2016-05-10 01:33:12 +08:00
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< li > compute property/atom command< / li >
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< div class = "section" id = "compute-property-atom-command" >
< span id = "index-0" > < / span > < h1 > compute property/atom 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 = "nb" > property< / span > < span class = "o" > /< / span > < span class = "n" > atom< / 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 > property/atom = style name of this compute command< / li >
< li > input = one or more atom attributes< / li >
< / ul >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > possible< / span > < span class = "n" > attributes< / span > < span class = "o" > =< / span > < span class = "nb" > id< / span > < span class = "p" > ,< / span > < span class = "n" > mol< / span > < span class = "p" > ,< / span > < span class = "n" > proc< / span > < span class = "p" > ,< / span > < span class = "nb" > type< / span > < span class = "p" > ,< / span > < span class = "n" > mass< / span > < span class = "p" > ,< / span >
< span class = "n" > x< / span > < span class = "p" > ,< / span > < span class = "n" > y< / span > < span class = "p" > ,< / span > < span class = "n" > z< / span > < span class = "p" > ,< / span > < span class = "n" > xs< / span > < span class = "p" > ,< / span > < span class = "n" > ys< / span > < span class = "p" > ,< / span > < span class = "n" > zs< / span > < span class = "p" > ,< / span > < span class = "n" > xu< / span > < span class = "p" > ,< / span > < span class = "n" > yu< / span > < span class = "p" > ,< / span > < span class = "n" > zu< / span > < span class = "p" > ,< / span > < span class = "n" > ix< / span > < span class = "p" > ,< / span > < span class = "n" > iy< / span > < span class = "p" > ,< / span > < span class = "n" > iz< / span > < span class = "p" > ,< / span >
< span class = "n" > vx< / span > < span class = "p" > ,< / span > < span class = "n" > vy< / span > < span class = "p" > ,< / span > < span class = "n" > vz< / span > < span class = "p" > ,< / span > < span class = "n" > fx< / span > < span class = "p" > ,< / span > < span class = "n" > fy< / span > < span class = "p" > ,< / span > < span class = "n" > fz< / span > < span class = "p" > ,< / span >
< span class = "n" > q< / span > < span class = "p" > ,< / span > < span class = "n" > mux< / span > < span class = "p" > ,< / span > < span class = "n" > muy< / span > < span class = "p" > ,< / span > < span class = "n" > muz< / span > < span class = "p" > ,< / span > < span class = "n" > mu< / span > < span class = "p" > ,< / span >
< span class = "n" > radius< / span > < span class = "p" > ,< / span > < span class = "n" > diameter< / span > < span class = "p" > ,< / span > < span class = "n" > omegax< / span > < span class = "p" > ,< / span > < span class = "n" > omegay< / span > < span class = "p" > ,< / span > < span class = "n" > omegaz< / span > < span class = "p" > ,< / span >
< span class = "n" > angmomx< / span > < span class = "p" > ,< / span > < span class = "n" > angmomy< / span > < span class = "p" > ,< / span > < span class = "n" > angmomz< / span > < span class = "p" > ,< / span >
< span class = "n" > shapex< / span > < span class = "p" > ,< / span > < span class = "n" > shapey< / span > < span class = "p" > ,< / span > < span class = "n" > shapez< / span > < span class = "p" > ,< / span >
< span class = "n" > quatw< / span > < span class = "p" > ,< / span > < span class = "n" > quati< / span > < span class = "p" > ,< / span > < span class = "n" > quatj< / span > < span class = "p" > ,< / span > < span class = "n" > quatk< / span > < span class = "p" > ,< / span > < span class = "n" > tqx< / span > < span class = "p" > ,< / span > < span class = "n" > tqy< / span > < span class = "p" > ,< / span > < span class = "n" > tqz< / span > < span class = "p" > ,< / span >
< span class = "n" > end1x< / span > < span class = "p" > ,< / span > < span class = "n" > end1y< / span > < span class = "p" > ,< / span > < span class = "n" > end1z< / span > < span class = "p" > ,< / span > < span class = "n" > end2x< / span > < span class = "p" > ,< / span > < span class = "n" > end2y< / span > < span class = "p" > ,< / span > < span class = "n" > end2z< / span > < span class = "p" > ,< / span >
< span class = "n" > corner1x< / span > < span class = "p" > ,< / span > < span class = "n" > corner1y< / span > < span class = "p" > ,< / span > < span class = "n" > corner1z< / span > < span class = "p" > ,< / span >
