forked from lijiext/lammps
778 lines
38 KiB
Plaintext
778 lines
38 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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fix rigid command :h3
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fix rigid/nve command :h3
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fix rigid/nvt command :h3
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fix rigid/npt command :h3
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fix rigid/nph command :h3
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fix rigid/small command :h3
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fix rigid/nve/small command :h3
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fix rigid/nvt/small command :h3
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fix rigid/npt/small command :h3
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fix rigid/nph/small command :h3
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[Syntax:]
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fix ID group-ID style bodystyle args keyword values ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {rigid/small} or {rigid/nve/small} or {rigid/nvt/small} or {rigid/npt/small} or {rigid/nph/small} :l
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bodystyle = {single} or {molecule} or {group} :l
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{single} args = none
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{molecule} args = none
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{group} args = N groupID1 groupID2 ...
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N = # of groups
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groupID1, groupID2, ... = list of N group IDs :pre
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zero or more keyword/value pairs may be appended :l
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keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l
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{langevin} values = Tstart Tstop Tperiod seed
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Tstart,Tstop = desired temperature at start/stop of run (temperature units)
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Tdamp = temperature damping parameter (time units)
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seed = random number seed to use for white noise (positive integer)
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{temp} values = Tstart Tstop Tdamp
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Tstart,Tstop = desired temperature at start/stop of run (temperature units)
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Tdamp = temperature damping parameter (time units)
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{iso} or {aniso} values = Pstart Pstop Pdamp
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Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
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Pdamp = pressure damping parameter (time units)
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{x} or {y} or {z} values = Pstart Pstop Pdamp
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Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
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Pdamp = stress damping parameter (time units)
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{couple} = {none} or {xyz} or {xy} or {yz} or {xz}
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{tparam} values = Tchain Titer Torder
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Tchain = length of Nose/Hoover thermostat chain
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Titer = number of thermostat iterations performed
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Torder = 3 or 5 = Yoshida-Suzuki integration parameters
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{pchain} values = Pchain
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Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
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{dilate} value = dilate-group-ID
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dilate-group-ID = only dilate atoms in this group due to barostat volume changes
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{force} values = M xflag yflag zflag
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M = which rigid body from 1-Nbody (see asterisk form below)
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xflag,yflag,zflag = off/on if component of center-of-mass force is active
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{torque} values = M xflag yflag zflag
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M = which rigid body from 1-Nbody (see asterisk form below)
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xflag,yflag,zflag = off/on if component of center-of-mass torque is active
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{infile} filename
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filename = file with per-body values of mass, center-of-mass, moments of inertia
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{mol} value = template-ID
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template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command :pre
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:ule
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[Examples:]
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fix 1 clump rigid single
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fix 1 clump rigid/small molecule
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fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
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fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
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fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
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fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
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fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
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fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
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fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
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fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
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fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre
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[Description:]
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Treat one or more sets of atoms as independent rigid bodies. This
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means that each timestep the total force and torque on each rigid body
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is computed as the sum of the forces and torques on its constituent
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particles. The coordinates, velocities, and orientations of the atoms
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in each body are then updated so that the body moves and rotates as a
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single entity.
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Examples of large rigid bodies are a colloidal particle, or portions
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of a biomolecule such as a protein.
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Example of small rigid bodies are patchy nanoparticles, such as those
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modeled in "this paper"_#Zhang by Sharon Glotzer's group, clumps of
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granular particles, lipid molecules consiting of one or more point
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dipoles connected to other spheroids or ellipsoids, irregular
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particles built from line segments (2d) or triangles (3d), and
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coarse-grain models of nano or colloidal particles consisting of a
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small number of constituent particles. Note that the "fix
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shake"_fix_shake.html command can also be used to rigidify small
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molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats
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the constituent atoms as point masses.
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These fixes also update the positions and velocities of the atoms in
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each rigid body via time integration, in the NVE, NVT, NPT, or NPH
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ensemble, as described below.
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There are two main variants of this fix, fix rigid and fix
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rigid/small. The NVE/NVT/NPT/NHT versions belong to one of the two
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variants, as their style names indicate.
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IMPORTANT NOTE: Not all of the {bodystyle} options and keyword/value
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options are available for both the {rigid} and {rigid/small} variants.
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See details below.
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The {rigid} variant is typically the best choice for a system with a
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small number of large rigid bodies, each of which can extend across
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the domain of many processors. It operates by creating a single
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global list of rigid bodies, which all processors contribute to.
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MPI_Allreduce operations are performed each timestep to sum the
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contributions from each processor to the force and torque on all the
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bodies. This operation will not scale well in parallel if large
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numbers of rigid bodies are simulated.
