DielectricPlanar

class maicos.modules.dielectricplanar.DielectricPlanar(atomgroups, dim=2, zmin=None, zmax=None, bin_width=0.5, refgroup=None, is_3d=False, sym=False, vac=False, unwrap=True, temperature=300, output_prefix='eps', concfreq=0, vcutwidth=0.1)

Bases: PlanarBase

Calculate planar dielectric profiles.

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

Also, please read and cite Schlaich et al.[1] and Refs. [2], [3].

Parameters:

• atomgroups (list[AtomGroup]) – a list of AtomGroup objects for which the calculations are performed.

• refgroup (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 to the center of the (changing) box.

• unwrap (bool) –

  When unwrap = 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.

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

• 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.

• jitter (float) –

  If jitter is not None, random numbers of the order of jitter (Å) are added to the atom positions.

  The appilication of a jitter is rationalized in possible aliasing effects when histogramming data, i.e., for spatial profiles. These aliasing effects can be stabilized with the application of a numerical jitter. The jitter value should be about the precision of the trajectory and will not alter the results of the histogram.

  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.

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

• is_3d (bool) – Use 3d-periodic boundary conditions, i.e., include the dipole correction for the interaction between periodic images [4].

• vac (bool) – Use vacuum boundary conditions instead of metallic (2D only!).

• sym (bool) – Symmetrize the profiles.

• temperature (float) – temperature (K)

• output_prefix (str) – Prefix for output files.

• vcutwidth (float) – Spacing of virtual cuts (bins) along the parallel directions.

results.bin_pos

Bin positions (in Å) ranging from zmin to zmax.

Type:

numpy.ndarray

results.eps_par

Reduced parallel dielectric profile \((\varepsilon_\parallel - 1)\) of the selected atomgroups

Type:

numpy.ndarray

results.deps_par

Uncertainty of parallel dielectric profile

Type:

numpy.ndarray

results.eps_par_self

Reduced self contribution of parallel dielectric profile \((\varepsilon_{\parallel,\mathrm{self}} - 1)\)

Type:

numpy.ndarray

results.eps_par_coll

Reduced collective contribution of parallel dielectric profile \((\varepsilon_{\parallel,\mathrm{coll}} - 1)\)

Type:

numpy.ndarray

results.eps_perp

Reduced inverse perpendicular dielectric profile \((\varepsilon^{-1}_\perp - 1)\)

Type:

numpy.ndarray

results.deps_perp

Uncertainty of inverse perpendicular dielectric profile

Type:

numpy.ndarray

results.eps_perp_self

Reduced self contribution of the inverse perpendicular dielectric profile \((\varepsilon^{-1}_{\perp,\mathrm{self}} - 1)\)

Type:

numpy.ndarray

results.eps_perp_coll

Reduced collective contribution of the inverse perpendicular dielectric profile \((\varepsilon^{-1}_{\perp,\mathrm{coll}} - 1)\)

Type:

numpy.ndarray

References

[1]

Alexander Schlaich, Ernst W. Knapp, and Roland R. Netz. Water Dielectric Effects in Planar Confinement. Phys. Rev. Lett., 117(4):048001, July 2016. doi:10.1103/PhysRevLett.117.048001.

[2]

Philip Loche, Cihan Ayaz, Amanuel Wolde-Kidan, Alexander Schlaich, and Roland R. Netz. Universal and Nonuniversal Aspects of Electrostatics in Aqueous Nanoconfinement. J. Phys. Chem. B, 124(21):4365–4371, May 2020. doi:10.1021/acs.jpcb.0c01967.

[3]

Douwe Jan Bonthuis, Stephan Gekle, and Roland R. Netz. Profile of the Static Permittivity Tensor of Water at Interfaces: Consequences for Capacitance, Hydration Interaction and Ion Adsorption. Langmuir, 28(20):7679–7694, 2012. doi:10.1021/la2051564.

[4]

Harry A. Stern and Scott E. Feller. Calculation of the dielectric permittivity profile for a nonuniform system: Application to a lipid bilayer simulation. The Journal of Chemical Physics, 118(7):3401–3412, February 2003. doi:10.1063/1.1537244.

save()

Save results.