From fe4e5afebaf7320ba5bed7f159c84bc5d1e5faec Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 06:23:02 -0700
Subject: Rename bos to bob
---
ml_exp/compound.py | 9 +++------
ml_exp/representations.py | 15 +++++++--------
2 files changed, 10 insertions(+), 14 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 1598fa482..4dbd8c95c 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -116,18 +116,15 @@ class Compound:
forces,
size=size)
- def gen_bos(self,
- size=23,
- stuff='bonds'):
+ def gen_bob(self,
+ size=23):
"""
Generate the Bag of Stuff for the compound.
size: compound size.
- stuff: elements of the bag, by default the known bag of bonds.
"""
self.bos = bag_of_stuff(self.cm,
self.atoms,
- size=size,
- stuff=stuff)
+ size=size)
def read_xyz(self,
filename):
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index ea079595e..d4e79c7d9 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -308,10 +308,9 @@ def check_bond(bags,
return False, None
-def bag_of_stuff(cm,
+def bag_of_bonds(cm,
atoms,
- size=23,
- stuff='bonds'):
+ size=23):
"""
Creates the Bag of Bonds using the Coulomb Matrix.
cm: coulomb matrix.
@@ -366,19 +365,19 @@ generated as the vector of eigenvalues, try (re-)generating the CM.')
bonds.append(''.join(sorted([a_i, a_j])))
bonds = atom_list + bonds
- # Create the final vector for the bos.
- bos = np.zeros(bond_size, dtype=float)
+ # Create the final vector for the bob.
+ bob = np.zeros(bond_size, dtype=float)
c_i = 0
for i, bond in enumerate(bonds):
checker = check_bond(bags, bond)
if checker[0]:
for j, num in enumerate(sorted(bags[checker[1]][1:])[::-1]):
- # Use c_i as the index for bos if the zero padding should
+ # Use c_i as the index for bob if the zero padding should
# be at the end of the vector instead of between each bond.
- bos[i*size + j] = num
+ bob[i*size + j] = num
c_i += 1
else:
print(f'Error. Bond {bond} from bond list coudn\'t be found',
'in the bags list. This could be a case where the atom',
'is only present oncce in the molecule.')
- return bos
+ return bob
--
cgit v1.2.3-70-g09d2
From d71927fc791e51bf383b88bd3d943d8e3311ee8a Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 06:23:28 -0700
Subject: Rename bos to bob
---
ml_exp/compound.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 4dbd8c95c..98e31532f 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -46,7 +46,7 @@ class Compound:
self.cm = None
self.ljm = None
self.am = None
- self.bos = None
+ self.bob = None
if xyz is not None:
self.read_xyz(xyz)
@@ -122,7 +122,7 @@ class Compound:
Generate the Bag of Stuff for the compound.
size: compound size.
"""
- self.bos = bag_of_stuff(self.cm,
+ self.bob = bag_of_stuff(self.cm,
self.atoms,
size=size)
--
cgit v1.2.3-70-g09d2
From 6dd33013265ce38122a623b285e0b39f2496aaf8 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 07:19:46 -0700
Subject: Rewrite fnm
---
ml_exp/compound.py | 33 +++++++++++++++++----------
ml_exp/representations.py | 58 ++++++++++++++++-------------------------------
2 files changed, 40 insertions(+), 51 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 98e31532f..ceace6984 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -33,20 +33,29 @@ class Compound:
Initialization of the Compound.
xyz: (path to) the xyz file.
"""
+ # General compound data.
self.name = None
-
self.n = None
- self.extra = None # In case a comment is in the compound file.
+ self.extra = None
self.atoms = None
self.atoms_nc = None
self.coordinates = None
self.pbe0 = None
self.delta = None
+ # Computed data.
self.cm = None
self.ljm = None
+ self.fnm = None
self.am = None
self.bob = None
+ self.bo_atoms = None
+ self.bok_cx = None
+ self.bof = None
+
+ # Helping data.
+ self.bonds = None
+ self.forces = None
if xyz is not None:
self.read_xyz(xyz)
@@ -103,17 +112,17 @@ class Compound:
bohr_ru: if radius units should be in bohr's radius units.
"""
# First, generate the first neighor matrix.
- fnm, bonds, forces = first_neighbor_matrix(self.coordinates,
- self.atoms_nc,
- self.atoms,
- size=size,
- use_forces=use_forces,
- bohr_ru=bohr_ru)
-
+ fnm_data = first_neighbor_matrix(self.coordinates,
+ self.atoms_nc,
+ self.atoms,
+ size=size,
+ use_forces=use_forces,
+ bohr_ru=bohr_ru)
+ self.fnm, self.bonds, self.forces = fnm_data
# Now, generate the adjacency matrix.
- self.am = adjacency_matrix(fnm,
- bonds,
- forces,
+ self.am = adjacency_matrix(self.fnm,
+ self.bonds,
+ self.forces,
size=size)
def gen_bob(self,
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index d4e79c7d9..515821290 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -181,11 +181,11 @@ def first_neighbor_matrix(coords,
bohr_ru: if radius units should be in bohr's radius units.
