IO: Implement write_snapshot_xdmf().
This subroutine stores an XDMF file which is a wrapper to HDF5 files for easy reading simulation data to visualization tools like Paraview or Visit. This subroutine is based on the one written by Pierre Kestener. Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
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src/io.F90
233
src/io.F90
@ -458,6 +458,7 @@ module io
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! import external variables
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!
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use evolution , only : time
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use mpitools , only : master
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! local variables are not implicit by default
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!
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@ -479,6 +480,9 @@ module io
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! store variable snapshot file
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!
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call write_snapshot_h5()
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if (with_xdmf) then
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call write_snapshot_xdmf()
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end if
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#endif /* HDF5 */
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! increase the snapshot counter and calculate the next snapshot time
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@ -7264,6 +7268,235 @@ module io
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!-------------------------------------------------------------------------------
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!
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end subroutine read_5d_array_double_h5
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!
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!===============================================================================
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!
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! subroutine WRITE_SNAPSHOT_XDMF:
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! ------------------------------
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!
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! Subroutine writes an XDMF file per snapshot per MPI process.
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! XDMF file is just a wrapper which helps to load data in a visualization
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! tools like Paraview or Visit.
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!
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! Based on the subroutine by Pierre Kestener
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! (see https://bitbucket.org/pkestene/amun-code).
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!
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!
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!===============================================================================
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!
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subroutine write_snapshot_xdmf()
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! import procedures and variables from other modules
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!
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use blocks , only : block_data, list_data
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use blocks , only : get_dblocks
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use equations , only : nv, pvars
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use mpitools , only : nproc
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use coordinates , only : in, jn, kn
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use coordinates , only : adx, ady, adz
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use coordinates , only : ng
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use evolution , only : time
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! local variables are not implicit by default
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!
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implicit none
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! local pointers
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!
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type(block_data), pointer :: pdata
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! local variables
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!
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character(len=64) :: fname, hname
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character(len=128) :: stmp, ttmp, sdim, bdim, pdim
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integer(kind=4) :: l, p
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integer(kind=4) :: ip, jp, kp
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! local arrays
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!
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integer, dimension(12) :: slab
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! local parameters
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!
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integer, parameter :: xdmf = 101
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!
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!-------------------------------------------------------------------------------
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!
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! prepare the XDMF and HDF5 file names
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write(fname, "(a1,i6.6,'_',i5.5,'.xdmf')") ftype, isnap, nproc
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write(hname, "(a1,i6.6,'_',i5.5,'.h5' )") ftype, isnap, nproc
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! open the XDMF file
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!
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open (unit = xdmf, file = fname, status = 'replace')
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! write the header
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!
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write(xdmf, "(a)") '<?xml version="1.0" encoding="UTF-8"?>'
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write(xdmf, "(a)") '<Xdmf Version="2.2"' &
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// ' xmlns:xi="http://www.w3.org/2003/XInclude">'
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write(xdmf, "(a)") ' <Domain>'
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write(stmp, "(a,i5.5)") 'region_', nproc
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write(xdmf, "(a)") ' <Grid Name="' // trim(adjustl(stmp)) &
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// '" GridType="Collection" CollectionType="Spatial">'
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write(stmp, "(1g15.8)") time
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write(xdmf, "(a)") ' <Time TimeType="Single" Value="' &
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// trim(adjustl(stmp)) // '"/>'
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! do not proceed if there are not data block on this processor
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!
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if (get_dblocks() > 0) then
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! prepare dimensions
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!
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ip = in + 1
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jp = jn + 1
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#if NDIMS == 3
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kp = kn + 1
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#endif /* NDIMS == 3 */
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#if NDIMS == 3
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write(stmp, "(1i8)") kn
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write(ttmp, "(1i8)") jn
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stmp = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
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write(ttmp, "(1i8)") in
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#else /* NDIMS == 3 */
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write(stmp, "(1i8)") jn
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write(ttmp, "(1i8)") in
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#endif /* NDIMS == 3 */
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bdim = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
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#if NDIMS == 3
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write(stmp, "(1i8)") 1
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#else /* NDIMS == 3 */
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write(stmp, "(1i8)") kn
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#endif /* NDIMS == 3 */
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write(ttmp, "(1i8)") jn
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stmp = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
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write(ttmp, "(1i8)") in
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stmp = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
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write(ttmp, "(1i8)") get_dblocks()
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sdim = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
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! prepare slab indices
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!
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#if NDIMS == 3
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if (with_ghosts) then
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slab(:) = (/ ng, ng, ng, -1, 1, 1, 1, 1, kn, jn, in, 1 /)
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else
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slab(:) = (/ 0, 0, 0, -1, 1, 1, 1, 1, kn, jn, in, 1 /)
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end if
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#else /* NDIMS == 3 */
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if (with_ghosts) then
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slab(:) = (/ 0, ng, ng, -1, 1, 1, 1, 1, 1, jn, in, 1 /)
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else
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slab(:) = (/ 0, 0, 0, -1, 1, 1, 1, 1, 1, jn, in, 1 /)
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end if
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#endif /* NDIMS == 3 */
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! iterate over all data blocks
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!
