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fpakc/src/modules/mesh/inout/vtu/moduleMeshOutputVTU.f90
Jorge Gonzalez 2c55913501 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).
2023-02-07 16:02:36 +01:00

461 lines
16 KiB
Fortran
Raw Blame History

MODULE moduleMeshOutputVTU
CONTAINS
SUBROUTINE writeHeader(nNodes, nCells, fileID)
USE moduleMesh
IMPLICIT NONE
INTEGER, INTENT(in):: nNodes, nCells
INTEGER, INTENT(in):: fileID
WRITE(fileID,"(A)") '<?xml version="1.0"?>'
WRITE(fileID,"(2X, A)") '<VTKFile type="UnstructuredGrid">'
WRITE(fileID,"(4X, A,ES20.6E3,A)") '<UnstructuredGrid>'
WRITE(fileID,"(6X, A, I10, A, I10, A)") '<Piece NumberOfPoints="', nNodes, '" NumberOfCells="', nCells, '">'
END SUBROUTINE writeHeader
SUBROUTINE writeFooter(fileID)
IMPLICIT NONE
INTEGER, INTENT(in):: fileID
WRITE(fileID,"(6X, A)") '</Piece>'
WRITE(fileID,"(4X, A)") '</UnstructuredGrid>'
WRITE(fileID,"(2X, A)") '</VTKFile>'
END SUBROUTINE writeFooter
FUNCTION getCellType(cell) RESULT(indexType)
USE moduleMesh3DCart
USE moduleMesh2DCyl
USE moduleMesh2DCart
USE moduleMesh1DRad
USE moduleMesh1DCart
USE moduleMesh0D
USE moduleErrors
IMPLICIT NONE
CLASS(meshCell), INTENT(in):: cell
INTEGER:: indexType
indexType = 0
SELECT TYPE(cell)
TYPE IS(meshCell3DCartTetra)
indexType = 10
TYPE IS(meshCell2DCylQuad)
indexType = 9
TYPE IS(meshCell2DCartQuad)
indexType = 9
TYPE IS(meshCell2DCylTria)
indexType = 5
TYPE IS(meshCell2DCartTria)
indexType = 5
TYPE IS(meshCell1DRadSegm)
indexType = 3
TYPE IS(meshCell1DCartSegm)
indexType = 3
TYPE IS(meshCell0D)
indexType = 1
CLASS DEFAULT
CALL criticalError('Cell not valid for VTU output', 'getCellType')
END SELECT
END FUNCTION getCellType
SUBROUTINE writeMesh(self, fileID)
USE moduleMesh
USE moduleRefParam
IMPLICIT NONE
CLASS(meshGeneric), INTENT(in):: self
INTEGER, INTENT(in):: fileID
INTEGER:: e
INTEGER:: offset(1:self%numCells), types(1:self%numCells)
!Write nodes coordinates
WRITE(fileID, "(8X, A)") '<Points>'
WRITE(fileID, "(10X,A)") '<DataArray type="Float32" NumberOfComponents="3" format="ascii">'
WRITE(fileID, "(6(ES20.6E3))") (self%nodes(e)%obj%getCoordinates()*L_ref, e = 1, self%numNodes)
WRITE(fileID, "(10X, A)") '</DataArray>'
WRITE(fileID, "(8X, A)") '</Points>'
WRITE(fileID, "(8X, A)") '<Cells>'
!Write nodes connectivity of each cell
WRITE(fileID, "(10X,A)") '<DataArray type="Int32" Name="connectivity" format="ascii">'
WRITE(fileID, "(6(I10))") (self%cells(e)%obj%getNodes(self%cells(e)%obj%nNodes) - 1, e = 1, self%numCells) !Array starts on 0
WRITE(fileID, "(10X, A)") '</DataArray>'
!Write offset of each cell
offset(1) = self%cells(1)%obj%nNodes
WRITE(fileID, "(10X,A)") '<DataArray type="Int32" Name="offsets" format="ascii">'
DO e = 2, self%numCells
offset(e) = offset(e - 1) + self%cells(e)%obj%nNodes
END DO
WRITE(fileID, "(6(I10))") offset
WRITE(fileID, "(10X, A)") '</DataArray>'
