From 0e893e29624cc35a6374ac8d1ff7124c9b6cb05c Mon Sep 17 00:00:00 2001
From: Judit Zador <jzador@sandia.gov>
Date: Fri, 7 Jun 2024 14:21:42 -0700
Subject: [PATCH 1/3] solution for IndexError when too many bonds created in
 Internals

---
 sella/internal.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/sella/internal.py b/sella/internal.py
index c2ffdbc..c9e539e 100644
--- a/sella/internal.py
+++ b/sella/internal.py
@@ -1375,6 +1375,9 @@ def find_all_bonds(
             labels[nbonds == 0] = -1
 
             for i, j in cwr(range(self.natoms), 2):
+                # do not consider bonds beyond max_bonds
+                #if i > max_bonds or j > max_bonds:
+                #    break
                 # do not add a bond between atoms belonging to the same
                 # bonding network fragment
                 if labels[i] == labels[j] and labels[i] != -1:
@@ -1393,12 +1396,16 @@ def find_all_bonds(
                             self.add_bond((i, j), ts)
                         except DuplicateInternalError:
                             continue
-                        c10y[i, nbonds[i]] = j
-                        nbonds[i] += 1
-                        c10y[j, nbonds[j]] = i
-                        nbonds[j] += 1
+                        if nbonds[i] < max_bonds and nbonds[j] < max_bonds:
+                            c10y[i, nbonds[i]] = j
+                            nbonds[i] += 1
+                            c10y[j, nbonds[j]] = i
+                            nbonds[j] += 1
+                        else:
+                            pass
             first_run = False
             scale *= 1.05
+            print(scale)
 
         if self.allow_fragments and nlabels != 1:
             assert nlabels > 1

From d2eb69e1ce023f91484ee2e4bf7b75cee5f367a5 Mon Sep 17 00:00:00 2001
From: Judit Zador <jzador@sandia.gov>
Date: Fri, 7 Jun 2024 14:24:35 -0700
Subject: [PATCH 2/3] removed comment from code

---
 sella/internal.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/sella/internal.py b/sella/internal.py
index c9e539e..a172f95 100644
--- a/sella/internal.py
+++ b/sella/internal.py
@@ -1375,9 +1375,6 @@ def find_all_bonds(
             labels[nbonds == 0] = -1
 
             for i, j in cwr(range(self.natoms), 2):
-                # do not consider bonds beyond max_bonds
-                #if i > max_bonds or j > max_bonds:
-                #    break
                 # do not add a bond between atoms belonging to the same
                 # bonding network fragment
                 if labels[i] == labels[j] and labels[i] != -1:

From aebd6b5ed12bae7731df7691206c30fd1a4486a6 Mon Sep 17 00:00:00 2001
From: Judit Zador <jzador@sandia.gov>
Date: Mon, 10 Jun 2024 15:37:19 -0700
Subject: [PATCH 3/3] removed unnecessary print

---
 sella/internal.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/sella/internal.py b/sella/internal.py
index a172f95..c1c63d7 100644
--- a/sella/internal.py
+++ b/sella/internal.py
@@ -1402,7 +1402,6 @@ def find_all_bonds(
                             pass
             first_run = False
             scale *= 1.05
-            print(scale)
 
         if self.allow_fragments and nlabels != 1:
             assert nlabels > 1