Update comment headers to new format (missed some in prev effort)

avogadro/command/qube.cpp

@@ -1,17 +1,6 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  Copyright 2014 Albert DeFusco University of Pittsburgh
-
-  This source code is released under the New BSD License, (the "License").
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 #include <avogadro/io/fileformatmanager.h>
 #include <avogadro/quantumio/gamessus.h>
@@ -28,15 +17,15 @@
 #include <sstream>
 #include <string>
 
-using Avogadro::Io::FileFormatManager;
 using Avogadro::Core::Cube;
-using Avogadro::Core::Molecule;
 using Avogadro::Core::GaussianSetTools;
+using Avogadro::Core::Molecule;
+using Avogadro::Io::FileFormatManager;
 using std::cin;
 using std::cout;
 using std::endl;
-using std::string;
 using std::ostringstream;
+using std::string;
 
 using Eigen::Vector3d;
 using Eigen::Vector3i;

avogadro/qtgui/insertfragmentdialog.cpp

@@ -1,17 +1,6 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  Copyright 2020 Geoffrey R. Hutchison
-
-  This source code is released under the New BSD License, (the "License").
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include "insertfragmentdialog.h"

avogadro/qtgui/scriptloader.cpp

@@ -1,15 +1,6 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  This source code is released under the New BSD License, (the "License").
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include "scriptloader.h"

avogadro/qtgui/scriptloader.h

@@ -1,15 +1,6 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  This source code is released under the New BSD License, (the "License").
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #ifndef AVOGADRO_QTGUI_SCRIPTLOADER_H
@@ -27,6 +18,9 @@ namespace QtGui {
 /**
  * @brief The ScriptLoader class finds and verifies different types of
  * python utility scripts.
+ *
+ * For example, finding all the "charge" scripts
+ * auto chargeScripts = ScriptLoader::scriptList("charge");
  */
 class AVOGADROQTGUI_EXPORT ScriptLoader : public QObject
 {

avogadro/qtplugins/bonding/bonding.h

@@ -1,7 +1,6 @@
 /******************************************************************************
   This source file is part of the Avogadro project.
-
-  This source code is released under the New BSD License, (the "License").
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #ifndef AVOGADRO_QTPLUGINS_BONDING_H

avogadro/qtplugins/commandscripts/command.cpp

@@ -1,6 +1,6 @@
 /******************************************************************************
   This source file is part of the Avogadro project.
-  This source code is released under the New BSD License, (the "License").
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include "command.h"

avogadro/qtplugins/commandscripts/command.h

@@ -1,6 +1,6 @@
 /******************************************************************************
   This source file is part of the Avogadro project.
-  This source code is released under the New BSD License, (the "License").
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #ifndef AVOGADRO_QTPLUGINS_COMMAND_H

avogadro/qtplugins/gamessinput/gamesshighlighter.h

@@ -1,17 +1,6 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  Copyright (C) 2009 Marcus D. Hanwell
-
-  This source code is released under the New BSD License, (the "License").
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #ifndef GAMESSHIGHLIGHTER_H

avogadro/qtplugins/measuretool/measuretool.cpp

@@ -1,11 +1,6 @@
 /******************************************************************************
   This source file is part of the Avogadro project.
-
-  Adapted from Avogadro 1.x with the following authors' permission:
-  Copyright 2007 Donald Ephraim Curtis
-  Copyright 2008 Marcus D. Hanwell
-
-  This source code is released under the New BSD License, (the "License").
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include "measuretool.h"
@@ -59,7 +54,8 @@ MeasureTool::MeasureTool(QObject* parent_)
        "\tDistances are measured between 1-2 and 2-3\n"
        "\tAngle is measured between 1-3 using 2 as the common point\n"
        "\tDihedral is measured between 1-2-3-4\n"
-       "Right Mouse: \tReset the measurements.").arg(shortcut));
+       "Right Mouse: \tReset the measurements.")
+      .arg(shortcut));
   setIcon();
 }
 

avogadro/rendering/dashedlinegeometry.cpp

@@ -1,6 +1,6 @@
 /******************************************************************************
   This source file is part of the Avogadro project.
-  This source code is released under the New BSD License, (the "License").
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include "dashedlinegeometry.h"
@@ -22,7 +22,7 @@
 namespace {
 #include "dashedline_fs.h"
 #include "dashedline_vs.h"
-}
+} // namespace
 
 using Avogadro::Vector3f;
 using Avogadro::Vector3ub;
@@ -46,8 +46,7 @@ class DashedLineGeometry::Private
 };
 
 DashedLineGeometry::DashedLineGeometry()
-  : m_lineWidth(1.0), m_lineCount(0),
-    m_color(255, 0, 0), m_opacity(255),
+  : m_lineWidth(1.0), m_lineCount(0), m_color(255, 0, 0), m_opacity(255),
     m_dirty(false), d(new Private)
 {
 }
@@ -159,8 +158,9 @@ void DashedLineGeometry::clear()
   m_dirty = true;
 }
 
