! $Id$
!
! Distributed IO (i.e. each process writes its own file data/procX)
!
! The file format written by output_snap() (and used, e.g. in var.dat)
! consists of the followinig Fortran records:
! 1. data(mx,my,mz,nvar)
! 2. t(1), x(mx), y(my), z(mz), dx(1), dy(1), dz(1), deltay(1)
! Here nvar denotes the number of slots, i.e. 1 for one scalar field, 3
! for one vector field, 8 for var.dat in the case of MHD with entropy.
!
! 04-nov-11/MR: IOSTAT handling generally introduced
! 16-nov-11/MR: calls to outlog adapted
! 10-Dec-2011/Bourdin.KIS: major cleanup
! 01-Jun-2015/Bourdin.KIS: outlog removed to see clear-text error messages
!
module Io
!
use Cdata
use Cparam, only: intlen, fnlen, max_int
use File_io, only: delete_file, file_exists
use Messages, only: fatal_error, warning, svn_id
!
implicit none
!
include 'io.h'
include 'record_types.h'
!
interface read_snap
module procedure read_snap_double
module procedure read_snap_single
endinterface
!
interface read_part
module procedure read_part_double
module procedure read_part_single
endinterface
!
interface read_globals
module procedure read_globals_double
module procedure read_globals_single
endinterface
!
interface input_grid
module procedure input_grid_double
module procedure input_grid_single
endinterface
!
interface input_proc_bounds
module procedure input_proc_bounds_double
module procedure input_proc_bounds_single
endinterface
!
! set ireset_tstart to 1 or 2 to coordinate divergent timestamp
integer, parameter :: MINT=1, MAXT=2
!
! Indicates if IO is done distributed (each proc writes into a procdir)
! or collectively (eg. by specialized IO-nodes or by MPI-IO).
!
logical :: lcollective_IO=.false.
character (len=labellen) :: IO_strategy="dist"
!
integer :: persist_last_id=-max_int
!
contains
!***********************************************************************
subroutine register_io
!
! dummy routine, generates separate directory for each processor.
! VAR#-files are written to the directory directory_snap which will
! be the same as directory, unless specified otherwise.
!
! 20-sep-02/wolf: coded
!
use Mpicomm, only: lroot
!
! identify version number
!
if (lroot) call svn_id("$Id$")
!
endsubroutine register_io
!***********************************************************************
subroutine finalize_io
!
endsubroutine finalize_io
!***********************************************************************
subroutine directory_names
!
! Set up the directory names:
! set directory name for the output (one subdirectory for each processor)
! if datadir_snap (where var.dat, VAR# go) is empty, initialize to datadir
!
! 02-oct-2002/wolf: coded
!
use General, only: directory_names_std
!
! check whether directory_snap contains `/proc0' -- if so, revert to the
! default name.
! Rationale: if directory_snap was not explicitly set in start.in, it
! will be written to param.nml as 'data/proc0', but this should in fact
! be data/procN on processor N.
!
if ((datadir_snap == '') .or. (index(datadir_snap,'proc0')>0)) &
datadir_snap = datadir
!
call directory_names_std(.true.)
!
endsubroutine directory_names
!***********************************************************************
subroutine output_snap(a,nv1,nv2,file)
!
! Write snapshot file, always write time and mesh, could add other things.
!
! 11-apr-97/axel: coded
! 13-Dec-2011/Bourdin.KIS: reworked
! 13-feb-2014/MR: made 'file' optional, 'a' assumed-shape (for downsampled output);
! moved donwsampling stuff to snapshot
!
use Mpicomm, only: start_serialize, end_serialize
use General, only: get_range_no, ioptest
!
real, dimension (:,:,:,:), intent(IN) :: a
integer, optional,intent(IN) :: nv1,nv2
character (len=*), optional,intent(IN) :: file
!
real :: t_sp ! t in single precision for backwards compatibility
integer :: na, ne
!
t_sp = real (t)
!
if (lserial_io) call start_serialize
if (present(file)) then
call delete_file(trim(directory_snap)//'/'//file)
open (lun_output, FILE=trim(directory_snap)//'/'//file, FORM='unformatted', status='new')
endif
na=ioptest(nv1,1)
ne=ioptest(nv2,mvar_io)
if (lroot .and. (ip <= 8)) print *, 'output_snap: nv1,nv2 =', na,ne
!
if (lwrite_2d) then
if (nx == 1) then
write (lun_output) a(l1,:,:,na:ne)
elseif (ny == 1) then
write (lun_output) a(:,m1,:,na:ne)
elseif (nz == 1) then
write (lun_output) a(:,:,n1,na:ne)
else
call fatal_error ('output_snap', 'lwrite_2d used for 3D simulation!')
endif
else
write (lun_output) a(:,:,:,na:ne)
endif
!
! Write shear at the end of x,y,z,dx,dy,dz.
! At some good moment we may want to treat deltay like with
! other modules and call a corresponding i/o parameter module.
!
if (lshear) then
write (lun_output) t_sp, x(1:size(a,1)), y(1:size(a,2)), z(1:size(a,3)), dx, dy, dz, deltay
else
write (lun_output) t_sp, x(1:size(a,1)), y(1:size(a,2)), z(1:size(a,3)), dx, dy, dz
endif
!
if (lserial_io) call end_serialize
!
endsubroutine output_snap
!***********************************************************************
subroutine output_snap_finalize
!
! Close snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: adapted from output_snap
!
use Mpicomm, only: end_serialize
!
if (persist_initialized) then
write (lun_output) id_block_PERSISTENT
persist_initialized = .false.
persist_last_id = -max_int
endif
!
close (lun_output)
!
if (lserial_io) call end_serialize
!
endsubroutine output_snap_finalize
!***********************************************************************
subroutine output_slice_position()
!
! Record slice positions.
!
! 13-nov-20/ccyang: wrapper
!
use HDF5_IO, only: hdf5_output_slice_position
!
call hdf5_output_slice_position()
!
endsubroutine output_slice_position
!***********************************************************************
subroutine output_slice(lwrite, time, label, suffix, pos, grid_pos, data)
!
! Append to a slice file
!
