Calculate Displacement Update (#75)

Resolves #74 
- Updated Changelog to note all changes
- Regenerated docs
- Updated copyright in Object class files
- Updated Object::calculateDisplacement function to calculate the net displacement when specifying and direction instead of the absolute displacement and updated the documentation accordingly
- Updated CalculateDisplacement units tests to check for negative displacement when specifying the displacement direction

CHANGELOG.md

@@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [v2.1.0] - 2020-07-25 - Build Update
+## [v2.1.0] - 2020-08-09 - Build and Bugfix Update
 
 ### Added
 - .travis.yml - Test builds for GCC 9
@@ -18,17 +18,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - README.md - Information about clang compiler support
 
 ### Changed
-- .travis.yml - Copyright years up 2020
+- .travis.yml - Copyright years up to 2020
 - .travis.yml - Test build OS from Ubuntu trusty to Ubuntu xenial and bionic
 - .travis.yml - Simplified how GCC versions are installed and configured
 - docs - Updated Doxygen documentation for v2.1.0 using Doxygen v1.8.18
 - Doxyfile - Project version to v2.1.0 and other adjustments for Doxygen version v1.8.18
-- LICENSE - Copyright years up 2020
-- makefile - Copyright years up 2020
+- LICENSE - Copyright years up to 2020
+- makefile - Copyright years up to 2020
 - makefile - Updated how the underlying compiler is detected now using 'mpicxx -show'
+- Object - Copyright years up to 2020
+- Object - Updated calculateDisplacement method to calculate net displacement when specifying a direction instead of the absolute displacement
 - README.md - Latest stable release version to v2.1.0
 - README.md - Updated description of testing configurations
-- Version - Copyright years up 2020
+- test.cpp (CalculateDisplacementTests) - Updated tests to check for negative net displacement when specifying a direction
+- Version - Copyright years up to 2020
 - Version - Current version string to v2.1.0
 
 ### Removed

docs/_object_8h_source.html

@@ -87,7 +87,7 @@
 <div class="title">Object.h</div>  </div>
 </div><!--header-->
 <div class="contents">
-<a href="_object_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// Copyright (c) 2017-2019 Michael C. Heiber</span></div>
+<a href="_object_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// Copyright (c) 2017-2020 Michael C. Heiber</span></div>
 <div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">// This source file is part of the KMC_Lattice project, which is subject to the MIT License.</span></div>
 <div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// For more information, see the LICENSE file that accompanies this software.</span></div>
 <div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// The KMC_Lattice project can be found on Github at https://github.com/MikeHeiber/KMC_Lattice</span></div>
@@ -156,7 +156,7 @@
 </div><!-- fragment --></div><!-- contents -->
 </div><!-- doc-content -->
 <div class="ttc" id="aclass_k_m_c___lattice_1_1_object_html_a7d3cf585bb696b0a550ca3ba19891dd3"><div class="ttname"><a href="class_k_m_c___lattice_1_1_object.html#a7d3cf585bb696b0a550ca3ba19891dd3">KMC_Lattice::Object::getObjectType</a></div><div class="ttdeci">virtual std::string getObjectType() const</div><div class="ttdoc">Gets the name of the Object class.</div><div class="ttdef"><b>Definition:</b> Object.cpp:56</div></div>
-<div class="ttc" id="aclass_k_m_c___lattice_1_1_object_html_a1831d9ef4058f8605c630cf68fc36b68"><div class="ttname"><a href="class_k_m_c___lattice_1_1_object.html#a1831d9ef4058f8605c630cf68fc36b68">KMC_Lattice::Object::calculateDisplacement</a></div><div class="ttdeci">double calculateDisplacement(const int direction=0) const</div><div class="ttdoc">Calculates the absolute displacement of the object from its starting coordinates in lattice units.</div><div class="ttdef"><b>Definition:</b> Object.cpp:29</div></div>
+<div class="ttc" id="aclass_k_m_c___lattice_1_1_object_html_a1831d9ef4058f8605c630cf68fc36b68"><div class="ttname"><a href="class_k_m_c___lattice_1_1_object.html#a1831d9ef4058f8605c630cf68fc36b68">KMC_Lattice::Object::calculateDisplacement</a></div><div class="ttdeci">double calculateDisplacement(const int direction=0) const</div><div class="ttdoc">Calculates the displacement of the object from its starting coordinates in lattice units.</div><div class="ttdef"><b>Definition:</b> Object.cpp:29</div></div>
 <div class="ttc" id="aclass_k_m_c___lattice_1_1_object_html_a3d2c9e1ec9c369bd99d65d3b56d7329d"><div class="ttname"><a href="class_k_m_c___lattice_1_1_object.html#a3d2c9e1ec9c369bd99d65d3b56d7329d">KMC_Lattice::Object::incrementDZ</a></div><div class="ttdeci">void incrementDZ(const int num)</div><div class="ttdoc">Increments the dz parameter, which is to be used when the Object crosses a z-direction periodic bound...</div><div class="ttdef"><b>Definition:</b> Object.cpp:72</div></div>
 <div class="ttc" id="a_utils_8h_html"><div class="ttname"><a href="_utils_8h.html">Utils.h</a></div></div>
 <div class="ttc" id="aclass_k_m_c___lattice_1_1_object_html_aefef862e9b7d6664f49c0187743dc757"><div class="ttname"><a href="class_k_m_c___lattice_1_1_object.html#aefef862e9b7d6664f49c0187743dc757">KMC_Lattice::Object::Object</a></div><div class="ttdeci">Object()</div><div class="ttdoc">Default constructor that creates an empty Object object.</div><div class="ttdef"><b>Definition:</b> Object.cpp:18</div></div>

