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compute_property_atom.txt
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.. index:: compute property/atom
compute property/atom command
=============================
Syntax
""""""
.. parsed-literal::
compute ID group-ID property/atom input1 input2 ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* property/atom = style name of this compute command
* input = one or more atom attributes
.. parsed-literal::
possible attributes = id, mol, proc, type, mass,
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
.. parsed-literal::
id = atom ID
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
.. parsed-literal::
PERI package per-atom properties:
vfrac = ???
s0 = ???
.. parsed-literal::
USER-EFF and USER-AWPMD package per-atom properties:
spin = electron spin
eradius = electron radius
ervel = electron radial velocity
erforce = electron radial force
.. parsed-literal::
USER-SPH package per-atom properties:
rho = ???
drho = ???
e = ???
de = ???
cv = ???
.. parsed-literal::
:doc:`fix property/atom <fix_property_atom>` per-atom properties:
i_name = custom integer vector with name
d_name = custom integer vector with name
Examples
""""""""
.. parsed-literal::
compute 1 all property/atom xs vx fx mux
compute 2 all property/atom type
compute 1 all property/atom ix iy iz
Description
"""""""""""
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
:ref:`output commands <howto_15>` that take computes as
inputs. See for example, the :doc:`compute reduce <compute_reduce>`,
:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`,
:doc:`fix ave/spatial <fix_ave_spatial>`, and :doc:`atom-style variable <variable>` commands.
The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning, with some
additional quantities that are only defined for certain :doc:`atom styles <atom_style>`. Basically, this augmented list gives an
input script access to any per-atom quantity stored by LAMMPS.
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. *shapex* if the particle is not an ellipsoid).
The additional quantities only accessible via this command, and not
directly via the :doc:`dump custom <dump>` command, are as follows.
*Shapex*, *shapey*, and *shapez* are defined for ellipsoidal particles
and define the 3d shape of each particle.
*Quatw*, *quati*, *quatj*, and *quatk* are defined for ellipsoidal
particles and body particles and store the 4-vector quaternion
representing the orientation of each particle. See the :doc:`set <set>`
command for an explanation of the quaternion vector.
*End1x*, *end1y*, *end1z*, *end2x*, *end2y*, *end2z*, are defined for
line segment particles and define the end points of each line segment.
*Corner1x*, *corner1y*, *corner1z*, *corner2x*, *corner2y*,
*corner2z*, *corner3x*, *corner3y*, *corner3z*, are defined for
triangular particles and define the corner points of each triangle.
*Nbonds* is available for all molecular atom styles and refers to the
number of explicit bonds assigned to an atom. Note that if the
:doc:`newton bond <newton>` command is set to *on*, 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 :doc:`newton bond off <newton>` is set,
it will be tallied with both atom I and atom J.
The *i_name* and *d_name* attributes refer to custom integer and
floating-point properties that have been added to each atom via the
:doc:`fix property/atom <fix_property_atom>` command. When that command
is used specific names are given to each attribute which are what is
specified as the "name" portion of *i_name* or *d_name*.
**Output info:**
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 :ref:`this section <howto_15>` for an overview of LAMMPS output
options.
The vector or array values will be in whatever :doc:`units <units>` the
corresponding attribute is in, e.g. velocity units for vx, charge
units for q, etc.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/spatial <fix_ave_spatial>`,
:doc:`fix property/atom <fix_property_atom>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
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