New functions to read VTU

Added a few functions to read .vtu meshes.

Output in .vtu changed to output data in 6 columns (seems to be the
    standard.)

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

@@ -1,8 +1,138 @@
-MODULE moduleMeshInputVTK
+MODULE moduleMeshInputVTU
   !Reads mesh in the VTU format
 
+  INTERFACE getValueFromLine
+    MODULE PROCEDURE getIntegerFromLine, getRealFromLine
+
+  END INTERFACE
+
   CONTAINS
-    SUBROUTINE initVTK(self)
+    FUNCTION findLine(fileID, text) RESULT(line)
+      USE moduleErrors
+      IMPLICIT NONE
+      
+      INTEGER, INTENT(in):: fileID
+      CHARACTER(*):: text
+      CHARACTER(LEN=256):: line
+      INTEGER:: error, found
+
+      error = 0
+      found = 0
+      !Reads all the file to find the 'text' string in a line
+      DO WHILE(error == 0 .AND. found == 0)
+        READ(fileID, "(A)", IOSTAT=error) line
+        found = INDEX(line, text)
+        IF (found > 0) THEN
+          EXIT
+
+        END IF
+      END DO
+
+      !If no line is found, return an error
+      IF (found == 0) THEN
+        CALL criticalError('String ' // text // ' not found in file.', 'findLine')
+
+      END IF
+
+    END FUNCTION findLine
+
+    SUBROUTINE getIntegerFromLine(line, label, valueInteger)
+      USE moduleErrors
+      IMPLICIT NONE
+
+      CHARACTER(LEN=256), INTENT(in):: line
+      CHARACTER(*), INTENT(in):: label
+      INTEGER, INTENT(out):: valueInteger
+      INTEGER:: labelStart, valueStart, valueEnd
+
+      labelStart = 0
+      labelStart = INDEX(line, label)
+      IF (labelStart == 0) THEN
+        CALL criticalError('Label '// label // ' not found in line', 'getValueFromLine')
+
+      END IF
+      valueStart = INDEX(line(labelStart:256), '"') + labelStart
+      valueEnd   = INDEX(line(valueStart:256), '"') + valueStart - 2
+      READ(line(valueStart:valueEnd), '(I10)') valueInteger
+
+    END SUBROUTINE getIntegerFromLine
+    
+    SUBROUTINE getRealFromLine(line, label, valueReal)
+      USE moduleErrors
+      IMPLICIT NONE
+
+      CHARACTER(LEN=256), INTENT(in):: line
+      CHARACTER(*), INTENT(in):: label
+      REAL(8), INTENT(out):: valueReal
+      INTEGER:: labelStart, valueStart, valueEnd
+
+      labelStart = 0
+      labelStart = INDEX(line, label)
+      IF (labelStart == 0) THEN
+        CALL criticalError('Label '// label // ' not found in line', 'getValueFromLine')
+
+      END IF
+      valueStart = INDEX(line(labelStart:256), '"') + labelStart
+      valueEnd   = INDEX(line(valueStart:256), '"') + valueStart - 2
+      READ(line(valueStart:valueEnd), '(F16.14)') valueReal
+
+    END SUBROUTINE getRealFromLine
+
+    SUBROUTINE readIntegerBlock(fileID, nData, array)
+      IMPLICIT NONE
+
+      INTEGER, INTENT(in):: fileID
+      INTEGER, INTENT(in):: nData
+      INTEGER, INTENT(out):: array(1:nData)
+      INTEGER:: iStart, iEnd, block
+
+      iStart = 0
+      iEnd = 0
+      block = 6 !Assumes block of data in 6 columns
+
+      DO WHILE (iStart < nData)
+        iStart = iStart + 1
+        iEnd   = iStart - 1 + block
+        PRINT *, iStart, iEnd
+        IF (iEnd > nData) THEN
+          iEnd = nData
+
+        END IF
+        READ(fileID, *) array(iStart:iEnd)
+        iStart = iEnd
+
+      END DO
+
+    END SUBROUTINE readIntegerBlock
+
+    SUBROUTINE readRealBlock(fileID, nData, array)
+      IMPLICIT NONE
+
+      INTEGER, INTENT(in):: fileID
+      INTEGER, INTENT(in):: nData
+      REAL(8), INTENT(out):: array(1:nData)
+      INTEGER:: iStart, iEnd, block
+
+      iStart = 0
+      iEnd = 0
+      block = 6 !Assumes block of data in 6 columns
+
+      DO WHILE (iStart < nData)
+        iStart = iStart + 1
+        iEnd   = iStart - 1 + block
+        PRINT *, iStart, iEnd
+        IF (iEnd > nData) THEN
+          iEnd = nData
+
+        END IF
+        READ(fileID, *) array(iStart:iEnd)
+        iStart = iEnd
+
+      END DO
+
+    END SUBROUTINE readRealBlock
+
+    SUBROUTINE initVTU(self)
       USE moduleMesh
       USE moduleMeshOutputVTU
       IMPLICIT NONE
@@ -20,7 +150,7 @@ MODULE moduleMeshInputVTK
       END SELECT
       self%readMesh    => readVTU
 
-    END SUBROUTINE initVTK
+    END SUBROUTINE initVTU
 
     SUBROUTINE readVTU(self, filename)
       USE moduleMesh3DCart
@@ -34,6 +164,34 @@ MODULE moduleMeshInputVTK
       CLASS(meshGeneric), INTENT(inout):: self
       CHARACTER(:), ALLOCATABLE, INTENT(in):: filename
       REAL(8):: r(1:3) !3 generic coordinates
+      INTEGER:: fileID, error, found
+      CHARACTER(LEN=256):: line
+      INTEGER:: numNodes, numElements
+      INTEGER, ALLOCATABLE, DIMENSION(:):: entitiesID, offsets
+
+      fileID = 10
+
+      OPEN(fileID, FILE=TRIM(filename))
+
+      !Find the number of nodes and elements (edges+cells) in the mesh.
+      line = findLine(fileID, '<Piece')
+      CALL getValueFromLine(line, 'NumberOfPoints', numNodes)
+      CALL getValueFromLine(line, 'NumberOfCells', numElements)
+      REWIND(fileID)
+
+      !Get the IDs of the cells to identify physical surfaces
+      line = findLine(fileID, 'Name="CellEntityIds"')
+      ALLOCATE(entitiesID(1:numElements))
+      CALL readIntegerBlock(fileID, numElements, entitiesID)
+      REWIND(fileID)
+
+      !Get the offsets to read connectivity
+      line = findLine(fileID, 'Name="offsets"')
+      ALLOCATE(offsets(1:numElements))
+      CALL readIntegerBlock(fileID, numElements, offsets)
+      REWIND(fileID)
+
+      CLOSE(fileID)
 
     END SUBROUTINE readVTU
 
@@ -47,4 +205,4 @@ MODULE moduleMeshInputVTK
 
     END SUBROUTINE readInitialVTU
 
-END MODULE moduleMeshInputVTK
+END MODULE moduleMeshInputVTU