! 13-nov-20/ccyang: wrapper
!
use HDF5_IO, only: hdf5_output_slice
!
logical, intent(in) :: lwrite
real, intent(in) :: time
character(len=*), intent(in) :: label, suffix
real, intent(in) :: pos
integer, intent(in) :: grid_pos
real, dimension(:,:), pointer :: data
!
call hdf5_output_slice(lwrite, time, label, suffix, pos, grid_pos, data)
!
endsubroutine output_slice
!***********************************************************************
subroutine output_part_snap(ipar, ap, mv, nv, file, label, ltruncate)
!
! Write particle snapshot file, always write mesh and time.
!
! 22-Oct-2018/PABourdin: adapted from output_snap
!
integer, intent(in) :: mv, nv
integer, dimension (mv), intent(in) :: ipar
real, dimension (mv,mparray), intent(in) :: ap
character (len=*), intent(in) :: file
character (len=*), optional, intent(in) :: label
logical, optional, intent(in) :: ltruncate
!
real :: t_sp ! t in single precision for backwards compatibility
!
t_sp = real (t)
open(lun_output,FILE=trim(directory_dist)//'/'//file,FORM='unformatted')
!
! write the number of particles present at the processor
write(lun_output) nv
if (nv /= 0) then
! write particle index
write(lun_output) ipar(1:nv)
! write particle data
write(lun_output) ap(1:nv,:)
endif
!
! write time and grid parameters
write(lun_output) t_sp, x, y, z, dx, dy, dz
!
close(lun_output)
!
endsubroutine output_part_snap
!***********************************************************************
subroutine output_stalker_init(num, nv, snap, ID)
!
! Open stalker particle snapshot file and initialize with snapshot time.
!
! 03-May-2019/PABourdin: coded
!
integer, intent(in) :: num, nv, snap
integer, dimension(nv), intent(in) :: ID
!
real :: t_sp
!
call output_stalker ('', 0, nv, (/ 0.0 /), num)
!
open (lun_output, file=trim(directory_dist)//'/particles_stalker.dat', form='unformatted', position='append')
!
! write the time, number, and ID of stalked particles at this processor
t_sp = t
write (lun_output) t_sp, nv
if (nv >= 1) write (lun_output) ID
!
endsubroutine output_stalker_init
!***********************************************************************
subroutine output_stalker(label, mv, nv, data, nvar, lfinalize)
!
! Write stalker particle quantity to snapshot file.
!
! 03-May-2019/PABourdin: coded
!
use General, only: loptest
!
character (len=*), intent(in) :: label
integer, intent(in) :: mv, nv
real, dimension (mv), intent(in) :: data
integer, intent(in), optional :: nvar
logical, intent(in), optional :: lfinalize
!
character (len=fnlen) :: dataset
real, dimension(:,:), allocatable, save :: stalk_data
integer, save :: pos = 0
!
if (loptest (lfinalize)) then
! deallocate temporary stalker particle space
if (pos > 0) then
write (lun_output) stalk_data
pos = 0
endif
if (allocated (stalk_data)) deallocate (stalk_data)
return
endif
!
if (present (nvar)) then
! allocate temporary stalker particle space
if (nv > 0) allocate (stalk_data (nvar, nv))
return
endif
!
if (nv > 0) then
! write stalker particles to temporary space
pos = pos + 1
stalk_data(pos,:) = data(1:nv)
endif
!
endsubroutine output_stalker
!***********************************************************************
subroutine output_part_finalize
!
! Close particle snapshot file.
!
! 03-May-2019/PABourdin: coded
!
call output_stalker ('', 0, 1, (/ 0.0 /), 0, lfinalize=.true.)
close (lun_output)
!
endsubroutine output_part_finalize
!***********************************************************************
subroutine output_pointmass(file, labels, fq, mv, nc)
!
! Write pointmass snapshot file with time.
!
! 26-Oct-2018/PABourdin: coded
!
character (len=*), intent(in) :: file
integer, intent(in) :: mv, nc
character (len=*), dimension (nc), intent(in) :: labels
real, dimension (mv,nc), intent(in) :: fq
!
if (.not. lroot) return
!
open(lun_output,FILE=trim(directory_snap)//'/'//trim(file),FORM='unformatted')
write(lun_output) mv
if (mv > 0) write(lun_output) fq
write(lun_output) t
close(lun_output)
if (ip<=10) print*,'written pointmass snapshot ', trim (file)
!
endsubroutine output_pointmass
!***********************************************************************
logical function init_write_persist(file)
!
! Initialize writing of persistent data to snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in), optional :: file
!
character (len=fnlen), save :: filename=""
!
persist_last_id = -max_int
init_write_persist = .false.
!
if (present (file)) then
filename = file
persist_initialized = .false.
return
endif
!
if (filename /= "") then
close (lun_output)
call delete_file(trim (directory_snap)//'/'//filename)
open (lun_output, FILE=trim (directory_snap)//'/'//filename, FORM='unformatted', status='new')
filename = ""
endif
!
if (lroot .and. (ip <= 9)) write (*,*) 'begin persistent block'
write (lun_output) id_block_PERSISTENT
init_write_persist = .false.
persist_initialized = .true.
!
endfunction init_write_persist
!***********************************************************************
logical function write_persist_id(label, id)
!
! Write persistent data to snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in) :: label
integer, intent(in) :: id
!
!write(20+iproc,*) 'write_persist_id, label, persist_initialized=',label,persist_initialized
write_persist_id = .true.
if (.not. persist_initialized) write_persist_id = init_write_persist()
if (.not. persist_initialized) return
!
if (persist_last_id /= id) then
write (lun_output) id
persist_last_id = id
endif
!
write_persist_id = .false.
!
endfunction write_persist_id
!***********************************************************************
logical function write_persist_logical_0D(label, id, value)
!
! Write persistent data to snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in) :: label
integer, intent(in) :: id
logical, intent(in) :: value
!
write_persist_logical_0D = .true.
if (write_persist_id (label, id)) return
!
write (lun_output) value
write_persist_logical_0D = .false.
!
endfunction write_persist_logical_0D
!***********************************************************************
logical function write_persist_logical_1D(label, id, value)
!
