Merge pull request #11 from MikeHeiber/development

Development v2.0-beta.2 Candidate2

Author: MikeHeiber

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-<div class="title">KMC_Lattice Documentation</div>  </div>
+<div class="title">KMC_Lattice </div>  </div>
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+<div class="textblock"><h2>General Information</h2>
+<p>This object-oriented C++ software package contains a general framework for lattice kinetic Monte Carlo (KMC) simulations. This framework consists of a number of utility functions and base classes that must be extended to create a fully operational KMC simulation. The goal of this package is to be robust and flexible so that users can easily develop KMC simulations for a wide variety of different scientific problems without the need to start from scratch. Try it out on <a href="https://github.com/MikeHeiber/KMC_Lattice">Github</a>.</p>
+<p>This KMC_Lattice package implements several event recalculation options for creating computationally efficient simulations. The package is designed to be usable on a personal computer and on high performance computing clusters. A simple example implementation of this general KMC framework can be found in the <a href="https://github.com/MikeHeiber/KMC_Lattice_example">KMC_Lattice_example</a> package. To see a more complete implementation for simulating a complex system, check out the <a href="https://github.com/MikeHeiber/Excimontec">Excimontec</a> software package that is used for simulating organic semiconductor materials and devices.</p>
+<p>For further reading about kinetic Monte Carlo simulations, a nice overview of the theory and algorithm can be found here:</p>
+<p><a href="http://www.fml.t.u-tokyo.ac.jp/~izumi/CMS/MC/Introduction_kMC.pdf">Introduction to the Kinetic Monte Carlo Method by Arthur Voter, Los Alamos National Lab</a></p>
+<h2>Work Together</h2>
+<p>If you would like to contribute to the development of this project or would like some help in building a KMC simulation for your specific scientific problem, please contact me to discuss a collaboration. You can check out my KMC research and other work on <a href="https://www.researchgate.net/profile/Michael_Heiber">Researchgate</a>.</p>
+<h2>Package Contents</h2>
+<p><a class="el" href="class_object.html" title="This base class contains the basic properties of a KMC simulation object and the functions needed to ...">Object</a> class - This base class can be extended to represent any entity that one would like to simulate. It could represent an electron, atom, molecule, organism, etc. depending on the application. The <a class="el" href="class_object.html" title="This base class contains the basic properties of a KMC simulation object and the functions needed to ...">Object</a> class contains the fundamental properties and back-end operations that any given entity simulation would require.</p>
+<p><a class="el" href="class_lattice.html" title="This class contains the properties of a three-dimensional lattice and the functions needed to interac...">Lattice</a> class - This class implements a lattice, its boundary conditions, and keeps track of its occupancy.</p>
+<p><a class="el" href="class_event.html" title="This base class contains the basic properties of a KMC simulation event and the functions needed to i...">Event</a> class - This base class can be extended to represent any process/mechanism/transition that one would like to simulate. It could represent a hopping motion event, a reaction event, etc. depending on the application. Typically, derived events are associated with a particular derived object. The <a class="el" href="class_event.html" title="This base class contains the basic properties of a KMC simulation event and the functions needed to i...">Event</a> class contains the fundamental properties and back-end operations that any given state transition would require.</p>
+<p><a class="el" href="class_site.html" title="This base class contains the basic properties of a lattice site and the functions needed to interact ...">Site</a> class - This base class can be extended to represent the lattice sites that make up the simulation medium/environment. Added site properties can be used to implement interactions between the simulation environment and the objects, which then affect the events. For example, site energies can be assigned to derived site classes to account for inhomogeneous systems.</p>
+<p><a class="el" href="class_simulation.html" title="This abstract base class contains the basic properties of a KMC simulation and the functions needed t...">Simulation</a> class - This base class can be extended to manage all derived objects and their associated events. The <a class="el" href="class_simulation.html" title="This abstract base class contains the basic properties of a KMC simulation and the functions needed t...">Simulation</a> class contains the fundamental properties and back-end operations that most simulations would require.</p>
+<p><a class="el" href="namespace_utils.html" title="This namespace provides useful constants and utility functions. ">Utils</a> - This file contain a number of useful utility functions, scientific constants, etc. that can then be used throughout the software package.</p>
+<p>Detailed API documentation for these classes and the entire KMC_Lattice package can be viewed <a href="https://mikeheiber.github.io/KMC_Lattice/">here</a>. </p>
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