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Make mesh converter compatible with random entity tag. #3

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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,9 @@
*.out
*.app

# System files osx
**/.DS_Store

# Directories
obj/
bin/
15 changes: 10 additions & 5 deletions mesh_converter/src/mod.f90
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Expand Up @@ -32,6 +32,11 @@ module gmshMod
integer :: numSurfaces
integer :: numVolumes

integer, allocatable :: Point_Tags(:)
integer, allocatable :: Curve_Tags(:)
integer, allocatable :: Surface_Tags(:)
integer, allocatable :: Volume_Tags(:)

integer, allocatable :: Point_numPhysicalTags(:)
integer, allocatable :: Curve_numPhysicalTags(:)
integer, allocatable :: Surface_numPhysicalTags(:)
Expand All @@ -42,12 +47,12 @@ module gmshMod
integer, allocatable :: Surface_physicalTags(:,:)
integer, allocatable :: Volume_physicalTags(:,:)
end type gmshEntityType

type gmshNodeType
integer :: numNodeBlocks
integer :: numNodes
integer :: minNodeTag
integer :: maxNodeTag
integer :: numNodeBlocks
integer :: numNodes
integer :: minNodeTag
integer :: maxNodeTag
integer,allocatable :: numNodesInBlock(:)
real(kind=8),allocatable :: coord(:,:)
end type gmshNodeType
Expand Down
82 changes: 47 additions & 35 deletions mesh_converter/src/readFiles.f90
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Expand Up @@ -330,7 +330,7 @@ subroutine readGmshMsh(lM)

! Entities
call gmsh_readentities(fid)

! Nodes
! Please note not all nodes are grid points, e.g. center of the circle.
call gmsh_readnodes(fid)
Expand All @@ -357,7 +357,7 @@ subroutine readGmshMsh(lM)
end do

lM%fname = "mesh-complete.mesh"

return
end subroutine readGmshMsh
!***********************************************************************
Expand Down Expand Up @@ -398,7 +398,7 @@ subroutine gmsh_readphysicalnames(lM, fid)
integer, intent(inout) :: fid

integer :: i, n

rewind(fid)
call findKwrd(fid, "$PhysicalNames")
read(fid,*) n
Expand Down Expand Up @@ -432,7 +432,7 @@ subroutine gmsh_readnodes(fid)

integer :: i, j, itemp
integer, allocatable :: NodeTag(:)

rewind(fid)
call findKwrd(fid, "$Nodes")
read(fid,*) gmshNodes%numNodeBlocks, gmshNodes%numNodes, &
Expand All @@ -441,7 +441,7 @@ subroutine gmsh_readnodes(fid)
allocate(gmshNodes%numNodesInBlock(gmshNodes%numNodeBlocks))
allocate(NodeTag(gmshNodes%numNodes))
allocate(gmshNodes%coord(3,gmshNodes%numNodes))

! read coordiantes block by block
do i = 1, gmshNodes%numNodeBlocks
read(fid,*) itemp, itemp, itemp, gmshNodes%numNodesInBlock(i)
Expand All @@ -453,7 +453,7 @@ subroutine gmsh_readnodes(fid)
read(fid,*) gmshNodes%coord(:,NodeTag(j))
end do
end do

return
end subroutine gmsh_readnodes
!***********************************************************************
Expand Down Expand Up @@ -498,9 +498,9 @@ subroutine gmsh_readelements(fid)
case(9)
gmshElements%eNoN(i) = 6 ! 6-node second order triangle
case(10)
gmshElements%eNoN(i) = 9 ! 9-node second order quadrangle
gmshElements%eNoN(i) = 9 ! 9-node second order quadrangle
case(11)
gmshElements%eNoN(i) = 10 ! 10-node second order tetrahedron
gmshElements%eNoN(i) = 10 ! 10-node second order tetrahedron
case(12)
gmshElements%eNoN(i) = 27 ! 27-node second order hexahedron
case(15)
Expand All @@ -509,7 +509,7 @@ subroutine gmsh_readelements(fid)
gmshElements%eNoN(i) = 8 ! 8-node second order quadrangle
case(17)
gmshElements%eNoN(i) = 20 ! 20-node second order hexahedron
case default
case default
write(stdout,ftab4) "ERROR: elelment type not defined!"
end select

