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< title > compute reduce command — LAMMPS documentation< / title >
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< li > compute reduce 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-reduce-command" >
< span id = "index-0" > < / span > < h1 > compute reduce command< a class = "headerlink" href = "#compute-reduce-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "compute-reduce-region-command" >
< h1 > compute reduce/region command< a class = "headerlink" href = "#compute-reduce-region-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 style arg mode input1 input2 ... keyword args ...
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command< / li >
< li > style = < em > reduce< / em > or < em > reduce/region< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > reduce< / em > arg = none
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< em > reduce/region< / em > arg = region-ID
region-ID = ID of region to use for choosing atoms
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< / pre >
< ul class = "simple" >
< li > mode = < em > sum< / em > or < em > min< / em > or < em > max< / em > or < em > ave< / em > or < em > sumsq< / em > or < em > avesq< / em > < / li >
< li > one or more inputs can be listed< / li >
< li > input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name< / li >
< / ul >
< div class = "highlight-python" > < div class = "highlight" > < pre > x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
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c_ID = per-atom or local vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
f_ID = per-atom or local vector calculated by a fix with ID
f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name
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< / pre > < / div >
< / div >
< ul class = "simple" >
< li > zero or more keyword/args pairs may be appended< / li >
< li > keyword = < em > replace< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > replace< / em > args = vec1 vec2
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vec1 = reduced value from this input vector will be replaced
vec2 = replace it with vec1[N] where N is index of max/min value from vec2
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< / pre >
< / div >
< div class = "section" id = "examples" >
< 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 reduce sum c_force
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compute 1 all reduce/region subbox sum c_force
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compute 2 all reduce min c_press[2] f_ave v_myKE
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compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Define a calculation that “ reduces” one or more vector inputs into
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scalar values, one per listed input. The inputs can be per-atom or
local quantities; they cannot be global quantities. Atom attributes
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are per-atom quantities, < a class = "reference internal" href = "compute.html" > < em > computes< / em > < / a > and < a class = "reference internal" href = "fix.html" > < em > fixes< / em > < / a >
may generate any of the three kinds of quantities, and < a class = "reference internal" href = "variable.html" > < em > atom-style variables< / em > < / a > generate per-atom quantities. See the
< a class = "reference external" href = "variable" > variable< / a > command and its special functions which can
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perform the same operations as the compute reduce command on global
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vectors.< / p >
< p > The reduction operation is specified by the < em > mode< / em > setting. The < em > sum< / em >
option adds the values in the vector into a global total. The < em > min< / em >
or < em > max< / em > options find the minimum or maximum value across all vector
values. The < em > ave< / em > setting adds the vector values into a global total,
then divides by the number of values in the vector. The < em > sumsq< / em >
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option sums the square of the values in the vector into a global
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total. The < em > avesq< / em > setting does the same as < em > sumsq< / em > , then divdes the
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sum of squares by the number of values. The last two options can be
useful for calculating the variance of some quantity, e.g. variance =
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sumsq - ave^2.< / p >
< p > Each listed input is operated on independently. For per-atom inputs,
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the group specified with this command means only atoms within the
group contribute to the result. For per-atom inputs, if the compute
reduce/region command is used, the atoms must also currently be within
the region. Note that an input that produces per-atom quantities may
define its own group which affects the quantities it returns. For
example, if a compute is used as an input which generates a per-atom
vector, it will generate values of 0.0 for atoms that are not in the
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group specified for that compute.< / p >
< p > Each listed input can be an atom attribute (position, velocity, force
component) or can be the result of a < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > or
< a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > or the evaluation of an atom-style
< a class = "reference internal" href = "variable.html" > < em > variable< / em > < / a > .< / p >
< p > The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
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self-explanatory. Note that other atom attributes can be used as
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inputs to this fix by using the < a class = "reference internal" href = "compute_property_atom.html" > < em > compute property/atom< / em > < / a > command and then specifying
an input value from that compute.< / p >
< p > If a value begins with “ < a href = "#id1" > < span class = "problematic" id = "id2" > c_< / span > < / a > ” , a compute ID must follow which has been
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previously defined in the input script. Computes can generate
per-atom or local quantities. See the individual
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< a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > doc page for details. If no bracketed integer
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is appended, the vector calculated by the compute is used. If a
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bracketed integer is appended, the Ith column of the array calculated
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by the compute is used. Users can also write code for their own
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compute styles and < a class = "reference internal" href = "Section_modify.html" > < em > add them to LAMMPS< / em > < / a > .< / p >
< p > If a value begins with “ < a href = "#id3" > < span class = "problematic" id = "id4" > f_< / span > < / a > ” , a fix ID must follow which has been
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previously defined in the input script. Fixes can generate per-atom
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or local quantities. See the individual < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > doc page for
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details. Note that some fixes only produce their values on certain
timesteps, which must be compatible with when compute reduce
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references the values, else an error results. If no bracketed integer
is appended, the vector calculated by the fix is used. If a bracketed
integer is appended, the Ith column of the array calculated by the fix
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is used. Users can also write code for their own fix style and < a class = "reference internal" href = "Section_modify.html" > < em > add them to LAMMPS< / em > < / a > .< / p >
< p > If a value begins with “ < a href = "#id5" > < span class = "problematic" id = "id6" > v_< / span > < / a > ” , a variable name must follow which has
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been previously defined in the input script. It must be an
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< a class = "reference internal" href = "variable.html" > < em > atom-style variable< / em > < / a > . Atom-style variables can
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reference thermodynamic keywords and various per-atom attributes, or
invoke other computes, fixes, or variables when they are evaluated, so
this is a very general means of generating per-atom quantities to
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reduce.< / p >
< hr class = "docutils" / >
< p > If the < em > replace< / em > keyword is used, two indices < em > vec1< / em > and < em > vec2< / em > are
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specified, where each index ranges from 1 to the # of input values.
