From 0c91ee8b6c968457cff1d968cf69add73902bd11 Mon Sep 17 00:00:00 2001
From: David Luevano <55825613+luevano@users.noreply.github.com>
Date: Thu, 20 Feb 2020 19:02:23 -0700
Subject: Clean main
---
ml_exp/__main__.py | 51 ++++++---------------------------------------------
1 file changed, 6 insertions(+), 45 deletions(-)
diff --git a/ml_exp/__main__.py b/ml_exp/__main__.py
index aaeb18714..83abb918e 100644
--- a/ml_exp/__main__.py
+++ b/ml_exp/__main__.py
@@ -22,50 +22,11 @@ SOFTWARE.
"""
# from ml_exp.do_ml import do_ml
# from ml_exp.misc import plot_benchmarks
-from ml_exp.read_qm7_data import read_qm7_data
-from ml_exp.adj_matrix import fneig_matrix, adj_matrix
-from ml_exp.c_matrix import c_matrix
-from ml_exp.bob import bob
-from ml_exp.bostuff import bok_cx
+# from ml_exp.read_qm7_data import read_qm7_data
+# from ml_exp.adj_matrix import fneig_matrix, adj_matrix
+# from ml_exp.c_matrix import c_matrix
+# from ml_exp.bob import bob
+# from ml_exp.bostuff import bok_cx
if __name__ == '__main__':
- """
- do_ml(min_training_size=1500,
- max_training_size=2000,
- training_increment_size=500,
- test_size=None,
- ljm_diag_value=None,
- ljm_sigma=1.0,
- ljm_epsilon=1.0,
- r_seed=111,
- save_benchmarks=False,
- show_msgs=True)
- """
- # plot_benchmarks()
- """
- xyz, nc, pbe0, delta, atoms = read_qm7_data(return_atoms=True)
- for i in range(1):
- fnm, bonds, forces = fneig_matrix(atoms[i], xyz[i], nc[i], True)
- am = adj_matrix(bonds, forces)
-
- print(f'{i} first neighbor matrix\n{fnm}')
- print(f'{i} bond list\n{bonds}')
- print(f'{i} force list\n{forces}')
- print(f'{i} adjacency matrix\n{am}')
- print('-'*30)
- print('OK!')
- """
- xyz, nc, pbe0, delta, atoms = read_qm7_data(return_atoms=True)
- for i in range(1):
- cm = c_matrix(xyz[i], nc[i], as_eig=False)
- bob_i = bob(cm, atoms[i])
-
- print(f'{i} coulomb matrix\n{cm}')
- print(f'{i} bag of bonds\n{bob}')
-
- fnm, bonds = fneig_matrix(atoms[i], xyz[i], nc[i], False)
- am = adj_matrix(fnm, bonds, None)
- bok_cx_i = bok_cx(am, atoms[i])
-
- print(f'{i} adjacency matrix\n{am}')
- print(f'{i} bag of k_cx\n{bok_cx_i}')
+ print('Ok!')
--
cgit v1.2.3-70-g09d2
From 7a83a6e48a7503848bf1a4abd448f7858dca71e0 Mon Sep 17 00:00:00 2001
From: David Luevano <55825613+luevano@users.noreply.github.com>
Date: Thu, 20 Feb 2020 19:54:46 -0700
Subject: Add basic compound object
---
ml_exp/__main__.py | 8 --------
ml_exp/compound.py | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 51 insertions(+), 8 deletions(-)
create mode 100644 ml_exp/compound.py
diff --git a/ml_exp/__main__.py b/ml_exp/__main__.py
index 83abb918e..3cb515d85 100644
--- a/ml_exp/__main__.py
+++ b/ml_exp/__main__.py
@@ -20,13 +20,5 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
-# from ml_exp.do_ml import do_ml
-# from ml_exp.misc import plot_benchmarks
-# from ml_exp.read_qm7_data import read_qm7_data
-# from ml_exp.adj_matrix import fneig_matrix, adj_matrix
-# from ml_exp.c_matrix import c_matrix
-# from ml_exp.bob import bob
-# from ml_exp.bostuff import bok_cx
-
if __name__ == '__main__':
print('Ok!')
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
new file mode 100644
index 000000000..6fd46fc3a
--- /dev/null
+++ b/ml_exp/compound.py
@@ -0,0 +1,51 @@
+"""MIT License
+
+Copyright (c) 2019 David Luevano Alvarado
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+import numpy as np
+
+
+class Compound:
+ def __init__(self, xyz=None):
+ self.n = None
+ self.atoms = None
+ self.coordinates = None
+
+ if xyz is not None:
+ self.read_xyz(xyz)
+
+ def read_xyz(self, filename):
+ """
+ Reads an xyz file and adds the corresponding data to the Compound.
+ filename: (path to) the xyz file.
+ """
+ with open(filename, 'r') as f:
+ lines = f.readlines()
+
+ self.n = int(lines[0])
+ self.atoms = []
+ self.coordinates = np.empty((self.n, 3), dtype=float)
+
+ for i, atom in enumerate(lines[2:self.n + 2]):
+ atom_d = atom.split()
+
+ self.atoms.append(atom_d[0])
+ self.coordinates[i] = np.asarray(atom_d[1:4], dtype=float)
--
cgit v1.2.3-70-g09d2
From 96eade3b9f72c5d1fa5bae27ba82a2cd23e1e200 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 17:16:22 -0700
Subject: Add nuclear charge
---
ml_exp/compound.py | 11 ++++
ml_exp/data.py | 141 ++++++++++++++++++++++++++++++++++++++++++++++++
ml_exp/read_qm7_data.py | 11 ++++
3 files changed, 163 insertions(+)
create mode 100644 ml_exp/data.py
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 6fd46fc3a..cfa3e0322 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -21,13 +21,22 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
import numpy as np
+from ml_exp.data import NUCLEAR_CHARGE
class Compound:
def __init__(self, xyz=None):
+ # empty_array = np.asarray([], dtype=float)
+
self.n = None
self.atoms = None
+ self.atoms_nc = None
self.coordinates = None
+ self.energy = None
+
+ self.coulomb_matrix = None
+ self.lennard_jones_matrix = None
+ self.bob = None
if xyz is not None:
self.read_xyz(xyz)
@@ -42,10 +51,12 @@ class Compound:
self.n = int(lines[0])
self.atoms = []
+ self.atoms_nc = np.empty(self.n, dtype=int)
self.coordinates = np.empty((self.n, 3), dtype=float)
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)
diff --git a/ml_exp/data.py b/ml_exp/data.py
new file mode 100644
index 000000000..243aff168
--- /dev/null
+++ b/ml_exp/data.py
@@ -0,0 +1,141 @@
+"""MIT License
+
+Copyright (c) 2019 David Luevano Alvarado
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+NUCLEAR_CHARGE = {
+ 'H': 1,
+ 'He': 2,
+ 'Li': 3,
+ 'Be': 4,
+ 'B': 5,
+ 'C': 6,
+ 'N': 7,
+ 'O': 8,
+ 'F': 9,
+ 'Ne': 10,
+ 'Na': 11,
+ 'Mg': 12,
+ 'Al': 13,
+ 'Si': 14,
+ 'P': 15,
+ 'S': 16,
+ 'Cl': 17,
+ 'Ar': 18,
+ 'K': 19,
+ 'Ca': 20,
+ 'Sc': 21,
+ 'Ti': 22,
+ 'V': 23,
+ 'Cr': 24,
+ 'Mn': 25,
+ 'Fe': 26,
+ 'Co': 27,
+ 'Ni': 28,
+ 'Cu': 29,
+ 'Zn': 30,
+ 'Ga': 31,
+ 'Ge': 32,
+ 'As': 33,
+ 'Se': 34,
+ 'Br': 35,
+ 'Kr': 36,
+ 'Rb': 37,
+ 'Sr': 38,
+ 'Y': 39,
+ 'Zr': 40,
+ 'Nb': 41,
+ 'Mo': 42,
+ 'Tc': 43,
+ 'Ru': 44,
+ 'Rh': 45,
+ 'Pd': 46,
+ 'Ag': 47,
+ 'Cd': 48,
+ 'In': 49,
+ 'Sn': 50,
+ 'Sb': 51,
+ 'Te': 52,
+ 'I': 53,
+ 'Xe': 54,
+ 'Cs': 55,
+ 'Ba': 56,
+ 'La': 57,
+ 'Ce': 58,
+ 'Pr': 59,
+ 'Nd': 60,
+ 'Pm': 61,
+ 'Sm': 62,
+ 'Eu': 63,
+ 'Gd': 64,
+ 'Tb': 65,
+ 'Dy': 66,
+ 'Ho': 67,
+ 'Er': 68,
+ 'Tm': 69,
+ 'Yb': 70,
+ 'Lu': 71,
+ 'Hf': 72,
+ 'Ta': 73,
+ 'W': 74,
+ 'Re': 75,
+ 'Os': 76,
+ 'Ir': 77,
+ 'Pt': 78,
+ 'Au': 79,
+ 'Hg': 80,
+ 'Tl': 81,
+ 'Pb': 82,
+ 'Bi': 83,
+ 'Po': 84,
+ 'At': 85,
+ 'Rn': 86,
+ 'Fr': 87,
+ 'Ra': 88,
+ 'Ac': 89,
+ 'Th': 90,
+ 'Pa': 91,
+ 'U': 92,
+ 'Np': 93,
+ 'Pu': 94,
+ 'Am': 95,
+ 'Cm': 96,
+ 'Bk': 97,
+ 'Cf': 98,
+ 'Es': 99,
+ 'Fm': 100,
+ 'Md': 101,
+ 'No': 102,
+ 'Lr': 103,
+ 'Rf': 104,
+ 'Db': 105,
+ 'Sg': 106,
+ 'Bh': 107,
+ 'Hs': 108,
+ 'Mt': 109,
+ 'Ds ': 110,
+ 'Rg ': 111,
+ 'Cn ': 112,
+ 'Nh': 113,
+ 'Fl': 114,
+ 'Mc': 115,
+ 'Lv': 116,
+ 'Ts': 117,
+ 'Og': 118}
diff --git a/ml_exp/read_qm7_data.py b/ml_exp/read_qm7_data.py
index 81be05a17..63c48195c 100644
--- a/ml_exp/read_qm7_data.py
+++ b/ml_exp/read_qm7_data.py
@@ -49,6 +49,17 @@ def read_nc_data(data_path):
return {line[2]: int(line[0]) for line in lines}
+# For use in the rewriting of the code (from functional programming to object
+# oriented programming-ish)
+def print_nc(nc_data):
+ """
+ Prints the nuclear charge data to the terminal.
+ nc_data: dict of nc.
+ """
+ for key in nc_data.keys():
+ print(f'\'{key}\': {nc_data[key]},')
+
+
# 'hof_qm7.txt.txt' retrieved from
# https://github.com/qmlcode/tutorial
def read_db_data(zi_data,
--
cgit v1.2.3-70-g09d2
From 4ce7823359a144973c667f488e5fa39e5d3f8acc Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 17:21:21 -0700
Subject: Remove unused function
---
ml_exp/compound.py | 3 +++
ml_exp/read_qm7_data.py | 34 ----------------------------------
2 files changed, 3 insertions(+), 34 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index cfa3e0322..9536767a7 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -41,6 +41,9 @@ class Compound:
if xyz is not None:
self.read_xyz(xyz)
+ def gen_cm(self):
+ pass
+
def read_xyz(self, filename):
"""
Reads an xyz file and adds the corresponding data to the Compound.
diff --git a/ml_exp/read_qm7_data.py b/ml_exp/read_qm7_data.py
index 63c48195c..666f9c3fc 100644
--- a/ml_exp/read_qm7_data.py
+++ b/ml_exp/read_qm7_data.py
@@ -21,10 +21,8 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
import os
-import time
import numpy as np
import random
-from ml_exp.misc import printc
# 'periodic_table_of_elements.txt' retrieved from
@@ -139,35 +137,3 @@ def read_db_data(zi_data,
if return_atoms:
return molecules, nuclear_charge, energy_pbe0, energy_delta, atoms
return molecules, nuclear_charge, energy_pbe0, energy_delta
-
-
-def read_qm7_data(data_path='data',
- r_seed=111,
- return_atoms=False):
- """
- Reads all the qm7 data.
- data_path: path to the data directory.
- r_seed: random seed to use for the shuffling.
- return_atoms: if atom list should be returned.
- """
- tic = time.perf_counter()
- printc('Data reading started.', 'CYAN')
-
- init_path = os.getcwd()
- os.chdir(data_path)
- data_path = os.getcwd()
-
- zi_data = read_nc_data(data_path)
- if return_atoms:
- molecules, nuclear_charge, energy_pbe0, energy_delta, atoms = \
- read_db_data(zi_data, data_path, r_seed, return_atoms)
- else:
- molecules, nuclear_charge, energy_pbe0, energy_delta = \
- read_db_data(zi_data, data_path, r_seed)
-
- os.chdir(init_path)
- toc = time.perf_counter()
- printc('\tData reading took {:.4f} seconds.'.format(toc-tic), 'GREEN')
- if return_atoms:
- return molecules, nuclear_charge, energy_pbe0, energy_delta, atoms
- return molecules, nuclear_charge, energy_pbe0, energy_delta
--
cgit v1.2.3-70-g09d2
From 2dd24b5f7dfa5c43acd8e4281dab22f178a5019e Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 17:25:25 -0700
Subject: Remove unused function
---
ml_exp/c_matrix.py | 33 ---------------------------------
1 file changed, 33 deletions(-)
diff --git a/ml_exp/c_matrix.py b/ml_exp/c_matrix.py
index 00034a660..ac942d473 100644
--- a/ml_exp/c_matrix.py
+++ b/ml_exp/c_matrix.py
@@ -20,11 +20,9 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
-import time
import math
import numpy as np
from numpy.linalg import eig
-from ml_exp.misc import printc
def c_matrix(mol_data,
@@ -146,34 +144,3 @@ def c_matrix(mol_data,
return np.sort(eig(cm)[0])[::-1]
else:
return cm
-
-
-def c_matrix_multiple(mol_data,
- nc_data,
- pipe=None,
- max_len=25,
- as_eig=True,
- bohr_radius_units=False):
- """
- Calculates the Coulomb Matrix of multiple molecules.
- mol_data: molecule data, matrix of atom coordinates.
- nc_data: nuclear charge data, array of atom data.
- pipe: for multiprocessing purposes. Sends the data calculated
- through a pipe.
- max_len: maximum amount of atoms in molecule.
- as_eig: if data should be returned as matrix or array of eigenvalues.
- bohr_radius_units: if units should be in bohr's radius units.
- """
- printc('Coulomb Matrices calculation started.', 'CYAN')
- tic = time.perf_counter()
-
- cm_data = np.array([c_matrix(mol, nc, max_len, as_eig, bohr_radius_units)
- for mol, nc in zip(mol_data, nc_data)])
-
- toc = time.perf_counter()
- printc('\tCM calculation took {:.4f} seconds.'.format(toc - tic), 'GREEN')
-
- if pipe:
- pipe.send(cm_data)
-
- return cm_data
--
cgit v1.2.3-70-g09d2
From f6fd349a822d6dd2f7172a90c6c35d1eb36f5c95 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 17:26:26 -0700
Subject: Move cmatrix to representations
---
ml_exp/c_matrix.py | 146 -----------------------------------------------------
1 file changed, 146 deletions(-)
delete mode 100644 ml_exp/c_matrix.py
diff --git a/ml_exp/c_matrix.py b/ml_exp/c_matrix.py
deleted file mode 100644
index ac942d473..000000000
--- a/ml_exp/c_matrix.py
+++ /dev/null
@@ -1,146 +0,0 @@
-"""MIT License
-
-Copyright (c) 2019 David Luevano Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-import math
-import numpy as np
-from numpy.linalg import eig
-
-
-def c_matrix(mol_data,
- nc_data,
- max_len=25,
- as_eig=True,
- bohr_radius_units=False):
- """
- Creates the Coulomb Matrix from the molecule data given.
- mol_data: molecule data, matrix of atom coordinates.
- nc_data: nuclear charge data, array of atom data.
- max_len: maximum amount of atoms in molecule.
- as_eig: if data should be returned as matrix or array of eigenvalues.
- bohr_radius_units: if units should be in bohr's radius units.
- """
- if bohr_radius_units:
- conversion_rate = 0.52917721067
- else:
- conversion_rate = 1
-
- mol_n = len(mol_data)
- mol_nr = range(mol_n)
-
- if not mol_n == len(nc_data):
- print(''.join(['Error. Molecule matrix dimension is different ',
- 'than the nuclear charge array dimension.']))
- else:
- if max_len < mol_n:
- print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
- 'greater than max_len. Using mol_n.']))
- max_len = None
-
- if max_len:
- cm = np.zeros((max_len, max_len))
- ml_r = range(max_len)
-
- # Actual calculation of the coulomb matrix.
- for i in ml_r:
- if i < mol_n:
- x_i = mol_data[i, 0]
- y_i = mol_data[i, 1]
- z_i = mol_data[i, 2]
- Z_i = nc_data[i]
- else:
- break
-
- for j in ml_r:
- if j < mol_n:
- x_j = mol_data[j, 0]
- y_j = mol_data[j, 1]
- z_j = mol_data[j, 2]
- Z_j = nc_data[j]
-
- x = (x_i-x_j)**2
- y = (y_i-y_j)**2
- z = (z_i-z_j)**2
-
- if i == j:
- cm[i, j] = (0.5*Z_i**2.4)
- else:
- cm[i, j] = (conversion_rate*Z_i*Z_j/math.sqrt(x
- + y
- + z))
- else:
- break
-
- # Now the value will be returned.
- if as_eig:
- cm_sorted = np.sort(eig(cm)[0])[::-1]
- # Thanks to SO for the following lines of code.
- # https://stackoverflow.com/a/43011036
-
- # Keep zeros at the end.
- mask = cm_sorted != 0.
- f_mask = mask.sum(0, keepdims=1) >\
- np.arange(cm_sorted.shape[0]-1, -1, -1)
-
- f_mask = f_mask[::-1]
- cm_sorted[f_mask] = cm_sorted[mask]
- cm_sorted[~f_mask] = 0.
-
- return cm_sorted
-
- else:
- return cm
-
- else:
- cm_temp = []
- # Actual calculation of the coulomb matrix.
- for i in mol_nr:
- x_i = mol_data[i, 0]
- y_i = mol_data[i, 1]
- z_i = mol_data[i, 2]
- Z_i = nc_data[i]
-
- cm_row = []
- for j in mol_nr:
- x_j = mol_data[j, 0]
- y_j = mol_data[j, 1]
- z_j = mol_data[j, 2]
- Z_j = nc_data[j]
-
- x = (x_i-x_j)**2
- y = (y_i-y_j)**2
- z = (z_i-z_j)**2
-
- if i == j:
- cm_row.append(0.5*Z_i**2.4)
- else:
- cm_row.append(conversion_rate*Z_i*Z_j/math.sqrt(x
- + y
- + z))
-
- cm_temp.append(np.array(cm_row))
-
- cm = np.array(cm_temp)
- # Now the value will be returned.
