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< title > compute vacf command — LAMMPS 15 May 2015 version documentation< / title >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
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< li > compute vacf 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-vacf-command" >
< span id = "index-0" > < / span > < h1 > compute vacf command< a class = "headerlink" href = "#compute-vacf-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 vacf
< / pre > < / div >
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< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command< / li >
< li > vacf = style name of this compute command< / li >
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< 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 vacf
compute 1 upper vacf
< / pre > < / div >
< / div >
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< 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 velocity auto-correlation
function (VACF), averaged over a group of atoms. Each atom’ s
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contribution to the VACF is its current velocity vector dotted into
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its initial velocity vector at the time the compute was specified.< / p >
< p > A vector of four quantites is calculated by this compute. The first 3
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elements of the vector are vx * vx0 (and similarly for the y and z
components), summed and averaged over atoms in the group. Vx is the
current x-component of velocity for the atom, vx0 is the initial
x-component of velocity for the atom. The 4th element of the vector
is the total VACF, i.e. (vx*vx0 + vy*vy0 + vz*vz0), summed and
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averaged over atoms in the group.< / p >
< p > The integral of the VACF versus time is proportional to the diffusion
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coefficient of the diffusing atoms. This can be computed in the
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following manner, using the < a class = "reference internal" href = "variable.html" > < em > variable trap()< / em > < / a > function:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute 2 all vacf
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fix 5 all vector 1 c_2[4]
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variable diff equal dt*trap(f_5)
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thermo_style custom step v_diff
< / pre > < / div >
< / div >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > If you want the quantities calculated by this compute
to be continuous when running from a < a class = "reference internal" href = "read_restart.html" > < em > restart file< / em > < / a > ,
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then you should use the same ID for this compute, as in the original
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run. This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
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correctly with time=0 atom velocities from the restart file.< / p >
< / div >
< p > < strong > Output info:< / strong > < / p >
< p > This compute calculates a global vector of length 4, which can be
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accessed by indices 1-4 by any command that uses global vector values
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from a compute as input. See < a class = "reference internal" href = "Section_howto.html#howto-15" > < span > this section< / span > < / a > for an overview of LAMMPS output
options.< / p >
< p > The vector values are “ intensive” . The vector values will be in
velocity^2 < a class = "reference internal" href = "units.html" > < em > units< / em > < / a > .< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< blockquote >
< div > none< / div > < / blockquote >
< / 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 = "compute_msd.html" > < em > compute msd< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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