forked from lijiext/lammps
155 lines
7.2 KiB
HTML
155 lines
7.2 KiB
HTML
<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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<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>compute 1 all rdf 100
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compute 1 all rdf 100 1 1
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compute 1 all rdf 100 * 3
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compute 1 fluid rdf 500 1 1 1 2 2 1 2 2
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compute 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>IMPORTANT NOTE: If you have a bonded system, then the settings of
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<A HREF = "special_bonds.html">special_bonds</A> command can remove pairwise
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interactions between atoms in the same bond, angle, or dihedral. This
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is the default setting for the <A HREF = "special_bonds.html">special_bonds</A>
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command, and means those pairwise interactions do not appear in the
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neighbor list. Because this fix uses the neighbor list, it also means
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those pairs will not be included in the RDF. One way to get around
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this, is to write a dump file, and use the <A HREF = "rerun.html">rerun</A> command
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to compute the RDF for snapshots in the dump file. The rerun script
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can use a <A HREF = "special_bonds.html">special_bonds</A> command that includes all
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pairs in the neighbor list.
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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 a
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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 compute 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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</UL>
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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 bin's thin
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shell in 3d (or the area of the bin's thin ring in 2d).
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</P>
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<P>A coordination number coord(r) is also calculated, which is the number
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of atoms of type <I>jtypeN</I> within the current bin or closer, averaged
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over atoms of type <I>itypeN</I>. This is calculated as the area- or
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volume-weighted sum of g(r) values over all bins up to and including
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the current bin, multiplied by the global average volume density of
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atoms of type jtypeN.
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</P>
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<P>The simplest way to output the results of the compute rdf calculation
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to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A> command, for
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example:
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</P>
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<PRE>compute myRDF all rdf 50
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fix 1 all ave/time 100 1 100 c_myRDF file tmp.rdf mode vector
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</PRE>
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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#howto_15">Section_howto 15</A> for an overview of
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LAMMPS output options.
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</P>
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<P>The array values calculated by this compute are all "intensive".
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</P>
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<P>The first column of array values will be in distance
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<A HREF = "units.html">units</A>. The g(r) columns of array values are normalized
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numbers >= 0.0. The coordination number columns of array values are
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also numbers >= 0.0.
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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 can use the <A HREF = "rerun.html">rerun</A> command to post-process
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a dump file. The definition of g(r) used by LAMMPS is only appropriate
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for characterizing atoms that are uniformly distributed throughout the
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simulation cell. In such cases, the coordination number is still
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correct and meaningful. As an example, if a large simulation cell
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contains only one atom of type <I>itypeN</I> and one of <I>jtypeN</I>, then g(r)
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will register an arbitrarily large spike at whatever distance they
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happen to be at, and zero everywhere else. coord(r) will show a step
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change from zero to one at the location of the spike in g(r).
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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_time.html">fix ave/time</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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