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Creating of nodes and edges in .vtu format

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Moving forward making vtu an independent format.

Now fpakc can generate nodes and edges from vtu input.
Next step is cells.

Some minor corrections in gmsh2 format to unify statements.
The reading of meshes needs a good overhaul.

Testing all geometries with vtu is gonna be fun...
This commit is contained in:
Jorge Gonzalez 2023-02-05 19:35:49 +01:00
commit 43a7421795
4 changed files with 220 additions and 43 deletions
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48
src/modules/init/moduleInput.f90
View file

@ -860,8 +860,13 @@ MODULE moduleInput
SUBROUTINE readGeometry(config)
USE moduleMesh
USE moduleMeshInputGmsh2, ONLY: initGmsh2
USE moduleMeshInputVTU, ONLY: initVTU, readVTU !TEMPORARY TO TEST VTU OUTPUT
USE moduleMeshInputVTU, ONLY: initVTU
USE moduleMeshInput0D, ONLY: init0D
USE moduleMesh3DCart
USE moduleMesh2DCyl
USE moduleMesh2DCart
USE moduleMesh1DRad
USE moduleMesh1DCart
USE moduleErrors
USE moduleOutput
USE moduleRefParam
@ -959,7 +964,34 @@ MODULE moduleInput
END SELECT
!Get the type of mesh
!Link the procedure to connect meshes
SELECT CASE(mesh%dimen)
CASE(3)
mesh%connectMesh => connectMesh3DCart
CASE(2)
SELECT CASE(mesh%geometry)
CASE("Cyl")
mesh%connectMesh => connectMesh2DCyl
CASE("Cart")
mesh%connectMesh => connectMesh2DCart
END SELECT
CASE(1)
SELECT CASE(mesh%geometry)
CASE("Rad")
mesh%connectMesh => connectMesh1DRad
CASE("Cart")
mesh%connectMesh => connectMesh1DCart
END SELECT
END SELECT
!Get the format of mesh
CALL config%get(object // '.meshType', meshFormat, found)
SELECT CASE(meshFormat)
CASE ("gmsh2")
@ -969,14 +1001,22 @@ MODULE moduleInput
END IF
CASE ("vtu")
CALL initVTU(mesh)
IF (doubleMesh) THEN
CALL initVTU(meshColl)
END IF
CASE DEFAULT
CALL criticalError('Mesh format ' // meshFormat // ' not defined.', 'readGeometry')
END SELECT
!Reads the mesh file
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

