fix rigid command — LIGGGHTS v3.X documentation

# fix rigid command

# fix rigid/nve command

# fix rigid/nvt command

# fix rigid/npt command

# fix rigid/nph command

# fix rigid/small command

## Syntax

    fix ID group-ID style bodystyle args keyword values ...

- ID, group-ID are documented in fix command
- style = rigid
- bodystyle = single or molecule or group

    single args = none
    molecule args = none
    group args = N groupID1 groupID2 ...
      N = # of groups
      groupID1, groupID2, ... = list of N group IDs

- zero or more keyword/value pairs may be appended
- keyword = or temp or iso or aniso or x or y or z or couple or tparam or pchain or dilate or force or torque or infile

    langevin values = Tstart Tstop Tperiod seed
      Tstart,Tstop = desired temperature at start/stop of run (temperature units)
      Tdamp = temperature damping parameter (time units)
      seed = random number seed to use for white noise (prime number greater 10000)
    temp values = Tstart Tstop Tdamp
      Tstart,Tstop = desired temperature at start/stop of run (temperature units)
      Tdamp = temperature damping parameter (time units)
    iso or aniso values = Pstart Pstop Pdamp
      Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
      Pdamp = pressure damping parameter (time units)
    x or y or z values = Pstart Pstop Pdamp
      Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
      Pdamp = stress damping parameter (time units)
    couple = none or xyz or xy or yz or xz
    tparam values = Tchain Titer Torder
      Tchain = length of Nose/Hoover thermostat chain
      Titer = number of thermostat iterations performed
      Torder = 3 or 5 = Yoshida-Suzuki integration parameters
    pchain values = Pchain
      Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
    dilate value = dilate-group-ID
      dilate-group-ID = only dilate atoms in this group due to barostat volume changes
    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
    infile filename
      filename = file with per-body values of mass, center-of-mass, moments of inertia

## Examples

    fix 1 clump rigid single
    fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off

## Description

Treat one or more sets of atoms as independent rigid bodies. This means that each timestep the total force and torque on each rigid body is computed as the sum of the forces and torques on its constituent particles and the coordinates, velocities, and orientations of the atoms in each body are updated so that the body moves and rotates as a single entity.

Examples of large rigid bodies are a large colloidal particle, or portions of a large biomolecule such as a protein.

Example of small rigid bodies are patchy nanoparticles, such as those modeled in this paper by Sharon Glotzer’s group, clumps of granular particles, lipid molecules consiting of one or more point dipoles connected to other spheroids or ellipsoids, irregular particles built from line segments (2d) or triangles (3d), and coarse-grain models of nano or colloidal particles consisting of a small number of constituent particles. Note that the `fix shake` command can also be used to rigidify small molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats the constituent atoms as point masses.

These fixes also update the positions and velocities of the atoms in each rigid body via time integration, in the NVE ensemble.

Warning

Not all of the bodystyle options and keyword/value options are available for both the rigid and rigid/small variants. See details below.

The rigid variant is typically the best choice for a system with a small number of large rigid bodies, each of which can extend across the domain of many processors. It operates by creating a single global list of rigid bodies, which all processors contribute to. MPI_Allreduce operations are performed each timestep to sum the contributions from each processor to the force and torque on all the bodies. This operation will not scale well in parallel if large numbers of rigid bodies are simulated.

Which of the two variants is faster for a particular problem is hard to predict. The best way to decide is to perform a short test run. Both variants should give identical numerical answers for short runs. Long runs should give statistically similar results, but round-off differences will accumulate to produce divergent trajectories.

Warning

You should not update the atoms in rigid bodies via other time-integration fixes (e.g. fix nve), or you will be integrating their motion more than once each timestep. When performing a hybrid simulation with some atoms in rigid bodies, and some not, a separate time integration fix like fix nve should be used for the non-rigid particles.

Warning

These fixes are overkill if you simply want to hold a collection of atoms stationary or 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).

Each rigid 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. This option is only allowed for fix rigid and its sub-styles.

