def test_xtc_reporter_append(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) xtcfile = os.path.join(tmpdir, 'traj.xtc') xtcfile_cp = os.path.join(tmpdir, 'traj_cp.xtc') checkpoint = os.path.join(tmpdir, 'checkpoint.chk') reporter = XTCReporter(xtcfile, 2) simulation.reporters.append(reporter) simulation.reporters.append(CheckpointReporter(checkpoint, 10)) simulation.step(10) reporter.close() shutil.copyfile(xtcfile, xtcfile_cp) 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.loadCheckpoint(checkpoint) reporter = XTCReporter(xtcfile, 2, append=True) simulation.reporters.append(reporter) simulation.step(10) reporter.close() xtc_traj = md.load(xtcfile, top=get_fn('native.pdb')) xtc_traj_cp = md.load(xtcfile_cp, top=get_fn('native.pdb')) eq(xtc_traj.xyz[:5], xtc_traj_cp.xyz) eq(xtc_traj.n_frames, 10) eq(xtc_traj_cp.n_frames, 5) eq(xtc_traj.time[:5], xtc_traj_cp.time)
def test_xtc_reporter_append(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) xtcfile = os.path.join(tmpdir, 'traj.xtc') xtcfile_cp = os.path.join(tmpdir, 'traj_cp.xtc') checkpoint = os.path.join(tmpdir, 'checkpoint.chk') reporter = XTCReporter(xtcfile, 2) simulation.reporters.append(reporter) simulation.reporters.append(CheckpointReporter(checkpoint, 10)) simulation.step(10) reporter.close() shutil.copyfile(xtcfile, xtcfile_cp) 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.loadCheckpoint(checkpoint) reporter = XTCReporter(xtcfile, 2, append=True) simulation.reporters.append(reporter) simulation.step(10) reporter.close() xtc_traj = md.load(xtcfile, top=get_fn('native.pdb')) xtc_traj_cp = md.load(xtcfile_cp, top=get_fn('native.pdb')) eq(xtc_traj.xyz[:5], xtc_traj_cp.xyz) eq(xtc_traj.n_frames, 10) eq(xtc_traj_cp.n_frames, 5) eq(xtc_traj.time[:5], xtc_traj_cp.time)
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_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(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') 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)