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fix TRZ file reader on big-endian architectures #1425

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rathann wants to merge 12 commits into from
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fix TRZ file reader on big-endian architectures #1425

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51649ad
use correct int types
rathann Jun 9, 2017
280dc13
relax test_symmetry test due to lower precision on 32bit
rathann Jun 9, 2017
1f61efd
Aesthetic fixes to test_gro
richardjgowers Jun 12, 2017
b3adb1b
Added tests for issue #1395
richardjgowers Jun 12, 2017
6baf47e
Added lib.util.ltruncate_integer
richardjgowers Jun 12, 2017
46768e5
Changed coordinate writers to use ltruncate_int
richardjgowers Jun 12, 2017
6a3e427
More work on making indexing arrays use intp (#1362)
richardjgowers Jun 12, 2017
9a34b0f
Explicitly define __hash__ for groups
jbarnoud Jun 13, 2017
180216f
Merge remote-tracking branch 'upstream/develop' into develop
rathann Jun 18, 2017
059f664
fix int type in asserts in TestDownshiftArrays
rathann Jun 18, 2017
b9084b0
Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…
rathann Jun 22, 2017
efa4628
fix TRZ file reader on big-endian arches
rathann Jun 22, 2017
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134 changes: 67 additions & 67 deletions package/MDAnalysis/coordinates/TRZ.py
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Original file line number Diff line number Diff line change
Expand Up @@ -180,58 +180,58 @@ def __init__(self, trzfilename, n_atoms=None, **kwargs):
**self._ts_kwargs)

# structured dtype of a single trajectory frame
readarg = str(n_atoms) + 'f4'
readarg = str(n_atoms) + '<f4'
frame_contents = [
('p1', 'i4'),
('nframe', 'i4'),
('ntrj', 'i4'),
('natoms', 'i4'),
('treal', 'f8'),
('p2', '2i4'),
('box', '9f8'),
('p3', '2i4'),
('pressure', 'f8'),
('ptensor', '6f8'),
('p4', '3i4'),
('etot', 'f8'),
('ptot', 'f8'),
('ek', 'f8'),
('T', 'f8'),
('p5', '6i4'),
('p1', '<i4'),
('nframe', '<i4'),
('ntrj', '<i4'),
('natoms', '<i4'),
('treal', '<f8'),
('p2', '<2i4'),
('box', '<9f8'),
('p3', '<2i4'),
('pressure', '<f8'),
('ptensor', '<6f8'),
('p4', '<3i4'),
('etot', '<f8'),
('ptot', '<f8'),
('ek', '<f8'),
('T', '<f8'),
('p5', '<6i4'),
('rx', readarg),
('pad2', '2i4'),
('pad2', '<2i4'),
('ry', readarg),
('pad3', '2i4'),
('pad3', '<2i4'),
('rz', readarg),
('pad4', '2i4'),
('pad4', '<2i4'),
('vx', readarg),
('pad5', '2i4'),
('pad5', '<2i4'),
('vy', readarg),
('pad6', '2i4'),
('pad6', '<2i4'),
('vz', readarg)]
if not self.has_force:
frame_contents += [('pad7', 'i4')]
frame_contents += [('pad7', '<i4')]
else:
frame_contents += [
('pad7', '2i4'),
('pad7', '<2i4'),
('fx', readarg),
('pad8', '2i4'),
('pad8', '<2i4'),
('fy', readarg),
('pad9', '2i4'),
('pad9', '<2i4'),
('fz', readarg),
('pad10', 'i4')]
('pad10', '<i4')]
self._dtype = np.dtype(frame_contents)

self._read_next_timestep()

def _read_trz_header(self):
"""Reads the header of the trz trajectory"""
self._headerdtype = np.dtype([
('p1', 'i4'),
('p1', '<i4'),
('title', '80c'),
('p2', '2i4'),
('force', 'i4'),
('p3', 'i4')])
('p2', '<2i4'),
('force', '<i4'),
('p3', '<i4')])
data = np.fromfile(self.trzfile, dtype=self._headerdtype, count=1)
self.title = ''.join(c.decode('utf-8') for c in data['title'][0]).strip()
if data['force'] == 10:
Expand Down Expand Up @@ -478,52 +478,52 @@ def __init__(self, filename, n_atoms, title='TRZ', convert_units=None):

self._writeheader(title)

floatsize = str(n_atoms) + 'f4'
floatsize = str(n_atoms) + '<f4'
self.frameDtype = np.dtype([
('p1a', 'i4'),
('nframe', 'i4'),
('ntrj', 'i4'),
('natoms', 'i4'),
('treal', 'f8'),
('p1b', 'i4'),
('p2a', 'i4'),
('box', '9f8'),
('p2b', 'i4'),
('p3a', 'i4'),
('pressure', 'f8'),
('ptensor', '6f8'),
('p3b', 'i4'),
('p4a', 'i4'),
('six', 'i4'),
('etot', 'f8'),
('ptot', 'f8'),
('ek', 'f8'),
('T', 'f8'),
('blanks', '2f8'),
('p4b', 'i4'),
('p5a', 'i4'),
('p1a', '<i4'),
('nframe', '<i4'),
('ntrj', '<i4'),
('natoms', '<i4'),
('treal', '<f8'),
('p1b', '<i4'),
('p2a', '<i4'),
('box', '<9f8'),
('p2b', '<i4'),
('p3a', '<i4'),
('pressure', '<f8'),
('ptensor', '<6f8'),
('p3b', '<i4'),
('p4a', '<i4'),
('six', '<i4'),
('etot', '<f8'),
('ptot', '<f8'),
('ek', '<f8'),
('T', '<f8'),
('blanks', '<2f8'),
('p4b', '<i4'),
('p5a', '<i4'),
('rx', floatsize),
('p5b', 'i4'),
('p6a', 'i4'),
('p5b', '<i4'),
('p6a', '<i4'),
('ry', floatsize),
('p6b', 'i4'),
('p7a', 'i4'),
('p6b', '<i4'),
('p7a', '<i4'),
('rz', floatsize),
('p7b', 'i4'),
('p8a', 'i4'),
('p7b', '<i4'),
('p8a', '<i4'),
('vx', floatsize),
('p8b', 'i4'),
('p9a', 'i4'),
('p8b', '<i4'),
('p9a', '<i4'),
('vy', floatsize),
('p9b', 'i4'),
('p10a', 'i4'),
('p9b', '<i4'),
('p10a', '<i4'),
('vz', floatsize),
('p10b', 'i4')])
('p10b', '<i4')])

def _writeheader(self, title):
hdt = np.dtype([
('pad1', 'i4'), ('title', '80c'), ('pad2', 'i4'),
('pad3', 'i4'), ('nrec', 'i4'), ('pad4', 'i4')])
('pad1', '<i4'), ('title', '80c'), ('pad2', '<i4'),
('pad3', '<i4'), ('nrec', '<i4'), ('pad4', '<i4')])
out = np.zeros((), dtype=hdt)
out['pad1'], out['pad2'] = 80, 80
out['title'] = title + ' ' * (80 - len(title))
Expand Down