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l = 0
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pdata => list_data
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do while(associated(pdata))
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! store block geometry information
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!
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write(stmp, "(1i9.9)") pdata%meta%id
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write(xdmf, "(a)") ' <Grid Name="block_' &
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// trim(adjustl(stmp)) // '">'
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#if NDIMS == 3
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write(stmp, "(1i8)") kp
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write(ttmp, "(1i8)") jp
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stmp = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
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write(ttmp, "(1i8)") ip
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stmp = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
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write(xdmf, "(a)") ' <Topology TopologyType="3DCoRectMesh"' &
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// ' Dimensions="' // trim(adjustl(stmp)) // '"/>'
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write(xdmf, "(a)") ' <Geometry GeometryType="ORIGIN_DXDYDZ">'
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write(stmp, "(3e16.8)") pdata%meta%zmin, pdata%meta%ymin &
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, pdata%meta%xmin
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write(xdmf, "(a)") ' <DataItem Name="Origin" NumberType="Float"' &
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// ' Precision="4" Dimensions="3" Format="XML">' &
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// trim(adjustl(stmp)) // '</DataItem>'
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write(stmp, "(3e16.8)") adz(pdata%meta%level), ady(pdata%meta%level) &
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, adx(pdata%meta%level)
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write(xdmf, "(a)") ' <DataItem Name="Spacing" NumberType="Float"' &
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// ' Precision="4" Dimensions="3" Format="XML">' &
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// trim(adjustl(stmp)) // '</DataItem>'
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#else /* NDIMS == 3 */
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write(stmp, "(1i8)") jp
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write(ttmp, "(1i8)") ip
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stmp = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
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write(xdmf, "(a)") ' <Topology TopologyType="2DCoRectMesh"' &
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// ' Dimensions="' // trim(adjustl(stmp)) // '"/>'
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write(xdmf, "(a)") ' <Geometry GeometryType="ORIGIN_DXDY">'
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write(stmp, "(2e16.8)") pdata%meta%ymin, pdata%meta%xmin
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write(xdmf, "(a)") ' <DataItem Name="Origin" NumberType="Float"' &
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// ' Precision="4" Dimensions="2" Format="XML">' &
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// trim(adjustl(stmp)) // '</DataItem>'
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write(stmp, "(2e16.8)") ady(pdata%meta%level), adx(pdata%meta%level)
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write(xdmf, "(a)") ' <DataItem Name="Spacing" NumberType="Float"' &
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// ' Precision="4" Dimensions="2" Format="XML">' &
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// trim(adjustl(stmp)) // '</DataItem>'
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#endif /* NDIMS == 3 */
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write(xdmf, "(a)") ' </Geometry>'
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! convert slab dimensions to string
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!
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slab(4) = l
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write(pdim, "(1i8)") slab(1)
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do p = 2, 12
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write(ttmp, "(1i8)") slab(p)
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pdim = trim(adjustl(pdim)) // ' ' // trim(adjustl(ttmp))
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end do
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! loop over all variables and store their information
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!
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do p = 1, nv
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write(xdmf, "(a)") ' <Attribute Name="' &
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// trim(adjustl(pvars(p))) &
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// '" AttributeType="Scalar" Center="Cell">'
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write(xdmf, "(a)") ' <DataItem ItemType="Hyperslab"' &
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// ' Dimensions="' // trim(adjustl(bdim)) &
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// '" Type="HyperSlab">'
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write(xdmf, "(a)") ' <DataItem Dimensions="3 4" Format="XML">' &
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// trim(adjustl(pdim)) // '</DataItem>'
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write(ttmp, "(a,':/variables/',a)") trim(hname), trim(pvars(p))
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write(xdmf, "(a)") ' <DataItem NumberType="Float"' &
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// ' Precision="8" Dimensions="' &
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// trim(adjustl(sdim)) // '" Format="HDF">' &
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// trim(adjustl(ttmp)) // '</DataItem>'
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write(xdmf, "(a)") ' </DataItem>'
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write(xdmf, "(a)") ' </Attribute>'
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end do
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! close grid structure for the current block
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!
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write(xdmf,"(a)") ' </Grid>'
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l = l + 1
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pdata => pdata%next
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end do
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end if ! get_dblocks() > 0
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! close the XDMF structures
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!
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write(xdmf, "(a)") ' </Grid>'
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write(xdmf, "(a)") ' </Domain>'
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write(xdmf, "(a)") '</Xdmf>'
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! close the XDMF file
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!
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close(xdmf)
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!-------------------------------------------------------------------------------
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!
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end subroutine write_snapshot_xdmf
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#endif /* HDF5 */
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!===============================================================================
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