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75.395 57.395 +75.395 c 57.883 75.395 58.273 75.52 58.566 75.77 c 58.855 76.012 59.004 +76.34 59.004 76.754 c 59.004 76.941 58.965 77.125 58.895 77.301 c 58.82 +77.48 58.691 77.688 58.504 77.926 c 58.449 77.988 58.277 78.168 57.988 78.457 + c 57.707 78.75 57.309 79.156 56.801 79.676 c h +56.801 79.676 m f +60.484 70.629 m 61.266 70.629 l 61.754 71.402 62.117 72.156 62.359 72.895 + c 62.609 73.625 62.734 74.355 62.734 75.082 c 62.734 75.813 62.609 76.547 + 62.359 77.285 c 62.117 78.027 61.754 78.773 61.266 79.535 c 60.484 79.535 + l 60.922 78.793 61.242 78.059 61.453 77.316 c 61.672 76.578 61.781 75.832 + 61.781 75.082 c 61.781 74.332 61.672 73.594 61.453 72.863 c 61.242 72.125 + 60.922 71.379 60.484 70.629 c h +60.484 70.629 m f +Q Q +showpage +%%Trailer +end +%%EOF diff --git a/doc/user-manual/fpakc_UserManual.pdf b/doc/user-manual/fpakc_UserManual.pdf index 5321ba4..1666f42 100644 Binary files a/doc/user-manual/fpakc_UserManual.pdf and b/doc/user-manual/fpakc_UserManual.pdf differ diff --git a/doc/user-manual/fpakc_UserManual.tex b/doc/user-manual/fpakc_UserManual.tex index 845cc9a..e572331 100644 --- a/doc/user-manual/fpakc_UserManual.tex +++ b/doc/user-manual/fpakc_UserManual.tex @@ -1,5 +1,5 @@ \documentclass[10pt,a4paper,twoside]{book} -%\usepackage[latin1]{inputenc} +\usepackage[latin1]{inputenc} \usepackage{amsmath} \usepackage{amsfonts} \usepackage{amssymb} @@ -460,10 +460,6 @@ make \begin{itemize} \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. This has to be in ASCII format. - \item \textbf{text}: Plain text file format only intended for 1D cases. - This has to be in ASCII format and comma separated. - The first column represents the position and the second column the physical ID of the node. - Values have to be $1$ (left boundary), $2$ (right boundary), or $0$ (no boundary.) \end{itemize} \item \textbf{meshFile}: Character. Mesh filename. diff --git a/src/makefile b/src/makefile index 83cf8db..247c7d2 100644 --- a/src/makefile +++ b/src/makefile @@ -9,7 +9,6 @@ OBJECTS = $(OBJDIR)/moduleMesh.o $(OBJDIR)/moduleMeshBoundary.o $(OBJDIR)/module $(OBJDIR)/moduleMeshInputVTU.o $(OBJDIR)/moduleMeshOutputVTU.o \ $(OBJDIR)/moduleMeshInputGmsh2.o $(OBJDIR)/moduleMeshOutputGmsh2.o \ $(OBJDIR)/moduleMeshInput0D.o $(OBJDIR)/moduleMeshOutput0D.o \ - $(OBJDIR)/moduleMeshInputText.o $(OBJDIR)/moduleMeshOutputText.o \ $(OBJDIR)/moduleMesh3DCart.o \ $(OBJDIR)/moduleMesh2DCyl.o \ $(OBJDIR)/moduleMesh2DCart.o \ diff --git a/src/modules/init/moduleInput.f90 b/src/modules/init/moduleInput.f90 index 74da279..9a8ace6 100644 --- a/src/modules/init/moduleInput.f90 +++ b/src/modules/init/moduleInput.f90 @@ -910,7 +910,6 @@ MODULE moduleInput USE moduleMeshInputGmsh2, ONLY: initGmsh2 USE moduleMeshInputVTU, ONLY: initVTU USE moduleMeshInput0D, ONLY: init0D - USE moduleMeshInputText, ONLY: initText USE moduleMesh3DCart USE moduleMesh2DCyl USE moduleMesh2DCart @@ -1059,20 +1058,6 @@ MODULE moduleInput END IF - case ("text") - !Check if the geometry is right. - if (mesh%dimen /= 1) then - call criticalError("Text mesh is only allowed for 1D geometries", 'readGeometry') - - end if - - !Read the mesh - call initText(mesh) - if (doubleMesh) then - call initText(meshColl) - - end if - CASE DEFAULT CALL criticalError('Mesh format ' // meshFormat // ' not defined.', 'readGeometry') diff --git a/src/modules/mesh/inout/makefile b/src/modules/mesh/inout/makefile index 1b8883d..a93161d 100644 --- a/src/modules/mesh/inout/makefile +++ b/src/modules/mesh/inout/makefile @@ -1,4 +1,4 @@ -all: vtu.o gmsh2.o 0D.o text.o +all: vtu.o gmsh2.o 0D.o vtu.o: moduleMeshInoutCommon.o $(MAKE) -C vtu all @@ -9,8 +9,5 @@ gmsh2.o: 0D.o: $(MAKE) -C 0D all -text.o: - $(MAKE) -C text all - %.o: %.f90 $(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@ diff --git a/src/modules/mesh/inout/text/makefile b/src/modules/mesh/inout/text/makefile deleted file mode 100644 index 26d0f10..0000000 --- a/src/modules/mesh/inout/text/makefile +++ /dev/null @@ -1,7 +0,0 @@ -all: moduleMeshInputText.o moduleMeshOutputText.o - -moduleMeshInputText.o: moduleMeshOutputText.o moduleMeshInputText.f90 - $(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@ - -%.o: %.f90 - $(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@ diff --git a/src/modules/mesh/inout/text/moduleMeshInputText.f90 b/src/modules/mesh/inout/text/moduleMeshInputText.f90 deleted file mode 100644 index a41e6d3..0000000 --- a/src/modules/mesh/inout/text/moduleMeshInputText.f90 +++ /dev/null @@ -1,232 +0,0 @@ -module moduleMeshInputText - !The mesh is stored as a column-wise text file. - !Aimed for simple geometries in 1D - - contains - !Inits the text mesh - subroutine initText(self) - use moduleMesh - use moduleMeshOutputText - implicit none - - class(meshGeneric), intent(inout), target:: self - - if (associated(meshForMCC,self)) then - self%printColl => printCollText - - end if - - select type(self) - type is (meshParticles) - self%printOutput => printOutputText - self%printEM => printEMText - self%printAverage => printAverageText - - self%readInitial => readInitialText - - end select - - self%readMesh => readText - - end subroutine initText - - !Reads the text mesh - subroutine readText(self, filename) - use moduleMesh - use moduleMesh1DCart - use moduleMesh1DRad - use moduleErrors - implicit none - - class(meshGeneric), intent(inout):: self - character(:), allocatable, intent(in):: filename !Dummy file, not used - integer:: fileID, reason - character(len=256):: line - integer:: nNodes - real(8):: r(1:3) !dummy 3D coordinate - integer:: physicalID - integer:: n, c - integer, allocatable:: p(:) - integer:: bt - - fileID = 10 - - open(fileID, file=trim(filename)) - - !Skip header - read(fileID, *) - - !Get number of nodes - nNodes = 0 - do - read(fileID, *, iostat=reason) line - - if (reason > 0) then - call criticalError('Error reading mesh file', 'readText') - - else if (reason < 0) then - exit - - else if (len(line) > 0) then - nNodes = nNodes + 1 - - end if - - end do - - if (nNodes == 0) then - call criticalError('No nodes read in mesh file', 'readText') - - end if - - self%numNodes = nNodes - allocate(self%nodes(1:self%numNodes)) - - SELECT TYPE(self) - TYPE IS(meshParticles) - ALLOCATE(self%K(1:self%numNodes, 1:self%numNodes)) - ALLOCATE(self%IPIV(1:self%numNodes, 1:self%numNodes)) - self%K = 0.D0 - self%IPIV = 0 - - END SELECT - - self%numCells = nNodes - 1 - allocate(self%cells(1:self%numCells)) - - select type(self) - type is (meshParticles) - self%numEdges = 2 - - allocate(self%edges(1:self%numEdges)) - - end select - - !Read the mesh now - rewind(fileID) - - !Skip header - read(fileID, *) - - !Allocate nodes and edges - do n = 1, self%numNodes - r = 0.D0 - - read(fileID, *) r(1), physicalID - - select case(self%geometry) - case("Cart") - allocate(meshNode1DCart:: self%nodes(n)%obj) - - case("Rad") - allocate(meshNode1DRad:: self%nodes(n)%obj) - - end select - - !Init nodes - call self%nodes(n)%obj%init(n, r) - - !Allocate edges if required) - select type(self) - type is (meshParticles) - if ((physicalID == 1) .or. (physicalID == 2)) then - select case(self%geometry) - case("Cart") - allocate(meshEdge1DCart:: self%edges(physicalID)%obj) - - case("Rad") - allocate(meshEdge1DRad:: self%edges(physicalID)%obj) - - end select - - allocate(p(1)) - p(1) = n - bt = getBoundaryId(physicalID) - call self%edges(physicalID)%obj%init(physicalID, p, physicalID, physicalID) - deallocate(p) - - end if - - end select - - end do - - !Allocate cells - n = 1 - allocate(p(1:2)) - do c = 1, self%numCells - p(1) = n - n = n + 1 - p(2) = n - - select case(self%geometry) - case("Cart") - allocate(meshCell1DCartSegm:: self%cells(c)%obj) - - case("Rad") - allocate(meshCell1DRadSegm:: self%cells(c)%obj) - - end select - - call self%cells(c)%obj%init(c, p, self%nodes) - - - end do - deallocate(p) - - close(fileID) - - !Call mesh connectivity - CALL self%connectMesh - - end subroutine readText - - subroutine readInitialText(filename, density, velocity, temperature) - use moduleErrors - implicit none - - character(:), allocatable, intent(in):: filename - real(8), allocatable, intent(out), dimension(:):: density - real(8), allocatable, intent(out), dimension(:,:):: velocity - real(8), allocatable, intent(out), dimension(:):: temperature - integer:: fileID, reason - character(len=256):: line - integer:: nNodes - integer:: n - - fileID = 10 - - open(fileID, file=trim(filename)) - - do - read(fileID, *, iostat=reason) line - - if (reason > 0) then - call criticalError('Error reading mesh file', 'readText') - - else if (reason < 0) then - exit - - else if (len(line) > 0) then - nNodes = nNodes + 1 - - end if - - end do - - allocate(density(1:nNodes)) - allocate(velocity(1:nNodes, 1:3)) - allocate(temperature(1:nNodes)) - - rewind(fileID) - - do n = 1, nNodes - read(fileID, *) density(n), velocity(n, 1:3), temperature(n) - - end do - - close(fileID) - - end subroutine readInitialText - -end module moduleMeshInputText diff --git a/src/modules/mesh/inout/text/moduleMeshOutputText.f90 b/src/modules/mesh/inout/text/moduleMeshOutputText.f90 deleted file mode 100644 index d69ddda..0000000 --- a/src/modules/mesh/inout/text/moduleMeshOutputText.f90 +++ /dev/null @@ -1,265 +0,0 @@ -module moduleMeshOutputText - contains - - subroutine writeSpeciesOutput(self, fileID, speciesIndex) - use moduleMesh - use moduleOutput - use moduleRefParam, only: L_ref - implicit none - - class(meshParticles), INTENT(in):: self - integer, intent(in):: fileID - integer, intent(in):: speciesIndex - real(8):: r(1:3) - type(outputFormat):: output - integer:: n - - do n = 1, self%numNodes - r = self%nodes(n)%obj%getCoordinates() - call calculateOutput(self%nodes(n)%obj%output(speciesIndex), output, self%nodes(n)%obj%v, species(speciesIndex)%obj) - - write(fileID, '(5(ES0.6E3,","),ES0.6E3)') r(1)*L_ref, output%density, output%velocity, output%temperature - - end do - - end subroutine writeSpeciesOutput - - subroutine writeCollOutput(self, fileID) - use moduleMesh - use moduleCollisions - use moduleRefParam, only: L_ref - implicit none - - class(meshGeneric), intent(in):: self - integer, intent(in):: fileID - integer:: n, k, c - - do n = 1, self%numCells - write(fileID, '(I0)', advance='no') n - - do k = 1, nCollPairs - do c = 1, interactionMatrix(k)%amount - write(fileID, '(",",I0)', advance='no') self%cells(n)%obj%tallyColl(k)%tally(c) - - end do - - end do - write(fileID, *) - - end do - - end subroutine writeCollOutput - - subroutine writeEMOutput(self, fileID) - use moduleMesh - use moduleRefParam, only: L_ref, Volt_ref, B_ref, EF_ref - implicit none - - class(meshParticles), intent(in):: self - integer, intent(in):: fileID - integer:: n, c - real(8):: r(1:3), Xi(1:3) - - do n = 1, self%numNodes - r = self%nodes(n)%obj%getCoordinates() - if (n == self%numNodes) then - Xi = (/ 1.D0, 0.D0, 0.D0 /) - c = self%numNodes - 1 - - else - Xi = (/ 0.D0, 0.D0, 0.D0 /) - c = n - - end if - - associate(output => self%nodes(n)%obj%emData) - write(fileID, '(7(ES0.6E3,","),ES0.6E3)') r(1)*L_ref, & - output%phi*Volt_ref, & - self%cells(c)%obj%gatherElectricField(Xi)*EF_ref, & - output%B*B_ref - - end associate - - end do - - end subroutine writeEMOutput - - subroutine writeAverage(self, fileIDMean, & - fileIDDeviation, & - speciesIndex) - - use moduleMesh - use moduleOutput - use moduleAverage - use moduleRefParam, only: L_ref - implicit none - - class(meshParticles), intent(in):: self - integer, intent(in):: fileIDMean, fileIDDeviation - INTEGER, intent(in):: speciesIndex - real(8):: r(1:3) - type(outputFormat):: outputMean - type(outputFormat):: outputDeviation - integer:: n - - do n = 1, self%numNodes - r = self%nodes(n)%obj%getCoordinates() - - call calculateOutput(averageScheme(n)%mean%output(speciesIndex), outputMean, & - self%nodes(n)%obj%v, species(speciesIndex)%obj) - - write(fileIDMean, '(5(ES0.6E3,","),ES0.6E3)') r(1)*L_ref, outputMean%density, outputMean%velocity, outputMean%temperature - - call calculateOutput(averageScheme(n)%deviation%output(speciesIndex), outputDeviation, & - self%nodes(n)%obj%v, species(speciesIndex)%obj) - - write(fileIDDeviation, '(5(ES0.6E3,","),ES0.6E3)') r(1)*L_ref, outputDeviation%density, outputDeviation%velocity, outputDeviation%temperature - - end do - - end subroutine writeAverage - - subroutine printOutputText(self) - use moduleMesh - use moduleSpecies - use moduleMeshInoutCommon - use moduleCaseParam, ONLY: timeStep - implicit none - - class(meshParticles), intent(in):: self - - INTEGER:: s, fileID - character(:), allocatable:: fileName - - fileID = 60 - - do s = 1, nSpecies - fileName = formatFileName(prefix, species(s)%obj%name, 