- if as_eig:
- return np.sort(eig(cm)[0])[::-1]
- else:
- return cm
--
cgit v1.2.3-70-g09d2
From d6b381e1ea629879b9855989b0f753632ea9df2a Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 17:33:41 -0700
Subject: Refactor code, size is 23 not 25
---
ml_exp/representations.py | 145 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 145 insertions(+)
create mode 100644 ml_exp/representations.py
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
new file mode 100644
index 000000000..830e51707
--- /dev/null
+++ b/ml_exp/representations.py
@@ -0,0 +1,145 @@
+"""MIT License
+
+Copyright (c) 2019 David Luevano Alvarado
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+import math
+import numpy as np
+
+
+def coulomb_matrix(coords,
+ nc,
+ size=23,
+ as_eig=True,
+ bohr_radius_units=False):
+ """
+ Creates the Coulomb Matrix from the molecule data given.
+ coords: compound coordinates.
+ nc: nuclear charge data.
+ size: compound size.
+ as_eig: if data should be returned as matrix or array of eigenvalues.
+ bohr_radius_units: if units should be in bohr's radius units.
+ """
+ if bohr_radius_units:
+ conversion_rate = 0.52917721067
+ else:
+ conversion_rate = 1
+
+ mol_n = len(coords)
+ mol_nr = range(mol_n)
+
+ if not mol_n == len(nc):
+ print(''.join(['Error. Molecule matrix dimension is different ',
+ 'than the nuclear charge array dimension.']))
+ else:
+ if size < mol_n:
+ print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
+ 'greater than size. Using mol_n.']))
+ size = None
+
+ if size:
+ cm = np.zeros((size, size))
+ ml_r = range(size)
+
+ # Actual calculation of the coulomb matrix.
+ for i in ml_r:
+ if i < mol_n:
+ x_i = coords[i, 0]
+ y_i = coords[i, 1]
+ z_i = coords[i, 2]
+ Z_i = nc[i]
+ else:
+ break
+
+ for j in ml_r:
+ if j < mol_n:
+ x_j = coords[j, 0]
+ y_j = coords[j, 1]
+ z_j = coords[j, 2]
+ Z_j = nc[j]
+
+ x = (x_i-x_j)**2
+ y = (y_i-y_j)**2
+ z = (z_i-z_j)**2
+
+ if i == j:
+ cm[i, j] = (0.5*Z_i**2.4)
+ else:
+ cm[i, j] = (conversion_rate*Z_i*Z_j/math.sqrt(x
+ + y
+ + z))
+ else:
+ break
+
+ # Now the value will be returned.
+ if as_eig:
+ cm_sorted = np.sort(np.linalg.eig(cm)[0])[::-1]
+ # Thanks to SO for the following lines of code.
+ # https://stackoverflow.com/a/43011036
+
+ # Keep zeros at the end.
+ mask = cm_sorted != 0.
+ f_mask = mask.sum(0, keepdims=1) >\
+ np.arange(cm_sorted.shape[0]-1, -1, -1)
+
+ f_mask = f_mask[::-1]
+ cm_sorted[f_mask] = cm_sorted[mask]
+ cm_sorted[~f_mask] = 0.
+
+ return cm_sorted
+
+ else:
+ return cm
+
+ else:
+ cm_temp = []
+ # Actual calculation of the coulomb matrix.
+ for i in mol_nr:
+ x_i = coords[i, 0]
+ y_i = coords[i, 1]
+ z_i = coords[i, 2]
+ Z_i = nc[i]
+
+ cm_row = []
+ for j in mol_nr:
+ x_j = coords[j, 0]
+ y_j = coords[j, 1]
+ z_j = coords[j, 2]
+ Z_j = nc[j]
+
+ x = (x_i-x_j)**2
+ y = (y_i-y_j)**2
+ z = (z_i-z_j)**2
+
+ if i == j:
+ cm_row.append(0.5*Z_i**2.4)
+ else:
+ cm_row.append(conversion_rate*Z_i*Z_j/math.sqrt(x
+ + y
+ + z))
+
+ cm_temp.append(np.array(cm_row))
+
+ cm = np.array(cm_temp)
+ # Now the value will be returned.
+ if as_eig:
+ return np.sort(np.linalg.eig(cm)[0])[::-1]
+ else:
+ return cm
--
cgit v1.2.3-70-g09d2
From 02cb17d411e9a1bc2fe5c6bcf75695f23f340648 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 17:44:34 -0700
Subject: Add exception
---
ml_exp/representations.py | 158 +++++++++++++++++++++++-----------------------
1 file changed, 79 insertions(+), 79 deletions(-)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 830e51707..50b78e548 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -42,83 +42,34 @@ def coulomb_matrix(coords,
else:
conversion_rate = 1
- mol_n = len(coords)
- mol_nr = range(mol_n)
+ n = coords.shape[0]
+ nr = range(n)
- if not mol_n == len(nc):
- print(''.join(['Error. Molecule matrix dimension is different ',
- 'than the nuclear charge array dimension.']))
- else:
- if size < mol_n:
- print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
- 'greater than size. Using mol_n.']))
- size = None
-
- if size:
- cm = np.zeros((size, size))
- ml_r = range(size)
-
- # Actual calculation of the coulomb matrix.
- for i in ml_r:
- if i < mol_n:
- x_i = coords[i, 0]
- y_i = coords[i, 1]
- z_i = coords[i, 2]
- Z_i = nc[i]
- else:
- break
-
- for j in ml_r:
- if j < mol_n:
- x_j = coords[j, 0]
- y_j = coords[j, 1]
- z_j = coords[j, 2]
- Z_j = nc[j]
-
- x = (x_i-x_j)**2
- y = (y_i-y_j)**2
- z = (z_i-z_j)**2
-
- if i == j:
- cm[i, j] = (0.5*Z_i**2.4)
- else:
- cm[i, j] = (conversion_rate*Z_i*Z_j/math.sqrt(x
- + y
- + z))
- else:
- break
-
- # Now the value will be returned.
- if as_eig:
- cm_sorted = np.sort(np.linalg.eig(cm)[0])[::-1]
- # Thanks to SO for the following lines of code.
- # https://stackoverflow.com/a/43011036
+ if not n == nc.shape[0]:
+ raise ValueError('Compound size is different than the nuclear charge\
+ size. Arrays are not of the right shape.')
- # Keep zeros at the end.
- mask = cm_sorted != 0.
- f_mask = mask.sum(0, keepdims=1) >\
- np.arange(cm_sorted.shape[0]-1, -1, -1)
+ if size < n:
+ print(''.join(['Error. Molecule matrix dimension (n) is ',
+ 'greater than size. Using n.']))
+ size = None
- f_mask = f_mask[::-1]
- cm_sorted[f_mask] = cm_sorted[mask]
- cm_sorted[~f_mask] = 0.
+ if size:
+ cm = np.zeros((size, size))
+ ml_r = range(size)
- return cm_sorted
-
- else:
- return cm
-
- else:
- cm_temp = []
- # Actual calculation of the coulomb matrix.
- for i in mol_nr:
+ # Actual calculation of the coulomb matrix.
+ for i in ml_r:
+ if i < n:
x_i = coords[i, 0]
y_i = coords[i, 1]
z_i = coords[i, 2]
Z_i = nc[i]
+ else:
+ break
- cm_row = []
- for j in mol_nr:
+ for j in ml_r:
+ if j < n:
x_j = coords[j, 0]
y_j = coords[j, 1]
z_j = coords[j, 2]
@@ -129,17 +80,66 @@ def coulomb_matrix(coords,
z = (z_i-z_j)**2
if i == j:
- cm_row.append(0.5*Z_i**2.4)
+ cm[i, j] = (0.5*Z_i**2.4)
else:
- cm_row.append(conversion_rate*Z_i*Z_j/math.sqrt(x
- + y
- + z))
+ cm[i, j] = (conversion_rate*Z_i*Z_j/math.sqrt(x
+ + y
+ + z))
+ else:
+ break
- cm_temp.append(np.array(cm_row))
+ # Now the value will be returned.
+ if as_eig:
+ cm_sorted = np.sort(np.linalg.eig(cm)[0])[::-1]
+ # Thanks to SO for the following lines of code.
+ # https://stackoverflow.com/a/43011036
- cm = np.array(cm_temp)
- # Now the value will be returned.
- if as_eig:
- return np.sort(np.linalg.eig(cm)[0])[::-1]
- else:
- return cm
+ # Keep zeros at the end.
+ mask = cm_sorted != 0.
+ f_mask = mask.sum(0, keepdims=1) >\
+ np.arange(cm_sorted.shape[0]-1, -1, -1)
+
+ f_mask = f_mask[::-1]
+ cm_sorted[f_mask] = cm_sorted[mask]
+ cm_sorted[~f_mask] = 0.
+
+ return cm_sorted
+
+ else:
+ return cm
+
+ else:
+ cm_temp = []
+ # Actual calculation of the coulomb matrix.
+ for i in nr:
+ x_i = coords[i, 0]
+ y_i = coords[i, 1]
+ z_i = coords[i, 2]
+ Z_i = nc[i]
+
+ cm_row = []
+ for j in nr:
+ x_j = coords[j, 0]
+ y_j = coords[j, 1]
+ z_j = coords[j, 2]
+ Z_j = nc[j]
+
+ x = (x_i-x_j)**2
+ y = (y_i-y_j)**2
+ z = (z_i-z_j)**2
+
+ if i == j:
+ cm_row.append(0.5*Z_i**2.4)
+ else:
+ cm_row.append(conversion_rate*Z_i*Z_j/math.sqrt(x
+ + y
+ + z))
+
+ cm_temp.append(np.array(cm_row))
+
+ cm = np.array(cm_temp)
+ # Now the value will be returned.
+ if as_eig:
+ return np.sort(np.linalg.eig(cm)[0])[::-1]
+ else:
+ return cm
--
cgit v1.2.3-70-g09d2
From bb5e608f0ca6491e1abfd7fd25d2f28ff6c96e6b Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 17:58:13 -0700
Subject: Rewrite cmatrix
---
ml_exp/representations.py | 111 +++++++++++++++-------------------------------
1 file changed, 35 insertions(+), 76 deletions(-)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 50b78e548..bbc538ae6 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -38,87 +38,36 @@ def coulomb_matrix(coords,
bohr_radius_units: if units should be in bohr's radius units.
"""
if bohr_radius_units:
- conversion_rate = 0.52917721067
+ cr = 0.52917721067
else:
- conversion_rate = 1
+ cr = 1
n = coords.shape[0]
- nr = range(n)
if not n == nc.shape[0]:
raise ValueError('Compound size is different than the nuclear charge\
size. Arrays are not of the right shape.')
if size < n:
- print(''.join(['Error. Molecule matrix dimension (n) is ',
- 'greater than size. Using n.']))
- size = None
-
- if size:
- cm = np.zeros((size, size))
- ml_r = range(size)
-
- # Actual calculation of the coulomb matrix.
- for i in ml_r:
- if i < n:
- x_i = coords[i, 0]
- y_i = coords[i, 1]
- z_i = coords[i, 2]
- Z_i = nc[i]
- else:
- break
-
- for j in ml_r:
- if j < n:
- x_j = coords[j, 0]
- y_j = coords[j, 1]
- z_j = coords[j, 2]
- Z_j = nc[j]
-
- x = (x_i-x_j)**2
- y = (y_i-y_j)**2
- z = (z_i-z_j)**2
-
- if i == j:
- cm[i, j] = (0.5*Z_i**2.4)
- else:
- cm[i, j] = (conversion_rate*Z_i*Z_j/math.sqrt(x
- + y
- + z))
- else:
- break
-
- # Now the value will be returned.
- if as_eig:
- cm_sorted = np.sort(np.linalg.eig(cm)[0])[::-1]
- # Thanks to SO for the following lines of code.
- # https://stackoverflow.com/a/43011036
+ print('Error. Compound size (n) is greater han (size). Using (n)\
+ instead of (size).')
+ size = n
- # Keep zeros at the end.
- mask = cm_sorted != 0.
- f_mask = mask.sum(0, keepdims=1) >\
- np.arange(cm_sorted.shape[0]-1, -1, -1)
-
- f_mask = f_mask[::-1]
- cm_sorted[f_mask] = cm_sorted[mask]
- cm_sorted[~f_mask] = 0.
-
- return cm_sorted
-
- else:
- return cm
+ nr = range(size)
+ cm = np.empty((size, size), dtype=float)
- else:
- cm_temp = []
- # Actual calculation of the coulomb matrix.
- for i in nr:
+ # Actual calculation of the coulomb matrix.
+ for i in nr:
+ if i < n:
x_i = coords[i, 0]
y_i = coords[i, 1]
z_i = coords[i, 2]
Z_i = nc[i]
+ else:
+ break
- cm_row = []
- for j in nr:
+ for j in nr:
+ if j < n:
x_j = coords[j, 0]
y_j = coords[j, 1]
z_j = coords[j, 2]
@@ -129,17 +78,27 @@ def coulomb_matrix(coords,
z = (z_i-z_j)**2
if i == j:
- cm_row.append(0.5*Z_i**2.4)
+ cm[i, j] = (0.5*Z_i**2.4)
else:
- cm_row.append(conversion_rate*Z_i*Z_j/math.sqrt(x
- + y
- + z))
+ cm[i, j] = (cr*Z_i*Z_j/math.sqrt(x + y + z))
+ else:
+ break
- cm_temp.append(np.array(cm_row))
+ # Now the value will be returned.
+ if as_eig:
+ cm_sorted = np.sort(np.linalg.eig(cm)[0])[::-1]
+ # Thanks to SO for the following lines of code.
+ # https://stackoverflow.com/a/43011036
- cm = np.array(cm_temp)
- # Now the value will be returned.
- if as_eig:
- return np.sort(np.linalg.eig(cm)[0])[::-1]
- else:
- return cm
+ # Keep zeros at the end.
+ mask = cm_sorted != 0.
+ f_mask = mask.sum(0, keepdims=1) >\
+ np.arange(cm_sorted.shape[0]-1, -1, -1)
+
+ f_mask = f_mask[::-1]
+ cm_sorted[f_mask] = cm_sorted[mask]
+ cm_sorted[~f_mask] = 0.
+
+ return cm_sorted
+ else:
+ return cm
--
cgit v1.2.3-70-g09d2
From efaa8eeb58d8e19d32f94ec4e91ec794574dfd32 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 18:13:33 -0700
Subject: Coulomb matrix done, fix init
---
ml_exp/__init__.py | 27 ++++-----------------------
ml_exp/compound.py | 28 ++++++++++++++++++++++++----
ml_exp/representations.py | 10 +++++-----
3 files changed, 33 insertions(+), 32 deletions(-)
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index 06425f6a2..8e803b37e 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -20,29 +20,10 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
-from ml_exp.read_qm7_data import read_nc_data, read_db_data, read_qm7_data
-from ml_exp.c_matrix import c_matrix, c_matrix_multiple
-from ml_exp.lj_matrix import lj_matrix, lj_matrix_multiple
-from ml_exp.frob_norm import frob_norm
-from ml_exp.gauss_kernel import gauss_kernel
-from ml_exp.cholesky_solve import cholesky_solve
-from ml_exp.do_ml import do_ml
-from ml_exp.parallel_create_matrices import parallel_create_matrices
-from ml_exp.misc import plot_benchmarks
-
+from ml_exp.compound import Compound
+from ml_exp.representations import coulomb_matrix
# If somebody does "from package import *", this is what they will
# be able to access:
-__all__ = ['read_nc_data',
- 'read_db_data',
- 'read_qm7_data',
- 'c_matrix',
- 'c_matrix_multiple',
- 'lj_matrix',
- 'lj_matrix_multiple',
- 'frob_norm',
- 'gauss_kernel',
- 'cholesky_solve',
- 'do_ml',
- 'parallel_create_matrices',
- 'plot_benchmarks']
+__all__ = ['Compound',
+ 'coulomb_matrix']
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 9536767a7..3ea377826 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -22,10 +22,16 @@ SOFTWARE.
"""
import numpy as np
from ml_exp.data import NUCLEAR_CHARGE
+from ml_exp.representations import coulomb_matrix
class Compound:
- def __init__(self, xyz=None):
+ def __init__(self,
+ xyz=None):
+ """
+ Initialization of the Compound.
+ xyz: (path to) the xyz file.
+ """
# empty_array = np.asarray([], dtype=float)
self.n = None
@@ -41,10 +47,24 @@ class Compound:
if xyz is not None:
self.read_xyz(xyz)
- def gen_cm(self):
- pass
+ def gen_cm(self,
+ size=23,
+ as_eig=True,
+ bohr_ru=False):
+ """
+ Generate the Coulomb Matrix for the compund.
+ size: compound size.
+ as_eig: if the representation should be as the eigenvalues.
+ bhor_ru: if radius units should be in bohr's radius units.
+ """
+ self.coulomb_matrix = coulomb_matrix(self.coordinates,
+ self.atoms_nc,
+ size=size,
+ as_eig=as_eig,
+ bhor_ru=bohr_ru)
- def read_xyz(self, filename):
+ def read_xyz(self,
+ filename):
"""
Reads an xyz file and adds the corresponding data to the Compound.
filename: (path to) the xyz file.
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index bbc538ae6..c503c310d 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -28,16 +28,16 @@ def coulomb_matrix(coords,
nc,
size=23,
as_eig=True,
- bohr_radius_units=False):
+ bhor_ru=False):
"""
Creates the Coulomb Matrix from the molecule data given.
coords: compound coordinates.
nc: nuclear charge data.
size: compound size.
- as_eig: if data should be returned as matrix or array of eigenvalues.
- bohr_radius_units: if units should be in bohr's radius units.
+ as_eig: if the representation should be as the eigenvalues.
+ bhor_ru: if radius units should be in bohr's radius units.
"""
- if bohr_radius_units:
+ if bhor_ru:
cr = 0.52917721067
else:
cr = 1
@@ -54,7 +54,7 @@ def coulomb_matrix(coords,
size = n
nr = range(size)
- cm = np.empty((size, size), dtype=float)
+ cm = np.zeros((size, size), dtype=float)
# Actual calculation of the coulomb matrix.
for i in nr:
--
cgit v1.2.3-70-g09d2
From 8a108f8757027750f825c6ef9dd55adb4c09def0 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 18:20:22 -0700
Subject: Remove unused function
---
ml_exp/lj_matrix.py | 46 ----------------------------------------------
1 file changed, 46 deletions(-)
diff --git a/ml_exp/lj_matrix.py b/ml_exp/lj_matrix.py
index 549790755..5e3e89678 100644
--- a/ml_exp/lj_matrix.py
+++ b/ml_exp/lj_matrix.py
@@ -20,11 +20,9 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
-import time
import math
import numpy as np
from numpy.linalg import eig
-from ml_exp.misc import printc
def lj_matrix(mol_data,
@@ -176,47 +174,3 @@ def lj_matrix(mol_data,
return np.sort(eig(lj)[0])[::-1]
else:
return lj
-
-
-def lj_matrix_multiple(mol_data,
- nc_data,
- pipe=None,
- diag_value=None,
- sigma=1.0,
- epsilon=1.0,
- max_len=25,
- as_eig=True,
- bohr_radius_units=False):
- """
- Calculates the Lennard-Jones Matrix of multiple molecules.