For bodystyle molecule, each set of atoms in the fix group with a different molecule ID is treated as a rigid body. This option is allowed for fix rigid and fix rigid/small, and their sub-styles. Note that atoms with a molecule ID = 0 will be treated as a single rigid body. For a system with atomic solvent (typically this is atoms with molecule ID = 0) surrounding rigid bodies, this may not be what you want. Thus you should be careful to use a fix group that only includes atoms you want to be part of rigid bodies.

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. This option is only allowed for fix rigid and its sub-styles.

Warning

To compute the initial center-of-mass position and other properties of each rigid body, the image flags for each atom in the body are used to “unwrap” the atom coordinates. Thus you must insure that these image flags are consistent so that the unwrapping creates a valid rigid body (one where the atoms are close together), particularly if the atoms in a single rigid body straddle a periodic boundary. This means the input data file or restart file must define the image flags for each atom consistently or that you have used the set command to specify them correctly. If a dimension is non-periodic then the image flag of each atom must be 0 in that dimension, else an error is generated.

The force and torque keywords discussed next are only allowed for fix rigid and its sub-styles.

By default, each rigid body is acted on by other atoms which induce an external force and torque on its center of mass, causing it to translate and rotate. Components of the external 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, or if you wish it to rotate or translate continuously unaffected by interactions with other particles. 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. Otherwise the initial translational or angular momentum the body has will persist.

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 typically define one fix rigid or fix rigid/small command which includes all the desired rigid bodies. LIGGGHTS(R)-PUBLIC will allow multiple rigid fixes to be defined, but it is more expensive.

The constituent particles within a rigid body can be point particles (the default in LIGGGHTS(R)-PUBLIC) or finite-size particles, such as spheres or ellipsoids or line segments or triangles. See the atom_style sphere and ellipsoid and line and tri commands for more details on these kinds of particles. Finite-size particles contribute differently to the moment of inertia of a rigid body than do point particles. Finite-size particles can also experience torque (e.g. due to frictional granular interactions) and have an orientation. These contributions are accounted for by these fixes.

Forces between particles within a body do not contribute to the external force or torque on the body. Thus for computational efficiency, you may wish to turn off pairwise and bond interactions between particles within each rigid body. The neigh_modify exclude and delete_bonds commands are used to do this. For finite-size particles this also means the particles can be highly overlapped when creating the rigid body.

The rigid style performs constant NVE time integration based on Richardson iterations.

The infile keyword allows a file of rigid body attributes to be read in from a file, rather then having LIGGGHTS(R)-PUBLIC compute them. There are 3 such attributes: the total mass of the rigid body, its center-of-mass position, and its 6 moments of inertia. For rigid bodies consisting of point particles or non-overlapping finite-size particles, LIGGGHTS(R)-PUBLIC can compute these values accurately. However, for rigid bodies consisting of finite-size particles which overlap each other, LIGGGHTS(R)-PUBLIC will ignore the overlaps when computing these 3 attributes. The amount of error this induces depends on the amount of overlap. To avoid this issue, the values can be pre-computed (e.g. using Monte Carlo integration).

The format of the file is as follows. Note that the file does not have to list attributes for every rigid body integrated by fix rigid. Only bodies which the file specifies will have their computed attributes overridden. The file can contain initial blank lines or comment lines starting with “#” which are ignored. The first non-blank, non-comment line should list N = the number of lines to follow. The N successive lines contain the following information:

    ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
    ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
    ...
    IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz

The rigid body IDs are all positive integers. For the single bodystyle, only an ID of 1 can be used. For the group bodystyle, IDs from 1 to Ng can be used where Ng is the number of specified groups. For the molecule bodystyle, use the molecule ID for the atoms in a specific rigid body as the rigid body ID.

The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are self-explanatory. The center-of-mass should be consistent with what is calculated for the position of the rigid body with all its atoms unwrapped by their respective image flags. If this produces a center-of-mass that is outside the simulation box, LIGGGHTS(R)-PUBLIC wraps it back into the box. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the simulation box XYZ axes, not with respect to the prinicpal axes of the rigid body itself. LIGGGHTS(R)-PUBLIC performs the latter calculation internally.