!Write type of each cell
WRITE(fileID, "(10X,A)") '<DataArray type="Int32" Name="types" format="ascii">'
DO e = 1, self%numCells
types(e) = getCellType(self%cells(e)%obj)
END DO
WRITE(fileID, "(6(I10))") types
WRITE(fileID, "(10X, A)") '</DataArray>'
WRITE(fileID, "(8X, A)") '</Cells>'
END SUBROUTINE writeMesh
SUBROUTINE writeSpeciesOutput(self, fileID, speciesIndex)
USE moduleMesh
USE moduleOutput
IMPLICIT NONE
CLASS(meshParticles), INTENT(in):: self
INTEGER, INTENT(in):: fileID
INTEGER, INTENT(in):: speciesIndex
TYPE(outputFormat):: output(1:self%numNodes)
INTEGER:: n
DO n = 1, self%numNodes
CALL calculateOutput(self%nodes(n)%obj%output(speciesIndex), output(n), self%nodes(n)%obj%v, species(speciesIndex)%obj)
END DO
!Write node data
WRITE(fileID,"(8X,A)") '<PointData>'
!Write density
WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Density (m^-3)" NumberOfComponents="1">'
WRITE(fileID,"(6(ES20.6E3))") (output(n)%density, n = 1, self%numNodes)
WRITE(fileID,"(10X,A)") '</DataArray>'
!Write velocity
WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Velocity (m s^-1)" NumberOfComponents="3">'
WRITE(fileID,"(6(ES20.6E3))") (output(n)%velocity, n = 1, self%numNodes)
WRITE(fileID,"(10X,A)") '</DataArray>'
!Write pressure
WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Pressure (Pa)" NumberOfComponents="1">'
WRITE(fileID,"(6(ES20.6E3))") (output(n)%pressure, n = 1, self%numNodes)
WRITE(fileID,"(10X,A)") '</DataArray>'
!Write temperature
WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Temperature (K)" NumberOfComponents="1">'
WRITE(fileID,"(6(ES20.6E3))") (output(n)%temperature, n = 1, self%numNodes)
WRITE(fileID,"(10X,A)") '</DataArray>'
!End node data
WRITE(fileID,"(8X,A)") '</PointData>'
END SUBROUTINE writeSpeciesOutput
SUBROUTINE writeCollOutput(self,fileID)
USE moduleMesh
USE moduleCollisions
IMPLICIT NONE
CLASS(meshGeneric), INTENT(in):: self
INTEGER, INTENT(in):: fileID
INTEGER:: k, c, n
CHARACTER(:), ALLOCATABLE:: title
CHARACTER (LEN=2):: cString
WRITE(fileID,"(8X,A)") '<CellData>'
DO k = 1, nCollPairs
DO c = 1, interactionMatrix(k)%amount
WRITE(cString, "(I2)") c
title = 'Pair ' // interactionMatrix(k)%sp_i%name // '-' // interactionMatrix(k)%sp_j%name // ' collision ' // cString
WRITE(fileID,"(10X,A, A, A)") '<DataArray type="Float64" Name="',title, '" NumberOfComponents="1">'
WRITE(fileID, "(6(I10))") (self%cells(n)%obj%tallyColl(k)%tally(c), n = 1, self%numCells)
WRITE(fileID, "(10X, A)") '</DataArray>'
END DO
END DO
WRITE(fileID,"(8X,A)") '</CellData>'
END SUBROUTINE writeCollOutput
SUBROUTINE writeEM(self, fileID)
USE moduleMesh
USE moduleRefParam
IMPLICIT NONE
CLASS(meshParticles), INTENT(in):: self
INTEGER, INTENT(in):: fileID
INTEGER:: n
REAL(8):: Xi(1:3)
!Points in nodes
WRITE(fileID,"(8X,A)") '<PointData>'
!Electric potential
WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Potential (V)" NumberOfComponents="1">'
