Command Line switches

The driver program can set various CrystalFp parameters from the command line and produces (if needed) answers as csv files.

At a minimum the program requires a POSCAR file containing the structures. To use energy related functionality, a file containing energies (one floating point value per line in the same order as the structures in the POSCAR file) is required.

To list the available numerical options for –fingerprint-method –distance-method and –grouping-method simply follow the switch by help.

To list –scatterplot-param and –analysis-param param names simply enter h h after the switch.

Usage:
    cfp [options] POSCARfile [ENERGIESfile]

-v  --verbose (optional argument)
        Verbose level (if no argument, defaults to 1)

-?  -h  --help (no argument)
        This help

-t  --elements (required argument)
        List of chemical elements to be assigned to POSCAR atoms

-es  --max-step  --end-step (required argument)
        Last step to load (default: all)

-ss  --start-step (required argument)
        First step to load (default: first)

-et  --energy-per-structure (no argument)
        Energy from file is per structure, not per atom

-e  --energy-threshold (required argument)
        Energy threshold

-r  --threshold-from-min (required argument)
        Threshold from minimum energy

-c  --cutoff-distance (required argument)
        Fingerprint forced cutoff distance

-n  --nano-clusters  --nanoclusters (no argument)
        The structures are nanoclusters, not crystals

-b  --bin-size (required argument)
        Bin size for the pseudo-diffraction methods

-p  --peak-size (required argument)
        Peak smearing size

-x  --force-dim (required argument)
        Force to this value the total length of the fingerprint (valid only on reloading from checkpoint)

-chk  --checkpoint-dir (required argument)
        Set fingerprint checkpoint directory

-i  --ignore-checkpoint (no argument)
        Ignore previous checkpoint

-f  --fingerprint-method (required argument)
        Compute fingerprints using the given method ('help' to list all methods)

-d  --distance-method (required argument)
        Compute distances using the given method ('help' to list all methods)

-g  --grouping-method (required argument)
        Grouping method ('help' to list all methods)

-gt  --grouping-threshold (required argument)
        Grouping max distance threshold

-k  --k (required argument)
        K value needed by some grouping algorithm

-s  --summary (required argument)
        Output a summary file to be used by another program

-fo  --fld-fingerprints (required argument)
        Output fingerprints in FLD AVS format

-do  --fld-distances (required argument)
        Output distance matrix in FLD AVS format

-sd  --sorted-distances (required argument)
        Output distances in increasing order

-rd  --remove-dupl (optional argument)
        Remove duplicates substituting them with a representative structure and writing the map of indices to file

-a  --analysis (required argument)
        Create a chart for the given analysis method (can be: ax,ay or ax)

-af  --analysis-file (required argument)
        File output for analysis

-ap  --analysis-param (multiple arguments)
        Pass one parameter for the given analysis method as: code value (code: bins, part)

-sc  --scatterplot (no argument)
        Create a scatterplot

-sf  --scatterplot-file (required argument)
        File output for scatter plot

-df  --diagnostic-file (required argument)
        File output for diagnostic chart assocated to the scatterplot

-sp  --scatterplot-param (multiple arguments)
        Pass one parameter for the scatterplot as: code value (code: retry, energy, iterations, kind, diagnostic, timestep, mass, stiffness, damping, perturb, bins, wobble)