Add GSD Logger and Pressure Tensor #53
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chrisjonesBSU
commented
Sep 19, 2023
| logger.add(thermo_props, quantities=self.log_quantities) | ||
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| for f in self._forcefield: | ||
| logger.add(f, quantities=["energy"]) | ||
| gsd_logger.add(f, quantities=["energy"]) |
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@marjanAlbouye if I add "force" to this list, will that log the average forces (not per-particle forces) just like it does for energy?
marjanalbooyeh
approved these changes
Sep 19, 2023
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LGTM! Thank you Chris.
Maybe adding a relevant unit test that checks whether all the intended values are logged could be helpful here.
We can access the logged values from a frame of gsd like this:
gsd_traj = gsd.hoomd.open("trajectory.gsd", "rb")
frame = gsd_traj[0]
logged_keys = frame.log.keys()
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## main #53 +/- ##
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+ Coverage 93.83% 93.85% +0.01%
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Files 18 18
Lines 1347 1351 +4
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+ Hits 1264 1268 +4
Misses 83 83
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This PR sets up a separate logger for the GSD writer and logs energy, thermodynamic quantities and the pressure tensor to the GSD file.