Added test for no drift correction

Former-commit-id: fac7926

kinisi/parser.py

@@ -66,6 +66,7 @@ def __init__(self,
         self.time_step = time_step
         self.step_skip = step_skip
         self.indices = indices
+        self.drift_indices = drift_indices
         self.memory_limit = memory_limit
         self.min_dt = min_dt
         self.max_dt = max_dt
@@ -669,7 +670,7 @@ class MDAnalysisParser(Parser):
         must be set to None for this to function. Molecules can be specificed as a list of lists of indices.
         This inner lists must all be on the same length.
     :param masses: Optional, list of masses associated with the indices in specie_indices. Must be same shape as specie_indices.
-    :param framework_indices: Optional, list of framework indices to be used to correct framework drift.
+    :param framework_indices: Optional, list of framework indices to be used to correct framework drift. If an empty list is passed no drift correction will be performed.
     """
 
     def __init__(self,

kinisi/tests/inputs/example_LAMMPS_drift.data

@@ -0,0 +1,23 @@
+9 atoms
+2 atom types
+
+0 10 xlo xhi
+0 10 ylo yhi
+0 10 zlo zhi
+
+Masses
+
+1 1
+2 16
+
+Atoms # full
+
+1 0 1 0.0 5.0 5.0 5.0 0 0 0
+2 0 2 0.0 2.5 2.5 2.5 0 0 0
+3 0 2 0.0 7.5 2.5 2.5 0 0 0
+4 0 2 0.0 2.5 7.5 2.5 0 0 0
+5 0 2 0.0 2.5 2.5 7.5 0 0 0
+6 0 2 0.0 7.5 7.5 2.5 0 0 0
+7 0 2 0.0 7.5 2.5 7.5 0 0 0
+8 0 2 0.0 2.5 7.5 7.5 0 0 0
+9 0 2 0.0 7.5 7.5 7.5 0 0 0

kinisi/tests/inputs/example_LAMMPS_drift.traj

@@ -0,0 +1,72 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+9
+ITEM: BOX BOUNDS pp pp pp
+0 10
+0 10
+0 10
+ITEM: ATOMS id type xs ys zs
+1	1	0.5	0.5	0.5
+2	2	0.25	0.25	0.25
+3	2	0.75	0.25	0.25
+4	2	0.25	0.75	0.25
+5	2	0.25	0.25	0.75
+6	2	0.75	0.75	0.25
+7	2	0.75	0.25	0.75
+8	2	0.25	0.75	0.75
+9	2	0.75	0.75	0.75
+ITEM: TIMESTEP
+1
+ITEM: NUMBER OF ATOMS
+9
+ITEM: BOX BOUNDS pp pp pp
+0 10
+0 10
+0 10
+ITEM: ATOMS id type xs ys zs
+1	1	0.5	0.5	0.5
+2	2	0.23	0.23	0.23
+3	2	0.73	0.23	0.23
+4	2	0.23	0.73	0.23
+5	2	0.23	0.23	0.73
+6	2	0.73	0.73	0.23
+7	2	0.73	0.23	0.73
+8	2	0.23	0.73	0.73
+9	2	0.73	0.73	0.73
+ITEM: TIMESTEP
+2
+ITEM: NUMBER OF ATOMS
+9
+ITEM: BOX BOUNDS pp pp pp
+0 10
+0 10
+0 10
+ITEM: ATOMS id type xs ys zs
+1	1	0.5	0.5	0.5
+2	2	0.21	0.21	0.21
+3	2	0.71	0.21	0.21
+4	2	0.21	0.71	0.21
+5	2	0.21	0.21	0.71
+6	2	0.71	0.71	0.21
+7	2	0.71	0.21	0.71
+8	2	0.21	0.71	0.71
+9	2	0.71	0.71	0.71
+ITEM: TIMESTEP
+3
+ITEM: NUMBER OF ATOMS
+9
+ITEM: BOX BOUNDS pp pp pp
+0 10
+0 10
+0 10
+ITEM: ATOMS id type xs ys zs
+1	1	0.5	0.5	0.5
+2	2	0.15	0.15	0.15
+3	2	0.65	0.15	0.15
+4	2	0.15	0.65	0.15
+5	2	0.15	0.15	0.65
+6	2	0.65	0.65	0.15
+7	2	0.65	0.15	0.65
+8	2	0.15	0.65	0.65
+9	2	0.65	0.65	0.65

kinisi/tests/test_parser.py

@@ -209,6 +209,23 @@ def test_mda_init_with_COM(self):
         assert_almost_equal(data.step_skip, 1)
         assert_equal(data.indices, [0])
         assert_almost_equal(data.coords_check, [[[0.382421597, 0.2087361, 0.2]]])
+
+    def test_mda_inti_with_empty_framwork_indices(self):
+        xd = mda.Universe(os.path.join(os.path.dirname(kinisi.__file__), 'tests/inputs/example_LAMMPS_drift.data'),
+                          os.path.join(os.path.dirname(kinisi.__file__), 'tests/inputs/example_LAMMPS_drift.traj'),
+                          topology_format='DATA',
+                          format='LAMMPSDUMP')
+        da_params = {
+            'specie': '1',
+            'time_step': 1,
+            'step_skip': 1,
+            'framework_indices':[]
+        }
+        data = parser.MDAnalysisParser(xd, **da_params)
+        assert_almost_equal(data.time_step, 1)
+        assert_almost_equal(data.step_skip, 1)
+        assert_equal(data.indices, [0])
+        assert_equal(data.drift_indices, [])
 
     def test_get_matrix(self):
         matrix = parser._get_matrix([10, 10, 10, 90, 90, 90])