From 67cc0022d77ff5b8313c090cbff097a55599348f Mon Sep 17 00:00:00 2001
From: Aritz Erkiaga <aerkiaga3@gmail.com>
Date: Wed, 13 Jul 2022 21:46:10 +0200
Subject: [PATCH] Workaround charge models locking up or not running

Signed-off-by: Aritz Erkiaga <aerkiaga3@gmail.com>
---
 avogadro/core/molecule.cpp                 | 1 +
 avogadro/qtplugins/openbabel/obcharges.cpp | 4 ++++
 2 files changed, 5 insertions(+)

diff --git a/avogadro/core/molecule.cpp b/avogadro/core/molecule.cpp
index f2f814cb8a..da19638982 100644
--- a/avogadro/core/molecule.cpp
+++ b/avogadro/core/molecule.cpp
@@ -258,6 +258,7 @@ MatrixX Molecule::partialCharges(const std::string& type) const
     return search->second; // value from the map
   } else {
     MatrixX charges(atomCount(), 1);
+    charges.fill(0.0);
     return charges;
   }
 }
diff --git a/avogadro/qtplugins/openbabel/obcharges.cpp b/avogadro/qtplugins/openbabel/obcharges.cpp
index 68641ea344..b2c2c9d405 100644
--- a/avogadro/qtplugins/openbabel/obcharges.cpp
+++ b/avogadro/qtplugins/openbabel/obcharges.cpp
@@ -198,6 +198,10 @@ MatrixX OBCharges::partialCharges(Core::Molecule& molecule) const
     charges(i, 0) = output[i];
   }
 
+  // workaround failed runs causing the code to freeze
+  if (abs(charges(0, 0)) < 0.00001)
+    charges(0, 0) = 0.0001;
+
   // cache the charges and allow them to show up in output
   molecule.setPartialCharges(m_identifier, charges);
   return charges;