Syntax:
fix ID group-ID shake tol iter N keyword values ...
b values = one or more bond types a values = one or more angle types t values = one or more atom types m value = one or more mass values
Examples:
fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2 fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31
Description:
Apply bond and angle constraints to specified bonds and angles in the simulation. This typically enables a longer timestep.
Each timestep the specified bonds and angles are reset to their equilibrium lengths and angular values via the well-known SHAKE algorithm. This is done by applying an additional constraint force so that the new positions preserve the desired atom separations. The equations for the additional force are solved via an iterative method that typically converges to an accurate solution in a few iterations. The desired tolerance (e.g. 1.0e-4 = 1 part in 10000) and maximum # of iterations are specified as arguments. Setting the N argument will print statistics to the screen and log file about regarding the lengths of bonds and angles that are being constrained. Small delta values mean SHAKE is doing a good job.
In LAMMPS, only small clusters of atoms can be constrained. This is so the constraint calculation for a cluster can be performed by a single processor, to enable good parallel performance. A cluster is defined as a central atom connected to others in the cluster by constrained bonds. LAMMPS allows for the following kinds of clusters to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or one central atom bonded to 2 others and the angle between the 3 atoms also constrained. This means water molecules or CH2 or CH3 groups may be constrained, but not all the C-C backbone bonds of a long polymer chain.
The b keyword lists bond types that will be constrained. The t keyword lists atom types. All bonds connected to an atom of the specified type will be constrained. The m keyword lists atom masses. All bonds connected to atoms of the specified masses will be constrained (within a fudge factor of MASSDELTA specified in fix_shake.cpp). The a keyword lists angle types. If both bonds in the angle are constrained then the angle will also be constrained if its type is in the list.
For all keywords, a particular bond is only constrained if both atoms in the bond are in the group specified with the SHAKE fix.
The degrees-of-freedom removed by SHAKE bonds and angles are accounted for in temperature and pressure computations. Similarly, the SHAKE contribution to the pressure of the system (virial) is also accounted for.
IMPORTANT NOTE: This command works by using the current forces on atoms to caculate an additional constraint force which when added will leave the atoms in positions that satisfy the SHAKE constraints (e.g. bond length) after the next time integration step. If you define fixes (e.g. fix efield) that add additional force to the atoms after fix shake operates, then this fix will not take them into account and the time integration will typically not satisfy the SHAKE constraints. The solution for this is to make sure that fix shake is defined in your input script after any other fixes which add or change forces (to atoms that fix shake operates on).
Styles with a cuda 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 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 package. They are only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.
You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
See 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 this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.
Restrictions:
For computational efficiency, there can only be one shake fix defined in a simulation.
If you use a tolerance that is too large or a max-iteration count that is too small, the constraints will not be enforced very strongly, which can lead to poor energy conservation. You can test for this in your system by running a constant NVE simulation with a particular set of SHAKE parameters and monitoring the energy versus time.
Related commands: none
Default: none