From 6ad25bb4cd5822fa84d1c4cec54952c6fd8df2f6 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Thu, 27 Feb 2020 21:41:41 -0700
Subject: Add rest of the descriptors
---
ml_exp/do_ml.py | 95 ++++++++++++++++++++++++++++++++++++++++++---------------
1 file 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()
--
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