forked from lijiext/lammps
171 lines
7.2 KiB
Plaintext
171 lines
7.2 KiB
Plaintext
.. index:: compute rdf
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compute rdf command
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===================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* rdf = style name of this compute command
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* Nbin = number of RDF bins
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* itypeN = central atom type for Nth RDF histogram (see asterisk form below)
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* jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below)
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Examples
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""""""""
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.. parsed-literal::
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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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Description
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"""""""""""
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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 *Nbin* bins from 0.0 to the maximum force cutoff
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defined by the :doc:`pair_style <pair_style>` 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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.. note::
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If you have a bonded system, then the settings of
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:doc:`special_bonds <special_bonds>` 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 :doc:`special_bonds <special_bonds>`
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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. This does not apply when
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using long-range coulomb (\ *coul/long*\ , *coul/msm*\ , *coul/wolf* or
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similar. One way to get around this would be to set special_bond
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scaling factors to very tiny numbers that are not exactly zero
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(e.g. 1.0e-50). Another workaround is to write a dump file, and use
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the :doc:`rerun <rerun>` command to compute the RDF for snapshots in the
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dump file. The rerun script can use a
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:doc:`special_bonds <special_bonds>` command that includes all pairs in
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the neighbor list.
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The *itypeN* and *jtypeN* 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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*itype*\ ,\ *jtype* pair.
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The *itypeN* and *jtypeN* 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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If both *itypeN* and *jtypeN* 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 *itypeN*
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are the central atom, and atoms of type *jtypeN* are the distribution
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atom. If either *itypeN* and *jtypeN* 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 *itypeN* are the central atom, and atoms of any of the range of
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types represented by *jtypeN* are the distribution atom.
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Pairwise distances are generated by looping over a pairwise neighbor
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list, just as they would be in a :doc:`pair_style <pair_style>`
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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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* atoms I,J are both in the specified compute group
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* the distance between atoms I,J is less than the maximum force cutoff
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* the type of the I atom matches itypeN (one or a range of types)
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* the type of the J atom matches jtypeN (one or a range of types)
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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 *itypeN* and *jtypeN*
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arguments are specified.
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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 *jtypeN* were uniformly distributed. Thus it
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involves the count of *itypeN* atoms, the count of *jtypeN* 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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A coordination number coord(r) is also calculated, which is the number
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of atoms of type *jtypeN* within the current bin or closer, averaged
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over atoms of type *itypeN*\ . 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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The simplest way to output the results of the compute rdf calculation
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to a file is to use the :doc:`fix ave/time <fix_ave_time>` command, for
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example:
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.. parsed-literal::
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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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**Output info:**
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This compute calculates a global array with the number of rows =
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*Nbins*\ , 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 *itypeN* versus
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*jtypeN* 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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:ref:`Section_howto 15 <howto_15>` for an overview of
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LAMMPS output options.
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The array values calculated by this compute are all "intensive".
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The first column of array values will be in distance
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:doc:`units <units>`. 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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Restrictions
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""""""""""""
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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 :doc:`rerun <rerun>` command to post-process
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a dump file and set the cutoff for the potential to be longer in the
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rerun script. Note that in the rerun context, the force cutoff is
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arbitrary, since you aren't running dynamics and thus are not changing
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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
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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 *itypeN* and one of *jtypeN*\ , 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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Related commands
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""""""""""""""""
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:doc:`fix ave/time <fix_ave_time>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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