NOTE: Bond distance of carbon to other elements
are (for atoms present in the qm7 dataset):
- C: 1.20 - 1.54 A (Edited to 1.19 - 1.54 A)
- H: 1.06 - 1.12 A
- O: 1.43 - 2.15 A
- N: 1.47 - 2.10 A
- S: 1.81 - 2.55 A
+ C: 1.19 - 1.54 A, 1.0
+ H: 1.06 - 1.12 A, 1.0
+ O: 1.43 - 2.15 A, 0.8
+ N: 1.47 - 2.10 A, 1.0
+ S: 1.81 - 2.55 A, 0.7
"""
if bohr_ru:
cr = 0.52917721067
@@ -210,7 +210,11 @@ size. Arrays are not of the right shape.')
cn_bond = sorted(['C', 'N'])
cs_bond = sorted(['C', 'S'])
- fnm = np.zeros((size, size), dtype=float)
+ pos_bonds = {cc_bond: (1.19, 1.54), ch_bond: (1.06, 1.12),
+ co_bond: (1.43, 2.15), cn_bond: (1.47, 2.19),
+ cs_bond: (1.81, 2.55)}
+
+ fnm = np.zeros((size, size), dtype=bool)
bonds = []
forces = []
@@ -219,39 +223,15 @@ size. Arrays are not of the right shape.')
# Ignore the diagonal.
if i != j:
bond = sorted([atoms[i], atoms[j]])
- rv = xyz_i - xyz_j
- r = np.linalg.norm(rv)/cr
-
- # Check for each type of bond.
- if (cc_bond == bond) and (r >= 1.19 and r <= 1.54):
- fnm[i, j] = 1.0
- if j > i:
- bonds.append((i, j))
- if use_forces:
- forces.append(rv*nc[i]*nc[j]/r**3)
- elif (ch_bond == bond) and (r >= 1.06 and r <= 1.12):
- fnm[i, j] = 1.0
- if j > i:
- bonds.append((i, j))
- if use_forces:
- forces.append(rv*nc[i]*nc[j]/r**3)
- elif (co_bond == bond) and (r >= 1.43 and r <= 2.15):
- fnm[i, j] = 0.8
- if j > i:
- bonds.append((i, j))
- if use_forces:
- forces.append(rv*nc[i]*nc[j]/r**3)
- elif (cn_bond == bond) and (r >= 1.47 and r <= 2.10):
- fnm[i, j] = 1.0
- if j > i:
- bonds.append((i, j))
- if use_forces:
- forces.append(rv*nc[i]*nc[j]/r**3)
- elif (cs_bond == bond) and (r >= 1.81 and r <= 2.55):
- fnm[i, j] = 0.7
- if j > i:
- bonds.append((i, j))
- if use_forces:
+ if bond in pos_bonds.keys():
+ r_min = pos_bonds[bond][0]
+ r_max = pos_bonds[bond][1]
+ rv = xyz_i - xyz_j
+ r = np.linalg.norm(rv)/cr
+ if r >= r_min and r <= r_max:
+ fnm[i, j] = True
+ if j > i:
+ bonds.append((i, j))
forces.append(rv*nc[i]*nc[j]/r**3)
return fnm, bonds, forces
--
cgit v1.2.3-70-g09d2
From 5bf923679707fd1603a6f73ca4d0ae8ec39e7858 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 07:40:33 -0700
Subject: Almost completely rewrite fnm to hd
---
ml_exp/__init__.py | 4 ++--
ml_exp/compound.py | 38 +++++++++++++++++++++++---------------
ml_exp/representations.py | 36 +++++++++++++++++++-----------------
3 files changed, 44 insertions(+), 34 deletions(-)
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index 48ece56c8..9e64d7754 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -22,7 +22,7 @@ SOFTWARE.
"""
from ml_exp.compound import Compound
from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
- first_neighbor_matrix, adjacency_matrix, check_bond, bag_of_stuff
+ get_helping_data, adjacency_matrix, check_bond, bag_of_stuff
from ml_exp.math import cholesky_solve
from ml_exp.qm7db import qm7db
from ml_exp.do_ml import simple_ml, do_ml
@@ -30,7 +30,7 @@ from ml_exp.do_ml import simple_ml, do_ml
__all__ = ['Compound',
'coulomb_matrix',
'lennard_jones_matrix',
- 'first_neighbor_matrix',
+ 'get_helping_data',
'adjacency_matrix',
'check_bond',
'bag_of_stuff',
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index ceace6984..26e393510 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -23,7 +23,7 @@ SOFTWARE.
import numpy as np
from ml_exp.data import NUCLEAR_CHARGE
from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
- first_neighbor_matrix, adjacency_matrix, bag_of_stuff
+ get_helping_data, adjacency_matrix, bag_of_stuff
class Compound:
@@ -46,7 +46,6 @@ class Compound:
# Computed data.
self.cm = None
self.ljm = None
- self.fnm = None
self.am = None
self.bob = None
self.bo_atoms = None
@@ -54,8 +53,11 @@ class Compound:
self.bof = None
# Helping data.
+ self.fnm = None
self.bonds = None
- self.forces = None
+ self.bonds_i = None
+ self.bonds_k = None
+ self.bonds_f = None
if xyz is not None:
self.read_xyz(xyz)
@@ -101,28 +103,34 @@ class Compound:
as_eig=as_eig,
bohr_ru=bohr_ru)
- def gen_am(self,
- use_forces=False,
+ def gen_hd(self,
size=23,
bohr_ru=False):
"""
+ Generate the helping data for use in Adjacency Matrix, for example.
+ size: compund size.
+ bohr_ru: if radius units should be in bohr's radius units.
