forked from lijiext/lammps
102 lines
4.1 KiB
Plaintext
102 lines
4.1 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 shake command :h3
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[Syntax:]
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fix ID group-ID shake tol iter N keyword values ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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shake = style name of this fix command :l
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tol = accuracy tolerance of SHAKE solution :l
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iter = max # of iterations in each SHAKE solution :l
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N = print SHAKE statistics every this many timesteps (0 = never) :l
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one or more keyword/value pairs are appended :l
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keyword = {b} or {a} or {t} or {m} :l
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{b} values = one or more bond types
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{a} values = one or more angle types
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{t} values = one or more atom types
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{m} value = one or more mass values :pre
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:ule
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[Examples:]
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fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
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fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 :pre
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[Description:]
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Apply bond and angle constraints to specified bonds and angles in the
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simulation. This typically enables a longer timestep.
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Each timestep the specified bonds and angles are reset to their
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equilibrium lengths and angular values via the well-known SHAKE
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algorithm. This is done by applying an additional constraint force so
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that the new positions preserve the desired atom separations. The
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equations for the additional force are solved via an iterative method
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that typically converges to an accurate solution in a few iterations.
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The desired tolerance (e.g. 1.0e-4 = 1 part in 10000) and maximum # of
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iterations are specified as arguments. Setting the N argument will
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print statistics to the screen and log file about regarding the
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lengths of bonds and angles that are being constrained. Small delta
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values mean SHAKE is doing a good job.
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In LAMMPS, only small clusters of atoms can be constrained. This is
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so the constraint calculation for a cluster can be performed by a
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single processor, to enable good parallel performance. A cluster is
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defined as a central atom connected to others in the cluster by
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constrained bonds. LAMMPS allows for the following kinds of clusters
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to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or
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one central atom bonded to 2 others and the angle between the 3 atoms
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also constrained. This means water molecules or CH2 or CH3 groups may
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be constrained, but not all the C-C backbone bonds of a long polymer
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chain.
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The {b} keyword lists bond types that will be constrained. The {t}
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keyword lists atom types. All bonds connected to an atom of the
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specified type will be constrained. The {m} keyword lists atom
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masses. All bonds connected to atoms of the specified masses will be
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constrained (within a fudge factor of MASSDELTA specified in
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fix_shake.cpp). The {a} keyword lists angle types. If both bonds in
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the angle are constrained then the angle will also be constrained if
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its type is in the list.
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For all keywords, a particular bond is only constrained if both atoms
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in the bond are in the group specified with the SHAKE fix.
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The degrees-of-freedom removed by SHAKE bonds and angles are accounted
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for in temperature and pressure computations. Similarly, the SHAKE
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contribution to the pressure of the system (virial) is also accounted
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for.
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix. No global scalar or vector or per-atom
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quantities are stored by this fix for access by various "output
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commands"_Section_howto.html#4_15. No parameter of this fix can be
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used with the {start/stop} keywords of the "run"_run.html command.
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This fix is not invoked during "energy minimization"_minimize.html.
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[Restrictions:]
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For computational efficiency, there can only be one shake fix defined
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in a simulation.
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If you use a tolerance that is too large or a max-iteration count that
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is too small, the constraints will not be enforced very strongly,
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which can lead to poor energy conservation. You can test for this in
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your system by running a constant NVE simulation with a particular set
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of SHAKE parameters and monitoring the energy versus time.
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[Related commands:] none
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[Default:] none
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