AMDAT

multibodies

A multibody is an entity that consists of multiple particles (each with its own trajectory). Multibodies are tracked and analyzed via multibody_lists, each of which contains a list of many multibodies that may change with time. These objects allow for analysis of internal degrees of freedom of multiparticle entities. In general, no multibodies are defined at the beginning of an instance of AMDAT. This is distinct from the case of trajectory_list, where the underlying trajectories in many cases already exist at the beginning of an AMDAT run (since they consist of particles created during trajectory file read-in). Therefore, some methods create multibodies themselves, which are organized into multibody_lists for analysis. Others merely create new multibody_lists storing existing multibodies.

Commands that create multibodies and multibody lists

Command	Effect
create_multibodies	Creates multibodies based upon specified locations within molecules
comover_multibodies	Creates multibodies comprised of particles that remain neighbors based on some distance cutoff. (In beta, not ready for general use, may be removed.)
relative_displacement_strings	Creates multibodies comprised of particles that move together. (In beta, not ready for general use, may be removed.)
string_multibodies	Builds multibodies comprised of ‘stringlike’ collective displacements

Commands that create new multibody lists from existing multibodies or delete multibody lists

Command	Effect
combine_multibody_lists	Creates a new multibody_list by merging a set of existing multibody_lists
region_multibody_list	Creates a new multibody_list by sorting an existing multibody_list into spatial bins based on their centroid or center of mass location
region_bead_multibody_list	Creates a new multibody_list by sorting an existing multibody_list into spatial bins based their constituent beads lying within a specified region
threshold_multibody_list	Creates a new multibody_list by downselecting a multibody_list based on the number of bodies in each multibody.
delete_multibody_list	Deletes an existing multibody_list and frees the associated memory. Does not delete the underlying multibodies themselves.

Analyzing multibody lists

The target multibody_list for these analysis tools is generally provided as an argument within the command line itself.

Command	Effect	Output
flatten_multibodies	Generates a trajectory_list containing all particles in multibodies in the specified multibody_list.	new trajectory_list
gyration_radius	Computes the mean multibody gyration radius of for the multibodies in a specified multibody_list.	Tab-demarcated data file
orientational_correlation	Calculates the orientational correlation of 2-body multibodies with an externally defined vector.	Tab-demarcated data file
raf	Computes the reorientation autocorrelation function for a list of 2-body multibodies.	Tab-demarcated data file
size_statistics	Reports statistics on the distribution of the number of bodies in multibodies in a given multibody_list.	Tab-demarcated data file
baf	Deprecated and planned for removal.	-

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