'csv', timeStep) - write(*, "(6X,A15,A)") "Creating file: ", fileName - open (fileID, file = path // folder // '/' // fileName) - - write(fileID, '(5(A,","),A)') 'Position (m)', & - 'Density (m^-3)', & - 'Velocity (m s^-1):0', 'Velocity (m s^-1):1', 'Velocity (m s^-1):2', & - 'Temperature (K)' - - call writeSpeciesOutput(self, fileID, s) - - close(fileID) - - end do - - end subroutine printOutputText - - subroutine printCollText(self) - use moduleMesh - use moduleOutput - use moduleMeshInoutCommon - use moduleCaseParam, only: timeStep - implicit none - - class(meshGeneric), intent(in):: self - integer:: fileID - character(:), allocatable:: fileName - integer:: k, c - character (len=2):: cString - - fileID = 62 - - if (collOutput) then - fileName = formatFileName(prefix, 'Collisions', 'csv', timeStep) - write(*, "(6X,A15,A)") "Creating file: ", fileName - open (fileID, file = path // folder // '/' // fileName) - - write(fileID, '(A)', advance='no') "Cell" - do k = 1, nCollPairs - do c = 1, interactionMatrix(k)%amount - write(cString, "(I2)") c - write(fileID, '(",",A)', advance='no') 'Pair ' // interactionMatrix(k)%sp_i%name // '-' // interactionMatrix(k)%sp_j%name // ' collision ' // cString - - end do - end do - - write(fileID, *) - - call writeCollOutput(self, fileID) - - close(fileID) - - end if - - end subroutine printCollText - - subroutine printEMText(self) - use moduleMesh - use moduleMeshInoutCommon - use moduleCaseParam, only: timeStep - implicit none - - class(meshParticles), intent(in):: self - integer:: fileID - character(:), allocatable:: fileName - - fileID = 64 - - if (emOutput) then - fileName = formatFileName(prefix, 'EMField', 'csv', timeStep) - write(*, "(6X,A15,A)") "Creating file: ", fileName - open (fileID, file = path // folder // '/' // fileName) - - write(fileID, '(8(A,","),A)') 'Position (m)', & - 'Potential (V)', & - 'Electric Field (V m^-1):0', 'Electric Field (V m^-1):1', 'Electric Field (V m^-1):2', & - 'Magnetic Field (T):0', 'Magnetic Field (T):1', 'Magnetic Field (T):2' - - call writeEMOutput(self, fileID) - - close(fileID) - - end if - - end subroutine printEMText - - subroutine printAverageText(self) - use moduleMesh - use moduleSpecies - use moduleMeshInoutCommon - implicit none - - class(meshParticles), intent(in):: self - integer:: s - integer:: fileIDMean, fileIDDeviation - character(:), allocatable:: fileNameMean, fileNameDeviation - - fileIDMean = 66 - fileIDDeviation = 67 - - do s = 1, nSpecies - fileNameMean = formatFileName('Average_mean', species(s)%obj%name, 'csv', timeStep) - write(*, "(6X,A15,A)") "Creating file: ", fileNameMean - open (fileIDMean, file = path // folder // '/' // fileNameMean) - - write(fileIDMean, '(5(A,","),A)') 'Position (m)', & - 'Density, mean (m^-3)', & - 'Velocity, mean (m s^-1):0', 'Velocity (m s^-1):1', 'Velocity (m s^-1):2', & - 'Temperature, mean (K)' - - fileNameDeviation = formatFileName('Average_deviation', species(s)%obj%name, 'csv', timeStep) - write(*, "(6X,A15,A)") "Creating file: ", fileNameDeviation - open (fileIDDeviation, file = path // folder // '/' // fileNameDeviation) - - write(fileIDDeviation, '(5(A,","),A)') 'Position (m)', & - 