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Lammps Support #348

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Lammps Support #348

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e5ccd50
Add lammps file generation and parsing
jaclark5 Feb 5, 2024
93bc158
Update formatting
jaclark5 Feb 5, 2024
606d7f1
Update variables in generated files
jaclark5 Feb 5, 2024
ed085b6
Add input for mbar
jaclark5 Feb 5, 2024
d64101a
Remove print
jaclark5 Feb 5, 2024
df567ea
Bug fix file outputs
jaclark5 Feb 5, 2024
b92901e
Bug fix file format
jaclark5 Feb 5, 2024
a3c5355
Bug fix param start, add dataframe for potential
jaclark5 Feb 7, 2024
0508cbc
Bug fix loops in mbar generation
jaclark5 Feb 7, 2024
79c7d7d
Add precision values for processing lammps input files
jaclark5 Feb 20, 2024
d2c1e6a
Merge branch 'master' into lammps
jaclark5 Feb 20, 2024
7d01677
Add error catch for column definition in extract_u_nk
jaclark5 Feb 20, 2024
1288fd0
Add abs to nblocks calc
jaclark5 Feb 22, 2024
304b924
Bug fix, nblocks
jaclark5 Feb 22, 2024
552c0d3
Add calculation of beta based on lammps units
jaclark5 Mar 13, 2024
32daa07
Update module docstring
jaclark5 Mar 13, 2024
5ca4199
Add name to author list
jaclark5 Mar 13, 2024
d9b62d2
Added to changelog
jaclark5 Mar 13, 2024
03f55b8
Update docs
jaclark5 Mar 13, 2024
22a62b0
Run Black
jaclark5 Mar 13, 2024
22d72ac
Sort lambda values for consistent output
jaclark5 Jun 10, 2024
5f8fb71
Update lammps.extract_dHdl defaults
jaclark5 Jul 9, 2024
23bc5c5
Update error for lambda values
jaclark5 Jul 15, 2024
d8e7092
Update extract_dHdl* to use prec
jaclark5 Jul 15, 2024
fc6b16c
Update changelog
jaclark5 Jul 24, 2024
809c6f0
update parsing.lammps.py docstrings
jaclark5 Jul 24, 2024
bdb14c6
Run Black
jaclark5 Jul 24, 2024
fe94f2a
Add ensemble support
jaclark5 Aug 21, 2024
fa5a539
Bug fix, inputs for extract_dHdl
jaclark5 Aug 23, 2024
8da4b99
Add LAMMPS unit conversion for pV term in npt u_r
jaclark5 Aug 30, 2024
2d5fe48
Fixed kT multiplication issue in dHdl
jaclark5 Aug 30, 2024
bd2c23a
Resolve deprecation warnings
jaclark5 Sep 3, 2024
4c736f6
Merge branch 'master' into lammps
jaclark5 Sep 5, 2024
e1d6e87
Resolve pandas depreication warning
jaclark5 Sep 13, 2024
9eb22a1
Moving average (#381)
jaclark5 Sep 14, 2024
ac8c479
Added to changelog
jaclark5 Mar 13, 2024
7331f28
initial CITATION.cff file
orbeckst Sep 11, 2024
ab91db5
add JOSS paper as preferred citation to CITATION
orbeckst Sep 11, 2024
d12d662
added references for MBAR and equilibration detection
orbeckst Sep 11, 2024
5969444
inserted additional JOSS paper authors in software author list
orbeckst Sep 11, 2024
7e96f64
updated CHANGES and AUTHORS for 2.3.3
orbeckst Sep 11, 2024
a241777
add authors to CITATION who had NOT been in AUTHORS
orbeckst Sep 12, 2024
d97d682
add @jaclark5 to AUTHORS and CITATION.cff
orbeckst Sep 16, 2024
cf4a307
Resolve bug in bar_model.delta_f_ creation (#397)
jaclark5 Sep 17, 2024
b16f177
black-formatted files
orbeckst Sep 17, 2024
a3b2c08
replace setup.py,cfg with pyproject.toml
orbeckst Sep 17, 2024
4379343
house-keeping
orbeckst Sep 17, 2024
263a431
make repo title identical to JOSS paper title (#404)
orbeckst Sep 19, 2024
f6ad696
[doc] tutorial: use alchemlyb.concat (#399)
orbeckst Sep 19, 2024
752cd64
Update version
jaclark5 Sep 19, 2024
7c07226
Merge branch 'master' into lammps
jaclark5 Sep 19, 2024
35c6de5
Formatting
jaclark5 Sep 19, 2024
b8a8c9e
FutureWarning
jaclark5 Sep 19, 2024
98fd197
Added commenting extract_u_nk
jaclark5 Sep 24, 2024
1dd796b
Add names, bug fix dHdl
jaclark5 Oct 22, 2024
337aac5
Merge branch 'master' into lammps
jaclark5 Oct 22, 2024
0e2a312
Bug fix columns, add name attribute
jaclark5 Nov 12, 2024
224ca08
Merge branch 'master' into lammps
jaclark5 Nov 12, 2024
0fb967b
Merge branch 'master' into lammps
jaclark5 Nov 15, 2024
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1 change: 1 addition & 0 deletions CHANGES
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Expand Up @@ -19,6 +19,7 @@ The rules for this file:
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
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1 change: 1 addition & 0 deletions docs/parsing.rst
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Expand Up @@ -240,4 +240,5 @@ See the documentation for the package you are using for more details on parser u
namd
gomc
parquet
lammps

14 changes: 14 additions & 0 deletions docs/parsing/alchemlyb.parsing.lammps.rst
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@@ -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
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