Cosine and SOAP Deduplication Tool

Supports single .xyz file or folder with multiple .xyz files.

Install

pip install .

Useage

COSOAP [-h] [-i INPUT_PATH] [-p NPROC] [-m {fps,threshold}] [-n NUM] [-s SIMLT] [-a ATOMS] [-r RCUT]

optional arguments:

  -h, --help            
                    show this help message and exit
                    
  -i INPUT_PATH, --input INPUT_PATH
                    Input: single .xyz/.extxyz file or folder
                    
  -p NPROC, --nproc NPROC
                    Number of processes
                    
  -m {fps,threshold}, --mode {fps,threshold}
                    Selection mode: 'fps' (select fixed N) or 'threshold' (remove duplicates). Default: fps
                    
  -n NUM, --num NUM     
                    [FPS Mode] Total number of structures to select. Default: 1000
  
  -s SIMLT, --simlT SIMLT
                    [Threshold Mode] Similarity threshold (1 - cosine). Default: 0.005
                    
  -a ATOMS, --atoms ATOMS
                    SOAP centers (e.g. 'C H O')
                    
  -r RCUT, --rcut RCUT  
                    SOAP cutoff radius

Output files:

train.xyz       : Unique labeled structures

test.xyz        : Similar labeled structures (for validation)


soap_cache/     : Cached descriptors (reused on rerun)