def testReportersPBC(self):
""" Test NetCDF and ASCII restart and trajectory reporters (w/ PBC) """
system = amber_solv.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8*u.angstroms)
integrator = mm.LangevinIntegrator(300*u.kelvin, 5.0/u.picoseconds,
1.0*u.femtoseconds)
sim = app.Simulation(amber_solv.topology, system, integrator)
sim.context.setPositions(amber_solv.positions)
sim.reporters.extend([
NetCDFReporter(get_fn('traj.nc', written=True), 1,
vels=True, frcs=True),
MdcrdReporter(get_fn('traj.mdcrd', written=True), 1),
RestartReporter(get_fn('restart.ncrst', written=True), 1,
netcdf=True),
RestartReporter(get_fn('restart.rst7', written=True), 1)
])
sim.step(5)
for reporter in sim.reporters: reporter.finalize()
ntraj = NetCDFTraj.open_old(get_fn('traj.nc', written=True))
atraj = AmberMdcrd(get_fn('traj.mdcrd', written=True),
amber_solv.ptr('natom'), True, mode='r')
nrst = NetCDFRestart.open_old(get_fn('restart.ncrst', written=True))
arst = AmberAsciiRestart(get_fn('restart.rst7', written=True), 'r')
self.assertEqual(ntraj.frame, 5)
self.assertEqual(atraj.frame, 5)
self.assertTrue(ntraj.hasvels)
self.assertTrue(ntraj.hasfrcs)
for i in range(ntraj.frame):
for x1, x2 in zip(ntraj.box[i], atraj.box[i]):
self.assertAlmostEqual(x1, x2, places=3)
self.assertEqual(len(nrst.box), 6)
self.assertEqual(len(arst.box), 6)
def test_reporters_pbc(self):
""" Test NetCDF and ASCII restart and trajectory reporters (w/ PBC) """
systemsolv = load_file(self.get_fn('ildn.solv.top'),
xyz=self.get_fn('ildn.solv.gro'))
system = systemsolv.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8 * u.angstroms)
integrator = mm.LangevinIntegrator(300 * u.kelvin, 5.0 / u.picoseconds,
1.0 * u.femtoseconds)
sim = app.Simulation(systemsolv.topology, system, integrator, CPU)
sim.context.setPositions(systemsolv.positions)
sim.reporters.extend([
NetCDFReporter(self.get_fn('traj.nc', written=True),
1,
vels=True,
frcs=True),
MdcrdReporter(self.get_fn('traj.mdcrd', written=True), 1),
RestartReporter(self.get_fn('restart.ncrst', written=True),
1,
netcdf=True),
RestartReporter(self.get_fn('restart.rst7', written=True), 1),
StateDataReporter(self.get_fn('state.o', written=True),
1,
volume=True,
density=True,
systemMass=1)
])
sim.step(5)
for reporter in sim.reporters:
reporter.finalize()
ntraj = NetCDFTraj.open_old(self.get_fn('traj.nc', written=True))
atraj = AmberMdcrd(self.get_fn('traj.mdcrd', written=True),
len(systemsolv.atoms),
True,
mode='r')
nrst = NetCDFRestart.open_old(
self.get_fn('restart.ncrst', written=True))
arst = AmberAsciiRestart(self.get_fn('restart.rst7', written=True),
'r')
self.assertEqual(ntraj.frame, 5)
self.assertEqual(atraj.frame, 5)
self.assertTrue(ntraj.hasvels)
self.assertTrue(ntraj.hasfrcs)
for i in range(ntraj.frame):
for x1, x2 in zip(ntraj.box[i], atraj.box[i]):
self.assertAlmostEqual(x1, x2, places=3)
self.assertEqual(len(nrst.box), 6)
self.assertEqual(len(arst.box), 6)
# Make sure the EnergyMinimizerReporter does not fail
f = StringIO()
rep = EnergyMinimizerReporter(f, volume=True)
rep.report(sim)
rep.finalize()
def test_reporters_pbc(self):
""" Test NetCDF and ASCII restart and trajectory reporters (w/ PBC) """
systemsolv = load_file(get_fn('ildn.solv.top'), xyz=get_fn('ildn.solv.gro'))