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The {rigid/small} variant is typically best for a system with a large
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number of small rigid bodies. Each body is assigned to the atom
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closest to the geometrical center of the body. The fix operates using
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local lists of rigid bodies owned by each processor and information is
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exchanged and summed via local communication between neighboring
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processors when ghost atom info is accumlated.
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IMPORTANT NOTE: To use {rigid/small} the ghost atom cutoff must be
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large enough to span the distance between the atom that owns the body
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and every other atom in the body. This distance value is printed out
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when the rigid bodies are defined. If the
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"pair_style"_pair_style.html cutoff plus neighbor skin does not span
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this distance, then you should use the "communicate
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cutoff"_communicate.html command with a setting epsilon larger than
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the distance.
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Which of the two variants is faster for a particular problem is hard
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to predict. The best way to decide is to perform a short test run.
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Both variants should give identical numerical answers for short runs.
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Long runs should give statistically similar results, but round-off
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differences may accumulate to produce divergent trajectories.
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IMPORTANT NOTE: You should not update the atoms in rigid bodies via
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other time-integration fixes (e.g. "fix nve"_fix_nve.html, "fix
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nvt"_fix_nvt.html, "fix npt"_fix_npt.html), or you will be integrating
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their motion more than once each timestep. When performing a hybrid
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simulation with some atoms in rigid bodies, and some not, a separate
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time integration fix like "fix nve"_fix_nve.html or "fix
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nvt"_fix_nh.html should be used for the non-rigid particles.
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IMPORTANT NOTE: These fixes are overkill if you simply want to hold a
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collection of atoms stationary or have them move with a constant
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velocity. A simpler way to hold atoms stationary is to not include
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those atoms in your time integration fix. E.g. use "fix 1 mobile nve"
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instead of "fix 1 all nve", where "mobile" is the group of atoms that
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you want to move. You can move atoms with a constant velocity by
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assigning them an initial velocity (via the "velocity"_velocity.html
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command), setting the force on them to 0.0 (via the "fix
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setforce"_fix_setforce.html command), and integrating them as usual
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(e.g. via the "fix nve"_fix_nve.html command).
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IMPORTANT NOTE: The aggregate properties of each rigid body are
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calculated one time at the start of the first simulation run after
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this fix is specified. The properties include the position and
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velocity of the center-of-mass of the body, its moments of inertia,
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and its angular momentum. This is done using the properties of the
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constituent atoms of the body at that point in time (or see the
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{infile} keyword option). Thereafter, changing properties of
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individual atoms in the body will have no effect on a rigid body's
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dynamics, unless they effect the "pair_style"_pair_style.html
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interactions that individual particles are part of. For example, you
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might think you could displace the atoms in a body or add a large
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velocity to each atom in a body to make it move in a desired direction
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before a 2nd run is performed, using the "set"_set.html or
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"displace_atoms"_displace_atoms.html or "velocity"_velocity.html
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command. But these commands will not affect the internal attributes
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of the body, and the position and velocity or individual atoms in the
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body will be reset when time integration starts.
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:line
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Each rigid body must have two or more atoms. An atom can belong to at
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most one rigid body. Which atoms are in which bodies can be defined
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via several options.
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IMPORTANT NOTE: With fix rigid/small, which requires bodystyle
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{molecule}, you can define a system that has no rigid bodies
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initially. This is useful when you are using the {mol} keyword in
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conjunction with another fix that is adding rigid bodies on-the-fly,
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such as "fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html.
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For bodystyle {single} the entire fix group of atoms is treated as one
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rigid body. This option is only allowed for fix rigid and its
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sub-styles.
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For bodystyle {molecule}, each set of atoms in the fix group with a
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different molecule ID is treated as a rigid body. This option is
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allowed for fix rigid and fix rigid/small, and their sub-styles. Note
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that atoms with a molecule ID = 0 will be treated as a single rigid
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body. For a system with atomic solvent (typically this is atoms with
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molecule ID = 0) surrounding rigid bodies, this may not be what you
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want. Thus you should be careful to use a fix group that only
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includes atoms you want to be part of rigid bodies.
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For bodystyle {group}, each of the listed groups is treated as a
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separate rigid body. Only atoms that are also in the fix group are
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included in each rigid body. This option is only allowed for fix
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rigid and its sub-styles.
