CVWriter

class cvpack.reporting.CVWriter(variable, value=False, emass=False, allowReinitialization=False)

A custom writer for reporting collective variable data.

Parameters:

• variable (CollectiveVariable) – The collective variable whose values and/or effective masses will be reported.

• value (bool) – If True, report the values of the collective variable.

• emass (bool) – If True, report the effective masses of the collective variable.

• allowReinitialization (bool) – Whether to allow context reinitialization when the collective variable shares its force group with other forces (see CollectiveVariable.getValue()).

Examples

>>> import cvpack
>>> import openmm
>>> from cvpack.reporting import StateDataReporter, CVWriter
>>> from math import pi
>>> 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")
>>> phi.addToSystem(model.system)
>>> psi = cvpack.Torsion(6, 8, 14, 16, name="psi")
>>> psi.addToSystem(model.system)
>>> reporter = StateDataReporter(
...     stdout,
...     100,
...     writers=[
...         CVWriter(phi, value=True, emass=True),
...         CVWriter(psi, value=True, emass=True),
...     ],
...     step=True,
... )
>>> integrator = openmm.LangevinIntegrator(
...     300 * unit.kelvin,
...     1 / unit.picosecond,
...     2 * unit.femtosecond,
... )
>>> integrator.setRandomNumberSeed(1234)
>>> # Integrate only the physical forces, so phi and psi do not bias the dynamics
>>> integrator.setIntegrationForceGroups({0})
>>> 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","phi (rad)",...,"emass[psi] (nm**2 Da/(rad**2))"
100,-2.4309...,0.0404...,2.7368...,0.0497...
200,-2.0470...,0.0386...,2.2298...,0.0456...
300,-2.4721...,0.0424...,2.2528...,0.0422...
400,-2.4032...,0.0406...,-3.1341...,0.0546...
500,-2.8165...,0.0460...,-2.5845...,0.0458...
600,-2.6256...,0.0401...,3.1382...,0.0509...
700,-2.4156...,0.0463...,2.1037...,0.0406...
800,-2.3871...,0.0372...,1.8683...,0.0408...
900,-1.8631...,0.0322...,2.0393...,0.0374...
1000,-1.0804...,0.0240...,1.8363...,0.0354...

Methods

getHeaders()

Gets a list of strings containing the headers to be added to the report.

Return type:

list[str]

getValues(simulation)

Gets a list of floats containing the values to be added to the report.

Parameters:

simulation (Simulation) – The simulation object.

Return type:

list[float]