47
src/modules/mesh/inout/gmsh2/moduleMeshInputGmsh2.f90
View file

@ -71,30 +71,26 @@ MODULE moduleMeshInputGmsh2
SELECT CASE(self%dimen)
CASE(3)
ALLOCATE(meshNode3Dcart::self%nodes(n)%obj)
self%connectMesh => connectMesh3DCart
CASE(2)
SELECT CASE(self%geometry)
CASE("Cyl")
ALLOCATE(meshNode2DCyl:: self%nodes(n)%obj)
self%connectMesh => connectMesh2DCyl
CASE("Cart")
ALLOCATE(meshNode2DCart:: self%nodes(n)%obj)
self%connectMesh => connectMesh2DCart
END SELECT
r(3) = 0.D0
CASE(1)
SELECT CASE(self%geometry)
CASE("Rad")
ALLOCATE(meshNode1DRad:: self%nodes(n)%obj)
self%connectMesh => connectMesh1DRad
CASE("Cart")
ALLOCATE(meshNode1DCart:: self%nodes(n)%obj)
self%connectMesh => connectMesh1DCart
END SELECT
r(2:3) = 0.D0
@ -111,7 +107,7 @@ MODULE moduleMeshInputGmsh2
!Reads total number of elements (no nodes)
READ(10, *) totalNumElem
!conts edges and volume elements
!Count edges and volume elements
SELECT TYPE(self)
TYPE IS(meshParticles)
self%numEdges = 0
@ -151,7 +147,7 @@ MODULE moduleMeshInputGmsh2
END SELECT
!Allocates arrays
!Allocates array of cells
ALLOCATE(self%cells(1:self%numCells))
SELECT TYPE(self)
@ -179,45 +175,30 @@ MODULE moduleMeshInputGmsh2
END SELECT
CASE (2)
ALLOCATE(p(1:2))
READ(10,*) n, elemType, eTemp, boundaryType, eTemp, p(1:2)
!Associate boundary condition procedure.
bt = getBoundaryId(boundaryType)
SELECT CASE(self%geometry)
CASE("Cyl")
ALLOCATE(p(1:2))
READ(10,*) n, elemType, eTemp, boundaryType, eTemp, p(1:2)
!Associate boundary condition procedure.
bt = getBoundaryId(boundaryType)
ALLOCATE(meshEdge2DCyl:: self%edges(e)%obj)
CASE("Cart")
ALLOCATE(p(1:2))
READ(10,*) n, elemType, eTemp, boundaryType, eTemp, p(1:2)
!Associate boundary condition procedure.
bt = getBoundaryId(boundaryType)
ALLOCATE(meshEdge2DCart:: self%edges(e)%obj)
END SELECT
CASE(1)
ALLOCATE(p(1:1))
READ(10, *) n, elemType, eTemp, boundaryType, eTemp, p(1)
!Associate boundary condition
bt = getBoundaryId(boundaryType)
SELECT CASE(self%geometry)
CASE("Rad")
ALLOCATE(p(1:1))
READ(10, *) n, elemType, eTemp, boundaryType, eTemp, p(1)
!Associate boundary condition
bt = getBoundaryId(boundaryType)
ALLOCATE(meshEdge1DRad:: self%edges(e)%obj)
CASE("Cart")
ALLOCATE(p(1:1))
READ(10, *) n, elemType, eTemp, boundaryType, eTemp, p(1)
!Associate boundary condition
bt = getBoundaryId(boundaryType)
ALLOCATE(meshEdge1DCart:: self%edges(e)%obj)
END SELECT
@ -231,9 +212,9 @@ MODULE moduleMeshInputGmsh2
END SELECT
!Read and initialize volumes
!Read and initialize cells
DO e = 1, self%numCells
!Reads the volume according to the geometry
!Read the cell according to the geometry
SELECT CASE(self%dimen)
CASE(3)
READ(10, *) n, elemType

