DielectricSphere#

class maicos.modules.dielectricsphere.DielectricSphere(atomgroup, bin_width=0.1, temperature=300, output_prefix='eps_sph', refgroup=None, concfreq=0, rmin=0, rmax=None, unwrap=True)[source]#

Bases: SphereBase

Calculate 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.

Also, please read andcite [1].

Parameters:

  • atomgroup (AtomGroup) – A AtomGroup 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

  • 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) – temperature (K)

  • output_prefix (str) – Prefix for output_prefix 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

save()[source]#

Save result.