+ """
+ hp = get_helping_data(self.coordinates,
+ self.nc,
+ self.atoms,
+ size=size,
+ bohr_ru=bohr_ru)
+
+ self.fnm, self.bonds, self.bonds_i, self.bonds_k, self.bonds_f = hp
+
+ def gen_am(self,
+ use_forces=False,
+ size=23):
+ """
Generate the Adjacency Matrix for the compund.
use_forces: if the use of forces instead of k_cx should be used.
size: compound size.
bohr_ru: if radius units should be in bohr's radius units.
"""
- # First, generate the first neighor matrix.
- fnm_data = first_neighbor_matrix(self.coordinates,
- self.atoms_nc,
- self.atoms,
- size=size,
- use_forces=use_forces,
- bohr_ru=bohr_ru)
- self.fnm, self.bonds, self.forces = fnm_data
- # Now, generate the adjacency matrix.
self.am = adjacency_matrix(self.fnm,
self.bonds,
- self.forces,
+ self.bonds_f,
size=size)
def gen_bob(self,
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 515821290..5e684314b 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -166,18 +166,17 @@ size. Arrays are not of the right shape.')
return lj
-def first_neighbor_matrix(coords,
- nc,
- atoms,
- size=23,
- use_forces=False,
- bohr_ru=False):
+def get_helping_data(coords,
+ nc,
+ atoms,
+ size=23,
+ bohr_ru=False):
"""
- Creates the First Neighbor Matrix from the molecule data given.
+ Creates helping data such as the First Neighbor Matrix for the compound.
coords: compound coordinates.
nc: nuclear charge data.
atoms: list of atoms.
- use_forces: if the use of forces instead of k_cx should be used.
+ size: compund size.
bohr_ru: if radius units should be in bohr's radius units.
NOTE: Bond distance of carbon to other elements
are (for atoms present in the qm7 dataset):
@@ -209,15 +208,15 @@ size. Arrays are not of the right shape.')
co_bond = sorted(['C', 'O'])
cn_bond = sorted(['C', 'N'])
cs_bond = sorted(['C', 'S'])
-
- pos_bonds = {cc_bond: (1.19, 1.54), ch_bond: (1.06, 1.12),
- co_bond: (1.43, 2.15), cn_bond: (1.47, 2.19),
- cs_bond: (1.81, 2.55)}
+ pos_bonds = {cc_bond: (1.19, 1.54, 1.0), ch_bond: (1.06, 1.12, 1.0),
+ co_bond: (1.43, 2.15, 0.8), cn_bond: (1.47, 2.19, 1.0),
+ cs_bond: (1.81, 2.55, 0.7)}
fnm = np.zeros((size, size), dtype=bool)
-
bonds = []
- forces = []
+ bonds_i = []
+ bonds_k = []
+ bonds_f = []
for i, xyz_i in enumerate(coords):
for j, xyz_j in enumerate(coords):
# Ignore the diagonal.
@@ -230,11 +229,14 @@ size. Arrays are not of the right shape.')
r = np.linalg.norm(rv)/cr
if r >= r_min and r <= r_max:
fnm[i, j] = True
+ # Only add to the list if in the upper triangle.
if j > i:
- bonds.append((i, j))
- forces.append(rv*nc[i]*nc[j]/r**3)
+ bonds.append(bond)
+ bonds_i.append((i, j))
+ bonds_k.append(pos_bonds[bond][2])
+ bonds_f.append(rv*nc[i]*nc[j]/r**3)
- return fnm, bonds, forces
+ return fnm, bonds, bonds_i, bonds_k, bonds_f
def adjacency_matrix(fnm,
--
cgit v1.2.3-70-g09d2
From 96df3d1b5e1de08d543991172f1fb1845b073018 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 07:40:56 -0700
Subject: Fix typo
---
ml_exp/compound.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 26e393510..23c66ec27 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -111,13 +111,13 @@ class Compound:
size: compund size.
bohr_ru: if radius units should be in bohr's radius units.
"""
- hp = get_helping_data(self.coordinates,
+ hd = get_helping_data(self.coordinates,
self.nc,
self.atoms,
size=size,
bohr_ru=bohr_ru)
- self.fnm, self.bonds, self.bonds_i, self.bonds_k, self.bonds_f = hp
+ self.fnm, self.bonds, self.bonds_i, self.bonds_k, self.bonds_f = hd
def gen_am(self,
use_forces=False,
--
cgit v1.2.3-70-g09d2
From e289a2de7a461a1194a47350e5339dce082972e7 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 07:42:25 -0700
Subject: Fix typo
---
ml_exp/__init__.py | 4 ++--
ml_exp/compound.py | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index 9e64d7754..4d672efd7 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -22,7 +22,7 @@ SOFTWARE.
"""
from ml_exp.compound import Compound
from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
- get_helping_data, adjacency_matrix, check_bond, bag_of_stuff
+ get_helping_data, adjacency_matrix, check_bond, bag_of_bonds
from ml_exp.math import cholesky_solve
from ml_exp.qm7db import qm7db
from ml_exp.do_ml import simple_ml, do_ml
@@ -33,7 +33,7 @@ __all__ = ['Compound',
'get_helping_data',
'adjacency_matrix',
'check_bond',
- 'bag_of_stuff',
+ 'bag_of_bonds',
'cholesky_solve',
'qm7db',
'simple_ml',
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 23c66ec27..ec5085797 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -23,7 +23,7 @@ SOFTWARE.
import numpy as np
from ml_exp.data import NUCLEAR_CHARGE
from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
- get_helping_data, adjacency_matrix, bag_of_stuff
+ get_helping_data, adjacency_matrix, bag_of_bonds
class Compound:
@@ -139,7 +139,7 @@ class Compound:
Generate the Bag of Stuff for the compound.
size: compound size.