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IMPORTANT NOTE: To compute the initial center-of-mass position and
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other properties of each rigid body, the image flags for each atom in
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the body are used to "unwrap" the atom coordinates. Thus you must
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insure that these image flags are consistent so that the unwrapping
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creates a valid rigid body (one where the atoms are close together),
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particularly if the atoms in a single rigid body straddle a periodic
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boundary. This means the input data file or restart file must define
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the image flags for each atom consistently or that you have used the
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"set"_set.html command to specify them correctly. If a dimension is
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non-periodic then the image flag of each atom must be 0 in that
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dimension, else an error is generated.
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The {force} and {torque} keywords discussed next are only allowed for
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fix rigid and its sub-styles.
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By default, each rigid body is acted on by other atoms which induce an
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external force and torque on its center of mass, causing it to
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translate and rotate. Components of the external center-of-mass force
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and torque can be turned off by the {force} and {torque} keywords.
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This may be useful if you wish a body to rotate but not translate, or
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vice versa, or if you wish it to rotate or translate continuously
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unaffected by interactions with other particles. Note that if you
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expect a rigid body not to move or rotate by using these keywords, you
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must insure its initial center-of-mass translational or angular
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velocity is 0.0. Otherwise the initial translational or angular
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momentum the body has will persist.
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An xflag, yflag, or zflag set to {off} means turn off the component of
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force of torque in that dimension. A setting of {on} means turn on
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the component, which is the default. Which rigid body(s) the settings
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apply to is determined by the first argument of the {force} and
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{torque} keywords. It can be an integer M from 1 to Nbody, where
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Nbody is the number of rigid bodies defined. A wild-card asterisk can
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be used in place of, or in conjunction with, the M argument to set the
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flags for multiple rigid bodies. This takes the form "*" or "*n" or
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"n*" or "m*n". If N = the number of rigid bodies, then an asterisk
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with no numeric values means all bodies from 1 to N. A leading
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asterisk means all bodies from 1 to n (inclusive). A trailing
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asterisk means all bodies from n to N (inclusive). A middle asterisk
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means all types from m to n (inclusive). Note that you can use the
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{force} or {torque} keywords as many times as you like. If a
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particular rigid body has its component flags set multiple times, the
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settings from the final keyword are used.
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IMPORTANT NOTE: For computational efficiency, you may wish to turn off
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pairwise and bond interactions within each rigid body, as they no
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longer contribute to the motion. The "neigh_modify
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exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html
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commands are used to do this. If the rigid bodies have strongly
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overalapping atoms, you may need to turn off these interactions to
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avoid numerical problems due to large equal/opposite intra-body forces
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swamping the contribution of small inter-body forces.
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For computational efficiency, you should typically define one fix
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rigid or fix rigid/small command which includes all the desired rigid
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bodies. LAMMPS will allow multiple rigid fixes to be defined, but it
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is more expensive.
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:line
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The constituent particles within a rigid body can be point particles
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(the default in LAMMPS) or finite-size particles, such as spheres or
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ellipsoids or line segments or triangles. See the "atom_style sphere
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and ellipsoid and line and tri"_atom_style.html commands for more
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details on these kinds of particles. Finite-size particles contribute
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differently to the moment of inertia of a rigid body than do point
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particles. Finite-size particles can also experience torque (e.g. due
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to "frictional granular interactions"_pair_gran.html) and have an
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orientation. These contributions are accounted for by these fixes.
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Forces between particles within a body do not contribute to the
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external force or torque on the body. Thus for computational
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efficiency, you may wish to turn off pairwise and bond interactions
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between particles within each rigid body. The "neigh_modify
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exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html
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commands are used to do this. For finite-size particles this also
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means the particles can be highly overlapped when creating the rigid
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body.
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:line
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The {rigid} and {rigid/small} and {rigid/nve} styles perform constant
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NVE time integration. The only difference is that the {rigid} and
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{rigid/small} styles use an integration technique based on Richardson
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iterations. The {rigid/nve} style uses the methods described in the
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paper by "Miller"_#Miller, which are thought to provide better energy
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conservation than an iterative approach.
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The {rigid/nvt} and {rigid/nvt/small} styles performs constant NVT
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integration using a Nose/Hoover thermostat with chains as described
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originally in "(Hoover)"_#Hoover and "(Martyna)"_#Martyna, which
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thermostats both the translational and rotational degrees of freedom
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of the rigid bodies. The rigid-body algorithm used by {rigid/nvt}
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is described in the paper by "Kamberaj"_#Kamberaj.
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The {rigid/npt} and {rigid/nph} (and their /small counterparts) styles
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perform constant NPT or NPH integration using a Nose/Hoover barostat
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with chains. For the NPT case, the same Nose/Hoover thermostat is also
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used as with {rigid/nvt}.
