Manual page for apps.ACorr program

ACorr is a tool for computing various correlations and autocorrelations on time-series. The program reads a file with data observations in a flat format: several columns and many rows. By default it calculates an autocorrelation function for a given column [by default for the first one] for time steps in the range of [0,t_max], where t_max can be specified by option -acorr.tmax. It is also possible to calculate crosscorrelation between two columns or autocorretation of vectors

-acorr.atime=<T|F> Calculate autocorrelation time.
-acorr.block_variance=<column ids> calculate variance in blocks as a function of a block size (see Andrew R. Leach “Molecular Modeling”, p. 305)
-acorr.crosscorrelation=<column ids> provides column indexes (counting from 1) to calculate correlation between the two data columns.
-acorr.max_err=<value> maximum relative error to restrict the range for autocorrelation time estimation. If the option is not used, autocorrelation time is fit over the range defined by -acorr.tmax option
-acorr.tmax=<number> provides the upper limit for the autocorrelation function argument. If the option is not used, the limit is set to 1/20 of the data range.
-acorr.vector=<column ids> provides column indexes (counting from 1) to calculate autocorrelation of vectors.
-h print a brief summary of available options
-help=<name-part> print a help message on the screen - ANSI terminal version with visual enhancements. If <name-part> argumen is given, the program will print only these options that contains that substring
-help.dox=<name> print a help message in doxygen (*.dox) format on the screen for the ACorr program
-help.md=<name> print a help message in markdown (*.md) format on the screen
-help.option=<option-name> print a help message for a single option on the screen.
-help.plain=<name-part> print a help message on the screen - plain text version. If <name-part> argumen is given, the program will print only these options that contains that substring
-in.column.index=<number> provides a column index for input data. By default the first column is used
-in.column.indexes=<numbers> provides column indexes (counting from 1) for input data.
-in.fname=<file name> provides a name of a file with input data
-in.fnames=<file names> provides a number of input file names
-mute suppress all messages from a given package or class, e.g. “-mute=jbcl.data.formats”, or “-mute=jbcl.calc.structural.Crmsd”. It is also possible to switch of a whole branch from the jbcl library, e.g. “-mute=jbcl.data” will mute all comming from jbcl.data.formats,jbcl.data.types, jbcl.data.dict and jbcl.data.basic. To switch all the messages, say: “-mute=jbcl” or simply “-mute” because the default behaviour is to mute everything. This option is executed AFTER -verbose, so user may increase verbosity level to a desired valueand then selectively switch off logging from some packages
-out.fname=<file name> provides an output file name
-stat.normalize=<value> Normalizes a KDE estimator or a histrogram to a given value, by default to 1.0
-verbose=<integer> Sets up a verbosity level to a given value. The argument should be an integer from the rangefrom 0 (no messages at all, which is equivalent to -mute=jbcl) to 6 when everything is logged. See -mute for additional information.

EXAMPLES

      (1) Reads a file "data" and computes autocorrelation for the second
column
    java apps.ACorr -i=data -o=autocorr -acorr.tmax=100 -c=2


      (2) Reads a bunch of files from independent experiments and calculate
autocorrelation of a vector (columns 2, 3 and 4). Relaxation time will
be computed as well by fitting a curve to the region where the relative
error does not exceed 0.1 (as defined with -acorr.max_err option)
    java apps.ACorr -in.fnames=data1,data2,data3 -acorr.tmax=100 -acorr.vector=2,3,4 -acorr.max_err=0.1