"""
- self.bob = bag_of_stuff(self.cm,
+ self.bob = bag_of_bonds(self.cm,
self.atoms,
size=size)
--
cgit v1.2.3-70-g09d2
From 759b48a965470ac18910951b2cb0599d371d1808 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 07:46:27 -0700
Subject: bos to bob
---
ml_exp/do_ml.py | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/ml_exp/do_ml.py b/ml_exp/do_ml.py
index d8ee415bf..3cb67675f 100644
--- a/ml_exp/do_ml.py
+++ b/ml_exp/do_ml.py
@@ -168,9 +168,8 @@ def do_ml(db_path='data',
compound.gen_am(use_forces=use_forces,
size=size,
bohr_ru=bohr_ru)
- if 'BOS' in identifiers:
- compound.gen_bos(size=size,
- stuff=stuff)
+ if 'BOB' in identifiers:
+ compound.gen_bob(size=size)
# Create a numpy array for the descriptors.
if 'CM' in identifiers:
@@ -179,8 +178,8 @@ def do_ml(db_path='data',
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)
+ if 'BOB' in identifiers:
+ bob_data = np.array([comp.bob for comp in compounds], dtype=float)
toc = time.perf_counter()
tictoc = toc - tic
@@ -212,8 +211,8 @@ def do_ml(db_path='data',
sigma=sigma,
identifier='CM',
show_msgs=show_msgs)
- if 'BOS' in identifiers:
- bos_mae, bos_tictoc = simple_ml(bos_data,
+ if 'BOB' in identifiers:
+ bob_mae, bob_tictoc = simple_ml(bob_data,
energy_pbe0,
training_size=training_size,
test_size=test_size,
--
cgit v1.2.3-70-g09d2
From da6b1428cda40534b820642d8e9be398d7fee8be Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 09:06:54 -0700
Subject: Rewrite kernel, gotta fix adj mat
---
ml_exp/compound.py | 1 -
ml_exp/do_ml.py | 29 +++++++++++++++++++++++------
ml_exp/kernels.py | 25 ++++++++++++++++++-------
3 files changed, 41 insertions(+), 14 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index ec5085797..f603ddd4e 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -126,7 +126,6 @@ class Compound:
Generate the Adjacency Matrix for the compund.
use_forces: if the use of forces instead of k_cx should be used.
size: compound size.
- bohr_ru: if radius units should be in bohr's radius units.
"""
self.am = adjacency_matrix(self.fnm,
self.bonds,
diff --git a/ml_exp/do_ml.py b/ml_exp/do_ml.py
index 3cb67675f..758bf01ae 100644
--- a/ml_exp/do_ml.py
+++ b/ml_exp/do_ml.py
@@ -33,6 +33,7 @@ def simple_ml(descriptors,
training_size,
test_size=None,
sigma=1000.0,
+ opt=True,
identifier=None,
show_msgs=True):
"""
@@ -43,6 +44,7 @@ def simple_ml(descriptors,
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.
+ opt: if the optimized algorithm should be used. For benchmarking purposes.
identifier: string with the name of the descriptor used.
show_msgs: if debug messages should be shown.
NOTE: identifier is just a string and is only for identification purposes.
@@ -76,13 +78,21 @@ def simple_ml(descriptors,
X_training = descriptors[:training_size]
Y_training = energies[:training_size]
- K_training = gaussian_kernel(X_training, X_training, sigma)
- alpha = cholesky_solve(K_training, Y_training)
+ K_training = gaussian_kernel(X_training,
+ X_training,
+ sigma,
+ opt=opt)
+ alpha = cholesky_solve(K_training,
+ Y_training)
X_test = descriptors[-test_size:]
Y_test = energies[-test_size:]
- K_test = gaussian_kernel(X_test, X_training, sigma)
- Y_predicted = np.dot(K_test, alpha)
+ K_test = gaussian_kernel(X_test,
+ X_training,
+ sigma,
+ opt=opt)
+ Y_predicted = np.dot(K_test,
+ alpha)
mae = np.mean(np.abs(Y_predicted - Y_test))
if show_msgs:
@@ -113,6 +123,7 @@ def do_ml(db_path='data',
training_size=1500,
test_size=None,
sigma=1000.0,
+ opt=True,
identifiers=["CM"],
show_msgs=True):
"""
@@ -132,6 +143,7 @@ def do_ml(db_path='data',
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.
+ opt: if the optimized algorithm should be used. For benchmarking purposes.
identifiers: list of names (strings) of descriptors to use.
show_msgs: if debug messages should be shown.