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The barostat parameters are specified using one or more of the {iso},
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{aniso}, {x}, {y}, {z} and {couple} keywords. These keywords give you
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the ability to specify 3 diagonal components of the external stress
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tensor, and to couple these components together so that the dimensions
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they represent are varied together during a constant-pressure
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simulation. The effects of these keywords are similar to those
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defined in "fix npt/nph"_fix_nh.html
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NOTE: Currently the {rigid/npt} and {rigid/nph} (and their /small
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counterparts) styles do not support triclinic (non-orthongonal) boxes.
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The target pressures for each of the 6 components of the stress tensor
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can be specified independently via the {x}, {y}, {z} keywords, which
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correspond to the 3 simulation box dimensions. For each component,
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the external pressure or tensor component at each timestep is a ramped
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value during the run from {Pstart} to {Pstop}. If a target pressure is
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specified for a component, then the corresponding box dimension will
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change during a simulation. For example, if the {y} keyword is used,
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the y-box length will change. A box dimension will not change if that
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component is not specified, although you have the option to change
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that dimension via the "fix deform"_fix_deform.html command.
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For all barostat keywords, the {Pdamp} parameter operates like the
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{Tdamp} parameter, determining the time scale on which pressure is
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relaxed. For example, a value of 10.0 means to relax the pressure in
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a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
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the "units"_units.html command).
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Regardless of what atoms are in the fix group (the only atoms which
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are time integrated), a global pressure or stress tensor is computed
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for all atoms. Similarly, when the size of the simulation box is
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changed, all atoms are re-scaled to new positions, unless the keyword
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{dilate} is specified with a {dilate-group-ID} for a group that
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represents a subset of the atoms. This can be useful, for example, to
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leave the coordinates of atoms in a solid substrate unchanged and
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controlling the pressure of a surrounding fluid. Another example is a
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system consisting of rigid bodies and point particles where the
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barostat is only coupled with the rigid bodies. This option should be
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used with care, since it can be unphysical to dilate some atoms and
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not others, because it can introduce large, instantaneous
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displacements between a pair of atoms (one dilated, one not) that are
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far from the dilation origin.
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The {couple} keyword allows two or three of the diagonal components of
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the pressure tensor to be "coupled" together. The value specified
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with the keyword determines which are coupled. For example, {xz}
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means the {Pxx} and {Pzz} components of the stress tensor are coupled.
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{Xyz} means all 3 diagonal components are coupled. Coupling means two
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things: the instantaneous stress will be computed as an average of the
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corresponding diagonal components, and the coupled box dimensions will
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be changed together in lockstep, meaning coupled dimensions will be
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dilated or contracted by the same percentage every timestep. The
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{Pstart}, {Pstop}, {Pdamp} parameters for any coupled dimensions must
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be identical. {Couple xyz} can be used for a 2d simulation; the {z}
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dimension is simply ignored.
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The {iso} and {aniso} keywords are simply shortcuts that are
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equivalent to specifying several other keywords together.
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The keyword {iso} means couple all 3 diagonal components together when
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pressure is computed (hydrostatic pressure), and dilate/contract the
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dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
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specifying these 4 keywords:
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x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple xyz :pre
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The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled
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independently using the {Pxx}, {Pyy}, and {Pzz} components of the
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stress tensor as the driving forces, and the specified scalar external
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pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
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these 4 keywords:
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x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple none :pre
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:line
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The keyword/value option pairs are used in the following ways.
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The {langevin} and {temp} and {tparam} keywords perform thermostatting
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of the rigid bodies, altering both their translational and rotational
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degrees of freedom. What is meant by "temperature" of a collection of
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rigid bodies and how it can be monitored via the fix output is
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discussed below.
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The {langevin} keyword applies a Langevin thermostat to the constant
|
|
NVE time integration performed by either the {rigid} or {rigid/small}
|
|
or {rigid/nve} styles. It cannot be used with the {rigid/nvt} style.
|
|
The desired temperature at each timestep is a ramped value during the
|
|
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
|
|
time units and determines how rapidly the temperature is relaxed. For
|
|
example, a value of 100.0 means to relax the temperature in a timespan
|
|
of (roughly) 100 time units (tau or fmsec or psec - see the
|
|
"units"_units.html command). The random # {seed} must be a positive
|
|
integer.
|
|
|
|
The way that Langevin thermostatting operates is explained on the "fix
|
|
langevin"_fix_langevin.html doc page. If you wish to simply viscously
|
|
damp the rotational motion without thermostatting, you can set
|
|
{Tstart} and {Tstop} to 0.0, which means only the viscous drag term in
|
|
the Langevin thermostat will be applied. See the discussion on the
|
|
"fix viscous"_doc/fix_viscous.html doc page for details.
