LAMMPS is run from the command line, reading commands from a file via the -in lmp_serial lammps/src/lmp_serial < src # content files for LAMMPS documentation html # HTML version of the LAMMPS manual (see html/) tools # tools and settings for building the. The LAMMPS “version” is the date when it was released, such as 1 The LAMMPS documentation is organized into the following sections.
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ID, group-ID are documented in fix command. 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 documenration 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. 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.
Each body must have pammps 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 groupeach of the vocumentation 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 moleculeeach set of atoms in the group with a different molecule ID is treated as a rigid body. For option filesets 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 as an integer from 1 to M the number of rigid bodies.
fix poems — LAMMPS documentation
Type is any integer; it is lammpe 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. A connection between a pair of rigid bodies is inferred if one atom is common to both bodies. 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.
For computational efficiency, you should only define one fix poems which includes all the desired rigid bodies.
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 lqmmps only correct if forces within the bodies have been turned off, and there is only a single fix poems defined.
No information about this fix is written to binary restart files. No global or per-atom quantities are stored by this fix for access by various output commands.
This fix is not invoked during energy minimization. Examples fix 3 fluid poems group clump1 clump2 clump3 fix 3 fluid poems file cluster.
Description Treats one or more sets of atoms as coupled rigid bodies. Each line of the file specifies a rigid body in the following format: