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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# 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 Lesser GNU Public Licence, v2.1 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 pytest
import numpy as np
from numpy.testing import assert_equal, assert_almost_equal
import MDAnalysis as mda
from MDAnalysis.coordinates.GMS import GMSReader
from MDAnalysisTests.datafiles import GMS_ASYMOPT, GMS_ASYMSURF, GMS_SYMOPT
class _GMSBase(object):
@pytest.fixture()
def u(self):
return mda.Universe(self.filename)
def test_n_frames(self, u):
assert_equal(
u.trajectory.n_frames,
self.n_frames,
err_msg="Wrong number of frames read from {}".format(self.flavour),
)
def test_random_access(self, u):
u = u
pos1 = u.atoms[-1].position
u.trajectory.next()
u.trajectory.next()
pos3 = u.atoms[-1].position
u.trajectory[0]
assert_equal(u.atoms[-1].position, pos1)
u.trajectory[2]
assert_equal(u.atoms[-1].position, pos3)
@staticmethod
def _calcFD(u):
u.trajectory.rewind()
pp = u.trajectory.ts._pos[0] - u.trajectory.ts._pos[3]
z1 = np.sqrt(sum(pp**2))
for i in range(5):
u.trajectory.next()
pp = u.trajectory.ts._pos[0] - u.trajectory.ts._pos[3]
z2 = np.sqrt(sum(pp**2))
return z1 - z2
def test_rewind(self, u):
u.trajectory.rewind()
assert_equal(u.trajectory.ts.frame, 0, "rewinding to frame 0")
def test_next(self, u):
u.trajectory.rewind()
u.trajectory.next()
assert_equal(u.trajectory.ts.frame, 1, "loading frame 1")
def test_dt(self, u):
assert_almost_equal(
u.trajectory.dt, 1.0, 4, err_msg="wrong timestep dt"
)
def test_step5distances(self, u):
assert_almost_equal(
self._calcFD(u),
self.step5d,
decimal=5,
err_msg="Wrong 1-4 atom distance change after "
"5 steps for {}".format(self.flavour),
)
class TestGMSReader(_GMSBase):
n_frames = 21
flavour = "GAMESS C1 optimization"
step5d = -0.0484664
filename = GMS_ASYMOPT
class TestGMSReaderSO(_GMSBase):
n_frames = 8
flavour = "GAMESS D4H optimization"
step5d = 0.227637
filename = GMS_SYMOPT
class TestGMSReaderASS(_GMSBase):
n_frames = 10
flavour = "GAMESS C1 surface"
step5d = -0.499996
filename = GMS_ASYMSURF
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