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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