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new features and bugfixes on seissolxdmf and seissolxdmfwriter #17

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new features and bugfixes on seissolxdmf and seissolxdmfwriter #17

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Thomas-Ulrich
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@Thomas-Ulrich Thomas-Ulrich commented Jun 14, 2024 •
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  • fix format of extracted seissol output (
    <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
    should appear only once and not at each time step. Paraview was not complaining about that, but SeisSol/Sampler does.
  • print available variables when the variable to read is not available.
  • replace corrupted time-steps (typically the last one when seissol is interrupted writing) with nans instead of 0s.
  • change setup.py to pyproject.toml (more recent format).
  • remove indices larger than number of output times, avoiding such kind of issue:
(base) ulrich@ulrich-ThinkPad-T490s:~/trash$ seissol_output_extractor dyn_0100_coh0.25_1_B1.2_C0.2_R0.8-fault.xdmf --time "i2,i10,i10000"
args.variables was set to all and now contains ['ASl', 'DS', 'Mud', 'PSR', 'P_n', 'Pn0', 'RT', 'SRd', 'SRs', 'Sld', 'Sls', 'StV', 'T_d', 'T_s', 'Td0', 'Ts0', 'Vr', 'fault-tag', 'partition']
Writing hdf5 output with compression enabled (compression_level=4). 
Use --compression=0 if you want to speed-up data extraction.
ASl: 0it [00:00, ?it/s]time step 10000 of ASl is corrupted, replacing with nans
ASl: 3it [00:00, 562.26it/s]
DS: 0it [00:00, ?it/s]time step 10000 of DS is corrupted, replacing with nans
DS: 3it [00:00, 650.78it/s]
Mud: 0it [00:00, ?it/s]time step 10000 of Mud is corrupted, replacing with nans
Mud: 3it [00:00, 579.30it/s]
PSR: 0it [00:00, ?it/s]time step 10000 of PSR is corrupted, replacing with nans
PSR: 3it [00:00, 652.71it/s]
P_n: 0it [00:00, ?it/s]time step 10000 of P_n is corrupted, replacing with nans
P_n: 3it [00:00, 504.04it/s]
Pn0: 0it [00:00, ?it/s]time step 10000 of Pn0 is corrupted, replacing with nans
Pn0: 3it [00:00, 449.73it/s]
RT: 0it [00:00, ?it/s]time step 10000 of RT is corrupted, replacing with nans
RT: 3it [00:00, 625.98it/s]
SRd: 0it [00:00, ?it/s]time step 10000 of SRd is corrupted, replacing with nans
SRd: 3it [00:00, 392.54it/s]
SRs: 0it [00:00, ?it/s]time step 10000 of SRs is corrupted, replacing with nans
SRs: 3it [00:00, 484.20it/s]
Sld: 0it [00:00, ?it/s]time step 10000 of Sld is corrupted, replacing with nans
Sld: 3it [00:00, 432.31it/s]
Sls: 0it [00:00, ?it/s]time step 10000 of Sls is corrupted, replacing with nans
Sls: 3it [00:00, 476.35it/s]
StV: 0it [00:00, ?it/s]time step 10000 of StV is corrupted, replacing with nans
StV: 3it [00:00, 879.62it/s]
T_d: 0it [00:00, ?it/s]time step 10000 of T_d is corrupted, replacing with nans
T_d: 3it [00:00, 467.35it/s]
T_s: 0it [00:00, ?it/s]time step 10000 of T_s is corrupted, replacing with nans
T_s: 3it [00:00, 312.45it/s]
Td0: 0it [00:00, ?it/s]time step 10000 of Td0 is corrupted, replacing with nans
Td0: 3it [00:00, 403.18it/s]
Ts0: 0it [00:00, ?it/s]time step 10000 of Ts0 is corrupted, replacing with nans
Ts0: 3it [00:00, 377.98it/s]
Vr: 0it [00:00, ?it/s]time step 10000 of Vr is corrupted, replacing with nans
Vr: 3it [00:00, 430.92it/s]
done writing dyn_0100_coh0.25_1_B1.2_C0.2_R0.8_extracted-fault.h5
Traceback (most recent call last):
  File "/home/ulrich/mambaforge/bin/seissol_output_extractor", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/ulrich/mambaforge/lib/python3.12/site-packages/seissolxdmfwriter/seissol_output_extractor.py", line 201, in main
    sxw.write_from_seissol_output(
  File "/home/ulrich/mambaforge/lib/python3.12/site-packages/seissolxdmfwriter/seissolxdmfwriter.py", line 512, in write_from_seissol_output
    [sx.ReadTimes()[k] for k in time_indices],
     ~~~~~~~~~~~~~~^^^
IndexError: list index out of range

-- add regionFilter option to filter for fault-tag or locationFlags

(base) ulrich@ulrich-ThinkPad-T490s:~/trash$ seissol_output_extractor dyn_0100_coh0.25_1_B1.2_C0.2_R0.8-fault.xdmf --time "i2,i10,i10000" --regionFilter "3,4,50" --xRange 0 10000  --zRange " -1000" 10000
Regions to filter: [3, 4, 50]
cell count after region filtering: 23638/23638
/home/ulrich/mambaforge/lib/python3.12/site-packages/seissolxdmfwriter/seissol_output_extractor.py:186: UserWarning: spatial filtering significantly slows down this script
  warn("spatial filtering significantly slows down this script")
cell count after spatial filtering: 97/23638
args.variables was set to all and now contains ['ASl', 'DS', 'Mud', 'PSR', 'P_n', 'Pn0', 'RT', 'SRd', 'SRs', 'Sld', 'Sls', 'StV', 'T_d', 'T_s', 'Td0', 'Ts0', 'Vr', 'fault-tag', 'partition']
Writing hdf5 output with compression enabled (compression_level=4). 
Use --compression=0 if you want to speed-up data extraction.
ASl: 2it [00:00, 1028.90it/s]
DS: 2it [00:00, 1156.25it/s]
Mud: 2it [00:00, 1033.97it/s]
PSR: 2it [00:00, 664.60it/s]
P_n: 2it [00:00, 961.78it/s]
Pn0: 2it [00:00, 1108.43it/s]
RT: 2it [00:00, 1223.72it/s]
SRd: 2it [00:00, 1116.99it/s]
SRs: 2it [00:00, 1142.71it/s]
Sld: 2it [00:00, 1164.44it/s]
Sls: 2it [00:00, 1083.94it/s]
StV: 2it [00:00, 1209.43it/s]
T_d: 2it [00:00, 1235.98it/s]
T_s: 2it [00:00, 1159.45it/s]
Td0: 2it [00:00, 1159.61it/s]
Ts0: 2it [00:00, 1147.24it/s]
Vr: 2it [00:00, 1233.26it/s]
done writing dyn_0100_coh0.25_1_B1.2_C0.2_R0.8_extracted-fault.h5
done writing dyn_0100_coh0.25_1_B1.2_C0.2_R0.8_extracted-fault.xdmf
full path: /home/ulrich/trash/dyn_0100_coh0.25_1_B1.2_C0.2_R0.8_extracted-fault.xdmf

@palgunadi1993
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hi Thomas,
I also want to add bug on this line:
https://github.com/SeisSol/Visualization/blob/master/seissolxdmf/seissolxdmf/seissolxdmf.py#L285

should it be self.ReadDataChunk()?

Thanks.
Kadek

@Thomas-Ulrich Thomas-Ulrich changed the title small updates on seissolxdmf and seissolxdmfwriter new features and bugfixes on seissolxdmf and seissolxdmfwriter Feb 11, 2025
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@Thomas-Ulrich @palgunadi1993