idZddlZddlmZmZddlmZddlm Z m Z ddl m Z e j e ddd d [ Gd d eZdS)z Dielectric --- :mod:`MDAnalysis.analysis.dielectric` =========================================================== :Authors: Mattia Felice Palermo, Philip Loche :Year: 2022 :Copyright: Lesser GNU Public License v2.1+ N) constantsconvert) AnalysisBase)dueDoi) NoDataErrorz10.1080/00268978300102721zDielectric analysiszMDAnalysis.analysis.dielectricT) descriptionpath cite_modulec6eZdZdZdfd ZdZdZdZxZS) DielectricConstantu Computes the average dipole moment .. math:: \boldsymbol M = \sum_i q_i \boldsymbol r_i where :math:`q_i` is the charge and :math:`\boldsymbol r_i` the position of atom :math:`i` in the given :class:`MDAnalysis.core.groups.AtomGroup`. Also, the static dielectric constant .. math:: \varepsilon = 1 + \frac{\langle M^2 \rangle - \langle M \rangle^2} {3 \varepsilon_ 0 V k_B T} is calculated for a system in tin foil boundary conditions, which is the usual case if electrostatics are handled with a Ewald summation technique. See [Neumann1983]_ for details on the derivation. .. warning:: Applying this class requires that no free charges, such as ions or charged fragments, are present in the simulation. Parameters ---------- atomgroup : MDAnalysis.core.groups.AtomGroup Atomgroup on which the analysis is executed temperature : float Temperature (Kelvin) at which the system has been simulated make_whole : bool Make molecules whole; If the input already contains whole molecules this can be disabled to gain speedup verbose : bool Show detailed progress of the calculation Attributes ---------- results.M : numpy.ndarray Directional dependant dipole moment :math:`\langle \boldsymbol M \rangle` in :math:`eÅ`. results.M2 : numpy.ndarray Directional dependant squared dipole moment :math:`\langle \boldsymbol M^2 \rangle` in :math:`(eÅ)^2` results.fluct : float Directional dependant dipole moment fluctuation :math:`\langle \boldsymbol M^2 \rangle - \langle \boldsymbol M \rangle^2` in :math:`(eÅ)^2` results.eps : numpy.ndarray Directional dependant static dielectric constant results.eps_mean : float Static dielectric constant Example ------- Create a :class:`DielectricConstant` instance by supplying an :class:`~MDAnalysis.core.groups.AtomGroup`, then use the :meth:`run` method:: import MDAnalysis as mda from MDAnalysis.analysis.dielectric import DielectricConstant from MDAnalysisTests.datafiles import PSF_TRICLINIC, DCD_TRICLINIC # Load a pure water system universe = mda.Universe(PSF_TRICLINIC, DCD_TRICLINIC) diel = DielectricConstant(universe.atoms) diel.run() print(diel.results) The static dielectric constant of the provided atomgroup is saved within the :class:`~MDAnalysis.analysis.base.Results` attribute. .. versionadded:: 2.1.0 ,Tc tt|j|jjfi|||_||_||_dSN)superr __init__universe trajectory atomgroup temperature make_whole)selfrrrkwargs __class__s h/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/analysis/dielectric.pyrzDielectricConstant.__init__sW0 $''0   )  -3   #&$ct|jdstdtj|jdddst dd |_tjd |j _ tjd |j _ tjd |j _ tjd |j _ d |j _dS) Nchargesz#No charges defined given atomgroup. fragments)compoundggh㈵>)atolzPAnalysis for non-neutral systems or systems with free charges are not available.r)hasattrrrnpallclose total_chargeNotImplementedErrorvolumezerosresultsMM2fluctepseps_meanrs r_preparezDielectricConstant._preparest~y11 ECDD D{ N ' ' ' = =s    &   ! (1++ Xa[[ 8A;;  ! rcD|jr|j|xj|jjjjjz c_tj|jj |jj }|j xj |z c_ |j xj ||zz c_ dSr)rrunwrapr(rrtsr$dotr positionsr*r+r,)rr+s r _single_framez DielectricConstant._single_frames ? $ N ! ! # # # t~.9<CC F4>)4>+C D D ! 1q5 rc>|jxj|jzc_|jxj|jzc_|xj|jzc_|jj|jj|jjzz |j_|jjt tddd|jz|jztdzz |j_ |jj |j_ |jxj dz c_ |jxj dz c_ dS)NBoltzmann_constantzkJ/moleVelectric_constant) r*r+n_framesr,r(r-rrrr.meanr/r0s r _concludezDielectricConstant._concludes $-' 4=( t}$ !\_t|~ /NN <- I23Xt D D k +, -  !% 0 5 5 7 7  A "r)rT) __name__ __module__ __qualname____doc__rr1r7r? __classcell__)rs@rr r 1swKKZ%%%%%%"""(!!!#######rr )rCnumpyr$MDAnalysis.unitsrrMDAnalysis.analysis.baserMDAnalysis.duerrMDAnalysis.exceptionsrciter rrrLs0////////111111########------C#$$% )  E#E#E#E#E#E#E#E#E#E#r