Expand All @@ -526,7 +526,7 @@ subroutine gmsh_readelements(fid)
call findKwrd(fid, "$Elements")
read(fid,*)
do i = 1, gmshElements%numElementBlocks
read(fid,*)
read(fid,*)
eNoN = gmshElements%eNoN(i)
do j = 1, gmshElements%numElementsInBlock(i)
ie = ie+1
Expand Down Expand Up @@ -559,8 +559,10 @@ subroutine gmsh_readentities(fid)

! Point entites
if (gmshEntities%numPoints > 0) then
allocate(gmshEntities%Point_Tags(gmshEntities%numPoints))
allocate(gmshEntities%Point_numPhysicalTags(gmshEntities%numPoints))
allocate(gmshEntities%Point_PhysicalTags(gmshEntities%numPoints,maxNumTags))
gmshEntities%Point_Tags = 0
gmshEntities%Point_numPhysicalTags = 0
gmshEntities%Point_PhysicalTags = 0

Expand All @@ -572,16 +574,19 @@ subroutine gmsh_readentities(fid)
elseif (numPhysicalTags == 1) then
BACKSPACE(fid)
read(fid,*) Tag, rtemp, rtemp, rtemp, numPhysicalTags, PhysicalTags
gmshEntities%Point_numPhysicalTags(Tag) = 1
gmshEntities%Point_PhysicalTags(Tag,1) = PhysicalTags
gmshEntities%Point_Tags(i) = Tag
gmshEntities%Point_numPhysicalTags(i) = 1
gmshEntities%Point_PhysicalTags(i,1) = PhysicalTags
end if
end do
end if

! Curve entites
if (gmshEntities%numCurves > 0) then
allocate(gmshEntities%Curve_Tags(gmshEntities%numCurves))
allocate(gmshEntities%Curve_numPhysicalTags(gmshEntities%numCurves))
allocate(gmshEntities%Curve_PhysicalTags(gmshEntities%numCurves,maxNumTags))
gmshEntities%Curve_Tags = 0
gmshEntities%Curve_numPhysicalTags = 0
gmshEntities%Curve_PhysicalTags = 0

Expand All @@ -593,16 +598,19 @@ subroutine gmsh_readentities(fid)
elseif (numPhysicalTags == 1) then
BACKSPACE(fid)
read(fid,*) Tag, rtemp, rtemp, rtemp, rtemp, rtemp, rtemp, numPhysicalTags, PhysicalTags
gmshEntities%Curve_numPhysicalTags(Tag) = 1
gmshEntities%Curve_PhysicalTags(Tag,1) = PhysicalTags
gmshEntities%Curve_Tags(i) = Tag
gmshEntities%Curve_numPhysicalTags(i) = 1
gmshEntities%Curve_PhysicalTags(i,1) = PhysicalTags
end if
end do
end if

! Surface entites
if (gmshEntities%numSurfaces > 0) then
allocate(gmshEntities%Surface_Tags(gmshEntities%numSurfaces))
allocate(gmshEntities%Surface_numPhysicalTags(gmshEntities%numSurfaces))
allocate(gmshEntities%Surface_PhysicalTags(gmshEntities%numSurfaces,maxNumTags))
gmshEntities%Surface_Tags = 0
gmshEntities%Surface_numPhysicalTags = 0
gmshEntities%Surface_PhysicalTags = 0

Expand All @@ -614,16 +622,19 @@ subroutine gmsh_readentities(fid)
elseif (numPhysicalTags == 1) then
BACKSPACE(fid)
read(fid,*) Tag, rtemp, rtemp, rtemp, rtemp, rtemp, rtemp, numPhysicalTags, PhysicalTags
gmshEntities%Surface_numPhysicalTags(Tag) = 1
gmshEntities%Surface_PhysicalTags(Tag,1) = PhysicalTags
gmshEntities%Surface_Tags(i) = Tag
gmshEntities%Surface_numPhysicalTags(i) = 1
gmshEntities%Surface_PhysicalTags(i,1) = PhysicalTags
end if
end do
end if

