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Rewrite H5MD module #4480

Merged
merged 9 commits into from
Apr 4, 2022
Merged

Rewrite H5MD module #4480

merged 9 commits into from
Apr 4, 2022

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jngrad
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@jngrad jngrad commented Mar 24, 2022

Description of changes:

  • make H5md a standard ScriptInterface class
  • make H5md checkpointable (API change: positional argument file_path is now a keyword argument)
  • make H5MD specifications accessible from the python interface
    • users can now decide which datasets (e.g. particle properties) are written to the trajectory
    • data can only be appended to an existing file if it has the same H5MD specifications
    • C++ developers can now add extra particle properties to the H5MD specifications with relative ease
    • Lees-Edwards boundary conditions are now part of the H5MD specifications
  • fix cryptic errors:
    • the H5md class is now usable in an interactive session
    • physical units are now optional
  • document how to parse H5MD files with various open source tools
  • document how to reconstruct the unfolded trajectory (fix for mailing list thread "Unwrapped coordinates in H5MD format")

jngrad and others added 8 commits March 22, 2022 23:26
@jngrad @pdebuyl
core: Store Lees-Edwards offset in H5MD output
514516d 
Co-authored-by: Pierre de Buyl <pdebuyl@pdebuyl.be>
@jngrad
core: Fix typo in const overload
465fc90
@jngrad
core: Refactor H5MD
12d86e0 
Don't throw an OSError when the h5md file is written from an
interactive session (leave the parameters/files/script field empty).
Make H5MD utility functions static.
@jngrad
python: Make H5md a script interface class
068360e 
Make properties read-only. Disable checkpointing. Allow writing H5MD
files without physical units. Add physical units to the box length
and Lees-Edwards offset.
@jngrad
docs: Rewrite H5MD feature documentation
cabd2d5
@jngrad
Implement dynamic H5MD specifications
2acb8aa 
Let the user select which properties to write to H5MD files. When
appending data to an existing H5MD file, the H5MD specifications
must match.
@jngrad
Implement H5MD checkpointing
4bc6eb6
@jngrad
tests: Check H5md edge cases
bd4dbb8
@jngrad jngrad added this to the Espresso 4.2 milestone Mar 24, 2022
@jngrad jngrad marked this pull request as ready for review March 24, 2022 17:00
@jngrad jngrad requested a review from itischler March 24, 2022 17:01
@jngrad jngrad added the automerge Merge with kodiak label Apr 4, 2022
@kodiakhq kodiakhq bot merged commit d1e0be5 into espressomd:python Apr 4, 2022
@jngrad jngrad deleted the h5md_maintenance branch April 4, 2022 18:31
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@reinaual reinaual reinaual approved these changes

@itischler itischler Awaiting requested review from itischler

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