LAMMPS support for chainreader (#4170)

* Generalize continuous check

* Bug fix parent method and chain implementation

* Update changelog and docs

* Update error output string

* Bug fix parenthesis

* Bug fix parent method and chain implementation

* Update changelog and docs

* simplify fix

* Address small reviewer comments

* Add test for consistent, expected time between frames

* Add check for timesteps

package/CHANGELOG

@@ -23,8 +23,11 @@ Fixes
     (PR #4163, Issue #4159)
 
 Enhancements
+  * LAMMPSDump Reader use of `continuous` option to stitch trajectories
+    (Issue #3546)
 
 Changes
+  * Add definition of ts.data['time'] in LAMMPSDump Reader (Issue #3546)
   * As per NEP29 the minimum supported version has been raised to 1.22. We
     have opted to pin to a minimum of 1.22.3 to avoid known issues on some
     platforms.

package/MDAnalysis/coordinates/LAMMPS.py

@@ -595,6 +595,7 @@ def _read_next_timestep(self):
         f.readline()  # ITEM TIMESTEP
         step_num = int(f.readline())
         ts.data['step'] = step_num
+        ts.data['time'] = step_num * ts.dt
 
         f.readline()  # ITEM NUMBER OF ATOMS
         n_atoms = int(f.readline())

package/MDAnalysis/coordinates/chain.py

@@ -191,7 +191,7 @@ class ChainReader(base.ReaderBase):
         what frames are used with the continuous option.
 
     The default chainreader will read all frames. The continuous option is
-    currently only supported for XTC and TRR files.
+    currently only supported for XTC, TRR, and LAMMPSDUMP files.
 
     Notes
     -----
@@ -299,7 +299,7 @@ def __init__(self, filenames, skip=1, dt=None, continuous=False,
 
         # calculate new start_frames to have a time continuous trajectory.
         if continuous:
-            check_allowed_filetypes(self.readers, ['XTC', 'TRR'])
+            check_allowed_filetypes(self.readers, ['XTC', 'TRR', "LAMMPSDUMP"])
             if np.any(np.array(n_frames) == 1):
                 raise RuntimeError("ChainReader: Need at least two frames in "
                                    "every trajectory with continuous=True")

testsuite/MDAnalysisTests/coordinates/test_chainreader.py

@@ -33,7 +33,9 @@
 import MDAnalysis as mda
 from MDAnalysis.transformations import translate
 from MDAnalysisTests.datafiles import (PDB, PSF, CRD, DCD,
-                                       GRO, XTC, TRR, PDB_small, PDB_closed)
+                                       GRO, XTC, TRR, PDB_small, PDB_closed,
+                                       LAMMPS_chain, LAMMPSDUMP_chain1,
+                                       LAMMPSDUMP_chain2,)
 from MDAnalysisTests.util import no_warning
 
 
@@ -206,6 +208,18 @@ def test_set_all_format_tuples(self):
         assert universe.trajectory.n_frames == 21
         assert_equal(universe.trajectory.filenames, [PDB, XTC, TRR])
 
+    def test_set_all_format_lammps(self):
+        universe = mda.Universe(
+            LAMMPS_chain, [LAMMPSDUMP_chain1, LAMMPSDUMP_chain2], 
+            format="LAMMPSDUMP", continuous=True)
+        assert universe.trajectory.n_frames == 11
+
+        # Test whether the amount of time between frames is consistently = 1
+        time_values = np.array([ts.time for ts in universe.trajectory])
+        dt_array = time_values[1:]-time_values[:-1]
+        assert np.unique(dt_array) == 1
+        assert_equal(time_values, np.arange(11))
+
     def test_set_format_tuples_and_format(self):
         universe = mda.Universe(GRO, [(PDB, 'pdb'), GRO, GRO, (XTC, 'xtc'), 
                                       (TRR, 'trr')], format='gro')