! Write persistent data to snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in) :: label
integer, intent(in) :: id
logical, dimension(:), intent(in) :: value
!
write_persist_logical_1D = .true.
if (write_persist_id (label, id)) return
!
write (lun_output) value
write_persist_logical_1D = .false.
!
endfunction write_persist_logical_1D
!***********************************************************************
logical function write_persist_int_0D(label, id, value)
!
! Write persistent data to snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in) :: label
integer, intent(in) :: id
integer, intent(in) :: value
!
write_persist_int_0D = .true.
if (write_persist_id (label, id)) return
!
write (lun_output) value
write_persist_int_0D = .false.
!
endfunction write_persist_int_0D
!***********************************************************************
logical function write_persist_int_1D(label, id, value)
!
! Write persistent data to snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in) :: label
integer, intent(in) :: id
integer, dimension(:), intent(in) :: value
!
write_persist_int_1D = .true.
if (write_persist_id (label, id)) return
!
write (lun_output) value
write_persist_int_1D = .false.
!
endfunction write_persist_int_1D
!***********************************************************************
logical function write_persist_real_0D(label, id, value)
!
! Write persistent data to snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in) :: label
integer, intent(in) :: id
real, intent(in) :: value
!
write_persist_real_0D = .true.
if (write_persist_id (label, id)) return
!
write (lun_output) value
write_persist_real_0D = .false.
!
endfunction write_persist_real_0D
!***********************************************************************
logical function write_persist_real_1D(label, id, value)
!
! Write persistent data to snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in) :: label
integer, intent(in) :: id
real, dimension(:), intent(in) :: value
!
write_persist_real_1D = .true.
if (write_persist_id (label, id)) return
!
write (lun_output) value
write_persist_real_1D = .false.
!
endfunction write_persist_real_1D
!***********************************************************************
logical function write_persist_torus_rect(label, id, value)
!
! Write persistent data to snapshot file.
!
! 16-May-2020/MR: coded
!
use Geometrical_types
character (len=*), intent(in) :: label
integer, intent(in) :: id
type(torus_rect), intent(in) :: value
!
write_persist_torus_rect = .true.
if (write_persist_id (label, id)) return
!
!write (lun_output) value
write_persist_torus_rect = .false.
!
endfunction write_persist_torus_rect
!***********************************************************************
subroutine input_snap(file,a,nv,mode)
!
! manages reading of snapshot from different precision
!
! 24-oct-13/MR: coded
!
character (len=*), intent(in) :: file
integer, intent(in) :: nv, mode
real, dimension (mx,my,mz,nv), intent(out) :: a
real(KIND=rkind8), dimension(:,:,:,:), allocatable :: adb
real(KIND=rkind4), dimension(:,:,:,:), allocatable :: asg
real(KIND=rkind8), dimension(:), allocatable :: xdb,ydb,zdb
real(KIND=rkind4), dimension(:), allocatable :: xsg,ysg,zsg
real(KIND=rkind8) :: dxdb,dydb,dzdb,deltaydb
real(KIND=rkind4) :: dxsg,dysg,dzsg,deltaysg
if (lread_from_other_prec) then
if (kind(a)==rkind4) then
allocate(adb(mx,my,mz,nv),xdb(mx),ydb(my),zdb(mz))
call read_snap(file,adb,xdb,ydb,zdb,dxdb,dydb,dzdb,deltaydb,nv,mode)
a=adb; x=xdb; y=ydb; z=zdb; dx=dxdb; dy=dydb; dz=dzdb; deltay=deltaydb
elseif (kind(a)==rkind8) then
allocate(asg(mx,my,mz,nv),xsg(mx),ysg(my),zsg(mz))
call read_snap(file,asg,xsg,ysg,zsg,dxsg,dysg,dzsg,deltaysg,nv,mode)
a=asg; x=xsg; y=ysg; z=zsg; dx=dxsg; dy=dysg; dz=dzsg; deltay=deltaysg
endif
else
call read_snap(file,a,x,y,z,dx,dy,dz,deltay,nv,mode)
endif
endsubroutine input_snap
!***********************************************************************
subroutine read_snap_single(file,a,x,y,z,dx,dy,dz,deltay,nv,mode)
!
! Read snapshot file in single precision, possibly with mesh and time (if mode=1).
!
! 24-oct-13/MR: derived from input_snap
! 28-oct-13/MR: consistency check for t_sp relaxed for restart from different precision
! 6-mar-14/MR: if timestamp of snapshot inconsistent, now three choices:
! if ireset_tstart= 0: cancel program
! = MINT, tstart unspecified: use minimum time of all var.dat
! for start
! = MAXT, tstart unspecified: use maximum time of all var.dat
! for start
! > 0, tstart specified: use this value
! 13-feb-20/MR: added possibility to omit a range of variables when reading the snapshot,
! range is defined as [ivar_omi1,ivar_omi2]
! 22-oct-20/MR: outsourced code shared with read_snap_double into io_dist.h
! Added "rescue mechanism": if snapshot is not properly readable,
! reding is tried from the (min. 11, max. 26) neighboring
! processors' snaphots.
!
use Mpicomm, only: start_serialize, end_serialize, mpibcast, mpibcast_real, mpiallreduce_or, &
stop_it, mpiallreduce_min, mpiallreduce_max, MPI_COMM_PENCIL, &
mpisend_char, mpirecv_char, mpiallreduce_and
use Syscalls, only: islink, system_cmd, readlink, extract_str
use General, only: itoa, find_proc, atoi
!
character (len=*), intent(in) :: file
integer, intent(in) :: nv, mode
real(KIND=rkind4), dimension (mx,my,mz,nv), intent(out) :: a
!
real(KIND=rkind4) :: t_sp, t_red
real(KIND=rkind4), intent(out) :: dx, dy, dz, deltay
real(KIND=rkind4), dimension (mx), intent(out) :: x
real(KIND=rkind4), dimension (my), intent(out) :: y
real(KIND=rkind4), dimension (mz), intent(out) :: z
real(KIND=rkind4), dimension(:,:,:,:), allocatable :: tmp_omit,tmp
!
include 'io_dist.h'
!
endsubroutine read_snap_single
!***********************************************************************
subroutine read_snap_double(file,a,x,y,z,dx,dy,dz,deltay,nv,mode)
!
