First version of vtu file format

After some testing and making things a bit better and more general, I am
quite happy with the implementation of vtu and it seems that it is
working (at least as good as Gmsh2).

There are some procedures that might be useful for other XML-like
formats that might be moved in the future to the common module (I am
    thinking right now in the implementation of a general format like
    XDMF3).

doc/user-manual/fpakc_UserManual.tex

@@ -448,10 +448,11 @@ make
                                \end{itemize}
           \item \textbf{meshType}: Character.
                                    Format of mesh file.
+                                   The output will be written in the same format as specified here.
                                    Accepted formats are:
                                    \begin{itemize}
-                                     \item \textbf{gmsh2}: \Gls{gmsh} file format in version 2.0.
+                                     \item \textbf{gmsh2}: \Gls{gmsh} file format in version 2.0. This has to be in ASCII format.
-                                     \item \textbf{vtu}: \Gls{vtu} file format.
+                                     \item \textbf{vtu}: \Gls{vtu} file format. This has to be in ASCII format.
                                    \end{itemize}
           \item \textbf{meshFile}: Character.
                                    Mesh filename.

src/makefile

@@ -5,6 +5,7 @@ OBJECTS = $(OBJDIR)/moduleMesh.o $(OBJDIR)/moduleMeshBoundary.o $(OBJDIR)/module
 			  	$(OBJDIR)/moduleCollisions.o $(OBJDIR)/moduleTable.o $(OBJDIR)/moduleParallel.o \
 			  	$(OBJDIR)/moduleEM.o $(OBJDIR)/moduleRandom.o $(OBJDIR)/moduleMath.o \
 					$(OBJDIR)/moduleProbe.o $(OBJDIR)/moduleAverage.o \
+					$(OBJDIR)/moduleMeshInoutCommon.o \
 			  	$(OBJDIR)/moduleMeshInputVTU.o $(OBJDIR)/moduleMeshOutputVTU.o \
 			  	$(OBJDIR)/moduleMeshInputGmsh2.o $(OBJDIR)/moduleMeshOutputGmsh2.o \
 			  	$(OBJDIR)/moduleMeshInput0D.o $(OBJDIR)/moduleMeshOutput0D.o \

src/modules/mesh/inout/gmsh2/moduleMeshOutputGmsh2.f90

@@ -85,6 +85,7 @@ MODULE moduleMeshOutputGmsh2
       USE moduleRefParam
       USE moduleSpecies
       USE moduleOutput
+      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
@@ -93,13 +94,11 @@ MODULE moduleMeshOutputGmsh2
       TYPE(outputFormat):: output(1:self%numNodes)
       REAL(8):: time
       CHARACTER(:), ALLOCATABLE:: fileName
-      CHARACTER (LEN=iterationDigits):: tstring
 
       time = DBLE(t)*tauMin*ti_ref
 
       DO i = 1, nSpecies
-        WRITE(tstring, iterationFormat) t
+        fileName = formatFileName(prefix, species(i)%obj%name, 'msh', t)
-        fileName= 'OUTPUT_' // tstring// '_' // species(i)%obj%name // '.msh'
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (60, file = path // folder // '/' //  fileName)
 
@@ -142,6 +141,7 @@ MODULE moduleMeshOutputGmsh2
       USE moduleCaseParam
       USE moduleCollisions
       USE moduleOutput
+      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(in):: self
@@ -151,7 +151,6 @@ MODULE moduleMeshOutputGmsh2
       INTEGER:: n
       REAL(8):: time
       CHARACTER(:), ALLOCATABLE:: fileName
-      CHARACTER (LEN=iterationDigits):: tString
       CHARACTER(:), ALLOCATABLE:: title
       CHARACTER (LEN=2):: cString
 
@@ -169,9 +168,8 @@ MODULE moduleMeshOutputGmsh2
 
       IF (collOutput) THEN
         time = DBLE(t)*tauMin*ti_ref
-        WRITE(tString, iterationFormat) t
 
-        fileName='OUTPUT_' // tString// '_Collisions.msh'
+        fileName = formatFileName(prefix, 'Collisions', 'msh', t)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (60, file = path // folder // '/' //  fileName)
 
@@ -203,6 +201,7 @@ MODULE moduleMeshOutputGmsh2
       USE moduleRefParam
       USE moduleCaseParam
       USE moduleOutput
+      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
@@ -210,16 +209,14 @@ MODULE moduleMeshOutputGmsh2
       INTEGER:: n, e
       REAL(8):: time
       CHARACTER(:), ALLOCATABLE:: fileName
-      CHARACTER (LEN=iterationDigits):: tstring
       REAL(8):: Xi(1:3)
 
       Xi = (/ 0.D0, 0.D0, 0.D0 /)
 
       IF (emOutput) THEN
         time = DBLE(t)*tauMin*ti_ref
-        WRITE(tstring, iterationFormat) t
 
-        fileName='OUTPUT_' // tstring// '_EMField.msh'
+        fileName = formatFileName(prefix, 'Collisions', 'msh', t)
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (20, file = path // folder // '/' //  fileName)
 
@@ -256,6 +253,7 @@ MODULE moduleMeshOutputGmsh2
       USE moduleSpecies
       USE moduleOutput
       USE moduleAverage
+      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
@@ -265,11 +263,11 @@ MODULE moduleMeshOutputGmsh2
       INTEGER:: fileMean=10, fileDeviation=20
 
