0b5d71537a
fixes formatting issues due to tabs, permission issues and a few typos and badly worded text.
186 lines
7.5 KiB
Plaintext
186 lines
7.5 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute rigid/local command :h3
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[Syntax:]
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compute ID group-ID rigid/local rigidID input1 input2 ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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rigid/local = style name of this compute command :l
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rigidID = ID of fix rigid/small command or one of its variants :l
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input = one or more rigid body attributes :l
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possible attributes = id, mol, mass,
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x, y, z, xu, yu, zu, ix, iy, iz
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vx, vy, vz, fx, fy, fz,
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omegax, omegay, omegaz,
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angmomx, angmomy, angmomz,
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quatw, quati, quatj, quatk,
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tqx, tqy, tqz,
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inertiax, inertiay, inertiaz
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id = atom ID of atom within body which owns body properties
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mol = molecule ID used to define body in "fix rigid/small"_fix_rigid.html command
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mass = total mass of body
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x,y,z = center of mass coords of body
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xu,yu,zu = unwrapped center of mass coords of body
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ix,iy,iz = box image that the center of mass is in
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vx,vy,vz = center of mass velocities
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fx,fy,fz = force of center of mass
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omegax,omegay,omegaz = angular velocity of body
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angmomx,angmomy,angmomz = angular momentum of body
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quatw,quati,quatj,quatk = quaternion components for body
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tqx,tqy,tqz = torque on body
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inertiax,inertiay,inertiaz = diagonalized moments of inertia of body :pre
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:ule
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[Examples:]
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compute 1 all rigid/local myRigid mol x y z :pre
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[Description:]
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Define a computation that simply stores rigid body attributes for
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rigid bodies defined by the "fix rigid/small"_fix_rigid.html command
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or one of its NVE, NVT, NPT, NPH variants. The data is stored as
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local data so it can be accessed by other "output
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commands"_Section_howto.html#howto_15 that process local data, such as
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the "compute reduce"_compute_reduce.html or "dump local"_dump.html
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commands.
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Note that this command only works with the "fix
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rigid/small"_fix_rigid.html command or its variants, not the fix rigid
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command and its variants. The ID of the "fix
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rigid/small"_fix_rigid.html command used to define rigid bodies must
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be specified as {rigidID}. The "fix rigid"_fix_rigid.html command is
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typically used to define a handful of (potentially very large) rigid
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bodies. It outputs similar per-body information as this command
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directly from the fix as global data; see the "fix
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rigid"_fix_rigid.html doc page for details
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The local data stored by this command is generated by looping over all
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the atoms owned on a processor. If the atom is not in the specified
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{group-ID} or is not part of a rigid body it is skipped. If it is not
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the atom within a body that is assigned to store the body information
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it is skipped (only one atom per body is so assigned). If it is the
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assigned atom, then the info for that body is output. This means that
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information for N bodies is generated. N may be less than the # of
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bodies defined by the fix rigid command, if the atoms in some bodies
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are not in the {group-ID}.
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NOTE: Which atom in a body owns the body info is determined internal
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to LAMMPS; it's the one nearest the geometric center of the body.
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Typically you should avoid this complication, by defining the group
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associated with this fix to include/exclude entire bodies.
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Note that as atoms and bodies migrate from processor to processor,
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there will be no consistent ordering of the entries within the local
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vector or array from one timestep to the next.
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Here is an example of how to use this compute to dump rigid body info
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to a file:
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compute 1 all rigid/local myRigid mol x y z fx fy fz
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dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\] c_1\[6\] c_1\[7\] :pre
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:line
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This section explains the rigid body attributes that can be specified.
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The {id} attribute is the atomID of the atom which owns the rigid body, which is
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assigned by the "fix rigid/small"_fix_rigid.html command.
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The {mol} attribute is the molecule ID of the rigid body. It should
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be the molecule ID which all of the atoms in the body belong to, since
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that is how the "fix rigid/small"_fix_rigid.html command defines its
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rigid bodies.
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The {mass} attribute is the total mass of the rigid body.
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There are two options for outputting the coordinates of the center of
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mass (COM) of the body. The {x}, {y}, {z} attributes write the COM
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"unscaled", in the appropriate distance "units"_units.html (Angstroms,
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sigma, etc). Use {xu}, {yu}, {zu} if you want the COM "unwrapped" by
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the image flags for each atobody. Unwrapped means that if the body
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COM has passed thru a periodic boundary one or more times, the value
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is generated what the COM coordinate would be if it had not been
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wrapped back into the periodic box.
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The image flags for the body can be generated directly using the {ix},
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{iy}, {iz} attributes. For periodic dimensions, they specify which
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image of the simulation box the COM is considered to be in. An image
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of 0 means it is inside the box as defined. A value of 2 means add 2
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box lengths to get the true value. A value of -1 means subtract 1 box
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length to get the true value. LAMMPS updates these flags as the rigid
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body COMs cross periodic boundaries during the simulation.
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The {vx}, {vy}, {vz}, {fx}, {fy}, {fz} attributes are components of
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the COM velocity and force on the COM of the body.
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The {omegax}, {omegay}, and {omegaz} attributes are the angular
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velocity componennts of the body around its COM.
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The {angmomx}, {angmomy}, and {angmomz} attributes are the angular
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momentum components of the body around its COM.
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The {quatw}, {quati}, {quatj}, and {quatk} attributes are the
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components of the 4-vector quaternion representing the orientation of
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the rigid body. See the "set"_set.html command for an explanation of
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the quaternion vector.
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The {angmomx}, {angmomy}, and {angmomz} attributes are the angular
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momentum components of the body around its COM.
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The {tqx}, {tqy}, {tqz} attributes are components of the torque acting
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on the body around its COM.
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The {inertiax}, {inertiay}, {inertiaz} attributes are components of
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diagonalized inertia tensor for the body, i.e the 3 moments of inertia
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for the body around its principal axes, as computed internally by
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LAMMPS.
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:line
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[Output info:]
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This compute calculates a local vector or local array depending on the
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number of keywords. The length of the vector or number of rows in the
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array is the number of rigid bodies. If a single keyword is
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specified, a local vector is produced. If two or more keywords are
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specified, a local array is produced where the number of columns = the
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number of keywords. The vector or array can be accessed by any
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command that uses local values from a compute as input. See "this
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section"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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The vector or array values will be in whatever "units"_units.html the
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corresponding attribute is in:
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id,mol = unitless
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mass = mass units
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x,y,z and xy,yu,zu = distance units
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vx,vy,vz = velocity units
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fx,fy,fz = force units
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omegax,omegay,omegaz = radians/time units
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angmomx,angmomy,angmomz = mass*distance^2/time units
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quatw,quati,quatj,quatk = unitless
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tqx,tqy,tqz = torque units
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inertiax,inertiay,inertiaz = mass*distance^2 units :ul
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[Restrictions:]
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This compute is part of the RIGID package. It is only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"dump local"_dump.html, "compute reduce"_compute_reduce.html
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[Default:] none
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