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Added groundwork for HDF5 support
Currently there is an indexing error with the HDF write statement.
This commit is contained in:
Sterling Harper
parent
73826aa2fd
commit
e0936553cb
2 changed files with 91 additions and 9 deletions
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@ -21,7 +21,7 @@ DEBUG = no
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PROFILE = no
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OPTIMIZE = no
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MPI = no
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HDF5 = no
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HDF5 = yes
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PETSC = no
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#===============================================================================
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@ -29,7 +29,7 @@ PETSC = no
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#===============================================================================
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MPI_DIR = /opt/mpich/3.0.4-$(COMPILER)
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HDF5_DIR = /opt/hdf5/1.8.11-$(COMPILER)
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HDF5_DIR = /usr/local/hdf5
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PHDF5_DIR = /opt/phdf5/1.8.11-$(COMPILER)
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PETSC_DIR = /opt/petsc/3.3-p6-$(COMPILER)
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@ -5,8 +5,22 @@ module particle_track
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!use output_interface only: file_create, file_close, write_double1Darray
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use string, only: to_str
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#ifdef HDF5
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use hdf5
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#endif
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implicit none
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#ifdef HDF5
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integer, private :: hdf5_err ! HDF5 error code
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integer(HID_T), private :: track_dset ! dataset handle
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integer(HID_T), private :: track_dspace ! master dataspace handle
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integer(HID_T), private :: track_selspace ! selected dataspace handle
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integer(HID_T), private :: track_fh ! HDF5 file handle
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integer(HID_T), private :: cparms ! chunk parameters
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integer(HSIZE_T), private :: n_tracks ! total number of tracks
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#endif
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contains
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!===============================================================================
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@ -19,13 +33,35 @@ contains
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subroutine initialize_particle_track()
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character(MAX_FILE_LEN) :: filename
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! Replace the following with '#ifdef HDF5'.
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#if 0
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integer(HSIZE_T) :: dims(2), max_dims(2), i
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integer(HID_T) :: cparms
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integer(HID_T) :: dapl
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#endif
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filename = trim(path_output) // 'track_' // trim(to_str(current_batch)) &
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// '_' // trim(to_str(current_gen)) // '_' // trim(to_str(p % id)) &
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// '.binary'
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open(UNIT=UNIT_TRACK, FILE=filename, STATUS='replace', &
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ACCESS='stream')
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!file_create(filename, 'serial')
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// '_' // trim(to_str(current_gen)) // '_' // trim(to_str(p % id))
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! Replace the following with '#ifdef HDF5'.
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#if 0
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filename = filename // '.h5'
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call h5fcreate_f(filename, H5F_ACC_TRUNC_F, track_fh, hdf5_err)
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dims = (/3, 1/)
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i = 3
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max_dims = (/i, H5S_UNLIMITED_F/)
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call h5screate_simple_f(2, dims, track_dspace, hdf5_err, max_dims)
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call h5pcreate_f(H5P_DATASET_CREATE_F, cparms, hdf5_err)
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call h5pset_chunk_f(cparms, 2, dims, hdf5_err)
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call h5pset_fill_value_f(cparms, H5T_NATIVE_DOUBLE, 0, hdf5_err)
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call h5dcreate_f(track_fh, 'coordinates', H5T_NATIVE_DOUBLE, track_dspace, &
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track_dset, hdf5_err, cparms)
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n_tracks = 1
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#else
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filename = filename // '.binary'
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open(UNIT=UNIT_TRACK, FILE=filename, ACTION="write", &
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STATUS='replace', ACCESS='stream')
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#endif
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end subroutine initialize_particle_track
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@ -38,8 +74,40 @@ contains
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!===============================================================================
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subroutine write_particle_track()
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! Replace the following with '#ifdef HDF5'.
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#if 0
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integer(HSIZE_T) :: dims(2), max_dims(2), offset(2), i
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integer(HSIZE_T), parameter :: cnt(2) = (/3, 1/), write_dims(2) = (/3, 1/)
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real(8) :: coords(3, 1)
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integer(HSIZE_T) :: test
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i = 3
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dims = (/i, n_tracks/)
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call h5dget_space_f(track_dset, track_dspace, hdf5_err)
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call h5dset_extent_f(track_dset, dims, hdf5_err)
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call h5dget_space_f(track_dset, track_dspace, hdf5_err)
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i = 1
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offset = (/i, n_tracks/)
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call h5sselect_hyperslab_f(track_dspace, H5S_SELECT_SET_F, offset, cnt, &
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hdf5_err)
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!call h5sget_select_npoints_f(track_dspace, test, hdf5_err)
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print *, test
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coords(:, 1) = p % coord0 % xyz
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print *, coords
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if (n_tracks<20) then
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call h5dwrite_f(track_dset, H5T_NATIVE_DOUBLE, coords, &
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write_dims, hdf5_err, file_space_id=track_dspace)
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end if
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!call h5sselect_hyperslab_f(track_dspace, H5S_SELECT_SET_F, offset, dims, &
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! hdf5_err)
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!i = 3
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n_tracks = n_tracks + 1
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!dims = (/i, n_tracks/)
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!call h5sset_extent_simple_f(track_dspace, 2, dims, max_dims, hdf5_err)
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!call h5dset_extent_f(track_dset, dims, hdf5_err)
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#else
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write(UNIT_TRACK) p % coord0 % xyz
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!write_double1Darray(p % coord0 % xyz, 'coordinates', 3)
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#endif
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end subroutine write_particle_track
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!===============================================================================
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@ -49,8 +117,22 @@ contains
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!===============================================================================
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subroutine finalize_particle_track()
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! Replace the following with '#ifdef HDF5'.
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#if 0
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integer(HSIZE_T) :: dims(2), max_dims(2), i
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call h5sget_simple_extent_dims_f(track_dspace, dims, max_dims, hdf5_err)
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!i = 3
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!dims = (/i, dims(2)-1/)
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!call h5dextend_f(track_dset, dims, hdf5_err)
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call h5dclose_f(track_dset, hdf5_err)
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call h5sclose_f(track_dspace, hdf5_err)
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call h5pclose_f(cparms, hdf5_err)
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call h5fclose_f(track_fh, hdf5_err)
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#else
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close(UNIT=UNIT_TRACK)
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!file_close('serial')
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#endif
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end subroutine finalize_particle_track
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end module particle_track
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