WRITE(fileID,"(6(ES20.6E3))") (self%nodes(n)%obj%emData%phi*Volt_ref, n = 1, self%numNodes)
WRITE(fileID,"(10X,A)") '</DataArray>'
!Magnetic Field
WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Magnetic Field (T)" NumberOfComponents="3">'
WRITE(fileID,"(6(ES20.6E3))") (self%nodes(n)%obj%emData%B*B_ref, n = 1, self%numNodes)
WRITE(fileID,"(10X,A)") '</DataArray>'
WRITE(fileID,"(8X,A)") '</PointData>'
!Cell Data
Xi = (/ 0.D0, 0.D0, 0.D0 /)
WRITE(fileID,"(8X,A)") '<CellData>'
!Electric field
WRITE(fileID,"(10X,A, A, A)") '<DataArray type="Float64" Name="Electric Field (V m^-1)" NumberOfComponents="3">'
WRITE(fileID, "(6(ES20.6E3))") (self%cells(n)%obj%gatherElectricField(Xi)*EF_ref, n = 1, self%numCells)
WRITE(fileID,"(10X,A)") '</DataArray>'
WRITE(fileID,"(8X,A)") '</CellData>'
END SUBROUTINE writeEM
SUBROUTINE writeCollection(fileID, t, fileNameStep, fileNameCollection)
USE moduleCaseParam
USE moduleOutput
USE moduleRefParam
IMPLICIT NONE
INTEGER:: fileID
INTEGER, INTENT(in):: t
CHARACTER(*):: fileNameStep, fileNameCollection
IF (t == tInitial) THEN
!Create collection file
WRITE(*, "(6X,A15,A)") "Creating file: ", fileNameCollection
OPEN (fileID + 1, file = path // folder // '/' // fileNameCollection)
WRITE (fileID + 1, "(A)") '<VTKFile type="Collection">'
WRITE (fileID + 1, "(2X, A)") '<Collection>'
CLOSE(fileID + 1)
END IF
!Write iteration file in collection
OPEN (fileID + 1, file = path // folder // '/' // fileNameCollection, ACCESS='APPEND')
WRITE(fileID + 1, "(4X, A, ES20.6E3, A, A, A)") '<DataSet timestep="', DBLE(t)*tauMin*ti_ref,'" file="', fileNameStep,'"/>'
!Close collection file
IF (t == tFinal) THEN
WRITE (fileID + 1, "(2X, A)") '</Collection>'
WRITE (fileID + 1, "(A)") '</VTKFile>'
END IF
CLOSE(fileID + 1)
END SUBROUTINE writeCollection
SUBROUTINE writeAverage(self, fileIDMean, fileIDDeviation, speciesIndex)
USE moduleMesh
USE moduleOutput
USE moduleAverage
IMPLICIT NONE
CLASS(meshParticles), INTENT(in):: self
INTEGER, INTENT(in):: fileIDMean, fileIDDeviation
INTEGER, INTENT(in):: speciesIndex
TYPE(outputFormat):: outputMean(1:self%numNodes)
TYPE(outputFormat):: outputDeviation(1:self%numNodes)
INTEGER:: n
DO n = 1, self%numNodes
CALL calculateOutput(averageScheme(n)%mean%output(speciesIndex), outputMean(n), &
self%nodes(n)%obj%v, species(speciesIndex)%obj)
CALL calculateOutput(averageScheme(n)%deviation%output(speciesIndex), outputDeviation(n), &
self%nodes(n)%obj%v, species(speciesIndex)%obj)
END DO
!Write node data
WRITE(fileIDMean, "(8X,A)") '<PointData>'
WRITE(fileIDDeviation,"(8X,A)") '<PointData>'
!Write density
WRITE(fileIDMean, "(10X,A)") '<DataArray type="Float64" Name="Density, mean (m^-3)" NumberOfComponents="1">'
WRITE(fileIDDeviation,"(10X,A)") '<DataArray type="Float64" Name="Density, deviation (m^-3)" NumberOfComponents="1">'