|
|
|
|
IMPORTANT NOTE: When the {langevin} keyword is used with fix rigid
|
|
versus fix rigid/small, different dynamics will result for parallel
|
|
runs. This is because of the way random numbers are used in the two
|
|
cases. The dynamics for the two cases should be statistically
|
|
similar, but will not be identical, even for a single timestep.
|
|
|
|
The {temp} and {tparam} keywords apply a Nose/Hoover thermostat to the
|
|
NVT time integration performed by the {rigid/nvt} style. They cannot
|
|
be used with the {rigid} or {rigid/small} or {rigid/nve} styles. The
|
|
desired temperature at each timestep is a ramped value during the run
|
|
from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in time
|
|
units and determines how rapidly the temperature is relaxed. For
|
|
example, a value of 100.0 means to relax the temperature in a timespan
|
|
of (roughly) 100 time units (tau or fmsec or psec - see the
|
|
"units"_units.html command).
|
|
|
|
Nose/Hoover chains are used in conjunction with this thermostat. The
|
|
{tparam} keyword can optionally be used to change the chain settings
|
|
used. {Tchain} is the number of thermostats in the Nose Hoover chain.
|
|
This value, along with {Tdamp} can be varied to dampen undesirable
|
|
oscillations in temperature that can occur in a simulation. As a rule
|
|
of thumb, increasing the chain length should lead to smaller
|
|
oscillations. The keyword {pchain} specifies the number of
|
|
thermostats in the chain thermostatting the barostat degrees of
|
|
freedom.
|
|
|
|
IMPORTANT NOTE: There are alternate ways to thermostat a system of
|
|
rigid bodies. You can use "fix langevin"_fix_langevin.html to treat
|
|
the individual particles in the rigid bodies as effectively immersed
|
|
in an implicit solvent, e.g. a Brownian dynamics model. For hybrid
|
|
systems with both rigid bodies and solvent particles, you can
|
|
thermostat only the solvent particles that surround one or more rigid
|
|
bodies by appropriate choice of groups in the compute and fix commands
|
|
for temperature and thermostatting. The solvent interactions with the
|
|
rigid bodies should then effectively thermostat the rigid body
|
|
temperature as well without use of the Langevin or Nose/Hoover options
|
|
associated with the fix rigid commands.
|
|
|
|
:line
|
|
|
|
The {mol} keyword can only be used with fix rigid/small. It must be
|
|
used when other commands, such as "fix deposit"_fix_deposit.html or
|
|
"fix pour"_fix_pour.html, add rigid bodies on-the-fly during a
|
|
simulation. You specify a {template-ID} previously defined using the
|
|
"molecule"_molecule.html command, which reads a file that defines the
|
|
molecule. You must use the same {template-ID} that the other fix
|
|
which is adding rigid bodies uses. The coordinates, atom types, atom
|
|
diameters, center-of-mass, and moments of inertia can be specified in
|
|
the molecule file. See the "molecule"_molecule.html command for
|
|
details. The only settings required to be in this file are the
|
|
coordinates and types of atoms in the molecule, in which case the
|
|
molecule command calculates the other quantities itself.
|
|
|
|
Note that these other fixes create new rigid bodies, in addition to
|
|
those defined initially by this fix via the {bodystyle} setting.
|
|
|
|
Also note that when using the {mol} keyword, extra restart information
|
|
about all rigid bodies is written out whenever a restart file is
|
|
written out. See the IMPORTANT NOTE in the next section for details.
|
|
|
|
:line
|
|
|
|
The {infile} keyword allows a file of rigid body attributes to be read
|
|
in from a file, rather then having LAMMPS compute them. There are 3
|
|
such attributes: the total mass of the rigid body, its center-of-mass
|
|
position, and its 6 moments of inertia. For rigid bodies consisting
|
|
of point particles or non-overlapping finite-size particles, LAMMPS
|
|
can compute these values accurately. However, for rigid bodies
|
|
consisting of finite-size particles which overlap each other, LAMMPS
|
|
will ignore the overlaps when computing these 3 attributes. The
|
|
amount of error this induces depends on the amount of overlap. To
|
|
avoid this issue, the values can be pre-computed (e.g. using Monte
|
|
Carlo integration).
|
|
|
|
The format of the file is as follows. Note that the file does not
|
|
have to list attributes for every rigid body integrated by fix rigid.
|
|
Only bodies which the file specifies will have their computed
|
|
attributes overridden. The file can contain initial blank lines or
|
|
comment lines starting with "#" which are ignored. The first
|
|
non-blank, non-comment line should list N = the number of lines to
|
|
follow. The N successive lines contain the following information:
|
|
|
|
ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz
|
|
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz
|
|
...
