Lammps Support (#348)

* Add lammps file generation and parsing

* Update formatting

* Update variables in generated files

* Add input for mbar

* Remove print

* Bug fix file outputs

* Bug fix file format

* Bug fix param start, add dataframe for potential

* Bug fix loops in mbar generation

* Add precision values for processing lammps input files

* Add error catch for column definition in extract_u_nk

* Add abs to nblocks calc

* Bug fix, nblocks

* Add calculation of beta based on lammps units
Add generation of u_nk and dHdl from linearly related dependencies

* Update module docstring

* Add name to author list

* Added to changelog

* Update docs

* Run Black

* Sort lambda values for consistent output

* Update lammps.extract_dHdl defaults

* Update error for lambda values

* Update extract_dHdl* to use prec

* update parsing.lammps.py docstrings

* Run Black

* Add ensemble support

* Bug fix, inputs for extract_dHdl

* Add LAMMPS unit conversion for pV term in npt u_r

* Fixed kT multiplication issue in dHdl

* Resolve deprecation warnings

* Resolve pandas depreication warning

* Moving average (#381)

* Add moving_average function for visualization and convergence testing

* Update versionadded

* Run Black

* Bug fix bar_.py states

* Update Changelog

* Update the docs

* Add tests

* Formatting to align with Black

* Update tests

* Refactor moving_average to align with forward_backward_convergence function

* Update tests

* Update test_convergence and lambda tests in convergence.moving_average

* Adjust convergence.py and tests for codecoverage

* black

* Update moving_average to block_average for more accurate descriptive name

* Address reviewer comments

* Update test to align with changed handling of dfs of different length in block_average

* Remove incorrect popagation of error in BAR

* Add tests and error catch for ill constructed BAR input, u_nk

* black

* Updated version comments

---------

Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>

* Added to changelog

* initial CITATION.cff file

- generated with https://bit.ly/cffinit
- authors and order from AUTHORS
- affiliations and ORCID from JOSS paper
- emails from paper or individuals

Co-authored-by: David L. Dotson <dotsdl@gmail.com>

* add JOSS paper as preferred citation to CITATION

- inferred DOI from proof
- assume final acceptance in 2024...

* added references for MBAR and equilibration detection

* inserted additional JOSS paper authors in software author list

- added David Mobley @davidlmobley (original conception and design of alchemlyb)
- added Michael Shirts @mrshirts (original conception and design of alchemlyb)

* updated CHANGES and AUTHORS for 2.3.3

- CHANGES: bump to 2.3.3
- add reminder to AUTHORS to also update CITATION.cff

* add authors to CITATION who had NOT been in AUTHORS

Added all authors that were mentioned in the Acknowledgements of the JOSS
paper but were not in AUTHORS

- Wei-Tse Hsu @wehs7661 (2020) for code clean-up in a732380
- Jan Janssen  @jan-janssen (2022) for creating the conda-forge package
- Shujie Fan @VOD555 (2022) for initial code for fractional equilibration time
- Helmut Carter @helmutcarter (2024) for doc fix in #356

* add @jaclark5 to AUTHORS and CITATION.cff

AUTHORS entry had been forgotten in PR #381

* Resolve bug in bar_model.delta_f_ creation (#397)

* fix bug introduced in PR #381: there was a change to creating the delta_f_ matrix,
  which resulted in the columns and indices being tuples that were in the wrong order 
  for single lambda computations.
* ensure that columns are in the correct order by explicitly sorting
* add a test for the delta_f_ columns

* black-formatted files

* replace setup.py,cfg with pyproject.toml

- fix #385
- use pyproject.toml instead of setup.py (note: may need to change README for PyPi to exclude
  banners)
- remove versioneer and use versioningit (use alchemlyb.__version__ directly where
  the version is needed, e.g., for sphinx docs)
- updated CHANGES for 2.4.0

* house-keeping

- gitignore _version
- ignore commits for blame that contain black-reformatting
  (in particular we forgot to include #280)

* make repo title identical to JOSS paper title (#404)

- close #402
- use same title in CITATION.cff for paper and project
  (required for the JOSS paper publication #71)
- added DOI for preferred citation in note because that is the
  only hint that shows up on zenodo)

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

replace `pandas.concat()` with `alchemlyb.concat()` in the tutorial (given that we explicitly tell users to use it)

* Update version

* Formatting

* FutureWarning

* Added commenting extract_u_nk

* Add names, bug fix dHdl

* Bug fix columns, add name attribute

* Add testing

* Black, add handling for compressed files

* Black for lammps parsing and handling compressed files

* Address code coverage

* Address test issues

* Address test issues

* Fix test issue

* Add tol parameter to lammps.extract_u_nk for case where rounding errors are greater than machine precision

* Update docstrings and tests for filenames and scaling factors

* Abstract ensemble check and add description of main functions

* ruff mypy

* Remove unused variable

* ruff remove dHdl.mul()

* Update module docstring

* Coverage

* ruff

* Fix code block

* Update module docstring

* Update src/alchemlyb/parsing/lammps.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Fix inverted logic

* ruff

---------

Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
Co-authored-by: David L. Dotson <dotsdl@gmail.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: 4 people

.gitignore

@@ -6,7 +6,7 @@ build
 docs/_build/
 src/alchemlyb.egg-info/
 __pycache__
-.coverage.*
+.coverage*
 *~
 dist/
 

CHANGES

@@ -34,6 +34,7 @@ Changes
 Enhancements
   - Added matrices for entropy and enthalpy for MBAR (PR #406)
   - Parallelise read and preprocess for ABFE workflow. (PR #371)
+  - Add support for LAMMPS FEP files (Issue #349, PR #348)
 
 
 09/19/2024 orbeckst, jaclark5

docs/parsing.rst

@@ -240,4 +240,5 @@ See the documentation for the package you are using for more details on parser u
     namd
     gomc
     parquet
+    lammps
 

docs/parsing/alchemlyb.parsing.lammps.rst

@@ -0,0 +1,14 @@
+LAMMPS Parsing
+=============
+.. automodule:: alchemlyb.parsing.lammps
+
+API Reference
+-------------
+This submodule includes these parsing functions:
+
+.. autofunction:: alchemlyb.parsing.lammps.extract_dHdl
+.. autofunction:: alchemlyb.parsing.lammps.extract_u_nk
+.. autofunction:: alchemlyb.parsing.lammps.extract_dHdl_from_u_n
+.. autofunction:: alchemlyb.parsing.lammps.extract_u_nk_from_u_n
+.. autofunction:: alchemlyb.parsing.lammps.extract_H
+.. autofunction:: alchemlyb.parsing.lammps.beta_from_units