! Read snapshot file in double precision, possibly with mesh and time (if mode=1).
!
! 24-oct-13/MR: derived from input_snap
! 28-oct-13/MR: consistency check for t_sp relaxed for restart from different precision
! 6-mar-14/MR: if timestamp of snapshot inconsistent, now three choices:
! if ireset_tstart= 0: cancel program
! = MINT, tstart unspecified: use minimum time of all var.dat
! for start
! = MAXT, tstart unspecified: use maximum time of all var.dat
! for start
! > 0, tstart specified: use this value
!
use Mpicomm, only: start_serialize, end_serialize, mpibcast, mpibcast_real, mpiallreduce_or, &
stop_it, mpiallreduce_min, mpiallreduce_max, MPI_COMM_PENCIL, &
mpisend_char, mpirecv_char,mpiallreduce_and
use Syscalls, only: islink, system_cmd, readlink, extract_str
use General, only: itoa, find_proc, atoi
!
character (len=*), intent(in) :: file
integer, intent(in) :: nv, mode
real(KIND=rkind8), dimension (mx,my,mz,nv), intent(out) :: a
!
real(KIND=rkind8) :: t_sp, t_red
real(KIND=rkind8), intent(out) :: dx, dy, dz, deltay
real(KIND=rkind8), dimension (mx), intent(out) :: x
real(KIND=rkind8), dimension (my), intent(out) :: y
real(KIND=rkind8), dimension (mz), intent(out) :: z
real(KIND=rkind8), dimension(:,:,:,:), allocatable :: tmp_omit,tmp
include 'io_dist.h'
!
endsubroutine read_snap_double
!***********************************************************************
subroutine input_snap_finalize
!
! Close snapshot file.
!
! 11-apr-97/axel: coded
! 13-Dec-2011/Bourdin.KIS: reworked
!
use Mpicomm, only: end_serialize
use Syscalls, only: system_cmd
!
close (lun_input)
if (snaplink/='') then
call system_cmd('rm -f '//snaplink)
snaplink=''
endif
if (lserial_io) call end_serialize
!
endsubroutine input_snap_finalize
!***********************************************************************
subroutine input_slice_real_arr(file, time, pos, data)
!
! Read a slice file.
!
! 13-nov-20/ccyang: wrapper
!
use HDF5_IO, only: hdf5_input_slice
!
character(len=*), intent(in) :: file
real, intent(out):: time, pos
real, dimension(:,:,:), intent(out):: data
!
call hdf5_input_slice(file, time, pos, data)
!
endsubroutine input_slice_real_arr
!***********************************************************************
subroutine input_slice_scat_arr(file, pos, data, ivar, nt)
!
! Read a slice file.
!
! 13-nov-20/ccyang: wrapper
!
use General, only: scattered_array
use HDF5_IO, only: hdf5_input_slice
!
character(len=*), intent(in) :: file
real, intent(out):: pos
type(scattered_array), pointer :: data !intent(inout)
integer, intent(in) :: ivar
integer, intent(out):: nt
!
call hdf5_input_slice(file, pos, data, ivar, nt)
!
endsubroutine input_slice_scat_arr
!***********************************************************************
subroutine input_part_snap(ipar, ap, mv, nv, npar_total, file, label)
!
! Read particle snapshot file, mesh and time are read in 'input_snap'.
!
! 24-Oct-2018/PABourdin: apadpted and moved to IO module
!
use Mpicomm, only: mpireduce_sum_int
!
integer :: mparray_tmp=1
integer, intent(in) :: mv
integer, dimension (mv), intent(out) :: ipar
real, dimension (mv,mparray), intent(out) :: ap
integer, intent(out) :: nv, npar_total
character (len=*), intent(in) :: file
character (len=*), optional, intent(in) :: label
!
open (lun_input, FILE=trim(directory_dist)//'/'//file, FORM='unformatted')
! Read number of particles for this processor.
read (lun_input) nv
if (nv > 0) then
! Read particle number identifier and then particle data.
read (lun_input) ipar(1:nv)
if (lread_oldsnap_nosink) then
if (lroot) print*,'read old snapshot file (but without sink particles)'
read (lun_input) ap(1:nv,1:mparray-1)
mparray_tmp=mparray !(trick to prevent compiler problem for mparray=0)
ap(1:nv,mparray_tmp)=0.0
else
read (lun_input) ap(1:nv,:)
endif
endif
close (lun_input)
if (ip<=8 .and. lroot) print*, 'input_particles: read ', file
!
! Sum the total number of all particles on the root processor.
call mpireduce_sum_int (nv, npar_total)
!
endsubroutine input_part_snap
!***********************************************************************
subroutine input_pointmass(file, labels, fq, mv, nc)
!
! Read pointmass snapshot file.
!
! 26-Oct-2018/PABourdin: coded
!
use Mpicomm, only: mpibcast_real
!
character (len=*), intent(in) :: file
integer, intent(in) :: mv, nc
character (len=*), dimension (nc), intent(in) :: labels
real, dimension (mv,nc), intent(out) :: fq
!
integer :: mv_in
!
if (lroot) then
if (ip<=8) print*, 'read pointmass snapshot', trim (file)
open(lun_input,FILE=trim(directory_snap)//'/'//trim(file),FORM='unformatted')
read(lun_input) mv_in
if (mv_in /= mv) call fatal_error("input_pointmass","dimensions differ between file and 'fq' array")
if (mv_in > 0) read(lun_input) fq
close(lun_input)
endif
!
call mpibcast_real(fq,(/mv,nc/))
!
endsubroutine input_pointmass
!***********************************************************************
logical function init_read_persist(file)
!
! Initialize writing of persistent data to persistent file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
use File_io, only: file_exists
use Mpicomm, only: mpibcast_logical, MPI_COMM_WORLD
!
character (len=*), intent(in), optional :: file
!
init_read_persist = .true.
