i>dZddlmZddlZddlZddlmZmZddl m Z ddl m Z ddl mZGddeZGd d eZdS) aK Linear Density --- :mod:`MDAnalysis.analysis.lineardensity` =========================================================== A tool to compute mass and charge density profiles along the three cartesian axes [xyz] of the simulation cell. Works only for orthorombic, fixed volume cells (thus for simulations in canonical NVT ensemble). N) AnalysisBaseResults) constants) deprecate) ResultsGroupc@eZdZdZdddddZdZfdZfd ZxZS) rzFrom version 3.0.0 onwards, some entries in Results will be renamed. See the docstring for LinearDensity for details. The Results class is defined here to implement deprecation warnings for the user. mass_densitymass_density_stddevcharge_densitycharge_density_stddev)pospos_stdcharchar_stdc^tjd|d|j|dtdS)N`zB` is deprecated and will be removed in version 3.0.0. Please use `z ` instead.)warningswarn_deprecation_dictDeprecationWarning)selfkeys k/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/analysis/lineardensity.py_deprecation_warningzResults._deprecation_warning7sT  C C C1#6 C C C      c||jvrH||tt||j|Stt||SN)rkeysrsuperr __getitem__)rr __class__s rr zResults.__getitem__>s~ $(--// / /  % %c * * *$''33&s+ Wd##//444rc||jvr"|||j|}tt||Sr)rrrrr __getattr__)rattrr!s rr#zResults.__getattr__Fs\ 4)..00 0 0  % %d + + +)$/DWd##//555r) __name__ __module__ __qualname____doc__rrr r# __classcell__r!s@rrr+s<< ( +    55555666666666rrceZdZdZdZedZdfd ZedZ dZ d Z d Z e d d d dZxZS) LinearDensityaLinear density profile Parameters ---------- select : AtomGroup any atomgroup grouping : str {'atoms', 'residues', 'segments', 'fragments'} Density profiles will be computed either on the atom positions (in the case of 'atoms') or on the center of mass of the specified grouping unit ('residues', 'segments', or 'fragments'). binsize : float Bin width in Angstrom used to build linear density histograms. Defines the resolution of the resulting density profile (smaller --> higher resolution) verbose : bool, optional Show detailed progress of the calculation if set to ``True`` Attributes ---------- results.x.dim : int index of the [xyz] axes results.x.mass_density : numpy.ndarray mass density in :math:`g \cdot cm^{-3}` in [xyz] direction results.x.mass_density_stddev : numpy.ndarray standard deviation of the mass density in [xyz] direction results.x.charge_density : numpy.ndarray charge density in :math:`\mathrm{e} \cdot mol \cdot cm^{-3}` in [xyz] direction results.x.charge_density_stddev : numpy.ndarray standard deviation of the charge density in [xyz] direction results.x.pos: numpy.ndarray Alias to the :attr:`results.x.mass_density` attribute. .. deprecated:: 2.2.0 Will be removed in MDAnalysis 3.0.0. Please use :attr:`results.x.mass_density` instead. results.x.pos_std: numpy.ndarray Alias to the :attr:`results.x.mass_density_stddev` attribute. .. deprecated:: 2.2.0 Will be removed in MDAnalysis 3.0.0. Please use :attr:`results.x.mass_density_stddev` instead. results.x.char: numpy.ndarray Alias to the :attr:`results.x.charge_density` attribute. .. deprecated:: 2.2.0 Will be removed in MDAnalysis 3.0.0. Please use :attr:`results.x.charge_density` instead. results.x.char_std: numpy.ndarray Alias to the :attr:`results.x.charge_density_stddev` attribute. .. deprecated:: 2.2.0 Will be removed in MDAnalysis 3.0.0. Please use :attr:`results.x.charge_density_stddev` instead. results.x.slice_volume : float volume of bin in [xyz] direction results.x.hist_bin_edges : numpy.ndarray edges of histogram bins for mass/charge densities, useful for, e.g., plotting of histogram data. Note: These density units are likely to be changed in the future. Example ------- First create a :class:`LinearDensity` object