       DO i = 1, nSpecies
-        fileName= 'Average_mean_' // species(i)%obj%name // '.msh'
+        fileName = formatFileName('Average_mean', species(i)%obj%name, 'msh')
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (fileMean, file = path // folder // '/' //  fileName)
 
-        fileName= 'Average_deviation_' // species(i)%obj%name // '.msh'
+        fileName = formatFileName('Average_deviation', species(i)%obj%name, 'msh')
         WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
         OPEN (filedeviation, file = path // folder // '/' //  fileName)
 

src/modules/mesh/inout/makefile

@@ -1,6 +1,6 @@
 all: vtu.o gmsh2.o 0D.o
 
-vtu.o:
+vtu.o: moduleMeshInoutCommon.o
 	$(MAKE) -C vtu all
 
 gmsh2.o:
@@ -8,3 +8,6 @@ gmsh2.o:
 
 0D.o:
 	$(MAKE) -C 0D all
+
+%.o: %.f90
+	$(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@

src/modules/mesh/inout/moduleMeshInoutCommon.f90

@@ -0,0 +1,27 @@
+MODULE moduleMeshInoutCommon
+
+  CHARACTER(LEN=4):: prefix = 'Step'
+
+  CONTAINS
+    PURE FUNCTION formatFileName(prefix, suffix, extension, t) RESULT(fileName)
+      USE moduleOutput
+      IMPLICIT NONE
+
+      CHARACTER(*), INTENT(in):: prefix, suffix, extension
+      INTEGER, INTENT(in), OPTIONAL:: t
+      CHARACTER (LEN=iterationDigits):: tString
+      CHARACTER(:), ALLOCATABLE:: fileName
+
+      IF (PRESENT(t)) THEN
+        WRITE(tString, iterationFormat) t
+        fileName = prefix //  '_' // tString // '_' // suffix // '.' // extension
+
+      ELSE
+        fileName = prefix //  '_' // suffix // '.' // extension
+
+      END IF
+
+    END FUNCTION formatFileName
+
+
+END MODULE moduleMeshInoutCommon

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

@@ -1,29 +1,7 @@
 MODULE moduleMeshOutputVTU
 
-  CHARACTER(LEN=6):: prefix = 'OUTPUT'
-
   CONTAINS
 
-    PURE FUNCTION formatFileName(prefix, suffix, extension, t) RESULT(fileName)
-      USE moduleOutput
-      IMPLICIT NONE
-
-      CHARACTER(*), INTENT(in):: prefix, suffix, extension
-      INTEGER, INTENT(in), OPTIONAL:: t
-      CHARACTER (LEN=iterationDigits):: tString
-      CHARACTER(:), ALLOCATABLE:: fileName
-
-      IF (PRESENT(t)) THEN
-        WRITE(tString, iterationFormat) t
-        fileName = prefix //  '_' // tString // '_' // suffix // '.' // extension
-
-      ELSE
-        fileName = prefix //  '_' // suffix // '.' // extension
-
-      END IF
-
-    END FUNCTION formatFileName
-
     SUBROUTINE writeHeader(nNodes, nCells, fileID)
       USE moduleMesh
       IMPLICIT NONE
@@ -332,6 +310,7 @@ MODULE moduleMeshOutputVTU
     SUBROUTINE printOutputVTU(self,t)
       USE moduleMesh
       USE moduleSpecies
+      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
@@ -358,7 +337,7 @@ MODULE moduleMeshOutputVTU
         CLOSE(fileID)
 
         !Write collection file for time plotting
-        fileNameCollection = formatFileName(prefix, 'Collection_' // species(i)%obj%name, 'pvd')
+        fileNameCollection = formatFileName('Collection', species(i)%obj%name, 'pvd')
         CALL writeCollection(fileID, t, fileName, filenameCollection)
 
       END DO
@@ -368,6 +347,7 @@ MODULE moduleMeshOutputVTU
     SUBROUTINE printCollVTU(self,t)
       USE moduleMesh
       USE moduleOutput
+      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(in):: self
@@ -395,7 +375,7 @@ MODULE moduleMeshOutputVTU
         CLOSE(fileID)
 
         !Write collection file for time plotting
-        fileNameCollection = formatFileName(prefix, 'Collection_Collisions', 'pvd')
+        fileNameCollection = formatFileName('Collection', 'Collisions', 'pvd')
         CALL writeCollection(fileID, t, fileName, filenameCollection)
 
       END IF
@@ -404,6 +384,7 @@ MODULE moduleMeshOutputVTU
 
     SUBROUTINE printEMVTU(self, t)
       USE moduleMesh
+      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
@@ -429,7 +410,7 @@ MODULE moduleMeshOutputVTU
         CLOSE(fileID)
 
         !Write collection file for time plotting
-        fileNameCollection = formatFileName(prefix, 'Collection_EMField', 'pvd')
+        fileNameCollection = formatFileName('Collection', 'EMField', 'pvd')
         CALL writeCollection(fileID, t, fileName, filenameCollection)
 
       END IF
@@ -439,6 +420,7 @@ MODULE moduleMeshOutputVTU
     SUBROUTINE printAverageVTU(self)
       USE moduleMesh
       USE moduleSpecies
+      USE moduleMeshInoutCommon
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self