204 lines
8.0 KiB
ReStructuredText
204 lines
8.0 KiB
ReStructuredText
.. index:: compute property/atom
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compute property/atom command
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=============================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID property/atom input1 input2 ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* property/atom = style name of this compute command
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* input = one or more atom attributes
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.. parsed-literal::
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possible attributes = id, mol, proc, type, mass,
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x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
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vx, vy, vz, fx, fy, fz,
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q, mux, muy, muz, mu,
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spx, spy, spz, sp, fmx, fmy, fmz,
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nbonds,
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radius, diameter, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz,
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shapex,shapey, shapez,
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quatw, quati, quatj, quatk, tqx, tqy, tqz,
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end1x, end1y, end1z, end2x, end2y, end2z,
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corner1x, corner1y, corner1z,
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corner2x, corner2y, corner2z,
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corner3x, corner3y, corner3z,
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i_name, d_name, i2_name[I], d2_name[I],
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vfrac, s0, spin, eradius, ervel, erforce,
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rho, drho, e, de, cv, buckling,
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.. parsed-literal::
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*id* = atom ID
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*mol* = molecule ID
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*proc* = ID of processor that owns atom
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*type* = atom type
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*mass* = atom mass
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*x,y,z* = unscaled atom coordinates
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*xs,ys,zs* = scaled atom coordinates
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*xu,yu,zu* = unwrapped atom coordinates
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*ix,iy,iz* = box image that the atom is in
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*vx,vy,vz* = atom velocities
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*fx,fy,fz* = forces on atoms
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*q* = atom charge
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*mux,muy,muz* = orientation of dipole moment of atom
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*mu* = magnitude of dipole moment of atom
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*spx, spy, spz* = direction of the atomic magnetic spin
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*sp* = magintude of atomic magnetic spin moment
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*fmx, fmy, fmz* = magnetic force
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*nbonds* = number of bonds assigned to an atom
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*radius,diameter* = radius,diameter of spherical particle
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*omegax,omegay,omegaz* = angular velocity of spherical particle
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*angmomx,angmomy,angmomz* = angular momentum of aspherical particle
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*shapex,shapey,shapez* = 3 diameters of aspherical particle
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*quatw,quati,quatj,quatk* = quaternion components for aspherical or body particles
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*tqx,tqy,tqz* = torque on finite-size particles
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*end12x, end12y, end12z* = end points of line segment
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*corner123x, corner123y, corner123z* = corner points of triangle
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*i_name* = custom integer vector with name
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*d_name* = custom floating point vector with name
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*i2_name[I]* = Ith column of custom integer array with name
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*d2_name[I]* = Ith column of custom floating-point array with name
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.. parsed-literal::
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PERI package per-atom properties:
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vfrac = volume fraction
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s0 = max stretch of any bond a particle is part of
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.. parsed-literal::
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EFF and AWPMD package per-atom properties:
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spin = electron spin
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eradius = electron radius
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ervel = electron radial velocity
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erforce = electron radial force
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.. parsed-literal::
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SPH package per-atom properties:
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rho = density of SPH particles
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drho = change in density
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e = energy
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de = change in thermal energy
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cv = heat capacity
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.. parsed-literal::
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MESONT package per-atom properties:
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buckling = buckling flag used in mesoscopic simulation of nanotubes
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Examples
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""""""""
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.. code-block:: LAMMPS
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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
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compute 3 all property/atom sp spx spy spz
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compute 1 all property/atom i_myFlag d_Sxyz[1] d_Sxyz[3]
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Description
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"""""""""""
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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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:doc:`output commands <Howto_output>` that take computes as inputs.
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See for example, the :doc:`compute reduce <compute_reduce>`, :doc:`fix
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ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`,
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:doc:`fix ave/chunk <fix_ave_chunk>`, and :doc:`atom-style variable
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<variable>` commands.
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The list of possible attributes is essentially the same as that used
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by the :doc:`dump custom <dump>` command, which describes their
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meaning, with some additional quantities that are only defined for
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certain :doc:`atom styles <atom_style>`. The goal of this augmented
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list gives an input script access to any per-atom quantity stored by
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LAMMPS.
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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
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quantities that are not defined for a particular particle in the group
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(e.g. *shapex* if the particle is not an ellipsoid).
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Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
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per-atom integer and floating-point vectors or arrays that have been
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added via the :doc:`fix property/atom <fix_property_atom>` command.
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When that command is used specific names are given to each attribute
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which are the "name" portion of these attributes. For arrays *i2_name*
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and *d2_name*, the column of the array must also be included following
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the name in brackets: e.g. d2_xyz[2], i2_mySpin[3].
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The additional quantities only accessible via this command, and not
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directly via the :doc:`dump custom <dump>` command, are as follows.
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*Nbonds* 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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:doc:`newton bond <newton>` command is set to *on*\ , which is the
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default, then every bond in the system is assigned to only one of the
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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 :doc:`newton bond off <newton>` is
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set, it will be tallied with both atom I and atom J.
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*Shapex*, *shapey*, and *shapez* are defined for ellipsoidal particles
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and define the 3d shape of each particle.
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*Quatw*, *quati*, *quatj*, and *quatk* 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 :doc:`set <set>`
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command for an explanation of the quaternion vector.
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*End1x*, *end1y*, *end1z*, *end2x*, *end2y*, *end2z*, are
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defined for line segment particles and define the end points of each
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line segment.
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*Corner1x*, *corner1y*, *corner1z*, *corner2x*, *corner2y*,
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*corner2z*, *corner3x*, *corner3y*, *corner3z*, are defined for
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triangular particles and define the corner points of each triangle.
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In addition, the various per-atom quantities listed above for specific
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packages are only accessible by this command.
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Output info
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"""""""""""
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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
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per-atom vector is produced. If two or more inputs are specified, a
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per-atom array is produced where the number of columns = the number of
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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 the :doc:`Howto output
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<Howto_output>` page for an overview of LAMMPS output options.
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The vector or array values will be in whatever :doc:`units <units>` the
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corresponding attribute is in, e.g. velocity units for vx, charge
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units for q, etc.
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For the spin quantities, sp is in the units of the Bohr magneton, spx,
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spy, and spz are unitless quantities, and fmx, fmy and fmz are given
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in rad/THz.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`,
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:doc::doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk
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:doc:<fix_ave_chunk>`, `fix property/atom <fix_property_atom>`
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Default
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"""""""
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none
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