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The replace keyword can only be used if the < em > mode< / em > is < em > min< / em > or < em > max< / em > .
It works as follows. A min/max is computed as usual on the < em > vec2< / em >
input vector. The index N of that value within < em > vec2< / em > is also stored.
Then, instead of performing a min/max on the < em > vec1< / em > input vector, the
stored index is used to select the Nth element of the < em > vec1< / em > vector.< / p >
< p > Thus, for example, if you wish to use this compute to find the bond
with maximum stretch, you can do it as follows:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute 1 all property/local batom1 batom2
compute 2 all bond/local dist
compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
thermo_style custom step temp c_3[1] c_3[2] c_3[3]
< / pre > < / div >
< / div >
< p > The first two input values in the compute reduce command are vectors
with the IDs of the 2 atoms in each bond, using the < a class = "reference internal" href = "compute_property_local.html" > < em > compute property/local< / em > < / a > command. The last input
value is bond distance, using the < a class = "reference internal" href = "compute_bond_local.html" > < em > compute bond/local< / em > < / a > command. Instead of taking the
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max of the two atom ID vectors, which does not yield useful
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information in this context, the < em > replace< / em > keywords will extract the
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atom IDs for the two atoms in the bond of maximum stretch. These atom
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IDs and the bond stretch will be printed with thermodynamic output.< / p >
< hr class = "docutils" / >
< p > If a single input is specified this compute produces a global scalar
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value. If multiple inputs are specified, this compute produces a
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global vector of values, the length of which is equal to the number of
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inputs specified.< / p >
< p > As discussed below, for the < em > sum< / em > and < em > sumsq< / em > modes, the value(s)
produced by this compute are all “ extensive” , meaning their value
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scales linearly with the number of atoms involved. If normalized
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values are desired, this compute can be accessed by the < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style custom< / em > < / a > command with < a class = "reference internal" href = "thermo_modify.html" > < em > thermo_modify norm yes< / em > < / a > set as an option. Or it can be accessed by a
< a class = "reference internal" href = "variable.html" > < em > variable< / em > < / a > that divides by the appropriate atom count.< / p >
< hr class = "docutils" / >
< p > < strong > Output info:< / strong > < / p >
< p > This compute calculates a global scalar if a single input value is
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specified or a global vector of length N where N is the number of
inputs, and which can be accessed by indices 1 to N. These values can
be used by any command that uses global scalar or vector values from a
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compute as input. See < a class = "reference internal" href = "Section_howto.html#howto-15" > < span > Section_howto 15< / span > < / a >
for an overview of LAMMPS output options.< / p >
< p > All the scalar or vector values calculated by this compute are
“ intensive” , except when the < em > sum< / em > or < em > sumsq< / em > modes are used on
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per-atom or local vectors, in which case the calculated values are
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“ extensive” .< / p >
< p > The scalar or vector values will be in whatever < a class = "reference internal" href = "units.html" > < em > units< / em > < / a > the
quantities being reduced are in.< / 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.html" > < em > compute< / em > < / a > , < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > , < a class = "reference internal" href = "variable.html" > < em > variable< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
< / div >
< / div >
< / div >
< / div >
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< hr / >
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© Copyright 2013 Sandia Corporation.
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