2006-09-22 00:22:34 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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2007-03-28 00:58:07 +08:00
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<H3>fix shake command
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2006-09-22 00:22:34 +08:00
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID shake tol iter N keyword values ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>shake = style name of this fix command
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<LI>tol = accuracy tolerance of SHAKE solution
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<LI>iter = max # of iterations in each SHAKE solution
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<LI>N = print SHAKE statistics every this many timesteps (0 = never)
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<LI>one or more keyword/value pairs are appended
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<LI>keyword = <I>b</I> or <I>a</I> or <I>t</I> or <I>m</I>
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<PRE> <I>b</I> values = one or more bond types
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<I>a</I> values = one or more angle types
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<I>t</I> values = one or more atom types
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<I>m</I> value = one or more mass values
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>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
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>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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</P>
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<P>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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</P>
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<P>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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2008-03-01 09:13:20 +08:00
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also constrained. This means water molecules or CH2 or CH3 groups may
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2006-09-22 00:22:34 +08:00
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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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</P>
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<P>The <I>b</I> keyword lists bond types that will be constrained. The <I>t</I>
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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 <I>m</I> 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 <I>a</I> 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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</P>
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<P>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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</P>
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<P>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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2008-01-10 23:50:00 +08:00
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contribution to the pressure of the system (virial) is also accounted
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for.
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2006-09-22 00:22:34 +08:00
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</P>
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2007-10-11 06:28:11 +08:00
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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2007-06-26 08:03:39 +08:00
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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2007-10-11 06:28:11 +08:00
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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 <A HREF = "Section_howto.html#4_15">output
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commands</A>. No parameter of this fix can be
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used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
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This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
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2007-06-26 08:03:39 +08:00
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</P>
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2006-09-22 00:22:34 +08:00
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<P><B>Restrictions:</B>
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</P>
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<P>For computational efficiency, there can only be one shake fix defined
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in a simulation.
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</P>
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<P>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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</P>
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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