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diff --git a/java/docs/feature/RadialDistributionFunction.html b/java/docs/feature/RadialDistributionFunction.html deleted file mode 100644 index 09d9600..0000000 --- a/java/docs/feature/RadialDistributionFunction.html +++ /dev/null @@ -1,230 +0,0 @@ -<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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