fix poems command

Syntax

fix ID group-ID poems keyword values

  • ID, group-ID are documented in fix command

  • poems = style name of this fix command

  • keyword = group or file or molecule

    group values = list of group IDs
molecule values = none
file values = filename

Examples

fix 3 fluid poems group clump1 clump2 clump3
fix 3 fluid poems file cluster.list

Description

Treats one or more sets of atoms as coupled rigid bodies. This means that each timestep the total force and torque on each rigid body is computed and the coordinates and velocities of the atoms are updated so that the collection of bodies move as a coupled set. This can be useful for treating a large biomolecule as a collection of connected, coarse-grained particles.

The coupling, associated motion constraints, and time integration is performed by the software package Parallelizable Open source Efficient Multibody Software (POEMS) which computes the constrained rigid-body motion of articulated (jointed) multibody systems (Anderson). POEMS was written and is distributed by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee, and other members of his group at Rensselaer Polytechnic Institute (RPI). Rudranarayan developed the LAMMPS/POEMS interface. For copyright information on POEMS and other details, please refer to the documents in the poems directory distributed with LAMMPS.

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, temp/rescale, langevin).

Each body must have a non-degenerate inertia tensor, which means if must contain at least 3 non-collinear atoms. Which atoms are in which bodies can be defined via several options.

For option group, each of the listed groups is treated as a rigid body. Note that only atoms that are also in the fix group are included in each rigid body.

For option molecule, each set of atoms in the group with a different molecule ID is treated as a rigid body.

For option file, sets of atoms are read from the specified file and each set is treated as a rigid body. Each line of the file specifies a rigid body in the following format:

ID type atom1-ID atom2-ID atom3-ID …

ID as an integer from 1 to M (the number of rigid bodies). Type is any integer; it is not used by the fix poems command. The remaining arguments are IDs of atoms in the rigid body, each typically from 1 to N (the number of atoms in the system). Only atoms that are also in the fix group are included in each rigid body. Blank lines and lines that begin with ‘#’ are skipped.

A connection between a pair of rigid bodies is inferred if one atom is common to both bodies. The POEMS solver treats that atom as a spherical joint with 3 degrees of freedom. Currently, a collection of bodies can only be connected by joints as a linear chain. The entire collection of rigid bodies can represent one or more chains. Other connection topologies (tree, ring) are not allowed, but will be added later. Note that if no joints exist, it is more efficient to use the fix rigid command to simulate the system.

When the poems fix is defined, it will print out statistics on the total # of clusters, bodies, joints, atoms involved. A cluster in this context means a set of rigid bodies connected by joints.

For computational efficiency, you should 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 can be used to do this if each rigid body is a group.

For computational efficiency, you should only define one fix poems which includes all the desired rigid bodies. LAMMPS will allow multiple poems fixes to be defined, but it is more expensive.

The degrees-of-freedom removed by coupled rigid bodies are accounted for in temperature and pressure computations. Similarly, the rigid body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix poems defined.

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

No information about this fix is written to binary restart files.

The fix_modify virial option is supported by this fix to add the contribution due to the added forces and torques on atoms to both the global pressure and per-atom stress of the system via the compute pressure and compute stress/atom commands. The former can be accessed by thermodynamic output. The default setting for this fix is fix_modify virial yes.

The fix_modify bodyforces option is supported by this fix style to set whether per-body forces and torques are computed early or late in a timestep, i.e. at the post-force stage or at the final-integrate stage, respectively.

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

This fix is part of the POEMS package. It is only enabled if LAMMPS was built with that package, which also requires the POEMS library be built and linked with LAMMPS. See the Build package page for more info.

Default

none

(Anderson) Anderson, Mukherjee, Critchley, Ziegler, and Lipton “POEMS: Parallelizable Open-source Efficient Multibody Software “, Engineering With Computers (2006). (link to paper)