A FileReader like thorn that uses InterpolateLocalUniform to interpolate the data read in onto the new grid.
IOUtil [1] defines a file reading interface via the IO parameters filereader_ID_dir, filereader_ID_files, filereader_ID_vars parameters. IOUtil uses the checkpoint recovery routines to read grid variable data from disk. This requires that the grid resolution used to write the files agrees with the resolution using when reading in data and that, for each refinement level, the to be read in region is fully contained in the corresponding refinement level in the source files.
ReadInterpolate relaxes this restriction by allowing arbitrary changes in resolution and grid structure in between source files and simulation. It uses Cactus local interpolation operators CCTK_InterpLocalUniform to interpolate data using the highest resolution source data available for each target grid point.
It provides parameters files and only_these_datasets that mirror IOUtil’s parameters to select files and datasets in IO::filereader_ID_dir.
Auxiliary parameters are provided to fine tune what is read and to control the interpolator.
ReadInterpolate takes input data \(\psi \) on a grid patch described by its origin \(\vec O\), grid spacing \(\Delta \vec x\) and shape \(\vec N\). Data is interpolated to the coordinates of the simulation grid \(\vec x\) using Cactus’ interpolation operators: \(\psi (\vec x) = L(\psi , \vec x; \vec O, \Delta \vec x, \vec N)\).
For a target point \(\vec x\) multiple datasets in the source files may contain this physical coordinate. When this happens the following selection algorithm applies:
unless the candidate datasets overlaps the outer boundary of the current grid, require that there are at least cctk_nghostzones or interpolator_half_width extra points for use by the interpolator. This may involve using an off-centered interpolation stencil for points near the outer boundary. Then
if reading in data from time level 0, pick the largest refinement level dataset that contains the point, otherwise pick the refinement level that matches the refinement level of the target point. This assumes that the files were written at a timestep when all refinement level align in time and that the timestep in the data files and simulation are identical. Setting
Once a source data set has been selected its data and the target coordinate triplet are passed to CCTK_InterpLocalUniform for interpolation.
This thorn is intended as an initial data thorn, scheduling itself in the CCTK_INITIAL time bin of Cactus.
This thorn is part of the Einstein Toolkit in the EinsteinInitialData repository.
To use this thorn, set IO::filereader_ID_dir to the directory containing the data files, set ReadInterpolate’s files to the base names of the file to read and only_these_datasets to a comma separated list of regular expressions to match the datasets to read. To obtain the list of data sets present in the file the h5ls tool, which is part of HDF5, can be used. The parameter max_number_of_read_variables must be set to the expected number of grid variables to be read.
If desired read in data can be moved to a different position on the grid using shift_read_datasets_by[3] which relocates the origin of the coordinates in the read in data to the given coordinate triplet.
ReadInterpolate attempts to avoid one sided interpolation as much as possible, yet tried to allow reading in data at the outer boundaries of the grid. A heuristic is used to allow one sided derivatives there. This requires changing interpolator_pars to allow off centered interpolation stencils.
A number of parameters are provided to select which datasets to read:
minimum_reflevel
ignore any datasets with refinement level less than this,
maximum_reflevel
ignore any datasets with refinement level higher than this,
Some Carpet version contain a bug and do not set origin correctly for cell centered grids (it is off by half a grid point, i.e. it does not take the staggering into account). This option fixes this issue by offsetting all datasets that should be offset. Setting fix_cell_centered_origins adds an offset to correct for this. This is incorrect for files where Carpet already used the correct origin. This parameter only affects cell centered input data.
Interpolation parameters ReadInterpolate uses interpolator_name as the local interpolator to interpolate read in data to simulation grid points. It passes interpolator_vars to the interpolator. The default values select AEILocalInterp’s Hermite interpolator and forbid off centered interpolation stencils or extrapolation.
ReadInterpolate uses epsilon as a fuzziness parameter when determining if a point is contained in a read in dataset. This may require changes for very large grids.
When deciding if a read in dataset is large enough to allow for interpolation without off centered stencils ReadInterpolate requires knowledge about the stencil width of the chosen interpolation operator. This can be explicitly specified as interpolator_half_width or alternatively assumed to be cctk_nghostzones if this parameter is set to -1, which is the default.
This makes sure that the interpolator does not off center the interpolation stencil if there are insufficient points to interpolate, which can happen if there are insufficient ghost-zones for the interpolation method used, and can lead to processor-number dependent results.
ReadInterpolate is no aware of any symmetry conditions used in either the simulation used to produce the data files the current simulation. Thus it will interpolated into symmetry points in the same manner as for outer boundary points. In these situations the parameter enforce_symmetries_after_reading to apply symmetry boundary conditions after having read in all data. This does not enable ReadInterpolate to read in data produced on, for example, an octant grid and provide data on a full grid.