- mol_data: molecule data, matrix of atom coordinates.
- nc_data: nuclear charge data, array of atom data.
- pipe: for multiprocessing purposes. Sends the data calculated
- through a pipe.
- diag_value: if special diagonal value is to be used.
- sigma: sigma value.
- epsilon: epsilon value.
- max_len: maximum amount of atoms in molecule.
- as_eig: if data should be returned as matrix or array of eigenvalues.
- bohr_radius_units: if units should be in bohr's radius units.
- """
- printc('L-J Matrices calculation started.', 'CYAN')
- tic = time.perf_counter()
-
- ljm_data = np.array([lj_matrix(mol,
- nc,
- diag_value,
- sigma,
- epsilon,
- max_len,
- as_eig,
- bohr_radius_units)
- for mol, nc in zip(mol_data, nc_data)])
-
- toc = time.perf_counter()
- printc('\tL-JM calculation took {:.4f} seconds.'.format(toc-tic), 'GREEN')
-
- if pipe:
- pipe.send(ljm_data)
-
- return ljm_data
--
cgit v1.2.3-70-g09d2
From a2463470b639a743189deece071654ed03791c3c Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 19:00:34 -0700
Subject: Moved ljmatrix to representations, rewrote code
---
ml_exp/lj_matrix.py | 176 ----------------------------------------------
ml_exp/representations.py | 102 +++++++++++++++++++++++++++
2 files changed, 102 insertions(+), 176 deletions(-)
delete mode 100644 ml_exp/lj_matrix.py
diff --git a/ml_exp/lj_matrix.py b/ml_exp/lj_matrix.py
deleted file mode 100644
index 5e3e89678..000000000
--- a/ml_exp/lj_matrix.py
+++ /dev/null
@@ -1,176 +0,0 @@
-"""MIT License
-
-Copyright (c) 2019 David Luevano Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-import math
-import numpy as np
-from numpy.linalg import eig
-
-
-def lj_matrix(mol_data,
- nc_data,
- diag_value=None,
- sigma=1.0,
- epsilon=1.0,
- max_len=25,
- as_eig=True,
- bohr_radius_units=False):
- """
- Creates the Lennard-Jones Matrix from the molecule data given.
- mol_data: molecule data, matrix of atom coordinates.
- nc_data: nuclear charge data, array of atom data.
- diag_value: if special diagonal value is to be used.
- sigma: sigma value.
- epsilon: epsilon value.
- max_len: maximum amount of atoms in molecule.
- as_eig: if data should be returned as matrix or array of eigenvalues.
- bohr_radius_units: if units should be in bohr's radius units.
- """
- if bohr_radius_units:
- conversion_rate = 0.52917721067
- else:
- conversion_rate = 1
-
- mol_n = len(mol_data)
- mol_nr = range(mol_n)
-
- if not mol_n == len(nc_data):
- print(''.join(['Error. Molecule matrix dimension is different ',
- 'than the nuclear charge array dimension.']))
- else:
- if max_len < mol_n:
- print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
- 'greater than max_len. Using mol_n.']))
- max_len = None
-
- if max_len:
- lj = np.zeros((max_len, max_len))
- ml_r = range(max_len)
-
- # Actual calculation of the coulomb matrix.
- for i in ml_r:
- if i < mol_n:
- x_i = mol_data[i, 0]
- y_i = mol_data[i, 1]
- z_i = mol_data[i, 2]
- Z_i = nc_data[i]
- else:
- break
-
- for j in ml_r:
- if j < mol_n:
- x_j = mol_data[j, 0]
- y_j = mol_data[j, 1]
- z_j = mol_data[j, 2]
-
- x = (x_i-x_j)**2
- y = (y_i-y_j)**2
- z = (z_i-z_j)**2
-
- if i == j:
- if diag_value is None:
- lj[i, j] = (0.5*Z_i**2.4)
- else:
- lj[i, j] = diag_value
- else:
- # Calculations are done after i==j is checked
- # so no division by zero is done.
-
- # A little play with r exponents
- # so no square root is calculated.
- # Conversion factor is included in r^2.
-
- # 1/r^2
- r_2 = sigma**2/(conversion_rate**2*(x + y + z))
-
- r_6 = math.pow(r_2, 3)
- r_12 = math.pow(r_6, 2)
- lj[i, j] = (4*epsilon*(r_12 - r_6))
- else:
- break
-
- # Now the value will be returned.
- if as_eig:
- lj_sorted = np.sort(eig(lj)[0])[::-1]
- # Thanks to SO for the following lines of code.
- # https://stackoverflow.com/a/43011036
-
- # Keep zeros at the end.
- mask = lj_sorted != 0.
- f_mask = mask.sum(0, keepdims=1) >\
- np.arange(lj_sorted.shape[0]-1, -1, -1)
-
- f_mask = f_mask[::-1]
- lj_sorted[f_mask] = lj_sorted[mask]
- lj_sorted[~f_mask] = 0.
-
- return lj_sorted
-
- else:
- return lj
-
- else:
- lj_temp = []
- # Actual calculation of the coulomb matrix.
- for i in mol_nr:
- x_i = mol_data[i, 0]
- y_i = mol_data[i, 1]
- z_i = mol_data[i, 2]
- Z_i = nc_data[i]
-
- lj_row = []
- for j in mol_nr:
- x_j = mol_data[j, 0]
- y_j = mol_data[j, 1]
- z_j = mol_data[j, 2]
-
- x = (x_i-x_j)**2
- y = (y_i-y_j)**2
- z = (z_i-z_j)**2
-
- if i == j:
- if not diag_value:
- lj_row.append(0.5*Z_i**2.4)
- else:
- lj_row.append(diag_value)
- else:
- # Calculations are done after i==j is checked
- # so no division by zero is done.
-
- # A little play with r exponents
- # so no square root is calculated.
- # Conversion factor is included in r^2.
-
- # 1/r^2
- r_2 = sigma**2/(conversion_rate**2*(x + y + z))
-
- r_6 = math.pow(r_2, 3)
- r_12 = math.pow(r_6, 2)
- lj_row.append(4*epsilon*(r_12 - r_6))
-
- lj_temp.append(np.array(lj_row))
-
- lj = np.array(lj_temp)
- # Now the value will be returned.
- if as_eig:
- return np.sort(eig(lj)[0])[::-1]
- else:
- return lj
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index c503c310d..b4edef8a5 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -102,3 +102,105 @@ def coulomb_matrix(coords,
return cm_sorted
else:
return cm
+
+
+def lennard_jones_matrix(coords,
+ nc,
+ diag_value=None,
+ sigma=1.0,
+ epsilon=1.0,
+ size=23,
+ as_eig=True,
+ bhor_ru=False):
+ """
+ Creates the Lennard-Jones Matrix from the molecule data given.
+ coords: compound coordinates.
+ nc: nuclear charge data.
+ diag_value: if special diagonal value is to be used.
+ sigma: sigma value.
+ epsilon: epsilon value.
+ size: compound size.
+ as_eig: if the representation should be as the eigenvalues.
+ bhor_ru: if radius units should be in bohr's radius units.
+ """
+ if bhor_ru:
+ cr = 0.52917721067
+ else:
+ cr = 1
+
+ n = coords.shape[0]
+
+ if not n == nc.shape[0]:
+ raise ValueError('Compound size is different than the nuclear charge\
+ size. Arrays are not of the right shape.')
+
+ if size < n:
+ print('Error. Compound size (n) is greater han (size). Using (n)\
+ instead of (size).')
+ size = n
+
+ nr = range(size)
+ lj = np.zeros((size, size), dtype=float)
+
+ # Actual calculation of the lennard-jones matrix.
+ for i in nr:
+ if i < n:
+ x_i = coords[i, 0]
+ y_i = coords[i, 1]
+ z_i = coords[i, 2]
+ Z_i = nc[i]
+ else:
+ break
+
+ for j in nr:
+ if j < n:
+ x_j = coords[j, 0]
+ y_j = coords[j, 1]
+ z_j = coords[j, 2]
+ # Never really used because when needed it is equal to Z_i.
+ # Z_j = nc[j]
+
+ x = (x_i-x_j)**2
+ y = (y_i-y_j)**2
+ z = (z_i-z_j)**2
+
+ if i == j:
+ if diag_value is None:
+ lj[i, j] = (0.5*Z_i**2.4)
+ else:
+ lj[i, j] = diag_value
+ else:
+ # Calculations are done after i==j is checked
+ # so no division by zero is done.
+
+ # A little play with r exponents
+ # so no square root is calculated.
+ # Conversion factor is included in r^2.
+
+ # 1/r^2
+ r_2 = sigma**2/(cr**2*(x + y + z))
+
+ r_6 = math.pow(r_2, 3)
+ r_12 = math.pow(r_6, 2)
+ lj[i, j] = (4*epsilon*(r_12 - r_6))
+ else:
+ break
+
+ # Now the value will be returned.
+ if as_eig:
+ lj_sorted = np.sort(np.linalg.eig(lj)[0])[::-1]
+ # Thanks to SO for the following lines of code.
+ # https://stackoverflow.com/a/43011036
+
+ # Keep zeros at the end.
+ mask = lj_sorted != 0.
+ f_mask = mask.sum(0, keepdims=1) >\
+ np.arange(lj_sorted.shape[0]-1, -1, -1)
+
+ f_mask = f_mask[::-1]
+ lj_sorted[f_mask] = lj_sorted[mask]
+ lj_sorted[~f_mask] = 0.
+
+ return lj_sorted
+ else:
+ return lj
--
cgit v1.2.3-70-g09d2
From 5ba008a928d34c49e431f32b5161f624d780c254 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 19:06:36 -0700
Subject: Add ljmatrix to compound
---
ml_exp/compound.py | 41 +++++++++++++++++++++++++++++++++--------
1 file changed, 33 insertions(+), 8 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 3ea377826..d74f1230a 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -22,7 +22,7 @@ SOFTWARE.
"""
import numpy as np
from ml_exp.data import NUCLEAR_CHARGE
-from ml_exp.representations import coulomb_matrix
+from ml_exp.representations import coulomb_matrix, lennard_jones_matrix
class Compound:
@@ -40,8 +40,8 @@ class Compound:
self.coordinates = None
self.energy = None
- self.coulomb_matrix = None
- self.lennard_jones_matrix = None
+ self.c_matrix = None
+ self.lj_matrix = None
self.bob = None
if xyz is not None:
@@ -57,11 +57,36 @@ class Compound:
as_eig: if the representation should be as the eigenvalues.
bhor_ru: if radius units should be in bohr's radius units.
"""
- self.coulomb_matrix = coulomb_matrix(self.coordinates,
- self.atoms_nc,
- size=size,
- as_eig=as_eig,
- bhor_ru=bohr_ru)
+ self.c_matrix = coulomb_matrix(self.coordinates,
+ self.atoms_nc,
+ size=size,
+ as_eig=as_eig,
+ bhor_ru=bohr_ru)
+
+ def gen_lj(self,
+ diag_value=None,
+ sigma=1.0,
+ epsilon=1.0,
+ size=23,
+ as_eig=True,
+ bohr_ru=False):
+ """
+ Generate the Lennard-Jones Matrix for the compund.
+ diag_value: if special diagonal value is to be used.
+ sigma: sigma value.
+ epsilon: epsilon value.
+ size: compound size.
+ as_eig: if the representation should be as the eigenvalues.
+ bhor_ru: if radius units should be in bohr's radius units.
+ """
+ self.lj_matrix = lennard_jones_matrix(self.coordinates,
+ self.atoms_nc,
+ diag_value=diag_value,
+ sigma=sigma,
+ epsilon=epsilon,
+ size=size,
+ as_eig=as_eig,
+ bhor_ru=bohr_ru)
def read_xyz(self,
filename):
--
cgit v1.2.3-70-g09d2
From 05d97a15d822400f7018a4381593c2638c6ad577 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 19:18:24 -0700
Subject: Refactor code
---
ml_exp/compound.py | 44 ++++++++++++++++++++++----------------------
1 file changed, 22 insertions(+), 22 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index d74f1230a..c6d5f8a64 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -40,8 +40,8 @@ class Compound:
self.coordinates = None
self.energy = None
- self.c_matrix = None
- self.lj_matrix = None
+ self.cm = None
+ self.ljm = None
self.bob = None
if xyz is not None:
@@ -57,19 +57,19 @@ class Compound:
as_eig: if the representation should be as the eigenvalues.
bhor_ru: if radius units should be in bohr's radius units.
"""
- self.c_matrix = coulomb_matrix(self.coordinates,
- self.atoms_nc,
- size=size,
- as_eig=as_eig,
- bhor_ru=bohr_ru)
+ self.cm = coulomb_matrix(self.coordinates,
+ self.atoms_nc,
+ size=size,
+ as_eig=as_eig,
+ bhor_ru=bohr_ru)
- def gen_lj(self,
- diag_value=None,
- sigma=1.0,
- epsilon=1.0,
- size=23,
- as_eig=True,
- bohr_ru=False):
+ def gen_ljm(self,
+ diag_value=None,
+ sigma=1.0,
+ epsilon=1.0,
+ size=23,
+ as_eig=True,
+ bohr_ru=False):
"""
Generate the Lennard-Jones Matrix for the compund.
diag_value: if special diagonal value is to be used.
@@ -79,14 +79,14 @@ class Compound:
as_eig: if the representation should be as the eigenvalues.
bhor_ru: if radius units should be in bohr's radius units.
"""
- self.lj_matrix = lennard_jones_matrix(self.coordinates,
- self.atoms_nc,
- diag_value=diag_value,
- sigma=sigma,
- epsilon=epsilon,
- size=size,
- as_eig=as_eig,
- bhor_ru=bohr_ru)
+ self.ljm = lennard_jones_matrix(self.coordinates,
+ self.atoms_nc,
+ diag_value=diag_value,
+ sigma=sigma,
+ epsilon=epsilon,
+ size=size,
+ as_eig=as_eig,
+ bhor_ru=bohr_ru)
def read_xyz(self,
filename):
--
cgit v1.2.3-70-g09d2
From a7d605f094e81c5139530560e26eb0ff9be8ec82 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 19:21:18 -0700
Subject: Add ljm to init
---
ml_exp/__init__.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index 8e803b37e..f5ec7068b 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -21,9 +21,10 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
from ml_exp.compound import Compound
-from ml_exp.representations import coulomb_matrix
+from ml_exp.representations import coulomb_matrix, lennard_jones_matrix
# If somebody does "from package import *", this is what they will
# be able to access:
__all__ = ['Compound',
- 'coulomb_matrix']
+ 'coulomb_matrix',
+ 'lennard_jones_matrix']
--
cgit v1.2.3-70-g09d2
From 4f95e38f1943856f9a0581c06ea603ffb6283d47 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 22 Feb 2020 16:02:12 -0700
Subject: Move adj matrix to representations
---
ml_exp/adj_matrix.py | 131 ----------------------------------------------
ml_exp/representations.py | 108 ++++++++++++++++++++++++++++++++++++++
2 files changed, 108 insertions(+), 131 deletions(-)
delete mode 100644 ml_exp/adj_matrix.py
diff --git a/ml_exp/adj_matrix.py b/ml_exp/adj_matrix.py
deleted file mode 100644
index de484b5be..000000000
--- a/ml_exp/adj_matrix.py
+++ /dev/null
@@ -1,131 +0,0 @@
-"""MIT License
-
-Copyright (c) 2019 David Luevano Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-from numpy import array, zeros, dot
-from numpy.linalg import norm
-from ml_exp.misc import printc
-
-
-def fneig_matrix(atoms,
- xyz,
- nc=None,
- use_forces=False):
- """
- Creates the first neighbor matrix of the given molecule data.
- atoms: list of atoms.
- xyz: matrix of atomic coords.
- nc: nuclear charge info.
- use_forces: if the use of forces instead of k_cx should be used.
- NOTE: Bond distance of carbon to other elements
- are (for atoms present in the qm7 dataset):
- C: 1.20 - 1.53 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
- """
- if use_forces and nc is None:
- printc(f'Error. use_forces={use_forces} but nc={nc}', 'RED')
- return None
- # 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'])
-
- # Number of atoms, empty matrix and bond list.
- n = len(atoms)
- fnm = array(zeros((n, n)), dtype=float)
- bonds = []
- forces = []
- for i, xyz_i in enumerate(xyz):
- for j, xyz_j in enumerate(xyz):
- # Ignore the diagonal.
- if i != j:
- bond = sorted([atoms[i], atoms[j]])
- rv = xyz_i - xyz_j
- r = norm(rv)
- # Check for each type of bond.
- if (cc_bond == bond) and (r >= 1.20 and r <= 1.53):
- 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:
- forces.append(rv*nc[i]*nc[j]/r**3)
- if use_forces:
- return fnm, bonds, forces
- return fnm, bonds
-
-
-def adj_matrix(fneig_matrix,
- bonds,
- forces=None,
- max_len=25):
- """
- Calculates the adjacency matrix given the bond list.
- bonds: list of bonds (tuple of indexes).
- max_len: maximum amount of atoms in molecule.
- forces: list of forces.
- """
- n = len(bonds)
-
- if max_len < n:
- print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
- 'greater than max_len. Using mol_n.']))
- max_len = n
-
- am = array(zeros((max_len, max_len)))
- for i, bond_i in enumerate(bonds):
- for j, bond_j in enumerate(bonds):
- # Ignore the diagonal.
- if i != j:
- if (bond_i[0] in bond_j) or (bond_i[1] in bond_j):
- if forces:
- am[i, j] = dot(forces[i], forces[j])
- else:
- am[i, j] = fneig_matrix[bond_i[0], bond_i[1]]
- return am
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index b4edef8a5..f503b5987 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -204,3 +204,111 @@ def lennard_jones_matrix(coords,
return lj_sorted
else:
return lj
+
+
+def fneig_matrix(atoms,
+ xyz,
+ nc=None,
+ use_forces=False):
+ """
+ Creates the first neighbor matrix of the given molecule data.
+ atoms: list of atoms.
+ xyz: matrix of atomic coords.
+ nc: nuclear charge info.
+ use_forces: if the use of forces instead of k_cx should be used.
+ NOTE: Bond distance of carbon to other elements
+ are (for atoms present in the qm7 dataset):
+ C: 1.20 - 1.53 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
+ """
+ if use_forces and nc is None:
+ # print(f'Error. use_forces={use_forces} but nc={nc}', 'RED')
+ return None
+ # 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'])
+
+ # Number of atoms, empty matrix and bond list.
+ n = len(atoms)
+ fnm = np.empty((n, n), dtype=float)
+ bonds = []
+ forces = []
+ for i, xyz_i in enumerate(xyz):
+ for j, xyz_j in enumerate(xyz):
+
+ # Ignore the diagonal.
+ if i != j:
+ bond = sorted([atoms[i], atoms[j]])
+ rv = xyz_i - xyz_j
+ r = np.linalg.norm(rv)
+
+ # Check for each type of bond.
+ if (cc_bond == bond) and (r >= 1.20 and r <= 1.53):
+ 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:
+ forces.append(rv*nc[i]*nc[j]/r**3)
+ if use_forces:
+ return fnm, bonds, forces
+ return fnm, bonds
+
+
+def adj_matrix(fneig_matrix,
+ bonds,
+ forces=None,
+ max_len=25):
+ """
+ Calculates the adjacency matrix given the bond list.
