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< title > compute property/atom command — LAMMPS 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 property/atom command< / li >
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< a href = "http://lammps.sandia.gov" > Website< / a >
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< span id = "index-0" > < / span > < h1 > compute property/atom command< a class = "headerlink" href = "#compute-property-atom-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 property/atom input1 input2 ...
< / 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 > property/atom = style name of this compute command< / li >
< li > input = one or more atom attributes< / li >
< / ul >
< div class = "highlight-python" > < div class = "highlight" > < pre > possible attributes = id, mol, proc, type, mass,
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x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
end1x, end1y, end1z, end2x, end2y, end2z,
corner1x, corner1y, corner1z,
corner2x, corner2y, corner2z,
corner3x, corner3y, corner3z,
nbonds,
vfrac, s0,
spin, eradius, ervel, erforce,
rho, drho, e, de, cv,
i_name, d_name
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< / pre > < / div >
< / div >
< div class = "highlight-python" > < div class = "highlight" > < pre > id = atom ID
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mol = molecule ID
proc = ID of processor that owns atom
type = atom type
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
xu,yu,zu = unwrapped atom coordinates
ix,iy,iz = box image that the atom is in
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
tqx,tqy,tqz = torque on finite-size particles
end12x, end12y, end12z = end points of line segment
corner123x, corner123y, corner123z = corner points of triangle
nbonds = number of bonds assigned to an atom
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< / pre > < / div >
< / div >
< div class = "highlight-python" > < div class = "highlight" > < pre > PERI package per-atom properties:
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vfrac = ???
s0 = ???
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< / pre > < / div >
< / div >
< div class = "highlight-python" > < div class = "highlight" > < pre > USER-EFF and USER-AWPMD package per-atom properties:
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spin = electron spin
eradius = electron radius
ervel = electron radial velocity
erforce = electron radial force
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< / pre > < / div >
< / div >
< div class = "highlight-python" > < div class = "highlight" > < pre > USER-SPH package per-atom properties:
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rho = ???
drho = ???
e = ???
de = ???
cv = ???
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< / pre > < / div >
< / div >
< pre class = "literal-block" >
< a class = "reference internal" href = "fix_property_atom.html" > < em > fix property/atom< / em > < / a > per-atom properties:
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i_name = custom integer vector with name
d_name = custom integer vector with name
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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 property/atom xs vx fx mux
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compute 2 all property/atom type
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compute 1 all property/atom ix iy iz
< / 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 computation that simply stores atom attributes for each atom
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in the group. This is useful so that the values can be used by other
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< a class = "reference internal" href = "Section_howto.html#howto-15" > < span > output commands< / span > < / a > that take computes as
inputs. See for example, the < a class = "reference internal" href = "compute_reduce.html" > < em > compute reduce< / em > < / a > ,
< a class = "reference internal" href = "fix_ave_atom.html" > < em > fix ave/atom< / em > < / a > , < a class = "reference internal" href = "fix_ave_histo.html" > < em > fix ave/histo< / em > < / a > ,
< a class = "reference internal" href = "fix_ave_spatial.html" > < em > fix ave/spatial< / em > < / a > , and < a class = "reference internal" href = "variable.html" > < em > atom-style variable< / em > < / a > commands.< / p >
< p > The list of possible attributes is the same as that used by the < a class = "reference internal" href = "dump.html" > < em > dump custom< / em > < / a > command, which describes their meaning, with some
additional quantities that are only defined for certain < a class = "reference internal" href = "atom_style.html" > < em > atom styles< / em > < / 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
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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
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(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" > < em > dump custom< / em > < / 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
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particles and body particles and store the 4-vector quaternion
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representing the orientation of each particle. See the < a class = "reference internal" href = "set.html" > < em > set< / em > < / 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
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number of explicit bonds assigned to an atom. Note that if the
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< a class = "reference internal" href = "newton.html" > < em > newton bond< / em > < / a > command is set to < em > on< / em > , which is the
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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
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for either atom I or atom J. If < a class = "reference internal" href = "newton.html" > < em > newton bond off< / em > < / 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
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floating-point properties that have been added to each atom via the
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< a class = "reference internal" href = "fix_property_atom.html" > < em > fix property/atom< / em > < / a > command. When that command
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is used specific names are given to each attribute which are what is
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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
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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
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per-atom values 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 or array values will be in whatever < a class = "reference internal" href = "units.html" > < em > units< / em > < / a > the
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corresponding attribute is in, e.g. velocity units for vx, charge
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units for q, etc.< / 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 = "dump.html" > < em > dump custom< / em > < / a > , < a class = "reference internal" href = "compute_reduce.html" > < em > compute reduce< / em > < / a > , < a class = "reference internal" href = "fix_ave_atom.html" > < em > fix ave/atom< / em > < / a > , < a class = "reference internal" href = "fix_ave_spatial.html" > < em > fix ave/spatial< / em > < / a > ,
< a class = "reference internal" href = "fix_property_atom.html" > < em > fix property/atom< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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© Copyright 2013 Sandia Corporation.
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