diff options
| -rw-r--r-- | ml_exp/do_ml.py | 95 |
1 files changed, 70 insertions, 25 deletions
diff --git a/ml_exp/do_ml.py b/ml_exp/do_ml.py index 40243d413..d8ee415bf 100644 --- a/ml_exp/do_ml.py +++ b/ml_exp/do_ml.py @@ -106,10 +106,14 @@ def do_ml(db_path='data', lj_sigma=1.0, lj_epsilon=1.0, use_forces=False, + stuff='bonds', size=23, as_eig=True, bohr_ru=False, + training_size=1500, + test_size=None, sigma=1000.0, + identifiers=["CM"], show_msgs=True): """ Main function that does the whole ML process. @@ -120,12 +124,20 @@ def do_ml(db_path='data', lj_sigma: sigma value. lj_epsilon: epsilon value. use_forces: if the use of forces instead of k_cx should be used. + stuff: elements of the bag, by default the known bag of bonds. size: compound size. as_eig: if the representation should be as the eigenvalues. bohr_ru: if radius units should be in bohr's radius units. + training_size: size of the training set to use. + test_size: size of the test set to use. If no size is given, + the last remaining molecules are used. sigma: depth of the kernel. + identifiers: list of names (strings) of descriptors to use. show_msgs: if debug messages should be shown. """ + if type(identifiers) != list: + raise TypeError('\'identifiers\' is not a list.') + init_time = time.perf_counter() # Data reading. @@ -141,24 +153,34 @@ def do_ml(db_path='data', # Matrices calculation. tic = time.perf_counter() for compound in compounds: - compound.gen_cm(size=size, - as_eig=as_eig, - bohr_ru=bohr_ru) - compound.gen_ljm(diag_value=diag_value, - sigma=lj_sigma, - epsilon=lj_epsilon, - size=size, - as_eig=as_eig, - bohr_ru=bohr_ru) - compound.gen_am(use_forces=use_forces, - size=size, - bohr_ru=bohr_ru) + if 'CM' in identifiers: + compound.gen_cm(size=size, + as_eig=as_eig, + bohr_ru=bohr_ru) + if 'LJM' in identifiers: + compound.gen_ljm(diag_value=diag_value, + sigma=lj_sigma, + epsilon=lj_epsilon, + size=size, + as_eig=as_eig, + bohr_ru=bohr_ru) + if 'AM' in identifiers: + compound.gen_am(use_forces=use_forces, + size=size, + bohr_ru=bohr_ru) + if 'BOS' in identifiers: + compound.gen_bos(size=size, + stuff=stuff) # Create a numpy array for the descriptors. - cm_data = np.array([compound.cm for compound in compounds], dtype=float) - ljm_data = np.array([compound.ljm for compound in compounds], dtype=float) - am_data = np.array([compound.cm for compound in compounds], dtype=float) - print(cm_data.shape, ljm_data.shape, am_data.shape) + if 'CM' in identifiers: + cm_data = np.array([comp.cm for comp in compounds], dtype=float) + if 'LJM' in identifiers: + ljm_data = np.array([comp.ljm for comp in compounds], dtype=float) + if 'AM' in identifiers: + am_data = np.array([comp.cm for comp in compounds], dtype=float) + if 'BOS' in identifiers: + bos_data = np.array([comp.bos for comp in compounds], dtype=float) toc = time.perf_counter() tictoc = toc - tic @@ -166,15 +188,38 @@ def do_ml(db_path='data', printc(f'Matrices calculation took {tictoc:.4f} seconds.', 'CYAN') # ML calculation. - # CM - cm_mae, cm_tictoc = simple_ml(cm_data, - energy_pbe0, - training_size=5000, - test_size=1500, - sigma=1000.0, - identifier='CM', - show_msgs=show_msgs) - print(cm_mae, cm_tictoc) + if 'CM' in identifiers: + cm_mae, cm_tictoc = simple_ml(cm_data, + energy_pbe0, + training_size=training_size, + test_size=test_size, + sigma=sigma, + identifier='CM', + show_msgs=show_msgs) + if 'LJM' in identifiers: + ljm_mae, ljm_tictoc = simple_ml(ljm_data, + energy_pbe0, + training_size=training_size, + test_size=test_size, + sigma=sigma, + identifier='LJM', + show_msgs=show_msgs) + if 'AM' in identifiers: + am_mae, am_tictoc = simple_ml(am_data, + energy_pbe0, + training_size=training_size, + test_size=test_size, + sigma=sigma, + identifier='CM', + show_msgs=show_msgs) + if 'BOS' in identifiers: + bos_mae, bos_tictoc = simple_ml(bos_data, + energy_pbe0, + training_size=training_size, + test_size=test_size, + sigma=sigma, + identifier='CM', + show_msgs=show_msgs) # End of program end_time = time.perf_counter() |