'Density, deviation (m^-3)', & - 'Velocity, deviation (m s^-1):0', 'Velocity (m s^-1):1', 'Velocity (m s^-1):2', & - 'Temperature, deviation (K)' - - call writeAverage(self, fileIDMean, fileIDDeviation, s) - - close(fileIDMean) - close(fileIDDeviation) - - end do - - end subroutine printAverageText - -end module moduleMeshOutputText diff --git a/src/modules/mesh/inout/vtu/moduleMeshInputVTU.f90 b/src/modules/mesh/inout/vtu/moduleMeshInputVTU.f90 index c7b89b5..e07db01 100644 --- a/src/modules/mesh/inout/vtu/moduleMeshInputVTU.f90 +++ b/src/modules/mesh/inout/vtu/moduleMeshInputVTU.f90 @@ -548,8 +548,6 @@ MODULE moduleMeshInputVTU CALL readDataBlock(fileID, numNodes, temperature) REWIND(fileID) - close(fileID) - END SUBROUTINE readInitialVTU END MODULE moduleMeshInputVTU diff --git a/src/modules/mesh/inout/vtu/moduleMeshOutputVTU.f90 b/src/modules/mesh/inout/vtu/moduleMeshOutputVTU.f90 index 8e8f91a..81e4bbf 100644 --- a/src/modules/mesh/inout/vtu/moduleMeshOutputVTU.f90 +++ b/src/modules/mesh/inout/vtu/moduleMeshOutputVTU.f90 @@ -11,7 +11,7 @@ MODULE moduleMeshOutputVTU WRITE(fileID,"(A)") '' WRITE(fileID,"(2X, A)") '' - WRITE(fileID,"(4X, A)") '' + WRITE(fileID,"(4X, A,ES20.6E3,A)") '' WRITE(fileID,"(6X, A, I10, A, I10, A)") '' END SUBROUTINE writeHeader diff --git a/src/modules/mesh/moduleMesh.f90 b/src/modules/mesh/moduleMesh.f90 index 01b03c7..7ab3914 100644 --- a/src/modules/mesh/moduleMesh.f90 +++ b/src/modules/mesh/moduleMesh.f90 @@ -344,10 +344,10 @@ MODULE moduleMesh !Array of cell elements TYPE(meshCellCont), ALLOCATABLE:: cells(:) !PROCEDURES SPECIFIC OF FILE TYPE - PROCEDURE(readMesh_interface), POINTER, PASS:: readMesh => NULL() - PROCEDURE(readInitial_interface), POINTER, NOPASS:: readInitial => NULL() - PROCEDURE(connectMesh_interface), POINTER, PASS:: connectMesh => NULL() - PROCEDURE(printColl_interface), POINTER, PASS:: printColl => NULL() + PROCEDURE(readMesh_interface), POINTER, PASS:: readMesh => NULL() + PROCEDURE(readInitial_interface), POINTER, NOPASS:: readInitial => NULL() + PROCEDURE(connectMesh_interface), POINTER, PASS:: connectMesh => NULL() + PROCEDURE(printColl_interface), POINTER, PASS:: printColl => NULL() CONTAINS !GENERIC PROCEDURES PROCEDURE, PASS:: doCollisions @@ -499,29 +499,28 @@ MODULE moduleMesh IMPLICIT NONE CLASS(meshParticles), INTENT(inout):: self - INTEGER:: c + INTEGER:: e + INTEGER:: nNodes INTEGER, ALLOCATABLE:: n(:) REAL(8), ALLOCATABLE:: localK(:,:) INTEGER:: i, j - DO c = 1, self%numCells - associate(nNodes => self%cells(c)%obj%nNodes) - ALLOCATE(n(1:nNodes)) - ALLOCATE(localK(1:nNodes, 1:nNodes)) - n = self%cells(c)%obj%getNodes(nNodes) - localK = self%cells(c)%obj%elemK(nNodes) + DO e = 1, self%numCells + nNodes = self%cells(e)%obj%nNodes + ALLOCATE(n(1:nNodes)) + ALLOCATE(localK(1:nNodes, 1:nNodes)) + n = self%cells(e)%obj%getNodes(nNodes) + localK = self%cells(e)%obj%elemK(nNodes) - DO i = 1, nNodes - DO j = 1, nNodes - self%K(n(i), n(j)) = self%K(n(i), n(j)) + localK(i, j) - - END DO + DO i = 1, nNodes + DO j = 1, nNodes + self%K(n(i), n(j)) = self%K(n(i), n(j)) + localK(i, j) END DO - DEALLOCATE(n, localK) + END DO - end associate + DEALLOCATE(n, localK) END DO