DL_POLY HISTORY may contain cells even for non-periodic simulations

package/CHANGELOG

@@ -18,11 +18,13 @@ The rules for this file:
          calcraven，xiki-tempula, mieczyslaw, manuel.nuno.melo, PicoCentauri,
          hanatok, rmeli, aditya-kamath, tirkarthi, LeonardoBarneschi, hejamu,
          biogen98, orioncohen, z3y50n, hp115, ojeda-e, thadanipaarth, HenryKobin,
-         1ut, sulays, ahy3nz
+         1ut, sulays, ahy3nz, fiszczyp
 
   * 2.0.0
 
 Fixes
+  * DL_POLY HISTORY file may contain unit cell dimensions even if there are
+    no periodic boundary conditions (imcom=0) (Issue #3314, PR #3312).
   * New RDKitConverter cache system to fix issue #2958 (PR #2942)
   * Fixed OpenMM converter documentation not showing up in the Converters
     section (Issue #3262, PR #2882)
@@ -186,7 +188,7 @@ Changes
   * Adds a `force` parameter to the RDKitConverter to allow conversion of
     molecules with no hydrogen atom, and a `set_converter_cache_size` function
     to change how many items are retained in the cache (PR #2942)
-  * `hydrogenbonds.WaterBridgeAnalysis.generate_table()` now returns the table; as previously, 
+  * `hydrogenbonds.WaterBridgeAnalysis.generate_table()` now returns the table; as previously,
     it also generates the `table` attribute but the attribute will be removed in 3.0.0.
   * `hydrogenbonds.WaterBridgeAnalysis` now stores data using the
     `hydrogenbonds.WaterBridgeAnalysis.results` attribute
@@ -198,7 +200,7 @@ Changes
     passes keyword arguments to the underlying converter. It can also be used
     as `convert_to.lowercase_pkg_name()` for tab-completion (PR #2882)
   * `analysis.polymer.PersistenceLength` class now stores `lb`,
-    `lp` and `fit` using the `analysis.base.Results` class 
+    `lp` and `fit` using the `analysis.base.Results` class
     (Issues #3289, #3291)
   * `analysis.hole2.HoleAnalysis` now stores ``sphpdbs``, ``outfiles``
     and ``profiles`` in the `analysis.base.Results` class (Issues #3261, #3269)
@@ -282,13 +284,13 @@ Deprecations
   * The `hydrogenbonds.WaterBridgeAnalysis.network` attribute is now deprecated
     in favour of `hydrogenbonds.WaterBridgeAnalysis.results.network`. It will be
     removed in 3.0.0 (Issue #3261, Issue #3270)
-  * The `analysis.Contacts.timeseries` attribute is now deprecated in favour of 
+  * The `analysis.Contacts.timeseries` attribute is now deprecated in favour of
     `analysis.Contacts.results.timeseries`. It will be removed in 3.0.0
     (Issue #3261)
   * In 3.0.0 the ParmEd classes will only be accessible from the
     `MDAnalysis.converters` module.
   * The `analysis.polymer.PersistenceLength.lb`,
-    `analysis.polymer.PersistenceLength.lp` and 
+    `analysis.polymer.PersistenceLength.lp` and
     `analysis.polymer.PersistenceLength.fit` attributes are now deprecated in
     favour of `analysis.polymer.PersistenceLength.results.lb`,
     `analysis.polymer.PersistenceLength.results.lp` and
@@ -371,15 +373,15 @@ Deprecations
     replaced with hydrogenbonds.WaterBridgeAnalysis (#3111)
   * TPRParser indexing resids from 0 by default is deprecated.
     From 2.0 TPRParser will index resids from 1 by default.
-  
+
 
 Enhancements
   * Added `get_connections` method to get bonds, angles, dihedrals, etc.
     with or without atoms outside the group (Issues #1264, #2821, PR #3160)
   * Added `tpr_resid_from_one` keyword to select whether TPRParser
     indexes resids from 0 or 1 (Issue #2364, PR #3153)
 
-    
+
 01/17/21 richardjgowers, IAlibay, orbeckst, tylerjereddy, jbarnoud,
          yuxuanzhuang, lilyminium, VOD555, p-j-smith, bieniekmateusz,
          calcraven, ianmkenney, rcrehuet, manuel.nuno.melo, hanatok
@@ -465,7 +467,7 @@ Fixes
   * n_components correctly selects PCA components (Issue #2623)
   * Use internal residue indices instead of resids for similarity and connectivity
     selections (Issues #2669 and #2672, PR #2673)
-  * Checks for cryo-em 1 A^3 default CRYST1 record, 
+  * Checks for cryo-em 1 A^3 default CRYST1 record,
     disabling setting of box dimensions if found (Issue #2599)
   * mdamath.angles now returns np.pi instead of -np.pi in cases of
     lower bound roundoff errors. (Issue #2632, PR #2634)
@@ -527,7 +529,7 @@ Fixes
 Enhancements
   * Added support for FHI-AIMS input files (PR #2705)
   * vastly improved support for 32-bit Windows (PR #2696)
-  * Added methods to compute the root-mean-square-inner-product of subspaces 
+  * Added methods to compute the root-mean-square-inner-product of subspaces
     and the cumulative overlap of a vector in a subspace for PCA (PR #2613)
   * Added .frames and .times arrays to AnalysisBase (Issue #2661)
   * Added elements attribute to PDBParser (Issue #2553, #2647)
@@ -574,7 +576,7 @@ Enhancements
 
