Merge pull request #12 from MikeHeiber/development

v2.0-beta.3 Development

Author: MikeHeiber

Doxyfile

@@ -1,4 +1,4 @@
-# Doxyfile 1.8.13
+# Doxyfile 1.8.14
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -20,8 +20,8 @@
 # This tag specifies the encoding used for all characters in the config file
 # that follow. The default is UTF-8 which is also the encoding used for all text
 # before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
-# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
-# for the list of possible encodings.
+# built into libc) for the transcoding. See
+# https://www.gnu.org/software/libiconv/ for the list of possible encodings.
 # The default value is: UTF-8.
 
 DOXYFILE_ENCODING      = UTF-8
@@ -38,7 +38,7 @@ PROJECT_NAME           = KMC_Lattice
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v2.0-beta.2
+PROJECT_NUMBER         = v2.0-beta.3
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -337,7 +337,7 @@ BUILTIN_STL_SUPPORT    = NO
 CPP_CLI_SUPPORT        = NO
 
 # Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
-# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
+# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen
 # will parse them like normal C++ but will assume all classes use public instead
 # of private inheritance when no explicit protection keyword is present.
 # The default value is: NO.
@@ -708,7 +708,7 @@ LAYOUT_FILE            =
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
 # extension is automatically appended if omitted. This requires the bibtex tool
-# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
+# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
 # For LaTeX the style of the bibliography can be controlled using
 # LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
 # search path. See also \cite for info how to create references.
@@ -795,7 +795,7 @@ INPUT                  = Z:\Software_Projects\Local\KMC_Lattice\
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
 # libiconv (or the iconv built into libc) for the transcoding. See the libiconv
-# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# documentation (see: https://www.gnu.org/software/libiconv/) for the list of
 # possible encodings.
 # The default value is: UTF-8.
 
@@ -1043,7 +1043,7 @@ SOURCE_TOOLTIPS        = YES
 # If the USE_HTAGS tag is set to YES then the references to source code will
 # point to the HTML generated by the htags(1) tool instead of doxygen built-in
 # source browser. The htags tool is part of GNU's global source tagging system
-# (see http://www.gnu.org/software/global/global.html). You will need version
+# (see https://www.gnu.org/software/global/global.html). You will need version
 # 4.8.6 or higher.
 #
 # To use it do the following:
@@ -1089,6 +1089,17 @@ CLANG_ASSISTED_PARSING = NO
 
 CLANG_OPTIONS          = 
 
+# If clang assisted parsing is enabled you can provide the clang parser with the
+# path to the compilation database (see:
+# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) used when the files
+# were built. This is equivalent to specifying the "-p" option to a clang tool,
+# such as clang-check. These options will then be pased to the parser.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse-libclang=ON option for CMake.
+# The default value is: 0.
+
+CLANG_COMPILATION_DATABASE_PATH= 0
+
 #---------------------------------------------------------------------------
 # Configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
@@ -1207,7 +1218,7 @@ HTML_EXTRA_FILES       =
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
 # will adjust the colors in the style sheet and background images according to
 # this color. Hue is specified as an angle on a colorwheel, see
-# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# https://en.wikipedia.org/wiki/Hue for more information. For instance the value
 # 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
 # purple, and 360 is red again.
 # Minimum value: 0, maximum value: 359, default value: 220.
@@ -1243,6 +1254,17 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
+# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
+# documentation will contain a main index with vertical navigation menus that
+# are dynamically created via Javascript. If disabled, the navigation index will
+# consists of multiple levels of tabs that are statically embedded in every HTML
+# page. Disable this option to support browsers that do not have Javascript,
+# like the Qt help browser.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_MENUS     = YES
+
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded.
@@ -1266,12 +1288,12 @@ HTML_INDEX_NUM_ENTRIES = 100
 
 # If the GENERATE_DOCSET tag is set to YES, additional index files will be
 # generated that can be used as input for Apple's Xcode 3 integrated development
-# environment (see: http://developer.apple.com/tools/xcode/), introduced with
+# environment (see: https://developer.apple.com/tools/xcode/), introduced with
 # OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
 # Makefile in the HTML output directory. Running make will produce the docset in
 # that directory and running make install will install the docset in
 # ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
-# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# startup. See https://developer.apple.com/tools/creatingdocsetswithdoxygen.html
 # for more information.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
@@ -1387,40 +1409,37 @@ QCH_FILE               =
 
