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docs/Machine_Learning_Force_Fields
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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 :
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- ``input_file ``: specifies the input file name.
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- ``output_prefix ``: specifies the prefix of the output files
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- ``sizes ``: creates chunks of different sizes.
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**Subset counts **
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- ``MD ``: structures obtained from Molecular Dynamics (MD) simulation. Adjust according to your data.
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- ``PCA ``: structures obtained from Principal Component Analysis (PCA).
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- ``PCA_Surface ``: Surface'focused structures from PCA sampling.
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- ``Random ``: Randomly selected structures for additional diversity.
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- ``contamination ``: Fraction of outliers removed by Isolation Forest.
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**SOAP ** refers to **Smooth Overlap of Atomic Positions **:
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- ``species ``: adjust according to your model.
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- ``r_cut ``: a cutoff for the neighbouring environment.
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- ``n_max ``: max number of radial basis functions (RBF).
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- ``l_max ``: max degree of shperical harmonics.
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- ``sigma ``: the width of smearing.
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- The output files contain:
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+ The output files contain:
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* `consolidated_dataset `: a chunk of dataset with the most diverse structures (preferred for ML training).
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* `MD_random_dataset `: random structures picked from MD data.
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* `random_dataset `: random structures from the whole dataset.
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- Choose the subset preferred for your method and convert according `xyz ` file to `npz ` format using:
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+ Choose the subset preferred for your method and convert according `xyz ` file to `npz ` format using:
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.. code-block :: bash
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