163
src/modules/mesh/inout/vtu/moduleMeshInputVTU.f90
View file

@ -124,7 +124,6 @@ MODULE moduleMeshInputVTU
DO WHILE (iStart < nData)
iStart = iStart + 1
iEnd = iStart - 1 + block
PRINT *, iStart, iEnd
IF (iEnd > nData) THEN
iEnd = nData
@ -173,6 +172,9 @@ MODULE moduleMeshInputVTU
INTEGER:: numNodes, numElements
INTEGER, ALLOCATABLE, DIMENSION(:):: entitiesID, offsets, connectivity, types
REAL(8), ALLOCATABLE, DIMENSION(:):: coordinates
INTEGER:: n, e, c
INTEGER, ALLOCATABLE:: p(:)
INTEGER:: bt
fileID = 10
@ -200,6 +202,8 @@ MODULE moduleMeshInputVTU
line = findline(fileID, 'Name="connectivity"')
ALLOCATE(connectivity(1:MAXVAL(offsets)))
CALL readDataBlock(fileID, MAXVAL(offsets), connectivity)
!Shift connectivity to start in 1
connectivity = connectivity + 1
REWIND(fileID)
!Get the type of elements
@ -217,7 +221,164 @@ MODULE moduleMeshInputVTU
CLOSE(fileID)
!All relevant information from the .vtu file has been read. Time to build the mesh.
self%numNodes = numNodes
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
DO n = 1, self%numNodes
!Get the coordinates for each direction
r(1) = coordinates(3*(n-1)+1)
r(2) = coordinates(3*(n-1)+2)
r(3) = coordinates(3*(n-1)+3)
SELECT CASE(self%dimen)
CASE(3)
ALLOCATE(meshNode3Dcart::self%nodes(n)%obj)
CASE(2)
SELECT CASE(self%geometry)
CASE("Cyl")
ALLOCATE(meshNode2DCyl:: self%nodes(n)%obj)
CASE("Cart")
ALLOCATE(meshNode2DCart:: self%nodes(n)%obj)
END SELECT
r(3) = 0.D0
CASE(1)
SELECT CASE(self%geometry)
CASE("Rad")
ALLOCATE(meshNode1DRad:: self%nodes(n)%obj)
CASE("Cart")
ALLOCATE(meshNode1DCart:: self%nodes(n)%obj)
END SELECT
r(2:3) = 0.D0
END SELECT
CALL self%nodes(n)%obj%init(n, r)
END DO
!Count the number of edges
SELECT TYPE(self)
TYPE IS(meshParticles)
SELECT CASE(self%dimen)
CASE(3)
!Edges are triangles, type 5 in VTK
self%numEdges = COUNT(types==5)
CASE(2)
!Edges are segments, type 3 in VTK
self%numEdges = COUNT(types==3)
CASE(1)
!Edges are nodes, type 1 in VTK
self%numEdges = COUNT(types==1)
END SELECT
self%numCells = numElements - self%numEdges
!Allocate array of edges
ALLOCATE(self%edges(1:self%numEdges))
TYPE IS(meshCollisions)
self%numCells = numElements
END SELECT
!Allocates array of cells
ALLOCATE(self%cells(1:self%numCells))
!Read edges
e = 0
c = 0
SELECT TYPE(self)
TYPE IS(meshParticles)
DO n = 1, numElements
SELECT CASE(self%dimen)
CASE(3)
IF (types(n) == 5) THEN
e = e + 1
ALLOCATE(meshEdge3DCartTria:: self%edges(e)%obj)
ALLOCATE(p(1:3))
p(1) = connectivity(offsets(n) - 2)
p(2) = connectivity(offsets(n) - 1)
p(3) = connectivity(offsets(n))
!Associate boundary condition procedure.
bt = getBoundaryId(entitiesID(n))
!Allocate edge
CALL self%edges(e)%obj%init(n, p, bt, entitiesID(n))
DEALLOCATE(p)
END IF
CASE(2)
IF (types(n) == 3) THEN
e = e+1
ALLOCATE(p(1:2))
p(1) = connectivity(offsets(n) - 1)
p(2) = connectivity(offsets(n))
!Associate boundary condition procedure.
bt = getBoundaryId(entitiesID(n))
SELECT CASE(self%geometry)
CASE("Cyl")
ALLOCATE(meshEdge2DCyl:: self%edges(e)%obj)
CASE("Cart")
ALLOCATE(meshEdge2DCart:: self%edges(e)%obj)
END SELECT
!Allocate edge
CALL self%edges(e)%obj%init(n, p, bt, entitiesID(n))
DEALLOCATE(p)
END IF
CASE(1)
IF (types(n) == 3) THEN
e = e + 1
ALLOCATE(p(1:1))
p(1) = connectivity(offsets(n))
!Associate boundary condition procedure.
bt = getBoundaryId(entitiesID(n))
SELECT CASE(self%geometry)
CASE("Rad")
ALLOCATE(meshEdge1DRad:: self%edges(e)%obj)
CASE("Cart")
ALLOCATE(meshEdge1DCart:: self%edges(e)%obj)
END SELECT
CALL self%edges(e)%obj%init(n, p, bt, entitiesID(n))
DEALLOCATE(p)
END IF
END SELECT
END DO
END SELECT
END SUBROUTINE readVTU
SUBROUTINE readInitialVTU(filename, density, velocity, temperature)

5
src/modules/solver/moduleSolver.f90
View file

@ -514,7 +514,6 @@ MODULE moduleSolver
USE moduleSpecies
USE moduleCompTime
USE moduleProbe
USE moduleMeshOutputVTU !TEMPORARY TO TEST VTU OUTPUT
IMPLICIT NONE
INTEGER, INTENT(in):: t
@ -528,11 +527,8 @@ MODULE moduleSolver
CALL outputProbes(t)
CALL mesh%printOutput(t)
CALL printOutputVTU(mesh, t) !TEMPORARY TO TEST VTU OUTPUT
IF (ASSOCIATED(meshForMCC)) CALL meshForMCC%printColl(t)
IF (ASSOCIATED(meshForMCC)) CALL printCollVTU(meshForMCC,t) !TEMPORARY TO TEST VTU OUTPUT
CALL mesh%printEM(t)
CALL printEMVTU(mesh, t) !TEMPORARY TO TEST VTU OUTPUT
WRITE(*, "(5X,A21,I10,A1,I10)") "t/tFinal: ", t, "/", tFinal
WRITE(*, "(5X,A21,I10)") "Particles: ", nPartOld
IF (t == 0) THEN
@ -565,7 +561,6 @@ MODULE moduleSolver
!Output average values
IF (useAverage .AND. t == tFinal) THEN
CALL mesh%printAverage()
CALL printAverageVTU(mesh) !TEMPORARY TO TEST VTU OUTPUT
END IF