ReadInterpolate assumes that data files were written by CarpetIOHDF5 and may not work with files written by PUGH’s IOHDF5.
This thorn is intended as an initial data thorn, however since it is generic it does not extend ADMBase’s or HydroBase’s initial_XXX parameters.
ReadInterpolate can be used to read data into curvilinear grids set up by Llama but cannot read data from curvilinear grids.
The test suite file admhydro.par shows how to use ReadInterpolate to read in metric and fluid variables:
ActiveThorns = "ReadInterpolate" # ReadInterpolate ignore these but they are required to allocate storage ADMBase::initial_data = "Cartesian Minkowski" ADMBase::initial_lapse = "one" ADMBase::initial_shift = "zero" ADMBase::initial_dtlapse = "zero" ADMBase::initial_dtshift = "zero" HydroBase::initial_hydro = "zero" IO::filereader_ID_dir = "tov_write" ReadInterpolate::files = "alp rho" ReadInterpolate::max_number_of_read_variables = 2 ReadInterpolate::shift_read_datasets_by[0] = +3.14 ReadInterpolate::shift_read_datasets_by[1] = -42 ReadInterpolate::shift_read_datasets_by[2] = -6
Please use the Einstein Toolkit ticket system to report issues.
This thorn was originally inspired by SpEC’s [2] ReadTensorsFromDiskWithMap item and developed to read in single neutron star data produced by THC [3] into GRHydro [4]. It has been found useful to in combination with CT_MultiLevel since then.
David Radice and Philipp Mösta provided bug reports and comments during the time this thorn was developed.
[1] https://bitbucket.org/cactuscode/cactusbase/src/master/IOUtil/
[2] Spectral Einstein Code, https://www.black-holes.org/code/SpEC.html
[3] WhiskyTHC: The General-Relativistic Templated Hydrodynamics Code, http://personal.psu.edu/dur566/whiskythc.html
[4] GRHydro is an evolution code for a general-purpose 3D relativistic hydrodynamics, https://bitbucket.org/einsteintoolkit/einsteinevolve/src/master/GRHydro/
| enforce_symmetries_after_reading | Scope: private | BOOLEAN |
| Description: apply symmetry boundary conditions after reading data
| ||
| Default: no | ||
| epsilon | Scope: private | REAL |
| Description: Tolerance when deciding if a grid point lies within an overlap region
| ||
| Range | Default: 1e-12 | |
| 0:* | any positive number, should be similar to AEILocalInterp’s
tolerance
| |
| files | Scope: private | STRING |
| Description: List of basenames of files to read in as initial data (e.g. omit the .file_XXX.h5 part)
| ||
| Range | Default: (none) | |
| .+ | Space-separated list of initial data filenames
| |
 | An empty string for not recovering initial data
| |
| fix_cell_centered_origins | Scope: private | BOOLEAN |
| Description: offset rl>1 cell centered input data by half a grid step to fix broken HDF5 files
| ||
| Default: no | ||
| interpolator_half_width | Scope: private | INT |
| Description: maximum number of points to one side of the interpolated location the interpolator
uses
| ||
| Range | Default: -1 | |
| 1:* | this is similar to cctk_nghostzones, 1 for linear and constant
interpolation
| |
| 2:* | 2nd for second order and 3rd interpolation
| |
| -1 | use cctk_nghostzones
| |
| interpolator_name | Scope: private | STRING |
| Description: Which interpolator should I use
| ||
| Range | Default: Hermite polynomial interpolation | |
| .+ | Any nonempty string
| |
| interpolator_pars | Scope: private | STRING |
| Description: Parameters for the interpolator
| ||
| Range | Default: order=3 boundary_off_centering_tolerance={1e12 1e12 1e12 1e12 1e12 1e12} boundary_extrapolation_tolerance={1e-12 1e-12 1e-12 1e-12 1e-12 1e-12} | |
| .* | ”Any string that Util_TableSetFromStr ing() will take”
| |
| max_number_of_read_variables | Scope: private | INT |
| Description: how many variables will be read in?