"""
@@ -165,9 +177,10 @@ def do_ml(db_path='data',
as_eig=as_eig,
bohr_ru=bohr_ru)
if 'AM' in identifiers:
- compound.gen_am(use_forces=use_forces,
- size=size,
+ compound.gen_hd(size=size,
bohr_ru=bohr_ru)
+ compound.gen_am(use_forces=use_forces,
+ size=size)
if 'BOB' in identifiers:
compound.gen_bob(size=size)
@@ -193,6 +206,7 @@ def do_ml(db_path='data',
training_size=training_size,
test_size=test_size,
sigma=sigma,
+ opt=opt,
identifier='CM',
show_msgs=show_msgs)
if 'LJM' in identifiers:
@@ -201,6 +215,7 @@ def do_ml(db_path='data',
training_size=training_size,
test_size=test_size,
sigma=sigma,
+ opt=opt,
identifier='LJM',
show_msgs=show_msgs)
if 'AM' in identifiers:
@@ -209,6 +224,7 @@ def do_ml(db_path='data',
training_size=training_size,
test_size=test_size,
sigma=sigma,
+ opt=opt,
identifier='CM',
show_msgs=show_msgs)
if 'BOB' in identifiers:
@@ -217,6 +233,7 @@ def do_ml(db_path='data',
training_size=training_size,
test_size=test_size,
sigma=sigma,
+ opt=opt,
identifier='CM',
show_msgs=show_msgs)
diff --git a/ml_exp/kernels.py b/ml_exp/kernels.py
index 3914ffc20..e6855f97e 100644
--- a/ml_exp/kernels.py
+++ b/ml_exp/kernels.py
@@ -26,20 +26,31 @@ import numpy as np
def gaussian_kernel(X1,
X2,
- sigma):
+ sigma,
+ opt=True):
"""
Calculates the Gaussian Kernel.
X1: first representations.
X2: second representations.
sigma: kernel width.
+ opt: if the optimized algorithm should be used. For benchmarking purposes.
"""
- inv_sigma = -0.5 / (sigma*sigma)
+ i_sigma = -0.5 / (sigma*sigma)
K = np.zeros((X1.shape[0], X2.shape[0]), dtype=float)
- for i, x1 in enumerate(X1):
- for j, x2 in enumerate(X2):
- f_norm = np.linalg.norm(x1 - x2)
- # print(f_norm)
- K[i, j] = math.exp(inv_sigma * f_norm)
+ if opt:
+ # Faster way of calculating the kernel.
+ for i, x1 in enumerate(X1):
+ if X2.ndim == 3:
+ norm = np.linalg.norm(X2 - x1, axis=(1, 2))
+ else:
+ norm = np.linalg.norm(X2 - x1, axis=-1)
+ K[i, :] = np.exp(i_sigma * np.square(norm))
+ else:
+ for i, x1 in enumerate(X1):
+ for j, x2 in enumerate(X2):
+ f_norm = np.linalg.norm(x2 - x1)
+ # print(f_norm)
+ K[i, j] = math.exp(i_sigma * f_norm**2)
return K
--
cgit v1.2.3-70-g09d2
From 2db295947a75ab0347ba0e11b98564da9d228c6a Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 09:08:22 -0700
Subject: Temp fix for adj mat
---
ml_exp/representations.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 5e684314b..5e99627df 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -242,12 +242,14 @@ size. Arrays are not of the right shape.')
def adjacency_matrix(fnm,
bonds,
forces,
+ use_forces=False,
size=22):
"""
Calculates the adjacency matrix given the bond list.
fnm: first neighbour matrix.
bonds: list of bonds (tuple of indexes).
forces: list of forces.
+ use_forces: if the use of forces instead of k_cx should be used.
size: compund size.
"""
n = len(bonds)
@@ -264,7 +266,7 @@ def adjacency_matrix(fnm,
# Ignore the diagonal.
if i != j:
if (bond_i[0] in bond_j) or (bond_i[1] in bond_j):
- if forces:
+ if use_forces:
am[i, j] = np.dot(forces[i], forces[j])
else:
am[i, j] = fnm[bond_i[0], bond_i[1]]
--
cgit v1.2.3-70-g09d2
From cf6c2d1bdb4bba9d4e3db035d26efd874b5ed230 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 09:13:10 -0700
Subject: Forgot one save
---
ml_exp/compound.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index f603ddd4e..e2b7ab7fd 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -130,6 +130,7 @@ class Compound:
self.am = adjacency_matrix(self.fnm,
self.bonds,
self.bonds_f,
+ use_forces=use_forces,
size=size)
def gen_bob(self,
--
cgit v1.2.3-70-g09d2
From 1384a40fb90f9118410d5473634ddbff8b628841 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 09:22:57 -0700
Subject: Change " to \
---
ml_exp/do_ml.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/ml_exp/do_ml.py b/ml_exp/do_ml.py
index 758bf01ae..db50cc8fa 100644
--- a/ml_exp/do_ml.py
+++ b/ml_exp/do_ml.py
@@ -124,7 +124,7 @@ def do_ml(db_path='data',
test_size=None,
sigma=1000.0,
opt=True,
- identifiers=["CM"],
+ identifiers=['CM'],
show_msgs=True):
"""
Main function that does the whole ML process.
--
cgit v1.2.3-70-g09d2
From 9e90b73721edf370f7be9c77aba8431bbe762bdb Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 11:31:40 -0700
Subject: float to np float)
---
ml_exp/kernels.py | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/ml_exp/kernels.py b/ml_exp/kernels.py
index e6855f97e..feaf9a990 100644
--- a/ml_exp/kernels.py
+++ b/ml_exp/kernels.py
@@ -37,9 +37,9 @@ def gaussian_kernel(X1,
"""
i_sigma = -0.5 / (sigma*sigma)
- K = np.zeros((X1.shape[0], X2.shape[0]), dtype=float)
+ K = np.zeros((X1.shape[0], X2.shape[0]), dtype=np.float64)
if opt:
- # Faster way of calculating the kernel.
