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New functions to read VTU

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Added a few functions to read .vtu meshes.

Output in .vtu changed to output data in 6 columns (seems to be the
    standard.)
This commit is contained in:
Jorge Gonzalez 2023-02-05 16:23:37 +01:00
commit 63fd8fdb91
3 changed files with 192 additions and 56 deletions
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4
src/modules/init/moduleInput.f90
View file

@ -860,6 +860,7 @@ MODULE moduleInput
SUBROUTINE readGeometry(config)
USE moduleMesh
USE moduleMeshInputGmsh2, ONLY: initGmsh2
USE moduleMeshInputVTU, ONLY: initVTU, readVTU !TEMPORARY TO TEST VTU OUTPUT
USE moduleMeshInput0D, ONLY: init0D
USE moduleErrors
USE moduleOutput
@ -873,6 +874,7 @@ MODULE moduleInput
LOGICAL:: found
CHARACTER(:), ALLOCATABLE:: meshFormat, meshFile
REAL(8):: volume
CHARACTER(:), ALLOCATABLE:: meshFileVTU !Temporary to test VTU OUTPUT
object = 'geometry'
@ -973,6 +975,8 @@ MODULE moduleInput
CALL config%get(object // '.meshFile', meshFile, found)
pathMeshParticle = path // meshFile
CALL mesh%readMesh(pathMeshParticle)
meshFileVTU = '/home/jorge/fpakc/runs/cylFlow/mesh.vtu' !TEMPORARY TO TEST VTU OUTPUT
CALL readVTU(mesh, meshFileVTU) !TEMPORARY TO TEST VTU OUTPUT
DEALLOCATE(meshFile)
IF (doubleMesh) THEN
!Reads the mesh file for collisions

166
src/modules/mesh/inout/vtu/moduleMeshInputVTU.f90
View file

@ -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

78
src/modules/mesh/inout/vtu/moduleMeshOutputVTU.f90
View file

@ -103,45 +103,37 @@ MODULE moduleMeshOutputVTU
CLASS(meshGeneric), INTENT(in):: self
INTEGER, INTENT(in):: fileID
CHARACTER(LEN=25):: nodeFormat
CHARACTER(LEN=25):: cellFormat
INTEGER:: e
INTEGER:: offset
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(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, "(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">'
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, "(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 = 0
offset(1) = self%cells(1)%obj%nNodes
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
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
WRITE(cellFormat, "(A,I1,A)") "(I10)"
WRITE(fileID, cellFormat, advance="no") getCellType(self%cells(e)%obj)
types(e) = getCellType(self%cells(e)%obj)
END DO
WRITE(fileID, "(6(I10))") types
WRITE(fileID, "(10X, A)") '</DataArray>'
WRITE(fileID, "(8X, A)") '</Cells>'
@ -156,7 +148,6 @@ MODULE moduleMeshOutputVTU
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
@ -168,23 +159,19 @@ MODULE moduleMeshOutputVTU
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,"(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(nodeFormat, "(A,I10, A)") "(", self%numNodes, "(3(ES20.6E3)))"
WRITE(fileID,nodeFormat) (output(n)%velocity, n = 1, self%numNodes)
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(nodeFormat, "(A,I10, A)") "(", self%numNodes, "(1(ES20.6E3)))"
WRITE(fileID,nodeFormat) (output(n)%pressure, n = 1, self%numNodes)
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(nodeFormat, "(A,I10, A)") "(", self%numNodes, "(1(ES20.6E3)))"
WRITE(fileID,nodeFormat) (output(n)%temperature, n = 1, self%numNodes)
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>'
@ -201,7 +188,6 @@ MODULE moduleMeshOutputVTU
INTEGER:: k, c, n
CHARACTER(:), ALLOCATABLE:: title
CHARACTER (LEN=2):: cString
CHARACTER(LEN=25):: cellFormat
WRITE(fileID,"(8X,A)") '<CellData>'
DO k = 1, nCollPairs
@ -209,8 +195,7 @@ MODULE moduleMeshOutputVTU
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, "(6(I10))") (self%cells(n)%obj%tallyColl(k)%tally(c), n = 1, self%numCells)
WRITE(fileID, "(10X, A)") '</DataArray>'
END DO
@ -226,33 +211,27 @@ MODULE moduleMeshOutputVTU
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,"(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(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,"(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(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, "(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>'
@ -303,7 +282,6 @@ MODULE moduleMeshOutputVTU
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
@ -320,33 +298,29 @@ MODULE moduleMeshOutputVTU
!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, "(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(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, "(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(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, "(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(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, "(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