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doc/html/_sources/fix_shake.txt
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doc/html/_sources/fix_shake.txt
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.. index:: fix shake
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fix shake command
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=================
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fix shake/cuda command
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======================
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fix rattle 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 tol iter N constraint values ... keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* style = shake or rattle = style name of this fix command
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* tol = accuracy tolerance of SHAKE solution
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* iter = max # of iterations in each SHAKE solution
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* N = print SHAKE statistics every this many timesteps (0 = never)
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* one or more constraint/value pairs are appended
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* constraint = *b* or *a* or *t* or *m*
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.. parsed-literal::
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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
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* zero or more keyword/value pairs may be appended
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* keyword = *mol*
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.. parsed-literal::
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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 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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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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fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol
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Description
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"""""""""""
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Apply bond and angle constraints to specified bonds and angles in the
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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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**SHAKE vs RATTLE:**
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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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(:ref:`Ryckaert et al. (1977) <Ryckaert>`). 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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(:ref:`Andersen (1983) <Andersen>`).
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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* at time *n*\ , for
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*i*\ =1,...,\ *N*\ , where *N* is the number of sites of our reference
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molecule. The distance vector between sites *i* and *j* is given by
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.. image:: Eqs/fix_rattle_rij.jpg
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:align: center
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The constraints can then be formulated as
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.. image:: Eqs/fix_rattle_constraints.jpg
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:align: center
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The SHAKE algorithm satisfies the first condition, i.e. the sites at
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time *n+1* 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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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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**SHAKE:**
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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 SHAKE algorithm
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(:ref:`Ryckaert et al. (1977) <Ryckaert>`). 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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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* constraint lists bond types that will be constrained. The *t*
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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 *m* constraint 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* 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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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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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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.. note::
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This command works by using the current forces on atoms to
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caculate an additional constraint force which when added will leave
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the atoms in positions that satisfy the SHAKE constraints (e.g. bond
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length) after the next time integration step. If you define fixes
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(e.g. :doc:`fix efield <fix_efield>`) that add additional force to the
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atoms after fix shake operates, then this fix will not take them into
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account and the time integration will typically not satisfy the SHAKE
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constraints. The solution for this is to make sure that fix shake is
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defined in your input script after any other fixes which add or change
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forces (to atoms that fix shake operates on).
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----------
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The *mol* keyword should be used when other commands, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>`, 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 *template-ID* previously defined
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using the :doc:`molecule <molecule>` command, which reads a file that
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defines the molecule. You must use the same *template-ID* 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 :doc:`molecule <molecule>` 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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----------
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Styles with a *cuda* 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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:doc:`Section_accelerate <Section_accelerate>` 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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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 :ref:`Making LAMMPS <start_3>` section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
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use the :doc:`suffix <suffix>` command in your input script.
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See :doc:`Section_accelerate <Section_accelerate>` of the manual for
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more instructions on how to use the accelerated styles effectively.
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----------
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**RATTLE:**
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The velocity constraints lead to a linear system of equations which
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can be solved analytically. The implementation of the algorithm in
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LAMMPS closely follows (:ref:`Andersen (1983) <Andersen>`).
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.. note::
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The fix rattle command modifies forces and velocities and thus
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should be defined after all other integration fixes in your input
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script. If you define other fixes that modify velocities or forces
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after fix rattle operates, then fix rattle will not take them into
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account and the overall time integration will typically not satisfy
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the RATTLE constraints. You can check whether the constraints work
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correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp
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to 1 and recompiling LAMMPS.
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about these fixes is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
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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 :ref:`output commands <howto_15>`. No parameter of these fixes
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can be used with the *start/stop* keywords of the :doc:`run <run>`
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command. These fixes are not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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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 :ref:`Making LAMMPS <start_3>` section for more info.
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For computational efficiency, there can only be one shake or rattle
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fix defined 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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SHAKE or RATTLE should not be used to contrain an angle at 180 degrees
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(e.g. linear CO2 molecule). This causes numeric difficulties.
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**Related commands:** none
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**Default:** none
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----------
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.. _Ryckaert:
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**(Ryckaert)** 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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.. _Andersen:
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**(Andersen)** H. Andersen, J of Comp Phys, 52, 24-34 (1983).
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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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