StateDataReporter

class cvpack.reporting.StateDataReporter(file, reportInterval, writers=(), **kwargs)

An extended version of OpenMM’s openmm.app.StateDataReporter class that includes custom writers for reporting additional simulation data.

A custom writer is an object that includes the following methods:

1. getHeaders: returns a list of strings containing the headers to be added to the report. It must have the following signature:

def getHeaders(self) -> List[str]:
    pass

2. getValues: returns a list of floats containing the values to be added to the report at a given time step. It must have the following signature:

def getValues(self, simulation: openmm.app.Simulation) -> List[float]:
    pass

3. initialize (optional): performs any necessary setup before the first report. If present, it must have the following signature:

def initialize(self, simulation: openmm.app.Simulation) -> None:
    pass

Parameters:

• file (str | TextIOBase) – The file to write to. This can be a file name or a file object.

• reportInterval (int) – The interval (in time steps) at which to report data.

• writers (Iterable[CustomWriter]) – A sequence of custom writers.

• **kwargs – Additional keyword arguments to be passed to the StateDataReporter constructor.

Examples

>>> import cvpack
>>> import openmm
>>> from math import pi
>>> from cvpack import reporting
>>> from openmm import app, unit
>>> from sys import stdout
>>> from openmmtools import testsystems
>>> model = testsystems.AlanineDipeptideVacuum()
>>> phi = cvpack.Torsion(4, 6, 8, 14, name="phi")
>>> psi = cvpack.Torsion(6, 8, 14, 16, name="psi")
>>> umbrella = cvpack.MetaCollectiveVariable(
...     f"0.5*kappa*(min(dphi,{2*pi}-dphi)^2+min(dpsi,{2*pi}-dpsi)^2)"
...     "; dphi=abs(phi-phi0); dpsi=abs(psi-psi0)",
...     [phi, psi],
...     unit.kilojoules_per_mole,
...     name="umbrella",
...     kappa=100 * unit.kilojoules_per_mole/unit.radian**2,
...     phi0=5*pi/6 * unit.radian,
...     psi0=-5*pi/6 * unit.radian,
... )
>>> reporter = reporting.StateDataReporter(
...     stdout,
...     100,
...     writers=[
...         reporting.CVWriter(umbrella, value=True, emass=True),
...         reporting.MetaCVWriter(
...             umbrella,
...             values=["phi", "psi"],
...             emasses=["phi", "psi"],
...             parameters=["phi0", "psi0"],
...             derivatives=["phi0", "psi0"],
...         ),
...     ],
...     step=True,
... )
>>> integrator = openmm.LangevinIntegrator(
...     300 * unit.kelvin,
...     1 / unit.picosecond,
...     2 * unit.femtosecond,
... )
>>> integrator.setRandomNumberSeed(1234)
>>> umbrella.addToSystem(model.system)
>>> simulation = app.Simulation(model.topology, model.system, integrator)
>>> simulation.context.setPositions(model.positions)
>>> simulation.context.setVelocitiesToTemperature(300 * unit.kelvin, 5678)
>>> simulation.reporters.append(reporter)
>>> simulation.step(1000)
#"Step","umbrella (kJ/mol)",...,"d[umbrella]/d[psi0] (kJ/(mol rad))"
100,2.2775...,-20.519...
200,3.0913...,0.7804...
300,25.466...,49.272...
400,2.5009...,-10.012...
500,1.3608...,-8.9529...
600,2.9577...,23.049...
700,8.1081...,25.068...
800,0.3278...,-0.4481...
900,1.2975...,9.5528...
1000,3.6413...,21.986...