forked from lijiext/lammps
872 lines
40 KiB
Plaintext
872 lines
40 KiB
Plaintext
.. index:: fix rigid
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fix rigid command
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=================
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fix rigid/nve command
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=====================
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fix rigid/nvt command
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=====================
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fix rigid/npt command
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=====================
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fix rigid/nph command
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=====================
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fix rigid/small command
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=======================
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fix rigid/nve/small command
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===========================
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fix rigid/nvt/small command
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===========================
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fix rigid/npt/small command
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===========================
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fix rigid/nph/small command
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===========================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID style bodystyle args keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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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*
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* bodystyle = *single* or *molecule* or *group*
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.. parsed-literal::
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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
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* zero or more keyword/value pairs may be appended
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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*
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.. parsed-literal::
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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 :doc:`molecule <molecule>` command
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Examples
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""""""""
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.. parsed-literal::
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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
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Description
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"""""""""""
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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 :ref:`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 :doc:`fix shake <fix_shake>` 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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.. note::
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Not all of the *bodystyle* options and keyword/value options are
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available for both the *rigid* and *rigid/small* variants. See
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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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.. note::
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To use *rigid/small* the ghost atom cutoff must be large enough
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to span the distance between the atom that owns the body and every
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other atom in the body. This distance value is printed out when the
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rigid bodies are defined. If the :doc:`pair_style <pair_style>` cutoff
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plus neighbor skin does not span this distance, then you should use
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the :doc:`comm_modify cutoff <comm_modify>` command with a setting
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epsilon larger than 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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.. note::
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You should not update the atoms in rigid bodies via other
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time-integration fixes (e.g. :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`), 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 :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>` should be used for the non-rigid particles.
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.. note::
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These fixes are overkill if you simply want to hold a collection
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of atoms stationary or have them move with a constant velocity. A
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simpler way to hold atoms stationary is to not include those atoms in
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your time integration fix. E.g. use "fix 1 mobile nve" instead of
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"fix 1 all nve", where "mobile" is the group of atoms that you want to
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move. You can move atoms with a constant velocity by assigning them
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an initial velocity (via the :doc:`velocity <velocity>` command),
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setting the force on them to 0.0 (via the :doc:`fix setforce <fix_setforce>` command), and integrating them as usual
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(e.g. via the :doc:`fix nve <fix_nve>` command).
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.. note::
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The aggregate properties of each rigid body are calculated one
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time at the start of the first simulation run after this fix is
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specified. The properties include the position and velocity of the
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center-of-mass of the body, its moments of inertia, and its angular
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momentum. This is done using the properties of the constituent atoms
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of the body at that point in time (or see the *infile* keyword
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option). Thereafter, changing properties of individual atoms in the
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body will have no effect on a rigid body's dynamics, unless they
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effect the :doc:`pair_style <pair_style>` interactions that individual
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particles are part of. For example, you might think you could
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displace the atoms in a body or add a large velocity to each atom in a
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body to make it move in a desired direction before a 2nd run is
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performed, using the :doc:`set <set>` or
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:doc:`displace_atoms <displace_atoms>` or :doc:`velocity <velocity>`
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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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----------
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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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.. note::
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With fix rigid/small, which requires bodystyle *molecule*, you
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can define a system that has no rigid bodies initially. This is
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useful when you are using the *mol* keyword in conjunction with
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another fix that is adding rigid bodies on-the-fly, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>`.