< span class = "n" > corner2x< / span > < span class = "p" > ,< / span > < span class = "n" > corner2y< / span > < span class = "p" > ,< / span > < span class = "n" > corner2z< / span > < span class = "p" > ,< / span >
< span class = "n" > corner3x< / span > < span class = "p" > ,< / span > < span class = "n" > corner3y< / span > < span class = "p" > ,< / span > < span class = "n" > corner3z< / span > < span class = "p" > ,< / span >
< span class = "n" > nbonds< / span > < span class = "p" > ,< / span >
< span class = "n" > vfrac< / span > < span class = "p" > ,< / span > < span class = "n" > s0< / span > < span class = "p" > ,< / span >
< span class = "n" > spin< / span > < span class = "p" > ,< / span > < span class = "n" > eradius< / span > < span class = "p" > ,< / span > < span class = "n" > ervel< / span > < span class = "p" > ,< / span > < span class = "n" > erforce< / span > < span class = "p" > ,< / span >
< span class = "n" > rho< / span > < span class = "p" > ,< / span > < span class = "n" > drho< / span > < span class = "p" > ,< / span > < span class = "n" > e< / span > < span class = "p" > ,< / span > < span class = "n" > de< / span > < span class = "p" > ,< / span > < span class = "n" > cv< / span > < span class = "p" > ,< / span >
< span class = "n" > i_name< / span > < span class = "p" > ,< / span > < span class = "n" > d_name< / span >
< / pre > < / div >
< / div >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "nb" > id< / span > < span class = "o" > =< / span > < span class = "n" > atom< / span > < span class = "n" > ID< / span >
< span class = "n" > mol< / span > < span class = "o" > =< / span > < span class = "n" > molecule< / span > < span class = "n" > ID< / span >
< span class = "n" > proc< / span > < span class = "o" > =< / span > < span class = "n" > ID< / span > < span class = "n" > of< / span > < span class = "n" > processor< / span > < span class = "n" > that< / span > < span class = "n" > owns< / span > < span class = "n" > atom< / span >
< span class = "nb" > type< / span > < span class = "o" > =< / span > < span class = "n" > atom< / span > < span class = "nb" > type< / span >
< span class = "n" > mass< / span > < span class = "o" > =< / span > < span class = "n" > atom< / span > < span class = "n" > mass< / span >
< span class = "n" > x< / span > < span class = "p" > ,< / span > < span class = "n" > y< / span > < span class = "p" > ,< / span > < span class = "n" > z< / span > < span class = "o" > =< / span > < span class = "n" > unscaled< / span > < span class = "n" > atom< / span > < span class = "n" > coordinates< / span >
< span class = "n" > xs< / span > < span class = "p" > ,< / span > < span class = "n" > ys< / span > < span class = "p" > ,< / span > < span class = "n" > zs< / span > < span class = "o" > =< / span > < span class = "n" > scaled< / span > < span class = "n" > atom< / span > < span class = "n" > coordinates< / span >
< span class = "n" > xu< / span > < span class = "p" > ,< / span > < span class = "n" > yu< / span > < span class = "p" > ,< / span > < span class = "n" > zu< / span > < span class = "o" > =< / span > < span class = "n" > unwrapped< / span > < span class = "n" > atom< / span > < span class = "n" > coordinates< / span >
< span class = "n" > ix< / span > < span class = "p" > ,< / span > < span class = "n" > iy< / span > < span class = "p" > ,< / span > < span class = "n" > iz< / span > < span class = "o" > =< / span > < span class = "n" > box< / span > < span class = "n" > image< / span > < span class = "n" > that< / span > < span class = "n" > the< / span > < span class = "n" > atom< / span > < span class = "ow" > is< / span > < span class = "ow" > in< / span >
< span class = "n" > vx< / span > < span class = "p" > ,< / span > < span class = "n" > vy< / span > < span class = "p" > ,< / span > < span class = "n" > vz< / span > < span class = "o" > =< / span > < span class = "n" > atom< / span > < span class = "n" > velocities< / span >
< span class = "n" > fx< / span > < span class = "p" > ,< / span > < span class = "n" > fy< / span > < span class = "p" > ,< / span > < span class = "n" > fz< / span > < span class = "o" > =< / span > < span class = "n" > forces< / span > < span class = "n" > on< / span > < span class = "n" > atoms< / span >
< span class = "n" > q< / span > < span class = "o" > =< / span > < span class = "n" > atom< / span > < span class = "n" > charge< / span >
