forked from lijiext/lammps
131 lines
5.8 KiB
HTML
131 lines
5.8 KiB
HTML
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>compute rdf command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>rdf = style name of this compute command
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<LI>Nbin = number of RDF bins
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<LI>itypeN = central atom type for Nth RDF histogram (see asterisk form below)
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<LI>jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all rdf 100
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fix 1 all rdf 100 1 1
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fix 1 all rdf 100 * 3
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fix 1 fluid rdf 500 1 1 1 2 2 1 2 2
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fix 1 fluid rdf 500 1*3 2 5 *10
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that calculates the radial distribution function
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(RDF), also called g(r), and the coordination number for a group of
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particles. Both are calculated in histogram form by binning pairwise
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distances into <I>Nbin</I> bins from 0.0 to the maximum force cutoff
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defined by the <A HREF = "pair_style.html">pair_style</A> command. The bins are of
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uniform size in radial distance. Thus a single bin encompasses a thin
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shell of distances in 3d and a thin ring of distances in 2d.
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</P>
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<P>The <I>itypeN</I> and <I>jtypeN</I> arguments are optional. These arguments
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must come in pairs. If no pairs are listed, then a single histogram
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is computed for g(r) between all atom types. If one or more pairs are
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listed, then a separate histogram is generated for each
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<I>itype</I>,<I>jtype</I> pair.
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</P>
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<P>The <I>itypeN</I> and <I>jtypeN</I> settings can be specified in one of two
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ways. An explicit numeric value can be used, as in the 4th example
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above. Or a wild-card asterisk can be used to specify a range of atom
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types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
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number of atom types, then an asterisk with no numeric values means
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all types from 1 to N. A leading asterisk means all types from 1 to n
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(inclusive). A trailing asterisk means all types from n to N
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(inclusive). A middle asterisk means all types from m to n
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(inclusive).
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</P>
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<P>If both <I>itypeN</I> and <I>jtypeN</I> are single values, as in the 4th example
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above, this means that a g(r) is computed where atoms of type <I>itypeN</I>
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are the central atom, and atoms of type <I>jtypeN</I> are the distribution
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atom. If either <I>itypeN</I> and <I>jtypeN</I> represent a range of values via
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the wild-card asterisk, as in the 5th example above, this means that a
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g(r) is computed where atoms of any of the range of types represented
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by <I>itypeN</I> are the central atom, and atoms of any of the range of
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types represented by <I>jtypeN</I> are the distribution atom.
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</P>
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<P>Pairwise distances are generated by looping over a pairwise neighbor
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list, just as they would be in a <A HREF = "pair_style.html">pair_style</A>
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computation. The distance between two atoms I and J is included in
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a specific histogram if the following criteria are met:
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</P>
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<UL><LI>atoms I,J are both in the specified fix group
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<LI>the distance between atoms I,J is less than the maximum force cutoff
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<LI>the type of the I atom matches itypeN (one or a range of types)
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<LI>the type of the J atom matches jtypeN (one or a range of types)
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<LI>the I,J interaction is included in the neighbor list
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</UL>
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<P>The last point is relevant for molecular systems with bonds, because
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if two atoms I,J are involved in 1-2, 1-3, 1-4 interactions within the
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molecular topology, their pairwise interaction may be turned off, and
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thus they will not appear in the neighbor list, and will not
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contribute to g(r). More specifically, this is true of pairs with a
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weighting factor of 0.0; pairs with a non-zero weighting factor are
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included. The weighting factors for 1-2, 1-3, and 1-4 pairwise
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interactions is set by the <A HREF = "special_bonds.html">special_bonds</A> command.
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</P>
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<P>It is OK if a particular pairwise distance is included in more than
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one individual histogram, due to the way the <I>itypeN</I> and <I>jtypeN</I>
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arguments are specified.
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</P>
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<P>The g(r) value for a bin is calculated from the histogram count by
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scaling it by the idealized number of how many counts there would be
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if atoms of type <I>jtypeN</I> were uniformly distributed. Thus it
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involves the count of <I>itypeN</I> atoms, the count of <I>jtypeN</I> atoms, the
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volume of the entire simulation box, and the volume of the thin bin
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shell in 3d (or the area of the thin bin ring in 2d).
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</P>
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<P>A coordination number coord(r) is also calculated, which is the sum of
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g(r) values for all bins up to and including the current bin.
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</P>
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<P><B>Output info:</B>
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</P>
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<P>This compute calculates a global array with the number of rows =
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<I>Nbins</I>, and the number of columns = 1 + 2*Npairs, where Npairs is the
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number of I,J pairings specified. The first column has the bin
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coordinate (center of the bin), Each successive set of 2 columns has
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the g(r) and coord(r) values for a specific set of <I>itypeN</I> versus
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<I>jtypeN</I> interactions, as described above. These values can be used
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by any command that uses a global values from a compute as input. See
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<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
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output options.
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</P>
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<P>The array values calculated by this compute are all "intensive", since
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they are normalized, meaning they are independent of the number of
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atoms in the simulation.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>The RDF is not computed for distances longer than the force cutoff,
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since processors (in parallel) don't know about atom coordinates for
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atoms further away than that distance. If you want an RDF for larger
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distances, you'll need to post-process a dump file.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_ave_histo.html">fix ave/histo</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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