Warning

If you use the infile keyword and write restart files during a simulation, then each time a restart file is written, the fix also write an auxiliary restart file with the name rfile.rigid, where “rfile” is the name of the restart file, e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary file is in the same format described above and contains info on the current center-of-mass and 6 moments of inertia. Thus it can be used in a new input script that restarts the run and re-specifies a rigid fix using an infile keyword and the appropriate filename. Note that the auxiliary file will contain one line for every rigid body, even if the original file only listed a subset of the rigid bodies.

Warning

The periodic image flags of atoms in rigid bodies are altered so that the rigid body can be reconstructed correctly when it straddles periodic boundaries. The atom image flags are not incremented/decremented as they would be for non-rigid atoms as the rigid body crosses periodic boundaries. Specifically, they are set so that the center-of-mass (COM) of the rigid body always remains inside the simulation box.

This means that if you output per-atom image flags you cannot interpret them as you normally would. I.e. 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. Likewise the compute msd will not compute the expected mean-squared displacement for such atoms if the body moves across periodic boundaries. 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.

Here are details on how, you can post-process a dump file to calculate a diffusion coefficient for rigid bodies, using the altered per-atom image flags written to a dump file. The image flags for atoms in the same rigid body can be used to unwrap the body and calculate its center-of-mass (COM). As mentioned above, this COM will always be inside the simulation box. Thus it will “jump” from one side of the box to the other when the COM crosses a periodic boundary. If you keep track of the jumps, you can effectively “unwrap” the COM and use that value to track the displacement of each rigid body, and thus the mean-squared displacement (MSD) of an ensemble of bodies, and thus a diffusion coefficient.

Note that fix rigid does define image flags for each rigid body, which are incremented when the center-of-mass of the rigid body crosses a periodic boundary in the usual way. These image flags have the same meaning as atom images (see the “dump” command) and can be accessed and output as described below.

## Restart, fix_modify, output, run start/stop, minimize info

No information is written to binary restart files. read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.

The fix_modify energy option is supported by the rigid/nvt fix to add the energy change induced by the thermostatting to the system’s potential energy as part of thermodynamic output.

The fix_modify temp and press options are supported by the rigid/npt and rigid/nph fixes to change the computes used to calculate the instantaneous pressure tensor. Note that the rigid/nvt fix does not use any external compute to compute instantaneous temperature.

The fixes compute a global scalar which can be accessed by various output commands. The scalar value calculated by these fixes is “intensive”. The scalar is the current temperature of the collection of rigid bodies. This is averaged over all rigid bodies and their translational and rotational degrees of freedom. The translational energy of a rigid body is 1/2 m v^2, where m = total mass of the body and v = the velocity of its center of mass. The rotational energy of a rigid body is 1/2 I w^2, where I = the moment of inertia tensor of the body and w = its angular velocity. Degrees of freedom constrained by the force and torque keywords are removed from this calculation, but only for the rigid and rigid/nve fixes.

This fix computes a global array of values which can be accessed by various output commands. The number of rows in the array is equal to the number of rigid bodies. The number of columns is 15. Thus for each rigid body, 15 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, the xyz components of the torque acting on the COM, and the xyz image flags of the COM, which have the same meaning as image flags for atom positions (see the “dump” command). The force and torque values in the array 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 ordering of the rigid bodies (by row in the array) 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 array values calculated by these fixes are “intensive”, meaning they are independent of the number of atoms in the simulation.

No parameter of these fixes can be used with the start/stop keywords of the run command. These fixes are not invoked during `energy minimization`.

## Restrictions

> none

## 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. Also Tchain = Pchain = 10, Titer = 1, Torder = 3.

(Hoover) Hoover, Phys Rev A, 31, 1695 (1985).

(Kamberaj) Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).

(Martyna) Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992); Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.

(Miller) Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, J Chem Phys, 116, 8649 (2002).

(Zhang) Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).