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Psydac's outputs

Structure

Psydac has a class meant to take care of outputing simulation results. This class, named OuputManager is located in psydac/api/postprocessing.py. It writes FemSpace related information in the Yaml syntax. The file looks like this:

ndim: 2
fields: file.h5 # Name of the fields file
patches:
- name: patch_0
  breakpoints:
  - [0.0, 0.25, 0.5, 0.75, 1.0]
  - [0.0, 0.25, 0.5, 0.75, 1.0]
  scalar_spaces:
  - name: Scalar_space
    ldim: 2
    kind: l2
    dtype: <class 'float'>
    rational: false
    periodic: [false, false]
    degree: [1, 1]
    multiplicity: [1, 1]
    basis: [B, B]
    knots:
    - [0.0, 0.0, 0.25, 0.5, 0.75, 1.0, 1.0]
    - [0.0, 0.0, 0.25, 0.5, 0.75, 1.0, 1.0]
  - &id001
    name: Vector_space[0]
    ldim: 2
    kind: undefined
    dtype: <class 'float'>
    rational: false
    periodic: [false, false]
    degree: [1, 2]
    multiplicity: [1, 1]
    basis: [B, B]
    knots:
    - [0.0, 0.0, 0.25, 0.5, 0.75, 1.0, 1.0]
    - [0.0, 0.0, 0.0, 0.25, 0.5, 0.75, 1.0, 1.0, 1.0]
  - &id002
    name: Vector_space[1]
    ldim: 2
    kind: undefined
    dtype: <class 'float'>
    rational: false
    periodic: [false, false]
    degree: [2, 1]
    multiplicity: [1, 1]
    basis: [B, B]
    knots:
    - [0.0, 0.0, 0.0, 0.25, 0.5, 0.75, 1.0, 1.0, 1.0]
    - [0.0, 0.0, 0.25, 0.5, 0.75, 1.0, 1.0]
  vector_spaces:
  - name: Vector_space
    kind: hcurl
    components:
    - *id001
    - *id002
- name: patch_1
  breakpoints:
  - [1.0, 1.25, 1.5, 1.75, 2.0]
  - [0.0, 0.25, 0.5, 0.75, 1.0]
  scalar_spaces:
  - name: Scalar_space
    ldim: 2
    kind: l2
    dtype: <class 'float'>
    rational: false
    periodic: [false, false]
    degree: [1, 1]
    multiplicity: [1, 1]
    basis: [B, B]
    knots:
    - [1.0, 1.0, 1.25, 1.5, 1.75, 2.0, 2.0]
    - [0.0, 0.0, 0.25, 0.5, 0.75, 1.0, 1.0]

The field coefficients are saved to the HDF5 format in the following manner :

file.h5
    attribute: spaces # name of the aforementioned Yaml file
    static/
        scalar_space_1/
            field_s1_1
            field_s1_2
            ....
            field_s1_n
        vector_space_1_[0]/
            attribute: parent_space # 'vector_space_1'
            field_v1_1_[0]
                attribute: parent_field # 'field_v1_1'
        vector_space_1_[1]/
            attribute: parent_space # 'vector_space_1'
            field_v1_1_[1]
                attribute: parent_field # 'field_v1_1'
        ...
    snapshot_1/
        attribute: t
        attribute: ts
        space_1/
        ...
        space_n/
    ...
    snapshot_n/

In addition to that, Psydac also features the PostProcessManager class to read those files, recreate all the FemSpace and FemField objects and export them to VTK.

Usage of class OutputManager

An instance of the OutputManager class is created at the beginning of the simulation, by specifying the following:

  1. The name of the YAML file (e.g. spaces.yaml) where the information about all FEM spaces will be written, and
  2. The name of the HDF5 file (e.g. fields.h5) where the coefficients of all FEM fields will be written.

References to the available FEM spaces are given to the OutputManager object through the add_spaces(**kwargs) method, and the corresponding YAML file is created upon calling the method export_space_info(). In order to inform the OutputManager object that the next fields to be exported are time-independent, the user should call the set_static() method. In the case of time-dependent fields, the user should prepare a time snapshot (which is defined for a specific integer time step ts and time value t) by calling the method add_snapshot(t, ts). In both cases the fields are exported to the HDF5 file through a call to the method export_fields(**kwargs). Here is a usage example:

# SymPDE Layer
# Discretization
# V0h and V1h are discretized SymPDE Space
# u0 and u1 are FemFields belonging to either of those spaces
output_m = OutputManager('spaces.yml', 'fields.h5')

output_m.add_spaces(V0=V0h, V1=V1h)
output_m.export_space_info() # Writes the space information to Yaml

output_m.set_static() # Tells the object to save in /static/
output_m.export_fields(u0_static=u0, u1_static=u1) # Actually does the saving

output_m.add_snapshot(t=0., ts=0)
# The line above tells the object to:
# 1. create the group snapshot_x with attribute t and ts
# 2. save in this snapshot
output_m.export_fields(u0=u0, u1=u1)

Usage of class PostProcessManager

Typically the PostProcessManager class is used in a separate post-processing script, which is run after the simulation has finished. In essence it evaluates the FEM fields over a uniform grid (applying the appropriate push-forward operations) and exports the values to a VTK file (or a sequence of files in the case of a time series). An instance of the PostProcessManager class is created by specifying the following:

  1. The name of the geometry file (in HDF5 format) which defines the geometry or the topological domain from which the geometry is derived.
  2. The name of the YAML file that contains the information about the FEM spaces
  3. The name of the HDF5 file that contains the coefficients of all the FEM fields

In order to export the fields to a VTK file, the user needs to call the method export_to_vtk(base_name, grid, npts_per_cell, snapshots, fields), where:

  1. base_name is the base name for the VTK output files.
  2. grid is either a user specified evaluation grid or None.
  3. npts_per_cell specifies the refinement in the case of a uniform grid.
  4. snapshots specifies which time snapshots should be extracted from the HDF5 file (none in the case of static fields)
  5. fields is a tuple of h5_field_name.

Here is a usage example:

# geometry.h5 is where the domain comes from. See PostProcessManager's docstring for more information
post = PostProcessManager(geometry_file='geometry.h5', space_file='spaces.yml', fields_file='fields.h5')

# See PostProcessManager.export_to_vtk's and TensorFemSpace.eval_fields' docstrings for more information
post.export_to_vtk('filename_vtk', grid=grid, npts_per_cell=npts_per_cell, snapshots='all', fields = ('u0', 'u1'))

Further Examples

Further examples are present in the following files:

  • examples/poisson_3d_target_torus.py
  • examples/sample_multipatch_parallel.py
  • examples/notebooks/Poisson_non_periodic.ipynb
  • psydac/api/tests/test_postprocessing.py