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# Trajectory tests
#
# Written by Konrad Hinsen
#
import unittest
from MMTK import *
from MMTK.Trajectory import Trajectory, SnapshotGenerator, TrajectoryOutput
from Scientific import N
import os
class InfiniteUniverseTest:
def setUp(self):
self.universe = InfiniteUniverse()
self.universe.addObject(Molecule('water',
position = Vector(-0.2, 0., 0.)))
self.universe.addObject(Molecule('water',
position = Vector(0.2, 0., 0.)))
class OrthorhombicUniverseTest:
def setUp(self):
self.universe = OrthorhombicPeriodicUniverse((1., 1., 0.5))
self.universe.addObject(Molecule('water',
position = Vector(-0.2, 0., 0.)))
self.universe.addObject(Molecule('water',
position = Vector(0.2, 0., 0.)))
class ParallelepipedicUniverseTest:
def setUp(self):
self.universe = ParallelepipedicPeriodicUniverse((Vector(1., 0., 0.),
Vector(0., 1., 0.),
Vector(0.5, 0., 0.5)))
self.universe.addObject(Molecule('water',
position = Vector(-0.2, 0., 0.)))
self.universe.addObject(Molecule('water',
position = Vector(0.2, 0., 0.)))
class SinglePrecisionTest:
double_precision = False
tolerance = 1.e-7
class DoublePrecisionTest:
double_precision = True
tolerance = 1.e-15
class TrajectoryTest:
def tearDown(self):
try:
os.remove('test.nc')
except OSError:
pass
def test_snapshot(self):
initial = self.universe.copyConfiguration()
transformation = Translation(Vector(0.,0.,0.01)) \
* Rotation(Vector(0.,0.,1.), 1.*Units.deg)
trajectory = Trajectory(self.universe, "test.nc", "w",
"trajectory test",
double_precision = self.double_precision)
snapshot = SnapshotGenerator(self.universe,
actions = [TrajectoryOutput(trajectory,
["all"],
0, None, 1)])
snapshot()
for i in range(100):
self.universe.setConfiguration(
self.universe.contiguousObjectConfiguration())
self.universe.applyTransformation(transformation)
self.universe.foldCoordinatesIntoBox()
snapshot()
trajectory.close()
self.universe.setConfiguration(initial)
trajectory = Trajectory(None, "test.nc")
t_universe = trajectory.universe
for i in range(101):
configuration = self.universe.configuration()
t_configuration = trajectory[i]['configuration']
max_diff = N.maximum.reduce(N.ravel(N.fabs(configuration.array
- t_configuration.array)))
self.assert_(max_diff < self.tolerance)
if configuration.cell_parameters is not None:
max_diff = N.maximum.reduce(N.fabs(configuration.cell_parameters
- t_configuration.cell_parameters))
self.assert_(max_diff < self.tolerance)
self.universe.setConfiguration(
self.universe.contiguousObjectConfiguration())
self.universe.applyTransformation(transformation)
self.universe.foldCoordinatesIntoBox()
trajectory.close()
class InfiniteUniverseTestSP(unittest.TestCase,
InfiniteUniverseTest,
TrajectoryTest,
SinglePrecisionTest):
setUp = InfiniteUniverseTest.setUp
class InfiniteUniverseTestDP(unittest.TestCase,
InfiniteUniverseTest,
TrajectoryTest,
DoublePrecisionTest):
setUp = InfiniteUniverseTest.setUp
tearDown = TrajectoryTest.tearDown
class OrthorhombicUniverseTestSP(unittest.TestCase,
OrthorhombicUniverseTest,
TrajectoryTest,
SinglePrecisionTest):
setUp = OrthorhombicUniverseTest.setUp
tearDown = TrajectoryTest.tearDown
class OrthorhombicUniverseTestDP(unittest.TestCase,
OrthorhombicUniverseTest,
TrajectoryTest,
DoublePrecisionTest):
setUp = OrthorhombicUniverseTest.setUp
tearDown = TrajectoryTest.tearDown
class ParallelepipedicUniverseTestSP(unittest.TestCase,
ParallelepipedicUniverseTest,
TrajectoryTest,
SinglePrecisionTest):
setUp = ParallelepipedicUniverseTest.setUp
tearDown = TrajectoryTest.tearDown
class ParallelepipedicUniverseTestDP(unittest.TestCase,
ParallelepipedicUniverseTest,
TrajectoryTest,
DoublePrecisionTest):
setUp = ParallelepipedicUniverseTest.setUp
tearDown = TrajectoryTest.tearDown
def suite():
loader = unittest.TestLoader()
s = unittest.TestSuite()
s.addTest(loader.loadTestsFromTestCase(InfiniteUniverseTestSP))
s.addTest(loader.loadTestsFromTestCase(InfiniteUniverseTestDP))
s.addTest(loader.loadTestsFromTestCase(OrthorhombicUniverseTestSP))
s.addTest(loader.loadTestsFromTestCase(OrthorhombicUniverseTestDP))
s.addTest(loader.loadTestsFromTestCase(ParallelepipedicUniverseTestSP))
s.addTest(loader.loadTestsFromTestCase(ParallelepipedicUniverseTestDP))
return s
if __name__ == '__main__':
unittest.main()
|
