Postlammps

A tool for performing post-processing with LAMMPS log files or OpenMM state data reports.

Installation

git clone https://github.com/atoms-ufrj/postlammps<br> cd postlammps<br> make<br> sudo make install<br>

Usage

Usage: postlammps [options] action [args] property-1 [property-2 ...]<br>

• action = acfun or block or fluct or histo or ineff or print or props or sampl or stats<br>
  • acfun args = maxtime<br>
  • block args = none<br>
  • fluct args = maxtime<br>
  • histo args = nbins<br>
  • ineff args = none<br>
  • print args = none<br>
  • props args = none<br>
  • sampl args = none<br>
  • stats args = none<br>

Actions

acfun: Computes autocorrelation functions from zero to maxtime<br> block: Performs normalization group blocking analysis<br> fluct: Computes normalized fluctuation autocorrelation functions from zero to maxtime<br> histo: Builds histograms with specified number of bins<br> ineff: Computes statistical inefficiencies and uncertainties<br> print: Prints the values of the selected properties<br> props: Lists all properties available in the log file<br> sampl: Samples uncorrelated points from the original data<br> stats: Computes basic statistics<br>

Options

-in: Specifies the name of the log file to be processed<br> -p: Tells postlammps to read a plain data file instead of a lammps log file<br> -mm: Tells postlammps to read an OpenMM state-data report<br> -e n: Skips n lines after every property reading<br> -d delimiter: Specifies the item delimiter used for output<br> delimiter = space or comma or semicolon or tab<br> -nt: Does not print property titles<br> -c X: Consider only the last X% of data<br> -r X Y: Consider only data within a specified range<br>

Notes

• If option -in is not used, postlammps operates in the standard input.<br>
• A plain data file contains the property titles in the first line and the property values in the subsequent lines.<br>