system = systemsolv.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8*u.angstroms)
integrator = mm.LangevinIntegrator(300*u.kelvin, 5.0/u.picoseconds,
1.0*u.femtoseconds)
sim = app.Simulation(systemsolv.topology, system, integrator, CPU)
sim.context.setPositions(systemsolv.positions)
sim.reporters.extend([
NetCDFReporter(get_fn('traj.nc', written=True), 1,
vels=True, frcs=True),
MdcrdReporter(get_fn('traj.mdcrd', written=True), 1),
RestartReporter(get_fn('restart.ncrst', written=True), 1,
netcdf=True),
RestartReporter(get_fn('restart.rst7', written=True), 1),
StateDataReporter(get_fn('state.o', written=True), 1,
volume=True, density=True, systemMass=1)
])
sim.step(5)
for reporter in sim.reporters: reporter.finalize()
ntraj = NetCDFTraj.open_old(get_fn('traj.nc', written=True))
atraj = AmberMdcrd(get_fn('traj.mdcrd', written=True),
len(systemsolv.atoms), True, mode='r')
nrst = NetCDFRestart.open_old(get_fn('restart.ncrst', written=True))
arst = AmberAsciiRestart(get_fn('restart.rst7', written=True), 'r')
self.assertEqual(ntraj.frame, 5)
self.assertEqual(atraj.frame, 5)
self.assertTrue(ntraj.hasvels)
self.assertTrue(ntraj.hasfrcs)
for i in range(ntraj.frame):
for x1, x2 in zip(ntraj.box[i], atraj.box[i]):
self.assertAlmostEqual(x1, x2, places=3)
self.assertEqual(len(nrst.box), 6)
self.assertEqual(len(arst.box), 6)
# Make sure the EnergyMinimizerReporter does not fail
f = StringIO()
rep = EnergyMinimizerReporter(f, volume=True)
rep.report(sim)
rep.finalize()
def testReporters(self):
""" Test NetCDF and ASCII restart and trajectory reporters (no PBC) """
system = amber_gas.createSystem()
integrator = mm.LangevinIntegrator(300*u.kelvin, 5.0/u.picoseconds,
1.0*u.femtoseconds)
sim = app.Simulation(amber_gas.topology, system, integrator, platform=mm.Platform.getPlatformByName('CPU'))
sim.context.setPositions(amber_gas.positions)
sim.reporters.extend([
NetCDFReporter(get_fn('traj1.nc', written=True), 10),
NetCDFReporter(get_fn('traj2.nc', written=True), 10, vels=True),
NetCDFReporter(get_fn('traj3.nc', written=True), 10, frcs=True),
NetCDFReporter(get_fn('traj4.nc', written=True), 10, vels=True,
frcs=True),
NetCDFReporter(get_fn('traj5.nc', written=True), 10, crds=False,
vels=True),
NetCDFReporter(get_fn('traj6.nc', written=True), 10, crds=False,
frcs=True),
NetCDFReporter(get_fn('traj7.nc', written=True), 10, crds=False,
vels=True, frcs=True),
MdcrdReporter(get_fn('traj1.mdcrd', written=True), 10),
MdcrdReporter(get_fn('traj2.mdcrd', written=True), 10,
crds=False, vels=True),
MdcrdReporter(get_fn('traj3.mdcrd', written=True), 10,
crds=False, frcs=True),
RestartReporter(get_fn('restart.ncrst', written=True), 10,
write_multiple=True, netcdf=True),
RestartReporter(get_fn('restart.rst7', written=True), 10)
])
sim.step(500)
for reporter in sim.reporters: reporter.finalize()
self.assertEqual(len(os.listdir(get_fn('writes'))), 61)
ntraj = [NetCDFTraj.open_old(get_fn('traj1.nc', written=True)),
NetCDFTraj.open_old(get_fn('traj2.nc', written=True)),
NetCDFTraj.open_old(get_fn('traj3.nc', written=True)),
NetCDFTraj.open_old(get_fn('traj4.nc', written=True)),
NetCDFTraj.open_old(get_fn('traj5.nc', written=True)),
NetCDFTraj.open_old(get_fn('traj6.nc', written=True)),
NetCDFTraj.open_old(get_fn('traj7.nc', written=True))]
