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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 1666f42..5321ba4 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 e572331..845cc9a 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} @@ -460,6 +460,10 @@ 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 247c7d2..83cf8db 100644 --- a/src/makefile +++ b/src/makefile @@ -9,6 +9,7 @@ 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 9a8ace6..74da279 100644 --- a/src/modules/init/moduleInput.f90 +++ b/src/modules/init/moduleInput.f90 @@ -910,6 +910,7 @@ MODULE moduleInput USE moduleMeshInputGmsh2, ONLY: initGmsh2 USE moduleMeshInputVTU, ONLY: initVTU USE moduleMeshInput0D, ONLY: init0D + USE moduleMeshInputText, ONLY: initText USE moduleMesh3DCart USE moduleMesh2DCyl USE moduleMesh2DCart @@ -1058,6 +1059,20 @@ 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 a93161d..1b8883d 100644 --- a/src/modules/mesh/inout/makefile +++ b/src/modules/mesh/inout/makefile @@ -1,4 +1,4 @@ -all: vtu.o gmsh2.o 0D.o +all: vtu.o gmsh2.o 0D.o text.o vtu.o: moduleMeshInoutCommon.o $(MAKE) -C vtu all @@ -9,5 +9,8 @@ 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 new file mode 100644 index 0000000..26d0f10 --- /dev/null +++ b/src/modules/mesh/inout/text/makefile @@ -0,0 +1,7 @@ +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 new file mode 100644 index 0000000..a41e6d3 --- /dev/null +++ b/src/modules/mesh/inout/text/moduleMeshInputText.f90 @@ -0,0 +1,232 @@ +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 new file mode 100644 index 0000000..d69ddda --- /dev/null +++ b/src/modules/mesh/inout/text/moduleMeshOutputText.f90 @@ -0,0 +1,265 @@ +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 e07db01..c7b89b5 100644 --- a/src/modules/mesh/inout/vtu/moduleMeshInputVTU.f90 +++ b/src/modules/mesh/inout/vtu/moduleMeshInputVTU.f90 @@ -548,6 +548,8 @@ 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 81e4bbf..8e8f91a 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,ES20.6E3,A)") '' + WRITE(fileID,"(4X, 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 7ab3914..01b03c7 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 @@ -499,28 +499,29 @@ MODULE moduleMesh IMPLICIT NONE CLASS(meshParticles), INTENT(inout):: self - INTEGER:: e - INTEGER:: nNodes + INTEGER:: c INTEGER, ALLOCATABLE:: n(:) REAL(8), ALLOCATABLE:: localK(:,:) INTEGER:: i, j - 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 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 i = 1, nNodes - DO j = 1, nNodes - self%K(n(i), n(j)) = self%K(n(i), n(j)) + localK(i, j) + 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 END DO - END DO + DEALLOCATE(n, localK) - DEALLOCATE(n, localK) + end associate END DO