! Volume entites
if (gmshEntities%numVolumes > 0) then
allocate(gmshEntities%Volume_Tags(gmshEntities%numVolumes))
allocate(gmshEntities%Volume_numPhysicalTags(gmshEntities%numVolumes))
allocate(gmshEntities%Volume_PhysicalTags(gmshEntities%numVolumes,maxNumTags))
gmshEntities%Volume_Tags = 0
gmshEntities%Volume_numPhysicalTags = 0
gmshEntities%Volume_PhysicalTags = 0

Expand All @@ -635,8 +646,9 @@ subroutine gmsh_readentities(fid)
elseif (numPhysicalTags == 1) then
BACKSPACE(fid)
read(fid,*) Tag, rtemp, rtemp, rtemp, rtemp, rtemp, rtemp, numPhysicalTags, PhysicalTags
gmshEntities%Volume_numPhysicalTags(Tag) = 1
gmshEntities%Volume_PhysicalTags(Tag,1) = PhysicalTags
gmshEntities%Volume_Tags(i) = Tag
gmshEntities%Volume_numPhysicalTags(i) = 1
gmshEntities%Volume_PhysicalTags(i,1) = PhysicalTags
end if
end do
end if
Expand Down Expand Up @@ -666,7 +678,7 @@ subroutine gmsh_bodymesh(lM)
physicalTag = gmshPhysicalNames%physicalTag(i)
j = j+1
name = gmshPhysicalNames%name(i)
end if
end if
end do
if (j .gt. 1) then
write(stdout,ftab4) "ERROR: can only handle one body mesh."
Expand All @@ -677,8 +689,8 @@ subroutine gmsh_bodymesh(lM)
stop
end if

! Using the physical tag to determine the
! surface tag (entity tag) for 2D problem or
! Using the physical tag to determine the
! surface tag (entity tag) for 2D problem or
! volume tag (entity tag) for 3D problem.
! Please note that there might be multiple entity tags
! for one physical tag.
Expand All @@ -690,7 +702,7 @@ subroutine gmsh_bodymesh(lM)
do j = 1, gmshEntities%Surface_numPhysicalTags(i)
if (physicalTag .eq. gmshEntities%Surface_PhysicalTags(i,j)) then
numEntityTags = numEntityTags + 1
entityTag(numEntityTags) = i
entityTag(numEntityTags) = gmshEntities%Surface_Tags(i)
end if
end do
end do
Expand All @@ -702,7 +714,7 @@ subroutine gmsh_bodymesh(lM)
do j = 1, gmshEntities%Volume_numPhysicalTags(i)
if (physicalTag .eq. gmshEntities%Volume_PhysicalTags(i,j)) then
numEntityTags = numEntityTags + 1
entityTag(numEntityTags) = i
entityTag(numEntityTags) = gmshEntities%Volume_Tags(i)
end if
end do
end do
Expand All @@ -721,7 +733,7 @@ subroutine gmsh_bodymesh(lM)
if (gmshElements%ElementDim(i) .eq. lM%nsd) then
if (gmshElements%EntityTag(i) .eq. Tag) then
lM%eNoN = gmshElements%eNoN(i)
if (.not. allocated(gIEN)) &
if (.not. allocated(gIEN)) &
allocate(gIEN(lM%eNoN,gmshElements%numElements))
gIEN(1:lM%eNoN,nEl+1:nEl + gmshElements%numElementsinBlock(i)) = &
gmshElements%conn(1:lM%eNoN,j+1:j+gmshElements%numElementsinBlock(i))
Expand Down Expand Up @@ -788,7 +800,7 @@ subroutine gmsh_boundarymesh(lM)
logical,allocatable :: flag(:)

