def test_reporter(tmpdir, get_fn):
pdb = PDBFile(get_fn('native.pdb'))
forcefield = ForceField('amber99sbildn.xml', 'amber99_obc.xml')
# NO PERIODIC BOUNDARY CONDITIONS
system = forcefield.createSystem(pdb.topology, nonbondedMethod=CutoffNonPeriodic,
nonbondedCutoff=1.0 * nanometers, constraints=HBonds, rigidWater=True)
integrator = LangevinIntegrator(300 * kelvin, 1.0 / picoseconds, 2.0 * femtoseconds)
integrator.setConstraintTolerance(0.00001)
platform = Platform.getPlatformByName('Reference')
simulation = Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(300 * kelvin)
tmpdir = str(tmpdir)
hdf5file = os.path.join(tmpdir, 'traj.h5')
ncfile = os.path.join(tmpdir, 'traj.nc')
dcdfile = os.path.join(tmpdir, 'traj.dcd')
xtcfile = os.path.join(tmpdir, 'traj.xtc')
reporter = HDF5Reporter(hdf5file, 2, coordinates=True, time=True,
cell=True, potentialEnergy=True, kineticEnergy=True, temperature=True,
velocities=True)
reporter2 = NetCDFReporter(ncfile, 2, coordinates=True, time=True, cell=True)
reporter3 = DCDReporter(dcdfile, 2)
reporter4 = XTCReporter(xtcfile, 2)
simulation.reporters.append(reporter)
simulation.reporters.append(reporter2)
simulation.reporters.append(reporter3)
simulation.reporters.append(reporter4)
simulation.step(100)
reporter.close()
reporter2.close()
reporter3.close()
reporter4.close()
with HDF5TrajectoryFile(hdf5file) as f:
got = f.read()
eq(got.temperature.shape, (50,))
eq(got.potentialEnergy.shape, (50,))
eq(got.kineticEnergy.shape, (50,))
eq(got.coordinates.shape, (50, 22, 3))
eq(got.velocities.shape, (50, 22, 3))
eq(got.cell_lengths, None)
eq(got.cell_angles, None)
eq(got.time, 0.002 * 2 * (1 + np.arange(50)))
assert f.topology == md.load(get_fn('native.pdb')).top
with NetCDFTrajectoryFile(ncfile) as f:
xyz, time, cell_lengths, cell_angles = f.read()
eq(cell_lengths, None)
eq(cell_angles, None)
eq(time, 0.002 * 2 * (1 + np.arange(50)))
hdf5_traj = md.load(hdf5file)
dcd_traj = md.load(dcdfile, top=get_fn('native.pdb'))
netcdf_traj = md.load(ncfile, top=get_fn('native.pdb'))
xtc_traj = md.load(xtcfile, top=get_fn('native.pdb'))
# we don't have to convert units here, because md.load already
# handles that
assert hdf5_traj.unitcell_vectors is None
eq(hdf5_traj.xyz, netcdf_traj.xyz)
eq(hdf5_traj.unitcell_vectors, netcdf_traj.unitcell_vectors)
eq(hdf5_traj.time, netcdf_traj.time)
eq(xtc_traj.time, netcdf_traj.time)
eq(dcd_traj.xyz, hdf5_traj.xyz)
eq(xtc_traj.xyz, dcd_traj.xyz, decimal=3)
def test_reporter():
tempdir = os.path.join(dir, 'test1')
os.makedirs(tempdir)
pdb = PDBFile(get_fn('native.pdb'))
forcefield = ForceField('amber99sbildn.xml', 'amber99_obc.xml')
# NO PERIODIC BOUNDARY CONDITIONS
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=CutoffNonPeriodic,
nonbondedCutoff=1.0 * nanometers,
constraints=HBonds,
rigidWater=True)
integrator = LangevinIntegrator(300 * kelvin, 1.0 / picoseconds,
2.0 * femtoseconds)
integrator.setConstraintTolerance(0.00001)
platform = Platform.getPlatformByName('Reference')
simulation = Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(300 * kelvin)
hdf5file = os.path.join(tempdir, 'traj.h5')
ncfile = os.path.join(tempdir, 'traj.nc')
dcdfile = os.path.join(tempdir, 'traj.dcd')
reporter = HDF5Reporter(hdf5file,
2,
coordinates=True,
time=True,
cell=True,
potentialEnergy=True,
kineticEnergy=True,
