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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 >
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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 > compute gyration 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-gyration-command" >
< span id = "index-0" > < / span > < h1 > compute gyration command< / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< / h2 >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > compute< / span > < span class = "n" > ID< / span > < span class = "n" > group< / span > < span class = "o" > -< / span > < span class = "n" > ID< / span > < span class = "n" > gyration< / span >
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< li > ID, group-ID are documented in < a class = "reference internal" href = "compute.html" > < span class = "doc" > compute< / span > < / a > command< / li >
< li > gyration = style name of this compute command< / li >
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< h2 > Examples< / h2 >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > compute< / span > < span class = "mi" > 1< / span > < span class = "n" > molecule< / span > < span class = "n" > gyration< / span >
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< h2 > Description< / h2 >
< p > Define a computation that calculates the radius of gyration Rg of the
group of atoms, including all effects due to atoms passing thru
periodic boundaries.< / p >
< p > Rg is a measure of the size of the group of atoms, and is computed as
the square root of the Rg^2 value in this formula< / p >
< img alt = "_images/compute_gyration.jpg" class = "align-center" src = "_images/compute_gyration.jpg" / >
< p > where M is the total mass of the group, Rcm is the center-of-mass
position of the group, and the sum is over all atoms in the group.< / p >
< p > A Rg^2 tensor, stored as a 6-element vector, is also calculated by
this compute. The formula for the components of the tensor is the
same as the above formula, except that (Ri - Rcm)^2 is replaced by
(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6
components of the vector are ordered xx, yy, zz, xy, xz, yz. Note
that unlike the scalar Rg, each of the 6 values of the tensor is
effectively a “ squared” value, since the cross-terms may be negative
and taking a sqrt() would be invalid.< / p >
< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > The coordinates of an atom contribute to Rg in “ unwrapped” form,
by using the image flags associated with each atom. See the < a class = "reference internal" href = "dump.html" > < span class = "doc" > dump custom< / span > < / a > command for a discussion of “ unwrapped” coordinates.
See the Atoms section of the < a class = "reference internal" href = "read_data.html" > < span class = "doc" > read_data< / span > < / a > command for a
discussion of image flags and how they are set for each atom. You can
reset the image flags (e.g. to 0) before invoking this compute by
using the < a class = "reference internal" href = "set.html" > < span class = "doc" > set image< / span > < / a > command.< / p >
< / div >
< p > < strong > Output info:< / strong > < / p >
< p > This compute calculates a global scalar (Rg) and a global vector of
length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These
values can be used by any command that uses a global scalar value or
vector values from a compute as input. See < a class = "reference internal" href = "Section_howto.html#howto-15" > < span class = "std std-ref" > Section_howto 15< / span > < / a > for an overview of LAMMPS output
options.< / p >
< p > The scalar and vector values calculated by this compute are
“ intensive” . The scalar and vector values will be in distance and
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distance^2 < a class = "reference internal" href = "units.html" > < span class = "doc" > units< / span > < / a > respectively.< / p >
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< div class = "section" id = "restrictions" >
< h2 > Restrictions< / h2 >
< blockquote >
< div > none< / div > < / blockquote >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< / h2 >
< p > < a class = "reference internal" href = "compute_gyration_chunk.html" > < span class = "doc" > compute gyration/chunk< / span > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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