DielectricCylinder

class maicos.DielectricCylinder(atomgroup: AtomGroup, bin_width: float = 0.1, temperature: float = 300, single: bool = False, output_prefix: str = 'eps_cyl', refgroup: AtomGroup | None = None, concfreq: int = 0, jitter: float = 0.0, dim: int = 2, rmin: float = 0, rmax: float | None = None, zmin: float | None = None, zmax: float | None = None, vcutwidth: float = 0.1, unwrap: bool = True, pack: bool = True)

Bases: CylinderBase

Cylindrical dielectric profiles.

Computes the axial \(\varepsilon_z(r)\) and inverse radial \(\varepsilon_r^{-1}(r)\) components of the cylindrical dielectric tensor \(\varepsilon\). The components are binned along the radial direction of the cylinder. The \(z\)-axis of the cylinder is pointing in the direction given by the dim parameter. The center of the cylinder is either located at the center of the simulation box (default) or at 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 component along the \(z\)-axis is used. For further information on the correlation analysis please refer to 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.

• pack (bool) –

  When True, molecules are put back into the unit cell. This is required because MAICoS only takes into account molecules that are inside the unit cell.

  If the input contains molecules that are already packed, speed up the calculation by disabling packing with pack=False.

• 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.

• dim ({0, 1, 2}) – Dimension for binning (x=0, y=1, z=1).

• zmin (float) –

  Minimal coordinate for evaluation (in Å) with respect to the center of mass of the refgroup.

  If zmin=None, all coordinates down to the lower cell boundary are taken into account.

• zmax (float) –

  Maximal coordinate for evaluation (in Å) with respect to the center of mass of the refgroup.

  If zmax = None, all coordinates up to the upper cell boundary are taken into account.

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

• 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.

• temperature (float) – Reference temperature (K)

• single (bool) – For a single chain of molecules the average of \(M\) is zero. This flag sets \(\langle M \rangle = 0\).

results.bin_pos

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

Type:

numpy.ndarray

results.eps_z

Reduced axial dielectric profile \((\varepsilon_z(r) - 1)\) of the selected atomgroup

Type:

numpy.ndarray

results.deps_z

Estimated uncertainty of axial dielectric profile

Type:

numpy.ndarray

results.eps_r

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

Type:

numpy.ndarray

results.deps_r

Estimated uncertainty of inverse radial dielectric profile

Type:

numpy.ndarray

References

[1]

Philip Loche, Cihan Ayaz, Alexander Schlaich, Yuki Uematsu, and Roland R. Netz. Giant Axial Dielectric Response in Water-Filled Nanotubes and Effective Electrostatic Ion–Ion Interactions from a Tensorial Dielectric Model. J. Phys. Chem. B, 123(50):10850–10857, December 2019. doi:10.1021/acs.jpcb.9b09269.

save() → None

Save results of analysis to file specified by output.