CrystalFp
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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)