2006-09-22 00:22:34 +08:00
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<HTML>
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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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2011-06-09 05:46:03 +08:00
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<H3>fix shake/cuda command
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</H3>
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2015-03-05 06:27:27 +08:00
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<H3>fix rattle command
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</H3>
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2006-09-22 00:22:34 +08:00
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<P><B>Syntax:</B>
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</P>
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2015-03-05 06:27:27 +08:00
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<PRE>fix ID group-ID style tol iter N constraint values ... keyword value ...
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2006-09-22 00:22:34 +08:00
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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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2015-03-05 06:27:27 +08:00
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<LI>style = shake or rattle = style name of this fix command
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2006-09-22 00:22:34 +08:00
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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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2014-01-08 02:06:02 +08:00
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<LI>one or more constraint/value pairs are appended
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2006-09-22 00:22:34 +08:00
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2014-01-08 02:06:02 +08:00
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<LI>constraint = <I>b</I> or <I>a</I> or <I>t</I> or <I>m</I>
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2006-09-22 00:22:34 +08:00
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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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2014-01-08 02:06:02 +08:00
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>mol</I>
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<PRE> <I>mol</I> value = template-ID
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template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
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</PRE>
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2006-09-22 00:22:34 +08:00
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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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2014-01-08 02:06:02 +08:00
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fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31
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2015-03-05 06:27:27 +08:00
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fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol
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fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31
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2015-03-05 06:08:07 +08:00
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fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol
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</PRE>
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2006-09-22 00:22:34 +08:00
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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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2015-03-05 06:27:27 +08:00
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simulation by either the SHAKE or RATTLE algorithms. This typically
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enables a longer timestep.
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</P>
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<P><B>SHAKE vs RATTLE:</B>
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</P>
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<P>The SHAKE algorithm was invented for schemes such as standard Verlet
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timesteppnig, where only the coordinates are integrated and the
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velocities are approximated as finite differences to the trajectories
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(<A HREF = "#Ryckaert">Ryckaert et al. (1977)</A>). If the velocities are
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integrated explicitly, as with velocity Verlet which is what LAMMPS
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uses as an integration method, a second set of constraining forces is
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required in order to eliminate velocity components along the bonds
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(<A HREF = "#Andersen">Andersen (1983)</A>).
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</P>
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<P>In order to formulate individual constraints for SHAKE and RATTLE,
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focus on a single molecule whose bonds are constrained. Let Ri and Vi
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be the position and velocity of atom <I>i</I> at time <I>n</I>, for
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<I>i</I>=1,...,<I>N</I>, where <I>N</I> is the number of sites of our reference
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molecule. The distance vector between sites <I>i</I> and <I>j</I> is given by
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</P>
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<CENTER><IMG SRC = "Eqs/fix_rattle_rij.jpg">
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</CENTER>
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<P>The constraints can then be formulated as
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2015-03-05 06:08:07 +08:00
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</P>
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<CENTER><IMG SRC = "Eqs/fix_rattle_constraints.jpg">
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</CENTER>
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2015-03-05 06:27:27 +08:00
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<P>The SHAKE algorithm satisfies the first condition, i.e. the sites at
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time <I>n+1</I> will have the desired separations Dij immediately after the
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coordinates are integrated. If we also enforce the second condition,
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the velocity components along the bonds will vanish. RATTLE satisfies
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both conditions. As implemented in LAMMPS, fix rattle uses fix shake
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2015-03-05 06:28:12 +08:00
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for satisfying the coordinate constraints. Therefore the settings and
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optional keywords are the same for both fixes, and all the information
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below about SHAKE is also relevant for RATTLE.
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2015-03-05 06:08:07 +08:00
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</P>
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<P><B>SHAKE:</B>
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</P>
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2006-09-22 00:22:34 +08:00
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<P>Each timestep the specified bonds and angles are reset to their
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2015-03-05 06:27:27 +08:00
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equilibrium lengths and angular values via the SHAKE algorithm
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(<A HREF = "#Ryckaert">Ryckaert et al. (1977)</A>). This is done by applying an
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additional constraint force so that the new positions preserve the
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desired atom separations. The equations for the additional force are
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solved via an iterative method that typically converges to an accurate
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solution in a few iterations. The desired tolerance (e.g. 1.0e-4 = 1
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part in 10000) and maximum # of iterations are specified as arguments.
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Setting the N argument will print statistics to the screen and log
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file about regarding the lengths of bonds and angles that are being
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constrained. Small delta values mean SHAKE is doing a good job.
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2006-09-22 00:22:34 +08:00
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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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2014-01-08 02:06:02 +08:00
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<P>The <I>b</I> constraint lists bond types that will be constrained. The <I>t</I>
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constraint lists atom types. All bonds connected to an atom of the
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specified type will be constrained. The <I>m</I> constraint lists atom
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2006-09-22 00:22:34 +08:00
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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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2014-01-08 02:06:02 +08:00
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fix_shake.cpp). The <I>a</I> constraint lists angle types. If both bonds
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in the angle are constrained then the angle will also be constrained
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if its type is in the list.
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2006-09-22 00:22:34 +08:00
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</P>
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2014-01-08 02:06:02 +08:00
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<P>For all constraints, a particular bond is only constrained if both
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atoms in the bond are in the group specified with the SHAKE fix.
