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fix up some more package designations and clean up some legacy formatting

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Axel Kohlmeyer
2021-07-25 20:23:37 -04:00
parent 18b1e10be8
commit 5a79429f03
592 changed files with 2074 additions and 2019 deletions
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10
doc/src/compute_rdf.rst
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@ -55,7 +55,7 @@ shell of distances in 3d and a thin ring of distances in 2d.
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses a neighbor list, it also means
those pairs will not be included in the RDF. This does not apply when
using long-range coulomb interactions (\ *coul/long*\ , *coul/msm*\ ,
using long-range coulomb interactions (\ *coul/long*, *coul/msm*,
*coul/wolf* 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
@ -94,7 +94,7 @@ The *itypeN* and *jtypeN* arguments are optional. These arguments
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
*itype*\ ,\ *jtype* pair.
*itype*,\ *jtype* pair.
The *itypeN* and *jtypeN* settings can be specified in one of two
ways. An explicit numeric value can be used, as in the fourth example
@ -156,13 +156,13 @@ Output info
"""""""""""
This compute calculates a global array with the number of rows =
*Nbins*\ , and the number of columns = 1 + 2\*Npairs, where Npairs is the
*Nbins*, and the number of columns = 1 + 2\*Npairs, where Npairs is the
number of I,J pairings specified. The first column has the bin
coordinate (center of the bin), Each successive set of 2 columns has
the g(r) and coord(r) values for a specific set of *itypeN* versus
*jtypeN* interactions, as described above. These values can be used
by any command that uses a global values from a compute as input. See
the :doc:`Howto output <Howto_output>` doc page for an overview of
the :doc:`Howto output <Howto_output>` page for an overview of
LAMMPS output options.
The array values calculated by this compute are all "intensive".
@ -186,7 +186,7 @@ your model. The definition of g(r) used by LAMMPS is only appropriate
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
contains only one atom of type *itypeN* and one of *jtypeN*\ , then g(r)
contains only one atom of type *itypeN* and one of *jtypeN*, then g(r)
will register an arbitrarily large spike at whatever distance they
happen to be at, and zero everywhere else. Coord(r) will show a step
change from zero to one at the location of the spike in g(r).