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Post-Processing Scripts

Contents

Transform

awl2struct.py is a script to transform the generated L, W, A, X to the cif format.

python awl2struct.py --output_path YOUR_PATH --label SPACE_GROUP --num_io_process 40
  • output_path: the path to read the generated L, W, A, X and save the cif files
  • label: the label to save the cif files, which is the space group number
  • num_io_process: the number of processes

Structure and Composition Validity

compute_metrics.py is a script to calculate the structure and composition validity of the generated structures.

python ../scripts/compute_metrics.py --root_path YOUR_PATH --filename YOUR_FILE --output_path ./ --num_io_process 40
  • root_path: the path to the dataset
  • filename: the filename of the generated structures
  • num_io_process: the number of processes

Novelty and Uniqueness

compute_metrics_matbench.py is a script to calculate the novelty and uniqueness of the generated structures.

python ../scripts/compute_metrics_matbench.py --train_path TRAIN_PATH --test_path TEST_PATH --gen_path GEN_PATH --output_path OUTPUT_PATH --label SPACE_GROUP --num_io_process 40
  • train_path: the path to the training dataset
  • test_path: the path to the test dataset
  • gen_path: the path to the generated dataset
  • output_path: the path to save the metrics results
  • label: the label to save the metrics results, which is the space group number g
  • num_io_process: the number of processes

Note that the training, test, and generated datasets should contain the structures within the same space group g which is specified in the command --label.

Relaxation

matgl_relax.py is a script to relax the generated structures using the matgl package. You can install the matgl following the instructions in the matgl repository.

python matgl_relax.py --restore_path RESTORE_PATH --filename FILENAME --relaxation --model_path MODEL_PATH
  • restore_path: the path to the generated structures
  • filename: the filename of the generated structures
  • relaxation: whether to relax the structures, if not specified, the script will only predict the energy of the structures without relaxation
  • model_path: the path to the matgl model checkpoint

Energy Above the Hull

e_above_hull.py is a script to calculate the energy above the hull of the generated structures based on the Materials Project database. To calculate the energy above the hull, the API key of the Materials Project is required, which can be obtained from the Materials Project website. Furthermore, the mp_api package should be installed.

python e_above_hull.py --restore_path RESTORE_PATH --filename FILENAME --api_key API_KEY --label LABEL --relaxation
  • restore_path: the path to the structures
  • filename: the filename of the structures
  • api_key: the API key of the Materials Project
  • label: the label to save the energy above the hull file
  • relaxation: whether to calculate the energy above the hull based on the relaxed structures

Embedding Visualization

plot_embeddings.py is a script to visualize the correlation of the learned embedding vectors of different elements.

python plot_embeddings.py --restore_path RESTORE_PATH
  • restore_path: the path to the model checkpoint

Structure Visualization

structure_visualization.ipynb is a notebook to visualize the generated structures.