ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

enable per-atom custom arrays in addition to vectors

Browse Source
This commit is contained in:
Steve Plimpton
2020-09-04 11:33:49 -06:00
parent d00807ee9a
commit d1442b0538
23 changed files with 1390 additions and 722 deletions
Download Patch File Download Diff File Expand all files Collapse all files

117
doc/src/compute_property_atom.rst
View File

@ -20,7 +20,8 @@ Syntax
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
sp, spx, spy, spz, fmx, fmy, fmz,
spx, spy, spz, sp, fmx, fmy, fmz,
nbonds,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
@ -29,42 +30,42 @@ Syntax
corner1x, corner1y, corner1z,
corner2x, corner2y, corner2z,
corner3x, corner3y, corner3z,
nbonds,
buckling,
vfrac, s0,
spin, eradius, ervel, erforce,
rho, drho, e, de, cv,
i_name, d_name
i_name, d_name, i2_name[I], d2_name[I],
vfrac, s0, spin, eradius, ervel, erforce,
rho, drho, e, de, cv, buckling
.. 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
sp = atomic magnetic spin moment
spx, spy, spz = direction of the atomic magnetic spin
fmx, fmy, fmz = magnetic force
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
buckling = buckling flag used in mesoscopic simulation of nanotubes
*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
*spx, spy, spz* = direction of the atomic magnetic spin
*sp* = magintude of atomic magnetic spin moment
*fmx, fmy, fmz* = magnetic force
*nbonds* = number of bonds assigned to an 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
*i_name* = custom integer vector with name
*d_name* = custom floating point vector with name
*i2_name[I]* = Ith column of custom integer array with name
*d2_name[I]* = Ith column of custom floating-point array with name
.. parsed-literal::
@ -91,9 +92,8 @@ Syntax
.. 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
USER-MESONT package per-atom properties:
buckling = buckling flag used in mesoscopic simulation of nanotubes
Examples
""""""""
@ -104,6 +104,7 @@ Examples
compute 2 all property/atom type
compute 1 all property/atom ix iy iz
compute 3 all property/atom sp spx spy spz
compute 1 all property/atom i_myFlag d_Sxyz[1] d_Sxyz[3]
Description
"""""""""""
@ -116,20 +117,37 @@ 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>` 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 list of possible attributes is essentially 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>`. The goal of 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).
Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
per-atom integer and floating-point vectors or arrays that have been
added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these attributes. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets: e.g. d2_xyz[2], i2_mySpin[3].
The additional quantities only accessible via this command, and not
directly via the :doc:`dump custom <dump>` command, are as follows.
*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.
*Shapex*\ , *shapey*\ , and *shapez* are defined for ellipsoidal particles
and define the 3d shape of each particle.
@ -146,19 +164,8 @@ line segment.
*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*.
In addition, the various per-atom quantities listed above for specific
packages are only accessible by this command.
Output info
"""""""""""