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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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.. note::
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To compute the initial center-of-mass position and other
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properties of each rigid body, the image flags for each atom in the
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body are used to "unwrap" the atom coordinates. Thus you must insure
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that these image flags are consistent so that the unwrapping creates a
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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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:doc:`set <set>` 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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.. note::
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For computational efficiency, you may wish to turn off pairwise
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and bond interactions within each rigid body, as they no longer
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contribute to the motion. The :doc:`neigh_modify exclude <neigh_modify>` and :doc:`delete_bonds <delete_bonds>`
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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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----------
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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 :doc:`atom_style sphere and ellipsoid and line and tri <atom_style>` 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 :doc:`frictional granular interactions <pair_gran>`) 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 :doc:`neigh_modify exclude <neigh_modify>` and :doc:`delete_bonds <delete_bonds>`
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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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----------
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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 :ref:`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 :ref:`(Hoover) <Hoover>` and :ref:`(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 :ref:`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 :doc:`fix npt/nph <fix_nh>`
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.. note::
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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 :doc:`fix deform <fix_deform>` 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 :doc:`units <units>` 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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.. parsed-literal::
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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
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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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.. parsed-literal::
|
|
|
|
x Pstart Pstop Pdamp
|
|
y Pstart Pstop Pdamp
|
|
z Pstart Pstop Pdamp
|
|
couple none
|
|
|
|
|
|
----------
|
|
|
|
|
|
The keyword/value option pairs are used in the following ways.
|
|
|
|
The *langevin* and *temp* and *tparam* keywords perform thermostatting
|
|
of the rigid bodies, altering both their translational and rotational
|
|
degrees of freedom. What is meant by "temperature" of a collection of
|
|
rigid bodies and how it can be monitored via the fix output is
|
|
discussed below.
|
|
|
|
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
|
|
:doc:`units <units>` command). The random # *seed* must be a positive
|
|
integer.
|
|
|
|
The way that Langevin thermostatting operates is explained on the :doc:`fix langevin <fix_langevin>` 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
|
|
:doc:`fix viscous <fix_viscous>` doc page for details.
|
|
|
|
.. 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
|
|
:doc:`units <units>` 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.
|
|
|
|
.. note::
|
|
|
|
There are alternate ways to thermostat a system of rigid bodies.
|
|
You can use :doc:`fix langevin <fix_langevin>` 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.
|
|
|
|
|
|
----------
|
|
|
|
|
|
The *mol* keyword can only be used with fix rigid/small. It must be
|
|
used when other commands, such as :doc:`fix deposit <fix_deposit>` or
|
|
:doc:`fix pour <fix_pour>`, add rigid bodies on-the-fly during a
|
|
simulation. You specify a *template-ID* previously defined using the
|
|
:doc:`molecule <molecule>` 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 :doc:`molecule <molecule>` 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 NOTE in the next section for details.
|
|
|
|
|
|
----------
|
|
|
|
|
|
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 5
|
|
such attributes: the total mass of the rigid body, its center-of-mass
|
|
position, its 6 moments of inertia, its center-of-mass velocity, and
|
|
the 3 image flags of the center-of-mass position. 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 4
|
|
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:
|
|
|
|
.. parsed-literal::
|
|
|
|
ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
|
|
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
|
|
...
|
|
IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
|
|
|
|
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. The
|
|
(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you
|
|
wish the body to have no initial motion.
|
|
|
|
The (ixcm,iycm,izcm) values are the image flags of the center of mass
|
|
of the body. For periodic dimensions, they specify which image of the
|
|
simulation box the body is considered to be in. An image of 0 means
|
|
it is inside the box as defined. A value of 2 means add 2 box lengths
|
|
to get the true value. A value of -1 means subtract 1 box length to
|
|
get the true value. LAMMPS updates these flags as the rigid bodies
|
|
cross periodic boundaries during the simulation.
|
|
|
|
.. 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.
|
|
|
|
|
|
----------
|
|
|
|
|
|
If you use a :doc:`temperature compute <compute>` 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).
|
|
|
|
.. 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.
|
|
|
|
|
|
----------
|
|
|
|
|
|
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 :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, and :doc:`fix nph <fix_nh>`.