-size_t DashedLineGeometry::addDashedLine(const Vector3f &start, const Vector3f &end,
-                                       const Vector4ub &rgba, int dashCount)
+size_t DashedLineGeometry::addDashedLine(const Vector3f& start,
+                                         const Vector3f& end,
+                                         const Vector4ub& rgba, int dashCount)
 {
   const int vertexCount = 2 * dashCount;
   Vector3f delta = (end - start) / (vertexCount - 1);
@@ -176,17 +176,18 @@ size_t DashedLineGeometry::addDashedLine(const Vector3f &start, const Vector3f &
   return m_lineCount - 1;
 }
 
-size_t DashedLineGeometry::addDashedLine(const Vector3f &start, const Vector3f &end,
-                                       const Vector3ub &rgb, int dashCount)
+size_t DashedLineGeometry::addDashedLine(const Vector3f& start,
+                                         const Vector3f& end,
+                                         const Vector3ub& rgb, int dashCount)
 {
   Vector4ub rgba = Vector4ub(rgb(0), rgb(1), rgb(2), m_opacity);
   return addDashedLine(start, end, rgba, dashCount);
 }
 
-size_t DashedLineGeometry::addDashedLine(const Vector3f &start, const Vector3f &end,
-                                       int dashCount)
+size_t DashedLineGeometry::addDashedLine(const Vector3f& start,
+                                         const Vector3f& end, int dashCount)
 {
   return addDashedLine(start, end, m_color, dashCount);
 }
 
-} // End namespace Avogadro
+} // namespace Avogadro::Rendering

avogadro/rendering/dashedlinegeometry.h

@@ -1,6 +1,6 @@
 /******************************************************************************
   This source file is part of the Avogadro project.
-  This source code is released under the New BSD License, (the "License").
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #ifndef AVOGADRO_RENDERING_DASHEDLINEGEOMETRY_H
@@ -27,9 +27,7 @@ class AVOGADRORENDERING_EXPORT DashedLineGeometry : public Drawable
     Vector3f vertex; // 12 bytes
     Vector4ub color; //  4 bytes
 
-    PackedVertex(const Vector3f &v, const Vector4ub &c)
-      : vertex(v), color(c)
-    {}
+    PackedVertex(const Vector3f& v, const Vector4ub& c) : vertex(v), color(c) {}
     static int vertexOffset() { return 0; }
     static int colorOffset() { return static_cast<int>(sizeof(Vector3f)); }
   };
@@ -69,12 +67,12 @@ class AVOGADRORENDERING_EXPORT DashedLineGeometry : public Drawable
    * @return The index of the first vertex added by this call.
    * @{
    */
-  size_t addDashedLine(const Vector3f &start, const Vector3f &end,
-                      const Vector4ub& color, int dashCount);
-  size_t addDashedLine(const Vector3f &start, const Vector3f &end,
-                      const Vector3ub& color, int dashCount);
-  size_t addDashedLine(const Vector3f &start, const Vector3f &end,
-                      int dashCount);
+  size_t addDashedLine(const Vector3f& start, const Vector3f& end,
+                       const Vector4ub& color, int dashCount);
+  size_t addDashedLine(const Vector3f& start, const Vector3f& end,
+                       const Vector3ub& color, int dashCount);
+  size_t addDashedLine(const Vector3f& start, const Vector3f& end,
+                       int dashCount);
   /** @} */
 
   /**
@@ -112,7 +110,7 @@ class AVOGADRORENDERING_EXPORT DashedLineGeometry : public Drawable
   Core::Array<PackedVertex> m_vertices;
   float m_lineWidth;
   int m_lineCount;
-  
+
   Vector3ub m_color;
   unsigned char m_opacity;
 
@@ -122,7 +120,8 @@ class AVOGADRORENDERING_EXPORT DashedLineGeometry : public Drawable
   Private* d;
 };
 
-inline DashedLineGeometry& DashedLineGeometry::operator=(DashedLineGeometry other)
+inline DashedLineGeometry& DashedLineGeometry::operator=(
+  DashedLineGeometry other)
 {
   using std::swap;
   swap(*this, other);

tests/core/arraytest.cpp

@@ -1,17 +1,6 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  Copyright 2011-2012 Kitware, Inc.
-
-  This source code is released under the New BSD License, (the "License").
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include <gtest/gtest.h>

tests/core/atomtest.cpp

@@ -1,27 +1,16 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  Copyright 2011-2012 Kitware, Inc.
-
-  This source code is released under the New BSD License, (the "License").
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include <gtest/gtest.h>
 
 #include <avogadro/core/molecule.h>
 
-using Avogadro::Core::Molecule;
-using Avogadro::Core::Atom;
 using Avogadro::Vector2;
 using Avogadro::Vector3;
+using Avogadro::Core::Atom;
+using Avogadro::Core::Molecule;
 
 TEST(AtomTest, setAtomicNumber)
 {

tests/core/atomtypertest.cpp

@@ -1,17 +1,6 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  Copyright 2013 Kitware, Inc.
-
-  This source code is released under the New BSD License, (the "License").
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include <gtest/gtest.h>
@@ -40,6 +29,7 @@ TEST(AtomTyper, singleAtomTyping)
   public:
     MassTyper() : AtomTyper<double>(nullptr) {}
     Array<double>& typesRef() { return m_types; }
+
   protected:
     double type(const Atom& atom)
     {

tests/core/basissettest.cpp

@@ -1,17 +1,6 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  Copyright 2011-2012 Kitware, Inc.
-
-  This source code is released under the New BSD License, (the "License").
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include <gtest/gtest.h>