Syntax:
fix ID group-ID rigid bodystyle args keyword values ...
single args = none molecule args = none group args = N groupID1 groupID2 ... N = # of groups groupID1, groupID2, ... = list of N group IDs
force values = M xflag yflag zflag M = which rigid body from 1-Nbody (see asterisk form below) xflag,yflag,zflag = off/on if component of center-of-mass force is active torque values = M xflag yflag zflag M = which rigid body from 1-Nbody (see asterisk form below) xflag,yflag,zflag = off/on if component of center-of-mass torque is active
Examples:
fix 1 clump rigid single fix 1 clump rigid single force 1 off off on fix 1 polychains rigid molecule fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on fix 2 fluid rigid group 3 clump1 clump2 clump3 fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
Description:
Treat one or more sets of atoms as an independent rigid body. This means that each timestep the total force and torque on each rigid body is computed and the coordinates and velocities of the atoms in each body are updated so that they move as a rigid body. This can be useful for freezing one or more portions of a large biomolecule, or for simulating a system of colloidal particles.
IMPORTANT NOTE: This fix is overkill if you just want to hold group of atoms stationary of have them move with a constant velocity. A simpler way to hold atoms stationary is to not include those atoms in your time integration fix. E.g. use "fix 1 mobile nve" instead of "fix 1 all nve", where "mobile" is the group of atoms that you want to move. You can move atoms with a constant velocity by assigning them an initial velocity (via the velocity command), setting the force on them to 0.0 (via the fix setforce command), and integrating them as usual (e.g. via the fix nve command).
IMPORTANT NOTE: This fix updates the positions and velocities of the rigid atoms with a constant-energy time integration, so you should not update the same atoms via other fixes (e.g. nve, nvt, npt).
Each body must have two or more atoms. An atom can belong to at most one rigid body. Which atoms are in which bodies can be defined via several options.
For bodystyle single the entire fix group of atoms is treated as one rigid body.
For bodystyle molecule, each set of atoms in the fix group with a different molecule ID is treated as a rigid body.
For bodystyle group, each of the listed groups is treated as a separate rigid body. Only atoms that are also in the fix group are included in each rigid body.
By default, each rigid body is acted on by other atoms which induce a force and torque on its center of mass, causing it to translate and rotate. Components of the center-of-mass force and torque can be turned off by the force and torque keywords. This may be useful if you wish a body to rotate but not translate, or vice versa. Note that if you expect a rigid body not to move or rotate by using these keywords, you must insure its initial center-of-mass translational or angular velocity is 0.0.
An xflag, yflag, or zflag set to off means turn off the component of force of torque in that dimension. A setting of on means turn on the component, which is the default. Which rigid body(s) the settings apply to is determined by the first argument of the force and torque keywords. It can be an integer M from 1 to Nbody, where Nbody is the number of rigid bodies defined. A wild-card asterisk can be used in place of, or in conjunction with, the M argument to set the flags for multiple rigid bodies. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of rigid bodies, then an asterisk with no numeric values means all bodies from 1 to N. A leading asterisk means all bodies from 1 to n (inclusive). A trailing asterisk means all bodies from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). Note that you can use the force or torque keywords as many times as you like. If a particular rigid body has its component flags set multiple times, the settings from the final keyword are used.
For computational efficiency, you may wish to turn off pairwise and bond interactions within each rigid body, as they no longer contribute to the motion. The neigh_modify exclude and delete_bonds commands are used to do this.
For computational efficiency, you should define one fix rigid which includes all the desired rigid bodies. LAMMPS will allow multiple rigid fixes to be defined, but it is more expensive.
This fix uses constant-energy integration, so you may need to impose additional constraints to control the temperature of an ensemble of rigid bodies. You can use fix langevin for this purpose to treat the system as effectively immersed in an implicit solvent, e.g. a Brownian dynamics model. Or you can thermostat only the non-rigid atoms that surround one or more rigid bodies (i.e. explicit solvent) by appropriate choice of groups in the compute and fix commands for temperature and thermostatting.
If you do calculate a temperature for the rigid bodies, the degrees-of-freedom removed by each rigid body are accounted for in the temperature (and pressure) computation, but only if the temperature group includes the entire rigid body. Rigid bodies in 3d have 6 degrees of freedom (3 translational, 3 rotational), except for dimers which only have 5. Rigid bodies in 2d have 3 degrees of freedom. Note that linear rigid bodies in 3d of three or more atoms also have 5 degrees of freedom instead of 6, but LAMMPS will not detect this. So you should use the compute_modify command to subtract an additional degree of freedom per rigid body. You may also wish to explicitly subtract additional degrees-of-freedom if you use the force and torque keywords to eliminate certain motions of the rigid body, as LAMMPS does not do this automatically.
The rigid body contribution to the pressure of the system (virial) is also accounted for by this fix.
IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are modified when the center-of-mass of the rigid body moves across a periodic boundary. They are not incremented/decremented as they would be for non-rigid atoms. This change does not affect dynamics, but means that any diagnostic computation based on the atomic image flag values must be adjusted accordingly. For example, the fix msd will not compute the expected mean-squared displacement for such atoms, and the image flag values written to a dump file will be different than they would be if the atoms were not in a rigid body. It also means that if you have bonds between a pair of rigid bodies and the bond straddles a periodic boundary, you cannot use the replicate command to increase the system size.
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.
This fix computes a global vector of quantities which can be accessed by various output commands. For each rigid body, 12 values are stored: the xyz coords of the center of mass (COM), the xyz components of the COM velocity, the xyz components of the force acting on the COM, and the xyz components of the torque acting on the COM. The force and torque values in the vector are not affected by the force and torque keywords in the fix rigid command; they reflect values before any changes are made by those keywords.
The total length of the vector is 12*Nbody where Nbody is the number of rigid bodies defined by the fix. Thus the 15th value in the vector would be the z-coord of the COM of the 2nd rigid body. LAMMPS chooses the ordering of the rigid bodies internally. The ordering of the rigid bodies is as follows. For the single keyword there is just one rigid body. For the molecule keyword, the bodies are ordered by ascending molecule ID. For the group keyword, the list of group IDs determines the ordering of bodies. The vector values calculated by this fix are "intensive", meaning they are independent of the number of atoms in the simulation.
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:
This fix performs an MPI_Allreduce each timestep that is proportional in length to the number of rigid bodies. Hence it will not scale well in parallel if large numbers of rigid bodies are simulated.
If the atoms in a single rigid body initially straddle a periodic boundary, the input data file must define the image flags for each atom correctly, so that LAMMPS can "unwrap" the atoms into a valid rigid body.
Related commands:
delete_bonds, neigh_modify exclude
Default:
The option defaults are force * on on on and torque * on on on meaning all rigid bodies are acted on by center-of-mass force and torque.