docs/class_k_m_c___lattice_1_1_object.html

@@ -108,7 +108,7 @@
 <tr class="memdesc:a3cc5166f14876fb0a6ceebbdd19d5b40"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructor that creates and initializes a usable <a class="el" href="class_k_m_c___lattice_1_1_object.html" title="This base class contains the basic properties of a KMC simulation object and the functions needed to ...">Object</a> object.  <a href="class_k_m_c___lattice_1_1_object.html#a3cc5166f14876fb0a6ceebbdd19d5b40">More...</a><br /></td></tr>
 <tr class="separator:a3cc5166f14876fb0a6ceebbdd19d5b40"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a1831d9ef4058f8605c630cf68fc36b68"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_k_m_c___lattice_1_1_object.html#a1831d9ef4058f8605c630cf68fc36b68">calculateDisplacement</a> (const int direction=0) const</td></tr>
-<tr class="memdesc:a1831d9ef4058f8605c630cf68fc36b68"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the absolute displacement of the object from its starting coordinates in lattice units.  <a href="class_k_m_c___lattice_1_1_object.html#a1831d9ef4058f8605c630cf68fc36b68">More...</a><br /></td></tr>
+<tr class="memdesc:a1831d9ef4058f8605c630cf68fc36b68"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the displacement of the object from its starting coordinates in lattice units.  <a href="class_k_m_c___lattice_1_1_object.html#a1831d9ef4058f8605c630cf68fc36b68">More...</a><br /></td></tr>
 <tr class="separator:a1831d9ef4058f8605c630cf68fc36b68"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a83a7bab6def0127d9a9a867a5f7f7ca8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="struct_k_m_c___lattice_1_1_coords.html">Coords</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_k_m_c___lattice_1_1_object.html#a83a7bab6def0127d9a9a867a5f7f7ca8">getCoords</a> () const</td></tr>
 <tr class="memdesc:a83a7bab6def0127d9a9a867a5f7f7ca8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the current coordinates of the <a class="el" href="class_k_m_c___lattice_1_1_object.html" title="This base class contains the basic properties of a KMC simulation object and the functions needed to ...">Object</a>.  <a href="class_k_m_c___lattice_1_1_object.html#a83a7bab6def0127d9a9a867a5f7f7ca8">More...</a><br /></td></tr>
@@ -148,7 +148,7 @@
 <div class="textblock"><p>This base class contains the basic properties of a KMC simulation object and the functions needed to interact with it. </p>
 <p>This base class is designed to work with the <a class="el" href="class_k_m_c___lattice_1_1_simulation.html" title="This abstract base class contains the basic properties of a KMC simulation and the functions needed t...">Simulation</a> class to construct a KMC simulation. This base class is intended to be extended to create classes that represent specific types of objects. </p><dl class="section copyright"><dt>Copyright</dt><dd>MIT License. For more information, see the LICENSE file that accompanies this software package. </dd></dl>
 <dl class="section author"><dt>Author</dt><dd>Michael C. Heiber </dd></dl>
-<dl class="section date"><dt>Date</dt><dd>2017-2019 </dd></dl>
+<dl class="section date"><dt>Date</dt><dd>2017-2020 </dd></dl>
 </div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
 <a id="a2f950c46bb2903eda745a8082dee201e"></a>
 <h2 class="memtitle"><span class="permalink"><a href="#a2f950c46bb2903eda745a8082dee201e">&#9670;&nbsp;</a></span>~Object()</h2>
@@ -257,10 +257,10 @@ <h2 class="memtitle"><span class="permalink"><a href="#a1831d9ef4058f8605c630cf6
       </table>
 </div><div class="memdoc">
 