!
if (present (file)) then
if (lroot) init_read_persist = .not. file_exists (trim (directory_snap)//'/'//file)
call mpibcast_logical(init_read_persist,comm=MPI_COMM_WORLD)
if (init_read_persist) return
endif
!
if (present (file)) then
close (lun_input)
open (lun_input, FILE=trim (directory_snap)//'/'//file, FORM='unformatted', status='old')
endif
!
if (lroot .and. (ip <= 9)) write (*,*) 'begin persistent block'
init_read_persist = .false.
!
endfunction init_read_persist
!***********************************************************************
logical function persist_exists(label)
!
! Dummy routine
!
! 12-Oct-2019/PABourdin: coded
!
character (len=*), intent(in) :: label
!
persist_exists = .false.
!
endfunction persist_exists
!***********************************************************************
logical function read_persist_id(label, id, lerror_prone)
!
! Read persistent block ID from snapshot file.
! Each persist data block starts with a unique ID followed by the data.
! Both are Fortran records. Returns a positive ID number on success.
!
! 17-Feb-2012/Bourdin.KIS: coded
!
use Mpicomm, only: mpibcast_int, MPI_COMM_WORLD
!
character (len=*), intent(in) :: label
integer, intent(out) :: id
logical, intent(in), optional :: lerror_prone
!
logical :: lcatch_error
integer :: io_err
!
lcatch_error = .false.
if (present (lerror_prone)) lcatch_error = lerror_prone
!
if (lroot .and. (ip <= 9)) write (*,*) 'read persistent ID '//trim (label)
if (lcatch_error) then
read (lun_input, iostat=io_err) id
if (io_err /= 0) id = -max_int
else
read (lun_input) id
endif
!
call mpibcast_int(id,comm=MPI_COMM_WORLD)
!
read_persist_id = .false.
if (id == -max_int) read_persist_id = .true.
!
endfunction read_persist_id
!***********************************************************************
logical function read_persist_logical_0D(label, value)
!
! Read persistent data from snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in) :: label
logical, intent(out) :: value
!
read (lun_input) value
read_persist_logical_0D = .false.
!
endfunction read_persist_logical_0D
!***********************************************************************
logical function read_persist_logical_1D(label, value)
!
! Read persistent data from snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in) :: label
logical, dimension(:), intent(out) :: value
!
read (lun_input) value
read_persist_logical_1D = .false.
!
endfunction read_persist_logical_1D
!***********************************************************************
logical function read_persist_int_0D(label, value)
!
! Read persistent data from snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in) :: label
integer, intent(out) :: value
!
read (lun_input) value
read_persist_int_0D = .false.
!
endfunction read_persist_int_0D
!***********************************************************************
logical function read_persist_int_1D(label, value)
!
! Read persistent data from snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
!
character (len=*), intent(in) :: label
integer, dimension(:), intent(out) :: value
!
read (lun_input) value
read_persist_int_1D = .false.
!
endfunction read_persist_int_1D
!***********************************************************************
logical function read_persist_real_0D(label, value)
!
! Read persistent data from snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
! 23-oct-2013/MR: modified for reading of different precision
!
character (len=*), intent(in) :: label
real, intent(out) :: value
!
real(KIND=rkind8) :: vdb
real(KIND=rkind4) :: vsg
!
if (lread_from_other_prec) then
if (kind(value)==rkind4) then
read (lun_input) vdb
value=vdb
elseif (kind(value)==rkind8) then
read (lun_input) vsg
value=vsg
endif
else
read (lun_input) value
endif
read_persist_real_0D = .false.
!
endfunction read_persist_real_0D
!***********************************************************************
logical function read_persist_real_1D(label, value)
!
! Read persistent data from snapshot file.
!
! 13-Dec-2011/Bourdin.KIS: coded
! 23-oct-2013/MR: modified for reading of different precision
!
character (len=*), intent(in) :: label
real, dimension(:), intent(out) :: value
!
real(KIND=rkind8), dimension(:), allocatable :: vdb
real(KIND=rkind4), dimension(:), allocatable :: vsg
!
if (lread_from_other_prec) then
if (kind(value)==rkind4) then
allocate(vdb(size(value)))
read (lun_input) vdb
value=vdb
elseif (kind(value)==rkind8) then
allocate(vsg(size(value)))
read (lun_input) vsg
value=vsg
endif
else
read (lun_input) value
endif
!
read_persist_real_1D = .false.
!
endfunction read_persist_real_1D
!***********************************************************************
logical function read_persist_torus_rect(label,value)
!
! Read persistent data from snapshot file.
!
! 16-May-2020/MR: coded
!
use Geometrical_types
character (len=*), intent(in) :: label
type(torus_rect), intent(out) :: value
!
!read (lun_input) value
read_persist_torus_rect = .false.
!
endfunction read_persist_torus_rect
!***********************************************************************
subroutine output_globals(file, a, nv, label)
!
! Write snapshot file of globals, ignoring mesh.
!
! 10-nov-06/tony: coded
!
use Mpicomm, only: start_serialize, end_serialize
!
integer :: nv
real, dimension (mx,my,mz,nv) :: a
character (len=*) :: file
character (len=*), intent(in), optional :: label
!
if (lserial_io) call start_serialize
open(lun_output,FILE=trim(directory_snap)//'/'//file,FORM='unformatted',status='replace')
!
if (lwrite_2d) then
if (nx==1) then
write(lun_output) a(4,:,:,:)
elseif (ny==1) then
write(lun_output) a(:,4,:,:)
elseif (nz==1) then
write(lun_output) a(:,:,4,:)
else
call fatal_error('output_globals','lwrite_2d used for 3-D simulation!')
endif
else
write(lun_output) a
endif
close(lun_output)
!
if (lserial_io) call end_serialize
!
endsubroutine output_globals
!***********************************************************************
subroutine input_globals(file, a, nv)
!
! Read globals snapshot file, ignoring mesh.
!
