Using this file can construct KRR model, and then apply the KRR model to relax structures of Au25 clusters. requirement python code: numpy, dscribe(1.0.0 version), ase In data directory, Au25-0-Vacuum-fix-gold contains force fields files. 1, Constructing KRR and GPR models (our final model) In the "data" directory, "iniS.xyz", "ini_dftE", "ini_groE" are used for construnct the MBTR-KRR-FF-AL and MBTR-GPR-FF-AL model. To construct KRR and GPR model, it is need to use the bash script ("save_model.sh") to run "save_model.py" (sbatch save_model.sh), then the models are constructed and saved. 2, Mean absolute erro of energy To compute the MAE, we can use KRR model to predict energies. The function "calculate" in "gromacs_ml_calculator_gpr1.py" can be used to predict DFT energies. Then the prediction can compared with reference energy and force ("data/new_1000_test_dft" and "data/new_1000_test_gro"). 3, Using our saved model to relax structures In the "data" directory, we proveided 100 GROMACS relaxed structures and their DFT energies ("test_for_100relax.xyz" and "test_for_100relax"). To relax these 100 structures with our ML models, it is need to use the bash script ("runs.sh") to run "01-relax-test.py" (sbatch runs.sh).

2023