Dielectric constant modules#
Epsilon bulk#
Description#
Compute dipole moment fluctuations and static dielectric constant.
Parameters#
- atomgroupAtomGroup
Atomgroup on which the analysis is executed
- make_wholebool
Make molecules whole; If the input already contains whole molecules this can be disabled to gain speedup
- temperaturefloat
temperature (K)
- outputstr
Output filename.
- concfreqint
Default number of frames after which results are calculated and files refreshed. If 0 results are only calculated at the end of the analysis and not saved by default.
- verbosebool
Turn on more logging and debugging
Attributes#
- results.Mnumpy.ndarray
Directional dependant dipole moment :math:langle boldsymbol M rangle` in \(eÅ\).
- results.M2numpy.ndarray
Directional dependant squared dipole moment \(\langle \boldsymbol M^2 \rangle\) in \((eÅ)^2\)
- results.fluctfloat
Directional dependant dipole moment fluctuation \(\langle \boldsymbol M^2 \rangle - \langle \boldsymbol M \rangle^2\) in \((eÅ)^2\)
- results.epsnumpy.ndarray
Directional dependant static dielectric constant
- results.eps_meanfloat
Static dielectric constant
Epsilon planar#
Description#
Calculate planar dielectric profiles.
See Schlaich, et al., Phys. Rev. Lett., vol. 117 (2016) for details
Parameters#
- atomgroupslist[AtomGroup]
a list of
AtomGroupfor which the dielectric profiles are calculated- dimint
Dimension for binning (x=0, y=1, z=2)
- binwidthfloat
binwidth (nanometer)
- comgroupAtomGroup
Perform the binning relative to the center of mass of the selected group.
- centerbool
Perform the binning relative to the center of the (changing) box.
- zminfloat
minimal coordinate for evaluation (nm)
- zmaxfloat
maximal coordinate for evaluation (nm). If None the whole box is taken into account.
- xybool
Use 2D slab geometry
- vacbool
Use vacuum boundary conditions instead of metallic (2D only!).
- symbool
symmetrize the profiles
- make_wholebool
Make molecules whole; If the input already contains whole molecules this can be disabled to gain speedup
- temperaturefloat
temperature (K)
- output_prefixstr
Prefix for output files
- concfreqint
Default number of frames after which results are calculated and files refreshed. If 0 results are only calculated at the end of the analysis and not saved by default.
- verbosebool
Turn on more logging and debugging
Attributes#
- results.zlist
bins
- results.dens_meannp.ndarray
eps_par: Parallel dielectric profile (ε_∥ - 1)
- results.deps_parnp.ndarray
Error of parallel dielectric profile
- results.eps_par_selfnp.ndarray
Self contribution of parallel dielectric profile
- results.eps_par_collnp.ndarray
Collective contribution of parallel dielectric profile
- results.eps_perpnp.ndarray
Inverse perpendicular dielectric profile (ε^{-1}_⟂ - 1)
- results.deps_perpnp.ndarray
Error of inverse perpendicular dielectric profile
- results.eps_par_selfnp.ndarray
Self contribution of Inverse perpendicular dielectric profile
- results.eps_perp_collnp.ndarray
Collective contribution of Inverse perpendicular dielectric profile
Epsilon cylinder#
Description#
Calculate cylindrical dielectric profiles.
Components are calculated along the axial (z) and radial (along xy) direction at the system’s center of mass.
Parameters#
- atomgroupAtomGroup
AtomGroupfor which the dielectric profiles are calculated- geometrystr
A structure file without water from which com is calculated.
- radiusfloat
Radius of the cylinder (nm)
- binwidthfloat
Bindiwdth the binwidth (nm)
- variable_drbool
Use a variable binwidth, where the volume is kept fixed.
- lengthfloat
Length of the cylinder (nm)
- make_wholebool
Make molecules whole; If the input already contains whole molecules this can be disabled to gain speedup
- temperaturefloat
temperature (K)
- singlebool
“1D” line of watermolecules
- output_prefixstr
Prefix for output_prefix files
- concfreqint
Default number of frames after which results are calculated and files refreshed. If 0 results are only calculated at the end of the analysis and not saved by default.
- verbosebool
Turn on more logging and debugging
Attributes#
- results.rnp.ndarray
bins
- results.eps_axnp.ndarray
Parallel dielectric profile (ε_∥)
- results.deps_axnp.ndarray
Error of parallel dielectric profile
- results.eps_radnp.ndarray
Inverse perpendicular dielectric profile (ε^{-1}_⟂)
- results.deps_radnp.ndarray
Error of inverse perpendicular dielectric profile
Dielectric spectrum#
Description#
Compute the linear dielectric spectrum.
This module, given molecular dynamics trajectory data, produces a .txt file containing the complex dielectric function as a function of the (linear, not radial - i.e. \(\nu\) or \(f\), rather than \(\omega\)) frequency, along with the associated standard deviations. The algorithm is based on the Fluctuation Dissipation Relation (FDR): \(\chi(f) = -1/(3 V k_B T \varepsilon_0) FT[\theta(t) \langle P(0) dP(t)/dt\rangle]\). By default, the polarization trajectory, time series array and the average system volume are saved in the working directory, and the data are reloaded from these files if they are present. Lin-log and log-log plots of the susceptibility are also produced by default.
Parameters#
- atomgroupAtomGroup
Atomgroup on which the analysis is executed
- make_wholebool
Make molecules whole; If the input already contains whole molecules this can be disabled to gain speedup
- temperaturefloat
Reference temperature.
- output_prefixstr
Prefix for the output files.
- segsint
Sets the number of segments the trajectory is broken into.
- dffloat
The desired frequency spacing in THz. This determines the minimum frequency about which there is data. Overrides segs option.
- noplotsbool
Prevents plots from being generated.
- plotformat str
Allows the user to choose the format of generated plots (choose from ‘pdf’, ‘png’, ‘jpg’, ‘eps’)
- yminfloat
Manually sets the minimum lower bound for the log-log plot.
- binsint
Determines the number of bins used for data averaging; (this parameter sets the upper limit). The data are by default binned logarithmically. This helps to reduce noise, particularly in the high-frequency domain, and also prevents plot files from being too large.
- binafterint
The number of low-frequency data points that are left unbinned.
- nobinbool
Prevents the data from being binned altogether. This can result in very large plot files and errors.
- verbosebool
Turn on more logging and debugging
Attributes#
results