pencil.io.fort2h5
Contains the functions to read old Fortran binary simulation data and write snapshots in hdf5 (data/allprocs/VAR*.h5 files), video slices to data/slices/uu1_xy.h5, etc. and averages to data/averages/xy.h5, etc
Functions
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Copy a simulation snapshot set written in Fortran binary to hdf5. |
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Copy a simulation set of video slices written in Fortran binary to hdf5. |
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Copy a simulation set of video slices written in Fortran binary to hdf5. |
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Copy a simulation object written in Fortran binary to hdf5. |
Module Contents
- pencil.io.fort2h5.var2h5(newdir, olddir, allfile_names, todatadir, fromdatadir, snap_by_proc, precision, lpersist, quiet, nghost, settings, param, grid, x, y, z, lshear, lremove_old_snapshots, indx, trimall=False, l_mpi=False, driver=None, comm=None, rank=0, size=1)
Copy a simulation snapshot set written in Fortran binary to hdf5.
call signature:
- var2h5(newdir, olddir, allfile_names, todatadir, fromdatadir, snap_by_proc,
precision, lpersist, quiet, nghost, settings, param, grid, x, y, z, lshear, lremove_old_snapshots, indx, trimall=False, l_mpi=False, driver=None, comm=None, rank=0, size=1
)
Keyword arguments:
- newdir:
String path to simulation destination directory.
- olddir:
String path to simulation destination directory.
- allfile_names:
A list of names of the snapshot files to be written, e.g. VAR0.
- todatadir:
Directory to which the data is stored.
- fromdatadir:
Directory from which the data is collected.
- snap_by_proc:
Read and write snapshots by procdir of the fortran binary tree
- precision:
Single ‘f’ or double ‘d’ precision for new data.
- lpersist:
option to include persistent variables from snapshots.
- quiet
Option not to print output.
- nghost:
Number of ghost zones.
- settings
simulation properties.
- param
simulation Param object.
- grid
simulation Grid object.
- xyz:
xyz arrays of the domain with ghost zones.
- lshear:
Flag for the shear.
- lremove_old_snapshots:
If True the old snapshots will be deleted once the new snapshot has been saved.
- indx:
List of variable indices in the f-array.
- trimall:
Strip ghost zones from snapshots
- l_mpi:
Applying MPI parallel process
- driver:
HDF5 file io driver either None or mpio
- comm:
MPI library calls
- rank:
Integer ID of processor
- size:
Number of MPI processes
- pencil.io.fort2h5.slices2h5(newdir, olddir, grid, todatadir='data/slices', fromdatadir='data', precision='d', quiet=True, lremove_old_slices=False, lsplit_slices=False, l_mpi=False, driver=None, comm=None, rank=0, size=1, vlarge=1000000000)
Copy a simulation set of video slices written in Fortran binary to hdf5.
call signature:
- slices2h5(newdir, olddir, grid,
todatadir=’data/slices’, fromdatadir=’data’, precision=’d’, quiet=True, lremove_old_slices=False, lsplit_slices=False, l_mpi=False, driver=None, comm=None, rank=0, size=1, vlarge=1000000000):
Keyword arguments:
- newdir:
String path to simulation destination directory.
- olddir:
String path to simulation destination directory.
- grid
simulation Grid object.
- todatadir:
Directory to which the data is stored.
- fromdatadir:
Directory from which the data is collected.
- precision:
Single ‘f’ or double ‘d’ precision for new data.
- quiet:
Option not to print output.
- lremove_old_slices:
If True the old video slices will be deleted once the new slices have been saved.
