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Add 'PairIJ Coeffs' section to the list of sections in LAMMPS parser #3959

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merged 17 commits into from
Jan 6, 2023
Merged

Add 'PairIJ Coeffs' section to the list of sections in LAMMPS parser #3959

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ee10b65
Add 'PairIJ Coeffs' section to the list of sections in LAMMPS parser.…
mglagolev Dec 15, 2022
9277e7a
Updating AUTHORS and CHANGELOG
mglagolev Dec 16, 2022
383423f
Adding a simple test
mglagolev Dec 16, 2022
2299045
Revert "Adding a simple test"
mglagolev Dec 22, 2022
8269b20
Adding test for LAMMPS PairIJ Coeffs file to test_lammpsdata
mglagolev Dec 22, 2022
4edbdca
Merge remote-tracking branch 'upstream/develop' into lammps_topology_…
mglagolev Dec 23, 2022
48b771e
Revert "Adding test for LAMMPS PairIJ Coeffs file to test_lammpsdata"
mglagolev Dec 24, 2022
357dc9c
Adding the zipped test datafile and class
mglagolev Dec 24, 2022
9130850
Implementing requested changes
mglagolev Dec 28, 2022
8d8786c
Bugfix to pass the tests; adding whitespace to pass darker lint
mglagolev Jan 4, 2023
4b5885e
Bugfix
mglagolev Jan 4, 2023
49421fe
Merge branch 'develop' into lammps_topology_add_pairij
mglagolev Jan 4, 2023
b0beae3
Merging
mglagolev Jan 4, 2023
6624fda
Merge branch 'lammps_topology_add_pairij' of http://github.com/mglago…
mglagolev Jan 4, 2023
4330ed4
Remove a duplicate record due to a merging mess
mglagolev Jan 4, 2023
4e134a6
Fixing the format
mglagolev Jan 4, 2023
d8fc45a
Fixing the PEP8 violation
mglagolev Jan 4, 2023
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1 change: 1 addition & 0 deletions package/AUTHORS
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Expand Up @@ -201,6 +201,7 @@ Chronological list of authors
- Jake Fennick
- Utsav Khatu
- Patricio Barletta
- Mikhail Glagolev


External code
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5 changes: 4 additions & 1 deletion package/CHANGELOG
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Expand Up @@ -13,11 +13,14 @@ The rules for this file:
* release numbers follow "Semantic Versioning" http://semver.org

------------------------------------------------------------------------------
??/??/?? IAlibay, pgbarletta

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Suggested change

Please don't add the extra line here (we try to keep the format of this file reasonably strict to make life easier on releases).

??/??/?? IAlibay, pgbarletta, mglagolev

* 2.5.0

Fixes
* Add 'PairIJ Coeffs' to the list of sections in LAMMPSParser.py
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(Issue #3336)

Enhancements

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1 change: 1 addition & 0 deletions package/MDAnalysis/topology/LAMMPSParser.py
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Expand Up @@ -119,6 +119,7 @@
'Impropers',
'Pair',
'Pair LJCoeffs',
'PairIJ Coeffs',
'Bond Coeffs',
'Angle Coeffs',
'Dihedral Coeffs',
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Binary file added testsuite/MDAnalysisTests/data/lammps/pairij_coeffs.data.bz2
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2 changes: 2 additions & 0 deletions testsuite/MDAnalysisTests/datafiles.py
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Expand Up @@ -142,6 +142,7 @@
"LAMMPShyd", "LAMMPShyd2",
"LAMMPSdata_deletedatoms", # with deleted atoms
"LAMMPSdata_triclinic", # lammpsdata file to test triclinic dimension parsing, albite with most atoms deleted
"LAMMPSdata_PairIJ", # lammps datafile with a PairIJ Coeffs section
"LAMMPSDUMP",
"LAMMPSDUMP_long", # lammpsdump file with a few zeros sprinkled in the first column first frame
"LAMMPSDUMP_allcoords", # lammpsdump file with all coordinate conventions (x,xs,xu,xsu) present, from LAMMPS rdf example
Expand Down Expand Up @@ -513,6 +514,7 @@
LAMMPShyd2 = resource_filename(__name__, "data/lammps/hydrogen-class1.data2")
LAMMPSdata_deletedatoms = resource_filename(__name__, 'data/lammps/deletedatoms.data')
LAMMPSdata_triclinic = resource_filename(__name__, "data/lammps/albite_triclinic.data")
LAMMPSdata_PairIJ = resource_filename(__name__, "data/lammps/pairij_coeffs.data.bz2")
LAMMPSDUMP = resource_filename(__name__, "data/lammps/wat.lammpstrj.bz2")
LAMMPSDUMP_long = resource_filename(__name__, "data/lammps/wat.lammpstrj_long.bz2")
LAMMPSDUMP_allcoords = resource_filename(__name__, "data/lammps/spce_all_coords.lammpstrj.bz2")
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21 changes: 21 additions & 0 deletions testsuite/MDAnalysisTests/topology/test_lammpsdata.py
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Expand Up @@ -36,6 +36,7 @@
LAMMPSdata_deletedatoms,
LAMMPSDUMP,
LAMMPSDUMP_long,
LAMMPSdata_PairIJ,
)


Expand Down Expand Up @@ -179,6 +180,26 @@ def test_traj(self, filename):
dtype=np.float32))

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class TestLammpsDataPairIJ(LammpsBase):
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"""Tests the reading of lammps .data topology file with a
PairIJ Coeffs section
"""

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@IAlibay IAlibay Jan 4, 2023 •
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Suggested change

No worries about the darker linting, as long as it's not breaching PEP8 it ends up just black trying to enforce its style.

That being said the above "whitespace on an empty line" is a PEP8 violation (I suspect the suggested edit here won't work well, essentially the empty line is fine, but it can't have any whitespaces on it)

Sorry about this, as @orbeckst explains re: keeping maintenance costs down, we end up requiring a lot of weird formatting rules that do tend to be rather unfriendly to new contributors :(

expected_attrs = ['types', 'resids', 'masses',
'bonds', 'angles', 'dihedrals', 'impropers']
ref_filename = LAMMPSdata_PairIJ
expected_n_atoms = 800
expected_n_atom_types = 2
expected_n_residues = 1
ref_n_bonds = 799
ref_bond = (397, 398)
ref_n_angles = 390
ref_angle = (722, 723, 724)
ref_n_dihedrals = 385
ref_dihedral = (722, 723, 724, 725)
ref_n_impropers = 0

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LAMMPS_NORESID = """\
LAMMPS data file via write_data, version 11 Aug 2017, timestep = 0

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