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Added subdirectory to particlesPath as per standard. #971

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Added subdirectory to particlesPath as per standard. #971

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DavidSagan
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Added subdirectory to particlesPath as per standard.

@ChristopherMayes
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This doesn't seem to make a valid file. In bmad-doc/tao_examples/optics_matching:

Tao> write beam -at end
[INFO] tao_write_cmd:
    Written: beam_1.hdf5

Tao> sp h5dump beam_1.hdf5 
h5dump error: unable to open file "beam_1.hdf5"

@ChristopherMayes
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One line:

tao -init $ACC_ROOT_DIR/bmad-doc/tao_examples/optics_matching/tao.init -noplot -command "beamon;write beam -at end;sp h5dump beam_1.hdf5"

Tao: set global track_type = beam

Tao: write beam -at end
[ERROR | 2024-MAY-28 20:38:55] hdf5_open_file:
    CANNOT CREATE FILE FOR WRITING: beam_1.hdf5
[INFO] tao_write_cmd:
    Written: beam_1.hdf5

Tao: sp h5dump beam_1.hdf5
h5dump error: unable to open file "beam_1.hdf5"

@DavidSagan
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@ChristopherMayes I'm not seeing these problems.

@ChristopherMayes
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Okay, I must have made a mistake. But @DavidSagan could you put in a better description here about what the change is?

@ChristopherMayes
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I tried openpmd-validator on this, and it gives:

openPMD_check_h5 -i beam_1.hdf5
Error: Attribute openPMDextension in `/` is not of type 'uint32' (is 'bytes_')!
Error: Attribute iterationEncoding (required) does NOT exist in `/`!
Error: Attribute iterationFormat (required) does NOT exist in `/`!
Warning: Attribute author (recommended) does NOT exist in `/`!
Error: Attribute date in `/` does not satisfy format ('2024-05-29 09:08:46' should be in format '^[0-9]{4}-[0-9]{2}-[0-9]{2} [0-9]{2}:[0-9]{2}:[0-9]{2} [\+|-][0-9]{4}$')!
Traceback (most recent call last):
  File "/Users/chrisonian/Code/mambaforge/envs/devel/bin/openPMD_check_h5", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/chrisonian/Code/mambaforge/envs/devel/lib/python3.12/site-packages/openpmd_validator/check_h5.py", line 931, in main
    result_array = check_file(file_name, verbose, force_extension_pic)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/chrisonian/Code/mambaforge/envs/devel/lib/python3.12/site-packages/openpmd_validator/check_h5.py", line 917, in check_file
    extensionStates = get_extensions(f, verbose)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/chrisonian/Code/mambaforge/envs/devel/lib/python3.12/site-packages/openpmd_validator/check_h5.py", line 116, in get_extensions
    if (bitmask & extensionIDs) == bitmask:
        ~~~~~~~~^~~~~~~~~~~~~~
TypeError: ufunc 'bitwise_and' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

@DavidSagan
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DavidSagan commented May 29, 2024 •
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Stuff like iterationEncoding should not be required. @ChristopherMayes See openPMD/openPMD-standard#232

@DavidSagan
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The change is: using axisLabels to determine storage order instead of gridDataOrder.

@DavidSagan
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And I fixed the date problem.

@ChristopherMayes
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Now I see:

openPMD_check_h5 -i beam_1.hdf5
Error: Attribute openPMDextension in `/` is not of type 'uint32' (is 'bytes_')!
Error: Attribute iterationEncoding (required) does NOT exist in `/`!
Error: Attribute iterationFormat (required) does NOT exist in `/`!
Warning: Attribute author (recommended) does NOT exist in `/`!
Traceback (most recent call last):
  File "/Users/chrisonian/Code/mambaforge/envs/devel/bin/openPMD_check_h5", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/chrisonian/Code/mambaforge/envs/devel/lib/python3.12/site-packages/openpmd_validator/check_h5.py", line 931, in main
    result_array = check_file(file_name, verbose, force_extension_pic)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/chrisonian/Code/mambaforge/envs/devel/lib/python3.12/site-packages/openpmd_validator/check_h5.py", line 917, in check_file
    extensionStates = get_extensions(f, verbose)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/chrisonian/Code/mambaforge/envs/devel/lib/python3.12/site-packages/openpmd_validator/check_h5.py", line 116, in get_extensions
    if (bitmask & extensionIDs) == bitmask:
        ~~~~~~~~^~~~~~~~~~~~~~
TypeError: ufunc 'bitwise_and' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

@ChristopherMayes
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Example file with this new code:
beam_1.hdf5.zip

@ChristopherMayes
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The change is: using axisLabels to determine storage order instead of gridDataOrder.

Well it looks like you are adding species in the paths as well.

@DavidSagan
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@ChristopherMayes I moved axisLabels one level higher as discussed. Be aware that the "old" field grid files also have an axisLabels attribute in the same spot but the order with the old files does not reflect the storage order. So you need to check to see if gridDataOrder exists and, if so, use that.

@ChristopherMayes
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I have corresponding changes in ChristopherMayes/openPMD-beamphysics#60.

@DavidSagan
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I will merge when you give the OK.

@ChristopherMayes
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I'd like the openPMD-validator [(version: 2.0.0) to pass with these new files. https://github.com/openPMD/openPMD-validator/tree/2.0.X

Currently is gives:

openPMD_check_h5 -i beam_1.hdf5 
Error: Attribute iterationEncoding (required) does NOT exist in `/`!
Error: Attribute iterationFormat (required) does NOT exist in `/`!
Warning: Attribute author (recommended) does NOT exist in `/`!
Error: Attribute date in `/` does not satisfy format ('2023-07-20 15:54:07' should be in format '^[0-9]{4}-[0-9]{2}-[0-9]{2} [0-9]{2}:[0-9]{2}:[0-9]{2} [\+|-][0-9]{4}$')!
Found 1 iteration(s)
Error: Attribute time (required) does NOT exist in `/data/00001`!
Error: Attribute dt (required) does NOT exist in `/data/00001`!
Warning: Attribute timeUnitSI (recommended) does NOT exist in `/data/00001`!
Result: 5 Errors and 2 Warnings.

This is related to openPMD/openPMD-standard#232.

This was referenced Jun 1, 2024
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@ax3l
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ax3l commented Jul 31, 2024 •
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Hi @DavidSagan @ChristopherMayes, can you attach here in a comment the new file (as zip) so I can check it with the validator as I update it?

@ax3l ax3l mentioned this pull request Jul 31, 2024
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@DavidSagan
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@ChristopherMayes You have a file to post on hand. Yes?

@ChristopherMayes
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Here is an example: particles_from_bmad_pr971.h5.zip

@ChristopherMayes
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@ax3l does that work for you?

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3 participants
@DavidSagan @ChristopherMayes @ax3l