-<p>Calculates the absolute displacement of the object from its starting coordinates in lattice units. </p>
+<p>Calculates the displacement of the object from its starting coordinates in lattice units. </p>
 <p>The function accounts for when periodic boundaries are crossed to determine the real displacement distance. </p><dl class="params"><dt>Parameters</dt><dd>
   <table class="params">
-    <tr><td class="paramname">direction</td><td>is an optional parameter that specifies whether the displacement only along a particular Cartesian direction should be calculated. When direction is not set, the default three-dimensional displacement is calculated, but when set to 1, 2, or 3, the function calculates the displacement only in the x-, y-, and z-directions, respectively. </td></tr>
+    <tr><td class="paramname">direction</td><td>is an optional parameter that specifies whether the displacement only along a particular Cartesian direction should be calculated. When direction is not set, the default three-dimensional absolute displacement is calculated, but when set to 1, 2, or 3, the function calculates the net displacement only in the x-, y-, and z-directions, respectively. </td></tr>
   </table>
   </dd>
 </dl>

src/Object.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2017-2019 Michael C. Heiber
+// Copyright (c) 2017-2020 Michael C. Heiber
 // This source file is part of the KMC_Lattice project, which is subject to the MIT License.
 // For more information, see the LICENSE file that accompanies this software.
 // The KMC_Lattice project can be found on Github at https://github.com/MikeHeiber/KMC_Lattice
@@ -31,11 +31,11 @@ namespace KMC_Lattice {
 		case 0:
 			return sqrt((coords_current.x + dx - coords_initial.x)*(coords_current.x + dx - coords_initial.x) + (coords_current.y + dy - coords_initial.y)*(coords_current.y + dy - coords_initial.y) + (coords_current.z + dz - coords_initial.z)*(coords_current.z + dz - coords_initial.z));
 		case 1:
-			return abs(coords_current.x + dx - coords_initial.x);
+			return coords_current.x + dx - coords_initial.x;
 		case 2:
-			return abs(coords_current.y + dy - coords_initial.y);
+			return coords_current.y + dy - coords_initial.y;
 		case 3:
-			return abs(coords_current.z + dz - coords_initial.z);
+			return coords_current.z + dz - coords_initial.z;
 		default:
 			throw invalid_argument("Error! Specified direction input parameter is invalid.");
 		}

src/Object.h

@@ -1,4 +1,4 @@
-// Copyright (c) 2017-2019 Michael C. Heiber
+// Copyright (c) 2017-2020 Michael C. Heiber
 // This source file is part of the KMC_Lattice project, which is subject to the MIT License.
 // For more information, see the LICENSE file that accompanies this software.
 // The KMC_Lattice project can be found on Github at https://github.com/MikeHeiber/KMC_Lattice
@@ -20,7 +20,7 @@ namespace KMC_Lattice {
 	//! base class is intended to be extended to create classes that represent specific types of objects. 
 	//! \copyright MIT License.  For more information, see the LICENSE file that accompanies this software package.
 	//! \author Michael C. Heiber
-	//! \date 2017-2019
+	//! \date 2017-2020
 	class Object {
 	public:
 		//! Default virtual destructor needed by the base class.
@@ -35,11 +35,11 @@ namespace KMC_Lattice {
 		//! \param start_coords is the Coords struct that defines the starting coordinates of the Object.
 		Object(const double time, const int tag_num, const Coords& start_coords);
 
