2016-05-10 01:33:12 +08:00
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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_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 bond/local 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-bond-local-command" >
< span id = "index-0" > < / span > < h1 > compute bond/local 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" > bond< / span > < span class = "o" > /< / span > < span class = "n" > local< / span > < span class = "n" > input1< / span > < span class = "n" > input2< / span > < span class = "o" > ...< / span >
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "compute.html" > < span class = "doc" > compute< / span > < / a > command< / li >
< li > bond/local = style name of this compute command< / li >
< li > one or more keywords may be appended< / li >
< li > keyword = < em > dist< / em > or < em > eng< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > dist< / em > = bond distance
< em > eng< / em > = bond energy
< em > force< / em > = bond force
< / pre >
< / div >
< div class = "section" id = "examples" >
< 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 = "nb" > all< / span > < span class = "n" > bond< / span > < span class = "o" > /< / span > < span class = "n" > local< / span > < span class = "n" > eng< / span >
< span class = "n" > compute< / span > < span class = "mi" > 1< / span > < span class = "nb" > all< / span > < span class = "n" > bond< / span > < span class = "o" > /< / span > < span class = "n" > local< / span > < span class = "n" > dist< / span > < span class = "n" > eng< / span > < span class = "n" > force< / span >
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< / h2 >
< p > Define a computation that calculates properties of individual bond
interactions. The number of datums generated, aggregated across all
processors, equals the number of bonds in the system, modified
by the group parameter as explained below.< / p >
< p > The local data stored by this command is generated by looping over all
the atoms owned on a processor and their bonds. A bond will only be
included if both atoms in the bond are in the specified compute group.
Any bonds that have been broken (see the < a class = "reference internal" href = "bond_style.html" > < span class = "doc" > bond_style< / span > < / a >
command) by setting their bond type to 0 are not included. Bonds that
have been turned off (see the < a class = "reference internal" href = "fix_shake.html" > < span class = "doc" > fix shake< / span > < / a > or
< a class = "reference internal" href = "delete_bonds.html" > < span class = "doc" > delete_bonds< / span > < / a > commands) by setting their bond type
negative are written into the file, but their energy will be 0.0.< / p >
< p > Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, bond output from the < a class = "reference internal" href = "compute_property_local.html" > < span class = "doc" > compute property/local< / span > < / a > command can be combined
with data from this command and output by the < a class = "reference internal" href = "dump.html" > < span class = "doc" > dump local< / span > < / a >
command in a consistent way.< / p >
< p > Here is an example of how to do this:< / p >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > compute< / span > < span class = "mi" > 1< / span > < span class = "nb" > all< / span > < span class = "nb" > property< / span > < span class = "o" > /< / span > < span class = "n" > local< / span > < span class = "n" > batom1< / span > < span class = "n" > batom2< / span > < span class = "n" > btype< / span >
< span class = "n" > compute< / span > < span class = "mi" > 2< / span > < span class = "nb" > all< / span > < span class = "n" > bond< / span > < span class = "o" > /< / span > < span class = "n" > local< / span > < span class = "n" > dist< / span > < span class = "n" > eng< / span >
< span class = "n" > dump< / span > < span class = "mi" > 1< / span > < span class = "nb" > all< / span > < span class = "n" > local< / span > < span class = "mi" > 1000< / span > < span class = "n" > tmp< / span > < span class = "o" > .< / span > < span class = "n" > dump< / span > < span class = "n" > index< / span > < span class = "n" > c_1< / span > < span class = "p" > [< / span > < span class = "mi" > 1< / span > < span class = "p" > ]< / span > < span class = "n" > c_1< / span > < span class = "p" > [< / span > < span class = "mi" > 2< / span > < span class = "p" > ]< / span > < span class = "n" > c_1< / span > < span class = "p" > [< / span > < span class = "mi" > 3< / span > < span class = "p" > ]< / span > < span class = "n" > c_2< / span > < span class = "p" > [< / span > < span class = "mi" > 1< / span > < span class = "p" > ]< / span > < span class = "n" > c_2< / span > < span class = "p" > [< / span > < span class = "mi" > 2< / span > < span class = "p" > ]< / span >
< / pre > < / div >
< / div >
< p > < strong > Output info:< / strong > < / p >
< p > This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of bonds. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See < a class = "reference internal" href = "Section_howto.html#howto-15" > < span class = "std std-ref" > this section< / span > < / a > for an overview of LAMMPS output
options.< / p >
2016-05-10 05:12:06 +08:00
< p > The output for < em > dist< / em > will be in distance < a class = "reference internal" href = "units.html" > < span class = "doc" > units< / span > < / a > . The
output for < em > eng< / em > will be in energy < a class = "reference internal" href = "units.html" > < span class = "doc" > units< / span > < / a > . The output for
< em > force< / em > will be in force < a class = "reference internal" href = "units.html" > < span class = "doc" > units< / span > < / a > .< / p >
2016-05-10 01:33:12 +08:00
< / div >
< 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 = "dump.html" > < span class = "doc" > dump local< / span > < / a > , < a class = "reference internal" href = "compute_property_local.html" > < span class = "doc" > compute property/local< / span > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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