Dielectric constant modules¶
Epsilon bulk¶
Description¶
Compute dipole moment fluctuations and static dielectric constant.
Inputs
- param outfreq (float)
Number of frames after which the output is updated.
- param output (str)
Output filename.
- param temperature (float)
temperature (K)
- param bpbc (bool)
do not make broken molecules whole again (only works if molecule is smaller than shortest
box vector
Outputs
- returns (dict)
- M: Directional dependant dipole moment
\(\langle \boldsymbol M \rangle\) in \(eÅ\).
- M2: Directional dependant squared dipole moment
\(\langle \boldsymbol M^2 \rangle\) in \((eÅ)^2\)
- fluct: Directional dependant dipole moment fluctuation
\(\langle \boldsymbol M^2 \rangle - \langle \boldsymbol M \rangle^2\) in \((eÅ)^2\)
eps: Directional dependant static dielectric constant
eps_mean: Static dielectric constant
Epsilon planar¶
Description¶
Calculate planar dielectric profiles. See Schlaich, et al., Phys. Rev. Lett., vol. 117 (2016) for details
Inputs :param output_prefix (str): Prefix for output files :param zmin (float): minimal coordinate for evaluation (nm) :param zmax (float): maximal coordinate for evaluation (nm) :param temperature (float): temperature (K) :param outfreq (int): Default number of frames after which output files are refreshed. :param b2d (bool): Use 2d slab geometry :param vac (bool): Use vacuum boundary conditions instead of metallic (2D only!). :param bsym (bool): symmetrize the profiles :param bpbc (bool): Do not make broken molecules whole again (only works if
molecule is smaller than shortest box vector
Outputs :param dim (int): Dimension for binning (0=X, 1=Y, 2=Z) :param binwidth (float): binwidth (nanometer) :param comgroup (str): Perform the binning relative to the center of mass of the selected group.With comgroup the center option is also used. :param center (bool): Perform the binning relative to the center of the (changing) box.
- returns (dict)
z: Bin positions
eps_par: Parallel dielectric profile (ε_∥ - 1)
deps_par: Error of parallel dielectric profile
eps_par_self: Self contribution of parallel dielectric profile
eps_par_coll: Collective contribution of parallel dielectric profile
eps_perp: Inverse perpendicular dielectric profile (ε^{-1}_⟂ - 1)
deps_perp: Error of inverse perpendicular dielectric profile
eps_par_self: Self contribution of Inverse perpendicular dielectric profile
eps_perp_coll: 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.
Inputs
- param output_prefix (str)
Prefix for output_prefix files
- param geometry (str)
A structure file without water from which com is calculated.
- param radius (float)
Radius of the cylinder (nm)
- param binwidth (float)
Bindiwdth the binwidth (nm)
- param variable_dr (bool)
Use a variable binwidth, where the volume is kept fixed.
- param length (float)
Length of the cylinder (nm)
- param outfreq (int)
Default number of frames after which output files are refreshed.
- param temperature (float)
temperature (K)
- param single (bool)
“1D” line of watermolecules
- param bpbc (bool)
Do not make broken molecules whole again (only works if molecule is smaller than shortest box vector
Outputs
- returns (dict)
r: Bin positions
eps_ax: Parallel dielectric profile (ε_∥)
deps_ax: Error of parallel dielectric profile
eps_rad: Inverse perpendicular dielectric profile (ε^{-1}_⟂)
deps_rad: Error of inverse perpendicular dielectric profile
Dielectric spectrum¶
Description¶
Computes 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 epsilon_0) FT{theta(t) <P(0) dP(t)/dt>}. 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.
Inputs
- param recalc (bool)
Forces to recalculate the polarization, regardless if it is already present.
- param temperature (float)
Reference temperature.
- param output_prefix (str)
Prefix for the output files.
- param segs (int)
Sets the number of segments the trajectory is broken into.
- param df (float)
The desired frequency spacing in THz. This determines the minimum frequency about which there is data. Overrides -segs option.
- param noplots (bool)
Prevents plots from being generated.
- param plotformat (str)
Allows the user to choose the format of generated plots (choose from ‘pdf’, ‘png’, ‘jpg’, ‘eps’)
- param ymin (float)
Manually sets the minimum lower bound for the log-log plot.
- param bins (int)
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.
- param binafter (int)
The number of low-frequency data points that are left unbinned.
- param nobin (bool)
Prevents the data from being binned altogether. This can result in very large plot files and errors.
Outputs :returns (dict): TODO