atraj = [AmberMdcrd(get_fn('traj1.mdcrd', written=True),
amber_gas.ptr('natom'), hasbox=False, mode='r'),
AmberMdcrd(get_fn('traj2.mdcrd', written=True),
amber_gas.ptr('natom'), hasbox=False, mode='r'),
AmberMdcrd(get_fn('traj3.mdcrd', written=True),
amber_gas.ptr('natom'), hasbox=False, mode='r')]
for traj in ntraj:
self.assertEqual(traj.frame, 50)
self.assertEqual(traj.Conventions, 'AMBER')
self.assertEqual(traj.ConventionVersion, '1.0')
self.assertEqual(traj.application, 'AmberTools')
self.assertEqual(traj.program, 'ParmEd')
self.assertFalse(traj.hasbox)
self.assertTrue(ntraj[0].hascrds)
self.assertFalse(ntraj[0].hasvels)
self.assertFalse(ntraj[0].hasfrcs)
self.assertTrue(ntraj[1].hascrds)
self.assertTrue(ntraj[1].hasvels)
self.assertFalse(ntraj[1].hasfrcs)
self.assertTrue(ntraj[2].hascrds)
self.assertFalse(ntraj[2].hasvels)
self.assertTrue(ntraj[2].hasfrcs)
self.assertTrue(ntraj[3].hascrds)
self.assertTrue(ntraj[3].hasvels)
self.assertTrue(ntraj[3].hasfrcs)
self.assertFalse(ntraj[4].hascrds)
self.assertTrue(ntraj[4].hasvels)
self.assertFalse(ntraj[4].hasfrcs)
self.assertFalse(ntraj[5].hascrds)
self.assertFalse(ntraj[5].hasvels)
self.assertTrue(ntraj[5].hasfrcs)
self.assertFalse(ntraj[6].hascrds)
self.assertTrue(ntraj[6].hasvels)
self.assertTrue(ntraj[6].hasfrcs)
for i in (0, 2, 3, 4, 5, 6): ntraj[i].close() # still need the 2nd
for traj in atraj: traj.close()
# Now test the NetCDF restart files
fn = get_fn('restart.ncrst.%d', written=True)
for i, j in enumerate(range(10, 501, 10)):
ncrst = NetCDFRestart.open_old(fn % j)
self.assertEqual(ncrst.coordinates.shape, (1, 25, 3))
self.assertEqual(ncrst.velocities.shape, (1, 25, 3))
np.testing.assert_allclose(ncrst.coordinates[0],
ntraj[1].coordinates[i])
np.testing.assert_allclose(ncrst.velocities[0],
ntraj[1].velocities[i], rtol=1e-6)
# Now test the ASCII restart file
f = AmberAsciiRestart(get_fn('restart.rst7', written=True), 'r')
# Compare to ncrst and make sure it's the same data
np.testing.assert_allclose(ncrst.coordinates, f.coordinates, rtol=1e-4)
np.testing.assert_allclose(ncrst.velocities, f.velocities, rtol=1e-4)
def test_reporters(self):
""" Test NetCDF and ASCII restart and trajectory reporters (no PBC) """
with self.assertRaises(ValueError):
NetCDFReporter(self.get_fn('blah', written=True), 1, crds=False)
with self.assertRaises(ValueError):
MdcrdReporter(self.get_fn('blah', written=True), 1, crds=False)
with self.assertRaises(ValueError):
MdcrdReporter(self.get_fn('blah', written=True),
1,
crds=True,
vels=True)
system = self.amber_gas.createSystem()
integrator = mm.LangevinIntegrator(300 * u.kelvin, 5.0 / u.picoseconds,
1.0 * u.femtoseconds)
sim = app.Simulation(self.amber_gas.topology,
system,
integrator,
platform=CPU)
sim.context.setPositions(self.amber_gas.positions)
sim.reporters.extend([
NetCDFReporter(self.get_fn('traj1.nc', written=True), 10),
NetCDFReporter(self.get_fn('traj2.nc', written=True),
10,
vels=True),
NetCDFReporter(self.get_fn('traj3.nc', written=True),
10,
frcs=True),
NetCDFReporter(self.get_fn('traj4.nc', written=True),
10,
vels=True,
frcs=True),
NetCDFReporter(self.get_fn('traj5.nc', written=True),
10,
crds=False,
vels=True),
NetCDFReporter(self.get_fn('traj6.nc', written=True),
10,
crds=False,
frcs=True),
NetCDFReporter(self.get_fn('traj7.nc', written=True),
