NetCDFReporter

class mdhelper.openmm.reporter.NetCDFReporter(file: str, interval: int, append: bool = False, periodic: bool = None, *, velocities: bool = False, forces: bool = False, subset: slice | ndarray[int] | Topology = None)

Bases: object

A NetCDF trajectory reporter for OpenMM that can report velocities and forces in addition to time and coordinates for all particles in the simulation or just a subset.

Parameters:

filestr

Filename of NetCDF file to which the data is saved. If file does not have the .nc extension, it will automatically be appended.

intervalint

Interval (in timesteps) at which to write frames.

appendbool, keyword-only, default: False

If True, the existing NetCDF file is opened for data to be appended to. If False, a new NetCDF file is opened (and will clobber an existing file with the same name).

periodicbool, keyword-only, optional

Specifies whether particle positions should be translated so the center of every molecule lies in the same periodic box. If None (the default), it will automatically decide whether to translate molecules based on whether the system being simulated uses periodic boundary conditions.

velocitiesbool, keyword-only, default: False

Specifies whether particle velocities should be written to file.

forcesbool, keyword-only, default: False

Specifies whether forces exerted on particles should be written to file.

subsetslice, numpy.ndarray, or openmm.app.Topology, keyword-only, optional

Slice or array containing the indices of particles to report data for. If an OpenMM topology is provided instead, the indices are determined from the atoms found in the topology.

Methods

describeNextReport	Get information about the next report this NetCDF reporter will generate.
report	Generate a report.

describeNextReport(simulation: Simulation) → tuple[int, bool, bool, bool, bool, bool]

Get information about the next report this NetCDF reporter will generate.

Parameters:

simulationopenmm.app.Simulation

OpenMM simulation to generate a report for.

Returns:

reporttuple

A six-element tuple containing

1. the number of steps until the next report,

2. whether the report will require coordinates,

3. whether the report will require velocities,

4. whether the report will require forces,

5. whether the report will require energies, and

6. whether coordinates should be wrapped to lie in a single periodic box.

report(simulation: Simulation, state: State) → None

Generate a report.

Parameters:

simulationopenmm.app.Simulation

OpenMM simulation to generate a report for.

stateopenmm.State

Current OpenMM simulation state.