Fix LAMMPS DCD writer compatibility with base tests

package/AUTHORS

@@ -287,6 +287,7 @@ Chronological list of authors
   - Francesco Siciliani
   - Akshit Boora
   - Sumit Saraswat
+  - Nayan Sharma
 
 
 External code

package/MDAnalysis/coordinates/LAMMPS.py

@@ -223,6 +223,23 @@ def __init__(self, dcdfilename, **kwargs):
                 raise ValueError(f"LAMMPS DCDReader: unknown unit {unit}")
         super(DCDReader, self).__init__(dcdfilename, **kwargs)
 
+    def Writer(self, filename, n_atoms=None, **kwargs):
+        """Return a DCD writer with the correct LAMMPS time conversion."""
+        if n_atoms is None:
+            n_atoms = self.n_atoms
+
+        dt = units.convert(self.ts.dt, "ps", "fs") / units.convert(
+            1.0, "ps", "AKMA"
+        )
+
+        return DCD.DCDWriter(
+            filename,
+            n_atoms=n_atoms,
+            dt=dt,
+            convert_units=self.convert_units,
+            **kwargs,
+        )
+
 
 class DATAReader(base.SingleFrameReaderBase):
     """Reads a single frame of coordinate information from a LAMMPS DATA file.

testsuite/MDAnalysisTests/coordinates/base.py

@@ -858,15 +858,15 @@ def test_write_different_box(self, ref, universe, tmpdir):
     def test_write_trajectory_atomgroup(self, ref, reader, universe, tmpdir):
         outfile = "write-atoms-test." + ref.ext
         with tmpdir.as_cwd():
-            with ref.writer(outfile, universe.atoms.n_atoms) as w:
+            with reader.Writer(outfile) as w:
                 for ts in universe.trajectory:
                     w.write(universe.atoms)
             self._check_copy(outfile, ref, reader)
 
     def test_write_trajectory_universe(self, ref, reader, universe, tmpdir):
         outfile = "write-uni-test." + ref.ext
         with tmpdir.as_cwd():
-            with ref.writer(outfile, universe.atoms.n_atoms) as w:
+            with reader.Writer(outfile) as w:
                 for ts in universe.trajectory:
                     w.write(universe)
             self._check_copy(outfile, ref, reader)
@@ -924,12 +924,12 @@ def test_no_container(self, ref, tmpdir):
                 with pytest.raises(TypeError):
                     ref.writer("foo")
 
-    def test_write_not_changing_ts(self, ref, universe, tmpdir):
+    def test_write_not_changing_ts(self, ref, reader, universe, tmpdir):
         outfile = "write-not-changing-ts." + ref.ext
 
         copy_ts = universe.trajectory.ts.copy()
         with tmpdir.as_cwd():
-            with ref.writer(outfile, n_atoms=5) as W:
+            with reader.Writer(outfile, n_atoms=universe.atoms.n_atoms) as W:
                 W.write(universe)
                 assert_timestep_almost_equal(copy_ts, universe.trajectory.ts)
 

testsuite/MDAnalysisTests/coordinates/test_lammps.py

@@ -28,6 +28,8 @@
 
 import MDAnalysis as mda
 from MDAnalysis import NoDataError
+from MDAnalysis.coordinates.LAMMPS import DCDReader
+from MDAnalysis.coordinates.DCD import DCDWriter
 
 from numpy.testing import assert_equal, assert_allclose
 
@@ -38,6 +40,11 @@
     RefLAMMPSDataDCD,
     RefLAMMPSDataAdditionalColumns,
 )
+from MDAnalysisTests.coordinates.base import (
+    BaseReference,
+    BaseReaderTest,
+    BaseWriterTest,
+)
 from MDAnalysisTests.datafiles import (
     LAMMPScnt,
     LAMMPShyd,
@@ -328,7 +335,75 @@ def test_n_angles(self, LAMMPSDATA_partial):
 # need more tests of the LAMMPS DCDReader
 
 
-class TestLAMMPSDCDReader(RefLAMMPSDataDCD):
+class LAMMPSDCDReference(BaseReference):
+    def __init__(self):
+        super().__init__()
+        self.topology = RefLAMMPSDataDCD.topology
+        self.trajectory = RefLAMMPSDataDCD.trajectory
+        self.reader = DCDReader
+
+        self.writer = DCDWriter
+        self.mean_dimensions = RefLAMMPSDataDCD.mean_dimensions
+        trajectory = self.reader(self.trajectory)
+
+        self.n_atoms = trajectory.n_atoms
+        self.n_frames = len(trajectory)
+        self.dt = trajectory.dt
+        self.totaltime = trajectory.totaltime
+        self.aux_lowf_data = [
+            [2**0],
+            [np.nan],
+            [np.nan],
+            [np.nan],
+            [2**1],
+        ]
+        self.aux_highf_data = [
+            [2**0],
+            [2**1],
+            [2**2],
+            [2**3],
+            [2**4],
+        ]
+        self.ext = "dcd"
+
+        self.first_frame = trajectory[0].copy()
+        self.second_frame = trajectory[1].copy()
+        self.last_frame = trajectory[-1].copy()
+        self.jump_to_frame = trajectory[3].copy()
+        for i, frame in enumerate(
+            [
+                self.first_frame,
+                self.second_frame,
+                self.last_frame,
+                self.jump_to_frame,
+            ]
+        ):
+            frame.aux.lowf = np.array(self.aux_lowf_data[[0, 1, 4, 3][i]])
+            frame.aux.highf = np.array(self.aux_highf_data[[0, 1, 4, 3][i]])
+
+        self.dimensions = self.first_frame.dimensions.copy()
+        self.dimensions_second_frame = self.second_frame.dimensions.copy()
+        self.volume = self.first_frame.volume
+
+        trajectory.close()
+
+    def iter_ts(self, i):
+        trajectory = self.reader(self.trajectory)
+        ts = trajectory[i].copy()
+        trajectory.close()
+
+        ts.aux.lowf = np.array(self.aux_lowf_data[i])
+        ts.aux.highf = np.array(self.aux_highf_data[i])
+
+        return ts
+
+
+class TestLAMMPSDCDReader(BaseReaderTest, RefLAMMPSDataDCD):
+    @staticmethod
+    @pytest.fixture(scope="class")
+    def ref():
+        return LAMMPSDCDReference()
+
     flavor = "LAMMPS"
 
     @pytest.fixture(scope="class")
@@ -409,7 +484,16 @@ def wrong_load(unit="GARBAGE"):
             wrong_load()
 
 
-class TestLAMMPSDCDWriter(RefLAMMPSDataDCD):
+class TestLAMMPSDCDWriter(BaseWriterTest, RefLAMMPSDataDCD):
+    @pytest.fixture()
+    def universe(self):
+        return mda.Universe(self.topology, self.trajectory, format=self.format)
+
+    @staticmethod
+    @pytest.fixture(scope="class")
+    def ref():
+        return LAMMPSDCDReference()
+
     flavor = "LAMMPS"
 
     @pytest.fixture(scope="class")