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< title > compute rdf command — LAMMPS documentation< / title >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_start.html" > 2. Getting Started< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_commands.html" > 3. Commands< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_accelerate.html" > 5. Accelerating LAMMPS performance< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_perf.html" > 8. Performance & scalability< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_tools.html" > 9. Additional tools< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_python.html" > 11. Python interface to LAMMPS< / a > < / li >
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< li > compute rdf command< / li >
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< a href = "http://lammps.sandia.gov" > Website< / a >
< a href = "Section_commands.html#comm" > Commands< / a >
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< div class = "section" id = "compute-rdf-command" >
< span id = "index-0" > < / span > < h1 > compute rdf command< a class = "headerlink" href = "#compute-rdf-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ...
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command< / li >
< li > rdf = style name of this compute command< / li >
< li > Nbin = number of RDF bins< / li >
< li > itypeN = central atom type for Nth RDF histogram (see asterisk form below)< / li >
< li > jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below)< / li >
< / ul >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute 1 all rdf 100
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compute 1 all rdf 100 1 1
compute 1 all rdf 100 * 3
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
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< 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
particles. Both are calculated in histogram form by binning pairwise
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distances into < em > Nbin< / em > bins from 0.0 to the maximum force cutoff
defined by the < a class = "reference internal" href = "pair_style.html" > < em > pair_style< / em > < / 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.< / p >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
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< p class = "last" > If you have a bonded system, then the settings of
< a class = "reference internal" href = "special_bonds.html" > < em > special_bonds< / em > < / 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 class = "reference internal" href = "special_bonds.html" > < em > special_bonds< / em > < / a >
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command, and means those pairwise interactions do not appear in the
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. This does not apply when
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using long-range coulomb (< em > coul/long< / em > , < em > coul/msm< / em > , < em > coul/wolf< / em > or
similar. One way to get around this would be to set special_bond
scaling factors to very tiny numbers that are not exactly zero
(e.g. 1.0e-50). Another workaround is to write a dump file, and use
the < a class = "reference internal" href = "rerun.html" > < em > rerun< / em > < / a > command to compute the RDF for snapshots in the
dump file. The rerun script can use a
< a class = "reference internal" href = "special_bonds.html" > < em > special_bonds< / em > < / a > command that includes all pairs in
the neighbor list.< / p >
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< / div >
< p > The < em > itypeN< / em > and < em > jtypeN< / em > arguments are optional. These arguments
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must come in pairs. If no pairs are listed, then a single histogram
is computed for g(r) between all atom types. If one or more pairs are
listed, then a separate histogram is generated for each
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< em > itype< / em > ,*jtype* pair.< / p >
< p > The < em > itypeN< / em > and < em > jtypeN< / em > 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
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 “ < em > n” or “ n< / em > ” or “ m*n” . If N = the
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number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
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(inclusive).< / p >
< p > If both < em > itypeN< / em > and < em > jtypeN< / em > are single values, as in the 4th example
above, this means that a g(r) is computed where atoms of type < em > itypeN< / em >
are the central atom, and atoms of type < em > jtypeN< / em > are the distribution
atom. If either < em > itypeN< / em > and < em > jtypeN< / em > represent a range of values via
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the wild-card asterisk, as in the 5th example above, this means that a
g(r) is computed where atoms of any of the range of types represented
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by < em > itypeN< / em > are the central atom, and atoms of any of the range of
types represented by < em > jtypeN< / em > are the distribution atom.< / p >
< p > Pairwise distances are generated by looping over a pairwise neighbor
list, just as they would be in a < a class = "reference internal" href = "pair_style.html" > < em > pair_style< / em > < / 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:< / p >
< ul class = "simple" >
< li > atoms I,J are both in the specified compute group< / li >
< li > the distance between atoms I,J is less than the maximum force cutoff< / li >
< li > the type of the I atom matches itypeN (one or a range of types)< / li >
< li > the type of the J atom matches jtypeN (one or a range of types)< / li >
< / ul >
< p > It is OK if a particular pairwise distance is included in more than
one individual histogram, due to the way the < em > itypeN< / em > and < em > jtypeN< / em >
arguments are specified.< / p >
< 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 < em > jtypeN< / em > were uniformly distributed. Thus it
involves the count of < em > itypeN< / em > atoms, the count of < em > jtypeN< / em > atoms, the
volume of the entire simulation box, and the volume of the bin’ s thin
shell in 3d (or the area of the bin’ s thin ring in 2d).< / p >
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< p > A coordination number coord(r) is also calculated, which is the number
of atoms of type < em > jtypeN< / em > within the current bin or closer, averaged
over atoms of type < em > itypeN< / em > . 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
the current bin, multiplied by the global average volume density of
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atoms of type jtypeN.< / p >
< p > The simplest way to output the results of the compute rdf calculation
to a file is to use the < a class = "reference internal" href = "fix_ave_time.html" > < em > fix ave/time< / em > < / a > command, for
example:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute myRDF all rdf 50
fix 1 all ave/time 100 1 100 c_myRDF file tmp.rdf mode vector
< / pre > < / div >
< / div >
< p > < strong > Output info:< / strong > < / p >
< p > This compute calculates a global array with the number of rows =
< em > Nbins< / em > , 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
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 < em > itypeN< / em > versus
< em > jtypeN< / em > 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 class = "reference internal" href = "Section_howto.html#howto-15" > < span > Section_howto 15< / span > < / a > for an overview of
LAMMPS output options.< / p >
< p > The array values calculated by this compute are all “ intensive” .< / p >
< p > The first column of array values will be in distance
< a class = "reference internal" href = "units.html" > < em > units< / em > < / a > . The g(r) columns of array values are normalized
numbers > = 0.0. The coordination number columns of array values are
also numbers > = 0.0.< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The RDF is not computed for distances longer than the force cutoff,
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 class = "reference internal" href = "rerun.html" > < em > rerun< / em > < / a > command to post-process
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a dump file and set the cutoff for the potential to be longer in the
rerun script. Note that in the rerun context, the force cutoff is
arbitrary, since you aren’ t running dynamics and thus are not changing
your model. The definition of g(r) used by LAMMPS is only appropriate
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for characterizing atoms that are uniformly distributed throughout the
simulation cell. In such cases, the coordination number is still
correct and meaningful. As an example, if a large simulation cell
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contains only one atom of type < em > itypeN< / em > and one of < em > jtypeN< / em > , 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).< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "fix_ave_time.html" > < em > fix ave/time< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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