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1.4.2 release - Bug fixes, new features #347

Merged
merged 67 commits into from
Sep 15, 2024
Merged

1.4.2 release - Bug fixes, new features #347

merged 67 commits into from
Sep 15, 2024

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YuuuXie
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@YuuuXie YuuuXie commented Mar 15, 2023

Summary

Bug fixes for no stress labels and pylammps sanity check. Pylammps restart feature. B1 descriptors

  • Fix 1: flare on-the-fly training with no stress label (debug by Julia, for integrated with CP2K)
  • Fix 2: flare offline training with no stress label
  • Fix 3: single atom energies were not added to lammps energy in PyLammps during sanity check comparing lammps energy and sgp energy, now added. (reported by Daniil)
  • Feature 1: allow PyLammps (on-the-fly training with lammps) to restart. Previously, after each DFT call, LAMMPS starts a new MD, so the time history required by NVT or NPT is lost, and the temperature ramping did not work. Now the "restart" file is used, so the temperature ramping should work.
  • Added references and related work to the documentation
  • Adjust the dependency option order in the installation guide in docs, since the conda dependencies likely cause issue

Checklist

Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.

Before a pull request can be merged, the following items must be checked:

  • Code is in the standard Python style.
    Run Black on your local machine.
  • Docstrings have been added in the Sphinx docstring format.
  • Type annotations are highly encouraged.
  • Tests have been added for any new functionality or bug fixes.
  • All existing tests pass.
  • The version number in flare/_version.py is updated. We are using a version number format a.b.c
    • If this PR fixes bugs, update version number to a.b.c+1
    • If this PR adds new features, update version number to a.b+1.0
    • If this PR includes significant changes in framework or interface, update version number to a+1.0.0

Note that the CI system will run all the above checks. But it will be much more
efficient if you already fix most errors prior to submitting the PR.

YuuuXie and others added 30 commits December 13, 2022 14:58
Fix pickling errors of CP2K within OTF training
@YuuuXie YuuuXie marked this pull request as draft April 27, 2023 15:25
@YuuuXie YuuuXie changed the title 1.4.0 Bug fixes for no stress labels and pylammps sanity check. Pylammps restart feature. B1 descriptors 1.4.0 release - Bug fixes, new features Apr 27, 2023
YuuuXie and others added 21 commits April 27, 2023 11:47
bug fixes: Kuu_jitter, sparse_descriptor initialization
1.4.0 Add b1 descriptors: merge to development
changed the extxyz import in calculate method of FakeDFT to read only the relevant frame from the file instead of the entire file on each call. This makes the FakeDFT method significantly faster.
Time step  is set to 0.5 fs
Origin print :

*-Frame: 1
Simulation Time:      0.001 ps

updated print:
*-Frame: 1
Simulation Time:     0.0005 ps
Update FakeDFT to only import relevant frame
Update output.py: fix time printing, with the time step with 0.5 fs
Merged three recent pull requests for bug fixes
@jonpvandermause jonpvandermause self-assigned this Sep 15, 2024
@jonpvandermause jonpvandermause marked this pull request as ready for review September 15, 2024 13:59
@jonpvandermause jonpvandermause changed the title 1.4.0 release - Bug fixes, new features 1.4.2 release - Bug fixes, new features Sep 15, 2024
@jonpvandermause jonpvandermause merged commit 8bb4b4d into master Sep 15, 2024
16 checks passed
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6 participants