temperature=True,
velocities=True)
reporter2 = NetCDFReporter(ncfile,
2,
coordinates=True,
time=True,
cell=True)
reporter3 = DCDReporter(dcdfile, 2)
simulation.reporters.append(reporter)
simulation.reporters.append(reporter2)
simulation.reporters.append(reporter3)
simulation.step(100)
reporter.close()
reporter2.close()
reporter3.close()
with HDF5TrajectoryFile(hdf5file) as f:
got = f.read()
eq(got.temperature.shape, (50, ))
eq(got.potentialEnergy.shape, (50, ))
eq(got.kineticEnergy.shape, (50, ))
eq(got.coordinates.shape, (50, 22, 3))
eq(got.velocities.shape, (50, 22, 3))
eq(got.cell_lengths, None)
eq(got.cell_angles, None)
eq(got.time, 0.002 * 2 * (1 + np.arange(50)))
assert f.topology == md.load(get_fn('native.pdb')).top
with NetCDFTrajectoryFile(ncfile) as f:
xyz, time, cell_lengths, cell_angles = f.read()
eq(cell_lengths, None)
eq(cell_angles, None)
eq(time, 0.002 * 2 * (1 + np.arange(50)))
hdf5_traj = md.load(hdf5file)
dcd_traj = md.load(dcdfile, top=get_fn('native.pdb'))
netcdf_traj = md.load(ncfile, top=get_fn('native.pdb'))
# we don't have to convert units here, because md.load already
# handles that
assert hdf5_traj.unitcell_vectors is None
eq(hdf5_traj.xyz, netcdf_traj.xyz)
eq(hdf5_traj.unitcell_vectors, netcdf_traj.unitcell_vectors)
eq(hdf5_traj.time, netcdf_traj.time)
eq(dcd_traj.xyz, hdf5_traj.xyz)
def test_reporter_subset(tmpdir, get_fn):
pdb = PDBFile(get_fn('native2.pdb'))
pdb.topology.setUnitCellDimensions([2, 2, 2])
forcefield = ForceField('amber99sbildn.xml', 'amber99_obc.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=CutoffPeriodic,
nonbondedCutoff=1 * nanometers, constraints=HBonds, rigidWater=True)
integrator = LangevinIntegrator(300 * kelvin, 1.0 / picoseconds, 2.0 * femtoseconds)
integrator.setConstraintTolerance(0.00001)
platform = Platform.getPlatformByName('Reference')
simulation = Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(300 * kelvin)
tmpdir = str(tmpdir)
hdf5file = os.path.join(tmpdir, 'traj.h5')
ncfile = os.path.join(tmpdir, 'traj.nc')
dcdfile = os.path.join(tmpdir, 'traj.dcd')
xtcfile = os.path.join(tmpdir, 'traj.xtc')
atomSubset = [0, 1, 2, 4, 5]
reporter = HDF5Reporter(hdf5file, 2, coordinates=True, time=True,
cell=True, potentialEnergy=True, kineticEnergy=True, temperature=True,
velocities=True, atomSubset=atomSubset)
reporter2 = NetCDFReporter(ncfile, 2, coordinates=True, time=True,
cell=True, atomSubset=atomSubset)
reporter3 = DCDReporter(dcdfile, 2, atomSubset=atomSubset)
reporter4 = XTCReporter(xtcfile, 2, atomSubset=atomSubset)
simulation.reporters.append(reporter)
simulation.reporters.append(reporter2)
simulation.reporters.append(reporter3)
simulation.reporters.append(reporter4)
simulation.step(100)
reporter.close()
reporter2.close()
reporter3.close()
reporter4.close()
t = md.load(get_fn('native.pdb'))
t.restrict_atoms(atomSubset)
with HDF5TrajectoryFile(hdf5file) as f:
got = f.read()
eq(got.temperature.shape, (50,))
eq(got.potentialEnergy.shape, (50,))
eq(got.kineticEnergy.shape, (50,))
eq(got.coordinates.shape, (50, len(atomSubset), 3))
eq(got.velocities.shape, (50, len(atomSubset), 3))
eq(got.cell_lengths, 2 * np.ones((50, 3)))
eq(got.cell_angles, 90 * np.ones((50, 3)))
eq(got.time, 0.002 * 2 * (1 + np.arange(50)))
assert f.topology == md.load(get_fn('native.pdb'), atom_indices=atomSubset).topology