+ # Faster way of calculating the kernel (no numba support).
for i, x1 in enumerate(X1):
if X2.ndim == 3:
norm = np.linalg.norm(X2 - x1, axis=(1, 2))
@@ -50,7 +50,6 @@ def gaussian_kernel(X1,
for i, x1 in enumerate(X1):
for j, x2 in enumerate(X2):
f_norm = np.linalg.norm(x2 - x1)
- # print(f_norm)
K[i, j] = math.exp(i_sigma * f_norm**2)
return K
--
cgit v1.2.3-70-g09d2
From 53c84552df5c7a7e1f084b0aec8eac63f7813e52 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 11:45:17 -0700
Subject: Change dtypes to np dtypes
---
ml_exp/compound.py | 8 ++++----
ml_exp/do_ml.py | 8 ++++----
ml_exp/math.py | 4 ++--
ml_exp/qm7db.py | 8 ++++----
ml_exp/representations.py | 10 +++++-----
5 files changed, 19 insertions(+), 19 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index e2b7ab7fd..4428e9164 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -153,15 +153,15 @@ class Compound:
lines = f.readlines()
self.name = filename.split('/')[-1]
- self.n = int(lines[0])
+ self.n = np.int32(lines[0])
self.extra = lines[1]
self.atoms = []
- self.atoms_nc = np.empty(self.n, dtype=int)
- self.coordinates = np.empty((self.n, 3), dtype=float)
+ self.atoms_nc = np.empty(self.n, dtype=np.int64)
+ self.coordinates = np.empty((self.n, 3), dtype=np.float64)
for i, atom in enumerate(lines[2:self.n + 2]):
atom_d = atom.split()
self.atoms.append(atom_d[0])
self.atoms_nc[i] = NUCLEAR_CHARGE[atom_d[0]]
- self.coordinates[i] = np.asarray(atom_d[1:4], dtype=float)
+ self.coordinates[i] = np.asarray(atom_d[1:4], dtype=np.float64)
diff --git a/ml_exp/do_ml.py b/ml_exp/do_ml.py
index db50cc8fa..04f8abe87 100644
--- a/ml_exp/do_ml.py
+++ b/ml_exp/do_ml.py
@@ -186,13 +186,13 @@ def do_ml(db_path='data',
# Create a numpy array for the descriptors.
if 'CM' in identifiers:
- cm_data = np.array([comp.cm for comp in compounds], dtype=float)
+ cm_data = np.array([comp.cm for comp in compounds], dtype=np.float64)
if 'LJM' in identifiers:
- ljm_data = np.array([comp.ljm for comp in compounds], dtype=float)
+ ljm_data = np.array([comp.ljm for comp in compounds], dtype=np.float64)
if 'AM' in identifiers:
- am_data = np.array([comp.cm for comp in compounds], dtype=float)
+ am_data = np.array([comp.cm for comp in compounds], dtype=np.float64)
if 'BOB' in identifiers:
- bob_data = np.array([comp.bob for comp in compounds], dtype=float)
+ bob_data = np.array([comp.bob for comp in compounds], dtype=np.float64)
toc = time.perf_counter()
tictoc = toc - tic
diff --git a/ml_exp/math.py b/ml_exp/math.py
index da1fdf08f..253abe5d2 100644
--- a/ml_exp/math.py
+++ b/ml_exp/math.py
@@ -39,7 +39,7 @@ def cholesky_solve(K,
size = K.shape[0]
# Solve Lx=y for x.
- x = np.zeros(size, dtype=float)
+ x = np.zeros(size, dtype=np.float64)
x[0] = y[0] / L[0, 0]
for i in range(1, size):
temp_sum = 0.0
@@ -49,7 +49,7 @@ def cholesky_solve(K,
# Now, solve LTa=x for a.
L2 = L.T
- a = np.zeros(size, dtype=float)
+ a = np.zeros(size, dtype=np.float64)
a[size - 1] = x[size - 1] / L2[size - 1, size - 1]
for i in range(0, size - 1)[::-1]:
temp_sum = 0.0
diff --git a/ml_exp/qm7db.py b/ml_exp/qm7db.py
index 3fd46b6bc..3ba2c5814 100644
--- a/ml_exp/qm7db.py
+++ b/ml_exp/qm7db.py
@@ -42,14 +42,14 @@ def qm7db(db_path='data',
for i, line in enumerate(lines):
line = line.split()
compounds.append(Compound(f'{db_path}/{line[0]}'))
- compounds[i].pbe0 = float(line[1])
- compounds[i].delta = float(line[1]) - float(line[2])
+ compounds[i].pbe0 = np.float64(line[1])
+ compounds[i].delta = np.float64(line[1]) - np.float64(line[2])
if is_shuffled:
random.seed(r_seed)
random.shuffle(compounds)
- e_pbe0 = np.array([compound.pbe0 for compound in compounds], dtype=float)
- e_delta = np.array([compound.delta for compound in compounds], dtype=float)
+ e_pbe0 = np.array([comp.pbe0 for comp in compounds], dtype=np.float64)
+ e_delta = np.array([comp.delta for comp in compounds], dtype=np.float64)
return compounds, e_pbe0, e_delta
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 5e99627df..31259c79c 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -53,7 +53,7 @@ size. Arrays are not of the right shape.')
'instead of (size).')
size = n
- cm = np.zeros((size, size), dtype=float)
+ cm = np.zeros((size, size), dtype=np.float64)
# Actual calculation of the coulomb matrix.
for i, xyz_i in enumerate(coords):
@@ -120,7 +120,7 @@ size. Arrays are not of the right shape.')