< span class = "n" > mux< / span > < span class = "p" > ,< / span > < span class = "n" > muy< / span > < span class = "p" > ,< / span > < span class = "n" > muz< / span > < span class = "o" > =< / span > < span class = "n" > orientation< / span > < span class = "n" > of< / span > < span class = "n" > dipole< / span > < span class = "n" > moment< / span > < span class = "n" > of< / span > < span class = "n" > atom< / span >
< span class = "n" > mu< / span > < span class = "o" > =< / span > < span class = "n" > magnitude< / span > < span class = "n" > of< / span > < span class = "n" > dipole< / span > < span class = "n" > moment< / span > < span class = "n" > of< / span > < span class = "n" > atom< / span >
< span class = "n" > radius< / span > < span class = "p" > ,< / span > < span class = "n" > diameter< / span > < span class = "o" > =< / span > < span class = "n" > radius< / span > < span class = "p" > ,< / span > < span class = "n" > diameter< / span > < span class = "n" > of< / span > < span class = "n" > spherical< / span > < span class = "n" > particle< / span >
< span class = "n" > omegax< / span > < span class = "p" > ,< / span > < span class = "n" > omegay< / span > < span class = "p" > ,< / span > < span class = "n" > omegaz< / span > < span class = "o" > =< / span > < span class = "n" > angular< / span > < span class = "n" > velocity< / span > < span class = "n" > of< / span > < span class = "n" > spherical< / span > < span class = "n" > particle< / span >
< span class = "n" > angmomx< / span > < span class = "p" > ,< / span > < span class = "n" > angmomy< / span > < span class = "p" > ,< / span > < span class = "n" > angmomz< / span > < span class = "o" > =< / span > < span class = "n" > angular< / span > < span class = "n" > momentum< / span > < span class = "n" > of< / span > < span class = "n" > aspherical< / span > < span class = "n" > particle< / span >
< span class = "n" > shapex< / span > < span class = "p" > ,< / span > < span class = "n" > shapey< / span > < span class = "p" > ,< / span > < span class = "n" > shapez< / span > < span class = "o" > =< / span > < span class = "mi" > 3< / span > < span class = "n" > diameters< / span > < span class = "n" > of< / span > < span class = "n" > aspherical< / span > < span class = "n" > particle< / span >
< span class = "n" > quatw< / span > < span class = "p" > ,< / span > < span class = "n" > quati< / span > < span class = "p" > ,< / span > < span class = "n" > quatj< / span > < span class = "p" > ,< / span > < span class = "n" > quatk< / span > < span class = "o" > =< / span > < span class = "n" > quaternion< / span > < span class = "n" > components< / span > < span class = "k" > for< / span > < span class = "n" > aspherical< / span > < span class = "ow" > or< / span > < span class = "n" > body< / span > < span class = "n" > particles< / span >
< span class = "n" > tqx< / span > < span class = "p" > ,< / span > < span class = "n" > tqy< / span > < span class = "p" > ,< / span > < span class = "n" > tqz< / span > < span class = "o" > =< / span > < span class = "n" > torque< / span > < span class = "n" > on< / span > < span class = "n" > finite< / span > < span class = "o" > -< / span > < span class = "n" > size< / span > < span class = "n" > particles< / span >
< span class = "n" > end12x< / span > < span class = "p" > ,< / span > < span class = "n" > end12y< / span > < span class = "p" > ,< / span > < span class = "n" > end12z< / span > < span class = "o" > =< / span > < span class = "n" > end< / span > < span class = "n" > points< / span > < span class = "n" > of< / span > < span class = "n" > line< / span > < span class = "n" > segment< / span >
< span class = "n" > corner123x< / span > < span class = "p" > ,< / span > < span class = "n" > corner123y< / span > < span class = "p" > ,< / span > < span class = "n" > corner123z< / span > < span class = "o" > =< / span > < span class = "n" > corner< / span > < span class = "n" > points< / span > < span class = "n" > of< / span > < span class = "n" > triangle< / span >
< span class = "n" > nbonds< / span > < span class = "o" > =< / span > < span class = "n" > number< / span > < span class = "n" > of< / span > < span class = "n" > bonds< / span > < span class = "n" > assigned< / span > < span class = "n" > to< / span > < span class = "n" > an< / span > < span class = "n" > atom< / span >
< / pre > < / div >
< / div >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > PERI package per-atom properties:
vfrac = ???
