fix rigid/meso command¶
fix ID group-ID rigid/meso bodystyle args keyword values ...
ID, group-ID are documented in fix command
rigid/meso = style name of this fix command
bodystyle = single or molecule or group
single args = none molecule args = none custom args = i_propname or v_varname i_propname = an integer property defined via fix property/atom v_varname = an atom-style or atomfile-style variable 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 = reinit or force or torque or infile
reinit = yes or no 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
fix 1 ellipsoid rigid/meso single fix 1 rods rigid/meso molecule fix 1 spheres rigid/meso single force 1 off off on fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on fix 2 spheres rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off
Treat one or more sets of mesoscopic SPH/SDPD particles 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. The coordinates and velocities of the particles in each body are then updated so that the body moves and rotates as a single entity using the methods described in the paper by (Miller). Density and internal energy of the particles will also be updated. This is implemented by creating internal data structures for each rigid body and performing time integration on these data structures. Positions and velocities of the constituent particles are regenerated from the rigid body data structures in every time step. This restricts which operations and fixes can be applied to rigid bodies. See below for a detailed discussion.
The operation of this fix is exactly like that described by the fix rigid/nve command, except that particles’ density, internal energy and extrapolated velocity are also updated.
You should not update the particles in rigid bodies via other time-integration fixes (e.g. fix sph, fix sph/stationary), or you will have conflicting updates to positions and velocities resulting in unphysical behavior in most cases. When performing a hybrid simulation with some atoms in rigid bodies, and some not, a separate time integration fix like fix sph should be used for the non-rigid particles.
These fixes are overkill if you simply want to hold a collection of particles stationary or have them move with a constant velocity. To hold particles stationary use fix sph/stationary instead. If you would like to move particles with a constant velocity use fix meso/move.
The aggregate properties of each rigid body are calculated at the start of a simulation run and are maintained in internal data structures. The properties include the position and velocity of the center-of-mass of the body, its moments of inertia, and its angular momentum. This is done using the properties of the constituent particles of the body at that point in time (or see the infile keyword option). Thereafter, changing these properties of individual particles in the body will have no effect on a rigid body’s dynamics, unless they effect any computation of per-particle forces or torques. If the keyword reinit is set to yes (the default), the rigid body data structures will be recreated at the beginning of each run command; if the keyword reinit is set to no, the rigid body data structures will be built only at the very first run command and maintained for as long as the rigid fix is defined. For example, you might think you could displace the particles in a body or add a large velocity to each particle in a body to make it move in a desired direction before a second run is performed, using the set or displace_atoms or velocity commands. But these commands will not affect the internal attributes of the body unless reinit is set to yes. With reinit set to no (or using the infile option, which implies reinit no) the position and velocity of individual particles in the body will be reset when time integration starts again.
Each rigid body must have two or more particles. A particle can belong to at most one rigid body. Which particles are in which bodies can be defined via several options.
For bodystyle single the entire fix group of particles is treated as one rigid body.
For bodystyle molecule, particles are grouped into rigid bodies by their respective molecule IDs: each set of particles in the fix group with the same molecule ID is treated as a different rigid body. Note that particles with a molecule ID = 0 will be treated as a single rigid body. For a system with solvent (typically this is particles 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 particles you want to be part of rigid bodies.
Bodystyle custom is similar to bodystyle molecule except that it is more flexible in using other per-atom properties to define the sets of particles that form rigid bodies. An integer vector defined by the fix property/atom command can be used. Or an atom-style or atomfile-style variable can be used; the floating-point value produced by the variable is rounded to an integer. As with bodystyle molecule, each set of particles in the fix groups with the same integer value is treated as a different rigid body. Since fix property/atom vectors and atom-style variables produce values for all particles, you should be careful to use a fix group that only includes particles you want to be part of rigid bodies.
For bodystyle group, each of the listed groups is treated as a separate rigid body. Only particles that are also in the fix group are included in each rigid body.
To compute the initial center-of-mass position and other properties of each rigid body, the image flags for each particle in the body are used to “unwrap” the particle coordinates. Thus you must insure that these image flags are consistent so that the unwrapping creates a valid rigid body (one where the particles are close together) , particularly if the particles 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 particle 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 particle must be 0 in that dimension, else an error is generated.
By default, each rigid body is acted on by other particles 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 or 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 bodies 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 should typically define one fix rigid/meso command which includes all the desired rigid bodies. LAMMPS will allow multiple rigid/meso fixes to be defined, but it is more expensive.
The keyword/value option pairs are used in the following ways.
The reinit keyword determines, whether the rigid body properties are re-initialized between run commands. With the option yes (the default) this is done, with the option no this is not done. Turning off the re-initialization can be helpful to protect rigid bodies against unphysical manipulations between runs or when properties cannot be easily re-computed (e.g. when read from a file). When using the infile keyword, the reinit option is automatically set to no.
The infile keyword allows a file of rigid body attributes to be read in from a file, rather then having LAMMPS compute them. There are 5 such attributes: the total mass of the rigid body, its center-of-mass position, its 6 moments of inertia, its center-of-mass velocity, and the 3 image flags of the center-of-mass position. For rigid bodies consisting of point particles or non-overlapping finite-size particles, LAMMPS can compute these values accurately. However, for rigid bodies consisting of finite-size particles which overlap each other, LAMMPS will ignore the overlaps when computing these 4 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 vxcm vycm vzcm lx ly lz ixcm iycm izcm ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm ... IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
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, LAMMPS 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 principal axes of the rigid body itself. LAMMPS performs the latter calculation internally.
The (vxcm,vycm,vzcm) values are the velocity of the center of mass. The (lx,ly,lz) values are the angular momentum of the body. The (vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you wish the body to have no initial motion.
The (ixcm,iycm,izcm) values are the image flags of the center of mass of the body. For periodic dimensions, they specify which image of the simulation box the body is considered to be in. An image of 0 means it is inside the box as defined. A value of 2 means add 2 box lengths to get the true value. A value of -1 means subtract 1 box length to get the true value. LAMMPS updates these flags as the rigid bodies cross periodic boundaries during the simulation.
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. 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.
Restart, fix_modify, output, run start/stop, minimize info¶
No information is written to binary restart files. If the infile keyword is used, an auxiliary file is written out with rigid body information each time a restart file is written, as explained above for the infile keyword.
None of the fix_modify options are relevant to this fix.
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 28. Thus for each rigid body, 28 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 components of the 4-vector quaternion representing the orientation of the rigid body, the xyz components of the angular velocity of the body around its COM, the xyz components of the torque acting on the COM, the 3 principal components of the moment of inertia, the xyz components of the angular momentum of the body around its COM, and the xyz image flags of the COM.
The center of mass (COM) for each body is similar to unwrapped coordinates written to a dump file. It will always be inside (or slightly outside) the simulation box. The image flags have the same meaning as image flags for particle positions (see the “dump” command). This means you can calculate the unwrapped COM by applying the image flags to the COM, the same as when unwrapped coordinates are written to a dump file.
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 this fix are “intensive”, meaning they are independent of the number of particles 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.
This fix is part of the USER-SDPD package and also depends on the RIGID package. It is only enabled if LAMMPS was built with both packages. See the Build package doc page for more info.
This fix requires that atoms store density and internal energy as defined by the atom_style sph command.
All particles in the group must be mesoscopic SPH/SDPD particles.
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 reinit = yes.
(Miller) Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, J Chem Phys, 116, 8649 (2002).