WRITE(fileIDMean, "(6(ES20.6E3))") (outputMean(n)%density, n = 1, self%numNodes)
WRITE(fileIDDeviation,"(6(ES20.6E3))") (outputDeviation(n)%density, n = 1, self%numNodes)
WRITE(fileIDMean,"(10X,A)") '</DataArray>'
WRITE(fileIDDeviation,"(10X,A)") '</DataArray>'
!Write velocity
WRITE(fileIDMean, "(10X,A)") '<DataArray type="Float64" Name="Velocity, mean (m s^-1)" NumberOfComponents="3">'
WRITE(fileIDDeviation,"(10X,A)") '<DataArray type="Float64" Name="Velocity, deviation (m s^-1)" NumberOfComponents="3">'
WRITE(fileIDMean, "(6(ES20.6E3))") (outputMean(n)%velocity, n = 1, self%numNodes)
WRITE(fileIDDeviation,"(6(ES20.6E3))") (outputDeviation(n)%velocity, n = 1, self%numNodes)
WRITE(fileIDMean, "(10X,A)") '</DataArray>'
WRITE(fileIDDeviation,"(10X,A)") '</DataArray>'
!Write pressure
WRITE(fileIDMean, "(10X,A)") '<DataArray type="Float64" Name="Pressure, mean (Pa)" NumberOfComponents="1">'
WRITE(fileIDDeviation,"(10X,A)") '<DataArray type="Float64" Name="Pressure, deviation (Pa)" NumberOfComponents="1">'
WRITE(fileIDMean, "(6(ES20.6E3))") (outputMean(n)%pressure, n = 1, self%numNodes)
WRITE(fileIDDeviation,"(6(ES20.6E3))") (outputDeviation(n)%pressure, n = 1, self%numNodes)
WRITE(fileIDMean, "(10X,A)") '</DataArray>'
WRITE(fileIDDeviation,"(10X,A)") '</DataArray>'
!Write temperature
WRITE(fileIDMean, "(10X,A)") '<DataArray type="Float64" Name="Temperature, mean (K)" NumberOfComponents="1">'
WRITE(fileIDDeviation,"(10X,A)") '<DataArray type="Float64" Name="Temperature, deviation (K)" NumberOfComponents="1">'
WRITE(fileIDMean, "(6(ES20.6E3))") (outputMean(n)%temperature, n = 1, self%numNodes)
WRITE(fileIDDeviation,"(6(ES20.6E3))") (outputDeviation(n)%temperature, n = 1, self%numNodes)
WRITE(fileIDMean, "(10X,A)") '</DataArray>'
WRITE(fileIDDeviation,"(10X,A)") '</DataArray>'
!End node data
WRITE(fileIDMean, "(8X,A)") '</PointData>'
WRITE(fileIDDeviation,"(8X,A)") '</PointData>'
END SUBROUTINE writeAverage
SUBROUTINE printOutputVTU(self,t)
USE moduleMesh
USE moduleSpecies
USE moduleMeshInoutCommon
IMPLICIT NONE
CLASS(meshParticles), INTENT(in):: self
INTEGER, INTENT(in):: t
INTEGER:: n, i, fileID
CHARACTER(:), ALLOCATABLE:: fileName, fileNameCollection
TYPE(outputFormat):: output(1:self%numNodes)
fileID = 60
DO i = 1, nSpecies
fileName = formatFileName(prefix, species(i)%obj%name, 'vtu', t)
WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
OPEN (fileID, file = path // folder // '/' // fileName)
CALL writeHeader(self%numNodes, self%numCells, fileID)
CALL writeMesh(self, fileID)
CALL writeSpeciesOutput(self, fileID, i)
CALL writeFooter(fileID)
CLOSE(fileID)
!Write collection file for time plotting
fileNameCollection = formatFileName('Collection', species(i)%obj%name, 'pvd')
CALL writeCollection(fileID, t, fileName, filenameCollection)
END DO
END SUBROUTINE printOutputVTU
SUBROUTINE printCollVTU(self,t)
USE moduleMesh
USE moduleOutput
USE moduleMeshInoutCommon
IMPLICIT NONE
CLASS(meshGeneric), INTENT(in):: self
INTEGER, INTENT(in):: t
INTEGER:: n, i, fileID
CHARACTER(:), ALLOCATABLE:: fileName, fileNameCollection
CHARACTER (LEN=iterationDigits):: tstring
TYPE(outputFormat):: output(1:self%numNodes)
fileID = 62
IF (collOutput) THEN
fileName = formatFileName(prefix, 'Collisions', 'vtu', t)
WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
OPEN (fileID, file = path // folder // '/' // fileName)
CALL writeHeader(self%numNodes, self%numCells, fileID)
CALL writeMesh(self, fileID)
CALL writeCollOutput(self, fileID)
CALL writeFooter(fileID)
CLOSE(fileID)
!Write collection file for time plotting
fileNameCollection = formatFileName('Collection', 'Collisions', 'pvd')
CALL writeCollection(fileID, t, fileName, filenameCollection)
END IF
END SUBROUTINE printCollVTU
SUBROUTINE printEMVTU(self, t)
USE moduleMesh
USE moduleMeshInoutCommon
IMPLICIT NONE
CLASS(meshParticles), INTENT(in):: self
INTEGER, INTENT(in):: t
INTEGER:: fileID
CHARACTER(:), ALLOCATABLE:: fileName, fileNameCollection
fileID = 64
IF (emOutput) THEN
fileName = formatFileName(prefix, 'EMField', 'vtu', t)
WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
OPEN (fileID, file = path // folder // '/' // fileName)
CALL writeHeader(self%numNodes, self%numCells, fileID)
CALL writeMesh(self, fileID)
CALL writeEM(self, fileID)
CALL writeFooter(fileID)
CLOSE(fileID)
!Write collection file for time plotting
fileNameCollection = formatFileName('Collection', 'EMField', 'pvd')
CALL writeCollection(fileID, t, fileName, filenameCollection)
END IF
END SUBROUTINE printEMVTU
SUBROUTINE printAverageVTU(self)
USE moduleMesh
USE moduleSpecies
USE moduleMeshInoutCommon
IMPLICIT NONE
CLASS(meshParticles), INTENT(in):: self
INTEGER:: n, i, fileIDMean, fileIDDeviation
CHARACTER(:), ALLOCATABLE:: fileNameMean, fileNameDeviation
TYPE(outputFormat):: output(1:self%numNodes)
fileIDMean = 66
fileIDDeviation = 67
DO i = 1, nSpecies
fileNameMean = formatFileName('Average_mean', species(i)%obj%name, 'vtu')
WRITE(*, "(6X,A15,A)") "Creating file: ", fileNameMean
OPEN (fileIDMean, file = path // folder // '/' // fileNameMean)
fileNameDeviation = formatFileName('Average_deviation', species(i)%obj%name, 'vtu')
WRITE(*, "(6X,A15,A)") "Creating file: ", fileNameDeviation
OPEN (fileIDDeviation, file = path // folder // '/' // fileNameDeviation)
CALL writeHeader(self%numNodes, self%numCells, fileIDMean)
CALL writeHeader(self%numNodes, self%numCells, fileIDDeviation)
CALL writeMesh(self, fileIDMean)
CALL writeMesh(self, fileIDDeviation)
CALL writeAverage(self, fileIDMean, fileIDDeviation, i)
CALL writeFooter(fileIDMean)
CALL writeFooter(fileIDDeviation)
CLOSE(fileIDMean)
CLOSE(fileIDDeviation)
END DO
END SUBROUTINE printAverageVTU
END MODULE moduleMeshOutputVTU
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