! 10-nov-06/tony: coded
!
use Mpicomm, only: start_serialize,end_serialize
!
character (len=*) :: file
integer :: nv
real, dimension (mx,my,mz,nv) :: a
!
real(KIND=rkind8), dimension(:,:,:,:), allocatable :: adb
real(KIND=rkind4), dimension(:,:,:,:), allocatable :: asg
!
if (lserial_io) call start_serialize
!
open(lun_input,FILE=trim(directory_snap)//'/'//file,FORM='unformatted',status='old')
if (lread_from_other_prec) then
if (kind(a)==rkind4) then
allocate(adb(mx,my,mz,nv))
call read_globals(adb)
a=adb
elseif (kind(a)==rkind8) then
allocate(asg(mx,my,mz,nv))
call read_globals(asg)
a=asg
endif
else
call read_globals(a)
endif
close(lun_input)
!
if (lserial_io) call end_serialize
!
endsubroutine input_globals
!***********************************************************************
subroutine read_globals_double(a)
!
! Read globals snapshot file in double precision
!
! 23-oct-13/MR : derived from input_globals
!
real(KIND=rkind8), dimension (:,:,:,:) :: a
!
if (lwrite_2d) then
if (nx==1) then
read(lun_input) a(4,:,:,:)
elseif (ny==1) then
read(lun_input) a(:,4,:,:)
elseif (nz==1) then
read(lun_input) a(:,:,4,:)
else
call fatal_error('input_globals','lwrite_2d used for 3-D simulation!')
endif
else
read(lun_input) a
endif
!
endsubroutine read_globals_double
!***********************************************************************
subroutine read_globals_single(a)
!
! Read globals snapshot file in single precision
!
! 23-oct-13/MR : derived from input_globals
!
real(KIND=rkind4), dimension (:,:,:,:) :: a
!
if (lwrite_2d) then
if (nx==1) then
read(lun_input) a(4,:,:,:)
elseif (ny==1) then
read(lun_input) a(:,4,:,:)
elseif (nz==1) then
read(lun_input) a(:,:,4,:)
else
call fatal_error('input_globals','lwrite_2d used for 3-D simulation!')
endif
else
read(lun_input) a
endif
!
endsubroutine read_globals_single
!***********************************************************************
subroutine log_filename_to_file(file,flist)
!
! In the directory containing `filename', append one line to file
! `flist' containing the file part of filename
!
use General, only: parse_filename, safe_character_assign
!
character (len=*) :: file,flist
!
character (len=fnlen) :: dir,fpart
!
call parse_filename(file,dir,fpart)
if (dir == '.') call safe_character_assign(dir,directory_snap)
!
open(lun_output,FILE=trim(dir)//'/'//flist,POSITION='append')
write(lun_output,'(A,1x,e16.8)') trim(fpart), t
close(lun_output)
!
if (lcopysnapshots_exp) then
if (lroot) then
open(lun_output,FILE=trim(datadir)//'/move-me.list',POSITION='append')
write(lun_output,'(A)') trim(fpart)
close(lun_output)
endif
endif
!
endsubroutine log_filename_to_file
!***********************************************************************
subroutine wgrid(file,mxout,myout,mzout,lwrite)
!
! Write processor-local part of grid coordinates.
!
! 21-jan-02/wolf: coded
! 15-jun-03/axel: Lx,Ly,Lz are now written to file (Tony noticed the mistake)
! 30-sep-13/MR : optional parameters mxout,myout,mzout added
! to be able to output coordinate vectors with lengths differing from
! mx,my,mz
! 25-Aug-2016/PABourdin: now a global "grid.dat" is always written from all IO modules
! 5-oct-2016/MR: modifications for output of downsampled grid
!
use Mpicomm, only: collect_grid
use General, only: ioptest, loptest
!
character (len=*) :: file
integer, optional :: mxout,myout,mzout
logical, optional :: lwrite
!
integer :: mxout1,myout1,mzout1
real, dimension (:), allocatable :: gx, gy, gz
integer :: alloc_err
real :: t_sp ! t in single precision for backwards compatibility
!
if (loptest(lwrite,.not.luse_oldgrid)) then
mxout1=ioptest(mxout,mx)
myout1=ioptest(myout,my)
mzout1=ioptest(mzout,mz)
!
t_sp = real (t)
open (lun_output,FILE=trim(directory)//'/'//file,FORM='unformatted',status='replace')
write(lun_output) t_sp,x(:mxout1),y(:myout1),z(:mzout1),dx,dy,dz
write(lun_output) dx,dy,dz
write(lun_output) Lx,Ly,Lz
write(lun_output) dx_1(:mxout1),dy_1(:myout1),dz_1(:mzout1)
write(lun_output) dx_tilde(:mxout1),dy_tilde(:myout1),dz_tilde(:mzout1)
close(lun_output)
!
if (lyang) return ! grid collection only needed on Yin grid, as grids are identical
! write also a global "data/allprocs/grid.dat"
if (lroot) then
if (ldownsampling) then
allocate (gx(ceiling(real(nxgrid)/downsampl(1))+2*nghost), &
gy(ceiling(real(nygrid)/downsampl(2))+2*nghost), &
gz(ceiling(real(nzgrid)/downsampl(3))+2*nghost), stat=alloc_err)
else
allocate (gx(nxgrid+2*nghost), gy(nygrid+2*nghost), gz(nzgrid+2*nghost), stat=alloc_err)
endif
if (alloc_err > 0) call fatal_error ('wgrid', 'Could not allocate memory for gx,gy,gz', .true.)
!
open (lun_output, FILE=trim(directory_collect)//'/'//file, FORM='unformatted', status='replace')
t_sp = real (t)
endif
call collect_grid(x(:mxout1), y(:myout1), z(:mzout1), gx, gy, gz)
if (lroot) then
write (lun_output) t_sp, gx, gy, gz, dx, dy, dz
write (lun_output) dx, dy, dz
write (lun_output) Lx, Ly, Lz
endif
call collect_grid(dx_1(:mxout1), dy_1(:myout1), dz_1(:mzout1), gx, gy, gz)
if (lroot) write (lun_output) gx, gy, gz
call collect_grid(dx_tilde(:mxout1), dy_tilde(:myout1), dz_tilde(:mzout1), gx, gy, gz)
if (lroot) then
write (lun_output) gx, gy, gz
close (lun_output)
deallocate(gx,gy,gz)
endif
endif
!
endsubroutine wgrid
!***********************************************************************
subroutine input_grid_single(x,y,z,dx,dy,dz,Lx,Ly,Lz,dx_1,dy_1,dz_1,dx_tilde,dy_tilde,dz_tilde)
!