+ bonds: list of bonds (tuple of indexes).
+ max_len: maximum amount of atoms in molecule.
+ forces: list of forces.
+ """
+ n = len(bonds)
+
+ if max_len < n:
+ print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
+ 'greater than max_len. Using mol_n.']))
+ max_len = n
+
+ am = np.empty((max_len, max_len), dtype=float)
+ for i, bond_i in enumerate(bonds):
+ for j, bond_j in enumerate(bonds):
+ # Ignore the diagonal.
+ if i != j:
+ if (bond_i[0] in bond_j) or (bond_i[1] in bond_j):
+ if forces:
+ am[i, j] = np.dot(forces[i], forces[j])
+ else:
+ am[i, j] = fneig_matrix[bond_i[0], bond_i[1]]
+ return am
--
cgit v1.2.3-70-g09d2
From 2572f9581b24547692a5654a1d452690a2cbcad6 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 22 Feb 2020 16:36:40 -0700
Subject: Add adj matrix to compound)
---
ml_exp/compound.py | 35 ++++++++++++++++---
ml_exp/representations.py | 89 ++++++++++++++++++++++++++++-------------------
2 files changed, 83 insertions(+), 41 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index c6d5f8a64..d4dc9b7c0 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -22,7 +22,8 @@ SOFTWARE.
"""
import numpy as np
from ml_exp.data import NUCLEAR_CHARGE
-from ml_exp.representations import coulomb_matrix, lennard_jones_matrix
+from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
+ first_neighbor_matrix, adjacency_matrix
class Compound:
@@ -42,6 +43,7 @@ class Compound:
self.cm = None
self.ljm = None
+ self.am = None
self.bob = None
if xyz is not None:
@@ -55,13 +57,13 @@ class Compound:
Generate the Coulomb Matrix for the compund.
size: compound size.
as_eig: if the representation should be as the eigenvalues.
- bhor_ru: if radius units should be in bohr's radius units.
+ bohr_ru: if radius units should be in bohr's radius units.
"""
self.cm = coulomb_matrix(self.coordinates,
self.atoms_nc,
size=size,
as_eig=as_eig,
- bhor_ru=bohr_ru)
+ bohr_ru=bohr_ru)
def gen_ljm(self,
diag_value=None,
@@ -77,7 +79,7 @@ class Compound:
epsilon: epsilon value.
size: compound size.
as_eig: if the representation should be as the eigenvalues.
- bhor_ru: if radius units should be in bohr's radius units.
+ bohr_ru: if radius units should be in bohr's radius units.
"""
self.ljm = lennard_jones_matrix(self.coordinates,
self.atoms_nc,
@@ -86,7 +88,30 @@ class Compound:
epsilon=epsilon,
size=size,
as_eig=as_eig,
- bhor_ru=bohr_ru)
+ bohr_ru=bohr_ru)
+
+ def gen_am(self,
+ use_forces=False,
+ size=23,
+ bohr_ru=False):
+ """
+ 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, bonds, forces = first_neighbor_matrix(self.coordinates,
+ self.atoms_nc,
+ self.atoms,
+ use_forces=use_forces,
+ bohr_ru=bohr_ru)
+
+ # Now, generate the adjacency matrix.
+ self.am = adjacency_matrix(fnm,
+ bonds,
+ forces,
+ size=size)
def read_xyz(self,
filename):
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index f503b5987..483da2898 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -28,16 +28,16 @@ def coulomb_matrix(coords,
nc,
size=23,
as_eig=True,
- bhor_ru=False):
+ bohr_ru=False):
"""
Creates the Coulomb Matrix from the molecule data given.
coords: compound coordinates.
nc: nuclear charge data.
size: compound size.
as_eig: if the representation should be as the eigenvalues.
- bhor_ru: if radius units should be in bohr's radius units.
+ bohr_ru: if radius units should be in bohr's radius units.
"""
- if bhor_ru:
+ if bohr_ru:
cr = 0.52917721067
else:
cr = 1
@@ -111,7 +111,7 @@ def lennard_jones_matrix(coords,
epsilon=1.0,
size=23,
as_eig=True,
- bhor_ru=False):
+ bohr_ru=False):
"""
Creates the Lennard-Jones Matrix from the molecule data given.
coords: compound coordinates.
@@ -121,9 +121,9 @@ def lennard_jones_matrix(coords,
epsilon: epsilon value.
size: compound size.
as_eig: if the representation should be as the eigenvalues.
- bhor_ru: if radius units should be in bohr's radius units.
+ bohr_ru: if radius units should be in bohr's radius units.
"""
- if bhor_ru:
+ if bohr_ru:
cr = 0.52917721067
else:
cr = 1
@@ -206,16 +206,18 @@ def lennard_jones_matrix(coords,
return lj
-def fneig_matrix(atoms,
- xyz,
- nc=None,
- use_forces=False):
+def first_neighbor_matrix(coords,
+ nc,
+ atoms,
+ use_forces=False,
+ bohr_ru=False):
"""
- Creates the first neighbor matrix of the given molecule data.
+ Creates the First Neighbor Matrix from the molecule data given.
+ coords: compound coordinates.
+ nc: nuclear charge data.
atoms: list of atoms.
- xyz: matrix of atomic coords.
- nc: nuclear charge info.
use_forces: if the use of forces instead of k_cx should be used.
+ 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 - 1.53 A
@@ -224,9 +226,17 @@ def fneig_matrix(atoms,
N: 1.47 - 2.10 A
S: 1.81 - 2.55 A
"""
- if use_forces and nc is None:
- # print(f'Error. use_forces={use_forces} but nc={nc}', 'RED')
- return None
+ if bohr_ru:
+ cr = 0.52917721067
+ else:
+ cr = 1
+
+ n = coords.shape[0]
+
+ if not n == nc.shape[0]:
+ raise ValueError('Compound size is different than the nuclear charge\
+ size. Arrays are not of the right shape.')
+
# Possible bonds.
cc_bond = sorted(['C', 'C'])
ch_bond = sorted(['C', 'H'])
@@ -234,19 +244,21 @@ def fneig_matrix(atoms,
cn_bond = sorted(['C', 'N'])
cs_bond = sorted(['C', 'S'])
- # Number of atoms, empty matrix and bond list.
- n = len(atoms)
- fnm = np.empty((n, n), dtype=float)
+ if use_forces:
+ fnm = np.empty((n, n), dtype=float)
+ else:
+ fnm = np.empty((n, n), dtype=int)
+
bonds = []
forces = []
- for i, xyz_i in enumerate(xyz):
- for j, xyz_j in enumerate(xyz):
+ for i, xyz_i in enumerate(coords):
+ for j, xyz_j in enumerate(coords):
# Ignore the diagonal.
if i != j:
bond = sorted([atoms[i], atoms[j]])
rv = xyz_i - xyz_j
- r = np.linalg.norm(rv)
+ r = np.linalg.norm(rv)/cr
# Check for each type of bond.
if (cc_bond == bond) and (r >= 1.20 and r <= 1.53):
@@ -279,29 +291,33 @@ def fneig_matrix(atoms,
bonds.append((i, j))
if use_forces:
forces.append(rv*nc[i]*nc[j]/r**3)
- if use_forces:
- return fnm, bonds, forces
- return fnm, bonds
+
+ return fnm, bonds, forces
-def adj_matrix(fneig_matrix,
- bonds,
- forces=None,
- max_len=25):
+def adjacency_matrix(fnm,
+ bonds,
+ forces,
+ size=23):
"""
Calculates the adjacency matrix given the bond list.
+ fnm: first neighbour matrix.
bonds: list of bonds (tuple of indexes).
- max_len: maximum amount of atoms in molecule.
forces: list of forces.
+ size: compund size.
"""
n = len(bonds)
- if max_len < n:
- print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
- 'greater than max_len. Using mol_n.']))
- max_len = n
+ if size < n:
+ print('Error. Compound size (n) is greater han (size). Using (n)\
+ instead of (size).')
+ size = n
+
+ if forces:
+ am = np.empty((size, size), dtype=float)
+ else:
+ am = np.empty((size, size), dtype=int)
- am = np.empty((max_len, max_len), dtype=float)
for i, bond_i in enumerate(bonds):
for j, bond_j in enumerate(bonds):
# Ignore the diagonal.
@@ -310,5 +326,6 @@ def adj_matrix(fneig_matrix,
if forces:
am[i, j] = np.dot(forces[i], forces[j])
else:
- am[i, j] = fneig_matrix[bond_i[0], bond_i[1]]
+ am[i, j] = fnm[bond_i[0], bond_i[1]]
+
return am
--
cgit v1.2.3-70-g09d2
From fb4307513ddda06742bbe4d542c2716c0d67c06d Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 22 Feb 2020 16:56:05 -0700
Subject: Refactor code
---
ml_exp/representations.py | 93 +++++++++++++----------------------------------
1 file changed, 26 insertions(+), 67 deletions(-)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 483da2898..354611190 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -20,7 +20,6 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
-import math
import numpy as np
@@ -53,36 +52,17 @@ def coulomb_matrix(coords,
instead of (size).')
size = n
- nr = range(size)
cm = np.zeros((size, size), dtype=float)
# Actual calculation of the coulomb matrix.
- for i in nr:
- if i < n:
- x_i = coords[i, 0]
- y_i = coords[i, 1]
- z_i = coords[i, 2]
- Z_i = nc[i]
- else:
- break
-
- for j in nr:
- if j < n:
- x_j = coords[j, 0]
- y_j = coords[j, 1]
- z_j = coords[j, 2]
- Z_j = nc[j]
-
- x = (x_i-x_j)**2
- y = (y_i-y_j)**2
- z = (z_i-z_j)**2
-
- if i == j:
- cm[i, j] = (0.5*Z_i**2.4)
- else:
- cm[i, j] = (cr*Z_i*Z_j/math.sqrt(x + y + z))
+ for i, xyz_i in enumerate(coords):
+ for j, xyz_j in enumerate(coords):
+ rv = xyz_i - xyz_j
+ r = np.linalg.norm(rv)/cr
+ if i == j:
+ cm[i, j] = (0.5*nc[i]**2.4)
else:
- break
+ cm[i, j] = nc[i]*nc[j]/r
# Now the value will be returned.
if as_eig:
@@ -139,52 +119,31 @@ def lennard_jones_matrix(coords,
instead of (size).')
size = n
- nr = range(size)
lj = np.zeros((size, size), dtype=float)
# Actual calculation of the lennard-jones matrix.
- for i in nr:
- if i < n:
- x_i = coords[i, 0]
- y_i = coords[i, 1]
- z_i = coords[i, 2]
- Z_i = nc[i]
- else:
- break
-
- for j in nr:
- if j < n:
- x_j = coords[j, 0]
- y_j = coords[j, 1]
- z_j = coords[j, 2]
- # Never really used because when needed it is equal to Z_i.
- # Z_j = nc[j]
-
- x = (x_i-x_j)**2
- y = (y_i-y_j)**2
- z = (z_i-z_j)**2
-
- if i == j:
- if diag_value is None:
- lj[i, j] = (0.5*Z_i**2.4)
- else:
- lj[i, j] = diag_value
+ for i, xyz_i in enumerate(coords):
+ for j, xyz_j in enumerate(coords):
+ if i == j:
+ if diag_value is None:
+ lj[i, j] = (0.5*nc[i]**2.4)
else:
- # Calculations are done after i==j is checked
- # so no division by zero is done.
-
- # A little play with r exponents
- # so no square root is calculated.
- # Conversion factor is included in r^2.
+ lj[i, j] = diag_value
+ else:
+ # Calculations are done after i==j is checked
+ # so no division by zero is done.
- # 1/r^2
- r_2 = sigma**2/(cr**2*(x + y + z))
+ # A little play with r exponents
+ # so no square root is calculated.
+ # Conversion factor is included in r^2.
+ rv = xyz_i - xyz_j
+ r = sigma*np.linalg.norm(rv)/cr
- r_6 = math.pow(r_2, 3)
- r_12 = math.pow(r_6, 2)
- lj[i, j] = (4*epsilon*(r_12 - r_6))
- else:
- break
+ # 1/r^n
+ r_2 = 1/r**2
+ r_6 = r_2**3
+ r_12 = r_6**2
+ lj[i, j] = (4*epsilon*(r_12 - r_6))
# Now the value will be returned.
if as_eig:
--
cgit v1.2.3-70-g09d2
From 8d0a22b9fdef41ece399468423cb533768d0e631 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 22 Feb 2020 17:12:32 -0700
Subject: Add tests
---
ml_exp/__main__.py | 11 ++++++++++-
ml_exp/representations.py | 4 ++--
2 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/ml_exp/__main__.py b/ml_exp/__main__.py
index 3cb515d85..cb8a9a3f1 100644
--- a/ml_exp/__main__.py
+++ b/ml_exp/__main__.py
@@ -20,5 +20,14 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
+from ml_exp.compound import Compound
+
+
if __name__ == '__main__':
- print('Ok!')
+ print('Initialize test')
+ test = []
+ for i in range(1, 10):
+ test.append(Compound(f'/home/luevano/py/ml_exp/data/qm7/000{i}.xyz'))
+ test[i-1].gen_cm(size=1, as_eig=False)
+ test[i-1].gen_ljm(size=1, as_eig=False)
+ test[i-1].gen_am(size=1)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 354611190..ae870f3b0 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -273,9 +273,9 @@ def adjacency_matrix(fnm,
size = n
if forces:
- am = np.empty((size, size), dtype=float)
+ am = np.zeros((size, size), dtype=float)
else:
- am = np.empty((size, size), dtype=int)
+ am = np.zeros((size, size), dtype=int)
for i, bond_i in enumerate(bonds):
for j, bond_j in enumerate(bonds):
--
cgit v1.2.3-70-g09d2
From 85198178482767d2831ddf3762e5e6eeafa990bd Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 22 Feb 2020 18:37:50 -0700
Subject: Fix bug, current errors present on adj matrix
---
ml_exp/__main__.py | 3 ---
ml_exp/representations.py | 16 ++++++++--------
2 files changed, 8 insertions(+), 11 deletions(-)
diff --git a/ml_exp/__main__.py b/ml_exp/__main__.py
index cb8a9a3f1..17119623e 100644
--- a/ml_exp/__main__.py
+++ b/ml_exp/__main__.py
@@ -28,6 +28,3 @@ if __name__ == '__main__':
test = []
for i in range(1, 10):
test.append(Compound(f'/home/luevano/py/ml_exp/data/qm7/000{i}.xyz'))
- test[i-1].gen_cm(size=1, as_eig=False)
- test[i-1].gen_ljm(size=1, as_eig=False)
- test[i-1].gen_am(size=1)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index ae870f3b0..796d15f98 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -48,8 +48,8 @@ def coulomb_matrix(coords,
size. Arrays are not of the right shape.')
if size < n:
- print('Error. Compound size (n) is greater han (size). Using (n)\
- instead of (size).')
+ print('Error. Compound size (n) is greater han (size). Using (n)',
+ 'instead of (size).')
size = n
cm = np.zeros((size, size), dtype=float)
@@ -115,8 +115,8 @@ def lennard_jones_matrix(coords,
size. Arrays are not of the right shape.')
if size < n:
- print('Error. Compound size (n) is greater han (size). Using (n)\
- instead of (size).')
+ print('Error. Compound size (n) is greater han (size). Using (n)',
+ 'instead of (size).')
size = n
lj = np.zeros((size, size), dtype=float)
@@ -137,10 +137,10 @@ def lennard_jones_matrix(coords,
# so no square root is calculated.
# Conversion factor is included in r^2.
rv = xyz_i - xyz_j
- r = sigma*np.linalg.norm(rv)/cr
+ r = np.linalg.norm(rv)/cr
# 1/r^n
- r_2 = 1/r**2
+ r_2 = sigma**2/r**2
r_6 = r_2**3
r_12 = r_6**2
lj[i, j] = (4*epsilon*(r_12 - r_6))
@@ -204,9 +204,9 @@ def first_neighbor_matrix(coords,
cs_bond = sorted(['C', 'S'])
if use_forces:
- fnm = np.empty((n, n), dtype=float)
+ fnm = np.zeros((n, n), dtype=float)
else:
- fnm = np.empty((n, n), dtype=int)
+ fnm = np.zeros((n, n), dtype=int)
bonds = []
forces = []
--
cgit v1.2.3-70-g09d2
From db47ff8606b14e4cdddc0e317972c3515b9c788b Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sun, 23 Feb 2020 21:03:39 -0700
Subject: Fix adj matrix issue with cc bonds)
---
ml_exp/__main__.py | 11 ++++++++---
ml_exp/compound.py | 6 ++++--
ml_exp/representations.py | 29 ++++++++++++++---------------
3 files changed, 26 insertions(+), 20 deletions(-)
diff --git a/ml_exp/__main__.py b/ml_exp/__main__.py
index 17119623e..124ce8cd9 100644
--- a/ml_exp/__main__.py
+++ b/ml_exp/__main__.py
@@ -25,6 +25,11 @@ from ml_exp.compound import Compound
if __name__ == '__main__':
print('Initialize test')
- test = []
- for i in range(1, 10):
- test.append(Compound(f'/home/luevano/py/ml_exp/data/qm7/000{i}.xyz'))
+ mol_name = '/home/luevano/py/ml_exp/data/qm7/0004.xyz'
+ mol = Compound(mol_name)
+ mol.gen_cm(size=1, as_eig=False)
+ mol.gen_ljm(size=1, as_eig=False)
+ mol.gen_am(size=1)
+
+ print(mol.n, mol.atoms, mol.atoms_nc)
+ print(mol.am)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index d4dc9b7c0..d499e6b83 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -39,7 +39,8 @@ class Compound:
self.atoms = None
self.atoms_nc = None
self.coordinates = None
- self.energy = None
+ self.pbe0 = None
+ self.delta = None
self.cm = None
self.ljm = None
@@ -91,8 +92,8 @@ class Compound:
bohr_ru=bohr_ru)
def gen_am(self,
- use_forces=False,
size=23,
+ use_forces=False,
bohr_ru=False):
"""
Generate the Adjacency Matrix for the compund.
@@ -104,6 +105,7 @@ class Compound:
fnm, bonds, forces = first_neighbor_matrix(self.coordinates,
self.atoms_nc,
self.atoms,
+ size=size,
use_forces=use_forces,
bohr_ru=bohr_ru)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 796d15f98..11c30dfd2 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -39,7 +39,7 @@ def coulomb_matrix(coords,
if bohr_ru:
cr = 0.52917721067
else:
- cr = 1
+ cr = 1.0
n = coords.shape[0]
@@ -106,7 +106,7 @@ def lennard_jones_matrix(coords,
if bohr_ru:
cr = 0.52917721067
else:
- cr = 1
+ cr = 1.0
n = coords.shape[0]
@@ -168,6 +168,7 @@ def lennard_jones_matrix(coords,
def first_neighbor_matrix(coords,
nc,
atoms,
+ size=23,
use_forces=False,
bohr_ru=False):
"""
@@ -179,7 +180,7 @@ 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 - 1.53 A
+ 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
@@ -188,7 +189,7 @@ def first_neighbor_matrix(coords,
if bohr_ru:
cr = 0.52917721067
else:
- cr = 1
+ cr = 1.0
n = coords.shape[0]
@@ -196,6 +197,11 @@ def first_neighbor_matrix(coords,
raise ValueError('Compound size is different than the nuclear charge\
size. Arrays are not of the right shape.')