testsuite/MDAnalysisTests/data/lammps/chain_dump_1.lammpstrj

@@ -0,0 +1,186 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+22
+ITEM: BOX BOUNDS pp pp pp
+0.0000000000000000e+00 1.0000000000000000e+01
+0.0000000000000000e+00 1.0000000000000000e+01
+0.0000000000000000e+00 1.0000000000000000e+01
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+13 0 2 0 3.42556 5.80345 1.03172
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+22 0 2 0 1.59082 3.31475 4.97774
+11 0 2 0 3.42477 4.70658 3.66179
+1 0 1 0 5.19899 5.00015 5.48947
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+14 0 2 0 6.62547 4.95874 6.02809
+19 0 2 0 7.08926 4.30542 5.23948
+20 0 2 0 7.0361 5.90606 5.4861
+15 0 2 0 4.22366 9.62949 5.40626
+21 0 2 0 4.17191 8.57808 5.01616
+6 0 2 0 8.27587 8.45465 4.67567
+18 0 2 0 1.26168 1.6929 8.0355
+3 0 2 0 3.45325 5.51395 8.67997
+9 0 2 0 5.19513 5.29517 8.55806
+5 0 2 0 6.55796 3.99289 9.54127
+7 0 2 0 7.62242 6.3979 9.73197
+8 0 2 0 6.88523 4.51143 6.98553
+17 0 2 0 9.17665 6.50396 7.07893
+12 0 2 0 7.07863 9.62566 7.36101
+ITEM: TIMESTEP
+1
+ITEM: NUMBER OF ATOMS
+22
+ITEM: BOX BOUNDS pp pp pp
+0.0000000000000000e+00 1.0000000000000000e+01
+0.0000000000000000e+00 1.0000000000000000e+01
+0.0000000000000000e+00 1.0000000000000000e+01
+ITEM: ATOMS id mol type q xu yu zu
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+13 0 2 0 3.43361 5.81743 1.05571
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+20 0 2 0 7.03647 5.90326 5.48498
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+21 0 2 0 4.17371 8.58414 5.00718
+6 0 2 0 8.25895 8.45456 4.65529
+18 0 2 0 1.24399 1.69158 8.02878
+3 0 2 0 3.44983 5.48966 8.7051
+9 0 2 0 5.18181 5.2815 8.56656
+5 0 2 0 6.56395 3.97275 9.5395
+7 0 2 0 7.61969 6.40413 9.72323
+8 0 2 0 6.88059 4.52138 6.98398
+17 0 2 0 9.19784 6.49329 7.08897
+12 0 2 0 7.1015 9.62409 7.37619
+ITEM: TIMESTEP
+2
+ITEM: NUMBER OF ATOMS
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+ITEM: BOX BOUNDS pp pp pp
+0.0000000000000000e+00 1.0000000000000000e+01
+0.0000000000000000e+00 1.0000000000000000e+01
+0.0000000000000000e+00 1.0000000000000000e+01
+ITEM: ATOMS id mol type q xu yu zu
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+13 0 2 0 3.44167 5.83141 1.07969
+16 0 2 0 0.0401567 8.70118 0.263043
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+1 0 1 0 5.21537 4.99476 5.45525
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+14 0 2 0 6.61824 5.02819 6.07806
+19 0 2 0 7.17033 4.32411 5.2502
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+6 0 2 0 8.24203 8.45447 4.63492
+18 0 2 0 1.2263 1.69026 8.02205
+3 0 2 0 3.44645 5.46536 8.73023
+9 0 2 0 5.16846 5.26782 8.57506
+5 0 2 0 6.56988 3.95258 9.53777
+7 0 2 0 7.61696 6.41036 9.71449
+8 0 2 0 6.87604 4.53115 6.98274
+17 0 2 0 9.21902 6.48262 7.09901
+12 0 2 0 7.12436 9.62251 7.39137
+ITEM: TIMESTEP
+3
+ITEM: NUMBER OF ATOMS
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+ITEM: BOX BOUNDS pp pp pp
+0.0000000000000000e+00 1.0000000000000000e+01
+0.0000000000000000e+00 1.0000000000000000e+01
+0.0000000000000000e+00 1.0000000000000000e+01
+ITEM: ATOMS id mol type q xu yu zu
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+ITEM: TIMESTEP
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+ITEM: TIMESTEP
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+ITEM: NUMBER OF ATOMS
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+ITEM: BOX BOUNDS pp pp pp
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+0.0000000000000000e+00 1.0000000000000000e+01
+0.0000000000000000e+00 1.0000000000000000e+01
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