|
|
IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz :pre
|
|
|
|
The rigid body IDs are all positive integers. For the {single}
|
|
bodystyle, only an ID of 1 can be used. For the {group} bodystyle,
|
|
IDs from 1 to Ng can be used where Ng is the number of specified
|
|
groups. For the {molecule} bodystyle, use the molecule ID for the
|
|
atoms in a specific rigid body as the rigid body ID.
|
|
|
|
The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are
|
|
self-explanatory. The center-of-mass should be consistent with what
|
|
is calculated for the position of the rigid body with all its atoms
|
|
unwrapped by their respective image flags. If this produces a
|
|
center-of-mass that is outside the simulation box, LAMMPS wraps it
|
|
back into the box. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
|
|
should be the values consistent with the current orientation of the
|
|
rigid body around its center of mass. The values are with respect to
|
|
the simulation box XYZ axes, not with respect to the prinicpal axes of
|
|
the rigid body itself. LAMMPS performs the latter calculation
|
|
internally. The (vxcm,vycm,vzcm) values are the velocity of the
|
|
center of mass. The (lx,ly,lz) values are the angular momentum of the
|
|
body. These last 6 values can simply be set to 0 if you wish the
|
|
body to have no initial motion.
|
|
|
|
IMPORTANT NOTE: If you use the {infile} or {mol} keywords and write
|
|
restart files during a simulation, then each time a restart file is
|
|
written, the fix also write an auxiliary restart file with the name
|
|
rfile.rigid, where "rfile" is the name of the restart file,
|
|
e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary
|
|
file is in the same format described above. Thus it can be used in a
|
|
new input script that restarts the run and re-specifies a rigid fix
|
|
using an {infile} keyword and the appropriate filename. Note that the
|
|
auxiliary file will contain one line for every rigid body, even if the
|
|
original file only listed a subset of the rigid bodies.
|
|
|
|
:line
|
|
|
|
If you use a "temperature compute"_compute.html with a group that
|
|
includes particles in rigid bodies, the degrees-of-freedom removed by
|
|
each rigid body are accounted for in the temperature (and pressure)
|
|
computation, but only if the temperature group includes all the
|
|
particles in a particular rigid body.
|
|
|
|
A 3d rigid body has 6 degrees of freedom (3 translational, 3
|
|
rotational), except for a collection of point particles lying on a
|
|
straight line, which has only 5, e.g a dimer. A 2d rigid body has 3
|
|
degrees of freedom (2 translational, 1 rotational).
|
|
|
|
IMPORTANT NOTE: You may wish to explicitly subtract additional
|
|
degrees-of-freedom if you use the {force} and {torque} keywords to
|
|
eliminate certain motions of one or more rigid bodies. LAMMPS does
|
|
not do this automatically.
|
|
|
|
The rigid body contribution to the pressure of the system (virial) is
|
|
also accounted for by this fix.
|
|
|
|
:line
|
|
|
|
If your simlulation is a hybrid model with a mixture of rigid bodies
|
|
and non-rigid particles (e.g. solvent) there are several ways these
|
|
rigid fixes can be used in tandem with "fix nve"_fix_nve.html, "fix
|
|
nvt"_fix_nh.html, "fix npt"_fix_nh.html, and "fix nph"_fix_nh.html.
|
|
|
|
If you wish to perform NVE dynamics (no thermostatting or
|
|
barostatting), use fix rigid or fix rigid/nve to integrate the rigid
|
|
bodies, and "fix nve"_fix_nve.html to integrate the non-rigid
|
|
particles.
|
|
|
|
If you wish to perform NVT dynamics (thermostatting, but no
|
|
barostatting), you can use fix rigid/nvt for the rigid bodies, and any
|
|
thermostatting fix for the non-rigid particles ("fix nvt"_fix_nh.html,
|
|
"fix langevin"_fix_langevin.html, "fix
|
|
temp/berendsen"_fix_temp_berendsen.html). You can also use fix rigid
|
|
or fix rigid/nve for the rigid bodies and thermostat them using "fix
|
|
langevin"_fix_langevin.html on the group that contains all the
|
|
particles in the rigid bodies. The net force added by "fix
|
|
langevin"_fix_langevin.html to each rigid body effectively thermostats
|
|
its translational center-of-mass motion. Not sure how well it does at
|
|
thermostatting its rotational motion.