s0 = ???
< / pre > < / div >
< / div >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > USER< / span > < span class = "o" > -< / span > < span class = "n" > EFF< / span > < span class = "ow" > and< / span > < span class = "n" > USER< / span > < span class = "o" > -< / span > < span class = "n" > AWPMD< / span > < span class = "n" > package< / span > < span class = "n" > per< / span > < span class = "o" > -< / span > < span class = "n" > atom< / span > < span class = "n" > properties< / span > < span class = "p" > :< / span >
< span class = "n" > spin< / span > < span class = "o" > =< / span > < span class = "n" > electron< / span > < span class = "n" > spin< / span >
< span class = "n" > eradius< / span > < span class = "o" > =< / span > < span class = "n" > electron< / span > < span class = "n" > radius< / span >
< span class = "n" > ervel< / span > < span class = "o" > =< / span > < span class = "n" > electron< / span > < span class = "n" > radial< / span > < span class = "n" > velocity< / span >
< span class = "n" > erforce< / span > < span class = "o" > =< / span > < span class = "n" > electron< / span > < span class = "n" > radial< / span > < span class = "n" > force< / span >
< / pre > < / div >
< / div >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > USER-SPH package per-atom properties:
rho = ???
drho = ???
e = ???
de = ???
cv = ???
< / pre > < / div >
< / div >
< pre class = "literal-block" >
< a class = "reference internal" href = "fix_property_atom.html" > < span class = "doc" > fix property/atom< / span > < / a > per-atom properties:
i_name = custom integer vector with name
d_name = custom integer vector with name
< / 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 = "nb" > property< / span > < span class = "o" > /< / span > < span class = "n" > atom< / span > < span class = "n" > xs< / span > < span class = "n" > vx< / span > < span class = "n" > fx< / span > < span class = "n" > mux< / span >
< span class = "n" > compute< / span > < span class = "mi" > 2< / span > < span class = "nb" > all< / span > < span class = "nb" > property< / span > < span class = "o" > /< / span > < span class = "n" > atom< / span > < span class = "nb" > type< / 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" > atom< / span > < span class = "n" > ix< / span > < span class = "n" > iy< / span > < span class = "n" > iz< / span >
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< / h2 >
< p > Define a computation that simply stores atom attributes for each atom
in the group. This is useful so that the values can be used by other
< a class = "reference internal" href = "Section_howto.html#howto-15" > < span class = "std std-ref" > output commands< / span > < / a > that take computes as
inputs. See for example, the < a class = "reference internal" href = "compute_reduce.html" > < span class = "doc" > compute reduce< / span > < / a > ,
< a class = "reference internal" href = "fix_ave_atom.html" > < span class = "doc" > fix ave/atom< / span > < / a > , < a class = "reference internal" href = "fix_ave_histo.html" > < span class = "doc" > fix ave/histo< / span > < / a > ,
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< a class = "reference internal" href = "fix_ave_chunk.html" > < span class = "doc" > fix ave/chunk< / span > < / a > , and < a class = "reference internal" href = "variable.html" > < span class = "doc" > atom-style variable< / span > < / a > commands.< / p >
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< p > The list of possible attributes is the same as that used by the < a class = "reference internal" href = "dump.html" > < span class = "doc" > dump custom< / span > < / a > command, which describes their meaning, with some
additional quantities that are only defined for certain < a class = "reference internal" href = "atom_style.html" > < span class = "doc" > atom styles< / span > < / a > . Basically, this augmented list gives an
input script access to any per-atom quantity stored by LAMMPS.< / p >
< p > The values are stored in a per-atom vector or array as discussed
below. Zeroes are stored for atoms not in the specified group or for
quantities that are not defined for a particular particle in the group