| ||
| Range | Default: 1 | |
| 1:* | any positive number
| |
| maximum_reflevel | Scope: private | INT |
| Description: ignore any datasets with refinement level higher than this
| ||
| Range | Default: 1000 | |
| 0:* | maximum refinement level to keep
| |
| minimum_reflevel | Scope: private | INT |
| Description: ignore any datasets with refinement level less than this
| ||
| Range | Default: (none) | |
| 0:* | minimum refinement level to keep
| |
| only_these_datasets | Scope: private | STRING |
| Description: comma separated list of dataset regular expression patterns to consider for reading
| ||
| Range | Default: (none) | |
| .+ | any valid Cactus regular expression
| |
| see [1] below | refinement level 6, all metric
| |
| :g[xyz][xyz],:rho | metric and rho everywhere
| |
[1]
ADMBASE[:][:]g[xyz][xyz].*rl=6
| shift_read_datasets_by | Scope: private | REAL |
| Description: add to all read in coordinates
| ||
| Range | Default: 0.0 | |
| *:* | what used to be origin in datasets appear here
| |
| test | Scope: private | KEYWORD |
| Description: control how test data is used
| ||
| Range | Default: no | |
| no | do not use test data
| |
| generate | generate test data
| |
| compare | compare read data to test data
| |
| verbosity | Scope: private | INT |
| Description: how much diagnostic output to produce
| ||
| Range | Default: 1 | |
| 0:0 | only errors
| |
| 1:1 | warn about suspicous states
| |
| 2:* | more and more detailed debug output (values up to 10 are defined.
10 is very verbose.)
| |
| filereader_id_dir | Scope: shared from IO | STRING |
Implements:
readinterpolate
Inherits:
grid
| Group Names | Variable Names | Details | |
| reflevelseen | reflevelseen | compact | 0 |
| description | highest refinement level in source data that overlaps this point so far | ||
| dimensions | 3 | ||
| distribution | DEFAULT | ||
| group type | GF | ||
| tags | Checkpoint=”no” Prolongation=”none” | ||
| timelevels | 1 | ||
| vararray_size | max_number_of_read_variables | ||
| variable type | INT | ||
| interpthispoint | interpthispoint | compact | 0 |
| description | fill this point this time around | ||
| dimensions | 3 | ||
| distribution | DEFAULT | ||
| group type | GF | ||
| tags | Checkpoint=”no” Prolongation=”none” | ||
| timelevels | 1 | ||
| variable type | INT | ||
| interp_coords | compact | 0 | |
| interp_x | description | coordinate arrays for the interpolator | |
| interp_y | dimensions | 3 | |
| interp_z | distribution | DEFAULT | |
| interp_data | group type | GF | |
| tags | Checkpoint=”no” Prolongation=”none” | ||
| timelevels | 1 | ||
| variable type | REAL | ||
| test_values | test_values | compact | 0 |
| description | store values for test | ||
| dimensions | 3 | ||
| distribution | DEFAULT | ||
| group type | GF | ||
| tags | Checkpoint=”yes” ProlongationOperator=”none” | ||
| timelevels | 3 | ||
| variable type | REAL | ||
| test_results | test_results | compact | 0 |
| description | difference values for test | ||
| dimensions | 3 | ||
| distribution | DEFAULT | ||
| group type | GF | ||
| tags | Checkpoint=”no” ProlongationOperator=”none” | ||
| timelevels | 1 | ||
| variable type | REAL | ||
Uses header:
carpet.hh
This section lists all the variables which are assigned storage by thorn EinsteinInitialData/ReadInterpolate. Storage can either last for the duration of the run (Always means that if this thorn is activated storage will be assigned, Conditional means that if this thorn is activated storage will be assigned for the duration of the run if some condition is met), or can be turned on for the duration of a schedule function.
| Conditional: | |
| test_values[3] test_results | |
CCTK_PARAMCHECK (conditional)
readinterpolate_paramcheck
sanity check given parameters
| Language: | c | |
| Options: | global | |
| Type: | function | |
CCTK_INITIAL (conditional)
readinterpolate_readdata
read in datasets from disk
| After: | admbase_initialdata | |
| hydrobase_initial | ||
| Before: | admbase_postinitial | |
| hydrobase_prim2coninitial | ||
| Type: | group | |
ReadInterpolate_ReadData (conditional)
readinterpolate_read
read in datasets
| Language: | c | |
| Options: | level | |
| Storage: | reflevelseen | |
| interpthispoint | ||
| interp_coords | ||
| Type: | function | |
CCTK_POSTPOSTINITIAL (conditional)
readinterpolate_freecache
free memory used for dataset caches
| Language: | c | |
| Options: | global | |
| Type: | function | |
ReadInterpolate_ReadData (conditional)
readinterpolate_enforcesymmetry
enforce symmeries if desired
| After: | readinterpolate_read | |
| Language: | c | |
| Options: | level | |
| Type: | function | |
ReadInterpolate_ReadData (conditional)
applybcs
apply symmetry conditions to read in variables
| After: | readinterpolate_enforcesymmetry | |
| Type: | group | |
CCTK_INITIAL (conditional)
readinterpolate_generatetestdata
generate polynomial test data
| Language: | c | |
| Type: | function | |
CCTK_POSTPOSTINITIAL (conditional)
readinterpolate_comparetestdata
compare to polynomial test data
| Language: | c | |
| Type: | function | |
| Alias Name: | Function Name: |
| ApplyBCs | ReadInterpolate_ApplyBCs |