|
|
|
|
If you with to perform NPT or NPH dynamics (barostatting), you cannot
|
|
use both "fix npt"_fix_nh.html and fix rigid/npt (or the nph
|
|
variants). This is because there can only be one fix which monitors
|
|
the global pressure and changes the simulation box dimensions. So you
|
|
have 3 choices:
|
|
|
|
Use fix rigid/npt for the rigid bodies. Use the {dilate} all option
|
|
so that it will dilate the positions of the non-rigid particles as
|
|
well. Use "fix nvt"_fix_nh.html (or any other thermostat) for the
|
|
non-rigid particles. :ulb,l
|
|
|
|
Use "fix npt"_fix_nh.html for the group of non-rigid particles. Use
|
|
the {dilate} all option so that it will dilate the center-of-mass
|
|
positions of the rigid bodies as well. Use fix rigid/nvt for the
|
|
rigid bodies. :l
|
|
|
|
Use "fix press/berendsen"_fix_press_berendsen.html to compute the
|
|
pressure and change the box dimensions. Use fix rigid/nvt for the
|
|
rigid bodies. Use "fix nvt"_fix_nh.thml (or any other thermostat) for
|
|
the non-rigid particles. :l,ule
|
|
|
|
In all case, the rigid bodies and non-rigid particles both contribute
|
|
to the global pressure and the box is scaled the same by any of the
|
|
barostatting fixes.
|
|
|
|
You could even use the 2nd and 3rd options for a non-hybrid simulation
|
|
consisting of only rigid bodies, assuming you give "fix
|
|
npt"_fix_nh.html an empty group, though it's an odd thing to do. The
|
|
barostatting fixes ("fix npt"_fix_nh.html and "fix
|
|
press/berensen"_fix_press_berendsen.html) will monitor the pressure
|
|
and change the box dimensions, but not time integrate any particles.
|
|
The integration of the rigid bodies will be performed by fix
|
|
rigid/nvt.
|
|
|
|
:line
|
|
|
|
Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
|
functionally the same as the corresponding style without the suffix.
|
|
They have been optimized to run faster, depending on your available
|
|
hardware, as discussed in "Section_accelerate"_Section_accelerate.html
|
|
of the manual. The accelerated styles take the same arguments and
|
|
should produce the same results, except for round-off and precision
|
|
issues.
|
|
|
|
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
|
|
KOKKOS, USER-OMP and OPT packages, respectively. They are only
|
|
enabled if LAMMPS was built with those packages. See the "Making
|
|
LAMMPS"_Section_start.html#start_3 section for more info.
|
|
|
|
You can specify the accelerated styles explicitly in your input script
|
|
by including their suffix, or you can use the "-suffix command-line
|
|
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
|
|
use the "suffix"_suffix.html command in your input script.
|
|
|
|
See "Section_accelerate"_Section_accelerate.html of the manual for
|
|
more instructions on how to use the accelerated styles effectively.
|
|
|
|
:line
|
|
|
|
[Restart, fix_modify, output, run start/stop, minimize info:]
|
|
|
|
No information about the {rigid} and {rigid/small} and {rigid/nve}
|
|
fixes are written to "binary restart files"_restart.html. The
|
|
exception is if the {infile} or {mol} keyword is used, in which case
|
|
an auxiliary file is written out with rigid body information each time
|
|
a restart file is written, as explained above for the {infile}
|
|
keyword. For style {rigid/nvt} the state of the Nose/Hoover
|
|
thermostat is written to "binary restart files"_restart.html. See the
|
|
"read_restart"_read_restart.html command for info on how to re-specify
|
|
a fix in an input script that reads a restart file, so that the
|
|
operation of the fix continues in an uninterrupted fashion.
|
|
|
|
The "fix_modify"_fix_modify.html {energy} option is supported by the
|
|
rigid/nvt fix to add the energy change induced by the thermostatting
|
|
to the system's potential energy as part of "thermodynamic
|
|
output"_thermo_style.html.
|
|
|
|
The "fix_modify"_fix_modify.html {temp} and {press} options are
|
|
supported by the rigid/npt and rigid/nph fixes to change the computes used
|
|
to calculate the instantaneous pressure tensor. Note that the rigid/nvt fix
|
|
does not use any external compute to compute instantaneous temperature.
|
|
|
|
The {rigid} and {rigid/small} and {rigid/nve} fixes compute a global
|
|
scalar which can be accessed by various "output
|
|
commands"_Section_howto.html#howto_15. The scalar value calculated by
|
|
these fixes is "intensive". The scalar is the current temperature of
|
|
the collection of rigid bodies. This is averaged over all rigid
|
|
bodies and their translational and rotational degrees of freedom. The
|
|
translational energy of a rigid body is 1/2 m v^2, where m = total
|
|
mass of the body and v = the velocity of its center of mass. The
|
|
rotational energy of a rigid body is 1/2 I w^2, where I = the moment
|
|
of inertia tensor of the body and w = its angular velocity. Degrees
|
|
of freedom constrained by the {force} and {torque} keywords are
|
|
removed from this calculation, but only for the {rigid} and
|
|
{rigid/nve} fixes.
