9 @@ MODULE moduleMeshInputVTU
       INTEGER:: numNodes, numElements
       INTEGER, ALLOCATABLE, DIMENSION(:):: entitiesID, offsets, connectivity, types
       REAL(8), ALLOCATABLE, DIMENSION(:):: coordinates
+      INTEGER:: n, e, c
+      INTEGER, ALLOCATABLE:: p(:)
+      INTEGER:: bt
 
       fileID = 10
 
@@ -200,6 +202,8 @@ MODULE moduleMeshInputVTU
       line = findline(fileID, 'Name="connectivity"')
       ALLOCATE(connectivity(1:MAXVAL(offsets)))
       CALL readDataBlock(fileID, MAXVAL(offsets), connectivity)
+      !Shift connectivity to start in 1
+      connectivity = connectivity + 1
       REWIND(fileID)
 
       !Get the type of elements
@@ -217,7 +221,164 @@ MODULE moduleMeshInputVTU
       CLOSE(fileID)
 
       !All relevant information from the .vtu file has been read. Time to build the mesh.
+      self%numNodes = numNodes
+      ALLOCATE(self%nodes(1:self%numNodes))
+      SELECT TYPE(self)
+      TYPE IS(meshParticles)
+        ALLOCATE(self%K(1:self%numNodes, 1:self%numNodes))
+        ALLOCATE(self%IPIV(1:self%numNodes, 1:self%numNodes))
+        self%K = 0.D0
+        self%IPIV = 0
 
+      END SELECT
+
+      DO n = 1, self%numNodes
+        !Get the coordinates for each direction
+        r(1) = coordinates(3*(n-1)+1)
+        r(2) = coordinates(3*(n-1)+2)
+        r(3) = coordinates(3*(n-1)+3)
+
+        SELECT CASE(self%dimen)
+        CASE(3)
+          ALLOCATE(meshNode3Dcart::self%nodes(n)%obj)
+
+        CASE(2)
+          SELECT CASE(self%geometry)
+          CASE("Cyl")
+            ALLOCATE(meshNode2DCyl:: self%nodes(n)%obj)
+
+          CASE("Cart")
+            ALLOCATE(meshNode2DCart:: self%nodes(n)%obj)
+
+          END SELECT
+
+          r(3) = 0.D0
+
+        CASE(1)
+          SELECT CASE(self%geometry)
+          CASE("Rad")
+            ALLOCATE(meshNode1DRad:: self%nodes(n)%obj)
+
+          CASE("Cart")
+            ALLOCATE(meshNode1DCart:: self%nodes(n)%obj)
+
+          END SELECT
+          r(2:3) = 0.D0
+
+        END SELECT
+        CALL self%nodes(n)%obj%init(n, r)
+
+      END DO
+
+      !Count the number of edges
+      SELECT TYPE(self)
+      TYPE IS(meshParticles)
+        SELECT CASE(self%dimen)
+        CASE(3)
+          !Edges are triangles, type 5 in VTK
+          self%numEdges = COUNT(types==5)
+        
+        CASE(2)
+          !Edges are segments, type 3 in VTK
+          self%numEdges = COUNT(types==3)
+
+        CASE(1)
+          !Edges are nodes, type 1 in VTK
+          self%numEdges = COUNT(types==1)
+        
+        END SELECT
+
+        self%numCells = numElements - self%numEdges
+        !Allocate array of edges
+        ALLOCATE(self%edges(1:self%numEdges))
+
+      TYPE IS(meshCollisions)
+        self%numCells = numElements
+
+      END SELECT
+
+      !Allocates array of cells
+      ALLOCATE(self%cells(1:self%numCells))
+
+      !Read edges
+      e = 0
+      c = 0
+      SELECT TYPE(self)
+      TYPE IS(meshParticles)
+        DO n = 1, numElements
+          SELECT CASE(self%dimen)
+          CASE(3)
+            IF (types(n) == 5) THEN
+              e = e + 1
+              ALLOCATE(meshEdge3DCartTria:: self%edges(e)%obj)
+              ALLOCATE(p(1:3))
+
+              p(1) = connectivity(offsets(n) - 2)
+              p(2) = connectivity(offsets(n) - 1)
+              p(3) = connectivity(offsets(n))
+
+              !Associate boundary condition procedure.
+              bt = getBoundaryId(entitiesID(n))
+
+              !Allocate edge
+              CALL self%edges(e)%obj%init(n, p, bt, entitiesID(n))
+              DEALLOCATE(p)
+
+            END IF
+
+          CASE(2)
+            IF (types(n) == 3) THEN
+              e = e+1
+              ALLOCATE(p(1:2))
+              p(1) = connectivity(offsets(n) - 1)
+              p(2) = connectivity(offsets(n))
+
+              !Associate boundary condition procedure.
+              bt = getBoundaryId(entitiesID(n))
+
+              SELECT CASE(self%geometry)
+              CASE("Cyl")
+                ALLOCATE(meshEdge2DCyl:: self%edges(e)%obj)
+
+              CASE("Cart")
+                ALLOCATE(meshEdge2DCart:: self%edges(e)%obj)
+
+              END SELECT
+
+              !Allocate edge
+              CALL self%edges(e)%obj%init(n, p, bt, entitiesID(n))
+              DEALLOCATE(p)
+
+            END IF
+
+          CASE(1)
+            IF (types(n) == 3) THEN
+              e = e + 1
+              ALLOCATE(p(1:1))
+              p(1) = connectivity(offsets(n))
+
+              !Associate boundary condition procedure.
+              bt = getBoundaryId(entitiesID(n))
+              SELECT CASE(self%geometry)
+              CASE("Rad")
+                ALLOCATE(meshEdge1DRad:: self%edges(e)%obj)
+
+              CASE("Cart")
+                ALLOCATE(meshEdge1DCart:: self%edges(e)%obj)
+
+              END SELECT
+
+              CALL self%edges(e)%obj%init(n, p, bt, entitiesID(n))
+              DEALLOCATE(p)
+
+            END IF
+
+          END SELECT
+
+        END DO
+
+      END SELECT
+        
     END SUBROUTINE readVTU
 
     SUBROUTINE readInitialVTU(filename, density, velocity, temperature)