DielectricSphere

class maicos.DielectricSphere(atomgroup: AtomGroup, bin_width: float = 0.1, temperature: float = 300, output_prefix: str = 'eps_sph', refgroup: AtomGroup | None = None, concfreq: int = 0, jitter: float = 0.0, rmin: float = 0, rmax: float | None = None, unwrap: bool = True)

Bases: SphereBase

Spherical dielectric profiles.

Components are calculated along the radial (\(r\)) direction either with respect to the center of the simulation box or the center of mass of the refgroup, if provided.

For usage, please refer to How-to: Dielectric constant and for details on the theory see Dielectric constant measurement.

For correlation analysis, the radial (\(r\)) component is used. For further information on the correlation analysis please refer to maicos.core.base.AnalysisBase or the General design section.

Also, please read and cite [1].

Parameters:

• atomgroup (MDAnalysis.core.groups.AtomGroup) – A AtomGroup for which the calculations are performed.

• unwrap (bool) –

  When True, molecules that are broken due to the periodic boundary conditions are made whole.

  If the input contains molecules that are already whole, speed up the calculation by disabling unwrap. To do so, use the flag -no-unwrap when using MAICoS from the command line, or use unwrap=False when using MAICoS from the Python interpreter.

  Note: Molecules containing virtual sites (e.g. TIP4P water models) are not currently supported in MDAnalysis. In this case, you need to provide unwrapped trajectory files directly, and disable unwrap. Trajectories can be unwrapped, for example, using the trjconv command of GROMACS.

• refgroup (MDAnalysis.core.groups.AtomGroup) – Reference AtomGroup used for the calculation. If refgroup is provided, the calculation is performed relative to the center of mass of the AtomGroup. If refgroup is None the calculations are performed with respect to the center of the (changing) box.

• jitter (float) –

  Magnitude of the random noise to add to the atomic positions.

  A jitter can be used to stabilize the aliasing effects sometimes appearing when histogramming data. The jitter value should be about the precision of the trajectory. In that case, using jitter will not alter the results of the histogram. If jitter = 0.0 (default), the original atomic positions are kept unchanged.

  You can estimate the precision of the positions in your trajectory with maicos.lib.util.trajectory_precision(). Note that if the precision is not the same for all frames, the smallest precision should be used.

• concfreq (int) – When concfreq (for conclude frequency) is larger than 0, the conclude function is called and the output files are written every concfreq frames.

• rmin (float) – Minimal radial coordinate relative to the center of mass of the refgroup for evaluation (in Å).

• rmax (float) –

  Maximal radial coordinate relative to the center of mass of the refgroup for evaluation (in Å).

  If rmax=None, the box extension is taken.

• bin_width (float) – Width of the bins (in Å).

• temperature (float) – Reference temperature (K)

• output_prefix (str) – Prefix for output files.

results.bin_pos

Bin positions (in Å) ranging from rmin to rmax.

Type:

numpy.ndarray

results.eps_rad

Reduced inverse radial dielectric profile (\(\varepsilon^{-1}_r - 1)\)

Type:

numpy.ndarray

results.deps_rad

Uncertainty of inverse radial dielectric profile

Type:

numpy.ndarray

References

[1]

Christian Schaaf and Stephan Gekle. Dielectric response of the water hydration layer around spherical solutes. Phys. Rev. E, 92(3):032718, September 2015. doi:10.1103/PhysRevE.92.032718.

save() → None

Save results of analysis to file specified by output.