 # The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
 # Project output. For more information please see Qt Help Project / Namespace
-# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# (see: http://doc.qt.io/qt-4.8/qthelpproject.html#namespace).
 # The default value is: org.doxygen.Project.
 # This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_NAMESPACE          = org.doxygen.Project
 
 # The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
 # Help Project output. For more information please see Qt Help Project / Virtual
-# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
-# folders).
+# Folders (see: http://doc.qt.io/qt-4.8/qthelpproject.html#virtual-folders).
 # The default value is: doc.
 # This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_VIRTUAL_FOLDER     = doc
 
 # If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
 # filter to add. For more information please see Qt Help Project / Custom
-# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
-# filters).
+# Filters (see: http://doc.qt.io/qt-4.8/qthelpproject.html#custom-filters).
 # This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_CUST_FILTER_NAME   = 
 
 # The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
 # custom filter to add. For more information please see Qt Help Project / Custom
-# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
-# filters).
+# Filters (see: http://doc.qt.io/qt-4.8/qthelpproject.html#custom-filters).
 # This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_CUST_FILTER_ATTRS  = 
 
 # The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
 # project's filter section matches. Qt Help Project / Filter Attributes (see:
-# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# http://doc.qt.io/qt-4.8/qthelpproject.html#filter-attributes).
 # This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_SECT_FILTER_ATTRS  = 
@@ -1513,7 +1532,7 @@ EXT_LINKS_IN_WINDOW    = NO
 
 FORMULA_FONTSIZE       = 10
 
-# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# Use the FORMULA_TRANSPARENT tag to determine whether or not the images
 # generated for formulas are transparent PNGs. Transparent PNGs are not
 # supported properly for IE 6.0, but are supported on all modern browsers.
 #
@@ -1525,7 +1544,7 @@ FORMULA_FONTSIZE       = 10
 FORMULA_TRANSPARENT    = YES
 
 # Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
-# http://www.mathjax.org) which uses client side Javascript for the rendering
+# https://www.mathjax.org) which uses client side Javascript for the rendering
 # instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
 # installed or if you want to formulas look prettier in the HTML output. When
 # enabled you may also need to install MathJax separately and configure the path
@@ -1552,7 +1571,7 @@ MATHJAX_FORMAT         = HTML-CSS
 # MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
 # Content Delivery Network so you can quickly see the result without installing
 # MathJax. However, it is strongly recommended to install a local copy of
-# MathJax from http://www.mathjax.org before deployment.
+# MathJax from https://www.mathjax.org before deployment.
 # The default value is: http://cdn.mathjax.org/mathjax/latest.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
@@ -1614,7 +1633,7 @@ SERVER_BASED_SEARCH    = NO
 #
 # Doxygen ships with an example indexer (doxyindexer) and search engine
 # (doxysearch.cgi) which are based on the open source search engine library
-# Xapian (see: http://xapian.org/).
+# Xapian (see: https://xapian.org/).
 #
 # See the section "External Indexing and Searching" for details.
 # The default value is: NO.
@@ -1627,7 +1646,7 @@ EXTERNAL_SEARCH        = NO
 #
 # Doxygen ships with an example indexer (doxyindexer) and search engine
 # (doxysearch.cgi) which are based on the open source search engine library
-# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Xapian (see: https://xapian.org/). See the section "External Indexing and
 # Searching" for details.
 # This tag requires that the tag SEARCHENGINE is set to YES.
 
@@ -1814,7 +1833,7 @@ LATEX_SOURCE_CODE      = NO
 
 # The LATEX_BIB_STYLE tag can be used to specify the style to use for the
 # bibliography, e.g. plainnat, or ieeetr. See
-# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
 # The default value is: plain.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
@@ -1997,9 +2016,9 @@ DOCBOOK_PROGRAMLISTING = NO
 #---------------------------------------------------------------------------
 
 # If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
-# AutoGen Definitions (see http://autogen.sf.net) file that captures the
-# structure of the code including all documentation. Note that this feature is
-# still experimental and incomplete at the moment.
+# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures
+# the structure of the code including all documentation. Note that this feature
+# is still experimental and incomplete at the moment.
 # The default value is: NO.
 