by supplying a selection, then use the :meth:`run` method. Finally access the results stored in results, i.e. the mass density in the x direction. .. code-block:: python ldens = LinearDensity(selection) ldens.run() print(ldens.results.x.mass_density) Alternatively, other types of grouping can be selected using the ``grouping`` keyword. For example to calculate the density based on a grouping of the :class:`~MDAnalysis.core.groups.ResidueGroup` of the input :class:`~MDAnalysis.core.groups.AtomGroup`. .. code-block:: python ldens = LinearDensity(selection, grouping='residues', binsize=1.0) ldens.run() .. versionadded:: 0.14.0 .. versionchanged:: 1.0.0 Support for the ``start``, ``stop``, and ``step`` keywords has been removed. These should instead be passed to :meth:`LinearDensity.run`. The ``save()`` method was also removed, you can use ``np.savetxt()`` or ``np.save()`` on the :attr:`LinearDensity.results` dictionary contents instead. .. versionchanged:: 1.0.0 Changed `selection` keyword to `select` .. versionchanged:: 2.0.0 Results are now instances of :class:`~MDAnalysis.core.analysis.Results` allowing access via key and attribute. .. versionchanged:: 2.2.0 * Fixed a bug that caused LinearDensity to fail if grouping="residues" or grouping="segments" were set. * Residues, segments, and fragments will be analysed based on their centre of mass, not centre of geometry as previously stated. * LinearDensity now works with updating atom groups. * Added new result container :attr:`results.x.hist_bin_edges`. It contains the bin edges of the histrogram bins for calculated densities and can be used for easier plotting of histogram data. .. versionchanged:: 2.10.0 * Introduced :meth:`get_supported_backends` allowing for parallel execution on :mod:`multiprocessing` and :mod:`dask` backends. * Removed undocumented and unused attribute :attr:`totalmass`. .. deprecated:: 2.2.0 The `results` dictionary has been changed and the attributes :attr:`results.x.pos`, :attr:`results.x.pos_std`, :attr:`results.x.char` and :attr:`results.x.char_std` are now deprecated. They will be removed in 3.0.0. Please use :attr:`results.x.mass_density`, :attr:`results.x.mass_density_stddev`, :attr:`results.x.charge_density`, and :attr:`results.x.charge_density_stddev` instead. TcdS)N)serialmultiprocessingdask)clss rget_supported_backendsz$LinearDensity.get_supported_backendss   ratoms?c ptt|j|jjfi||g|_|j|_||_||_td|j d<td|j d<td|j d<|jj dd|_ tj |j |_|j |jzt }||_|j|z }gd |_|j D]\}|j |d }|||j |d <|jD])} tj|j|j || <*]|jd kr0|jdj|_|jdj|_dS|jd vrX|jd|j|_|jd|j|_dSt3|jd)Nr)dimxyzr r r r r7 slice_volumer4residuessegments fragmentscompound# is not a valid value for grouping.)rr,__init__universe trajectory_ags _universebinsizegroupingrresults dimensionsnpprodvolumeastypeintmaxnbinsrzerosmassescharges total_mass total_chargeAttributeError) rselectrMrLkwargsbins slices_volr7idxrr!s rrGzLinearDensity.__init__s'+mT""+ O &  *0   H  ! $NNN S#NNN S#NNN S.3BQB7gdo.. 4</77<<XXZZ [4'     < > >C,s#E*C0:3DL n -y > >)+$*)=)= S!#&& > =G # #)A,-DK9Q</DLLL ]C C C)A,114=1IIDK9Q<44dm4LLDLLL!=EEE rc vtjd|Dd}tjd|Dd}tjd|Dd}tjd|Dd}t|dd|dd|dd |||| S) Ncg|] }|d S)r r1.0entrys r z4LinearDensity._custom_aggregator..s 8 8 8uU> " 8 8 8rr)axiscg|] }|d S)r r1rds rrgz4LinearDensity._custom_aggregator..s ? ? ?eU( ) ? ? ?rcg|] }|d S)r r1rds rrgz4LinearDensity._custom_aggregator..s : : :U# $ : : :rcg|] }|d S)r r1rds rrgz4LinearDensity._custom_aggregator.. s A A AU* + A A Arr7r?hist_bin_edges)r7r?rlr r r r )rPsumr)rNr r r r s r_custom_aggregatorz LinearDensity._custom_aggregatorsv 8 8 8 8 8q   !f ? ?w ? ? ?a    : :' : : :   !# A A A A A! ! !  5! 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