lammps updates

imdclient/data/lammps_v3.in

@@ -51,19 +51,18 @@ velocity all create 300 102939 dist gaussian mom yes rot yes
 # this is equlibration process.
 fix 1 all nve 
 # <Dump all the atoms to the file dump.min>
-dump dump_1 all custom 100 trj.dump id type x y z ix iy iz vx vy vz 
-
-
-
+# DCD lines are commented. These lines were used to create the true trajectory
+# dump dcd1 all dcd 1 lammps_trj.dcd 
+# dump_modify dcd1 unwrap yes
 
 ## IMD settings
 # https://docs.lammps.org/fix_imd.html
-fix 2 all imd 8888 version 3 unwrap on nowait off time off
+fix 2 all imd 8888 version 3 unwrap on nowait off time on
 
 ## Run MD sim
 # run with active settings as many runs as required. timestep*No. of. steps =10ps
 run 1000 
-undump dump_1 # Stop dumping information to the dump file.
+# undump dcd1 # Stop dumping information to the dump file.
 unfix 1
 # Unfix the NVE. Additional lines if any will assume that this fix is off.
 #End

imdclient/tests/base.py

@@ -3,6 +3,11 @@
 import os
 from .utils import run_sim_and_wait
 import MDAnalysis as mda
+from MDAnalysisTests.coordinates.base import assert_timestep_almost_equal
+
+import logging
+
+logger = logging.getLogger("imdclient.IMDClient")
 
 
 class IMDv3IntegrationTest:
@@ -15,6 +20,7 @@ def simulation(self, tmp_path, command, match_string):
         yield p
         os.chdir(old_cwd)
         p.kill()
+        logger.debug("Killed simulation process")
         p.wait()
 
     @pytest.fixture()
@@ -27,24 +33,22 @@ def universe(self, simulation, universe_kwargs, topology):
         return u
 
     @pytest.fixture()
-    def store_imd_traj(self, universe, topology, traj_path, universe_kwargs):
+    def store_imd_traj(self, universe):
         timesteps = []
         for ts in universe.trajectory:
             timesteps.append(ts.copy())
         return timesteps
 
     @pytest.fixture()
-    def true_universe(
-        self, topology, traj_path, universe_kwargs, store_imd_traj
-    ):
+    def true_universe(self, topology, true_trajectory, universe_kwargs):
         return mda.Universe(
             topology,
-            traj_path,
+            true_trajectory,
             **universe_kwargs,
         )
 
     def test_compare_imd_to_true_traj(self, store_imd_traj, true_universe):
-        for i, (imd_ts, true_ts) in enumerate(
-            zip(store_imd_traj, true_universe.trajectory)
-        ):
-            assert imd_ts == true_ts
+        for i in range(len(true_universe.trajectory)):
+            assert_timestep_almost_equal(
+                true_universe.trajectory[i], store_imd_traj[i], decimal=3
+            )

imdclient/tests/datafiles.py

@@ -20,5 +20,6 @@
 
 LAMMPS_TOPOL = (_data_ref / "lammps_topol.data").as_posix()
 LAMMPS_IN = (_data_ref / "lammps_v3.in").as_posix()
+LAMMPS_TRAJ = (_data_ref / "lammps_trj.dcd").as_posix()
 
 del resources

imdclient/tests/test_lammps.py

@@ -6,7 +6,7 @@
 import logging
 from .utils import run_sim_and_wait, get_free_port
 from .base import IMDv3IntegrationTest
-from .datafiles import LAMMPS_IN, LAMMPS_TOPOL
+from .datafiles import LAMMPS_IN, LAMMPS_TOPOL, LAMMPS_TRAJ
 
 # NOTE: removeme
 from imdclient.IMDREADER import IMDReader
@@ -37,11 +37,8 @@ def topology(self):
         return LAMMPS_TOPOL
 
     @pytest.fixture()
-    def traj_path(self):
-        """Relative path of the trajectory file within `tmp_dir`.
-        Allows comparison of large trajectory files without storing them in the repo.
-        """
-        return Path("trj.dump")
+    def true_trajectory(self):
+        return LAMMPS_TRAJ
 
     @pytest.fixture()
     def universe_kwargs(self):