10,
crds=False,
vels=True,
frcs=True),
MdcrdReporter(self.get_fn('traj1.mdcrd', written=True), 10),
MdcrdReporter(self.get_fn('traj2.mdcrd', written=True),
10,
crds=False,
vels=True),
MdcrdReporter(self.get_fn('traj3.mdcrd', written=True),
10,
crds=False,
frcs=True),
RestartReporter(self.get_fn('restart.ncrst', written=True),
10,
write_multiple=True,
netcdf=True),
RestartReporter(self.get_fn('restart.rst7', written=True), 10),
])
sim.step(500)
for reporter in sim.reporters:
reporter.finalize()
self.assertEqual(len(os.listdir(self._temporary_directory.name)), 61)
ntraj = [
NetCDFTraj.open_old(self.get_fn('traj1.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj2.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj3.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj4.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj5.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj6.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj7.nc', written=True))
]
atraj = [
AmberMdcrd(self.get_fn('traj1.mdcrd', written=True),
self.amber_gas.ptr('natom'),
hasbox=False,
mode='r'),
AmberMdcrd(self.get_fn('traj2.mdcrd', written=True),
self.amber_gas.ptr('natom'),
hasbox=False,
mode='r'),
AmberMdcrd(self.get_fn('traj3.mdcrd', written=True),
self.amber_gas.ptr('natom'),
hasbox=False,
mode='r'),
]
for traj in ntraj:
self.assertEqual(traj.frame, 50)
self.assertEqual(traj.Conventions, 'AMBER')
self.assertEqual(traj.ConventionVersion, '1.0')
self.assertEqual(traj.application, 'AmberTools')
self.assertEqual(traj.program, 'ParmEd')
self.assertFalse(traj.hasbox)
self.assertTrue(ntraj[0].hascrds)
self.assertFalse(ntraj[0].hasvels)
self.assertFalse(ntraj[0].hasfrcs)
self.assertTrue(ntraj[1].hascrds)
self.assertTrue(ntraj[1].hasvels)
self.assertFalse(ntraj[1].hasfrcs)
self.assertTrue(ntraj[2].hascrds)
self.assertFalse(ntraj[2].hasvels)
self.assertTrue(ntraj[2].hasfrcs)
self.assertTrue(ntraj[3].hascrds)
self.assertTrue(ntraj[3].hasvels)
self.assertTrue(ntraj[3].hasfrcs)
self.assertFalse(ntraj[4].hascrds)
self.assertTrue(ntraj[4].hasvels)
self.assertFalse(ntraj[4].hasfrcs)
self.assertFalse(ntraj[5].hascrds)
self.assertFalse(ntraj[5].hasvels)
self.assertTrue(ntraj[5].hasfrcs)
self.assertFalse(ntraj[6].hascrds)
self.assertTrue(ntraj[6].hasvels)
self.assertTrue(ntraj[6].hasfrcs)
for i in (0, 2, 3, 4, 5, 6):
ntraj[i].close() # still need the 2nd
for traj in atraj:
traj.close()
# Now test the NetCDF restart files
fn = self.get_fn('restart.ncrst.%d', written=True)
for i, j in enumerate(range(10, 501, 10)):
ncrst = NetCDFRestart.open_old(fn % j)
self.assertEqual(ncrst.coordinates.shape, (1, 25, 3))
self.assertEqual(ncrst.velocities.shape, (1, 25, 3))
np.testing.assert_allclose(ncrst.coordinates[0],
ntraj[1].coordinates[i])
np.testing.assert_allclose(ncrst.velocities[0],
ntraj[1].velocities[i],
rtol=1e-6)
# Now test the ASCII restart file
f = AmberAsciiRestart(self.get_fn('restart.rst7', written=True), 'r')
# Compare to ncrst and make sure it's the same data
np.testing.assert_allclose(ncrst.coordinates, f.coordinates, atol=1e-3)
np.testing.assert_allclose(ncrst.velocities, f.velocities, rtol=1e-3)
# Make sure the EnergyMinimizerReporter does not fail
f = StringIO()
rep = EnergyMinimizerReporter(f)
rep.report(sim, frame=10)
rep.finalize()
