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
cd postlammps
make
sudo make install

Usage

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

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

Actions

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

Options

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

Notes

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