'instead of (size).')
size = n
- lj = np.zeros((size, size), dtype=float)
+ lj = np.zeros((size, size), dtype=np.float64)
# Actual calculation of the lennard-jones matrix.
for i, xyz_i in enumerate(coords):
@@ -259,7 +259,7 @@ def adjacency_matrix(fnm,
instead of (size).')
size = n
- am = np.zeros((size, size), dtype=float)
+ am = np.zeros((size, size), dtype=np.float64)
for i, bond_i in enumerate(bonds):
for j, bond_j in enumerate(bonds):
@@ -317,7 +317,7 @@ generated as the vector of eigenvalues, try (re-)generating the CM.')
size = n
# Bond max length, calculated using only the upper triangular matrix.
- bond_size = int((size * size - size)/2 + size)
+ bond_size = np.int32((size * size - size)/2 + size)
# List where each bag data is stored.
bags = []
@@ -350,7 +350,7 @@ generated as the vector of eigenvalues, try (re-)generating the CM.')
bonds = atom_list + bonds
# Create the final vector for the bob.
- bob = np.zeros(bond_size, dtype=float)
+ bob = np.zeros(bond_size, dtype=np.float64)
c_i = 0
for i, bond in enumerate(bonds):
checker = check_bond(bags, bond)
--
cgit v1.2.3-70-g09d2
From 4a3f602aab73bb0304a237ddca5d9f3fa8867001 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 14:07:24 -0700
Subject: Fix bugs
---
ml_exp/do_ml.py | 4 ++--
ml_exp/representations.py | 4 +++-
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/ml_exp/do_ml.py b/ml_exp/do_ml.py
index 04f8abe87..5054b2b06 100644
--- a/ml_exp/do_ml.py
+++ b/ml_exp/do_ml.py
@@ -225,7 +225,7 @@ def do_ml(db_path='data',
test_size=test_size,
sigma=sigma,
opt=opt,
- identifier='CM',
+ identifier='AM',
show_msgs=show_msgs)
if 'BOB' in identifiers:
bob_mae, bob_tictoc = simple_ml(bob_data,
@@ -234,7 +234,7 @@ def do_ml(db_path='data',
test_size=test_size,
sigma=sigma,
opt=opt,
- identifier='CM',
+ identifier='BOB',
show_msgs=show_msgs)
# End of program
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 31259c79c..6b5d26bcb 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -358,10 +358,12 @@ generated as the vector of eigenvalues, try (re-)generating the CM.')
for j, num in enumerate(sorted(bags[checker[1]][1:])[::-1]):
# Use c_i as the index for bob if the zero padding should
# be at the end of the vector instead of between each bond.
- bob[i*size + j] = num
+ # bob[i*size + j] = num
+ bob[c_i] = num
c_i += 1
else:
print(f'Error. Bond {bond} from bond list coudn\'t be found',
'in the bags list. This could be a case where the atom',
'is only present oncce in the molecule.')
+
return bob
--
cgit v1.2.3-70-g09d2
From 62cef5f1782caf4ff379cd021744b98be4be6c8b Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Mon, 2 Mar 2020 12:01:58 -0700
Subject: Fix bug
---
ml_exp/compound.py | 16 ++++++++--------
ml_exp/do_ml.py | 6 ++++++
ml_exp/representations.py | 44 ++++++++++++++++++++++++--------------------
3 files changed, 38 insertions(+), 28 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 4428e9164..6c8525195 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -38,7 +38,7 @@ class Compound:
self.n = None
self.extra = None
self.atoms = None
- self.atoms_nc = None
+ self.nc = None
self.coordinates = None
self.pbe0 = None
self.delta = None
@@ -73,7 +73,7 @@ class Compound:
bohr_ru: if radius units should be in bohr's radius units.
"""
self.cm = coulomb_matrix(self.coordinates,
- self.atoms_nc,
+ self.nc,
size=size,
as_eig=as_eig,
bohr_ru=bohr_ru)
@@ -95,7 +95,7 @@ class Compound:
bohr_ru: if radius units should be in bohr's radius units.
"""
self.ljm = lennard_jones_matrix(self.coordinates,
- self.atoms_nc,
+ self.nc,
diag_value=diag_value,
sigma=sigma,
epsilon=epsilon,
@@ -112,8 +112,8 @@ class Compound:
bohr_ru: if radius units should be in bohr's radius units.
"""
hd = get_helping_data(self.coordinates,
- self.nc,
self.atoms,
+ self.nc,
size=size,
bohr_ru=bohr_ru)
@@ -127,8 +127,8 @@ class Compound:
use_forces: if the use of forces instead of k_cx should be used.
size: compound size.
