Merge branch 'master' into reconnection
This commit is contained in:
commit
4c54692ad2
327
src/io.F90
327
src/io.F90
@ -126,6 +126,10 @@ module io
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!
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!
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logical , save :: with_ghosts = .true.
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logical , save :: with_ghosts = .true.
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|
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! a flag to determine if XDMF files should be generated
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!
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logical , save :: with_xdmf = .false.
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! local variables to store the number of processors and maximum level read from
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! local variables to store the number of processors and maximum level read from
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! the restart file
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! the restart file
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!
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!
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@ -195,6 +199,7 @@ module io
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! local variables
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! local variables
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!
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!
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character(len=255) :: ghosts = "on"
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character(len=255) :: ghosts = "on"
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character(len=255) :: xdmf = "off"
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integer :: dd, hh, mm, ss
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integer :: dd, hh, mm, ss
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!
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!
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!-------------------------------------------------------------------------------
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!-------------------------------------------------------------------------------
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@ -226,6 +231,10 @@ module io
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!
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!
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call get_parameter_string ("include_ghosts" , ghosts )
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call get_parameter_string ("include_ghosts" , ghosts )
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! get the flag determining if the XDMF files should be generated
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!
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call get_parameter_string ("generate_xdmf" , xdmf )
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! check ghost cell storing flag
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! check ghost cell storing flag
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!
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!
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select case(trim(ghosts))
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select case(trim(ghosts))
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@ -235,6 +244,15 @@ module io
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with_ghosts = .true.
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with_ghosts = .true.
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end select
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end select
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! check flag for generating XDMF files
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!
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select case(trim(xdmf))
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case ("off", "OFF", "n", "N", "false", "FALSE", "no", "NO")
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with_xdmf = .false.
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case default
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with_xdmf = .true.
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end select
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! return the run number
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! return the run number
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!
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!
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irun = max(1, nrest)
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irun = max(1, nrest)
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@ -251,6 +269,11 @@ module io
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else
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else
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write (*,"(4x,a21,2x,'=',1x,a)") "with ghosts cells ", "off"
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write (*,"(4x,a21,2x,'=',1x,a)") "with ghosts cells ", "off"
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end if
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end if
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if (with_xdmf) then
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write (*,"(4x,a21,2x,'=',1x,a)") "generate XDMF files ", "on"
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else
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write (*,"(4x,a21,2x,'=',1x,a)") "generate XDMF files ", "off"
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end if
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write (*,"(4x,a21,2x,'=',1x,e9.2)") "snapshot interval ", hsnap
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write (*,"(4x,a21,2x,'=',1x,e9.2)") "snapshot interval ", hsnap
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if (hrest > 0.0d+00) then
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if (hrest > 0.0d+00) then
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dd = int(hrest / 2.4d+01)
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dd = int(hrest / 2.4d+01)
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@ -435,6 +458,7 @@ module io
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! import external variables
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! import external variables
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!
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!
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use evolution , only : time
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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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! local variables are not implicit by default
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!
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!
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@ -456,6 +480,10 @@ module io
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! store variable snapshot file
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! store variable snapshot file
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!
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!
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call write_snapshot_h5()
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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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if (master) call write_snapshot_xdmf_master()
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end if
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#endif /* HDF5 */
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#endif /* HDF5 */
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! increase the snapshot counter and calculate the next snapshot time
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! increase the snapshot counter and calculate the next snapshot time
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@ -7241,6 +7269,305 @@ module io
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!-------------------------------------------------------------------------------
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!-------------------------------------------------------------------------------
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!
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!
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end subroutine read_5d_array_double_h5
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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, "(1i16)") nproc
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write(xdmf, "(a)") ' <Grid Name="region_' // 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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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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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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|
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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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|
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! store block geometry information
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|
!
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write(stmp, "(1i16)") 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">' &
|
||||||
|
// trim(adjustl(stmp)) // '</DataItem>'
|
||||||
|
write(stmp, "(2e16.8)") ady(pdata%meta%level), adx(pdata%meta%level)
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||||||
|
write(xdmf, "(a)") ' <DataItem Name="Spacing" NumberType="Float"' &
|
||||||
|
// ' Precision="4" Dimensions="2" Format="XML">' &
|
||||||
|
// trim(adjustl(stmp)) // '</DataItem>'
|
||||||
|
#endif /* NDIMS == 3 */
|
||||||
|
write(xdmf, "(a)") ' </Geometry>'
|
||||||
|
|
||||||
|
! convert slab dimensions to string
|
||||||
|
!
|
||||||
|
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)
|
||||||
|
pdim = trim(adjustl(pdim)) // ' ' // trim(adjustl(ttmp))
|
||||||
|
end do
|
||||||
|
|
||||||
|
! loop over all variables and store their information
|
||||||
|
!
