Improve xdr cython

package/CHANGELOG

@@ -19,6 +19,8 @@ The rules for this file:
  * 2.4.0
 
 Fixes
+  * XTC and TRR readers now fail with IOError when a status except EOK (=0) is
+    detected on reading a frame instead of silently continuing
   * Consolidate license files across MDAnalysis library packages (PR #3939)
   * Kwargs passed through to `MemoryReader` when using `transfer_to_memory()`
     and `in_memory=True`.
@@ -37,6 +39,10 @@ Fixes
     (e.g. bonds, angles) (PR #3779).
 
 Enhancements
+  * Improve C content of libxdr Cython, add `read_direct` methods to read 
+    coordinates, velocities and forces directly into memoryviews of `Timestep`
+    attributes, make `TRR` timestep have positions, velocities and forces on
+    `__init__`. (Issue #3891 PR  #3892).
   * Improve C content of libdcd Cython (Issue #3882, PR #3888)
   * The timeseries method for exporting coordinates from multiple frames to a
     NumPy array was added to ProtoReader (PR #3890)

package/MDAnalysis/coordinates/TRR.py

@@ -31,6 +31,7 @@
 MDAnalysis.coordinates.XTC: Read and write GROMACS XTC trajectory files.
 MDAnalysis.coordinates.XDR: BaseReader/Writer for XDR based formats
 """
+import errno
 from . import base
 from .XDR import XDRBaseReader, XDRBaseWriter
 from ..lib.formats.libmdaxdr import TRRFile
@@ -151,6 +152,28 @@ class TRRReader(XDRBaseReader):
     _writer = TRRWriter
     _file = TRRFile
 
+    def _read_next_timestep(self, ts=None):
+        """copy next frame into timestep
+
+        versionadded:: 2.4.0
+            TRRReader implements this method so that it can use
+            read_direct_xvf to read the data directly into the timestep
+            rather than copying it from a temporary array.
+        """
+        if self._frame == self.n_frames - 1:
+            raise IOError(errno.EIO, 'trying to go over trajectory limit')
+        if ts is None:
+            ts = self.ts
+        # allocate arrays to read into, will set to proper values
+        # in _frame_to_ts
+        ts.has_positions = True
+        ts.has_velocities = True
+        ts.has_forces = True
+        frame = self._xdr.read_direct_xvf(ts.positions, ts.velocities, ts.forces)
+        self._frame += 1
+        self._frame_to_ts(frame, ts)
+        return ts
+
     def _frame_to_ts(self, frame, ts):
         """convert a trr-frame to a mda TimeStep"""
         ts.time = frame.time

package/MDAnalysis/coordinates/XDR.py

@@ -120,7 +120,8 @@ class XDRBaseReader(base.ReaderBase):
        XDR offsets read from trajectory if offsets file read-in fails
     .. versionchanged:: 2.0.0
        Add a InterProcessLock when generating offsets
-
+    .. versionchanged:: 2.4.0
+       Use a direct read into ts attributes
     """
     @store_init_arguments
     def __init__(self, filename, convert_units=True, sub=None,
@@ -288,17 +289,6 @@ def _read_frame(self, i):
             timestep = self._read_next_timestep()
         return timestep
 
-    def _read_next_timestep(self, ts=None):
-        """copy next frame into timestep"""
-        if self._frame == self.n_frames - 1:
-            raise IOError(errno.EIO, 'trying to go over trajectory limit')
-        if ts is None:
-            ts = self.ts
-        frame = self._xdr.read()
-        self._frame += 1
-        self._frame_to_ts(frame, ts)
-        return ts
-
     def Writer(self, filename, n_atoms=None, **kwargs):
         """Return writer for trajectory format"""
         if n_atoms is None:

package/MDAnalysis/coordinates/XTC.py

@@ -31,6 +31,8 @@
 MDAnalysis.coordinates.TRR: Read and write GROMACS TRR trajectory files.
 MDAnalysis.coordinates.XDR: BaseReader/Writer for XDR based formats
 """
+
+import errno
 from . import base
 from .XDR import XDRBaseReader, XDRBaseWriter
 from ..lib.formats.libmdaxdr import XTCFile
@@ -130,12 +132,35 @@ class XTCReader(XDRBaseReader):
     See :ref:`Notes on offsets <offsets-label>` for more information about
     offsets.
 