+ if size < n:
+ print('Error. Compound size (n) is greater han (size). Using (n)',
+ 'instead of (size).')
+ size = n
+
# Possible bonds.
cc_bond = sorted(['C', 'C'])
ch_bond = sorted(['C', 'H'])
@@ -203,16 +209,12 @@ def first_neighbor_matrix(coords,
cn_bond = sorted(['C', 'N'])
cs_bond = sorted(['C', 'S'])
- if use_forces:
- fnm = np.zeros((n, n), dtype=float)
- else:
- fnm = np.zeros((n, n), dtype=int)
+ fnm = np.zeros((size, size), dtype=float)
bonds = []
forces = []
for i, xyz_i in enumerate(coords):
for j, xyz_j in enumerate(coords):
-
# Ignore the diagonal.
if i != j:
bond = sorted([atoms[i], atoms[j]])
@@ -220,7 +222,7 @@ def first_neighbor_matrix(coords,
r = np.linalg.norm(rv)/cr
# Check for each type of bond.
- if (cc_bond == bond) and (r >= 1.20 and r <= 1.53):
+ if (cc_bond == bond) and (r >= 1.19 and r <= 1.54):
fnm[i, j] = 1.0
if j > i:
bonds.append((i, j))
@@ -257,7 +259,7 @@ def first_neighbor_matrix(coords,
def adjacency_matrix(fnm,
bonds,
forces,
- size=23):
+ size=22):
"""
Calculates the adjacency matrix given the bond list.
fnm: first neighbour matrix.
@@ -272,10 +274,7 @@ def adjacency_matrix(fnm,
instead of (size).')
size = n
- if forces:
- am = np.zeros((size, size), dtype=float)
- else:
- am = np.zeros((size, size), dtype=int)
+ am = np.zeros((size, size), dtype=float)
for i, bond_i in enumerate(bonds):
for j, bond_j in enumerate(bonds):
--
cgit v1.2.3-70-g09d2
From 54e69de6126afb321c0ea575ede595347ffc121c Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sun, 23 Feb 2020 21:07:54 -0700
Subject: Add fnm and am to init
---
ml_exp/__init__.py | 7 +++++--
ml_exp/__main__.py | 12 ++----------
2 files changed, 7 insertions(+), 12 deletions(-)
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index f5ec7068b..d81f0999a 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -21,10 +21,13 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
from ml_exp.compound import Compound
-from ml_exp.representations import coulomb_matrix, lennard_jones_matrix
+from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
+ first_neighbor_matrix, adjacency_matrix
# If somebody does "from package import *", this is what they will
# be able to access:
__all__ = ['Compound',
'coulomb_matrix',
- 'lennard_jones_matrix']
+ 'lennard_jones_matrix',
+ 'first_neighbor_matrix',
+ 'adjacency_matrix']
diff --git a/ml_exp/__main__.py b/ml_exp/__main__.py
index 124ce8cd9..44b492103 100644
--- a/ml_exp/__main__.py
+++ b/ml_exp/__main__.py
@@ -20,16 +20,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
-from ml_exp.compound import Compound
+# from ml_exp.compound import Compound
if __name__ == '__main__':
- print('Initialize test')
- mol_name = '/home/luevano/py/ml_exp/data/qm7/0004.xyz'
- mol = Compound(mol_name)
- mol.gen_cm(size=1, as_eig=False)
- mol.gen_ljm(size=1, as_eig=False)
- mol.gen_am(size=1)
-
- print(mol.n, mol.atoms, mol.atoms_nc)
- print(mol.am)
+ print('OK!')
--
cgit v1.2.3-70-g09d2
From 336654366a0e0a15263bd0d93bcb81ef48fcb040 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sun, 23 Feb 2020 21:12:00 -0700
Subject: Remove bag of stuff
---
ml_exp/bostuff.py | 99 -------------------------------------------------------
1 file changed, 99 deletions(-)
delete mode 100644 ml_exp/bostuff.py
diff --git a/ml_exp/bostuff.py b/ml_exp/bostuff.py
deleted file mode 100644
index 1741e26cd..000000000
--- a/ml_exp/bostuff.py
+++ /dev/null
@@ -1,99 +0,0 @@
-"""MIT License
-
-Copyright (c) 2019 David Luevano Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-from numpy import array, zeros
-from collections import Counter
-from ml_exp.bob import check_bond
-
-
-def bok_cx(adj_matrix,
- atoms,
- max_n=25,
- max_bond_len=325):
- """
- Creates the bag of k_cx using the adjacency matrix data.
- adj_matrix: adjacency matrix.
- max_n: maximum amount of atoms.
- max_bond_len: maximum amount of bonds in molecule.
- """
- n = len(atoms)
- bond_n = (n * n - n) / 2 + n
- n_r = range(n)
-
- if max_n < n:
- print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
- 'greater than max_len. Using mol_n.']))
- max_n = n
-
- if max_bond_len < bond_n:
- print(''.join(['Error. Molecule bond length (bond_n) is ',
- 'greater than max_bond_len. Using bond_n.']))
- max_bond_len = bond_n
-
- # List where each bag data is stored.
- bags = []
- for i in n_r:
- for j in n_r:
- # Work only in the upper triangle of the coulomb matrix.
- if j >= i:
- # Get the string of the current bond.
- if i == j:
- current_bond = atoms[i]
- else:
- current_bond = ''.join(sorted([atoms[i], atoms[j]]))
-
- # Check if that bond is already in a bag.
- checker = check_bond(bags, current_bond)
- # Either create a new bag or add values to an existing one.
- if not checker[0]:
- bags.append([current_bond, adj_matrix[i, j]])
- else:
- bags[checker[1]].append(adj_matrix[i, j])
-
- # Create the actual bond list ordered.
- atom_counter = Counter(atoms)
- atom_list = sorted(list(set(atoms)))
- bonds = []
- for i, a_i in enumerate(atom_list):
- if atom_counter[a_i] > 1:
- for a_j in atom_list[i:]:
- bonds.append(''.join(sorted([a_i, a_j])))
- bonds = atom_list + bonds
-
- # Create the final vector for the bok_cx.
- bok_cx = array(zeros(max_bond_len), 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 bok_cx if the zero padding should
- # be at the end of the vector instead of between each bond.
- bok_cx[i*max_n + j] = num
- c_i += 1
- # This is set to false because this was a debugging measure.
- else:
- print(''.join([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 once',
- ' in the molecule.']))
- return bok_cx
--
cgit v1.2.3-70-g09d2
From 321681e542509869568e9ed610d821c1d9d9d5e6 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sun, 23 Feb 2020 21:16:16 -0700
Subject: Move bob to representations
---
ml_exp/bob.py | 117 ----------------------------------------------
ml_exp/representations.py | 94 +++++++++++++++++++++++++++++++++++++
2 files changed, 94 insertions(+), 117 deletions(-)
delete mode 100644 ml_exp/bob.py
diff --git a/ml_exp/bob.py b/ml_exp/bob.py
deleted file mode 100644
index 86efecdb4..000000000
--- a/ml_exp/bob.py
+++ /dev/null
@@ -1,117 +0,0 @@
-"""MIT License
-
-Copyright (c) 2019 David Luevano Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-from numpy import array, zeros
-from collections import Counter
-
-
-def check_bond(bags,
- bond):
- """
- Checks if a bond is in a bag.
- bags: list of bags, containing a bag per entry, which in turn
- contains a list of bond-values.
- bond: bond to check.
- """
- if bags == []:
- return False, None
-
- for i, bag in enumerate(bags):
- if bag[0] == bond:
- return True, i
-
- return False, None
-
-
-def bob(c_matrix,
- atoms,
- max_n=25,
- max_bond_len=325):
- """
- Creates the bag of bond using the coulomb matrix data.
- c_matrix: coulomb matrix.
- atoms: list of atoms.
- max_n: maximum amount of atoms.
- max_bond_len: maximum amount of bonds in molecule.
- """
- n = len(atoms)
- bond_n = (n * n - n) / 2 + n
- n_r = range(n)
-
- if max_n < n:
- print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
- 'greater than max_len. Using mol_n.']))
- max_n = n
-
- if max_bond_len < bond_n:
- print(''.join(['Error. Molecule bond lenght (bond_n) is ',
- 'greater than max_bond_len. Using bond_n.']))
- max_bond_len = bond_n
-
- # List where each bag data is stored.
- bags = []
- for i in n_r:
- for j in n_r:
- # Work only in the upper triangle of the coulomb matrix.
- if j >= i:
- # Get the string of the current bond.
- if i == j:
- current_bond = atoms[i]
- else:
- current_bond = ''.join(sorted([atoms[i], atoms[j]]))
-
- # Check if that bond is already in a bag.
- checker = check_bond(bags, current_bond)
- # Either create a new bag or add values to an existing one.
- if not checker[0]:
- bags.append([current_bond, c_matrix[i, j]])
- else:
- bags[checker[1]].append(c_matrix[i, j])
-
- # Create the actual bond list ordered.
- atom_counter = Counter(atoms)
- atom_list = sorted(list(set(atoms)))
- bonds = []
- for i, a_i in enumerate(atom_list):
- if atom_counter[a_i] > 1:
- for a_j in atom_list[i:]:
- bonds.append(''.join(sorted([a_i, a_j])))
- bonds = atom_list + bonds
-
- # Create the final vector for the bob.
- bob = array(zeros(max_bond_len), 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 bob if the zero padding should
- # be at the end of the vector instead of between each bond.
- bob[i*max_n + j] = num
- c_i += 1
- # This is set to false because this was a debugging measure.
- else:
- print(''.join([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 once',
- ' in the molecule.']))
- return bob
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 11c30dfd2..3119a4a88 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -21,6 +21,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
import numpy as np
+from collections import Counter
def coulomb_matrix(coords,
@@ -287,3 +288,96 @@ def adjacency_matrix(fnm,
am[i, j] = fnm[bond_i[0], bond_i[1]]
return am
+
+
+def check_bond(bags,
+ bond):
+ """
+ Checks if a bond is in a bag.
+ bags: list of bags, containing a bag per entry, which in turn
+ contains a list of bond-values.
+ bond: bond to check.
+ """
+ if bags == []:
+ return False, None
+
+ for i, bag in enumerate(bags):
+ if bag[0] == bond:
+ return True, i
+
+ return False, None
+
+
+def bob(c_matrix,
+ atoms,
+ max_n=25,
+ max_bond_len=325):
+ """
+ Creates the bag of bond using the coulomb matrix data.
+ c_matrix: coulomb matrix.
+ atoms: list of atoms.
+ max_n: maximum amount of atoms.
+ max_bond_len: maximum amount of bonds in molecule.
+ """
+ n = len(atoms)
+ bond_n = (n * n - n) / 2 + n
+ n_r = range(n)
+
+ if max_n < n:
+ print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
+ 'greater than max_len. Using mol_n.']))
+ max_n = n
+
+ if max_bond_len < bond_n:
+ print(''.join(['Error. Molecule bond lenght (bond_n) is ',
+ 'greater than max_bond_len. Using bond_n.']))
+ max_bond_len = bond_n
+
+ # List where each bag data is stored.
+ bags = []
+ for i in n_r:
+ for j in n_r:
+ # Work only in the upper triangle of the coulomb matrix.
+ if j >= i:
+ # Get the string of the current bond.
+ if i == j:
+ current_bond = atoms[i]
+ else:
+ current_bond = ''.join(sorted([atoms[i], atoms[j]]))
+
+ # Check if that bond is already in a bag.
+ checker = check_bond(bags, current_bond)
+ # Either create a new bag or add values to an existing one.
+ if not checker[0]:
+ bags.append([current_bond, c_matrix[i, j]])
+ else:
+ bags[checker[1]].append(c_matrix[i, j])
+
+ # Create the actual bond list ordered.
+ atom_counter = Counter(atoms)
+ atom_list = sorted(list(set(atoms)))
+ bonds = []
+ for i, a_i in enumerate(atom_list):
+ if atom_counter[a_i] > 1:
+ for a_j in atom_list[i:]:
+ bonds.append(''.join(sorted([a_i, a_j])))
+ bonds = atom_list + bonds
+
+ # Create the final vector for the bob.
+ bob = array(zeros(max_bond_len), 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 bob if the zero padding should
+ # be at the end of the vector instead of between each bond.
+ bob[i*max_n + j] = num
+ c_i += 1
+ # This is set to false because this was a debugging measure.
+ else:
+ print(''.join([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 once',
+ ' in the molecule.']))
+ return bob
--
cgit v1.2.3-70-g09d2
From 2c8a05c20fbfec9d6c34a83958b694a7611b6cf1 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sun, 23 Feb 2020 21:45:06 -0700
Subject: Refactor bag of sutff in representations
---
ml_exp/compound.py | 2 +-
ml_exp/representations.py | 73 +++++++++++++++++++++++------------------------
2 files changed, 36 insertions(+), 39 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index d499e6b83..595078d55 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -45,7 +45,7 @@ class Compound:
self.cm = None
self.ljm = None
self.am = None
- self.bob = None
+ self.bos = None
if xyz is not None:
self.read_xyz(xyz)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 3119a4a88..a85fee11f 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -45,8 +45,8 @@ def coulomb_matrix(coords,
n = coords.shape[0]
if not n == nc.shape[0]:
- raise ValueError('Compound size is different than the nuclear charge\
- size. Arrays are not of the right shape.')
+ raise ValueError('Compound size is different than the nuclear charge \
+size. Arrays are not of the right shape.')
if size < n:
print('Error. Compound size (n) is greater han (size). Using (n)',
@@ -112,8 +112,8 @@ def lennard_jones_matrix(coords,
n = coords.shape[0]
if not n == nc.shape[0]:
- raise ValueError('Compound size is different than the nuclear charge\
- size. Arrays are not of the right shape.')
+ raise ValueError('Compound size is different than the nuclear charge \
+size. Arrays are not of the right shape.')
if size < n:
print('Error. Compound size (n) is greater han (size). Using (n)',
@@ -195,8 +195,8 @@ def first_neighbor_matrix(coords,
n = coords.shape[0]
if not n == nc.shape[0]:
- raise ValueError('Compound size is different than the nuclear charge\
- size. Arrays are not of the right shape.')
+ raise ValueError('Compound size is different than the nuclear charge \
+size. Arrays are not of the right shape.')
if size < n:
print('Error. Compound size (n) is greater han (size). Using (n)',
@@ -295,7 +295,7 @@ def check_bond(bags,
"""
Checks if a bond is in a bag.
bags: list of bags, containing a bag per entry, which in turn
- contains a list of bond-values.
+ contains a list of bond-values.
bond: bond to check.
"""
if bags == []:
@@ -308,50 +308,49 @@ def check_bond(bags,
return False, None
-def bob(c_matrix,
- atoms,
- max_n=25,
- max_bond_len=325):
+def bag_of(cm,
+ atoms,
+ stuff='bonds',
+ size=23):
"""
- Creates the bag of bond using the coulomb matrix data.
- c_matrix: coulomb matrix.
+ Creates the Bag of Bonds using the Coulomb Matrix.
+ cm: coulomb matrix.
atoms: list of atoms.
- max_n: maximum amount of atoms.
- max_bond_len: maximum amount of bonds in molecule.
+ size: maximum amount of atoms.
"""
+ if cm is None:
+ raise ValueError('Coulomb Matrix hasn\'t been initialized for the \
+current compound.')
+
n = len(atoms)
- bond_n = (n * n - n) / 2 + n
- n_r = range(n)
- if max_n < n:
- print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
- 'greater than max_len. Using mol_n.']))
- max_n = n
+ if size < n:
+ print('Error. Compound size (n) is greater han (size). Using (n)',
+ 'instead of (size).')
+ size = n
- if max_bond_len < bond_n:
- print(''.join(['Error. Molecule bond lenght (bond_n) is ',
- 'greater than max_bond_len. Using bond_n.']))
- max_bond_len = bond_n
+ # Bond max length, calculated using only the upper triangular matrix.
+ bond_size = (size * size - size)/2 + size
# List where each bag data is stored.
bags = []
- for i in n_r:
- for j in n_r:
+ for i, atom_i in enumerate(atoms):
+ for j, atom_j in enumerate(atoms):
# Work only in the upper triangle of the coulomb matrix.
if j >= i:
# Get the string of the current bond.
if i == j:
- current_bond = atoms[i]
+ current_bond = atom_i
else:
- current_bond = ''.join(sorted([atoms[i], atoms[j]]))
+ current_bond = ''.join(sorted([atom_i, atom_j]))
# Check if that bond is already in a bag.
checker = check_bond(bags, current_bond)
# Either create a new bag or add values to an existing one.
if not checker[0]:
- bags.append([current_bond, c_matrix[i, j]])
+ bags.append([current_bond, cm[i, j]])
else:
- bags[checker[1]].append(c_matrix[i, j])
+ bags[checker[1]].append(cm[i, j])
# Create the actual bond list ordered.
atom_counter = Counter(atoms)
@@ -364,7 +363,7 @@ def bob(c_matrix,
bonds = atom_list + bonds
# Create the final vector for the bob.
- bob = array(zeros(max_bond_len), dtype=float)
+ bob = np.zeros(bond_size, dtype=float)
c_i = 0
for i, bond in enumerate(bonds):
checker = check_bond(bags, bond)
@@ -372,12 +371,10 @@ def bob(c_matrix,
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*max_n + j] = num
+ bob[i*size + j] = num
c_i += 1
- # This is set to false because this was a debugging measure.
else:
- print(''.join([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 once',
- ' in the molecule.']))
+ 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 b82b90ec609ee80629f1e7f4b8a03cbbb53a0f21 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sun, 23 Feb 2020 21:45:45 -0700
Subject: Edit bag of stuff function name
---
ml_exp/representations.py | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index a85fee11f..1fe55aa5f 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -308,15 +308,15 @@ def check_bond(bags,
return False, None
-def bag_of(cm,
- atoms,
- stuff='bonds',
- size=23):
+def bag_of_stuff(cm,
+ atoms,
+ stuff='bonds',
+ size=23):
"""
Creates the Bag of Bonds using the Coulomb Matrix.
cm: coulomb matrix.
atoms: list of atoms.
- size: maximum amount of atoms.
+ size: compound size.