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2006-09-22 00:22:34 +08:00
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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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2012-01-20 23:13:16 +08:00
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<P>IMPORTANT NOTE: This command works by using the current forces on
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atoms to caculate an additional constraint force which when added will
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leave the atoms in positions that satisfy the SHAKE constraints
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(e.g. bond length) after the next time integration step. If you
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define fixes (e.g. <A HREF = "fix_efield.html">fix efield</A>) that add additional
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force to the atoms after fix shake operates, then this fix will not
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take them into account and the time integration will typically not
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satisfy the SHAKE constraints. The solution for this is to make sure
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that fix shake is defined in your input script after any other fixes
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which add or change forces (to atoms that fix shake operates on).
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</P>
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2011-06-09 05:46:03 +08:00
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<HR>
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2014-01-08 02:06:02 +08:00
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<P>The <I>mol</I> keyword should be used when other commands, such as <A HREF = "fix_deposit.html">fix
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deposit</A> or <A HREF = "fix_pour.html">fix pour</A>, add molecules
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on-the-fly during a simulation, and you wish to contrain the new
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molecules via SHAKE. You specify a <I>template-ID</I> previously defined
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using the <A HREF = "molecule.html">molecule</A> command, which reads a file that
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defines the molecule. You must use the same <I>template-ID</I> that the
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command adding molecules uses. The coordinates, atom types, special
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bond restrictions, and SHAKE info can be specified in the molecule
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file. See the <A HREF = "molecule.html">molecule</A> command for details. The only
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settings required to be in this file (by this command) are the SHAKE
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info of atoms in the molecule.
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</P>
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<HR>
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2011-06-09 05:46:03 +08:00
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<P>Styles with a <I>cuda</I> suffix are functionally the same as the
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corresponding style without the suffix. They have been optimized to
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run faster, depending on your available hardware, as discussed in
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2011-12-14 04:35:35 +08:00
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<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
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accelerated styles take the same arguments and should produce the same
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results, except for round-off and precision issues.
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2011-06-09 05:46:03 +08:00
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</P>
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2011-08-27 02:53:00 +08:00
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<P>These accelerated styles are part of the USER-CUDA package. They are
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only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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2011-06-09 05:46:03 +08:00
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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2012-01-28 07:39:14 +08:00
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by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
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2011-08-26 00:46:23 +08:00
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switch</A> when you invoke LAMMPS, or you can
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use the <A HREF = "suffix.html">suffix</A> command in your input script.
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2011-06-09 05:46:03 +08:00
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</P>
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2011-12-14 04:35:35 +08:00
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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more instructions on how to use the accelerated styles effectively.
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2011-06-09 05:46:03 +08:00
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</P>
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<HR>
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2015-03-05 06:08:07 +08:00
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<P><B>RATTLE:</B>
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</P>
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<P>The velocity constraints lead to a linear system of equations which
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2015-03-05 06:27:27 +08:00
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can be solved analytically. The implementation of the algorithm in
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2015-03-05 07:01:51 +08:00
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LAMMPS closely follows (<A HREF = "#Andersen">Andersen (1983)</A>).
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2015-03-05 06:27:27 +08:00
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</P>
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<P>IMPORTANT NOTE: The fix rattle command modifies forces and velocities
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and thus should be defined after all other integration fixes in your
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input script. If you define other fixes that modify velocities or
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forces after fix rattle operates, then fix rattle will not take them
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into account and the overall time integration will typically not
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satisfy the RATTLE constraints. You can check whether the constraints
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work correctly by setting the value of RATTLE_DEBUG in
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src/fix_rattle.cpp to 1 and recompiling LAMMPS.
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2015-03-05 06:08:07 +08:00
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</P>
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<HR>
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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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2015-03-05 06:27:27 +08:00
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<P>No information about these fixes is written to <A HREF = "restart.html">binary restart
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2007-06-26 08:03:39 +08:00
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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2015-03-05 06:27:27 +08:00
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are relevant to these fixes. No global or per-atom quantities are
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stored by these fixes for access by various <A HREF = "Section_howto.html#howto_15">output
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commands</A>. No parameter of these fixes
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can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
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command. These fixes are not invoked during <A HREF = "minimize.html">energy
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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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2015-03-05 06:27:27 +08:00
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<P>These fixes are part of the RIGID package. They are only enabled if
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LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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2014-01-08 04:59:37 +08:00
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LAMMPS</A> section for more info.
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</P>
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2015-03-05 06:27:27 +08:00
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<P>For computational efficiency, there can only be one shake or rattle
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fix defined in a simulation.
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2006-09-22 00:22:34 +08:00
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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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2015-03-05 06:08:07 +08:00
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<HR>
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<A NAME = "Ryckaert"></A>
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<P><B>(Ryckaert)</B> J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen,
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J of Comp Phys, 23, 327-341 (1977).
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2015-03-05 06:08:07 +08:00
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</P>
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<A NAME = "Andersen"></A>
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2015-03-06 23:36:22 +08:00
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<P><B>(Andersen)</B> H. Andersen, J of Comp Phys, 52, 24-34 (1983).
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2015-03-05 06:08:07 +08:00
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</P>
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2006-09-22 00:22:34 +08:00
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</HTML>
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