+
+
     """
     format = 'XTC'
     units = {'time': 'ps', 'length': 'nm'}
     _writer = XTCWriter
     _file = XTCFile
 
+    def _read_next_timestep(self, ts=None):
+        """
+        copy next frame into timestep
+
+        versionadded:: 2.4.0
+            XTCReader implements this method so that it can use
+            read_direct_x method of XTCFile to read the data directly
+            into the timestep rather than copying it from a temporary array.
+        """
+        if self._frame == self.n_frames - 1:
+            raise IOError(errno.EIO, 'trying to go over trajectory limit')
+        if ts is None:
+            ts = self.ts
+        if ts.has_positions:
+            frame = self._xdr.read_direct_x(ts.positions)
+        else:
+            frame = self._xdr.read()
+        self._frame += 1
+        self._frame_to_ts(frame, ts)
+        return ts
+
     def _frame_to_ts(self, frame, ts):
         """convert a xtc-frame to a mda TimeStep"""
         ts.frame = self._frame

package/MDAnalysis/lib/formats/libmdaxdr.pxd

@@ -0,0 +1,110 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+#
+# MDAnalysis --- https://www.mdanalysis.org
+# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
+# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
+# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
+# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
+# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
+# doi: 10.25080/majora-629e541a-00e
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+
+import numpy as np
+cimport numpy as np
+
+np.import_array()
+from libc.stdint cimport int64_t
+
+from libc.stdio cimport SEEK_SET, SEEK_CUR, SEEK_END
+
+cdef extern from 'include/xdrfile.h':
+    ctypedef struct XDRFILE:
+        pass
+
+    XDRFILE* xdrfile_open (char * path, char * mode)
+    int xdrfile_close (XDRFILE * xfp)
+    int xdr_seek(XDRFILE *xfp, int64_t pos, int whence)
+    int64_t xdr_tell(XDRFILE *xfp)
+    ctypedef float matrix[3][3]
+    ctypedef float rvec[3]
+
+
+cdef extern from 'include/xdrfile_xtc.h':
+    int read_xtc_natoms(char * fname, int * natoms)
+    int read_xtc(XDRFILE * xfp, int natoms, int * step, float * time, matrix box,
+                 rvec * x, float * prec)
+    int write_xtc(XDRFILE * xfp, int natoms, int step, float time, matrix box,
+                  rvec * x, float prec)
+
+
+
+cdef extern from 'include/xdrfile_trr.h':
+    int read_trr_natoms(char *fname, int *natoms)
+    int read_trr(XDRFILE *xfp, int natoms, int *step, float *time, float *_lambda,
+                 matrix box, rvec *x, rvec *v, rvec *f, int *has_prop)
+    int write_trr(XDRFILE *xfp, int natoms, int step, float time, float _lambda,
+                  matrix box, rvec *x, rvec *v, rvec *f)
+
+
+cdef extern from 'include/xtc_seek.h':
+    int read_xtc_n_frames(char *fn, int *n_frames, int *est_nframes, int64_t **offsets)
+
+
+cdef extern from 'include/trr_seek.h':
+    int read_trr_n_frames(char *fn, int *n_frames, int *est_nframes, int64_t **offsets)
+
+
+cdef class _XDRFile:
+    """Base python wrapper for gromacs-xdr formats
+
+    This class can be similar to the normal file objects in python. The read()
+    function will return a frame and all information in it instead of a single
+    line. Additionally the context-manager protocoll is supported as well.
+
+    Note
+    ----
+    This class can't be initialized; use one of the subclasses :class:`XTCFile` or :class:`TRRFile`.
+    """
+    # number of atoms
+    cdef readonly int n_atoms
+    # whether the file is open
+    cdef int is_open
+    # whether we have reached the end of the file
+    cdef int reached_eof
+    # the XDR file pointer
+    cdef XDRFILE *xfp
+    # the name of the xdr file 
+    cdef readonly fname
+    # the current frame in the file
+    cdef int current_frame
+    # the file mode
+    cdef str mode
+    # the simulation box
+    cdef np.ndarray box
+    # numpy array of offsets into the fle 
+    cdef np.ndarray _offsets
+    # whether we have the offsets
+    cdef readonly int _has_offsets
+
+
+cdef class XTCFile(_XDRFile):
+    """File-like wrapper for gromacs XTC files."""
+    # precision of the XTC file
+    cdef float precision
+
+
+
+cdef class TRRFile(_XDRFile):
+    """File-like wrapper for gromacs TRR files"""