Code

Lammps Support#348

Code

Open

jaclark5 wants to merge 61 commits intoalchemistry:masteralchemistry/alchemlyb:masterfrom jaclark5:lammpsjaclark5/alchemlyb:lammpsCopy head branch name to clipboard

+2,174-1

Commits

Commits on Feb 5, 2024

• Add lammps file generation and parsing

  jaclark5

  committed
  e5ccd50

• Update formatting

  jaclark5

  committed
  93bc158

• Update variables in generated files

  jaclark5

  committed
  606d7f1

• Add input for mbar

  jaclark5

  committed
  ed085b6

• Remove print

  jaclark5

  committed
  d64101a

• Bug fix file outputs

  jaclark5

  committed
  df567ea

• Bug fix file format

  jaclark5

  committed
  b92901e

Commits on Feb 7, 2024

• Bug fix param start, add dataframe for potential

  jaclark5

  committed
  a3c5355

• Bug fix loops in mbar generation

  jaclark5

  committed
  0508cbc

Commits on Feb 20, 2024

• Add precision values for processing lammps input files

  jaclark5

  committed
  79c7d7d

• Merge branch 'master' into lammps

  jaclark5

  committed
  d2c1e6a

• Add error catch for column definition in extract_u_nk

  jaclark5

  committed
  7d01677

Commits on Feb 22, 2024

• Add abs to nblocks calc

  jaclark5

  committed
  1288fd0

• Bug fix, nblocks

  jaclark5

  committed
  304b924

Commits on Mar 13, 2024

• Add calculation of beta based on lammps units

  Show description for 552c0d3
  jaclark5

  committed
  552c0d3

• Update module docstring

  jaclark5

  committed
  32daa07

• Add name to author list

  jaclark5

  committed
  5ca4199

• Added to changelog

  jaclark5

  committed
  d9b62d2

• Update docs

  jaclark5

  committed
  03f55b8

• Run Black

  jaclark5

  committed
  22a62b0

Commits on Jul 24, 2024

• Sort lambda values for consistent output

  jaclark5

  committed
  22d72ac

• Update lammps.extract_dHdl defaults

  jaclark5

  committed
  5f8fb71

• Update error for lambda values

  jaclark5

  committed
  23bc5c5

• Update extract_dHdl* to use prec

  jaclark5

  committed
  d8e7092

• Update changelog

  jaclark5

  committed
  fc6b16c

• update parsing.lammps.py docstrings

  jaclark5

  committed
  809c6f0

• Run Black

  jaclark5

  committed
  bdb14c6

Commits on Aug 21, 2024

• Add ensemble support

  jaclark5

  committed
  fe94f2a

Commits on Aug 23, 2024

• Bug fix, inputs for extract_dHdl

  jaclark5

  committed
  fa5a539

Commits on Aug 30, 2024

• Add LAMMPS unit conversion for pV term in npt u_r

  jaclark5

  committed
  8da4b99

• Fixed kT multiplication issue in dHdl

  jaclark5

  committed
  2d5fe48

Commits on Sep 3, 2024

• Resolve deprecation warnings

  jaclark5

  committed
  bd2c23a

Commits on Sep 5, 2024

• Merge branch 'master' into lammps

  jaclark5

  authored
  4c736f6

Commits on Sep 13, 2024

• Resolve pandas depreication warning

  jaclark5

  committed
  e1d6e87

Commits on Sep 19, 2024

• Moving average (alchemistry#381)

  Show description for 9eb22a1
  

  jaclark5

  and

  orbeckst

  committed
  9eb22a1

• Added to changelog

  jaclark5

  committed
  ac8c479

• initial CITATION.cff file

  Show description for 7331f28
  

  2 peopleauthored and

  jaclark5

  committed
  7331f28

• add JOSS paper as preferred citation to CITATION

  Show description for ab91db5
  

  orbeckst

  authored and

  jaclark5

  committed
  ab91db5

• added references for MBAR and equilibration detection

  

  orbeckst

  authored and

  jaclark5

  committed
  d12d662

• inserted additional JOSS paper authors in software author list

  Show description for 5969444
  

  orbeckst

  authored and

  jaclark5

  committed
  5969444

• updated CHANGES and AUTHORS for 2.3.3

  Show description for 7e96f64
  

  orbeckst

  authored and

  jaclark5

  committed
  7e96f64

• add authors to CITATION who had NOT been in AUTHORS

  Show description for a241777
  

  orbeckst

  authored and

  jaclark5

  committed
  a241777

• add @jaclark5 to AUTHORS and CITATION.cff

  Show description for d97d682
  

  orbeckst

  authored and

  jaclark5

  committed
  d97d682

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

  Show description for cf4a307
  jaclark5

  committed
  cf4a307

• black-formatted files

  

  orbeckst

  authored and

  jaclark5

  committed
  b16f177

• replace setup.py,cfg with pyproject.toml

  Show description for a3b2c08
  

  orbeckst

  authored and

  jaclark5

  committed
  a3b2c08

• house-keeping

  Show description for 4379343
  

  orbeckst

  authored and

  jaclark5

  committed
  4379343

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

  Show description for 263a431
  

  orbeckst

  authored and

  jaclark5

  committed
  263a431

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

  Show description for f6ad696
  

  orbeckst

  authored and

  jaclark5

  committed
  f6ad696

• Update version

  jaclark5

  committed
  752cd64

• Merge branch 'master' into lammps

  jaclark5

  committed
  7c07226

• Formatting

  jaclark5

  committed
  35c6de5

• FutureWarning

  jaclark5

  committed
  b8a8c9e

Commits on Sep 24, 2024

• Added commenting extract_u_nk

  jaclark5

  committed
  98fd197

Commits on Oct 22, 2024

• Add names, bug fix dHdl

  jaclark5

  committed
  1dd796b

• Merge branch 'master' into lammps

  jaclark5

  committed
  337aac5

Commits on Nov 12, 2024

• Bug fix columns, add name attribute

  jaclark5

  committed
  0e2a312

• Merge branch 'master' into lammps

  jaclark5

  committed
  224ca08

Commits on Nov 15, 2024

• Merge branch 'master' into lammps

  jaclark5

  committed
  0fb967b

Commits on Nov 17, 2024

• Add testing

  jaclark5

  committed
  ffe2d77

Commits on Dec 20, 2024

• Merge branch 'master' into lammps

  jaclark5

  committed
  8257659