|
||||||
|
do p = 1, nv
|
||||||
|
|
||||||
|
write(xdmf, "(a)") ' <Attribute Name="' &
|
||||||
|
// trim(adjustl(pvars(p))) &
|
||||||
|
// '" AttributeType="Scalar" Center="Cell">'
|
||||||
|
write(xdmf, "(a)") ' <DataItem ItemType="Hyperslab"' &
|
||||||
|
// ' Dimensions="' // trim(adjustl(bdim)) &
|
||||||
|
// '" Type="HyperSlab">'
|
||||||
|
write(xdmf, "(a)") ' <DataItem Dimensions="3 4" Format="XML">' &
|
||||||
|
// trim(adjustl(pdim)) // '</DataItem>'
|
||||||
|
write(ttmp, "(a,':/variables/',a)") trim(hname), trim(pvars(p))
|
||||||
|
write(xdmf, "(a)") ' <DataItem NumberType="Float"' &
|
||||||
|
// ' Precision="8" Dimensions="' &
|
||||||
|
// trim(adjustl(sdim)) // '" Format="HDF">' &
|
||||||
|
// trim(adjustl(ttmp)) // '</DataItem>'
|
||||||
|
write(xdmf, "(a)") ' </DataItem>'
|
||||||
|
write(xdmf, "(a)") ' </Attribute>'
|
||||||
|
|
||||||
|
end do
|
||||||
|
|
||||||
|
! close grid structure for the current block
|
||||||
|
!
|
||||||
|
write(xdmf,"(a)") ' </Grid>'
|
||||||
|
|
||||||
|
l = l + 1
|
||||||
|
pdata => pdata%next
|
||||||
|
end do
|
||||||
|
|
||||||
|
end if ! get_dblocks() > 0
|
||||||
|
|
||||||
|
! close the XDMF structures
|
||||||
|
!
|
||||||
|
write(xdmf, "(a)") ' </Grid>'
|
||||||
|
write(xdmf, "(a)") ' </Domain>'
|
||||||
|
write(xdmf, "(a)") '</Xdmf>'
|
||||||
|
|
||||||
|
! close the XDMF file
|
||||||
|
!
|
||||||
|
close(xdmf)
|
||||||
|
|
||||||
|
!-------------------------------------------------------------------------------
|
||||||
|
!
|
||||||
|
end subroutine write_snapshot_xdmf
|
||||||
|
!
|
||||||
|
!===============================================================================
|
||||||
|
!
|
||||||
|
! subroutine WRITE_SNAPSHOT_XDMF_MASTER:
|
||||||
|
! -------------------------------------
|
||||||
|
!
|
||||||
|
! Subroutine writes one XDMF file per snapshot in root MPI process to gather
|
||||||
|
! all MPI subdomains.
|
||||||
|
!
|
||||||
|
! Based on the subroutine by Pierre Kestener
|
||||||
|
! (see https://bitbucket.org/pkestene/amun-code).
|
||||||
|
!
|
||||||
|
!
|
||||||
|
!===============================================================================
|
||||||
|
!
|
||||||
|
subroutine write_snapshot_xdmf_master()
|
||||||
|
|
||||||
|
! import procedures and variables from other modules
|
||||||
|
!
|
||||||
|
use mpitools , only : npmax
|
||||||
|
|
||||||
|
! local variables are not implicit by default
|
||||||
|
!
|
||||||
|
implicit none
|
||||||
|
|
||||||
|
! local variables
|
||||||
|
!
|
||||||
|
character(len=64) :: fname, pname
|
||||||
|
integer(kind=4) :: np
|
||||||
|
|
||||||
|
! local parameters
|
||||||
|
!
|
||||||
|
integer, parameter :: xdmf = 102
|
||||||
|
!
|
||||||
|
!-------------------------------------------------------------------------------
|
||||||
|
!
|
||||||
|
! prepare the XDMF and HDF5 file names
|
||||||
|
|
||||||
|
write(fname, "(a1,i6.6,'.xdmf')") ftype, isnap
|
||||||
|
|
||||||
|
! open the XDMF file
|
||||||
|
!
|
||||||
|
open (unit = xdmf, file = fname, status = 'replace')
|
||||||
|
|
||||||
|
! write the header
|
||||||
|
!
|
||||||
|
write(xdmf, "(a)") '<?xml version="1.0" encoding="UTF-8"?>'
|
||||||
|
write(xdmf, "(a)") '<Xdmf Version="2.2"' &
|
||||||
|
// ' xmlns:xi="http://www.w3.org/2003/XInclude">'
|
||||||
|
write(xdmf, "(a)") ' <Domain Name="GatherMPISubDomains">'
|
||||||
|
write(xdmf, "(a)") ' <Grid Name="FullDomain"' &
|
||||||
|
// ' GridType="Collection" CollectionType="Spatial">'
|
||||||
|
|
||||||
|
! write references to MPI subdomain files
|
||||||
|
!
|
||||||
|
do np = 0, npmax
|
||||||
|
write(pname, "(a1,i6.6,'_',i5.5,'.xdmf')") ftype, isnap, np
|
||||||
|
write(xdmf, "(a)") ' <xi:include href="' // trim(pname) &
|
||||||
|
// '" xpointer="xpointer(//Xdmf/Domain/Grid)"/>'
|
||||||
|
end do
|
||||||
|
|
||||||
|
! close the XDMF structures
|
||||||
|
!
|
||||||
|
write(xdmf, "(a)") ' </Grid>'
|
||||||
|
write(xdmf, "(a)") ' </Domain>'
|
||||||
|
write(xdmf, "(a)") '</Xdmf>'
|
||||||
|
|
||||||
|
! close the XDMF file
|
||||||
|
!
|
||||||
|
close(xdmf)
|
||||||
|
|
||||||
|
!-------------------------------------------------------------------------------
|
||||||
|
!
|
||||||
|
end subroutine write_snapshot_xdmf_master
|
||||||
#endif /* HDF5 */
|
#endif /* HDF5 */
|
||||||
|
|
||||||
!===============================================================================
|
!===============================================================================
|
||||||
|
|||||||
Loading…
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Reference in New Issue
Block a user