The utilities included here are typically quick text-processing utilities that perform simple manipulations such as smoothing data, sorting/histogramming, translating one format to another, etc. These utilities are UNIX-based, are designed to be used in conjunction with the standard UNIX utilities sed, awk, and grep to build elegant pipelines for the processing of data streams. A basic understanding of these standard UNIX utilities will enable the user to perform analyses of data from xyz, car, psf, and other common formats.
vacuumms Provides the release version of VACUUMMS and the options with which it was built.
avg calculates average value of input set sum calculates sum of input set max returns maximum value from input set min returns minimum value from input set std returns standard deviation (provide mean on command line) from input set miss Finds the missing number in a series of values from input set
loge the natural logs log10 the logs base 10 exp the exponentials sqrt the square roots sq the squares pow the input values raised to the power specified on the command line recip output the reciprocal of the input expr_add the input values plus the quantity specified on the command line expr_multiply the input values multiplied by the quantity specified on the command line stream_multiply like expr_multiply, but accepts multiple quantities on the command line
dst2hst Transforms a distribution to a histogram wdst2hst Transforms a weighted distribution to a histogram
add Adds a list of tabulated functions. In: list of files (two fields, separated by tabs) on the command line Out: A tabulated function the sum of the input functions. normalize In: Tabulated function Out: Normalized tabulated function sew Accepts a list of tabulated functions, sews them together columnwise to generate a single output
uniq In: List of cavities in .cav format Out: List of unique cavities in .cav format a2b In: 2 files of .cfg format, same number of lines Out: a list of distances from pt A (1st file) to pt B (2nd file) dwf For estimating Debye-Waller factor... generates a list of squares of distances from first to second smooth In: A tabulated function Out: Smoothed version of function cram In: A .gfg format list of atoms, plus box dimensions (at command line) Out: A .gfg format list of atoms, wrapped for the periodic boundary condition. povheader Writes a povray header, according to params specified on command line stack_tiffs Takes a stack of 2D tiff images and converts them to a single 3D tiff replicate_gfg Takes a 3D configuration and copies it into the 26 surrounding periodic boxes. replicate_cav Takes a 3D configuration of cavities and copies it into the 26 surrounding periodic boxes. ftw_cuda Checks to see if a CUDA-capable device is present truncate Capture a subset of gfg data by specifying two corners of a bounding box. ck Count number of lines .cav format read clustercat In: Individual clusters of cavities Out: Multiple clusters of cavities
stream2slice slices a data stream into files with the specified number of lines fvi2tiff generates a 3D TIFF from fvi data cfg2gfg adds columns (default values of 1.0f for sigma and epsilon) gfg2pov generates povray format from gfg gfgc2pov generates povray format from gfgc fvi2pov generates povray format from fvi data cav2pov generates povray format from cavity list vis2pov generates povray format from vis cav2vis generates vis format from cav cfg2vis generates vis format from cfg gfg2fvi A utility for generating free volume index/FVI data from configuration/gfg; requires GPU and CUDA utils sgfg2fvi Serial version of utility for generating free volume index/FVI data from configuration/gfg