| Command | Effect |
|---|---|
create_bin_list |
Creates a list of all trajectories based on a binning scheme |
remove_bin_list |
Deletes a bin list from memory |
Analysis commands that target trajectory list objects
Similarly to trajectory_list, these commands’ syntax includes a “type” line, which has the name of the analysis method, followed by a “target” line. This target line involves specifying a defined trajectory_bin_list and a trajectory_list. Analysis will occur on a bin-by-bin basis as determined by the trajectory_bin_list specified. Only those particles included in the specified trajectory_list at each time will be employed in the analysis. The syntax of the target line is as follows.
bin_list <name of trajectory_bin_list> <name of trajectory_list> <persistence check? 0 or 1 (optional)>
Put another way, this takes the intersection of the trajectory_list and each bin of the trajectory_bin_list, and performs the calculation on each bin individually. The analysis will in general output a separate tab-demarcated file for each bin, which may produce a large number of files. An ending will be appended to the name of each output file with the bin indicies (e.g. <output file>.2.1.2.bindata)
The optional argument <persistence check> specifies whether or not, for dynamic analyses, the algorithm retains only particles that are in the bin at start and end times of a given time gap. The default is zero, meaning this check is not performed.
| Command | Effect | Output |
|---|---|---|
composition |
Calculates the composition and number density. | Tab demarcated data file |
find_edge |
Finds the leading edge of a set of particles along a vector. | Tab demarcated data file |
incremental_mean_displacement |
Calculates mean displacement of particles as a function of time. | Tab demarcated data file. |
isfs |
Calculates the self-part of the intermediate scattering function. | Tab demarcated 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 demarcated data file |
msd_2d |
Calculates the two-dimensional mean-square displacement. | Tab demarcated data file |
structure_factor |
Computes the structure factor. | Tab demarcated data file |
trajectory_list_decay |
Computes an autocorrelation function for inclusion in the trajectory_list. |
Tab demarcated 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. |
write_bin_xyz |
Writes xyz files for all bins. | Series of xyz trajectory files |