(e.g. < em > shapex< / em > if the particle is not an ellipsoid).< / p >
< p > The additional quantities only accessible via this command, and not
directly via the < a class = "reference internal" href = "dump.html" > < span class = "doc" > dump custom< / span > < / a > command, are as follows.< / p >
< p > < em > Shapex< / em > , < em > shapey< / em > , and < em > shapez< / em > are defined for ellipsoidal particles
and define the 3d shape of each particle.< / p >
< p > < em > Quatw< / em > , < em > quati< / em > , < em > quatj< / em > , and < em > quatk< / em > are defined for ellipsoidal
particles and body particles and store the 4-vector quaternion
representing the orientation of each particle. See the < a class = "reference internal" href = "set.html" > < span class = "doc" > set< / span > < / a >
command for an explanation of the quaternion vector.< / p >
< p > < em > End1x< / em > , < em > end1y< / em > , < em > end1z< / em > , < em > end2x< / em > , < em > end2y< / em > , < em > end2z< / em > , are defined for
line segment particles and define the end points of each line segment.< / p >
< p > < em > Corner1x< / em > , < em > corner1y< / em > , < em > corner1z< / em > , < em > corner2x< / em > , < em > corner2y< / em > ,
< em > corner2z< / em > , < em > corner3x< / em > , < em > corner3y< / em > , < em > corner3z< / em > , are defined for
triangular particles and define the corner points of each triangle.< / p >
< p > < em > Nbonds< / em > is available for all molecular atom styles and refers to the
number of explicit bonds assigned to an atom. Note that if the
< a class = "reference internal" href = "newton.html" > < span class = "doc" > newton bond< / span > < / a > command is set to < em > on< / em > , which is the
default, then every bond in the system is assigned to only one of the
two atoms in the bond. Thus a bond between atoms I,J may be tallied
for either atom I or atom J. If < a class = "reference internal" href = "newton.html" > < span class = "doc" > newton bond off< / span > < / a > is set,
it will be tallied with both atom I and atom J.< / p >
< p > The < em > i_name< / em > and < em > d_name< / em > attributes refer to custom integer and
floating-point properties that have been added to each atom via the
< a class = "reference internal" href = "fix_property_atom.html" > < span class = "doc" > fix property/atom< / span > < / a > command. When that command
is used specific names are given to each attribute which are what is
specified as the “ name” portion of < em > i_name< / em > or < em > d_name< / em > .< / p >
< p > < strong > Output info:< / strong > < / p >
< p > This compute calculates a per-atom vector or per-atom array depending
on the number of input values. If a single input is specified, a
per-atom vector is produced. If two or more inputs are specified, a
per-atom array is produced where the number of columns = the number of
inputs. The vector or array can be accessed by any command that uses
per-atom 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 >
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< p > The vector or array values will be in whatever < a class = "reference internal" href = "units.html" > < span class = "doc" > units< / span > < / a > the
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corresponding attribute is in, e.g. velocity units for vx, charge
units for q, etc.< / p >
< / 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 >
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< p > < a class = "reference internal" href = "dump.html" > < span class = "doc" > dump custom< / span > < / a > , < a class = "reference internal" href = "compute_reduce.html" > < span class = "doc" > compute reduce< / span > < / a > , < a class = "reference internal" href = "fix_ave_atom.html" > < span class = "doc" > fix ave/atom< / span > < / a > , < a class = "reference internal" href = "fix_ave_chunk.html" > < span class = "doc" > fix ave/chunk< / span > < / a > ,
2016-05-10 01:33:12 +08:00
< a class = "reference internal" href = "fix_property_atom.html" > < span class = "doc" > fix property/atom< / span > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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