From 7494d56888d3d8eda8f5b2c732c3685ff8006ff9 Mon Sep 17 00:00:00 2001
From: David Luevano <55825613+luevano@users.noreply.github.com>
Date: Fri, 24 Jan 2020 09:16:19 -0700
Subject: Add special values and force values
---
ml_exp/__main__.py | 5 +++--
ml_exp/adj_matrix.py | 53 ++++++++++++++++++++++++++++++++++++++++------------
2 files changed, 44 insertions(+), 14 deletions(-)
diff --git a/ml_exp/__main__.py b/ml_exp/__main__.py
index 63708e75c..6d62333e2 100644
--- a/ml_exp/__main__.py
+++ b/ml_exp/__main__.py
@@ -41,11 +41,12 @@ if __name__ == '__main__':
# plot_benchmarks()
xyz, nc, pbe0, delta, atoms = read_qm7_data(return_atoms=True)
for i in range(1):
- fnm, bonds = fneig_matrix(atoms[i], xyz[i])
- am = adj_matrix(bonds)
+ 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!')
diff --git a/ml_exp/adj_matrix.py b/ml_exp/adj_matrix.py
index 1fbbe0555..27ad158dc 100644
--- a/ml_exp/adj_matrix.py
+++ b/ml_exp/adj_matrix.py
@@ -20,24 +20,32 @@ 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 numpy import array, zeros, dot
from numpy.linalg import norm
+from ml_exp.misc import printc
def fneig_matrix(atoms,
- xyz):
+ 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.
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'])
@@ -45,35 +53,54 @@ def fneig_matrix(atoms,
# Number of atoms, empty matrix and bond list.
n = len(atoms)
- fnm = array(zeros((n, n)))
+ 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]])
- r = norm(xyz_i - xyz_j)
+ rv = xyz_i - xyz_j
+ r = norm(rv)
# Check for each type of bond.
- if (ch_bond == bond) and (r >= 1.06 and r <= 1.12):
- fnm[i, j] = 1
+ 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] = 0.5
+ 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] = 1
+ 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
+ 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] = 1
+ 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(bonds):
+def adj_matrix(bonds,
+ forces=None):
"""
Calculates the adjacency matrix given the bond list.
bonds: list of bonds (tuple of indexes).
@@ -85,6 +112,8 @@ def adj_matrix(bonds):
# Ignore the diagonal.
if i != j:
if (bond_i[0] in bond_j) or (bond_i[1] in bond_j):
- am[i, j] = 1
-
+ if forces:
+ am[i, j] = dot(forces[i], forces[j])
+ else:
+ am[i, j] = 1
return am
--
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