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lines changed Original file line number Diff line number Diff line change @@ -508,26 +508,29 @@ Detailed Explanation of YAML Input :
508508- ``input_file ``: specifies the input file name.
509509- ``output_prefix ``: specifies the prefix of the output files
510510- ``sizes ``: creates chunks of different sizes.
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511512**Subset counts **
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512514- ``MD ``: structures obtained from Molecular Dynamics (MD) simulation. Adjust according to your data.
513515- ``PCA ``: structures obtained from Principal Component Analysis (PCA).
514516- ``PCA_Surface ``: Surface'focused structures from PCA sampling.
515517- ``Random ``: Randomly selected structures for additional diversity.
516518- ``contamination ``: Fraction of outliers removed by Isolation Forest.
517519
518520**SOAP ** refers to **Smooth Overlap of Atomic Positions **:
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519522- ``species ``: adjust according to your model.
520523- ``r_cut ``: a cutoff for the neighbouring environment.
521524- ``n_max ``: max number of radial basis functions (RBF).
522525- ``l_max ``: max degree of shperical harmonics.
523526- ``sigma ``: the width of smearing.
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525- The output files contain:
528+ The output files contain:
526529 * `consolidated_dataset `: a chunk of dataset with the most diverse structures (preferred for ML training).
527530 * `MD_random_dataset `: random structures picked from MD data.
528531 * `random_dataset `: random structures from the whole dataset.
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530- Choose the subset preferred for your method and convert according `xyz ` file to `npz ` format using:
533+ Choose the subset preferred for your method and convert according `xyz ` file to `npz ` format using:
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532535 .. code-block :: bash
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