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diff --git a/java/docs/feature/RadialDistributionFunction.html b/java/docs/feature/RadialDistributionFunction.html new file mode 100644 index 0000000..09d9600 --- /dev/null +++ b/java/docs/feature/RadialDistributionFunction.html @@ -0,0 +1,230 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.RADIALDISTRIBUTIONFUNCTION" +></A +>Radial distribution function (RDF)</H2 +><P +>The radial distribution function (RDF) [<A +HREF="bibliography.html#MSG99" +>msg99</A +>,<A +HREF="bibliography.html#WFZ04B" +>wfz04b</A +>] can be interpreted as the probability distribution of finding an atom in a spherical volume of +radius <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>r</B +></SPAN +>. +<DIV +CLASS="EQUATION" +><A +NAME="AEN14" +></A +><P +><B +>Equation 1. Radial distribution function</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/rdf.gif" +ALIGN="CENTER"></P +></DIV +></DIV +> +where <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>r<SUB +>ij</SUB +></B +></SPAN +> is the geometrical distance between the atoms +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +> and atom <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>j</B +></SPAN +>, <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>w<SUB +>i</SUB +></B +></SPAN +> +and <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>w<SUB +>j</SUB +></B +></SPAN +> are the atom properties of the atoms <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +> and +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>j</B +></SPAN +>. <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>B</B +></SPAN +> is the smoothing parameter +(fuzziness of the distance <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>r<SUB +>ij</SUB +></B +></SPAN +>) for the interatomic distance and +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>f</B +></SPAN +> the scaling factor.</P +><P +>If <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>B</B +></SPAN +> aims to infinity the RDF code approximates to the autocorrelation function () and the fuzziness +of the distance <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>r<SUB +>ij</SUB +></B +></SPAN +> vanishes. So the RDF code can be treated as a generalized +autocorrelation function.</P +><P +>The RDF user parameters can be defined in the <TT +CLASS="FILENAME" +>joelib.properties</TT +>-file, otherwise the default parameters will be used:</P +><PRE +CLASS="PROGRAMLISTING" +>jcompchem.joelib.desc.types.RadialDistributionFunction.minSphericalVolume = 0.2 +joelib.desc.types.RadialDistributionFunction.maxSphericalVolume = 10.0 +joelib.desc.types.RadialDistributionFunction.sphericalVolumeResolution = 0.2 +joelib.desc.types.RadialDistributionFunction.smoothingFactor = 25</PRE +><P +>Optional the RDF can be calculated with protonated molecules, but you must be sure that all available atom +properties are calculated with hydrogens also. Because this is not the standard, this option should be only used by developers.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +><A +HREF="bibliography.html" +ACCESSKEY="N" +>Next</A +></TD +></TR +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
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