 GENERATE_AUTOGEN_DEF   = NO

Lattice.cpp

@@ -6,6 +6,7 @@
 #include "Lattice.h"
 
 using namespace std;
+using namespace Utils;
 
 Lattice::Lattice() {
 
@@ -222,6 +223,10 @@ int Lattice::getWidth() const{
 	return Width;
 }
 
+double Lattice::getVolume() const {
+	return ((Length*Width*Height*1e-7*Unit_size)*1e-7*Unit_size)*1e-7*Unit_size;
+}
+
 bool Lattice::isOccupied(const Coords& coords) const{
 	return site_ptrs[getSiteIndex(coords)]->isOccupied();
 }

Lattice.h

@@ -181,6 +181,9 @@ class Lattice{
 		//! \return The unit size property of the lattice.
 		double getUnitSize() const;
 
+		//! \brief Gets the volume of the lattice in cm^-3.
+		double getVolume() const;
+
 		//! \brief Gets the y-direction size of the lattice, the width.
 		//! \return The Width property of the lattice, which is the y-direction size.
 		int getWidth() const;

Simulation.cpp

@@ -45,7 +45,7 @@ void Simulation::init(const Parameters_Simulation& params, const int id) {
 }
 
 
-list<Event*>::iterator Simulation::addEvent(Event* event_ptr) {
+list<Event*>::const_iterator Simulation::addEvent(Event* event_ptr) {
 	event_ptrs.push_back(event_ptr);
 	return --event_ptrs.end();
 }
@@ -64,7 +64,7 @@ void Simulation::addObject(Object* object_ptr) {
 	N_events_executed++;
 }
 
-list<Event*>::iterator Simulation::chooseNextEvent() {
+list<Event*>::const_iterator Simulation::chooseNextEvent() {
 	auto event_target_it = event_ptrs.begin();
 	if (event_ptrs.size() > 1) {
 		for (auto it = ++event_ptrs.begin(); it != event_ptrs.end(); ++it) {
@@ -162,6 +162,10 @@ double Simulation::getTime() const {
 	return time_sim;
 }
 
+double Simulation::getVolume() const {
+	return lattice.getVolume();
+}
+
 bool Simulation::isLoggingEnabled() const {
 	return Enable_logging;
 }

Simulation.h

@@ -110,6 +110,9 @@ class Simulation{
 		//! Get the current simulation time in units of seconds.
         double getTime() const;
 
+		//! Get the simulation box volume in cm^-3
+		double getVolume() const;
+
 		//! \brief Checks whether or not logging is enabled.
 		//! \details This is primarily used for debugging purposes.
 		//! \return true if logging is enabled.
@@ -140,7 +143,7 @@ class Simulation{
 		//! \brief Adds a pointer to an Event object to the event list and returns the iterator to its position in the list.
 		//! \param event_ptr is the input Event pointer.
 		//! \return A list iterator that indicates where in the event list the newly added Event pointer is located.
-		std::list<Event*>::iterator addEvent(Event* event_ptr);
+		std::list<Event*>::const_iterator addEvent(Event* event_ptr);
 
 		//! \brief Adds a pointer to an Object object to the object list.
 		//! \param object_ptr is the input Object pointer.
@@ -149,7 +152,7 @@ class Simulation{
 		//! \brief Searches the event list and determines which event will be executed next.
 		//! \details Chooses the event that has the smallest execution time.
 		//! \return A list iterator points to an Event pointer in event list that has been selected to be executed next.
-		std::list<Event*>::iterator chooseNextEvent();
+		std::list<Event*>::const_iterator chooseNextEvent();
 
 		//! \brief Constructs and returns a vector of pointers to all Object objects that are to have their events recalculated/
 		//! \param coords_start is the Coords struct that designates the starting coordinates of an event.

Utils.h

@@ -205,15 +205,8 @@ namespace Utils {
 			result = 1;
 			return result;
 		}
-		int exponent_abs;
-		if (exponent < 0) {
-			exponent_abs = -exponent;
-		}
-		else {
-			exponent_abs = exponent;
-		}
 		result = base;
-		for (int i = 1; i < exponent_abs; i++) {
+		for (int i = 1; i < abs(exponent); i++) {
 			result *= base;
 		}
 		if (exponent < 0) {

docs/_event_8h_source.html

@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">KMC_Lattice
-   &#160;<span id="projectnumber">v2.0-beta.2</span>
+   &#160;<span id="projectnumber">v2.0-beta.3</span>
    </div>
    <div id="projectbrief">A general framework for three-dimensional lattice kinetic Monte Carlo simulations</div>
   </td>

docs/_lattice_8h_source.html

@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">KMC_Lattice
-   &#160;<span id="projectnumber">v2.0-beta.2</span>
+   &#160;<span id="projectnumber">v2.0-beta.3</span>
    </div>
    <div id="projectbrief">A general framework for three-dimensional lattice kinetic Monte Carlo simulations</div>
   </td>