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

* Add 'PairIJ Coeffs' section to the list of sections in LAMMPS parser. This ensures correct processing of LAMMPS data files

* Updating AUTHORS and CHANGELOG

* Adding a simple test

* Revert "Adding a simple test"

This reverts commit 383423f.

The test needs to be integrated into the test_lammpsdata.py
instead of a separate script, and the sample datafile needs
to be placed in the appropriate directory.

* Adding test for LAMMPS PairIJ Coeffs file to test_lammpsdata

* Revert "Adding test for LAMMPS PairIJ Coeffs file to test_lammpsdata"

This reverts commit 8269b20.

* Adding the zipped test datafile and class

* Implementing requested changes

* Bugfix to pass the tests; adding whitespace to pass darker lint

* Bugfix

* Merging

* Remove a duplicate record due to a merging mess

* Fixing the format

* Fixing the PEP8 violation

Author: mglagolev

package/AUTHORS

@@ -201,6 +201,7 @@ Chronological list of authors
   - Jake Fennick
   - Utsav Khatu
   - Patricio Barletta
+  - Mikhail Glagolev
 
 
 External code

package/CHANGELOG

@@ -13,11 +13,13 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/?? IAlibay, pgbarletta
+??/??/?? IAlibay, pgbarletta, mglagolev
 
  * 2.5.0
 
 Fixes
+  * Add 'PairIJ Coeffs' to the list of sections in LAMMPSParser.py
+    (Issue #3336)
 
 Enhancements
 

package/MDAnalysis/topology/LAMMPSParser.py

@@ -119,6 +119,7 @@
     'Impropers',
     'Pair',
     'Pair LJCoeffs',
+    'PairIJ Coeffs',
     'Bond Coeffs',
     'Angle Coeffs',
     'Dihedral Coeffs',

testsuite/MDAnalysisTests/data/lammps/pairij_coeffs.data.bz2

@@ -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
@@ -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")

testsuite/MDAnalysisTests/datafiles.py

@@ -36,6 +36,7 @@
     LAMMPSdata_deletedatoms,
     LAMMPSDUMP,
     LAMMPSDUMP_long,
+    LAMMPSdata_PairIJ,
 )
 
 
@@ -179,6 +180,26 @@ def test_traj(self, filename):
                               dtype=np.float32))
 
 
+class TestLammpsDataPairIJ(LammpsBase):
+    """Tests the reading of lammps .data topology file with a
+    PairIJ Coeffs section
+    """
+
+    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
+
+
 LAMMPS_NORESID = """\
 LAMMPS data file via write_data, version 11 Aug 2017, timestep = 0