! Read grid in single precision
!
! 23-oct-13/MR: derived from input_grid
!
real(KIND=rkind4), intent(OUT) :: dx,dy,dz,Lx,Ly,Lz
real(KIND=rkind4), dimension (mx),intent(OUT) :: x,dx_1,dx_tilde
real(KIND=rkind4), dimension (my),intent(OUT) :: y,dy_1,dy_tilde
real(KIND=rkind4), dimension (mz),intent(OUT) :: z,dz_1,dz_tilde
!
integer :: io_err
real(KIND=rkind4) :: t_sp ! t in single precision for backwards compatibility
!
read(lun_input) t_sp,x,y,z,dx,dy,dz
read(lun_input) dx,dy,dz
read(lun_input, iostat=io_err) Lx,Ly,Lz
if (io_err < 0) then
! End-Of-File: give notification that box dimensions are not read.
! This should only happen when reading old files.
! We should allow this for the time being.
call warning ('input_grid', "Lx,Ly,Lz are not yet in grid.dat")
else
read(lun_input) dx_1,dy_1,dz_1
read(lun_input) dx_tilde,dy_tilde,dz_tilde
endif
!
endsubroutine input_grid_single
!***********************************************************************
subroutine input_grid_double(x,y,z,dx,dy,dz,Lx,Ly,Lz,dx_1,dy_1,dz_1,dx_tilde,dy_tilde,dz_tilde)
!
! Read grid in double precision
!
! 23-oct-13/MR: derived from input_grid
!
real(KIND=rkind8), intent(OUT) :: dx,dy,dz,Lx,Ly,Lz
real(KIND=rkind8), dimension (mx),intent(OUT) :: x,dx_1,dx_tilde
real(KIND=rkind8), dimension (my),intent(OUT) :: y,dy_1,dy_tilde
real(KIND=rkind8), dimension (mz),intent(OUT) :: z,dz_1,dz_tilde
!
integer :: io_err
real(KIND=rkind8) :: t_sp ! t in double precision for backwards compatibility
!
read(lun_input) t_sp,x,y,z,dx,dy,dz
read(lun_input) dx,dy,dz
read(lun_input, iostat=io_err) Lx,Ly,Lz
if (io_err < 0) then
! End-Of-File: give notification that box dimensions are not read.
! This should only happen when reading old files.
! We should allow this for the time being.
call warning ('input_grid_double', "Lx,Ly,Lz are not yet in grid.dat")
else
read(lun_input) dx_1,dy_1,dz_1
read(lun_input) dx_tilde,dy_tilde,dz_tilde
endif
!
endsubroutine input_grid_double
!***********************************************************************
subroutine rgrid (file)
!
! Read processor-local part of grid coordinates.
!
! 21-jan-02/wolf: coded
! 15-jun-03/axel: Lx,Ly,Lz are now read in from file (Tony noticed the mistake)
! 24-oct-13/MR : handling of reading from different precision introduced
! 28-oct-13/MR : added overwriting of grid.dat if restart from different precision
! 3-mar-15/MR : calculation of d[xyz]2_bound added: contain twice the distances of
! three neighbouring points from the boundary point
! 15-apr-15/MR : automatic detection of precision added; doesn't work for old files
! which don't contain Lx, Ly, Lz etc.
!
use File_io, only: file_size
!
character (len=*) :: file
!
integer :: datasize, filesize
integer, parameter :: nrec=5
logical :: lotherprec
!
real(KIND=rkind8), dimension(:), allocatable :: xdb,ydb,zdb,dx_1db,dy_1db,dz_1db,dx_tildedb,dy_tildedb,dz_tildedb
real(KIND=rkind4), dimension(:), allocatable :: xsg,ysg,zsg,dx_1sg,dy_1sg,dz_1sg,dx_tildesg,dy_tildesg,dz_tildesg
real(KIND=rkind8) :: dxdb,dydb,dzdb,Lxdb,Lydb,Lzdb
real(KIND=rkind4) :: dxsg,dysg,dzsg,Lxsg,Lysg,Lzsg
open(lun_input,FILE=trim(directory)//'/'//file,FORM='unformatted',status='old')
lotherprec=.false.
if (lread_from_other_prec) then
datasize = 3*(mx+my+mz) + 10
filesize = file_size(trim(directory)//'/'//file) - 8*nrec ! length without record marker
!
if (kind(x)==rkind4) then
lotherprec = filesize/=4*datasize
if (lotherprec) then
allocate(xdb(mx),ydb(my),zdb(mz),dx_1db(mx),dy_1db(my),dz_1db(mz),dx_tildedb(mx),dy_tildedb(my),dz_tildedb(mz))
call input_grid(xdb,ydb,zdb,dxdb,dydb,dzdb,Lxdb,Lydb,Lzdb, &
dx_1db,dy_1db,dz_1db,dx_tildedb,dy_tildedb,dz_tildedb)
x=xdb; y=ydb; z=zdb; dx=dxdb; dy=dydb; dz=dzdb
Lx=Lxdb; Ly=Lydb; Lz=Lzdb; dx_1=dx_1db; dy_1=dy_1db; dz_1=dz_1db
dx_tilde=dx_tildedb; dy_tilde=dy_tildedb; dz_tilde=dz_tildedb
endif
elseif (kind(x)==rkind8) then
lotherprec = filesize/=8*datasize
if (lotherprec) then
allocate(xsg(mx),ysg(my),zsg(mz),dx_1sg(mx),dy_1sg(my),dz_1sg(mz),dx_tildesg(mx),dy_tildesg(my),dz_tildesg(mz))
call input_grid(xsg,ysg,zsg,dxsg,dysg,dzsg,Lxsg,Lysg,Lzsg, &
dx_1sg,dy_1sg,dz_1sg,dx_tildesg,dy_tildesg,dz_tildesg)
x=xsg; y=ysg; z=zsg; dx=dxsg; dy=dysg; dz=dzsg
Lx=Lxsg; Ly=Lysg; Lz=Lzsg; dx_1=dx_1sg; dy_1=dy_1sg; dz_1=dz_1sg;
dx_tilde=dx_tildesg; dy_tilde=dy_tildesg; dz_tilde=dz_tildesg
endif
endif
endif
if (.not.lotherprec) &
call input_grid(x,y,z,dx,dy,dz,Lx,Ly,Lz,dx_1,dy_1,dz_1,dx_tilde,dy_tilde,dz_tilde)
close(lun_input)
!
if (lotherprec) call wgrid(file,lwrite=.true.) ! perhaps not necessary
!