-		//! \brief Calculates the absolute displacement of the object from its starting coordinates in lattice units.
+		//! \brief Calculates the displacement of the object from its starting coordinates in lattice units.
 		//! \details The function accounts for when periodic boundaries are crossed to determine the real 
 		//! displacement distance.
 		//! \param direction is an optional parameter that specifies whether the displacement only along a particular Cartesian direction should be calculated.
-		//! When direction is not set, the default three-dimensional displacement is calculated, but when set to 1, 2, or 3, the function calculates the displacement
+		//! When direction is not set, the default three-dimensional absolute displacement is calculated, but when set to 1, 2, or 3, the function calculates the net displacement
 		//! only in the x-, y-, and z-directions, respectively.
 		double calculateDisplacement(const int direction = 0) const;
 

test/test.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2017-2019 Michael C. Heiber
+// Copyright (c) 2017-2020 Michael C. Heiber
 // This source file is part of the KMC_Lattice project, which is subject to the MIT License.
 // For more information, see the LICENSE file that accompanies this software.
 // The KMC_Lattice project can be found on Github at https://github.com/MikeHeiber/KMC_Lattice
@@ -1555,29 +1555,29 @@ namespace ObjectTests {
 		EXPECT_DOUBLE_EQ(1.0, object1.calculateDisplacement(0));
 		EXPECT_DOUBLE_EQ(0.0, object1.calculateDisplacement(1));
 		EXPECT_DOUBLE_EQ(0.0, object1.calculateDisplacement(2));
-		EXPECT_DOUBLE_EQ(1.0, object1.calculateDisplacement(3));
+		EXPECT_DOUBLE_EQ(-1.0, object1.calculateDisplacement(3));
 		object1.setCoords({ 49,49,49 });
 		object1.incrementDX(-50);
 		object1.incrementDY(-50);
 		EXPECT_DOUBLE_EQ(sqrt(3), object1.calculateDisplacement());
 		EXPECT_DOUBLE_EQ(sqrt(3), object1.calculateDisplacement(0));
-		EXPECT_DOUBLE_EQ(1.0, object1.calculateDisplacement(1));
-		EXPECT_DOUBLE_EQ(1.0, object1.calculateDisplacement(2));
-		EXPECT_DOUBLE_EQ(1.0, object1.calculateDisplacement(3));
+		EXPECT_DOUBLE_EQ(-1.0, object1.calculateDisplacement(1));
+		EXPECT_DOUBLE_EQ(-1.0, object1.calculateDisplacement(2));
+		EXPECT_DOUBLE_EQ(-1.0, object1.calculateDisplacement(3));
 		object1.setCoords({ 49,0,49 });
 		object1.incrementDY(50);
 		EXPECT_DOUBLE_EQ(sqrt(2), object1.calculateDisplacement());
 		EXPECT_DOUBLE_EQ(sqrt(2), object1.calculateDisplacement(0));
-		EXPECT_DOUBLE_EQ(1.0, object1.calculateDisplacement(1));
+		EXPECT_DOUBLE_EQ(-1.0, object1.calculateDisplacement(1));
 		EXPECT_DOUBLE_EQ(0.0, object1.calculateDisplacement(2));
-		EXPECT_DOUBLE_EQ(1.0, object1.calculateDisplacement(3));
+		EXPECT_DOUBLE_EQ(-1.0, object1.calculateDisplacement(3));
 		object1.resetInitialCoords({ 5,5,5 });
 		object1.setCoords({ 4,4,4 });
 		EXPECT_DOUBLE_EQ(sqrt(3), object1.calculateDisplacement());
 		EXPECT_DOUBLE_EQ(sqrt(3), object1.calculateDisplacement(0));
-		EXPECT_DOUBLE_EQ(1.0, object1.calculateDisplacement(1));
-		EXPECT_DOUBLE_EQ(1.0, object1.calculateDisplacement(2));
-		EXPECT_DOUBLE_EQ(1.0, object1.calculateDisplacement(3));
+		EXPECT_DOUBLE_EQ(-1.0, object1.calculateDisplacement(1));
+		EXPECT_DOUBLE_EQ(-1.0, object1.calculateDisplacement(2));
+		EXPECT_DOUBLE_EQ(-1.0, object1.calculateDisplacement(3));
 		// Check invalid direction parameter usage
 		EXPECT_THROW(object1.calculateDisplacement(4), invalid_argument);
 	}