AMDAT

trajectory_list

trajectory_lists are the foundational data object in AMDAT. A trajectory_list stores a list of particles for analysis, which may (or may not) vary with the time frame in the trajectory. Some trajectory_lists are static and contain a fixed list of particles for analysis. Some are dynamic and may contain different particles at each time step or in each time block (in exponential or blocked time schemes).

Creating and manipulating trajectory lists

There are many methods of creating trajectory_list objects. The simplest way to create a static trajectory list is the create_list command, which allow the user to select particles based on molecular species, atom types, or other characteristics within the chemical structure of the system. More complex methods may perform some analysis on a trajectory list or some other data object and generate a dynamical trajectory_list based on some analysis of the system. A table of commands that create or destroy trajectory_list objects follows.

Commands that create or destroy trajectory_list objects

Command	Effect
create_list	Creates a static list of particle trajectories.
combine_trajectories	Creates a new list of trajectories by merging multiple existing of existing trajectory_list objects.
delete_trajectory_list	Deletes an existing trajectory_list, freeing up the associated memory.
flatten_multibodies	Creates a trajectory list comprised of all trajectories in a set of multibodies.
invert_list	Creates a new trajectory list by inverting an existing trajectory list and then intersecting it with a second list.
thresholded_list	Creates a list of trajectories by applying a value threshold to a specified value_list.
traj_list_from_bin_list	Creates a trajectory_list object from a bin of a trajectory_bin_list

In addition to the above, all commands that create multibodies also create an associated trajectory_list comprised of either the centroids or centers of mass of the multibodies, as specified by the user. See the multibodies page for more information.

Analyzing trajectory lists

Most trajectory analysis methods consist of two lines, where the first line (the “type” line) defines the type of analysis to be performed and the output file, and the second line (the “target” line) specifies the atoms or molecules on which the analysis is to be performed. The target line generally has the syntax

list <name of trajectory_list to be analyzed>

Some trajectory analysis methods must be provided two targets, which are specified via two consecutive lines below the command itself. The overall structure is then as follows.

<Analysis command> <keywords>
list <name of trajectory_list 1 for analysis>
list <name of trajectory_list 2 for analysis>

A large number of analysis tools target trajectory_list objects.

Analysis commands that target trajectory_list objects

Command	Effect	Output
clustered_list	Generates a new trajectory list by finding clustered particles in the original list.	New trajectory_list
compare_gaussian	Finds points where the self Van Hove crosses the Gaussian approximation to the self Van Hove.	Tab demarkated data file
composition	Calculates the composition and number density.	Tab demarkated data file
composition_vs_time	Calculates and outputs the composition and number density as a function of time.	Tab demarkated data file
create_distance_neighborlist	Constructs a neighborlist object based on a distance cutoff criterion	neighbor_list
create_voronoi_neighborlist	Constructs a neighborlist object based on the voronoi tesselation	neighbor_list
displacement_list	Computes the displacement of each particle at some time separation and stores the results in a value_list	Tab demarkated data file and value_list
displacement_dist	Computes the displacement of each particle at some time separation and reports a distribution	Tab demarcated data file.
displacement_map	Generates maps of particle displacement magnitude and writes to pdb files with value beta specifying displacement.	PDB file
incremental_mean_displacement	Calculates mean displacement of particles as a function of time.	Tab demarcated data file.
isf_list	Calculate full intermediate scattering function	Tab demarkated data file
isfs	Calculates the self-part of the intermediate scattering function.	Tab demarkated data file
mean_closest_distance	Calculates the average distance between particles in two distinct trajectory_lists.	Tab demarkated data file
mean_displacement	Calculates the mean (not mean square) displacement vector of all particles as a function of time.	Tab demarcated data file
msd	Calculates the mean-square displacement.	Tab demarkated data file
msd_2d	Calculates the two-dimensional mean-square displacement.	Tab demarkated data file
n_fold	Calculates mean and time dependence of n-fold order parameter and writes maps to files.	Tab demarkated data file and a PDB file
ngp	Calculates non-Gaussian parameter of the mean squared displacement.	Tab demarkated data file
rnf	Computes the mean number of particles in shells around a set of central particles	Tab demarcated data file
rdf	Computes the radial distribution function.	Tab demarkated data file
rgtensor_stats	Calculates statistics describing the radius of gyration tensor characterizing particle trajectories as a function of time.	Tab demarkated data file
stiffness_dist	Calculates distribution of inverse Debye-Waller factor values 1/u2.	Tab demarkated data file
strings	Analyzes ‘stringlike’ collective motion. Planned for deprecation in favor of string_multibodies.	Tab demarkated data file.
streamlined_strings	Functionality unknown. Requires additional investigation.	Tab demarkated data file.
string_multibodies	Builds multibodies comprised of ‘stringlike’ collective displacements	multibody_list
structure_factor	Computes the structure factor.	Tab demarkated data file
trajectory_list_decay	Computes an autocorrelation function for inclusion in the trajectory_list.	Tab demarkated data file
u2dist	Calculates distribution of square displacements at a specified time.	Tab demarkated data file
unsteady_velocity	Calculates mean velocity as a function of time, provided that velocities were read in at file read time.	Tab demarcated data file.
vac_fourier	Calculates fourier transform of velocity autocorrelation function.	Tab demarkated data file
vac_function	Calculates velocity autocorrelation function by taking two derivatives of the mean-square-displacement.	Tab demarkated data file
vhd	Calculates distinct part of the Van Hove function.	Tab demarkated data file
vhs	Calculates self-part of the Van Hove function.	Tab demarkated data file
vht	Adds together previously computed vhd and vhs.	Tab demarkated data file
write_list_trajectory	Writes to file an xyz trajectory from a trajectory list.	Trajectory file in wrapped xyz format
write_list_trajectory_full	Writes to file an xyz trajectory from a trajectory list.	Trajectory file in wrapped xyz format
write_single_particle	Writes an xyz file from a single particle, in which its locations at distinct times are written out at a single time.	xyz trajectory file
find_fast	Deprecated; does not work properly. In principle find particles that are ‘fast’ based on the above comparison between the self Van Hove and Gaussian approximation.	-
find_fast_fixedthreshold	Finds fast particles based on displacements higher than some value. Likely to become deprecated in favor of valuelist approach.	new trajectory_list
find_between	Finds particles with displacements in some value range. Likely to become deprecated in favor of valuelist approach.	new trajectory_list
gyration_radius	Deprecated; to be removed.	-
isf	Deprecated; to be removed.	-
radial_debye_waller	Computes dwf as a function of distance from (0,0,0). Planned for deprecation.
vector_autocorrelation_function	Computes autocorrelation function for a specified set of vectors. Essentially replaced by raf multibody functionality and planned for deprecation.	Tab-demarcated data file.

Finally, there are a small number of analysis tools that do not directly run on trajectory_lists, but output some transformation of a prior analysis performed on a trajectory list.

Command	Effect	Output
isfd	Deprecated and likely incorrect; to be removed.	-
structure_factor_from_rdf	Performs a fourier transform on data from a prior rdf calculation to arrive at a structure factor.	Tab demarcated data file

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