These sections provide an overview of what SPPARKS can do, describe what it means for SPPARKS to be an open-source code, and acknowledge the funding and people who have contributed to SPPARKS.1.1 What is SPPARKS
SPPARKS is a Monte Carlo code that has algorithms for kinetic Monte Carlo (KMC), rejection KMC (rKMC), and Metropolis Monte Carlo (MMC). On-lattice and off-lattice applications with spatial sites on which "events" occur can be simulated in parallel.
KMC is also called true KMC or rejection-free KMC. rKMC is also called null-event MC. In a generic sense the code's KMC and rKMC solvers catalog a list of events, each with an associated probability, choose a single event to perform, and advance time by the correct amount. Events may be chosen individually at random, or a sweep of enumarated sites can be performed to select possible events in a more ordered fashion.
Note that rKMC is different from Metropolis MC, which is sometimes called thermodynamic-equilibrium MC or barrier-free MC, in that rKMC still uses rates to define events, often associated with the rate for the system to cross some energy barrier. Thus both KMC and rKMC track the dynamic evolution of a system in a time-accurate manner as events are performed. Metropolis MC is typically used to sample states from a system in equilibrium or to drive a system to equilibrium (energy minimization). It does this be performing (possibly) non-physical events. As such it has no requirement to sample events with the correct relative probabilities or to limit itself to physical events (e.g. it can change an atom to a new species). Because of this it also does not evolve the system in a time-accurate manner; in general there is no "time" associated with Metropolis MC events.
Applications are implemented in SPPARKS which define events and their probabilities and acceptance/rejection criteria. They are coupled to solvers or sweepers to perform KMC or rKMC simulations. The KMC or rKMC options for an application in SPPARKS can be written to define rates based on energy differences between the initial and final state of an event and a Metropolis-style accept/reject criterion based on the Boltzmann factor SPPARKS will then perform a Metropolis-style Monte Carlo simulation.
In parallel, a geometric partitioning of the simulation domain is performed. Sub-partitioning of processor domains into colors or quadrants (2d) and octants (3d) is done to enable multiple events to be performed on multiple processors simultaneously. Communication of boundary information is performed as needed.
Parallelism can also be invoked to perform multiple runs on a collection of processors, for statistical puposes.
SPPARKS is designed to be easy to modify and extend. For example, new solvers and sweeping rules can be added, as can new applications. Applications can define new commands which are read from the input script.
SPPARKS is written in C++. It runs on single-processor desktop or laptop machines, but for some applications, can also run on parallel computers. SPPARKS will run on any parallel machine that compiles C++ and supports the MPI message-passing library. This includes distributed- or shared-memory machines.
SPPARKS is a freely-available open-source code. See the SPPARKS WWW Site for download information. It is distributed under the terms of the GNU Public License (GPL), or sometimes by request under the terms of the GNU Lesser General Public License (LGPL), which means you can use or modify the code however you wish. The only restrictions imposed by the GPL or LGPL are on how you distribute the code further. See this section for a brief discussion of the open-source philosophy.
These are three kinds of applications in SPPARKS:
On-lattice applications define static event sites with a fixed neighbor connectivity. Off-lattice applications define mobile event sites such as particles. A particle's neighbors are typically specified by a cutoff distance. General applications have no spatial component.
The set of on-lattice applications currently in SPPARKS are:
The set of off-lattice applications currently in SPPARKS are:
The set of general applications currently in SPPARKS are:
These are the KMC solvers currently available in SPPARKS and their scaling properties:
Our group has written and released a separate toolkit called Pizza.py which provides tools which can be used to setup, analyze, plot, and visualize data for SPPARKS simulations. Pizza.py is written in Python and is available for download from the Pizza.py WWW site.
SPPARKS comes with no warranty of any kind. As each source file states in its header, it is a copyrighted code that is distributed free-of- charge, under the terms of the GNU Public License (GPL), or sometimes by request under the terms of the GNU Lesser General Public License (LGPL). This is often referred to as open-source distribution - see www.gnu.org or www.opensource.org for more details. The legal text of the GPL or LGPL is in the LICENSE file that is included in the SPPARKS distribution.
Here is a summary of what the GPL means for SPPARKS users:
(1) Anyone is free to use, modify, or extend SPPARKS in any way they choose, including for commercial purposes.
(2) If you distribute a modified version of SPPARKS, it must remain open-source, meaning you distribute source code under the terms of the GPL. You should clearly annotate such a code as a derivative version of SPPARKS.
(3) If you distribute any code that used SPPARKS source code, including calling it as a library, then that must also be open-source, meaning you distribute its source code under the terms of the GPL.
(4) If you give SPPARKS files to someone else, the GPL LICENSE file and source file headers (including the copyright and GPL notices) should remain part of the code.
In the spirit of an open-source code, if you use SPPARKS for something useful or if you fix a bug or add a new feature or applicaton to the code, let us know. We would like to include your contribution in the released version of the code and/or advertise your success on our WWW page.
SPPARKS is distributed by Sandia National Laboratories. SPPARKS development has been funded by the US Department of Energy (DOE), through its LDRD and ASC programs.
The primary authors of SPPARKS are Steve Plimpton, Aidan Thompson, and Alex Slepoy. They can be contacted via email: email@example.com, firstname.lastname@example.org, email@example.com.
The following Sandians have also contributed to the design and ideas in SPPARKS: