First step towards reading .vtu mesh

Just setting up the required functions.
This commit is contained in:
Jorge Gonzalez 2023-02-04 15:41:13 +01:00
commit f5be04587a
11 changed files with 78 additions and 31 deletions

View file

@ -0,0 +1,505 @@
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
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
CHARACTER(LEN=25):: nodeFormat
CHARACTER(LEN=25):: cellFormat
INTEGER:: e
INTEGER:: offset
!Write nodes coordinates
WRITE(fileID, "(8X, A)") '<Points>'
WRITE(fileID, "(10X,A)") '<DataArray type="Float32" NumberOfComponents="3" format="ascii">'
WRITE(nodeFormat, "(A,I10, A)") "(", self%numNodes, "(3(ES20.6E3)))"
WRITE(fileID, nodeFormat) (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">'
DO e = 1, self%numCells
WRITE(cellFormat, "(A,I1,A)") "(",self%cells(e)%obj%nNodes,"(I10))"
WRITE(fileID, cellFormat, advance="no") self%cells(e)%obj%getNodes(self%cells(e)%obj%nNodes) - 1 !Array starts on 0
END DO
WRITE(fileID, "(10X, A)") '</DataArray>'
!Write offset of each cell
offset = 0
WRITE(fileID, "(10X,A)") '<DataArray type="Int32" Name="offsets" format="ascii">'
DO e = 1, self%numCells
WRITE(cellFormat, "(A,I1,A)") "(I10)"
offset = offset + self%cells(e)%obj%nNodes
WRITE(fileID, cellFormat, advance="no") offset
END DO
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
WRITE(cellFormat, "(A,I1,A)") "(I10)"
WRITE(fileID, cellFormat, advance="no") getCellType(self%cells(e)%obj)
END DO
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)
CHARACTER(LEN=25):: nodeFormat
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(nodeFormat, "(A,I10, A)") "(", self%numNodes, "(1(ES20.6E3)))"
WRITE(fileID,nodeFormat) (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(nodeFormat, "(A,I10, A)") "(", self%numNodes, "(3(ES20.6E3)))"
WRITE(fileID,nodeFormat) (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(nodeFormat, "(A,I10, A)") "(", self%numNodes, "(1(ES20.6E3)))"
WRITE(fileID,nodeFormat) (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(nodeFormat, "(A,I10, A)") "(", self%numNodes, "(1(ES20.6E3)))"
WRITE(fileID,nodeFormat) (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
CHARACTER(LEN=25):: cellFormat
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(cellFormat, "(A,I10, A)") "(", self%numCells, "(I10))"
WRITE(fileID, cellFormat) (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
CHARACTER(LEN=25):: nodeFormat
CHARACTER(LEN=25):: cellFormat
INTEGER:: n
REAL(8):: Xi(1:3)
Xi = (/ 0.D0, 0.D0, 0.D0 /)
!Points in nodes
WRITE(fileID,"(8X,A)") '<PointData>'
!Electric potential
WRITE(fileID,"(10X,A)") '<DataArray type="Float64" Name="Potential (V)" NumberOfComponents="1">'
WRITE(nodeFormat, "(A,I10, A)") "(", self%numNodes, "(1(ES20.6E3)))"
WRITE(fileID,nodeFormat) (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(nodeFormat, "(A,I10, A)") "(", self%numNodes, "(3(ES20.6E3)))"
WRITE(fileID,nodeFormat) (self%nodes(n)%obj%emData%B*B_ref, n = 1, self%numNodes)
WRITE(fileID,"(10X,A)") '</DataArray>'
WRITE(fileID,"(8X,A)") '</PointData>'
!Cell Data
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(cellFormat, "(A,I10, A)") "(", self%numCells, "(3(ES20.6E3)))"
WRITE(fileID, cellFormat) (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)
CHARACTER(LEN=25):: nodeFormat
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(nodeFormat,"(A,I10, A)") "(", self%numNodes, "(1(ES20.6E3)))"
WRITE(fileIDMean, nodeFormat) (outputMean(n)%density, n = 1, self%numNodes)
WRITE(fileIDDeviation,nodeFormat) (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(nodeFormat,"(A,I10, A)") "(", self%numNodes, "(3(ES20.6E3)))"
WRITE(fileIDMean, nodeFormat) (outputMean(n)%velocity, n = 1, self%numNodes)
WRITE(fileIDDeviation,nodeFormat) (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(nodeFormat,"(A,I10, A)") "(", self%numNodes, "(1(ES20.6E3)))"
WRITE(fileIDMean, nodeFormat) (outputMean(n)%pressure, n = 1, self%numNodes)
WRITE(fileIDDeviation,nodeFormat) (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(nodeFormat,"(A,I10, A)") "(", self%numNodes, "(1(ES20.6E3)))"
WRITE(fileIDMean, nodeFormat) (outputMean(n)%temperature, n = 1, self%numNodes)
WRITE(fileIDDeviation,nodeFormat) (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
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(prefix, '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
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(prefix, 'Collection_Collisions', 'pvd')
CALL writeCollection(fileID, t, fileName, filenameCollection)
END IF
END SUBROUTINE printCollVTU
SUBROUTINE printEMVTU(self, t)
USE moduleMesh
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(prefix, 'Collection_EMField', 'pvd')
CALL writeCollection(fileID, t, fileName, filenameCollection)
END IF
END SUBROUTINE printEMVTU
SUBROUTINE printAverageVTU(self)
USE moduleMesh
USE moduleSpecies
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