185 lines
7.4 KiB
ReStructuredText
185 lines
7.4 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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sp, spx, spy, spz, fmx, fmy, fmz,
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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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nbonds,
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vfrac, s0,
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spin, eradius, ervel, erforce,
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rho, drho, e, de, cv,
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i_name, d_name
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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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sp = atomic magnetic spin moment
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spx, spy, spz = direction of the atomic magnetic spin
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fmx, fmy, fmz = magnetic force
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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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nbonds = number of bonds assigned to an atom
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.. parsed-literal::
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PERI package per-atom properties:
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vfrac = ???
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s0 = ???
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.. parsed-literal::
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USER-EFF and USER-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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USER-SPH package per-atom properties:
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rho = ???
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drho = ???
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e = ???
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de = ???
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cv = ???
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.. parsed-literal::
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:doc:`fix property/atom <fix_property_atom>` per-atom properties:
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i_name = custom integer vector with name
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d_name = custom integer vector with name
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Examples
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""""""""
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.. parsed-literal::
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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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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. See
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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/chunk <fix_ave_chunk>`, and :doc:`atom-style variable <variable>`
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commands.
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The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning, with some
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additional quantities that are only defined for certain :doc:`atom styles <atom_style>`. Basically, this augmented list gives an
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input script access to any per-atom quantity stored by 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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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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*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 defined for
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line segment particles and define the end points of each 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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*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 set,
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it will be tallied with both atom I and atom J.
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The *i\_name* and *d\_name* 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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:doc:`fix property/atom <fix_property_atom>` 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 *i\_name* or *d\_name*.
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**Output info:**
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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 <Howto_output>` doc page for an overview of LAMMPS output
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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>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
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:doc:`fix property/atom <fix_property_atom>`
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**Default:** none
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