! debug output
!
if (ip<=4.and.lroot) then
print*,'rgrid: Lx,Ly,Lz=',Lx,Ly,Lz
print*,'rgrid: dx,dy,dz=',dx,dy,dz
endif
!
endsubroutine rgrid
!***********************************************************************
subroutine wproc_bounds(file)
!
! Export processor boundaries to file.
!
! 22-Feb-2012/PABourdin: adapted from io_dist
! 27-nov-2020/ccyang: make the file single
!
character(len=*), intent(in) :: file
!
integer :: ierr
!
! Only one process is needed.
!
if (.not. lroot) return
!
! Write proc[xyz]_bounds.
!
open (lun_output, FILE=file, FORM='unformatted', IOSTAT=ierr, status='replace')
if (ierr /= 0) call fatal_error("wproc_bounds", "Cannot open " // trim(file))
write (lun_output) procx_bounds
write (lun_output) procy_bounds
write (lun_output) procz_bounds
close (lun_output)
!
endsubroutine wproc_bounds
!***********************************************************************
subroutine rproc_bounds(file)
!
! Import processor boundaries from file.
!
! 10-jul-08/kapelrud: coded
! 16-Feb-2012/Bourdin.KIS: rewritten
!
character (len=*) :: file
!
real(KIND=rkind4), dimension(0:nprocx):: procx_boundssg
real(KIND=rkind4), dimension(0:nprocy):: procy_boundssg
real(KIND=rkind4), dimension(0:nprocz):: procz_boundssg
!
real(KIND=rkind8), dimension(0:nprocx):: procx_boundsdb
real(KIND=rkind8), dimension(0:nprocy):: procy_boundsdb
real(KIND=rkind8), dimension(0:nprocz):: procz_boundsdb
!
open(lun_input,FILE=file,FORM='unformatted',status='old')
if (lread_from_other_prec) then
if (kind(x)==rkind4) then
call input_proc_bounds(procx_boundsdb,procy_boundsdb,procz_boundsdb)
procx_bounds=procx_boundsdb; procy_bounds=procy_boundsdb; procz_bounds=procz_boundsdb
elseif (kind(x)==rkind8) then
call input_proc_bounds(procx_boundssg,procy_boundssg,procz_boundssg)
procx_bounds=procx_boundssg; procy_bounds=procy_boundssg; procz_bounds=procz_boundssg
endif
else
call input_proc_bounds(procx_bounds,procy_bounds,procz_bounds)
endif
close(lun_output)
!
endsubroutine rproc_bounds
!***********************************************************************
subroutine input_proc_bounds_double(procx_bounds,procy_bounds,procz_bounds)
!
! Import processor boundaries from file.in double precision
!
! 23-oct-13/MR: derivced from rproc_bounds
!
real(KIND=rkind8), dimension(0:nprocx), intent(OUT):: procx_bounds
real(KIND=rkind8), dimension(0:nprocy), intent(OUT):: procy_bounds
real(KIND=rkind8), dimension(0:nprocz), intent(OUT):: procz_bounds
!
read(lun_input) procx_bounds
read(lun_input) procy_bounds
read(lun_input) procz_bounds
!
endsubroutine input_proc_bounds_double
!***********************************************************************
subroutine input_proc_bounds_single(procx_bounds,procy_bounds,procz_bounds)
!
! Import processor boundaries from file.in single precision
!
! 23-oct-13/MR: derived from rproc_bounds
!
real(KIND=rkind4), dimension(0:nprocx), intent(OUT):: procx_bounds
real(KIND=rkind4), dimension(0:nprocy), intent(OUT):: procy_bounds
real(KIND=rkind4), dimension(0:nprocz), intent(OUT):: procz_bounds
!
read(lun_input) procx_bounds
read(lun_input) procy_bounds
read(lun_input) procz_bounds
!
endsubroutine input_proc_bounds_single
!***********************************************************************
function read_part_double(lun,a,omit) result (ios)
!
! Reads part of array, stored on disk, defined by range of variable indices ivar_omit(1):ivar_omit(2)
! into array a. Uses dummy buffer omit of size (:,:,:,1:ivar_omit(2)-ivar_omit(1)+1).
!
! 31-mar-21/MR: coded
!
integer, intent(IN) :: lun
real(KIND=rkind8), dimension(:,:,:,:), intent(OUT) :: a, omit
integer :: ios
if (ivar_omit(1)==1) then
read (lun,iostat=ios) omit,a
elseif (ivar_omit(1)>1) then
read (lun,iostat=ios) a(:,:,:,:ivar_omit(1)-1),omit,a(:,:,:,ivar_omit(1):)
else
read (lun,iostat=ios) a
endif
endfunction read_part_double
!***********************************************************************
function read_part_single(lun,a,omit) result (ios)
!
! Reads part of array, stored on disk, defined by range of variable indices ivar_omit(1):ivar_omit(2)
! into array a. Uses dummy buffer omit of size (:,:,:,1:ivar_omit(2)-ivar_omit(1)+1).
!
! 31-mar-21/MR: coded
!
integer, intent(IN) :: lun
real(KIND=rkind4), dimension(:,:,:,:), intent(OUT) :: a, omit
integer :: ios
if (ivar_omit(1)==1) then
read (lun,iostat=ios) omit,a
elseif (ivar_omit(1)>1) then
read (lun,iostat=ios) a(:,:,:,:ivar_omit(1)-1),omit,a(:,:,:,ivar_omit(1):)
else
read (lun,iostat=ios) a
endif
endfunction read_part_single
!***********************************************************************
endmodule Io