From 6dd33013265ce38122a623b285e0b39f2496aaf8 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 07:19:46 -0700
Subject: Rewrite fnm
---
ml_exp/compound.py | 33 +++++++++++++++++----------
ml_exp/representations.py | 58 ++++++++++++++++-------------------------------
2 files changed, 40 insertions(+), 51 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 98e31532f..ceace6984 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -33,20 +33,29 @@ class Compound:
Initialization of the Compound.
xyz: (path to) the xyz file.
"""
+ # General compound data.
self.name = None
-
self.n = None
- self.extra = None # In case a comment is in the compound file.
+ self.extra = None
self.atoms = None
self.atoms_nc = None
self.coordinates = None
self.pbe0 = None
self.delta = None
+ # Computed data.
self.cm = None
self.ljm = None
+ self.fnm = None
self.am = None
self.bob = None
+ self.bo_atoms = None
+ self.bok_cx = None
+ self.bof = None
+
+ # Helping data.
+ self.bonds = None
+ self.forces = None
if xyz is not None:
self.read_xyz(xyz)
@@ -103,17 +112,17 @@ class Compound:
bohr_ru: if radius units should be in bohr's radius units.
"""
# First, generate the first neighor matrix.
- fnm, bonds, forces = first_neighbor_matrix(self.coordinates,
- self.atoms_nc,
- self.atoms,
- size=size,
- use_forces=use_forces,
- bohr_ru=bohr_ru)
-
+ fnm_data = first_neighbor_matrix(self.coordinates,
+ self.atoms_nc,
+ self.atoms,
+ size=size,
+ use_forces=use_forces,
+ bohr_ru=bohr_ru)
+ self.fnm, self.bonds, self.forces = fnm_data
# Now, generate the adjacency matrix.
- self.am = adjacency_matrix(fnm,
- bonds,
- forces,
+ self.am = adjacency_matrix(self.fnm,
+ self.bonds,
+ self.forces,
size=size)
def gen_bob(self,
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index d4e79c7d9..515821290 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -181,11 +181,11 @@ def first_neighbor_matrix(coords,
bohr_ru: if radius units should be in bohr's radius units.
NOTE: Bond distance of carbon to other elements
are (for atoms present in the qm7 dataset):
- C: 1.20 - 1.54 A (Edited to 1.19 - 1.54 A)
- H: 1.06 - 1.12 A
- O: 1.43 - 2.15 A
- N: 1.47 - 2.10 A
- S: 1.81 - 2.55 A
+ C: 1.19 - 1.54 A, 1.0
+ H: 1.06 - 1.12 A, 1.0
+ O: 1.43 - 2.15 A, 0.8
+ N: 1.47 - 2.10 A, 1.0
+ S: 1.81 - 2.55 A, 0.7
"""
if bohr_ru:
cr = 0.52917721067
@@ -210,7 +210,11 @@ size. Arrays are not of the right shape.')
cn_bond = sorted(['C', 'N'])
cs_bond = sorted(['C', 'S'])
- fnm = np.zeros((size, size), dtype=float)
+ pos_bonds = {cc_bond: (1.19, 1.54), ch_bond: (1.06, 1.12),
+ co_bond: (1.43, 2.15), cn_bond: (1.47, 2.19),
+ cs_bond: (1.81, 2.55)}
+
+ fnm = np.zeros((size, size), dtype=bool)
bonds = []
forces = []
@@ -219,39 +223,15 @@ size. Arrays are not of the right shape.')
# Ignore the diagonal.
if i != j:
bond = sorted([atoms[i], atoms[j]])
- rv = xyz_i - xyz_j
- r = np.linalg.norm(rv)/cr
-
- # Check for each type of bond.
- if (cc_bond == bond) and (r >= 1.19 and r <= 1.54):
- fnm[i, j] = 1.0
- if j > i:
- bonds.append((i, j))
- if use_forces:
- forces.append(rv*nc[i]*nc[j]/r**3)
- elif (ch_bond == bond) and (r >= 1.06 and r <= 1.12):
- fnm[i, j] = 1.0
- if j > i:
- bonds.append((i, j))
- if use_forces:
- forces.append(rv*nc[i]*nc[j]/r**3)
- elif (co_bond == bond) and (r >= 1.43 and r <= 2.15):
- fnm[i, j] = 0.8
- if j > i:
- bonds.append((i, j))
- if use_forces:
- forces.append(rv*nc[i]*nc[j]/r**3)
- elif (cn_bond == bond) and (r >= 1.47 and r <= 2.10):
- fnm[i, j] = 1.0
- if j > i:
- bonds.append((i, j))
- if use_forces:
- forces.append(rv*nc[i]*nc[j]/r**3)
- elif (cs_bond == bond) and (r >= 1.81 and r <= 2.55):
- fnm[i, j] = 0.7
- if j > i:
- bonds.append((i, j))
- if use_forces:
+ if bond in pos_bonds.keys():
+ r_min = pos_bonds[bond][0]
+ r_max = pos_bonds[bond][1]
+ rv = xyz_i - xyz_j
+ r = np.linalg.norm(rv)/cr
+ if r >= r_min and r <= r_max:
+ fnm[i, j] = True
+ if j > i:
+ bonds.append((i, j))
forces.append(rv*nc[i]*nc[j]/r**3)
return fnm, bonds, forces
--
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