 Changes
   * Unused `MDAnalysis.lib.mdamath._angle` has been removed (Issue #2650)
-  * Refactored dihedral selections and Ramachandran.__init__ to speed up 
+  * Refactored dihedral selections and Ramachandran.__init__ to speed up
     dihedral selections for faster tests (Issue #2671, PR #2706)
   * Removes the deprecated `t0`, `tf`, and `dtmax` from
     :class:Waterdynamics.SurvivalProbability. Instead the `start`, `stop` and

package/MDAnalysis/coordinates/DLPoly.py

@@ -1,5 +1,5 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #
 # MDAnalysis --- https://www.mdanalysis.org
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
@@ -152,10 +152,19 @@ def __init__(self, filename, **kwargs):
         # "private" file handle
         self._file = util.anyopen(self.filename, 'r')
         self.title = self._file.readline().strip()
-        self._levcfg, self._imcon, self.n_atoms = np.int64(self._file.readline().split()[:3])
+        header = np.int64(self._file.readline().split())
+        self._levcfg, self._imcon, self.n_atoms, _, _ = header
         self._has_vels = True if self._levcfg > 0 else False
         self._has_forces = True if self._levcfg == 2 else False
 
+        rwnd = self._file.tell()
+        self._file.readline()
+        if (len(self._file.readline().split())) == 3:
+            self._has_cell = True
+        else:
+            self._has_cell = False
+        self._file.seek(rwnd)
+
         self.ts = self._Timestep(self.n_atoms,
                                  velocities=self._has_vels,
                                  forces=self._has_forces,
@@ -169,7 +178,8 @@ def _read_next_timestep(self, ts=None):
         line = self._file.readline()  # timestep line
         if not line.startswith('timestep'):
             raise IOError
-        if not self._imcon == 0:
+
+        if self._has_cell:
             ts._unitcell[0] = self._file.readline().split()
             ts._unitcell[1] = self._file.readline().split()
             ts._unitcell[2] = self._file.readline().split()
@@ -193,11 +203,12 @@ def _read_next_timestep(self, ts=None):
                 ts._velocities[i] = self._file.readline().split()
             if self._has_forces:
                 ts._forces[i] = self._file.readline().split()
+            i += 1
 
         if ids:
             ids = np.array(ids)
             # if ids aren't strictly sequential
-            if not all(ids == (np.arange(self.n_atoms) + 1)):
+            if not np.all(ids == (np.arange(self.n_atoms) + 1)):
                 order = np.argsort(ids)
                 ts._pos[:] = ts._pos[order]
                 if self._has_vels:
@@ -216,31 +227,17 @@ def _read_frame(self, frame):
 
     @property
     def n_frames(self):
-        try:
-            return self._n_frames
-        except AttributeError:
-            self._n_frames = self._read_n_frames()
-            return self._n_frames
-
-    def _read_n_frames(self):
-        """Read the number of frames, and the offset for each frame
-
-        offset[i] - returns the offset in bytes to seek into the file to be
-                    just before the frame starts
-        """
-        offsets = self._offsets = []
+        # Second line is traj_key, imcom, n_atoms, n_frames, n_records
+        offsets = []
 
         with open(self.filename, 'r') as f:
-            n_frames = 0
-
-            f.readline()
             f.readline()
+            n_frames = int(f.readline().split()[3])
             position = f.tell()
             line = f.readline()
             while line.startswith('timestep'):
                 offsets.append(position)
-                n_frames += 1
-                if not self._imcon == 0:  # box info
+                if self._has_cell:
                     f.readline()
                     f.readline()
                     f.readline()
@@ -254,6 +251,7 @@ def _read_n_frames(self):
                 position = f.tell()
                 line = f.readline()
 
+        self._offsets = offsets
         return n_frames
 
     def _reopen(self):

package/MDAnalysis/topology/DLPolyParser.py

@@ -129,16 +129,14 @@ def parse(self, **kwargs):
         with openany(self.filename) as inf:
             inf.readline()
             levcfg, imcon, megatm = np.int64(inf.readline().split()[:3])
-            inf.readline()
-            if not imcon == 0:
-                inf.readline()
-                inf.readline()
-                inf.readline()
 
             names = []
             ids = []
 
             line = inf.readline()
+            while not len(line.split()) == 5:
+                line = inf.readline()
+
             while line and not line.startswith('timestep'):
                 name = line[:8].strip()
                 names.append(name)
@@ -169,7 +167,7 @@ def parse(self, **kwargs):
 
         atomtypes = guessers.guess_types(names)
         masses = guessers.guess_masses(atomtypes)
-            
+
         attrs = [
             Atomnames(names),
             Atomids(ids),