"""
- self.am = adjacency_matrix(self.fnm,
- self.bonds,
+ self.am = adjacency_matrix(self.bonds_i,
+ self.bonds_k,
self.bonds_f,
use_forces=use_forces,
size=size)
@@ -156,12 +156,12 @@ class Compound:
self.n = np.int32(lines[0])
self.extra = lines[1]
self.atoms = []
- self.atoms_nc = np.empty(self.n, dtype=np.int64)
+ self.nc = np.empty(self.n, dtype=np.int64)
self.coordinates = np.empty((self.n, 3), dtype=np.float64)
for i, atom in enumerate(lines[2:self.n + 2]):
atom_d = atom.split()
self.atoms.append(atom_d[0])
- self.atoms_nc[i] = NUCLEAR_CHARGE[atom_d[0]]
+ self.nc[i] = NUCLEAR_CHARGE[atom_d[0]]
self.coordinates[i] = np.asarray(atom_d[1:4], dtype=np.float64)
diff --git a/ml_exp/do_ml.py b/ml_exp/do_ml.py
index 5054b2b06..5efd13690 100644
--- a/ml_exp/do_ml.py
+++ b/ml_exp/do_ml.py
@@ -176,11 +176,13 @@ def do_ml(db_path='data',
size=size,
as_eig=as_eig,
bohr_ru=bohr_ru)
+ """
if 'AM' in identifiers:
compound.gen_hd(size=size,
bohr_ru=bohr_ru)
compound.gen_am(use_forces=use_forces,
size=size)
+ """
if 'BOB' in identifiers:
compound.gen_bob(size=size)
@@ -189,8 +191,10 @@ def do_ml(db_path='data',
cm_data = np.array([comp.cm for comp in compounds], dtype=np.float64)
if 'LJM' in identifiers:
ljm_data = np.array([comp.ljm for comp in compounds], dtype=np.float64)
+ """
if 'AM' in identifiers:
am_data = np.array([comp.cm for comp in compounds], dtype=np.float64)
+ """
if 'BOB' in identifiers:
bob_data = np.array([comp.bob for comp in compounds], dtype=np.float64)
@@ -218,6 +222,7 @@ def do_ml(db_path='data',
opt=opt,
identifier='LJM',
show_msgs=show_msgs)
+ """
if 'AM' in identifiers:
am_mae, am_tictoc = simple_ml(am_data,
energy_pbe0,
@@ -227,6 +232,7 @@ def do_ml(db_path='data',
opt=opt,
identifier='AM',
show_msgs=show_msgs)
+ """
if 'BOB' in identifiers:
bob_mae, bob_tictoc = simple_ml(bob_data,
energy_pbe0,
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 6b5d26bcb..be567d67a 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -167,15 +167,15 @@ size. Arrays are not of the right shape.')
def get_helping_data(coords,
- nc,
atoms,
+ nc,
size=23,
bohr_ru=False):
"""
Creates helping data such as the First Neighbor Matrix for the compound.
coords: compound coordinates.
- nc: nuclear charge data.
atoms: list of atoms.
+ nc: nuclear charge data.
size: compund size.
bohr_ru: if radius units should be in bohr's radius units.
NOTE: Bond distance of carbon to other elements
@@ -203,11 +203,11 @@ size. Arrays are not of the right shape.')
size = n
# Possible bonds.
- cc_bond = sorted(['C', 'C'])
- ch_bond = sorted(['C', 'H'])
- co_bond = sorted(['C', 'O'])
- cn_bond = sorted(['C', 'N'])
- cs_bond = sorted(['C', 'S'])
+ cc_bond = ''.join(sorted(['C', 'C']))
+ ch_bond = ''.join(sorted(['C', 'H']))
+ co_bond = ''.join(sorted(['C', 'O']))
+ cn_bond = ''.join(sorted(['C', 'N']))
+ cs_bond = ''.join(sorted(['C', 'S']))
pos_bonds = {cc_bond: (1.19, 1.54, 1.0), ch_bond: (1.06, 1.12, 1.0),
co_bond: (1.43, 2.15, 0.8), cn_bond: (1.47, 2.19, 1.0),
cs_bond: (1.81, 2.55, 0.7)}
@@ -221,7 +221,7 @@ size. Arrays are not of the right shape.')
for j, xyz_j in enumerate(coords):
# Ignore the diagonal.
if i != j:
- bond = sorted([atoms[i], atoms[j]])
+ bond = ''.join(sorted([atoms[i], atoms[j]]))
if bond in pos_bonds.keys():
r_min = pos_bonds[bond][0]
r_max = pos_bonds[bond][1]
@@ -239,21 +239,25 @@ size. Arrays are not of the right shape.')
return fnm, bonds, bonds_i, bonds_k, bonds_f
-def adjacency_matrix(fnm,
- bonds,
- forces,
+def adjacency_matrix(bonds_i,
+ bonds_k,
+ bonds_f,
use_forces=False,
- size=22):
+ size=23):
"""
Calculates the adjacency matrix given the bond list.
- fnm: first neighbour matrix.
- bonds: list of bonds (tuple of indexes).
- forces: list of forces.
+ bonds: list of bond names.
+ bonds_i: list of bond indexes (tuple of indexes).
+ bonds_k: list of k_cx values.
+ bonds_f: list of force values.
use_forces: if the use of forces instead of k_cx should be used.
size: compund size.
"""
- n = len(bonds)
+ if bonds_i is None:
+ raise ValueError('The helping data hasn\'t been initialized for\
+the current compound.')
+ n = len(bonds_i)
if size < n:
print('Error. Compound size (n) is greater han (size). Using (n)\
instead of (size).')
@@ -261,15 +265,15 @@ def adjacency_matrix(fnm,
am = np.zeros((size, size), dtype=np.float64)
- for i, bond_i in enumerate(bonds):
- for j, bond_j in enumerate(bonds):
+ for i, bond_i in enumerate(bonds_i):
+ for j, bond_j in enumerate(bonds_i):
# Ignore the diagonal.
if i != j:
if (bond_i[0] in bond_j) or (bond_i[1] in bond_j):
if use_forces:
- am[i, j] = np.dot(forces[i], forces[j])
+ am[i, j] = np.dot(bonds_f[i], bonds_f[j])
else:
- am[i, j] = fnm[bond_i[0], bond_i[1]]
+ am[i, j] = bonds_k[i]
return am
--
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