"""
if cm is None:
raise ValueError('Coulomb Matrix hasn\'t been initialized for the \
--
cgit v1.2.3-70-g09d2
From b300e365d0886695b0d0220aad1be6cb38cf3c36 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sun, 23 Feb 2020 22:06:30 -0700
Subject: Add bos to compound, and bugfix to bos
---
ml_exp/__init__.py | 6 ++++--
ml_exp/compound.py | 15 ++++++++++++++-
ml_exp/representations.py | 20 ++++++++++++--------
3 files changed, 30 insertions(+), 11 deletions(-)
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index d81f0999a..dcb10a1df 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
+ first_neighbor_matrix, adjacency_matrix, check_bond, bag_of_stuff
# If somebody does "from package import *", this is what they will
# be able to access:
@@ -30,4 +30,6 @@ __all__ = ['Compound',
'coulomb_matrix',
'lennard_jones_matrix',
'first_neighbor_matrix',
- 'adjacency_matrix']
+ 'adjacency_matrix',
+ 'check_bond',
+ 'bag_of_stuff']
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 595078d55..8b6af0ae9 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
+ first_neighbor_matrix, adjacency_matrix, bag_of_stuff
class Compound:
@@ -115,6 +115,19 @@ class Compound:
forces,
size=size)
+ def gen_bos(self,
+ size=23,
+ stuff='bonds'):
+ """
+ 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)
+
def read_xyz(self,
filename):
"""
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 1fe55aa5f..ea079595e 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -310,8 +310,8 @@ def check_bond(bags,
def bag_of_stuff(cm,
atoms,
- stuff='bonds',
- size=23):
+ size=23,
+ stuff='bonds'):
"""
Creates the Bag of Bonds using the Coulomb Matrix.
cm: coulomb matrix.
@@ -322,6 +322,10 @@ def bag_of_stuff(cm,
raise ValueError('Coulomb Matrix hasn\'t been initialized for the \
current compound.')
+ if cm.ndim == 1:
+ raise ValueError('Coulomb Matrix (CM) dimension is 1. Maybe it was \
+generated as the vector of eigenvalues, try (re-)generating the CM.')
+
n = len(atoms)
if size < n:
@@ -330,7 +334,7 @@ current compound.')
size = n
# Bond max length, calculated using only the upper triangular matrix.
- bond_size = (size * size - size)/2 + size
+ bond_size = int((size * size - size)/2 + size)
# List where each bag data is stored.
bags = []
@@ -362,19 +366,19 @@ current compound.')
bonds.append(''.join(sorted([a_i, a_j])))
bonds = atom_list + bonds
- # Create the final vector for the bob.
- bob = np.zeros(bond_size, dtype=float)
+ # Create the final vector for the bos.
+ bos = 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 bob if the zero padding should
+ # Use c_i as the index for bos if the zero padding should
# be at the end of the vector instead of between each bond.
- bob[i*size + j] = num
+ bos[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 bob
+ return bos
--
cgit v1.2.3-70-g09d2
From adbc889949b8399353ab166b5d9c15734f1f0bb8 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 25 Feb 2020 20:41:09 -0700
Subject: Move frob norm and cholesky solve to math
---
ml_exp/cholesky_solve.py | 64 ---------------------------------
ml_exp/frob_norm.py | 51 ---------------------------
ml_exp/gauss_kernel.py | 49 --------------------------
ml_exp/kernels.py | 49 ++++++++++++++++++++++++++
ml_exp/math.py | 92 ++++++++++++++++++++++++++++++++++++++++++++++++
5 files changed, 141 insertions(+), 164 deletions(-)
delete mode 100644 ml_exp/cholesky_solve.py
delete mode 100644 ml_exp/frob_norm.py
delete mode 100644 ml_exp/gauss_kernel.py
create mode 100644 ml_exp/kernels.py
create mode 100644 ml_exp/math.py
diff --git a/ml_exp/cholesky_solve.py b/ml_exp/cholesky_solve.py
deleted file mode 100644
index bc6a572a3..000000000
--- a/ml_exp/cholesky_solve.py
+++ /dev/null
@@ -1,64 +0,0 @@
-"""MIT License
-
-Copyright (c) 2019 David Luevano Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-import numpy as np
-from numpy.linalg import cholesky
-
-
-def cholesky_solve(K, y):
- """
- Applies Cholesky decomposition to obtain the 'alpha coeficients'.
- K: kernel.
- y: known parameters.
- """
- # The initial mathematical problem is to solve Ka=y.
-
- # First, add a small lambda value.
- K[np.diag_indices_from(K)] += 1e-8
-
- # Get the Cholesky decomposition of the kernel.
- L = cholesky(K)
- size = len(L)
-
- # Solve Lx=y for x.
- x = np.zeros(size)
- x[0] = y[0] / L[0, 0]
- for i in range(1, size):
- temp_sum = 0.0
- for j in range(i):
- temp_sum += L[i, j] * x[j]
- x[i] = (y[i] - temp_sum) / L[i, i]
-
- # Now, solve LTa=x for a.
- L2 = L.T
- a = np.zeros(size)
- a_ms = size - 1
- a[a_ms] = x[a_ms] / L2[a_ms, a_ms]
- # Because of the form of L2 (upper triangular matriz), an inversion of
- # range() needs to be done.
- for i in range(0, a_ms)[::-1]:
- temp_sum = 0.0
- for j in range(i, size)[::-1]:
- temp_sum += L2[i, j] * a[j]
- a[i] = (x[i] - temp_sum) / L2[i, i]
-
- return a
diff --git a/ml_exp/frob_norm.py b/ml_exp/frob_norm.py
deleted file mode 100644
index 4c3a2945d..000000000
--- a/ml_exp/frob_norm.py
+++ /dev/null
@@ -1,51 +0,0 @@
-"""MIT License
-
-Copyright (c) 2019 David Luevano Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-import math
-
-
-def frob_norm(array):
- """
- Calculates the frobenius norm of a given array or matrix.
- array: array of data.
- """
-
- arr_sh_len = len(array.shape)
- arr_range = range(len(array))
- fn = 0.0
-
- # If it is a 'vector'.
- if arr_sh_len == 1:
- for i in arr_range:
- fn += array[i]*array[i]
-
- return math.sqrt(fn)
-
- # If it is a matrix.
- elif arr_sh_len == 2:
- for i in arr_range:
- for j in arr_range:
- fn += array[i, j]*array[i, j]
-
- return math.sqrt(fn)
- else:
- print('Error. Array size greater than 2 ({}).'.format(arr_sh_len))
diff --git a/ml_exp/gauss_kernel.py b/ml_exp/gauss_kernel.py
deleted file mode 100644
index 834d62408..000000000
--- a/ml_exp/gauss_kernel.py
+++ /dev/null
@@ -1,49 +0,0 @@
-"""MIT License
-
-Copyright (c) 2019 David Luevano Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-import math
-import numpy as np
-from ml_exp.frob_norm import frob_norm
-
-
-def gauss_kernel(X_1, X_2, sigma):
- """
- Calculates the Gaussian Kernel.
- X_1: first representations.
- X_2: second representations.
- sigma: kernel width.
- """
- x1_l = len(X_1)
- x1_range = range(x1_l)
- x2_l = len(X_2)
- x2_range = range(x2_l)
-
- inv_sigma = -0.5 / (sigma*sigma)
-
- K = np.zeros((x1_l, x2_l))
- for i in x1_range:
- for j in x2_range:
- f_norm = frob_norm(X_1[i] - X_2[j])
- # print(f_norm)
- K[i, j] = math.exp(inv_sigma * f_norm)
-
- return K
diff --git a/ml_exp/kernels.py b/ml_exp/kernels.py
new file mode 100644
index 000000000..834d62408
--- /dev/null
+++ b/ml_exp/kernels.py
@@ -0,0 +1,49 @@
+"""MIT License
+
+Copyright (c) 2019 David Luevano Alvarado
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+import math
+import numpy as np
+from ml_exp.frob_norm import frob_norm
+
+
+def gauss_kernel(X_1, X_2, sigma):
+ """
+ Calculates the Gaussian Kernel.
+ X_1: first representations.
+ X_2: second representations.
+ sigma: kernel width.
+ """
+ x1_l = len(X_1)
+ x1_range = range(x1_l)
+ x2_l = len(X_2)
+ x2_range = range(x2_l)
+
+ inv_sigma = -0.5 / (sigma*sigma)
+
+ K = np.zeros((x1_l, x2_l))
+ for i in x1_range:
+ for j in x2_range:
+ f_norm = frob_norm(X_1[i] - X_2[j])
+ # print(f_norm)
+ K[i, j] = math.exp(inv_sigma * f_norm)
+
+ return K
diff --git a/ml_exp/math.py b/ml_exp/math.py
new file mode 100644
index 000000000..781985118
--- /dev/null
+++ b/ml_exp/math.py
@@ -0,0 +1,92 @@
+"""MIT License
+
+Copyright (c) 2019 David Luevano Alvarado
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+import numpy as np
+import math
+
+
+def frob_norm(array):
+ """
+ Calculates the frobenius norm of a given array or matrix.
+ array: array of data.
+ """
+
+ arr_sh_len = len(array.shape)
+ arr_range = range(len(array))
+ fn = 0.0
+
+ # If it is a 'vector'.
+ if arr_sh_len == 1:
+ for i in arr_range:
+ fn += array[i]*array[i]
+
+ return math.sqrt(fn)
+
+ # If it is a matrix.
+ elif arr_sh_len == 2:
+ for i in arr_range:
+ for j in arr_range:
+ fn += array[i, j]*array[i, j]
+
+ return math.sqrt(fn)
+ else:
+ print('Error. Array size greater than 2 ({}).'.format(arr_sh_len))
+
+
+def cholesky_solve(K, y):
+ """
+ Applies Cholesky decomposition to obtain the 'alpha coeficients'.
+ K: kernel.
+ y: known parameters.
+ """
+ # The initial mathematical problem is to solve Ka=y.
+
+ # First, add a small lambda value.
+ K[np.diag_indices_from(K)] += 1e-8
+
+ # Get the Cholesky decomposition of the kernel.
+ L = np.linalg.cholesky(K)
+ size = len(L)
+
+ # Solve Lx=y for x.
+ x = np.zeros(size)
+ x[0] = y[0] / L[0, 0]
+ for i in range(1, size):
+ temp_sum = 0.0
+ for j in range(i):
+ temp_sum += L[i, j] * x[j]
+ x[i] = (y[i] - temp_sum) / L[i, i]
+
+ # Now, solve LTa=x for a.
+ L2 = L.T
+ a = np.zeros(size)
+ a_ms = size - 1
+ a[a_ms] = x[a_ms] / L2[a_ms, a_ms]
+ # Because of the form of L2 (upper triangular matriz), an inversion of
+ # range() needs to be done.
+ for i in range(0, a_ms)[::-1]:
+ temp_sum = 0.0
+ for j in range(i, size)[::-1]:
+ temp_sum += L2[i, j] * a[j]
+ a[i] = (x[i] - temp_sum) / L2[i, i]
+
+ return a
--
cgit v1.2.3-70-g09d2
From 2bdd175a6eb1f6edd8689987fef1a29fc1043da1 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 25 Feb 2020 20:42:15 -0700
Subject: Remove frobnorm, already in numpy
---
ml_exp/math.py | 29 -----------------------------
1 file changed, 29 deletions(-)
diff --git a/ml_exp/math.py b/ml_exp/math.py
index 781985118..e7c8dcabc 100644
--- a/ml_exp/math.py
+++ b/ml_exp/math.py
@@ -21,35 +21,6 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
import numpy as np
-import math
-
-
-def frob_norm(array):
- """
- Calculates the frobenius norm of a given array or matrix.
- array: array of data.
- """
-
- arr_sh_len = len(array.shape)
- arr_range = range(len(array))
- fn = 0.0
-
- # If it is a 'vector'.
- if arr_sh_len == 1:
- for i in arr_range:
- fn += array[i]*array[i]
-
- return math.sqrt(fn)
-
- # If it is a matrix.
- elif arr_sh_len == 2:
- for i in arr_range:
- for j in arr_range:
- fn += array[i, j]*array[i, j]
-
- return math.sqrt(fn)
- else:
- print('Error. Array size greater than 2 ({}).'.format(arr_sh_len))
def cholesky_solve(K, y):
--
cgit v1.2.3-70-g09d2
From d1b84b91f4b94b717de477e47b22946fd42be0db Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 25 Feb 2020 20:52:08 -0700
Subject: Refactor gauss kernel, more natural syntax
---
ml_exp/__init__.py | 4 +++-
ml_exp/kernels.py | 22 +++++++++-------------
2 files changed, 12 insertions(+), 14 deletions(-)
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index dcb10a1df..e9dd83eae 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -23,6 +23,7 @@ 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
+from ml_exp.math import cholesky_solve
# If somebody does "from package import *", this is what they will
# be able to access:
@@ -32,4 +33,5 @@ __all__ = ['Compound',
'first_neighbor_matrix',
'adjacency_matrix',
'check_bond',
- 'bag_of_stuff']
+ 'bag_of_stuff',
+ 'cholesky_solve']
diff --git a/ml_exp/kernels.py b/ml_exp/kernels.py
index 834d62408..7a61a1e1e 100644
--- a/ml_exp/kernels.py
+++ b/ml_exp/kernels.py
@@ -22,27 +22,23 @@ SOFTWARE.
"""
import math
import numpy as np
-from ml_exp.frob_norm import frob_norm
-def gauss_kernel(X_1, X_2, sigma):
+def gaussian_kernel(X1,
+ X2,
+ sigma):
"""
Calculates the Gaussian Kernel.
- X_1: first representations.
- X_2: second representations.
+ X1: first representations.
+ X2: second representations.
sigma: kernel width.
"""
- x1_l = len(X_1)
- x1_range = range(x1_l)
- x2_l = len(X_2)
- x2_range = range(x2_l)
-
inv_sigma = -0.5 / (sigma*sigma)
- K = np.zeros((x1_l, x2_l))
- for i in x1_range:
- for j in x2_range:
- f_norm = frob_norm(X_1[i] - X_2[j])
+ K = np.zeros((X1.shape[0], X2.shape[0]), dtype=float)
+ for i in X1:
+ for j in X2:
+ f_norm = np.linalg.norm(i - j)
# print(f_norm)
K[i, j] = math.exp(inv_sigma * f_norm)
--
cgit v1.2.3-70-g09d2
From 0b35ed647ec4d786b488082dd98bb91ca0f5cc05 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 25 Feb 2020 20:54:01 -0700
Subject: Placeholder
---
ml_exp/__main__.py | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/ml_exp/__main__.py b/ml_exp/__main__.py
index 44b492103..0d9b87bad 100644
--- a/ml_exp/__main__.py
+++ b/ml_exp/__main__.py
@@ -20,8 +20,5 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
-# from ml_exp.compound import Compound
-
-
if __name__ == '__main__':
- print('OK!')
+ print('Everything OK!\n\tThis is a placeholder.')
--
cgit v1.2.3-70-g09d2
From 339954ffc95c29327d33e3e2697fea1cf8e9427d Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 25 Feb 2020 21:03:31 -0700
Subject: Remove unused functions
---
ml_exp/read_qm7_data.py | 33 ---------------------------------
1 file changed, 33 deletions(-)
diff --git a/ml_exp/read_qm7_data.py b/ml_exp/read_qm7_data.py
index 666f9c3fc..3017ac429 100644
--- a/ml_exp/read_qm7_data.py
+++ b/ml_exp/read_qm7_data.py
@@ -25,39 +25,6 @@ import numpy as np
import random
-# 'periodic_table_of_elements.txt' retrieved from
-# https://gist.github.com/GoodmanSciences/c2dd862cd38f21b0ad36b8f96b4bf1ee
-def read_nc_data(data_path):
- """
- Reads nuclear charge data from file and returns a dictionary.
- data_path: path to the data directory.
- """
- fname = 'periodic_table_of_elements.txt'
- with open(''.join([data_path, '/', fname]), 'r') as infile:
- temp_lines = infile.readlines()
-
- del temp_lines[0]
-
- lines = []
- for temp_line in temp_lines:
- new_line = temp_line.split(sep=',')
- lines.append(new_line)
-
- # Dictionary of nuclear charge.
- return {line[2]: int(line[0]) for line in lines}
-
-
-# For use in the rewriting of the code (from functional programming to object
-# oriented programming-ish)
-def print_nc(nc_data):
- """
- Prints the nuclear charge data to the terminal.
- nc_data: dict of nc.
- """
- for key in nc_data.keys():
- print(f'\'{key}\': {nc_data[key]},')
-
-
# 'hof_qm7.txt.txt' retrieved from
# https://github.com/qmlcode/tutorial
def read_db_data(zi_data,
--
cgit v1.2.3-70-g09d2
From 3c8a53f42a4a90d3cc235fc4e4132556b9cd74fa Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 25 Feb 2020 21:06:10 -0700
Subject: Rename function
---
ml_exp/qm7db.py | 106 ++++++++++++++++++++++++++++++++++++++++++++++++
ml_exp/read_qm7_data.py | 106 ------------------------------------------------
2 files changed, 106 insertions(+), 106 deletions(-)
create mode 100644 ml_exp/qm7db.py
delete mode 100644 ml_exp/read_qm7_data.py
diff --git a/ml_exp/qm7db.py b/ml_exp/qm7db.py
new file mode 100644
index 000000000..e584bc123
--- /dev/null
+++ b/ml_exp/qm7db.py
@@ -0,0 +1,106 @@
+"""MIT License
+
+Copyright (c) 2019 David Luevano Alvarado
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+import os
+import numpy as np
+import random
+
+
+# 'hof_qm7.txt.txt' retrieved from
+# https://github.com/qmlcode/tutorial
+def qm7db(zi_data,
+ data_path,
+ r_seed=111,
+ return_atoms=False):
+ """
+ Reads molecule database and extracts
+ its contents as usable variables.
+ zi_data: dictionary containing nuclear charge data.
+ data_path: path to the data directory.
+ r_seed: random seed to use for the shuffling.
+ return_atoms: if atom list should be returned.
+ """
+ os.chdir(data_path)
+
+ fname = 'hof_qm7.txt'
+ with open(fname, 'r') as infile:
+ lines = infile.readlines()
+
+ # Temporary energy dictionary.
+ energy_temp = dict()
+
+ for line in lines:
+ xyz_data = line.split()
+
+ xyz_name = xyz_data[0]
+ hof = float(xyz_data[1])
+ dftb = float(xyz_data[2])
+ # print(xyz_name, hof, dftb)
+
+ energy_temp[xyz_name] = np.array([hof, hof - dftb])
+
+ # Use a random seed.
+ random.seed(r_seed)
+
+ et_keys = list(energy_temp.keys())
+ random.shuffle(et_keys)
+
+ # Temporary energy dictionary, shuffled.
+ energy_temp_shuffled = dict()
+ for key in et_keys:
+ energy_temp_shuffled.update({key: energy_temp[key]})
+
+ mol_data = []
+ mol_nc_data = []
+ atoms = []
+ # Actual reading of the xyz files.
+ for i, k in enumerate(energy_temp_shuffled.keys()):
+ with open(k, 'r') as xyz_file:
+ lines = xyz_file.readlines()
+
+ len_lines = len(lines)
+ mol_temp_data = []
+ mol_nc_temp_data = np.array(np.zeros(len_lines-2))
+ atoms_temp = []
+ for j, line in enumerate(lines[2:len_lines]):
+ line_list = line.split()
+
+ atoms_temp.append(line_list[0])
+ mol_nc_temp_data[j] = float(zi_data[line_list[0]])
+ line_data = np.array(np.asarray(line_list[1:4], dtype=float))
+ mol_temp_data.append(line_data)
+
+ mol_data.append(mol_temp_data)
+ mol_nc_data.append(mol_nc_temp_data)
+ atoms.append(atoms_temp)
+
+ # Convert everything to a numpy array.