|
|
|
|
If you wish to perform NVE dynamics (no thermostatting or
|
|
barostatting), use fix rigid or fix rigid/nve to integrate the rigid
|
|
bodies, and :doc:`fix nve <fix_nve>` 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 (:doc:`fix nvt <fix_nh>`,
|
|
:doc:`fix langevin <fix_langevin>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`). You can also use fix rigid
|
|
or fix rigid/nve for the rigid bodies and thermostat them using :doc:`fix langevin <fix_langevin>` on the group that contains all the
|
|
particles in the rigid bodies. The net force added by :doc:`fix langevin <fix_langevin>` 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 :doc:`fix npt <fix_nh>` 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 :doc:`fix nvt <fix_nh>` (or any other thermostat) for the
|
|
non-rigid particles.
|
|
* Use :doc:`fix npt <fix_nh>` 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.
|
|
* Use :doc:`fix press/berendsen <fix_press_berendsen>` 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.
|
|
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 :doc:`fix npt <fix_nh>` an empty group, though it's an odd thing to do. The
|
|
barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen <fix_press_berendsen>`) 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.
|
|
|
|
|
|
----------
|
|
|
|
|
|
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 :doc:`Section_accelerate <Section_accelerate>`
|
|
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 :ref:`Making LAMMPS <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 :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
|
|
use the :doc:`suffix <suffix>` command in your input script.
|
|
|
|
See :doc:`Section_accelerate <Section_accelerate>` of the manual for
|
|
more instructions on how to use the accelerated styles effectively.
|
|
|
|
|
|
----------
|
|
|
|
|
|
Restart, fix_modify, output, run start/stop, minimize info
|
|
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
|
|
|
No information about the *rigid* and *rigid/small* and *rigid/nve*
|
|
fixes are written to :doc:`binary restart files <restart>`. 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 :doc:`binary restart files <restart>`. See the
|
|
:doc:`read_restart <read_restart>` 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 :doc:`fix_modify <fix_modify>` *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 :doc:`thermodynamic output <thermo_style>`.
|
|
|
|
The :doc:`fix_modify <fix_modify>` *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 :ref:`output commands <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 :ref:`output commands <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 :ref:`output commands <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 :doc:`run <run>` command. These fixes are not invoked during
|
|
:doc:`energy minimization <minimize>`.
|
|
|
|
|
|
----------
|
|
|
|
|
|
Restrictions
|
|
""""""""""""
|
|
|
|
|
|
These fixes are all part of the RIGID package. It is only enabled if
|
|
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
|
|
|
|
Assigning a temperature via the :doc:`velocity create <velocity>`
|
|
command to a system with :doc:`rigid bodies <fix_rigid>` 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 :doc:`run 0 <run>` command, which
|
|
insures all DOFs are accounted for properly, and then rescale the
|
|
temperature to the desired value before performing a simulation. For
|
|
example:
|
|
|
|
.. parsed-literal::
|
|
|
|
velocity all create 300.0 12345
|
|
run 0 # temperature may not be 300K
|
|
velocity all scale 300.0 # now it should be
|
|
|
|
Related commands
|
|
""""""""""""""""
|
|
|
|
:doc:`delete_bonds <delete_bonds>`, :doc:`neigh_modify <neigh_modify>`
|
|
exclude, :doc:`fix shake <fix_shake>`
|
|
|
|
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.
|
|
|
|
|
|
----------
|
|
|
|
|
|
.. _Hoover:
|
|
|
|
|
|
|
|
**(Hoover)** Hoover, Phys Rev A, 31, 1695 (1985).
|
|
|
|
.. _Kamberaj:
|
|
|
|
|
|
|
|
**(Kamberaj)** Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).
|
|
|
|
.. _Martyna:
|
|
|
|
|
|
|
|
**(Martyna)** Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
|
|
Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
|
|
|
|
.. _Miller:
|
|
|
|
|
|
|
|
**(Miller)** Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
|
|
J Chem Phys, 116, 8649 (2002).
|
|
|
|
.. _Zhang:
|
|
|
|
|
|
|
|
**(Zhang)** Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).
|
|
|
|
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|
.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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