Versatile command that can do several things based on the keyword that follows. The general structure is as follows.
value_list <keyword> <arguments>
A list of keywords and associated arguments is as follows.
value_list threshold_value <value list name> <new trajectory list to create> <threshold keyword> <threshold1> <optional: threshold 2>
Constructs a new trajectory list, by selecting only those particles with values in the selected value list that are above, below, or between selected threshold values.
<threshold keyword> may be greater, less, or between. When greater, <threshold1> sets the value above which particles are selected and <threshold2> is not used. When less, <threshold1> sets the value below which particles are selected and <threshold2> is not used. When between, <threshold1> sets the value above which particles are selected and <threshold2> sets the value below which particles are selected.
value_list threshold_percentile <value list name> <new trajectory list to create> <threshold keyword> <percentile threshold1> <optional: percentile threshold 2>
Constructs a new trajectory list, by selecting only those particles whose values in the selected value list are in a specified percentile range (among all values in the list), either above, below, or between selected threshold percentile values.
<threshold keyword> may be greater, less, or between. When greater, <threshold1> sets the percentile value above which particles are selected and <threshold2> is not used. When less, <threshold1> sets the percentile value below which particles are selected and <threshold2> is not used. When between, <threshold1> sets the value above which particles are selected and <threshold2> sets the percentile value below which particles are selected.
value_list write_pdb <value list name> <output file name stem> <value time index> <position time index> <optional: maximum value to write out>
Writes out a .pdb file in which the value in the beta column is drawn from a value list. This can readily allow visualization of the system with particles colored by a computed per-particle value in VMD or OVITO. <output file name stem> is the filename prior to the .pdb suffix, which will be added by AMDAT before writing. <value time index> specifies the time at which the value will be drawn from the value list. <position time index> specifies the time at which the configuration will be written. The optional maximum value argument will set a largest value to be written to the beta value in the pdb file; any value higher than this will be reduced to this value. This can help in visualization work where a small number of high values can ‘blow out’ the color scale.