+ molecules = np.array([np.array(mol) for mol in mol_data])
+ nuclear_charge = np.array([nc_d for nc_d in mol_nc_data])
+ energy_pbe0 = np.array([energy_temp_shuffled[k][0]
+ for k in energy_temp_shuffled.keys()])
+ energy_delta = np.array([energy_temp_shuffled[k][1]
+ for k in energy_temp_shuffled.keys()])
+
+ if return_atoms:
+ return molecules, nuclear_charge, energy_pbe0, energy_delta, atoms
+ return molecules, nuclear_charge, energy_pbe0, energy_delta
diff --git a/ml_exp/read_qm7_data.py b/ml_exp/read_qm7_data.py
deleted file mode 100644
index 3017ac429..000000000
--- a/ml_exp/read_qm7_data.py
+++ /dev/null
@@ -1,106 +0,0 @@
-"""MIT License
-
-Copyright (c) 2019 David Luevano Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-import os
-import numpy as np
-import random
-
-
-# 'hof_qm7.txt.txt' retrieved from
-# https://github.com/qmlcode/tutorial
-def read_db_data(zi_data,
- data_path,
- r_seed=111,
- return_atoms=False):
- """
- Reads molecule database and extracts
- its contents as usable variables.
- zi_data: dictionary containing nuclear charge data.
- data_path: path to the data directory.
- r_seed: random seed to use for the shuffling.
- return_atoms: if atom list should be returned.
- """
- os.chdir(data_path)
-
- fname = 'hof_qm7.txt'
- with open(fname, 'r') as infile:
- lines = infile.readlines()
-
- # Temporary energy dictionary.
- energy_temp = dict()
-
- for line in lines:
- xyz_data = line.split()
-
- xyz_name = xyz_data[0]
- hof = float(xyz_data[1])
- dftb = float(xyz_data[2])
- # print(xyz_name, hof, dftb)
-
- energy_temp[xyz_name] = np.array([hof, hof - dftb])
-
- # Use a random seed.
- random.seed(r_seed)
-
- et_keys = list(energy_temp.keys())
- random.shuffle(et_keys)
-
- # Temporary energy dictionary, shuffled.
- energy_temp_shuffled = dict()
- for key in et_keys:
- energy_temp_shuffled.update({key: energy_temp[key]})
-
- mol_data = []
- mol_nc_data = []
- atoms = []
- # Actual reading of the xyz files.
- for i, k in enumerate(energy_temp_shuffled.keys()):
- with open(k, 'r') as xyz_file:
- lines = xyz_file.readlines()
-
- len_lines = len(lines)
- mol_temp_data = []
- mol_nc_temp_data = np.array(np.zeros(len_lines-2))
- atoms_temp = []
- for j, line in enumerate(lines[2:len_lines]):
- line_list = line.split()
-
- atoms_temp.append(line_list[0])
- mol_nc_temp_data[j] = float(zi_data[line_list[0]])
- line_data = np.array(np.asarray(line_list[1:4], dtype=float))
- mol_temp_data.append(line_data)
-
- mol_data.append(mol_temp_data)
- mol_nc_data.append(mol_nc_temp_data)
- atoms.append(atoms_temp)
-
- # Convert everything to a numpy array.
- molecules = np.array([np.array(mol) for mol in mol_data])
- nuclear_charge = np.array([nc_d for nc_d in mol_nc_data])
- energy_pbe0 = np.array([energy_temp_shuffled[k][0]
- for k in energy_temp_shuffled.keys()])
- energy_delta = np.array([energy_temp_shuffled[k][1]
- for k in energy_temp_shuffled.keys()])
-
- if return_atoms:
- return molecules, nuclear_charge, energy_pbe0, energy_delta, atoms
- return molecules, nuclear_charge, energy_pbe0, energy_delta
--
cgit v1.2.3-70-g09d2
From 2185e43ffdbf70a06cb894549fc7ff09f9c90cc3 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 25 Feb 2020 21:09:49 -0700
Subject: Refactor code
---
ml_exp/qm7db.py | 17 ++++++-----------
1 file changed, 6 insertions(+), 11 deletions(-)
diff --git a/ml_exp/qm7db.py b/ml_exp/qm7db.py
index e584bc123..4a7beaed6 100644
--- a/ml_exp/qm7db.py
+++ b/ml_exp/qm7db.py
@@ -27,17 +27,14 @@ import random
# 'hof_qm7.txt.txt' retrieved from
# https://github.com/qmlcode/tutorial
-def qm7db(zi_data,
+def qm7db(nc,
data_path,
- r_seed=111,
- return_atoms=False):
+ r_seed=111):
"""
- Reads molecule database and extracts
- its contents as usable variables.
- zi_data: dictionary containing nuclear charge data.
+ Creates a list of compounds with the qm7 database.
+ nc: dictionary containing nuclear charge data.
data_path: path to the data directory.
r_seed: random seed to use for the shuffling.
- return_atoms: if atom list should be returned.
"""
os.chdir(data_path)
@@ -85,7 +82,7 @@ def qm7db(zi_data,
line_list = line.split()
atoms_temp.append(line_list[0])
- mol_nc_temp_data[j] = float(zi_data[line_list[0]])
+ mol_nc_temp_data[j] = float(nc[line_list[0]])
line_data = np.array(np.asarray(line_list[1:4], dtype=float))
mol_temp_data.append(line_data)
@@ -101,6 +98,4 @@ def qm7db(zi_data,
energy_delta = np.array([energy_temp_shuffled[k][1]
for k in energy_temp_shuffled.keys()])
- if return_atoms:
- return molecules, nuclear_charge, energy_pbe0, energy_delta, atoms
- return molecules, nuclear_charge, energy_pbe0, energy_delta
+ return molecules, nuclear_charge, energy_pbe0, energy_delta, atoms
--
cgit v1.2.3-70-g09d2
From 39d7b86cfb578b491c8cbf99905e67f7f7937dc9 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 25 Feb 2020 21:13:33 -0700
Subject: Refactor code
---
ml_exp/qm7db.py | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/ml_exp/qm7db.py b/ml_exp/qm7db.py
index 4a7beaed6..1f1115ba0 100644
--- a/ml_exp/qm7db.py
+++ b/ml_exp/qm7db.py
@@ -20,7 +20,6 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
-import os
import numpy as np
import random
@@ -28,19 +27,18 @@ import random
# 'hof_qm7.txt.txt' retrieved from
# https://github.com/qmlcode/tutorial
def qm7db(nc,
- data_path,
+ db_path='data',
r_seed=111):
"""
Creates a list of compounds with the qm7 database.
nc: dictionary containing nuclear charge data.
- data_path: path to the data directory.
+ db_path: path to the database directory.
r_seed: random seed to use for the shuffling.
"""
- os.chdir(data_path)
- fname = 'hof_qm7.txt'
- with open(fname, 'r') as infile:
- lines = infile.readlines()
+ fname = f'{db_path}/hof_qm7.txt'
+ with open(fname, 'r') as f:
+ lines = f.readlines()
# Temporary energy dictionary.
energy_temp = dict()
--
cgit v1.2.3-70-g09d2
From d064df5d045a5502f273814252debdb564df3ffc Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Wed, 26 Feb 2020 04:47:44 -0700
Subject: Refactor code
---
ml_exp/math.py | 23 ++++++++++-------------
1 file changed, 10 insertions(+), 13 deletions(-)
diff --git a/ml_exp/math.py b/ml_exp/math.py
index e7c8dcabc..da1fdf08f 100644
--- a/ml_exp/math.py
+++ b/ml_exp/math.py
@@ -23,23 +23,23 @@ SOFTWARE.
import numpy as np
-def cholesky_solve(K, y):
+def cholesky_solve(K,
+ y):
"""
- Applies Cholesky decomposition to obtain the 'alpha coeficients'.
+ Applies Cholesky decomposition to solve Ka=y. Where a are the alpha
+ coeficients.
K: kernel.
y: known parameters.
"""
- # The initial mathematical problem is to solve Ka=y.
-
- # First, add a small lambda value.
+ # Add a small lambda value.
K[np.diag_indices_from(K)] += 1e-8
# Get the Cholesky decomposition of the kernel.
L = np.linalg.cholesky(K)
- size = len(L)
+ size = K.shape[0]
# Solve Lx=y for x.
- x = np.zeros(size)
+ x = np.zeros(size, dtype=float)
x[0] = y[0] / L[0, 0]
for i in range(1, size):
temp_sum = 0.0
@@ -49,12 +49,9 @@ def cholesky_solve(K, y):
# Now, solve LTa=x for a.
L2 = L.T
- a = np.zeros(size)
- a_ms = size - 1
- a[a_ms] = x[a_ms] / L2[a_ms, a_ms]
- # Because of the form of L2 (upper triangular matriz), an inversion of
- # range() needs to be done.
- for i in range(0, a_ms)[::-1]:
+ a = np.zeros(size, dtype=float)
+ a[size - 1] = x[size - 1] / L2[size - 1, size - 1]
+ for i in range(0, size - 1)[::-1]:
temp_sum = 0.0
for j in range(i, size)[::-1]:
temp_sum += L2[i, j] * a[j]
--
cgit v1.2.3-70-g09d2
From 5a85580b5f99484b957b65326ec5a19ab627d801 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Wed, 26 Feb 2020 05:26:21 -0700
Subject: Optimize qm7db reading for the rewrite
---
ml_exp/__init__.py | 2 --
ml_exp/compound.py | 3 ++-
ml_exp/qm7db.py | 68 +++++++++++-------------------------------------------
3 files changed, 16 insertions(+), 57 deletions(-)
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index e9dd83eae..d685e7ccc 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -25,8 +25,6 @@ from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
first_neighbor_matrix, adjacency_matrix, check_bond, bag_of_stuff
from ml_exp.math import cholesky_solve
-# If somebody does "from package import *", this is what they will
-# be able to access:
__all__ = ['Compound',
'coulomb_matrix',
'lennard_jones_matrix',
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 8b6af0ae9..0a8b89610 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -33,7 +33,7 @@ class Compound:
Initialization of the Compound.
xyz: (path to) the xyz file.
"""
- # empty_array = np.asarray([], dtype=float)
+ self.name = None
self.n = None
self.atoms = None
@@ -137,6 +137,7 @@ class Compound:
with open(filename, 'r') as f:
lines = f.readlines()
+ self.name = filename.split('/')[-1]
self.n = int(lines[0])
self.atoms = []
self.atoms_nc = np.empty(self.n, dtype=int)
diff --git a/ml_exp/qm7db.py b/ml_exp/qm7db.py
index 1f1115ba0..f9950c317 100644
--- a/ml_exp/qm7db.py
+++ b/ml_exp/qm7db.py
@@ -20,6 +20,7 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
+from ml_exp.compound import Compound
import numpy as np
import random
@@ -28,72 +29,31 @@ import random
# https://github.com/qmlcode/tutorial
def qm7db(nc,
db_path='data',
+ is_shuffled=True,
r_seed=111):
"""
Creates a list of compounds with the qm7 database.
nc: dictionary containing nuclear charge data.
db_path: path to the database directory.
+ is_shuffled: if the resulting list of compounds should be shuffled.
r_seed: random seed to use for the shuffling.
"""
-
fname = f'{db_path}/hof_qm7.txt'
with open(fname, 'r') as f:
lines = f.readlines()
- # Temporary energy dictionary.
- energy_temp = dict()
-
- for line in lines:
- xyz_data = line.split()
-
- xyz_name = xyz_data[0]
- hof = float(xyz_data[1])
- dftb = float(xyz_data[2])
- # print(xyz_name, hof, dftb)
+ compounds = []
+ 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])
- energy_temp[xyz_name] = np.array([hof, hof - dftb])
-
- # Use a random seed.
+ # Shuffle the compounds list
random.seed(r_seed)
+ random.shuffle(compounds)
- et_keys = list(energy_temp.keys())
- random.shuffle(et_keys)
-
- # Temporary energy dictionary, shuffled.
- energy_temp_shuffled = dict()
- for key in et_keys:
- energy_temp_shuffled.update({key: energy_temp[key]})
-
- mol_data = []
- mol_nc_data = []
- atoms = []
- # Actual reading of the xyz files.
- for i, k in enumerate(energy_temp_shuffled.keys()):
- with open(k, 'r') as xyz_file:
- lines = xyz_file.readlines()
-
- len_lines = len(lines)
- mol_temp_data = []
- mol_nc_temp_data = np.array(np.zeros(len_lines-2))
- atoms_temp = []
- for j, line in enumerate(lines[2:len_lines]):
- line_list = line.split()
-
- atoms_temp.append(line_list[0])
- mol_nc_temp_data[j] = float(nc[line_list[0]])
- line_data = np.array(np.asarray(line_list[1:4], dtype=float))
- mol_temp_data.append(line_data)
-
- mol_data.append(mol_temp_data)
- mol_nc_data.append(mol_nc_temp_data)
- atoms.append(atoms_temp)
-
- # Convert everything to a numpy array.
- molecules = np.array([np.array(mol) for mol in mol_data])
- nuclear_charge = np.array([nc_d for nc_d in mol_nc_data])
- energy_pbe0 = np.array([energy_temp_shuffled[k][0]
- for k in energy_temp_shuffled.keys()])
- energy_delta = np.array([energy_temp_shuffled[k][1]
- for k in energy_temp_shuffled.keys()])
+ e_pbe0 = np.array([compound.pbe0 for compound in compounds], dtype=float)
+ e_delta = np.array([compound.delta for compound in compounds], dtype=float)
- return molecules, nuclear_charge, energy_pbe0, energy_delta, atoms
+ return compounds, e_pbe0, e_delta
--
cgit v1.2.3-70-g09d2
From a0e73407bfef3569a994c07d5bb9c8df97518e30 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Wed, 26 Feb 2020 05:32:35 -0700
Subject: Add feature
---
ml_exp/compound.py | 2 ++
ml_exp/qm7db.py | 6 +++---
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 0a8b89610..9c7102860 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -36,6 +36,7 @@ class Compound:
self.name = None
self.n = None
+ self.extra = None # In case a comment is in the compound file.
self.atoms = None
self.atoms_nc = None
self.coordinates = None
@@ -139,6 +140,7 @@ class Compound:
self.name = filename.split('/')[-1]
self.n = int(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)
diff --git a/ml_exp/qm7db.py b/ml_exp/qm7db.py
index f9950c317..8d2453f45 100644
--- a/ml_exp/qm7db.py
+++ b/ml_exp/qm7db.py
@@ -49,9 +49,9 @@ def qm7db(nc,
compounds[i].pbe0 = float(line[1])
compounds[i].delta = float(line[1]) - float(line[2])
- # Shuffle the compounds list
- random.seed(r_seed)
- random.shuffle(compounds)
+ 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)
--
cgit v1.2.3-70-g09d2
From b209f5e79ce45e6a4d5b442f10217806d078d5a6 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Wed, 26 Feb 2020 05:40:44 -0700
Subject: Update requirements
---
requirements.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/requirements.txt b/requirements.txt
index 437e0428a..4b242770c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,3 @@
colorama==0.4.3
numpy==1.18.1
-pandas==0.25.3
\ No newline at end of file
+pandas==1.0.1
--
cgit v1.2.3-70-g09d2
From e18a909d18481e5e292882b3b1dd2ad8d693d097 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Wed, 26 Feb 2020 05:53:54 -0700
Subject: Revise printc
---
ml_exp/__init__.py | 4 +++-
ml_exp/misc.py | 38 +++++++++++++++++---------------------
2 files changed, 20 insertions(+), 22 deletions(-)
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index d685e7ccc..c62141a58 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -24,6 +24,7 @@ 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
from ml_exp.math import cholesky_solve
+from ml_exp.qm7db import qm7db
__all__ = ['Compound',
'coulomb_matrix',
@@ -32,4 +33,5 @@ __all__ = ['Compound',
'adjacency_matrix',
'check_bond',
'bag_of_stuff',
- 'cholesky_solve']
+ 'cholesky_solve',
+ 'qm7db']
diff --git a/ml_exp/misc.py b/ml_exp/misc.py
index e9142b05f..4bd68eefc 100644
--- a/ml_exp/misc.py
+++ b/ml_exp/misc.py
@@ -29,29 +29,25 @@ init()
def printc(text, color):
"""
Prints texts normaly, but in color. Using colorama.
- text: string with the text to print.
+ text: text to print.
color: color to be used, same as available in colorama.
"""
- color_dic = {'BLACK': Fore.BLACK,
- 'RED': Fore.RED,
- 'GREEN': Fore.GREEN,
- 'YELLOW': Fore.YELLOW,
- 'BLUE': Fore.BLUE,
- 'MAGENTA': Fore.MAGENTA,
- 'CYAN': Fore.CYAN,
- 'WHITE': Fore.WHITE,
- 'RESET': Fore.RESET}
-
- color_dic_keys = color_dic.keys()
- if color not in color_dic_keys:
- print(Fore.RED
- + '\'{}\' not found, using default color.'.format(color)
- + Style.RESET_ALL)
- actual_color = Fore.RESET
- else:
- actual_color = color_dic[color]
-
- print(actual_color + text + Style.RESET_ALL)
+ color = color.upper()
+ colors = {'BLACK': Fore.BLACK,
+ 'RED': Fore.RED,
+ 'GREEN': Fore.GREEN,
+ 'YELLOW': Fore.YELLOW,
+ 'BLUE': Fore.BLUE,
+ 'MAGENTA': Fore.MAGENTA,
+ 'CYAN': Fore.CYAN,
+ 'WHITE': Fore.WHITE,
+ 'RESET': Fore.RESET}
+
+ av_colors = colors.keys()
+ if color not in av_colors:
+ raise KeyError(f'{color} not found.')
+
+ print(colors[color] + text + Style.RESET_ALL)
def plot_benchmarks():
--
cgit v1.2.3-70-g09d2
From eeea8ff03aeae2367f8db4e4f0d65cccf708d434 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Wed, 26 Feb 2020 21:20:10 -0700
Subject: Remove unused function
---
ml_exp/parallel_create_matrices.py | 85 --------------------------------------
1 file changed, 85 deletions(-)
delete mode 100644 ml_exp/parallel_create_matrices.py
diff --git a/ml_exp/parallel_create_matrices.py b/ml_exp/parallel_create_matrices.py
deleted file mode 100644
index a68122d48..000000000
--- a/ml_exp/parallel_create_matrices.py
+++ /dev/null
@@ -1,85 +0,0 @@
-"""MIT License
-
-Copyright (c) 2019 David Luevano Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-from multiprocessing import Process, Pipe
-from ml_exp.c_matrix import c_matrix_multiple
-from ml_exp.lj_matrix import lj_matrix_multiple
-
-
-def parallel_create_matrices(mol_data,
- nc_data,
- ljm_diag_value=None,
- ljm_sigma=1.0,
- ljm_epsilon=1.0,
- max_len=25,
- as_eig=True,
- bohr_radius_units=False):
- """
- Creates the Coulomb and L-J matrices in parallel.
- mol_data: molecule data, matrix of atom coordinates.
- nc_data: nuclear charge data, array of atom data.
- ljm_diag_value: if special diagonal value is to be used for lj matrix.
- ljm_sigma: sigma value for lj matrix.
- ljm_epsilon: psilon value for lj matrix.
- max_len: maximum amount of atoms in molecule.
- as_eig: if data should be returned as matrix or array of eigenvalues.
- bohr_radius_units: if units should be in bohr's radius units.
- """
-
- # Matrices calculation.
- procs = []
- pipes = []
-
- cm_recv, cm_send = Pipe(False)
- p1 = Process(target=c_matrix_multiple,
- args=(mol_data,
- nc_data,
- cm_send,
- max_len,
- as_eig,
- bohr_radius_units))
- procs.append(p1)
- pipes.append(cm_recv)
- p1.start()
-
- ljm_recv, ljm_send = Pipe(False)
- p2 = Process(target=lj_matrix_multiple,
- args=(mol_data,
- nc_data,
- ljm_send,
- ljm_diag_value,
- ljm_sigma,
- ljm_epsilon,
- max_len,
- as_eig,
- bohr_radius_units))
- procs.append(p2)
- pipes.append(ljm_recv)
- p2.start()
-
- cm_data = pipes[0].recv()
- ljm_data = pipes[1].recv()
-
- for proc in procs:
- proc.join()
-
- return cm_data, ljm_data
--
cgit v1.2.3-70-g09d2
From 4d759471c3e92381bb6e8b91083b8dea5ec49b02 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Thu, 27 Feb 2020 15:31:23 -0700
Subject: Rewrite basic ml function
---
ml_exp/do_ml.py | 218 ++++++++++++--------------------------------------------
1 file changed, 45 insertions(+), 173 deletions(-)
diff --git a/ml_exp/do_ml.py b/ml_exp/do_ml.py
index 110242a1d..de4d4061c 100644
--- a/ml_exp/do_ml.py
+++ b/ml_exp/do_ml.py
@@ -22,206 +22,78 @@ SOFTWARE.
"""
import time
import numpy as np
-from multiprocessing import Process, Pipe
from ml_exp.misc import printc
-from ml_exp.gauss_kernel import gauss_kernel
-from ml_exp.cholesky_solve import cholesky_solve
-from ml_exp.read_qm7_data import read_qm7_data
-from ml_exp.parallel_create_matrices import parallel_create_matrices
-
-
-def ml(desc_data,
- energy_data,
- training_size,
- desc_type=None,
- pipe=None,
- test_size=None,
- sigma=1000.0,
- show_msgs=True):
+from ml_exp.kernels import gaussian_kernel
+from ml_exp.math import cholesky_solve
+# from ml_exp.qm7db import qm7db
+
+
+def simple_ml(descriptors,
+ energies,
+ training_size,
+ identifier=None,
+ test_size=None,
+ sigma=1000.0,
+ show_msgs=True):
"""
- Does the ML methodology.
- desc_data: descriptor (or representation) data.
- energy_data: energy data associated with desc_data.
+ Basic ML methodology for a single descriptor type.
+ descriptors: array of descriptors.
+ energies: array of energies.
training_size: size of the training set to use.
- desc_type: string with the name of the descriptor used.
- pipe: for multiprocessing purposes. Sends the data calculated
- through a pipe.
+ identifier: string with the name of the descriptor used.
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.
- show_msgs: Show debug messages or not.
- NOTE: desc_type is just a string and is only for identification purposes.
+ show_msgs: if debu messages should be shown.
+ NOTE: identifier is just a string and is only for identification purposes.
Also, training is done with the first part of the data and
- testing with the ending part of the data.
+ testing with the ending part of the data.
"""
tic = time.perf_counter()
# Initial calculations for later use.
- d_len = len(desc_data)
- e_len = len(energy_data)
+ data_size = descriptors.shape[0]
- if not desc_type:
- desc_type = 'NOT SPECIFIED'
+ if not identifier:
+ identifier = 'NOT SPECIFIED'
- if d_len != e_len:
- printc(''.join(['ERROR. Descriptor data size different ',
- 'than energy data size.']), 'RED')
- return None
+ if not data_size == energies.shape[0]:
+ raise ValueError('Energies size is different than descriptors size.')
- if training_size >= d_len:
- printc('ERROR. Training size greater or equal than data size.', 'RED')
- return None
+ if training_size >= data_size:
+ raise ValueError('Training size is greater or equal to the data size.')
+ # If test_size is not set, it is set to a maximum size of 1500.
if not test_size:
- test_size = d_len - training_size
+ test_size = data_size - training_size
if test_size > 1500:
test_size = 1500
if show_msgs:
- printc('{} ML started.'.format(desc_type), 'GREEN')
- printc('\tTraining size: {}'.format(training_size), 'CYAN')
- printc('\tTest size: {}'.format(test_size), 'CYAN')
- printc('\tSigma: {}'.format(sigma), 'CYAN')
+ printc(f'{identifier} ML started.', 'GREEN')
+ printc(f'\tTraining size: {training_size}', 'CYAN')
+ printc(f'\tTest size: {test_size}', 'CYAN')
+ printc(f'\tSigma: {test_size}', 'CYAN')
- X_training = desc_data[:training_size]
- Y_training = energy_data[:training_size]
- K_training = gauss_kernel(X_training, X_training, sigma)
- alpha_ = cholesky_solve(K_training, Y_training)
+ 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)
- X_test = desc_data[-test_size:]
- Y_test = energy_data[-test_size:]
- K_test = gauss_kernel(X_test, X_training, sigma)
- Y_predicted = np.dot(K_test, alpha_)
+ 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)
mae = np.mean(np.abs(Y_predicted - Y_test))
if show_msgs:
- printc('\tMAE for {}: {:.4f}'.format(desc_type, mae), 'GREEN')
+ printc('\tMAE for {identifier}: {mae:.4f}', 'GREEN')
toc = time.perf_counter()
tictoc = toc - tic
if show_msgs:
- printc('\t{} ML took {:.4f} seconds.'.format(desc_type, tictoc),
- 'GREEN')
- printc('\t\tTraining size: {}'.format(training_size), 'CYAN')
- printc('\t\tTest size: {}'.format(test_size), 'CYAN')
- printc('\t\tSigma: {}'.format(sigma), 'CYAN')
-
- if pipe:
- pipe.send([desc_type, training_size, test_size, sigma, mae, tictoc])
+ printc(f'\t{identifier} ML took {tictoc:.4f} seconds.', 'GREEN')
+ printc(f'\t\tTraining size: {training_size}', 'CYAN')
+ printc(f'\t\tTest size: {test_size}', 'CYAN')
+ printc(f'\t\tSigma: {sigma}', 'CYAN')
return mae, tictoc
-
-
-def do_ml(min_training_size,
- max_training_size=None,
- training_increment_size=500,
- test_size=None,
- ljm_diag_value=None,
- ljm_sigma=1.0,
- ljm_epsilon=1.0,
- r_seed=111,
- save_benchmarks=False,
- max_len=25,
- as_eig=True,
- bohr_radius_units=False,
- sigma=1000.0,
- show_msgs=True):
- """
- Main function that does the whole ML process.
- min_training_size: minimum training size.
- max_training_size: maximum training size.
- training_increment_size: training increment size.
- test_size: size of the test set to use. If no size is given,
- the last remaining molecules are used.
- ljm_diag_value: if a special diagonal value should be used in lj matrix.
- ljm_sigma: sigma value for lj matrix.
- ljm_epsilon: epsilon value for lj matrix.
- r_seed: random seed to use for the shuffling.
- save_benchmarks: if benchmarks should be saved.
- max_len: maximum amount of atoms in molecule.
- as_eig: if data should be returned as matrix or array of eigenvalues.
- bohr_radius_units: if units should be in bohr's radius units.
- sigma: depth of the kernel.
- show_msgs: Show debug messages or not.
- """
- # Initialization time.
- init_time = time.perf_counter()
- if not max_training_size:
- max_training_size = min_training_size + training_increment_size
-
- # Data reading.
- molecules, nuclear_charge, energy_pbe0, energy_delta =\
- read_qm7_data(r_seed=r_seed)
-
- # Matrices calculation.
- cm_data, ljm_data = parallel_create_matrices(molecules,
- nuclear_charge,
- ljm_diag_value,
- ljm_sigma,
- ljm_epsilon,
- max_len,
- as_eig,
- bohr_radius_units)
-
- # ML calculation.
- procs = []
- cm_pipes = []
- ljm_pipes = []
- for i in range(min_training_size,
- max_training_size + 1,
- training_increment_size):
- cm_recv, cm_send = Pipe(False)
- p1 = Process(target=ml,
- args=(cm_data,
- energy_pbe0,
- i,
- 'CM',
- cm_send,
- test_size,
- sigma,
- show_msgs))
- procs.append(p1)
- cm_pipes.append(cm_recv)
- p1.start()
-
- ljm_recv, ljm_send = Pipe(False)
- p2 = Process(target=ml,
- args=(ljm_data,
- energy_pbe0,
- i,
- 'L-JM',
- ljm_send,
- test_size,
- sigma,
- show_msgs))
- procs.append(p2)
- ljm_pipes.append(ljm_recv)
- p2.start()
-
- cm_bench_results = []
- ljm_bench_results = []
- for cd_pipe, ljd_pipe in zip(cm_pipes, ljm_pipes):
- cm_bench_results.append(cd_pipe.recv())
- ljm_bench_results.append(ljd_pipe.recv())
-
- for proc in procs:
- proc.join()
-
- if save_benchmarks:
- with open('data\\benchmarks.csv', 'a') as save_file:
- # save_file.write(''.join(['ml_type,tr_size,te_size,kernel_s,',
- # 'mae,time,lj_s,lj_e,date_ran\n']))
- ltime = time.localtime()[:3][::-1]
- ljm_se = ',' + str(ljm_sigma) + ',' + str(ljm_epsilon) + ','
- date = '/'.join([str(field) for field in ltime])
- for cm, ljm, in zip(cm_bench_results, ljm_bench_results):
- cm_text = ','.join([str(field) for field in cm])\
- + ',' + date + '\n'
- ljm_text = ','.join([str(field) for field in ljm])\
- + ljm_se + date + '\n'
- save_file.write(cm_text)
- save_file.write(ljm_text)
-
- # End of program
- end_time = time.perf_counter()
- printc('Program took {:.4f} seconds.'.format(end_time - init_time),
- 'CYAN')
--
cgit v1.2.3-70-g09d2
From a8dc304d0c85b3db76986f109bdcd7a530bd3045 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Thu, 27 Feb 2020 15:42:02 -0700
Subject: Fix bug
---
ml_exp/qm7db.py | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
diff --git a/ml_exp/qm7db.py b/ml_exp/qm7db.py
index 8d2453f45..3fd46b6bc 100644
--- a/ml_exp/qm7db.py
+++ b/ml_exp/qm7db.py
@@ -25,15 +25,11 @@ import numpy as np
import random
-# 'hof_qm7.txt.txt' retrieved from
-# https://github.com/qmlcode/tutorial
-def qm7db(nc,
- db_path='data',
+def qm7db(db_path='data',
is_shuffled=True,
r_seed=111):
"""
Creates a list of compounds with the qm7 database.
- nc: dictionary containing nuclear charge data.
db_path: path to the database directory.
is_shuffled: if the resulting list of compounds should be shuffled.
r_seed: random seed to use for the shuffling.
--
cgit v1.2.3-70-g09d2
From b937df41c1c5e996be94a3a690908ea989e281dc Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Thu, 27 Feb 2020 15:59:38 -0700
Subject: Placeholder function, test
---
ml_exp/do_ml.py | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++++++--
1 file changed, 54 insertions(+), 2 deletions(-)
diff --git a/ml_exp/do_ml.py b/ml_exp/do_ml.py
index de4d4061c..f32480367 100644
--- a/ml_exp/do_ml.py
+++ b/ml_exp/do_ml.py
@@ -25,7 +25,7 @@ import numpy as np
from ml_exp.misc import printc
from ml_exp.kernels import gaussian_kernel
from ml_exp.math import cholesky_solve
-# from ml_exp.qm7db import qm7db
+from ml_exp.qm7db import qm7db
def simple_ml(descriptors,
@@ -44,7 +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.
- show_msgs: if debu messages should be shown.
+ show_msgs: if debug messages should be shown.
NOTE: identifier is just a string and is only for identification purposes.
Also, training is done with the first part of the data and
testing with the ending part of the data.
@@ -97,3 +97,55 @@ def simple_ml(descriptors,
printc(f'\t\tSigma: {sigma}', 'CYAN')
return mae, tictoc
+
+
+def do_ml(db_path='data',
+ is_shuffled=True,
+ r_seed=111,
+ show_msgs=True):
+ """
+ Main function that does the whole ML process.
+ training_size: minimum training size.
+ test_size: size of the test set to use. If no size is given,
+ the last remaining molecules are used.
+ ljm_diag_value: if a special diagonal value should be used in lj matrix.
+ ljm_sigma: sigma value for lj matrix.
+ ljm_epsilon: epsilon value for lj matrix.
+ r_seed: random seed to use for the shuffling.
+ save_benchmarks: if benchmarks should be saved.
+ size: maximum amount of atoms in molecule.
+ as_eig: if data should be returned as matrix or array of eigenvalues.
+ bohr_radius_units: if units should be in bohr's radius units.
+ sigma: depth of the kernel.
+ show_msgs: if debug messages should be shown.
+ """
+ init_time = time.perf_counter()
+
+ # Data reading.
+ tic = time.perf_counter()
+ compounds, energy_pbe0, energy_delta = qm7db(db_path=db_path,
+ is_shuffled=is_shuffled,
+ r_seed=r_seed)
+ toc = time.perf_counter()
+ tictoc = toc - tic
+ if show_msgs:
+ printc(f'Data reading took {tictoc:.4f} seconds.', 'CYAN')
+
+ # Matrices calculation.
+ tic = time.perf_counter()
+ for compound in compounds:
+ compound.gen_cm()
+ compound.gen_ljm()
+ compound.gen_am()
+ toc = time.perf_counter()
+ tictoc = toc - tic
+ if show_msgs:
+ printc(f'Matrices calculation took {tictoc:.4f} seconds.', 'CYAN')
+
+ # ML calculation.
+ # PLHLDR
+
+ # End of program
+ end_time = time.perf_counter()
+ totaltime = end_time - init_time
+ printc(f'Program took {totaltime:.4f} seconds.', 'CYAN')
--
cgit v1.2.3-70-g09d2
From c4d30a346d114185ab93eb5e88e241b922b5a538 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Thu, 27 Feb 2020 16:50:57 -0700
Subject: Add simple ml methodology, fix bugs
---
ml_exp/__init__.py | 5 ++++-
ml_exp/compound.py | 2 +-
ml_exp/do_ml.py | 65 ++++++++++++++++++++++++++++++++++++++++--------------
ml_exp/kernels.py | 6 ++---
4 files changed, 56 insertions(+), 22 deletions(-)
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index c62141a58..48ece56c8 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -25,6 +25,7 @@ from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
first_neighbor_matrix, 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
__all__ = ['Compound',
'coulomb_matrix',
@@ -34,4 +35,6 @@ __all__ = ['Compound',
'check_bond',
'bag_of_stuff',
'cholesky_solve',
- 'qm7db']
+ 'qm7db',
+ 'simple_ml',
+ 'do_ml']
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 9c7102860..1598fa482 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -93,8 +93,8 @@ class Compound:
bohr_ru=bohr_ru)
def gen_am(self,
- size=23,
use_forces=False,
+ size=23,
bohr_ru=False):
"""
Generate the Adjacency Matrix for the compund.
diff --git a/ml_exp/do_ml.py b/ml_exp/do_ml.py
index f32480367..40243d413 100644
--- a/ml_exp/do_ml.py
+++ b/ml_exp/do_ml.py
@@ -31,19 +31,19 @@ from ml_exp.qm7db import qm7db
def simple_ml(descriptors,
energies,
training_size,
- identifier=None,
test_size=None,
sigma=1000.0,
+ identifier=None,
show_msgs=True):
"""
Basic ML methodology for a single descriptor type.
descriptors: array of descriptors.
energies: array of energies.
training_size: size of the training set to use.
- identifier: string with the name of the descriptor used.
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.
+ 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.
Also, training is done with the first part of the data and
@@ -86,7 +86,7 @@ def simple_ml(descriptors,
mae = np.mean(np.abs(Y_predicted - Y_test))
if show_msgs:
- printc('\tMAE for {identifier}: {mae:.4f}', 'GREEN')
+ printc(f'\tMAE for {identifier}: {mae:.4f}', 'GREEN')
toc = time.perf_counter()
tictoc = toc - tic
@@ -102,20 +102,27 @@ def simple_ml(descriptors,
def do_ml(db_path='data',
is_shuffled=True,
r_seed=111,
+ diag_value=None,
+ lj_sigma=1.0,
+ lj_epsilon=1.0,
+ use_forces=False,
+ size=23,
+ as_eig=True,
+ bohr_ru=False,
+ sigma=1000.0,
show_msgs=True):
"""
Main function that does the whole ML process.
- training_size: minimum training size.
- test_size: size of the test set to use. If no size is given,
- the last remaining molecules are used.
- ljm_diag_value: if a special diagonal value should be used in lj matrix.
- ljm_sigma: sigma value for lj matrix.
- ljm_epsilon: epsilon value for lj matrix.
+ db_path: path to the database directory.
+ is_shuffled: if the resulting list of compounds should be shuffled.
r_seed: random seed to use for the shuffling.
- save_benchmarks: if benchmarks should be saved.
- size: maximum amount of atoms in molecule.
- as_eig: if data should be returned as matrix or array of eigenvalues.
- bohr_radius_units: if units should be in bohr's radius units.
+ diag_value: if special diagonal value is to be used.
+ lj_sigma: sigma value.
+ lj_epsilon: epsilon value.
+ use_forces: if the use of forces instead of k_cx should be used.
+ 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.
sigma: depth of the kernel.
show_msgs: if debug messages should be shown.
"""
@@ -134,16 +141,40 @@ def do_ml(db_path='data',
# Matrices calculation.
tic = time.perf_counter()
for compound in compounds:
- compound.gen_cm()
- compound.gen_ljm()
- compound.gen_am()
+ 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)
+
+ # 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)
+
toc = time.perf_counter()
tictoc = toc - tic
if show_msgs:
printc(f'Matrices calculation took {tictoc:.4f} seconds.', 'CYAN')
# ML calculation.
- # PLHLDR
+ # 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)
# End of program
end_time = time.perf_counter()
diff --git a/ml_exp/kernels.py b/ml_exp/kernels.py
index 7a61a1e1e..3914ffc20 100644
--- a/ml_exp/kernels.py
+++ b/ml_exp/kernels.py
@@ -36,9 +36,9 @@ def gaussian_kernel(X1,
inv_sigma = -0.5 / (sigma*sigma)
K = np.zeros((X1.shape[0], X2.shape[0]), dtype=float)
- for i in X1:
- for j in X2:
- f_norm = np.linalg.norm(i - j)
+ 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)
--
cgit v1.2.3-70-g09d2
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()
--
cgit v1.2.3-70-g09d2