! For boundary points, it requires two global-to-local mappings.
! g2l: since we need to remove some unnecessary points in gmshNodes,
! g2l: since we need to remove some unnecessary points in gmshNodes,
! this mapping is built to contruct the body mesh
! lg2l: when writing boundaries to vtp files, we need a local connectivity
! system, this mapping maps **body mesh**, i.e. after g2l, to local.
Expand All @@ -810,7 +822,7 @@ subroutine gmsh_boundarymesh(lM)
sharedelem(k,numshared(k)) = i
end do
end do

lM%nFa = 0
do i = 1, gmshPhysicalNames%num
if (gmshPhysicalNames%dimension(i) .eq. lM%nsd-1) then
Expand All @@ -823,7 +835,7 @@ subroutine gmsh_boundarymesh(lM)
if (gmshPhysicalNames%dimension(i) .eq. lM%nsd-1) then
j = j + 1
physicalTag(j) = gmshPhysicalNames%physicalTag(i)
lM%fa(j)%fname = gmshPhysicalNames%name(i)
lM%fa(j)%fname = gmshPhysicalNames%name(i)
end if
end do

Expand All @@ -844,7 +856,7 @@ subroutine gmsh_boundarymesh(lM)
do k = 1, gmshEntities%Curve_numPhysicalTags(j)
if (physicalTag(iFa) .eq. gmshEntities%Curve_physicalTags(j,k)) then
numEntityTags = numEntityTags + 1
entityTag(numEntityTags) = j
entityTag(numEntityTags) = gmshEntities%Curve_Tags(j)
end if
end do
end do
Expand All @@ -857,15 +869,15 @@ subroutine gmsh_boundarymesh(lM)
do k = 1, gmshEntities%Surface_numPhysicalTags(j)
if (physicalTag(iFa) .eq. gmshEntities%Surface_physicalTags(j,k)) then
numEntityTags = numEntityTags + 1
entityTag(numEntityTags) = j
entityTag(numEntityTags) = gmshEntities%Surface_Tags(j)
end if
end do
end do
end if
if (numEntityTags .eq. 0) then
write(stdout,ftab4) "ERROR: cannot find corresponding entitiy."
stop
end if
end if

! raw connectivity for boundary mesh
nEl = 0
Expand All @@ -877,7 +889,7 @@ subroutine gmsh_boundarymesh(lM)
if (gmshElements%EntityTag(i) .eq. Tag) then
eNoN = gmshElements%eNoN(i)
! lM%fa(iFa)%eNoN = eNoN
if (.not. allocated(gIEN)) &
if (.not. allocated(gIEN)) &
allocate(gIEN(eNoN,gmshElements%numElements))
numinBlocks = gmshElements%numElementsinBlock(i)
gIEN(1:eNoN,nEl+1:nEl+numinBlocks) = gmshElements%conn(1:eNoN,j+1:j+numinBlocks)
Expand All @@ -888,7 +900,7 @@ subroutine gmsh_boundarymesh(lM)
j = j + gmshElements%numElementsInBlock(i)
end do
end do

! first global to local mapping
do i = 1, nEl
do j = 1, eNoN
Expand Down Expand Up @@ -920,7 +932,7 @@ subroutine gmsh_boundarymesh(lM)
lM%fa(iFa)%x(:,j) = lM%x(:,i)
end if
end do
! DO NOT convert gIEN to local IEN yet
! DO NOT convert gIEN to local IEN yet
allocate(lM%fa(iFa)%IEN(lM%fa(iFa)%eNoN,lM%fa(iFa)%nEl))
lM%fa(iFa)%IEN = gIEN(:,1:lM%fa(iFa)%nEl)

Expand All @@ -933,7 +945,7 @@ subroutine gmsh_boundarymesh(lM)
do k = 1, numshared(ii)
flag = .FALSE.
ie = sharedelem(ii,k)
do j = 1, lM%fa(iFa)%eNoN
do j = 1, lM%fa(iFa)%eNoN
do l = 1, lM%eNoN
if (gIEN(j,i) .eq. lM%IEN(l,ie)) then
flag(j) = .TRUE.
Expand All @@ -944,7 +956,7 @@ subroutine gmsh_boundarymesh(lM)
if (ALL(flag)) then
lM%fa(iFa)%gE(i) = ie
exit
end if
end if
end do
end do

Expand Down