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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
from MDAnalysis import units
class TestUnitEncoding(object):
def test_unicode(self):
try:
assert_equal(units.lengthUnit_factor["\u212b"], 1.0)
except KeyError:
raise AssertionError("Unicode symbol for Angtrom not supported")
def test_unicode_encoding_with_symbol(self):
try:
assert_equal(units.lengthUnit_factor["Å"], 1.0)
except KeyError:
raise AssertionError(
"UTF-8-encoded symbol for Angtrom not supported"
)
class TestConstants(object):
# CODATA 2010 (NIST): http://physics.nist.gov/cuu/Constants/
# (accessed 2015-02-15)
# Add a reference value to this dict for every entry in
# units.constants
constants_reference = (
("N_Avogadro", 6.02214129e23), # mol**-1
("elementary_charge", 1.602176565e-19), # As
("calorie", 4.184), # J
("Boltzmann_constant", 8.314462159e-3), # KJ (mol K)**-1
("Boltzman_constant", 8.314462159e-3), # remove in 2.8.0
("electric_constant", 5.526350e-3), # As (Angstroms Volts)**-1
)
@pytest.mark.parametrize("name, value", constants_reference)
def test_constant(self, name, value):
assert_almost_equal(units.constants[name], value)
def test_boltzmann_typo_deprecation(self):
wmsg = (
"Please use 'Boltzmann_constant' henceforth. The key "
"'Boltzman_constant' was a typo and will be removed "
"in MDAnalysis 2.8.0."
)
with pytest.warns(DeprecationWarning, match=wmsg):
units.constants["Boltzman_constant"]
class TestConversion(object):
@staticmethod
def _assert_almost_equal_convert(value, u1, u2, ref):
val = units.convert(value, u1, u2)
assert_almost_equal(
val, ref, err_msg="Conversion {0} --> {1} failed".format(u1, u2)
)
nm = 12.34567
A = nm * 10.0
@pytest.mark.parametrize(
"quantity, unit1, unit2, ref",
(
(nm, "nm", "A", A),
(A, "Angstrom", "nm", nm),
(A, "\u212b", "nm", nm),
),
)
def test_length(self, quantity, unit1, unit2, ref):
self._assert_almost_equal_convert(quantity, unit1, unit2, ref)
@pytest.mark.parametrize(
"quantity, unit1, unit2, ref",
(
(1, "ps", "AKMA", 20.45482949774598),
(1, "AKMA", "ps", 0.04888821),
(1, "ps", "ms", 1e-9),
(1, "ms", "ps", 1e9),
(1, "ps", "us", 1e-6),
(1, "us", "ps", 1e6),
(1, "\u03BCs", "ps", 1e6),
(1, "fs", "ns", 1e-6),
),
)
def test_time(self, quantity, unit1, unit2, ref):
self._assert_almost_equal_convert(quantity, unit1, unit2, ref)
@pytest.mark.parametrize(
"quantity, unit1, unit2, ref",
(
(1, "kcal/mol", "kJ/mol", 4.184),
(1, "kcal/mol", "eV", 0.0433641),
),
)
def test_energy(self, quantity, unit1, unit2, ref):
self._assert_almost_equal_convert(quantity, unit1, unit2, ref)
@pytest.mark.parametrize(
"quantity, unit1, unit2, ref",
(
(1, "kJ/(mol*A)", "J/m", 1.66053892103219e-11),
(2.5, "kJ/(mol*nm)", "kJ/(mol*A)", 0.25),
(1, "kcal/(mol*Angstrom)", "kJ/(mol*Angstrom)", 4.184),
),
)
def test_force(self, quantity, unit1, unit2, ref):
self._assert_almost_equal_convert(quantity, unit1, unit2, ref)
@pytest.mark.parametrize(
"quantity, unit1, unit2, ref",
(
(1, "A/ps", "m/s", 1e-10 / 1e-12),
(1, "A/ps", "nm/ps", 0.1),
(1, "A/ps", "pm/ps", 1e2),
(1, "A/ms", "A/ps", 1e-9),
(1, "A/us", "A/ps", 1e-6),
(1, "A/\u03BCs", "A/ps", 1e-6),
(1, "\u212b/\u03BCs", "A/ps", 1e-6),
(1, "A/fs", "A/ps", 1e3),
(1, "A/ps", "A/fs", 1e-3),
(1, "A/ns", "A/ms", 1e6),
(1, "\u212b/ns", "A/ms", 1e6),
(1, "A/ps", "A/ps", 1.0),
(1, "nm/ns", "pm/ps", 1.0),
(1, "m/s", "A/fs", 1e-5),
(1, "A/AKMA", "A/ps", 1 / 4.888821e-2),
),
)
def test_speed(self, quantity, unit1, unit2, ref):
self._assert_almost_equal_convert(quantity, unit1, unit2, ref)
@pytest.mark.parametrize(
"quantity, unit1, unit2", ((nm, "Stone", "nm"), (nm, "nm", "Stone"))
)
def test_unit_unknown(self, quantity, unit1, unit2):
with pytest.raises(ValueError):
units.convert(quantity, unit1, unit2)
def test_unit_unconvertable(self):
nm = 12.34567
A = nm * 10.0
with pytest.raises(ValueError):
units.convert(A, "A", "ps")
class TestBaseUnits:
@staticmethod
@pytest.fixture
def ref():
# This is a copy of the dictionary we expect.
# We want to know if base units are added or altered.
ref = {
"length": "A",
"time": "ps",
"energy": "kJ/mol",
"charge": "e",
"force": "kJ/(mol*A)",
"speed": "A/ps",
}
return ref
def test_MDANALYSIS_BASE_UNITS_correct(self, ref):
assert ref == units.MDANALYSIS_BASE_UNITS
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