|
|
|
|
The {rigid/nvt}, {rigid/npt}, and {rigid/nph} fixes compute a global
|
|
scalar which can be accessed by various "output
|
|
commands"_Section_howto.html#howto_15. The scalar value calculated by
|
|
these fixes is "extensive". The scalar is the cumulative energy
|
|
change due to the thermostatting and barostatting the fix performs.
|
|
|
|
All of the {rigid} fixes except {rigid/small} compute a global array
|
|
of values which can be accessed by various "output
|
|
commands"_Section_howto.html#howto_15. The number of rows in the
|
|
array is equal to the number of rigid bodies. The number of columns
|
|
is 15. Thus for each rigid body, 15 values are stored: the xyz coords
|
|
of the center of mass (COM), the xyz components of the COM velocity,
|
|
the xyz components of the force acting on the COM, the xyz components
|
|
of the torque acting on the COM, and the xyz image flags of the COM.
|
|
|
|
The center of mass (COM) for each body is similar to unwrapped
|
|
coordinates written to a dump file. It will always be inside (or
|
|
slightly outside) the simulation box. The image flags have the same
|
|
meaning as image flags for atom positions (see the "dump" command).
|
|
This means you can calculate the unwrapped COM by applying the image
|
|
flags to the COM, the same as when unwrapped coordinates are written
|
|
to a dump file.
|
|
|
|
The force and torque values in the array are not affected by the
|
|
{force} and {torque} keywords in the fix rigid command; they reflect
|
|
values before any changes are made by those keywords.
|
|
|
|
The ordering of the rigid bodies (by row in the array) is as follows.
|
|
For the {single} keyword there is just one rigid body. For the
|
|
{molecule} keyword, the bodies are ordered by ascending molecule ID.
|
|
For the {group} keyword, the list of group IDs determines the ordering
|
|
of bodies.
|
|
|
|
The array values calculated by these fixes are "intensive", meaning
|
|
they are independent of the number of atoms in the simulation.
|
|
|
|
No parameter of these fixes can be used with the {start/stop} keywords
|
|
of the "run"_run.html command. These fixes are not invoked during
|
|
"energy minimization"_minimize.html.
|
|
|
|
:line
|
|
|
|
[Restrictions:]
|
|
|
|
These fixes are all part of the RIGID package. It is only enabled if
|
|
LAMMPS was built with that package. See the "Making
|
|
LAMMPS"_Section_start.html#start_3 section for more info.
|
|
|
|
Assigning a temperature via the "velocity create"_velocity.html
|
|
command to a system with "rigid bodies"_fix_rigid.html may not have
|
|
the desired outcome for two reasons. First, the velocity command can
|
|
be invoked before the rigid-body fix is invoked or initialized and the
|
|
number of adjusted degrees of freedom (DOFs) is known. Thus it is not
|
|
possible to compute the target temperature correctly. Second, the
|
|
assigned velocities may be partially canceled when constraints are
|
|
first enforced, leading to a different temperature than desired. A
|
|
workaround for this is to perform a "run 0"_run.html command, which
|
|
insures all DOFs are accounted for properly, and then rescale the
|
|
temperature to the desired value before performing a simulation. For
|
|
example:
|
|
|
|
velocity all create 300.0 12345
|
|
run 0 # temperature may not be 300K
|
|
velocity all scale 300.0 # now it should be :pre
|
|
|
|
[Related commands:]
|
|
|
|
"delete_bonds"_delete_bonds.html, "neigh_modify"_neigh_modify.html
|
|
exclude, "fix shake"_fix_shake.html
|
|
|
|
[Default:]
|
|
|
|
The option defaults are force * on on on and torque * on on on,
|
|
meaning all rigid bodies are acted on by center-of-mass force and
|
|
torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3.
|
|
|
|
:line
|
|
|
|
:link(Hoover)
|
|
[(Hoover)] Hoover, Phys Rev A, 31, 1695 (1985).
|
|
|
|
:link(Kamberaj)
|
|
[(Kamberaj)] Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).
|
|
|
|
:link(Martyna)
|
|
[(Martyna)] Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
|
|
Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
|
|
|
|
:link(Miller)
|
|
[(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
|
|
J Chem Phys, 116, 8649 (2002).
|
|
|
|
:link(Zhang)
|
|
[(Zhang)] Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).
|