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Lammps Support#348

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jaclark5 wants to merge 67 commits intoalchemistry:masteralchemistry/alchemlyb:masterfrom jaclark5:lammpsjaclark5/alchemlyb:lammpsCopy head branch name to clipboard

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Commits

Commits on Feb 5, 2024

• Add lammps file generation and parsing

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• Update formatting

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• Update variables in generated files

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• Add input for mbar

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• Remove print

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• Bug fix file outputs

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• Bug fix file format

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Commits on Feb 7, 2024

• Bug fix param start, add dataframe for potential

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• Bug fix loops in mbar generation

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Commits on Feb 20, 2024

• Add precision values for processing lammps input files

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  committed
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• Merge branch 'master' into lammps

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• Add error catch for column definition in extract_u_nk

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Commits on Feb 22, 2024

• Add abs to nblocks calc

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• Bug fix, nblocks

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Commits on Mar 13, 2024

• Add calculation of beta based on lammps units

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• Update module docstring

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• Add name to author list

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• Added to changelog

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• Update docs

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• Run Black

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Commits on Jul 24, 2024

• Sort lambda values for consistent output

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• Update lammps.extract_dHdl defaults

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• Update error for lambda values

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• Update extract_dHdl* to use prec

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• Update changelog

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• update parsing.lammps.py docstrings

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• Run Black

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Commits on Aug 21, 2024

• Add ensemble support

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Commits on Aug 23, 2024

• Bug fix, inputs for extract_dHdl

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Commits on Aug 30, 2024

• Add LAMMPS unit conversion for pV term in npt u_r

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  8da4b99

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• Fixed kT multiplication issue in dHdl

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Commits on Sep 3, 2024

• Resolve deprecation warnings

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Commits on Sep 5, 2024

• Merge branch 'master' into lammps

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Commits on Sep 13, 2024

• Resolve pandas depreication warning

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Commits on Sep 19, 2024

• Moving average (alchemistry#381)

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• Added to changelog

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• initial CITATION.cff file

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  2 peopleauthored and

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• add JOSS paper as preferred citation to CITATION

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• added references for MBAR and equilibration detection

  

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• inserted additional JOSS paper authors in software author list

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• updated CHANGES and AUTHORS for 2.3.3

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• add authors to CITATION who had NOT been in AUTHORS

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• add @jaclark5 to AUTHORS and CITATION.cff

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• Resolve bug in bar_model.delta_f_ creation (alchemistry#397)

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• black-formatted files

  

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• replace setup.py,cfg with pyproject.toml

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• house-keeping

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• make repo title identical to JOSS paper title (alchemistry#404)

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• [doc] tutorial: use alchemlyb.concat (alchemistry#399)

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• Update version

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• Merge branch 'master' into lammps

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• Formatting

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• FutureWarning

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Commits on Sep 24, 2024

• Added commenting extract_u_nk

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Commits on Oct 22, 2024

• Add names, bug fix dHdl

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• Merge branch 'master' into lammps

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Commits on Nov 12, 2024

• Bug fix columns, add name attribute

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• Merge branch 'master' into lammps

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Commits on Nov 15, 2024

• Merge branch 'master' into lammps

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Commits on Nov 17, 2024

• Add testing

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Commits on Dec 20, 2024

• Merge branch 'master' into lammps

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Commits on Jan 2, 2025

• Black, add handling for compressed files

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• Black for lammps parsing and handling compressed files

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Commits on Jan 5, 2025

• Address code coverage

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• Address test issues

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• Address test issues

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• Fix test issue

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