- lsplit_slices:
Read the video slices in iterative chunks for large memory
- l_mpi:
Applying MPI parallel process
- driver:
HDF5 file io driver either None or mpio
- comm:
MPI library calls
- rank:
Integer ID of processor
- size:
Number of MPI processes
- vlarge:
Limit size of file without chunking
- pencil.io.fort2h5.aver2h5(newdir, olddir, todatadir='data/averages', fromdatadir='data', l2D=True, precision='d', quiet=True, lremove_old_averages=False, aver_by_proc=False, laver2D=False, l_mpi=False, driver=None, comm=None, rank=0, size=1)
Copy a simulation set of video slices written in Fortran binary to hdf5.
call signature:
- aver2h5(newdir, olddir,
todatadir=’data/averages’, fromdatadir=’data’, l2D=True, precision=’d’, quiet=True, lremove_old_averages=False, aver_by_proc=False, laver2D=False, l_mpi=False, driver=None, comm=None, rank=0, size=1):
Keyword arguments:
- newdir:
String path to simulation destination directory.
- olddir:
String path to simulation destination directory.
- todatadir:
Directory to which the data is stored.
- fromdatadir:
Directory from which the data is collected.
- l2D
Option to include 2D averages if the file sizes are not too large
- precision:
Single ‘f’ or double ‘d’ precision for new data.
- quiet
Option not to print output.
- lremove_old_averages:
If True the old averages data will be deleted once the new h5 data has been saved.
- aver_by_proc
Option to read old binary files by processor and write in parallel
- laver2D
If True apply to each plane_list ‘y’, ‘z’ and load each variable sequentially
- l_mpi:
Applying MPI parallel process
- driver:
HDF5 file io driver either None or mpio
- comm:
MPI library calls
- rank:
Integer ID of processor
- size:
Number of MPI processes
- pencil.io.fort2h5.sim2h5(newdir='.', olddir='.', varfile_names=None, todatadir='data/allprocs', fromdatadir='data', precision='d', nghost=3, lpersist=True, x=None, y=None, z=None, lshear=False, snap_by_proc=False, aver_by_proc=False, lremove_old_snapshots=False, lremove_old_slices=False, lread_all_videoslices=False, vlarge=100000000, lremove_old_averages=False, execute=False, quiet=True, l2D=True, lvars=True, lvids=True, laver=True, laver2D=False, lremove_deprecated_vids=False, lsplit_slices=False)
Copy a simulation object written in Fortran binary to hdf5. The default is to copy all snapshots from/to the current simulation directory. Optionally the old files can be removed to
call signature:
- sim2h5(newdir=’.’, olddir=’.’, varfile_names=None,
todatadir=’data/allprocs’, fromdatadir=’data’, precision=’d’, nghost=3, lpersist=False, x=None, y=None, z=None, lshear=False, snap_by_proc=False, aver_by_proc=False, lremove_old_snapshots=False, lremove_old_slices=False, lread_all_videoslices=True, lremove_old_averages=False, execute=False, quiet=True, l2D=True, lvars=True, lvids=True, laver=True)
Keyword arguments:
- olddir:
String path to simulation source directory. Path may be relative or absolute.
- newdir:
String path to simulation destination directory. Path may be relative or absolute.
- varfile_names:
A list of names of the snapshot files to be written, e.g. VAR0 If None all varfiles in olddir+’/data/proc0/’ will be converted
- todatadir:
Directory to which the data is stored.
- fromdatadir:
Directory from which the data is collected.
- precision:
Single ‘f’ or double ‘d’ precision for new data.
- nghost:
Number of ghost zones. TODO: handle switching size of ghost zones.
- lpersist:
option to include persistent variables from snapshots.
- xyz:
xyz arrays of the domain with ghost zones. This will normally be obtained from Grid object, but facility to redefine an alternative grid value.
- lshear:
Flag for the shear.
- execute:
optional confirmation required if lremove_old.
- lremove_old_snapshots:
If True the old snapshot data will be deleted once the new h5 data has been saved.
- lremove_old_slices:
If True the old video slice data will be deleted once the new h5 data has been saved.
- lremove_old_averages:
If True the old averages data will be deleted once the new h5 data has been saved.
- aver_by_proc
Option to read old binary files by processor and write in parallel
- laver2D
If True apply to each plane_list ‘y’, ‘z’ and load each variable sequentially
- l_mpi:
Applying MPI parallel process
- driver:
HDF5 file io driver either None or mpio
- comm:
MPI library calls
- rank:
Integer ID of processor
- size:
Number of MPI processes