mdtraj.reporters.HDF5Reporter¶
-
class
mdtraj.reporters.
HDF5Reporter
(file, reportInterval, coordinates=True, time=True, cell=True, potentialEnergy=True, kineticEnergy=True, temperature=True, velocities=False, atomSubset=None)¶ HDF5Reporter stores a molecular dynamics trajectory in the HDF5 format.
This object supports saving all kinds of information from the simulation – more than any other trajectory format. In addition to all of the options, the topology of the system will also (of course) be stored in the file. All of the information is compressed, so the size of the file is not much different than DCD, despite the added flexibility.
- Parameters
- filestr, or HDF5TrajectoryFile
Either an open HDF5TrajecoryFile object to write to, or a string specifying the filename of a new HDF5 file to save the trajectory to.
- reportIntervalint
The interval (in time steps) at which to write frames.
- coordinatesbool
Whether to write the coordinates to the file.
- timebool
Whether to write the current time to the file.
- cellbool
Whether to write the current unit cell dimensions to the file.
- potentialEnergybool
Whether to write the potential energy to the file.
- kineticEnergybool
Whether to write the kinetic energy to the file.
- temperaturebool
Whether to write the instantaneous temperature to the file.
- velocitiesbool
Whether to write the velocities to the file.
- atomSubsetarray_like, default=None
Only write a subset of the atoms, with these (zero based) indices to the file. If None, all of the atoms will be written to disk.
Notes
If you use the
atomSubset
option to write only a subset of the atoms to disk, thekineticEnergy
,potentialEnergy
, andtemperature
fields will not change. They will still refer to the energy and temperature of the whole system, and are not “subsetted” to only include the energy of your subsystem.Examples
>>> simulation = Simulation(topology, system, integrator) >>> h5_reporter = HDF5Reporter('traj.h5', 100) >>> simulation.reporters.append(h5_reporter) >>> simulation.step(10000)
>>> traj = mdtraj.trajectory.load('traj.lh5')
- Attributes
- backend
Methods
close
(self)Close the underlying trajectory file
describeNextReport
(self, simulation)Get information about the next report this object will generate.
report
(self, simulation, state)Generate a report.
-
__init__
(self, file, reportInterval, coordinates=True, time=True, cell=True, potentialEnergy=True, kineticEnergy=True, temperature=True, velocities=False, atomSubset=None)¶ Create a HDF5Reporter.
Methods
__init__
(self, file, reportInterval[, …])Create a HDF5Reporter.
close
(self)Close the underlying trajectory file
describeNextReport
(self, simulation)Get information about the next report this object will generate.
report
(self, simulation, state)Generate a report.
Attributes
backend