with NetCDFTrajectoryFile(ncfile) as f:
xyz, time, cell_lengths, cell_angles = f.read()
eq(cell_lengths, 20 * np.ones((50, 3)))
eq(cell_angles, 90 * np.ones((50, 3)))
eq(time, 0.002 * 2 * (1 + np.arange(50)))
eq(xyz.shape, (50, len(atomSubset), 3))
hdf5_traj = md.load(hdf5file)
dcd_traj = md.load(dcdfile, top=hdf5_traj)
netcdf_traj = md.load(ncfile, top=hdf5_traj)
xtc_traj = md.load(xtcfile, top=hdf5_traj)
# we don't have to convert units here, because md.load already handles that
eq(hdf5_traj.xyz, netcdf_traj.xyz)
eq(hdf5_traj.unitcell_vectors, netcdf_traj.unitcell_vectors)
eq(hdf5_traj.time, netcdf_traj.time)
eq(xtc_traj.time, netcdf_traj.time)
eq(dcd_traj.xyz, hdf5_traj.xyz)
eq(xtc_traj.xyz, hdf5_traj.xyz)
eq(dcd_traj.unitcell_vectors, hdf5_traj.unitcell_vectors)
def test_reporter_subset():
tempdir = os.path.join(dir, 'test2')
os.makedirs(tempdir)
pdb = PDBFile(get_fn('native2.pdb'))
pdb.topology.setUnitCellDimensions([2, 2, 2])
forcefield = ForceField('amber99sbildn.xml', 'amber99_obc.xml')
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=CutoffPeriodic,
nonbondedCutoff=1 * nanometers,
constraints=HBonds,
rigidWater=True)
integrator = LangevinIntegrator(300 * kelvin, 1.0 / picoseconds,
2.0 * femtoseconds)
integrator.setConstraintTolerance(0.00001)
platform = Platform.getPlatformByName('Reference')
simulation = Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(300 * kelvin)
hdf5file = os.path.join(tempdir, 'traj.h5')
ncfile = os.path.join(tempdir, 'traj.nc')
dcdfile = os.path.join(tempdir, 'traj.dcd')
atomSubset = [0, 1, 2, 4, 5]
reporter = HDF5Reporter(hdf5file,
2,
coordinates=True,
time=True,
cell=True,
potentialEnergy=True,
kineticEnergy=True,
temperature=True,
velocities=True,
atomSubset=atomSubset)
reporter2 = NetCDFReporter(ncfile,
2,
coordinates=True,
time=True,
cell=True,
atomSubset=atomSubset)
reporter3 = DCDReporter(dcdfile, 2, atomSubset=atomSubset)
simulation.reporters.append(reporter)
simulation.reporters.append(reporter2)
simulation.reporters.append(reporter3)
simulation.step(100)
reporter.close()
reporter2.close()
reporter3.close()
t = md.load(get_fn('native.pdb'))
t.restrict_atoms(atomSubset)
with HDF5TrajectoryFile(hdf5file) as f:
got = f.read()
eq(got.temperature.shape, (50, ))
eq(got.potentialEnergy.shape, (50, ))
eq(got.kineticEnergy.shape, (50, ))
eq(got.coordinates.shape, (50, len(atomSubset), 3))
eq(got.velocities.shape, (50, len(atomSubset), 3))
eq(got.cell_lengths, 2 * np.ones((50, 3)))
eq(got.cell_angles, 90 * np.ones((50, 3)))
eq(got.time, 0.002 * 2 * (1 + np.arange(50)))
assert f.topology == md.load(get_fn('native.pdb'),
atom_indices=atomSubset).topology
with NetCDFTrajectoryFile(ncfile) as f:
xyz, time, cell_lengths, cell_angles = f.read()
eq(cell_lengths, 20 * np.ones((50, 3)))
eq(cell_angles, 90 * np.ones((50, 3)))
eq(time, 0.002 * 2 * (1 + np.arange(50)))
eq(xyz.shape, (50, len(atomSubset), 3))
hdf5_traj = md.load(hdf5file)
dcd_traj = md.load(dcdfile, top=hdf5_traj)
netcdf_traj = md.load(ncfile, top=hdf5_traj)
# we don't have to convert units here, because md.load already handles
# that
eq(hdf5_traj.xyz, netcdf_traj.xyz)
eq(hdf5_traj.unitcell_vectors, netcdf_traj.unitcell_vectors)
eq(hdf5_traj.time, netcdf_traj.time)
eq(dcd_traj.xyz, hdf5_traj.xyz)
eq(dcd_traj.unitcell_vectors, hdf5_traj.unitcell_vectors)
